{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T14:00:17Z","timestamp":1785420017132,"version":"3.56.0"},"reference-count":126,"publisher":"MDPI AG","issue":"7","license":[{"start":{"date-parts":[[2026,6,30]],"date-time":"2026-06-30T00:00:00Z","timestamp":1782777600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Science, Technology & Innovative Funding Authority","award":["5884"],"award-info":[{"award-number":["5884"]}]},{"name":"Grant Office of the Faculty of Medicine, Assiut University","award":["2016-12-28-009"],"award-info":[{"award-number":["2016-12-28-009"]}]},{"award":["2016-12-28-009"],"award-info":[{"award-number":["2016-12-28-009"]}],"id":[{"id":"https:\/\/ror.org\/01jaj8n65","id-type":"ROR","asserted-by":"publisher"}]},{"name":"BBSRC research","award":["BB\/R017689\/1"],"award-info":[{"award-number":["BB\/R017689\/1"]}]},{"name":"BBSRC research","award":["BB\/Y007603\/1"],"award-info":[{"award-number":["BB\/Y007603\/1"]}]},{"name":"UKRI\u2019s Research England"},{"id":[{"id":"https:\/\/ror.org\/02wxr8x18","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>Escherichia coli is increasingly recognised as an important cause of ventilator-associated pneumonia (VAP), particularly in intensive care units (ICUs) with high antimicrobial selective pressure. Unlike classical respiratory pathogens, ICU-associated E. coli often originates from the patient\u2019s intestinal microbiota and harbours a complex mobilome enriched with antimicrobial resistance determinants. In this study, a total of 200 nosocomial endotracheal aspirate samples were aseptically collected from patients admitted to the Respiratory ICU at Assiut University hospital. Antimicrobial susceptibility testing, serotyping and screening for various virulence and antimicrobial resistance genes (e.g., extended-spectrum \u03b2-lactamase (ESBL) and carbapenems genes) were carried out. In total, E. coli isolates were recovered from 54\/200 (27%) endotracheal aspirates, with a high prevalence of multidrug resistance (MDR) observed (74.1%). Resistance to \u03b2-lactams was common with phenotypic evidence suggestive of ESBL production detected in 64.8% of isolates. Genome sequencing of three MDR E. coli isolates confirmed that they carried multiple antimicrobial resistance genes, which included ESBL genes (e.g., blaCTX-M-15 and blaTEM-1B). Each strain was also found to be high-risk extraintestinal pathogenic E. coli (ExPEC) clones, belonging to either sequence type ST131 or ST405. These findings support an endogenous infection model for VAP, whereby ICU selective pressure favours highly mobile, multidrug-resistant E. coli lineages adapted for extraintestinal survival. The high production of ESBLs and the prevalence of carbapenemase genes highlight the urgent need for molecular surveillance and antimicrobial stewardship strategies for the control of such high-priority pathogens in this part of the world.<\/jats:p>","DOI":"10.3390\/microorganisms14071438","type":"journal-article","created":{"date-parts":[[2026,6,30]],"date-time":"2026-06-30T16:56:55Z","timestamp":1782838615000},"page":"1438","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Antimicrobial Resistance and Comparative Genome Analysis of High-Risk Escherichia coli Strains Isolated from Ventilator-Associated Pneumonia Cases in Egyptian ICUs"],"prefix":"10.3390","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1840-4858","authenticated-orcid":false,"given":"Shaymaa","family":"Yusuf","sequence":"first","affiliation":[{"name":"Microbiology and Immunology Department, Faculty of Veterinary Medicine, Assiut University, Assiut 71515, Egypt"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mona H.","family":"Abdel-Rahim","sequence":"additional","affiliation":[{"name":"Medical Microbiology and Immunology Department, Faculty of Medicine, Assiut University, Assiut 71515, Egypt"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Omnia","family":"El-Badawy","sequence":"additional","affiliation":[{"name":"Medical Microbiology and Immunology Department, Faculty of Medicine, Assiut University, Assiut 71515, Egypt"},{"name":"Department of Basic Medical Sciences, Badr University in Assiut (BUA), Assiut 19592, Egypt"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Safy","family":"Hadiya","sequence":"additional","affiliation":[{"name":"Assiut International Center of Nanomedicine, Al-Rajhy Liver Hospital, Assiut University, Assiut 71515, Egypt"},{"name":"Microbiology and Immunology Department, School of Biotechnology, Badr University in Assiut, Assiut 19592, Egypt"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amany G.","family":"Thabit","sequence":"additional","affiliation":[{"name":"Medical Microbiology and Immunology Department, Faculty of Medicine, Assiut University, Assiut 71515, Egypt"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Radwa","family":"Abdelwahab","sequence":"additional","affiliation":[{"name":"Medical Microbiology and Immunology Department, Faculty of Medicine, Assiut University, Assiut 71515, Egypt"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Heba A.","family":"Hammad","sequence":"additional","affiliation":[{"name":"Medical Microbiology and Immunology Department, Faculty of Medicine, Assiut University, Assiut 71515, Egypt"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shabaan H.","family":"Ahmed","sequence":"additional","affiliation":[{"name":"Medical Microbiology and Immunology Department, Faculty of Medicine, Assiut University, Assiut 71515, Egypt"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1166-0480","authenticated-orcid":false,"given":"Mohamed","family":"Samir","sequence":"additional","affiliation":[{"name":"Department of Zoonoses, Faculty of Veterinary Medicine, Zagazig University, Zagazig 44519, Egypt"},{"name":"School of Science, Faculty of Engineering and Science, University of Greenwich, Medway campus, Kent ME4 4TB, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaoqiang","family":"Liu","sequence":"additional","affiliation":[{"name":"College of Veterinary Medicine, Northwest A&F University, Xianyang 712100, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4672-3514","authenticated-orcid":false,"given":"Douglas F.","family":"Browning","sequence":"additional","affiliation":[{"name":"Biosciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK"},{"name":"Aston Institute for Membrane Excellence, Aston University, Birmingham B4 7ET, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sherine A.","family":"Aly","sequence":"additional","affiliation":[{"name":"Medical Microbiology and Immunology Department, Faculty of Medicine, Assiut University, Assiut 71515, Egypt"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,6,30]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Aiesh, B.M., Qashou, R., Shemmessian, G., Swaileh, M.W., Abutaha, S.A., Sabateen, A., Barqawi, A.-K., AbuTaha, A., and Zyoud, S.H. (2023). Nosocomial infections in the surgical intensive care unit: An observational retrospective study from a large tertiary hospital in Palestine. BMC Infect. Dis., 23.","DOI":"10.1186\/s12879-023-08677-z"},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Ramos, S., Silva, V., Dapkevicius, M.L.E., Cani\u00e7a, M., Tejedor-Junco, M.T., Igrejas, G., and Poeta, P. (2020). Escherichia coli as Commensal and Pathogenic Bacteria Among Food-Producing Animals: Health Implications of Extended Spectrum \u03b2-lactamase (ESBL) Production. Animals, 10.","DOI":"10.3390\/ani10122239"},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Braz, V.S., Melchior, K., and Moreira, C.G. (2020). Escherichia coli as a Multifaceted Pathogenic and Versatile Bacterium. Front. Cell. Infect. Microbiol., 10.","DOI":"10.3389\/fcimb.2020.548492"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1038\/nrmicro818","article-title":"Pathogenic Escherichia coli","volume":"2","author":"Kaper","year":"2004","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"AME-0014-2020","DOI":"10.1128\/microbiolspec.AME-0014-2020","article-title":"Distinguishing Pathovars from Nonpathovars: Escherichia coli","volume":"8","author":"Riley","year":"2020","journal-title":"Microbiol. Spectr."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"888","DOI":"10.1007\/s00134-020-05980-0","article-title":"Ventilator-associated pneumonia in adults: A narrative review","volume":"46","author":"Papazian","year":"2020","journal-title":"Intensiv. Care Med."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"115564","DOI":"10.1016\/j.biopha.2023.115564","article-title":"Combatting resistance: Understanding multi-drug resistant pathogens in intensive care units","volume":"167","author":"Teng","year":"2023","journal-title":"Biomed. Pharmacother."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"146","DOI":"10.1016\/j.jhin.2024.03.004","article-title":"Bacteriology of endotracheal tube biofilms and antibiotic resistance: A systematic review","volume":"147","author":"Mishra","year":"2024","journal-title":"J. Hosp. Infect."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"58","DOI":"10.1111\/1758-2229.12019","article-title":"The Clermont Escherichia coli phylo-typing method revisited: Improvement of specificity and detection of new phylo-groups","volume":"5","author":"Clermont","year":"2013","journal-title":"Environ. Microbiol. Rep."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"610403","DOI":"10.1155\/2015\/610403","article-title":"Diarrheagenic Escherichia coli phylogroups are associated with antibiotic resistance and duration of diarrheal episode","volume":"2015","author":"Mosquito","year":"2015","journal-title":"Sci. World J."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"728","DOI":"10.1038\/nrmicro3093","article-title":"MLST revisited: The gene-by-gene approach to bacterial genomics","volume":"11","author":"Maiden","year":"2013","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Fratamico, P.M., DebRoy, C., Liu, Y., Needleman, D.S., Baranzoni, G.M., and Feng, P. (2016). Advances in Molecular Serotyping and Subtyping of Escherichia coli. Front. Microbiol., 7.","DOI":"10.3389\/fmicb.2016.00644"},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Martins, J.C.L., Gon\u00e7alves, A., Fernandes, C., Cabecinha, E., Monteiro, S., Guedes, H., Almeida, G., Garcia, J., da Silva, G.J., and Varandas, S. (2024). Multidrug-Resistant Escherichia coli Accumulated by Freshwater Bivalves: An Underestimated Risk for Public Health?. Pathogens, 13.","DOI":"10.3390\/pathogens13080617"},{"key":"ref_14","first-page":"4","article-title":"Phylotyping and Serotyping of Escherichia coli Isolates from Poultry Faecal Samples","volume":"23","author":"Lakheshar","year":"2022","journal-title":"Vet. Pract."},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Pakbin, B., Br\u00fcck, W.M., and Rossen, J.W.A. (2021). Virulence Factors of Enteric Pathogenic Escherichia coli: A Review. Int. J. Mol. Sci., 22.","DOI":"10.20944\/preprints202108.0348.v1"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"50","DOI":"10.2478\/jccm-2018-0011","article-title":"Endotracheal Tube Biofilm and its Impact on the Pathogenesis of Ventilator-Associated Pneumonia","volume":"4","author":"Diaconu","year":"2018","journal-title":"J. Crit. Care Med."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"2747","DOI":"10.2147\/IDR.S219696","article-title":"Characterization of antibiotic resistance and virulence factors of Escherichia coli strains isolated from Iranian inpatients with urinary tract infections","volume":"12","author":"Haghighatpanah","year":"2019","journal-title":"Infect. Drug Resist."},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Sora, V.M., Meroni, G., Martino, P.A., Soggiu, A., Bonizzi, L., and Zecconi, A. (2021). Extraintestinal Pathogenic Escherichia coli: Virulence Factors and Antibiotic Resistance. Pathogens, 10.","DOI":"10.3390\/pathogens10111355"},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Kathayat, D., Lokesh, D., Ranjit, S., and Rajashekara, G. (2021). Avian Pathogenic Escherichia coli (APEC): An Overview of Virulence and Pathogenesis Factors, Zoonotic Potential, and Control Strategies. Pathogens, 10.","DOI":"10.3390\/pathogens10040467"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"213","DOI":"10.11604\/pamj.2020.37.213.24988","article-title":"Prevalence of extended-spectrum \u03b2-lactamase (ESBL) and molecular detection of blaTEM, blaSHV and blaCTX-M genotypes among Enterobacteriaceae isolates from patients in Khartoum, Sudan","volume":"37","author":"Dirar","year":"2020","journal-title":"Pan Afr. Med. J."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1033","DOI":"10.1016\/S1473-3099(25)00118-5","article-title":"The WHO Bacterial Priority Pathogens List 2024: A prioritisation study to guide research, development, and public health strategies against antimicrobial resistance","volume":"25","author":"Sati","year":"2025","journal-title":"Lancet Infect. Dis."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"e00115-18","DOI":"10.1128\/CMR.00115-18","article-title":"NDM Metallo-\u03b2-Lactamases and Their Bacterial Producers in Health Care Settings","volume":"32","author":"Wu","year":"2019","journal-title":"Clin. Microbiol. Rev."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1111\/nyas.14223","article-title":"Plasmid evolution in carbapenemase-producing Enterobacteriaceae: A review","volume":"1457","author":"Kopotsa","year":"2019","journal-title":"Ann. N. Y. Acad. Sci."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"S9","DOI":"10.1093\/infdis\/jiw402","article-title":"Interplay Between Antibiotic Resistance and Virulence During Disease Promoted by Multidrug-Resistant Bacteria","volume":"215","author":"Geisinger","year":"2017","journal-title":"J. Infect. Dis."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"e61","DOI":"10.1093\/cid\/ciw353","article-title":"Management of Adults with Hospital-acquired and Ventilator-associated Pneumonia: 2016 Clinical Practice Guidelines by the Infectious Diseases Society of America and the American Thoracic Society","volume":"63","author":"Kalil","year":"2016","journal-title":"Clin. Infect. Dis."},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Jorgensen, J.H., Carroll, K.C., Funke, G., Pfaller, M.A., Landry, M.L., and Richter, S.S. (2015). Escherichia, Shigella, and Salmonella. Manual of Clinical Microbiology, Wiley.","DOI":"10.1128\/9781555817381"},{"key":"ref_27","unstructured":"Clinical & Laboratory Standards Institute (CLSI) (2025). Performance Standards for Antimicrobial Susceptibility Testing, CLSI. [35th ed.]."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"34900","DOI":"10.1074\/jbc.M505333200","article-title":"High Resolution crystal structures of the trans-enamine intermediates formed by sulbactam and clavulanic acid and E166A SHV-1 \u03b2-lactamase","volume":"280","author":"Padayatti","year":"2005","journal-title":"J. Biol. Chem."},{"key":"ref_29","first-page":"189","article-title":"Modified Hodge test: A simple and effective test for detection of carbapenemase production","volume":"3","author":"Amjad","year":"2011","journal-title":"Iran. J. Microbiol."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"3798","DOI":"10.1128\/JCM.40.10.3798-3801.2002","article-title":"Imipenem-EDTA disk method for differentiation of metallo-\u03b2-lactamase-producing clinical isolates of Pseudomonas spp. and Acinetobacter spp.","volume":"40","author":"Yong","year":"2002","journal-title":"J. Clin. Microbiol."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1016\/S0580-9517(08)70447-1","article-title":"2 Serotyping of Escherichia coli","volume":"14","year":"1984","journal-title":"Methods Microbiol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"3107","DOI":"10.1111\/1462-2920.14713","article-title":"Characterization and rapid identification of phylogroup G in Escherichia coli, a lineage with high virulence and antibiotic resistance potential","volume":"21","author":"Clermont","year":"2019","journal-title":"Environ. Microbiol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1080\/21505594.2020.1859852","article-title":"Antimicrobial resistance and gene regulation in Enteroaggregative Escherichia coli from Egyptian children with diarrhoea: Similarities and differences","volume":"12","author":"Abdelwahab","year":"2021","journal-title":"Virulence"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: A flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing","volume":"19","author":"Bankevich","year":"2012","journal-title":"J. Comput. Biol."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: Rapid prokaryotic genome annotation","volume":"30","author":"Seemann","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"1355","DOI":"10.1128\/JCM.06094-11","article-title":"Multilocus sequence typing of total-genome-sequenced bacteria","volume":"50","author":"Larsen","year":"2012","journal-title":"J. Clin. Microbiol."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"2410","DOI":"10.1128\/JCM.00008-15","article-title":"Rapid and Easy In Silico Serotyping of Escherichia coli Isolates by Use of Whole-Genome Sequencing Data","volume":"53","author":"Joensen","year":"2015","journal-title":"J. Clin. Microbiol."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"3895","DOI":"10.1128\/AAC.02412-14","article-title":"In silico detection and typing of plasmids. Antimicrob using PlasmidFinder and plasmid multilocus sequence typing","volume":"58","author":"Carattoli","year":"2014","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"3491","DOI":"10.1093\/jac\/dkaa345","article-title":"ResFinder 4.0 for predictions of phenotypes from genotypes","volume":"75","author":"Bortolaia","year":"2020","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"1501","DOI":"10.1128\/JCM.03617-13","article-title":"Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli","volume":"52","author":"Joensen","year":"2014","journal-title":"J. Clin. Microbiol."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"e01269-20","DOI":"10.1128\/JCM.01269-20","article-title":"In Silico Genotyping of Escherichia coli Isolates for Extraintestinal Virulence Genes by Use of Whole-Genome Sequencing Data","volume":"58","author":"Tetzschner","year":"2020","journal-title":"J. Clin. Microbiol."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"btag129","DOI":"10.1093\/bioinformatics\/btag129","article-title":"Whole-genome prediction of bacterial pathogenic capacity on novel bacteria using protein language models with PathogenFinder2","volume":"42","author":"Florensa","year":"2026","journal-title":"Bioinformatics"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"e000143","DOI":"10.1099\/acmi.0.000143","article-title":"Easy phylotyping of Escherichia coli via the EzClermont web app and command-line tool","volume":"2","author":"Waters","year":"2020","journal-title":"Access Microbiol."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"944","DOI":"10.1093\/bioinformatics\/16.10.944","article-title":"Artemis: Sequence visualization and annotation","volume":"16","author":"Rutherford","year":"2000","journal-title":"Bioinformatics"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"W484","DOI":"10.1093\/nar\/gkad326","article-title":"Proksee: In-depth characterization and visualization of bacterial genomes","volume":"51","author":"Grant","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"3422","DOI":"10.1093\/bioinformatics\/bti553","article-title":"ACT: The Artemis Comparison Tool","volume":"21","author":"Carver","year":"2005","journal-title":"Bioinformatics"},{"key":"ref_48","unstructured":"(2025, November 09). The NCBI Pathogen Detection Project, Available online: https:\/\/www.ncbi.nlm.nih.gov\/pathogens\/."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"D757","DOI":"10.1093\/nar\/gkae902","article-title":"EnteroBase in 2025: Exploring the genomic epidemiology of bacterial pathogens","volume":"53","author":"Dyer","year":"2025","journal-title":"Nucleic Acids Res."},{"key":"ref_50","doi-asserted-by":"crossref","unstructured":"Saratto, T., Visuri, K., Lehtinen, J., Ortega-Sanz, I., Steenwyk, J.L., and Sihvonen, S. (2025). Solu: A cloud platform for real-time genomic pathogen surveillance. BMC Bioinform., 26.","DOI":"10.1186\/s12859-024-06005-z"},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"1530","DOI":"10.1093\/molbev\/msaa015","article-title":"IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era","volume":"37","author":"Minh","year":"2020","journal-title":"Mol. Biol. Evol."},{"key":"ref_52","doi-asserted-by":"crossref","unstructured":"Kocsis, B., Guly\u00e1s, D., and Szab\u00f3, D. (2022). Emergence and Dissemination of Extraintestinal Pathogenic High-Risk International Clones of Escherichia coli. Life, 12.","DOI":"10.3390\/life12122077"},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1007\/s40121-025-01254-8","article-title":"Dual Transmission Dynamics of Carbapenem Resistance in Pediatric Oncology: Plasmid-Mediated and Clonal Spread of blaNDM-5 Enterobacterales","volume":"15","author":"Jalal","year":"2026","journal-title":"Infect. Dis. Ther."},{"key":"ref_54","doi-asserted-by":"crossref","unstructured":"Zakaria, A.S., Edward, E.A., and Mohamed, N.M. (2022). Pathogenicity Islands in Uropathogenic Escherichia coli Clinical Isolate of the Globally Disseminated O25:H4-ST131 Pandemic Clonal Lineage: First Report from Egypt. Antibiotics, 11.","DOI":"10.3390\/antibiotics11111620"},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"2640","DOI":"10.1093\/jac\/dks261","article-title":"Identification of acquired antimicrobial resistance genes","volume":"67","author":"Zankari","year":"2012","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"3066","DOI":"10.1093\/jac\/dkw258","article-title":"Impact of AAC(6\u2032)-Ib-cr in combination with chromosomal-mediated mechanisms on clinical quinolone resistance in Escherichia coli","volume":"71","author":"Machuca","year":"2016","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"2538","DOI":"10.1128\/JCM.00737-17","article-title":"Development of a Web Tool for Escherichia coli Subtyping Based on fimH Alleles","volume":"55","author":"Roer","year":"2017","journal-title":"J. Clin. Microbiol."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"1091","DOI":"10.1111\/1574-6976.12076","article-title":"Coping with low pH: Molecular strategies in neutralophilic bacteria","volume":"38","author":"Lund","year":"2014","journal-title":"FEMS Microbiol. Rev."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"2360","DOI":"10.1128\/AEM.02634-07","article-title":"Evolution of the iss Gene in Escherichia coli","volume":"74","author":"Johnson","year":"2008","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"827","DOI":"10.4049\/jimmunol.148.3.827","article-title":"Role of TraT protein, an anticomplementary protein produced in Escherichia coli by R100 factor, in serum resistance","volume":"148","author":"Pramoonjago","year":"1992","journal-title":"J. Immunol."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1016\/j.vetmic.2011.05.023","article-title":"The Ins and Outs of siderophore mediated iron uptake by extra-intestinal pathogenic Escherichia coli","volume":"153","author":"Caza","year":"2011","journal-title":"Veter. Microbiol."},{"key":"ref_62","doi-asserted-by":"crossref","unstructured":"Ja\u00e9n-Luchoro, D., Kahnamouei, A., Yazdanshenas, S., Lindblom, A., Samuelsson, E., \u00c5hr\u00e9n, C., and Karami, N. (2023). Comparative Genomic Analysis of ST131 Subclade C2 of ESBL-Producing E. coli Isolates from Patients with Recurrent and Sporadic Urinary Tract Infections. Microorganisms, 11.","DOI":"10.3390\/microorganisms11071622"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"5963","DOI":"10.1128\/AEM.00786-09","article-title":"Antimicrobial resistance-conferring plasmids with similarity to virulence plasmids from avian pathogenic Escherichia coli strains in Salmonella enterica serovar kentucky isolates from poultry","volume":"75","author":"Fricke","year":"2009","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_64","doi-asserted-by":"crossref","unstructured":"Abdelwahab, R., Alhammadi, M.M., Yasir, M., Hassan, E.A., Ahmed, E.H., Abu-Faddan, N.H., Daef, E.A., Busby, S.J.W., and Browning, D.F. (2026). Antimicrobial Resistance and Comparative Genome Analysis of High-Risk Escherichia coli Strains Isolated from Egyptian Children with Diarrhoea. Microorganisms, 14.","DOI":"10.3390\/microorganisms14010247"},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"5694","DOI":"10.1073\/pnas.1322678111","article-title":"Global dissemination of a multidrug resistant Escherichia coli clone","volume":"111","author":"Petty","year":"2014","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"17394","DOI":"10.1038\/s41598-019-54004-5","article-title":"An Escherichia coli ST131 pangenome atlas reveals population structure and evolution across 4,071 isolates","volume":"9","author":"Decano","year":"2019","journal-title":"Sci. Rep."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"2907","DOI":"10.3201\/eid2612.201221","article-title":"Trends in Population Dynamics of Escherichia coli Sequence Type 131, Calgary, Alberta, Canada, 2006\u20132016","volume":"26","author":"Peirano","year":"2020","journal-title":"Emerg. Infect. Dis."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"494","DOI":"10.1038\/s41467-023-43854-3","article-title":"Global emergence of a hypervirulent carbapenem-resistant Escherichia coli ST410 clone","volume":"15","author":"Ba","year":"2024","journal-title":"Nat. Commun."},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"e575","DOI":"10.1016\/S2666-5247(21)00149-X","article-title":"Key parameters for genomics-based real-time detection and tracking of multidrug-resistant bacteria: A systematic analysis","volume":"2","author":"Gorrie","year":"2021","journal-title":"Lancet Microbe"},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"561","DOI":"10.2147\/IDR.S232943","article-title":"Characterization of the IncFII-IncFIB(pB171) Plasmid Carrying blaNDM-5 in Escherichia coli ST405 Clinical Isolate in Japan","volume":"13","author":"Takayama","year":"2020","journal-title":"Infect. Drug Resist."},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"168","DOI":"10.1186\/s12931-024-02779-1","article-title":"Multidrug-resistant pathogens and ventilator-associated pneumonia in critically ill COVID-19 and non-COVID-19 patients: A prospective observational monocentric comparative study","volume":"25","author":"Montrucchio","year":"2024","journal-title":"Respir. Res."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"1491","DOI":"10.1016\/j.cmi.2025.05.026","article-title":"Incidence, microbiology, and mortality of ventilation-associated pneumonia in a large Italian cohort of critically ill patients: Results from the PROSAFE project","volume":"31","author":"Colaneri","year":"2025","journal-title":"Clin. Microbiol. Infect."},{"key":"ref_73","doi-asserted-by":"crossref","unstructured":"Elsheikh, M., Kuriyama, A., Goto, Y., Takahashi, Y., Toyama, M., Nishikawa, Y., El Heniedy, M.A., Abdelraouf, Y.M., Okada, H., and Nakayama, T. (2024). Incidence and predictors of ventilator-associated pneumonia using a competing risk analysis: A single-center prospective cohort study in Egypt. BMC Infect. Dis., 24.","DOI":"10.1186\/s12879-024-09909-6"},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"655","DOI":"10.1080\/17476348.2025.2493366","article-title":"The pathogenesis of ventilator-associated pneumonia: Old and new mechanisms","volume":"19","author":"Ulsamer","year":"2025","journal-title":"Expert Rev. Respir. Med."},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"92","DOI":"10.12688\/f1000research.129080.1","article-title":"Hospital-acquired and ventilator-associated pneumonia caused by multidrug-resistant Gram-negative pathogens: Understanding epidemiology, resistance patterns, and implications with COVID-19","volume":"12","author":"Halat","year":"2023","journal-title":"F1000Research"},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"1527","DOI":"10.1007\/s40121-023-00820-2","article-title":"Antimicrobial Resistance in Ventilator-Associated Pneumonia: Predictive Microbiology and Evidence-Based Therapy","volume":"12","author":"Alnimr","year":"2023","journal-title":"Infect. Dis. Ther."},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"509","DOI":"10.1089\/mdr.2018.0249","article-title":"Patterns of Fluoroquinolone Resistance in Enterobacteriaceae Isolated from the Assiut University Hospitals, Egypt: A Comparative Study","volume":"25","author":"Hadiya","year":"2019","journal-title":"Microb. Drug Resist."},{"key":"ref_78","doi-asserted-by":"crossref","unstructured":"Kilinc, M. (2025). Antibiotic Resistance and Mortality in ICU Patients: A Retrospective Analysis of First Culture Growth Results. Antibiotics, 14.","DOI":"10.3390\/antibiotics14030290"},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"S521","DOI":"10.1093\/cid\/ciz824","article-title":"Epidemiology and Diagnostics of Carbapenem Resistance in Gram-negative Bacteria","volume":"69","author":"Nordmann","year":"2019","journal-title":"Clin. Infect. Dis."},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1186\/s13756-024-01497-z","article-title":"Prevalence and molecular characterization of ESBL-producing Enterobacteriaceae in Egypt: A systematic review and meta-analysis of hospital and community-acquired infections","volume":"13","author":"Azzam","year":"2024","journal-title":"Antimicrob. Resist. Infect. Control"},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"107275","DOI":"10.1016\/j.micpath.2024.107275","article-title":"Emerging threats: Antimicrobial resistance in extended-spectrum beta-lactamase and carbapenem-resistant Escherichia coli","volume":"200","author":"Aljohni","year":"2025","journal-title":"Microb. Pathog."},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"e0289524","DOI":"10.1128\/spectrum.02895-24","article-title":"Genetic characteristics and risk factors of extended-spectrum \u03b2-lactamase-producing Escherichia coli in Chinese intensive care unit: A prospective molecular epidemiology study","volume":"13","author":"Ding","year":"2025","journal-title":"Microbiol. Spectr."},{"key":"ref_83","doi-asserted-by":"crossref","first-page":"e0057421","DOI":"10.1128\/AAC.00574-21","article-title":"Evolutionary Trajectories toward Ceftazidime-Avibactam Resistance in Klebsiella pneumoniae Clinical Isolates","volume":"65","author":"Carattoli","year":"2021","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"102392","DOI":"10.1016\/j.plasmid.2018.12.001","article-title":"Contemporary IncI1 plasmids involved in the transmission and spread of antimicrobial resistance in Enterobacteriaceae","volume":"118","author":"Carattoli","year":"2021","journal-title":"Plasmid"},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"107668","DOI":"10.1016\/j.ijantimicag.2025.107668","article-title":"A systematic review and meta-analysis of the global epidemiology of carbapenem-resistant Escherichia coli","volume":"67","author":"Walker","year":"2026","journal-title":"Int. J. Antimicrob. Agents"},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1186\/s12941-025-00778-8","article-title":"Emergence and polyclonal dissemination of NDM-5\/OXA-181 carbapenemase-producing Escherichia coli in the French Indian Ocean territories","volume":"24","author":"Vedani","year":"2025","journal-title":"Ann. Clin. Microbiol. Antimicrob."},{"key":"ref_87","doi-asserted-by":"crossref","first-page":"e00135-18","DOI":"10.1128\/CMR.00135-18","article-title":"Global Extraintestinal Pathogenic Escherichia coli (ExPEC) Lineages","volume":"32","author":"Manges","year":"2019","journal-title":"Clin. Microbiol. Rev."},{"key":"ref_88","doi-asserted-by":"crossref","first-page":"8881117","DOI":"10.1155\/ijm\/8881117","article-title":"Virulence, Phylogenetic Grouping, and Antimicrobial Resistance Traits of Extraintestinal Escherichia coli in Clinical Isolates From Northwest Mexico","volume":"2025","year":"2025","journal-title":"Int. J. Microbiol."},{"key":"ref_89","doi-asserted-by":"crossref","first-page":"5949","DOI":"10.1007\/s11033-023-08532-z","article-title":"Evaluation of presence of clone ST131 and biofilm formation in ESBL producing and non-producing Escherichia coli strains","volume":"50","author":"Celebi","year":"2023","journal-title":"Mol. Biol. Rep."},{"key":"ref_90","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1186\/s12931-025-03204-x","article-title":"Whole genome comparisons reveal gut-to-lung translocation of Escherichia coli and Burkholderia cenocepacia in two cases of ventilator-associated pneumonia in ICU patients","volume":"26","author":"Gao","year":"2025","journal-title":"Respir. Res."},{"key":"ref_91","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1016\/S2213-2600(15)00427-0","article-title":"The microbiome and critical illness","volume":"4","author":"Dickson","year":"2016","journal-title":"Lancet Respir. Med."},{"key":"ref_92","doi-asserted-by":"crossref","first-page":"e0312823","DOI":"10.1128\/spectrum.03128-23","article-title":"Longitudinal genomic surveillance of multidrug-resistant Escherichia coli carriage in critical care patients","volume":"12","author":"Khoury","year":"2024","journal-title":"Microbiol. Spectr."},{"key":"ref_93","doi-asserted-by":"crossref","unstructured":"Bok, E., Mazurek-Popczyk, J., Wojciech, M., and Baldy-Chudzik, K. (2025). Extraintestinal traits of pathogenicity and sequence type lineages in commensal Escherichia coli from adults and young children: Genotypic and phenotypic profiles. Front. Microbiol., 16.","DOI":"10.3389\/fmicb.2025.1579685"},{"key":"ref_94","doi-asserted-by":"crossref","unstructured":"Santos, A.C.M., Silva, R.S., Vieira, M.A.M., Niero, C.V., Ribeiro, M.S.F., Guth, B.E.C., Gomes, T.A.T., and Silva, R.M. (2025). The diverse virulence potential of atypical enteropathogenic Escherichia coli isolated from diarrhea: The emergence of a hybrid pathotype?. Front. Microbiol., 16.","DOI":"10.3389\/fmicb.2025.1599350"},{"key":"ref_95","doi-asserted-by":"crossref","first-page":"e01361-14","DOI":"10.1128\/mBio.01361-14","article-title":"Membership and Behavior of ultra-low-diversity pathogen communities present in the gut of humans during prolonged critical illness","volume":"5","author":"Zaborin","year":"2014","journal-title":"mBio"},{"key":"ref_96","doi-asserted-by":"crossref","first-page":"386","DOI":"10.30699\/ijp.2021.521669.2556","article-title":"Molecular Characterization of Antibiotic Resistance Associated with TEM and CTX-M ESBL in Uropathogenic E. coli Strains Isolated from Outpatients","volume":"16","author":"Farzi","year":"2021","journal-title":"Iran. J. Pathol."},{"key":"ref_97","doi-asserted-by":"crossref","first-page":"4445","DOI":"10.1128\/JCM.40.12.4445-4449.2002","article-title":"Differences in virulence factors among clinical isolates of Escherichia coli causing cystitis and pyelonephritis in women and prostatitis in men","volume":"40","author":"Ruiz","year":"2002","journal-title":"J. Clin. Microbiol."},{"key":"ref_98","doi-asserted-by":"crossref","unstructured":"Machado, E., Coque, T.M., Cant\u00f3n, R., Sousa, J.C., and Peixe, L. (2013). Commensal Enterobacteriaceae as reservoirs of extended-spectrum beta-lactamases, integrons, and sul genes in Portugal. Front. Microbiol., 4.","DOI":"10.3389\/fmicb.2013.00080"},{"key":"ref_99","doi-asserted-by":"crossref","first-page":"920","DOI":"10.1093\/infdis\/173.4.920","article-title":"A Novel multiply primed polymerase chain reaction assay for identification of variant papG genes encoding the Gal(1-4)Gal-binding PapG adhesins of Escherichia coli","volume":"173","author":"Johnson","year":"1996","journal-title":"J. Infect. Dis."},{"key":"ref_100","doi-asserted-by":"crossref","first-page":"2056","DOI":"10.1128\/AEM.07320-11","article-title":"Human-associated extended-spectrum \u03b2-lactamase in the Antarctic","volume":"78","author":"Stedt","year":"2012","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_101","doi-asserted-by":"crossref","first-page":"490","DOI":"10.1128\/AAC.01025-12","article-title":"Clonal composition and community clustering of drug-susceptible and -resistant Escherichia coli isolates from bloodstream infections","volume":"57","author":"Diep","year":"2013","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_102","doi-asserted-by":"crossref","first-page":"961","DOI":"10.3346\/jkms.2005.20.6.961","article-title":"Emergence and wide dissemination of CTX-M-type ESBLs, and CMY-2- and DHA-1-type AmpC \u03b2-lactamases in Korean respiratory isolates of Klebsiella pneumoniae","volume":"20","author":"Yum","year":"2005","journal-title":"J. Korean Med. Sci."},{"key":"ref_103","doi-asserted-by":"crossref","unstructured":"Tanaka, M., Hanawa, T., Suda, T., Tanji, Y., Minh, L.N., Kondo, K., Azam, A.H., Kiga, K., Yonetani, S., and Yashiro, R. (2025). Comparative analysis of virulence-associated genes in ESBL-producing Escherichia coli isolates from bloodstream and urinary tract infections. Front. Microbiol., 16.","DOI":"10.1101\/2024.08.21.608955"},{"key":"ref_104","doi-asserted-by":"crossref","unstructured":"Huang, S., Dai, W., Sun, S., Zhang, X., and Zhang, L. (2012). Prevalence of plasmid-mediated quinolone resistance and aminoglycoside resistance determinants among carbapeneme non-susceptible Enterobacter cloacae. PLoS ONE, 7.","DOI":"10.1371\/journal.pone.0047636"},{"key":"ref_105","doi-asserted-by":"crossref","first-page":"1189","DOI":"10.1128\/jcm.30.5.1189-1193.1992","article-title":"Rapid and specific detection of the pap, afa, and sfa adhesin-encoding operons in uropathogenic Escherichia coli strains by polymerase chain reaction","volume":"30","author":"Archambaud","year":"1992","journal-title":"J. Clin. Microbiol."},{"key":"ref_106","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1086\/315217","article-title":"Extended virulence genotypes of Escherichia coli strains from patients with urosepsis in relation to phylogeny and host compromise","volume":"181","author":"Johnson","year":"2000","journal-title":"J. Infect. Dis."},{"key":"ref_107","doi-asserted-by":"crossref","first-page":"1889","DOI":"10.1128\/AEM.03222-15","article-title":"Characteristics of CTX-M Extended-Spectrum \u03b2-Lactamase-Producing Escherichia coli Strains Isolated from Multiple Rivers in Southern Taiwan","volume":"82","author":"Chen","year":"2016","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_108","doi-asserted-by":"crossref","first-page":"1939","DOI":"10.1128\/AAC.45.6.1939-1940.2001","article-title":"Carbapenem-resistant Klebsiella pneumoniae in Singapore producing IMP-1 \u03b2-lactamase and lacking an outer membrane protein","volume":"45","author":"Koh","year":"2001","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_109","doi-asserted-by":"crossref","first-page":"1234","DOI":"10.1093\/jac\/dkn111","article-title":"Prevalence of Qnr determinants among bloodstream isolates of Escherichia coli and Klebsiella pneumoniae in a Taiwanese Hospital, 1999\u20132005","volume":"61","author":"Wu","year":"2008","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_110","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1111\/j.1574-695X.1995.tb00179.x","article-title":"Detection of urovirulence factors in Escherichia coli by multiplex polymerase chain reaction","volume":"12","author":"Yamamoto","year":"1995","journal-title":"FEMS Immunol. Med. Microbiol."},{"key":"ref_111","doi-asserted-by":"crossref","first-page":"490","DOI":"10.1111\/j.1469-0691.2007.01694.x","article-title":"Emergence and spread of carbapenem-resistant strains of Acinetobacter baumannii in a tertiary-care hospital in Poland","volume":"13","author":"Wroblewska","year":"2007","journal-title":"Clin. Microbiol. Infect."},{"key":"ref_112","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1016\/j.diagmicrobio.2010.12.002","article-title":"Multiplex PCR for detection of acquired carbapenemase genes","volume":"70","author":"Poirel","year":"2011","journal-title":"Diagn. Microbiol. Infect. Dis."},{"key":"ref_113","doi-asserted-by":"crossref","first-page":"1179","DOI":"10.1099\/mic.0.27809-0","article-title":"ibeA, a virulence factor of avian pathogenic Escherichia coli","volume":"151","author":"Germon","year":"2005","journal-title":"Microbiology"},{"key":"ref_114","doi-asserted-by":"crossref","first-page":"580","DOI":"10.1099\/jmm.0.016188-0","article-title":"A novel IS26 structure surrounds bla CTX-M genes in different plasmids from German clinical Escherichia coli isolates","volume":"59","author":"Cullik","year":"2010","journal-title":"J. Med. Microbiol."},{"key":"ref_115","doi-asserted-by":"crossref","first-page":"e17514","DOI":"10.5812\/jjm.17514","article-title":"Virulence Genes and Antimicrobial Resistance Pattern in Uropathogenic Escherichia coli Isolated from Hospitalized Patients in Kashan, Iran","volume":"8","author":"Neamati","year":"2015","journal-title":"Jundishapur J. Microbiol."},{"key":"ref_116","doi-asserted-by":"crossref","first-page":"240","DOI":"10.1016\/j.jgar.2023.12.032","article-title":"Genomic insights into a blaNDM-5-carrying Escherichia coli ST167 isolate recovered from faecal sample of a healthy individual in China","volume":"36","author":"Li","year":"2024","journal-title":"J. Glob. Antimicrob. Resist."},{"key":"ref_117","doi-asserted-by":"crossref","first-page":"16457","DOI":"10.1038\/s41598-019-52859-2","article-title":"The Resistome, Mobilome, Virulome and Phylogenomics of Multidrug-Resistant Escherichia coli Clinical Isolates from Pretoria, South Africa","volume":"9","author":"Mbelle","year":"2019","journal-title":"Sci. Rep."},{"key":"ref_118","doi-asserted-by":"crossref","first-page":"924","DOI":"10.3201\/eid2805.212535","article-title":"Genomic Epidemiology of Global Carbapenemase-Producing Escherichia coli, 2015\u20132017","volume":"28","author":"Peirano","year":"2022","journal-title":"Emerg. Infect. Dis."},{"key":"ref_119","doi-asserted-by":"crossref","unstructured":"Ramadan, H., Soliman, A.M., Hiott, L.M., Elbediwi, M., Woodley, T.A., Chattaway, M.A., Jenkins, C., Frye, J.G., and Jackson, C.R. (2021). Emergence of Multidrug-Resistant Escherichia coli Producing CTX-M, MCR-1, and FosA in Retail Food from Egypt. Front. Cell. Infect. Microbiol., 11.","DOI":"10.3389\/fcimb.2021.681588"},{"key":"ref_120","doi-asserted-by":"crossref","first-page":"e30","DOI":"10.1038\/emi.2016.24","article-title":"First identification of NDM-5 associated with OXA-181 in Escherichia coli from Egypt","volume":"5","author":"Gamal","year":"2016","journal-title":"Emerg. Microbes Infect."},{"key":"ref_121","doi-asserted-by":"crossref","first-page":"324","DOI":"10.1111\/zph.12676","article-title":"Circulation of emerging NDM-5-producing Escherichia coli among humans and dogs in Egypt","volume":"67","author":"Ramadan","year":"2020","journal-title":"Zoonoses Public Health"},{"key":"ref_122","doi-asserted-by":"crossref","first-page":"e02084-20","DOI":"10.1128\/AAC.02084-20","article-title":"Coproduction of Tet(X7) Conferring High-Level Tigecycline Resistance, Fosfomycin FosA4, and Colistin Mcr-1.1 in Escherichia coli Strains from Chickens in Egypt","volume":"65","author":"Soliman","year":"2021","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_123","doi-asserted-by":"crossref","unstructured":"Soliman, A.M., Ramadan, H., Shimamoto, T., Komatsu, T., Maruyama, F., and Shimamoto, T. (2025). Detection and Genomic Characteristics of NDM-19- and QnrS11-Producing O101:H5 Escherichia coli Strain Phylogroup A: ST167 from a Poultry Farm in Egypt. Microorganisms, 13.","DOI":"10.3390\/microorganisms13081769"},{"key":"ref_124","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1186\/s13059-018-1540-z","article-title":"SKESA: Strategic k-mer extension for scrupulous assemblies","volume":"19","author":"Souvorov","year":"2018","journal-title":"Genome Biol."},{"key":"ref_125","doi-asserted-by":"crossref","first-page":"390","DOI":"10.1038\/s41598-017-18910-w","article-title":"Cryptic transmission of ST405 Escherichia coli carrying bla NDM-4 in hospital","volume":"8","author":"Zhang","year":"2018","journal-title":"Sci. Rep."},{"key":"ref_126","doi-asserted-by":"crossref","first-page":"e01924-18","DOI":"10.1128\/AAC.01924-18","article-title":"Spreading Patterns of NDM-Producing Enterobacteriaceae in Clinical and Environmental Settings in Yangon, Myanmar","volume":"63","author":"Sugawara","year":"2019","journal-title":"Antimicrob. Agents Chemother."}],"container-title":["Microorganisms"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-2607\/14\/7\/1438\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,6,30]],"date-time":"2026-06-30T17:33:02Z","timestamp":1782840782000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-2607\/14\/7\/1438"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,6,30]]},"references-count":126,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2026,7]]}},"alternative-id":["microorganisms14071438"],"URL":"https:\/\/doi.org\/10.3390\/microorganisms14071438","relation":{},"ISSN":["2076-2607"],"issn-type":[{"value":"2076-2607","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,6,30]]}}}