Svea Sachse

Evaluation of a Polymerase Chain Reaction Assay for Pathogen Detection in Septic Patients under Routine Condition: An Observational Study

Background Treatment of septic shock relies on appropriate antimicrobial therapy. Current culture based methods deliver final results after days, which may delay potentially lifesaving adjustments in antimicrobial therapy. This study was undertaken to compare PCR with blood culture results under routine conditions regarding 1. impact on antimicrobial therapy, and 2. time to result, in patients with presumed sepsis. Methodology/Principal Findings This was an observational study in a 50 beds ICU of a university hospital. In 245 patients with suspected sepsis, 311 concomitant blood cultures and blood for multiplex PCR (VYOO®) were obtained. 45 of 311 blood cultures (14.5%) and 94 of 311 PCRs (30.1%) were positive. However, blood culture or microbiological sampling from the presumed site of infection rarely confirmed PCR results and vice versa. Median time to positivity and interquartile range were 24.2 (18.0, 27.5) hours for the PCR and 68 (52.2, 88.5) hours for BC (p<0.01). PCR median time to result was dependent on technician availability (53.5 hours on Saturdays, 7.2 hours under optimal logistic conditions). PCR results showed good correlation with procalcitonin (p<0.001). In 34% of patients with positive PCRs antimicrobial therapy was considered inadequate according to assessment of clinical arbitrators including 5 patients with vancomycin-resistant enterococci (VRE), 3 cases with multiresistant staphylococci, and 4 patients with fungi. Conclusions The results of this observational study support the hypothesis that PCR results are available faster, are more frequently positive, and may result in earlier adjustment of antimicrobial therapy. However, shorter time to result can only be fully exploited when the laboratory is adequately staffed for a 24 hour/7 day service, or when point of care/automated assay systems become available.

Culture Independent Raman Spectroscopic Identification of Urinary Tract Infection Pathogens: A Proof of Principle Study

Urinary tract infection (UTI) is a very common infection. Up to every second woman will experience at least one UTI episode during her lifetime. The gold standard for identifying the infectious microorganisms is the urine culture. However, culture methods are time-consuming and need at least 24 h until the results are available. Here, we report about a culture independent identification procedure by using Raman microspectroscopy in combination with innovative chemometrics. We investigated, for the first time directly, urine samples by Raman microspectroscopy on a single-cell level. In a first step, a database of eleven important UTI bacterial species, which were grown in sterile filtered urine, was built up. A support vector machine (SVM) was used to generate a statistical model, which allows a classification of this data set with an accuracy of 92% on a species level. This model was afterward used to identify infected urine samples of ten patients directly without a preceding culture step. Thereby, we were able to determine the predominant bacterial species (seven Escherichia coli and three Enterococcus faecalis ) for all ten patient samples. These results demonstrate that Raman microspectroscopy in combination with support vector machines allow an identification of important UTI bacteria within two hours without the need of a culture step.

Truncated Human Cytidylate-Phosphate-Deoxyguanylate-Binding Protein for Improved Nucleic Acid Amplification Technique-Based Detection of Bacterial Species in Human Samples

ABSTRACT A trunk of human cytidylate-phosphate-deoxyguanylate-binding protein/CXXC finger protein 1 (CFP1), immobilized onto an aminohexyl-Sepharose column, can be used as a preanalytical tool for the selective enrichment of bacterial DNA from mixed solutions with high amounts of human background DNA for nucleic acid amplification technique-based detection of pathogens. The transcriptional activator protein exhibits a high affinity for nonmethylated CpG dinucleotide motifs, which are differentially distributed in prokaryotic and higher eukaryotic genomes. The feasibility of the affinity chromatography (AC) step was tested with DNA from severely septic patients. AC using 16S rRNA gene primers substantially increased PCR sensitivity. Approximately 90% of eukaryotic DNA was removed, which significantly increased the signal-to-noise ratio. Threshold cycle values revealed that sensitivity was elevated at least 10-fold. The change in the ratio of bacterial DNA to human DNA increased from 26% to 74% the likelihood of culture-independent PCR-based identification of bacterial presence. Compared to the results seen with blood culture (which is the clinical gold standard for systemic infections, exhibiting 28% positives), the combination of AC and PCR achieves a significant increase in sensitivity and contributes to shortening the time to results for the initiation of guided antibiotic therapy.

Identification of bacterial DNA in neutrocytic and non-neutrocytic cirrhotic ascites by means of a multiplex polymerase chain reaction

Background: Even though bacterial cultures of ascitic fluid are negative in up to 65% of the cases of spontaneous bacterial peritonitis (SBP); bacterial DNA (bactDNA) has been frequently detected in episodes of SBP as well as in culture‐negative non‐neutrocytic ascites.

Attributable costs of patients with candidemia and potential implications of polymerase chain reaction–based pathogen detection on antifungal therapy in patients with sepsis

PURPOSE The purposes of this study were to calculate attributable costs of candidemia in patients with severe sepsis and to obtain preliminary data regarding the potential effects of polymerase chain reaction-based pathogen detection on antifungal therapy for these patients. METHODS Patients treated between 2004 and 2010 because of severe sepsis were included into this retrospective analysis. The hospital management provided annual fixed costs per patient-day; data for variable intensive care unit costs were taken from the literature. Multiplex polymerase chain reaction (PCR) was used (VYOO, SIRS-Lab, Jena, Germany) for pathogen detection in the blood. RESULTS Thirty-two patients with candidemia were identified. Of 874 patients with sepsis, propensity score matching found 32 corresponding patients with sepsis but without candida infection but similar risk factors for developing candidemia. Attributable costs of candidemia were 7713.79 Euro (cost increase, 19.4%). Initiation of antifungal therapy was reduced from 67.5 (52.4, 90) hours in the group, where candida infection was determined by blood culture, to 31.0 (28.0, 37.5; P < .01) hours after detection by multiplex PCR. CONCLUSIONS Candidemia increases costs of care in patients with septic shock. Polymerase chain reaction-based pathogen detection significantly reduces the time to initiation of antifungal therapy. This might impact on the clinical course of the disease but need to be confirmed in further trials.

Coexistence of Borrelia spp. and Babesia spp. in Ixodes ricinus ticks in Middle Germany.

Altogether, 430 nymphs and 570 adult Ixodes ricinus ticks were collected in 2006 (n = 506) and 2007 (n = 494) from a forest area in Middle Germany (Thuringia). Single ticks were investigated by polymerase chain reaction and restriction fragment length polymorphism or sequencing for Borrelia spp. (ospA gene) and Babesia spp. (18S rRNA gene). Overall, 27.0% (270/1000) were infected with Borrelia species. Out of these, Borrelia garinii was detected most frequently (133/270)-especially, OspA serotype 6 (51/270), followed by Bo. burgdorferi (70/270), Bo. afzelii (42/270), Bo. valaisiana subgroup I (28/270), not typable Borrelia spp. (5/270), Bo. spielmanii (3/270), Bo. valaisiana subgroup II (2/270), and Bo. lusitaniae (1/270). In 1.4% of investigated ticks mixed infections with several Borrelia spp. occurred. Babesia spp.-specific DNA was detected in 5.0% of ticks. Babesia microti was slightly more prevalent (28/50) than Babesia divergens (20/50). Moreover, 5.9% (16/270) of Borrelia spp.-infected ticks were coinfected with Babesia spp. Knowledge on the degree of heterogeneity of Borrelia species and OspA types is prerequisite not only for local risk assessment, but also for diagnostic test and vaccine development.

Distinct Different Contributions of the Alternative and Classical Complement Activation Pathway for the Innate Host Response during Sepsis

Complement activation represents a crucial innate defense mechanism to invading microorganisms, but there is an eminent lack of understanding of the separate contribution of the different complement activation pathways to the host response during sepsis. We therefore investigated different innate host immune responses during cecal ligation and puncture (CLP)-induced sepsis in mice lacking either the alternative (fD−/−) or classical (C1q−/−) complement activation pathway. Both knockout mice strains showed a significantly reduced survival and increased organ dysfunction when compared with control mice. Surprisingly, fD−/− mice demonstrated a compensated bacterial clearance capacity as control mice at 6 h post CLP, whereas C1q−/− mice were already overwhelmed by bacterial growth at this time point. Interestingly, at 24 h after CLP, fD−/− mice failed to clear bacteria in a way comparable to control mice. However, both knockout mice strains showed compromised C3 cleavage during sepsis. Investigating potential causes for this discrepancy, we were able to demonstrate that despite normal bacterial clearance capacity early during the onset of sepsis, fD−/− mice displayed increased inflammatory cytokine generation and neutrophil recruitment into lungs and blood when compared with both control- and C1q−/− mice, indicating a potential loss of control over these immune responses. Further in vitro experiments revealed a strongly increased Nf-κB activation capacity in isolated neutrophils from fD−/− mice, supporting this hypothesis. Our results provide evidence for the new concept that the alternative complement activation pathway exerts a distinctly different contribution to the innate host response during sepsis when compared with the classical pathway.

Co-circulation of Emerging Tick-Borne Pathogens in Middle Germany

From May until October 2007, a total of 658 Ixodes ricinus ticks were collected off birds (189), rodents (273), and vegetation (196) in a certain area of Middle Germany and investigated for infection with Babesia spp., Anaplasma phagocytophilum, and Rickettsia spp. Overall, 13.1% (86/658) of the ticks were infected with at least one pathogen; co-infections occurred in 0.6% (4/658). Babesia spp. specific DNA was detected in 9.7% (64/658) of the ticks, 1.4% (9/658) were infected with A. phagocytophilum, and 2.6% (17/658) harbored rickettsiae. At least two different Rickettsia species were identified: Rickettsia monacensis and Rickettsia helvetica. Our study provides first interesting insights into the circulation and co-circulation of several emerging pathogens not only in ticks parasitizing birds and small mammals as potential reservoirs but also in questing ticks in a single natural habitat.

Genetic characterization and barcoding of taxa in the genus Wolffia Horkel ex Schleid. (Lemnaceae) as revealed by two plastidic markers and amplified fragment length polymorphism (AFLP)

The genus Wolffia of the duckweed family (Lemnaceae) contains the smallest flowering plants. Presently, 11 species are recognized and categorized mainly on the basis of morphology. Because of extreme reduction of structure of all species, molecular methods are especially required for barcoding and identification of species and clones of this genus. We applied AFLP combined with Bayesian analysis of population structure to 66 clones covering all 11 species. Nine clusters were identified: (1) W. angusta and W. microscopica (only one clone), (2) W. arrhiza, (3) W. cylindracea (except one clone that might be a transition form), (4) W. australiana, (5) W. globosa, (6) W. globosa, W. neglecta, and W. borealis, (7) W. brasiliensis, and W. columbiana, (8) W. columbiana, (9) W. elongata. Furthermore, we investigated the sequences of plastidic regions rps16 (54 clones) and rpl16 (55 clones), and identified the following species: W. angusta, W. australiana, W. brasiliensis, W. cylindracea, W. elongata, W. microscopica, and W. neglecta. Wolffia globosa has been separated into two groups by both methods. One group which consists only of clones from North America and East Asia was labelled here “typical W. globosa”. The other group of W. globosa, termed operationally “W. neglecta”, contains also clones of W. neglecta and shows high similarity to W. borealis. None of the methods recognized W. borealis as a distinct species. Although each clone could be characterized individually by AFLP and plastidic sequences, and most species could be bar-coded, the presently available data are not sufficient to identify all taxa of Wolffia.

Comparison of multilocus sequence typing, RAPD, and MALDI-TOF mass spectrometry for typing of β-lactam–resistant Klebsiella pneumoniae strains

Extended spectrum of β-lactam (ESBL) resistance of Klebsiella pneumoniae has become an increasing problem in hospital infections. Typing of isolates is important to establish the intrahospital surveillance of resistant clones. In this study, the discriminatory potential of randomly amplified polymorphic DNA and matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) analyses were compared with multilocus sequence typing (MLST) by using 17 β-lactam-resistant K. pneumoniae isolates of different genotypes. MLST alleles were distributed in 8 sequence types (STs). Among ESBL strains of the same ST, the presence of different β-lactamase genes was common. RAPD band patterns also revealed 8 types that corresponded to MLST-defined genotypes in 15 out of 17 cases. MALDI-TOF analysis could differentiate 5 clusters of strains. The results of this work show that RAPD may be usable as a rapid screening method for the intrahospital surveillance of K. pneumoniae, allowing a discrimination of clonally related strains. MALDI-TOF-based typing was not strongly corresponding to genotyping and warrants further investigation.