{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T11:45:04Z","timestamp":1790682304553,"version":"4.1.0"},"reference-count":70,"publisher":"Public Library of Science (PLoS)","issue":"7","license":[{"start":{"date-parts":[[2021,7,26]],"date-time":"2021-07-26T00:00:00Z","timestamp":1627257600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"universit\u00e9 des sciences et de la technologie d\u2019oran mohamed boudiaf"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"abstract":"<jats:p>The purpose of the study was to characterize the resistome, virulome, mobilome and Clustered Regularly Interspaced Short Palindromic Repeats-associated (CRISPR-Cas) system of extended-spectrum \u03b2-lactamase producing<jats:italic>Klebsiella pneumoniae<\/jats:italic>(ESBL-KP) clinical isolates and to determine their phylogenetic relatedness. The isolates were from Algeria, isolated at the University Hospital Establishment of Oran, between 2011 and 2012. ESBL-KP isolates (n = 193) were screened for several antibiotic resistance genes (ARGs) using qPCR followed by Pulsed-Field Gel Electrophoresis (PFGE). Representative isolates were selected from PFGE clusters and subjected to whole-genome sequencing (WGS). Genomic characterization of the WGS data by studying prophages, CRISPR-Cas systems, Multi-Locus Sequence Typing (MLST), serotype, ARGs, virulence genes, plasmid replicons, and their pMLST. Phylogenetic and comparative genomic were done using core genome MLST and SNP-Based analysis. Generally, the ESBL-KP isolates were polyclonal. The whole genome sequences of nineteen isolates were taken of main PFGE clusters. Sixteen sequence types (ST) were found including high-risk clones ST14, ST23, ST37, and ST147. Serotypes K1 (n = 1), K2 (n = 2), K3 (n = 1), K31 (n = 1), K62 (n = 1), and K151 (n = 1) are associated with hyper-virulence. CRISPR-Cas system was found in 47.4%, typed I-E and I-E*. About ARGs, from 193 ESBL-KP, the majority of strains were multidrug-resistant, the CTX-M-1 enzyme was predominant (99%) and the prevalence of plasmid-mediated quinolone resistance (PMQR) genes was high with<jats:italic>aac(6\u2032)-lb-cr<\/jats:italic>(72.5%) and<jats:italic>qnr\u2019s<\/jats:italic>(65.8%). From 19 sequenced isolates we identified ESBL, AmpC, and carbapenemase genes:<jats:italic>bla<\/jats:italic><jats:sub><jats:italic>CTX-M-15<\/jats:italic><\/jats:sub>(n = 19),<jats:italic>bla<\/jats:italic><jats:sub><jats:italic>OXA-48<\/jats:italic><\/jats:sub>(n = 1),<jats:italic>bla<\/jats:italic><jats:sub><jats:italic>CMY-2<\/jats:italic><\/jats:sub>(n = 2), and<jats:italic>bla<\/jats:italic><jats:sub><jats:italic>CMY-16<\/jats:italic><\/jats:sub>(n = 2), as well as non-ESBL genes:<jats:italic>qnrB1<\/jats:italic>(n = 12),<jats:italic>qnrS1<\/jats:italic>(n = 1) and<jats:italic>armA<\/jats:italic>(n = 2). We found IncF, IncN, IncL\/M, IncA\/C2, and Col replicon types, at least once per isolate. This study is the first to report<jats:italic>qnrS<\/jats:italic>in ESBL-KP in Algeria. Our analysis shows the concerning co-existence of virulence and resistance genes and would support that genomic surveillance should be a high priority in the hospital environment.<\/jats:p>","DOI":"10.1371\/journal.pone.0254805","type":"journal-article","created":{"date-parts":[[2021,7,26]],"date-time":"2021-07-26T17:34:42Z","timestamp":1627320882000},"page":"e0254805","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":12,"title":["High-risk clones of extended-spectrum \u03b2-lactamase-producing Klebsiella pneumoniae isolated from the University Hospital Establishment of Oran, Algeria (2011\u20132012)"],"prefix":"10.1371","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3966-6080","authenticated-orcid":true,"given":"Assia","family":"Zemmour","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Radia","family":"Dali-Yahia","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Makaoui","family":"Maatallah","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nadjia","family":"Saidi-Ouahrani","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bouabdallah","family":"Rahmani","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nora","family":"Benhamouche","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hissa M.","family":"Al-Farsi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christian G.","family":"Giske","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2021,7,26]]},"reference":[{"issue":"6","key":"pone.0254805.ref001","doi-asserted-by":"crossref","first-page":"2529","DOI":"10.1128\/iai.60.6.2529-2535.1992","article-title":"Mechanisms of Klebsiella pneumoniae resistance to complement-mediated killing","volume":"60","author":"S Merino","year":"1992","journal-title":"Infect Immun"},{"issue":"4","key":"pone.0254805.ref002","doi-asserted-by":"crossref","first-page":"657","DOI":"10.1128\/CMR.18.4.657-686.2005","article-title":"Extended-spectrum b-lactamases: a clinical update","volume":"18","author":"DL Paterson","year":"2005","journal-title":"Clin Microbiol 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