DNA polymorphisms in methicillin-susceptible and methicillin-resistant strains of Staphylococcus aureus

Methicillin-Resistant Staphylococcus aureus: Molecular Characterization, Evolution, and Epidemiology

Staphylococcus aureus, a major human pathogen, has a collection of virulence factors and the ability to acquire resistance to most antibiotics. This ability is further augmented by constant emergence of new clones, making S. aureus a "superbug." Clinical use of methicillin has led to the appearance of methicillin-resistant S. aureus (MRSA). The past few decades have witnessed the existence of new MRSA clones. Unlike traditional MRSA residing in hospitals, the new clones can invade community settings and infect people without predisposing risk factors. This evolution continues with the buildup of the MRSA reservoir in companion and food animals. This review focuses on imparting a better understanding of MRSA evolution and its molecular characterization and epidemiology. We first describe the origin of MRSA, with emphasis on the diverse nature of staphylococcal cassette chromosome mec (SCCmec). mecA and its new homologues (mecB, mecC, and mecD), SCCmec types (13 SCCmec types have been discovered to date), and their classification criteria are discussed. The review then describes various typing methods applied to study the molecular epidemiology and evolutionary nature of MRSA. Starting with the historical methods and continuing to the advanced whole-genome approaches, typing of collections of MRSA has shed light on the origin, spread, and evolutionary pathways of MRSA clones.

Epidemiological typing of methicillin-resistant Staphylococcus aureus (MRSA): spa typing versus pulsed-field gel electrophoresis

Molecular methods based on sequencing, such as spa typing, have facilitated epidemiological typing of bacterial isolates compared to the gold standard pulsed-field gel electrophoresis (PFGE), a technically more demanding method. We studied methicillin-resistant Staphylococcus aureus (MRSA) in 4 Swedish counties from 2003 through 2005, and compared spa typing and PFGE results to epidemiological data. Of 280 MRSA isolates, 91 were from sporadic cases and 189 were associated with 35 outbreaks. A total of 50 spa types and 74 PFGE patterns were detected. 60 (21%) of the MRSA isolates carried the Panton-Valentine leukocidin (PVL) genes. 12 of the PVL-positive MRSA were healthcare associated. 25 of the spa types and 31 of the PFGE patterns were associated with outbreaks. In 1 of the outbreaks we found isolates with different but closely related spa types, and in 6 of the outbreaks we observed isolates with different but related PFGE patterns. In this low-endemic setting, with outbreaks limited in time and place, we found spa typing to be a useful tool for epidemiological typing of MRSA, due to its rapidity, accessibility, ease of use, and standardized nomenclature.

Molecular and epidemiological evidence for spread of multiresistant methicillin-susceptible Staphylococcus aureus strains in hospitals

The excision of the staphylococcal chromosomal cassette mec (SCCmec) from methicillin-resistant Staphylococcus aureus (MRSA) strains results in methicillin-susceptible S. aureus (MSSA) strains. In order to determine the proportion and diversity of multidrug-resistant MSSA (MR-MSSA) strains derived from MRSA strains, 247 mecA-negative isolates recovered in 60 French hospitals between 2002 and 2004 were characterized. The spa types of all strains were determined, and a subset of the strains (n = 30) was further genotyped by multilocus sequence typing. The IDI-MRSA assay was used to test the isolates for the presence of the SCCmec element, which was detected in 68% of all isolates analyzed. Molecular analysis of the samples suggested that 92% of the MR-MSSA isolates were derived from MRSA clones of diverse genetic backgrounds, of which the clone of sequence type 8 and SCCmec type IV(A) accounted for most of the samples. High variations in incidence data and differences in the molecular characteristics of the isolates from one hospital to another indicate that the emergence of MR-MSSA resulted from independent SCCmec excisions from epidemic MRSA isolates, as well as the diffusion of methicillin-susceptible strains after the loss of SCCmec. MR-MSSA could constitute a useful model for the study of the respective genetic and environmental factors involved in the dissemination of S. aureus in hospitals.

Virtual digest identification of secondary enzymes for use in pulsed-field gel electrophoresis of Staphylococcus aureus

Pulsed-field gel electrophoresis (PFGE) is currently the gold standard for methicillin-resistant Staphylococcus aureus (MRSA) typing but only one enzyme, SmaI, is currently used for restriction digest. We report the use of virtual digestion to identify enzymes for S. aureus PFGE. Two enzymes (EagI and SacII) were identified and successfully used to characterize two sets of S. aureus isolates, 12 USA300, and 14 additional MRSA isolates comprised of seven SmaI patterns. Phylogenetic analysis of patterns generated by all enzymes determined that the USA300 MRSAs are identical. In contrast, digestion with EagI or SacII resolved one to two band differences among three MRSA pattern sets that were not detected using SmaI. These results demonstrate that a second enzyme may detect differences in S. aureus isolates not detected by single enzyme digestion. However, because isolates differing by one to two bands are considered identical, such discrimination may not be clinically or epidemiologically relevant.

Geographic dissemination of methicillin-resistant Staphylococcus aureus strains: a French regional study

The aim of this study was to compare methicillin-resistant Staphylococcus aureus strains collected in eight hospitals located in the same region of France (Brittany) over a short period (January 1999-July 2000). Ninety-two isolates of methicillin-resistant S. aureus were characterised by their pulsotype and their antibiotype. Pulsotype analysis permitted the definition of three clusters. Two of them comprised 83% of the studied isolates. Phenotypic analysis showed two major antibiotypes, widespread in Brittany but with a heterogeneous geographic distribution and one antibiotype fitting the definition of glycopeptide intermediate S. aureus. These data argue for the high epidemicity of methicillin-resistant S. aureus among the same region.

Significance of methicillin-resistant Staphylococcus aureus (MRSA) survey in a university teaching hospital

We experienced a methicillin-resistant Staphylococcus aureus (MRSA) outbreak in two wards at our medical school teaching hospital during the period of July-September 1997. To determine whether these MRSA clinical isolates were associated with environmental factors, we conducted two sequential MRSA surveys of the hospital staff and surroundings in wards with outbreaks (wards 1 and 2) and in one ward without an outbreak (ward 3) in April 1998 (ward 1 only) and in March 1999 (wards 1, 2, and 3). In the two sequential surveys, MRSA strains were detected mainly from white coats. MRSA strains isolated from fingers in the first survey were decreased in the second survey. The pulsed-field gel electrophoresis (PFGE) patterns of the strains isolated in the two surveys were classified into five types (A-E). Type D, including the outbreak pattern of the MRSA in ward 1 in 1997, was reduced between the first and second surveys by managing microbiological hygiene, suggesting that the outbreak was controlled in ward 1. On the other hand, the strains isolated in the second survey in ward 2 were mainly type E, which was also common among clinical isolates from ward 2 during the latter half of 1998 to 1999. This suggested a high probability of cross-infection between the patients and the hospital staff in the ward. Our observations suggest that doctors and nurses should be cautious that their coats might be contaminated with the prevailing strains of MRSA. We also concluded that the surveys were very useful for the successful management of MRSA infections.

Evaluation of antibacterial efficacy of drugs for urinary tract infections by genotyping based on pulsed-field gel electrophoresis (PFGE)

We attempted to determine whether the same bacterium isolated from patients with urinary tract infections (UTI) before and after treatment with antimicrobial agents was of the same strain ("persisted") or of a different strain ("changed"). Furthermore, to verify the effectiveness of antimicrobial agents for UTI, we investigated whether bacterial strains could be classified as persisted or changed based on their electrophoretic patterns in pulsed-field gel electrophoresis (PFGE). We examined eight species of bacteria ( Enterococcus avium, Staphylococcus epidermidis, Pseudomonas fluorescens, Serratia marcescens, Citrobacter freundii, Enterobacter cloacae, Enterobacter aerogenes, and Escherichia coli), consisting of 41 strains (19 pairs isolated before and after treatment with antimicrobial agents) isolated from patients with complicated UTI. It was concluded that all bacteria were unchanged, based on the clinical effect on bacteriuria. The chromosomal DNA of these bacteria was digested with restriction enzymes and classified based on their electrophoretic pattern in PFGE. A comparison of the patterns of the fragments revealed that 14 pairs were indistinguishable before and after treatment, 3 pairs were closely related, 1 pair was possibly related, and 1 pair was different. These results demonstrated that 18 pairs of isolates (indistinguishable, closely related, and possibly related) were highly likely to be continued infections by the same strain, and that 1 pair (different) had been replaced by another strain. Based on these results, we believe that bacterium genotyping by PFGE is a more effective method for evaluating the antibacterial efficacy of antimicrobial agents.

Nine-year surveillance of methicillin-resistant Staphylococcus aureus in a hospital suggests instability of mecA DNA region in an epidemic strain

The distributions of the antibiotic resistance patterns in a population of Staphylococcus aureus isolates from a teaching hospital were studied over a 9-year period. The results indicate the existence of successive major epidemic methicillin-resistant strains and the emergence of a methicillin-susceptible strain with an unusual resistance pattern. Our findings suggest that this methicillin-susceptible S. aureus strain could be derived from the dominant gentamicin-susceptible methicillin-resistant S. aureus strain with the loss of a 40-kb DNA fragment.

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.

Epidemiological study of staphylococcal colonization and cross-infection in two West African Hospitals

Surveillance in two medium-size (250-300 beds) hospitals located in the most populated islands of Cape Verde was undertaken in July 1997 in order to obtain data concerning nasal carriage of staphylococci. Nasal swabs (172) taken from inpatients and health care workers (HCW) from different internment services yielded 68 Staphylococcus aureus and 105 coagulase-negative staphylococcal (CNS) isolates, demonstrating extensive colonization of both inpatients and HCW by S. aureus (carriage rate 41%) and CNS (carriage rate 65%). The most frequent CNS species were S. epidermidis and S. haemolyticus. Three species--S. aureus, S. epidermidis, and S. sciuri-were recovered from wound swabs. The antibiotic susceptibility profiles of S. aureus and CNS differed sharply: all 68 S. aureus were resistant to penicillin but were fully susceptible to oxacillin as well as the other antimicrobial agents tested-gentamicin; erythromycin, except for three strains; ciprofloxacin; sulfamethoxazole-trimethoprim, except for two strains; vancomycin; and amoxicillin/clavulanate. In contrast, most (91/105) of CNS were resistant to both penicillin and oxacillin, and a variable but substantial proportion of CNS isolates also carried multiresistant traits to gentamicin, erythromycin, sulfamethoxazole-trimethoprim, and amoxicillin/clavulanate. The analysis by PFGE of the methicillin-susceptible S. aureus (MSSA) and the methicillin-resistant S. epidermidis (MRSE) strains provided evidence for extensive cross-infection and cross-colonization from HCW to patients.

Characterization of MRSA transmission in an emergency medical center by sequence analysis of the 3'-end region of the coagulase gene

The distribution of methicillin-resistant Staphylococcus aureus (MRSA) isolates at the St. Marianna University affiliated emergency medical center (EMC) was studied by sequence analysis of the 3'-end region of the coagulase gene. We collected a total of 42 MRSA isolates, consisting of 20 strains from the hospital environment, 13 strains from the nostrils or fingers of medical staff, and 9 strains from inpatients in the EMC. We compared our results with those from 27 stock strains of known coagulase serotype and 2 strains reported in the literature. All 69 strains tested have four to six tandem repeats in the 3'-end region of the coagulase gene. Among the 42 MRSA isolates collected, the base sequence of the 3'-end region of the coagulase gene was identical in 28 of them (67%). The number of isolates originating from the hospital environment, medical staff, and patients, respectively, that were identical to this representative strain were 18 (90%), 6 (46%), and 4 (44%). Phylogenetic analysis using the DNA sequences of the tandem repeat region demonstrated that almost all strains from the patients formed a concordant cluster with the representative strain from the hospital ward. We also assessed the value of sequence analysis of the 3'-end region of the coagulase gene as an epidemiological marker. Our results indicate that sequence analysis of the 3'-end region of the coagulase gene of MRSA may be a potent epidemiologic typing system.

Genotypic and phenotypic differentiation of an antifungal biocontrol strain belonging to Bacillus subtilis

Physiological and molecular fingerprints of biotechnologically relevant rhizobacteria are necessary for registration, patenting, recognition and quality checking of the strains. To characterize the biological control agent, Bacillus subtilis B2g, the strain was compared with other plant-associated B. subtilis isolates. Phenotypic characterization included biochemical and nutritional properties, in vitro activity and analysis of potential antagonistic mechanisms towards several plant pathogenic fungi. According to the phenotypic characteristics, it was not possible to differentiate the biocontrol agent from the other strains, although the enzymatic fingerprint was unique. Genotypic diversity among the isolates was characterized by molecular fingerprinting methods using REP-PCR (repetitive extragenomic palindromic PCR), and macrorestriction of genomic DNA and electrophoretic separation of DNA fragments by pulsed-field gel electrophoresis (PFGE). A protocol for PFGE analysis using restriction enzyme SfiI for B. subtilis was developed. PFGE typing of B. subtilis B2g resulted in a unique fingerprint. Therefore, it was possible to differentiate B. subtilis B2g, the biocontrol agent of Phytovit, from other antifungal B. subtilis isolates.

[Methicillin-resistant Staphylococcus aureus: factors responsible for its incidence]

INTRODUCTION

How can we explain that the proportion of methicillin-resistant Staphylococcus aureus (MRSA) varies between the European countries, ranging from < 1% in Scandinavia to > 30% in Spain, France and Italy? This paper is aimed at attempting to determine factors at the origin of the spreading of endemic MRSA strains as of the early 1980s. Those strains are characterized by their ability to develop resistance to current antibiotics and make treatment of severe and deep infections more complex.

CURRENT KNOWLEDGE AND KEY POINTS

Differences in the virulence of MRSA strains and that of susceptible strains appear unlikely. MRSA prevalence seems to be a growing problem, especially in Southern Europe where rates of resistance to other anti-staphylococcal antibiotics are high. General policies for antibiotic therapy as well as the implementation of strategies for prevention and control of MRSA might be responsible for such rates. Indeed, once MRSA is introduced into a facility without control program, this multiresistant bacteria rapidly spreads within the hospital and becomes endemic, expanding its reservoir. FUTURE PROSPECTS ET PROJECTS: Due to the introduction of new methods in microbiology and communication, infection control measures including procedures for isolation and identification of MRSA reservoirs are still feasible; however, their implementation requires human and material resources. Areas requiring improvement in the detection of MRSA outbreaks are identified in this paper, with particular emphasis on the need for national surveillance of MRSA prevalence and reappraisal of MRSA control strategies in French hospitals.

Comparison of protein A gene sequencing with pulsed-field gel electrophoresis and epidemiologic data for molecular typing of methicillin-resistant Staphylococcus aureus

The epidemiologic relatedness of methicillin-resistant Staphylococcus aureus (MRSA) isolates is currently determined by analysis of chromosomal DNA restriction patterns by pulsed-field gel electrophoresis (PFGE). We have evaluated an alternative typing system (MicroSeq StaphTrack Kit; Perkin-Elmer Biosystems) based on the sequence analysis of the chromosomally encoded polymorphic repeat X region of the S. aureus protein A (spa) gene. A total of 69 clinical MRSA isolates were divided into 18 groups according to the number and nucleotide sequences of the spa repeats. Molecular typing results obtained both by spa sequencing and from the PFGE patterns were concordant except for one group, which contained 20 isolates recovered over a 2-year period from hospitalized patients at the Mayo Clinic. Although the spa typing patterns were indistinguishable for those isolates, PFGE analysis yielded seven related but distinguishable patterns. Further coagulase gene sequence analysis subtyped those 20 strains into four groups which followed distinct temporal and geographic distributions. During a 2-year epidemic period there were up to 7 fragment changes in PFGE patterns among epidemiologically related isolates, suggesting that PFGE may be unsuitable for long-term typing of strains involved in epidemics. Although more limited than PFGE in discriminatory power, spa sequencing analysis could be used as a screening method for typing of MRSA strains because of the shorter turnaround time, ease of use, and the inherent advantages of sequence analysis, storage, and sharing of information.

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.

Follow-up of Staphylococcus aureus nasal carriage after 8 years: redefining the persistent carrier state

Studies of Staphylococcus aureus nasal carriage have distinguished three carriage patterns: persistent, intermittent, and noncarriage. The criteria used to identify these carriage patterns have been inconsistent. In 1988 the S. aureus nasal carrier index, i.e., the proportion of nasal swab specimen cultures yielding S. aureus, was determined for 91 staff members of various departments of a large university hospital by obtaining weekly nasal swab specimens for culture over a 12-week period. Thirty-three (36%) persons had carrier indices of 0.80 or higher, 15 (17%) had indices between 0.1 and 0.7, and 43 (47%) had indices of zero. In 1995, 17 individuals with carrier indices of 0.80 or higher in 1988 were available for reexamination. For 12 (71%) of these individuals, S. aureus was again isolated from a single nasal swab, i.e., from each individual with a 1988 carrier index of 1.0 but from only half of those with indices below 1.0. Genotyping (by randomly amplified polymorphic DNA analysis and pulsed-field gel electrophoresis) of all S. aureus strains showed that strains isolated from only three individuals, all with 1988 carrier indices of 1.0, in 1988 and 1995 showed genetic similarity. In conclusion, persistent S. aureus nasal carriage is a unique characteristic of a fraction of the population, and the attribute "persistent" should be confined to those individuals for whom serial nasal swab specimen cultures consistently yield S. aureus.

Epidemiological typing of extended-spectrum beta-lactamase-producing Klebsiella pneumoniae isolates by pulsed-field gel electrophoresis and antibiotic susceptibility patterns

Over a 16-month period, Klebsiella pneumoniae isolates from 102 patients admitted to a university hospital in Liege (Belgium) produced extended-spectrum beta-lactamases. Pulsed-field gel electrophoresis of genome macrorestriction patterns with XbaI and antibiotic susceptibility patterns subdivided 39 isolates into eight clonally related groups. Two of them were implicated in the course of this outbreak. They were responsible for successive waves of infection or colonization in different wards of the hospital while the others were encountered sporadically. A beta-lactamase with an isoelectric point of 7.6 and consistent with type SHV-2 characterized all nine isolates chosen among both major groups.

Characterization of erythromycin-resistant isolates of Staphylococcus aureus recovered in the United States from 1958 through 1969

We tested 16 erythromycin-resistant clinical isolates of S. aureus, recovered from patients hospitalized in the United States from 1958 to 1969, for the presence of ermA, ermB, and ermC by using PCR. Fifteen of 16 isolates contained at least one copy of ermA; the remaining isolate, which was also clindamycin resistant, contained ermB. Eight of the 15 isolates harboring ermA, all of which were inducible, contained a single copy of the gene in the chromosome, while the remaining seven isolates had two copies of the gene. ermB was plasmid encoded and mediated constitutive resistance to erythromycin.

Molecular typing of Staphylococcus aureus based on PCR restriction fragment length polymorphism and DNA sequence analysis of the coagulase gene

A typing procedure for Staphylococcus aureus was developed based on improved PCR amplification of the coagulase gene and restriction fragment length polymorphism (RFLP) analysis of the product. All coagulase-positive staphylococci produced a single PCR amplification product of either 875, 660, 603, or 547 bp. Those strains of epidemic methicillin-resistant S. aureus 16 (EMRSA-16) studied all gave a product of 547 bp. PCR products were digested with AluI and CfoI, and the fragments were separated by gel electrophoresis. Ten distinct RFLP patterns were found among 85 isolates of methicillin-resistant S. aureus (MRSA) and 10 propagating strains (PS) of methicillin-sensitive S. aureus (MSSA) examined. RFLP patterns 1, 2, and 3 were specific to strains of EMRSA-3, -15, and -16, respectively. By contrast, RFLP patterns 4 and 5 were seen with a heterogeneous collection of strains, together with drug-resistant forms of S. aureus isolated in Europe and four propagating strains used for the international phage set. RFLP pattern 6 was given by the Airedale isolate and PS 95. RFLP pattern 7 encompassed EMRSA-2 (isolate 331), PS 94, and PS 96. An isolate from Germany gave RFLP pattern 8. Eight strains of MSSA gave patterns similar to those of methicillin-resistant strains (RFLP patterns 3, 4, 5, 6, and 7), but two, PS 42E and PS 71, gave unique RFLP patterns 9 and 10, respectively. The coagulase gene PCR products for 24 isolates of MRSA and two isolates of MSSA were sequenced for both strands. The sequences were aligned, and evolutionary lineages were inferred based on pairwise distances between isolates.

Methicillin-resistant Staphylococcus aureus versus the burn patient

Methicillin-resistant Staphylococcus aureus (MRSA) has become a frequent cause of nosocomial infection, its increasing prevalence posing serious therapeutic and infection control problems within the hospital environment. MRSA is a major challenge to the burn patient, with potential to cause significant morbidity and mortality. Burn patients have been shown to become colonised and infected more readily than other patient groups. Extensive burn injuries are particularly susceptible to infection as a result of the disruption of the normal skin barrier and accompanying depression of immune responses. Extended hospitalisation and antibiotic therapy have been identified as additional risk factors for MRSA carriage and infection. Microbial surveillance, epidemiological studies and the introduction of strict infection control regimes can reduce the prevalence of MRSA but may be insufficient for eradication or prevention of outbreak situations. Recognition of the clinical importance of MRSA to the burn patient highlights the need to take appropriate measures to minimise transmission and infection in this vulnerable group of patients.

Evolution of an endemic methicillin-resistant Staphylococcus aureus population in an Australian hospital from 1967 to 1996

The evolution over 30 years of a population of methicillin-resistant Staphylococcus aureus (MRSA) from a tertiary referral hospital was studied by phylogenetic analysis of SmaI-generated restriction fragment length polymorphisms (RFLPs). The results suggest that a new clone of MRSA appeared at the hospital in the early 1980s, which, although usually retaining its ancestral phage-type, developed four different RFLP pulsotypes in the next 16 years. This finding indicates that multiple RFLP patterns in MRSA do not necessarily represent multiple clones deriving from different mec gene transfer events. Such variation within a clone may be significant in the interpretation of RFLP patterns during outbreaks and emphasizes the need to use two typing methods in studies of such populations. Since the appearance of new clones of MRSA is a relatively rare event, cross-infection control is paramount in the prevention of MRSA dissemination.

Typing of nosocomial strains of Serratia marcescens: comparison of pulsed-field gel electrophoresis of macrorestriction fragments with biotyping, esterase typing and ribotyping

Fifty nosocomial isolates of Serratia marcescens, collected in six Belgian hospitals between 1986 and 1990, were characterized by using pulsed-field gel electrophoresis (PFGE) with XbaI. The results were compared with those previously obtained by three other methods: biotyping, esterase electrophoresis typing and ribotyping with EcoRI and HindIII. Macrorestriction analysis (42 PFGE groups) and esterase typing (42 zymotypes) proved to be the most discriminating, followed by ribotyping (28 ribotypes) and biotyping (10 biochemical profiles). Biotyping would serve as a screen to identify isolates, due to its accessibility. Esterase typing provided a reliable tool to make subdivisions within biotypes because of congruence between biochemical groups and esterase patterns. Additional discrimination was still achieved by ribotyping and PFGE. It is concluded that the combined results of these four markers were useful for distinguishing all epidemic and sporadic isolates.

Genetic analysis of equine methicillin-resistant Staphylococcus aureus by pulsed-field gel electrophoresis

Pulsed-field gel electrophoresis (PFGE) was used to determine genetic relationships among 15 methicillin-resistant Staphylococcus aureus (MRSA) isolates from mares with metritis and from a stallion with dermatitis in Hokkaido. All the 15 isolates showed phage pattern 6/47/54/75, coagulase type IV, and enterotoxin type A. The restriction endonuclease SmaI cut their genomic DNAs into 15 or 16 fragments ranging in size from 8 to 630 kb. Fourteen of the 15 isolates showed the same PFGE pattern, whereas the remaining one appeared to be closely related. The 9 human MRSA isolates showing the same phenotypic characteristics as the horse isolates gave different PFGE patterns from those of the horse isolates.

Pulsed-field gel electrophoresis of Staphylococcus hyicus and Staphylococcus chromogenes genomic DNA and its taxonomic, epidemiologic and ecologic applications in veterinary medicine

One hundred and thirty-eight strains of Staphylococcus hyicus and 21 strains of S. chromogenes isolated from animals were analyzed by pulsed-field gel electrophoresis (PFGE) after restriction endonuclease Smal digestion of chromosomal DNA. Eighty-eight strains of S. hyicus from pigs with or without exudative epidermitis (EE) generated 16 to 26 fragments in the size range of < 1 to 485 kb, and yielded 39 different patterns. With regard to the strains from pigs with EE, PFGE patterns differed according to the country of origin. Outbreaks of EE occurring on four separate pig farms in Japan involved S. hyicus with different PFGE patterns. The PFGE patterns shown by S. hyicus strains from 4 kinds of animals were compared. Strains from pigs differed from those isolated from chickens (n = 45; 18 to 24 fragments of < 1 to 425 kb), cows (n = 3; 17 to 19 fragments of < 1 to 475 kb), and goats (n = 2; 16 or 17 fragments of < 1 to 1,125 kb). Also, each of the chicken, cow and goat strains had a host-specific fragment. The results suggest that PFGE analysis might be a useful marker for distinguishing ecovars within S. hyicus. In contrast, strains of S. chromogenes from pigs and cows generated 17 to 24 fragments ranging from < 1 to 545 kb. The PFGE patterns of S. chromogenes strains were more highly conserved than those of S. hyicus. S. chromogenes strains could be distinguished from S. hyicus strains by fragments within the range of 305 to 545 kb. The results indicate that PFGE analysis could be used to distinguish between S. hyicus and S. chromogenes. We conclude that PFGE analysis is a useful tool not only for species or strain identification but also for epidemiologic or ecologic studies of S. hyicus and S. chromogenes.

Two clones of methicillin-resistant Staphylococcus aureus in Poland

OBJECTIVE: To evaluate relatedness among methicillin-resistant Staphylococcus aureus (MRSA) strains isolated in Poland. METHODS: Ninety-three MRSA hospital isolates were collected from different regions in Poland from 1990 to 1992. Strains were analyzed with respect to heterogeneity of methicillin resistance, phage types, resistance patterns, crystal violet staining, chromosomal DNA SmaI restriction patterns by PFGE, ERIC1 and ERIC2 AP-PCR types and DNA repeat polymorphism within the protein A gene. Resistance to methicillin was confirmed by the detection of the mecA gene by PCR. RESULTS: The combined results of typing methods demonstrate that all MRSA strains analyzed could be easily divided into two distinct clones (clonally related strains). The first consisted of strains with clear heterogeneous expression of resistance to methicillin (34 isolates) and the second showed more homogeneous resistance (59 isolates). In this study the best method for epidemiologic analysis of MRSA was found to be PFGE. A good correlation between the epidemic behavior of MRSA and a high number of repetitive DNA units within the protein A gene was observed. CONCLUSIONS: Results show that in Poland two distinct clones of epidemic MRSA have circulated in the past, easily discriminated by pheno- and genotyping methods, and both could be found together in a single hospital.

Molecular and phage typing of Staphylococcus aureus harbouring cryptic conjugative plasmids

The spread of antibiotic resistant-bacterial pathogens in a hospital could be due to the spread of a resistant strain or the spread of a resistance plasmid among unrelated strains. In this study the relatedness of Staphylococcus aureus isolates carrying identical cryptic conjugative plasmids was determined by a combination of resistance profiles, plasmid patterns, pulsed field gel electrophoresis of SmaI digested chromosomal DNA and phage typing. Results of the different typing techniques were in agreement to one another and demonstrated that the isolates were of three different types. The results suggested that a cryptic conjugative plasmid had spread to different S. aureus isolates in the hospital. This is an example of plasmid spread as opposed to strain spread.

Genomic diversity of mec regulator genes in methicillin-resistant Staphylococcus aureus and Staphylococcus epidermidis

Low-affinity penicillin-binding protein PBP-2a encoded by mecA is closely related to methicillin resistance in staphylococci, and expression of PBP-2a is controlled by regulator elements encoded by mecR1 and mecI which are located adjacent to mecA on the chromosome. Deletion or mutation which occurred in mec regulator gene is considered to be associated with constitutive production of PBP-2a. The distribution of the mec regulator genes in 176 strains of Staphylococcus aureus and 33 strains of S. epidermidis isolated from a single hospital was studied by polymerase chain reaction amplification. Most clinical isolates of methicillin-resistant S. aureus (MRSA) (94.3%) and S. epidermidis (MRSE) (83.9%) possessed both mecI and mecR1 genes (type I), whereas no mec regulator genes were detected in mecA-negative isolates. In contrast, 7 MRSA and 5 MRSE isolates were found to have incomplete regulator genes, and they were classified into three groups; strains which lacked only mecI gene (type II), strains which lacked mecI and 3'-end of mecR1 gene (type III), and strains which lacked both regulator genes (type IV). Analysis of mecI gene from all the strains having mecI by restriction fragment length polymorphism after Mse I digestion indicated that three MRSA strains possessed one of the known point mutations identified previously. These findings indicated the predominance of a single type of MRSA possessing both mecI and mecR1 in the study period and also suggested a high genomic diversity in mec regulator region of staphylococci.

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 the clonal diversity of Staphylococcus aureus methicillin-resistant strains isolated at João Pessoa, state of Paraíba. Brazil

To investigate the clonal diversity of Staphylococcus aureus strains isolated at João Pessoa, State of Paraíba, Brazil, digested genomic DNA were studied by pulsed-field gel electrophoresis (PFGE) in nine methicillin-resistant strains (MRSA) and three methicillin-sensitive strains (MSSA), selected among 67 isolates based on their antimicrobial susceptibility and epidemiology. The isolates were obtained between April and November 1992 from the Hospital of the Federal University of Paraíba, located in João Pessoa. Two MRAS isolates from the Oswaldo Cruz Hospital, São Paulo, Brazil, including an epidemic strain previously detected from different hospitals at the country were used as control. Five different patterns, were demonstrated by MRSA isolated in João Pessoa and these patterns were described in several epidemiologically unrelated hospitals in São Paulo. Our results suggest the interstate dissemination of a MRSA clone in João Pessoa which is similar to that described in other cities of Brazil.

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.

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.

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

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

Genetic variability among Chlamydia trachomatis reference and clinical strains analyzed by pulsed-field gel electrophoresis

Pulsed-field gel electrophoresis (PFGE) was applied to Chlamydia trachomatis reference strains representing each of the 18 serovars and to 29 clinical isolates from genital specimens collected in Bordeaux, France, or Malmö, Sweden. Comparison of the fingerprint patterns of the reference strains revealed a high level of polymorphism of the total DNA when SmaI was used (14 profiles), whereas the other enzymes, Sse8387I and ApaI, showed fewer differences. Some serovars, considered to be closely related on the basis of their antigenic determinants located on the major outer membrane protein (MOMP), such as D and Da or I and Ia, were shown to be different after PFGE of their genomic DNAs. However, serovars B and Ba and serovars L2 and L2a had identical patterns after analysis with the three endonucleases. When applied to clinical isolates, which were typed by restriction fragment length polymorphism analysis of the MOMP gene, PFGE allowed the detection of intragenotype polymorphisms and showed the identity of two strains successively isolated from the same patient. This technique seems to be an efficient tool for epidemiological studies when used in addition to serotyping or genotyping by restriction fragment length polymorphism analysis of the MOMP gene.

Genetic variation in Staphylococcus aureus coagulase genes: potential and limits for use as epidemiological marker

To perform coagulase gene typing, the repeated units encoding hypervariable regions of the Staphylococcus aureus coagulase gene were amplified by the PCR technique; this was followed by AluI restriction enzyme digestion and analysis of restriction fragment length polymorphism (RFLP) patterns. In order to assess the discriminatory power of this typing method, 30 epidemiologically unrelated S. aureus strains which differed by their pulsed-field gel electrophoresis patterns were examined. Although 18 of the 30 strains had unique and unshared AluI RFLP patterns, there were only four observed patterns in the remaining 12 strains. This finding indicated that unrelated strains may share identical AluI RFLP patterns. To elucidate the degree of genetic variation in the C-terminus-encoding loci within the coagulase genes, the PCR products of these 12 strains were subjected to Taq polymerase-mediated sequencing. Sequence analysis confirmed the AluI recognition sites in each of the four RFLP groups and demonstrated that AluI appears to yield the highest RFLP in restriction enzyme analysis. By their DNA sequences the majority of strains sharing common AluI groups could be clearly differentiated from each other and revealed between 93.2 and 98.5% homology. When we determined the nucleotide sequences of two strains after six subcultivations no significant alterations were observed. Because the discriminatory power of the current coagulase gene typing method is not great enough to be used as the sole method to type S. aureus, additional techniques are necessary. Sequence analysis of the repeated unit-encoding region for the typing of S. aureus may be potentially useful as an alternative to other current molecular typing techniques.

Characterization of Staphylococcus intermedius from healthy dogs and cases of superficial pyoderma by DNA restriction endonuclease patterns

In order to study the possible clonal relation of Staphyloccocus (S.) intermedius from canine superficial pyoderma and from healthy carriers, isolates from pustular swabs and from vaginal, nasal and normal skin sabs were typed using macrorestriction analysis with Sma I and pulsed-field gel electrophoresis. From the size of the resulting fragments the size of the chromosome of S. intermedius could be determined to be roughly 1500 +/- 200 kb on the average. The fingerprints were very heterogeneous though characteristically distinct from patterns of (human) S. aureus as published by others. Strains from superficial pyoderma were not found to be more similar to each other than strains from healthy carriers. Therefore it was concluded that strains from this type of skin infection probably did not belong to a certain subpopulation of S. intermedius, which might have indicated a higher virulence of these strains.

Typing of Staphylococcus aureus by amplification of the 16S-23S rRNA intergenic spacer sequences

The possibility of using polymorphisms in the spacer regions between 16S and 23S rRNA genes in order to type Staphylococcus aureus has been evaluated. To this purpose, DNA extracted from 74 independent isolates was amplified making use of a pair of primers complementary to conserved regions in the 16S and 23S genes. We have demonstrated that the method provides a good discrimination between unrelated isolates, giving better results when methicillin-sensitive strains are considered. Moreover, the amplification profiles were reproducible and all strains were typable. Given these results, and the technical simplicity of the process, we propose PCR-ribotyping to be taken into consideration as a method for typing S. aureus.

Molecular epidemiology for local outbreaks of methicillin resistant Staphylococcus aureus (MRSA). The need for several methods

Subtyping isolates may be useful for epidemiological studies of methicillin-resistant-Staphylococcus aureus (MRSA) outbreaks. Among subtyping methods, DNA-based techniques have been applied very effectively for this purpose. An outbreak of MRSA infections took place in one hospital in Barcelona early during 1991. From the beginning of the outbreak to December 92, 70 MRSA isolates from different patients and sources were collected. All strains were evaluated by restriction endonuclease analysis of plasmid DNA (REAP) and macrorestriction endonuclease analysis of genomic DNA using Sma I and pulsed-field-gel-electrophoresis (PFGE). Plasmid screening and REAP using Hind III demonstrated two plasmid subtypes: subtype A showing a large plasmid, and subtype B showing the same large plasmid plus a smaller one. Subtypes A and B corresponded to the more recent and older isolates, respectively, suggesting the loss of the small plasmid during the epidemic. PFGE using Sma I displayed two closely related profiles (PFGE subtype A and A'; CS = 0.90). These subtypes were different from those subtypes exhibited from 4 methicillin-susceptible-Staphylococcus aureus (MSSA) isolates from the same hospital and from 2 epidemiologically unrelated MRSA isolates. Almost all isolates showing PFGE subtype A preceded those isolates showing PFGE subtype A'. This fact and the similarity between both subtypes suggested minor chromosomal DNA rearrangement during the outbreak from a unique strain. While PFGE using Sma I is a useful tool in evaluation of clonal dissemination, our data suggest epidemic or local outbreaks may need several methods to best delineate the source and spread of MRSA strains. The reproducibility and discriminatory power of REAP makes it a useful adjunct in this context.

Identification and characterization of Serpulina hyodysenteriae by restriction enzyme analysis and Southern blot analysis

Chromosomal DNA restriction enzyme analysis and Southern blot hybridization were used to characterize Serpulina hyodysenteriae strains. When chromosomal DNAs from selected strains (reference serotypes) of S. hyodysenteriae were digested with the restriction endonuclease Sau3A and hybridized with a 1.1-kb S. hyodysenteriae-specific DNA probe, a common 3-kb band was always detected in S. hyodysenteriae strains but was absent from Serpulina innocens strains. When the chromosomal DNA was digested with the restriction endonuclease Asp 700 and hybridized with two S. hyodysenteriae-specific DNA probes (0.75 and 1.1 kb of DNA), distinct hybridization patterns for each S. hyodysenteriae reference strain and the Australian isolate S. hyodysenteriae 5380 were detected. Neither the 1.1-kb nor the 0.75-kb DNA probe hybridized with Asp 700- or Sau3A-digested S. innocens chromosomal DNA. The presence of the 3-kb Sau3A DNA fragment in S. hyodysenteriae reference strains from diverse geographical locations shows that this fragment is conserved among S. hyodysenteriae strains and can be used as a species-specific marker. Restriction endonuclease analysis and Southern blot hybridization with these well-defined DNA probes are reliable and accurate methods for species-specific and strain-specific identification of S. hyodysenteriae.

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.

Application of genomic DNA subtyping by pulsed field gel electrophoresis and restriction enzyme analysis of plasmid DNA to characterize methicillin-resistant Staphylococcus aureus from two nosocomial outbreaks

Pulsed-field gel electrophoresis (PFGE) and restriction enzyme analysis of plasmid DNA (REAP) were applied to study the epidemiologic relationship among methicillin-resistant Staphylococcus aureus (MRSA) isolates from outbreaks in two hospitals in São Paulo, Brazil: 82 MRSA isolates, 73 from a university hospital and nine from a general adult intensive care unit of a private hospital, were collected from 62 patients: 95% of the MRSAs were also resistant to gentamicin and ciprofloxacin. REAP subtyping of both collections identified six different subtypes: 55 (72.6%) MRSAs from the university hospital and nine isolates from the private hospital shared the same epidemic REAP subtype. Discrimination by restriction of genomic DNA with Sma I followed by PFGE enabled the identification of 14 DNA subtypes. Based on the combined REAP-genomic DNA subtype, the predominant subtype in the university hospital was A/A (44 isolates) whereas the epidemic subtype in the private hospital was A/M (seven isolates). The application of two typing methods showed better discrimination among MRSAs than did either method alone.

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.

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.