A Clinical Strain with Carried by an Integrative and Conjugative Element in China

Overview

Journal Front Microbiol

Specialty Microbiology

Date 2022 Aug 15

PMID 35966707

Authors

Lin Zheng

Xinfang Zhang

Lingwei Zhu

Gejin Lu

Jiayao Guan

Mingwei Liu

Jie Jing

Shiwen Sun

Ying Wang

Yang Sun

Xue Ji

Bowen Jiang

Jun Chen

Jun Liu

Ping Chen

Xuejun Guo

Affiliations

Soon will be listed here.

Abstract

Objective: To precisely determine the species of a carbapenem-resistant strain 1809276 isolated from the urine of a Chinese patient and analyze its integrative and conjugative element (ICE) formation mechanism.

Methods: Single-molecule real-time (SMRT) sequencing was carried out on strain 18091276 to obtain the complete chromosome and plasmid (pCN1276) sequences, and average nucleotide identity (ANI) was used for precise species identification. The ICEs in GenBank with the same integrase structure as ICE were aligned. At the same time, the transfer ability of and the antibiotic sensitivity of 18091276 were tested.

Results: This bacterium was , and its drug resistance mechanism is the capture of the gene cassette by the Tn-like type 1 integron (- ) to form In before its capture by the ΔTn-carrying ICE . The acquisition of confers carbapenem resistance to 18091276.

Conclusion: The formation of -carrying ICE , its further integration into the chromosomes, and transposition and recombination of other elements promote bacterial gene accumulation and transmission.

Citing Articles

Characterization of a novel multi-resistant Pseudomonas juntendi strain from China with chromosomal bla and a megaplasmid coharboring bla and bla.

Jiang S, Li Y, Bi K, Yang S, Xia H, Li S BMC Genomics. 2024; 25(1):774.

PMID: 39118048 PMC: 11311922. DOI: 10.1186/s12864-024-10688-2.

Comprehensive insights into the impact of bacterial indole-3-acetic acid on sensory preferences in Drosophila melanogaster.

Aziz R, Ramesh P, Suchithra K, Stothard P, Narayana V, Raghu S Sci Rep. 2024; 14(1):8311.

PMID: 38594449 PMC: 11003987. DOI: 10.1038/s41598-024-58829-7.

Update on Accepted Novel Bacterial Isolates Derived from Human Clinical Specimens and Taxonomic Revisions Published in 2020 and 2021.

Munson E, Carroll K J Clin Microbiol. 2022; 61(1):e0028222.

PMID: 36533910 PMC: 9879126. DOI: 10.1128/jcm.00282-22.

References

Boratyn G, Camacho C, Cooper P, Coulouris G, Fong A, Ma N . BLAST: a more efficient report with usability improvements. Nucleic Acids Res. 2013; 41(Web Server issue):W29-33. PMC: 3692093. DOI: 10.1093/nar/gkt282. View

Edwards U, Rogall T, Blocker H, Emde M, Bottger E . Isolation and direct complete nucleotide determination of entire genes. Characterization of a gene coding for 16S ribosomal RNA. Nucleic Acids Res. 1989; 17(19):7843-53. PMC: 334891. DOI: 10.1093/nar/17.19.7843. View

Alcock B, Raphenya A, Lau T, Tsang K, Bouchard M, Edalatmand A . CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Res. 2019; 48(D1):D517-D525. PMC: 7145624. DOI: 10.1093/nar/gkz935. View

Johnson C, Grossman A . Integrative and Conjugative Elements (ICEs): What They Do and How They Work. Annu Rev Genet. 2015; 49:577-601. PMC: 5180612. DOI: 10.1146/annurev-genet-112414-055018. View

Nandi T, Ong C, Singh A, Boddey J, Atkins T, Sarkar-Tyson M . A genomic survey of positive selection in Burkholderia pseudomallei provides insights into the evolution of accidental virulence. PLoS Pathog. 2010; 6(4):e1000845. PMC: 2848565. DOI: 10.1371/journal.ppat.1000845. View

Bortolaia V, Kaas R, Ruppe E, Roberts M, Schwarz S, Cattoir V . ResFinder 4.0 for predictions of phenotypes from genotypes. J Antimicrob Chemother. 2020; 75(12):3491-3500. PMC: 7662176. DOI: 10.1093/jac/dkaa345. View

Xiang G, Lan K, Cai Y, Liao K, Zhao M, Tao J . Clinical Molecular and Genomic Epidemiology of in China. Front Microbiol. 2021; 12:744291. PMC: 8507844. DOI: 10.3389/fmicb.2021.744291. View

Yoon S, Ha S, Lim J, Kwon S, Chun J . A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek. 2017; 110(10):1281-1286. DOI: 10.1007/s10482-017-0844-4. View

Labbate M, Case R, Stokes H . The integron/gene cassette system: an active player in bacterial adaptation. Methods Mol Biol. 2009; 532:103-25. DOI: 10.1007/978-1-60327-853-9_6. View

10.

Grindley N, Reed R . Transpositional recombination in prokaryotes. Annu Rev Biochem. 1985; 54:863-96. DOI: 10.1146/annurev.bi.54.070185.004243. View

11.

Yano H, Miyakoshi M, Ohshima K, Tabata M, Nagata Y, Hattori M . Complete nucleotide sequence of TOL plasmid pDK1 provides evidence for evolutionary history of IncP-7 catabolic plasmids. J Bacteriol. 2010; 192(17):4337-47. PMC: 2937381. DOI: 10.1128/JB.00359-10. View

12.

Varani A, Siguier P, Gourbeyre E, Charneau V, Chandler M . ISsaga is an ensemble of web-based methods for high throughput identification and semi-automatic annotation of insertion sequences in prokaryotic genomes. Genome Biol. 2011; 12(3):R30. PMC: 3129680. DOI: 10.1186/gb-2011-12-3-r30. View

13.

Walsh T, Toleman M, Poirel L, Nordmann P . Metallo-beta-lactamases: the quiet before the storm?. Clin Microbiol Rev. 2005; 18(2):306-25. PMC: 1082798. DOI: 10.1128/CMR.18.2.306-325.2005. View

14.

Zong Z . The complex genetic context of blaPER-1 flanked by miniature inverted-repeat transposable elements in Acinetobacter johnsonii. PLoS One. 2014; 9(2):e90046. PMC: 3934969. DOI: 10.1371/journal.pone.0090046. View

15.

Peix A, Ramirez-Bahena M, Velazquez E . The current status on the taxonomy of Pseudomonas revisited: An update. Infect Genet Evol. 2017; 57:106-116. DOI: 10.1016/j.meegid.2017.10.026. View

16.

Brettin T, Davis J, Disz T, Edwards R, Gerdes S, Olsen G . RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep. 2015; 5:8365. PMC: 4322359. DOI: 10.1038/srep08365. View

17.

Diene S, Rolain J . Carbapenemase genes and genetic platforms in Gram-negative bacilli: Enterobacteriaceae, Pseudomonas and Acinetobacter species. Clin Microbiol Infect. 2014; 20(9):831-8. DOI: 10.1111/1469-0691.12655. View

18.

Brovedan M, Marchiaro P, Diaz M, Faccone D, Corso A, Pasteran F . Pseudomonas putida group species as reservoirs of mobilizable Tn402-like class 1 integrons carrying bla metallo-β-lactamase genes. Infect Genet Evol. 2021; 96:105131. DOI: 10.1016/j.meegid.2021.105131. View

19.

Rowland S, Boocock M, Burke M, Rice P, Stark W . The protein-protein interactions required for assembly of the Tn3 resolution synapse. Mol Microbiol. 2021; 114(6):952-965. DOI: 10.1111/mmi.14579. View

20.

Liu M, Li X, Xie Y, Bi D, Sun J, Li J . ICEberg 2.0: an updated database of bacterial integrative and conjugative elements. Nucleic Acids Res. 2018; 47(D1):D660-D665. PMC: 6323972. DOI: 10.1093/nar/gky1123. View