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Publications (112)
There is a constant need to reduce turn-around times and keep costs as low as possible for the carriage screening of GBS in pregnant patients. Laboratory automation might provide an edge in this field. The objectives of the present study were: i) to compare the performance of the direct chromID™ Strepto B agar (CA) plating against LIM-broth enriche...
The objective of this study was to assess the clinical performances of PhenoMATRIX and PhenoMATRIX PLUS for the screening of methicillin-resistant Staphylococcus aureus (MRSA) from nasal and inguinal/perineal ESwabs using chromogenic media. The automated performances were compared to the manual reading. Additionally, we evaluated PhenoMATRIX PLUS f...
The objective of this study was to evaluate the performance of the Copan Colibrí™ against the manual preparation of the MALDI targets. We analyzed 416 (31 different species) non-duplicate strains covering the most important species identified in clinical routine. We also assessed the intra-strain repeatability between the comparable methods. We the...
Introduction
Rapid molecular tests could accelerate the control of extended-spectrum beta-lactamase-producing Enterobacterales (ESBL-PE) and carbapenemase-producing organisms (CPO) in intensive care units (ICUs).
Objective and methods
This interventional 12-month cohort study compared a loop-mediated isothermal amplification (LAMP) assay performed...
Timely and accurate detection of Group B Streptococcus (GBS) carriage in pregnant women allows for targeted peripartum prophylaxis. Replacing culture-based screening by molecular biology assays enables faster results obtention, better targeted antibiotic prophylaxis, and reduces the laboratory workload. Here, we present a comparative analysis betwe...
The objective of this study was to evaluate the accuracy and robustness of a fully automated EUCAST RAST (rapid antimicrobial susceptibility test) directly from positive blood culture and to appreciate its implementation constraints. This study was conducted in two phases: (i) spiked blood culture bottles (BCs) using 779 non-duplicate clinical isol...
The purpose of this study is to identify predictive factors associated with missed diagnosis of B. pertussis–B. holmesii co-infection by assessing the analytical performance of a commercially available multiplexed PCR assay and by building a prediction model based on clinical signs and symptoms for detecting co-infections. This is a retrospective s...
Background:
Nontuberculous mycobacteria (NTM) are increasingly identified in industrialized countries, and their role as pathogens is more frequently recognized. The relative prevalence of NTM strains shows an important geographical variability. Thus, establishing the local relative prevalence of NTM strains is relevant and useful for clinicians....
Background
Escherichia coli sequence type (ST) 131 H30 is an emerging multidrug resistant subclone, known to spread and cause outbreaks in long-term care facilities (LTCFs).
Objectives and methods
From 2010 through 2020, we performed 11 yearly surveillance studies for determining the prevalence of digestive carriage of ESBL-producing E. coli (ESBL...
The objective of this study was to evaluate the performances of the automated digital imaging of Gram-stained slides against manual microscopy. Four hundred forty-three identified Gram-stained slides were included in this study. When both methods agreed, we considered the results as correct, and no further examination was carried out. Whenever the...
Background
Diagnosis of Mycobacterium tuberculosis (MTB) infection can be confirmed by Xpert assays within hours. However, when sample size does not allow performing both culture and Xpert, or if Xpert is negative, then formal diagnosis of MTB relies on culture and time to detection of growth (TDG) becomes critical for clinical management.
Objecti...
The purpose of the present study was to assess the agreement at the categorical level between the VITEK ® 2 system and the Colibri TM coupled to the Radian TM under real routine laboratory conditions. The 675 non-duplicate clinical strains included in this study (249 Enterobacterales-isolates, 198 Pseudomonas aeruginosa , 107 Staphylococcus aureus...
Objectives
To assess the extent to which food items are a source of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (ESBL-Ec) and ESBL-producing Klebsiella pneumoniae (ESBL-Kp) for humans in five European cities.
Methods
We sampled 122 human polluted (hp)-environments (sewers and polluted rivers, as a proxy of human contamination)...
False-positive results in the diagnostic of meningitis and encephalitis pose important challenges. This study aimed to determine false-positive rates for Haemophilus influenzae in cerebrospinal fluids evaluated by the BioFire FilmArray® Meningitis/Encephalitis Panel. We conducted a retrospective study of all H. influenzae-positive FilmArray®. Menin...
Objectives
This study aimed to determine rates and risk factors of ESBL-producing Enterobacteriaceae (ESBL-PE) acquisition and transmission within households after hospital discharge of an ESBL-PE-positive index patient.
Methods
2-year prospective cohort study in 5 European cities. Patients colonised with ESBL-producing Escherichia coli (ESBL-Ec)...
Clinical microbiology laboratories are the first line to combat and handle infectious diseases and antibiotic resistance, including newly emerging ones. Although most clinical laboratories still rely on conventional methods, a cascade of technological changes, driven by digital imaging and high-throughput sequencing, will revolutionize the manageme...
Using computerized time-stamps, we compared the turnaround-times (TAT) for urine samples and screening ESwabs of MRSA, VRE, and ESBL carriage in the bacteriology laboratory of Geneva University Hospitals between January and December 2017 (period preceding the implementation of the WASPLabTM) with the same specimen types analyzed between January and...
In essence, automation can be driven by several of the following incentives: increased processing capacity of the laboratory, better costs control through processes standardization, optimized traceability, or improved workflows to reduce turnaround times (TAT). This project aims at presenting an overview of the project management and change managem...
The objectives of this study were to define the shortest incubation times on the WASPLab for reliable MALDI-TOF/MS-based species identification and for the preparation of a 0.5 McFarland suspension for antimicrobial disk diffusion susceptibility testing using short subcultures growing on solid culture media inoculated by positive blood cultures spi...
Invasive meningococcal disease (IMD), caused by Neisseria meningitidis (Nm) strains, is a life-threatening but vaccine-preventable condition. Bexsero is a four-component vaccine that offers broad protection against Nm of serogroup B (NmB), particularly common in Europe. In Switzerland, Bexsero has not yet been licensed and no information is availab...
Capnocytophaga canisis an uncommon cause of septic shock. Only three cases have been previously reported in the literature. Inthis article, we describe the case of a 70-year-old male admitted to the intensive care unit for septic shock of unknown origin. Onday 2, one anaerobic bottle out of the two sets taken at admission turned positive with Gram-...
Streptococcus suis is a facultative anaerobic gram-positive bacteria which can cause severe infections in pigs, such as meningitis, septicaemia and endocarditis. This pathogen causes significant economic losses in the porcine industry worldwide. Furthermore, S. suis has emerged recently as a human zoonotic pathogen. It causes meningitis, with possi...
Objective: The aim of the present study was to assess whether the WASPLab automation enables faster detection of vancomycin-resistant Enterococcus (VRE) on chromogenic VRE-specific plates by shortening the incubation time.
Methods: Ninety different VRE culture negative rectal ESwab specimens were spiked with various concentrations (ranging from 3 ×...
Objectives:
This study investigated the agreement at the categorical level between the Copan WASPLab incorporating the BioRad expert system against the SIRscan 2000 automatic for antimicrobial disk diffusion susceptibility testing.
Methods:
The 338 clinical strains (67 Pseudomonas aeruginosa, 19 methicillin-resistant Staphylococcus aureus (MRSA)...
Background
Active surveillance and contact precautions may prevent cross-transmission of ESBL-producing Enterobacteriaceae and CPE. Culture-based methods delaying results might increase risk of cross-transmission, and lead to unnecessary preemptive contact precautions. This observational cohort study compared rapid Loop-Mediated Isothermal Amplific...
Objectives:
The aim of this study was to evaluate the possibility of using a PCR-based panel to identify bacterial and fungal bloodstream infections in the setting of suspected or confirmed viral haemorrhagic fever.
Methods:
The accuracy of the FilmArray® Blood Culture Identification Panel (BCID) assay was assessed to identify the common bacteri...
The most common causes of infective endocarditis (IE) are Staphylococcus, Streptococcus, Enterococcus, and HACEK-related organisms. In 15–30% of the IE cases, standard blood cultures remain sterile. We aimed at identifying the causative agent of a blood-culture-negative IE by whole metagenome shotgun sequencing (WMGS). A 54-year old woman diagnosed...
Objectives:
Intestinal carriage with extended spectrum β-lactamase Enterobacteriaceae (ESBL-E) and carbapenemase-producing Enterobacteriaceae (CPE) can persist for months. We aimed to evaluate whether oral antibiotics followed by faecal microbiota transplantation (FMT) can eradicate intestinal carriage with ESBL-E/CPE.
Methods:
Randomized, open-...
Purpose
To compare bacteria recovered by standard cultures and metataxonomics, particularly with regard to ventilator-associated pneumonia (VAP) pathogens, and to determine if the presence of particular bacteria or microbiota in tracheal and oropharyngeal secretions during the course of intubation was associated with the development of VAP.
Method...
Objective:
The aim was to evaluate whether laboratory automation (inoculation and automated incubation combined with timely defined high-resolution digital imaging) may help reduce the time required to obtain reliable culture analysis results.
Methods:
We compared the results obtained by WASPLab automation against WASP-based automated inoculatio...
Horizontal transfer of plasmid-mediated antibiotic resistance has rarely been documented in vivo. Utilizing long-read (Oxford Nanopore) and short-read (Illumina) sequencing, we confirmed that a gut-colonizing Escherichia coli and a hypervirulent Klebsiella pneumoniae ST23, isolated from a surgical site culture of a patient receiving cefuroxime ther...
The Roche Cobas 6800 CT/NG assay was compared to the Abbott m2000 Real Time CT/NG assay for detecting Chlamydia trachomatis and Neisseria gonorrhoeae in 714 specimens referred to the bacteriology laboratory at Geneva University Hospitals, between November 2017 and March 2018, and in nine external quality controls for molecular diagnostics (seven fr...
Purpose:
Eight confirmed cases of Legionnaires’ disease were identified at the Geneva University Hospitals between 28 July 2017 and 02 August 2017, leading to a detailed outbreak investigation.
Methods:
Legionnaires’ disease cases were defined according to Swiss and European (ELDSNet) consensus guidelines. An outbreak investigation task force wa...
Here, we sequenced DNA extracted from a necrotic hepatic lesion from a patient with suspected chronic hepatic brucelloma but negative culture results. Although most of the taxonomically classified sequencing reads corresponded to human genome sequences, our data suggest that whole-metagenome shotgun sequencing may be used together with other tests...
[This corrects the article DOI: 10.1186/s13756-017-0285-x.].
Background
Many outbreaks due to Serratia marcescens among neonates have been described in the literature but little is known about the role of whole genome sequencing in outbreak analysis and management. Methods
Between February and March 2013, 2 neonates and 2 infants previously hospitalised in the neonatal unit of a tertiary care centre in Switz...
Background
The aim of this pilot study was to investigate the extent of oropharyngeal Kingella kingae carriage during the first 6 months of life. Methods
We conducted a monocentric transversal pilot study on healthy children younger than 6 months in order to define the oropharyngeal carriage rate. Participants were recruited between December 2013 a...
Background:
Kingella kingae has been increasingly identified in patients with osteoarticular infections. Our main objective was to evaluate the association between carriage of K. kingae in the oropharynx of preschool children and osteoarticular infections.
Methods:
We conducted this prospective case-control study in 2 tertiary care pediatric hos...
Background: Ecthyma gangrenosum (EG) are necrotic lesions that develop in the context of Pseudomonas aeruginosa bacteremia. Isolated reports describe EG in the setting of non-Pseudomonal infections. In a patient with EG, initial blood cultures showed Escherichia coli, and almost occulted P. aeruginosa bacteremia. Based on the clinical picture we su...
Background:
Sepsis is an important cause of morbidity and mortality in neonates and clinicians are typically required to administer empiric antibiotics while waiting for blood culture results. However, prolonged and inappropriate use of antibiotics is associated with various complications and adverse events. Better tools to rapidly rule out bacter...
Objectives:
The aim of the present work was to investigate the potential roles of PBPs, efflux pumps, and slow drug influx for imipenem heteroresistance in nontypeable Haemophilus influenzae (NTHi).
Methods:
The 59 NTHi clinical isolates examined in this study were collected at Geneva University Hospitals between 2009 and 2014. Alterations in PB...
Objectives:
Empiric therapy of methicillin-susceptible Staphylococcus aureus (MSSA) with vancomycin is associated with poorer outcome than targeted therapy with beta-lactams. Our objective was to evaluate if rapid determination of methicillin resistance shortens the time from Gram stain to targeted antimicrobial therapy in staphylococcal bacteraem...
Background
The role of asymptomatic carriers of toxigenic Clostridium difficile (TCD) in nosocomial cross-transmission remains debatable. Moreover, its relevance in the elderly has been sparsely studied. Objectives
To assess asymptomatic TCD carriage in an acute care geriatric population. Methods
We performed a prospective cohort study at the 296-b...
Background:
Kingella kingae is currently recognized as a significant pathogen of the pediatric population. Nevertheless, the possibility for adults to serve as a reservoir of healthy carriers has not been studied.
Method:
We conducted a monocentric transversal study on 228 healthy adults to define the carriage rate. Participants were recruited a...
The degree of bacterial contamination of stethoscopes can vary significantly following a physical examination.
OBJECTIVE
To conduct a prospective study to investigate the impact of various environmental and patient characteristics on stethoscope contamination.
METHODS
Following a standardized examination, the levels of bacterial contamination of...
Determinants of Successful Methicillin-Resistant Staphylococcus aureus Decolonization - Volume 37 Issue 6 - Elodie von Dach, Caroline Landelle, Americo Agostinho, Thomas Haustein, Patrice François, Gesuele Renzi, Jacques Schrenzel, Stephan Harbarth
This study determined the antibiotic susceptibility profile and genetic mechanisms of β-lactam resistance in 27 clinical strains of Acinetobacter baumannii isolated at the University Hospitals of Geneva, Switzerland. The antimicrobial susceptibility testing was performed using Etest and the disc diffusion method in accordance with CLSI guidelines....
The purpose of this study was to analyze the molecular mechanisms of ampicillin-resistant Haemophilus influenzae isolated in Geneva, Switzerland. We investigated the association between specific patterns of amino acid substitutions in penicillin-binding protein 3 (with or without β-lactamase production) and β-lactam susceptibility. Another main foc...
The aim of this study was to investigate changes in oropharyngeal K. kingae carriage during the first four years of life, including seasonal variation and comparison of asymptomatic carriage with cases of invasive osteoarticular infections (OAI).
Oropharyngeal bacterial K. kingae carriage was screened in 744 healthy children aged 7 to 48 months bet...
The etiologic agents of acute gastroenteritis are diverse. The diagnosis of bacterial pathogens is particularly challenging given the large amount of vastly diverse indigenous gastrointestinal organisms present in stool. Multiple methods must be used by the clinical microbiology laboratories to diagnose the cause of acute gastroenteritis, including...
PLEX-ID uses polymerase chain reaction-electrospray ionization/mass spectrometry for rapid identification of infectious agents in clinical samples. We evaluated its concordance with our centre's standard methods (SM) for bacterial and fungal detection in bronchoalveolar lavage (BAL) fluid in a prospective observational cohort study. The primary out...
Carbapenemase-producing enterobacteria (CPE) spread all over the world during the last years, causing serious infections with increasing frequency. Very few new drugs active against CPE are expected to be clinically available. Studies summarized in this review show that there is yet room to improve our therapeutic approaches, in the treatment of in...
Objectives:
Precise assessment of potential therapeutic synergy, antagonism or indifference between antimicrobial agents currently depends on time-consuming and hard-to-standardize in vitro chequerboard titration methods. We here present a method based on a novel two-dimensional antibiotic gradient technique named Xact™.
Methods:
We used a test...
The spread of microorganisms in hospitals is an important public health threat, and yet few studies have assessed how human microbial communities (microbiota) evolve in the hospital setting. Studies conducted so far have mainly focused on a limited number of bacterial species, mostly pathogenic ones and primarily during outbreaks. We explored the b...
OBJECTIVE: To test the hypothesis that methicillin-susceptible Staphylococcus aureus (MSSA) carriage may protect against nosocomial methicillin-resistant S. aureus (MRSA) acquisition by competing for colonization of the anterior nares.
DESIGN: Prospective cohort and nested case-control study.
SETTING: Swiss university hospital.
PATIENTS: All adult...
Objective:
Determine the prevalence of extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae (ESBL-PE) contamination of food and colonization of food handlers in a hospital kitchen and compare retrieved ESBL-PE strains with patient isolates.
Design:
Cross-sectional study.
Setting:
A 2,200-bed tertiary care university hospital in Sw...
Objectives
To compare the contamination level of physicians’ hands and stethoscopes and to explore the risk of cross-transmission of microorganisms through the use of stethoscopes.
Patients and Methods
We conducted a structured prospective study between January 1, 2009, and May 31, 2009, involving 83 inpatients at a Swiss university teaching hospi...
Emerging strain of Stapylococcus aureus (S. aureus) producer of the Panton-Valentine Leukocidine (PVL+) are becoming a new issue in public health. Those bacteria are accountable for serious cutaneous infection with a necrotic evolution, necrotizing pneumonia and severe osteoarticular infection. These last infections can be life-threatening and are...
Wards cohorting infected orthopaedic patients may be particularly prone to transmitting extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-E). We analyze their epidemic pattern by performing molecular typing of ESBL-E isolated from patients and healthcare workers (HCW) from our septic ward. Between March 2010 and November 2011, 186...
In order to evaluate the intrafamilial oropharyngeal transmission of Kingella kingae we conducted a prospective study among pairs of siblings. We found that 55% of children who suffered from osteoarticular infections due to K. kingae, and 40 % of asymptomatic carriers of K. kingae had siblings with positive oropharyngeal carriage.
Changes within the MRSA population of single hospitals have been observed with certain clones replacing others. Surveillance of the genetic diversity within a hospital provides useful epidemiological data. Staphylococcal chromosomic cassettes (SCCmec) of MRSA isolates are routinely determined at HUG.
Objectives:
Extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-E) are an increasingly frequent cause of infections in the community and the healthcare setting. In this study, we aimed to investigate whether intestinal carriage of ESBL-E can be eradicated.
Methods:
We conducted a double-blind, randomized, placebo-controlled, single-...
Kingella kingae is a Gram-negative bacterium that is today recognized as the major cause of joint and bone infections in young children. This microorganism is a member of the normal flora of the oropharynx, and the carriage rate among children under 4 years of age is approximately 10%. K. kingae is transmitted from child to child through close pers...
