Genome-wide antibiotic resistance and virulence profiling of Pseudomonas Aeruginosa isolated from clinical samples in Lebanon. (c2017)

Abstract

Extensively drug resistant Pseudomonas aeruginosa (XDR) are a great worldwide public health concern. P. aeruginosa is a Gram-negative opportunistic pathogen associated with a broad range of infections. It causes acute skin, lung, urinary tract infections and sepsis. It can also cause chronic infections in the pulmonary passages of individuals with cystic fibrosis. P. aeruginosa is widespread in nature lurking on diverse habitats including animals, plants, soil, in-animate objects and hospital settings. In this study, 18 P. aeurginosa clinical isolates were collected from the American University of Beirut Medical Center in Lebanon and were used for identification, phylogenetic analysis and detection of porin (oprL, oprI and oprD), efflux pumps (mexA, mexC and mexE) and exotoxin genes (exoU and exoS). Illumina paired-end libraries for twelve representative isolates were prepared and sequenced. The initial assemblies produced an average genome size of 6.8 Mb, G+C% content of 65.90-66.30% and 116-396 contigs. In silico MLST typing revealed that the isolates belonged to six MLST types: ST-233, ST-235, ST-296, ST-654, ST-1182 and ST-1233. Antimicrobial susceptibility testing showed that all except PA43, were XDR. Genomic analysis revealed the presence of several β-lactamases encoding genes (blaPAO, blaOXA-50, blaOXA-4, blaIMP-15, blaGES-1 and/or blaVIM-2 genes) and the aac(6')Ib-cr gene conferring aminoglycoside resistance. Additionally, all the 18 isolates carried mexC and mexE conferring ciprofloxacin resistance. exoS and exoU toxing encoding genes were detected in 56% and 39% of the isolates, respectively, and phiCTX was the most common detected plasmid in this study. In this study the comparative analysis of P. aeruginosa genomes isolated from clinical samples in Lebanon, revealed many antibiotic resistance and virulence factor genes, a large number of genes that are involved in regulation, catabolism, transport, and efflux of organic compounds contributing to the remarkable ability of this bacterium to adapt to a wide range of environmental niches. The emergence and spread of XDR P. aeruginosa, which constitute a therapeutic problem of serious concern, emphasize the importance of having effective laboratory detection systems and infection control measures.