
==== Front
Microbiol Resour Announc
Microbiol Resour Announc
mra
Microbiology Resource Announcements
2576-098X
American Society for Microbiology 1752 N St., N.W., Washington, DC

39162452
mra00497-24
10.1128/mra.00497-24
mra.00497-24
Genome Sequences
genomics-and-proteomicsGenomics and ProteomicsDraft genomes of one Staphylococcus haemolyticus and five Staphylococcus lugdunensis strains isolated from catheterized urine samples of females
Appleberry Helen 1
Anjum Haaris 2
Cage Taleah 1
Jarm Kayla 2
Khan Haashir 1
Proctor Lizzie 1
Saroca Junelle 2
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

Kula Alex 1 2
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, Illinois, USA
Editor Klepac-Ceraj Vanja Department of Biological Sciences, Wellesley College , Wellesley, Massachusetts, USA

Address correspondence to Catherine Putonti, cputonti@luc.edu
The authors declare no conflict of interest.

9 2024
20 8 2024
20 8 2024
13 9 e00497-2411 5 2024
07 7 2024
Copyright © 2024 Appleberry et al.
2024
Appleberry 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

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.

KEYWORDS

Staphylococcus haemolyticus
Staphylococcus lugdunensis
urinary microbiome
urobiome
rUTI
OAB
Loyola University Chicago (LUC) Mulcahy Scholars Program Appleberry Helen cover-dateSeptember 2024
==== Body
pmcANNOUNCEMENT

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% CO2 for 24 hours at 35°C. Liquid tryptone soy medium was inoculated with single colonies from these plates and incubated in 5% CO2 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.

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	

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.

ACKNOWLEDGMENTS

We 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 six strains.
==== Refs
REFERENCES

1 Bieber L, Kahlmeter G. 2010. Staphylococcus lugdunensis in several niches of the normal skin flora. Clin Microbiol Infect 16 :385–388. doi:10.1111/j.1469-0691.2009.02813.x 19519842
2 Byrd AL, Belkaid Y, Segre JA. 2018. The human skin microbiome. Nat Rev Microbiol 16 :143–155. doi:10.1038/nrmicro.2017.157 29332945
3 Heilbronner S, Foster TJ. 2021. Staphylococcus lugdunensis: a skin commensal with invasive pathogenic potential. Clin Microbiol Rev 34 :e00205-20. doi:10.1128/CMR.00205-20 33361142
4 Rossi CC, Ahmad F, Giambiagi-deMarval M. 2024. Staphylococcus haemolyticus: an updated review on nosocomial infections, antimicrobial resistance, virulence, genetic traits, and strategies for combating this emerging opportunistic pathogen. Microbiol Res 282 :127652. doi:10.1016/j.micres.2024.127652 38432015
5 Moreland RB, Choi BI, Geaman W, Gonzalez C, Hochstedler-Kramer BR, John J, Kaindl J, Kesav N, Lamichhane J, Lucio L, Saxena M, Sharma A, Tinawi L, Vanek ME, Putonti C, Brubaker L, Wolfe AJ. 2023. Beyond the usual suspects: emerging uropathogens in the microbiome age. Front Urol 3 :1212590. doi:10.3389/fruro.2023.1212590
6 Haile DT, Hughes J, Vetter E, Kohner P, Snyder R, Patel R, Cockerill FR III. 2002. Frequency of isolation of Staphylococcus lugdunensisin consecutive urine cultures and relationship to urinary tract infection. J Clin Microbiol 40 :654–656. doi:10.1128/JCM.40.2.654-656.2002 11825988
7 Wu P, Chen Y, Zhao J, Zhang G, Chen J, Wang J, Zhang H. 2017. Urinary microbiome and psychological factors in women with overactive bladder. Front Cell Infect Microbiol 7 :488. doi:10.3389/fcimb.2017.00488 29230385
8 Khan Z, Healey GD, Paravati R, Berry N, Rees E, Margarit L, Gonzalez D, Emery S, Conlan RS. 2021. Chronic urinary infection in overactive bladder syndrome: a prospective, blinded case control study. Front Cell Infect Microbiol 11 :752275. doi:10.3389/fcimb.2021.752275 34660348
9 Halverson T, Mueller ER, Brubaker L, Wolfe AJ. 2022. Symptom improvement with mirabegron treatment is associated with urobiome changes in adult women. Int Urogynecol J 33 :1319–1328. doi:10.1007/s00192-022-05190-w 35412069
10 Halverson T, Mueller ER, Brubaker L, Wolfe AJ. 2023. Urobiome changes differ based on OAB treatment in adult females. Int Urogynecol J 34 :1271–1277. doi:10.1007/s00192-022-05416-x 36422657
11 Burnett LA, Hochstedler BR, Weldon K, Wolfe AJ, Brubaker L. 2021. Recurrent urinary tract infection: association of clinical profiles with urobiome composition in women. Neurourol Urodyn 40 :1479–1489. doi:10.1002/nau.24707 34036621
12 Hochstedler BR, Burnett L, Price TK, Jung C, Wolfe AJ, Brubaker L. 2022. Urinary microbiota of women with recurrent urinary tract infection: collection and culture methods. Int Urogynecol J 33 :563–570. doi:10.1007/s00192-021-04780-4 33852041
13 Thomas-White K, Taege S, Limeira R, Brincat C, Joyce C, Hilt EE, Mac-Daniel L, Radek KA, Brubaker L, Mueller ER, Wolfe AJ. 2020. Vaginal estrogen therapy is associated with increased Lactobacillus in the urine of postmenopausal women with overactive bladder symptoms. Am J Obstet Gynecol 223 :727. doi:10.1016/j.ajog.2020.08.006
14 Price TK, Dune T, Hilt EE, Thomas-White KJ, Kliethermes S, Brincat C, Brubaker L, Wolfe AJ, Mueller ER, Schreckenberger PC. 2016. The clinical urine culture: enhanced techniques improve detection of clinically relevant microorganisms. J Clin Microbiol 54 :1216–1222. doi:10.1128/JCM.00044-16 26962083
15 Hilt EE, McKinley K, Pearce MM, Rosenfeld AB, Zilliox MJ, Mueller ER, Brubaker L, Gai X, Wolfe AJ, Schreckenberger PC. 2014. Urine is not sterile: use of enhanced urine culture techniques to detect resident bacterial flora in the adult female bladder. J Clin Microbiol 52 :871–876. doi:10.1128/JCM.02876-13 24371246
16 Olson RD, Assaf R, Brettin T, Conrad N, Cucinell C, Davis JJ, Dempsey DM, Dickerman A, Dietrich EM, Kenyon RW, et al. . 2023. Introducing the bacterial and viral bioinformatics resource center (BV-BRC): a resource combining PATRIC, IRDand ViPR. Nucleic Acids Res 51 :D678–D689. doi:10.1093/nar/gkac1003 36350631
17 Wick RR, Judd LM, Gorrie CL, Holt KE. 2017. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLOS Comput Biol 13 :e1005595. doi:10.1371/journal.pcbi.1005595 28594827
18 Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, Cuomo CA, Zeng Q, Wortman J, Young SK, Earl AM. 2014. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 9 :e112963. doi:10.1371/journal.pone.0112963 25409509
19 Meier-Kolthoff JP, Göker M. 2019. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 10 :2182. doi:10.1038/s41467-019-10210-3 31097708
20 Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, Ostell J. 2016. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 44 :6614–6624. doi:10.1093/nar/gkw569 27342282
21 Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. 2015. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 25 :1043–1055. doi:10.1101/gr.186072.114 25977477
