Genomic surveillance of Salmonella spp. in the Philippines during 2013-2014

Marietta L Lagrada; Silvia Argimón; Janice B Borlasa; Jaywardeen P Abad; June M Gayeta; Melissa L Masim; Agnettah M Olorosa; Victoria Cohen; Benjamin Jeffrey; Khalil Abudahab; Sonia B Sia; Charmian M Hufano; John Stelling; Matthew T G Holden; David M Aanensen; Celia C Carlos

doi:10.1101/2022.02.14.480363

Genomic surveillance of Salmonella spp. in the Philippines during 2013-2014

Marietta L Lagrada^*, Silvia Argimón, Janice B Borlasa, Jaywardeen P Abad, June M Gayeta, Melissa L Masim, Agnettah M Olorosa, Victoria Cohen, Benjamin Jeffrey, Khalil Abudahab, Sonia B Sia, Charmian M Hufano, John Stelling, Matthew T G Holden, David M Aanensen, Celia C Carlos

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

Abstract

BACKGROUND: Increasing antimicrobial resistance (AMR) in Salmonella has been observed in the Philippines. We aimed to characterise the population and AMR mechanisms of Salmonella with whole genome sequencing (WGS) and compare it with laboratory surveillance methods.

METHODS: The serotype, multilocus sequence type, AMR genes and relatedness between isolates were determined from the genomes of 148 Salmonella Typhi (S. Typhi) and 65 non-typhoidal Salmonella (NTS) collected by the Antimicrobial Resistance Surveillance Program during 2013-2014. Genotypic serotypes and AMR prediction were compared with phenotypic data.

RESULTS: AMR rates in S. Typhi were low, with sparse acquisition of mutations associated with reduced susceptibility to fluoroquinolones or extended-spectrum beta-lactamases (ESBL) genes. By contrast, 75% of NTS isolates were insusceptible to at least one antimicrobial, with more than half carrying mutations and/or genes linked to fluoroquinolone resistance. ESBL genes were detected in five genomes, which also carried other AMR determinants. The population of S. Typhi was dominated by likely endemic genotype 3.0, which caused a putative local outbreak. The main NTS clades were global epidemic S. Enteritidis ST11 and S. Typhimurium monophasic variant (I,4,[5],12: i: -) ST34.

CONCLUSION: We provide the first genomic characterisation of Salmonella from the Philippines and evidence of WGS utility for ongoing surveillance.

Original language	English
Article number	trac080
Pages (from-to)	1202-1213
Number of pages	12
Journal	Transactions of the Royal Society of Tropical Medicine and Hygiene
Volume	116
Issue number	12
Early online date	23 Aug 2022
DOIs	https://doi.org/10.1101/2022.02.14.480363 https://doi.org/10.1093/trstmh/trac080
Publication status	Published - 1 Dec 2022

Keywords

Antimicrobial drug resistance
Epidemiology/surveillance
Genomics
Salmonella
Typhoid fever
Whole genome sequencing

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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© The Author(s) 2022. Published by Oxford University Press on behalf of Royal Society of Tropical Medicine and Hygiene. This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/ by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited.
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Cite this

Lagrada, M. L., Argimón, S., Borlasa, J. B., Abad, J. P., Gayeta, J. M., Masim, M. L., Olorosa, A. M., Cohen, V., Jeffrey, B., Abudahab, K., Sia, S. B., Hufano, C. M., Stelling, J., Holden, M. T. G., Aanensen, D. M., & Carlos, C. C. (2022). Genomic surveillance of Salmonella spp. in the Philippines during 2013-2014. Transactions of the Royal Society of Tropical Medicine and Hygiene, 116(12), 1202-1213. Article trac080. https://doi.org/10.1101/2022.02.14.480363, https://doi.org/10.1093/trstmh/trac080

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title = "Genomic surveillance of Salmonella spp. in the Philippines during 2013-2014",

abstract = "BACKGROUND: Increasing antimicrobial resistance (AMR) in Salmonella has been observed in the Philippines. We aimed to characterise the population and AMR mechanisms of Salmonella with whole genome sequencing (WGS) and compare it with laboratory surveillance methods.METHODS: The serotype, multilocus sequence type, AMR genes and relatedness between isolates were determined from the genomes of 148 Salmonella Typhi (S. Typhi) and 65 non-typhoidal Salmonella (NTS) collected by the Antimicrobial Resistance Surveillance Program during 2013-2014. Genotypic serotypes and AMR prediction were compared with phenotypic data.RESULTS: AMR rates in S. Typhi were low, with sparse acquisition of mutations associated with reduced susceptibility to fluoroquinolones or extended-spectrum beta-lactamases (ESBL) genes. By contrast, 75% of NTS isolates were insusceptible to at least one antimicrobial, with more than half carrying mutations and/or genes linked to fluoroquinolone resistance. ESBL genes were detected in five genomes, which also carried other AMR determinants. The population of S. Typhi was dominated by likely endemic genotype 3.0, which caused a putative local outbreak. The main NTS clades were global epidemic S. Enteritidis ST11 and S. Typhimurium monophasic variant (I,4,[5],12: i: -) ST34.CONCLUSION: We provide the first genomic characterisation of Salmonella from the Philippines and evidence of WGS utility for ongoing surveillance.",

keywords = "Antimicrobial drug resistance, Epidemiology/surveillance, Genomics, Salmonella, Typhoid fever, Whole genome sequencing",

author = "Lagrada, {Marietta L} and Silvia Argim{\'o}n and Borlasa, {Janice B} and Abad, {Jaywardeen P} and Gayeta, {June M} and Masim, {Melissa L} and Olorosa, {Agnettah M} and Victoria Cohen and Benjamin Jeffrey and Khalil Abudahab and Sia, {Sonia B} and Hufano, {Charmian M} and John Stelling and Holden, {Matthew T G} and Aanensen, {David M} and Carlos, {Celia C}",

note = "Funding: This work was supported by a Newton Fund award from the Medical Research Council (UK) MR/N019296/1 and the Philippine Council for Health Research and Development. This work was also partially supported by research grant U01CA207167 from the U.S. National Institutes of Health. SA and DMA were additionally supported by the National Institute for Health Research (UK) Global Health Research Unit on genomic Surveillance of AMR [16_136_111] and by the Centre for Genomic Pathogen Surveillance.",

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doi = "10.1101/2022.02.14.480363",

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Lagrada, ML, Argimón, S, Borlasa, JB, Abad, JP, Gayeta, JM, Masim, ML, Olorosa, AM, Cohen, V, Jeffrey, B, Abudahab, K, Sia, SB, Hufano, CM, Stelling, J, Holden, MTG, Aanensen, DM & Carlos, CC 2022, 'Genomic surveillance of Salmonella spp. in the Philippines during 2013-2014', Transactions of the Royal Society of Tropical Medicine and Hygiene, vol. 116, no. 12, trac080, pp. 1202-1213. https://doi.org/10.1101/2022.02.14.480363, https://doi.org/10.1093/trstmh/trac080

TY - JOUR

T1 - Genomic surveillance of Salmonella spp. in the Philippines during 2013-2014

AU - Lagrada, Marietta L

AU - Argimón, Silvia

AU - Borlasa, Janice B

AU - Abad, Jaywardeen P

AU - Gayeta, June M

AU - Masim, Melissa L

AU - Olorosa, Agnettah M

AU - Cohen, Victoria

AU - Jeffrey, Benjamin

AU - Abudahab, Khalil

AU - Sia, Sonia B

AU - Hufano, Charmian M

AU - Stelling, John

AU - Holden, Matthew T G

AU - Aanensen, David M

AU - Carlos, Celia C

N1 - Funding: This work was supported by a Newton Fund award from the Medical Research Council (UK) MR/N019296/1 and the Philippine Council for Health Research and Development. This work was also partially supported by research grant U01CA207167 from the U.S. National Institutes of Health. SA and DMA were additionally supported by the National Institute for Health Research (UK) Global Health Research Unit on genomic Surveillance of AMR [16_136_111] and by the Centre for Genomic Pathogen Surveillance.

PY - 2022/12/1

Y1 - 2022/12/1

N2 - BACKGROUND: Increasing antimicrobial resistance (AMR) in Salmonella has been observed in the Philippines. We aimed to characterise the population and AMR mechanisms of Salmonella with whole genome sequencing (WGS) and compare it with laboratory surveillance methods.METHODS: The serotype, multilocus sequence type, AMR genes and relatedness between isolates were determined from the genomes of 148 Salmonella Typhi (S. Typhi) and 65 non-typhoidal Salmonella (NTS) collected by the Antimicrobial Resistance Surveillance Program during 2013-2014. Genotypic serotypes and AMR prediction were compared with phenotypic data.RESULTS: AMR rates in S. Typhi were low, with sparse acquisition of mutations associated with reduced susceptibility to fluoroquinolones or extended-spectrum beta-lactamases (ESBL) genes. By contrast, 75% of NTS isolates were insusceptible to at least one antimicrobial, with more than half carrying mutations and/or genes linked to fluoroquinolone resistance. ESBL genes were detected in five genomes, which also carried other AMR determinants. The population of S. Typhi was dominated by likely endemic genotype 3.0, which caused a putative local outbreak. The main NTS clades were global epidemic S. Enteritidis ST11 and S. Typhimurium monophasic variant (I,4,[5],12: i: -) ST34.CONCLUSION: We provide the first genomic characterisation of Salmonella from the Philippines and evidence of WGS utility for ongoing surveillance.

AB - BACKGROUND: Increasing antimicrobial resistance (AMR) in Salmonella has been observed in the Philippines. We aimed to characterise the population and AMR mechanisms of Salmonella with whole genome sequencing (WGS) and compare it with laboratory surveillance methods.METHODS: The serotype, multilocus sequence type, AMR genes and relatedness between isolates were determined from the genomes of 148 Salmonella Typhi (S. Typhi) and 65 non-typhoidal Salmonella (NTS) collected by the Antimicrobial Resistance Surveillance Program during 2013-2014. Genotypic serotypes and AMR prediction were compared with phenotypic data.RESULTS: AMR rates in S. Typhi were low, with sparse acquisition of mutations associated with reduced susceptibility to fluoroquinolones or extended-spectrum beta-lactamases (ESBL) genes. By contrast, 75% of NTS isolates were insusceptible to at least one antimicrobial, with more than half carrying mutations and/or genes linked to fluoroquinolone resistance. ESBL genes were detected in five genomes, which also carried other AMR determinants. The population of S. Typhi was dominated by likely endemic genotype 3.0, which caused a putative local outbreak. The main NTS clades were global epidemic S. Enteritidis ST11 and S. Typhimurium monophasic variant (I,4,[5],12: i: -) ST34.CONCLUSION: We provide the first genomic characterisation of Salmonella from the Philippines and evidence of WGS utility for ongoing surveillance.

KW - Antimicrobial drug resistance

KW - Epidemiology/surveillance

KW - Genomics

KW - Salmonella

KW - Typhoid fever

KW - Whole genome sequencing

U2 - 10.1101/2022.02.14.480363

DO - 10.1101/2022.02.14.480363

M3 - Article

C2 - 35999186

SN - 0035-9203

VL - 116

SP - 1202

EP - 1213

JO - Transactions of the Royal Society of Tropical Medicine and Hygiene

JF - Transactions of the Royal Society of Tropical Medicine and Hygiene

IS - 12

M1 - trac080

ER -

Genomic surveillance of Salmonella spp. in the Philippines during 2013-2014

Abstract

Keywords

UN SDGs

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