Next Article in Journal
Characteristics of COVID-19 Breakthrough Infections among Vaccinated Individuals and Associated Risk Factors: A Systematic Review
Next Article in Special Issue
Diagnostic Methods of Common Intestinal Protozoa: Current and Future Immunological and Molecular Methods
Previous Article in Journal
Zoonotic Flavivirus Exposure in Peri-Urban and Suburban Pig-Keeping in Hanoi, Vietnam, and the Knowledge and Preventive Practices of Pig Farmers
Previous Article in Special Issue
Prevalence of Intestinal Parasitic Infections among Children in Europe over the Last Five Years
 
 
Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
Journals
TropicalMed
Volume 7
Issue 5
10.3390/tropicalmed7050080
tropicalmed-logo
Submit to this Journal Review for this Journal Propose a Special Issue
► Article Menu

Article Menu

share Share announcement Help format_quote Cite question_answer Discuss in SciProfiles thumb_up
...
Endorse textsms
...
Comment
first_page
settings
Order Article Reprints
Font Type:
Arial Georgia Verdana
Font Size:
Aa Aa Aa
Line Spacing:
Column Width:
Background:
Review

Acute Viral Gastrointestinal (GI) Infections in the Tropics—A Role for Cartridge-Based Multiplex PCR Panels?

by
Stefanie Kramme
1,
Theo Dähne
2,
Alexey Fomenko
2 and
Marcus Panning
2,*
1
Institute for Infection Prevention and Hospital Epidemiology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
2
Institute of Virology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
*
Author to whom correspondence should be addressed.
Trop. Med. Infect. Dis. 2022, 7(5), 80; https://0-doi-org.brum.beds.ac.uk/10.3390/tropicalmed7050080
Submission received: 23 March 2022 / Revised: 16 May 2022 / Accepted: 17 May 2022 / Published: 19 May 2022
(This article belongs to the Special Issue Diarrheagenic Pathogens and Gastrointestinal Infections)
Versions Notes

Abstract

:
Acute gastroenteritis (AGE) contributes to increased morbidity and mortality worldwide. In particular, children in resource-poor settings suffer from frequent episodes of diarrhea. A variety of pathogens, including bacteria, viruses, fungi, and protozoa, can cause AGE. Common viruses associated with AGE are norovirus, rotavirus, astrovirus, adenovirus, and sapovirus. Due to their similar clinical presentation, AGE pathogens cannot be distinguished on clinical grounds rendering the etiological diagnosis challenging. However, reliable diagnosis is essential for individual and public health reasons, e.g., to limit transmission, for appropriate antibiotic use, prognostic appreciation, and vaccination programs. Therefore, high-quality data derived by accurate diagnostics are important to improve global health. In Western industrialized countries, diagnosis relies on microbiological testing, including culture methods, microscopy, immunochromatography, and single-target molecular methods. Recently, multiplex PCR or syndromic panels have been introduced, which simultaneously analyze for multiple pathogens in a very short time. A further technological advancement is cartridge-based syndromic panels, which allow for near patient/point-of-care testing independently from a laboratory. In resource-poor tropical regions, however, laboratory diagnosis is rarely established, and there are little routine laboratory data on the epidemiology of viral AGE pathogens. Limiting factors for the implementation of syndromic panels are high costs, sophisticated equipment, and the need for trained personnel. In addition, pilot studies have shown a large number of viral (co-)detections among healthy controls, thus further challenging their clinical utilization. Hence, there are little evidence-based data on the impact of multiplex syndromic panels from resource-limited regions. Here, we aim to provide a brief overview of what is known about the use of syndromic panels for virus-associated AGE in tropical regions and to address future challenges.

1. Introduction

Acute gastroenteritis (AGE) is associated with a high disease burden worldwide. On a global scale, it is estimated that 2 billion cases occur each year [1].
In industrialized countries, AGE has a great impact on individual and public health but to a lesser extent on mortality. Here, the elderly population and immunosuppressed patients are at the highest risk for severe and sometimes fatal courses [2,3,4]. A wide range of pathogens, including bacteria, viruses, fungi, and protozoa, can cause AGE.
On the contrary, in resource-limited regions, such as low- and middle-income countries (LMIC), morbidity and mortality can be very high and account for a considerable proportion of emergency department visits, hospitalizations, and, ultimately, deaths. Children, in particular, constitute the most vulnerable population in tropical regions; around 2 million deaths occur each year, mainly those with malnutrition [5].
Based on data from a large multicentric children cohort study from eight resource-poor sites (Bangladesh, Brazil, India, Nepal, Pakistan, Peru, South Africa, and Tanzania), a predominant viral cause (36.4%) could be identified by quantitative RT-PCR, followed by bacterial (25.0%) and parasitic (3.5%) (Etiology, Risk Factors, and Interactions of Enteric Infections and Malnutrition and the Consequences for Child Health and Development (MAL-ED), [6]).
Common viruses associated with childhood AGE in the resource-poor settings, in descending order, are rotavirus, enteric adenovirus (types 40/41), sapovirus, norovirus, and astrovirus [6,7,8].
Virus transmission is facilitated by unfavorable socioeconomic levels with cramped and crowded households, malnutrition, contaminated water or food, poor sanitation and hygiene, and climatic conditions that allow environmental contamination by pathogens [9]. All of these could possibly explain the high disease burden of AGE in developing countries, where large and explosive outbreaks can occur (e.g., in refugee camps) [10]. Outbreaks can also occur, e.g., in hospitals, long-term care facilities (LTCF), or nursing homes.
Traditional methods for the detection of AGE pathogens include laborious and time-consuming stool cultures, antigen detection methods, and microscopy. In addition, all of these traditional techniques are less sensitive and specific compared to nucleic acid amplification techniques (NAT) [11]. However, timely diagnosis may prevent adverse patient outcomes and stop further spread by rapid isolation precautions, e.g., in a hospital or an LTCF setting. Patients may benefit from rapid and appropriate diagnosis, avoiding erroneous prescription of antibiotics, concomitant side effects, and antibiotic-resistance related issues. Of note, a study with 414 patients performed in India using a molecular multiplex panel registered the use of antibiotics in 90% of patients with a viral causative agent [12].
Molecular methods have undoubtedly revolutionized clinical virology in the past decades and helped to improve our understanding of the epidemiology of virus-associated AGE. Using NAT, norovirus was shown to be a key AGE pathogen causing nearly a fifth of all cases of AGE [13]. With the advent of recently introduced multiplex PCR panels, a comprehensive and simultaneous analysis of up to 20 different pathogens is possible within a very short time and minimal hands-on time. This allows for a syndromic testing approach since these panels test for pathogens associated with a specific infectious syndrome. As of yet, these panels are primarily available for respiratory tract and gastrointestinal infections. Although multiplex testing is increasingly utilized in many industrialized countries, data from, e.g., Africa or tropical settings, are scarce.
Data on the clinical impact (i.e., antibiotic prescription, auxiliary testing, isolation, length of hospital stay) of syndromic panels, even from industrialized regions, are lacking at large and are, to some extent, controversial. According to the health technology assessment report by Freeman et al., multiplex testing for gastrointestinal pathogens leads to a higher number of positive results than conventional testing. However, the clinical significance of these additional positive results is unclear as test-treatment trials are lacking. Therefore, no conclusion can be drawn whether the additional positive results lead to overdiagnosis or improved patient management [14].
Further important hurdles for their implementation are high costs, the need for sophisticated equipment, and the lack of evidence-based criteria for their clinical use. Especially for bacterial AGE pathogens, it is imperative to discriminate between true infection and colonization. Quantitative data from PCR-based methods might help to distinguish active infection from colonization but warrant careful interpretation and standardization [6,15,16]. Unlike bacterial AGE, there is no approved therapy for most viral infections, except for symptomatic treatment and isolation. Importantly, rotavirus vaccines are now widely used for the prevention of rotavirus-associated gastroenteritis. To control the success of vaccination programs, reliable detection methods are of importance. This gives rise to the notion that molecular methods are not only important for individuals but also for public health in many countries worldwide. Finally, the cost-effectiveness of molecular methods is hard to assess not only in resource-rich countries, as prerequisites as laboratory equipment and test costs, reimbursement, and other variables are significantly different from country to country. Having this in mind, it is evident that clinical guidelines do not recommend universal testing of all patients presenting with diarrheal symptoms.
Here, we summarize what is known about the use of multiplex syndromic panels for the detection of virus-associated AGE in resource-limited regions.

2. Methods

We conducted a literature search using the terms shown in Table 1. We searched the Medline database and retrieved a total of 596 studies. We included 27 articles and our own experience to set up a brief narrative review on the use of syndromic panels for virus-associated AGE in tropical regions [5,6,12,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36]. Exclusion criteria were population outside LMIC and singleplex PCR; we did not apply any year filters or age restrictions to the target population. We focused on technical aspects and the clinical impact of syndromic panels. Finally, we suggest directions for future research.

3. Technical and Pre-Analytical Considerations

In general, before the introduction of novel diagnostic methods in a laboratory or hospital, it is advisable to perform change management to define, e.g., the clinical needs, the indication to order a test, and to anticipate possible pitfalls [37]. Loderstadt and colleagues present a detailed overview of various issues, including regulatory ones for the molecular detection of bacteria associated with AGE in the tropics [38].
The challenges in AGE diagnosis are partly explainable by the fact that stool is a complex material due to its variable content of PCR inhibitors, which depend on the patient’s diet, gut microbiome, lifestyle, and environmental factors such as exposure to animals or unimproved sanitation infrastructure [38,39]. Substances such as urea, hemoglobin, heparin, polysaccharides, chlorophyll from vegetables, bile salts, and glycolipids have been identified as inhibitors and are possible factors for false-negative results [39,40]. Especially in the tropical setting, this challenge is considerable since here, necessary requirements such as refrigerated or frozen storage and transport are not always guaranteed, either due to a lack of logistics or interruptions in the cold chain due to electrical interruptions, which poses the risk of degradation of the unextracted nucleic acid in the samples due to suboptimal storage conditions. Attempts have been made to counteract this problem through sample storage on Flinders Technology Associates® (FTA) cards at ambient temperature. The FTA® paper card is a fiber-membrane-based system impregnated with chemicals that lyse cells, cell nuclei, organelles, and nucleic acid. The released nucleic acids bind tightly in the fibers of the FTA® matrix, which protects the nucleic acids from damaging substances such as nucleases and thus reduces degradation [41]. The application of this technology for storage has been evaluated primarily for bacterial DNA in stool samples, as viral RNA is considered an unstable molecule due to the ubiquitous presence of RNAases. Hence, a systematic review of FTA® cards for the preservation of viral RNA found only one trial in which FTA® cards were used for stool samples. Here, promising results were shown for rotavirus detection both in vitro under different storage temperatures and under field conditions, while another study published after the search of the systematic review investigated different enteropathogens [22,42]. The study showed that FTA® card-based storage has the lowest sensitivity for noroviruses compared to bacterial pathogens [43]. A promising, cost-effective alternative to commercially available paper matrix cards for the storage and preservation of stool specimens was proposed by Cromeans et al., who modified universal nucleic acid extraction buffer (UNEX) to impregnate a self-developed cellulose filter disc (UNEXP disc). Suspensions of norovirus-positive stool samples (n = 54) were applied to UNEXP discs; after two weeks of storage at room temperature on the UNEXP discs, all samples showed norovirus RT-qPCR positive. A subset of seven samples was stored for three months and found RT-qPCR positive. In addition, genotyping was successful in 76% (41/54) of the samples [44]. Further research on FTA® card and UNEXP cards for other AGE viruses and under different storage conditions and durations would therefore be desirable.
Technically, a wide variety of molecular laboratory-developed tests (LDT) as well as commercial assays are available to detect AGE pathogens [45]. The Luminex GPP assay was one of the first syndromic assays for GI pathogens on the market. It is a truly laboratory-based workflow, as it requires separate nucleic acid extraction and (in previous versions) post-PCR processing steps. In a similar fashion, the Fast Track Diagnostics gastroenteritis panel offers real-time PCR-based multiplex testing. These conventional multiplex panels allow for batch testing of up to 96 samples but require sophisticated technical equipment. These technical prerequisites obviously limit their application in remote and/or resource-limited regions. However, a recent study showed that the detection rate increased over conventional methods [12]. A real-time PCR system is not available in many tropical regions due to cost, lack of equipment, and high technical demand on the staff, and therefore, the data on the routine use of PCR for AGE diagnosis are limited [25].
Most studies evaluating AGEs in resource-limited settings with multiplex PCR transfer the stool samples to industrialized countries or occasionally to remote urban laboratories with sufficient infrastructure [30,36,46].
The majority of studies are epidemiological and address the question of detection of coinfection in AGE in specific regions.
However, the question of the utility of multiplex diagnostics in the LMIC setting is unclear, and in particular, the frequent multiple pathogen detection complicates this circumstance by making treatment decisions difficult. It is conceivable that the possibility of differentiating between bacterial and viral pathogens may reduce the use of antibiotics. However, if multiple pathogens are detected without differentiation between infection and colonization, the opposite is also conceivable with increased costs due to antibiotic overuse and the development of antimicrobial resistance [29].
Likewise, the question of cost-effectiveness analysis of conventional multiplex PCR diagnostics for the detection of AGE in resource-limited settings is largely unanswered. For example, only a study conducted in India by Mitra et al. showed that similar test accuracy can be achieved at a lower cost using in-house designed multiplex PCR compared to commercially available real-time assay (FTD Viral Gastroenteritis kit) [35].
Technological advancements are cartridge-based syndromic panels, i.e., no separate nucleic acid extraction and amplification/detection steps are necessary. This approach allows for rapid and point of care testing independently from diagnostic laboratories. These panels display very fast turn-around and minimal hands-on time but require specialized equipment from the respective manufacturer [47]. Currently, the BioFire Film Array Gastrointestinal Panel and the QIAstat Gastrointestinal (GI) Panel are examples of commercially available cartridge-based assays (Table 2).
Pre-analytical considerations should also include the panel composition and the epidemiology of the analyzed pathogens. Major viral targets included in AGE multiplex panels are adenovirus 40/41, astrovirus, norovirus genogroup I/II, rotavirus A, and, in some assays, sapovirus. These pathogens represent the most important viral causes of AGE (Table 3). Before the introduction of a novel diagnostic technique, the analytical sensitivity or the limit of detection needs to be known for every target. Comparison studies of current syndromic panels have demonstrated equivalent or even superior performance to reference assays [45,48,49]. Not surprisingly, performance data varied between panels but also within panels with respect to specific pathogens [50,51]. Frequently, overall sensitivity is shown but might be critically low for selected targets [17]. In addition, genotypes can influence performance. For adenovirus, the most common types seen in AGE are included (types 40/41) in most assays. However, regionally circulating virus types might influence the reliability of results. Critically, validation studies conducted in tropical regions remain scarce but are of importance. Commercial panels include fixed combinations of pathogens and do not allow them to be customized, e.g., to local needs or seasonality of pathogens. It is well known that in temperate regions, norovirus and rotavirus typically occur in the colder month of the year (“winter vomiting disease”). In tropical regions, however, explosive outbreaks can occur with hundreds of cases due to the consumption of contaminated water irrespective of seasonality. On the contrary, selected pathogens may be rare overall, and consequently, the positive predictive value is very low. In addition, the introduction of the rotavirus vaccine also has an impact on the pretest probability and should be taken into account. Thus, knowledge about patients‘ vaccination status is of interest since rotavirus vaccination may also yield a positive PCR result for an indeterminate time period post vaccination [52]. In this respect, LDTs allow for greater flexibility as only locally relevant pathogens can be included. Finally, many available assays do have a CE label, which limits, e.g., the selection of the sample specimen type to those endorsed by the manufacturer. If alternative specimens are to be tested, extensive validation needs to be done to account for regulatory issues.
One of the most promising benefits of the new syndromic cartridge-based panels is the reduced hands-on and turn-around time. They can provide comprehensive results in <2 h. This might lead to rapid and more targeted therapy, more informed decision making regarding isolation, and optimized patient management [53].

4. Clinical Impact and Current Evidence

As with any diagnostic testing, the indication should be inferred in light of local epidemiological considerations and the clinical presentation. Current reviews do not universally recommend diagnostic multiplex testing in every patient with suspected diarrheal diseases [54]. Our literature search yielded only 13 studies reporting on the use of multiplex PCR panels for AGE in tropical settings. Critically, many of these studies were conducted in tropical regions, but the multiplex analysis was performed by study partners, e.g., in Europe [15,17]. In addition, these studies were not designed to assess the clinical impact of multiplex testing on patient care and public health. This certainly limits the interpretation of the usability of multiplex testing in tropical settings.
In industrialized regions, a study evaluated the impact of another platform, the FilmArray GIP, on length of stay and patient isolation. This study found that patients spent considerable time without appropriate isolation methods in the hospital, whereas other patients were placed under contact precautions without cause [53]. Another study has shown that costs for the clinical laboratory increased, but overall, there were savings for the hospital [55]. Claas et al. reported that 65% of positive results were from pathogens not specifically ordered by the treating physician [56]. The clinical impact is much harder to assess in resource-limited settings where it became apparent that in children, numerous pathogens can be detected in cases with diarrhea as well as in asymptomatic controls [17]. Another study on infectious diarrhea including adult patients with persistent diarrhea and asymptomatic controls came to a similar conclusion in that positive results need confirmation of an active infection state [5]. These findings emphasize that it requires careful analysis of the local setting (i.e., patient population: adult versus pediatric, ambulatory versus in-hospital, immune status/previous antibiotic treatment, travel associated) and to evaluate the implementation of new methods in the local laboratory. The integrated stewardship concept addresses these concerns and might help in decision making when implementing syndromic panels [57].
For some patients, a more tailored approach would be more effective but not possible with the fixed combinations delivered by the manufacturers. It seems advisable to develop algorithms, which patient should be tested using which method. This apparently needs a cross-sectional and collaborative effort of all involved partners within a hospital or in primary care. However, in industrialized settings and even more so in resource-limited settings, there are still limited evidence-based data available to support a favorable benefit–risk ratio. In a meta-analysis including 162 norovirus outbreaks, implementation of infection control measures reduced patient case counts and length of hospital stay 0.6 and 0.7 fold, respectively, emphasizing the value of rapid and accurate diagnostics [58]. However, these data lack the economic impact, which is of particular relevance for low-income settings.
To conclude, although syndromic panels have been available for some time, there are still no general recommendations for the routine use of multiplex syndromic panels in patients presenting with AGE neither in industrialized nor in resource-poor settings. Thus, the question of the role of syndromic panels in the tropics remains open.

5. Outlook and Perspectives

Syndromic panels represent the spearhead of novel diagnostic tools not only for AGE. They have been proven to deliver fast and accurate results in multiple comparison studies and will help to advance our understanding of the epidemiology of AGE. This might lead to improved patient care but needs further (ideally multicenter and prospective) studies in, e.g., different settings, specific patient groups, and geographical locations. High costs of syndromic panels have significantly hindered their widespread implementation in routine diagnostic laboratories. This holds even more true for their use in resource-poor countries. Therefore, cost-effectiveness analyses are needed to allow state-of-the-art testing in remote settings. In addition, future research should be dedicated to coming to evidence-based recommendations on their use in different settings. Finally, cost-effectiveness and shortcomings have to be communicated between the laboratory, clinicians, practitioners, and other stakeholders.

Author Contributions

Conceptualization, A.F. and M.P.; Methodology, A.F.; Software and Formal Analysis, T.D. and A.F.; Writing—Original Draft Preparation, S.K. and M.P.; Writing—Review and Editing, S.K., T.D., A.F. and M.P. All authors have read and agreed to the published version of the manuscript.

Funding

This study was in part funded by BMBF-Verbundprojekt “COVIRES”, Fkz.: 13GW0540C.

Institutional Review Board Statement

Not applicable.

Informed Consent Statement

Not applicable.

Data Availability Statement

Not applicable.

Conflicts of Interest

The authors declare no conflict of interest.

References

  1. Farthing, M.; Salam, M.A.; Lindberg, G.; Dite, P.; Khalif, I.; Salazar-Lindo, E.; Ramakrishna, B.S.; Goh, K.-L.; Alan, T.; Aamir, G.K.; et al. Acute diarrhea in adults and children: A global perspective. J. Clin. Gastroenterol. 2013, 47, 12–20. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  2. Jagai, J.S.; Smith, G.S.; Schmid, J.E.; Wade, T.J. Trends in gastroenteritis-associated mortality in the United States, 1985–2005: Variations by ICD-9 and ICD-10 codes. BMC Gastroenterol. 2014, 14, 211. [Google Scholar] [CrossRef] [Green Version]
  3. Balachandran, N.; Cates, J.; Kambhampati, A.; Marconi, V.; Brown, S.T.; Rodriguez–Barradas, M.C.; Beenhouwer, D.; Holodniy, M.; Lucero-Obusan, C.A.; Cardemil, C.; et al. 702. Risk Factors for Acute Gastroenteritis Among Patients Hospitalized in 5 Veterans Affairs Medical Centers, 2016–2019. Open Forum Infect. Dis. 2021, 8, S451. [Google Scholar] [CrossRef]
  4. Troeger, C.; Blacker, B.F.; Khalil, I.A.; Rao, P.C.; Cao, S.; Zimsen, S.R.M.; Albertson, S.B.; Stanaway, J.D.; Deshpande, A.; Abebe, Z.; et al. Estimates of the global, regional, and national morbidity, mortality, and aetiologies of diarrhoea in 195 countries: A systematic analysis for the Global Burden of Disease Study 2016. Lancet Infect. Dis. 2018, 18, 1211–1228. [Google Scholar] [CrossRef] [Green Version]
  5. Becker, S.; Chatigre, J.; Gohou, J.-P.; Coulibaly, J.; Leuppi, R.; Polman, K.; Chappuis, F.; Mertens, P.; Herrmann, M.; N’Goran, E.; et al. Combined stool-based multiplex PCR and microscopy for enhanced pathogen detection in patients with persistent diarrhoea and asymptomatic controls from Côte d’Ivoire. Clin. Microbiol. Infect. 2015, 21, 591.e1–591.e10. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  6. Platts-Mills, J.A.; Liu, J.; Rogawski, E.T.; Kabir, F.; Lertsethtakarn, P.; Siguas, M.; Khan, S.S.; Praharaj, I.; Murei, A.; Nshama, R.; et al. Use of quantitative molecular diagnostic methods to assess the aetiology, burden, and clinical characteristics of diarrhoea in children in low-resource settings: A reanalysis of the MAL-ED cohort study. Lancet Glob. Health 2018, 6, e1309–e1318. [Google Scholar] [CrossRef] [Green Version]
  7. Wilhelmi, I.; Roman, E.; Sanchez-Fauquier, A. Viruses causing gastroenteritis. Clin. Microbiol. Infect. 2003, 9, 247–262. [Google Scholar] [CrossRef] [Green Version]
  8. Desselberger, U. Viral gastroenteritis. Medical 2017, 45, 690–694. [Google Scholar] [CrossRef]
  9. Andersson, M.E.; Elfving, K.; Shakely, D.; Nilsson, S.; Msellem, M.; Trollfors, B.; Mårtensson, A.; Björkman, A.; Lindh, M. Rapid Clearance and Frequent Reinfection With Enteric Pathogens Among Children With Acute Diarrhea in Zanzibar. Clin. Infect. Dis. Off. Publ. Infect. Dis. Soc. Am. 2017, 65, 1371–1377. [Google Scholar] [CrossRef]
  10. Veronica, D.C.; Monika, T.-W.; Nadine, L.; Rolf, K.; Herbert, P.; David, D.C.; Berrilli, F.; Kaboré, Y.; D’Alfonso, R. Application of Luminex Gastrointestinal Pathogen Panel to human stool samples from Côte d’Ivoire. J. Infect. Dev. Ctries. 2015, 9, 884–889. [Google Scholar]
  11. Cybulski, R.J.; Bateman, A.C.; Bourassa, L.; Bryan, A.; Beail, B.; Matsumoto, J.; Cookson, B.T.; Fang, F.C. Clinical Impact of a Multiplex Gastrointestinal Polymerase Chain Reaction Panel in Patients with Acute Gastroenteritis. Clin. Infect. Dis. 2018, 67, 1688–1696. [Google Scholar] [CrossRef] [PubMed]
  12. Ghoshal, U.; Tejan, N.; Sisodia, J.; Verma, S.; Prasad, N.; Uc, G. The utility of multiplex polymerase chain reaction for diagnosis of infectious diarrhoea in a tropical country. Indian J. Med. Microbiol. 2021, 39, 323–327. [Google Scholar] [CrossRef] [PubMed]
  13. Ahmed, S.M.; Hall, A.J.; Robinson, A.E.; Verhoef, L.; Premkumar, P.; Parashar, U.D.; Koopmans, M.; Lopman, B.A. Global prevalence of norovirus in cases of gastroenteritis: A systematic review and meta-analysis. Lancet Infect. Dis. 2014, 14, 725–730. [Google Scholar] [CrossRef] [Green Version]
  14. Freeman, K.; Mistry, H.; Tsertsvadze, A.; Royle, P.; McCarthy, N.; Taylor-Phillips, S.; Manuel, R.; Mason, J. Multiplex tests to identify gastrointestinal bacteria, viruses and parasites in people with suspected infectious gastroenteritis: A systematic review and economic analysis. Heal. Technol. Assess. 2017, 21, 1–188. [Google Scholar] [CrossRef]
  15. Eibach, D.; Krumkamp, R.; Hahn, A.; Sarpong, N.; Adu-Sarkodie, Y.; Leva, A.; Käsmaier, J.; Panning, M.; May, J.; Tannich, E. Application of a multiplex PCR assay for the detection of gastrointestinal pathogens in a rural African setting. BMC Infect. Dis. 2016, 16, 150. [Google Scholar] [CrossRef] [Green Version]
  16. Liu, J.; Kibiki, G.; Maro, V.; Maro, A.; Kumburu, H.; Swai, N.; Taniuchi, M.; Gratz, J.; Toney, D.; Kang, G.; et al. Multiplex reverse transcription PCR Luminex assay for detection and quantitation of viral agents of gastroenteritis. J. Clin. Virol. Off. Publ. Pan Am. Soc. Clin. Virol. 2011, 50, 308–313. [Google Scholar] [CrossRef] [Green Version]
  17. De Rauw, K.; Detemmerman, L.; Breynaert, J.; Pierard, D. Detection of Shiga toxin-producing and other diarrheagenic Escherichia coli by the BioFire FilmArray(R) Gastrointestinal Panel in human fecal samples. Eur. J. Clin. Microbiol. Infect Dis. 2016, 35, 1479–1486. [Google Scholar] [CrossRef]
  18. Goldfarb, D.M.; Steenhoff, A.P.; Pernica, J.M.; Chong, S.; Luinstra, K.; Mokomane, M.; Mazhani, L.; Quaye, I.; Goercke, I.; Mahony, J.; et al. Evaluation of Anatomically Designed Flocked Rectal Swabs for Molecular Detection of Enteric Pathogens in Children Admitted to Hospital with Severe Gastroenteritis in Botswana. J. Clin. Microbiol. 2014, 52, 3922–3927. [Google Scholar] [CrossRef] [Green Version]
  19. Platts-Mills, J.A.; Swai, N.; Saidi, Q.; Amour, C.; Gratz, J.; Liu, J.; Kumburu, H.; Mduma, E.; McCormick, B.J.J.; Svensen, E.; et al. Association Between Stool Enteropathogen Quantity and Disease in Tanzanian Children Using TaqMan Array Cards: A Nested Case-Control Study. Am. J. Trop. Med. Hyg. 2014, 90, 133–138. [Google Scholar] [CrossRef] [Green Version]
  20. Kurokawa, M.; Ono, K.; Ishiyama, S.; Rai, S.K. Evaluation of rapid diagnostic methods for pediatric viral diarrhea using samples collected in Nepal and Japan. Med. Coll. J. 2004, 6, 78–82. [Google Scholar]
  21. Lertsethtakarn, P.; Silapong, S.; Sakpaisal, P.; Serichantalergs, O.; Ruamsap, N.; Lurchachaiwong, W.; Anuras, S.; Platts-Mills, J.A.; Liu, J.; Houpt, E.R.; et al. Travelers’ Diarrhea in Thailand: A Quantitative Analysis Using TaqMan® Array Card. Clin. Infect. Dis. Off. Publ. Infect. Dis. Soc. Am. 2018, 67, 120–127. [Google Scholar] [CrossRef] [PubMed]
  22. Tam, K.I.; Esona, M.D.; Williams, A.; Ndze, V.N.; Boula, A.; Bowen, M.D. Evaluation of BBL Sensi-Discs and FTA(R) cards as sampling devices for detection of rotavirus in stool samples. J. Virol. Methods 2015, 222, 41–46. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  23. Philip, C.O.; Koech, M.; Kipkemoi, N.; Kirera, R.; Ndonye, J.; Ombogo, A.; Kirui, M.; Kipkirui, E.; Danboise, B.; Hulseberg, C.; et al. Evaluation of the performance of a multiplex reverse transcription polymerase chain reaction kit as a potential diagnostic and surveillance kit for rotavirus in Kenya. Trop. Dis. Travel Med. Vaccines 2019, 5, 12. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  24. Walker, C.R.; Lechiile, K.; Mokomane, M.; Steenhoff, A.P.; Arscott-Mills, T.; Pernica, J.M.; Goldfarb, D.M. Evaluation of Anatomically Designed Flocked Rectal Swabs for Use with the BioFire FilmArray Gastrointestinal Panel for Detection of Enteric Pathogens in Children Admitted to Hospital with Severe Gastroenteritis. J. Clin. Microbiol. 2019, 57, e00962-19. [Google Scholar] [CrossRef]
  25. Duong, V.T.; Phat, V.V.; Tuyen, H.T.; Dung, T.T.N.; Trung, P.D.; Minh, P.V.; Tu, L.T.P.; Campbell, J.I.; Le Phuc, H.; Ha, T.T.T.; et al. Evaluation of Luminex xTAG Gastrointestinal Pathogen Panel Assay for Detection of Multiple Diarrheal Pathogens in Fecal Samples in Vietnam. J. Clin. Microbiol. 2016, 54, 1094–1100. [Google Scholar] [CrossRef] [Green Version]
  26. Kabayiza, J.C.; Andersson, M.E.; Nilsson, S.; Baribwira, C.; Muhirwa, G.; Bergström, T.; Lindh, M. Diarrhoeagenic microbes by real-time PCR in Rwandan children under 5 years of age with acute gastroenteritis. Clin. Microbiol. Infect. Off. Publ. Eur. Soc. Clin. Microbiol. Infect. Dis. 2014, 20, O1128-35. [Google Scholar] [CrossRef] [Green Version]
  27. Kabayiza, J.C.; Andersson, M.E.; Nilsson, S.; Bergström, T.; Muhirwa, G.; Lindh, M. Real-time PCR identification of agents causing diarrhea in Rwandan children less than 5 years of age. Pediatr. Infect. Dis. J. 2014, 33, 1037–1042. [Google Scholar] [CrossRef]
  28. Pernica, J.M.; Steenhoff, A.P.; Welch, H.; Mokomane, M.; Quaye, I.; Arscott-Mills, T.; Mazhani, L.; Lechiile, K.; Mahony, J.; Smieja, M.; et al. Correlation of Clinical Outcomes With Multiplex Molecular Testing of Stool From Children Admitted to Hospital With Gastroenteritis in Botswana. J. Pediatric Infect. Dis. Soc. 2016, 5, 312–318. [Google Scholar] [CrossRef] [Green Version]
  29. Gaensbauer, J.T.; Lamb, M.; Calvimontes, D.M.; Asturias, E.J.; Kamidani, S.; Contreras-Roldan, I.L.; Dominguez, S.R.; Robinson, C.C.; Zacarias, A.; Berman, S.; et al. Identification of Enteropathogens by Multiplex PCR among Rural and Urban Guatemalan Children with Acute Diarrhea. Am. J. Trop. Med. Hyg. 2019, 101, 534–540. [Google Scholar] [CrossRef]
  30. Elfving, K.; Andersson, M.; Msellem, M.I.; Welinder-Olsson, C.; Petzold, M.; Björkman, A.; Trollfors, B.; Mårtensson, A.; Lindh, M. Real-time PCR threshold cycle cutoffs help to identify agents causing acute childhood diarrhea in Zanzibar. J. Clin. Microbiol. 2014, 52, 916–923. [Google Scholar] [CrossRef] [Green Version]
  31. Gosselin, K.B.; Aboud, S.; McDonald, C.M.; Moyo, S.; Khavari, N.; Manji, K.; Kisenge, R.; Fawzi, W.; Kellogg, M.; Tran, H.Q.; et al. Etiology of Diarrhea, Nutritional Outcomes, and Novel Intestinal Biomarkers in Tanzanian Infants. J. Pediatric Gastroenterol. Nutr. 2017, 64, 104–108. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  32. Seid, L.; Stokes, W.; Bayih, A.G.; Getie, S.; Abere, A.; Tesfa, H.; Pillai, D.R. Molecular detection of Enteropathogens from diarrheic stool of HIV positive patients in Gondar, Ethiopia. BMC Infect. Dis. 2018, 18, 354. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  33. Mokomane, M.; Tate, J.E.; Steenhoff, A.P.; Esona, M.D.; Bowen, M.D.; Lechiile, K.; Pernica, J.M.; Kasvosve, I.; Parashar, U.D.; Goldfarb, D.M. Evaluation of the Influence of Gastrointestinal Coinfections on Rotavirus Vaccine Effectiveness in Botswana. Pediatric Infect. Dis. J. 2018, 37, e58–e62. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  34. Taniuchi, M.; Sobuz, S.U.; Begum, S.; Platts-Mills, J.A.; Liu, J.; Yang, Z.; Wang, X.Q.; Petri, W.A., Jr.; Haque, R.; Houpt, E.R. Etiology of diarrhea in Bangladeshi infants in the first year of life analyzed using molecular methods. J. Infect. Dis. 2013, 208, 1794–1802. [Google Scholar] [CrossRef] [Green Version]
  35. Mitra, S.; Nayak, M.K.; Majumdar, A.; Sinha, A.; Chatterjee, S.; Deb, A.; Chawla-Sarkar, M.; Dutta, S. Development and evaluation of a multiplex conventional reverse-transcription polymerase chain reaction assay for detection of common viral pathogens causing acute gastroenteritis. Diagn. Microbiol. Infect. Dis. 2020, 97, 115061. [Google Scholar] [CrossRef] [PubMed]
  36. Pelkonen, T.; Dos Santos, M.D.; Roine, I.; Dos Anjos, E.; Freitas, C.; Peltola, H.; Laakso, S.; Kirveskari, J. Potential Diarrheal Pathogens Common Also in Healthy Children in Angola. Pediatric Infect. Dis. J. 2018, 37, 424–428. [Google Scholar] [CrossRef] [Green Version]
  37. Zanella, M.-C.; Meylan, P.; Kaiser, L. Syndromic panels or ‘panel syndrome’? A perspective through the lens of respiratory tract infections. Clin. Microbiol. Infect. 2020, 26, 665–668. [Google Scholar] [CrossRef]
  38. Loderstädt, U.; Hagen, R.; Hahn, A.; Frickmann, H. New Developments in PCR-Based Diagnostics for Bacterial Pathogens Causing Gastrointestinal Infections—A Narrative Mini-Review on Challenges in the Tropics. Trop. Med. Infect. Dis. 2021, 6, 96. [Google Scholar] [CrossRef]
  39. Schrader, C.; Schielke, A.; Ellerbroek, L.; Johne, R. PCR inhibitors-occurrence, properties and removal. J. Appl. Microbiol. 2012, 113, 1014–1026. [Google Scholar] [CrossRef]
  40. Oikarinen, S.; Tauriainen, S.; Viskari, H.; Simell, O.; Knip, M.; Virtanen, S.; Hyöty, H. PCR inhibition in stool samples in relation to age of infants. J. Clin. Virol. 2009, 44, 211–214. [Google Scholar] [CrossRef]
  41. Picard-Meyer, E.; Barrat, J.; Cliquet, F. Use of filter paper (FTA®) technology for sampling, recovery and molecular characterisation of rabies viruses. J. Virol. Methods 2007, 140, 174–182. [Google Scholar] [CrossRef] [PubMed]
  42. Cardona-Ospina, J.A.; Villalba-Miranda, M.F.; Palechor-Ocampo, L.A.; Mancilla, L.I.; Sepúlveda-Arias, J.C. A systematic review of FTA cards® as a tool for viral RNA preservation in fieldwork: Are they safe and effective? Prev. Vet. Med. 2019, 172, 104772. [Google Scholar] [CrossRef] [PubMed]
  43. Lalani, T.; Tisdale, M.D.; Liu, J.; Mitra, I.; Philip, C.; Odundo, E.; Reyes, F.; Simons, M.P.; Fraser, J.A.; Hutley, E.; et al. Comparison of stool collection and storage on Whatman FTA Elute cards versus frozen stool for enteropathogen detection using the TaqMan Array Card PCR assay. PLoS ONE 2018, 13, e0202178. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  44. Cromeans, T.; Jothikumar, N.; Lee, J.; Collins, N.; Burns, C.C.; Hill, V.R.; Vinjé, J. A new solid matrix for preservation of viral nucleic acid from clinical specimens at ambient temperature. J. Virol. Methods 2019, 274, 113732. [Google Scholar] [CrossRef] [PubMed]
  45. Zhang, H.; Morrison, S.; Tang, Y.-W. Multiplex Polymerase Chain Reaction Tests for Detection of Pathogens Associated with Gastroenteritis. Clin. Lab. Med. 2015, 35, 461–486. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  46. Rogawski, E.T.; Liu, J.-L.; Platts-Mills, J.; Kabir, F.; Lertsethtakarn, P.; Siguas, M.; Khan, S.S.; Praharaj, I.; Murei, A.; Nshama, R.; et al. Use of quantitative molecular diagnostic methods to investigate the effect of enteropathogen infections on linear growth in children in low-resource settings: Longitudinal analysis of results from the MAL-ED cohort study. Lancet Glob. Health 2018, 6, e1319–e1328. [Google Scholar] [CrossRef] [Green Version]
  47. Spina, A.; Kerr, K.; Cormican, M.; Barbut, F.; Eigentler, A.; Zerva, L.; Tassios, P.; Popescu, G.; Rafila, A.; Eerola, E.; et al. Spectrum of enteropathogens detected by the FilmArray GI Panel in a multicentre study of community-acquired gastroenteritis. Clin. Microbiol. Infect. 2015, 21, 719–728. [Google Scholar] [CrossRef] [Green Version]
  48. Machiels, J.D.; Cremers, A.; Van Bergen-Verkuyten, M.C.G.T.; Paardekoper-Strijbosch, S.J.M.; Frijns, K.C.J.; Wertheim, H.F.L.; Rahamat-Langendoen, J.; Melchers, W.J.G. Impact of the BioFire FilmArray gastrointestinal panel on patient care and infection control. PLoS ONE 2020, 15, e0228596. [Google Scholar] [CrossRef]
  49. Buss, S.N.; Leber, A.; Chapin, K.; Fey, P.D.; Bankowski, M.J.; Jones, M.K.; Rogatcheva, M.; Kanack, K.J.; Bourzac, K.M. Multicenter Evaluation of the BioFire FilmArray Gastrointestinal Panel for Etiologic Diagnosis of Infectious Gastroenteritis. J. Clin. Microbiol. 2015, 53, 915–925. [Google Scholar] [CrossRef] [Green Version]
  50. Zhan, Z.; Guo, J.; Xiao, Y.; He, Z.; Xia, X.; Huang, Z.; Guan, H.; Ling, X.; Li, J.; Diao, B.; et al. Comparison of BioFire FilmArray gastrointestinal panel versus Luminex xTAG Gastrointestinal Pathogen Panel (xTAG GPP) for diarrheal pathogen detection in China. Int. J. Infect. Dis. 2020, 99, 414–420. [Google Scholar] [CrossRef]
  51. Huang, R.S.; Johnson, C.L.; Pritchard, L.; Hepler, R.; Ton, T.T.; Dunn, J.J. Performance of the Verigene(R) enteric pathogens test, Biofire FilmArray gastrointestinal panel and Luminex xTAG(R) gastrointestinal pathogen panel for detection of common enteric pathogens. Diagn. Microbiol. Infect. Dis. 2016, 86, 336–339. [Google Scholar] [CrossRef] [PubMed]
  52. Yen, C.; Jakob, K.; Esona, M.D.; Peckham, X.; Rausch, J.; Hull, J.J.; Whittier, S.; Gentsch, J.R.; LaRussa, P. Detection of fecal shedding of rotavirus vaccine in infants following their first dose of pentavalent rotavirus vaccine. Vaccine 2011, 29, 4151–4155. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  53. Rand, K.H.; Tremblay, E.E.; Hoidal, M.; Fisher, L.B.; Grau, K.R.; Karst, S.M. Multiplex gastrointestinal pathogen panels: Implications for infection control. Diagn. Microbiol. Infect. Dis. 2015, 82, 154–157. [Google Scholar] [CrossRef] [PubMed]
  54. Ramanan, P.; Bryson, A.L.; Binnicker, M.J.; Pritt, B.S.; Patel, R. Syndromic Panel-Based Testing in Clinical Microbiology. Clin. Microbiol. Rev. 2018, 31, e00024-17. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  55. Goldenberg, S.D.; Bacelar, M.; Brazier, P.; Bisnauthsing, K.; Edgeworth, J.D. A cost benefit analysis of the Luminex xTAG Gastrointestinal Pathogen Panel for detection of infectious gastroenteritis in hospitalised patients. J. Infect. 2015, 70, 504–511. [Google Scholar] [CrossRef] [Green Version]
  56. Claas, E.C.; Burnham, C.A.; Mazzulli, T.; Templeton, K.; Topin, F. Performance of the xTAG(R) gastrointestinal pathogen panel, a multiplex molecular assay for simultaneous detection of bacterial, viral, and parasitic causes of infectious gastroenteritis. J. Microbiol. Biotechnol. 2013, 23, 1041–1045. [Google Scholar] [CrossRef] [Green Version]
  57. Dik, J.H.; Poelman, R.; Friedrich, A.W.; Niesters, H.G.M.; Rossen, J.W.A.; Sinha, B. Integrated Stewardship Model Comprising Antimicrobial, Infection Prevention, and Diagnostic Stewardship (AID Stewardship). J. Clin. Microbiol. 2017, 55, 3306–3307. [Google Scholar] [CrossRef] [Green Version]
  58. Adams, C.; Peterson, S.R.; Hall, A.J.; Parashar, U.; Lopman, B.A. Associations of infection control measures and norovirus outbreak outcomes in healthcare settings: A systematic review and meta-analysis. Expert Rev. Anti-Infect. Ther. 2022, 20, 279–290. [Google Scholar] [CrossRef]
Table
Table 1. Literature search strategy for MEDLINE.
Table 1. Literature search strategy for MEDLINE.
Search NoSearch Strategy
1africa* [Title/Abstract]
2resource-poor [Title/Abstract]
3tropic* [Title/Abstract]
4(low income [Title/Abstract]) OR (middle income [Title/Abstract])
5equatorial region [Title/Abstract]
6developing countries [Title/Abstract]
7“Poverty Areas” [Mesh]
8“Africa” [Mesh]
9“Developing Countries” [Mesh]
10“Molecular Diagnostic Techniques” [Mesh]
11“Polymerase Chain Reaction” [Mesh]
12“Real-Time Polymerase Chain Reaction” [Mesh]
13“Reverse Transcriptase Polymerase Chain Reaction” [Mesh]
14“Multiplex Polymerase Chain Reaction” [Mesh]
15“Nucleic Acid Amplification Techniques” [Mesh]
16PCR [Title/Abstract] OR polymerase chain reaction [Title/Abstract] OR nucleic acid amplification [Title/Abstract]
17(syndromic panel* [Title/Abstract]) OR (syndromic multiplex [Title/Abstract]) OR (syndromic test* [Title/Abstract])
18(cartridge-based real-time PCR[Title/Abstract]) OR (cartridge-based PCR[Title/Abstract]) OR (cartridge-based test* [Title/Abstract]) OR (cartridge-based NAAT [Title/Abstract]) OR (cartridge-based Nucleic Acid Amplification Test [Title/Abstract])
19“Viruses” [Mesh]
20viral [Title/Abstract] OR virus [Title/Abstract]
21“Sapovirus” [Mesh]
22“Rotavirus Infections” [Mesh]
23“Rotavirus” [Mesh]
24“norovirus” [MeSH Terms]
25“Avastrovirus” [Mesh]
26“Adenoviridae” [Mesh]
27“Adenoviridae Infections” [Mesh]
28“Astroviridae” [Mesh]
29sapovir* or rotavir* or norovir* or astrovir* or adenovir*
30“Gastroenteritis” [Mesh]
31“Diarrhea” [Mesh]
32gastroenteritis [Title/Abstract] OR enteritis [Title/Abstract] OR gastrointestinal infec-tion [Title/Abstract] OR diarrhea [Title/Abstract] OR travellers disease [Title/Abstract]
33#1 OR #2 OR #3 OR #4 OR #5 OR #6 OR #7 OR #8 OR #9
34#10 OR #11 OR #12 OR #13 OR #14 OR #15 OR #16 OR #17 OR #18
35#19 or #20 or #21 or #22 or #23 or #24 or #25 or #26 or #27 or #28 or #29
36#30 or #31 or #32
37#33 and #34 and #35 and #36
Table
Table 2. Currently available cartridge-based commercial multiplex panels for AG pathogens.
Table 2. Currently available cartridge-based commercial multiplex panels for AG pathogens.
ManufacturerGastrointestinal Panel
BiomerieuxFilmArray Gastrointestinal (GI) Panel
LuminexVerigene Enteric Pathogens Test
QiagenQIAstat-Dx Gastrointestinal Panel
Table
Table 3. Baseline characteristics of frequently included pathogens in multiplex PCR panels.
Table 3. Baseline characteristics of frequently included pathogens in multiplex PCR panels.
VirusMode of TransmissionTarget PopulationIncubation Period (Days)Clinical SignificanceVaccination
SapovirusFecal–oral; food and waterInfants and young children; adults less frequently1–2Mild to moderate gastroenteritisNo
RotavirusFecal–oral; food and waterInfants and young children; adults less frequently1–2Moderate to severe gastroenteritis, including severe dehydration; hospital-acquired infections occurYes
NorovirusFecal–oral; food and water; possibly via aerosolsAll age groups1–2Moderate to severe gastroenteritis, including hospital-acquired infections; prolonged shedding in immunocompromised patientsNo
AstrovirusFecal–oral; food and waterYoung children; adults less frequently1–2Mild to moderate gastroenteritis, including asymptomatic infectionsNo
AdenovirusFecal–oral; food and waterInfants and young children; adults less frequently>7Moderate to severe gastroenteritis, including hospital-acquired infections; possible persistence in immunocompromised patientsNo
Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Share and Cite

MDPI and ACS Style

Kramme, S.; Dähne, T.; Fomenko, A.; Panning, M. Acute Viral Gastrointestinal (GI) Infections in the Tropics—A Role for Cartridge-Based Multiplex PCR Panels? Trop. Med. Infect. Dis. 2022, 7, 80. https://0-doi-org.brum.beds.ac.uk/10.3390/tropicalmed7050080

AMA Style

Kramme S, Dähne T, Fomenko A, Panning M. Acute Viral Gastrointestinal (GI) Infections in the Tropics—A Role for Cartridge-Based Multiplex PCR Panels? Tropical Medicine and Infectious Disease. 2022; 7(5):80. https://0-doi-org.brum.beds.ac.uk/10.3390/tropicalmed7050080

Chicago/Turabian Style

Kramme, Stefanie, Theo Dähne, Alexey Fomenko, and Marcus Panning. 2022. "Acute Viral Gastrointestinal (GI) Infections in the Tropics—A Role for Cartridge-Based Multiplex PCR Panels?" Tropical Medicine and Infectious Disease 7, no. 5: 80. https://0-doi-org.brum.beds.ac.uk/10.3390/tropicalmed7050080

Article Metrics

Back to TopTop