The hygiene hypothesis, the COVID pandemic, and consequences for the human microbiome

The potential importance of the built-environment microbiome and its impact on human health

There is increasing evidence that interactions between microbes and their hosts not only play a role in determining health and disease but also in emotions, thought, and behavior. Built environments greatly influence microbiome exposures because of their built-in highly specific microbiomes coproduced with myriad metaorganisms including humans, pets, plants, rodents, and insects. Seemingly static built structures host complex ecologies of microorganisms that are only starting to be mapped. These microbial ecologies of built environments are directly and interdependently affected by social, spatial, and technological norms. Advances in technology have made these organisms visible and forced the scientific community and architects to rethink gene-environment and microbe interactions respectively. Thus, built environment design must consider the microbiome, and research involving host-microbiome interaction must consider the built-environment. This paradigm shift becomes increasingly important as evidence grows that contemporary built environments are steadily reducing the microbial diversity essential for human health, well-being, and resilience while accelerating the symptoms of human chronic diseases including environmental allergies, and other more life-altering diseases. New models of design are required to balance maximizing exposure to microbial diversity while minimizing exposure to human-associated diseases. Sustained trans-disciplinary research across time (evolutionary, historical, and generational) and space (cultural and geographical) is needed to develop experimental design protocols that address multigenerational multispecies health and health equity in built environments.

Unveiling the gut-eye axis: how microbial metabolites influence ocular health and disease

The intricate interplay between the gut microbiota and ocular health has surpassed conventional medical beliefs, fundamentally reshaping our understanding of organ interconnectivity. This review investigates into the intricate relationship between gut microbiota-derived metabolites and their consequential impact on ocular health and disease pathogenesis. By examining the role of specific metabolites, such as short-chain fatty acids (SCFAs) like butyrate and bile acids (BAs), herein we elucidate their significant contributions to ocular pathologies, thought-provoking the traditional belief of organ sterility, particularly in the field of ophthalmology. Highlighting the dynamic nature of the gut microbiota and its profound influence on ocular health, this review underlines the necessity of comprehending the complex workings of the gut-eye axis, an emerging field of science ready for further exploration and scrutiny. While acknowledging the therapeutic promise in manipulating the gut microbiome and its metabolites, the available literature advocates for a targeted, precise approach. Instead of broad interventions, it emphasizes the potential of exploiting specific microbiome-related metabolites as a focused strategy. This targeted approach compared to a precision tool rather than a broad-spectrum solution, aims to explore the therapeutic applications of microbiome-related metabolites in the context of various retinal diseases. By proposing a nuanced strategy targeted at specific microbial metabolites, this review suggests that addressing specific deficiencies or imbalances through microbiome-related metabolites might yield expedited and pronounced outcomes in systemic health, extending to the eye. This focused strategy holds the potential in bypassing the irregularity associated with manipulating microbes themselves, paving a more efficient pathway toward desired outcomes in optimizing gut health and its implications for retinal diseases.

Social and environmental transmission spread different sets of gut microbes in wild mice

Gut microbes shape many aspects of organismal biology, yet how these key bacteria transmit among hosts in natural populations remains poorly understood. Recent work in mammals has emphasized either transmission through social contacts or indirect transmission through environmental contact, but the relative importance of different routes has not been directly assessed. Here we used a novel radio-frequency identification-based tracking system to collect long-term high-resolution data on social relationships, space use and microhabitat in a wild population of mice (Apodemus sylvaticus), while regularly characterizing their gut microbiota with 16S ribosomal RNA profiling. Through probabilistic modelling of the resulting data, we identify positive and statistically distinct signals of social and environmental transmission, captured by social networks and overlap in home ranges, respectively. Strikingly, microorganisms with distinct biological attributes drove these different transmission signals. While the social network effect on microbiota was driven by anaerobic bacteria, the effect of shared space was most influenced by aerotolerant spore-forming bacteria. These findings support the prediction that social contact is important for the transfer of microorganisms with low oxygen tolerance, while those that can tolerate oxygen or form spores may be able to transmit indirectly through the environment. Overall, these results suggest social and environmental transmission routes can spread biologically distinct members of the mammalian gut microbiota.

Examining Sound, Light, and Vibrations as Tools to Manage Microbes and Support Holobionts, Ecosystems, and Technologies

The vast array of interconnected microorganisms across Earth's ecosystems and within holobionts has been called the "Internet of Microbes." Bacteria and archaea are masters of energy and information collection, storage, transformation, and dissemination using both "wired" and wireless (at a distance) functions. Specific tools affecting microbial energy and information functions offer effective strategies for managing microbial populations within, between, and beyond holobionts. This narrative review focuses on microbial management using a subset of physical modifiers of microbes: sound and light (as well as related vibrations). These are examined as follows: (1) as tools for managing microbial populations, (2) as tools to support new technologies, (3) as tools for healing humans and other holobionts, and (4) as potential safety dangers for microbial populations and their holobionts. Given microbial sensitivity to sound, light, and vibrations, it is critical that we assign a higher priority to the effects of these physical factors on microbial populations and microbe-laden holobionts. We conclude that specific sound, light, and/or vibrational conditions are significant therapeutic tools that can help support useful microbial populations and help to address the ongoing challenges of holobiont disease. We also caution that inappropriate sound, light, and/or vibration exposure can represent significant hazards that require greater recognition.

[New aspects in etiology and treatment of adolescent anorexia nervosa-a postulated bio-psycho-social model and the impact of the COVID-19 pandemic]

Anorexia nervosa is one of the most frequent chronic disorders of adolescence associated with a high mortality. During the COVID-19-pandemic, the number of hospitalized children and adolescents with anorexia nervosa significantly increased. This article outlines new research findings to decode the etiology of this serious disorder, especially a genetic disposition and changes of metabolism. Against the background of increasing rates during the COVID-19 pandemic, the importance of the gene-environment interaction is discussed, and new treatment forms are described. Besides the development of new biological treatment strategies, there is also some important progress in psychotherapeutic interventions. Carers should always be integrated when treating children and adolescents with anorexia nervosa, which is especially emphasized in the new "home treatment" setting. The new concept of anorexia nervosa as a metabo-psychiatric disorder gives us hope for new research ideas and treatment strategies in this often-debilitating disorder of childhood and adolescence.

Impact of COVID-19 on nationwide pediatric complicated sinusitis trends throughout 2018-2022

OBJECTIVES

To describe and analyze the trends of pediatric sinusitis cases from 2018 to 2022 across the country utilizing the Pediatric Hospital Information System (PHIS) database focusing on volumes, socioeconomics, and severity of cases.

STUDY DESIGN

Retrospective Cohort Study.

METHODS

A retrospective cohort study using the Pediatric Health Information System (PHIS) database, which consists of 50 children's hospitals was performed. Regions were defined according to PHIS guidelines. We evaluated percentage of sinusitis cases demographic and socioeconomic information and subgrouped by region throughout 2018-2022.

RESULTS

In all regions there were a greater number of sinusitis cases post-COVID compared to pre-COVID, with notable increases in major and extreme severity. The years 2020 and 2021 saw a decrease in total sinusitis cases in all locations. Both surgical intervention and severity of sinusitis were significant factors affecting length of stay. Age and severity were the most significant predictors regarding the odds of having sinus surgery. Age and insurance type were significant predictors of severity, with increasing age and government insurance associated with higher odds of major or extreme severity of sinusitis.

CONCLUSIONS

There appears to be a trend of both increased number and worsening severity of acute sinusitis cases in the post-COVID era compared to pre-COVID. There was a decrease in cases in 2020-2021 during the pandemic, consistent with trends of other communicable diseases.

Increase in Streptococcal Necrotizing Fasciitis During and After the Coronavirus Disease 2019 Pandemic

Background: Necrotizing fasciitis (NF) is a life-threatening and rare condition. However, we report and analyze a remarkably high number of NF cases during the coronavirus disease 2019 (COVID-19) pandemic and especially in the first months after the COVID-19 pandemic. Patients and Methods: We conducted a retrospective analysis of 17 cases of NF treated in our clinic between January and May 2023. Data were collected on demographics, comorbidities, risk factors, laboratory findings, and clinical outcomes. For each individual case two risk indicating scores, the Laboratory Risk Indicator for Necrotizing Fasciitis (LRINEC) and Laboratory and Anamnestic Risk Indicator for Necrotizing Fasciitis (LARINF) were calculated. Results: In the pandemic years 2021 and 2022 there were 21 and 30 patients with NF, respectively, treated in our clinic. Of the 17 included NF cases in this study from January until May 2023, 16 cases required intensive care unit (ICU) admission, six cases required limb amputation, and four cases resulted in death. The microbiologic examination revealed seven cases of polymicrobial infections, eight cases of monomicrobial infections primarily caused by Streptococcus pyogenes, and two cases without microbial growth. The LRINEC score showed a sensitivity of 82%, whereas the LARINF score demonstrated a sensitivity of 100% for identifying cases of NF. Conclusions: This study highlights a notable increase in NF during and after the COVID-19 pandemic, predominantly associated with Streptococcus pyogenes-induced infections. These cases demonstrate a highly aggressive nature, leading to limb amputation or death in more than half of the cases.

Shared governance in the plant holobiont and implications for one health

The holobiont Holobiont theory is more than 80 years old, while the importance of microbial communities for plant holobionts was already identified by Lorenz Hiltner more than a century ago. Both concepts are strongly supported by results from the new field of microbiome research. Here, we present ecological and genetic features of the plant holobiont that underpin principles of a shared governance between hosts and microbes and summarize the relevance of plant holobionts in the context of global change. Moreover, we uncover knowledge gaps that arise when integrating plant holobionts in the broader perspective of the holobiome as well as one and planetary health concepts. Action is needed to consider interacting holobionts at the holobiome scale, for prediction and control of microbiome function to improve human and environmental health outcomes.

Use of immunology in news and YouTube videos in the context of COVID-19: politicisation and information bubbles

Background

The COVID-19 pandemic propelled immunology into global news and social media, resulting in the potential for misinterpreting and misusing complex scientific concepts.

Objective

To study the extent to which immunology is discussed in news articles and YouTube videos in English and Italian, and if related scientific concepts are used to support specific political or ideological narratives in the context of COVID-19.

Methods

In English and Italian we searched the period 11/09/2019 to 11/09/2022 on YouTube, using the software Mozdeh, for videos mentioning COVID-19 and one of nine immunological concepts: antibody-dependent enhancement, anergy, cytokine storm, herd immunity, hygiene hypothesis, immunity debt, original antigenic sin, oxidative stress and viral interference. We repeated this using MediaCloud for news articles.Four samples of 200 articles/videos were obtained from the randomised data gathered and analysed for mentions of concepts, stance on vaccines, masks, lockdown, social distancing, and political signifiers.

Results

Vaccine-negative information was higher in videos than news (8-fold in English, 6-fold in Italian) and higher in Italian than English (4-fold in news, 3-fold in videos). We also observed the existence of information bubbles, where a negative stance towards one intervention was associated with a negative stance to other linked ideas. Some immunological concepts (immunity debt, viral interference, anergy and original antigenic sin) were associated with anti-vaccine or anti-NPI (non-pharmacological intervention) views. Videos in English mentioned politics more frequently than those in Italian and, in all media and languages, politics was more frequently mentioned in anti-guidelines and anti-vaccine media by a factor of 3 in video and of 3-5 in news.

Conclusion

There is evidence that some immunological concepts are used to provide credibility to specific narratives and ideological views. The existence of information bubbles supports the concept of the "rabbit hole" effect, where interest in unconventional views/media leads to ever more extreme algorithmic recommendations.

Impact of SARS-CoV-2 Vaccination or Infection on the Safety and Efficacy of Aesthetic Injections: A Systematic Review

BACKGROUND

Aesthetic injections have become increasingly popular for maintaining a youthful appearance. However, with the rise of SARS-CoV-2, there have been concerns about potential complications. This study aims to summarize and understand the complications that occur in individuals who have received cosmetic injections after SARS-CoV-2 infection or vaccination. By doing so, we hope to provide recommendations to minimize these complications and ensure the safety of aesthetic treatments in the current COVID-19 era.

METHODS

The PRISMA guidelines, the Preferred Reporting Program for Systematic Reviews and Meta-Analyses, were used for this review. Databases including PubMed, EMBASE, Medline, Web of Science and ScienceDirect were searched. The last search time of each database was May 10, 2023. In addition, relevant references were manually searched.

RESULTS

A total of 26 studies containing 139 patients were searched. The complication with the highest percentage of reported patients was delayed inflammatory response (DIR) (n = 68; 48.92%), followed by diminished efficacy (n = 45; 32.37%) and filler reaction (n = 12; 8.63%). The remaining complications include hypersensitivity reactions, symptomatic hypercalcemia, sub-acute hypersensitive reactions, hyperalgesia, infection, fat necrosis and granulomatous reaction.

CONCLUSIONS

Cosmetic injectable procedures are generally safe but may have adverse effects, particularly during the pandemic. It is important for individuals to fully understand these risks beforehand. Clinicians should be knowledgeable about adverse event mechanisms and management to prevent issues. Industry leaders should strengthen risk management efforts to ensure safe and steady development of cosmetic injections. Overall, a comprehensive understanding, effective communication and risk management are crucial for the safe use of cosmetic injectable procedures.

LEVEL OF EVIDENCE III

This journal requires that authors assign a level of evidence to each article. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the online Instructions to Authors at www.springer.com/00266 .

Development and management of gastrointestinal symptoms in long-term COVID-19

Background

Emerging evidence reveals that SARS-CoV-2 possesses the capability to disrupt the gastrointestinal (GI) homeostasis, resulting in the long-term symptoms such as loss of appetite, diarrhea, gastroesophageal reflux, and nausea. In the current review, we summarized recent reports regarding the long-term effects of COVID-19 (long COVID) on the gastrointestine.

Objective

To provide a narrative review of abundant clinical evidence regarding the development and management of long-term GI symptoms in COVID-19 patients.

Results

Long-term persistent digestive symptoms are exhibited in a majority of long-COVID patients. SARS-CoV-2 infection of intestinal epithelial cells, cytokine storm, gut dysbiosis, therapeutic drugs, psychological factors and exacerbation of primary underlying diseases lead to long-term GI symptoms in COVID-19 patients. Interventions like probiotics, prebiotics, fecal microbiota transplantation, and antibiotics are proved to be beneficial in preserving intestinal microecological homeostasis and alleviating GI symptoms.

Conclusion

Timely diagnosis and treatment of GI symptoms in long-COVID patients hold great significance as they may contribute to the mitigation of severe conditions and ultimately lead to the improvement of outcomes of the patients.

Bacterial Proteases as Potentially Exploitable Modulators of SARS-CoV-2 Infection: Logic from the Literature, Informatics, and Inspiration from the Dog

(1) Background: The COVID-19 pandemic left many intriguing mysteries. Retrospective vulnerability trends tie as strongly to odd demographics as to exposure profiles, genetics, health, or prior medical history. This article documents the importance of nasal microbiome profiles in distinguishing infection rate trends among differentially affected subgroups. (2) Hypothesis: From a detailed literature survey, microbiome profiling experiments, bioinformatics, and molecular simulations, we propose that specific commensal bacterial species in the Pseudomonadales genus confer protection against SARS-CoV-2 infections by expressing proteases that may interfere with the proteolytic priming of the Spike protein. (3) Evidence: Various reports have found elevated Moraxella fractions in the nasal microbiomes of subpopulations with higher resistance to COVID-19 (e.g., adolescents, COVID-19-resistant children, people with strong dietary diversity, and omnivorous canines) and less abundant ones in vulnerable subsets (the elderly, people with narrower diets, carnivorous cats and foxes), along with bioinformatic evidence that Moraxella bacteria express proteases with notable homology to human TMPRSS2. Simulations suggest that these proteases may proteolyze the SARS-CoV-2 spike protein in a manner that interferes with TMPRSS2 priming.

Assessing the Impact of the COVID-19 Pandemic on the Severity of Pediatric Inflammatory Bowel Disease Admissions and New Diagnoses

Introduction

The COVID-19 pandemic has introduced new challenges to the diagnosis and management of pediatric inflammatory bowel disease (IBD). Many patients have had only limited access to their providers through telemedicine, and many chose to delay nonemergent treatment.

Methods

A retrospective chart review of patients with IBD seen by the Pediatric Gastroenterology Division at Doernbecher Children's Hospital from January 2018 to August 2021 was conducted. The study cohort was divided into 2 groups: those presenting before the onset of the COVID-19 pandemic (January 1, 2018 to February 28, 2020) and those presenting during the pandemic (March 1, 2020 to August 1, 2021). Variables collected included: age, sex, race, ethnicity, IBD type, insurance type, location of residence. Primary outcome measures selected focused on disease severity, initial type of treatment, or surgical intervention offered. A subgroup analysis of the new diagnosis patients was performed. Data were analyzed using independent t-tests, chi-squared analysis, and Wilcoxon rank sum tests.

Results

Two hundred and eleven patients met inclusion criteria, 107 (72 new diagnoses, 35 admissions) within the pre-COVID epoch and 104 (67 new diagnoses, 37 admissions) within the during-COVID epoch. Patients in the during-COVID epoch had higher fecal calprotectin level and were more likely to be started on a biologic as initial treatment. Patients admitted during COVID for IBD flare were more likely to require surgical intervention. Subgroup analysis of newly diagnosed patients revealed higher incidence of comorbid depression and anxiety.

Conclusions

Our review identified increased disease severity in newly diagnosed pediatric patients with IBD as well as pediatric patients admitted for flare during COVID. Increases in anxiety and depression rates during COVID may have contributed to worsened disease severity.

The MothersBabies Study, an Australian Prospective Cohort Study Analyzing the Microbiome in the Preconception and Perinatal Period to Determine Risk of Adverse Pregnancy, Postpartum, and Child-Related Health Outcomes: Study Protocol

The microbiome has emerged as a key determinant of human health and reproduction, with recent evidence suggesting a dysbiotic microbiome is implicated in adverse perinatal health outcomes. The existing research has been limited by the sample collection and timing, cohort design, sample design, and lack of data on the preconception microbiome. This prospective, longitudinal cohort study will recruit 2000 Australian women, in order to fully explore the role of the microbiome in the development of adverse perinatal outcomes. Participants are enrolled for a maximum of 7 years, from 1 year preconception, through to 5 years postpartum. Assessment occurs every three months until pregnancy occurs, then during Trimester 1 (5 + 0-12 + 6 weeks gestation), Trimester 2 (20 + 0-24 + 6 weeks gestation), Trimester 3 (32 + 0-36 + 6 weeks gestation), and postpartum at 1 week, 2 months, 6 months, and then annually from 1 to 5 years. At each assessment, maternal participants self-collect oral, skin, vaginal, urine, and stool samples. Oral, skin, urine, and stool samples will be collected from children. Blood samples will be obtained from maternal participants who can access a study collection center. The measurements taken will include anthropometric, blood pressure, heart rate, and serum hormonal and metabolic parameters. Validated self-report questionnaires will be administered to assess diet, physical activity, mental health, and child developmental milestones. Medications, medical, surgical, obstetric history, the impact of COVID-19, living environments, and pregnancy and child health outcomes will be recorded. Multiomic bioinformatic and statistical analyses will assess the association between participants who developed high-risk and low-risk pregnancies, adverse postnatal conditions, and/or childhood disease, and their microbiome for the different sample types.

Is a Lower Dose of More Bioavailable Iron (18-mg Ferrous Bisglycinate) Noninferior to 60-mg Ferrous Sulfate in Increasing Ferritin Concentrations While Reducing Gut Inflammation and Enteropathogen Detection in Cambodian Women? A Randomized Controlled Noninferiority Trial

BACKGROUND

Global guidelines recommend untargeted iron supplementation for women in regions of anemia prevalence ≥40%, such as Cambodia. However, the potential harms of untargeted iron on the gut have not been rigorously studied in women and likely vary depending on iron dose and form.

OBJECTIVES

We investigated if a lower dose of a highly bioavailable iron amino acid chelate was as effective as the standard dose of iron salts in increasing ferritin concentrations and whether any differences were observed in gut inflammation or enteropathogen detection.

METHODS

A double-blind, randomized placebo-controlled noninferiority trial was conducted in Cambodia. Nonpregnant women (n = 480, 18-45 y) were randomly assigned to 60-mg ferrous sulfate, 18-mg ferrous bisglycinate, or placebo for 12 wk. Nonfasting blood and stool specimens were collected at baseline and 12 wk. Ferritin and fecal calprotectin were measured with an ELISA. A molecular assay was used to detect 11 enteropathogens in a random subset of n = 100 women. Generalized linear mixed-effects models were used to estimate the adjusted mean difference in ferritin concentrations at 12 wk (primary outcome), as compared with our 'a priori' noninferiority margin of 20 μg/L.

RESULTS

Baseline anemia and iron deficiency prevalence was low (17% and 6%, respectively). The adjusted mean difference in ferritin concentrations between the iron groups was 14.6 (95% confidence interval [CI]: 7.6, 21.6) μg/L. Mean ferritin concentration at 12 wk was higher in the ferrous sulfate (99 [95% CI: 95, 103] μg/L, P < 0.001) than in ferrous bisglycinate (84 [95% CI: 80, 88] μg/L) and placebo groups (78 [95% CI: 74, 82] μg/L). No differences in fecal calprotectin concentrations or enteropathogen detection were observed across groups at 12 wk.

CONCLUSIONS

Ferrous bisglycinate (18-mg) was not as effective as ferrous sulfate (60-mg) in increasing ferritin concentrations and did not differentially influence biomarkers of gut health in this predominantly iron-replete population of Cambodian women. This trial was registered at clinicaltrials.gov registry as NCT04017598.

The Effect of Oral Iron Supplementation on Gut Microbial Composition: a Secondary Analysis of a Double-Blind, Randomized Controlled Trial among Cambodian Women of Reproductive Age

The World Health Organization recommends untargeted iron supplementation for women of reproductive age (WRA) in countries where anemia prevalence is greater than 40%, such as Cambodia. Iron supplements, however, often have poor bioavailability, so the majority remains unabsorbed in the colon. The gut houses many iron-dependent bacterial enteropathogens; thus, providing iron to individuals may be more harmful than helpful. We examined the effects of two oral iron supplements with differing bioavailability on the gut microbiomes in Cambodian WRA. This study is a secondary analysis of a double-blind, randomized controlled trial of oral iron supplementation in Cambodian WRA. For 12 weeks, participants received ferrous sulfate, ferrous bisglycinate, or placebo. Participants provided stool samples at baseline and 12 weeks. A subset of stool samples (n = 172), representing the three groups, were randomly selected for gut microbial analysis by 16S rRNA gene sequencing and targeted real-time PCR (qPCR). At baseline, 1% of women had iron-deficiency anemia. The most abundant gut phyla were Bacteroidota (45.7%) and Firmicutes (42.1%). Iron supplementation did not alter gut microbial diversity. Ferrous bisglycinate increased the relative abundance of Enterobacteriaceae, and there was a trend towards an increase in the relative abundance of Escherichia-Shigella. qPCR detected an increase in the enteropathogenic Escherichia coli (EPEC) virulence gene, bfpA, in the group that received ferrous sulfate. Thus, iron supplementation did not affect overall gut bacterial diversity in predominantly iron-replete Cambodian WRA, however, evidence does suggest an increase in relative abundance within the broad family Enterobacteriaceae associated with ferrous bisglycinate use. IMPORTANCE To the best of our knowledge, this is the first published study to characterize the effects of oral iron supplementation on the gut microbiomes of Cambodian WRA. Our study found that iron supplementation with ferrous bisglycinate increases the relative abundance of Enterobacteriaceae, which is a family of bacteria that includes many Gram-negative enteric pathogens like Salmonella, Shigella, and Escherichia coli. Using qPCR for additional analysis, we were able to detect genes associated with enteropathogenic E. coli, a type of diarrheagenic E. coli known to be present around the world, including water systems in Cambodia. The current WHO guidelines recommend blanket (untargeted) iron supplementation for Cambodian WRA despite a lack of studies in this population examining iron's effect on the gut microbiome. This study can facilitate future research that may inform evidence-based global practice and policy.

Severity and mortality associated with COVID-19 among children hospitalised in tertiary care centres in India: a cohort study

Background

It is critical to identify high-risk groups among children with COVID-19 from low-income and middle-income countries (LMICs) to facilitate the optimum use of health system resources. The study aims to describe the severity and mortality of different clinical phenotypes of COVID-19 in a large cohort of children admitted to tertiary care hospitals in India.

Methods

Children aged 0-19 years with evidence of SARS-CoV-2 infection (real time polymerase chain reaction or rapid antigen test positive) or exposure (anti-SARS-CoV-2 antibody, or history of contact with SARS-CoV-2) were enrolled in the study, between January 2021 and March 2022 across five tertiary hospitals in India. All study participants enrolled prospectively and retrospectively were followed up for three months after discharge. COVID-19 was classified into severe (Multisystem Inflammatory Syndrome in Children (MIS-C), severe acute COVID-19, 'unclassified') or non-severe disease. The mortality rates were estimated in different phenotypes.

Findings

Among 2468 eligible children enrolled, 2148 were hospitalised. Signs of illness were present in 1688 (79%) children with 1090 (65%) having severe disease. High mortality was reported in MIS-C (18.6%), severe acute COVID-19 (13.3%) and the unclassified severe COVID-19 disease (12.3%). Mortality remained high (17.5%) when modified MIS-C criteria was used. Non-severe COVID-19 disease had 14.1% mortality when associated with comorbidity.

Interpretation

Our findings have important public health implications for low resource settings. The high mortality underscores the need for better preparedness for timely diagnosis and management of COVID-19. Children with associated comorbidity or coinfections are a vulnerable group and need special attention. MIS-C requires context specific diagnostic criteria for low resource settings. It is important to evaluate the clinical, epidemiological and health system-related risk factors associated with severe COVID-19 and mortality in children from LMICs.

Funding

Department of Biotechnology, Govt of India and Department of Maternal, Child and Adolescent Health and Aging, WHO, Geneva, Switzerland.

A higher number of SARS-COV-2 infections in quilombola communities than in the local population in Brazil

The historical and social vulnerability of quilombola communities in Brazil can make them especially fragile in the face of COVID-19, considering that several individuals have precarious health systems and inadequate access to water. This work aimed to characterize the frequency of SARS-COV-2 infections and the presence of IgM and IgG SARS-CoV-2 antibodies in quilombola populations and their relationship with the presence of risk factors or preexisting chronic diseases in the quilombola communities. We analyzed the sociodemographic and clinical characteristics, serological status, comorbidities, and symptoms of 1,994 individuals (478 males and 1,536 females) from 18 Brazilian municipalities in the State of Sergipe of quilombola communities, which were evaluated at different epidemiological weeks, starting at the 32nd (August 6th) and ending at the 40th (October 3rd) epidemiological week. More than 70% of studied families live in rural areas and they have an extreme poverty social status. Although we found a higher number of SARS-COV-2 infections in quilombola communities than in the local population, their SARS-CoV-2 reactivity and IgM and IgG positivity varied across the communities investigated. Arterial hypertension was the most risk factor, being found in 27.8% of the individuals (9.5% in stage 1, 10.8% in stage 2, and 7.5% in stage 3). The most common COVID-19 symptoms and comorbidities were headache, runny nose, flu, and dyslipidemia. However, most individuals were asymptomatic (79.9%). Our data indicate that mass testing must be incorporated into public policy to improve the health care system available to quilombola populations during a future pandemic or epidemic.

Gut microbiota in COVID-19: key microbial changes, potential mechanisms and clinical applications

The gastrointestinal tract is involved in coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The gut microbiota has important roles in viral entry receptor angiotensin-converting enzyme 2 (ACE2) expression, immune homeostasis, and crosstalk between the gut and lungs, the 'gut-lung axis'. Emerging preclinical and clinical studies indicate that the gut microbiota might contribute to COVID-19 pathogenesis and disease outcomes; SARS-CoV-2 infection was associated with altered intestinal microbiota and correlated with inflammatory and immune responses. Here, we discuss the cutting-edge evidence on the interactions between SARS-CoV-2 infection and the gut microbiota, key microbial changes in relation to COVID-19 severity and host immune dysregulations with the possible underlying mechanisms, and the conceivable consequences of the pandemic on the human microbiome and post-pandemic health. Finally, potential modulatory strategies of the gut microbiota are discussed. These insights could shed light on the development of microbiota-based interventions for COVID-19.

Incidence of pediatric tonsillitis, otitis and upper respiratory infectious entities in the pre and post COVID-19 quarantine eras

BACKGROUND

At this point of the COVID-19 pandemic, with the worldwide loosening of health restrictions, there has been an observed jump in infectious load especially of the upper airways.Aims/Objectives: To shed light on children's immunity and potential health risks after the COVID-19 pandemic.

METHODS

A retrospective chart review from May 2019 to January 2022. Pediatric patients with a discharge diagnosis suggestive of an upper respiratory or ENT infection were included. The sample was divided into three groups according to the date of presentation.

RESULTS

A total 4356 patients were diagnosed with ENT infectious aetiology. The mean age was 4.69 years. The three periods studied were: Period-1 (May 2019-January 2020), period-2 (February 2020-April 2021) and period-3 (May 2021-January 2022). The distribution of adenoiditis and MEE is the same across all periods (p > .05). The incidence of URTI, AOM and tonsillitis were significantly highest during period-3 followed by period-1, which in turn was significantly higher than during period-2 (p < .05). The incidence of sinusitis was the highest during period-3 (p < .001).

CONCLUSION

There seems to be a heightened susceptibility to acute infection in children after the pandemic.Significance: It is important to keep in mind the changes in microbiota and implement measures to promote healthy gut flora, timely vaccination, and prompt medical interventions.Summary BoxWhat is already known: We already know that quarantine has significantly decreased infectious load especially in children.This study adds an objective assessment of this decrease with an assessment of the infectious load post-quarantine.This study is a model for future pandemics on the importance of vaccinations and the importance of microbiota changes after pandemics.

Unintended Consequences of COVID-19 Non-Pharmaceutical Interventions (NPIs) for Population Health and Health Inequalities

Since the start of the COVID-19 pandemic in early 2020, governments around the world have adopted an array of measures intended to control the transmission of the SARS-CoV-2 virus, using both pharmaceutical and non-pharmaceutical interventions (NPIs). NPIs are public health interventions that do not rely on vaccines or medicines and include policies such as lockdowns, stay-at-home orders, school closures, and travel restrictions. Although the intention was to slow viral transmission, emerging research indicates that these NPIs have also had unintended consequences for other aspects of public health. Hence, we conducted a narrative review of studies investigating these unintended consequences of NPIs, with a particular emphasis on mental health and on lifestyle risk factors for non-communicable diseases (NCD): physical activity (PA), overweight and obesity, alcohol consumption, and tobacco smoking. We reviewed the scientific literature using combinations of search terms such as 'COVID-19', 'pandemic', 'lockdowns', 'mental health', 'physical activity', and 'obesity'. NPIs were found to have considerable adverse consequences for mental health, physical activity, and overweight and obesity. The impacts on alcohol and tobacco consumption varied greatly within and between studies. The variability in consequences for different groups implies increased health inequalities by age, sex/gender, socioeconomic status, pre-existing lifestyle, and place of residence. In conclusion, a proper assessment of the use of NPIs in attempts to control the spread of the pandemic should be weighed against the potential adverse impacts on other aspects of public health. Our findings should also be of relevance for future pandemic preparedness and pandemic response teams.

The Association between Previous Antibiotic Consumption and SARS-CoV-2 Infection: A Population-Based Case-Control Study

Background: The susceptibility to SARS-CoV-2 infection is complex and not yet fully elucidated, being related to many variables; these include human microbiome and immune status, which are both affected for a long period by antibiotic use. We therefore aimed to examine the association of previous antibiotic consumption and SARS-CoV-2 infection in a large-scale population-based study with control of known confounders. Methods: A matched case–control study was performed utilizing the electronic medical records of a large Health Maintenance Organization. Cases were subjects with confirmed SARS-CoV-2 infection (n = 31,260), matched individually (1:4 ratio) to controls without a positive SARS-CoV-2 test (n = 125,039). The possible association between previous antibiotic use and SARS-CoV-2 infection was determined by comparing antibiotic consumption in the previous 6 and 12 months between the cases and controls. For each antibiotic consumed we calculated the odds ratio (OR) for documented SARS-CoV-2 infection, 95% confidence interval (CI), and p-value using univariate and multivariate analyses. Results: The association between previous antibiotic consumption and SARS-CoV-2 infection was complex and bi-directional. In the multivariate analysis, phenoxymethylpenicillin was associated with increased rate of SARS-CoV-2 infection (OR 1.110, 95% CI: 1.036–1.191) while decreased rates were associated with previous consumption of trimethoprim-sulfonamides (OR 0.783, 95% CI: 0.632–0.971) and azithromycin (OR 0.882, 95% CI: 0.829–0.938). Fluroquinolones were associated with decreased rates (OR 0.923, 95% CI: 0.861–0.989) only in the univariate analysis. Previous consumption of other antibiotics had no significant association with SARS-CoV-2 infection. Conclusions: Previous consumption of certain antibiotic agents has an independent significant association with increased or decreased rates of SARS-CoV-2 infection. Plausible mechanisms, that should be further elucidated, are mainly antibiotic effects on the human microbiome and immune modulation.

A Healthy Vaginal Microbiota Remains Stable during Oral Probiotic Supplementation: A Randomised Controlled Trial

The primary objective of this randomised, placebo-controlled, triple-blind study was to assess whether orally consumed Lactobacillus acidophilus La-14 (La-14) and Lacticaseibacillus rhamnosus HN001 (HN001) colonise a healthy human vagina. Furthermore, potential effects on vaginal microbiota and immune markers were explored. Fifty women devoid of vaginal complaints (Nugent score 0-3 and vaginal pH ≤ 4.5) were randomised into a 2-week intervention with either La-14 and HN001 as the verum product or a comparable placebo. Vaginal swab samples were collected at baseline, after one and two weeks of intervention, and after a one-week follow-up, for assessing colonisation of the supplemented lactobacilli, vaginal microbiota, and six specific immune markers. Colonisation of L. acidophilus and L. rhamnosus was not observed above the assay detection limit (5.29 and 5.11 log 10 genomes/swab for L. acidophilus and L. rhamnosus, respectively). Vaginal microbiotas remained stable and predominated by lactobacilli throughout the intervention, and vaginal pH remained optimal (at least 90% of participants in both groups had pH 4.0 or 4.5 throughout the study). Immune markers elafin and human β-defensin 3 (HBD-3) were significantly decreased in the verum group (p = 0.022 and p = 0.028, respectively) but did not correlate with any microbiota changes. Adverse events raised no safety concerns, and no undesired changes in the vaginal microbiota or immune markers were detected.

The Pandemic and Your Skin—Direct and Indirect Impact of COVID-19

Apart from well-known respiratory symptoms, less frequent symptoms also appear as a direct result of COVID-19 infection, or as indirect effects of the recommended quarantine and related lifestyle changes. The impact of the COVID-19 pandemic on human skin is predominantly focused on in this article. Cutaneous manifestations, including redness, chilblain-like symptoms (COVID toes), hives or urticaria rash, water blisters, and fishing net-like red-blue patterns on the skin, may appear as accompanying or as systemic COVID-19 symptoms with potential lesions at different skin sites. These symptoms were related to skin phototypes and vitamin D deficiency. Moreover, Black, Asian, and minority ethnic origin patients are found to be more sensitive to COVID-19 infection than Caucasians because of vitamin D deficiency. The region of population with lighter skin phototypes have a significantly higher chance to develop cutaneous manifestations than population with dark skin. In addition, adverse effects, such as skin barrier damage and irritation, may also occur due to extensive personal protective equipment usage (e.g., masks, protective suits, and a few others) and predominately alcohol-based sanitizers. This manuscript covers various aspects of COVID-19 and its clinical skin manifestations.

Associations of disordered eating with the intestinal microbiota and short-chain fatty acids among young adults with type 1 diabetes

BACKGROUND AND AIMS

Disordered eating (DE) in type 1 diabetes (T1D) includes insulin restriction for weight loss with serious complications. Gut microbiota-derived short chain fatty acids (SCFA) may benefit host metabolism but are reduced in T1D. We evaluated the hypothesis that DE and insulin restriction were associated with reduced SCFA-producing gut microbes, SCFA, and intestinal microbial diversity in adults with T1D.

METHODS AND RESULTS

We collected stool samples at four timepoints in a hypothesis-generating gut microbiome pilot study ancillary to a weight management pilot in young adults with T1D. 16S ribosomal RNA gene sequencing measured the normalized abundance of SCFA-producing intestinal microbes. Gas-chromatography mass-spectrometry measured SCFA (total, acetate, butyrate, and propionate). The Diabetes Eating Problem Survey-Revised (DEPS-R) assessed DE and insulin restriction. Covariate-adjusted and Bonferroni-corrected generalized estimating equations modeled the associations. COVID-19 interrupted data collection, so models were repeated restricted to pre-COVID-19 data. Data were available for 45 participants at 109 visits, which included 42 participants at 65 visits pre-COVID-19. Participants reported restricting insulin "At least sometimes" at 53.3% of visits. Pre-COVID-19, each 5-point DEPS-R increase was associated with a -0.34 (95% CI -0.56, -0.13, p = 0.07) lower normalized abundance of genus Anaerostipes; and the normalized abundance of Lachnospira genus was -0.94 (95% CI -1.5, -0.42), p = 0.02 lower when insulin restriction was reported "At least sometimes" compared to "Rarely or Never".

CONCLUSION

DE and insulin restriction were associated with a reduced abundance of SCFA-producing gut microbes pre-COVID-19. Additional studies are needed to confirm these associations to inform microbiota-based therapies in T1D.

COVID-19: The Ethno-Geographic Perspective of Differential Immunity

Coronavirus disease 2019 (COVID-19), the agent behind the worst global pandemic of the 21st century (COVID-19), is primarily a respiratory-disease-causing virus called SARS-CoV-2 that is responsible for millions of new cases (incidence) and deaths (mortalities) worldwide. Many factors have played a role in the differential morbidity and mortality experienced by nations and ethnicities against SARS-CoV-2, such as the quality of primary medical health facilities or enabling economies. At the same time, the most important variable, i.e., the subsequent ability of individuals to be immunologically sensitive or resistant to the infection, has not been properly discussed before. Despite having excellent medical facilities, an astounding issue arose when some developed countries experienced higher morbidity and mortality compared with their relatively underdeveloped counterparts. Hence, this investigative review attempts to analyze the issue from an angle of previously undiscussed genetic, epigenetic, and molecular immune resistance mechanisms in correlation with the pathophysiology of SARS-CoV-2 and varied ethnicity-based immunological responses against it. The biological factors discussed here include the overall landscape of human microbiota, endogenous retroviral genes spliced into the human genome, and copy number variation, and how they could modulate the innate and adaptive immune systems that put a certain ethnic genetic architecture at a higher risk of SARS-CoV-2 infection than others. Considering an array of these factors in their entirety may help explain the geographic disparity of disease incidence, severity, and subsequent mortality associated with the disease while at the same time encouraging scientists to design new experimental approaches to investigation.

Ancient pathogens provide a window into health and well-being

This perspective draws on the record of ancient pathogen genomes and microbiomes illuminating patterns of infectious disease over the course of the Holocene in order to address the following question. How did major changes in living circumstances involving the transition to and intensification of farming alter pathogens and their distributions? Answers to this question via ancient DNA research provide a rapidly expanding picture of pathogen evolution and in concert with archaeological and historical data, give a temporal and behavioral context for heath in the past that is relevant for challenges facing the world today, including the rise of novel pathogens.

Shifting pattern of gut microbiota in pregnant women two decades apart - an observational study

BACKGROUND

Past decades have witnessed a decrease in environmental biodiversity. We hypothesized a similar decrease in indigenous gut microbiota diversity, which may have contributed to the obesity epidemic.

OBJECTIVE

To investigate the changes in the composition and function of the gut microbiota in pregnant women over a period of 20 years.

STUDY DESIGN

Altogether 124 pregnant women (41 overweight and matched 83 normal weight) pregnant in 1997, 2007 or 2017 were included in the study. The gut microbiota composition was assessed from fecal samples obtained at 32 weeks of gestation by 16S rRNA gene sequencing. Fecal short chain fatty acid (SCFA) profiles were measured by gas chromatography mass spectrometry (GC-MS).

RESULTS

Distinct gut microbiota profiles were detected in pregnant women from 1997, 2007 and 2017 (PERMANOVA Bray-Curtis R2 = 0.029, p = 0.001). The women pregnant in 1997 exhibited significantly higher microbiota richness and diversity as compared to those pregnant in 2007 and 2017. The total concentration of fecal SCFAs was significantly higher in the pregnant women in 1997 compared to those in 2007 and 2017. Significant differences in gut microbiota composition between normal weight and overweight women were manifest in 1997 but not in 2007 or 2017.

CONCLUSIONS

The decrease in intestinal microbiota richness and diversity over two decades occurred in parallel with the decline in biodiversity in our natural surroundings. It appears that the gut microbiota of pregnant women has changed over time to a composition typical for overweight individuals.

The Gut Microbiome of Children during the COVID-19 Pandemic

The gut microbiome has been shown to play a critical role in maintaining a healthy state. Dysbiosis of the gut microbiome is involved in modulating disease severity and potentially contributes to long-term outcomes in adults with COVID-19. Due to children having a significantly lower risk of severe illness and limited sample availability, much less is known about the role of the gut microbiome in children with COVID-19. It is well recognized that the developing gut microbiome of children differs from that of adults, but it is unclear if this difference contributes to the different clinical presentations and complications. In this review, we discuss the current knowledge of the gut microbiome in children with COVID-19, with gut microbiome dysbiosis being found in pediatric COVID-19 but specific taxa change often differing from those described in adults. Additionally, we discuss possible mechanisms of how the gut microbiome may mediate the presentation and complications of COVID-19 in children and the potential role for microbial therapeutics.

Exiting the Anthropocene: Achieving personal and planetary health in the 21st century

Planetary health provides a perspective of ecological interdependence that connects the health and vitality of individuals, communities, and Earth's natural systems. It includes the social, political, and economic ecosystems that influence both individuals and whole societies. In an era of interconnected grand challenges threatening health of all systems at all scales, planetary health provides a framework for cross-sectoral collaboration and unified systems approaches to solutions. The field of allergy is at the forefront of these efforts. Allergic conditions are a sentinel measure of environmental impact on human health in early life-illuminating how ecological changes affect immune development and predispose to a wider range of inflammatory noncommunicable diseases (NCDs). This shows how adverse macroscale ecology in the Anthropocene penetrates to the molecular level of personal and microscale ecology, including the microbial systems at the foundations of all ecosystems. It provides the basis for more integrated efforts to address widespread environmental degradation and adverse effects of maladaptive urbanization, food systems, lifestyle behaviors, and socioeconomic disadvantage. Nature-based solutions and efforts to improve nature-relatedness are crucial for restoring symbiosis, balance, and mutualism in every sense, recognizing that both personal lifestyle choices and collective structural actions are needed in tandem. Ultimately, meaningful ecological approaches will depend on placing greater emphasis on psychological and cultural dimensions such as mindfulness, values, and moral wisdom to ensure a sustainable and resilient future.

Nasopharyngeal microbiome of COVID-19 patients revealed a distinct bacterial profile in deceased and recovered individuals

The bacterial co-infections in SARS-CoV-2 patients remained the least explored subject of clinical manifestations that may also determine the disease severity. Nasopharyngeal microbial community structure within SARS-CoV-2 infected patients could reveal interesting microbiome dynamics that may influence the disease outcomes. Here, in this research study, we analyzed distinct nasopharyngeal microbiome profile in the deceased (n = 48) and recovered (n = 29) COVID-19 patients and compared it with control SARS-CoV-2 negative individuals (control) (n = 33). The nasal microbiome composition of the three groups varies significantly (PERMANOVA, p-value <0.001), where deceased patients showed higher species richness compared to the recovered and control groups. Pathogenic genera, including Corynebacterium (LDA score 5.51), Staphylococcus, Serratia, Klebsiella and their corresponding species were determined as biomarkers (p-value <0.05, LDA cutoff 4.0) in the deceased COVID-19 patients. Ochrobactrum (LDA score 5.79), and Burkholderia (LDA 5.29), were found in the recovered group which harbors ordinal bacteria (p-value <0.05, LDA-4.0) as biomarkers. Similarly, Pseudomonas (LDA score 6.19), and several healthy nasal cavity commensals including Veillonella, and Porphyromonas, were biomarkers for the control individuals. Healthy commensal bacteria may trigger the immune response and alter the viral infection susceptibility and thus, may play important role and possible recovery that needs to be further explored. This research finding provide vital information and have significant implications for understanding the microbial diversity of COVID-19 patients. However, additional studies are needed to address the microbiome-based therapeutics and diagnostics interventions.

Type 1 diabetes incidence in children and adolescents during the COVID-19 pandemic in Germany

AIMS/HYPOTHESIS

The aim of this study was to analyze the incidence of type 1 diabetes in children and adolescents (<20 years of age) during the COVID-19 pandemic (3/2020 to 12/2021) in Germany.

METHODS

The present study was based on the IQVIA longitudinal prescription database (LRx), All persons (age ≤ 20 years) with new insulin prescriptions from 2016 to 2021 (index date) were selected and stratified by age group. Weekly (age-specific) data were used to forecast the prescription incidence for the pandemic period based on pre-pandemic data and to explore the relationship between weekly reported age-specific COVID-19 incidences and type 1 diabetes incidence and rate ratios of observed vs. predicted diabetes incidence respectively.

RESULTS

During the pre-pandemic period, there was a stable higher insulin prescription incidence during the winter period and a lower insulin prescription incidence during summer. During the pandemic period, there was less seasonal variation in incidence related to the finding that the observed incidence during summer in 2002 and 2021 was 44 % and 65 %, higher, respectively, than the expected incidence based on pre-pandemic year. We did not find any cross-correlations between the COVID-19 incidence and the type 1 diabetes incidence for any age group. Likewise, there were no cross-correlations between the COVID-19 incidence and the incidence rate ratios of observed incidences to predicted incidences.

CONCLUSIONS/INTERPRETATION

During the COVID-19 pandemic, there was less seasonal variation in the incidence of type 1 diabetes (defined by new insulin prescriptions), with higher observed than expected incidences during summer. We found no evidence that the increase in type 1 diabetes incidence during the COVID-19 pandemic relates to direct effects of COVID-19 pandemic.

The Intestinal Microbiota and Short-Chain Fatty Acids in Association with Advanced Metrics of Glycemia and Adiposity Among Young Adults with Type 1 Diabetes and Overweight or Obesity

Background

Comanagement of glycemia and adiposity is the cornerstone of cardiometabolic risk reduction in type 1 diabetes (T1D), but targets are often not met. The intestinal microbiota and microbiota-derived short-chain fatty acids (SCFAs) influence glycemia and adiposity but have not been sufficiently investigated in longstanding T1D.

Objectives

We evaluated the hypothesis that an increased abundance of SCFA-producing gut microbes, fecal SCFAs, and intestinal microbial diversity were associated with improved glycemia but increased adiposity in young adults with longstanding T1D.

Methods

Participants provided stool samples at ≤4 time points (NCT03651622: https://clinicaltrials.gov/ct2/show/NCT03651622). Sequencing of the 16S ribosomal RNA gene measured abundances of SCFA-producing intestinal microbes. GC-MS measured total and specific SCFAs (acetate, butyrate, propionate). DXA (body fat percentage and percentage lean mass) and anthropometrics (BMI) measured adiposity. Continuous glucose monitoring [percentage of time in range (70-180 mg/dL), above range (>180 mg/dL), and below range (54-69 mg/dL)] and glycated hemoglobin (i.e., HbA1c) assessed glycemia. Adjusted and Bonferroni-corrected generalized estimating equations modeled the associations of SCFA-producing gut microbes, fecal SCFAs, and intestinal microbial diversity with glycemia and adiposity. COVID-19 interrupted data collection, so models were repeated restricted to pre-COVID-19 visits.

Results

Data were available for ≤45 participants at 101 visits (including 40 participants at 54 visits pre-COVID-19). Abundance of Eubacterium hallii was associated inversely with BMI (all data). Pre-COVID-19, increased fecal propionate was associated with increased percentage of time above range and reduced percentage of time in target and below range; and abundances of 3 SCFA-producing taxa (Ruminococcus gnavus, Eubacterium ventriosum, and Lachnospira) were associated inversely with body fat percentage, of which two microbes were positively associated with percentage lean mass. Abundance of Anaerostipes was associated with reduced percentage of time in range (all data) and with increased body fat percentage and reduced percentage lean mass (pre-COVID-19).

Conclusions

Unexpectedly, fecal propionate was associated with detriment to glycemia, whereas most SCFA-producing intestinal microbes were associated with benefit to adiposity. Future studies should confirm these associations and determine their potential causal linkages in T1D.This study is registered at clinical.trials.gov (NCT03651622; https://clinicaltrials.gov/ct2/show/NCT03651622).

Effects of physical distancing by COVID-19 pandemic on diet quality, neurological and immunological markers, and fecal microbiota of Brazilian older women

Physical distancing was used to prevent transmission of COVID-19, however there are concerns that this may promote harmful impacts on health, such as reduced levels of physical practice and changes in food intake and gut microbiota composition. This study evaluated the impacts of 6 months physical distancing on Brazilian older women upon body mass index (BMI), strength, physical activity level (IPAQ), eating habits, neurological markers (brain-derived neurotrophic factor-BDNF and cortisol), cytokines (IL-2, IL-5, IL-6, IL-10, interferon-IFN-γ, tumor necrosis factor-TNF-α), aging-associated markers (vascular endothelial growth factor-VEGF, insulin-like growth factor-IGF-1, klotho and thymic stromal lymphopoietin-TSLP), besides specific groups of fecal microbiota. Fifteen women, over 60 years old, residents of São Paulo state (Brazil), were evaluated in March and in September 2020. The older adult women, with a mean age 66 ± 6.2 years presented significantly increased BMI and high effect size for non-protective foods consumption, reduced light physical activity and strength 6 months following the physical distancing. Furthermore, the serum concentration of IFN-γ, IGF-1, and IFN-γ/IL-5 were significantly higher, while lower concentration of IL-2 and IL-5 were observed 6 months after the physical distancing. Significant increase was noted only to Blautia spp. abundance after 6 months of physical distancing. Several correlations were observed at both before and after physical distancing, however, interestingly, many of them were lost or inverted 6 months following, while new ones emerged. Taken together, these results showed that lifestyle changes and stress conditions addressed by physical distancing from the COVID-19 pandemic impacted the health of older women included in the present study. Therefore, future follow-up studies are essential to propose interventions in order to restore the health conditions observed before the pandemic period, and thus to maintain the quality of life of older adults in different socioeconomic contexts.

Gut and oral microbiota associations with viral mitigation behaviors during the COVID-19 pandemic

Imposition of social and health behavior mitigations are important control measures in response to the coronavirus disease 2019 (COVID-19) pandemic caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Although postulated that these measures may impact the human microbiota including losses in diversity from heightened hygiene and social distancing measures, this hypothesis remains to be tested. Other impacts on the microbiota and host mental and physical health status associations from these measures are also not well-studied. Here we examine changes in stool and oral microbiota by analyzing 16S rRNA gene sequence taxonomic profiles from the same individuals during pre-pandemic (before March 2020) and early pandemic (May-November 2020) phases. During the early pandemic phase, individuals were also surveyed using questionnaires to report health histories, anxiety, depression, sleep and other lifestyle behaviors in a cohort of predominantly Caucasian adults (mean age = 61.5 years) with the majority reporting at least one underlying co-morbidity. We identified changes in microbiota (stool n = 288; oral n = 89) between pre-pandemic and early pandemic time points from the same subject and associated these differences with questionnaire responses using linear statistical models and hierarchical clustering of microbiota composition coupled to logistic regression. While a trend in loss of diversity was identified between pre-pandemic and early pandemic time points it was not statistically significant. Paired difference analyses between individuals identified fewer significant changes between pre-pandemic and early pandemic microbiota in those who reported fewer comorbidities. Cluster transition analyses of stool and saliva microbiota determined most individuals remained in the same cluster assignments from the pre-pandemic to early pandemic period. Individuals with microbiota that shifted in composition, causing them to depart a pre-pandemic cluster, reported more health issues and pandemic-associated worries. Collectively, our study identified that stool and saliva microbiota from the pre-pandemic to early pandemic periods largely exhibited ecological stability (especially stool microbiota) with most associations in loss of diversity or changes in composition related to more reported health issues and pandemic-associated worries. Longitudinal observational cohorts are necessary to monitor the microbiome in response to pandemics and changes in public health measures.

Postscript: A pandemic read on African health and environmental histories

This postscript reflects on this special issue's contributions for readers preoccupied with the COVID-19 pandemic. First, these articles on African environment and health underscore that past process of and interventions into land use and human health have cumulative effects on disease emergence and re-emergence. Relatedly, although multiple epidemics have affected the African continent and other parts of the world over the past century, global health institutions and actors have sidelined or forgotten these epidemics. These analyses draw our attention to the historical production and mobilization of specific concepts which frame what questions are asked, how they are answered, and the material solutions provided or withheld. And finally, these pieces highlight the ethical stakes of agricultural, conservation, and health interventions, reminding us that the African continent's histories are fraught with inequities from colonial and postcolonial extractive relations and racist assumptions that have undermined livelihoods, food security and health. As African states, institutions, and global health critics politick for vaccine equity and deplore the inequitable access to COVID-19 vaccines in African countries compared to the rest of the world, these articles remind us that these long-standing inequities should catalyze fundamental change.

COVID-19 severity is associated with population-level gut microbiome variations

The human gut microbiome interacts with many diseases, with recent small studies suggesting a link with COVID-19 severity. Exploring this association at the population-level may provide novel insights and help to explain differences in COVID-19 severity between countries. We explore whether there is an association between the gut microbiome of people within different countries and the severity of COVID-19, measured as hospitalisation rate. We use data from the large (n = 3,055) open-access gut microbiome repository curatedMetagenomicData, as well as demographic and country-level metadata. Twelve countries were placed into two groups (high/low) according to COVID-19 hospitalisation rate before December 2020 (ourworldindata.com). We use an unsupervised machine learning method, Topological Data Analysis (TDA). This method analyses both the local geometry and global topology of a high-dimensional dataset, making it particularly suitable for population-level microbiome data. We report an association of distinct baseline population-level gut microbiome signatures with COVID-19 severity. This was found both with a PERMANOVA, as well as with TDA. Specifically, it suggests an association of anti-inflammatory bacteria, including Bifidobacteria species and Eubacterium rectale, with lower severity, and pro-inflammatory bacteria such as Prevotella copri with higher severity. This study also reports a significant impact of country-level confounders, specifically of the proportion of over 70-year-olds in the population, GDP, and human development index. Further interventional studies should examine whether these relationships are causal, as well as considering the contribution of other variables such as genetics, lifestyle, policy, and healthcare system. The results of this study support the value of a population-level association design in microbiome research in general and for the microbiome-COVID-19 relationship, in particular. Finally, this research underscores the potential of TDA for microbiome studies, and in identifying novel associations.

Pathways to community transmission of COVID-19 due to rapid evaporation of respiratory virulets

HYPOTHESIS

The formation of virus-laden colloidal respiratory microdroplets - the sneeze or cough virulets and their evaporation driven miniaturization in the open air are found to have a significant impact on the community transmission of COVID-19 pandemic.

SIMULATION DETAILS

We simulate the motions and trajectories of virulets by employing laminar fluid flow coupled with droplet tracing physics. A force field analysis has been included considering the gravity, drag, and inertial forces to unleash some of the finer features of virulet trajectories leading to the droplet and airborne transmissions of the virus. Furthermore, an analytical model corroborates temperature (T) and relative humidity (RH) controlled droplet miniaturization.

RESULTS

The study elucidates that the tiny (1-50 µm) and intermediate (60-100 µm) size ranged virulets tend to form bioaerosol and facilitate an airborne transmission while the virulets of larger dimensions (300 to 500 µm) are more prone to gravity dominated droplet transmission. Subsequently, the mapping between the T and RH guided miniaturization of virulets with the COVID-19 cases for six different cities across the globe justifies the significant contribution of miniaturization-based bioaerosol formation for community transmission of the pandemic.

Incidence of Type 1 Diabetes in Children and Adolescents During the COVID-19 Pandemic in Germany: Results From the DPV Registry

OBJECTIVE

The aim of this study was to investigate the incidence of type 1 diabetes in children and adolescents during the coronavirus disease 2019 (COVID-19) pandemic in Germany compared with previous years.

RESEARCH DESIGN AND METHODS

Based on data from the multicenter German Diabetes Prospective Follow-up Registry, we analyzed the incidence of type 1 diabetes per 100,000 patient-years in children and adolescents from 1 January 2020 through 30 June 2021. Using Poisson regression models, expected incidences for 2020/21 were estimated based on the data from 2011 to 2019 and compared with observed incidences in 2020/21 by estimating incidence rate ratios (IRRs) with 95% CIs.

RESULTS

From 1 January 2020 to 30 June 2021, 5,162 children and adolescents with new-onset type 1 diabetes in Germany were registered. The observed incidence in 2020/21 was significantly higher than the expected incidence (24.4 [95% CI 23.6-25.2] vs. 21.2 [20.5-21.9]; IRR 1.15 [1.10-1.20]; P < 0.001). IRRs were significantly elevated in June 2020 (IRR 1.43 [1.07-1.90]; P = 0.003), July 2020 (IRR 1.48 [1.12-1.96]; P < 0.001), March 2021 (IRR 1.29 [1.01-1.65]; P = 0.028), and June 2021 (IRR 1.39 [1.04-1.85]; P = 0.010).

CONCLUSIONS

A significant increase in the incidence of type 1 diabetes in children was observed during the COVID-19 pandemic, with a delay in the peak incidence of type 1 diabetes by ∼3 months after the peak COVID-19 incidence and also after pandemic containment measures. The underlying causes are yet unknown. However, indirect rather than direct effects of the pandemic are more likely to be the cause.

Pandemics, past and present: The role of biological anthropology in interdisciplinary pandemic studies

Biological anthropologists are ideally suited for the study of pandemics given their strengths in human biology, health, culture, and behavior, yet pandemics have historically not been a major focus of research. The COVID‐19 pandemic has reinforced the need to understand pandemic causes and unequal consequences at multiple levels. Insights from past pandemics can strengthen the knowledge base and inform the study of current and future pandemics through an anthropological lens. In this paper, we discuss the distinctive social and epidemiological features of pandemics, as well as the ways in which biological anthropologists have previously studied infectious diseases, epidemics, and pandemics. We then review interdisciplinary research on three pandemics–1918 influenza, 2009 influenza, and COVID‐19–focusing on persistent social inequalities in morbidity and mortality related to sex and gender; race, ethnicity, and Indigeneity; and pre‐existing health and disability. Following this review of the current state of pandemic research on these topics, we conclude with a discussion of ways biological anthropologists can contribute to this field moving forward. Biological anthropologists can add rich historical and cross‐cultural depth to the study of pandemics, provide insights into the biosocial complexities of pandemics using the theory of syndemics, investigate the social and health impacts of stress and stigma, and address important methodological and ethical issues. As COVID‐19 is unlikely to be the last global pandemic, stronger involvement of biological anthropology in pandemic studies and public health policy and research is vital.

Privacy Risks in Microbiome Research: Public Perspectives before and during a Global Pandemic

We assessed public perspectives of microbiome research privacy risks before and after a nationwide emergency was declared in the United States regarding the Covid-19 pandemic. From January to July of 2020, we conducted an online survey of perceived privacy risks of microbiome research among U.S. adults. Among 3,106 participants (the preemergency group), most expressed that the microbiome posed privacy risks similar to those associated with DNA (60.3%) or medical records (50.6%) and that they would prefer detailed explanations (70.2%) of risk in consent materials. Only 8.9% reported moderate to high familiarity with microbiome privacy risks. In adjusted analyses, individuals who participated in the study after the Covid-19 emergency was declared (the Covid-19 emergency group) were less likely to express that microbiome privacy risks were similar to those of DNA or medical records and more likely to report familiarity with the privacy risks of microbiomes. There was a trend toward increased concern after the Covid-19 emergency was declared (p = 0.053). Overall, the study revealed that many U.S. adults believe that microbiome privacy risks are similar to those associated with DNA or medical records, and they prefer detailed explanations in consent documents. Individuals who participated after the Covid-19 emergency was declared reported greater knowledge of microbiome privacy risks but had more concern.

Endotracheal tube microbiome in hospitalized patients defined largely by hospital environment

Background

Studies of the respiratory tract microbiome primarily focus on airway and lung microbial diversity, but it is still unclear how these microbial communities may be affected by intubation and long periods in intensive care units (ICU), an aspect that today could aid in the understanding of COVID19 progression and disease severity. This study aimed to explore and characterize the endotracheal tube (ETT) microbiome by analyzing ETT-associated microbial communities.

Methods

This descriptive study was carried out on adult patients subjected to invasive mechanical ventilation from 2 to 21 days. ETT samples were obtained from 115 patients from ICU units in two hospitals. Bacteria isolated from endotracheal tubes belonging to the ESKAPE group were analyzed for biofilm formation using crystal violet quantification. Microbial profiles were obtained using Illumina sequencing of 16S rRNA gene.

Results

The ETT microbiome was mainly composed by the phyla Proteobacteria, Firmicutes and Bacteroidetes. Microbiome composition correlated with the ICU in which patients were hospitalized, while intubation time and diagnosis of ventilator-associated pneumonia (VAP) did not show any significant association.

Conclusion

These results suggest that the ICU environment, or medical practices, could be a key to microbial colonization and have a direct influence on the ETT microbiomes of patients that require mechanical ventilation.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12931-022-02086-7.

Preschool Environment: Teacher Experiences during the COVID-19 Pandemic in Ghana

Background: In Ghana, the COVID-19 pandemic led to the government’s decision to shut down schools for nearly nine months. This study explores the experiences of preschool teachers in Ghana during the COVID-19 pandemic. Methods: The study was carried out using the Qualitative Description approach and aspects of Albert Bandura’s Social Learning Theory. Twenty-five teachers agreed to carry out face-to-face interviews with the researchers. An audio recorder device was used to record the interviews, with each interview lasting between 35–55 min. The analysis was carried out by two researchers who served as coders, and MAXQDA 2022 (VERBI Software GmbH) was used to do the analysis. Results: All twenty-five participants indicated their awareness of COVID-19. Participants said they were so “Scared” when they heard about COVID-19 that it could spell the doom for all humanity. Participants also talked about the extra workload that came upon them as a result of the pandemic and the “financial challenges” that they went through during the pandemic because they had no income since they were not teaching. Study participants indicated that one benefit of the pandemic was the heightened awareness of the need to practice hygienic behavior in their classroom. Conclusion: Participants’ beliefs about the virus being lethal led to mask wearing and the practice of hygienic behavior. Thus, although the COVID-19 pandemic negatively impacted the emotional and financial status of the studied participants, a positive outcome was the participants’ awareness of the need to practice positive health behavior, which will contribute to the overall health and safety of everyone in the preschool environment.

The Role of Exposomes in the Pathophysiology of Autoimmune Diseases II: Pathogens

In our continuing examination of the role of exposomes in autoimmune disease, we use this review to focus on pathogens. Infections are major contributors to the pathophysiology of autoimmune diseases through various mechanisms, foremost being molecular mimicry, when the structural similarity between the pathogen and a human tissue antigen leads to autoimmune reactivity and even autoimmune disease. The three best examples of this are oral pathogens, SARS-CoV-2, and the herpesviruses. Oral pathogens reach the gut, disturb the microbiota, increase gut permeability, cause local inflammation, and generate autoantigens, leading to systemic inflammation, multiple autoimmune reactivities, and systemic autoimmunity. The COVID-19 pandemic put the spotlight on SARS-CoV-2, which has been called “the autoimmune virus.” We explore in detail the evidence supporting this. We also describe how viruses, in particular herpesviruses, have a role in the induction of many different autoimmune diseases, detailing the various mechanisms involved. Lastly, we discuss the microbiome and the beneficial microbiota that populate it. We look at the role of the gut microbiome in autoimmune disorders, because of its role in regulating the immune system. Dysbiosis of the microbiota in the gut microbiome can lead to multiple autoimmune disorders. We conclude that understanding the precise roles and relationships shared by all these factors that comprise the exposome and identifying early events and root causes of these disorders can help us to develop more targeted therapeutic protocols for the management of this worldwide epidemic of autoimmunity.

An insight to the therapeutic potential of algae-derived sulfated polysaccharides and polyunsaturated fatty acids: Focusing on the COVID-19

Covid-19 pandemic severely affected human health worldwide. The rapidly increasing COVID-19 cases and successive mutations of the virus have made it a major challenge for scientists to find the best and efficient drug/vaccine/strategy to counteract the virus pathogenesis. As a result of research in scientific databases, regulating the immune system and its responses with nutrients and nutritional interventions is the most critical solution to prevent and combat this infection. Also, modulating other organs such as the intestine with these compounds can lead to the vaccines' effectiveness. Marine resources, mainly algae, are rich sources of nutrients and bioactive compounds with known immunomodulatory properties and the gut microbiome regulations. According to the purpose of the review, algae-derived bioactive compounds with immunomodulatory activities, sulfated polysaccharides, and polyunsaturated fatty acids have a good effect on the immune system. In addition, they have probiotic/prebiotic properties in the intestine and modulate the gut microbiomes; therefore, they can increase the effectiveness of vaccines produced. Thus, they with respectable safety, immune regulation, and modulation of microbiota have potential therapeutic against infections, especially COVID-19. They can also be employed as promising candidates for the prevention and treatment of viral infections, such as COVID-19.

Effect of the COVID-19 Pandemic on Rates of Ninety-Day Peri-Prosthetic Joint and Surgical Site Infections after Primary Total Joint Arthroplasty: A Multicenter, Retrospective Study

Background: The impact of the coronavirus 2019 (COVID-19) pandemic on the rate of primary total joint arthroplasty (TJA) peri-prosthetic joint infection (PJI) and superficial surgical site infections (SSI) is currently unknown. The purpose of this multicenter study was to evaluate any changes in the rates of 90-day PJI or 30-day SSI, including trends in microbiology of the infections, during the COVID-19 pandemic compared to the three years prior. Patients and Methods: An Institutional Review Board-approved, multicenter, retrospective study was conducted with five participating academic institutions across two healthcare systems in the northeastern United States. Primary TJA patients from the years 2017-2019 were grouped as a pre-COVID-19 pandemic cohort and patients from the year 2020 were grouped as a COVID-19 pandemic cohort. Differences in patient demographics, PJI, SSI, and microbiology between the two cohorts were assessed. Results: A total of 14,844 TJAs in the pre-COVID-19 pandemic cohort and 5,453 TJAs in the COVID-19 pandemic cohort were evaluated. There were no substantial differences of the combined 90-day PJI and 30-day superficial SSI rates between the pre-COVID-19 pandemic cohort (0.35%) compared with the COVID-19 pandemic cohort (0.26%; p = 0.303). Conclusions: This study did not find any change in the rates of 90-day PJI or 30-day superficial SSI in patients undergoing primary TJA between a pre-COVID-19 pandemic and COVID-19 pandemic cohort. Larger national database studies may identify small but substantial differences in 90-day PJI and 30-day superficial SSI rates between these two time periods. Our data may support continued efforts to maintain high compliance with hand hygiene, use of personal protective equipment, and limited hospital visitation whenever possible.

mRNA Vaccines: Why Is the Biology of Retroposition Ignored?

The major advantage of mRNA vaccines over more conventional approaches is their potential for rapid development and large-scale deployment in pandemic situations. In the current COVID-19 crisis, two mRNA COVID-19 vaccines have been conditionally approved and broadly applied, while others are still in clinical trials. However, there is no previous experience with the use of mRNA vaccines on a large scale in the general population. This warrants a careful evaluation of mRNA vaccine safety properties by considering all available knowledge about mRNA molecular biology and evolution. Here, I discuss the pervasive claim that mRNA-based vaccines cannot alter genomes. Surprisingly, this notion is widely stated in the mRNA vaccine literature but never supported by referencing any primary scientific papers that would specifically address this question. This discrepancy becomes even more puzzling if one considers previous work on the molecular and evolutionary aspects of retroposition in murine and human populations that clearly documents the frequent integration of mRNA molecules into genomes, including clinical contexts. By performing basic comparisons, I show that the sequence features of mRNA vaccines meet all known requirements for retroposition using L1 elements-the most abundant autonomously active retrotransposons in the human genome. In fact, many factors associated with mRNA vaccines increase the possibility of their L1-mediated retroposition. I conclude that is unfounded to a priori assume that mRNA-based therapeutics do not impact genomes and that the route to genome integration of vaccine mRNAs via endogenous L1 retroelements is easily conceivable. This implies that we urgently need experimental studies that would rigorously test for the potential retroposition of vaccine mRNAs. At present, the insertional mutagenesis safety of mRNA-based vaccines should be considered unresolved.