Emergence of a Clinical Escherichia coli Sequence Type 131 Strain Carrying a Chromosomal bla KPC-2 Gene

Dairong Wang; Xinli Mu; Ying Chen; Dongdong Zhao; Ying Fu; Yan Jiang; Yiwei Zhu; Jingjing Quan; Xiaoting Hua; Guofeng Mao; Xi Li; Yunsong Yu

doi:10.3389/fmicb.2020.586764

Emergence of a Clinical Escherichia coli Sequence Type 131 Strain Carrying a Chromosomal bla _KPC-2 Gene

Front Microbiol. 2020 Nov 13:11:586764. doi: 10.3389/fmicb.2020.586764. eCollection 2020.

Authors

Dairong Wang^{1

2}, Xinli Mu^{1

3}, Ying Chen^{1

3}, Dongdong Zhao^{1

3}, Ying Fu^{3

4}, Yan Jiang^{1

3}, Yiwei Zhu^{1

3}, Jingjing Quan^{1

3}, Xiaoting Hua^{1

3}, Guofeng Mao⁵, Xi Li⁶, Yunsong Yu^{1

3}

Affiliations

¹ Department of Infectious Diseases, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, China.
² Blood Center of Zhejiang Province, Hangzhou, China.
³ Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou, China.
⁴ Department of Clinical Laboratory, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, China.
⁵ Department of Laboratory Medicine, Shaoxing People's Hospital, Shaoxing, China.
⁶ Centre of Laboratory Medicine, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China.

Abstract

Objectives: Bacteria carrying the Klebsiella pneumoniae carbapenemase genes have rapidly spread worldwide and have become a great threat to public health. The bla _KPC-2 gene has been primarily located on plasmids cocirculating in various strains. However, chromosomal integration of the bla _KPC _-2 gene in Escherichia coli has not been reported. In the present study, we report the detection of the first clinical strain of E. coli ST131 with a bla _KPC _-2 gene, which integrated in the chromosome. E. coli strain EC3385 was identified and subjected to susceptibility testing and genotyping. The complete genome sequences of this strain and four Proteus mirabilis strains were obtained. Chromosomal integration of the bla _KPC-2 gene was confirmed using a combination of short- and long-read sequencing. Comparative genetic analyses were performed and the origin of the chromosomal location of the bla _KPC-2 gene was further analyzed. Whole-genome sequencing revealed that strain EC3385 belonged to the ST131 type and possessed various resistance and virulence genes. Sequence analysis showed that the bla _KPC-2 gene was carried in a 24-kb insertion sequence on the chromosome. This insertion sequence possessed high sequence similarity to previously reported bla _KPC-2 -habouring plasmids of P. mirabilis in China. To the best of our knowledge, this is the first report of a clinical ST131 E. coli strain carrying bla _KPC-2 on the chromosome. The bla _KPC-2 gene was probably horizontally transferred from the P. mirabilis plasmid to the E. coli chromosome by the IS26 element, indicating that P. mirabilis might be an important reservoir of bla _KPC-2 gene for E. coli. Furthermore, the E. coli ST131 strain carrying the chromosomal bla _KPC _-2 gene could be further spread due to its carbapenem resistance and high virulence. It is imperative to perform active surveillance to prevent further dissemination of KPC-2 type carbapenemase-producing isolates.

Keywords: E. coli; KPC-2; cre; resistance mechanism; whole genome sequencing.