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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

39083712
mra00487-24
10.1128/mra.00487-24
mra.00487-24
Genome Sequences
genomics-and-proteomicsGenomics and ProteomicsDraft genome sequences of four Corynebacterium amycolatum strains isolated from female urine samples
Kula Alex 1 2
Chilton Grace 1 2
Damaso James 2
Golzar Yusef 2
Rushnaiwala Fatima 1 2
Appleberry Helen 1
https://orcid.org/0000-0003-4532-0545
Wolfe Alan J. 3
https://orcid.org/0000-0003-3049-5991
Putonti Catherine 1 2 3 cputonti@luc.edu

1 Department of Biology, Loyola University Chicago , Chicago, Illinois, USA
2 Bioinformatics Program, Loyola University Chicago , Chicago, Illinois, USA
3 Department of Microbiology and Immunology, Loyola University Chicago , Maywood, 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
31 7 2024
31 7 2024
13 9 e00487-2414 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

Corynebacterium amycolatum is an emerging pathogen of the urinary tract. Here, we present the draft genomes for four strains isolated from urine collected from symptomatic and asymptomatic female participants.

KEYWORDS

Corynebacterium amycolatum
urinary tract infection
urobiome
OAB
rUTI
Loyola University Chicago (LUC) Mulcahy Scholars Program Appleberry Helen cover-dateSeptember 2024
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pmcANNOUNCEMENT

Although Corynebacterium amycolatum is a commensal member of the skin flora, it is an opportunistic pathogen associated with cellulitis, endocarditis, peritonitis, and sepsis (1). Strains of this species also have been isolated from urinary samples (2) and posited to be an opportunistic pathogen of the urinary tract (3). To further investigate the genomic content of C. amycolatum strains from the urinary tract, here we present four genomes: UMB3517 and UMB3010, isolated from catheterized urine samples from females with overactive bladder (OAB) symptoms, UMB7578, isolated from a voided urine sample from a female diagnosed with recurrent urinary tract infections (rUTIs), and UMB0362, isolated from a catheterized urine sample from an asymptomatic (healthy) female.

Urine samples were collected as part of prior institutional review board (IRB) approved studies [see Table 1; (4–7)]. Strains were isolated from the sample using the expanded quantitative urine culture (EQUC) method (8) for the Loyola Urinary Education and Research Collaborative (LUEREC) collection. Prior to banking the strains, the genus and species were determined by matrix-assisted laser desorption ionization-time of flight (MALDI-TOF), as previously described (9). The frozen stock was obtained from the collection and streaked on a Brain Heart Infusion (BHI) agar plate and incubated at 35°C in 5% CO2 for 24 h. A single colony was selected and grown in liquid BHI medium under the same culture conditions. DNA was extracted using a DNeasy Blood and Tissue Kit (Qiagen), following the manufacturer’s instructions for Gram-positive organisms. Sequencing and library preparation were performed by SeqCoast Genomics (Portsmouth, NH). Samples were prepared with an Illumina DNA Prep tagmentation kit and sequenced with the Illumina NextSeq2000 platform (2 × 150 bp reads). Assemblies were performed using BV-BRC v3.35.5 (10) with the “auto” parameter. Briefly, the raw reads were trimmed using Trim Galore v0.6.5 (https://github.com/FelixKrueger/TrimGalore) and assembled using Unicycler v0.4.8 (11), followed by polishing with Pilon v1.23 (12). The genome assemblies were annotated using the BV-BRC Genome Annotation tool (10) and the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) v6.7 (13); the latter is the publicly available annotation. Genome coverage, completeness, and contamination were calculated by BV-BRC. Virulence factor screening was performed using the VFanalyzer tool (14). Unless specified otherwise, default parameters were used for all software tools.

TABLE 1 Genome statistics and strain isolation source details

Strain	UMB0362	UMB3010	UMB3517	UMB7578	
SRA Accession no.	SRR28710892	SRR28710896	SRR28710897	SRR28710893	
Assembly Accession no.	JBCGES000000000	JBCGEV000000000	JBCGEW000000000	JBCGET000000000	
No. of raw reads	2,044,004	1,780,282	2,784,774	2,504,768	
Assembly length (bp)	2,503,085	2,456,972	2,501,019	2,554,220	
G + C (%)	58.76	58.93	58.85	58.7	
No. of contigs	53	44	32	49	
Contigs N50 (bp)	127,036	107,160	216,091	135,435	
Coverage (x)	115.19	102.27	146.26	135.60	
Completeness (%)	100	100	100	100	
Contamination (%)	0.4	0.6	0.4	0.6	
Symptom status	Asymptomatic	OAB	OAB	rUTI	
IRB no. (Institution)	LU206449 (LUC)	LU207152 (LUC)	LU207152 (LUC)	170077AW (UCSD)	
Study reference	(7)	(4)	(4)	(5, 6)	

Table 1 lists the genome assembly statistics for the four C. amycolatum strains. Virulence factor predictions for all four genome assemblies identified genes associated with siderophore-dependent iron uptake (irp6A, irp6B, and irp6C), regulation (dtxR, mprB, senX3, sigA/proV, and whiB3), and other virulence-associated classes. The virulence factor profiles for these four strains are congruent with those noted in the recent pangenomic study of the 26 publicly available genome assemblies for the species (15). The authors of this prior study suggest that these virulence factors were acquired via horizontal gene transfer, enabling the invasive phenotype observed in strains responsible for infections (15). Further sequencing and subsequent investigation of C. amycolatum genomes is needed to understand the prevalence of horizontal gene transfer in this species.

ACKNOWLEDGMENTS

The authors wish to acknowledge the study participants who consented to donate urine, the clinical members of LUEREC who recruited those participants and collected their urine, and members of the Wolfe lab who processed the samples. 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

Table 1 lists the SRA accession numbers and assembly accession numbers for the four strains.
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