{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,1]],"date-time":"2026-07-01T02:56:36Z","timestamp":1782874596600,"version":"3.54.5"},"reference-count":96,"publisher":"MDPI AG","issue":"1","license":[{"start":{"date-parts":[[2026,1,21]],"date-time":"2026-01-21T00:00:00Z","timestamp":1768953600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Egyptian Ministry of Higher Education"},{"DOI":"10.13039\/501100000268","name":"Medical School, Assiut University","doi-asserted-by":"publisher","award":["BB\/R017689\/1"],"award-info":[{"award-number":["BB\/R017689\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000268","name":"Medical School, Assiut University","doi-asserted-by":"publisher","award":["BB\/Y007603\/1"],"award-info":[{"award-number":["BB\/Y007603\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Princess Nourah bint Abdulrahman University Researchers Supporting Project","award":["PNURSP2026R898"],"award-info":[{"award-number":["PNURSP2026R898"]}]},{"name":"Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>Escherichia coli is an important human pathogen that is able to cause a variety of infections, which can result in diarrhoea, urinary tract infections, sepsis, and even meningitis, depending on the pathotype of the infecting strain. Like many Gram-negative bacteria, E. coli is becoming increasingly resistant to many frontline antibiotics, including third-generation cephalosporins and carbapenems, which are often considered the antibiotics of last resort for these infections. This is particularly the case in Egypt, where multidrug-resistant (MDR) E. coli is highly prevalent. However, in spite of this, few Egyptian MDR E. coli strains have been fully characterised by genome sequencing. Here, we present the genome sequences of ten highly MDR E. coli strains, which were isolated from children who presented with diarrhoea at the Outpatients Clinic of Assiut University Children\u2019s Hospital in Assiut, Egypt. We report that they carry multiple antimicrobial resistance genes, which includes extended spectrum \u03b2-lactamase genes, as well as blaNDM and blaOXA carbapenemase genes, likely encoded on IncX3 and IncF plasmids. Many of these strains were also found to be high-risk extra-intestinal pathogenic E. coli (ExPEC) clones belonging to sequence types ST167, ST410, and ST617. Thus, their presence in the Egyptian paediatric population is particularly worrying, and this highlights the need for increased surveillance of high-priority pathogens in this part of the world.<\/jats:p>","DOI":"10.3390\/microorganisms14010247","type":"journal-article","created":{"date-parts":[[2026,1,21]],"date-time":"2026-01-21T08:48:08Z","timestamp":1768985288000},"page":"247","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Antimicrobial Resistance and Comparative Genome Analysis of High-Risk Escherichia coli Strains Isolated from Egyptian Children with Diarrhoea"],"prefix":"10.3390","volume":"14","author":[{"given":"Radwa","family":"Abdelwahab","sequence":"first","affiliation":[{"name":"Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK"},{"name":"Faculty of Medicine, Assiut University, Assiut 71515, Egypt"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-6920-1161","authenticated-orcid":false,"given":"Munirah M.","family":"Alhammadi","sequence":"additional","affiliation":[{"name":"Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9437-2996","authenticated-orcid":false,"given":"Muhammad","family":"Yasir","sequence":"additional","affiliation":[{"name":"Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ehsan A.","family":"Hassan","sequence":"additional","affiliation":[{"name":"Faculty of Medicine, Assiut University, Assiut 71515, Egypt"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Entsar H.","family":"Ahmed","sequence":"additional","affiliation":[{"name":"Faculty of Medicine, Assiut University, Assiut 71515, Egypt"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nagla H.","family":"Abu-Faddan","sequence":"additional","affiliation":[{"name":"Faculty of Medicine, Assiut University, Assiut 71515, Egypt"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Enas A.","family":"Daef","sequence":"additional","affiliation":[{"name":"Faculty of Medicine, Assiut University, Assiut 71515, Egypt"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephen J. W.","family":"Busby","sequence":"additional","affiliation":[{"name":"Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK"}],"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":"College of Health and Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,1,21]]},"reference":[{"key":"ref_1","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_2","doi-asserted-by":"crossref","first-page":"AME0014-2020","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_3","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_4","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_5","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. New York Acad. Sci."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"501","DOI":"10.1111\/joim.12342","article-title":"Global dissemination of extensively drug-resistant carbapenemase-producing Enterobacteriaceae: Clinical perspectives on detection, treatment and infection control","volume":"277","author":"Giske","year":"2015","journal-title":"J. Intern. Med."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"113","DOI":"10.4103\/2221-6189.259110","article-title":"Integron frequency of Escherichia coli strains from patients with urinary tract infection in Southwest of Iran","volume":"8","author":"Alkhudhairy","year":"2019","journal-title":"J. Acute Dis."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"1638","DOI":"10.1128\/JCM.02316-16","article-title":"In Vitro Activity of Imipenem against Carbapenemase-Positive Enterobacteriaceae Isolates Collected by the SMART Global Surveillance Program from 2008 to 2014","volume":"55","author":"Karlowsky","year":"2017","journal-title":"J. Clin. Microbiol."},{"key":"ref_9","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_10","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_11","doi-asserted-by":"crossref","first-page":"832","DOI":"10.1016\/j.jgar.2020.07.015","article-title":"Draft genome sequence of a bla(NDM-1)- and bla(OXA-244)-carrying multidrug-resistant Escherichia coli D-ST69 clinical isolate from Egypt","volume":"22","author":"Soliman","year":"2020","journal-title":"J. Glob. Antimicrob. Resist."},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Mohamed, N.M., Zakaria, A.S., and Edward, E.A. (2022). Genomic Characterization of International High-Risk Clone ST410 Escherichia coli Co-Harboring ESBL-Encoding Genes and bla(NDM-5) on IncFIA\/IncFIB\/IncFII\/IncQ1 Multireplicon Plasmid and Carrying a Chromosome-Borne bla(CMY-2) from Egypt. Antibiotics, 11.","DOI":"10.3390\/antibiotics11081031"},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Braun, S.D., Rezk, S., Brandt, C., Reinicke, M., Diezel, C., M\u00fcller, E., Frankenfeld, K., Kr\u00e4hmer, D., Monecke, S., and Ehricht, R. (2024). Tracking Multidrug Resistance in Gram-Negative Bacteria in Alexandria, Egypt (2020-2023): An Integrated Analysis of Patient Data and Diagnostic Tools. Antibiotics, 13.","DOI":"10.3390\/antibiotics13121185"},{"key":"ref_14","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_15","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_16","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_17","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_18","doi-asserted-by":"crossref","unstructured":"Wick, R.R., Judd, L.M., Gorrie, C.L., and Holt, K.E. (2017). Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput. Biol., 13.","DOI":"10.1371\/journal.pcbi.1005595"},{"key":"ref_19","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_20","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_21","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_22","doi-asserted-by":"crossref","first-page":"3895","DOI":"10.1128\/AAC.02412-14","article-title":"In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing","volume":"58","author":"Carattoli","year":"2014","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_23","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_24","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":"Johnson","year":"2020","journal-title":"J. Clin. Microbiol."},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Cosentino, S., Voldby Larsen, M., M\u00f8ller Aarestrup, F., and Lund, O. (2013). PathogenFinder--distinguishing friend from foe using bacterial whole genome sequence data. PLoS ONE, 8, Erratum in PLoS ONE. 2013, 8.","DOI":"10.1371\/annotation\/b84e1af7-c127-45c3-be22-76abd977600f"},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Ferrer Florensa, A., Almagro Armenteros, J.J., Kaas, R.S., Conradsen Clausen, P.T.L., Nielsen, H., Rost, B., and Aarestrup, F.M. (2025). Whole-genome prediction of bacterial pathogenic capacity on novel bacteria using protein language models, with PathogenFinder2. bioRxiv.","DOI":"10.1101\/2025.04.12.648497"},{"key":"ref_27","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_28","doi-asserted-by":"crossref","first-page":"acmi000143","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_29","doi-asserted-by":"crossref","first-page":"D32","DOI":"10.1093\/nar\/gkj014","article-title":"ISfinder: The reference centre for bacterial insertion sequences","volume":"34","author":"Siguier","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"W16","DOI":"10.1093\/nar\/gkw387","article-title":"PHASTER: A better, faster version of the PHAST phage search tool","volume":"44","author":"Arndt","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref_31","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_32","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_33","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_34","doi-asserted-by":"crossref","first-page":"W45","DOI":"10.1093\/nar\/gkaf397","article-title":"AutoMLST2: A web server for phylogeny and microbial taxonomy","volume":"53","author":"Pourmohsenin","year":"2025","journal-title":"Nucleic Acids Res"},{"key":"ref_35","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_36","unstructured":"(2025, November 09). The NCBI Pathogen Detection Project; National Center for Biotechnology Information: Bethesda, MD, USA; National Library of Medicine: Bethesda, MD, USA; National Institutes of Health: Bethesda, MD, USA, 2016, Available online: https:\/\/www.ncbi.nlm.nih.gov\/pathogens\/."},{"key":"ref_37","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_38","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_39","doi-asserted-by":"crossref","first-page":"8200","DOI":"10.1038\/s41467-025-63477-0","article-title":"Emergence of a carbapenem-resistant atypical uropathogenic Escherichia coli clone as an increasing cause of urinary tract infection","volume":"16","author":"Walker","year":"2025","journal-title":"Nat. Commun."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"e00337-18","DOI":"10.1128\/mSphere.00337-18","article-title":"Escherichia coli Sequence Type 410 Is Causing New International High-Risk Clones","volume":"3","author":"Roer","year":"2018","journal-title":"mSphere"},{"key":"ref_41","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_42","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1111\/j.1469-0691.2011.03570.x","article-title":"Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: An international expert proposal for interim standard definitions for acquired resistance","volume":"18","author":"Magiorakos","year":"2012","journal-title":"Clin. Microbiol. Infect."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"e00269-20","DOI":"10.1128\/mSphere.00269-20","article-title":"Novel Insights and Features of the NDM-5-Producing Escherichia coli Sequence Type 167 High-Risk Clone","volume":"5","author":"Villa","year":"2020","journal-title":"mSphere"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1038\/s42003-023-05745-7","article-title":"Carbapenem-resistant Escherichia coli exhibit diverse spatiotemporal epidemiological characteristics across the globe","volume":"7","author":"Huang","year":"2024","journal-title":"Commun. Biol."},{"key":"ref_45","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_46","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_47","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_48","doi-asserted-by":"crossref","first-page":"e29642","DOI":"10.1016\/j.heliyon.2024.e29642","article-title":"Characterization of bla(NDM-19)-producing IncX3 plasmid isolated from carbapenem-resistant Escherichia coli and Klebsiella pneumoniae","volume":"10","author":"Moussa","year":"2024","journal-title":"Heliyon"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1186\/s13073-019-0699-6","article-title":"Stepwise evolution and convergent recombination underlie the global dissemination of carbapenemase-producing Escherichia coli","volume":"12","author":"Cabanel","year":"2020","journal-title":"Genome Med."},{"key":"ref_50","doi-asserted-by":"crossref","unstructured":"Mahazu, S., Prah, I., Ayibieke, A., Sato, W., Hayashi, T., Suzuki, T., Iwanaga, S., Ablordey, A., and Saito, R. (2021). Possible Dissemination of Escherichia coli Sequence Type 410 Closely Related to B4\/H24RxC in Ghana. Front. Microbiol., 12.","DOI":"10.3389\/fmicb.2021.770130"},{"key":"ref_51","doi-asserted-by":"crossref","unstructured":"Chudejova, K., Kraftova, L., Mattioni Marchetti, V., Hrabak, J., Papagiannitsis, C.C., and Bitar, I. (2021). Genetic Plurality of OXA\/NDM-Encoding Features Characterized From Enterobacterales Recovered From Czech Hospitals. Front. Microbiol., 12.","DOI":"10.3389\/fmicb.2021.641415"},{"key":"ref_52","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."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1007\/s11033-020-06047-5","article-title":"The first evaluation relationship of integron genes and the multidrug-resistance in class A ESBLs genes in enteropathogenic Escherichia coli strains isolated from children with diarrhea in Southwestern Iran","volume":"48","author":"Jomehzadeh","year":"2021","journal-title":"Mol. Biol. Rep."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"820","DOI":"10.3923\/jbs.2009.820.824","article-title":"Detection of Shiga Toxin Producing E. coli Strains Isolated from Stool Samples of Patients with Diarrhea in Abadan Hospitals, Iran","volume":"9","author":"Jomezadeh","year":"2009","journal-title":"J. Biol. Sci."},{"key":"ref_55","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_56","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_57","doi-asserted-by":"crossref","first-page":"683","DOI":"10.1099\/jmm.0.054262-0","article-title":"Prevalence of enteroaggregative Escherichia coli and its virulence-related genes in a case-control study among children from north-eastern Brazil","volume":"62","author":"Lima","year":"2013","journal-title":"J. Med. Microbiol."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"314","DOI":"10.1093\/femsre\/fuaa008","article-title":"Molecular determinants of surface colonisation in diarrhoeagenic Escherichia coli (DEC): From bacterial adhesion to biofilm formation","volume":"44","author":"Ageorges","year":"2020","journal-title":"FEMS Microbiol. Rev."},{"key":"ref_59","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_60","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":"Vet. Microbiol."},{"key":"ref_61","doi-asserted-by":"crossref","unstructured":"Boisen, N., \u00d8sterlund, M.T., Joensen, K.G., Santiago, A.E., Mandomando, I., Cravioto, A., Chattaway, M.A., Gonyar, L.A., Overballe-Petersen, S., and Stine, O.C. (2020). Redefining enteroaggregative Escherichia coli (EAEC): Genomic characterization of epidemiological EAEC strains. PLoS Neglected Trop. Dis., 14.","DOI":"10.1371\/journal.pntd.0008613"},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1016\/j.ijmm.2012.03.002","article-title":"Virulence factors and phylogenetic grouping of Escherichia coli isolates from patients with bacteraemia of urinary tract origin relate to sex and hospital- vs. community-acquired origin","volume":"302","author":"Lundgren","year":"2012","journal-title":"Int. J. Med. Microbiol."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"2097","DOI":"10.1099\/mic.0.27499-0","article-title":"Comparison of Escherichia coli isolates implicated in human urinary tract infection and avian colibacillosis","volume":"151","author":"Giddings","year":"2005","journal-title":"Microbiology"},{"key":"ref_64","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_65","doi-asserted-by":"crossref","first-page":"UTI-0006-2012","DOI":"10.1128\/microbiolspec.UTI-0006-2012","article-title":"Reservoirs of Extraintestinal Pathogenic Escherichia coli","volume":"3","author":"Manges","year":"2015","journal-title":"Microbiol. Spectr."},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"1127","DOI":"10.1016\/S0022-5347(01)65154-1","article-title":"Genetic evidence supporting the fecal-perineal-urethral hypothesis in cystitis caused by Escherichia coli","volume":"157","author":"Yamamoto","year":"1997","journal-title":"J. Urol."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"116079","DOI":"10.1016\/j.watres.2020.116079","article-title":"Genotypic and phenotypic traits of bla(CTX-M)-carrying Escherichia coli strains from an UV-C-treated wastewater effluent","volume":"184","author":"Tavares","year":"2020","journal-title":"Water Res."},{"key":"ref_68","doi-asserted-by":"crossref","unstructured":"Maga\u00f1a-Liz\u00e1rraga, J.A., G\u00f3mez-Gil, B., Rend\u00f3n-Maldonado, J.G., Delgado-Vargas, F., Vega-L\u00f3pez, I.F., and B\u00e1ez-Flores, M.E. (2022). Genomic Profiling of Antibiotic-Resistant Escherichia coli Isolates from Surface Water of Agricultural Drainage in North-Western Mexico: Detection of the International High-Risk Lineages ST410 and ST617. Microorganisms, 10.","DOI":"10.3390\/microorganisms10030662"},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"e00757-15","DOI":"10.1128\/genomeA.00757-15","article-title":"Whole-Genome Sequences of Multidrug-Resistant Escherichia coli Strains Sharing the Same Sequence Type (ST410) and Isolated from Human and Avian Sources in Italy","volume":"3","author":"Accogli","year":"2015","journal-title":"Genome Announc."},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"e00990-20","DOI":"10.1128\/mSphere.00990-20","article-title":"Genetic Determinants of Resistance to Extended-Spectrum Cephalosporin and Fluoroquinolone in Escherichia coli Isolated from Diseased Pigs in the United States","volume":"5","author":"Hayer","year":"2020","journal-title":"mSphere"},{"key":"ref_71","doi-asserted-by":"crossref","unstructured":"Lee, S., An, J.U., Guk, J.H., Song, H., Yi, S., Kim, W.H., and Cho, S. (2021). Prevalence, Characteristics and Clonal Distribution of Extended-Spectrum \u03b2-Lactamase- and AmpC \u03b2-Lactamase-Producing Escherichia coli Following the Swine Production Stages, and Potential Risks to Humans. Front. Microbiol., 12.","DOI":"10.3389\/fmicb.2021.710747"},{"key":"ref_72","doi-asserted-by":"crossref","unstructured":"Haley, B.J., Kim, S.W., Salaheen, S., Hovingh, E., and Van Kessel, J.A.S. (2022). Virulome and genome analyses identify associations between antimicrobial resistance genes and virulence factors in highly drug-resistant Escherichia coli isolated from veal calves. PLoS ONE, 17.","DOI":"10.1371\/journal.pone.0265445"},{"key":"ref_73","doi-asserted-by":"crossref","unstructured":"Nittayasut, N., Yindee, J., Boonkham, P., Yata, T., Suanpairintr, N., and Chanchaithong, P. (2021). Multiple and High-Risk Clones of Extended-Spectrum Cephalosporin-Resistant and bla(NDM-5)-Harbouring Uropathogenic Escherichia coli from Cats and Dogs in Thailand. Antibiotics, 10.","DOI":"10.3390\/antibiotics10111374"},{"key":"ref_74","doi-asserted-by":"crossref","unstructured":"Aslam, B., Khurshid, M., Arshad, M.I., Muzammil, S., Rasool, M., Yasmeen, N., Shah, T., Chaudhry, T.H., Rasool, M.H., and Shahid, A. (2021). Antibiotic Resistance: One Health One World Outlook. Front. Cell. Infect. Microbiol., 11, Erratum in Front. Cell. Infect. 2024, 14, 1488430.","DOI":"10.3389\/fcimb.2021.771510"},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"240","DOI":"10.1016\/j.jgar.2023.12.032","article-title":"Genomic insights into a bla(NDM-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_76","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1016\/j.diagmicrobio.2018.11.007","article-title":"Characterization of an NDM-19-producing Klebsiella pneumoniae strain harboring 2 resistance plasmids from China","volume":"93","author":"Liu","year":"2019","journal-title":"Diagn. Microbiol. Infect. Dis."},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"114851","DOI":"10.1016\/j.diagmicrobio.2019.06.003","article-title":"Detection of NDM-19, a novel variant of the New Delhi metallo-\u03b2-lactamase with increased carbapenemase activity under zinc-limited conditions, in Switzerland","volume":"95","author":"Mancini","year":"2019","journal-title":"Diagn. Microbiol. Infect. Dis."},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"e01542-17","DOI":"10.1128\/genomeA.01542-17","article-title":"Complete Nucleotide Sequence of an Escherichia coli Sequence Type 410 Strain Carrying bla(NDM-5) on an IncF Multidrug Resistance Plasmid and bla(OXA-181) on an IncX3 Plasmid","volume":"6","author":"Roer","year":"2018","journal-title":"Genome Announc."},{"key":"ref_79","doi-asserted-by":"crossref","unstructured":"Oh, S., Nam, S.K., Chang, H.E., and Park, K.U. (2022). Comparative Analysis of Short- and Long-Read Sequencing of Vancomycin-Resistant Enterococci for Application to Molecular Epidemiology. Front. Cell. Infect. Microbiol., 12.","DOI":"10.3389\/fcimb.2022.857801"},{"key":"ref_80","doi-asserted-by":"crossref","unstructured":"Therrien, D.A., Konganti, K., Gill, J.J., Davis, B.W., Hillhouse, A.E., Michalik, J., Cross, H.R., Smith, G.C., Taylor, T.M., and Riggs, P.K. (2021). Complete Whole Genome Sequences of Escherichia coli Surrogate Strains and Comparison of Sequence Methods with Application to the Food Industry. Microorganisms, 9.","DOI":"10.3390\/microorganisms9030608"},{"key":"ref_81","doi-asserted-by":"crossref","unstructured":"Hammad, H.A., Abdelwahab, R., Browning, D.F., and Aly, S.A. (2025). Genome Characterization of Carbapenem-Resistant Hypervirulent Klebsiella pneumoniae Strains, Carrying Hybrid Resistance-Virulence IncHI1B\/FIB Plasmids, Isolated from an Egyptian Pediatric ICU. Microorganisms, 13.","DOI":"10.3390\/microorganisms13051058"},{"key":"ref_82","doi-asserted-by":"crossref","unstructured":"Bizri, A.R., El-Fattah, A.A., Bazaraa, H.M., Al Ramahi, J.W., Matar, M., Ali, R.A.N., El Masry, R., Moussa, J., Abbas, A.J.A., and Aziz, M.A. (2023). Antimicrobial resistance landscape and COVID-19 impact in Egypt, Iraq, Jordan, and Lebanon: A survey-based study and expert opinion. PLoS ONE, 18.","DOI":"10.1371\/journal.pone.0288550"},{"key":"ref_83","doi-asserted-by":"crossref","first-page":"1905","DOI":"10.2147\/IDR.S298920","article-title":"Landscape of Multidrug-Resistant Gram-Negative Infections in Egypt: Survey and Literature Review","volume":"14","author":"Elsharnouby","year":"2021","journal-title":"Infect. Drug Resist."},{"key":"ref_84","unstructured":"Egyptian_Drug_Authority (2025, November 09). National Guidance for the Rational Use of Duplicate Antimicrobial Therapy, Available online: https:\/\/www.edaegypt.gov.eg\/media\/yvsalsgc\/national-guidance-for-the-rational-use-of-duplicate.pdf."},{"key":"ref_85","unstructured":"Egyptian_Drug_Authority (2025, November 09). National Guidelines for Preauthorization of Restricted Antimicrobials in Hospitals National Antimicrobial Rational Use Committee, Available online: https:\/\/www.edaegypt.gov.eg\/media\/0suhvkon\/edrex-gl-cap-care-012-national-guidelines-for-preauthorization-of-restricted-antimicrobials-in-hospitals-2022-1-_.pdf."},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1016\/j.jiph.2009.09.004","article-title":"Self-medication with antibiotics in the ambulatory care setting within the Euro-Mediterranean region; results from the ARMed project","volume":"2","author":"Scicluna","year":"2009","journal-title":"J. Infect. Public Health"},{"key":"ref_87","doi-asserted-by":"crossref","first-page":"104","DOI":"10.1186\/s13756-024-01458-6","article-title":"Pharmacies and use of antibiotics: A cross sectional study in 19 Arab countries","volume":"13","author":"Hafez","year":"2024","journal-title":"Antimicrob. Resist. Infect. Control"},{"key":"ref_88","doi-asserted-by":"crossref","unstructured":"Elkhadry, S.W., and Tahoon, M.A.H. (2024). Health literacy and its association with antibiotic use and knowledge of antibiotic among Egyptian population: Cross sectional study. BMC Public Health, 24.","DOI":"10.1186\/s12889-024-19668-3"},{"key":"ref_89","doi-asserted-by":"crossref","first-page":"233","DOI":"10.3390\/antibiotics3020233","article-title":"Understanding Antibiotic Use in Minya District, Egypt: Physician and Pharmacist Prescribing and the Factors Influencing Their Practices","volume":"3","author":"Dooling","year":"2014","journal-title":"Antibiotics"},{"key":"ref_90","doi-asserted-by":"crossref","first-page":"1972","DOI":"10.1016\/S0140-6736(23)02508-4","article-title":"Antimicrobial resistance in the ongoing Gaza war: A silent threat","volume":"402","author":"Moussally","year":"2023","journal-title":"Lancet"},{"key":"ref_91","doi-asserted-by":"crossref","first-page":"e0167924","DOI":"10.1128\/msystems.01679-24","article-title":"Antimicrobial resistance in a protracted war setting: A review of the literature from Palestine","volume":"10","author":"Kumar","year":"2025","journal-title":"mSystems"},{"key":"ref_92","doi-asserted-by":"crossref","unstructured":"El Aila, N.A., and El Aish, K.I.A. (2025). Six-year antimicrobial resistance patterns of Escherichia coli isolates from different hospitals in Gaza, Palestine. BMC Microbiol., 25.","DOI":"10.1186\/s12866-025-04335-3"},{"key":"ref_93","unstructured":"(2014). Performance Standards for Antimicrobial Susceptibility Testing. Standard No. CLSI Document M100-S24. Twenty-Fourth Informational Supplement."},{"key":"ref_94","doi-asserted-by":"crossref","first-page":"322","DOI":"10.1038\/s42003-019-0569-1","article-title":"Key evolutionary events in the emergence of a globally disseminated, carbapenem resistant clone in the Escherichia coli ST410 lineage","volume":"2","author":"Feng","year":"2019","journal-title":"Commun. Biol."},{"key":"ref_95","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_96","doi-asserted-by":"crossref","first-page":"dlaf058","DOI":"10.1093\/jacamr\/dlaf058","article-title":"Genomic diversity of clinically relevant bacterial pathogens from an acute care hospital in Suva, Fiji","volume":"7","author":"Hawkey","year":"2025","journal-title":"JAC-Antimicrob. Resist."}],"container-title":["Microorganisms"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-2607\/14\/1\/247\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,23]],"date-time":"2026-01-23T05:31:50Z","timestamp":1769146310000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-2607\/14\/1\/247"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,1,21]]},"references-count":96,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,1]]}},"alternative-id":["microorganisms14010247"],"URL":"https:\/\/doi.org\/10.3390\/microorganisms14010247","relation":{},"ISSN":["2076-2607"],"issn-type":[{"value":"2076-2607","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,1,21]]}}}