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The Journal of Antimicrobial... Aug 2019Routine sequencing of MRSA could bring about significant improvements to outbreak detection and investigation. Sequencing is commonly performed using DNA extracted from...
BACKGROUND
Routine sequencing of MRSA could bring about significant improvements to outbreak detection and investigation. Sequencing is commonly performed using DNA extracted from a pure culture, but overcoming the delay associated with this step could reduce the time to infection control interventions.
OBJECTIVES
To develop and evaluate rapid sequencing of MRSA using primary clinical cultures.
METHODS
Patients with samples submitted to the clinical laboratory at the Cambridge University Hospitals NHS Foundation Trust from which MRSA was isolated were identified, the routine laboratory culture plates obtained and DNA extraction and sequencing performed.
RESULTS
An evaluation of routine MRSA cultures from 30 patients demonstrated that direct sequencing from bacterial colonies picked from four different culture media was feasible. The 30 clinical MRSA isolates were sequenced on the day of plate retrieval over five runs and passed quality control metrics for sequencing depth and coverage. The maximum contamination detected using Kraken was 1.09% fragments, which were identified as Prevotella dentalis. The most common contaminants were other staphylococcal species (25 isolate sequences) and Burkholderia dolosa (11 isolate sequences). Core genome pairwise SNP analysis to identify clusters based on isolates that were ≤50 SNPs different was used to triage cases for further investigation. This identified three clusters, but more detailed genomic and epidemiological evaluation excluded an acute outbreak.
CONCLUSIONS
Rapid sequencing of MRSA from clinical culture plates is feasible and reduces the delay associated with purity culture prior to DNA extraction.
Topics: Colony Count, Microbial; DNA, Bacterial; Genome, Bacterial; Genomics; Humans; Methicillin-Resistant Staphylococcus aureus; Sequence Analysis, DNA; Staphylococcal Infections
PubMed: 31039248
DOI: 10.1093/jac/dkz170 -
The Journal of Biological Chemistry Sep 2013A gene cluster involved in N-glycan metabolism was identified in the genome of Bacteroides thetaiotaomicron VPI-5482. This gene cluster encodes a major facilitator...
A gene cluster involved in N-glycan metabolism was identified in the genome of Bacteroides thetaiotaomicron VPI-5482. This gene cluster encodes a major facilitator superfamily transporter, a starch utilization system-like transporter consisting of a TonB-dependent oligosaccharide transporter and an outer membrane lipoprotein, four glycoside hydrolases (α-mannosidase, β-N-acetylhexosaminidase, exo-α-sialidase, and endo-β-N-acetylglucosaminidase), and a phosphorylase (BT1033) with unknown function. It was demonstrated that BT1033 catalyzed the reversible phosphorolysis of β-1,4-D-mannosyl-N-acetyl-D-glucosamine in a typical sequential Bi Bi mechanism. These results indicate that BT1033 plays a crucial role as a key enzyme in the N-glycan catabolism where β-1,4-D-mannosyl-N-acetyl-D-glucosamine is liberated from N-glycans by sequential glycoside hydrolase-catalyzed reactions, transported into the cell, and intracellularly converted into α-D-mannose 1-phosphate and N-acetyl-D-glucosamine. In addition, intestinal anaerobic bacteria such as Bacteroides fragilis, Bacteroides helcogenes, Bacteroides salanitronis, Bacteroides vulgatus, Prevotella denticola, Prevotella dentalis, Prevotella melaninogenica, Parabacteroides distasonis, and Alistipes finegoldii were also suggested to possess the similar metabolic pathway for N-glycans. A notable feature of the new metabolic pathway for N-glycans is the more efficient use of ATP-stored energy, in comparison with the conventional pathway where β-mannosidase and ATP-dependent hexokinase participate, because it is possible to directly phosphorylate the D-mannose residue of β-1,4-D-mannosyl-N-acetyl-D-glucosamine to enter glycolysis. This is the first report of a metabolic pathway for N-glycans that includes a phosphorylase. We propose 4-O-β-D-mannopyranosyl-N-acetyl-D-glucosamine:phosphate α-D-mannosyltransferase as the systematic name and β-1,4-D-mannosyl-N-acetyl-D-glucosamine phosphorylase as the short name for BT1033.
Topics: Acetylglucosamine; Adenosine Triphosphate; Bacterial Proteins; Bacteroides; Biological Transport, Active; Glucans; Multigene Family; Phosphorylases
PubMed: 23943617
DOI: 10.1074/jbc.M113.469080 -
Frontiers in Microbiology 2024Pigs are widely used as animal models in various studies related to humans. The interaction between the gut microbiota and the host has significant effects on the host's...
Pigs are widely used as animal models in various studies related to humans. The interaction between the gut microbiota and the host has significant effects on the host's health and disease status. However, although there have been many studies investigating the pig gut microbiota, the findings have been inconsistent due to variations in rearing conditions. Interactions between the gut microbiota and host have not been fully explored in pigs. Specific pathogen-free (SPF) pigs are ideal non-primate large animals to study the interactions between the gut microbiota and the host. In this study, we performed high-throughput sequencing analysis of the gut microbiota and the gut tissue transcriptome of six SPF pigs to provide a systematic understanding of the composition, function, and spatial distribution of gut microbiota in SPF pigs. We identified significant differences in microbial diversity and functionality among different gastrointestinal tract sites. Metagenomics data analysis revealed significant differences in alpha diversity and beta diversity of microbiota in different gastrointestinal sites of SPF pigs. Additionally, transcriptomic data indicated significant differences in gene expression as well as KEGG and GO functional enrichment between the small intestine and large intestine. Furthermore, by combining microbial metagenomics and host transcriptomics analyses, specific correlations were found between gut microbiota and host genes. These included a negative correlation between the gene and , possibly related to bacterial metabolic pathways involving vitamin B12, and a positive correlation between the gene and , possibly because both are involved in fatty acid metabolism. These findings lay the groundwork for further exploration of the co-evolution between the microbiota and the host, specifically in relation to nutrition, metabolism, and immunity. In conclusion, we have elucidated the diversity of the gut microbiota in SPF pigs and conducted a detailed investigation into the interactions between the gut microbiota and host gene expression. These results contribute to our understanding of the intricate dynamics between the gut microbiota and the host, offering important references for advancements in life science research, bioproduct production, and sustainable development in animal husbandry.
PubMed: 38800748
DOI: 10.3389/fmicb.2024.1402807 -
Journal of Clinical Neuroscience :... Feb 2020Abscesses associated with tumors are a rare entity. Imaging to differentiate abscess from other entities is often non-diagnostic, and often the source of infection is...
INTRODUCTION
Abscesses associated with tumors are a rare entity. Imaging to differentiate abscess from other entities is often non-diagnostic, and often the source of infection is unknown. We present an unusual case of peritumoral abscess infected with both gram-negative and gram-positive bacteria.
METHODS
A 70-year-old, previously healthy male presented with a 1-day history of right-sided facial weakness sparing the forehead, as well as concomitant right upper and lower extremity numbness. A homogenously enhancing mass with adjacent rim-enhancing lesion with diffusion restricting cavity seen on magnetic resonance imaging (MRI) raised the possibility of abscess.
RESULTS
Separate biopsy specimens of both the tumor and adjacent fluid collection during drainage of the collection confirmed World Health Organization (WHO) grade I meningioma and bacterial abscess containing Streptococcus constellatus, Fusobacterium species, Prevotella dentalis, and Parvimonas micra. The histologic diagnosis therefore confirmed the preoperative radiologic findings of two different but associated lesions. Investigations to determine a definitive source of infection were inconclusive, including urinalysis, blood cultures, respiratory cultures, endoscopy, and an orthopantomogram.
CONCLUSIONS
Gram-negative and gram-positive bacteria can both be culprits in the formation of peritumoral abscess. Although the source of infection is unconfirmed, the presence of oropharyngeal flora in the abscess suggests a subclinical odontogenic infection with hematogenous spread to the tumor and adjacent brain.
Topics: Aged; Brain Abscess; Gram-Negative Bacterial Infections; Gram-Positive Bacterial Infections; Humans; Male; Meningeal Neoplasms; Meningioma
PubMed: 31864828
DOI: 10.1016/j.jocn.2019.11.033