<p>Co-Occurrence of <em>mcr-9</em> and <em>bla</em>_NDM-1 in <em>Enterobacter cloacae</em> Isolated from a Patient with Bloodstream Infection</p>

Abstract

Background: Bloodstream infection (BSI) caused by carbapenem-resistant Enterobacteriaceae are potentially life-threatening related to poorer outcomes. Colistin is considered one of the lastresort treatments against human infections caused by multidrug-resistant (MDR) Gram-negative bacteria. Therefore, emergence of strains from the blood that co-harboring mcr and carbapenem resistance genes were considered as a serious problem. Purpose: In this study, two mcr-9-harboring MDR Enterobacter cloacae isolates BSI034 and BSI072 recovered from BSI patients were identified, one of which co-harbored mcr-9 and bla NDM-1. The genetic characteristics of the MDR plasmid needed to be clarified. Methods: S1-PFGE and Southern blotting were conducted to determine the location of mcr-9. Whole-genome sequencing was performed to obtain the complete genome and plasmid sequences. The resistome and virulence genes of the strains, accompanied by the genetic characteristics of mcr-9-and bla NDM-1 -harboring plasmids, were analyzed. Results: Whole-genome sequencing showed that BSI034 harbored mcr-9-carrying IncHI2type pBSI034-MCR9 and bla NDM-1 -carrying IncX3-type pBSI034-NDM1. The 278,517 bp pBSI034-MCR9 carried mcr-9 along with the other 19 resistance genes. mcr-9 was flanked by IS903B (1057 bp) and IS26 (820 bp) in the same orientation. In addition to resistance genes, strain BSI034 also carried a chromosome-located Yersinia high-pathogenicity island, which harbored genes of yersiniabactin biosynthesis operon ybtSXQPAUTE, irp1/2, and fyuA. Conclusion:We described the complete genome and mcr-9/bla NDM-1 -co-harboring plasmid of E. cloacae from a BSI patient. Notable differences were observed within mosaic modules between pBSI034-MCR9 and other mcr-9-harboring plasmids due to extensive recombination via horizontal gene transfer.

First Report of Coexistence of blaSFO–1 and blaNDM–1 β-Lactamase Genes as Well as Colistin Resistance Gene mcr-9 in a Transferrable Plasmid of a Clinical Isolate of Enterobacter hormaechei

“…Like the classical IncHI2 plasmids, the p1575-1 plasmid held a complete conjugative system, and the conjugation frequencies ranged from 0.5 × 10 −6 to 2 × 10 −6 per donor cell. The IncHI2-type conjugative plasmids harboring mcr-9 were also discovered previously, and the conjugation frequencies of those plasmid were 10 −4 (Lin et al, 2020) or 2.03 × 10 −7 (−5.42 × 10 −8 ) (Cha et al, 2020), which were similar to our findings. Through the analysis, we identified the complete conjugative modules on the plasmid p1575-1, strongly suggesting that p1575-1 could be transferred autonomously.…”

“…Not like the blaNDM-1, which receives widespread attention, the bla SFO−1 gene is not included in the routine surveillance, but it could be an effective weapon that various gram-negative bacteria could use to resist β-lactams (Matsumoto and Inoue, 1999); therefore, the prevalence of the coexistence of the bla SFO−1 gene and carbapenemase genes might be underestimated. Some studies reported the coexistence of bla SFO−1 and bla NDM−1 β-lactamase genes and fosfomycin resistance gene fosA3 in Escherichia coli clinical isolate (Zhao et al, 2015) and the co-occurrence of mcr-9 and bla NDM−1 in Enterobacter cloacae (Yuan et al, 2019;Faccone et al, 2020;Lin et al, 2020). However, in this study, we not only found the coexistence of mcr-9 and bla NDM−1 , but also a rare gene bla SFO−1 was detected on the same transferable plasmid.…”

Emergence of IncHI2 Plasmids With Mobilized Colistin Resistance (mcr)-9 Gene in ESBL-Producing, Multidrug-Resistant Salmonella Typhimurium and Its Monophasic Variant ST34 From Food-Producing Animals in Italy

“…In our three selected isolates, mcr-9 was demonstrated to be located on IncHI2/IncHI2A plasmids by the hybrid (Illumina-Oxford Nanopore) approach, together with other AMR genes conferring resistance to different antimicrobial classes, including the bla SHV −12 ESBL gene type detected in the two plasmids of pig origin, and different genes involved in heavy metals metabolism. Similarly, previous findings detected IncHI2-or IncHI2A-type plasmids in mcr-9 positive Enterobacteriaceae, often together with other resistance determinants (including HPCIAs) and to heavy metals mainly from human patients (Carroll et al, 2019;Chavda et al, 2019;Kieffer et al, 2019;Bitar et al, 2020;Faccone et al, 2020;Kananizadeh et al, 2020;Lin et al, 2020;Osei Sekyere et al, 2020;Soliman et al, 2020;Tsui et al, 2020;Umeda et al, 2020;Elbediwi et al, 2021;Marchetti et al, 2021;Sun et al, 2021), and also from animal (Börjesson et al, 2020;Yuan et al, 2019;Borowiak et al, 2020;Haenni et al, 2020;Leite et al, 2020), food (Borowiak et al, 2020;Sadek et al, 2020;Tyson et al, 2020), and environmental (Kamathewatta et al, 2020) sources. Few reports also described mcr-9 integrated into the chromosome of Citrobacter (Ribeiro et al, 2021) and Salmonella (Pan et al, 2020;Tyson et al, 2020) isolates, with a genetic context similar to the structure observed in mcr-9-harboring plasmid sequences, suggesting a possible mcr-9 transfer as a gene cassette between plasmids and chromosomes (Pan et al, 2020).…”

Genomic Characterization of Salmonella enterica Isolates From Retail Meat in Beijing, China

“…The two plasmids IncX4 and IncI2 may increase the fitness of the host and become the major plasmid types driving the dissemination of the mcr-1 gene ( Wu et al, 2018 ). In the present study, we validated the presence of the mcr-9 gene commonly on large plasmids ( Lin et al, 2020 ). Colistin has been used for decades in veterinary medicine and as a last-resort drug to treat infections in humans ( Kempf et al, 2016 ).…”