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Little is known about the mucosal microflora of the colon and rectum at the time of elective surgery. Our objective was to determine the concentrations of anaerobic and aerobic bacteria associated with the mucosa of the mechanically prepared large bowel. Ten patients were studied after a standard polyethylene glycol-electrolyte lavage preparation. No patient had taken antibiotics in the preceding four weeks. Sterile wire brushes passed through the colonoscope during advancement were used to culture the rectal, transverse colon, and cecal mucosa. Total anaerobic, aerobic, Gram-positive, and enteric bacterial counts were determined along with specific cultures for Bacteroides fragilis, Clostridium difficile, Escherichia coli, Pseudomonas aeruginosa, enterococcus, and staphylococcus species. The results showed that there was a significant increase (P < 0.01) in aerobes, anaerobes, enterics, Gram positives, B. fragilis, and E. coli mucosal counts with proximal progression. Aerobes showed a steady gradient, while anaerobes demonstrated an increase from the rectum to the transverse colon but no change between the transverse colon and cecum. We conclude that, in the prepared bowel, there is an increase in the mucosal bacterial counts in the more proximal portions of the bowel. The results may serve as a baseline for future studies on the mucosal-associated bacteria of the large intestine.

The COVID-19 pandemic has demonstrated a clear need for high-throughput, multiplexed, and sensitive assays for detecting SARS-CoV-2 and other respiratory viruses as well as their emerging variants. Here, we present microfluidic CARMEN (mCARMEN), a cost-effective virus and variant detection platform that combines CRISPR-based diagnostics and microfluidics with a streamlined workflow for clinical use. We developed the mCARMEN respiratory virus panel (RVP) and demonstrated its diagnostic-grade performance on 533 patient specimens in an academic setting and then 166 specimens in a clinical setting. We further developed a panel to distinguish 6 SARS-CoV-2 variant lineages, including Delta and Omicron, and evaluated it on 106 patient specimens, with near-perfect concordance to sequencing-based variant classification. Lastly, we implemented a combined Cas13 and Cas12 approach that enables quantitative measurement of viral copies in samples. mCARMEN enables high-throughput surveillance of multiple viruses and variants simultaneously.

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