Literature Review: Gastrointestinal infections

Multiplex RT-PCR for rapid detection of viruses commonly causing diarrhoea in pediatric patients
Thongprachum A, Khamrin P, Pham NT, Takanashi S, Okitsu S, et al. J Med Virol 2017; 89(5): 818–824
Multiplex RT-PCR method using five sets of panel primers was developed for the detection of diarrhoeal viruses, including rotavirus A, B, and C, adenovirus, astrovirus, norovirus GI and GII, sapovirus, Aichi virus, parechovirus, enterovirus, cosavirus, bocavirus, and Saffold virus. The sensitivity of the method was evaluated and tested with 751 fecal specimens collected from Japanese children with acute diarrhoea. Several kinds of viruses were detected in 528 out of 751 (70.3%) fecal specimens. Mixed-infection with different viruses in clinical specimens could also be effectively detected. The method proved to be reliable with highly sensitive and specific and useful for routine diagnosis.

Evaluation of diagnostic accuracy of two rapid stool antigen tests using an immunochromatographic assay to detect Helicobacter pylori
da Silva-Etto JMK1, Mattar R2, Villares-Lopes CA1, Marques SB1, Carrilho FJ. Clin Biochem 2017; pii: S0009–9120(17)30129–7
OBJECTIVES: The stool antigen assay for H. pylori infection diagnosis with monoclonal antibodies is a simple and recommended technique by the Maastricht V/Florence consensus report. Recently, Pylori K-Set K-1219 (Coris Bioconcept Sprl, Belgium) and HP-F23 (Symbiosys, Brazil) have been made commercially available in Brazil. Thus, the aim of this study was to evaluate the diagnostic accuracies of these two rapid stool antigen tests by immunochromatographic assays (index tests) for the clinical practice.
DESIGN AND METHODS: A total of 98 patients who underwent upper gastrointestinal endoscopy and 13C-urea breath test entered the study. H. pylori infection status was defined by the combination of the rapid urease test and the 13C-urea breath test (reference standard). Two observers who were aware of H. pylori status performed the reading of index tests. Diagnostic accuracy (sensitivity, specificity, positive predictive value, negative predictive value with 95% confidence intervals, positive likelihood ratio, negative likelihood ratio and kappa index measure of agreement) were determined.
RESULTS: The index tests where in perfect agreement with the H. pylori status with kappa values of 0.87 for Pylori K-Set K-1219 and 0.92 for HP-F23. The sensitivity of HP-F23 was 97.9% (IC95%: 87.5–100) and specificity was 93.8% (IC95%; 84-97.2).The positive likelihood ratio was 15.8, and the negative likelihood ratio was 0.02. The Pylori K-Set K-1219 had a sensitivity of 87.7% (IC95%: 74.5–94.9) and a specificity of 100% (IC95%: 91.6-100); the positive likelihood ratio was infinity, and the negative likelihood ratio was 0.1. The test line on the cassette device of HP-F23 was stronger than of the Pylori K-Set K-1219.
CONCLUSION: The HP-F23 test performed better in clinical practice. Nonetheless, the 13C-urea breath test is more reliable technique. Moreover, caution must be paid to the trace or clear pale test line readings that were observed in false positive and false negative results, leading to incorrect management of the patient.

Development of an LPS-based ELISA for diagnosis of Yersinia enterocolitica O:3 infections in Danish patients: a follow-up study
Dalby T, Rasmussen E, Schiellerup P, Krogfelt KA. BMC Microbiol 2017; 17(1): 125
BACKGROUND: The bacterium Yersinia enterocolitica causes gastroenteritis in humans. The study aimed to develop a diagnostic enzyme-linked immunosorbent assay (ELISA) for detection of Y. enterocolitica O:3 LPS antibodies in sera from Danish patients with suspected Y. enterocolitica O:3 gastrointestinal infection. As a part of this, antibody decay profiles after culture confirmed Y. enteritis were studied.
RESULTS: An ELISA using Y. enterocolitica O:3 LPS as the coating antigen was developed for measuring IgA, IgG and IgM specific antibodies. A longitudinal collection of 220 sera drawn between 20 and 1053 days after onset of symptoms from 85 adult Danish patients with verified Y. enteritis were examined. A control group of 100 sera from healthy Danish blood-donors were analysed in order to determine the cut-off for interpretation of results. Serum samples from 62 out of 81 patients who delivered either the first or the second sample were found positive for specific antibodies against Y. enterocolitica O:3 LPS (77%). For samples collected within 60 days after onset of symptoms (n = 48) sensitivities of 58%, 42% and 79% for IgA, IgG and IgM antibodies were found. A sensitivity of 81% was found for these samples when using the definition of a positive result in either IgA, IgG or IgM as a combined positive. All samples received up to 36 days after onset of symptoms (n=10) were found to be positive using this definition. For the period 61 to 90 days after onset of symptoms (n=32), a combined sensitivity of 63% was found. The antibody levels as well as decay profiles for the three different immunoglobulin classes for the individual patients exhibited a large degree of variation.
CONCLUSIONS: Using a definition of positive as a positive result for either IgA, IgG or IgM antibodies, a diagnostic sensitivity of 81% was achieved for samples received within 60 days after onset of symptoms. In particular, the levels of specific IgM antibodies were elevated. In comparison, the standard tube-agglutination assay achieved a sensitivity of 60% on the same samples. The sensitivity of the ELISA decreased the longer the duration of time since onset of symptoms. The ELISA was highly specific for Yersinia when testing sera from individuals with confirmed gastrointestinal infections by other bacteria. Moreover, the knowledge gained from this longitudinal study of antibody decay profiles can be used in future epidemiological studies of seroprevalence.

The development of a multiplex real-time RT-PCR for the detection of adenovirus, astrovirus, rotavirus and sapovirus from stool samples
Bennett S, Gunson RN. J Virol Methods 2017; 242: 30–34
Viral gastroenteritis is a major health problem with significant morbidity and economic consequences. Viral gastroenteritis is caused by a number of viruses, including norovirus, rotavirus, adenovirus, astrovirus, and sapovirus. Conventional diagnosis is based on direct antigen detection and electron microscopy, however enzyme immunoassay’s are insensitive and not available for all relevant pathogens, and electron microscope (EM) is no longer routinely carried out in most laboratories. Most laboratories now offer norovirus real-time PCR testing however the availability of other assays is variable. Commercial methods for the detection of inflectional intestinal disease (IID) are available but these can be expensive and are not commonly used. This paper describes the development of a single multiplex assay for the simultaneous detection of adenovirus, astrovirus, rotavirus and sapovirus from stool samples. The multiplex was evaluated by assessing endpoint sensitivity, specificity, panel of clinical samples, quality control (QC) panel and the robustness and reproducibility of the multiplex.
Cholera rapid test with enrichment step has diagnostic performance equivalent to culture
Ontweka LN, Deng LO, Rauzier J, Debes AK, Tadesse F, et al. PLoS One 2016; 11(12): e0168257
Cholera rapid diagnostic tests (RDT) could play a central role in outbreak detection and surveillance in low-resource settings, but their modest performance has hindered their broad adoption. The addition of an enrichment step may improve test specificity. We describe the results of a prospective diagnostic evaluation of the Crystal VC RDT (Span Diagnostics, India) with enrichment step and of culture, each compared to polymerase chain reaction (PCR), during a cholera outbreak in South Sudan. RDTs were performed on alkaline peptone water inoculated with stool and incubated for 4-6 hours at ambient temperature. Cholera culture was performed from wet filter paper inoculated with stool. Molecular detection of Vibrio cholerae O1 by PCR was done from dry Whatman 903 filter papers inoculated with stool, and from wet filter paper supernatant. In August and September 2015, 101 consecutive suspected cholera cases were enrolled, of which 36 were confirmed by PCR. The enriched RDT had 86.1% (95% CI: 70.5–95.3) sensitivity and 100% (95% CI: 94.4–100) specificity compared to PCR as the reference standard. The sensitivity of culture versus PCR was 83.3% (95% CI: 67.2–93.6) for culture performed on site and 72.2% (95% CI: 54.8–85.8) at the international reference laboratory, where samples were tested after an average delay of two months after sample collection, and specificity was 98.5% (95% CI: 91.7–100) and 100% (95% CI: 94.5–100), respectively. The RDT with enrichment showed performance comparable to that of culture and could be a sustainable alternative to culture confirmation where laboratory capacity is limited.

Clinical and analytical evaluation of a single-vial stool collection device with formalin-free fixative for improved processing and comprehensive detection of gastrointestinal parasites
Couturier BA, Jensen R, Arias N, Heffron M, Gubler E, et al. J Clin Microbiol 2015; 53(8): 2539–2548
Microscopic examination of feces is a standard laboratory method for diagnosing gastrointestinal parasite infections. In North America, the ovum and parasite (O&P) examination is typically performed using stool that is chemically fixed in polyvinyl alcohol (PVA) and formalin, after which the stool is concentrated by filtration to enhance sensitivity. Mini Parasep solvent-free (SF) tubes allow collection and concentration within a single collection vial. The goal of the study was to determine whether consolidated processing and concentration with the Parasep tubes using an alcohol-based fixative (Alcorfix) provide O&P examinations equivalent to or better than those done by processing of PVA-formalin-fixed stool using a SpinCon concentration device. Parasep tubes revealed filtration performance equivalent to that of the SpinCon concentration device using PVA-formalin-fixed stool containing protozoa. Specimens cocollected in Parasep tubes containing PVA-formalin and Alcorfix revealed comparable morphology and staining for various protozoa. Alcorfix effectively fixed live Cryptosporidium and microsporidia such that morphology and staining were conserved for modified acid-fast and modified trichrome stains. A work flow analysis revealed significant time savings for batches of 10 or 30 O&P specimens in tubes with Alcorfix compared to the amount of time that it took to analyse the same number of specimens in tubes with PVA-formalin. The direct hands-on time savings with Mini Parasep tubes were 17 min and 41 s and 32 min and 1 s for batches of 10 and 30 specimens, respectively. Parasep tubes containing Alcorfix provide significant work flow advantages to laboratories that process medium to high volumes of O&P specimens by streamlining processing and converting to a single tube. These improvements in work flow, reduction of the amount of formalin used in the laboratory, and equivalent microscopy results are attractive advancements in O&P testing for North American diagnostic parasitology laboratories.

Chemiluminescent immunoassays for the laboratory diagnosis of Clostridium difficile infection
Makristathis A, Zeller I, Mitteregger D, Kundi M, Hirschl AM. Eur J Clin Microbiol Infect Dis 2017; 36(7): 1253–1259
For the microbiological diagnosis of a Clostridium difficile infection (CDI), a two-test algorithm consisting of a C. difficile glutamate dehydrogenase (GDH)-immunoassay followed by a toxin-immunoassay in positive cases is widely used. In this study, two chemiluminescent immunoassays (CLIAs), one for GDH and the other for the toxins A and B, have been evaluated systematically using appropriate reference methods. Three-hundred diarrhoeal stool specimens submitted for CDI diagnosis were analysed by the LIAISON CLIAs (DiaSorin). Toxigenic culture (TC) and cell cytotoxicity assay (CCTA) were used as “gold standard” reference methods. In addition, GDH and toxin A and B enzyme immunoassays (EIAs), C. diff Chek-60 and toxin A/B II (TechLab), and the Cepheid Xpert C. difficile polymerase chain reaction (PCR) were performed. C. difficile was grown in 42 (14%), TC was positive in 35 (11.7%) and CCTA in 25 (8.3%) cases. CLIAs were more sensitive but less specific than the respective EIAs. Using culture as reference, the sensitivity of the GDH CLIA was 100%. In comparison to CCTA sensitivity, specificity, positive predictive value and negative predictive value of the two-test algorithm were 88, 99.3, 91.7 and 98.9% by CLIAs and 72, 99.6, 94.7 and 97.5% by EIAs. Discrepant results by CLIAs were more frequent than that by EIAs (9% vs. 6.3%); in those cases, PCR allowed for the accurate detection of toxigenic strains. Due to performance characteristics and testing comfort, CLIAs in combination with PCR represent a favourable option for the rapid laboratory C. difficile diagnostics.
Detection and differentiation of norovirus genogroups I and II from clinical stool specimens using real-time PCR
Ramanan P, Espy MJ, Khare R, Binnicker MJ. Diagn Microbiol Infect Dis 2017; 87(4): 325–327
A real-time RT-PCR assay was designed to detect and differentiate norovirus genogroups I (GI) and II (GII), with primers and probes targeting the nonstructural polyprotein gene. Stool samples (n=100) submitted for routine testing by the BioFire FilmArray® GI panel were also tested by the norovirus GI/GII real-time PCR assays. When compared to the FilmArray GI panel, the norovirus real-time PCR assay demonstrated a sensitivity of 77.5% (62/80) and specificity of 95% (19/20). Specimens yielding discordant results (n=19) were tested at two outside laboratories for adjudication. Following discordant resolution, the adjusted sensitivity and specificity of the norovirus real-time PCR assays were 96.9% (63/65) and 100% (35/35), respectively. These results suggest that the real-time PCR assays are able to accurately detect and differentiate norovirus GI/GII from clinical stool specimens. Furthermore, our report highlights a potential issue with the specificity of the BioFire FilmArray® norovirus assay, which warrants additional investigation.

Limited diagnostic value of a multiplexed gastrointestinal pathogen panel for the detection of adenovirus infection in an oncology patient population
McMillen T, Lee YJ, Kamboj M, Babady NE. J Clin Virol 2017; 94: 37–41
BACKGROUND: Diagnosis of adenovirus infections in transplant patients may be accomplished using either plasma or stool samples. IVD-cleared multiplexed gastrointestinal (GI) PCR panels offer an option for rapid testing of stool samples but most only target adenovirus (HAdV) types F40/41.
OBJECTIVES: Given the potential significance of a positive adenovirus test in an immunocompromised patient, we sought to determine the frequency of type 40/41 in our patient population and the utility of a readily available multiplexed, FDA-cleared GI Panel for the detection of adenovirus infections.
STUDY DESIGN: A total of 215 specimens from immunocompromised patients mostly with hematologic malignancy or transplant recipients were evaluated including 107 plasma samples, 85 stool samples and 23 respiratory samples. Genotyping was performed successfully on 122 specimens.
RESULTS: The most common type detected in all samples including stools was adenovirus C/2. In a subset of patients with multiple specimen types tested, similar types were detected in all samples.
CONCLUSIONS: Although adenovirus F40/41 is the most common enteric type, adenovirus C/2 was the most common type identified in stools and subsequently plasma samples of our patient population. Implementation of assays that have wide reactivity for most adenovirus types is essential for optimal diagnostic yield.

Synergistic effect of hyperglycemia and Helicobacter pylori infection status on colorectal adenoma risk
Hu KC, Wu MS, Chu CH, Wang HY, Lin SC, et al. J Clin Endocrinol Metab 2017; 102(8): 2744–2750
CONTEXT: Both Helicobacter pylori and type 2 diabetes mellitus are possible risk factors for colon adenoma.
OBJECTIVE: The purpose of this study was to assess the interaction between H. pylori and hyperglycemia status on the risk of colon adenoma.
DESIGN, SETTING, AND PARTICIPANTS: This was a cross-sectional, retrospective study conducted at the MacKay Memorial Hospital, Taiwan. The study included 3943 subjects aged >40 years undergoing bidirectional gastrointestinal endoscopy on the same day between July 2006 and June 2015. All subjects had a gastric biopsy specimen tested for H. pylori.
MAIN OUTCOME MEASURE: Colon adenoma with and without H. pylori infection at different hemoglobin A1c (HbA1c) levels.
RESULTS: The prevalence of colorectal adenomas in patients who were H. pylori-positive and H. pylori-negative was 37.3% and 27.29%, respectively. Multivariate logistic regression analysis identified male sex, age, body mass index, H. pylori infection, and HbA1c ≥6.5% as independent risk factors for adenoma; use of hypoglycemic agents decreased this risk. The prevalence of adenoma was increased with elevated HbA1c levels regardless of H. pylori status. The odds ratio (OR) for adenoma was 1.44 (95% confidence interval [CI], 1.20 to 1.73) if H. pylori was present or 1.68 (95% CI, 1.05 to 2.70) in patients who were H. pylori-negative but had HbA1c ≥7.0%. If both conditions were present, the OR was 4.79 (95% CI, 2.92 to 7.84). A 1% increase in HbA1c was associated with an increased prevalence of adenoma by 42.4% in H. pylori-positive subjects.
CONCLUSIONS: The combination of H. pylori infection and elevated HbA1c is associated with an increased risk of colon adenoma.