Emergence of a Multidrug-Resistant Co-Carrying a New Variant and Genes Recovered from a Urinary Tract Infection.

Background: Carbapenem-resistant Enterobacterales (CRE) are a significant threat to worldwide public health, resulting in increased morbidity, death, hospitalization time and healthcare expenses. Here, the genomic and phylogenetic characteristics of a multidrug-resistant isolate carrying both the new variant and gene obtained from a urinary tract infection in China are investigated.

Methods: Antimicrobial susceptibility of 779 was evaluated by using the broth microdilution method. Short-read Illumina NovaSeq 6000 and long-read Oxford Nanopore MinION platforms were applied to sequence the bacterial whole genomic DNA and then de novo assembled. The genome sequence was annotated using the NCBI Prokaryotic Genome Annotation Pipeline and further subjected to identify the sequence type (ST), capsular type, and antibiotic resistance genes. BacWGSTdb 2.0 was used to perform the core genome multilocus sequence typing (cgMLST) analysis with other closely related isolates deposited in the public database.

Results: 779 was resistant to aztreonam, levofloxacin, fosfomycin, cefoxitin, cefepime, cefotaxime, imipenem, meropenem, polymyxin, and tigecycline. The complete genome sequence of 779 is made up of nine contigs totaling 5,667,876 bp, including one chromosome and eight plasmids. The isolate was assigned to ST101, serotype O-:H31, and phylogroup B1. The colistin resistance gene (located in a 242,460 bp IncHI2/IncHI2A plasmid) and the β-lactam resistance gene (located in a 46,161 bp IncX3 plasmid) were among the 27 antimicrobial resistance genes discovered. The closest relative of 779, another ST101 strain ( 443) obtained from a sewage sample in Shandong, China in 2015, differs by only 24 cgMLST alleles.

Conclusion: We discovered the first multidrug-resistant ST101 strain with plasmid-mediated variant and gene in China. These findings would help us to better understanding the genomic traits, antimicrobial resistance mechanisms and epidemiological aspects of this bacterial pathogen.