Genetic Characterization of Colistin-Resistant Salmonella enterica ST34 Co-Harbouring Plasmid-Borne mcr-1, bla_CTX-M-15 and bla_KPC-2 Recovered from a Paediatric Patient in Shenzhen, China

Abstract

Background

Since 2015, plasmid-borne mcr-1 has been reported in various bacterial strains in the clinical setting globally. However, the transmission mechanisms of this gene in Salmonella are not well defined. This study aimed to characterize the genomic features of a Salmonella enterica ST34 isolate, which carried a mcr-1, mapped to a carbapenemase and extended spectrum β-lactamase encoding gene located on the IncX4 plasmid.

Methods

Salmonella enterica was recovered from a diarrheal paediatric patient in Shenzhen, China. Antimicrobial susceptibility testing was performed by using the VITEK 2 system. Drug resistance genes were identified using targeted primers and Sanger sequencing. The transferability and genome location of mcr-1 was determined by performing conjugation, S1-PFGE and Southern blot hybridization analysis. WGS was performed by Illumina MiSeq sequencing and was assembled using the A5-Miseq pipeline, and gene annotation was performed using RAST 2.0. The database Centre for Genomic Epidemiology’s website was used to identify resistance genes and sequence types (STs).

Results

We found that the isolate was extensively drug resistant and belonging to ST34, carrying an IncX4 plasmid with mcr-1, bla_KPC-2 and bla_CTX-M-15. We also noticed that genes bla_PAO, fosA, catB, the mutation in oprD and mexT (MexEF-OprN efflux regulator), and exotoxin-encoding genes (exoS, exoY and exoT) were associated with resistance and virulence in the genome. In addition, heavy metal resistance genes as silP and silE were determined.

Conclusion

This study highlights the potential risk of ST34 of Salmonella enterica serotype Typhimurium carrying multiple drug resistance encoding genes in a single IncX4 plasmid.

Keywords:

• Salmonella enterica
• MCR-1
• KPC-1
• CTX-M-15
• paediatric patient

Data Sharing Statement

All data files mentioned in this manuscript are available.

Ethics Approval and Consent to Participate

The study was conducted according to the guidelines of the Declaration of Helsinki, and approved by the Institutional Ethics Committee, Shenzhen Children’s Hospital, Reference number: 2018 (013) on dated 2018/09/03.

Informed Consent Statement

Due to the retrospective nature of the study, the Ethics Committee of Shenzhen Children’s Hospital, Shenzhen determined that patients’ consent was not required. The clinical isolate samples used in this research were part of the routine hospital laboratory procedure No personal patient’s information was used, data were kept confidentially and in compliance with the Declaration of Helsinki.

Acknowledgments

We would like to thank Prof. Ma Lian and Dr. Chen Xiaowen from the pediatric research institute, Shenzhen Children’s Hospital for their constant support of this project and Dr. Sunil Kumar Shahu from BGI, Shenzhen, for genome assembly.

Author Contributions

All authors made a significant contribution to the work reported, whether that is in the conception, study design, execution, acquisition of data, analysis and interpretation, or in all these areas; took part in drafting, revising or critically reviewing the article; gave final approval of the version to be published; have agreed on the journal to which the article has been submitted; and also agree to be accountable for all aspects of the work.

Disclosure

The authors declare no conflicts of interest in this work.

Additional information

Funding

(1) Shenzhen Fund for Guangdong Provincial High-Level Clinical Key Specialties (No. funded this research SZGSP012), and (2) Shenzhen Key Medical Discipline Construction Fund (No. SZXK034).