Coexistence of Two Genes Carried on IncX3 and IncFII Plasmids in an Isolate Revealed by Illumina and Nanopore Sequencing

Overview

Journal Front Microbiol

Specialty Microbiology

Date 2020 Mar 3

PMID 32117184

Citations 7

Authors

Lang Yang

Yanfeng Lin

Lanfen Lu

Mei Xue

Hui Ma

Xuguang Guo

Kaiying Wang

Peihan Li

Xinying Du

Kezong Qi

Peng Li

Hongbin Song

Affiliations

Soon will be listed here.

Abstract

The emergence of carbapenem-resistant poses a significant threat to public health worldwide. Here, we reported a multidrug-resistant strain with two different -carrying plasmids from China. Illumina short-read and MinION long-read whole genome sequencing were performed. Genomic analysis found that one gene together with was located on a 55-kb IncX3 plasmid, while the other gene was on a novel 68-kb IncFII plasmid. Susceptibility testing and quantitative reverse transcription PCR results further indicated that the transconjugants with the IncX3 plasmid exhibited higher-level carbapenem resistance and expression of than those with both plasmids or the IncFII plasmid. Two other β-lactamase genes ( and ) were also detected on another 160-kb IncF plasmid. This is the first report of coexistence of two -carrying plasmids in a single bacterial isolate, highlighting the genetic complexity of NDM-5 carbapenemase circulation, and the urgent need for continued active surveillance.

Citing Articles

Molecular epidemiology and comparative genomics of carbapenemase-producing isolates from 19 tertiary hospitals in China from 2019 to 2020.

Ko W, Tseng S, Chou C, Li T, Li R, Zhang Y Front Microbiol. 2023; 14:1056399.

PMID: 37152734 PMC: 10160391. DOI: 10.3389/fmicb.2023.1056399.

Global prevalence, characteristics, and future prospects of IncX3 plasmids: A review.

Guo X, Chen R, Wang Q, Li C, Ge H, Qiao J Front Microbiol. 2022; 13:979558.

PMID: 36147856 PMC: 9485871. DOI: 10.3389/fmicb.2022.979558.

Role of Chromosome- and/or Plasmid-Located on the Carbapenem Resistance and the Gene Stability in Escherichia coli.

Sakamoto N, Akeda Y, Sugawara Y, Matsumoto Y, Motooka D, Iida T Microbiol Spectr. 2022; 10(4):e0058722.

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Characterization of NDM-5 Carbapenemase-Encoding Gene ( ) - Positive Multidrug Resistant Commensal from Diarrheal Patients.

Chowdhury G, Ramamurthy T, Das B, Ghosh D, Okamoto K, Miyoshi S Infect Drug Resist. 2022; 15:3631-3642.

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References

Wu W, Espedido B, Feng Y, Zong Z . Citrobacter freundii carrying blaKPC-2 and blaNDM-1: characterization by whole genome sequencing. Sci Rep. 2016; 6:30670. PMC: 4964652. DOI: 10.1038/srep30670. View

Elumalai S, Muthu G, Selvam R, Ramesh S . Detection of TEM-, SHV- and CTX-M-type β-lactamase production among clinical isolates of Salmonella species. J Med Microbiol. 2014; 63(Pt 7):962-967. DOI: 10.1099/jmm.0.068486-0. View

Kanamori H, Parobek C, Juliano J, Johnson J, Johnston B, Johnson T . Genomic Analysis of Multidrug-Resistant Escherichia coli from North Carolina Community Hospitals: Ongoing Circulation of CTX-M-Producing ST131-30Rx and ST131-30R1 Strains. Antimicrob Agents Chemother. 2017; 61(8). PMC: 5527606. DOI: 10.1128/AAC.00912-17. View

Aziz R, Bartels D, Best A, DeJongh M, Disz T, Edwards R . The RAST Server: rapid annotations using subsystems technology. BMC Genomics. 2008; 9:75. PMC: 2265698. DOI: 10.1186/1471-2164-9-75. View

Livak K, Schmittgen T . Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods. 2002; 25(4):402-8. DOI: 10.1006/meth.2001.1262. View

Zong Z, Zhang X . blaNDM-1-carrying Acinetobacter johnsonii detected in hospital sewage. J Antimicrob Chemother. 2013; 68(5):1007-10. DOI: 10.1093/jac/dks505. View

Yong D, Toleman M, Giske C, Cho H, Sundman K, Lee K . Characterization of a new metallo-beta-lactamase gene, bla(NDM-1), and a novel erythromycin esterase gene carried on a unique genetic structure in Klebsiella pneumoniae sequence type 14 from India. Antimicrob Agents Chemother. 2009; 53(12):5046-54. PMC: 2786356. DOI: 10.1128/AAC.00774-09. View

Feng Y, Liu L, McNally A, Zong Z . Coexistence of Two Genes on an IncF Plasmid as Revealed by Nanopore Sequencing. Antimicrob Agents Chemother. 2018; 62(5). PMC: 5923099. DOI: 10.1128/AAC.00110-18. View

Pu X, Pan J, Gu Y, Zheng W, Li J, Yu H . Complete Sequences and Characterization of Two Novel Plasmids Carrying aac(6')-Ib-cr and qnrS Gene in Shigella flexneri. Microb Drug Resist. 2015; 22(2):115-22. DOI: 10.1089/mdr.2015.0082. View

10.

Stamatakis A . RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014; 30(9):1312-3. PMC: 3998144. DOI: 10.1093/bioinformatics/btu033. View

11.

Jovcic B, Lepsanovic Z, Begovic J, Rakonjac B, Perovanovic J, Topisirovic L . The clinical isolate Pseudomonas aeruginosa MMA83 carries two copies of the blaNDM-1 gene in a novel genetic context. Antimicrob Agents Chemother. 2013; 57(7):3405-7. PMC: 3697382. DOI: 10.1128/AAC.02312-12. View

12.

Yu L, Li W, Qi K, Wang S, Chen X, Ni J . McbR is involved in biofilm formation and H2O2 stress response in avian pathogenic Escherichia coli X40. Poult Sci. 2019; 98(9):4094-4103. DOI: 10.3382/ps/pez205. View

13.

Zurfluh K, Klumpp J, Nuesch-Inderbinen M, Stephan R . Full-Length Nucleotide Sequences of mcr-1-Harboring Plasmids Isolated from Extended-Spectrum-β-Lactamase-Producing Escherichia coli Isolates of Different Origins. Antimicrob Agents Chemother. 2016; 60(9):5589-91. PMC: 4997865. DOI: 10.1128/AAC.00935-16. View

14.

Wick R, Judd L, Gorrie C, Holt K . Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol. 2017; 13(6):e1005595. PMC: 5481147. DOI: 10.1371/journal.pcbi.1005595. View

15.

Nahid F, Zahra R, Sandegren L . A blaOXA-181-harbouring multi-resistant ST147 Klebsiella pneumoniae isolate from Pakistan that represent an intermediate stage towards pan-drug resistance. PLoS One. 2017; 12(12):e0189438. PMC: 5722313. DOI: 10.1371/journal.pone.0189438. View

16.

Krishnaraju M, Kamatchi C, Jha A, Devasena N, Vennila R, Sumathi G . Complete sequencing of an IncX3 plasmid carrying blaNDM-5 allele reveals an early stage in the dissemination of the blaNDM gene. Indian J Med Microbiol. 2015; 33(1):30-8. DOI: 10.4103/0255-0857.148373. View

17.

Cornaglia G, Giamarellou H, Rossolini G . Metallo-β-lactamases: a last frontier for β-lactams?. Lancet Infect Dis. 2011; 11(5):381-93. DOI: 10.1016/S1473-3099(11)70056-1. View

18.

Ruan Z, Feng Y . BacWGSTdb, a database for genotyping and source tracking bacterial pathogens. Nucleic Acids Res. 2015; 44(D1):D682-7. PMC: 4702769. DOI: 10.1093/nar/gkv1004. View

19.

Runcharoen C, Raven K, Reuter S, Kallonen T, Paksanont S, Thammachote J . Whole genome sequencing of ESBL-producing Escherichia coli isolated from patients, farm waste and canals in Thailand. Genome Med. 2017; 9(1):81. PMC: 5588602. DOI: 10.1186/s13073-017-0471-8. View

20.

Carattoli A, Zankari E, Garcia-Fernandez A, Larsen M, Lund O, Villa L . In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother. 2014; 58(7):3895-903. PMC: 4068535. DOI: 10.1128/AAC.02412-14. View