Australian rates of campylobacteriosis are among the highest in developed countries, yet only limited work has been done to characterize Campylobacter spp. in Australian retail products. We performed whole genome sequencing (WGS) on 331 C. coli and 285 C. jejuni from retail chicken meat, as well as beef, chicken, lamb and pork offal (organs). Campylobacter isolates were highly diverse, with 113 sequence types (STs) including 38 novel STs, identified from 616 isolates. Genomic analysis suggests very low levels (2.3-15.3%) of resistance to aminoglycoside, beta-lactam, fluoroquinolone, macrolide and tetracycline antibiotics. A majority (>90%) of isolates (52/56) possessing the fluoroquinolone resistanceassociated T86I mutation in the gyrA gene belonged to ST860, ST2083 or ST7323. The 44 pork offal isolates were highly diverse, representing 33 STs (11 novel STs) and harboured genes associated with resistance to aminoglycosides, lincosamides and macrolides not generally found in isolates from other sources. Prevalence of multidrug resistant genotypes was very low (<5%), but tenfold higher in C. coli than C. jejuni. This study highlights that Campylobacter spp. from retail products in Australia are highly genotypically diverse and important differences in antimicrobial resistance exist between Campylobacter species and animal sources.

Clostridium difficile infections (CDIs) are some of the most common hospital-associated infections worldwide. Approximately 5% of the general population is colonised with the pathogen, but most are protected from disease by normal intestinal flora or immune responses to toxins. We developed a stochastic compartmental model of CDI in hospitals that captures the condition of the host's gut flora and the role of adaptive immune responses. A novel, derivative-based method for sensitivity analysis of individual-level outcomes was developed and applied to the model. The model reproduced the observed incidence and recurrence rates for hospitals with high and moderate incidence of hospital-acquired CDI. In both scenarios, the reproduction number for within-hospital transmission was less than 1 (0.67 and 0.44, respectively), but the proportion colonised with C. difficile at discharge (7.3 and 6.1%, respectively) exceeded the proportion colonised at admission (5%). The transmission and prevalence of CDI were most sensitive to the average length of stay and the transmission rate of the pathogen. Recurrent infections were most strongly affected by the treatment success rate and the immune profile of patients. Transmission within hospitals is substantial and leads to a net export of colonised individuals to the broader community. However, within-hospital transmission alone is insufficient to sustain endemic conditions in hospitals without the constant importation of colonised individuals. Improved hygiene practices to reduce transmission from symptomatic and asymptomatic individuals and reduced length of stay are most likely to reduce within-hospital transmission and infections; however, these interventions are likely to have a smaller effect on the probability of recurrence. Immunising inpatients against the toxins produced by C. difficile will reduce the incidence of CDI but may increase transmission.

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Clostridium difficile infections (CDIs) affect patients in hospitals and in the community, but the relative importance of transmission in each setting is unknown. We developed a mathematical model of C. difficile transmission in a hospital and surrounding community that included infants, adults and transmission from animal reservoirs. We assessed the role of these transmission routes in maintaining disease and evaluated the recommended classification system for hospital- and community-acquired CDIs. The reproduction number in the hospital was <1 (range: 0.16–0.46) for all scenarios. Outside the hospital, the reproduction number was >1 for nearly all scenarios without transmission from animal reservoirs (range: 1.0–1.34). However, the reproduction number for the human population was <1 if a minority (>3.5–26.0%) of human exposures originated from animal reservoirs. Symptomatic adults accounted for <10% transmission in the community. Under conservative assumptions, infants accounted for 17% of community transmission. An estimated 33–40% of community-acquired cases were reported but 28–39% of these reported cases were misclassified as hospital-acquired by recommended definitions. Transmission could be plausibly sustained by asymptomatically colonised adults and infants in the community or exposure to animal reservoirs, but not hospital transmission alone. Under-reporting of community-onset cases and systematic misclassification underplays the role of community transmission.

Bhutan experienced its largest and first nation-wide dengue epidemic in 2019. The cases in 2019 were greater than the total number of cases in all the previous years. This study aimed to characterize the spatiotemporal patterns and effective reproduction number of this explosive epidemic. Weekly notified dengue cases were extracted from the National Early Warning, Alert, Response and Surveillance (NEWARS) database to describe the spatial and temporal patterns of the epidemic. The time-varying, temperature-adjusted cohort effective reproduction number was estimated over the course of the epidemic. The dengue epidemic occurred between 29 April and 8 December 2019 over 32 weeks, and included 5935 cases. During the epidemic, dengue expanded from six to 44 subdistricts. The effective reproduction number was <3 for most of the epidemic period, except for a ≈1 month period of explosive growth, coinciding with the monsoon season and school vacations, when the effective reproduction number peaked >30 and after which the effective reproduction number declined steadily. Interventions were only initiated 6 weeks after the end of the period of explosive growth. This finding highlights the need to reinforce the national preparedness plan for outbreak response, and to enable the early detection of cases and timely response.