Isolation, Identification, Antimicrobial Resistance, Genotyping, and Whole-Genome Sequencing Analysis of Enteritidis Isolated from a Food-Poisoning Incident

Overview

Journal Pol J Microbiol

Specialty Microbiology

Date 2024 Mar 4

PMID 38437471

Authors

Zhuru Hou

Benjin Xu

Ling Liu

Rongrong Yan

Jinjing Zhang

Affiliations

Soon will be listed here.

Abstract

is a common pathogen in humans and animals that causes food poisoning and infection, threatening public health safety. We aimed to investigate the genome structure, drug resistance, virulence characteristics, and genetic relationship of a strain isolated from patients with food poisoning. The pathogen strain 21A was collected from the feces of patients with food poisoning, and its minimum inhibitory concentration against commonly used antibiotics was determined using the strip test and Kirby-Bauer disk methods. Subsequently, WGS analysis was used to reveal the genome structural characteristics and the carrying status of resistance genes and virulence genes of strain 21A. In addition, an MLST-based minimum spanning tree and an SNP-based systematic spanning tree were constructed to investigate its genetic evolutionary characteristics. The strain 21A was identified by mass spectrometry as , which was found to show resistance to ampicillin, piperacillin, sulbactam, levofloxacin, and ciprofloxacin. The WGS and bioinformatics analyses revealed this strain as Enteritidis belonging to ST11, which is common in China, containing various resistance genes and significant virulence characteristics. Strain 21A was closely related to the SJTUF strains, a series strains from animal, food and clinical sources, as well as from Shanghai, China, which were located in the same evolutionary clade. According to the genetic makeup of strain 21A, the change G > A was found to be the most common variation. We have comprehensively analyzed the genomic characteristics, drug resistance phenotype, virulence phenotype, and genetic evolution relationship of . Enteritidis strain 21A, which will contribute towards an in-depth understanding of the pathogenic mechanism of . Enteritidis and the effective prevention and control of foodborne diseases.

Citing Articles

Antimicrobial resistance and genome characteristics of Salmonella enteritidis from Huzhou, China.

Yan W, Xu D, Chen L, Wu X PLoS One. 2024; 19(6):e0304621.

PMID: 38833480 PMC: 11149840. DOI: 10.1371/journal.pone.0304621.

References

Mohammed B . Identification and bioinformatic analysis of invA gene of Salmonella in free range chicken. Braz J Biol. 2022; 84:e263363. DOI: 10.1590/1519-6984.263363. View

Li H, Durbin R . Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009; 25(14):1754-60. PMC: 2705234. DOI: 10.1093/bioinformatics/btp324. View

Johnson R, Fais C, Parmar M, Cheruvara H, Marshall R, Hesketh S . Cryo-EM Structure and Molecular Dynamics Analysis of the Fluoroquinolone Resistant Mutant of the AcrB Transporter from . Microorganisms. 2020; 8(6). PMC: 7355581. DOI: 10.3390/microorganisms8060943. View

Li H, Durbin R . Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics. 2010; 26(5):589-95. PMC: 2828108. DOI: 10.1093/bioinformatics/btp698. View

Cao G, Zhao S, Kuang D, Hsu C, Yin L, Luo Y . Geography shapes the genomics and antimicrobial resistance of Salmonella enterica Serovar Enteritidis isolated from humans. Sci Rep. 2023; 13(1):1331. PMC: 9873609. DOI: 10.1038/s41598-022-24150-4. View

Zwama M, Nishino K . Ever-Adapting RND Efflux Pumps in Gram-Negative Multidrug-Resistant Pathogens: A Race against Time. Antibiotics (Basel). 2021; 10(7). PMC: 8300642. DOI: 10.3390/antibiotics10070774. View

DePristo M, Banks E, Poplin R, Garimella K, Maguire J, Hartl C . A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011; 43(5):491-8. PMC: 3083463. DOI: 10.1038/ng.806. View

Zhou X, Xu L, Xu X, Zhu Y, Suo Y, Shi C . Antimicrobial Resistance and Molecular Characterization of Salmonella enterica Serovar Enteritidis from Retail Chicken Products in Shanghai, China. Foodborne Pathog Dis. 2018; 15(6):346-352. DOI: 10.1089/fpd.2017.2387. View

Soubeiga A, Kpoda D, Compaore M, Somda-Belemlougri A, Kaseko N, Rouamba S . Molecular Characterization and the Antimicrobial Resistance Profile of spp. Isolated from Ready-to-Eat Foods in Ouagadougou, Burkina Faso. Int J Microbiol. 2022; 2022:9640828. PMC: 9668442. DOI: 10.1155/2022/9640828. View

10.

Zhang Y, Liu K, Zhang Z, Tian S, Liu M, Li X . A Severe Gastroenteritis Outbreak of Serovar Enteritidis Linked to Contaminated Egg Fried Rice, China, 2021. Front Microbiol. 2021; 12:779749. PMC: 8645860. DOI: 10.3389/fmicb.2021.779749. View

11.

Fardsanei F, Mehdi Soltan Dallal M, Douraghi M, Memariani H, Bakhshi B, Zahraei Salehi T . Antimicrobial resistance, virulence genes and genetic relatedness of Salmonella enterica serotype Enteritidis isolates recovered from human gastroenteritis in Tehran, Iran. J Glob Antimicrob Resist. 2017; 12:220-226. DOI: 10.1016/j.jgar.2017.10.005. View

12.

Wang L, Li Y, Liu Y, Zuo L, Li Y, Wu S . Salmonella spv locus affects type I interferon response and the chemotaxis of neutrophils via suppressing autophagy. Fish Shellfish Immunol. 2019; 87:721-729. DOI: 10.1016/j.fsi.2019.02.009. View

13.

Zhou X, Li M, Xu L, Shi C, Shi X . Characterization of Antibiotic Resistance Genes, Plasmids, Biofilm Formation, and Invasion Capacity of Enteritidis Isolates from Children with Gastroenteritis. Microb Drug Resist. 2019; 25(8):1191-1198. DOI: 10.1089/mdr.2018.0421. View

14.

Lu X, Zhai P, Liu Z, Deng L, Zhang T, Wu X . Comparison of Antibiotic Resistance Profiles of Isolates from Retail Meats in Nanchang, China, in Two Periods. Foodborne Pathog Dis. 2023; 20(6):237-243. DOI: 10.1089/fpd.2022.0067. View

15.

McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A . The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010; 20(9):1297-303. PMC: 2928508. DOI: 10.1101/gr.107524.110. View

16.

Chen J, Ed-Dra A, Zhou H, Wu B, Zhang Y, Yue M . Antimicrobial resistance and genomic investigation of non-typhoidal isolated from outpatients in Shaoxing city, China. Front Public Health. 2022; 10:988317. PMC: 9513250. DOI: 10.3389/fpubh.2022.988317. View

17.

Jones P, Binns D, Chang H, Fraser M, Li W, McAnulla C . InterProScan 5: genome-scale protein function classification. Bioinformatics. 2014; 30(9):1236-40. PMC: 3998142. DOI: 10.1093/bioinformatics/btu031. View

18.

Galperin M, Makarova K, Wolf Y, Koonin E . Expanded microbial genome coverage and improved protein family annotation in the COG database. Nucleic Acids Res. 2014; 43(Database issue):D261-9. PMC: 4383993. DOI: 10.1093/nar/gku1223. View

19.

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

20.

Wang X, Wang H, Li T, Liu F, Cheng Y, Guo X . Characterization of Salmonella spp. isolated from chickens in Central China. BMC Vet Res. 2020; 16(1):299. PMC: 7441611. DOI: 10.1186/s12917-020-02513-1. View