Influences of bovine colostrum on nasal swab microbiome and viral upper respiratory tract infections - A case report.
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ABSTRACT:
SUBMITTER: Alsayed A
PROVIDER: S-EPMC7437540 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:The upper respiratory tract (URT) hosts a complex microbial community of commensal microorganisms and potential pathogens. Analyzing the composition and nature of the healthy URT microbiota and how it changes over time will contribute to a better understanding of the pathogenesis of pneumonia and otitis. A longitudinal study was conducted including 174 Holstein calves that were divided in four groups: healthy calves, calves diagnosed with pneumonia, otitis or both diseases. Deep pharyngeal swabs were collected on days 3, 14, 28, and 35 of life, and next-generation sequencing of the 16S rRNA gene as well as quantitative PCR was performed. The URT of Holstein dairy calves aged 3 to 35 days revealed to host a highly diverse bacterial community. The relative abundances of the bacterial genera Mannheimia, Moraxella, and Mycoplasma were significantly higher in diseased versus healthy animals, and the total bacterial load of newborn calves at day 3 was higher for animals that developed pneumonia than for healthy animals. Our results corroborate the existing knowledge that species of Mannheimia and Mycoplasma are important pathogens in pneumonia and otitis. Furthermore, they suggest that species of Moraxella can potentially cause the same disorders (pneumonia and otitis), and that high neonatal bacterial load is a key contributor to the development of pneumonia.
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Project description:The urgent need for large-scale diagnostic testing for SARS-CoV-2 has prompted pursuit of sample-collection methods of sufficient sensitivity to replace sampling of the nasopharynx (NP). Among these alternatives is collection of nasal-swab samples, which can be performed by the patient, avoiding the need for healthcare personnel and personal protective equipment. Previous studies have reached opposing conclusions regarding whether nasal sampling is concordant or discordant with NP. To resolve this disagreement, we compared nasal and NP specimens collected by healthcare workers in a cohort consisting of individuals clinically suspected of COVID-19 and outpatients known to be SARS-CoV-2 RT-PCR positive undergoing follow-up. We investigated three different transport conditions, including traditional viral transport media (VTM) and dry swabs, for each of two different nasal-swab collection protocols on a total of 308 study participants, and compared categorical results and Ct values to those from standard NP swabs collected at the same time from the same patients. All testing was performed by RT-PCR on the Abbott SARS-CoV-2 RealTime EUA (limit of detection [LoD], 100 copies viral genomic RNA/mL transport medium). We found high concordance (Cohen's kappa >0.8) only for patients with viral loads above 1,000 copies/mL. Those with viral loads below 1,000 copies/mL, the majority in our cohort, exhibited low concordance (Cohen's kappa = 0.49); most of these would have been missed by nasal testing alone. Previous reports of high concordance may have resulted from use of assays with higher LoD (?1,000 copies/mL). These findings counsel caution in use of nasal testing in healthcare settings and contact-tracing efforts, as opposed to screening of asymptomatic, low-prevalence, low-risk populations. Nasal testing is an adjunct, not a replacement, for NP.
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Project description:Bovine coronavirus (BCoV) is a causative agent of respiratory and enteric diseases in cattle and calves. BCoV infection was also evident in captive wild ruminants. Recently, water deer are recognized as the most common wildlife to approach farmhouses and livestock barns in Korea. Therefore, we investigated 77 nasal swab samples from non-captive wild water deer (Hydropotes inermis) between November 2016 and September 2017 and identified three samples positive for coronavirus, indicating potential for respiratory shedding. The full genomic sequences of the water deer coronavirus were closely related to BCoV (>98%). Therefore, effective biosecurity system in bovine farms would be necessary to prevent contact between farm ruminants and free-ranging wild water deer.
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Project description:Detection by tandem mass spectrometry of a specific subset of SARS-CoV-2 viral peptides to illustrate the potential of shotgun proteomics for clinical diagnostic.
2020-07-23 | PXD019686 | Pride
Project description:BackgroundBovine respiratory disease (BRD) is an ongoing health and economic challenge in the dairy and beef cattle industries. Multiple risk factors make an animal susceptible to BRD. The presence of Mannheimia haemolytica, Pasteurella multocida, Histophilus somni, and Mycoplasma bovis in lung tissues have been associated with BRD mortalities, but they are also commonly present in the upper respiratory tract of healthy animals. This study aims to compare the cattle nasal microbiome (diversity, composition and community interaction) and the abundance of BRD pathogens (by qPCR) in the nasal microbiome of Holstein steers that are apparently healthy (Healthy group, n = 75) or with BRD clinical signs (BRD group, n = 58). We then used random forest models based on nasal microbial community and qPCR results to classify healthy and BRD-affected animals and determined the agreement with the visual clinical signs. Additionally, co-occurring species pairs were identified in visually BRD or healthy animal groups.ResultsCattle in the BRD group had lower alpha diversity than pen-mates in the healthy group. Amplicon sequence variants (ASVs) from Trueperella pyogenes, Bibersteinia and Mycoplasma spp. were increased in relative abundance in the BRD group, while ASVs from Mycoplasma bovirhinis and Clostridium sensu stricto were increased in the healthy group. Prevalence of H. somni (98%) and P. multocida (97%) was high regardless of BRD clinical signs whereas M. haemolytica (81 and 61%, respectively) and M. bovis (74 and 51%, respectively) were more prevalent in the BRD group than the healthy group. In the BRD group, the abundance of M. haemolytica and M. bovis was increased, while H. somni abundance was decreased. Visual observation of clinical signs agreed with classification by the nasal microbial community (misclassification rate of 32%) and qPCR results (misclassification rate 34%). Co-occurrence analysis demonstrated that the nasal microbiome of BRD-affected cattle presented fewer bacterial associations than healthy cattle.ConclusionsThis study offers insight into the prevalence and abundance of BRD pathogens and the differences in the nasal microbiome between healthy and BRD animals. This suggests that nasal bacterial communities provide a potential platform for future studies and potential pen-side diagnostic testing.
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Project description:Bovine nasal swabs viral metagenome Raw sequence reads
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Project description:The human respiratory tract is heavily exposed to microorganisms. Viral respiratory tract pathogens, like RSV, influenza and rhinoviruses cause major morbidity and mortality from respiratory tract disease. Furthermore, as viruses have limited means of transmission, viruses that cause pathogenicity in other tissues may be transmitted through the respiratory tract. It is therefore important to chart the human virome in this compartment. We have studied nasopharyngeal aspirate samples submitted to the Karolinska University Laboratory, Stockholm, Sweden from March 2004 to May 2005 for diagnosis of respiratory tract infections. We have used a metagenomic sequencing strategy to characterize viruses, as this provides the most unbiased view of the samples. Virus enrichment followed by 454 sequencing resulted in totally 703,790 reads and 110,931 of these were found to be of viral origin by using an automated classification pipeline. The snapshot of the respiratory tract virome of these 210 patients revealed 39 species and many more strains of viruses. Most of the viral sequences were classified into one of three major families; Paramyxoviridae, Picornaviridae or Orthomyxoviridae. The study also identified one novel type of Rhinovirus C, and identified a number of previously undescribed viral genetic fragments of unknown origin.
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2023-04-01 | E-MTAB-12791 | biostudies-arrayexpress
Project description:Performing a proper nasal and oropharyngeal swab procedure is essential in the screening of COVID-19 infection. The video illustration of nasal and oropharyngeal swab is presented (Video S1). To correctly perform the nasopharyngeal swab, the patient must be seated comfortably with the back of their head against the headrest. The swab is inserted in the nose horizontally, along an imaginary line between the nostril and the ear. Oropharyngeal sampling is easier to perform. The swab is directed toward the rear wall of the oropharynx and it is rotated a few times before removal. After taking the sample, it is necessary to insert both swabs in the same tube, breaking the rod with one swift and controlled movement. Finally, carefully reset the cap. It appears to be extremely important to properly collect nasopharyngeal and oropharyngeal swabs in order to minimize the false negative rate among COVID-19 positive patients.
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