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Ulanova M, Tsang RSW, Goldfarb DM, Smieja M, Huska B, Luinstra K, Le Saux N. Prevalence of Haemophilus influenzae in the nasopharynx of children from regions with varying incidence of invasive H. influenzae serotype a disease: Canadian Immunization Research Network (CIRN) study. Int J Circumpolar Health 2024; 83:2371111. [PMID: 38941555 PMCID: PMC11216270 DOI: 10.1080/22423982.2024.2371111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Accepted: 06/18/2024] [Indexed: 06/30/2024] Open
Abstract
Haemophilus influenzae serotype a (Hia) has recently emerged as an important cause of invasive disease in the North American Arctic and Sub-Arctic regions, mainly affecting young Indigenous children. In this study, we addressed the question of whether the prevalence of Hia and all H. influenzae in the nasopharynx differed between paediatric populations from regions with high versus low incidence of invasive Hia disease. Nasopharyngeal specimens from children with acute respiratory tract infections (ARTI) collected for routine diagnostic detection of respiratory viruses were analysed with molecular-genetic methods to identify and serotype H. influenzae. In Nunavut, a region with a high incidence of invasive Hia disease, all H. influenzae and particularly Hia were found in the nasopharynx of 60.6% and 3.0% children. In Southern Ontario (Hamilton region), where Hia invasive disease is rare, the frequencies of all H. influenzae and Hia detection were 38.5% and 0.6%, respectively. In both cohorts, non-typeable H. influenzae was prevalent (57.0% and 37.9%, respectively). Considering that Hia is an important cause of severe invasive disease in Nunavut children, 3% prevalence of Hia among children with ARTI can reflect continuing circulation of the pathogen in the Northern communities that may result in invasive disease outbreaks.
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Affiliation(s)
- Marina Ulanova
- Medical Sciences, NOSM University, Thunder Bay, ON, Canada
| | - Raymond SW Tsang
- Vaccine Preventable Bacterial Diseases, National Microbiology Laboratory Branch, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - David M. Goldfarb
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Marek Smieja
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
- Virology, Hamilton Regional Laboratory Medicine Association, St. Joseph’s Healthcare, Hamilton, ON, Canada
| | - Brenda Huska
- Medical Sciences, NOSM University, Thunder Bay, ON, Canada
| | - Kathy Luinstra
- Virology, Hamilton Regional Laboratory Medicine Association, St. Joseph’s Healthcare, Hamilton, ON, Canada
| | - Nicole Le Saux
- Division of Infectious Disease, University of Ottawa, Ottawa, ON, Canada
- Division of Infectious Diseases, Children’s Hospital of Eastern Ontario (CHEO), Ottawa, ON, Canada
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2
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Sandybayev N, Beloussov V, Strochkov V, Solomadin M, Granica J, Yegorov S. Metagenomic profiling of nasopharyngeal samples from adults with acute respiratory infection. ROYAL SOCIETY OPEN SCIENCE 2024; 11:240108. [PMID: 39076360 PMCID: PMC11286146 DOI: 10.1098/rsos.240108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 05/20/2024] [Indexed: 07/31/2024]
Abstract
Diagnosis of acute respiratory infections (ARIs) is challenging due to the broad diversity of potential microbial causes. We used metagenomic next-generation sequencing (mNGS) to analyze the nasopharyngeal virome of ARI patients, who had undergone testing with a clinical multiplex PCR panel (Amplisens ARVI-screen-FRT). We collected nasopharyngeal swabs from 49 outpatient adults, 32 of whom had ARI symptoms and were PCR-positive, and 4 asymptomatic controls in Kazakhstan during Spring 2021. We assessed the biodiversity of the mNGS-derived virome and concordance with PCR results. PCR identified common ARI viruses in 65% of the symptomatic cases. mNGS revealed viral taxa consisting of human, non-human eukaryotic and bacteriophage groups, comprising 15, 11 and 28 genera, respectively. Notable ARI-associated human viruses included rhinovirus (16.3%), betaherpesvirus 7 (14.3%) and Epstein-Barr virus (8.16%). The primary phage hosts were Streptococcus spp. (32.7%), Pseudomonas aeruginosa (24.5%) and Burkholderia spp. (20.4%). In total, 47% of ARIs were linked solely to bacterial pathogens, a third to viral-bacterial co-infections, and less than 10% to only viral infections by mNGS. PCR showed low concordance with mNGS, except for rhinovirus. These results underscore the importance of broad diagnostic methods and question the effectiveness of commonly used PCR panels in ARI diagnosis.
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Affiliation(s)
- Nurlan Sandybayev
- Kazakhstan-Japan Innovation Centre, Kazakh National Agrarian Research University (KazNARU), Almaty, Kazakhstan
| | - Vyacheslav Beloussov
- Kazakhstan-Japan Innovation Centre, Kazakh National Agrarian Research University (KazNARU), Almaty, Kazakhstan
- TreeGene Molecular Genetics Laboratory, Almaty, Kazakhstan
| | - Vitaliy Strochkov
- Kazakhstan-Japan Innovation Centre, Kazakh National Agrarian Research University (KazNARU), Almaty, Kazakhstan
| | - Maxim Solomadin
- School of Pharmacy, Karaganda Medical University, Karaganda, Kazakhstan
| | - Joanna Granica
- TreeGene Molecular Genetics Laboratory, Almaty, Kazakhstan
| | - Sergey Yegorov
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster Immunology Research Centre; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Department of Biology, School of Sciences and Humanities, Nazarbayev University, Astana, Kazakhstan
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3
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Perdijk O, Azzoni R, Marsland BJ. The microbiome: an integral player in immune homeostasis and inflammation in the respiratory tract. Physiol Rev 2024; 104:835-879. [PMID: 38059886 DOI: 10.1152/physrev.00020.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 11/07/2023] [Accepted: 11/30/2023] [Indexed: 12/08/2023] Open
Abstract
The last decade of microbiome research has highlighted its fundamental role in systemic immune and metabolic homeostasis. The microbiome plays a prominent role during gestation and into early life, when maternal lifestyle factors shape immune development of the newborn. Breast milk further shapes gut colonization, supporting the development of tolerance to commensal bacteria and harmless antigens while preventing outgrowth of pathogens. Environmental microbial and lifestyle factors that disrupt this process can dysregulate immune homeostasis, predisposing infants to atopic disease and childhood asthma. In health, the low-biomass lung microbiome, together with inhaled environmental microbial constituents, establishes the immunological set point that is necessary to maintain pulmonary immune defense. However, in disease perturbations to immunological and physiological processes allow the upper respiratory tract to act as a reservoir of pathogenic bacteria, which can colonize the diseased lung and cause severe inflammation. Studying these host-microbe interactions in respiratory diseases holds great promise to stratify patients for suitable treatment regimens and biomarker discovery to predict disease progression. Preclinical studies show that commensal gut microbes are in a constant flux of cell division and death, releasing microbial constituents, metabolic by-products, and vesicles that shape the immune system and can protect against respiratory diseases. The next major advances may come from testing and utilizing these microbial factors for clinical benefit and exploiting the predictive power of the microbiome by employing multiomics analysis approaches.
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Affiliation(s)
- Olaf Perdijk
- Department of Immunology, School of Translational Science, Monash University, Melbourne, Victoria, Australia
| | - Rossana Azzoni
- Department of Immunology, School of Translational Science, Monash University, Melbourne, Victoria, Australia
| | - Benjamin J Marsland
- Department of Immunology, School of Translational Science, Monash University, Melbourne, Victoria, Australia
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4
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Li R, Li J, Zhou X. Lung microbiome: new insights into the pathogenesis of respiratory diseases. Signal Transduct Target Ther 2024; 9:19. [PMID: 38228603 DOI: 10.1038/s41392-023-01722-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 10/25/2023] [Accepted: 11/22/2023] [Indexed: 01/18/2024] Open
Abstract
The lungs were long thought to be sterile until technical advances uncovered the presence of the lung microbial community. The microbiome of healthy lungs is mainly derived from the upper respiratory tract (URT) microbiome but also has its own characteristic flora. The selection mechanisms in the lung, including clearance by coughing, pulmonary macrophages, the oscillation of respiratory cilia, and bacterial inhibition by alveolar surfactant, keep the microbiome transient and mobile, which is different from the microbiome in other organs. The pulmonary bacteriome has been intensively studied recently, but relatively little research has focused on the mycobiome and virome. This up-to-date review retrospectively summarizes the lung microbiome's history, composition, and function. We focus on the interaction of the lung microbiome with the oropharynx and gut microbiome and emphasize the role it plays in the innate and adaptive immune responses. More importantly, we focus on multiple respiratory diseases, including asthma, chronic obstructive pulmonary disease (COPD), fibrosis, bronchiectasis, and pneumonia. The impact of the lung microbiome on coronavirus disease 2019 (COVID-19) and lung cancer has also been comprehensively studied. Furthermore, by summarizing the therapeutic potential of the lung microbiome in lung diseases and examining the shortcomings of the field, we propose an outlook of the direction of lung microbiome research.
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Affiliation(s)
- Ruomeng Li
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Jing Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, China.
| | - Xikun Zhou
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China.
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5
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Bhagchandani T, Nikita, Verma A, Tandon R. Exploring the Human Virome: Composition, Dynamics, and Implications for Health and Disease. Curr Microbiol 2023; 81:16. [PMID: 38006423 DOI: 10.1007/s00284-023-03537-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 10/24/2023] [Indexed: 11/27/2023]
Abstract
Humans are colonized by large number of microorganisms-bacteria, fungi, and viruses. The overall genome of entire viruses that either lives on or inside the human body makes up the human virome and is indeed an essential fraction of the human metagenome. Humans are constantly exposed to viruses as they are ubiquitously present on earth. The human virobiota encompasses eukaryotic viruses, bacteriophages, retroviruses, and even giant viruses. With the advent of Next-generation sequencing (NGS) and ongoing development of numerous bioinformatic softwares, identification and taxonomic characterization of viruses have become easier. The viruses are abundantly present in humans; these can be pathogenic or commensal. The viral communities occupy various niches in the human body. The viruses start colonizing the infant gut soon after birth in a stepwise fashion and the viral composition diversify according to their feeding habits. Various factors such as diet, age, medications, etc. influence and shape the human virome. The viruses interact with the host immune system and these interactions have beneficial or detrimental effects on their host. The virome composition and abundance change during the course of disease and these alterations impact the immune system. Hence, the virome population in healthy and disease conditions influences the human host in numerous ways. This review presents an overview of assembly and composition of the human virome in healthy asymptomatic individuals, changes in the virome profiles, and host-virome interactions in various disease states.
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Affiliation(s)
- Tannu Bhagchandani
- Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Nikita
- Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Anjali Verma
- Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Ravi Tandon
- Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India.
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6
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Hong S, Li D, Wei Y, Zheng Y, Cai J, Zheng H, Zhang X, Deng Y, Han D, Wang J, Chen L, Li S, Qiu W, Ren M, Zou L. Epidemiology of respiratory pathogens in patients with acute respiratory tract infection in Xiamen, China: A retrospective survey from 2020 to 2022. Heliyon 2023; 9:e22302. [PMID: 38053876 PMCID: PMC10694312 DOI: 10.1016/j.heliyon.2023.e22302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 11/08/2023] [Accepted: 11/09/2023] [Indexed: 12/07/2023] Open
Abstract
Acute respiratory tract infections (ARTI) are caused by respiratory pathogens and range from asymptomatic infections to severe respiratory diseases. These diseases can be life threatening with high morbidity and mortality worldwide. Under the pandemic of coronavirus disease 2019 (COVID-19), little has been reported about the pathogen etiologies and epidemiology of patients suffering from ARTI of all age in Xiamen. Region-specific surveillance in individuals with ARTI of all ages was performed in Xiamen from January 2020 to October 2022. Here, we observed the epidemiological characteristics of thirteen pathogens within ARTI patients and further revealed the difference of that between upper respiratory tract infections (URTI) and lower respiratory tract infections (LRTI). In total 56.36 % (2358/4184) of the ARTI patients were positive for at least one respiratory pathogen. Rhinovirus (RVs, 29.22 %), influenza A (FluA, 19.59 %), respiratory syncytial virus (RSV, 18.36 %), metapneumovirus (MPV, 13.91 %), and adenovirus (ADV, 10.31 %) were the five leading respiratory pathogens. Respiratory pathogens displayed age- and season-specific patterns, even between URTI and LRTI. Compared with other groups, a higher proportion of FluA (52.17 % and 68.75 %, respectively) infection was found in the adult group and the elder group, while the lower proportion of RVs (14.11 % and 11.11 %) infection was also observed in them. Although ARTI cases circulated throughout the year, RVs, FluB, and BoV peaked in autumn, and FluA circulated more in summer. Besides, the co-infectious rate was 8.7 % with the most common for RVs. Logistic regression analyses revealed the correlations between respiratory pathogens and disease types. These results are essential for replenishing epidemiological characteristics of common respiratory pathogens that caused ARTI in Xiamen during the epidemic of COVID-19, and a better understanding of it might optimize the local prevention and clinical control.
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Affiliation(s)
- Shan Hong
- Department of Pediatrics, The Fifth Hospital of Xiamen, Xiamen, Fujian, China
| | - Dan Li
- Key Laboratory of Digital Technology in Medical Diagnostics of Zhejiang Province, Dian Diagnostics Group Co., Ltd., Hangzhou, Zhejiang, China
| | - Yanli Wei
- Department of General Practice, The Fifth Hospital of Xiamen, Xiamen, Fujian, China
| | - Yilin Zheng
- Department of Pediatrics, The Fifth Hospital of Xiamen, Xiamen, Fujian, China
| | - Jiading Cai
- Department of General Practice, The Fifth Hospital of Xiamen, Xiamen, Fujian, China
| | - Heping Zheng
- Department of Intensive Care Unit, The Fifth Hospital of Xiamen, Xiamen, Fujian, China
| | - Xuan Zhang
- Key Laboratory of Digital Technology in Medical Diagnostics of Zhejiang Province, Dian Diagnostics Group Co., Ltd., Hangzhou, Zhejiang, China
| | - Yulin Deng
- Department of Pediatrics, The Fifth Hospital of Xiamen, Xiamen, Fujian, China
| | - Dandan Han
- Department of Pediatrics, The Fifth Hospital of Xiamen, Xiamen, Fujian, China
| | - Jia Wang
- Department of Pediatrics, The Fifth Hospital of Xiamen, Xiamen, Fujian, China
| | - Linlin Chen
- Department of Pediatrics, The Fifth Hospital of Xiamen, Xiamen, Fujian, China
| | - Shujing Li
- Department of Pediatrics, The Fifth Hospital of Xiamen, Xiamen, Fujian, China
| | - Weiping Qiu
- Department of General Practice, The Fifth Hospital of Xiamen, Xiamen, Fujian, China
| | - Min Ren
- Department of Pediatrics, The Fifth Hospital of Xiamen, Xiamen, Fujian, China
| | - Liangneng Zou
- Department of General Practice, The Fifth Hospital of Xiamen, Xiamen, Fujian, China
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7
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Mattila S, Sarlin S, Heikkilä R, Leinonen E, Nurmi V, Riikonen J, Paalanne N, Honkila M, Huhtamäki H, Pokka T, Koskela U, Renko M, Tapiainen T. Nasopharyngeal detection of atypical bacteria by multiplex polymerase chain reaction panel in acutely ill children was associated with an increased risk of pneumonia. Acta Paediatr 2023; 112:830-836. [PMID: 36644932 DOI: 10.1111/apa.16672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/10/2023] [Accepted: 01/13/2023] [Indexed: 01/17/2023]
Abstract
AIM We aimed to assess whether detection of respiratory bacteria by multiplex polymerase chain reaction (PCR) testing associates with clinical outcomes in acutely ill children. METHODS This cross-sectional study enrolled children under the age of 18 with a suspected respiratory infection treated in a paediatric emergency department of Oulu University Hospital, Finland from January 2015 through December 2015. Nasopharyngeal samples were routinely analysed for 16 respiratory viruses and later, after storage, analysed with a multiplex PCR panel for seven respiratory bacteria. RESULTS At least one bacterial pathogen was detected in 600 out of the 1195 children (50%). The mean age was 3.3 (SD 3.7) years and 54% were boys. Atypical bacteria were associated with a risk of pneumonia (adjusted odds ratio [aOR] 14.1, 95% CI 3.98-50.1). Co-detection of rhinovirus with Streptococcus pneumoniae was not associated with risk of pneumonia (aOR 2.39, 95% CI 0.78-7.30). Detection of Streptococcus pneumoniae, Haemophilus influenzae or both was not associated with the risk of hospital admission or prescription of antibiotics. CONCLUSION Nasopharyngeal detection of atypical bacteria in acutely ill children was associated with a markedly increased risk of pneumonia. The clinical utility of wide testing for other respiratory bacteria needs further evaluation.
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Affiliation(s)
- Suvi Mattila
- Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Oulu, Finland.,Research Unit of Clinical Medicine and Medical Research Center Oulu, University of Oulu, Oulu, Finland
| | - Suvi Sarlin
- Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Oulu, Finland.,Research Unit of Clinical Medicine and Medical Research Center Oulu, University of Oulu, Oulu, Finland
| | - Reetta Heikkilä
- Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Oulu, Finland
| | - Emilia Leinonen
- Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Oulu, Finland
| | - Violetta Nurmi
- Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Oulu, Finland
| | - Jonni Riikonen
- Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Oulu, Finland
| | - Niko Paalanne
- Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Oulu, Finland.,Research Unit of Clinical Medicine and Medical Research Center Oulu, University of Oulu, Oulu, Finland
| | - Minna Honkila
- Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Oulu, Finland.,Research Unit of Clinical Medicine and Medical Research Center Oulu, University of Oulu, Oulu, Finland
| | - Heikki Huhtamäki
- Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Oulu, Finland.,Research Unit of Clinical Medicine and Medical Research Center Oulu, University of Oulu, Oulu, Finland
| | - Tytti Pokka
- Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Oulu, Finland.,Research Unit of Clinical Medicine and Medical Research Center Oulu, University of Oulu, Oulu, Finland
| | - Ulla Koskela
- Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Oulu, Finland.,Research Unit of Clinical Medicine and Medical Research Center Oulu, University of Oulu, Oulu, Finland
| | - Marjo Renko
- Department of Pediatrics and Adolescent Medicine, Kuopio University Hospital, Kuopio, Finland.,University of Eastern Finland, Kuopio, Finland
| | - Terhi Tapiainen
- Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Oulu, Finland.,Research Unit of Clinical Medicine and Medical Research Center Oulu, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland
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Bjornsdottir B, Benitez Hernandez U, Haraldsson A, Thors V. Febrile Children with Pneumonia Have Higher Nasopharyngeal Bacterial Load Than Other Children with Fever. Pathogens 2023; 12:517. [PMID: 37111403 PMCID: PMC10143154 DOI: 10.3390/pathogens12040517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 03/15/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023] Open
Abstract
Febrile episodes are common in children and the most frequent reason for attending emergency services. Although most infections have a benign and self-limiting course, severe and sometimes life-threatening infections occur. This prospective study describes a cohort of children presenting to a single-centre pediatric emergency department (ED) with suspected invasive bacterial infection, and explores the relationships between nasopharyngeal microbes and outcomes. All children attending the ED who had a blood culture taken were offered to participate over a two-year period. In addition to conventional medical care, a nasopharyngeal swab was obtained., which was analysed for respiratory viruses and three bacterial species using a quantitative PCR. Fisher's exact test, Wilcoxon rank sum, and multivariable models were used for statistical analyses of the 196 children (75% younger than four years) who were enrolled and had sufficient data for analysis; 92 had severe infections according to the study protocol, while five had bloodstream infections. Radiologically confirmed pneumonia was the most common severe infection found in 44/92 patients. The presence of respiratory viruses and the carriage of Streptococcus pneumoniae and Haemophilus influenzae were associated with a higher risk of pneumonia. Higher density colonisation with these bacteria were independent risk factors for pneumonia, whereas Moraxella catarrhalis carriage was associated with lower risk. Our data support the hypothesis that higher nasopharyngeal density of pneumococci and H. influenzae could play a role in the development of bacterial pneumonia in children. A preceding viral infection of the respiratory tract may be a trigger and play a role in the progression to severe lower respiratory tract infection.
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Affiliation(s)
- Bryndis Bjornsdottir
- Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
- Department of Science/Biostatistics, Landspitali University Hospital, 101 Reykjavik, Iceland
| | | | - Asgeir Haraldsson
- Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
- Children’s Hospital Iceland, Landspitali University Hospital, 101 Reykjavik, Iceland
| | - Valtyr Thors
- Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
- Children’s Hospital Iceland, Landspitali University Hospital, 101 Reykjavik, Iceland
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Abbott P, Frede C, Hu WCY, Lujic S, Trankle S, Campbell L, Gunasekera H, Walsh R, Leach AJ, Morris P, Kong K, Reath J. Acute otitis media symptoms and symptom scales in research with Aboriginal and Torres Strait Islander children. PLoS One 2023; 18:e0280926. [PMID: 36821636 PMCID: PMC9949645 DOI: 10.1371/journal.pone.0280926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 12/29/2022] [Indexed: 02/24/2023] Open
Abstract
BACKGROUND Aboriginal and Torres Strait Islander children experience a high burden of otitis media. We collected data on symptoms associated with acute otitis media (AOM) in a clinical trial involving children receiving primary care at urban Aboriginal Medical Services. Two scales were employed to monitor symptoms over time: the AOM-Severity of Symptoms scale (AOM-SOS) and the AOM-Faces Scale (AOM-FS). This study took place at a mid-point of the un-blinded trial. METHODS We examined symptoms at enrolment and day 7, and compared the scales for trends, and bivariate correlation (Spearman's rho) over 14 days. Responsiveness of the scales to clinical change was determined by Friedman's test of trend in two subgroups stratified by day 7 AOM status. We interviewed parents/carers and research officers regarding their experience of the scales and analysed data thematically. RESULTS Data derived from 224 children (18 months to 16 years; median 3.6 years). Common symptoms associated with AOM at baseline were runny nose (40%), cough (38%) and irritability (36%). More than one third had no or minimal symptoms at baseline according to AOM-SOS (1-2/10) and AOM-FS scores (1-2/7). The scales performed similarly, and were moderately correlated, at all study points. Although scores decreased from day 0 to 14, trends and mean scores were the same whether AOM was persistent or resolved at day 7. Users preferred the simplicity of the AOM-FS but encountered challenges when interpreting it. CONCLUSION We found minimally symptomatic AOM was common among Aboriginal and Torres Strait Islander children in urban settings. The AOM-SOS and AOM-FS functioned similarly. However, it is likely the scales measured concurrent symptoms related to upper respiratory tract infections, given they did not differentiate children with persistent or resolved AOM based on stringent diagnostic criteria. This appears to limit the research and clinical value of the scales in monitoring AOM treatment among Aboriginal and Torres Strait Islander children.
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Affiliation(s)
- Penelope Abbott
- Department of General Practice, Western Sydney University, Campbelltown, New South Wales, Australia
- * E-mail:
| | - Caitlin Frede
- Department of General Practice, Western Sydney University, Campbelltown, New South Wales, Australia
| | - Wendy C. Y. Hu
- Medical Education Unit, School of Medicine, Western Sydney University, Campbelltown, New South Wales, Australia
| | - Sanja Lujic
- Centre for Big Data Research in Health, University of New South Wales, Sydney, New South Wales, Australia
| | - Steven Trankle
- Department of General Practice, Western Sydney University, Campbelltown, New South Wales, Australia
| | - Letitia Campbell
- Kalwun Development Corporation, Gold Coast, Queensland, Australia
| | - Hasantha Gunasekera
- Children’s Hospital Westmead Clinical School, Sydney University, Sydney, New South Wales, Australia
| | - Robyn Walsh
- Department of General Practice, Western Sydney University, Campbelltown, New South Wales, Australia
| | - Amanda J. Leach
- Child Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Peter Morris
- Child Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Kelvin Kong
- School of Medicine and Public Health, University of Newcastle, Newcastle, New South Wales, Australia
| | - Jennifer Reath
- Department of General Practice, Western Sydney University, Campbelltown, New South Wales, Australia
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10
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Lane S, Hilliam Y, Bomberger JM. Microbial and Immune Regulation of the Gut-Lung Axis during Viral-Bacterial Coinfection. J Bacteriol 2023; 205:e0029522. [PMID: 36409130 PMCID: PMC9879096 DOI: 10.1128/jb.00295-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Viral-bacterial coinfections of the respiratory tract have long been associated with worsened disease outcomes. Clinical and basic research studies demonstrate that these infections are driven via complex interactions between the infecting pathogens, microbiome, and host immune response, although how these interactions contribute to disease progression is still not fully understood. Research over the last decade shows that the gut has a significant role in mediating respiratory outcomes, in a phenomenon known as the "gut-lung axis." Emerging literature demonstrates that acute respiratory viruses can modulate the gut-lung axis, suggesting that dysregulation of gut-lung cross talk may be a contributing factor during respiratory coinfection. This review will summarize the current literature regarding modulation of the gut-lung axis during acute respiratory infection, with a focus on the role of the microbiome, secondary infections, and the host immune response.
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Affiliation(s)
- Sidney Lane
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Yasmin Hilliam
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Jennifer M. Bomberger
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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11
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Orzołek I, Ambrożej D, Makrinioti H, Zhu Z, Jartti T, Feleszko W. Severe bronchiolitis profiling as the first step towards prevention of asthma. Allergol Immunopathol (Madr) 2023; 51:99-107. [PMID: 37169566 DOI: 10.15586/aei.v51i3.788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 02/07/2023] [Indexed: 05/13/2023]
Abstract
Bronchiolitis is the most common respiratory infection leading to hospitalization and constitutes a significant healthcare burden. The two main viral agents causing bronchiolitis, respiratory syncytial virus (RSV) and rhinovirus (RV), have distinct cytopathic, immune response, and clinical characteristics. Different approaches have been suggested for subtyping bronchiolitis based on viral etiology, atopic status, transcriptome profiles in blood, airway metabolome, lipidomic data, and airway microbiota. The highest risk of asthma at school age has been in a subgroup of bronchiolitis characterized by older age, high prevalence of RV infection, previous breathing problems, and/or eczema. Regarding solely viral etiology, RV-bronchiolitis in infancy has been linked to a nearly three times higher risk of developing asthma than RSV-bronchiolitis. Although treatment with betamimetics and systemic corticosteroids has been found ineffective in bronchiolitis overall, it can be beneficial for infants with severe RV bronchiolitis. Thus, there is a need to develop a more individualized therapeutic approach for bronchiolitis and follow-up strategies for infants at higher risk of asthma in the future perspective.
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Affiliation(s)
- Izabela Orzołek
- Department of Pediatric Pneumonology and Allergy, Medical University of Warsaw, Warsaw, Poland
| | - Dominika Ambrożej
- Department of Pediatric Pneumonology and Allergy, Medical University of Warsaw, Warsaw, Poland
- Doctoral School, Medical University of Warsaw, Warsaw, Poland
| | - Heidi Makrinioti
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Zhaozhong Zhu
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Tuomas Jartti
- PEDEGO Research Unit, University of Oulu, Oulu, Finland
- Department of Pediatrics and Adolescent Medicine, University of Oulu, Oulu, Finland
- Department of Pediatrics and Adolescent Medicine, Turku University Hospital and University of Turku, Turku, Finland
| | - Wojciech Feleszko
- Department of Pediatric Pneumonology and Allergy, Medical University of Warsaw, Warsaw, Poland;
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12
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Zuurbier RP, Bogaert D, de Steenhuijsen Piters WAA, Arp K, Chu MLJN, Sanders EAM, van Houten MA. Asymptomatic Viral Presence in Early Life Precedes Recurrence of Respiratory Tract Infections. Pediatr Infect Dis J 2023; 42:59-65. [PMID: 36476532 DOI: 10.1097/inf.0000000000003732] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Respiratory tract infections (RTIs) in infants are often caused by viruses. Although respiratory syncytial virus (RSV), influenza virus and human metapneumovirus (hMPV) can be considered the most pathogenic viruses in children, rhinovirus (RV) is often found in asymptomatic infants as well. Little is known about the health consequences of viral presence, especially early in life. We aimed to examine the dynamics of (a)symptomatic viral presence and relate early viral detection to susceptibility to RTIs in infants. METHODS In a prospective birth cohort of 117 infants, we tested 1304 nasopharyngeal samples obtained from 11 consecutive regular sampling moments, and during acute RTIs across the first year of life for 17 respiratory viruses by quantitative PCR. Associations between viral presence, viral (sub)type, viral load, viral co-detection and symptoms were tested by generalized estimating equation (GEE) models. RESULTS RV was the most detected virus. RV was negatively associated [GEE: adjusted odds ratio (aOR) 0.41 (95% CI 0.18-0.92)], and hMPV, RSV, parainfluenza 2 and 4 and human coronavirus HKU1 were positively associated with an acute RTI. Asymptomatic RV in early life was, however, associated with increased susceptibility to and recurrence of RTIs later in the first year of life (Kaplan-Meier survival analysis: P = 0.022). CONCLUSIONS Respiratory viruses, including the seasonal human coronaviruses, are often detected in infants, and are often asymptomatic. Early life RV presence is, though negatively associated with an acute RTI, associated with future susceptibility to and recurrence of RTIs. Further studies on potential ecologic or immunologic mechanisms are needed to understand these observations.
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Affiliation(s)
- Roy P Zuurbier
- From the Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Utrecht
- Spaarne Gasthuis Academy, Hoofddorp and Haarlem, The Netherlands
| | - Debby Bogaert
- From the Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Utrecht
- Medical Research Council and University of Edinburgh Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Kayleigh Arp
- From the Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Utrecht
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Mei Ling J N Chu
- From the Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Utrecht
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Elisabeth A M Sanders
- From the Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Utrecht
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Marlies A van Houten
- Spaarne Gasthuis Academy, Hoofddorp and Haarlem, The Netherlands
- Department of Pediatrics, Spaarne Gasthuis, Hoofddorp and Haarlem, The Netherlands
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13
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Consonni A, Miglietti M, De Luca CMG, Cazzaniga FA, Ciullini A, Dellarole IL, Bufano G, Di Fonzo A, Giaccone G, Baggi F, Moda F. Approaching the Gut and Nasal Microbiota in Parkinson's Disease in the Era of the Seed Amplification Assays. Brain Sci 2022; 12:1579. [PMID: 36421902 PMCID: PMC9688507 DOI: 10.3390/brainsci12111579] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 11/10/2022] [Accepted: 11/17/2022] [Indexed: 10/30/2023] Open
Abstract
Parkinson's disease (PD) is a neurodegenerative disorder often associated with pre-motor symptoms involving both gastrointestinal and olfactory tissues. PD patients frequently suffer from hyposmia, hyposalivation, dysphagia and gastrointestinal dysfunctions. During the last few years it has been speculated that microbial agents could play a crucial role in PD. In particular, alterations of the microbiota composition (dysbiosis) might contribute to the formation of misfolded α-synuclein, which is believed to be the leading cause of PD. However, while several findings confirmed that there might be an important link between intestinal microbiota alterations and PD onset, little is known about the potential contribution of the nasal microbiota. Here, we describe the latest findings on this topic by considering that more than 80% of patients with PD develop remarkable olfactory deficits in their prodromal disease stage. Therefore, the nasal microbiota might contribute to PD, eventually boosting the gut microbiota in promoting disease onset. Finally, we present the applications of the seed amplification assays to the study of the gut and olfactory mucosa of PD patients, and how they could be exploited to investigate whether pathogenic bacteria present in the gut and the nose might promote α-synuclein misfolding and aggregation.
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Affiliation(s)
- Alessandra Consonni
- Division of Neurology 4-Neuroimmunology and Neuromuscular Diseases, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
| | - Martina Miglietti
- Division of Neurology 4-Neuroimmunology and Neuromuscular Diseases, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
| | - Chiara Maria Giulia De Luca
- Division of Neurology 5-Neuropathology, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
| | - Federico Angelo Cazzaniga
- Division of Neurology 5-Neuropathology, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
| | - Arianna Ciullini
- Division of Neurology 5-Neuropathology, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
| | - Ilaria Linda Dellarole
- Division of Neurology 5-Neuropathology, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
| | - Giuseppe Bufano
- Division of Neurology 5-Neuropathology, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
| | - Alessio Di Fonzo
- Division of Neurology, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Giorgio Giaccone
- Division of Neurology 5-Neuropathology, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
| | - Fulvio Baggi
- Division of Neurology 4-Neuroimmunology and Neuromuscular Diseases, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
| | - Fabio Moda
- Division of Neurology 5-Neuropathology, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
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14
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Takashima MD, Grimwood K, Sly PD, Lambert SB, Ware RS. Interference between rhinovirus and other RNA respiratory viruses in the first 2-years of life: A longitudinal community-based birth cohort study. J Clin Virol 2022; 155:105249. [PMID: 35939878 DOI: 10.1016/j.jcv.2022.105249] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 07/27/2022] [Accepted: 07/30/2022] [Indexed: 10/16/2022]
Abstract
BACKGROUND Cross-sectional studies report negative associations between rhinovirus and other RNA respiratory viruses. However, longitudinal studies with frequent, serial sampling are needed to identify the directionality of this relationship and its nature. OBJECTIVE To investigate the association between rhinovirus and other RNA respiratory viruses detected 1-week apart. METHODS The Observational Research in Childhood Infectious Diseases cohort study was conducted in Brisbane, Australia (2010-2014). Parents collected nasal swabs weekly from birth until age 2-years. Swabs were analysed by real-time polymerase chain reaction. The association between new rhinovirus detections and five other RNA viruses (influenza, respiratory syncytial virus, parainfluenza viruses, seasonal human coronaviruses, and human metapneumovirus) in paired swabs 1-week apart were investigated. RESULTS Overall, 157 children provided 8,101 swabs, from which 4,672 paired swabs 1-week apart were analysed. New rhinovirus detections were negatively associated with new pooled RNA respiratory virus detections 1-week later (adjusted odds ratio (aOR) 0.48; 95% confidence interval (CI): 0.13-0.83), as were pooled RNA virus detections with new rhinovirus detections the following week (aOR 0.34; 95%CI: 0.09-0.60). At the individual species level, rhinovirus had the strongest negative association with new seasonal human coronavirus detections in the subsequent week (aOR 0.34; 95%CI: 0.120.95) and respiratory syncytial virus had the strongest negative association with rhinovirus 1-week later (aOR 0.21; 95%CI: 0.050.88). CONCLUSION A strong, negative bidirectional association was observed between rhinovirus and other RNA viruses in a longitudinal study of a community-based cohort of young Australian children. This suggests within-host interference between RNA respiratory viruses.
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Affiliation(s)
- Mari D Takashima
- Menzies Health Institute Queensland and School of Medicine and Dentistry, Griffith University, Gold Coast 4222, Queensland, Australia.
| | - Keith Grimwood
- Menzies Health Institute Queensland and School of Medicine and Dentistry, Griffith University, Gold Coast 4222, Queensland, Australia; Departments of Infectious Diseases and Paediatrics, Gold Coast Health, Gold Coast 4215, Queensland, Australia
| | - Peter D Sly
- Children's Health and Environment Program, Child Health Research Centre, The University of Queensland, South Brisbane 4101, Queensland, Australia; Australian Infectious Diseases Research Centre, The University of Queensland, St Lucia 4072, Queensland, Australia
| | - Stephen B Lambert
- UQ Centre for Clinical Research, The University of Queensland, Herston 4006, Queensland, Australia; National Centre for Immunisation Research and Surveillance, Westmead 2145, New South Wales, Australia
| | - Robert S Ware
- Menzies Health Institute Queensland and School of Medicine and Dentistry, Griffith University, Gold Coast 4222, Queensland, Australia
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15
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Hwang JK, Na JY, Kim J, Oh JW, Kim YJ, Choi YJ. Age-Specific Characteristics of Adult and Pediatric Respiratory Viral Infections: A Retrospective Single-Center Study. J Clin Med 2022; 11:jcm11113197. [PMID: 35683584 PMCID: PMC9181129 DOI: 10.3390/jcm11113197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 05/26/2022] [Accepted: 05/31/2022] [Indexed: 11/16/2022] Open
Abstract
This study aimed to identify age-specific characteristics of respiratory viral infections. Hospitalized patients with confirmed viral respiratory infections were included in the sample. The patients were divided into the pediatric group (<19 years old) and the adult group (≥19 years old). The groups were then subdivided based on age: 0−6, 7−12, 13−18, 19−49, 50−64, and ≥65 years old. These groups were compared to evaluate the differences in the pattern of respiratory viral infections. Among a total of 4058 pediatric patients (mean age 3.0 ± 2.9 years, n = 1793 females), 2829 (48.9%) had mono-infections, while 1229 (51.1%) had co-infections. Co-infections were the most common in the 0−6-year-old group (31.6%). Among 1550 adult patients (mean age 70.2 ± 15.3 years, n = 710 females), 1307 (85.6%) had mono-infections and 243 (14.4%) had co-infections. Co-infections were most common in the ≥65-year-old group (16.8%). Viral infection and co-infection rates decreased with age in pediatric patients but increased with increasing age in adults. In pediatric patients, the rates of viral infections and co-infections were high; the rate of co-infections was higher in younger patients. In adult patients, the rates of viral infections and co-infections were lower than those in pediatric patients; the rate of co-infections was higher in older patients.
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Affiliation(s)
- Jae Kyoon Hwang
- Department of Pediatrics, Hanyang University Guri Hospital, Guri 11923, Korea; (J.K.H.); (J.-W.O.)
| | - Jae Yoon Na
- Department of Pediatrics, Hanyang University Seoul Hospital, Seoul 04763, Korea; (J.Y.N.); (J.K.); (Y.J.K.)
| | - Jihye Kim
- Department of Pediatrics, Hanyang University Seoul Hospital, Seoul 04763, Korea; (J.Y.N.); (J.K.); (Y.J.K.)
| | - Jae-Won Oh
- Department of Pediatrics, Hanyang University Guri Hospital, Guri 11923, Korea; (J.K.H.); (J.-W.O.)
- Department of Pediatrics, College of Medicine, Hanyang University, Seoul 04763, Korea
| | - Yong Joo Kim
- Department of Pediatrics, Hanyang University Seoul Hospital, Seoul 04763, Korea; (J.Y.N.); (J.K.); (Y.J.K.)
- Department of Pediatrics, College of Medicine, Hanyang University, Seoul 04763, Korea
| | - Young-Jin Choi
- Department of Pediatrics, Hanyang University Guri Hospital, Guri 11923, Korea; (J.K.H.); (J.-W.O.)
- Correspondence:
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16
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Clearance of mixed biofilms of Streptococcus pneumoniae and methicillin-susceptible/resistant Staphylococcus aureus by antioxidants N-acetyl-L-cysteine and cysteamine. Sci Rep 2022; 12:6668. [PMID: 35461321 PMCID: PMC9035182 DOI: 10.1038/s41598-022-10609-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 04/07/2022] [Indexed: 12/01/2022] Open
Abstract
Biofilm-associated infections are of great concern because they are associated with antibiotic resistance and immune evasion. Co-colonization by Staphylococcus aureus and Streptococcus pneumoniae is possible and a threat in clinical practice. We investigated the interaction between S. aureus and S. pneumoniae in mixed biofilms and tested new antibiofilm therapies with antioxidants N-acetyl-l-cysteine (NAC) and cysteamine (Cys). We developed two in vitro S. aureus–S. pneumoniae mixed biofilms in 96-well polystyrene microtiter plates and we treated in vitro biofilms with Cys and NAC analyzing their effect by CV staining and viable plate counting. S. pneumoniae needed a higher proportion of cells in the inoculum and planktonic culture to reach a similar population rate in the mixed biofilm. We demonstrated the effect of Cys in preventing S. aureus biofilms and S. aureus–S. pneumoniae mixed biofilms. Moreover, administration of 5 mg/ml of NAC nearly eradicated the S. pneumoniae population and killed nearly 94% of MSSA cells and 99% of MRSA cells in the mixed biofilms. The methicillin resistance background did not change the antioxidants effect in S. aureus. These results identify NAC and Cys as promising repurposed drug candidates for the prevention and treatment of mixed biofilms by S. pneumoniae and S. aureus.
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17
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Gupta A, Karyakarte R, Joshi S, Das R, Jani K, Shouche Y, Sharma A. Nasopharyngeal microbiome reveals the prevalence of opportunistic pathogens in SARS-CoV-2 infected individuals and their association with host types. Microbes Infect 2022; 24:104880. [PMID: 34425246 PMCID: PMC8379005 DOI: 10.1016/j.micinf.2021.104880] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/03/2021] [Accepted: 08/06/2021] [Indexed: 02/09/2023]
Abstract
The novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is causing a severe global health emergency owing to its highly infectious nature. Although the symptoms of SARS-CoV-2 are well known but its impact on nasopharyngeal microbiome is poorly studied. The present cross-sectional study was intended to understand the perturbation in the nasopharyngeal microbiome composition within the infected (n = 63) and non-infected (n = 26) individuals using 16S rRNA gene based targeted amplicon sequencing and their association with host types and the prevalence of opportunistic pathogens at the stage of infection. The results confirmed that number of OTUs were significantly (p < 0.05) decreased in the SARS-CoV-2 infected individuals in comparison to non-infected individuals. Pairwise Wilcoxon test showed a significant (p < 0.05) increase in the abundance of Proteobacteria in infected individuals compared to non-infected ones and vice-versa for Fusobacteria and Bacteroidetes. Similarity percentage (SIMPER) analysis showed the increment in the abundance of opportunistic pathogens (Haemophilus, Stenotrophomonas, Acinetobacter, Moraxella, Corynebacterium 1, Gemella, Ralstonia, and Pseudomonas) involved in secondary infection. Furthermore, this study highlighted the microbial community structure of individuals within and across the families. In this study, we also performed the assesment of microbiome associated with host types (age and genders) and COVID-19 conditions (symptomatic and asymptomatic). The data suggested that the host types/conditions during the COVID-19 infection are potential factors in enrichment of specific bacterial communities in upper respiratory tract.
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Affiliation(s)
- Abhishek Gupta
- DBT-National Centre for Cell Science, Pune, Maharashtra, 411007, India
| | - Rajesh Karyakarte
- Byramjee Jeejeebhoy Government Medical College, Pune, Maharashtra, 411001, India
| | - Suvarna Joshi
- Byramjee Jeejeebhoy Government Medical College, Pune, Maharashtra, 411001, India
| | - Rashmita Das
- Byramjee Jeejeebhoy Government Medical College, Pune, Maharashtra, 411001, India
| | - Kunal Jani
- DBT-National Centre for Cell Science, Pune, Maharashtra, 411007, India
| | - Yogesh Shouche
- DBT-National Centre for Cell Science, Pune, Maharashtra, 411007, India
| | - Avinash Sharma
- DBT-National Centre for Cell Science, Pune, Maharashtra, 411007, India.
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18
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de Steenhuijsen Piters WAA, Watson RL, de Koff EM, Hasrat R, Arp K, Chu MLJN, de Groot PCM, van Houten MA, Sanders EAM, Bogaert D. Early-life viral infections are associated with disadvantageous immune and microbiota profiles and recurrent respiratory infections. Nat Microbiol 2022; 7:224-237. [PMID: 35058634 DOI: 10.1038/s41564-021-01043-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 12/06/2021] [Indexed: 12/17/2022]
Abstract
The respiratory tract is populated by a specialized microbial ecosystem, which is seeded during and directly following birth. Perturbed development of the respiratory microbial community in early-life has been associated with higher susceptibility to respiratory tract infections (RTIs). Given a consistent gap in time between first signs of aberrant microbial maturation and the observation of the first RTIs, we hypothesized that early-life host-microbe cross-talk plays a role in this process. We therefore investigated viral presence, gene expression profiles and nasopharyngeal microbiota from birth until 12 months of age in 114 healthy infants. We show that the strongest dynamics in gene expression profiles occurred within the first days of life, mostly involving Toll-like receptor (TLR) and inflammasome signalling. These gene expression dynamics coincided with rapid microbial niche differentiation. Early asymptomatic viral infection co-occurred with stronger interferon activity, which was related to specific microbiota dynamics following, including early enrichment of Moraxella and Haemophilus spp. These microbial trajectories were in turn related to a higher number of subsequent (viral) RTIs over the first year of life. Using a multi-omic approach, we found evidence for species-specific host-microbe interactions related to consecutive susceptibility to RTIs. Although further work will be needed to confirm causality of our findings, together these data indicate that early-life viral encounters could impact subsequent host-microbe cross-talk, which is linked to later-life infections.
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Affiliation(s)
- Wouter A A de Steenhuijsen Piters
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Utrecht, the Netherlands
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Rebecca L Watson
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Emma M de Koff
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Utrecht, the Netherlands
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
- Spaarne Gasthuis Academy, Hoofddorp and Haarlem, the Netherlands
| | - Raiza Hasrat
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Utrecht, the Netherlands
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Kayleigh Arp
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Utrecht, the Netherlands
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Mei Ling J N Chu
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Utrecht, the Netherlands
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Pieter C M de Groot
- Department of Obstetrics and Gynaecology, Spaarne Gasthuis, Hoofddorp and Haarlem, the Netherlands
| | - Marlies A van Houten
- Spaarne Gasthuis Academy, Hoofddorp and Haarlem, the Netherlands
- Department of Paediatrics, Spaarne Gasthuis, Hoofddorp and Haarlem, the Netherlands
| | - Elisabeth A M Sanders
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Utrecht, the Netherlands
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Debby Bogaert
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Utrecht, the Netherlands.
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands.
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK.
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19
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Otheo E, Rodríguez M, Moraleda C, Domínguez-Rodríguez S, Martín MD, Herreros ML, Vázquez C, Folgueira MD, Pérez-Rivilla A, Jensen J, López A, Berzosa A, Sanz de Santaeufemia FJ, Jiménez AB, Sainz T, Llorente M, Santos M, Garrote E, Muñoz C, Sánchez P, Illán M, Coca A, Barrios A, Pacheco M, Arquero C, Gutiérrez L, Epalza C, Rojo P, Serna-Pascual M, Mota I, Moreno S, Galán JC, Tagarro A. Viruses and Mycoplasma pneumoniae are the main etiological agents of community-acquired pneumonia in hospitalized pediatric patients in Spain. Pediatr Pulmonol 2022; 57:253-263. [PMID: 34633153 DOI: 10.1002/ppul.25721] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 09/22/2021] [Accepted: 10/08/2021] [Indexed: 11/08/2022]
Abstract
OBJECTIVES To describe the etiology of community-acquired pneumonia (CAP) in hospitalized children in Spain and analyze the predictors of the etiology. HYPOTHESIS The different etiological groups of pediatric CAP are associated with different clinical, radiographic, and analytical data. DESIGN Observational, multicenter, and prospective study. PATIENT SELECTION This study included children aged 1 month to 17 years with CAP, who were hospitalized between April 2012 and May 2019. METHODS An extensive microbiological workup was performed. The clinical, radiographic, and analytical parameters were analyzed for three etiological groups. RESULTS Among the 495 children included, at least one causative pathogen was identified in 262 (52.9%): pathogenic viruses in 155/262 (59.2%); atypical bacteria (AB), mainly Mycoplasma pneumonia, in 84/262 (32.1%); and typical bacteria (TyB) in 40/262 (15.3%). Consolidation was observed in 89/138 (64.5%) patients with viral CAP, 74/84 (88.1%) with CAP caused by AB, and 40/40 (100%) with CAP caused by TyB. Para-pneumonic pleural effusion (PPE) was observed in 112/495 (22.6%) patients, of which 61/112 (54.5%) presented a likely causative pathogen: viruses in 12/61 (19.7%); AB in 23/61 (37.7%); and TyB in 26/61 (42.6%). Viral etiology was significantly frequent in young patients and in those with low oxygen saturation, wheezing, no consolidation, and high lymphocyte counts. CAP patients with AB as the etiological agent had a significantly longer and less serious course as compared to those with other causative pathogens. CONCLUSIONS Viruses and M. pneumoniae are the main causes of pediatric CAP in Spain. Wheezing, young age, and no consolidation on radiographs are indicative of viral etiology. Viruses and AB can also cause PPE. Since only a few cases can be directly attributed to TyB, the indications for antibiotics must be carefully considered in each patient.
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Affiliation(s)
- Enrique Otheo
- Department of Pediatrics, Hospital Universitario Ramón y Cajal, Universidad de Alcalá, Madrid, Spain
| | - Mario Rodríguez
- Department of Microbiology, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal para la Investigación Sanitaria (IRYCIS), Madrid, Spain.,Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Cinta Moraleda
- Fundación para la Investigación Biomédica del Hospital 12 de Octubre, Madrid, Spain.,RITIP (Translational Research Network in Pediatric Infectious Diseases), Madrid, Spain.,Pediatric Infectious Diseases Unit, Department of Pediatrics, Hospital Universitario 12 de Octubre, Madrid, Spain.,Pediatric Research and Clinical Trials Unit (UPIC), Instituto de Investigación Sanitaria Hospital 12 de Octubre (IMAS12), Madrid, Spain
| | - Sara Domínguez-Rodríguez
- Fundación para la Investigación Biomédica del Hospital 12 de Octubre, Madrid, Spain.,RITIP (Translational Research Network in Pediatric Infectious Diseases), Madrid, Spain.,Pediatric Research and Clinical Trials Unit (UPIC), Instituto de Investigación Sanitaria Hospital 12 de Octubre (IMAS12), Madrid, Spain
| | - María D Martín
- Department of Microbiology, Laboratorio BR Salud, Hospital Universitario Infanta Sofía, San Sebastián de los Reyes, Madrid, Spain
| | - María L Herreros
- Department of Pediatrics, Hospital Universitario Infanta Sofía, San Sebastián de los Reyes, Madrid, Spain
| | - Carmen Vázquez
- Department of Pediatrics, Hospital Universitario Ramón y Cajal, Universidad de Alcalá, Madrid, Spain
| | - María D Folgueira
- Department of Microbiology, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Hospital 12 de Octubre (IMAS12), Madrid, Spain
| | - Alfredo Pérez-Rivilla
- Department of Microbiology, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Hospital 12 de Octubre (IMAS12), Madrid, Spain
| | - Julia Jensen
- Department of Pediatrics, Hospital Infanta Cristina , Parla, Madrid, Spain
| | - Agustín López
- Department of Pediatrics, Hospital Universitario Puerta de Hierro, Majadahonda, Madrid, Spain
| | - Arantxa Berzosa
- Department of Pediatrics, Hospital Universitario de Getafe, Getafe, Madrid, Spain
| | | | - Ana B Jiménez
- Department of Pediatrics, Fundación Jiménez Díaz, Madrid, Spain
| | - Talía Sainz
- RITIP (Translational Research Network in Pediatric Infectious Diseases), Madrid, Spain.,Department of Pediatrics, Infectious and Tropical Diseases, Hospital Universitario La Paz, Instituto Investigación Hospital La Paz (IDIPAZ), Madrid, Spain
| | - Marta Llorente
- Department of Pediatrics, Hospital Universitario del Sureste, Arganda del Rey, Madrid, Spain
| | - Mar Santos
- RITIP (Translational Research Network in Pediatric Infectious Diseases), Madrid, Spain.,Pediatric Infectious Diseases Unit, Hospital Universitario Gregorio Marañón, Madrid, Spain
| | - Elisa Garrote
- Department of Pediatrics, Hospital Universitario Basurto, Bilbao, Vizcaya, Spain
| | - Cristina Muñoz
- Department of Pediatrics, Hospital General de Villalba, Villalba, Madrid, Spain
| | - Paula Sánchez
- Pediatric Infectious Diseases, Immunology and Rheumatology Unit, Hospital Universitario Virgen del Rocío, Instituto de Biomedicina de Sevilla (IBIS), Seville, Spain
| | - Marta Illán
- Department of Pediatrics, Hospital Clínico San Carlos, Madrid, Spain
| | - Ana Coca
- Pediatric Intensive Care Unit, Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - Ana Barrios
- Department of Pediatrics, Hospital Universitario Infanta Sofía, San Sebastián de los Reyes, Madrid, Spain
| | - Mónica Pacheco
- Department of Pediatrics, Hospital Universitario Infanta Sofía, San Sebastián de los Reyes, Madrid, Spain
| | - Carmen Arquero
- Department of Pediatrics, Hospital Universitario Infanta Sofía, San Sebastián de los Reyes, Madrid, Spain
| | - Lourdes Gutiérrez
- Fundación para la Investigación Biomédica del Hospital 12 de Octubre, Madrid, Spain.,RITIP (Translational Research Network in Pediatric Infectious Diseases), Madrid, Spain.,Pediatric Research and Clinical Trials Unit (UPIC), Instituto de Investigación Sanitaria Hospital 12 de Octubre (IMAS12), Madrid, Spain
| | - Cristina Epalza
- Fundación para la Investigación Biomédica del Hospital 12 de Octubre, Madrid, Spain.,RITIP (Translational Research Network in Pediatric Infectious Diseases), Madrid, Spain.,Pediatric Infectious Diseases Unit, Department of Pediatrics, Hospital Universitario 12 de Octubre, Madrid, Spain.,Pediatric Research and Clinical Trials Unit (UPIC), Instituto de Investigación Sanitaria Hospital 12 de Octubre (IMAS12), Madrid, Spain
| | - Pablo Rojo
- Fundación para la Investigación Biomédica del Hospital 12 de Octubre, Madrid, Spain.,RITIP (Translational Research Network in Pediatric Infectious Diseases), Madrid, Spain.,Pediatric Infectious Diseases Unit, Department of Pediatrics, Hospital Universitario 12 de Octubre, Madrid, Spain.,Pediatric Research and Clinical Trials Unit (UPIC), Instituto de Investigación Sanitaria Hospital 12 de Octubre (IMAS12), Madrid, Spain.,Department of Pediatrics, Universidad Complutense de Madrid, Madrid, Spain
| | - Miquel Serna-Pascual
- Fundación para la Investigación Biomédica del Hospital 12 de Octubre, Madrid, Spain.,RITIP (Translational Research Network in Pediatric Infectious Diseases), Madrid, Spain.,Pediatric Research and Clinical Trials Unit (UPIC), Instituto de Investigación Sanitaria Hospital 12 de Octubre (IMAS12), Madrid, Spain
| | - Inmaculada Mota
- Department of Radiology, Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - Santiago Moreno
- Department of Infectious Diseases, Hospital Universitario Ramón y Cajal, Universidad de Alcalá, Madrid, Spain
| | - Juan C Galán
- Department of Microbiology, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal para la Investigación Sanitaria (IRYCIS), Madrid, Spain.,Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Alfredo Tagarro
- Fundación para la Investigación Biomédica del Hospital 12 de Octubre, Madrid, Spain.,RITIP (Translational Research Network in Pediatric Infectious Diseases), Madrid, Spain.,Pediatric Research and Clinical Trials Unit (UPIC), Instituto de Investigación Sanitaria Hospital 12 de Octubre (IMAS12), Madrid, Spain.,Department of Pediatrics, Hospital Universitario Infanta Sofía, San Sebastián de los Reyes, Madrid, Spain.,Pediatrics Research Group, Universidad Europea de Madrid, Madrid, Spain
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20
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Viles WD, Madan JC, Li H, Karagas MR, Hoen AG. INFORMATION CONTENT OF HIGH-ORDER ASSOCIATIONS OF THE HUMAN GUT MICROBIOTA NETWORK. Ann Appl Stat 2021; 15:1788-1807. [PMID: 35342498 PMCID: PMC8955221 DOI: 10.1214/21-aoas1449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/26/2024]
Abstract
The human gastrointestinal tract is an environment that hosts an ecosystem of microorganisms essential to human health. Vital biological processes emerge from fundamental inter- and intra-species molecular interactions that influence the assembly and composition of the gut microbiota ecology. Here we quantify the complexity of the ecological relationships within the human infant gut microbiota ecosystem as a function of the information contained in the nonlinear associations of a sequence of increasingly-specified maximum entropy representations of the system. Our paradigm frames the ecological state, in terms of the presence or absence of individual microbial ecological units that are identified by amplicon sequence variants (ASV) in the gut microenvironment, as a function of both the ecological states of its neighboring units and, in a departure from standard graphical model representations, the associations among the units within its neighborhood. We characterize the order of the system based on the relative quantity of statistical information encoded by high-order statistical associations of the infant gut microbiota.
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Affiliation(s)
- Weston D. Viles
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth
| | | | - Hongzhe Li
- Department of Biostatistics and Epidemiology, Perelman School of Medicine, University of Pennsylvania
| | | | - Anne G. Hoen
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth
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21
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Prospective Study of the Performance of Parent-Collected Nasal and Saliva Swab Samples, Compared with Nurse-Collected Swab Samples, for the Molecular Detection of Respiratory Microorganisms. Microbiol Spectr 2021; 9:e0016421. [PMID: 34756077 PMCID: PMC8579848 DOI: 10.1128/spectrum.00164-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Respiratory tract infections (RTIs) are ubiquitous among children in the community. A prospective observational study was performed to evaluate the diagnostic performance and quality of at-home parent-collected (PC) nasal and saliva swab samples, compared to nurse-collected (NC) swab samples, from children with RTI symptoms. Children with RTI symptoms were swabbed at home on the same day by a parent and a nurse. We compared the performance of PC swab samples as the test with NC swab samples as the reference for the detection of respiratory pathogen gene targets by reverse transcriptase PCR, with quality assessment using a human gene. PC and NC paired nasal and saliva swab samples were collected from 91 and 92 children, respectively. Performance and interrater agreement (Cohen's κ) of PC versus NC nasal swab samples for viruses combined showed sensitivity of 91.6% (95% confidence interval [CI], 85.47 to 95.73%) and κ of 0.84 (95% CI, 0.79 to 0.88), respectively; the respective values for bacteria combined were 91.4% (95% CI, 86.85 to 94.87%) and κ of 0.85 (95% CI, 0.80 to 0.89). In saliva samples, viral and bacterial sensitivities were lower at 69.0% (95% CI, 57.47 to 79.76%) and 78.1% (95% CI, 71.60 to 83.76%), as were κ values at 0.64 (95% CI, 0.53 to 0.72) and 0.70 (95% CI, 0.65 to 0.76), respectively. Quality assessment for human biological material (18S rRNA) indicated perfect interrater agreement. At-home PC nasal swab samples performed comparably to NC swab samples, whereas PC saliva swab samples lacked sensitivity for the detection of respiratory microbes. IMPORTANCE RTIs are ubiquitous among children. Diagnosis involves a swab sample being taken by a health professional, which places a considerable burden on community health care systems, given the number of cases involved. The coronavirus disease 2019 (COVID-19) pandemic has seen an increase in the at-home self-collection of upper respiratory tract swab samples without the involvement of health professionals. It is advised that parents conduct or supervise swabbing of children. Surprisingly, few studies have addressed the quality of PC swab samples for subsequent identification of respiratory pathogens. We compared NC and PC nasal and saliva swab samples taken from the same child with RTI symptoms, for detection of respiratory pathogens. The PC nasal swab samples performed comparably to NC samples, whereas saliva swab samples lacked sensitivity for the detection of respiratory microbes. Collection of swab samples by parents would greatly reduce the burden on community nurses without reducing the effectiveness of diagnoses.
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22
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Kang HM, Kang JH. Effects of nasopharyngeal microbiota in respiratory infections and allergies. Clin Exp Pediatr 2021; 64:543-551. [PMID: 33872488 PMCID: PMC8566799 DOI: 10.3345/cep.2020.01452] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 04/02/2021] [Indexed: 11/27/2022] Open
Abstract
The human microbiome, which consists of a collective cluster of commensal, symbiotic, and pathogenic microorganisms living in the human body, plays a key role in host health and immunity. The human nasal cavity harbors commensal bacteria that suppress the colonization of opportunistic pathogens. However, dysbiosis of the nasal microbial community is associated with many diseases, such as acute respiratory infections including otitis media, sinusitis and bronchitis and allergic respiratory diseases including asthma. The nasopharyngeal acquisition of pneumococcus, which exists as a pathobiont in the nasal cavity, is the initial step in virtually all pneumococcal diseases. Although the factors influencing nasal colonization and elimination are not fully understood, the adhesion of opportunistic pathogens to nasopharyngeal mucosa receptors and the eliciting of immune responses in the host are implicated in addition to bacterial microbiota properties and colonization resistance dynamics. Probiotics or synbiotic interventions may show promising and effective roles in the adjunctive treatment of dysbiosis; however, more studies are needed to characterize how these interventions can be applied in clinical practice in the future.
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Affiliation(s)
- Hyun Mi Kang
- Division of Pediatric Infectious Diseases, Departments of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jin Han Kang
- Division of Pediatric Infectious Diseases, Departments of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Korea
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23
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Penela-Sánchez D, González-de-Audicana J, Armero G, Henares D, Esteva C, de-Sevilla MF, Ricart S, Jordan I, Brotons P, Cabrerizo M, Muñoz-Almagro C, Launes C. Lower Respiratory Tract Infection and Genus Enterovirus in Children Requiring Intensive Care: Clinical Manifestations and Impact of Viral Co-Infections. Viruses 2021; 13:2059. [PMID: 34696489 PMCID: PMC8541154 DOI: 10.3390/v13102059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 10/07/2021] [Accepted: 10/08/2021] [Indexed: 12/15/2022] Open
Abstract
Infection by rhinovirus (RV) and enterovirus (EV) in children ranges from asymptomatic infection to severe lower respiratory tract infection (LRTI). This cohort study evaluates the clinical impact of RV/EV species, alone or in codetection with other viruses, in young children with severe LRTI. Seventy-one patients aged less than 5 years and admitted to the Paediatric Intensive Care Unit (PICU) of a reference children's hospital with RV or EV (RV/EV) LRTI were prospectively included from 1/2018 to 3/2020. A commercial PCR assay for multiple respiratory pathogens was performed in respiratory specimens. In 22/71, RV/EV + respiratory syncytial virus (RSV) was found, and 18/71 had RV/EV + multiple viral detections. Patients with single RV/EV detection required invasive mechanical ventilation (IMV) as frequently as those with RSV codetection, whereas none of those with multiple viral codetections required IMV. Species were determined in 60 samples, 58 being RV. No EV-A, EV-C, or EV-D68 were detected. RV-B and EV-B were only found in patients with other respiratory virus codetections. There were not any associations between RV/EV species and severity outcomes. To conclude, RV/EV detection alone was observed in young children with severe disease, while multiple viral codetections may result in reduced clinical severity. Differences in pathogenicity between RV and EV species could not be drawn.
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Affiliation(s)
- Daniel Penela-Sánchez
- Paediatrics Department, Hospital Sant Joan de Déu, 08195 Barcelona, Spain; (D.P.-S.); (G.A.); (M.-F.d.-S.); (S.R.)
- Paediatrics Intensive Care Unit, Hospital Sant Joan de Déu, 08195 Barcelona, Spain;
| | - Jon González-de-Audicana
- Enterovirus and Viral Gastroenteritis Unit, Centro Nacional de Microbiología, Instituto Carlos III, 28222 Madrid, Spain; (J.G.-d.-A.); (M.C.)
| | - Georgina Armero
- Paediatrics Department, Hospital Sant Joan de Déu, 08195 Barcelona, Spain; (D.P.-S.); (G.A.); (M.-F.d.-S.); (S.R.)
- Paediatrics Intensive Care Unit, Hospital Sant Joan de Déu, 08195 Barcelona, Spain;
| | - Desiree Henares
- Grupo de Investigación en Enfermedades Infecciosas Pediátricas, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, 08195 Barcelona, Spain; (D.H.); (C.E.); (P.B.); (C.M.-A.)
- Molecular Microbiology Department, Hospital Sant Joan de Déu, 08195 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Cristina Esteva
- Grupo de Investigación en Enfermedades Infecciosas Pediátricas, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, 08195 Barcelona, Spain; (D.H.); (C.E.); (P.B.); (C.M.-A.)
- Molecular Microbiology Department, Hospital Sant Joan de Déu, 08195 Barcelona, Spain
| | - Mariona-Fernández de-Sevilla
- Paediatrics Department, Hospital Sant Joan de Déu, 08195 Barcelona, Spain; (D.P.-S.); (G.A.); (M.-F.d.-S.); (S.R.)
- Grupo de Investigación en Enfermedades Infecciosas Pediátricas, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, 08195 Barcelona, Spain; (D.H.); (C.E.); (P.B.); (C.M.-A.)
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Paediatrics Department, Faculty of Medicine and Health Sciences, Universitat de Barcelona, 08007 Barcelona, Spain
| | - Silvia Ricart
- Paediatrics Department, Hospital Sant Joan de Déu, 08195 Barcelona, Spain; (D.P.-S.); (G.A.); (M.-F.d.-S.); (S.R.)
- Paediatrics Department, Faculty of Medicine and Health Sciences, Universitat de Barcelona, 08007 Barcelona, Spain
| | - Iolanda Jordan
- Paediatrics Intensive Care Unit, Hospital Sant Joan de Déu, 08195 Barcelona, Spain;
- Grupo de Investigación en Enfermedades Infecciosas Pediátricas, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, 08195 Barcelona, Spain; (D.H.); (C.E.); (P.B.); (C.M.-A.)
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Paediatrics Department, Faculty of Medicine and Health Sciences, Universitat de Barcelona, 08007 Barcelona, Spain
| | - Pedro Brotons
- Grupo de Investigación en Enfermedades Infecciosas Pediátricas, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, 08195 Barcelona, Spain; (D.H.); (C.E.); (P.B.); (C.M.-A.)
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Department of Medicine, School of Medicine, Universitat Internacional de Catalunya, 08017 Barcelona, Spain
| | - María Cabrerizo
- Enterovirus and Viral Gastroenteritis Unit, Centro Nacional de Microbiología, Instituto Carlos III, 28222 Madrid, Spain; (J.G.-d.-A.); (M.C.)
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Carmen Muñoz-Almagro
- Grupo de Investigación en Enfermedades Infecciosas Pediátricas, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, 08195 Barcelona, Spain; (D.H.); (C.E.); (P.B.); (C.M.-A.)
- Molecular Microbiology Department, Hospital Sant Joan de Déu, 08195 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Department of Medicine, School of Medicine, Universitat Internacional de Catalunya, 08017 Barcelona, Spain
| | - Cristian Launes
- Paediatrics Department, Hospital Sant Joan de Déu, 08195 Barcelona, Spain; (D.P.-S.); (G.A.); (M.-F.d.-S.); (S.R.)
- Grupo de Investigación en Enfermedades Infecciosas Pediátricas, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, 08195 Barcelona, Spain; (D.H.); (C.E.); (P.B.); (C.M.-A.)
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Paediatrics Department, Faculty of Medicine and Health Sciences, Universitat de Barcelona, 08007 Barcelona, Spain
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24
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Jinhage M, Hermansson A, Gisselsson-Solén M. Nasopharyngeal cultures in children with AOM - A retrospective study on bacteriological findings and impact on management. Int J Pediatr Otorhinolaryngol 2021; 149:110848. [PMID: 34304116 DOI: 10.1016/j.ijporl.2021.110848] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 06/09/2021] [Accepted: 07/18/2021] [Indexed: 11/27/2022]
Abstract
BACKGROUND Despite a far from perfect correlation with middle ear growth, nasopharyngeal cultures are sometimes used in children with acute otitis media (AOM) in order to have some idea of the causative pathogen. How these cultures are used in clinical practice and to what extent they influence clinical management has not previously been studied. The objective with this study was to investigate in what circumstances nasopharyngeal cultures are performed in children with AOM, what the bacteriological results are and to what extent cultures influence clinical management. METHODS All nasopharyngeal cultures taken in clinical practice from children with AOM in the county of Skåne, Sweden, during 2017-2018 were retrieved together with details from the medical charts two months prior to and one month after the culture. Information about the reason for culturing, the bacteriological result, and whether this result changed the management of the child, was retrieved from the charts. RESULTS During the 2 years, 978 nasopharyngeal cultures were taken in children with AOM. The most common reasons for obtaining a culture was a recurrence of AOM (40%) or treatment failure (22%). Many of the children had ongoing or recent antibiotic treatment. M. catarrhalis was the most commonly identified pathogen (53%), followed by H. influenzae (30%) and S. pneumoniae (14%). Resistance rates were low, and the most commonly identified resistant pathogen was betalactamase-negative ampicillin-resistant H. influenzae. One in five cultures led to a change in management, such as a change of antibiotics or an additional check-up. This was most commonly seen in association with H. influenzae, reflecting clinical practice in Sweden, where AOM is primarily treated with penicillin V. CONCLUSION Despite not having a perfect correlation with middle ear growth, nasopharyngeal cultures can provide clues about suitable alternative antibiotics in cases of treatment failure, and they can help monitoring nasopharyngeal carriage and resistance rates.
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Affiliation(s)
- Malin Jinhage
- Skåne University Hospital, Sweden; Department of Otorhinolaryngology, Head and Neck Surgery, Lund University Hospital, 22185, Lund, Sweden.
| | - Ann Hermansson
- Department of Otorhinolaryngology, Head and Neck Surgery, Lund University Hospital, 22185, Lund, Sweden
| | - Marie Gisselsson-Solén
- Department of Otorhinolaryngology, Head and Neck Surgery, Lund University Hospital, 22185, Lund, Sweden
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25
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Diaz-Diaz A, Bunsow E, Garcia-Maurino C, Moore-Clingenpeel M, Naples J, Juergensen A, Mertz S, Wang H, Leber AL, Gern J, Hall MW, Cohen DM, Ramilo O, Mejias A. Nasopharyngeal Codetection of H. influenzae and S. pneumoniae and Respiratory Syncytial Virus Disease Outcomes in Children. J Infect Dis 2021; 225:912-923. [PMID: 34543409 DOI: 10.1093/infdis/jiab481] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 09/16/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The role of nasopharyngeal bacteria on RSV disease has been underestimated. We measured the frequency and quantitative detection of potentially pathogenic bacteria in the upper respiratory tract of infants with RSV infection over seven respiratory seasons, and their impact on clinical outcomes. METHODS Children <2 years old with mild (outpatients; n=115) or severe (inpatients; n=566) RSV infection, and matched healthy controls (n=161) were prospectively enrolled. Nasopharyngeal samples were obtained for RSV, S. pneumoniae, S. aureus, M. catarrhalis, and H. influenzae detection and quantitation by PCR. Multivariable models were constructed to identify variables predictive of severe disease. RESULTS S. pneumoniae, H. influenzae, and M. catarrhalis, but not S. aureus, were detected more frequently in RSV-infected children (84%) than healthy controls (46%; p<0.001). Detection of S. pneumoniae and/or H. influenzae was associated with fever, more frequent antibiotic treatment, worse radiologic findings, and higher neutrophil counts (p<0.01). In adjusted analyses S. pneumoniae/H. influenzae co-detection was associated with greater odds (OR; 95% CI) of hospitalization (2.25 [1.07-4.74), higher disease severity scores (1.93 [1.14-3.26]), prolonged oxygen administration (2.23 [1.01-4.91]), and longer hospitalization (2.53 [1.33-4.79]). CONCLUSIONS Nasopharyngeal co-detection of S. pneumoniae and H. influenzae in infants with RSV infection is associated with increased disease severity.
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Affiliation(s)
- Alejandro Diaz-Diaz
- Division of Infectious Diseases, Department of Pediatrics, Nationwide Children's Hospital-The Ohio State University College of Medicine, Columbus, OH, USA
| | - Eleonora Bunsow
- Center for Vaccines & Immunity, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Cristina Garcia-Maurino
- Center for Vaccines & Immunity, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Melissa Moore-Clingenpeel
- Biostatistics Resource Core, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Jeffrey Naples
- Division of Critical Care Medicine, Department of Pediatrics, Nationwide Children's Hospital, Columbus, OH, USA
| | - Alexis Juergensen
- Center for Vaccines & Immunity, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Sara Mertz
- Center for Vaccines & Immunity, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Huanyu Wang
- Department of Laboratory Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Amy L Leber
- Department of Laboratory Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - James Gern
- Department of Pediatrics. University of Wisconsin, School of Medicine and Public Health. Madison WI, USA
| | - Mark W Hall
- Division of Critical Care Medicine, Department of Pediatrics, Nationwide Children's Hospital, Columbus, OH, USA
| | - Daniel M Cohen
- Division of Emergency Medicine, Department of Pediatrics, Nationwide Children's Hospital, Columbus, OH, USA
| | - Octavio Ramilo
- Division of Infectious Diseases, Department of Pediatrics, Nationwide Children's Hospital-The Ohio State University College of Medicine, Columbus, OH, USA.,Center for Vaccines & Immunity, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Asuncion Mejias
- Division of Infectious Diseases, Department of Pediatrics, Nationwide Children's Hospital-The Ohio State University College of Medicine, Columbus, OH, USA.,Center for Vaccines & Immunity, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
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26
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Nesbitt H, Burke C, Haghi M. Manipulation of the Upper Respiratory Microbiota to Reduce Incidence and Severity of Upper Respiratory Viral Infections: A Literature Review. Front Microbiol 2021; 12:713703. [PMID: 34512591 PMCID: PMC8432964 DOI: 10.3389/fmicb.2021.713703] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 08/06/2021] [Indexed: 12/12/2022] Open
Abstract
There is a high incidence of upper respiratory viral infections in the human population, with infection severity being unique to each individual. Upper respiratory viruses have been associated previously with secondary bacterial infection, however, several cross-sectional studies analyzed in the literature indicate that an inverse relationship can also occur. Pathobiont abundance and/or bacterial dysbiosis can impair epithelial integrity and predispose an individual to viral infection. In this review we describe common commensal microorganisms that have the capacity to reduce the abundance of pathobionts and maintain bacterial symbiosis in the upper respiratory tract and discuss the potential and limitations of localized probiotic formulations of commensal bacteria to reduce the incidence and severity of viral infections.
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Affiliation(s)
- Henry Nesbitt
- Discipline of Pharmacy, Graduate School Health, University of Technology Sydney, Sydney, NSW, Australia
| | - Catherine Burke
- School of Life Sciences, University of Technology Sydney, Sydney, NSW, Australia
| | - Mehra Haghi
- Discipline of Pharmacy, Graduate School Health, University of Technology Sydney, Sydney, NSW, Australia
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27
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Li ZJ, Zhang HY, Ren LL, Lu QB, Ren X, Zhang CH, Wang YF, Lin SH, Zhang XA, Li J, Zhao SW, Yi ZG, Chen X, Yang ZS, Meng L, Wang XH, Liu YL, Wang X, Cui AL, Lai SJ, Jiang T, Yuan Y, Shi LS, Liu MY, Zhu YL, Zhang AR, Zhang ZJ, Yang Y, Ward MP, Feng LZ, Jing HQ, Huang LY, Xu WB, Chen Y, Wu JG, Yuan ZH, Li MF, Wang Y, Wang LP, Fang LQ, Liu W, Hay SI, Gao GF, Yang WZ. Etiological and epidemiological features of acute respiratory infections in China. Nat Commun 2021; 12:5026. [PMID: 34408158 PMCID: PMC8373954 DOI: 10.1038/s41467-021-25120-6] [Citation(s) in RCA: 116] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 07/26/2021] [Indexed: 12/18/2022] Open
Abstract
Nationwide prospective surveillance of all-age patients with acute respiratory infections was conducted in China between 2009‒2019. Here we report the etiological and epidemiological features of the 231,107 eligible patients enrolled in this analysis. Children <5 years old and school-age children have the highest viral positivity rate (46.9%) and bacterial positivity rate (30.9%). Influenza virus, respiratory syncytial virus and human rhinovirus are the three leading viral pathogens with proportions of 28.5%, 16.8% and 16.7%, and Streptococcus pneumoniae, Mycoplasma pneumoniae and Klebsiella pneumoniae are the three leading bacterial pathogens (29.9%, 18.6% and 15.8%). Negative interactions between viruses and positive interactions between viral and bacterial pathogens are common. A Join-Point analysis reveals the age-specific positivity rate and how this varied for individual pathogens. These data indicate that differential priorities for diagnosis, prevention and control should be highlighted in terms of acute respiratory tract infection patients' demography, geographic locations and season of illness in China.
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Affiliation(s)
- Zhong-Jie Li
- Division of Infectious Disease, Key Laboratory of Surveillance and Early-warning on Infectious Disease, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hai-Yang Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Li-Li Ren
- Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qing-Bin Lu
- Department of Laboratorial Science and Technology, School of Public Health, Peking University, Beijing, China
| | - Xiang Ren
- Division of Infectious Disease, Key Laboratory of Surveillance and Early-warning on Infectious Disease, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Cui-Hong Zhang
- Division of Infectious Disease, Key Laboratory of Surveillance and Early-warning on Infectious Disease, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yi-Fei Wang
- Division of Infectious Disease, Key Laboratory of Surveillance and Early-warning on Infectious Disease, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Sheng-Hong Lin
- Division of Infectious Disease, Key Laboratory of Surveillance and Early-warning on Infectious Disease, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiao-Ai Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jun Li
- Sun Yat-sen University, Guangzhou, China
| | - Shi-Wen Zhao
- Yunnan Center for Disease Control and Prevention, Kunming, China
| | - Zhi-Gang Yi
- Shanghai Public Health Clinical Center, Shanghai, China
| | - Xiao Chen
- Zhejiang University, Hangzhou, China
| | - Zuo-Sen Yang
- Liaoning Provincial Center for Disease Control and Prevention, Shenyang, China
| | - Lei Meng
- Gansu Provincial Center for Disease Control and Prevention, Lanzhou, China
| | - Xin-Hua Wang
- Gansu Provincial Center for Disease Control and Prevention, Lanzhou, China
| | | | - Xin Wang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Ai-Li Cui
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Sheng-Jie Lai
- Division of Infectious Disease, Key Laboratory of Surveillance and Early-warning on Infectious Disease, Chinese Center for Disease Control and Prevention, Beijing, China.,School of Geography and Environmental Science, University of Southampton, Southampton, UK.,School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Tao Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yang Yuan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lu-Sha Shi
- Division of Infectious Disease, Key Laboratory of Surveillance and Early-warning on Infectious Disease, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Meng-Yang Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yu-Liang Zhu
- Division of Infectious Disease, Key Laboratory of Surveillance and Early-warning on Infectious Disease, Chinese Center for Disease Control and Prevention, Beijing, China
| | - An-Ran Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zhi-Jie Zhang
- Department of Epidemiology and Health Statistics, School of Public Health, Fudan University, Shanghai, China
| | - Yang Yang
- Department of Biostatistics, College of Public Health and Health Professions, and Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Michael P Ward
- Sydney School of Veterinary Science, The University of Sydney, Camden, NSW, Australia
| | - Lu-Zhao Feng
- Division of Infectious Disease, Key Laboratory of Surveillance and Early-warning on Infectious Disease, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Huai-Qi Jing
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Liu-Yu Huang
- The Institute for Disease Prevention and Control of PLA, Beijing, China
| | - Wen-Bo Xu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yu Chen
- Zhejiang University, Hangzhou, China
| | | | | | | | - Yu Wang
- Chinese Centre for Disease Control and Prevention, Beijing, China
| | - Li-Ping Wang
- Division of Infectious Disease, Key Laboratory of Surveillance and Early-warning on Infectious Disease, Chinese Center for Disease Control and Prevention, Beijing, China.
| | - Li-Qun Fang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China.
| | - Wei Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China.
| | - Simon I Hay
- Department of Health Metrics Sciences, School of Medicine, University of Washington, Seattle, WA, USA.,Institute for Health Metrics and Evaluation, University of Washington, Seattle, WA, USA
| | - George F Gao
- Chinese Centre for Disease Control and Prevention, Beijing, China
| | - Wei-Zhong Yang
- Chinese Centre for Disease Control and Prevention, Beijing, China
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Hullegie S, Venekamp RP, van Dongen TMA, Hay AD, Moore MV, Little P, Schilder AGM, Damoiseaux RAMJ. Prevalence and Antimicrobial Resistance of Bacteria in Children With Acute Otitis Media and Ear Discharge: A Systematic Review. Pediatr Infect Dis J 2021; 40:756-762. [PMID: 34166300 PMCID: PMC8274581 DOI: 10.1097/inf.0000000000003134] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/15/2021] [Indexed: 11/26/2022]
Abstract
BACKGROUND Of children with acute otitis media (AOM), 15%-20% present with acute onset ear discharge due to a spontaneous perforation of the tympanic membrane (AOMd). This review aims to quantify the prevalence and antimicrobial resistance (AMR) status of bacteria in children with AOMd in the pneumococcal conjugate vaccine (PCV) era. METHODS Systematic searches were performed in PubMed, EMBASE and Cochrane Library from inception to June 7, 2019. Two reviewers extracted relevant data and assessed risk of bias independently. All English studies reporting any prevalence and/or AMR data of bacterial middle ear isolates from children with AOMd were included. Risk of bias was assessed using the Joanna Briggs Institute Critical Appraisal checklist. RESULTS Of 4088 unique records retrieved, 19 studies (10,560 children) were included. Overall quality was judged good. Streptococcus pneumoniae (median 26.1%, range 9.1%-47.9%), Haemophilus influenzae (median 18.8%, range 3.9%-55.3%), Staphylococcus aureus (median 12.3%, range 2.3%-34.9%) and Streptococcus pyogenes (median 11.8%, range 1.0%-30.9%) were the most prevalent bacteria. In 76.0% (median, range 48.7%-100.0%, 19 studies, 1,429 children) any bacterium was identified. AMR data were sparse and mainly limited to S. pneumoniae. We found no evidence of a clear shift in the prevalence of bacteria and AMR over time. CONCLUSIONS In children with AOMd, S. pneumoniae and H. influenzae are the 2 predominant bacteria, followed by S. aureus and S. pyogenes in the post-PCV era. AMR data are sparse and no clearly change over time was observed. Ongoing surveillance of the microbiology profile in children with AOMd is warranted to guide antibiotic selection and to assess the impact of children's PCV status.
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Affiliation(s)
- Saskia Hullegie
- From the Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Roderick P. Venekamp
- From the Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Thijs M. A. van Dongen
- From the Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Alastair D. Hay
- Centre for Academic Primary Care, Bristol Medical School: Population Health Sciences, University of Bristol, Bristol
| | - Michael V. Moore
- Primary Care and Population Sciences Unit, Aldermoor Health Centre, University of Southampton, Southampton
| | - Paul Little
- Primary Care and Population Sciences Unit, Aldermoor Health Centre, University of Southampton, Southampton
| | - Anne G. M. Schilder
- From the Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- NIHR UCLH BRC, evidENT, Ear Institute, University College London, London, United Kingdom
| | - Roger A. M. J. Damoiseaux
- From the Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
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Abstract
The nasopharyngeal microbiome is a dynamic microbial interface of the aerodigestive tract, and a diagnostic window in the fight against respiratory infections and antimicrobial resistance. As its constituent bacteria, viruses and mycobacteria become better understood and sampling accuracy improves, diagnostics of the nasopharynx could guide more personalized care of infections of surrounding areas including the lungs, ears and sinuses. This review will summarize the current literature from a clinical perspective and highlight its growing importance in diagnostics and infectious disease management.
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Affiliation(s)
- Matthew Flynn
- School of Biomedical Sciences, Ulster University, Coleraine BT52 1SA, UK
- Otolaryngology Department, Queen Elizabeth University Hospital, Glasgow G51 4TF, UK
| | - James Dooley
- School of Biomedical Sciences, Ulster University, Coleraine BT52 1SA, UK
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30
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Khan T, Das RS, Chaudhary A, Chatterjee J, Bhattacharya SD. Association of nasopharyngeal viruses and pathogenic bacteria in children and their parents with and without HIV. Pneumonia (Nathan) 2021; 13:8. [PMID: 33947476 PMCID: PMC8096464 DOI: 10.1186/s41479-021-00088-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 04/21/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Bacteria and respiratory viruses co-occur in the nasopharynx, and their interactions may impact pathogenesis of invasive disease. Associations of viruses and bacteria in the nasopharynx may be affected by HIV. METHODS We conducted a nested case-control study from a larger cohort study of banked nasopharyngeal swabs from families with and without HIV in West Bengal India, to look at the association of viruses and bacteria in the nasopharynx of parents and children when they are asymptomatic. Quantitative polymerase chain reaction for 4 bacteria and 21 respiratory viruses was run on 92 random nasopharyngeal swabs from children--49 from children living with HIV (CLH) and 43 from HIV uninfected children (HUC)-- and 77 swabs from their parents (44 parents of CLH and 33 parents of HUC). RESULTS Bacteria was found in 67% of children, viruses in 45%, and both in 27% of child samples. Staphylococcus aureus (53%) was the most common bacteria, followed by Streptococcus pneumoniae (pneumococcus) (37%) in children and parents (53, 20%). Regardless of HIV status, viruses were detected in higher numbers (44%) in children than their parents (30%) (p = 0.049), particularly rhinovirus (p = 0.02). Human rhinovirus was the most frequently found virus in both CLH and HUC. Children with adenovirus were at six times increased risk of also having pneumococcus (Odds ratio OR 6, 95% CI 1.12-31.9) regardless of HIV status. In addition, the presence of rhinovirus in children was associated with increased pneumococcal density (Regression coeff 4.5, 1.14-7.9). In CLH the presence of rhinovirus increased the risk of pneumococcal colonization by nearly sixteen times (OR 15.6, 1.66-146.4), and, pneumococcus and S. aureus dual colonization by nearly nine times (OR 8.7). CONCLUSIONS Children more frequently carried viruses regardless of HIV status. In CLH the presence of rhinovirus, the most frequently detected virus, significantly increased co-colonization with pneumococcus and S. aureus.
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Affiliation(s)
- Tila Khan
- School of Medical Science & Technology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302 India
| | - Ranjan Saurav Das
- School of Medical Science & Technology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302 India
| | - Amrita Chaudhary
- School of Medical Science & Technology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302 India
| | - Jyotirmoy Chatterjee
- School of Medical Science & Technology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302 India
| | - Sangeeta Das Bhattacharya
- School of Medical Science & Technology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302 India
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31
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Liu Z, Ma A, Mathé E, Merling M, Ma Q, Liu B. Network analyses in microbiome based on high-throughput multi-omics data. Brief Bioinform 2021; 22:1639-1655. [PMID: 32047891 PMCID: PMC7986608 DOI: 10.1093/bib/bbaa005] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 01/07/2020] [Accepted: 01/08/2020] [Indexed: 02/06/2023] Open
Abstract
Together with various hosts and environments, ubiquitous microbes interact closely with each other forming an intertwined system or community. Of interest, shifts of the relationships between microbes and their hosts or environments are associated with critical diseases and ecological changes. While advances in high-throughput Omics technologies offer a great opportunity for understanding the structures and functions of microbiome, it is still challenging to analyse and interpret the omics data. Specifically, the heterogeneity and diversity of microbial communities, compounded with the large size of the datasets, impose a tremendous challenge to mechanistically elucidate the complex communities. Fortunately, network analyses provide an efficient way to tackle this problem, and several network approaches have been proposed to improve this understanding recently. Here, we systemically illustrate these network theories that have been used in biological and biomedical research. Then, we review existing network modelling methods of microbial studies at multiple layers from metagenomics to metabolomics and further to multi-omics. Lastly, we discuss the limitations of present studies and provide a perspective for further directions in support of the understanding of microbial communities.
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Affiliation(s)
- Zhaoqian Liu
- Department of Biomedical Informatics, College of Medicine, the Ohio State University, Columbus, OH 43210, USA
| | - Anjun Ma
- Department of Biomedical Informatics, College of Medicine, the Ohio State University, Columbus, OH 43210, USA
| | - Ewy Mathé
- Department of Biomedical Informatics, College of Medicine, the Ohio State University, Columbus, OH 43210, USA
| | - Marlena Merling
- Department of Biomedical Informatics, College of Medicine, the Ohio State University, Columbus, OH 43210, USA
| | - Qin Ma
- Department of Biomedical Informatics, College of Medicine, the Ohio State University, Columbus, OH 43210, USA
| | - Bingqiang Liu
- Department of Biomedical Informatics, College of Medicine, the Ohio State University, Columbus, OH 43210, USA
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32
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Dysbiosis in Pediatrics Is Associated with Respiratory Infections: Is There a Place for Bacterial-Derived Products? Microorganisms 2021; 9:microorganisms9020448. [PMID: 33671586 PMCID: PMC7926342 DOI: 10.3390/microorganisms9020448] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/12/2021] [Accepted: 02/17/2021] [Indexed: 12/22/2022] Open
Abstract
Respiratory tract infections (RTIs) are common in childhood because of the physiologic immaturity of the immune system, a microbial community under development in addition to other genetic, physiological, environmental and social factors. RTIs tend to recur and severe lower viral RTIs in early childhood are not uncommon and are associated with increased risk of respiratory disorders later in life, including recurrent wheezing and asthma. Therefore, a better understanding of the main players and mechanisms involved in respiratory morbidity is necessary for a prompt and improved care as well as for primary prevention. The inter-talks between human immune components and microbiota as well as their main functions have been recently unraveled; nevertheless, more is still to be discovered or understood in the above medical conditions. The aim of this review paper is to provide the most up-to-date overview on dysbiosis in pre-school children and its association with RTIs and their complications. The potential role of non-harmful bacterial-derived products, according to the old hygiene hypothesis and the most recent trained-innate immunity concept, will be discussed together with the need of proof-of-concept studies and larger clinical trials with immunological and microbiological endpoints.
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33
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Understanding Human Microbiota Offers Novel and Promising Therapeutic Options against Candida Infections. Pathogens 2021; 10:pathogens10020183. [PMID: 33572162 PMCID: PMC7915436 DOI: 10.3390/pathogens10020183] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 01/20/2021] [Accepted: 02/02/2021] [Indexed: 12/12/2022] Open
Abstract
Human fungal pathogens particularly of Candida species are one of the major causes of hospital acquired infections in immunocompromised patients. The limited arsenal of antifungal drugs to treat Candida infections with concomitant evolution of multidrug resistant strains further complicates the management of these infections. Therefore, deployment of novel strategies to surmount the Candida infections requires immediate attention. The human body is a dynamic ecosystem having microbiota usually involving symbionts that benefit from the host, but in turn may act as commensal organisms or affect positively (mutualism) or negatively (pathogenic) the physiology and nourishment of the host. The composition of human microbiota has garnered a lot of recent attention, and despite the common occurrence of Candida spp. within the microbiota, there is still an incomplete picture of relationships between Candida spp. and other microorganism, as well as how such associations are governed. These relationships could be important to have a more holistic understanding of the human microbiota and its connection to Candida infections. Understanding the mechanisms behind commensalism and pathogenesis is vital for the development of efficient therapeutic strategies for these Candida infections. The concept of host-microbiota crosstalk plays critical roles in human health and microbiota dysbiosis and is responsible for various pathologies. Through this review, we attempted to analyze the types of human microbiota and provide an update on the current understanding in the context of health and Candida infections. The information in this article will help as a resource for development of targeted microbial therapies such as pre-/pro-biotics and microbiota transplant that has gained advantage in recent times over antibiotics and established as novel therapeutic strategy.
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34
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Jullien S, Sharma R, Lhamu Mynak M, Henares D, Muñoz-Almagro C, Bassat Q. Pneumococcal nasopharyngeal carriage among Bhutanese children hospitalized with clinical pneumonia: serotypes and viral co-infection. BMC Infect Dis 2020; 20:940. [PMID: 33297987 PMCID: PMC7725031 DOI: 10.1186/s12879-020-05674-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 11/30/2020] [Indexed: 10/26/2022] Open
Abstract
BACKGROUND Pneumococcal nasopharyngeal colonization (PNC) generally precedes pneumococcal disease. The purpose of this study was to determine the prevalence of PNC and to identify the pneumococcal serotypes circulating among Bhutanese children under five years of age admitted with clinical pneumonia, before the introduction of pneumococcal conjugate vaccine (PCV13) in the country. We also aimed to contribute to the understanding of the interplay between PNC and viral co-infection among this population. METHODS This was a prospective study conducted at the Jigme Dorji Wangchuck National Referral Hospital in Bhutan over 12 consecutive months. Children aged 2 to 59 months admitted with WHO-defined clinical pneumonia were eligible for recruitment. We collected blood for bacterial culture and molecular identification of S. pneumoniae, and nasopharyngeal washing for screening of respiratory viruses, and for the detection and capsular typing of S. pneumoniae by real-time polymerase chain reaction (RT-PCR). RESULTS Overall, 189 children were recruited, and PNC was tested in 121 of them (64.0%). PNC was found in 76/121 children (62.8%) and S. pneumoniae was identified in blood (both by culture and RT-PCR) in a single child. Respiratory viruses were detected in a similar proportion among children with (62/70; 88.6%) and without PNC (36/40; 90.0%; p = 1.000), but rhinovirus detection was less common among children with PNC (20/70; 28.6% versus 19/40; 47.5%; p = 0.046). Capsular typing identified 30 different serotypes. Thirty-nine children (51.3%) were colonised with two to five different serotypes. A third of the children presented with serotypes considered highly invasive. Over half of the children (44/76; 57.9%) were carrying at least one serotype included in PCV13. CONCLUSIONS This study provides baseline information on the status of PNC among Bhutanese children admitted with clinical pneumonia prior to the introduction of PCV13, which is valuable to monitor its potential impact. PCV13 could theoretically have averted up to 58% of the pneumococcal infections among the children in this study, suggesting a future role for the vaccine to significantly reduce the burden associated with S. pneumoniae in Bhutan.
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Affiliation(s)
- Sophie Jullien
- Barcelona Institute for Global Health (ISGlobal), Hospital Clinic, Universitat de Barcelona, Barcelona, Spain. .,Jigme Dorji Wangchuck National Referral Hospital, Thimphu, Bhutan.
| | - Ragunath Sharma
- Jigme Dorji Wangchuck National Referral Hospital, Thimphu, Bhutan
| | - Mimi Lhamu Mynak
- Jigme Dorji Wangchuck National Referral Hospital, Thimphu, Bhutan
| | - Desiree Henares
- Instituto de Recerca Pediatrica, Hospital Sant Joan de Deu (University of Barcelona), Barcelona, Spain.,CIBER of Epidemiology and Public Health CIBERESP, Madrid, Spain
| | - Carmen Muñoz-Almagro
- Instituto de Recerca Pediatrica, Hospital Sant Joan de Deu (University of Barcelona), Barcelona, Spain.,CIBER of Epidemiology and Public Health CIBERESP, Madrid, Spain.,Department of Medicine, Universitat Internacional of Catalunya, Barcelona, Spain
| | - Quique Bassat
- Barcelona Institute for Global Health (ISGlobal), Hospital Clinic, Universitat de Barcelona, Barcelona, Spain.,CIBER of Epidemiology and Public Health CIBERESP, Madrid, Spain.,Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain.,Pediatric Infectious Diseases Unit, Pediatrics Department, Hospital Sant Joan de Déu (University of Barcelona), Barcelona, Spain.,Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
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35
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Chen J, Tian C, Cheng X, Wang R, Zhou H, Zeng X. A case of asymptomatic SARS-CoV-2 infection followed by secondary community acquired pneumonia. Quant Imaging Med Surg 2020; 10:2208-2211. [PMID: 33139999 DOI: 10.21037/qims-20-847] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Jiaxiang Chen
- Guizhou University School of Medicine, Guiyang, China.,Department of Medical Imaging, Guizhou Provincial People's Hospital, Guiyang, China
| | - Chong Tian
- Department of Medical Imaging, Guizhou Provincial People's Hospital, Guiyang, China
| | - Xinge Cheng
- Department of Graduate School, Zunyi Medical University, Zunyi, China
| | - Rongpin Wang
- Department of Medical Imaging, Guizhou Provincial People's Hospital, Guiyang, China
| | - Hourong Zhou
- Department of Medical Imaging, Guizhou Provincial People's Hospital, Guiyang, China.,Department of Research and Education, Jiangjunshan Hospital of Guizhou Province, Guiyang, China
| | - Xianchun Zeng
- Department of Medical Imaging, Guizhou Provincial People's Hospital, Guiyang, China
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36
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Grimwood K, Lambert SB, Ware RS. Endemic Non-SARS-CoV-2 Human Coronaviruses in a Community-Based Australian Birth Cohort. Pediatrics 2020; 146:peds.2020-009316. [PMID: 32887791 DOI: 10.1542/peds.2020-009316] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/27/2020] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND AND OBJECTIVES The coronavirus (CoV) disease 2019 pandemic has drawn attention to the CoV virus family. However, in community settings, there is limited information on these viruses in healthy children. We explored the epidemiology of the 4 endemic (non-severe acute respiratory syndrome CoV 2) human coronaviruses (HCoVs) by species, including acute illness episodes, risk factors, and health care burden in Australian children in the first 2 years of life. METHODS The Observational Research in Childhood Infectious Diseases community-based cohort was a prospective study of acute respiratory illnesses in children from birth until their second birthday. Parents recorded daily symptoms, maintained an illness-burden diary, and collected weekly nasal swabs, which were tested for 17 respiratory viruses, including HCoVs, by real-time polymerase chain reaction assays. RESULTS Overall, 158 children participating in Observational Research in Childhood Infectious Diseases provided 11 126 weekly swabs, of which 168 were HCoV-positive involving 130 incident episodes. HCoV-NL63 and HCoV-OC43 were most commonly detected, accounting for two-thirds of episodes. Whereas 30 children had different HCoVs detected on different occasions, 7 were reinfected with the same species. HCoV incidence in the first 2 years of life was 0.76 episodes per child-year (95% confidence interval [CI] 0.63 to 0.91), being greatest in the second year (1.06; 95% CI 0.84 to 1.33) and during winter (1.32; 95% CI 1.02 to 1.71). Fifty percent of HCoV episodes were symptomatic, and 24.2% led to health care contact. CONCLUSIONS In children, HCoV infections are common, recurrent, and frequently asymptomatic. In future studies, researchers should determine transmission pathways and immune mechanisms.
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Affiliation(s)
- Keith Grimwood
- School of Medicine and Menzies Health Institute Queensland, Griffith University, Southport, Queensland, Australia; .,Departments of Paediatrics and Infectious Diseases, Gold Coast Health, Southport, Queensland, Australia; and
| | - Stephen B Lambert
- National Centre for Epidemiology and Population Health, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Robert S Ware
- School of Medicine and Menzies Health Institute Queensland, Griffith University, Southport, Queensland, Australia
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37
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Miellet WR, van Veldhuizen J, Nicolaie MA, Mariman R, Bootsma HJ, Bosch T, Rots NY, Sanders EAM, van Beek J, Trzciński K. Influenza-like Illness Exacerbates Pneumococcal Carriage in Older Adults. Clin Infect Dis 2020; 73:e2680-e2689. [PMID: 33124669 DOI: 10.1093/cid/ciaa1551] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND In older adults pneumococcal disease is strongly associated with respiratory viral infections, but the impact of viruses on Streptococcus pneumoniae carriage prevalence and load remains poorly understood. Here, we investigated the effects of influenza-like illness (ILI) on pneumococcal carriage in community-dwelling older adults. METHODS We investigated the presence of pneumococcal DNA in saliva samples collected in the 2014/2015 influenza season from 232 individuals aged ≥60 years at ILI-onset, followed by sampling 2-3 weeks and 7-9 weeks after the first sample. We also sampled 194 age-matched controls twice 2-3 weeks apart. Pneumococcal DNA was detected with quantitative-PCRs targeting piaB and lytA genes in raw and in culture-enriched saliva. Bacterial and pneumococcal abundances were determined in raw saliva with 16S and piaB quantification. RESULTS The prevalence of pneumococcus-positive samples was highest at onset of ILI (18% or 42/232) and lowest among controls (13% or 26/194, and 11% or 22/194, at the first and second sampling moment, respectively), though these differences were not significant. Pneumococcal carriage was associated with exposure to young children (OR:2.71, 95%CI 1.51-5.02, p<0.001), and among asymptomatic controls with presence of rhinovirus infection (OR:4.23; 95%CI 1.16-14.22, p<0.05). When compared with carriers among controls, pneumococcal absolute abundances were significantly higher at onset of ILI (p<0.01), and remained elevated beyond recovery from ILI (p<0.05). Finally, pneumococcal abundances were highest in carriage events newly-detected after ILI-onset (estimated geometric mean 1.21E -5, 95%CI 2.48E -7-2.41E -5, compared with pre-existing carriage). CONCLUSIONS ILI exacerbates pneumococcal colonization of the airways in older adults, and this effect persists beyond recovery from ILI.
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Affiliation(s)
- Willem R Miellet
- Centre for Infectious Disease Control Netherlands, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands.,Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, The Netherlands
| | - Janieke van Veldhuizen
- Centre for Infectious Disease Control Netherlands, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Mioara A Nicolaie
- Centre for Infectious Disease Control Netherlands, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands.,Centre for Nutrition, Prevention and Care, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Rob Mariman
- Centre for Infectious Disease Control Netherlands, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Hester J Bootsma
- Centre for Infectious Disease Control Netherlands, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Thijs Bosch
- Centre for Infectious Disease Control Netherlands, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Nynke Y Rots
- Centre for Infectious Disease Control Netherlands, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Elisabeth A M Sanders
- Centre for Infectious Disease Control Netherlands, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands.,Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, The Netherlands
| | - Josine van Beek
- Centre for Infectious Disease Control Netherlands, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Krzysztof Trzciński
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, The Netherlands
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Muhandule Birindwa A, Gonzales-Siles L, Nordén R, Geravandi S, Tumusifu Manegabe J, Morisho L, Saili Mushobekwa S, Andersson R, Skovbjerg S. High bacterial and viral load in the upper respiratory tract of children in the Democratic Republic of the Congo. PLoS One 2020; 15:e0240922. [PMID: 33119683 PMCID: PMC7595347 DOI: 10.1371/journal.pone.0240922] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 10/05/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Respiratory pathogens including Streptococcus pneumoniae and Haemophilus influenzae, are implicated in the pathogenicity of acute lower respiratory infection (ALRI). These are also commonly found in both healthy and sick children. In this study, we describe the first data on the most frequent bacteria and viruses detected in the nasopharynx of children from the general population in the Eastern DR Congo. METHODS From January 2014 to June 2015, nasopharyngeal samples from 375 children aged from 2 to 60 months attending health centres for immunisation or growth monitoring were included in the study. Multiplex real-time PCR assays were used for detection of 15 different viruses and 5 bacterial species and for determination of pneumococcal serotypes/serogroups in the nasopharyngeal secretions. RESULTS High levels of S. pneumoniae were detected in 77% of cases, and H. influenzae in 51%. Rhinovirus and enterovirus were the most commonly found viruses, while respiratory syncytial virus (RSV) was rare (1%). Co-occurrence of both bacteria and viruses at high levels was detected in 33% of the children. The pneumococcal load was higher in those children who lived in a dwelling with an indoor kitchen area with an open fire, i.e. a kitchen with an open fire for cooking located inside the dwelling with the resultant smoke passing to the living room and/or bedrooms; this was also higher in children from rural areas as compared to children from urban areas or children not living in a dwelling with an indoor kitchen area with an open fire/not living in this type of dwelling. Immunization with 2-3 doses of PCV13 was associated with lower rates of pneumococcal detection. Half of the identified serotypes were non-PCV13 serotypes. The most common non-PCV13 serotypes/serogroups were 15BC, 10A, and 12F, while 5, 6, and 19F were the most prevalent PCV13 serotypes/serogroups. CONCLUSIONS The burden of respiratory pathogens including S. pneumoniae in Congolese children was high but relatively few children had RSV. Non-PCV13 serotypes/serogroups became predominant soon after PCV13 was introduced in DR Congo.
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Affiliation(s)
- Archippe Muhandule Birindwa
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Panzi Hospital, Bukavu, Democratic Republic of the Congo
- Université Evangélique en Afrique, Bukavu, Democratic Republic of the Congo
- Institut Superieur Technique Medical, Uvira, Democratic Republic of the Congo
- * E-mail: ,
| | - Lucia Gonzales-Siles
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Rickard Nordén
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Region Västra Götaland, Sweden
| | - Shadi Geravandi
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | | | | | | | - Rune Andersson
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Region Västra Götaland, Sweden
| | - Susann Skovbjerg
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Region Västra Götaland, Sweden
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Barcik W, Boutin RCT, Sokolowska M, Finlay BB. The Role of Lung and Gut Microbiota in the Pathology of Asthma. Immunity 2020; 52:241-255. [PMID: 32075727 PMCID: PMC7128389 DOI: 10.1016/j.immuni.2020.01.007] [Citation(s) in RCA: 303] [Impact Index Per Article: 75.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 12/30/2019] [Accepted: 01/20/2020] [Indexed: 02/08/2023]
Abstract
Asthma is a common chronic respiratory disease affecting more than 300 million people worldwide. Clinical features of asthma and its immunological and molecular etiology vary significantly among patients. An understanding of the complexities of asthma has evolved to the point where precision medicine approaches, including microbiome analysis, are being increasingly recognized as an important part of disease management. Lung and gut microbiota play several important roles in the development, regulation, and maintenance of healthy immune responses. Dysbiosis and subsequent dysregulation of microbiota-related immunological processes affect the onset of the disease, its clinical characteristics, and responses to treatment. Bacteria and viruses are the most extensively studied microorganisms relating to asthma pathogenesis, but other microbes, including fungi and even archaea, can potently influence airway inflammation. This review focuses on recently discovered connections between lung and gut microbiota, including bacteria, fungi, viruses, and archaea, and their influence on asthma.
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Affiliation(s)
- Weronika Barcik
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Rozlyn C T Boutin
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Milena Sokolowska
- Swiss Institute of Allergy and Asthma Research, University of Zurich, Davos, Switzerland; Christine Kühne - Center for Allergy Research and Education (CK-CARE), Davos, Switzerland
| | - B Brett Finlay
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada.
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40
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Effects of 10-valent pneumococcal conjugate (PCV10) vaccination on the nasopharyngeal microbiome. Vaccine 2020; 38:1436-1443. [DOI: 10.1016/j.vaccine.2019.11.079] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 11/19/2019] [Accepted: 11/28/2019] [Indexed: 01/02/2023]
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Hoang VT, Dao TL, Ly TDA, Belhouchat K, Chaht KL, Gaudart J, Mrenda BM, Drali T, Yezli S, Alotaibi B, Fournier PE, Raoult D, Parola P, de Santi VP, Gautret P. The dynamics and interactions of respiratory pathogen carriage among French pilgrims during the 2018 Hajj. Emerg Microbes Infect 2019; 8:1701-1710. [PMID: 31749410 PMCID: PMC6882464 DOI: 10.1080/22221751.2019.1693247] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
We conducted this study to describe the dynamics of the acquisition of respiratory pathogens, their potential interactions and risk factors for possible lower respiratory tract infection symptoms (LRTI) among French pilgrims during the 2018 Hajj. Each participant underwent four successive systematic nasopharyngeal swabs before and during their stay in Saudi Arabia. Carriage of the main respiratory pathogens was assessed by PCR. 121 pilgrims were included and 93.4% reported respiratory symptoms during the study period. The acquisition of rhinovirus, coronaviruses and Staphylococcus aureus occurred soon after arrival in Saudi Arabia and rates decreased gradually after days 5 and 6. In contrast, Streptococcus pneumoniae and Klebsiella pneumoniae carriage increased progressively until the end of the stay in Saudi Arabia. Haemophilus influenzae and Moraxella catarrhalis carriage increased starting around days 12 and 13, following an initial clearance. Influenza viruses were rarely isolated. We observed an independent positive mutual association between S. aureus and rhinovirus carriage and between H. influenzae and M. catarrhalis carriage. Dual carriage of H. influenzae and M. catarrhalis was strongly associated with S. pneumoniae carriage (OR = 6.22). Finally, our model showed that M. catarrhalis carriage was negatively associated with K. pneumoniae carriage. Chronic respiratory disease was associated with symptoms of LRTI. K. pneumoniae, M. catarrhalis-S. aureus and H. influenzae-rhinovirus dual carriage was associated with LRTI symptoms. Our data suggest that RTIs at the Hajj are a result of complex interactions between a number of respiratory viruses and bacteria.
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Affiliation(s)
- Van-Thuan Hoang
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France.,IHU-Méditerranée Infection, Marseille, France.,Thai Binh University of Medicine and Pharmacy, Thai Binh, Viet Nam
| | - Thi-Loi Dao
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France.,IHU-Méditerranée Infection, Marseille, France.,Thai Binh University of Medicine and Pharmacy, Thai Binh, Viet Nam
| | - Tran Duc Anh Ly
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Khadidja Belhouchat
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Kamel Larbi Chaht
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Jean Gaudart
- Aix Marseille Univ, INSERM, IRD, SESSTIM UMR1252, Faculty of Medicine Marseille, France.,APHM, La Timone Hospital, Biostatistics & ICT Marseille, France
| | | | - Tassadit Drali
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Saber Yezli
- The Global Centre for Mass Gatherings Medicine, Ministry of Health, Riyadh, Saudi Arabia
| | - Badriah Alotaibi
- The Global Centre for Mass Gatherings Medicine, Ministry of Health, Riyadh, Saudi Arabia
| | - Pierre-Edouard Fournier
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Didier Raoult
- IHU-Méditerranée Infection, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
| | - Philippe Parola
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Vincent Pommier de Santi
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France.,IHU-Méditerranée Infection, Marseille, France.,French Military Centre for Epidemiology and Public Health, Marseille, France
| | - Philippe Gautret
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
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Caballero MT, Bianchi AM, Nuño A, Ferretti AJP, Polack LM, Remondino I, Rodriguez MG, Orizzonte L, Vallone F, Bergel E, Polack FP. Mortality Associated With Acute Respiratory Infections Among Children at Home. J Infect Dis 2019; 219:358-364. [PMID: 30165655 PMCID: PMC6325348 DOI: 10.1093/infdis/jiy517] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 08/23/2018] [Indexed: 12/11/2022] Open
Abstract
Background Numerous deaths in children aged <5 years in the developing world occur at home. Acute respiratory infections (ARIs) are thought to play an important role in these deaths. Risk factors and pathogens linked to fatal episodes remain unclear. Methods A case-control study among low-income children aged <5 years was performed in Buenos Aires, Argentina, to define risk factors and viral pathogens among those who died of ARI at home. Results A total of 278 families of children aged <5 years (of whom 104 died and 174 were healthy controls) participated in the study. A total of 87.5% of ARI-associated deaths occurred among infants aged <12 months. The estimated mortality rate due to ARI among infants was 5.02 deaths/1000 live births. Dying at home from ARI was associated with living in a crowded home (odds ratio [OR], 3.73; 95% confidence interval [CI], 1.41-9.88), having an adolescent mother (OR, 4.89; 95% CI, 1.37-17.38), lacking running water in the home (OR, 4.39; 95% CI, 1.11-17.38), incomplete vaccinations for age (OR, 3.39; 95% CI, 1.20-9.62), admission to a neonatal intensive care unit (OR, 7.17; 95% CI, 2.21-23.27), and no emergency department visit during the ARI episode (OR, 72.32; 95% CI, 4.82-1085.6). The at-home death rate due to respiratory syncytial virus infection among infants was 0.26 deaths/100 live births and that due to influenza was 0.07 deaths/1000 live births. Conclusions Social vulnerabilities underlie at-home mortality due to ARI. Mortality rates due to RSV and influenza virus infection are high among infants at home and are similar to those reported for hospitalized children.
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Affiliation(s)
| | | | - Alejandra Nuño
- Secretaria de Salud de Lomas de Zamora, Buenos Aires, Argentina
| | | | | | - Ines Remondino
- Secretaria de Salud de Florencio Varela, Buenos Aires, Argentina
| | | | | | | | - Eduardo Bergel
- Instituto de Efectividad Clinica y Sanitaria, Buenos Aires, Argentina
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Kumpitsch C, Koskinen K, Schöpf V, Moissl-Eichinger C. The microbiome of the upper respiratory tract in health and disease. BMC Biol 2019; 17:87. [PMID: 31699101 PMCID: PMC6836414 DOI: 10.1186/s12915-019-0703-z] [Citation(s) in RCA: 217] [Impact Index Per Article: 43.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 09/19/2019] [Indexed: 02/08/2023] Open
Abstract
The human upper respiratory tract (URT) offers a variety of niches for microbial colonization. Local microbial communities are shaped by the different characteristics of the specific location within the URT, but also by the interaction with both external and intrinsic factors, such as ageing, diseases, immune responses, olfactory function, and lifestyle habits such as smoking. We summarize here the current knowledge about the URT microbiome in health and disease, discuss methodological issues, and consider the potential of the nasal microbiome to be used for medical diagnostics and as a target for therapy.
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Affiliation(s)
- Christina Kumpitsch
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Neue Stiftingtalstraße 6, 8010 Graz, Austria
| | - Kaisa Koskinen
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Neue Stiftingtalstraße 6, 8010 Graz, Austria
| | - Veronika Schöpf
- Institute of Psychology, University of Graz, Universitaetsplatz 2, 8010 Graz, Austria
- BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria
- Present address: Medical University Vienna, Spitalgasse 23, 1090 Vienna, Austria
| | - Christine Moissl-Eichinger
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Neue Stiftingtalstraße 6, 8010 Graz, Austria
- BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria
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44
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Dano ID, Ousmane S, Moumouni K, Lagare A, Issa I, Testa J. Risk factors associated with Streptococcus pneumonia carriage in children under five years old with acute respiratory infection in Niger. Pan Afr Med J 2019; 33:239. [PMID: 31692895 PMCID: PMC6814941 DOI: 10.11604/pamj.2019.33.239.15945] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 04/14/2019] [Indexed: 01/12/2023] Open
Abstract
Introduction Streptococcus pneumonia is a leading cause of bacterial pneumonia, meningitis and sepsis in children, and pneumococcal carriage is an important source of horizontal spread of these pathogens within the community. Methods A questionnaire was addressed to parents for the collection of sociodemographic and medical information. Nasopharyngeal swabbing was processed using a molecular method. We used logistic regression models to examine independent associations between pneumococcal carriage and potential risk factors. All associations with a p-value of < 0.25 in the bivariate regression analyses were subsequently entered in the multivariate regression model. Results A total of 637 children aged 1 to 59 months admitted for acute respiratory infection were included. The rate of respiratory virus carriage was 76%, whereas that of bacteria was 47% and that of bacteria-virus co-colonization was 42%. A bivariate analysis showed that carriage was not related to gender, father's or mother's education level, father's occupation, type of housing or lighting, or passive exposure to cigarette smoking in the house. It was also not linked to complete vaccination with PCV-13 or PPSV-23 and antibiotic treatment prior to hospitalization. A multivariate analysis showed that carriage was related to age greater than 3 months, maternal occupation, house flooring type, and co-colonization of another bacterium and virus. Conclusion These results can be helpful to understand the dynamics of pneumococcal nasopharyngeal colonization; they confirm the interest of vaccinating infants before the age of 3 months with appropriate vaccine to prevent spread nasopharyngeal colonization and pneumococcal diseases in children.
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Affiliation(s)
- Ibrahim Dan Dano
- Centre de Recherche Médicale et Sanitaire (CERMES), 634 Boulevard de la Nation, Niamey, Niger
| | - Sani Ousmane
- Centre de Recherche Médicale et Sanitaire (CERMES), 634 Boulevard de la Nation, Niamey, Niger
| | - Kamaye Moumouni
- Hôpital National de Niamey (HNN), Service de Pédiatrie A, Niamey, Niger
| | - Adamou Lagare
- Centre de Recherche Médicale et Sanitaire (CERMES), 634 Boulevard de la Nation, Niamey, Niger
| | - Idi Issa
- Centre de Recherche Médicale et Sanitaire (CERMES), 634 Boulevard de la Nation, Niamey, Niger
| | - Jean Testa
- Centre de Recherche Médicale et Sanitaire (CERMES), 634 Boulevard de la Nation, Niamey, Niger
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Huang R, McGrath SP, Hirsch PR, Clark IM, Storkey J, Wu L, Zhou J, Liang Y. Plant-microbe networks in soil are weakened by century-long use of inorganic fertilizers. Microb Biotechnol 2019; 12:1464-1475. [PMID: 31536680 PMCID: PMC6801139 DOI: 10.1111/1751-7915.13487] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 08/23/2019] [Accepted: 08/26/2019] [Indexed: 11/28/2022] Open
Abstract
Understanding the changes in plant-microbe interactions is critically important for predicting ecosystem functioning in response to human-induced environmental changes such as nitrogen (N) addition. In this study, the effects of a century-long fertilization treatment (> 150 years) on the networks between plants and soil microbial functional communities, detected by GeoChip, in grassland were determined in the Park Grass Experiment at Rothamsted Research, UK. Our results showed that plants and soil microbes have a consistent response to long-term fertilization-both richness and diversity of plants and soil microbes are significantly decreased, as well as microbial functional genes involved in soil carbon (C), nitrogen (N) and phosphorus (P) cycling. The network-based analyses showed that long-term fertilization decreased the complexity of networks between plant and microbial functional communities in terms of node numbers, connectivity, network density and the clustering coefficient. Similarly, within the soil microbial community, the strength of microbial associations was also weakened in response to long-term fertilization. Mantel path analysis showed that soil C and N contents were the main factors affecting the network between plants and microbes. Our results indicate that century-long fertilization weakens the plant-microbe networks, which is important in improving our understanding of grassland ecosystem functions and stability under long-term agriculture management.
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Affiliation(s)
- Ruilin Huang
- State Key Laboratory of Soil and Sustainable AgricultureInstitute of Soil ScienceChinese Academy of SciencesNanjing210008China
- University of Chinese Academy of SciencesNo. 19A Yuquan RoadBeijing100049China
| | | | | | - Ian M. Clark
- Rothamsted ResearchHarpendenHertfordshireAL5 2JQUK
| | | | - Liyou Wu
- Institute for Environmental GenomicsDepartment of Microbiology & Plant BiologySchool of Civil Engineering and Environmental SciencesUniversity of OklahomaNormanOK73019USA
| | - Jizhong Zhou
- Institute for Environmental GenomicsDepartment of Microbiology & Plant BiologySchool of Civil Engineering and Environmental SciencesUniversity of OklahomaNormanOK73019USA
- State Key Joint Laboratory of Environment Simulation and Pollution ControlSchool of EnvironmentTsinghua UniversityBeijing100084China
| | - Yuting Liang
- State Key Laboratory of Soil and Sustainable AgricultureInstitute of Soil ScienceChinese Academy of SciencesNanjing210008China
- University of Chinese Academy of SciencesNo. 19A Yuquan RoadBeijing100049China
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Uddin SMI, Englund JA, Kuypers JY, Chu HY, Steinhoff MC, Khatry SK, LeClerq SC, Tielsch JM, Mullany LC, Shrestha L, Katz J. Burden and Risk Factors for Coronavirus Infections in Infants in Rural Nepal. Clin Infect Dis 2019; 67:1507-1514. [PMID: 29668900 PMCID: PMC6206108 DOI: 10.1093/cid/ciy317] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 04/12/2018] [Indexed: 12/12/2022] Open
Abstract
Background Knowledge of risk factors for symptomatic human coronavirus (HCoV) infections in children in community settings is limited. We estimated the disease burden and impact of birth-related, maternal, household, and seasonal factors on HCoV infections among children from birth to 6 months old in rural Nepal. Methods Prospective, active, weekly surveillance for acute respiratory infections (ARIs) was conducted in infants over a period of 3 years during 2 consecutive, population-based randomized trials of maternal influenza immunization. Midnasal swabs were collected for acute respiratory symptoms and tested for HCoV and other viruses by reverse-transcription polymerase chain reaction. Association between HCoV incidence and potential risk factors was modeled using Poisson regression. Results Overall, 282 of 3505 (8%) infants experienced an HCoV ARI within the first 6 months of life. HCoV incidence overall was 255.6 (95% confidence interval [CI], 227.3–286.5) per 1000 person-years, and was more than twice as high among nonneonates than among neonates (incidence rate ratio [IRR], 2.53; 95% CI, 1.52–4.21). HCoV ARI incidence was also positively associated with the number of children <5 years of age per room in a household (IRR, 1.13; 95% CI, 1.01–1.28). Of the 296 HCoV infections detected, 46% were coinfections with other respiratory viruses. While HCoVs were detected throughout the study period, seasonal variation was also observed, with incidence peaking in 2 winters (December–February) and 1 autumn (September–November). Conclusions HCoV is associated with a substantial proportion of illnesses among young infants in rural Nepal. There is an increased risk of HCoV infection beyond the first month of life.
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Affiliation(s)
- S M Iftekhar Uddin
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | | | - Jane Y Kuypers
- Molecular Virology Laboratory, School of Medicine, Seattle
| | - Helen Y Chu
- Harborview Medical Center, University of Washington, Seattle
| | - Mark C Steinhoff
- Global Health Center, Cincinnati Children's Hospital Medical Center, Ohio
| | | | - Steve C LeClerq
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland.,Nepal Nutrition Intervention Project-Sarlahi, Kathmandu
| | - James M Tielsch
- Department of Global Health, Milken Institute School of Public Health, George Washington University, D.C
| | - Luke C Mullany
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Laxman Shrestha
- Department of Pediatrics and Child Health, Institute of Medicine, Tribhuvan University, Kathmandu, Nepal
| | - Joanne Katz
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
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Rowe HM, Karlsson E, Echlin H, Chang TC, Wang L, van Opijnen T, Pounds SB, Schultz-Cherry S, Rosch JW. Bacterial Factors Required for Transmission of Streptococcus pneumoniae in Mammalian Hosts. Cell Host Microbe 2019; 25:884-891.e6. [PMID: 31126758 DOI: 10.1016/j.chom.2019.04.012] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 02/18/2019] [Accepted: 04/02/2019] [Indexed: 02/06/2023]
Abstract
The capacity of Streptococcus pneumoniae to successfully transmit and colonize new human hosts is a critical aspect of pneumococcal population biology and a prerequisite for invasive disease. However, the bacterial mechanisms underlying this process remain largely unknown. To identify bacterial factors required for transmission, we conducted a high-throughput genetic screen with a transposon sequencing (Tn-seq) library of a pneumococcal strain in a ferret transmission model. Key players in both metabolism and transcriptional regulation were identified as required for efficient bacterial transmission. Targeted deletion of the putative C3-degrading protease CppA, iron transporter PiaA, or competence regulatory histidine kinase ComD significantly decreased transmissibility in a mouse model, further validating the screen. Maternal vaccination with recombinant surface-exposed PiaA and CppA alone or in combination blocked transmission in offspring and were more effective than capsule-based vaccines. These data underscore the possibility of targeting pneumococcal transmission as a means of eliminating invasive disease in the population.
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Affiliation(s)
- Hannah M Rowe
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Erik Karlsson
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Haley Echlin
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Ti-Cheng Chang
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Lei Wang
- Department of Biostatistics, St Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Stanley B Pounds
- Department of Biostatistics, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Stacey Schultz-Cherry
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Jason W Rosch
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA.
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Douros K, Kotzia D, Kottaridi C, Giotas A, Boutopoulou B, Bozas E, Matziou V, Priftis K, Papaevangelou V. Evidence for respiratory viruses interactions in asymptomatic preschool-aged children. Allergol Immunopathol (Madr) 2019; 47:260-264. [PMID: 30454860 PMCID: PMC7126143 DOI: 10.1016/j.aller.2018.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 07/22/2018] [Accepted: 07/24/2018] [Indexed: 11/16/2022]
Abstract
Aim To prospectively evaluate interferences between viruses of the upper respiratory tract in asymptomatic preschool children. Methods Nasal-pharyngeal swabs from 233 preschool aged children were prospectively collected over four consecutive time periods, during one school year. The samples were tested using a RT-PCR DNA/RNA microarray system for nine respiratory viruses. Results Respiratory syncytial virus (RSV) was a predictor of the presence of influenza virus (INFL) (OR: 9.12, CI: 1.52–54.75, p = 0.016), and similarly, INFL predicted the presence of RSV (OR: 4.01, CI: 1.14–14.16, p = 0.030). Also, rhinovirus (RV) was a predictor of adenovirus (ADV) presence (OR: 3.66, CI: 1.10–12.14, p = 0.034), and similarly, ADV predicted the presence of RV (OR: 4.05, CI: 1.02–16.05, p = 0.046). No other significant associations between viruses were observed. Conclusion Our results indicate that respiratory viruses found in carrier stage in asymptomatic children may interact with other viruses and even facilitate their settling in the upper respiratory tract. The pathophysiological role of these interactions is not yet clear.
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Thors V, Christensen H, Morales-Aza B, Oliver E, Sikora P, Vipond I, Muir P, Finn A. High-density Bacterial Nasal Carriage in Children Is Transient and Associated With Respiratory Viral Infections-Implications for Transmission Dynamics. Pediatr Infect Dis J 2019; 38:533-538. [PMID: 30985547 DOI: 10.1097/inf.0000000000002256] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
BACKGROUND This longitudinal study describes the associations between respiratory viral infections, rhinitis and the prevalence and density of the common nasopharyngeal bacterial colonizers, Streptococcus pneumoniae (Sp), Moraxella catarrhalis (Mc), Haemophilus influenzae (Hi) and Staphylococcus aureus. METHODS In an observational cohort study, 161 children attending day care centers in Bristol, United Kingdom, were recruited. Monthly nasopharyngeal swabs were taken and stored frozen in Skim-milk, tryptone, glucose and glycerin broth (STGG) broth. Quantitative polymerase chain reaction was used for detection of respiratory viruses and 4 bacterial species. t tests and logistic regression models were used for analysis. RESULTS The frequent colonisers, Sp, Mc and Hi were more frequently found at high density in contrast to Staphylococcus aureus although temporally, high-density carriage was short lived. Respiratory viral infections and symptoms of rhinitis were both independently and consistently associated with higher bacterial density with an observed 2-fold increase in density for Sp, Mc and Hi (P = 0.004-0.017). CONCLUSIONS For Sp and Hi, the association between young age and higher bacterial DNA density was explained by more frequent viral infection and increased nasal discharge, while the associations between some viral specie's and some bacterial species' density appear to be stronger than others. Increased colonization density and rhinitis may promote transmission of these commonly carried organisms.
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Affiliation(s)
- Valtyr Thors
- From the School of Cellular and Molecular Medicine, University of Bristol, Education Centre, Bristol, United Kingdom
- Children's Hospital, Landspitali University Hospital Iceland, Reykjavik, Iceland
| | | | - Begonia Morales-Aza
- From the School of Cellular and Molecular Medicine, University of Bristol, Education Centre, Bristol, United Kingdom
| | - Elizabeth Oliver
- From the School of Cellular and Molecular Medicine, University of Bristol, Education Centre, Bristol, United Kingdom
| | - Paulina Sikora
- From the School of Cellular and Molecular Medicine, University of Bristol, Education Centre, Bristol, United Kingdom
| | - Ian Vipond
- Public Health Laboratory Bristol, Public Health England, Southmead Hospital, Bristol, United Kingdom
| | - Peter Muir
- Public Health Laboratory Bristol, Public Health England, Southmead Hospital, Bristol, United Kingdom
| | - Adam Finn
- From the School of Cellular and Molecular Medicine, University of Bristol, Education Centre, Bristol, United Kingdom
- School of Population Health Sciences, University of Bristol
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50
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Abdulgader SM, Robberts L, Ramjith J, Nduru PM, Dube F, Gardner-Lubbe S, Zar HJ, Nicol MP. Longitudinal Population Dynamics of Staphylococcus aureus in the Nasopharynx During the First Year of Life. Front Genet 2019; 10:198. [PMID: 30930937 PMCID: PMC6428701 DOI: 10.3389/fgene.2019.00198] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 02/25/2019] [Indexed: 11/22/2022] Open
Abstract
Background:Staphylococcus aureus colonization is a risk factor for invasive disease. Few studies have used strain genotype data to study S. aureus acquisition and carriage patterns. We investigated S. aureus nasopharyngeal carriage in infants in an intensively sampled South African birth cohort. Methods: Nasopharyngeal swabs were collected at birth and fortnightly from 137 infants through their first year of life. S. aureus was characterized by spa-typing. The incidence of S. aureus acquisition, and median carriage duration for each genotype was determined. S. aureus carriage patterns were defined by combining the carrier index (proportion of samples testing positive for S. aureus) with genotype diversity measures. Persistent or prolonged carriage were defined by a carrier index ≥0.8 or ≥0.5, respectively. Risk factors for time to acquisition of S. aureus were determined. Results: Eighty eight percent (121/137) of infants acquired S. aureus at least once. The incidence of acquisition at the species and genotype level was 1.83 and 2.8 episodes per child-year, respectively. No children had persistent carriage (defined as carrier index of >0.8). At the species level 6% had prolonged carriage, while only 2% had prolonged carriage with the same genotype. Carrier index correlated with the absolute number of spa-CCs carried by each infant (r = 0.5; 95% CI 0.35–0.62). Time to first acquisition of S. aureus was shorter in children from households with ≥5 individuals (HR 1.06, 95% CI 1.07–1.43), with S. aureus carrier mothers (HR; 1.5, 95% CI 1.2–2.47), or with a positive tuberculin skin test during the first year of life (HR; 1.81, 95% CI 0.97–3.3). Conclusion: Using measures of genotype diversity, we showed that S. aureus NP carriage is highly dynamic in infants. Prolonged carriage with a single strain occurred rarely; persistent carriage was not observed. A correlation was observed between carrier index and genotype diversity.
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Affiliation(s)
- Shima M Abdulgader
- Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Lourens Robberts
- Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Jordache Ramjith
- Division of Epidemiology and Biostatistics, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa
| | - Polite M Nduru
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital and SA-MRC Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Felix Dube
- Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,Department of Molecular and Cell Biology, Faculty of Science, University of Cape Town, Cape Town, South Africa
| | - Sugnet Gardner-Lubbe
- Department of Statistics and Actuarial Science, Stellenbosch University, Stellenbosch, South Africa
| | - Heather J Zar
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital and SA-MRC Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Mark P Nicol
- Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,Institute of Infectious Disease & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,School of Biomedical Sciences, University of Western Australia, Perth, WA, Australia
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