Evaluation of the Staph-Zym system with staphylococci isolated from bovine intramammary infections

High-throughput molecular identification of Staphylococcus spp. isolated from a clean room facility in an environmental monitoring program

BACKGROUND

The staphylococci are one of the most common environmental isolates found in clean room facility. Consequently, isolation followed by comprehensive and accurate identification is an essential step in any environmental monitoring program.

FINDINGS

We have used the API Staph identification kit (bioMérieux, France) which depends on the expression of metabolic activities and or morphological features to identify the Staphylococcus isolates. The API staphylococci showed low sensitivity in the identification of some species, so we performed molecular methods based on PCR based fingerprinting of glyceraldehyde-3-phosphate dehydrogenase encoding gene as useful taxonomic tool for examining Staphylococcus isolates.

CONCLUSIONS

Our results showed that PCR protocol used in this study which depends on genotypic features was relatively accurate, rapid, sensitive and superior in the identification of at least 7 species of Staphylococcus than API Staph which depends on phenotypic features.

Identification of Staphylococcus spp. by PCR-restriction fragment length polymorphism of gap gene

Oligonucleotide primers specific for the Staphylococcus aureus gap gene were previously designed to identify 12 Staphylococcus spp. by PCR. In the present study, AluI digestion of PCR-generated products rendered distinctive restriction fragment length polymorphism patterns that allowed 24 Staphylococcus spp. to be identified with high specificity.

Glyceraldehyde-3-phosphate dehydrogenase-encoding gene as a useful taxonomic tool for Staphylococcus spp

The gap gene of Staphylococcus aureus, encoding glyceraldehyde-3-phosphate dehydrogenase, was used as a target to amplify a 933-bp DNA fragment by PCR with a pair of primers 26 and 25 nucleotides in length. PCR products, detected by agarose gel electrophoresis, were also amplified from 12 Staphylococcus spp. analyzed previously. Hybridization with an internal 279-bp DNA fragment probe was positive in all PCR-positive samples. No PCR products were amplified when other gram-positive and gram-negative bacterial genera were analyzed using the same pair of primers. AluI digestion of PCR-generated products gave 12 different restriction fragment length polymorphism (RFLP) patterns, one for each species analyzed. However, we could detect two intraspecies RFLP patterns in Staphylococcus epidermidis, Staphylococcus hominis, and Staphylococcus simulans which were different from the other species. An identical RFLP pattern was observed for 112 S. aureus isolates from humans, cows, and sheep. The sensitivity of the PCR assays was very high, with a detection limit for S. aureus cells of 20 CFU when cells were suspended in saline. PCR amplification of the gap gene has the potential for rapid identification of at least 12 species belonging to the genus Staphylococcus, as it is highly specific.

Rapid identification and typing of Staphylococcus aureus by PCR-restriction fragment length polymorphism analysis of the aroA gene

The Staphylococcus aureus aroA gene, which encodes 5-enolpyruvylshikimate-3-phosphate synthase, was used as a target for the amplification of a 1,153-bp DNA fragment by PCR with a pair of primers of 24 and 19 nucleotides. The PCR products, which were detected by agarose gel electrophoresis, were amplified from all S. aureus strains so far analyzed (reference strains and isolates from cows and sheep with mastitis, as well as 59 isolates from humans involved in four confirmed outbreaks). Hybridization with an internal 536-bp DNA fragment probe was positive for all PCR-positive samples. No PCR products were amplified when other Staphylococcus spp. or genera were analyzed by using the same pair of primers. The detection limit for S. aureus cells was 20 CFU when the cells were suspended in saline; however, the sensitivity of the PCR was lower (5 x 10(2) CFU) when S. aureus cells were suspended in sterilized whole milk. TaqI digestion of the PCR-generated products rendered two different restriction fragment length polymorphism patterns with the cow and sheep strains tested, and these patterns corresponded to the two different patterns obtained by antibiotic susceptibility tests. Analysis of the 59 human isolates by our easy and rapid protocol rendered results similar to those of other assays.

Use of enzyme tests in characterization and identification of aerobic and facultatively anaerobic gram-positive cocci

The contribution of enzyme tests to the accurate and rapid routine identification of gram-positive cocci is introduced. The current taxonomy of the genera of aerobic and facultatively anaerobic cocci based on genotypic and phenotypic characterization is reviewed. The clinical and economic importance of members of these taxa is briefly summarized. Tables summarizing test schemes and kits available for the identification of staphylococci, enterococci, and streptococci on the basis of general requirements, number of tests, number of taxa, test classes, and completion times are discussed. Enzyme tests included in each scheme are compared on the basis of their synthetic moiety. The current understanding of the activity of enzymes important for classification and identification of the major groups, methods of testing, and relevance to the ease and speed of identification are reviewed. Publications describing the use of different identification kits are listed, and overall identification successes and problems are discussed. The relationships between the results of conventional biochemical and rapid enzyme tests are described and considered. The use of synthetic substrates for the detection of glycosidases and peptidases is reviewed, and the advantages of fluorogenic synthetic moieties are discussed. The relevance of enzyme tests to accurate and meaningful rapid routine identification is discussed.

A comparison of methods used in species identification of coagulase-negative staphylococci isolated from the milk of sheep

Thirty reference strains of staphylococci, 76 strains isolated from confirmed cases of subclinical mastitis and 10 strains from the teat tip skin and the mouth of sucking lambs were assigned to species using four biochemical methods. These were the commercially available micromethods API Staph and Staph-Zym; the specialized laboratory method Rosco Set and Reactions in Standard Laboratory Culture Media (SLCM). The Rosco Set assigned species to all the strains, the SLCM to 96.5%, the Staph-zym to 86.1% and the API Staph to 81.4%. API Staph and the SLCM favoured the 'aureus' group with the 'epidermidis' second, while the reverse was true for the other two methods. All the identification methods assigned the same species to only 29% of the tested isolates, causing considerable variation in the number of species identified within each group. This variation indicates that reported species prevalence from cases of ovine mastitis should be viewed with caution.

Evaluation of the Staph-Zym system in the identification of staphylococci isolated from ovine milk and the ewe environment

The Staph-Zym and the Rosco Set methods were used to assign species to 142 strains of staphylococci isolated from the milk of sheep with subclinical intramammary infection or teat skin, mouth of lambs or milking machine teat cups. One hundred eleven of the same strains were also tested by Standard Laboratory Culture Media. The Rosco Set assigned species to all strains tested, but the other two methods were unable to assign species to a similar proportion of isolates. Seventy six (68.5%) of the strains tested with all three methods were not assigned the same species, each method shown a preference for particular species. The Staph-Zym and the Rosco Set identified most of the strains as members of the "epidermidis" group with the "aureus" second, while the reverse was observed with the Standard Laboratory Culture Media. Only in the case of Staphylococcus epidermidis all methods were in close agreement. When the results of the Staph-Zym and the Rosco Set are compared, although they agree on the predominant group, they disagree on the predominant species within the same group.

Staphylococcal and other bacterial species associated with intramammary infections in Danish dairy herds

Four thousand six hundred forty-five quarter milk samples from 1179 cows from 20 commercial dairy herds were examined in order to determine the prevalence of bacterial species. A total of 859 isolates from 839 (18.1%) culture positive samples could be assigned to 34 different species and subspecies. Diagnostics of staphylococcal species was based on conventional procedures able to differentiate between all 36 species and subspecies presently acknowledged. Staphylococcus aureus was found in 10.2% of the samples and was the most common species isolated. Streptococcus dysgalactiae (1.6%) and Streptococcus uberis (1.4%) were the second and third most common species isolated. Seventeen different coagulase negative staphylococcal species (CNS) were found in 4.1% of the samples. The most frequently isolated CNS were S. epidermidis (1.3%), S. chromogenes (1.0%) and S. simulans (0.7%). Isolates of S. aureus were phage typed, and isolates of S. epidermidis were investigated by phage typing, antibiogram typing, and biotyping. A total of 378 (79.9%) isolates of S. aureus could be typed by phages, assigning them to 18 different phage types. However, 6 phage types accounted for 92.1% of the typable isolates. One to 2 phage types predominated within each herd. Eleven (18%) isolates of S. epidermidis could be typed by phages, assigning the isolates to 3 different types. Biotyping of S. epidermidis produced a total of 8 different types, the most common accounting for 29.5% of the isolates. A total of 6 different antibiogram types were observed among all isolates of S. epidermidis. Resistance towards penicillin (36.1%), tetracycline (9.8%) and streptomycin (9.8%), were recorded in the isolates of S. epidermidis. However, 35 (57.4%) of the isolates were susceptible to all 12 antibiotics tested.

Evaluation of Staph ID 32 system and Staph-Zym system for identification of coagulase-negative staphylococci

The purpose of the investigation was to evaluate two commercially available identification systems: a new modification of the Staph-Zym system (Rosco, Tåstrup, Denmark) and the Staph ID 32 API system (API System, BioMérieux, Paris, France). A local standard method to be used in routine laboratories was also evaluated. A total of 200 staphylococcal isolates, including strains from both the American Type Culture Collection and the Czechoslovak Collection of Microorganisms as well as 89 clinical isolates, were used in tests of all three identification systems. The Staph ID 32 API system identified from 50 to 100% of the reference strains and 82.1% of the clinical isolates correctly. The Staph-Zym system identified from 90 to 100% of the reference strains and 82.1% of the clinical isolates correctly. Most misidentifications were of minor importance, but in both systems major failures appeared (Staphylococcus aureus was identified as a coagulase-negative staphylococcus). Both systems needed backup from a reference laboratory to determine if two isolates were of the same strain.

Staphylococcal and other bacterial species associated with intramammary infections in Danish dairy herds

Four thousand six hundred forty-five quarter milk samples from 1179 cows from 20 commercial dairy herds were examined in order to determine the prevalence of bacterial species. A total of 859 isolates from 839 (18.1%) culture positive samples could be assigned to 34 different species and subspecies. Diagnostics of staphylococcal species was based on conventional procedures able to differentiate between all 36 species and subspecies presently acknowledged. Staphylococcus aureus was found in 10.2% of the samples and was the most common species isolated. Streptococcus dysgalactiae (1.6%) and Streptococcus uberis (1.4%) were the second and third most common species isolated. Seventeen different coagulase negative staphylococcal species (CNS) were found in 4.1% of the samples. The most frequently isolated CNS were S. epidermidis (1.3%), S. chromogenes (1.0%) and S. simulans (0.7%). Isolates of S. aureus were phage typed, and isolates of S. epidermidis were investigated by phage typing, antibiogram typing, and biotyping. A total of 378 (79.9%) isolates of S. aureus could be typed by phages, assigning them to 18 different phage types. However, 6 phage types accounted for 92.1% of the typable isolates. One to 2 phage types predominated within each herd. Eleven (18%) isolates of S. epidermidis could be typed by phages, assigning the isolates to 3 different types. Biotyping of S. epidermidis produced a total of 8 different types, the most common accounting for 29.5% of the isolates. A total of 6 different antibiogram types were observed among all isolates of S. epidermidis. Resistance towards penicillin (36.1%), tetracycline (9.8%) and streptomycin (9.8%), were recorded in the isolates of S. epidermidis. However, 35 (57.4%) of the isolates were susceptible to all 12 antibiotics tested.

Comparison of genotypic and phenotypic methods for species identification of coagulase-negative staphylococcal isolates from blood cultures

Coagulase-negative staphylococci are often isolated from blood cultures. Simple methods are needed for correct identification of those species most frequently found. In this study, PCR methods were developed for the identification of S. epidermidis and S. haemolyticus, based on DNA sequences in their 16S rDNA. The results obtained by these methods were compared with those obtained using a number of phenotypic methods, including two commercial kits API Staph and Staphzyme. Fifteen type collection strains and 133 blood culture isolates were tested. The sensitivity of the PCR for identification of S. epidermidis was 99% compared with API Staph, but the specificity was lower, 94%, because of positive results also for S. capitis. The results by the PCR for identification of S. haemolyticus correlated closely with the Staphzyme results, 13 isolates being identified by Staphzyme and 16 by the PCR. API Staph, however, identified only four clinical isolates as S. haemolyticus, probably too few. Among the individual phenotypic tests performed, a trehalose-mannitol agar method and a desferrioxamine disc diffusion test for the identification of S. epidermidis were found to be very accurate. Anaerobic growth after overnight incubation could be used to distinguish S. epidermidis from S. hominis. The conclusion is that a majority of all Gram-positive, catalase-positive and coagulase-negative blood culture isolates can be typed as regards species level using only a few genotypic and/or phenotypic tests.

A simple identification scheme for coagulase negative staphylococci from bovine mastitis

Coagulase-negative staphylococci from cases of bovine mastitis were identified to species level by using an identification scheme based on a three-plate test system which tested for DNase on DNA agar, for protease on calcium caseinate agar, and for the organism's sensitivity to novobiocin, desferrioxaminine (deferoxamine) and fosfomycin by agar diffusion tests. Testing for the inhibition of Staphylococcus delta haemolysin (Skalka 1991) can replace the protease tests.

Identification of veterinary pathogens by use of commercial identification systems and new trends in antimicrobial susceptibility testing of veterinary pathogens

Veterinary diagnostic microbiology is a unique specialty within microbiology. Although isolation and identification techniques are similar to those used for human pathogens, many veterinary pathogens require unique cultivation or identification procedures. Commercial identification systems provide rapid, accurate identification of human pathogens. However, the accuracy of these systems with veterinary pathogens varies widely depending on the bacterial species and the host animal from which it was isolated. Increased numbers of veterinary strains or species in the data bases of the various systems would improve their accuracy. Current procedures and interpretive criteria used for antimicrobial susceptibility testing of veterinary pathogens are based on guidelines used for human pathogens. The validity of these guidelines for use with veterinary pathogens has not been established. As with fastidious human pathogens, standardized methodologies and quality control isolates are needed for tests of organisms such as Actinobacillus pleuropneumoniae and Haemophilus somnus. Furthermore, interpretive criteria for veterinary antimicrobial agents based on the MIC for veterinary pathogens, the pharmacokinetics of the antimicrobial agent in the host animal, and in vivo efficacy of the antimicrobial agent are needed. This article reviews both the commercial identification systems evaluated with veterinary pathogens and current methods for performing and interpreting antimicrobial susceptibility tests with veterinary pathogens. Recommendations for future improvements in both areas are discussed.

Detecting methicillin-resistant Staphylococcus epidermidis--disc diffusion, broth breakpoint or polymerase chain reaction?

Growth conditions are important for the expression of resistance to methicillin among staphylococci. Consequently a phenotypic susceptibility test has to be chosen carefully to avoid false susceptible results. In this study we wanted to devise rapid and simple phenotypic tests whose results completely correlate with the presence of the methicillin resistance gene, mecA. A simplified polymerase chain reaction (PCR) method not needing separate DNA extraction from the tested bacteria was used to amplify a 449 bp region of the mecA gene. One hundred and ten strains of S. epidermidis were tested. The results were in complete agreement with those from a broth tube breakpoint test, known to identify more strains as resistant than does the method recommended by NCCLS. In disc diffusion test it was possible to clearly distinguish resistant from susceptible strains by using discs containing oxacillin, cephalexin and cephradine. A 5 micrograms cephradine disc was further analysed by testing another 441 consecutive clinical isolates of staphylococci. All resistant coagulase-negative staphylococci grew out to the edge of this disc, whereas susceptible strains showed an inhibition zone at least 10 mm in diameter. The 5 micrograms cephradine disc is recommended for routine work. The PCR method and broth tube breakpoint test are both reliable reference methods.

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.