Characterization of carbapenem non-susceptible Gram-negative Bacilli isolated from the feces of 10,000 inpatients in Southern China

Background Carbapenem non-susceptible Gram-negative bacilli (CNS-GNB) were dominant pathogen causing clinical infections. The human intestine was important reservoir of GNB, but there were few studies to analysis the prevalence of fecal colonization with them. Methods Fecal samples were collected from hosiptal screening test for GNB was conducted by using home-made MacConkey agar. Antimicrobial susceptibility was determined by the automatic microbiology analyzer and drug-resistant genes were characterized by polymerase chain reaction assays and DNA sequencing. The whole genome sequencing were used to analysis the characteristic of genetic structure of the isolates. Results A total of 680 CNS-GNB were collected. Acinetobacter spp. were the dominant species (33.8%) of the 22 genera. Carbapenemase genes were identified in 307 isolates (45.1%), including 206 (30.3%) blaNDM; 51 (7.5%) blaVIM−2, 48 (7.1%) blaIMP, and seven (1.0%) blaKPC−2. The blaNDM genes were first detected in three isolates, Providencia vermicola, Achromobacter spp., and Cupriavidus gilardii. Co-existence of blaVIM and blaIMP genes was detected in five isolates; Achromobacter co-producing VIM and IMP has not been previously reported. The mcr-1 gene was identified in five strains of Acinetobacter and one strain of K. pneumoniae. In addition, we detected seven isolates harboring the blaAFM−1 gene, a novel metallo-β-lactamase gene. This was first genomic analysis of ST11 K. pneumoniae co-producing NDM-5 and mcr-1, which revealed that blaNDM-5 and mcr-1 are located on two different plasmids. The plasmid harboring blaNDM-5, which was composed of a typical IncX3-type backbone, and the mcr-1 gene, was located between an IS30-like element ISApl1 and a PAP2-like encoding gene in the IncHI2-type plasmid. Conclusions the overall prevalence of fecal carriage of CNS-GNB in 10,000 stool samples was 7.45%, and more than half of CNS-GNB produced carbapenemase. Most CNS-GNB cases were associated with infectious disease, multiple hospitalizations, or long-term care, and a high prevalence of underlying disease.