Detection of gastrointestinal pathogens in oncology patients by highly multiplexed molecular panels

Abstract

We compared the frequency of gastrointestinal (GI) pathogen detection in an oncology patient population by two multiplexed molecular assays, the Luminex xTAG® GI Pathogen Panel (GPP, which identifies 14 GI pathogens) and the BioFire GI pathogen panel (BFGP, which identifies 22 GI pathogens). We additionally reviewed the clinical characteristics of patients tested with both panels. A total of 200 prospectively collected and 81 archived stool samples were tested by both panels. In the prospective cohort, the GPP and BFGP identified a pathogen in 33.5% (95% CI: 27.3–40.35%) and 39.6% (95% CI: 33.0%–46.6%) of samples respectively (p=0.25). The BFGP detected significantly more pathogens than the GPP (p=0.038) with 21.3% of samples positive for targets only detected by the BFGP. The concordance between the assays was very good at 91.1% (κ=0.8, 95% CI=0.7–0.9) when considering only pathogens detected by both assays. The most frequent pathogens detected were Clostridium difficile, Norovirus, Campylobacter and Salmonella species. On the archived samples, the BFGP was positive in 92.6% of samples but detected more pathogens than the GPP (86 vs 97, p=0.033), including both targets unique to the BFGP and targets common to both panels. A pathogen was more frequently detected in patients with hematological malignancies than solid tumors and in ambulatory patients compared to hospitalized patients but these differences were not statistically significant. Overall, the detection rates were similar for both the GPP and the BFGP and the latter detected more than one pathogen in additional patients. The impact of increased detection of GI pathogens by multiplexed panels on the clinical care of oncology patients will require further investigation.

Mucosal microbiota of intestinal polyps reveals putative biomarkers of colorectal cancer

“…3 ). Interestingly, these taxa are commonly found in patients with CRC 57 , with the Fusobacterium genus frequently being associated with tumor progression 58 . Moreover, CpT samples possessed microbial genera commonly involved in development of intestinal disease or pathologies, such as Streptococcus (taxonomic trend prevalence of 80.00% in CpT) and Gemella (taxonomic trend prevalence of 80% in CpT) 59 , 60 .…”

Molecular detection of Enteropathogens from diarrheic stool of HIV positive patients in Gondar, Ethiopia

“…In contrast, detection of diarrheagenic E. coli strains are much lower when examining stool from patients in developed countries, highlighting their common frequency in sanitation poor settings [19]. Even in asymptomatic individuals, prevalence of diarrheagenic strains of E. coli are high in developing countries.…”

Approach to fever in patients with neutropenia: a review of diagnosis and management

“…Notably, Clostridioides difficile was the most common pathogen identified in these studies, and less expensive testing is available to test for C. difficile alone. 39 – 41 There are some limitations with using GI PCR panels in neutropenic patients, including some notable gaps in the current panels available, such as Strongyloides stercoralis , cytomegalovirus, and certain strains of adenovirus. 42 In addition, these tests do not differentiate colonization from active infection; thus, detection of an organism on the PCR panel does not rule out non-infectious etiologies like GVHD.…”

“…37,38 A few studies have evaluated the use of the GI PCR panels in cancer patients. 29,[39][40][41] Results from the studies comparing the GI PCR panels to conventional testing in this population demonstrated significantly improved pathogen identification. 29,40,41 It is unclear how many patients were presenting with FN or how the GI PCR panels influenced clinical outcomes in these studies, but they highlight the ability of these tests to improve diagnosis of infectious diarrhea in cancer patients.…”

“…29,[39][40][41] Results from the studies comparing the GI PCR panels to conventional testing in this population demonstrated significantly improved pathogen identification. 29,40,41 It is unclear how many patients were presenting with FN or how the GI PCR panels influenced clinical outcomes in these studies, but they highlight the ability of these tests to improve diagnosis of infectious diarrhea in cancer patients. Notably, Clostridioides difficile was the most common pathogen identified in these studies, and less expensive testing is available to test for C. difficile alone.…”