Usability of rectal swabs for microbiome sampling in a cohort study of hematological and oncological patients

Abstract

Objectives Large-scale clinical studies investigating associations between intestinal microbiota signatures and human diseases usually rely on stool samples. However, the timing of repeated stool sample collection cannot be predefined in longitudinal settings. Rectal swabs, being straightforward to obtain, have the potential to overcome this drawback. Therefore, we assessed the usability of rectal swabs for microbiome sampling in a cohort of hematological and oncological patients. Study design We used a pipeline for intestinal microbiota analysis from deep rectal swabs which was established and validated with test samples and negative controls. Consecutively, a cohort of patients from hematology and oncology wards was established and weekly deep rectal swabs taken during their admissions and re-admissions. Results Validation of our newly developed pipeline for intestinal microbiota analysis from rectal swabs revealed consistent and reproducible results. Over a period of nine months, 418 rectal swabs were collected longitudinally from 41 patients. Adherence to the intended sampling protocol was 97%. After DNA extraction, sequencing, read pre-processing and filtering of chimeric sequences, 405 of 418 samples (96.9%) were eligible for further analyses. Follow-up samples and those taken under current antibiotic exposure showed a significant decrease in alpha diversity as compared to baseline samples. Microbial domination occurred most frequently by Enterococcaceae (99 samples, 24.4%) on family level and Enterococcus (90 samples, 22.2%) on genus level. Furthermore, we noticed a high abundance of potential skin commensals in 99 samples (24.4%). Summary Deep rectal swabs were shown to be reliable for microbiome sampling and analysis, with practical advantages related to high sampling adherence, easy timing, transport and storage. The relatively high abundance of putative skin commensals in this patient cohort may be of potential interest and should be further investigated. Generally, previous findings on alpha diversity dynamics obtained from stool samples were confirmed.

Pre- and Post-Race Intestinal Microbiota in Long-Distance Sled Dogs and Associations with Performance

“…It is also possible that the storage of the samples directly after collection (freezing at −20 • C) before transport in a cold box and then freezing at -80°C was not optimal for preservation of DNA, but this was the same for all samples collected at the race. Although rectal swabs have been shown to give reliable results in studies of the intestinal microbiota in humans [29], direct comparison of the results from our study with those of other studies may be difficult due to the major influence of extraction method on composition and diversity [30,31].…”

Prevalence of Vancomycin-Resistant Enterococcus (VRE) in Companion Animals: The First Meta-Analysis and Systematic Review

“…However, the opposite is the case with animals, as most fecal samples are obtained from the environment. For animals, rectal swabbing is typically difficult and involves a great deal of planning and expertise [ 53 ]. A good technique for sample collection is that which reduces DNA lyses or alteration for molecular studies, as many studies have shown how important it is for sample collection and storage, library preparation, and DNA extraction using a standardized procedure [ 54 , 55 , 56 ].…”

Antimicrobial resistance gene prevalence in a population of patients with advanced dementia is related to specific pathobionts

“…Second, we were limited by the original SPREAD population, in which few subjects 463 received only a single antimicrobial during the course of the study; this makes it difficult to say 464 whether the temporal variability we observed was widespread in the cohort, although the fact that 465 there were frequently high pathobiont levels observed in the larger metagenomics dataset we used 466 to test our multiple linear regression suggests that this may be the case. Third, in this study we 467 worked with rectal swabs, which are similar but not identical to fecal samples and may be 468 susceptible to cross-contamination from urinary pathogens or skin flora, particularly in incontinent 469 advanced dementia patients [152][153][154][155]. Fourth, metagenomic assembly has limitations.…”