Biology subjects

Johnson, P. D. R.

Publications and source records attributed to Johnson, P. D. R..

6 recordsLinked to original sources

bioRxiv2025

Defining new Buruli ulcer endemic areas in urban southeastern Australia using bacterial genomics-informed possum excreta surveys

Buruli ulcer (BU) in southeastern Australia is a zoonosis caused by infection with Mycobacterium ulcerans. Australian native possums are a major wildlife reservoir and infected possums shed M. ulcerans in their excreta, with mosquitoes being the major transmitting vector in this region. BU is geographically restricted and this feature, combined with an average 4.8-month incubation period, makes tracking M. ulcerans environmental spread and timely identification of new BU endemic areas challenging. While human movement complicates transmission tracing, we used the highly territorial behaviour of native possums and high-resolution pathogen genomics to confidently identify new BU endemic areas in Melbournes inner northwest and southern suburbs of Geelong. Using pathogen genomic phylodynamic modelling, we estimated that M. ulcerans was introduced to these areas 2-6 years before the emergence of human BU cases. This study shows how possum excreta surveys combined with pathogen genome data can pinpoint new BU endemic areas, thus providing critical local knowledge for targeted public health interventions to reduce exposure risk and ensure early diagnosis.

microbiology↗

bioRxiv2024

Mycobacterium ulcerans challenge strain selection for a Buruli ulcer controlled human infection model

Critical scientific questions remain regarding infection with Mycobacterium ulcerans, the organism responsible for the neglected tropical disease, Buruli ulcer (BU). A controlled human infection model has the potential to accelerate our knowledge of the immunological correlates of disease, to test prophylactic interventions and novel therapeutics. Here we present microbiological evidence supporting M. ulcerans JKD8049 as a suitable human challenge strain. This non-genetically modified Australian isolate is susceptible to clinically relevant antibiotics, can be cultured in animal-free and surfactant-free media, can be enumerated for precise dosing, and has stable viability following cryopreservation. Infectious challenge of humans with JKD8049 is anticipated to imitate natural infection, as M. ulcerans JKD8049 is genetically stable following in vitro passage and produces the key virulence factor, mycolactone. Also reported are considerations for the manufacture, storage, and administration of M. ulcerans JKD8049 for controlled human infection.

microbiology↗

bioRxiv2023

Season of transmission of Ross River/Barmah Forest Virus and Mycobacterium ulcerans closely align in southeastern Australia, supporting mosquitoes as the vector of Buruli ulcer

Ross River Virus and Barmah Forest Virus infections (alphaviruses) have short incubation periods and are transmitted to humans by mosquitoes. Mycobacterium ulcerans infection (Buruli ulcer) has a much longer incubation period and its mode of transmission is contested. We studied the relationship between month of notification of alphavirus infections and Buruli ulcer in the temperate Australian state of Victoria over the six-year period, 2017-2022. Using cross-correlation, a signal processing technique, we found that a five-month temporal shift in month of Buruli ulcer notification provided optimal alignment with month of alphavirus notification. This closely matches the previously determined 5-month Buruli ulcer incubation period. Inferred transmission of both conditions showed coordinated maxima in summer and autumn and coordinated minima in winter and spring. The close alignment in season of transmission of alphavirus infection and Buruli ulcer in Victoria supports mosquitoes as the primary local vector of M. ulcerans.

microbiology↗

bioRxiv2023

Mycobacterium ulcerans not detected by PCR on human skin in Buruli ulcer endemic areas of south eastern Australia

IntroductionMycobacterium ulcerans (MU) causes Buruli ulcer (BU), a geographically restricted infection that can result in skin loss, contracture, and permanent scarring. Lesion-location maps compiled from more than 640 cases in south eastern Australia suggest biting insects are likely involved in transmission, but it is unclear whether MU is brought by insects to their target or if MU is already on the skin and inoculation is an opportunistic event that need not be insect dependent. MethodsWe validated a PCR swab detection assay and defined its dynamic range using laboratory cultured M. ulcerans and fresh pigskin. We invited volunteers in Buruli-endemic and non-endemic areas to sample their skin surfaces with self-collected skin swabs tested by IS2404 quantitative PCR. ResultsPigskin validation experiments established a limit-of-detection of 0.06 CFU/cm2 at a qPCR cycle threshold (Ct) of 35. Fifty-seven volunteers returned their self-collected kits of 4 swabs (bilateral ankles, calves, wrists, forearms), 10 from control areas and 47 from endemic areas. Collection was timed to coincide with the known peak-transmission period of Buruli. All swabs from human volunteers tested negative (Ct [≥]35). ConclusionsM. ulcerans was not detected on the skin of humans from highly BU endemic areas. Author SummaryBuruli ulcer (BU) incidence is increasing in temperate south eastern Australia. We have yet to develop public health programs to assist people avoid BU partly because the precise mode of transmission is contentious. Recent research has shown that environmental contamination with M. ulcerans (the cause of BU) is widespread in endemic areas as a result of faecal shedding from infected possums that live close to humans, although direct human-possum contact is rare. We investigated the possibility that the skin of humans in endemic areas could become transiently contaminated with M. ulcerans while outdoors. If this were the case then BU prevention programs could be developed around skin protection and regular washing/showering. To study this possibility, we developed a sensitive skin swab PCR-assay that we tested using a pigskin laboratory model so we could be confident in our results. We asked volunteers to collect their own skin swabs after spending at least 4 hours outside during the known period of peak Buruli transmission. Fifty seven volunteers returned swab sets for testing. Our results were negative. We did not find evidence that humans in our endemic zone have M. ulcerans contamination on their skin.

microbiology↗

bioRxiv2022

Structured surveys of Australian native possum excreta predict Buruli ulcer occurrence in humans

Buruli ulcer (BU) is a neglected tropical disease caused by infection of subcutaneous tissue with Mycobacterium ulcerans. BU is commonly reported across rural regions of Central and West Africa but has been increasing dramatically in temperate southeast Australia around the major metropolitan city of Melbourne. Previous research has shown that Australian native possums are reservoirs of M. ulcerans and that they shed the bacteria in their fecal material (excreta). Field surveys show that locales where possums harbor M. ulcerans overlap with human cases of BU, raising the possibility of using possum excreta surveys to predict the risk of disease occurrence in humans. We thus established a highly structured 12-month possum excreta surveillance program across an area of 350 km2 in the Mornington Peninsula area 70 km south of Melbourne, Australia. The primary objective of our study was to assess if M. ulcerans surveillance of possum excreta provided useful information for predicting future human BU case locations. Over two sampling campaigns in summer and winter, we collected 2282 possum excreta specimens of which 11% were PCR positive for M. ulcerans-specific DNA. Using the spatial scanning statistical tool SatScan, we observed non-random, co-correlated clustering of both M. ulcerans positive possum excreta and human BU cases. We next trained a statistical model with the Mornington Peninsula excreta survey data to predict the future likelihood of human BU cases occurring in the region. By observing where human BU cases subsequently occurred, we show that the excreta model performance was superior to a null model trained using the previous years human BU case incidence data (AUC 0.66 vs 0.55). We then used data unseen by the excreta-informed model from a new survey of 661 possum excreta specimens in Geelong, a geographically separate BU endemic area to the southwest of Melbourne, to prospectively predict the location of human BU cases in that region. As for the Mornington Peninsula, the excreta-based BU prediction model outperformed the null model (AUC 0.75 vs 0.50) and pinpointed specific locations in Geelong where interventions could be deployed to interrupt disease spread. This study highlights the One Health nature of BU by confirming a quantitative relationship between possum excreta shedding of M. ulcerans and humans developing BU. The excreta survey-informed modeling we have described will be a powerful tool for efficient targeting of public health responses to stop BU.

microbiology↗

bioRxiv2017

A target-specific assay for rapid and quantitative detection of Mycobacterium chimaera DNA in environmental and clinical specimens

Mycobacterium chimaera is an opportunistic environmental mycobacterium, belonging to the Mycobacterium intracellulare complex. Although most commonly associated with pulmonary disease, there has been growing awareness of invasive M. chimaera infections following cardiac surgery. Investigations suggest world-wide spread of a specific M. chimaera clone, associated with contaminated hospital heater-cooler units used during the surgery. Given the global dissemination of this clone, its potential to cause invasive disease, and the laboriousness of current culture-based diagnostic methods, there is a pressing need to develop rapid and accurate diagnostic assays, specific for M. chimaera. Here, we assessed 354 mycobacterial genome sequences and confirmed that M. chimaera is a phylogenetically coherent group. In silico comparisons indicated six DNA regions present only in M. chimaera. We targeted one of these regions and developed a TaqMan qPCR assay for M. chimaera with a detection limit of 10 CFU in whole blood. In vitro screening against DNA extracted from 40 other mycobacteria and 22 bacterial species from 21 diverse genera confirmed in silico predicted specificity for M. chimaera. Screening 33 water samples from heater cooler units with this assay highlighted the increased sensitivity of PCR compared to culture, with 15 of 23 culture negative samples positive by M. chimaera qPCR. We have thus developed a robust molecular assay that can be readily and rapidly deployed to screen clinical and environmental specimens for M. chimaera.

microbiology↗