Lessons learned: drive-through COVID-19 clinic testing during an adaptive epidemic response and a point-of-care test assessment of a computer-read rapid lateral flow immunoassay with fluorescence-based detection.

Background. The COVID-19 pandemic demonstrated a need for robust SARS-CoV-2 test evaluation infrastructure to underpin biosecurity and protect the population during a pandemic health emergency.Gap statement. The first generation of rapid antigen tests was less accurate than molecular methods due to their inherent sensitivity and specificity shortfalls, compounded by the consequences of self-testing. This created a need for more accurate point-of-care SARS-CoV-2 detection methods.Aim. Here we present the lessons-learned during the COVID-19 emergency response in Western Australia including the detailed set-up, evaluation and operation of rapid antigen test in a state-run drive-through sample collection service during the COVID-19 pandemic after the strict border shutdown ended.Methods. We report a conformity assessment of a novel, second-generation rapid antigen test (Virulizer) comprising a technician-operated rapid lateral flow immunoassay with fluorescence-based detection.Results. The Virulizer rapid antigen test demonstrated up to 100% sensitivity (95% CI: 61.0-100%), 91.94% specificity (95% CI: 82.5-96.5%) and 92.65% accuracy when compared to a commercial PCR assay method. Wide confidence intervals in our series reflect the limits of small sample size. Nevertheless, the Virulizer assay performance was well-suited to point-of-care screening for SARS-CoV-2 in a drive-through clinic setting.Conclusion. The adaptive evaluation process necessary under changing pandemic conditions enabled assessment of a simple sample collection and point-of-care testing process, and showed how this system could be rapidly deployed for SARS-CoV-2 testing, including to regional and remote settings.

Speaking of sepsis: semantics, syntax, and slang.

Medical language is in a constant state of evolution. Its grammar and vocabulary are not fixed by rigid rules. The interdisciplinary field of sepsis has become a meeting point for new insights arising from advances in systems biology, epidemiology, mechanistic understandings of disease process and antimicrobial interventions. This convergence has gained from our recent experience of SARS-CoV-2 infection and COVID-19 and possibilities inferred from emerging information technology. Biomedical descriptors have diverged along disciplinary lines creating an unfortunate disconnect between clinical and laboratory-based terminology. The resulting confusion between clinically determined sepsis and laboratory verified bloodstream infection raises practical questions that affect daily operational processes in the ward, clinic and laboratory. There is an urgent need to understand how the clinical sepsis pathway and corresponding clinical laboratory workflow can be better aligned as a single coherent entity. There is also an implicit need to understand how this process should produce actionable information in a timely and orderly manner, and identify residual obselete terminology that has crept into common usage. A widely accepted sepsis epistemology, ontology and heuristic will help us improve our clinical management of sepsis.

Case Study: Applying Rapid Flow Cytometry Analysis to CAPD Effluent.

Peritoneal dialysis (PD) peritonitis cases require rapid clinical interventions to ensure the best possible patient outcomes. Culture-dependent microbiology tools are slow and cannot provide clinicians with evidence to guide antimicrobial prescription practices in an appropriate time frame. Genotypic methods have met with limited success for analyzing continuous ambulatory PD effluent, with most centers still relying on culture-dependent microbiology. We present a case study in which we apply flow cytometry techniques to antibiotic-compromised effluent. We demonstrate, with supporting evidence, direct enumeration of bacterial and human immune cells, with results reported within 2 hours of receiving the clinical specimen.

Clinical features and outcome of patients with cutaneous melioidosis during a nosocomial outbreak in a temperate region of Australia.

Six cases of cutaneous melioidosis from southwestern Australia, a non-endemic region occurred as a result of Burkholderia pseudomallei contamination of normal saline that was used for irrigating superficial wounds. Treatment with parenteral meropenem, given by continuous infusion for 2 weeks, followed by oral antibiotics was successful in all cases.

Prevalence of oropharyngeal antibiotic-resistant flora among residents of aged care facilities: a pilot study.

Residents in 11 long-term care facilities, and presenting to a single tertiary hospital site, were sampled to estimate prevalence of oropharyngeal colonization with resistant Gram-negative bacteria. From 124 residents, only one isolate (0.8%; 95% confidence interval 0.0%, 4.4) was multi-resistant (an extended-spectrum ß-lactamase producing Escherichia coli) indicating that different treatment recommendations for respiratory infections in this population may not be justified.

Comparison of methods for AmpC ß-lactamase detection in Enterobacteriaceae.

AmpC ß-lactamases (Bla(AmpC)) are an emerging group of antimicrobial resistance determinants. The lack of an agreed Bla(AmpC) detection method hinders investigation of their epidemiology and understanding of their clinical significance. This study compared the sensitivity and specificity of phenotypic methods of Bla(AmpC) detection in a collection of 246 Enterobacteriaceae with a diverse range of ß-lactam resistance profiles. The Bla(AmpC) screening methods evaluated were based on cephamycin, ceftazidime and cefepime susceptibility. These were compared with Bla(AmpC) screening using conventional ESBL detection methods. The confirmatory methods evaluated were biologically based assays, inhibitor-based assays, an AmpC Etest and a rapid chromogenic assay. A multiplex nucleic acid amplification test and the three-dimensional enzyme extraction assay were used as reference methods. Bla(AmpC) activity was present in 74 isolates. The majority of the enzymes were plasmid-encoded and belonged to the CMY, DHA and EBC families. The screening methods had sensitivities between 47 and 99 % and specificities of 45-95 %. The performance of confirmatory tests varied widely, ranging in sensitivity from 19 % to 97 % and in specificity from 88 % to 100 %. Only the Tris-EDTA and MAST ID D68C disc tests had a sensitivity and a specificity above 90 %. Further investigation is needed to establish the most suitable enzyme substrates, inhibitor types, inhibitor concentrations and interpretative cut-offs in order to refine the inhibitor-based methods. A simple disc-based protocol using cefoxitin non-susceptibility as a screening tool, followed by the Tris-EDTA method for confirmation, detects Bla(AmpC) activity with 95 % sensitivity and 98 % specificity.

Zoonotic tuberculosis: on the decline.

Mycobacterium bovis is a zoonotic member of the Mycobacterium tuberculosis complex responsible for a clinical syndrome indistinguishable from that due to M. tuberculosis. In Australia, infection with M. bovis has historically been associated with employment in the livestock industry or immigration from countries in which animal disease is endemic. It currently accounts for 0.2% of all human cases of tuberculosis within Australia. This paper describes a case of pulmonary M. bovis in a butcher and reviews factors responsible for the declining incidence of this disease in Australia.

Procalcitonin and C-reactive protein in severe 2009 H1N1 influenza infection.

PURPOSE: To examine whether, in an adult intensive care unit (ICU), procalcitonin or C-reactive protein (CRP) levels discriminated between 2009 H1N1 influenza infection and community-acquired pneumonia of bacterial origin. METHODS: A retrospective observational study performed at an Australian hospital over a 4-month winter period during the 2009 H1N1 influenza pandemic. Levels on admission of procalcitonin and CRP were compared between patients admitted to the ICU with community-acquired pneumonia of bacterial and 2009 H1N1 origin. RESULTS: Compared to those with bacterial or mixed infection (n = 9), patients with 2009 H1N1 infection (n = 16) were significantly more likely to have bilateral chest X-ray infiltrates, lower APACHE scores, more prolonged lengths of stay in ICU and lower white cell count, procalcitonin and CRP levels. Using a cutoff of >0.8 ng/ml, the sensitivity and specificity of procalcitonin for detection of patients with bacterial/mixed infection were 100 and 62%, respectively. A CRP cutoff of >200 mg/l best identified patients with bacterial/mixed infection (sensitivity 100%, specificity 87.5%). In combination, procalcitonin levels >0.8 ng/ml and CRP >200 mg/l had optimal sensitivity (100%), specificity (94%), negative predictive value (100%) and positive predictive value (90%). Receiver-operating characteristic curve analysis suggested the diagnostic accuracy of procalcitonin may be inferior to CRP in this setting. CONCLUSIONS: Procalcitonin measurement potentially assists in the discrimination between severe lower respiratory tract infections of bacterial and 2009 H1N1 origin, although less effectively than CRP. Low values, particularly when combined with low CRP levels, suggested bacterial infection, alone or in combination with influenza, was unlikely.

Melioidosis in northern Australia, 2001-02.

Melioidosis, caused by the gram negative bacterium Burkholderia pseudomallei, is endemic in northern Australia. Using data collated from centres in Western Australia, the Northern Territory and Queensland, this report describes the epidemiology of this disease between 1 November, 2001 and 31 October, 2002. There were 47 cases seen during this period with an average annual incidence of 5.8 cases per 100,000 population. In Indigenous Australians, an incidence of 25.5 cases per 100,000 population was seen. The timing and location of cases was generally correlated with rainfall across northern Australia. A case-cluster in a Queensland community was associated with post-cyclonic flooding. Risk factors included diabetes, alcohol-related problems and renal disease. Pneumonia (51%) was the most common clinical diagnosis. The mortality rate attributable to melioidosis was 21 per cent, although a number of other patients died of underlying disease. Despite improvements in recognition and treatment, melioidosis is still associated with a high morbidity and mortality, particularly in Indigenous Australians.