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

Genomic characterization of antimicrobial-resistant Salmonella enterica in chicken meat from wet markets in Metro Manila, Philippines

The emergence of multidrug-resistant (MDR) Salmonella is recognized as a significant public health problem worldwide. This study investigated the occurrence of MDR Salmonella serovars in chicken meat from wet markets in Metro Manila, Philippines from February to July 2022. Using whole genome sequencing (WGS) and phenotypic antimicrobial resistance (AMR) testing, the serovar, drug resistance, and virulence profiles of Salmonella isolates were characterized. Out of 253 chicken cut samples, 95 S. enterica isolates representing 15 distinct serovars were recovered. The most common was S. enterica serovar Infantis (51.58%), followed by S. Brancaster (9.47%), S. Anatum (7.37%), S. London (7.37%), S. Uganda (6.32%), and S. Derby (4.21%). Phenotypic AMR testing revealed that 73.68% of the isolates were resistant to at least one drug class, and 45.26% were MDR. A wide array of antimicrobial resistance genes (ARGs) associated with resistance to 12 different drug classes was identified, including three β-lactamase gene variants: bla CTX-M-65, bla TEM-1, and bla TEM-176. Some of these ARGs were located on MDR plasmids, such as those on IncFIB(K)_1_Kpn3, IncFIA(HI1)_1_HI1, and IncX1_1. A total of 131 virulence genes were detected, some of which conferred pESI-like characteristics to S. Infantis. These findings highlight a potential public health risk posed by pathogenic MDR Salmonella in chicken meat and underscore the urgent need for further research and coordinated AMR surveillance in the Philippines, aiming to stimulate national efforts to combat AMR.

Genomic analysis of Salmonella enterica from Metropolitan Manila abattoirs and markets reveals insights into circulating virulence and antimicrobial resistance genotypes

The integration of next-generation sequencing into the identification and characterization of resistant and virulent strains as well as the routine surveillance of foodborne pathogens such as Salmonella enterica have not yet been accomplished in the Philippines. This study investigated the antimicrobial profiles, virulence, and susceptibility of the 105 S. enterica isolates from swine and chicken samples obtained from slaughterhouses and public wet markets in Metropolitan Manila using whole-genome sequence analysis. Four predominant serovars were identified in genotypic serotyping, namely, Infantis (26.7%), Anatum (19.1%), Rissen (18.1%), and London (13.3%). Phenotypic antimicrobial resistance (AMR) profiling revealed that 65% of the isolates were resistant to at least one antibiotic, 37% were multidrug resistant (MDR), and 57% were extended-spectrum β-lactamase producers. Bioinformatic analysis revealed that isolates had resistance genes and plasmids belonging to the Col and Inc plasmid families that confer resistance against tetracycline (64%), sulfonamide (56%), and streptomycin (56%). Further analyses revealed the presence of 155 virulence genes, 42 of which were serovar-specific. The virulence genes primarily code for host immune system modulators, iron acquisition enzyme complexes, host cell invasion proteins, as well as proteins that allow intracellular and intramacrophage survival. This study showed that virulent MDR S. enterica and several phenotypic and genotypic AMR patterns were present in the food chain. It serves as a foundation to understand the current AMR status in the Philippines food chain and to prompt the creation of preventative measures and efficient treatments against foodborne pathogens.

Global diversity and antimicrobial resistance of typhoid fever pathogens: Insights from a meta-analysis of 13,000 Salmonella Typhi genomes

BACKGROUND

The Global Typhoid Genomics Consortium was established to bring together the typhoid research community to aggregate and analyse Salmonella enterica serovar Typhi (Typhi) genomic data to inform public health action. This analysis, which marks 22 years since the publication of the first Typhi genome, represents the largest Typhi genome sequence collection to date (n=13,000).

METHODS

This is a meta-analysis of global genotype and antimicrobial resistance (AMR) determinants extracted from previously sequenced genome data and analysed using consistent methods implemented in open analysis platforms GenoTyphi and Pathogenwatch.

RESULTS

Compared with previous global snapshots, the data highlight that genotype 4.3.1 (H58) has not spread beyond Asia and Eastern/Southern Africa; in other regions, distinct genotypes dominate and have independently evolved AMR. Data gaps remain in many parts of the world, and we show the potential of travel-associated sequences to provide informal 'sentinel' surveillance for such locations. The data indicate that ciprofloxacin non-susceptibility (>1 resistance determinant) is widespread across geographies and genotypes, with high-level ciprofloxacin resistance (≥3 determinants) reaching 20% prevalence in South Asia. Extensively drug-resistant (XDR) typhoid has become dominant in Pakistan (70% in 2020) but has not yet become established elsewhere. Ceftriaxone resistance has emerged in eight non-XDR genotypes, including a ciprofloxacin-resistant lineage (4.3.1.2.1) in India. Azithromycin resistance mutations were detected at low prevalence in South Asia, including in two common ciprofloxacin-resistant genotypes.

CONCLUSIONS

The consortium's aim is to encourage continued data sharing and collaboration to monitor the emergence and global spread of AMR Typhi, and to inform decision-making around the introduction of typhoid conjugate vaccines (TCVs) and other prevention and control strategies.

FUNDING

No specific funding was awarded for this meta-analysis. Coordinators were supported by fellowships from the European Union (ZAD received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 845681), the Wellcome Trust (SB, Wellcome Trust Senior Fellowship), and the National Health and Medical Research Council (DJI is supported by an NHMRC Investigator Grant [GNT1195210]).