Whole-genome Sequencing of Antimicrobial-resistant Isolates from a Carcass

Overview

Journal Data Brief

Date 2023 Feb 23

PMID 36819900

Authors

Trung Thanh Nguyen

Hoa Vinh Le

Da Pham Xuan

Trung Nghia Vu

Minh Hong Nguyen

Huyen Thi Thanh Tran

Affiliations

Soon will be listed here.

Abstract

is one of the most common agents of foodborne bacterial illness with poultry being an important reservoir. The indiscriminate use of antimicrobial compounds in poultry farming increasingly leads to antimicrobial-resistant (AMR) which threatens the health of both animals and humans. Antimicrobial-resistant from the poultry can spread to human through the direct contact with infected poultry or fecal contaminated environments. Antimicrobial-resistant especially fluoroquinolone-resistant nontyphoidal is in the list of global health concern stated by the World Health Organization (WHO). Here we report the whole-genome sequencing data and de novo genome assemble of antimicrobial-resistant strains S8 and S9 from the carcass collected in Vietnam. Genomic DNA of were extracted and subjected to whole-genome sequencing using Illumina MiSeq platform. The genome size of antimicrobial-resistant strain S8 is 4,707,459 bp with a GC-content of 52.38%, containing 10 antimicrobial resistant genes. The genome size of antimicrobial-resistant strain S9 is 4,923,944 bp with a GC-content of 52,39%, containing 10 antimicrobial resistance genes. Our data provided the insights on antimicrobial resistant genes of isolates from the carcass, which help to understand the infection mechanism of antimicrobial-resistant in human.

References

Assefa S, Keane T, Otto T, Newbold C, Berriman M . ABACAS: algorithm-based automatic contiguation of assembled sequences. Bioinformatics. 2009; 25(15):1968-9. PMC: 2712343. DOI: 10.1093/bioinformatics/btp347. View

Bolger A, Lohse M, Usadel B . Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014; 30(15):2114-20. PMC: 4103590. DOI: 10.1093/bioinformatics/btu170. View

Vo A, van Duijkeren E, Fluit A, Heck M, Verbruggen A, Maas H . Distribution of Salmonella enterica serovars from humans, livestock and meat in Vietnam and the dominance of Salmonella Typhimurium phage type 90. Vet Microbiol. 2005; 113(1-2):153-8. DOI: 10.1016/j.vetmic.2005.10.034. View

Chen L, Yang J, Yu J, Yao Z, Sun L, Shen Y . VFDB: a reference database for bacterial virulence factors. Nucleic Acids Res. 2004; 33(Database issue):D325-8. PMC: 539962. DOI: 10.1093/nar/gki008. View

Feldgarden M, Brover V, Gonzalez-Escalona N, Frye J, Haendiges J, Haft D . AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence. Sci Rep. 2021; 11(1):12728. PMC: 8208984. DOI: 10.1038/s41598-021-91456-0. View

Yoshida C, Kruczkiewicz P, Laing C, Lingohr E, Gannon V, Nash J . The Salmonella In Silico Typing Resource (SISTR): An Open Web-Accessible Tool for Rapidly Typing and Subtyping Draft Salmonella Genome Assemblies. PLoS One. 2016; 11(1):e0147101. PMC: 4723315. DOI: 10.1371/journal.pone.0147101. View

Ta Y, Nguyen T, To P, Pham D, Le H, Nguyen Thi G . Quantification, serovars, and antibiotic resistance of salmonella isolated from retail raw chicken meat in Vietnam. J Food Prot. 2014; 77(1):57-66. DOI: 10.4315/0362-028X.JFP-13-221. View

Pornsukarom S, Van Vliet A, Thakur S . Whole genome sequencing analysis of multiple Salmonella serovars provides insights into phylogenetic relatedness, antimicrobial resistance, and virulence markers across humans, food animals and agriculture environmental sources. BMC Genomics. 2018; 19(1):801. PMC: 6218967. DOI: 10.1186/s12864-018-5137-4. View

Nghiem M, Nguyen V, Nguyen T, Nguyen T, Vo T . Antimicrobial resistance gene expression associated with multidrug resistant Salmonella spp. isolated from retail meat in Hanoi, Vietnam. Int Microbiol. 2017; 20(2):85-93. DOI: 10.2436/20.1501.01.288. View

10.

Bankevich A, Nurk S, Antipov D, Gurevich A, Dvorkin M, Kulikov A . SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012; 19(5):455-77. PMC: 3342519. DOI: 10.1089/cmb.2012.0021. View

11.

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