Genetic characterisation of a complex class 1 integron in an NDM-1-producing Citrobacter freundii ST396 clinical strain isolated from a urine sample

Zhonghong Li; Yanfeng Lin; Lanfen Lu; Kaiying Wang; Lang Yang; Peihan Li; Jinhui Li; Leili Jia; Peng Li; Hongbin Song

doi:10.1016/j.jgar.2020.08.002

Genetic characterisation of a complex class 1 integron in an NDM-1-producing Citrobacter freundii ST396 clinical strain isolated from a urine sample

J Glob Antimicrob Resist. 2020 Dec:23:64-66. doi: 10.1016/j.jgar.2020.08.002. Epub 2020 Aug 18.

Authors

Zhonghong Li¹, Yanfeng Lin², Lanfen Lu³, Kaiying Wang², Lang Yang², Peihan Li², Jinhui Li⁴, Leili Jia⁴, Peng Li⁵, Hongbin Song⁶

Affiliations

¹ Center for Disease Control and Prevention of PLA, 20 DongDa Street, Fengtai District, Beijing 100071, China; College of Environmental and Chemical Engineering, Nanchang Hangkong University, Nanchang, Jiangxi 330063, China.
² Center for Disease Control and Prevention of PLA, 20 DongDa Street, Fengtai District, Beijing 100071, China; Academy of Military Medical Sciences, Academy of Military Sciences, Beijing 100850, China.
³ Department of Laboratory, Sun Yat-Sen University affiliated Zhongshan Hospital, Zhongshan, Guangdong 528400, China.
⁴ Center for Disease Control and Prevention of PLA, 20 DongDa Street, Fengtai District, Beijing 100071, China.
⁵ Center for Disease Control and Prevention of PLA, 20 DongDa Street, Fengtai District, Beijing 100071, China. Electronic address: jiekenlee@126.com.
⁶ Center for Disease Control and Prevention of PLA, 20 DongDa Street, Fengtai District, Beijing 100071, China. Electronic address: hongbinsong@263.net.

PMID: 32818668
DOI: 10.1016/j.jgar.2020.08.002

Abstract

Objectives: The aim of this study was to characterise a multidrug-resistant (MDR) Citrobacter freundii strain carrying a bla_NDM-1-harbouring conjugative IncA/C2-type plasmid in China.

Methods: The whole genome of C. freundii strain L75 was sequenced both on HiSeq® (Novogene Corp., China) and GridION X5 (GrandOmics Biosciences Co., Ltd.) platforms. De novo genome assembly, genome annotation, multilocus sequence typing (MLST) and plasmid replicon typing were performed.

Results: Citrobacter freundii L75 was assigned to ST396 and contains a 5.1-Mb chromosome and two plasmids (∼146 kb and ∼73 kb) designated pCf75 and pCf76, respectively. The antibiotic resistance determinants bla_NDM-1, sul1, sul2, arr-3, mph(A), aadA16, aph(3")-Ib, aac(3)-IId, aph(6)-Id, aac(6')-Ib-cr and dfrA27 were located on plasmid pCf75, whilst bla_CMY-78 was chromosomally encoded. A 22.1-kb MDR-encoding region (MDRR) in a complex class 1 integron contained all of the resistance genes of plasmid pCf75.

Conclusions: We detected and characterised a plasmid carrying a novel MDRR in which a complex class 1 integron plays an essential role. In addition, this study provides fresh genomic insights into the diversity of C. freundii ST396 prevalent in Guangzhou Province, China, and underscores the increasing clinical relevance of the IncA/C2 plasmid family.

Keywords: Citrobacter freundii; Integrons; NDM-1; Plasmids; ST396; β-Lactamase.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

China
Citrobacter freundii* / genetics
Enterobacteriaceae Infections*
Humans
Integrons
Microbial Sensitivity Tests
Multilocus Sequence Typing
beta-Lactamases

Substances

beta-Lactamases
beta-lactamase NDM-1