Impact of Gut Microbiota on Immunogenicity to Covid-19 Vaccines in Plwh

Background: Immune responses to SARS-CoV-2 vaccines in people living with HIV (PLWH) have been the focus of several recent studies. As the gut microbiome can influence vaccine immunogenicity, in this study we are the first to investigate whether the baseline gut microbiota can predict immune responses to the BNT162b2 SARS-CoV-2 vaccine in people living with HIV (PLWH) and healthy controls (HC). Method(s): Fecal samples were collected from PLWH (n=68) and HC (n=75) at baseline, prior to the first vaccine dose, to extract DNA for 16S rRNA sequencing. The individuals were part of the COVAXID Clinical trial, where humoral and cellular responses to SARS-CoV-2 vaccine were evaluated on day 35 after the first dose. Comprehensive bioinformatic tools were used for bacterial identification to further reveal the associations between gut microbiota and SARS-CoV-2 antibody, spike CD4+ T cell responses, and clinical parameters such as age, gender, CD4/CD8 ratio, and length of antiretroviral (ART) treatment. Result(s): At day 35 post vaccination, HC showed significantly higher spike IgG titers than PLWH (p=0.0001). Interestingly, both phylogenetic and alpha-diversity were negatively correlated with antibody titers, in the whole cohort and within groups. Similarly, individuals with low alpha-diversity had higher levels of spike specific CD4+T-cell responses. Agathobacter, Lactobacillus, Bacteroides, and Lachnospira were positively correlated with both antibody levels and spike-specific CD4+ T-cell responses while Methanobrevibacter, Marvinbryantia, Cloacibacillus, and Succinivibrio have a negative one. Within the PLWH group, the gut microbiota taxa associated with CD4+ counts, such as Lachnospira (p=0.002), Oscillibacter (p=0.019) and Flavonifractor (p=0.017), were found to be positively correlated with spike IgG levels. Additionally, the length of ART treatment and CD4/CD8 ratio displayed a positive association with bacterial diversity. Notably, different microbiome profiles and immune status in PLWH, affect their immune responses to vaccination. Conclusion(s): Our results show potential associations between gut microbiota diversity and spike IgG responses after COVID-19 vaccination. These findings were consistent in the whole cohort, albeit group differences between the microbiome compositions in PLWH and HC were observed. Based on our findings, we propose that microbiome modulation could optimize immunogenicity to SARS-Cov-2 vaccines.

COVID-19: DIARRHEA, INFLAMMATION AND INTESTINAL MICROBIOTA

Introduction: Increased inflammatory cytokines has been observed in COVID-19 patients and there is evidence showing an alteration in gut-microbiota composition. SARS-CoV-2 can cause gastrointestinal symptoms, such as diarrhea. Evidence of an altered gut-microbiota composition and cytokines levels in COVID-19 diarrhea patients is lacking. Objectives: To compare serum cytokine levels and gut microbiota between COVID-19 diarrhea (D-COVID- 19) and non-diarrhea (NonD-COVID-19) patients and non- COVID-19 controls (HC). Material and methods: We included 143 hospitalized COVID-19 patients (positive quantitative reverse transcription PCR) in a single University Hospital, and 53 ambulatory HC (negative rapid serological test) were included. Blood and stool samples were collected at hospital admission in COVID-19 patients and at the time of HC recruitment. 27- pro and anti-inflammatory cytokines (Bio-Plex Pro™, Bio- Rad) were measured. Gut microbiota composition and diversity profiles were characterized by sequencing the 16S rRNA gene V3-V4 region amplified using DNA extracted from stool samples. Bioinformatics analysis was performed with QIIME2 software. First, we compare cytokine levels between COVID- 19 and HC and then COVID-19 with and without diarrhea. All comparisons were adjusted for age, sex, and BMI with linear regression. Results: The mean age in COVID-19 patients was 54 +/- 15 years (F=50%) and 52 +/- 8 (F=62%) for HC. Diarrhea was present in 19 (13.29%) of COVID-19 patients. COVID-19 patients had significative higher levels of: IL- 1ra, IL-2, IL-6, IL-7, IL-8, IL-13, IP-10 and PDGF-bb. Significant lower values of: IL-9, FGF -basic, MIP-1β, TNF-α were observed in D-COVID-19 compared to NonD-COVID-19. COVID-19 patients had a significant reduction of bacterial species (p=0.0001), and diversity and complexity of the bacterial community (Shannon's index) (p=0.0001) compared to the HC. There was no difference between D-COVID-19 and NonD-COVID-19. There were also changes in the composition of the microbiota associated with COVID-19. At the phylum level, COVID-19 patients showed a significant decrease in Actinobacteria and Firmicutes, and an increase in Bacteroidetes. At species level, an increase of 4 species of the genus Bacteroides was observed in COVID-19 patients. 31 very diverse bacterial species were found, all decreased in D-COVID-19. Conclusions: An alteration in serum cytokine levels was observed between COVID-19 and HC. D-COVID-19 had a decrease in some proinflammatory cytokines. A significant decrease in richness and species diversity of gutmicrobiota was observed in COVID-19 patients compared to HC, but no significant differences were observed between D-COVID-19 and NonD-COVID-19. However, in D-COVID- 19, a decrease in some bacterial species was observed.(Table Presented)(Figure Presented)

Gut Microbiota Disruption in COVID-19 or Post-COVID Illness Association with severity biomarkers: A Possible Role of Pre / Pro-biotics in manipulating microflora.

Coronavirus disease (COVID-19), a coronavirus-induced illness attributed to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission, is thought to have first emerged on November 17, 2019. According to World Health Organization (WHO). COVID-19 has been linked to 379,223,560 documented occurrences and 5,693,245 fatalities globally as of 1st Feb 2022. Influenza A virus that has also been discovered diarrhea and gastrointestinal discomfort was found in the infected person, highlighting the need of monitoring them for gastro intestinal tract (GIT) symptoms regardless of whether the sickness is respiration related. The majority of the microbiome in the intestines is Firmicutes and Bacteroidetes, while Bacteroidetes, Proteobacteria, and Firmicutes are found in the lungs. Although most people overcome SARS-CoV-2 infections, many people continue to have symptoms months after the original sickness, called Long-COVID or Post COVID. The term "post-COVID-19 symptoms" refers to those that occur with or after COVID-19 and last for more than 12 weeks (long-COVID-19). The possible understanding of biological components such as inflammatory, immunological, metabolic activity biomarkers in peripheral blood is needed to evaluate the study. Therefore, this article aims to review the informative data that supports the idea underlying the disruption mechanisms of the microbiome of the gastrointestinal tract in the acute COVID-19 or post-COVID-mediated elevation of severity biomarkers.

Assessment of wastewater and microbiological characteristics from selected hospitals in Umuahia metropolis

There is an increasing universal awareness of environmental problems arising as a result of COVID- 19 pandemic and pollution especially in Nigeria. Among the source of this problem is effluent discharge from industries, particularly hospitals in arable farmlands and environs. Two outstanding hospital were purposively selected;Madonna Catholic Hospital and Abia Specialist Hospital in Umuahia, Abia State. Their wastewater samples were collected from three different wards;maternity, general private, and general out-patients department (GOPD) wards. Results obtained show significant variation in physiochemical properties in some wards and heavy metals across all wards. Seven bacteria species;Staphylococcus aureus, Escherichia coli, Klesbsiella pneumonia, Pseudomonas aeruginosa, Proteus vulgaris, Bacteriod sp and Streptococcus pyogenes and one fungi specie- Candida albican were recorded from the samples. The bacterial load in Madonna ranged from 209.04 to 232.95cfu/ml in January, February, and March each and was statistically the same in the three wards (p>0.05). Fungi load ranged from 1.58 to 2.35cfu/ml in January, February, and March each and also significantly different at (p>0.05). The frequency of microbial characteristics isolated in the two hospital wastewater ranged from 33 to 100% with 100% of Staphylococcus aureus and Escherichia coli in all the wards, while other species varied significantly between 67 and 33% each. The results of the isolated bacteria from hospital wastewater showed resistivity to the tested antibiotics, and as therapeutic agents. Therefore, results call for need for urgent attention to be given to the discharge of wastewater from hospitals to ensure that food production around the environment is not contaminated.

Effects of recombinant porcine Lactobacillus reuteri secreting expression of bovine lactoferrin peptides on growth performance of newborn piglets and protective effect against diarrhea virus infection

This experiment was conducted to investigate the effects of recombinant porcine Lactobacillus reuteri secreting bovine lactoferrin peptide (LFCA) on growth performance of newborn piglets and the protective effect on porcine transmissible gastroenteritis virus (TGEV)infection which caused piglet diarrhea. Experiment 1:thirty-six one-day-old newborn piglets with an average body weight of about 1.5 kg were randomly divided into 3 groups, which were pPG-LFCA/LR-CO21 group, pPG/LR-CO21 group and control group, each group with 12 piglets. Piglets in each group were orally administered recombinant porcine Lactobacillus reuteri expressing LFCA pPG-LFCA/LR-CO21, containing empty vector plasmid PPG/LR-CO21 and equal volume phosphate buffer (PBS);oral administration continued for 3 days, and the observation time after oral administration was 14 d. During the period, piglets were fed freely, and the changes of body weight and diarrhea were recorded. Experiment 2:thirty one-day-old newborn piglets with an average body weight of about 1.5 kg were randomly divided into 5 groups and given TGEV with a half tissue culture infection dose (TCID50) of 10-7.50/mL by oral administration of 1, 3, 6, 9 and 12 mL, respectively. The observation period of 7 d was set to analyze the conditions of half lethal dose. Experiment 3:another thirty-two newborn piglets with an average body weight of about 1.5 kg were selected as experimental animals and randomly divided into 4 groups, with 8 piglets in each group. The groups were pPG-LFCA/LR-CO21 group, pPG/LR-CO21 group, control group and TGEV infect group. There were 8 replicates in each group and 1 piglet in each replicate. Each head of the experimental group was orally fed ppG-LFCA/LR-CO21, pPG/LR-CO21 and equal volume of PBS at a dose of 2..1010 CFU per day for 1 consecutive week. At 8 days of age, TGEV was infected by oral administration at half lethal dose, and samples were collected after 7 days of infection. The weight change and diarrhea of each group of piglets were recorded;hematoxylin-eosin staining was used to detect the length of intestinal villi and the depth of crypts;enzyme linked immunosorbent assay (ELISA) was used to determine total serum total immunoglobulin G (IgG) and total secretory immunoglobulin A (sIgA) antibody contents. RT-qPCR was used to detect the mRNA relative expression levels of Claudin-1, Occludin, tight junction protein-1 (ZO-1), inflammatory cytokines interleukin-6 (IL-6), interleukin-8 (IL-8), interferon-P (IFN-P), tumor necrosis factor-a (TNF-a) and Toll-like receptor 2 (TLR2). The flora structure of the contents of the piglet's cecum was analyzed. After oral recombinant porcine Lactobacillusreuteri, compared with the control group, the average daily gain of newborn piglets in the pPG-LFCA/LR-CO21 group was significantly increased (P < 0.01), while the diarrhea rate was significantly decreased (P < 0.01). Compared with TGEV infection group, the average daily gain of piglets in pPG-LFCA/LR-CO21 group was increased and diarrhea rate was decreased, and the differences were significant (P < 0.05). Villus height and the ratio of villus height to crypt depth in jejunum and ileum were significantly increased (P < 0.05). The contents of total IgG and intestinal mucosal total sIgA antibody in serum of piglets were significantly increased (P < 0.05);the mRNA relative expression levels of tight junction protein-related genes Claudin-1, Occludin and ZO-1 in intestinal mucosal tissue were extremely significantly increased (P < 0.01), and the serum TNF-a content was extremely significantly decreased (P < 0.01). Serum IFN-P, IL-6, IL-8 and TLR2 contents were significantly increased (P < 0.01), and the survival rate of piglets was improved. The analysis of the bacterial diversity in the contents of the piglets' cecum showed that the proportion of normal intestinal flora of piglets decreased after TGEV infection. Compared with the TGEV infect group, the proportion of pathogenic bacteria Bacteroides in piglet's intestinal flora decreased by o

Evaluation of Rates of Culture Positive Blood Stream Pathogens Prior to and during the SARS-CoV-2 Pandemic: A Multicenter Evaluation

Background. Bacterial co-infections or super-infections are well-characterized complications of viral infections, further increasing morbidity and mortality of global viral pandemics. We evaluated trends in the incidence of culture positive gram-negative (GN), gram-positive (GP), and fungal/yeast pathogens from a blood source in hospitalized patients at US hospitals before and during the SARS-CoV-2 pandemic. Methods: This was a multi-center, retrospective cohort analysis of all hospitalized patients from 267 US acute care facilities with >1-day inpatient admission between 7/1/19-5/19/21 (BD Insights Research Database [Becton, Dickinson and Company, Franklin Lakes, NJ]). SARS-CoV-2 infection was identified by a positive PCR during or ≤7 days prior to hospitalization. All admissions with a non-contaminant culture positive GN, GP, and fungal/yeast pathogen from a blood source were evaluated prior to and during the SARS-CoV-2 pandemic as rates per 1,000 admissions (p< .05 for significance). Results. There were 2,001,793 admissions in the pre-SARS-CoV-2 period (7/2019-2/2020) and 2,875,219 admissions during the SARS-CoV-2 pandemic. Incidence of GN/GP blood stream pathogens was significantly higher prior to the SARS-CoV-2 pandemic than during the pandemic. Higher rates of blood stream pathogens occurred in those who were tested for SARS-CoV-2, but all non-tested patients had significantly lower rates than pre-pandemic. Rates of Candida spp., Enterococcus spp., Serratia marcescens, and Enterobacter cloacae were higher in SARS-CoV-2 positive patients compared to pre-pandemic patients. Compared to the prior pandemic period, the incidence of B. fragilis, Streptococcus, Enterococcus and Candida were higher among those tested for SARS-CoV-2 but were negative. Conclusion. In general, rates of positive blood cultures for bacterial pathogens were either lower or similar during the SARS-CoV-2 period compared to the pre-SARS-CoV-2 pandemic period. The patients that were tested for SARS-CoV-2 but were positive who had higher rates of infection than prior may indicate the similarity in viral and bacterial clinical presentation. Further evaluation of higher rates of Enterococcus and Candida in the pandemic period are warranted.

Tools for interpretation of wastewater SARS-CoV-2 temporal and spatial trends demonstrated with data collected in the San Francisco Bay Area.

Wastewater surveillance for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA can be integrated with COVID-19 case data to inform timely pandemic response. However, more research is needed to apply and develop systematic methods to interpret the true SARS-CoV-2 signal from noise introduced in wastewater samples (e.g., from sewer conditions, sampling and extraction methods, etc.). In this study, raw wastewater was collected weekly from five sewersheds and one residential facility. The concentrations of SARS-CoV-2 in wastewater samples were compared to geocoded COVID-19 clinical testing data. SARS-CoV-2 was reliably detected (95% positivity) in frozen wastewater samples when reported daily new COVID-19 cases were 2.4 or more per 100,000 people. To adjust for variation in sample fecal content, four normalization biomarkers were evaluated: crAssphage, pepper mild mottle virus, Bacteroides ribosomal RNA (rRNA), and human 18S rRNA. Of these, crAssphage displayed the least spatial and temporal variability. Both unnormalized SARS-CoV-2 RNA signal and signal normalized to crAssphage had positive and significant correlation with clinical testing data (Kendall's Tau-b (τ)=0.43 and 0.38, respectively), but no normalization biomarker strengthened the correlation with clinical testing data. Locational dependencies and the date associated with testing data impacted the lead time of wastewater for clinical trends, and no lead time was observed when the sample collection date (versus the result date) was used for both wastewater and clinical testing data. This study supports that trends in wastewater surveillance data reflect trends in COVID-19 disease occurrence and presents tools that could be applied to make wastewater signal more interpretable and comparable across studies.