From the Guidelines

A stool culture is not always necessary when ordering separate stool bacterial testing.

The decision to perform a stool culture should be based on the clinical presentation and epidemiologic risk factors of the patient, as outlined in the 2017 Infectious Diseases Society of America clinical practice guidelines for the diagnosis and management of infectious diarrhea 1.
Stool testing should be performed for specific pathogens, such as Salmonella, Shigella, Campylobacter, Yersinia, C. difficile, and STEC, in people with diarrhea accompanied by fever, bloody or mucoid stools, severe abdominal cramping or tenderness, or signs of sepsis 1.
However, in some cases, such as when enteric fever or bacteremia is suspected, culture-independent diagnostic testing, including panel-based multiplex molecular diagnostics, may be sufficient, and culture-dependent diagnostic testing may not be necessary 1.
The yield of stool cultures can be low, with estimates ranging from 0.9% to 5.8% for various enteric pathogens 1.

In cases of inflammatory diarrhea, a thorough microbiological assessment, including stool culture, may be necessary to aid in diagnosis and prevent unnecessary procedures or treatments 1.
In patients with a high risk of complications, such as immunocompromised individuals or those with certain high-risk conditions, stool culture may be warranted, even if the yield is low 1.
In outbreaks of diarrheal illness, stool culture may be necessary to detect and investigate the outbreak, and to provide appropriate follow-up recommendations for patients 1.

From the Research

The necessity of stool culture when ordering separate stool bacterial testing is debatable, with some studies suggesting that it may not be necessary in all cases 2, 3.
A study published in 2022 found that metagenomics-based stool testing approach could simultaneously provide diagnostic and public health information, and may be more routinely applied in clinical and public health laboratories as cost, speed, and analytics improve 4.
Another study published in 2020 found that stool cultures had a very low yield of detecting an underlying pathogen in patients with acute gastroenteritis, and played little to no role in patient management for the vast majority of patients 2.

A study published in 2002 found that clinical predictors of positive stool culture in adult patients with acute infectious diarrhea included summer season, fever, duration of abdominal pain, and requirement of IV fluid therapy 5.
However, another study published in 1988 found that bacterial stool culture and ova and parasite identification were not indicated for patients with nosocomial diarrhea, and that elimination of these unnecessary stool tests would have saved the hospital approximately $7530 in the 18-month study period 3.

A study published in 2015 compared the time-motion analysis of conventional stool culture and the BD MAX™ Enteric Bacterial Panel (EBP), and found that the EBP resulted in significant time savings and a shorter time-to-result for patients with acute bacterial diarrhea 6.
The study found that with conventional culture, negative culture results were available from 41:14:27 to 54:17:19, while with EBP, positive and negative results were available from 2:28:40 to 3:33:39 6.