Draft genome sequence data of the multidrug-resistant bacterium Staphylococcus haemolyticus 010503B isolated from an aerosol sample in a hospital waiting area in Thailand

Staphylococcus haemolyticus 010503B is a multidrug-resistant bacterium isolated from an outpatient clinic in a hospital waiting area in Thailand. Here we present the draft genome sequence of S. haemolyticus 010503B. The paired-end reads were generated on the Illumina NextSeq 550 sequencer using genomic DNA from the pure culture of S. haemolyticus 010503B. The draft genome consisted of 114 contigs with a total size of 2,457,654 base pairs, an N50 of 57,312 base pairs and a GC content of 32.60%. The dDDH between 010503B and Staphylococcus haemolyticus SM 131T was 91.9%, identifying the strain as Staphylococcus haemolyticus. The data presented holds promise for bacterial classification, comparative genomics, analysing antimicrobial resistance comprehensively, and assessing bacterial virulence factors of S. haemolyticus. The draft genome sequence data has been deposited at NCBI under Bioproject accession number PRJNA550309.

Staphylococcus haemolyticus 010503B is a multidrug-resistant bacterium isolated from an outpatient clinic in a hospital waiting area in Thailand.Here we present the draft genome sequence of S. haemolyticus 010503B.The paired-end reads were generated on the Illumina NextSeq 550 sequencer using genomic DNA from the pure culture of S. haemolyticus 010503B.The draft genome consisted of 114 contigs with a total size of 2,457,654 base pairs, an N50 of 57,312 base pairs and a GC content of 32.60%.The dDDH between 010503B and Staphylococcus haemolyticus SM 131 T was 91.9%, identifying the strain as Staphylococcus haemolyticus .The data presented holds promise for bacterial classification, comparative genomics, analysing antimicrobial resistance comprehensively, and assessing bacterial virulence factors of S. haemolyticus .The draft genome sequence data has been deposited at NCBI under Bioproject accession number PRJNA550309.DNA was extracted using the PureLink TM Genomic DNA Mini Kit and sequenced on an Illumina NextSeq 550.AfterQC v0.9.6 was used for adapter trimming and quality filtering.Genome assembly was performed using Unicycler v0.5.0 and assembly metrics were determined using QUAST v5.0.2.Genome quality was assessed using CheckM v1.1.2.Digital DNA-DNA hybridisations and a phylogenomic tree were analysed using the Type (Strain) Genome Server.Genomic map was generated by Proksee.Genome annotation was performed using the NCBI Prokaryotic Genome Annotation Pipeline.Identification of antimicrobial resistance genes and prediction of resistance phenotypes were performed using ResFinder v4.3.3.

Data source location
Staphylococcus haemolyticus 010503B was obtained from an aerosol sample collected in a waiting area at Thammasat University Hospital, located at latitude 14.07341 and longitude 100.61513 in Thailand.

Value of the Data
• The draft genome sequence of S. haemolyticus 010503B has potential value for scientific studies in the fields of bacterial taxonomy and ecology, particularly in relation to the identification and distribution of taxa.• The draft genome sequence of S. haemolyticus 010503B provides potential benefits for comparative genomic research on other Staphylococcus species with multidrug resistance.• Elucidating the genome sequence of S. haemolyticus 010503B can potentially aid in the identification of antimicrobial resistance genes and the prediction of drug resistance profiles.

Data Description
Here we present the draft genome sequence data of S. haemolyticus 010503B ( Fig. 1 ), including its gene clusters with antimicrobial resistance genes and the predicted of phenotypes.
The genome consisted of 114 contigs with a total size of 2,457,654 bp, an N50 value of 57,312 bp and a GC content of 32.60% ( Table 1 ).

Bacterial isolation and identification
Aerosol samples were collected using an Andersen six-stage impactor (BGI Inc, Waltham, MA) in the patient waiting area for medical examinations, outpatient clinics at Thammasat University Hospital, Pathum Thani Province, Thailand.An Andersen six-stage impactor with a volume of 28.3 L/min for 15 min (BGI Inc, Waltham, MA) was placed on the floor at a height of 1.5 m.At each stage of the sterilised impactor, a medium plate containing Baird Parker Agar (BPA) (Oxoid, UK) was placed.After aerosol sampling, BPA plates were incubated at 37 °C for 48 h.A single colony of strain 010503B was plated on Luria-Bertani (LB) agar by cross-streaking and stored in LB broth with 25% glycerol at -80 °C for long-term storage.

Genomic DNA preparation
The genomic DNA (gDNA) was extracted from overnight cultures of the strain 010503B grown in LB broth, utilizing the PureLink TM Genomic DNA Mini Kit in accordance with the manufacturer's instructions.Subsequently, agarose gel electrophoresis and NanoDrop spectrophotometry (Thermo Scientific, USA) were utilized to evaluate the quality of the gDNA.

Whole genome sequencing and assembly
The Nextera XT DNA library preparation kit (Illumina, San Diego, CA, USA) was used to generate sequencing libraries from 1 ng of DNA.The NextSeq 550 sequencer was used to acquire raw sequencing reads using the NextSeq 500/550 high output kit v2.5 (300 cycles, 2 × 150-bp reads) manufactured by Illumina.Quality assessments, adapter trimming, and quality filtering were performed using AfterQC v0.9.6 with the default settings [1] .De novo genome assembly was performed using the raw reads and Unicycler v0.5.0 with default settings [2] .The assessment of genome assembly metrics was performed using QUAST v5.0.2, employing the default parameters [3] .

Taxonomic identification of the strain
The assessment of genome quality was conducted using CheckM v1.1.2,employing the default settings [4] .The analysis of digital DNA-DNA hybridization (dDDH) and a phylogenomic tree, derived from the whole genome sequences of 010503B and its related type strains, was conducted using the Type (Strain) Genome Server (TYGS) [5] .

Genome annotation and antimicrobial gene prediction
A genomic map of 010503B was generated by Proksee [6] , and the genome was annotated using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) with default settings [7] .In addition, whole genome sequence (WGS)-based antimicrobial susceptibility testing was performed using ResFinder v4.3.3 with default settings [8] .

Limitations
The use of next-generation sequencing techniques generates vast quantities of data.However, de novo genome assemblies resulting from this data often display significant deficiencies in completeness.The current assemblies possess shortcomings that render them vulnerable to annotation errors, particularly regarding the imprecise estimation of genes that could possibly exist in the draft genome of 010503B.

Ethics Statement
This work does not involve human or animal subjects and the authors declare that this manuscript is original and has not been published elsewhere.

Data Availability
Draft genome sequence data of the multidrug-resistant bacterium Staphylococcus haemolyticus 010503B isolated from an aerosol sample in a patient waiting area, Thammasat University Hospital, Thailand (Original data) (Genbank).
© 2024 The Authors.Published by Elsevier Inc.This is an open access article under the CC BY license ( http://creativecommons.org/licenses/by/4.0/ )

Table 1
Genomic features and assembly statistics for S. haemolyticus 010503B.

Table 2
Identification of antimicrobial resistance genes and prediction of resistance phenotypes from the 010503B genome sequence.Phylogenomic tree reconstructed using whole-genome sequence data from S. haemolyticus 010503B and its closely related type strain on the TYGS platform.Branch numbers were determined based on pseudo-bootstrap support values greater than 60% from 100 replicates using Genome Blast Distance Phylogeny (GBDP), with an average branch support of 88.0%.