Publications

@article{Kyomukama2026,

title = {Discovery of synergistic drug combinations for E. coli from drug information, pathogen response and disease microenvironment data},

author = {Racheal Claire Kyomukama and Moses Ainembabazi and Henry Mutegeki and Patricia Nabisubi and Fredrick Elishama Kakembo and Gloria Loyce Nankoma and Kevin Cissy Nabukeera and Andrew Walakira and Ronald Galiwango},

doi = {10.1186/s44398-026-00023-y},

issn = {3005-1924},

year  = {2026},

date = {2026-12-00},

urldate = {2026-12-00},

journal = {BMC Artif. Intell.},

volume = {2},

number = {1},

publisher = {Springer Science and Business Media LLC},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Nuwamanya2025,

title = {Societal Economic Burden of Antibiotic Resistance in Uganda: A Cost of Illness Study},

author = {Elly Nuwamanya and Jonathan Mayito and Stephen Okoboi and Ronald Galiwango and Dathan Byonanebye and Suzan Nakasendwa and Flavia Dhikusooka and Janet Nabisere and Vivian Twemanye and Conrad Tumwine and Mackline Hope and Reuben Kiggundu and Ellon Twinomuhwezi and Lumbwe Chola and Joseph Babigumira and Thorkild Tylleskär and Francis Kakooza and Andrew Kambugu},

doi = {10.1007/s41669-025-00625-8},

issn = {2509-4254},

year  = {2026},

date = {2026-03-00},

urldate = {2026-03-00},

journal = {PharmacoEconomics Open},

volume = {10},

number = {2},

pages = {305--316},

publisher = {Springer Science and Business Media LLC},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Nakasendwa2026,

title = {Antibiotic use among patients admitted to tertiary hospitals in Uganda: a trend analysis of 2020–2023 point prevalence surveys},

author = {Suzan Nakasendwa and Jonathan Mayito and Vivian Twemanye and Conrad Tumwine and Reuben Kiggundu and Ronald Galiwango and Elly Nuwamanya and James Muleme and Flavia Dhikusooka and Herman Mwanja and Ellon Twinomuhwezi and Harriet Akello and Morries Seru and Hope Mackline and Dathan M Byonanebye and Francis Kakooza and Andrew Kambugu},

doi = {10.1136/bmjopen-2025-110251},

issn = {2044-6055},

year  = {2026},

date = {2026-03-00},

urldate = {2026-03-00},

journal = {BMJ Open},

volume = {16},

number = {3},

publisher = {BMJ},

abstract = {<jats:sec>

                    <jats:title>Objective</jats:title>

                    <jats:p>Limited data exist on temporal changes in antibiotic use in low and middle-income countries. We evaluated trends in antibiotic use at tertiary hospitals in Uganda.</jats:p>

                  </jats:sec>

                  <jats:sec>

                    <jats:title>Design</jats:title>

                    <jats:p>Retrospective trend analysis of a repeated point prevalence survey (PPS).</jats:p>

                  </jats:sec>

                  <jats:sec>

                    <jats:title>Setting and participants</jats:title>

                    <jats:p>This study utilised antibiotic use data from quarterly PPS conducted among inpatients at nine regional referral hospitals in Uganda between October 2020 and December 2023.</jats:p>

                  </jats:sec>

                  <jats:sec>

                    <jats:title>Outcome measures</jats:title>

                    <jats:p>

                      We determined the proportions of antibiotic use, prescriptions guided by culture and sensitivity tests (CST), WHO AWaRe (

                      <jats:italic>Access, Watch and Reserve</jats:italic>

                      ) categories, and prescriptions without documented indication. Linear regression was used to derive slope coefficients and 95% confidence interval (CI).

                    </jats:p>

                  </jats:sec>

                  <jats:sec>

                    <jats:title>Results</jats:title>

                    <jats:p>

                      Of 15,154 patients surveyed, 8,892 (58.7%) received systemic antibiotics. The median age was 23 years (IQR: 11–38), 5,338 (60.5%) were female, and 4,583 (51.5%) were on treatment for infectious syndromes, including sepsis (1,400, 15.7%) and pneumonia (867, 9.8%). The drug utilisation index (DU75) consisted of ceftriaxone, metronidazole, gentamicin and ampicillin, which accounted for 76.9% (12,291/15,989) of total antibiotic use. The distribution of prescribed antibiotics was 46.6% Access, 45.5% Watch, 0.1% Reserve and 7.7% unrecommended combinations. Overall, 5,402 (60.8%) prescriptions were aligned with national guidelines, 2,147 (24.1%) prescriptions were issued without an indication, and CST guided 271 (3%) prescriptions. Over time, there was no significant change in antibiotic prescription prevalence (slope=0.09, CI −0.93 to 1.10) and prescriptions without indication (slope=−0.70, CI −1.79 to 3.98). However, adherence to treatment guidelines (slope=2.06, CI 0.14 to 3.98) and prescriptions based on CST results (slope=0.62, CI 0.12 to 1.13) significantly increased, while ‘

                      <jats:italic>Watch’</jats:italic>

                      antibiotics prescriptions decreased (slope=−0.40, CI −0.63 to –0.17).

                    </jats:p>

                  </jats:sec>

                  <jats:sec>

                    <jats:title>Conclusions</jats:title>

                    <jats:p>

                      The antibiotic prescription rate remained high, with no significant change over time. Improvements were seen in adherence to treatment guidelines, use of CST and reduced use of ‘

                      <jats:italic>Watch’</jats:italic>

                      antibiotics. Strengthening antibiotic stewardship is recommended to further improve practices.

                    </jats:p>

                  </jats:sec>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Kiggundu2026,

title = {Leveraging disease outbreak news to strengthen the global response to antimicrobial resistance: a call for action},

author = {Reuben Kiggundu and J. P. Waswa and Herman Mwanja and Mackline Hope and Andrew Kambugu and Francis Kakooza and Dathan M. Byonanebye},

doi = {10.3389/fpubh.2025.1710596},

issn = {2296-2565},

year  = {2026},

date = {2026-01-07},

urldate = {2026-01-07},

journal = {Front. Public Health},

volume = {13},

publisher = {Frontiers Media SA},

abstract = {<jats:p>Antimicrobial resistance (AMR) is an escalating global health threat, with low- and middle-income countries (LMICs) bearing the greatest burden as healthcare facilities become breeding grounds for resistant pathogens, leading to increased morbidity, mortality, and straining of already limited resources. The World Health Organization’s Disease Outbreak News (DONs) has proven invaluable for early warnings and coordinated responses to infectious disease outbreaks like Ebola and COVID-19, yet AMR events remain largely absent from this system, leading to under-detection, limited global visibility, and ineffective interventions. In this paper, we review the historical evolution of DONs, its supporting frameworks, and the dynamics of AMR outbreaks in LMIC healthcare settings to explore how DONs could be adapted for AMR. We recommend standardizing AMR outbreaks reporting, integrating DONs into response efforts, linking AMR surveillance to DONs workflows, and expanding the definition of Public Health Emergencies of International Concern (PHEIC) to include high-morbidity AMR events, steps that would elevate AMR from a “silent pandemic” to a visible priority.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Twemanye2026,

title = {Implementation of the WHO Point Prevalence Surveys on Antibiotic Use in a Low-Income Country: Experiences and lessons learned from Uganda},

author = {Vivian Twemanye and Conrad Tumwine and Herman Mwanja and Morries Seru and Harriet Akello and Hope Mackline and Elly Nuwamanya and Suzan Nakasendwa and Ellon Twinomuhwezi and Richard Walwema and Jonathan Mayito and Dathan Byonanebye and Francis Kakooza and Andrew Kambugu and Reuben Kiggundu},

doi = {10.12688/wellcomeopenres.25045.1},

issn = {2398-502X},

year  = {2026},

date = {2026-01-06},

urldate = {2026-01-06},

journal = {Wellcome Open Res},

volume = {11},

publisher = {F1000 Research Ltd},

abstract = {<ns3:p>Background Antimicrobial resistance (AMR) poses a significant challenge to global health, especially in low- and middle-income countries (LMICs). The World Health Organization (WHO) recommends point prevalence surveys (PPS) as a standardized method for monitoring antibiotic use in hospitals. This manuscript describes Uganda’s experience and lessons learned in implementing the World Health Organisation Point Prevalence Survey methodology (WPPS) in high-volume tertiary hospitals. Methods The WPPS methodology was adapted to align with the health system in Uganda, the existing policies, and information systems, prioritizing inpatient points of care with high antibiotic use, and involving multidisciplinary teams in data collection, capacity building, and continuous quality improvement initiatives. Digitization of the paper-based WPPS tool enhanced and streamlined data collection, reduced errors, and improved data accessibility. Conducting quarterly surveys based on similar methodologies, provided sufficient data points that allowed tracking of trends and gauged the effectiveness of AMS interventions over time, helping to overcome the limitations of single surveys or sparse snapshot data. Results Implementation of the WPPS was feasible and provided actionable outputs on antibiotic prescribing patterns. The approach facilitated capacity building, continuous quality improvement, and the ability to monitor trends in antimicrobial use over time. Key observations from implementation and routine feedback included inadequate documentation of prescriptions and their indications, limited digitalization of patient records, and challenges in integrating WPPS data with broader AMR surveillance systems. Conclusion Uganda’s experience suggests that the WPPS offers a feasible solution for gathering actionable data on antibiotic prescription patterns, which is essential for informing antimicrobial stewardship programmes and supporting policy decisions as intended. Leveraging these insights can strengthen surveillance in Uganda and could guide the development and implementation of AMR surveillance and monitoring frameworks in other LMICs. Strengthening integration with national AMR surveillance frameworks could further enhance the utility of these data in guiding interventions.</ns3:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Mwanja2025,

title = {Epidemiology of Bloodstream Bacterial Infections and Missed Opportunities to Detect and Respond to Possible Outbreaks Due to Drug-Resistant Bacteria in Hospitals in Uganda: A Review of Retrospective National AMR Surveillance Data 2020 to 2023},

author = {Herman Mwanja and Reuben Kiggundu and Richard Walwema and Fahad Lwigale and JP. Waswa and Mackline Hope and Morgan Otita and Conrad Tumwine and Daniel Bulwadda and Andrew Kambugu and Dathan Byonanebye and Francis Kakooza},

doi = {10.12688/wellcomeopenres.24366.1},

issn = {2398-502X},

year  = {2025},

date = {2025-12-10},

urldate = {2025-12-10},

journal = {Wellcome Open Res},

volume = {10},

publisher = {F1000 Research Ltd},

abstract = {<ns3:p>

                    Background Antimicrobial resistance (AMR) poses a critical global health threat, with low- and middle-income countries (LMICs) facing systemic challenges in the detection and response to outbreaks of resistant pathogens. Despite Uganda establishing a national AMR surveillance system, there are no systems for the real-time detection of AMR outbreaks due to limited laboratory capacity, standardised protocols and data management systems. Methods This study involved a retrospective analysis of blood culture data collected from ten sentinel AMR surveillance sites (tertiary hospitals) across Uganda between October 2020 and December 2023 to evaluate AMR patterns, identify resistance alerts, and missed AMR outbreaks. Blood culture data from 2,572 patients were analysed using WHONET-SaTScan software to generate isolate listing summaries, identify resistance alerts of public health importance, and detect spatial-temporal clusters that signal potential outbreaks of resistant bacteria. Results Bacterial growth was observed in 17.1% (441/2,572) of blood samples. The key isolated pathogens included

                    <ns3:italic>Staphylococcus aureus</ns3:italic>

                    19.1% (86/441), Coagulase-negative

                    <ns3:italic>Staphylococci</ns3:italic>

                    34.7% (153/441), and

                    <ns3:italic>Escherichia coli</ns3:italic>

                    7.5% (33/441). Critical AMR alerts included 13.6% (60/441) cases of extended-spectrum β-lactamase (ESBL)-producing Enterobacterales and 3.6% (16/441) carbapenem-resistant isolates, alongside high-priority resistance mechanisms such as methicillin-resistant

                    <ns3:italic>Staphylococcus aureus</ns3:italic>

                    (15/441) and vancomycin-resistant

                    <ns3:italic>Enterococci</ns3:italic>

                    1.4% (6/441). Spatial-temporal analysis revealed seven significant clusters (possible outbreaks) across three sites, including a 12-day

                    <ns3:italic>Enterococcus</ns3:italic>

                    species cluster in a paediatric ward and a multi-ward

                    <ns3:italic>Staphylococcus aureus</ns3:italic>

                    outbreak. Conclusions This study reveals a significant burden of drug-resistant bloodstream infections in Ugandan hospitals and shows that key outbreak signals and possible outbreaks went unnoticed. Strengthening surveillance with real-time alerts, better data use, and targeted responses is critical to controlling the spread of resistant bacteria in Uganda and similar settings.

                  </ns3:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Mutegeki2025,

title = {There is urgent need for a Global Data Resource for Antimicrobial PK/PD: CAMO-Net GDR Initiative},

author = {Henry Mutegeki and Alison H. Holmes and Daudi Jjingo and Ronald Galiwango and Andrew Kambugu and Nusrat Shafiq and Kerri Hill-Cawthorne and William Hope and Shampa Das},

doi = {10.1038/s41467-025-64707-1},

issn = {2041-1723},

year  = {2025},

date = {2025-12-00},

urldate = {2025-12-00},

journal = {Nat Commun},

volume = {16},

number = {1},

publisher = {Springer Science and Business Media LLC},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Bonaconsa2025b,

title = {Exploring the influence of communication and team dynamics relating to infection care on intensive care unit patient discussions: Insights from sociograms and team reflexivity},

author = {C. Bonaconsa and E. Charani and D. Van den Bergh and I. Joubert and M. Mendelson},

doi = {10.1016/j.jcrc.2025.155127},

issn = {0883-9441},

year  = {2025},

date = {2025-10-00},

urldate = {2025-10-00},

journal = {Journal of Critical Care},

volume = {89},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{deBritto-Costa2025,

title = {Understanding context to plan antimicrobial stewardship: A mixed-method study in a Brazilian urban primary care},

author = {Letícia Fernandes de Britto-Costa and Vítor Falcão de Oliveira and Maria Tereza Pepe Razzolini and Fátima L.S. Nunes and Gabriela Tonon de Oliveira Xavier and Erika Regina Manuli and Fábio Eudes Leal and Regina Maura Zetone Grespan and Cibele Cristine Remondes Sequeira and Meiryellen Midiã Macedo and Ester Cerdeira Sabino and Alison Holmes and Silvia Figueiredo Costa and Anna S. Levin and Maria Clara Padoveze},

doi = {10.1016/j.ajic.2025.02.005},

issn = {0196-6553},

year  = {2025},

date = {2025-05-00},

urldate = {2025-05-00},

journal = {American Journal of Infection Control},

volume = {53},

number = {5},

pages = {619--627},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Shutt2025b,

title = {The intersection of the social determinants of health and antimicrobial resistance in human populations: a systematic review},

author = {Alison E. Shutt and Diane Ashiru-Oredope and James Price and Maria Clara Padoveze and Nusrat Shafiq and Emma Carter and Amrita Ghataure and Sameed Shariq and Alison H Holmes and Esmita Charani},

doi = {10.1136/bmjgh-2024-017389},

issn = {2059-7908},

year  = {2025},

date = {2025-05-00},

urldate = {2025-05-00},

journal = {BMJ Glob Health},

volume = {10},

number = {5},

publisher = {BMJ},

abstract = {<jats:sec>

                  <jats:title>Introduction</jats:title>

                  <jats:p>The social determinants of health (SDoH) impact the emergence and spread of antimicrobial resistance (AMR). We conducted a systematic review of literature mapping evidence on the intersection of SDoH, drug-resistant infections, antibiotic use, and public-facing interventions.</jats:p>

               </jats:sec>

               <jats:sec>

                  <jats:title>Methods</jats:title>

                  <jats:p>Following Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines, Ovid MEDLINE, Ovid EMBASE, the Cochrane Library, PsycINFO and Scopus were searched for published evidence in English between 2000 and 2022. Covidence software was used for data extraction. The evidence was mapped to the SDoH frameworks and the systematic review objectives.</jats:p>

               </jats:sec>

               <jats:sec>

                  <jats:title>Results</jats:title>

                  <jats:p>Of 17 252 retrieved papers, 16 636 were included in title and abstract review, with 153 included in data extraction (126 empirical studies and 27 papers with secondary data). Of these, 92/126 (73%) were quantitative, 23/126 (18%) qualitative and 11/126 (9 %) mixed methods. There was evidence from high income 60/126 (47%), lower-middle income 41/126 (33%), low income 14 (11%) and upper-middle income 11 (9%) countries.</jats:p>

                  <jats:p>There is limited evidence associated with the complete range of SDoH in different populations. Reported determinants affecting the risk of exposure to and spread of AMR include (a) socioeconomic status and the associated impact on health seeking behaviours, (b) housing—living in a deprived area and overcrowding and (c) knowledge linked with education affecting practices, exacerbated by interconnected complexity with the associated influence of socioeconomic status. A gap in understanding the upstream systems which create inequality and negatively impact SDoH is evident. Numerous definitions are used to identify vulnerable populations. There is very limited research examining specific population groups, for example, traveller communities and the disabled. Reported interventions focus on awareness programmes with little evidence on sustained behaviour change.</jats:p>

               </jats:sec>

               <jats:sec>

                  <jats:title>Conclusions</jats:title>

                  <jats:p>This review identified the need to (a) develop policies and context-specific solutions to manage upstream determinants, (b) include population groups where current evidence is limited and (c) prioritise community-based research using co-production methods.</jats:p>

               </jats:sec>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Sekaggya-Wiltshire2025b,

title = {Therapeutic drug monitoring for antimicrobial agents for people living with HIV (TAP)},

author = {Christine Sekaggya-Wiltshire and Eva Agnes Laker Odongpiny and Francis Williams Ojara and Isabella Kyohairwe and Reuben Kiggundu and Hope Mackline and Catriona Waitt and Aida N Kawuma and Allan Kengo and Allan Buzibye and Noela Owarwo and Francis Kakooza and Andrew Kambugu},

doi = {10.12688/wellcomeopenres.22707.2},

issn = {2398-502X},

year  = {2025},

date = {2025-04-22},

urldate = {2025-04-22},

journal = {Wellcome Open Res},

volume = {9},

publisher = {F1000 Research Ltd},

abstract = {<ns5:p>Background Antimicrobial resistance (AMR) is a growing health concern, particularly in Africa, and is predicted to become the leading cause of death after cancer by 2050. Factors like overuse or inappropriate use of antibiotics contribute to this crisis. People living with HIV (PLWH) are particularly vulnerable to AMR with potential drug-drug interactions between antiretroviral and antimicrobial agents against common organisms like <ns5:italic>Mycobacterium tuberculosis.</ns5:italic> There is limited data on the concentrations of commonly used antimicrobial agents in people living with HIV in resource-limited settings. Therapeutic Drug Monitoring (TDM) offers a promising approach to optimize antibiotic dosing and improve treatment outcomes for those with sub-optimal drug concentrations. TDM has been recommended for PLWH on anti-tuberculosis treatment due to sub-optimal drug concentrations found in a significant proportion of those with TB. Objectives The main objectives of this study are to determine the concentrations of selected antimicrobial agents in people living with HIV requiring antimicrobial therapy and to assess the utility of therapeutic drug monitoring in achieving therapeutic targets for PLWH receiving rifampicin and isoniazid for the treatment of tuberculosis. Methods This prospective observational study will enroll adult PLWH receiving amoxicillin, azithromycin, ciprofloxacin, rifampicin, isoniazid, or ceftriaxone. Concentrations of these antibiotics will be measured locally using validated liquid chromatography mass spectrometry methods and high-performance liquid chromatography with ultraviolet detection. TDM with dose adjustment will be performed in a subset of participants on TB treatment. Pharmacokinetic parameters will be estimated using non-linear mixed effects models. Results This study was reviewed and approved by the research and ethics committee in February 2024. Participant enrolment began in September 2024. Conclusions We anticipate that the findings from this research will characterize pharmacokinetic and pharmacodynamics relationships to predict treatment response for optimal antimicrobial therapeutic and anti-tuberculosis dosing among people living with HIV (PLWH). Clinical registration The study is registered with Pan African Clinical Trials Registry, registration number PACTR202409710100607, registration date 07 August 2024, <ns5:ext-link xmlns:ns6="http://www.w3.org/1999/xlink" ext-link-type="uri" ns6:href="https://pactr.samrc.ac.za/TrialDisplay.aspx?TrialID=31764">pactr.samrc.ac.za/TrialDisplay.aspx?TrialID=31764</ns5:ext-link></ns5:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Hope2025,

title = {Combining antibiotics to tackle antimicrobial resistance},

author = {William Hope and Sumathi Nambiar and Seamus O’Brien and Michael Sharland and David L. Paterson and Mo Yin and Ian H. Gilbert and Michael Ferguson and Sharon J. Peacock and Iain Buchan and Nada Reza and Vineet Dubey and Christopher A. Darlow and Alessandro Gerada and Alex Howard and and Helen Alexander and Megan Berkessel and Miguel Camera and Christopher Dowson and Simon Foster and Charlotte Green and Freya Harrison and Jay Hinton and Julia Hubbard and Tim Miles and Neil Ranson and Christopher Schofield and Brendan Wren},

doi = {10.1038/s41564-025-01969-x},

issn = {2058-5276},

year  = {2025},

date = {2025-04-00},

urldate = {2025-04-00},

journal = {Nat Microbiol},

volume = {10},

number = {4},

pages = {813--816},

publisher = {Springer Science and Business Media LLC},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Pandey2025,

title = {A systematic review of antibiotic drug shortages and the strategies employed for managing these shortages},

author = {Avaneesh Kumar Pandey and Jennifer Cohn and Vrinda Nampoothiri and Uttara Gadde and Amrita Ghataure and Ashish Kumar Kakkar and Yogendra, Kumar Gupta and Samir Malhotra and Oluchi Mbamalu and Marc Mendelson and Anne-Grete Märtson and Sanjeev Singh and Thomas Tängdén and Nusrat Shafiq and Esmita Charani},

doi = {10.1016/j.cmi.2024.09.023},

issn = {1198-743X},

year  = {2025},

date = {2025-03-00},

urldate = {2025-03-00},

journal = {Clinical Microbiology and Infection},

volume = {31},

number = {3},

pages = {345--353},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Tängdén2025b,

title = {Comprised access to antibiotics — the growing problem of availability and responsible use},

author = {Thomas Tängdén and Esmita Charani},

doi = {10.1016/j.cmi.2024.11.036},

issn = {1198-743X},

year  = {2025},

date = {2025-03-00},

urldate = {2025-03-00},

journal = {Clinical Microbiology and Infection},

volume = {31},

number = {3},

pages = {331--332},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Otaalo2025,

title = {Evaluating the appropriateness of prescribing antibiotics among persons with HIV (PWH) enrolled in routine cohorts at the Infectious Diseases Institute Clinic, Kampala, Uganda:  A study protocol},

author = {Brian Otaalo and Joseph Musaazi and Herman Mwanja and Derek Ngabirano and Reuben Kiggundu and Eva Agnes Laker Odongpiny and Francis Kakooza and Andrew Kambugu and Noela C. Owarwo and Barbara Castelnuovo},

doi = {10.12688/wellcomeopenres.23532.1},

issn = {2398-502X},

year  = {2025},

date = {2025-02-07},

urldate = {2025-02-07},

journal = {Wellcome Open Res},

volume = {10},

publisher = {F1000 Research Ltd},

abstract = {<ns3:p>Introduction Antimicrobial resistance is a global health threat and people living with HIV are at an increased risk. Inappropriate antibiotic use is one of the major driving factors for antimicrobial resistance, and a lot of irrational antibiotic use happens in outpatient clinics. This may be worse in resource-limited settings which face challenges in diagnosis and have drug shortages. There is limited information about the appropriateness of antibiotic prescriptions and their safety in people living with HIV especially in out-patient settings. Our study aims to assess the appropriateness and safety of antibiotic prescriptions among people living with HIV at the Infectious Diseases Institute, Kampala, Uganda. Methods We will conduct a review of medical records (charts and electronic medical records) of persons with HIV attending a tertiary out-patient HIV clinic in Kampala with an antibiotic prescription between January 2016- December 2022. We will stratify and randomly sample charts of patients receiving routine care and those having a visit when they were screened for tuberculosis. We will also include all patients who had visits in the urgent care unit, and visits of pregnant women. We will abstract data from both electrical and paper-based medical records. The appropriateness of an antibiotic prescription will be assessed using Uganda’s clinical guidelines for the corresponding period as a reference. The safety of antibiotic prescriptions in pregnancy will be assessed in line with the Swedish classification system. Patient characteristics at the time of antibiotic prescription will be summarized using descriptive statistics. Appropriateness and safety will be reported as a proportion of overall prescriptions.</ns3:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{B.2025,

title = {Advances in diagnosis and prognosis of bacteraemia, bloodstream infection, and sepsis using machine learning: A comprehensive living literature review},

author = {Hernandez B. and Ming D.K. and Rawson T.M. and Bolton W. and Wilson R. and Vasikasin V. and Daniels J. and Rodriguez-Manzano J. and Davies F.J. and Georgiou P. and Holmes A.H.},

doi = {10.1016/j.artmed.2024.103008},

issn = {0933-3657},

year  = {2025},

date = {2025-02-00},

urldate = {2025-02-00},

journal = {Artificial Intelligence in Medicine},

volume = {160},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Nampoothiri2025b,

title = {Evolution of pharmacist roles in antimicrobial stewardship: A 20-year systematic review},

author = {Vrinda Nampoothiri and Mohamed Hisham and Oluchi Mbamalu and Zubair Umer Mohamed and Sanjeev K. Singh and Esmita Charani},

doi = {10.1016/j.ijid.2024.107306},

issn = {1201-9712},

year  = {2025},

date = {2025-02-00},

urldate = {2025-02-00},

journal = {International Journal of Infectious Diseases},

volume = {151},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Batheja2025b,

title = {Understanding gender inequities in antimicrobial resistance: role of biology, behaviour and gender norms},

author = {Deepshikha Batheja and Srishti Goel and Esmita Charani},

doi = {10.1136/bmjgh-2024-016711},

issn = {2059-7908},

year  = {2025},

date = {2025-01-00},

urldate = {2025-01-00},

journal = {BMJ Glob Health},

volume = {10},

number = {1},

publisher = {BMJ},

abstract = {<jats:p>Antimicrobial resistance (AMR) poses a critical public health threat, with gendered implications that are often overlooked. Key drivers of bacterial AMR include the misuse of antibiotics, inadequate water, sanitation and hygiene infrastructure and poor infection control practices. Persistent gender discrimination exacerbates these issues, resulting in disparities in healthcare access and outcomes. This review explores how biological, sociocultural and behavioural factors contribute to the differential incidence of AMR in women. We present a conceptual framework to understand how gender norms influence antibiotic use and AMR. Differences in infection susceptibility, health-seeking behaviours, the ability to access and afford essential antibiotics and quality healthcare and appropriate diagnosis and management by healthcare providers across genders highlight the necessity for gender-sensitive approaches. Addressing gender dynamics within the health workforce and fostering inclusive policies is crucial for effectively mitigating AMR. Integrating intersectional and life course approaches into AMR mitigation strategies is essential to manage the changing health needs of women and other vulnerable groups.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{VanDenBergh2024b,

title = {Defining and responding to the contextual drivers for implementation of antimicrobial stewardship in 14 neonatal units in South Africa},

author = {Dena Van Den Bergh and Esmita Charani and Angela Dramowski and Ama Sakoa Annor and Michelle Gijzelaar and Angeliki Messina and Andriette Van Jaarsveld and Debra A Goff and Pavel Prusakov and Liezl Balfour and Adrie Bekker and Azraa Cassim and Nelesh P Govender and Sandi L Holgate and Sonya Kolman and Hafsah Tootla and Natalie Schellack and Kessendri Reddy and Christine Fisher and Lucinda Conradie and Anika Van Niekerk and Anje Laubscher and Pearl Alexander and Thanusha Naidoo and Magdel Dippenaar and Colleen Bamford and Sharnel Brits and Pinky Chirwa and Hannelie Erasmus and Pieter Ekermans and Lerina Rungen and Teresa Kriel and Dini Mawela and Simthembile Mjekula and Maphoshane Nchabeleng and Ronald Nhari and Marli Janse Van Rensburg and Pablo J Sánchez and Adrian Brink and and Azraa Cassim and Firdose Nakwa and Reenu Thomas and Alison Van Kwawegen and Jeannette Wadula and Ama Sakoa Annor and Dini Mawela and Masego Moncho and Martha Tshipo Motau and Maphoshane Nchabeleng and Sharnel Brits and Willem Breytenbach and Ilse Els-Goussard and Erika Grotepass and Alida Portland and Hafsah Tootla and Ayesha Arendse and Christine Fisher and Amanda Khumalo and Simthembile Mjekula and Shakti Pillay and Abdul Qayyum Kader and Chetna Govind and Vinesh Moodley and Thanusha Naidoo and Lerina Rungen and Pearl Alexander and John Berlyn and Owen Dreyer and Arisna Maharaj and Dawie Peens and Madeleine Pieters and Emma van Schalkwyk and Marlon Starr and Colleen Bamford and Teresa Kriel and Mariska van der Wal and Veliswa Mgudlwa and Colette Beukes and James Macdonald and Ronald Nhari and Tanya Ndou and Gladys Rapoone and Antia Taljaard and Marina Aucamp and Lucinda Conradie and Hafsah Tootla and Anika van Niekerk and Vindana Chibabhai and Pinky Chirwa and Sonya Kolman and Selebaleng Nchwee and Dina Bruwer and Magdel Dippenaar and Hannelie Erasmus and Madaleen Olivier and Lea van der Westhuizen and Juanita Coetzee and Pieter Ekermans and Marleen Engelbrecht and Marli Janse van Rensburg and Lindie van Tonder and Tarina Bester and Zanli van Blerk and Anje Laubscher and Johnny Lotter and Liesl Venter and Heinrich du Toit and Jennifer Coetzee and Deleen Bartman and Adrie Bekker and Sandi Holgate and Kessendri Reddy and Sinethemba Hloyi and Trudie Isobel and Leticia Radloff},

doi = {10.1093/jacamr/dlae222},

issn = {2632-1823},

year  = {2024},

date = {2024-12-26},

urldate = {2024-12-26},

volume = {7},

number = {1},

publisher = {Oxford University Press (OUP)},

abstract = {<jats:title>Abstract</jats:title>

               <jats:sec>

                  <jats:title>Background</jats:title>

                  <jats:p>Research on the contextual drivers of antimicrobial stewardship (AMS) programme interventions in neonatal units is limited.</jats:p>

               </jats:sec>

               <jats:sec>

                  <jats:title>Methods</jats:title>

                  <jats:p>As part of a prospective mixed-methods multidisciplinary neonatal AMS (NeoAMS) interventional study in 14 South African hospitals, we applied a three-phased process to assess implementation barriers and contextual drivers experienced by participating health professionals. The study included: (Phase one; P1) a survey of pre-intervention barriers and enablers; (P2) written feedback during the study intervention phase; and (P3) semi-structured exit interviews.</jats:p>

               </jats:sec>

               <jats:sec>

                  <jats:title>Results</jats:title>

                  <jats:p>Respondents to the P1 survey (n = 100) identified 15 barriers, 9 in the domain of personnel resources, including staffing, time and workload constraints. Other barriers related to limited access to antimicrobial use and surveillance trends, complexity of neonatal care, absence of multidisciplinary team (MDT) AMS and change resistance. For P2, written feedback during implementation (n = 42) confirmed that the MDT approach facilitated systems changes, including policy adaptations, process improvements, strengthened infection control practices, and expansion of AMS MDT roles. MDT benefits were described as aligned team purpose, improved communication, and knowledge sharing. Reported challenges included time to meet and building trust. In P3 interviews (n = 42), improved interpersonal communication, trust, personal growth and confidence building were cited as highlights of working in multidisciplinary AMS teams. Extending the MDT approach to other hospitals, training more health professionals in AMS and increasing management involvement were identified as priorities going forward.</jats:p>

               </jats:sec>

               <jats:sec>

                  <jats:title>Conclusions</jats:title>

                  <jats:p>Understanding the organizational and interprofessional context for NeoAMS implementation enabled an MDT approach to develop and optimize neonatal AMS with potential for adoption in similar resource-constrained settings.</jats:p>

               </jats:sec>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ahmad2024,

title = {Systems Policy Analysis for Antimicrobial Resistance Targeted Action (SPAARTA): A Research Protocol},

author = {Raheelah Ahmad and Nina Zhu and Rishabh Jain and Jyoti Joshi and Mirfin Mpundu and Paola Amigo Gutierrez and Alison Holmes and Tillman Weyde and Rifat Atun},

doi = {10.12688/wellcomeopenres.22923.1},

issn = {2398-502X},

year  = {2024},

date = {2024-12-02},

urldate = {2024-12-02},

journal = {Wellcome Open Res},

volume = {9},

publisher = {F1000 Research Ltd},

abstract = {<ns3:p>Background The majority of countries (64%) have an Antimicrobial Resistance (AMR) National Action Plan (NAP V.1.0), but many remain unimplemented, and lack funding for interventions. Intervention selection requires a systematic approach to explain and predict progress. Looking beyond AMR is important to ensure the capture of systemic factors at the country level, which can impede or accelerate success. Aim To provide innovative policy analysis to allow country comparison and refine targeted action, while developing and implementing NAPs (V.2.0). Methods Mixed-method multi-country case study of policies and implementation strategies to address AMR across One Health. Starting with 17 countries, the sample includes each WHO region and emerging economies. This investigation of structures, processes, and outcomes has three components: a. Textual analysis of peer-reviewed literature, policy documents, global and national progress reports, validated by global and in-country experts. An all-language article search conducted for 2000-2024, using broad search terms: ‘Antimicrobial resistance policies’, ‘national action plan’, ‘surveillance’, ‘AMR systems’ supplemented by hand searches. Deductive analysis using multi-disciplinary frameworks including the Expert Consensus for Implementation Research (ERIC). b. Longitudinal quantitative analysis assessing country contextual determinants and Antimicrobial Use (AMU) and AMR outcomes. Data from global health indicator repositories and international and national AMU and AMR surveillance networks are analysed using econometrics and machine learning approaches. c. Interactive Tableau dashboard development to display insights from a & b to allow visualisation and comparison of case-country AMR intervention context and components. Discussion This protocol provides a systematic, transparent approach for countries to benchmark their own AMR strategies. The interactive dashboard will allow comparisons between country clusters by geography or economy, and enable rapid knowledge mobilisation among strategic and operational stakeholders including policy makers and planners. This protocol facilitates others to perform this structured assessment and nominate their country for the next wave of analysis.</ns3:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Hibbard2024,

title = {Antimicrobial stewardship: a definition with a One Health perspective},

author = {Rebecca Hibbard and Marc Mendelson and Stephen W. Page and Jorge Pinto Ferreira and Céline Pulcini and Mathilde C. Paul and Céline Faverjon},

doi = {10.1038/s44259-024-00031-w},

issn = {2731-8745},

year  = {2024},

date = {2024-12-00},

urldate = {2024-12-00},

journal = {npj Antimicrob Resist},

volume = {2},

number = {1},

publisher = {Springer Science and Business Media LLC},

abstract = {<jats:title>Abstract</jats:title><jats:p>Antimicrobial stewardship (AMS) is a commonly advocated approach to address antimicrobial resistance. However, AMS is often defined in different ways depending on where it is applied, such that a range of definitions is now in use. These definitions may be functional and well-structured for a given context but are often ill-adapted for collaborative work, creating difficulties for intersectoral communication on AMS and complicating the design, implementation, and evaluation of AMS interventions from a One Health perspective. Using boundary object theory, we identified three key elements common to AMS in different settings in the human and animal health sectors—a sense of collective and temporal responsibility, flexibility in scale and scope, and contextual contingency. Based on these findings, we propose a definition for antimicrobial stewardship applicable to the human and animal health sectors, intended to facilitate intersectoral communication and cooperation. Further directions of this work could include the application of the definition to develop indicators for evaluating stewardship interventions and the extension of the definition to incorporate elements pertinent to plant and ecosystem health.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{deOliveira2024,

title = {Colonisation by multidrug-resistant organisms in health workers in primary care: narrow spectrum oral antimicrobials are a risk factor},

author = {Vítor Falcão de Oliveira and Letícia Fernandes de Britto-Costa and Gabrielly Lacerda de Aragão and Nazareno Scaccia and Ana Carolina Mamana and Marina Farrel Côrtes and Maura Salaroli de Oliveira and Bruno de Melo Tavares and Erika Regina Manuli and Fábio Eudes Leal and Gabriela Tonon de Oliveira Xavier and Regina Maura Zetone Grespan and Cibele Cristine Remondes Sequeira and Fatima L. S. Nunes and Milena Dropa and Solange Martone-Rocha and Maria Tereza Pepe Razzolini and Ester Cerdeira Sabino and Maria Clara Padoveze and Alison Holmes and Silvia F. Costa and Anna S. Levin and and Ícaro Boszczowski and Ana Rubia Guedes Vinhole and Ana Paula Marchi and Sania Alves dos Santos and Sueli F. Raymundo and Ana Rocío Cárdenas Maita and Guilherme Crepaldi Esposito and Marcio Oikawa and Milena Borges and Marta Angela Marcondes and Raquel da Silva Terezam and Pedro Casini and Maria deda LourdesSilva and Mônica Tilli Reis Pessoa Conde and Jaqueline de Pierri and Meiryellen Midiã Macedo and Viviane Aparecida Ramos},

doi = {10.1007/s10096-024-04953-1},

issn = {1435-4373},

year  = {2024},

date = {2024-12-00},

urldate = {2024-12-00},

journal = {Eur J Clin Microbiol Infect Dis},

volume = {43},

number = {12},

pages = {2323--2333},

publisher = {Springer Science and Business Media LLC},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Babirye2024,

title = {Machine learning-based prediction of antibiotic resistance in Mycobacterium tuberculosis clinical isolates from Uganda},

author = {Sandra Ruth Babirye and Mike Nsubuga and Gerald Mboowa and Charles Batte and Ronald Galiwango and David Patrick Kateete},

doi = {10.1186/s12879-024-10282-7},

issn = {1471-2334},

year  = {2024},

date = {2024-12-00},

urldate = {2024-12-00},

journal = {BMC Infect Dis},

volume = {24},

number = {1},

publisher = {Springer Science and Business Media LLC},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Howard2024d,

title = {Personalised antimicrobial susceptibility testing with clinical prediction modelling informs appropriate antibiotic use},

author = {Alex Howard and David M. Hughes and Peter L. Green and Anoop Velluva and Alessandro Gerada and Simon Maskell and Iain E. Buchan and William Hope},

doi = {10.1038/s41467-024-54192-3},

issn = {2041-1723},

year  = {2024},

date = {2024-12-00},

urldate = {2024-12-00},

journal = {Nat Commun},

volume = {15},

number = {1},

publisher = {Springer Science and Business Media LLC},

abstract = {<jats:title>Abstract</jats:title><jats:p>Antimicrobial susceptibility testing is a key weapon against antimicrobial resistance. Diagnostic microbiology laboratories use one-size-fits-all testing approaches that are often imprecise, inefficient, and inequitable. Here, we report a personalised approach that adapts laboratory testing for urinary tract infection to maximise the number of appropriate treatment options for each patient. We develop and assess susceptibility prediction models for 12 antibiotics on real-world healthcare data using an individual-level simulation study. When combined with decision thresholds that prioritise selection of World Health Organisation Access category antibiotics (those least likely to induce antimicrobial resistance), the personalised approach delivers more susceptible results (results that encourage prescription of that antibiotic) per specimen for Access category antibiotics than a standard testing approach, without compromising provision of susceptible results overall. Here, we show that personalised antimicrobial susceptibility testing could help tackle antimicrobial resistance by safely providing more Access category antibiotic treatment options to clinicians managing urinary tract infection.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Hope2024,

title = {Progress on implementing the WHO-GLASS recommendations on priority pathogen-antibiotic sensitivity testing in Africa: A scoping review},

author = {Mackline Hope and Reuben Kiggundu and Dickson Tabajjwa and Conrad Tumwine and Fahad Lwigale and Herman Mwanja and J. P. Waswa and Jonathan Mayito and Daniel Bulwadda and Dathan M. Byonanebye and Francis Kakooza and Andrew Kambugu},

doi = {10.12688/wellcomeopenres.23133.1},

issn = {2398-502X},

year  = {2024},

date = {2024-11-22},

urldate = {2024-11-22},

journal = {Wellcome Open Res},

volume = {9},

publisher = {F1000 Research Ltd},

abstract = {<ns3:p>Introduction The World Health Organization global antimicrobial resistance surveillance system (GLASS) was rolled out in 2015 to guide antimicrobial resistance (AMR) surveillance. However, its implementation in Africa has not been fully evaluated. We conducted a scoping review to establish the progress of implementing the WHO 2015 GLASS manual in Africa. Methods We used MeSH terms to comprehensively search electronic databases (MEDLINE and Embase) for articles from Africa published in English between January 2016 and December 2023. The Arksey and O'Malley's methodological framework for scoping reviews was employed. Data were collected on compliance with WHO GLASS recommendations for AMR surveillance-priority samples, pathogens, and pathogen-antibiotic combinations and analysed using Microsoft Excel. Results Overall, 13,185 articles were identified. 7,409 were duplicates, and 5,141 articles were excluded based on titles and abstracts. 609 full-text articles were reviewed, and 147 were selected for data extraction. Of the 147 selected articles, 78.9% had been published between 2020 and 2023; 57.8% were from Eastern Africa. 93.9% of articles were on cross-sectional studies. 96.6% included only one priority sample type; blood (n=56), urine (n=64), and stool (n=22). Of the 60 articles that focused on blood as a priority sample type, 71.7%, 68.3%, 68.3%, 36.7%, 30%, and 10% reported recovery of <ns3:italic>Escherichia coli</ns3:italic>, <ns3:italic>Staphylococcus aureus, Klebsiella pneumoniae</ns3:italic>, <ns3:italic>Acinetobacter baumannii</ns3:italic>, <ns3:italic>Salmonella</ns3:italic> species and <ns3:italic>Streptococcus pneumoniae,</ns3:italic> respectively. <ns3:italic>Salmonella</ns3:italic> and <ns3:italic>Shigella</ns3:italic> species were reported to have been recovered from 91.3% and 73.9% of the 23 articles that focused on stool. <ns3:italic>E. coli</ns3:italic> and <ns3:italic>K. pneumoniae</ns3:italic> recoveries were also reported from 94.2% and 68.1% of the 69 articles that focused on urine. No article in this review reported having tested all the recommended WHO GLASS pathogen-antibiotic combinations for specific pathogens. Conclusion Progress has been made in implementing the GLASS recommendations in Africa, but adoption varies across countries limiting standardisation and comparability of data.</ns3:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Hope2024b,

title = {Progress of Implementation of World Health Organization Global Antimicrobial Resistance Surveillance System Recommendations on Priority Pathogen-Antibiotic Sensitivity Testing in Africa: Protocol for a Scoping Review},

author = {Mackline Hope and Reuben Kiggundu and Dathan M Byonanebye and Jonathan Mayito and Dickson Tabajjwa and Fahad Lwigale and Conrad Tumwine and Herman Mwanja and Andrew Kambugu and Francis Kakooza},

doi = {10.2196/58140},

issn = {1929-0748},

year  = {2024},

date = {2024-11-15},

urldate = {2024-11-15},

journal = {JMIR Res Protoc},

volume = {13},

publisher = {JMIR Publications Inc.},

abstract = {<jats:sec>

            <jats:title>Background</jats:title>

            <jats:p>Antimicrobial resistance (AMR) is a major global public health concern, particularly in low- and middle-income countries where resources and infrastructure for an adequate response are limited. The World Health Organization (WHO) Global Antimicrobial Resistance Surveillance System (GLASS) was introduced in 2016 to address these challenges, outlining recommendations for priority pathogen-antibiotic combinations. Despite this initiative, implementation in Africa remains understudied. This scoping review aims to assess the current state of implementing WHO GLASS recommendations on antimicrobial sensitivity testing (AST) in Africa.</jats:p>

          </jats:sec>

          <jats:sec>

            <jats:title>Objective</jats:title>

            <jats:p>The primary objective of this study is to determine the current state of implementing the WHO GLASS recommendations on AST for priority pathogen-antimicrobial combinations. The review will further document if the reporting of AST results is according to “susceptible,” “intermediate,” and “resistant” recommendations according to GLASS.</jats:p>

          </jats:sec>

          <jats:sec>

            <jats:title>Methods</jats:title>

            <jats:p>Following the methodological framework by Arksey and O’Malley, studies published between January 2016 and November 2023 will be included. Search strategies will target electronic databases, including MEDLINE, Scopus, CINAHL, and Embase. Eligible studies will document isolates tested for antimicrobial sensitivity, focusing on WHO-priority specimens and pathogens. Data extraction will focus on key study characteristics, study context, population, and adherence to WHO GLASS recommendations on AST. Descriptive statistics involving summarizing the quantitative data extracted through measures of central tendency and variation will be used. Covidence and Microsoft Excel software will be used. This study will systematically identify, collate, and analyze relevant studies and data sources based on clear inclusion criteria to provide a clear picture of the progress achieved in the implementation of the WHO GLASS recommendations. Areas for further improvement will be documented to inform future efforts to strengthen GLASS implementation for enhanced AMR surveillance in Africa.</jats:p>

          </jats:sec>

          <jats:sec>

            <jats:title>Results</jats:title>

            <jats:p>The study results are expected in August 2024.</jats:p>

          </jats:sec>

          <jats:sec>

            <jats:title>Conclusions</jats:title>

            <jats:p>To our knowledge, this scoping review will be the first to comprehensively examine the implementation of WHO GLASS recommendations in Africa, shedding light on the challenges and successes of AMR surveillance in the region. Addressing these issues aims to contribute to global efforts to combat AMR.</jats:p>

          </jats:sec>

          <jats:sec>

            <jats:title>International Registered Report Identifier (IRRID)</jats:title>

            <jats:p>PRR1-10.2196/58140</jats:p>

          </jats:sec>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Mayito2024d,

title = {Combating Antimicrobial Resistance Through a Data-Driven Approach to Optimize Antibiotic Use and Improve Patient Outcomes: Protocol for a Mixed Methods Study},

author = {Jonathan Mayito and Conrad Tumwine and Ronald Galiwango and Elly Nuwamanya and Suzan Nakasendwa and Mackline Hope and Reuben Kiggundu and Dathan M Byonanebye and Flavia Dhikusooka and Vivian Twemanye and Andrew Kambugu and Francis Kakooza},

doi = {10.2196/58116},

issn = {1929-0748},

year  = {2024},

date = {2024-11-08},

urldate = {2024-11-08},

journal = {JMIR Res Protoc},

volume = {13},

publisher = {JMIR Publications Inc.},

abstract = {<jats:sec>

                    <jats:title>Background</jats:title>

                    <jats:p>It is projected that drug-resistant infections will lead to 10 million deaths annually by 2050 if left unabated. Despite this threat, surveillance data from resource-limited settings are scarce and often lack antimicrobial resistance (AMR)–related clinical outcomes and economic burden. We aim to build an AMR and antimicrobial use (AMU) data warehouse, describe the trends of resistance and antibiotic use, determine the economic burden of AMR in Uganda, and develop a machine learning algorithm to predict AMR-related clinical outcomes.</jats:p>

                  </jats:sec>

                  <jats:sec>

                    <jats:title>Objective</jats:title>

                    <jats:p>The overall objective of the study is to use data-driven approaches to optimize antibiotic use and combat antimicrobial-resistant infections in Uganda. We aim to (1) build a dynamic AMR and antimicrobial use and consumption (AMUC) data warehouse to support research in AMR and AMUC to inform AMR-related interventions and public health policy, (2) evaluate the trends in AMR and antibiotic use based on annual antibiotic and point prevalence survey data collected at 9 regional referral hospitals over a 5-year period, (3) develop a machine learning model to predict the clinical outcomes of patients with bacterial infectious syndromes due to drug-resistant pathogens, and (4) estimate the annual economic burden of AMR in Uganda using the cost-of-illness approach.</jats:p>

                  </jats:sec>

                  <jats:sec>

                    <jats:title>Methods</jats:title>

                    <jats:p>We will conduct a study involving data curation, machine learning–based modeling, and cost-of-illness analysis using AMR and AMU data abstracted from procurement, human resources, and clinical records of patients with bacterial infectious syndromes at 9 regional referral hospitals in Uganda collected between 2018 and 2026. We will use data curation procedures, FLAIR (Findable, Linkable, Accessible, Interactable and Repeatable) principles, and role-based access control to build a robust and dynamic AMR and AMU data warehouse. We will also apply machine learning algorithms to model AMR-related clinical outcomes, advanced statistical analysis to study AMR and AMU trends, and cost-of-illness analysis to determine the AMR-related economic burden.</jats:p>

                  </jats:sec>

                  <jats:sec>

                    <jats:title>Results</jats:title>

                    <jats:p>The study received funding from the Wellcome Trust through the Centers for Antimicrobial Optimisation Network (CAMO-Net) in April 2023. As of October 28, 2024, we completed data warehouse development, which is now under testing; completed data curation of the historical Fleming Fund surveillance data (2020-2023); and collected retrospective AMR records for 599 patients that contained clinical outcomes and cost-of-illness economic burden data across 9 surveillance sites for objectives 3 and 4, respectively.</jats:p>

                  </jats:sec>

                  <jats:sec>

                    <jats:title>Conclusions</jats:title>

                    <jats:p>The data warehouse will promote access to rich and interlinked AMR and AMU data sets to answer AMR program and research questions using a wide evidence base. The AMR-related clinical outcomes model and cost data will facilitate improvement in the clinical management of AMR patients and guide resource allocation to support AMR surveillance and interventions.</jats:p>

                  </jats:sec>

                  <jats:sec>

                    <jats:title>International Registered Report Identifier (IRRID)</jats:title>

                    <jats:p>PRR1-10.2196/58116</jats:p>

                  </jats:sec>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Gerada2024d,

title = {Simulation to optimize the laboratory diagnosis of bacteremia},

author = {Alessandro Gerada and Gareth Roberts and Alex Howard and Nada Reza and Anoop Velluva and Conor Rosato and Peter L. Green and William Hope},

editor = {Siu-Kei Chow},

doi = {10.1128/spectrum.01449-24},

issn = {2165-0497},

year  = {2024},

date = {2024-11-05},

urldate = {2024-11-05},

journal = {Microbiol Spectr},

volume = {12},

number = {11},

publisher = {American Society for Microbiology},

abstract = {<jats:title>ABSTRACT</jats:title>

          <jats:sec>

            <jats:title/>

            <jats:p>Blood cultures are central to the management of patients with sepsis and bloodstream infection. Clinical decisions depend on the timely availability of laboratory information, which, in turn, depends on the optimal laboratory processing of specimens. Discrete event simulation (DES) offers insights into where optimization efforts can be targeted. Here, we generate a detailed process map of blood culture processing within a laboratory and use it to build a simulator. Direct observation of laboratory staff processing blood cultures was used to generate a flowchart of the blood culture laboratory pathway. Retrospective routinely collected data were combined with direct observations to generate probability distributions over the time taken for each event. These data were used to inform the DES model. A sensitivity analysis explored the impact of staff availability on turnaround times. A flowchart of the blood culture pathway was constructed, spanning labeling, incubation, organism identification, and antimicrobial susceptibility testing. Thirteen processes in earlier stages of the pathway, not otherwise captured by routinely collected data, were timed using direct observations. Observations revealed that specimen processing is predominantly batched. Another eight processes were timed using retrospective data. A simulator was built using DES. Sensitivity analysis revealed that specimen progression through the simulation was especially sensitive to laboratory technician availability. Gram stain reporting time was also sensitive to laboratory scientist availability. Our laboratory simulation model has wide-ranging applications for the optimization of laboratory processes and effective implementation of the changes required for faster and more accurate results.</jats:p>

          </jats:sec>

          <jats:sec>

            <jats:title>IMPORTANCE</jats:title>

            <jats:p>Optimization of laboratory pathways and resource availability has a direct impact on the clinical management of patients with bloodstream infection. This research offers an insight into the laboratory processing of blood cultures at a system level and allows clinical microbiology laboratories to explore the impact of changes to processes and resources.</jats:p>

          </jats:sec>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Bhandari2024,

title = {Addressing Challenges in Antibiotic Access: Barriers, Implications and Strategies for Solution},

author = {Ritika Kondel Bhandari and Avaneesh Kumar Pandey and Samir Malhotra and Ashish Kumar Kakkar and Sanjeev Singh and Jennifer Cohn and Alison Holmes and Esmita Charani and Nusrat Shafiq},

doi = {10.1007/s40290-024-00538-7},

issn = {1179-1993},

year  = {2024},

date = {2024-11-00},

urldate = {2024-11-00},

journal = {Pharm Med},

volume = {38},

number = {6},

pages = {387--397},

publisher = {Springer Science and Business Media LLC},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Mwanja2024,

title = {Utility of syndromic surveillance for the surveillance of healthcare-associated infections in resource-limited settings: a narrative review},

author = {Herman Mwanja and J. P. Waswa and Reuben Kiggundu and Hope Mackline and Daniel Bulwadda and Dathan M. Byonanebye and Andrew Kambugu and Francis Kakooza},

doi = {10.3389/fmicb.2024.1493511},

issn = {1664-302X},

year  = {2024},

date = {2024-10-21},

urldate = {2024-10-21},

journal = {Front. Microbiol.},

volume = {15},

publisher = {Frontiers Media SA},

abstract = {<jats:p>Globally, Healthcare-associated infections (HCAIs) pose a significant threat to patient safety and healthcare systems. In low- and middle-income countries (LMICs), the lack of adequate resources to manage HCAIs, as well as the weak healthcare system, further exacerbate the burden of these infections. Traditional surveillance methods that rely on laboratory tests are cost-intensive and impractical in these settings, leading to ineffective monitoring and delayed management of HCAIs. The rates of HCAIs in resource-limited settings have not been well established for most LMICs, despite their negative consequences. This is partly due to costs associated with surveillance systems. Syndromic surveillance, a part of active surveillance, focuses on clinical observations and symptoms rather than laboratory confirmation for HCAI detection. Its cost-effectiveness and efficiency make it a beneficial approach for monitoring HCAIs in LMICs. It provides for early warning capabilities, enabling timely identification and response to potential HCAI outbreaks. Syndromic surveillance is highly sensitive and this helps balance the challenge of low sensitivity of laboratory-based surveillance systems. If syndromic surveillance is used hand-in-hand with laboratory-based surveillance systems, it will greatly contribute to establishing the true burden of HAIs in resource-limited settings. Additionally, its flexibility allows for adaptation to different healthcare settings and integration into existing health information systems, facilitating data-driven decision-making and resource allocation. Such a system would augment the event-based surveillance system that is based on alerts and rumours for early detection of events of outbreak potential. If well streamlined and targeted, to monitor priority HCAIs such as surgical site infections, hospital-acquired pneumonia, diarrheal illnesses, the cost and burden of the effects from these infections could be reduced. This approach would offer early detection capabilities and could be expanded into nationwide HCAI surveillance networks with standardised data collection, healthcare worker training, real-time reporting mechanisms, stakeholder collaboration, and continuous monitoring and evaluation. Syndromic surveillance offers a promising strategy for combating HCAIs in LMICs. It provides early warning capabilities, conserves resources, and enhances patient safety. Effective implementation depends on strategic interventions, stakeholder collaboration, and ongoing monitoring and evaluation to ensure sustained effectiveness in HCAI detection and response.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Useh2024b,

title = {Awareness of infection care terms among outpatients and carers in a public health facility: a cross-sectional survey},

author = {Ebruphiyo Ruth Useh and Bongeka Mfeketo and Okuhle Mbengo and Innocent Karangwa and Timothy Pennel and Adam Boutall and Salome Maswime and Linda Pohl and Esmita Charani and Marc Mendelson and Oluchi Mbamalu},

doi = {10.12688/wellcomeopenres.20162.2},

issn = {2398-502X},

year  = {2024},

date = {2024-10-09},

urldate = {2024-10-09},

journal = {Wellcome Open Res},

volume = {8},

publisher = {F1000 Research Ltd},

abstract = {<ns3:p>Background As healthcare recipients and individuals affected by antimicrobial resistance (AMR), patients and their carers can be engaged in infection prevention and control (IPC) and antimicrobial stewardship (AMS) initiatives to manage AMR. To effectively participate in these initiatives, patients and carers need to understand general terms used in infection care. We explored awareness of commonly used infection-related terms among patients and carers in the surgical out-patient of a tertiary academic hospital. Methods Self-administered paper survey distributed among out-patients from August to September 2022. Categorical variables were analysed using Chi squared test. Significance was set as p-value of < 0.05. Content analysis identified terms commonly used by patients when talking about infections. Results Overall, 896 out of 1,269 respondents (response rate 70.6%), with a 1:3 male to female ratio were included. Most respondents were patients (75%), with a minimum of high school education (91.2%) and a surgical history (60.3%). <ns3:italic>Surgical wound infection</ns3:italic> was the most familiar term to participants. While many respondents had not heard of Methicillin-resistant Staphylococcus aureus (<ns3:italic>MRSA</ns3:italic>) (92.3%, n=754) or <ns3:italic>antimicrobial resistance</ns3:italic> (92.8%, n=755), significantly more were aware of the descriptions provided for these terms (13.7% and 33.0%, respectively; p<0.001). Participants considered <ns3:italic>antibiotic resistance</ns3:italic> to be a condition in which the body rejects, resists, or does not respond to antibiotics. Conclusions Findings show dissonance between patients’ awareness of and healthcare workers’ use of infection-care terms, highlighting the need for relatable and accessible terms in infection-care engagement initiatives. More than half of respondents acknowledged that patient engagement responsibility is everyone’s, underscoring the need for contextually fit and relevant communication strategies to advance patient engagement and infection awareness.</ns3:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Howard2024c,

title = {Bayesian estimation of the prevalence of antimicrobial resistance: a mathematical modelling study},

author = {Alex Howard and Peter L Green and Anoop Velluva and Alessandro Gerada and David M Hughes and Charlotte Brookfield and William Hope and Iain Buchan},

doi = {10.1093/jac/dkae230},

issn = {1460-2091},

year  = {2024},

date = {2024-09-03},

urldate = {2024-09-03},

volume = {79},

number = {9},

pages = {2317--2326},

publisher = {Oxford University Press (OUP)},

abstract = {<jats:title>Abstract</jats:title>

               <jats:sec>

                  <jats:title>Background</jats:title>

                  <jats:p>Estimates of the prevalence of antimicrobial resistance (AMR) underpin effective antimicrobial stewardship, infection prevention and control, and optimal deployment of antimicrobial agents. Typically, the prevalence of AMR is determined from real-world antimicrobial susceptibility data that are time delimited, sparse, and often biased, potentially resulting in harmful and wasteful decision-making. Frequentist methods are resource intensive because they rely on large datasets.</jats:p>

               </jats:sec>

               <jats:sec>

                  <jats:title>Objectives</jats:title>

                  <jats:p>To determine whether a Bayesian approach could present a more reliable and more resource-efficient way to estimate population prevalence of AMR than traditional frequentist methods.</jats:p>

               </jats:sec>

               <jats:sec>

                  <jats:title>Methods</jats:title>

                  <jats:p>Retrospectively collected, open-source, real-world pseudonymized healthcare data were used to develop a Bayesian approach for estimating the prevalence of AMR by combination with prior AMR information from a contextualized review of literature. Iterative random sampling and cross-validation were used to assess the predictive accuracy and potential resource efficiency of the Bayesian approach compared with a standard frequentist approach.</jats:p>

               </jats:sec>

               <jats:sec>

                  <jats:title>Results</jats:title>

                  <jats:p>Bayesian estimation of AMR prevalence made fewer extreme estimation errors than a frequentist estimation approach [n = 74 (6.4%) versus n = 136 (11.8%)] and required fewer observed antimicrobial susceptibility results per pathogen on average [mean = 28.8 (SD = 22.1) versus mean = 34.4 (SD = 30.1)] to avoid any extreme estimation errors in 50 iterations of the cross-validation. The Bayesian approach was maximally effective and efficient for drug–pathogen combinations where the actual prevalence of resistance was not close to 0% or 100%.</jats:p>

               </jats:sec>

               <jats:sec>

                  <jats:title>Conclusions</jats:title>

                  <jats:p>Bayesian estimation of the prevalence of AMR could provide a simple, resource-efficient approach to better inform population infection management where uncertainty about AMR prevalence is high.</jats:p>

               </jats:sec>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Anyaduba2024,

title = {Offsetting Dense Particle Sedimentation in Microfluidic Systems},

author = {Tochukwu Dubem Anyaduba and Jesus Rodriguez-Manzano},

doi = {10.3390/mi15091063},

issn = {2072-666X},

year  = {2024},

date = {2024-09-00},

urldate = {2024-09-00},

journal = {Micromachines},

volume = {15},

number = {9},

publisher = {MDPI AG},

abstract = {<jats:p>Sedimentation is an undesirable phenomenon that complicates the design of microsystems that exploit dense microparticles as delivery tools, especially in biotechnological applications. It often informs the integration of continuous mixing modules, consequently impacting the system footprint, cost, and complexity. The impact of sedimentation is significantly worse in systems designed with the intent of particle metering or binary encapsulation in droplets. Circumventing this problem involves the unsatisfactory adoption of gel microparticles as an alternative. This paper presents two solutions—a hydrodynamic solution that changes the particle sedimentation trajectory relative to a flow-rate dependent resultant force, and induced hindered settling (i-HS), which exploits Richardson–Zaki (RZ) corrections of Stokes’ law. The hydrodynamic solution was validated using a multi-well fluidic multiplexing and particle metering manifold. Computational image analysis of multiplex metering efficiency using this method showed an average reduction in well-to-well variation in particle concentration from 45% (Q = 1 mL/min, n = 32 total wells) to 17% (Q = 10 mL/min, n = 48 total wells). By exploiting a physical property (cloud point) of surfactants in the bead suspension in vials, the i-HS achieved a 58% reduction in the sedimentation rate. This effect results from the surfactant phase change, which increases the turbidity (transient increase in particle concentration), thereby exploiting the RZ theories. Both methods can be used independently or synergistically to eliminate bead settling in microsystems or to minimize particle sedimentation</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Pandey2024,

title = {A systematic review of antibiotic drug shortages and the strategies employed for managing these shortages},

author = {Avaneesh Kumar Pandey and Jennifer Cohn and Vrinda Nampoothiri and Uttara Gadde and Amrita Ghataure and Ashish Kumar Kakkar and Yogendra, Kumar Gupta and Samir Malhotra and Oluchi Mbamalu and Marc Mendelson and Anne-Grete Märtson and Sanjeev Singh and Thomas Tängdén and Nusrat Shafiq and Esmita Charani},

doi = {10.1016/j.cmi.2024.09.023},

issn = {1198-743X},

year  = {2024},

date = {2024-09-00},

urldate = {2024-09-00},

journal = {Clinical Microbiology and Infection},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Gerada2024c,

title = {AIgarMIC: a Python package for automated interpretationof agar dilution minimum inhibitory concentration assays},

author = {Alessandro Gerada and Nicholas Harper and Alex Howard and William Hope},

doi = {10.21105/joss.06826},

issn = {2475-9066},

year  = {2024},

date = {2024-09-00},

urldate = {2024-09-00},

journal = {JOSS},

volume = {9},

number = {101},

publisher = {The Open Journal},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Cohn2024d,

title = {Accelerating antibiotic access and stewardship: a new model to safeguard public health},

author = {Jennifer Cohn and Marc Mendelson and Souha S Kanj and Nusrat Shafiq and Icaro Boszczowski and Ramanan Laxminarayan},

doi = {10.1016/s1473-3099(24)00070-7},

issn = {1473-3099},

year  = {2024},

date = {2024-09-00},

urldate = {2024-09-00},

journal = {The Lancet Infectious Diseases},

volume = {24},

number = {9},

pages = {e584--e590},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Blank2024,

title = {Exploring real-world vancomycin target attainment in neonatal intensive care in the context of Staphylococcal infections: a retrospective observational cohort study},

author = {Michael Blank and Richard C. Wilson and Yu Wan and Joanna Peters and Frances Davies and Lidia Tyszczuk and Bruno Pichon and Alaa Riezk and Alicia Demirjian and Colin Stewart Brown and Mark Gilchrist and Alison H. Holmes and Timothy Miles Rawson},

doi = {10.1016/j.jinf.2024.106191},

issn = {0163-4453},

year  = {2024},

date = {2024-08-00},

urldate = {2024-08-00},

journal = {Journal of Infection},

volume = {89},

number = {2},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Charani2024,

title = {Power Relations in Optimisation of Therapies and Equity in Access to Antibiotics (PROTEA) Study: investigating the intersection of socio-economic and cultural drivers on antimicrobial resistance (AMR) and its influence on healthcare access and health-providing behaviours in India and South Africa},

author = {Esmita Charani and Sipho Dlamini and Anastasia Koch and Sanjeev Singh and Rebecca Hodes and Ramanan Laxminarayan and Deepshikha Batheja and Elelwani Ramugondo and Arunima Sehgal Mukherjee and Marc Mendelson},

doi = {10.12688/wellcomeopenres.20193.1},

issn = {2398-502X},

year  = {2024},

date = {2024-07-24},

urldate = {2024-07-24},

journal = {Wellcome Open Res},

volume = {9},

publisher = {F1000 Research Ltd},

abstract = {<ns5:p>Across social structures within society, including healthcare, power relations manifest according to gender, socioeconomic status, race, ethnicity, and class influencing infection related healthcare access and health providing-behaviours. Therefore, accounting for sociocultural drivers, including gender, race, and class, and their influence on economic status can improve healthcare access and health-providing behaviours in infection prevention and control (IPC) as well as antibiotic use, which in turn helps mitigate the spread of antimicrobial resistance (AMR). This Wellcome funded research will investigate how and why the social determinants of health and economic status influence how people seek, experience, and provide healthcare for suspected or proven (bacterial) infections and how these factors influence antibiotic prescribing and use in South Africa (upper middle-income country) and India (lower middle-income country). The aim of this body of work is to, (1) define and estimate the sociocultural and economic drivers for AMR in different resource settings, (2) design, implement and evaluate context-sensitive IPC and antimicrobial stewardship (AMS) interventions, and (3) inform policy and strategy for AMR mitigation. The population will be healthcare workers (HCWs), patients, and their carers across acute medical and surgical pathways where IPC and antibiotic-related healthcare access and health-providing behaviours will be studied. Qualitative methods will include ethnographic research, semi-structured in-depth interviews, and focus groups with healthcare providers, patients and carers. Quantitative analysis of bedside observational data from hospitals and population level data on antibiotic use will study the various predictors of AMR using bivariable and multivariable regression analyses. The research will provide high-quality evidence on how social determinants intersect with health, social well-being, and vulnerability in IPC practices and antibiotic use. Using this knowledge we will: 1) design, implement, and measure effects of interventions accounting for these factors; 2) provide a toolkit for advocacy for actors in AMR, and healthcare to assist them to promote dialogue, including policy dialogue on this issue. This work directly benefits the target population and informs healthcare services and practice across the participating countries with potential for wider translation. The setting will be hospitals in South Africa (middle-income country) and India (lower middle-income country). The population will be healthcare workers (HCWs), patients, and their carers across acute medical and surgical pathways where IPC and antibiotic-related health-seeking and health-providing behaviours will be studied. These populations represent communities most affected by infections and AMR because existing interventions do not address a) differences in how surgical versus medical teams manage infections; b) the role of the wider social network of individuals on their decision-making, c) intersection of the social determinants of health including race, gender, socioeconomic deprivation with AMR.</ns5:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Reza2024b,

title = {Challenges for global antibiotic regimen planning and establishing antimicrobial resistance targets: implications for the WHO Essential Medicines List and AWaRe antibiotic book dosing},

author = {Nada Reza and Alessandro Gerada and Katharine E. Stott and Alex Howard and Mike Sharland and William Hope},

editor = {Graeme N. Forrest},

doi = {10.1128/cmr.00139-23},

issn = {1098-6618},

year  = {2024},

date = {2024-06-13},

urldate = {2024-06-13},

journal = {Clin Microbiol Rev},

volume = {37},

number = {2},

publisher = {American Society for Microbiology},

abstract = {<jats:title>SUMMARY</jats:title>

          <jats:p>

            The World Health Organisation’s 2022 AWaRe Book provides guidance for the use of 39 antibiotics to treat 35 infections in primary healthcare and hospital facilities. We review the evidence underpinning suggested dosing regimens. Few (

            <jats:italic>n</jats:italic>

            = 18) population pharmacokinetic studies exist for key oral AWaRe antibiotics, largely conducted in homogenous and unrepresentative populations hindering robust estimates of drug exposures. Databases of minimum inhibitory concentration distributions are limited, especially for community pathogen-antibiotic combinations. Minimum inhibitory concentration data sources are not routinely reported and lack regional diversity and community representation. Of studies defining a pharmacodynamic target for ß-lactams (

            <jats:italic>n</jats:italic>

            = 80), 42 (52.5%) differed from traditionally accepted 30%–50% time above minimum inhibitory concentration targets. Heterogeneity in model systems and pharmacodynamic endpoints is common, and models generally use intravenous ß-lactams. One-size-fits-all pharmacodynamic targets are used for regimen planning despite complexity in drug-pathogen-disease combinations. We present solutions to enable the development of global evidence-based antibiotic dosing guidance that provides adequate treatment in the context of the increasing prevalence of antimicrobial resistance and, moreover, minimizes the emergence of resistance.

          </jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Okeke2024d,

title = {The scope of the antimicrobial resistance challenge},

author = {Iruka N Okeke and Marlieke E A de Kraker and Thomas P Van Boeckel and Chirag K Kumar and Heike Schmitt and Ana C Gales and Silvia Bertagnolio and Mike Sharland and Ramanan Laxminarayan},

doi = {10.1016/s0140-6736(24)00876-6},

issn = {0140-6736},

year  = {2024},

date = {2024-06-00},

urldate = {2024-06-00},

journal = {The Lancet},

volume = {403},

number = {10442},

pages = {2426--2438},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Lewnard2024d,

title = {Burden of bacterial antimicrobial resistance in low-income and middle-income countries avertible by existing interventions: an evidence review and modelling analysis},

author = {Joseph A Lewnard and Esmita Charani and Alec Gleason and Li Yang Hsu and Wasif Ali Khan and Abhilasha Karkey and Clare I R Chandler and Tapfumanei Mashe and Ejaz Ahmed Khan and Andre N H Bulabula and Pilar Donado-Godoy and Ramanan Laxminarayan},

doi = {10.1016/s0140-6736(24)00862-6},

issn = {0140-6736},

year  = {2024},

date = {2024-06-00},

urldate = {2024-06-00},

journal = {The Lancet},

volume = {403},

number = {10442},

pages = {2439--2454},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Mendelson2024f,

title = {Ensuring progress on sustainable access to effective antibiotics at the 2024 UN General Assembly: a target-based approach},

author = {Marc Mendelson and Joseph A Lewnard and Mike Sharland and Aislinn Cook and Koen B Pouwels and Yewande Alimi and Mirfin Mpundu and Evelyn Wesangula and Jeffrey Scott Weese and John-Arne Røttingen and Ramanan Laxminarayan},

doi = {10.1016/s0140-6736(24)01019-5},

issn = {0140-6736},

year  = {2024},

date = {2024-06-00},

urldate = {2024-06-00},

journal = {The Lancet},

volume = {403},

number = {10443},

pages = {2551--2564},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Nampoothiri2024h,

title = {Pharmacist roles in antimicrobial stewardship: a qualitative study from India, South Africa and the United Kingdom},

author = {Vrinda Nampoothiri and Oluchi Mbamalu and Marc Mendelson and Sanjeev Singh and Esmita Charani},

doi = {10.1093/jacamr/dlae047},

issn = {2632-1823},

year  = {2024},

date = {2024-05-06},

urldate = {2024-05-06},

volume = {6},

number = {3},

publisher = {Oxford University Press (OUP)},

abstract = {<jats:title>Abstract</jats:title>

               <jats:sec>

                  <jats:title>Objective</jats:title>

                  <jats:p>To explore pharmacist roles in antimicrobial stewardship (AMS) in India, South Africa (SA), United Kingdom (UK) and the factors that contribute to their participation in the programme in these countries.</jats:p>

               </jats:sec>

               <jats:sec>

                  <jats:title>Methods</jats:title>

                  <jats:p>Data were collected between April 2019 and March 2022 through semi-structured interviews with key AMS stakeholders from India (Kerala); SA (Western Cape province) and the UK (England). Interviews were conducted face to face or via Zoom and Skype platforms, audio recordings were transcribed verbatim and thematically analysed using a grounded theory approach aided by NVivo 12 software.</jats:p>

               </jats:sec>

               <jats:sec>

                  <jats:title>Results</jats:title>

                  <jats:p>We interviewed 38 key AMS stakeholders (pharmacists and doctors). India and the UK have dedicated AMS pharmacists (Doctor of Pharmacy and Master of Pharmacy graduates with opportunities for additional post-graduate qualifications respectively). Pharmacists in the UK lead AMS programmes, while in India, predominantly in the private sector, pharmacists drive AMS in collaboration with clinicians. In SA, pharmacists (Bachelor of Pharmacy graduates) participate in AMS out of their own commitment in addition to their pharmacy responsibilities. Private sector pharmacists drive AMS while public sector pharmacists participate in clinician-led AMS programmes. Current pharmacy curricula do not provide adequate training in AMS, and this limitation shapes pharmacist roles and acceptance in AMS among clinicians in India and SA. Support of mentors (doctors/senior pharmacists) and self-motivated learning are key factors for effective pharmacist involvement in AMS.</jats:p>

               </jats:sec>

               <jats:sec>

                  <jats:title>Conclusions</jats:title>

                  <jats:p>A contextually developed, standardized and accessible AMS training programme along with pharmacy curricula modification to include AMS, may facilitate prominent pharmacist roles in AMS.</jats:p>

               </jats:sec>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Gerada2024b,

title = {Determination of minimum inhibitory concentrations using machine-learning-assisted agar dilution},

author = {Alessandro Gerada and Nicholas Harper and Alex Howard and Nada Reza and William Hope},

editor = {Kileen L. Shier},

doi = {10.1128/spectrum.04209-23},

issn = {2165-0497},

year  = {2024},

date = {2024-05-02},

urldate = {2024-05-02},

journal = {Microbiol Spectr},

volume = {12},

number = {5},

publisher = {American Society for Microbiology},

abstract = {<jats:title>ABSTRACT</jats:title>

          <jats:sec>

            <jats:title/>

            <jats:p>

              Effective policy to address the global threat of antimicrobial resistance requires robust antimicrobial susceptibility data. Traditional methods for measuring minimum inhibitory concentration (MIC) are resource intensive, subject to human error, and require considerable infrastructure. AIgarMIC streamlines and standardizes MIC measurement and is especially valuable for large-scale surveillance activities. MICs were measured using agar dilution for

              <jats:italic>n</jats:italic>

              = 10 antibiotics against clinical Enterobacterales isolates (

              <jats:italic>n</jats:italic>

              = 1,086) obtained from a large tertiary hospital microbiology laboratory.

              <jats:italic>Escherichia coli</jats:italic>

              (

              <jats:italic>n</jats:italic>

              = 827, 76%) was the most common organism. Photographs of agar plates were divided into smaller images covering one inoculation site. A labeled data set of colony images was created and used to train a convolutional neural network to classify images based on whether a bacterial colony was present (first-step model). If growth was present, a second-step model determined whether colony morphology suggested antimicrobial growth inhibition. The ability of the AI to determine MIC was then compared with standard visual determination. The first-step model classified bacterial growth as present/absent with 94.3% accuracy. The second-step model classified colonies as “inhibited” or “good growth” with 88.6% accuracy. For the determination of MIC, the rate of essential agreement was 98.9% (644/651), with a bias of −7.8%, compared with manual annotation. AIgarMIC uses artificial intelligence to automate endpoint assessments for agar dilution and potentially increases throughput without bespoke equipment. AIgarMIC reduces laboratory barriers to generating high-quality MIC data that can be used for large-scale surveillance programs.

            </jats:p>

          </jats:sec>

          <jats:sec>

            <jats:title>IMPORTANCE</jats:title>

            <jats:p>This research uses modern artificial intelligence and machine-learning approaches to standardize and automate the interpretation of agar dilution minimum inhibitory concentration testing. Artificial intelligence is currently of significant topical interest to researchers and clinicians. In our manuscript, we demonstrate a use-case in the microbiology laboratory and present validation data for the model’s performance against manual interpretation.</jats:p>

          </jats:sec>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2024e,

title = {Why We Need to Change How We Talk About Infectious Disease},

doi = {10.1001/amajethics.2024.390},

issn = {2376-6980},

year  = {2024},

date = {2024-05-01},

urldate = {2024-05-01},

volume = {26},

number = {5},

pages = {E390--398},

publisher = {American Medical Association (AMA)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Abel2024,

title = {System-wide approaches to antimicrobial therapy and antimicrobial resistance in the UK: the AMR-X framework},

author = {Kathryn Abel and Emily Agnew and James Amos and Natalie Armstrong and Darius Armstrong-James and Thomas Ashfield and Stephen Aston and J Kenneth Baillie and Steven Baldwin and Gavin Barlow and Victoria Bartle and Julia Bielicki and Colin Brown and Enitan Carrol and Michelle Clements and Graham Cooke and Aaron Dane and Paul Dark and Jeremy Day and Anthony de-Soyza and Andrew Dowsey and Stephanie Evans and David Eyre and Timothy Felton and Tom Fowler and Robbie Foy and Karen Gannon and Alessandro Gerada and Anna Goodman and Tracy Harman and Gail Hayward and Alison Holmes and Susan Hopkins and Philip Howard and Alexander Howard and Yingfen Hsia and Gwen Knight and Nick Lemoine and James Koh and Alasdair Macgowan and Charis Marwick and Catrin Moore and Seamus O’Brien and Raymond Oppong and Sharon Peacock and Sarah Pett and Koen Pouwels and Chris Queree and Najib Rahman and Mark Sculpher and Laura Shallcross and Michael Sharland and Jasvinder Singh and Karen Stoddart and Emma Thomas-Jones and Andrew Townsend and Andrew Ustianowski and Tjeerd Van Staa and Sarah Walker and Peter White and Paul Wilson and Iain Buchan and Beth Woods and Peter Bower and Martin Llewelyn and William Hope},

doi = {10.1016/s2666-5247(24)00003-x},

issn = {2666-5247},

year  = {2024},

date = {2024-05-00},

urldate = {2024-05-00},

journal = {The Lancet Microbe},

volume = {5},

number = {5},

pages = {e500--e507},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Nampoothiri2024g,

title = {Current state of education, training and practices in antimicrobial stewardship among pharmacy students: A cross-sectional survey from Kerala, India},

author = {Vrinda Nampoothiri and Esmita Charani and Sanjeev Singh},

doi = {10.1016/j.ijmmb.2024.100607},

issn = {0255-0857},

year  = {2024},

date = {2024-05-00},

urldate = {2024-05-00},

journal = {Indian Journal of Medical Microbiology},

volume = {49},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Mayito2024,

title = {Characterization of Antibiotic Resistance in Select Tertiary Hospitals in Uganda: An Evaluation of 2020 to 2023 Routine Surveillance Data},

author = {Jonathan Mayito and Daniel Kibombo and Charles Olaro and Susan Nabadda and Consolata Guma and Immaculate Nabukenya and Andrew Busuge and Flavia Dhikusooka and Alex Andema and Peter Mukobi and Nathan Onyachi and Ben Watmon and Stephen Obbo and Alfred Yayi and James Elima and Celestine Barigye and Filbert J. Nyeko and Ibrahim Mugerwa and Musa Sekamatte and Joel Bazira and Richard Walwema and Mohammed Lamorde and Francis Kakooza and Henry Kajumbula},

doi = {10.3390/tropicalmed9040077},

issn = {2414-6366},

year  = {2024},

date = {2024-04-00},

urldate = {2024-04-00},

journal = {TropicalMed},

volume = {9},

number = {4},

publisher = {MDPI AG},

abstract = {<jats:p>Antimicrobial resistance (AMR) is a public health concern in Uganda. We sought to conduct an extended profiling of AMR burden at selected Ugandan tertiary hospitals. We analyzed routine surveillance data collected between October 2020 and March 2023 from 10 tertiary hospitals. The analysis was stratified according to the hospital unit, age, gender, specimen type, and time. Up to 2754 isolates were recovered, primarily from pus: 1443 (52.4%); urine: 1035 (37.6%); and blood: 245 (8.9%). Most pathogens were Staphylococcus aureus, 1020 (37%), Escherichia coli, 808 (29.3%), and Klebsiella spp., 200 (7.3%). Only 28% of Escherichia coli and 42% of the other Enterobacterales were susceptible to ceftriaxone, while only 44% of Staphylococcus aureus were susceptible to methicillin (56% were MRSA). Enterococcus spp. susceptibility to vancomycin was 72%. The 5–24-year-old had 8% lower ampicillin susceptibility than the >65-year-old, while the 25–44-year-old had 8% lower ciprofloxacin susceptibility than the >65-year-old. The 0–4-year-old had 8% higher ciprofloxacin susceptibility. Only erythromycin susceptibility varied by sex, being higher in males. Escherichia coli ciprofloxacin susceptibility in blood (57%) was higher than in urine (39%) or pus (28%), as was ceftriaxone susceptibility in blood (44%) versus urine (34%) or pus (14%). Klebsiella spp. susceptibility to ciprofloxacin and meropenem decreased by 55% and 47%, respectively, during the evaluation period. During the same period, Escherichia coli ciprofloxacin susceptibility decreased by 40%, while Staphylococcus aureus gentamicin susceptibility decreased by 37%. Resistance was high across the Access and Watch antibiotic categories, varying with time, age, sex, specimen type, and hospital unit. Effective antimicrobial stewardship targeted at the critical AMR drivers is urgently needed.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Mendelson2024,

title = {Antimicrobial resistance and the great divide: inequity in priorities and agendas between the Global North and the Global South threatens global mitigation of antimicrobial resistance},

author = {Marc Mendelson and Ramanan Laxminarayan and Direk Limmathurotsakul and Samuel Kariuki and Martha Gyansa-Lutterodt and Esmita Charani and Sanjeev Singh and Kamini Walia and Ana C Gales and Mirfin Mpundu},

doi = {10.1016/s2214-109x(23)00554-5},

issn = {2214-109X},

year  = {2024},

date = {2024-03-00},

urldate = {2024-03-00},

journal = {The Lancet Global Health},

volume = {12},

number = {3},

pages = {e516--e521},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Bonaconsa2024g,

title = {Optimizing infection control and antimicrobial stewardship bedside discussion: a scoping review of existing evidence on effective healthcare communication in hospitals},

author = {Candice Bonaconsa and Oluchi Mbamalu and Surya Surendran and Anu George and Marc Mendelson and Esmita Charani},

doi = {10.1016/j.cmi.2023.12.011},

issn = {1198-743X},

year  = {2024},

date = {2024-03-00},

urldate = {2024-03-00},

journal = {Clinical Microbiology and Infection},

volume = {30},

number = {3},

pages = {336--352},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Johnson2024,

title = {A model-based approach to estimating the prevalence of disease combinations in South Africa},

author = {Leigh F Johnson and Reshma Kassanjee and Naomi Folb and Sarah Bennett and Andrew Boulle and Naomi S Levitt and Robyn Curran and Kirsty Bobrow and Rifqah A Roomaney and Max O Bachmann and Lara R Fairall},

doi = {10.1136/bmjgh-2023-013376},

issn = {2059-7908},

year  = {2024},

date = {2024-02-00},

urldate = {2024-02-00},

journal = {BMJ Glob Health},

volume = {9},

number = {2},

publisher = {BMJ},

abstract = {<jats:sec><jats:title>Background</jats:title><jats:p>The development of strategies to better detect and manage patients with multiple long-term conditions requires estimates of the most prevalent condition combinations. However, standard meta-analysis tools are not well suited to synthesising heterogeneous multimorbidity data.</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>We developed a statistical model to synthesise data on associations between diseases and nationally representative prevalence estimates and applied the model to South Africa. Published and unpublished data were reviewed, and meta-regression analysis was conducted to assess pairwise associations between 10 conditions: arthritis, asthma, chronic obstructive pulmonary disease (COPD), depression, diabetes, HIV, hypertension, ischaemic heart disease (IHD), stroke and tuberculosis. The national prevalence of each condition in individuals aged 15 and older was then independently estimated, and these estimates were integrated with the ORs from the meta-regressions in a statistical model, to estimate the national prevalence of each condition combination.</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>The strongest disease associations in South Africa are between COPD and asthma (OR 14.6, 95% CI 10.3 to 19.9), COPD and IHD (OR 9.2, 95% CI 8.3 to 10.2) and IHD and stroke (OR 7.2, 95% CI 5.9 to 8.4). The most prevalent condition combinations in individuals aged 15+ are hypertension and arthritis (7.6%, 95% CI 5.8% to 9.5%), hypertension and diabetes (7.5%, 95% CI 6.4% to 8.6%) and hypertension and HIV (4.8%, 95% CI 3.3% to 6.6%). The average numbers of comorbidities are greatest in the case of COPD (2.3, 95% CI 2.1 to 2.6), stroke (2.1, 95% CI 1.8 to 2.4) and IHD (1.9, 95% CI 1.6 to 2.2).</jats:p></jats:sec><jats:sec><jats:title>Conclusion</jats:title><jats:p>South Africa has high levels of HIV, hypertension, diabetes and arthritis, by international standards, and these are reflected in the most prevalent condition combinations. However, less prevalent conditions such as COPD, stroke and IHD contribute disproportionately to the multimorbidity burden, with high rates of comorbidity. This modelling approach can be used in other settings to characterise the most important disease combinations and levels of comorbidity.</jats:p></jats:sec>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Riezk2024,

title = {A low-volume LC/MS method for highly sensitive monitoring of phenoxymethylpenicillin, benzylpenicillin, and probenecid in human serum},

author = {Alaa Riezk and Richard C. Wilson and Anthony E. G. Cass and Alison H. Holmes and Timothy M. Rawson},

doi = {10.1039/d3ay01816d},

issn = {1759-9679},

year  = {2024},

date = {2024-01-25},

urldate = {2024-01-25},

journal = {Anal. Methods},

volume = {16},

number = {4},

pages = {558--565},

publisher = {Royal Society of Chemistry (RSC)},

abstract = {<jats:p>Fast and highly sensitive analysis of phenoxymethylpenicillin, benzylpenicillin and probenecid in human serum using a triple quadrupole LC/MS method for therapeutic drug monitoring.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{10.12688/wellcomeopenres.22923.1,

title = {Systems Policy Analysis for Antimicrobial Resistance Targeted Action (SPAARTA): A Research Protocol [version 1; peer review: awaiting peer review]},

author = {R Ahmad and N Zhu and R Jain and J Joshi and M Mpundu and PA Gutierrez and A Holmes and T Weyde and R Atun},

doi = {10.12688/wellcomeopenres.22923.1},

year  = {2024},

date = {2024-01-01},

urldate = {2024-01-01},

journal = {Wellcome Open Research},

volume = {9},

number = {700},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{doi:10.1021/acs.analchem.4c00319,

title = {Rapid, Portable, and Electricity-free Sample Extraction Method for Enhanced Molecular Diagnostics in Resource-Limited Settings},

author = {Ivana Pennisi and Matthew L. Cavuto and Luca Miglietta and Kenny Malpartida-Cardenas and Oliver W. Stringer and Katerina-Theresa Mantikas and Ruth Reid and Rebecca Frise and Nicolas Moser and Paul Randell and Frances Davies and Frances Bolt and Wendy Barclay and Alison Holmes and Pantelis Georgiou and Jesus Rodriguez-Manzano},

url = {https://doi.org/10.1021/acs.analchem.4c00319},

doi = {10.1021/acs.analchem.4c00319},

year  = {2024},

date = {2024-01-01},

urldate = {2024-01-01},

journal = {Analytical Chemistry},

volume = {96},

number = {28},

pages = {11181-11188},

note = {PMID: 38967089},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{MENDELSON20242551,

title = {Ensuring progress on sustainable access to effective antibiotics at the 2024 UN General Assembly: a target-based approach},

author = {Marc Mendelson and Joseph A Lewnard and Mike Sharland and Aislinn Cook and Koen B Pouwels and Yewande Alimi and Mirfin Mpundu and Evelyn Wesangula and Jeffrey Scott Weese and John-Arne Røttingen and Ramanan Laxminarayan},

url = {https://www.sciencedirect.com/science/article/pii/S0140673624010195},

doi = {https://doi.org/10.1016/S0140-6736(24)01019-5},

issn = {0140-6736},

year  = {2024},

date = {2024-01-01},

urldate = {2024-01-01},

journal = {The Lancet},

volume = {403},

number = {10443},

pages = {2551-2564},

abstract = {Summary 

Rising antimicrobial resistance (AMR) is a global health crisis for countries of all economic levels, alongside the broader challenge of access to antibiotics. As a result, development goals for child survival, healthy ageing, poverty reduction, and food security are at risk. Preserving antimicrobial effectiveness, a global public good, requires political will, targets, accountability frameworks, and funding. The upcoming second high-level meeting on AMR at the UN General Assembly (UNGA) in September, 2024, is evidence of political interest in addressing the problem of AMR, but action on targets, accountability, and funding, absent from the 2016 UNGA resolution, is needed. We propose ambitious yet achievable global targets for 2030 (relative to a prepandemic 2019 baseline): a 10% reduction in mortality from AMR; a 20% reduction in inappropriate human antibiotic use; and a 30% reduction in inappropriate animal antibiotic use. Given national variation in current levels of antibiotic use, these goals (termed the 10–20–30 by 2030) should be met within a framework of universal access to effective antibiotics. The WHO Access, Watch, Reserve (AWARE) system can be used to define, monitor, and evaluate appropriate levels of antibiotic use and access. Some countries should increase access to narrow-spectrum, safe, and affordable (Access) antibiotics, whereas others should discourage the inappropriate use of broader-spectrum (Watch) and last-resort (Reserve) antibiotics; AWARE targets should use a risk-based, burden-adjusted approach. Improved infection prevention and control, access to clean water and sanitation, and vaccination coverage can offset the selection effects of increased antibiotic use in low-income settings. To ensure accountability and global scientific guidance and consensus, we call for the establishment of the Independent Panel on Antimicrobial Access and Resistance and the support of leaders from low-income and middle-income countries.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Shah2024,

title = {Antimicrobial stewardship and targeted therapies in the changing landscape of maternal sepsis},

author = {Nishel M Shah and Esmita Charani and Damien Ming and Fook-Choe Cheah and Mark R Johnson},

doi = {10.1016/j.jointm.2023.07.006},

issn = {2667-100X},

year  = {2024},

date = {2024-01-00},

urldate = {2024-01-00},

journal = {Journal of Intensive Medicine},

volume = {4},

number = {1},

pages = {46--61},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Howard2024b,

title = {Antimicrobial learning systems: an implementation blueprint for artificial intelligence to tackle antimicrobial resistance},

author = {Alex Howard and Stephen Aston and Alessandro Gerada and Nada Reza and Jason Bincalar and Henry Mwandumba and Tom Butterworth and William Hope and Iain Buchan},

doi = {10.1016/s2589-7500(23)00221-2},

issn = {2589-7500},

year  = {2024},

date = {2024-01-00},

urldate = {2024-01-00},

journal = {The Lancet Digital Health},

volume = {6},

number = {1},

pages = {e79--e86},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Bonaconsa2024f,

title = {Mentorship as an overlooked dimension of research capacity strengthening: how to embed value-driven practices in global health},

author = {Candice Bonaconsa and Vrinda Nampoothiri and Oluchi Mbamalu and Sipho Dlamini and Surya Surendran and Sanjeev K Singh and Raheelah Ahmad and Alison Holmes and Muneera A Rasheed and Marc Mendelson and Esmita Charani},

doi = {10.1136/bmjgh-2023-014394},

issn = {2059-7908},

year  = {2024},

date = {2024-01-00},

urldate = {2024-01-00},

journal = {BMJ Glob Health},

volume = {9},

number = {1},

publisher = {BMJ},

abstract = {<jats:p>Mentorship in global health remains an overlooked dimension of research partnerships. Commitment to effective mentorship models requires value-driven approaches. This includes having an understanding of (1) what mentorship means across different cultural and hierarchical boundaries in the health research environment, and (2) addressing entrenched power asymmetries across different aspects including funding, leadership, data and outputs, and capacity strengthening. Existing guidance towards equity and sustainability fails to inform how to navigate complex relationships which hinder effective mentorship models. We focus this perspective piece on human capacity strengthening in research partnerships through mentorship. Using a case study of a research partnership, we describe the lessons learnt and the challenges faced in the mentor mentee relationship while maintaining an effective and sustainable partnership. Human capacity strengthening must research projects and collaborations, and recognise local leadership and ownership. To be transformative and effective, practices need to be driven by common values across research teams.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Birgand2024b,

title = {Role of anaesthesia providers in infection-related care across the perioperative pathway: a global survey},

author = {Gabriel Birgand and Bruce Biccard and Antoine Deslandes and Oluchi Mbamalu and Candice Bonaconsa and Adam Boutall and Marc Mendelson and Marc Leone and Jules Ndoli and Andrew Leather and Alison Holmes and Ramani Moonesinghe and Esmita Charani},

doi = {10.1016/j.bja.2023.10.023},

issn = {0007-0912},

year  = {2024},

date = {2024-01-00},

urldate = {2024-01-00},

journal = {British Journal of Anaesthesia},

volume = {132},

number = {1},

pages = {197--200},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Surendran2024d,

title = {Visual Mapping of Operating Theater Team Dynamics and Communication for Reflexive Feedback and Surgical Practice Optimization},

author = {Surya Surendran and Candice Bonaconsa and Vrinda Nampoothiri and Oluchi Mbamalu and Anu George and Swetha Mallick and Sudheer OV and Alison Holmes and Marc Mendelson and Sanjeev Singh and Gabriel Birgand and Esmita Charani},

doi = {10.1097/as9.0000000000000463},

issn = {2691-3593},

year  = {2024},

date = {2024-00-00},

urldate = {2024-00-00},

volume = {5},

number = {3},

publisher = {Ovid Technologies (Wolters Kluwer Health)},

abstract = {<jats:sec>

            <jats:title>Background:</jats:title>

            <jats:p>Effective operating theater (OT) communication and teamwork are essential to optimal surgical outcomes. We mapped the OT team dynamics and infection control practices using visual methods to guide reflexive feedback and optimize perioperative practices.</jats:p>

          </jats:sec>

          <jats:sec>

            <jats:title>Methods:</jats:title>

            <jats:p>Data were gathered from adult gastrointestinal surgical teams at a tertiary hospital in India using observations, sociograms (communication mapping tool), and focus group discussions (FGDs). Our methods aimed to map team communication, roles and responsibilities in infection-related practices, and door openings. Qualitative data were thematically analyzed. Quantitative data were analyzed using descriptive statistics.</jats:p>

          </jats:sec>

          <jats:sec>

            <jats:title>Results:</jats:title>

            <jats:p>Data were gathered from 10 surgical procedures (over 51 hours) using 16 sociograms, 15 traffic flow maps, and 3 FGDs. Senior surgeons directly influence team hierarchies, dynamics, and communication. While the surgeons, anesthetic residents, and technicians lead most tasks during procedures, the scrub nurse acts as a mediator coordinating activity among role players across hierarchies. Failing to provide the scrub nurse with complete details of the planned surgery leads to multiple door openings to fetch equipment and disposables. Traffic flow observed in 15-minute intervals corresponds to a mean frequency of 56 door openings per hour (min: 16; max: 108), with implications for infection control. Implementing the World Health Organization surgical safety checklist was inconsistent across pathways and does not match reported compliance data.</jats:p>

          </jats:sec>

          <jats:sec>

            <jats:title>Conclusions:</jats:title>

            <jats:p>Human factors research is important in optimizing surgical teamwork. Using visual methods to provide feedback to perioperative teams on their communication patterns and behaviors, provided an opportunity for contextualized enhancement of infection prevention and control practices.</jats:p>

          </jats:sec>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{LeFevre2023,

title = {Preferences for onward health data use in the electronic age among maternity patients and providers in South Africa: a qualitative study},

author = {Amnesty LeFevre and Olivia Welte and Kearabetswe Moopelo and Nicki Tiffin and Gaolatlhe Mothoagae and Nobukhosi Ncube and Nasiphi Gwiji and Manape Shogole and Amy L. Slogrove and Nomakhawuta Moshani and Andrew Boulle and Jane Goudge and Frances Griffiths and Lee Fairlie and Ushma Mehta and Kerry Scott and Nirvana Pillay},

doi = {10.1080/26410397.2023.2274667},

issn = {2641-0397},

year  = {2023},

date = {2023-12-00},

urldate = {2023-12-00},

journal = {Sexual and Reproductive Health Matters},

volume = {31},

number = {4},

publisher = {Informa UK Limited},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Levin2023b,

title = {Launch of the São Paulo Wellcome Trust-funded multidisciplinary research program on optimising antimicrobial use in highly populated urban environments},

author = {Anna S. Levin and Silvia F. Costa and Maria Tereza P. Razzolini and Maria Clara Padoveze and Fatima L.S. Nunes and Maura S. Oliveira and Maristela P. Freire and Bruno M. Tavares and Denise B. Assis and Vitor F. de Oliveira and Fabio E. Leal and Marta A. Marcondes and Milena Dropa and Mônica T.R.P. Conde and Marcio K. Oikawa and João E. Ferreira and Ester Sabino and Erika R. Manuli and Sueli F. Raymundo},

doi = {10.1016/j.lana.2023.100574},

issn = {2667-193X},

year  = {2023},

date = {2023-09-00},

urldate = {2023-09-00},

journal = {The Lancet Regional Health - Americas},

volume = {25},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Walia2023,

title = {How can lessons from the COVID-19 pandemic enhance antimicrobial resistance surveillance and stewardship?},

author = {Kamini Walia and Marc Mendelson and Gagandeep Kang and Ramasubramanian Venkatasubramanian and Rina Sinha and Sonam Vijay and Balaji Veeraraghavan and Buddha Basnyat and Camilla Rodrigues and Nitin Bansal and Pallab Ray and Purva Mathur and Ram Gopalakrishnan and Vinod C Ohri},

doi = {10.1016/s1473-3099(23)00124-x},

issn = {1473-3099},

year  = {2023},

date = {2023-08-00},

urldate = {2023-08-00},

journal = {The Lancet Infectious Diseases},

volume = {23},

number = {8},

pages = {e301--e309},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Howard2023,

title = {Antimicrobial treatment imprecision: an outcome-based model to close the data-to-action loop},

author = {Alex Howard and Nada Reza and Stephen Aston and Beth Woods and Alessandro Gerada and Iain Buchan and William Hope and Anne-Grete Märtson},

doi = {10.1016/s1473-3099(23)00367-5},

issn = {1473-3099},

year  = {2023},

date = {2023-08-00},

urldate = {2023-08-00},

journal = {The Lancet Infectious Diseases},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Mbamalu2023c,

title = {A survey of patient and public perceptions and awareness of SARS-CoV-2-related risks among participants in India and South Africa},

author = {Oluchi Mbamalu and Surya Surendran and Vrinda Nampoothiri and Candice Bonaconsa and Fabia Edathadathil and Nina Zhu and Vanessa Carter and Helen Lambert and Carolyn Tarrant and Raheelah Ahmad and Adrian Brink and Ebrahim Steenkamp and Alison Holmes and Sanjeev Singh and Esmita Charani and Marc Mendelson},

editor = {Abram L. Wagner},

doi = {10.1371/journal.pgph.0001078},

issn = {2767-3375},

year  = {2023},

date = {2023-07-10},

urldate = {2023-07-10},

journal = {PLOS Glob Public Health},

volume = {3},

number = {7},

publisher = {Public Library of Science (PLoS)},

abstract = {<jats:p>A cross-sectional survey among participants in India and South Africa to explore perceptions and awareness of SARS-CoV-2-related risks. Main outcome measures–proportion of participants aware of SARS-CoV-2, and their perception of infection risks as it related to their views and perceptions on vaccination, i.e., using COVID-19 vaccine uptake as proxy for awareness level. Self-administered questionnaires were used to collect data via web- and paper-based surveys over three months. Pearson’s Chi-squared test assessed relationships between variables; a p-value less than 0.05 was considered significant. There were 844 respondents (India: n = 660, South Africa: n = 184; response rate 87.6%), with a 61.1% vs 38.3% female to male ratio. Post-high-school or university education was the lowest qualification reported by most respondents in India (77.3%) and South Africa (79.3%). Sources of pandemic information were usually media and journal publications (73.2%), social media (64.6%), family and friends (47.7%) and government websites (46.2%). Most respondents correctly identified infection prevention measures (such as physical distancing, mask use), with 90.0% reporting improved hand hygiene practices since the pandemic. Hesitancy or refusal to accept the SARS-CoV-2 vaccine was reported among 17.9% and 50.9% of respondents in India and South Africa, respectively; reasons cited included rushed vaccine development and the futility of vaccines for what respondents considered a self-limiting flu-like illness. In South Africa, vaccine acceptance was associated with improved hand hygiene practices since the pandemic and flu vaccination in the preceding year. No relationship was noted between awareness and practice of infection prevention measures (such as hand hygiene) and socio-demographic factors such as employment status or availability of amenities. Pandemic response and infection prevention and control measures through vaccination campaigns should consider robust public engagement and contextually-fit communication strategies with multimodal, participatory online and offline initiatives to address public concerns, specifically towards vaccines developed for this pandemic and general vaccine hesitancy.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Charani2023,

title = {An analysis of existing national action plans for antimicrobial resistance—gaps and opportunities in strategies optimising antibiotic use in human populations},

author = {Esmita Charani and Marc Mendelson and Scott J C Pallett and Raheelah Ahmad and Mirfin Mpundu and Oluchi Mbamalu and Candice Bonaconsa and Vrinda Nampoothiri and Sanjeev Singh and Nathan Peiffer-Smadja and Vanesa Anton-Vazquez and Luke S P Moore and Jeroen Schouten and Tomislav Kostyanev and Vera Vlahović-Palčevski and Diamantis Kofteridis and Juliana Silva Corrêa and Alison H Holmes},

doi = {10.1016/s2214-109x(23)00019-0},

issn = {2214-109X},

year  = {2023},

date = {2023-03-00},

urldate = {2023-03-00},

journal = {The Lancet Global Health},

volume = {11},

number = {3},

pages = {e466--e474},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Mbamalu2023,

title = {Survey of healthcare worker perceptions of changes in infection control and antimicrobial stewardship practices in India and South Africa during the COVID-19 pandemic},

author = {Oluchi Mbamalu and Surya Surendran and Vrinda Nampoothiri and Candice Bonaconsa and Fabia Edathadathil and Nina Zhu and Helen Lambert and Carolyn Tarrant and Raheelah Ahmad and Adam Boutall and Adrian Brink and Ebrahim Steenkamp and Alison Holmes and Sanjeev Singh and Esmita Charani and Marc Mendelson},

doi = {10.1016/j.ijregi.2022.11.010},

issn = {2772-7076},

year  = {2023},

date = {2023-03-00},

urldate = {2023-03-00},

journal = {IJID Regions},

volume = {6},

pages = {90--98},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Riezk2023,

title = {A rapid, simple, high-performance liquid chromatography method for the clinical measurement of beta-lactam antibiotics in serum and interstitial fluid},

author = {Alaa Riezk and Richard C. Wilson and Timothy M. Rawson and Vasin Vasikasin and Paul Arkel and Trevor J. Ferris and Lisa D. Haigh and Anthony E. G. Cass and Alison H. Holmes},

doi = {10.1039/d2ay01276f},

issn = {1759-9679},

year  = {2023},

date = {2023-02-09},

urldate = {2023-02-09},

journal = {Anal. Methods},

volume = {15},

number = {6},

pages = {829--836},

publisher = {Royal Society of Chemistry (RSC)},

abstract = {<jats:p>A LC/MS method for the simultaneous quantitative measurement of three beta-lactam antibiotics in serum and interstitial fluid samples.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Riezk2023b,

title = {Triple quadrupole LC/MS method for the simultaneous quantitative measurement of cefiderocol and meropenem in serum},

author = {Alaa Riezk and Vasin Vasikasin and Richard C. Wilson and Timothy M. Rawson and James G. McLeod and Rishi Dhillon and Jamie Duckers and Anthony E. G. Cass and Alison H. Holmes},

doi = {10.1039/d2ay01459a},

issn = {1759-9679},

year  = {2023},

date = {2023-02-09},

urldate = {2023-02-09},

journal = {Anal. Methods},

volume = {15},

number = {6},

pages = {746--751},

publisher = {Royal Society of Chemistry (RSC)},

abstract = {<jats:p>LC/MS method for the simultaneous quantitative measurement of cefiderocol and meropenem in serum samples.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ashiru-Oredope2023,

title = {Global collaborations in antimicrobial stewardship: All hands on deck},

author = {Diane Ashiru-Oredope and Bradley J. Langford and Candice Bonaconsa and Vrinda Nampoothiri and Esmita Charani and Debra A. Goff},

doi = {10.1017/ash.2023.122},

issn = {2732-494X},

year  = {2023},

date = {2023-00-00},

urldate = {2023-00-00},

journal = {ASHE},

volume = {3},

number = {1},

publisher = {Cambridge University Press (CUP)},

abstract = {<jats:title>Abstract</jats:title>

	  <jats:p>Tackling antimicrobial resistance (AMR) through antimicrobial stewardship (AMS) interventions is a key objective within the World Health Organization (WHO)’s Global Action on AMR. We outline the reasons why global collaborations for AMS are needed. We provide examples of global collaborations, and we offer considerations when starting on a global health journey focused on AMS.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Mutemaringa2022,

title = {Record linkage for Routinely Collected Health Data in an African Health Information Exchange.},

author = {Themba Mutemaringa and Alexa Heekes and Andrew Boulle and Nicki Tiffin},

doi = {10.23889/ijpds.v7i3.2022},

issn = {2399-4908},

year  = {2022},

date = {2022-08-25},

urldate = {2022-08-25},

journal = {IJPDS},

volume = {7},

number = {3},

publisher = {Swansea University},

abstract = {<jats:p>Objectives



To describe the record linkage system that is currently implemented at the Provincial Health Data Centre (PHDC) in the Western Cape, South Africa

To assess its output to date with respect to types of matches and duplicates trends

To describe the errors affecting patient matching



ApproachWe apply a stepwise deterministic record linkage approach to link patient data that are routinely collected from health information systems in the Western Cape province of South Africa. Variables used in the linkage process include South African National Identity number (RSA ID), date of birth, year of birth, month of birth, day of birth, residential address and contact information. Matching records are established from sequentially running the data through multiple passes formed by various combinations of linkage variables. Descriptive analyses are used to estimate the extent of mismatches and duplication in the provincial patient master index (PMI).

Results



The proportion of duplicates dropped from approximately 16.8% in December 2015 to 9.6% in October 2020, indicating improved data linkage over time.

Duplicates mainly arise from spelling errors, and surname and first names carry most of the errors, with different first names and surname for the same individual in approximately 22% of duplicates.

Linkage is also affected by completeness, with less than 30 % completeness for the South African national identity (RSA ID) number which is mainly because RSA ID is not mandatory when seeking healthcare.



ConclusionLinkage improvement could be due to improved registration practices. Further improvements are possible by repeating data linkage where patients register before creating a new patient record following a failed search. This could use the PHDC linkage approach whilst leveraging all data in addition to search terms used by the clerk.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}