An MLST approach to support tracking of plasmids carrying OXA-48-like carbapenemase

Abstract

Objectives The prevalence of infections caused by OXA-48-like carbapenemase-producing organisms in Ireland has increased dramatically since 2011 and is an urgent public health issue. Genome-based high-resolution genotyping was used to analyse clinical isolates submitted to the Irish Carbapenemase-Producing Enterobacteriaceae Reference Laboratory Service for a 13 month period (2016–17). Methods A total of 109 OXA-48-producing non-duplicate clinical isolates from 16 submitting centres were sequenced. Using a gene-by-gene approach, isolate genomes were characterized by MLST and core genome MLST, and the presence of antimicrobial resistance determinants was determined. Reference mapping and a novel plasmid MLST-type approach was applied to determine plasmid background. Results The OXA-48-like-producing isolates were Escherichia coli (n = 56), Klebsiella spp. (n = 46) and Enterobacter cloacae (n = 7). Amongst the E. coli isolates there were 37 different STs and amongst the Klebsiella spp. isolates there were 27 different STs. blaOXA-48 was present in 105/109 (96.3%) of isolates. Based on mapping analysis and detection of the pOXA-48 IncL-type plasmid replicon and backbone genes, a pOXA-48-like plasmid was identified in 93/109 isolates (85.3%). The remaining isolates (n = 16; 14.7%) harboured blaOXA-48-like genes in unknown environments. Using a gene-by-gene approach two pOXA-48-like plasmid groups with 2/71 pOXA-48-like locus differences between them were identified. Conclusions In Ireland we found a diversity of genotypes associated with OXA-48-like-producing clinical isolates with the IncL pOXA-48 plasmid type predominating as the blaOXA-48 genetic environment. A plasmid MLST approach can rapidly identify plasmids associated with outbreaks and monitor spread of types temporally and geographically.

Genome evolution and the emergence of pathogenicity in avian Escherichia coli

“…Confirmation of the plasmidic context of specific genes may require that analyses are performed separately on miniprep plasmid extractions or the use of long read sequencing 117 . However, the prevalence of putative APEC plasmid genes among isolates from carriage and invasive disease can be determined using the gene-by-gene approach 37 , 38 , 118 employed here. Additionally, annotated gene lists were obtained for the following plasmids: pAPEC-O1-R 119 ; pAPEC-O2-R 120 ; pAPEC-O2-211A-ColV 121 ; pAPEC-O1-ColBM 54 ; p1ColV5155 122 ; pAPEC-O2-ColV 10 .…”

Pathogenicity of Clinical OXA-48 Isolates and Impact of the OXA-48 IncL Plasmid on Virulence and Bacterial Fitness

“…Of these, five plasmids were completely sequenced by both Illumina ® short-read and SMRT long-read technology revealing a sequence identity of each ≥99.9%. To analyze the 63 kb IncL plasmids of the 21 isolates, which were solely sequenced by short-read technology, the sequencing reads of each isolate were mapped to the complete sequence of the 63 kb plasmid IncL from EC7215 (Brehony et al, 2019). Thereby, a median coverage of >50 of each isolate to the reference sequence from EC7215 was noticed, suggesting the presence of highly similar plasmids in all these isolates (Supplementary Figure 1).…”

Carbapenem and colistin-resistant bacteria in North Lebanon: Coexistence of mcr-1 and NDM-4 genes in Escherichia coli

“…Moreover, OXA-48-producing E. cloacae isolates have been previously described in Lebanon by Hammoudi et al [16]. However, the clones ST109, ST135, and ST66 have been reported in patients from different countries in the world, including the Czech Republic, Ireland, and Croatia respectively [36][37][38].…”