{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,17]],"date-time":"2026-04-17T12:57:47Z","timestamp":1776430667013,"version":"3.51.2"},"reference-count":51,"publisher":"MDPI AG","issue":"4","license":[{"start":{"date-parts":[[2026,4,17]],"date-time":"2026-04-17T00:00:00Z","timestamp":1776384000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"EURGen-RefLabCap project"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>In 2023, the European Centre for Disease Prevention and Control surveillance report highlighted an increasing number of carbapenem-resistant Escherichia coli isolates carrying the less common blaNDM-5 variant in Europe. The aim of this study was to investigate the molecular epidemiology of NDM-producing (New Delhi metallo-\u03b2-lactamase) E. coli isolates collected in Croatia over a one-year period. A total of 160 carbapenemase-producing E. coli isolates were reported through national surveillance in Croatia between March 2023 and March 2024. Whole-genome sequencing was performed on 22 NDM-producing E. coli isolates. Phylogenetic analysis identified 17 sequence types, indicating high diversity and polyclonal spread. High variability in resistome profiles and co-occurrence of resistance genes across multiple antimicrobial classes indicate multidrug resistance. The predominant blaNDM variant was blaNDM-1 (77.27%), followed by blaNDM-5 (22.73%). Co-occurrence of blaNDM with extended-spectrum \u03b2-lactamase (ESBL) encoding genes was detected in 12\/22 isolates (54.55%). Plasmid analysis identified 22 different replicon types, with IncFII (54.54%) and IncA\/C2 (45.45%) being the most frequent. Our findings provide insights into the molecular epidemiology of NDM-producing E. coli at the national level, highlighting the presence of the blaNDM-5 variant. These results emphasize the need for genomic surveillance and strengthened infection control strategies to better understand and limit its spread.<\/jats:p>","DOI":"10.3390\/microorganisms14040909","type":"journal-article","created":{"date-parts":[[2026,4,17]],"date-time":"2026-04-17T11:53:46Z","timestamp":1776426826000},"page":"909","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Molecular Epidemiology of NDM-Producing Escherichia coli Isolates in Croatia from March 2023 to March 2024"],"prefix":"10.3390","volume":"14","author":[{"given":"Josip","family":"Ujevi\u0107","sequence":"first","affiliation":[{"name":"Department of Clinical Microbiology, University Hospital for Infectious Diseases \u201cDr. Fran Mihaljevi\u0107\u201d, 10000 Zagreb, Croatia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3554-3668","authenticated-orcid":false,"given":"Marko","family":"Jeli\u0107","sequence":"additional","affiliation":[{"name":"Department of Clinical Microbiology, University Hospital for Infectious Diseases \u201cDr. Fran Mihaljevi\u0107\u201d, 10000 Zagreb, Croatia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6232-1465","authenticated-orcid":false,"given":"Arjana","family":"Tambi\u0107 Andra\u0161evi\u0107","sequence":"additional","affiliation":[{"name":"Department of Clinical Microbiology, University Hospital for Infectious Diseases \u201cDr. Fran Mihaljevi\u0107\u201d, 10000 Zagreb, Croatia"},{"name":"Dental School of Medicine, University of Zagreb, 10000 Zagreb, Croatia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5542-9192","authenticated-orcid":false,"given":"Iva","family":"Buti\u0107","sequence":"additional","affiliation":[{"name":"Department of Clinical Microbiology, University Hospital for Infectious Diseases \u201cDr. Fran Mihaljevi\u0107\u201d, 10000 Zagreb, Croatia"},{"name":"Dental School of Medicine, University of Zagreb, 10000 Zagreb, Croatia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2026,4,17]]},"reference":[{"key":"ref_1","unstructured":"European Centre for Disease Prevention and Control, and World Health Organization (2022). Antimicrobial Resistance Surveillance in Europe 2022: 2020 Data, Publications Office of the European Union. Available online: https:\/\/www.ecdc.europa.eu\/sites\/default\/files\/documents\/Joint-WHO-ECDC-AMR-report-2022.pdf."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"629","DOI":"10.1016\/S0140-6736(21)02724-0","article-title":"Global burden of bacterial antimicrobial resistance in 2019: A systematic analysis","volume":"399","author":"Murray","year":"2022","journal-title":"Lancet"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"S28","DOI":"10.1093\/infdis\/jiw282","article-title":"The Epidemiology of Carbapenem-Resistant Enterobacteriaceae: The Impact and Evolution of a Global Menace","volume":"215","author":"Logan","year":"2017","journal-title":"J. Infect. Dis."},{"key":"ref_4","unstructured":"(2024, November 08). Growing Resistance to Last-Line Antibiotics: 2013. Available online: https:\/\/antibiotic.ecdc.europa.eu\/en\/publications-data\/growing-resistance-last-line-antibiotics-2013."},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Sheu, C.-C., Chang, Y.-T., Lin, S.-Y., Chen, Y.-H., and Hsueh, P.-R. (2019). Infections Caused by Carbapenem-Resistant Enterobacteriaceae: An Update on Therapeutic Options. Front. Microbiol., 10.","DOI":"10.3389\/fmicb.2019.00080"},{"key":"ref_6","first-page":"913","article-title":"Co-transfer of mcr-1 and mcr-3 variant in Escherichia coli ST1632 isolate in China: Silence is not always golden","volume":"45","author":"Li","year":"2025","journal-title":"Pak. Vet. J."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"16581","DOI":"10.1038\/s41598-025-98206-6","article-title":"Emergence of transferable tigecycline and eravacycline resistance gene tet(X4) in Escherichia coli isolates from Iran","volume":"15","author":"Haeili","year":"2025","journal-title":"Sci. Rep."},{"key":"ref_8","first-page":"390","article-title":"Prevalence and sequence analysis of Escherichia coli harboring colistin, gentamicin, streptomycin, tetracycline and quinolone resistance genes from commercial broilers","volume":"45","author":"Madni","year":"2025","journal-title":"Pak. Vet. J."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"6320","DOI":"10.1038\/s41598-025-90761-2","article-title":"Genomic insights into plasmid mediated AMR genes, virulence factors and mobile genetic elements in raw milk Escherichia coli from Gujarat, India","volume":"15","author":"Mangroliya","year":"2025","journal-title":"Sci. Rep."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1128\/microbiolspec.ARBA-0026-2017","article-title":"Antimicrobial Resistance in Escherichia coli","volume":"6","author":"Poirel","year":"2018","journal-title":"Microbiol. Spectr."},{"key":"ref_11","unstructured":"Tobin, E.H., and Zahra, F. (2026, March 22). Nosocomial Infections, StatPearls [Internet], Available online: https:\/\/www.ncbi.nlm.nih.gov\/books\/NBK559312\/."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"e01428-25","DOI":"10.1128\/mbio.01428-25","article-title":"Zoonotic Escherichia coli and urinary tract infections in Southern California","volume":"16","author":"Aziz","year":"2025","journal-title":"mBio"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"e443","DOI":"10.1016\/S2666-5247(22)00037-4","article-title":"Gut colonisation by extended-spectrum \u03b2-lactamase-producing Escherichia coli and its association with the gut microbiome and metabolome in Dutch adults: A matched case-control study","volume":"3","author":"Ducarmon","year":"2022","journal-title":"Lancet Microbe"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"5426","DOI":"10.1038\/s41467-025-61327-7","article-title":"Suppression of gut colonization by multidrug-resistant Escherichia coli clinical isolates through cooperative niche exclusion","volume":"16","author":"Wende","year":"2025","journal-title":"Nat. Commun."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1016\/j.phrs.2016.03.028","article-title":"Off-Target drug effects resulting in altered gene expression events with epigenetic and \u201cQuasi-Epigenetic origins\u201d","volume":"107","author":"Anderson","year":"2016","journal-title":"Pharmacol. Res."},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Capelo-Mart\u00ednez, J., and Igrejas, G. (2019). Beta-Lactams. Antibiotic Drug Resistance, Wiley. [1st ed.].","DOI":"10.1002\/9781119282549"},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"De Angelis, G., Del Giacomo, P., Posteraro, B., Sanguinetti, M., and Tumbarello, M. (2020). Molecular Mechanisms, Epidemiology, and Clinical Importance of \u03b2-Lactam Resistance in Enterobacteriaceae. Int. J. Mol. Sci., 21.","DOI":"10.3390\/ijms21145090"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1098\/rstb.1980.0049","article-title":"The structure of \u03b2-lactamases","volume":"289","author":"Ambler","year":"1980","journal-title":"Philos. Trans. R. Soc. Lond. B Biol. Sci."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"e00397-20","DOI":"10.1128\/AAC.00397-20","article-title":"Metallo-\u03b2-Lactamases: Structure, Function, Epidemiology, Treatment Options, and the Development Pipeline","volume":"64","author":"Boyd","year":"2020","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"917","DOI":"10.1080\/14756366.2017.1344235","article-title":"Beta-lactamase database (BLDB)\u2013structure and function","volume":"32","author":"Naas","year":"2017","journal-title":"J. Enzym. Inhib. Med. Chem."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"e00587-22","DOI":"10.1128\/spectrum.00587-22","article-title":"Role of Chromosome- and\/or Plasmid-Located blaNDM on the Carbapenem Resistance and the Gene Stability in Escherichia coli","volume":"10","author":"Sakamoto","year":"2022","journal-title":"Microbiol. Spectr."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"e00704-25","DOI":"10.1128\/msphere.00704-25","article-title":"Global geographic and genomic epidemiology analysis of carbapenem-resistant Escherichia coli carrying blaNDM-9","volume":"10","author":"Sheng","year":"2025","journal-title":"mSphere"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"2609","DOI":"10.1038\/s41598-021-82166-8","article-title":"Increasing New Delhi metallo-\u03b2-lactamase-positive Escherichia coli among carbapenem non-susceptible Enterobacteriaceae in Taiwan during 2016 to 2018","volume":"11","author":"Huang","year":"2021","journal-title":"Sci. Rep."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"dlab032","DOI":"10.1093\/jacamr\/dlab032","article-title":"Dissemination mechanisms of NDM genes in hospitalized patients","volume":"3","author":"Zhai","year":"2021","journal-title":"JAC-Antimicrob. Resist."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"dlae124","DOI":"10.1093\/jacamr\/dlae124","article-title":"Genomic characterization of carbapenemase-producing Enterobacterales from Dhaka food markets unveils the spread of high-risk antimicrobial-resistant clones and plasmids co-carrying blaNDM and mcr-1.1","volume":"6","author":"Nisa","year":"2024","journal-title":"JAC Antimicrob. Resist."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"114","DOI":"10.1186\/s13756-025-01639-x","article-title":"NDM-1 plasmid clustering reflects clonal transmission of Klebsiella pneumoniae ST147 in four hospitals in Berlin, Germany","volume":"14","author":"Weber","year":"2025","journal-title":"Antimicrob. Resist. Infect. Control"},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Li, L., Gao, Y., Wang, L., Lu, F., Ji, Q., Zhang, Y., Yang, S., Cheng, P., Sun, F., and Qu, S. (2024). The effects of NDM-5 on Escherichia coli and the screening of interacting proteins. Front. Microbiol., 15.","DOI":"10.3389\/fmicb.2024.1328572"},{"key":"ref_28","unstructured":"European Centre for Disease Prevention and Control (2023). Increase in Escherichia coli Isolates Carrying blaNDM-5 in the European Union\/European Economic Area, 2012\u20132022, ECDC."},{"key":"ref_29","unstructured":"Andrews, S. (2025, May 01). FastQC: A Quality Control Tool for High Throughput Sequence Data. Available online: https:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc\/."},{"key":"ref_30","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_31","doi-asserted-by":"crossref","first-page":"1072","DOI":"10.1093\/bioinformatics\/btt086","article-title":"QUAST: Quality assessment tool for genome assemblies","volume":"29","author":"Gurevich","year":"2013","journal-title":"Bioinformatics"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1128\/JCM.02452-13","article-title":"Rapid Whole-Genome Sequencing for Detection and Characterization of Microorganisms Directly from Clinical Samples","volume":"52","author":"Hasman","year":"2014","journal-title":"J. Clin. Microbiol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"1529","DOI":"10.1128\/JCM.02981-13","article-title":"Benchmarking of Methods for Genomic Taxonomy","volume":"52","author":"Larsen","year":"2014","journal-title":"J. Clin. Microbiol."},{"key":"ref_34","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_35","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_36","doi-asserted-by":"crossref","first-page":"12728","DOI":"10.1038\/s41598-021-91456-0","article-title":"AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence","volume":"11","author":"Feldgarden","year":"2021","journal-title":"Sci. Rep."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"524","DOI":"10.1186\/s13059-014-0524-x","article-title":"The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes","volume":"15","author":"Treangen","year":"2014","journal-title":"Genome Biol."},{"key":"ref_38","unstructured":"RStudio Team (2020). RStudio: Integrated Development for R, RStudio Team. Available online: https:\/\/posit.co."},{"key":"ref_39","unstructured":"WHO (2024). Bacterial Priority Pathogens List 2024: Bacterial Pathogens of Public Health Importance, to Guide Research, Development, and Strategies to Prevent and Control Antimicrobial Resistance, World Health Organization. [1st ed.]."},{"key":"ref_40","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_41","doi-asserted-by":"crossref","first-page":"1355","DOI":"10.1007\/s10096-022-04493-6","article-title":"Molecular analysis of OXA-48-producing Escherichia coli in Switzerland from 2019 to 2020","volume":"41","author":"Findlay","year":"2022","journal-title":"Eur. J. Clin. Microbiol. Infect. Dis."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"e01515-24","DOI":"10.1128\/jcm.01515-24","article-title":"Rapidly spreading Enterobacterales with OXA-48-like carbapenemases","volume":"63","author":"Peirano","year":"2025","journal-title":"J. Clin. Microbiol."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"2400727","DOI":"10.2807\/1560-7917.ES.2024.29.47.2400727","article-title":"Emergence of Escherichia coli ST131 carrying carbapenemase genes, European Union\/European Economic Area, August 2012 to May 2024","volume":"29","author":"Kohlenberg","year":"2024","journal-title":"Eurosurveillance"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"319","DOI":"10.2147\/IDR.S444117","article-title":"Molecular characteristics and antimicrobial susceptibility profiles of blaKPC-producing Escherichia coli isolated from a teaching hospital in Shanghai, China","volume":"17","author":"Cao","year":"2024","journal-title":"Infect. Drug Resist."},{"key":"ref_45","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_46","doi-asserted-by":"crossref","first-page":"565","DOI":"10.1128\/CMR.00116-14","article-title":"The Role of Epidemic Resistance Plasmids and International High-Risk Clones in the Spread of Multidrug-Resistant Enterobacteriaceae","volume":"28","author":"Mathers","year":"2015","journal-title":"Clin. Microbiol. Rev."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"106055","DOI":"10.1016\/j.psj.2025.106055","article-title":"Emerging threat of antimicrobial resistance determinants and plasmid replicon types acquisition by Escherichia coli of poultry and other food-producing animal origin in China: Local findings with global implications","volume":"104","author":"Shoaib","year":"2025","journal-title":"Poult. Sci."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1016\/j.rvsc.2022.05.016","article-title":"CpxR negatively regulates IncFII-replicon plasmid pEC011 conjugation by directly binding to multi-promoter regions","volume":"150","author":"Jia","year":"2022","journal-title":"Res. Vet. Sci."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"847","DOI":"10.1016\/j.csbj.2023.01.004","article-title":"Molecular epidemiology and genomic insights into the transmission of carbapenem-resistant NDM-producing Escherichia coli","volume":"21","author":"Xu","year":"2023","journal-title":"Comput. Struct. Biotechnol. J."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1016\/j.jgar.2023.12.006","article-title":"The occurrence of the carbapenemase gene, blaNDM-5, on a transmissible IncX3 plasmid in multidrug-resistant Escherichia coli isolated from a farm dog","volume":"36","author":"Daaboul","year":"2024","journal-title":"J. Glob. Antimicrob. Resist."},{"key":"ref_51","unstructured":"European Centre for Disease Prevention and Control, and World Health Organization (2023). Antimicrobial Resistance Surveillance in Europe 2023: 2021 Data, Publications Office of the European Union. Available online: https:\/\/www.ecdc.europa.eu\/sites\/default\/files\/documents\/Antimicrobial%20resistance%20surveillance%20in%20Europe%202023%20-%202021%20data.pdf."}],"container-title":["Microorganisms"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-2607\/14\/4\/909\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,4,17]],"date-time":"2026-04-17T12:12:32Z","timestamp":1776427952000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-2607\/14\/4\/909"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,4,17]]},"references-count":51,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2026,4]]}},"alternative-id":["microorganisms14040909"],"URL":"https:\/\/doi.org\/10.3390\/microorganisms14040909","relation":{},"ISSN":["2076-2607"],"issn-type":[{"value":"2076-2607","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,4,17]]}}}