Draft Genome Sequences of 12 Leuconostoc carnosum Strains Isolated from Cooked Ham Packaged in a Modified Atmosphere and from Fresh Sausages

Leuconostoc carnosum is a lactic acid bacterium that preferentially colonizes meat. In this work, we present the draft genome sequences of 12 Leuconostoc carnosum strains isolated from modified-atmosphere-packaged cooked ham and fresh sausages. Three strains harbor bacteriocin genes

Distribution of <i>salmonella</i> serovars in humans, foods, farm animals and environment, companion and wildlife animals in Singapore

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&ndash;2016 period, Salmonella ser. Enteritidis was consistently the predominating serovar attributing to &gt;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 (&le;3.0%). Most isolates (&gt;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

Metagenomics-Based Proficiency Test of Smoked Salmon Spiked with a Mock Community

peer reviewedAn inter-laboratory proficiency test was organized to assess the ability of participants to perform shotgun metagenomic sequencing of cold smoked salmon, experimentally spiked with a mock community composed of six bacteria, one parasite, one yeast, one DNA, and two RNA viruses. Each participant applied its in-house wet-lab workflow(s) to obtain the metagenomic dataset(s), which were then collected and analyzed using MG-RAST. A total of 27 datasets were analyzed. Sample pre-processing, DNA extraction protocol, library preparation kit, and sequencing platform, influenced the abundance of specific microorganisms of the mock community. Our results highlight that despite differences in wet-lab protocols, the reads corresponding to the mock community members spiked in the cold smoked salmon, were both detected and quantified in terms of relative abundance, in the metagenomic datasets, proving the suitability of shotgun metagenomic sequencing as a genomic tool to detect microorganisms belonging to different domains in the same food matrix. The implementation of standardized wet-lab protocols would highly facilitate the comparability of shotgun metagenomic sequencing dataset across laboratories and sectors. Moreover, there is a need for clearly defining a sequencing reads threshold, to consider pathogens as detected or undetected in a food sample

Development of a dairy-free fermented oat-based beverage with enhanced probiotic and bioactive properties

Lactobacillus fermentum PC1 with proven probiotic properties was used to ferment oats with added honey to develop a probiotic beverage with enhanced bioactive ingredients. The viable Lactobacilli were enumerated during the fermentation and storage at 4°C, as well as after exposure to simulated gastrointestinal tract conditions. Good survival was noted both during storage as well as when exposed to the in vitro digestive tract conditions. Comparative analysis of the antioxidant activity, total phenolic content, and phenolic composition indicated fermentation improved the total antioxidant capacity and phenolic acid concentration. An increase of more than 50% of gallic acid, catechin, vanillic acid, caffeic acid, p-coumaric acid, and ferulic acid was observed in the methanol extracts. Moreover, no significant decrease in the β-glucan content was noted during fermentation and storage. In conclusion, this fermented product has a great potential as a functional food with enhanced probiotic survival and increased bioactive ingredients.Nanyang Technological UniversityPublished versionThis work was supported by Ageing Research Institute for Society and Education (ARISE), Nanyang Technological University, Singapore. DW was supported from the funding of China Scholarship Council (grant no. 201906240301)

Food Safety in ASEAN : Pitfalls of Complacency

ASEAN food safety regulators may think it conservative to stick to testing for hazards in food, neglecting the need to base control in the notion of risk. This mindset however has a number of pitfalls, which can end up making the region more vulnerable to ‘unknown unknowns’ in food safety

Honeys with anti-inflammatory capacity can alter the elderly gut microbiota in an ex vivo gut model

The anti-inflammatory effect of different sourced honeys and the impact on elderly gut microbiota were studied in terms of chemical compositions, anti-inflammatory effect and gut microbiota modulating capacities. All four honeys suppressed the production of pro-inflammatory markers NO, IL-1β and IL-6 induced by lipopolysaccharide and promoted the expression of anti-inflammatory cytokines IL-10 in RAW 264.7 cells. Moreover, in the ex vivo batch gut model using elderly fecal microbiota (referred to as microcosm), it was showed that the addition of honeys increased the abundance of beneficial lactobacilli, decreased the abundance of potentially harmful Gram negative enteric bacteria, and exerted a beneficial effect on the production of short chain fatty acids. The concentration of gallic acid in honeys was positively correlated with the expression level of IL-10 and the abundance of lactobacilli. These findings indicate honeys with anti-inflammatory capacity have great potential for regulating the elderly gut microbiota which would lead to health benefits.Nanyang Technological UniversityWe sincerely thank the support from the funding of China Scholarship Council (grant no. 201906240301)

Characterization of Extended-Spectrum Beta-Lactamase-Producing Escherichia coli Isolates from Jurong Lake, Singapore with Whole-Genome-Sequencing

Background: The fast-spreading of Extended-Spectrum Beta-Lactamase-Producing Escherichia coli (ESBL-producing E. coli) and ESBL genes has become a big challenge to public health. The risk of spreading ESBL genes and pathogens in the environment and community has raised public health concern. The characterizing and whole-genome sequencing studies of ESBL-producing bacteria from reservoir water in Singapore is still limited. Materials and methods: The reservoir water sample was taken from two randomly selected sampling points of the Chinese Garden (Jurong river reservoir), which is a popular reservoir park in Singapore. The bacteria of the water sample were collected with 0.45 &micro;m filter membranes and enriched before processing with ESBL-producing E. coli screening. The collected ESBL positive isolates were further characterized by both phenotypic tests including disc diffusion and microdilution Minimum Inhibitory Concentration (MIC) test, and also genotypic test as whole-genome sequencing analysis. Besides, to investigate the transferability of the resistance gene, a conjugation test was performed with the J53 E. coli strain as the gene receptor. Result: Nine ESBL-producing E. coli isolates were collected and confirmed as ESBL-producing with both phenotypic and genotypic tests. A potential pathogen as ST131 clade A isolate was identified, and all isolates were determined to harbor a blaCTX-M gene. Among them, strain J1E4 was resistant to polymyxin E and confirmed to harboring a conjugatable mcr-1 gene. Further genetic environment analysis has reflected a conversed gene cluster formed by insert sequence (IS), blaCTX-M-15, and WbuC family cupin-fold metalloprotein, which may potentially jump from the plasmids to the chromosome. Conclusion: The first time we reported the whole genome sequencing (WGS) data of ESBL-producing E. coli including potential pathogen (ST131) present in reservoir water in Singapore. The ESBL-producing E. coli from reservoir water also carrying conjugatable colistin resistance genes which may become a risk to human health

Comparative genomics of Leuconostoc carnosum

Leuconostoc carnosum is a known colonizer of meat-related food matrices. It reaches remarkably high loads during the shelf life in packaged meat products and plays a role in spoilage, although preservative effects have been proposed for some strains. In this study, the draft genomes of 17 strains of L. carnosum (i.e., all the strains that have been sequenced so far) were compared to decipher their metabolic and functional potential and to determine their role in food transformations. Genome comparison and pathway reconstruction indicated that L. carnosum is a compact group of closely related heterofermentative bacteria sharing most of the metabolic features. Adaptation to a nitrogen-rich environment, such as meat, is evidenced by 23 peptidase genes identified in the core genome and by the autotrophy for nitrogen compounds including several amino acids, vitamins, and cofactors. Genes encoding the decarboxylases yielding biogenic amines were not present. All the strains harbored 1-4 of 32 different plasmids, bearing functions associated to proteins hydrolysis, transport of amino acids and oligopeptides, exopolysaccharides, and various resistances (e.g., to environmental stresses, bacteriophages, and heavy metals). Functions associated to bacteriocin synthesis, secretion, and immunity were also found in plasmids. While genes for lactococcin were found in most plasmids, only three harbored the genes for leucocin B, a class IIa antilisterial bacteriocin. Determinants of antibiotic resistances were absent in both plasmids and chromosomes.Published versio

Whole-genome sequencing of nontyphoidal Salmonella enterica isolates obtained from various meat types in Ghana

Here, we report the draft genome sequences of 16 nontyphoidal Salmonella enterica isolates obtained from locally produced meats in Tamale, Ghana, which are commonly consumed by most natives as an important protein source. The draft genomes will help provide a molecular snapshot of Salmonella enterica isolates found in these retail meats in Tamale.Published versio

Antimicrobial resistance risk assessment of vibrio parahaemolyticus isolated from farmed green mussels in Singapore

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.Nanyang Technological UniversitySingapore Food AgencyPublished versionThis research was funded by National Centre for Food Science, Singapore Food Agency, and Nanyang Technological University, School of Chemistry, Chemical Engineering and Biotechnology under grant number REQ0230976