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.

Figure 1.

Genomic surveillance of NTS from the Philippines, 2013–2014. (A) Phylogenetic tree of 65 isolates inferred from an alignment of 117 371 core genome SNP sites. (B) Subtree of 21 S. Enteritidis isolates. The tree leaves are coloured by sentinel site as indicated in (C). The trees are annotated with bootstrap values and the tree blocks indicate the distribution of the serological serotype, genoserotype, sequence types (STs), resistance phenotype for five antibiotics and acquired resistance genes and mutations. AMP: ampicillin; CRO: ceftriaxone; CHL: chloramphenicol; CIP: ciprofloxacin; SXT: sulphamethoxazole-trimetoprim. Origin of isolates. BGH: Baguio General Hospital and Medical Center; CMC: Cotabato Regional Hospital and Medical Center; CVM: Cagayan Valley Medical Center; DMC: Southern Philippines Medical Center; EVR: Eastern Visayas Regional Medical Center; FEU: Far Eastern University Hospital; JLM: Jose B. Lingad Memorial Regional Hospital; MAR: Mariano Marcos Memorial Hospital and Medical Center; NMC: Northern Mindanao Medical Center; RMC: Rizal Medical Center; SLH: San Lazaro Hospital; STU: University of Sto. Tomas Hospital; VSM: Vicente Sotto Memorial Medical Center; ZMC: Zamboanga City Medical Center. The full data are available at https://microreact.org/project/k2BC6hsaxYr1Eo5U9v71iJ-arspnts2013-2014.

Figure 2.

Genomic surveillance of S. Typhi from the Philippines, 2013–2014. (A) Phylogenetic tree of 148 isolates inferred from an alignment of 2094 SNP sites obtained after mapping the genome sequences to the complete genome of reference strain CT18 and masking regions of mobile genetic elements and recombination. The tree leaves are coloured by sentinel site and indicated on the map. BGH: Baguio General Hospital and Medical Center; BRT: Bicol Regional Training & Teaching Hospital; CMC: Cotabato Regional Hospital and Medical Center; CVM: Cagayan Valley Medical Center; DMC: Southern Philippines Medical Center; EVR: Eastern Visayas Regional Medical Center; FEU: Far Eastern University Hospital; GMH: Governor Celestino Gallares Memorial Hospital; MAR: Mariano Marcos Memorial Hospital and Medical Center; MMH: Corazon Locsin Montelibano Memorial Regional Hospital; NMC: Northern Mindanao Medical Center; STU: University of Sto. Tomas Hospital; VSM: Vicente Sotto Memorial Medical Center; ZMC: Zamboanga City Medical Center. The tree is annotated with subclades within genotype 3.0 (3.0.I and 3.0.II), a putative outbreak cluster (CMC) and bootstrap values on major branches. The tree blocks indicate the distribution of the sequence types (STs), genotype, resistance phenotype for six antibiotics and acquired resistance genes and mutations. AMP: ampicillin; CRO: ceftriaxone; CTX: cefixime; CHL: chloramphenicol; CIP: ciprofloxacin; SXT: sulphamethoxazole-trimetoprim. The data are available at https://microreact.org/project/kRW7Z2TLg3FEM7rmq8sZ1e. (B) Boxplot showing the distribution of the SNP differences between pairs of genomes from genotype 3.0 belonging both to subclade 3.0.I (red), both to subclade 3.0.II (green) or one to each subclade (blue). The horizontal line indicates the median and the box indicates the interquartile range.

Figure 3.

S. Typhi from the Philippines in global context. Phylogenetic trees of genomes belonging to genotypes 3.0, 3.2.1 and 4.1 from the Philippines and 19 other countries or regions, generated with Pathogenwatch. Genomes from countries sparsely represented but belonging to the same continent/region were grouped to simplify the tree annotation. The trees are also annotated with the distribution of resistance determinants identified by Pathogenwatch. The data are available at https://microreact.org/project/rym1Shfy7, https://microreact.org/project/i5GByUGqNuLR9sGdDRH5hA-global-sat-321 and https://microreact.org/project/pDqxJCq7YzYy6ibxEZ2Rgk-global-sat-41.