Hybrid Capture-based Targeted Next-generation Sequencing for Pathogen Identification in Culture-Negative, Refractory and Relapsing Peritonitis Associated with Peritoneal Dialysis: A Case Series

For millions of people living with kidney failure, a procedure called peritoneal dialysis offers a way to filter their blood using the lining of their own abdomen. A soft tube, or catheter, is placed into the belly, and a special fluid is pumped in to draw out waste. This fluid sits for a while, then is drained out. However, this life-sustaining process carries a serious risk: the lining of the belly can become inflamed and infected, a condition known as peritonitis. When this happens, the fluid usually turns cloudy, and the patient feels pain. Doctors have long relied on a standard method to find the cause: they take a sample of the fluid and try to grow the germs in a lab dish. If the dish remains empty after a few days, the infection is labeled "culture-negative." In these difficult cases, where the germs refuse to grow or the infection keeps coming back despite strong antibiotics, doctors are often left guessing. They might keep changing the antibiotics, hoping to hit the right target, but without knowing exactly what they are fighting, the treatment can fail, and the patient may lose the ability to use their dialysis catheter.

A team of researchers in Tianjin, China, decided to look closer at these stubborn cases using a new kind of technology. Instead of waiting for germs to grow in a dish, they used a method called hybrid capture-based targeted next-generation sequencing. This technique acts like a highly sensitive net that can fish out tiny genetic fragments from hundreds of thousands of different types of microbes—bacteria, fungi, and viruses—directly from the fluid. The researchers applied this tool to fourteen patients who were struggling with peritonitis that was either culture-negative, resistant to treatment, or prone to returning. They compared the results of this new genetic test against the old standard of growing bacteria in a lab. The findings revealed a significant gap in traditional diagnosis. While the standard lab culture found the cause in only about half of the cases, the genetic test identified a specific pathogen in nearly four out of every five patients. Most strikingly, the test uncovered that viruses were a major culprit in these difficult infections, a possibility that standard lab methods almost never detect.

The study focused on patients who had already been treated with antibiotics for several days without success. In eight of these cases, the traditional lab culture came back empty, showing no bacteria. Yet, when the researchers used the genetic test on the same fluid samples, they found evidence of infection in six of those eight patients. In total, the genetic test identified a virus in seven of the fourteen patients, which is half of the group. These viruses included types known as cytomegalovirus, Epstein-Barr virus, and others that often hide in the body and can wake up when the immune system is weak. The researchers were careful to distinguish between a virus that was simply passing through and one that was actually causing the illness. They defined a "clinically relevant" viral infection as one where the virus was found in the fluid, no other germ explained the symptoms, and the patient got better after receiving antiviral medicine. Six of the seven patients with viral findings met these strict criteria.

The patients with these viral infections presented a distinct picture compared to those with bacterial infections. Those with viruses had lower levels of inflammation markers in their blood and in the fluid draining from their bellies. Their white blood cell counts were lower, and the fluid was less cloudy than in the bacterial cases. Despite having milder signs of inflammation initially, these patients took longer to clear the infection completely. However, once their treatment was adjusted to include antiviral medication, all six patients with confirmed viral peritonitis recovered and were able to keep their dialysis catheters. In contrast, the group without detected viruses had a much harder time; only two out of seven patients in that group achieved full recovery, while the others had to switch to a different type of dialysis because their infections could not be controlled.

This research suggests that viruses are a common but overlooked cause of peritonitis in patients who do not respond to standard antibiotics. For decades, the medical community has suspected that viruses might play a role in these mysterious infections, but the tools to prove it were lacking. The study provides concrete evidence that when a patient with peritoneal dialysis has an infection that culture tests cannot find, or one that refuses to go away with antibiotics, a virus might be the reason. By using genetic sequencing to look for these invisible invaders, doctors can identify the true cause and switch to the right treatment, such as antiviral drugs, rather than continuing to prescribe antibiotics that do not work. While the study is small and based on a single hospital, it offers a new path forward for diagnosing and treating some of the most difficult cases of peritonitis, potentially saving the catheters and health of patients who would otherwise be left without a clear answer.