An Overview of the Molecular Methods in the Diagnosis of Gastrointestinal Infectious Diseases

Amjad, Muhammad

doi:10.1155/2020/8135724

Cited by 48 publications

(38 citation statements)

References 56 publications

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“…Morphological methods are frequently being executed first and then the molecular approaches are applied next. Furthermore, this trend is not an exclusive feature of oral fungal identification but is a trend in the entire field of microbiology and its subset mycology [ 8 , 76 – 79 ]. Figure 3(a ) shows that the morphological methods were the most used in the period from 2009 to 2014 and these were followed by the sugar fermentation and assimilation tests in the same period.…”

Section: Resultsmentioning

confidence: 99%

Oral mycobiome identification in atopic dermatitis, leukemia, and HIV patients – a systematic review

Sodré

Rodrigues

Vieira

et al. 2020

Journal of Oral Microbiology

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Introduction: Oral mycobiome profiling is important to understand host-pathogen interactions that occur in various diseases. Invasive fungal infections are particularly relevant for patients who have received chemotherapy and for those who have HIV infection. In addition, changes in fungal microbiota are associated with the worsening of chronic conditions like atopic dermatitis (AD). This work aims, through a systematic review, to analyze the methods used in previous studies to identify oral fungi and their most frequent species in patients with the following conditions: HIV infection, leukemia, and atopic dermatitis. Methods: A literature search was performed on several different databases. Inclusion criteria were: written in English or Portuguese; published between September 2009 and September 2019; analyzed oral fungi of HIV-infected, leukemia, or AD patients. Results: 21 studies were included and the most identified species was Candida. The predominant methods of identification were morphological (13/21) and sugar fermentation and assimilation tests (11/21). Polymerase chain reaction (PCR) was the most used molecular method (8/21) followed by sequencing techniques (3/21). Conclusions: Although morphological and biochemical tests are still used, they are associated with high-throughput sequencing techniques, due to their accuracy and time saving for profiling the predominant species in oral mycobiome.

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Section: Resultsmentioning

confidence: 99%

Oral mycobiome identification in atopic dermatitis, leukemia, and HIV patients – a systematic review

Sodré

Rodrigues

Vieira

et al. 2020

Journal of Oral Microbiology

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“…Among the multiplex NAATs that are CE marked but not FDA cleared are the Allplex™ Gastrointestinal Panel (Seegene, Seoul, South Korea), a multiplex assay with 23 targets including six parasites ( C. cayetanensis , Blastocystis sp., Cryptosporidium spp., Dientamoeba fragilis , E. histolytica , and G. duodenalis ) [ 51 ] and the QIAstat-Dx ® Gastrointestinal Panel (Qiagen, Hilden, Germany), which has 21 targets including four parasites ( C. cayetanensis , Cryptosporidium spp., E. histolytica , and G. duodenalis ) [ 51 ]. Similarly, the EasyScreen™ Enteric Protozoan Extended Detection Kit (Genetic Signatures, Newtown, Australia) has six protozoan and microsporidial targets, including C. cayetanensis .…”

Section: Molecular Diagnosismentioning

confidence: 99%

Cyclosporiasis—Updates on Clinical Presentation, Pathology, Clinical Diagnosis, and Treatment

Mathison

Pritt

2021

Microorganisms

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Cyclospora cayetanensis is an intestinal coccidian parasite transmitted to humans through the consumption of oocysts in fecally contaminated food and water. Infection is found worldwide and is highly endemic in tropical and subtropical regions with poor sanitation. Disease in developed countries is usually observed in travelers and in seasonal outbreaks associated with imported produce from endemic areas. Recently, summertime outbreaks in the United States have also been linked to locally grown produce. Cyclosporiasis causes a diarrheal illness which may be severe in infants, the elderly, and immunocompromised individuals. The increased adoption of highly sensitive molecular diagnostic tests, including commercially available multiplex panels for gastrointestinal pathogens, has facilitated the detection of infection and likely contributed to the increased reports of cases in developed countries. This manuscript reviews important aspects of the biology, epidemiology, and clinical manifestations of C. cayetanensis and provides an in-depth discussion of current laboratory diagnostic methods.

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“…Culturing most viruses that cause diarrhea is difficult. Other techniques for virus identification such as electron microscopy and immunoassay demand special expertise which is often lacking in many clinical diagnostic laboratories [ 5 , 6 ].…”

Section: Introductionmentioning

confidence: 99%

“…Multiplex polymerase chain reaction (PCR) based testing has been recently added to the list of microbiological diagnostic tools for several infectious diseases. It allows rapid and simultaneous amplification of several targets with good sensitivity and specificity [ 5 , 7 ]. Although used in some tertiary hospitals in the UAE, this method, has not yet been evaluated at a population level, where co-infections, as well as asymptomatic carriage of pathogens may exist.…”

Section: Introductionmentioning

confidence: 99%

Etiology of diarrhea by multiplex polymerase chain reaction among young children in the United Arab Emirates: a case-control study

et al. 2021

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Background Little is known about the etiology of childhood diarrhea in the United Arab Emirates (UAE) especially after the introduction of rotavirus vaccines. This study aimed to identify gastrointestinal pathogens in children with diarrhea (cases) and the carriage rate of these pathogens in asymptomatic children (controls). Methods Stool samples were collected from 203 cases and 73 controls who presented to two major hospitals in Al Ain city, UAE. Samples were analyzed with Allplex™ Gastrointestinal Full Panel Assay for common entero-pathogens. The association between diarrhea and the isolated pathogens was calculated in a multivariate logistic regression model. The adjusted attributable fractions (aAFs) were calculated for all pathogens significantly associated with cases. Results At least one pathogen was identified in 87 samples (42.8%) from cases and 17 (23.3%) from controls (P < 0.001). Rotavirus, norovirus GII and adenovirus were significantly more prevalent in cases. Their aAFs with 95% ci are 0.95 (0.64, 1.00) for rotavirus, 0.86 (0.38, 0.97) for norovirus GII and 0.84 (0.29, 0.96) for adenovirus. None of the 13 bacteria tested for were more commonly found in the cases than in controls. Cryptosporidium spp. were more significantly detected in cases than in controls. Co-infections occurred in 27.9% of the children. Viruses and parasites were significantly more likely to occur together only in the cases. Conclusions Multiplex PCR revealed high positivity rates in both cases and controls which demand a cautious interpretation. Rotavirus remains the main childhood diarrhea pathogen in UAE. Effective strategies are needed to better control rotavirus and other causative pathogens.

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An Overview of the Molecular Methods in the Diagnosis of Gastrointestinal Infectious Diseases

Cited by 48 publications

References 56 publications

Oral mycobiome identification in atopic dermatitis, leukemia, and HIV patients – a systematic review

Oral mycobiome identification in atopic dermatitis, leukemia, and HIV patients – a systematic review

Cyclosporiasis—Updates on Clinical Presentation, Pathology, Clinical Diagnosis, and Treatment

Etiology of diarrhea by multiplex polymerase chain reaction among young children in the United Arab Emirates: a case-control study

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