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 <sup>®</sup> 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 <sup>®</sup> 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 <sup>®</sup> 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

Longitudinal increase in the detection rate of Mycobacterium chimaera in heater-cooler device-derived water samples

Colonization with Mycobacterium chimaera and other nontuberculous mycobacteria (NTM) has been reported for heater-cooler devices (HCD) produced by several manufacturers. Up to now, exclusively LivaNova (London, UK) HCDs have been associated with M. chimaera infections after cardiac surgery. The vast majority of studies on HCD colonization were cross-sectional. We were interested in longitudinal dynamics of mycobacterial growth in HCD water samples and analyzed data of a prospective mycobacterial surveillance of five LivaNova 3T HCDs. Nontuberculous mycobacteria were isolated in 319 (48.0%, 21 water samples grew more than one mycobacterial species) of a total of 665 water samples. The most frequently detected species were M. chimaera (N= 247/319, 77.4%), Mycobacterium gordonae (46/319, 14.4%) and Mycobacterium paragordonae (34/319, 10.7%). Detection rates increased longitudinally for any NTM (odds ratio (OR) per year in use: 1.60, 95% CI 1.17-2.24, P<0.001) and for M. chimaera (OR per year in use: 1.67, 95% CI 1.11-2.57, P<0.01)

Update zum Zoonosepotential von Chlamydien

Knowledge of the obligate intracellular bacteria from the Chlamydiaceae family has increased significantly in recent years. Not only new chlamydia species, such as Chlamydia avium or C. buteonis in birds have been described, but also known chlamydia in new host species, such as C. psittaci in horses. This review article provides an up-to-date overview of the zoonotic potential of C. psittaci, C. abortus, C. caviae and C. felis and summarizes current findings on other chlamydia species in different animal species; supplemented by information on optimal sampling and pathogen detection

Клиническая значимость гене тической характеризации рака предстательной железы: обзор литературы

Molecular and genetic characterization of the prostate cancer seems to be a very relevant issue for clinical practice with regard to diagnostics, prognosis, treatment selection and assessment of therapy efficacy. A lot of fundamental studies assault the genetic basis of the disease and the differences in the phenotypic traits of prostate tumors. However, the significant gap is seen between the huge amount of studies to genetic characterization of prostate cancer, which often have a limited way to translation into the clinical practice or simply were not conceived to be so, and clinical practice. Substantial difficulties on the way are multifocality of the prostate carcinoma, inter- and intrafocal heterogeneity and abundance of recurrent genetic alterations, the role of which is understudied to date. In this review we have aimed at the providing an overview of the current studies, being the most close to translation in clinical practice. The common applications and problems are discussed.В последнее время предпринимаются многочисленные попытки выявления молекулярных генетических особенностей рака предстательной железы (РПЖ). Тем не менее, несмотря на большое количество исследовательских программ по молекулярной биологии и генетике, значение результатов этих работ остается неясным, а выводы имеют ограниченное применение в клинической практике. Во многом это связано с тем, что РПЖ характеризуется выраженной генетической гетерогенностью. Мы провели анализ литературы для выявления путей возможного клинического применения результатов фундаментальных генетических и молекулярно-биологических исследований в отношении РПЖ (трансляции в клинику), основных проблем, возникающих при этом, и перспектив развития данного направления

High Rates of Asymptomatic Mycoplasma genitalium Infections With High Proportion of Genotypic Resistance to First-Line Macrolide Treatment Among Men Who Have Sex With Men Enrolled in the Zurich Primary HIV Infection Study

Background Mycoplasma genitalium (Mg) is an emerging sexually transmitted pathogen among men who have sex with men (MSM). Resistance to recommended antimicrobial agents are of public health concern. Few data exist on Mg infections in MSM diagnosed with human immunodeficiency virus (HIV) during primary HIV infection. Methods Participants of the Zurich Primary HIV Study (ClinicalTrials.gov Identifier NCT00537966) were systematically offered screening for sexually transmitted infections (STIs) between April 2019 and September 2020. Screening was performed using an in-house polymerase chain reaction panel comprising Mg including genotypic resistance testing for macrolides and quinolones, Chlamydia trachomatis including serovars L1-L3, Neisseria gonorrhoeae, Treponema pallidum, and Hemophilus ducreyi. Results We screened 148 of 266 (55.6%) participants, with an overall total of 415 follow-up visits. Ninety-one percent were MSM. The incidence rate for all STIs was 47.0 (95% confidence interval [CI], 32.2-68.6) per 100 person-years. Mycoplasma genitalium was the most frequently detected pathogen: 30 participants (20%) presented with at least 1 Mg infection, corresponding to a period prevalence of 20.3% and incidence rate of 19.5 Mg infections (95% CI, 11.8-32.4). Most Mg infections (93%) were asymptomatic, and 9 (30%) participants showed spontaneous clearance. We detected high rates of antibiotic resistance: 73.3% to macrolides, 3.3% to quinolones, and 13.3% resistance to both antibiotics. Conclusions The high prevalence of mostly asymptomatic Mg infections and high rate of spontaneous clearance support cautious initiation for treatment. The high proportion of macrolide-resistant strains suggests that a genotypic determination of resistance should be standard of care. Moxifloxacin should be the preferred treatment option for symptomatic Mg infections among MSM if resistance testing is unavailable

Phenotypic and genotypic characterization of Neisseria gonorrhoeae isolates among individuals at high risk for sexually transmitted diseases in Zurich, Switzerland

Background: While ceftriaxone resistance remains scarce in Switzerland, global Neisseria gonorrhoeae (NG) antimicrobial resistance poses an urgent threat. This study describes clinical characteristics in MSM (men who have sex with men) diagnosed with NG infection and analyses NG resistance by phenotypic and genotypic means. Methods: Data of MSM enrolled in three clinical cohorts with a positive polymerase chain reaction test (PCR) for NG were analysed between January 2019 and December 2021 and linked with antibiotic susceptibility testing. Bacterial isolates were subjected to whole genome sequencing (WGS). Results: Of 142 participants, 141 (99%) were MSM and 118 (84%) living with HIV. Participants were treated with ceftriaxone ( N = 79), azithromycin ( N = 2), or a combination of both ( N = 61). No clinical or microbiological failures were observed. From 182 positive PCR samples taken, 23 were available for detailed analysis. Based on minimal inhibitory concentrations (MICs), all isolates were susceptible to ceftriaxone, gentamicin, cefixime, cefpodoxime, ertapenem, zoliflodacin, and spectinomycin. Resistance to azithromycin, tetracyclines and ciprofloxacin was observed in 10 (43%), 23 (100%) and 11 (48%) of the cases, respectively. Analysis of WGS data revealed combinations of resistance determinants that matched with the corresponding phenotypic resistance pattern of each isolate. Conclusion: Among the MSM diagnosed with NG mainly acquired in Switzerland, ceftriaxone MICs were low for a subset of bacterial isolates studied and no treatment failures were observed. For azithromycin, high occurrences of in vitro resistance were found. Gentamicin, cefixime, cefpodoxime, ertapenem, spectinomycin, and zoliflodacin displayed excellent in vitro activity against the 23 isolates underscoring their potential as alternative agents to ceftriaxone

Gene expression variation between distinct areas of breast cancer measured from paraffin-embedded tissue cores

BACKGROUND: Diagnosis and prognosis in breast cancer are mainly based on histology and immunohistochemistry of formalin-fixed, paraffin-embedded (FFPE) material. Recently, gene expression analysis was shown to elucidate the biological variance between tumors and molecular markers were identified that led to new classification systems that provided better prognostic and predictive parameters. Archived FFPE samples represent an ideal source of tissue for translational research, as millions of tissue blocks exist from routine diagnostics and from clinical studies. These should be exploited to provide clinicians with more accurate prognostic and predictive information. Unfortunately, RNA derived from FFPE material is partially degraded and chemically modified and reliable gene expression measurement has only become successful after implementing novel and optimized procedures for RNA isolation, demodification and detection. METHODS: In this study we used tissue cylinders as known from the construction of tissue microarrays. RNA was isolated with a robust protocol recently developed for RNA derived from FFPE material. Gene expression was measured by quantitative reverse transcription PCR. RESULTS: Sixteen tissue blocks from 7 patients diagnosed with multiple histological subtypes of breast cancer were available for this study. After verification of appropriate localization, sufficient RNA yield and quality, 30 tissue cores were available for gene expression measurement on TaqMan(R) Low Density Arrays (16 invasive ductal carcinoma (IDC), 8 ductal carcinoma in situ (DCIS) and 6 normal tissue), and 14 tissue cores were lost. Gene expression values were used to calculate scores representing the proliferation status (PRO), the estrogen receptor status and the HER2 status. The PRO scores measured from entire sections were similar to PRO scores determined from IDC tissue cores. Scores determined from normal tissue cores consistently revealed lower PRO scores than cores derived from IDC or DCIS of the same block or from different blocks of the same patient. CONCLUSION: We have developed optimized protocols for RNA isolation from histologically distinct areas. RNA prepared from FFPE tissue cores is suitable for gene expression measurement by quantitative PCR. Distinct molecular scores could be determined from different cores of the same tumor specimen

Digital Health Solutions to Reduce the Burden of Atherosclerotic Cardiovascular Disease Proposed by the CARRIER Consortium

Digital health is a promising tool to support people with an elevated risk for atherosclerotic cardiovascular disease (ASCVD) and patients with an established disease to improve cardiovascular outcomes. Many digital health initiatives have been developed and employed. However, barriers to their large-scale implementation have remained. This paper focuses on these barriers and presents solutions as proposed by the Dutch CARRIER (ie, Coronary ARtery disease: Risk estimations and Interventions for prevention and EaRly detection) consortium. We will focus in 4 sections on the following: (1) the development process of an eHealth solution that will include design thinking and cocreation with relevant stakeholders; (2) the modeling approach for two clinical prediction models (CPMs) to identify people at risk of developing ASCVD and to guide interventions; (3) description of a federated data infrastructure to train the CPMs and to provide the eHealth solution with relevant data; and (4) discussion of an ethical and legal framework for responsible data handling in health care. The Dutch CARRIER consortium consists of a collaboration between experts in the fields of eHealth development, ASCVD, public health, big data, as well as ethics and law. The consortium focuses on reducing the burden of ASCVD. We believe the future of health care is data driven and supported by digital health. Therefore, we hope that our research will not only facilitate CARRIER consortium but may also facilitate other future health care initiatives