Genomic data of Leptospira interrogans HP358 isolated from rodent captured from the human leptospirosis suspected areas of Selangor state, Malaysia.

The data provided in this article is the genomic sequence of new Leptospira isolate, Leptospira interrogans strain HP358 (L. interrogans HP358) isolated from rodent, Sundamys muelleri (S. muelleri), captured from the human leptospirosis suspected area, in forest environment, Hulu Perdik, Selangor. The kidney of the rodent was cultured, and the genomic DNA of pure Leptospira isolate was extracted and sequenced. The de novo assembly of genome generated 118 contigs with N50 of 133,176bp. The genome size of the L. interrogans HP358 was determined with a length of 4,808,724 and 35.01% G+C content with 229 subsystems, 5236 coding sequences and 39 RNAs. The whole genome shotgun project has been deposited in NCBI GenBank under the accession number JAFCYY000000000.1.

Specifications Table

Value of the Data

WGS of Leptospira interrogans HP358 reported in Malaysia, the whole genome sequence of this strain could provide fundamental knowledge and insight towards understanding its virulence and microbial properties.

The data, an important source towards understanding the relationship among Leptospira interrogans strains from Malaysia and other regions will benefit researchers, public health, health sector, veterinary and reference laboratories.

The data may provide valuable information in understanding the epidemiology and diagnostics of leptospirosis, defining the virulence properties, thereby could assist in developing informed policy in the design and implementation of leptospirosis control programme.

Data Description

The data reported in this article is the genomic data of whole genome sequencing (WGS) of Leptospira interrogans HP358 (L. interrogans HP358) with ST number ST238, a new ST number recorded in Leptospira MLST data base [1]. L. interrogans HP358 was isolated from the kidney of rodents, Sundamys muelleri (S. muelleri), captured from the human leptospirosis suspected area, in forest environment, Hulu Perdik, Selangor, Malaysia. S. muelleri is a species of rodent commonly found in Malaysia, Indonesia, Myanmar, Thailand and Philippines. The isolate was cultured in liquid Ellinghausen-McCullough-Johnson-Harris (EMJH) medium supplemented with Leptospira enrichment medium, rabbit and calf serum and 5-fluorouracil. The genome size of the L. interrogans HP358 contained a length of 4,808,724 nucleotides with G+C content of 35.01%, 229 subsystems, 5236 coding sequences and 39 RNAs.

Experimental Design, Materials and Methods

Bacterial culture and DNA extraction

The genomic DNA of L. interrogans HP358 was extracted using DNeasy Blood & Tissue kits (Qiagen, German) according to the manufacturer's instruction. The DNA library for WGS was prepared using the IGP-NGSP Illumina Library and subsequently sequenced using the Miseq instruments platform.

Whole genome sequencing and bioinformatic analysis

Approximately 99% of the genome was sequenced using 177 × sequencing coverage and generated a total of 2,902,368 paired reads of a 151-bp paired-end (Illumina, San Diego, CA). The sequencing data was deposited in the Sequence Read Archive (SRA) (Bio-sample accession number of SAMN16925409) under the bio-project accession number PRJNA680866. The quality of the raw sequences read was assessed using FastQC and then pre-processed using BBMap version 38.43 tool [2]. The adapters were trimmed and sequences read with less than 50bp were removed based on the phred quality score (below Q30) using BBDuk.sh [2]. The quality-filtered sequences were de novo assembled using SPAdes version 3.11.1 [3]. The de novo assembly of the genome generated 118 contigs with N50 of 133,176bp. The whole genome size of L. interrogans HP358 was determined with a length of 4,808,724 bp and G + C content of 35.01%. The draft genome of L. interrogans HP358 (Genome accession number of JAFCYY000000000) was annotated by the Rapid Annotation of microbial genomes using Subsystem Technology (RAST) [4] and showed 229 subsystems, 5 236 coding sequences and 39 RNAs.

The availability of this genome sequence would enable the comparative genomics study and understanding the phylogenetic relationship of this isolate with other Leptospira strains. The sequence data may play important role in understanding the key difference in the virulence level of different Leptospira isolates and subsequently increase the knowledge that determines the different clinical manifestation of leptospirosis. Therefore, the availability of this genome of local isolates provides genetic and epidemiological information about prevailing Leptospira species in Malaysia.

Ethics Statement

This research work was supported by the Ministry of Education, Malaysia through the Fundamental Research Grant Scheme (FRGS/1/2019/WAB13/UPM/02/2).

CRediT Author Statement

Noraini Philip: Conceptualization, Methodology, Software, Data curation, Investigation, Writing – original draft; Jaeyres Jani: Conceptualization, Methodology, Software, Data curation, Writing – review & editing; Nurul Natasya Azhari: Data curation, Investigation; Zamberi Sekawi: Conceptualization, Funding, Supervision; Vasantha Kumari Neela: Conceptualization, Funding, Supervision, Writing – review & editing.

Declaration of Competing Interest

The authors declare that they have no known competing financial interests or personal relationships which have or could be perceived to have influenced the work reported in this article.

Subject	Medicine and Public Health
Specific subject area	Microbiology, Leptospira
Type of data	Analyzed data
How data were acquired	The genomic data was acquired by whole genome sequencing conducted on Illumina Miseq instruments platform
Data format	Raw data and whole genome sequence data analysis.
Parameters of data collection	Genomic DNA was extracted from pure Leptospira culture at room temperature.
Description of data collection	Kidney from rodents (Sundamys muelleri) was cultured in EMJH medium and incubated at 28°C for growth of leptospires. It was filtered until a pure Leptospira culture was obtained.
Data source location	The rodent caught from forest in Hulu Perdik, Selangor, Malaysia
Data accessibility	Repository name:Data is publicly available at NCBI GenBank from the following links:https://www.ncbi.nlm.nih.gov/nuccore/JAFCYY000000000.1https://www.ncbi.nlm.nih.gov/bioproject/PRJNA680866https://www.ncbi.nlm.nih.gov/biosample/SAMN16925409