Draft genome sequences of Staphylococcus species isolated from urine samples from asymptomatic females

TL;DR

This paper presents draft genome sequences of four Staphylococcus species isolated from urine samples of asymptomatic females.

Contribution

The study provides new genomic data for Staphylococcus species commonly found in the female urinary tract.

Findings

Genome sequences of four Staphylococcus isolates were obtained from asymptomatic females.

The isolates include both uropathogenic and commensal species.

Abstract

The female urinary tract is host to several different Staphylococcus species, both uropathogens and commensals. To further investigate these species, we sequenced the genomes of four isolates from voided urine samples collected from asymptomatic (“healthy”) females: Staphylococcus aureus U215, Staphylococcus haemolyticus U117, and Staphylococcus hominis strains U224 and U226.

Tables

TABLE 1. Genome assembly statistics for S. aureus U215, S. haemolyticus U117, and S. hominis U224 and U226

Strain	U215	U117	U224	U226
Species designation	S. aureus	S. haemolyticus	S. hominis	S. hominis
ANI (%)	98.07a	98.70b	98.58c	98.80c
Assembly length (bp)	2,738,746	2,435,287	2,293,153	2,398,823
No. of contigs	46	82	51	41
Contigs N50 (bp)	176,606	65,388	86,826	146,863
Coverage (×)	193.88	166.08	438.37	413.62
# genes	2,737	2,471	2,329	2,433
# tRNAs	56	55	50	55
G + C (%)	32.70	32.54	31.33	31.39
Completeness (%)	98.08	99.25	91.55	89.78
Contamination (%)	0.39	0.06	3.77	5.06
No. of reads	3,784,218	2,653,578	8,473,308	8,992,872
SRA accession no.	SRR34298188	SRR34547675	SRR34298187	SRR34298186
Assembly accession no.	JBPFAR000000000	JBPFAQ000000000	JBPFAS000000000	JBPFAT000000000

Full text

ANNOUNCEMENT

Although typically associated with the skin and mucosa, Staphylococcus species also inhabit the urinary tract. While Staphylococcus aureus is a known uropathogen, it is not prevalent (1). However, coagulase-negative staphylococci species are common, in particular in the urine of females with urge urinary incontinence (2, 3). While some species are more frequently found, e.g., Staphylococcus epidermidis and Staphylococcus haemolyticus, others are rare, e.g., Staphylococcus hominis (2). Here, we present the draft genome assemblies of one S. aureus, one S. haemolyticus, and two S. hominis isolates from urine collected from four different self-identified “healthy” females who had not taken antibiotics within the last 6 months.

Participants in our institutional review board (IRB)-approved study (IRB no. 3603) were students at Loyola University Chicago (41.99872, −87.6577). Each participant was instructed to collect a first-morning, mid-stream urine sample. Within 1 hour of sampling, 100 µL of urine was spread on a mannitol salt (MS) agar plate and incubated for 24 hours at 35°C with 5% CO_2_. MS broth (1 mL) was inoculated with a morphologically distinct colony and incubated for 24 hours at 35°C with 5% CO_2_ without shaking. This process was repeated to purify the isolates. DNA was extracted using the DNeasy Blood and Tissue kit (Qiagen), following the manufacturer’s protocol for gram-positive bacteria. DNA was quantified via a Qubit fluorometer and then sent to SeqCoast (Portsmouth, NH USA) for library construction (Illumina DNA Prep tagmentation kit and unique dual indexes) and sequencing (Illumina NextSeq2000 platform; 2 × 150 bp reads). Prior to delivery from SeqCoast, DRAGEN v3.10.12 (Illumina) was used for read demultiplexing, read trimming, and run analytics.

Assembly was performed using the BV-BRC v3.51.7 web tool with the “auto” option (4). Raw reads were trimmed using trim_galore v0.6.5dev (https://github.com/FelixKrueger/TrimGalore), normalized via bbnorm v37.60 (https://sourceforge.net/projects/bbmap/), and assembled using Unicycler v0.4.8 (5), followed by two rounds of polishing with Pilon v1.24 (6). To determine the species of each isolate, taxonomic binning of raw reads was conducted via BV-BRC (which uses Kraken 2 [7]). The BV-BRC identified species was confirmed by JSpeciesWS (8), comparing each draft assembly to species representatives within the JSpeciesWS GenomesDB, and by NCBI upon submission. Genome annotations were generated by PGAP v6.10 (9). Completeness and contamination metrics were computed using CheckM v1.2.3 (10) upon submission to NCBI. Genomes were also examined for prophage sequences using PHASTER (11). Unless otherwise noted, default parameters were used for all software tools.

Table 1 lists the genome assembly statistics. While temperate phages of S. aureus have been shown to be significant drivers of the species’ evolution (12), the diversity of Staphylococcus-infecting phages has only recently been explored (13, 14). Intact prophage sequences were found in the S. aureus and S. hominis sequences. S. hominis U224 encoded for two phages, one of which is also present in the S. hominis U226 genome. Further characterization of Staphylococcus-infecting phages of the urinary tract is needed to ascertain their role in shaping these species for this environment.