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Published on: March 24, 2023
Trans-Regional and Cross-Host Spread of mcr-Carrying Plasmids Revealed by Complete Plasmid Sequences - 44 Countries,
Zhe Li1, Zhenpeng Li1, Yao Peng1
1State Key Laboratory of Infectious Disease Prevention and Control; National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
Background:
The surveillance of antimicrobial resistance genes (ARGs) and bacteria is one critical approach to prevent and control antimicrobial resistance (AMR). Next-generation sequencing (NGS) is a powerful tool in monitoring the emergence and spread of ARGs and resistant bacteria. The horizontal transfer of ARGs across host bacteria mediated by plasmids is a challenge in NGS surveillance for resistance because short-read sequencing can hardly generate the complete plasmid genome sequence, and the correlation between ARGs and plasmids are difficult to determine.
Methods:
The complete genome sequences of 455 mcr-carrying plasmids (pMCRs), and the data of their host bacteria and isolation regions were collected from the NCBI database. Genes of Inc types and ARGs were searched for each plasmid. The genome similarity of these plasmids was analyzed by pangenome clustering and genome alignment.
Results:
A total of 52 Inc types, including a variety of fusion plasmids containing 2 or more Inc types were identified in these pMCRs and carried by complex host bacteria. The cooccurrence of ARGs in pMCRs was generally observed, with an average of 3.9 ARGs per plasmid. Twenty-two clusters with consistent or highly similar sequences and gene compositions were identified by the pangenome clustering, which were characterized with distributions in different countries/regions, years or host bacteria in each cluster.
Discussion:
Based on the complete plasmid sequences, distribution of mcr genes in different Inc type plasmids, their co-existence with other AMRs, and transmission of one pMCR across regions and host bacteria can be revealed definitively. Complete plasmid genomes and comparisons in the laboratory network are necessary for spread tracing of ARG-carrying plasmids and risk assessment in AMR surveillance.
Insights
Complete plasmid sequencing is crucial for tracking antimicrobial resistance genes (ARGs) and understanding their spread. This study analyzed 455 mcr-carrying plasmids, revealing diverse Inc types and co-occurring ARGs, aiding in AMR surveillance.
Area of Science:
- Microbiology
- Genomics
- Public Health
Background:
- Antimicrobial resistance (AMR) surveillance is vital for control.
- Next-generation sequencing (NGS) aids in monitoring resistance genes (ARGs) and bacteria.
- Short-read sequencing limits complete plasmid analysis and ARG-plasmid correlation.
Purpose of the Study:
- To investigate the genomic characteristics of mcr-carrying plasmids (pMCRs).
- To understand the diversity and co-occurrence of ARGs within pMCRs.
- To assess the utility of complete plasmid sequences for AMR surveillance.
Main Methods:
- Collected 455 complete pMCR genome sequences from NCBI.
- Identified Inc types and ARGs for each plasmid.
- Analyzed plasmid genome similarity using pangenome clustering and alignment.
Main Results:
- Identified 52 Inc types in pMCRs, including fusion plasmids.
- Observed co-occurrence of ARGs, averaging 3.9 per plasmid.
- Defined 22 plasmid clusters with distinct geographical, temporal, or host distributions.
Conclusions:
- Complete plasmid sequences definitively reveal ARG distribution, co-existence, and transmission.
- Complete plasmid genomes are essential for tracing plasmid spread and AMR risk assessment.
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