Molecular characterization and replicon typing of plasmids encoding carbapenemases in Gram-negative bacteria

Background Carbapenem resistance in Gram-negative bacteria is an ongoing public-health problem of global dimensions leaving very few treatment options for severely infected patients. This study focuses on the dissemination of plasmid-borne carbapenemase genes in Gram-negative bacteria in Tamil Nadu, India. A total of 151 non-repetitive isolates belonging to 11 genera were collected from a diagnostic center in Tamil Nadu. Minimal inhibitory concentration of imipenem and meropenem were determined using micro-broth dilution method. E. coli pathotyping, Klebsiella serotyping, screening for beta-lactamases and plasmid incompatibility grouping was performed.Results E. coli (n=57) isolates were classified as, Enteropathogenic (n=12), Enteroaggregative (n=9), Enterohemorrhagic (n=8), Enterotoxigenic (n=3), Enteroinvasive (n=1) and unclassified E. coli (n=24). Of the 45 Klebsiella species, 14 were K1 whereas 11 were K2 serotype and in 20 Klebsiella serotype could not be determined. Other isolates (n=49) consisted of P. aeruginosa , S. typhi , E. cloacae , A. baumannii , S. marcescens , A. xylosoxidans , P. mirabilis and E. meningoseptica . Of the total number of isolates, 71% (n=107) and 68% (n=103) were found to be resistant to meropenem and imipenem respectively. The most prevalent beta-lactamase gene was bla NDM-1 (21%, 12/57) followed by bla OXA-181 (16%, 9/57) both detected in E. coli . Other carbapenemase genes detected were bla GES-9 (n=8), bla OXA-23 (n=7) and bla IMP-1 (n=3). Interestingly bla GES-1 (n=11), bla OXA-51 (n=9) were also detected. The unusual presence of bla OXA-23 was seen in E. coli (n=4), and bla OXA-23 and bla OXA-51 (IncA/C) in K. pneumoniae (n=3). Plasmid incompatibility (inc/rep) typing results showed that the plasmids carrying resistance genes (n=11) belonged to IncX, IncA/C, IncFIA-FIB and IncFIIA groups. Six E. coli isolates and one K. pneumoniae were able to transfer plasmid-borne carbapenemase ( bla NDM-1 , bla OXA-181 , bla GES-1 , bla GES-9 ) via conjugation.Conclusions This study highlights the prevalence of carbapenem resistance and the acquisition of plasmid-borne carbapenemase genes in unusual Gram-negative bacteria highlighting the role of evolution by generating microbial diversity.

Global phylogenetic analysis of Escherichia coli and plasmids carrying the mcr-1 gene indicates bacterial diversity but plasmid restriction

To understand the dynamics behind the worldwide spread of the mcr-1 gene, we determined the population structure of Escherichia coli and of mobile genetic elements (MGEs) carrying the mcr-1 gene. After a systematic review of the literature we included 65 E. coli whole genome sequences (WGS), adding 6 recently sequenced travel related isolates, and 312 MLST profiles. We included 219 MGEs described in 7 Enterobacteriaceae species isolated from human, animal and environmental samples. Despite a high overall diversity, 2 lineages were observed in the E. coli population that may function as reservoirs of the mcr-1 gene, the largest of which was linked to ST10, a sequence type known for its ubiquity in human faecal samples and in food samples. No genotypic clustering by geographical origin or isolation source was observed. Amongst a total of 13 plasmid incompatibility types, the Incl2, lncX4 and IncHI2 plasmids accounted for more than 90% of MGEs carrying the mcr-1 gene. We observed significant geographical clustering with regional spread of lncHI2 plasmids in Europe and Incl2 in Asia. These findings point towards promiscuous spread of the mcr-1 gene by efficient horizontal gene transfer dominated by a limited number of plasmid incompatibility types.