Genomic Diversity in Staphylococcus xylosus

Abstract

Staphylococcus xylosus is a commensal of the skin of humans and animals and a ubiquitous bacterium naturally present in food. It is one of the major starter cultures used for meat fermentation, but a few strains could potentially be hazardous and are related to animal opportunistic infections. To better understand the genetic diversity of S. xylosus intraspecies, suppressive and subtractive hybridization (SSH) was carried out with the S. xylosus C2a strain, a commensal of human skin, used as the driver for three tester strains, S04002 used as a starter culture, S04009 isolated from cow mastitis, and 00-1747, responsible for mouse dermatitis. SSH revealed 122 tester-specific fragments corresponding to 149 open reading frames (ORFs). A large proportion of these ORFs resembled genes involved in specific metabolisms. Analysis of the distribution of the tester-specific fragments in 20 S. xylosus strains of various origins showed that the S. xylosus species could be divided into two clusters with one composed only of potentially hazardous strains. The genetic content diversity of this species is colocalized in a region near the origin of replication of the chromosome. This region of speciation previously observed in the Staphylococcus genus corresponded in S. xylosus species to a strain-specific region potentially implicated in ecological fitness.

Staphylococcus xylosus is a commensal bacterium generally found inhabiting the skin and the mucous membranes of mammals and birds (15, 22). S. xylosus is ubiquitous, can be found in various niches (12, 25, 28), and persists in soils and on surfaces (32). In addition to its ability to form biofilms (29), the ubiquity of S. xylosus might be explained by its ability to adapt to different environments. S. xylosus is naturally present in raw meat and milk and is commonly used as a starter culture for their fermentation (14, 36). This species is virtually defined as a nonpathogenic Staphylococcus, but a few strains of S. xylosus are related to animal and human opportunistic infections (27, 33, 37, 39). Thus, most strains are commensal and useful in food while others could potentially be hazardous, showing the versatility of this species.

Genomes, and consequently phenotypes, can be highly heterogeneous in bacterial strains, even if they belong to the same species. Genomic comparative studies between all Staphylococcus sequenced genomes showed an average 78% identity (35). The 22% genetic variability observed within the Staphylococcus genus is also observed within species. Indeed, genetic diversity between 36 S. aureus strains using whole-genome DNA microarrays showed that 78% of genes were common to all strains and 22% of genes were strain specific and might play a role in adaptation to specialized niches (7). In a previous study with genomic DNA restriction and pulsed-field gel electrophoresis (PFGE) analysis of seven S. xylosus strains of various origins, we showed genomic diversity within this species, with variations of chromosome size and ribosomal operon (rrn) number (5). S. xylosus isolated from opportunistic infections seemed to have chromosomes up to 11% larger than strains isolated from the food environment (5). Genomic differences were also found between S. xylosus strains isolated from meat products by PFGE and randomly amplified polymorphic DNA analyses (5), but much remains to be learned about the genetic content differences. Strain-specific genes of S. xylosus are of major interest in explaining the versatility of this species. We expanded comparisons of S. xylosus strains by using suppressive and subtractive hybridization (SSH). This method provides comprehensive surveys of genome differences among closely related strains by facilitating the identification of DNA segments present in one genome (tester) but absent in another (driver). It has been widely used for the analysis of bacterial pathogen genomes to discover new epidemiological markers, virulence factors, and host specificity determinants (38). SSH was also successfully used to study genome plasticity or intraspecies genomic diversity (23, 30).

In this work, SSH was carried out between three S. xylosus tester strains: S. xylosus S04002, used as a starter culture, S. xylosus S04009, isolated from cow mastitis, and S. xylosus 00-1747, responsible for mouse dermatitis (39). S. xylosus C2a, a commensal of human skin, was used as a driver. The chromosomal organization of the S. xylosus C2a strain has been reported (5) and has constituted the starting point for studying the genetic diversity within this species. Specific DNA fragments of 29.7, 25.4, and 22.8 kb were isolated from the three SSH libraries obtained from S. xylosus S04002, S04009, and 00-1747, respectively. Their distributions among 20 S. xylosus strains were analyzed, and their locations in the respective chromosomes of the S. xylosus tester strains were determined.

MATERIALS AND METHODS

Strains.

The S. xylosus strains used in the study are listed in Table 1. S. xylosus C2a is derived from the type strain DSM20267 and is cured of its endogenous plasmid, pSX267 (11). The other strains are nonduplicate isolates of different origins. Bacteria were stored at −70°C. Cultures were grown in brain heart infusion broth or agar and incubated at 37°C for 16 h.

TABLE 1.

S. xylosus strains used in this study and their origins

Strain	Origin
C2aa	Derived from DSM20267, human skin
839	Meat starter
840	Meat starter
S01002	Meat starter
S01003	Meat starter
S01004	Meat starter
S01006	Meat starter
S01007	Meat starter
S01008	Meat starter
S04002a	Meat starter
S01001	Dairy starter
S04003	Dairy starter
S04009a	Cow mastitis
S04010	Cow mastitis
S04012	Cow mastitis
S04013	Cow mastitis
S04016	Cow mastitis
S04017	Cow mastitis
S04018	Cow mastitis
S04011	Goat mastitis
S04014	Goat mastitis
S04019	Goat mastitis
S04020	Goat mastitis
00-1747a	Mouse dermatitis

^aStrain used for SSH.

Pulsed-field gel electrophoresis.

Genomic DNA of S. xylosus strains was prepared in agarose plugs as described previously (21). Plugs were restricted with the endonuclease I-CeuI (New England Biolabs, United Kingdom) or SmaI enzyme (Promega, Charbonnière, France) according to the manufacturers' instructions. Fragments were separated by PFGE in 1% agarose gels in 0.5× Tris-borate-EDTA buffer on a CHEF-DR III apparatus (Bio-Rad, Ivry, France). Electrophoretic conditions were 50 s to 100 s for 6 h and 10 s to 30 s for 18 h or 50 s to 90 s for 22 h and then 1 s to 12 s for 13 h at 14°C at a constant voltage of 6 V·cm⁻¹ and an angle of 120° for the determination of specific subtracted fragment location. Lambda DNA concatemers were used as molecular size markers (Promega). After migration, gels were stained in ethidium bromide, digitized under UV light (Gel Doc 2000; Bio-Rad), and analyzed using the Quantity One quantitation software (Bio-Rad). Similarities between the PFGE profiles, based on band position, were derived by the Dice correlation coefficient with a maximum position tolerance of 2%. A hierarchical unweighted pair group method analysis was used to generate a dendrogram.

Chromosomal DNA and plasmid preparation.

Chromosomal DNA from S. xylosus was isolated by the method of Marmur (18). To isolate plasmid DNA from S. xylosus, cells were lysed with 16 μg/ml lysostaphin, and the QIAprep Miniprep kit (Qiagen, Courtaboeuf, France) was subsequently applied.

Suppressive-subtractive hybridizations and differential screening.

Three subtracted DNA libraries were generated following the recommendations for the Clontech PCR-Select bacterial genome subtraction kit (BD Biosciences Clontech, Erembodegem, Belgium). Genomic DNAs of S. xylosus strains S04002, S04009, and 00-1747 were used as the testers and that of S. xylosus C2a was used as a driver. To increase the proportion of chromosomal subtracted DNA, the endogenous plasmids of the tester strains were also used as drivers. Genomic and plasmid DNAs were digested by the appropriate RsaI enzyme. Suppression-subtractive hybridizations were carried out as recommended by the supplier except that hybridization temperatures were set at 61°C instead 63°C due to the low G+C content of Staphylococcus DNA. The pool of subtracted fragments was amplified by PCR using the Advantage cDNA polymerase (BD Biosciences Clontech). PCR products generated in each library were cloned into the pGEM-T Easy vector (Promega) according to the supplier's recommendations and transformed into Escherichia coli TG1 competent cells, which were then cultured on Luria-Bertani agar plates containing 100 μg/ml ampicillin, 50 μg/ml 5-bromo-4-chloro-3-indolyl-β-d-galactopyranoside, and 0.5 mM isopropyl thiogalactoside. Resulting transformants were individually grown in Luria-Bertani medium containing 100 μg/ml ampicillin in 96-well microtiter plates and stored in 20% glycerol at −70°C. Subtracted library clones were randomly selected as templates for PCR amplification using nested primers 1 and 2R, provided in the genome subtraction kit. PCR products were analyzed by agarose gel electrophoresis to verify the size of the inserts and the presence of one distinct amplified product. PCR products of each subtracted library were screened for tester-specific fragments using dot blot hybridization. They were arrayed in duplicate onto positively charged nylon membranes (Hybond N⁺; Amersham Biosciences, Orsay, France). One μg of RsaI-restricted genomic DNA from the driver and each tester DNA was randomly labeled with the Dig-High Prime system (Roche Applied Science, Neuilly sur Seine, France) and then used as probes to separately hybridize the blots. The digoxigenin-labeled probes were detected by the Dig color detection kit (Roche).

The distribution of tester-specific fragments was also evaluated among S. xylosus strains. Genomic DNAs from 20 strains (Table 1) were used as probes, as described above. The distribution of tester-specific fragments was analyzed by a complete linkage hierarchical cluster analysis using Microsoft Excel software with the XLStat add-in. A distance matrix was calculated by using Sokal and Sneath's (1) similarity coefficient to take into account positive (occurrence) and negative (nonoccurrence) matches.

DNA sequencing and analysis.

Plasmid DNA containing tester-specific inserts was isolated from individual clones using the NucleoSpin Plasmid QuickPure kit (Macherey-Nagel, Hoerdt, France). Sequencing reactions were performed using the BigDye terminator as recommended by the supplier (Applied Biosystems, Courtaboeuf, France) and analyzed by using an ABI 310 automated DNA sequencer. Bioinformatic analyses were performed from Web-based servers. The sequences were analyzed by BLASTX and/or BLASTN searches against the NCBI GenBank database. Based on the analysis, redundant sequences were identified and sequence assembly was done with the CAP3 program (http://bioinformatics.iastate.edu/aat/sas.html). ORF Finder and BLASTX analyses were performed on contigs. When no similarity was found, a PSI-BLAST analysis was performed.

Determination of chromosomal locations of subtracted sequences.

For Southern blotting, digested chromosomal DNAs of S. xylosus S04002, S04009, and 00-1747 strains separated by PFGE were passively transferred onto positively charged nylon membranes (Hybond-N⁺; Amersham Biosciences). Equal amounts of PCR amplicons of each tester-specific insert were pooled and randomly labeled using the Dig-High Prime system (Roche Applied Science). After hybridizations, detection was performed using the Dig chemiluminescence detection kit following the supplier's instructions (Roche Applied Science). To confirm the localization of tester-specific inserts, chromosomal DNA restriction fragments of interest were excised from the PFGE gel, rinsed three times for 30 min with 10 mM Tris-HCl, pH 8.5, and digested with RsaI (Promega) according to the supplier's recommendations. DNA fragments were thus extracted from agarose and purified before labeling with the AlkPhos direct labeling kit (Amersham Biosciences) and hybridized to the dot blot containing the subtracted unique sequence as described for the differential screening.

Nucleotide sequence accession numbers.

Insert sequences of the subtracted libraries have been deposited in GenBank and given accession numbers ER935832 to ER935953.

RESULTS AND DISCUSSION

PFGE analysis.

The 24 S. xylosus strains were characterized by PFGE patterns after genomic DNA restriction with the SmaI enzyme (Fig. 1). A large diversity of PFGE patterns was found between strains, as 18 distinct genetic profiles were observed. The genetic relatedness of the S. xylosus strains ranged from 10 to 100% (Fig. 1). Employing a cutoff similarity value of 70%, one cluster exclusively composed of S. xylosus strains used as a starter culture was identified, while all the other strains had their own macro-restriction profiles, except for the S01007 and S01004 strains, used as starter culture, and the strains S04016 and S04018, which were both cow mastitis isolates. Cluster analysis did not show any relationship between the origin of S. xylosus isolates and their SmaI PFGE results and confirmed the intraspecies genomic differences observed by Martin et al. (19). From our study, three strains with heterogenic profiles and of three different origins were chosen to represent S. xylosus genetic diversity: S. xylosus S04002, used as a starter culture; S04009, isolated from cow mastitis; 00-1747, responsible for mouse dermatitis.

FIG. 1.

Unweighted pair group method analysis dendrogram with Dice coefficient of PFGE profiles of 24 SmaI macro-restricted S. xylosus chromosomes.

Suppressive-subtractive hybridizations of S. xylosus C2a from S04002, S04009, or 00-1747.

Following SSH, three DNA subtraction libraries were created containing 192, 384, and 320 clones of putative specific DNAs of S. xylosus S04002, S04009, and 00-1747, respectively. The number of clones corresponded to the proportion of chromosome size differences of the three tester strains evaluated in our previous study (5). After PCR amplification of the cloned inserts, clones giving no amplicon or multiple amplicons were discarded. To check the specificity of cloned inserts of the three libraries, PCR products of the inserts were arrayed and hybridized with the genomic DNA probes of the three respective tester strains or the driver C2a strain. From S. xylosus S04002, S04009, and 00-1747 DNA subtraction libraries, a total of 75, 105, and 92 DNA fragments were found to be specific to the tester strains, respectively. All these DNA fragments were two-end sequenced, and 40, 43, and 39 different sequences were identified, respectively (Table 2). A total of 29.67, 22.78, and 25.42 kb were extracted from the S. xylosus S04002, S04009, and 00-1747 genomes, respectively. The sizes of these specific DNA fragments varied from 125 to 1,715 bp, with an average size of 700 bp. Their G+C contents were 30.3% for those of the S04002 subtracted library, 32.8% for the S04009 subtracted library, and 31.1% for the 00-1747 subtracted library. These GC percentages were at the lower limit of S. xylosus G+C content, estimated to be between 30 and 36% (31). SSH has thus been used successfully for the extraction of the differential genetic content of S. xylosus strains arising from various niches.

TABLE 2.

S. xylosus S04002-, S04009-, and 00-1747-specific sequences with significant protein matches in the GenBank database

Function group and predicted encoded protein	Fragment	E value	% Identity	Organism	Accession no.	Homology found
						S04002	S04009	00-1747
Metabolism
Biotin metabolism
Biotin synthase BioB	E5	2.00E-44	85	Staphylococcus aureus COL	ER935916	+
	E129	2.00E-34	80	S. aureus COL	ER935940	+
Adenosylmethionine-8-amino-7-oxononanoate aminotransferase BioA BioD	E5	1.00E-17	62	S. aureus Mu50	ER935916	+
	D128	6.00E-125	82	S. aureus COL	ER935891			+
	D128	4.00E-26	63	Staphylococcus epidermidis RP62A	ER935891			+
Myo-inositol catabolism
IolA	Mb262	5.00E-133	74	Bacillus licheniformis ATCC 14580	ER935857	+	+
	D76	6.00E-40	65	Geobacillus kaustophilus HTA426	ER935886			+
IolB	Mb11	1.00E-61	52	B. licheniformis ATCC 14580	ER935832	+	+
IolC	Mb11	7.00E-59	63	Bacillus halodurans C-125	ER935832	+	+
IolC (putative)	M141	1.00E-30	66	B. licheniformis ATCC 14580	ER935866	+	+
IolD	M141	8.00E-71	70	B. halodurans C-125	ER935866	+	+
IolG	E126	2.00E-64	50	Bacillus cereus E33L	ER935938	+
IolE	Mb118	2.00E-79	63	Clostridium tetani E88	ER935843	+	+
Pentose and glucuronate interconversion
d-Arabino-3-hexulose-6-phosphate formaldehyde lyase	E51	2.00E-14	95	Staphylococcus saprophyticus ATCC 15305	ER935923	+	+
Putative hexulose-6-phosphate synthase	E28	4.00E-75	95	S. saprophyticus ATCC 15305	ER935918	+	+
Putative 6-phospho-3-hexuloisomerase	E28	9.00E-77	83	S. saprophyticus ATCC 15305	ER935918	+	+
UTP-glucose-1-phosphate uridyltransferase	E36	7.00E-75	90	S. saprophyticus ATCC 15305	ER935921	+
2-dehydro-3-deoxyphosphogluconate aldolase	Mb275	3.00E-78	63	Bacillus thuringiensis serovar Israelensis ATCC 35646	ER935858		+	+
2-dehydro-3-deoxygluconokinase PfkB	D151	5.00E-63	55	Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293	ER935896			+
	D242	6.00E-29	49	Bacillus weihenstephanensis KBAB4	ER935906		+	+
Alpha/beta hydrolase fold family protein	Mb59	3.00E-27	52	Flavobacteriales bacterium HTCC2170	ER935840		+
Fructose and mannose metabolism
Phosphomannomutase	E127	4.00E-83	65	S. epidermidis RP62A	ER935939	+
Hexitol dehydrogenase	Mb27	4.00E-94	69	S. aureus COL	ER935835		+	+
	M139	1.00E-14	72	S. aureus COL	ER935864		+	+
Sorbitol dehydrogenase	M139	3.00E-10	62	S. aureus COL	ER935864		+	+
Fermentative metabolism
Acetoin (diacetyl) reductase ButA	E129	9.00E-57	81	S. epidermidis ATCC 12228	ER935940	+
α-Acetolactate synthase AlsS	E190	0.0	97	S. saprophyticus ATCC 15305	ER935953	+
Amino acid metabolism
Saccharopine dehydrogenase-related protein	D85	2.00E-04	54	Lactococcus lactis subsp. cremoris SK11	ER935887			+
	D218	2.00E-35	64	L. lactis subsp. cremoris SK11	ER935905			+
Sarcosine oxidase alpha subunit	D129	5.00E-77	51	B. thuringiensis serovar Konkukian 97-27	ER935892			+
Sarcosine oxidase beta subunit	D298	4.00E-45	41	B. cereus ATCC 14579	ER935912			+
Betaine aldehyde dehydrogenase	D298	9.00E-25	63	B. weihenstephanensis KBAB4	ER935912			+
Dihydrodipicolinate synthase	D176	2.00E-06	42	Rickettsia felis URRWXCal2	ER935899			+
Other
Lipase	E179	4.00E-92	92	S. saprophyticus	ER935951	+
Putative lipase	D218	2.00E-88	83	S. saprophyticus ATCC 15305	ER935905			+
UDP-glucose 4-epimerase	D44	2.00E-20	59	G. kaustophilus	ER935881			+
Dihydroorotase	D23	1.00E-71	56	B. cereus G9241	ER935879		+	+
Putative nucleoside diphosphate-sugar epimerase DTDP-D-glucose 4,6-dehydratase	D46	1.00E-55	82	S. saprophyticus ATCC 15305	ER935882		+	+
COG1670, putative acetyltransferase	D96	5.00E-45	54	S. saprophyticus ATCC 15305	ER935888		+	+
Aldehyde dehydrogenase AldA	D106	4.00E-55	69	Bacillus sp. B14905	ER935889			+
Riboflavin kinase RibR	D213	9.00E-10	40	B. subtilis subsp. subtilis 168	ER935904	+	+	+
COG2936, putative peptidase S9, prolyl oligopeptidase precursor	D273	5.00E-50	81	S. aureus RF122	ER935909			+
Similar to oxidoreductase	Mb127	8.00E-16	36	S. aureus Mu50	ER935844		+	+
COG0655, putative iron-sulfur flavoprotein (hypothetical protein SAS0063)	E184	1.00E-16	53	S. aureus MSSA476	ER935952	+
Short-chain alcohol dehydrogenase	E139	9.00E-73	98	S. saprophyticus ATCC 15305	ER935942	+
COG4221, putative short-chain alcohol dehydrogenase of unknown specificity	E51	2.00E-42	100	S. saprophyticus ATCC 15305	ER935923	+
COG1063, alcohol dehydrogenase	M65	2.00E-141	97	S. saprophyticus ATCC 15305	ER935860	+	+
Regulatory
Putative regulator of HxlAB (hexulose-6-phosphate synthase and 6-phospho-3-hexuloisomerase)	E111	1.00E-35	98	S. saprophyticus ATCC 15305	ER935932	+
Transcriptional regulator, LysR family probable AlsR regulator	E173	4.00E-37	33	Bacillus clausii KSM-K16	ER935950	+
Putative regulator of sorbitol operon	D7	4.00E-18	28	Clostridium beijerincki NCIMB 8052	ER935875			+
Sorbitol operon activator	D254	2.00E-24	39	C. beijerincki KSM-K16	ER935908			+
Transcriptional regulator putative hydrogen peroxide-inducible genes activator	E85	3.00E-81	99	S. saprophyticus ATCC 15305	ER935928	+	+
PTS multidomain regulator BglG	Mb48	6.00E-41	44	S. aureus MSSA476	ER935839		+
	D63	2.00E-16	45	S. aureus COL	ER935884		+	+
Putative PTS multidomain regulator EIIA putative fructose/mannitol specific	Mb147	6.00E-45	45	S. aureus MSSA476	ER935850		+	+
PTS system enzyme II B component putative sorbitol specific	M149	6.00E-35	87	S. aureus Mu50	ER935867		+	+
	D53	2.00E-36	84	S. aureus Mu50	ER935883		+	+
PTS transport system IIA component putative galactitol specific	D53	1.00E-07	44	S. aureus MRSA252	ER935883		+	+
Accessory gene regulator C agrC	E154	5.00E-110	83	S. saprophyticus ATCC 15305	ER935944	+
Protein SSP2020 putative ebsC transcription regulation protein	M160	6.00E-40	61	S. saprophyticus ATCC 15305	ER935868		+	+
NmrA-like transcriptional regulator	D11	8.00E-22	38	Salinispora tropica CNB-440	ER935876			+
Transcriptional regulator, LysR family domain protein	E184	4.00E-56	66	S. aureus MSSA476	ER935952	+
	E116	8.00E-13	46	S. aureus USA300	ER935933	+
Transcriptional regulator, GntR family/aminotransferase, class I	E3	1.00E-53	57	S. aureus COL	ER935914	+	+
	Mb46	1.00E-49	59	S. aureus COL	ER935838		+
	Mb145	9.00E-20	81	S. aureus COL	ER935849		+
COG1167, putative transcriptional regulator, GntR family	E100	2.00E-165	98	S. saprophyticus ATCC 15305	ER935929	+
Transcriptional regulator, AraC/XylS family	D141	2.00E-43	58	Oceanobacillus iheyensis HTE831	ER935895		+	+
COG1733, putative transcriptional regulator	E139	3.00E-17	93	S. saprophyticus ATCC 15305	ER935942	+	+
Cell membrane/surface structure
Putative autolysin (mannosyl-glycoprotein endo-β-N-acetylglucosamidase)	E73	3.00E-55	99	S. saprophyticus ATCC 15305	ER935926	+	+	+
	E130	2.00E-178	97	S. saprophyticus ATCC 15305	ER935941	+
Autolysin (mannosyl-glycoprotein endo-β-N-acetylglucosamidase)	D294	5.00E-07	66	S. epidermidis ATCC 12228	ER935911	+	+	+
67-kDa myosin-cross-reactive streptococcal antigen-like protein	E110	3.00E-26	94	S. epidermidis	ER935931	+
smart00255, putative Toll-interleukin receptor	D157	1.00E-35	69	S. aureus MSSA476	ER935897			+
Glycosyl transferase, family 2, CDP-glycerol:poly(glycerophosphate) glycerophosphotransferase	E121	1.00E-32	40	Clostridium phytofermentans ISDg	ER935935	+
Lipopolysaccharide modification acyltransferase	Mb127	8.00E-19	78	S. epidermidis ATCC 1228	ER935844		+	+
Biofilm-associated protein Bap	D137	1.00E-18	28	Staphylococcus hyicus	ER935894			+
LPXTG cell wall surface anchor family protein, hypothetical protein SSPP105	E25	1.00E-27	98	S. saprophyticus ATCC 15305	ER935917	+
Cell wall surface anchor family protein, hypothetical protein SSPP105	E34	2.00E-114	98	S. saprophyticus ATCC 15305	ER935920	+
Putative membrane protein of unknown function	D157	3.00E-05	36	S. saprophyticus ATCC 15305	ER935897			+
COG3152, predicted membrane protein	D158	0.056	31	Staphylococcus haemolyticus	ER935898			+
COG3949, SSP0396 uncharacterized membrane protein	D294	9.00E-24	39	S. saprophyticus ATCC 15305		+	+	+
Resistance
Methicillin resistance protein MecA1	Mb201	4.00E-38	52	Staphylococcus sciuri	ER935854		+
MecR1, methicillin resistance regulatory protein	M116	5.00E-73	58	S. aureus	ER935862		+
Metallothiol transferase FosB (fosfomycin resistance protein)	M130	3.00E-69	89	S. haemolyticus JCSC1435	ER935863		+
MphBM macrolide 2′-phosphotransferase II	M180	1.00E-92	86	S. aureus	ER935869		+	+
Micrococcin P1 peptide synthetase	Mb107	6.00E-123	58	Staphylococcus equorum	ER935842		+	+
Putative tetronasin resistance transmembrane protein	D178	3.00E-18	36	B. halodurans C-125	ER935901		+	+
Aminoglycoside adenyltransferase	D121	7.00E-51	79	S. saprophyticus ATCC 15305	ER935890			+
Arsenate reductase	E125	3,00E-73	100	S. xylosus plasmid Psx267	ER935937	+	+	+
Arsenic efflux pump protein	E125	2.00E-61	100	S. aureus	ER935937	+	+	+
Arsenic efflux pump membrane protein	D284	4.00E-19	100	S. xylosus(Psx267)	ER935910	+	+	+
Arsenic resistance operon repressor	D284	4.00E-49	89	S. aureus N315	ER935910	+	+	+
Membrane protein TerC, possibly involved in tellurium resistance	D16	1.00E-11	78	S. saprophyticus ATCC 15305	ER935877			+
Probable drug resistance transporter of EmrB/QacA family	Mb12	4.00E-19	46	Listeria monocytogenes 4b F2365	ER935833	+	+
Putative drug exporter of RND superfamily	E4	8.00E-91	74	S. saprophyticus ATCC 15305	ER935915	+
COG2329, putative antibiotic biosynthesis monooxygenase	M266	2.00E-27	55	S. aureus JH1	ER935873		+	+
Transport
l-lactate permease	E117	2.00E-47	92	S. saprophyticus ATCC 15305	ER935934	+
Na+:myo-inositol cotransporter	Mb42	1,00E-56	70	Bacillus clausii KSM-K16	ER935837	+	+
Amino acid permease-associated region lysine-specific permease precursor	D132	4.00E-58	53	Pseudomonas fluorescens PfO-1	ER935893			+
PTS enzyme IIC component putative galactitol specific I	M283	9.00E-34	57	Salmonella enterica serovar Typhimurium LT2	ER935874		+
Ferrous iron transport protein B	Mb142	8.00E-42	76	S. epidermidis RP62A	ER935848		+	+
ATPase copper transport	E158	4.00E-62	86	S. aureus USA300	ER935947	+
	D182	4.00E-110	85	S. aureus USA300	ER935902			+
Putative permease, putative role in amino acid adenylation	E157	2.00E-51	81	S. aureus USA300	ER935946	+	+
Putative permease of drug and metabolite transporter superfamily	E38	6.00E-122	98	S. saprophyticus ATCC 15305	ER935922	+	+
Putative transporter, EamA family	E77	8.00E-50	53	S. aureus Mu50	ER935927	+
Putative ABC-type nitrate sulfonate taurine bicarbonate transport system ATPase component	M237	3.00E-65	89	S. saprophyticus ATCC 15305	ER935871		+	+
TRAP-T family transporter, putative tripartite tricarboxylate transporter	D177	2.00E-17	49	Rhodobacter sphaeroides 2.4.1	ER935900		+	+
ABC transporter, ATP-binding/permease protein	D19	6.00E-18	73	S. aureus COL	ER935878			+
Putative ABC transporter permease	E61	1.00E-10	89	S. saprophyticus ATCC 15305	ER935925	+
Major facilitator family transporter	E142	3.00E-32	54	Listeria innocua Clip11262	ER935943	+		+
Putative permease of the major facilitator superfamily	D301	4.00E-20	96	S. saprophyticus ATCC 15305	ER935913			+
Phage-related and IS elements
IS605/IS200-like transposase	Mb168	3.00E-86	89	S. epidermidis ATCC 1228	ER935851		+	+
Recombinase Sin	E110	3.00E-75	94	S. epidermidis ATCC 12228	ER935931	+
Integrase	Mb194	7.00E-66	64	S. aureus RF122	ER935852		+
Phage infection protein	E168	0.0	99	S. epidermidis RP62A	ER935949	+		+
Phage terminase large subunit, 77ORF003	Mb33	5.00E-68	62	Bacteriophage 77	ER935836		+
ORF001	Mb66	3.00E-11	60	Bacteriophage 2638A	ER935841		+
ORF094	Mb66	7.00E-13	79	Bacteriophage 2638A	ER935841		+
ORF028	Mb66	3.00E-06	77	Bacteriophage 2638A	ER935841		+
Conserved phage protein probable ORF029 of bacteriophage 37	Mb131	1.00E-16	56	S. haemolyticus JCSC1435	ER935845		+
phiPVL ORF050-like protein	Mb133	3.00E-06	36	S. aureus USA300	ER935846		+
ORF025	Mb137	3.00E-08	51	Bacteriophage EW	ER935847		+
ORF60	Mb215	2.00E-06	46	S. phage 187	ER935856		+
ORF077	Mb215	0.012	41	Bacteriophage EW	ER935856		+
Capsid protein, 77ORF006	M85	7.00E-55	80	Bacteriophage 77	ER935861		+
77ORF042	M85	1.00E-12	47	Bacteriophage 77	ER935861		+
ORF001	M256	3.00E-59	59	Bacteriophage 2638A	ER935872		+
Phage helicase, C terminal	M200	2.00E-22	31	Clostridium thermocellum ATCC 27405	ER935870		+
Integrase, ORF010	D65	2.00E-30	56	Bacteriophage 52A	ER935885			+
Hypothetical protein SSPP103, phage infection protein	E160	3.00E-11		S. saprophyticus ATCC 15305	ER935948	+	+	+
Hypothetical protein SAR0381, probable phage protein	Mb279	5.00E-09	38	S. aureus MRSA252	ER935859		+
Unknown function
COG3877, unnamed protein product	E31	7.00E-37	79	S. haemolyticus JCSC1435	ER935919	+
Hypothetical protein SSP0169	E55	2.00E-09	85	S. saprophyticus ATCC 15305	ER935924	+
Similar to unknown protein SH2317	E108	7.00E-09	60	S. haemolyticus	ER935930	+
Hypothetical protein SE2200	E123	3.00E-09	89	S. epidermidis ATCC 12228	ER935936	+		+
Hypothetical protein SH0055	E156	1.00E-34	70	S. haemolyticus JCSC1435	ER935945	+
COG1284, uncharacterized conserved protein SSP1949	Mb26	2.00E-36	84	S. saprophyticus ATCC 15305	ER935834		+	+
Hypothetical protein cn33	Mb198	2.00E-19	37	S. epidermidis bacteriophage CNPH82	ER935853		+
Hypothetical protein SH1793	Mb215	0.001	54	S. haemolyticus JCSC1435	ER935856		+
Hypothetical protein, no similarity found	Mb213				ER935855		+
Hypothetical protein SAB0188	M139	7.00E-07	64	S. aureus RF122	ER935864		+	+
Hypothetical protein Mbar_A2529	M266	2.00E-12	30	Methanosarcina barkeri strain Fusaro	ER935873		+	+
Hypothetical protein	D39	8.00E-12	45	S. aureus Mu50	ER935880			+
Truncated hypothetical protein	D121	1.00E-10	83	S. saprophyticus ATCC 15305	ER935890			+
Hypothetical protein SSP2368	D197	4.00E-05	49	S. saprophyticus ATCC 15305	ER935903		+	+
No significant similarity found	M140				ER935865		+
No significant similarity found	D246				ER935907			+

Identification of specific sequences of S. xylosus S04002, S04009, and 00-1747 and a large proportion of specific metabolism sequences.

The 122 tester-specific fragments were analyzed by BLASTX and PSI-BLAST searches and led to the identification of 149 open reading frames (ORFs), as shown in Table 2. These ORFs were assigned to one of seven classes: metabolism, regulatory, cell membrane/surface structure, resistance, transport, phage-related structure, and IS elements and unknown functions. Fourteen ORFs resembled hypothetical bacterial genes of unknown function, while two fragments had no significant matches with known sequences. The other ORFs had significant similarity to sequences with known functions largely described in the Staphylococcus genus. However, for the S. xylosus 00-1747 strain, 20 of its 47 detected ORFs corresponded to genes from other bacterial genera (Table 2). A majority of ORFs seemed to be related to specific metabolisms as biotin, myo-inositol, and sorbitol, to amino acid and fermentative metabolisms, and to pentose and glucuronate interconversions (Table 2).

In the S. xylosus S04009 strain genome, fragments corresponding to five genes involved in myo-inositol metabolism as well as the Na⁺:myo-inositol cotransporter were subtracted (Table 2). Myo-inositol is a hexitol which is a constituent of virtually every living cell; it is synthesized by plants and is essential for humans and animals. Different bacterial species (Klebsiella spp., Salmonella spp., Pseudomonas spp., Bacillus subtilis, etc.) are able to use myo-inositol as carbohydrate source, but genes implicated in this catabolism have been described in few species (16). In Bacillus subtilis, two iol operons were described, including an operon of 10 genes, iolABCDEFGHIJ, and an operon of two genes, iolRS (40). Until now, these genes had never been described in a Staphylococcus genus.

Five ORFs of the S. xylosus 00-1747 strain were related to lysine and glycine metabolism genes, none of which corresponded to staphylococcal genes (Table 2). Sarcosine oxidase and betaine aldehyde dehydrogenase were shown to be implicated in metabolism of glycine betaine, an effective osmoprotectant (1, 4). Only betaine aldehyde dehydrogenase and dihydropicolinate synthase were identified in actual staphylococcal sequenced genomes, but these genes showed no significant match at the DNA level with these ORFs. Sarcosine oxidase and saccharopine dehydrogenase have never been observed in staphylococcal genomes. The fact that the S. xylosus 00-1747 strain contained numerous nonstaphylococcal homology ORFs might be explained by its origin. This strain was isolated from mouse dermatitis in Korea. The particular origin of this strain suggests that ecological and/or geographical divergences in S. xylosus species may exist.

From the S. xylosus meat starter S04002 subtraction, fragments corresponding to fermentative metabolism were found: an acetolactate synthase which transforms pyruvate in acetolactate, its regulator AlsR, and an acetoin dehydrogenase which transforms acetoin into diacetyl, as well as a lactate permease also implicated in anaerobic metabolism (Table 2). Acetoin and diacetyl are aroma compounds. Their production in fermented meat products has been characterized with a dairy product odor (20). Some S. xylosus strains produce these aroma compounds more than other staphylococcus species (34). This property is variable between S. xylosus strains, and a correlation between strain persistence in ripened meat and the capacity of strains to produce acetoin has been shown (9). In lactic acid bacteria isolated from fermented sausages, the production of acetoin is stimulated by a low pH and a low sugar concentration, conditions that could be found at the end of the ripening process (9). Recently, Fuchs et al. (8) showed that in S. aureus the production of acetoin and lactate was stimulated by anaerobic growth conditions.

The large number of differential genes predicted to be involved in metabolism strongly suggested a wide adaptation of S. xylosus strains to their environment and to the availability of the different substrates.

Horizontal transfer in S. xylosus S04009.

The S. xylosus S04009 strain isolated from cow mastitis showed 12 specific subtracted fragments corresponding to phage-related sequences (Table 2). The presence of at least three different bacteriophages, 77, 2638A, and EW, was deduced, and an IS605/IS200 transposase was also detected. Three phage-related proteins were found in S. xylosus S04002 and one in 00-1747 subtracted fragments. Phages in S. aureus are well studied: 37 phage genomes are reported in the GenBank database (3, 17). To our knowledge, there are few studies of phages from coagulase-negative staphylococci, and only two phages from Staphylococcus epidermidis have been completely sequenced and molecularly characterized (3). Other putative evidence of horizontal transfer in S. xylosus S04009 is the presence of specific sequences corresponding to antibiotic resistance as methicillin, fosfomycin, and macrolide resistance proteins (Table 2).

Particular S. xylosus surface structures.

Specific surface structures were found in the S. xylosus tester strains. The meat starter strain S. xylosus S04002 possessed a specific fragment corresponding to a 67-kDa myosin-cross-reactive streptococcal antigen-like protein. This protein family is thought to have structural features in common with the beta chain of the class II antigens. In Streptococcus pyogenes it reacts with antimyosin antibodies and plays a role in the pathogenesis of streptococcal infections (13). This gene is found in other Staphylococcus sequenced genomes, such as S. aureus, S. epidermidis, or Staphylococcus haemolyticus, but its function in those bacteria is still unknown. The S. xylosus 00-1747 strain implicated in mouse dermatitis contained a specific fragment resembling a Toll-interleukin receptor (TIR). Such a eukaryotic signal-mimicking molecule has been described in Salmonella enterica serovar Enteriditis (24). It was demonstrated that it is an important virulence factor in vivo by modulating host defense mechanisms involved in regulation of NF-κB and caspase activation. Experiments in mice infected with a Salmonella strain deficient in TIR showed reduced lethality. Predicted TIR-like domains are widespread and show an unusual distribution in bacterial species. A lateral transfer of this gene has been supposed (24).

Specific fragments shared by S. xylosus S04002, S04009, and 00-1747.

The presence of common fragments in the three S. xylosus tester strain chromosomes was detected by dot blot hybridization using genomic DNA of the three strains as a probe. The three strains shared only six specific fragments. Those six common fragments corresponded to arsenic resistance genes with the arsenate reductase and the arsenical efflux pump membrane protein, a riboflavin kinase, a hypothetical phage infection protein, and two fragments which were similar to an autolysin, a mannosyl-glycoprotein endo-β-N-acetylglucosamidase (Table 2).

Among the 122 specific fragments, 66 hybridized with S. xylosus S04009 genomic DNA. This mastitis isolate contained the highest number of specific fragments in its genome.

The S. xylosus strains S04009 and 00-1747 isolated from mastitis and dermatitis, respectively, shared the highest number of specific fragments, with 29 in common. They had specific sequences similar to a hexitol-specific PTS system, probably sorbitol specific. Indeed, other fragments related to sorbitol assimilation were isolated, such as a sorbitol dehydrogenase and the putative regulator of the sorbitol operon. Those two commensal strains also shared numerous specific DNA sequences implicated in resistance to antibiotics and other toxic components, such as tellurium, but also antibiotic synthesis-related sequences, such as a monooxygenase and a lipopeptide, micrococcin P1. These two strains also had in common the feoB gene, implicated in ferrous ion transport. This gene was identified in S. aureus and S. epidermidis genomes but had not been characterized (10). The ability to acquire iron (Fe) in a host is known to be an essential attribute of most pathogenic bacteria (2).

The meat starter strain S04002 and the strain S04009 isolated from mastitis shared 20 fragments. They have in common the iolABCDE myo-inositol genes but not the iolG gene, which was present in S04002 but absent in S04009. IolG corresponds to a myo-inositol 2-dehydrogenase, which is the first enzyme of myo-inositol catabolism, degrading the incoming myo-inositol into 2-keto-myo-inositol. The iolFHIJ and iolRS genes described in B. subtilis were not detected in the subtracted libraries (40). The gene iolR corresponds to a negative regulator of the iol operon, iolF is related to a myo-inositol transporter, and iolE codes for a 2-keto-myo-inositol dehydratase, while the functions of the other iol genes are still unclear in B. subtilis (40).

The meat starter S. xylosus S04002 had only nine fragments in common with the mouse dermatitis strain 00-1747. The biotin synthesis-related sequences obtained after genomic subtraction of these two strains seemed to be drastically different at the DNA level, and none of these fragments hybridized with the two genomic DNAs.

Conservation of tester-specific fragments within S. xylosus strains.

The extent of polymorphism among S. xylosus strains for the specific fragments was assessed. The RsaI-digested genomic DNAs of 20 different S. xylosus strains, 10 used as starters in the food industry and 10 isolated from cow or goat mastitis (Table 1), were hybridized with the 122 specific fragment sequences of the three tester strains. Four specific fragments (D39, D129, D137, and D158) from the S. xylosus 00-1747 library and four (Mb33, Mb66, M85, and M130) from the S. xylosus S04009 library were absent in the genomic DNA of the 20 S. xylosus strains. No specific fragment was present in all the S. xylosus genomes. The subtracted fragment most commonly found, which hybridized with 21 of the 23 S. xylosus strains (including the three tester strains), was fragment D294, corresponding to a hypothetical membrane protein and a CHAP domain corresponding to an amidase domain frequently found in autolysin precursor. A hierarchic ascendant classification gathered the strains into two clusters named I and II (Fig. 2).

FIG. 2.

Distribution of tester-specific fragments within S. xylosus strains.

Cluster I comprised five strains, all isolated from animal-associated opportunistic infections, sharing eight fragments: Mb26, Mb48, Mb147, M139, M149, D63, D96, and D213 (Table 2). These fragments corresponded to metabolic genes as PTS system specific to hexitol and its associated antiterminator Bgl, a sorbitol dehydrogenase, an acetyltransferase of unknown specificity, and a riboflavin kinase. Three of these fragments (Mb147, M139, and M149) corresponding to a hexitol assimilation system were absent in cluster II except one strain. The cluster could be divided into two subgroups named Ia and Ib. The Ia subgroup included the tester strain S. xylosus S04009 and the strain S04013, both isolated from cow mastitis. These two strains had 43 of the 122 specific fragments in common, 25 of which were from the S. xylosus S04009 library, showing a highly related genetic content between these two strains. Subgroup Ib comprised the tester strain S. xylosus 00-1747, isolated from mouse dermatitis, and two strains isolated from goat mastitis, S04019 and S04020. The genomes of these three strains shared 20 fragments, 9 of which were common to the genome of the tester strain S04009 of subgroup Ia.

Cluster II comprised 18 strains that shared a few fragments with cluster I, and they shared the E154 fragment, which was absent in cluster I except for one strain. This fragment corresponded to the accessory gene regulator C (agrC), which is a staphylococcal conserved regulator. It has been observed that there is a high genetic variability of the agr locus in Staphylococcus species and particularly in the agrC sequence (26). This variability was observed not only between Staphylococcus species but also between subpopulations of a single species (6). In S. aureus, agrD and agrC polymorphism permitted definition of a group broadly correlated with genotype which was correlated with pathotype (26). The existence of at least two different genotypic clusters (I and II) within the S. xylosus species was confirmed by the argC polymorphism distribution observed.

Cluster II could be divided into two subgroups named IIa and IIb. Subgroup IIa comprised the tester strain S04002 and the S01001 and S01008 strains of meat origin and six other strains isolated from mastitis (Fig. 2; Table 1). Within this heterogeneous subgroup, only two fragments were found to be in common: D294, described previously to be the most shared fragment between the 23 S. xylosus strains, and the fragment E154, already mentioned above. Subgroup IIb comprised eight S. xylosus strains used as starters (Fig. 2; Table 1) and one S. xylosus isolated from cow mastitis S04016. Twenty-one fragments were common between all these strains. They corresponded to the six myo-inositol metabolism genes (iolABCDEG), all the fermentative metabolism genes (als, acetoin reductase, and lactate permease genes), and the lipase gene (E179). The presence of iol genes in the majority of starter S. xylosus strains and their absence in the actual staphylococcal sequenced genomes indicate a specific and fortuitous acquisition of these genes by some S. xylosus strains. The presence of fermentative metabolism may be an adaptation to anaerobic growth conditions. In S. aureus, the overexpression of the genes implicated in butanediol fermentation and lactate production were recently observed under fermentative conditions (8). Adaptation to anaerobic conditions and lipase activity could procure a technological advantage for S. xylosus used in food processing.

Location of tester-specific fragments on their respective chromosomes.

The location of each specific fragment from the three DNA subtraction libraries was analyzed by Southern hybridization. Genomic DNAs of the S. xylosus S04002, S04009, and 00-1747 strains were digested with I-CeuI or SmaI, resolved by PFGE (Fig. 3), and blotted for Southern hybridization with a labeled pool of the specific fragments of each library. The specific fragments were located on the ∼1,100-kb I-CeuI fragment of each tester strain chromosome and on a few SmaI fragments. The specific fragments from the S. xylosus S04002 library were located on the 375-kb and 125-kb SmaI fragments, those of the S. xylosus S04009 were mainly on the 300-kb but also on the 150-kb, 100-kb, and 50-kb SmaI fragments, and the fragments of S. xylosus 00-1747 were located on the 400-kb and 100-kb SmaI fragments (Fig. 3). To confirm the probable colocalization of the SSH library-specific fragments, a second hybridization was performed using PFGE macro-restricted fragments as probes. The distribution of all the specific fragments from the three libraries is shown in Fig. 3. For each of the S. xylosus S04002, S04009, and 00-1747 subtracted libraries, more than 97.5% of inserts were located in the ∼1,100 kb I-CeuI fragment. Most of these fragments were located on the 300-/400-kb SmaI fragments on each S. xylosus tester strain, confirming that numerous specific fragments were colocalized on the S. xylosus S04002, S04009, and 00-1747 chromosomes. In a previous study we demonstrated by positioning the dnaA and gyrA genes, which are often found near the chromosome origin of replication of bacteria (oriC), that in S. xylosus C2a the origin of replication oriC was in the 1,138-kb I-CeuI and 365-kb SmaI fragments (5). To check if the colocalization region corresponded to the oriC of the three tester strain chromosomes, we hybridized dnaA and gyrA probes on I-CeuI or SmaI restriction fragments of S. xylosus S04002, S04009, and 00-1747 strains (data not shown). The genes dnaA and gyrA were located on the ∼1,100-kb I-CeuI fragment and on 300-/400-kb SmaI fragments of the three tester strains. Takeuchi et al. (35) observed in a comparative analysis of the S. haemolyticus genome with the seven S. aureus and the two S. epidermidis sequenced genomes that a region named the “oriC environ” emerged as a chromosomal region unique to each staphylococcal species. It dictates many biological features that characterize each staphylococcal species. For example, in the oriC environ of S. aureus, important virulence determinants such as protein A (spa), coagulase (coa), and the capsule locus [cap5(8)A to -P] were present. This oriC environ region was defined in the downstream region 30 kb from the oriC. It contained the staphylococcal cassette chromosomes, which might serve as a vehicle for introduction of exogenous genes into this region as well as insertion sequence elements and other recombinases serving to excise unused genes. A species-specific upstream region was also observed in some Staphylococcus strains. The authors' theory was that certain useful foreign genes were preserved by being transferred upstream of the oriC, protecting them from insertion sequence-mediated deletion occurring in the oriC environ. It was observed that the oriC environ was similar within a species but diverse among the different species, and the seven S. aureus sequenced strains had the downstream part of the oriC environ in common (35). In this study, we showed that the polymorphism of S. xylosus strains was principally centered on this oriC environ region, a species-specific region and also a strain-specific region in S. xylosus. Analysis of the differential genetic content of different S. xylosus demonstrated that this region is implicated in staphylococcal speciation but also actively participates in species evolution by the acquisition of new metabolism functions, like assimilation of new carbohydrate sources, antibiotic resistance, or factors possibly implicated in virulence. These strain-specific genes may be used as markers in epidemiological or evolutionary studies. The genomic evolution capacity is essential for ubiquitous species such as S. xylosus. Sequencing of this strain-specific “oriC environ” region in numerous Staphylococcus species and numerous strains within a species should provide a better understanding of staphylococcal genome plasticity and the genetic fitness of this genus in response to specialized niches.

FIG. 3.

PFGE patterns of the S. xylosus 00-1747, S04009, and S04002 tester strains. The percentage of specific fragments that hybridized with restriction fragments is detailed for each restriction pattern.