Construction of a chromosome map for the phage group II Staphylococcus aureus Ps55

Identification of Staphylococcus aureus based on PCR amplification of species specific genomic 826 bp sequence derived from a common 44-kb Sma I restriction fragment

Primers were designed for polymerase chain reaction (PCR)-amplification of a genomic sequence specific to Staphylococcus aureus strains. The sequence corresponds to a part of the 44-kb Sma I fragment (fragment L on the S. aureus NCTC 8325 restriction map) which was found to be common to strains of the S. aureus species (Pantůcek et al 1996, International Journal of Systematic Bacteriology, 46: 216-222). The labelled 44-kb Sma I restriction fragment derived from S. aureus NCTC 8325-4 was hybridized to the Eco RI restriction patterns of genomic DNA from 13 strains representing different macrorestriction types of S. aureus subsp. aureus. This made it possible to reveal the 2052 bp Eco RI restriction subfragment and to demonstrate its presence in all the tested strains. From the sequence of this subfragment, primers were designed by means of which the 826 bp amplicons were obtained in all 216 tested strains of S. aureus. No hybridization and PCR-products were observed in 40 collection strains of other staphylococcal species and subspecies as well as in 45 clinical strains of coagulase-negative staphylococci. These results lead us to the conclusion that the use of the above primers makes it possible to identify rapidly and reliably S. aureus strains of various provenance and different genotypes.

The two-component system ArlS-ArlR is a regulator of virulence gene expression in Staphylococcus aureus

Staphylococcus aureus is a major human pathogen that produces many virulence factors in a temporally regulated manner controlled by at least two global virulence regulatory loci (agr and sarA). We identified previously a two-component system, ArlS-ArlR, that modifies the activity of extracellular serine protease and may be involved in virulence regulation. Here, we show that mutations in either arlR or arlS increase the production of secreted proteins [alpha-toxin (Hla), beta-haemolysin, lipase, coagulase, serine protease (Ssp)] and especially protein A (Spa). Furthermore, the pattern of proteins secreted by both mutants was strikingly different from that of the wild-type strain. Transcriptional fusions showed that expression of hla, ssp and spa was higher in both mutants than in the wild-type strain, indicating that the arl operon decreases the production of virulence factors by downregulating the transcription of their genes. The arl mutation did not change spa expression in an agrA mutant or in a sarA mutant, suggesting that both the sarA and the agr loci are required for the action of arl on spa. Northern blot analyses indicated that the arl mutation increased the synthesis of both RNA II and RNA III, but decreased sarA transcription. Finally, arl was not autoregulated, but its expression was stimulated by agr and sarA. These results suggest that the Arl system interacts with both agr and sarA regulatory loci to modulate the virulence regulation network.

DNA heterogeneity of Staphylococcus aureus strains evaluated by SmaI and SgrAI pulsed-field gel electrophoresis in patients with impetigo

To our knowledge, no studies have previously been carried out on the heterogeneity and intrafamily colonization of impetigo Staphylococcus aureus strains obtained by powerful discriminating methods such as pulsed-field gel electrophoresis (PFGE). To explore this topic, macrorestriction patterns of S. aureus strains were analyzed after SmaI and SgrAI digestion. The two enzymes provided superimposable results. A total of ninety-seven S. aureus strains was found in the 26 families whose lesions and nasal and pharyngeal samples were examined. There were 39 strains which were different by PFGE, and of these, 24 were found in the lesions. Although 85% of impetigo patients showed nasal colonization and 58% showed pharyngeal colonization, only 54% of the patients had the same PFGE strain in the lesion and in the nose, and 35% in the lesion and the pharynx. In half of the 26 families, at least one member (mother, father, or relative) presented a S. aureus strain identical, by PFGE, to strains isolated in patients' lesions. Nineteen percent of mothers, 15% of fathers, and 19% of the other relatives presented nasal colonization with strains identical to those isolated in the children's lesions. Lesional strains showed higher antimicrobial resistance than nonlesional isolates.

The genomic diversity of coagulase-negative staphylococci associated with nosocomial infections

A total of 117 isolates of coagulase-negative staphylococci (CNS) were collected from patients in three medical centres. They were genotyped by pulsed-field gel electrophoresis (PFGE) following digestion with restriction enzymes SmaI and SstII. The isolates included Staphylococcus epidermidis, S. simulans, S. hominis, S. lugdunensis, S. capitis, S. saprophyticus, S. caprae and S. sciuri. They were collected at random from 82 patients and were associated with infected central venous lines, continuous ambulatory peritoneal dialysis (CAPD) catheters, endocarditis, osteomyelitis of prosthetic hips and internally fixed fractures. The genetic heterogeneity of the strains was demonstrated by PFGE profiles and two dendrograms. Though the strains were segregated into species, there was no clustering of the strains by type of infection, associated medical unit or geographical location of the patient. Numerous genotypes were identified, suggesting that no specific strains of CNS are associated with prosthetic related infection.

Evidence for a novel Chlorella virus-encoded alginate lyase

To clone the genes encoding lysis protein from a Chlorella virus, water samples were collected from 13 aquatic environments located in the Kanto area of Japan. Eight water samples contained plaque-forming viruses on Chlorella sp. NC64A, but no virus was detected in the other five samples. A novel Chlorella virus, CVN1, was isolated from the Inba-numa marsh sample. CVN1 genomic DNA was partially digested and shotgun cloned into pUC118 to identify the genomic region responsible for the lytic phenotype on Chlorella sp. NC64A. A DNA fragment which encoded two ORFs, ORF1 and ORF2, was obtained by antialgal assay. The ORF2 gene product, CL2, consisted of 333 amino acids showing antialgal activity not only on the original host of Chlorella sp. NC64A, but also on the heterogeneous hosts of Chlorella vulgaris C-27 and C. vulgaris C-207. CL2 showed a weak homology (19.8% amino acid identity) to mannuronate lyase SP2 from Turbo cornutus. CL2 in Escherichia coli cells was purified using a nickel chelate column. Lyase activity of purified CL2 on alginic acid was observed in an enzyme assay. The specific activity of purified CL2 was 2.1x10(-2) U mg(-1), the optimum pH for enzymatic activity was 10.5, and Ca(2+) was required for enzyme activity. This is the first report of a Chlorella virus protein with lyase activity.

The diverse and dynamic structure of bacterial genomes

Bacterial genome sizes, which range from 500 to 10,000 kbp, are within the current scope of operation of large-scale nucleotide sequence determination facilities. To date, 8 complete bacterial genomes have been sequenced, and at least 40 more will be completed in the near future. Such projects give wonderfully detailed information concerning the structure of the organism's genes and the overall organization of the sequenced genomes. It will be very important to put this incredible wealth of detail into a larger biological picture: How does this information apply to the genomes of related genera, related species, or even other individuals from the same species? Recent advances in pulsed-field gel electrophoretic technology have facilitated the construction of complete and accurate physical maps of bacterial chromosomes, and the many maps constructed in the past decade have revealed unexpected and substantial differences in genome size and organization even among closely related bacteria. This review focuses on this recently appreciated plasticity in structure of bacterial genomes, and diversity in genome size, replicon geometry, and chromosome number are discussed at inter- and intraspecies levels.

Chromosome map of Xanthomonas campestris pv. campestris 17 with locations of genes involved in xanthan gum synthesis and yellow pigmentation

No plasmid was detected in Xanthomonas campestris pv. campestris 17, a strain of the causative agent of black rot in cruciferous plants isolated in Taiwan. Its chromosome was cut by PacI, PmeI, and SwaI into five, two, and six fragments, respectively, and a size of 4.8 Mb was estimated by summing the fragment lengths in these digests. Based on the data obtained from partial digestion and Southern hybridization using probes common to pairs of the overlapping fragments or prepared from linking fragments, a circular physical map bearing the PacI, PmeI, and SwaI sites was constructed for the X. campestris pv. campestris 17 chromosome. Locations of eight eps loci involved in exopolysaccharide (xanthan gum) synthesis, two rrn operons each possessing an unique I-CeuI site, one pig cluster required for yellow pigmentation, and nine auxotrophic markers were determined, using mutants isolated by mutagenesis with Tn5(pfm)CmKm. This transposon contains a polylinker with sites for several rare-cutting restriction endonucleases located between the chloramphenicol resistance and kanamycin resistance (Kmr) genes, which upon insertion introduced additional sites into the chromosome. The recA and tdh genes, with known sequences, were mapped by tagging with the polylinker-Kmr segment from Tn5(pfm)CmKm. This is the first map for X. campestris and would be useful for genetic studies of this and related Xanthomonas species.

The genome of Staphylococcus aureus: a review

The genome of Staphylococcus aureus consists of a single circular chromosome (2.7-2.8 mbp) plus an assortment of extrachromosomal accessory genetic elements: conjugative and nonconjugative plasmids, mobile elements (IS, Tn, Hi), prophages and other variable elements. Plasmids (1-60 kbp) are classified into 4 classes and there are 15 known incompatibility groups. Mobile elements of the genome (0.8-18 kbp) appear in the chromosome or in plasmids of classes II and III. Prophages (45-60 kbp) are integrated in the bacterial chromosome, and they are UV- or mitomycin-inducible. Temperate bacteriophages of S. aureus are members of the Siphoviridae and the serological groups A, B and F occur most frequently. In the paper presented, the characteristics of chromosome, plasmids, transposons and other genetic elements of S. aureus genome are given and an alphabetical list of known genes of this species is included.

Prevalence and chromosomal map location of Staphylococcus aureus adhesin genes

Using genomic DNA from 25 unrelated strains and probes specific for each gene, we assessed the prevalence of the Staphylococcus aureus (Sa) adhesion genes cna, fnbA, fnbB, fib, clfA, fbpA, ebpS and map. All 25 strains encoded fib, clfA, ebpS, map and at least one of the fnb genes. fbpA and coa appeared to be allelic variants of the same gene with the fbpA variant being present in only four of 25 isolates. cna was present in 10 of 25 strains. Using Southern blot analysis of SmaI-digested genomic DNA resolved by pulsed-field gel electrophoresis, the adhesion genes were mapped to SmaI fragments A (ebpS), B (fib and clfA), C (fnbA/fnbB), E (fbpA), F (map) and G (cna). Despite variations in SmaI restriction profiles, co-localization of adhesin genes with genes known to map to specific SmaI fragments in the Sa 8325-4 chromosome strains suggests that the chromosomal location of each adhesin gene is conserved.