One Health Analysis of mcr -Carrying Plasmids and Emergence of mcr-10.1 in Three Species of Klebsiella Recovered from Humans in China

Abstract

Reports of mcr-1 and mcr-8 are common in China; however, few studies have reported mcr-9 and mcr-10 . One reason is that the newly described variants can be phenotypically colistin susceptible and thus may not be identified. The global dissemination of the mobile colistin resistance ( mcr ) gene illustrates how the use of colistin in veterinary medicine can affect human health, exemplifying the concept of One Health. This study screened for the existence of mcr variants (from mcr-1 to mcr-10 ) in a 5-year collection of clinical Klebsiella short-read whole-genome sequencing (WGS) data from a tertiary hospital in China (2013 to 2018) and aimed to identify the mechanisms of mcr spread. MICs were measured for the mcr -positive isolates, and long-read sequencing was performed to complete the mcr -positive genome sequences. Six variants ( mcr-1.1 , mcr-8.1 , mcr-8.2 , mcr-9.1 , mcr-9.2 , and mcr-10.1 ) were identified in 20 genomes, with plasmids from the IncFII K , IncHI2, IncI2, and IncX4 groups. Highly similar plasmids (coverage, >75%; nucleotide identity, >98.5%) isolated from silver gulls, chickens, pigs, wastewater treatment plants, and hospital sewage were identified in GenBank. The MICs of the mcr-1 - and mcr-8 -carrying isolates were ≥4 μg/mL; however, the MICs of the mcr-9 - and mcr-10 -carrying isolates ranged from 0.5 μg/mL to 1 μg/mL (colistin susceptible). The variants mcr-1 to mcr-9 were found only in Klebsiella pneumoniae , while mcr-10.1 was found in K. pneumoniae , Klebsiella quasipneumoniae subsp. quasipneumoniae , and Klebsiella variicola . A pair of inverted repeats (IRs) was identified for hsdSMR -IS Ec36 - mcr-10.1 - xerC ; IR-1 (5′- TCAAACGTA ) was inside the att L site of xerC , indicating that mcr-10.1 was originally integrated by xerC and mobilized by IS Ec36 afterwards. In conclusion, this is the first report of mcr-10.1 susceptible to colistin in three species of Klebsiella . This study shows the genetic events that happened to mcr-10.1 in a stepwise manner, with the first step being XerC integration and the second being IS Ec36 mobilization. Finally, this study also highlights mcr transmission between humans and nature. IMPORTANCE Reports of mcr-1 and mcr-8 are common in China; however, few studies have reported mcr-9 and mcr-10 . One reason is that the newly described variants can be phenotypically colistin susceptible and thus may not be identified. This study identified the mcr -positive clinical isolates by investigating WGS data for 2,855 Klebsiella isolates (including K. pneumoniae , K. quasipneumoniae subsp. quasipneumoniae , and K. variicola ) and found three mcr-9 and three mcr-10 cases (MICs, 0.5 μg/mL to 1 μg/mL; colistin susceptible). This study also reveals a pair of perfect 9-bp IRs of IS Ec36 and the precise mcr-10.1 integration and insertion events that happened to the IncFII K plasmids. A One Health analysis of highly similar plasmid structures from human and nonhuman sources emphasizes the plasmid transmission and evolution process.