Abstract
I applaud the recent publication by Jongjitaree et al., which assessed the ability for microbial next-generation sequencing (NGS) of preoperative urine to predict postoperative urinary tract infection (UTI) compared with culture and found that NGS could significantly improve detection of UTI-causative microbes in patients undergoing stone removal procedures. 1 These results mirror the enhanced sensitivity previously reported elsewhere. 2,3 The authors go on to recommend incorporating NGS alongside standard urine culture because of the high sensitivity observed and ability to better describe bacteria, which may only be otherwise described as “mixed urogenital flora.”
To bolster the recommendation for NGS as a standard in preoperative urine screening, I suggest considering results from a comparative efficacy trial I co-authored last year with colleagues. 3 The intervention in this study involved NGS guided antibiotic prophylaxis for patients undergoing kidney stone surgeries compared with a standard of care using urine culture screening, with antibiotic prophylaxis informed by empiric recommendations instead. The key takeaway was that postoperative UTI was reduced by 85%–100% when the prophylactic antibiotics were modified to target microbes, which were uniquely found by NGS. 3
Lastly, I want to clarify one technical detail on the NGS application as implemented by MicroGen DX (Lubbock, TX). A concern was noted that detection of microorganisms by NGS can be as high as 100% because NGS can “… identify all microbiomes, including nonpathogenic organisms, leading to reduced specificity.” 1 The protocol for NGS used by MicroGen DX involves a broad-range PCR step which requires that sufficient bacterial (or fungal) DNA must be present to warrant sequencing (i.e., end-point PCR). 4,5 This critical quality control step, among others, ensures that not all samples will return positive results because there must be a significant enough bioburden present. Further, all quantifiable species are not reported through the MicroGen DX workflow, only the “dominant” detected species reported greater than 2% relative abundance, which limits reporting of many organisms which are likely not relevant. 3,4
In summary, the work by Jongjitaree and colleagues is a welcome addition to the literature and shows the capacity for NGS applications to benefit patients undergoing urologic procedures with relatively high risk for postoperative UTI. Our own recent study complements the current work as a logical next step would be to develop a randomized controlled trial to demonstrate efficacy over standard of care urine culture. I look forward to seeing the impact of these studies on patient care and quality of life.