{"title":"The hospital sink drain microbiome as a melting pot for AMR transmission to nosocomial pathogens.","authors":"Gregory E McCallum, James P J Hall","doi":"10.1038/s44259-025-00137-9","DOIUrl":"10.1038/s44259-025-00137-9","url":null,"abstract":"<p><p>The hospital sink drain microbiome can harbour opportunistic pathogens and antimicrobial resistance genes (ARGs). Aspects of this habitat, such as exposure to disinfectants, antibiotics, nutrients, and body fluids could exacerbate horizontal gene transfer of ARGs and clinically impactful pathogen resistance. Here, we explore features of the hospital sink drain that may favour ARG acquisition and transmission, highlight studies providing evidence of transfer, and consider strategies to mitigate these risks.</p>","PeriodicalId":520007,"journal":{"name":"npj antimicrobials and resistance","volume":"3 1","pages":"68"},"PeriodicalIF":0.0,"publicationDate":"2025-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12307617/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144746747","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Adam Valcek, Carsten Kröger, Rubén de Dios, Ronan R McCarthy, Tom Coenye, M Stephen Trent, Nabil Karah, Bernt Eric Uhlin, Annika Y Classen, Paul G Higgins, Ingo Ebersberger, Maria-Halima Laaberki, Xavier Charpentier, Paolo Visca, Philip N Rather, Charles Van der Henst
{"title":"Inter- and intra-bacterial strain diversity remains the \"elephant in the (living) room\".","authors":"Adam Valcek, Carsten Kröger, Rubén de Dios, Ronan R McCarthy, Tom Coenye, M Stephen Trent, Nabil Karah, Bernt Eric Uhlin, Annika Y Classen, Paul G Higgins, Ingo Ebersberger, Maria-Halima Laaberki, Xavier Charpentier, Paolo Visca, Philip N Rather, Charles Van der Henst","doi":"10.1038/s44259-025-00138-8","DOIUrl":"10.1038/s44259-025-00138-8","url":null,"abstract":"<p><p>Acinetobacter baumannii is an opportunistic Gram-negative bacterial pathogen responsible for severe nosocomial infections worldwide. Resistance to last-resort antibiotics causes A. baumannii to be ranked as a top priority for the research and development of new antibiotics by the WHO and an urgent threat to public health by the CDC. It is also a member of the ESKAPE group comprising the most problematic antibiotic-resistant nosocomial pathogens. Resistance towards desiccation, disinfectants, reactive oxygen species, and the host immune system helps A. baumannii thrive in hospital settings and infect individuals compromised by lines, tubes, and indwelling devices. A. baumannii displays extensive genomic heterogeneity, yet recent studies show that this level of plasticity is also prevalent in lab strains widely used to study A. baumannii biology. Successive subculturing of widely used strains and spontaneous genetic variations results in significantly altered genotypes and phenotypes, often not recognized by the scientific community. In addition, the current strain designation methods do not allow efficient communication about such differences. Even presumably identical strains from established culture collections have been found to demonstrate genetic heterogeneity. The \"elephant in the (living) room\" refers to the risk but also the potential of the bi-partite problem concerning the high diversity amongst A. baumannii isolates (inter-strain variability), and the universal issue of microevolution (intra-strain variability). This is generally ignored as it is not referenced adequately in scientific publications. We aim to raise awareness about the current issues and the problematic consequences generated by intra- and inter-strain diversity based on modern examples of A. baumannii isolates. Therefore, this review provides cases of broadly used A. baumannii strains and their genetic and phenotypic differences.</p>","PeriodicalId":520007,"journal":{"name":"npj antimicrobials and resistance","volume":"3 1","pages":"67"},"PeriodicalIF":0.0,"publicationDate":"2025-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12297434/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144719347","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ivan Sugrue, Carolin Ade, Paula M O'Connor, Jan-Martin Daniel, Paolo Innocenti, Nico Kirsch, Nathaniel I Martin, Günther Weindl, Colin Hill, Tanja Schneider, R Paul Ross
{"title":"Trans-kingdom conservation of mechanism between bacterial actifensin and eukaryotic defensins.","authors":"Ivan Sugrue, Carolin Ade, Paula M O'Connor, Jan-Martin Daniel, Paolo Innocenti, Nico Kirsch, Nathaniel I Martin, Günther Weindl, Colin Hill, Tanja Schneider, R Paul Ross","doi":"10.1038/s44259-025-00135-x","DOIUrl":"10.1038/s44259-025-00135-x","url":null,"abstract":"<p><p>Antimicrobial peptides are defense molecules found across all domains of life holding promise for developing therapies against drug-resistant pathogens. Actifensin, from Actinomyces ruminicola DPC7226, exhibits potent activity against gram-positive bacteria and shares structural similarities with eukaryotic defensins. This study characterized actifensin's mechanism of action and therapeutic potential. The findings revealed that actifensin inhibits peptidoglycan synthesis by binding lipid II (Kd = 30 ± 20 nM). Unlike defensins, it also binds lipid I (Kd = 24 ± 27 nM) without significant difference, suggesting the N-acetyl glucosamine moiety of lipid II is not required for complexation. Membrane disruption was not observed with DiSC<sub>3</sub>(5) fluorescence, or synthetic unilamellar liposomes, indicating indirect cell death via cell wall weakening, visualised by phase contrast microscopy. Actifensin showed no haemolytic activity or toxicity up to 128 µg/ml in human erythrocytes and Hep G2 cells. The peptide was not immunogenic, demonstrating no induction of LDH release in PBMCs or any effect on TLR-mediated signalling. Structural motif analysis identified actifensin as part of a conserved trans-kingdom defensin subfamily, GXGCP, distinct from XTCD peptides in more recently evolved arthropods. These findings emphasise the conserved structure-function relationship of antimicrobials across kingdoms, suggesting a shared evolutionary history of defensins and highlight the therapeutic potential for them or their variants.</p>","PeriodicalId":520007,"journal":{"name":"npj antimicrobials and resistance","volume":"3 1","pages":"66"},"PeriodicalIF":0.0,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12284004/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144692991","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Pan-genus analysis and typing of antimicrobial resistance plasmids in Acinetobacter.","authors":"Liam A Tobin, Margaret M C Lam, Mehrad Hamidian","doi":"10.1038/s44259-025-00133-z","DOIUrl":"10.1038/s44259-025-00133-z","url":null,"abstract":"<p><p>Plasmids play a central role in horizontal gene transfer and bacterial adaptation, especially in the context of antimicrobial resistance (AMR) among opportunistic pathogens. Some members of the genus Acinetobacter are known for their role in hospital-acquired infections, harboring plasmids that facilitate rapid adaptation to selective pressures. However, the extent of plasmid diversity and evolutionary dynamics within Acinetobacter has not been fully elucidated. In this study, we analysed 1846 complete and non-redundant Acinetobacter plasmid sequences, identifying 166 novel Replicase (Rep) protein types and providing a significant update to the Acinetobacter Plasmid Typing (APT) scheme, which now comprises 257 Rep types. A detailed phylogenetic analysis of the prevailing R3-type Rep sequences reveals two distinct evolutionary clades (A and B) and several additional subclades. This phylogenetic structure suggests evolutionary pressures within all clades, potentially influenced by host species distribution and environmental factors. Analysis of these plasmids highlights diverse plasmid types involved in dissemination of AMR within the genus in different niches, underscoring both clinical and natural environments as reservoirs of Acinetobacter plasmids. Our findings provide a refined framework for tracking Acinetobacter plasmids, advancing our understanding of plasmid-mediated AMR spread and informing strategies to combat the spread of AMR in this critical genus.</p>","PeriodicalId":520007,"journal":{"name":"npj antimicrobials and resistance","volume":"3 1","pages":"65"},"PeriodicalIF":0.0,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12284255/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144692990","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Victor A Medina, Angela S García-Vega, Fernando Rodríguez, Enmanuel S Triviño-García, Jaime A Robledo, Aura L Leal, Julián C Galvis, Luis F Reyes, Iruka N Okeke, Natacha Couto, Emmanuelle A Kumaran, Georgina Lewis-Woodhouse, Silvia Argimon, Stefany A Arevalo, Anthony P Underwood, Xavier Fargetton, David M Aanensen, Maria P Donado-Godoy
{"title":"Epidemiological Genomics of Klebsiella pneumoniae isolates from hospitals across Colombia.","authors":"Victor A Medina, Angela S García-Vega, Fernando Rodríguez, Enmanuel S Triviño-García, Jaime A Robledo, Aura L Leal, Julián C Galvis, Luis F Reyes, Iruka N Okeke, Natacha Couto, Emmanuelle A Kumaran, Georgina Lewis-Woodhouse, Silvia Argimon, Stefany A Arevalo, Anthony P Underwood, Xavier Fargetton, David M Aanensen, Maria P Donado-Godoy","doi":"10.1038/s44259-025-00127-x","DOIUrl":"10.1038/s44259-025-00127-x","url":null,"abstract":"<p><p>Klebsiella pneumoniae is one of the most important nosocomial pathogens worldwide. In Colombia, K. pneumoniae has been identified as the second most frequent microbial etiologic agent of healthcare-associated infections. We conducted a prospective local study of 335 K. pneumoniae isolates in 26 nationwide hospitals from 2020 to 2021. We found that the spread of carbapenem resistance was mediated by successful clones belonging to sequence types (ST) such as ST11, ST1082, and ST307, related to intra-hospital infections. We observed that bla<sub>KPC</sub> remains the primary resistance mechanism to carbapenems and that, unlike other countries, ST11 strains commonly carry bla<sub>KPC-3</sub>. We identified the recent introduction and circulation of new sequence types with different resistance mechanisms and hypervirulence. Besides, we detected possible transmission events closely linked to carbapenemase-carrying strains, mainly in intensive care units. This study helps us understand how K. pneumoniae disseminates in Colombian hospitals and where to direct effective intervention measures.</p>","PeriodicalId":520007,"journal":{"name":"npj antimicrobials and resistance","volume":"3 1","pages":"64"},"PeriodicalIF":0.0,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12280007/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144683949","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jonathan J Y Teo, Eliza Xin Pei Ho, Amanda Hui Qi Ng, Shaun Hong Chuen How, Kern Rei Chng, Yiğit Can Ateş, Muhd Tarmidzi Fau'di, Kyaw Thu Aung, Niranjan Nagarajan
{"title":"Citywide metagenomic surveillance of food centres reveals local microbial signatures and antibiotic resistance gene enrichment.","authors":"Jonathan J Y Teo, Eliza Xin Pei Ho, Amanda Hui Qi Ng, Shaun Hong Chuen How, Kern Rei Chng, Yiğit Can Ateş, Muhd Tarmidzi Fau'di, Kyaw Thu Aung, Niranjan Nagarajan","doi":"10.1038/s44259-025-00132-0","DOIUrl":"10.1038/s44259-025-00132-0","url":null,"abstract":"<p><p>The distribution of microorganisms in built environments with high human traffic, such as food centres, can potentially have a significant impact on public health, particularly in the context of increasing worldwide incidence of food and fomite-related outbreaks. In many major Asian cities, public food centres are central to daily food consumption, yet there is a lack of baseline knowledge about their environmental microbiomes. We performed a city-wide metagenomic survey of food-centre microbiomes in Singapore, covering 16 centres and 240 samples, to map the abundances of microbial (bacteria, archaea, fungi, viruses) and non-microbial DNA across two timepoints. Food-centre microbiomes were found to be enriched in food-related DNA signatures compared to other environments, such as hospitals and offices, with specific food-microbe associations (e.g., Enterobacteriaceae and fish) and food DNA providing a partial explanation for the microbial profiles observed (44% of variation explained). Machine learning analysis identified a small set of microbial species (n = 22) that serve as highly accurate (>80%) location-specific signatures for various food centres, some of which persist even after 3 years. Profiling of antibiotic resistance genes (ARGs) and pathogens identified a surprising enrichment of ARGs in food centres relative to other non-healthcare environments (>2.5×), and an order of magnitude enrichment of key pathogenic species (e.g., Klebsiella pneumoniae, Enterobacter spp) even compared to hospital environments. These results highlight the contribution of diverse biotic and abiotic factors in shaping the unique microbiome profiles of different food-centre environments, and the potential for using metagenomic surveillance to understand the risk for infections and antibiotic resistance gene transmission.</p>","PeriodicalId":520007,"journal":{"name":"npj antimicrobials and resistance","volume":"3 1","pages":"63"},"PeriodicalIF":0.0,"publicationDate":"2025-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12238472/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144593732","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Cristina Calvo-Fernandez, Marta M Dolcet-Negre, Barbara Martin-Maldonado, Mario Pulido-Vadillo, Natalia Montero, Roger Such, Encarnación García-Vila, Jose F Delgado-Blas, Bruno Gonzalez-Zorn
{"title":"Human-wildlife ecological interactions shape Escherichia coli population and resistome in two sloth species from Costa Rica.","authors":"Cristina Calvo-Fernandez, Marta M Dolcet-Negre, Barbara Martin-Maldonado, Mario Pulido-Vadillo, Natalia Montero, Roger Such, Encarnación García-Vila, Jose F Delgado-Blas, Bruno Gonzalez-Zorn","doi":"10.1038/s44259-025-00134-y","DOIUrl":"10.1038/s44259-025-00134-y","url":null,"abstract":"<p><p>Antimicrobial resistance (AMR) is a global health concern, with natural ecosystems acting as reservoirs for resistant bacteria. We assessed AMR in Escherichia coli isolated from two wild sloth species in Costa Rica. E. coli from two-toed sloths (Choloepus hoffmanni), a species with greater mobility and a broader diet, showed resistance to sulfamethoxazole (25%), tetracycline (9.4%), chloramphenicol (6.3%), ampicillin (6.3%), trimethoprim (3.1%), and ciprofloxacin (3.1%), which correlated with the presence of resistance genes (tet(A), tet(B), bla<sub>TEM-1B</sub>, aph(3\")-Id, aph(6)-Id, sul2, qnrS1, floR and dfrA8). E. coli from three-toed sloths (Bradypus variegatus) showed 40% resistance to sulfamethoxazole despite no detected resistance genes, suggesting a regional effect. A significant negative correlation was found between AMR and distance to human-populated areas, highlighting anthropogenic impact on AMR spread. Notably, E. coli isolates from remote areas with no human impact indicate that some ecosystems remain unaffected. Preserving these areas is essential to protect environmental and public health.</p>","PeriodicalId":520007,"journal":{"name":"npj antimicrobials and resistance","volume":"3 1","pages":"62"},"PeriodicalIF":0.0,"publicationDate":"2025-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12229481/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144562555","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Joy R Paterson, Joshua M Wadsworth, Rebecca J Lee, Ping Hu, Jacob Biboy, Daniela Vollmer, Waldemar Vollmer, Jon Marles-Wright, Jana N Radin, Thomas E Kehl-Fie, Mary T Moran, Gary J Sharples
{"title":"Enhanced resistance of metal sequestering agents by reconfiguration of the Staphylococcus aureus cell wall.","authors":"Joy R Paterson, Joshua M Wadsworth, Rebecca J Lee, Ping Hu, Jacob Biboy, Daniela Vollmer, Waldemar Vollmer, Jon Marles-Wright, Jana N Radin, Thomas E Kehl-Fie, Mary T Moran, Gary J Sharples","doi":"10.1038/s44259-025-00131-1","DOIUrl":"10.1038/s44259-025-00131-1","url":null,"abstract":"<p><p>Chelators possess antibacterial properties linked to metal sequestration, simulating the action of nutritional immunity in preventing infection. To gain further insight into bacterial adaptation to metal restriction, we isolated mutants of Staphylococcus aureus with enhanced resistance to two synthetic chelators with therapeutic potential. Mutations were identified that altered peptidoglycan metabolism and teichoic acid modification, crucially affecting PBP2 and eliminating FmtA or VraF functionality. The resulting strains showed increased cell wall thickness, modified cell surface charge and varied in susceptibility to cell wall-targeting agents. In those mutants lacking either FmtA or VraF, the modifications substantially increased cell surface-associated calcium, offering protection against loss of manganese that was preferentially targeted by both chelators. Our phenotypic and cellular metal analyses identify the cell envelope of S. aureus as a key target for metal sequestering molecules. Peptidoglycan and teichoic acids, in particular, serve as key repositories for a subset of metal ions that safeguard against deprivation and can be altered to augment resistance to antibacterial chelators.</p>","PeriodicalId":520007,"journal":{"name":"npj antimicrobials and resistance","volume":"3 1","pages":"61"},"PeriodicalIF":0.0,"publicationDate":"2025-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12229560/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144562554","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Risk of multidrug resistance in Escherichia coli associated with routine antimicrobial prophylaxis on pig farms.","authors":"Ryohei Toya, Miki Okuno, Yosuke Sasaki, Keisuke Yoshihara, Yuichiro Deguchi, Debora Satie Nagano, Seiji Shimada, Yoshitoshi Ogura","doi":"10.1038/s44259-025-00130-2","DOIUrl":"10.1038/s44259-025-00130-2","url":null,"abstract":"<p><p>Although extensively studied, the association between antimicrobial usage and the emergence of antimicrobial resistance (AMR) in livestock still has unresolved aspects. This study analyzed the genomes of 195 Escherichia coli strains from pigs, a species with high antimicrobial consumption, across five production stages on 13 farms in Japan employing diverse antimicrobial administration strategies. A total of 61 acquired AMR genes (aARGs), spanning 13 distinct antimicrobial classes, were identified. A significant correlation was found between antimicrobial usage and the number of aARGs in E. coli strains. The four farms with the highest usage administered antimicrobials orally as routine prophylaxis during fattening. These farms showed significantly higher proportions of multidrug-resistant (MDR) genotypes at all stages compared to farms without routine prophylaxis. The number of frequently detected aARGs was more strongly correlated with total antimicrobial usage than with the usage of the corresponding antimicrobial classes. Co-occurrence network analysis suggested that genetic linkages among these aARGs may promote co-selection, thereby acting as a driving force in the emergence of MDR strains under routine prophylaxis treatment.</p>","PeriodicalId":520007,"journal":{"name":"npj antimicrobials and resistance","volume":"3 1","pages":"59"},"PeriodicalIF":0.0,"publicationDate":"2025-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12209429/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144532664","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Frank Chilanga, Keneth I Kasozi, Stella Mazeri, Gavin K Paterson, Adrian Muwonge
{"title":"A systematic review of antimicrobial resistance transmission inferences at the human-livestock interface in Africa.","authors":"Frank Chilanga, Keneth I Kasozi, Stella Mazeri, Gavin K Paterson, Adrian Muwonge","doi":"10.1038/s44259-025-00126-y","DOIUrl":"10.1038/s44259-025-00126-y","url":null,"abstract":"<p><p>The transmission of antibiotic-resistant bacteria across multi-species networks is a contributor to the global challenge of antimicrobial resistance (AMR). AMR transmission inferencing, a retrospective process, is critical for refining the evidence underpinning current control strategies. In Africa, where AMR is associated with an estimated 1.05 million deaths annually, it is crucial to evaluate how AMR transmission inferences are made and to consider their implications for achieving national action plan goals. Key questions that need to be addressed in these settings include: (a) How is transmission defined? (b) How are transmission studies designed? (c) Which pathogens or commensal bacteria are used to infer AMR transmission? (d) How granular and reliable is the data used to make transmission inferences? (e) Can the frequency of transmission events be quantified? and (f) Can the directionality of transmission between hosts be established? In this systematic review, we examine the evidence informing current control strategies by analysing 34 studies from Africa, involving 18,604 human and livestock samples and 16 sentinel bacteria. Transmission inferences largely rely on cross-sectional studies with limited sample representativeness. Gram-negative bacteria, mainly Escherichia coli (64.71%), form the basis of most inferences. Most inferences remain qualitative, and analyses often overlook uncertainty quantification. In addition, studies are potentially underpowered as only 25% of collected samples are used for transmission inferencing. Based on this analysis, we propose a framework that leverages the growing use of genomic epidemiology to infer AMR transmission with an aim of supporting the design and evaluation of targeted interventions.</p>","PeriodicalId":520007,"journal":{"name":"npj antimicrobials and resistance","volume":"3 1","pages":"58"},"PeriodicalIF":0.0,"publicationDate":"2025-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12209416/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144532662","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}