IncX4 Plasmid Carrying the New mcr-1.9 Gene Variant in a CTX-M-8-Producing Escherichia coli Isolate Recovered From Swine

Abstract

We studied a commensal colistin-resistant Escherichia coli isolated from a swine cecum sample collected at a slaughter, in Portugal. Antimicrobial susceptibility phenotype of E. coli LV23529 showed resistance to colistin at a minimum inhibitory concentration of 4 mg/L. Whole genome of E. coli LV23529 was sequenced using a MiSeq system and the assembled contigs were analyzed for the presence of antibiotic resistance and plasmid replicon types using bioinformatics tools. We report a novel mcr-1 gene variant (mcr-1.9), carried by an IncX4 plasmid, where one-point mutation at nucleotide T1238C leads to Val413Ala substitution. The mcr-1.9 genetic context was characterized by an IS26 element upstream of the mcr-pap2 element and by the absence of ISApl1. Bioinformatic analysis also revealed genes conferring resistance to β-lactams, sulphamethoxazole, trimethoprim, chloramphenicol and colistin, corresponding to the phenotype noticed. Moreover, we highlight the presence of mcr-1.9 plus blaCTX-M-8, a blaESBL gene rarely detected in Europe in isolates of animal origin; these two genes were located on different plasmids with 33,303 and 89,458 bp, respectively. MCR-1.9-harboring plasmid showed high identity to other X4-type mcr-1-harboring plasmids characterized worldwide, which strongly suggests that the presence of PMCR-encoding genes in food-producing animals, such as MCR-1.9, represent a potential threat to humans, as it is located in mobile genetic elements that have the potential to spread horizontally.

Genomic Characterization of Prevalent mcr-1, mcr-4, and mcr-5 Escherichia coli Within Swine Enteric Colibacillosis in Spain

“…Interestingly, almost all mcr-4 isolates belonged to the clonal group ST10-A (CH11-24) (García et al, 2018), which was shown to be highly present (more than 50%) within the mcr-1 diarrheagenic isolates of a second study (García-Meniño et al, 2018). Both studies reinforced other countries’ findings that the pig industry is an important reservoir of colistin-resistant E. coli , as well as being carriers of other additional risk genes such as bla ESBL genes (García et al, 2018; García-Meniño et al, 2018; Magistrali et al, 2018; Manageiro et al, 2019). Based on reported evidences (Beyrouthy et al, 2017; Gilrane et al, 2017), there is great concern about the in vivo acquisition of mcr- and bla ESBL -bearing plasmids by human E. coli isolates following treatment with colistin, or via animal transmission through direct contact or via food chain.…”

“…Since the mcr-1 plasmid gene was first described (Liu et al, 2016), it has been identified in members of the Enterobacteriaceae family encoded in different plasmid types, including IncI2, IncX4, IncHI1, IncHI2, IncFI, IncFII, IncP, IncK (Sun et al, 2018). Different authors corroborate that large conjugative plasmids of types IncHI2, IncX4 and IncI2 would be the maximum responsible for the dissemination of the mcr-1 gene among E. coli isolates from different sources and geographical locations (Doumith et al, 2016; Li et al, 2017; Manageiro et al, 2019). To date, other mcr genes (2–9) have been described (Carroll et al, 2019); among them, the mcr-4 and mcr-5 genes appear mostly encoded in small and non-conjugative ColE-like type plasmids (Sun et al, 2018).…”

Characteristics of Carbapenem-Resistant and Colistin-Resistant Escherichia coli Co-Producing NDM-1 and MCR-1 from Pig Farms in China

“…Plasmid prediction using whole genome sequences identified several putative types of plasmids harbored by the eight strains (Figure 4). Among these putative types of plasmids, IncHI2A, IncFIB(K), IncFII, IncFI1, IncR, IncHI2, and IncFIA plasmids carrying bla NDM-1 have been reported [33,34,35,36,37], while IncX4, IncFIB(K), IncFII, IncFI1, IncY, IncHI2, IncX1, and IncFIA plasmids carrying mcr-1 have been reported [38,39,40,41,42]. Although more accurate and reliable technologies such as the third-generation sequencing technologies are necessary for determining the accurate type and sequence of the plasmids, bioinformatical analysis using whole genome sequences revealed that an IncFII-type plasmid homologous to pHNEC55 (GenBank accession: KT879914) likely carried the bla NDM-1 gene, and an IncX4-type plasmid homologous to pIBMC_mcr1 (GenBank accession: MF449287) likely carried the mcr-1 gene, as the backbones of both plasmids were found in the genomes of the eight strains (Figure 5).…”

Colistin and its role in the Era of antibiotic resistance: an extended review (2000–2019)

“…Currently, 22 functional genetic variants of mcr-1 have been assigned [75][76][77][78][79][80][81][82], including mcr-1.1 [35], mcr-1.2 [83], mcr-1.3 [84], mcr-1.4 [85], mcr-1.5 [86], mcr-1.6 [87], mcr-1.7 [85], mcr-1.8 [43], mcr-1.9 [88], mcr-1.10 [75], mcr-1.11 [89], mcr-1.12 [43], mcr-1.13 [90], mcr-1.14 [71], and mcr-1.15 [91], while the other genetic variants from mcr-1.16 to mcr-1.22, were uploaded to NCBI GenBank (https://www.ncbi. nlm.nih.gov/nuccore/NG_065944.1).…”