Wei Ching Khor

Salmonella Saintpaul is a foodborne pathogen of public health relevance. This study characterised 79 S. Saintpaul isolates from human clinical and food sources collected in Singapore from 2015 to 2017. Isolates belonged to ST3602 (91.1%, n = 72), ST27 (6.33%, n = 5), ST49 (1.27%, n = 1) or ST50 (1.27%, n = 1). ST3602 predominated in both human (92.5%) and food (89.7%) isolates. Human and food isolates showed the highest resistance to penicillins and beta-lactam/beta-lactamase inhibitor combinations. The analysis identified beta-lactam resistance genes (bla_CTX-M-1, bla_TEM-1D), aminoglycoside resistance genes (aph(4)-Ia, aac(3)-IVa, aadA), and fluoroquinolone resistance genes (qnrS) as the most prevalent. Notably, 31.6% of isolates identified as extended-spectrum beta-lactamase (ESBL)-producing and all ESBL-positive isolates exhibited multidrug resistance. Plasmids were predicted in 75.9% (n = 60) of the isolates, with IncI1-I(Alpha) being the most common incompatibility group and showing a strong association with bla_CTX-M-1 (Fisher’s exact test, p < 0.001; Φ = 0.913). Single-nucleotide polymorphism (SNP) analysis revealed close genetic relatedness between chicken and human isolates at relatively low SNP distances (0–16 SNPs), suggesting potential shared transmission pathways. This study provides epidemiological insights and antimicrobial resistance landscape of S. Saintpaul in Singapore, informing strategies for food safety and public health surveillance.

The tilapia (Oreochromis) aquaculture industry in Malaysia has expanded rapidly to meet the increasing demand for animal protein. However, this growth is challenged by microbial infections, particularly those caused by the emerging pathogen Aeromonas dhakensis. This study aimed to investigate the microbial community composition across four distinct tilapia farming systems and assess associated water physicochemical parameters, with a focus on detecting the presence of A. dhakensis and elucidating its environmental associations. Water physicochemical parameters were measured to evaluate environmental conditions, microbial communities were characterized through 16S rDNA metabarcoding, and A. dhakensis was detected using both microbiological and molecular approaches. Principal component analysis (PCA) and canonical correspondence analysis (CCA) were employed to explore the influence of environmental variables and microbial community dynamics on pathogen occurrence. Our results indicated that floating cages exhibited higher levels of temperature, ammonium, and fecal coliform, while cement tanks showed signs of nutrient accumulation. PCA revealed that both systems were associated with degraded water quality. A total of 45 A. dhakensis strains with distinct fingerprints were isolated. The 16S metabarcoding revealed Proteobacteria, Actinobacteria, and Planctomycetota as the dominant phyla. Alpha diversity did not differ significantly among pond systems, while beta diversity revealed variations in microbial assemblages across aquaculture systems. CCA identified dissolved oxygen, temperature, macronutrients (phosphate, ammonium, nitrate, and nitrite), and turbidity as significant environmental drivers shaping the microbial community structure across the pond systems. In conclusion, this study highlights the importance of environmental factors, particularly dissolved oxygen, temperature, and nutrient levels, in shaping microbial community composition and potentially influencing the presence of pathogenic bacteria such as A. dhakensis. These findings underscore the need for improved environmental management in tilapia aquaculture to mitigate disease risks and support fish health.

Salmonella remains a significant foodborne pathogen globally with S. Typhimurium presenting as a frequently occurring serovar. This study aimed to characterize 67 S. Typhimurium isolates from humans, food, farms, and slaughterhouses collected in Singapore from 2016 to 2017. Using whole-genome sequencing analysis, the isolates were found to belong to either ST19 (n = 33) or ST36 (n = 34). ST36 predominated in human intestinal and chicken isolates, while human extra-intestinal and non-chicken food isolates belonged to ST19. Plasmids were predicted in 88.1% (n = 59) of the isolates with the most common incompatibility group profiles being IncFIB(S), IncFII(S) and IncQ1. IncFIB(S) (adjusted p-value < 0.05) and IncFII(S) (adjusted p-value < 0.05) were significantly more prevalent in ST19 isolates, while Col156 (adjusted p-value < 0.05) was more significantly found in ST36 isolates. ST36 isolates exhibited higher resistance to multiple antibiotic classes such as penicillins, phenicols, folate pathway inhibitors, aminoglycosides, β-lactam/β-lactamase inhibitor combinations, tetracyclines, and fluoroquinolones. Phylogenetics analysis suggested potential shared routes of transmission among human, chicken, farm and slaughterhouse environments. Taken together, this study offers a cross-sectional epidemiological insight into the genomic epidemiology and antimicrobial landscape of S. Typhimurium isolates in Singapore, informing strategies for future public health and food safety surveillance.

Staphylococcus aureus contamination of food and food contact surfaces is a public health concern given its virulent and antimicrobial-resistant properties worldwide. In this study, a total of 181 MSSA isolates were analyzed for SE genes, antimicrobial resistance patterns, and spa types. Overall, 24.9% of isolates were positive for SE gene detection, with sea being the most prevalent classical SE (18.8%). The most predominant sample sources for SE gene contamination were hand swabs for sea (6/48), meat dishes for seb (3/14) and seafood dishes for sec (2/24). Antimicrobial resistance was also observed at relatively high frequencies for the clinically important antibiotics penicillin G and ampicillin (both 54.7%), followed by tetracycline (14.9%) and azithromycin (8.8%). In addition, characterization of spa types revealed spa type t5078 to be the most predominant (40.3%), with significant associations between spa types t127 and t5521 and the sea gene. This study offers insights into the enterotoxin gene and antimicrobial resistance profiles of S. aureus in cooked or ready-to-eat food to inform future surveillance and epidemiological studies.

Vibrio parahaemolyticus, commonly found in seafood products, is responsible for gastroenteritis resulting from the consumption of undercooked seafood. Hence, there is a need to characterize and quantify the risk involved from this pathogen. However, there has been no study reporting the quantification of hemolytic antimicrobial-resistant (AMR) Vibrio parahaemolyticus in locally farmed shellfish in Singapore. In this study, ampicillin, penicillin G, tetracycline resistant, and non-AMR hemolytic V. parahaemolyticus were surveyed and quantified in green mussel samples from different premises in the food chain (farm and retail). The occurrence data showed that 31/45 (68.9%) of farmed green mussel samples, 6/6 (100%) farm water samples, and 41/45 (91.1%) retail shellfish samples detected the presence of hemolytic V. parahaemolyticus. V. parahaemolyticus counts ranged from 1.6–5.9 Log CFU/g in the retail shellfish samples and 1.0–2.9 Log CFU/g in the farm water samples. AMR risk assessments (ARRA), specifically for ampicillin, penicillin G, tetracycline, and hemolytic (non-AMR) scenarios were conducted for the full farm-to-home and partial retail-to-home chains. The hemolytic ARRA scenario estimated an average probability of illness of 5.7 × 10⁻³ and 1.2 × 10⁻² per serving for the full and partial chains, respectively, translating to 165 and 355 annual cases per total population or 2.9 and 6.2 cases per 100,000 population, respectively. The average probability of illness per year ratios for the three ARRAs to the hemolytic ARRA were 0.82, 0.81, and 0.47 (ampicillin, penicillin G, and tetracycline, respectively) for the full chain and 0.54, 0.39, and 0.09 (ampicillin, penicillin G, and tetracycline, respectively) for the partial chain. The sensitivity analysis showed that the overall cooking effect, initial concentrations of pathogenic V. parahaemolyticus, and harvest duration and harvest temperature were key variables influencing the risk estimates in all of the modelled ARRAs. The study findings can be used by relevant stakeholders to make informed decisions for risk management that improve food safety.

Vibrio parahaemolyticus is a causative pathogen for gastroenteritis involving the consumption of undercooked or raw seafood. However, there is a paucity of data regarding the quantitative detection of this pathogen in finfish, while no study reported the enumeration of haemolytic antimicrobial-resistant (AMR) V. parahaemolyticus. In this study, ampicillin-, penicillin G- and tetracycline-resistant and non-AMR haemolytic V. parahaemolyticus isolates were monitored and quantified in grey mullet samples reared locally from different premises within the food chain (farm and retail). Occurrence data for haemolytic V. parahaemolyticus were 13/45 (29%) in farm fish samples, 2/6 (one third) from farm water samples and 27/45 (60%) from retail fish samples. Microbial loads for haemolytic V. parahaemolyticus microbial loads ranged from 1.9 to 4.1 Log CFU/g in fish samples and 2.0 to 3.0 Log CFU/g in farm water samples. AMR risk assessments (ARRAs) for both the full farm-to-home and partial retail-to-home chains in the risk modelling framework were conducted, specifically for ampicillin, penicillin G, tetracycline and haemolytic (non-AMR) scenarios. The haemolytic ARRA predicted an average probability of illness of 2.9 × 10⁻⁴ and 4.5 × 10⁻⁵ per serving for the farm-to-home and retail-to-home chains, respectively, translating to 57 and 148 cases annually. The ratios of the average probability of illness per year for the three ARRAs to the haemolytic ARRA were 1.1 × 10⁻² and 3.0 × 10⁻⁴ (ampicillin and penicillin G, respectively) for the farm-to-home chain and 1.3, 1.6 and 0.4 (ampicillin, penicillin G and tetracycline, respectively) for the retail-to-home chain. Sensitivity analysis showed that the initial concentrations of haemolytic V. parahaemolyticus in the gills and intestines of the fish and the cooking and washing of the fish cavity were the major variables influencing risk outputs in all modelled ARRAs. The findings of this study are useful for relevant stakeholders to make informed decisions regarding risk management to improve overall food safety.

Aeromonas dhakensis is ubiquitous in aquatic habitats and can cause life-threatening septicaemia in humans. However, limited data are available on their antimicrobial susceptibility testing (AST) profiles. Hence, we aimed to examine their AST patterns using clinical (n = 94) and non-clinical (n = 23) isolates with dehydrated MicroScan microdilution. Carbapenem resistant isolates were further screened for genes related to carbapenem resistance using molecular assay. The isolates exhibited resistance to imipenem (76.9%), doripenem (62.4%), meropenem (41.9%), trimethoprim/sulfamethoxazole (11.1%), cefotaxime (8.5%), ceftazidime (6%), cefepime (1.7%) and aztreonam (0.9%), whereas all isolates were susceptible to amikacin. Clinical isolates showed significant association with resistance to doripenem, imipenem and meropenem compared to non-clinical isolates. These bla_cphA were detected in clinical isolates with resistance phenotypes: doripenem (67.2%, 45/67), imipenem (65.9%, 54/82) and meropenem (65.2%, 30/46). Our findings showed that the MicroScan microdilution method is suitable for the detection of carbapenem resistance in both clinical (48.9–87.2%) and non-clinical (4.3–13.0%) isolates. This study revealed that A. dhakensis isolates had relatively high carbapenem resistance, which may lead to potential treatment failure. Continued monitoring of aquatic sources with a larger sample size should be carried out to provide further insights.

Salmonella Enteritidis is a major foodborne pathogen worldwide. In this study, a total of 276 S. enteritidis isolates, collected between 2016 and 2017 from human, food and farm/slaughterhouse samples, were studied to enhance the understanding of the epidemiology of human salmonellosis in Singapore. Results showed all 276 isolates belonged either to ST1925 (70.3%) or ST11 (29.7%), with ST11 being significantly more frequent in extra-intestinal isolates and chicken isolates. Food isolates, most of which were from poultry, showed the highest prevalence of resistance (33–37%) against beta-lactams or beta-lactams/beta-lactamase inhibitor combination (ampicillin, piperacillin and ampicillin/sulbactam). The analysis showed the detection of genes associated with resistance to aminoglycoside genes (99.6%), tetracycline (55.1%), and beta-lactams (14.9%) of all isolates. Nine types of plasmids were found in 266 isolates; the most common incompatibility group profiles were IncFIB(S)-IncFII(S)-IncX1 (72.2%) and IncFIB(S)-IncFII(S) (15.8%). Most plasmid harbouring isolates from chicken (63.6%, 14/22) and from human (73.8%, 175/237) shared the same plasmid profile (IncFIB(S)-IncFII(S)-IncX1). SNP analysis showed clustering of several isolates from poultry food products and human isolates, suggesting phylogenetic relatedness among these isolates. Lastly, this study provides important epidemiological insights on the application of phenotypic and next-generation sequencing (NGS) tools for improved food safety and public health surveillance and outbreak investigation of S.enteritidis.

We analyzed the epidemiological distribution of Salmonella serovars in humans, foods, animals and the environment as a One-Health step towards identifying risk factors for human salmonellosis. Throughout the 2012–2016 period, Salmonella ser. Enteritidis was consistently the predominating serovar attributing to >20.0% of isolates in humans. Other most common serovars in humans include Salmonella ser. Stanley, Salmonella ser. Weltevreden, Salmonella ser. Typhimurium and Salmonella ser. 4,5,12:b:-(dT+). S. Enteritidis was also the most frequent serovar found among the isolates from chicken/chicken products (28.5%) and eggs/egg products (61.5%) during the same period. In contrast, S. Typhimurium (35.2%) and Salmonella ser. Derby (18.8%) were prevalent in pork/pork products. S. Weltevreden was more frequent in seafood (19.2%) than others (≤3.0%). Most isolates (>80.0%) from farms, companion and wildlife animals belonged to serovars other than S. Enteritidis or S. Typhimurium. Findings demonstrate the significance of a One-Health investigative approach to understand the epidemiology Salmonella for more effective and integrated surveillance systems.