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Misra A, Powell EA. Preanalytical Challenges of Molecular Microbiology Tests. Clin Lab Med 2024; 44:33-43. [PMID: 38280796 DOI: 10.1016/j.cll.2023.10.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2024]
Abstract
As infectious disease diagnostics increasingly incorporates molecular techniques, there are unique preanalytical concerns that must be considered. First, noninvasive specimen types that may be inadequate for culture-based diagnostics may be acceptable when using molecular tests. Second, specimen containers must be evaluated for the presence of substances that may interfere with amplification or sequencing reactions. Finally, the capacity of transport, storage, and processing conditions to maintain nucleic acid integrity and avoid contamination must be assessed. This review explores these issues and the effects they may have on result quality.
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Affiliation(s)
- Anisha Misra
- Department of Laboratory Medicine, Cleveland Clinic, Robert J. Tomsich Pathology and Laboratory Medicine Institute, 10300 Carnegie Avenue LL-1, Cleveland, OH 44195, USA
| | - Eleanor A Powell
- Department of Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, 3188 Bellevue Avenue, Cincinnati, OH 45219, USA.
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2
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Brendish NJ, Beard KR, Malachira AK, Tanner AR, Sanga-Nyirongo L, Gwiggner M, Cummings JRF, Moyses HE, Clark TW. Clinical impact of syndromic molecular point-of-care testing for gastrointestinal pathogens in adults hospitalised with suspected gastroenteritis (GastroPOC): a pragmatic, open-label, randomised controlled trial. THE LANCET. INFECTIOUS DISEASES 2023:S1473-3099(23)00066-X. [PMID: 37116527 DOI: 10.1016/s1473-3099(23)00066-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 01/25/2023] [Accepted: 02/03/2023] [Indexed: 04/30/2023]
Abstract
BACKGROUND Single-occupancy isolation rooms are a finite resource in UK hospitals but are crucial in preventing transmission of infection. Patients with suspected gastroenteritis are nursed in single-occupancy rooms, but delays in laboratory testing lead to non-infectious patients remaining isolated for prolonged periods unnecessarily. Rapid molecular test panels for gastrointestinal pathogens have a run time of around 1 h but their clinical impact is unknown. We aimed to evaluate the clinical impact of syndromic molecular point-of-care testing (mPOCT) for gastrointestinal pathogens in adult patients presenting to hospital with suspected gastroenteritis on single-occupancy room use and a range of other outcome measures. METHODS In this pragmatic, open-label, randomised controlled trial, we enrolled adults hospitalised with suspected gastroenteritis in a large UK hospital. Patients were randomly allocated (1:1) to receive syndromic mPOCT of stool or rectal samples, or to routine clinical care (control) with laboratory testing. The primary outcome was the duration of time in single-occupancy rooms assessed on a modified intention-to-treat basis. Secondary outcomes included the time to results, time to de-isolation, antibiotic use, and safety outcomes. The study was registered with ISRCTN, ISRCTN88918395, and is complete. FINDINGS Between March 20, 2017 and March 17, 2020, from 455 patients assessed for eligibility, we enrolled 278 patients, 138 assigned to mPOCT (one withdrawal) and 140 to the control group. The duration (geometric mean) of single-occupancy room isolation was 1·8 days (95% CI 1·5-2·2) in the mPOCT group compared with 2·6 days (2·2-3·0) in the control group (exponentiated coefficient 0·70 [95% CI 0·56 to 0·87]; p=0·0017). The median (IQR) time to results was 1·7 h (1·5-2·0) for mPOCT and 44·7 h (21·2-66·1) for the control group (p<0·0001). Time to de-isolation was 0·6 days (0·3-1·8) in the mPOCT group compared with 2·2 days (1·2-3·2) in the control group, (p<0·0001). Antibiotics were given in 89 (65%) of 137 in the mPOCT group and 66 (47%) of 140 in the control group (p=0·0028). There were no differences between groups in length of hospital stay, or in safety outcomes including mortality, intensive care unit admission, or readmission to hospital. INTERPRETATION mPOCT for gastrointestinal pathogens in patients with suspected gastroenteritis returned results more rapidly than conventional testing and was associated with a reduction in single-occupancy room use. However, these benefits need to be balanced against a potential increase in antibiotic use. FUNDING University Hospital Southampton NHS Foundation Trust.
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Affiliation(s)
- Nathan J Brendish
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK; NIHR Southampton Biomedical Research Centre and Clinical Research Facility, University Hospital Southampton NHS Foundation Trust, Southampton, UK; Department of Infection, University Hospital Southampton NHS Foundation Trust, Southampton, UK.
| | - Kate R Beard
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK; NIHR Southampton Biomedical Research Centre and Clinical Research Facility, University Hospital Southampton NHS Foundation Trust, Southampton, UK; Department of Infection, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Ahalya K Malachira
- Department of Infection, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Alex R Tanner
- Department of Infection, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Langizya Sanga-Nyirongo
- Department of Infection, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Markus Gwiggner
- Department of Gastroenterology, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - J R Fraser Cummings
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK; NIHR Southampton Biomedical Research Centre and Clinical Research Facility, University Hospital Southampton NHS Foundation Trust, Southampton, UK; Department of Gastroenterology, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Helen E Moyses
- NIHR Southampton Biomedical Research Centre and Clinical Research Facility, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Tristan W Clark
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK; NIHR Southampton Biomedical Research Centre and Clinical Research Facility, University Hospital Southampton NHS Foundation Trust, Southampton, UK; Department of Infection, University Hospital Southampton NHS Foundation Trust, Southampton, UK; University Hospital Southampton NHS Foundation Trust, Southampton, UK
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3
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Chadwick PR, Trainor E, Marsden GL, Mills S, Chadwick C, O'Brien SJ, Evans CM, Mullender C, Strazds P, Turner S, Weston V, Toleman MS, de Barros C, Kontkowski G, Bak A. Guidelines for the management of norovirus outbreaks in acute and community health and social care settings. J Hosp Infect 2023:S0195-6701(23)00043-9. [PMID: 36796728 DOI: 10.1016/j.jhin.2023.01.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 01/19/2023] [Accepted: 01/22/2023] [Indexed: 02/17/2023]
Affiliation(s)
| | - Eamonn Trainor
- Northern Care Alliance NHS Foundation Trust, Greater Manchester, UK.
| | - Gemma L Marsden
- Healthcare Infection Society, London, UK; Royal College of General Practitioners, London, UK
| | - Samuel Mills
- British Infection Association, Seafield, West Lothian, UK; Oxford University NHS Foundation Trust, Oxford, UK
| | | | | | - Cariad M Evans
- Sheffield Teaching Hospital NHS Foundation Trust, Sheffield, UK
| | | | - Pixy Strazds
- Infection Prevention Society, London, UK; St Andrew's Healthcare, Northampton, UK
| | - Sarah Turner
- Infection Prevention Society, London, UK; Stockport Council, Stockport, UK
| | - Valya Weston
- Healthcare Infection Society, London, UK; Infection Prevention Society, London, UK; NHS England, London, UK
| | - Michelle S Toleman
- Healthcare Infection Society, London, UK; Cambridge University Hospitals NHS Trust, Cambridge, UK
| | | | | | - Aggie Bak
- Healthcare Infection Society, London, UK
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Evaluation of a new fast in-house Real-Time PCR assay for detecting both Norovirus and toxigenic Clostridium difficile using fecal sample and rectal swab. Am J Infect Control 2022; 50:67-71. [PMID: 34461212 DOI: 10.1016/j.ajic.2021.08.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 08/23/2021] [Accepted: 08/23/2021] [Indexed: 12/31/2022]
Abstract
BACKGROUND Norovirus and toxigenic Clostridium difficile infections are the 2 most common causes of infectious gastroenteritis. Rapid and reliable detection of these to microorganisms is important to assess if contact precautions are indicated to prevent spreading and reduce cost of isolation. METHODS This study determines sensitivity and specificity of a new fast in-house PCR assay used on BD MAX platform to detect both norovirus and C difficile in 1 turn-over in clinical context. Furthermore, fecal samples as well as rectal swabs were used as analysis material to determine the accuracy of the new assay on a fecal samples and rectal swabs compared with standard methods. RESULTS From 227 included patients, 143 rectal swabs and 135 fecal samples obtained. The new in-house PCR showed a sensitivity of 73.3% and a specificity of 99.2% for norovirus on a fecal sample and a sensitivity of 57.1% and specificity 99.1% of for norovirus on a rectal swab. For C difficile a sensitivity of 100% and specificity of 100% on a fecal sample and a sensitivity of 90.9% and a specificity of 99.1% on a rectal swab was shown. The time consumption for detecting the 2 enteropathogens was reduced by half by using the new assay. CONCLUSIONS The new assay shows an acceptable sensitivity and specificity for C difficile and an acceptable specificity for norovirus when analysis was done on fecal samples and reduces half of the time consumption. Further research is needed to improve the accuracy of the new in-house PCR before clinical implication.
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Maasch JRMA, Arzika AM, Cook C, Lebas E, Pilotte N, Grant JR, Williams SA, Keenan JD, Lietman TM, Aiemjoy K. Rectal Swabs as an Alternative Sample Collection Method to Bulk Stool for the Real-Time PCR Detection of Giardia duodenalis. Am J Trop Med Hyg 2020; 103:1276-1282. [PMID: 32524959 PMCID: PMC7470573 DOI: 10.4269/ajtmh.19-0909] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 05/02/2020] [Indexed: 12/19/2022] Open
Abstract
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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Affiliation(s)
| | | | - Catherine Cook
- Proctor Foundation, University of California San Francisco, San Francisco, California
| | - Elodie Lebas
- Proctor Foundation, University of California San Francisco, San Francisco, California
| | - Nils Pilotte
- Department of Biological Sciences, Smith College, Northampton, Massachusetts
- Molecular and Cellular Biology Program, University of Massachusetts, Amherst, Massachusetts
| | - Jessica R. Grant
- Department of Biological Sciences, Smith College, Northampton, Massachusetts
| | - Steven A. Williams
- Department of Biological Sciences, Smith College, Northampton, Massachusetts
- Molecular and Cellular Biology Program, University of Massachusetts, Amherst, Massachusetts
| | - Jeremy D. Keenan
- Proctor Foundation, University of California San Francisco, San Francisco, California
| | - Thomas M. Lietman
- Proctor Foundation, University of California San Francisco, San Francisco, California
| | - Kristen Aiemjoy
- Proctor Foundation, University of California San Francisco, San Francisco, California
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California
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Culture of Rectal Swab Specimens for Enteric Bacterial Pathogens Decreases Time to Test Result While Preserving Assay Sensitivity Compared to Bulk Fecal Specimens. J Clin Microbiol 2019; 57:JCM.02077-18. [PMID: 30944186 DOI: 10.1128/jcm.02077-18] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Accepted: 03/22/2019] [Indexed: 01/26/2023] Open
Abstract
Diarrheal illness is a major cause of morbidity and mortality throughout the world, yet the etiologic agent of many cases of gastrointestinal illness remains unspecified, often due to the lack of convenient, timely, and sensitive diagnostic testing. Although bulk fecal specimens remain the recommended specimen type for enteric culture, rectal swabs may be an option preferred by clinicians and patients due to the convenience and timing of collection. However, the lack of data evaluating the sensitivity of rectal swabs compared to fecal specimens for detection of enteric pathogens precludes this specimen type from being recommended by national guidelines. In this study, we retrospectively reviewed 480 paired rectal swab and fecal specimens submitted for enteric culture to the Barnes-Jewish Hospital and St. Louis Children's Hospital microbiology laboratories in St. Louis, MO, from 2002 to 2017. We report 32% positivity of paired specimens with an overall agreement of 93% and Cohen's κ of 0.84 (95% confidence interval, 0.78 to 0.89). Additionally, we evaluated the time to result from the time of patient presentation to the health care setting and demonstrate that rectal swabs have a significantly shorter time to an actionable result than bulk fecal specimens (median, 67.4 h versus 78.4 h, respectively; P < 0.001). These findings indicate that rectal swabs facilitate on-demand culture-based testing with a sensitivity comparable to that of fecal specimens and thus should be recommended for enteric bacterial culture when bulk fecal specimens are unavailable.
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Kotar T, Pirš M, Steyer A, Cerar T, Šoba B, Skvarc M, Poljšak Prijatelj M, Lejko Zupanc T. Evaluation of rectal swab use for the determination of enteric pathogens: a prospective study of diarrhoea in adults. Clin Microbiol Infect 2018; 25:733-738. [PMID: 30315956 DOI: 10.1016/j.cmi.2018.09.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Revised: 09/27/2018] [Accepted: 09/30/2018] [Indexed: 10/28/2022]
Abstract
OBJECTIVES A stool sample is the sample of choice for microbiological testing of enteric pathogens causing diarrhoea, but a rectal swab can be a more practical alternative. A prospective observational study was performed to evaluate the diagnostic performance of flocked rectal swab specimens using the syndromic molecular approach to determine the aetiology of diarrhoea in adults. METHODS We compared the performance of rectal swabs with stool samples as the reference standard in determining viral, bacterial and protozoal pathogens using real-time multiplex PCR as well as standard stool culture. Paired samples of stool and rectal swab specimens were collected from 304 adult patients with diarrhoea, presented at the Department of Infectious Diseases, University Medical Centre Ljubljana, between June 2016 and August 2017. RESULTS Overall sensitivity of rectal swab samples in the syndromic molecular approach was 83.2% (95% CI 77.2%-88.1%). Pathogen group-specific analysis of rectal swabs showed sensitivity of 65.6% (95% CI 52.7%-77.1%) for viruses and 57.1% (95% CI 28.9%-82.3%) for parasites. For bacteria, sensitivity was 86.5% (95% CI 79.5%-91.8%) when PCR was performed and 61.4% (95% CI 52.4%-69.9%) when culture for bacteria was performed. Mean threshold cycle (Ct) values for most pathogens were higher in rectal swab specimens than in stool specimens. CONCLUSIONS Our results indicate that rectal swabs can be used in the diagnosis of diarrhoea in adults when stool specimens are not available or when rapid aetiological determination is needed. However, rectal swabs should be analysed using a molecular approach. The mean Ct value for most pathogens is higher in rectal swab specimens than in stool specimens.
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Affiliation(s)
- T Kotar
- Infectious Diseases, University Clinical Centre Ljubljana, Ljubljana, Slovenia.
| | - M Pirš
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - A Steyer
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - T Cerar
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - B Šoba
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - M Skvarc
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - M Poljšak Prijatelj
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - T Lejko Zupanc
- Infectious Diseases, University Clinical Centre Ljubljana, Ljubljana, Slovenia
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Gibory M, Haltbakk I, Flem E, Vainio K, Salamanca BV, Størdal K, Nordbø SA, Jakobsen K, Haarr E, Dudman SG. Rotavirus detection in bulk stool and rectal swab specimens in children with acute gastroenteritis in Norway. J Clin Virol 2017; 97:50-53. [DOI: 10.1016/j.jcv.2017.10.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 09/28/2017] [Accepted: 10/31/2017] [Indexed: 11/25/2022]
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Smith ZL, Dua A, Saeian K, Ledeboer NA, Graham MB, Aburajab M, Ballard DD, Khan AH, Dua KS. A Novel Protocol Obviates Endoscope Sampling for Carbapenem-Resistant Enterobacteriaceae: Experience of a Center with a Prior Outbreak. Dig Dis Sci 2017; 62:3100-3109. [PMID: 28681083 DOI: 10.1007/s10620-017-4669-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 06/27/2017] [Indexed: 12/09/2022]
Abstract
BACKGROUND Numerous published outbreaks, including one from our institution, have described endoscope-associated transmission of multidrug-resistant organisms (MDROs). Individual centers have adopted their own protocols to address this issue, including endoscope culture and sequestration. Endoscope culturing has drawbacks and may allow residual bacteria, including MDROs, to go undetected after high-level disinfection. AIM To report the outcome of our novel protocol, which does not utilize endoscope culturing, to address our outbreak. METHODS All patients undergoing procedures with elevator-containing endoscopes were asked to permit performance of a rectal swab. All endoscopes underwent high-level disinfection according to updated manufacturer's guidance. Additionally, ethylene oxide (EtO) sterilization was done in the high-risk settings of (1) positive response to a pre-procedure risk stratification questionnaire, (2) positive or indeterminate CRE polymerase chain reaction (PCR) from rectal swab, (3) refusal to consent for PCR or questionnaire, (4) purulent cholangitis or infected pancreatic fluid collections. Two endoscopes per weekend were sterilized on a rotational basis. RESULTS From September 1, 2015 to April 30, 2016, 556 endoscopy sessions were performed using elevator-containing endoscopes. Prompted EtO sterilization was done on 46 (8.3%) instances, 3 from positive/indeterminate PCR tests out of 530 samples (0.6%). No CRE transmission was observed during the study period. Damage or altered performance of endoscopes related to EtO was not observed. CONCLUSION In this pilot study, prompted EtO sterilization in high-risk patients has thus far eliminated endoscope-associated MDRO transmission, although no CRE infections were noted throughout the institution during the study period. Further studies and a larger patient sample will be required to validate these findings.
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Affiliation(s)
- Zachary L Smith
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA. .,Division of Gastroenterology and Hepatology, Medical College of Wisconsin, Milwaukee, WI, USA. .,Division of Gastroenterology, Washington University School of Medicine, 660 S Euclid Ave, Campus Box 8124, Saint Louis, MO, 63110, USA.
| | - Arshish Dua
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Kia Saeian
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA.,Division of Gastroenterology and Hepatology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Nathan A Ledeboer
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Mary Beth Graham
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA.,Division of Infectious Diseases, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Murad Aburajab
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA.,Division of Gastroenterology and Hepatology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Darren D Ballard
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA.,Division of Gastroenterology and Hepatology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Abdul H Khan
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA.,Division of Gastroenterology and Hepatology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Kulwinder S Dua
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA.,Division of Gastroenterology and Hepatology, Medical College of Wisconsin, Milwaukee, WI, USA
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Glisovic S, Eintracht S, Longtin Y, Oughton M, Brukner I. Rectal swab screening assays of public health importance in molecular diagnostics: Sample adequacy control. J Infect Public Health 2017; 11:234-237. [PMID: 28801105 DOI: 10.1016/j.jiph.2017.07.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 06/16/2017] [Accepted: 07/09/2017] [Indexed: 11/30/2022] Open
Abstract
Rectal swabs are routinely used by public health authorities to screen for multi-drug resistant enteric bacteria including vancomycin-resistant enterococci (VRE) and carbapenem-resistant enterobacteriaceae (CRE). Screening sensitivity can be influenced by the quality of the swabbing, whether performed by the patient (self-swabbing) or a healthcare practitioner. One common exclusion criterion for rectal swabs is absence of "visible soiling" from fecal matter. In our institution, this criterion excludes almost 10% of rectal swabs received in the microbiology laboratory. Furthermore, over 30% of patients in whom rectal swabs are cancelled will not be re-screened within the next 48h, resulting in delays in removing infection prevention measures. We describe two quantitative polymerase chain reaction (qPCR)-based assays, human RNAse P and eubacterial 16S rDNA, which might serve as suitable controls for sampling adequacy. However, lower amounts of amplifiable human DNA make the 16s rDNA assay a better candidate for sample adequacy control.
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Affiliation(s)
| | - Shaun Eintracht
- Medical Faculty, McGill University, Montreal, Quebec, Canada; SMBD-Jewish General Hospital, Montreal, Quebec, Canada
| | - Yves Longtin
- Medical Faculty, McGill University, Montreal, Quebec, Canada; SMBD-Jewish General Hospital, Montreal, Quebec, Canada
| | - Matthew Oughton
- Medical Faculty, McGill University, Montreal, Quebec, Canada; SMBD-Jewish General Hospital, Montreal, Quebec, Canada
| | - Ivan Brukner
- Medical Faculty, McGill University, Montreal, Quebec, Canada; SMBD-Jewish General Hospital, Montreal, Quebec, Canada.
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11
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Freedman SB, Xie J, Nettel-Aguirre A, Lee B, Chui L, Pang XL, Zhuo R, Parsons B, Dickinson JA, Vanderkooi OG, Ali S, Osterreicher L, Lowerison K, Tarr PI. Enteropathogen detection in children with diarrhoea, or vomiting, or both, comparing rectal flocked swabs with stool specimens: an outpatient cohort study. Lancet Gastroenterol Hepatol 2017; 2:662-669. [PMID: 28712662 DOI: 10.1016/s2468-1253(17)30160-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 05/10/2017] [Accepted: 05/18/2017] [Indexed: 12/17/2022]
Abstract
BACKGROUND Enteropathogen detection traditionally relies on diarrhoeal stool samples, but these are inconvenient to collect if they are not immediately available, leading to suboptimum return rates of samples and delayed or missed diagnostic opportunities. We sought to compare the enteropathogen yields of rectal swabs and stool specimens in children with diarrhoea or vomiting, or both. METHODS The Alberta Provincial Pediatric EnTeric Infection TEam (APPETITE) did a study in three outpatient cohorts in Calgary and Edmonton (AB, Canada)-children enrolled in the Pediatric Emergency Research Canada emergency departments, children receiving routine vaccinations at a Calgary health clinic, and symptomatic children who met criteria for treatment at home. Eligible participants were children younger than 18 years, with at least three episodes of vomiting or diarrhoea in the preceding 24 h and fewer than 7 days of symptoms. After excluding those enrolled within the previous fortnight, unable to follow-up, or having psychiatric illness, neutropenia, or requiring emergent care, we attempted to collect rectal swabs and stool from all participants. Specimens were tested with the multianalyte assay Luminex xTAG Gastrointestinal Pathogen Panel, an in-house five-virus panel and bacterial culture. Primary outcomes were comparative yield (calculated as the proportion of submitted paired specimens only in which at least one pathogen was identified) and overall yield (which calculated the proportion of study participants in whom at least one pathogen was identified in all specimens, where unsubmitted specimens were analysed as negative). We used McNemar's test to do pathogen-specific analyses, and generalised estimating equations (GEE) for the global (ie, any) pathogen analyses, with adjustments made for the presence of diarrhoea, location, and their interactions with specimen type. FINDINGS Between Dec 12, 2014, and Aug 31, 2016, we studied 1519 eligible participants, 1147 (76%) of whom provided stool specimens and 1514 (>99%) provided swab specimens. 871 (76%) of 1147 stool specimens and 1024 (68%) of 1514 swabs were positive for any pathogen (p<0·0001). Comparative yield adjusted odds ratios (ORs) for stool specimens relative to swabs were 1·24 (95% CI 1·11-1·38) in children with diarrhoea at presentation and 1·76 (1·47-2·11) in children without diarrhoea. GEE analysis identified an interaction between the presence of diarrhoea and specimen type (p=0·0011) and collection location (p=0·0078). In an overall yield analysis, pathogen yield was 57% (871 of 1519 children) for stool specimens and 67% (1024 of 1519 children) for rectal swabs, with an unadjusted OR of 0·65 (95% CI 0·59-0·72) for stool relative to swab. INTERPRETATION Rectal swabs should be done when enteropathogen identification and rapid detection are needed, appropriate molecular diagnostic technology is available, and a stool specimen is not immediately available. In view of their high yield, we urge that the recommendation against the use of rectal swabs as diagnostic specimens be reconsidered. FUNDING Alberta Innovates-Health Solutions Team Collaborative Research Innovation Opportunity.
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Affiliation(s)
- Stephen B Freedman
- Sections of Emergency Medicine and Gastroenterology, Department of Paediatrics, Alberta Children's Hospital, Alberta Children's Hospital Research Institute, University of Calgary, Cumming School of Medicine Calgary, AB, Canada.
| | - Jianling Xie
- Section of Pediatric Emergency Medicine, Alberta Children's Hospital, University of Calgary, Calgary, AB, Canada
| | - Alberto Nettel-Aguirre
- Departments of Paediatrics and of Community Health Sciences, Cumming School of Medicine, Faculty of Kinesiology, Alberta Children's Hospital, Alberta Children's Hospital Research Institute, O'Brien Population Health Institute, University of Calgary, Calgary, AB, Canada
| | - Bonita Lee
- Department of Paediatrics, Faculty of Medicine and Dentistry, Stollery Children's Hospital, Women and Children's Health Research Institute, University of Alberta, Edmonton, AB, Canada
| | - Linda Chui
- Provincial Laboratory for Public Health, Edmonton, AB, Canada; Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada
| | - Xiao-Li Pang
- Provincial Laboratory for Public Health, Edmonton, AB, Canada; Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada
| | - Ran Zhuo
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada
| | - Brendon Parsons
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada
| | - James A Dickinson
- Health Sciences Centre, Department of Family Medicine and Department of Community Health Sciences, University of Calgary, Calgary, AB, Canada
| | - Otto G Vanderkooi
- Departments of Paediatrics, Microbiology, Immunology, and Infectious Diseases, Pathology & Laboratory Medicine and Community Health Sciences and the Alberta Children's Hospital Research Institute, Alberta Children's Hospital, University of Calgary, Calgary, AB, Canada
| | - Samina Ali
- Department of Paediatrics, Faculty of Medicine and Dentistry, Stollery Children's Hospital, Women and Children's Health Research Institute, University of Alberta, Edmonton, AB, Canada
| | - Lara Osterreicher
- Provincial Clinical Programs, Health Link Alberta, Alberta Health Services, Edmonton, AB, Canada
| | - Karen Lowerison
- Section of Pediatric Emergency Medicine, Alberta Children's Hospital, University of Calgary, Calgary, AB, Canada
| | - Phillip I Tarr
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Paediatrics, Washington University School of Medicine, St Louis, MO, USA
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Abstract
Norovirus is an important cause of gastroenteritis outbreaks globally and the most prevalent cause of sporadic gastroenteritis in many regions. Rapid and accurate identification of causative viral agents is critical for outbreak investigation, disease surveillance, and management. Because norovirus is not cultivable and has a highly diversified and variable genome, it is difficult to develop diagnostic assays. Detection methods have evolved from electron microscopy to conventional end-point reverse transcription polymerase chain reaction (RT-PCR), immunoassay, real-time RT-PCR, other molecular technologies, and nanotechnology array-based assays. The status and features of various testing methods are summarized in this review.
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Affiliation(s)
- Xiaoli Pang
- Provincial Laboratory for Public Health, Walter Mackenzie Health Sciences Centre, University of Alberta Hospital, 8440 - 112 Street, Edmonton, Alberta T6G 2J2, Canada; Department of Laboratory Medicine and Pathology, University of Alberta, 8440-112 Street, Edmonton, Alberta T6G 2B7, Canada.
| | - Bonita E Lee
- Department of Pediatrics, University of Alberta, 11405, 87 Avenue, Edmonton, Alberta T6G 1C9, Canada
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