Multiplex polymerase chain reaction tests for detection of pathogens associated with gastroenteritis

Assessing the burden of viral co-infections in acute gastroenteritis in children: An eleven-year-long investigation

BACKGROUND

Acute gastroenteritis is an important cause of childhood morbidity and mortality worldwide. A number of pathogens are responsible for human acute gastroenteritis. The recent introduction of syndromic assays for the diagnosis of enteric infections, including a wide panel of enteric pathogens, has unveiled the frequency of mixed infections. This study was carried out to assess the burden of viral co-infections and the genetic diversity of the viruses detected in children hospitalized with acute gastroenteritis in Italy.

METHODS

A total of 4161 stool samples collected from diarrheic children over 11 years, from January 2008 to December 2018, were investigated for the presence of four enteric viruses, i.e. group A rotavirus, norovirus, astrovirus and adenovirus. The samples were initially screened by either molecular or immunochromatographic assays and subsequently confirmed by Real-time PCR and sequence analyses.

RESULTS

At least one viral agent was detected in 48.6 %of specimens. Rotavirus was the most prevalent virus (24.7 %) followed by norovirus (19.6 %), adenovirus (5.3 %) and astrovirus (3%). Co-infections were detected in 8.3 % of virus-positive patients, with common viral combination being rotavirus with norovirus (70.6 % of co-infections) or with astrovirus (9.6 %). A variety of viral genotypes was detected in co-infections and in single infections. Using Real-time PCR cycle thresholds as a proxy measure of fecal viral load, rotavirus was generally detected at higher levels in co-infected patients.

CONCLUSIONS

Combining and deciphering measurable indicators of viral load and epidemiological information could be useful for an accurate interpretation of viral co-infections.

Bacterial Imprinting Methods and Their Applications: An Overview

Microbial contaminations and infections are hazardous and pose crucial concerns for humans. They result in severe morbidity and mortality around the globe. Even though dish-culturing, polymerase chain reaction (PCR), an enzyme-linked immunosorbent assay (ELISA) exhibits accurate and reliable detection of bacteria but these methods are time-consuming, laborious, and expensive. This warrants early detection and quantification of bacteria for timely diagnosis and treatment. Bacteria imprinting ensures a solution for selective and early detection of bacteria by snagging them inside their imprinted cavities. This review provides an insight into MIPs based bacterial detection strategies, challenges, and future perspectives.

Development and evaluation of a multiplex conventional reverse-transcription polymerase chain reaction assay for detection of common viral pathogens causing acute gastroenteritis

Timely identification of etiological agents of enteric infections is necessary to reduce the burden of infantile diarrheal mortality. Nucleic acid amplification-based detection methods offer a quick, reliable way for diagnosis of microbes in clinical specimens. This study was undertaken to evaluate an easy-to-use, cost-effective multiplex conventional reverse-transcription polymerase chain reaction (RT-PCR) assay developed at the Indian Council of Medical Research-National Institute of Cholera and Enteric Diseases virology laboratory to identify 4 common enteric viruses (rotavirus, norovirus, adenovirus, astrovirus) in stool samples from patients who were being evaluated for acute diarrhea. On comparison with a commercially available real-time PCR method, significant agreement in sensitivity and specificity was observed. Though the turnaround time for RT-PCR was 6-8 h compared to 5-6 h for real-time PCR, the real-time PCR has high test cost (approximately 28 USD/2000 INR) for Fast-Track Diagnostics kit-based quantitative RT-PCR versus 6 USD or 400 INR for conventional multiplex RT-PCR/sample. Thus, the conventional RT-PCR method is expected to be adaptable at local hospitals and health cares in resource-poor settings.

Performance of the QIAstat-Dx Gastrointestinal Panel for Diagnosing Infectious Gastroenteritis

Detection and identification of enteropathogens that cause infectious gastroenteritis are essential steps for appropriate patient treatment and effective isolation precautions. Several syndrome-based tests have recently become available, with the gastrointestinal panel (GIP) assay on the QIAstat-Dx as the most recent addition to the syndromic testing landscape.

Detection and identification of enteropathogens that cause infectious gastroenteritis are essential steps for appropriate patient treatment and effective isolation precautions. Several syndrome-based tests have recently become available, with the gastrointestinal panel (GIP) assay on the QIAstat-Dx as the most recent addition to the syndromic testing landscape. The QIAstat-Dx GIP assay offers simultaneous testing for 24 bacterial, viral, and parasitic enteropathogens using a single test that reports the results in 70 min. In this study, we compared the performance of the GIP assay to laboratory-developed real-time PCR assays (LDTs), using 172 prospectively and retrospectively collected fecal samples from patients suspected to have infectious gastroenteritis. The GIP assay detected 97/107 enteropathogens (91%) that were detected by LDTs, and the overall agreement of results increased to 95% when excluding discrepant results with cycle threshold (C_T) values of >35. Further, the GIP assay detected 42 additional enteropathogens that were not detected, or tested, by LDTs. These included 35 diarrheagenic Escherichia coli targets for which the clinical relevance is unclear for most. The main advantage of the QIAstat-Dx system compared to other syndromic testing systems is the ability to generate C_T values that could help with the interpretation of results. However, compared to LDTs, the GIP assay is limited by flexibility and high-throughput testing. In conclusion, the GIP assay offers an easy, sample-to-answer workflow with a rapid detection of the most common enteropathogens and therefore has the potential to direct appropriate therapy and infection control precautions.

Inflammatory bowel disease masquerading as traveller's diarrhoea

Diarrhoea that occurs during or after recent travel is predominantly infectious in nature; however, in atypical or prolonged cases a broader range of aetiologies for diarrhoea must be considered, and a careful history and examination may reveal clues to more sinister causes of diarrhoea. We report two cases in which a recent travel history and a positive stool culture or polymerase chain reaction testing for bacterial pathogens delayed the diagnosis of ulcerative colitis. As a result of severe inflammatory bowel disease, colectomy was the final result in both cases. Early consideration of causes other than infection for traveller's diarrhoea may prevent unnecessary morbidity in young patients.

Application of biological variation and six sigma models to evaluate analytical quality of six HbA1c analyzers and design quality control strategy

Objective: To apply biological variation and six Sigma models to evaluate analysis performance of 6 HbA_1c analyzers and design the new quality control strategy. Method: We collected data of imprecision and inaccuracy from routine internal quality control (June 2017-December 2017) and proficiency test of NGSP, respectively. The coefficient of variance (CV)% and bias% were plotted in the biological variation and six sigma models. The new quality control strategy was designed by the sigma value and OPSpecs. The quality improvement was guided by the QGI. Results: The analytical performance of 6 HbA_1c analyzers in our laboratory were good in the routine model, However, 50% (3/6) and 67% (4/6) of the HbA_1c analyzers reached the acceptable level in the biological variation and six Sigma model, respectively. We also design personalized control strategy and promote quality improvement by combining the sigma value, OPSpecs, and QGI. Conclusions: Biological variation model and six sigma model could visually display the performance of 6 HbA_1c analyzers and personalized control strategy could be designed based on the sigma value, OPSpecs, and QGI.

Clinical Guideline Highlights for the Hospitalist: Clostridium difficile Infections in Children

GUIDELINE TITLE

Clinical Practice Guidelines for Clostridium difficile Infection in Adults and Children: 2017 Update by the Infectious Diseases Society of America (IDSA) and Society for Healthcare Epidemiology of America (SHEA).

RELEASE DATE

February 15, 2018 PRIOR VERSIONS: Cohen SH, Gerding DN, Johnson S, et al; Society for Healthcare Epidemiology of America; Infectious Diseases Society of America. Clinical practice guidelines for Clostridium difficile infection in adults: 2010 update by the Society for Healthcare Epidemiology of America (SHEA) and the Infectious Diseases Society of America (IDSA). Infect Control Hosp Epidemiol. 2010; 31:431-55.Gerding DN, Johnson S, Peterson LR, et al. Clostridium difficile-associated diarrhea and colitis. Infect Control Hosp Epidemiol 1995;16:459-477.

DEVELOPER

IDSA and SHEA.

FUNDING SOURCE

Support for this guideline was provided by the IDSA and SHEA.

TARGET POPULATION

Children and adults with Clostridium difficile infections.

Simultaneous Detection of Multiple Pathogenic Targets with Stem-Tagged Primer Sets

Simultaneous multiple gene detection is indispensable for the detection of various genes in a small sample obtained by an invasive method. A typical detection method is probe-based fluorescence melting curve analysis by means of real-time PCR. It is very limited because, for each target, a probe sequence with at least a different T_m must be designed. To overcome this limitation, we developed a simultaneous multiple gene detection method based on a giant amplicon molecular beacon. PCR was performed by attaching stem sequences with different T_m values to each primer set, and the melting T_m was measured by hybridizing the stem sequences at both ends of the amplified amplicon; this generated well-separated T_m signals. The important point here is that the stem sequence that produces the T_m signal is an arbitrarily selectable sequence unrelated to the target gene. Because it is arbitrarily selectable, the desired T_m can be freely adjusted. As a result, we succeeded in the simultaneous detection of four samples with the use of only one fluorophore. Theoretically, a combination of five fluorophores could detect more than 20 multiple genes simultaneously.

Primary care physician knowledge, attitudes, and diagnostic testing practices for norovirus and acute gastroenteritis

BACKGROUND

Norovirus is a leading cause of acute gastroenteritis (AGE) across the age spectrum; candidate vaccines are in clinical trials. While norovirus diagnostic testing is increasingly available, stool testing may not be performed routinely, which can hamper surveillance and burden of disease estimates. Additionally, lack of knowledge of the burden of disease may inhibit provider vaccine recommendations, which could affect coverage rates and ultimately the impact of the vaccine. Our objectives were to understand physicians' stool testing practices in outpatients with AGE, and physician knowledge of norovirus, in order to improve surveillance and prepare for vaccine introduction.

METHODS

Internet and mail survey on AGE, norovirus, and future norovirus vaccines conducted January to March 2018 among national networks of primary care pediatricians, family practice and general internal medicine physicians.

RESULTS

The response rate was 59% (820/1383). During peak AGE season, physicians estimated they ordered stool tests for a median of 15% (interquartile range: 5-33%) of their outpatients with AGE. Stool tests were reported as more often available for ova and parasites, Clostridioides difficile, and bacterial culture (>95% for all specialties) than for norovirus (6-33% across specialties); even when available, norovirus-specific tests were infrequently ordered. Most providers were unaware that norovirus is a leading cause of AGE across all age groups (Pediatricians 80%, Family Practice 86%, General Internal Medicine 89%) or that alcohol-based hand sanitizers are ineffective against norovirus (Pediatricians 51%, Family Practice 66%, General Internal Medicine 62%). Concerns cited as major barriers to implementing a future norovirus vaccine included if the vaccine is not covered by insurance (General Internal Medicine 64%, Pediatricians 67%, Family Practice 74%) and lack of adequate reimbursement for vaccination (Pediatricians 43%, General Internal Medicine 46%, Family Practice 50%). Factors that providers believed were 'not at all a barrier' or 'minor barrier' to new vaccine introduction included the belief that "my patients won't need this vaccine" (General Internal Medicine 78%, Family Practice 86%, Pediatricians 90%) and "my patients already get too many vaccines" (Family Practice 89%, General Internal Medicine 92%, Pediatricians 95%).

CONCLUSIONS

Primary care physicians had few concerns regarding future norovirus vaccine introduction, but have knowledge gaps on norovirus prevalence and hand hygiene for prevention. Also, physicians infrequently order stool tests for outpatients with AGE, which limits surveillance estimates that rely on physician-ordered stool diagnostics. Closing physician knowledge gaps on norovirus burden and transmission can help support norovirus vaccine introduction.

Gastroenteritis, Viral

Viral gastroenteritis (VGE) is an acute, self-limiting gastrointestinal infection caused by several viruses which most often trigger nausea, vomiting, abdominal pain and diarrhea. It is one of the most common human illnesses with its greatest impact on the very young and elderly. In the developing world, VGE can be life threatening whereas in most developed countries, it is self-limited and managed with hydration. Most agents of VGE are spread by the fecal oral route or may occur in explosive outbreaks due to food or water contamination. Control of these infections depends upon proper food handling, hand hygiene, clean water and the rotavirus vaccination of infants. This chapter will discuss the common viruses which cause this syndrome.

Development and evaluation of a Luminex xTAG assay for sulfonamide resistance genes in Escherichia coli and Salmonella isolates

Clinically occurring sulfonamide resistance in gram-negative bacteria is codified by several sul genes, mostly associated with the mobilized genetic elements named integrons, and integrons are frequently found in plasmids. There are four sul genes (sul1, sul2, sul3 and sul4) that encode resistance to sulfonamides. The aim of the present study was to develop a bead-based xTAG assay for the simultaneous detection of all four sul genes and related Class 1 integrons (int1) in Escherichia coli and Salmonella isolates. The limits of detection ranged from 10 to 1000 copies/μL of input purified plasmid DNA. Forty-one bacterial isolates from clinical samples were examined using the newly developed xTAG assay and also by conventional PCR to determine the relative performance of each. The results obtained by xTAG assay showed higher detection rates and accuracy for sul genes than conventional PCR. It indicated that the xTAG-multiplex PCR is a convenient method for rapid identification of sul genes.

Development of multiplex PCR for neglected infectious diseases

Scrub typhus, murine typhus, and leptospirosis are widely neglected infectious diseases caused by Orientia tsutsugamushi, Rickettsia typhi, and pathogenic Leptospira spp., respectively. Patients usually present with non-specific symptoms and therefore are commonly diagnosed with acute undifferentiated febrile illness. Consequently, patients face delayed treatment and increased mortality. Antibody-based serological test currently used as gold standard has limitations due to insufficient antibody titers, especially in the early phase of infection. In this study, we aimed to develop multiplex PCR to combine 3 primer pairs that target specific genes encoding 56-kDa TSA of O. tsutsugamushi, 17-kDa antigen of R. typhi, and LipL32 of L. Interrogans and evaluate its performance in comparison to the standard serological tests. Using EDTA blood samples of known patients, the sensitivity and specificity of our multiplex PCR was 100% and 70%, respectively. In addition, the assay was able to diagnose the co-infection of scrub typhus and leptospirosis. The assay may be useful in identifying causative agents during the early phase of these diseases, enabling prompt and appropriate treatment.

Scrub typhus, murine typhus, and leptospirosis are diagnosed as acute undifferentiated febrile illness. Diagnostic tests for these diseases depend on antibody detection. However, antibody detection is still limited by its tendency to return negative results during the early phase of aforementioned diseases. In this study, a novel multiplex PCR has been developed for detecting Orientia tsutsugamushi, Rickettsia typhi, and Leptospira interrogans that are simultaneously amplified in a single tube. The results have shown that multiplex PCR could be used as a diagnostic tool for detecting bacteria during the early phase of scrub typhus, murine typhus, and leptospirosis, allowing for administration of appropriate treatment.

Parasites in Human Stool: To Ignore or Not To Ignore?

Human stool contains a myriad of microorganisms, of which the vast majority are nonpathogenic and represent an important component of the healthy microbiome. The increasing use of molecular techniques has allowed the rapid identification of bacteria, viruses and parasites in human stool. This review focuses on the 3 main classes of parasite responsible for human disease, helminths, protozoa and ectoparasites, and highlights the importance of differentiating between pathogenic and nonpathogenic parasites.

Future management of viral diseases: role of new technologies and new approaches in microbial interactions

BACKGROUND

New technologies allow rapid detecting and counting of virus genomes in clinical specimens, defining susceptibility to specific antivirals, pinpointing molecular sequences correlated to virulence traits, and identifying viral and host factors driving resolution or chronicity of infections. As a result, during the past three decades the diagnostic virology laboratory has become crucial for patient care and an integral component of the multifarious armamentarium for patient management. This change in paradigm has caused obsolescence of methods once considered the reference standard of infectious disease diagnosis that were used to detect whole or specific components of virions in the specimen.

OBJECTIVES

This review provides an overview of standard and novel technologies applied to molecular diagnosis of viral infections and illustrates some crucial points for correcting interpretation of the laboratory data.

SOURCES

Peer-reviewed literature of topics pertinent to this review.

CONTENT AND IMPLICATIONS

New technologies are reinventing the way virologic diagnoses are made, with a conversion to new, simpler-to-use platforms. Although indicated for the same purpose, not all methods are equal and can yield different results. Further, tests identifying multiple analytes at once can detect microorganisms present or activated as a result of pathologic processes triggered by other pathogens or noninfectious causes. Thus, new directions will have to be taken in the way in which the diagnoses of viral diseases are performed. This represents a breakthrough in the clinical virology laboratory.

Post-mortem microbiology in sudden death: sampling protocols proposed in different clinical settings

BACKGROUND

Autopsies, including minimally invasive autopsies, are a powerful tool for determination of the cause of death. When a patient dies from an infection, microbiology is crucial to identify the causative organism. Post-mortem microbiology (PMM) aims to detect unexpected infections causing sudden deaths; confirm clinically suspected but unproven infection; evaluate the efficacy of antimicrobial therapy; identify emergent pathogens; and recognize medical errors. Additionally, the analysis of the thanatomicrobiome may help to estimate the post-mortem interval.

AIMS

The aim was to provide advice in the collection of PMM samples and to propose sampling guidelines for microbiologists advising autopsy pathologists facing different sudden death scenarios.

SOURCES

A multidisciplinary team with experts in various fields of microbiology and autopsies on behalf of the ESGFOR (ESCMID - European Society of Clinical Microbiology and Infectious Diseases - study group of forensic and post-mortem microbiology and in collaboration with the European Society of Pathology) developed this narrative review based on a literature search using MedLine and Scopus electronic databases supplemented with their own expertise.

CONTENT

These guidelines address measures to prevent sample contamination in autopsy microbiology; general PMM sampling technique; protocols for PMM sampling in different scenarios and using minimally invasive autopsy; and potential use of the evolving post-mortem microbiome to estimate the post-mortem interval.

IMPLICATIONS

Adequate sampling is paramount to identify the causative organism. Meaningful interpretation of PMM results requires careful evaluation in the context of clinical history, macroscopic and histological findings. Networking and closer collaboration among microbiologists and autopsy pathologists is vital to maximize the yield of PMM.

Automated Real-Time Collection of Pathogen-Specific Diagnostic Data: Syndromic Infectious Disease Epidemiology

Background

Health care and public health professionals rely on accurate, real-time monitoring of infectious diseases for outbreak preparedness and response. Early detection of outbreaks is improved by systems that are comprehensive and specific with respect to the pathogen but are rapid in reporting the data. It has proven difficult to implement these requirements on a large scale while maintaining patient privacy.

Objective

The aim of this study was to demonstrate the automated export, aggregation, and analysis of infectious disease diagnostic test results from clinical laboratories across the United States in a manner that protects patient confidentiality. We hypothesized that such a system could aid in monitoring the seasonal occurrence of respiratory pathogens and may have advantages with regard to scope and ease of reporting compared with existing surveillance systems.

Methods

We describe a system, BioFire Syndromic Trends, for rapid disease reporting that is syndrome-based but pathogen-specific. Deidentified patient test results from the BioFire FilmArray multiplex molecular diagnostic system are sent directly to a cloud database. Summaries of these data are displayed in near real time on the Syndromic Trends public website. We studied this dataset for the prevalence, seasonality, and coinfections of the 20 respiratory pathogens detected in over 362,000 patient samples acquired as a standard-of-care testing over the last 4 years from 20 clinical laboratories in the United States.

Results

The majority of pathogens show influenza-like seasonality, rhinovirus has fall and spring peaks, and adenovirus and the bacterial pathogens show constant detection over the year. The dataset can also be considered in an ecological framework; the viruses and bacteria detected by this test are parasites of a host (the human patient). Interestingly, the rate of pathogen codetections, on average 7.94% (28,741/362,101), matches predictions based on the relative abundance of organisms present.

Conclusions

Syndromic Trends preserves patient privacy by removing or obfuscating patient identifiers while still collecting much useful information about the bacterial and viral pathogens that they harbor. Test results are uploaded to the database within a few hours of completion compared with delays of up to 10 days for other diagnostic-based reporting systems. This work shows that the barriers to establishing epidemiology systems are no longer scientific and technical but rather administrative, involving questions of patient privacy and data ownership. We have demonstrated here that these barriers can be overcome. This first look at the resulting data stream suggests that Syndromic Trends will be able to provide high-resolution analysis of circulating respiratory pathogens and may aid in the detection of new outbreaks.

Detection of Norovirus by BD MAX™, Xpert® Norovirus, and xTAG® Gastrointestinal Pathogen Panel in stool and vomit samples

BACKGROUND

Norovirus is a leading cause of infectious gastroenteritis, characterized by outbreaks of diarrhoea and vomiting in closed settings. Nucleic acid amplification tests allow rapid and sensitive laboratory diagnosis of norovirus, with a number of commercial platforms now available.

OBJECTIVES

Evaluate the performance of the Becton Dickinson BD-MAX™System, Cepheid Xpert® Norovirus Assay, and Luminex xTAG® Gastrointestinal Pathogen Panel (GPP) for norovirus detection in stool. Assess the performance of the Xpert® Norovirus Assay and BD-MAX™ in vomit samples.

STUDY DESIGN

163 diarrhoeal stool samples were tested on four diagnostic systems (laboratory-defined real time RT-PCR (assigned as gold standard), BD MAX™, Xpert® Norovirus Assay, and xTAG® GPP). A further 70 vomit samples were tested on the Xpert and BD MAX platforms.

RESULTS

In stool, sensitivity and specificity of the BD-MAX™ was 96.8% and 100%, for Xpert® Norovirus Assay was 91.9% and 100%, and for xTAG® GPP was 79.0% and 87.1%. In vomit samples positive and negative percent agreement was 95.6% and 92.0%, between the BD-MAX™ and Xpert® Norovirus.

CONCLUSIONS

The BD-MAX™ System with user defined settings and the Xpert® Norovirus Assay showed acceptable sensitivity and specificity for detection of norovirus from stool and vomit. The xTAG GPP assay was less reliable for norovirus detection but can detect a number of other clinically useful enteropathogens. Clinical laboratories must consider skill mix, budget, and sample throughput to determine the best fit for their service.

Contribution of the FilmArray® Gastrointestinal Panel in the laboratory diagnosis of gastroenteritis in a cohort of children: a two-year prospective study

This study represents a 2-year picture of the epidemiology of enteric pathogens in children suffering from gastroenteritis using the FilmArray® Gastrointestinal Panel (FA-GP), a multiplex molecular assay that allows to simultaneously detect a large panel of pathogens independently of the etiological suspicion and to evaluate its potential contribution to the diagnosis compared to the conventional methods. A total of 1716 stool samples, collected from children with clinical suspicion of bacterial and/or viral gastroenteritis attending the University Hospital of Parma, was submitted to the FA-GP and, when an adequate aliquot was available, to electron microscopy (n = 1163) for virus detection and to an enterovirus-targeting real-time PCR (n = 1703). Specimens with positive results for Salmonella, Yersinia enterocolitica, Vibrio, diarrheagenic Escherichia coli/Shigella, Campylobacter, Plesiomonas shigelloides and/or parasites by the FA-GP were also submitted to conventional diagnostic methods. The FA-GP gave positive results in 958 (55.8%) cases, 64.8% from inpatients: 647 (67.5%) contained a single agent and 311 (32.5%) multiple agents, for a total of 1374 pathogens. Enteropathogenic E. coli, rotavirus, norovirus, toxigenic Clostridioides difficile, and sapovirus were the most commonly detected pathogens. A total of 812 additional agents (344 of which as single pathogen) was detected by the FA-GP and not included in the clinical suspicion. The overall recovery rate of the conventional methods from stools that resulted positive by the FA-GP was 38.6% for bacteria, 50% and 84.2% for Giardia intestinalis and Cryptosporidium, respectively, and ranged from 3.7% to 64.6% for viruses, if excluding all electron microscopy-negative astroviruses. Enterovirus, an agent not targeted by the FA-GP, was revealed in 9.6% (164/1703) of the examined samples, and in 52 cases it was the only agent detected. The results of this study allowed to extend the range of detectable pathogens independently of the clinical suspicion, to detect co-infections in almost one third of children positive for at least one agent and to show that conventional methods would have missed more than half of the enteric agents detected by the FA-GP.

Enhanced culture recovery of Campylobacter with modified Cary-Blair medium: A practical field experience

Modified Cary-Blair medium derived devices have been implemented in many laboratories to optimize culture recovery of common bacterial enteric pathogens. Our analysis constitutes the first report of routine laboratory experience supporting the idea that the use of such devices enhances Campylobacter recovery from stools.

Rapid diagnosis of parasitic diseases: current scenario and future needs

BACKGROUND

Parasitic diseases are one of the world's most devastating and prevalent infections, causing millions of morbidities and mortalities annually. In the past, many of these infections have been linked predominantly to tropical or subtropical areas. Nowadays, however, climatic and vector ecology changes, a significant increase in international travel, armed conflicts, and migration of humans and animals have influenced the transmission of some parasitic diseases from 'book pages' to reality in developed countries. It has also been noted that many patients who have never travelled to endemic areas suffer from blood-borne infections caused by protozoa. In the light of existing knowledge, this new trend can be explained by the fact that in the process of migration a large number of asymptomatic carriers become a part of the blood bank donor and transplant donor populations. Accurate and rapid diagnosis represents the crucial weapon in the fight against parasitic infections.

AIMS

To review old and new approaches for rapid diagnosis of parasitic infections.

SOURCES

Data for this review were obtained through searches of PubMed using combinations of the following terms: parasitological diagnostics, microscopy, lateral flow assays, immunochromatographic assays, multiplex-PCR, and transplantation.

CONTENT

In this review, we provide a brief account of the advantages and limitations of rapid methods for diagnosis of parasitic diseases and focus our attention on current and future research in this area. The approximate costs associated with the use of different techniques and their applicability in endemic and non-endemic areas are also discussed.

IMPLICATIONS

Microscopy remains the cornerstone of parasitological diagnostics, especially in the field and low-resource settings, and provides epidemiological assessment of parasite burden. However, increased use and availability of point-of-care tests and molecular assays in modern era allow more rapid and accurate diagnoses and increased sensitivity in the identification of parasitic infections.

Clinical Practice Guidelines for Clostridium difficile Infection in Adults and Children: 2017 Update by the Infectious Diseases Society of America (IDSA) and Society for Healthcare Epidemiology of America (SHEA)

A panel of experts was convened by the Infectious Diseases Society of America (IDSA) and Society for Healthcare Epidemiology of America (SHEA) to update the 2010 clinical practice guideline on Clostridium difficile infection (CDI) in adults. The update, which has incorporated recommendations for children (following the adult recommendations for epidemiology, diagnosis, and treatment), includes significant changes in the management of this infection and reflects the evolving controversy over best methods for diagnosis. Clostridium difficile remains the most important cause of healthcare-associated diarrhea and has become the most commonly identified cause of healthcare-associated infection in adults in the United States. Moreover, C. difficile has established itself as an important community pathogen. Although the prevalence of the epidemic and virulent ribotype 027 strain has declined markedly along with overall CDI rates in parts of Europe, it remains one of the most commonly identified strains in the United States where it causes a sizable minority of CDIs, especially healthcare-associated CDIs. This guideline updates recommendations regarding epidemiology, diagnosis, treatment, infection prevention, and environmental management.

Investigation and Analysis of Hemoglobin A1c Measurement Systems' Performance for 135 Laboratories in China

Background:

Hemoglobin A1c (HbA1c) measurement is of great value for the diagnosis and monitoring of diabetes. Many manufacturers have developed various experiments to determine the HbA1c concentration. However, the longitudinal use of these tests requires strict quality management. This study aimed to analyze the quality of HbA1c measurement systems in China using six sigma techniques to help improve their performances.

Methods:

A total of 135 laboratories were involved in this investigation in 2015. Bias values and coefficients of variation were collected from an HbA1c trueness verification external quality assessment program and an internal quality control program organized by the National Center of Clinical Laboratories in China. The sigma (σ) values and the quality goal index (QGI) were used to evaluate the performances of different groups, which were divided according to principles and instruments.

Results:

The majority of participants (88, 65.2%) were scored as “improvement needed (σ < 3)”, suggesting that the laboratories needed to improve their measurement performance. Only 8.2% (11/135) of the laboratories were scored as “world class (σ ≥ 6)”. Among all the 88 laboratories whose σ values were below 3, 52 (59.1%) and 23 (26.1%) laboratories needed to improve measurement precision (QGI <8.0) and trueness (QGI >1.2), respectively; the remaining laboratories (13, 14.8%) needed to improve both measurement precision and trueness. In addition, 16.1% (5/31) and 15.0% (3/20) of the laboratories in “TOSOH” and “ARKRAY” groups, respectively, were scored as “world class”, whereas none of the laboratories in “BIO-RAD” group were scored as “world class”.

Conclusions:

This study indicated that, although participating laboratories were laboratories with better performance in China, the performances were still unsatisfactory. Actions should be taken to improve HbA1c measurement performance before we can include HbA1c assays in diabetes diagnosis in China.

Interpretation and Relevance of Advanced Technique Results

Advanced techniques in the field of diagnostic microbiology have made amazing progress over the past 25 years due largely to a technological revolution in the molecular aspects of microbiology [1, 2]. In particular, rapid molecular methods for nucleic acid amplification and characterization combined with automation in the clinical microbiology laboratory as well as user-friendly software and robust laboratory informatics systems have significantly broadened the diagnostic capabilities of modern clinical microbiology laboratories. Molecular methods such as nucleic acid amplification tests (NAATs) rapidly are being developed and introduced in the clinical laboratory setting [3, 4]. Indeed, every section of the clinical microbiology laboratory, including bacteriology, mycology, mycobacteriology, parasitology, and virology, has benefited from these advanced techniques. Because of the rapid development and adaptation of these molecular techniques, the interpretation and relevance of the results produced by such molecular methods continues to lag behind. The purpose of this chapter is to review, update, and discuss the interpretation and relevance of results produced by these advanced molecular techniques.

Multiplex PCR for Detection and Identification of Microbial Pathogens

 Multiplexed nucleic acid-based tests for infectious disease have become a standard part of clinical laboratory practice. These tests provide a comprehensive syndrome-based approach to determine the etiological agent of disease. The technology underlying these different systems is reviewed here with a special focus on the BioFire FilmArray® platform. The literature on the clinical utility and cost-effectiveness of these platforms for respiratory, blood culture, and gastrointestinal infections is discussed. Although there are reports showing a clear benefit to the patient or to the healthcare system from adopting a syndromic molecular approach, it is also apparent that clinical laboratories and healthcare providers are still learning how to take full advantage of the new systems. Finally, some improvements to this technology that should appear in the next few years are discussed. These include automated pathogen-specific surveillance based on aggregating the data from these systems, a move toward point-of-care syndromic testing, and further decreases in time to result of the tests.

Laboratory diagnosis of cryptosporidiosis

Cryptosporidiosis is a major etiology of persistent and chronic diarrhea in children and immunocompromised patients. In addition, it is also one of the important pathogens causing zoonotic or waterborne outbreaks. A number of conventional and molecular tests are available, but each test is riddled with few limitations. Further, there is a need to develop point of care tests and multiplexed tests for simultaneous detection of multiple pathogens.

Portable device for the detection of colorimetric assays

In this work, a low-cost, portable device is developed to detect colorimetric assays for in-field and point-of-care (POC) analysis. The device can rapidly detect both pH values and nitrite concentrations of five different samples, simultaneously. After mixing samples with specific reagents, a high-resolution digital camera collects a picture of the sample, and a single-board computer processes the image in real time to identify the hue-saturation-value coordinates of the image. An internal light source reduces the effect of any ambient light so the device can accurately determine the corresponding pH values or nitrite concentrations. The device was purposefully designed to be low-cost, yet versatile, and the accuracy of the results have been compared to those from a conventional method. The results obtained for pH values have a mean standard deviation of 0.03 and a correlation coefficient R2 of 0.998. The detection of nitrites is between concentrations of 0.4-1.6 mg l-1, with a low detection limit of 0.2 mg l-1, and has a mean standard deviation of 0.073 and an R2 value of 0.999. The results represent great potential of the proposed portable device as an excellent analytical tool for POC colorimetric analysis and offer broad accessibility in resource-limited settings.

Portable device for the detection of colorimetric assays

In this work, a low-cost, portable device is developed to detect colorimetric assays for in-field and point-of-care (POC) analysis. The device can rapidly detect both pH values and nitrite concentrations of five different samples, simultaneously. After mixing samples with specific reagents, a high-resolution digital camera collects a picture of the sample, and a single-board computer processes the image in real time to identify the hue-saturation-value coordinates of the image. An internal light source reduces the effect of any ambient light so the device can accurately determine the corresponding pH values or nitrite concentrations. The device was purposefully designed to be low-cost, yet versatile, and the accuracy of the results have been compared to those from a conventional method. The results obtained for pH values have a mean standard deviation of 0.03 and a correlation coefficient R² of 0.998. The detection of nitrites is between concentrations of 0.4-1.6 mg l^-1, with a low detection limit of 0.2 mg l^-1, and has a mean standard deviation of 0.073 and an R² value of 0.999. The results represent great potential of the proposed portable device as an excellent analytical tool for POC colorimetric analysis and offer broad accessibility in resource-limited settings.

Evaluation of the multiplex PCR Allplex-GI assay in the detection of bacterial pathogens in diarrheic stool samples

Rapid and accurate detection of the pathogens that cause gastrointestinal infection is important for appropriate therapy and proper infection control. This study assesses the performance of a new molecular assay for simultaneous detection of 13 different gastrointestinal bacteria in stool specimens. Using the Allplex GI-Bacteria (AGI-BI/AGI-BII) assay, a total of 394 stool samples were tested and the results were compared with culturing on selective differential followed by identification by mass spectroscopy. Discordant results were analyzed by a different multiplex PCR method, the Fast-Track Diagnostics Bacterial gastroenteritis (FTD-BG). The routine method (RM) detected 109 (27.7%) positive samples and the Allplex-GI assay, 261 (66.2%). Analysis of discordant results revealed that the molecular assay detected 44 pathogens that were not detected by the RM, including 23 Campylobacter spp., 11 Salmonella spp, 3 Y. enterocolitica, 2 EIEC/Shigella spp, 2 E. coli 0157, 2 C. difficile and 1 Aeromonas spp. Five cases not detected by the molecular method were detected by the RM (3 Aeromonas spp, 1 Salmonella spp and 1 Y. enterocolitica). For all targets, the percentages of sensitivity and specificity were >95%, except for Aeromonas spp., which were 81% and 99% respectively. This study suggests that Allplex-GI multiplex PCR is a sensitive and specific assay that enables a rapid and accurate diagnosis of bacterial gastrointestinal infections.

A Decade of Development of Chromogenic Culture Media for Clinical Microbiology in an Era of Molecular Diagnostics

In the last 25 years, chromogenic culture media have found widespread application in diagnostic clinical microbiology. In the last decade, the range of media available to clinical laboratories has expanded greatly, allowing specific detection of additional pathogens, including Pseudomonas aeruginosa, group B streptococci, Clostridium difficile, Campylobacter spp., and Yersinia enterocolitica. New media have also been developed to screen for pathogens with acquired antimicrobial resistance, including vancomycin-resistant enterococci, carbapenem-resistant Acinetobacter spp., and Enterobacteriaceae with extended-spectrum β-lactamases and carbapenemases. This review seeks to explore the utility of chromogenic media in clinical microbiology, with particular attention given to media that have been commercialized in the last decade. The impact of laboratory automation and complementary technologies such as matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is also assessed. Finally, the review also seeks to demarcate the role of chromogenic media in an era of molecular diagnostics.

HIV and diarrhoea: what is new?

PURPOSE OF REVIEW

The review examines the changing causes and the investigation of infectious and noninfectious diarrhoea in individuals with HIV.

RECENT FINDINGS

Despite the excellent prognosis conferred by combination antiretroviral therapy, diarrhoea is still common in HIV-positive individuals and is associated with reduced quality of life and survival. There is increasing interest in the importance of Th17 and Th22 T cells in the maintenance of mucosal immunity within the gut, and in the role of the gut microbiome in gut homeostasis. Bacterial causes of HIV-associated diarrhoea continue to be important in resource-poor settings. In other settings, sexually transmitted enteric infections such as lymphogranuloma venereum and shigellosis are increasingly reported in men who have sex with men. HIV increases the risk of such infections and the presence of antimicrobial resistance. Parasitic causes of diarrhoea are more common in individuals with uncontrolled HIV and low CD4 counts. Noninfectious causes of diarrhoea include all classes of antiretroviral therapy, which is under-recognised as a cause of poor treatment adherence. Pancreatic dysfunction is remediable and the diagnostic workup of HIV-related diarrhoea should include faecal elastase measurements. New antimotility agents such as crofelemer may be useful in managing secretory diarrhoea symptoms.

SUMMARY

Clinicians looking after patients with HIV should ask about diarrhoeal symptoms, which are under-reported and may have a remediable infectious or noninfectious cause.

Comparison of three multiplex gastrointestinal platforms for the detection of gastroenteritis viruses

BACKGROUND

Viruses are major etiological agents of childhood gastroenteritis. In recent years, several molecular platforms for the detection of viral enteric pathogens have become available.

OBJECTIVE/STUDY DESIGN

We evaluated the performance of three multiplex platforms including Biofire's Gastrointestinal Panel (FilmArray), Luminex xTAG^® Gastrointestinal Pathogen Panel (GPP), and the TaqMan Array Card (TAC) for the detection of five gastroenteritis viruses using a coded panel of 300 archived stool samples.

RESULTS

The FilmArray detected a virus in 199 (96.1%) and the TAC in 172 (83.1%) of the 207 samples (187 samples positive for a single virus and 20 samples positive for more than one virus) whereas the GPP detected a virus in 100 (78.7%) of the 127 (97 positive for one virus and three positive for more than one virus) samples. Overall the clinical accuracy was highest for the FilmArray (98%) followed by TAC (97.2%) and GPP (96.9%). The sensitivity of the FilmArray, GPP and TAC platforms was highest for rotavirus (100%, 95.8%, and 89.6%, respectively) and lowest for adenovirus type 40/41 (97.4%, 57.9% and 68.4%). The specificity of the three platforms ranged from 95.6% (rotavirus) to 99.6% (norovirus/sapovirus) for the FilmArray, 99.6% (norovirus) to 100% (rotavirus/adenovirus) for GPP, and 98.9% (astrovirus) to 100% (rotavirus/sapovirus) for TAC.

CONCLUSION

The FilmArray demonstrated the best analytical performance followed by TAC. In recent years, the availability of multi-enteric molecular testing platforms has increased significantly and our data highlight the strengths and weaknesses of these platforms.

Quality specifications of routine clinical chemistry methods based on sigma metrics in performance evaluation

INTRODUCTION

Sigma metrics were applied to evaluate the performance of 20 routine chemistry assays, and individual quality control criteria were established based on the sigma values of different assays.

METHODS

Precisions were expressed as the average coefficient variations (CVs) of long-term two-level chemistry controls. The biases of the 20 assays were obtained from the results of trueness programs organized by National Center for Clinical Laboratories (NCCL, China) in 2016. Four different allowable total error (TEa) targets were chosen from biological variation (minimum, desirable, optimal), Clinical Laboratory Improvements Amendments (CLIA, US), Analytical Quality Specification for Routine Analytes in Clinical Chemistry (WS/T 403-2012, China) and the National Cholesterol Education Program (NECP).

RESULTS

The sigma values from different TEa targets varied. The TEa targets for ALT, AMY, Ca, CHOL, CK, Crea, GGT, K, LDH, Mg, Na, TG, TP, UA and Urea were chosen from WS/T 403-2012; the targets for ALP, AST and GLU were chosen from CLIA; the target for K was chosen from desirable biological variation; and the targets for HDL and LDL were chosen from the NECP. Individual quality criteria were established based on different sigma values.

CONCLUSIONS

Sigma metrics are an optimal tool to evaluate the performance of different assays. An assay with a high value could use a simple internal quality control rule, while an assay with a low value should be monitored strictly.

Current knowledge on the laboratory diagnosis of Clostridium difficile infection

Clostridium difficile (C. difficile) is a spore-forming, toxin-producing, gram-positive anaerobic bacterium that is the principal etiologic agent of antibiotic-associated diarrhea. Infection with C. difficile (CDI) is characterized by diarrhea in clinical syndromes that vary from self-limited to mild or severe. Since its initial recognition as the causative agent of pseudomembranous colitis, C. difficile has spread around the world. CDI is one of the most common healthcare-associated infections and a significant cause of morbidity and mortality among older adult hospitalized patients. Due to extensive antibiotic usage, the number of CDIs has increased. Diagnosis of CDI is often difficult and has a substantial impact on the management of patients with the disease, mainly with regards to antibiotic management. The diagnosis of CDI is primarily based on the clinical signs and symptoms and is only confirmed by laboratory testing. Despite the high burden of CDI and the increasing interest in the disease, episodes of CDI are often misdiagnosed. The reasons for misdiagnosis are the lack of clinical suspicion or the use of inappropriate tests. The proper diagnosis of CDI reduces transmission, prevents inadequate or unnecessary treatments, and assures best antibiotic treatment. We review the options for the laboratory diagnosis of CDI within the settings of the most accepted guidelines for CDI diagnosis, treatment, and prevention of CDI.

Exploiting Bacterial Whole-Genome Sequencing Data for Evaluation of Diagnostic Assays: Campylobacter Species Identification as a Case Study

The application of whole-genome sequencing (WGS) to problems in clinical microbiology has had a major impact on the field. Clinical laboratories are now using WGS for pathogen identification, antimicrobial susceptibility testing, and epidemiological typing. WGS data also represent a valuable resource for the development and evaluation of molecular diagnostic assays, which continue to play an important role in clinical microbiology. To demonstrate this application of WGS, this study used publicly available genomic data to evaluate a duplex real-time PCR (RT-PCR) assay that targets mapA and ceuE for the detection of Campylobacter jejuni and Campylobacter coli, leading global causes of bacterial gastroenteritis. In silico analyses of mapA and ceuE primer and probe sequences from 1,713 genetically diverse C. jejuni and C. coli genomes, supported by RT-PCR testing, indicated that the assay was robust, with 1,707 (99.7%) isolates correctly identified. The high specificity of the mapA-ceuE assay was the result of interspecies diversity and intraspecies conservation of the target genes in C. jejuni and C. coli Rare instances of a lack of specificity among C. coli isolates were due to introgression in mapA or sequence diversity in ceuE The results of this study illustrate how WGS can be exploited to evaluate molecular diagnostic assays by using publicly available data, online databases, and open-source software.

Multiplex Polymerase Chain Reaction for Detection of Gastrointestinal Pathogens in Migrant Workers in Qatar

The causes of infectious diarrhea among the migrant worker population in Qatar are not well understood. We conducted a prospective observational study to understand the demographic and clinical characteristics and infectious causes of diarrhea among migrant workers in Doha, Qatar. A total of 126 male workers presenting to the Qatar Red Crescent Worker's Health Center outpatient clinic or emergency department were studied over a 5-month period in 2015–2016. Epidemiologic surveys were administered to all subjects and the prevalence of 22 different stool pathogens was determined using multiplex polymerase chain reaction (PCR) (FilmArray^® Gastrointestinal PCR). A target pathogen was identified in 62.7% of subjects. Enteropathogenic Escherichia coli was the most prevalent pathogen and was detected in 24.6% of subjects, followed by Salmonella (22.2%), enteroaggregative E. coli (15.1%), Giardia lamblia (9.5%), and enterotoxigenic E. coli (8.7%). Multiple pathogens were identified in 49.3% of positive stool samples. In a multivariable analysis, the presence of a heart rate ≥ 90 (adjusted odds ratio [OR] = 3.7, 95% confidence interval [CI] = 1.4–10.0) and > 5 fecal leukocytes/high-power field (adjusted OR = 2.8, 95% CI = 1.2–7.0) were significant predictors of detecting an acute inflammatory pathogen by PCR. Use of multiplex PCR enabled the detection of gastrointestinal pathogens in a high proportion of cases, illustrating the utility of this diagnostic tool in epidemiologic studies of infectious diarrhea.

Performance of the Verigene® enteric pathogens test, Biofire FilmArray™ gastrointestinal panel and Luminex xTAG® gastrointestinal pathogen panel for detection of common enteric pathogens

BACKGROUND

Multiplex syndromic panels have the capability of identifying causes of diarrheal illness. This study evaluated the performance characteristics of three multiplex molecular assays for the detection of common stool pathogens.

METHODS

A total of 152 stool specimens were tested using three platforms: Verigene Enteric Pathogens Test (Verigene), Biofire FilmArray Gastrointestinal Panel (Biofire) and Luminex xTAG® Gastrointestinal Pathogen Panel (Luminex). Assays were assessed only for the targets common among all three; namely, Campylobacter, Salmonella, Shigella, Shiga toxin-producing E. coli (STEC), norovirus, and rotavirus.

RESULTS

The sensitivities (%) and specificities (%) of the assays were: Campylobacter, Biofire (100,100), Verigene (83.3,99.3), Luminex (91.7,100); Salmonella, Biofire (95.8,100), Verigene (83.3,100), Luminex (79.2,100); Shigella, Biofire (100,100), Verigene (95.4,99.1), Luminex (100,100); STEC, Biofire (100,100), Verigene (91.7,100), Luminex (91.7,100); norovirus, Biofire (94.7,99.3), Verigene (89.0,100), Luminex (89.5,100); and rotavirus, Biofire (100, 98.6), Verigene (71.4,100), Luminex (100,100).

CONCLUSIONS

All multiplex panels detected the majority of gastrointestinal pathogens when compared to conventional methods.

Novel bead-based platform for direct detection of unlabelled nucleic acids through Single Nucleobase Labelling

Over the last decade, circulating microRNAs have received attention as diagnostic and prognostic biomarkers. In particular, microRNA122 has been demonstrated to be an early and more sensitive indicator of drug-induced liver injury than the widely used biomarkers such as alanine aminotransferase and aspartate aminotransferase. Recently, microRNA122 has been used in vitro to assess the cellular toxicity of new drugs and as a biomarker for the development of a rapid test for drug overdose/liver damage. In this proof-of-concept study, we report a PCR-free and label-free detection method that has a limit of detection (3 standard deviations) of 15 fmoles of microRNA122, by integrating a dynamic chemical approach for "Single Nucleobase Labelling" with a bead-based platform (Luminex^®) thereby, in principle, demonstrating the exciting prospect of rapid and accurate profiling of any microRNAs related to diseases and toxicology.

Multiplex Molecular Panels for Diagnosis of Gastrointestinal Infection: Performance, Result Interpretation, and Cost-Effectiveness

Gastrointestinal disease is a major cause of morbidity and mortality worldwide, especially among young children and immunocompromised patients. Diarrhea may result from infection with a variety of microbial pathogens, including bacteria, viruses, or parasites. Historically, the diagnosis of infectious diarrhea has been made using microscopy, antigen tests, culture, and real-time PCR. A combination of these traditional tests is often required due to the inability to distinguish between infectious etiologies based on the clinical presentation alone. Recently, several multiplex molecular assays have been developed for the detection of gastrointestinal pathogens directly from clinical stool samples. These panels allow for the detection and identification of up to 20 pathogens in as little as 1 h. This review will focus on the multiplex molecular panels that have received clearance from the FDA for the diagnosis of diarrheal disease and will highlight issues related to test performance, result interpretation, and cost-effectiveness of these new molecular diagnostic tools.

Assessment of enzyme measurement procedures in China through a trueness verification program

BACKGROUND

Since 2003, the National Center for Clinical Laboratories (NCCL) has organized a network of reference laboratories and several survey programs to improve standardization in China.

METHODS

We analyzed the 2015 trueness verification program to assess the status of enzyme measurement standardization. Commutable serum-based materials were prepared and sent to 10 reference laboratories to assign target values for 2 enzymes (alanine aminotransferase-pyridoxal phosphate [ALT-pp] and γ-glutamyltransferase [GGT]) using IFCC reference measurement procedures.

RESULTS

Analytical performance was assessed for compliance to 3 indexes: trueness (bias), imprecision (CV), and accuracy (total error). Of the 250 participating laboratories, about half (≥124) used heterogeneous systems. More laboratories met the tolerance limit of imprecision than of trueness or accuracy. Except at the lowest concentration, the CV pass rates were >90% for the 2 enzymes. The optimal performance criterion derived from biological variation yielded pass rates for total error (ALT 77%, GGT 80%) that were higher than for bias (ALT 63%, GGT 73%).

CONCLUSIONS

PT/EQA results for commutable samples can be used to assess trueness against reference measurement procedures. Despite global and national standardization programs, bias remains a critical limitation of current enzyme measurement procedures in China.