Documenting elimination of co-circulating COVID-19 clusters using genomics in New South Wales, Australia.

OBJECTIVE: To adapt 'fishplots' to describe real-time evolution of SARS-CoV-2 genomic clusters. RESULTS: This novel analysis adapted the fishplot to depict the size and duration of circulating genomic clusters over time in New South Wales, Australia. It illuminated the effectiveness of interventions on the emergence, spread and eventual elimination of clusters and distilled genomic data into clear information to inform public health action.

Cholera outbreak in Forcibly Displaced Myanmar National (FDMN) from a small population segment in Cox's Bazar, Bangladesh, 2019.

BACKGROUND: Bangladesh experienced a sudden, large influx of forcibly displaced persons from Myanmar in August 2017. A cholera outbreak occurred in the displaced population during September-December 2019. This study aims to describe the epidemiologic characteristics of cholera patients who were hospitalized in diarrhea treatment centers (DTCs) and sought care from settlements of Forcibly Displaced Myanmar Nationals (FDMN) as well as host country nationals during the cholera outbreak. METHODS: Diarrhea Treatment Center (DTC) based surveillance was carried out among the FDMN and host population in Teknaf and Leda DTCs hospitalized for cholera during September-December 2019. RESULTS: During the study period, 147 individuals with cholera were hospitalized. The majority, 72% of patients reported to Leda DTC. Nearly 65% sought care from FDMN settlements. About 47% of the cholera individuals were children less than 5 years old and 42% were aged 15 years and more. Half of the cholera patients were females. FDMN often reported from Camp # 26 (45%), followed by Camp # 24 (36%), and Camp # 27 (12%). Eighty-two percent of the cholera patients reported watery diarrhea. Some or severe dehydration was observed in 65% of cholera individuals. Eighty-one percent of people with cholera received pre-packaged ORS at home. About 88% of FDMN cholera patients reported consumption of public tap water. Pit latrine without water seal was often used by FDMN cholera individuals (78%). CONCLUSION: Vigilance for cholera patients by routine surveillance, preparedness, and response readiness for surges and oral cholera vaccination campaigns can alleviate the threats of cholera.

An outbreak of acute jaundice syndrome (AJS) among the Rohingya refugees in Cox's Bazar, Bangladesh: Findings from enhanced epidemiological surveillance.

In the summer of 2017, an estimated 745,000 Rohingya fled to Bangladesh in what has been described as one of the largest and fastest growing refugee crises in the world. Among numerous health concerns, an outbreak of acute jaundice syndrome (AJS) was detected by the disease surveillance system in early 2018 among the refugee population. This paper describes the investigation into the increase in AJS cases, the process and results of the investigation, which were strongly suggestive of a large outbreak due to hepatitis A virus (HAV). An enhanced serological investigation was conducted between 28 February to 26 March 2018 to determine the etiologies and risk factors associated with the outbreak. A total of 275 samples were collected from 18 health facilities reporting AJS cases. Blood samples were collected from all patients fulfilling the study specific case definition and inclusion criteria, and tested for antibody responses using enzyme-linked immunosorbent assay (ELISA). Out of the 275 samples, 206 were positive for one of the agents tested. The laboratory results confirmed multiple etiologies including 154 (56%) samples tested positive for hepatitis A, 1 (0.4%) positive for hepatitis E, 36 (13%) positive for hepatitis B, 25 (9%) positive for hepatitis C, and 14 (5%) positive for leptospirosis. Among all specimens tested 24 (9%) showed evidence of co-infections with multiple etiologies. Hepatitis A and E are commonly found in refugee camps and have similar clinical presentations. In the absence of robust testing capacity when the epidemic was identified through syndromic reporting, a particular concern was that of a hepatitis E outbreak, for which immunity tends to be limited, and which may be particularly severe among pregnant women. This report highlights the challenges of identifying causative agents in such settings and the resources required to do so. Results from the month-long enhanced investigation did not point out widespread hepatitis E virus (HEV) transmission, but instead strongly suggested a large-scale hepatitis A outbreak of milder consequences, and highlighted a number of other concomitant causes of AJS (acute hepatitis B, hepatitis C, Leptospirosis), albeit most likely at sporadic level. Results strengthen the need for further water and sanitation interventions and are a stark reminder of the risk of other epidemics transmitted through similar routes in such settings, particularly dysentery and cholera. It also highlights the need to ensure clinical management capacity for potentially chronic conditions in this vulnerable population.

An outbreak investigation of scrub typhus in Western Province, Solomon Islands, 2014.

OBJECTIVE: To identify the etiology and risk factors of undifferentiated fever in a cluster of patients in Western Province, Solomon Islands, May 2014. METHODS: An outbreak investigation with a case control study was conducted. A case was defined as an inpatient in one hospital in Western Province, Solomon Islands with high fever (> 38.5 °C) and a negative malaria microscopy test admitted between 1 and 31 May 2014. Asymptomatic controls matched with the cases residentially were recruited in a ratio of 1:2. Serum samples from the subjects were tested for rickettsial infections using indirect micro-immunofluorescence assay. RESULTS: Nine cases met the outbreak case definition. All cases were male. An eschar was noted in five cases (55%), and one developed pneumonitis. We did not identify any environmental factors associated with illness. Serum samples of all five follow-up cases (100%) had strong-positive IgG responses to scrub typhus. All but one control (10%) had a moderate response against scrub typhus. Four controls had low levels of antibodies against spotted fever group rickettsia, and only one had a low-level response to typhus group rickettsia. DISCUSSION: This outbreak represents the first laboratory-confirmed outbreak of scrub typhus in the Western Province of Solomon Islands. The results suggest that rickettsial infections are more common than currently recognized as a cause of an acute febrile illness. A revised clinical case definition for rickettsial infections and treatment guidelines were developed and shared with provincial health staff for better surveillance and response to future outbreaks of a similar kind.

An outbreak investigation of congenital rubella syndrome in Solomon Islands, 2013.

INTRODUCTION: During May 2012, a rubella outbreak was declared in Solomon Islands. A suspected case of congenital rubella syndrome (CRS) was reported from one hospital 11 months later in 2013. This report describes the subsequent CRS investigation, findings and measures implemented. METHODS: Prospective CRS surveillance was conducted at the newborn nursery, paediatric and post-natal wards, and the paediatric cardiology and ophthalmology clinics of the study hospital from April to July 2013. Retrospective case finding by reviewing medical records was also undertaken to identify additional cases born between January and March 2013 for the same wards and clinics. Cases were identified using established World Health Organization case definitions for CRS. RESULTS: A total of 13 CRS cases were identified, including two laboratory-confirmed, four clinically confirmed and seven suspected cases. Five CRS cases were retrospectively identified, including four suspected and one clinically confirmed case. There was no geospatial clustering of residences. The mothers of the cases were aged between 20 and 36 years. Three of the six mothers available for interview recalled an acute illness with rash during the first trimester of pregnancy. DISCUSSION: Additional CRS cases not captured in this investigation are likely. Caring for CRS cases is a challenge in resource-poor settings. Rubella vaccination is safe and effective and can prevent the serious consequences of CRS. Well planned and funded vaccination activities can prevent future CRS cases.

Vector-control response in a post-flood disaster setting, Honiara, Solomon Islands, 2014.

PROBLEM: The close quartering and exposed living conditions in evacuation centres and the potential increase in vector density after flooding in Solomon Islands resulted in an increased risk of exposure for the occupants to vectorborne diseases. CONTEXT: In April 2014, Solomon Islands experienced a flash flooding event that affected many areas and displaced a large number of people. In the capital, Honiara, nearly 10 000 people were housed in emergency evacuation centres at the peak of the post-flood emergency. At the time of the floods, the number of dengue cases was increasing, following a record outbreak in 2013. ACTION: The National Vector Borne Disease Control Programme with the assistance of the World Health Organization implemented an emergency vector-control response plan to provide protection to the at-risk populations in the evacuation centres. The National Surveillance Unit also activated an early warning disease surveillance system to monitor communicable diseases, including dengue and malaria. OUTCOME: Timely and strategic application of the emergency interventions probably prevented an increase in dengue and malaria cases in the affected areas. DISCUSSION: Rapid and appropriate precautionary vector-control measures applied in a post-natural disaster setting can prevent and mitigate vectorborne disease incidences. Collecting vector surveillance data allows better analysis of vector-control operations' effectiveness.

Increased Rotavirus Prevalence in Diarrheal Outbreak Precipitated by Localized Flooding, Solomon Islands, 2014.

Flooding on 1 of the Solomon Islands precipitated a nationwide epidemic of diarrhea that spread to regions unaffected by flooding and caused >6,000 cases and 27 deaths. Rotavirus was identified in 38% of case-patients tested in the city with the most flooding. Outbreak potential related to weather reinforces the need for global rotavirus vaccination.

Salmonella Typhimurium and Outbreaks of Egg-Associated Disease in Australia, 2001 to 2011.

INTRODUCTION: Salmonellosis is a significant public health problem, with eggs frequently identified as a food vehicle during outbreak investigations. Salmonella enterica serovar Typhimurium and Salmonella enterica serovar Enteritidis are the two most frequently identified causes of egg-associated disease in industrialized countries. In Australia, a comprehensive review of egg-associated outbreaks has not been previously undertaken. METHODS: Using a national register of foodborne outbreaks, we undertook a descriptive review of egg-associated outbreaks between 2001 and 2011. Included in our review was additional detail from the findings of trace back investigations conducted to the farm level. Evidence classifications were developed and applied to each outbreak based on descriptive and analytical epidemiology, food safety investigations, and microbiological testing of clinical, food, and trace back-derived samples. RESULTS: Over the study period, the proportion of foodborne Salmonella outbreaks linked to eggs increased significantly (p < 0.001). In total, 166 outbreaks were identified, with 90% caused by Salmonella Typhimurium. The majority of outbreaks were linked to commercial food providers, with raw egg use the major contributing factor. These events resulted in more than 3200 cases, more than 650 hospitalizations, and at least 4 deaths. Fifty-four percent of investigations used analytical epidemiology, food microbiology, and trace back microbiology to demonstrate links between human illness and eggs. Trace back investigations identified S. enterica indistinguishable from outbreak-associated clinical or food samples on 50% of sampled egg farms. CONCLUSION: Effective control of egg-associated salmonellosis remains a challenge in Australia, with Salmonella Typhimurium dominating as the causative serotype in outbreak events. Although outbreaks predominantly occur in the settings of restaurants, the high recovery rate of indistinguishable Salmonella on epidemiologically implicated egg farms suggests that further efforts to minimize infection pressure at the primary production level are needed in Australia.

Parechovirus Genotype 3 Outbreak among Infants, New South Wales, Australia, 2013-2014.

From October 2013 through February 2014, human parechovirus genotype 3 infection was identified in 183 infants in New South Wales, Australia. Of those infants, 57% were male and 95% required hospitalization. Common signs and symptoms were fever >38°C (86%), irritability (80%), tachycardia (68%), and rash (62%). Compared with affected infants in the Northern Hemisphere, infants in New South Wales were slightly older, both sexes were affected more equally, and rash occurred with considerably higher frequency. The New South Wales syndromic surveillance system, which uses near real-time emergency department and ambulance data, was useful for monitoring the outbreak. An alert distributed to clinicians reduced unnecessary hospitalization for patients with suspected sepsis.

Mass poisoning after consumption of a hawksbill turtle, Federated States of Micronesia, 2010.

BACKGROUND: Marine turtles of all species are capable of being toxic. On 17 October 2010, health authorities in the Federated States of Micronesia were notified of the sudden death of three children and the sickening of approximately 20 other people on Murilo Atoll in Chuuk State. The illnesses were suspected to be the result of mass consumption of a hawksbill turtle (Eretmochelys imbricata). An investigation team was assembled to confirm the cause of the outbreak, describe the epidemiology of cases and provide recommendations for control. METHODS: We conducted chart reviews, interviewed key informants, collected samples for laboratory analysis, performed environmental investigations and conducted a cohort study. RESULTS: Four children and two adults died in the outbreak and 95 others were sickened; 84% of those who ate the turtle became ill (n = 101). The relative risk for developing illness after consuming the turtle was 11.1 (95% confidence inteval: 4.8-25.9); there was a dose-dependent relationship between amount of turtle meat consumed and risk of illness. Environmental and epidemiological investigations revealed no alternative explanation for the mass illness. Laboratory testing failed to identify a causative agent. CONCLUSION: We concluded that turtle poisoning (also called chelonitoxism) was the cause of the outbreak on Murilo. The range of illness described in this investigation is consistent with previously reported cases of chelonitoxism. This devastating incident highlights the dangers, particularly to children, of consuming turtle meat. Future incidents are certain to occur unless action is taken to alter turtle-eating behaviour in coastal communities throughout the world.

Proportion of illness acquired by foodborne transmission for nine enteric pathogens in Australia: an expert elicitation.

BACKGROUND: Estimates of the burden of illness acquired from food inform public health policy and prioritize interventions. A key component of such estimates is the proportion of illnesses that are acquired by foodborne transmission. In view of the shortage of requisite data, these proportions are commonly obtained through a process known as expert elicitation. We report findings from an elicitation process used to assess the importance of the foodborne transmission route for nine pathogens in Australia, circa 2010. MATERIALS AND METHODS: Eleven experts were asked to estimate the proportion of illness acquired by five transmission routes: food, environmental, water, person, and zoonotic, together with a 90% certainty interval for foodborne transmission. Foodborne estimates and intervals from each expert were combined using both modified triangular and Program Evaluation and Review Technique (PERT) distributions, in @Risk version 6, to generate final distributions from which median estimates and 95% Credible Intervals (CrI) were calculated. RESULTS: Shiga toxin-producing Escherichia coli (STEC) was the only pathogen believed to have an important zoonotic transmission route, while norovirus, hepatitis A virus, non-STEC pathogenic E. coli, and Shigella spp. were all thought to be primarily spread from person to person. Foodborne transmission was the main route for Clostridium perfringens (98%, CrI: 84-100), Listeria monocytogenes (98%, CrI: 86-100), nontyphoidal Salmonella spp. (72%, CrI: 50-87), and Campylobacter spp. (77%, CrI: 60-90). Foodborne estimates using the modified triangular distribution had wider CrI than these calculated using the PERT distribution. CONCLUSIONS: Foodborne proportions for most pathogens in this study were the same or lower than those estimated circa 2000 in Australia, with the greatest decline for non-STEC pathogenic E. coli. Inclusion of certainty intervals from experts helps to quantify the precision of foodborne proportions. A decline in estimates of the foodborne proportion for common pathogens will influence final estimates of the burden of illness acquired from food.

Ongoing outbreak of dengue serotype-3 in Solomon Islands, January to May 2013.

INTRODUCTION: In January 2013, clinicians in Honiara, Solomon Islands noted several patients presenting with dengue-like illness. Serum from three cases tested positive for dengue by rapid diagnostic test. Subsequent increases in cases were reported, and the outbreak was confirmed as being dengue serotype-3 by further laboratory tests. This report describes the ongoing outbreak investigation, findings and response. METHODS: Enhanced dengue surveillance was implemented in the capital, Honiara, and in the provinces. This included training health staff on dengue case definitions, data collection and reporting. Vector surveillance was also conducted. RESULTS: From 3 January to 15 May 2013, 5254 cases of suspected dengue were reported (101.8 per 10 000 population), including 401 hospitalizations and six deaths. The median age of cases was 20 years (range zero to 90), and 86% were reported from Honiara. Both Aedes aegyti and Aedes albopictus were identified in Honiara. Outbreak response measures included clinical training seminars, vector control activities, implementation of diagnostic and case management protocols and a public communication campaign. DISCUSSION: This was the first large dengue outbreak documented in Solomon Islands. Factors that may have contributed to this outbreak include a largely susceptible population, the presence of a highly efficient dengue vector in Honiara, a high-density human population with numerous breeding sites and favourable weather conditions for mosquito proliferation. Although the number of cases has plateaued since 1 April, continued enhanced nationwide surveillance and response activities are necessary.

EpiReview: Typhoid fever, NSW, 2005-2011.

AIM: To examine trends in the incidence of typhoid fever in NSW to inform the development of prevention strategies. METHODS: Typhoid fever case notification data for the period 2005-2011 were extracted from the NSW Notifiable Conditions Information Management System. Population incidence rates were calculated and analysed by demographic variables. RESULTS: There were 250 case notifications of typhoid fever in NSW from 2005 to 2011, of which 240 are likely to have been acquired overseas. Case notifications remained relatively stable over the review period with the highest rates in Western Sydney Local Health District (10.9 per 100,000 population). Two-thirds (66.4%) of all case notifications are likely to have been acquired in South Asia, and about half of overseas-acquired case notifications were most likely to have been associated with travel to visit friends and relatives. Hospitalisation was required for 79.6% of cases where hospitalisation status was known. Prior typhoid vaccination was reported in 7% of cases in 2010 and 2011 where vaccination status was known. CONCLUSION: While typhoid fever rates remain low in NSW, case notifications of this preventable infection continue to be reported, particularly in travellers visiting friends and relatives in South Asia. Further research to better understand barriers to the use of preventive measures may be useful in targeting typhoid fever prevention messages in high-risk groups, particularly South Asian communities in NSW.

Influenza surveillance in the Pacific Island countries and territories during the 2009 pandemic: an observational study.

BACKGROUND: Historically, Pacific island countries and territories (PICTs) have been more severely affected by influenza pandemics than any other part of the world. We herein describe the emergence and epidemiologic characteristics of pandemic influenza H1N1 in PICTs from 2009 to 2010. METHODS: The World Health Organization gathered reports of influenza-like-illness and laboratory-confirmed pandemic H1N1 cases from all 23 Pacific island countries and territories, from April 2009 through August 2010. Data were gathered through weekly email reports from Pacific island countries and territories and through email or telephone follow-up. RESULTS: Pacific island countries and territories started detecting pandemic H1N1 cases in June 2009, firstly in French Polynesia, with the last new detection occurring in August 2009 in Tuvalu. Nineteen Pacific island countries and territories reported 1,972 confirmed cases, peaking in August 2009. No confirmed pandemic H1N1 cases were identified in Niue, Pitcairn and Tokelau; the latter instituted strict maritime quarantine. Influenza-like-illness surveillance showed trends similar to surveillance of confirmed cases.Seven Pacific island countries and territories reported 21 deaths of confirmed pandemic H1N1. Case-patients died of acute respiratory distress syndrome or multi-organ failure, or both. The most reported pre-existing conditions were obesity, lung disease, heart disease, and pregnancy.Pacific island countries and territories instituted a variety of mitigation measures, including arrival health screening. Multiple partners facilitated influenza preparedness planning and outbreak response. CONCLUSIONS: Pandemic influenza spread rapidly throughout the Pacific despite enormous distances and relative isolation. Tokelau and Pitcairn may be the only jurisdictions to have remained pandemic-free. Despite being well-prepared, Pacific island countries and territories experienced significant morbidity and mortality, consistent with other indigenous and low-resource settings.For the first time, regional influenza-like-illness surveillance was conducted in the Pacific, allowing health authorities to monitor the pandemic's spread and severity in real-time.Future regional outbreak responses will likely benefit from the lessons learned during this outbreak.

Pacific-wide simplified syndromic surveillance for early warning of outbreaks.

The International Health Regulations require timely detection and response to outbreaks. Many attempts to set up an outbreak early warning system in Pacific island countries and territories (PICTs) have failed. Most were modelled on systems from large countries; large amounts of data often overwhelmed small public health teams. Many conditions required overseas laboratory confirmation, further reducing timeliness and completeness. To improve timeliness and reduce the data burden, simplified surveillance was proposed, with case definitions based on clinical signs and symptoms without the need for laboratory confirmation or information on symptoms, location, sex and age. After trials in three PICTs, this system was implemented throughout the Pacific. Enthusiastic adoption by public health staff resulted in 20 of 22 PICTs reporting weekly to the World Health Organization within 12 months of starting to use the system. In the first year, the system has detected many infectious disease outbreaks and facilitated timely implementation of control measures. For several Pacific countries and territories, this is the first functional and timely infectious disease surveillance system. When outbreak detection is the principal objective, simplification of surveillance should be a priority in countries with a limited public health system capacity.

Salmonellosis outbreak traced to playground sand, Australia, 2007-2009.

A community outbreak of gastroenteritis in Australia during 2007-2009 was caused by ingestion of playground sand contaminated with Salmonella enterica Paratyphi B, variant Java. The bacterium was also isolated from local wildlife. Findings support consideration of nonfood sources during salmonellosis outbreak investigations and indicate transmission through the animal-human interface.

Improving resolution of public health surveillance for human Salmonella enterica serovar Typhimurium infection: 3 years of prospective multiple-locus variable-number tandem-repeat analysis (MLVA).

BACKGROUND: Prospective typing of Salmonella enterica serovar Typhimurium (STM) by multiple-locus variable-number tandem-repeat analysis (MLVA) can assist in identifying clusters of STM cases that might otherwise have gone unrecognised, as well as sources of sporadic and outbreak cases. This paper describes the dynamics of human STM infection in a prospective study of STM MLVA typing for public health surveillance. METHODS: During a three-year period between August 2007 and September 2010 all confirmed STM isolates were fingerprinted using MLVA as part of the New South Wales (NSW) state public health surveillance program. RESULTS: A total of 4,920 STM isolates were typed and a subset of 4,377 human isolates was included in the analysis. The STM spectrum was dominated by a small number of phage types, including DT170 (44.6% of all isolates), DT135 (13.9%), DT9 (10.8%), DT44 (4.5%) and DT126 (4.5%). There was a difference in the discriminatory power of MLVA types within endemic phage types: Simpson's index of diversity ranged from 0.109 and 0.113 for DTs 9 and 135 to 0.172 and 0.269 for DTs 170 and 44, respectively. 66 distinct STM clusters were observed ranging in size from 5 to 180 cases and in duration from 4 weeks to 25 weeks. 43 clusters had novel MLVA types and 23 represented recurrences of previously recorded MLVA types. The diversity of the STM population remained relatively constant over time. The gradual increase in the number of STM cases during the study was not related to significant changes in the number of clusters or their size. 667 different MLVA types or patterns were observed. CONCLUSIONS: Prospective MLVA typing of STM allows the detection of community outbreaks and demonstrates the sustained level of STM diversity that accompanies the increasing incidence of human STM infections. The monitoring of novel and persistent MLVA types offers a new benchmark for STM surveillance.A part of this study was presented at the MEEGID × (Molecular Epidemiology and Evolutionary Genetics of Infectious Diseases) Conference, 3-5 November 2010, Amsterdam, The Netherlands.