Gastrointestinal Pathogens in Hospitalized Pediatric Patients in Northern Morocco: Insights from the BioFire® FilmArray® Gastrointestinal Panel

Hajar Sabri^1,2*, Reda Amrani Souhli^1,2, Youssra Amekran¹, Yousra El boussadni³, Karima Rissoul^1,2

Affiliation:

¹Microbiology-Virology Laboratory, General University Hospital Mohammed VI, Tangier, Morocco

²Department of Medical Biology, Faculty of Medicine and Pharmacy, Abdelmalek Essaadi University, Tangier, Morocco.

³Pediatrics Service, Faculty of Medicine and Pharmacy, Abdelmalek Essaadi University, Tangier, Morocco

*Corresponding author:

Hajar Sabri, Department of Medical Biology, Faculty of Medicine and Pharmacy, Abdelmalek Essaadi University, Tangier, Morocco.

Received: March 28, 2026;Accepted: April 02, 2026;Published: April 13, 2026

Introduction

Gastrointestinal infections (GIs) are a global pediatric health concern. They are among the leading causes of morbidity and mortality worldwide. disproportionately affecting children under five years of age [1,2]. Their clinical presentation (diarrhea, vomiting, abdominal pain, and fever) is largely nonspecific, making it difficult to identify the causative pathogen based on clinical findings alone [3]. Although stool culture remains a reference method, its turnaround time of 2 to 5 days, limited sensitivity, and inability to detect viral or parasitic agents restrict its clinical utility [4,5]. In the absence of an identified causative pathogen, empirical antibiotic therapy is commonly initiated, carrying risks of promoting antimicrobial resistance and potential harm in viral or self-limited infections [6-8].

In the last few years, there has been a significant progress in infections disease diagnostics, with the transition from traditional methods to syndromic-based diagnosis [9]. These methods use molecular assays that simultaneously detect several pathogens including bacteria, viruses, fungi and parasites within a few hours [10]. The BioFire® FilmArray® Gastrointestinal Panel (GIP) simultaneously targets 22 enteric pathogens and has shown high sensitivity and specificity in multiple clinical settings [4]. It requires minimal technical expertise, works directly from stool samples without prior culture, and has demonstrated high sensitivity and specificity across multiple clinical settings [4]. These features make it particularly useful in pediatric care, where a rapid and broad diagnostic workup is often needed [11]. Despite growing data on GIP performance in adult and mixed populations, few studies have looked at how detected pathogens differ by age group in hospitalized children [12].

This study was conducted at the General University Hospital Mohammed VI of Tangier, Morocco. It aimed to evaluate the distribution of gastrointestinal pathogens detected by the BioFire® FilmArray® GIP in hospitalized pediatric patients, to characterize age-specific differences in detection rates, and to describe co-infection patterns along with their clinical implications.

Materials and Methods

Study design and patients

This retrospective descriptive study analyzed 101 samples of pediatric patients who were admitted to the General University Hospital Mohammed VI of Tangier, Morocco, from June 2023 to January 2026, and underwent multiplex gastrointestinal panel (GIP) testing during the study period. We evaluated the results of samples of patients under 18 years old and both sexes were eligible for inclusion. Records with incomplete demographic or microbiological data were excluded.

Stool samples collected within routine clinical practice were examined using the BioFire® FilmArray® GI Panel at the request of an infectious disease specialist.

Data collection

For each pediatric patient, demographic and clinical data were extracted. Collected information included age, sex, clinical service of origin, symptoms, and GIP test results.

We categorized the samples into three groups: Group A,

young infants (<6 months), Group B, toddlers (6 months- 2

years), and Group C, children (>2 years). Clinical services were classified into general pediatrics, pediatric emergency, neonatal intensive care unit (ICU), pediatric ICU and Pediatric surgery.

Gastrointestinal panel testing

Stool samples were analyzed using the BioFire® FilmArray® Gastrointestinal (GI) Panel, a fully automated multiplex PCR system. The panel simultaneously detects 22 enteric pathogens, including 13 bacteria, 5 viruses, and 4 parasites, directly from stool specimens.

The bacterial pathogens included Campylobacter spp, (C. jejuni, C. coli, C. upsaliensis), Clostridioides dificile (toxin A/B), Plesiomonas shigelloides, Yersinia enterocolitica, Vibrio spp. (V. parahaemolyticus, V. vulnificus) and Vibrio Cholerae, and diarrheagenic Escherichia coli pathotypes (enteropathogenic E. coli (EPEC), enteroaggregative E. coli (EAEC), enterotoxigenic E. coli (ETEC), Shiga toxin producing E. coli (STEC), and E. coli O157).

Viral targets included Norovirus GI/GII, Rotavirus A, Adenovirus F (40/41), Astrovirus, and Sapovirus (I, II, IV, and V).

Parasitic targets included Giardia lamblia, Cryptosporidium spp., Entamoeba histolytica, and Cyclospora cayetanensis.

Statistical analysis

Data analysis was performed using SPSS version 26.0. Categorical variables were presented as frequencies and percentages. Comparisons between groups were performed using the chi-square test to assess associations between infection types and age groups. A p-value < 0.05 was considered statistically significant.

Results

A total of 101 pediatric patients were included: 61 males (60.4%) and 40 females (39.6%). They were distributed across three age groups: Group A (<6 months, n = 33), Group B (6 months–2 years, n = 32), and Group C (>2 years, n = 36). The most frequently reported symptom was diarrhea (73.3%), followed by vomiting (41.6%), fever (32.7%), and abdominal pain (15.8%). Most patients were admitted to the general pediatric ward (73.3%), with smaller proportions from the pediatric emergency unit (12.9%), neonatal Intensive Care Unit (ICU) (5.9%), and pediatric ICU (5.0%) (Table 1).

Among the 74 positive samples, single pathogen detection was observed in 30 samples (29.7%), whereas co- detections involving two or more pathogens were recorded in 44 samples (43.6%). Co-detection rates was strongly age- dependent, being the lowest in Group A (7/33,21.2%) and essentially higher in Group B (18/32, 56.3%) and Group C (19/36, 52.8%). Double detections cere the predominant co-detection pattern, representing 21 samples (20.8%), followed by triple detections in 15 samples (14.9%) and detections of four or more pathogens in 8 samples (7.9%) (Table 2).

Table 3 illustrates the distribution of all detected pathogens across the three age groups. The overall positivity rate was 73.3% (74/101), with a statistically significant increase across age groups: 51.5% in Group A (<6 months),

Table 1: Demographic and clinical characteristics of patients included in the study.

81.2% in Group B (6 months- 2 years), and 86.1% in Group

C (>2 years) (p = 0.002).

Bacterial pathogens accounted for the majority of detections, with EAEC and EPEC being the most prevalent (20.8% each), followed by Campylobacter (17.8%), Clostridium dificile toxin A/B (11.9%), and Salmonella (7.6%). STEC showed a statistically significant age- dependent increase, with no detections recorded in Group A and B compared to 13.9% in Group C (p=0.037). Although a comparable age-dependent gradient was noted for Shigella/EIEC, the observed difference did fell short of statistical significance (p=0.065). Among viral pathogens Norovirus GI/GII (12.9%) and Rotavirus A (11.9%) were identified across all age groups, while Adenovirus F 40/41 was detected exclusively in Group B (12.5%, p = 0.011). Parasitic pathogens followed a clear maturational gradient, with Giardia lamblia appearing in Group B (3.1%) and peaking in Group C (13.9%, p = 0.037), and Cryptosporidium exclusively identified to Group C (5.6%).

Table 4 summarizes the distribution of co-detected pathogen pairs across age groups, revealing both consistent and age-specific patterns. EAEC+ EPEC was the most frequent combination overall (n = 9), identified in all three groups, followed by EPEC + Campylobacter (n = 7), with a predominance Group A (n = 4). Age-specific co-detection patterns were observed in both Group B and Group C. In Group B, Adenovirus F 40/41, containing pairs and Norovirus GI/GII, Salmonella combination (n = 3) were identified. Whereas in Group C, ETEC-associated combinations were characterized including Giardia lamblia, Shigella, EIEC (n = 2). The absence of parasitic co-detections in Group A further support the age-dependent pattern of parasitic pathogen acquisition documented in this study.

Table 2: Positivity rates of BioFire® FilmArray® Gastrointestinal Panel pathogens.

Table 3: Distribution of pathogens according to age groups.

EPEC, enteropathogenic Escherichia coli; EAEC, enteroaggregative Escherichia coli; ETEC, enterotoxigenic Escherichia coli; STEC, Shiga toxin-producing Escherichia coli; EIEC, enteroinvasive Escherichia coli. * p < 0.05.

Table 4: Distribution of major co-detected pathogens by age group.

EPEC, enteropathogenic Escherichia coli; EAEC, enteroaggregative Escherichia coli; ETEC, enterotoxigenic Escherichia coli; STEC, Shiga toxin-producing Escherichia coli; EIEC, enteroinvasive Escherichia coli; C. dificile, Clostridium dificile.

Discussion

The overall positivity rate of 73.3% observed in our study is consistent with previously published data using the BioFire® FilmArray® GIP. Zhan et al. [13] reported a comparable rate of 65% in a Chinese multicenter study and Chung et al. [12] reported an overall positivity rate of 50.9% in a pediatric cohort, which is lower than the rate observed in our study. Multiplex gastrointestinal PCR panels results have described an age-related increase in enteropathogenic positivity; In a multicenter study using the same platform, children aged between one and five years receives significantly higher rates of positivity compared with infants younger than one year [4]. Likewise, Ho et al. [14] showed that age ≥1 year was independently associated with a greater likelihood of actionable gastrointestinal panel results, particularly in children aged 2–5 years. Consistent with these findings, our results showed increasing positivity with age, with the highest rate observed in children older than 2 years (86.1%).

Bacterial agents were predominant (71%), with EAEC and EPEC being the most frequently detected (20.8% each). Some recent molecular epidemiological investigations have shown that Enteropathogenic E. coli (EPEC) and Enteroaggregative E. coli (EAEC) are two of the most commonly reported diarrhoeagenic pathogens of acute diarrhea in children. In studies employing multiplex PCR panels, EPEC often ranks as the most prevalent pathotype detected, with EAEC also commonly identified at high rates, highlighting the contribution of these E. coli pathotypes towards the global pediatric diarrheal burden [15,16]. The high prevalence of diarrheagenic E. coli pathotypes in our study likely reflects local environmental and epidemiological conditions, as similarly reported in other developing-country settings [17]. STEC and Shigella/EIEC were both detected at significantly higher rates in older age groups (p = 0.037 and p = 0.065, respectively), consistent with the foodborne and environmental transmission dynamics of these pathogens, whose clinical relevance increase as children transition from exclusive breastfeeding to diversified dietary practices [17,18].

Among viral pathogens, Norovirus GI/GII (12.9%) and Rotavirus A (11.9%) were identified at similar rates across all age groups, reflecting their broad endemic transmission in pediatric populations with incomplete immunization coverage [19-21]. The persistent detection of Rotavirus A regardless of age may further sustained by the residual disruption of routine childhood vaccination programs in the post-COVID-19 era, with global routine vaccine uptake yet to fully recover to pre-pandemic levels as of 2023 [22,23].

The exclusive detection of Adenovirus F 40/41 in Group B (12.5%, p = 0.011) is consistent with the established age-specific distribution of enteric Adenovirus infection, selectively affecting children under 24 months, as documented in a North African pediatric study [24]. Parasitic pathogens demonstrated a well-defined age-dependent distribution, being entirely absent from Group A and progressively more frequent in older children. Giardia lamblia was detected in Group B (3.1%) and Group C (13.9%, p = 0.037), while Cryptosporidium was identified exclusively in two Group C patients only. A review on global prevalence confirms that Cryptosporidium and Giardia are major causes of GIs in children and are widely reports across different geographic regions [15]. This age-dependent pattern reflects the progressive increase in environmental pathogen exposure as children become more mobile and transition to shared food and school settings [25].

The clinical presentation in our study (diarrhea (73.3%), vomiting (41.6%), fever (32.7%), and abdominal pain (15.8%) fit the typical picture of acute gastroenteritis. Symptoms, however, do not in themselves prove cause, as organisms, including EPEC, EAEC, or Clostridium dificile, are often noted [26]. Every one of these is a known colonizer in the infant gut and has the potential to remain in stool without causing disease [27-29]. C. difficile is a well-documented example: asymptomatic colonization reaches as high as 50% in neonates and young infants, and a positive result in this age group requires a cautious clinical approach and not automatic therapy [15,30].

The profile of EPEC and EAEC is similar, and they have been widely shed by healthy children in resource- limited settings; environmental contaminants keep their fecal-oral circulation intact irrespective of clinical condition [17,31]. Further complicating the situation, the FilmArray® GIP is unable to distinguish typical forms from atypical EPEC strains [4]. Clinical studies show that typical strains harbor both the Locus of Enterocyte Effacement (LEE) and the adherence factor plasmid and are related to frank diarrheal disease, while atypical strains are devoid of this plasmid and act as low-virulence commensals in children exposed to polluted contexts [16,32]. Given that the assay targets the eae gene shared by the two variants, a positive EPEC signal might reflect colonization by a clinically silent strain as well as actual infection [33,34]. The detection of EPEC and EAEC should be interpreted with caution [34]. Both pathotypes are also commonly co-detected with other enteropathogens, which raise the debate about their actual mode of pathogenesis versus asymptomatic carriage [34,35]. In a large pediatric study E. coli pathotypes are frequently detected in healthy children without symptoms, indicating asymptomatic carriage where detection alone does not imply a clinical disease requiring [36]. These findings underscore the interpretative difficulties of syndromic molecular testing and the necessity of clinical correlation when making a causal association between detection and disease [37,38].

Co-detection between two or more pathogens was detected in 43.6% of samples compared to 31.5% for multicenter study (4), 30.2%, as reported by Spina et al. [27], and the 37.7% in Carmon et al. [39] in a hospitalized Israeli population [39]. Co-detections increased significantly with age: 21.2% in Group A compared with 56.3% in Group B and 52.8% in Group C. The interpretation of co-detections continues to be difficult since there are multiple pathogens, and different pathogens could present at once, hindering the detection of the primary causative agent [40]. This is complicated by the extended shedding of pathogens including Norovirus and Salmonella, where a positive PCR result may reflect a prior resolved infection rather than active disease [41].

In summary, these results reaffirm that the BioFire® FilmArray® GIP fills an important diagnostic gap in pediatric infectious gastroenteritis that has not been fully addressed by single-target assays or stool culture. Through rapid detection of 22 enteric pathogens within less than an hour, it enhances etiological assessment and supports timely bedside clinical decision-making in hospitalized children.

Limitations

The study was conducted in a single center with a relatively small simple size. Additionally, while the GIP provides a large and rapid detection of many gastrointestinal pathogens, it does not include certain viruses relevant in young infants, such as Enterovirus and Parechovirus.

Conclusion

This study highlights the diagnostic value of BioFire® FilmArray® GIP in hospitalized children with suspected gastroenteritis, particularly through the identification of age- related pathogen distribution patterns and co-detections not readily detected by conventional methods. Further studies integrating quantitative PCR are required to establish age-specific pathogen-load thresholds and strengthen antimicrobial stewardship in resource-limited pediatric settings.

Acknowledgments

The authors would like to thank the staff of the participating laboratory and hospital for their technical assistance and support during sample collection and analysis.

Funding Source

No external funding for this manuscript.

Financial Disclosure

All authors have indicated they have no financial

relationships relevant to this article to disclose.

Conflict of Interest

The authors have no potential conflicts to disclose.

Authors’ contributions

H.S and K.R, study conception and design. KR, supervision and critical evaluation. H.S and Y.A, writing and interpretation, R.A.S, data analysis. Y.E, reviewing.

References

1. Walker CLF, Rudan I, Liu L, et al. Global burden of childhood pneumonia and diarrhoea. Lancet 381 (2013): 1405-1416.
2. GBD 2016 DALYs and HALE Collaborators. Global, regional, and national disability-adjusted life-years (DALYs) for 333 diseases and injuries and healthy life expectancy (HALE) for 195 countries and territories, 1990-2016: a systematic analysis for the Global Burden of Disease Study 2016. Lancet 390 (2017): 1260-1344.
3. 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 78 (2024): 573-581.
4. Buss SN, Leber A, Chapin K, et Multicenter evaluation of the BioFire FilmArray gastrointestinal panel for etiologic diagnosis of infectious gastroenteritis. Journal of Clinical Microbiology 53 (2015): 915-925.
5. Fraij O, Castro N, de Leon Castro LA, et Stool cultures show a lack of impact in the management of acute gastroenteritis for hospitalized patients in the Bronx, New York. Gut Pathogens 12 (2020): 30.
6. Bruzzese E, Giannattasio A, Guarino A. Antibiotic treatment of acute gastroenteritis in children. F1000Research 7 (2018): 193.
7. Lim CJ, Kong DC, Stuart RL. Reducing inappropriate antibiotic prescribing in the residential care setting: current perspectives. Clinical Interventions in Aging 9 (2014): 165-177.
8. Kim YJ, Park KH, Park DA, et al. Guideline for the Antibiotic Use in Acute Gastroenteritis. Infection & Chemotherapy 51 (2019): 217-243.
9. Ligero-López J, García-Rodríguez J, Ruiz-Carrascoso
10. Diagnosis of gastrointestinal infections: comparison between traditional microbiology and a commercial syndromic molecular-based panel. FEMS Microbiology Letters 370 (2023): fnad122.
11. Dumkow LE, Worden LJ, Rao Syndromic diagnostic testing: a new way to approach patient care in the treatment of infectious diseases. Journal of Antimicrobial Chemotherapy 76 (2021): iii4-iii11.
12. Jiménez-Jiménez AB, Galán-Sánchez F, García-López Hortelano M, et al. Acute infectious gastroenteritis in childhood: the role of rapid multiplex molecular syndromic panels in diagnosis and clinical management. Revista Española de Quimioterapia 38 (2025): 258-277.
13. Chung YN, Jeon JS. Clinical Utility of FilmArray Gastrointestinal Panel among Newborn and Infant Patients in a Tertiary Hospital in American Journal of Biochemistry and Biotechnology 21 (2025): 56-59.
14. Zhan Z, Guo J, Xiao Y, et al. Comparison of BioFire FilmArray gastrointestinal panel versus Luminex xTAG Gastrointestinal Pathogen Panel (xTAG GPP) for diarrheal pathogen detection in China. International Journal of Infectious Diseases 99 (2020): 414-420.
15. Ho EC, Cotter JM, Thomas J, et al. Factors Associated With Actionable Gastrointestinal Panel Results in Hospitalized Hospital Pediatrics 13 (2023):1115-1123.
16. Bitilinyu-Bangoh JEV, Riesebosch S, Rebel M, et al. Prevalence of Cryptosporidium and Giardia infections in under-five children with diarrhoea in Blantyre, Malawi. BMC Infectious Diseases 24 (2024): 68.
17. Kaur P, Dudeja Pathophysiology of Enteropathogenic Escherichia coli-induced Diarrhea. Newborn 2 (2023):102-113.
18. Platts-Mills JA, Babji S, Bodhidatta L, et al. Pathogen- specific burdens of community diarrhoea in developing countries: a multisite birth cohort study (MAL-ED). Lancet Global Health 3 (2015): e564-e575.
19. Gharpure R, Marsh ZA, Tack DM, et al. Disparities in Incidence and Severity of Shigella Infections Among Children—Foodborne Diseases Active Surveillance Network (FoodNet), 2009-2018. Journal of the Pediatric Infectious Diseases Society (2021).
20. Riera-Montes M, O’Ryan M, Verstraeten T. Norovirus and Rotavirus Disease Severity in Children: Systematic Review and Meta-analysis. Pediatric Infectious Disease Journal 37 (2018): 501-505.
21. Hall AJ, Lopman BA, Payne DC, et Norovirus Disease in the United States. Emerging Infectious Diseases 19 (2013): 1198-1205.
22. Saha R, Lo M, De P, et al. Epidemiology of viral gastroenteritis in children and genetic diversity of rotavirus strains in Kolkata, West Bengal after introduction of rotavirus vaccine. Vaccine 45 (2025): 126637.
23. Burnett E, Parashar UD, Winn A, et Trends in Rotavirus Laboratory Detections and Internet Search Volume Before and After Rotavirus Vaccine Introduction and in the Context of the Coronavirus Disease 2019 Pandemic— United States, 2000–2021. Journal of Infectious Diseases 225 (2022): jiac062.
24. Jones Routine Vaccination Coverage — Worldwide, Morbidity and Mortality Weekly Report 73 (2024).
25. Sdiri-Loulizi K, Gharbi-Khélifi H, de Rougemont A, et al. Acute infantile gastroenteritis associated with human enteric viruses in Tunisia. Journal of Clinical Microbiology 46 (2008): 1349-1355.
26. Squire SA, Ryan U. Cryptosporidium and Giardia in Africa: current and future Parasites & Vectors 10 (2017): 195.
27. Truong J, Cointe A, Le Roux E, et al. Clinical impact of a gastrointestinal PCR panel in children with infectious diarrhoea. Archives of Disease in Childhood 107 (2022): 601-605.
28. Spina A, Kerr KG, Cormican M, et al. Spectrum of enteropathogens detected by the FilmArray GI Panel in a multicentre study of community-acquired Clinical Microbiology and Infection 21 (2015): 719-728.
29. Ochoa TJ, Barletta F, Contreras C, et New insights into the epidemiology of enteropathogenic Escherichia coli infection. Transactions of the Royal Society of Tropical Medicine and Hygiene 102 (2008): 852-856.
30. Singh T, Das S, Ramachandran VG, et al. Typical & atypical enteropathogenic Escherichia coli in diarrhoea & their role as carrier in children under five. Indian Journal of Medical Research 145 (2017): 551-557.
31. Brennhofer SA, Rogawski McQuade ET, Liu J, et al. Clostridioides difficile colonization among very young children in resource-limited settings. Clinical Microbiology and Infection 28 (2022): 996-1002.
32. Kehl A, Bader L, Kaiping AC, et al. Enteropathogenic Escherichia coli revisited - New insights into old EPEC isolates using whole genome sequencing. International Journal of Medical Microbiology 320 (2025): 151659.
33. Ahmad OM, Rukh S, Dos Santos Pereira S, et al. A Comprehensive Review of the Role of Virulence Factors in Enteropathogenic Escherichia coli-Induced Intestinal Injury. Cureus 17 (2025): e83475.
34. Hu J, Torres Enteropathogenic Escherichia coli: foe or innocent bystander? Clinical Microbiology and Infection 21 (2015): 729-734.
35. Kralicek SE, Sitaraman LM, Kuprys PV, et Clinical manifestations and stool load of atypical enteropathogenic E. coli infections in U.S. children and adults. Gastroenterology 163 (2022): 1321-1333.
36. Kaur P, Chakraborti A, Asea A. Enteroaggregative Escherichia coli: An Emerging Enteric Food Borne Pathogen. Interdisciplinary Perspectives on Infectious Diseases 2010 (2010): 254159.
37. Llorente MT, Muadica AS, Dashti A, et Molecular-based evidence for school transmission of enteroaggregative Escherichia coli among apparently healthy children attending nursery, infant, and primary schools in Madrid (Spain). European Journal of Pediatrics 184 (2025): 658.
38. Baker JM, Hasso-Agopsowicz M, Pitzer VE, et al. Association of enteropathogen detection with diarrhoea by age and high versus low child mortality settings: a systematic review and meta-analysis. Lancet Global Health 9 (2021): e1402-e1410.
39. Diaz JN, Iannotti LL, Louis Dulience SJ, et Prevalence of diarrheagenic Escherichia coli and impact on child health in Cap-Haitien, Haiti. PLOS Global Public Health 3 (2023): e0001863.
40. Carmon D, Rohana H, Azrad M, et The Impact of a Positive Biofire® FilmArray® Gastrointestinal Panel Result on Clinical Management and Outcomes. Diagnostics 13 (2023): 1094.
41. Potgieter N, Heine L, Ngandu JPK, et High Burden of Co-Infection with Multiple Enteric Pathogens in Children Suffering with Diarrhoea from Rural and Peri-Urban Communities in South Africa. Pathogens 12 (2023): 315.
42. Hadad L, Avelson N, Goldberger M, et Asymptomatic Shedding of Enteric Viruses in Young Children: Insights From a Year-Long Prospective Surveillance Study. Journal of Medical Virology 97 (2025): e70694.