First Genomic Characterization of blaVIM-1 and mcr-9-Coharbouring Enterobacter hormaechei Isolated from Food of Animal Origin

Abstract

We describe here the complete genome sequence of an Enterobacter hormaechei ST279 coharbouring blaVIM-1 and mcr-9 recovered from uncooked beef patty in June 2017, Egypt. The tested isolate was resistant to carbapenem but susceptible to colistin (minimum inhibitory concentration (MIC), 0.5 μg/mL). The antimicrobial susceptibility profile and conjugation experiments were performed. The entire genome was sequenced by the Illumina MiniSeq and Oxford Nanopore methods. The blaVIM-1 and mcr-9 genes are carried on the same IncHI2/pMLST1 plasmid, pMS37a (Size of 270.9 kb). The mcr-9 gene was located within the physical boundaries demarcated by two insertion elements IS903 (upstream) and IS1 (downstream) but did not possess the downstream regulatory genes (qseC/qseB) which regulate the expression of mcr-9. Therefore, the mcr-9 might be silently disseminated among carbapenem-resistant Enterobacterales. In addition to blaVIM-1 and mcr-9, plasmid pMS37a harbored various antibiotic resistance genes including aac(6’)-Il, ΔaadA22, aac(6’)-Ib-cr, sul1, dfrA1 and tetA. To the best of our knowledge, this is the first report of a blaVIM-1 and mcr-9-coharbouring E. hormaechei isolate of food origin worldwide. The identification of a multidrug-resistant VIM-1 and mcr-9 positive Enterobacter hormaechei isolate from food is worrisome as retail meat and meat products could serve as a vehicle for these MDR bacteria, which could be transferred between animals and humans through the food chain. It further highlights that Enterobacterales co-producing MCR and carbapenemases being found in the food chain indeed correspond to a One-Health issue, highlighting the need for serious steps to prevent their further dissemination.

Genomic Characterization of VIM and MCR Co-Producers: The First Two Clinical Cases, in Italy

“…On the other hand, IB2020 had mcr-9 on the chromosome in this gene’s cassette: mcr-9-wubC-qseC-qseB-exeA. This gene’s cassette was detected to express colistin resistance as presented in our IB2020 isolate [ 32 , 34 ]. Our results confirm and highlight some important aspects: the presence of mcr-9 determinants together with the two-component regulatory genes, can increase the gene expression, leading to colistin resistance whether on a plasmid or on the chromosome.…”

“…The reports of VIM and MCR co-production in ECC isolates are increasing, as described elsewhere [ 30 , 31 , 32 , 33 , 34 ]. The presence of mcr-9 -like genes bound by two insertion sequences as in p3849_IncHI2_mcr and as reported in Sadek et al 2020 and Bitar et al 2020 will not express colistin resistance and such plasmids can circulate silently until detected.…”

Prevalence and Traits of Mobile Colistin Resistance Gene Harbouring Isolates from Different Ecosystems in Africa

“…Inadequate husbandry and slaughterhouse facilities and unhygienic slaughtering techniques facilitate the contamination of animal-related products in Africa [ 53 ]. Six publications investigated the mcr gene in 211 isolates from foods of animal origin in Africa [ 36 , 50 , 54 – 57 ]. Twenty-nine strains were reported to harbour mcr -1 among the isolates tested.…”

“…coli carrying mcr -1 and one carbapenemase-producing ( bla VIM-1 ) Enterobacter hormaechei (isolated during 2017) carrying mcr -9 were detected among 129 COL-resistant Enterobacteriaceae (0.8%) isolated from samples of raw meat/RTE meat products collected from supermarkets, slaughterhouses, and butcher's shops [ 55 – 57 ], suggesting that farm-to-fork transmission of MGCB in Africa is facilitated by cross-contamination of meat in slaughterhouses (critical point of contamination by potentially multi to extensive resistant organisms). The mcr -1 and mcr -9 were on 64.4 kb IncI2 and 250 kb IncHI plasmids, respectively, and there were 22 other resistance genes (including ESBL, PMQR, and heavy metal resistance genes) belonging to five antimicrobial families in the mcr -positive strains [ 55 – 57 ] ( Table 2 ). This suggests that uncooked and half raw foods of animal origin are a source for the dissemination of multiresistant organisms coproducing MCR, ESBL, and carbapenemase in Africa, and that IncHI2 is a major driver of mcr -9/heavy metal resistance along the food production and supply chain in the Middle East.…”

“…This suggests that uncooked and half raw foods of animal origin are a source for the dissemination of multiresistant organisms coproducing MCR, ESBL, and carbapenemase in Africa, and that IncHI2 is a major driver of mcr -9/heavy metal resistance along the food production and supply chain in the Middle East. The mcr -1-positive strains were extensively diversified belonging to eight STs [ 56 , 57 ] ( Table 2 ), including pandemic and zoonotic HiR-ExPEC clones ST10 and ST58 (which dominated) [ 41 ], and conjugation was positive for mcr -1 and both mcr -9 and carbapenem-resistance encoding gene ( bla VIM-1 ) [ 56 , 57 ], implying that farm-to-plate transmission is a route for the dissemination of virulent mcr -containing strains capable of transferring genes encoding resistance against last-resort antimicrobials to other organisms (potentially acquired through handling/consumption of uncooked food of animal origin) in Africa. The presence of organisms resistant to COL and carbapenems in the food chains is alarming because diseases associated with these strains are often hard-to-treat and often are untreatable.…”