Evaluation of a multiplex gastrointestinal PCR panel for the aetiological diagnosis of infectious diarrhoea

Evaluation of non-invasive diagnostic tools for diarrhea: a systematic review of point-of-care tests and biomarkers

Background

Diarrhea is a prevalent condition affecting millions worldwide. However, current standard diagnostic methods have many drawbacks. This review examines various non-invasive point-of-care (POC) tests and biomarkers aiding rapid diagnosis of diarrhea from different causes.

Methods

PubMed, PubMed Central, ScienceDirect, Cochrane Library, and Google Scholar were searched from 2013 to present for relevant literature. Two reviewers independently assessed included studies' quality using the Critical Appraisal Skills Programme (CASP) checklist.

Results

The search yielded 1453 studies, of which 39 were included after screening and applying eligibility criteria. Polymerase chain reaction (PCR) was the POC test in 25 studies, providing consistent sensitivity and specificity. For biomarkers, C-reactive protein (CRP), fecal calprotectin, and procalcitonin offered high sensitivity and specificity for conditions like acute pediatric diarrhea, microscopic colitis, and inflammatory diarrhea, respectively.

Conclusion

PCR proved the ideal POC test for rapid diarrhea diagnosis, while the procalcitonin biomarker helps differentiate inflammatory from non-inflammatory diarrhea. Other reviewed tools also demonstrated promising diagnostic performance, though improvements in sensitivity, specificity, and usability are still needed.

Enhancing enteric pathogen detection: implementation and impact of multiplex PCR for improved diagnosis and surveillance

BACKGROUND

Syndromic surveillance of acute gastroenteritis plays a significant role in the diagnosis and management of gastrointestinal infections that are responsible for a substantial number of deaths globally, especially in developing countries. In Lebanon, there is a lack of national surveillance for acute gastroenteritis, and limited data exists regarding the prevalence of pathogens causing diarrhea. The one-year study aims to investigate the epidemiology of common gastrointestinal pathogens and compare our findings with causative agents of diarrhea reported by our study collaborative centers.

METHODS

A multicenter, cross-sectional study was conducted over a one-year period. A total of 271 samples were obtained from outpatients and inpatients presenting with symptoms of acute gastroenteritis at various healthcare facilities. The samples were then analyzed using Allplex gastrointestinal assay that identifies a panel of enteric pathogens.

RESULTS

Overall, enteropathogens were detected in 71% of the enrolled cases, 46% of those were identified in patients as single and 54% as mixed infections. Bacteria were observed in 48%, parasites in 12% and viruses in 11%. Bacterial infections were the most prevalent in all age groups. Enteroaggregative E. coli (26.5%), Enterotoxigenic E. coli (23.2%) and Enteropathogenic E. coli (20.3%) were the most frequently identified followed by Blastocystis hominis (15.5%) and Rotavirus (7.7%). Highest hospitalization rate occurred with rotavirus (63%), Enterotoxigenic E. coli (50%), Blastocystis hominis (45%) and Enteropathogenic E. coli (43%). Enteric pathogens were prevalent during summer, fall and winter seasons.

CONCLUSIONS

The adoption of multiplex real-time PCR assays in the diagnosis of gastrointestinal infections has identified gaps and improved the rates of detection for multiple pathogens. Our findings highlight the importance of conducting comprehensive surveillance to monitor enteric infections. The implementation of a syndromic testing panel can therefore provide healthcare professionals with timely and accurate information for more effective treatment and public health interventions.

Clinical performance evaluation of TAQPATH Enteric Bacterial Select Panel for the detection of common enteric bacterial pathogens in comparison to routine stool culture and other qPCR-based diagnostic tests

IMPORTANCE

Enteric bacterial infections caused by Salmonella, Shigella, pathogenic Escherichia coli, and Campylobacter represent one of the most common causes of infectious enteritis worldwide. The timely and accurate diagnosis of pathogens causing gastroenteritis is crucial for patient care, public health, and disease surveillance. While stool culture has long been the standard and highly specific method for detecting enteric pathogens, it is labor-intensive and time-consuming with limited sensitivity. To improve patient outcomes, there is a need to implement new cost-effective approaches for the detection of bacterial enteric pathogens with higher sensitivity and faster time to result. This study shows that multiplex real-time polymerase chain reaction-based tests, such as the TAQPATH Enteric Bacterial Select Panel, are accurate and cost-effective diagnostic alternatives for the detection and differentiation of the most common enteric bacterial pathogens, offering quicker time to result and higher sensitivity compared to routine stool culture.

Infectious Disease Pathology of the Gastrointestinal Tract: Diagnosing the Challenging Cases

Infectious diseases of the GI tract mimic a variety of other GI diseases, including chronic idiopathic inflammatory bowel disease and ischemia. It can be challenging to identify pathogens in tissue sections as well, as many trainees are not exposed to infectious disease pathology other than in the context of microbiology. Our ability to diagnose infections in formalin fixed, paraffin embedded material has grown exponentially with the advent of new histochemical and immunohistochemical stains, as well as more options for molecular testing. Correlating these diagnostic techniques with morphology has led to increasing understanding of the histologic patterns that are associated with specific pathogens.

Summer diarrhea in children: a monocentric French epidemiological observational study

Pediatric diarrhea is a major public health problem worldwide. In France, continuous surveillance shows a winter epidemic peak and a more modest summer recrudescence. Few studies describe the infectious agents responsible for pediatric summer diarrhea in France. The objectives were to estimate the prevalence of infectious diarrhea and describe the pathogens responsible for summer diarrhea in children; and to describe common factors that can be used as guidance on the etiology of these diarrheas. A cross-sectional, single-center, epidemiological observational study was conducted in the pediatric emergency department of a French hospital between June and September in 2019 and 2020. Multiplex gastrointestinal pathogen panels were used for diagnostics. A multiple correspondence analysis was used to determine profiles of patients. A total of 95 children were included, of whom 82.1% (78/95) were under five years old. The prevalence of infectious summer diarrhea was 81.1% (77/95, 95%CI 71.7-88.4%). A total of 126 infectious agents were detected (50.0% bacteria, 38.1% viruses, 11.9% parasites). The main enteric pathogens were enteropathogen Escherichia coli (24/126), rotavirus (17/126) and Salmonella (16/126). A co-detection was found in 51.9% (40/77) of cases. Four patient profiles, considering the severity and the pathogen involved, were highlighted.

Campylobacter spp. Prevalence in Santiago, Chile: A Study Based on Molecular Detection in Clinical Stool Samples from 2014 to 2019

Campylobacter spp. is an emerging cause of infectious diarrhea worldwide. In South American countries such as Chile, its prevalence is underestimated due to inadequate detection methods. Gastrointestinal multiplex PCR panels (GMP) permit rapid and sensitive detection of bacterial pathogens and provide important epidemiological information. This study aimed to analyze Campylobacter epidemiology using the results of molecular methods and to compare molecular detection results to those of culture methods. We performed a retrospective, descriptive analysis of Campylobacter spp. detected in clinical stool samples between 2014-2019 by GMP and culture. Within 16,582 specimens examined by GMP, Campylobacter was the most prevalent enteropathogenic bacteria (8.5%), followed by Salmonella spp. (3.9%), Shigella spp./enteroinvasive Escherichia coli (EIEC) (1.9%), and Yersinia enterocolitica (0.8%). The highest Campylobacter prevalence occurred in 2014/2015. Campylobacteriosis affected more males (57.2%) and adults from 19-65 years (47.9%) and showed a bimodal seasonality with summer and winter peaks. In 11,251 routine stool cultures, Campylobacter spp. was detected in 4.6%, mostly C. jejuni (89.6%). Among 4533 samples tested by GMP and culture in parallel, GMP showed a superior sensitivity (99.1% versus 50%, respectively). The study suggests that Campylobacter spp. is the most frequent bacterial enteropathogen in Chile.

Yersiniosis: a forgotten mimicker and confounder of Crohn’s disease

Yersiniosis is a zoonosis caused by the Yersinia bacterium. The route of infection is most commonly oral and is caused by consumption of Yersinia-contaminated food. The clinical presentations of chronic yersiniosis are abdominal pain, diarrhea, relapsing arthritis, and skin lesions, that is, nodular erythema. The diagnosis is based on culture-dependent identification of Yersinia in stool, positive serologic test results, or molecular techniques. The treatment of choice is combination antibiotic therapy. Mild forms of the disease do not usually require treatment. Yersiniosis frequently mimics or confounds other chronic intestinal and extraintestinal inflammatory conditions, particularly Crohn’s disease. Therefore, diagnosis of yersiniosis may be a challenge for medical practitioners. Not including Yersinia infection in the differential diagnosis of abdominal symptoms can lead to an incorrect diagnosis and inappropriate treatment. This review summarises the current knowledge of Yersinia enterocolitica and pseudotuberculosis infection, with special focus on differential diagnosis between this infection and Crohn’s disease.

Review of the role of gastrointestinal multiplex polymerase chain reaction in the management of diarrheal illness

Acute and chronic diarrheal illness secondary to gastrointestinal infection is a significant cause of morbidity and mortality around the world. A cornerstone of management includes prompt diagnosis and appropriate treatment of culprit pathogens. Timely diagnosis can improve patient care, assist in infection control, and prevent disease outbreaks. Historical methods of diagnosis include traditional culture methods and stool analysis. These are limited by long turnaround time and inability to simultaneously assess multiple pathogens. The advent of multiplexed nucleic acid amplification tests first began with the Food and Drug Administration-approved respiratory virus multiplex polymerase chain reaction (PCR) panel in 2009, followed by gastrointestinal infections in 2013, and neurological infections in 2014. We conducted a review of current literature pertaining to the clinical utility of a gastrointestinal multiplex PCR in management of acute and chronic diarrhea in patients. To date, seven platforms approved by the US Food and Drug Administration are used in detection of various bacterial, viral, and parasitic causative organisms for diagnosis of gastrointestinal infections. The sensitivity and specificity of each assay vary depending on the tested organism. Interpretation of a positive result has to be tailored to the clinical context. Further studies are required to establish the utility of gastrointestinal multiplex PCR from a cost-based perspective, whether specific enteropathogens such as Clostridioides difficile are better assessed with toxin gene detection and whether new parameters such as cycle threshold values can improve clinical application of test results.

Alteration of gut microbial composition associated with the therapeutic efficacy of fecal microbiota transplantation in Clostridium difficile infection

BACKGROUND/PURPOSE

Clostridium difficile infection (CDI) leads to a significant cause of hospital-acquired morbidity and mortality. Fecal microbiota transplantation (FMT) is effective to treat recurrent or refractory CDI (rCDI). However, the change of microbial composition contributed by FMT and its association with treatment outcomes is not well determined in Taiwan. We aimed to investigate the efficacy of FMT and the association with microbial alteration endemically.

METHODS

Twelve patients who received FMT for rCDI in Taipei Veterans General Hospital were prospectively enrolled from April 2019 to July 2020. The clinical assessments and fecal microbial analyses in comparison with fecal materials of unrelated donors were conducted before and after FMT.

RESULTS

The overall success rate of FMT for rCDI was 91.7%. A prominence of Proteobacteria, Gammaproteobacteria and Enterobacteriales were observed in the feces of patients with rCDI. Increased fecal phylogenetic diversities and a significant microbial dissimilarity were provided by successful FMT compared to patients before treatment. However, the distinctness was not obvious between patients' feces at baseline and after unsuccessful FMT. Moreover, dynamic change of fecal microbial composition after FMT was observed during follow-up but did not interrupt the treatment effects of FMT.

CONCLUSION

Gut dysbiosis commonly co-exists in patients with rCDI. Restoration of gut microbial communities by FMT provides a promising strategy to treat antibiotic-failed CDI, and the extent of microbial change would be related to the treatment outcomes of FMT. Besides, the effectiveness of FMT for CDI could be maintained even the gut microbiota has diverged over time.

Functions and potential of lipocalin-2 as fecal biomarker for acute gastrointestinal infections (review of literature)

Despite the visible progress in reducing morbidity and mortality from intestinal infections and acute diarrhea associated with them, especially in childhood, the problem of their diagnosis and treatment remains relevant. The article discusses the structure, function and application of lipocalin-2 in infectious diseases as a non-invasive biomarker of bacterial inflammation in the intestine.

Approach to the patient with infectious colitis: clinical features, work-up and treatment

PURPOSE OF REVIEW

To provide the definition, causes, and current recommendations for workup and treatment of acute infectious colitis in adults, a common medical problem of diverse cause.

RECENT FINDINGS

The management of acute colitis in adults depend upon establishment of cause. Most forms of infectious colitis are treatable with antimicrobials. Multiplex polymerase chain reaction (PCR) followed by guided culture on PCR-positive pathogens can often confirm active infection while standard culture methods provide isolates for antibiotic susceptibility testing, subtyping, and Whole Genome Sequencing.

SUMMARY

Patients with colitis may be suffering from a range of etiologies including infectious colitis, neutropenic colitis, drug-induced colitis, and inflammatory bowel disease. The present review was prepared to provide an approach to prompt diagnosis and management of acute colitis to prevent severe complications (e.g. dehydration and malnutrition, or toxic megacolon) and provide recommendations for antimicrobial therapy.

Mapping of aetiologies of gastroenteritis: a systematic review and meta-analysis of pathogens identified using a multiplex screening array

OBJECTIVE

Emergence of molecular methods to screen stools could provide a more complete picture of pathogens causing gastroenteritis, allowing to adequately treat patients whenever required but, so far, no aggregate data have been released. Our objective was to report pathogens identified in patients suffering from gastroenteritis using a multiplex molecular array.

DESIGN

Medline and Embase were searched for original publications reporting pathogens identified with FilmArray GI panel in patients suffering from gastroenteritis. Proportions of pathogens were extracted and pooled using a model with random effects.

RESULTS

Fourteen studies (17,815 patients) were included in the analysis. Among the 7,071 patients (39.7%) with positive FilmArray, identified pathogens were EPEC (27.5%), Clostridium difficile (19.3%), Norovirus (15.1%), EAEC (15%), Campylobacter spp (11.8%), Salmonella spp (8.1%), ETEC (7.3%), Rotavirus (7.3%), Sapovirus (7.1%), STEC (5.2%), Shigella/EIEC (4.9%), Giardia lamblia (4%), Adenovirus (3.8%), Cryptosporidium spp (3.8%), Astrovirus (2.8%), Yersinia enterocolitica (1.7%), Escherichia coli O157 (1.1%), Plesiomonas shigelloides (1.1%), Cyclospora cayetanensis (0.7%), Vibrio spp (0.5%), Vibrio cholerae (0.3%) and Entamoeba histolytica (0.3%). When considering only studies with control group (microbiological examination of the stools performed by other methods), FilmArray identified at least one pathogen in 48.2% of patients versus 16.7% when using comparative diagnostic methods.

CONCLUSIONS

FilmArray GI panel was positive in 39.7% of patients suffering from gastroenteritis. This proportion has to be mitigated by the carriage rates of identified organisms. Ultimately, restricted ordering of molecular panels to those patients who might benefit from specific treatment could provide medical value by swift identification of the pathogen and more targeted therapy.

Prevalence of Enteropathogens and Virulence Traits in Brazilian Children With and Without Diarrhea

The use of molecular diagnostics for pathogen detection in epidemiological studies have allowed us to get a wider view of the pathogens associated with diarrhea, but the presence of enteropathogens in asymptomatic individuals has raised several challenges in understanding the etiology of diarrhea, and the use of these platforms in clinical diagnosis as well. To characterize the presence of the most relevant bacterial enteropathogens in diarrheal episodes, we evaluated here the prevalence of diarrheagenic E. coli pathotypes, Salmonella spp., and Yersinia enterocolitica in stool samples of children with and without diarrhea using real-time quantitative PCR (qPCR). We found that the presence of genetic markers associated with bacterial pathogens was significantly higher in stool samples from the diarrhea group compared to the control (P < 0.001). Bacterial loads in samples positive for eae and aggR markers were also determined. Compared to samples from asymptomatic children, a significantly higher number of copies of the eae gene were found in diarrhea samples. Also, the presence of genetic markers associated with STEC strains with clinical significance was evaluated in eae-positive samples by high-throughput real-time PCR. The data presented herein demonstrated that asymptomatic children of an urban area in Brazil might be enteropathogen reservoirs, especially for STEC.

Performance Evaluation of the Novodiag Bacterial GE+ Multiplex PCR Assay

The bacteriological diagnosis of intestinal bacterial infections has historically been based on culture on agar plates. However, culture may lack sensitivity, and some enteropathogens, such as pathovars of Escherichia coli, may escape routine diagnosis. Our goal was to evaluate the analytical performance of the Novodiag Bacterial GE+ kit for the detection of enteropathogenic bacteria in acute community diarrhea. We included 251 stools in this study (198 retrospective and 53 prospective). The analytical performance was calculated using a composite reference standard (CRS) in the absence of a perfect gold standard (lack of sensitivity of culture). The CRS was defined as positive if culture was positive or, in case of a negative culture, if the BD Max extended enteric bacterial panel and/or other real-time PCR (RT-PCR) tests were positive. Of the 251 samples, 200 were positive, and 51 were negative. Overall sensitivities of the Novodiag Bacterial GE+ kit for Campylobacter sp., Salmonella sp., Shigella sp./enteroinvasive E. coli (EIEC), Yersinia enterocolitica, enterohemorrhagic E. coli (EHEC), and enterotoxigenic E. coli (ETEC) ranged from 98.98 to 100%, specificities ranged from 98.08 to 100%, positive predictive values (PPVs) ranged from 88.24 to 100%, and negative predictive values (NVPs) ranged from 99.36 to 100%. The analytical performance of the Novodiag Bacterial GE+ kit is excellent. It can be used as a routine tool in the rapid diagnosis of bacterial gastroenteritis. Despite the eNAT tube dilution of the primary sample, the detection of Salmonella sp. and EHEC was perfect. The kit has the advantage of only detecting pathogenic Y. enterocolitica Its performance for Campylobacter is very satisfactory.