Comparison of Stool Versus Rectal Swab Samples From Long-Term Acute Care Hospital (LTACH) Patients for Microbiota Analysis

Background. Stool is the standard specimen type for human gastrointestinal microbiota analysis. However, stool collection from in-patients can be challenging, making collection of rectal swabs a more feasible sampling approach. In this study, we compared the microbiota from stool and rectal swab samples to assess differences due to sample collection method. Methods. Stool was collected into a sterile container immediately after a bowel movement. Subsequently, rectal swab samples were collected within 10 minutes, and at 3, 6, and 12-27 hours later. Rectal samples were collected using a Dacron swab that was inserted 1-2 cm past the anal verge, then transferred to liquid Stuart medium for transport (BBL). Samples were stored at 4˚C for 1-26 hours, and then frozen at -80°C until analyzed. Total DNA was isolated using the MoBio PowerMag Soil DNA isolation kit. The V4 region of the 16S rRNA gene was PCR-amplified and sequenced using Illumina technology. Results. Eight stool and 30 swab samples were collected from 8 in-patients at one LTACH. Inter-individual microbiota differences were assessed by analysis of molecular variance (AMOVA) of the Yue and Clayton dissimilarity index (θYC). Grouping samples by patient regardless of sample collection method demonstrated significant differences among all patients (p-values: <0.001-0.029) compared to no overall difference between all stool and swab samples collected from individual patients (p-value: 0.976). Overall, microbial communities were similar in stool and swab samples collected from a patient, although minor shifts in the relative abundance of dominant organisms were noted over the 12-27-hour window. The θYC dissimilarity index between swab and stool samples was significantly lower within individuals (median 0.17, IQR 0.17) than between individuals (median 0.93, IQR 0.12) (Wilcoxon test p-value: <0.0001) indicating minimal differences between stool and swab specimens collected from the same individual over the sampling period. Conclusion. Minor differences in the microbial community were observed between stool and rectal swab samples over a 12-27-hour period. Rectal swabs are a suitable alternative to assessing the stool microbiota when fresh stool material is difficult to obtain. Disclosures. M. K. Hayden, Sage Products, Inc: Sage provided CHG product at no cost to a study on which I was PI, and on another study on which I am CoI., Sage provided CHG product at no cost to facilities involved in this study. Molnlycke: Molnlycke provided CHG product to participating facilities involved in a study on which I am CoI., Molnlycke provided CHG product to participating facilities involved in a study on which I am CoI