Antimicrobial susceptibility testing of Gram-positive and -negative bacterial isolates directly from spiked blood culture media with Raman spectroscopy.

Patients suffering from bacterial bloodstream infections have an increased risk of developing systematic inflammatory response syndrome (SIRS), which can result in rapid deterioration of the patients' health. Diagnostic methods for bacterial identification and antimicrobial susceptibility tests are time-consuming. The aim of this study was to investigate whether Raman spectroscopy would be able to rapidly provide an antimicrobial susceptibility profile from bacteria isolated directly from positive blood cultures. First, bacterial strains (n = 133) were inoculated in tryptic soy broth and incubated in the presence or absence of antibiotics for 5 h. Antimicrobial susceptibility profiles were analyzed by Raman spectroscopy. Subsequently, a selection of strains was isolated from blood cultures and analyzed similarly. VITEK®2 technology and broth dilution were used as the reference methods. Raman spectra from 67 antibiotic-susceptible strains showed discriminatory spectra in the absence or at low concentrations of antibiotics as compared to high antibiotic concentrations. For 66 antibiotic-resistant strains, no antimicrobial effect was observed on the bacterial Raman spectra. Full concordance with VITEK®2 data and broth dilution was obtained for the antibiotic-susceptible strains, 68 % and 98 %, respectively, for the resistant strains. Discriminative antimicrobial susceptibility testing (AST) profiles were obtained for all bacterial strains isolated from blood cultures, resulting in full concordance with the VITEK®2 data. It can be concluded that Raman spectroscopy is able to detect the antimicrobial susceptibility of bacterial species isolated from a positive blood culture bottle within 5 h. Although Raman spectroscopy is cheap and rapid, further optimization is required, to fulfill a great promise for future AST profiling technology development.

Raman spectroscopy-based identification of nosocomial outbreaks of the clonal bacterium Escherichia coli.

DNA-based techniques are frequently used to confirm the relatedness of putative outbreak isolates. These techniques often lack the discriminatory power when analyzing closely related microbes such as E. coli. Here the value of Raman spectroscopy as a typing tool for E. coli in a clinical setting was retrospectively evaluated.

Comparison of Raman spectroscopy and two molecular diagnostic methods for Burkholderia cepacia complex species identification.

OBJECTIVES: Burkholderia cepacia complex (Bcc) and Pseudomonas aeruginosa strains, colonize the respiratory tract of cyctic fibrosis patients. These strains are phenotypically difficult to discriminate, but differ greatly in their pathogenic potential and species identification is relevant. Here, three methods were compared for their diagnostic capacity. METHODS: A Bcc collection was analyzed with Raman spectroscopy, AFLP and rep-PCR analysis. RESULTS: Raman spectroscopy of 40 strains revealed high similarity. Rep-PCR and AFLP of respectively 96 and 112 strains revealed that Bcc strains could be distinguished from Pseudomonas strains. Both molecular methods allowed the identification of most Bcc species according to previous phenotypic and molecular characterization. CONCLUSION: Both AFLP and rep-PCR method data correspond with the previously reported species identification. However, Raman spectroscopy does not discriminate among P. aeruginosa and Bcc species and is therefore not useful as a diagnostic tool.

Discrimination of Aspergillus lentulus from Aspergillus fumigatus by Raman spectroscopy and MALDI-TOF MS.

In 2005, a new sibling species of Aspergillus fumigatus was discovered: Aspergillus lentulus. Both species can cause invasive fungal disease in immune-compromised patients. The species are morphologically very similar. Current techniques for identification are PCR-based or morphology-based. These techniques are labour-intense and not sufficiently discriminatory. Since A. lentulus is less susceptible to several antifungal agents, it is important to correctly identify the causative infectious agent in order to optimize antifungal therapy. In this study we determined whether Raman spectroscopy and/or MALDI-TOF MS were able to differentiate between A. lentulus and A. fumigatus. For 16 isolates of A. lentulus and 16 isolates of A. fumigatus, Raman spectra and peptide profiles were obtained using the Spectracell and MALDI-TOF MS (VITEK MS RUO, bioMérieux) respectively. In order to obtain reliable Raman spectra for A. fumigatus and A. lentulus, the culture medium needed to be adjusted to obtain colourless conidia. Only Raman spectra obtained from colourless conidia were reproducible and correctly identified 25 out of 32 (78 %) of the Aspergillus strains. For VITEK MS RUO, no medium adjustments were necessary. Pigmented conidia resulted in reproducible peptide profiles as well in this case. VITEK MS RUO correctly identified 100 % of the Aspergillus isolates, within a timeframe of approximately 54 h including culture. Of the two techniques studied here, VITEK MS RUO was superior to Raman spectroscopy in the discrimination of A. lentulus from A. fumigatus. VITEK MS RUO seems to be a successful technique in the daily identification of Aspergillus spp. within a limited timeframe.

Molecular diagnostic analysis of outbreak scenarios.

In the current laboratory assignment, technical aspects of the polymerase chain reaction (PCR) are integrated in the context of six different bacterial outbreak scenarios. The "Enterobacterial Repetitive Intergenic Consensus Sequence" (ERIC) PCR was used to analyze different outbreak scenarios. First, groups of 2-4 students determined optimal ERIC-PCR conditions to validate the protocol and subsequently applied ERIC-PCR to identify genetic relatedness among bacterial strains. Based on these genetic fingerprints, students selected the outbreak cases from the patient samples and assessed the risk factors for the outbreak scenario. Finally, students presented their findings during a classroom presentation. The results indicated that the assignment successfully facilitated student learning on the technical aspects of (ERIC) PCR and clearly demonstrated the practical application of PCR in a clinical diagnostic setting. Additionally, the assignment was highly appreciated by the students.

External quality assessment of the molecular diagnostics and genotyping of meticillin-resistant Staphylococcus aureus.

Two multicentre external quality assessments (EQA) for the molecular detection and genotyping of meticillin-resistant Staphylococcus aureus (MRSA) were arranged. Firstly, 11 samples containing various amounts of inactivated MRSA strains, meticillin-susceptible S. aureus (MSSA), meticillin-resistant coagulase-negative staphylococci (MRCoNS) or Escherichia coli were distributed to 82 laboratories. Samples containing 102 or 103 MRSA cells were correctly scored in only 16 and 46% of the datasets returned, respectively. Two of the used MSSA strains contained an SCCmec cassette lacking the mecA gene. There was a marked difference in the percentage of correct results for these two MSSA strains (37 and 39%) compared to the MSSA strain lacking the SCCmec cassette (88%). Secondly, a panel for MRSA genotyping, consisting of ten samples (two identical, three genetically related and five unique strains) was distributed to 19 laboratories. Seventy-three percent of the datasets recorded all samples correctly. Most pulsed-field gel electrophoresis (PFGE) protocols proved to be suboptimal, resulting in inferior resolution in the higher or lower fragment regions. The performance of molecular diagnostics for MRSA shows no significant changes since our first EQA in 2006. The first molecular typing results are encouraging. Both assessments indicate that programme expansion is required and that major performance discrepancies continue to exist.

Detection of colon flora in peritoneal drain fluid after colorectal surgery: can RT-PCR play a role in diagnosing anastomotic leakage?

A semi-quantitative Real-Time PCR strategy was developed to identify potential indicator organisms for anastomotic leakage in peritoneal drainage fluid, Escherichia coli and Enterococcus faecalis. The analytical performance of the amplification method was validated with 10 culture-positive and 7 culture-negative peritoneal drain fluid samples, obtained from 9 different patients with a colorectal anastomosis. Real-Time PCR results were fully concordant with the microbiological culture results. However, among the culture-negative samples, four false-positive RT-PCR results were found. All false-positives originated from a single patient with a surgical site infection. This may indicate an elevated sensitivity of the RT-PCR method. The results showed that the semi-quantitative RT-PCR method has a clear potential to be useful as a powerful tool in early detection of anastomotic leakage.

Replacement of methicillin-resistant Staphylococcus aureus clones in Hungary over time: a 10-year surveillance study.

The prevalence of methicillin-resistant Staphylococcus aureus (MRSA) in Hungary has been increasing and is now close to 20% among invasive isolates of S. aureus. In order to understand the evolution of MRSA in Hungary, two collections of isolates were studied: 22 representatives of a collection of 238 MRSA isolates recovered between 1994 and 1998, and a collection of 299 MRSA isolates recovered between 2001 and 2004. The isolates were first characterised by pulsed-field gel electrophoresis (PFGE) and were distributed into 19 different PFGE patterns. Representatives of each pattern were further characterised by spa typing, multilocus sequence typing (MLST) and staphylococcal cassette chromosome mec (SCCmec) typing. The Hungarian clone that was predominant in 1994-1998 (PFGE E, ST239-III) had almost disappeared in 2003-2004, being replaced by the Southern German clone (PFGE B, ST228-I) and the New York/Japan epidemic clone (PFGE A, ST5-II), which represented c. 85% of the 2001-2004 isolates. Thus, this study describes, for the first time, the co-dominance and extensive spread of the New York/Japan clone in a European country.

Comparison of Staphylococcus aureus isolates from bovine and human skin, milking equipment, and bovine milk by phage typing, pulsed-field gel electrophoresis, and binary typing.

Staphylococcus aureus isolates (n = 225) from bovine teat skin, human skin, milking equipment, and bovine milk were fingerprinted by pulsed-field gel electrophoresis (PFGE). Strains were compared to assess the role of skin and milking equipment as sources of S. aureus mastitis. PFGE of SmaI-digested genomic DNA identified 24 main types and 17 subtypes among isolates from 43 herds and discriminated between isolates from bovine teat skin and milk. Earlier, phage typing (L. K. Fox, M. Gershmann, D. D. Hancock, and C. T. Hutton, Cornell Vet. 81:183-193, 1991) had failed to discriminate between isolates from skin and milk. Skin isolates from humans belonged to the same pulsotypes as skin isolates from cows. Milking equipment harbored strains from skin as well as strains from milk. We conclude that S. aureus strains from skin and from milk can both be transmitted via the milking machine, but that skin strains are not an important source of intramammary S. aureus infections in dairy cows. A subset of 142 isolates was characterized by binary typing with DNA probes developed for typing of human S. aureus. Typeability and overall concordance with epidemiological data were lower for binary typing than for PFGE while discriminatory powers were similar. Within several PFGE types, binary typing discriminated between main types and subtypes and between isolates from different herds or sources. Thus, binary typing is not suitable as replacement for PFGE but may be useful in combination with PFGE to refine strain differentiation.

Rapid detection of methicillin resistance in Staphylococcus aureus isolates by the MRSA-screen latex agglutination test.

The slide agglutination test MRSA-Screen (Denka Seiken Co., Niigata, Japan) was compared with the mecA PCR ("gold standard") for the detection of methicillin resistance in Staphylococcus aureus. The MRSA-Screen test detected the penicillin-binding protein 2a (PBP2a) antigen in 87 of 90 genetically diverse methicillin-resistant S. aureus (MRSA) stock culture strains, leading to a sensitivity of 97%. The three discrepant MRSA strains displayed positive results only after induction of the mecA gene by exposure to methicillin. Both mecA PCR and MRSA-Screen displayed negative results among the methicillin-susceptible S. aureus strains (n = 106), as well as for Micrococcus spp. (n = 10), members of the family Enterobacteriaceae (n = 10), Streptococcus pneumoniae (n = 10), and Enterococcus spp. (n = 10) (specificity = 100%). Producing the same PBP2a antigen, all 10 methicillin-resistant Staphylococcus epidermidis strains score positived in both the latex test and the mecA PCR. Consequently, the MRSA-Screen test should be applied only after identification of the MRSA strain to the species level to rule out coagulase-negative staphylococci. In conclusion, due to excellent specificity and sensitivity the MRSA-Screen latex test has the potential to be successfully used for routine applications in the microbiology laboratory.

Distribution, antibiotic susceptibility and tolerance of bacterial isolates in culture-positive cases of endocarditis in The Netherlands.

During a two-year period data were collected nationwide in The Netherlands on 438 episodes of bacterial endocarditis (BE) in 432 patients. Of the strains isolated in these patients 419 were available for analysis. Of these, 326 were isolated in native valve endocarditis (NVE) and 93 in prosthetic valve endocarditis (PVE). Viridans streptococci, staphylococci and enterococci together constituted 87% of the isolates. More than 46% of the viridans streptococci consisted of Streptococcus sanguis. Enterococcus faecalis and Staphylococcus aureus were the predominant species in the late form of PVE. The majority of the viridans streptococci and haemolytic streptococci were highly susceptible to penicillin. Five of 35 strains of coagulase negative staphylococci were resistant to methicillin. Eleven percent of a random sample of the streptococci collected were tolerant to penicillin. After repeated exposure to a concentration gradient of an appropriate beta-lactam antibiotic, this figure increased to 49%. Of the staphylococci, 5-6% of the strains were tolerant before induction and 16-20% after induction. Of the Enterococcus strains (n = 40), 12.5% showed high-level resistance to one or more aminoglycoside.

Degree and stability of tolerance to penicillin in Streptococcus pyogenes.

The degree of antibiotic tolerance may be assessed by determining the tolerance percentage of a bacterial strain, defined as the surviving fraction of an inoculum that has been exposed for 24 hours to a high concentration of a beta-lactam antibiotic. In 61 clinical isolates of Streptococcus pyogenes, tolerance percentages ranged from 0 to 0.43. From the slopes of the killing curves it can be deduced that killing starts to be delayed at a tolerance percentage of 0.1. Although a tolerance percentage exceeding 0.1 was observed in 41.4% of the strains, the incidence of clinically relevant forms of tolerance is expected to occur in a smaller fraction of the strains. Tolerance percentages of two strains stored at 20 degrees C, 4 degrees C or -70 degrees C (tolerance percentages 0.43 and 0.36) decreased to 0.03 or less in six weeks. Tolerance percentages could be completely restored in these strains, but not in sensitive strains, by successive selection for this property on penicillin gradients of increasing concentration. In four strains isolated from a family outbreak, identical levels of tolerance percentage could be selected for with the same technique.

Determination of aminoglycosides in rat renal tissue by enzyme immunoassay.

The enzyme-multiplied immunoassay technique for the determination of gentamicin or amikacin in serum was evaluated for use in rat renal tissue. After the addition of either gentamicin or amikacin to tissue homogenate, the assay of the supernatant showed a reduced recovery, depending on the amount of renal tissue present per milliliter of homogenate. The recovery was independent of the amount of aminoglycoside added. This reduction could be due to either protein binding or interference with the enzyme-multiplied immunoassay technique by substances released from the renal tissue. When the enzyme-multiplied immunoassay technique is used for aminoglycoside assay in renal tissue, care should be taken to minimize the amount of tissue present in the homogenate or to correct for the decreased recovery.

Efficacy of ampicillin therapy in experimental listeriosis in mice with impaired T-cell-mediated immune response.

The importance of intact host defense mechanisms for successful antimicrobial therapy was investigated via a comparison of the activities of ampicillin against experimental Listeria monocytogenes infections in normal mice and congenitally athymic (nude) mice. Nude mice were used for these experiments because recovery from infection with this organism depends on development of cellular immunity induced specifically by a T-cell-mediated reaction. When infections ampicillin per mouse (32 doses of 25 mg each), which is twenty times the dose required for a cure of infections in normal mice (8 doses of 5 mg each), would not cure infections in nude mice. With a reduction in inoculum to 10(5) colony-forming units, cures were obtained with a total ampicillin dose of 800 mg (32 doses of 25 mg each), but not with 400 mg (16 doses of 25 mg each). These studies show clearly that the efficacy of ampicillin against infections with L. monocytogenes is dependent upon intact host defense mechanisms.