Performance of MALDI-TOF MS, real-time PCR, antigen detection, and automated biochemical testing for the identification of Burkholderia pseudomallei.

Burkholderia pseudomallei is the causative agent of melioidosis, a disease highly endemic to Southeast Asia and northern Australia, though the area of endemicity is expanding. Cases may occur in returning travelers or, rarely, from imported contaminated products. Identification of B. pseudomallei is challenging for laboratories that do not see this organism frequently, and misidentifications by matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) and automated biochemical testing have been reported. The in vitro diagnostic database for use with the Vitek MS has recently been updated to include B. pseudomallei and we aimed to validate the performance for identification in comparison to automated biochemical testing with the Vitek 2 GN card, quantitative real-time polymerase chain reaction (qPCR) targeting the type III secretion system, and capsular polysaccharide antigen detection using a lateral flow immunoassay (LFA). We tested a "derivation" cohort including geographically diverse B. pseudomallei and a range of closely related Burkholderia species, and a prospective "validation" cohort of B. pseudomallei and B. cepacia complex clinical isolates. MALDI-TOF MS had a sensitivity of 1.0 and specificity of 1.0 for the identification and differentiation of B. pseudomallei from related Burkholderia species when a certainty cutoff of 99.9% was used. In contrast, automated biochemical testing for B. pseudomallei identification had a sensitivity of 0.83 and specificity of 0.88. Both qPCR and LFA correctly identified all B. pseudomallei isolates with no false positives. Due to the high level of accuracy, we have now incorporated MALDI-TOF MS into our laboratory's B. pseudomallei identification workflow.IMPORTANCEBurkholderia pseudomallei causes melioidosis, a disease associated with high morbidity and mortality that disproportionately affects rural areas in Southeast Asia and northern Australia. The known area of endemicity is expanding and now includes the continental United States. Laboratory identification can be challenging which may result in missed or delayed diagnoses and poor patient outcomes. In this study, we compared mass spectrometry using an updated spectral database with multiple other methods for B. pseudomallei identification and found mass spectrometry highly accurate. We have therefore incorporated this fast and cost-effective method into our laboratory's workflow for B. pseudomallei identification.

Mycoplasma genitalium retrospective audit of Northern Territory isolates from 2022.

Abstract: The Northern Territory (NT) has the highest rates of sexually transmitted infections (STI) in Australia; however, the local prevalence of Mycoplasma genitalium (M. genitalium) has not been previously determined. This study was designed to review M. genitalium detection, to determine the regional NT prevalence and macrolide resistance rates. In our study the NT background prevalence of M. genitalium is 13%, with the highest detection rates occurring in central Australia and in correctional facility inmates. Symptomatic patients attending sexual health clinics have a positivity rate of 12%, but very high macrolide resistance. The decision to screen for M. genitalium should be based on several factors, including the prevalence of the infection in the local population; the availability of effective treatments; and the potential benefits and risks of detection and therapy.

Comprehensive observational study evaluating the enduring effectiveness of 4CMenB, the meningococcal B vaccine against gonococcal infections in the Northern Territory and South Australia, Australia: study protocol.

INTRODUCTION: The effectiveness of antibiotics for treating gonococcal infections is compromised due to escalating antibiotic resistance; and the development of an effective gonococcal vaccine has been challenging. Emerging evidence suggests that the licensed meningococcal B (MenB) vaccine, 4CMenB is effective against gonococcal infections due to cross-reacting antibodies and 95% genetic homology between the two bacteria, Neisseria meningitidis and Neisseria gonorrhoeae, that cause the diseases. This project aims to undertake epidemiological and genomic surveillance to evaluate the long-term protection of the 4CMenB vaccine against gonococcal infections in the Northern Territory (NT) and South Australia (SA), and to determine the potential benefit of a booster vaccine doses to provide longer-term protection against gonococcal infections. METHODS AND ANALYSES: This observational study will provide long-term evaluation results of the effectiveness of the 4CMenB vaccine against gonococcal infections at 4-7 years post 4CMenB programme implementation. Routine notifiable disease notifications will be the basis for assessing the impact of the vaccine on gonococcal infections. Pathology laboratories will provide data on the number and percentage of N. gonorrhoeae positive tests relative to all tests administered and will coordinate molecular sequencing for isolates. Genome sequencing results will be provided by SA Pathology and Territory Pathology/New South Wales Health Pathology, and linked with notification data by SA Health and NT Health. There are limitations in observational studies including the potential for confounding. Confounders will be analysed separately for each outcome/comparison. ETHICS AND DISSEMINATION: The protocol and all study documents have been reviewed and approved by the SA Department for Health and Well-being Human Research Ethics Committee (HREC/2022/HRE00308), and the evaluation will commence in the NT on receipt of approval from the NT Health and Menzies School of Health Research Human Research Ethics Committee. Results will be published in peer-reviewed journals and presented at scientific meetings and public forums.

Implementing a national programme of pathogen genomics for public health: the Australian Pathogen Genomics Program (AusPathoGen).

Delivering large-scale routine pathogen genomics surveillance for public health is of considerable interest, although translational research models that promote national-level implementation are not well defined. We describe the development and deployment of the Australian Pathogen Genomics Program (AusPathoGen), a comprehensive national partnership between academia, public health laboratories, and public health agencies that commenced in January, 2021. Successfully establishing and delivering a national programme requires inclusive and transparent collaboration between stakeholders, defined and clear focus on public health priorities, and support for strengthening national genomics capacity. Major enablers for delivering such a programme include technical solutions for data integration and analysis, such as the genomics surveillance platform AusTrakka, standard bioinformatic analysis methods, and national ethics and data sharing agreements that promote nationally integrated surveillance systems. Training of public health officials to interpret and act on genomic data is crucial, and evaluation and cost-effectiveness programmes will provide a benchmark and evidence for sustainable investment in genomics nationally and globally.

Spectrum of human Pasteurella species infections in tropical Australia.

BACKGROUND: Acquired zoonotic infections with Pasteurella bacterial species have a wide clinical spectrum of disease from invasive infections to localised bite-wound infections. METHODS: This study reviewed the spectrum of the demographic, clinical, temporal, and microbiological trends of laboratory confirmed Pasteurella species infections presenting to a single-centre tropical tertiary hospital over a twenty-year period. RESULTS: 195 episodes from 190 patients were included. 51.3% patients were female, and 20.5% Aboriginal or Torres Strait Islander peoples. Crude incidence of Pasteurella spp. infections increased from 1.5 per 100,000 population in 2000, to 11.4 per 100,000 population in 2021. There were 22 (11.3%) bloodstream infections, 22 (11.3%) invasive, 34 (17.4%) deep local, 98 (50.2%) superficial infections, and 19 (9.7%) other or unknown. Adults over 65 years of age accounted for the majority of bacteraemias (63.7%). More severe infections, including bacteraemia, invasive and deep local infections, were more common in lower limb infections and in those with underlying comorbidities. Animal contact with cats was more common in bloodstream infections (36.4%), but dog bites more common in invasive, deep local and superficial infections. 30-day all-cause mortality was low at 1.0%. Pasteurella multocida was most commonly identified (61.1%), but P. canis, P. dagmatis, and other Pasteurella infections were also noted. 67.7% of specimens were polymicrobial, with other significant organisms being Staphylococcus aureus, Streptococcus pyogenes, Group G Streptococcus and Pseudomonas aeruginosa. CONCLUSION: Pasteurella species remain clinically important pathogens, with the ability to cause severe and invasive infections with associated morbidity. Presentations to hospital are becoming more common, and the polymicrobial nature of bites wounds has implications for empiric antibiotic guidelines.

Characterisation of Corynebacterium diphtheriae isolates in the Northern Territory of Australia.

This article summarises our review of 41 Corynebacterium diphtheriae wound swab isolates from the tropical Northern Territory of Australia. On polymerase chain reaction and whole genome sequencing, no isolates were toxigenic strains.