Clostridioides difficile infection (CDI) epidemiology and patient characteristics in Switzerland.

OBJECTIVES: Clostridioides difficile infection (CDI) is a disease with high morbidity and mortality rates. The objective of this study was to describe CDI epidemiology and patient characteristics over a 5-year period in Switzerland and assess risk factors for mortality, recurrence and severe CDI. PATIENTS AND METHODS: We retrospectively included all consecutive CDI cases having occurred in adult patients hospitalized in two tertiary centers: the Lausanne University Hospital (1000 beds) and the University Hospital of Zurich (900 beds), between 2014 and 2018. Suspected cases of CDI were identified from the microbiology laboratory database on the basis of a positive test and confirmed by records review. RESULTS: During first CDI episodes, the median age was 67 years and the median Charlson comorbidity index (CCI) score was 5. All in all, 299 out of 826 patients (36.2%) had severe infection based on the Infectious Diseases Society of America criteria. In the multivariable analysis, CCI was associated with increased risk of mortality. None of the factors recorded on admission were significantly associated with increased risk of recurrence. In the multivariable analysis, male sex and CCI were associated with severity, while immunosuppression was associated with less severe presentation. CONCLUSIONS: If we did not identify any criteria on admission that could be predictive of recurrences, this could be explained the retrospective nature of the study. A higher comorbidity index is a key driver for severe CDI and mortality. Reporting of CDI is not mandatory in Switzerland; structuration of CDI reporting should be a short-term priority.

Diagnostic strategies for SARS-CoV-2 infection and interpretation of microbiological results.

BACKGROUND: To face the current COVID-19 pandemic, diagnostic tools are essential. It is recommended to use real-time RT-PCR for RNA viruses in order (a) to perform a rapid and accurate diagnostic, (b) to guide patient care and management and (c) to guide epidemiological strategies. Further studies are warranted to define the role of serological diagnosis and a possible correlation between serological response and prognosis. OBJECTIVES: The aim was to guide clinical microbiologists in the use of these diagnostic tests and clinicians in the interpretation of their results. SOURCES: A search of literature was performed through PubMed and Google Scholar using the keywords SARS-CoV-2, SARS-CoV-2 molecular diagnosis, SARS-CoV-2 immune response, SARS-CoV-2 serology/antibody testing, coronavirus diagnosis. CONTENT: The present review discusses performances, limitations and use of current and future diagnostic tests for SARS-CoV-2. IMPLICATIONS: Real-time RT-PCR remains the reference method for diagnosis of SARS-CoV-2 infection. On the other hand, notwithstanding its varying sensitivity according to the time of infection, serology represents a valid asset (a) to try to solve possible discrepancies between a highly suggestive clinical and radiological presentation and negative RT-PCR, (b) to solve discrepancies between different PCR assays and (c) for epidemiological purposes.

Evaluation of the BD Phoenix™ CPO Detect Test for the detection of carbapenemase producers.

OBJECTIVES: Becton-Dickinson recently developed the Phoenix™ CPO (carbapenemase-producing organism) Detect Test, a growth-based test embedded in Gram-negative (GN) panels for the detection and confirmation of bacteria producing class A, B and D carbapenemases. This study aimed to (a) determine the performance of the CPO test, and (b) assess its added value in routine diagnostic workflows. METHODS: The performance of the BD Phoenix CPO test was analysed retrospectively on a collection of 185 molecularly characterized strains, including 92 CPOs, and prospectively on 135 and 160 routine isolates with and without CPO suspicion, respectively. RESULTS: In the retrospective study the CPO test exhibited 92.4% accuracy (95%CI 87.6-95.8), 97.8% sensitivity (95%CI 92.4-99.7) and 87.1% specificity (95%CI 78.6-93.2) for carbapenemase detection. The CPO test provided a classification to class A, B, and D for 81.3% of detected carbapenemases with 94.6% accuracy (95%CI 86.7-98.5). In the prospective study the CPO test detection performance showed 77.8% accuracy (95%CI 68.8-84.5), 100% sensitivity (95%CI 91.2-100) and 67.8% specificity (95%CI 57.3-77.1) with 135 CPO-suspicious isolates and 98.8% accuracy and specificity (95%CI 95.6-99.9) with 160 non-CPO-suspicious isolates. Compared to routine testing, the implementation of the CPO test allowed a mean reduction of 21.3 h (95%CI 17.6-25) in turnaround time, 16.8 min (95%CI 13.4-20.2) in hands-on time, and 20.6 CHF (95%CI 16.5-24.8) in costs. CONCLUSIONS: The CPO test is reliable for the detection of CPO with a high sensitivity. However, the relatively low detection specificity required the use of additional confirmatory methods. The carbapenemase classification accuracy is robust in providing preliminary results before molecular characterization. Finally, the implementation of the test in routine workflows allowed a significant reduction in turnaround time, hands-on time and cost compared to the conventional approach.

A predation assay using amoebae to screen for virulence factors unearthed the first W. chondrophila inclusion membrane protein.

Waddlia chondrophila is an intracellular bacterium phylogenetically related to the well-studied human and animal pathogens of the Chlamydiaceae family. In the last decade, W. chondrophila was convincingly demonstrated to be associated with adverse pregnancy outcomes in humans and abortions in animals. All members of the phylum Chlamydiae possess a Type Three Secretion System that they use for delivering virulence proteins into the host cell cytosol to modulate their environment and create optimal conditions to complete their life cycle. To identify W. chondrophila virulence proteins, we used an original screening approach that combines a cosmid library with an assay monitoring resistance to predation by phagocytic amoebae. This technique combined with bioinformatic data allowed the identification of 28 candidate virulence proteins, including Wimp1, the first identified inclusion membrane protein of W. chondrophila.

Project management: importance for diagnostic laboratories.

BACKGROUND: The need for diagnostic laboratories to improve both quality and productivity alongside personnel shortages incite laboratory managers to constantly optimize laboratory workflows, organization, and technology. These continuous modifications of the laboratories should be conducted using efficient project and change management approaches to maximize the opportunities for successful completion of the project. AIM: This review aims at presenting a general overview of project management with an emphasis on selected critical aspects. SOURCES: Conventional project management tools and models, such as HERMES, described in the literature, associated personal experience, and educational courses on management have been used to illustrate this review. CONTENT: This review presents general guidelines of project management and highlights their importance for microbiology diagnostic laboratories. As an example, some critical aspects of project management will be illustrated with a project of automation, as experienced at the laboratories of bacteriology and hygiene of the University Hospital of Lausanne. It is important to define clearly beforehand the objective of a project, its perimeter, its costs, and its time frame including precise duration estimates of each step. Then, a project management plan including explanations and descriptions on how to manage, execute, and control the project is necessary to continuously monitor the progression of a project to achieve its defined goals. Moreover, a thorough risk analysis with contingency and mitigation measures should be performed at each phase of a project to minimize the impact of project failures. IMPLICATIONS: The increasing complexities of modern laboratories mean clinical microbiologists must use several management tools including project and change management to improve the outcome of major projects and activities.

Prevalence and diversity of Chlamydiales and other amoeba-resisting bacteria in domestic drinking water systems.

A growing number of human infections incriminate environmental bacteria that have evolved virulent mechanisms to resist amoebae and use them as a replicative niche. These bacteria are designated amoeba-resisting bacteria (ARB). Despite the isolation of these ARB in various human clinical samples, the possible source of infection remains undetermined in most cases. However, it is known that the ARB Legionella pneumophila, for instance, causes a respiratory infection in susceptible hosts after inhalation of contaminated water aerosols from various sources. The Chlamydiales order contains many ARB, such as Parachlamydia acanthamoebae or Simkania negevensis, previously implicated in human respiratory infections with no identified contamination sources. We thus investigated whether domestic water systems are a potential source of transmission of these Chlamydiales to humans by using amoebal culture and molecular methods. Other important ARB such as mycobacteria and Legionella were also investigated, as were their possible amoebal hosts. This work reports for the first time a very high prevalence and diversity of Chlamydiales in drinking water, being detected in 35 (72.9%) of 48 investigated domestic water systems, with members of the Parachlamydiaceae family being dominantly detected. Furthermore, various Legionella and mycobacteria species were also recovered, some species of which are known to be causal agents of human infections.

Comparative genomics of Neisseria meningitidis strains: new targets for molecular diagnostics.

In 2010, Jaton et al. (False-negative PCR result due to gene polymorphism: the example of Neisseria meningitidis. J Clin Microbiol 2010;48:4590-2) reported an isolate of Neisseria meningitidis serogroup B that was not detected by the ctrA quantitative real-time PCR (qRT-PCR) used in our diagnostic laboratory. Sequence analysis of ctrA revealed several single nucleotide polymorphisms responsible for the negative qRT-PCR. Therefore, we sequenced the genome of this isolate and performed comparative genomics to propose new gene targets for the specific detection of N. meningitidis from clinical specimens. We identified 11 genes as specific to N. meningitidis genomes and common to at least 177 (97%) of the 183 genomes available. Among them, three genes (metA, tauE and shlA) were selected to develop new qRT-PCRs for the detection of N. meningitidis DNA. The three qRT-PCRs were highly sensitive and specific, and they exhibited a good reproducibility when tested on plasmidic positive controls and genomic DNA extracted from strains of N. meningitidis and other relevant bacterial species. The clinical sensitivity and specificity of metA and tauE qRT-PCRs were both 100% based on a testing of cerebrospinal fluid samples positive for N. meningitidis or other clinically relevant bacteria. Despite a 100% specificity, the sensitivity of the shlA qRT-PCR was only 70%. We thus recommend using the metA and/or tauE qRT-PCRs developed here. To prevent PCR failure in the presence of new polymorphic strains, the detection of dual targets by duplex qRT-PCR would be more accurate and suitable for the diagnosis of N. meningitidis from clinical specimens.

Laboratory automation in clinical bacteriology: what system to choose?

Automation was introduced many years ago in several diagnostic disciplines such as chemistry, haematology and molecular biology. The first laboratory automation system for clinical bacteriology was released in 2006, and it rapidly proved its value by increasing productivity, allowing a continuous increase in sample volumes despite limited budgets and personnel shortages. Today, two major manufacturers, BD Kiestra and Copan, are commercializing partial or complete laboratory automation systems for bacteriology. The laboratory automation systems are rapidly evolving to provide improved hardware and software solutions to optimize laboratory efficiency. However, the complex parameters of the laboratory and automation systems must be considered to determine the best system for each given laboratory. We address several topics on laboratory automation that may help clinical bacteriologists to understand the particularities and operative modalities of the different systems. We present (a) a comparison of the engineering and technical features of the various elements composing the two different automated systems currently available, (b) the system workflows of partial and complete laboratory automation, which define the basis for laboratory reorganization required to optimize system efficiency, (c) the concept of digital imaging and telebacteriology, (d) the connectivity of laboratory automation to the laboratory information system, (e) the general advantages and disadvantages as well as the expected impacts provided by laboratory automation and (f) the laboratory data required to conduct a workflow assessment to determine the best configuration of an automated system for the laboratory activities and specificities.

Blood culture-based diagnosis of bacteraemia: state of the art.

Blood culture remains the best approach to identify the incriminating microorganisms when a bloodstream infection is suspected, and to guarantee that the antimicrobial treatment is adequate. Major improvements have been made in the last years to increase the sensitivity and specificity and to reduce the time to identification of microorganisms recovered from blood cultures. Among other factors, the introduction in clinical microbiology laboratories of the matrix-assisted laser desorption ionization time-of-flight mass spectrometry technology revolutionized the identification of microorganisms whereas the introduction of nucleic-acid-based methods, such as DNA hybridization or rapid PCR-based test, significantly reduce the time to results. Together with traditional antimicrobial susceptibility testing, new rapid methods for the detection of resistance mechanisms respond to major epidemiological concerns such as methicillin-resistant Staphylococcus aureus, extended-spectrum ß-lactamase or carbapenemases. This review presents and discusses the recent developments in microbial diagnosis of bloodstream infections based on blood cultures.

Roles of bovine Waddlia chondrophila and Chlamydia trachomatis in human preterm birth.

Waddlia chondrophila and Chlamydia trachomatis are intracellular bacteria associated with human miscarriage. We investigated their role in human preterm birth. Whereas presence of Chlamydia trachomatis DNA in genital tract was associated with human preterm birth, Waddlia was not, despite being present in women's genital tracts.

Undressing of Waddlia chondrophila to enrich its outer membrane proteins to develop a new species-specific ELISA.

Waddlia chondrophila, an obligate intracellular bacterium of the Chlamydiales order, is considered as an agent of bovine abortion and a likely cause of miscarriage in humans. Its role in respiratory diseases was questioned after the detection of its DNA in clinical samples taken from patients suffering from pneumonia or bronchiolitis. To better define the role of Waddlia in both miscarriage and pneumonia, a tool allowing large-scale serological investigations of Waddlia seropositivity is needed. Therefore, enriched outer membrane proteins of W. chondrophila were used as antigens to develop a specific ELISA. After thorough analytical optimization, the ELISA was validated by comparison with micro-immunofluorescence and it showed a sensitivity above 85% with 100% specificity. The ELISA was subsequently applied to human sera to specify the role of W. chondrophila in pneumonia. Overall, 3.6% of children showed antibody reactivity against W. chondrophila but no significant difference was observed between children with and without pneumonia. Proteomic analyses were then performed using mass spectrometry, highlighting members of the outer membrane protein family as the dominant proteins. The major Waddlia putative immunogenic proteins were identified by immunoblot using positive and negative human sera. The new ELISA represents an efficient tool with high throughput applications. Although no association with pneumonia and Waddlia seropositivity was observed, this ELISA could be used to specify the role of W. chondrophila in miscarriage and in other diseases.

Development of a real-time PCR for the specific detection of Waddlia chondrophila in clinical samples.

Waddlia chondrophila is considered as an emerging human pathogen likely involved in miscarriage and lower respiratory tract infections. Given the low sensitivity of cell culture to recover such an obligate intracellular bacteria, molecular-based diagnostic approaches are warranted. We thus developed a real-time PCR that amplifies Waddlia chondrophila DNA. Specific primers and probe were selected to target the 16S rRNA gene. The PCR specifically amplified W. chondrophila but did not amplify other related-bacteria such as Parachlamydia acanthamoebae, Simkania negevensis and Chlamydia pneumoniae. The PCR exhibited a good intra-run and inter-run reproducibility and a sensitivity of less than ten copies of the positive control. This real-time PCR was then applied to 32 nasopharyngeal aspirates taken from children with bronchiolitis not due to respiratory syncytial virus (RSV). Three samples revealed to be Waddlia positive, suggesting a possible role of this Chlamydia-related bacteria in this setting.

Mecanismo de accion del levonorgestrel en la anticoncepcion de emergencia

En esta revisión se actualiza el mecanismo de acción del levonorgestrel (LNG) usado en anticoncepción de emergencia. El análisis crítico de la estimación de la eficacia anticonceptiva del LNG indica que su tasa de falla es más alta que la publicada. El LNG aumenta la viscosidad del moco cervical impidiendo que los espermatozoides del reservorio cervical vayan a renovar la población espermática en el sitio de fecundación. Diversos autores han documentado que LNG suprime el pico preovulatorio de gonadotrofinas e interfiere con el proceso ovulatorio en la mujer y en modelos animales. Administrado después de la fecundación en rata y Cebus apella, no interfiere con la implantación del embrión. Se concluye que LNG previene el embarazo solamente cuando se administra en un momento del ciclo menstrual en el cual puede impedir la fecundación y que el método falla cuando la administración es más tardía.

Carcinoma verrugoso del cuello uterino: a propósito de un caso / Verrucous carcinoma of the uterine cervix: on purpose of 1 case

Se presenta un caso de carcinoma verrucoso del cuello uterino, se discute sus aspectos clínicos y anátomo-patológicos, y revisión de la literatura

Estudio de diseminación del cáncer de vesícula biliar: estudio anatomoclínico de 65 autopsias / Study of gallbladder cancer spread: anatomical and clinical study of 65 autopsies

Se analizan 65 autopsias de pacientes con Ca, vesicular realizadas en el Servicio de Anatomía Patológica, en el período 1960-1987. Se comprobó un mayor grado de diseminación del cáncer vesicular en mujeres, con importante predominio de metástasis peritoneales (p<0,001>. El tipo histológico más frecuente fue el adenocarcinoma tubular moderadamente diferenciado (25,3%). Se encontraron metástasis en 87% de los casos, predominando las metástasis hepáticas (70,8%), peritoneales (41,5%) y pulmonares (40%). El 66,2% de los pacientes presentó compromiso ganglionar, preferentemente en el grupo peripancreático (46,5%). Al evaluar el grado de diseminación visceral para el grupo ganglionar definido como regional, se comprobó la existencia de metástasis hepáticas en 74% y pulmonares en 39% de los casos. Es necesaria la identificación y sistematización minuciosa de los ganglios que drenan el área vesicular, tanto en el acto quirúrgico como en las necropsias, para poder definir el manejo terapéutico más racional, especialmente para los pacientes con cáncer vesicular en Estadio IV de Nevin

Seguimiento a largo plazo de mujeres tratadas con implantes anticonceptivos de Levonorgestrel Norplant / Long-term follow up of women treated with contraceptive implants of norplant levonorgestrel

Este trabajo describe el seguimiento a largo plazo de 376 mujeres que recibieron los implantes Norplant durante el período comprendido entre octubre de 1974 y mayo de 1979. En ciento diez de estos casos, se reemplazaron los implantes luego de diferentes plazos de uso del primer set. Los niveles promedios de levonorgestrel plasmático declinaron en forma paulatina a través de ocho años de uso continuo de las cápsulas Norplant (r=937). Los valores fueron 0,35 ng/ml, 0,29 ng/ml y 0,22 ng/ml durante el primer, quinto y octavo año de tratamiento, respectivamente. Luego de la extracción de Norplant y su reemplazo con un segundo set de implantes, los niveles de levonogestrel plasmático fueron similares a aquellos observados después de la primera inserción, tanto cuando se colocaron en el mismo lugar que el primer set como cuando se ubicaron en un área diferente. Se estableció que la vida media del levonorgestrel en plasma después del retiro de los implantes es de 42 ñ 16 h (x ñ D. S) y que sólo quedaban cantidades mínimas en circulación después de 96 h. Durante 18.530 meses-mujer de uso del primer set de implantes se produjeron diecinueve embarazos, once de ellos entre el sexto y octavo año de tratamiento. El índice de Pearl para los primeros cinco años de uso de implantes Norplant fue 0,63. En los 5.020 meses-mujer observadas durante el tratamiento con un segundo set de cápsulas no se ha producido ningún embarazo. Cincuenta y seis mujeres (14,9%) de las 376 usuarias del primer implante, y doce (10,9%) de las 110 mujeres que aceptaron el reemplazo de los implantes se retiraron del estudio por razones médicas, principalmente efectos secundarios asociados frecuentemente con la contracepción hormonal..