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 journalArticlepeer-review

1 Citation (Scopus)


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 languageEnglish
Article numbertrac080
Pages (from-to)1202-1213
Number of pages12
JournalTransactions of the Royal Society of Tropical Medicine and Hygiene
Issue number12
Early online date23 Aug 2022
Publication statusPublished - 1 Dec 2022


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


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