Multiplex polymerase chain reaction for detection of genes for Staphylococcus aureus thermonuclease and methicillin resistance and correlation with oxacillin resistance

Clonal dissemination of epidemic methicillin-resistant Staphylococcus aureus in Belgium and neighboring countries

OBJECTIVES

To determine the diversity of pulsed-field gel electrophoresis (PFGE) types among epidemic strains of methicillin-resistant Staphylococcus aureus (MRSA) recovered in Belgium, France, Germany and The Netherlands over the period 1981-94.

METHODS

MRSA strains collected in a multicenter survey in Belgium (n = 171) and from reference laboratories in neighboring countries (n = 102) were characterized by PFGE analysis using the SmaI enzyme.

RESULTS

In total, 32 PFGE types were found. Epidemic PFGE type 1, first recognized in 1984, accounted for 82% of Belgian strains (87% of hospitals) and 51% of European MRSA strains. Four other internationally epidemic PFGE types (types 8, 10, 11 and 12) were less widely disseminated and more recently detected (1991-94), each recovered from two or three countries. International spread of two PFGE types was linked to transfer of colonized patients to Dutch hospitals from another country where this type was frequently recovered.

CONCLUSIONS

Genotypic analysis indicated widespread distribution of several outbreak-associated MRSA strains over large European regions, which was in some instances related to interhospital patient transfer. These findings underscore the need for standardized international surveillance and control of MRSA transmission between healthcare institutions across Europe.

Multiplex PCR for detection of genes for Staphylococcus aureus enterotoxins, exfoliative toxins, toxic shock syndrome toxin 1, and methicillin resistance

A multiplex PCR assay for detection of genes for staphylococcal enterotoxins A to E (entA, entB, entC, entD, and entE), toxic shock syndrome toxin 1 (tst), exfoliative toxins A and B (etaA and etaB), and intrinsic methicillin resistance (mecA) was developed. Detection of femA was used as an internal positive control. The multiplex PCR assay combined the primers for sea to see and femA in one set and those for eta, etb, tst, mecA, and femA in the other set. Validation of the assay was performed using 176 human isolates of Staphylococcus aureus. This assay offers a very specific, quick, reliable, and inexpensive alternative to conventional PCR assays used in clinical laboratories to identify various staphylococcal toxin genes.

Clonal spread of staphylococci among patients with peritonitis associated with continuous ambulatory peritoneal dialysis

BACKGROUND

Peritonitis is the most important complication of continuous ambulatory peritoneal dialysis (CAPD). Coagulase-negative staphylococci (CNS) are the most common causes of peritonitis, only limited information is available regarding the distribution and epidemiology of different CNS species associated with CAPD peritonitis.

METHODS

CNS isolated from dialysis effluent from CAPD patients with peritonitis was identified by species and further analyzed with pulsed-field gel electrophoresis (PFGE).

RESULTS

A total of 216 microorganisms (206 bacteria and 10 Candida species) were isolated from 196 consecutive culture-positive CAPD samples obtained from 75 patients. One hundred and twenty-one (56%) isolates represented staphylococci. The four most frequently isolated staphylococcal species were Staphylococcus epidermidis (70 isolates), Staphylococcus aureus (31 isolates), Staphylococcus hemolyticus (10 isolates), and Staphylococcus hominis (4 isolates). PFGE analysis revealed the clonal spread among patients of three different clones of S. epidermidis and one clone of S. aureus among the investigated patients. Indistinguishable isolates of either S. epidermidis, S. hominis, or S. aureus were also isolated in repeated samples from several patients.

CONCLUSION

PFGE is a useful method for the epidemiological evaluation of staphylococci-associated CAPD infections and should replace older and less accurate methods, such as antibiotic sensitivity patterns. We recommend that CNS isolates from patients with CAPD-associated peritonitis should be saved for future investigations and typing, which would aid in the management of this patient category.

Correlation between the resistance genotype determined by multiplex PCR assays and the antibiotic susceptibility patterns of Staphylococcus aureus and Staphylococcus epidermidis

Clinical isolates of Staphylococcus aureus (a total of 206) and S. epidermidis (a total of 188) from various countries were tested with multiplex PCR assays to detect clinically relevant antibiotic resistance genes associated with staphylococci. The targeted genes are implicated in resistance to oxacillin (mecA), gentamicin ¿aac(6')-aph(2"), and erythromycin (ermA, ermB, ermC, and msrA). We found a nearly perfect correlation between genotypic and phenotypic analysis for most of these 394 strains, showing the following correlations: 98% for oxacillin resistance, 100% for gentamicin resistance, and 98.5% for erythromycin resistance. The discrepant results were (i) eight strains found to be positive by PCR for mecA or ermC but susceptible to the corresponding antibiotic based on disk diffusion and (ii) six strains of S. aureus found to be negative by PCR for mecA or for the four erythromycin resistance genes targeted but resistant to the corresponding antibiotic. In order to demonstrate in vitro that the eight susceptible strains harboring the resistance gene may become resistant, we subcultured the susceptible strains on media with increasing gradients of the antibiotic. We were able to select cells demonstrating a resistant phenotype for all of these eight strains carrying the resistance gene based on disk diffusion and MIC determinations. The four oxacillin-resistant strains negative for mecA were PCR positive for blaZ and had the phenotype of beta-lactamase hyperproducers, which could explain their borderline oxacillin resistance phenotype. The erythromycin resistance for the two strains found to be negative by PCR is probably associated with a novel mechanism. This study reiterates the usefulness of DNA-based assays for the detection of antibiotic resistance genes associated with staphylococcal infections.

Community strain of methicillin-resistant Staphylococcus aureus involved in a hospital outbreak

Western Australia (WA) has been able to prevent methicillin-resistant Staphylococcus aureus (MRSA) strains from outside of the state from becoming established in its hospitals. Recently, a single-strain outbreak of MRSA occurred in a WA metropolitan teaching hospital following admission of an infected patient from a remote community. The strain responsible for the outbreak was unrelated to any imported strains and spread rapidly in the hospital. Screening of two remote communities in the region from which the index case came revealed that 42% of the people in one community and 24% in the other carried MRSA. Isolates were typed by resistance pattern, plasmid analysis, contour-clamped homogeneous electric field electrophoresis, bacteriophage pattern, and coagulase gene restriction fragment length polymorphism. It was found that of the people carrying MRSA, 39% in the former community and 17% in the latter community were carrying an MRSA strain which was indistinguishable from the strain that caused the hospital outbreak.

Methods for the differentiation of microorganisms

Advances in analytical and diagnostic assays based on novel nucleic acid analyses techniques have revolutionized the application of molecular differentiation of microorganisms. Phenotypic typing schemes are now broadly supplemented by new genotyping methods which allow a more refined and detailed differentiation of closely related microorganisms, bacterial strains, isolates and pathogens on the DNA level. Bio-, sero- and phagetyping, antibiotic susceptibility tests, immunoblotting as well as multilocus enzyme- or polyacrylamide gel electrophoresis are now supported by the analysis of plasmid or chromosomal DNA restriction profiles, ribotyping, pulsed-field gel electrophoresis and polymerase- or ligase-chain reaction-based methods or direct sequencing technique to differentiate microorganisms. Some of these molecular techniques are also used in the field of virology to analyse and differentiate closely related sub- or genotypes. Few examples for the analysis and investigation of these usually small genomes will also be given.

Investigation of a cluster of Staphylococcus aureus invasive infection in the top end of the Northern Territory

INTRODUCTION

Staphylococcus aureus invasive infection remains a serious condition associated with considerable morbidity and mortality. Following notification of five cases at Royal Darwin Hospital (RDH), we searched for related cases, determined their epidemiological characteristics and attempted to identify the source of this apparent cluster.

METHODS

We reviewed RDH microbiology records between June 1996 and April 1997 for S. aureus isolates with similar antibiograms to notified cases. We used antibiotic resistance patterns, bacteriophage typing and two molecular typing techniques to subtype implicated isolates. Hospital records were reviewed for admission details and associated costs were estimated.

RESULTS

Fifty-four cluster-related isolates occurred in 47 separate presentations. The peak incidence was in the wet season. The most important risk factor for staphylococcal invasive infection was the presence of skin sores/scabies in 17/54 cases (31%), followed by intravascular line use in 14/54 (26%), open trauma in 11/54 (20%), underlying end stage renal failure and alcoholism each in ten of 54 (18%). The mean admission length was 30 days and antibiotics were given for an average of 23 days. Death due to S. aureus infection occurred in eight of 47 (17%) presentations. S. aureus pneumonia was community acquired in 12/13 patients (92%) and six of 13 (46%) died. Ten of 13 (80%) pneumonia patients had at least one other focus of S. aureus infection. The cost of antibiotics and hospital bed per presentation was approximately $16,000. Presentations with skin sores/scabies cost considerably more ($31,000). No common epidemiologic features were found for community or hospital acquired cases.

CONCLUSION

Considerable mortality and cost was attributable to cases of S. aureus invasive infection during this cluster; particularly those with community acquired pneumonia or skin sores/scabies. Staphylococcal antibiotic cover should be considered early for unwell patients presenting to hospital with pneumonia and other signs of potential S. aureus infection. It is appropriate to target public health efforts to prevent skin sores and to provide adequate treatment when they occur.

A rapid (20 h) solid screening medium for detecting methicillin-resistant Staphylococcus aureus

Methicillin aztreonam mannitol salt agar is a sensitive and reliable solid screening medium for detecting methicillin-resistant Staphylococcus aureus (MRSA). With this medium an incubation period of only 20 h is sufficient to either produce visible colonies of MRSA or to exclude MRSA (no staphylococcal colonies). Coagulase testing (requiring a further 6 h) enables coagulase-positive isolates to be provisionally reported as 'possible MRSA' 26-30 h after the swabs were collected. The medium supports growth of intrinsically resistant staphylococci including low-expression-class MRSA (methicillin minimum inhibitory concentration (MIC) 8-16 mg/L), but methicillin susceptible staphylococci and beta-lactamase hyperproducers are suppressed.

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.

Mechanisms of methicillin resistance in staphylococci

The continuously high prevalence of methicillin-resistant staphylococci (MRS) throughout the world is a constant threat to public health, owing to the multiresistant characteristics of these bacteria. Methicillin resistance is phenotypically associated with the presence of the penicillin-binding protein 2a (PBP2a) not present in susceptible staphylococci. This protein has a low binding affinity for beta-lactam antibiotics. It is a transpeptidase which may take over cell wall synthesis during antibiotic treatment when normally occurring PBPs are inactivated by ligating beta-lactams. PBP2a is encoded by the mecA gene, which is located in mec, a foreign DNA region. Expression of PBP2a is regulated by proteins encoded by the plasmid-borne blaR1-bla1 inducer-repressor system and the corresponding genomic mecRl-mecl system. The blaRl-blal products are important both for the regulation of beta-lactamase and for mecA expression. Methicillin resistance is influenced by a number of additional factors, e.g. the products of the chromosomal fem genes which are important in the synthesis of normal peptidoglycan precursor molecules. Inactivation of fem-genes results in structurally deficient precursors which are not accepted as cell wall building blocks by the ligating PBP2a transpeptidase during antibiotic treatment. This may result in reduced resistance to beta-lactam antibiotics. Inactivation of genes affecting autolysis has shown that autolytic enzymes are also of importance in the expression of methicillin resistance. Methicillin resistance has evolved among earth microorganisms for protection against exogenous or endogenous antibiotics. Presumably the mec region was originally transferred from coagulase negative staphylococci (CNS) to Staphylococcus aureus (SA). A single or a few events of this kind with little subsequent interspecies transfer had been anticipated. However, recent data suggest a continuous horizontal acquisition by S. aureus of mec, being unidirectional from CNS to SA. Methicillin resistance may also be associated with mechanisms independent of mecA, resulting in borderline methicillin resistance. These mechanisms include beta-lactamase hyperproduction, production of methicillinases, acquisition of structurally modified normal PBPs, or the appearance of small colony variants of SA. Most MRS are multiresistant, and the mec region may harbour several resistance determinants, resulting in a clustering of resistance genes within this region.

Rapid genotypic confirmation of methicillin resistance

Detection of phenotypic methicillin resistance in Staphylococcus aureus clinical strains by conventional disk diffusion testing is fraught with problems. We used gene amplification of the mecA locus by polymerase chain reaction (PCR), in conjunction with a capillary/air thermal cycler, to overcome both the inaccuracy of phenotypic methods and the lengthy processing times required for previous genotypic methods. The rapid PCR method correctly identified methicillin resistance in a consecutive series of 30 S. aureus isolates when compared with routine and reference phenotypic methods. The shorter processing time and smaller reagent volumes required for the air thermal cycler make same-day determination of methicillin resistance in clinical isolates feasible for diagnostic laboratories.

Comparison of PCR detection of mecA with standard susceptibility testing methods to determine methicillin resistance in coagulase-negative staphylococci

Approximately 75% of coagulase-negative staphylococci are resistant to methicillin, but it is suspected that even more resistance exists that is not detected by standard susceptibility assays. To determine the most accurate assay for measuring resistance, we compared the detection of mecA by PCR with detection by National Committee for Clinical Laboratory Standards methods using oxacillin as the class drug. Strains from 11 species of coagulase-negative staphylococci were selected such that 84% were susceptible by the broth microdilution method. Of 45 mecA-positive strains, 1 strain was unable to express the mecA gene product after induction and was not included in further analyses. For microdilution with 2% NaCl, the disk test without salt, and agar screen containing 4% NaCl plus-6 micrograms of oxacillin per ml, the sensitivities in detecting the 44 mecA-positive strains were 50, 84, and 70%, respectively, at 24 h and 77, 82, and 100%, respectively, at 48 h. The specificities of microdilution, disk, and agar screen in detecting the 97 strains lacking mecA were 100, 89, and 100%, respectively, at 24 h. Only the disk test proved to be less specific at 48 h (81%). Furthermore, for 10 of the mecA-positive strains plus an additional 8 strains subsequently added to the analyses, the MICs were 2 micrograms/ml at 24 h by the broth microdilution method; all 18 strains were positive for mecA by PCR. Thus, an oxacillin MIC of > or = 2 micrograms/ml indicated resistance and is probably a more appropriate breakpoint than the current National Committee for Clinical Laboratory Standards breakpoint of 4 micrograms/ml for coagulase-negative staphylococci. Strains for which MICs are < 2 micrograms/ml may be methicillin resistant and should be verified as susceptible by oxacillin agar screening with incubation for 48 h.

Evaluation of Rapid ATB Staph for 5-hour antimicrobial susceptibility testing of Staphylococcus aureus. Groupement pour le Dépistage, L'Etude et la Prévention des Infections Hospitalières-Groep ter Opsporing, Studie en Preventie van Infecties in de Ziekenhuizen

The accuracy of Rapid ATB Staph (bioMérieux, La Balme-Les Grottes, France) for detection of oxacillin resistance and for detection susceptibility to 11 other antimicrobial agents in 553 and 519 Staphylococcus aureus isolates, respectively, was evaluated by comparing results with those produced by oxacillin agar screen and agar dilution methods, respectively. Further characterization of isolates with discrepant results for oxacillin testing was done by PCR detection of the nuc and mecA genes. By oxacillin agar screening, there were 307 oxacillin-resistant and 246 oxacillin-susceptible isolates. Rapid ATB results were obtained in 5 h for 515 (93.2%) of the isolates tested. Rapid ATB showed 97.0% sensitivity for detection of oxacillin resistance, confirmed by the presence of the mecA gene. After repeat testing of isolates flagged by the ATB software as possible errors, sensitivity increased to 99% for oxacillin-resistant isolates. Essential agreement with agar dilution testing for susceptibility to amoxicillin-clavulanic acid, gentamicin, erythromycin, clindamycin, and ciprofloxacin, as estimated by Youden's J statistic, was > 0.90. Subpopulations of isolates with significantly increased MICs of amikacin, rifampin, and minocycline, indicating borderline susceptibility, were detected by Rapid ATB and categorized as resistant. Rapid ATB Staph showed adequate accuracy for detection within 5 h of the oxacillin- and multiple-drug-resistant S. aureus isolates currently prevalent in Belgium.

Revised interpretation of oxacillin MICs for Staphylococcus epidermidis based on mecA detection

In 1992 and 1993, at The Ohio State University Medical Center, a larger proportion of Staphylococcus epidermidis strains required oxacillin MICs of 1 to 2 micrograms/ml than did Staphylococcus aureus strains. mecA genotype was correlated with antimicrobial susceptibility for selected clinical S. epidermidis strains. All 14 strains that required oxacillin MICs of < or = 0.25 microgram/ml and 2 of 5 strains that required oxacillin MICs of 0.5 microgram/ml were susceptible by 1-microgram oxacillin disk test and were mecA negative. Three of 5 strains that required oxacillin MICs of 0.5 microgram/ml and all 18 strains that required oxacillin MICs of > or = 1.0 microgram/ml were resistant by oxacillin disk test and were mecA positive. Current National Committee for Clinical Laboratory Standards MIC interpretive criteria may underestimate methicillin resistance among S. epidermidis strains.

Direct identification of Staphylococcus aureus in blood cultures by detection of the gene encoding the thermostable nuclease or the gene product

This study compares methods for direct identification of S. aureus in blood cultures by detection of the thermonuclease (TNase) of this bacterium or the nuc gene encoding it. The protein was detected by an enzyme diffusion test in o-toluidine blue DNA agar with a test time of at least 4 h, by a monoclonal antibody (MAb)-based sandwich enzyme-linked immunosorbent assay (sELISA) with a test time of approximately 4 h, and by a MAb-based sandwich enzyme-linked immunofiltration assay (sELIFA) with a test time of 25-30 min (sample preparation included). The nuc gene was amplified by a polymerase chain reaction (PCR) with a test time (amplification plus detection) of approximately 3.5 h. The tests were optimized for direct examination of blood-containing cultures. All tests were positive with 67/67 blood cultures which grew S. aureus, negative with 35/35 cultures which grew coagulase-negative staphylococci, and negative with 37/37 cultures with various other bacteria. These results showed positive agreement with those of the commercial AccuProbe test but not with the StaphAurex agglutination kit. With an artificially seeded blood culture, minimum total times required (incubation plus testing) were as follows: nuc-PCR, 9.5 h; sELIFA, 12.5 h; enzymatic test, 16-36 h; AccuProbe, 14 h. Direct examination of both the nuc gene and the mecA gene encoding methicillin resistance demonstrated the mecA gene in all the coagulase-negative staphylococci (48.6%) which showed oxacillin resistance. The sELIFA had the particular advantage of its short test time, the PCR its high sensitivity and the possibility of simultaneous detection of the species-specific nuc gene and genes encoding other clinically important characters of the bacteria. These tests offer the prospect of direct application to a variety of clinical specimens for rapid diagnosis of S. aureus infection.

Testing of methicillin resistance by in vitro susceptibility and the presence of the mecA gene in clinical Staphylococcus aureus isolates in Finland

A total of 140 epidemiologically unrelated Staphylococcus aureus strains collected in Finland between 1983 and 1994 were sent to the reference laboratory with verified or suspected methicillin resistance. These strains and 37 S. aureus strains previously identified as methicillin-susceptible were retested using 5 different susceptibility test methods including agar screening, disc diffusion, growth around methicillin (25 micrograms) test strips and minimal inhibitory concentration (MIC) determinations by an agar dilution method and E-test. The isolates were also analyzed for the presence of the mecA gene by the polymerase chain reaction (PCR). Based on in vitro susceptibility, 69 strains were identified as methicillin-resistant and were positive for the mecA gene in PCR, while 84 strains were methicillin-susceptible and negative for this gene. Susceptibility testing gave conflicting results for 24 (14%) strains. When the tests were repeated in triplicate for each isolate, discrepant results were still achieved with 18 of the 24 strains in at least 2 different tests. Thus, based on in vitro susceptibility, these strains could not be definitely classified as resistant or susceptible to methicillin. Yet 7 of them were positive for the mecA gene as an indication of genetic resistance to methicillin. Corroborating earlier studies, these results illustrate the difficulty of detecting methicillin resistance/susceptibility based only on susceptibility testing and underscore the importance of confirming methicillin resistance in S. aureus in specialized laboratories.