Infectious disease diagnostics has been transformed by metagenomic next-generation sequencing (mNGS), an unbiased approach that detects bacteria, viruses, fungi, and parasites in a single assay. By sequencing all nucleic acids in a sample, mNGS overcomes the narrow detection scope and slow turnaround of conventional tests, substantially improving pathogen detection. In conditions such as meningitis/encephalitis, sepsis, and pneumonia, mNGS frequently identifies etiologies missed by routine diagnostic tests, thereby facilitating earlier pathogen-directed therapy and, in selected settings, improving clinical management and outcomes. This approach is particularly valuable for immunocompromised, pediatric, and intensive care unit (ICU) patients with atypical infections. Currently, clinical mNGS workflows primarily rely on short-read sequencing platforms (e.g., Illumina), whereas long-read platforms (e.g., Nanopore, PacBio) offer advantages for rapid or high-resolution applications. Optimized bioinformatics and stringent quality control are essential for reliable results. Beyond clinical diagnostics, mNGS provides valuable genetic data on antimicrobial resistance (AMR) and pathogen phylogeny, supporting public health and outbreak surveillance (e.g., wastewater monitoring and variant tracking). Current challenges include distinguishing colonization from infection, interpreting sequencing data quantitatively, and reducing cost and turnaround time. Looking ahead, emerging strategies such as targeted panels, rapid automated workflows, and host‑response integration are expected to further shorten time‑to‑result and improve diagnostic specificity. Parallel progress in ethical and regulatory frameworks remains essential to ensure responsible implementation. To support clinical adoption, a standardized framework for clinical interpretation of mNGS results, together with associated training, has been developed and implemented. Overall, mNGS is likely to become an increasingly important component of infectious disease diagnostics, with ongoing innovations expected to broaden its clinical and epidemiological impact.

Biliary tract infections (BTIs) present a significant therapeutic challenge, particularly in the face of increasing antimicrobial resistance. Bacteriophages, viruses that target and destroy bacteria, offer the potential for treating severe bacterial infections, although their use in BTIs has been limited. We describe an 88-year-old female with a complex and recurrent BTI caused by multiple bacteria, including multidrug-resistant Pseudomonas aeruginosa. Despite treatment with various antibiotics and percutaneous transhepatic cholangiodrainage (PTCD), her condition did not improve. As a final measure, we implemented personalized phage therapy in combination with antibiotics. An initial 9-day antibiotic treatment combined with a P. aeruginosa phage cocktail administered via PTCD fluid resulted in significant symptom relief. However, phage-resistant pathogens emerged, exhibiting resistance to all 100 double-stranded DNA (dsDNA) phages in our library due to genetic mutations affecting lipopolysaccharides biosynthesis. A second round of therapy with a double-stranded RNA (dsRNA) phage, phiYY, which targets O-antigen deficient mutants, was subsequently administered. Although complete eradication of P. aeruginosa was not achieved, the patient’s clinical symptoms were markedly improved. This case demonstrated the safety and efficacy of phage therapy in the treatment of BTIs and showcased the feasibility of employing dsRNA phages to combat the emergence of O-antigen-deficient bacterial mutants. However, it also underscores the considerable challenges in completely eradicating persistent P. aeruginosa infections, which may be attributed to bacterial heterogeneity, biofilm formation, and phage-resistant genetic mutations.