6th Clinical Microbiology Conference

Biography

Biography: Maria Luisa G. Daroy

Abstract

The Philippines is a hotspot for the emergence of antibiotic-resistant “superbugs,” such as fluoroquinolone-resistant E. coli and carbapenemase-carrying Klebsiellapneumoniae. This paper reports on the use of next-generation sequencing and bioinformatics techniques for the the genome-wide analysis of genetic variation influoroquinolone-resistant E. coli, carbapenem-resistant K. pneumoniae, ESBL-positive K. pneumoniae, and a carbapenem-resistant Stenotrophomonasmaltophila. These bacteria were isolated in 2013-2014 from clinical specimens of patients confinedat St. Luke’s Medical Center in Manila, Philippines. De novo assembly, primary structural and functional annotations, gene search and SNV analyses performed on pooled reads identified several resistance determinants. Plasmid-borne New Delhi β-lactamase genes, blaNDM-1 and blaNDM-7, were found in K. pneumoniae, as well asstop codon mutations in the ompK35 and ompK36 porin genes.SNVs in the genomes of susceptible and fluoroquinolone-resistant E. coli were identified in scaffolds derived from pooled reads, which were then mapped against reference sequences of two susceptible and one fluoroquinolone-resistant E. coli. In silico filtering of SNVs using a subtraction strategy selected for variants that may be associated with fluoroquinolone resistance in 23 genes involved in transport, respiratory chain, oxidative stress, iron metabolism and bacterial cell death. The functional association of these variants and putative pathways offluoroquinolone resistance involving them were derived by mining gene annotations. This strategy of combining whole genome analyses with in silico identification of significant variants and searching gene ontologies for functional associations is useful to guide functional genomics studies on the development of antibiotic resistance in common clinical pathogens like E. coli and K. pneumoniae.