Genomic analysis of chromosomal cointegrated bla NDM-1-carrying ICE and bla RSA-1-carrying IME from clinical multidrug resistant Aeromonas caviae

Xinhua Luo; Zhe Yin; Lianhua Yu; Jin Zhang; Dakang Hu; Mengqiao Xu; Peng Wang; Fengling Wang; Jiao Feng

doi:10.3389/fcimb.2023.1131059

Genomic analysis of chromosomal cointegrated bla _NDM-1-carrying ICE and bla _RSA-1-carrying IME from clinical multidrug resistant Aeromonas caviae

Front Cell Infect Microbiol. 2023 Mar 23:13:1131059. doi: 10.3389/fcimb.2023.1131059. eCollection 2023.

Authors

Xinhua Luo¹, Zhe Yin², Lianhua Yu¹, Jin Zhang¹, Dakang Hu¹, Mengqiao Xu¹, Peng Wang², Fengling Wang³, Jiao Feng⁴

Affiliations

¹ Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital, Taizhou, China.
² State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China.
³ Nanxiang Branch of Ruijin Hospital, Shanghai Jiaotong University, Shanghai, China.
⁴ Institutes of Biomedical Sciences, Shanxi University, Taiyuan, China.

Abstract

Introduction: The objective of this study is to thoroughly analyze the detailed genomic characteristics of clinical strain 211703 of Aeromonas caviae, which co-carrying bla _RSA-1 and bla _NDM-1 genes. 211703 was isolated from the patient's cerebrospinal fluid drainage sample in a Chinese tertiary hospital.

Methods: Carbapenemase NDM was detected by the immunocolloidal gold technique. The MIC values were determined by VITEK2. The whole genome sequence of 211703 was analyzed using phylogenetics, genomic comparison, and extensive dissection.

Results: This study revealed that 211703 only contained a single 4.78 Mb chromosome (61.8% GC content), and no plasmids were discovered in 211703. 15 different types of resistant genes were detected in the genome of 211703, including bla _RSA-1 harbored on integrative and mobilizable element (IME) Tn7413a, and bla _NDM-1 harbored on integrative and conjugative element (ICE). The ICE and IME were all carried on the chromosome of 211703 (c211703). Detailed comparison of related IMEs/ICEs showed that they shared similar conserved backbone regions, respectively. Comprehensive annotation revealed that bla _RSA-1 was carried by the gene cassette of a novel integron In2148 on Tn7413a, and bla _NDM-1 was captured by an insertion sequence ISCR14-like on the ICE of 211703. We speculated that mobile genetic elements (MGEs) such as ICE and IME facilitated the spread of resistance genes such as bla _RSA-1 and bla _NDM-1.

Discussion: In conclusion, this study provides an overall understanding of the genomic characterization of clinically isolated A. caviae 211703, and an in-depth discussion of multiple acquisition methods of drug resistance genes in Aeromonas. To the best of our knowledge, this is the first report of A. caviae carrying bla _RSA-1 even both bla _RSA-1 and bla _NDM-1, and this is the first bacterium carrying bla _RSA-1 isolated from the clinical setting.

Keywords: Aeromonas caviae; ICE; IME; blaNDM-1; blaRSA-1.

Publication types

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

MeSH terms

Aeromonas caviae*
Chromosomes
Genomics
Humans

Substances

beta-lactamase NDM-1
rabbit sperm membrane autoantigen

Grants and funding

This work was supported by the Foundation of Taizhou Science and Technology Bureau (22ywa43), the Medical and Health Science and Technology Project of Zhejiang Province (2023KY1323), the Key Laboratory of Microbiol Technology and Bioinformatics of Zhejiang Province Foundation (2021E10010KFJJ09), and the National Natural Science Foundation of China (82002207).