Core genome sequence analysis to characterize Salmonella enterica serovar Rissen ST469 from a swine production chain

Teerarat Prasertsee, Phongsakorn Chuammitri, Manu Deeudom, Nipa Chokesajjawatee, Pannita Santiyanont, Pakpoom Tadee, Aniroot Nuangmek, Phacharaporn Tadee, Samuel K. Sheppard, Ben Pascoe, Prapas Patchanee

Research output: Contribution to journalArticle

Abstract

Salmonella enterica subsp. enterica serotype Rissen is the predominant serotype found in Thai pork production and can be transmitted to humans through contamination of the food chain. This study was conducted to investigate the genetic relationships between serovar Rissen isolates from all levels of the pork production chain and evaluate the ability of the in silico antimicrobial resistance (AMR) genotypes to predict the phenotype of serovar Rissen. A total of 38 serovar Rissen isolates were tested against eight antibiotic agents by a disk diffusion method and the whole genomes of all isolates were sequenced to detect AMR genetic elements using the ResFinder database.A total of 86.84% of the isolates were resistant to tetracycline, followed by ampicillin (78.96%) and sulfonamide-trimethoprim (71.05%). Resistance to more than one antimicrobial agent was observed in 78.95% of the isolates, with the most common pattern showing resistance to ampicillin, chloramphenicol, streptomycin, sulfonamide-trimethoprim, and tetracycline. The results of genotypic AMR indicated that 89.47% of the isolates carried tet(A), 84.22% carried blaTEM-1B, 78.95% carried sul3, and 78.95% carried dfrA12. The genotypic prediction of phenotypic resistance resulted in a mean sensitivity of 97.45% and specificity of 75.48%. Analysis by core genome multilocus sequence typing (cgMLST) demonstrated that the Salmonella isolates from various sources and different locations shared many of the same core genome loci. This implies that serovar Rissen has infected every stage of the pork production process and that contamination can occur in every part of the production chain.
Original languageEnglish
Pages (from-to)68-74
Number of pages7
JournalInternational Journal of Food Microbiology
Volume304
Early online date28 May 2019
DOIs
Publication statusPublished - 2 Sep 2019

Keywords

  • Antimicrobial resistance
  • Core genome MLST
  • Pig production
  • Salmonella serovar Rissen
  • Whole genome sequencing

ASJC Scopus subject areas

  • Food Science
  • Microbiology

Cite this

Core genome sequence analysis to characterize Salmonella enterica serovar Rissen ST469 from a swine production chain. / Prasertsee, Teerarat; Chuammitri, Phongsakorn; Deeudom, Manu; Chokesajjawatee, Nipa; Santiyanont, Pannita; Tadee, Pakpoom; Nuangmek, Aniroot; Tadee, Phacharaporn; Sheppard, Samuel K.; Pascoe, Ben; Patchanee, Prapas.

In: International Journal of Food Microbiology, Vol. 304, 02.09.2019, p. 68-74.

Research output: Contribution to journalArticle

Prasertsee, T, Chuammitri, P, Deeudom, M, Chokesajjawatee, N, Santiyanont, P, Tadee, P, Nuangmek, A, Tadee, P, Sheppard, SK, Pascoe, B & Patchanee, P 2019, 'Core genome sequence analysis to characterize Salmonella enterica serovar Rissen ST469 from a swine production chain', International Journal of Food Microbiology, vol. 304, pp. 68-74. https://doi.org/10.1016/j.ijfoodmicro.2019.05.022
Prasertsee, Teerarat ; Chuammitri, Phongsakorn ; Deeudom, Manu ; Chokesajjawatee, Nipa ; Santiyanont, Pannita ; Tadee, Pakpoom ; Nuangmek, Aniroot ; Tadee, Phacharaporn ; Sheppard, Samuel K. ; Pascoe, Ben ; Patchanee, Prapas. / Core genome sequence analysis to characterize Salmonella enterica serovar Rissen ST469 from a swine production chain. In: International Journal of Food Microbiology. 2019 ; Vol. 304. pp. 68-74.
@article{37452e04634c4fe3b3d7e2d6fb55f02e,
title = "Core genome sequence analysis to characterize Salmonella enterica serovar Rissen ST469 from a swine production chain",
abstract = "Salmonella enterica subsp. enterica serotype Rissen is the predominant serotype found in Thai pork production and can be transmitted to humans through contamination of the food chain. This study was conducted to investigate the genetic relationships between serovar Rissen isolates from all levels of the pork production chain and evaluate the ability of the in silico antimicrobial resistance (AMR) genotypes to predict the phenotype of serovar Rissen. A total of 38 serovar Rissen isolates were tested against eight antibiotic agents by a disk diffusion method and the whole genomes of all isolates were sequenced to detect AMR genetic elements using the ResFinder database.A total of 86.84{\%} of the isolates were resistant to tetracycline, followed by ampicillin (78.96{\%}) and sulfonamide-trimethoprim (71.05{\%}). Resistance to more than one antimicrobial agent was observed in 78.95{\%} of the isolates, with the most common pattern showing resistance to ampicillin, chloramphenicol, streptomycin, sulfonamide-trimethoprim, and tetracycline. The results of genotypic AMR indicated that 89.47{\%} of the isolates carried tet(A), 84.22{\%} carried blaTEM-1B, 78.95{\%} carried sul3, and 78.95{\%} carried dfrA12. The genotypic prediction of phenotypic resistance resulted in a mean sensitivity of 97.45{\%} and specificity of 75.48{\%}. Analysis by core genome multilocus sequence typing (cgMLST) demonstrated that the Salmonella isolates from various sources and different locations shared many of the same core genome loci. This implies that serovar Rissen has infected every stage of the pork production process and that contamination can occur in every part of the production chain.",
keywords = "Antimicrobial resistance, Core genome MLST, Pig production, Salmonella serovar Rissen, Whole genome sequencing",
author = "Teerarat Prasertsee and Phongsakorn Chuammitri and Manu Deeudom and Nipa Chokesajjawatee and Pannita Santiyanont and Pakpoom Tadee and Aniroot Nuangmek and Phacharaporn Tadee and Sheppard, {Samuel K.} and Ben Pascoe and Prapas Patchanee",
year = "2019",
month = "9",
day = "2",
doi = "10.1016/j.ijfoodmicro.2019.05.022",
language = "English",
volume = "304",
pages = "68--74",
journal = "International Journal of Food Microbiology",
issn = "0168-1605",
publisher = "Elsevier",

}

TY - JOUR

T1 - Core genome sequence analysis to characterize Salmonella enterica serovar Rissen ST469 from a swine production chain

AU - Prasertsee, Teerarat

AU - Chuammitri, Phongsakorn

AU - Deeudom, Manu

AU - Chokesajjawatee, Nipa

AU - Santiyanont, Pannita

AU - Tadee, Pakpoom

AU - Nuangmek, Aniroot

AU - Tadee, Phacharaporn

AU - Sheppard, Samuel K.

AU - Pascoe, Ben

AU - Patchanee, Prapas

PY - 2019/9/2

Y1 - 2019/9/2

N2 - Salmonella enterica subsp. enterica serotype Rissen is the predominant serotype found in Thai pork production and can be transmitted to humans through contamination of the food chain. This study was conducted to investigate the genetic relationships between serovar Rissen isolates from all levels of the pork production chain and evaluate the ability of the in silico antimicrobial resistance (AMR) genotypes to predict the phenotype of serovar Rissen. A total of 38 serovar Rissen isolates were tested against eight antibiotic agents by a disk diffusion method and the whole genomes of all isolates were sequenced to detect AMR genetic elements using the ResFinder database.A total of 86.84% of the isolates were resistant to tetracycline, followed by ampicillin (78.96%) and sulfonamide-trimethoprim (71.05%). Resistance to more than one antimicrobial agent was observed in 78.95% of the isolates, with the most common pattern showing resistance to ampicillin, chloramphenicol, streptomycin, sulfonamide-trimethoprim, and tetracycline. The results of genotypic AMR indicated that 89.47% of the isolates carried tet(A), 84.22% carried blaTEM-1B, 78.95% carried sul3, and 78.95% carried dfrA12. The genotypic prediction of phenotypic resistance resulted in a mean sensitivity of 97.45% and specificity of 75.48%. Analysis by core genome multilocus sequence typing (cgMLST) demonstrated that the Salmonella isolates from various sources and different locations shared many of the same core genome loci. This implies that serovar Rissen has infected every stage of the pork production process and that contamination can occur in every part of the production chain.

AB - Salmonella enterica subsp. enterica serotype Rissen is the predominant serotype found in Thai pork production and can be transmitted to humans through contamination of the food chain. This study was conducted to investigate the genetic relationships between serovar Rissen isolates from all levels of the pork production chain and evaluate the ability of the in silico antimicrobial resistance (AMR) genotypes to predict the phenotype of serovar Rissen. A total of 38 serovar Rissen isolates were tested against eight antibiotic agents by a disk diffusion method and the whole genomes of all isolates were sequenced to detect AMR genetic elements using the ResFinder database.A total of 86.84% of the isolates were resistant to tetracycline, followed by ampicillin (78.96%) and sulfonamide-trimethoprim (71.05%). Resistance to more than one antimicrobial agent was observed in 78.95% of the isolates, with the most common pattern showing resistance to ampicillin, chloramphenicol, streptomycin, sulfonamide-trimethoprim, and tetracycline. The results of genotypic AMR indicated that 89.47% of the isolates carried tet(A), 84.22% carried blaTEM-1B, 78.95% carried sul3, and 78.95% carried dfrA12. The genotypic prediction of phenotypic resistance resulted in a mean sensitivity of 97.45% and specificity of 75.48%. Analysis by core genome multilocus sequence typing (cgMLST) demonstrated that the Salmonella isolates from various sources and different locations shared many of the same core genome loci. This implies that serovar Rissen has infected every stage of the pork production process and that contamination can occur in every part of the production chain.

KW - Antimicrobial resistance

KW - Core genome MLST

KW - Pig production

KW - Salmonella serovar Rissen

KW - Whole genome sequencing

UR - http://www.scopus.com/inward/record.url?scp=85066465939&partnerID=8YFLogxK

U2 - 10.1016/j.ijfoodmicro.2019.05.022

DO - 10.1016/j.ijfoodmicro.2019.05.022

M3 - Article

VL - 304

SP - 68

EP - 74

JO - International Journal of Food Microbiology

JF - International Journal of Food Microbiology

SN - 0168-1605

ER -