Systemic lupus erythematosus (SLE) is a chronic autoimmune disease involving multiple organs and system. Immune system disorder, T cell and B cell dysfunction, the use of corticosteroids and immunosuppressive agents result in low immunity and prone to infection in SLE patients. At the mean time, infection can also aggravate the activity of SLE . The infection site in SLE patients are widely distributed, and the most common infection sites were the lungs, followed by upper respiratory tracts and urinary tracts . A retrospective review performed in 3,831 hospitalized SLE patients revealed that in SLE death cases mainly dying from infection, Aspergillus fumigatus and Pneumocystis carinii were the two most commonly infected pathogens, and Cytomegalovirus was a frequent pathogen of polyinfection . It was worth noting that polyinfections were more frequent than single pathogen infection (60.5 vs. 39.5 %), including common bacteria, fungal infection, and cytomegalovirus, simultaneously the mortality was significantly higher.The mix infections caused by Aspergillus fumigatus as well as Pneumocystis jirovecii are serious and often lethal diseases in severely immunocompromised patients . Moreover the incidence of (IPA) and (PCP) increases with the extent of the underlying or therapeutic immunosuppression, and, especially for IPA, has a major impact on morbidity and mortality .
An enhancement of clinical awareness,a rapid and accurate diagnostic༌and precise management is crucial for early treatment in immunocompromised SLE patients. However in severely immunocompromised patients, simultaneous or secondary infections in Pneumocystis jirovecii pneumonia are mostly caused by bacterial pathogens, whereas fungal pathogens, especially Aspergillus fumigatus, are rarely diagnosed . Nowadays the diagnosis of Pneumocystis pneumonia (PCP) is usually achieved by examining stained smears of BALF for the presence of the organism, and the cloning and sequencing of Pneumocystis jiroveciiis provide an alternative method. Moreover, the diagnosis of IPA relies mainly on tissue culture and morphological analysis, which may bring drawbacks due to the limited culture positive rate and is sometimes time consuming . The introduction of biomarkers such as galactomannan (GM) and polymerase chain reaction (PCR) assays make big difference in the diagnosis of invasive pulmonary aspergillosis (IPA) . With advantages of high sensitivity, low cost and fast detection, however, PCR method requires the physician to raise a few suspicious pathogens prior to examination and is usually restricted to only limited range of pathogens. The radiographic evaluation still has difficulty to make the radiographic diagnosis of combined IPA and PCP. Therefore, these methods are not best applicable in certain clinical situations such as polyinfection in SLE patients.
Next-generation sequencing (NGS) or massively parallel sequencing, a method of simultaneously sequencing millions of fragments of DNA, has been rapidly adopted in the clinical laboratory. Under such circumstances, the implementation of NGS in clinical field enabled a fast and comparably accurate diagnostic tool for physicians,and most importantly, it does not require a predefined range of suspicious pathogens.NGS is an assay that can sequence the entire DNA/RNA of a sample, and this process does not need any primers or probes. It holds the promise of identifying most of the pathogens. Furthermore, NGS can generate billions of DNA/RNA sequences per run, and this enables metagenomic analysis. The principles of NGS in infectious diseases are composed of three main procedures, the identification of the nucleotides in the targeted samples, the comparison of these nucleotides against the catalogue of causative agents, and the decision-making progress whether the acquired sequences points to the possible etiological hypothesis . The first literature applying NGS in the diagnosis of infection was published in 2014, in which leptospira sequence were detected in the spinal fluid of neuroleptospirosis patient . Since then, multiple studies have reported the use of NGS in central nervous system, bloodstream, and respiratory infections [23–26]. The advantage of NGS is its potential to detect multiple pathogens simultaneously in one test while immunosuppressed patients are more likely to be the largest beneficiaries of NGS because they often have coinfections . The major challenge of clinical use of NGS is how to interpret the results and determine whether the microorganism whose sequences are identified is truly the causative pathogen. The nature of NGS tends to detect all nucleotide sequences not only from the samples but also those acquired from the contamination during clinical procedures or laboratory processing, and thus it is challenging to discriminate causative pathogens from normal microbes and environmental contaminants. A microbe found by NGS is usually considered a causative agent based in part or in total on the following clues or evidence: the coverage rate (species level) is significantly greater than that of any other microbe or that in the control materials, or the mapping read number is at the top of the microbes list ; the result is confirmed by traditional techniques such as culture, serological testing, PCR, Sanger sequencing, and histopathology; the sequence or read number or pathogen load is significantly reduced during the course of treatment ; and the patient improved after targeted antimicrobial agent treatment [28, 30, 31].
Detecting specific microorganisms by NGS is just the first step. However, not all microorganisms determined by NGS are relevant to infectious diseases, such as oral colonizing bacteria (e.g., Streptococcus parasanguinis, Streptococcus mitis, and Prevotella melaninogenica). Taken together, clinicians should identify the real pathogen according to both NGS and other examinations.
In our case, NGS identified Pneumocystis jirovecii and Aspergillus fumigatus the causative agent within 24 hours. The sequencing data, which was in consistent with the patient’s biological and morphologic evidence, clinical and radiological features, assisted clinical physicians in approaching the diagnosis of mixed infection apace and effectively. With the help of NGS on the rapid diagnosis, the patient’s chest radiograph displayed obvious absorption of bilateral lung inflammation after 6 days of target treatment. The limitation of this case study included lacking a validated quantification method to interpret the significance of the NGS result, and since the patient discharged from the hospital, her further condition couldn't be tracked.
In summary, we report a case of a SLE patient with simultaneous Pneumocystis pneumonia and invasive aspergillosis, and as we know it is the first documented case in SLE patients. This case highlights the challenges in the diagnosis and management of this rare dual infection and some of its devastating consequences.The introduction of next-generation sequencing applied to pathogen identification dramatically improves the ability to identify poly-infection that occasionally cause disease but lethal. It helps clinicians to make a rapid and precise diagnosis of infectious diseases in the near future.