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

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.

Serotype distribution and antimicrobial resistance of Streptococcus pneumoniae in the Philippines, 2012-2018.

OBJECTIVE: Data are scarce on the prevailing Streptococcus pneumoniae serotypes in the Philippines, including the relative antimicrobial resistance (AMR) of these bacteria. This study is designed to fill that gap by describing the serotype distribution and AMR of S. pneumoniae in the Philippines from 2012 to 2018. METHODS: S. pneumoniae isolates from clinical specimens were collected through the Philippine Department of Health Antimicrobial Resistance Surveillance Program from 1 January 2012 to 31 December 2018. Identification and antimicrobial susceptibility testing (AST) were performed using conventional and automated methods (Vitek2 Compact Automated Machine). AST for penicillin, erythromycin, co-trimoxazole, ceftriaxone and levofloxacin was done following the Clinical and Laboratory Standard Institute recommendations. Serotyping was done through slide agglutination following the Denka Seiken slide agglutination method. RESULTS: From a total of 307 isolates of S. pneumoniae, 32 serotypes were identified; the most frequently occurring were serotypes 1, 3, 5, 4, 18, 19A, 6B, 15 and 14. Many (n = 113, 36.53%) of the isolates were from those aged £5 years. Pneumococcal conjugate vaccine (PCV) coverage was as follows: PCV7 (32.69%), PCV10 (54.16%) and PCV13 (69.23%). The overall AMR of invasive S. pneumoniae isolates was low. Penicillin-resistant serotypes were 14, 19, 24, 4, 5, 1, 15, 6 and 32. DISCUSSION: With the inclusion of PCV13 in the National Immunization Program, continued monitoring of the prevailing serotypes of S. pneumoniae isolates in the Philippines is needed to guide disease and AMR control measures.