Evaluation of restriction endonuclease fingerprinting of chromosomal DNA and plasmid profile analysis for characterization of multiresistant coagulase-negative staphylococci in bacteremic neonates

Investigation of an outbreak of methicillin-resistant Staphylococcus aureus in patients with skin disease using DNA restriction patterns

OBJECTIVE

To investigate an outbreak of methicillin-resistant Staphylococcus aureus (MRSA) among patients using chromosomal typing of the isolates.

DESIGN

Comparison of epidemiological and clinical data to endonuclease restriction fragmentation analysis (RFA) of the MRSA isolates associated with an outbreak. Total DNA from the MRSA isolates was restricted with HINDIII and HAEIII for typing.

SETTING

Tertiary care academic medical center.

METHODS

An epidemiological investigation of an outbreak of MRSA among patients in private rooms was evaluated by routine infection control methods. The MRSA isolates from blood cultures of 7 patients and the nares of a nurse were collected during the outbreak. MRSA isolates from 23 patients not associated with the outbreak also were collected. The total DNA of the MRSA isolates were restricted with HINDIII and HAEIII and electrophoresed on 0.6% agarose gels.

RESULTS

MRSA from 4 of the 7 bacteremic patients and the nurse on the outbreak unit had the same endonuclease restriction pattern. The patients were linked in that they were compromised by severe psoriasis or skin ulcers, were on the unit during the same period, and had oatmeal baths in a common bathtub. Of 50 staff members screened, the nurse was the only person detected as colonized by the strain. The other 3 patients on the unit as well as the 23 patients in other locations not associated with the outbreak had MRSA isolates with different RFA patterns. The use of the bathtub was discontinued and further transmission of MRSA was stopped.

CONCLUSIONS

A comparison of the relatedness of MRSA by RFA demonstrated the uniqueness of the epidemiologically linked isolates and the utility of the RFA technique in the performance of routine infection control investigations.

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.

The utility of restriction endonuclease analysis and phage typing in the epidemiologic investigation of a Staphylococcus aureus outbreak in a neonatal nursery

Outbreaks of Staphylococcus aureus infections in neonatal units require prompt investigation and implementation of control measures. From January to March 1990, a marked increase in the number of S. aureus infections was observed in a neonatal nursery. Twenty-seven S. aureus isolates from 23 patients were analyzed by phage typing and restriction endonuclease analysis (REA). Only nine strains were differentiated by phage type. However, REA with HindIII, CfoI, and ClaI differentiated 20 strains. The REA results indicated that the outbreak was due to several different S. aureus strains and did not represent transmission of a single epidemic strain. REA may enable more accurate determination of the presence or absence of an epidemic strain during an outbreak than would traditional methods such as phage typing.

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.

Comparison of blood cultures with corresponding venipuncture site cultures of specimens from hospitalized premature neonates

We compared the presence and identities of isolates from blood culture samples obtained by percutaneous venipuncture with those of commensal skin organisms cultured from respective venipuncture sites after skin cleansing; 677 blood and skin site culture pairs from 488 infants were compared. Organisms grew in 58 blood cultures; nine of these cultures had corresponding venipuncture site cultures that also grew organisms. Forty-two blood culture isolates were coagulase-negative staphylococci; five of these were associated with similar venipuncture site cultures. According to restriction-endonuclease fingerprinting of chromosomal DNA and plasmid analysis, three pairs of blood and venipuncture site cultures were identical and two pairs were different. Thus only 7% (3/42) of coagulase-negative staphylococcal blood isolates were associated with identical contamination at the venipuncture site. We conclude that, if the venipuncture site has been carefully cleansed, the growth of coagulase-negative staphylococci in blood cultures of specimens from premature neonates indicates bacteremia rather than skin contamination in the vast majority of cases.

Molecular relatedness of Staphylococcus epidermidis isolates obtained during a platelet transfusion-associated episode of sepsis

Staphylococcus epidermidis was isolated from the blood of a 25-year-old pregnant woman following the administration of eight units of platelets. She had developed chills and a fever of 41.4 degrees C soon after the transfusions were completed. S. epidermidis was also obtained from all eight platelet units, as well as from the packed-erythrocyte unit associated with the first unit of platelets. The isolation of the same organism from these epidemiologically related sources provided us with the opportunity to phenotypically and genetically characterize the isolates. Several typing methods, including four molecular techniques, were used to increase our chances of finding any differences between the isolates under investigation. Phenotypic analyses demonstrated that S. epidermidis isolates from the patient, platelet units, and erythrocyte unit reacted in exactly the same manner in 15 biochemical tests, exhibited slime production, and had the same antibiotic susceptibility pattern. Genetic analyses, which included plasmid profiles, plasmid cross-hybridization, field inversion gel electrophoresis, and ribotyping, substantiated the relationships between the S. epidermidis isolates from the patient, platelet units, and erythrocyte unit. Eight S. epidermidis control strains unrelated to the case were found to differ significantly from the platelet-related strain.

Antigenic and genetic homogeneity of Streptococcus uberis strains from the bovine udder

DNA- fingerprints (Hind III) of Streptococcus uberis field isolates from New York State and Europe showed substantial homogeneity, but were different to those of the type strain of the newly proposed psychrophilic species S. parauberis. S. uberis strains had major SDS-heat extracted antigens of molecular masses (Mr) less than 14, 40-41, 42-43, 59-61, 80-86 and 118-122 kDa following immunoblotting with rabbit hyperimmune sera. Bovine sera and milk reacted with the 40-41 and 118-122 kDa antigens. Variations in the Mr of particular bands were too unevenly distributed to permit formation of subgroups. Although cross reactive, the sizes of the antigens of S. parauberis strain NCDO 2020 were substantially different to those of S. uberis, the most prominent antigen having a Mr of 50 kDa. The antigenic and genetic data therefore strongly support the introduction of S. parauberis as a distinct species. S. uberis strains reacted with antiserum to Lancefield groups B, E, G and P, their grouping reactions showing no correlation with DNA and immunoblot fingerprints. Lancefield grouping of S. uberis therefore appears to have little value in identification.

Molecular epidemiology of Staphylococcus haemolyticus strains isolated in an Albanian hospital

A recent outbreak of erythroderma in young children in an Albanian hospital was investigated. The etiology was not established, but Staphylococcus haemolyticus was frequently isolated from the affected children and from staff working in the same unit. Possible relationships among the isolates were investigated by using classical techniques (biotype, antimicrobial susceptibility, and extrachromosomal DNA pattern) and by restriction endonuclease analysis (REA) of total DNA. Control isolates of proven pathogenicity from hospitalized patients in Lyon, France were subjected to the same procedures. Distinct REA patterns were obtained after digestion with two enzymes in 7 of 10 isolates from five affected children. Six distinct patterns were observed in nine isolates from six staff members; two REA patterns from patient isolates and two from staff members were identical, and these were distinguishable by the other markers examined. Only two different REA patterns were found in the pathogenic control isolates despite the use of a third additional enzyme. Again, the isolates with the same REA patterns could be distinguished by their plasmid profile or antimicrobial resistance profile. REA of total DNA used in combination with other markers indicated that the Albanian isolates differed considerably, whereas the French pathogenic isolates showed little variability.

DNA fingerprinting of isolates of Staphylococcus aureus from newborns and their contacts

During a study on the epidemiology of Staphylococcus aureus colonization in newborns, mothers, and hospital staff, S. aureus was isolated from 536 of 1,945 specimens. Ninety-three isolates of S. aureus from the three groups of individuals were included in a study to evaluate the potential of DNA fingerprinting for strain differentiation. The 93 isolates were also phage typed and their plasmid profiles were analyzed. Cleavage of DNA with BamHI resulted in 13 different DNA restriction endonuclease band patterns (DNA REBPs), one of which consisted of eight isolates whose DNA was not cleaved with BamHI. The DNAs from these eight isolates were easily cleaved with HindIII. The different DNA REBPs were stable both during in vitro and in vivo growth and allowed strain differentiation within phage groups or types. We could not show any strong association between DNA REBP classes, phage types or groups, and plasmid profiles. Of the 93 isolates, 27 (29.0%) could not be phage typed and 12 (12.9%) lacked plasmids. We therefore conclude that DNA fingerprinting is a powerful tool, in addition to phage typing and plasmid profile analysis, for strain differentiation of S. aureus.

Evaluation of coagulase-negative staphylococci in blood cultures. A prospective clinical and microbiological study

Coagulase-negative staphylococci (CNS) are the commonest microorganisms in blood cultures, and sorting out patients with CNS septicemia from sample contamination a persistent problem. We prospectively evaluated 73 patients with CNS-positive blood cultures during 1 year and analysed the corresponding 122 isolates in order to determine the rate of septicemia and define the role of microbiological markers of identity such as plasmid profile for that purpose. Three patients had true septicemia, all of them with implanted foreign devices. The plasmid analysis, being the most reliable identity marker, had its greatest implication in reducing the intermediate group of patients clinically suspected of septicemia from 12 to 4. Strict clinical criteria and serial blood cultures are most important in sorting out patients with CNS septicemia from cases of sample contamination. In high risk patients--critically ill with implanted foreign devices--plasmid analysis or other reliable markers of identity are of great additional value.

Epidemiologic and clinical utility of typing systems for differentiating among strains of methicillin-resistant Staphylococcus aureus

Typing systems for differentiating among strains of methicillin-resistant Staphylococcus aureus (MRSA) can be valuable tools for the epidemiologist and the clinician. Specific criteria for evaluating such systems are typeability, reproducibility, and discriminatory power. An ideal typing system also would be rapid, inexpensive, technically simple, and readily available. Systems based on the detection of phenotypic variations include antimicrobial susceptibility testing, bacteriophage typing, multilocus enzyme electrophoresis, and electrophoretic methods such as protein electrophoresis and immunoblotting. Systems that directly detect genotypic variations include plasmid profile analysis, restriction enzyme analysis of plasmid DNA, restriction enzyme analysis of chromosomal DNA, Southern blot analysis of specific restriction fragment length polymorphisms, and pulse field gel electrophoresis. In general, the more widely available typing systems based on phenotypic assays and plasmid analysis have limitations in typeability and/or discriminatory power. The chromosomal DNA-based techniques, although promising, are unproven approaches still under active investigation.

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

Ribotyping consists of restriction endonuclease fingerprinting of ribosomal RNA (rRNA) genes visualized by Southern hybridization with an rRNA probe. This method was developed and compared with restriction endonuclease fingerprinting of chromosomal DNA for typing coagulase-negative staphylococci. Twenty-five American Type Culture Collection reference type strains and 53 clinical isolates were typed. Both methods clearly distinguished all 15 species of coagulase-negative staphylococci and most individual strains within each species. Except in the case of Staphylococcus warneri, ribotyping was most discriminating with the use of ClaI, one of eight endonucleases tested. HpaI and AvaI were more specific than ClaI for discrimination between strains of Staphylococcus warneri. The patterns produced by ribotyping were much simpler and thus easier to interpret than corresponding chromosomal fingerprints. However, ribotyping was slightly less discriminating. It is concluded that ribotyping offers an alternative method for molecular typing of coagulase-negative staphylococci. The application of both methods needs to be further evaluated in the clinical setting.