The role of the microbiota in respiratory virus-bacterial pathobiont relationships in the upper respiratory tract.

The mechanisms by which respiratory viruses predispose to secondary bacterial infections remain poorly characterized. Using 2,409 nasopharyngeal swabs from 300 infants in Botswana, we performed a detailed analysis of factors that influence the dynamics of bacterial pathobiont colonization during infancy. We quantify the extent to which viruses increase the acquisition of , , and .

Serotype epidemiology and antibiotic resistance of pneumococcal isolates colonizing infants in Botswana (2016-2019).

Background: In 2012, Botswana introduced 13-valent pneumococcal conjugate vaccine (PCV-13) to its childhood immunization program in a 3+0 schedule, achieving coverage rates of above 90% by 2014. In other settings, PCV introduction has been followed by an increase in carriage or disease caused by non-vaccine serotypes, including some serotypes with a high prevalence of antibiotic resistance.

Methods: We characterized the serotype epidemiology and antibiotic resistance of pneumococcal isolates cultured from nasopharyngeal samples collected from infants (≤12 months) in southeastern Botswana between 2016 and 2019.

Likelihood of hospitalization for a chronic respiratory condition following pediatric infection with enterovirus and rhinovirus strains.

Background: Rhino-enteroviruses, particularly enterovirus strain D68 (EV-D68), have been associated with severe respiratory distress in children. The goal of this study was to compare the long-term outcomes of children with EV-D68 infection to that of children with other enterovirus / rhinovirus.

Methods: Nasopharyngeal swabs from 174 children presenting with respiratory distress were tested by PCR for respiratory viruses.

Assessment of nasopharyngeal Streptococcus pneumoniae colonization does not permit discrimination between Canadian children with viral and bacterial respiratory infection: a matched-cohort cross-sectional study.

Background: Readily-available diagnostics do not reliably discriminate between viral and bacterial pediatric uncomplicated pneumonia, both of which are common. Some have suggested that assessment of pneumococcal carriage could be used to identify those children with bacterial pneumonia. The objective of this study was to determine if nasopharyngeal pneumococcal colonization patterns differed between children with definite viral disease, definite bacterial disease, and respiratory disease of indeterminate etiology.

Self-collected oral flocked swabs to measure prevalence of Epstein-Barr Virus antibodies and DNA amongst university students.

Epstein-Barr Virus (EBV) exposure and illness is common in undergraduate university students and may affect academic achievement, social life, and quality of life. We designed a study to measure EBV exposure (EBV-IgG, either Epstein-Barr nuclear antigen 1 (EBNA-1)-IgG or viral capsid antigen (VCA)-IgG) and current viral shedding (EBV-DNA) using self-collected oral swabs among university undergraduate students. Of 184 students enrolled, 129 (70.

Evaluation of the FecalSwab for Stool Specimen Storage and Molecular Detection of Enteropathogens on the BD Max System.

The FecalSwab system (Copan Italia, Brescia, Italy) is a convenient alternative to bulk stool for the diagnosis of enteric pathogens. Although the U.S.

Non-invasive detection of IgG antibodies from common pathogenic viruses using oral flocked swabs.

Salivary antibodies are useful in surveillance and vaccination studies. However, low antibody levels and degradation by endonucleases are problematic. Oral flocked swabs are a potential non-invasive alternative for detecting viral antibodies.

Paediatric critical illness associated with respiratory infection: a single-centre, retrospective cohort study.

Objectives: To describe critically ill children with respiratory infections, classify them by infection syndrome type and determine the prevalence of detection.

Study Design: A retrospective, single-centre cohort study. All children aged 2 months-18 years with presumed respiratory infection who were admitted to a tertiary hospital paediatric intensive care unit (PICU) between September 2015 and October 2016 were eligible.

The prevalence and clinical characteristics of pertussis-associated pneumonia among infants in Botswana.

Background: There are scant data on the prevalence and clinical course of pertussis disease among infants with pneumonia in low- and middle-income countries. While pertussis vaccination coverage is high (≥90%) among infants in Botswana, human immunodeficiency virus (HIV) infection affects nearly one-third of pregnancies. We aimed to evaluate the prevalence and clinical course of pertussis disease in a cohort of HIV-unexposed uninfected (HUU), HIV-exposed uninfected (HEU), and HIV-infected infants with pneumonia in Botswana.

Predictors of Poor Outcomes Among Infants With Respiratory Syncytial Virus-associated Acute Lower Respiratory Infection in Botswana.

Among children 1-23 months of age with respiratory syncytial virus-associated acute lower respiratory infection in Botswana, young age (<6 months), household use of wood as a cooking fuel, moderate or severe malnutrition and oxygen saturation <90% on room air were independent predictors of clinical nonresponse at 48 hours. Among HIV-uninfected infants less than six months of age, HIV exposure was associated with a higher risk of in-hospital mortality.

Pneumococcal Colonization and the Nasopharyngeal Microbiota of Children in Botswana.

Background: Nasopharyngeal colonization precedes infections caused by Streptococcus pneumoniae. A more detailed understanding of interactions between S. pneumoniae and the nasopharyngeal microbiota of children could inform strategies to prevent pneumococcal infections.

The Nasopharyngeal Microbiota of Children With Respiratory Infections in Botswana.

Background: Nearly half of child pneumonia deaths occur in sub-Saharan Africa. Microbial communities in the nasopharynx are a reservoir for pneumonia pathogens and remain poorly described in African children.

Methods: Nasopharyngeal swabs were collected from children with pneumonia (N = 204), children with upper respiratory infection symptoms (N = 55) and healthy children (N = 60) in Botswana between April 2012 and April 2014.

A comparison of flocked swabs and traditional swabs, using multiplex real-time PCR for detection of common gastroenteritis pathogens in Botswana.

We compared the performance of flocked and matched traditional rectal swabs collected from 236 children admitted with gastroenteritis in Botswana. All samples were tested using real time multiplex-PCR assays for nine enteric pathogens. There was a 20% higher detection of Shigella from flocked swabs, but most other pathogens had similar detection rates.

Ease, Comfort, and Performance of the HerSwab Vaginal Self-Sampling Device for the Detection of Chlamydia trachomatis and Neisseria gonorrhoeae.

Background: Many sexually transmitted diseases are asymptomatic in the lower genital tract and can cause upper tract complications if left untreated. Self-collected vaginal (SCV) swabs enable the accurate detection of many sexually transmitted infections and give women the option of collecting their own samples while providing them with privacy and convenience.

Methods: We compared SCV samples collected and transported dry using the HerSwab device to physician-collected vaginal (PCV) Aptima swabs for the detection of Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG), and measured patients' ease and comfort with self-collection.

Throat and nasal swabs for molecular detection of respiratory viruses in acute pharyngitis.

Background: Detection of specific respiratory viruses is important for surveillance programs, where nasopharyngeal or nasal swabs have traditionally been used. Our objective was to determine whether sampling with a throat swab provides incremental benefit-when used in conjunction with a nasal swab-to detect respiratory viruses among patients with acute pharyngitis in the outpatient setting.

Findings: Among 83 university students with acute pharyngitis, we detected respiratory viruses with molecular assays on two samples collected per student: with a flocked nasal mid-turbinate swab and a rayon throat swab.

Clinical severity of pediatric respiratory illness with enterovirus D68 compared with rhinovirus or other enterovirus genotypes.

Background: Enterovirus D68 (EV-D68) resulted in a reported increase in the number of children needing hospital or critical care admission because of respiratory insufficiency during 2014. It remains unclear, however, whether EV-D68 infections were more severe than rhinovirus or non-EV-D68 enterovirus infections.

Methods: We evaluated consecutive children presenting to a pediatric hospital between Aug.

Comparison of asymptomatic and symptomatic rhinovirus infections in university students: incidence, species diversity, and viral load.

Human rhinovirus (HRV) infections are common but poorly characterized in university students. Thus, we characterized asymptomatic and symptomatic HRV infections by incidence, species diversity, and viral load of 502 university students during September and October of 2010 and 2011 from nasal swabs and electronically submitted symptom questionnaires. We tested all symptomatic students and randomly sampled participants who remained asymptomatic (n=25/week, over 8 weeks each study year) on a weekly basis by real-time PCR and sequenced HRV positives.

Association of respiratory viruses with outcomes of severe childhood pneumonia in Botswana.

Background: The highest incidence of childhood acute lower respiratory tract infection (ALRI) is in low- and middle-income countries. Few studies examined whether detection of respiratory viruses predicts ALRI outcomes in these settings.

Methods: We conducted prospective cohort and case-control studies of children 1-23 months of age in Botswana.

Evaluation of anatomically designed flocked rectal swabs for molecular detection of enteric pathogens in children admitted to hospital with severe gastroenteritis in Botswana.

Two-hundred eighty matched bulk stool and anatomically designed flocked rectal swab samples were collected from children admitted to the hospital with acute diarrhea in Botswana. Their parents were asked about the acceptability of the swab collection method compared with bulk stool sampling. All samples underwent identical testing with a validated 15-target (9 bacterial, 3 viral, and 3 parasite) commercial multiplex PCR assay.

Vitamin D3 and gargling for the prevention of upper respiratory tract infections: a randomized controlled trial.

Background: We undertook a 2X2 factorial, randomized controlled trial (RCT) to assess whether vitamin D3 supplementation (10,000 international units per week) versus placebo and gargling versus no gargling could prevent viral, clinical upper respiratory tract infection (URTI) in university students.

Methods: We randomized 600 students into 4 treatment arms: 1) vitamin D3 and gargling, 2) placebo and gargling, 3) vitamin D3 and no gargling, and 4) placebo and no gargling. Students completed weekly electronic surveys and submitted self-collected mid-turbinate nasal flocked swabs during September and October in 2010 or 2011.

The loss of topography in the microbial communities of the upper respiratory tract in the elderly.

Rationale: The microbial communities inhabiting the upper respiratory tract protect from respiratory infection. The maturity of the immune system is a major influence on the composition of the microbiome and, in youth, the microbiota and immune system are believed to mature in tandem. With age, immune function declines and susceptibility to respiratory infection increases.

Co-circulation of multiple genotypes of human rhinovirus during a large outbreak of respiratory illness in a veterans' long-term care home.

Background: Human rhinoviruses (HRVs) are a well-recognized cause of long-term care home (LTCH) outbreaks of respiratory illness. However, there are limited data on the molecular epidemiology of the HRV types involved.

Objectives: To determine whether a large respiratory outbreak in a LTCH was caused by a single type of HRV, and to describe the clinical impact of the outbreak.

Use of an improved quantitative polymerase chain reaction assay to determine differences in human rhinovirus viral loads in different populations.

Human rhinoviruses (HRV) frequently cause acute respiratory infections and chronic respiratory disease exacerbations. However, testing is not generally offered. We developed a modified HRV quantitative polymerase chain reaction (qPCR) assay to assess viral loads in the community and hospital patients.

Evaluation and clinical validation of an alcohol-based transport medium for preservation and inactivation of respiratory viruses.

The clinical and public health importance of influenza and other respiratory viruses has accelerated the development of highly sensitive molecular diagnostics, but data are limited regarding preanalytical stages of diagnostic testing. We evaluated CyMol, an alcohol-based transport medium, for its ability to maintain specimen integrity for up to 21 days of storage at various temperatures; for its ability to inactivate virus; and for its compatibility with antigen- or nucleic acid-based diagnostics for respiratory viruses in clinical samples. In mock-infected samples, both universal transport medium (UTM-RT) and CyMol maintained equivalent viral quantities for at least 14 days at room temperature or colder, whereas a dry swab collection maintained viral quantities only if refrigerated or frozen.