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Clin Infect Dis. 2019 Nov 5. pii: ciz1068. doi: 10.1093/cid/ciz1068. [Epub ahead of print]

Impact of a Multiplexed PCR Panel on Identifying Diarrheal Pathogens in Hematopoietic Cell Transplant Recipients.

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NewYork-Presbyterian Hospital/Weill Cornell Medical Center, New York, NY, USA.
Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.
Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY, USA.
Transplantation-Oncology Infectious Diseases Program, Division of Infectious Diseases, Weill Cornell Medicine, New York, NY, USA.
Division of Gastroenterology, Weill Cornell Medicine, New York, NY, USA.



Diarrhea is common and associated with substantial morbidity among hematopoietic cell transplant (HCT) recipients, but the etiology is often not identified. Multiplexed PCR assays increase the detection of diarrheal pathogens, but the impact of this technology in this population has not been evaluated.


Our center replaced stool cultures and other conventional microbiological methods with the FilmArray® Gastrointestinal Panel (GI PCR) in June 2016. We reviewed all adult patients who received a HCT from June 2014-May 2015 (pre-GI PCR, n=163) and from June 2016-May 2017 (post-GI PCR, n=182) and followed them for one year after transplantation. Clostridioides difficile infection was diagnosed by an independent PCR test in both cohorts.


The proportion of patients with ≥1 identified infectious diarrheal pathogen increased from 25% to 37% after implementation of GI PCR (p=0.01). Eight patients (5%) in the pre-GI PCR cohort tested positive for a pathogen other than C. difficile, vs. 49 patients (27%) in the post-GI PCR cohort (p<0.001). The most common non-C. difficile diarrheal pathogens in the post-GI PCR cohort were enteropathogenic Escherichia coli (n=14, 8%), norovirus (n=14, 8%), and Yersinia enterocolitica (n=7, 4%). The percentage of diarrheal episodes with an identified infectious etiology increased from 14% to 23% (p=0.001). Median total costs of stool testing per patient did not increase (pre: $473; post: $425; p=0.25).


Infectious etiologies of diarrhea were identified in a higher proportion of HCT recipients after replacing conventional stool testing with a multiplexed PCR assay, without an increase in testing costs.


diagnosis; diarrhea; multiplexed PCR; stem cell transplant


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