Complete Genome Sequence of a New Zealand Mycobacterium tuberculosis Strain Responsible for Ongoing Transmission over the Past 30 Years.

We report here the complete genome sequence of Mycobacterium tuberculosis strain Colonial S-type 1 (CS1), which has been responsible for ongoing outbreaks of tuberculosis in New Zealand over the past 30 years. CS1 appears to be highly transmissible, with greater rates of progression to active disease, compared to other circulating M. tuberculosis strains; therefore, comparison of its genomic content is of interest.

Tiotropium treatment for bronchiectasis: a randomised, placebo-controlled, crossover trial.

BACKGROUND: Tiotropium via the HandiHaler device is an established long-acting, anticholinergic bronchodilator that prevents exacerbations and improves lung function in patients with chronic obstructive pulmonary disease. We hypothesised that tiotropium would reduce pulmonary exacerbations and improve lung function in patients with stable bronchiectasis and airflow limitation, and assessed the effect of tiotropium on these outcomes. METHODS: In a randomised, double-blind, two-period crossover trial, we recruited adult patients from three hospitals in New Zealand. Patients were excluded if they had a smoking history of >20 pack-years. Patients were assigned to either the tiotropium-placebo or placebo-tiotropium sequence in a 1:1 ratio, using randomly permuted blocks stratified by centre. Participants and investigators were masked to treatment allocation. Eligible patients received tiotropium 18 µg via HandiHaler daily for 6 months followed by 6 months of placebo, or vice versa, with a washout period of 4 weeks. The primary end-point was rate of event-based exacerbations during the 6-month period. Primary analyses were carried out in an intention-to-treat set. RESULTS: 90 patients were randomly assigned and 85 completed both treatment cycles. The rate of exacerbations was 2.17 per year under the tiotropium treatment and 2.27 per year under placebo (rate ratio 0.96, 95% CI 0.72-1.27; p=0.77). Tiotropium, compared with placebo, improved forced expiratory volume in 1 s by 58 mL (95% CI 23-92 mL; p=0.002). Adverse events were similar under both treatments. CONCLUSIONS: Tiotropium via HandiHaler over 6 months significantly improved lung function but not frequency of exacerbations. Further research is required to understand the clinical context and significance of these findings.

Long-term macrolide antibiotics for the treatment of bronchiectasis in adults: an individual participant data meta-analysis.

BACKGROUND: Bronchiectasis guidelines recommend long-term macrolide treatment for patients with three or more exacerbations per year without Pseudomonas aeruginosa infection. Randomised controlled trials suggest that long-term macrolide treatment can prevent exacerbations in adult patients with bronchiectasis, but these individual studies have been too small to do meaningful subgroup analyses. We did a systematic review and individual patient data (IPD) meta-analysis to explore macrolide benefit in subpopulations, including those in which macrolide therapy is not currently recommended. METHODS: We searched MEDLINE, Embase, the Cochrane Central Register of Controlled Trials, and Web of Science from Jan 1, 2000, to Sept 30, 2018, to identify double blind, randomised, placebo-controlled trials of macrolide antibiotics in adult patients with bronchiectasis. We applied no language restrictions. Randomised controlled trials were eligible if treatment was defined a priori as long term and had a primary or secondary outcome of bronchiectasis exacerbations. Studies in patients with cystic fibrosis bronchiectasis were excluded. The primary outcome of the meta-analysis was frequency of exacerbations requiring treatment with antibiotics. Secondary endpoints were time to first exacerbation, change in quality of life according to the St George's Respiratory Questionnaire (SGRQ), and change in FEV1. IPD meta-analysis was done using fixed effects models adjusting for age, sex, FEV1, and trial. We did prespecified subgroup analyses for each of the primary and secondary endpoints using one-step meta-analysis only. Subgroups were defined by age, sex, previous exacerbation frequency, smoking status, inhaled corticosteroid use at baseline, body-mass index at baseline, cause, C-reactive protein at baseline, baseline FEV1 percentage of predicted, SGRQ total score, and Pseudomonas aeruginosa in sputum culture at baseline. The meta-analysis is registered with the PROSPERO international register of systematic reviews, number CRD42018102908. FINDINGS: Of 234 identified studies, we included three randomised controlled trials, and IPD was obtained for 341 participants. Macrolide antibiotics reduced the frequency of exacerbations (adjusted incidence rate ratio [IRR] 0·49, 95% CI 0·36 to 0·66; p<0·0001). We also found that macrolide treatment improved the time to first exacerbation (adjusted hazard ratio 0·46, 0·34 to 0·61; p<0·0001) and was associated with improved quality of life measured by the SGRQ (mean improvement 2·93 points, 0·03 to 5·83; p=0·048). Macrolides were not associated with a significant improvement in FEV1 (67 mL at 1 year, -22 to 112; p=0·14). Effect estimates in prespecified subgroup analyses revealed a reduced frequency of exacerbations in all prespecified subgroups, including a high level of benefit in patients with P aeruginosa infection (IRR 0·36, 0·18-0·72; p=0·0044) and in patients with one to two exacerbations per year (0·37, 0·16-0·88; p=0·025). Studies were rated as low risk of bias across all domains. INTERPRETATION: Long-term macrolide treatment significantly reduces the frequency of exacerbations in patients with bronchiectasis, with similar benefits observed in all subgroups based on patient characteristics. This finding suggests that macrolides might be considered in patients in whom macrolides are not indicated according to the current guidelines, particularly if alternative approaches to reduce exacerbations have been unsuccessful. However, downsides of long-term macrolide treatment must also be taken into account. FUNDING: European Respiratory Society.

Dispersal of Mycobacterium tuberculosis Driven by Historical European Trade in the South Pacific.

Mycobacterium tuberculosis (Mtb) is a globally distributed bacterial pathogen whose population structure has largely been shaped by the activities of its obligate human host. Oceania was the last major global region to be reached by Europeans and is the last region for which the dispersal and evolution of Mtb remains largely unexplored. Here, we investigated the evolutionary history of the Euro-American L4.4 sublineage and its dispersal to the South Pacific. Using a phylodynamics approach and a dataset of 236 global Mtb L4.4 genomes we have traced the origins and dispersal of L4.4 strains to New Zealand. These strains are predominantly found in indigenous Maori and Pacific people and we identify a clade of European, likely French, origin that is prevalent in indigenous populations in both New Zealand and Canada. Molecular dating suggests the expansion of European trade networks in the early 19th century drove the dispersal of this clade to the South Pacific. We also identify historical and social factors within the region that have contributed to the local spread and expansion of these strains, including recent Pacific migrations to New Zealand and the rapid urbanization of Maori in the 20th century. Our results offer new insight into the expansion and dispersal of Mtb in the South Pacific and provide a striking example of the role of historical European migrations in the global dispersal of Mtb.

Cardiac dysfunction in exacerbations of chronic obstructive pulmonary disease is often not detected by electrocardiogram and chest radiographs.

BACKGROUND: Cardiac dysfunction is common in exacerbations of chronic obstructive pulmonary disease (COPD), even in patients without clinically suspected cardiac disorders. AIM: To investigate associations between electrocardiogram (ECG) and chest radiograph abnormalities and biochemical evidence of cardiac dysfunction (N-terminal pro-B-type natriuretic peptide and troponin T) in patients hospitalised with exacerbations of COPD at Waikato Hospital. METHODS: Independent examiners, blinded to NT-proBNP and troponin T levels, assessed ECG for tachycardia, atrial fibrillation, ventricular hypertrophy and ischaemic changes in 389 patients and chest radiographs for signs of heart failure in 350 patients. Associations between electrocardiographic and radiographic abnormalities with at least moderate interrater agreement and cardiac biomarkers were analysed. RESULTS: High NT-proBNP values (>220 pmol/L) were associated with atrial fibrillation (22 vs 6%), right ventricular hypertrophy (24 vs 15%), left ventricular hypertrophy (15 vs 4%), ischaemia (59 vs 33%) and cardiomegaly (42 vs 20%). High troponin T values (>0.03ug/L or high-sensitivity >50 ng/L) were associated with tachycardia (65 vs 41%), right ventricular hypertrophy (26 vs 15%) and ischaemia (60 vs 36%). None of the electrocardiographic or radiographic abnormalities was sensitive or specific for cardiac biomarker abnormalities. Ischaemia on ECG was the best indicator for raised NT-proBNP (sensitivity 59%, specificity 67%). Tachycardia and ischaemia were the best indicators of raised troponin T (sensitivity 65 and 60%, specificity 59 and 64% respectively). CONCLUSIONS: ECG and chest radiograph abnormalities have poor sensitivity and specificity for diagnosing acute cardiac dysfunction in exacerbations of COPD. Cardiac biomarkers provide additional diagnostic information about acute cardiac dysfunction in exacerbations of COPD.

Rapid molecular diagnosis of the Mycobacterium tuberculosis Rangipo strain responsible for the largest recurring TB cluster in New Zealand.

Despite New Zealand being a low-tuberculosis (TB) burden country, there are disproportionately high rates of TB in particular populations. Here, we report a rapid molecular diagnosis of the Mycobacterium tuberculosis Rangipo strain responsible for the largest recurring TB cluster in New Zealand.

Whole genome sequencing of Mycobacterium tuberculosis reveals slow growth and low mutation rates during latent infections in humans.

Very little is known about the growth and mutation rates of Mycobacterium tuberculosis during latent infection in humans. However, studies in rhesus macaques have suggested that latent infections have mutation rates that are higher than that observed during active tuberculosis disease. Elevated mutation rates are presumed risk factors for the development of drug resistance. Therefore, the investigation of mutation rates during human latency is of high importance. We performed whole genome mutation analysis of M. tuberculosis isolates from a multi-decade tuberculosis outbreak of the New Zealand Rangipo strain. We used epidemiological and phylogenetic analysis to identify four cases of tuberculosis acquired from the same index case. Two of the tuberculosis cases occurred within two years of exposure and were classified as recently transmitted tuberculosis. Two other cases occurred more than 20 years after exposure and were classified as reactivation of latent M. tuberculosis infections. Mutation rates were compared between the two recently transmitted pairs versus the two latent pairs. Mean mutation rates assuming 20 hour generation times were 5.5 X 10(-10) mutations/bp/generation for recently transmitted tuberculosis and 7.3 X 10(-11) mutations/bp/generation for latent tuberculosis. Generation time versus mutation rate curves were also significantly higher for recently transmitted tuberculosis across all replication rates (p = 0.006). Assuming identical replication and mutation rates among all isolates in the final two years before disease reactivation, the u 20 hr mutation rate attributable to the remaining latent period was 1.6 × 10(-11) mutations/bp/generation, or approximately 30 fold less than that calculated during the two years immediately before disease. Mutations attributable to oxidative stress as might be caused by bacterial exposure to the host immune system were not increased in latent infections. In conclusion, we did not find any evidence to suggest elevated mutation rates during tuberculosis latency in humans, unlike the situation in rhesus macaques.

Biomarkers of cardiac dysfunction and mortality from community-acquired pneumonia in adults.

BACKGROUND: Cardiac dysfunction is common in acute respiratory diseases and may influence prognosis. We hypothesised that blood levels of N-terminal B-type natriuretic peptide (NT-proBNP) and high-sensitivity Troponin T would predict mortality in adults with community-acquired pneumonia. METHODS AND FINDINGS: A prospective cohort of 474 consecutive patients admitted with community-acquired pneumonia to two New Zealand hospitals over one year. Blood taken on admission was available for 453 patients and was analysed for NT-proBNP and Troponin T. Elevated levels of NT-proBNP (>220 pmol/L) were present in 148 (33%) and 86 (19%) of these patients respectively. Among the 26 patients who died within 30 days of admission, 23 (89%) had a raised NT-proBNP and 14 (53%) had a raised Troponin T level on admission compared to 125 (29%) and 72 (17%) of the 427 who survived (p values<0.001). Both NT-proBNP and Troponin T predicted 30-day mortality in age-adjusted analysis but after mutual adjustment for the other cardiac biomarker and the Pneumonia Severity Index, a raised N-terminal pro-brain natriuretic peptide remained a predictor of 30-day mortality (OR = 5.3, 95% CI 1.4-19.8, p = 0.013) but Troponin T did not (OR = 1.3, 95% CI 0.5-3.2, p = 0.630). The areas under the receiver-operating curves to predict 30-day mortality were similar for NT-proBNP (0.88) and the Pneumonia Severity Index (0.87). CONCLUSIONS: Elevated N-terminal B-type natriuretic peptide is a strong predictor of mortality from community-acquired pneumonia independent of clinical prognostic indicators. The pathophysiological basis for this is unknown but suggests that cardiac involvement may be an under-recognised determinant of outcome in pneumonia and may require a different approach to treatment. In the meantime, measurement of B-type natriuretic peptides may help to assess prognosis.

Azithromycin for prevention of exacerbations in non-cystic fibrosis bronchiectasis (EMBRACE): a randomised, double-blind, placebo-controlled trial.

BACKGROUND: Azithromycin is a macrolide antibiotic with anti-inflammatory and immunomodulatory properties. We tested the hypothesis that azithromycin would decrease the frequency of exacerbations, increase lung function, and improve health-related quality of life in patients with non-cystic fibrosis bronchiectasis. METHODS: We undertook a randomised, double-blind, placebo-controlled trial at three centres in New Zealand. Between Feb 12, 2008, and Oct 15, 2009, we enrolled patients who were 18 years or older, had had at least one pulmonary exacerbation requiring antibiotic treatment in the past year, and had a diagnosis of bronchiectasis defined by high-resolution CT scan. We randomly assigned patients to receive 500 mg azithromycin or placebo three times a week for 6 months in a 1:1 ratio, with a permuted block size of six and sequential assignment stratified by centre. Participants, research assistants, and investigators were masked to treatment allocation. The coprimary endpoints were rate of event-based exacerbations in the 6-month treatment period, change in forced expiratory volume in 1 s (FEV(1)) before bronchodilation, and change in total score on St George's respiratory questionnaire (SGRQ). Analyses were by intention to treat. This study is registered with the Australian New Zealand Clinical Trials Registry, number ACTRN12607000641493. FINDINGS: 71 patients were in the azithromycin group and 70 in the placebo group. The rate of event-based exacerbations was 0·59 per patient in the azithromycin group and 1·57 per patient in the placebo group in the 6-month treatment period (rate ratio 0·38, 95% CI 0·26-0·54; p<0·0001). Prebronchodilator FEV(1) did not change from baseline in the azithromycin group and decreased by 0·04 L in the placebo group, but the difference was not significant (0·04 L, 95% CI -0·03 to 0·12; p=0·251). Additionally, change in SGRQ total score did not differ between the azithromycin (-5·17 units) and placebo groups (-1·92 units; difference -3·25, 95% CI -7·21 to 0·72; p=0·108). INTERPRETATION: Azithromycin is a new option for prevention of exacerbations in patients with non-cystic fibrosis bronchiectasis with a history of at least one exacerbation in the past year. FUNDING: Health Research Council of New Zealand and Auckland District Health Board Charitable Trust.

Biochemical markers of cardiac dysfunction predict mortality in acute exacerbations of COPD.

BACKGROUND: Retrospective studies suggest that plasma levels of N-terminal pro-brain natriuretic peptide (NT-proBNP) and cardiac troponin T are often elevated in patients with acute exacerbations of chronic obstructive pulmonary disease (COPD) and are associated with increased mortality. These cardiac biomarkers were investigated in an unselected cohort of patients admitted to hospital with exacerbations of COPD. METHODS: Consecutive patients with physician-diagnosed COPD exacerbation but without clinical evidence of acute cardiac disease admitted to a public hospital over a 1 year period were studied prospectively. NT-proBNP and troponin T were measured on admission. The primary end point was all-cause mortality at 30 days. RESULTS: Elevated NT-proBNP (>220 pmol/l) was present in 65/244 patients (27.5%) and significantly predicted 30-day mortality (OR 9.0, 95% CI 3.1 to 26.2, p<0.001). Elevated troponin T (>0.03 µg/l) was found in 40/241 patients (16.6%) and also predicted 30-day mortality (OR 6.3, 95% CI 2.4 to 16.5, p<0.001). These associations persisted after adjusting for other clinical and laboratory predictors of mortality (arterial CO(2) pressure (Paco(2)), body mass index and CURB65 score). NT-proBNP and troponin T levels appeared to have additive associations with mortality: 30-day mortality among patients with abnormalities of both NT-proBNP and troponin T was 15-fold higher than among patients with normal values. CONCLUSION: Elevated levels of NT-proBNP and troponin T are strong predictors of early mortality among patients admitted to hospital with acute exacerbations of COPD independently of other known prognostic indicators. The pathophysiological basis for this is unknown, but indicates that cardiac involvement in exacerbations of COPD may be an important determinant of prognosis.

Vitamin D, innate immunity and outcomes in community acquired pneumonia.

BACKGROUND AND OBJECTIVE: Vitamin D regulates the production of the antimicrobial peptides cathelicidin and beta-defensin-2, which play an important role in the innate immune response to infection. We hypothesized that vitamin D deficiency would be associated with lower levels of these peptides and worse outcomes in patients admitted to hospital with community acquired pneumonia. METHODS: Associations between mortality and serum levels of 25-hydroxyvitamin D, cathelicidin and beta-defensin-2 were investigated in a prospective cohort of 112 patients admitted with community acquired pneumonia during winter. RESULTS: Severe 25-hydroxyvitamin D deficiency (<30nmol/L) was common in this population (15%) and was associated with a higher 30-day mortality compared with patients with sufficient 25-hydroxyvitamin D (>50nmol/L) (odds ratio 12.7, 95% confidence interval: 2.2-73.3, P=0.004). These associations were not explained by differences in age, comorbidities, or the severity of the acute illness. Neither cathelicidin nor beta-defensin-2 levels predicted mortality, although there was a trend towards increased mortality with lower cathelicidin (P=0.053). Neither cathelicidin nor beta-defensin-2 levels correlated with 25-hydroxyvitamin D. CONCLUSIONS: 25-hydroxyvitamin D deficiency is associated with increased mortality in patients admitted to hospital with community acquired pneumonia during winter. Contrary to our hypothesis, 25-hydroxyvitamin D levels were not associated with levels of cathelicidin or beta-defensin-2.

Predicting early mortality in acute exacerbation of chronic obstructive pulmonary disease using the CURB65 score.

BACKGROUND AND OBJECTIVE: Hospitalization for exacerbation of COPD is associated with a high risk of mortality. A risk-prediction model using information easily obtained on admission could help to identify high-risk individuals. The CURB65 score was developed to predict mortality risk in community acquired pneumonia. A retrospective study found that this score was also associated with mortality in COPD exacerbations. We conducted a prospective study to assess the utility of the CURB65 score in acute COPD exacerbations. METHODS: Consecutive patients with physician diagnosed COPD exacerbations admitted to a public hospital during a 1-year period were studied prospectively. The CURB65 scores were calculated from information obtained at initial hospital presentation. CURB65 = one point each for Confusion, Urea > 7 mmol/L, Respiratory rate ≥ 30/min, low Blood pressure, age ≥ 65 years. RESULTS: 30-day mortality data were available for 249 of 252 patients. CURB65 scores on admission significantly predicted risk of death during the hospital admission and at 30 days. The 30-day mortality by score groups were: low risk (scores 0-1) 2.0% (2/98), moderate risk (score 2) 6.7% (6/90) and high risk (scores 3-5) 21.3% (13/61). CURB65 scores were not predictive of 1-year mortality. CONCLUSIONS: A simple 6-point score based on confusion, blood urea, respiratory rate, blood pressure and age can be used to stratify patients with COPD exacerbation into different management groups. The CURB65 score was as effective in predicting early mortality in our cohort of acute COPD exacerbations as it was in previous cohorts with community acquired pneumonia. Our findings suggest that CURB65 scores can help clinicians to assess patients with exacerbation of COPD.

Pulmonary embolism outcome: a prospective evaluation of CT pulmonary angiographic clot burden score and ECG score.

OBJECTIVE: The purpose of this study was to establish whether a correlation exists between the CT pulmonary angiographic clot burden score, the ECG score at diagnosis, and the 12-month mortality rate among patients diagnosed with pulmonary embolism. SUBJECTS AND METHODS: A total of 523 consecutive patients who underwent CT pulmonary angiography for a suspected moderate to high pretest probability of pulmonary embolism were recruited from March 2003 to October 2004. There were 105 patients with positive CT pulmonary angiography examinations. Two consultant respiratory physicians and two consultant radiologists independently and prospectively calculated an ECG score and a quantified pulmonary artery clot burden, respectively. Twelve-month follow-up was completed in all patients. RESULTS: The mean ECG score was 2.36 (SD, 2.84) and the mean clot burden score percentage was 23.74% (16.8%). Poor correlation (r = 0.09) was seen between the average ECG score and the average clot burden score percentage (p = 0.39) at diagnosis. Thirteen patients had died at the 12-month follow-up. The mean ECG score for those patients who were alive was 2.4 (2.91) and for those who had died was 2.03 (2.34) at 12 months (p = 0.65). The mean clot burden score percentage for those patients who were alive was 24% (17%) and for those who had died was 22.1% (15.7%) at 12 months (p < 0.73). CONCLUSION: No statistically significant association was seen between ECG score and CT pulmonary angiographic clot burden at diagnosis and the 12-month all-cause mortality rate of patients diagnosed with pulmonary embolism.

Maori have a much higher incidence of community-acquired pneumonia and pneumococcal pneumonia than non-Maori: findings from two New Zealand hospitals.

To determine the incidence rates of community-acquired pneumonia and pneumococcal pneumonia requiring hospitalisation among Maori and non-Maori, an observational study was conducted in Christchurch and Hamilton. Self-reported data were collected using an interviewer-administered questionnaire. Routine clinical, radiological, and microbiological techniques were used apart from the BinaxNow pneumococcal antigen test for diagnosis of this infection. Census data was used to determine the denominator for statistical analyses. The pneumonia rate overall was 3.03 times higher among Maori than non-Maori (p<0.001). Differences were significant for each 10-year age group from age 45-74 years (p<0.05). The rate of pneumococcal pneumonia was 3.23 fold higher for Maori than non-Maori (p<0.001), but it did not reach statistical significance in the age-related comparisons. These ethnic disparities are of major concern, and policy planners should consider further interventions to improve the efficacy of current anti-smoking campaigns and to undertake studies of conjugate pneumococcal vaccines for Maori.