Association of symptomatic upper respiratory tract infections with the alteration of the oropharyngeal microbiome in a cohort of school children in Côte d'Ivoire.

Introduction: The oropharyngeal microbiome plays an important role in protection against infectious agents when in balance. Despite use of vaccines and antibiotic therapy to prevent respiratory tract infections, they remain one of the major causes of mortality and morbidity in Low- and middle-income countries. Hence the need to explore other approaches to prevention by identifying microbial biomarkers that could be leveraged to modify the microbiota in order to enhance protection against pathogenic bacteria. The aim of this study was to analyze the oropharyngeal microbiome (OPM) of schoolchildren in Côte d'Ivoire presenting symptoms of upper respiratory tract infections (URTI) for better prevention strategy. Methods: Primary schools' children in Korhogo (n = 37) and Abidjan (n = 39) were followed for six months with monthly oropharyngeal sampling. Clinical diagnostic of URT infection was performed and nucleic acid extracted from oropharyngeal swabs were used for 16S rRNA metagenomic analysis and RT-PCR. Results: The clinical examination of children's throat in Abidjan and Korhogo identified respectively 17 (43.59%) and 15 (40.54%) participants with visible symptoms of URTIs, with 26 episodes of infection in Abidjan and 24 in Korhogo. Carriage of Haemophilus influenzae (12%), Streptococcus pneumoniae (6%) and SARS-CoV-2 (6%) was confirmed by PCR. A significant difference in alpha diversity was found between children colonized by S. pneumoniae and those that were not (p = 0.022). There was also a significant difference in alpha diversity between children colonised with H. influenzae and those who were not (p = 0.017). No significant difference was found for SARS-CoV-2. Sphingomonas, Ralstonia and Rothia were significantly enriched in non-carriers of S. pneumoniae; Actinobacillus was significantly enriched in non-carriers of H. influenzae; Actinobacillus and Porphyromonas were significantly enriched in non-carriers of SARS-CoV-2 (p < 0.001). Discussion: Nearly 40% of children showed clinical symptoms of infection not related to geographical location. The OPM showed an imbalance during H. influenzae and S. pneumoniae carriage. This study provides a baseline understanding of microbiome markers in URTIs in children for future research, to develop targeted interventions aimed at restoring the microbial balance and reducing the symptoms associated with RTIs.

Narrative review of application of metagenomic approaches to study the link between oropharyngeal microbiome and infectious diseases.

Context: Viral and bacterial infections are major causes of morbidity and mortality worldwide. The oropharyngeal microbiome could play an important role in preventing invasion of viral and bacterial pathogens by modulating its content and the host's innate immune response. Next Generation Sequencing (NGS) technologies now enable in-depth study of the genomes of microbial communities. The objective of this review is to highlight how metagenomics has contributed to establish links between changes in the oropharyngeal microbiome and emergence of bacterial and viral diseases. Method: Two search engines, PubMed and Google scholar were used with filters to focus searches on peer-reviewed original articles published between January 2010 and September 2022. Different keywords were used and only articles with metagenomic approaches were included. Results: This review shows that there were few articles studying the link between oropharyngeal microbiome and infectious diseases. Studies on viruses using metagenomic techniques have been growing exponentially in recent years due to the Covid-19 pandemic. This review shows that most studies still focus on the basic identification of microorganisms in different disease states and multiple microorganisms (Alloprevotella, Prevotella, Bacteroides, Haemophilus, Streptococcus, Klebsiella sp., Acinetobacter sp…), have been associated with development of infections such as childhood wheezing, influenza, Covid-19, pneumonia, meningitis, and tuberculosis. Conclusion: The oropharyngeal microbiome, despite its importance, remains poorly studied. A limited number of articles were identified but this number has increased exponentially since 2020 due to research conducted on Covid-19. These studies have shown that metagenomic has contributed to the unbiased identification of bacteria that could be used as biomarkers of various diseases and that further research is now needed to capitalize on those findings for human health benefit.

Factors associated with acute malnutrition among children aged 6-59 months in Haiti, Burkina Faso and Madagascar: A pooled analysis.

BACKGROUND: Acute malnutrition is one of the main causes of morbidity and mortality among children under 5 years worldwide, and Action Contre la Faim (ACF) aims to address its causes and consequences. To better tailor humanitarian programs, ACF conducts standardized contextual studies called Link NCAs (Nutrition Causal Analysis), to identify factors associated with severe acute malnutrition (SAM) and moderate acute malnutrition (MAM). Data from three Link NCAs performed in 2018 and 2019 in Haiti, Burkina Faso and Madagascar were used to explore the prevalence of malnutrition by different indicators and associated risk factors among children aged 6-59 months. METHODS: Cross-sectional data, collected via household surveys applying two-stage cluster sampling, were pooled to build a sample of 1,356 children. Recommended anthropometric thresholds were used to define SAM (Weight-for-Height Z-score (WHZ) <-3 or Mid-upper Arm Circumference (MUAC) <115 mm and/or presence oedema), MAM (-3≤WHZ<-2 or 115≤MUAC<125 mm) and global acute malnutrition GAM (SAM or MAM) among children. Multivariate analyses for each anthropometric indicator were performed using logistic mixed models and adjusting for potential confounders. RESULTS: The prevalence of acute malnutrition was the highest in Madagascar. The risk of having GAM and MAM varied across countries, while the risk of having SAM varied across clusters. Being male, suffering from diarrhea, and having unwashed face and hands, were significantly associated with GAM by WHZ with adjusted odds ratio of 1.9 [95%Confidence interval (CI):1.1-3.2], 1.7 (95%CI: 1.0-3.1) and 1.9 (95%CI: 1.0-3.6) respectively. These factors were also associated with MAM by WHZ. None of the studied factors was significantly associated with SAM, which could be due to a small sample size. CONCLUSION: These results obtained from a large sample contribute to the evidence of the factors associated with undernutrition in children aged 6-59 months. Further research with larger sample sizes is needed to confirm these results.

Mothers' and health workers' exposure to breastmilk substitutes promotions in Abidjan, Côte d'Ivoire.

Marketing of breastmilk substitutes (BMS) continues to undermine breastfeeding globally, and low income countries experiencing rapid economic growth are especially vulnerable as expanding BMS markets. The objective of the study was to understand the prevalence of exposure to BMS promotions among mothers of children 0-23 months, the frequency and type of contacts between BMS companies and health workers and the presence of educational/informational materials and branded equipment associated with such companies in health facilities in Abidjan using the World Health Organization's NetCode protocol. The methods included structured interviews with health workers and mothers and observations of equipment/materials in a sample of 42 facilities, 330 mothers and 129 health workers. Descriptive statistics were produced, and chi-squared tests were used to assess differences by child age and facility type. Forty-three per cent of mothers were advised to feed BMS products in the past 6 months, with a significantly higher percentage of mothers of older children (6-23 months) advised compared to infants 0-5 months. Two thirds (66%) of mothers had seen promotions outside of facilities. Among health workers, 63% were contacted by BMS companies, and only 8% were familiar with the International Code of Marketing of BMS. Differences were found between public/private facilities in the types of requests BMS companies made to health workers. Strong actions are needed in Côte d'Ivoire to prevent BMS promotion in the health system, including increasing health workers' knowledge of the International Code and national regulations, monitoring violations and reaching mothers and families to promote optimal breastfeeding practices.