ABSTRACT
Intro: It is hypothesized that metagenomics could contribute to the effective sentinel surveillance of emerging infections to identify plausible cause of respiratory symptoms in the population. Method(s): This study forms part of a longitudinal household cohort study involving the collection of respiratory symptoms and vaccination history in Hong Kong. As a pilot, selected households were provided with swab collection kit for collecting nasopharyngeal and throat samples when there was an influenza-like illness (ILI) during a 4-month presumptive period of the year's winter influenza season. Sequence-Independent Single Primer Amplification (SISPA) and nanopore metagenomic sequencing were performed. After basecalling, demultiplexing, and quality filtering, taxonomic classification was done. Unclassified and host reads were removed and only taxon with over 0.1% abundance were included in the analysis. Finding(s): Between December 2021 and April 2022, of 101 collection kits delivered, 36 (36%) participants returned the samples. Two (6%) had previous COVID-19 diagnosis and almost all (97%) received at least one dose of COVID-19 vaccination. Metagenomics sequencing was performed on 13 samples collected from participants when ILI was present. Of the 1,592,219 reads obtained, 5308 taxa were identified and 136 had over 0.1% abundance, including 128 bacteria, 6 fungi, and 1 virus, which was a bacteriophage. The five most abundant genera of bacteria included Neisseria (19%), Streptococcus (10%), Haemophilus (9%), Veillonella (3%), and Rothia (3%). Haemophilus parainfluenzae was the most abundant species with 97,542 (6%) reads, followed by Neisseria meningitides (5%). Other bacteria identified included Rothia mucilaginosa, Acinetobacter baumannii, Lautropia mirabilis, Veillonella atypica, Streptococcus salivarius, and Streptococcus pneumonia. Inter-participant abundance profile was significantly different (p<0.001). Conclusion(s): The absence of viral infections identified echoed the extremely low proportion (3/21986, or 0.01%) of respiratory specimens testing positive for influenza virus by the government laboratory during the same period. The metagenomic profile could be useful for identifying the likely ILI-causing pathogen.Copyright © 2023
ABSTRACT
The oral cavity, like the lungs, is often referred to as the <<ecological niche of commensal, symbiotic, and pathogenic or-ganisms,>> and the emigration and elimination of microbes between them are constant, ensuring a healthy distribution of saprophytic microorganisms that maintains organ, tissue, and immune homeostasis. The prolonged hospital stays due to COVID-19 complications, cross-infection, oxygenation therapy through the mask or incubation, and long-term intravenous infusions limit the patient's ability to care about the oral cavity, regularly clean teeth, floss interdental, etc., which creates extremely favorable conditions for colonization by aerobic and anaerobic pathogens of the oral cavity and periodontal pockets and leads to the rapid progression of chronic generalized periodontitis in this category of patients in the future. The goal of the study was to assess the state of the microbiome of the periodontal pockets of dental patients in the post-covid period. Methods. The object of the study was 140 patients with generalized periodontitis of the I and II stages of development in the chronic course (GP), among which 80 patients had coronavirus disease in the closest past. The patients were randomized by age, sex, and stage of GP development. The diagnosis of periodontal disease was established according to the classification by Danilevskyi. The bacteriological material for aerobic and facultative anaerobic microflora and yeast-like fungi was collected from periodontal pockets with a calibrated bacteriological loop and immediately seeded on blood agar. Results. Significant qualitative and quantitative changes in the nature of the oral microbiocenosis were observed in patients with GP after the recent coronavirus disease, compared with similar patients who did not suffer from COVID-19. We have noticed almost complete disappearance of bacteria that belong to the transient representatives of the oral microflora such as Neisseria, corynebacteria (diphtheria), micrococci, and lac-tobacilli. The main resident representatives of the oral microflora, i.e., alpha-hemolytic Streptococci of the mitis group, were found in all healthy individuals and patients of groups A and C, but in 30.0 +/- 4.58% of patients in group B, alpha-hemolytic streptococci in the contents of periodontal pockets are present in quantities not available for detection by the applied method (<2.7 lg CCU/mL). In terms of species, Streptococcus oralis and Streptococcus salivarius are more characteris-tic in gingival crevicular fluid in healthy individuals (93.8% of selected strains). In 68.4 +/- 3.32% of patients in group A, 64.0 +/- 3.43% of patients in group B, and 67.5 +/- 3.76% of patients in group C, the dominant species were Streptococcus gordonii and Streptococcus sanguinis (p<0.01), which increased pathogenic potential as they produce streptolysin-O, inhibit complement activation, bind to fibronectine, actively form biofilms on the surface of tooth enamel and gum epithelial surface, and can act as an initiator of adhesion of periodontal pathogens. The other representatives of the resident microflora of the oral cavity - Stomatococcus mucilaginosus and Veillonella parvula for the patients of group C are also found in periodontal pockets with a significantly lower index of persistence and minimal population level. In the post-covid period, both the population level and the frequency of colonization of periodontal pockets by Staphylo-cocci and beta-hemolytic Streptococci decreases rapidly. For these patient groups, unlike for those that did not suffer from COVID-19, we did not find any case of colonization with Staphylococcus aureus, as well as beta-hemolytic Streptococci and Epidermal staphylococcus were also absent. The most characteristic in the post-covid period is a decrease in the proportion of alpha-hemolytic Streptococci, an increase in the proportion of yeast-like fungi of Candida species, as well as the appearance of a significant number of gram-negative rod-shaped bacteria (Enterobacteria and Pseudomonads). In periodontal patien s, the microbial count is approximately 2 orders of magnitude lower than in those with GP who did not suffer from COVID-19 (p<0.05). Conclusions. The overpassed coronavirus disease due to intensive antibiotic therapy leads to a marked decrease in the number of viable saprophytic microorganisms in the periodontal pockets of patients with GP. In the post-covid period for the patients with GP, there is a decrease in the level of colonization of periodontal pockets by species of resident oral microflora - alpha-hemolytic Streptococci, reduction of resident micro-organism's species, and almost complete disappearance of transient microflora. On the other hand, the frequency of colonization of periodontal pockets by fungi species, enterobacteria, and pseudomonads significantly increases. There are more expressed disorders in the periodontal pocket's microbiome for the patients with a severe and complicated course of coronavirus disease, such as post-covid pulmonary fibrosis, which requires reconsideration of approaches to therapeutic and pharmacological treatment in this category of patients.Copyright © 2022, Zabolotny Institute of Microbiology and Virology, NAS of Ukraine. All rights reserved.
ABSTRACT
SARS-CoV-2 has had a profound impact on the human population in the last 24 months. This includes dramatic changes in lifestyle, hygiene, and altered food sources/consumption patterns, which could directly impact the small bowel microbiome on an individual and perhaps even at a population level. To date, this has not been examined. Here, we compare small bowel microbial profiles in subjects before SARS-CoV-2 and intra-pandemic. Methods: The REIMAGINE study is a large-scale study using validated methods for duodenal aspirate collection and microbiome sequencing in subjects undergoing upper endoscopy. Subjects were divided into 2 groups: pre-pandemic, from February 2019 to March 2020;and intrapandemic, from April 2021 to September 2021. Groups were matched for gender, age, and BMI. Duodenal aspirates were collected, and microbial DNA was isolated using the MagAttract PowerSoilDNA Kit. V3 and V4 libraries were sequenced on a MiSeq. Reference-based Operational Taxonomic Unit clustering was performed using SILVA v132 database. Taxonomic analysis was performed with CLC Microbial Genomics Module v.2.5 and MicrobiomeAnalyst, and duodenal microbial alpha- and beta-diversity indices were calculated. Significance was determined by Wilcox test. Results: In total 94 subjects were included in the analysis. The overall duodenal microbiome profile (beta-diversity) of intra-pandemic subjects (n=38, mean age= 51 ± 18, mean BMI =23.9 ± 4.7) was significantly different from pre-pandemic subjects (n=56, mean age= 51 ± 15, mean BMI = 25.24 ± 4.9)(p<0.002, Fig1A), with no significant changes in duodenal microbial alpha diversity between groups (Fig1B). Significant duodenal microbial taxonomic differences were identified between groups, including changes in the relative abundance (RA) of 2 phyla, 3 classes, 6 orders, 4 families and 23 genera (Fig2A). At the phylum level, Actinobacteria RA was significantly decreased in the intra vs. the pre group (FC=-1.99, P=9.83E-8, Fig2B). Additionally, at the genus level, RA of Rothia (P= 6.85E-7), Pseudomonas (P=0.0376), and Escherichia (P=0.0092) were significantly decreased in the intra group (Fig2A). Of note, the phylum Deinococcus (P=0.0016) was increased in the intra vs. the pre group (Fig2B). Conclusion: In this first study examining the effect of the COVID-19 pandemic on the small bowel microbiome, we show substantial changes in microbial profiles intra-pandemic as compared to pre-pandemic. The duodenal microbiome of intra-pandemic subjects was associated with less disrupter bacteria (Escherichia and Pseudomonas), commonly associated with GI disorders. In contrast, Deinococcus phylum was increased intra-pandemic. This phylum includes organisms resistant to sanitation and increased in the nasal passage of people during the pandemic. The short and long term impact of these changes on human health require further study.(Figure Presented)
ABSTRACT
Monitoring severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on surfaces is emerging as an important tool for identifying past exposure to individuals shedding viral RNA. Our past work demonstrated that SARS-CoV-2 reverse transcription-quantitative PCR (RT-qPCR) signals from surfaces can identify when infected individuals have touched surfaces and when they have been present in hospital rooms or schools. However, the sensitivity and specificity of surface sampling as a method for detecting the presence of a SARS-CoV-2 positive individual, as well as guidance about where to sample, has not been established. To address these questions and to test whether our past observations linking SARS-CoV-2 abundance to Rothia sp. in hospitals also hold in a residential setting, we performed a detailed spatial sampling of three isolation housing units, assessing each sample for SARS-CoV-2 abundance by RT-qPCR, linking the results to 16S rRNA gene amplicon sequences (to assess the bacterial community at each location), and to the Cq value of the contemporaneous clinical test. Our results showed that the highest SARS-CoV-2 load in this setting is on touched surfaces, such as light switches and faucets, but a detectable signal was present in many untouched surfaces (e.g., floors) that may be more relevant in settings, such as schools where mask-wearing is enforced. As in past studies, the bacterial community predicts which samples are positive for SARS-CoV-2, with Rothia sp. showing a positive association. IMPORTANCE Surface sampling for detecting SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19), is increasingly being used to locate infected individuals. We tested which indoor surfaces had high versus low viral loads by collecting 381 samples from three residential units where infected individuals resided, and interpreted the results in terms of whether SARS-CoV-2 was likely transmitted directly (e.g., touching a light switch) or indirectly (e.g., by droplets or aerosols settling). We found the highest loads where the subject touched the surface directly, although enough virus was detected on indirectly contacted surfaces to make such locations useful for sampling (e.g., in schools, where students did not touch the light switches and also wore masks such that they had no opportunity to touch their face and then the object). We also documented links between the bacteria present in a sample and the SARS-CoV-2 virus, consistent with earlier studies.