Comparison of four genotyping assays for epidemiological study of methicillin-resistant Staphylococcus aureus

Historic methicillin-resistant Staphylococcus aureus: expanding current knowledge using molecular epidemiological characterization of a Swiss legacy collection

BACKGROUND

Few methicillin-resistant Staphylococcus aureus (MRSA) from the early years of its global emergence have been sequenced. Knowledge about evolutionary factors promoting the success of specific MRSA multi-locus sequence types (MLSTs) remains scarce. We aimed to characterize a legacy MRSA collection isolated from 1965 to 1987 and compare it against publicly available international and local genomes.

METHODS

We accessed 451 historic (1965-1987) MRSA isolates stored in the Culture Collection of Switzerland, mostly collected from the Zurich region. We determined phenotypic antimicrobial resistance (AMR) and performed whole genome sequencing (WGS) using Illumina short-read sequencing on all isolates and long-read sequencing on a selection with Oxford Nanopore Technology. For context, we included 103 publicly available international assemblies from 1960 to 1992 and sequenced 1207 modern Swiss MRSA isolates from 2007 to 2022. We analyzed the core genome (cg)MLST and predicted SCCmec cassette types, AMR, and virulence genes.

RESULTS

Among the 451 historic Swiss MRSA isolates, we found 17 sequence types (STs) of which 11 have been previously described. Two STs were novel combinations of known loci and six isolates carried previously unsubmitted MLST alleles, representing five new STs (ST7843, ST7844, ST7837, ST7839, and ST7842). Most isolates (83% 376/451) represented ST247-MRSA-I isolated in the 1960s, followed by ST7844 (6% 25/451), a novel single locus variant (SLV) of ST239. Analysis by cgMLST indicated that isolates belonging to ST7844-MRSA-III cluster within the diversity of ST239-MRSA-III. Early MRSA were predominantly from clonal complex (CC)8. From 1980 to the end of the twentieth century, we observed that CC22 and CC5 as well as CC8 were present, both locally and internationally.

CONCLUSIONS

The combined analysis of 1761 historic and contemporary MRSA isolates across more than 50 years uncovered novel STs and allowed us a glimpse into the lineage flux between Swiss-German and international MRSA across time.

Analysis of Salmonella enterica Serovar Typhi by Outer Membrane Protein (OMP) Profiling, Random Amplification of Polymorphic DNA (RAPD) and Pulsed Field Gel Electrophoresis (PFGE)

A number of countries, including developed countries, still have typhoid fever as a major problem resulting in frequent outbreaks. The importance of controlling spread of typhoid fever is well known and necessitates periodic studies to delineate epidemiological relationships. Although phage typing remains to be the preferred conventional method for characterisation of typhoid bacilli, it is of limited use due to prevalence of few predominant phage types in the country like India. Therefore, an effort has been made to assess three molecular methods [Outer Membrane Protein (OMP) Profiling, Random Amplification of Polymorphic DNA (RAPD) and Pulsed Field Gel Electrophoresis (PFGE)] for typing of Salmonella enterica serovar Typhi. 128 Salmonella enterica serovar Typhi isolates were identified using biotyping and serotyping followed by antimicrobial susceptibility testing. These isolates were further subjected to OMP analysis, RAPD and PFGE. PFGE (114 unique clusters) was found to be the most discriminatory method followed by RAPD (94 unique clusters) and OMP profiling (50 unique clusters). Multidrug resistant strains were well discriminated by all three methods used in the study. PFGE still remains the most preferred method for detailed epidemiological investigations. However, random amplification of polymorphic DNA and outer membrane protein profiling can also be considered for molecular discrimination of the isolates in the laboratories lacking high-end facilities.

Multiple-locus variable number tandem repeat analysis of Staphylococcus aureus: comparison with pulsed-field gel electrophoresis and spa-typing

Background

Molecular typing of methicillin-resistant Staphylococcus aureus (MRSA) is required to study the routes and rates of transmission of this pathogen. Currently available typing techniques are either resource-intensive or have limited discriminatory ability. Multiple-locus variable number tandem repeat analysis (MLVA) may provide an alternative high throughput molecular typing tool with high epidemiological resolution.

Methodology/Principal Findings

A new MLVA scheme for S. aureus was validated using 1681 S. aureus isolates collected from Dutch patients and 100 isolates from pigs. MLVA using 8 tandem repeat loci was performed in 2 multiplex PCRs and the fluorescently labeled PCR products were accurately sized on an automated DNA sequencer. The assessed number of repeats was used to create MLVA profiles consisting of strings of 8 integers that were used for categorical clustering. MLVA yielded 511 types that clustered into 11 distinct MLVA complexes which appeared to coincide with MLST clonal complexes. MLVA was at least as discriminatory as PFGE and twice as discriminatory as spa-sequence typing. There was considerable congruence between MLVA, spa-sequence typing and PFGE, at the MLVA complex level with group separation values of 95.1% and 89.2%. MLVA could not discriminate between pig-related MRSA strains isolated from humans and pigs, corroborating the high degree of relationship. MLVA was also superior in the grouping of MRSA isolates previously assigned to temporal-spatial clusters with indistinguishable SpaTypes, demonstrating its enhanced epidemiological usefulness.

Conclusions

The MLVA described in this study is a high throughput, relatively low cost genotyping method for S. aureus that yields discrete and unambiguous data that can be used to assign biological meaningful genotypes and complexes and can be used for interlaboratory comparisons in network accessible databases. Results suggest that MLVA offsets the disadvantages of other high discriminatory typing approaches and represents a promising tool for hospital, national and international molecular epidemiology.

Molecular characterisation of Staphylococcus aureus strains isolated from small and large ruminants reveals a host rather than tissue specificity

Staphylococcus aureus is an important pathogen in domestic ruminants. The main objective of this study was to determine the similarity of epidemiologically unrelated S. aureus isolates from bovine, ovine, and caprine hosts regardless the locus of isolation (nares and udder). By pulsed-field gel electrophoresis, seven major pulsotypes were identified among 153 isolates recovered from 12 different regions of France as well as from Brazil, the USA and Belgium. Typing of the accessory gene regulator (agr) and capsular (cap) serotype was carried out on all the isolates and revealed the predominance of agr I and III and of cap8 regardless the ruminant host species. Screening for methicilin-resistant S. aureus (MRSA) was carried out by disk diffusion and revealed a prevalence of only 3.2% of MRSA among the strains tested. These results suggest the existence of a host rather than tissue specificity among S. aureus isolates colonising the ruminant species and suggest a limited transmission of those isolates between large (bovine) and small (ovine-caprine) ruminants. The agr class and cap types correlated with pulsotype clusters rather than with a specific host species. Antimicrobial resistance appears not to have contributed to the predominance of any given genotypes, and MRSA prevalence appears very low in ruminant isolates.

Application of molecular techniques to the study of hospital infection

Nosocomial infections are an important source of morbidity and mortality in hospital settings, afflicting an estimated 2 million patients in United States each year. This number represents up to 5% of hospitalized patients and results in an estimated 88,000 deaths and 4.5 billion dollars in excess health care costs. Increasingly, hospital-acquired infections with multidrug-resistant pathogens represent a major problem in patients. Understanding pathogen relatedness is essential for determining the epidemiology of nosocomial infections and aiding in the design of rational pathogen control methods. The role of pathogen typing is to determine whether epidemiologically related isolates are also genetically related. To determine molecular relatedness of isolates for epidemiologic investigation, new technologies based on DNA, or molecular analysis, are methods of choice. These DNA-based molecular methodologies include pulsed-field gel electrophoresis (PFGE), PCR-based typing methods, and multilocus sequence analysis. Establishing clonality of pathogens can aid in the identification of the source (environmental or personnel) of organisms, distinguish infectious from noninfectious strains, and distinguish relapse from reinfection. The integration of molecular typing with conventional hospital epidemiologic surveillance has been proven to be cost-effective due to the associated reduction in the number of nosocomial infections. Cost-effectiveness is maximized through the collaboration of the laboratory, through epidemiologic typing, and the infection control department during epidemiologic investigations.

Use of an automated multiple-locus, variable-number tandem repeat-based method for rapid and high-throughput genotyping of Staphylococcus aureus isolates

Fast and reliable genotyping methods that allow real-time epidemiological surveillance would be instrumental to monitoring of the spread of methicillin-resistant Staphylococcus aureus. We describe an automated variable-number tandem repeat-based method for the rapid genotyping of Staphylococcus aureus. Multiplex PCR amplifications with eight primer pairs that target gene regions with variable numbers of tandem repeats were resolved by microcapillary electrophoresis and automatically assessed by cluster analysis. This genotyping technique was evaluated for its discriminatory power and reproducibility with clinical isolates of various origins, including a panel of control strains previously characterized by several typing methods and collections from either long-term carriers or defined nosocomial outbreaks. All steps of this new procedure were developed to ensure a rapid turnaround time and moderate cost. The results obtained suggest that this rapid approach is a valuable tool for the genotyping of S. aureus isolates in real time.

Distribution of mecA among methicillin-resistant clinical staphylococcal strains isolated at hospitals in Naples, Italy

Two hundred and twenty strains of Staphylococcus isolated in Naples, Italy, were surveyed for the distribution of the mecA, the structural gene for penicillin-binding protein 2a, which is the genetic determinant for methicillin-resistance in staphylococci. Screening by a cloned mecA, revealed that of 220 strains, 43 were methicillin-resistant (19.5%) and 177 were methicillin-susceptible (80.5%). Among the 43 resistant strains 23 (53.5%) carried mecA in their genome and 20 (46.5%) did not carry mecA, in spite of their resistance to methicillin. Every group was submitted to the AP-PCR profiling. A quantitative analysis of the patterns divided strains into four different clusters for methicillin-resistant mecA-negative and two different clusters for methicillin-resistant mecA-positive with primer 1, while no clusters were noted with primer 7. We conclude that these clinical isolates from our area, were not found to belong to a single clone, although the predominance of four methicillin-resistant mecA-negative genotypes were noted.

Dynamics of bacterial colonisation in the respiratory tract of patients with cystic fibrosis

Mutations in the human genome may result in altered phenotypes. The cystic fibrosis (CF) patient, for instance, suffers from an aberrant composition of the epithelial lining of the gastrointestinal and respiratory tract. In this particular case, a single point mutation in the cystic fibrosis conductance regulator (CFTR) gene results in major physiological changes resulting in ecological changes that generate a niche particularly attractive to a selected set of microbial pathogens. We here present a review on the dynamics of the bacterial populations inhabiting the CF lung. Studies focusing on Staphylococcus aureus, Haemophilus influenzae and Pseudomonas aeruginosa will be summarised and discussed, whereas the technology used for microbial characterisation will be shortly highlighted. Emphasis, however, will be on those studies that assessed the genetic diversity among clinical isolates that were obtained over prolonged periods of time, enabling the distinction between persistent colonisation versus frequent re-infection by the selected pathogens. Evolutionary adaptation of pathogens to the CF lung is a common theme in many of these studies.

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.

Subtyping of MRSA isolates belonging to a widely disseminated clonal group by polymorphism of the dru sequences in mec-associated DNA

During the past 7 years the "Berlin epidemic MRSA" has spread throughout whole Germany. SmaI macrorestriction patterns of this clonal group are rather stable as are the length polymorphisms at the 3' end of the coagulase gene and the x-region of spa. However, the dru region (direct repeat units) of mec-associated DNA exhibits a length polymorphism due to deletion of one or more direct repeat units. Five different subclones could be discriminated by dru region length polymorphism. Location of deletions and of a few point mutations allow a delineation of these subclones.

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.

DNA heterogeneity of Staphylococcus aureus strains evaluated by SmaI and SgrAI pulsed-field gel electrophoresis in patients with impetigo

To our knowledge, no studies have previously been carried out on the heterogeneity and intrafamily colonization of impetigo Staphylococcus aureus strains obtained by powerful discriminating methods such as pulsed-field gel electrophoresis (PFGE). To explore this topic, macrorestriction patterns of S. aureus strains were analyzed after SmaI and SgrAI digestion. The two enzymes provided superimposable results. A total of ninety-seven S. aureus strains was found in the 26 families whose lesions and nasal and pharyngeal samples were examined. There were 39 strains which were different by PFGE, and of these, 24 were found in the lesions. Although 85% of impetigo patients showed nasal colonization and 58% showed pharyngeal colonization, only 54% of the patients had the same PFGE strain in the lesion and in the nose, and 35% in the lesion and the pharynx. In half of the 26 families, at least one member (mother, father, or relative) presented a S. aureus strain identical, by PFGE, to strains isolated in patients' lesions. Nineteen percent of mothers, 15% of fathers, and 19% of the other relatives presented nasal colonization with strains identical to those isolated in the children's lesions. Lesional strains showed higher antimicrobial resistance than nonlesional isolates.

Persistence of Legionella pneumophila in a hospital's water system: a 13-year survey

OBJECTIVE

To describe the molecular epidemiology of Legionella pneumophila infections in the University of Iowa Hospitals and Clinics (UIHC).

DESIGN

Molecular epidemiological study using pulsed-field gel electrophoresis (PFGE).

SETTING

A large university teaching hospital. ISOLATES: All surviving isolates obtained from culture-proven nosocomial L. pneumophila infections and all surviving isolates obtained from the University of Iowa Hospital and Clinics' water supply between 1981 and 1993.

RESULTS

Thirty-three isolates from culture-proven nosocomial cases of L. pneumophila pneumonia were available for typing. PFGE of genomic DNA from the clinical isolates identified six different strains. However, only strain C (16 cases) and strain D (13 cases) caused more than 1 case. Strain C caused clusters of nosocomial infection in 1981, 1986, and 1993 and also caused 4 sporadic cases. Strain D caused a cluster in 1987 and 1988 plus 4 sporadic cases. Of the six strains causing clinical infections, only strains C and D were identified in water samples. PFGE identified three strains in the water supply, of which strains C and D caused clinical disease and also persisted in the water supply during most of the study period.

CONCLUSION

Specific strains of L. pneumophila can colonize hospital water supplies and cause nosocomial infections over long periods of time.

Nasal carriage of staphylococcus aureus and epidemiology of surgical-site infections in a Sudanese university hospital

Surgical site infections (SSI) due to Staphylococcus aureus among 256 male and 158 female patients (mean age, 28 years) undergoing elective surgery at the Soba University Hospital (Khartoum, Sudan) were studied. During an 11-month study period all patients were analyzed for nasal carriage of S. aureus at the time of admission. Follow-up of the development of SSI proceeded until 4 weeks after the operations. In addition, nasal swabs were obtained periodically during the same period from 82 members of the staff. In order to discriminate autoinfection from cross infection, bacterial isolates were typed by random amplification of polymorphic DNA (RAPD), pulsed-field gel electrophoresis (PFGE) of DNA macrorestriction fragments, and restriction fragment length polymorphism analysis of the protein A and coagulase genes. Preoperative cultures revealed the presence of S. aureus in the noses of 98 patients (24%). The overall number of postsurgical wound infections in the entire group was 57 (14%), 24 of which were due to S. aureus. Only 6 of the 98 nasal S. aureus carriers suffered from wound infections by the same species. In these six cases the infecting strain could not be genetically discriminated from the nasal inhabitant, substantiating autoinfection. However, nasal carriage of S. aureus is not a significant risk factor for the development of SSI in this setting (6 of 98 patients with autoinfection versus 18 of 316 patients [414 - 98 patients] with cross infection; P = 0.81), most probably due to the fact that noncarriers are at a significant and relatively large risk for acquiring an independent S. aureus SSI. The other S. aureus strains causing SSI showed a high degree of genetic heterogeneity, demonstrating that it is not an epidemic strain that is causing the SSI. Among the staff personnel screened, 47.4% did not carry S. aureus in the nose at any time during the study period, whereas 13. 2% persistently carried a single strain in the nose. Another 39.5% could be classified as intermittent carriers. When strains derived from staff personnel were genetically typed, it was demonstrated that most of the strains represented genetic variants clearly differing from the isolates causing SSI. On the other hand, possible cross colonization among staff personnel and even cross infection from staff personnel to patients or from patient to patient were demonstrated in some cases, but epidemic spread of a single strain or a few clonally related strains of S. aureus could be excluded.

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.

Outbreak of Staphylococcus schleiferi wound infections: strain characterization by randomly amplified polymorphic DNA analysis, PCR ribotyping, conventional ribotyping, and pulsed-field gel electrophoresis

Within a 1-year period, six surgical-site infections (SSI) caused by Staphylococcus schleiferi were observed in the department of cardiac surgery of Ignatius Hospital, Breda, The Netherlands. Since outbreaks caused by this species of coagulase-negative staphylococci have not been described before, an extensive environmental survey and a case control study were performed in combination with molecular typing of the causative microorganism in order to identify potential sources of infection. Variability, as detected by four different genotyping methods (random amplification of polymorphic DNA [RAPD], conventional and PCR-mediated ribotyping, and pulsed-field gel electrophoresis [PFGE] of DNA macro restriction fragments), appeared to be limited both among the clinical isolates and among several control strains obtained from various unrelated sources. Among unrelated strains, RAPD and PCR-mediated ribotyping identified two types only, whereas seven different types were identified in a relatively concordant manner by conventional ribotyping and PFGE. The latter two procedures proved to be the most useful tools for tracking the epidemiology of S. schleiferi. Four of the outbreak-related strains were identical by both methods, and two isolates showed limited differences. In the search for a potential source of S. schleiferi infection, two slightly different PFGE types were encountered on several occasions in the nose of a single surgeon. These strains were, however, clearly different from the outbreak type. In contrast, S. schleiferi cultures remained negative for two persons identified on the basis of case control analysis. It was demonstrated that SSI caused by S. schleiferi had a clinical impact for patients comparable to that of a wound infection caused by Staphylococcus aureus. This report describes the first well-documented outbreak of S. schleiferi infection. A source of the outbreak was not detected.

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.

Simultaneous persistence of methicillin-resistant and methicillin-susceptible clones of Staphylococcus aureus in a neonatal ward of a Warsaw hospital

Fifty-seven methicillin-resistant Staphylococcus aureus (MRSA) isolates from babies (N = 31), carriers amongst health care workers (N = 16; 10% of all staff members) and the environment (N = 10); 39 MSSA isolates, from babies (N = 18), health care workers (N = 5) and environment (N = 16) were analysed. The strains were from the neonatal ward of a teaching hospital in Warsaw and were collected over a period of 16 months (1993/1994). The isolates were characterized by phage-typing, arbitrary-primed polymerase chain reaction (AP PCR), DNA repeat polymorphism within the protein A gene and the resistance pattern to antimicrobial agents. The presence of the mecA gene was determined by PCR. MRSA were classified as heterogeneously resistant to methicillin, susceptible to other antimicrobial agents and, except for three isolates, appeared to be genotypically almost identical. The first example of mupirocin resistant MRSA in Poland was documented. Amongst MSSA isolates, increased variability was seen, however, the persistence of one predominate clone of MSSA was shown. In this particular hospital environment, several different strains of both MRSA and MSSA were capable of maintaining persistent colonization.

Increasing incidence and widespread dissemination of methicillin-resistant Staphylococcus aureus (MRSA) in hospitals in central Europe, with special reference to German hospitals

OBJECTIVE: to present data on prevalence and interregional spread of methicillin-resistant Staphylococcus aureus (MRSA) in Germany. METHODS: A nationwide collection of MRSA isolates from nosocomial infections in 143 hospitals was established from isolates (n=4368) sent to a microbiological reference center during 1993--95. As chosen by distinguishable resistance phenotypes at each time of occurrence during the study period, 1830 isolates were subjected to molecular typing by means of Smal macrorestriction patterns, PCR for RNA gene spacer patterns, and PCR for patterns of DNA stretches flanked by the ERIC-2 sequence and flanked by Tn916 and ribosomal binding site. In addition, data from a multicenter study on the incidence of antibiotic resistance have been analyzed (32 centers, 637 S. aureus isolates). RESULTS: In 1995 the prevalence of MRSA among S. aureus isolates was 8.7% overall in central Europe (including Germany), in comparison to 1.7% in 1990. From 1993 until now, a continuous interregional dissemination of six epidemic strains, which were identified by molecular typing, was recorded. Besides these epidemic strains, 15 MRSA strains were identified which could not be allocated to the epidemic MRSA or to the known clonal groups of the species S. aureus. MRSA from three cases of sporadic nosocomial infections exhibited characteristics of the clonal group of S. aureus with the capacity for toxic shock syndrome formation. The pattern of one MRSA corresponded to those of the S. aureus group exhibiting phage pattern 94,96. CONCLUSIONS: The prevalence of MRSA has increased in central Europe (and Germany) during the last 5 years, to 8.7%. The main source of infection with MRSA is obviously interregional dissemination of epidemic strains. At the same time, the mecA gene has been acquired by strains previously sensitive to methicillin.

Molecular epidemiology of Staphylococcus aureus strains colonizing the lungs of related and unrelated cystic fibrosis patients

BACKGROUND: Cystic fibrosis (CF) patients can become persistently colonized with Staphylococcus aureus. This is initiated at an early age and may continue until or sometimes even during adolescence. Little is known about the epidemiology and cross-infectivity of S. aureus in CF patients, whether via the environment or person to person. METHODS: S. aureus isolates (n=189) from six unrelated CF patients and six pairs of CF siblings were genetically typed by arbitrary primed polymerase chain reaction (AP-PCR) assays. RESULTS: This longitudinal study revealed 35 different genotypes among the 189 isolates; the median number of types in a patient was three (range 1--6). One common S. aureus genotype was found in six patients and involved 20% of all isolates analyzed. Ultimately, in most of the patients long-term colonization with a single genotype was observed. In several, but certainly not all, pairs the siblings became persistently colonized with isolates that could not be discriminated by the typing method used; different S. aureus genotypes were isolated on an incidental but relatively frequent basis. Only one pair of siblings never shared identical isolates at any time during the screening period. CONCLUSIONS: In five of six cases, identical isolates were shared by CF siblings at a certain time. This suggests intra-family transmission or the presence of a common environmental source. The fact that in most of the CF sibling pairs different genotypes of S. aureus caused the ultimate long-term colonization indicates that, despite regular cross-colonization, patient characteristics select the S. aureus strain best adapted to the affected lung. Some genotypes may be particularly prevalent in the CF patient population, but additional studies are needed to confirm this.

Use of pulsed-field gel electrophoresis to investigate an outbreak of Serratia marcescens

Pulsed-field gel electrophoresis (PFGE) typing was applied to the epidemiological investigation of 20 Serratia marcescens isolates collected from urine specimens of 17 patients and three urinals over a 2-month period. Twenty-five epidemiologically unrelated strains were also tested to determine the discriminatory power of PFGE. The PFGE fingerprints of each isolate were consistent in three different tests. The 20 outbreak isolates had an identical PFGE fingerprint pattern, while the epidemiologically unrelated strains demonstrated unique PFGE fingerprint patterns. The source of the outbreak was inadequately disinfected urinals. We conclude that PFGE served as a highly discriminatory and reproducible method for the epidemiological investigation of the outbreak of S. marcescens infection addressed by this study.

Changes in major populations of methicillin-resistant Staphylococcus aureus in Belgium

A total of 102 epidemic methicillin-resistant Staphylococcus aureus (MRSA) isolates collected in 13 Belgian hospitals during two periods (1981-1985 and 1991-1992) were tested for phage-type, for the presence of aminoglycoside-modifying enzymes (AME), and examined by arbitrarily primed polymerase chain reaction (AP-PCR). All isolates, but five, belonged to a few distinct phage-types of group III. Most isolates expressed a combination of AAC(6')-APH(2") with APH(3')III, and ANT(4',4") or both. Both phage-typing and AME suggested a change in the MRSA population between the two periods but the AP-PCR method revealed only slight differences.

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.

Typing of Staphylococcus aureus by PCR for DNA sequences flanked by transposon Tn916 target region and ribosomal binding site

The continuous intra- and interhospital spread of multiresistant Staphylococcus aureus demands a rapid molecular typing system. This study describes the fingerprinting of S. aureus by PCR amplification of DNA sequences flanked by the target site for transposon Tn916 and the ribosomal binding site and neighboring nucleotides (target 916-Shine-Dalgarno PCR [tar 916-shida PCR]). Both starting points for PCR are known to be randomly distributed on the S. aureus chromosome. By use of SmaI-macrorestriction patterns as the reference method it was shown that this PCR genotyping discriminates among strains of the major clonal groups of the species S. aureus (strains with phage patterns 29, +, 94, 96, and 95 as well as group II and group III patterns) and identifies the six epidemic methicillin-resistant S. aureus strains prevalent in German hospitals. All of the investigated strains including methicillin-sensitive. S. aureus were typeable. Tar 916-shida patterns are stable during the dissemination of epidemic methicillin-resistant S. aureus among different hospitals.

Typing of Pseudomonas aeruginosa strains from patients with cystic fibrosis: phenotyping versus genotyping

OBJECTIVE: To assess the discriminatory power of two genotypic and two phenotypic techniques by analysis of Pseudomonas aeruginosa sputum isolates obtained with long term intervals from 29 independent cystic fibrosis (CF) patients. METHODS: Fifty-eight strains of P. aeruginosa were subjected to serotyping and pyocin production was assessed. Arbitrarily primed polymerase chain reaction (AP PCR) and pulsed-field gel electrophoresis (PFGE) were applied in order to detect genetic polymorphisms. RESULTS: From the results of different typing techniques, it appeared that the numbers of separate types varied between 11 and 43, and the percentage of identical P. aeruginosa pairs from individual patients varied between 51% and 72%, depending on the test system used. AP PCR and PFGE displayed enhanced resolution when compared to serotyping and pyocin typing; both DNA typing techniques generated concordant results, although differences in resolution are apparent. This results in 15% discordance, which may be the result of differences in the definitions of (sub)clonal relatedness as applied for AP PCR and PFGE, respectively. CONCLUSIONS: Molecular typing techniques are superior to phenotyping where P. aeruginosa is concerned. AP PCR is a fast and useful technique for determining clonality among P. aeruginosa strains from chronically colonized CF patients. It is clear, however, that the interpretation of data and comparative analysis of PFGE and AP PCR results necessitates additional (international) standardization and the development of practical guidelines.

Molecular typing of Salmonella typhi strains from Dhaka (Bangladesh) and development of DNA probes identifying plasmid-encoded multidrug-resistant isolates

Seventy-eight Salmonella typhi strains isolated in 1994 and 1995 from patients living in Dhaka, Bangladesh, were subjected to phage typing, ribotyping, IS200 fingerprinting, and PCR fingerprinting. The collection displayed a high degree of genetic homogeneity, because restricted numbers of phage types and DNA fingerprints were observed. A significant number of the S. typhi strains (67%) were demonstrated to be multiple drug resistant (MDR). The vast majority of the MDR strains were resistant to chloramphenicol, ampicillin, trimethoprim, streptomycin, sulfamethoxazole, and tetracycline (R type CATmSSuT), a resistance phenotype that has also frequently been observed in India. Only two strains displayed a distinct MDR phenotype, R type AT-mSSuT. Pulsed-field gel electrophoresis demonstrated the presence of large plasmids exclusively in the MDR strains of both R types. The plasmids present in the S. typhi strains of R type CATmSSuT could be conjugated to Escherichia coli and resulted in the complete transfer of the MDR phenotype. PCR fingerprinting allowed discrimination of MDR and susceptible strains. The DNA fragments enabling discrimination of MDR and susceptible S. typhi strains by PCR were useful genetic markers for identifying MDR encoded by large plasmids of the H1 incompatibility group.

Novel BOX repeat PCR assay for high-resolution typing of Streptococcus pneumoniae strains

Typing data obtained by specifically targeting a single, high-stringency PCR at the pneumococcal BOX repeat element for 28 strains of Streptococcus pneumoniae completely corroborated the resolutions attained by five genotypic procedures as described by Hermans et al. (P.W.M. Hermans, M. Sluijter, T. Hoogenboezem, H. Heersma, A. van Belkum, and R. de Groot, J. Clin. Microbiol. 33:1606-1612, 1995). All pairs of strains, except one, derived from both the cerebrospinal fluid and blood of the same individual were shown to be identical. Moreover, other, epidemiologically unrelated isolates were demonstrated to be unique. Considering the combined data from the five typing techniques applied previously as the "gold standard," the single BOX PCR test demonstrated excellent resolving powers while maintaining epidemiological linkage.

Comparison of an improved RAPD fingerprinting with different typing methods for discriminating clinical isolates of Staphylococcus spp

Different epidemiological markers were used to characterize 2 Staphylococcus epidermidis and 8 Staphylococcus aureus strains isolated from patients with severe infections. We compared random amplified polymorphic DNA (RAPD) fingerprints, biotypes, antibiotic assays, plasmid profiles and chromosomal DNA restriction endonuclease analysis (REA). Data analysis based on numerical taxonomy methods indicates that RAPD and REA give similar results allowing a good discrimination of the two species and of each isolate. The RAPD method is easier and faster than REA, but the reproducibility of RAPD fingerprints obtained in independent experiments can be problematic. We have found simple technical devices to improve the reproducibility of the RAPD procedure which is therefore a very useful tool in epidemiology for identification and characterization of Staphylococcus spp.

Investigation into the repeated recovery of coagulase-negative staphylococci from blood taken at the end of cardiopulmonary by-pass

Forty-six strains of coagulase-negative staphylococci (CNS) were typed by biochemical reactivity, antibiotic susceptibility pattern, macrorestriction analysis by pulsed-field gel electrophoresis (PFGE) and arbitrary primed polymerase chain reaction (AP PCR). Twenty-four strains were obtained in 1993 from blood cultures of as many patients coupled to a heart-lung machine during cardiac surgery. Since over 30% of the latter belonged to a single type, it was concluded that during the year of analysis a single clone of CNS persisted in this hospital setting. Subsequent epidemiological surveillance putatively identified four possible carriers among surgical personnel. For this reason, 22 strains collected from the hands and nose of two cardiac surgeons and two perfusionists were also tested; none were identical to the persistent clone. Thus either the operation equipment was colonized longitudinally or the causative CNS had disappeared from the suspect individuals' flora. Longitudinal monitoring of CNS infections by various techniques gives a valuable insight into nosocomial epidemiology and elucidates the complexity of the CNS colonization.

Multicenter evaluation of arbitrarily primed PCR for typing of Staphylococcus aureus strains

Fifty-nine isolates of Staphylococcus aureus and a single strain of Staphylococcus intermedius were typed by arbitrarily primed PCR (AP-PCR). To study reproducibility and discriminatory abilities, AP-PCR was carried out in seven laboratories with a standardized amplification protocol, template DNA isolated in a single institution, and a common set of three primers with different resolving powers. The 60 strains could be divided into 16 to 30 different genetic types, depending on the laboratory. This difference in resolution was due to differences in technical procedures (as shown by the deliberate introduction of experimental variables) and/or the interpretation of the DNA fingerprints. However, this did not hamper the epidemiologically correct clustering of related strains. The average number of different genotypes identified exceeded those of the more traditional typing strategies (F. C. Tenover, R. Arbeit, G. Archer, J. Biddle, S. Byrne, R. Goering, G. Hancock, G. A. Hebert, B. Hill, R. Hollis, W. R. Jarvis, B. Kreiswirth, W. Eisner, J. Maslow, L. K. McDougal, J. M. Miller, M. Mulligan, and M. A. Pfaller, J. Clin. Microbiol. 32:407-415, 1994). Comparison of AP-PCR with pulsed-field gel electrophoresis (PFGE) indicated the existence of strains with constant PFGE types but variable AP-PCR types. The reverse (constant AP-PCR and variable PFGE patterns) was also observed. This indicates additional resolution for combined analyses. It is concluded that AP-PCR is well suited for genetic analysis and monitoring of nosocomial spreading of staphylococci. The interlaboratory reproducibility of DNA-banding patterns and the intralaboratory standardization need improvement.

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.