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Missa KF, Diallo K, Bla KB, Tuo KJ, Gboko KDT, Tiémélé LS, Ouattara AF, Gragnon BG, Ngoi JM, Wilkinson RJ, Awandare GA, Bonfoh B. Association of symptomatic upper respiratory tract infections with the alteration of the oropharyngeal microbiome in a cohort of school children in Côte d'Ivoire. Front Microbiol 2024; 15:1412923. [PMID: 38993497 PMCID: PMC11238735 DOI: 10.3389/fmicb.2024.1412923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 05/29/2024] [Indexed: 07/13/2024] Open
Abstract
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.
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Affiliation(s)
- Kouassi Firmin Missa
- Direction de la Recherche et du Développement, Centre Suisse de Recherches Scientifiques en Côte d'Ivoire, Abidjan, Côte d'Ivoire
- Laboratoire de Biologie et Santé, UFR Biosciences, Université Félix Houphouët Boigny de Cocody, Abidjan, Côte d'Ivoire
| | - Kanny Diallo
- Direction de la Recherche et du Développement, Centre Suisse de Recherches Scientifiques en Côte d'Ivoire, Abidjan, Côte d'Ivoire
- West African Centre for Cell Biology of Infectious Pathogens, Accra, Ghana
| | - Kouakou Brice Bla
- Laboratoire de Biologie et Santé, UFR Biosciences, Université Félix Houphouët Boigny de Cocody, Abidjan, Côte d'Ivoire
| | - Kolotioloman Jérémie Tuo
- Direction de la Recherche et du Développement, Centre Suisse de Recherches Scientifiques en Côte d'Ivoire, Abidjan, Côte d'Ivoire
- Laboratoire de Microbiologie, Biotechnologies et Bio-informatique, Institut National Polytechnique Félix Houphouët-Boigny, Yamoussoukro, Côte d'Ivoire
| | - Kossia Debia Thérèse Gboko
- Direction de la Recherche et du Développement, Centre Suisse de Recherches Scientifiques en Côte d'Ivoire, Abidjan, Côte d'Ivoire
| | - Laurent-Simon Tiémélé
- Direction de la Recherche et du Développement, Centre Suisse de Recherches Scientifiques en Côte d'Ivoire, Abidjan, Côte d'Ivoire
| | - Allassane Foungoye Ouattara
- Direction de la Recherche et du Développement, Centre Suisse de Recherches Scientifiques en Côte d'Ivoire, Abidjan, Côte d'Ivoire
- Laboratoire de Cytologie et Biologie Animale, Université Nangui Abrogoua, Abidjan, Côte d'Ivoire
| | - Biego Guillaume Gragnon
- Laboratoire de Cytologie et Biologie Animale, Université Nangui Abrogoua, Abidjan, Côte d'Ivoire
| | | | - Robert J Wilkinson
- Laboratoire National d'Appui au Développement Agricole, Laboratoire Régional de Korhogo, Korhogo, Côte d'Ivoire
- The Francis Crick Institute, London, United Kingdom
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Gordon A Awandare
- West African Centre for Cell Biology of Infectious Pathogens, Accra, Ghana
| | - Bassirou Bonfoh
- Direction de la Recherche et du Développement, Centre Suisse de Recherches Scientifiques en Côte d'Ivoire, Abidjan, Côte d'Ivoire
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Diallo K, Missa KF, Tuo JK, Amoikon TLS, Bla BK, Bonfoh B. Narrative review of application of metagenomic approaches to study the link between oropharyngeal microbiome and infectious diseases. Front Microbiol 2023; 14:1292526. [PMID: 38163063 PMCID: PMC10755466 DOI: 10.3389/fmicb.2023.1292526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 11/20/2023] [Indexed: 01/03/2024] Open
Abstract
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.
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Affiliation(s)
- Kanny Diallo
- Centre Suisse de Recherches Scientifiques en Côte d’Ivoire (CSRS), Abidjan, Côte d’Ivoire
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
| | - Kouassi Firmin Missa
- Centre Suisse de Recherches Scientifiques en Côte d’Ivoire (CSRS), Abidjan, Côte d’Ivoire
- Université Félix Houphouët Boigny de Cocody, Abidjan, Côte d’Ivoire
| | - Jeremie Kolotioloman Tuo
- Centre Suisse de Recherches Scientifiques en Côte d’Ivoire (CSRS), Abidjan, Côte d’Ivoire
- Institut National Polytechnique Félix Houphouët-Boigny (INP-HB), Yamoussoukro, Côte d’Ivoire
| | | | - Brice K. Bla
- Université Félix Houphouët Boigny de Cocody, Abidjan, Côte d’Ivoire
| | - Bassirou Bonfoh
- Centre Suisse de Recherches Scientifiques en Côte d’Ivoire (CSRS), Abidjan, Côte d’Ivoire
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Wang X, Shao Z, Zhu M, Li B, You M, Chen X. The correlation of the intestinal with pharyngeal microbiota in early neonates. Front Microbiol 2023; 14:1225352. [PMID: 37601350 PMCID: PMC10434775 DOI: 10.3389/fmicb.2023.1225352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 07/11/2023] [Indexed: 08/22/2023] Open
Abstract
Introduction The gut-lung axis has long been recognized as an important mechanism affecting intestinal and lung immunity. Still, few studies have examined the correlation between the intestinal and pharyngeal microbiota in early neonates, especially when feeding patterns are one of the main drivers of microbiota development. Methods To explore the composition and function of intestinal and pharyngeal microbiota and to analyze the effect of limited formula feeding on the initial microbiota colonization in early full-term neonates, we characterized the stool and oropharyngeal microbiota of 20 healthy full-term newborns sampled on days 0 and 5-7 after birth using 16S rRNA gene sequencing. Based on the sequencing results, a comparison was made of the compositions and functions of the intestinal and oropharyngeal microbiota for analysis. Results and discussion At the phylum level, Firmicutes, Actinobacteria, Proteobacteria, and Bacteroidetes were the most abundant in both niches. At the genus level, the species of pioneer bacteria were rich in the intestine and oropharynx but low in abundance on day 0. On days 5-7, Bifidobacterium (25.40%) and Escherichia-Shigella (22.16%) were dominant in the intestine, while Streptococcus (38.40%) and Staphylococcus (23.13%) were dominant in the oropharynx. There were eight core bacteria genera in the intestine and oropharynx on days 5-7, which were Bifidobacterium, Escherichia-Shigella, Staphylococcus, Streptococcus, Bacteroides, Parabacteroides, Rothia, and Acinetobacter. As indicated by PICRUSt analysis, on days 5-7, the intestinal microbiota was more predictive than the oropharyngeal microbiota in transcription, metabolism, cell motility, cellular processes and signaling, and organismal system function in the KEGG pathway. Compared to exclusive breastfeeding, limited formula feeding (40-60%) had no significant effect on the neonatal intestinal and oropharyngeal microbiota composition during the initial colonization period. Our results suggest that the initial colonization of microbiota is closely related to the ecological niche environment in the intestine and oropharynx, with their core microbiota being closely correlated. We found that early limited formula feeding could not significantly affect the initial colonization of microbiota in the intestine and oropharynx.
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Affiliation(s)
- Xuejuan Wang
- Department of Neonatal, Shanghai Pudong New Area Health Maternal and Child Health Hospital, Shanghai, China
- Department of Pediatric, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Zhiying Shao
- Department of Neonatal, Shanghai Pudong New Area Health Maternal and Child Health Hospital, Shanghai, China
| | - Minrong Zhu
- Department of Neonatal, Shanghai Pudong New Area Health Maternal and Child Health Hospital, Shanghai, China
| | - Bingjie Li
- Department of Pediatric, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Mingyu You
- Department of Pediatric, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xiaoqing Chen
- Department of Pediatric, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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Next-Generation Sequencing Results Vary Between Cultured and Uncultured Microbes. Curr Microbiol 2022; 79:187. [PMID: 35524899 DOI: 10.1007/s00284-022-02865-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 04/05/2022] [Indexed: 11/03/2022]
Abstract
Next-generation sequencing (NGS) technology has led to innovations in environmental metagenomics and investigations involving humans and microbes. However, it is necessary to analyze the components that will affect analysis of the method upon processing a large amount of information. In particular, the processing method after sample collection affects the NGS results, and it is necessary to check for inaccurate results. Here, we show that the microbial communities obtained from fingertip samples differ from those obtained from fingertips remaining on mobile phones and desks, when cultured or not for 24 h. We also confirmed changes in microbial communities in fingertip samples from desks incubated for 2, 4, 8, 16, and 24 h. Samples of prints from mobile phones that are considerably vulnerable to external factors were not analyzed. Ratios of Firmicutes and Bacillus were, respectively, increased in cultures at the phylum and species levels. Collectively, we identified bacterial species that can aid in determining whether a sample has been cultured. In addition, although microbial communities differed depending on sample types, we confirmed changes after culture for 4 and 8 h. However, since this study is a sample limited to three types, it is necessary to analyze other types of samples in the same way and check whether they are applicable to all types. This strategy can verify the suitability of samples for deriving informative results from cultured or uncultured bacterial communities.
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Wang X, Xu X, Chen Y, Li Z, Zhang M, Zhao C, Lian B, Zhao J, Guo Y, Liu Q. Liu Shen Capsule Alters Airway Microbiota Composition and Metabolite Profiles in Healthy Humans. Front Pharmacol 2022; 12:824180. [PMID: 35153770 PMCID: PMC8831732 DOI: 10.3389/fphar.2021.824180] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 12/31/2021] [Indexed: 12/31/2022] Open
Abstract
Alteration in airway microbiota composition and perturbations in microbe-metabolites interactions have been proposed as markers of many diseases. Liu Shen (LS) capsule, a traditional Chinese medicine, was proved as favorable in treating respiratory diseases. However, the effects of the LS capsule in terms of regulating human microorganisms and metabolite profiles are not well known. This study aimed to define and compare the respiratory microbiota composition and circulating and fecal metabolite profiles before and after LS capsule administration. A total of 30 healthy volunteers were recruited. The pharyngeal swab samples were collected for 16S rRNA gene sequencing. The serum and fecal samples were collected to analyze the non-targeted ultra-performance liquid chromatography–tandem mass spectrometry metabolomics. The airway microbial compositions were profoundly altered after LS capsule administration, as evidenced by increased microbial diversity and altered microbial taxa distribution. The increasing abundance of bacterial Bifidobacteria, and Lactobacillus characterized the after-administration groups, and the increasing of abundance bacterial Proteobacteria, Veillonella, Prevotella, Neisseria, and Actinomyces characterized the before-administration groups. Significant discriminations were observed in both serum and fecal metabolic profiles between the before- and after-administration groups. A total number of 134 and 71 significant HMDB taxonomic metabolites including glycerophospholipids, fatty acyls, and prenol lipids in the serum and fecal samples were identified respectively between the before- and after-administration groups. The integrated analysis showed that some altered airway microbiota phylum, such as Bacteroidetes and Proteobacteria, significantly correlated with metabolites in serum and fecal. Hence, our study reported the alternations in the composition and functions of the airway microbial community and the changes in circulating and fecal metabolite profiles after LS capsule administration in healthy humans, thus providing a novel insight into the mechanisms underlying the role of LS capsule treating and preventing related diseases.
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Affiliation(s)
- Xuerui Wang
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Basic Research with Traditional Chinese Medicine on Infectious Diseases, Beijing, China
- Beijing Institute of Chinese Medicine, Beijing, China
| | - Xiaolong Xu
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Basic Research with Traditional Chinese Medicine on Infectious Diseases, Beijing, China
- Beijing Institute of Chinese Medicine, Beijing, China
| | - Yishan Chen
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Zhenxuan Li
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Mina Zhang
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Chunxia Zhao
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Bo Lian
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Jingxia Zhao
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, China
- Beijing Institute of Chinese Medicine, Beijing, China
| | - Yuhong Guo
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Qingquan Liu
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Basic Research with Traditional Chinese Medicine on Infectious Diseases, Beijing, China
- Beijing Institute of Chinese Medicine, Beijing, China
- *Correspondence: Qingquan Liu,
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Loman BR, Shrestha CL, Kotha K, Minta A, Zhang S, Mejias A, Bailey MT, Creary S, Kopp BT. Upper airway microbiome changes in children with sickle cell disease during vaso-occlusive and acute chest syndrome episodes. Am J Hematol 2020; 95:E289-E292. [PMID: 32644239 DOI: 10.1002/ajh.25931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/02/2020] [Accepted: 07/06/2020] [Indexed: 11/11/2022]
Affiliation(s)
- Brett R Loman
- Center for Microbial Pathogenesis, The Abigail Wexner Research Institute, Columbus, Ohio
| | - Chandra L Shrestha
- Center for Microbial Pathogenesis, The Abigail Wexner Research Institute, Columbus, Ohio
| | - Kavitha Kotha
- Division of Pulmonary Medicine, Nationwide Children's Hospital, Columbus, Ohio
| | - Abena Minta
- Center for Microbial Pathogenesis, The Abigail Wexner Research Institute, Columbus, Ohio
| | - Shuzhong Zhang
- Center for Microbial Pathogenesis, The Abigail Wexner Research Institute, Columbus, Ohio
| | - Asuncion Mejias
- Center for Vaccines and Immunity, The Abigail Wexner Research Institute, Columbus, Ohio
| | - Michael T Bailey
- Center for Microbial Pathogenesis, The Abigail Wexner Research Institute, Columbus, Ohio
| | - Susan Creary
- Center for Innovation in Pediatric Practice, The Abigail Wexner Research Institute, Columbus, Ohio
- Division of Hematology/Oncology/BMT, Nationwide Children's Hospital, Columbus, Ohio
| | - Benjamin T Kopp
- Center for Microbial Pathogenesis, The Abigail Wexner Research Institute, Columbus, Ohio
- Division of Pulmonary Medicine, Nationwide Children's Hospital, Columbus, Ohio
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Maleki A, Mirnaseri Z, Kouhsari E, Taherikalani M, Pakzad I, Mohammadi J, Sadeghifard N. Asymptomatic carriers of Neisseria meningitidis and Moraxella catarrhalis in healthy children. New Microbes New Infect 2020; 36:100691. [PMID: 32514361 PMCID: PMC7267740 DOI: 10.1016/j.nmni.2020.100691] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 04/19/2020] [Accepted: 05/02/2020] [Indexed: 12/17/2022] Open
Abstract
There is a close correlation between asymptomatic oropharyngeal colonization by bacterial pathogens and paediatric respiratory diseases. Evaluation of the frequency of asymptomatic carriers of Neisseria meningitidis and Moraxella catarrhalis in healthy children was the main aim of the current study. In this cross-sectional study, 123 oropharyngeal swabs were collected from children between 2 and 6 years old in kindergartens of Ilam, Iran. Moraxella catarrhalis and N. meningitidis were identified using phenotypic and genotypic assays. In addition, the occurrence of the virulence factors (ctrA and uspA1) and iron uptake (tbpA) genes was evaluated by PCR. Results showed that 21 M. catarrhalis isolates and 17 N. meningitidis isolates were identified by conventional microbiological and biochemical methods, but the RT-PCR assay detected that 18 and 8 isolates were positive for M. catarrhalis and N. meningitidis, respectively. The tbpA gene was positive in all N. meningitidis and M. catarrhalis isolates. Seven isolates were positive for the ctrA gene in N. meningitidis and seven isolates were positive for the uspA1 gene in M. catarrhalis. These pathogenic bacteria often occurred as asymptomatic carriage of N. meningitidis in children from large families with low economic status, which reflects the importance of the environment and socio-economic level of families in the distribution of these potentially pathogenic bacteria in the oropharynx of children. Monitoring for the carriage of potential pathogenic bacteria in the nasopharynx of healthy children is important as this can predispose to infectious diseases; common exposure to human respiratory bacterial pathogens is a further risk factor.
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Affiliation(s)
- A. Maleki
- Clinical Microbiology Research Centre, Ilam University of Medical Sciences, Ilam, Iran
| | - Z. Mirnaseri
- Clinical Microbiology Research Centre, Ilam University of Medical Sciences, Ilam, Iran
| | - E. Kouhsari
- Clinical Microbiology Research Centre, Ilam University of Medical Sciences, Ilam, Iran
| | - M. Taherikalani
- Razi Herbal Medicines Research Centre & Department of Microbiology, School of Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran
| | - I. Pakzad
- Clinical Microbiology Research Centre, Ilam University of Medical Sciences, Ilam, Iran
| | - J. Mohammadi
- Clinical Microbiology Research Centre, Ilam University of Medical Sciences, Ilam, Iran
| | - N. Sadeghifard
- Clinical Microbiology Research Centre, Ilam University of Medical Sciences, Ilam, Iran
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