Operational challenges of the Philippine Antimicrobial Resistance Surveillance Program during the COVID-19 pandemic.

Problem: Operation of the Philippine Antimicrobial Resistance Surveillance Program (ARSP) has been affected by the coronavirus disease 2019 (COVID-19) pandemic, during which time difficulties in maintaining laboratory functions, staffing levels and participation were reported. Context: The COVID-19 pandemic has increased pressure on most health systems and programmes in the Philippines, including ARSP. As ARSP is the source of national data on antimicrobial resistance (AMR) trends, there are concerns that the negative effects of the pandemic may have impacted the quality of data produced. Action: We describe disruptions to laboratory operations, personnel availability and participation in ARSP surveillance, and their impact on reported data for 2020. Outcome: Surveillance operations were challenged by reallocation of human, infrastructure and financial resources for pandemic response among both the sentinel sites and the coordinating laboratory, the Antimicrobial Resistance Surveillance Reference Laboratory. There was a decrease in the amount of data submitted to the surveillance system, as well as in the number of isolates sent to the reference laboratory for confirmation of bacterial identification and antimicrobial susceptibility testing. Nevertheless, overall performance scores of the sentinel sites for most parameters were comparable to 2019, the year before the pandemic. Discussion: The impact of operational changes to ARSP due to the pandemic needs to be considered when analysing AMR surveillance data from 2020. Automation of data submission, good working relationships between the coordinating laboratory and sentinel sites, and supply chain system strengthening were identified as key to maintaining AMR surveillance during the COVID-19 pandemic.

Genomic surveillance of Neisseria gonorrhoeae in the Philippines, 2013-2014.

Antimicrobial-resistant Neisseria gonorrhoeae is a major threat to public health and is of particular concern in the Western Pacific Region, where the incidence of gonorrhoea is high. The Antimicrobial Resistance Surveillance Program (ARSP) has been capturing information on resistant gonorrhoea since 1996, but genomic epidemiology studies on this pathogen are lacking in the Philippines. We sequenced the whole genomes of 21 N. gonorrhoeae isolates collected in 2013-2014 by ARSP. The multilocus sequence type, multiantigen sequence type, presence of determinants of antimicrobial resistance and relatedness among the isolates were all derived from the sequence data. The concordance between phenotypic and genotypic resistance was also determined. Ten of 21 isolates were resistant to penicillin, ciprofloxacin and tetracycline, due mainly to the presence of the blaTEM gene, the S91F mutation in the gyrA gene and the tetM gene, respectively. None of the isolates was resistant to ceftriaxone or cefixime. The concordance between phenotypic and genotypic resistance was 92.38% overall for five antibiotics in four classes. Despite the small number of isolates studied, they were genetically diverse, as shown by the sequence types, the N. gonorrhoeae multiantigen sequence typing types and the tree. Comparison with global genomes placed the Philippine genomes within global lineage A and led to the identification of an international transmission route. This first genomic survey of N. gonorrhoeae isolates collected by ARSP will be used to contextualize prospective surveillance. It highlights the importance of genomic surveillance in the Western Pacific and other endemic regions for understanding the spread of drug-resistant gonorrhoea worldwide.

Integrating whole-genome sequencing within the National Antimicrobial Resistance Surveillance Program in the Philippines.

National networks of laboratory-based surveillance of antimicrobial resistance (AMR) monitor resistance trends and disseminate these data to AMR stakeholders. Whole-genome sequencing (WGS) can support surveillance by pinpointing resistance mechanisms and uncovering transmission patterns. However, genomic surveillance is rare in low- and middle-income countries. Here, we implement WGS within the established Antimicrobial Resistance Surveillance Program of the Philippines via a binational collaboration. In parallel, we characterize bacterial populations of key bug-drug combinations via a retrospective sequencing survey. By linking the resistance phenotypes to genomic data, we reveal the interplay of genetic lineages (strains), AMR mechanisms, and AMR vehicles underlying the expansion of specific resistance phenotypes that coincide with the growing carbapenem resistance rates observed since 2010. Our results enhance our understanding of the drivers of carbapenem resistance in the Philippines, while also serving as the genetic background to contextualize ongoing local prospective surveillance.