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Murray, M.

Publications and source records attributed to Murray, M..

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Genome wide association with quantitative resistance phenotypes in Mycobacterium tuberculosis reveals novel resistance genes and regulatory regions

Drug resistance is threatening attempts at tuberculosis epidemic control. Molecular diagnostics for drug resistance that rely on the detection of resistance-related mutations could expedite patient care and accelerate progress in TB eradication. We performed minimum inhibitory concentration testing for 12 anti-TB drugs together with Illumina whole genome sequencing on 1452 clinical Mycobacterium tuberculosis (MTB) isolates. We then used a linear mixed model to evaluate genome wide associations between mutations in MTB genes or noncoding regions and drug resistance, followed by validation of our findings in an independent dataset of 792 patient isolates. Novel associations at 13 genomic loci were confirmed in the validation set, with 2 involving noncoding regions. We found promoter mutations to have smaller average effects on resistance levels than gene body mutations in genes where both can contribute to resistance. Enabled by a quantitative measure of resistance, we estimated the heritability of the resistance phenotype to 11 anti-TB drugs and identify a lower than expected contribution from known resistance genes. We also report the proportion of variation in resistance levels explained by the novel loci identified here. This study highlights the complexity of the genomic mechanisms associated with the MTB resistance phenotype, including the relatively large number of potentially causative or compensatory loci, and emphasizes the contribution of the noncoding portion of the genome.

evolutionary biology

Rifampicin and rifabutin resistance in 1000 Mycobacterium tuberculosis clinical isolates

SynopsisDrug resistant tuberculosis (TB) remains a public health challenge with limited treatment options and high associated mortality. Rifamycins are among the most potent anti-TB drugs, and the loss of susceptibility to these agents, a hallmark of MDR TB, is considered a substantial therapeutic challenge. Rifamycins are known to target the RpoB subunit of RNA polymerase; however, our understanding of how rifamycin resistance is genetically encoded remains incomplete. Here we investigated rpoB genetic diversity and cross resistance between the two rifamycin drugs rifampicin (RIF) and rifabutin (RFB). We performed whole genome sequencing of 1005 MTB clinical isolates and measured minimum inhibitory concentration (MIC) to both agents on 7H10 agar using the indirect proportion method. Of the 1005 isolates, 767 were RIF resistant, and of these, 211 (27%) were sensitive to RFB at the critical concentration of 0.5ug/ml; 101/211 isolates had the rpoB mutation D435V (E.coli D516V). Isolates with discrepant resistance (RIF R and RFB S) 16.9 times more likely to harbor a D435V mutation as those resistant to both agents (OR 95% CI 10.5-27.9, P-value <10-40). To further understand this discrepancy, we generated both D435V and S450L (E.coli S531L) rpoB mutants in a laboratory strain and measured their antibiotic susceptibility using the alamar blue reduction assay. Compared with wildtype, D435V increased the 50% inhibitory concentration (IC50) to both RIF and RFB, however in both cases to a lesser degree than the S450L mutation. The observation that the rpoB D435V mutation produces an increase in the IC50 for both drugs contrasts with findings from previous smaller studies that suggested that isolates with D435V mutation remain RFB susceptible despite being RIF resistant. Our finding thus suggests that the recommended critical testing concentration for RFB should be revised.

evolutionary biology

Spatial-temporal clustering analysis of yaws on Lihir Island, Papua New Guinea to enhance planning and implementation of eradication programs

BackgroundIn the global program for the eradication of yaws, assessments of the prevalence of the disease are used to decide where to initiate mass treatment. However, the smallest administrative unit which should be used as the basis for making decisions is not clear. We investigated spatial and temporal clustering of yaws to help inform the choice of implementation unit.\n\nMethodology/Principal findingsWe analyzed 11 years of passive surveillance data on incident yaws cases (n = 1448) from Lihir Island, Papua New Guinea. After adjusting for age, sex, and trends in health-seeking, we detected three non-overlapping spatiotemporal clusters (p < 1 x 10-17, p = 1.4 x 10-14, p = 1.4 x 10-8). These lasted from 28 to 47 months in duration and each encompassed between 4 and 6 villages. We also assessed spatial clustering of prevalent yaws cases (n = 532) that had been detected in 7 biannual active case finding surveys beginning in 2013. We identified 1 statistically significant cluster in each survey. We considered the possibility that schools that serve multiple villages might be loci of transmission, but we found no evidence that incident cases of yaws among 8- to 14-year-olds clustered within primary school attendance areas (p = 0.684).\n\nConclusions/SignificanceThese clusters likely reflect transmission of yaws across village boundaries; villages may be epidemiologically linked to a degree such that mass drug administration may be more effectively implemented at a spatial scale larger than the individual village.\n\nAuthor SummaryThe World Health Organization aims to eradicate yaws using mass drug administration (MDA), which consists of treating everyone in an administrative unit with antibiotics. The administrative unit in a country which is used as the basis for making decisions about implementing MDA is called the implementation unit. Prevalence assessments are used to identify endemic communities for mass treatment programs, but the spatial scale (e.g. village, sub-district, district, or province) at which mass treatment should be implemented is currently unclear. The choice of implementation unit depends on many factors; one of these is the underlying transmission patterns of the disease. Using data from Lihir Island, Papua New Guinea, we found that geographic clusters of yaws often spanned multiple villages. These clusters likely reflect transmission of the infectious disease across village boundaries and suggest that it may be best to implement MDA at a spatial scale larger than the individual village, for example at sub-district level.

epidemiology

Downregulation of the central noradrenergic system by Toxoplasma gondii infection

The parasitic protozoan Toxoplasma gondii becomes encysted in brain and muscle tissue during chronic infection, a stage that was previously thought to be dormant but has been found to be active and associated with physiological effects in the host. Dysregulation of catecholamines in the CNS has previously been observed in chronically-infected animals. In the study described here, the noradrenergic system was suppressed with decreased levels of norepinephrine in brains of infected animals and in infected neuronal cells in vitro. Expression of dopamine {beta}-hydroxylase (DBH), essential for synthesis of norepinephrine from dopamine, was the most differentially-expressed gene in infections in vitro and was down-regulated in infected brain tissue, particularly in the prefrontal cortex and dorsal locus coeruleus/pons region. The down-regulated DBH expression in infected rat catecholaminergic and human neuronal cells corresponded with decreased norepinephrine and increased dopamine. As the DBH suppression was observed in vitro, this effect is not caused by neuroinflammation. Silencing of DBH expression was specific for T. gondii infection and was not observed with CMV infection. The noradrenergic-linked behaviors of sociability and arousal were altered in chronically-infected animals, with a high correlation between DBH expression and infection intensity. These findings together provide a plausible mechanism to explain prior discrepancies in changes to CNS neurotransmitters levels with infection. The suppression of norepinephrine synthesis observed here may, in part, explain behavioural effects of infection, associations with mental illness, and neurological consequences of infection such as the loss of coordination and motor impairments associated with human toxoplasmosis.

microbiology

Catching up to a fast-moving target: Evaluation of a health system strengthening intervention in rural Rwanda 2005-2010 using data from repeated cross-sectional surveys

IntroductionAlthough Rwandas health system underwent major reforms and improvements after the 1994 Genocide, the health system and population health in the southeast lagged behind other areas. In 2005 Partners In Health and the Rwandan Ministry of Health began a health system strengthening intervention in this region.\n\nMethodsCombining results from the 2005 and 2010 Demographic and Health Surveys with those from a supplemental 2010 survey, we compared changes in health system output indicators and population health outcomes between 2005 and 2010 as reported by 21,338 women living in the intervention area and similar rural areas, controlling for potential confounding by economic and demographic variables.\n\nResultsOverall health system coverage improved similarly in both regions between 2005 and 2010, with an indicator of composite coverage of child health interventions increasing from 57.9% to 75.0% in the intervention area and from 58.7% to 73.8% in other rural areas. Despite experiencing poorer health outcomes in 2005, the intervention area caught up to or exceeded other rural areas on 23 of 25 indicators. Most notably, under-five mortality declined by an annual rate of 12.8% in the intervention area, from 229.8 to 83.2 deaths per 1000 live births, and by 8.9% in other rural areas, from 157.7 to 75.8 deaths per 1000 live births. Improvements were most dramatic among the poorest households.\n\nConclusionWe observed dramatic improvements in population health outcomes including under-five mortality between 2005 and 2010 in rural Rwanda generally, and in the intervention area specifically.\n\nSUMMARY BOXO_ST_ABSWhat is already known about this topic?C_ST_ABSO_LIMuch of the evidence that health system strengthening in rural Africa has improved health outcomes comes from studies of targeted regional interventions such as performance based financing or community health worker programs, rather than integrated interventions that encompass multiple components including infrastructure and supply chain investments, health management information system, workforce training and incentives at all levels, community health workers, and free services for poor patients.\nC_LIO_LIIn addition to these experimental or quasi-experimental studies, a series of case studies have documented individual nations, pathways to achieving millennium development goal 4 target, the reduction of under-five mortality by two thirds between 1990 and 2015.\nC_LIO_LIThese reports suggest that improvements in coverage of reproductive, maternal and child health indicators explain some, but not all, of the decline in child mortality and that these successes occurred in the context of national gains in health, nutrition and food security, sanitation, poverty reduction, and access to clean water.\nC_LI\n\nWhat are the new findings?O_LICoverage of most maternal and child health care interventions improved at a similar pace in our rural intervention area and other rural areas.\nC_LIO_LIDespite experiencing poorer health outcomes in 2005, our rural intervention area caught up to or exceeded other rural areas on 23 of 25 population health indicators by 2010.\nC_LIO_LIInfant and under-5 mortality declined in our rural intervention area even more precipitously than in other rural areas of Rwanda between 2005 and 2010.\nC_LI\n\nHow might this influence practice?O_LIThe process of strengthening national health systems often involves trade-offs between a focus on first testing individual programs that distributed widely, as is often practiced by pilot programs with multilateral institutions, or implementing multiple simultaneous programs locally. Our results show that integrated health system strengthening interventions can be locally adapted to enable the rapid expansion of health care coverage as well as dramatic improvements in population health outcomes.\nC_LIO_LIIntegrated multi-level interventions can also help narrow the health care coverage and outcome gap between richer and poorer members of a society.\nC_LIO_LINational governments can leverage nongovernmental partners to achieve the health related sustainable development goals through joint implementation of national health policy.\nC_LI

epidemiology