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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.
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COVID-19 , Quarentena , Austrália/epidemiologia , Surtos de Doenças , Humanos , SARS-CoV-2RESUMO
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.
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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.
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Guias de Prática Clínica como Assunto , Tuberculose/microbiologia , Austrália , Humanos , Laboratórios/normas , Mycobacterium tuberculosis , Tuberculose/diagnósticoRESUMO
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.
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Infecções por Escherichia coli/microbiologia , Genoma Bacteriano , Epidemiologia Molecular , Toxina Shiga/genética , Escherichia coli Shiga Toxigênica/genética , Escherichia coli Shiga Toxigênica/isolamento & purificação , Austrália/epidemiologia , Simulação por Computador , Farmacorresistência Bacteriana/genética , Infecções por Escherichia coli/epidemiologia , Escherichia coli O157/genética , Proteínas de Escherichia coli/genética , Evolução Molecular , Humanos , Tipagem de Sequências Multilocus , Mutação , Fenótipo , Filogenia , Saúde Pública , Sorotipagem , Escherichia coli Shiga Toxigênica/classificação , Sequenciamento Completo do GenomaAssuntos
Antibacterianos/administração & dosagem , Bacteriemia/diagnóstico , Bacteriófagos/fisiologia , Infecções por Yersinia pseudotuberculosis/diagnóstico , Yersinia pseudotuberculosis/isolamento & purificação , Idoso , Bacteriemia/tratamento farmacológico , Bacteriemia/microbiologia , Técnicas de Tipagem Bacteriana , Ceftriaxona/administração & dosagem , Ciprofloxacina/administração & dosagem , Diagnóstico Diferencial , Feminino , Humanos , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz , Yersinia pseudotuberculosis/genética , Infecções por Yersinia pseudotuberculosis/tratamento farmacológico , Infecções por Yersinia pseudotuberculosis/microbiologiaRESUMO
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.
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Infecções por Burkholderia/microbiologia , Burkholderia/isolamento & purificação , Clorexidina , Infecção Hospitalar/microbiologia , Surtos de Doenças , Desinfetantes , Austrália/epidemiologia , Burkholderia/genética , Infecções por Burkholderia/epidemiologia , Infecção Hospitalar/epidemiologia , Humanos , Unidades de Terapia Intensiva , Antissépticos Bucais , Filogenia , Polimorfismo de Nucleotídeo Único/genética , Centros de Atenção Terciária , Sequenciamento Completo do GenomaAssuntos
Técnicas Bacteriológicas/métodos , Burkholderia pseudomallei/isolamento & purificação , Melioidose/diagnóstico , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz , Burkholderia/química , Burkholderia/imunologia , Burkholderia/isolamento & purificação , Burkholderia pseudomallei/química , Burkholderia pseudomallei/imunologia , Diagnóstico Precoce , Humanos , Imunoensaio , Masculino , Melioidose/microbiologia , Pessoa de Meia-Idade , Sensibilidade e EspecificidadeRESUMO
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.
RESUMO
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.
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DNA Bacteriano/genética , DNA Bacteriano/isolamento & purificação , Técnicas de Diagnóstico Molecular/métodos , Infecções por Mycobacterium/diagnóstico , Mycobacterium/genética , Mycobacterium/isolamento & purificação , Reação em Cadeia da Polimerase/métodos , Humanos , Infecções por Mycobacterium/microbiologia , Sensibilidade e EspecificidadeRESUMO
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.
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Testes de Liberação de Interferon-gama , Tuberculose Latente/diagnóstico , Tuberculose Latente/microbiologia , Mycobacterium tuberculosis , Adulto , Fatores Etários , Contagem de Linfócito CD4 , Criança , Coinfecção , Análise Custo-Benefício , Infecções por HIV/imunologia , Infecções por HIV/virologia , Pessoal de Saúde , Humanos , Hospedeiro Imunocomprometido , Tuberculose Latente/transmissão , Guias de Prática Clínica como Assunto , Tuberculose/diagnóstico , Tuberculose/microbiologia , Tuberculose/transmissãoAssuntos
Actinobacteria/isolamento & purificação , Doenças Transmissíveis Importadas/diagnóstico , Doenças Transmissíveis Importadas/patologia , Infecções por Bactérias Gram-Positivas/diagnóstico , Infecções por Bactérias Gram-Positivas/patologia , Dermatopatias Bacterianas/diagnóstico , Dermatopatias Bacterianas/patologia , Actinobacteria/classificação , Adulto , Técnicas Bacteriológicas , DNA Bacteriano/química , DNA Bacteriano/genética , DNA Ribossômico/química , DNA Ribossômico/genética , Feminino , Humanos , Microscopia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Homologia de Sequência , ViagemAssuntos
Actinobacteria/isolamento & purificação , Doenças Transmissíveis Importadas/diagnóstico , Doenças Transmissíveis Importadas/patologia , Infecções por Bactérias Gram-Positivas/diagnóstico , Infecções por Bactérias Gram-Positivas/patologia , Dermatopatias Bacterianas/diagnóstico , Dermatopatias Bacterianas/patologia , Actinobacteria/classificação , Adulto , Técnicas Bacteriológicas , DNA Bacteriano/química , DNA Bacteriano/genética , DNA Ribossômico/química , DNA Ribossômico/genética , Feminino , Humanos , Microscopia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Homologia de Sequência , ViagemRESUMO
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.
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Técnicas de Diagnóstico Molecular/métodos , Infecções por Mycobacterium não Tuberculosas/diagnóstico , Micobactérias não Tuberculosas/isolamento & purificação , Reação em Cadeia da Polimerase em Tempo Real/métodos , Infecções Respiratórias/diagnóstico , Humanos , Sensibilidade e EspecificidadeRESUMO
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.
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Burkholderia pseudomallei , Clima Desértico , Melioidose/epidemiologia , Melioidose/microbiologia , Chuva , Características de Residência , Austrália/epidemiologia , Geografia , História do Século XXI , Humanos , Melioidose/históriaRESUMO
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.
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Técnicas Bacteriológicas/métodos , Penicilinase/análise , Infecções Estafilocócicas/microbiologia , Staphylococcus aureus/enzimologia , Austrália , Humanos , Fenótipo , Sensibilidade e Especificidade , Staphylococcus aureus/isolamento & purificaçãoRESUMO
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.
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Otárias , Mycobacterium/classificação , Mycobacterium/isolamento & purificação , Tuberculose Pulmonar/veterinária , Animais , Evolução Fatal , Masculino , Tuberculose Pulmonar/microbiologia , Tuberculose Pulmonar/patologiaRESUMO
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.
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Farmacorresistência Bacteriana Múltipla , Mycobacterium tuberculosis/isolamento & purificação , Tuberculose Resistente a Múltiplos Medicamentos/epidemiologia , Tuberculose Pulmonar/epidemiologia , Adolescente , Adulto , Distribuição por Idade , Idoso , Relatórios Anuais como Assunto , Antituberculosos/uso terapêutico , Austrália/epidemiologia , Criança , Pré-Escolar , Notificação de Doenças/estatística & dados numéricos , Emigração e Imigração , Monitoramento Epidemiológico , Feminino , Humanos , Incidência , Laboratórios , Masculino , Testes de Sensibilidade Microbiana , Pessoa de Meia-Idade , Mycobacterium tuberculosis/efeitos dos fármacos , Mycobacterium tuberculosis/crescimento & desenvolvimento , Estudos Retrospectivos , Distribuição por Sexo , Tuberculose Resistente a Múltiplos Medicamentos/tratamento farmacológico , Tuberculose Resistente a Múltiplos Medicamentos/etnologia , Tuberculose Resistente a Múltiplos Medicamentos/microbiologia , Tuberculose Pulmonar/tratamento farmacológico , Tuberculose Pulmonar/etnologia , Tuberculose Pulmonar/microbiologia , População BrancaRESUMO
BACKGROUND: Vitamin D (vitD) and L-arginine have important antimycobacterial effects in humans. Adjunctive therapy with these agents has the potential to improve outcomes in active tuberculosis (TB). METHODS: In a 4-arm randomised, double-blind, placebo-controlled factorial trial in adults with smear-positive pulmonary tuberculosis (PTB) in Timika, Indonesia, we tested the effect of oral adjunctive vitD 50,000 IU 4-weekly or matching placebo, and L-arginine 6.0 g daily or matching placebo, for 8 weeks, on proportions of participants with negative 4-week sputum culture, and on an 8-week clinical score (weight, FEV1, cough, sputum, haemoptysis). All participants with available endpoints were included in analyses according to the study arm to which they were originally assigned. Adults with new smear-positive PTB were eligible. The trial was registered at ClinicalTrials.gov NCT00677339. RESULTS: 200 participants were enrolled, less than the intended sample size: 50 received L-arginine + active vitD, 49 received L-arginine + placebo vit D, 51 received placebo L-arginine + active vitD and 50 received placebo L-arginine + placebo vitD. According to the factorial model, 99 people received arginine, 101 placebo arginine, 101 vitamin D, 99 placebo vitamin D. Results for the primary endpoints were available in 155 (4-week culture) and 167 (clinical score) participants. Sputum culture conversion was achieved by week 4 in 48/76 (63%) participants in the active L-arginine versus 48/79 (61%) in placebo L-arginine arms (risk difference -3%, 95% CI -19 to 13%), and in 44/75 (59%) in the active vitD versus 52/80 (65%) in the placebo vitD arms (risk difference 7%, 95% CI -9 to 22%). The mean clinical outcome score also did not differ between study arms. There were no effects of the interventions on adverse event rates including hypercalcaemia, or other secondary outcomes. CONCLUSION: Neither vitD nor L-arginine supplementation, at the doses administered and with the power attained, affected TB outcomes. REGISTRY: ClinicalTrials.gov. Registry number: NCT00677339.