Genomic characteristics of prospectively sequenced from respiratory and non-respiratory sources.

Understanding the differences between strains isolated from respiratory and non-respiratory sources may inform clinical care and control strategies. We examined demographic and genomic characteristics of all culture-confirmed cultures isolated from respiratory and non-respiratory sources in New South Wales, Australia, from January 2017 to December 2021, using logistic regression models. strains from 1,831 patients were sequenced; 64.

Exploring programmatic indicators of tuberculosis control that incorporate routine sequencing in low incidence settings: a comprehensive (2017-2021) patient cohort analysis.

Background: Routine whole genome sequencing of has been implemented with increasing frequency. However, its value for tuberculosis (TB) control programs beyond individual case management and enhanced drug resistance detection has not yet been explored.

Methods: We analysed routine sequencing data of culture-confirmed TB cases notified between 1st January 2017 and 31st December 2021 in New South Wales (NSW), Australia.

Genomic markers of drug resistance in populations with minority variants.

Minority variants of harboring mutations conferring resistance can become dominant populations during tuberculosis (TB) treatment, leading to treatment failure. Our understanding of drug-resistant within-host subpopulations and the frequency of resistance-conferring mutations in minority variants remains limited. sequences recovered from liquid cultures of culture-confirmed TB cases notified between January 2017 and December 2021 in New South Wales, Australia were examined.

Value of routine whole genome sequencing for Mycobacterium tuberculosis drug resistance detection.

Routine whole genome sequencing (WGS) of pathogens is becoming more feasible as sequencing costs decrease and access to benchtop sequencing equipment and bioinformatics pipelines increases. This study examined the added value gained from implementing routine WGS of all Mycobacterium tuberculosis isolates in New South Wales, Australia. Drug resistance markers inferred from WGS data were compared to commercial genotypic drug susceptibility testing (DST) assays and conventional phenotypic DST in all isolates sequenced between 2016 and 2019.

Use of GeneXpert MTB/RIF on a single pooled sputum specimen to exclude pulmonary tuberculosis among hospital inpatients placed in respiratory isolation.

Background: Patients with suspected pulmonary tuberculosis (PTB) are usually placed in respiratory isolation awaiting three sputum smear microscopy results for acid-fast bacilli (3AFB). GeneXpert MTB/RIF (Xpert) on a pooled sample from two sputa may allow for more rapid de-isolation.

Objectives: To compare the sensitivity and negative predictive value (NPV) of Xpert performed on a single pooled sputum sample ('pooled Xpert') to 3AFB, in order to exclude PTB in patients placed in respiratory isolation.

Genome-wide comparison of Corynebacterium diphtheriae isolates from Australia identifies differences in the Pan-genomes between respiratory and cutaneous strains.

Background: Corynebacterium diphtheriae is the main etiological agent of diphtheria, a global disease causing life-threatening infections, particularly in infants and children. Vaccination with diphtheria toxoid protects against infection with potent toxin producing strains. However a growing number of apparently non-toxigenic but potentially invasive C.

Mutations associated with in vitro resistance to bedaquiline in Mycobacterium tuberculosis isolates in Australia.

Genome-wide analysis of 517 Mycobacterium tuberculosis isolates from New South Wales, Australia, have identified previously reported and 8 new mutations in Rv0678 and atpE genes linked to in vitro resistance to bedaquiline, a new class of antimycobacterial drugs. These mutations were present in 2.9% of prospectively sequenced genomes but in 10.

Recurrence of tuberculosis in a low-incidence setting: a retrospective cross-sectional study augmented by whole genome sequencing.

Background: The recurrence of tuberculosis (TB) disease in treated patients can serve as a marker of the efficacy of TB control programs. Recurrent disease represents either endogenous reactivation with the same strain of Mycobacterium tuberculosis due to non-compliance or inadequate therapy or exogenous reinfection with a new strain. Genotyping or whole genome sequencing (WGS) of M.

Comparison of quantitative PCR and culture-based methods for evaluating dispersal of Bacillus thuringiensis endospores at a bioterrorism hoax crime scene.

Since the anthrax mail attacks of 2001, law enforcement agencies have processed thousands of suspicious mail incidents globally, many of which are hoax bioterrorism threats. Bio-insecticide preparations containing Bacillus thuringiensis (Bt) spores have been involved in several such threats in Australia, leading to the requirement for rapid and sensitive detection techniques for this organism, a close relative of Bacillus anthracis. Here we describe the development of a quantitative PCR (qPCR) method for the detection of Bt crystal toxin gene cry1, and evaluation of the method's effectiveness during a hoax bioterrorism event in 2009.

Tuberculosis in Australia: bacteriologically confirmed cases and drug resistance, 2004: a report of the Australian Mycobacterium Reference Laboratory Network.

The Australian Mycobacterium Reference Laboratory Network collected and analysed laboratory data on new cases of disease caused by Mycobacterium tuberculosis complex in the year 2004. A total of 787 cases were identified by bacteriology, representing an annual reporting rate of 3.9 cases per 100,000 population.

Tuberculosis in Australia: bacteriologically confirmed cases and drug resistance, 2003. A report of the Australian Mycobacterium Reference Laboratory Network.

The Australian Mycobacterium Reference Laboratory Network collected and analysed laboratory data on new cases of disease caused by Mycobacterium tuberculosis complex in the year 2003. A total of 784 cases were identified by bacteriology, representing an annual reporting rate of 3.9 cases of laboratory confirmed tuberculosis per 100,000 population.