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Microbiol Resour Announc
Microbiol Resour Announc
mra
Microbiology Resource Announcements
2576-098X
American Society for Microbiology 1752 N St., N.W., Washington, DC

39162462
mra00488-24
10.1128/mra.00488-24
mra.00488-24
Genome Sequences
genomics-and-proteomicsGenomics and ProteomicsTwo draft genome assemblies of Staphylococcus aureus strains isolated from a cheek swab of a healthy female participant
Kula Alex 1 2
Jablonska Sandra 1 2
Avalos Lexi 1
Jensen Tyler 2
Appleberry Helen 1
https://orcid.org/0000-0003-3049-5991
Putonti Catherine 1 2 cputonti@luc.edu

1 Department of Biology, Loyola University Chicago , Chicago, Illinois, USA
2 Bioinformatics Program, Loyola University Chicago , Chicago, Illinois, USA
Editor Rasko David University of Maryland School of Medicine , Baltimore, Maryland, USA

Address correspondence to Catherine Putonti, cputonti@luc.edu
The authors declare no conflict of interest.

9 2024
20 8 2024
20 8 2024
13 9 e00488-2410 5 2024
08 7 2024
Copyright © 2024 Kula et al.
2024
Kula et al.
https://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

ABSTRACT

Staphylococcus aureus is an opportunistic pathogen often commensal within the nasal and oral cavities. Here we present the genomes of S. aureus O139-S and O139-NS, both isolated from the cheek swab of a healthy female participant. While found in the same sample, the two strains displayed distinct colony morphologies.

KEYWORDS

Staphylococcus aureus
cheek
oral microbiome
Loyola University Chicago (LUC) Mulcahy Scholars Program Appleberry Helen Loyola University Chicago (LUC) Carbon Fellowship Program Jablonska Sandra cover-dateSeptember 2024
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pmcANNOUNCEMENT

In many healthy people, Staphylococcus aureus resides in the nasal and oral flora (1, 2). S. aureus produces a variety of immune evasion molecules and host-specific mobile genetic elements that have contributed to its persistence in different host species, not just humans [see reference (3)]. Multi-drug resistance (MDR) among S. aureus strains has been of concern for decades now (https://www.cdc.gov/infectioncontrol/guidelines/mdro/), and methicillin-resistant S. aureus (MRSA) remains a global health concern [see reference (4)]. Antibiotic resistance and even MDR rates have been identified among these “commensal” S. aureus strains (2, 5). Here, we present two S. aureus draft genome assemblies, both isolated from the cheek swab of a healthy female participant. Plating of these two strains consistently displayed different colony morphologies.

The strains were isolated from storage solution (Amies media) from an oral swab (BD BBL CultureSwab) as part of an IRB-approved study (Loyola University Chicago, #3603). Females were enrolled in the study if they were between the ages of 18 and 25 and had not taken antibiotics in the past 6 months. Samples were processed within 1 hour of receipt. Swabs were swirled and squeezed in the storage media prior to spreading the solution on Mannitol Salt Phenol Red (MS) Agar and incubated for 24 hours at 35°C with 5% CO2. Each distinct colony morphology was then picked and grown in MS broth and incubated with the same culture conditions. This process was repeated to purify the strain. DNA was extracted from the liquid culture using the DNeasy Blood and Tissue Kit (Qiagen), following the protocol for Gram-positive species. DNA was then sent to SeqCoast (Portsmouth, NH) where DNA libraries were constructed using the Illumina DNA Prep tagmentation kit with unique dual indexes. Libraries were sequenced on the Illumina NextSeq2000 platform producing 2 × 150 bp paired-end reads. The Bacterial and Viral Bioinformatics Resource Center (BV-BRC) webtool v3.35.5 was used to assemble the genomes with the “auto” option (6). Trim Galore v0.6.5 (https://github.com/FelixKrueger/TrimGalore) and Unicycler v0.4.8 (7) were used for trimming and assembly, respectively. Assemblies were then refined using Pilon v1.23 (8). BV-BRC was also used to calculate genome coverage, completeness, and contamination as well as conduct variant analysis. Genome annotations were produced using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) v6.7 (9). Antibiotic resistance genes were identified using ResFinder v4.5.0 (10, 11), specifying the Klebsiella species. Unless otherwise specified, default parameters were used for all software tools.

Table 1 lists the assembly statistics for the two strains. Variant analysis identified 25 sites of variation, including nonsynonymous mutations in annotated transposases (IS4 family) and in superantigen-encoding pathogenicity islands (SaPI). We can only speculate that these mutations contributed to the observed different colony morphologies. Both genomes encode for blaZ, suggestive of resistance to penicillin. The fact that the individual from whom these strains were isolated had not taken antibiotics recently may contribute to the fact that only blaZ was encoded in these genomes.

TABLE 1 Genome statistics for S. aureus O139-S and O139-NS

Strain	O139-S	O139-NS	
No. of Raw Reads	3,037,190	2,357,462	
Assembly Length (bp)	2,830,754	2,831,334	
G + C (%)	32.74	32.74	
No. of Contigs	69	68	
Contigs N50 (bp)	150,179	150,179	
Coverage (x)	139.17	117.42	
Completeness (%)	100	100	
Contamination (%)	0	0	

ACKNOWLEDGMENTS

We wish to acknowledge the study participant who consented to provide samples for this study. This work was part of a course-based undergraduate research experience at Loyola University Chicago through the support of the College of Arts and Sciences.

DATA AVAILABILITY

Raw reads are publicly available in the SRA database, with accession nos. SRR28706146 (O139-S) and SRR28706145 (O139-NS). This Whole Genome Shotgun project has been deposited in DDBJ/ENA/GenBank under the accession nos. JBCGEA000000000 (O139-S) and JBCGDZ000000000 (O138-NS). The versions described in this paper are the first version.
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