title: Genome sequencing and comparative analysis of an NDM-1-producing Klebsiella pneumoniae ST15 isolated from a refugee patient.
abstract: The escalating problem of antibiotic resistance, specifically cabarpenemase and extended-spectrum β-lacatamase (ESBL) producing K. pneumoniae strains, is directly correlated with increased patient morbidity and mortality and prolonged hospitalization and costs. In this study, a comprehensive genomic analysis encompassing the resistomics, virulence repertoire and mobile genetic elements of an NDM-1 positive ESBL-producing K. pneumoniae EA-MEH ST15 isolated from a urine sample collected from a Syrian refugee was conducted. Illumina paired-end libraries were prepared and sequenced resulting in 892,300 high-quality reads. The initial assembly produced 329 contigs with a combined 5,954,825 bp and a 56.5% G+C content. Resistome analysis revealed the presence of several β-lactamases including NDM-1, SHV-28, CTX-M-15 and OXA-1 in addition to 18 other genes encoding for resistance, among which are aph(3')-Ia, aac(6')Ib-cr, armA, strB, strA and aadA2 genes. Additionally, five plasmids IncFIB(Mar), IncHI1B, IncFIB(pKPHS1), IncFIB(K) and IncFII(K) and four integrated phages were detected. In silico MLST analysis revealed that the isolate was of sequence type ST15. To our knowledge this is the first in-depth genomic analysis of a NDM-1 positive K. pneumoniae ST15 in Lebanon associated with the recent population migration. The potential dissemination of such MDR strains is an important public health concern.
authors.affiliation: a Department of Natural Sciences, School of Arts and Sciences , Lebanese American University , Byblos , Lebanon.
authors.forename: Tamara
authors.initials: T
authors.lastname: Salloum
authors.affiliation: a Department of Natural Sciences, School of Arts and Sciences , Lebanese American University , Byblos , Lebanon.
authors.forename: Harout
authors.initials: H
authors.lastname: Arabaghian
authors.affiliation: a Department of Natural Sciences, School of Arts and Sciences , Lebanese American University , Byblos , Lebanon.
authors.forename: Sahar
authors.initials: S
authors.lastname: Alousi
authors.affiliation: b Clinical Laboratory , The Middle East Institute of Health , Bsalim , Lebanon.
authors.forename: Edmond
authors.initials: E
authors.lastname: Abboud
authors.affiliation: a Department of Natural Sciences, School of Arts and Sciences , Lebanese American University , Byblos , Lebanon.
authors.forename: Sima
authors.identifier: http://orcid.org/0000-0002-3653-8940
authors.initials: S
authors.lastname: Tokajian
mesh_terms: D000369:Aged, 80 and over; D001482:Base Composition; D024881:Drug Resistance, Bacterial; D016680:Genome, Bacterial; D006801:Humans; D020071:Interspersed Repetitive Sequences; D007710:Klebsiella Infections / Q000382:microbiology*; D007711:Klebsiella pneumoniae / Q000201:enzymology* / Q000235:genetics* / Q000302:isolation & purification; D008297:Male; D039002:Prophages / Q000235:genetics; D012036:Refugees; D017422:Sequence Analysis, DNA; D037521:Virulence Factors / Q000235:genetics; D000073336:Whole Genome Sequencing; D001618:beta-Lactamases / Q000378:metabolism*
chemical_list: D037521:Virulence Factors; D001618:beta-Lactamases; C552864:beta-lactamase NDM-1
keywords: ESBL; Klebsiella pneumoniae; MDR; Middle East; NDM-1; SHV-28; ST15; draft-genome sequencing