First Report of Pathogenic Bacterium Kalamiella piersonii Isolated from Urine of a Kidney Stone Patient: Draft Genome and Evidence for Role in Struvite Crystallization

Punchappady Devasya Rekha; Asif Hameed; Muhammed A P Manzoor; Mangesh V Suryavanshi; Sudeep D Ghate; A B Arun; Sneha S Rao; Athmika; Sukesh Kumar Bajire; M Mujeeburahiman; C-C Young

doi:10.3390/pathogens9090711

First Report of Pathogenic Bacterium Kalamiella piersonii Isolated from Urine of a Kidney Stone Patient: Draft Genome and Evidence for Role in Struvite Crystallization

Pathogens. 2020 Aug 29;9(9):711. doi: 10.3390/pathogens9090711.

Authors

Affiliations

¹ Yenepoya Research Centre, Yenepoya Deemed to be University, Mangalore 575018, India.
² Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 40227, Taiwan.
³ Department of Urology, Yenepoya Medical College and Hospital, Yenepoya Deemed to be University, Mangalore 575018, India.

Abstract

Uropathogenic bacteria are widely distributed in the environment and urinary tract infection is implicated in kidney stone disease. Here, we report on a urease negative bacterium Kalamiella piersonii (strain YU22) isolated from the urine of a struvite stone (MgNH₄PO₄·6H₂O) patient. The closest species, K. piersonii IIIF1SW-P2^T was reported from International Space Station samples. However, there are no earlier reports on its human association. Using whole genome and experimental analysis, its involvement in urinary tract colonization and struvite crystallization was explored. The strain YU22 showed many virulence factors that are needed for host cell invasion and colonization including cell adhesion factors, swimming and swarming motilities, biofilm and siderophore among others. In vitro infection studies in HEK-293T cells demonstrated the host cell attachment and killing. It was able to utilize amino acids as sole carbon source and showed growth in synthetic and healthy urine establishing metabolic adaptation to urinary tract. Increased pH and availability of ammonium ions from amino acid breakdown promoted struvite crystallization. The results from this study support the involvement of urease negative uropathogen in the struvite lithogenesis. Further studies on other isolates of K. peirsonii are warranted to assess its health risks.

Keywords: amino acid metabolism; asparaginase; lithogenesis; media alkalization; motility and biofilm; struvite; synthetic urine; urea carboxylase; uropathogen; virulence.