Two draft genome assemblies of Staphylococcus aureus strains isolated from a cheek swab of a healthy female participant

TL;DR

This paper presents two draft genomes of Staphylococcus aureus strains from a healthy person's cheek swab.

Contribution

The novelty lies in isolating and sequencing two distinct S. aureus strains from the same sample of a healthy individual.

Findings

Two S. aureus strains (O139-S and O139-NS) were isolated from a single cheek swab.

The strains showed distinct colony morphologies despite originating from the same sample.

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.

Tables

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

Full text

ANNOUNCEMENT

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% CO_2_. 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.