Diagnostic challenges in peritoneal dialysis-associated peritonitis with atypical and rare pathogens: A new era of metagenomic next-generation sequencing precision diagnosis

Welcome to AudioScholar. Today we're covering "Diagnostic challenges in peritoneal dialysis-associated peritonitis with atypical and rare pathogens: A new era of metagenomic next-generation sequencing precision diagnosis," by Dong X and colleagues, published in *Peritoneal Dialysis International: Journal of the International Society for Peritoneal Dialysis*.

Peritonitis remains a major complication for patients on peritoneal dialysis, often leading to treatment failure, catheter removal, and a switch to hemodialysis. While standard guidelines have improved diagnosis by recommending inoculation of peritoneal fluid into blood culture bottles, a significant challenge persists: culture-negative peritonitis. In some centers, this can account for up to 40 percent of cases. This diagnostic gap is particularly wide when the culprits are atypical or rare pathogens—like mycobacteria, fungi, or certain viruses—which either grow very slowly or not at all in standard culture media. This delay in identifying the causative organism can lead to inappropriate empirical antibiotic therapy, worse outcomes, and higher mortality. This paper reviews the evidence for a newer technology, metagenomic next-generation sequencing, or mNGS, as a tool to close this diagnostic gap.

This article is a review, synthesizing the findings from numerous recent studies and case reports to build a case for the clinical utility of mNGS in diagnosing peritoneal dialysis-associated peritonitis. Unlike traditional culture, which tries to grow living organisms from a sample, mNGS takes an unbiased approach. It extracts all the genetic material—both DNA and RNA—directly from a clinical sample, in this case, the peritoneal dialysate. It then sequences millions of these genetic fragments and uses powerful bioinformatics to match them against vast databases of microbial genomes. This allows for the identification of bacteria, fungi, viruses, and parasites all in one test, without needing a pre-specified target and without the need for the organism to be viable or culturable.

The authors compile evidence suggesting that mNGS offers significant advantages over conventional culture. A key benefit is a higher diagnostic yield. One single-center study cited in the review found that the pathogen detection rate with mNGS was significantly higher than with traditional culture—specifically, 87 percent versus 60 percent. Another study reported a sensitivity of nearly 97 percent for mNGS, compared to about 71 percent for the blood culture bottle method. This advantage is especially pronounced in patients who have already started antibiotics, a common scenario where culture sensitivity drops significantly. In one study of patients already on antibiotics, mNGS had a positive rate of 92 percent, while culture only identified a pathogen in 38 percent of cases.

Another major advantage is speed. Traditional culture and sensitivity testing can take several days. The review highlights that mNGS can deliver results in about 25 hours, a dramatic reduction from the average of 89 hours for culture-based methods. This rapid turnaround allows for much earlier adjustment of antimicrobial therapy, potentially reducing the use of broad-spectrum agents and minimizing the risk of treatment failure or resistance.

The central argument of the paper is the unique ability of mNGS to identify the atypical and difficult-to-culture pathogens that cause the most diagnostic headaches. For instance, tuberculous peritonitis is notoriously difficult to diagnose, as acid-fast bacilli culture can take over six weeks. mNGS can detect *Mycobacterium tuberculosis* DNA much more rapidly. The same applies to non-tuberculous mycobacteria, which can be mistaken for exit-site infections. The review also points to the utility of mNGS in diagnosing fungal peritonitis, a condition with high mortality where early diagnosis and catheter removal are critical. Finally, the technology can identify pathogens that are almost never sought with standard methods, such as *Ureaplasma*, anaerobes, and even viruses like human herpesvirus, which have been detected in peritoneal fluid using mNGS. The technology is also adept at identifying polymicrobial infections, which may be present in about 15 percent of cases.

However, the authors provide a balanced perspective, detailing the significant limitations of mNGS that currently prevent it from replacing culture as the standard of care. The most immediate barrier is cost. A single mNGS test can run from several hundred to over a thousand dollars, which is often not covered by insurance and is a major hurdle for routine clinical use, though prices are expected to fall.

A critical clinical limitation is that mNGS cannot perform antibiotic susceptibility testing. It detects genetic sequences, but it doesn't provide a living organism to test against a panel of antibiotics. While it can identify known antibiotic resistance genes, the presence of a gene doesn't always perfectly predict the organism's actual resistance phenotype in the patient. Therefore, conventional culture remains essential for guiding specific antibiotic choices.

Furthermore, interpretation of mNGS results requires clinical expertise. The test is so sensitive that it can't distinguish between DNA from a live, replicating pathogen and residual DNA from dead organisms or environmental contaminants. A clinician must correlate the sequencing report with the clinical picture. A high number of sequence reads from a known pathogen is significant, but a few reads from a common skin contaminant might just be noise. This distinction is crucial to avoid over-treating contamination as infection. The paper also notes a potential for false negatives, as some bacteria with thick cell walls, like *Streptococcus*, can be difficult to break open for DNA extraction, occasionally making culture more sensitive for these specific organisms.

So, what's the clinical bottom line? Metagenomic next-generation sequencing is a powerful new diagnostic tool, but it's not a first-line test for every case of peritonitis. It should be considered an adjunct to, not a replacement for, standard culture. The authors suggest its use should be prioritized for specific, challenging clinical scenarios. These include cases of culture-negative peritonitis where the patient is failing to improve on empirical therapy. It is also particularly valuable for patients with recurrent or relapsing peritonitis, and for those who are immunocompromised or have complex medical histories. If you have a high suspicion for an unusual pathogen like tuberculosis or a fungus, or if your patient was already on broad-spectrum antibiotics before a good dialysate sample could be collected, mNGS could provide the diagnostic clarity that culture cannot. The key is to use it selectively in diagnostically difficult situations and to always interpret the results within the broader clinical context of the patient.

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