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 gram-negative bacilli (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 genus (33.8%, 230/680) of the 22 genera. Carbapenemase genes were identified in 307 isolates (45.1%, 307/680), including 206 (30.3%, 206/680) bla NDM ; 51 (7.5%, 51/680) bla VIM-2 , 48 (7.1%, 48/680) bla IMP , and seven (1.0%, 7/680) bla KPC-2 . The bla NDM genes were first detected in three isolates, Providencia vermicola , Achromobacter spp. , and Cupriavidus gilardii . Co-existence of bla VIM and bla IMP 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 Klebsiella pneumoniae . In addition, we detected seven isolates harboring the bla AFM-1 gene, a novel metallo-β-lactamase gene. This was first genomic analysis of ST11 Klebsiella 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% (745/10000), and CNS-GNB producing carbapenemase were up to 45.1% (307/680). Most CNS-GNB cases were associated with infectious disease, multiple hospitalizations, or long-term care, and a high prevalence of underlying disease.