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

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.

The Study of Genetic Relationship Among Third Generation Cephalosporin-resistant Salmonella enterica Strains by ERIC-PCR

Background and Objectives:

Salmonella is an important food-borne pathogen responsible for disease in humans and animals. The aim of this study was to investigate the genetic relationship among third generation cephalosporin-resistant Salmonella enterica strains by Enterobacterial Repetitive Intergenic Consensus (ERIC)-PCR.

Methods:

The study included all Salmonella isolates obtained from clinical cases in a pediatric hospital in Tehran, Iran during 2006 to 2009. Antimicrobial susceptibility testing was performed according to the Clinical and Laboratory Standards Institute. The genetic relationship between third generation cephalosporins-resistant Salmonella enterica strains was determined using ERIC-PCR.

Results:

Of 136 Salmonella enterica isolates recovered from pediatric patients, six isolates including four Salmonella enterica serotype Infantis and two Salmonella enterica serotype Enteritidis showed an extended-spectrum cephalosporins resistant phenotype. ERIC-PCR differentiated Salmonella enterica serotypes Infantis and Enteritidis into 2 distinct clusters arbitrarily named as E1 and E2. Profile E1 was found in two Salmonella enterica serotype Enteritidis isolates, and profile E2 was found in four Salmonella enterica serotype Infantis isolates.

Conclusion:

Extended-spectrum cephalosporins resistant Salmonella could be attributed to a few predominant serotypes including Enteritidis and Infantis in this study. Genetic analysis using ERIC-PCR showed that closely related clones are responsible for the occurrence of extended-spectrum cephalosporins resistant Salmonella infection in Tehran.

Molecular diagnostics of clinically important staphylococci

Bacterial species of the genus Staphylococcus known as important human and animal pathogens are the cause of a number of severe infectious diseases. Apart from the major pathogen Staphylococcus aureus, other species until recently considered to be nonpathogenic may also be involved in serious infections. Rapid and accurate identification of the disease-causing agent is therefore prerequisite for disease control and epidemiological surveillance. Modern methods for identification and typing of bacterial species are based on genome analysis and have many advantages compared to phenotypic methods. The genotypic methods currently used in molecular diagnostics of staphylococcal species, particularly of S. aureus, are reviewed. Attention is also paid to new molecular methods with the highest discriminatory power. Efforts made to achieve interlaboratory reproducibility of diagnostic methods are presented.

Typing of Clostridium perfringens strains by use of Random Amplified Polymorphic DNA (RAPD) system in comparison with zymotyping

The definition of strain clonality postulates that strains showed identical phenotypic and genetic traits are likely to descend from a common ancestor even if they were isolated from different sources and locations. Regarding this definition, non-epidemiologically linked strains might be clonal strains. To overcome this ambiguity, the discriminatory capability of RAPD typing was assessed firstly on eight Clostridium perfringens strains proven to be chromosomally different with one being the mutant of another one. Thirteen primers were tested but only two were able to differentiate seven of the eight strains. With none of the used primers it was possible to differentiate the parental strain and its mutant harboring an insertion of 180 kb. The four most discriminant primers were retained to determine the RAPD fingerprints of a further 20 previously zymotyped strains from which seventeen were unrelated. To compare the two typing systems, the zymotype of the eight chromosomally different strains was determined. Thus, the discriminatory index was calculated on the basis of 25 unrelated C. perfringens strains. This was 0.97 with RAPD typing and 0.99 with zymotyping. From these results we conclude that the RAPD typing which is less fastidious than zymotyping can be used as an epidemiological marker for C. perfringens.

Validation of pulsed-field gel electrophoresis and spa typing for long-term, nationwide epidemiological surveillance studies of Staphylococcus aureus infections

Pulsed-field gel electrophoresis (PFGE) of genomic macrorestriction fragments has been used by the Belgian Reference Laboratory for Staphylococci for national hospital surveys of methicillin-resistant Staphylococcus aureus since 1992. The sequencing of the polymorphic X region of the protein A gene (spa typing) offers significant advantages over PFGE in terms of speed, ease of interpretation, and exportability. To validate its potential use for national surveillance, we evaluated the robustness of spa typing compared with that of PFGE based on a collection of 217 S. aureus strains representative of the Belgian S. aureus epidemiology during the last 13 years. spa typing and PFGE both showed high discriminatory power (discriminatory indexes of 0.98 and 0.96, respectively) and achieved high concordance (95.9%) in type classification. Both methods also showed good concordance with multilocus sequence typing (MLST) (95.5%). However, we observed occasional "violations" of MLST clonal complex assignment by spa typing. Our results suggest that both PFGE and spa typing are reliable methods for long-term, nationwide epidemiological surveillance studies. We suggest that spa typing, which is a single-locus-based method, should preferably be used in combination with additional markers, such as staphylococcal cassette chromosome mec typing or resistance or virulence gene detection.

Effectiveness of a hospital-wide selective screening programme for methicillin-resistant Staphylococcus aureus (MRSA) carriers at hospital admission to prevent hospital-acquired MRSA infections

Screening of potential MRSA-positive patients at hospital admission is recommended in German and international guidelines. This policy has been shown to be effective in reducing the frequency of nosocomial MRSA transmissions in the event of an outbreak, but the influence of screening on reducing hospital-acquired MRSA infections in a hospital setting where MRSA is endemic is not yet well-documented. This study describes the effect of hospital-wide screening of defined risk groups in a 700-bed acute care hospital during a period of 19 months. In a cohort study with a 19-month control period, the frequencies of hospital-acquired MRSA infections were compared with and without screening. In the control period, there were 119 MRSA-positive patients, of whom 48 had a hospital-acquired MRSA infection. On the basis of this frequency, a predicted total of 73.2 hospital-acquired MRSA infections was calculated for the screening period, but only 52% of the expected number (38 hospital-acquired MRSA infections) were observed, i.e., 48% of the predicted number of hospital-acquired MRSA infections were prevented by the screening programme. The screening programme was performed with minimal effort and can therefore be recommended as an effective measure to help prevent hospital-acquired MRSA infections.

A change in Belgian epidemic methicillin-resistant Staphylococcus aureus phage types in 2000: phenotypic and genotypic characterization of isolates from a general hospital

During 2000, new methicillin-resistant Staphylococcus aureus (MRSA) epidemic phage types became preponderant in Belgium. In the present study, phenotypic and genotypic characteristics of 130 MRSA isolates from a general Belgian hospital were investigated. The MRSA nature of the isolates was confirmed by coagulase test, oxacillin screen plate test and detection of the mecA gene by polymerase chain reaction. Phage typing categorized the MRSA strains into two main groups: the [O]* types and the [J]* types. SmaI macrorestriction analysis by pulsed-field gel electrophoresis gave the same pulsotype in the majority of strains. All strains of the [O]* and [J]* groups, except one, belonged to this pulsotype. Aminoglycoside-modifying-enzyme genes could only be detected in a minority of strains. Although the epidemic phage types of the mid-1990s appear to have been supplanted by the [O]* and [J]* groups, the MRSA population examined showed a remarkably uniform profile corresponding to the previous major clone B.

Pulsed-field gel electrophoresis typing of oxacillin-resistant Staphylococcus aureus isolates from the United States: establishing a national database

Oxacillin-resistant Staphylococcus aureus (ORSA) is a virulent pathogen responsible for both health care-associated and community onset disease. We used SmaI-digested genomic DNA separated by pulsed-field gel electrophoresis (PFGE) to characterize 957 S. aureus isolates and establish a database of PFGE patterns. In addition to PFGE patterns of U.S. strains, the database contains patterns of representative epidemic-type strains from the United Kingdom, Canada, and Australia; previously described ORSA clonal-type isolates; 13 vancomycin-intermediate S. aureus (VISA) isolates, and two high-level vancomycin-resistant, vanA-positive strains (VRSA). Among the isolates from the United States, we identified eight lineages, designated as pulsed-field types (PFTs) USA100 through USA800, seven of which included both ORSA and oxacillin-susceptible S. aureus isolates. With the exception of the PFT pairs USA100 and USA800, and USA300 and USA500, each of the PFTs had a unique multilocus sequence type and spa type motif. The USA100 PFT, previously designated as the New York/Tokyo clone, was the most common PFT in the database, representing 44% of the ORSA isolates. USA100 isolates were typically multiresistant and included all but one of the U.S. VISA strains and both VRSA isolates. Multiresistant ORSA isolates from the USA200, -500, and -600 PFTs have PFGE patterns similar to those of previously described epidemic strains from Europe and Australia. The USA300 and -400 PFTs contained community isolates resistant only to beta-lactam drugs and erythromycin. Noticeably absent from the U.S. database were isolates with the previously described Brazilian and EMRSA15 PFGE patterns. These data suggest that there are a limited number of ORSA genotypes present in the United States.

Ten years phage-typing of Belgian clinical methicillin-resistant Staphylococcus aureus isolates (1992–2001)

Gradual changes have been observed in the phage-types of methicillin-resistant Staphylococcus aureus (MRSA) isolates from Belgian hospitals. A total of 6551 isolates, collected in 93 Belgian hospitals over 10 years (1992-2001), was examined. A decreasing incidence of the main early Belgian epidemic phage-types ([A], [B], [H]*, Jo*) was observed. Since 1997 and 2000, a new series of phage-types ([Hv]*, [J]*, [O]*), which were likely related to the previous group [H]*, have been noted. The general trends were confirmed in two particular hospitals. Local epidemic and/or endemic phage-types were also encountered.

Molecular typing of methicillin-resistant Staphylococcus aureus: can PCR replace pulsed-field gel electrophoresis?

Pulsed-field gel electrophoresis (PFGE) is considered the "gold standard" for molecular typing of methicillin-resistant Staphylococcus aureus (MRSA). However, the method is time-consuming and expensive, and its discriminatory power may not be necessary in outbreak situations. We used a rapid multiplex PCR-based method with published primers and compared the results with those obtained by PFGE. A total of 75 clinical isolates were typed: 59 strains originated from our prospectively collected clinical strains and were epidemiologically unrelated; 16 strains came from an outbreak that was epidemiologically well defined in time and space. A primer mix of the spa gene, the coa gene, and the hypervariable region adjacent to mecA gene was used for multiplex PCR. Both PFGE and PCR clustered the 75 strains into 41 different genotypes. Concordance of the results was 100% for strains originating from the outbreak. Overall, both methods produced concordant results in 72% of cases. A total of 16% were clustered together by PFGE, but not by PCR and 12% were clustered together by PCR but not by PFGE, respectively. The turnaround time was only 8 h for PCR but 5 days for PFGE. This PCR-based method is excellent for rapid and inexpensive typing of MRSA in an outbreak setting, but the discriminatory power and reproducibility are still insufficient to replace PFGE in longitudinal studies in the endemic setting.

Comparison of arbitrarily primed-polymerase chain reaction and pulse-field gel electrophoresis for characterizing methicillin-resistant Staphylococcus aureus

AIMS

The aim of this study was to analyse genotypes for clinical isolates of methicillin-resistant Staphylococcus aureus (MRSA), including hetero-vancomycin-resistant Staph. aureus (VRSA), at a Japanese university hospital.

METHODS AND RESULTS

Seventy-eight clinical isolates of MRSA were analysed by arbitrarily primed-polymerase chain reaction (AP-PCR) using ERIC2 primer and by pulse-field gel electrophoresis (PFGE) following SmaI digestion. Analyses of the nine genotypes and 28 subtypes defined by PFGE, and of the three genotypes and 22 subtypes defined by AP-PCR, both facilitated epidemiological tracing. Used in combination, AP-PCR and PFGE provided more precise classification than the use of a single genotyping method. The six hetero-VRSA isolates were classified into four genotypes defined by the combination of both methods, but these genotypes contained non-VRSA isolates.

CONCLUSIONS

The results suggest that both PFGE and AP-PCR are useful in discriminating MRSA, but not hetero-VRSA, isolates for epidemiological analysis.

SIGNIFICANCE AND IMPACT OF THE STUDY

Combining the results of PFGE with the results of AP-PCR can provide more detail differentiation of MRSA and hetero-MRSA isolates than either method alone.

Bacteraemia caused by coagulase-negative staphylococci exhibiting decreased susceptibility to teicoplanin

The purpose of our study was to assess the prevalence of coagulase-negative staphylococci (CoNS) isolates with reduced susceptibility to glycopeptides among the isolates responsible for bloodstream infections and to describe the epidemiology of these isolates. CoNS isolates from bloodstream infections were collected and characterized by analysis of antibiotic susceptibility and restriction fragment length polymorphism using pulsed-field gel electrophoresis. The medical records of patients with positive cultures and trends in glycopeptide use were reviewed to determine the effect of previous antibiotic treatment on the susceptibility profile of these organisms. The crude incidence of CoNS bacteraemia was 0.51 per 1000 days of hospitalization. The 15 (28.8%) strains identified as having decreased susceptibility to teicoplanin by the reference method were all hospital-acquired and displayed 13 different DNA patterns. The relative risk of harbouring strains with decreased susceptibility to teicoplanin was 3.55 among patients previously treated with vancomycin (confidence interval 95%: 2.15-5.85). The teicoplanin consumption in our institution was constant and represented about 27% of the glycopeptide consumption in daily defined doses. The implementation of programmes aiming to reduce the unnecessary use of glycopeptides should have a significant impact on the reduced-susceptibility rate because strains probably become resistant as a result of antibiotic pressure.

Epidemiologic genotyping of methicillin-resistant Staphylococcus aureus by pulsed-field gel electrophoresis at a university hospital and comparison with antibiotyping and protein A and coagulase gene polymorphisms

A total of 124 methicillin-resistant Staphylococcus aureus (MRSA) isolates were ascertained at the University Hospital of the Canary Islands between January 1997 and April 2000. Genotyping included pulsed-field gel electrophoresis (PFGE) (SmaI digestion) and PCR-restriction fragment length polymorphism (PCR-RFLP) analysis for the coagulase (coa) and protein A (spa) genes. Antibiotic resistance was the main phenotypic marker correlated with genotyping results. Three main PFGE types were detected: A (with 12 subtypes), B (with 2 subtypes), and C. PFGE type A1 was the most commonly found (61% of isolates) and the one responsible for all the epidemic outbreaks. Other genetics markers used (coa and spa RFLPs) were significantly correlated with the PFGE types detected (P < 0.001). These PCR-RFLP assays were useful as molecular markers for a quick, preliminary study of MRSA outbreaks.

Molecular epidemiology of methicillin-resistant Staphylococcus aureus in Colombian hospitals: dominance of a single unique multidrug-resistant clone

The first study on the molecular characterization of methicillin-resistant Staphylococcus aureus (MRSA) isolates from Colombia was performed as part of a global surveillance established by the CEM/NET Initiative, under Project RESIST. Seventy-six MRSA isolates recovered from five hospitals during 1996-1998 were analyzed by the hybridization of ClaI restriction digests with mecA- and Tn554-specific probes, and by pulsed-field gel electrophoresis (PFGE) of chromosomal SmaI digests. All MRSA isolates, with one exception, belonged to a single clonal type II::NH::D. This clone, which was previously described among MRSA isolates recovered in the early 1990s in European and New York and South American hospitals, showed resistance to beta-lactam antibiotics only and appeared to be associated almost exclusively with pediatric infections ("Pediatric clone" of MRSA). While sharing identical molecular typing properties with the Pediatric clone, the Colombian isolates differed by extensive multidrug resistance and were recovered from patients of all ages. It is also noteworthy that the Brazilian clone of MRSA (XI::B::B), another multidrug-resistant international clone currently widely spread in Brazil, Argentina, Uruguay, Chile, and also in several European countries, was completely absent from this set of isolates from Colombia.

Enterobacterial repetitive intergenic consensus sequence-based PCR (ERIC-PCR); its ability to differentiate Streptococcus pyogenes strains and applicability to the study of outbreaks of streptococcal infection

We evaluated the ability of enterobacterial repetitive intergenic consensus sequence-based PCR (ERIC-PCR) to differentiate 95 Streptococcus pyogenes strains with M or T serotypes isolated from sporadic streptococcal infections as compared with M or T serotypings and pulsed-field gel electrophoresis (PFGE). Although the ERIC-PCR had less discriminatory power, defined as the ability to divide the strains with the same serotypes into the different sub-types, than PFGE, it consistently classified the strains into 16 patterns with a high correlation with M or T serotyping. The PCR method further discriminated 4 M or T serotypes into sub-types. The application of ERIC-PCR to 5 outbreaks of streptococcal infection produced the results that agreed closely with those of T serotyping and PFGE. ERIC-PCR has sufficient discriminatory power and is a quick and relatively easy technique, making it useful for routine epidemiological investigations.

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.

Antibiotic susceptibility and genotypic characterization of methicillin-resistant Staphylococcus aureus strains in eastern France

We studied changes over four years in the characteristics of methicillin-resistant Staphylococcus aureus (MRSA) strains isolated in a French university hospital by analysis of antibiotic susceptibility and restriction fragment length polymorphism using pulsed field gel electrophoresis. Changes were considered in relation to regional and national frameworks. The proportion of gentamicin-susceptible methicillin-resistant S. aureus (GS-MRSA) among MRSA increased from 22.6% in 1994 to 86.8% in 1998. We first isolated strains of GS-MRSA susceptible to tobramycin and amikacin (TKS-MRSA) in 1996 from patients in eight wards. The number of TKS-MRSA strains per 100 MRSA was 6.1 in 1997, 14.5 in 1998, and 18.9 in 1999. Pattern A, the major DNA pattern identified, accounted for 78.6% of isolates in 1998. This pattern was found in TKS-MRSA and TKR-MRSA strains, but not in Gentamicin-resistant MRSA strains (GR-MRSA). Fitness analysis showed that GR-MRSA strains had much lower replication rates than GS-MRSA strains, but there was no difference between TKS-MRSA and TKR-MRSA strains. Aminoglycoside consumption remained constant between 1994 and 1998. The spread of TKS-MRSA in our hospital since 1996 may relate to the "total use threshold", as the level of tobramycin/amikacin use is below that required for selection of TKR-MRSA.

Antibiotic susceptibility and genotypic characterization of Haemophilus influenzae strains isolated from nasopharyngeal specimens from children in day-care centers in eastern France

OBJECTIVE

To determine the overall carriage rate for Haemophilus influenzae in young children in day-care centers, the frequency of resistance to various classes of antibiotic, and the clonal relationship between isolates of the various resistant phenotypes.

METHODS

Nasopharyngeal (NP) specimens were obtained and cultured on chocolate agar with bacitracin. Antibiotic susceptibility testing and serotyping were performed for all isolates. The genetic polymorphism of ampicillin-susceptible and beta-lactamase-producing isolates was studied by pulsed-field gel electrophoresis using SmaI.

RESULTS

Of the 596 NP secretion cultures, 152 (25.5%) were positive for H. influenzae. Sixty-four (42.1%) isolates produced beta-lactamase and two (1.3%) were ampicillin resistant but did not produce beta-lactamase. We were unable to serotype 150 isolates; one isolate belonged to capsular serotype e and one to serotype f. Forty-six major DNA patterns were identified among 76 randomized isolates. beta-lactamase producing isolates more frequently showed EP than ampicillin-susceptible isolates P < 10(-4). The frequency of isolates with EP was significantly lower in day-care centers attended by less than 20 children than in those attended by more than 20 children (P = 0.020).

CONCLUSIONS

Resistance due to beta-lactamase production has disseminated in some day-care centers, mostly by person-to-person spread but also via the possible conjugal transfer of large plasmids between strains. The size of day-care centers may affect the risk of transmission.

Clinical and molecular epidemiology of chromosome-mediated resistance to third-generation cephalosporins in Enterobacter isolates in eastern France

OBJECTIVE

To determine both the prevalence of group I beta-lactamase-related resistance and the clinical setting in which resistance to expanded-spectrum cephalosporins occurs.

METHODS

Isolates of Enterobacter spp. were sensitivity tested to a range of antibiotics, and selected isolates were DNA fingerprinted by pulsed-field gel electrophoresis. The medical records of all patients with positive cultures for Enterobacter spp. were reviewed to determine the effect of previous antibiotic treatment on the susceptibility profile of these organisms.

RESULTS

The crude incidence of colonization/infection (n = 315) was 0.51 per 100 patients and 0.73 per 1000 days of hospitalization. The 4-day and 7-day Kaplan-Meier rates of colonization/infection with Enterobacter were estimated to be 7.57% (standard deviation (SD = 3.26%) and 4.16% (SD = 2.88%)), respectively. The time lag to colonization/infection with isolates producing large amounts of Bush group 1 beta-lactamase (HLBL) (27.35 +/- 27.30 days) was significantly different from that to colonization/infection with wild-type isolates (13.59 +/- 17.93 days) (P = 0.036). Ninety-six isolates (30.5%) demonstrated acquired resistance to expanded-spectrum cephalosporins: 34 isolates (10.8%) produced extended-spectrum beta-lactamase, and 62 isolates (19.7%) produced HLBL. The 89 Enterobacter isolates susceptible to third-generation cephalosporins yielded 84 major DNA patterns, and the 45 HLBL isolates yielded 38 major DNA patterns. The risk of colonization/infection with HLBL-producing Enterobacter was higher in cases of antimicrobial treatment with third-generation cephalosporins or a fluoroquinolone, and in cases of urinary tract colonization/infection.

CONCLUSIONS

The judicious use in hospitals of both expanded-spectrum cephalosporins and other antibiotics such as fluoroquinolones is necessary to curtail the emergence of resistance in Enterobacter spp.

Clinical and molecular epidemiology of hospital Enterococcus faecium isolates in eastern France. Members of Réseau Franc-Comtois de Lutte contr les Infections Nosocomiales

We carried out a surveillance study of Enterococcus faecium isolates in the Franche-Comtéregion of France over three years. Clinical and epidemiological strains were characterized by antibiotype and genotype (pulsed field gel electrophoresis, PFGE). Three case-control studies were performed to identify risk factors for colonization/infection with three defined resistant phenotypes (amoxycillin, high-level gentamicin and high-level kanamycin). The crude incidence of colonization/infection was 0.156%, and 68.8% of cases were classified as hospital-acquired. Incidence did not differ according to the type of hospitalization (middle term or acute care). The urinary tract was the major site of infection. Resistance rates were: 45.8% (amoxycillin), 18.7% (high-level gentamicin), 61.4% (high-level kanamycin) and 3.1% (vancomycin). No isolate produced b-lactamase and one isolate carried the vanA gene. PFGE revealed two major epidemic patterns each including resistant strains isolated in different hospitals and during different periods in the study. Previous antimicrobial treatment was not identified as a risk factor for colonization/infection with any resistant phenotype. Despite the low frequency of vancomycin-resistant isolates in this study, resistant strains were widely disseminated and had characteristics enabling them to persist and spread. If these strains acquired the vanA gene, the risk of an outbreak would be large. So, the prevalence of vancomycin-resistant E. faecium in hospitals should be carefully monitored in the future.

Analysis of a mini-outbreak of methicillin-resistant Staphylococcus aureus in a surgical ward by using arbitrarily primed-polymerase chain reaction

In November 1995, an increase was noticed in the number of methicillin-resistant Staphylococcus aureus (MRSA) isolates from a surgical ward at Hacettepe University Hospital. All MRSA isolates obtained from clinical specimens in this ward (14 MRSA isolates from wound cultures of 10 patients) were collected prospectively for 10 weeks. Surveillance cultures were taken from ward personnel (nose cultures from 4 physicians, 7 nurses, 1 secretary, 1 waiter), 2 surgical dressing containers and 1 nebulizer. MRSA was isolated from one of the surgical dressing containers, the nebulizer and nose cultures of 3 physicians, 3 nurses and the ward secretary. Arbitrarily primed polymerase chain reaction (AP-PCR) analysis showed that most MRSA isolates belonged to 2 major clones (pattern A, pattern B). Pattern A was the most frequent one and was present in 4 clinical isolates, surgical dressing container-1. Pattern B was identified in 3 clinical isolates and nose culture of physician-3. AP-PCR analysis revealed that this mini-MRSA outbreak was caused by contamination of surgical dressing container with MRSA and nasal MRSA carriage in ward staff. AP-PCR seems to be a valuable typing method for analysis of nosocomial MRSA outbreaks because of its simplicity and rapidity.

Genetic homogeneity among methicillin-resistant Staphylococcus aureus strains from Saudi Arabia

Ninety-four strains of methicillin-resistant Staphylococcus aureus (MRSA) were collected from patients nursed in several hospitals in Saudi Arabia, before they were referred to King Faisal Specialist Hospital and Research Centre for tertiary care. The hospitals were from geographically diverse regions and as such the entirety of Saudi Arabia was covered. All strains were genetically typed by random amplification of polymorphic DNA (RAPD) analysis using three different primers and a representative subset of the strains was analyzed with pulsed-field gel electrophoresis (PFGE) as well. It was concluded that 87 out of 94 (93%) belong to a single clonally related lineage of MRSA. In the other 7 cases, the DNA banding patterns were shown to differ only slightly from those determined for the clonal type. PFGE analysis confirmed the homogeneity of the collection of strains. When the RAPD and PFGE fingerprints obtained for the Saudi clone were compared to those generated for a collection of MRSA with a more diverse geographical background, it was shown that the clonal type from Saudi Arabia was not identical to any of these MRSA strains. Our data provide another example of the capacity of certain MRSA clones to expand through entire nations and establish themselves permanently among large number of hospitals and, consequently, even larger numbers of patients.

Spread of a methicillin-resistant and multiresistant epidemic clone of Staphylococcus aureus in Argentina

One hundred forty-eight recent methicillin-resistant Staphylococcus aureus (MRSA) isolates collected from 13 hospitals in Argentina were examined for antibiotic susceptibility and clonal type, using hybridization with DNA probes specific for mecA and Tn554, and pulsed-field gel electrophoresis (PFGE) of chromosomal SmaI digests. The majority of the isolates (62.2%) shared the common PFGE B pattern and carried variants of mecA and Tn554 polymorphs characteristic of an MRSA clone widely spread in Brazilian hospitals. Similarly to the Brazilian isolates, the MRSA clone recovered in the Argentinian hospitals (XI::B::B) and its close relatives (XI::B'::B, XI::AA::B, XI::M::B, XI::omega omega::B, and III::W::B) showed susceptibility to spectinomycin and resistance to numerous antibacterial agents, including beta-lactams, tetracycline, aminoglycosides, macrolides, trimethoprim/sulfamethoxazole, ciprofloxacin, and fosfomycin, and more than 60% of the isolates were also resistant to chloramphenicol and rifampin. The XI::B::B MRSA clone represented the majority of isolates recovered in most of the hospitals, nine of which were located in the city of Buenos Aires, three in the province of Buenos Aires, and one in the province of Tucumán, 1,312 km northwest of the city of Buenos Aires. The observations document further geographic expansion of this South American MRSA clone across national boundaries.

Several different clones present during the penetration phase of resistant Streptococcus pneumoniae in the city of Malmö, Sweden

A rapid increase in the prevalence of Streptococcus pneumoniae with reduced sensitivity to penicillin (MIC > or = 0.12 microgram/mL) was noted among clinical isolates during a 15-month period in 1994-1995 in the city of Malmö, Sweden. All first-time clinical isolates (n = 178) were consecutively collected and investigated for genetic relatedness with BOX-A PCR and arbitrarily primed (AP) PCR. An improved method for chromosomal DNA extraction and the use of three reliable discriminatory primers for AP-PCR of S. pneumoniae are described. Using molecular fingerprinting, 30 different genotypes were discerned among the 178 isolates. The majority (87%) of isolates belonged to serogroups 6, 9, 15, 19, and 23. Resistance patterns and serogrouping indicated the presence of at least three major phenotypic clones. DNA fingerprinting in conjunction with minimum inhibitory concentration (MIC) values, resistance patterns, and epidemiological data confirmed the existence of two clones belonging to serogroups 6 and 9. Of the 178 isolates, 82% were from children of preschool age, most of whom attended day-care centers. We conclude that abundant S. pneumoniae strains with MICs > or = 0.12 microgram/mL for penicillin were present in the city of Malmö during the study period. At least two genetically discrete clones causing clinical illness were identified, and attendance at day-care centers may be a major factor in the spread of these strains.

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.

Multilocus sequence typing for characterization of methicillin-resistant and methicillin-susceptible clones of Staphylococcus aureus

A multilocus sequence typing (MLST) scheme has been developed for Staphylococcus aureus. The sequences of internal fragments of seven housekeeping genes were obtained for 155 S. aureus isolates from patients with community-acquired and hospital-acquired invasive disease in the Oxford, United Kingdom, area. Fifty-three different allelic profiles were identified, and 17 of these were represented by at least two isolates. The MLST scheme was highly discriminatory and was validated by showing that pairs of isolates with the same allelic profile produced very similar SmaI restriction fragment patterns by pulsed-field gel electrophoresis. All 22 isolates with the most prevalent allelic profile were methicillin-resistant S. aureus (MRSA) isolates and had allelic profiles identical to that of a reference strain of the epidemic MRSA clone 16 (EMRSA-16). Four MRSA isolates that were identical in allelic profile to the other major epidemic MRSA clone prevalent in British hospitals (clone EMRSA-15) were also identified. The majority of isolates (81%) were methicillin-susceptible S. aureus (MSSA) isolates, and seven MSSA clones included five or more isolates. Three of the MSSA clones included at least five isolates from patients with community-acquired invasive disease and may represent virulent clones with an increased ability to cause disease in otherwise healthy individuals. The most prevalent MSSA clone (17 isolates) was very closely related to EMRSA-16, and the success of the latter clone at causing disease in hospitals may be due to its emergence from a virulent MSSA clone that was already a major cause of invasive disease in both the community and hospital settings. MLST provides an unambiguous method for assigning MRSA and MSSA isolates to known clones or assigning them as novel clones via the Internet.

Molecular typing of fluoroquinolone-resistant and fluoroquinolone-susceptible Escherichia coli isolated from blood of neutropenic cancer patients in a single center

OBJECTIVE: To investigate the molecular epidemiology of fluoroquinolone-resistant (FQ-R) and fluoroquinolone-susceptible (FQ-S) bacteremic Escherichia coli isolates from neutropenic patients by pulsed-field gel electrophoresis (PFGE) and random amplified polymorphic DNA (RAPD) analysis. METHODS: Nineteen FQ-R and 27 FQ-S isolates of E. coli, obtained from patients on a hematologic ward over a 7-year period, were genotyped by PFGE and RAPD using two different random primers (1247 and 1283). RESULTS: PFGE analysis was able to type all FQ-S isolates and most (17/19, 89%) FQ-R isolates of E. coli. All isolates were genotypically unrelated, with the exception of two indistinguishable FQ-R isolates from different patients in the same period. RAPD analysis typed all isolates, including those FQ-R isolates untypable by PFGE, but was unable to distinguish between some isolates that were different by PFGE. Using primer 1247, RAPD analysis identified six pairs and one triad, while primer 1283 identified seven pairs and one triad of indistinguishable isolates. CONCLUSIONS: No spread of epidemic FQ-R or FQ-S E. coli isolates was documented among neutropenic patients. RAPD analysis is a powerful genotyping method, but appeared to be less reproducible and discriminatory than PFGE for investigating E. coli isolates.

Value of enterobacterial repetitive intergenic consensus PCR for study of Pasteurella multocida strains isolated from mouths of dogs

Fifty-six Pasteurella multocida strains (40 P. multocida subsp. septica and 16 P. multocida subsp. multocida strains) isolated from the mouths of 56 dogs among the 134 living in a French canine military training center (132e Groupe Cynophile de l'Armée de Terre, Suippes, France) were studied by use of enterobacterial repetitive intergenic consensus-PCR (ERIC-PCR) and restriction fragment length polymorphism (RFLP) techniques. Both techniques showed genomic heterogeneity of the strains studied. However, RFLP was more discriminatory than ERIC-PCR for differentiating P. multocida strains. All but three pairs of strains were discriminated by RFLP, suggesting a limited circulation of strains between these dogs living in proximity. Although ERIC-PCR is easier and faster to perform, it cannot be recommended for epidemiological studies of P. multocida strains.

PCR-RFLP analysis of the coagulase gene of Staphylococcus aureus: application to the differentiation of epidemic and sporadic methicillin-resistant strains

Preventing cross-infection with epidemic strains of methicillin-resistant Staphylococcus aureus (MRSA) requires effective control measures. These call for simple, rapid, discriminatory and reproducible methods for typing this pathogen. In this study 140 isolates/strains from 105 hospitals in England and Wales, representing 72 diverse phage types, were analysed by bacteriophage typing and PCR coagulase (coa) gene restriction fragment length polymorphism (RFLP). Isolates gave a coa gene PCR product that was either 660 base pairs (bp), 603 bp or 547 pb in size. The PCR products were digested with Alu I and Cfo I, and the fragments separated by gel electrophoresis. Eight coa gene RFLP patterns, numbered 1 to 8, were observed. Pattern 3 was most common (N = 25 isolates), followed by patterns 2 and 5 (18 isolates each), pattern 1 (14 isolates), pattern 4 (11 isolates), pattern 7 (10 isolates), pattern 8 (eight isolates) and pattern 6 (six isolates). Isolates of the same phage type often gave different coa gene RFLP patterns, and the patterns within the epidemic types EMRSA-03, EMRSA-15 and EMRSA-16 were heterogeneous. Thus, representatives of EMRSA-03 were subtyped to coa RFLP patterns 1 and 2, those of EMRSA-05 to coa RFLP patterns 1, 2, 7 and 8, and those for EMRSA-16 to coa RFLP patterns 2, 3, 4, 5 and 6. The range of patterns within single phage types of S. aureus could help to discriminate between isolates/strains, and in a hierarchical approach coa gene RFLP could occupy an intermediate position between phage typing and pulsed-field gel electrophoresis (PFGE).

Clinical and molecular epidemiology of hospital Enterococcus faecalis isolates in eastern France

OBJECTIVE: To report on the occurrence of Enterococcus faecalis hospital isolates obtained during 1 year in hospitals in the Franche-Comté region of France. METHODS: Clinical isolates of E. faecalis of different antibiotic susceptibility phenotypes from hospitalized patients were characterized by pulsed-field gel electrophoresis. Patients with positive cultures were investigated by three case-control studies to identify risk factors for colonization/infection. RESULTS: The crude incidence of colonization/infection was 2.37%, and 4-day and 7-day colonization rates after admission were 10.0% and 6.36%, respectively. The rates of high-level resistance to kanamycin (HLKR) and to gentamicin (HLGR) were 47.1% and 7.1%, respectively. No isolate was resistant to glycopeptides or produced beta-lactamase. The 209 hospital isolates obtained during the study yielded 98 major DNA patterns, of which two were major epidemic patterns including HLKR isolates. No single factor was significantly associated with colonization/infection by HLKR isolates. The length of hospitalization before isolation was associated with colonization by HLGR isolates. CONCLUSIONS: The isolation frequency of E. faecalis strains with acquired resistance to aminoglycoside antibiotics, and the wide dissemination of resistant strains with characteristics that allow them to persist and spread, argue for further large prospective surveys of clinical isolates of E. faecalis in hospitals.

Intercontinental spread of a multidrug-resistant methicillin-resistant Staphylococcus aureus clone

Two hundred ten methicillin-resistant Staphylococcus aureus (MRSA) isolates recovered between 1990 and 1997 from three Portuguese hospitals located in Lisbon and Oporto were analyzed by molecular fingerprinting techniques. The hybridization of ClaI restriction digests with the mecA- and Tn554-specific DNA probes combined with pulsed-field gel electrophoresis documented the abrupt appearance and extensive intrahospital spread of the Brazilian epidemic MRSA clone in the 1995 samples of each one of the three hospitals analyzed-suggesting the intercontinental transfer of this strain from Brazil to Portugal. The appearance of this clone may challenge the dominance of another highly epidemic imported clone-the Iberian MRSA, currently the most widely spread MRSA clone in Portuguese hospitals.

Clonal identification of Aeromonas hydrophila strains using randomly amplified polymorphic DNA analysis

The suitability of arbitrary primer polymerase chain reaction (RAPD) as a typing technique was evaluated by comparing it with pulsed-field gel electrophoresis (PFGE) to characterize Aeromonas hydrophila strains isolated from a cluster of hospital-acquired infections. Five isolates from patients and 10 isolates from the water supply were compared to 10 epidemiologically unrelated strains isolated from patients and rivers. Two methods were used to prepare DNA and two primers (AP3 and AP5) were selected. The discriminatory power was better with the extractive DNA preparation than the boiling method. The discrimination of closely related from less related strains by PCR using AP3 was consistent with that by PFGE: water supply of Cholet hospital contaminated with Aeromonas species was not the source of the cluster of hospital infections and only two patients were infected with clonally-related strains. RAPD using primer AP3 was simpler, cheaper, and quicker to perform than pulsed-field gel electrophoresis and is well suited for the epidemiological study of A. hydrophila isolates.

Repetitive sequence-based PCR versus pulsed-field gel electrophoresis for typing of Enterococcus faecalis at the subspecies level

Repetitive sequence-based PCR was compared to pulsed-field gel electrophoresis (PFGE) for the ability to discriminate Enterococcus faecalis isolates at the subspecies level. The BOXA2R primer, derived from repetitive sequences in Streptococcus pneumoniae, was applied to 41 isolates of E. faecalis collected from various sources. The REP1R-Dt and REP2-Dt primers, derived from the gram-negative repetitive extragenic palindromic element, were also applied to 18 selected isolates. Of the 41 isolates examined, 7 were beta-lactamase producing and 8 were vancomycin resistant. By PFGE, 17 isolates had distinct patterns; the other 24 were classified into eight different clonal groups. By PCR using the BOXA2R primer, 16 isolates generated distinct patterns; the other 25 were classified into nine different clonal groups. There were only minor differences in the PCR results obtained by using the BOXA2R primer and the REP1R-Dt and REP2-Dt primers. Two isolates among vancomycin-resistant enterococci from the greater Houston, Tex., area were related by PFGE, distinct by PCR with the BOXA2R primer, and related by PCR with the REP1R-Dt and REP2-Dt primers. Clonal relationships among the remaining 39 isolates were similar by both PFGE and PCR. PCR reliably discriminated all epidemiologically unrelated isolates. Although PCR is less time consuming than PFGE, PCR results were more difficult to interpret than PFGE results, perhaps because fewer bands were generated by PCR than by PFGE and some PCR products were inconsistently seen.

Typing of Staphylococcus aureus and Staphylococcus epidermidis strains by PCR analysis of inter-IS256 spacer length polymorphisms

IS256 elements are present in multiple copies in the staphylococcal genome, either flanking the transposon Tn4001 or independent of it. PCR-based analysis of inter-IS256 spacer polymorphisms was developed for typing of methicillin-resistant Staphylococcus aureus (MRSA) and Staphylococcus epidermidis strains. Using SmaI macrorestriction analysis resolved by pulsed-field gel electrophoresis (PFGE) as the reference method for MRSA typing, excellent reproducibility (100%), discriminatory power (97%), and in vivo stability were observed. Good concordance of the results with those of other molecular typing methods was found for two MRSA collections. Inter-IS256 PCR analysis of a U.S. collection of MRSA strains (n = 36), previously characterized by 15 typing methods, showed more limited discrimination. Agreement was 78% with PFGE analysis and 83% with ribotyping (HindIII). Analysis of a second set of Belgian MRSA strains (n = 17), categorized into two widespread epidemic clones by PFGE analysis, showed 65% agreement. For typing of S. epidermidis strains (n = 26), inter-IS256 PCR showed complete typeability (100%) and good discriminatory power (85%). Inter-IS256 PCR analysis is proposed as an efficient molecular typing assay for epidemiological studies of MRSA or S. epidermidis isolates.

Association of mutations in grlA and gyrA topoisomerase genes with resistance to ciprofloxacin in epidemic and sporadic isolates of methicillin-resistant Staphylococcus aureus

The types of topoisomerase alterations in genomically diverse epidemic and sporadic strains of methicillin- and fluoroquinolone-resistant Staphylococcus aureus isolated from European hospitals between 1984 and 1994 were characterized. Convergent dual mutations in gyrA (codon 83, 84, or 88) and grlA (codon 79 and/or 80) were found in all strains exhibiting high-level resistance to ciprofloxacin (MIC, 16 to > or = 128 microg/ml). In some epidemic strains, the resistant phenotype and genotype appeared in the 1990s and persisted thereafter.

Epidemiologically related and unrelated strains of Pseudomonas aeruginosa serotype O12 cannot be distinguished by phenotypic and genotypic typing

A clonal origin for European isolates of antibiotic multi-resistant Pseudomonas aeruginosa serotype O12 has been suggested. This study was designed to assess the value and limitations of several typing methods for the investigation of outbreaks due to this serotype. In Hôpital de Rodez, France, this organism is endemic, and a prospective clinical epidemiological study was undertaken over a 15 month period, encompassing all patients at the hospital from whom P. aeruginosa O12 was isolated. All isolates were examined by auxanogram, antibiogram, phage-typing, electrophoresis of esterases and pulsed-field gel electrophoresis of DNA. The results suggest that (1) the methods used did not clearly differentiate between clinically-related and epidemiologically-unrelated European isolates, (2) in Hôpital de Rodez, while some isolates were likely to have been transmitted from patient-to-patient, most infections or colonizations with this organism were sporadic and their origin is unknown. The limits of typing methods for the investigation of outbreaks of nosocomial infection with multi-resistant P. aeruginosa O12 are emphasized.

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.

Monitoring Persistence of Coagulase-Negative Staphylococci in a Hematology Department Using Phenotypic and Genotypic Strategies

Objective:

To determine persistence of coagulase-negative staphylococci (CNS) on a hematology-oncology ward and to determine the value of phenotypic and genotypic procedures for establishing clonality among CNS isolates.

Design:

Strains of CNS isolated from bacteremic patients (n=139) were typed by biochemical reactivity, antibiotic susceptibility, DNA macrorestriction analysis by pulsed-field gel electrophoresis (PFGE), and arbitrary primed polymerase chain reaction (AP PCR). Coagulase-negative staphylococci were subgrouped in a random collection (n=20) used for the evaluation of the typing procedures and a collection of 119 CNS isolates from hematologic patients displaying multiple bacteremic episodes.

Results:

Analysis of the reference collection demonstrated the usefulness of the DNA typing procedures, indicating that AP PCR and PFGE can be used for epidemiologic typing of CNS in a concordant fashion. Certain strains appeared to be permanent colonizers of the hematology ward or ward-related personnel. In individual patients, persistent colonization by a single type was demonstrated. However, a number of patients also experienced bacteremic episodes caused by CNS belonging to different types.

Conclusion:

We conclude that monitoring of CNS infections on a hematology ward by various genotypic techniques provides insight into nosocomial epidemiology and elucidates the complexity of the infections taking place. DNA typing is preferred over phenotypic procedures and can identify persistent CNS strains in a given location.