The DataHarmonizer: a tool for faster data harmonization, validation, aggregation and analysis of pathogen genomics contextual information.

Pathogen genomics is a critical tool for public health surveillance, infection control, outbreak investigations as well as research. In order to make use of pathogen genomics data, they must be interpreted using contextual data (metadata). Contextual data include sample metadata, laboratory methods, patient demographics, clinical outcomes and epidemiological information. However, the variability in how contextual information is captured by different authorities and how it is encoded in different databases poses challenges for data interpretation, integration and their use/re-use. The DataHarmonizer is a template-driven spreadsheet application for harmonizing, validating and transforming genomics contextual data into submission-ready formats for public or private repositories. The tool's web browser-based JavaScript environment enables validation and its offline functionality and local installation increases data security. The DataHarmonizer was developed to address the data sharing needs that arose during the COVID-19 pandemic, and was used by members of the Canadian COVID Genomics Network (CanCOGeN) to harmonize SARS-CoV-2 contextual data for national surveillance and for public repository submission. In order to support coordination of international surveillance efforts, we have partnered with the Public Health Alliance for Genomic Epidemiology to also provide a template conforming to its SARS-CoV-2 contextual data specification for use worldwide. Templates are also being developed for One Health and foodborne pathogens. Overall, the DataHarmonizer tool improves the effectiveness and fidelity of contextual data capture as well as its subsequent usability. Harmonization of contextual information across authorities, platforms and systems globally improves interoperability and reusability of data for concerted public health and research initiatives to fight the current pandemic and future public health emergencies. While initially developed for the COVID-19 pandemic, its expansion to other data management applications and pathogens is already underway.

Economic evaluation of covered stents for transjugular intrahepatic portosystemic stent shunt in patients with variceal bleeding and refractory ascites secondary to cirrhosis.

OBJECTIVES: Transjugular intrahepatic portosystemic stent shunt (TIPSS) is clinically effective in variceal bleeding and refractory ascites; however, the cost-effectiveness of TIPSS has yet to be evaluated in the UK. This study aimed to establish the cost-effectiveness of (i) pre-emptive TIPSS versus endoscopic band ligation (EBL) in populations with variceal bleeding and (ii) TIPSS versus large volume paracentesis (LVP) in refractory ascites. METHODS: A cost-utility analysis was conducted with the perspective including healthcare costs and quality-adjusted life years (QALYs). A Markov model was constructed with a 2-year time horizon, health states for mortality and survival and probabilities for the development of variceal bleeding, ascites and hepatic encephalopathy. A survival analysis was conducted to extrapolate 12-month to 24-month mortality for the refractory ascites indication. Uncertainty was analysed in deterministic and probabilistic sensitivity analyses. RESULTS: TIPSS was cost-effective (dominant) and cost saving for both indications. For variceal bleeding, pre-emptive TIPSS resulted in 0.209 additional QALYs, and saved £600 per patient compared with EBL. TIPSS had a very high probability of being cost-effective (95%) but was not cost saving in scenario analyses driven by rates of variceal rebleeding. For refractory ascites, TIPSS resulted in 0.526 additional QALYs and saved £17 983 per patient and had a 100% probability of being cost-effective and cost saving when compared with LVP. CONCLUSIONS: TIPSS is a cost-effective intervention for variceal bleeding and refractory ascites. TIPSS is highly cost-saving for refractory ascites. Robust randomised trial data are required to confirm whether pre-emptive TIPSS is cost saving for variceal bleeding.

Autorepressor PsrA is required for optimal Legionella pneumophila growth in Acanthamoeba castellanii protozoa.

Legionella pneumophila possesses a unique intracellular lifecycle featuring distinct morphological stages that include replicative forms and transmissive cyst forms. Expression of genes associated with virulence traits and cyst morphogenesis is concomitant, and governed by a complex stringent response based-regulatory network and the stationary phase sigma factor RpoS. In Pseudomonas spp., rpoS expression is controlled by the autorepressor PsrA, and orthologs of PsrA and RpoS are required for cyst formation in Azotobacter. Here we report that the L. pneumophila psrA ortholog, expressed as a leaderless monocistronic transcript, is also an autorepressor, but is not a regulator of rpoS expression. Further, the binding site sequence recognized by L. pneumophila PsrA is different from that of Pseudomonas PsrA, suggesting a repertoire of target genes unique to L. pneumophila. While PsrA was dispensable for growth in human U937-derived macrophages, lack of PsrA affected bacterial intracellular growth in Acanthamoeba castellanii protozoa, but also increased the quantity of poly-3-hydroxybutyrate (PHB) inclusions in matured transmissive cysts. Interestingly, overexpression of PsrA increased the size and bacterial load of the replicative vacuole in both host cell types. Taken together, we report that PsrA is a host-specific requirement for optimal temporal progression of L. pneumophila intracellular lifecycle in A. castellanii.

Ecological niche adaptation of Salmonella Typhimurium U288 is associated with altered pathogenicity and reduced zoonotic potential.

The emergence of new bacterial pathogens is a continuing challenge for agriculture and food safety. Salmonella Typhimurium is a major cause of foodborne illness worldwide, with pigs a major zoonotic reservoir. Two phylogenetically distinct variants, U288 and ST34, emerged in UK pigs around the same time but present different risk to food safety. Here we show using genomic epidemiology that ST34 accounts for over half of all S. Typhimurium infections in people while U288 less than 2%. That the U288 clade evolved in the recent past by acquiring AMR genes, indels in the virulence plasmid pU288-1, and accumulation of loss-of-function polymorphisms in coding sequences. U288 replicates more slowly and is more sensitive to desiccation than ST34 isolates and exhibited distinct pathogenicity in the murine model of colitis and in pigs. U288 infection was more disseminated in the lymph nodes while ST34 were recovered in greater numbers in the intestinal contents. These data are consistent with the evolution of S. Typhimurium U288 adaptation to pigs that may determine their reduced zoonotic potential.

Pseudomonas chlororaphis PA23 metabolites protect against protozoan grazing by the predator Acanthamoeba castellanii.

BACKGROUND: Pseudomonas chlororaphis strain PA23 is a biocontrol agent that is able to protect canola against the pathogenic fungus Sclerotinia sclerotiorum. This bacterium secretes a number of metabolites that contribute to fungal antagonism, including pyrrolnitrin (PRN), phenazine (PHZ), hydrogen cyanide (HCN) and degradative enzymes. In order to be successful, a biocontrol agent must be able to persist in the environment and avoid the threat of grazing predators. The focus of the current study was to investigate whether PA23 is able to resist grazing by the protozoan predator Acanthamoeba castellanii (Ac) and to define the role of bacterial metabolites in the PA23-Ac interaction. METHODS: Ac was co-cultured with PA23 WT and a panel of derivative strains for a period of 15 days, and bacteria and amoebae were enumerated on days 1, 5, 10 and 15. Ac was subsequently incubated in the presence of purified PRN, PHZ, and KCN and viability was assessed at 24, 48 and 72 h. Chemotactic assays were conducted to assess whether PA23 compounds exhibit repellent or attractant properties towards Ac. Finally, PA23 grown in the presence and absence of amoebae was subject to phenotypic characterization and gene expression analyses. RESULTS: PRN, PHZ and HCN were found to contribute to PA23 toxicity towards Ac trophozoites, either by killing or inducing cyst formation. This is the first report of PHZ-mediated toxicity towards amoebae. In chemotaxis assays, amoebae preferentially migrated towards regulatory mutants devoid of extracellular metabolite production as well as a PRN mutant, indicating this antibiotic has repellent properties. Co-culturing of bacteria with amoebae led to elevated expression of the PA23 phzI/phzR quorum-sensing (QS) genes and phzA and prnA, which are under QS control. PHZ and PRN levels were similarly increased in Ac co-cultures, suggesting that PA23 can respond to predator cues and upregulate expression of toxins accordingly. CONCLUSIONS: PA23 compounds including PRN, PHZ and HCN exhibited both toxic and repellent effects on Ac. Co-culturing of bacteria and amoebae lead to changes in bacterial gene expression and secondary metabolite production, suggesting that PA23 can sense the presence of these would-be predators and adjust its physiology in response.

Mutation of hilD in a Salmonella Derby lineage linked to swine adaptation and reduced risk to human health.

Salmonella enterica variants exhibit diverse host adaptation, outcome of infection, and associated risk to food safety. Analysis of the distribution of Salmonella enterica serovar Derby (S. Derby) subtypes in human and swine identified isolates with a distinct PFGE profile that were significantly under-represented in human infections, consistent with further host adaptation to swine. Here we show that isolates with this PFGE profile form a distinct phylogenetic sub-clade within S. Derby and exhibit a profound reduction in invasion of human epithelial cells, and a relatively small reduction in swine epithelial cells. A single missense mutation in hilD, that encodes the master-regulator of the Salmonella Pathogenicity Island 1 (SPI-1), was present in the adapted lineage. The missense mutation resulted in a loss of function of HilD that accounted for reduced invasion in human epithelial cells. The relatively small impact of the mutation on interaction with swine cells was consistent with an alternative mechanism of invasion in this pathogen-host combination.

Evolution of Salmonella within Hosts.

Within-host evolution has resulted in thousands of variants of Salmonella that exhibit remarkable diversity in host range and disease outcome, from broad host range to exquisite host restriction, causing gastroenteritis to disseminated disease such as typhoid fever. Within-host evolution is a continuing process driven by genomic variation that occurs during each infection, potentiating adaptation to a new niche resulting from changes in animal husbandry, the use of antimicrobials, and emergence of immune compromised populations. We discuss key advances in our understanding of the evolution of Salmonella within the host, inferred from (i) the process of host adaptation of Salmonella pathovars in the past, and (ii) direct observation of the generation of variation and selection of beneficial traits during single infections.

Legionella pneumophila OxyR Is a Redundant Transcriptional Regulator That Contributes to Expression Control of the Two-Component CpxRA System.

Nominally an environmental organism, Legionella pneumophila is an intracellular parasite of protozoa but is also the causative agent of the pneumonia termed Legionnaires' disease, which results from inhalation of aerosolized bacteria by susceptible humans. Coordination of gene expression by a number of identified regulatory factors, including OxyR, assists L. pneumophila in adapting to the stresses of changing environments. L. pneumophila OxyR (OxyRLp) is an ortholog of Escherichia coli OxyR; however, OxyRLp was shown elsewhere to be functionally divergent, such that it acts as a transcription regulator independently of the oxidative stress response. In this study, the use of improved gene deletion methods has enabled us to generate an unmarked in-frame deletion of oxyR in L. pneumophila Lack of OxyRLp did not affect in vitro growth or intracellular growth in Acanthamoeba castellanii protozoa and U937-derived macrophages. The expression of OxyRLp does not appear to be regulated by CpxR, even though purified recombinant CpxR bound a DNA sequence similar to that reported for CpxR elsewhere. Surprisingly, a lack of OxyRLp resulted in elevated activity of the promoters located upstream of icmR and the lpg1441-cpxA operon, and OxyRLp directly bound to these promoter regions, suggesting that OxyRLp is a direct repressor. Interestingly, a strain overexpressing OxyRLp demonstrated reduced intracellular growth in A. castellanii but not in U937-derived macrophages, suggesting that balanced expression control of the two-component CpxRA system is necessary for survival in protozoa. Taken together, this study suggests that OxyRLp is a functionally redundant transcriptional regulator in L. pneumophila under the conditions evaluated herein.IMPORTANCELegionella pneumophila is an environmental pathogen, with its transmission to the human host dependent upon its ability to replicate in protozoa and survive within its aquatic niche. Understanding the genetic factors that contribute to L. pneumophila survival within each of these unique environments will be key to limiting future point-source outbreaks of Legionnaires' disease. The transcriptional regulator L. pneumophila OxyR (OxyRLp) has been previously identified as a potential regulator of virulence traits warranting further investigation. This study demonstrated that oxyR is nonessential for L. pneumophila survival in vitro and in vivo via mutational analysis. While the mechanisms of how OxyRLp expression is regulated remain elusive, this study shows that OxyRLp negatively regulates the expression of the cpxRA two-component system necessary for intracellular survival in protozoa.

The CpxRA two-component system contributes to Legionella pneumophila virulence.

The bacterium Legionella pneumophila is capable of intracellular replication within freshwater protozoa as well as human macrophages, the latter of which results in the serious pneumonia Legionnaires' disease. A primary factor involved in these host cell interactions is the Dot/Icm Type IV secretion system responsible for translocating effector proteins needed to establish and maintain the bacterial replicative niche. Several regulatory factors have been identified to control the expression of the Dot/Icm system and effectors, one of which is the CpxRA two-component system, suggesting essentiality for virulence. In this study, we generated cpxR, cpxA and cpxRA in-frame null mutant strains to further delineate the role of the CpxRA system in bacterial survival and virulence. We found that cpxR is essential for intracellular replication within Acanthamoeba castellanii, but not in U937-derived macrophages. Transcriptome analysis revealed that CpxRA regulates a large number of virulence-associated proteins including Dot/Icm effectors as well as Type II secreted substrates. Furthermore, the cpxR and cpxRA mutant strains were more sodium resistant than the parental strain Lp02, and cpxRA expression reaches maximal levels during postexponential phase. Taken together, our findings suggest the CpxRA system is a key contributor to L. pneumophila virulence in protozoa via virulence factor regulation.

Identification of vacuoles containing extraintestinal differentiated forms of Legionella pneumophila in colonized Caenorhabditis elegans soil nematodes.

Legionella pneumophila, a causative agent of Legionnaires' disease, is a facultative intracellular parasite of freshwater protozoa. Legionella pneumophila features a unique developmental network that involves several developmental forms including the infectious cyst forms. Reservoirs of L. pneumophila include natural and man-made freshwater systems; however, recent studies have shown that isolates of L. pneumophila can also be obtained directly from garden potting soil suggesting the presence of an additional reservoir. A previous study employing the metazoan Caenorhabditis elegans, a member of the Rhabditidae family of free-living soil nematodes, demonstrated that the intestinal lumen can be colonized with L. pneumophila. While both replicative forms and differentiated forms were observed in C. elegans, these morphologically distinct forms were initially observed to be restricted to the intestinal lumen. Using live DIC imaging coupled with focused transmission electron microscopy analyses, we report here that L. pneumophila is able to invade and establish Legionella-containing vacuoles (LCVs) in the intestinal cells. In addition, LCVs containing replicative and differentiated cyst forms were observed in the pseudocoelomic cavity and gonadal tissue of nematodes colonized with L. pneumophila. Furthermore, establishment of LCVs in the gonadal tissue was Dot/Icm dependent and required the presence of the endocytic factor RME-1 to gain access to maturing oocytes. Our findings are novel as this is the first report, to our knowledge, of extraintestinal LCVs containing L. pneumophila cyst forms in C. elegans tissues, highlighting the potential of soil-dwelling nematodes as an alternate environmental reservoir for L. pneumophila.

Regulatory control of temporally expressed integration host factor (IHF) in Legionella pneumophila.

Legionella pneumophila, an intracellular parasite of protozoa, possesses a distinct dimorphic life cycle that alternates between the vegetative replicative form and the resilient but highly infectious cyst form. Previously, temporally expressed heterodimeric integration host factor (IHF) was shown to be required for differentiation into the cyst form. However, the precise regulatory mechanisms controlling the expression of IHF have not been identified. Microplate kinetic assays with GFP reporter promoter fusion constructs in wild-type, Δihf, ΔrpoS and ΔletA mutant strain backgrounds were employed to assess differences in expression levels of ihfA, ihfB, rsmY and rsmZ. Loss of IHF, RsmY and RsmZ expression in various mutant strain backgrounds was confirmed by quantitative PCR. Here we report that the stationary phase sigma factor RpoS is a positive regulator of IHF, whereas IHF appears to act as a positive autoregulator assisting RpoS. Bioinformatic analyses identified a set of IHF binding sites upstream of one RpoS binding site in the promoter region for both ihfA and ihfB. Recombinant IHF protein bound ihfA and ihfB promoter regions in vitro, confirming the functionality of these IHF binding sites that may assist in the bending of the promoter DNA to facilitate transcription activation of ihfA and ihfB by RpoS. Interestingly, the consensus binding site for IHF is very similar to that of the two-component response regulator LetA. LetA negatively regulates transcription of ihfA and ihfB, implying titrational regulatory control by LetA and IHF. Along with LetA, IHF was found to positively regulate expression of the non-coding regulatory RNAs RsmY and RsmZ responsible for the de-repression of CsrA-repressed transcripts associated with cyst formation, and coordinated post-exponential virulent phenotypes. Taken together, these observations indicate that IHF may have more of an integral role in the global regulatory system governing the transition from replicative to cyst forms than previously thought.

The relationship between dating violence and suicidal behaviors in a national sample of adolescents.

Relationship violence is a common problem faced by adolescents in the United States. In general, adolescents are at higher risk for relationship victimization than adults (Silverman, Raj, Mucci, & Hathaway, 2001), and females between the ages of 16 and 24 years are at the highest risk of relationship victimization (Rennison, 2001). This study uses data from the 2007 Youth Risk Behavior Surveillance (YRBSS) System (or referred to as Youth Risk Behavior Survey [YRBS]; N = 11,781) of adolescents between the ages of 14 and 17 years to estimate two logistic regression models on the association between relationship violence and suicidal behaviors controlling for variables such as sexual assault and drug use. The findings indicated that victimized adolescents are at higher risk for planning and/or attempting suicide compared to nonvictimized adolescents. Implications for research and practice are explored.

Coral recovery may not herald the return of fishes on damaged coral reefs.

The dynamic nature of coral reefs offers a rare opportunity to examine the response of ecosystems to disruption due to climate change. In 1998, the Great Barrier Reef experienced widespread coral bleaching and mortality. As a result, cryptobenthic fish assemblages underwent a dramatic phase-shift. Thirteen years, and up to 96 fish generations later, the cryptobenthic fish assemblage has not returned to its pre-bleach configuration. This is despite coral abundances returning to, or exceeding, pre-bleach values. The post-bleach fish assemblage exhibits no evidence of recovery. If these short-lived fish species are a model for their longer-lived counterparts, they suggest that (1) the full effects of the 1998 bleaching event on long-lived fish populations have yet to be seen, (2) it may take decades, or more, before recovery or regeneration of these long-lived species will begin, and (3) fish assemblages may not recover to their previous composition despite the return of corals.

Quantifying relative diver effects in underwater visual censuses.

Diver-based Underwater Visual Censuses (UVCs), particularly transect-based surveys, are key tools in the study of coral reef fish ecology. These techniques, however, have inherent problems that make it difficult to collect accurate numerical data. One of these problems is the diver effect (defined as the reaction of fish to a diver). Although widely recognised, its effects have yet to be quantified and the extent of taxonomic variation remains to be determined. We therefore examined relative diver effects on a reef fish assemblage on the Great Barrier Reef. Using common UVC methods, the recorded abundance of seven reef fish groups were significantly affected by the ongoing presence of SCUBA divers. Overall, the diver effect resulted in a 52% decrease in the mean number of individuals recorded, with declines of up to 70% in individual families. Although the diver effect appears to be a significant problem, UVCs remain a useful approach for quantifying spatial and temporal variation in relative fish abundances, especially if using methods that minimise the exposure of fishes to divers. Fixed distance transects using tapes or lines deployed by a second diver (or GPS-calibrated timed swims) would appear to maximise fish counts and minimise diver effects.

Vulnerable people, groups, and populations: societal view.

Vulnerability, the susceptibility to harm, results from an interaction between the resources available to individuals and communities and the life challenges they face. Vulnerability results from developmental problems, personal incapacities, disadvantaged social status, inadequacy of interpersonal networks and supports, degraded neighborhoods and environments, and the complex interactions of these factors over the life course. The priority given to varying vulnerabilities, or their neglect, reflects social values. Vulnerability may arise from individual, community, or larger population challenges and requires different types of policy interventions--from social and economic development of neighborhoods and communities, and educational and income policies, to individual medical interventions.

Change in prevalence of psychiatric disorders from ages 21 to 30 in a community sample.

The authors examined change and demonstrated variation in the prevalence of psychiatric disorders from ages 21 to 30 in a prospective community study (n = 352) using generalized estimating equations and investigated effects of past and recent psychiatric disorder on emerging adult functioning (at age 30). Results revealed significant declines in 12-month prevalence of phobia and substance use disorders from ages 21 to 30 but not in depression or posttraumatic stress disorder. Males were at significantly higher risk for lifetime substance use disorders; females were at higher risk for lifetime depression, phobia, and PTSD. Twelve-month and lifetime disorder were associated with impaired global functioning at age 30. Internalizing disorders were associated with impaired interpersonal functioning, whereas externalizing disorders were associated with impaired socioeconomic functioning. Results of this study have implications for mental health service planning in emerging adulthood.

Adolescent suicidal ideation as predictive of psychopathology, suicidal behavior, and compromised functioning at age 30.

OBJECTIVE: The purpose of this study was to examine whether suicidal ideation in a community population of adolescents represents normative adolescent angst or is predictive of psychopathology, suicidal and problem behaviors, and compromised functioning 15 years after onset. METHOD: Participants were 346 largely Caucasian individuals who were part of a single-age cohort from a working class community and whose development had been traced prospectively from ages 5 to 30. Those with suicidal ideation at age 15 were compared to those without suicidal ideation at age 15 on measures of psychopathology, suicidal ideation and behavior, problem behaviors, and adult functioning at age 30. Gender differences were assessed across all domains. RESULTS: At age 30, there were marked differences between adolescents with suicidal ideation and adolescents without suicidal ideation of both genders in most domains examined. Subjects with suicidal ideation were twice as likely to have an axis I disorder, nearly 12 times more likely to have attempted suicide by age 30, and 15 times more likely to have expressed suicidal thoughts in the past 4 years. Subjects with suicidal ideation had more problem behaviors and poorer overall functioning as assessed by multiple informants. Their self-perceptions of coping ability, self-esteem, and interpersonal relations were also lower. Although subjects with suicidal ideation among both genders had higher levels of psychopathology, suicidal ideation and behavior, and problem behaviors at age 30, male subjects with suicidal ideation had lower salaries and socioeconomic status and were less likely to have achieved residential independence. CONCLUSIONS: Findings underscore the importance of considering suicidal ideation in adolescence as a marker of severe distress and a predictor of compromised functioning, indicating the need for early identification and continued intervention.

Evaluation of factors associated with positive IgM capture ELISA results in equids with clinical signs compatible with West Nile virus infection: 1,017 cases (2003).

OBJECTIVE: To describe the prevalence of West Nile virus (WNV) infection and evaluate factors associated with positive IgM capture ELISA results in equids with clinical signs compatible with WNV infection. DESIGN: Retrospective case series. SAMPLE POPULATION: Laboratory submission forms from 1,104 equids tested for WNV in Colorado in 2003. PROCEDURES: Submission forms accompanying samples submitted for detection of WNV via IgM capture ELISA were obtained from the Colorado state veterinarian and diagnostic laboratories performing the tests. Data on signalment, clinical signs, history of vaccination against WNV, and assay results were collected from laboratory submission forms. Equids with clinical signs compatible with WNV infection in which IgM capture ELISA results were positive were considered as case equids. RESULTS: 1,104 equids were tested for WNV; 1,017 (92.1%) had clinical signs compatible with WNV infection. Among equids with clinical signs compatible with WNV infection, the odds of testing positive for WNV via IgM capture ELISA were lower in males and in vaccinated equids and higher in equids with moderate and severe illness, compared with females, unvaccinated equids, and equids with mild illness. CONCLUSIONS AND CLINICAL RELEVANCE: Among equids with clinical signs compatible with WNV infection, vaccination against WNV, severity of clinical signs, duration of illness, and region in Colorado were associated with increased risk of having a positive IgM capture ELISA result.