Low immunity is frequently encountered among patients undergoing long-term radiotherapy and chemotherapy for cancer, patients with autoimmune diseases, patients with kidney diseases, and others[4, 5]. In our case, this patient has a history of three months of methylprednisolone for kidney disease and exhibits a low CD3+, CD4+ and CD8+ T cell counts, which is indicative of a compromised immune status. Immunocompromised patients often suffer from a polymicrobial pulmonary infection, such as P. jirovecii, Nocardia farcinica. P. jirovecii is a severe fungal infection that has a high prevalence in immunocompromised individuals, CD4+ lymphocyte counts < 200 cells/ul and corticosteroid use are risk factors for P.jirovecii colonization[6]. Early diagnosis and medication are important for good prognosis, however, diagnosis of P. jirovecii remains challenging due to its atypical clinical manifestations and low sensitivity and specificity of current diagnostic methods[7]. Nocardia farcinica is a weak acidic actinomycete that is widely present in soil, water and air. Inhalation of spores or fragments of hyphae results in pulmonary nocardiosis, about 50 percent of norcardiosis occurs in immunocompromised settings while Nocardia farcinica is more common than other Norcardia species [8–10]. The variable clinical manifestation and the difficulty in pathogen detection often lead to delays in the treatment of norcardiosis patients. Recently, several studies illustrated that compared to conventional methods, mNGS had a satisfactory diagnostic value in P. jirovecii and Norcardia farcinica diagnoses, reducing the detection turnaround time[11–13]. As reported, the application of mNGS corrected misdiagnosed tuberculosis, diagnosed a rare case of multisystem infection and a multi-site infection by Norcardia farcinica, and illustrated the competence of mNGS in the diagnosis of Norcardia spp. [14–16].
The mNGS technique is a promising approach for detecting co-pathogens in mixed pulmonary infection, with key advantages in speed and sensitivity[17]. In cases where multiple pathogens coexist, such as in immunocompromised patients, mNGS can significantly simplify the diagnostic process by identifying bacteria, fungi, parasites, and viruses concurrently. Unlike traditional methods that often rely on prior hypotheses and targeted testing, mNGS is unbiased and can detect even atypical, rare, or emerging pathogens. The high detection sensitivity of mNGS, coupled with its ability to detect unculturable organisms, makes it superior to culture-based methods[18].
In our case, given the history of methylprednisolone usage and the low CD4+ T cells count, they are indeed high-risk factors for opportunistic infection caused by P.jirovecii, A.fumigates, N.farcinica, and CMV. These pathogens are commonly found in immunocompromised individuals, but a simultaneous infection with all four of them is extremely rare. To the best of our knowledge, this is the first reported case of all four pathogens being detected in a single BALF sample using the mNGS technology in China. The conventional diagnostic methods, often struggle with detecting multiple pathogens simultaneously due to their limitations in sensitivity, specificity, throughput, and the need for pre-hypotheses. These limitations can lead to delays in diagnosis and poor prognosis, particularly in cases where multiple pathogens are involved. Although the current gold standard for diagnosing invasive pulmonary aspergillus is based on histopathological evidence and a positive tissue aspergillus polymerase chain reaction (PCR), these two diagnostic methods are invasive. Especially considering the severity of this patient's condition, it is challenging to clinically apply of these invasive diagnostic methods.
The rapid and comprehensive pathogen detection capability of mNGS technology can significantly guide the rational use of antibiotics[19, 20]. In this case, the mNGS results assisted clinical doctors in prescribing VCZ for the treatment of Aspergillus fumigatus infection and ganciclovir for the treatment of CMV infection, both of which played a crucial role in the successful management and treatment of the patient’s disease, highlighting the value of mNGS in precision medicine. Given the patient's severe condition and based on clinical experience, the use of VCZ for antifungal treatment is appropriate. The post-treatment microbiological test results also confirm the effectiveness of the medication.
In conclusion, patients in immunocompromised states often suffer from polymicrobial pulmonary infection. Compared to the limitations of traditional diagnostic methods, the mNGS technology has shown significant potential in enhancing the diagnosis and treatment of such complex and challenging infectious cases.