Rapid diagnosis of disseminated Mycobacterium mucogenicum infection in formalin-fixed, paraffin-embedded specimen using next-generation sequencing: A case report

Abstract

Background: Mycobacterium mucogenicum (M. mucogenicum) belongs to the group of rapidly growing Nontuberculous mycobacteria. This microorganism is associated with a wide spectrum of infectious diseases. Due to a low detection rate or the time required for conventional culture methodology, a rapid and broad-spectrum method is necessary to identify rare pathogens.

Case summary: A 12-year-old immunocompetent girl presented with painful masses for five months. The first mass was found in the right upper quadrant of the abdomen, and was about 1 cm × 1.5 cm in size, tough but pliable in texture, with an irregular margin and tenderness. An abscess gradually formed and ulcerated with suppuration of the mass. Three new masses appeared on the back one by one. Chest computed tomography showed patchy and streaky cloudy opacities in both lungs. Needle aspiration of the abscess was performed, but the smear and conventional culture were negative, and the pathological examination showed no pathogens. We then performed next-generation sequencing using a formalin-fixed, paraffin-embedded specimen to identify the pathogen. A significantly high abundance of M. mucogenicum was detected. The patient's abscesses gradually decreased in size, while inflammation in both lungs improved following 12-wk of treatment. No recurrence was observed four months after the end of the one-year treatment period.

Conclusion: Next-generation sequencing is a promising tool for the rapid and accurate diagnosis of rare pathogens, even when using a formalin-fixed, paraffin-embedded specimen.

Keywords: Case report; Disseminated infection; Formalin-fixed, paraffin-embedded specimen; Mycobacterium mucogenicum; Next-generation sequencing; Rapid diagnosis.

Figure 1

These images show the successive changes (from A to D) of the skin lesion on the lower right back over several months up to September 30, 2018.

Figure 2

The chest computed tomography on September 21, 2018 shows a massive pleural effusion on the left, a small pleural effusion on the right, patchy and streaky cloudy opacities on both lungs, suggesting inflammation. A: The sagittal plane; B: The horizontal plane.

Figure 3

The pathological manifestations of abscess tissue on the lower right back shows numerous lymphocytes and neutrophils infiltration, a small number of multinuclear giant cells and granulation tissues were found, which confirmed suppurative and granulomatous inflammation. A: Magnification of 200 ×, B: Magnification of 400 ×.

Figure 4

Sequencing results and phylogenetic analysis show nucleotide positions in the Mycobacterium mucogenicum genome.

Figure 5

These images show the four wounds on the 12^th day after anti-nontuberculous mycobacteria treatment. A: A mass on the right upper abdomen; B: A mass on the left lower back; C: Two masses on the right back.

Figure 6

These images show the four wounds on the 90^th day after anti-nontuberculous mycobacteria treatment. A: A mass on the right upper abdomen, B: A mass on the left lower back; C: Two masses on the right back.

Figure 7

The chest computed tomography on January 23, 2019 shows pleural effusion on both sides were absorbed completely, and patchy and streaky cloudy opacities on both lungs were improved compared with the images in Figure 2. A: The sagittal plane; B: The horizontal plane.

Figure 8

This image shows two masses on the right back in February, 2021.