Background In urban Australia, the burden of shigellosis is either in returning travelers from shigellosis-endemic regions or in men who have sex with men (MSM). Here, we combine genomic data with comprehensive epidemiological data on sexual exposure and travel to describe the spread of multidrug-resistant Shigella lineages. Methods A population-level study of all cultured Shigella isolates in the state of Victoria, Australia, was undertaken from 1 January 2016 through 31 March 2018. Antimicrobial susceptibility testing, whole-genome sequencing, and bioinformatic analyses of 545 Shigella isolates were performed at the Microbiological Diagnostic Unit Public Health Laboratory. Risk factor data on travel and sexual exposure were collected through enhanced surveillance forms or by interviews. Results Rates of antimicrobial resistance were high, with 17.6% (95/541) and 50.6% (274/541) resistance to ciprofloxacin and azithromycin, respectively. There were strong associations between antimicrobial resistance, phylogeny, and epidemiology. Specifically, 2 major MSM-associated lineages were identified: a Shigellasonnei lineage (n = 159) and a Shigella flexneri 2a lineage (n = 105). Of concern, 147/159 (92.4%) of isolates within the S. sonnei MSM-associated lineage harbored mutations associated with reduced susceptibility to recommended oral antimicrobials: namely, azithromycin, trimethoprim-sulfamethoxazole, and ciprofloxacin. Long-read sequencing demonstrated global dissemination of multidrug-resistant plasmids across Shigella species and lineages, but predominantly associated with MSM isolates. Conclusions Our contemporary data highlight the ongoing public health threat posed by resistant Shigella, both in Australia and globally. Urgent multidisciplinary public health measures are required to interrupt transmission and prevent infection.

Background A cornerstone of Australia's ability to control COVID-19 has been effective border control with an extensive supervised quarantine programme. However, a rapid recrudescence of COVID-19 was observed in the state of Victoria in June, 2020. We aim to describe the genomic findings that located the source of this second wave and show the role of genomic epidemiology in the successful elimination of COVID-19 for a second time in Australia.Methods In this observational, genomic epidemiological study, we did genomic sequencing of all laboratoryconfirmed cases of COVID-19 diagnosed in Victoria, Australia between Jan 25, 2020, and Jan 31, 2021. We did phylogenetic analyses, genomic cluster discovery, and integrated results with epidemiological data (detailed information on demographics, risk factors, and exposure) collected via interview by the Victorian Government Department of Health. Genomic transmission networks were used to group multiple genomic clusters when epidemiological and genomic data suggested they arose from a single importation event and diversified within Victoria. To identify transmission of emergent lineages between Victoria and other states or territories in Australia, all publicly available SARS-CoV-2 sequences uploaded before Feb 11, 2021, were obtained from the national sequence sharing programme AusTrakka, and epidemiological data were obtained from the submitting laboratories. We did phylodynamic analyses to estimate the growth rate, doubling time, and number of days from the first local infection to the collection of the first sequenced genome for the dominant local cluster, and compared our growth estimates to previously published estimates from a similar growth phase of lineage B.1.1.7 (also known as the Alpha variant) in the UK.

Objectives To assess variations by time of year and hospital in the uptake of influenza and pertussis vaccinations by pregnant women in Victoria; to identify factors associated with vaccination uptake. Design, setting Retrospective analysis of data in the Victorian Perinatal Data Collection (VPDC), a population surveillance system for obstetric conditions, procedures, and pregnancy and birth outcomes. Participants Women whose pregnancies ended in a live or stillbirth during July 2015 – June 2017. Main outcome measures Influenza and pertussis vaccinations during pregnancy. Results 153 980 pregnancies in 67 hospitals ended during July 2015 – June 2017; 59 968 pregnant women (39.0%) were vaccinated against influenza and 98 583 (64.0%) against pertussis. Coverage varied by pregnancy end date, rising for influenza during winter and spring, but for pertussis rising continuously across the two years from 37.5% to 82.2%. Differences between hospitals in coverage were marked. Factors associated with vaccination included greater maternal age, primigravidity, early antenatal care, and GP‐led care. The odds of vaccination were statistically significantly lower for women born overseas and those who smoked during pregnancy; the odds of vaccination were also lower for Aboriginal and Torres Strait Islander women. Conclusions Pertussis vaccination of pregnant women in Victoria has increased, but influenza vaccination rates remain moderate and variable. Structural changes at the system level may improve maternal vaccination rates. Embedding the delivery of maternal vaccination programs in antenatal care pathways should be a priority.

Cryptosporidiosis is one of the most common waterborne diseases reported worldwide. Outbreaks of this gastrointestinal disease, which is caused by the Cryptosporidium parasite, are often attributed to public swimming pools and municipal water supplies. Between the months of January and April in 2009, New South Wales, Australia, experienced the largest waterborne cryptosporidiosis outbreak reported in Australia to date. Through the course of the contamination event, 1,141 individuals became infected with Cryptosporidium. Health authorities in New South Wales indicated that public swimming pool use was a contributing factor in the outbreak. To identify the Cryptosporidium species responsible for the outbreak, fecal samples from infected patients were collected from hospitals and pathology companies throughout New South Wales for genetic analyses. Genetic characterization of Cryptosporidium oocysts from the fecal samples identified the anthroponotic Cryptosporidium hominis IbA10G2 subtype as the causative parasite. Equal proportions of infections were found in males and females, and an increased susceptibility was observed in the 0-to 4-year age group. Spatiotemporal analysis indicated that the outbreak was primarily confined to the densely populated coastal cities of Sydney and Newcastle.

Objective: Recent studies have used Bayesian methods to predict timing of influenza epidemics many weeks in advance, but there is no documented evaluation of how such forecasts might support the day-to-day operations of public health staff. Methods:During the 2015 influenza season in Melbourne, Australia, weekly forecasts were presented at Health Department surveillance unit meetings, where they were evaluated and updated in light of expert opinion to improve their accuracy and usefulness.Results: Predictive capacity of the model was substantially limited by delays in reporting and processing arising from an unprecedented number of notifications, disproportionate to seasonal intensity. Adjustment of the predictive algorithm to account for these delays and increased reporting propensity improved both current situational awareness and forecasting accuracy. Conclusions:Collaborative engagement with public health practitioners in model development improved understanding of the context and limitations of emerging surveillance data. Incorporation of these insights in a quantitative model resulted in more robust estimates of disease activity for public health use. Implications for public health:In addition to predicting future disease trends, forecasting methods can quantify the impact of delays in data availability and variable reporting practice on the accuracy of current epidemic assessment. Such evidence supports investment in systems capacity.

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Mycobacterium tuberculosis is primarily a pathogen of humans. Infections have been reported in animal species and it is emerging as a significant disease of elephants in the care of humans. With the close association between humans and animals, transmission can occur. In November 2010, a clinically healthy Asian elephant in an Australian zoo was found to be shedding M. tuberculosis; in September 2011, a sick chimpanzee at the same zoo was diagnosed with tuberculosis caused by an indistinguishable strain of M. tuberculosis. Investigations included staff and animal screening. Four staff had tuberculin skin test conversions associated with spending at least 10 hours within the elephant enclosure; none had disease. Six chimpanzees had suspected infection. A pathway of transmission between the animals could not be confirmed. Tuberculosis in an elephant can be transmissible to people in close contact and to other animals more remotely. The mechanism for transmission from elephants requires further investigation.

Genital Chlamydia trachomatis is a sexually transmissible bacterial infection that is asymptomatic in the majority of infected individuals and is associated with significant short-term and long-term morbidity. The population prevalence of the infection appears to be increasing. C. trachomatis is of public health significance because of the impacts of untreated disease on reproductive outcomes, transmission of other sexually acquired infections, and the costs to health systems. At the individual level, C. trachomatis infection is readily treatable with antibiotics, although antibiotic resistance appears to be increasing. At the population level, public health control of spread of infection is more problematic. Approaches to control include primary preventive activities, increased access to testing and treatment for people with or at risk of infection, partner notification and treatment, and screening either opportunistically or as part of an organized population screening program. A combination of all of the above approaches is likely to be required to have a significant effect on the burden of disease associated with genital chlamdyia infection and to reduce population prevalence. The development of a vaccine for genital chlamydia infection could significantly reduce the public health burden associated with infection; however a vaccine is not expected to be available in the near future.