Genomic surveillance of Salmonella spp. in the Philippines during 2013-2014.
antimicrobial drug resistance
epidemiology/surveillance
genomics
salmonella
typhoid fever
whole genome sequencing
Journal
Transactions of the Royal Society of Tropical Medicine and Hygiene
ISSN: 1878-3503
Titre abrégé: Trans R Soc Trop Med Hyg
Pays: England
ID NLM: 7506129
Informations de publication
Date de publication:
02 12 2022
02 12 2022
Historique:
received:
04
04
2022
revised:
08
07
2022
accepted:
04
08
2022
pubmed:
24
8
2022
medline:
7
12
2022
entrez:
23
8
2022
Statut:
ppublish
Résumé
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. 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. 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. We provide the first genomic characterisation of Salmonella from the Philippines and evidence of WGS utility for ongoing surveillance.
Sections du résumé
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.
Identifiants
pubmed: 35999186
pii: 6674273
doi: 10.1093/trstmh/trac080
pmc: PMC9717386
doi:
Substances chimiques
Fluoroquinolones
0
Anti-Bacterial Agents
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
1202-1213Subventions
Organisme : Department of Health
Pays : United Kingdom
Organisme : Medical Research Council
ID : MR/N019296/1
Pays : United Kingdom
Organisme : NCI NIH HHS
ID : U01 CA207167
Pays : United States
Informations de copyright
© The Author(s) 2022. Published by Oxford University Press on behalf of Royal Society of Tropical Medicine and Hygiene.
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