Genome sequencing and comparative analysis of an NDM-1-producing <i>Klebsiella pneumoniae</i> ST15 isolated from a refugee patient

<p>The escalating problem of antibiotic resistance, specifically cabarpenemase and extended-spectrum β-lacatamase (ESBL) producing <i>K. pneumoniae</i> 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 <i>K. pneumoniae</i> 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 <i>aph(3′)</i>-<i>Ia, aac(6′)Ib</i>-<i>cr, armA, strB, strA</i> and <i>aadA2</i> genes. Additionally, five plasmids IncFIB(Mar), IncHI1B, IncFIB(pKPHS1), IncFIB(K) and IncFII(K) and four integrated phages were detected. <i>In silico</i> 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 <i>K. pneumoniae</i> ST15 in Lebanon associated with the recent population migration. The potential dissemination of such MDR strains is an important public health concern.</p