Isolation and whole genomic analysis of mesophilic bacterium Pseudoglutamicibacter cumminsii in epithelial mesothelioma

Our plain-English summary of Isolation and whole genomic analysis of mesophilic bacterium Pseudoglutamicibacter cumminsii in epithelial mesothelioma, by N. Xu, K. Wu, T. La, et al (Heliyon, 2024).

The study

• Authors: N. Xu, K. Wu, T. La, B. Cao
• Journal: Heliyon
• Published: 2024;10(15):e35617
• Cited by: 1 article, as counted by NIH iCite
• Read it: PubMed · Publisher · Free full text

Abstract

The relationship between bacteria and tumors has been the hot spot of clinical research in recent years. Pseudoglutamicibacter cumminsii is an aerobic Gram-positive bacterium commonly found in soil. Recent studies have identified P. cumminsii in patients with cutaneous and urinary tract infections. However, little is known on its pathogenesis as well as involvement in other clinical symptoms. In this study, we first report the isolation of P. cumminsii in blood of an epithelial mesothelioma patient. The clinical and laboratory characteristics of P. cumminsii were first described and evaluated. The pure colony of P. cumminsii was then identified using automated microorganism identification system and mass spectrum. The whole genome of the newly identified strain was sequenced with third generation sequencing (TGS). The assembled genome was further annotated and analyzed. Whole genomic and comparative genomic analysis revealed that the isolated P. cumminsii strain in this study had a genome size of 2,179,930 bp and had considerable unique genes compared with strains reported in previous findings. Further phylogenetic analysis showed that this strain had divergent phylogenetic relationship with other P. cumminsii strains. Based on these results, the newly found P. cumminsii strain was named P. cumminsii XJ001 (PC1). Virulence analysis identified a total of 71 pathogenic genes with potential roles in adherence, immune modulation, nutrition/metabolism, and regulation in PC1. Functional analysis demonstrated that the annotated genes in PC1 were mainly clustered into amino acid metabolism (168 genes), carbohydrate metabolism (107 genes), cofactor and vitamin metabolisms (98 genes), and energy metabolism (68 genes). Specifically, six genes including yodJ, idh, katA, pyk, sodA, and glsA were identified within cancer pathways, and their corresponding homologous genes have been documented with precise roles in human cancer. Collectively, the above results first identified P. cumminsii in the blood of tumor patients and further provide whole genomic landscape of the newly identified PC1 strain, shedding light on future studies of bacteria in tumorigenesis.

© 2024 The Authors.

In plain English

This was a single-patient report combined with whole genome sequencing of a bacterial isolate. A 36-year-old man admitted to the Second Affiliated Hospital of Xi'an Jiaotong University on 1 May 2018 with abdominal effusion and a lower abdominal mass was diagnosed with epithelial mesothelioma after peritoneal biopsy and immunohistology; PET-CT findings were described as consistent with abdominal malignant mesothelioma. In the article's introduction the authors state that epithelial mesothelioma is primarily caused by exposure to asbestos fibers; no exposure history for this patient was reported. Two blood cultures grew a Gram-positive organism that VITEK 2 Compact could not identify but mass spectrometry identified as Pseudoglutamicibacter cumminsii, named strain XJ001 (PC1). Nanopore sequencing gave a genome of 2,179,930 bp with 1922 genes, 61.23 % GC content, 96 unique genes versus five reference strains, average nucleotide identity of 94.50 % to 97.24 %, and 71 potential virulence factors. Six genes (yodJ, idh, katA, pyk, sodA, glsA) fell in KEGG cancer pathways. The authors noted no direct evidence linking the infection to tumor progression.

We wrote this plain-English summary from the full article with the help of AI, and a second AI model checked each sentence against the article. It is not the authors' wording; the abstract and the article are their own account.

What the study did and found

• Design: Single-case clinical report with bacterial isolation and whole genome (third-generation Nanopore) sequencing and comparative genomic analysis
• Who was studied: One 36-year-old male patient with epithelial (abdominal) mesothelioma admitted 1 May 2018 to the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China; blood cultures taken in August 2018
• Exposure: No exposure assessment; the study concerns bloodstream isolation of the bacterium Pseudoglutamicibacter cumminsii. The authors state in the introduction that epithelial mesothelioma is primarily caused by asbestos fiber exposure
• Main results:
  • Diagnosis in this patient: peritoneal puncture tissue showed CK(+), VIM(−), EMA(+), D2-40 small focus (+), CR(+), CK5/6(+), P53(+), CK-L(+), TTF(−), CDX2(−), PSA(−), KI67(+) 20 %, leading to a diagnosis of epithelial mesothelioma
  • Both blood cultures from the patient turned positive (after 24 h 33 min and 20 h 29 min); the isolate could not be identified by VITEK 2 Compact but was confirmed as P. cumminsii by mass spectrometry
  • Genome of the isolate (PC1): 2,179,930 bp total, 1,922,406 bp annotated, 1922 genes, GC content 61.23 %
  • Average nucleotide identity between PC1 and the five reference P. cumminsii strains ranged from 94.50 % to 97.24 %
  • PC1 and the five reference strains shared 1542 core genes and 2474 pan genes
  • PC1 had 96 unique genes compared with the five reference strains
  • Virulence analysis of PC1 found 71 potential virulence factors, most in nutritional/metabolic factors (23 genes), immune modulation (13), regulation (12), adherence (7)
  • KEGG annotation of PC1: 168 genes in amino acid metabolism, 107 in carbohydrate metabolism, 98 in metabolism of cofactors and vitamins, 68 in energy metabolism; six genes (yodJ, idh, katA, pyk, sodA, glsA) in the Cancer: overview category
  • Phylogenetic trees based on core/pan genes and gene families placed PC1 apart from the other five strains
• The authors' conclusion: The authors concluded that these results will contribute to understanding of P. cumminsii's role in cancer, particularly mesothelioma
• Limitations the authors state:
  • No direct evidence linking P. cumminsii infection to tumor progression
  • Lack of gene expression data
  • The authors state the relationship between the infection and tumorigenesis is unclear, offering two alternative explanations

Topics

Medical terms in this study, explained in our Lexicon: Mesothelioma, Carcinogenesis.

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