Whole-Genome Sequencing of SARS-CoV-2 from Quarantine Hotel Outbreak.

Hotel quarantine for international travelers has been used to prevent coronavirus disease spread into Australia. A quarantine hotel-associated community outbreak was detected in South Australia. Real-time genomic sequencing enabled rapid confirmation tracking the outbreak to a recently returned traveler and linked 2 cases of infection in travelers at the same facility.

Burkholderia lata Infections from Intrinsically Contaminated Chlorhexidine Mouthwash, Australia, 2016.

Burkholderia lata was isolated from 8 intensive care patients at 2 tertiary hospitals in Australia. Whole-genome sequencing demonstrated that clinical and environmental isolates originated from a batch of contaminated commercial chlorhexidine mouthwash. Genomic analysis identified efflux pump-encoding genes as potential facilitators of bacterial persistence within this biocide.

Target-Specific Assay for Rapid and Quantitative Detection of Mycobacterium chimaera DNA.

Mycobacterium chimaera is an opportunistic environmental mycobacterium belonging to the Mycobacterium avium-M. intracellulare complex. Although most commonly associated with pulmonary disease, there has been growing awareness of invasive M. chimaera infections following cardiac surgery. Investigations suggest worldwide 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 quantitative PCR (qPCR) assay for M. chimaera with a detection limit of 100 CFU/ml in whole blood spiked with bacteria. In vitro screening against DNA extracted from 40 other mycobacterial species and 22 bacterial species from 21 diverse genera confirmed the 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.

Position statement on interferon-γ release assays for the detection of latent tuberculosis infection.

Interferon-y release assays (IGRAs), such as the Quantiferon (QIFN) TB-Gold Plus assay (Qiagen, Hilden, Germany) and the T-SPOT.TB test (Oxford Immunotec Limited, Abingdon, United Kingdom), are marketed as a substitute for the tuberculin skin test (TST) for the detection of latent tuberculosis infection (LTBI). The relative merits of IGRAs and TST have been hotly debated over the last decade. The specificity of IGRAs has been optimised by using Mycobacterium tuberculosis-specific antigens. However, IGRAs are functional in vitro T-cell-based assays that may lack reproducibility due to specimen collection, transport, processing and kit manufacturing issues. Longitudinal studies comparing the ability of IGRAs and TST to predict the future development of active tuberculosis disease (TB) are the ultimate arbiters on the respective utility of these assays. Three meta-analyses addressing this comparison have now been published and clinical experience with IGRAs is accumulating. The systematic reviews show that IGRAs and TST have similar (but poor) ability to identify patients with LTBI at risk of developing active TB disease. The improved specificity of IGRAs however may reduce the number of patients requiring preventative therapy. Based on these meta-analyses, The National Tuberculosis Advisory Committee (NTAC) now recommends either TST or an IGRA for the investigation of LTBI in most circumstances. Both tests may be used in patients where the risk of progression to active TB disease is high and the disease sequelae potentially severe (eg. LTBI testing in immunocompromised patients or those commencing anti-tumour necrosis factor-a (TNF) therapy). Neither test should be used in the investigation of active TB disease (though TST and/or IGRA may be used as supplementary tests in paediatric cases). The choice of test for serial testing in healthcare workers (HCWs) remains controversial. A preference remains for TST in this circumstance because IGRAs have been bedevilled by higher rates of reversions and conversions when used for serial testing. These recommendations supersede all previous NTAC IGRA statements.

Culture-Independent Detection of Nontuberculous Mycobacteria in Clinical Respiratory Samples.

Culture-based detection of nontuberculous Mycobacteria (NTM) in respiratory samples is time consuming and can be subject to overgrowth by nonmycobacterial bacteria. We describe a single-reaction TaqMan quantitative PCR assay for the direct detection of NTM species in clinical samples that is specific, sensitive, and robust.

Endemic melioidosis in residents of desert region after atypically intense rainfall in central Australia, 2011.

After heavy rains and flooding during early 2011 in the normally arid interior of Australia, melioidosis was diagnosed in 6 persons over a 4-month period. Although the precise global distribution of the causal bacterium Burkholderia pseudomallei remains to be determined, this organism can clearly survive in harsh and even desert environments outside the wet tropics.

Performance of phenotypic tests for detection of penicillinase in Staphylococcus aureus isolates from Australia.

Recent studies have shown that chromogenic cephalosporin tests are inferior to disc zone edge tests in detecting penicillinase in Staphylococcus aureus isolates, resulting in a change to CLSI and EUCAST guidelines in 2012. We sought to confirm these findings using Australian isolates and compare the performance of the CLSI and EUCAST methods, which use different disc strengths, penicillin at 10 units (P10) and 1 unit (P1), respectively. Using blaZ PCR as the reference standard, the sensitivities of the tests for detection of penicillinase production were as follows: Cefinase disc test, 24/38 isolates (63%); P10 disc zone edge test, 34/38 isolates (89%); P10 disc diameter test, 25/38 isolates (66%); P1 disc zone edge test, 38/38 isolates (100%); and P1 disc diameter test, 38/38 isolates (100%). We also found that the P10 disc zone edge test reading was interpreted differently by the clinical laboratory and the study investigators in 11% of instances. Our findings support those of previous studies showing that chromogenic cephalosporin-based ß-lactamase tests are inferior to disc methods in detecting S. aureus penicillinase. We also conclude that the EUCAST method using the P1 disc has the best performance, particularly because the P1 disc zone diameter reading closely correlated with penicillinase production and reading of the disc zone diameter is less subjective than reading of the zone edge.

Tuberculosis in Australia: bacteriologically-confirmed cases and drug resistance, 2011. A report of the Australian Mycobacterium Reference Laboratory Network.

The Australian Mycobacterium Reference Laboratory Network collects and analyses laboratory data on new cases of disease caused by the Mycobacterium tuberculosis complex. In 2011, a total of 1,057 cases were identified bacteriologically; an annual reporting rate of 4.6 cases per 100,000 population. Eighteen children aged less than 15 years plus an additional 11 children from the Torres Strait Protected Zone had bacteriologically-confirmed tuberculosis. Results of in vitro drug susceptibility testing were available for 1,056 isolates for isoniazid, rifampicin, ethambutol, and pyrazinamide. A total of 107 (10.0%) isolates of M. tuberculosis were resistant to at least one of these anti-tuberculosis agents. Resistance to at least isoniazid and rifampicin (defined as multi-drug resistance, MDR) was detected in 25 (2.4%) isolates; 18 were from the respiratory tract (sputum n=14, bronchoscopy n=3, tissue n=1). Ten (55.6%) of the MDR-TB-positive sputum specimens were smear-positive, as was a single sample from a lymph node. Ten patients with MDR-TB were Papua New Guinea (PNG) nationals in the Torres Strait Protected Zone. If these PNG nationals are excluded from the analysis, the underlying MDR-TB rate in Australia was 1.4%. No cases of extensively drug-resistant TB (defined as MDR-TB with additional resistance to a fluoroquinolone and an injectable agent) were detected in 2011.

Mycobacterium pinnipedii tuberculosis in a free-ranging Australian fur seal (Arctocephalus pusillus doriferus) in South Australia.

This report describes the first case in South Australia, Australia, of Mycobacterium pinnipedii tuberculosis in a free-ranging Australian fur seal (Arctocephalus pusillus doriferus). Severe pyogranulomatous pleuropneumonia with intrahistocytic acid-fast beaded filamentous bacilli was seen on histology. M. pinnipedii was confirmed by full 24-loci mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) typing. Spillover concerns for public health and cattle are discussed.

Survey of Klebsiella pneumoniae bacteraemia in two South Australian hospitals and detection of hypermucoviscous phenotype and magA/rmpA genotypes in K . pneumoniae isolates.

PURPOSE: Clinical patterns of Klebsiella pneumoniae bacteraemia vary geographically. An invasive syndrome involving abscess formation has emerged in recent years. Putative virulence factors associated with this syndrome include colony hypermucoviscosity, and magA and rmpA genes. We studied epidemiologic and microbiologic characteristics of K. pneumoniae bacteraemia at two South Australian hospitals and identified cases of K. pneumoniae invasive syndrome. We determined the frequency of the hypermucoviscosity, magA and rmpA genes among bacteraemic and selected non-bacteraemic isolates. METHODS: Thirty-one patients with K. pneumoniae bacteraemia treated between June 2010 and July 2011 were included. Existing records were examined for relevant clinical and microbiological data. Urinary and wound isolates were also examined. Hypermucoviscosity was identified by a positive string test, whilst polymerase chain reaction detected magA and rmpA positive isolates. RESULTS: Of 31 blood culture isolates, 22 were associated with community-acquired infection. Biliary infection was the commonest source, occurring in ten patients. Three patients had K. pneumoniae invasive syndrome, all of Asian extraction (p = 0.0044). Four blood isolates demonstrated one or more of hypermucoviscosity, magA or rmpA; three were from patients with liver abscesses. Liver abscess isolates were all K1 serotype and had similar PFGE profiles. CONCLUSIONS: This study augments understanding of local epidemiology and microbiology of K. pneumoniae bacteraemia. It confirms local emergence of K. pneumoniae invasive syndrome and implicates the role of magA and rmpA genes in its pathogenesis.

Tuberculosis in Australia: bacteriologically confirmed cases and drug resistance, 2010. A report of the Australian Mycobacterium Reference Laboratory Network.

The Australian Mycobacterium Reference Laboratory Network collects and analyses laboratory data on new cases of disease caused by the Mycobacterium tuberculosis complex. In 2010, a total of 1,051 cases were identified by bacteriology; an annual reporting rate of 4.7 cases per 100,000 population. Twelve children aged less than 10 years had bacteriologically-confirmed tuberculosis. Results of in vitro drug susceptibility testing were available for 1,050 isolates for isoniazid (INH), rifampicin (RIF), ethambutol (EMB), and pyrazinamide (PYZ). A total of 126 (12%) isolates of M. tuberculosis were resistant to at least one of these anti-tuberculosis agents. Resistance to at least INH and RIF (defined as multi-drug resistance, MDR) was detected in 37 (3.5%) isolates, including three Australians with extensive travel in high burden TB countries; 33 were from the respiratory tract (sputum n=28, bronchoscopy n=5). Nineteen (65.5%) of the MDR-TB-positive sputum specimens were smear-positive, as were single samples from bronchoscopy and urine. Sixteen patients with MDR-TB were from the Torres Strait Protected Zone. If these Papa New Guinea nationals are excluded from the analysis, the underlying MDR-TB rate in Australian isolates was 2.0%. One case of extensively drug-resistant TB (defined as MDR-TB with additional resistance to a fluoroquinolone and an injectable agent) was detected in 2010.

The Royal College of Pathologists of Australasia (RCPA) position statement on COVID-19.

For the detection of early COVID-19 disease, RCPA supports the use of molecular tests for SARS-CoV-2 and strongly opposes the introduction of COVID-19 IgG/IgM rapid tests for this purpose.

Revised guidelines for Australian laboratories performing mycobacteriology testing.

Mycobacteriology laboratories play a key role in tuberculosis (TB) control by providing phenotypic and molecular diagnostics, by performing molecular typing to aid contact tracing, and by supporting research and similar laboratories in Australia's neighbouring countries where TB is prevalent. The National Tuberculosis Advisory Committee (NTAC) published a set of laboratory guidelines in 2006 aiming to document the infrastructure, equipment, staffing and work practices required for safe high-quality work in Australian mycobacteriology laboratories. These revised guidelines have the same aims and have been through a similar extensive consultative peer-review process involving the Mycobacterium Reference Laboratory (MRL) network, the Mycobacterium Special Interest Group (SIG) of the Australian Society for Microbiology (ASM), and other relevant national bodies. This revised document contains several significant changes reflecting the publication of new biosafety guidelines and tuberculosis standards by various national and international organisations, technology developments - such as the MPT64-based immunochromatographic tests (ICTs) and the Xpert MTB/RIF assay, and updated work practices in mycobacteriology laboratories. The biosafety recommendations affirm the latest Australian/New Zealand Standard 2243.3: 2010 and promote a biorisk assessment approach that, in addition to the risk categorisation of the organism, also considers the characteristics of the procedure being performed. Using this biorisk assessment approach, limited manipulations, such as Ziehl-Neelsen (ZN) microscopy, MPT64 ICTs, and culture inactivation/DNA extraction for molecular testing, may be performed on a positive TB culture in a PC2 laboratory with additional features and work practices. Other significant changes include recommendations on the integration of MPT64 ICTs and novel molecular tests into TB laboratory workflows to provide rapid accurate results that improve the care of TB patients. This revised document supersedes the original 2006 publication. NTAC will periodically review these guidelines and provide updates as new laboratory technologies become available.

Emergence and divergence of major lineages of Shiga-toxin-producing Escherichia coli in Australia.

Shiga-toxin-producing Escherichia coli (STEC) infection is an important global cause of foodborne disease. To date however, genomics-based studies of STEC have been predominately focused upon STEC collected in the Northern Hemisphere. Here, we demonstrate the population structure of 485 STEC isolates in Australia, and show that several clonal groups (CGs) common to Australia were infrequently detected in a representative selection of contemporary STEC genomes from around the globe. Further, phylogenetic analysis demonstrated that lineage II of the global O157:H7 STEC was most prevalent in Australia, and was characterized by a frameshift mutation in flgF, resulting in the H-non-motile phenotype. Strong concordance between in silico and phenotypic serotyping was observed, along with concordance between in silico and conventional detection of stx genes. These data represent the most comprehensive STEC analysis from the Southern Hemisphere, and provide a framework for future national genomics-based surveillance of STEC in Australia.

Draft Genome Sequences of Two Enterobacter cloacae subsp. cloacae Strains Isolated from Australian Hematology Patients with Bacteremia.

Enterobacter cloacae is a common member of the gut microbiota in healthy individuals. However, it is also an opportunistic pathogen, capable of causing bacteremia. We report the draft genomes of two Enterobacter cloacae subspecies cloacae strains isolated from hematology patients with bacteremia. Both isolates carry genes encoding extended-spectrum ß-lactamases.