Whole genome capture of vector-borne pathogens from mixed DNA samples: a case study of Borrelia burgdorferi.

BACKGROUND: Rapid and accurate retrieval of whole genome sequences of human pathogens from disease vectors or animal reservoirs will enable fine-resolution studies of pathogen epidemiological and evolutionary dynamics. However, next generation sequencing technologies have not yet been fully harnessed for the study of vector-borne and zoonotic pathogens, due to the difficulty of obtaining high-quality pathogen sequence data directly from field specimens with a high ratio of host to pathogen DNA. RESULTS: We addressed this challenge by using custom probes for multiplexed hybrid capture to enrich for and sequence 30 Borrelia burgdorferi genomes from field samples of its arthropod vector. Hybrid capture enabled sequencing of nearly the complete genome (~99.5 %) of the Borrelia burgdorferi pathogen with 132-fold coverage, and identification of up to 12,291 single nucleotide polymorphisms per genome. CONCLUSIONS: The proprosed culture-independent method enables efficient whole genome capture and sequencing of pathogens directly from arthropod vectors, thus making population genomic study of vector-borne and zoonotic infectious diseases economically feasible and scalable. Furthermore, given the similarities of invertebrate field specimens to other mixed DNA templates characterized by a high ratio of host to pathogen DNA, we discuss the potential applicabilty of hybrid capture for genomic study across diverse study systems.

Multi-criteria decision analysis as an innovative approach to managing zoonoses: results from a study on Lyme disease in Canada.

BACKGROUND: Zoonoses are a growing international threat interacting at the human-animal-environment interface and call for transdisciplinary and multi-sectoral approaches in order to achieve effective disease management. The recent emergence of Lyme disease in Quebec, Canada is a good example of a complex health issue for which the public health sector must find protective interventions. Traditional preventive and control interventions can have important environmental, social and economic impacts and as a result, decision-making requires a systems approach capable of integrating these multiple aspects of interventions. This paper presents the results from a study of a multi-criteria decision analysis (MCDA) approach for the management of Lyme disease in Quebec, Canada. MCDA methods allow a comparison of interventions or alternatives based on multiple criteria. METHODS: MCDA models were developed to assess various prevention and control decision criteria pertinent to a comprehensive management of Lyme disease: a first model was developed for surveillance interventions and a second was developed for control interventions. Multi-criteria analyses were conducted under two epidemiological scenarios: a disease emergence scenario and an epidemic scenario. RESULTS: In general, we observed a good level of agreement between stakeholders. For the surveillance model, the three preferred interventions were: active surveillance of vectors by flagging or dragging, active surveillance of vectors by trapping of small rodents and passive surveillance of vectors of human origin. For the control interventions model, basic preventive communications, human vaccination and small scale landscaping were the three preferred interventions. Scenarios were found to only have a small effect on the group ranking of interventions in the control model. CONCLUSIONS: MCDA was used to structure key decision criteria and capture the complexity of Lyme disease management. This facilitated the identification of gaps in the scientific literature and enabled a clear identification of complementary interventions that could be used to improve the relevance and acceptability of proposed prevention and control strategy. Overall, MCDA presents itself as an interesting systematic approach for public health planning and zoonoses management with a "One Health" perspective.

Integration and visualization of host-pathogen data related to infectious diseases.

MOTIVATION: Infectious disease research is generating an increasing amount of disparate data on pathogenic systems. There is a growing need for resources that effectively integrate, analyze, deliver and visualize these data, both to improve our understanding of infectious diseases and to facilitate the development of strategies for disease control and prevention. RESULTS: We have developed Disease View, an online host-pathogen resource that enables infectious disease-centric access, analysis and visualization of host-pathogen interactions. In this resource, we associate infectious diseases with corresponding pathogens, provide information on pathogens, pathogen virulence genes and the genetic and chemical evidences for the human genes that are associated with the diseases. We also deliver the relationships between pathogens, genes and diseases in an interactive graph and provide the geolocation reports of associated diseases around the globe in real time. Unlike many other resources, we have applied an iterative, user-centered design process to the entire resource development, including data acquisition, analysis and visualization. AVAILABILITY AND IMPLEMENTATION: Freely available at http://www.patricbrc.org; all major web browsers supported. CONTACT: cmao@vbi.vt.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Two boundaries separate Borrelia burgdorferi populations in North America.

Understanding the spread of infectious diseases is crucial for implementing effective control measures. For this, it is important to obtain information on the contemporary population structure of a disease agent and to infer the evolutionary processes that may have shaped it. Here, we investigate on a continental scale the population structure of Borrelia burgdorferi, the causative agent of Lyme borreliosis (LB), a tick-borne disease, in North America. We test the hypothesis that the observed population structure is congruent with recent population expansions and that these were preceded by bottlenecks mostly likely caused by the near extirpation in the 1900s of hosts required for sustaining tick populations. Multilocus sequence typing and complementary population analytical tools were used to evaluate B. burgdorferi samples collected in the Northeastern, Upper Midwestern, and Far-Western United States and Canada. The spatial distribution of sequence types (STs) and inferred population boundaries suggest that the current populations are geographically separated. One major population boundary separated western B. burgdorferi populations transmitted by Ixodes pacificus in California from Eastern populations transmitted by I. scapularis; the other divided Midwestern and Northeastern populations. However, populations from all three regions were genetically closely related. Together, our findings suggest that although the contemporary populations of North American B. burgdorferi now comprise three geographically separated subpopulations with no or limited gene flow among them, they arose from a common ancestral population. A comparative analysis of the B. burgdorferi outer surface protein C (ospC) gene revealed novel linkages and provides additional insights into the genetic characteristics of strains.

Phylogeography of Lyme borreliosis-group spirochetes and methicillin-resistant Staphylococcus aureus.

Multilocus sequence typing (MLST) and multilocus sequence analysis (MLSA) have revolutionized understanding the global epidemiology of many medically relevant bacteria utilizing a number, mostly seven, of housekeeping genes. A more recent introduction, single nucleotide polymorphisms (SNPs), constitutes an even more powerful tool for bacterial typing, population genetic studies and phylogeography. The introduction of massive parallel sequencing has made genome re-sequencing and SNP discovery more economical for investigations of microbial organisms. In this paper we review phylogeographic studies on Lyme borreliosis (LB)-group spirochetes and methicillin-resistant Staphylococcus aureus (MRSA). Members of the LB-group spirochetes are tick-transmitted zoonotic bacteria that have many hosts and differ in their degree of host specialism, constituting a highly complex system. MRSA is a directly transmitted pathogen that may be acquired by contact with infected people, animals or MRSA-contaminated objects. For the LB-group spirochetes, MLSA has proved a powerful tool for species assignment and phylogeographic investigations while for S. aureus, genome-wide SNP data have been used to study the very short-term evolution of two important MRSA lineages, ST239 and ST225. These data are detailed in this review.

Phylogeography of Borrelia burgdorferi in the eastern United States reflects multiple independent Lyme disease emergence events.

Since its first description in coastal Connecticut in 1976, both the incidence of Lyme disease and the geographic extent of endemic areas in the US have increased dramatically. The rapid expansion of Lyme disease into its current distribution in the eastern half of the US has been due to the range expansion of the tick vector, Ixodes scapularis, upon which the causative agent, Borrelia burgdorferi is dependent for transmission to humans. In this study, we examined the phylogeographic population structure of B. burgdorferi throughout the range of I. scapularis-borne Lyme disease using multilocus sequence typing based on bacterial housekeeping genes. We show that B. burgdorferi populations from the Northeast and Midwest are genetically distinct, but phylogenetically related. Our findings provide strong evidence of prehistoric population size expansion and east-to-west radiation of descendent clones from founding sequence types in the Northeast. Estimates of the time scale of divergence of northeastern and midwestern populations suggest that B. burgdorferi was present in these regions of North America many thousands of years before European settlements. We conclude that B. burgdorferi populations have recently reemerged independently out of separate relict foci, where they have persisted since precolonial times.

Effect of expanded US recommendations for seasonal influenza vaccination: comparison of two pediatric emergency departments in the United States and Canada.

BACKGROUND: Starting in the 2006/2007 influenza season, the US Advisory Committee on Immunization Practices expanded its recommendations for seasonal influenza vaccination to include healthy children aged 24-59 months. The parallel Canadian organization, the National Advisory Committee on Immunization, did not at that time issue a similar recommendation, thereby creating a natural experiment to evaluate the effect of the policy in the United States. METHODS: We examined data for 2000/2001 through 2008/2009 and estimated relative changes in visits to the emergency department for influenza-like illness at two pediatric hospitals, one in Boston, Massachusetts, and the other in Montréal, Quebec, following the US policy change. Models were adjusted for virologic factors, seasonal trends and all-cause utilization of the emergency department. RESULTS: Of 1 043 989 visits to the emergency departments of the two hospitals for any reason during the study period, 114 657 visits were related to influenza-like illness. Adjusted models estimated a 34% decline in rates of influenza-like illness among children two to four years old in the US hospital relative to the Canadian hospital (rate ratio 0.66, 95% confidence interval 0.58-0.75) following the 2006 policy change of the Advisory Committee on Immunization Practices. This was accompanied by more modest declines of 11% to 18% for the other age groups studied. INTERPRETATION: The divergence in influenza rates among children in the US and Canadian sample populations after institution of the US policy to vaccinate children two to four years of age is evidence that the recommendation of the US Advisory Committee on Immunization Practices resulted in a reduction in influenza-related morbidity in the target group and may have indirectly affected other pediatric age groups. Provincial adoption of the 2010 recommendation of the National Advisory Committee on Immunization in Canada to vaccinate children two to four years of age might positively affect influenza morbidity in Canada.

Spatially explicit multi-criteria decision analysis for managing vector-borne diseases.

The complex epidemiology of vector-borne diseases creates significant challenges in the design and delivery of prevention and control strategies, especially in light of rapid social and environmental changes. Spatial models for predicting disease risk based on environmental factors such as climate and landscape have been developed for a number of important vector-borne diseases. The resulting risk maps have proven value for highlighting areas for targeting public health programs. However, these methods generally only offer technical information on the spatial distribution of disease risk itself, which may be incomplete for making decisions in a complex situation. In prioritizing surveillance and intervention strategies, decision-makers often also need to consider spatially explicit information on other important dimensions, such as the regional specificity of public acceptance, population vulnerability, resource availability, intervention effectiveness, and land use. There is a need for a unified strategy for supporting public health decision making that integrates available data for assessing spatially explicit disease risk, with other criteria, to implement effective prevention and control strategies. Multi-criteria decision analysis (MCDA) is a decision support tool that allows for the consideration of diverse quantitative and qualitative criteria using both data-driven and qualitative indicators for evaluating alternative strategies with transparency and stakeholder participation. Here we propose a MCDA-based approach to the development of geospatial models and spatially explicit decision support tools for the management of vector-borne diseases. We describe the conceptual framework that MCDA offers as well as technical considerations, approaches to implementation and expected outcomes. We conclude that MCDA is a powerful tool that offers tremendous potential for use in public health decision-making in general and vector-borne disease management in particular.

Genotypic diversity of Borrelia burgdorferi strains detected in Ixodes scapularis larvae collected from North American songbirds.

We genotyped Borrelia burgdorferi strains detected in larvae of Ixodes scapularis removed from songbirds and compared them with those found in host-seeking I. scapularis nymphs sampled throughout the eastern United States. Birds are capable of transmitting most known genotypes, albeit at different frequencies than expected based on genotypes found among host-seeking nymphs.

Evidence-based tool for triggering school closures during influenza outbreaks, Japan.

Guidelines available to school administrators to support school closure decisions during influenza outbreaks are usually not evidence-based. Using empirical data on absentee rates of elementary school students in Japan, we developed a simple and practical algorithm for determining the optimal timing of school closures for control of influenza outbreaks.

Fetal exposures and perinatal influences on the stool microbiota of premature infants.

OBJECTIVE: To test the hypothesis that maternal complications significantly affect gut colonization patterns in very low birth weight infants. METHODS: Forty-nine serial stool samples were obtained weekly from nine extremely premature infants enrolled in a prospective longitudinal study. Sequencing of the bacterial 16S rRNA gene from stool samples was performed to approximate the intestinal microbiome. Linear mixed effects models were used to evaluate relationships between perinatal complications and intestinal microbiome development. RESULTS: Subjects with prenatal exposure to a non-sterile intrauterine environment, i.e. prolonged preterm premature rupture of membranes (PPPROM) and chorioamnionitis exposure, were found to have a relatively higher abundance of potentially pathogenic bacteria in the stool across all time points compared to subjects without those exposures, irrespective of exposure to postnatal antibiotics. Compared with those delivered by Caesarean section, vaginally delivered subjects were found to have significantly lower diversity of stool microbiota across all time points, with lower abundance of many genera, most in the family Enterobacteriaceae. CONCLUSIONS: We identified persistently increased potential pathogen abundance in the developing stool microbiota of subjects exposed to a non-sterile uterine environment. Maternal complications appear to significantly influence the diversity and bacterial composition of the stool microbiota of premature infants, with findings persisting over time.

Identification of SNPs associated with variola virus virulence.

BACKGROUND: Decades after the eradication of smallpox, its etiological agent, variola virus (VARV), remains a threat as a potential bioweapon. Outbreaks of smallpox around the time of the global eradication effort exhibited variable case fatality rates (CFRs), likely attributable in part to complex viral genetic determinants of smallpox virulence. We aimed to identify genome-wide single nucleotide polymorphisms associated with CFR. We evaluated unadjusted and outbreak geographic location-adjusted models of single SNPs and two- and three-way interactions between SNPs. FINDINGS: Using the data mining approach multifactor dimensionality reduction (MDR), we identified five VARV SNPs in models significantly associated with CFR. The top performing unadjusted model and adjusted models both revealed the same two-way gene-gene interaction. We discuss the biological plausibility of the influence of the SNPs identified these and other significant models on the strain-specific virulence of VARV. CONCLUSIONS: We have identified genetic loci in the VARV genome that are statistically associated with VARV virulence as measured by CFR. While our ability to infer a causal relationship between the specific SNPs identified in our analysis and VARV virulence is limited, our results suggest that smallpox severity is in part associated with VARV strain variation and that VARV virulence may be determined by multiple genetic loci. This study represents the first application of MDR to the identification of pathogen gene-gene interactions for predicting infectious disease outbreak severity.

Human risk of infection with Borrelia burgdorferi, the Lyme disease agent, in eastern United States.

The geographic pattern of human risk for infection with Borrelia burgdorferi sensu stricto, the tick-borne pathogen that causes Lyme disease, was mapped for the eastern United States. The map is based on standardized field sampling in 304 sites of the density of Ixodes scapularis host-seeking nymphs infected with B. burgdorferi, which is closely associated with human infection risk. Risk factors for the presence and density of infected nymphs were used to model a continuous 8 km×8 km resolution predictive surface of human risk, including confidence intervals for each pixel. Discontinuous Lyme disease risk foci were identified in the Northeast and upper Midwest, with a transitional zone including sites with uninfected I. scapularis populations. Given frequent under- and over-diagnoses of Lyme disease, this map could act as a tool to guide surveillance, control, and prevention efforts and act as a baseline for studies tracking the spread of infection.

Characteristics of US public schools with reported cases of novel influenza A (H1N1).

OBJECTIVE: The 2009 pandemic of influenza A (H1N1) has disproportionately affected children and young adults, resulting in attention by public health officials and the news media on schools as important settings for disease transmission and spread. We aimed to characterize US schools affected by novel influenza A (H1N1) relative to other schools in the same communities. METHODS: A database of US school-related cases was obtained by electronic news media monitoring for early reports of novel H1N1 influenza between April 23 and June 8, 2009. We performed a matched case-control study of 32 public primary and secondary schools that had one or more confirmed cases of H1N1 influenza and 6815 control schools located in the same 23 counties as case schools. RESULTS: Compared with controls from the same county, schools with reports of confirmed cases of H1N1 influenza were less likely to have a high proportion of economically disadvantaged students (adjusted odds ratio (aOR) 0.385; 95% confidence interval (CI) 0.166-0.894) and less likely to have older students (aOR 0.792; 95% CI 0.670-0.938). CONCLUSIONS: We conclude that public schools with younger, more affluent students may be considered sentinels of the epidemic and may have played a role in its initial spread.

Niche partitioning of Borrelia burgdorferi and Borrelia miyamotoi in the same tick vector and mammalian reservoir species.

The Lyme borreliosis agent Borrelia burgdorferi and the relapsing fever group species Borrelia miyamotoi co-occur in the United States. We used species-specific, quantitative polymerase chain reaction to study both species in the blood and skin of Peromyscus leucopus mice and host-seeking Ixodes scapularis nymphs at a Connecticut site. Bacteremias with B. burgdorferi or B. miyamotoi were most prevalent during periods of greatest activity for nymphs or larvae, respectively. Whereas B. burgdorferi was 30-fold more frequent than B. miyamotoi in skin biopsies and mice had higher densities of B. burgdorferi densities in the skin than in the blood, B. miyamotoi densities were higher in blood than skin. In a survey of host-seeking nymphs in 11 northern states, infection prevalences for B. burgdorferi and B. miyamotoi averaged approximately 0.20 and approximately 0.02, respectively. Co-infections of P. leucopus or I. scapularis with both B. burgdorferi and B. miyamotoi were neither more nor less common than random expectations.

Effects of tick control by acaricide self-treatment of white-tailed deer on host-seeking tick infection prevalence and entomologic risk for Ixodes scapularis-borne pathogens.

We evaluated the effects of tick control by acaricide self-treatment of white-tailed deer on the infection prevalence and entomologic risk for three Ixodes scapularis-borne bacteria in host-seeking ticks. Ticks were collected from vegetation in areas treated with the "4-Poster" device and from control areas over a 6-year period in five geographically diverse study locations in the Northeastern United States and tested for infection with two known agents of human disease, Borrelia burgdorferi and Anaplasma phagocytophilum, and for a novel relapsing fever-group spirochete related to Borrelia miyamotoi. Overall, 38.2% of adults and 12.5% of nymphs were infected with B. burgdorferi; 8.5% of adults and 4.2% of nymphs were infected with A. phagocytophilum; and 1.9% of adults and 0.8% of nymphs were infected with B. miyamotoi. In most cases, treatment with the 4-Poster device was not associated with changes in the prevalence of infection with any of these three microorganisms among nymphal or adult ticks. However, the density of nymphs infected with B. burgdorferi, and consequently the entomologic risk for Lyme disease, was reduced overall by 68% in treated areas compared to control areas among the five study sites at the end of the study. The frequency of bacterial coinfections in ticks was generally equal to the product of the proportion of ticks infected with a single bacterium, indicating that enzootic maintenance of these pathogens is independent. We conclude that controlling ticks on deer by self-application of acaricide results in an overall decrease in the human risk for exposure to these three bacterial agents, which is due solely to a reduction in tick density.