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Acute Medicine & Surgery 2024Altered gut microbiota has been proposed as one of the causes of exacerbation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2/COVID-19) from the...
AIM
Altered gut microbiota has been proposed as one of the causes of exacerbation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2/COVID-19) from the perspective of the gut-lung axis. We aimed to evaluate gut microbiota in mechanically ventilated patients with COVID-19 prior to using antibiotics.
METHODS
We retrospectively selected for enrollment COVID-19 patients who required mechanical ventilation on admission but who had not used antibiotics before admission to observe the influence of SARS-Cov-2 on gut microbiota. Fecal samples were collected serially on admission and were evaluated by 16S rRNA gene deep sequencing.
RESULTS
The phylum of Bacteroidetes decreased, and those of Firmicutes and Actinobacteria increased in COVID-19 patients compared with those in healthy controls ( < 0.001). The main commensals of , , and at the genus level were significantly decreased in the COVID-19 patients, and opportunistic bacteria including , , , , and were increased ( < 0.001). α-Diversity and β-diversity in COVID-19 patients significantly changed compared with those in the healthy controls.
CONCLUSION
The commensal gut microbiota were altered, and opportunistic bacteria increased in patients with severe COVID-19 who required mechanical ventilation on admission.
PubMed: 38213715
DOI: 10.1002/ams2.923 -
BMC Microbiology Jan 2024Reliable species identification of cultured isolates is essential in clinical bacteriology. We established a new study algorithm named NOVA - Novel Organism Verification...
Novel Organism Verification and Analysis (NOVA) study: identification of 35 clinical isolates representing potentially novel bacterial taxa using a pipeline based on whole genome sequencing.
BACKGROUND
Reliable species identification of cultured isolates is essential in clinical bacteriology. We established a new study algorithm named NOVA - Novel Organism Verification and Analysis to systematically analyze bacterial isolates that cannot be characterized by conventional identification procedures MALDI-TOF MS and partial 16 S rRNA gene sequencing using Whole Genome Sequencing (WGS).
RESULTS
We identified a total of 35 bacterial strains that represent potentially novel species. Corynebacterium sp. (n = 6) and Schaalia sp. (n = 5) were the predominant genera. Two strains each were identified within the genera Anaerococcus, Clostridium, Desulfovibrio, and Peptoniphilus, and one new species was detected within Citrobacter, Dermabacter, Helcococcus, Lancefieldella, Neisseria, Ochrobactrum (Brucella), Paenibacillus, Pantoea, Porphyromonas, Pseudoclavibacter, Pseudomonas, Psychrobacter, Pusillimonas, Rothia, Sneathia, and Tessaracoccus. Twenty-seven of 35 strains were isolated from deep tissue specimens or blood cultures. Seven out of 35 isolated strains identified were clinically relevant. In addition, 26 bacterial strains that could only be identified at the species level using WGS analysis, were mainly organisms that have been identified/classified very recently.
CONCLUSION
Our new algorithm proved to be a powerful tool for detection and identification of novel bacterial organisms. Publicly available clinical and genomic data may help to better understand their clinical and ecological role. Our identification of 35 novel strains, 7 of which appear to be clinically relevant, shows the wide range of undescribed pathogens yet to define.
Topics: Bacteria; Whole Genome Sequencing; Corynebacterium; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; RNA, Ribosomal, 16S; Bacterial Typing Techniques
PubMed: 38178003
DOI: 10.1186/s12866-023-03163-7 -
Germs Sep 2023The annual incidence of infective endocarditis (IE) is 3-9 cases per 100000 in developed countries and most cases are due to staphylococci and streptococci. IE due to...
INTRODUCTION
The annual incidence of infective endocarditis (IE) is 3-9 cases per 100000 in developed countries and most cases are due to staphylococci and streptococci. IE due to Gram-positive anaerobic cocci (GPAC) is very rare.
CASE REPORT
We present a case of a 38-year-old female with bacteremia and infective endocarditis of the native mitral valve. She presented with fever, chills, and abdominal pain. A computed tomographic scan of the abdomen showed splenic abscesses. Blood cultures and broad-range PCR from the splenic abscess sample were negative. Transthoracic echocardiography showed a mobile filamentous structure on the atrial side of the anterior mitral leaflet which was suggestive for infective endocarditis. Karius test (cell-free microbial DNA testing) showed Gram-positive anaerobic cocci She was successfully treated with antibiotics.
CONCLUSIONS
In cases of infection with fastidious organisms like GPACs, the use of next-generation sequencing (NGS) can allow the correct identification of culprit pathogens and streamlined treatment.
PubMed: 38146378
DOI: 10.18683/germs.2023.1396 -
Gut Pathogens Dec 2023Critical illness and care within the intensive care unit (ICU) leads to profound changes in the composition of the gut microbiome. The impact of such changes on the...
BACKGROUND
Critical illness and care within the intensive care unit (ICU) leads to profound changes in the composition of the gut microbiome. The impact of such changes on the patients and their subsequent disease course remains uncertain. We hypothesized that specific changes in the gut microbiome would be more harmful than others, leading to increased mortality in critically ill patients.
METHODS
This was a prospective cohort study of critically ill adults in the ICU. We obtained rectal swabs from 52 patients and assessed the composition the gut microbiome using 16 S rRNA gene sequencing. We followed patients throughout their ICU course and evaluated their mortality rate at 28 days following admission to the ICU. We used selbal, a machine learning method, to identify the balance of microbial taxa most closely associated with 28-day mortality.
RESULTS
We found that a proportional ratio of four taxa could be used to distinguish patients with a higher risk of mortality from patients with a lower risk of mortality (p = .02). We named this binarized ratio our microbiome mortality index (MMI). Patients with a high MMI had a higher 28-day mortality compared to those with a low MMI (hazard ratio, 2.2, 95% confidence interval 1.1-4.3), and remained significant after adjustment for other ICU mortality predictors, including the presence of the acute respiratory distress syndrome (ARDS) and the Acute Physiology and Chronic Health Evaluation (APACHE II) score (hazard ratio, 2.5, 95% confidence interval 1.4-4.7). High mortality was driven by taxa from the Anaerococcus (genus) and Enterobacteriaceae (family), while lower mortality was driven by Parasutterella and Campylobacter (genera).
CONCLUSIONS
Dysbiosis in the gut of critically ill patients is an independent risk factor for increased mortality at 28 days after adjustment for clinically significant confounders. Gut dysbiosis may represent a potential therapeutic target for future ICU interventions.
PubMed: 38115015
DOI: 10.1186/s13099-023-00567-8 -
Cancers Oct 2023Breast cancer (BC) is the leading cause of cancer mortality among women in Ethiopia. Overall, women of African ancestry have the highest death toll due to BC compared to...
Breast cancer (BC) is the leading cause of cancer mortality among women in Ethiopia. Overall, women of African ancestry have the highest death toll due to BC compared to other racial/ethnic groups. The cause of the disparity in mortality is unclear. Recently, studies conducted in the United States and other high-income countries highlighted the role of microbial dysbiosis in BC initiation, tumor growth, and treatment outcome. However, the extent to which inter-individual differences in the makeup of microbiota are associated with clinical and histopathological outcomes in Ethiopian women has not been studied. The goal of our study was to profile the microbiome in breast tumor and normal adjacent to tumor (NAT) tissues of the same donor and to identify associations between microbial composition and abundance and clinicopathological factors in Ethiopian women with BC. We identified 14 microbiota genera in breast tumor tissues that were distinct from NAT tissues, of which , , , , and were most significantly decreased in breast tumors compared to NAT tissues. Several microbial genera significantly differed by clinicopathological factors in Ethiopian women with BC. Specifically, the genus more strongly correlated with aggressive triple negative (TNBC) and basal-like breast tumors. The genera , , , and most strongly correlated with HER2-E tumors. Luminal A and luminal B tumors also correlated with but not as strongly as HER2-E tumors. A relatively higher abundance of the genus most significantly correlated with advanced-stage breast tumors compared to early-stage tumors. This is the first study to report an association between breast microbial dysbiosis and clinicopathological factors in Ethiopian women.
PubMed: 37835588
DOI: 10.3390/cancers15194893 -
Frontiers in Microbiology 2023Dried distillers' grains with solubles (DDGS) are rich in nutrients, and partially alternative feeding of DDGS effectively reduces cost of feed and improves animals'...
Dried distillers' grains with solubles (DDGS) are rich in nutrients, and partially alternative feeding of DDGS effectively reduces cost of feed and improves animals' growth. We used 16S rDNA gene sequencing and LC/MS-based metabolomics to explore the effect of feeding cattle with a basal diet (BD) and a Jiang-flavor DDGS diet (replaces 25% concentrate of the diet) on microbiome and metabolome of ruminal and cecal contents in Guanling yellow cattle. The results showed that the ruminal and cecal contents shared the same dominance of , and in two groups. The ruminal dominant genera were , , and ; and the cecal dominant genera were , , and . Linear discriminant analysis effect size analysis (LDA > 2, < 0.05) revealed the significantly differential bacteria enriched in the DDGS group, including , and in the ruminal contents, which was associated with degradation of plant polysaccharides. Besides, , , and in the cecal contents were involved in fatty acid metabolism. Compared with the BD group, 20 significantly different metabolites obtained in the ruminal contents of DDGS group were down-regulated ( < 0.05), and based on them, 4 significantly different metabolic pathways ( < 0.05) were enriched including "Linoleic acid metabolism," "Biosynthesis of unsaturated fatty acids," "Taste transduction," and "Carbohydrate digestion and absorption." There were 65 significantly different metabolites (47 were upregulated, 18 were downregulated) in the cecal contents of DDGS group when compared with the BD group, and 4 significantly different metabolic pathways ( < 0.05) were enriched including "Longevity regulating pathway," "Bile secretion," "Choline metabolism in cancer," and "HIF-1 signaling pathway." Spearman analysis revealed close negative relationships between the top 20 significantly differential metabolites and in the ruminal contents. Bacteria with high relevance to cecal differential metabolites were , , and that affect specific metabolic pathways in cattle. Collectively, our results suggest that feeding cattle with a DDGS diet improves the microbial structure and the metabolic patterns of lipids and carbohydrates, thus contributing to the utilization efficiency of nutrients and physical health to some extent. Our findings will provide scientific reference for the utilization of DDGS as feed in cattle industry.
PubMed: 37789852
DOI: 10.3389/fmicb.2023.1171563 -
Asian Journal of Surgery Jan 2024We investigated the characteristics of the microbial community of the nasal sinuses in patients with chronic rhinosinusitis with nasal polyps (CRSwNP) and identified the...
BACKGROUND
We investigated the characteristics of the microbial community of the nasal sinuses in patients with chronic rhinosinusitis with nasal polyps (CRSwNP) and identified the correlations of the nasal microbiome with the inflammatory microenvironment of the nasal cavity.
METHODOLOGY
We collected matched nasal secretion and polyp tissue samples from 77 CRSwNP patients. Then, we extracted microbial DNA from cotton swabs, used high-throughput sequencing technology based on 16S ribosomal RNA (rRNA) to detect the bacterial community composition, and detected cytokines such as interleukin (IL)-5, IL-8, IL-17a, IL-17e, IL-18, IL-27 and interferon (INF)-gamma in the polyp tissue samples using Luminex. Eosinophils and neutrophils in the peripheral blood and polyp tissue were counted, and the relationships between inflammatory factors or inflammatory cell counts and nasal microbial diversity were analyzed.
RESULTS
Among the inflammatory factors evaluated, IL-5 had a positive rate of 32.47%, IFN-γ had a positive rate of 84.42%, IL-17A and IL-17E had positive rates of 75.32%, IL-18 had a positive rate of 94.81%, IL-27 had a positive rate of 68.83%, and IL-8 had a positive rate of 100%. IL-17a and IL-27 were negatively correlated with both Enterobacter and Anaerococcus, IL-8 was negatively correlated with both Enterobacter and Staphylococcus, IL-18 was positively correlated with Candidatus Arthromitus and negatively correlated with Haemophilus, and IL-27 was positively correlated with Faecalibaculum. Lactobacillus and Enterococcus were positively correlated with the degree of neutrophil infiltration in nasal polyp tissue.
CONCLUSIONS
In Southwest China, inflammation of the nasal polyps exhibits a variety of patterns. Enterobacteria and anaerobic bacteria may be correlated with the inflammatory pattern of nasal polyps. The neutrophil-mediated inflammatory response plays an important role in patients with CRSwNP in Southwest China.
Topics: Humans; Interleukin-17; Nasal Polyps; Rhinitis; Interleukin-18; Interleukin-27; Interleukin-8; Rhinosinusitis; Sinusitis; Chronic Disease
PubMed: 37659949
DOI: 10.1016/j.asjsur.2023.08.096 -
Kidney360 Oct 2023, , , and are the most common genera in the anterior nares. The nasal abundance of is inversely correlated with the nasal abundance of . Peritoneal dialysis patients...
KEY POINTS
, , , and are the most common genera in the anterior nares. The nasal abundance of is inversely correlated with the nasal abundance of . Peritoneal dialysis patients have a distinctly diverse representation of and in their anterior nares.
BACKGROUND
The nasal passages harbor both commensal and pathogenic bacteria that can be associated with infectious complications. The nasal microbiome in peritoneal dialysis (PD) patients, however, has not been well characterized. In this study, we sought to characterize the anterior nasal microbiota in PD patients and assess its association with PD peritonitis.
METHODS
In this study, we recruited 32 PD patients, 37 kidney transplant (KTx) recipients, and 22 living donor/healthy control (HC) participants and collected their anterior nasal swabs at a single point in time. We followed the PD patients for future development of peritonitis. We performed 16S ribosomal RNA (rRNA) gene sequencing of the V4–V5 hypervariable region to determine the nasal microbiota. We compared nasal abundance of common genera among the three groups using Wilcoxon rank-sum test with Benjamini–Hochberg adjustment. DESeq2 was also used to compare the groups at the amplicon sequence variant levels.
RESULTS
In the entire cohort, the most abundant genera in the nasal microbiota included , , , and . Correlational analyses revealed a significant inverse relationship between the nasal abundance of and that of . PD patients have a higher nasal abundance of than KTx recipients and HC participants. PD patients have a more diverse representation of and than KTx recipients and HC participants. PD patients who concurrently have or who developed future peritonitis had a numerically higher nasal abundance of than PD patients who did not develop peritonitis.
CONCLUSIONS
We find a distinct nasal microbiota signature in PD patients compared with KTx recipients and HC participants. Given the potential relationship between the nasal pathogenic bacteria and infectious complications, further studies are needed to define the nasal microbiota associated with these infectious complications and to conduct studies on the manipulation of the nasal microbiota to prevent such complications.
Topics: Humans; Nose; Peritoneal Dialysis; Microbiota
PubMed: 37642987
DOI: 10.34067/KID.0000000000000249 -
Scientific Reports Aug 2023The non-filarial and non-communicable disease podoconiosis affects around 4 million people and is characterized by severe leg lymphedema accompanied with painful...
The non-filarial and non-communicable disease podoconiosis affects around 4 million people and is characterized by severe leg lymphedema accompanied with painful intermittent acute inflammatory episodes, called acute dermatolymphangioadenitis (ADLA) attacks. Risk factors have been associated with the disease but the mechanisms of pathophysiology remain uncertain. Lymphedema can lead to skin lesions, which can serve as entry points for bacteria that may cause ADLA attacks leading to progression of the lymphedema. However, the microbiome of the skin of affected legs from podoconiosis individuals remains unclear. Thus, we analysed the skin microbiome of podoconiosis legs using next generation sequencing. We revealed a positive correlation between increasing lymphedema severity and non-commensal anaerobic bacteria, especially Anaerococcus provencensis, as well as a negative correlation with the presence of Corynebacterium, a constituent of normal skin flora. Disease symptoms were generally linked to higher microbial diversity and richness, which deviated from the normal composition of the skin. These findings show an association of distinct bacterial taxa with lymphedema stages, highlighting the important role of bacteria for the pathogenesis of podoconiosis and might enable a selection of better treatment regimens to manage ADLA attacks and disease progression.
Topics: Humans; Elephantiasis; Bacteria, Anaerobic; Leg; Lymphedema; Skin
PubMed: 37612446
DOI: 10.1038/s41598-023-40765-7 -
International Wound Journal Nov 2023Identifying the microbiome within chronic diabetic foot ulcers is essential if effective antimicrobial therapies are to be administered. Using culture and 16S rRNA gene...
Identifying the microbiome within chronic diabetic foot ulcers is essential if effective antimicrobial therapies are to be administered. Using culture and 16S rRNA gene sequencing, the aim of this study was to compare the microbiome of paired tissue scraping samples with swab samples, collected from participants during attendance at a high-risk foot clinic. The mean richness of cultured swab and tissue scraping samples was consistent, with anaerobes infrequently isolated from both sample types. Comparing percentage frequencies of detection of selected genera of known and potential pathogens namely Staphylococcus, Streptococcus, Enterococcus, Corynebacterium, Enterobacteriaceae and Pseudomonas from cultured and sequenced swab and tissue scrapings indicated that both collection methods captured varying percentages of all the selected genera. The mean abundance of sequenced samples was not significantly different between swabs and tissue scrapings. The mean richness or number of distinct operational taxonomic units (OTUs) and Shannon's H diversity index were not significantly different between the two collection methods. The mean relative abundance of the selected genera of known and potential pathogens, including anaerobes Anaerococcus and Finegoldia, was higher in swabs compared with tissue scrapings and significantly so in Staphylococcus and Pseudomonas genera. Multivariate analyses confirmed no significant differences between the bacterial community compositions of the paired samples. These results suggest that tissue scrapings and swabs can effectively capture the microbiome of chronic DFUs using culture and 16S rRNA gene sequencing.
Topics: Humans; Diabetic Foot; RNA, Ribosomal, 16S; Bacteria; Microbiota; Foot; Staphylococcus; Pseudomonas; Diabetes Mellitus
PubMed: 37501084
DOI: 10.1111/iwj.14267