NGS-Based Gastrointestinal Pathogen Panel: Introduction, Sampling Method, and Applications

Gastrointestinal (GI) infections can be caused by a combination of viruses, bacteria, and parasites. In a stool specimen, the gastrointestinal pathogen panel concurrently searches for the presence of many disease-causing microbes.

In a stool sample, GI pathogen panels are used to collectively screen for the existence of numerous disease-causing (pathogenic viruses, bacteria, and/or parasites and assist to identify a GI infection. A GI pathogen panel can be used in combination with other examinations, such as a stool culture or an ova and parasite analysis (O&P), to help treat the symptoms, since there are several causes of GI infections. The genetic material of the microbes being examined is identified by the GI pathogen panel. The quantity of microbes tested and their form depend on the composition of the panel used. While some panels may be restricted to testing for a few bacteria, for example, which are the most prevalent causes of GI infections, other panels may be more extensive and test a range of bacteria, viruses, and parasites. Viruses such as norovirus or adenovirus, bacteria such as Campylobacter, Salmonella or Clostridium difficile, and parasites such as Giardia or Cryptosporidium are some of the microbes that may be identified.

Stool culture to detect pathogenic bacteria, an ova, and parasite examination (O&P) exam to identify parasites, and/or various other tests, such as antigen tests, have been used in traditional testing.

Stool sampling:

1. A fresh stool sample obtained in a sterile bottle should not be tainted by feces or water in the stool sample.;

2. Stools can either be brought to the laboratory within two hours of processing or moved to special vials containing preservative solutions for transport.

These tests are helpful, but some bacteria in culture can be difficult to develop effectively, some parasites can be overlooked if they are found in limited numbers, and virus testing is not regularly available. Many examinations are often labor-intensive, and when a healthcare professional has a conclusive response, it can take 2-3 days or more.

GI Pathogen Panel Applications

In public health and clinical microbiology, next-generation sequencing (NGS) has begun to gain interest. Cost-efficient research and fast processing time are given by NGS. It has also been used for illustrating bacterial outbreaks in therapeutic environments and has been proposed for the real-time typing and monitoring of pathogens in real-time.

Up until recently, NGS was predominantly used on bacterial isolates. However, the technologies can be implemented directly to clinical samples, possibly advancing diagnostics and resulting in even more rapid diagnostic results, as illustrated for urinary tract infections. Moreover, the identification of Clostridium difficile by NGS has lately been shown to be correlated with existing laboratory testing and metagenomics sequencing has been used on a restricted number of patient stool samples to identify pathogens. NGS provides identification of tolerance and virulence genes in addition to species detection, which will help shorten the time required to begin pathogen-directed therapy.

In one research, in 34 of the 38 conventionally positive bacterial samples, the NGS-based approach provided the identification of the same bacterial pathogens as the classical approach and predicted the suspected pathogens in five of the 11 negative samples. Overall, the NGS-based approach made pathogen identification equivalent to traditional diagnostics feasible and the approach could be applied for all pathogens to be identified.


  1. Guthrie JL, Gardy JL. A brief primer on genomic epidemiology: lessons learned from Mycobacterium tuberculosis. Annals of the New York Academy of Sciences. 2017, 1388(1).
  2. Gwinn M, MacCannell DR, Khabbaz RF. Integrating advanced molecular technologies into public health. Journal of clinical microbiology. 2017, 55(3).

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