Segregated by Wealth, Health, and Development: An Analysis of Pre-School Child Health in a Medium-Sized German City.

The School Entry Examination (SEE) can be used to identify children with current health issues, developmental delays, and risk factors for later diseases. This study analyzes the health status of preschool children in a German city with considerable socio-economic differences among its quarters. We used secondary data from SEEs 2016-2019 from the entire city (8417 children), which we divided into quarters with low (LSEB), medium (MSEB), and high socioeconomic burden (HSEB). In HSEB quarters, 11.3% of children were overweight as opposed to 5.3% in LSEB quarters. In HSEB quarters, 17.2% of children had sub-par cognitive development in contrast to 1.5% in LSEB quarters. For overall sub-par development, LSEB quarters had a prevalence of 3.3%, whereas, in HSEB quarters, 35.8% of children received this result. Logistic regression was used to determine the influence of the city quarter on the outcome of overall sub-par development. Here, considerable disparities among HSEB and LSEB quarters remained after adjustment for parents' employment status and education. Pre-school children in HSEB quarters showed a higher risk for later disease than children in LSEB quarters. The city quarter had an association with child health and development that should be considered in the formulation of interventions.

Sick and Tired-Sociodemographic and Psychosocial Characteristics of Asylum Seekers Awaiting an Appointment for Psychotherapy.

BACKGROUND: An EU directive holds the EU member states responsible for implementing the provision of health care for asylum seekers. However, current literature indicates insufficient care for asylum seekers in the German health system. This article aims to characterize the situation of the client population on the waiting list of a psychosocial center (PSZ). METHODS: We conducted a retrospective observational study based on client files in Halle (Saale), Germany. We included 437 adults who were on the PSZ waiting list between 2016 and 2019. Questionnaires that collected information on the clientele at two different times were analyzed. RESULTS: The average waiting time for psychotherapy was 50 weeks. In total, 85.6% of the 188 respondents reported sleep disorders (n = 161), 65.4% of clients reported pain (n = 123) and 54.8% suicide attempts/suicidal thoughts (n = 54). In the 16-week waiting period in which the clients waited for an initial appointment with a psychologist, the residence status deteriorated in 21.3% (n = 40). CONCLUSION: Improving asylum seekers' access to the German health system is urgently needed in order to prevent unnecessary suffering in the future and to comply with EU law.

CRHP Finder, a webtool for the detection of clarithromycin resistance in Helicobacter pylori from whole-genome sequencing data.

BACKGROUND: Resistance to clarithromycin in Helicobacter pylori (H pylori) is mediated by mutations in the domain V of the 23S rRNA gene (A2142G, A2143G, A2142C). Other polymorphisms in the 23S rRNA gene have been reported to cause low-level clarithromycin resistance but their importance is still under debate. In this study, we aimed to develop and evaluate the CRHP Finder webtool for detection of the most common mutations mediating clarithromycin resistance from whole-genome sequencing (WGS) data. Moreover, we included an analysis of 23 H pylori strains from Danish patients between January 2017 and September 2019 in Copenhagen, Denmark. MATERIALS AND METHODS: The CRHP Finder detects the fraction of each of the four nucleotides in nucleotide positions 2142, 2143, 2182, 2244 and 2712 of the 23S rRNA gene in H pylori (E coli numbering) by aligning raw sequencing reads (fastq format) with k-mer alignment (KMA). The nucleotide distribution in each position is compared to previously described point mutations mediating clarithromycin resistance in H pylori, and a genotypic prediction of the clarithromycin resistance phenotype is presented as output. For validation of the CRHP webtool, 137 fastq paired-end sequencing datasets originating from a well-characterized strain collection of H pylori were analyzed. RESULTS: The CRHP Finder correctly identified all resistance mutations reported in the sequencing data of 137 H pylori strains. In the 23 Danish H pylori strains, CRHP Finder detected A2143G (13%) in all resistant strains, and T2182C (13%) and C2244T (4,3%) nucleotide exchanges in only susceptible strains. CONCLUSION: In this study, we present the validation of the first webtool for H pylori resistance prediction based on the detection of 23S rRNA mutations (A2142C, A2142G, A2143G, T2182C, C2244T, T2712C) from WGS data of H pylori.

[COVID-19: Knowledge, risk perception and strategies for handling the pandemic]. / COVID-19: Wissensstand, Risikowahrnehmung und Umgang mit der Pandemie.

INTRODUCTION: In order to stem the spread of an epidemic, widespread adherence to safety measures and their acceptance within the German population are of key importance. This survey examines the levels of knowledge and the perception of risk within the population and analyses implementation and adherence to the recommended and legally mandated safety measures in the early phase of the COVID-19 pandemic. METHODS: In March 2020, participants registered on the HeReCa-Online-Panel from Saxony-Anhalt, Berlin and Schleswig Holstein were invited to complete a 65-question survey. RESULTS: 1048 respondents answered the questionnaire, which amounts to a response of 3.5%. 83% of respondents stated that they felt themselves to be well-informed or very well-informed concerning COVID-19 and the coronavirus. The majority of respondents reported fears for the well-being of family members (60%) or the health of the German population as a whole (45%); 79% reported concerns regarding adverse economic impacts. 79% of respondents have implemented individual protective measures, such as reducing social contacts and maintaining the recommended physical distance in public spaces. Most respondents regarded the government-mandated safety measures as predominantly reasonable and appropriate. CONCLUSIONS: In the early phase of the pandemic, most people kept themselves informed about of COVID-19 and started to take individual measures for risk reduction. Acceptance of governmental measures to stem the spread of the pandemic was high.

Does Preoperative Decolonization Reduce Surgical Site Infections in Elective Orthopaedic Surgery? A Prospective Randomized Controlled Trial.

BACKGROUND: Surgical site infections (SSIs) after elective orthopaedic surgery are very stressful for patients due to frequent rehospitalizations with reoperations and poorer functional outcomes. Prevention of such events is therefore crucial. Although an evidence-based consensus is still lacking, preoperative decolonization could decrease SSI. Specifically, more information is needed about the effect of a preoperative decolonization procedure on SSI proportions in both Staphylococcus aureus carriers and non-S. aureus carriers after general orthopaedic surgery. QUESTIONS/PURPOSES: Our study addressed the following questions: (1) Does preoperative decolonization reduce the risk of SSI after general elective orthopaedic surgery in patients colonized with S. aureus? (2) Does preoperative decolonization reduce the risk of SSI among patients who are not colonized with S. aureus? METHODS: In this prospective, randomized, single-blinded trial, we recruited patients undergoing general elective orthopaedic surgery in one tertiary care center in Switzerland. Between November 2014 and September 2017, 1318 of 1897 screened patients were enrolled. Patients were allocated into either the S. aureus carrier group (35%, 465 of 1318 patients) or the noncarrier group (65%, 853 of 1318 patients) according to screening culture results. In the S. aureus group, 232 patients were allocated to the intervention arm and 233 were allocated to the control arm. Intervention was 5 days of daily chlorhexidine showers and mupirocin nasal ointment twice a day. Of the 853 noncarriers, 426 were allocated to the intervention arm and 427 were allocated to the control arm. All patients in both groups were analyzed in an intention-to-treat manner. The primary endpoint was SSI occurrence at 90 days postoperative and the secondary endpoint was SSI occurrence at 30 days postoperative.The initial sample size calculation was made for the S. aureus carrier group. Based on the literature review, a 4% proportion of SSI was expected in the control group. Thus, 726 carriers would have been needed to detect a relative risk reduction of 80% with a power of 80% at a two-sided α-error of 0.048 (adjusted for interim analysis). Assuming carrier prevalence of 27%, 2690 patients would have been needed in total. An interim analysis was performed after including half of the targeted S. aureus carriers (363 of 726). Based on the low infection rate in the control group (one of 179), a new sample size of 15,000 patients would have been needed. This was deemed not feasible and the trial was stopped prematurely. RESULTS: Among carriers, there was no difference in the risk of SSI between the intervention and control arms (decolonized SSI risk: 0.4% [one of 232], control SSI risk: 0.4% [one of 233], risk difference: 0.0% [95% CI -1.2% to 1.2%], stratified for randomization stratification factors; p > 0.999). For noncarriers, there was no difference in risk between the intervention and control arms (decolonized SSI risk: 0.2% [one of 426], control SSI risk: 0.2% [one of 247], stratified risk difference: -0.0% [95% CI -0.7 to 0.6]; p = 0.973). CONCLUSIONS: We found no difference in the risk of SSI between the decolonization and control groups, both in S. aureus carriers and noncarriers. Because of the low event numbers, no definite conclusion about efficacy of routine preoperative decolonization can be drawn. The results, however, may be helpful in future meta-analyses. LEVEL OF EVIDENCE: Level II, therapeutic study.

Mycoplasma penetrans bacteremia in an immunocompromised patient detected by metagenomic sequencing: a case report.

BACKGROUND: Mycoplasma sp. are well recognized as etiological agents of respiratory and sexually transmitted disease. Mycoplasma penetrans, a species of Mycoplasma sp., has been frequently detected in HIV-positive patients and associated with the progression of HIV-associated disease. To date, there is only a single case report describing M. penetrans as the causative agent of a severe respiratory tract infection in a HIV-negative patient. CASE PRESENTATION: In this report, we describe the case of M. penetrans bacteremia in a HIV-negative, 38-year-old, female, immunocompromised, solid organ transplant patient (combined kidney and pancreas transplantation in 2016), who was admitted to our hospital with anemic uterine bleeding and fever of 38.3 °C. Several hours before her admission at our university hospital, a latex bladder catheter was inserted into her uterus and she complained about fatigue, dizziness and ongoing vaginal bleeding. Laboratory examination showed severe anemia, but microbiological examination was inconspicuous (culture negative vaginal and cervical smears, negative urine culture). Bacterial blood cultures showed a growth signal after 4 h, but microscopic examination with Gram staining and subcultures on different agar media did not identify bacterial pathogens. To identify the bacterial cause of malignancy in the patient, metagenomic sequencing of the blood culture was performed that identified M. penetrans. CONCLUSION: Metagenomic sequencing identified M. penetrans in an immunosuppressed patient with culture-negative bacteremia. Clinicians should be aware of the opportunistic potential of M. penetrans that may cause severe infections in certain vulnerable patient populations and the limitations of culture and Gram staining for confirming the presence of fastidious bacterial pathogens like Mycoplasma spp.

Comparison of the Diagnostic Performance of qPCR, Sanger Sequencing, and Whole-Genome Sequencing in Determining Clarithromycin and Levofloxacin Resistance in Helicobacter pylori.

Helicobacter pylori antibiotic resistance is increasing worldwide, emphasizing the urgent need for more rapid resistance detection prior to the administration of H. pylori eradication regimens. Macrolides and fluoroquinolones are widely used to treat H. pylori. In this study, we aimed to compare the diagnostic performance of A) 23SrDNA qPCR (with melting curve analysis) and an in-house developed gyrA qPCR followed by Sanger sequencing with a commercial IVD-marked hybridization probe assay (for 23SrDNA and gyrA) using 142 gastric biopsies (skipping culturing) and B) the same two qPCR for 23SrDNA and gyrA (including Sanger sequencing) with whole-genome sequencing (WGS) and phenotypic characterization of clarithromycin and levofloxacin resistance using 76 cultured isolates. The sensitivity of both qPCRs was 100% compared to that of the commercial IVD-marked hybridization probe assay for the detection of H. pylori in gastric biopsies (without resistance testing). The specificity of the qPCR gyrA followed by Sanger sequencing was 100%, indicating that the best sequence identity was always H. pylori. The results show good agreement between molecular tests, especially between qPCR (inclusive Sanger sequencing) and WGS. Discrepancies (concerning mutated or wild type of positive H. pylori gastric biopsies) were observed between Sanger sequencing of the gyrA gene and the corresponding commercial hybridization probe assay, mostly because the high sequence diversity of the gyrA gene even at positions adjacent to the relevant codons of 87 and 91 interfered with obtaining correct results from the hybridization probe assay. Interestingly, we found several mixed sequences, indicating mixed populations in the gastric biopsies (direct detection without culturing). There was a high percentage of both levofloxacin and clarithromycin resistance in gastric biopsies (both between 22% and 29%, direct detection in gastric biopsies). Therefore, we recommend analyzing both targets in parallel. We confirmed that phenotypic resistance is highly correlated with the associated mutations. We concluded that the two qPCR followed by Sanger sequencing of the gyrA gene is a fast, cost-effective and comprehensive method for resistance testing of H. pylori directly in gastric biopsies.

Review of current diagnostic methods and advances in Helicobacter pylori diagnostics in the era of next generation sequencing.

Helicobacter pylori (H. pylori) infection is highly prevalent in the human population and may lead to severe gastrointestinal pathology including gastric and duodenal ulcers, mucosa associated tissue lymphoma and gastric adenocarcinoma. In recent years, an alarming increase in antimicrobial resistance and subsequently failing empiric H. pylori eradication therapies have been noted worldwide, also in many European countries. Therefore, rapid and accurate determination of H. pylori's antibiotic susceptibility prior to the administration of eradication regimens becomes ever more important. Traditionally, detection of H.pylori and its antimicrobial resistance is done by culture and phenotypic drug susceptibility testing that are cumbersome with a long turn-around-time. Recent advances in diagnostics provide new tools, like real-time polymerase chain reaction (PCR) and line probe assays, to diagnose H. pylori infection and antimicrobial resistance to certain antibiotics, directly from clinical specimens. Moreover, high-throughput whole genome sequencing technologies allow the rapid analysis of the pathogen's genome, thereby allowing identification of resistance mutations and associated antibiotic resistance. In the first part of this review, we will give an overview on currently available diagnostic methods for detection of H. pylori and its drug resistance and their implementation in H. pylori management. The second part of the review focusses on the use of next generation sequencing technology in H. pylori research. To this end, we conducted a literature search for original research articles in English using the terms "Helicobacter", "transcriptomic", "transcriptome", "next generation sequencing" and "whole genome sequencing". This review is aimed to bridge the gap between current diagnostic practice (histology, rapid urease test, H. pylori culture, PCR and line probe assays) and new sequencing technologies and their potential implementation in diagnostic laboratory settings in order to complement the currently recommended H. pylori management guidelines and subsequently improve public health.

Rapid Characterization of Virulence Determinants in Helicobacter pylori Isolated from Non-Atrophic Gastritis Patients by Next-Generation Sequencing.

Helicobacter pylori is a major human pathogen that causes a wide range of gastrointestinal pathology. Progression of H. pylori induced gastritis to more severe disease has been found to highly correlate with the array of virulence factors expressed by the pathogen. The objective of this study was twofold: first, to characterize the genetic diversity of H. pylori strains isolated from 41 non-atrophic gastritis patients in Switzerland, an issue that has not been investigated to date. And second, to assess the prevalence and sequence variation of H. pylori virulence factors (cagA, vacA, iceA and dupA) and genes encoding outer membrane proteins (OMPs; babA, babB, sabA, sabB, hopZ, hopQ and oipA) by whole genome sequencing (WGS) using an Illumina MiSeq platform. WGS identified high genetic diversity in the analyzed H. pylori strains. Most H. pylori isolates were assigned to hpEurope (95.0%, 39/41), and the remaining ones (5.0%, 2/41) to hpEastAsia, subpopulation hspEAsia. Analysis of virulence factors revealed that 43.9% of the strains were cagA-positive, and the vacA s1 allele was detected in 56.0% of the isolates. The presence of cagA was found to be significantly associated (P < 0.001) with the presence of vacA s1, babA2 and hopQ allele 1 as well as expression of oipA. Moreover, we found an association between the grade of gastritis and H. pylori abundance in the gastric mucosa, respectively and the presence of cagA, vacA s1 and hopQ allele 1. Among our 41 gastritis patients, we identified seven patients infected with H. pylori strains that carried a specific combination of virulence factors (i.e., cagA, vacA s1 allele and babA2 allele), recently implicated in the development of more severe gastrointestinal pathology, like peptic ulcer disease and even gastric cancer. To this end, WGS can be employed for rapid and detailed characterization of virulence determinants in H. pylori, providing valuable insights into the pathogenic capacity of the bacterium. This could ultimately lead to a higher level of personalized treatment and management of patients suffering from H. pylori associated infections.

Population-based inference of aminoglycoside resistance mechanisms in Escherichia coli.

BACKGROUND: Interpretative reading of antimicrobial susceptibility test (AST) results allows inferring biochemical resistance mechanisms from resistance phenotypes. For aminoglycosides, however, correlations between resistance pathways inferred on the basis of the European Committee on Antimicrobial Susceptibility Testing (EUCAST) clinical breakpoints and expert rules versus genotypes are generally poor. This study aimed at developing and validating a decision tree based on resistance phenotypes determined by disc diffusion and based on epidemiological cut-offs (ECOFFs) to infer the corresponding resistance mechanisms in Escherichia coli. METHODS: Phenotypic antibiotic susceptibility of thirty wild-type and 458 aminoglycoside-resistant E. coli clinical isolates was determined by disc diffusion and the genomes were sequenced. Based on well-defined cut-offs, we developed a phenotype-based algorithm (Aminoglycoside Resistance Mechanism Inference Algorithm - ARMIA) to infer the biochemical mechanisms responsible for the corresponding aminoglycoside resistance phenotypes. The mechanisms inferred from susceptibility to kanamycin, tobramycin and gentamicin were analysed using ARMIA- or EUCAST-based AST interpretation and validated by whole genome sequencing (WGS) of the host bacteria. FINDINGS: ARMIA-based inference of resistance mechanisms and WGS data were congruent in 441/458 isolates (96·3%). In contrast, there was a poor correlation between resistance mechanisms inferred using EUCAST CBPs/expert rules and WGS data (418/488, 85·6%). Based on the assumption that resistance mechanisms can result in therapeutic failure, EUCAST produced 63 (12·9%) very major errors (vME), compared to only 2 (0·4%) vME with ARMIA. When used for detection and identification of resistance mechanisms, ARMIA resolved >95% vMEs generated by EUCAST-based AST interpretation. INTERPRETATION: This study demonstrates that ECOFF-based analysis of AST data of only four aminoglycosides provides accurate information on the resistance mechanisms in E. coli. Since aminoglycoside resistance mechanisms, despite having in certain cases a minimal effect on the minimal inhibitory concentration, may compromise the bactericidal activity of aminoglycosides, prompt detection of resistance mechanisms is crucial for therapy. Using ARMIA as an interpretative rule set for editing AST results allows for better predictions of in vivo activity of this drug class.

Defining threshold values in microscopic examination and qPCR for optimal performance of line probe assays for resistance detection in Mycobacterium tuberculosis complex.

Line probe assays enable rapid detection of drug-resistant Mycobacterium tuberculosis directly from clinical specimens. This study shows that defining threshold values in microscopic examination or PCR detection of M. tuberculosis optimizes line probe assay efficiency, thereby avoiding costs and loss of time due to unnecessary molecular testing.

Menstrual toxic shock syndrome: case report and systematic review of the literature.

Menstrual toxic shock syndrome (mTSS) is a life-threatening disease caused by superantigen-producing Staphylococcus aureus. Incidence ranges from 0·03 to 0·50 cases per 100 000 people, with overall mortality around 8%. In this Grand Round, we present the case of a previously healthy 23-year-old menstruating woman who was diagnosed with mTSS after she presented at our hospital with a septic condition for the second time. The diagnosis was confirmed by fulfilment of the clinical criteria outlined by the US Centers for Disease Control and Prevention (CDC; fever, rash, desquamation, hypotension, and multi-system involvement) as well as a nasal swab positive for the S aureus strain and presence of the gene encoding for toxic shock syndrome toxin 1 (TSST-1). In the early 1980s, when mTSS was first described, use of tampons was considered the main risk factor. Today, the complex interplay between pathogenic factors of S aureus, immunological mechanisms of the host, and changes in the vaginal ecosystem during menstruation has broadened current understanding of the disease, and the CDC criteria have appreciable limitations in everyday clinical practice.

Evaluation of the AID AmpC line probe assay for molecular detection of AmpC-producing Enterobacterales.

OBJECTIVES: In this study, the commercially available AID AmpC line probe assay (LPA) was evaluated for detection of plasmid-mediatedblaAmpC ß-lactamase genes in Enterobacterales as well as chromosomal mutations in the blaAmpC promoter/attenuator regions in Escherichia coli. METHODS: Accuracy of the AID AmpC probes was assessed using Enterobacterales clinical isolates harbouring diverse plasmid-mediated AmpC enzymes (ACC, ACT, DHA, FOX, CMY and MOX) and E. coli clinical isolates with mutations in the chromosomal blaAmpC promoter/attenuator regions. The diagnostic performance of the AID AmpC LPA for blaAmpC detection directly from clinical specimens was determined using 99 clinical urine specimens with bacterial cell counts >105CFU/mL and the results were compared with culture-based phenotypic drug susceptibility testing (DST). RESULTS: Detection of blaAmpC genes in Enterobacterales clinical isolates showed 100% congruence with phenotypic DST results. The AID AmpC LPA showed 100% specificity [95% confidence interval (CI) 96-100%] and 100% sensitivity (95% CI 75-100%) for detection of plasmid-meditated blaAmpC and E. coli genomic blaAmpC promoter/attenuator mutations directly from clinical urine specimens. The AID AmpC LPA detected three AmpC-producers in urine specimens with bacterial cell counts >105CFU/mL that were missed by culture-based phenotypic DST, thereby displaying higher diagnostic sensitivity. CONCLUSION: The AID AmpC LPA is an accurate, sensitive and easy-to-use test that can be readily implemented in any diagnostic laboratory for molecular detection of blaAmpC genes in Enterobacterales.

Genetic Determinants and Prediction of Antibiotic Resistance Phenotypes in Helicobacter pylori.

Helicobacter pylori is a major human pathogen. Diagnosis of H. pylori infection and determination of its antibiotic susceptibility still mainly rely on culture and phenotypic drug susceptibility testing (DST) that is time-consuming and laborious. Whole genome sequencing (WGS) has recently emerged in medical microbiology as a diagnostic tool for reliable drug resistance prediction in bacterial pathogens. The aim of this study was to compare phenotypic DST results with the predictions based on the presence of genetic determinants identified in the H. pylori genome using WGS. Phenotypic resistance to clarithromycin, metronidazole, tetracycline, levofloxacin, and rifampicin was determined in 140 clinical H. pylori isolates by E-Test®, and the occurrence of certain single nucleotide polymorphisms (SNPs) in target genes was determined by WGS. Overall, there was a high congruence of >99% between phenotypic DST results for clarithromycin, levofloxacin, and rifampicin and SNPs identified in the 23S rRNA, gyrA, and rpoB gene. However, it was not possible to infer a resistance phenotype for metronidazole based on the occurrence of distinct SNPs in frxA and rdxA. All 140 H. pylori isolates analysed in this study were susceptible to tetracycline, which was in accordance with the absence of double or triple nucleotide substitutions in the 16S rRNA gene.

Light availability impacts structure and function of phototrophic stream biofilms across domains and trophic levels.

Phototrophic biofilms are ubiquitous in freshwater and marine environments where they are critical for biogeochemical cycling, food webs and in industrial applications. In streams, phototrophic biofilms dominate benthic microbial life and harbour an immense prokaryotic and eukaryotic microbial biodiversity with biotic interactions across domains and trophic levels. Here, we examine how community structure and function of these biofilms respond to varying light availability, as the crucial energy source for phototrophic biofilms. Using metatranscriptomics, we found that under light limitation-dominant phototrophs, including diatoms and cyanobacteria, displayed a remarkable plasticity in their photosynthetic machinery manifested as higher abundance of messenger RNAs (mRNAs) involved in photosynthesis and chloroplast ribosomal RNA. Under higher light availability, bacterial mRNAs involved in phosphorus metabolism, mainly from Betaproteobacteria and Cyanobacteria, increased, likely compensating for nutrient depletion in thick biofilms with high biomass. Consumers, including diverse ciliates, displayed community shifts indicating preferential grazing on algae instead of bacteria under higher light. For the first time, we show that the functional integrity of stream biofilms under variable light availability is maintained by structure-function adaptations on several trophic levels. Our findings shed new light on complex biofilms, or "microbial jungles", where in analogy to forests, diverse and multitrophic level communities lend stability to ecosystem functioning. This multitrophic level perspective, coupling metatranscriptomics to process measurements, could advance understanding of microbial-driven ecosystems beyond biofilms, including planktonic and soil environments.

Detection of respiratory bacterial pathogens causing atypical pneumonia by multiplex Lightmix® RT-PCR.

Pneumonia is a severe infectious disease. In addition to common viruses and bacterial pathogens (e.g. Streptococcus pneumoniae), fastidious respiratory pathogens like Chlamydia pneumoniae, Mycoplasma pneumoniae and Legionella spp. can cause severe atypical pneumonia. They do not respond to penicillin derivatives, which may cause failure of antibiotic empirical therapy. The same applies for infections with B. pertussis and B. parapertussis, the cause of pertussis disease, that may present atypically and need to be treated with macrolides. Moreover, these fastidious bacteria are difficult to identify by culture or serology, and therefore often remain undetected. Thus, rapid and accurate identification of bacterial pathogens causing atypical pneumonia is crucial. We performed a retrospective method evaluation study to evaluate the diagnostic performance of the new, commercially available Lightmix® multiplex RT-PCR assay that detects these fastidious bacterial pathogens causing atypical pneumonia. In this retrospective study, 368 clinical respiratory specimens, obtained from patients suffering from atypical pneumonia that have been tested negative for the presence of common agents of pneumonia by culture and viral PCR, were investigated. These clinical specimens have been previously characterized by singleplex RT-PCR assays in our diagnostic laboratory and were used to evaluate the diagnostic performance of the respiratory multiplex Lightmix® RT-PCR. The multiplex RT-PCR displayed a limit of detection between 5 and 10 DNA copies for different in-panel organisms and showed identical performance characteristics with respect to specificity and sensitivity as in-house singleplex RT-PCRs for pathogen detection. The Lightmix® multiplex RT-PCR assay represents a low-cost, time-saving and accurate diagnostic tool with high throughput potential. The time-to-result using an automated DNA extraction device for respiratory specimens followed by multiplex RT-PCR detection was below 4 h, which is expected to significantly improve diagnostics for atypical pneumonia-associated bacterial pathogens.

A novel RT-PCR for the detection of Helicobacter pylori and identification of clarithromycin resistance mediated by mutations in the 23S rRNA gene.

In this study we evaluated the commercially available LightMix® RT-PCR assay for Helicobacter pylori detection and identification of clarithromycin (CLR) resistance in culture and clinical specimens (gastric biopsies and stool). The H. pylori LightMix® RT-PCR detects a 97bp long fragment of the 23S rRNA gene and allows the identification of 3 distinct point mutations conferring CLR resistance via melting curve analysis. The performance of the H. pylori LightMix® RT-PCR was evaluated using a set of 60 H. pylori strains showing phenotypical CLR susceptibility or CLR resistance (Minimum inhibitory concentrations from 0.016 to 256mg/L). We found high concordance (95%) between phenotypical CLR resistance screening by E-Test® and the Lightmix® RT-PCR. Discrepant results were verified by sequencing of the 23S rRNA gene that always confirmed the results obtained by Lightmix® RT-PCR. Furthermore, H. pylori was detected in clinical biopsy and stool specimens by Lightmix® RT-PCR that identified the correct H. pylori genotype. The LightMix® RT-PCR is an accurate, sensitive and easy to use test for H. pylori and CLR resistance detection and can therefore be readily implemented in any diagnostic laboratory.

Pathogen Identification by Multiplex LightMix Real-Time PCR Assay in Patients with Meningitis and Culture-Negative Cerebrospinal Fluid Specimens.

Acute bacterial meningitis is a medical emergency, and delays in initiating effective antimicrobial therapy result in increased morbidity and mortality. Culture-based methods, thus far considered the "gold standard" for identifying bacterial microorganisms, require 24 to 48 h to provide a diagnosis. In addition, antimicrobial therapy is often started prior to clinical sample collection, thereby decreasing the probability of confirming the bacterial pathogen by culture-based methods. To enable a fast and accurate detection of the most important bacterial pathogens causing meningitis, namely, Streptococcus pneumoniae, Haemophilus influenzae, Neisseria meningitidis, Streptococcus agalactiae, and Listeria monocytogenes, we evaluated a commercially available multiplex LightMix real-time PCR (RT-PCR) in 220 cerebrospinal fluid (CSF) specimens. The majority of CSF samples were collected by lumbar puncture, but we also included some CSF samples from patients with symptoms of meningitis from the neurology department that were recovered from shunts. CSF samples were analyzed by multiplex RT-PCR enabling a first diagnosis within a few hours after sample arrival at our institute. In contrast, bacterial identification took between 24 and 48 h by culture. Overall, a high agreement of bacterial identification between culture and multiplex RT-PCR was observed (99%). Moreover, multiplex RT-PCR enabled the detection of pathogens, S. pneumoniae (n = 2), S. agalactiae (n = 1), and N. meningitidis (n = 1), in four culture-negative samples. As a complement to classical bacteriological CSF culture, the LightMix RT-PCR assay proved to be valuable by improving the rapidity and accuracy of the diagnosis of bacterial meningitis.

Variability in gene content and expression of the thioredoxin system in Oenococcus oeni.

The thioredoxin system protects against oxidative stress through the reversible oxidation of the thioredoxin active center dithiol to a disulphide. The genome of Oenococcus oeni PSU-1 contains three thioredoxin genes (trxA1, trxA2, trxA3), one thioredoxin reductase (trxB) and one ferredoxin reductase (fdr) which, until recently, was annotated as a second thioredoxin reductase. For the first time, the entire thioredoxin system in several O. oeni strains isolated from wine has been analysed. Comparisons at the DNA and protein levels have been undertaken between sequences from O. oeni and other genera and species, and the genera Leuconostoc and Lactobacillus were found to present the highest similarities. The gene most frequently absent from a collection of 34 strains and the sequences annotated in the NCBI database was trxA1. Moreover, phylogenetic analysis suggested that this gene was horizontally transferred from Lactobacillus to O. oeni. Strain-dependent expression profiles were determined in rich and in wine-like media. General over-expression was detected after inoculation into wine-like medium, with trxA3 being the most highly expressed gene. The increased transcriptional levels of the thioredoxin genes are indicative of the crucial role of this system in the O. oeni response to wine harsh conditions.