Genetic drift and purifying selection shape within-host influenza A virus populations during natural swine infections

Patterns of within-host influenza A virus (IAV) diversity and evolution have been described in natural human infections, but these patterns remain poorly characterized in non-human hosts. Elucidating these dynamics is important to better understand IAV biology and the evolutionary processes that govern spillover into humans. Here, we sampled an IAV outbreak in pigs during a week-long county fair to characterize viral diversity and evolution in this important reservoir host. Nasal wipes were collected on a daily basis from all pigs present at the fair, yielding up to 421 samples per day. Subtyping of PCR-positive samples revealed the co-circulation of H1N1 and H3N2 subtype swine IAVs. PCR-positive samples with robust Ct values were deep-sequenced, yielding 506 sequenced samples from a total of 253 pigs. Based on higher-depth re-sequenced data from a subset of these initially sequenced samples (260 samples from 168 pigs), we characterized patterns of within-host IAV genetic diversity and evolution. We find that IAV genetic diversity in single-subtype infected pigs is low, with the majority of intrahost Single Nucleotide Variants (iSNVs) present at frequencies of <10%. The ratio of the number of nonsynonymous to the number of synonymous iSNVs is significantly lower than under the neutral expectation, indicating that purifying selection shapes patterns of within-host viral diversity in swine. The dynamic turnover of iSNVs and their pronounced frequency changes further indicate that genetic drift also plays an important role in shaping IAV populations within pigs. Taken together, our results highlight similarities in patterns of IAV genetic diversity and evolution between humans and swine, including the role of stochastic processes in shaping within-host IAV dynamics.

Standardizing clinical culture specimen collection in Ethiopia: a training-of-trainers

BACKGROUND

Proper specimen collection is central to improving patient care by ensuring optimal yield of diagnostic tests, guiding appropriate management, and targeting treatment. The purpose of this article is to describe the development and implementation of a training-of-trainers educational program designed to improve clinical culture specimen collection among healthcare personnel (HCP) in Ethiopia.

METHODS

A Clinical Specimen Collection training package was created consisting of a Trainer's Manual, Reference Manual, Assessment Tools, Step-by-Step Instruction Guides (i.e., job aides), and Core Module PowerPoint Slides.

RESULTS

A two-day course was used in training 16 master trainers and 47 facility-based trainers responsible for cascading trainings on clinical specimen collection to HCP at the pre-service, in-service, or national-levels. The Clinical Specimen Collection Package is offered online via The Ohio State University's CANVAS online platform.

CONCLUSIONS

The training-of-trainers approach may be an effective model for development of enhanced specimen collection practices in low-resource countries.

Spatio-temporal impacts of aerial adulticide applications on populations of West Nile virus vector mosquitoes

BACKGROUND

Aerial applications of insecticides that target adult mosquitoes are widely used to reduce transmission of West Nile virus to humans during periods of epidemic risk. However, estimates of the reduction in abundance following these treatments typically focus on single events, rely on pre-defined, untreated control sites and can vary widely due to stochastic variation in population dynamics and trapping success unrelated to the treatment.

METHODS

To overcome these limitations, we developed generalized additive models fitted to mosquito surveillance data collected from CO2-baited traps in Sacramento and Yolo counties, California from 2006 to 2017. The models accounted for the expected spatial and temporal trends in the abundance of adult female Culex (Cx.) tarsalis and Cx. pipiens in the absence of aerial spraying. Estimates for the magnitude of deviation from baseline abundance following aerial spray events were obtained from the models.

RESULTS

At 1-week post-treatment with full spatial coverage of the trapping area by pyrethroid or pyrethrin products, Cx. pipiens abundance was reduced by a mean of 52.4% (95% confidence intrval [CI] - 65.6, - 36.5%) while the use of at least one organophosphate pesticide resulted in a mean reduction of 76.2% (95% CI - 82.8, - 67.9%). For Cx. tarsalis, at 1-week post-treatment with full coverage there was a reduction in abundance of 30.7% (95% CI - 54.5, 2.5%). Pesticide class was not a significant factor contributing to the reduction. In comparison, repetition of spraying over three to four consecutive weeks resulted in similar estimates for Cx. pipiens and estimates of somewhat smaller magnitude for Cx. tarsalis.

CONCLUSIONS

Aerial adulticides are effective for achieving a rapid short-term reduction of the abundance of the primary West Nile virus vectors, Cx. tarsalis and Cx. pipiens. A larger magnitude of reduction was estimated in Cx. pipiens, possibly due to the species' focal distribution. Effects of aerial sprays on Cx. tarsalis populations are likely modulated by the species' large dispersal ability, population sizes and vast productive larval habitat present in the study area. Our modeling approach provides a new way to estimate effects of public health pesticides on vector populations using routinely collected observational data and accounting for spatio-temporal trends and contextual factors like weather and habitat. This approach does not require pre-selected control sites and expands upon past studies that have focused on the effects of individual aerial treatment events.

Simulation-free estimation of an individual-based SEIR model for evaluating nonpharmaceutical interventions with an application to COVID-19 in the District of Columbia

The ongoing COVID-19 pandemic has overwhelmingly demonstrated the need to accurately evaluate the effects of implementing new or altering existing nonpharmaceutical interventions. Since these interventions applied at the societal level cannot be evaluated through traditional experimental means, public health officials and other decision makers must rely on statistical and mathematical epidemiological models. Nonpharmaceutical interventions are typically focused on contacts between members of a population, and yet most epidemiological models rely on homogeneous mixing which has repeatedly been shown to be an unrealistic representation of contact patterns. An alternative approach is individual based models (IBMs), but these are often time intensive and computationally expensive to implement, requiring a high degree of expertise and computational resources. More often, decision makers need to know the effects of potential public policy decisions in a very short time window using limited resources. This paper presents a computation algorithm for an IBM designed to evaluate nonpharmaceutical interventions. By utilizing recursive relationships, our method can quickly compute the expected epidemiological outcomes even for large populations based on any arbitrary contact network. We utilize our methods to evaluate the effects of various mitigation measures in the District of Columbia, USA, at various times and to various degrees. Rcode for our method is provided in the supplementry material, thereby allowing others to utilize our approach for other regions.

Performance of nucleocapsid and spike-based SARS-CoV-2 serologic assays

There is an urgent need for an accurate antibody test for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We have developed 3 ELISA methods, trimer spike IgA, trimer spike IgG, and nucleocapsid IgG, for detecting anti-SARS-CoV-2 antibodies. We evaluated their performance along with four commercial ELISAs, EDI™ Novel Coronavirus COVID-19 ELISA IgG and IgM, Euroimmun Anti-SARS-CoV-2 ELISA IgG and IgA, and one lateral flow assay, DPP® COVID-19 IgM/IgG System (Chembio). Both sensitivity and specificity were evaluated and the probable causes of false-positive reactions were determined. The assays were evaluated using 300 pre-epidemic samples and 100 PCR-confirmed COVID-19 samples. The sensitivities and specificities of the assays were as follows: 90%/100% (in-house trimer spike IgA), 90%/99.3% (in-house trimer spike IgG), 89%/98.3% (in-house nucleocapsid IgG), 73.7%/100% (EDI nucleocapsid IgM), 84.5%/95.1% (EDI nucleocapsid IgG), 95%/93.7% (Euroimmun S1 IgA), 82.8%/99.7% (Euroimmun S1 IgG), 82.0%/91.7% (Chembio nucleocapsid IgM), 92%/93.3% (Chembio nucleocapsid IgG). The presumed causes of false positive results from pre-epidemic samples in commercial and in-house assays were mixed. In some cases, assays lacked reproducibility. In other cases, reactivity was abrogated by competitive inhibition (spiking the sample with the same antigen that was used for coating ELISAs prior to performing the assay), suggesting positive reaction could be attributed to the presence of antibodies against these antigens. In other cases, reactivity was consistently detected but not abrogated by the spiking, suggesting positive reaction was not attributed to the presence of antibodies against these antigens. Overall, there was wide variability in assay performance using our samples, with in-house tests exhibiting the highest combined sensitivity and specificity. The causes of "false positivity" in pre-epidemic samples may be due to plasma antibodies apparently reacting with the corresponding antigen, or spurious reactivity may be directed against non-specific components in the assay system. Identification of these targets will be essential to improving assay performance.

Endotoxin clustering with allergens in house dust and asthma outcomes in a U.S. national study

BACKGROUND

Endotoxin is ubiquitous in the environment, but its clustering with indoor allergens is not well characterized. This study examined the clustering patterns of endotoxin with allergens in house dust and their association with asthma outcomes.

METHODS

We analyzed data from 6963 participants of the 2005-2006 National Health and Nutrition Examination Survey. House dust sampled from bedroom floor and bedding was evaluated for endotoxin and allergens from fungi, cockroach, dog, cat, mites, and rodents. Two-step cluster analysis and logistic regressions were performed to identify the clustering patterns and their associations with current asthma and wheeze in the past 12 months, adjusting for covariates.

RESULTS

Of the homes, 17.8% had low endotoxin and allergen levels in house dust (Cluster 1). High endotoxin level clustered with Alternaria and pet allergens in the homes of participants with a high socioeconomic status who own pets (Cluster 2) (48.9%). High endotoxin clustered with Aspergillus, dust mites, cockroach, and rodent allergens in the homes of participants with low socioeconomic status (Cluster 3) (33.3%). Compared to Cluster 1, Cluster 2 was associated with higher asthma prevalence (OR 1.42, 95% CI: 1.06-1.91) and wheeze (OR 1.32, 95% CI: 1.07-1.63). Cluster 3 was positively associated with wheeze only in participants sensitized to inhalant allergens (OR 1.42, 95% CI: 1.06-1.91) or exposed to tobacco smoke (OR 1.72, 95% CI: 1.15-2.60).

CONCLUSIONS

The clustering of endotoxin with allergens in dust from homes with pets or of people with low socioeconomic status is associated with asthma and wheeze.

Rickettsia felis identified in two fatal cases of acute meningoencephalitis

BACKGROUND

Rickettsia felis has recently emerged worldwide as a cause of human illness. Typically causing mild, undifferentiated fever, it has been implicated in several cases of non-fatal neurological disease in Mexico and Sweden. Its distribution and pathogenicity in Southeast Asia is poorly understood.

METHODOLOGY/PRINCIPAL FINDINGS

We retroactively tested cerebrospinal fluid (CSF) or sera from 64 adult patients admitted to hospital in North Sulawesi, Indonesia with acute neurological disease. Rickettsia felis DNA was identified in the CSF of two fatal cases of meningoencephalitis using multi-locus sequence typing semi-nested PCR followed by Sanger sequencing. DNA from both cases had 100% sequence homologies to the R. felis reference strain URRWXCal2 for the 17-kDa and ompB genes, and 99.91% to gltA.

CONCLUSION/SIGNIFICANCE

The identification of R. felis in the CSF of two fatal cases of meningoencephalitis in Indonesia suggests the distribution and pathogenicity of this emerging vector-borne bacteria might be greater than generally recognized. Typically Rickettsia are susceptible to the tetracyclines and greater knowledge of R. felis endemicity in Indonesia should lead to better management of some acute neurological cases.

Onset Trajectories of Sexting and Other Sexual Behaviors Across High School: A Longitudinal Growth Mixture Modeling Approach

Sexting is receiving substantial scholarly attention and is now considered commonplace in adolescence. Little is known, however, about the normative contexts and the development of adolescent sexting behavior, including the initiation of sexting in relation to other sexual behaviors. In this study, we used growth mixture modeling to identify classes of onset trajectories for sexual behaviors across high school. Participants included 429 high school students (54% female) who completed annual assessments of sexual behavior over a three-year period. We identified four distinct classes: postponement (9%) with no behaviors other than hand-holding and kissing initiated by Grade 11, gradual onset (44%) with sexting and other sexual behaviors emerging incrementally across high school, continuous onset (32%) with sexting and other sexual behaviors within the first three years of high school, early onset (15%) with initiation of sexting and all other sexual behaviors prior to or by the end of Grade 9. Boys were more likely than girls to be members of the postponement versus gradual onset class, while Black students were more likely than White students to be members of the early versus gradual onset class. Sexting behavior appears to be common in adolescence and co-emerges with genital contact behavior across varying trajectories of sexual development. These findings provide the foundation for contextualizing sexting within normative sexual development. Further, this information can inform efforts to promote sexual health.

Influenza-associated pneumonia hospitalizations in Uganda, 2013-2016

BACKGROUND

Influenza is an important contributor to acute respiratory illness, including pneumonia, and results in substantial morbidity and mortality globally. Understanding the local burden of influenza-associated severe disease can inform decisions on allocation of resources toward influenza control programs. Currently, there is no national influenza vaccination program in Uganda.

METHODS

In this study, we used data on pneumonia hospitalizations that were collected and reported through the Health Management Information System (HMIS) of the Ministry of Health, Uganda, and the laboratory-confirmed influenza positivity data from severe acute respiratory illness (SARI) surveillance in three districts (Wakiso, Mbarara, and Tororo) to estimate the age-specific incidence of influenza-associated pneumonia hospitalizations from January 2013 through December 2016.

RESULTS

The overall estimated mean annual rate of pneumonia hospitalizations in the three districts was 371 (95% confidence interval [CI] 323-434) per 100,000 persons, and was highest among children aged <5 years (1,524 [95% CI 1,286-1,849]) compared to persons aged ≥5 years (123 [95% CI 105-144]) per 100,000 persons. The estimated mean annual rate of influenza-associated pneumonia hospitalization was 34 (95% CI 23-48) per 100,000 persons (116 [95% CI 78-165] and 16 [95% CI 6-28] per 100,000 persons among children aged <5 years and those ≥5 years, respectively). Among children aged <5 years, the rate of hospitalized influenza-associated pneumonia was highest among those who were <2 years old (178 [95% CI 109-265] per 100,000 persons). Over the period of analysis, the estimated mean annual number of hospitalized influenza-associated pneumonia cases in the three districts ranged between 672 and 1,436, of which over 70% represent children aged <5 years.

CONCLUSIONS

The burden of influenza-associated pneumonia hospitalizations was substantial in Uganda, and was highest among young children aged <5 years. Influenza vaccination may be considered, especially for very young children.

Human response to live plague vaccine EV, Almaty region, Kazakhstan, 2014-2015

Background

In Kazakhstan, a live plague vaccine EV 76 NIIEG has been used for plague prophylaxis since the mid-1930s. Vaccination is administered yearly among people living in plague-enzootic areas. Similar practices are used in other former Soviet Union countries. Yet, to this day, the effectiveness period of the vaccine is unknown. It is also not clear how different factors can affect the effectiveness of the vaccine over time.

Methods

We surveyed changes in antibody levels specific for F1 antigens of Yersinia pestis among vaccinated people 4, 8, and 12 months post- vaccination. Blood samples were taken from the participants of the study for producing sera, which was later analyzed using indirect hemagglutination reaction with antigenic erythrocyte assay (micromethod) for identifying antibodies to F1 Y.pestis.

Results

In first-time-receivers of the plague vaccine, antibody titer reached the highest level of antibody that represents a conditionally protective titer after 4 months, dropped drastically after 8 months, and dropped again after 12 months. Similar results were obtained among those who have been vaccinated previously. However, in that group, the percentage of people with a level of antibody that represents a conditionally protective titer remained statistically significant even after 8 and 12 months.

Conclusion

Based on the results of this study, we recommend initiating vaccination campaigns for the medical and veterinary staff, as well as the general population four months prior to the springtime epizootics of plague among wild rodents.

Invasive Streptococcus pneumoniae infection among hospitalized patients in Jingzhou city, China, 2010-2012

BACKGROUND

Streptococcus pneumoniae (Sp) is a leading cause of bacterial pneumonia, meningitis, and sepsis and a major source of morbidity and mortality worldwide. Invasive pneumococcal disease (IPD) is defined as isolation of Sp from a normally sterile site, including blood or cerebrospinal fluid. The aim of this study is to describe outcomes as well as clinical and epidemiological characteristics of hospitalized IPD case patients in central China.

METHODS

We conducted surveillance for IPD among children and adults from April 5, 2010 to September 30, 2012, in four major hospitals in Jingzhou City, Hubei Province. We collected demographic, clinical, and outcome data for all enrolled hospitalized patients with severe acute respiratory infection (SARI) or meningitis, and collected blood, urine, and cerebrospinal fluid (CSF) for laboratory testing for Sp infections. Collected data were entered into Epidata software and imported into SPSS for analysis.

RESULTS

We enrolled 22,375 patients, including 22,202 (99%) with SARI and 173 (1%) with meningitis. One hundred and eighteen (118, 3%) with either SARI or meningitis were Sp positive, 32 (0.8%) from blood/CSF culture, and 87 (5%) from urine antigen testing. Of those 118 patients, 57% were aged ≥65 years and nearly 100% received antibiotics during hospitalization. None were previously vaccinated with 7-valent pneumococcal conjugate vaccine (PCV 7), 23-valent pneumococcal polysaccharide vaccine, or seasonal influenza vaccine. The main serotypes identified were 14, 12, 3, 1, 19F, 4, 5, 9V, 15 and 18C, corresponding to serotype coverage rates of 42%, 63%, and 77% for PCV7, PCV10, and PCV13, respectively.

CONCLUSIONS

Further work is needed to expand access to pneumococcal vaccination in China, both among children and potentially among the elderly, and inappropriate use of antibiotics is a widespread and serious problem in China.

Smoke-Free Multi-unit Housing Policies Show Promise in Reducing Secondhand Smoke Exposure Among Racially and Ethnically Diverse, Low-Income Seniors

Secondhand smoke (SHS) exposure is a public health issue for residents of multi-unit housing (MUH) properties. We evaluated the impact of smoke-free policy implementation on reported SHS exposure among racially, ethnically diverse seniors living in low-income MUH properties. In Spring 2013 and Summer 2014, we surveyed residents (n = 960) at 15 MUH properties in Broward and Miami-Dade Counties, Florida. The percentage of residents reporting SHS exposure within their apartments from elsewhere in or around their building decreased from 31.1 %, before policy implementation, to 23.6 % at follow-up (p = 0.02). In multivariate analysis of non-smoking residents after policy implementation, residents who reported having one or more comorbidities were two times more likely to report SHS exposure (aOR 2.23, 95 % CI 1.12-4.40). Considering the vulnerability of low-income seniors to SHS exposure, our findings are relevant to residents, property owners/managers, and public health professionals making decisions about smoke-free policies for MUH properties in which seniors reside.

Reporting to parents on children's exposures to asthma triggers in low-income and public housing, an interview-based case study of ethics, environmental literacy, individual action, and public health benefits

BACKGROUND

Emerging evidence about the effects of endocrine disruptors on asthma symptoms suggests new opportunities to reduce asthma by changing personal environments. Right-to-know ethics supports returning personal results for these chemicals to participants, so they can make decisions to reduce exposures. Yet researchers and institutional review boards have been reluctant to approve results reports in low-income communities, which are disproportionately affected by asthma. Concerns include limited literacy, lack of resources to reduce exposures, co-occurring stressors, and lack of models for effective reporting. To better understand the ethical and public health implications of returning personal results in low-income communities, we investigated parents' experiences of learning their children's environmental chemical and biomonitoring results in the Green Housing Study of asthma.

METHODS

The Green Housing Study measured indoor chemical exposures, allergens, and children's asthma symptoms in "green"-renovated public housing and control sites in metro-Boston and Cincinnati in 2011-2013. We developed reports for parents of children in the study, including results for their child and community. We observed community meetings where results were reported, and metro-Boston residents participated in semi-structured interviews in 2015 about their report-back experience. Interviews were systematically coded and analyzed.

RESULTS

Report-back was positively received, contributed to greater understanding, built trust between researchers and participants, and facilitated action to improve health. Sampling visits and community meetings also contributed to creating a positive study experience for participants. Participants were able to make changes in their homes, such as altering product use and habits that may reduce asthma symptoms, though some faced roadblocks from family members. Participants also gained access to medical resources, though some felt that clinicians were not responsive. Participants wanted larger scale change from government or industry and wanted researchers to leverage study results to achieve change.

CONCLUSIONS

Report-back on environmental chemical exposures in low-income communities can enhance research benefits by engaging residents with personally relevant information that informs and motivates actions to reduce exposure to asthma triggers. Ethical practices in research should support deliberative report-back in vulnerable communities.

Trends of racial and ethnic disparities in virologic suppression among women in the HIV Outpatient Study, USA, 2010-2015

In the United States, women accounted for 19% of new HIV diagnoses in 2015 and were less likely to reach virologic suppression when compared to men. We assessed trends and disparities in virologic suppression among HIV-positive women to inform HIV treatment strategies. Data were from a prospective cohort of the HIV Outpatient Study and collected at nine United States HIV clinics. We included women aged ≥18 years, with ≥1 visit, who were prescribed antiretroviral therapy, and had ≥1 viral load test performed between 2010 and 2015. We defined virologic suppression as viral load <50 copies/mL and calculated adjusted prevalence ratios (aPR) with 95% confidence intervals (CI) for virologic suppression by race/ethnicity and year of measure. Generalized estimating equations were used for multivariable analyses to assess factors associated with virologic suppression. Among 809 women (median age = 44 years), 482 (60%) were black, 177 (22%) white, 150 (19%) Hispanic/Latina. Virologic suppression was less prevalent among black women (73%) compared with Hispanic/Latina women (83%) and white women (91%). In multivariable analyses, not achieving virologic suppression was more likely among black women (aPR = 2.13; CI = 1.50–3.02) or Hispanic/Latina women (aPR = 1.66; CI = 1.08–2.56) compared with white women, and among women who attended public clinics (aPR = 1.42; CI = 1.07–1.87) compared with those who attended a private clinic. Between 2010 and 2015, virologic suppression among HIV-positive women increased from 68% to 83%, but racial/ethnic disparities persisted. Black and Hispanic/Latina women had significantly lower rates of virologic suppression than white women. Interventions targeting virologic suppression improvement among HIV-positive women of color, especially those who attend public clinics, are warranted.

Epidemiologic comparisons of soccer-related injuries presenting to emergency departments and reported within high school and collegiate settings

BACKGROUND

Few studies compare sports injury patterns in different settings. This study described the epidemiology of soccer injuries presenting to emergency departments (EDs) and compared injuries presenting to EDs to injuries presenting to collegiate and high school athletic trainers (ATs).

METHODS

Soccer-related injuries (product code 1267) in the National Electronic Injury Surveillance System (NEISS) that were sustained by individuals at least two years of age in 2004-2013 were included. High School Reporting Information Online (HS RIO) data for high school soccer injuries during the 2005/06-2013/14 academic years were compared to NEISS data for those aged 14-17 years in 2005-2013. National Collegiate Athletic Association Injury Surveillance Program (NCAA-ISP) data for collegiate soccer injuries during the 2009/10-2013/14 academic years were compared to NEISS data for those aged 18-22 years in 2009-2013. All datasets included weights to calculate national estimates. Injury proportion ratios (IPRs) with 95% confidence intervals (CIs) compared nationally estimated injury distributions between the HS RIO/NCAA-ISP and NEISS data subsets.

RESULTS

During the study period, 63,258 soccer-related injuries were captured by NEISS, which translates to an estimated 2,039,250 injuries seen at US EDs nationwide. Commonly injured body parts included the head/face (19.1%), ankle (17.6%), hand/wrist (15.3%), and knee (12.2%). Common diagnoses included sprains/strains (34.0%), fractures (22.2%), and contusions (17.7%). Compared to their respective age ranges in NEISS, sprains/strains comprised a larger proportion of injuries in HS RIO (48.3% vs. 33.7%; IPR = 1.38; 95% CI: 1.33, 1.42) and NCAA-ISP (51.3% vs. 37.0%; IPR = 1.39; 95% CI: 1.31, 1.46). In contrast, fractures comprised a smaller proportion of injuries in HS RIO than in NEISS (7.5% vs. 18.6%; IPR = 0.43; 95% CI: 0.39, 0.47) and NCAA-ISP (2.8% vs. 15.7%; IPR = 0.18; 95% CI: 0.14, 0.22).

CONCLUSIONS

ATs more commonly reported injuries that are easily diagnosed and treated (e.g., sprains/strains); EDs more commonly reported injuries with longer recovery times and rehabilitation (e.g., fractures). Although ED surveillance data can identify the most severe sports-related injuries, high school and college sports surveillance may better describe the breadth of sports-related injuries. Our findings may provide further support for school-based sports medicine professionals, but further research is needed to comprehensively examine the potential economic and health-related benefits.

Evaluation of a nurse practitioner-physician task-sharing model for multidrug-resistant tuberculosis in South Africa

Background

Treatment success rates for multidrug-resistant tuberculosis (MDR-TB) in South Africa remain close to 50%. Lack of access to timely, decentralized care is a contributing factor. We evaluated MDR-TB treatment outcomes from a clinical cohort with task-sharing between a clinical nurse practitioner (CNP) and a medical officer (MO).

Methods

We completed a retrospective evaluation of outcomes from a prospective, programmatically-based MDR-TB cohort who were enrolled and received care between 2012 and 2015 at a peri-urban hospital in KwaZulu-Natal, South Africa. Treatment was provided by either by a CNP or MO.

Findings

The cohort included 197 participants with a median age of 33 years, 51% female, and 74% co-infected with HIV. The CNP initiated 123 participants on treatment. Overall MDR-TB treatment success rate in this cohort was 57.9%, significantly higher than the South African national average of 45% in 2012 (p<0·0001) and similar to the provincal average of 60% (p = NS). There were no significant differences by provider type: treatment success was 61% for patients initiated by the CNP and 52.7% for those initiated by the MO.

Interpretation

Clinics that adopted a task sharing approach for MDR-TB demonstrated greater treatment success rates than the national average. Task-sharing between the CNP and MO did not adversely impact treatment outcome with similar success rates noted. Task-sharing is a feasible option for South Africa to support decentralization without compromising patient outcomes. Models that allow sharing of responsibility for MDR-TB may optimize the use of human resources and improve access to care.

Epidemiology, clinical features and risk factors for human rabies and animal bites during an outbreak of rabies in Maputo and Matola cities, Mozambique, 2014: Implications for public health interventions for rabies control

Background

In Mozambique, the majority of rabies outbreaks are unreported and data on the epidemiological features of human rabies and animal bites are scarce. An outbreak of human rabies in adjacent Maputo and Matola cities in 2014 prompted us to investigate the epidemiology, clinical features and risk factors of human rabies and animal bites in the two cities.

Methodology/Principal findings

We reviewed cases of human rabies and animal bites from April to July 2014, and carried out a community investigation in July and August in the neighborhoods where cases of human rabies resided. This investigation included collection of clinical, demographic and epidemiological information and a case control study to investigate the risk factors associated with human rabies. Fourteen cases of human rabies were detected in Maputo (n = 10) and Matola (n = 3) cities and neighbouring Boane district (n = 1) between April and August 2014, all of whom had been admitted to hospital. All had a recent history of dog bite. Of the 14 rabid dogs, only one had been immunized. 819 cases of animal bites were registered, of which 64.6% (529/819) were from Maputo City. Dogs were responsible for 97.8% (801/819) of all animal bites, but only 27.0% (126/467) were immunized. Factors significantly associated with human rabies were: age <15 years (p = 0.05), bite by stray dog (p = 0.002), deep wound (p = 0.02), bite in the head (p = 0.001), bite by unimmunized dog (p = 0.01), no use of soap and water (p = 0.001), and no post-exposure prophylaxis (p = 0.01).

Conclusions/Significance

Implementation of control measures for rabies is poor in Maputo and Matola cities, where cases of human rabies were strongly associated with bites by stray and unvaccinated dogs and irregular implementation of post-exposure measures.

Rabies is a deadly neglected virus that causes an estimated 59,000 deaths each year worldwide. In 2014, an outbreak of human rabies in adjacent Maputo and Matola cities prompted us to investigate the epidemiology and risk factors of human rabies and animal bites in the two cities. We reviewed cases of human rabies and animal bites through both health facility and community investigations and carried out a case control study in affected neighborhoods. We found a total of 14 unreported human rabies cases in a four month period, and 819 cases of animal bites in a three month retrospective review of records. Dogs were responsible for all rabid bites and for 97.8% of animal bites. None of the rabid dogs had been vaccinated. Factors significantly associated with human rabies were: age <15 years, bite by a stray dog, deep wound, bite in the head, bite by an unimmunized dog, failure to use soap and water to cleanse the wound, and to vaccinate after the bite. We concluded that the poor implementation of control measures for rabies had led to the outbreak and recommended strengthening implementation, particularly in rapidly urbanizing areas.

Mosquitoes on a plane: Disinsection will not stop the spread of vector-borne pathogens, a simulation study

Mosquito-borne diseases are increasingly being recognized as global threats, with increased air travel accelerating their occurrence in travelers and their spread to new locations. Since the early days of aviation, concern over the possible transportation of infected mosquitoes has led to recommendations to disinsect aircraft. Despite rare reports of mosquitoes, most likely transported on aircraft, infecting people far from endemics areas, it is unclear how important the role of incidentally transported mosquitoes is compared to the role of traveling humans. We used data for Plasmodium falciparum and dengue viruses to estimate the probability of introduction of these pathogens by mosquitoes and by humans via aircraft under ideal conditions. The probability of introduction of either pathogen by mosquitoes is low due to few mosquitoes being found on aircraft, low infection prevalence among mosquitoes, and high mortality. Even without disinsection, introduction via infected human travelers was far more likely than introduction by infected mosquitoes; more than 1000 times more likely for P. falciparum and more than 200 times more likely for dengue viruses. Even in the absence of disinsection and under the most favorable conditions, introduction of mosquito-borne pathogens via air travel is far more likely to occur as a result of an infected human travelling rather than the incidental transportation of infected mosquitoes. Thus, while disinsection may serve a role in preventing the spread of vector species and other invasive insects, it is unlikely to impact the spread of mosquito-borne pathogens.

Measuring changes in transmission of neglected tropical diseases, malaria, and enteric pathogens from quantitative antibody levels

BACKGROUND

Serological antibody levels are a sensitive marker of pathogen exposure, and advances in multiplex assays have created enormous potential for large-scale, integrated infectious disease surveillance. Most methods to analyze antibody measurements reduce quantitative antibody levels to seropositive and seronegative groups, but this can be difficult for many pathogens and may provide lower resolution information than quantitative levels. Analysis methods have predominantly maintained a single disease focus, yet integrated surveillance platforms would benefit from methodologies that work across diverse pathogens included in multiplex assays.

METHODS/PRINCIPAL FINDINGS

We developed an approach to measure changes in transmission from quantitative antibody levels that can be applied to diverse pathogens of global importance. We compared age-dependent immunoglobulin G curves in repeated cross-sectional surveys between populations with differences in transmission for multiple pathogens, including: lymphatic filariasis (Wuchereria bancrofti) measured before and after mass drug administration on Mauke, Cook Islands, malaria (Plasmodium falciparum) before and after a combined insecticide and mass drug administration intervention in the Garki project, Nigeria, and enteric protozoans (Cryptosporidium parvum, Giardia intestinalis, Entamoeba histolytica), bacteria (enterotoxigenic Escherichia coli, Salmonella spp.), and viruses (norovirus groups I and II) in children living in Haiti and the USA. Age-dependent antibody curves fit with ensemble machine learning followed a characteristic shape across pathogens that aligned with predictions from basic mechanisms of humoral immunity. Differences in pathogen transmission led to shifts in fitted antibody curves that were remarkably consistent across pathogens, assays, and populations. Mean antibody levels correlated strongly with traditional measures of transmission intensity, such as the entomological inoculation rate for P. falciparum (Spearman's rho = 0.75). In both high- and low transmission settings, mean antibody curves revealed changes in population mean antibody levels that were masked by seroprevalence measures because changes took place above or below the seropositivity cutoff.

CONCLUSIONS/SIGNIFICANCE

Age-dependent antibody curves and summary means provided a robust and sensitive measure of changes in transmission, with greatest sensitivity among young children. The method generalizes to pathogens that can be measured in high-throughput, multiplex serological assays, and scales to surveillance activities that require high spatiotemporal resolution. Our results suggest quantitative antibody levels will be particularly useful to measure differences in exposure for pathogens that elicit a transient antibody response or for monitoring populations with very high- or very low transmission, when seroprevalence is less informative. The approach represents a new opportunity to conduct integrated serological surveillance for neglected tropical diseases, malaria, and other infectious diseases with well-defined antigen targets.

Challenges and Strategies for Prevention of Multidrug-Resistant Organism Transmission in Nursing Homes

PURPOSE OF REVIEW

Nursing home residents are at high risk for colonization and infection with bacterial pathogens that are multidrug-resistant organisms (MDROs). We discuss challenges and potential solutions to support implementing effective infection prevention and control practices in nursing homes.

RECENT FINDINGS

Challenges include a paucity of evidence that addresses MDRO transmission during the care of nursing home residents, limited staff resources in nursing homes, insufficient infection prevention education in nursing homes, and perceptions by nursing home staff that isolation and contact precautions negatively influence the well being of their residents. A small number of studies provide evidence that specifically address these challenges. Their outcomes support a paradigm shift that moves infection prevention and control practices away from a pathogen-specific approach and toward one that focuses on resident risk factors.

Prevalence and clinical presentation of Rickettsia, Coxiella, Leptospira, Bartonella and chikungunya virus infections among hospital-based febrile patients from December 2008 to November 2009 in Bangladesh

BACKGROUND

We conducted a study to identify Rickettsia, Coxiella, Leptospira, Bartonella, and Chikungunya virus infections among febrile patients presenting at hospitals in Bangladesh.

METHODS

We collected blood samples from patients at six tertiary hospitals from December 2008 to November 2009 and performed laboratory tests at the United States Centers for Disease Control and Prevention (CDC).

RESULTS

Out of 720 enrolled patients, 263 (37%) were infected with Rickettsia; 132 patients had immunofluorescence antibody titer >64 against spotted fever, 63 patients against scrub typhus fever and 10 patients against typhus fever. Ten patients were identified with Coxiella. We isolated Leptospira from two patients and Bartonella from one patient. Ten patients had antibodies against Chikungunya virus. The proportion of patients who died was higher with rickettsial fever (5%) compared to those without a diagnosis of rickettsial infection (2%). None of the patients were initially diagnosed with rickettsial fever.

CONCLUSIONS

Rickettsial infections are frequent yet under-recognized cause of febrile illness in Bangladesh. Clinical guidelines should be revised so that local clinicians can diagnose rickettsial infections and provide appropriate drug treatment.

Viral deep sequencing needs an adaptive approach: IRMA, the iterative refinement meta-assembler

BACKGROUND

Deep sequencing makes it possible to observe low-frequency viral variants and sub-populations with greater accuracy and sensitivity than ever before. Existing platforms can be used to multiplex a large number of samples; however, analysis of the resulting data is complex and involves separating barcoded samples and various read manipulation processes ending in final assembly. Many assembly tools were designed with larger genomes and higher fidelity polymerases in mind and do not perform well with reads derived from highly variable viral genomes. Reference-based assemblers may leave gaps in viral assemblies while de novo assemblers may struggle to assemble unique genomes.

RESULTS

The IRMA (iterative refinement meta-assembler) pipeline solves the problem of viral variation by the iterative optimization of read gathering and assembly. As with all reference-based assembly, reads are included in assembly when they match consensus template sets; however, IRMA provides for on-the-fly reference editing, correction, and optional elongation without the need for additional reference selection. This increases both read depth and breadth. IRMA also focuses on quality control, error correction, indel reporting, variant calling and variant phasing. In fact, IRMA's ability to detect and phase minor variants is one of its most distinguishing features. We have built modules for influenza and ebolavirus. We demonstrate usage and provide calibration data from mixture experiments. Methods for variant calling, phasing, and error estimation/correction have been redesigned to meet the needs of viral genomic sequencing.

CONCLUSION

IRMA provides a robust next-generation sequencing assembly solution that is adapted to the needs and characteristics of viral genomes. The software solves issues related to the genetic diversity of viruses while providing customized variant calling, phasing, and quality control. IRMA is freely available for non-commercial use on Linux and Mac OS X and has been parallelized for high-throughput computing.

Translating Research into Practice: Employing Community-Based Mixed Methods Approaches to Address Chronic Disease and Depression Among Latinos

The co-occurrence of depression and chronic diseases is often under-recognized, under-treated, and under-studied. Among Latinos, complex structural and cultural barriers exist which complicate the translation of chronic disease self-management programs (CDSMP) for this population. To better understand those barriers and deliver a CDSMP designed to best meet local needs, a community-based, mixed methods study was designed. Formative research was conducted through focus groups with Latinos with chronic illness and minor depression (ICD) and family members to obtain insight into perceived needs and interviews with stakeholders to assess barriers and facilitators to the adoption of CDSMPs. Analytic Hierarchy Process was employed to determine core elements of a CDSMP for ICDs, family members, and the promotores who deliver these programs. Findings guided the transcreation of a CDSMP. This study offers a promising model for enhancing the effects of evidence-based interventions and emphasizes the importance of meeting differing needs within the local population.

The role of researchers in disseminating evidence to public health practice settings: a cross-sectional study

BACKGROUND

Evidence-based public health interventions, which research has demonstrated offer the most promise for improving the population's health, are not always utilized in practice settings. The extent to which dissemination from researchers to public health practice settings occurs is not widely understood. This study examines the extent to which public health researchers in the United States are disseminating their research findings to local and state public health departments.

METHODS

In a 2012, nationwide study, an online questionnaire was administered to 266 researchers from the National Institutes of Health, the Centers for Disease Control and Prevention, and universities to determine dissemination practices. Logistic regression analyses were used to examine the association between dissemination to state and/or local health departments and respondent characteristics, facilitators, and barriers to dissemination.

RESULTS

Slightly over half of the respondents (58%) disseminated their findings to local and/or state health departments. After adjusting for other respondent characteristics, respondents were more likely to disseminate their findings to health departments if they worked for a university Prevention Research Center or the Centers for Disease Control and Prevention, or received their degree more than 20 years ago. Those who had ever worked in a practice or policy setting, those who thought dissemination was important to their own research and/or to the work of their unit/department, and those who had expectations set by their employers and/or funding agencies were more likely to disseminate after adjusting for work place, graduate degree and/or fellowship in public health, and the year the highest academic degree was received.

CONCLUSIONS

There is still room for improvement in strengthening dissemination ties between researchers and public health practice settings, and decreasing the barriers researchers face during the dissemination process. Researchers could better utilize national programs or workshops, knowledge brokers, or opportunities provided through academic institutions to become more proficient in dissemination practices.