Nanopore 16S rRNA sequencing reveals alterations in nasopharyngeal microbiome and enrichment of Mycobacterium and Mycoplasma in patients with COVID 19

The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) is a major global health concern. This virus infects the upper respiratory tract and causes pneumonia-like symptoms. So far, few studies have shown that respiratory infections alter nasopharyngeal (NP) microbiome diversity and enrich opportunistic pathogens. In this study, we have sequenced the 16S rRNA variable regions, V1 through V9, extracted from NP samples of control and COVID-19 (symptomatic and asymptomatic) participants using the Oxford Nanopore technology. Comprehensive bioinformatics analysis investigating the alpha/beta diversities, non-metric multidimensional scaling, correlation studies, canonical correspondence analysis, linear discriminate analysis, and dysbiosis index analysis revealed control and COVID-19-specific NP microbiomes. We observed significant dysbiosis in COVID-19 NP microbiome with abundance of opportunistic pathogens such as Cutibacterium, Corynebacterium, Oerskovia, and Cellulomonas in asymptomatic patients, and of Streptomyces and Mycobacteriaceae family in symptomatic patients. Furthermore, we observed sharp rise in enrichment of opportunistic pathogens in symptomatic patients, with abundance of Mycobacteria and Mycoplasma, which strongly correlated with the occurrences of chest pain and fever. Our findings contribute novel insights regarding emergence of opportunistic pathogens in COVID-19 patients and their relationship with symptoms, suggesting their potential role in coinfections.

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Long-read 16S-seq reveals nasopharynx microbial dysbiosis and enrichment of Mycobacterium and Mycoplasma in COVID-19 patients: A source of co-infection

10.21203/rs.3.rs-1149233/v1 ◽

2021 ◽

Author(s):

Punit Prasad ◽

Soumendu Mahapatra ◽

Rasmita Mishra ◽

Krushna Chandra Murmu ◽

Shifu Aggarwal ◽

...

Keyword(s):

Microbial Diversity ◽

Respiratory Infections ◽

Health Concern ◽

Upper Respiratory Tract ◽

Opportunistic Pathogens ◽

Variable Regions ◽

Microbial Dysbiosis ◽

Asymptomatic Patients ◽

Oxford Nanopore ◽

Long Read

Abstract Background The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) is a major global health concern. This virus infects the upper respiratory tract and causes pneumonia-like symptoms. So far, few studies have shown alterations in nasopharyngeal (NP) microbial diversity, enrichment of opportunistic pathogens and their role in co-infections during respiratory infections. Therefore, we hypothesized that microbial diversity changes, with increase in the population of opportunistic pathogens, during SARS-CoV2 infection in the nasopharynx which may be involved in co-infection in COVID-19 patients. Methods The 16S rRNA variable regions, V1-V9, of NP samples of control and COVID-19 (symptomatic and asymptomatic) patients were sequenced using the Oxford Nanopore™ technology. Comprehensive bioinformatics analysis for determining alpha/beta diversities, non-metric multidimensional scaling, correlation studies, canonical correspondence analysis, linear discriminate analysis, and dysbiosis index were used to analyze the control and COVID-19-specific NP microbiomes. Results We observed significant dysbiosis in COVID-19 NP microbiome with increase in abundance of opportunistic pathogens at genus and species levels in asymptomatic/symptomatic patients. The significant abundance of Mycobacteria spp. and Mycoplasma spp. in symptomatic patients suggest their association and role in co-infections in COVID-19 patients. Furthermore, we found strong correlation of enrichment of Mycobacteria and Mycoplasma with the occurrences of chest pain and fever in symptomatic COVID-19 patients. Conclusion This is the first study from India to show the abundance of Mycobacteria and Mycoplasma opportunistic pathogens in non-hospitalized COVID-19 patients and their relationship with symptoms, indicating the possibility of co-infections.

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The role of the local microbial ecosystem in respiratory health and disease

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2014.0294 ◽

2015 ◽

Vol 370 (1675) ◽

pp. 20140294 ◽

Cited By ~ 96

Author(s):

Wouter A. A. de Steenhuijsen Piters ◽

Elisabeth A. M. Sanders ◽

Debby Bogaert

Keyword(s):

Respiratory Tract ◽

Respiratory Tract Infections ◽

Respiratory Infections ◽

Bacterial Overgrowth ◽

Health Concern ◽

High Morbidity ◽

Upper Respiratory Tract ◽

Colonization Resistance ◽

Upper Respiratory ◽

Tract Infections

Respiratory tract infections are a major global health concern, accounting for high morbidity and mortality, especially in young children and elderly individuals. Traditionally, highly common bacterial respiratory tract infections, including otitis media and pneumonia, were thought to be caused by a limited number of pathogens including Streptococcus pneumoniae and Haemophilus influenzae . However, these pathogens are also frequently observed commensal residents of the upper respiratory tract (URT) and form—together with harmless commensal bacteria, viruses and fungi—intricate ecological networks, collectively known as the ‘microbiome’. Analogous to the gut microbiome, the respiratory microbiome at equilibrium is thought to be beneficial to the host by priming the immune system and providing colonization resistance, while an imbalanced ecosystem might predispose to bacterial overgrowth and development of respiratory infections. We postulate that specific ecological perturbations of the bacterial communities in the URT can occur in response to various lifestyle or environmental effectors, leading to diminished colonization resistance, loss of containment of newly acquired or resident pathogens, preluding bacterial overgrowth, ultimately resulting in local or systemic bacterial infections. Here, we review the current body of literature regarding niche-specific upper respiratory microbiota profiles within human hosts and the changes occurring within these profiles that are associated with respiratory infections.

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Viral etiology and epidemiology of pediatric patients hospitalized for acute respiratory tract infections in Macao: a retrospective study from 2014 to 2017

BMC Infectious Diseases ◽

10.1186/s12879-021-05996-x ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Cheng Lei ◽

Lisong Yang ◽

Cheong Tat Lou ◽

Fan Yang ◽

Kin Ian SiTou ◽

...

Keyword(s):

Respiratory Tract ◽

Lower Respiratory Tract ◽

Respiratory Tract Infections ◽

Pediatric Patients ◽

Respiratory Infections ◽

Upper Respiratory Tract ◽

Viral Etiology ◽

Upper Respiratory ◽

Syncytial Virus ◽

Tract Infections

Abstract Background Acute respiratory infections (ARIs) are among the leading causes of hospitalization in children. Understanding the local dominant viral etiologies is important to inform infection control practices and clinical management. This study aimed to investigate the viral etiology and epidemiology of respiratory infections among pediatric inpatients in Macao. Methods A retrospective study using electronic health records between 2014 and 2017 at Kiang Wu Hospital was performed. Nasopharyngeal swab specimens were obtained from hospitalized children aged 13 years or younger with respiratory tract diseases. xMAP multiplex assays were employed to detect respiratory agents including 10 respiratory viruses. Data were analyzed to describe the frequency and seasonality. Results Of the 4880 children enrolled in the study, 3767 (77.1%) were positive for at least one of the 13 viral pathogens tested, of which 2707 (55.5%) being male and 2635 (70.0%) under 2 years old. Among the positive results, there were 3091 (82.0%) single infections and 676 (18.0%) multiple infections. The predominant viruses included human rhinovirus/enterovirus (HRV/EV 27.4%), adenovirus (ADV, 15.8%), respiratory syncytial virus B (RSVB, 7.8%) and respiratory syncytial virus A (RSVA, 7.8%). The detection of viral infection was the most prevalent in autumn (960/1176, 81.6%), followed by spring (1095/1406, 77.9%), winter (768/992, 77.4%), and summer (944/1306, 72.3%), with HRV/EV and ADV being most commonly detected throughout the 4 years of study period. The detection rate of viral infection was highest among ARI patients presented with croup (123/141, 87.2%), followed by lower respiratory tract infection (1924/2356, 81.7%) and upper respiratory tract infection (1720/2383, 72.2%). FluA, FluB and ADV were positive factors for upper respiratory tract infections. On the other hand, infection with RSVA, RSVB, PIV3, PIV4, HMPV, and EV/RHV were positively associated with lower respiratory tract infections; and PIV1, PIV2, and PIV3 were positively associated with croup. Conclusions This is the first study in Macao to determine the viral etiology and epidemiology of pediatric patients hospitalized for ARIs. The study findings can contribute to the awareness of pathogen, appropriate preventative measure, accurate diagnosis, and proper clinical management of respiratory viral infections among children in Macao.

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TIRYAQ-E-ARBA (A POLY HERBAL UNANI FORMULATION) IN FIGHTING AGAINST COVID 19 LIKE CONDITIONS – UNANI PERSPECTIVE

Indian Journal of Unani Medicine ◽

10.53390/ijum.v13i1.3 ◽

2020 ◽

Vol 13 (1) ◽

Author(s):

Nafisa Qibriya Khan ◽

A. H. Farooqui ◽

Syed Ayesha Fatima ◽

Jalil Ahmad ◽

Tausif S. Khan

Keyword(s):

Respiratory Infections ◽

Transmission Rate ◽

Multiple Organ ◽

World Health ◽

Upper Respiratory Tract ◽

Health Crisis ◽

Unani Medicine ◽

The World ◽

Health Organization ◽

Almost All

Coronavirus disease 2019 (COVID-19) is a pandemic disease of modern time with unique and rapid transmission rate and affected almost all the nations without respecting any border. Coronavirus disease 2019 (COVID-19) is arguably the biggest health crisis the world has faced in 21st century. It is an infectious disease and declared pandemic by the World Health Organization. The coronavirus disease 2019 (COVID-19) outbreak, which originated in Wuhan, China, has now spread to 192 countries and administrative regions infecting nearly 800,000 individuals of all ages as of 31 March 2020. Though most infected individuals exhibit mild symptoms including fever, upper respiratory tract symptoms, shortness of breath, and diarrhoea, or are asymptomatic altogether, severe cases of infection can lead to pneumonia, multiple organ failure, and death. Globally, at least 7900 deaths have been directly attributed to COVID19, and this number is expected to rise with the ongoing epidemic. This is particularly crucial as the current outbreak involves a new pathogen (SARS-CoV-2), on which limited knowledge exists of its infectivity and clinical profile. Research is in progress on therapeutic efficacy of various agents including anti-malarials (Chloroquine and Hydroxychloroquine), antiviral drugs, and convalescent serum of recovered patients. Unani system of medicine is one of the traditional systems of medicine which is being explored for providing preventive, supportive and rehabilitative care to patients. Unani system of medicine has a detailed description of drugs that are utilized in many infectious diseases, including respiratory infections. Immune response is essential to eliminate virus and to preclude disease progression to severe stages. Therefore, it is important to summarize the evidence regarding the preventive measures, control options such as immune-stimulator and prophylactic treatment in Unani medicine against Covid19. This review summarizes various pharmacological actions of Unani formulation Tiryaq-e-Arba in Unani literature and various reported pharmacological activities which can possibly provide prevention, control and reduction of complications of this deadly disease.

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Principles of Judicious Use of Antimicrobial Agents for Pediatric Upper Respiratory Tract Infections

PEDIATRICS ◽

10.1542/peds.101.s1.163 ◽

1998 ◽

Vol 101 (Supplement_1) ◽

pp. 163-165 ◽

Cited By ~ 11

Author(s):

Scott F. Dowell ◽

S. Michael Marcy ◽

William R. Phillips ◽

Michael A. Gerber ◽

Benjamin Schwartz

Keyword(s):

Respiratory Tract ◽

Antimicrobial Agents ◽

Respiratory Infections ◽

The United States ◽

Antimicrobial Treatment ◽

Antimicrobial Use ◽

Upper Respiratory Tract ◽

Oral Agents ◽

Upper Respiratory ◽

Tract Infections

This article introduces a set of principles to define judicious antimicrobial use for five conditions that account for the majority of outpatient antimicrobial use in the United States. Data from the National Center for Health Statistics indicate that in recent years, approximately three fourths of all outpatient antibiotics have been prescribed for otitis media, sinusitis, bronchitis, pharyngitis, or nonspecific upper respiratory tract infection.1Antimicrobial drug use rates are highest for children1; therefore, the pediatric age group represents the focus for the present guidelines. The evidence-based principles presented here are focused on situations in which antimicrobial therapy could be curtailed without compromising patient care. They are not formulated as comprehensive management strategies. For most upper respiratory infections that require antimicrobial treatment, there are several appropriate oral agents from which to choose. Although the general principles of selecting narrow-spectrum agents with the fewest side effects and lowest cost are important, the principles that follow include few specific antibiotic selection recommendations.

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Prescription Surveillance and Polymerase Chain Reaction Testing to Identify Pathogens during Outbreaks of Infection

BioMed Research International ◽

10.1155/2013/746053 ◽

2013 ◽

Vol 2013 ◽

pp. 1-7 ◽

Cited By ~ 1

Author(s):

Hiroaki Sugiura ◽

Tsuguto Fujimoto ◽

Tamie Sugawara ◽

Nozomu Hanaoka ◽

Masami Konagaya ◽

...

Keyword(s):

Polymerase Chain Reaction ◽

Syndromic Surveillance ◽

Respiratory Infections ◽

Emerging Infectious Diseases ◽

Upper Respiratory Tract ◽

Chain Reaction ◽

Specific Pathogen ◽

Polymerase Chain ◽

Syncytial Virus ◽

Tract Infections

Syndromic surveillance, including prescription surveillance, offers a rapid method for the early detection of agents of bioterrorism and emerging infectious diseases. However, it has the disadvantage of not considering definitive diagnoses. Here, we attempted to definitively diagnose pathogens using polymerase chain reaction (PCR) immediately after the prescription surveillance system detected an outbreak. Specimens were collected from 50 patients with respiratory infections. PCR was used to identify the pathogens, which included 14 types of common respiratory viruses andMycoplasma pneumoniae. Infectious agents includingM. pneumoniae, respiratory syncytial virus (RSV), rhinovirus, enterovirus, and parainfluenza virus were detected in 54% of patients. For the rapid RSV diagnosis kit, sensitivity was 80% and specificity was 85%. For the rapid adenovirus diagnosis kit, no positive results were obtained; therefore, sensitivity could not be calculated and specificity was 100%. Many patients were found to be treated for upper respiratory tract infections without the diagnosis of a specific pathogen. In Japan, an outbreak ofM. pneumoniaeinfection began in 2011, and our results suggested that this outbreak may have included false-positive cases. By combining syndromic surveillance and PCR, we were able to rapidly and accurately identify causative pathogens during a recent respiratory infection outbreak.

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Medical Consultations After Typhoon Haiyan in a Field Hospital in the Philippines

Disaster Medicine and Public Health Preparedness ◽

10.1017/dmp.2019.99 ◽

2019 ◽

Vol 14 (1) ◽

pp. 34-38

Author(s):

Julita Gil Cuesta ◽

Joris Adriaan Frank van Loenhout ◽

Maria Lourdes de Lara Banquesio ◽

Masniza Mustaffa ◽

Debarati Guha-Sapir

Keyword(s):

Respiratory Tract Infections ◽

Respiratory Infections ◽

District Hospital ◽

The Philippines ◽

Upper Respiratory Tract ◽

Field Hospital ◽

Adult Men ◽

Medical Consultations ◽

Upper Respiratory ◽

Tract Infections

ABSTRACTIntroduction and Objectives:Typhoon Haiyan partially destroyed the Ormoc District Hospital in the Philippines. A field hospital was established to replace its outpatient department for 5 weeks. We investigated the reasons for medical consultation in the field hospital.Methods:We described the consultations by sex, age, week, and diagnosis according to the Surveillance in Post-Extreme Emergencies and Disasters system. We compared the number and proportion of upper respiratory tract infections (URTIs) with a control season in 2014.Results:We included 6785 consultations, 55.9% from women. The majority of consultations were communicable diseases (88.2%) followed by noncommunicable (7.1%) and injuries (5.6%). Males suffered more often from injuries than women (66.0% vs 34.0%). Consultations due to injuries decreased from 10.0% in the first to 2.9% in the last week. The most frequent diagnosis over the study period was acute respiratory infections (ARIs) (73.1%), of which 83.0% were children. The number of daily URTIs was higher than in a similar 2014 period.Conclusions:ARI was the most prevalent diagnosis. We recommend ARI treatments being fully accessible after such a disaster. During the first week, injury prevention should focus on adult men. Studies after natural disasters should include control periods to better understand disease distribution, ultimately improving the prioritization in disasters.

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Multi-modality detection of SARS-CoV-2 in faecal donor samples for transplantation and in asymptomatic emergency surgical admissions

10.1101/2021.02.02.21250934 ◽

2021 ◽

Author(s):

Susan E Manzoor ◽

Shafquat Zaman ◽

Celina Whalley ◽

David Inglis ◽

Andrew Bosworth ◽

...

Keyword(s):

Digital Pcr ◽

Upper Respiratory Tract ◽

Clearance Time ◽

Evidence Based Treatment ◽

Dilution Series ◽

Acute Presentation ◽

Asymptomatic Patients ◽

Upper Respiratory ◽

Low Levels ◽

Surgical Unit

ABSTRACTIntroductionFaecal transplantation is an evidence based treatment for Clostridiodes difficile. Patients infected with SARS-CoV-2 have been shown to shed the virus in stool for up to 33 days, well beyond the average clearance time for upper respiratory tract shedding. We carried out an analytical and clinical validation of reverse-transcriptase quantitative (RT-qPCR) as well as LAMP, LamPORE and droplet digital PCR in the detection of SARS-CoV-2 RNA in stool from donated samples for FMT, spiked samples and asymptomatic inpatients in an acute surgical unit.MethodsKilled SARS-CoV-2 viral lysate and extracted RNA was spiked into donor stool & FMT and a linear dilution series from 10−1 to 10−5 and tested via RT-qPCR, LAMP, LamPORE and ddPCR against SARS-CoV-2. Patients admitted to the critical care unit with symptomatic SARS-CoV-2 and sequential asymptomatic patients from acute presentation to an acute surgical unit were also tested.ResultsIn a linear dilution series, detection of the lowest dilution series was found to be 8 copies per microlitre of sample. Spiked lysate samples down to 10−2 dilution were detected in FMT samples using RTQPCR, LamPORE and ddPCR and down to 10−1 with LAMP. In symptomatic patients 5/12 had detectable SARS-CoV-2 in stool via RT-qPCR and 6/12 via LamPORE, and in 1/97 asymptomatic patients via RT-qPCR.ConclusionsRT-qPCR can be detected in FMT donor samples using RT-qPCR, LamPORE and ddPCR to low levels using validated pathways. As previously demonstrated, nearly half of symptomatic and less than one percent of asymptomatic patients had detectable SARS-CoV-2 in stool.

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Disinfection performance of a drinking water bottle system with a UVC LED cap against waterborne pathogens and heterotrophic contaminants

10.1101/2021.06.02.446792 ◽

2021 ◽

Author(s):

Richard M Mariita ◽

Sebastien A Blumenstein ◽

Christian M Beckert ◽

Thomas Gombas ◽

Rajul V Randive

Keyword(s):

Public Health ◽

16S Rrna ◽

16S Rrna Gene ◽

Heterotrophic Bacteria ◽

Health Concern ◽

Plate Count ◽

Rrna Gene ◽

Public Health Concern ◽

Worst Case ◽

The 16S Rrna Gene

Background: The purgaty One systems (cap+bottle) are portable stainless-steel water bottles with ultraviolet subtype C (UVC) disinfection capability. This study examines the bottle design, verifies disinfection performance against Escherichia coli, Pseudomonas aeruginosa, Vibrio cholerae and heterotrophic contaminants and addresses the public health relevance of heterotrophic bacteria. Methods: Bottles were inoculated with bacterial strains and disinfection efficacy examined using colony forming unit (CFU) assay. The heterotrophic plate count (HPC) method was used to determine the disinfection performance against environmental contaminants at day 0 and after 3 days of water stagnation. All UVC irradiation experiments were performed under stagnant conditions to confirm that the preset application cycle of 55 seconds offers the desired disinfection performance under worst-case condition. To determine the effectiveness of purgaty One systems (cap+bottle) in disinfection, inactivation efficacy or log reduction value (LRV) was determined using bacteria concentration between UVC ON condition and controls (UVC OFF). The study utilized the 16S rRNA gene for isolate characterization by identifying HPC bacteria to confirm if they belong to groups that are of public health concern. Results: Purgaty One systems fitted with Klaran UVC LEDs achieved 99.99% inactivation (LRV4) efficacy against E. coli and 99.9% inactivation (LRV3) against P. aeruginosa, V. cholerae and heterotrophic contaminants. Based on the 16S rRNA gene analyses, the study determined that the identified HPC isolates enriched by UVC irradiation are of rare public health concern. Conclusion: The bottles satisfactorily inactivated the target pathogenic bacteria and HPC contaminants even after 3 days of water stagnation.

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Evaluation of the microbial community structure of potable water samples from occupied and unoccupied buildings using16S rRNA amplicon sequencing

10.1101/2020.07.17.209346 ◽

2020 ◽

Author(s):

Kimothy L Smith ◽

Howard A Shuman ◽

Douglas Findeisen

Keyword(s):

Microbial Community ◽

16S Rrna ◽

Water Samples ◽

Ad Hoc ◽

Microbial Community Composition ◽

Amplicon Sequencing ◽

The Other ◽

Water Usage ◽

16S Rrna Amplicon Sequencing ◽

Oxford Nanopore

AbstractWe conducted two studies of water samples from buildings with normal occupancy and water usage compared to water from buildings that were unoccupied with little or no water usage due to the COVID-19 shutdown. Study 1 had 52 water samples obtained ad hoc from buildings in four metropolitan locations in different states in the US and a range of building types. Study 2 had 36 water samples obtained from two buildings in one metropolitan location with matched water sample types. One of the buildings had been continuously occupied, and the other substantially vacant for approximately 3 months. All water samples were analyzed using 16S rRNA amplicon sequencing with a MinION from Oxford Nanopore Technologies. More than 127 genera of bacteria were identified, including genera with members that are known to include more than 50 putative frank and opportunistic pathogens. While specific results varied among sample locations, 16S rRNA amplicon abundance and the diversity of bacteria were higher in water samples from unoccupied buildings than normally occupied buildings as was the abundance of sequenced amplicons of genera known to include pathogenic bacterial members. In both studies Legionella amplicon abundance was relatively small compared to the abundance of the other bacteria in the samples. Indeed, when present, the relative abundance of Legionella amplicons was lower in samples from unoccupied buildings. Legionella did not predominate in any of the water samples and were found, on average, in 9.6% of samples in Study 1 and 8.3% of samples in Study 2.SynopsisComparison of microbial community composition in the plumbing of occupied and unoccupied buildings during the COVID-19 pandemic shutdown.

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