AUTHOR=Tokajian Sima , Eisen Jonathan A. , Jospin Guillaume , Farra Anna , Coil David A. 

TITLE=Whole genome sequencing of extended-spectrum β-lactamase producing Klebsiella pneumoniae isolated from a patient in Lebanon

JOURNAL=Frontiers in Cellular and Infection Microbiology

VOLUME=5

YEAR=2015

URL=https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2015.00032

DOI=10.3389/fcimb.2015.00032

ISSN=2235-2988

ABSTRACT=<p><bold>Objective:</bold> The emergence of extended-spectrum β-lactamase (ESBL)-producing bacteria is now a critical concern. The ESBL-producing <italic>Klebsiella pneumoniae</italic> constitutes one of the most common multidrug-resistant (MDR) groups of gram-negative bacteria involved in nosocomial infections worldwide. In this study we report on the molecular characterization through whole genome sequencing of an ESBL-producing <italic>K. pneumoniae</italic> strain, LAU-KP1, isolated from a stool sample from a patient admitted for a gastrointestinal procedure/surgery at the Lebanese Amrican University Medical Center-Rizk Hospital (LAUMCRH) in Lebanon.</p><p><bold>Methods:</bold> Illumina paired-end libraries were prepared and sequenced, which resulted in 4,220,969 high-quality reads. All sequence processing and assembly were performed using the A5 assembly pipeline.</p><p><bold>Results:</bold> The initial assembly produced 86 contigs, for which no scaffolding was obtained. The final collection of contigs was submitted to GenBank. The final draft genome sequence consists of a combined 5,632,663 bases with 57% G+C content. Automated annotation was performed using the RAST annotation server. Sequencing analysis revealed that the isolate harbored different β-lactamase genes, including <italic>bla</italic><sub>oxa−1</sub>, <italic>bla</italic><sub>CTX−M−15</sub>, <italic>bla</italic><sub>SHV−11</sub>, and <italic>bla</italic><sub>TEM−1b</sub>. The isolate was also characterized by the concomitant presence of other resistance determinants most notably <italic>acc(6′)-lb-cr</italic> and <italic>qnrb1</italic>. The entire plasmid content was also investigated and revealed homology with four major plasmids pKPN-IT, pBS512_2, pRSF1010_SL1344, and pKPN3.</p><p><bold>Conclusions:</bold> The potential role of <italic>K. pneumonia</italic> as a reservoir for ESBL genes and other resistance determinants is along with the presence of key factors that favor the spread of antimicrobial resistance a clear cause of concern and the problem that Carbapenem-non-susceptible ESBL isolates are posing in hospitals should be reconsidered through systematic exploration and molecular characterization.</p>