Epidemiological, Clinical, and Phylogenetic Characteristics of the First SARS-CoV-2 Transmission in a Nursing Home of Singapore: A Prospective Observational Investigation.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission has resulted in a significant burden among nursing home facilities globally. This prospective observational cohort study aims to define the potential sources of introduction and characteristics of SARS-CoV-2 transmission of the first nursing home facility in Singapore. An epidemiological serial point-prevalence survey of SARS-CoV-2 was conducted among 108 residents and 56 healthcare staff (HCS). In the current study, 14 (13%) residents and two (3.6%) HCS were diagnosed with coronavirus disease 2019 (COVID-19), with a case fatality rate (CFR) of 28.6% (4/14) among the residents. The median age of the infected residents was 86.5 [interquartile range (IQR) 78.5-88] and 85.7% were women. Five residents were symptomatic (35.7%) and the others were asymptomatic (64.3%). A higher proportion of residents who succumbed to COVID-19 had hypertension than those who recovered. The SARS-CoV-2 whole-genome sequencing showed lineage B.6 which is rare globally but common regionally during the early phase of the pandemic. Household transmission is a potential source of introduction into the nursing home, with at least six epidemiologically linked secondary cases. Male residents were less implicated due to the staff segregation plan by block. Among residents, a higher proportion of the non-survivors were asymptomatic and had hypertension compared with survivors.

Whole-genome sequencing of the rare Salmonella enterica serovar Anfo isolated from food handlers.

Field investigations were conducted after a small cluster of food poisoning involving six cases was reported. While no stool samples were available from the cases for microbiological testing, Salmonella species was found to be present in the stools of food handlers with gastroenteritis symptoms. Four Salmonella isolates recovered from the food handlers were retrospectively investigated at the genome level using whole-genome sequencing (WGS). WGS showed that S. Anfo (antigenic formulae 39:y:1,2), a rarely isolated serovar, caused infections in the food handlers. S. Anfo analysed in this study contained virulence factors required for causing disease. They did not contain any antibiotic resistance genes or plasmid. The epidemiologically related isolates differed to each other by a maximum of one single nucleotide polymorphism. WGS was useful in identifying rare Salmonella serovars and it is potentially more cost-effective than traditional serotyping methods. It can also confidently group epidemiologically related isolates belonging to S. Anfo.

Retrospective genome-wide comparisons of Salmonella enterica serovar Enteritidis from suspected outbreaks in Singapore.

The number of salmonellosis cases in Singapore has increased over the years. Salmonella enterica serovar Enteritidis has always been the most predominant serovar in the last five years. The National Public Health Laboratory assisted outbreak investigations by performing multilocus variable number tandem repeat analysis (MLVA) on isolates that were collected at the time of the investigations. Isolates were defined as belonging to a particular cluster if they had identical MLVA patterns. Whilst MLVA has been instrumental in outbreak investigations, it may not be useful when outbreaks are caused by an endemic MLVA type. In this study, we analysed 67 isolates from 12 suspected outbreaks with known epidemiological links to explore the use of next-generation sequencing (NGS) for defining outbreaks. We found that NGS can confidently group isolates into their respective outbreaks. The isolates from each suspected outbreak were closely related and differed by a maximum of 3 single nucleotide polymorphisms (SNPs). They were also clearly separated from isolates that belonged to different suspected outbreaks. This study provides an important insight and further evidence on the value of NGS for routine surveillance and outbreak detection of S. Enteritidis.

Melioidosis, Singapore, 2003-2014.

In contrast with northern Australia and Thailand, in Singapore the incidence of melioidosis and co-incidence of melioidosis and pneumonia have declined. Burkholderia pseudomallei deep abscesses increased 20.4% during 2003-2014. These trends could not be explained by the environmental and climatic factors conventionally ascribed to melioidosis.

Group B Streptococcus Serotype III Sequence Type 283 Bacteremia Associated with Consumption of Raw Fish, Singapore.

We conducted a retrospective study of 40 case-patients and 58 controls as part of a nationwide investigation of a group B Streptococcus outbreak in Singapore in 2015. Eating a Chinese-style raw fish dish (yusheng) was a major risk factor for bacteremia, particularly caused by serotype III sequence type 283.

Epidemic resurgence of dengue fever in Singapore in 2013-2014: A virological and entomological perspective.

BACKGROUND: Dengue resurged in Singapore during 2013-14, causing an outbreak with unprecedented number of cases in the country. In the present study, we summarise the epidemiological, virological and entomological findings gathered through the dengue surveillance programme and highlight the drivers of the epidemic. We also describe how the surveillance system facilitated the preparedness to moderate epidemic transmission of dengue in the country. METHODS: The case surveillance was based on a mandatory notification system that requires all medical practitioners to report clinically-suspected and laboratory-confirmed cases within 24 hours. The circulating Dengue virus (DENV) populations were monitored through an island wide virus surveillance programme aimed at determining the serotypes and genotypes of circulating virus strains. Entomological surveillance included adult Aedes surveillance as well as premise checks for larval breeding. RESULTS: A switch in the dominant serotype from DENV-2 to DENV-1 in March 2013 signalled a potential spike in cases, and the alert was corroborated by an increase in average Aedes house index. The alert triggered preparedness and early response to moderate the impending outbreak. The two-year outbreak led to 22,170 cases in 2013 and 18,338 in 2014, corresponding to an incidence rate of 410.6 and 335.0 per 100,000 population, respectively. DENV-1 was the dominant serotype in 2013 (61.7 %, n = 5,071) and 2014 (79.2 %, n = 5,226), contributed largely by a newly-introduced DENV-1 genotype III strain. The percentage of houses with Ae. aegypti breeding increased significantly (p < 0.001) from 2012 (annual average of 0.07 %) to 2013 (annual average of 0.14 %), followed by a drop in 2014 (annual average of 0.10 %). Aedes breeding data further showed a wide spread distribution of Ae. aegypti in the country that corresponded with the dengue case distribution pattern in 2013 and 2014. The adult Aedes data from 34 gravitrap sentinel sites revealed that approximately 1/3 of the monitored sites remained at high risk of DENV transmission in 2013. CONCLUSIONS: The culmination of the latest epidemic is likely to be due to a number of demographic, social, virological, entomological, immunological, climatic and ecological factors that contribute to DENV transmission. A multi-pronged approach backed by the epidemiological, virological and entomological understanding paved way to moderate the case burden through an integrated vector management approach.

Ministry of Health Clinical Practice Guidelines: Prevention, Diagnosis and Management of Tuberculosis.

The Ministry of Health (MOH) has developed the clinical practice guidelines on Prevention, Diagnosis and Management of Tuberculosis to provide doctors and patients in Singapore with evidence-based treatment for tuberculosis. This article reproduces the introduction and executive summary (with recommendations from the guidelines) from the MOH clinical practice guidelines on Prevention, Diagnosis and Management of Tuberculosis, for the information of SMJ readers. The chapters and page numbers mentioned in the reproduced extract refer to the full text of the guidelines, which are available from the Ministry of Health website: http://www.moh.gov.sg/content/moh_web/healthprofessionalsportal/doctors/guidelines/cpg_medical.html. The recommendations should be used with reference to the full text of the guidelines. Following this article are multiple choice questions based on the full text of the guidelines.

Progress towards measles elimination in Singapore.

OBJECTIVE: We describe the epidemiological trends of measles in Singapore in relation to its progress towards measles elimination and identify gaps in fulfilling the World Health Organization Western Pacific Regional Office regional measles elimination criteria. METHODS: Epidemiological data on measles maintained by the Communicable Diseases Division, Ministry of Health from 1981 to 2012 were collated and analysed. Data on measles vaccination coverage were obtained from the National Immunization Registry and School Health Services, Health Promotion Board. To assess the seroprevalence of the population, the findings of periodic seroepidemiological surveys on measles were traced and reviewed. FINDINGS: With the successful implementation of the National Childhood Immunization Programme using the monovalent measles vaccine, measles incidence declined from 88.5 cases per 100,000 in 1984 to 6.9 per 100,000 in 1991. Resurgences were observed in 1992, 1993 and 1997. A 'catch-up' vaccination programme using the trivalent measles, mumps and rubella (MMR) vaccine was conducted in 1997, followed by introduction of the two-dose vaccination schedule in January 1998. Measles incidence subsequently declined sharply to 2.9 per 100,000 in 1998. Vaccination coverage was maintained at 95% for the first dose and 92-94% for the second dose. Seroprevalence surveys showed seropositivity for measles IgG antibodies in over 95% of adults in 2004, and in 83.1% of children aged 1-17 years in 2008-2010. Sporadic cases with occasional clusters of two or more cases continued to occur among the unvaccinated population, especially children aged below 4 years. The predominant measles virus genotype has shifted from D9 to the B3 and G3 genotypes, which are endemic in neighbouring countries. CONCLUSION: Singapore has made good progress towards the elimination of endemic measles. To further eliminate sporadic cases of measles, the national immunisation schedule has recently been amended to vaccinate children with 2 doses of MMR vaccine before 2 years of age.

Influenza-associated hospitalizations, Singapore, 2004-2008 and 2010-2012.

Studies of influenza-associated hospitalizations in tropical settings are lacking. To increase understanding of the effect of influenza in Singapore, we estimated the age-specific influenza-associated hospitalizations for pneumonia and influenza during 2004-2008 and 2010-2012. The rate of hospitalization was 28.3/100,000 person-years during 2004-2008 and 29.6/100,000 person-years during 2010-2012. The age-specific influenza-associated hospitalization rates followed a J-shaped pattern: rates in persons >75 years of age and in children <6 months of age were >47 times and >26 times higher, respectively, than those for persons 25-44 years of age. Across all ages during these 2 study periods, ≈12% of the hospitalizations for pneumonia and influenza were attributable to influenza. The rates and proportions of hospitalizations for influenza, particularly among the very young and the elderly, are considerable in Singapore and highlight the importance of vaccination in protecting populations at risk.

The Singapore field epidemiology service: insights into outbreak management.

Field epidemiology involves the implementation of quick and targeted public health interventions with the aid of epidemiological methods. In this article, we share our practical experiences in outbreak management and in safeguarding the population against novel diseases. Given that cities represent the financial nexuses of the global economy, global health security necessitates the safeguard of cities against epidemic diseases. Singapore's public health landscape has undergone a systemic and irreversible shift with global connectivity, rapid urbanization, ecological change, increased affluence, as well as shifting demographic patterns over the past two decades. Concomitantly, the threat of epidemics, ranging from severe acute respiratory syndrome and influenza A (H1N1) to the resurgence of vector-borne diseases as well as the rise of modern lifestyle-related outbreaks, have worsened difficulties in safeguarding public health amidst much elusiveness and unpredictability. One critical factor that has helped the country overcome these innate and man-made public health vulnerabilities is the development of a resilient field epidemiology service, which includes our enhancement of surveillance and response capacities for outbreak management, and investment in public health leadership. We offer herein the Singapore story as a case study in meeting the challenges of disease control in our modern built environment.

Epidemiology and control of chikungunya fever in Singapore.

OBJECTIVES: We conducted an epidemiological review of the chikungunya fever situation in Singapore and described the measures taken to prevent the chikungunya virus from becoming entrenched in the tropical city-state. METHODS: All laboratory-confirmed cases and outbreak investigation reports maintained by the Communicable Diseases Division, Ministry of Health, and Aedes mosquito surveillance data obtained by the National Environment Agency during the period 2006 and 2009 were reviewed and analysed. RESULTS: Sporadic cases were imported into Singapore until the first local transmission occurred in an urban area where Aedes aegypti was the predominant vector. Subsequent introduction of a mutant viral strain (A226V) in early 2008 resulted in the rapid spread to suburban and rural areas where Aedes albopictus was the primary vector. 1072 cases including 812 (75.7%) indigenous cases were reported. The main sources of importation were India and Malaysia. Foreign contract workers were identified as high-risk for indigenous infections. CONCLUSIONS: The disease was successfully brought under control through aggressive vector control measures directed at A. albopictus. Although the incidence has sharply declined since January 2009, a high degree of vigilance is maintained to prevent a recurrence of epidemic transmission which can occur even with a well-established nationwide mosquito control programme.

Home air-conditioning, traffic exposure, and asthma and allergic symptoms among preschool children.

Epidemiological data suggest that traffic exposures can influence asthma and allergic symptoms among preschool children; however, there is no information on risk reduction via home air-conditioning (AC). The aim of this study is to evaluate the associations of self-reported traffic densities with asthma and allergic symptoms among preschool children and determine whether AC is an effect modifier. A cross-sectional study adopting an expanded and modified ISAAC--International Study of Asthma and Allergies in Childhood conducted on randomly selected 2994 children living in homes without any indoor risk factors. Specific information on demographics, indoor home risk factors, and traffic variables were obtained. Adjusted prevalence ratios (PR) and 95% confidence interval (CI) were determined by Cox proportional hazard regression model with assumption of a constant risk period controlled for covariates. We found dose-response significant relationships between validated self-reported traffic densities and asthma and rhinitis symptoms. Among children sleeping in non-air-conditioned homes, there were stronger associations between asthma and rhinitis symptoms studied. PRs for heavy traffic density were 2.06 for wheeze (95% CI 0.97-4.38), 2.89 for asthma (1.14-7.32), 1.73 for rhinitis (1.00-2.99), and 3.39 for rhinoconjunctivitis (1.24-9.27). There were no associations found for children sleeping in air-conditioned homes. Our results suggest that AC in the bedroom modifies the health effects of traffic among preschool children. This finding suggests that attention should also be paid to ventilation characteristics of the homes to remediate health-related traffic pollution problems.

An outbreak of gastroenteritis caused by Salmonella enterica serotype Enteritidis traced to cream cakes.

INTRODUCTION: This paper describes the epidemiological, microbiological and environmental investigations conducted during an outbreak of Salmonella gastroenteritis in Singapore. METHODS: A case-control study was undertaken to identify the vehicle of transmission. Microbiological testing was performed on faecal, food and environmental samples. Isolates of Salmonella were further characterized by phage typing and ribotyping. RESULTS: There were 216 gastroenteritis cases reported from 20 November to 4 December 2007. The causative agent was identified as Salmonella enterica subspecies enterica serotype Enteritidis for 14 out of 20 cases tested. The vehicle of transmission was traced to cream cakes produced by a bakery and sold at its retail outlets (P < 0.001, OR = 143.00, 95% Cl = 27.23-759.10). More than two-thirds of the 40 Salmonella strains isolated from hospitalized cases, food samples and asymptomatic food handlers were of phage type 1; the others reacted but did not conform to any phage type. The phage types correlated well with their unique antibiograms. The ribotype patterns of 22 selected isolates tested were highly similar, indicating genetic relatedness. The dendrogram of the strains from the outbreak showed distinct clustering and correlation compared to the non-outbreak strains, confirming a common source of infection. DISCUSSION: The cream cakes were likely contaminated by one of the ingredients used in the icing. Cross-contamination down the production line and subsequent storage of cakes at ambient temperatures for a prolonged period before consumption could have contributed to the outbreak.

An outbreak of gastroenteritis caused by Salmonella enterica serotype Enteritidis traced to cream cakes

Introduction:This paper describes the epidemiological, microbiological and environmental investigations conducted during an outbreak of Salmonella gastroenteritis in Singapore. Methods:A case-control study was undertaken to identify the vehicle of transmission. Microbiological testing was performed on faecal, food and environmental samples. Isolates of Salmonella were further characterized by phage typing and ribotyping. Results:There were 216 gastroenteritis cases reported from 20 November to 4 December 2007. The causative agent was identified as Salmonella enterica subspecies enterica serotype Enteritidis for 14 out of 20 cases tested. The vehicle of transmission was traced to cream cakes produced by a bakery and sold at its retail outlets ( P Salmonella strains isolated from hospitalized cases, food samples and asymptomatic food handlers were of phage type 1; the others reacted but did not conform to any phage type. The phage types correlated well with their unique antibiograms. The ribotype patterns of 22 selected isolates tested were highly similar, indicating genetic relatedness. The dendrogram of the strains from the outbreak showed distinct clustering and correlation compared to the non-outbreak strains, confirming a common source of infection. Discussion:The cream cakes were likely contaminated by one of the ingredients used in the icing. Cross-contamination down the production line and subsequent storage of cakes at ambient temperatures for a prolonged period before consumption could have resulted in the outbreak.

Entomologic and molecular investigation into Plasmodium vivax transmission in Singapore, 2009.

BACKGROUND: Singapore has been certified malaria free since November 1982 by the World Health Organization and despite occasional local transmission, the country has maintained the standing. In 2009, three clusters of malaria cases were reported in Singapore. METHODS: Epidemiological, entomological and molecular studies were carried out to investigate the three clusters, namely Mandai-Sungei Kadut, Jurong Island and Sembawang. RESULTS: A total of 29 malaria patients, with no recent travel history, were reported in the three clusters. Molecular analysis based on the msp3α and msp1 genes showed two independent local transmissions: one in Mandai-Sungei Kadut and another in Sembawang. Almost all cases within each cluster were epidemiologically linked. In Jurong Island cluster, epidemiological link remains uncertain, as almost all cases had a unique genetic profile. Only two cases shared a common profile and were found to be linked to the Mandai-Sungei Kadut cluster. Entomological investigation found Anopheles sinensis to be the predominant Anopheline in the two areas where local transmission of P. vivax was confirmed. Anopheles sinensis was found to be attracted to human bait and bites as early as 19:45 hrs. However, all Anopheles mosquitoes caught were negative for sporozoites and oocysts by dissection. CONCLUSION: Investigation of P. vivax cases from the three cluster areas confirmed the occurrence of local transmission in two areas. Although An. sinensis was the predominant Anopheline found in areas with confirmed transmission, the vector/s responsible for the outbreaks still remains cryptic.

Outbreak of novel influenza A (H1N1-2009) linked to a dance club.

INTRODUCTION: This paper describes the epidemiology and control of a community outbreak of novel influenza A (H1N1-2009) originating from a dance club in Singapore between June and July 2009. MATERIALS AND METHODS: Cases of novel influenza A (H1N1-2009) were confirmed using in-house probe-based real-time polymerase chain reaction (PCR). Contact tracing teams from the Singapore Ministry of Health obtained epidemiological information from all cases via telephone. RESULTS: A total of 48 cases were identified in this outbreak, of which 36 (75%) cases were patrons and dance club staff, and 12 (25%) cases were household members and social contacts. Mathematical modelling showed that this outbreak had a reproductive number of 1.9 to 2.1, which was similar to values calculated from outbreaks in naïve populations in other countries. CONCLUSION: This transmission risk occurred within an enclosed space with patrons engaged in intimate social activities, suggesting that dance clubs are places conducive for the spread of the virus.

International health regulations: lessons from the influenza pandemic in Singapore.

INTRODUCTION: Singapore's defense against imported novel influenza A (H1N1-2009) comprised public health measures in compliance with the World Health Organization's (WHO) International Health Regulations (IHR), 2005. We report herein on the epidemiology and control of the fi rst 350 cases notified between May and June 2009. MATERIALS AND METHODS: We investigated the fi rst 350 laboratory-confirmed cases of novel influenza A (H1N1-2009) identified from the healthcare institutions between 27 May and 25 June 2009. Epidemiological details of these cases were retrieved and analysed. Contact tracing and active case finding were also instituted for each reported case, and relevant particulars including flight information were provided to WHO and overseas counterparts. RESULTS: The fi rst 350 novel influenza A (H1N1-2009) cases comprised 221(63%) imported cases, 124 (35%) locally acquired cases and 5 (2%) cases with unknown source. The imported cases consisted of three waves involving the United States (US), Australia and Southeast Asia. In the fi rst wave, 11 (69%) of the 16 imported cases had visited the US within seven days prior to their onset of illness between 25 May and 4 June 2009. In the second wave, 20 (74%) of the 27 imported cases between 5 June and 12 June had travelled to Melbourne, Australia. In the third wave, 90 (51%) of the 178 imported cases between 13 June and 25 June were acquired from intra-regional travel in Southeast Asia. Specifically, 49 cases were from the Philippines and 40 (82%) of them had travelled to Manila. A total of 667 communications were effected through the IHR mechanism; a majority within 24 hours of disease notification. CONCLUSION: Singapore experienced an unprecedented need for international cooperation in surveillance and response to this novel Influenza A (H1N1-2009) pandemic. The IHR mechanism served as a useful channel to engage in regional cooperation concerning disease surveillance and data sharing, but requires improvement.

Dengue virus surveillance for early warning, Singapore.

In Singapore, after a major outbreak of dengue in 2005, another outbreak occurred in 2007. Laboratory-based surveillance detected a switch from dengue virus serotype 1 (DENV-1) to DENV-2. Phylogenetic analysis showed a clade replacement within DENV-2 cosmopolitan genotype, which accompanied the predominant serotype switch, and cocirculation of multiple genotypes of DENV-3.