Metatranscriptomic analysis of host response and vaginal microbiome of patients with severe COVID-19

Xiao, Meng; Lu, Bo; Ding, Rui; Liu, Xia; Wu, Xian; Li, Yaqian; Li, Xudong; Qiu, Lin; Zhang, Zhibo; Xie, Jing; Chen, Yu; Zhang, Dong; Dong, Liting; Zhang, Meiling; Ji, Peng; Yang, Hua; Kudihna, Timothy; Xu, Yingchun; Li, Taisheng; Yi, Chengqi; Zhu, Lan

doi:10.1007/s11427-021-2091-0

Cited by 7 publications

(6 citation statements)

References 10 publications

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“…Furthermore, we also observed a higher vaginal microbial heterogeneity among infected women compared to controls. This high heterogeneity was previously observed in a metagenomic study with postmenopausal women (56), where not only microbial but also the proportion of bacterial transcript varied considerably among SARS-CoV-2 infected participants in that study (56). Such inter-individual variation may be due to the differences in the personal physiological response to SARS-CoV-2, disease severity, individual's hormonal profile (e.g., early, or late in pregnancy), and health status.…”

Section: Discussionsupporting

confidence: 59%

“…Compositional vaginal microbiota changes observed in pregnant women with active SARS-CoV-2 infection may be the consequence of alterations in the vaginal epithelial environment ( 55 ) and the immune system interaction. Although viral particles of SARS-CoV-2 have not been detected in the vaginal fluid ( 56-58 ), this pulmonary infection promotes strong systemic inflammatory responses ( 59 ). This pro-inflammatory immune tone on the epitheliums, including the vagina, may limit or favor the survival of certain taxa.…”

Section: Discussionmentioning

confidence: 99%

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Impact of SARS-CoV-2 on the microbiota of pregnant women and their infants

Leftwich

Vargas-Robles

Rojas-Correa

et al. 2022

Preprint

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The microbiome inherited at birth exerts marked effects on immune programming with long-term health consequences. Here, we demonstrated that the gut, vaginal, and oral microbial diversity of pregnant women with SARS-CoV-2 infection is reduced, and women with early infections exhibit a different vaginal microbiota composition compared to healthy controls at the time of delivery. Accordingly, infants born to pregnant women with early SARS-CoV-2 infection exhibit a unique oral microbiota dominated by Streptococcus species. Together, we demonstrated that SARS-CoV-2 infections during pregnancy, particularly early infections, are associated with lasting changes in the microbiome of pregnant women compromising the initial microbial seed of their infant. Our results highlight the importance of further exploring the impact of SARS-CoV-2 on the infant's microbiome-dependent immune programming.

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Section: Discussionsupporting

confidence: 59%

Section: Discussionmentioning

confidence: 99%

Impact of SARS-CoV-2 on the microbiota of pregnant women and their infants

Leftwich

Vargas-Robles

Rojas-Correa

et al. 2022

Preprint

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“…The first [20] was an extended time-series survey of 39 participants and was not included as its size would not significantly increment our power. The second [26] interrogated the vaginal metatranscriptome and host response during severe SARS-CoV-2 infection; raw data for this study were not available at the accession number given in the article. Owing to this, and the potential confounding introduced by viral infection and intensive care admission, this dataset was also excluded.…”

Section: Resultsmentioning

confidence: 99%

Vaginal metatranscriptome meta-analysis reveals functional BV subgroups and novel colonisation strategies

Dos Santos,

Copeland,

Macklaim

et al. 2024

Preprint

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The application of '-omics' technologies to study bacterial vaginosis (BV) has uncovered vast differences in composition and scale between the vaginal microbiomes of healthy and BV patients. Compared to amplicon sequencing and shotgun metagenomic approaches focusing on a single or few species, investigating the transcriptome of the vaginal microbiome at a system-wide level can provide insight into the functions which are actively expressed and differential between states of health and disease. We conducted a meta-analysis of vaginal metatranscriptomes from three studies, split into exploratory (n = 44) and validation (n = 297) datasets, accounting for the compositional nature of sequencing data and differences in scale between healthy and BV microbiomes. Conducting differential abundance analyses on the exploratory dataset, we identified a multitude of strategies employed by microbes associated with states of health and BV to evade host cationic antimicrobial peptides (CAMPs); putative mechanisms used by BV-associated species to resist and counteract the low vaginal pH; and potential approaches to disrupt vaginal epithelial integrity so as to establish sites for adherence and biofilm formation. Moreover, we identified several distinct functional subgroups within the BV population, distinguished by genes involved in motility, chemotaxis, biofilm formation and co-factor biosynthesis. After defining molecular states of health and BV in the validation dataset using KEGG orthology terms rather than community state types, differential abundance analysis confirmed earlier observations regarding CAMP resistance and compromising epithelial barrier integrity in healthy and BV microbiomes, and also supported the existence of motile vs. non-motile subgroups in the BV population. Our findings highlight a need to focus on functional rather than taxonomic differences when considering the role of microbiomes in disease and identify pathways for further research as potential BV treatment targets.

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“…Aolymat et al indicated that the incidence of abnormal vaginal discharge, genital itching, and lower abdominal pain was significantly increased during COVID-19 infection compared to pre-infection. 29 In the study by Xiao et al 30 using a TRACE-seq-based metatranscriptomic analysis, there were significant differences in the vaginal microbiome between the COVID-19 group and the healthy control groups. Compared to healthy controls, patients with COVID-19 had higher intragroup heterogeneity of vaginal microbiota structure, more frequent vaginal dysbacteriosis, and more frequent detection of bacterial vaginosis (BV) pathogens, such as Mycoplasma spp., Gardnerella spp., Ureaplasma spp., Bacteroides spp., and Atopobium spp.…”

Section: Discussionmentioning

confidence: 99%

Effect of COVID-19 on Menstruation and Lower Reproductive Tract Health

Li,

Bai,

Xiang

et al. 2023

IJWH

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Background: To evaluate the dynamically impact of the coronavirus disease 2019 (COVID-19) on the female reproductive system. Methods: An online survey was shared to women of reproductive age who had been infected with COVID-19 and recovered in China between January and March 2023. Results: In total, 610 women of childbearing age completed the menstrual component of the survey and 82.6% (n=504) women selfpurchased medications without hospitalization. 254 women were menstruating during COVID-19 infection. 66.9% of them reported changes in menstruation, including cycle length (64.7%), menstrual flow (72.4%), and duration (53%), compared to pre-COVID-19. COVID-19-related chest tightness (OR: 9.5; 95% CI: 1.9-46.3), COVID-19-related stress (OR: 18.4; 95% CI: 1.4-249.7), and COVID-19-related low mood (OR: 6.2; 95% CI: 1.4-28.2) were associated with these menstrual changes. However, over 73% of women who menstruated during and after COVID-19 regained their pre-infection menstrual cycle (73%), duration (79.6%), and flow (75.2%) during their first menstruation after COVID-19 recovery. Compared to pre-infection, 19.7% (n=124) women reported changes in lower reproductive tract during COVID-19, including volume and color of vaginal discharge, vulvar pruritus, and vaginitis. These changes were significantly increased in those with a history of pelvic inflammatory disease (OR: 12.1; 95% CI: 3.1-48.2), ovarian cysts (OR: 4.9; 95% CI: 1.2-19.4), and vaginitis (OR: 5.5; 95% CI: 2.1-14.4) prior to COVID-19. However, 52.4% reported that their lower reproductive tract health had returned to its pre-infection within the first month after recovery from COVID-19, while 73.5% reported a return to the pre-infection within 2 months. Conclusion: Changes in menstruation and lower reproductive tract associated with COVID-19 are transient. Menstruation and lower reproductive tract health will gradually return to pre-COVID-19 status within 2 months of recovery, which can help alleviate excessive concerns about the effects of COVID-19 on the reproductive system.

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Metatranscriptomic analysis of host response and vaginal microbiome of patients with severe COVID-19

Cited by 7 publications

References 10 publications

Impact of SARS-CoV-2 on the microbiota of pregnant women and their infants

Impact of SARS-CoV-2 on the microbiota of pregnant women and their infants

Vaginal metatranscriptome meta-analysis reveals functional BV subgroups and novel colonisation strategies

Effect of COVID-19 on Menstruation and Lower Reproductive Tract Health

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