Comparison of PCR-based methods for typing Staphylococcus aureus isolates

In this study, we compared the potentials of (i) a multiplex PCR-based multilocus variable-number tandem repeat (VNTR) assay; (ii) a triplex PCR coamplifying fragments of spa, coa, and the hypervariable region adjacent to the mecA gene; (iii) restriction profile analysis of the STAR repetitive element; (iv) randomly amplified polymorphic DNA analysis; (v) inter-IS256 PCR; and (vi) rep-MP3 PCR. Multilocus VNTR typing and triplex PCR (coa, spa, and hypervariable region) approaches showed excellent reproducibility and high discriminatory power; however, only multilocus VNTR typing could distinguish all pulsed-field gel electrophoresis and spa types. Multilocus VNTR typing appears to be the most useful PCR-based method for the rapid genotyping of Staphylococcus aureus strains.     

Analysis of different molecular methods for typing methicillin-resistant Staphylococcus aureus isolates belonging to the Brazilian epidemic clone

The extensive geographic spread of MRSA isolates belonging to the Brazilian epidemic clone (BEC) limited the value of pulsed-field gel electrophoresis (PFGE) in epidemiological studies of outbreaks caused by these strains. Thus, the discriminatory power of eight different molecular methods was evaluated in an attempt to establish a methodology for genotyping BEC isolates involved in intra-hospital outbreaks. BEC isolates from five hospitals in Teresina City, Piaui State were genotyped by conventional electrophoresis or PFGE of Cla I- or Sma I-digested genomic DNA hybridised with specific labelled mecA, Tn554, IS257 and IS256 probes. The combination of PFGE with Cla I/mecA, Cla I/Tn554, Cla I/IS257, Sma I/mecA and Sma I/IS257 probe-fingerprinting techniques provided a very poor discriminatory power for BEC strains. Although Cla I/IS256 fingerprinting discriminated 17 different polymorphisms among the isolates displaying PFGE A1 pattern, this strategy was not reproducible. In contrast, the combination of PFGE and Sma I/IS256 polymorphisms differentiated BEC isolates into nine stable polymorphisms. Thus combination of PFGE and hybridisation with IS256 probe may be recommended as a useful means of typing BEC strains involved in intra-hospital infections.     

Comparison of molecular and conventional methods for typing of enteroviral isolates

Twenty-eight enteroviral isolates obtained from various clinical specimens were typed by Lim-Benyesh-Melnick (LBM) pool-based neutralization, PCR-restriction fragment length polymorphism (RFLP), and partial sequencing of the VP1 region of the enteroviral genome. Sequencing was found to be a good alternative to LBM typing, while PCR-RFLP was inadequate for identification of enteroviral isolates.     

Multilocus sequence typing of intercontinental bovine Staphylococcus aureus isolates

A total of 258 bovine-associated Staphylococcus aureus isolates from the United States, Chile, and the United Kingdom, plus the reference isolate S. aureus Newbould 305 (NCIMB 702892), were analyzed by multilocus sequence typing (MLST). A collection of previously characterized United Kingdom isolates were also included in the analysis. The results demonstrated that MLST is suitable for the differentiation of bovine S. aureus isolates from various sites (milk, teat skin, milking machine unit liners, hands, and bedding) and countries. The theory of the host specificity of S. aureus is supported by the detection of a previously undescribed clonal complex that comprised 87.4% of the isolates studied, with representatives from all geographic locations investigated. This suggests that a single clonal group has achieved a widespread distribution and is responsible for the majority of infections. Some sequence types (STs; ST25, ST115, ST124, and ST126) demonstrated site specificity, as they were significantly (P < 0.05) associated with milk or teat skin.     

DNA macroarray for identification and typing of Staphylococcus aureus isolates

A DNA macroarray containing 465 intragenic amplicons was designed to identify Staphylococcus aureus at the species level and to type S. aureus isolates. The genes selected included those encoding (i) S. aureus-specific proteins, (ii) staphylococcal and enterococcal proteins mediating antibiotic resistance and factors involved in their expression, (iii) putative virulence proteins and factors controlling their expression, and (iv) proteins produced by mobile elements. The macroarray was hybridized with the cellular DNAs of 80 S. aureus clinical isolates that were previously typed by analyses of their antibiograms and SmaI patterns. The set selected contained unrelated, endemic, and outbreak-related isolates belonging to 45 SmaI genotypes. In a gene content dendrogram, the 80 isolates were distributed into 52 clusters. The outbreak-related isolates were linked in the same or a closely related cluster(s). Clustering based on gene content provided a better discrimination than SmaI pattern analysis for the tested mecA(+) isolates that were endemic to Europe. All of the antibiotic resistance genes detected could be correlated with their corresponding phenotypes, except for one isolate which carried a mecA gene without being resistant. The 16 isolates responsible for bone infections were distinguishable from the 12 isolates from uninfected nasal carriers by a significantly higher prevalence of the sdrD gene coding for a putative SD (serine-aspartate) adhesin (in 15 and 7 isolates, respectively). In conclusion, the macroarray designed for this study offers an attractive and rapid typing method which has the advantage of providing additional information concerning the gene content of the isolate of interest.     

External quality assessment of molecular typing of Staphylococcus aureus isolates by a network of laboratories

A network of laboratories designated Centres for Molecular Diagnosis was funded in 2000 by Belgian National Health Insurance to provide clinically relevant molecular diagnostic tests. These included typing of nosocomial pathogens as a service to local hospital infection control programs. Two external quality assessment (EQA) surveys were performed in 2001 and 2003 to evaluate the proficiencies of the laboratories at Staphylococcus aureus typing. EQA panels included S. aureus isolates with either indistinguishable, clonally related, or unrelated pulsed-field gel electrophoresis (PFGE) patterns. A hypothetical hospital outbreak problem was also submitted for analysis. Typeability, reproducibility, discrimination (D) index, and epidemiological concordance were evaluated. Ten centers participated in each survey. Seven centers performed PFGE analysis, while others used repetitive-element or randomly amplified polymorphic DNA PCR, amplified fragment length polymorphism, or spa typing. Full typeability (100%) was achieved by all centers, and all but one showed 100% reproducibility. Discrimination was appropriate (D index, >or=96%) for centers performing PFGE analysis but not for all those using other methods (D index range, 72% to 97%). Correct answers to the epidemiological questions were provided by 7/10 and 10/10 centers in 2001 and 2003, respectively. Individual feedback of results was provided to each center together with specific technical recommendations for improving performance. Our findings indicate that surveys of lab proficiency are useful for validation and optimization of molecular typing services to local hospital infection control programs.     

Comparison of traditional and molecular methods for typing nontoxigenic strains ofCorynebacterium diphtheriae

Thirty-eight nontoxigenic strains ofCorynebacterium diphtheriae isolated between 1987 and 1992 from clinical specimens of French patients were typed by biotyping, antibiograms, bacteriophage typing, ribotyping, and restriction analysis by pulsed-field gel electrophoresis (PFGE). Excellent correlation occurred between the genotypes defined by PFGESfil profiles or by ribotypeBstEll profiles. Genotyping revealed seven genotype patterns among the 26 biotype mitis isolates, five among the nine biotype gravis isolates, and three among the three biotype belfanti isolates. Phage typing was nonreactive for nine of the 38 isolates. A combination of all the typing methods led to the identification of 19 different types ofCorynebacterium diphtheriae.     

Molecular and phenotypic typing of Staphylococcus aureus isolates from rabbit meat

Twenty-six Staphylococcus aureus isolates were recovered from rabbit carcasses and cuts during a period of seven months. Samples from 51 different animals, flocks and farms were obtained from five establishments in four Spanish provinces. To determine their diversity and possible origin, isolates were typed by three molecular and three phenotypic methods. PFGE, with the highest discrimination index (D=0.966), identified 19 patterns (more than one band difference) and 10 types (more than three band differences). Based on > or = 90% similarity, RAPD (D=0.877) produced nine patterns while ribotyping (D=0.786) produced seven types. On the basis of biotyping (D=0.644), 11 isolates belonged to human ecovars and 15 to the non-host-specific crystal violet type C (NHS CV:C) biotypes. By direct phage typing (D=0.761), 17 isolates were lysed by human phages into groups II (8 isolates), III (5 isolates), I/III (2 isolates) and V (2 isolates). The overall resistance to antimicrobials (D=0.783) was 76.9%, with most isolates being resistant to tetracycline (61.5%) and penicillin G (26.9%). PFGE showed that samples from each processing plant carried different S. aureus types, some of them persisting over time. There also was evidence of interestablishment dissemination of genetically related clones, most of them belonging to the PFGE type A and phenotype "NHS CV:C biotypes-3A/3C/55/71 phage type", which is highly virulent for European commercial rabbitries. The ubiquity of the virulent phenotype, as well as the high incidence of resistance to antibiotics with application in human medicine, is a matter of concern in public and animal health.     

Comparison of typing methods for Clostridium difficile isolates.

A simple discriminative typing method for Clostridium difficile has been developed. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of whole-cell proteins and restriction enzyme analysis are relatively simple techniques but are difficult to evaluate, especially the restriction enzyme analysis. Immunoblotting and restriction fragment length polymorphism typing facilitate simple discrimination of patterns.     

Evaluation of electrophoretic methods for typing methicillin-resistant Staphylococcus aureus

Three electrophoretic methods of typing methicillin-resistant Staphylococcus aureus (MRSA) strains--plasmid profiles (PP), whole-cell protein profiles (WCPP) and immunoblotting profiles (IP)--were evaluated and compared with phage typing. The results obtained with isolates from 12 outbreaks were compared both within the outbreaks, to determine the consistency of results, and between outbreaks. There was generally good agreement between the typing methods but in only six outbreaks did all four methods indicate the same relationship between isolates. WCPP comprised more than 50 bands; when differences occurred, they were seen in only a few bands. In contrast, IP comprised only one or two major bands and the differences were much easier to interpret. The PPs of many of the isolates were similar; many isolates contained a plasmid of mol. wt (18-25) x 10(6). In several outbreaks both WCPP and IP showed minor differences between isolates that were not apparent with phage typing. When comparisons were made between the 12 index strains and an isolate representing the London epidemic MRSA strain, phage typing and WCPP were the most discriminatory methods; both gave nine distinct patterns, whereas there were eight IPs and only six PPs amongst the 13 strains. It was concluded that both WCPP and IP could provide valuable epidemiological data on MRSA and that IP was the easiest of the three methods to interpret.     

Comparison of multilocus sequence typing and pulsed-field gel electrophoresis as tools for typing Staphylococcus aureus isolates in a microepidemiological setting

Multilocus sequence typing (MLST) of Staphylococcus aureus is well suited to the study of global or long-term epidemiology, but its role in local epidemiology has not been defined. The present study has compared MLST with pulsed-field gel electrophoresis (PFGE) by using S. aureus isolates associated with carriage and disease in a busy regional renal unit. One hundred forty-four patients were prospectively recruited, of whom 103 were receiving hemodialysis and 41 were on continuous ambulatory peritoneal dialysis. Three nasal swab specimens were obtained 1 month apart on entering the study. A nasal swab was positive for S. aureus on at least one occasion in 50 patients (35%). Typing of the 104 carriage isolates demonstrated 21 PFGE types and 21 sequence types (STs). Thirty-one carriers had two or more positive nasal swabs; of these, the isolates in all swabs from a given carrier had identical PFGE types for 29 carriers; the isolates in all of the same 29 swabs had identical STs. The carriage strain in two patients changed both PFGE type and STs during the period of swabbing. Eight patients (6%) had an episode of S. aureus bacteremia during the 12-month study period, and two of these were nasal carriers. One of these invasive isolates had the same PFGE type and ST as the carriage isolate. There were no differences between Simpson's index of diversity for PFGE and Simpson's index of diversity for MLST for both invasive and carriage isolates, suggesting that the two methods have very similar discriminatory abilities. We conclude that PFGE and MLST performed equally in this study.     

Comparison of molecular typing methods for Candida albicans.

Four molecular approaches to determining the types of Candida albicans strains were compared. The strains used were those whose repeated DNA (ribosomal and mitochondrial) EcoRI restriction fragment length polymorphisms (RFLP) were determined by Stevens et al. (D. A. Stevens, F. C. Odds, and S. Scherer, Rev. Infect. Dis. 12:258-266, 1990). Scherer and Stevens (S. Scherer and D. A. Stevens, Proc. Natl. Acad. Sci. USA 85:1452-1456, 1988) used the same strains to examine the Southern blots of genomic EcoRI digests probed with the repeated sequence 27A. The results of these investigators were compared with determinations of RFLPs generated from repeated DNA by the enzyme HinfI and examination of the karyotypes of strains under two sets of conditions, one for the smaller chromosomes and one for the larger ones. Analysis of RFLPs of repeated DNA is most convenient but shows the lowest degree of resolution. Use of the repeated sequence and use of karyotype have very high resolution, but the former method is more convenient than the latter. HinfI digestion is more sensitive than EcoRI digestion but equally convenient. By using all four methods, separate types were identified for 18 of the 20 strains examined.     

Comparison of five repetitive-sequence-based PCR typing methods for molecular discrimination of Salmonella enterica isolates

Five repetitive-element PCR (rep-PCR) techniques [primer sets ERIC1R-ERIC2 and REP1R-REP2I and primers ERIC2, BOXA1R, and (GTG)5] were evaluated for the discrimination of Salmonella enterica isolates at the serotype level. On the basis of number, even distribution over the whole fingerprint, and clarity of bands in the fingerprints, the enterobacterial repetitive intergenic consensus (ERIC) primer set and the (GTG)5 primer were chosen for use in the following experiments. For these two primer sets, reproducibility was tested on different lysates of five selected serotypes of Salmonella in the same PCR by using three different PCR runs. Reproducibility was poor between different PCR runs but high within the same PCR run. Furthermore, 80 different serotypes and five isolates which were not typeable by serotyping were fingerprinted. All strains were typeable by the ERIC primer set and the (GTG)5 primer and generated unique fingerprints, except for some strains with incomplete antigenic codes. Finally, 55 genetically different strains belonging to 10 serotypes were fingerprinted to examine the genetic diversity of the rep-PCR within serotypes. This experiment showed that one serotype did not always correlate to only one ERIC or (GTG)5 fingerprint but that the fingerprint heterogeneity within a serotype was limited. In epidemiological studies, ERIC- and/or (GTG)5-PCR can be used to limit the number of strains that have to be serotyped. The reproducibility of isolates in one PCR run, the discriminatory power, and the genetic diversity (stability) of the fingerprint were similar for the Eric primer set and the (GTG)5 primer, so both are equally able to discriminate Salmonella serotypes.     

Molecular typing and distribution of Staphylococcus aureus isolates in Eastern Canadian dairy herds

Macrorestriction analysis of SmaI-digested chromosomal DNA, using pulsed field gel electrophoresis (PFGE) was performed to type and estimate genetic relationships among 288 Staphylococcus aureus isolates recovered from 58 Eastern Canadian dairy herds. In addition, a subset of the collection was phage typed and evaluated for sensitivity to 10 antimicrobial compounds. Of 288 isolates recovered, 29 distinct PFGE types were identified. Based on estimates of genetic relationships, the PFGE types were assigned to six lineage groups, designated A through F. Of all of the isolates, ca. 93% were assigned to lineage groups A, D, or F. In 58.6% of herds, only a single PFGE type was recovered, while the remainder had two to four types. Of the 212 isolates evaluated for antimicrobial resistance, 24.5% were resistant to one or more antimicrobials. Resistance to penicillin (9.9%) was most common, followed by resistance to sulfadimethoxine (7.5%). Isolates resistant to multiple antibiotics were rare. A total of 63% of isolates responded to phages from groups 1 and 3, and 32.8% could not be typed with any of the phage strains used. The other 4.1% belonged to a variety of phage types. Most of the PFGE lineage group A and F isolates corresponded to phage groups 3 and 1, respectively, and most group D isolates were not typeable. PFGE typing had better discriminatory power than phage typing in defining the relatedness of the S. aureus isolates. Distribution of PFGE types and phage types was independent across regions and within herds.     

烧伤病房金黄色葡萄球菌分离株的分子分型及其耐药性

BACKGROUND: Methicillin-resistant Staphylococcus aureus (MRSA) infection had been a global problem up to 1980s, and it has become a leading pathogen giving rise to nosocomial infections now. OBJECTIVE: To determine the molecular types and drug susceptibilities of Staphylococcus aureus prevailed in burn ward, and to provide a basis for preventing and controlling MRSA intections. METHODS: A total of 53 Staphylococcus aureus strains were collected from the burn ward in the Urumqi General Hospital of Lanzhou Military Region of Chinese PLA. These MRSA strains were identified by PCR and cefoxitin disc diffusion test, and all MRSA strains were typed by spa, SCCmec and MLST typing. In the meanwhile, antibiotic susceptibilities of 17 kinds of drugs, such as oxacillin, to Staphylococcus aureus were also determined, and drug resistance of different types of Staphylococcus aureus especially MRSA, was analyzed. RESULTS AND CONCLUSION:Among 53 Staphylococcus aureus strains, 43 were identified as MRSA, containing determined for amplification of meoA (n=41) and positive for cefoxitin disc diffusion test (n=2). Three SCCmec types, four spa types, and three ST types were found. The major predominant clone was ST239-MRSA-III-t030 (90.7%), with highest resistant to oxacillin and other nine antibiotics. In conclusion, the higher MRSA isolation rate from the burn ward, and ST239-MRSA-III-t030, as the predominant clone, presents with an outbreak in the burn ward and stronger resistance to many different families of antibiotics.       

Epidemiological typing of methicillin-resistant Staphylococcus aureus outbreak isolates by pulsed-field gel electrophoresis and antibiogram

Methicillin-resistant Staphylococcus aureus (MRSA) is one of the most common nosocomial pathogens. In April 1997, there were five MRSA-infected patients among 16 patients in the Neonatal Intensive Care Unit (NICU), Seoul National University Hospital, which is a tertiary-care hospital with 1,500 beds. The infections had spread from twin patients with MRSA who had transferred from Hospital C. MRSA was isolated from the axilla of 15 (94%) of the 16 patients, including the two patients with obvious infections. Three (19%) of 16 doctors and nine (30%) of 30 nurses had MRSA colonization of the anterior nares. Six different PFGE patterns (A through F) were identified in the 53 isolates of MRSA tested. Twelve of 13 isolates from infected sites of five patients showed pattern F. Three MRSA strains obtained from hospital C showed closely or possibly related pattern F. MRSA of type F was isolated from three of 16 patients' axilla, and one of 3 doctors' and three of 30 nurses' nasal swabs. The antibiogram code for 12 of 13 MRSA isolates from five infected patients was 66,754. PFGE patterns of these isolates were either F, F1, F2 or Fa. Only one of three strains isolated from clinical specimens of patients in Hospital C showed the antibiogram code 66754, although they were all PFGE types F1 and Fa. In conclusion, the presumptive sources of the outbreak of MRSA infection in NICU were the twin patients transferred from hospital C. Antibiogram correlated reasonably well to the PFGE type. An effective notification system is needed when a MRSA-infected patient is transferred to another hospital to control the spread of the infection.     

Comparison of molecular typing methods for characterization of Staphylococcus epidermidis: proposal for clone definition

In the present study we give some direction on the selection of the most appropriate typing method(s) to be used for the characterization of Staphylococcus epidermidis, in view of the most recent findings on the evolution, population structure, and epidemiology of this species. In order to achieve this aim, quantitative assessment of the correlation of the results of three typing methods—pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), and staphylococcal chromosomal cassette mec (SCCmec) typing, which target different regions of the chromosome that evolve at different rates—was performed. In order to evaluate the discriminatory ability and the strength and direction of the correlation of the different typing methods, Simpson's index of diversity (SID), the adjusted Rand coefficient (AR), and the Wallace coefficient (W) were calculated. PFGE was the most discriminatory method (SID = 99%), followed by MLST (SID = 90%) and SCCmec typing (SID = 75%). The values of AR and W (0.10 < AR < 0.30; 0.50 < W < 0.75) indicated that the partition of the same isolate collection by PFGE, MLST, and SCCmec typing provided results that had only a poor correlation with each other. However, the information provided by the combination of PFGE and SCCmec enabled the prediction of the results obtained by MLST at the level of the clonal complex with a high degree of precision (W > 0.90). We propose that clones of S. epidermidis be defined by the combination of the PFGE type followed by the SCCmec type, which provides reliable information on the short-term epidemiology and the ability to predict with consistency long-term clonal evolution.     

Lectin typing of methicillin-resistant Staphylococcus aureus

This study reports the patterns of agglutination of 77 clinical isolates of methicillin-resistant Staphylococcus aureus by 32 commercially available lectins. Cell suspensions were not pre-treated. Each isolate was cultured on three media: Columbia blood agar, trypticase-soy agar and Chapman Stone agar. The lectins agglutinating each isolate varied widely depending on culture medium; only five isolates were agglutinated by the same set of lectins regardless of the culture medium used. Lectin typing could be a useful epidemiological tool, but it is necessary to standardise assay conditions (notably culture medium) to enable meaningful comparison of the results produced by different research groups or centres.     

Usefulness of three probes in typing isolates of methicillin-resistant Staphylococcus aureus (MRSA)

Fifty-nine epidemiologically unrelated methicillin-resistant Staphylococcus aureus (MRSA) isolates from different geographical areas and 23 phage-type 77 MRSA isolates from France were investigated. Cellular DNA, digested with restriction endonucleases EcoRI or HindIII, was probed with plasmids carrying the gene encoding 16S rRNA (pBA2), the gene aacA-aphD (pSF815A) and the gene aacA-aphD plus part of IS256 (pIP1307). When probed with pBA2, most of the unrelated isolates displayed the same hybridisation pattern. A greater diversity in patterns was detected in gentamicin-resistant strains with the two other probes. The most accurate fingerprinting of these isolates was obtained with the probe pIP1307. Moreover, this probe appeared to be useful for tracing the phage-type 77 epidemic MRSA isolates widespread in French hospitals.     

Methicillin resistance among isolates of Staphylococcus aureus: antibiotic sensitivity pattern & phage typing

Out of 3988 clinical specimens from hospital admitted patients 230 strains of Staphylococcus aureus were isolated, 45 strains (19.56%) were Methicillin resistance Staphylococcus aureus (MRSA). All MRSA strains were beta lactamase producers. Multidrug resistance was observed among MRSA strains more commonly than in methicillin sensitive strains of Staphylococcus aureus (MSSA). Maximum strains were resistant to penicillin (100%), co-trimoxa zole (97%) & chloramphenicol (93.33%). As least resistant to gentamicin & ciprofloxacin shown by MRSA, these drugs can be used in few situations after susceptibility test. All strains of MRSA were sensitive to vancomicin (100%). Majority of strains (34 out of 45) showed MIC values of 4 ug/ml. Twenty eight out of 44 strains were non typable using routine phages. Study revealed that MRSA with associated multidrug resistance is common in this region. There is need to develop local set of MRSA phages for improvement of typability.