Whole-genome comparative analysis of carbapenem-resistant Escherichia coli isolated from hospitalized patients in Lebanon. (c2016)

Abstract

Antibiotic resistant bacteria that are challenging and nearly impossible to treat are becoming more prevalent and this is resulting in an urgent public health concern. The horizontal gene transfer of antibiotic resistance genes between bacteria as well as the complex antibiotic resistance mechanisms involved have aided in the production of an extensive spectrum of bacterial species with multi-drug resistant patterns. Resistance mechanisms of Gram-negative bacteria, such as extraintestinal Escherichia coli (ExPEC), vary extensively and the emergence of extended spectrum β-lactamases (ESBLs) as well as carbapenemases have compromised the effectiveness of the majority of antibiotics. ExPEC is one of the major causes of community- and nosocomial-acquired infections. Distinct from intestinal pathogens and commensals, ExPEC causes infections of the bloodstream, respiratory tract, urinary tract, peritoneum and cerebrospinal fluid. The universal burden of diseases caused by such a microorganism is staggering and hundreds of thousands of people are annually affected. In this study, 27 carbapenem resistant ExPEC isolates were recovered from hospitalized patients at the AUBMC (American University of Beirut Medical Center) and were used for identification, phylogenetic typing and molecular detection of associated antibiotic resistance genes (OXA, SHV, TEM, CTX-M and CTX-M-15). High-throughput sequencing was performed on ten isolates and bioinformatic tools were utilized to identify resistance and virulence determinants, plasmids, and phages. Overall, out of the 27 isolates, 59.6 %, 51.9 %, 7.4 %, 88.9 % and 63 % carried the blaOXA, blaTEM, blaSHV, blaCTX-M and blaCTX-M-15 genes, respectively. The distribution of the isolates among the different phylogenetic groups was as follows: 5 (18.5 %) belonged to group A, 3 (11.1 %) group B1, 6 (22.2 %) group B2 and 13 (48.2 %) group D. The average genome was 5.2 Mb with an average of 224–342 contigs and a G+C % content of 50.49 % – 50.79 %. The isolates were derived from 7 different lineages: ST- 405 (ECC153, ECC157, ECC173 and ECC188), ST-205 (EC 174), ST-410 (ECC194), ST-448 (ECC161), ST-617 (ECC202), ST-1284 (ECC167) and ST-648 (ECC149). Analysis revealed that these isolates harbored different β-lactamase genes including blaOXA-1, blaOXA-10, blaOXA-181, blaTEM-1b, blaCTX-M-15, blaCMY-2, blaCMY-42 in addition to aac(6')Ib-cr gene which confers tetracycline and aminoglycoside resistance among others. To the best of our knowledge, this is the first detection of blaOXA-181 encoding E. coli from Lebanon in addition to it being the first comprehensive genome-wide comparative analysis of carbapenem resistant ExPEC isolates. The pandemic potential of these ExPEC strains merits further large-scale comparative and functional genomic studies to better understand the biology of this clinically important bacterium.