DiFei Academic丨A case report on mNGS identification of pulmonary infection complicated by air cyst caused by Streptomyces albus

Introduction

In January 2024, Li Fuxiang’s team from the Department of Critical Care Medicine of the Western Theater Command General Hospital of the Chinese People’s Liberation Army cooperated with Difei Medical toFrontiers in Cellular and Infection Microbiology(IF=5.7)The magazine published a rare case report.The patient had necrotizing pneumonia and air cysts caused by Streptomyces albus infection. The strains were identified through whole-genome sequencing (WGS) combined with phylogenetic analysis, and the diagnosis and identification of rare opportunistic pathogens by mNGS technology were explored. ability.

Research Background

Streptomyces are a group of Gram-positive soil microorganisms that are filamentous and branched.Because it can produce rich and diverse secondary metabolites, it has been widely used in clinical medicine. However, it is also a potential human pathogen and mainly exists in patients with low immune function.

Of the reported cases of Streptomyces infections, only a few have been described as relevant to humans, with the most common infection being actinomycomas, although rare invasive infections can also be caused.A retrospective study of Streptomyces isolates identified in clinical samples from a French microbiology laboratory found that nearly half of the patients had invasive infections.Therefore, the significance of Streptomyces as an opportunistic pathogen cannot be ignored.

Case presentation

A 75-year-old male patient was admitted to the hospital because of symptoms of chest tightness, dyspnea accompanied by cough and a small amount of brown sputum that had worsened for 4 days. His symptoms began to appear ten days before admission.The patient was a farmer with long-term exposure to soil and hay, had a long history of smoking, and had no history of tuberculosis, chronic respiratory disease, or congenital immunodeficiency.One month ago, he fell down and suffered multiple fractures of his right rib. He applied unidentified herbal medicine to the skin of the closed fractures.

Admission diagnosis and treatment

On admission, the patient's body temperature was 36.7°C, blood pressure was 122/76 mm Hg, pulse rate was 109/min, respiratory rate was 42/min, and blood oxygen saturation in room air was 88%.The patient was conscious, with scattered ecchymoses visible on the right neck, shoulder and chest, and no obvious enlargement of superficial lymph nodes.

Laboratory tests: elevated neutrophils (94.5%) and elevated C-reactive protein (283.91mg/L).The white blood cell count and other values ​​were normal.Chest computed tomography (CT) showed patchy high-density shadows and air cysts in the right upper lung (Figure 1 A1 ~ A3).

Figure 1 Serial chest HRCT scans performed during hospitalization and after discharge.

During hospitalization, the patient underwent tracheal intubation and invasive mechanical ventilation due to respiratory failure.Bedside fiberoptic bronchoscopy showed a large amount of brown purulent secretions in the bronchus of the upper lobe of the right lung, and bronchoalveolar lavage fluid (BALF) was collected.Considering the possibility of community-acquired pneumonia, intravenous infusion of piperacillin-tazobactam and levofloxacin was initially administered.

Further examination and treatment

On the 5th day after admission, BALF culture results showed Gram-positive, branching, non-acidic fast filamentous bacilli, with visible aerial hyphae of organismal development, clearly visible in lactophenol cotton blue staining (Figures 2 and 3) .The bacteria formed white, dry, wrinkled small colonies on blood agar. After 72 hours of aerobic growth, they became velvety and formed white aerial hyphae (Figure 4).Initial empiric therapy was changed to linezolid and amikacin.After the patient's respiratory failure improved significantly, the tracheal intubation was removed and an oronasal mask was used for non-invasive ventilation.

On the 8th day after admission, a reexamination of the chest CT showed that the patchy shadows merged into enlarged lobulated consolidation shadows, and a new left pleural effusion appeared, indicating that the initial treatment (Figure 1B1 ~ B3) was ineffective.The minimum inhibitory concentration was determined using the broth microdilution method, and the bacteria were sensitive to clarithromycin, amikacin, and linezolid.Add the above antibiotics for 15 days.

On the 20th day after admission, chest CT showed consolidation in the right lung and gradual reduction in volume (Figure 1 C1~C3).

Figure 2-4 Gram stain; Lactophenol cotton blue staining and blood agar culture results

Prognosis of treatment

After discharge, the patient continued to receive clarithromycin treatment for 2 months. A follow-up chest CT performed 2 months later showed that the lesion had been absorbed and both lungs (Figure 1D1~D3) had expanded.The patient had no recurrence of infection.

WGSComparison of results with hemolytic genes

High-throughput sequencing was used to identify and obtain the full genome of the pathogen, which was found to be similar to Streptomyces albicans with 100% coverage and similarity.Using the BV-BRC information system, closely related Streptomyces species in the NCBI database and different strains with published complete genome sequences were used to analyze and draw a phylogenetic tree with this strain (Figure 5). It was found that the strain in this case is closely related to the white network chain. The mold strains MDJK11 are clustered together.

Figure 5 Phylogenetic tree constructed based on NCBI whole genome sequence

The Streptomyces albus strain has strong hemolytic activity, and the hemolytic activity was obvious after 72 hours of culture (Figure 4).Comparing the gene sequences of the reported strains with previously reported genes that induce hemolysis (Table 1),The results showed that the 16S ribosomal RNA gene (MT304816.1) of B. hyodysenteriae strain G423 and the FilA5 gene (MH638271.1) of Streptomyces filipinensis strain DSM 40112 were comparable.Therefore, these genes may be related to the hemolytic activity of PRJNA922082.

Table 1 Putative hemolysin genes and alignment results in the PRJNA922082 genome

Outcome and Prognosis

After nearly 3 months of treatment with clarithromycin, the patient's condition improved and the infection did not recur.

Summarize

1. This article describes a case of severe pneumonia caused by infection with Streptomyces albicans due to normal immune function, and the identification of Streptomyces albicans using WGS and phylogenetic analysis.

2. The diagnosis and treatment of Streptomyces infection described in this case may provide a reference for the clinical management of such patients.For high-risk patients suspected of rare pathogen infection, WGS testing can be performed to further explore the triggering factors, disease course, treatment and evolution of Streptomyces isolates.

3. The susceptibility factors, disease course, treatment, and evolution of Streptomyces isolates still require further study.

references:

Liu J, Xu Z, Bai Y, Feng J, Xu L and Li F (2024) Streptomyces albireticuli lung infection managed as a pulmonary air cyst: a case report and literature review. Front. Cell. Infect. Microbiol. 13:1296491. doi: 10.3389/fcimb.2023.1296491.

Compiler: Aoki Reviewer: Jia, Zixi Typesetting: Lin