Molecular epidemiology of colistin-resistant Enterobacteriaceae in inpatient and avian isolates from China: high prevalence of mcr-negative Klebsiella pneumoniae

- Higher prevalence rate of MCR-1 among avian compared with inpatient isolates of K. pneumoniae and E. coli in mainland China.
- Three fourths of colistin-resistant K. pneumoniae (ColRKP) isolates were mcr-negative.
- The chromosomal genes ramA, pmrB, and phoQ were not associated with colistin resistance in ColRKP.
- The existing chromosomal and transferable mechanisms do not explain colistin resistance in mcr-negative ColRKP.
- MCR-1 combined with upregulated PmrB contributed to low-level colistin resistance in colistin-resistant E. coli (ColREC).

Whether chromosomal and transmissible mechanisms contribute simultaneously to colistin resistance in Klebsiella pneumoniae and Escherichia coli remains unknown. This study aims to identify the underlying mechanisms of colistin resistance in inpatient and avian K. pneumoniae and E. coli in China. We retrospectively screened 2353 Enterobacteriaceae isolates from inpatients at multiple centers during 2011-2014, and 168 avian isolates from one slaughterhouse in 2013 for the presence of MCR-1/MCR-2. Mutations and transcriptional levels of the chromosomal RamA, PhoPQ, and PmrAB genes were determined by PCR and RT-qPCR. The transferability and genetic characteristics of the underlying colistin-resistance genes were detected by conjugation and whole-genome sequencing. The MIC90 for colistin in colistin-resistant K. pneumoniae (ColRKP, 128 mg/L, N = 17) was 16-fold higher than in colistin-resistant E. coli (ColREC, 8 mg/L, N = 33). The dominant sequence types of ColRKP were ST2018 and ST37, whereas ColREC displayed diversity. The chromosomal genes ramA, pmrB, and phoQ were not associated with colistin resistance in ColRKP. The transcriptional levels of PmrB in ColREC were 7.5-fold greater than in colistin-susceptible isolates. The carrying rates of MCR-1 in ColREC and ColRKP were 100% (33/33) and 23.5% (4/17), respectively. Plasmid IncI2 (~60 kb) carrying MCR-1 could be transferred to recipient E. coli EC600 with frequencies ranging from 8.74 × 10−6 to 1.31 × 10−4. No transferable genes were identified in mcr-1-negative ColRKP. MCR-1 combined with upregulated PmrB was associated with low-level colistin resistance in ColREC. However, two-thirds of the ColRKP isolates were mcr-negative and need to be studied further.