Molecular techniques open up new vistas for typing of coagulase-negative staphylococci

Simplified and reliable scheme for species-level identification of Staphylococcus clinical isolates

Reliable and rapid identification of staphylococcal strains continues to be a problem faced by many microbiology laboratories. This study evaluates a simplified method that uses a flowchart to assist in the identification of 12 clinical species of Staphylococcus, including eight subspecies. A total of 198 isolates and 11 control strains were identified by the reference method, which employed 22 tests. The results were compared with those obtained by two other methods: an automated system (MicroScan WalkAway) and a simplified method composed of nine tests. The simplified scheme showed an accuracy of 98.5%, while the automated method showed an accuracy of 79.3% (P < 0.001), in identifying staphylococcal species. Atypical phenotypic profiles were detected by both the reference (55.6%) and the simplified (19.7%) methods. The simplified method proposed here was shown to be reliable, with the advantage of being more practical and economic than the reference method.

Acute postoperative endophthalmitis caused by Staphylococcus lugdunensis

Acute postoperative endophthalmitis caused by Staphylococcus lugdunensis is infrequently reported in clinical studies. Five cases of acute postcataract surgery endophthalmitis caused by S. lugdunensis were taken from a multicenter prospective study conducted in four university-affiliated hospitals in France (2004 to 2005). These cases were characterized by severe ocular inflammation occurring with a mean delay of 7.6 days after cataract surgery, severe visual loss (hand motions or less in three cases), and dense infiltration of the vitreous. Each of these patients was initially treated by using a standard protocol with intravitreal (vancomycin and ceftazidime), systemic, and topical antibiotics. Given the severity of the endophthalmitis, even though bacteria were sensitive to intravitreal antibiotics, pars plana vitrectomy was needed in four cases. The final visual prognosis was complicated by severe retinal detachment in three cases. The microbiological diagnosis was reached by using conventional cultures with specific biochemical tests and eubacterial PCR amplification followed by direct sequencing.

Occurance of Staphylococcus nepalensis strains in different sources including human clinical material

Five isolates of coagulase-negative staphylococci were obtained from human urine, the gastrointestinal tract of squirrel monkeys, pig skin and from the environment. All key biochemical characteristics of the tested strains corresponded with the description of Staphylococcus xylosus species. However, partial 16S rRNA gene sequences obtained from analysed strains corresponded with those of Staphylococcus nepalensis reference strains, except for two strains which differed in one residue. Ribotyping with EcoRI and HindIII restriction enzymes, whole cell protein profile analysis performed by SDS-PAGE and SmaI macrorestriction analysis were used for more precise characterization and identification of the analysed strains. Obtained results showed that EcoRI and HindIII ribotyping and whole cell protein fingerprinting are suitable and reliable methods for the differentiation of S. nepalensis strains from the other novobiocin resistant staphylococci, whereas macrorestriction analysis was found to be a good tool for strain typing. The isolation of S. nepalensis is sporadic, and according to our best knowledge this study is the first report of the occurrence of this species in human clinical material as well as in other sources.

Staphylococcus equorum and Staphylococcus succinus isolated from human clinical specimens

A polyphasic identification approach was applied to a group of 11 novobiocin-resistant staphylococci isolated from human clinical materials. Phenotypic characteristics obtained by both commercial and conventional tests assigned eight strains as Staphylococcus xylosus and three strains as ambiguous S. xylosus/Staphylococcus equorum. In contrast to biotyping, ribotyping with EcoRI and HindIII restriction endonucleases and whole-cell protein fingerprinting assigned six analysed strains as S. equorum, and five strains as Staphylococcus succinus. Confirmation of the identification was done by partial 16S rRNA gene sequencing and S. equorum isolates were verified by a PCR assay targeting the sodA gene. From the data it has been implied that ribotyping and whole-cell protein analysis can be used to differentiate between the biochemically almost indistinguishable species S. xylosus, S. equorum and S. succinus. The present study confirms what is believed to be the first occurrence of S. equorum in a relevant human clinical material in the Czech Republic and describes what is believed to be the first-ever isolation of S. succinus from human clinical material.

Identification and molecular characterization of mannitol salt positive, coagulase-negative staphylococci from nasal samples of medical personnel and students

The identification of mannitol salt positive, coagulase-negative staphylococci (CNS) is often disregarded when Staphylococcus aureus is screened in clinical samples using mannitol salt agar. However, the emergence of CNS as important human pathogens has indicated that reliable methods for the identification of clinically significant CNS are of great importance in understanding the epidemiology of infections caused by them. The identification and molecular characterization of mannitol salt positive CNS from nasal samples of medical personnel and students is reported here. A total of 84 mannitol salt positive staphylococcal isolates were obtained from 240 nasal samples, of which 15 were CNS. The API STAPH system classified the CNS isolates into six species, and one-third of the isolates were identified with confidence levels of <80 %. 16S-23S rRNA intergenic spacer length polymorphism analysis (ITS-PCR) identified only two species (Staphylococcus haemolyticus and Staphylococcus saprophyticus). This identification was confirmed by antibiotyping, species-specific PCR and PFGE. The results from this study indicate that ITS-PCR is a potentially useful and reliable tool, enabling hospital laboratories to obtain rapid, full and accurate identification of CNS at the species level.

The investigation of Staphylococcus aureus and coagulase-negative staphylococci nasal carriage among patients undergoing haemodialysis

The frequency of nasal staphylococcal colonization among haemodialysed patients was investigated. The swabs were collected in 1998 and 2004 from 28 and 43 patients, respectively. Staphylococcus aureus colonization rates were 57.1% and 27.9% in 1998 and 2004, respectively. Twenty-six coagulase-negative staphylococci (CNS) isolates were cultured: S. epidermidis (21), S. lugdunensis (2), single S. haemolyticus, S. warneri, and S. capitits isolates. One S. aureus and 10 CNS isolates were methicillin resistant. The methicillin-resistant S. aureus (MRSA) was resistant to beta-lactams, tetracycline, and harbored the pvl gene encoding the Panton-Valentine leukocidin. The decrease in S. aureus colonization at 6-year interval was observed. The presence of the pvl gene and a favorable antibiotic susceptibility pattern of the MRSA suggest that the isolate was a member of community-acquired MRSA (CA-MRSA). Concluding, screening of haemodialysed patients for staphylococcal colonization accompanied by characterization of cultured isolates is important to understand its epidemiology and to develop infection prevention measures and treatment strategies.

RAPD for the typing of coagulase-negative staphylococci implicated in catheter-related bloodstream infection

OBJECTIVES

A rapid random amplification of polymorphic DNA (RAPD) technique was developed to distinguish between strains of coagulase-negative staphylococci (CoNS) involved in central venous catheter (CVC)-related bloodstream infection. Its performance was compared with that of pulsed-field gel electrophoresis (PFGE).

METHODS

Patients at the University Hospital Birmingham NHS Foundation Trust, U.K. who underwent stem cell transplantation and were diagnosed with CVC-related bloodstream infection due to CoNS whilst on the bone marrow transplant unit were studied. Isolates of CoNS were genotyped by PFGE and RAPD, the latter employing a single primer and a simple DNA extraction method.

RESULTS

Both RAPD and PFGE were highly discriminatory (Simpson's diversity index, 0.96 and 0.99, respectively). Within the 49 isolates obtained from blood cultures of 33 patients, 20 distinct strains were identified by PFGE and 25 by RAPD. Of the 25 strains identified by RAPD, nine clusters of CoNS contained isolates from multiple patients, suggesting limited nosocomial spread. However, there was no significant association between time of inpatient stay and infection due to any particular strain.

CONCLUSION

The RAPD technique presented allows CoNS strains to be genotyped with high discrimination within 4h, facilitating real-time epidemiological investigations. In this study, no single strain of CoNS was associated with a significant number of CVC-related bloodstream infections.

Rapid and reliable identification of Staphylococcus equorum by a species-specific PCR assay targeting the sodA gene

Rapid and reliable identification of Staphylococcus (S.) equorum was achieved by species-specific PCR assays. A set of primers targeting the manganese-dependent superoxide dismutase (sodA) gene of S. equorum was designed. Species-specificity of the primer set was evaluated by using a total of 112 strains (including 27 reference strains of the DSM collection), representing 26 different species of the genus Staphylococcus, 3 species of the genus Kocuria, and different strains of Macrococcus caseolyticus. By using primers SdAEqF and SdAEqR the expected PCR fragment was obtained only when DNA from S. equorum strains was used as template. The rapidity (about 4 h from DNA isolation to results) and reliability of the PCR procedures established suggests that the method may be profitably applied for specific detection and identification of S. equorum strains.

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.

Ribotyping and a study of transmission of Staphylococcus aureus collected from food preparation facilities

Food poisoning from Staphylococcus aureus is sometimes caused by improper handling of food items in food preparation facilities. Prevention of contamination by employees is particularly important in facilities where a significant amount of food preparation is performed by hand. Some experiments have been performed to describe bacterial cross-contamination in the food preparation process, but there have been few studies of cross-contamination in actual food preparation facilities. Aiming to shed light on the transmission of S. aureus in food preparation facilities, this study collected samples of 66 strains of this bacterium from the fingers of food preparation staff, foodstuffs, prepared foods, cooking utensils, and cooking equipment and typed them with the ribotyping method. S. aureus from the same ribogroup was detected on the hands of a study participant, a faucet, knife, frying pan, and a salad, indicating that bacteria found on the hands of the study participant was transmitted to cooking utensils and prepared foods. Transmission (from a faucet to a frying pan handle) of bacteria by another person, a third party, was also detected.

Design and evaluation of specific PCR primers for rapid and reliable identification of Staphylococcus xylosus strains isolated from dry fermented sausages

Rapid and reliable identification of Staphylococcus xylosus was achieved by species-specific PCR assays. Two sets of primers, targeting on xylulokinase (xylB) and 60 kDa heat-shock protein (hsp60) genes of S. xylosus, respectively, were designed. Species-specificity of both sets of primers was evaluated by using 27 reference strains of the DSM collection, representing 23 different species of the Staphylococcus genus and 3 species of the Kocuria genus. Moreover, 90 wild strains isolated from different fermented dry sausages were included in the analysis. By using primers xylB-F and xylB-R the expected PCR fragment was obtained only when DNA from S. xylosus was used. By contrast, amplification performed by using primers xylHs-F and xylHs-R produced a single PCR fragment, of the expected length, when DNA from S. xylosus, S. haemolyticus, S. intermedius and S. kloosii were used as template. Nevertheless, AluI digestion of the xylHs-F/xylHs-R PCR fragment allowed a clear differentiation of these 4 species. The rapidity (about 4 h from DNA isolation to results) and reliability of the PCR procedures established suggests that the method may be profitably applied for specific detection and identification of S. xylosus strains.

Combining Denaturing Gradient Gel Electrophoresis of 16S rDNA V3 Region and 16S–23S rDNA Spacer Region Polymorphism Analyses for the Identification of Staphylococci from Italian Fermented Sausages

Separation of amplified V3 region from 16S rDNA by denaturing gradient gel electrophoresis (PCR-DGGE) and 16S-23S rDNA intergenic spacer region polymorphism (ISR-PCR) analyses were tested as tool for differentiation of staphylococcal strains commonly isolated from fermented sausages. Variable V3 regions of 25 staphylococcal reference strains and 96 wild strains of species belonging to the genera Staphylococcus, Micrococcus and Kocuria were analyzed. PCR-DGGE profiles obtained were species-specific for S. sciuri, S. haemolyticus, S. hominis, S. auricularis, S. condimenti, S. kloosi, S. vitulus, S. succinus, S. pasteuri, S. capitis and S. (Macrococcus) caseolyticus. Moreover, 7 groups could be distinguished gathering the remaining species as result of the separation of the V3 rDNA amplicons in DGGE. Furthermore, the combination of the results obtained by PCR-DGGE and ISR-PCR analyses allowed a clear differentiation of all the staphylococcal species analysed, with exception of the pairs S. equorum-S. cohnii and S. carnosus-S. schleiferi. The suitability of both molecular techniques and of the combination their results for the identification of staphylococci was validated analysing partial nucleotide sequence of the 16S rDNA of a representative number of wild strains.