Determination of penicillin susceptibility of Streptococcus pneumoniae using the polymerase chain reaction

Rapid identification of penicillin and macrolide resistance genes and simultaneous quantification of Streptococcus pneumoniae in purulent sputum samples by use of a novel real-time multiplex PCR assay

We evaluated a real-time quantitative PCR combined with a multiplex PCR assay for the quantification of Streptococcus pneumoniae and the simultaneous detection of drug-resistant genes by gel-based PCR, using purulent sputum samples. This assay correctly quantified S. pneumoniae and identified their penicillin and erythromycin susceptibilities directly from samples within 3 h.

Rapid detection of antibacterial resistance in emerging Gram-positive cocci

Effective infection control efforts obviously depend on the performance of the laboratory to detect emerging resistant pathogens accurately and confirm resistance patterns by additional methods to conventional or automated systems. Conventional methods still remain the predominant approaches for detection and identification of bacteria and resistance patterns. However, the estimated time for conventional tests to detect resistance is at least 24-48 h for methicillin-resistant Staphylococcus aureus, vancomycin-resistant enterococci and other epidemiologically important pathogens. Most of the tests used for rapid detection require bacterial growth in culture. There is an important clinical need for rapid detection of bacteria directly from patient samples. Rapid methods based on immunological or molecular technologies have contributed significantly. Molecular assays for several resistance markers are reliable, such as for mecA in staphylococci and vanA in enterococci. However, for other resistance markers, there is a lack of field testing. Cost-effectiveness of rapid detection of antibacterial resistance is another concern. Molecular assays would be useful for tertiary hospitals considering the investment costs and requirement of expert laboratory staff. For smaller centres, rapid tests based on immunological techniques may be a better choice.

Determination of penicillin resistance in Streptococcus pneumoniae isolates from southern Brazil by PCR

OBJECTIVE

To demonstrate the potential clinical applicability of the PCR technique to the early detection of bacterial resistance in Streptococcus pneumoniae.

METHODS

We studied 153 samples of S. pneumoniae, isolated from different anatomic sites, using polymerase chain reaction (PCR) for the detection of specific amplicons from genes that code for penicillin-binding proteins (PBP) 1a, 2b and 2x, which are responsible for penicillin resistance in this organism. The occurrence of these mutated genes was correlated with the minimum inhibitory concentration (MIC) of penicillin, determined by the agar dilution test.

RESULTS

The rate of penicillin resistance in S. pneumoniae in Porto Alegre, Brazil was 22.8% (16.3% intermediate resistance and 6.5% high resistance). In a statistically significant proportion of cases (p < 0.05), penicillin-susceptible samples had no amplicons, intermediate samples had only one (generally from PBP 2x), and highly resistant samples had amplicons from all three PBPs investigated.

CONCLUSION

These results suggest that penicillin resistance in S. pneumoniae in southern Brazil is on the increase, but is still lower than in other countries, and that PCR could be used for its early detection.

Identical penicillin-binding domains in penicillin-binding proteins of Streptococcus pneumoniae clinical isolates with different levels of beta-lactam resistance

We have sequenced the penicillin-binding domains of the complete repertoire of penicillin-binding proteins and MurM from 22 clinical isolates of Streptococcus pneumoniae that span a wide range of beta-lactam resistance levels. Evidence of mosaicism was found in the genes encoding PBP 1a, PBP 2b, PBP 2x, MurM, and, possibly, PBP 2a. Five isolates were found to have identical PBP and MurM sequences, even though the MICs for penicillin G ranged from 0.25 to 2.0 mg/liter. When the sequences encoding PBP 1a, PBP 2b, and PBP 2x from one of these isolates were used to transform laboratory strain R6, the resulting strain had a resistance level higher than that of the less resistant isolates carrying that PBP set but lower than that of the most resistant isolates carrying that PBP set. This result demonstrates that if the R6 strain is arbitrarily defined as the standard genotype, some wild genetic backgrounds can either increase or decrease the PBP-based resistance phenotype.

A reação em cadeia da polimerase na detecção da resistência à penicilina em Streptococcus pneumoniae

INTRODUÇÃO: O Streptococcus pneumoniae é o mais freqüente agente etiológico de infecções respiratórias adquiridas na comunidade e sua resistência aos antimicrobianos tem aumentado nos últimos anos. A determinação da resistência é feita rotineiramente por método lento que depende do crescimento em cultura e determinação da concentração inibitória mínima (CIM). A reação em cadeia da polimerase (PCR) detecta os genes responsáveis pela resistência do Streptococcus pneumoniae a penicilina em cerca de 8 horas. OBJETIVO: Comparar a PCR com o método da CIM no diagnóstico da resistência da Streptococcus pneumoniae a penicilina. MÉTODO: Foram estudadas 153 amostras de Streptococcus pneumoniae, isoladas de diferentes sítios anatômicos, usando-se para detecção de mutações nos genes que codificam as proteínas ligadoras de penicilina 1a, 2b e 2x, responsáveis pela resistência à penicilina. A ocorrência das mutações foi correlacionada com a CIM de penicilina, determinada pelo teste de difusão em ágar. RESULTADOS: A resistência global à penicilina do Streptococcus pneumoniae foi de 22,8% (16,3% de resistência intermediária e 6,5% de resistência alta). Em proporções estatisticamente significativas, as amostras sensíveis à penicilina não tinham mutações, as intermediárias apenas uma, geralmente na proteína ligadora de penicilina 2x, e as altamente resistentes tinham mutações nas três proteínas investigadas. CONCLUSÃO: A PCR é um método rápido para a detecção da resistência à penicilina do Streptococcus pneumoniae, que poderá vir a ser utilizado na prática clínica.

Resistance to beta-lactams and glycopeptides in staphylococci and streptococci

Molecular mechanisms of the action of beta-lactam and glycopeptide antibiotics, as well as genetic background and phenotypical features of the resistance of staphylococci, streptococci and enterococci to these antibiotics are reviewed. Furthermore, susceptibility patterns concerning beta-lactam and glycopeptide drugs of staphylococcal, streptococcal, as well as enterococcal strains isolated from clinical specimens at the Semmelweis University of Medicine, Budapest, Hungary between January 1997 and December 2000 are also presented.

Rapid real-time PCR for determination of penicillin susceptibility in pneumococcal meningitis, including culture-negative cases

A novel real-time PCR-hybridization assay was developed for the rapid (<1 h) detection of penicillin susceptibility in Streptococcus pneumoniae. When applied to 24 pneumococcal DNA-positive cerebrospinal fluid extracts, penicillin-sensitive S. pneumoniae was detected in all instances. Real-time PCR proved more sensitive than culture, microscopy, or antigen detection and provided susceptibility data even in culture-negative cases.

Molecular detection of antimicrobial resistance

The determination of antimicrobial susceptibility of a clinical isolate, especially with increasing resistance, is often crucial for the optimal antimicrobial therapy of infected patients. Nucleic acid-based assays for the detection of resistance may offer advantages over phenotypic assays. Examples are the detection of the methicillin resistance-encoding mecA gene in staphylococci, rifampin resistance in Mycobacterium tuberculosis, and the spread of resistance determinants across the globe. However, molecular assays for the detection of resistance have a number of limitations. New resistance mechanisms may be missed, and in some cases the number of different genes makes generating an assay too costly to compete with phenotypic assays. In addition, proper quality control for molecular assays poses a problem for many laboratories, and this results in questionable results at best. The development of new molecular techniques, e.g., PCR using molecular beacons and DNA chips, expands the possibilities for monitoring resistance. Although molecular techniques for the detection of antimicrobial resistance clearly are winning a place in routine diagnostics, phenotypic assays are still the method of choice for most resistance determinations. In this review, we describe the applications of molecular techniques for the detection of antimicrobial resistance and the current state of the art.

Rationalised prescribing for community acquired pneumonia: a closed loop audit

AIMS

To audit the management of community acquired pneumonia before and after the introduction of a protocol. To determine the aetiology of pneumonia using routine investigations and polymerase chain reaction (PCR).

METHODS

Retrospective and prospective audit following the introduction of a management protocol. Prospective cases were investigated routinely and with PCR on blood and nasopharyngeal aspirate.

RESULTS

There was a significant increase in rational prescribing following introduction of the protocol with 75% of children receiving intravenous penicillin or erythromycin compared with 26% beforehand. Of 89 children in the prospective group, 51 microbiological diagnoses were achieved in 48 children. Seven children had Streptococcus pneumoniae infection, 14 had Mycoplasma infection, six had pertussis, and one had Chlamydia pneumoniae infection. Twenty three children had a viral cause of which respiratory syncytial virus was commonest.

CONCLUSIONS

Introduction of the protocol led to improved prescribing. PCR increased the diagnostic yield and the results support the management protocol.

Community-acquired pneumonia

Community-acquired pneumonia (CAP) remains a leading cause of morbidity and mortality worldwide and has significant financial implications for health-care systems. The epidemiology and fundamental biology of the disease has evolved, reflecting the human immunodeficiency virus pandemic, increasing world travel, and, as always, poverty. The promise held out by molecular diagnostic technology has yet to deliver in this arena, and antibiotic resistance continues to drive the quest for new antimicrobial agents. The emergence of multidrug-resistant Streptococcus pneumoniae, the microorganism most often implicated as a cause of CAP, continues to threaten treatment options. The evolution of this organism, the persistently high mortality rate associated with CAP, and increasing health-care costs have prompted the publication of guidelines by various authorities that can be used to assist in the initial assessment of the patient and then guide empirical antimicrobial therapy. It is unclear whether these guidelines will have significant impact on cost and mortality, although the trend toward a rational and evidence-based approach to antimicrobial therapy must be a goal to aspire to.

Molecular techniques for the diagnosis of respiratory bacterial infection

DNA amplification techniques are now available for all of the major respiratory bacterial pathogens. The most important recent developments have been in the application of these techniques to routine clinical practice. A major problem for rapid techniques is the need to provide susceptibility results. Effective susceptibility techniques have now been described for Streptococcus pneumoniae and Mycobacterium tuberculosis. It has also been possible to use amplification techniques to monitor the response to antituberculosis chemotherapy by monitoring mRNA in sputum samples. The added sensitivity the amplification-based techniques give over conventional culture techniques is valuable not only in enhancing diagnosis, which allows the use of less invasive specimens, but also in opening new investigative areas in the pathogenesis of respiratory conditions.

Detection of penicillin susceptibility in Streptococcus pneumoniae by pbp2b PCR-restriction fragment length polymorphism analysis

A PCR-restriction fragment length polymorphism strategy directed against the pbp2b gene was evaluated for identification of penicillin susceptibility. A total of 106 United Kingdom (U.K.), 30 Danish, and 11 Papua New Guinean strains were tested. Of the U.K. strains, all the susceptible and all but one of the resistant isolates were correctly assigned. By using conventional definitions of "not resistant" and "not susceptible," the sensitivities were 97. 5 and 94.4%, the specificities were 100 and 98.9%, the positive predictive values were 100 and 94.4%, and the negative predictive values were 93.1 and 98.9%, respectively. This technique may allow susceptible (MIC, <0.1 mg/liter) and resistant (MIC, >1 mg/liter) isolates to be distinguished in a single PCR.