Patterns of viral pathogens causing upper respiratory tract infections among symptomatic children in Mwanza, Tanzania

The Epidemiological Features and Pathogen Spectrum of Respiratory Tract Infections, Istanbul, Türkiye, from 2021 to 2023

Respiratory tract infections (RTIs) can lead to both recurrent seasonal epidemic outbreaks and devastating pandemics. The aim of this study was to evaluate the epidemiologic characteristics and pathogen spectrum of RTIs using a multiplex RT-PCR panel. A total of 9354 cases with suspected RTIs between February 2021 and July 2023 were included in this study. A total of 11,048 nasopharyngeal and oropharyngeal samples from these patients were analyzed for 23 respiratory tract pathogens using multiplex RT-PCR. H. influenzae and S. pneumoniae were considered as colonizing bacteria. At least one pathogen was detected in 70.66% of the samples; viral pathogens were detected in 48.41% of the samples, bacterial pathogens were detected in 16.06% of the samples, and viral + bacterial pathogens were detected in 35.53% of the samples. The most frequently detected viral pathogen was rhinovirus/enterovirus (RV/EV) (19.99%). Interestingly, in 2021, respiratory syncytial virus A/B showed atypical activity and replaced RV/EV as the most prevalent pathogen. Human bocavirus, H. influenzae, and S. pneumoniae were detected at higher rates in males (p: 0.038, p: 0.042, and p: 0.035, respectively), while SARS-CoV-2 and B. pertussis were detected at higher rates in females (p < 0.001 and p: 0.033). RTIs were found at higher rates in children (p < 0.001). SARS-CoV-2 and human coronaviruses 229E were detected at higher rates in adults (p < 0.001 and p: 0.001). This comprehensive study with a large sample size investigating RTI pathogens was the first in Türkiye. Understanding the current viral circulation using multiplex RT-PCR panels enables clinicians to predict the most likely pathogens affecting patients and contributes to patient management, in addition to anticipating potential threats.

Seasonal variation of asymptomatic viral and bacterial nasopharyngeal carriage in rural Senegal

BACKGROUND

The surveillance of respiratory pathogens in rural areas of West Africa has, to date, largely been focussed on symptoms. In this prospective study conducted prior to the COVID-19 pandemic, we aimed to assess the asymptomatic prevalence of respiratory pathogen carriage in a group of individuals living in a rural area of Senegalese.

METHODS

Longitudinal follow up was performed through monthly nasopharyngeal swabbing during the dry season and weekly swabbing during the rainy season. We enrolled 15 individuals from the village of Ndiop. A total of 368 nasopharyngeal swabs were collected over a one-year period. We investigated the prevalence of 18 respiratory viruses and eight respiratory bacteria in different age groups using singleplex and multiplex PCR.

RESULTS

In total, 19.56% of the samples (72/368) were positive for respiratory viruses and 13.60% of the samples (50/368) were positive for respiratory bacteria. Coronaviruses (19/72, 26.39%), adenoviruses (17/72, 23.61%), rhinoviruses (14/72, 19.44%), Streptococcus pneumoniae (17/50, 34%), and Moraxella catarrhalis (15/50, 30%) were the most frequently detected viruses. Interestingly, the carriage of respiratory pathogens was shown to be more frequent during the rainy season, as pluviometry was shown to be positively associated with the occurrence of respiratory viruses such as influenza (P = .0078, r2 =.523) and RSV (P = .0055, r2 =.554).

CONCLUSIONS

Our results show a non-negligible circulation of respiratory pathogens in a rural area in Senegal (West Africa) with an underestimated proportion of asymptomatic individuals. This study highlights the fact that the circulation of viruses and bacteria in the community has been overlooked.

Influence of Microbiota on Clinical Expressions of Respiratory Viral Infections

Respiratory infections, mainly due to viruses, are among the leading causes of worldwide morbidity and mortality. We investigated the prevalence of viruses and bacteria in a cross-sectional survey conducted in Dielmo, a village in rural Senegal with a population of 481 inhabitants. Nasopharyngeal sampling was performed in 50 symptomatic subjects and 101 asymptomatic subjects. Symptomatic subjects were defined as individuals presenting with clinical signs of respiratory infection, whereas asymptomatic subjects were recruited in the same households. The identification of pathogens was performed by polymerase chain reaction for 18 respiratory viruses and eight respiratory bacteria. The prevalence results for respiratory viruses detected in each study group demonstrated that 83.6% of symptomatic samples were positive for at least one respiratory virus, and 21.8% were detected in asymptomatic samples. Influenza A (P = 0.0001), metapneumovirus (P = 0.04), and enterovirus (P = 0.001) were significantly more prevalent in symptomatic patients. Overall, 82.0% of symptomatic subjects and 26.9% of asymptomatic subjects were positive for at least one respiratory bacterium. The most frequent pathogenic bacteria detected were Moraxella catarrhalis (56%) and Streptococcus pneumoniae (48.0%) among symptomatic individuals, whereas in asymptomatic subjects Corynebacterium propinquum was more prevalent (18%). A principal component analysis showed that parainfluenzas 2 and 4 were associated with asymptomatic subjects, whereas influenza A was associated with the presence of symptoms. Considering these results, a large epidemiological surveillance of the circulation of these respiratory pathogens in the general population should be conducted to provide a better understanding of their carriage and to potentially prevent epidemics.

Personal and Household Hygiene Measures for Preventing Upper Respiratory Tract Infections among Children: A Cross-Sectional Survey of Parental Knowledge, Attitudes, and Practices

Personal and household hygiene measures are important for preventing upper respiratory tract infections (URTIs) and other infectious diseases, including coronavirus disease 2019 (COVID-19). An online survey recruited 414 eligible parents in Hong Kong to study their hygiene knowledge, attitudes, and practices (KAPs) regarding the prevention of URTIs among their children. The average knowledge score was high (10.2/12.0), but some misconceptions were identified. The majority of the participants agreed that good personal hygiene (93.5%) and good environmental hygiene (92.8%) can prevent URTIs. The average score for hand hygiene practices was high (3.78/4.00), but only 56.8% of the parents always performed hand hygiene before touching their mouths, noses, or eyes. In terms of environmental hygiene, only some household items were disinfected with disinfectants (door handles in 69.8% of the households, toilet seats in 60.4% of the households, the floor in 42.8% of the households, dining chairs in 24.2% of the households, and dining tables in 20.5% of the households). A higher knowledge score was associated with parents having tertiary educational levels or above, working as healthcare professionals, living in private residential flats or staff quarters, or having household incomes of HKD 70,000 or above. The results of multiple regression analyses also indicated that parents who were healthcare professionals and with higher household income had a better parental knowledge of hygiene measures after adjusting the attitude score. For hand hygiene, parents who achieved higher attitude scores obtained higher practice scores. Under the fifth wave of the COVID-19 epidemic, there were some misconceptions regarding hygiene among parents. Any health promotion program should target parents regarding taking proper personal and household hygienic measures, especially for those who had relatively lower socio-economic status and/or from a non-healthcare background. Motivating attitudes toward hand hygiene can lead to better practices.

Simultaneous Detection of Multiple Respiratory Viruses Among SARS-CoV-2-positive and negative Patients by Multiplex TaqMan One-step Real-time PCR

Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has clinical manifestations similar to other common respiratory viral infections. There are limited data on the frequency of viral respiratory coinfection among patients infected with SARS-CoV-2 in Iran. Objectives: This cross-sectional study investigated the prevalence of multiple respiratory viruses among SARS-CoV-2-positive and negative patients during the coronavirus disease 2019 (COVID-19) pandemic in Iran. Methods: We included oropharyngeal/nasopharyngeal swab specimens of patients suspected of COVID-19 from December 2020 to March 2021. A reliable multiplex TaqMan one-step real-time PCR method was employed to detect 17 viral respiratory pathogens simultaneously. Descriptive analyses were performed to characterize the specimens concerning age, gender, clinical manifestations, and underlying disease. Results: Multiple respiratory viruses with a frequency of 18.78% were detected in 197 studied patients. Human metapneumovirus was the most prevalent pathogen detected in both SARS-CoV-2-positive (n = 7, 7.7%) and negative (n = 7, 6.6%) patients. Moreover, the frequency rate of viral infection was almost the same in both SARS-CoV-2-positive (18.68%) and negative (18.86%) patients. Altogether, there were no differences in baseline demographic characteristics such as age, sex, clinical symptoms, and comorbidities between the two groups (P > 0.05). Conclusions: The data presented here expand our understanding of the epidemiology of multiple types of viral respiratory pathogens in suspected COVID-19 patients. Therefore, simultaneous screening of other viral respiratory pathogens will be helpful for clinicians and researchers interested in the control of viral respiratory tract infections.

Bacterial Gut Microbiota and Infections During Early Childhood

Gut microbiota composition during the first years of life is variable, dynamic and influenced by both prenatal and postnatal factors, such as maternal antibiotics administered during labor, delivery mode, maternal diet, breastfeeding, and/or antibiotic consumption during infancy. Furthermore, the microbiota displays bidirectional interactions with infectious agents, either through direct microbiota-microorganism interactions or indirectly through various stimuli of the host immune system. Here we review these interactions during childhood until 5 years of life, focusing on bacterial microbiota, the most common gastrointestinal and respiratory infections and two well characterized gastrointestinal diseases related to dysbiosis (necrotizing enterocolitis and Clostridioides difficile infection). To date, most peer-reviewed studies on the bacterial microbiota in childhood have been cross-sectional and have reported patterns of gut dysbiosis during infections as compared to healthy controls; prospective studies suggest that most children progressively return to a "healthy microbiota status" following infection. Animal models and/or studies focusing on specific preventive and therapeutic interventions, such as probiotic administration and fecal transplantation, support the role of the bacterial gut microbiota in modulating both enteric and respiratory infections. A more in depth understanding of the mechanisms involved in the establishment and maintenance of the early bacterial microbiota, focusing on specific components of the microbiota-immunity-infectious agent axis is necessary in order to better define potential preventive or therapeutic tools against significant infections in children.

Seasonal Coronaviruses and Other Neglected Respiratory Viruses: A Global Perspective and a Local Snapshot

Respiratory viral infections are the leading cause of morbidity and mortality in the world; however, there are several groups of viruses that are insufficiently routinely sought for, and can thus be considered neglected from a diagnostic and clinical standpoint. Timely detection of seasonality of certain respiratory viruses (e.g., enveloped viruses such as seasonal coronaviruses) in the local context can aid substantially in targeted and cost-effective utilization of viral diagnostic approaches. For the other, non-enveloped and year-round viruses (i.e., rhinovirus, adenovirus, and bocavirus), a continuous virological diagnosis needs to be implemented in clinical laboratories to more effectively address the aetiology of respiratory infections, and assess the overall impact of these viruses on disease burden. While the coronavirus disease 2019 (COVID-19) pandemic is still actively unfolding, we aimed to emphasize the persistent role of seasonal coronaviruses, rhinoviruses, adenoviruses and bocaviruses in the aetiology of respiratory infections. Consequently, this paper concentrates on the burden and epidemiological trends of aforementioned viral groups on a global level, but also provides a snapshot of their prevalence patterns in Croatia in order to underscore the potential implications of viral seasonality. An overall global prevalence in respiratory tract infections was found to be between 0.5 and 18.4% for seasonal coronaviruses, between 13 and 59% for rhinoviruses, between 1 and 36% for human adenoviruses, and between 1 and 56.8% for human bocaviruses. A Croatian dataset on patients with respiratory tract infection and younger than 18 years of age has revealed a fairly high prevalence of rhinoviruses (33.4%), with much lower prevalence of adenoviruses (15.6%), seasonal coronaviruses (7.1%), and bocaviruses (5.3%). These insights represent a relevant discussion point in the context of the COVID-19 pandemic where the testing of non-SARS-CoV-2 viruses has been limited in many settings, making the monitoring of disease burden associated with other respiratory viruses rather difficult.

Polyphenol-Rich Larix decidua Bark Extract with Antimicrobial Activity against Respiratory-Tract Pathogens: A Novel Bioactive Ingredient with Potential Pharmaceutical and Nutraceutical Applications

Larch (Larix decidua) bark is a sawmill waste, traditionally used for antiseptic, expectorant and dermatological (wound healing, eczema, psoriasis) purposes. In this work, we developed a food-grade dry larch bark extract (LBE) from sawmill by-products using hydro-alcoholic extraction. The antibacterial activity of LBE was evaluated against respiratory-tract pathogens, i.e., Staphylococcus aureus, Streptococcus pyogenes, Streptococcus pneumoniae, Klebsiella pneumoniae, Pseudomonas aeruginosa and Haemophilus influenza, and it was compared to that of grapefruit seed extract (GSE), a commercially available raw material commonly proposed as antibacterial ingredient for over-the-counter products. Procyanidins (PACs) and other polyphenols contents in LBE were determined by HPLC-FLD-MS and HPLC-DAD-MSⁿ, respectively. The antimicrobial activity of LBE and GSE was assessed using the micro-plate dilution technique in concentration range of 2-200 µg/mL, and the safety of these dosages was assessed in cellular and animal models. LBE showed considerable contents of PACs (15% w/w; especially B-type) and other polyphenols (3.8% w/w), among which the characteristic spiropolyphenols larixinol and epilarixinol were identified, together with the flavonoids isoquercitrin and rutin, already reported as growth inhibitors of different respiratory-tract pathogens. LBE showed higher antimicrobial activity compared to GSE, demonstrated by a growth inhibition range of 10-40% towards five of six strains tested, compared to 10-15% of GSE. These results suggest that LBE may represent a natural and sustainable source of active compounds with antibacterial activity for pharmaceutical and nutraceutical applications.