{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,4]],"date-time":"2025-11-04T23:50:17Z","timestamp":1762300217066,"version":"build-2065373602"},"reference-count":45,"publisher":"MDPI AG","issue":"11","license":[{"start":{"date-parts":[[2022,11,12]],"date-time":"2022-11-12T00:00:00Z","timestamp":1668211200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001871","name":"FCT (Funda\u00e7\u00e3o para a Ci\u00eancia e Tecnologia) through CESAM","doi-asserted-by":"publisher","award":["UIDP\/50017\/2020+UIDB\/50017\/2020 + LA\/P\/0094\/2020","UIDB\/04004\/2020","SFRH\/BD\/145147\/2019","CEECIND\/00977\/2020"],"award-info":[{"award-number":["UIDP\/50017\/2020+UIDB\/50017\/2020 + LA\/P\/0094\/2020","UIDB\/04004\/2020","SFRH\/BD\/145147\/2019","CEECIND\/00977\/2020"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"CFE","doi-asserted-by":"publisher","award":["UIDP\/50017\/2020+UIDB\/50017\/2020 + LA\/P\/0094\/2020","UIDB\/04004\/2020","SFRH\/BD\/145147\/2019","CEECIND\/00977\/2020"],"award-info":[{"award-number":["UIDP\/50017\/2020+UIDB\/50017\/2020 + LA\/P\/0094\/2020","UIDB\/04004\/2020","SFRH\/BD\/145147\/2019","CEECIND\/00977\/2020"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"Rafael Tavares","doi-asserted-by":"publisher","award":["UIDP\/50017\/2020+UIDB\/50017\/2020 + LA\/P\/0094\/2020","UIDB\/04004\/2020","SFRH\/BD\/145147\/2019","CEECIND\/00977\/2020"],"award-info":[{"award-number":["UIDP\/50017\/2020+UIDB\/50017\/2020 + LA\/P\/0094\/2020","UIDB\/04004\/2020","SFRH\/BD\/145147\/2019","CEECIND\/00977\/2020"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"Marta Tac\u00e3o","doi-asserted-by":"publisher","award":["UIDP\/50017\/2020+UIDB\/50017\/2020 + LA\/P\/0094\/2020","UIDB\/04004\/2020","SFRH\/BD\/145147\/2019","CEECIND\/00977\/2020"],"award-info":[{"award-number":["UIDP\/50017\/2020+UIDB\/50017\/2020 + LA\/P\/0094\/2020","UIDB\/04004\/2020","SFRH\/BD\/145147\/2019","CEECIND\/00977\/2020"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>Background: New Delhi metallo-beta-lactamase (NDM) has been spreading across the globe, but the causes of its success are poorly understood. We characterized a blaNDM-5-positive Escherichia coli strain from a Portuguese hospital and conducted comparative genomic analyses to understand the role of clonal background and horizontal gene transfer in blaNDM-5 dissemination. Methods: After blaNDM PCR screening and genome sequencing, Ec355340 was subjected to mating, transformation, and plasmid curing assays and MICs determination for several antibiotics. Comparison with data compiled from public databases was performed. Results: blaNDM-5 was in a complex integron co-located in a FIB-FII plasmid (pEc355340_NDM-5). The mating assays were unsuccessful, but plasmid transformation into a susceptible host led to resistance to all beta-lactams and to sulfamethoxazole-trimethoprim. The profile of virulence genes (n = 73) was compatible with extraintestinal pathogenesis. An analysis of genomes from public databases suggested that blaNDM-5 has rarely been associated with ST156 strains (such as Ec355340), while is has frequently been found on strains of the ST10 clonal complex. However, ST156 may play a role in the co-spreading of blaNDM and mcr genes. Regardless, comparative genomics confirmed the presence of blaNDM in similar complex integrons in plasmids (48\/100 plasmids most similar to pEc355340_NDM-5) and ST156 genomes (20\/41 blaNDM-positive genomes). Conclusions: blaNDM-5 and other blaNDM variants were more frequently associated to complex integrons than previously reported and, therefore, these platforms may be important drivers in their dissemination. The identification of blaNDM-5 for the first time in Portugal could be a game-changer in the current Portuguese antibiotic resistance scenario, as this gene encodes a higher-level resistance phenotype, and its spread may be facilitated due to the association with complex integrons.<\/jats:p>","DOI":"10.3390\/microorganisms10112243","type":"journal-article","created":{"date-parts":[[2022,11,14]],"date-time":"2022-11-14T02:34:58Z","timestamp":1668393298000},"page":"2243","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Report and Comparative Genomics of an NDM-5-Producing Escherichia coli in a Portuguese Hospital: Complex Class 1 Integrons as Important Players in blaNDM Spread"],"prefix":"10.3390","volume":"10","author":[{"given":"Rafael D. S.","family":"Tavares","sequence":"first","affiliation":[{"name":"Centre for Functional Ecology (CFE), Department of Life Sciences, University of Coimbra, Cal\u00e7ada Martim de Freitas, 3000-456 Coimbra, Portugal"},{"name":"Centre for Environmental and Marine Studies (CESAM) and Department of Biology, University of Aveiro, Campus Universit\u00e1rio Santiago, 3810-193 Aveiro, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7965-4928","authenticated-orcid":false,"given":"Marta","family":"Tac\u00e3o","sequence":"additional","affiliation":[{"name":"Centre for Environmental and Marine Studies (CESAM) and Department of Biology, University of Aveiro, Campus Universit\u00e1rio Santiago, 3810-193 Aveiro, Portugal"}]},{"given":"Elmano","family":"Ramalheira","sequence":"additional","affiliation":[{"name":"Servi\u00e7o de Patologia Cl\u00ednica, Centro Hospitalar do Baixo Vouga-EPE, Avenida Artur Ravara, 3810-501 Aveiro, Portugal"}]},{"given":"S\u00f3nia","family":"Ferreira","sequence":"additional","affiliation":[{"name":"Servi\u00e7o de Patologia Cl\u00ednica, Centro Hospitalar do Baixo Vouga-EPE, Avenida Artur Ravara, 3810-501 Aveiro, Portugal"},{"name":"Department of Medical Sciences, University of Aveiro, Campus Universit\u00e1rio Santiago, 3810-193 Aveiro, Portugal"},{"name":"Instituto de Educa\u00e7\u00e3o e Cidadania, Largo da Igreja, Mamarrosa, 3770-033 Aveiro, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7717-4939","authenticated-orcid":false,"given":"Isabel","family":"Henriques","sequence":"additional","affiliation":[{"name":"Centre for Functional Ecology (CFE), Department of Life Sciences, University of Coimbra, Cal\u00e7ada Martim de Freitas, 3000-456 Coimbra, Portugal"}]}],"member":"1968","published-online":{"date-parts":[[2022,11,12]]},"reference":[{"key":"ref_1","unstructured":"O\u2019Neill, J. (2022, January 01). Review on Antimicrobial Resistance. Antimicrobial Resistance: Tackling a Crisis for the Health and Wealth of Nations. Available online: https:\/\/amr-review.org\/Publications.html."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1016\/j.molmed.2012.03.003","article-title":"Carbapenem resistance in Enterobacteriaceae: Here is the storm!","volume":"18","author":"Nordmann","year":"2012","journal-title":"Trends Mol. Med."},{"key":"ref_3","unstructured":"WHO (World Health Organization) (2022, January 01). Global Priority List of Antibiotic-Resistant Bacteria to Guide Research, Discovery, and Development of New Antibiotics. Available online: https:\/\/www.who.int\/medicines\/publications\/en\/."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"ofy150","DOI":"10.1093\/ofid\/ofy150","article-title":"Association between carbapenem resistance and mortality among adult, hospitalized patients with serious infections due to Enterobacteriaceae: Results of a systematic literature review and meta-analysis","volume":"5","author":"Martin","year":"2018","journal-title":"Open Forum Infect. Dis."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"5046","DOI":"10.1128\/AAC.00774-09","article-title":"Characterization of a new metallo-beta-lactamase gene, blaNDM-1, and a novel erythromycin esterase gene carried on a unique genetic structure in Klebsiella pneumoniae sequence type 14 from India","volume":"53","author":"Yong","year":"2009","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"588","DOI":"10.1016\/j.tim.2011.09.005","article-title":"The emerging NDM carbapenemases","volume":"19","author":"Nordmann","year":"2011","journal-title":"Trends Microbiol."},{"key":"ref_7","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_8","doi-asserted-by":"crossref","first-page":"e00115","DOI":"10.1128\/CMR.00115-18","article-title":"NDM metallo-beta-lactamases and their bacterial producers in health care settings","volume":"32","author":"Wu","year":"2019","journal-title":"Clin. Microbiol. Rev."},{"key":"ref_9","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_10","doi-asserted-by":"crossref","first-page":"104588","DOI":"10.1016\/j.meegid.2020.104588","article-title":"Evolving trends of New Delhi Metallo-beta-lactamase (NDM) variants: A threat to antimicrobial resistance","volume":"86","author":"Farhat","year":"2020","journal-title":"Infect. Genet. Evol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"284","DOI":"10.1016\/j.jgar.2019.06.008","article-title":"Frequency distribution, genotypes and prevalent sequence types of New Delhi metallo-beta-lactamase-producing Escherichia coli among clinical isolates around the world: A review","volume":"19","author":"Dadashi","year":"2019","journal-title":"J. Glob. Antimicrob. Resist."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"e01077-15","DOI":"10.1128\/genomeA.01077-15","article-title":"Draft genome sequence of the first NDM-1-producing Providencia stuartii strain isolated in Portugal","volume":"3","author":"Manageiro","year":"2015","journal-title":"Genome Announc."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"903","DOI":"10.1093\/jac\/dkz542","article-title":"Occurrence of NDM-1-producing Morganella morganii and Proteus mirabilis in a single patient in Portugal: Probable in vivo transfer by conjugation","volume":"75","author":"Goncalves","year":"2020","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"113913","DOI":"10.1016\/j.envpol.2020.113913","article-title":"Occurrence of carbapenemase-producing Enterobacteriaceae in a Portuguese river: blaNDM, blaKPC and blaGES among the detected genes","volume":"260","author":"Teixeira","year":"2020","journal-title":"Environ. Pollut."},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Mendes, G., Ramalho, J.F., Duarte, A., Pedrosa, A., Silva, A.C., M\u00e9ndez, L., and Caneiras, C. (2022). First outbreak of NDM-1-Producing Klebsiella pneumoniae ST11 in a Portuguese Hospital Centre during the COVID-19 pandemic. Microorganisms, 10.","DOI":"10.3390\/microorganisms10020251"},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Novais, \u00c2., Ferraz, R.V., Viana, M., da Costa, P.M., and Peixe, L. (2022). NDM-1 introduction in Portugal through a ST11 KL105 Klebsiella pneumoniae widespread in Europe. Antibiotics, 11.","DOI":"10.3390\/antibiotics11010092"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"5952","DOI":"10.1128\/AAC.05108-11","article-title":"A novel variant, NDM-5, of the New Delhi metallo-\u03b2-lactamase in a multidrug-resistant Escherichia coli ST648 isolate recovered from a patient in the United Kingdom","volume":"55","author":"Hornsey","year":"2011","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"729952","DOI":"10.3389\/fmicb.2021.729952","article-title":"Genetic diversity and characteristics of blaNDM-positive plasmids in Escherichia coli","volume":"12","author":"Zhang","year":"2021","journal-title":"Front. Microbiol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"116079","DOI":"10.1016\/j.watres.2020.116079","article-title":"Genotypic and phenotypic traits of blaCTX-M-carrying Escherichia coli strains from an UV-C-treated wastewater effluent","volume":"184","author":"Tavares","year":"2020","journal-title":"Water Res."},{"key":"ref_20","first-page":"71","article-title":"Comparative genomics of the conjugation region of F-like plasmids: Five shades of F","volume":"3","author":"Moncalian","year":"2016","journal-title":"Front. Mol. Biosci."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1111\/1574-6968.12419","article-title":"Bacterial self-defence: How Escherichia coli evades serum killing","volume":"354","author":"Miajlovic","year":"2014","journal-title":"FEMS Microbiol. Lett."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1186\/s13099-019-0290-0","article-title":"Virulence factors, prevalence and potential transmission of extraintestinal pathogenic Escherichia coli isolated from different sources: Recent reports","volume":"11","author":"Sarowska","year":"2019","journal-title":"Gut Pathog."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"2023","DOI":"10.3201\/eid2312.170883","article-title":"High rate of MCR-1-producing Escherichia coli and Klebsiella pneumoniae among pigs, Portugal","volume":"23","author":"Kieffer","year":"2017","journal-title":"Emerg. Infect. Dis."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"995","DOI":"10.1111\/1462-2920.12231","article-title":"Quinolone-resistant Escherichia coli isolated from birds of prey in Portugal are genetically distinct from those isolated from water environments and gulls in Portugal, Spain and Sweden","volume":"16","author":"Vredenburg","year":"2014","journal-title":"Environ. Microbiol."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"1899","DOI":"10.3389\/fmicb.2017.01899","article-title":"Genetic background and expression of the new qepA4 gene variant recovered in clinical TEM-1- and CMY-2-producing Escherichia coli","volume":"8","author":"Manageiro","year":"2017","journal-title":"Front. Microbiol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"1518","DOI":"10.1111\/1462-2920.15930","article-title":"Phylogenomics, epigenomics, virulome, and mobilome of Gram-negative bacteria co-resistant to carbapenems and polymyxins: A One-Health systematic review and meta-analyses","volume":"24","author":"Ramaloko","year":"2022","journal-title":"Environ. Microbiol."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1089\/mdr.2010.0132","article-title":"The CTX-M conundrum: Dissemination of plasmids and Escherichia coli clones","volume":"17","author":"Naseer","year":"2011","journal-title":"Microb. Drug Resist."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"483","DOI":"10.3389\/fmicb.2020.00483","article-title":"Analysis of COMPASS, a new comprehensive plasmid database revealed prevalence of multireplicon and extensive diversity of IncF plasmids","volume":"11","author":"Douarre","year":"2020","journal-title":"Front. Microbiol."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"2518","DOI":"10.1093\/jac\/dkq347","article-title":"Replicon sequence typing of IncF plasmids carrying virulence and resistance determinants","volume":"65","author":"Villa","year":"2010","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"3981","DOI":"10.2147\/IDR.S236766","article-title":"Emergence of almost identical F36:A-:B32 plasmids carrying blaNDM-5 and qepA in Escherichia coli from both Pakistan and Canada","volume":"12","author":"Baloch","year":"2019","journal-title":"Infect. Drug Resist."},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Li, J., Lan, R., Xiong, Y., Ye, C., Yuan, M., Liu, X., Chen, X., Yu, D., Liu, B., and Lin, W. (2014). Sequential isolation in a patient of Raoultella planticola and Escherichia coli bearing a novel ISCR1 element carrying blaNDM-1. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0089893"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"2472","DOI":"10.3389\/fmicb.2019.02472","article-title":"Complex class 1 integron in a clinical Escherichia coli strain from Vietnam carrying both mcr-1 and blaNDM-1","volume":"10","author":"Tran","year":"2019","journal-title":"Front. Microbiol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"64","DOI":"10.1016\/j.jgar.2020.08.002","article-title":"Genetic characterisation of a complex class 1 integron in an NDM-1-producing Citrobacter freundii ST396 clinical strain isolated from a urine sample","volume":"23","author":"Li","year":"2020","journal-title":"J. Glob. Antimicrob. Resist."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"1131","DOI":"10.1038\/s41467-022-28819-2","article-title":"Role of mobile genetic elements in the global dissemination of the carbapenem resistance gene blaNDM","volume":"13","author":"Acman","year":"2022","journal-title":"Nat. Commun."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"16260","DOI":"10.1038\/nmicrobiol.2016.260","article-title":"Comprehensive resistome analysis reveals the prevalence of NDM and MCR-1 in Chinese poultry production","volume":"2","author":"Wang","year":"2017","journal-title":"Nat. Microbiol."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"1535","DOI":"10.1038\/ismej.2017.38","article-title":"Class 1 integrons are low-cost structures in Escherichia coli","volume":"11","author":"Lacotte","year":"2017","journal-title":"ISME J."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"242","DOI":"10.3389\/fcimb.2017.00242","article-title":"Decreased fitness and virulence in ST10 Escherichia coli harboring blaNDM-5 and mcr-1 against a ST4981 strain with blaNDM-5","volume":"7","author":"Zhang","year":"2017","journal-title":"Front. Cell Infect. Microbiol."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"739","DOI":"10.1016\/j.ijantimicag.2018.01.023","article-title":"The prevalence of colistin resistance in Escherichia coli and Klebsiella pneumoniae isolated from food animals in China: Coexistence of mcr-1 and blaNDM with low fitness cost","volume":"51","author":"Wang","year":"2018","journal-title":"Int. J. Antimicrob. Agents"},{"key":"ref_39","doi-asserted-by":"crossref","unstructured":"Ma, T., Fu, J., Xie, N., Ma, S., Lei, L., Zhai, W., Shen, Y., Sun, C., Wang, S., and Shen, Z. (2020). Fitness cost of blaNDM-5-carrying p3R-IncX3 plasmids in wild-type NDM-free Enterobacteriaceae. Microorganisms, 8.","DOI":"10.3390\/microorganisms8030377"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"5873","DOI":"10.1128\/AAC.01019-15","article-title":"Carbapenemase-producing Klebsiella pneumoniae, a key pathogen set for global nosocomial dominance","volume":"59","author":"Pitout","year":"2015","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_41","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_42","first-page":"25","article-title":"Genomic fingerprinting of bacteria using repetitive sequence-based polymerase chain reaction","volume":"5","author":"Versalovic","year":"1994","journal-title":"Methods Mol. Cell. Biol."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"490","DOI":"10.1093\/jac\/dkp498","article-title":"Development of a set of multiplex PCR assays for the detection of genes encoding important beta-lactamases in Enterobacteriaceae","volume":"65","author":"Dallenne","year":"2010","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"6461","DOI":"10.1128\/AEM.00271-06","article-title":"Biochemical and molecular characterization of tetracycline-resistant Aeromonas veronii isolates from catfish","volume":"72","author":"Nawaz","year":"2006","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1099\/00222615-22-2-125","article-title":"Distribution and genetic location of Tn7 in trimethoprim-resistant Escherichia coli","volume":"22","author":"Kraft","year":"1986","journal-title":"J. Med. Microbiol."}],"container-title":["Microorganisms"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-2607\/10\/11\/2243\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T01:17:06Z","timestamp":1760145426000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-2607\/10\/11\/2243"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,11,12]]},"references-count":45,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2022,11]]}},"alternative-id":["microorganisms10112243"],"URL":"https:\/\/doi.org\/10.3390\/microorganisms10112243","relation":{},"ISSN":["2076-2607"],"issn-type":[{"type":"electronic","value":"2076-2607"}],"subject":[],"published":{"date-parts":[[2022,11,12]]}}}