Whole genome analysis of Gram-negative bacteria using the EPISEQ CS application and other bioinformatic platforms

Abstract

To determine genomic characteristics and molecular epidemiology of carbapenem non-susceptible K. pneumoniae, E. coli, A. baumannii, and P. aeruginosa from medical centers of Mexico using whole genome sequencing (WGS) data analyzed with the EPISEQ® CS application and other bioinformatic platforms. Clinical isolates collected from 28 centers in Mexico included carbapenem-non-susceptible Klebsiella pneumoniae (n = 22), Escherichia coli (n = 24), Acinetobacter baumannii (n = 16), and Pseudomonas aeruginosa (n = 13). Isolates were subjected to WGS using the Illumina (MiSeq) platform. FASTQ files were uploaded to the EPISEQ® CS application for analysis. Additionally, the tools Kleborate v2.0.4 and Pathogenwatch were used as comparators for Klebsiella genomes, and the bacterial whole genome sequence typing database (BacWGSTdb) was used for E. coli and A. baumannii. For K. pneumoniae, both bioinformatic approaches detected multiple genes encoding aminoglycoside, quinolone, and phenicol resistance and the presence of blaNDM-1 explained carbapenem non-susceptibility in 18 strains and blaKPC-3 in four strains. Regarding E. coli, both EPISEQ® CS and BacWGSTdb analyses detected multiple virulence and resistance genes: 20 of 24 (83.3%) strains carried blaNDM, three of 24 (12.4%) carried blaOXA-232, and one carried blaOXA-181. Genes that confer resistance to aminoglycosides, tetracyclines, sulfonamides, phenicols, trimethoprim, and macrolides were also detected by both platforms. Regarding A. baumannii, the most frequent carbapenemase-encoding gene detected by both platforms was blaOXA-72, followed by blaOXA-66. Both approaches detected similar genes for aminoglycosides, carbapenems, tetracyclines, phenicols, and sulfonamides. Regarding P. aeruginosa, blaVIM, blaIMP, and blaGES were the more frequently detected. Multiple virulence genes were detected in all strains. EPISEQ® CS compared to the other available platforms, enabled a comprehensive resistance and virulence analysis, providing a reliable method for bacterial strain typing and characterization of virulome and resistome.