Mitochondrial genome diversity of Balamuthia mandrillaris revealed by a fatal case of granulomatous amoebic encephalitis

Cherie Tsz-Yiu Law; Thirapa Nivesvivat; Qing Xiong; Kasem Kulkeaw; Ling Shi; Pichet Ruenchit; Detchvijitr Suwanpakdee; Piradee Suwanpakdee; Nongnat Tongkrajang; Patsharaporn T Sarasombath; Stephen Kwok-Wing Tsui

doi:10.3389/fmicb.2023.1162963

Mitochondrial genome diversity of Balamuthia mandrillaris revealed by a fatal case of granulomatous amoebic encephalitis

Front Microbiol. 2023 May 5:14:1162963. doi: 10.3389/fmicb.2023.1162963. eCollection 2023.

Authors

Cherie Tsz-Yiu Law^{1

2}, Thirapa Nivesvivat³, Qing Xiong^{1

2}, Kasem Kulkeaw⁴, Ling Shi^{1

2}, Pichet Ruenchit⁴, Detchvijitr Suwanpakdee³, Piradee Suwanpakdee⁵, Nongnat Tongkrajang⁴, Patsharaporn T Sarasombath⁴, Stephen Kwok-Wing Tsui^{1

2}

Affiliations

¹ School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.
² Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.
³ Infectious Disease Unit, Department of Pediatrics, Phramongkutklao Hospital, Bangkok, Thailand.
⁴ Siriraj Integrative Center for Neglected Parasitic Diseases, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.
⁵ Neurology Division, Department of Pediatrics, Phramongkutklao Hospital, Bangkok, Thailand.

Abstract

Introduction: Balamuthia (B.) mandrillaris is a free-living amoeba that can cause rare yet fatal granulomatous amoebic encephalitis (GAE). However, efficacious treatment for GAE is currently unavailable, especially when genomic studies on B. mandrillaris are limited.

Methods: In this study, B. mandrillaris strain KM-20 was isolated from the brain tissue of a GAE patient, and its mitochondrial genome was de novo assembled using high-coverage Nanopore long reads and Illumina short reads.

Results and discussion: Phylogenetic and comparative analyses revealed a range of diversification in the mitochondrial genome of KM-20 and nine other B. mandrillaris strains. According to the mitochondrial genome alignment, one of the most variable regions was observed in the ribosomal protein S3 (rps3), which was caused by an array of novel protein tandem repeats. The repeating units in the rps3 protein tandem region present significant copy number variations (CNVs) among B. mandrillaris strains and suggest KM-20 as the most divergent strain for its highly variable sequence and highest copy number in rps3. Moreover, mitochondrial heteroplasmy was observed in strain V039, and two genotypes of rps3 are caused by the CNVs in the tandem repeats. Taken together, the copy number and sequence variations of the protein tandem repeats enable rps3 to be a perfect target for clinical genotyping assay for B. mandrillaris. The mitochondrial genome diversity of B. mandrillaris paves the way to investigate the phylogeny and diversification of pathogenic amoebae.

Keywords: Balamuthia mandrillaris; free-living amoeba; genotyping; granulomatous amoebic encephalitis; mitochondrial genome; neglected diseases; ribosomal protein S3.