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# The benefits of molecular testing in acute gastroenteritis diagnosis
- URL: https://med-techinsights.com/the-benefits-of-molecular-testing-in-acute-gastroenteritis-diagnosis/
- Published: 2026-05-11T14:26:27.000Z
- Updated: 2026-10-23T02:40:08.000Z
- Description: Diarrhoea caused by acute gastroenteritis continues to place a heavy burden on global health systems. Although many people recover quickly with only short lived issues, such as vomiting, nausea, abdominal pain or cramping, the condition can also lead to far more severe outcomes.1 In 2021, diarrhoea
- Author: Oliver Johnson
- Tags: Insights, Research & Development

Diarrhoea caused by acute gastroenteritis continues to place a heavy burden on global health systems. Although many people recover quickly with only short lived issues, such as vomiting, nausea, abdominal pain or cramping, the condition can also lead to far more severe outcomes.1 In 2021, diarrhoea accounted for more than one million deaths around the world and remained the leading cause of mortality in children under five.2 In Europe, a study reported that 771,834 people were discharged from hospital annually for all-cause acute gastroenteritis.3 The illness often begins abruptly and resolves without medical intervention, but symptoms can occasionally include blood in the stool and may require clinical attention.1

###### **The pathogens responsible**

Figures from 2023 show that bacterial causes of acute gastroenteritis continued to rise. *Campylobacter* topped the list again, with *Salmonella* following as the second most commonly reported pathogen, and both increased in numbers compared with 2022.4 Shiga toxin-producing *Escherichia coli* (STEC) was third, with *Yersinia enterocolitica* appearing next in the rankings.4 Traveller’s diarrhoea, however, tends to be dominated by different organisms. Depending on the destination, the leading culprits are usually enterotoxigenic and enteroaggregative *E. coli*, as well as *Shigella*, though the prevalence of each varies widely between regions.5

Given the overlap in clinical presentation across a wide range of pathogens, accurate diagnostic pathways are central to guiding appropriate testing and treatment. Rapid identification helps clinicians to select the right approach and supports infection control efforts. This is especially important for suspected STEC infections, as Shiga toxins are known to cause haemolytic uraemic syndrome (HUS).6 In HUS, red blood cells become damaged and platelet levels fall, which in turn can progress to kidney injury.6 Although strains producing Shiga toxin 2 – particularly Stx2a – are most often implicated in HUS, Stx1a can also play a role, especially when it occurs alongside Stx2a.7,8 Testing strategies must therefore cover all eventualities, and molecular assays fit well here because they offer a fast and reliable way to identify both toxins, with positive samples typically forwarded to public health laboratories for culture-based confirmation and further characterisation.9

Beyond main causative pathogens, which are commonly recommended for testing in most national guidelines, there are more controversial targets.10 *Aeromonas* species are key examples: they are widespread in water sources and frequently colonise healthy individuals, but current evidence offers little support for a clear pathogenic role in diarrhoeal disease.11 Similar questions arise with *Clostridioides difficile*, which can be carried asymptomatically, but is particularly problematic in high risk patients such as older adults, individuals recently exposed to antibiotics, patients undergoing prolonged hospital or care home stays, those receiving acid-suppressive therapy, and people with weakened immune systems.12 Most guidance recommends reserving *C. difficile* testing for patients with substantial or persistent diarrhoea and relevant clinical risk factors, typically within a multistep approach to confirming toxin-producing strains.13

###### **A modern approach to GI diagnostics**

Whatever the cause, accurate and timely diagnosis plays a central role in managing gastrointestinal infections and supports effective treatment decisions. However, traditional approaches, including culture-based methods, have well-known drawbacks; they can be slow, often taking several days to pinpoint the relevant organism, which increases the risk of delayed or inappropriate therapy and reduces the opportunity for swift, targeted intervention.14

Molecular diagnostics have transformed GI testing, offering far greater sensitivity and markedly shorter turnaround times.15 Studies show that for organisms such as *Salmonella spp.*, *Shigella spp*., *Vibrio spp.* and *Campylobacter*, molecular methods can detect up to 50% more infections than conventional techniques.14 They also generate results within hours rather than days, enabling clinicians to act sooner and tailor treatment appropriately.14,15 Faster detection not only supports better patient outcomes but also helps guide timely isolation and other infection control measures.15

Multiplex molecular panels offer clear benefits by enabling simultaneous detection of several pathogens from a single sample. Although evidence on their broader clinical impact is still emerging, early findings are encouraging. A 2024 study in the US reported that routine panel use in paediatric emergency settings led to the identification of more organisms with clinical significance and reduced return visits by 21%.16 Additional research from a tertiary care centre – also in the US – showed that multiplex testing lessened the need for further diagnostic work, including follow-up laboratory tests and abdominal imaging, and contributed to a decline in prescribing unnecessary antibiotics. When test costs and downstream savings were combined, it was estimated that multiplex testing cut expenses by $293.61 per patient.14–17

Evidence from European healthcare settings highlights similar financial advantages of multiplex molecular testing. In one evaluation, Goldenburg *et al18* reported that although laboratories faced higher initial costs, the introduction of multiplex panels cut total isolation days from 2,202 to 1,447 within eight months, yielding net savings of £66,765 that more than compensated for the initial investment.18 A separate economic study reached comparable conclusions, showing that while multiplex enteric panels cost more than culture, they ultimately saved €27 per acute gastroenteritis episode overall and €185 per episode in children.19 These savings were attributed mainly to shorter hospital stays, fewer emergency visits and a lower likelihood of readmission.19

But what is the real cost of culture-based methods? One US study calculated that each culture required $10.37 in technologists’ time alone, based on a $27 per hour wage, and that positive results could take as long as 96 hours to finalise.20 Although molecular tests have higher direct costs, they tend to lower overall healthcare spending by delivering faster answers, reducing unnecessary treatments and cutting down on additional investigations.14

###### **Conclusion**

Above all, acute gastroenteritis remains a major global health issue, and the overlap in symptoms across many pathogens means laboratory testing is essential for accurate diagnosis. Evidence is mounting that molecular assays provide rapid, reliable identification, supporting appropriate treatment and helping to limit onward transmission.21 Although these assays perform extremely well, they complement rather than replace culture, which remains vital for susceptibility testing, strain typing and a thorough investigation of outbreaks.22 Public health bodies continue to recommend following up positive molecular results with targeted culture to allow full characterisation and population surveillance.23 Ultimately, using both approaches together in a complementary way gives healthcare teams the tools to strengthen routine diagnostics and improve outcomes for patients and public health alike.

**References:**

1\. Adedire O, Love NK, Hughes HE, Buchan I, Vivancos R, Elliot AJ. Early Detection and Monitoring of Gastrointestinal Infections Using Syndromic Surveillance: A Systematic Review. *Int J Environ Res Public Health*. 2024;21(4):489\. doi:10.3390/ijerph21040489

2\. Kyu HH, Vongpradith A, Dominguez RMV, et al. Global, regional, and national age-sex-specific burden of diarrhoeal diseases, their risk factors, and aetiologies, 1990–2021, for 204 countries and territories: a systematic analysis for the Global Burden of Disease Study 2021\. *Lancet Infect Dis*. 2025;25(5):519-536\. doi:10.1016/S1473-3099(24)00691-1

3\. Calduch EN, Cattaert T, Verstraeten T. Model estimates of hospitalization discharge rates for norovirus gastroenteritis in Europe, 2004–2015\. *BMC Infect Dis*. 2021;21(1):757\. doi:10.1186/s12879-021-06421-z

4\. The European Union One Health 2023 Zoonoses report. *EFSA Journal*. 2024;22(12). doi:10.2903/j.efsa.2024.9106

5\. Vila J. New molecular diagnostic tools in traveller’s diarrhea. *J Travel Med*. 2017;24(suppl\_1):S23-S28\. doi:10.1093/jtm/taw071

6\. Kakoullis L, Papachristodoulou E, Chra P, Panos G. Shiga toxin-induced haemolytic uraemic syndrome and the role of antibiotics: a global overview. *Journal of Infection*. 2019;79(2):75-94\. doi:10.1016/J.JINF.2019.05.018

7\. Melton-Celsa AR. Shiga Toxin (Stx) Classification, Structure, and Function. In: *Enterohemorrhagic Escherichia Coli and Other Shiga Toxin‐Producing E. Coli*. John Wiley & Sons, Ltd; 2015:37-53\. doi:[https://doi.org/10.1128/9781555818791.ch3](https://doi.org/10.1128/9781555818791.ch3?ref=med-techinsights.com)

8\. Costigan C, Wildes DM, Riordan M, Awan A, Gorman KM. Why exclude children with Shiga toxin genotype 1 alone from hemolytic uremic syndrome screening? *J Pediatr*. 2021;238:344-345\. doi:10.1016/j.jpeds.2021.07.060

9\. Vallières E, Saint-Jean M, Rallu F. Comparison of three different methods for detection of Shiga toxin-producing Escherichia coli in a tertiary pediatric care center. *J Clin Microbiol*. 2013;51(2):481-486\. doi:10.1128/JCM.02219-12

10\. Vallières E, Saint-Jean M, Rallu F. Comparison of three different methods for detection of Shiga toxin-producing Escherichia coli in a tertiary pediatric care center. *J Clin Microbiol*. 2013;51(2):481-486\. doi:10.1128/JCM.02219-12

11\. Michael JJ, L AS, J MC. Plesiomonas shigelloides Revisited. *Clin Microbiol Rev*. 2016;29(2):349-374\. doi:10.1128/cmr.00103-15

12\. Mada PK, Alam MU. *Clostridioides Difficile Infection*. 2025.

13\. McDonald LC, Gerding DN, Johnson S, et al. 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). *Clinical Infectious Diseases*. 2018;66(7):e1-e48\. doi:10.1093/cid/cix1085

14\. Beal SG, Tremblay EE, Toffel S, Velez L, Rand KH. A Gastrointestinal PCR Panel Improves Clinical Management and Lowers Health Care Costs. *J Clin Microbiol*. 2018;56(1). doi:10.1128/JCM.01457-17

15\. Zhang H, Morrison S, Tang YW. Multiplex Polymerase Chain Reaction Tests for Detection of Pathogens Associated with Gastroenteritis. *Clin Lab Med*. 2015;35(2):461-486\. doi:10.1016/j.cll.2015.02.006

16\. Pavia AT, Cohen DM, Leber AL, et al. Clinical Impact of Multiplex Molecular Diagnostic Testing in Children With Acute Gastroenteritis Presenting to an Emergency Department: A Multicenter Prospective Study. *Clinical Infectious Diseases*. 2024;78(3):573-581\. doi:10.1093/cid/ciad710

17\. Lewinski MA, Alby K, Babady NE, et al. Exploring the Utility of Multiplex Infectious Disease Panel Testing for Diagnosis of Infection in Different Body Sites: A Joint Report of the Association for Molecular Pathology, American Society for Microbiology, Infectious Diseases Society of America, and Pan American Society for Clinical Virology. *The Journal of Molecular Diagnostics*. 2023;25(12):857-875\. doi:[https://doi.org/10.1016/j.jmoldx.2023.08.005](https://doi.org/10.1016/j.jmoldx.2023.08.005?ref=med-techinsights.com)

18\. Goldenberg SD, Bacelar M, Brazier P, Bisnauthsing K, Edgeworth JD. A cost benefit analysis of the Luminex xTAG Gastrointestinal Pathogen Panel for detection of infectious gastroenteritis in hospitalised patients. *Journal of Infection*. 2015;70(5):504-511\. doi:[https://doi.org/10.1016/j.jinf.2014.11.009](https://doi.org/10.1016/j.jinf.2014.11.009?ref=med-techinsights.com)

19\. Ferrer J, Giménez E, Carretero D, et al. BD MAX Enteric Bacterial, Bacterial Plus, and Virus Panels for Diagnosis of Acute Infectious Gastroenteritis: a Cost-Benefit Analysis. *Microbiol Spectr*. 2022;10(5). doi:[https://doi.org/10.1128/spectrum.00880-22](https://doi.org/10.1128/spectrum.00880-22?ref=med-techinsights.com)

20\. Beal SG, Mesfin M, Ciurca J, Smith G, Gander RM. *Evaluation of Costs, Technologists’ Time and Turn‐around Times for Conventional Stool Cultures.* 2013.

21\. 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(5):80\. doi:10.3390/tropicalmed7050080

22\. Fleckenstein JM, Matthew Kuhlmann F, Sheikh A. Acute Bacterial Gastroenteritis. *Gastroenterol Clin North Am*. 2021;50(2):283-304\. doi:10.1016/j.gtc.2021.02.002

23\. Aphl. *Submission of Enteric Pathogens from Positive Culture‐Independent Diagnostic Test Specimens to Public Health: Interim Guidelines*.