Multidrug resistant (MDR)
Escherichia coli
strains that carry extended-spectrum β-lactamases (ESBLs) or colistin resistance gene
mcr-1
have been identified in the human gut at an increasing incidence worldwide. In this study, we isolated and characterized MDR Enterobacteriaceae from the gut microbiota of healthy Singaporeans and show that the detection rates for ESBL-producing and
mcr
-positive Enterobacteriaceae are 25.7% (28/109) and 7.3% (8/109), respectively. Whole-genome sequencing analysis of the 37
E. coli
isolates assigned them into 25 sequence types and six different phylogroups, suggesting that the MDR
E. coli
gut colonizers are highly diverse. We then analysed the genetic context of the resistance genes and found that composite transposons played important roles in the co-transfer of
bla
CTX-M-15/55
and
qnrS1
, as well as the acquisition of
mcr-1
. Furthermore, comparative genomic analysis showed that 12 of the 37 MDR
E. coli
isolates showed high similarity to ESBL-producing
E. coli
isolates from raw meat products in local markets. By analyzing the core genome SNPs shared by these isolates, we identified possible clonal transmission of a MDR
E. coli
clone between human and raw meat, as well as a group of highly similar IncI2 (Delta) plasmids that might be responsible for the dissemination of
mcr-1
in a much wider geographic region. Together, these results suggest that antibiotic resistance may be transmitted between different environmental settings by the expansion of MDR
E. coli
clones, as well as by the dissemination of resistance plasmids.
Importance
The human gut can harbor both antibiotic resistant and virulent
E. coli
which may subsequently cause infections. In this study, we found that MDR
E. coli
isolates from the gut of healthy Singaporeans carry a diverse range of antibiotic resistance mechanisms and virulence factor genes, and are highly diverse to each other. By comparing their genomes with the ESBL-producing
E. coli
isolates from raw meat products that were sampled at a similar time from local markets, we detected a MDR
E. coli
clone that was possibly transmitted between humans and raw meat products. Furthermore, we also found that a group of resistance plasmids might be responsible for the dissemination of colistin resistance gene
mcr-1
in Singapore, Malaysia and Europe. Our findings call for better countermeasures to block the transmission of antibiotic resistance.
Comparative genomic analysis reveals a high prevalence of inter-species in vivo transfer of carbapenem-resistance plasmids in patients with haematological malignancies
