Seasonal variation of respiratory pathogen colonization in asymptomatic health care professionals: A single-center, cross-sectional, 2-season observational study

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

BACKGROUND

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

METHODS

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

RESULTS

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

CONCLUSIONS

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

The Upper Airway Microbiota, Environmental Exposures, Inflammation, and Disease

Along with playing vital roles in pathogen exclusion and immune system priming, the upper airways (UAs) and their microbiota are essential for myriad physiological functions such as conditioning and transferring inhaled air. Dysbiosis, a microbial imbalance, is linked with various diseases and significantly impedes the quality of one’s life. Daily inhaled exposures and/or underlying conditions contribute to adverse changes to the UA microbiota. Such variations in the microbial community exacerbate UA and pulmonary disorders via modulating inflammatory and immune pathways. Hence, exploring the UA microbiota’s role in maintaining homeostasis is imperative. The microbial composition and subsequent relationship with airborne exposures, inflammation, and disease are crucial for strategizing innovating UA diagnostics and therapeutics. The development of a healthy UA microbiota early in life contributes to normal respiratory development and function in the succeeding years. Although different UA cavities present a unique microbial profile, geriatrics have similar microbes across their UAs. This lost community segregation may contribute to inflammation and disease, as it stimulates disadvantageous microbial–microbial and microbial–host interactions. Varying inflammatory profiles are associated with specific microbial compositions, while the same is true for many disease conditions and environmental exposures. A shift in the microbial composition is also detected upon the administration of numerous therapeutics, highlighting other beneficial and adverse side effects. This review examines the role of the UA microbiota in achieving homeostasis, and the impact on the UAs of environmental airborne pollutants, inflammation, and disease.

Antigen-Presenting Cells in the Airways: Moderating Asymptomatic Bacterial Carriage

Bacterial respiratory tract infections (RTIs) are a major global health burden, and the role of antigen-presenting cells (APCs) in mounting an immune response to contain and clear invading pathogens is well-described. However, most encounters between a host and a bacterial pathogen do not result in symptomatic infection, but in asymptomatic carriage instead. The fact that a pathogen will cause infection in one individual, but not in another does not appear to be directly related to bacterial density, but rather depend on qualitative differences in the host response. Understanding the interactions between respiratory pathogens and airway APCs that result in asymptomatic carriage, will provide better insight into the factors that can skew this interaction towards infection. This review will discuss the currently available knowledge on airway APCs in the context of asymptomatic bacterial carriage along the entire respiratory tract. Furthermore, in order to interpret past and futures studies into this topic, we propose a standardized nomenclature of the different stages of carriage and infection, based on the pathogen’s position with regard to the epithelium and the amount of inflammation present.

Respiratory Tract Microecology and Bronchopulmonary Dysplasia in Preterm Infants

Bronchopulmonary dysplasia (BPD) is a severe respiratory complication in preterm infants. Although the etiology and pathogenesis of BPD are complex and remain to be clarified, recent studies have reported a certain correlation between the microecological environment of the respiratory tract and BPD. Changes in respiratory tract microecology, such as abnormal microbial diversity and altered evolutional patterns, are observed prior to the development of BPD in premature infants. Therefore, research on the colonization and evolution of neonatal respiratory tract microecology and its relationship with BPD is expected to provide new ideas for its prevention and treatment. In this paper, we review microecological changes in the respiratory tract and the mechanisms by which they can lead to BPD in preterm infants.

Birth during the moderate weather seasons is associated with early onset of type 1 diabetes in the Mediterranean area

AIM

To assess the association of seasonal and perinatal parameters with early age of type 1 diabetes (T1D) onset.

METHODS

A cross-sectional review of all medical records of T1D patients born between the years 1990 and 2005, and diagnosed before/by the age of 10 years, from 13 university-affiliated paediatric medical centres in Israel, was performed. Data included: gender, ethnicity, seasons of birth and disease onset, birth gestational age and weight, and autoimmune diseases of the probands and their first-degree family members. Statistical analysis included the Chi-square test or Mann-Whitney test, as appropriate and multivariate regression analysis.

RESULTS

Enrolled were 1571 T1D patients at a median age of T1D onset 6.9 years (IQR 4.4,8.4); 336 of them presented before 4 years of age. The median age of this group was 2.5 years (IQR 1.7,3.2), and of the 1235 patients who presented after 4 years of age, median presentation age was 7.5 years (IQR 6.1,8.8). Multivariate regression analysis demonstrated that a more recent birth year; OR = 1.06, 95% CI 1.02-1.1, P = 0.003, and birth during the moderate weather months (September, October, March, and April) were significantly associated with younger age at T1D onset; OR = 1.68, 95% CI 1.17-2.4, P = 0.005.

CONCLUSIONS

Our novel finding demonstrates the association between younger than 4 years old age at presentation and birth during moderate weather months. The results also support previous reports, that there is a slight increase in the annual incidence of T1D in the youngest age groups.

Panel 7 - Pathogenesis of otitis media - a review of the literature between 2015 and 2019

OBJECTIVE

To perform a comprehensive review of the literature from July 2015 to June 2019 on the pathogenesis of otitis media. Bacteria, viruses and the role of the microbiome as well as the host response are discussed. Directions for future research are also suggested.

DATA SOURCES

PubMed database of the National Library of Medicine.

REVIEW METHODS

PubMed was searched for any papers pertaining to OM pathogenesis between July 2015 and June 2019. If in English, abstracts were assessed individually for their relevance and included in the report. Members of the panel drafted the report based on these searches and on new data presented at the 20th International Symposium on Recent Advances in Otitis Media.

CONCLUSIONS

The main themes that arose in OM pathogenesis were around the need for symptomatic viral infections to develop disease. Different populations potentially having different mechanisms of pathogenesis. Novel bacterial otopathogens are emerging and need to be monitored. Animal models need to continue to be developed and used to understand disease pathogenesis.

IMPLICATIONS FOR PRACTICE

The findings in the pathogenesis panel have several implications for both research and clinical practice. The most urgent areas appear to be to continue monitoring the emergence of novel otopathogens, and the need to develop prevention and preventative therapies that do not rely on antibiotics and protect against the development of the initial OM episode.

Use of whole-genome sequencing in the molecular investigation of care-associated HCoV-OC43 infections in a hematopoietic stem cell transplant unit

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HCoV−OC43 is involved in healthcare–associated infections.

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HCoV−OC43 genotypes B, E, F and G are identified.

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Asian and European strains of HCoV−OC43 circulate among patients.

Background

While respiratory viral infections are recognized as a frequent cause of illness in hematopoietic stem cell transplantation (HSCT) recipients, HCoV−OC43 infections have rarely been investigated as healthcare-associated infections in this population.

Objectives

In this report, HCoV−OC43 isolates collected from HSCT patients were retrospectively characterized to identify potential clusters of infection that may stand for a hospital transmission.

Study design

Whole-genome and S gene sequences were obtained from nasal swabs using next-generation sequencing and phylogenetic trees were constructed. Similar identity matrix and determination of the most common ancestor were used to compare clusters of patient’s sequences. Amino acids substitutions were analysed.

Results

Genotypes B, E, F and G were identified. Two clusters of patients were defined from chronological data and phylogenetic trees. Analyses of amino acids substitutions of the S protein sequences identified substitutions specific for genotype F strains circulating among European people.

Conclusions

HCoV−OC43 may be implicated in healthcare-associated infections.

Approche syndromique multiplexe en réanimation

Le développement récent des nouveaux tests de diagnostic rapide par PCR multiplexe à visée syndromique, capables de détecter plusieurs dizaines de pathogènes en quelques heures, a entraîné un changement de paradigme en microbiologie et en pratique clinique. Plusieurs d’entre eux, comme les panels pour détecter les germes en cause dans les bactériémies, les infections respiratoires hautes ou basses et les méningoencéphalites, sont déjà disponibles et peuvent apporter une aide dans le diagnostic des infections chez les patients de réanimation. Bien que ces nouvelles techniques présentent des avantages évidents pour le dénombrement de micro-organismes et parfois pour la détection simultanée de gènes de résistance, pour les délais d’exécution et de rendus de résultats, elles présentent cependant certains défis, comme l’évaluation de leurs performances réelles, leur coût très élevé, le choix des stratégies d’utilisation et l’interprétation clinicobiologique des résultats. Dans cet article, nous avons passé en revue les différents tests qui peuvent ou pourront aider les réanimateurs dans leur pratique quotidienne, relevé leurs limites et leur impact bénéfique potentiel sur le soin des patients.

Diversity of upper respiratory tract infections and prevalence of Streptococcus pneumoniae colonization among patients with fever and flu-like symptoms

BACKGROUND

Many upper respiratory pathogens cause similar symptoms. In China, routine molecular tests for upper respiratory pathogens are not widely performed and antibiotics abuse in treating upper respiratory tract infections (URTIs) is a major public health concern.

METHODS

We performed qualitative real-time PCR tests to detect common upper respiratory tract pathogens including 9 viruses and 3 bacteria in 1221 nasopharyngeal swabs from patients with fever and influenza-like symptoms in a Chinese city. A quantitative real-time PCR was also performed to measure the bacterial density of the colonizing Streptococcus pneumoniae in these samples.

RESULTS

We found very diverse pathogens including 81.7% viruses, 11.6% bacteria and 6.7% mixed viruses and bacteria. S. pneumoniae colonization was found in 8.0% of the cases but most of them had low bacterial density (Mean = 3.9 log cfu/ml). We also discovered an increase of S. pneumoniae colonization frequency (but not the density) in patients with detectable upper respiratory tract pathogens, in a pathogen variety-dependent manner.

CONCLUSIONS

Our study provided strong evidence against empiric antibiotic use for treating URTIs, and highlighted a strong need for improving the diagnostic capacity for URTIs by using more molecular testing in China.

Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia

Influenza and other respiratory viral infections are the most common type of acute respiratory infection. Viral infections predispose patients to secondary bacterial infections, which often have a more severe clinical course. The mechanisms underlying post-viral bacterial infections are complex, and include multifactorial processes mediated by interactions between viruses, bacteria, and the host immune system. Studies over the past 15 years have demonstrated that unique microbial communities reside on the mucosal surfaces of the gastrointestinal tract and the respiratory tract, which have both direct and indirect effects on host defense against viral infections. In addition, antiviral immune responses induced by acute respiratory infections such as influenza are associated with changes in microbial composition and function (“dysbiosis”) in the respiratory and gastrointestinal tract, which in turn may alter subsequent immune function against secondary bacterial infection or alter the dynamics of inter-microbial interactions, thereby enhancing the proliferation of potentially pathogenic bacterial species. In this review, we summarize the literature on the interactions between host microbial communities and host defense, and how influenza, and other acute respiratory viral infections disrupt these interactions, thereby contributing to the pathogenesis of secondary bacterial infections.

Nosocomial Outbreak of Upper Respiratory Tract Infection With β-Lactamase-Negative Ampicillin-Resistant Nontypeable Haemophilus influenzae

OBJECTIVETo describe the epidemiologic features of an outbreak of an acute respiratory tract infection (ARI) caused by β-lactamase-negative ampicillin-resistant (BLNAR) nontypeable Haemophilus influenzae (NTHi) in an acute-care ward.DESIGNCross-sectional case-control study.SETTINGAn acute-care ward (ward A) in a general hospital of Kochi in western Japan.METHODSPatients who shared a room with an index patient and all staff in ward A were screened and followed from July 1 to August 31, 2015. Sputum or throat swab samples were collected from participants and tested by culture and polymerase chain reaction (PCR). The association between detected pathogens and ARI development among all participants was examined. A case-control study was conducted to identify risk factors for disease.RESULTSIn total, 78 participants, including the index patient, were enrolled. Of all participants, 27 (34.6%) developed mild respiratory symptoms during a 3-week period: 24 were diagnosed as upper respiratory tract infections, and 3 were diagnosed as lower respiratory tract infections. The presence of BLNAR NTHi was confirmed in 13 participants, and multilocus sequence typing demonstrated that these isolates belonged to sequence type 159. All isolates showed identical pulsed-field gel electrophoresis patterns. The presence of BLNAR NTHi was strongly associated with ARI development, whereas viruses were not associated with the disease. Multivariate analyses demonstrated that a history of contact with the index patient was independently associated with ARI caused by BLNAR NTHi.CONCLUSIONSBLNAR NTHi has the potential to cause upper respiratory tract infections among adults and to spread rapidly in hospital settings.Infect Control Hosp Epidemiol 2018;39:652-659.

Impact of respiratory viruses in the neonatal intensive care unit

OBJECTIVE

To describe the epidemiology and clinical impact of respiratory viruses in a neonatal intensive care unit (NICU).

STUDY DESIGN

We conducted a retrospective observational study of infants with respiratory viruses detected by multiplex reverse-transcriptase PCR from May 2012 to May 2017. The proportion of symptomatic vs. asymptomatic infants and associated morbidity were assessed. The association of infection prevention and control (IP&C) strategies and transmission was ascertained.

RESULTS

Respiratory viruses were detected in 83 infants representing 86 unique episodes during which infants remained asymptomatic in 15 (17%). Of the 71 symptomatic episodes, only 45% were associated with increased respiratory and/or nutritional support. Rhinovirus/enteroviruses were most common (69%) and involved nine of 12 transmission events. IP&C strategies including restricting visitors <12 years of age and screening exposed infants were associated with decreased transmission rates.

CONCLUSIONS

NICU patients can be asymptomatic carriers of respiratory viruses. Identification of such infants is important to prevent transmission in the NICU.

Prevalence of and risk factors for nasal methicillin-resistant Staphylococcus aureus colonization among children in central Taiwan

BACKGROUND/PURPOSE

Staphylococcus aureus (S. aureus) causes diseases ranging from mild skin infections to invasive diseases. Carriage of S. aureus, including methicillin-resistant S. aureus (MRSA), is a significant risk factor for subsequent staphylococcal infection. Several studies discussed MRSA colonization in Taiwan, but mostly in northern Taiwan. This is the first study that estimates the prevalence of MRSA nasal colonization in healthy children and identifies the potential risk factors in central Taiwan.

METHODS

A total of 3144 healthy children aged 2-60 months who visited Taichung Veterans General Hospital (TCVGH) were screened for nasal S. aureus carriage from July 2005 to December 2010. Questionnaires included demographic information and potential risk factors for carriage of S. aureus were completed by parents/guardians.

RESULTS

Prevalence of MSSA and MRSA were 12.09% and 5.25%, respectively. The youngest group aged 2-6 months had the highest S. aureus carriage rate, and the carriage rate revealed a peak in summer. The nasal colonization of Streptococcus pneumoniae (S. pneumoniae) was a protective factor against S. aureus colonization. 85% of the MRSA colonizing isolates belonged to clonal complex 59/staphylococcal cassette chromosome type IV or V_T, the local community clone in Taiwan.

CONCLUSION

An increasing trend of MRSA nasal carriage rate in Taiwan had been brought forward, however, it was not observed in central Taiwan during the period of 2005-2010. We found a summer peak on both MRSA and MSSA carriages.

Composition and immunological significance of the upper respiratory tract microbiota

The intestinal microbiota is essential for nutrient acquisition, immune development, and exclusion of invading pathogens. The upper respiratory tract (URT) microbiota is less well studied and does not appear to abide by many of the paradigms of the gastrointestinal tract. Decades of carriage studies in children have demonstrated that microbe–microbe competition and collusion occurs in the URT. Whether colonization with common pathogens (e.g., Staphylococcus aureus and Streptococcus pneumoniae) alters immune development or susceptibility to respiratory conditions is just beginning to be understood. Herein, we discuss the biogeography of the URT microbiota, the succession and evolution of the microbiota through the life course, and discuss the evidence for microbe–microbe interactions in colonization and infection.