Rectal swab screening assays of public health importance in molecular diagnostics: Sample adequacy control

Glisovic, Sanja; Eintracht, Shaun; Longtin, Yves; Oughton, Matthew; Brukner, Ivan

doi:10.1016/j.jiph.2017.07.009

Cited by 16 publications

(22 citation statements)

References 25 publications

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“…Evidence to support the requirement of visible pigment is sparse. In one study, approximately 10% of rectal swab specimens received in the microbiology laboratory were excluded from processing due to the absence of visible pigment (9), and an unknown proportion were not even submitted from the point of collection for similar reasons. The absence of visible pigment on a swab is presumed to indicate that the stool sample on the swab is inadequate, but no published data support the superior sensitivity of swabs with visible feces.…”

mentioning

confidence: 99%

Pigment Visibility on Rectal Swabs Used To Detect Enteropathogens: a Prospective Cohort Study

et al. 2019

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Data are lacking regarding the impact of visible pigment on rectal swab diagnostic accuracy. We describe the test characteristics of rectal swabs with and without pigment in children with gastroenteritis. Between December 2014 and September 2017, children (age, <18 years) with ≥3 episodes of vomiting and/or diarrhea in a 24-h period and symptoms for <7 days were enrolled through two pediatric emergency departments and from a province-wide nursing telephone advice line in Alberta, Canada. Specimens were analyzed by employing nucleic acid amplification panels. The primary outcomes were the sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) for the rectal swabs, with stool specimen results being used as the reference standard. An enteropathogen was detected in 76.0% (1,399/1,841) of the paired specimens. A total of 54.4% (1,001/1841) of the swabs had visible pigment. The respective enteropathogen detection characteristics of swabs with and without visible pigment were as follows: 92.2% (95% confidence interval [CI], 90.0%, 94.0%) versus 83.7% (95% CI, 80.5%, 86.4%) for sensitivity, 94.3% (95% CI, 90.5%, 96.6%) versus 91.2% (95% CI, 86.3%, 94.5%) for specificity, 97.9% (95% CI, 96.4%, 98.8%) versus 96.5% (95% CI, 94.5%, 97.8%) for PPV, and 80.9% (95% CI, 76.0%, 85.1%) versus 65.8% (95% CI, 60.0%, 71.1%) for NPV. Processing of swabs without visible pigment would increase the rate of identification of positive swabs from 50.0% (682/1,365) to 88.3% (1,205/1,365). There is a modest decrease in the reliability of a negative test on swabs without evidence of pigment, but the overall yield is significantly greater when they are not excluded from testing. Hence, rectal swabs without visible feces should not be routinely rejected from testing.

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confidence: 99%

Pigment Visibility on Rectal Swabs Used To Detect Enteropathogens: a Prospective Cohort Study

et al. 2019

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“…Clinical diagnostic guidelines generally assume a positive relationship between visible soiling with fecal matter and the diagnostic utility of rectal swabs. 44 However, recent interrogations of this relationship have concluded that testing rectal swabs that lack visible feces is worthwhile for the PCR detection of common enteric bacteria and viruses. 44,45 Our results further corroborate this conclusion in the context of a protozoan diagnostic, as we observed no difference in rectal swab sensitivity when controlling for visible feces.…”

Section: Discussionmentioning

confidence: 99%

“…44 However, recent interrogations of this relationship have concluded that testing rectal swabs that lack visible feces is worthwhile for the PCR detection of common enteric bacteria and viruses. 44,45 Our results further corroborate this conclusion in the context of a protozoan diagnostic, as we observed no difference in rectal swab sensitivity when controlling for visible feces. There was an indication that C q values were slightly lower in rectal swabs with visible stool, although the difference was not statistically significant.…”

Section: Discussionmentioning

confidence: 99%

Rectal Swabs as an Alternative Sample Collection Method to Bulk Stool for the Real-Time PCR Detection of Giardia duodenalis

Maasch

Arzika

Cook

et al. 2020

The American Journal of Tropical Medicine and Hygiene

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Though bulk stool remains the gold standard specimen type for enteropathogen diagnosis, rectal swabs may offer comparable sensitivity with greater ease of collection for select pathogens. This study sought to evaluate the validity and reproducibility of rectal swabs as a sample collection method for the molecular diagnosis of Giardia duodenalis. Paired rectal swab and bulk stool samples were collected from 86 children ages 0-4 years living in southwest Niger, with duplicate samples collected among a subset of 50 children. Infection was detected using a previously validated real-time PCR diagnostic targeting the small subunit ribosomal RNA gene. Giardia duodenalis was detected in 65.5% (55/84) of bulk stool samples and 44.0% (37/84) of swab samples. The kappa evaluating test agreement was 0.81 (95% CI: 0.54-1.00) among duplicate stool samples (N = 49) and 0.75 (95% CI: 0.47-1.00) among duplicate rectal swabs (N = 48). Diagnostic sensitivity was 93% (95% CI: 84-98) by bulk stool and 63% (95% CI: 49-75) by rectal swabs. When restricting to the lowest three quartiles of bulk stool quantitation cycle values (an indication of relatively high parasite load), sensitivity by rectal swabs increased to 78.0% (95% CI: 64-89, P < 0.0001). These findings suggest that rectal swabs provide less sensitive and reproducible results than bulk stool for the real-time PCR diagnosis of G. duodenalis. However, their fair sensitivity for higher parasite loads suggests that swabs may be a useful tool for detecting higher burden infections when stool collection is excessively expensive or logistically challenging.

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“…Described tcdB qPCR assay was validated with multiple commercial assays in the past (C difficile Quick Check Complete, Alere; BD Max, BD and BD GeneOhm, BD) and used over last 10 years in our institution to detect symptomatic patients which are positive for tcdB biomarker. The relative normalization of samples was obtained using universal 16S rDNA amplicons, as a measure of total bacterial load, as described [23]. The qPCR was performed on Roche Light Cycler 480 instrument, following PCR program: hold at 94 o C for 2 minutes and cycling of 45x (94 o C, 10sec, and following by priming, elongation and acquisition of fluorescence at 50 o C for 20 seconds).…”

Section: Methodsmentioning

confidence: 99%

Absolute versus relative presentation of tcdB Clostridium difficile biomarker

Brukner¹,

Eintracht²,

Forgetta³

et al. 2019

Integr Mol Med

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Clostridium difficile infection is the major etiologic agent of antibiotic-associated pseudomembranous colitis, a disease that can be fatal if unrecognized, or untreated. On average, there are 15000 deaths and 500000 new cases per year, in the USA. Diagnostic biomarkers currently used are the tcdB gene, or its gene product (toxin B). Clinical interpretation of the assay is particularly challenging: (1) biomarker detection is possible without manifestation of symptoms and (2) missing biomarker due to assay sensitivity limitations can be fatal. To resolve clinical uncertainty, quantitative analysis has been considered. Despite multiple efforts, a quantitative tcdB/toxB threshold with a meaningful clinical impact has yet to be established. Herein we shed light as to why mass/volume-based normalisations were fruitless in the past. Specifically, measuring total bacterial flora (using "universal bacterial" 16S qPCR rDNA assay) to calculate relative abundance of C difficile, we demonstrate a strong and significant negative correlation between tcdB biomarker of C difficile (R 2 =0.73, N=227, P=10 -39 ) and the rest of gut microorganisms. The new parameter (Cq (toxB)-Cq (16SrDNA)) is calculated from two biomarkers, is independent of sampling variability and inherently incorporates the destructive character of C difficile on the rest of micro-flora. By incorporating relative abundance of tcdB (in context of the total bacterial flora), and correcting for "biomass wash-out/dilution effects of acute diarrhea , these biomarkers could collectively enhance the predictive value of CDI testing.

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Rectal swab screening assays of public health importance in molecular diagnostics: Sample adequacy control

Cited by 16 publications

References 25 publications

Pigment Visibility on Rectal Swabs Used To Detect Enteropathogens: a Prospective Cohort Study

Pigment Visibility on Rectal Swabs Used To Detect Enteropathogens: a Prospective Cohort Study

Rectal Swabs as an Alternative Sample Collection Method to Bulk Stool for the Real-Time PCR Detection of Giardia duodenalis

Absolute versus relative presentation of tcdB Clostridium difficile biomarker

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