Draft genomes of one Staphylococcus haemolyticus and five Staphylococcus lugdunensis strains isolated from catheterized urine samples of females

TL;DR

This paper presents draft genomes of six staphylococcus strains isolated from urine samples of women with urinary tract symptoms.

Contribution

The novel contribution is the draft genome sequencing of one S. haemolyticus and five S. lugdunensis strains from catheterized urine samples.

Findings

Draft genomes of five S. lugdunensis and one S. haemolyticus strains were sequenced.

The strains were isolated from catheterized urine samples of females with lower urinary tract symptoms.

Abstract

Although Staphylococcus haemolyticus and Staphylococcus lugdunensis are members of the normal human flora, they also can cause infection. Here, we present the draft genomes of five strains of S. lugdunensis and one strain of S. haemolyticus isolated from transurethral catheterized urine samples from different females experiencing lower urinary tract symptoms.

Tables

TABLE 1. Genome assembly and strain information for the 1 S. haemolyticus and 5 S. lugdunensis strains isolated from the urobiome

Strain	S. haemolyticus UMB3106B	S. lugdunensis UMB1735	S. lugdunensis UMB5747	S. lugdunensis UMB7308	S. lugdunensis UMB8915	S. lugdunensis UMB8974
No. of Raw Reads	2,584,846	2,130,040	2,186,190	2,157,860	1,915,472	2,971,182
Assembly Length (bp)	2,414,972	2,526,737	2,538,396	2,542,811	2,496,650	2,537,671
G + C (%)	32.74	33.68	33.65	33.64	33.77	33.65
No. of Contigs	62	22	28	27	15	32
Contigs N50 (bp)	106,858	285,955	188,585	369,218	629,127	188,585
Coverage (x)	136.19	119.72	118.19	111.41	103.87	145.19
Completeness (%)	99.31	97.61	97.69	97.66	96.47	97.69
Contamination (%)	0	0.32	0.34	0.34	0.38	0.34
Symptom Status	rUTI	OAB	OAB	OAB	OAB	OAB
IRB Protocol No. (Institution)	170077AW (UCSD)	LU207152 (LUC)	LU207152 (LUC)	LU207152 (LUC)	LU207102 (LUC)	LU207102 (LUC)
Study Reference(s)	11, 12	13	13	13	9, 10	9, 10
SRA Accession No.	SRR28710902	SRR28710913	SRR28710895	SRR28710912	SRR28710910	SRR28710914
Assembly Accession No.	JBCGEY000000000	JBCGEQ000000000	JBCGER000000000	JBCGEP000000000	JBCGEO000000000	JBCGEZ000000000

Full text

ANNOUNCEMENT

Staphylococcus haemolyticus and Staphylococcus lugdunensis are coagulase-negative staphylococci (CoNS) and “commensal” members of the skin microbiota (1, 2). However, both are known opportunistic pathogens (3, 4). While S. haemolyticus is the second-most frequently isolated CoNS from urine samples, incidences of S. haemolyticus-associated urinary tract infections (UTIs) are rising (5). S. lugdunensis is recognized as a rare cause of UTIs, while also a part of the nonpathogenic flora of the urobiome (6). Here, we present a S. haemolyticus strain, isolated from the urine of a female diagnosed with recurrent UTI (rUTI), and five S. lugdunensis strains, isolated from five different females with overactive bladder (OAB) symptoms. While prior studies have found instances in which Staphylococcus sp. have been more abundant in the urinary microbiota of individuals with OAB, it is unknown if this is associated with the symptoms observed (7, 8).

These urine samples were collected as part of prior IRB-approved studies (see Table 1) (9–13). The strains were cultured from the urine samples by the enhanced quantitative urine culture (EQUC) method (14). Species identification was determined using a matrix-assisted laser desorption ionization-time of flight mass spectrometer (MALDI-TOF MS; Bruker Daltonics, Billerica, MA) as previously described (15), and the isolates were stored at −80°C in the Loyola Urinary Education and Research Collaborative (LUEREC) collection. Samples were retrieved from this collection and streaked on tryptone soy agar (TSA) plates and were incubated in 5% CO_2_ for 24 hours at 35°C. Liquid tryptone soy medium was inoculated with single colonies from these plates and incubated in 5% CO_2_ for 24 hours at 35°C. DNA was extracted from the liquid cultures with the DNeasy Blood and Tissue Kit (Qiagen), following the manufacturer's protocol for Gram-positive species. DNA was sent to SeqCoast (Portsmouth, NH) for library preparation using the DNA Prep tagmentation kit (Illumina) and unique dual indexes. These libraries were then sequenced by SeqCoast on the Illumina NextSeq2000 platform with a 300-cycle flow cell kit (2 × 150 bp reads). The BV-BRC website, v3.35.5 (16), was used for genome assembly with the “auto” parameter. There the reads were trimmed by trim_galore v0.6.5dev (https://github.com/FelixKrueger/TrimGalore), assembled by Unicycler v0.4.8 (17), and polished with Pilon v1.23 (18). Taxonomy was confirmed with the Type Strain Genome Server (TYGS) (19). Assemblies were annotated by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) v.6.7 (20). Coverage was calculated by BV-BRC; genome completeness and contamination were computed by CheckM v1.2.2 (21) upon submission to NCBI. Default parameters were used unless otherwise specified.

Information regarding the sequencing of these six strains, S. haemolyticus UMB3106B and S. lugdunensis UMB1735, UMB5747, UMB7308, UMB8915, and UMB8974, can be found in Table 1. For both species, the number of sequenced isolates from the urinary tract is limited. Further sequencing of Staphylococcus isolates from the urine of individuals with OAB is needed to explore associations between symptoms and CoNS species.