Plasmid-Mediated Co-Occurrence of mcr-1.1 in Extended-Spectrum β-Lactamase (ESBL)-Producing Escherichia coli Isolated From the Indigenous Seminomadic Community in Malaysia

Abstract

The growing prevalence of commensal antibiotic resistant Escherichia coli poses a significant concern for the global spread of antibiotic resistance. Stool samples (n = 35) from a seminomadic indigenous community in Malaysia, the Jehai, were screened for multidrug-resistant bacteria, specifically the extended-spectrum β-lactamase (ESBL) producers. Subsequently, whole-genome sequencing was used to provide genomic insights into eight ESBL-producing E. coli that colonised eight individuals. The ESBL E. coli isolates carry resistance genes from various antibiotic classes such as the β-lactams (bla _TEM, bla _CTX-M-15 and bla _CTX-M-55), quinolones (gyrA, qnrS and qnrS1) and aminoglycosides (aph(3')-Ia, aph(6)-Id and aac(3)-IId). Three concerning convergence of ESBL, colistin and metal resistance determinants, with three plasmids from H-type lineage harbouring bla _CTX-M and mcr-1.1 genes were identified. Using the Oxford Nanopore Technology (ONT) Native Barcoding Kit (SQK-NBD114.24) in conjunction with the R10.4.1 flow cell, which achieved an average read accuracy (Q > 10) of 99.84%, we further characterised the mcr-1.1-bearing plasmids, ranging in size from 25 to 28 kb, from three strains of E. coli. This report represents the first whole genome analysis of multidrug-resistant bacteria, specifically those resistant to colistin, found within the indigenous population in Malaysia. It strongly indicates that the pertinent issue of colistin resistance in the country is far more significant than previously estimated.

Keywords: antimicrobial resistance; colistin resistance; extended-spectrum β-lactamase Escherichia coli; mcr-1 gene; remote indigenous community; rural health.

Figure 1

GrapeTree view showing the MLST phylogenetic relationships among the E. coli global strains from the EnteroBase. It consists of the five STs identified in this study.

Figure 2

A midpoint-rooted maximum likelihood tree of Malaysian E. coli strains (n = 32) depicts the abundance of AMR genes and the interlinkage of the representative AMR gene classes across different phylogroups. A coloured box indicated the presence of AMR genes. A box with a corresponding lighter shade indicates an absence.

Figure 3

Genome wide stress response gene profile of the Malaysian E. coli isolates. Blue box denotes present and white box denotes absent.

Figure 4

Genome wide virulence gene profile of the Malaysian E. coli isolates. Red box denotes present and white box denotes absent.

Figure 5

Circular comparative analysis of the mcr1.1 bearing plasmids identified in the current study. The plasmid pMCR1-59,496 isolated from K. pneumoniae (OP950836.1) was used as a reference. AMR genes and insertion sequence elements were labelled at the outmost ring.