Genome-wide identification of cis DNA methylation quantitative trait loci in three Southeast Asian Populations.

DNA methylation (DNAm) is an epigenetic modification that acts to regulate gene transcription, is essential for cellular processes and plays an important role in complex traits and disease. Variation in DNAm levels is influenced by both genetic and environmental factors. Several studies have examined the extent to which common genetic variation influences DNAm (i.e. mQTLs), however, an improved understanding of mQTLs across diverse human populations is needed to increase their utility in integrative genomic studies in order to further our understanding of complex trait and disease biology. Here, we systematically examine cis-mQTLs in three Southeast Asian populations in the Singapore Integrative Omics (iOmics) Study, comprised of Chinese (n = 93), Indians (n = 83) and Malays (n = 78). A total of 24 851 cis-mQTL probes were associated with at least one SNP in meta- and ethnicity-specific analyses at a stringent significance level. These cis-mQTL probes show significant differences in local SNP heritability between the ethnicities, enrichment in functionally relevant regions using data from the Roadmap Epigenomics Mapping Consortium and are associated with nearby genes and complex traits due to pleiotropy. Importantly, DNAm prediction performance and the replication of cis-mQTLs both within iOmics and between two independent mQTL studies in European and Bangladeshi individuals is best when the genetic distance between the ethnicities is small, with differences in cis-mQTLs likely due to differences in allele frequency and linkage disequilibrium. This study highlights the importance of, and opportunities from, extending investigation of the genetic control of DNAm to Southeast Asian populations.

Extended-Spectrum ß-Lactamase-Producing and mcr-1-Positive Escherichia coli from the Gut Microbiota of Healthy Singaporeans.

Multidrug-resistant (MDR) Escherichia coli strains that carry extended-spectrum ß-lactamases (ESBLs) or colistin resistance gene mcr-1 have been identified in the human gut at an increasing incidence worldwide. In this study, we isolated and characterized MDR Enterobacteriaceae from the gut microbiota of healthy Singaporeans and show that the detection rates for ESBL-producing and mcr-positive Enterobacteriaceae are 25.7% (28/109) and 7.3% (8/109), respectively. Whole-genome sequencing analysis of the 37 E. coli isolates assigned them into 25 sequence types and 6 different phylogroups, suggesting that the MDR E. coli gut colonizers are highly diverse. We then analyzed the genetic context of the resistance genes and found that composite transposons played important roles in the cotransfer of blaCTX-M-15/55 and qnrS1, as well as the acquisition of mcr-1. Furthermore, comparative genomic analysis showed that 12 of the 37 MDR E. coli isolates showed high similarity to ESBL-producing E. coli isolates from raw meat products in local markets. By analyzing the core genome single nucleotide polymorphisms (SNPs) shared by these isolates, we identified possible clonal transmission of an MDR E. coli clone between human and raw meat, as well as a group of highly similar IncI2 (Delta) plasmids that might be responsible for the dissemination of mcr-1 in a much wider geographic region. Together, these results suggest that antibiotic resistance may be transmitted between different environmental settings by the expansion of MDR E. coli clones, as well as by the dissemination of resistance plasmids. IMPORTANCE The human gut can harbor both antibiotic-resistant and virulent Escherichia coli which may subsequently cause infections. In this study, we found that multidrug-resistant (MDR) E. coli isolates from the gut of healthy Singaporeans carry a diverse range of antibiotic resistance mechanisms and virulence factor genes and are highly diverse. By comparing their genomes with the extended-spectrum ß-lactamase (ESBL)-producing E. coli isolates from raw meat products that were sampled at a similar time from local markets, we detected an MDR E. coli clone that was possibly transmitted between humans and raw meat products. Furthermore, we also found that a group of resistance plasmids might be responsible for the dissemination of colistin resistance gene mcr-1 in Singapore, Malaysia, and Europe. Our findings call for better countermeasures to block the transmission of antibiotic resistance.

Consumption of Foods With Higher Energy Intake Rates is Associated With Greater Energy Intake, Adiposity, and Cardiovascular Risk Factors in Adults.

BACKGROUND: Both high energy density and fast eating rates contribute to excess energy intakes. The energy intake rate (EIR; kcal/min) combines both the energy density (kcal/g) and eating rate (g/min) of a food to quantify the typical rate at which calories of different foods are ingested. OBJECTIVES: We describe the EIRs of diets in a multi-ethnic Asian population, and examine relationships between the consumption of high-EIR foods and total energy intake, body composition, and cardio-metabolic risk factors. METHODS: Diet and lifestyle data from the Singapore Multi-Ethnic Cohort 2 (n = 7011; 21-75 y), were collected through interviewer-administrated questionnaires. The EIR for each of the 269 foods was calculated as the product of its eating rate and energy density. Multivariable models were used to examine associations between the relative consumption of foods with higher and lower EIRs and energy intake, body composition, and cardio-metabolic risks, after adjusting for age, sex, ethnicity, education level, physical activity, smoking status, and alcohol drinking status. RESULTS: Individuals with higher daily energy intakes and with obesity consumed a significantly larger percentage of their energy from high-EIR foods, with a smaller relative intake of lower-EIR foods. Individuals with raised serum cholesterol also consumed a significantly higher proportion of high-EIR foods, whereas those without hypertension consumed a larger percentage of energy intake from low-EIR foods. Individuals classified as having a "very high" dietary EIR had a significantly 1.3 kg higher body weight (95% CI, 0.2-1.5; P = 0.013), 0.4 kg/m2 higher BMI (95% CI, 0.03-0.8; P = 0.037), and 1.2 cm larger waist circumference (95% CI, 0.2-2.2; P = 0.010), and were more likely to have abdominal overweight (OR, 1.3; 95% CI, 1.1-1.5; P < 0.001) than those with a "low" dietary EIR. CONCLUSIONS: Comparing foods by their EIRs summarizes the combined impact of energy density and eating rate, and may identify foods and dietary patterns that are associated with obesogenic eating styles and higher diet-related cardiovascular disease risk in an Asian population.

Emergence of tigecycline- and eravacycline-resistant Tet(X4)-producing Enterobacteriaceae in the gut microbiota of healthy Singaporeans.

OBJECTIVES: The recently discovered tigecycline-inactivating enzyme Tet(X4) can confer high-level tigecycline resistance on its hosts, which makes it a public health concern. This study focused on isolation and screening of Tet(X4)-positive Enterobacteriaceae from the gut microbiota of a cohort of healthy individuals in Singapore. METHODS: MinION and Illumina sequencing was performed to obtain the complete genome sequences of Escherichia coli 2EC1-1 and 94EC. Subsequently, 109 human faecal samples were screened retrospectively for eravacycline-resistant Enterobacteriaceae strains, which were further tested for tet(X4) by PCR. The taxonomy of the isolated strains was determined by 16S rRNA gene PCR and Sanger sequencing. RESULTS: Comparative genomic analysis of E. coli 2EC1-1 and 94EC revealed that both carry tet(X4), which is encoded by IncI1-type plasmids p2EC1-1 and p94EC-2, respectively. Retrospective screening of faecal samples collected from 109 healthy individuals showed that the faecal carriage rate of Tet(X4)-producing Enterobacteriaceae is 10.1% (95% CI = 5.1%-17.3%), suggesting that tet(X4) is widely distributed in the gut microbiota of healthy individuals in Singapore. CONCLUSIONS: To the best of our knowledge, this is the first report on the prevalence of tet(X4) in the gut microbiota of a healthy human cohort, as well as the first description of this resistance mechanism outside of China. Our findings suggest that surveillance of tet(X4) in community settings is vital to monitor the spread of this resistance mechanism.

Development and validation of the Rapid Positive Mental Health Instrument (R-PMHI) for measuring mental health outcomes in the population.

BACKGROUND: The multidimensional Positive Mental Health Instrument (PMHI) has 47 items and six subscales. This study aimed to develop and validate a short unidimensional version of the PMHI among Singapore's adult resident population. METHODS: Using pooled data from three earlier studies (n = 1050), PMHI items were reduced by Partial Credit Rasch Model (PCRM) runs in a random split-half sample, while psychometric properties of the resulting measure were tested through confirmatory factor analysis (CFA), item response theory-graded response model and internal consistency reliability in the other half. Its reliability, construct and concurrent validity, agreement with the original scale, floor and ceiling effect, and scale estimates were further investigated in an external representative general population sample (n = 1925). RESULTS: The average age of the participants was around 41 years. Four PCRM re-runs for item selection resulted in a 6-item unidimensional Rapid PMHI (R-PMHI). CFA confirmed the unidimensional structure of the R-PMHI in the internal (RMSEA = 0.075, CFI = 0.985, TLI = 0.974) and external (RMSEA = 0.051, CFI = 0.992, TLI = 0.987) validation samples. In the external validation sample, the R-PMHI met concurrent validity criteria, showing high agreement with the 47-item version with intra-class correlation coefficient of 0.872 (95% CI: 0.861 to 0.882) and low floor and ceiling effects. Weight-adjusted mean (SE, 95% CI) R-PMHI score in the population was 4.86 (0.2, 4.82-4.90). CONCLUSION: The unidimensional 6-item R-PMHI offers brevity over the original multidimensional measure while appropriately representing the positive mental health construct. Prospective studies are needed to assess its responsiveness and test-retest reliability.

Psychometric properties and population norms of the positive mental health instrument in a representative multi-ethnic Asian population.

BACKGROUND: Measures of mental well-being and positive mental health (PMH) have been largely developed and used in Western populations, however, data on representative Asian communities are lacking. Using data from a population sample, this study sought to establish psychometric properties and norms of the PMH Instrument (PMH-I), a measure of positive mental health developed in Singapore. METHODS: We conducted a nationally representative survey among 1925 adults aged 18-79 years of Chinese, Malay, Indian or other ethnicity. Participants reported socio-demographic characteristics and completed the PMH-I along with measures of health-related quality of life (HRQoL) and psychological distress. Construct validity of the PMH-I was assessed using confirmatory factor analysis and concurrent validity was tested through correlation with other psychological measures. Normative PMH values and differences in population subgroups were estimated. RESULTS: The six-factor-higher-order structure of the PMH-I comprising six subscales of general coping, emotional support, spirituality, interpersonal skills, personal growth and autonomy and global affect was confirmed. Concurrent validity was shown through significant positive correlation of the total PMH score and its subscales with HRQoL and an inverse correlation with psychological distress. Weighted age, gender and ethnicity-specific norms were derived for the Singapore population. Total PMH was significantly higher in participants aged over 40 years as compared with 18-29 year olds and in non-Chinese ethnic groups as compared with Chinese. These differences were observed for all PMH-I subscales, with the exception of emotional support and interpersonal skills score differences by age. In contrast, gender, marital status, and education level were significantly associated with some of the subscales, but not with total PMH. CONCLUSIONS: These results support the psychometric properties of the PMH-I in a multi-ethnic Asian population sample. The generalizable population-based norms support the application of the PMH-I for measuring mental health and assessing its determinants within the Singapore general population.

Adequacy of public health communications on H7N9 and MERS in Singapore: insights from a community based cross-sectional study.

BACKGROUND: Singapore remains vulnerable to worldwide epidemics due to high air traffic with other countries This study aims to measure the public's awareness of the Middle East Respiratory Syndrome (MERS) and Avian Influenza A (H7N9), identify population groups who are uninformed or misinformed about the diseases, understand their choice of outbreak information source, and assess the effectiveness of communication channels in Singapore. METHODS: A cross-sectional study, comprising of face-to-face interviews, was conducted between June and December 2013 to assess the public's awareness and knowledge of MERS and H7N9, including their choice of information source. Respondents were randomly selected and recruited from 3 existing cohort studies. An opportunistic sampling approach was also used to recruit new participants or members in the same household through referrals from existing participants. RESULTS: Out of 2969 participants, 53.2% and 79.4% were not aware of H7N9 and MERS respectively. Participants who were older and better educated were most likely to hear about the diseases. The mean total knowledge score was 9.2 (S.D ± 2.3) out of 20, and 5.9 (S.D ± 1.2) out of 10 for H7N9 and MERS respectively. Participants who were Chinese, more educated and older had better knowledge of the diseases. Television and radio were the primary sources of outbreak information regardless of socio-demographic factors. CONCLUSION: Heightening education of infectious outbreaks through appropriate media to the young and less educated could increase awareness.

Epidemiology and Relative Severity of Influenza Subtypes in Singapore in the Post-Pandemic Period from 2009 to 2010.

BACKGROUND: After 2009, pandemic influenza A(H1N1) [A(H1N1)pdm09] cocirculated with A(H3N2) and B in Singapore. METHODS: A cohort of 760 participants contributed demographic data and up to 4 blood samples each from October 2009 to September 2010. We compared epidemiology of the 3 subtypes and investigated evidence for heterotypic immunity through multivariable logistic regression using a generalized estimating equation. To examine age-related differences in severity between subtypes, we used LOESS (locally weighted smoothing) plots of hospitalization to infection ratios and explored birth cohort effects referencing the pandemic years (1957; 1968). RESULTS: Having more household members aged 5-19 years and frequent public transport use increased risk of infection, while preexisting antibodies against the same subtype (odds ratio [OR], 0.61; P = .002) and previous influenza infection against heterotypic infections (OR, 0.32; P = .045) were protective. A(H1N1)pdm09 severity peaked in those born around 1957, while A(H3N2) severity was least in the youngest individuals and increased until it surpassed A(H1N1)pdm09 in those born in 1952 or earlier. Further analysis showed that severity of A(H1N1)pdm09 was less than that for A(H3N2) in those born in 1956 or earlier (P = .021) and vice versa for those born in 1968 or later (P < .001), with no difference in those born between 1957 and 1967 (P = .632). CONCLUSIONS: Our findings suggest that childhood exposures had long-term impact on immune responses consistent with the theory of antigenic sin. This, plus observations on short-term cross-protection, have implications for vaccination and influenza epidemic and pandemic mitigation strategies.

Insights into the genetic structure and diversity of 38 South Asian Indians from deep whole-genome sequencing.

South Asia possesses a significant amount of genetic diversity due to considerable intergroup differences in culture and language. There have been numerous reports on the genetic structure of Asian Indians, although these have mostly relied on genotyping microarrays or targeted sequencing of the mitochondria and Y chromosomes. Asian Indians in Singapore are primarily descendants of immigrants from Dravidian-language-speaking states in south India, and 38 individuals from the general population underwent deep whole-genome sequencing with a target coverage of 30X as part of the Singapore Sequencing Indian Project (SSIP). The genetic structure and diversity of these samples were compared against samples from the Singapore Sequencing Malay Project and populations in Phase 1 of the 1,000 Genomes Project (1 KGP). SSIP samples exhibited greater intra-population genetic diversity and possessed higher heterozygous-to-homozygous genotype ratio than other Asian populations. When compared against a panel of well-defined Asian Indians, the genetic makeup of the SSIP samples was closely related to South Indians. However, even though the SSIP samples clustered distinctly from the Europeans in the global population structure analysis with autosomal SNPs, eight samples were assigned to mitochondrial haplogroups that were predominantly present in Europeans and possessed higher European admixture than the remaining samples. An analysis of the relative relatedness between SSIP with two archaic hominins (Denisovan, Neanderthal) identified higher ancient admixture in East Asian populations than in SSIP. The data resource for these samples is publicly available and is expected to serve as a valuable complement to the South Asian samples in Phase 3 of 1 KGP.

Predicting HLA alleles from high-resolution SNP data in three Southeast Asian populations.

The major histocompatibility complex (MHC) containing the classical human leukocyte antigen (HLA) Class I and Class II genes is among the most polymorphic and diverse regions in the human genome. Despite the clinical importance of identifying the HLA types, very few databases jointly characterize densely genotyped single nucleotide polymorphisms (SNPs) and HLA alleles in the same samples. To date, the HapMap presents the only public resource that provides a SNP reference panel for predicting HLA alleles, constructed with four collections of individuals of north-western European, northern Han Chinese, cosmopolitan Japanese and Yoruba Nigerian ancestry. Owing to complex patterns of linkage disequilibrium in this region, it is unclear whether the HapMap reference panels can be appropriately utilized for other populations. Here, we describe a public resource for the Singapore Genome Variation Project with: (i) dense genotyping across ∼ 9000 SNPs in the MHC; (ii) four-digit HLA typing for eight Class I and Class II loci, in 96 southern Han Chinese, 89 Southeast Asian Malays and 83 Tamil Indians. This resource provides population estimates of the frequencies of HLA alleles at these eight loci in the three population groups, particularly for HLA-DPA1 and HLA-DPB1 that were not assayed in HapMap. Comparing between population-specific reference panels and a cosmopolitan panel created from all four HapMap populations, we demonstrate that more accurate imputation is obtained with population-specific panels than with the cosmopolitan panel, especially for the Malays and Indians but even when imputing between northern and southern Han Chinese. As with SNP imputation, common HLA alleles were imputed with greater accuracy than low-frequency variants.

Deep whole-genome sequencing of 100 southeast Asian Malays.

Whole-genome sequencing across multiple samples in a population provides an unprecedented opportunity for comprehensively characterizing the polymorphic variants in the population. Although the 1000 Genomes Project (1KGP) has offered brief insights into the value of population-level sequencing, the low coverage has compromised the ability to confidently detect rare and low-frequency variants. In addition, the composition of populations in the 1KGP is not complete, despite the fact that the study design has been extended to more than 2,500 samples from more than 20 population groups. The Malays are one of the Austronesian groups predominantly present in Southeast Asia and Oceania, and the Singapore Sequencing Malay Project (SSMP) aims to perform deep whole-genome sequencing of 100 healthy Malays. By sequencing at a minimum of 30× coverage, we have illustrated the higher sensitivity at detecting low-frequency and rare variants and the ability to investigate the presence of hotspots of functional mutations. Compared to the low-pass sequencing in the 1KGP, the deeper coverage allows more functional variants to be identified for each person. A comparison of the fidelity of genotype imputation of Malays indicated that a population-specific reference panel, such as the SSMP, outperforms a cosmopolitan panel with larger number of individuals for common SNPs. For lower-frequency (<5%) markers, a larger number of individuals might have to be whole-genome sequenced so that the accuracy currently afforded by the 1KGP can be achieved. The SSMP data are expected to be the benchmark for evaluating the value of deep population-level sequencing versus low-pass sequencing, especially in populations that are poorly represented in population-genetics studies.

Evaluation of Equations for Predicting 24-Hour Urinary Sodium Excretion from Casual Urine Samples in Asian Adults.

BACKGROUND: The collection of 24-h urine samples for the estimation of sodium intake is burdensome, and the utility of spot urine samples in Southeast Asian populations is unclear. OBJECTIVE: We aimed to assess the validity of prediction equations with the use of spot urine concentrations. METHODS: A sample of 144 Singapore residents of Chinese, Malay, and Indian ethnicity aged 18-79 y were recruited from the Singapore Health 2 Study conducted in 2014. Participants collected urine for 24 h in multiple small bottles on a single day. To determine the optimal collection time for a spot urine sample, a 1-mL sample was taken from a random bottle collected in the morning, afternoon, and evening. Published equations and a newly derived equation were used to predict 24-h sodium excretion from spot urine samples. RESULTS: The mean ± SD concentration of sodium from the 24-h urine sample was 125 ± 53.4 mmol/d, which is equivalent to 7.2 ± 3.1 g salt. Bland-Altman plots showed good agreement at the group level between estimated and actual 24-h sodium excretion, with biases for the morning period of -3.5 mmol (95% CI: -14.8, 7.8 mmol; new equation) and 1.46 mmol (95% CI: -10.0, 13.0 mmol; Intersalt equation). A larger bias of 25.7 mmol (95% CI: 12.2, 39.3 mmol) was observed for the Tanaka equation in the morning period. The prediction accuracy did not differ significantly for spot urine samples collected at different times of the day or at a random time of day (P = 0.11-0.76). CONCLUSION: This study suggests that the application of both our own newly derived equation and the Intersalt equation to spot urine concentrations may be useful in predicting group means for 24-h sodium excretion in urban Asian populations.

Comparison of tet(X4)-containing contigs assembled from metagenomic sequencing data with plasmid sequences of isolates from a cohort of healthy subjects.

Recently discovered tet(X) gene variants have provided new insights into microbial antibiotic resistance mechanisms and their potential consequences for public health. This study focused on detection, analysis, and characterization of Tet(X4)-positive Enterobacterales from the gut microbiota of a healthy cohort of individuals in Singapore using cultivation-dependent and cultivation-independent approaches. Twelve Tet(X4)-positive Enterobacterales strains that were previously obtained from the cohort were fully genome-sequenced and comparatively analyzed. A metagenomic sequencing (MS) data set of the same samples was mined for contigs that harbored the tet(X4) resistance gene. The sequences of tet(X4)-containing contigs and plasmids sequences were compared. The presence of the resistance genes floR and estT (previously annotated as catD) was detected in the same cassette in 10 and 12 out of the 12 tet(X4)-carrying plasmids, respectively. MS detected tet(X4)-containing contigs in 2 out of the 109 subjects, while cultivation-dependent analysis previously reported a prevalence of 10.1%. The tet(X4)-containing sequences assembled from MS data are relatively short (~14 to 33 kb) but show high similarity to the respective plasmid sequences of the isolates. Our findings show that MS can complement efforts in the surveillance of antibiotic resistance genes for clinical samples, while it has a lower sensitivity than a cultivation-based method when the target organism has a low abundance. Further optimization is required if MS is to be utilized in antibiotic resistance surveillance.IMPORTANCEThe global rise in antibiotic resistance makes it necessary to develop and apply new approaches to detect and monitor the prevalence of antibiotic resistance genes in human populations. In this regard, of particular interest are resistances against last-resort antibiotics, such as tigecycline. In this study, we show that metagenomic sequencing can help to detect high abundance of the tigecycline resistance gene tet(X4) in fecal samples from a cohort of healthy human subjects. However, cultivation-based approaches currently remain the most reliable and cost-effective method for detection of antibiotic-resistant bacteria.

Mutual Exclusion of Methanobrevibacter Species in the Human Gut Microbiota Facilitates Directed Cultivation of a Candidatus Methanobrevibacter Intestini Representative.

Methanogenic Archaea (methanogens) are a phylogenetically diverse group of microorganisms and are considered to be the most abundant archaeal representatives in the human gut. However, the gut methanogen diversity of human populations in many global regions remains poorly investigated. Here, we report the abundance and diversity of gut methanogenic Archaea in a multi-ethnic cohort of healthy Singaporeans by using a concerted approach of metagenomic sequencing, 16S rRNA gene amplicon sequencing, and quantitative PCR. Our results indicate a mutual exclusion of Methanobrevibacter species, i.e., the highly prevalent Methanobrevibacter smithii and the less prevalent Candidatus Methanobrevibacter intestini in more than 80% of the samples when using an amplicon sequencing-based approach. Leveraging on this finding, we were able to select a fecal sample to isolate a representative strain, TLL-48-HuF1, for Candidatus Methanobrevibacter intestini. The analyzed physiological parameters of M. smithii DSM 861T and strain TLL-48-HuF1 suggest high similarity of the two species. Comparative genome analysis and the mutual exclusion of the Methanobrevibacter species indicate potentially different niche adaptation strategies in the human host, which may support the designation of Candidatus M. intestini as a novel species. IMPORTANCE Methanogens are important hydrogen consumers in the gut and are associated with differing host health. Here, we determine the prevalence and abundance of archaeal species in the guts of a multi-ethnic cohort of healthy Singapore residents. While Methanobrevibacter smithii is the most prevalent and abundant methanogen in the human gut of local subjects, the recently proposed Candidatus Methanobrevibacter intestini is the abundant methanogen in a minority of individuals that harbor them. The observed potential mutual exclusion of M. smithii and Ca. M. intestini provides further support to the proposal that the two physiologically similar strains may belong to different Methanobrevibacter species.

Contrasting SARS-CoV-2 epidemics in Singapore: cohort studies in migrant workers and the general population.

IMPORTANCE: Since January 2020, Singapore has implemented comprehensive measures to suppress SARS-CoV-2. Despite this, the country has experienced contrasting epidemics, with limited transmission in the community and explosive outbreaks in migrant worker dormitories. OBJECTIVE: To estimate SARS-CoV-2 infection incidence among migrant workers and the general population in Singapore. DESIGN: Prospective serological cohort studies. SETTING: Two cohort studies - in a migrant worker dormitory and in the general population in Singapore. PARTICIPANTS: 478 residents of a SARS-CoV-2-affected migrant worker dormitory were followed up between May and July 2020, with blood samples collected on recruitment and after 2 and 6 weeks. In addition, 937 community-dwelling adult Singapore residents, for whom pre-pandemic sera were available, were recruited. These individuals also provided a serum sample on recruitment in November/December 2020. EXPOSURE: Exposure to SARS-CoV-2 in a densely populated migrant worker dormitory and in the general population. MAIN OUTCOMES AND MEASURES: The main outcome measures were the incidences of SARS-CoV-2 infection in migrant workers and in the general population, as determined by the detection of neutralizing antibodies against SARS-CoV-2, and adjusting for assay sensitivity and specificity using a Bayesian modeling framework. RESULTS: No evidence of community SARS-CoV-2 exposure was found in Singapore prior to September 2019. It was estimated that < 2 per 1000 adult residents in the community were infected with SARS-CoV-2 in 2020 (cumulative seroprevalence: 0.16%; 95% CrI: 0.008-0.72%). Comparison with comprehensive national case notification data suggested that around 1 in 4 infections in the general population were associated with symptoms. In contrast, in the migrant worker cohort, almost two-thirds had been infected by July 2020 (cumulative seroprevalence: 63.8%; 95% CrI: 57.9-70.3%); no symptoms were reported in almost all of these infections. CONCLUSIONS AND RELEVANCE: Our findings demonstrate that SARS-CoV-2 suppression is possible with strict and rapid implementation of border restrictions, case isolation, contact tracing, quarantining, and social-distancing measures. However, the risk of large-scale epidemics in densely populated environments requires specific consideration in preparedness planning. Prioritization of these settings in vaccination strategies should minimize the risk of future resurgences and potential spillover of transmission to the wider community.

Genome-centric analysis of short and long read metagenomes reveals uncharacterized microbiome diversity in Southeast Asians.

Despite extensive efforts to address it, the vastness of uncharacterized 'dark matter' microbial genetic diversity can impact short-read sequencing based metagenomic studies. Population-specific biases in genomic reference databases can further compound this problem. Leveraging advances in hybrid assembly (using short and long reads) and Hi-C technologies in a cross-sectional survey, we deeply characterized 109 gut microbiomes from three ethnicities in Singapore to comprehensively reconstruct 4497 medium and high-quality metagenome assembled genomes, 1708 of which were missing in short-read only analysis and with >28× N50 improvement. Species-level clustering identified 70 (>10% of total) novel gut species out of 685, improved reference genomes for 363 species (53% of total), and discovered 3413 strains unique to these populations. Among the top 10 most abundant gut bacteria in our study, one of the species and >80% of strains were unrepresented in existing databases. Annotation of biosynthetic gene clusters (BGCs) uncovered more than 27,000 BGCs with a large fraction (36-88%) unrepresented in current databases, and with several unique clusters predicted to produce bacteriocins that could significantly alter microbiome community structure. These results reveal significant uncharacterized gut microbial diversity in Southeast Asian populations and highlight the utility of hybrid metagenomic references for bioprospecting and disease-focused studies.

Cancer Screening Knowledge and Behavior in a Multi-Ethnic Asian Population: The Singapore Community Health Study.

BACKGROUND: Cancer has become the leading cause of mortality in Singapore and among other Asian populations worldwide. Despite the presence of National Cancer Screening programmes in Singapore, less than half of the population has had timely screening according to guidelines. The underlying factors of poor cancer screening rates and health outcomes among Asian ethnic groups remain poorly understood. We therefore examined cancer screening participation rates and screening behavior in a multi-ethnic Singapore population. METHODS: We collected data from 7,125 respondents of the 2015-2016 Singapore Community Health Study. Factors associated with cervical, breast, and colorectal cancer screening were evaluated using modified Poisson regression. Adjusted prevalence ratios were computed with 95% confidence intervals after adjusting for confounders. RESULTS: The mean age of the respondents was 57.7 ± 10.9 years; 58.9% were female and were predominately Chinese (73.0%), followed by Malay (14.2%), and Indian (10.9%). Less than half of the respondents in the recommended age groups had undergone cancer screening (cervical, 43%; breast, 35.1%; colorectal, 27.3%). Malay respondents were significantly less likely to screen as recommended for cervical (aPR = 0.75, CI = 0.65-0.86, p < 0.001), breast (aPR = 0.83, CI = 0.68-0.99, p = 0.045), and colorectal cancer (aPR = 0.55, CI = 0.44-0.68, p < 0.001), as compared to Chinese respondents. Respondents who had obtained lower secondary level education were 42% more likely to screen for cervical cancer (aPR = 1.42, CI = 1.23-1.64, p < 0.001), and 22% more likely to screen for breast cancer (aPR = 1.22, CI = 1.02-1.46, p = 0.032), compared to those with primary level education and below. Respondents with a household income ≥S$10,000/month were 71% more likely to screen for breast cancer (aPR = 1.71, CI = 1.37-2.13, p < 0.001), as compared with <$2,000/month. CONCLUSIONS: Ethnicity and socio-economic status were significantly associated with lower uptake of cancer screening tests in Singapore. To improve the screening uptake among disadvantaged groups, a multi-faceted approach is needed that addresses the barriers to screening such as the adequacy of subsidy schemes and ethnic differences.

Highly functional virus-specific cellular immune response in asymptomatic SARS-CoV-2 infection.

The efficacy of virus-specific T cells in clearing pathogens involves a fine balance between antiviral and inflammatory features. SARS-CoV-2-specific T cells in individuals who clear SARS-CoV-2 without symptoms could reveal nonpathological yet protective characteristics. We longitudinally studied SARS-CoV-2-specific T cells in a cohort of asymptomatic (n = 85) and symptomatic (n = 75) COVID-19 patients after seroconversion. We quantified T cells reactive to structural proteins (M, NP, and Spike) using ELISpot and cytokine secretion in whole blood. Frequencies of SARS-CoV-2-specific T cells were similar between asymptomatic and symptomatic individuals, but the former showed an increased IFN-γ and IL-2 production. This was associated with a proportional secretion of IL-10 and proinflammatory cytokines (IL-6, TNF-α, and IL-1ß) only in asymptomatic infection, while a disproportionate secretion of inflammatory cytokines was triggered by SARS-CoV-2-specific T cell activation in symptomatic individuals. Thus, asymptomatic SARS-CoV-2-infected individuals are not characterized by weak antiviral immunity; on the contrary, they mount a highly functional virus-specific cellular immune response.

Association Between Self-Reported Eating Rate, Energy Intake, and Cardiovascular Risk Factors in a Multi-Ethnic Asian Population.

Eating faster is associated with greater body mass index (BMI), but less is known about the relationships between eating rate, energy intake, body composition, and cardio-metabolic risk factors in different Asian ethnic groups. Using data from the Singapore Multi-Ethnic Cohort (n = 7011; 21-75 y), we investigated associations between self-reported eating rate (SRER), with energy intake, body composition, blood pressure, and blood lipids. SRER and lifestyle was assessed using interviewer-administered questionnaires. Multivariable models were used to examine the associations of SRER with energy intake, body composition, blood pressure, and blood lipids after adjusting for covariates. General and abdominal overweight were defined as BMI ≥ 23 kg/m2 and waist circumference > 90cm (men) and > 80cm (women), respectively. On average, faster eaters (vs. slower eaters) consumed 105kcal/day more (p = 0.034), had ~5kg higher body weight (p < 0.001), 1.3 kg/m2 higher BMI (p < 0.001), and 3.1cm larger waist-circumference (p < 0.001). Faster eaters had significantly higher blood pressure, circulating triglycerides, and total-to-high-density lipoprotein cholesterol ratio than slower eaters. Faster eaters were twice as likely to develop general (multivariable-OR: 2.2;95%CI,1.8-2.6; p < 0.001), and abdominal (OR:1.8;95%CI, 1.5-2.2; p < 0.001) overweight than slower eaters. This association was observed across all subgroups by age, sex, and ethnicity. Findings suggest that SRER is a robust behavioral marker for increased risk of higher energy intake, obesity, and poor cardio-metabolic health, and a modifiable behavioral risk-factor for obesity prevention.

Cohort profile: the Singapore diabetic cohort study.

PURPOSE: The diabetic cohort (DC) was set up to study the determinants of complications in individuals with type 2 diabetes and examine the role of genetic, physiological and lifestyle factors in the development of complications in these individuals. PARTICIPANTS: A total of 14 033 adult participants with type 2 diabetes were recruited from multiple public sector polyclinics and hospital outpatient clinics in Singapore between November 2004 and November 2010. The first round of follow-up was conducted for 4131 participants between 2012 and 2016; the second round of follow-up started in 2016 and is expected to end in 2021. A questionnaire survey, physical assessments, blood and urine sample collection were conducted at recruitment and each follow-up visit. The data set also includes genetic data and linkage to medical and administrative records for recruited participants. FINDINGS TO DATE: Data from the cohort have been used to identify determinants of diabetes and related complications. The longitudinal data of medical records have been used to analyse diabetes control over time and its related outcomes. The cohort has also contributed to the identification of genetic loci associated with type 2 diabetes and diabetic kidney disease in collaboration with other large cohort studies. About 25 scientific papers based on the DC data have been published up to May 2019. FUTURE PLANS: The rich data in DC can be used for various types of research to study disease-related complications in patients with type 2 diabetes. We plan to further investigate disease progression and new biomarkers for common diabetic complications, including diabetic kidney disease and diabetic neuropathy.