Model selection, hummingbird natural history, and biological hypotheses: a response to Sazatornil et al.

We have previously suggested that a shift from bee to hummingbird pollination, in concert with floral architecture modifications, occurred at the crown of Salvia subgenus Calosphace in North America ca. 20 mya (Kriebel et al. 2020 and references therein). Sazatornil et al. (2022), using a hidden states model, challenged these assertions, arguing that bees were the ancestral pollinator of subg. Calosphace and claiming that hummingbirds could not have been the ancestral pollinator of subg. Calosphace because hummingbirds were not contemporaneous with crown subg. Calosphace in North America. Here, using a variety of models, we demonstrate that most analyses support hummingbirds as ancestral pollinators of subg. Calosphace and show that Sazatornil et al. (2022) erroneously concluded that hummingbirds were absent from North America ca. 20 mya. We contend that "biological realism" - based on timing and placement of hummingbirds in Mexico ca. 20 mya and the correlative evolution of hummingbird associated floral traits - must be considered when comparing models based on fit and complexity, including hidden states models.

SARS-CoV-2 Outbreak Dynamics in an Isolated US Military Recruit Training Center With Rigorous Prevention Measures.

BACKGROUND: Marine recruits training at Parris Island experienced an unexpectedly high rate of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, despite preventive measures including a supervised, 2-week, pre-entry quarantine. We characterize SARS-CoV-2 transmission in this cohort. METHODS: Between May and November 2020, we monitored 2,469 unvaccinated, mostly male, Marine recruits prospectively during basic training. If participants tested negative for SARS-CoV-2 by quantitative polymerase chain reaction (qPCR) at the end of quarantine, they were transferred to the training site in segregated companies and underwent biweekly testing for 6 weeks. We assessed the effects of coronavirus disease 2019 (COVID-19) prevention measures on other respiratory infections with passive surveillance data, performed phylogenetic analysis, and modeled transmission dynamics and testing regimens. RESULTS: Preventive measures were associated with drastically lower rates of other respiratory illnesses. However, among the trainees, 1,107 (44.8%) tested SARS-CoV-2-positive, with either mild or no symptoms. Phylogenetic analysis of viral genomes from 580 participants revealed that all cases but one were linked to five independent introductions, each characterized by accumulation of mutations across and within companies, and similar viral isolates in individuals from the same company. Variation in company transmission rates (mean reproduction number R 0 ; 5.5 [95% confidence interval [CI], 5.0, 6.1]) could be accounted for by multiple initial cases within a company and superspreader events. Simulations indicate that frequent rapid-report testing with case isolation may minimize outbreaks. CONCLUSIONS: Transmission of wild-type SARS-CoV-2 among Marine recruits was approximately twice that seen in the community. Insights from SARS-CoV-2 outbreak dynamics and mutations spread in a remote, congregate setting may inform effective mitigation strategies.

Assessing the Effects of Measles Virus Infections on Childhood Infectious Disease Mortality in Brazil.

BACKGROUND: Measles virus infection induces acute immunosuppression for weeks following infection, and also impairs preexisting immunological memory, resulting in "immune amnesia" that can last for years. Both mechanisms predispose the host to severe outcomes of subsequent infections. Therefore, measles dynamics could potentially affect the epidemiology of other infectious diseases. METHODS: To examine this hypothesis, we analyzed the annual mortality rates of children aged 1-9 years in Brazil from 1980 to 1995. We calculated the correlation between nonmeasles infectious disease mortality rates and measles mortality rates using linear and negative-binomial models, with 3 methods to control the confounding effects of time. We also estimated the duration of measles-induced immunomodulation. RESULTS: The mortality rates of nonmeasles infectious diseases and measles virus infection were highly correlated. This positive correlation remained significant after removing the time trends. We found no evidence of long-term measles immunomodulation beyond 1 year. CONCLUSIONS: These results support that measles virus infection could increase the mortality of other infectious diseases. The short lag identified for measles effects (<1 year) implies that acute immunosuppression was potentially driving this effect in Brazil. Overall, our study indicates disproportionate contributions of measles to childhood infectious disease mortality, highlighting the importance of measles vaccination.

The impact of COVID-19 nonpharmaceutical interventions on the future dynamics of endemic infections.

Nonpharmaceutical interventions (NPIs) have been employed to reduce the transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), yet these measures are already having similar effects on other directly transmitted, endemic diseases. Disruptions to the seasonal transmission patterns of these diseases may have consequences for the timing and severity of future outbreaks. Here we consider the implications of SARS-CoV-2 NPIs for two endemic infections circulating in the United States of America: respiratory syncytial virus (RSV) and seasonal influenza. Using laboratory surveillance data from 2020, we estimate that RSV transmission declined by at least 20% in the United States at the start of the NPI period. We simulate future trajectories of both RSV and influenza, using an epidemic model. As susceptibility increases over the NPI period, we find that substantial outbreaks of RSV may occur in future years, with peak outbreaks likely occurring in the winter of 2021-2022. Longer NPIs, in general, lead to larger future outbreaks although they may display complex interactions with baseline seasonality. Results for influenza broadly echo this picture, but are more uncertain; future outbreaks are likely dependent on the transmissibility and evolutionary dynamics of circulating strains.

Epidemic dynamics of respiratory syncytial virus in current and future climates.

A key question for infectious disease dynamics is the impact of the climate on future burden. Here, we evaluate the climate drivers of respiratory syncytial virus (RSV), an important determinant of disease in young children. We combine a dataset of county-level observations from the US with state-level observations from Mexico, spanning much of the global range of climatological conditions. Using a combination of nonlinear epidemic models with statistical techniques, we find consistent patterns of climate drivers at a continental scale explaining latitudinal differences in the dynamics and timing of local epidemics. Strikingly, estimated effects of precipitation and humidity on transmission mirror prior results for influenza. We couple our model with projections for future climate, to show that temperature-driven increases to humidity may lead to a northward shift in the dynamic patterns observed and that the likelihood of severe outbreaks of RSV hinges on projections for extreme rainfall.

Amphitropical disjunctions in New World Menthinae: Three Pliocene dispersals to South America following late Miocene dispersal to North America from the Old World.

PREMISE OF THE STUDY: The subtribe Menthinae (Lamiaceae), with 35 genera and 750 species, is among the largest and most economically important subtribes within the mint family. Most genera of Menthinae are found exclusively in the New World, where the group has a virtually continuous distribution ranging from temperate North America to southern South America. In this study, we explored the presence, timing, and origin of amphitropical disjuncts within Menthinae. METHODS: Our analyses were based on a data set consisting of 89 taxa and the nuclear ribosomal DNA markers ITS and ETS. Phylogenetic relationships were determined under maximum likelihood and Bayesian criteria, divergence times were estimated with the program BEAST, and ancestral range estimated with BioGeoBEARS. KEY RESULTS: A North Atlantic Land Bridge migration event at about 10.6 Ma is inferred from western Eurasia to North America. New World Menthinae spread rapidly across North America, and then into Central and South America. Several of the large speciose genera are not monophyletic with nuclear rDNA, a finding mirrored with previous chloroplast DNA results. Three amphitropical disjunctions involving North and southern South America clades, one including a southeastern South American clade with several genera, were inferred to have occurred within the past 5 Myr. CONCLUSIONS: Although three New World Menthinae genera occur in both North and South America, none exhibit an amphitropical disjunction. However, three clades exhibit amphitropical disjunctions, all dating to the early Pliocene, and all involve jump dispersals to either southeastern or southwestern South America from southeastern North America.

Identifying Hotspots of Multidrug-Resistant Tuberculosis Transmission Using Spatial and Molecular Genetic Data.

BACKGROUND: We aimed to identify and determine the etiology of "hotspots" of concentrated multidrug-resistant tuberculosis (MDR-tuberculosis) risk in Lima, Peru. METHODS: From 2009 to 2012, we conducted a prospective cohort study among households of tuberculosis cases from 106 health center (HC) areas in Lima, Peru. All notified tuberculosis cases and their household contacts were followed for 1 year. Symptomatic individuals were screened by microscopy and culture; positive cultures were tested for drug susceptibility (DST) and genotyped by 24-loci mycobacterial interspersed repetitive units-variable-number tandem repeats (MIRU-VNTR). RESULTS: 3286 individuals with culture-confirmed disease, DST, and 24-loci MIRU-VNTR were included in our analysis. Our analysis reveals: (1) heterogeneity in annual per-capita incidence of tuberculosis and MDR-tuberculosis by HC, with a rate of MDR-tuberculosis 89 times greater (95% confidence interval [CI], 54,185) in the most-affected versus the least-affected HC; (2) high risk for MDR-tuberculosis in a region spanning several HCs (odds ratio = 3.19, 95% CI, 2.33, 4.36); and (3) spatial aggregation of MDR-tuberculosis genotypes, suggesting localized transmission. CONCLUSIONS: These findings reveal that localized transmission is an important driver of the epidemic of MDR-tuberculosis in Lima. Efforts to interrupt transmission may be most effective if targeted to this area of the city.

Global trends in antimicrobial use in food animals.

Demand for animal protein for human consumption is rising globally at an unprecedented rate. Modern animal production practices are associated with regular use of antimicrobials, potentially increasing selection pressure on bacteria to become resistant. Despite the significant potential consequences for antimicrobial resistance, there has been no quantitative measurement of global antimicrobial consumption by livestock. We address this gap by using Bayesian statistical models combining maps of livestock densities, economic projections of demand for meat products, and current estimates of antimicrobial consumption in high-income countries to map antimicrobial use in food animals for 2010 and 2030. We estimate that the global average annual consumption of antimicrobials per kilogram of animal produced was 45 mg⋅kg(-1), 148 mg⋅kg(-1), and 172 mg⋅kg(-1) for cattle, chicken, and pigs, respectively. Starting from this baseline, we estimate that between 2010 and 2030, the global consumption of antimicrobials will increase by 67%, from 63,151 ± 1,560 tons to 105,596 ± 3,605 tons. Up to a third of the increase in consumption in livestock between 2010 and 2030 is imputable to shifting production practices in middle-income countries where extensive farming systems will be replaced by large-scale intensive farming operations that routinely use antimicrobials in subtherapeutic doses. For Brazil, Russia, India, China, and South Africa, the increase in antimicrobial consumption will be 99%, up to seven times the projected population growth in this group of countries. Better understanding of the consequences of the uninhibited growth in veterinary antimicrobial consumption is needed to assess its potential effects on animal and human health.

Age-specific risks of tuberculosis infection from household and community exposures and opportunities for interventions in a high-burden setting.

We analyzed data from a large population-based prospective cohort study of household contacts of tuberculosis patients in Lima, Peru, to estimate the importance of within-household transmission relative to community-based transmission. We identified all adults (older than 15 years of age) who had incident pulmonary tuberculosis diagnosed at any of 106 public health centers in Lima from September 2009 to August 2012. A total of 14,041 household contacts of 3,446 index patients were assessed for tuberculosis infection and disease. We compared the prevalence of latent tuberculosis infection (LTBI) among persons who had received the Bacillus Calmette-Guérin vaccine in households with and without a microbiologically confirmed index case to estimate the age-specific risk of infection and excess risk of LTBI from household and community exposures. We found that the risk of infection from household and community sources increased from birth until 20 years of age. However, a large proportion of infections among child and young-adult household contacts could have been the result of household exposure. Excess infection risk associated with household exposure accounted for 58% (95% confidence interval: 47, 66) of LTBI prevalence among exposed children younger than 1 year of age, 48% (95% confidence interval: 39, 57) among 10-year-old children, and 44% (95% confidence interval: 34, 51) among 15-year-old adolescents. These findings suggest that expanded access to preventive therapy for older children and young-adult household contacts of known tuberculosis cases may be beneficial.

Manejo de desechos en: Hospital Escuela Universitario, San Felipe e Instituto Hondureño de Seguridad Social / Management of waste in the Hospital Escuela, San Felipe and Instituto Hondureño de Seguridad Social

El manejo de los residuos intrahospitalarios es un aspecto que forma parte de la gestión hospitalaria, cuya finalidad es preservar la bioseguridad de los empleados y pacientes en las diferentes áreas, así como la protección del medio ambiente. Objetivo: caracterizar el manejo intrahospitalario de los desechos generados en diferentes áreas de los hospitales: Escuela Universitario, San Felipe y el Instituto Hondureño de Seguridad Social (IHSS). Material y Métodos: estudio descriptivo sobre el manejo de desechos intrahospitalarios, realizado durante el mes de marzo del año 2014 en las instituciones mencionadas. Se evaluaron las áreas: quirófano, sala de oncología, sala de cirugía, servicio de rayos x y servicio de laboratorio. Se recopilaron los datos mediante la anotación de observaciones hechas por los empleados y los investigadores. Resultados: en las salas de cirugía general se observó inadecuada segregación de los desechos bioinfecciosos. En cada centro hospitalario existen áreas específicas destinadas y señalizadas para el almacenamiento de los desechos previo a su eliminación. En las áreas de rayos x, laboratorio y sala de oncología, se observó inadecuada segregación de los desechos a pesar de existir recipientes rotulados y afiches que brindan ejemplos de segregación adecuada; en el área de quirófano en los tres hospitales, existe una adecuada segregación de los desechos. El transporte interno de los desechos es realizado incorrectamente, no cuenta con un número adecuado de carros especiales para su transporte, de manera que los empleados encargados lo hacen manualmente, exponiéndose a enfermarse, a sí mismo, otros empleados, pacientes y público en general. Conclusión: el personal está segregando inadecuadamente los desechos, a pesar que cada hospital cuenta con un reglamento establecido para su manejo...(AU)

Bacillus Calmette-Guérin and isoniazid preventive therapy protect contacts of patients with tuberculosis.

RATIONALE: Individuals living with patients with tuberculosis (TB) are at elevated risk of infection and disease, with children at greatest risk. The World Health Organization recommends isoniazid preventive therapy (IPT) for HIV-positive contacts and those younger than 5 years. Despite these recommendations, household-level IPT programs are rarely implemented in high TB burden settings. Evidence is scarce about the age-specific efficacy of interventions, such as IPT and bacillus Calmette-Guérin (BCG) vaccination for preventing TB disease among exposed contacts. OBJECTIVES: We estimate the age-specific efficacy of IPT and BCG for preventing TB disease using data from a large observational prospective cohort study of household contacts of patients with TB in Lima, Peru. METHODS: We identified all adults (>15 yr) with incident pulmonary TB (index cases) diagnosed at 106 public health centers in Lima from September 2009 to August 2012. Among 14,041 household contacts (of 3,446 index cases) assessed for infection and disease during the year-long follow-up period, we identified 462 additional TB cases. We estimate risk ratios (RR) for pulmonary TB associated with BCG, IPT, and latent TB infection. MEASUREMENTS AND MAIN RESULTS: BCG confers protection against coprevalent and incident TB among HIV-negative children younger than 10 years (RR, 0.35; 95% confidence interval, 0.19-0.66). IPT confers protection against incident TB among HIV-negative contacts younger than 30 years (RR, 0.33; 95% confidence interval, 0.20-0.54). Risk of incident TB associated with latent TB infection is greatest for children younger than 5 years and decreases with age. CONCLUSIONS: These findings support the use of IPT in older children and young-adult household contacts, in addition to children younger than 5 years.

Understanding reduced rotavirus vaccine efficacy in low socio-economic settings.

INTRODUCTION: Rotavirus vaccine efficacy ranges from >90% in high socio-economic settings (SES) to 50% in low SES. With the imminent introduction of rotavirus vaccine in low SES countries, understanding reasons for reduced efficacy in these settings could identify strategies to improve vaccine performance. METHODS: We developed a mathematical model to predict rotavirus vaccine efficacy in high, middle and low SES based on data specific for each setting on incidence, protection conferred by natural infection and immune response to vaccination. We then examined factors affecting efficacy. RESULTS: Vaccination was predicted to prevent 93%, 86% and 51% of severe rotavirus gastroenteritis in high, middle and low SES, respectively. Also predicted was that vaccines are most effective against severe disease and efficacy declines with age in low but not high SES. Reduced immunogenicity of vaccination and reduced protection conferred by natural infection are the main factors that compromise efficacy in low SES. DISCUSSION: The continued risk of severe disease in non-primary natural infections in low SES is a key factor underpinning reduced efficacy of rotavirus vaccines. Predicted efficacy was remarkably consistent with observed clinical trial results from different SES, validating the model. The phenomenon of reduced vaccine efficacy can be predicted by intrinsic immunological and epidemiological factors of low SES populations. Modifying aspects of the vaccine (e.g. improving immunogenicity in low SES) and vaccination program (e.g. additional doses) may bring improvements.

A geographic zone method to describe intra-articular pathology in hip arthroscopy: cadaveric study and preliminary report.

PURPOSE: Our purpose was to develop an alternative method to divide the acetabulum and femoral head into different zones based on anatomic landmarks clearly visible during arthroscopy to facilitate reporting the geographic location of intra-articular injuries. METHODS: Two vertical lines are positioned across the acetabulum aligned with the anterior and posterior limits of the acetabular notch. A horizontal line is positioned aligned with the superior limit of the notch perpendicular to the previous lines. The lines divide the acetabulum into 6 zones. Numbers are assigned to each zone in consecutive order. Zone 1 is the anterior-inferior acetabulum. The numbers progress around the notch until zone 5 is assigned to the posterior-inferior acetabulum. Zone 6 is the acetabular notch. The same method is applied to the femoral head. Six experienced hip arthroscopists were instructed in the zone and clock-face methods and were asked to identify and describe the geographic locations of lesions at the acetabular rim, acetabular cartilage, and femoral head in the same cadaveric specimen. RESULTS: The zone method was more reproducible than the clock-face method in the geographic description of intra-articular injuries on the acetabulum and the femoral head. CONCLUSIONS: Among a group of expert hip arthroscopists, the zone method was more reproducible than the clock-face method. CLINICAL RELEVANCE: The presented method divides the acetabulum into 6 different zones based on the acetabular notch. The zones are the same for right- and left-side hips. The same method is applied for the femoral head allowing, for the first time, a geographic description of pathology.

Microsporidiosis en pacientes con diarrea crónica y sida, hiv asintomáticos y pacientes con diarrea aguda / Microsporidiosis in patients with chronic diarrhea and aids, asymptomatic hiv and patients with acute diarrhea

Microsporidia are intracellular protozoa that mainly affect AIDS patients and chronic diarrhea, caused by the strains Enterocytozoon bieneusi and septata intestinalis, is the most common clinical manifestation. The diagnosis is made in intestinal biopsies, however the recently developed trichomic stain with chromotrope 2R, is able to detect microsporidia in stools and has a good correlation with the biopsy. Using this technique, we studied 43 asymptomatic HIV infected subjects, 89 AIDS patients with chronic diarrhea and 186 patients with acute diarrhea as controls. Thirty three percent of patients with AIDS, 16.3 percent of HIV infected subjects and none of the individuals with acute diarrhea had microsporidia in their stools (p<0.05). In 15 patients with AIDS we detected intermitted stool microsporidia shedding; this finding should encourage repetitive examinations in negative cases. The trichomic stain for microsporidia is proposed as a routine test in AIDS patients with diarrhea