Public health interventions successfully mitigated multiple incursions of SARS-CoV-2 Delta variant in the Australian Capital Territory.

The COVID-19 pandemic has presented a unique opportunity to understand how real-time pathogen genomics can be used for large-scale outbreak investigations. On 12 August 2021, the Australian Capital Territory (ACT) detected an incursion of the SARS-CoV-2 Delta (B.1.617.2) variant. Prior to this date, SARS-CoV-2 had been eliminated locally since 7 July 2020. Several public health interventions were rapidly implemented in response to the incursion, including a territory-wide lockdown and comprehensive contact tracing. The ACT has not previously used pathogen genomics at a population level in an outbreak response; therefore, this incursion also presented an opportunity to investigate the utility of genomic sequencing to support contact tracing efforts in the ACT. Sequencing of >75% of the 1793 laboratory-confirmed cases during the 3 months following the initial notification identified at least 13 independent incursions with onwards spread in the community. Stratification of cases by genomic cluster revealed that distinct cohorts were affected by the different incursions. Two incursions resulted in most of the community transmission during the study period, with persistent transmission in vulnerable sections of the community. Ultimately, both major incursions were successfully mitigated through public health interventions, including COVID-19 vaccines. The high rates of SARS-CoV-2 sequencing in the ACT and the relatively small population size facilitated detailed investigations of the patterns of virus transmission, revealing insights beyond those gathered from traditional contact tracing alone. Genomic sequencing was critical to disentangling complex transmission chains to target interventions appropriately.

Lessons from a COVID-19 outbreak in the disability support sector, Australian Capital Territory, August 2021.

Abstract: People with disability are at higher risk of severe outcomes from SARS-CoV-2 infection. Due to complex client needs and available staffing, disability support providers (DSP) were limited in their ability to mitigate the introduction of SARS-CoV-2 into disability support settings. This report describes the characteristics of a Delta variant outbreak associated with a single DSP in Canberra, Australian Capital Territory (ACT), in August 2021. We calculated attack rates for workplace exposure sites and households, using the number of people present at workplaces and households as the denominator. Thirty confirmed cases were identified, comprised of 13 support workers, six clients, and 11 household and other contacts. The median age of cases was 30.5 years (range 1 to 80 years) and 5 cases (17%) were hospitalised. No cases were admitted to an intensive care unit (ICU) or died. Twenty-two percent of people in close contact with confirmed SARS-CoV-2 cases in this cluster (23/103) subsequently tested positive to SARS-CoV-2. Investigations identified multiple primary cases, with one primary case the likely infection source for at least 17 other cases. Despite the majority being eligible for vaccination, only two cases were fully vaccinated (two doses > 14 days before exposure). The mean secondary attack rate at workplace sites (15% or 12/80 close contacts infected) was lower than the tertiary attack rate (47.8% or 11/23 close contacts infected). The overall risk of contracting SARS-CoV-2 in DSP-related work sites was lower than for household settings (relative risk: 0.42; 95% confidence interval: 0.21-0.82). These findings demonstrate the importance of ongoing collaboration between governments and the disability support sector. Development and delivery of targeted health messaging to people with disability and to disability support workers, regarding infection control in the home setting, and identification of enablers for vaccination, should be the highest priorities from this collaboration.

Cohorting children in a childcare setting: a strategy to reduce SARS-CoV-2 Delta transmission, August-September 2021.

Background: Childcare centres can be high-risk settings for SARS-CoV-2 transmission due to age, vaccination status, and infection control challenges. We describe the epidemiology and clinical characteristics of a childcare SARS-CoV-2 Delta outbreak. When the outbreak occurred, little was known about the transmission dynamics of SARS-CoV-2 ancestral and Delta strains among children. Vaccinations for coronavirus disease 2019 (COVID-19) were not mandatory for childcare staff, and children (< 12 years) were ineligible. Methods: A retrospective cohort design of childcare attendees was used to investigate age-cohorts exposure and transmission of SARS-CoV-2. We defined a case as a person who tested positive to SARS-CoV-2; we defined a close contact as a person who attended the childcare during 16-20 August 2021. Childcare centre exposures were defined by three cohorts: younger children (0-< 2.5 years) with designated staff; older children (2.5-5 years) with designated staff; and a staff-only group that moved between both age cohorts. We calculated the number and proportion of SARS-CoV-2 Delta infections, symptom profile and severity in children and adults, secondary attack rates, and relative risks (RR) with 95% confidence intervals (CIs) to compare age-cohort exposures and SARS-CoV-2 infection. Results: There were 38 outbreak cases that tested positive to SARS-CoV-2 Delta infection, comprising one primary case, 11 childcare attendees and 26 household members. Child attendees were in two non-interacting groups, 0-< 2.5 years and 2.5-5 years, with designated staff, separate rooms, and independent ventilation. The greatest risk of infection to childcare attendees was in the < 2.5 years age cohort which had a secondary attack rate of 41% and were five times more likely to be infected with SARS-CoV-2 (RR = 5.73; 95% CI: 1.37-23.86; p ≤ 0.01). No identified transmission (n = 0/21) occurred in the ≥ 2.5 years age cohort. Conclusion: Young children play an important role in SARS-CoV-2 Delta transmission to their peers and staff in childcare settings and to household members. Cohorting may be effective at limiting the propagation of SARS-CoV-2 in childcare settings. These findings highlight a need for multi-layered mitigation strategies and implementation support to manage respiratory infection control challenges at childcares. If prevention measures are not in place, this may facilitate ongoing transmission in these settings and into the broader community.

How do general practitioners test and treat gonococcal infections in the Australian Capital Territory? Implications for disease surveillance and control.

Abstract: The incidence of Neisseria gonorrhoeae (gonorrhoea) and Treponema pallidum (syphilis) infections in the Australian Capital Territory (ACT) has increased since 2014 in people reporting heterosexual exposure. This population is more likely to present to general practice rather than to specialised sexual health clinics, with potential implications for disease surveillance and control. This study aimed to explore: conformity of self-reported clinical practice with sexually transmitted infection guidelines in general practice; gaps in sexual health knowledge and skills; and areas for improved support from ACT Health Communicable Disease Control. A cross-sectional survey of general practitioners (GPs) and nurse practitioners (NPs) practicing in the ACT was conducted in December 2020, using a 17-item questionnaire and semi-structured interviews. Twenty-three GPs and one NP returned completed surveys (response rate 5.3%); four GPs and one NP participated in interviews. In its complex setting of competing demands, GP practice may not always meet national guidelines. In response to clinical vignettes, although all GPs ordered investigations for gonorrhoea, only 25% of these met the gold-standard by including endocervical or vaginal swabs. With respect to assessing antimicrobial sensitivities to guide treatment, only 58% correctly reported following up a positive gonococcal polymerase chain reaction test with a culture. Around two-thirds of respondents (62.5%) identified the appropriate antibiotic therapy and 75% correctly identified the responsibility of the diagnosing clinician to discuss contact tracing with the patient. Suggestions for increased support focussed on education, communication efficiency, and providing a 'safety net' for follow up.

Pens down: An outbreak of the B.1.617.2 SARS-CoV-2 variant in an Australian high school, August 2021.

Background: Little is known about the transmission dynamics of the B.1.617.2 (Delta) variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) among children and young adolescents. We investigated an outbreak in an Australian high school, with limited public health mitigation measures in place, to understand the school activities associated with transmission, and the role of young adolescents in spreading SARS-CoV-2. Methods: All 1,164 school attendees were monitored for SARS-CoV-2 infection through their mandated 14-day quarantine period. A cohort study design was used to investigate the effect of contact with the index case in different classes on the transmission of SARS-CoV-2, and the effect of vaccination among household contacts on becoming infected by SARS-CoV-2. Results: There were 48 outbreak cases, including 14 students and one teacher who likely acquired their infection at the school. Attack rates among students in the index case's classes ranged from 0% to 45%. The greatest risk of infection for students in the same grade attending a class with the index case were from the drama class (risk ratio, RR: 111.6; 95% confidence interval (95% CI): 14.88-837.19) and the personal development, health, and physical education class (RR: 7.45: 95% CI: 2.27-24.44). The overall household attack rate was 57%, and household contacts who were not fully vaccinated were 2.9 times more likely (95% CI: 1.07-7.87) to become cases than were effectively-vaccinated household contacts. Conclusion: Children can play an important role in the transmission of the Delta variant of SARS-CoV-2 within schools and at home. Transmission in this outbreak was largely associated with active, practical lessons that had close contact between students. This study demonstrates that the absence of public health and social measures in a low-incidence context resulted in the rapid spread of coronavirus disease 2019 (COVID-19) within an educational setting. These findings reinforce the role of public health and social measures and vaccinations to reduce airborne transmission and to enable a safe face-to-face learning environment.

Kebabs with a side of Salmonella: Two outbreaks of Salmonella linked to kebab shops in Canberra, ACT.

Abstract: We report two outbreaks of Salmonella associated with kebab shops in Canberra, Australian Capital Territory, detected through routine surveillance. The first consisted of 12 cases of Salmonella Agona, nine of whom reported eating chicken from the same kebab shop. The second consisted of two cases of Salmonella Virchow who both reported eating chicken from another (unrelated) kebab shop. Environmental investigations identified similar food safety issues at both businesses, including improper cleaning of kebab shaving equipment and serving cut rotisserie meat without further cooking. Environmental samples detected Salmonella genomically linked to the respective outbreak cases. These outbreaks highlight the importance of appropriate cleaning and sanitising of kebab shaving equipment and the use of a second cook step after kebab meat is shaved from the rotisserie.

Donuts for weight loss? A norovirus outbreak associated with a bakery in the Australian Capital Territory.

Background: An outbreak of gastroenteritis was investigated following complaints of illness after eating donuts from a food premises in the Australian Capital Territory (ACT). Methods: Food poisoning complainants and contacts were surveyed using a standard gastroenteritis questionnaire including menu items from the food premises. Descriptive analyses were performed on data collected for all responses. A case-control study was conducted for a group of 140 people at a catered function. Food safety inspections were conducted with food and environmental samples tested at the ACT Government Analytical Laboratory. Stool specimens were collected from cases who were ill at the time of interview. Neither active case finding, nor viral testing of food or environmental samples, could be conducted. Results: Three hundred and one people were surveyed, and 215 individuals (71.4%) reported vomiting and/or diarrhoea following consumption of a donut purchased from the business over a five-day period. All ill respondents reported eating a donut. The medians of incubation period and illness duration were 34 hours (interquartile range, IQR: 29-42 hours) and 48 hours (IQR: 29-72 hours) respectively. Diarrhoea, vomiting and abdominal pain were the most commonly reported symptoms. Eight out of 11 specimens collected from ill individuals were positive for norovirus. For the case-control study, data from 59 attendees were collected, with an attack rate of 46% (27/59). Eating any kind of filled donut was associated with a person becoming ill (odds ratio: 10.4; 95% confidence interval: 1.18-478.13). No single flavour was identified as the likely source of infection. Elevated levels of coliforms were present in two samples of donut filling obtained during the food safety inspection. Conclusion: Donuts are a novel vehicle for norovirus infection. This implicated pathogen, plus evidence collected at the food premises suggestive of faecal contamination, indicates the source of this outbreak was likely an ill food handler. The findings of this outbreak highlight the importance of excluding food handlers from work while ill. While this was one of the largest foodborne outbreaks investigated in the ACT, the true extent of illness remains unknown. Active case finding should be pursued to determine the magnitude of outbreaks.

Vaccine breakthrough infections in a highly-vaccinated Australian population during a SARS-CoV-2 Delta outbreak.

Abstract: Over 80% of residents in the Australian Capital Territory were fully vaccinated within 10 weeks of a SARS-CoV-2 Delta variant outbreak. Of the outbreak's 1,545 cases, 10% were breakthrough infections. The incidence of infections among fully- and partially-vaccinated people was 98.5% and 90% lower, respectively, than for unvaccinated people.

Tobacco smoking and mortality among Aboriginal and Torres Strait Islander adults in Australia.

BACKGROUND: Despite generally high smoking prevalences, stemming from colonization, the relationship of smoking to mortality has not been quantified reliably in an Indigenous population. We investigate smoking and mortality among Aboriginal and Torres Strait Islander adults in Australia, where current adult daily smoking prevalence is 40.2%. METHODS: A prospective study of 1388 cardiovascular disease- and cancer-free Aboriginal adults aged ≥45 years, of the 267 153 45 and Up Study participants randomly sampled from the New South Wales general population over 2006-09. Questionnaire and mortality data were linked (through the Centre for Health Record Linkage) to mid-2019. Adjusted hazard ratios (called relative risks, RRs) for all-cause mortality-among current- and past- versus never-smokers-were estimated overall, by smoking intensity and by age at cessation. Smoking-attributable fractions and associated deaths were estimated. RESULTS: Over 14 586 person-years' follow-up (median 10.6 years), 162 deaths accrued. Mortality RRs [95% confidence interval (CI)] were 3.90 (2.52-6.04) for current- and 1.95 (1.32-2.90) for past- versus never-smokers, with age heterogeneity. RRs increased with smoking intensity, to 4.29 (2.15-8.57) in current-smokers of ≥25 cigarettes/day. Compared with never-smokers, RRs were 1.48 (0.85-2.57) for those quitting at <45 years of age and 2.21 (1.29-3.80) at 45-54 years. Never-smokers lived an average >10 years longer than current-smokers. Around half of deaths among adults aged ≥45 years were attributable to smoking, exceeding 10 000 deaths in the past decade. CONCLUSIONS: In this population, >80% of never-smokers would survive to 75 years, versus ∼40% of current-smokers. Quitting at all ages examined had substantial benefits versus continuing smoking; those quitting before age 45 years had mortality risks similar to never-smokers. Smoking causes half of deaths in older Aboriginal and Torres Strait Islander adults; Indigenous tobacco control must receive increased priority.

Two carbapenemase-producing Enterobacteriaceae outbreaks detected retrospectively by whole-genome sequencing at an Australian tertiary hospital.

In 2014, two genetically-linked cases of carbapenemase-producing Enterobacteriaceae (CPE) were detected at the Canberra Hospital (TCH), prompting an investigation and response that appeared to contain transmission. We report a 2017 retrospective investigation into cases of CPE in the Australian Capital Territory (ACT) that aimed to identify clusters and transmission mechanisms. Cases detected between 2012 and 2016 were identified from the hospital laboratory information system. Whole-genome sequencing (WGS) was performed retrospectively on stored isolates. Seventy-two cases were identified, with nearly 90% of isolates containing blaIMP genes. Using multilocus sequence type (ST) data, we identified two small outbreaks of CPE containing blaIMP-4 (Enterobacter cloacae complex ST24, n = 7; Citrobacter freundii ST8, n = 10), each spanning over three years. Epidemiological and environmental evidence implicate environmental reservoirs and carriers undetected by routine infection prevention and control investigations.

Free range eggs does not mean safe eggs: an outbreak of Salmonella Typhimurium linked to free range eggs.

An outbreak of Salmonella enterica serovar Typhimurium with closely related Multiple Locus Variable-number Tandem Repeat Analysis (MLVA) patterns was detected by routine surveillance by the Australian Capital Territory Health Protection Service in May 2018. The outbreak consisted of three cases in 2018 (MLVA 03-10-10-09-496) and one in 2016 (MLVA 03-10-09-09-496), who reported eating home-cooked eggs from the same local producer. Environmental investigations found significant problems with egg cleaning, hand hygiene and documentation of food safety procedures on farm. Environmental samples collected from the farm were found to have the same MLVA pattern as the 2018 cases. Although poor farm practices most likely led to contamination of the eggs, this outbreak highlights the need for consumer education about safe handling of eggs in the home.

Evaluation of Australia's Enhanced Invasive Pneumococcal Disease (IPD) Surveillance Program.

Australia's Enhanced Invasive Pneumococcal Disease Surveillance Program is part of the National Notifiable Diseases Surveillance System, and is coordinated by the Enhanced Invasive Pneumococcal Disease Surveillance Working Group (EIPDSWG). This first evaluation of the surveillance program aimed to evaluate its performance against a number of attributes, identify ways in which surveillance may be improved, and make recommendations to the EIPDSWG. We conducted literature and document reviews; key informant interviews; an online stakeholder survey; and descriptive analyses of a subset of surveillance data. The program is complex, but has proved useful for detecting serotype replacement in response to the national infant vaccination program-informing a change to the recommended vaccine in 2011. The program is less useful for monitoring targeted programs in other high-risk groups, because complete data for cases aged between five and 50 years are not routinely collected in the largest jurisdictions and data collection is hampered by the absence of accessible electronic health records. Lack of support for reference laboratories for antimicrobial susceptibility testing, and data entry and transmission problems in some jurisdictions, have reduced the utility of the program for surveillance of antimicrobial resistance (AMR). Priority recommendations to the EIPDSWG focus on collecting complete data for all cases, to allow matching of serotypes to vaccines and surveillance of vaccine failures, while ensuring stakeholders can easily access useful surveillance data at the level of detail they require. Efforts should also be made to improve AMR data completeness, and to explore the feasibility of whole-genome sequencing methods for monitoring resistance.