Changes in the Nasal Microbiota of Pigs Following Single or Co-Infection with Porcine Reproductive and Respiratory Syndrome and Swine Influenza A Viruses

Chrun, Tiphany; Ragione, Roberto M. La; Graham, Simon P.; Tchilian, Elma

doi:10.3390/pathogens10101225

Cited by 9 publications

(11 citation statements)

References 42 publications

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“…Finally, the presence of an "uncultured" Neisseriaceae member that was most abundant in our community-dwelling SARS-CoV-2-infected group is interesting. This family has been previously reported as a "core" nasopharyngeal microbiome taxon [28] and has been shown to be associated with swine influenza co-infection [29]. However, it's role in SARS-CoV-2 infection remains unclear.…”

Section: Plos Onementioning

confidence: 99%

Alterations in the nasopharyngeal microbiome associated with SARS-CoV-2 infection status and disease severity

et al. 2022

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Objectives The COVID-19 pandemic and ensuing public health emergency has emphasized the need to study SARS-CoV-2 pathogenesis. The human microbiome has been shown to regulate the host immune system and may influence host susceptibility to viral infection, as well as disease severity. Several studies have assessed whether compositional alterations in the nasopharyngeal microbiota are associated with SARS-CoV-2 infection. However, the results of these studies were varied, and many did not account for disease severity. This study aims to examine whether compositional differences in the nasopharyngeal microbiota are associated with SARS-CoV-2 infection status and disease severity. Methods We performed Nanopore full-length 16S rRNA sequencing on 194 nasopharyngeal swab specimens from hospitalized and community-dwelling SARS-CoV-2-infected and uninfected individuals. Sequence data analysis was performed using the BugSeq 16S analysis pipeline. Results We found significant beta (PERMANOVA p < 0.05), but not alpha (Kruskal-Wallis p > 0.05) diversity differences in the nasopharyngeal microbiota among our study groups. We identified several differentially abundant taxa associated with SARS-CoV-2 infection status and disease severity using ALDEx2. Finally, we observed a trend towards higher abundance of Enterobacteriaceae in specimens from hospitalized SARS-CoV-2-infected patients. Conclusions This study identified several alterations in the nasopharyngeal microbiome associated with SARS-CoV-2 infection status and disease severity. Understanding the role of the microbiome in infection susceptibility and severity may open new avenues of research for disease prevention and treatment.

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Section: Plos Onementioning

confidence: 99%

Alterations in the nasopharyngeal microbiome associated with SARS-CoV-2 infection status and disease severity

et al. 2022

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“…There are many unanswered questions about the impact of changes in the upper respiratory microbiota on PRDC infections. Initial investigations into the impact of IAV on the nasal microbiota of pigs examined animals only during the acute phase of infection or utilized small group sizes, which can reduce confidence in the analysis [ 10 , 11 ]. Additionally, previous research has shown co-infections between IAV and important swine respiratory pathobionts or pathogens alter the host response to infection and worsen the severity of disease [ 18 – 22 ].…”

Section: Discussionmentioning

confidence: 99%

“…Two studies have investigated the effect of IAV infection on the swine nasal microbiota. One evaluated the acute phase of IAV infection (through day 5 post-challenge), while the other investigated through the resolution of IAV infection to day 31 post-challenge [ 10 , 11 ]. Both studies found reduced microbial richness post-challenge with IAV, but no change in the time-dependent development of the microbiota [ 10 , 11 ].…”

Section: Introductionmentioning

confidence: 99%

“…One evaluated the acute phase of IAV infection (through day 5 post-challenge), while the other investigated through the resolution of IAV infection to day 31 post-challenge [ 10 , 11 ]. Both studies found reduced microbial richness post-challenge with IAV, but no change in the time-dependent development of the microbiota [ 10 , 11 ]. However, small group sizes and inter-animal variation may have impacted the results of these studies.…”

Section: Introductionmentioning

confidence: 99%

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Resilience of swine nasal microbiota to influenza A virus challenge in a longitudinal study

Hau

Nielsen

Mou

et al. 2023

Vet Res

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Influenza A virus (IAV) is an important contributing pathogen of porcine respiratory disease complex (PRDC) infections. Evidence in humans has shown that IAV can disturb the nasal microbiota and increase host susceptibility to bacterial secondary infections. Few, small-scale studies have examined the impact of IAV infection on the swine nasal microbiota. To better understand the effects of IAV infection on the nasal microbiota and its potential indirect impacts on the respiratory health of the host, a larger, longitudinal study was undertaken to characterize the diversity and community composition of the nasal microbiota of pigs challenged with an H3N2 IAV. The microbiome of challenged pigs was compared with non-challenged animals over a 6-week period using 16S rRNA gene sequencing and analysis workflows to characterize the microbiota. Minimal changes to microbial diversity and community structure were seen between the IAV infected and control animals the first 10 days post-IAV infection. However, on days 14 and 21, the microbial populations were significantly different between the two groups. Compared to the control, there were several genera showing significant increases in abundance in the IAV group during acute infection, such as Actinobacillus and Streptococcus. The results here highlight areas for future investigation, including the implications of these changes post-infection on host susceptibility to secondary bacterial respiratory infections.

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“…Finally, the presence of an "uncultured" Neisseriaceae member that was most abundant in our community-dwelling SARS-CoV-2-infected group is interesting. This family has been previously reported as a "core" nasopharyngeal microbiome taxon [26] and has been shown to be associated with swine influenza co-infection [27]. However, it's role in SARS-CoV-2 infection remains unclear.…”

Section: Discussionmentioning

confidence: 99%

Alterations in the Nasopharyngeal Microbiome Associated with SARS-CoV-2 Infection Status and Disease Severity

Gauthier

Locher

MacDonald

et al. 2022

Preprint

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Objectives: The COVID-19 pandemic and ensuing public health emergency has emphasized the need to study SARS-CoV-2 pathogenesis. The human microbiome has been shown to regulate the host immune system and may influence host susceptibility to viral infection, as well as disease severity. Several studies have assessed whether compositional alterations in the nasopharyngeal microbiota are associated with SARS-CoV-2 infection. However, the results of these studies were varied, and many did not account for disease severity. This study aims to examine whether compositional differences in the nasopharyngeal microbiota are associated with SARS-CoV-2 infection status and disease severity. Methods: We performed Nanopore full-length 16S rRNA sequencing on 194 nasopharyngeal swab specimens from hospitalized and community-dwelling SARS-CoV-2-infected and uninfected individuals. Sequence data analysis was performed using the BugSeq 16S analysis pipeline. Results: We found significant beta (PERMANOVA p < 0.05), but not alpha (Kruskal-Wallis p > 0.05) diversity differences in the nasopharyngeal microbiota among our study groups. We identified several differentially abundant taxa associated with SARS-CoV-2 infection status and disease severity using ALDEx2. Finally, we observed a trend towards higher abundance of Enterobacteriaceae in specimens from hospitalized SARS-CoV-2-infected patients. Conclusions: This study identified several alterations in the nasopharyngeal microbiome associated with SARS-CoV-2 infection status and disease severity. Understanding the role of the microbiome in infection susceptibility and severity may open new avenues of research for disease prevention and treatment.

show abstract

Changes in the Nasal Microbiota of Pigs Following Single or Co-Infection with Porcine Reproductive and Respiratory Syndrome and Swine Influenza A Viruses

Cited by 9 publications

References 42 publications

Alterations in the nasopharyngeal microbiome associated with SARS-CoV-2 infection status and disease severity

Alterations in the nasopharyngeal microbiome associated with SARS-CoV-2 infection status and disease severity

Resilience of swine nasal microbiota to influenza A virus challenge in a longitudinal study

Alterations in the Nasopharyngeal Microbiome Associated with SARS-CoV-2 Infection Status and Disease Severity

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