ProbeTools: designing hybridization probes for targeted genomic sequencing of diverse and hypervariable viral taxa

Background

Sequencing viruses in many specimens is hindered by excessive background material from hosts, microbiota, and environmental organisms. Consequently, enrichment of target genomic material is necessary for practical high-throughput viral genome sequencing. Hybridization probes are widely used for enrichment in many fields, but their application to viral sequencing faces a major obstacle: it is difficult to design panels of probe oligo sequences that broadly target many viral taxa due to their rapid evolution, extensive diversity, and genetic hypervariability. To address this challenge, we created ProbeTools, a package of bioinformatic tools for generating effective viral capture panels, and for assessing coverage of target sequences by probe panel designs in silico. In this study, we validated ProbeTools by designing a panel of 3600 probes for subtyping the hypervariable haemagglutinin (HA) and neuraminidase (NA) genome segments of avian-origin influenza A viruses (AIVs). Using in silico assessment of AIV reference sequences and in vitro capture on egg-cultured viral isolates, we demonstrated effective performance by our custom AIV panel and ProbeTools’ suitability for challenging viral probe design applications.

Results

Based on ProbeTool’s in silico analysis, our panel provided broadly inclusive coverage of 14,772 HA and 11,967 NA reference sequences. For each reference sequence, we calculated the percentage of nucleotide positions covered by our panel in silico; 90% of HA and NA references sequences had at least 90.8 and 95.1% of their nucleotide positions covered respectively. We also observed effective in vitro capture on a representative collection of 23 egg-cultured AIVs that included isolates from wild birds, poultry, and humans and representatives from all HA and NA subtypes. Forty-two of forty-six HA and NA segments had over 98.3% of their nucleotide positions significantly enriched by our custom panel. These in vitro results were further used to validate ProbeTools’ in silico coverage assessment algorithm; 89.2% of in silico predictions were concordant with in vitro results.

Conclusions

ProbeTools generated an effective panel for subtyping AIVs that can be deployed for genomic surveillance, outbreak prevention, and pandemic preparedness. Effective probe design against hypervariable AIV targets also validated ProbeTools’ design and coverage assessment algorithms, demonstrating their suitability for other challenging viral capture applications.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08790-4.

Metagenomic Analysis of the Pediatric-Onset Multiple Sclerosis Gut Microbiome

BACKGROUND AND OBJECTIVES

Little is known of the functional potential of the gut microbiome in pediatric-onset multiple sclerosis (MS). We performed metagenomic analyses using stool samples from individuals with pediatric-onset MS and unaffected controls.

METHODS

Persons ≤21 years old enrolled in the Canadian Pediatric Demyelinating Disease Network providing a stool sample were eligible. Twenty patients with MS (McDonald criteria) with symptom onset <18 years were matched to 20 controls by sex, age (±3 years), stool consistency, and race. Microbial taxonomy and functional potentials were estimated from stool sample-derived metagenomic reads and compared by disease status (MS vs controls) and disease-modifying drug (DMD) exposure using alpha diversity, relative abundance, and prevalence using Wilcoxon rank sum, ALDEx2, and Fisher exact tests, respectively.

RESULTS

Individuals with MS were aged 13.6 years (mean) at symptom onset and 8 were DMD-naive. Mean ages at stool sample were 16.1 and 15.4 years for MS and control participants, respectively; 80% were girls. Alpha diversity of enzymes and proteins did not differ by disease or DMD status (p > 0.20), but metabolic pathways, gene annotations, and microbial taxonomy did. Individuals with MS (vs controls) exhibited higher methanogenesis prevalence (odds ratio 10, p = 0.044) and Methanobrevibacter abundance (log₂ fold change [LFC] 1.7, p = 0.0014), but lower homolactic fermentation abundance (LFC -0.48, p = 0.039). Differences by DMD status included lower phosphate butyryl transferase for DMD-naive vs exposed patients with MS (LFC -1.0, p = 0.033).

DISCUSSION

The gut microbiome's functional potential and taxonomy differed between individuals with pediatric-onset MS vs controls, including higher prevalence of a methane-producing pathway from Archaea and depletion of the lactate fermentation pathway. DMD exposure was associated with butyrate-producing enzyme enrichment. Together these findings indicate that the gut microbiome of individuals with MS may have a disturbed functional potential.

Extraction and Detection of Avian Influenza Virus From Wetland Sediment Using Enrichment-Based Targeted Resequencing

Early virus detection and characterization is key to successful avian influenza virus (AIV) surveillance for the health of humans as well as domestic poultry. We explored a novel sampling approach and molecular strategy using sediment from wetlands and outdoor waterbodies on poultry farms as a population-level proxy of AIV activity in waterfowls. RNA was extracted using the MoBio RNA PowerSoil Total RNA isolation kit with additional chloroform extraction steps to reduce PCR inhibition. AIV matrix protein (MP) gene was detected in 42/345 (12.2%) samples by RT-qPCR; an additional 64 (18.6%) samples showed evidence of amplification below the threshold and were categorized as “suspect positive.” Enrichment-based targeted resequencing (TR) identified AIV sequences in 79/345 (22.9%) samples. TR probes were designed for MP, hemagglutinin (HA), and neuraminidase (NA), however PB2 and PA were also identified. Although RT-qPCR and TR only had fair-moderate agreement, RT-qPCR positivity was predictive of TR-positivity both when using only strictly positive RT-qPCR samples (OR = 11.29) and when coding suspect positives as positive (OR = 7.56). This indicates that RT-qPCR could be used as a screening tool to select samples for virus characterization by TR and that future studies should consider RT-qPCR suspect positives to be positive samples for subsequent resequencing when avoiding false negatives is the priority, for instance in a diagnostic test, and to consider suspect positives to be negative samples when cost efficiency over a large number of samples is the priority, for instance in a surveillance program. A total of 13 HA (H1-7, H9-13, H16) and 9 NA (N1-9) subtypes were identified, with a maximum of 8 HA and 8 NA subtypes detected in a single sample. The optimized RNA extraction and targeted resequencing methods provided increased virus detection and subtyping characterization that could be implemented in an AIV surveillance system.

TARGETED RESEQUENCING OF WETLAND SEDIMENT AS A TOOL FOR AVIAN INFLUENZA VIRUS SURVEILLANCE

Surveillance methods for avian influenza virus (AIV) based upon collecting and testing samples from individual wild birds have several significant limitations primarily related to the difficulties associated with obtaining samples. Because AIVs are shed in waterfowl feces, the use of environmental substrates where waterfowl feces accumulate may overcome some of these limitations. However, these substrates are difficult to analyze using traditional diagnostic techniques, such as virus culture and PCR, because of virus inactivation, RNA degradation, low concentration of target RNA, microbial complexity, presence of inhibitory substances, and other factors. We investigated the use of a genomics-based approach called targeted resequencing to detect and characterize AIVs in wetland sediments during the 2014-15 North American highly pathogenic avian influenza outbreak. We identified AIV in 20.6% (71/345) sediment samples obtained from wetlands (n=15) and outdoor waterbodies on AIV-infected poultry farms (n=10) in British Columbia, Canada (the first area affected during the outbreak). Thirteen hemagglutinin (HA) and nine neuraminidase (NA) subtypes were detected, including H5, N1, and N8 sequences that clustered with other sequences associated with the North American outbreak. Additionally, as many as eight HA and eight NA subtypes could be detected in a single sediment sample. This proof-of-concept study shows the potential utility of sediment sampling coupled with genomics-based analysis as a tool for AIV surveillance.

Influenza Classification Suite: An automated Galaxy workflow for rapid influenza sequence analysis

Influenza viruses continually evolve to evade population immunity, and the different lineages are assigned into clades based on shared mutations. We have developed a publicly available computational workflow, the Influenza Classification Suite, for rapid clade mapping of sequenced influenza viruses. This suite provides a user‐friendly workflow implemented in Galaxy to automate clade calling and antigenic site extraction. Workflow input includes clade definition and amino acid index array files, which can be customized to identify any clades of interest. The Influenza Classification Suite provides rapid, high‐resolution understanding of circulating influenza strain evolution to inform influenza vaccine effectiveness and the need for potential vaccine reformulation.

mTORC2-AKT signaling to ATP-citrate lyase drives brown adipogenesis and de novo lipogenesis

mTORC2 phosphorylates AKT in a hydrophobic motif site that is a biomarker of insulin sensitivity. In brown adipocytes, mTORC2 regulates glucose and lipid metabolism, however the mechanism has been unclear because downstream AKT signaling appears unaffected by mTORC2 loss. Here, by applying immunoblotting, targeted phosphoproteomics and metabolite profiling, we identify ATP-citrate lyase (ACLY) as a distinctly mTORC2-sensitive AKT substrate in brown preadipocytes. mTORC2 appears dispensable for most other AKT actions examined, indicating a previously unappreciated selectivity in mTORC2-AKT signaling. Rescue experiments suggest brown preadipocytes require the mTORC2/AKT/ACLY pathway to induce PPAR-gamma and establish the epigenetic landscape during differentiation. Evidence in mature brown adipocytes also suggests mTORC2 acts through ACLY to increase carbohydrate response element binding protein (ChREBP) activity, histone acetylation, and gluco-lipogenic gene expression. Substrate utilization studies additionally implicate mTORC2 in promoting acetyl-CoA synthesis from acetate through acetyl-CoA synthetase 2 (ACSS2). These data suggest that a principal mTORC2 action is controlling nuclear-cytoplasmic acetyl-CoA synthesis.

mTORC2 activates Akt, a regulator of cell growth and metabolism, however, the role of mTORC2 in adipocytes is incompletely understood. Here the authors report that a mTORC2-Akt axis specifically activates ACLY to promote lipid synthesis and histone acetylation during brown adipocyte differentiation.

An evaluation of systemic reforms of public hospitals: the Sanming model in China

Low- and middle-income countries (LMICs) have been searching for effective strategies to reform their inefficient and wasteful public hospitals. Recently, China developed a model of systemic reforms called the Sanming model to address the inefficiency and waste at public hospitals. In this article, we explain and evaluate how the Sanming model reformed its 22 public hospitals in 2013 by simultaneously restructuring the hospital governance structure, altering the payment system to hospitals, and realigning physicians' incentives. By employing the difference-in-difference (DID) method and using the hospital-level data from 187 public hospitals in Fujian province, we find that the Sanming model has reduced medical costs significantly without measurably sacrificing clinical quality and productive efficiency. The systemic reform, on average, has reduced the medical care cost per outpatient visit and per inpatient admission by 6.1% (P-value = 0.0445) and 15.4% (P-value < 0.001), respectively. It is largely accomplished through a decrease in drug expenditures per outpatient visit and per inpatient admission of about 29% (P-value < 0.001) and 53% (P-value < 0.001). These results show that the Sanming model has achieved at least a short-term success in improving the performance of the public hospitals. These findings suggest that such a systemic transformation of public hospitals, where the governance structure, payment system and physician compensation methods are aligned, are crucial to improving their performance; it holds critical lessons for China and other LMICs.

Human Activity Determines the Presence of Integron-Associated and Antibiotic Resistance Genes in Southwestern British Columbia

The dissemination of antibiotic resistant bacteria from anthropogenic sources into the environment poses an emerging public health threat. Antibiotic resistance genes (ARGs) and gene-capturing systems such as integron-associated integrase genes (intI) play a key role in alterations of microbial communities and the spread of antibiotic resistant bacteria into the environment. In order to assess the effect of anthropogenic activities on watersheds in southwestern British Columbia, the presence of putative antibiotic resistance and integrase genes was analyzed in the microbiome of agricultural, urban influenced, and protected watersheds. A metagenomics approach and high-throughput quantitative PCR (HT qPCR) were used to screen for elements of resistance including ARGs and intI. Metagenomic sequencing of bacterial genomic DNA was used to characterize the resistome of microbial communities present in watersheds over a 1-year period. There was a low prevalence of ARGs relative to the microbial population (<1%). Analysis of the metagenomic sequences detected a total of 60 elements of resistance including 46 ARGs, intI1, and groEL/intI1 genes and 12 quaternary ammonium compounds (qac) resistance genes across all watershed locations. The relative abundance and richness of ARGs was found to be highest in agriculture impacted watersheds compared to urban and protected watersheds. A downstream transport pattern was observed in the impacted watersheds (urban and agricultural) during dry months. Similar to other reports, this study found a strong association between intI1 and ARGs (e.g., sul1), an association which may be used as a proxy for anthropogenic activities. Chemical analysis of water samples for three major groups of antibiotics was below the detection limit. However, the high richness and gene copy numbers (GCNs) of ARGs in impacted sites suggest that the effects of effluents on microbial communities are occurring even at low concentrations of antimicrobials in the water column. Antibiotic resistance and integrase genes in a year-long metagenomic study showed that ARGs were driven mainly by environmental factors from anthropogenized sites in agriculture and urban watersheds. Environmental factors such as land-use and water quality parameters accounted for 45% of the variability observed in watershed locations.

MentaLiST - A fast MLST caller for large MLST schemes

MLST (multi-locus sequence typing) is a classic technique for genotyping bacteria, widely applied for pathogen outbreak surveillance. Traditionally, MLST is based on identifying sequence types from a small number of housekeeping genes. With the increasing availability of whole-genome sequencing data, MLST methods have evolved towards larger typing schemes, based on a few hundred genes [core genome MLST (cgMLST)] to a few thousand genes [whole genome MLST (wgMLST)]. Such large-scale MLST schemes have been shown to provide a finer resolution and are increasingly used in various contexts such as hospital outbreaks or foodborne pathogen outbreaks. This methodological shift raises new computational challenges, especially given the large size of the schemes involved. Very few available MLST callers are currently capable of dealing with large MLST schemes. We introduce MentaLiST, a new MLST caller, based on a k-mer voting algorithm and written in the Julia language, specifically designed and implemented to handle large typing schemes. We test it on real and simulated data to show that MentaLiST is faster than any other available MLST caller while providing the same or better accuracy, and is capable of dealing with MLST schemes with up to thousands of genes while requiring limited computational resources. MentaLiST source code and easy installation instructions using a Conda package are available at https://github.com/WGS-TB/MentaLiST.

SNVPhyl: a single nucleotide variant phylogenomics pipeline for microbial genomic epidemiology

The recent widespread application of whole-genome sequencing (WGS) for microbial disease investigations has spurred the development of new bioinformatics tools, including a notable proliferation of phylogenomics pipelines designed for infectious disease surveillance and outbreak investigation. Transitioning the use of WGS data out of the research laboratory and into the front lines of surveillance and outbreak response requires user-friendly, reproducible and scalable pipelines that have been well validated. Single Nucleotide Variant Phylogenomics (SNVPhyl) is a bioinformatics pipeline for identifying high-quality single-nucleotide variants (SNVs) and constructing a whole-genome phylogeny from a collection of WGS reads and a reference genome. Individual pipeline components are integrated into the Galaxy bioinformatics framework, enabling data analysis in a user-friendly, reproducible and scalable environment. We show that SNVPhyl can detect SNVs with high sensitivity and specificity, and identify and remove regions of high SNV density (indicative of recombination). SNVPhyl is able to correctly distinguish outbreak from non-outbreak isolates across a range of variant-calling settings, sequencing-coverage thresholds or in the presence of contamination. SNVPhyl is available as a Galaxy workflow, Docker and virtual machine images, and a Unix-based command-line application. SNVPhyl is released under the Apache 2.0 license and available at http://snvphyl.readthedocs.io/ or at https://github.com/phac-nml/snvphyl-galaxy.

Metagenomic Investigation of Plasma in Individuals with ME/CFS Highlights the Importance of Technical Controls to Elucidate Contamination and Batch Effects

Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is a debilitating disease causing indefinite fatigue. ME/CFS has long been hypothesised to have an infectious cause; however, no specific infectious agent has been identified. We used metagenomics to analyse the RNA from plasma samples from 25 individuals with ME/CFS and compare their microbial content to technical controls as well as three control groups: individuals with alternatively diagnosed chronic Lyme syndrome (N = 13), systemic lupus erythematosus (N = 11), and healthy controls (N = 25). We found that the majority of sequencing reads were removed during host subtraction, thus there was very low microbial RNA content in the plasma. The effects of sample batching and contamination during sample processing proved to outweigh the effects of study group on microbial RNA content, as the few differences in bacterial or viral RNA abundance we did observe between study groups were most likely caused by contamination and batch effects. Our results highlight the importance of including negative controls in all metagenomic analyses, since there was considerable overlap between bacterial content identified in study samples and control samples. For example, Proteobacteria, Firmicutes, Actinobacteria, and Bacteriodes were found in both study samples and plasma-free negative controls. Many of the taxonomic groups we saw in our plasma-free negative control samples have previously been associated with diseases, including ME/CFS, demonstrating how incorrect conclusions may arise if controls are not used and batch effects not accounted for.

Uncovering effects of antibiotics on the host and microbiota using transkingdom gene networks

OBJECTIVE

Despite widespread use of antibiotics for the treatment of life-threatening infections and for research on the role of commensal microbiota, our understanding of their effects on the host is still very limited.

DESIGN

Using a popular mouse model of microbiota depletion by a cocktail of antibiotics, we analysed the effects of antibiotics by combining intestinal transcriptome together with metagenomic analysis of the gut microbiota. In order to identify specific microbes and microbial genes that influence the host phenotype in antibiotic-treated mice, we developed and applied analysis of the transkingdom network.

RESULTS

We found that most antibiotic-induced alterations in the gut can be explained by three factors: depletion of the microbiota; direct effects of antibiotics on host tissues and the effects of remaining antibiotic-resistant microbes. Normal microbiota depletion mostly led to downregulation of different aspects of immunity. The two other factors (antibiotic direct effects on host tissues and antibiotic-resistant microbes) primarily inhibited mitochondrial gene expression and amounts of active mitochondria, increasing epithelial cell death. By reconstructing and analysing the transkingdom network, we discovered that these toxic effects were mediated by virulence/quorum sensing in antibiotic-resistant bacteria, a finding further validated using in vitro experiments.

CONCLUSIONS

In addition to revealing mechanisms of antibiotic-induced alterations, this study also describes a new bioinformatics approach that predicts microbial components that regulate host functions and establishes a comprehensive resource on what, why and how antibiotics affect the gut in a widely used mouse model of microbiota depletion by antibiotics.

Harnessing the privatisation of China's fragmented health-care delivery

Although China's 2009 health-care reform has made impressive progress in expansion of insurance coverage, much work remains to improve its wasteful health-care delivery. Particularly, the Chinese health-care system faces substantial challenges in its transformation from a profit-driven public hospital-centred system to an integrated primary care-based delivery system that is cost effective and of better quality to respond to the changing population needs. An additional challenge is the government's latest strategy to promote private investment for hospitals. In this Review, we discuss how China's health-care system would perform if hospital privatisation combined with hospital-centred fragmented delivery were to prevail--population health outcomes would suffer; health-care expenditures would escalate, with patients bearing increasing costs; and a two-tiered system would emerge in which access and quality of care are decided by ability to pay. We then propose an alternative pathway that includes the reform of public hospitals to pursue the public interest and be more accountable, with public hospitals as the benchmarks against which private hospitals would have to compete, with performance-based purchasing, and with population-based capitation payment to catalyse coordinated care. Any decision to further expand the for-profit private hospital market should not be made without objective assessment of its effect on China's health-policy goals.

Sparse distance-based learning for simultaneous multiclass classification and feature selection of metagenomic data

MOTIVATION

Direct sequencing of microbes in human ecosystems (the human microbiome) has complemented single genome cultivation and sequencing to understand and explore the impact of commensal microbes on human health. As sequencing technologies improve and costs decline, the sophistication of data has outgrown available computational methods. While several existing machine learning methods have been adapted for analyzing microbiome data recently, there is not yet an efficient and dedicated algorithm available for multiclass classification of human microbiota.

RESULTS

By combining instance-based and model-based learning, we propose a novel sparse distance-based learning method for simultaneous class prediction and feature (variable or taxa, which is used interchangeably) selection from multiple treatment populations on the basis of 16S rRNA sequence count data. Our proposed method simultaneously minimizes the intraclass distance and maximizes the interclass distance with many fewer estimated parameters than other methods. It is very efficient for problems with small sample sizes and unbalanced classes, which are common in metagenomic studies. We implemented this method in a MATLAB toolbox called MetaDistance. We also propose several approaches for data normalization and variance stabilization transformation in MetaDistance. We validate this method on several real and simulated 16S rRNA datasets to show that it outperforms existing methods for classifying metagenomic data. This article is the first to address simultaneous multifeature selection and class prediction with metagenomic count data.

AVAILABILITY

The MATLAB toolbox is freely available online at http://metadistance.igs.umaryland.edu/.

CONTACT

zliu@umm.edu

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Realignment of incentives for health-care providers in China

Inappropriate incentives as part of China's fee-for-service payment system have resulted in rapid cost increase, inefficiencies, poor quality, unaffordable health care, and an erosion of medical ethics. To reverse these outcomes, a strategy of experimentation to realign incentives for providers with the social goals of improvement in quality and efficiency has been initiated in China. This Review shows how lessons that have been learned from international experiences have been improved further in China by realignment of the incentives for providers towards prevention and primary care, and incorporation of a treatment protocol for hospital services. Although many experiments are new, preliminary evidence suggests a potential to produce savings in costs. However, because these experiments have not been scientifically assessed in China, evidence of their effects on quality and health outcome is largely missing. Although a reform of the provider's payment can be an effective short-term strategy, professional ethics need to be re-established and incentives changed to alter the profit motives of Chinese hospitals and physicians alike. When hospitals are given incentives to achieve maximum profit, incentives for hospitals and physicians must be separated.

The role of patient-to-patient transmission in the acquisition of imipenem-resistant Pseudomonas aeruginosa colonization in the intensive care unit

BACKGROUND

Imipenem-resistant Pseudomonas aeruginosa (IRPA) is an emerging problem. The causal role of antibiotic selective pressure versus patient-to-patient transmission has not been assessed using a large cohort.

METHODS

Patients who were admitted to the medical and surgical intensive care units (ICUs) at the University of Maryland Medical Center from 2001 through 2006 had multiple perianal culture samples collected. Using pulsed-field gel electrophoresis (PFGE), the number of patients who acquired IRPA as a result of patient-to-patient transmission was determined. We also analyzed a subset of patients who had a previous surveillance culture that grew an imipenem-susceptible P. aeruginosa (ISPA) and a subsequent culture that grew IRPA.

RESULTS

Our cohort consisted of 7071 patients. Three hundred patients were colonized with IRPA. 151 patients had positive culture findings at ICU admission, and 149 patients acquired an IRPA. Among the patients who acquired IRPA, 46 (31%) had a PFGE pattern similar to that for another isolate, and 38 (26%) were found to be colonized with an ISPA on the basis of earlier culture results. Of the 38-patient subset, 28 (74%) had identical PFGE patterns.

CONCLUSIONS

Our data showed that, of those cases of IRPA acquisition, 46 (31%) were defined as cases of patient-to-patient transmission, and 28 (19%) were cases of acquisition by the patients' endogenous flora.

Development of an effective public health screening program to assess hearing disabilities among newborns in Shanghai: a prospective cohort study

BACKGROUND

An effective, systematic program of screening, diagnosis and intervention against hearing loss in infants could help them avoid developmental impediments and could help society stem preventable healthcare burdens. We assessed the feasibility and outcomes of a new public health universal newborn hearing screening program (UNHSP) for neonates born in Shanghai.

METHODS

From March 2002 to June 2007, we conducted a two-stage hearing loss screening program for neonates born at all 105 delivery hospitals in Shanghai. Institutional participants in the program followed standardized testing criteria and procedures. The first stage of screening occurred in the hospital during the third day post-birth; positive infants underwent a second-stage outpatient screening on Day 42. Positive infants were examined at clinical diagnosis centres, and interventions were conducted at rehabilitation centres. In 2003, a random sample of parents were interviewed about the program, and their level of stress over learning their child screened positive were recorded and analyzed.

FINDINGS

Overall, our program screened 72.98% of eligible infants and provided effective interventions within six months to 86.31% of those with hearing oss. During the 5-year study, first-stage screenings assessed 90.85% of 616,880 eligible infants and found 12.16% positive. Day 42 screenings had a 65.68% participation rate and a positive rate of 14.75%. Of these, 0.146% were deemed permanently hearing impaired within three months of birth. Parental satisfaction measures exceeded 90%.

INTERPRETATION

A government-sponsored public health program to screen, diagnose, treat and provide interventions for all newborns with permanently hearing impairment can be effectively implemented and can achieve outcomes that surpass comparable clinical initiatives.

Ill health and its potential influence on household consumptions in rural China

Ill health is very expensive and could have significant impact on household consumptions. The purpose of this study is to examine the differences in household consumption patterns among households with or without ill health family member(s) in rural China. We also examine the opportunity cost of ill health by estimating the marginal effects of medical spending on consumption patterns. The data used in this study are from the baseline survey of a community-based rural health insurance study in a poor rural area of China conducted in 2002. The unit of analysis in this study is the household; 4553 households are included in this survey. Fractional Logit model is used as our prediction model. Ill health is measured by the presence of hospitalization and presence of diagnosed chronic disease(s) in a household. Findings from this study reveal that ill health and medical expenditure reduces household investment in human capital, physical capital for farm production, and other consumptions that are critical to human well-being. Subgroup analysis displayed that the impacts of medical expenditure on household consumption patterns described above are more significant in low-income households than in high-income households. In addition, the decline of the percentages of other consumptions is much larger for households with hospitalization than for households with chronic diseases.

Adverse selection in a voluntary Rural Mutual Health Care health insurance scheme in China

This study examines adverse selection in a subsidized voluntary health insurance scheme, the Rural Mutual Health Care (RMHC) scheme, in a poor rural area of China. The study was made possible by a unique longitudinal data set: the total sample includes 3492 rural residents from 1020 households. Logistic regression was employed for the data analysis. The results show that although this subsidized scheme achieved a considerable high enrollment rate of 71% of rural residents, adverse selection still exists. In general, individuals with worse health status are more likely to enroll in RMHC than individuals with better health status. Although the household is set as the enrollment unit for the RMHC for the purpose of reducing adverse selection, nearly 1/3 of enrolled households are actually only partially enrolled. Furthermore, we found that adverse selection mainly occurs in partially enrolled households. The non-enrolled individuals in partially enrolled households have the best health status, while the enrolled individuals in partially enrolled households have the worst health status. Pre-RMHC, medical expenditure for enrolled individuals in partially enrolled households was 206.6 yuan per capita per year, which is 1.7 times as much as the pre-RMHC medical expenditure for non-enrolled individuals in partially enrolled households. The study also reveals that the pre-enrolled medical expenditure per capita per year of enrolled individuals was 9.6% higher than the pre-enrolled medical expenditure of all residents, including both enrolled and non-enrolled individuals. In conclusion, although the subsidized RMHC scheme reached a very high enrollment rate and the household is set as the enrollment unit for the purpose of reducing adverse selection, adverse selection still exists, especially within partially enrolled households. Voluntary RMHC will not be financially sustainable if the adverse selection is not fully taken into account.

Community-based health insurance in poor rural China: the distribution of net benefits

The collapse of China's Cooperative Medical System (CMS) in 1978 resulted in the lack of an organized financing scheme for health care, adversely affecting rural farmers' access to health care, especially among the poor. The Chinese government recently announced a policy to re-establish some forms of community-based insurance (CBI). Many existing schemes involve low premiums but high co-payments. We hypothesized that such benefit design leads to unequal distribution of the "net benefits" (NB)--benefits net of payment--because even though low premiums are more affordable to poor farmers, high co-payments may have a significant deterrent effect on the poor in the use of services in CBI. To test this hypothesis empirically, we estimated the probability of farmers joining a re-established CBI using logistic regression, and the utilization of health care services for those who joined the scheme using the two-part model. Based on the estimations, we predicted the distribution of NB among those who joined the CBI and for the entire population in the community. Our data came from a household survey of 4160 members of 1173 households conducted in six villages in Fengshan Township, Guizhou Province, China. Three principal findings emerged from this study. First, income is an important factor influencing farmers' decision to join a CBI despite the premium representing a very small fraction of household income. Secondly, both income and health status influence enrollees' utilization of health services: richer/sicker participants obtain greater NB from the CBI than poorer/healthier members, meaning that the poorer/healthier participants subsidize the rich/sick. Thirdly, wealthy farmers benefit the most from the CBI with low premium and high co-payment features at every level of health status. In conclusion, policy recommendations related to the improvement of the benefit distribution of CBI schemes are made based on the results from this study.

Social capital and farmer's willingness-to-join a newly established community-based health insurance in rural China

In 2002, China announced a new funding strategy that would reestablish community-based health insurance (CHI) in rural areas, whereby the Chinese government will entice farmers' participation by providing each participant an annual subsidy of 10-20 Yuan (US 1.25-2.50 dollars). However, there is no evidence demonstrating how many farmers would be willing-to-join (WTJ) such newly developed government subsidized voluntary-based CHI scheme and what factors influence farmers' willingness-to-join. In this study, we examine the probability of farmers' willingness-to-join such CHI under the different scenarios of government subsidy and individual contribution, and also explore factors that influence farmers' willingness-to-join with the emphasis on social capital. The study is based on data collected from a 2002 household survey conducted in Fengsan Township, located in China's Guizhou Province. Logistic regression is used in the analysis. The findings from this study show that even with the government subsidy to the premium, the probability of WTJ the new voluntary-based CHI only reach 50%. The results also indicate that community level social capital, as measured by reciprocity index, and individual level social capital, as measured by trust index, are significantly and positively associated with the probability of farmers' WTJ newly developed government subsidized CHI. Policy recommendations have been made based on those findings.

The impact of quality on the demand for outpatient services in Cyprus

Health policy reforms in a number of countries seek to improve provider quality by sharpening the incentives they face, for example by exposing them to greater competition. For this to succeed, patients must be responsive to quality in their choice of provider. This paper uses data from Cyprus to estimate the effect of quality on patients' choice between public and private outpatient care. It improves on the existing literature by using a more comprehensive set of quality attributes which allows the dimensions of quality that have the largest effect on patient choice of provider to be identified. We also introduce an innovative way of measuring patients' perceptions of quality in a household survey. We find that patients' choice of provider is sensitive to quality, and that interpersonal quality is more important than either technical quality or system-related factors.

IslandPath: aiding detection of genomic islands in prokaryotes

Genomic islands (clusters of genes of potential horizontal origin in a prokaryotic genome) are frequently associated with a particular adaptation of a microbe that is of medical, agricultural or environmental importance, such as antibiotic resistance, pathogen virulence, or metal resistance. While many sequence features associated with such islands have been adopted separately in applications for analysis of genomic islands, including pathogenicity islands, there is no single application that integrates multiple features for island detection. IslandPath is a network service which incorporates multiple DNA signals and genome annotation features into a graphical display of a bacterial or archaeal genome, to aid the detection of genomic islands.

AVAILABILITY

This application is available at http://www.pathogenomics.sfu.ca/islandpath and the source code is freely available, under GNU public licence, from the authors.

SUPPLEMENTARY INFORMATION

An online help file, which includes analyses of the utility of IslandPath, can be found at http://www.pathogenomics.sfu.ca/islandpath/current/islandhelp.html

Effectiveness of community health financing in meeting the cost of illness

How to finance and provide health care for the more than 1.3 billion rural poor and informal sector workers in low- and middle-income countries is one of the greatest challenges facing the international development community. This article presents the main findings from an extensive survey of the literature of community financing arrangements, and selected experiences from the Asia and Africa regions. Most community financing schemes have evolved in the context of severe economic constraints, political instability, and lack of good governance. Micro-level household data analysis indicates that community financing improves access by rural and informal sector workers to needed heath care and provides them with some financial protection against the cost of illness. Macro-level cross-country analysis gives empirical support to the hypothesis that risk-sharing in health financing matters in terms of its impact on both the level and distribution of health, financial fairness and responsiveness indicators. The background research done for this article points to five key policies available to governments to improve the effectiveness and sustainability of existing community financing schemes. This includes: (a) increased and well-targeted subsidies to pay for the premiums of low-income populations; (b) insurance to protect against expenditure fluctuations and re-insurance to enlarge the effective size of small risk pools; (c) effective prevention and case management techniques to limit expenditure fluctuations; (d) technical support to strengthen the management capacity of local schemes; and (e) establishment and strengthening of links with the formal financing and provider networks.

Transformation of ministries of health in the era of health reform: the case of Colombia

Ministries of health are being called upon to lead major health reforms; at the same time they must reform themselves to become more modern institutions and assume new and different functions and roles in the more dynamic reformed system. The literature on public administration and on health reform has recommended many processes of institutional reform and development, building on private sector management techniques, popularized by 'reinventing government' and 'total quality management'. More recently, thoughtful insights have emphasized improving public management through a focus on creating 'public value'; on political, as well as administrative, leadership; improving institutional performance through strengthening the 'task networks' of organizations needed to achieve strategic objectives; and creating a learning culture within the organization. This article applies these recent approaches to the specific needs of ministries of health in order to improve their capacity to lead major health reforms. This combined approach is then used to analyze and make recommendations to the Ministry of Health in Colombia where the authors were providing technical support for a major new health reform.

4 x 4 vertical-cavity surface-emitting laser (VCSEL) and metal-semiconductor-metal (MSM) optical backplane demonstrator system

We describe a system demonstrator based on vertical-cavity surface-emitting lasers, metal-semiconductor-metal detectors, printed circuit board (PCB) level optoelectronic device packaging, a compact bulk optical relay, and novel barrel/PCB optomechanics. The entire system was constructed in a standard VME electrical backplane chassis and was capable of operating at >1.7 Gbit/s of aggregate data capacity. In addition to the component technologies developed, we describe operational testing and characterization of the demonstrator.

Ethnic distribution of the glutathione transferase Mu 1-1 (GSTM1) null genotype in 1473 individuals and application to bladder cancer susceptibility

Polycyclic aromatic hydrocarbons, found in cigarette smoke, food and industrial materials, are potential human carcinogens. Deficiency of detoxifying enzymes, such as glutathione transferases, may affect the metabolic fates of these chemicals and raise cancer risks in exposed individuals. The GSTM1 null genotype is a common form of glutathione transferase deficiency. Because knowledge of its ethnic distribution would be useful in epidemiologic studies, we measured the frequencies of the GSTM1 null genotype among healthy blacks, whites, Asian Indians, Chinese, Japanese, Koreans, Filipinos, Samoans and Hispanics. Rapid genotyping was done by use of a PCR assay, with dried blood spots on blotter paper as DNA templates. The frequency of the null genotype ranged from 0.31 among blacks to 0.88 among Samoans. The PCR assay was also applied to a pilot study of 114 bladder cancer cases from Kaiser Permanente Medical Center, Harbor City, California. DNA for these cases was obtained from paraffin-embedded surgical specimens. The overall odds ratio for bladder cancer with the GSTM1 null genotype was 1.4 (95% confidence interval 0.94-2.1), indicating no statistical difference in null genotype frequencies among bladder cancer patients compared to a healthy population. Large epidemiologic studies, which can be accomplished with dried blood spots or paraffin-embedded tissue specimens, may be useful for further assessment.

Small-group judgment methods for determining resource-based relative values

National telephone surveys used in the Resource-Based Relative Value Scale Study produce reliable and valid relative values of work, but phone surveys are expensive and time consuming. We evaluated three small-group processes as alternatives. We compared national survey work estimates for 38 surgical services to those generated by panels of 11 and 19 highly qualified general surgeons using 1) single-round mail survey; 2) Delphi multiple-round ratings; and 3) modified Delphi with face-to-face discussion. Single-round mail-survey ratings were closest to the national survey; average differences were 11.0% and 12.6%. Delphi feedback led to increased differences: typical values differed by 14.6% and 15.2%. Face-to-face discussion led to still further divergence (21.0%). Single-round mail survey of a small number of experts provides relative work values that compare more favorably to those of the national survey than those obtained from Delphi multiple-round ratings or modified Delphi with face-to-face discussion.

Cellular targets and host genes in multistage carcinogenesis

Recent studies indicate that although cellular DNA is the critical target in the action of initiating carcinogens, specific membrane-associated receptors mediate the actions of certain tumor promoters. A stereochemical model is presented to explain how three different types of tumor promoters (phorbol esters, indole alkaloids, and polyacetates) can interact with the same class of cellular receptors. Multistage chemical carcinogenesis might involve progressive alterations in the expression of cellular DNA sequences homologous to oncogenes and regulatory sequences in certain retroviruses. We found that the oncogene c-mos is not rearranged or expressed in a series of carcinogen-transformed murine C3H 10T112 cells. These cells do express, however, a unique set of poly(A)+ RNAs that contain sequences homologous to the Moloney leukemia virus long terminal repeat sequence. Studies are in progress to determine the significance of this finding with respect to the carcinogenic process.