First Identification of a Multidrug-Resistant Pseudomonas putida Co-Carrying Five β-Lactam Resistance Genes Recovered from a Urinary Tract Infection in China

Danni Bao; Linyao Huang; Jianxin Yan; Yexuzi Li; Zhi Ruan; Tian Jiang

doi:10.2147/IDR.S366567

First Identification of a Multidrug-Resistant Pseudomonas putida Co-Carrying Five β-Lactam Resistance Genes Recovered from a Urinary Tract Infection in China

Infect Drug Resist. 2022 Apr 28:15:2229-2234. doi: 10.2147/IDR.S366567. eCollection 2022.

Authors

Danni Bao^{1

2}, Linyao Huang³, Jianxin Yan³, Yexuzi Li⁴, Zhi Ruan², Tian Jiang^{2

3}

Affiliations

¹ Department of Clinical Laboratory, Sanmen People's Hospital, Taizhou, Zhejiang, 317100, People's Republic of China.
² Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310016, People's Republic of China.
³ Department of Clinical Laboratory, The Affiliated Wenling Hospital, Wenzhou Medical University, Wenling, 317500, People's Republic of China.
⁴ Department of Critical Care Medicine, The Affiliated Wenling Hospital, Wenzhou Medical University, Wenling, 317500, People's Republic of China.

Abstract

The emergence of multidrug-resistant Pseudomonas spp. in the clinical settings has heightened public awareness. Here, we described the genomic characteristics of a P. putida isolate co-carrying five β-lactam resistance genes recovered from a urinary tract infection in China. Whole-genome sequencing was performed using Illumina NovaSeq 6000 and Oxford Nanopore MinION platforms. The genome sequence was annotated and further subjected to identify the sequence type (ST), antibiotic resistance and virulence genes. Phylogenetic analysis of 193 P. putida strains stored in NCBI public database based on core genome single nucleotide polymorphism (cgSNP) strategy were also performed and visualized. Our study indicated that P. putida PP_2463 was resistant to a wide range of antimicrobial agents tested, including aminoglycosides, carbapenems and fluoroquinolones. The complete genome sequence of P. putida PP_2463 is made up of one chromosome and two plasmids, which could be assigned to a new sequence type (ST) 148. The co-occurrence of β-lactam resistance genes bla _IPM-15, bla _PME-1, bla _CARB-2, and bla _NDM-1 were first identified in P. putida, and a novel β-lactamase gene located in the chromosome were among the antimicrobial resistance genes discovered. The closest relative of P. putida PP_2463 was identified in 2012 from a urine sample in China, with a difference of 143 SNPs. Along with the presence of multiple β-lactamase genes and mobile genetic elements, the multidrug-resistant phenotype suggests a significant potential as an antibiotic resistance reservoir for Pseudomonas spp.

Keywords: Pseudomonas putida; blaCARB-2; blaIPM-15; blaNDM-5; blaPME-1; multidrug-resistance; urinary tract infection; whole genome sequencing.

Grants and funding

This study was supported by Zhejiang Provincial Medical and Health Science and Technology Plan (2022RC299), Scientific Research Fund of Taizhou Science and Technology Bureau (20ywb152), Scientific Research Fund of Wenling Science and Technology Bureau (2021S00229, 2020S0180116).