Bacterial culture followed by antimicrobial susceptibility testing is considered the gold standard method for diagnosis of bacterial infections. Culture is typically performed in reference laboratories and takes three to five days to furnish a definitive result. The long delay necessitates that either the patient must wait for the results to receive an evidence-based antimicrobial prescription, or the provider must initiate an empirical treatment, and modify it as needed, once the culture results are available; both of which can lead to improper or unnecessary antimicrobial use and patient suffering. As such, culture is used only sparingly in resource limited settings with minimal antimicrobial stewardship oversight such as the veterinary sector. 
Failure Points for Bacterial Culture
While bacterial culture is generally accepted as the gold standard method for diagnosis of bacterial infectious diseases, the accuracy and utility of culture depends on four factors, namely: the method of sample collection, the storage container/swab/media used, how the sample is shipped, and finally when the sample is plated by the reference laboratory.
- Method of Collection: For some clinical conditions, such as collecting urine for a suspected UTI, urine can be collected by mid-stream free catch, catheter, or by cystocentesis. Each method has a different risk for introducing contaminating bacteria, with the first be the most likely and the last the least likely to cause in an erroneous result. A study comparing urine collection methods in cats and dogs reported 35 and 8.6 percent discrepant culture results for midstream samples and cystocentesis samples, respectively, between immediate and delayed plating of samples . Another study comparing urine collection methods reported bacterial growth in 0, 26, and 85 percent of samples collected by cystocentesis, catheterization, and the midstream urine collection respectively, in clinically normal dogs. 
- Storage Container: A significant factor influencing accuracy of culture results is sample collection and storage kits where different collection tubes, swab types and transport media can affect bacterial concentrations. For example, in a study, E. coli counts in dog urine samples declined by six-fold and 358-fold in urine transport tubes and silicone-coated clot tubes, respectively, when stored at room temperature for 24 hours . Another study on bacterial culture on abscesses found only 54, 56, and 73 percent of all the bacterial strains present in the samples were identified when samples were collected using inoculation loops, viscose swabs, and polyurethane swabs, respectively .
- Shipping Time: The effect of different collection tubes/swab types/transportation media can be exacerbated by shipping temperature conditions and the length of time in transit. Most samples tested in reference laboratories are shipped, and even for overnight express options, the average time to delivery is 19 hours.  This delay has a significant impact on the results as it can lower the concentration of clinically significant bacterial while allowing time for the concentration of resident and contaminating flora to increase. These changes can lead to false positive and negative test results. 
- Time to plating at reference laboratory: Most clinicians have plenty of stories of culture results taking sometimes a week or more for results for common bacterial infections. Barring a massive weather-caused shipping delay, the most likely explanation is a delay at the reference laboratory for plating samples. Every lost hour increases the chances of an erroneous result, and arguably harms the health of pets that were placed on the wrong therapy from the start.
Culture negative infections explained
Thirty percent of surgical site infections are found to be culture negative. Some of these culture negative infections are caused by anaerobes which do not readily grow in routine culture. Others are caused by biofilms, which account for 60-85 percent of bacterial infections in the developed world, and the bacteria that cause biofilms are notoriously hard to culture.  Lastly, there are some infections that are caused by bacteria which are stressed (due to host responses or antimicrobial therapy) and remain in a “viable, but not culturable” state but can be readily detected by PCR. 
Regardless of the reason, techniques such as qPCR can often definitively identify the causative pathogen, even for samples that come back negative by culture.
Bacterial culture for diagnosis of urinary tract infections- is this the best we can do?
Approximately 30 percent of symptomatic UTI cases in women have negative culture results . These negative results effectively rule out UTI as the reasons for the symptoms and dangerously take the focus away from an infection. Recent studies have revealed that the reasons for negative test results is that standard culture poorly detects common uropathogens. In one study, standard urine culture missed 67 percent of uropathogens overall in symptomatic patients. Another study reported that culture was positive for uropathogens in less than 10 percent of symptomatic UTI patients when compared to DNA sequencing.  Yet another study found 90 percent of the culture negative urine samples were positive for Escherichia coli by qPCR. In short, there is enough evidence to suggest that in most of the culture negative symptomatic UTI cases there is an underlying infection that can be diagnosed using other means that are often molecular based.
Culture is especially poor in detecting bacteria in tissues that are dormant and in deep-seated infections such as chronic cystitis. There is a growing collection of evidence pertaining to the failure of culture to detect a variety of infections, questioning its status as the gold standard method. Furthermore, the days required to get culture results and the false negative and false positive risk associated with such a delay, further contribute to the reasons why culture is not more frequently used in veterinary medicine. Emerging molecular diagnostic technologies such as qPCR have been shown to provide very accurate results, particularly when employed at the point-of-care, where it is possible to avoid the inaccuracies introduced by improper storage conditions and delayed time to testing due to shipping. As these technologies become more common, it is expected that clinicians will more frequently strive for a proper diagnosis before deciding how best to treat the patient.