Escherichia coli ST542 Co-Harbouring blaNDM-1 and mcr-1 in a Pig Farm, China

Carbapenems are potent antibiotics utilized to treat serious infections caused by multidrug-resistant (MDR) Gramnegative bacteria. 1However, the clinical use of carbapenems has led to the emergence and global dissemination of carbapenem-resistant Enterobacteriaceae (CRE), which pose a significant threat to effective clinical therapy. 1 The genes encoding carbapenemases, particularly the New Delhi metallo--lactamase gene bla NDM , have been widely distributed among humans and detected in animals, food, and the environment. 1,2Colistin is considered as the last therapeutic resort for treating MDR Gram-negative bacteria, especially CRE bacteria. 1,3However, its efficacy has been undermined by the emergence of various antimicrobial resistance mechanisms, such as mutations in the two-component regulatory systems PmrA-PmrB and PhoP-PhoQ. 3Particularly, the global spread of plasmid-mediated colistin resistance gene mcr, first identified in 2015, has further exacerbated this issue. 3Here, we report the recent identification of Escherichia coli ST542 strains co-producing MCR-1 and NDM-1 isolated from a pig farm in Yangzhou, China.On 17 May 2022, a total of 126 samples were collected from a pig farm in Yangzhou, China, including pig feces (n = 93), feed (n = 3), pig drinking water (n = 5), and floor swabs from pens (n = 25).A single sample was collected per pig, with no more than five samples taken from pigs in the same house.The samples were incubated in buffered peptone water (BPW) broth for 18-24 hours and subsequently inoculated onto MacConkey agar.One suspected E. coli isolate was selected from each sample and confirmed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.In total, 107 E. coli isolates were obtained, among which three (2.80%) isolates, namely YZ22PE67, YZ22PE68 and YZ22PE106 from pig feces co-carried the bla NDM-1 and mcr-1 genes, confirmed by PCR and sequencing as previously described. 3,4Minimum inhibitory concentrations (MICs) of 16 antimicrobial agents were determined using the microdilution method (cationadjusted Mueller-Hinton broth) or the agar dilution method (Mueller-Hinton agar; limited to fosfomycin).E. coli ATCC 25922 served as the quality control strain.Results were interpreted according to the Clinical and Laboratory Standards Institute (CLSI) M100, 32 nd edition, or the European Committee on Antimicrobial Susceptibility Testing (EUCAST; www.eucast.org).As shown in Table 1, three NDM-and MCR-producing E. coli isolates were resistant to meropenem and colistin, as well as to ampicillin, cefazolin, cefotaxime, streptomycin, tetracycline, chloramphenicol, florfenicol, sulfamethoxazole/trimethoprim.However, they remained susceptible to gentamicin, amikacin, tigecycline, nalidixic acid, ciprofloxacin, and fosfomycin (Table S1).To further characterize these E. coli isolates, whole-genome sequencing was performed using Illumina HiSeq technology (Illumina, San Diego, CA, USA).The library was prepared with the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs, USA), generating 150 bp paired-end reads.Subsequently, genomic DNA was