Application of metagenomic next-generation sequencing as an adjunct to conventional microbiological testing for the diagnosis of infection in kidney transplant recipients.

BACKGROUND

Kidney transplant recipients are highly susceptible to opportunistic and nosocomial infections that demand rapid and accurate diagnosis due to the broad and complex spectrum of pathogens. Conventional microbiological testing (CMT) is often limited, particularly when patients are already receiving antimicrobial therapy at the time of sampling. This study aimed to evaluate the clinical value of metagenomic next-generation sequencing (mNGS) as a complementary diagnostic approach to CMT, with a focus on concordance and discrepancies between the two methods across peripheral blood, sputum, bronchoalveolar lavage fluid (BALF), and urine samples.

METHODS

We conducted a retrospective study of kidney transplant recipients with suspected infections who underwent simultaneous mNGS and CMT testing between March 2022 and May 2024. The impact of prior antibiotic exposure on diagnostic yield was assessed. Detection of antimicrobial resistance (AMR) genes by mNGS and subsequent modifications in anti-infective management were also analyzed.

RESULTS

A total of 243 samples (57 blood, 96 sputum, 71 BALF, 19 urine) were included. Across all sample types, mNGS demonstrated significantly higher positive rates than CMT (blood: 78.95% vs 21.05%; BALF: 90.14% vs 19.72%; sputum: 92.71% vs 20.83%; urine: 89.47% vs 36.84%; all P<0.001). Prior antibiotic exposure markedly reduced CMT positivity but had minimal impact on mNGS detection. Concordance analysis showed 40.35% of samples were positive by both methods, while 60.1% were negative by CMT but positive by mNGS. In addition to pathogens identified by CMT, mNGS detected a broader range of microorganisms, including viruses (e.g., cytomegalovirus, Epstein-Barr virus, SARS-CoV-2), fungi (Pneumocystis jirovecii), and parasites (Strongyloides stercoralis, Toxoplasma gondii). Overall, mNGS-guided results refined antibiotic treatment strategies in 110 cases (60.11%).

CONCLUSION

mNGS serves as a valuable adjunct to CMT in kidney transplant recipients, providing rapid and comprehensive pathogen identification. However, from a health economics perspective, mNGS should be applied selectively according to clinical needs, rather than as a universal first-line diagnostic method.