Coexistence of <i>tet</i> (X4), <i>mcr-1</i> , and <i>bla</i> _NDM-5 in ST6775 <i>Escherichia coli</i> Isolates of Animal Origin in China

Abstract

Emergence of pathogens harboring multiple resistance genes incurs great concerns. Cooccurrence of mobile resistance genes conferring resistance to tigecycline, colistin, and carbapenems in Escherichia coli has not been investigated. This study aimed to characterize three E. coli isolates coharboring <i>tet</i>(X4), <i>mcr-1</i>, and <i>bla</i>_NDM-5. Isolates coharboring <i>tet</i>(X4), <i>mcr-1</i>, and <i>bla</i>_NDM-5 were identified and characterized by PCR, Sanger sequencing, antimicrobial susceptibility testing, conjugation assays, Illumina sequencing, nanopore sequencing, and bioinformatic analysis. Three E. coli isolates carrying <i>tet</i>(X4), <i>mcr-1</i>, and <i>bla</i>_NDM-5 were identified from pigeons in China. They were resistant to almost all antimicrobials except enrofloxacin. <i>tet</i>(X4) and <i>bla</i>_NDM-5 could be conjugated into E. coli C600, but <i>mcr-1</i> was nontransferable in three isolates. Three isolates belonged to sequence type 6775 (ST6775), and clonal dissemination of isolates carrying <i>tet</i>(X4), <i>mcr-1</i>, and <i>bla</i>_NDM-5 existed in the pigeon farm. Genetic analysis revealed that <i>mcr-1</i> mediated by the Tn<i>6330</i> was located on the chromosome, <i>tet</i>(X4) was located on the IncFII plasmid, and <i>bla</i>_NDM-5 was located on the IncX3 plasmid. We first characterized the E. coli isolates carrying <i>tet</i>(X4), <i>mcr-1</i>, and <i>bla</i>_NDM-5 simultaneously. Relevant measures should be taken to decrease the prevalence of pathogens carrying <i>tet</i>(X4), <i>mcr-1</i>, and <i>bla</i>_NDM-5. <b>IMPORTANCE</b> Tigecycline and colistin are regarded as vital antimicrobials to treat multidrug-resistant (MDR) bacterial infections, such as that caused by carbapenemase-producing <i>Enterobacteriaceae</i> (CPE). Cooccurrence of mobile resistance genes conferring resistance to last-resort antimicrobials in E. coli remains unknown. Here, we characterized E. coli strains coharboring <i>tet</i>(X4), <i>mcr-1</i>, and <i>bla</i>_NDM-5 phenotypically and genetically. Resistance genes <i>tet</i>(X4), <i>mcr-1</i>, and <i>bla</i>_NDM-5 were located on transposons or plasmids that were mobile genetic elements related to the capture, accumulation, and dissemination of such important resistance genes. The emergence of E. coli isolates carrying <i>tet</i>(X4), <i>mcr-1</i>, and <i>bla</i>_NDM-5 highlights the importance of monitoring the coexistence of novel mobile resistance genes in different settings with a One Health approach. Risk of transmission of such MDR pathogens from animals to humans should be evaluated comprehensively.