Study of the resistome of human microbial communities using a targeted panel of antibiotic resistance genes in COVID-19 patients

Aim. To study overall drug resistance genes (resistome) in the human gut microbiome and the changes in these genes during COVID-19 in-hospital therapy. Materials and methods. A single-center retrospective cohort study was conducted. Only cases with laboratory-confirmed SARS-CoV-2 RNA using polymerase chain reaction in oro-/nasopharyngeal swab samples were subject to analysis. The patients with a documented history of or current comorbidities of the hepatobiliary system, malignant neoplasms of any localization, systemic and autoimmune diseases, as well as pregnant women were excluded. Feces were collected from all study subjects for subsequent metagenomic sequencing. The final cohort was divided into two groups depending on the disease severity: mild (group 1) and severe (group 2). Within group 2, five subgroups were formed, depending on the use of antibacterial drugs (ABD): group 2A (receiving ABD), group 2AC (receiving ABD before hospitalization), group 2AD (receiving ABD during hospitalization), group 2AE (receiving ABD during and before hospitalization), group 2B (not receiving ABD). Results. The median number of antibiotic resistance (ABR) genes (cumulative at all time points) was significantly higher in the group of patients treated with ABD: 81.0 (95% CI 73.8–84.5) vs. 51.0 (95% CI 31.1–68.4). In the group of patients treated with ABD (2A), the average number of multidrug resistance genes (efflux systems) was significantly higher than in controls (group 2B): 47.0 (95% CI 46.0–51.2) vs. 21.5 (95% CI 7.0–43.9). Patients with severe coronavirus infection tended to have a higher median number of ABR genes but without statistical significance. Patients in the severe COVID-19 group who did not receive ABD before and during hospitalization also had more resistance genes than the patients in the comparison group. Conclusion. This study demonstrated that fewer ABR genes were identified in the group with a milder disease than in the group with a more severe disease associated with more ABR genes, with the following five being the most common: SULI, MSRC, ACRE, EFMA, SAT

ACI-1 beta-lactamase is widespread across human gut microbiomes in Negativicutes due to transposons harboured by tailed prophages

Antibiotic resistance is increasing among pathogens, and the human microbiome contains a reservoir of antibiotic resistance genes. Acidaminococcus intestini is the first Negativicute bacterium (Gram-negative Firmicute) shown to be resistant to beta-lactam antibiotics. Resistance is conferred by the aci1 gene, but its evolutionary history and prevalence remain obscure. We discovered that ACI-1 proteins are phylogenetically distinct from beta-lactamases of Gram-positive Firmicutes and that aci1 occurs in bacteria scattered across the Negativicute clade, suggesting lateral gene transfer. In the reference A. intestini RyC-MR95 genome, we found transposons residing within a tailed prophage context are likely vehicles for aci1's mobility. We found aci1 in 56 (4.4%) of 1,267 human gut metagenomes, mostly hosted within A. intestini, and, where could be determined, mostly within a consistent mobile element constellation. These samples are from Europe, China and the USA, showing that aci1 is distributed globally. We found that for most Negativicute assemblies with aci1, the prophage observed in A. instestini is absent, but in all cases aci1 is flanked by varying transposons. The chimeric mobile elements we identify here likely have a complex evolutionary history and potentially provide multiple complementary mechanisms for antibiotic resistance gene transfer both within and between cells

Phigaro: high-throughput prophage sequence annotation

Phigaro is a standalone command-line application that is able to detect prophage regions taking raw genome and metagenome assemblies as an input. It also produces dynamic annotated 'prophage genome maps' and marks possible transposon insertion spots inside prophages. It is applicable for mining prophage regions from large metagenomic datasets

A Cross-Sectional Study of the Gut Microbiota Composition in Moscow Long-Livers

The aim was to assess the gut microbiota of long-livers from Moscow. This study included two groups of patients who signed their consent to participate. The group of long-livers (LL) included 20 participants aged 97–100 years (4 men and 16 women). The second group included 22 participants aged 60–76 years (6 men) without clinical manifestations of chronic diseases (healthy elderly). Gut microbiota was studied by 16S rRNA sequencing. Long-livers underwent a complex geriatric assessment as well as expanded blood biochemistry. Gut microbiota composition in the cohorts was also compared with microbiome in long-livers from Japan and Italy. Russian long-livers’ microbiome contained more beneficial bacteria than healthy elderly including Ruminococcaceae, Christensenellaceae, Lactobacillaceae families. Conditional pathogens like Veillonellaceae, Mogibacteriaceae, Alcaligenaceae, Peptococcaceae, Peptostreptococcaceae were more abundant in the healthy elderly. Compared with Italian and Japanese microbiome LL, the Russian LL appeared to be more similar to the Italian cohort. Bifidobacterium/Coprococcus and Faecalibacterium/Coprococcus balances were associated with femoral and carotid intima–media thickness, respectively. Bifidobacterium/Coriobacteriaceae balance was assessed with the folic acid level and Faecalibacterium/Coriobacteriaceae_u the with Mini Nutritional Assessment score. Long-livers’ microbiome appeared to be unexpectedly balanced. The high representation of beneficial bacteria in long-livers may prevent them from low-grade inflammation and thus protect them from the development of atherosclerosis and other aging-associated conditions

Metagenomic Profiles of the Intestinal Virome of Long-Livers

The microbial community of the human intestine is important for maintaining human health. It has been reported that the gut microbiome changes with age, and it can be enrichedwith certain beneficial bacteria while also losing certain commensal bacteria.Little is known about the gut virome of long-livers. Our research aimed to extract, sequence and analyze the viral fraction of long-livers’ gut microbiota in comparison with those of young adults and the elderly. We were thereby able to characterize the gut virome profiles and viral diversity of three age groups. Keywords: aging, gut microbiome, viral metagenomics, bacteriophage

Metagenomic Profiles of the Intestinal Virome of Long-Livers

The microbial community of the human intestine is important for maintaining human health. It has been reported that the gut microbiome changes with age, and it can be enrichedwith certain beneficial bacteria while also losing certain commensal bacteria.Little is known about the gut virome of long-livers. Our research aimed to extract, sequence and analyze the viral fraction of long-livers' gut microbiota in comparison with those of young adults and the elderly. We were thereby able to characterize the gut virome profiles and viral diversity of three age groups. Keywords: aging, gut microbiome, viral metagenomics, bacteriophage

Draft genomes of Enterococcus faecium strains isolated from human feces before and after eradication therapy against Helicobacter pylori

The abundance of Enterococci in the human intestinal microbiota environment is usually < 0.1% of the total bacterial fraction. The multiple resistance to antibiotics of the opportunistic Enterococcus spp. is alarming for the world medical community because of their high prevalence among clinically significant strains of microorganisms. Enterococci are able to collect different mobile genetic elements and transmit resistance to antibiotics to wide range of Gram-positive and Gram-negative species of microorganisms, including the transmission of vancomycin resistance to methicillin-resistant strains of Staphylococcus aureus. The number of infections caused by antibiotics resistant strains of Enterococcus spp. is increasing. Here we present a draft genomes of Enterococcus faecium strains. These strains were isolated from human feces before and after (1 month) Helicobacter pylori eradication therapy. The samples were subject to whole-genome sequencing using Illumina HiSeq. 2500 platform. The data is available at NCBI https://www.ncbi.nlm.nih.gov/bioproject/PRJNA412824

Microbial Signatures in COVID-19: Distinguishing Mild and Severe Disease via Gut Microbiota

The COVID-19 pandemic, caused by the SARS-CoV-2 virus, has significantly impacted global healthcare, underscoring the importance of exploring the virus’s effects on infected individuals beyond treatments and vaccines. Notably, recent findings suggest that SARS-CoV-2 can infect the gut, thereby altering the gut microbiota. This study aimed to analyze the gut microbiota composition differences between COVID-19 patients experiencing mild and severe symptoms. We conducted 16S rRNA metagenomic sequencing on fecal samples from 49 mild and 43 severe COVID-19 cases upon hospital admission. Our analysis identified a differential abundance of specific bacterial species associated with the severity of the disease. Severely affected patients showed an association with Enterococcus faecium, Akkermansia muciniphila, and others, while milder cases were linked to Faecalibacterium prausnitzii, Alistipes putredinis, Blautia faecis, and additional species. Furthermore, a network analysis using SPIEC-EASI indicated keystone taxa and highlighted structural differences in bacterial connectivity, with a notable disruption in the severe group. Our study highlights the diverse impacts of SARS-CoV-2 on the gut microbiome among both mild and severe COVID-19 patients, showcasing a spectrum of microbial responses to the virus. Importantly, these findings align, to some extent, with observations from other studies on COVID-19 gut microbiomes, despite variations in methodologies. The findings from this study, based on retrospective data, establish a foundation for future prospective research to confirm the role of the gut microbiome as a predictive biomarker for the severity of COVID-19