Typing of coagulase-negative staphylococci by Southern hybridization of chromosomal DNA fingerprints using a ribosomal RNA probe

Use of tuf as a target for sequence-based identification of Gram-positive cocci of the genus Enterococcus, Streptococcus, coagulase-negative Staphylococcus, and Lactococcus

Background

Accurate identification of isolates belonging to genus Enterococcus, Streptococcus, coagulase-negative Staphylococcus, and Lactococcus at the species level is necessary to provide a better understanding of their pathogenic potential, to aid in making clinical decisions, and to conduct epidemiologic investigations,especially when large blind samples must be analyzed. It is useful to simultaneously identify species in different genera using a single primer pair.

Methods

We developed a primer pair based on the tuf gene (encoding elongation factor) sequence to identify 56 Gram-positive cocci isolates.

Results

The target sequences were amplified from all 56 samples. The sequencing results and the phylogenetic tree derived from the partial tuf gene sequences identified the isolates as three enterococcal species, two lactococcal species, two staphylococcal species, and six streptococcal species, as well as eight isolates that were novel species of the genus Streptococcus. Partial gene sequence analysis of the sodA, dnaK, and 16S RNA genes confirmed the results obtained by tuf gene sequencing.

Conclusion

Based on the uniform amplification of the tuf gene from all samples and the ability to identify all isolates at both the genus and species levels, we conclude that the primer pair developed in this research provides a powerful tool for identifying these organisms in clinical laboratories where large blind samples are used.

Genetic classification and distinguishing of Staphylococcus species based on different partial gap, 16S rRNA, hsp60, rpoB, sodA, and tuf gene sequences

The analysis of 16S rRNA gene sequences has been the technique generally used to study the evolution and taxonomy of staphylococci. However, the results of this method do not correspond to the results of polyphasic taxonomy, and the related species cannot always be distinguished from each other. Thus, new phylogenetic markers for Staphylococcus spp. are needed. We partially sequenced the gap gene (approximately 931 bp), which encodes the glyceraldehyde-3-phosphate dehydrogenase, for 27 Staphylococcus species. The partial sequences had 24.3 to 96% interspecies homology and were useful in the identification of staphylococcal species (F. Layer, B. Ghebremedhin, W. König, and B. König, J. Microbiol. Methods 70:542-549, 2007). The DNA sequence similarities of the partial staphylococcal gap sequences were found to be lower than those of 16S rRNA (approximately 97%), rpoB (approximately 86%), hsp60 (approximately 82%), and sodA (approximately 78%). Phylogenetically derived trees revealed four statistically supported groups: S. hyicus/S. intermedius, S. sciuri, S. haemolyticus/S. simulans, and S. aureus/epidermidis. The branching of S. auricularis, S. cohnii subsp. cohnii, and the heterogeneous S. saprophyticus group, comprising S. saprophyticus subsp. saprophyticus and S. equorum subsp. equorum, was not reliable. Thus, the phylogenetic analysis based on the gap gene sequences revealed similarities between the dendrograms based on other gene sequences (e.g., the S. hyicus/S. intermedius and S. sciuri groups) as well as differences, e.g., the grouping of S. arlettae and S. kloosii in the gap-based tree. From our results, we propose the partial sequencing of the gap gene as an alternative molecular tool for the taxonomical analysis of Staphylococcus species and for decreasing the possibility of misidentification.

Species-level identification of clinical staphylococcal isolates based on polymerase chain reaction--restriction fragment length polymorphism analysis of a partial groEL gene sequence

A pair of degenerate primers that amplified, by polymerase chain reaction (PCR), a partial groEL gene sequence (550 bp) was used for the identification of the 12 most common human staphylococcal pathogens. The amplified products were digested by AluI endonuclease, and distinctive PCR restriction fragment length polymorphism (RFLP) patterns for reference strains were obtained. This protocol was validated by the identification of 89 clinical staphylococcal isolates, and the results were compared with those obtained by the reference biochemical identification, showing 100% concordant results. Two species, Staphylococcus aureus and Staphylococcus lugdunensis, showed intraspecies polymorphisms on their PCR-RFLP patterns. All strains were also identified using the API Staph ID test (bioMérieux, Durham, NC) and the MicroScan WalkAway automated system (Dade Behring, West Sacramento, CA). When 17 Staphylococcus isolates were tested in a blind experiment by the PCR-RFLP of the groEL gene method, all strains were also correctly identified. We propose the PCR-RFLP of the groEL gene with AluI as a reliable and reproducible method for identification of Staphylococcus spp.

Differentiation of Staphylococcus spp. by terminal-restriction fragment length polymorphism analysis of glyceraldehyde-3-phosphate dehydrogenase-encoding gene

Classical phenotypic and biochemical testing do not lead to correct identification of the distinct Staphylococcus species. Therefore, the aim of our study was to develop a method for the reliable and accurate determination of distinct Staphylococcus species. In the present study, the 931-934-bp partial sequences of the glyceraldehyde-3-phosphate dehydrogenase-encoding (gap) gene of 28 validly described Staphylococcus species were amplified and sequenced. By using the respective sequence information we performed a terminal-restriction fragment length polymorphism (T-RFLP) analysis. For T-RFLP the partial gap gene was amplified with double-fluorescently labelled primers and digested with the restriction enzymes DdeI, BspHI and TaqI. Distinctive T-RFLP patterns were rendered by the use of capillary electrophoresis with laser-induced fluorescence detection. This molecular method allowed us to identify all 28 Staphylococcus species with high specificity. This was validated by analysis of 34 Staphylococcus epidermidis and 28 Staphylococcus haemolyticus isolates. These results demonstrate the feasibility and applicability of the T-RFLP method based on the partial gap gene sequences for rapid and accurate species identification.

Identification of staphylococci by 16S internal transcribed spacer rRNA gene restriction fragment length polymorphism

The capacity of 16S internal transcribed spacer (16S-ITS) rRNA gene RFLP to differentiate 16 type strains and nine clinical isolates of staphylococci was evaluated. The 16S rRNA gene was amplified together with the ITS region and the amplification products were digested with TaqI restriction enzyme. Analysis of the 16S-ITS rRNA gene RFLP profiles differentiated each of the 16 type strains into distinct RFLP haplotypes.

Identification of coagulase-negative staphylococci other than Staphylococcus epidermidis by automated ribotyping

As routine identification of coagulase-negative staphylococci is problematic, the performance of automated ribotyping was evaluated for identification of coagulase-negative staphylococci other than Staphylococcus epidermidis. In total, 177 isolates were tested, comprising 149 isolates from blood samples, 15 isolates that were not identified by internal transcribed spacer (ITS)-PCR in a previous study, and 13 reference strains. The identification results were compared with those obtained by the API 20 Staph system, with standard phenotypic and molecular methods as reference. Most (n = 166; 93.8%) isolates were identified correctly by automated ribotyping. For 61 isolates, API 20 Staph and ribotyping were in agreement, but for 105 isolates, ribotyping provided correct identification and API 20 Staph did not. Four isolates not identified by automated ribotyping were recognised correctly by API 20 Staph. The remaining seven isolates could not be identified by either of the two methods. Automated ribotyping was able to distinguish Staphylococcus capitis reliably from Staphylococcus caprae. The results demonstrate the value of automated ribotyping for identification of coagulase-negative Staphylococcus (CoNS) isolates from human sources and may help to clarify the clinical relevance of CoNS species. In addition, automated ribotyping was able to detect polymorphisms that may be useful for epidemiological purposes within S. capitis, Staphylococcus hominis, Staphylococcus haemolyticus, Staphylococcus simulans, S. caprae, Staphylococcus warneri, Staphylococcus lugdunensis, Staphylococcus schleiferi, Staphylococcus sciuri, Staphylococcus pasteuri and Staphylococcus xylosus.

Phenotypic and genotypic characterisation of blood isolates of coagulase-negative staphylococci in the newborn

Coagulase-negative staphylococci (CNS) are the leading cause of late-onset sepsis in newborns (>72 h of age). Our aim was to determine whether phenotypic and/or genotypic differences existed between blood isolates of CNS regarded as inducers of sepsis or as contaminants. Ninety-seven bloodisolates of CNS recovered from newborns at the neonatal intensive care unit, Orebro, Sweden in 1983-1997 were analysed. Twenty-nine of them (30%) were classified as sepsis isolates and 68 (70%) as contaminants. The most prevalent species was Staphylococcus epidermidis (n=59). Staphylococcus haemolyticus (n=16) was most often isolated from newborns with the lowest gestational age and birth weight. Biochemical typing using the Phene Plate system (PhP) and genotyping using pulsed-field gel electrophoresis (PFGE) showed that the S. epidermidis isolates regarded as inducers of sepsis (n=16) were more homogeneous than isolates considered contaminants (n=37). One main genotypic group, representing seven (44%) isolates, was identified among the sepsis isolates. Phenotypically the S. epidermidis sepsis isolates comprised three major clusters. In contrast, among the S. epidermidis contaminants, eight genotypic groups and two phenotypic clusters were identified. The dominating genotypic group among the sepsis isolates of S. epidermidis may represent strains with higher invasive capacity.

rpoB gene sequence-based identification of Staphylococcus species

The complete sequence of rpoB, the gene encoding the beta subunit of RNA polymerase was determined for Staphylococcus saccharolyticus, Staphylococcus lugdunensis, S taphylococcus caprae, and Staphylococcus intermedius and partial sequences were obtained for an additional 27 Staphylococcus species. The complete rpoB sequences varied in length from 3,452 to 3,845 bp and had a 36.8 to 39.2% GC content. The partial sequences had 71.6 to 93.6% interspecies homology and exhibited a 0.08 to 0.8% intraspecific divergence. With a few exceptions, the phylogenetic relationships inferred from the partial rpoB sequences were in agreement with those previously derived from DNA-DNA hybridization studies and analyses of 16S ribosomal DNA gene sequences and partial HSP60 gene sequences. The staphylococcal rpoB sequence database we established enabled us to develop a molecular method for identifying Staphylococcus isolates by PCR followed by direct sequencing of the 751-bp amplicon. In blind tests, this method correctly identified 10 Staphylococcus isolates, and no positive results were obtained with 10 non-Staphylococcus gram-positive and gram-negative bacterial isolates. We propose partial sequencing of the rpoB gene as a new tool for the accurate identification of Staphylococcus isolates.

Rapid species identification of coagulase negative Staphylococci by rRNA spacer length polymorphism analysis

OBJECTIVES

The identification of coagulase-negative staphylococci (CNS) is carried out mainly through conventional methods, commercial identification kits, and molecular biology-based methods. We evaluated the efficiency of PCR analysis of tRNA intergenic spacer length polymorphism (tDNA-ILP) and 16S-23S intergenic spacer length polymorphism (16S-23S ILP), and also that of restriction analysis of 16S-23S intergenic spacer amplification products (RA 16S-23S), for the rapid and accurate identification of CNS species.

METHODS

The PCR assays of rRNA spacer length polymorphisms were tested with nine reference type strains and 122 clinical isolates. The results were compared with those obtained by conventional methods and the Vitek system for clinical isolates.

RESULTS

Seventy-eight (63.9%) of 122 strains were identified as the same species with conventional identification, the Vitek GPI system, tDNA-ILP, and RA 16S-23S. The 16S-23S ILP analysis did not produce distinguishable PCR fragments. The results of tDNA-ILP analysis were in agreement with those of RA 16S-23S to the species level for 98.2% except for unknown patterns (eight isolates).

CONCLUSIONS

These results indicate that tDNA-ILP and RA 16S-23S analysis are potentially valuable tools for rapid and accurate CNS identification.

Molecular tracking of coagulase-negative staphylococcal isolates from catheter-related infections

Three molecular typing methods (pulsed-field electrophoresis, localization of the mecA gene, and probing the vicinity of mec) have been used for the characterization of 40 catheter-related isolates of coagulase-negative staphylococci (CNS) in 14 patients admitted to the same hospital. The 40 isolates yielded 14 different SmaI banding patterns and corresponding unique localizations of mecA, each associated with a unique ClaI mecA polymorph. In 6 of the 14 patients the contaminated skin at the catheter entry site was the source of 4 local infections and 2 cases of bacteremia. A contaminated hub was the origin of 2 local infections and 4 cases of bacteremia in 6 more patients. The remaining 2 patients had positive cultures from both skin and catheter hub. In each bacteremic patient, the CNS recovered from catheter-related sites (tip, skin, and/or hub) and the CNS recovered from blood were identical, but each of these matching isolates was unique to the particular patients, indicating a low rate of cross-infection from patient to patient. Although classical methods for typing CNS (e.g., biotype and antibiotype) are readily available for most hospital laboratories, they have limitations concerning reproducibility and discriminatory power. Molecular epidemiologic techniques can provide powerful support to traditional techniques in determining the etiologic role of CNS in the disease process.

Molecular characterization and LD(50) identify virulent isolates of Staphylococcus epidermidis from adult sepsis

Staphylococcus epidermidis plays an important role in infections of patients with implanted prosthetic devices. The exact clinical significance of recovered S. epidermidis from clinical specimens is difficult to assess, as they are inhabitants of the normal skin. In this study, 11 adults with clinical sepsis and blood cultures that grew only S. epidermidis were the host population. Bacterial virulence in vivo was determined by using the mouse LD(50) assay where the intravenous lethality was determined for each patient isolate. Bacterial dose (CFU x 10(9)) that produced lethality in 50% of the animals at 12 h was the value used for comparison. Restriction fragment length polymorphism (RFLP) analysis of chromosomal DNA by pulsed-field gel electrophoresis (PFGE) was used for identification of individual strains and their clonal organization. Confirmation of species assignment was done by RFLP analysis of 16S + 23S rRNA gene regions (ribotyping). Plasmid profile analysis was also conducted. Four of 11 blood isolates from adults with S. epidermidis sepsis had indistinguishable or closely related DNA patterns and were considered clone A. The same clone was previously seen to account for the majority of sepsis in a neonatal intensive care unit. There were significant differences in virulence characteristics of the S. epidermidis isolates. Clone A isolates produced lethality by LD(50) in mice at a dose averaging 2.35; clone B isolate at a dose of 2.54, and the remaining isolates, representing six distinct clones, were lethal to mice at significantly larger doses (3.51-5.17, average 4.16). These data suggest that individual clones of S. epidermidis isolated from septic adults have detectable differences in virulence as defined by an animal bioassay, and the more virulent clone is widespread.

Differentiation of Lactobacillus Species by Molecular Typing

A total of 64 type, reference, clinical, health food, and stock isolates of microaerophilic Lactobacillus species were examined by restriction fragment length polymorphisms. Of particular interest were members of six of the eight species most commonly recovered from the vaginas of healthy premenopausal women, namely, Lactobacillus jensenii, L. casei, L. rhamnosus, L. acidophilus, L. plantarum, and L. fermentum. Six main groupings were identified on the basis of ribotyping. This technique was able to classify fresh isolates to the species level. In the case of the ribotype A grouping for L. rhamnosus, differences between strains were evident by chromosome typing (chromotyping). Many isolates did not possess plasmids. Six L. rhamnosus strains isolated from four different health food products appeared to be identical to L. rhamnosus ATCC 21052. The molecular typing system is useful for identifying and differentiating Lactobacillus isolates. Studies of strains of potential importance to the urogenital flora should include molecular characterization as a means of comparing genetic traits with those of strains whose characteristics associated with colonization and antagonism against pathogens have been defined.

Characterization of coagulase-negative staphylococci by primer-specific polymerase chain reaction and ribotyping

OBJECTIVE: To analyze, by primer-specific polymerase chain reaction (PCR) and ribotyping, coagulase-negative staphylococci (CNS). METHODS: Forty-five clinical isolates of CNS were identified by the API ID32 STAPH system and ribotyping. Additionally, primer-specific PCR was evaluated for identification of clinical strains of Staphylococcus epidermidis. RESULTS: Forty-five isolates of CNS from neonates with nosocomial bacteremia were studied. The results of the S. epidermidis-specific PCR were compared with those obtained using ribotyping and the API ID32 STAPH system. Excellent congruence was found between primer-specific PCR and ribotyping. Primer-specific PCR proved to be a fast and reliable method for the identification of S. epidermidis strains. According to the primer-specific PCR and ribotyping analysis, a few CNS isolates were found to be incorrectly identified by the API ID32 STAPH system. CONCLUSIONS: Primer-specific PCR is a fast and reliable method for the identification of S. epidermidis. Primer-specific PCR in combination with ribotyping is a promising approach for studying the epidemiology of S. epidermidis and other CNS species in hospital.

Adhesion of coagulase-negative staphylococci grouped according to physico-chemical surface properties

Physico-chemical cell surface properties of 23 coagulase-negative staphylococcal strains, including contact angles, zeta potentials and elemental cell surface composition were measured, together with the adhesion of all strains to hexadecane. The data were employed in a hierarchical cluster analysis, revealing that the 23 strains comprised essentially four different groups. Groups I-III were somewhat similar to each other, but group IV was markedly distinguished from the other strains, predominantly through an elevated acidity of the cell surface. These group distinctions were not related to the presence of a capsule or slime on the strains. Adhesion of the strains to hexadecane depended critically on electrostatic interactions between the hexadecane and the staphylococci, and adhesion only occurred when the electrostatic repulsion between hexadecane and the micro-organisms was less than 500 kT at closest approach. Adhesion of six representative strains from all four groups in a parallel plate flow chamber to silicone rubber, an implant material with similar hydrophobicity to hexadecane, did not show such a critical dependence, nor did it relate with the group distinction. Possibly, microbial adhesion to substratum surfaces like silicone rubber is more complicated than adhesion to an ideally smooth and homogeneous hexadecane surface in an aqueous solution. Adhesion of all six strains to silicone rubber with an adsorbed conditioning film of plasma proteins was less than that to bare silicone rubber: initial deposition rates dropped from 2000-3000 cm-2 s-1 to 100-300 cm-2 s-1 after adsorption of plasma proteins, while the stationary end-point adhesion decreased from 10 x 10(6)-15 x 10(6) cm-2 to 1 x 10(6)-5 x 10(6) cm-2. The adhering staphylococci poorly withstood the passage of an air-bubble through the parallel plate flow chamber, regardless of the presence of a conditioning film, indicating a low affinity of these relatively hydrophilic strains for hydrophobic substratum surfaces.

Identification of Staphylococcus species and subspecies by the chaperonin 60 gene identification method and reverse checkerboard hybridization

A previous study (S. H. Goh et al., J. Clin. Microbiol. 34:818-823, 1996) demonstrated that a 600-bp region of the chaperonin 60 (Cpn60) genes from various bacterial isolates could be amplified by PCR with a pair of degenerate primers and that the products could be used as species-specific probes for Staphylococcus aureus, S. epidermidis, S. haemolyticus, S. lugdunensis, S. saprophyticus, and S. schleiferi. To further validate the utility of bacterial Cpn60 genes as universal targets for bacterial identification (ID), reverse checkerboard chemiluminescent hybridization experiments were performed with DNA probes from 34 different Staphylococcus species and subspecies. With the exception of probes from the Cpn60 genes of S. intermedius and S. delphini, which cross hybridized, all were species specific. Two subspecies of both S. capitis and S. cohnii were differentiated from one another, while DNAs from the two S. schleiferi subspecies cross hybridized. When 40 known Staphylococcus isolates were tested in a blind experiment by the Cpn60 gene method, 36 strains, representing six species and one subspecies (S. sciuri, S. caseolyticus, S. hominis, S. warneri, S. hyicus, S. haemolyticus, and S. capitis subsp. ureolyticus), were correctly identified. DNA from the four remaining isolates, known to be S. hyicus bovine strains, failed to hybridize to DNA from the S. hyicus target strain or any other Staphylococcus species. However, DNAs from these S. hyicus isolates did cross hybridize with each other. New DNA sequence data and evidence from previous studies suggest some genetic divergence between the two groups of S. hyicus isolates. Our results demonstrate that this Cpn60 gene-based ID method has the potential to be a basic method for bacterial ID. Studies are in progress to further validate the utility of this Cpn60 gene system for ID of Staphylococcus and other genera, including those of slow-growing microorganisms.

Identification of atypical strains of Staphylococcus epidermidis by use of molecular tools

Four atypical coagulase-negative staphylococcal (CNS) isolates from clinical sources were compared with Staphylococcus epidermidis strains by ribotyping. The ribotypes of the four strains shared close rDNA restriction profiles with those of the S. epidermidis strains used. The DNA sequence encoding 16S rRNA demonstrated 99.9% homology with S. epidermidis. S1 nuclease experiments showed that these atypical strains formed a homogeneous genomic group. DNA-DNA homologies between the S. epidermidis type strain CCM 2124 and the four CNS isolates ranged from 70 to 89%. The guanine-plus-cytosine content of the deoxyribonucleic acid of the four strains ranged from 31 to 32 mol%.

Combined use of ribotyping, PFGE typing and IS431 typing in the discrimination of nosocomial strains of methicillin-resistant Staphylococcus aureus

We have previously reported the phenotypic characterization of methicillin-resistant Staphylococcus aureus (MRSA) clinical strains isolated in Malaya University Hospital in the period 1987 to 1989 using antibiogram, coagulase typing, plasmid profiles, and phage typing. Here, we report the analysis of the same strains with three genotyping methods; ribotyping, pulsed-field gel electrophoresis (PFGE) typing, and IS431 typing (a restriction enzyme fragment length polymorphism analysis using an IS431 probe). Ribotyping could discriminate 46 clinical MRSA strains into 5 ribotypes, PFGE typing into 22 types, and IS431 typing into 15 types. Since the differences of the three genotyping patterns from strain to strain were quite independent from one another, the combined use of the three genotyping methods could discriminate 46 strains into 39 genotypes. Thus, the powerful discriminatory ability of the combination was demonstrated.

Identification and ribotyping of Staphylococcus xylosus and Staphylococcus equorum strains isolated from goat milk and cheese

Twenty-five strains of staphylococci isolated from goat milk and cheese were identified as belonging to the Staphylococcus xylosus/equorum group using the ID 32 Staph system (bioMérieux, Marcy-L'Etoile, France). This system, however, was not able to discriminate between these two species for 19 of the strains tested. Ribotyping was performed on these 25 strains, as well as on three reference strains of each of these two species. Hybridization membranes were scanned and analyzed using the Taxotron software package (Taxolab, Institut Pasteur, Paris, France). A dendrogram representation showed that ribotypes were distributed in two clear-cut clusters corresponding to S. equorum (21 strains) and S. xylosus (four strains).

HSP60 gene sequences as universal targets for microbial species identification: studies with coagulase-negative staphylococci

A set of universal degenerate primers which amplified, by PCR, a 600-bp oligomer encoding a portion of the 60-kDa heat shock protein (HSP60) of both Staphylococcus aureus and Staphylococcus epidermidis were developed. However, when used as a DNA probe, the 600-bp PCR product generated from S. epidermidis failed to cross-hybridize under high-stringency conditions with the genomic DNA of S. aureus and vice versa. To investigate whether species-specific sequences might exist within the highly conserved HSP60 genes among different staphylococci, digoxigenin-labelled HSP60 probes generated by the degenerate HSP60 primers were prepared from the six most commonly isolated Staphylococcus species (S. aureus 8325-4, S. epidermidis 9759, S. haemolyticus ATCC 29970, S. schleiferi ATCC 43808, S. saprophyticus KL122, and S. lugdunensis CRSN 850412). These probes were used for dot blot hybridization with genomic DNA of 58 reference and clinical isolates of Staphylococcus and non-Staphylococcus species. These six Staphylococcus species HSP60 probes correctly identified the entire set of staphylococcal isolates. The species specificity of these HSP60 probes was further demonstrated by dot blot hybridization with PCR-amplified DNA from mixed cultures of different Staphylococcus species and by the partial DNA sequences of these probes. In addition, sequence homology searches of the NCBI BLAST databases with these partial HSP60 DNA sequences yielded the highest matching scores for both S. epidermidis and S. aureus with the corresponding species-specified probes. Finally, the HSP60 degenerate primers were shown to amplify an anticipated 600-bp PCR product from all 29 Staphylococcus species and from all but 2 of 30 other microbial species, including various gram-positive and gram-negative bacteria, mycobacteria, and fungi. These preliminary data suggest the presence of species-specific sequence variation within the highly conserved HSP60 genes of staphylococci. Further work is required to determine whether these degenerate HSP60 primers may be exploited for species-specific microbic identification and phylogenetic investigation of staphylococci and perhaps other microorganisms in general.

Subspecies discrimination of staphylococci from revision arthroplasties by ribotyping

Sixty-six cultures of Staphylococcus spp. were obtained from bone and tissue samples collected from 37 patients during revision arthroplasties and were speciated and ribotyped to assess strain diversity in each species. There were 10 ribotypes among 51 isolates of S. epidermidis, three among three isolates of S. capitis, two among four isolates of S. aureus and two among two isolates of S. simulans. One ribotype was found among each of: two isolates of S. warneri; two isolates of S. haemolyticus and single isolates of S. cohnii and S. saprophyticus. Low molecular weight bands of ribotype patterns characterized one or two related species whereas high molecular weight bands were useful for distinguishing types within species. Specimens from 17 patients yielded more than one isolate of Staphylococcus spp. In 13 of these patients the isolates were representatives of a single species but in only eight did ribotyping show the isolates to be identical. The findings of multiple species and ribotypes from samples taken from the same patient may have implications for understanding the nature of infection in revision arthroplasty and for antibiotic therapy.

Food-initiated outbreak of methicillin-resistant Staphylococcus aureus analyzed by pheno- and genotyping

An outbreak of methicillin-resistant Staphylococcus aureus (MRSA) involving 27 patients and 14 health-care workers (HCW) was studied. The outbreak started in the hematology unit of the University Hospital Rotterdam, Dijkzigt, The Netherlands, and spread to the surgical unit. Twenty-one patients (77.8%) developed clinical disease, and five died. Subsequently, MRSA was detected in food and in the throat of one of the HCW who prepared food for hematology patients. Food contaminated by an HCW most likely caused the first case of MRSA septicemia. This route of transmission has not been described before. The outbreak strain was probably transmitted to the surgical unit by a colonized nurse, where it caused an explosive outbreak. Airborne probably transmitted to the surgical unit by a colonized nurse, where it caused an explosive outbreak. Airborne MRSA transmission played an important role in disseminating the organism. The outbreak was controlled within 6 months by intensifying surveillance, temporarily closing the affected wards, treating carriers, and instituting an MRSA ward outside the hospital. Phage typing, insertion sequence probing, protein A gene typing, and DNA fingerprinting by PCR revealed that all outbreak-related isolates were identical. By pulsed-field gel electrophoresis, all but one of the outbreak-related isolates were determined to be identical. Protein A gene typing identified numerous (11) repeat units in all outbreak-related isolates, which supports the suggestion that the outbreak strain may have been more virulent and more transmissible than other MRSA strains. Pheno- and genotyping studies underlined the value of DNA fingerprinting methods for investigation of MRSA epidemiology. Optimal discriminatory power was achieved by combining the results of four genotyping methods.

Identification and ribotypes of Staphylococcus caprae isolates isolated as human pathogens and from goat milk

We report five cases of human infection with Staphylococcus caprae. Two were community acquired (one case each of endocarditis and urinary tract infection); the other three were acquired in a hospital (two cases of bacteremia associated with intravenous access and one case of urinary tract infection). Analysis of human isolates and goat isolates from eight herds showed that they could be misidentified by some commercial identification systems but were clearly identified as S. caprae by ribotyping, according to their species-specific ribotype. Phylogenetic methods applied to the ribotypes did not reveal two distinct lineages corresponding to the goat and human origins of the isolates, although human ribotypes were clearly distinguishable by the presence of a core of four specific bands. The latter observation may reflect some degree of evolutionary change within the species between human and goat isolates.

Detection of genomic heterogeneity in Streptococcus suis isolates by DNA restriction fragment length polymorphisms of rRNA genes (ribotyping)

Whole-cell chromosomal digests of 54 isolates of Streptococcus suis encompassing all known serotypes from a geographically varied collection were examined by PstI restriction fragment length polymorphisms and then hybridized with a digoxigenin-11-dUTP-labeled cDNA probe transcribed from a mixture of 16S and 23S rRNAs from Escherichia coli MRE600. The hybridization patterns showed genetic heterogeneity within and between S. suis serotypes. Most isolates (87%) representing 28 serotypes contained a common band at approximately 1.8 kb. However, 13% of the isolates representing seven serotypes lacked the 1.8-kb band, indicating that the species as currently defined is diverse. Nonetheless, the 1.8-kb band may be a useful genotypic marker for identification of most S. suis isolates. We tested the ability of this technique to discriminate between virulent and avirulent S. suis type 2 isolates. A virulent strain of S. suis type 2 could be distinguished from avirulent strains by the presence of specific bands. No correlation was obvious between band pattern and hemolysin production.

Molecular epidemiology of Staphylococcus epidermidis isolates in a hematological unit during a 4-month survey

In order to study the strain variety, clonal stability and epidemiology of Staphylococcus epidermidis, isolates from all bacterial cultures taken when clinically indicated in 2 wards of the hematological unit of Helsinki University Hospital, during a 4-month period, were characterized by 3 typing methods: antibiogram, plasmid profile and ribotype. A total of 141 distinct S. epidermidis colonies, from 28 blood cultures and 37 cultures from other sources in 32 patients were studied. Plasmid profiles and ribopatterns revealed 47 different strains of which 16 were bacteremic. One of these strains caused bacteremia in 4 different patients over a 3-month period and it was isolated from blood on 7 different sampling occasions. The occurrence of this clone was constant; it was usually found in both of 2 blood culture bottles inoculated (6/7 pairs) and dominated among the 17 distinct S. epidermidis colonies studied from the positive bottles (94% of the total). The clones causing bacteremias in the 2 wards were distinct. These findings indicate that certain clones of S. epidermidis can predominate in hematological wards and that nosocomial transmission of S. epidermidis strains may occur among patients, particularly within the same ward.

Use of ribotyping in epidemiological surveillance of nosocomial outbreaks

Over the past few years, genotypic methods based on the study of bacterial DNA polymorphism have shown high discriminatory power for strain differentiation and superiority over most phenotypic methods commonly available in the clinical microbiology laboratory. Some of the methods used, however, required either a high level of technology and sophisticated equipment (e.g., pulsed-field gel electrophoresis) or species-specific reagents of restricted availability (randomly cloned DNA probes or gene-specific probes). Because ribotyping uses a universal probe (rRNA) and is a rather simple technology, particularly since the advent of nonradioactive labelling systems, it has been widely used for strain differentiation of most bacterial species involved in nosocomial outbreaks. In vitro and in vivo stability of the markers studied has been demonstrated. Although there may be limitation to this approach, ribotyping was found to be highly discriminative, particularly for typing members of the family Enterobacteriaceae, Pseudomonas cepacia, and Xanthomonas maltophilia. In many cases, it has improved the understanding of the mechanism of nosocomial acquisition of organisms by allowing a distinction between endogenous and exogenous infections. Among exogenous infections, it has distinguished between individual and epidemic strains, thus differentiating cross-infection from independent acquisition.

Update on clinical significance of coagulase-negative staphylococci

The clinical significance of coagulase-negative Staphylococcus species (CNS) continues to increase as strategies in medical practice lead to more invasive procedures. Hospitalized patients that are immunocompromised and/or suffering from chronic diseases are the most vulnerable to infection. Since CNS are widespread on the human body and are capable of producing very large populations, distinguishing the etiologic agent(s) from contaminating flora is a serious challenge. For this reason, culture identification should proceed to the species and strain levels. A much stronger case can be made for the identification of a CNS etiologic agent if the same strain is repeatedly isolated from a series of specimens as opposed to the isolation of different strains of one or more species. Strain identity initially can be based on colony morphology, and then one or more molecular approaches can be used to gain information on the genotype. Many of the CNS species are commonly resistant to antibiotics that are being indicated for staphylococcal infections, with the exception of vancomycin. The widespread use of antibiotics in hospitals has provided a reservoir of antibiotic-resistant genes. The main focus on mechanisms of pathogenesis has been with foreign body infections and the role of specific adhesins and slime produced by Staphylococcus epidermidis. Slime can reduce the immune response and opsonophagocytosis, thereby interfering with host defense mechanisms. As we become more aware of the various strategies used by CNS, we will be in a better position to compromise their defense mechanisms and improve treatment.

Epidemiological markers of coagulase-negative staphylococci

Several different epidemiological typing methods have been used in studies of coagulase-negative staphylococci; these include biotyping, antibiotic susceptibility pattern analysis, serological typing, phage typing, slime production detection, protein profile analysis, immunoblot fingerprinting and DNA typing. The most frequently used tests are antibiotic susceptibility and extrachromosomal DNA banding patterns. Comparison of chromosomal DNA restriction patterns is facilitated when the fragments are separated by pulsed-field electrophoresis. Typing variations occur quite frequently even in isolates of demonstrated clinical significance. Caution should therefore be exercised in denying the clinical relevance of coagulase-negative staphylococci, even when successive isolates show distinct typing differences.

Characterization of unrelated strains of Staphylococcus schleiferi by using ribosomal DNA fingerprinting, DNA restriction patterns, and plasmid profiles

The molecular characteristics of 31 unrelated strains of Staphylococcus schleiferi isolated from 13 hospitals between 1973 and 1991 were determined by ribosomal DNA fingerprinting by using a digoxigenin-labeled DNA probe, genomic DNA restriction patterns, and plasmid profiles. Only six strains harbored one or two plasmids. DNA restriction analysis, which was carried out with five endonucleases (EcoRI, HindIII, PstI, PvuII, and ClaI), did not allow us to discriminate between isolates. Ribotyping with HindIII, ClaI, or EcoRI enzymes generated six, seven, and nine distinct patterns, respectively. With the combination ClaI-EcoRI, 13 ribotypes were obtained among the 31 strains, suggesting a relative heterogeneity within the species. Moreover, all strains shared two or three common bands, according to the endonuclease used, which were relatively specific for S. schleiferi in comparison with the ribosomal banding patterns described for other coagulase-negative staphylococci. These results illustrate that ribotyping can be used for the epidemiological investigation of S. schleiferi isolates and possibly for taxonomic analysis in this species.

Characterization of Listeria strains from a foodborne listeriosis outbreak by rDNA gene restriction patterns compared to four other typing methods

The rDNA gene restriction patterns of 134 isolates of Listeria species were determined with pKK3535--a pBR322 derived plasmid containing an Escherichia coli rRNA operon--used as a probe following digestion of chromosomal DNA by EcoRI endonuclease. Nineteen reference and type strains representing all species and serotypes of Listeria showed 17 distinct ribotypes. One hundred and fifteen wild strains of Listeria monocytogenes were ribotyped and the results were compared to those of serotyping, phage typing, multilocus enzyme electrophoresis (MEE) and restriction endonuclease analysis (REA). Ninety-six Listeria monocytogenes serotype 4b wild strains displayed six distinct ribotypes (I-VI), 72% (69/96) of them clustering in two very close rDNA patterns (I and II) of eight and nine bands, respectively. The same 96 strains displayed six REA patterns and eight MEE electrotypes. Among the 96 Listeria monocytogenes 4b isolates, the 34 epidemic strains defined by phage typing and by epidemiological data all belonged to one ribotype (ribotype I) representing 56% of the strains belonging to this ribotype. These same 34 epidemic strains were also grouped by REA and MEE typing in a unique profile (REA-A) and MEE electrotype (ET 1). Twenty-two Listeria monocytogenes strains of serogroup 1/2 analyzed by rDNA typing showed nine distinct ribotypes. For the 96 Listeria monocytogenes 4b strains studied, the discriminatory index was highest for phage typing and for any combination including phage typing. Ribotyping appears to be a well reproducible molecular typing method and could be a useful complement to other typing methods for the epidemiological study of listeriosis.

rRNA gene restriction patterns as an epidemiological marker in nosocomial outbreaks of Staphylococcus aureus infections

rRNA gene restriction patterns (ribotyping) were compared with phage typing, serotyping, enterotoxins and exfoliatin production in the analysis of 26 Staphylococcus aureus strains isolated from two different nosocomial outbreaks. Total DNA was cleaved by EcoRI restriction endonuclease. After agarose gel electrophoresis and Southern transfer, the hybridization of the membranes was done with radiolabelled 16S rRNA gene from Bacillus subtilis inserted into a plasmid vector. Six to 13 fragments were visualized. A core of common fragments was discerned for all strains tested. A full correlation between ribotyping and conventional markers was observed in only one of the outbreaks studied. In both outbreaks, ribotyping proved helpful in characterizing otherwise untypable strains.

Usefulness of the ID32 staph system and a method based on rRNA gene restriction site polymorphism analysis for species and subspecies identification of staphylococcal clinical isolates

The usefulness of the ID32 Staph System and a method based on rRNA gene restriction site polymorphism was evaluated by the study of 42 staphylococcal clinical isolates phenotypically difficult to identify. The ID32 Staph micromethod and the genomic method are adapted for recognition of 27 and 31 staphylococcal taxa, respectively. The genomic method is based on a Dice analysis of the hybridization patterns obtained by cutting the cellular DNA either with EcoRI or with HindIII and by probing with pBA2, containing the Bacillus subtilis gene encoding 16S rRNA, labeled either with [alpha-32P]dCTP or with acetylaminofluorene. This study showed that the nonradioactive labeling provided a better resolution of the hybridizing bands than radioactive labeling. Of the 42 isolates selected, only 22 could be assigned to a staphylococcal species by the ID32 Staph System, whereas 35 could be identified by the genomic method. This latter method also enabled the screening of three unclassified isolates having hybridization patterns more closely related to each other than to any of the 31 staphylococcal taxa investigated. These three isolates could belong to a staphylococcal taxon not yet described.

Ribotyping of Helicobacter pylori from clinical specimens

Ribotyping is a method used to type strains of bacteria by analyzing the restriction enzyme digestion patterns of the rRNA genes. This method was applied to 126 strains of Helicobacter pylori from 100 unrelated symptomatic patients who had endoscopies done and to 15 strains from 15 infected subjects from seven families. Analysis of the rRNA gene patterns revealed 77 distinct ribotypes from the 100 patients. From 15 of these subjects, isolates were recovered from antral mucosal biopsies at follow-up endoscopy. All follow-up isolates from the same patient, with one exception, yielded identical digest patterns. This patient had strains with two distinct digest patterns obtained from a set of three isolates cultured from biopsy specimens taken at different times. Five patients who had isolates recovered from different sites in the stomach (antrum, gastric body, duodenum, and pyloric channel) showed ribotyping patterns which were identical for each patient yet distinct between patients. In seven family groups studied, identical digest patterns were detected in members of two families, with variability in strains detected among members of the remaining families. This study demonstrates that ribotyping provides a useful, reliable, reproducible, and highly discriminatory typing scheme for the study of H. pylori infection.

Comparative evaluation of a new molecular method for typing Staphylococcus epidermidis

The discriminatory powers of several techniques for typing Staphylococcus epidermidis were evaluated in an epidemiological study of bacteria isolated from intensive care patients and from neonates. Genomic DNA fingerprinting using BclI restriction endonuclease was an effective epidemiological marker. The distinct restriction fragment profiles produced with this enzyme were highlighted with specific probes in a Southern blot technique. Cloned Escherichia coli rRNA gene probes proved to have lower discriminatory power and be less suitable for intraspecies typing. However, a panel of random genomic Staphylococcus epidermidis DNA clones provided almost the same level of discrimination as the DNA fingerprinting technique and also provided a clearer profile. DNA and gene fingerprinting techniques were reproducible and highly discriminatory compared to typing based on antigen and plasmid profiles, antibiotic susceptibility patterns and biotypes.

Ribotyping of coagulase-negative staphylococci with special emphasis on intraspecific typing of Staphylococcus epidermidis

Coagulase-negative staphylococci (CoNS), particularly Staphylococcus epidermidis, are increasingly being recognized as opportunistic pathogens. They are often multiply antibiotic resistant and can cause nosocomial outbreaks. For clinical and epidemiological reasons, accurate species identification and typing are imperative. Ribotyping, i.e., the generation of characteristic fragment patterns by hybridization of restriction endonuclease fragments of total DNA with labeled standard rRNA from Escherichia coli, has been applied to CoNS for species identification by various investigators. The present study, involving 115 randomly collected clinical isolates of CoNS, provides ambiguous evidence with respect to those findings. Eighty six S. epidermidis strains were ribotyped intraspecifically. Eleven different ribotypes were found after digestion with EcoRI, and 10 were found with HindIII. A combination of the two restriction endonucleases resulted in an increase in the discriminatory power (DP) from 14.3 to 31.6%. A combination of ribotyping with biotyping raised the DP to a maximum of 48.6%. The reproducibility of ribotyping was 100% after greater than 400 generations of growth. No correlation between methicillin resistance and certain ribotypes among the S. epidermidis strains was observed. Ribotyping is considered a useful tool for the intraspecific typing of CoNS for epidemiological purposes. The DP can be increased by the use of additional restriction endonucleases.