Draft genomes of Neisseria perflava UMB0578, Proteus mirabilis UMB8339, and Enterococcus faecalis UMB7967 isolated from urine samples

TL;DR

This paper reports the draft genomes of three bacteria isolated from urine samples, which may help understand urinary tract microbiomes.

Contribution

The study provides new draft genome sequences of three bacterial isolates from urine.

Findings

Draft genome of Neisseria perflava UMB0578 was sequenced.

Draft genome of Proteus mirabilis UMB8339 was sequenced.

Draft genome of Enterococcus faecalis UMB7967 was sequenced.

Abstract

The urinary tract of females harbors a variety of microorganisms, both for those with and without symptoms. Here, we present the draft genome sequences of three isolates from urine samples—Neisseria perflava UMB0578, Proteus mirabilis UMB8339, and Enterococcus faecalis UMB7967.

Tables

TABLE 1. Genome assembly statistics

Strain	UMB0578	UMB8339	UMB7967
Species	N. perflava	P. mirabilis	E. faecalis
SRA accession no.	SRR28710915	SRR28710898	SRR28710894
Assembly accession no.	JBCGFA000000000	JBCGEX000000000	JBCGEU000000000
No. raw reads	1,699,568	1,535,364	3,035,810
Assembly length (bp)	2,273,827	3,722,531	2,908,311
G+C (%)	48.98	38.49	37.3
No. contigs	42	62	43
Contigs N50 (bp)	232,257	217,641	603,203
Coverage (×)	106.01	51.49	140.04
Completeness (%)	100	100	100
Contamination (%)	0.2	0	0

Full text

ANNOUNCEMENT

Recent efforts have been focused on cataloging the bacterial species of the urinary microbiota (1), and research has found that many species within the female urinary microbiota also inhabit the vaginal microbiota (2–4). As the most recent catalog of bacterial species diversity in the urinary tract shows, numerous taxa can be found in this ecological niche (1). While some are considered “commensal” or “transient,” those taxa associated with symptoms/diseases are significantly better studied. In our group’s continued effort to characterize and sequence strains from the urinary microbiota, here, we present the draft genome assemblies of three species: Neisseria perflava, Proteus mirabilis, and Enterococcus faecalis. While N. perflava is not associated with urinary tract infections, both P. mirabilis and E. faecalis are known causes of both uncomplicated and complicated urinary tract infections (UTIs) (5).

N. perflava UMB0578 was isolated from a catheterized urine sample from a female with stress urinary incontinence [IRB: LU204133, LU 204658, and LU206449 (Loyola University Chicago) (6)]. Both P. mirabilis UMB8339 and E. faecalis UMB7967 were isolated from voided urine samples from two different females diagnosed with recurrent UTI [IRB: 170077AW (University of California, San Diego) (7, 8)]. These strains were isolated using the expanded quantitative urine culture method (9); the taxonomy of these isolates was determined via matrix-assisted laser desorption ionization-time of flight, as previously described (10), and stored at −80°C in the Loyola Urinary Education and Research Collaborative (LUEREC) collection. We obtained samples from this collection and streaked the N. perflava isolate onto a nutrient broth (NB) agar plate and the P. mirabilis and E. faecalis isolates onto brain heart infusion agar plates. The N. perflava NB plate was incubated at 37°C for 48 hours; the other two plates were incubated at 35°C in 5% CO_2_ for 24 hours. For each, a single colony was selected and grown in their respective culture media under the above culture conditions. DNA extraction was performed using the DNeasy Blood and Tissue Kit (Qiagen), following the protocol for Gram-positive organisms, and sent to SeqCoast Genomics (Portsmouth, NH) for library construction, using the Illumina DNA Prep tagmentation kit, and sequencing on the Illumina NextSeq2000 platform. Raw reads (2 × 150 bp reads) were assembled using BV-BRC v3.35.5 (11) with the “auto” parameter. The raw reads were first trimmed using Trim Galore v0.6.5 (https://github.com/FelixKrueger/TrimGalore) and then assembled using Unicycler v0.4.8 (12). Assemblies were next polished with Pilon v1.23 (13). BV-BRC also was used to calculate genome coverage, completeness, and contamination. Genome annotations were produced using the NCBI Prokaryotic Genome Annotation Pipeline v6.7 (14). Unless otherwise specified, default parameters were used for all software tools.

Genome assembly statistics are provided in Table 1. Continued efforts to sequence both commensal and pathogenic species of the urinary microbiota are needed to better understand this community, both for symptomatic and asymptomatic individuals.