Readying the Applied Epidemiology Workforce for Emerging Areas of Public Health Practice.

CONTEXT: Epidemiologists are key professionals within the public health workforce. As the role of public health agencies changes over time, epidemiologists will need to adapt and develop new skill sets to work in emerging areas of (public health) practice (EAoPs), which are areas of practice that are new or are growing in interest and use. OBJECTIVE: This mixed-methods research study sought to explore the role and readiness of state health department epidemiologists in the United States to work in EAoPs. DESIGN: Three phases of data collection and analysis were conducted including secondary analysis of the Public Health Workforce Interests and Needs Survey, a survey of the designated state epidemiologist in all 50 states and the District of Columbia, and focus groups with early-, mid-, and senior-career epidemiologists working in state health departments. SETTING: Fifty state health departments and the District of Columbia. PARTICIPANTS: Epidemiologists working in state health departments. MAIN OUTCOME MEASURES: Identification of EAoPs relevant to epidemiologists, the role of epidemiologists in these EAoPs, and readiness of epidemiologists to work in EAoPs. RESULTS: Participant state health department epidemiologists indicated that the studied EAoPs were important to their work and that epidemiologists have some role in them. Key facilitators identified to working in EAoPs included supportive organizational strategy and leadership, dedicated time for training and work, cross-training across programs, and the development of crosscutting skills. CONCLUSIONS: There is much opportunity for epidemiologists to be more engaged in current EAoPs. Not only can epidemiologists supply relevant data but they can also bring skills and expertise to help improve the overall success of population health improvement work. Workforce development strategies should be implemented to ensure a nimble epidemiology workforce that can readily adapt to the needs of future public health practice.

Use of Job Classifications, Career Ladders, and the Applied Epidemiology Competencies to Support Recruitment, Retention, and Practice of State Health Department Epidemiologists.

CONTEXT: State health departments report that recruitment and retention of qualified epidemiologists is a significant challenge to ensuring epidemiology capacity to support essential public health services. OBJECTIVE: To collect information on the use of epidemiology job classifications, career ladders, and professional competencies in state health departments to inform workforce development activities that improve epidemiology capacity. DESIGN: Electronic survey of the designated state epidemiologist. SETTING: Fifty state health departments and the District of Columbia. PARTICIPANTS: State epidemiologists working in state health departments. MAIN OUTCOME MEASURES: Use and perceived benefit of epidemiology job classifications, career ladders, and professional competencies. RESULTS: All 50 states and the District of Columbia responded to the survey. Most state health departments reported having epidemiology-specific job classifications (n = 44, 90%) and career ladders (n = 36, 71%) in place. State epidemiologists strongly agreed or agreed that having an epidemiology-specific classification positively contributed to recruitment (n = 37, 84%) and retention (n = 29, 66%) of epidemiologists in their agency. State epidemiologists strongly agreed or agreed that having an epidemiology-specific career ladder positively contributed to recruitment (n = 24, 69%) and retention (n = 23, 66%) of epidemiologists in their agency. Only 10 (29%) state epidemiologists reported using the applied epidemiology competencies to develop or revise their jurisdiction's epidemiology career ladder. CONCLUSIONS: State health departments should implement well-maintained epidemiology-specific job classifications and career ladders that are based on current epidemiology competencies. Career ladders should be supported with opportunities for competency-based training to support career progression.

Training Needs and Awareness of Emerging Areas of Public Health Practice Among Epidemiologists Working in State Health Agency Central Offices in the United States, 2017.

CONTEXT: Epidemiologists working in state health agency central offices (SHA-CO) are key professionals working to monitor population health indicators. Assessing training needs to identify gaps is critical to ensuring a competent public health workforce. OBJECTIVE: The objective of this research was to identify training needs of SHA-CO epidemiologists and their awareness of emerging areas of public health practice (EAoP) using data from the 2017 Public Health Workforce Interests and Needs Survey (PH WINS). DESIGN: SHA-CO epidemiologists were surveyed in fall 2017 using a Web-based tool. Balanced repeated replication weights were used to account for complex sample design. Differences in responses by tenure, education level, and supervisory status were assessed using multinomial logistic regression. SETTING: Forty-seven state health agencies. PARTICIPANTS: Permanently employed SHA-CO epidemiologists. MAIN OUTCOME MEASURES: Training needs were identified by classifying skill gaps as those skills that participants self-reported as high relevance to day-to-day work but self-rated as having low proficiency. Awareness of EAoP was self-reported. RESULTS: Systems and strategic thinking and budget and financial management were the areas with the greatest training needs. For most skill domains, fewer participants reported skill gaps with increasing years of public health work experience. Participants with 16 or more years of work experience were less likely to be motivated by most training motivators listed by epidemiologists with 5 or fewer years of experience. The EAoP participants reported greatest awareness of evidence-based public health practice (67%), and the EAoP they reported hearing least about was Health in All Policies (14%). CONCLUSIONS: Stratified analyses by tenure identified important differences in training needs and motivators that employers can use to customize workforce development strategies. SHA-CO epidemiologists reported varying amounts of awareness of EAoP. Specialized training approaches may contribute to improved employee engagement and reduce skill gaps among SHA-CO epidemiologists.

Large Outbreak of Hepatitis C Virus Associated With Drug Diversion by a Healthcare Technician.

Background: In May 2012, the New Hampshire (NH) Division of Public Health Services (DPHS) was notified of 4 persons with newly diagnosed hepatitis C virus (HCV) infection at hospital X. Initial investigation suggested a common link to the hospital cardiac catheterization laboratory (CCL) because the infected persons included 3 CCL patients and a CCL technician. NH DPHS initiated an investigation to determine the source and control the outbreak. Methods: NH DPHS conducted site visits, case patient and employee interviews, medical record and medication use review, and employee and patient HCV testing using enzyme immunoassay for anti-HCV, reverse-transcription polymerase chain reaction for HCV RNA, nonstructural 5B (NS5B) and hypervariable region 1 (HVR1) sequencing, and quasispecies analysis. Results: HCV HVR1 analysis of the first 4 cases confirmed a common source of infection. HCV testing identified 32 of 1074 CCL patients infected with the outbreak strain, including 3 patients coinfected with >1 HCV strain. The epidemiologic investigation revealed evidence of drug diversion by the HCV-infected technician, evidenced by gaps in controlled medication control, higher fentanyl use during procedures for confirmed cases, and building card key access records documenting the presence of the technician during days when transmission occurred. The employee's status as a traveling technician led to a multistate investigation, which identified additional cases at prior employment sites. Conclusions: This is the largest laboratory-confirmed drug diversion-associated HCV outbreak published to date. Recommendations to reduce drug diversion risk and to conduct outbreak investigations are provided.

Phenological and distributional shifts in ichthyoplankton associated with recent warming in the northeast Pacific Ocean.

Understanding changes in the migratory and reproductive phenology of fish stocks in relation to climate change is critical for accurate ecosystem-based fisheries management. Relocation and changes in timing of reproduction can have dramatic effects upon the success of fish populations and throughout the food web. During anomalously warm conditions (1-4°C above normal) in the northeast Pacific Ocean during 2015-2016, we documented shifts in timing and spawning location of several pelagic fish stocks based on larval fish samples. Total larval concentrations in the northern California Current (NCC) during winter (January-March) 2015 and 2016 were the highest observed since annual collections first occurred in 1998, primarily due to increased abundances of Engraulis mordax (northern anchovy) and Sardinops sagax (Pacific sardine) larvae, which are normally summer spawning species in this region. Sardinops sagax and Merluccius productus (Pacific hake) exhibited an unprecedented early and northward spawning expansion during 2015-16. In addition, spawning duration was greatly increased for E. mordax, as the presence of larvae was observed throughout the majority of 2015-16, indicating prolonged and nearly continuous spawning of adults throughout the warm period. Larvae from all three of these species have never before been collected in the NCC as early in the year. In addition, other southern species were collected in the NCC during this period. This suggests that the spawning phenology and distribution of several ecologically and commercially important fish species dramatically and rapidly changed in response to the warming conditions occurring in 2014-2016, and could be an indication of future conditions under projected climate change. Changes in spawning timing and poleward migration of fish populations due to warmer ocean conditions or global climate change will negatively impact areas that were historically dependent on these fish, and change the food web structure of the areas that the fish move into with unforeseen consequences.

Assessment of Epidemiology Capacity in State Health Departments - United States, 2017.

In 2017, the Council of State and Territorial Epidemiologists performed its sixth periodic Epidemiology Capacity Assessment, a national assessment that evaluates trends in workforce size, funding, and epidemiology capacity among state health departments. A standardized web-based questionnaire was sent to the state epidemiologist in the 50 states, the District of Columbia (DC), and the U.S. territories and the Federated States of Micronesia inquiring about the number of current and optimal epidemiologist positions; sources of epidemiology activity and personnel funding; and each department's self-perceived capacity to lead activities, provide subject matter expertise, and obtain and manage resources for the four Essential Public Health Services (EPHS)* most closely linked to epidemiology. From 2013 to 2017, the number of state health department epidemiologists† increased 22%, from 2,752 to 3,369, the greatest number of workers since the first full Epidemiology Capacity Assessment enumeration in 2004. The federal government provided most (77%) of the funding for epidemiologic activities and personnel. Substantial to full capacity (50%-100%) was highest for investigating health problems (92% of health departments) and monitoring health status (84%), whereas capacity for evaluating effectiveness (39%) and applied research (29%) was considerably lower. An estimated additional 1,200 epidemiologists are needed to reach full capacity to conduct the four EPHS. Additional resources might be needed to ensure that state health department epidemiologists possess the specialized skills to deliver EPHS, particularly in evaluation and applied epidemiologic research.

Workplace Safety Concerns among Co-workers of Responder Returning from Ebola-Affected Country.

We surveyed public health co-workers regarding attitudes toward a physician who returned to New Hampshire after volunteering in the West African Ebola outbreak. An unexpectedly large (18.0%) proportion of staff expressed discomfort with the Ebola responder returning to work. Employers should take proactive steps to address employee fears and concerns.

Human outbreak of Salmonella Typhimurium associated with exposure to locally made chicken jerky pet treats, New Hampshire, 2013.

Pet treats and pet food can be contaminated with Salmonella and other pathogens, though they are infrequently implicated as the source of human outbreaks. In 2013, the New Hampshire Department of Health and Human Services investigated a cluster of Salmonella Typhimurium infections associated with contaminated locally made pet treats. Case-patients were interviewed with standardized questionnaires to assess food, animal, and social histories. Laboratory and environmental investigations were conducted, including testing of clinical specimens, implicated product, and environmental swabs. Between June and October 2013, a total of 43 ill persons were identified. Sixteen patients (37%) were hospitalized. Among 43 case-patients interviewed, the proportion exposed to dogs (95%) and pet treats (69%) in the 7 days prior to illness was statistically higher than among participants in a U.S. population-based telephone survey (61%, p<0.0001 and 16%, p<0.0001, respectively). On further interview, 38 (88%) reported exposure to Brand X Chicken Jerky, the maker of Brand X chicken jerky, or the facility in which it was made. Product testing isolated the outbreak strain from four of four Brand X Chicken Jerky samples, including an unopened package purchased at retail, opened packages collected from patient households, and unpackaged jerky obtained from the jerky maker. A site visit revealed inadequate processing of the chicken jerky, bare-hand contact with the finished product prior to packaging, and use of vacuum-sealed packaging, which may have enabled facultative anaerobic bacteria to proliferate. Seven (78%) of nine environmental swabs taken during the site visit also yielded the outbreak strain. Brand X Chicken Jerky was voluntarily recalled on September 9, 2013. Consumers should be made aware of the potential for locally made products to be exempt from regulation and for animals and animal food to carry pathogens that cause human illness, and be educated to perform hand hygiene after handling pet food or treats.

Salmonella typhimurium infections associated with peanut products.

BACKGROUND: Contaminated food ingredients can affect multiple products, each distributed through various channels and consumed in multiple settings. Beginning in November 2008, we investigated a nationwide outbreak of salmonella infections. METHODS: A case was defined as laboratory-confirmed infection with the outbreak strain of Salmonella Typhimurium occurring between September 1, 2008, and April 20, 2009. We conducted two case-control studies, product "trace-back," and environmental investigations. RESULTS: Among 714 case patients identified in 46 states, 166 (23%) were hospitalized and 9 (1%) died. In study 1, illness was associated with eating any peanut butter (matched odds ratio, 2.5; 95% confidence interval [CI], 1.3 to 5.3), peanut butter-containing products (matched odds ratio, 2.2; 95% CI, 1.1 to 4.7), and frozen chicken products (matched odds ratio, 4.6; 95% CI, 1.7 to 14.7). Investigations of focal clusters and single cases associated with nine institutions identified a single institutional brand of peanut butter (here called brand X) distributed to all facilities. In study 2, illness was associated with eating peanut butter outside the home (matched odds ratio, 3.9; 95% CI, 1.6 to 10.0) and two brands of peanut butter crackers (brand A: matched odds ratio, 17.2; 95% CI, 6.9 to 51.5; brand B: matched odds ratio, 3.6; 95% CI, 1.3 to 9.8). Both cracker brands were made from brand X peanut paste. The outbreak strain was isolated from brand X peanut butter, brand A crackers, and 15 other products. A total of 3918 peanut butter-containing products were recalled between January 10 and April 29, 2009. CONCLUSIONS: Contaminated peanut butter and peanut products caused a nationwide salmonellosis outbreak. Ingredient-driven outbreaks are challenging to detect and may lead to widespread contamination of numerous food products.

Evaluation of a multitarget real-time PCR assay for detection of Bordetella species during a pertussis outbreak in New Hampshire in 2011.

A multitarget real-time PCR assay with three targets, including insertion sequence 481 (IS481), IS1001, and an IS1001-like element, as well as pertussis toxin subunit S1 (ptxS1), for the detection of Bordetella species was evaluated during a pertussis outbreak. The sensitivity and specificity were 77 and 88% (PCR) and 66 and 100% (culture), respectively. All patients with an IS481 C(T) of <30 also tested positive by ptxS1 assay and were clinical pertussis cases. No patients with IS481 C(T) values of ≥40 tested positive by culture. Therefore, we recommend that culture be performed only for specimens with IS481 C(T) values of 30 ≤ CT <40.

Notes from the field: update on Lyme carditis, groups at high risk, and frequency of associated sudden cardiac death--United States.

On December 13, 2013, MMWR published a report describing three cases of sudden cardiac death associated with Lyme carditis. State public health departments and CDC conducted a follow-up investigation to determine 1) whether carditis was disproportionately common among certain demographic groups of patients diagnosed with Lyme disease, 2) the frequency of death among patients diagnosed with Lyme disease and Lyme carditis, and 3) whether any additional deaths potentially attributable to Lyme carditis could be identified. Lyme disease cases are reported to CDC through the Nationally Notifiable Disease Surveillance System; reporting of clinical features, including Lyme carditis, is optional. For surveillance purposes, Lyme carditis is defined as acute second-degree or third-degree atrioventricular conduction block accompanying a diagnosis of Lyme disease. During 2001-2010, a total of 256,373 Lyme disease case reports were submitted to CDC, of which 174,385 (68%) included clinical information. Among these, 1,876 (1.1%) were identified as cases of Lyme carditis. Median age of patients with Lyme carditis was 43 years (range = 1-99 years); 1,209 (65%) of the patients were male, which is disproportionately larger than the male proportion among patients with other clinical manifestations (p<0.001). Of cases with this information available, 69% were diagnosed during the months of June-August, and 42% patients had an accompanying erythema migrans, a characteristic rash. Relative to patients aged 55-59 years, carditis was more common among men aged 20-39 years, women aged 25-29 years, and persons aged ≥75 years.

Rebound activation of 5-HT neurons following SSRI discontinuation.

Cessation of therapy with a selective serotonin (5-HT) reuptake inhibitor (SSRI) is often associated with an early onset and disabling discontinuation syndrome, the mechanism of which is surprisingly little investigated. Here we determined the effect on 5-HT neurochemistry of discontinuation from the SSRI paroxetine. Paroxetine was administered repeatedly to mice (once daily, 12 days versus saline controls) and then either continued or discontinued for up to 5 days. Whereas brain tissue levels of 5-HT and/or its metabolite 5-HIAA tended to decrease during continuous paroxetine, levels increased above controls after discontinuation, notably in hippocampus. In microdialysis experiments continuous paroxetine elevated hippocampal extracellular 5-HT and this effect fell to saline control levels on discontinuation. However, depolarisation (high potassium)-evoked 5-HT release was reduced by continuous paroxetine but increased above controls post-discontinuation. Extracellular hippocampal 5-HIAA also decreased during continuous paroxetine and increased above controls post-discontinuation. Next, immunohistochemistry experiments found that paroxetine discontinuation increased c-Fos expression in midbrain 5-HT (TPH2 positive) neurons, adding further evidence for a hyperexcitable 5-HT system. The latter effect was recapitulated by 5-HT1A receptor antagonist administration although gene expression analysis could not confirm altered expression of 5-HT1A autoreceptors following paroxetine discontinuation. Finally, in behavioural experiments paroxetine discontinuation increased anxiety-like behaviour, which partially correlated in time with the measures of increased 5-HT function. In summary, this study reports evidence that, across a range of experiments, SSRI discontinuation triggers a rebound activation of 5-HT neurons. This effect is reminiscent of neural changes associated with various psychotropic drug withdrawal states, suggesting a common unifying mechanism.

The Pelagic Species Trait Database, an open data resource to support trait-based ocean research.

Trait-based frameworks are increasingly used for predicting how ecological communities respond to ongoing global change. As species range shifts result in novel encounters between predators and prey, identifying prey 'guilds', based on a suite of shared traits, can distill complex species interactions, and aid in predicting food web dynamics. To support advances in trait-based research in open-ocean systems, we present the Pelagic Species Trait Database, an extensive resource documenting functional traits of 529 pelagic fish and invertebrate species in a single, open-source repository. We synthesized literature sources and online resources, conducted morphometric analysis of species images, as well as laboratory analyses of trawl-captured specimens to collate traits describing 1) habitat use and behavior, 2) morphology, 3) nutritional quality, and 4) population status information. Species in the dataset primarily inhabit the California Current system and broader NE Pacific Ocean, but also includes pelagic species known to be consumed by top ocean predators from other ocean basins. The aim of this dataset is to enhance the use of trait-based approaches in marine ecosystems and for predator populations worldwide.

An updated end-to-end ecosystem model of the Northern California Current reflecting ecosystem changes due to recent marine heatwaves.

The Northern California Current is a highly productive marine upwelling ecosystem that is economically and ecologically important. It is home to both commercially harvested species and those that are federally listed under the U.S. Endangered Species Act. Recently, there has been a global shift from single-species fisheries management to ecosystem-based fisheries management, which acknowledges that more complex dynamics can reverberate through a food web. Here, we have integrated new research into an end-to-end ecosystem model (i.e., physics to fisheries) using data from long-term ocean surveys, phytoplankton satellite imagery paired with a vertically generalized production model, a recently assembled diet database, fishery catch information, species distribution models, and existing literature. This spatially-explicit model includes 90 living and detrital functional groups ranging from phytoplankton, krill, and forage fish to salmon, seabirds, and marine mammals, and nine fisheries that occur off the coast of Washington, Oregon, and Northern California. This model was updated from previous regional models to account for more recent changes in the Northern California Current (e.g., increases in market squid and some gelatinous zooplankton such as pyrosomes and salps), to expand the previous domain to increase the spatial resolution, to include data from previously unincorporated surveys, and to add improved characterization of endangered species, such as Chinook salmon (Oncorhynchus tshawytscha) and southern resident killer whales (Orcinus orca). Our model is mass-balanced, ecologically plausible, without extinctions, and stable over 150-year simulations. Ammonium and nitrate availability, total primary production rates, and model-derived phytoplankton time series are within realistic ranges. As we move towards holistic ecosystem-based fisheries management, we must continue to openly and collaboratively integrate our disparate datasets and collective knowledge to solve the intricate problems we face. As a tool for future research, we provide the data and code to use our ecosystem model.

Improved fixation quality provided by a Bessel beacon in an adaptive optics system.

PURPOSE: We investigate whether a structured probe beam that creates the beacon for use in a retinal imaging adaptive optics system can provide useful side effects. In particular we investigate whether a Bessel beam that is seen by the subject as a set of concentric rings has a dampening effect on fixation variations of the subject under observation. This calming effect would allow longer periods of observation, particularly for patients with abnormal fixation. METHOD: An experimental adaptive optics system developed for retinal imaging is used to monitor the fluctuations in aberrations for artificial and human subjects. The probe beam is alternated between a traditional beacon and one provided by a Bessel beam created by SLM. RESULTS: Time-frequency analysis is used to indicate the differences in power and time variation during fixation depending on whether the Bessel beam or the traditional beacon is employed. Comparison is made with the response for an artificial eye to discount systemic variations. CONCLUSION: Significant evidence is accrued to indicate the reduced fluctuations in fixation when the Bessel beam is employed to create the beacon.

Leveraging explanations in interactive machine learning: An overview.

Explanations have gained an increasing level of interest in the AI and Machine Learning (ML) communities in order to improve model transparency and allow users to form a mental model of a trained ML model. However, explanations can go beyond this one way communication as a mechanism to elicit user control, because once users understand, they can then provide feedback. The goal of this paper is to present an overview of research where explanations are combined with interactive capabilities as a mean to learn new models from scratch and to edit and debug existing ones. To this end, we draw a conceptual map of the state-of-the-art, grouping relevant approaches based on their intended purpose and on how they structure the interaction, highlighting similarities and differences between them. We also discuss open research issues and outline possible directions forward, with the hope of spurring further research on this blooming research topic.

Laboratory Criteria for Exclusion and Readmission of Potentially Infectious Persons in Sensitive Settings in the Age of Culture-Independent Diagnostic Tests: Report of a Multidisciplinary Workgroup.

Culture-independent diagnostic tests (CIDTs) are increasingly used for clinical diagnosis of gastrointestinal diseases such as salmonellosis, Shiga toxin-producing E. coli disease, and shigellosis because of their speed, convenience, and generally high-performance characteristics. These tests are also used to screen potentially infectious asymptomatic persons during outbreak investigations in sensitive settings such as childcare, food service, and healthcare. However, only limited performance data are available for CIDTs used on specimens from asymptomatic persons. The Association of Public Health Laboratories (APHL) and Council of State and Territorial Epidemiologists (CSTE) convened a workgroup to examine the available scientific data to inform interim decision-making related to exclusion and readmission criteria for potentially infectious persons in sensitive settings, the risks and benefits of different testing strategies, and to identify knowledge gaps for further research. This is the report on the Workgroup findings.

Ensuring Equitable COVID-19 Vaccine Allocation in New Hampshire: The First Eight Months toward a New Era.

The global coronavirus disease 2019 (COVID-19) pandemic has been exacerbated by social vulnerabilities and racial disparities, resulting in disproportionate morbidity and mortality that require continued attention to strategies that ensure equitable vaccine allocation. The State of New Hampshire (NH) developed a transparent framework to guide COVID-19 vaccine allocation plans, of which one key component was the allocation of 10% of vaccine supply to disproportionately impacted and highly vulnerable populations, predominantly identified through a national vulnerability index. The process, operational approaches, ethical challenges, and unanticipated consequences resulted in many valuable lessons learned. Equitable allocation of this limited and critical pandemic countermeasure required public understanding and engagement, which was achieved through a publicly available framework that was flexible, resourced using public funds, and widely communicated. Broad partnerships were also critical to addressing disparities in the delivery of vaccine. The lessons learned and described here will facilitate more nimble and equitable jurisdictional responses in future public health emergencies.

The bacteriology of pleural infection (TORPIDS): an exploratory metagenomics analysis through next generation sequencing.

BACKGROUND: Pleural infection is a common and severe disease with high morbidity and mortality worldwide. The knowledge of pleural infection bacteriology remains incomplete, as pathogen detection methods based on culture have insufficient sensitivity and are biased to selected microbes. We designed a study with the aim to discover and investigate the total microbiome of pleural infection and assess the correlation between bacterial patterns and 1-year survival of patients. METHODS: We assessed 243 pleural fluid samples from the PILOT study, a prospective observational study on pleural infection, with 16S rRNA next generation sequencing. 20 pleural fluid samples from patients with pleural effusion due to a non-infectious cause and ten PCR-grade water samples were used as controls. Downstream analysis was done with the DADA2 pipeline. We applied multivariate Cox regression analyses to investigate the association between bacterial patterns and 1-year survival of patients with pleural infection. FINDINGS: Pleural infection was predominately polymicrobial (192 [79%] of 243 samples), with diverse bacterial frequencies observed in monomicrobial and polymicrobial disease and in both community-acquired and hospital-acquired infection. Mixed anaerobes and other Gram-negative bacteria predominated in community-acquired polymicrobial infection whereas Streptococcus pneumoniae prevailed in monomicrobial cases. The presence of anaerobes (hazard ratio 0·46, 95% CI 0·24-0·86, p=0·015) or bacteria of the Streptococcus anginosus group (0·43, 0·19-0·97, p=0·043) was associated with better patient survival, whereas the presence (5·80, 2·37-14·21, p<0·0001) or dominance (3·97, 1·20-13·08, p=0·024) of Staphylococcus aureus was linked with lower survival. Moreover, dominance of Enterobacteriaceae was associated with higher risk of death (2·26, 1·03-4·93, p=0·041). INTERPRETATION: Pleural infection is a predominantly polymicrobial infection, explaining the requirement for broad spectrum antibiotic cover in most individuals. High mortality infection associated with S aureus and Enterobacteriaceae favours more aggressive, with a narrower spectrum, antibiotic strategies. FUNDING: UK Medical Research Council, National Institute for Health Research Oxford Biomedical Research Centre, Wellcome Trust, Oxfordshire Health Services Research Committee, Chinese Academy of Medical Sciences, and John Fell Fund.

Beyond immunity: quantifying the effects of host anti-parasite behavior on parasite transmission.

A host's first line of defense in response to the threat of parasitic infection is behavior, yet the efficacy of anti-parasite behaviors in reducing infection are rarely quantified relative to immunological defense mechanisms. Larval amphibians developing in aquatic habitats are at risk of infection from a diverse assemblage of pathogens, some of which cause substantial morbidity and mortality, suggesting that behavioral avoidance and resistance could be significant defensive strategies. To quantify the importance of anti-parasite behaviors in reducing infection, we exposed larval Pacific chorus frogs (Pseudacris regilla) to pathogenic trematodes (Ribeiroia and Echinostoma) in one of two experimental conditions: behaviorally active (unmanipulated) or behaviorally impaired (anesthetized). By quantifying both the number of successful and unsuccessful parasites, we show that host behavior reduces infection prevalence and intensity for both parasites. Anesthetized hosts were 20-39% more likely to become infected and, when infected, supported 2.8-fold more parasitic cysts. Echinostoma had a 60% lower infection success relative to the more deadly Ribeiroia and was also more vulnerable to behaviorally mediated reductions in transmission. For Ribeiroia, increases in host mass enhanced infection success, consistent with epidemiological theory, but this relationship was eroded among active hosts. Our results underscore the importance of host behavior in mitigating disease risk and suggest that, in some systems, anti-parasite behaviors can be as or more effective than immune-mediated defenses in reducing infection. Considering the severe pathologies induced by these and other pathogens of amphibians, we emphasize the value of a broader understanding of anti-parasite behaviors and how co-occurring stressors affect them.