{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,16]],"date-time":"2026-07-16T14:09:52Z","timestamp":1784210992001,"version":"3.55.0"},"reference-count":55,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,7,16]],"date-time":"2026-07-16T00:00:00Z","timestamp":1784160000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>The application of next-generation sequencing (NGS) is rapidly expanding for antimicrobial resistance (AMR) surveillance and clinical decision-making. However, despite a high AMR burden, many low- and middle-income countries lack the infrastructure and technical capacity required to implement sequencing-based approaches. To address this gap and demonstrate the practical application of the technology, we compared the performance of nanopore sequencing combined with real-time analysis using the EPI2ME platform in a mobile laboratory with that of a hybrid sequencing approach integrating Illumina short reads and nanopore long reads.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>\n                      In this exploratory diagnostic evaluation study, 25\n                      <jats:italic>Escherichia coli<\/jats:italic>\n                      isolates obtained through the German annual national AMR monitoring program were included. Isolates resistant to at least one\n                      <jats:italic>\u03b2<\/jats:italic>\n                      -lactam antibiotic were considered as resistant isolate. Genomic DNA was subjected to both Illumina and nanopore sequencing. Following the sequencing, the EPI2ME whole genome sequencing pipeline was used to detect and identify\n                      <jats:italic>\u03b2<\/jats:italic>\n                      -lactamase genes in\n                      <jats:italic>E. coli<\/jats:italic>\n                      isolates. As the comparator, both long and short read-based hybrid assemblies were used to detect and identify the\n                      <jats:italic>\u03b2<\/jats:italic>\n                      -lactamase genes. The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of the sequencing approaches were calculated against the phenotypic classification of\n                      <jats:italic>E. coli<\/jats:italic>\n                      isolates, treating the presence or absence of\n                      <jats:italic>\u03b2<\/jats:italic>\n                      -lactamase\u2013encoding genes as the genotypic predictor of\n                      <jats:italic>\u03b2<\/jats:italic>\n                      -lactam resistance.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      A total of 36\n                      <jats:italic>\u03b2<\/jats:italic>\n                      -lactamase\u2013encoding genes, predominantly from the\n                      <jats:italic>bla<\/jats:italic>\n                      <jats:sub>CTX-M<\/jats:sub>\n                      ,\n                      <jats:italic>bla<\/jats:italic>\n                      <jats:sub>SHV<\/jats:sub>\n                      , and\n                      <jats:italic>bla<\/jats:italic>\n                      <jats:sub>TEM<\/jats:sub>\n                      families, were detected. Both analytical approaches achieved a promising accuracy towards predicting\n                      <jats:italic>\u03b2<\/jats:italic>\n                      -lactam resistance. Moderate agreement was observed between methods, with an overall concordance of 68.9%. A distinct distribution pattern of\n                      <jats:italic>\u03b2<\/jats:italic>\n                      -lactamase genes was observed across the MIC ranges of the isolates for third-generation cephalosporins and the carbapenems.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Discussion<\/jats:title>\n                    <jats:p>These findings support the feasibility of deploying nanopore sequencing in mobile suitcase laboratories to strengthen AMR surveillance in food production systems. Given its portability, rapid turnaround time, and minimal infrastructure requirements, the approach may also have broader applications for One Health based AMR surveillance, clinical decision-making, and outbreak investigations in resource-limited settings.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fmicb.2026.1854040","type":"journal-article","created":{"date-parts":[[2026,7,16]],"date-time":"2026-07-16T13:27:36Z","timestamp":1784208456000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Nanopore sequencing in suitcase lab enables improved detection of \u03b2-lactamase genes in food-borne E. coli"],"prefix":"10.3389","volume":"17","author":[{"given":"Prakash","family":"Ghosh","sequence":"first","affiliation":[{"name":"Institute for Animal Hygiene and Veterinary Public Health, Leipzig University","place":["Leipzig, Germany"]},{"name":"Department of Empirical Health Economics, Technische Universit\u00e4t Berlin","place":["Berlin, Germany"]},{"name":"Nutrition Research Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b)","place":["Dhaka, Bangladesh"]},{"name":"One Network for Environment and Bioscience (ONEB)","place":["Dhaka, Bangladesh"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ulrike","family":"Binsker","sequence":"additional","affiliation":[{"name":"Department Biological Safety, German Federal Institute for Risk Assessment","place":["Berlin, Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rea Maja","family":"Kobialka","sequence":"additional","affiliation":[{"name":"Institute for Animal Hygiene and Veterinary Public Health, Leipzig University","place":["Leipzig, Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arianna","family":"Ceruti","sequence":"additional","affiliation":[{"name":"Institute for Animal Hygiene and Veterinary Public Health, Leipzig University","place":["Leipzig, Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Muhammad","family":"Asaduzzaman","sequence":"additional","affiliation":[{"name":"Department of Community Medicine and Global Health, Institute of Health and Society, Faculty of Medicine, University of Oslo","place":["Oslo, Norway"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Siddhartha Narayan","family":"Joardar","sequence":"additional","affiliation":[{"name":"Department of Veterinary Microbiology, West Bengal University of Animal and Fishery Sciences","place":["Kolkata, India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Asaduzzaman","family":"Asad","sequence":"additional","affiliation":[{"name":"Gut-Brain Axis Laboratory, Infectious Diseases Division, ICDDR, B","place":["Dhaka, Bangladesh"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Behrouz Alizadeh","family":"Savareh","sequence":"additional","affiliation":[{"name":"Institute for Animal Hygiene and Veterinary Public Health, Leipzig University","place":["Leipzig, Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Frimpong","sequence":"additional","affiliation":[{"name":"Department of Molecular Medicine, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology","place":["Kumasi, Ghana"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bhupesh","family":"Taneja","sequence":"additional","affiliation":[{"name":"CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB)","place":["New Delhi, India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martin","family":"Siegel","sequence":"additional","affiliation":[{"name":"Chair of General Economics, Health Economics and Econometrics, University of Greifswald","place":["Greifswald, Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yakhya","family":"Dieye","sequence":"additional","affiliation":[{"name":"Pole de Microbiologie, Institut de Pasteur de Dakar","place":["Dakar, Senegal"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Uwe","family":"Truyen","sequence":"additional","affiliation":[{"name":"Institute for Animal Hygiene and Veterinary Public Health, Leipzig University","place":["Leipzig, Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ahmed Abd","family":"El Wahed","sequence":"additional","affiliation":[{"name":"Institute for Animal Hygiene and Veterinary Public Health, Leipzig University","place":["Leipzig, Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,7,16]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1038\/s41591-023-02666-0","article-title":"An African one health network for antimicrobial resistance and neglected tropical diseases","volume":"30","author":"Abd El Wahed","year":"2024","journal-title":"Nat. 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Microbiol."},{"key":"ref23","doi-asserted-by":"publisher","first-page":"e35816","DOI":"10.1016\/j.heliyon.2024.e35816","article-title":"Sensitivity and specificity of Nanopore sequencing for detecting carbapenem and 3rd-generation cephalosporin-resistant Enterobacteriaceae in urine samples: real-time simulation with public antimicrobial resistance gene database","volume":"10","author":"Kawang","year":"2024","journal-title":"Heliyon."},{"key":"ref24","doi-asserted-by":"publisher","first-page":"116800","DOI":"10.1016\/j.diagmicrobio.2025.116800","article-title":"Field deployment of the mobile suitcase laboratory for rapid detection of Mpox virus in the Democratic Republic of the Congo","volume":"112","author":"Kobialka","year":"2025","journal-title":"Diagn. Microbiol. Infect. 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Microbiol."},{"key":"ref27","doi-asserted-by":"publisher","DOI":"10.1016\/j.lanmic.2025.101183","article-title":"Estimating the association of antimicrobial resistance genes with minimum inhibitory concentration in Escherichia coli: an observational study","volume":"6","author":"Lipworth","year":"2025","journal-title":"Lancet Microbe"},{"key":"ref28","doi-asserted-by":"publisher","DOI":"10.1016\/j.microc.2025.115471","article-title":"Antimicrobial resistance detection: rapid transition to point-of-care platforms","author":"Madaje","year":"2025","journal-title":"Microchem. J."},{"key":"ref29","doi-asserted-by":"publisher","first-page":"629","DOI":"10.1016\/S0140-6736(21)02724-0\/ATTACHMENT\/4504FC2B-08AE-46D6-BD75-80811DF8B5E6\/MMC1.PDF","article-title":"Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis","volume":"399","author":"Murray","year":"2022","journal-title":"Lancet"},{"key":"ref30","doi-asserted-by":"publisher","first-page":"1092556","DOI":"10.3389\/fmicb.2022.1092556","article-title":"\u0392-Lactam potentiators to re-sensitize resistant pathogens: discovery, development, clinical use and the way forward","volume":"13","author":"Narendrakumar","year":"2022","journal-title":"Front. Microbiol."},{"key":"ref31","doi-asserted-by":"publisher","first-page":"S17","DOI":"10.1093\/CID\/CIAA1581","article-title":"National estimates of healthcare costs associated with multidrug-resistant bacterial infections among hospitalized patients in the United States","volume":"72","author":"Nelson","year":"2021","journal-title":"Clin. Infect. Dis."},{"key":"ref32","volume-title":"Tackling Drug-Resistant Infections Globally: Final Report and Recommendations","author":"O\u2019Neill","year":"2016"},{"key":"ref33","doi-asserted-by":"publisher","DOI":"10.3390\/antibiotics14080827","article-title":"Nanopore sequencing-driven mapping of antimicrobial resistance genes in selected Escherichia coli isolates from pigs and poultry layers in Nigeria","volume":"14","author":"Ogunleye","year":"2025","journal-title":"Antibiotics"},{"key":"ref34","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2025.1753559","article-title":"Novel insights into antimicrobial-resistant, virulent and biofilm-forming Salmonella: molecular and phenotypic evidence from duck at the human-animal-environment interface","volume":"16","author":"Paul","year":"2026","journal-title":"Front. Microbiol."},{"key":"ref35","doi-asserted-by":"publisher","first-page":"29","DOI":"10.3390\/microorganisms9010029","article-title":"Identification of a blaVIM-1-carrying IncA\/C2 multiresistance plasmid in an Escherichia coli isolate recovered from the German food chain","volume":"9","author":"Pauly","year":"2021","journal-title":"Microorganisms"},{"key":"ref36","doi-asserted-by":"publisher","first-page":"154","DOI":"10.1016\/J.MIMET.2018.07.014","article-title":"Current antimicrobial susceptibility testing for beta-lactamase-producing Enterobacteriaceae in clinical settings","volume":"152","author":"Pereckaite","year":"2018","journal-title":"J. Microbiol. Methods"},{"key":"ref37","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1128\/AAC.48.1.15-22.2004","article-title":"Emergence of Oxacillinase-mediated resistance to imipenem in Klebsiella pneumoniae","volume":"48","author":"Poirel","year":"2004","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref38","doi-asserted-by":"publisher","first-page":"29531","DOI":"10.1038\/s41598-024-80660-3","article-title":"Evaluation of DNA extraction kits for long-read shotgun metagenomics using Oxford Nanopore sequencing for rapid taxonomic and antimicrobial resistance detection","volume":"14","author":"Purushothaman","year":"2024","journal-title":"Sci. Rep."},{"key":"ref39","doi-asserted-by":"publisher","first-page":"101237","DOI":"10.1016\/j.onehlt.2025.101237","article-title":"Prevalence of extended-spectrum beta-lactamase-producing Enterobacteriaceae isolated from animals in Bangladesh: a systematic review and meta-analysis","volume":"21","author":"Rahaman","year":"2025","journal-title":"One Health"},{"key":"ref40","doi-asserted-by":"publisher","DOI":"10.3389\/feduc.2021.710971","article-title":"Challenges and considerations for delivering bioinformatics training in LMICs: perspectives from Pan-African and Latin American bioinformatics networks","volume":"6","author":"Ras","year":"2021","journal-title":"Front Educ (Lausanne)."},{"key":"ref41","doi-asserted-by":"publisher","first-page":"46","DOI":"10.1017\/S1466252317000020","article-title":"Types and prevalence of extended-spectrum beta-lactamase producing Enterobacteriaceae in poultry","volume":"30","author":"Saliu","year":"2017","journal-title":"Anim. Health Res. Rev."},{"key":"ref42","doi-asserted-by":"publisher","first-page":"1808","DOI":"10.1021\/acsestwater.3c00794","article-title":"Rapid identification of bacterial composition in wastewater by combining reverse purification nucleic acid extraction and Nanopore sequencing","volume":"4","author":"Schurig","year":"2024","journal-title":"ACS EST Water"},{"key":"ref43","doi-asserted-by":"publisher","first-page":"738","DOI":"10.1093\/cid\/cix417","article-title":"Whole-genome sequencing accurately identifies resistance to extended-spectrum \u03b2-lactams for major gram-negative bacterial pathogens","volume":"65","author":"Shelburne","year":"2017","journal-title":"Clin. Infect. Dis."},{"key":"ref44","doi-asserted-by":"publisher","first-page":"e0017825","DOI":"10.1128\/jcm.00178-25","article-title":"Automated whole genome sequencing platform for bacterial strain typing in clinical microbiology laboratories","volume":"63","author":"Siddall","year":"2025","journal-title":"J. Clin. Microbiol."},{"key":"ref45","doi-asserted-by":"publisher","first-page":"1298248","DOI":"10.3389\/FSCI.2024.1298248","article-title":"Real-time genomic surveillance for enhanced control of infectious diseases and antimicrobial resistance","volume":"2","author":"Struelens","year":"2024","journal-title":"Front. Sci."},{"key":"ref46","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2025.1715467","article-title":"Evaluation of four DNA extraction kits for implementation of nanopore sequencing in routine surveillance of antimicrobial resistance in low-resource settings","volume":"16","author":"Thornval","year":"2025","journal-title":"Front. Microbiol."},{"key":"ref47","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41598-024-55865-1","article-title":"Multi-platform whole genome sequencing for tuberculosis clinical and surveillance applications","volume":"14","author":"Thorpe","year":"2024","journal-title":"Sci. Rep."},{"key":"ref48","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2016.01860","article-title":"Global antimicrobial stewardship: a closer look at the formidable implementation challenges","volume":"7","author":"Tiong","year":"2016","journal-title":"Front. Microbiol."},{"key":"ref49","doi-asserted-by":"publisher","first-page":"66","DOI":"10.3390\/antibiotics12040661","article-title":"Extended-spectrum \u03b2-lactamases (ESBL) producing bacteria in animals","volume":"12","author":"Tseng","year":"2023","journal-title":"Antibiotics"},{"key":"ref50","doi-asserted-by":"publisher","first-page":"10931","DOI":"10.1038\/s41598-018-29334-5","article-title":"Evaluation of Oxford Nanopore\u2019s MinION sequencing device for microbial whole genome sequencing applications","volume":"8","author":"Tyler","year":"2018","journal-title":"Sci. Rep."},{"key":"ref51","doi-asserted-by":"publisher","first-page":"526944","DOI":"10.3389\/FCIMB.2020.00308\/XML\/NLM","article-title":"Modern tools for rapid diagnostics of antimicrobial resistance","volume":"10","author":"Vasala","year":"2020","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"ref52","doi-asserted-by":"publisher","first-page":"e0107222","DOI":"10.1128\/AAC.01072-22","article-title":"Validation and application of long-read whole-genome sequencing for antimicrobial resistance gene detection and antimicrobial susceptibility testing","volume":"67","author":"Weinmaier","year":"2023","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref53","doi-asserted-by":"publisher","first-page":"129","DOI":"10.1186\/s13059-019-1727-y","article-title":"Performance of neural network basecalling tools for Oxford Nanopore sequencing","volume":"20","author":"Wick","year":"2019","journal-title":"Genome Biol."},{"key":"ref54","doi-asserted-by":"publisher","first-page":"13","DOI":"10.3389\/fmicb.2022.1073057","article-title":"Evaluation of multiplex nanopore sequencing for Salmonella serotype prediction and antimicrobial resistance gene and virulence gene detection","volume":"13","author":"Wu","year":"2023","journal-title":"Front. Microbiol."},{"key":"ref55","doi-asserted-by":"publisher","first-page":"1758","DOI":"10.1101\/gr.279829.124","article-title":"Accurate genotyping of three major respiratory bacterial pathogens with ONT R10.4.1 long-read sequencing","volume":"35","author":"Zidane","year":"2025","journal-title":"Genome Res."}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2026.1854040\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,16]],"date-time":"2026-07-16T13:27:37Z","timestamp":1784208457000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2026.1854040\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,7,16]]},"references-count":55,"alternative-id":["10.3389\/fmicb.2026.1854040"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2026.1854040","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,7,16]]},"article-number":"1854040"}}