Whole Genome Sequence of Pandoraea pnomenusa GXDRC_01 Isolated from a Clinical Sample, Gujarat, India
Vivek N. Upasani *
Genexplore Diagnostics and Research Centre Pvt. Ltd., 1201-1210, Iconic Shyamal, Shyamal Cross Road, Ahmedabad 380015, Gujarat, India.
Hetvi P. Patel
Genexplore Diagnostics and Research Centre Pvt. Ltd., 1201-1210, Iconic Shyamal, Shyamal Cross Road, Ahmedabad 380015, Gujarat, India.
Alpesh R. Patel
Genexplore Diagnostics and Research Centre Pvt. Ltd., 1201-1210, Iconic Shyamal, Shyamal Cross Road, Ahmedabad 380015, Gujarat, India.
Shiva S. Chettiar
Genexplore Diagnostics and Research Centre Pvt. Ltd., 1201-1210, Iconic Shyamal, Shyamal Cross Road, Ahmedabad 380015, Gujarat, India.
Sushma R. Shah
Department of Obstetrics and Gynaecology, Smt. NHL Municipal Medical College and SVPIMSR, Ellisbridge, Ahmedabad 380006, Gujarat, India.
Devendrasinh D. Jhala
Department of Zoology, School of Sciences, Gujarat University, Ahmedabad 380009, Gujarat, India.
*Author to whom correspondence should be addressed.
Abstract
Aim: This research aims to report the genome sequence of Pandoraea pnomenusa GXDRC_01 isolated from a pregnant woman, from western India.
Study Design: Vaginal swab sample collection, enrichment, screening on Blood Agar medium, gDNA extraction, NGS, and data analysis.
Place and Duration of Study: Molecular Biology Department, Genexplore Diagnostics and Research Centre Pvt. Ltd., Ahmedabad, India, between October 2024 and March 2025.
Methodology: High quality gDNA was isolated and quantified by Epoch. Identification of the bacterium was carried out by Vitek2 system and phylogenetic analysis. For WGS the library was prepared using Ion Xpress™ Plus Fragment Library Kit, and sequencing was carried out by NGS using Ion Torrent S5 Plus (550 Chip) (Thermo scientific, USA). Sequence data was assembled using SPAdes v. 4.0.0 and annotation was done by NCBI Prokaryotic Genome Annotation Pipeline (PGAP).
Results: The genome sequence of P. pnomenusa GXDRC_01 included 118 contigs with a calculated genome size of 5.4 Mb. The completeness of genome using CheckM analysis (V1.2.3) was 94.74% with 0.07% contamination.
Conclusion: A beta-proteobacteria was isolated from a vaginal swab sample obtained from a tertiary hospital in Ahmedabad, India. It was identified as Pandoraea pnomenusa, and the genome assembly code is GCA_050017075.1, and genome assembly identified as ASM5001707v1. This is the first report on the isolation and genome analysis of this gram-negative bacterium from the vaginal swab sample of a pregnant woman in India. It is important to report this gram-negative bacterium in vaginal flora as it is known to cause sepsis, bacteremia and cystic fibrosis.
Keywords: Pandoraea pnomenusa, WGS, vaginal swab, pregnant woman, emerging pathogen, LIM broth, NCBI PGAP, Ion Torrent S5, PPROM, GBS