Molecular epidemiology of tuberculosis in Tasmania and genomic characterisation of its first known multi-drug resistant case

Background:The origin and spread of tuberculosis (TB) in Tasmania and the types of strains of Mycobacteriumtuberculosis complex (MTBC) present in the population are largely unknown.Objective:The aim of this study was to perform the first genomic analysis of MTBC isolates from Tasmaniato better understand the epidemiology of TB in the state.Methods:Whole-genome sequencing was performed on cultured isolates of MTBC collected from2014–2016. Single-locus variant analysis was applied to determine the phylogeny of the isolatesand the presence of drug-resistance mutations. The genomic data were then cross-referencedagainst public health surveillance records on each of the cases.Results:We determined that 83.3% of TB cases in Tasmania from 2014–2016 occurred in non-Australianborn individuals. Two possible TB clusters were identified based on single locus variantanalysis, one from November-December 2014 (n = 2), with the second from MayAugust2015 (n = 4). We report here the first known isolate of multi-drug resistant (MDR)M. tuberculosis in Tasmania from 2016 for which we established its drug resistance mutationsand potential overseas origin. In addition, we characterised a case of M. bovis TB in aTasmanian-born person who presented in 2014, approximately 40 years after the last confirmedcase in the state’s bovids.Conclusions:TB in Tasmania is predominantly of overseas origin with genotypically-unique drug-susceptibleisolates of M. tuberculosis. However, the state also exhibits features of TB that areobserved in other jurisdictions, namely, the clustering of cases, and drug resistance. Earlydetection of TB and contact tracing, particularly of overseas-born cases, coordinated withrapid laboratory drug-susceptibility testing and molecular typing, will be essential for Tasmaniato reach the World Health Organisation’s TB eradication goals for low-incidencesettings

Influenza epidemiology in patients admitted to sentinel Australian hospitals in 2018: the Influenza Complications Alert Network (FluCAN)

TThe Influenza Complications Alert Network (FluCAN) is a sentinel hospital-based surveillance program that operates at sites in all jurisdictions in Australia. This report summarises the epidemiology of hospitalisations with laboratory-confirmed influenza during the 2018 influenza season. In this observational surveillance system, cases were defined as patients admitted to any of the 17 sentinel hospitals with influenza confirmed by nucleic acid detection. Data were also collected on a frequencymatched control group of influenza-negative patients admitted with acute respiratory infection. During the period 3 April to 31 October 2018 (the 2018 influenza season), 769 patients were admitted with confirmed influenza to one of 17 FluCAN sentinel hospitals. Of these, 30% were elderly (≥65 years), 28% were children (<16 years), 6.4% were Aboriginal and Torres Strait Islander peoples, 2.2% were pregnant and 66% had chronic comorbidities. A small proportion of FluCAN admissions were due to influenza B (13%). Estimated vaccine coverage was 77% in the elderly (≥65 years), 45% in nonelderly adults with medical comorbidities and 26% in children (<16 years) with medical comorbidities. The estimated vaccine effectiveness (VE) in the target population was 52% (95% CI: 37%, 63%). There were a smaller number of hospital admissions detected with confirmed influenza in this national observational surveillance system in 2018 than in 2017, with the demographic profile reflecting the change in circulating subtype from A/H3N2 to A/H1N1.We acknowledge the support of the Australian Government Department of Health and the Victorian Department of Health and Human Services for funding this system

GWAS meta-analysis of intrahepatic cholestasis of pregnancy implicates multiple hepatic genes and regulatory elements

Intrahepatic cholestasis of pregnancy (ICP) is a pregnancy-specific liver disorder affecting 0.5–2% of pregnancies. The majority of cases present in the third trimester with pruritus, elevated serum bile acids and abnormal serum liver tests. ICP is associated with an increased risk of adverse outcomes, including spontaneous preterm birth and stillbirth. Whilst rare mutations affecting hepatobiliary transporters contribute to the aetiology of ICP, the role of common genetic variation in ICP has not been systematically characterised to date. Here, we perform genome-wide association studies (GWAS) and meta-analyses for ICP across three studies including 1138 cases and 153,642 controls. Eleven loci achieve genome-wide significance and have been further investigated and fine-mapped using functional genomics approaches. Our results pinpoint common sequence variation in liver-enriched genes and liver-specific cis-regulatory elements as contributing mechanisms to ICP susceptibility

Intercontinental translocation of latent multidrug‐resistant tuberculosis to Australia demonstrated by whole genome sequencing

In 2016, there were an estimated 490 000 cases globally of multidrug- resistant (MDR) tuberculosis exhibiting resistance to isoniazid and rifampicin.1 The first case of MDR tuberculosis diagnosed in Tasmania occurred in 2016 in a Vietnamese- born person. Vietnam was the second highest reported country of birth for overseas- born patients with tuberculosis notified in Australia in 2014.2 The patient had previously tested positive for tuberculosis infection in an interferon- γ release assay test performed in Tasmania in early 2016, but at the time, the patient was asymptomatic and had a normal chest x- ray and a negative sputum culture. After an episode of colitis, a colon tissue biopsy specimen isolated Mycobacterium tuberculosis. Whole genome sequence of the isolate (TASMDR1), identified high confidence mutations for isoniazid, rifampicin, ethambutol and pyrazinamide, in accordance with the culture- based drug susceptibility testing, and, in addition, it identified a mutation associated with streptomycin resistance

State-Wide genomic and epidemiological analyses of Vancomycin-Resistant Enterococcus faecium in Tasmania’s Public Hospitals

From 2015 onwards, the number of vancomycin-resistant Enterococcus faecium (VREfm) isolates increased in Tasmania. Previously, we examined the transmission of VREfm at the Royal Hobart Hospital (RHH). In this study, we performed a state-wide analysis of VREfm from Tasmania’s four public acute hospitals. Whole-genome analysis was performed on 331 isolates collected from screening and clinical specimens of VREfm. In silico multi-locus sequence typing (MLST) was used to determine the relative abundance of broad sequence types (ST) across the state. Core genome MLST (cgMLST) was then applied to identify potential clades within the ST groupings followed by single-nucleotide polymorphic (SNP) analysis. This work revealed that differences in VREfm profiles are evident between the state’s two largest hospitals with the dominant vanA types being ST80 at the RHH and ST1421 at Launceston General Hospital (LGH). A higher number of VREfm cases were recorded at LGH (n = 54 clinical, n = 122 colonization) compared to the RHH (n = 14 clinical, n = 67 colonization) during the same time period, 2014–2016. Eleven of the clinical isolates from LGH were vanA and belonged to ST1421 (n = 8), ST1489 (n = 1), ST233 (n = 1), and ST80 (n = 1) whereas none of the clinical isolates from the RHH were vanA. For the recently described ST1421, cgMLST established the presence of individual clusters within this sequence type that were common to more than one hospital and that included isolates with a low amount of SNP variance (≤16 SNPs). A spatio-temporal analysis revealed that VREfm vanA ST1421 was first detected at the RHH in 2014 and an isolate belonging to the same cgMLST cluster was later collected at LGH in 2016. Inclusion of isolates from two smaller hospitals, the North West Regional Hospital (NRH) and the Mersey Community Hospital (MCH) found that ST1421 was present in both of these institutions in 2017. These findings illustrate the spread of a recently described sequence type of VREfm, ST1421, to multiple hospitals in an Australian state within a relatively short time span

High Peripheral Blood Th17 Percent Associated with Poor Lung Function in Cystic Fibrosis

<div><p>People with cystic fibrosis (CF) have been reported to make lung T cell responses that are biased towards T helper (Th) 2 or Th17. We hypothesized that CF-related T cell regulatory defects could be detected by analyzing CD4⁺ lymphocyte subsets in peripheral blood. Peripheral blood mononuclear cells from 42 CF patients (6 months–53 years old) and 78 healthy controls (2–61 years old) were analyzed for Th1 (IFN-γ⁺), Th2 (IL-4⁺), Th17 (IL-17⁺), Treg (FOXP3⁺), IL-10⁺ and TGF-β⁺ CD4⁺ cells. We observed higher proportions of Treg, IL-10⁺ and TGF-β⁺ CD4⁺ cells in CF adults (≥ 18 years old), but not children/adolescents, compared with controls. Within the CF group, high TGF-β⁺% was associated with chronic <i>Pseudomonas aeruginosa</i> lung infection (<i>p</i> < 0.006). We observed no significant differences between control and CF groups in the proportions of Th1, Th2 or Th17 cells, and no association within the CF group of any subset with sex, CFTR genotype, or clinical exacerbation. However, high Th17% was strongly associated with poor lung function (FEV1 % predicted) (<i>p</i> = 0.0008), and this association was strongest when both lung function testing and blood sampling were performed within one week. Our results are consistent with reports of CF as a Th17 disease and suggest that peripheral blood Th17 levels may be a surrogate marker of lung function in CF.</p></div

Comparison of demographics and CD4⁺ T cell subsets in control and cystic fibrosis groups.

<p><i>P</i>-values (Mann—Whitney) of significant differences are shown <b>bold.</b></p><p>Comparison of demographics and CD4⁺ T cell subsets in control and cystic fibrosis groups.</p

Emergence of Vancomycin-Resistant Enterococcus faecium at an Australian Hospital: A Whole Genome Sequencing Analysis

Abstract In 2015, a marked increase in vancomycin-resistant Enterococcus faecium (VREfm) isolation was detected at the Royal Hobart Hospital, Australia. The primary objective of this work was to examine the dynamics of VREfm transmission using whole genome data mapped to public health surveillance information. Screening and clinical isolates of VREfm from patients were typed for the specific vancomycin-resistance locus present. Of total isolates collected from 2014–2016 (n = 222), 15.3% and 84.7% harboured either the vanA or the vanB vancomycin-resistance locus, respectively. Whole-genome sequencing of 80 isolates was performed in conjunction with single-nucleotide polymorphic (SNP) analysis and in silico multi-locus sequence typing (MLST). Among the isolates sequenced, 5 phylogenetic clades were identified. The largest vanB clade belonged to MLST sequence type ST796 and contained clinical isolates from VREfm infections that clustered closely with isolates from colonised patients. Correlation of VREfm genotypes with spatio-temporal patient movements detected potential points of transmission within the hospital. ST80 emerged as the major vanA sequence type for which the most likely index case of a patient cluster was ascertained from SNP analyses. This work has identified the dominant clones associated with increased VREfm prevalence in a healthcare setting, and their likely direction of transmission

Comparison of CD4⁺ T cell subset percentages in adults and children in control and CF groups.

<p>*<i>P</i>-values (Mann—Whitney) of significant differences are shown <b>bold</b></p><p>Comparison of CD4⁺ T cell subset percentages in adults and children in control and CF groups.</p

Correlation of Th17% with FEV1% predicted depending on time between lung function testing and blood sampling.

<p>*<i>P</i>-values indicating significant differences are shown in <b>bold.</b></p><p>Correlation of Th17% with FEV1% predicted depending on time between lung function testing and blood sampling.</p