Numerical analysis of electrophoretic protein patterns of methicillin-resistant strains of Staphylococcus aureus

Bacterial Whole Cell Protein Profiling: Methodology, Applications and Constraints

Background:

In the era of modern microbiology, several methods are available for identification and typing of bacteria, including whole genome sequencing. However, in microbiological laboratories or hospitals where genomic based molecular typing methods and/or trained manpower are unavailable, whole cell protein profiling using sodium dodecyl sulfate polyacrylamide gel electrophoresis might be a useful alternative/supplementary method for bacterial identification, strain typing and epidemiology. Whole cell protein profiling by SDS-PAGE is based on the principle that under standard growth conditions, a bacterial strain expresses the same set of proteins, the pattern of which can be used for bacterial identification.

Objective:

The objective of this review is to assess the current status of whole cell protein profiling by SDS-PAGE and its advantages and constraints for bacterial identification and typing.

Results and Conclusions:

Several earlier and recent studies prove the potential and utility of this technique as an adjunct or supplementary method for bacterial identification, strain typing and epidemiology. There is no denying the fact that utility of this technique as an adjunct or supplementary method for bacterial identification and typing has already been demonstrated and its practical applications need to be evaluated further.

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 eletrophoresis 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.

SDS-PAGE and Gel IEF: Tool for Differentiation of Methicillin-Resistant and Methicillin-Sensitive Strains of Staphylococcus aureus

The methicillin-resistant Staphylococcus aureus causes difficult-to-treat healthcare-associated infections in humans. For fast and effective selection of an appropriate antibiotic therapy, it is essential to have rapid and reliable methods for differentiation of methicillin-resistant S. aureus from less dangerous methicillin-sensitive S. aureus. There have been many methods for the identification of methicillin-resistant S. aureus described but none has been accepted as an international standard. The most commonly used techniques such as phenotyping and genotyping have a few disadvantages, for instance, these techniques are not reproducible and stable. In addition, they are time-consuming, expensive, and they are not capable to distinguish all S. aureus strains. In this study, the methicillin-resistant and methicillin-sensitive S. aureus isolates obtained from patients were extracted in hot water. The released proteins were characterised by sodium dodecyl sulphate polyacrylamide gel electrophoresis and gel isoelectric focusing. These two methods were able to differentiate among tested bacterial strains. The proposed methods are time saving, they are applicable in standard biochemical laboratories, and they do not require any expensive equipment.

Methicillin-resistant Staphylococcal aureus evolution in Australia over 35 years

Australia has a long association methicillin-resistant Staphylococcus aureus (MRSA). Its unique geographic and demographic features have led to the emergence and spread of three types of MRSA over 35 years. Classical multiresistant hospital-acquired MRSA were first noted in Australia in 1965. By the end of the 1970s, strains of this type of MRSA were well established in the complex tertiary care hospitals in the capital cities on the eastern seaboard of mainland Australia. Characterized by resistance to beta-lactams, erythromycin, tetracycline, gentamicin, and trimethoprim-sulfamethoxazole, these strains have persisted and diversified genetically and have acquired a variety of new resistances. They have proven pathogenicity and are a prominent cause of hospital infection in the endemic institutions. More recently they have become endemic in some central state tertiary care hospitals. Community-acquired strains of MRSA first appeared in the north of Western Australia in the mid-1980s. Strains have subsequently appeared in the south of the state and in the two adjacent central states, and are more frequently isolated from Aboriginal patients. Although harboring few or no additional resistances apart from resistance to beta-lactams initially, these strains are also accumulating additional resistances. A different variety of community-acquired MRSA has recently been noted in eastern Australia. It has a similar antibiogram to the western strains, but an entirely different epidemiology, resembling that currently being experienced in parts of New Zealand, and associated with patients of south Pacific island origin.

Molecular epidemiology of methicillin-resistant Staphylococcus aureus strains: state of affairs and tomorrow' s possibilities

Methicillin-resistant strains of Staphylococcus aureus (MRSA) have posed a clinical threat for nearly 40 years. During these years, an array of additional technologies suited for identification of MRSA below the species level has become available. The technologies, whether they assess phenotype or genotype, provide data that can be used for elucidation of the routes of dissemination of individual MRSA types. This review summarizes the current state of affairs with respect to the quality of the various laboratory techniques and includes descriptions of novel strategies such as binary typing and multilocus sequence typing (MLST). Drawbacks of procedures will be compared, and the value of molecular typing in the elucidation of complex biological phenomena, such as epidemicity, carriage, and reduced vancomycin susceptibility, will be indicated. Means for integrated assessment of bacterial biology, epidemiology, and population structure will be discussed.

Methicillin-resistant Staphylococcus aureus typing methods: which should be the international standard?

Methicillin-resistant Staphylococcus aureus (MRSA) has spread to all parts of the world. Effective control measures are dependent on a thorough knowledge of the organism's epidemiology which requires a typing technique that can be universally applied. Many typing methods have been developed for MRSA but none has been adopted as the internationally recognized standard. This review summarizes the information available on each in order to assess their suitability as a reference procedure. The majority of phenotypic and genotypic techniques are not sufficiently discriminatory, reproducible, stable or useful in an outbreak to be acceptable. The methods which do fulfil these requirements and have a potential for standardization, such as pulsed-field gel electrophoresis, binary typing or a combination of more rapid techniques, require further systematic evaluation.

Phylogenetic analysis of macrorestriction fragments as a measure of genetic relatedness in Staphylococcus aureus: the epidemiological impact of methicillin resistance

The present study was undertaken for the purpose of defining the epidemiology and genetic relatedness of Staphylococcus aureus strains in a region of Italy by investigating the molecular background for which resistance to methicillin, mediated by the acquisition of another penicillin-binding protein gene, is embedded. Restriction fragment length polymorphism (RFLP) data were used for phylogenetic analyses, since genetic distance values can be used as a general measure of the number of events generating distinct clones. The percentages of methicillin-resistant S. aureus (MRSA) isolates in a six-month period from inpatients and outpatients were, respectively, 12% (22 out of 180) and 0.4% (1 out of 257). On the basis of RFLP obtained after pulsed field gel electrophoresis (PFGE), it was possible to designate isolates as indistinguishable, closely related, possibly related and unrelated. We were able to demonstrate the occurrence of at least five distinct MRSA cross-infection episodes in two hospitals, four involving two patients each and one involving four patients. Phylogenetic analyses overcame the simple pairwise comparison of common bands between strains, and provided a comprehensive epidemiological scenario, identifying three major clusters of MRSA, including different levels of genetic relatedness, while excluding the circulation of a single clone in Italy. Moreover, multidimensional scaling analysis of the obtained genetic distance confirmed that MRSA strains belong to a restricted set of clones, thus demonstrating the relatedness of broad evolutionary lineages within the species S. aureus.

Phenotypic and genotypic characterization of nosocomial Staphylococcus aureus isolates from trauma patients

Staphylococcus aureus is a major cause of nosocomial infections. During the period from March 1992 to March 1994, the patients admitted to the intensive care unit of the University of Maryland Shock Trauma Center were monitored for the development of S. aureus infections. Among the 776 patients eligible for the study, 60 (7.7%) patients developed 65 incidents of nosocomial S. aureus infections. Of the clinical isolates, 43.1% possessed a polysaccharide type 5 capsule, 44.6% possessed a type 8 capsule, and the remaining 12.3% had capsules that were not typed by the type 5 or type 8 antibodies. Six antibiogram types were noted among the infection-related isolates, with the majority of the types being resistant only to penicillin and ampicillin. It was noted that the majority of cases of pneumonia were caused by relatively susceptible strains, while resistant strains were isolated from patients with bacteremia and other infections. Only 16 (6.3%) of the isolates were found to be methicillin-resistant S. aureus (MRSA). DNA fingerprinting by pulsed-field gel electrophoresis showed 36 different patterns, with characteristic patterns being found for MRSA strains and the strains with different capsular types. Clonal relationships were established, and the origins of the infection-related isolates in each patient were determined. We conclude that (i) nosocomial infection-related isolates from the shock trauma patients did not belong to a single clone, although the predominance of a methicillin-resistant genotype was noted, (ii) most infection-related S. aureus isolates were relatively susceptible to antibiotics, but a MRSA strain was endemic, and (iii) for practical purposes, the combination of the results of capsular and antibiogram typing can be used as a useful epidemiological marker.

Epidemiology of methicillin-resistant Staphylococcus aureus in a Warsaw hospital

Methicillin-resistant Staphylococcus aureus (MRSA) isolates were collected during two eight-month periods in 1991 and 1994, respectively. In order to study the epidemiology, all 74 strains were characterized by phage-typing, antibiotic resistance patterns and DNA-restriction map after cleavage with SmaI enzyme, and pulsed-filed gel electrophoresis (PFGE). These investigations confirmed that MRSA in the hospital, 1991 and 1994, was not due to the spread of one or two clones, but by the simultaneous occurrence of a few well characterized strains and sporadic, occurring strains of different phage-types. Some of these might have developed from the more commonly occurring strains. Isolates from 1994 were more resistant to antibiotics in vitro, than the 1991 isolates. The typing results also indicated that whilst most of the MRSA strains in 1994 were different compared with those of 1991, some of the strains might have been present in both years. The PFGE-typing was more discriminatory and gave a higher typability than the phage-typing, especially among the multiply resistant isolates of MRSA from 1994. Among the less resistant strains the phage-typability was high and with only few exceptions, there was a good correlation between PFGE-type and phage-type.

Quantitative Antibiogram as a Typing Method for the Prospective Epidemiological Surveillance and Control of MRSA Comparison with Molecular Typing

Objective:

Evaluation of the quantitative antibiogram as an epidemiological tool for the prospective typing of methicillin-resistantStaphylococcus aureus(MRSA), and comparison with ribotyping.

Methods:

The method is based on the multivariate analysis of inhibition zone diameters of antibiotics in disk diffusion tests. Five antibiotics were used (erythromycin, clindamycin, cotrimoxazole, gentamicin, and ciprofloxacin). Ribotyping was performed using seven restriction enzymes (EcoRV,HindIII,KpnI,PstI,EcoRI,SfuI, andBamHI).

Setting:

1,000-bed tertiary university medical center.

Results:

During a 1-year period, 31 patients were found to be infected or colonized with MRSA. Cluster analysis of antibiogram data showed nine distinct antibiotypes. Four antibiotypes were isolated from multiple patients (2, 4, 7, and 13, respectively). Five additional antibiotypes were isolated from the remaining five patients. When analyzed with respect to the epidemiological data, the method was found to be equivalent to ribotyping.

Among 206 staff members who were screened, six were carriers of MRSA. Both typing methods identified concordant of MRSA types in staff members and in the patients under their care.

Conclusions:

The quantitative antibiogram was found to be equivalent to ribotyping as an epidemiological tool for typing of MRSA in our setting. Thus, this simple, rapid, and readily available method appears to be suitable for the prospective surveillance and control of MRSA for hospitals that do not have molecular typing facilities and in which MRSA isolates are not uniformly resistant or susceptible to the antibiotics tested.

Comparison of DNA fingerprinting by PFGE and PCR-RFLP of the coagulase gene to distinguish MRSA isolates

Staphylococcus aureus isolates were collected from epidemiologically unrelated clinical sources in Japan between 1991 and 1993. A total of 40 isolates, five each of eight coagulase types, were analysed by polymerase chain reaction (PCR) of the coagulase gene, PCR-restriction fragment length polymorphism (RFLP) after AluI digestion, and pulsed-field gel electrophoresis (PFGE) of chromosomal DNA after SmaI digestion. The efficiency of discrimination among the isolates increased in the order of PCR < PCR-RFLP < PFGE, yielding five, 13 and 31 different types, respectively. To assess the clinical use of these methods, 42 additional methicillin-resistant S. aureus (MRSA) isolates collected from 27 inpatients in a hospital were analysed. PFGE and PCR-RFLP were able to discriminate 11 and four types, respectively. PFGE analysis detected cross-infection between four postoperative patients in an intensive-care unit, and in six neonates in intensive care. We conclude that of the three methods tested, PFGE analysis currently allows the most effective discrimination of MRSA strains.

Analysis of methicillin-resistant and methicillin-susceptible Staphylococcus aureus by a molecular typing method based on coagulase gene polymorphisms

A molecular typing method for Staphylococcus aureus based on coagulase gene polymorphisms (coagulase gene typing) was evaluated by examining a total of 240 isolates which comprised 210 methicillin-resistant S. aureus (MRSA) and 30 methicillin-susceptible S. aureus (MSSA) collected from a single hospital. By AluI restriction enzyme digestion of the PCR-amplified 3'-end region of the coagulase gene including 81-bp repeated units, the MRSA and MSSA isolates examined were divided into 6 and 12 restriction fragment length polymorphism (RFLP) patterns, respectively, whereas five patterns were commonly detected in MRSA and MSSA. MRSA isolates that showed a particular RFLP pattern were considered to be predominant in the hospital. Coagulase typing with type-specific antisera was also performed for all S. aureus isolates for comparison. Coagulase types II and VII were most frequently detected and included isolates with four and five different AluI RFLP patterns, respectively, whereas each of the other coagulase types corresponded to a single RFLP pattern. These results indicated that RFLP typing was more discriminatory than serological typing, for typing S. aureus and demonstrated its utility in epidemiologic investigation of S. aureus infection in hospitals.

Molecular genotyping of methicillin-resistant Staphylococcus aureus via fluorophore-enhanced repetitive-sequence PCR

Methicillin resistance in Staphylococcus aureus is a frequent cause of nosocomial and community-acquired infections. Accurate, rapid epidemiologic typing is crucial to the identification of the source and spread of infectious disease and could provide detailed information on the generation of methicillin-resistant S. aureus (MRSA) strains. The high degree of genetic relatedness of MRSA strains has precluded the use of more conventional methods of genetic fingerprinting. A rapid DNA fingerprinting method that exploits PCR amplification from a DNA repeat sequence in MRSA is described. The random chromosomal distribution of this repeat sequence provides an ideal target for detecting DNA fragment patterns specific to individual MRSA strains. Two PCR fingerprinting methods which use an oligonucleotide primer based on a repetitive sequence found in Mycoplasma pneumoniae are presented. The repetitive element sequence-based PCR (rep-PCR) and fluorophore-enhanced rep-PCR (FERP) can identify epidemic strains among background MRSA. The combination of oligonucleotide primers labeled with different fluorescent dyes allowed simultaneous FERP fingerprinting and mecA gene detection. Eight different fingerprint patterns were observed in MRSA strains collected from different sources. These techniques provide a rapid discriminatory means of molecular epidemiologic typing of MRSA involved in nosocomial infections.

Nasal carriage of Staphylococcus aureus and cross-contamination in a surgical intensive care unit: efficacy of mupirocin ointment

A six month prospective study was carried out in a surgical intensive care unit (SICU) of a university hospital to assess the incidence and routes of exogenous colonization by Staphylococcus aureus. A total of 157 patients were included in the study. One thousand one hundred and eleven specimens (nasal, surgical wound swabs, tracheal secretions obtained on admission and once a week thereafter, and all clinical specimens) were collected over a four month period from patients without nasal decontamination (A). They were compared with 729 specimens collected over a two month period from patients treated with nasal mupirocin ointment (B). All S. aureus strains were typed by restriction fragment length polymorphism (RFLP) pulsed-field gel electrophoresis after SmaI macrorestriction. The nasal colonization rates on admission were 25.5 and 32.7% in groups A and B, respectively. Thirty-one untreated patients (31.3%) and three patients (5.1%) treated with nasal ointment, acquired the nasal S. aureus in the SICU (P = 0.00027). Nasal carriers were more frequently colonized in the bronchopulmonary tract (Bp) and surgical wound (Sw) (62%) than patients who were not nasal carriers (14%) (P < 0.00001). The patterns were identical for nasal, Bp and Sw strains from the same patient. RFLP analysis characterized seven epidemic strains of methicillin-resistant S. aureus (MRSA) which colonized 60% of group A and 9% of group B patients (P < 0.00001). The bronchopulmonary tract infection rate was reduced in group B (P = 0.032). In conclusion, in an SICU, nasal carriage of S. aureus appeared to be the source of endogenous and cross-colonization. The use of nasal mupirocin ointment reduced the incidence of Bp and Sw colonization, as well as the MRSA infection rate.

Typing of Staphylococcus aureus strains by PCR-amplification of variable-length 16S-23S rDNA spacer regions: characterization of spacer sequences

To develop a rapid and accurate method of typing large numbers of clinical isolates of Staphylococcus aureus, the spacer region C of the rRNA operon [1391-507 (16S-23S)] was enzymically amplified from 322 strains. When the products were separated by denaturing PAGE, 15 variable-length rrn alleles were demonstrated, ranging in size from 906 to 1223 bp. The variable-length HpaII-digested region C [(region E; 1446-196 (16S-23S)] amplification products were cloned into M13mp18RF to sequence separate variable-length alleles. A total of 17 region E inserts were sequenced, aligned and divided into nine alleles by length (938-1174) and sequence properties. The 16S-23S spacer rDNA varied in length (303-551 bp) and in properties; three alleles contained a tRNAIle gene alone, two alleles contained a tRNAIle and a tRNAAla gene, and four alleles lacked tRNA genes. The sequences of two alleles showed less than 1% variation when isolated from two or three S. aureus strains. The 48 penicillin- and methicillin-sensitive strains were divided into 26 ribotypes; in contrast, the 274 methicillin-resistant S. aureus (MRSA) strains were divided into nine ribotypes (A-I) with 97% typing as either ribotype A or B (rrnL was missing in B). The sequence conservation of the rrn operons argues for the use of the 16S-23S spacer region as a stable and direct indicator of the evolutionary divergence of S. aureus strains.

Quantitative antibiogram typing using inhibition zone diameters compared with ribotyping for epidemiological typing of methicillin-resistant Staphylococcus aureus

Antibiogram typing of methicillin-resistant Staphylococcus aureus with selected antibiotics was evaluated as a primary epidemiological typing tool and compared with ribotyping. Antibiograms were derived with the Kirby-Bauer disk diffusion method by using erythromycin, clindamycin, cotrimoxazole, gentamicin, and ciprofloxacin. For typing, antibiogram data were analyzed by similarity analysis of disk zone diameters (quantitative antibiogram typing). One hundred seventy-two isolates were typed. Reproducibility reached 98% for the quantitative antibiogram and 100% for ribotyping. With three selected restriction enzymes (EcoRV, HindIII, and KpnI), 40 epidemiologically unrelated isolates could be classified into 21 ribotypes, whereas quantitative antibiogram typing classified these isolates into 19 groups. To evaluate the discriminatory power of the methods, we calculated an index of discrimination from data obtained with these 40 isolates. This index takes into consideration both the number of types defined by the typing method and their relative frequencies. With both ribotyping and quantitative antibiogram typing, high discrimination indices (0.972 and 0.954, respectively) were obtained. When epidemiological links between patients (ward, period of hospitalization, and contacts between staff and patients) were compared with the results of ribotyping or the quantitative antibiogram typing method, it appeared that both methods were able to discriminate epidemiological clusters, with only a few discrepancies. In conclusion, quantitative antibiogram typing, although not necessarily based on genomic markers, is a simple method which enables a reliable workup of methicillin-resistant S. aureus epidemic when sophisticated molecular typing methods are not available.

Cell surface hydrophobicity and adherence to extra-cellular matrix proteins in two collections of methicillin-resistant Staphylococcus aureus

Non-specific and specific mechanisms of adherence have been examined in two collections of methicillin-resistant Staphylococcus aureus (MRSA). Determination of hydrophobicity by salt aggregation, hydrophobicity indices and of adherence to the extra-cellular matrix proteins fibronectin, vitronectin, laminin and collagen type 1 have failed to reveal any correlation with phage-type, plasmid profile or antibiogram. Further, the strain collections, made over a period of years in two countries, differ markedly in their adherence characteristics; MRSA are heterogeneous in this respect. Such heterogeneity may explain the polarization of views on the epidemicity or 'virulence' of MRSA. With the exception of adherence to collagen a small group of methicillin sensitive S. aureus had characteristics intermediate between the two groups of MRSA.

Comparison of traditional and molecular methods of typing isolates of Staphylococcus aureus

Fifty-nine Staphylococcus aureus isolates and 1 isolate of Staphylococcus intermedius were typed by investigators at eight institutions by using either antibiograms, bacteriophage typing, biotyping, immunoblotting, insertion sequence typing with IS257/431, multilocus enzyme electrophoresis, restriction analysis of plasmid DNA, pulsed-field or field inversion gel electrophoresis, restriction analysis of PCR-amplified coagulase gene sequences, restriction fragment length polymorphism typing by using four staphylococcal genes as probes, or ribotyping. Isolates from four well-characterized outbreaks (n = 29) and a collection of organisms from two nursing homes were mixed with epidemiologically unrelated stock strains from the Centers for Disease Control and Prevention. Several isolates were included multiple times either within or between the sets of isolates to analyze the reproducibilities of the typing systems. Overall, the DNA-based techniques and immunoblotting were most effective in grouping outbreak-related strains, recognizing 27 to 29 of the 29 outbreak-related strains; however, they also tended to include 3 to 8 epidemiologically unrelated isolates in the same strain type. Restriction fragment length polymorphism methods with mec gene-associated loci were less useful than other techniques for typing oxacillin-susceptible isolates. Phage typing, plasmid DNA restriction analysis, and antibiogram analysis, the techniques most readily available to clinical laboratories, identified 23 to 26 of 29 outbreak-related isolates and assigned 0 to 6 unrelated isolates to outbreak strain types. No single technique was clearly superior to the others; however, biotyping, because it produced so many subtypes, did not effectively group outbreak-related strains of S. aureus.

Methicillin-resistant Staphylococcus aureus disease in a Portuguese hospital: characterization of clonal types by a combination of DNA typing methods

Fifteen pediatric patients as well as the five nursing staff of the Burn Unit of the Hospital D. Estefania in Lisbon, Portugal, were assayed at weekly intervals over a five-month period in order to identify the nature and number of methicillin-resistant Staphylococcus aureus (MRSA) clones associated with colonization and wound infection. Methicillin resistance was confirmed by a mec-specific DNA probe. MRSA isolates were classified into chromosomal types (clones) on the basis of a variety of techniques: (i) ribotyping; (ii) restriction digestion by the endonuclease ClaI followed by Southern hybridization with the mecA-specific DNA probe and (iii) by hybridization with Tn554; and (iv) pulsed-field electrophoresis (PFE) of SmaI digests followed by (v) Southern hybridization with the mecA DNA probe. A sixth, physiological technique (population analysis) was used to define the mode of phenotypic expression of methicillin resistance in each isolate. All isolates carried a single, common polymorph (ClaI type III) of the mecA gene. Hybridization with Tn554 resolved these isolates to two novel patterns (alpha and beta), of which one (Tn554 alpha) was predominant (90%). This pattern could be further resolved to four closely related PFE types (A through D). In contrast, all isolates with the Tn554 beta pattern belonged to an additional, grossly different PFE type E. The Tn554 beta class was also unique in that these bacteria carried the mecA gene in a SmaI fragment smaller (about 170 kb) than that found in the alpha type strains (194 kb). Most isolates (83%) showed a single heterogeneous (population analysis Class 3) mode of resistance expression. The data demonstrate the full capacity of the globally rare (ClaI type III) MRSA clone for colonization and virulence. The results also document the stability of the complex heterogeneous resistance phenotype as well as the stability of the chromosomal types under conditions of in vivo carriage over a period of several months. In a few isolates the same mecA polymorph was present in several, grossly different genetic backgrounds, suggesting horizontal transfer of the mecA gene.

Ribotypes and plasmid contents of Vibrio anguillarum strains in relation to serovar

Eighty-six strains of the 10 major agglutination types of Vibrio anguillarum (serovars O1 to O10) and 6 nontypeable strains of V. anguillarum have been characterized by ribotyping with a probe complementary to 16S and 23S rRNA of Escherichia coli and by plasmid profile analysis. Forty-four different ribotypes were observed with the restriction enzyme HindIII. Ribotype similarity was compared by using the Dice coefficient (Sd), and three significantly different levels of homogeneity within the V. anguillarum serovars were observed (serovars O1, O3A, O7, and O9, Sds of > 90%; serovars O2B, O4, and O10, Sds of 80 to 90%; serovars O2A, O3B, O5, and O8, Sds between 46 and 70%). None of the ribotype patterns of V. anguillarum strains were observed among 20 other Vibrio strains typed for comparison. By cluster analysis, the V. anguillarum strains were divided into a main cluster containing 83 strains, while all strains of serovar O3B, one strain (each) of serovars O2A, O5, and O8, and a nontypeable strain were separated from this cluster by at least 15% difference in similarity coefficients. Plasmids were demonstrated in only six strains other than serovar O1. In serovar O1, a 67- to 70-kilobase-pair (kb) plasmid molecule was present in 17 of 19 strains tested; of the two remaining strains, one strain harbored two plasmids (45 and 6.5 kb) and one strain had no plasmids.

Comparative study of the cellular fatty acids of methicillin-resistant and -susceptible Staphylococcus aureus

The cellular fatty acid compositions of 26 strains of methicillin-resistant Staphylococcus aureus (MRSA) and 17 strains of methicillin-susceptible S. aureus (MSSA) were analyzed by gas-liquid chromatography. The fatty acid compositions of the two groups were very similar with 16 identified components. The major fatty acids were Ci14 = 0, Ci15 = 0, C18 = 0 and C20 = 0. Among these fatty acids, the percentage of the Ci15 = 0 fatty acid component of MRSA strains (11.4 +/- 3.9%) was statistically higher than that of MSSA strains (6.2 +/- 2.4%) (p < 0.001). On the other hand, the percentage of the C20 = 0 fatty acid components of MRSA strains (20.2 +/- 8.8%) was statistically lower than that of MSSA strains (30.7 +/- 10.4%) (p < 0.001). The production of beta-lactamase and beta-hemolysin in both groups' strain was also unrelated to the relative amounts of the fatty acid components. These results indicated a statistical tendency for the percentage fatty acid compositions of the MRSA strains to be quantitatively different from those of the MSSA for both the Ci15 = 0 and C20 = 0 fatty acid components. Analysis of the fatty acid compositions may have an application in the differentiation of MRSA and MSSA strains.

Concordant clonal delineation of methicillin-resistant Staphylococcus aureus by macrorestriction analysis and polymerase chain reaction genome fingerprinting

Pulsed-field gel electrophoresis of DNA macrorestriction fragments (macrorestriction analysis) allows epidemiologic typing and delineation of genetic relatedness of methicillin-resistant Staphylococcus aureus (MRSA) by indexing variations in the global chromosome architecture. Polymerase chain reaction (PCR)-mediated genome fingerprinting can also discriminate MRSA strains by detecting locally variable DNA motifs. To assess the correlation between these methods, 48 epidemic MRSA strains collected from 20 hospitals over a 10-year period were tested in a blind comparison by (i) macrorestriction analysis with SstII or SmaI endonuclease and (ii) PCR fingerprinting with four primer sets aimed at the mecA gene, enterobacterial repetitive intergenic consensus sequences, and arbitrary sequences. Isolates were discriminated into 22 macrorestriction patterns and 15 PCR fingerprints. MRSA strains belonging to 12 distinct clones by macrorestriction analysis showed 11 distinct PCR genotypes distinguished by multiple band differences. In contrast, 34 of 37 MRSA strains found to be clonally related by macrorestriction analysis clustered in two highly related PCR genotypes that differed by a single DNA fragment (P < 0.0001). These data demonstrate concordant clonal delineation of epidemic MRSA by macrorestriction analysis and PCR fingerprinting and thereby indicate that the rapid PCR assay may be an efficient epidemiologic typing system.

Comparison of phage typing and DNA fingerprinting by polymerase chain reaction for discrimination of methicillin-resistant Staphylococcus aureus strains

A typing procedure for methicillin-resistant Staphylococcus aureus (MRSA) based on the polymerase chain reaction (PCR) amplification of both mecA sequences and variable DNA sequences as present in the prokaryotic genome has been developed. Two primers based on the sequences of DNA repeats as discovered in gram-negative members of the family Enterobacteriaceae allow detection of variable regions in the genome of a gram-positive bacterium such as S. aureus, as does a newly described arbitrary primer. This procedure, enabling the detection of 23 different genotypes in a collection of 48 MRSA isolates, was validated by comparisons with phage typing studies. It appeared that within the same group of isolates only 13 different phagovars could be identified. Combination of the results from both phage typing and genotyping allowed the discrimination of 34 of 48 isolates. However, depending on the primer-variable complexity of the PCR fingerprints, which could also be modulated by combination of PCR primers, clear homologies between the groups defined by either phage typing or fingerprinting were observed. An analysis of an MRSA outbreak in a geriatric institution showed a collection of genetically homogeneous isolates. In agreement with phage typing, PCR fingerprinting revealed the identical natures of the MRSA strains isolated from all patients.

Random amplified polymorphic DNA assay is less discriminant than pulsed-field gel electrophoresis for typing strains of methicillin-resistant Staphylococcus aureus

Twenty-six strains of methicillin-resistant Staphylococcus aureus with different pulsed-field gel electrophoresis fingerprints were tested by random amplified polymorphic DNA assay with three primers, resulting in 15 to 20 different random amplified polymorphic DNA fingerprints. By summing the results for the three primers, the number of different fingerprints increased to 25, but two strains could not be differentiated. We conclude that pulsed-field gel electrophoresis remains the best method of typing methicillin-resistant S. aureus strains.

Typing of Staphylococcus aureus by pulsed-field gel electrophoresis, zymotyping, capsular typing, and phage typing: resolution of clonal relationships

Sixty-nine Staphylococcus aureus isolates from two epidemiologically unrelated sources were typed by pulsed-field gel electrophoresis after SmaI digestion of chromosomal DNA (genome typing), and the results were compared with those obtained by other typing methods: phage typing with the international set of phages, capsular serotyping with monoclonal antibodies against capsular polysaccharides type 5 and 8, and zymotyping by polyacrylamide agarose electrophoresis for esterase polymorphism. A good correlation of S. aureus types was found by these four typing methods. Differentiation increased in the order capsular typing < zymotyping < phage typing < genome typing, yielding 2, 10, 20, and 26 different S. aureus types, respectively. Five of the 26 genome types were further divided into several subtypes revealing clonal relationships. When 36 French S. aureus isolates were compared with 33 German S. aureus isolates, 3 strains representing clonal populations were identical in both groups. S. aureus isolates from patients with cystic fibrosis were also typed at the beginning and the end of a 4-week summer camp for these patients. The results suggested a possible strain transmission during the summer camp. We conclude that genome typing by pulsed-field gel electrophoresis is a powerful tool not only for strain identification but also for the resolution of the clonal relationships of S. aureus strains.

Epidemiologic typing and delineation of genetic relatedness of methicillin-resistant Staphylococcus aureus by macrorestriction analysis of genomic DNA by using pulsed-field gel electrophoresis

To evaluate the usefulness of phenotypic and genotypic analyses for the epidemiologic typing of methicillin-resistant Staphylococcus aureus (MRSA), we characterized 64 epidemic MRSA isolates and 10 sporadic methicillin-susceptible S. aureus isolates from a university hospital and 18 MRSA isolates from hospitals in different geographical areas. Chromosomal DNA macrorestriction analysis with SstII was resolved by pulsed-field gel electrophoresis and compared with antibiotype analysis, phage type analysis, and standard genomic DNA restriction analysis with BglII. Indices of the discriminatory ability of these methods were 0.982, 0.959, 0.947, and 0.959, respectively. Macrorestriction patterns of 94% of MRSA isolates from patients, personnel, and the environment associated with a nosocomial outbreak were closely related (similarity coefficient, 85 to 100%). In contrast, methicillin-susceptible S. aureus isolates showed a marked diversity of macrorestriction patterns (median similarity, 41%). MRSA isolates from other geographical areas showed diverse macrorestriction patterns, with the exception of four isolates displaying identical or closely related patterns; these isolates were associated with concurrent outbreaks in four other Belgian hospitals. A concordance of genomic DNA macrorestriction typing with phenotypic methods was observed for 60 to 65% of MRSA isolates, and a concordance with standard DNA restriction analysis was found for 79 to 98% of these isolates. In conclusion, genomic DNA macrorestriction analysis was a useful complement to phenotypic methods for delineating epidemic isolates of MRSA, for identifying their nosocomial reservoirs, and for tracing their intra- and interhospital spread. The genetic relatedness of MRSA isolates, as estimated by this technique, appeared to correlate with their space-time clustering.

Clonal analysis of methicillin-resistant Staphylococcus aureus strains from intercontinental sources: association of the mec gene with divergent phylogenetic lineages implies dissemination by horizontal transfer and recombination

Genetic relationships among 254 isolates of Staphylococcus aureus resistant to methicillin recovered between 1961 and 1992 from nine countries on four continents were determined by analyzing electrophoretically demonstrable allelic variation at 15 chromosomal enzyme loci. Fifteen distinctive electrophoretic types, marking clones, were identified. The mec gene is harbored by many divergent phylogenetic lineages representing a large portion of the breadth of chromosomal diversity in the species, a result that is interpreted as evidence that multiple episodes of horizontal transfer and recombination have contributed to the spread of this resistance determinant in natural populations. Isolates recovered in the United Kingdom, Denmark, Switzerland, Egypt, and Uganda in the 1960s are of a single multilocus enzyme genotype and probably are progeny of an ancestral methicillin-resistant clone. There is geographic variation in the frequency of recovery of the common methicillin-resistant clones, an observation that may in part explain reported regional differences in natural history correlates of resistant organisms.

Typing of methicillin-resistant Staphylococcus aureus with an M13 repeat probe

A bacteriophage M13 tandem repeat has been used to probe EcoRI digested genomic DNA of methicillin-resistant Staphylococcus aureus (MRSA). The patterns generated were found to be useful in typing MRSA and generally confirmed the relationships that had previously been recognized in other studies based on antimicrobial resistance and plasmid profiles. The epidemic MRSA of London hospitals (EMRSA) and the majority of the epidemic MRSA of eastern Australian hospitals (EA MRSA) gave the same pattern. However, two isolates previously classified as EA MRSA gave a different pattern and a third another pattern. One isolate from Dublin, two isolates from Nuneaton and two isolates from Singapore gave the same pattern as the two EA MRSA. With the exception of the early or classic MRSA all the other isolates examined gave their own distinctive patterns. With one exception the classic MRSA belonged to a separate group. The exception was of particular interest because it gave the same pattern as the majority of the EA MRSA. This suggests that there may be an evolutionary relationship between some of the classic MRSA and the EMRSA of London and the EA MRSA of Australia.

DNA fingerprinting by pulsed-field gel electrophoresis is more effective than ribotyping in distinguishing among methicillin-resistant Staphylococcus aureus isolates

Pulsed-field gel electrophoresis (PFGE) after SmaI restriction of DNA from 239 methicillin-resistant Staphylococcus aureus isolates (from 142 patients) produced 26 different fingerprints. The deduced chromosome sizes ranged from 2,200 to 3,100 kb (+/- 100 kb). A total of 81 isolates taken from 65 patients were then typed by PFGE and ribotyping with ClaI, EcoRI, and HindIII. Ribotypes were less discriminating than PFGE. Ribotyping did not discriminate isolates from a given PFGE fingerprint into different subsets. PFGE may be a more effective epidemiological tool than ribotyping for the typing of methicillin-resistant S. aureus strains.

Biochemical and molecular characterization of Salmonella enterica serovar berta, and comparison of methods for typing

Strains of Salmonella enterica serovar berta (S. berta) from Denmark and seven other countries have been characterized with the aim of developing a rational typing strategy in connection with outbreak investigations. Biotyping divided the strains into H2S-positive (90%) and H2S-negative (10%) biovars. Six percent of the strains were resistant to one or more antimicrobial agents. Eighty-eight percent of the strains carried plasmids and 52 different plasmid profiles were recognized. Six of the common plasmid sizes in these profiles were shown by restriction enzyme analyses to contain more than one plasmid species. More than 90% of the strains had the same ribotype with the restriction enzymes Sma I and EcoR I and the same whole cell protein profile. Outer membrane protein profiles and isoenzyme profiles were identical in all S. berta analysed. Plasmid profiling in combination with restriction enzyme analysis of plasmids seemed to be the most rational typing strategy for S. berta. The results indicated that S. berta strains regardless of geographical source or host are possibly clonal in nature.

Differentiation of strains of Helicobacter pylori by numerical analysis of 1-D SDS-PAGE protein patterns: evidence for post-treatment recrudescence

Twenty-three pre- and post-treatment isolates of Helicobacter pylori from the antral mucosa of eight patients with dyspepsia and gastritis were compared using 1-D SDS PAGE of proteins. The protein patterns were highly reproducible and were used as the basis for two numerical analyses. The first, based on the total protein patterns, showed that a number of the strains did not cluster with their respective patient set. This was thought to be due to differences in both mobility and intensity of proteins in the major band region. The second analysis, based on partial patterns, excluding the major band region (51-68 kDa), divided the clinical isolates into clearly defined groups corresponding to the patient sets. Although there was a degree of heterogeneity with respect to protein pattern between the pre- and post-treatment isolates of some patients, there was nonetheless clear evidence that each patient was harbouring strains of only a single type. These results suggested that patients were not being reinfected with a different strain but that there was recrudescence of the pre-treatment strain. Protein 'fingerprints' provided a precise and reproducible means of strain differentiation, and revealed that in each patient the same strain persisted after drug therapy even though there was marked patient-to-patient strain variation.

The application of two-dimensional polyacrylamide gel electrophoresis to medical microbiology: molecular epidemiology of viruses and bacteria

A variety of molecular methods can be used to identify protein and nucleic acid markers with which to investigate the epidemiology of viruses and bacteria. This paper reviews the application of two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) for studying microbial molecular epidemiology. A small format 2-D PAGE system is described for locating protein markers in group B coxsackie viruses (CVB) and Haemophilus influenzae isolates. Representative isolates of CVB serotypes 2, 4, and 5 were compared by analysing the intracellular proteins present in CVB-infected HEp-2 cells by 2-D PAGE protein gels. Although some of the virus-induced proteins had similar electrophoretic mobilities, the three serotypes could be distinguished from each other on the basis of a major virus-induced protein of molecular weight between 39,000 and 43,000. Protein differences were demonstrated among six serotype 2 CVB (CVB-2) isolates. Four clinical CVB-2 isolates collected over a period of four months had indistinguishable two-dimensional protein profiles. Comparison of the two-dimensional protein profiles of cloned virus stocks prepared from a single clinical CVB isolate demonstrated that it was a heterogeneous virus population. The proteins of nontypable and type-b H. influenzae isolates were compared. Up to 160 proteins, detected by staining with Coomassie Brilliant Blue R, were resolved by 2-D PAGE. Although protein differences between individual bacterial isolates were detected, comparable two-dimensional protein profiles were found for the two groups of H. influenzae isolates. There was no similarity in the two-dimensional protein profiles of H. influenzae and Aeromonas. Potential protein markers were identified that may be useful in long-term studies of H. influenzae epidemiology.

Typing of methicillin resistant and susceptible Staphylococcus aureus strains by ribosomal RNA gene restriction patterns using a biotinylated probe

Nine methicillin-sensitive (MSSA) and 37 methicillin-resistant (MRSA) Staphylococcus aureus isolates of various phage types and resistotypes from seven countries were investigated. Chromosomal DNA was restricted with HindIII or EcoRI, Southern blotted and hybridised with a cDNA probe to 16S+23S rRNA derived from MRSA NCTC 10442. Resulting rDNA profiles could be differentiated on the basis of 22 patterns which were unaffected by changes in plasmid, transposon, enterotoxin A or phage content. Percentage similarity values were calculated using the Dice coefficient and UPGA clustering. Australian and epidemic (EMRSA-1) isolates from the UK showed a high degree of similarity, but the pattern was not unique and was also found in MSSA and other MRSA, e.g. NCTC 10442. An MSSA of phage group II was the most distinct isolate. The method shows potential as an additional tool in a complex typing system, types non-phage typable strains and may provide clues to the clonal evolution of MRSA and MSSA.

Pulsed field gel electrophoresis as a new epidemiological tool for monitoring methicillin-resistant Staphylococcus aureus in an intensive care unit

Pulsed field gel electrophoresis (PFGE) of bacterial DNA was used in a 1-month epidemiological study of methicillin-resistant Staphylococcus aureus (MRSA) in a 15-bed Intensive Care Unit (ICU). Patient and hospital staff carriage as well as distribution of MRSA in the ICU environment were investigated, and a total of 3802 samples produced 175 isolates. The stability and the reproducibility of the PFGE method were satisfactory. Moreover, the plasmid content of the strains so far examined had no influence on the PFGE profiles of the MRSA strains. The polymorphic profiles observed also account for the use of this method as an epidemiological tool for investigating MRSA. Among 30 patients who stayed more than 4 days in the unit, PFGE analysis showed 11 episodes of colonization in nine patients, whereas lysotyping and plasmid DNA analysis demonstrated only eight and seven such episodes in the same patients, respectively. The combination of PFGE with lysotyping and plasmid analysis may provide a greater discriminatory capacity between MRSA isolates.

DNA-DNA hybridization and analysis of restriction endonuclease and rRNA gene patterns of atypical (catalase-weak/negative) Campylobacter jejuni from paediatric blood and faecal cultures

Sixteen strains of atypical (catalase-weak or negative), hippurate-hydrolysing campylobacters from paediatric blood and faecal cultures were identified by DNA-DNA slot hybridization. All were closely related (greater than or equal to 67%) to Campylobacter jejuni and representative strains had G + C contents of 30 +/- 1 mol%. Numerical analysis of chromosomal DNA HaeIII digest patterns revealed two clusters of strains at the 55%S level corresponding to C. jejuni subsp. jejuni and C. jejuni subsp. doylei; most strains belonged to the latter subspecies. No two strains had identical patterns but within each subspecies two subgroups were identifiable, corresponding to Lior biotypes I and II. Southern blot hybridization analysis with a 16 + 23S rRNA cistron probe from Escherichia coli also showed differences between the various strains, and in a numerical analysis three groupings were formed at 70%S corresponding to C. jejuni subsp. jejuni Lior biotypes I and II, and C. jejuni subsp. doylei. Four of the subspecies doylei strains contained a 3.4-MDa plasmid. These analyses showed that catalase-negative C. jejuni subsp. jejuni were genomically distinguishable from C. jejuni subsp. doylei as were Lior biotypes within subsp. jejuni. Ability to produce catalase is not a feature common to all C. jejuni strains, and our results confirm that some strains of subspecies jejuni may be negative in that character although typical in other respects. DNA pattern heterogeneity was consistent with serological differences between strains.

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.

Investigation of a pseudo-outbreak of 'Pseudomonas thomasii' in a special-care baby unit by numerical analysis of SDS-PAGE protein patterns

Forty-two cultures of pseudomonas comprising 28 clinical isolates from a pseudo-outbreak on a Special-Care Baby Unit and 14 reference strains, including 9 type strains, of various Pseudomonas species, were characterized by one-dimensional sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) of whole-cell proteins. The protein patterns were highly reproducible and were used as the basis for a numerical analysis which divided the strains into 9 phenons. Two of the 28 clinical isolates were identified by biochemical tests as P. pickettii and their identification was confirmed by SDS-PAGE as they fell in the same phenon as the type strain of the species. The remaining 26 isolates, which could not be identified on phenotypic tests, fell in the same phenon as three reference strains of 'P. thomasii'. The protein patterns provided the first clear evidence that P. pickettii and 'P. thomasii' were separate taxa and that the 'outbreak' was polymicrobial in origin, in line with the probable aqueous source of contamination. We conclude that high-resolution SDS-PAGE of proteins provides an effective method of identifying and differentiating pseudomonads, especially where this cannot be done adequately using conventional biochemical tests.

Numerical analysis of SDS-PAGE protein patterns of Serratia marcescens: a comparison with other typing methods

Twenty-five cultures comprising 18 clinical isolates of Serratia marcescens from two hospitals, the type strain of S. marcescens, two reference strains of S. marinorubra, the type or a reference strain of three other Serratia species and a reference strain of undetermined species, were characterized by one-dimensional sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) of whole-cell proteins. The protein patterns were highly reproducible and were used as the basis of a numerical analysis which divided the clinical isolates into eight protein types. Comparison with O-serotyping indicated that the level of discrimination by SDS-PAGE was similar. As with O-serotyping, a secondary scheme, such as phage typing, is necessary to differentiate strains of the same protein type. We conclude that high-resolution SDS-PAGE of proteins provides an effective adjunct to other methods for typing isolates of S. marcescens.

Comparison of SDS-PAGE protein patterns with other typing methods for investigating the epidemiology of 'Klebsiella aerogenes'

Twenty-four cultures comprising 20 clinical isolates of 'Klebsiella aerogenes' from two hospitals, a reference strain of 'K. aerogenes' and the type strains of three other Klebsiella species, were characterized by one-dimensional sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) of whole-cell proteins. The protein patterns were highly reproducible and were used as the basis of a numerical analysis which divided the clinical isolates into 12 protein types. Comparison with established typing methods indicated that the level of discrimination of SDS-PAGE was similar to that achieved with conventional typing methods but the strains were grouped differently. Protein typing subdivided five serotype K3 isolates that could also be distinguished by phage typing. Conversely, three strains of protein type 11 were clearly distinguishable by both serotyping and phage typing. We conclude that high-resolution SDS-PAGE of proteins provides an effective adjunct to other methods for typing isolates of 'K. aerogenes'.

Numerical analysis of sodium dodecyl sulphate-polyacrylamide gel electrophoretic protein patterns for the classification, identification and typing of medically important bacteria

A numerical analysis of one-dimensional sodium dodecyl sulphate polyacrylamide gel electrophoretic protein patterns of three separate bacterial groups is described. Similarity between patterns was estimated using a correlation coefficient and is represented diagramatically by the unweighted pair-group with arithmetic averages method of clustering. Protein patterns were scanned using a laser densitometer interfaced directly to a microcomputer, where calculations were performed semi-automatically with specially written software. A method for the normalization of patterns from different gels is utilized. Whole cell protein patterns clearly distinguished strains representing various groups of Achromobacter. Similarly the two biovars of the Group EF-4 bacteria could be separated after analysis of partial "background patterns" as could the different species of Providencia. In addition, whole patterns could be used to type the various strains of P. rettgeri. These examples serve to illustrate the power, versatility and potential of the technique when applied to problems of classification, identification and typing of bacteria of medical interest. Its advantages and disadvantages, when compared to other available electrophoretic methodologies, are discussed, as is the future application of such technology to the hospital laboratory.