Dataset Information

Coverage evaluation of universal bacterial primers using the metagenomic datasets.

ABSTRACT: BACKGROUND: The coverage of universal primers for the bacterial 16S rRNA gene plays a crucial role in the correct understanding of microbial community structure. However, existing studies on primer coverage are limited by the lack of appropriate databases and are restricted to the domain level. Additionally, most studies do not account for the positional effect of single primer-template mismatches. In this study, we used 7 metagenomic datasets as well as the Ribosomal Database Project (RDP) to assess the coverage of 8 widely used bacterial primers. RESULTS: The coverage rates for bacterial primers were found to be overestimated by previous studies that only investigated the RDP because of PCR amplification bias in the sequence composition of the dataset. In the RDP, the non-coverage rates for all primers except 27F were ?6%, while in the metagenomic datasets, most were ?10%. If one considers that a single mismatch near the 3' end of the primer might greatly reduce PCR efficiency, then some phylum non-coverage rates would change by more than 20%. Primer binding-site sequence variants that could not pair with their corresponding primers are discussed. CONCLUSIONS: Our study revealed the potential bias introduced by the use of universal bacterial primers in the assessment of microbial communities. With the development of high-throughput, next-generation sequencing techniques, it will become feasible to sequence more of the hypervariable regions of the bacterial 16S rRNA gene. This, in turn, will lead to the more frequent use of the primers discussed here.

SUBMITTER: Mao DP

PROVIDER: S-EPMC3445835 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature

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Coverage evaluation of universal bacterial primers using the metagenomic datasets.

Mao Dan-Ping DP Zhou Quan Q Chen Chong-Yu CY Quan Zhe-Xue ZX

BMC microbiology 20120503

<h4>Background</h4>The coverage of universal primers for the bacterial 16S rRNA gene plays a crucial role in the correct understanding of microbial community structure. However, existing studies on primer coverage are limited by the lack of appropriate databases and are restricted to the domain level. Additionally, most studies do not account for the positional effect of single primer-template mismatches. In this study, we used 7 metagenomic datasets as well as the Ribosomal Database Project (RD ...[more]

PMID: 22554309

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Project description:BackgroundMass distribution of insecticide-treated nets (ITNs) is a cost-effective way to achieve universal coverage, but maintaining this coverage is more difficult. In addition to commonly used indicators, evaluation of universal coverage should include coverage of effective nets and changes in coverage over time.MethodsLongitudinal and cross-sectional household ITN surveys were carried out from 2010 to 2013 in six locations representing a variety of settings across western Kenya. Five indicators were used to evaluate the current status of universal coverage: 1) ITN ownership--proportion of households that own at least one ITN, 2) access index--ratio of the number of family members over the number of ITNs owned by that household, 3) operational coverage--proportion of the at-risk population potentially covered by ITNs, assuming one ITN for every two people, 4) effective coverage--population coverage of effective ITNs, and 5) usage--proportion of the population that used ITNs the previous night.ResultsITN ownership and operational coverage increased substantially from 2010 to 2013, but this increase was mostly due to the 2011 mass distribution campaign. In 2013, household ITN ownership was on average 84.4% (95% CI [78.4, 90.5]) across the six study areas, and operational coverage was 83.2% (95% CI [72.5, 93.8]). The ITN access rate was 59.1% (95% CI [56.6, 61.7]), and 40.8% (95% CI [38.3, 43.4]) of the people at risk needed more nets to achieve universal coverage. About 88.5% (95% CI [86.1, 90.9]) of the ITNs were below three years old and 16.5% (95% CI [12.1, 20.9]) of the ITNs had hole(s). The estimated effective long-lasting insecticide-treated net (LLIN) coverage was 70.5% (95 CI [58.7, 82.3]). Approximately 18.4% (95% CI [15.5, 21.4]) of the ITNs were shared by more than three persons, and the population ITN usage rate was about 75-87%. The reason for not using ITNs was almost exclusively "net not available".ConclusionCurrent methods of delivering ITNs, i.e., one mass campaign every five years and regular distribution of ITNs from health center can barely maintain the current effective coverage. Inaccessibility and loss of physical integrity of ITNs are major hindrances to achieving and maintaining universal coverage.

Project description:BackgroundMutuelles is a community-based health insurance program, established since 1999 by the Government of Rwanda as a key component of the national health strategy on providing universal health care. The objective of the study was to evaluate the impact of Mutuelles on achieving universal coverage of medical services and financial risk protection in its first eight years of implementation.Methods and findingsWe conducted a quantitative impact evaluation of Mutuelles between 2000 and 2008 using nationally-representative surveys. At the national and provincial levels, we traced the evolution of Mutuelles coverage and its impact on child and maternal care coverage from 2000 to 2008, as well as household catastrophic health payments from 2000 to 2006. At the individual level, we investigated the impact of Mutuelles' coverage on enrollees' medical care utilization using logistic regression. We focused on three target populations: the general population, under-five children, and women with delivery. At the household level, we used logistic regression to study the relationship between Mutuelles coverage and the probability of incurring catastrophic health spending. The main limitation was that due to insufficient data, we are not able to study the impact of Mutuelles on health outcomes, such as child and maternal mortalities, directly. The findings show that Mutuelles improved medical care utilization and protected households from catastrophic health spending. Among Mutuelles enrollees, those in the poorest expenditure quintile had a significantly lower rate of utilization and higher rate of catastrophic health spending. The findings are robust to various estimation methods and datasets.ConclusionsRwanda's experience suggests that community-based health insurance schemes can be effective tools for achieving universal health coverage even in the poorest settings. We suggest a future study on how eliminating Mutuelles copayments for the poorest will improve their healthcare utilization, lower their catastrophic health spending, and affect the finances of health care providers.

Dataset Information

Coverage evaluation of universal bacterial primers using the metagenomic datasets.

Publications

Coverage evaluation of universal bacterial primers using the metagenomic datasets.

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