ABSTRACT
Staphylococcus haemolyticus is an emerging, multidrug-resistant pathogen associated with healthcare infections. We report the whole-genome sequences of two human isolates, NGCE 403 (2.6 Mb, 33% GC content, 2,533 genes) and FSCC13 (2.6 Mb, 32.5% GC content, 2,586 genes), which provide insights into their virulence and resistance mechanisms.
KEYWORDS: Staphylococcus haemolyticus, antibiotic resistance, virulence gene, prophage, whole-genome sequencing
ANNOUNCEMENT
Staphylococcus haemolyticus, a coagulase-negative staphylococcal species, is frequently associated with bloodstream and device-related infections and is characterized by antibiotic resistance, biofilm formation, and adaptation to a variety of host-associated niches, complicating therapy and increasing infection risk (1, 2).
S. haemolyticus strains NGCE403 (from stool) and FSCC13 (from wound) were isolated from patients at a hospital in Dhaka (23.8041° N, 90.4152° E). The stool sample, homogenized in sterile PBS, and the wound swab were streaked onto mannitol salt agar and incubated at 37°C for 18–24 h. Pink colonies were subcultured on TSA (Thermo Scientific) and presumptively identified by Gram staining and catalase, oxidase, coagulase, urease, and novobiocin susceptibility tests (3). Isolates grown in tryptic soy broth at 37°C for 18-24 h were used for DNA extraction with the DNeasy Blood and Tissue Kit (QIAGEN). Nanopore sequencing libraries were prepared using the Rapid PCR Barcoding Kit (SQK-RPB004, Oxford Nanopore Technologies, UK) and sequenced using a FLO-MIN106 (R9.4.1) flow cell on the MinION Mk1C platform. Basecalling was performed using Super Accuracy mode in Guppy (v.5.0.11); trimming was performed using Porechop (v.0.2.3) (4); and filtration was performed using Filtlong (v.0.2.1) (5). Long-read assembly was performed using Flye (v.2.9) (6). Default parameters were used except where otherwise noted. Genome annotation was performed using the Prokaryotic Genome Annotation Pipeline (v.6.5) (7). Genome assemblies were analyzed with QUAST (v.5.3.0) (8), and read counts, N50, and coverage depth were calculated from raw FASTQ files using SeqKit (9) and custom Python scripts. Sequencing details for FSCC13 and NGCE403 are listed in Table 1. The draft genome of S. haemolyticus NGCE 403 contains 2,533 genes, including 2,109 protein-coding genes and 80 RNA genes (60 tRNAs), whereas the strain FSCC13 contains 2,586 genes, including 2,163 protein-coding genes and 79 RNA genes (59 tRNAs). By MLST 2.0 (10), the strains NGCE 403 and FSCC 13 were identified as ST 3 and ST 40, respectively. ResFinder (v.4.6.0) (11) identified aminoglycoside resistance genes, including aac(6′)-aph(2″), APH(3′)-IIIa, and ant(6)-Ia, alongside mecA for beta-lactam resistance in FSCC13. NGCE403 contained mecA, blaZ, and macrolide resistance genes msrA and mphC. Both strains shared genes such as vanY, vanT, norC, and sdrM, which confer resistance to glycopeptides, fluoroquinolones, and disinfectants. Mobile Element Finder (v.1.0.3) (12) detected one plasmid in NGCE403 and two in FSCC13, carrying resistance genes for erythromycin (ermC, mphC, and msrA), penicillin (blaZ), and chlorhexidine (qacA). Among the virulence factors, capsular polysaccharide (capA family protein), SasC (cell-cell adhesion), atl (autolysin), lip (lipase), nuc (nuclease), and cylR2 (cytolysin) were predicted in both strains. Strain FSCC13 uniquely harbored clfA (clumping factor), while strain NGCE403 uniquely contained fibrinogen-binding protein sdrC. PHASTEST (13) identified one prophage in NGCE403, which contains structural genes, a repressor, and integrase, suggesting potential virion production. FSCC13 has two prophages: one similar to the one in NGCE403 and another, likely cryptic, lacking structural genes. This genomic resource will enhance our understanding of lifestyle, immunotherapeutic, and chemotherapeutic approaches to control S. haemolyticus.
TABLE 1.
Genome assembly and strain information for the two S. haemolyticus strains
| Strain | Total reads | Read N50 (bp) | Assembly length (bp) | No. of contigs | Assembly N50 (bp) | GC (%) | Genome fraction (%) | Duplication ratio | Coverage (×, assembly) |
|---|---|---|---|---|---|---|---|---|---|
| FSCC13 | 105,245 | 4,729 | 2,594,099 | 8 | 610,788 | 32.5 | 89.022 | 1.011 | ≈161× |
| NGCE403 | 95,393 | 4,961 | 2,551,171 | 2 | 2,520,515 | 33 | 87.859 | 1.010 | ≈170× |
ACKNOWLEDGMENTS
This work was funded by the North South University Conference Travel and Research Grant (CTRG) 2020–2021 (grant no. CTRG-20/SHLS/18).
All experimental protocols and sample collection were approved by the North South University Institutional Review Board (IRB)/Ethical Review Committee under protocol number 2020/ORNSU/IRB/1109.
Fariza Shams and Maqsud Hossain: conceptualization, formal analysis, funding acquisition, investigation, methodology, supervision, and writing (original draft, review, and editing); Syeda Naushin Tabassum and Aura Rahman: data curation, formal analysis, software, and visualization; Nayma Haque Tonny, Pronoy Debnath, and Asifa Siddika Badhon: formal analysis and writing (review and editing); Abdus Sadique: formal analysis, investigation, project administration, resources, and supervision; Jahidul Alam: formal analysis, investigation, and resources.
Contributor Information
Fariza Shams, Email: fariza.shams@northsouth.edu.
Atmika Paudel, Fluxus Inc., Sunnyvale, California, USA.
DATA AVAILABILITY
The genome sequences of S. haemolyticus strain FSCC 13 and NGCE 403 have been deposited at DDBJ/ENA/GenBank under accession numbers JBNFUP000000000 and JBNFUQ000000000, respectively. The BioProject and BioSample accession numbers of S. haemolyticus strain FSCC13 are PRJNA1253103 and SAMN48065002, respectively. The BioProject and BioSample accession numbers of S. haemolyticus strain NGCE403 are PRJNA1253111 and SAMN48065039, respectively. Raw sequencing reads of S. haemolyticus strain FSCC13 and NGCE403 are available in the NCBI Sequence Read Archive at https://www.ncbi.nlm.nih.gov/sra/PRJNA1253103 and https://www.ncbi.nlm.nih.gov/sra/PRJNA1253111, respectively.
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Associated Data
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Data Availability Statement
The genome sequences of S. haemolyticus strain FSCC 13 and NGCE 403 have been deposited at DDBJ/ENA/GenBank under accession numbers JBNFUP000000000 and JBNFUQ000000000, respectively. The BioProject and BioSample accession numbers of S. haemolyticus strain FSCC13 are PRJNA1253103 and SAMN48065002, respectively. The BioProject and BioSample accession numbers of S. haemolyticus strain NGCE403 are PRJNA1253111 and SAMN48065039, respectively. Raw sequencing reads of S. haemolyticus strain FSCC13 and NGCE403 are available in the NCBI Sequence Read Archive at https://www.ncbi.nlm.nih.gov/sra/PRJNA1253103 and https://www.ncbi.nlm.nih.gov/sra/PRJNA1253111, respectively.