IncFIB-4.1 and IncFIB-4.2 Single-Replicon Plasmids: Small Backbones with Large Accessory Regions

Abstract

Purpose

To establish a typing scheme for IncFIB replicon and to dissect genomic features of IncFIB-4.1/4.2 single-replicon plasmids.

Methods

A total of 146 representative fully sequenced IncFIB-replicon-containing plasmids were selected to construct a phylogenetic tree of repB_IncFIB sequences. A collection of nine IncFIB-4.1/4.2 single-replicon plasmids from China were fully sequenced here and compared with the first sequenced IncFIB-4.1/4.2 single-replicon plasmids from GenBank to dissect their genomic diversity.

Results

In this study, a repB sequence-based scheme was proposed for grouping IncFIB replicon into seven primary types and further into 70 subtypes. A collection of nine IncFIB-4.1/4.2 single-replicon plasmids were fully sequenced here and compared with the first sequenced IncFIB-4.1/4.2 single-replicon plasmids from GenBank. These 11 plasmids had small backbones and shared only three key backbone markers repB together with its iterons, parABC, and stbD. Each plasmid contained one large accessory region (LAR) inserted into the backbone, and these 11 LARs had significantly distinct profiles of mobile genetic elements (MGEs) and resistance/metabolism gene loci. Antibiotic resistance regions (ARRs; the antibiotic resistance gene-containing genetic elements) were found in seven of these 11 LARs. Besides resistance genes, ARRs carried unit or composite transposons, integrons, and putative resistance units. IncFIB-4.1/4.2 single-replicon plasmids were important vectors of drug resistance genes. This was the first report of three novel MGEs: In1776, Tn6755, and Tn6857.

Conclusion

Data presented here provided a deeper insight into diversity and evolution of IncFIB replicon and IncFIB-4.1/4.2 single-replicon plasmids.

Keywords:

• IncFIB
• IncFIB-4 single-replicon plasmids
• large accessory regions
• antibiotic resistance regions
• In1776
• Tn6755
• Tn6857

Data Sharing Statement

The datasets generated for this study can be found in the complete nucleotide sequences of plasmids pBJ20-tetA, p71221-mphA, pW08291-tetA, pA2508-emrE, pL21-1NR, p10057-catA, p13294-1NR, pA1876-NR, and pA2359-IMP were submitted to GenBank under accession numbers MN310373, MN310374, MN310376, MN310379, MN423365, MN423364, MT570100, MT549899, and MN423363, respectively.

Ethics Statement

This study uses the clinical bacterial isolates obtained from the Chinese public hospitals as listed in Table S1. The local legislation did not require the study to be reviewed or approved by an ethics committee, because the bacterial isolates involved in this study was part of the routine hospital Laboratory procedures. The research involving biohazards and all related procedures were approved by the Biosafety Committee of the Beijing Institute of Microbiology and Epidemiology.

Acknowledgments

All experiments and data analyses were done in Dr. Dongsheng Zhou’s laboratory.

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 agree to be accountable for all aspects of the work.

Disclosure

The authors report no conflicts of interest in this work.

Additional information

Funding

This work was supported by the National Natural Science Foundation of China (Grant No. 3214100027), the Key Project Plan of Medical Science Research in Hebei Province under Grant 20181072, and the Foundation of State Key Laboratory of Pathogen and Biosecurity of China under Grant SKLPBS2116.