Effectiveness of favipiravir in COVID-19: a live systematic review
AbstractWe performed a systematic review and meta-analysis for the effectiveness of Favipiravir on  the fatality and the requirement of mechanical ventilation for the treatment of moderate to severe COVID-19 patients. We searched available literature and reported it by using PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines. Until June 1, 2021, we search ed PubMed, bioRxiv, medRxiv, ClinicalTrials.gov, Cochrane Central Register of Controlled Trials (CENTRAL), and Google Scholar by using the keywords “Favipiravir” and terms sy...
Source: European Journal of Clinical Microbiology and Infectious Diseases - August 4, 2021 Category: Microbiology Source Type: research

Impact of public health measures on the post-COVID-19 respiratory syncytial virus epidemics in France
This study described the consequences of public health measures on respiratory syncytial virus (RSV) severe infections in France, where an interseasonal resurgence of RSV occurred recently. All patients admitted to Necker Hospital (Paris) between August 2018 and April 2021 with a diagnosis of RSV-associated acute lung respiratory infection (ALRI) were enrolled. Characteristics of subjects with RSV-associated ALRI in 2020/2021 were compared to those infected during the two previous outbreaks. Overall, 664 inpatients were diagnosed with RSV-associated ALRI: 229, 183, and 252 during the 2018/2019, 2019/2020, and 2020/2021 out...
Source: European Journal of Clinical Microbiology and Infectious Diseases - August 4, 2021 Category: Microbiology Source Type: research

Accuracy of saliva and nasopharyngeal sampling for detection of SARS-CoV-2 in community screening: a multicentric cohort study
AbstractNasopharyngeal sampling for nucleic acid amplification testing (NAAT) is the standard diagnostic test of coronavirus disease 2019. Our objectives were to assess, in real-life conditions, the diagnostic accuracy of a nasopharyngeal point-of-care antigen (Ag) test and of saliva NAAT for detection of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in ambulatory care. This was a prospective cohort study from 19 October through 18 December 2020 in two community COVID-19 screening centers in Paris, France. Two nasopharyngeal swabs and one saliva sample were simultaneously collected. Diagnostic accuracies of ...
Source: European Journal of Clinical Microbiology and Infectious Diseases - August 3, 2021 Category: Microbiology Source Type: research

The role of mouthwash sampling in SARS-CoV-2 diagnosis
ConclusionsMW with normal saline, especially when tested by N gene, can effectively detect COVID-19 patients. Furthermore, this method was not inferior when compared to R and E genes of ONP swabs, which are common targets in many laboratories around the world. (Source: European Journal of Clinical Microbiology and Infectious Diseases)
Source: European Journal of Clinical Microbiology and Infectious Diseases - August 3, 2021 Category: Microbiology Source Type: research

Molecular testing for H. pylori clarithromycin and quinolone resistance: a prospective Chinese study
AbstractIn China, there is a high prevalence of antibiotic-resistantHelicobacter pylori infections in the population. The aim of the study was to assess a new ARMS-PCR test for detection ofH. pylori clarithromycin resistance (CR) and quinolone resistance (QR) mutations and evaluate the spectrum of antibiotic resistance in patients from three Chinese provinces. Sanger sequencing and multiplex ARMS-PCR were used to detectH. pylori CR and QR bacteria in gastric biopsy samples. Among the 1,182 patients enrolled with gastritis, 643 (54.4%) were positive forH. pylori. Of these, 371 (57.7%) had antibiotic-resistant strains, compr...
Source: European Journal of Clinical Microbiology and Infectious Diseases - July 21, 2021 Category: Microbiology Source Type: research

Molecular characterization of clinical carbapenem-resistant Enterobacterales from Qatar
AbstractOne hundred forty-nine carbapenem-resistantEnterobacterales from clinical samples obtained between April 2014 and November 2017 were subjected to whole genome sequencing and multi-locus sequence typing.Klebsiella pneumoniae (81, 54.4%) andEscherichia coli (38, 25.5%) were the most common species. Genes encoding metallo- β-lactamases were detected in 68 (45.8%) isolates, and OXA-48-like enzymes in 60 (40.3%).blaNDM-1 (45; 30.2%) andblaOXA-48 (29; 19.5%) were the most frequent. KPC-encoding genes were identified in 5 (3.6%) isolates. Most common sequence types wereE. coli ST410 (8; 21.1%) and ST38 (7; 18.4%), an...
Source: European Journal of Clinical Microbiology and Infectious Diseases - July 21, 2021 Category: Microbiology Source Type: research

Antimicrobial stewardship experience in paediatrics: first-year activity report
AbstractAntimicrobial resistance is one of the most relevant threats in public health worldwide. Strategies as antimicrobial stewardship programs, aiming to preserve our antibiotic armamentarium, have been implemented since 2007 in adult and paediatric patients. We aim to describe the first experience of a paediatric antimicrobial stewardship program. We conducted a retrospective observational study in a tertiary care children ’s hospital. A team composed of a microbiologist, an infectious diseases physician, and a paediatrician led the project. All positive blood and cerebrospinal fluid cultures and other biological...
Source: European Journal of Clinical Microbiology and Infectious Diseases - July 21, 2021 Category: Microbiology Source Type: research

Stepwise selection of mutation conferring fluroquinolone resistance: multisite MDR-TB cohort study
In this study, we demonstrate that fluroquinolone (FQ) is at risk of acquired drug resistance after continuous exposure. The reduced susceptibility is observed in subsequentMycobacterium tuberculosis isolates from patients without FQ exposure. The stepwise selection of mutation of increasing FQ resistance highlights the urgent need for monitoring FQ resistance in multidrug-resistant tuberculosis patients throughout the entire treatment course. (Source: European Journal of Clinical Microbiology and Infectious Diseases)
Source: European Journal of Clinical Microbiology and Infectious Diseases - July 21, 2021 Category: Microbiology Source Type: research

Annual variations of Haemophilus influenzae carriage among Hajj pilgrims
(Source: European Journal of Clinical Microbiology and Infectious Diseases)
Source: European Journal of Clinical Microbiology and Infectious Diseases - July 21, 2021 Category: Microbiology Source Type: research

Correction to: An evaluation of risk factors to predict target concentration non-attainment in critically ill patients prior to empiric β-lactam therapy
(Source: European Journal of Clinical Microbiology and Infectious Diseases)
Source: European Journal of Clinical Microbiology and Infectious Diseases - July 21, 2021 Category: Microbiology Source Type: research

Global molecular epidemiology of carbapenem-resistant Escherichia coli (2002 –2017)
AbstractThe emergence of carbapenem-resistant (CR)Escherichia coli obliges an assessment of such strains ’ molecular epidemiology. Accordingly, we characterized in detail a globally distributed collection of CRE. coli isolates, then explored for associations between geographical origin and bacterial traits, and between different bacterial traits. We used established PCR-based assays and broth microdilution MIC determinations to characterize 343 global CR (i.e., non-susceptible to  ≥ 1 carbapenem) extraintestinalE. coli isolates (2002 –2017) for diverse molecular traits—including phylogrou...
Source: European Journal of Clinical Microbiology and Infectious Diseases - July 19, 2021 Category: Microbiology Source Type: research

Correction to: Diagnostic performance of four SARS-CoV-2 antibody assays in patients with COVID-19 or with bacterial and non-SARS-CoV-2 viral respiratory infections
(Source: European Journal of Clinical Microbiology and Infectious Diseases)
Source: European Journal of Clinical Microbiology and Infectious Diseases - July 16, 2021 Category: Microbiology Source Type: research

Development of a loop-mediated isothermal amplification assay for the rapid detection of six common respiratory viruses
AbstractDue to the highly contagious and spreads quickly of respiratory infectious diseases (ADR), the availability of rapid, sensitive, and reliable diagnostic methods is essential for disease control. Here, we develop an approach based on loop-mediated isothermal amplification (LAMP) for the detection of influenza A virus (Flu A), Flu A subtypes H1N1and H3N2, influenza B virus (Flu B), respiratory syncytial virus (RSV) subtypes A and B, human adenovirus (HAdV), parainfluenza virus (PIV) subtypes 1 and 3, and human rhinovirus (HRV) simultaneously. We designed primers specific to detect respiratory viruses above, optimized...
Source: European Journal of Clinical Microbiology and Infectious Diseases - July 15, 2021 Category: Microbiology Source Type: research

Impact of a 4-year antimicrobial stewardship program implemented in a Greek tertiary hospital
This study aimed to investigate the effects of a 4-year antibiotic stewardship program (ASP) in a tertiary hospital. We monitored data for 2015 (pre-intervention) and 2016 –2019 (post-intervention) about antibiotic consumption (DDD/100 bed days),Clostridioides difficile infections (CDIs), resistance rates, length of stay (LOS), and annual antibiotic costs. Significant reductions were observed for total antibiotics/colistin/carbapenems/quinolones/tigecycline consumption and resistance rates ofPseudomonas aeruginosa,Klebsiella pneumoniae, and vancomycin-resistant enterococci. Considerable reductions occurred for LOS (4...
Source: European Journal of Clinical Microbiology and Infectious Diseases - July 15, 2021 Category: Microbiology Source Type: research

The prevalence and mortality of cryptococcal meningitis in patients with autoimmune diseases: a systematic review and meta-analysis
AbstractGrowing evidence suggests that autoimmune diseases (AIDs) are risk factors for cryptococcal meningitis (CM). Therefore, understanding the epidemiological and clinical profile of CM in patients with AIDs is important. This meta-analysis assessed the prevalence, clinical profiles, and clinical outcomes of CM in AIDs.  Studies on CM in patients with AIDs were searched for in PubMed, EMBASE, Web of Science, and China National Knowledge Infrastructure, and meta-analyses were performed using the statistical program of R. Nineteen studies with 36,631 patients with AIDs were analyzed. The overall pooled CM preval...
Source: European Journal of Clinical Microbiology and Infectious Diseases - July 14, 2021 Category: Microbiology Source Type: research

Population-based surveillance of Enterobacter cloacae complex causing blood stream infections in a centralized Canadian region
This study provided novel information aboutEnterobacter genomics in a well-defined human population. (Source: European Journal of Clinical Microbiology and Infectious Diseases)
Source: European Journal of Clinical Microbiology and Infectious Diseases - July 14, 2021 Category: Microbiology Source Type: research

The MOBILISE study: utilisation of ambulatory pumps in the inpatient setting to administer continuous antibiotic infusions —a randomised controlled trial
AbstractIn the inpatient setting, antibiotics are generally administered via bedside pumps with multiple daily dosing. Utilisation of a continuous antibiotic infusion (CAI) instead might have patient and nursing satisfaction, workflow efficiencies and infection control benefits. We aimed to study the utilisation of CAI in the inpatient setting for routine antibiotic administration. Patients receiving a peripherally inserted central venous catheter (PICC) for antibiotic administration were screened for the study. The patients were randomised to either (1) standard pump and intermittent antibiotic administration (IAA) or (2)...
Source: European Journal of Clinical Microbiology and Infectious Diseases - July 13, 2021 Category: Microbiology Source Type: research

Prognosis of rash and chilblain-like lesions among outpatients with COVID-19: a large cohort study
AbstractIn a large regional observational cohort study of adult ( ≥ 18 years), outpatients with COVID-19, prevalence, characteristics, and outcome of patients with rash and/or chilblain-like lesions (CLL), compared with population without cutaneous features, were studied. In total, 28,957 outpatients were included; the prevalence of rash and CCL were 9.5% and 3.7%, respectively. Presence of rash was significantly associated with presence of asthenia, shivers or myalgia, respiratory and gastro-intestinal symptoms, and anosmia/ageusia. The presence of CCL was associated with chest pain, chest oppression, nause...
Source: European Journal of Clinical Microbiology and Infectious Diseases - July 13, 2021 Category: Microbiology Source Type: research

C-reactive protein predicts persistent bacteremia caused by community-acquired methicillin-resistant Staphylococcus aureus strain
AbstractThere is limited data on persistent bacteremia (PB) caused by community-acquired methicillin-resistantStaphylococcus aureus (CA-MRSA). Here, we aimed to investigate the clinical and microbiological characteristics of PB caused by the major CA-MRSA strain in Korea (ST72-SCCmecIV). All adult patients withS.aureus bacteremia were prospectively investigated from August 2008 to December 2018. Patients with ST72 MRSA bacteremia were included in the study. Patients were stratified into the PB group (defined as positive blood cultures for  ≥ 3 days) and short bacteremia (SB) group. A total of 291 pati...
Source: European Journal of Clinical Microbiology and Infectious Diseases - July 10, 2021 Category: Microbiology Source Type: research

Lack of evidence for infectious SARS-CoV-2 in feces and sewage
AbstractThe SARS-CoV-2 can be excreted in feces and can reach sewage systems. Determining the presence of infective viral particles in feces and sewage is necessary to take adequate control measures and to elucidate new routes of transmission. Here, we have developed a sample concentration methodology that allows us to maintain viral infectivity. Feces of COVID-19 patients and wastewater samples have been analyzed both by molecular methods and cell culture. Our results show no evidence of infective viral particles, suggesting that fecal –oral transmission is not a primary route. However, larger-scale efforts are need...
Source: European Journal of Clinical Microbiology and Infectious Diseases - July 9, 2021 Category: Microbiology Source Type: research

Feasibility and utility of facemask sampling in the detection of SARS-CoV-2 during an ongoing pandemic
AbstractsEasy access to screening for timely identification and isolation of infectious COVID-19 patients remains crucial in sustaining the international efforts to control COVID-19 spread. A major barrier limiting broad-based screening is the lack of a simple, rapid, and cost-effective COVID-19 testing method. We evaluated the feasibility and utility of facemask sampling in a cohort of 42 COVID-19-positive and 36 COVID-19-negative patients. We used a prototype of Steri-Strips ™ (3 M) applied to the inner surface of looped surgical facemasks (Assure), which was worn by patients for a minimum wear time of 3 ...
Source: European Journal of Clinical Microbiology and Infectious Diseases - July 5, 2021 Category: Microbiology Source Type: research

Protective role of IL-18 in host defenses against group B Streptococcus
AbstractThe aim of this study was to investigate the role of IL-18, a member of the IL-1 family, in group BStreptococcus (GBS) infection. Both in a neonatal and adult model of GBS infection, IL-18-deficient animals were significantly more susceptible to infection than WT animals. The lack of IL18 was associated with a marked reduction in IFN- γ-levels after bacterial stimulation but did not play a significant role in the recruitment of PMN to sites of GBS infection. Collectively, our data document a fundamental function of IL-18 signaling in boosting the host immune responses against GBS infection. (Source: European ...
Source: European Journal of Clinical Microbiology and Infectious Diseases - July 4, 2021 Category: Microbiology Source Type: research

Current fluconazole treatment regimens result in under-dosing of critically ill adults during early therapy
ConclusionCurrent fluconazole dosing regimens do not achieve adequate early target attainment in critically ill adults, particularly in those who are overweight, have higher creatinine clearance, or are undergoing CRRT. Current fluconazole dosing strategies are generally inadequate to treat organisms with an MIC of ≥4 mg/L. (Source: European Journal of Clinical Microbiology and Infectious Diseases)
Source: European Journal of Clinical Microbiology and Infectious Diseases - June 16, 2021 Category: Microbiology Source Type: research

Comparison of time-to-positivity between two blood culture systems: a detailed analysis down to the genus-level
AbstractA recently developed, automated blood culture system and medium improve the time-to-positivity (TTP) for bacteremia. However, there have thus far been no genus-level analyses using this novel system. We evaluated and compared the changes in blood culture TTP between two systems: BacT/Alert 3D with a blood culture medium containing activated charcoal versus the more recent BacT/Alert Virtuo with a blood culture medium containing polymeric beads. This before-and-after study included blood cultures collected between July 2010 and April 2014 (3D, activated charcoal) and between July 2015 and April 2018 (Virtuo, polymer...
Source: European Journal of Clinical Microbiology and Infectious Diseases - June 16, 2021 Category: Microbiology Source Type: research

Differential genotypic signatures of Toll-like receptor polymorphisms among dengue-chikungunya mono- and co-infected Eastern Indian patients
This study underlined the importance of TLR7 and 8 SNPs towards mono-/co-infection of DENV/CHIKV, with certain genotypes associated with co-infection susceptibility. Moreover, it suggested a probable role of specific genotypes of TLR7 and 8 polymorphisms imparting high dengue/chikungunya viral load among co-infected patients. (Source: European Journal of Clinical Microbiology and Infectious Diseases)
Source: European Journal of Clinical Microbiology and Infectious Diseases - June 16, 2021 Category: Microbiology Source Type: research

Predictors of failure after fecal microbiota transplantation for recurrent Clostridioides difficile infection: a systematic review and meta-analysis
AbstractFecal microbiota transplantation (FMT) is a highly effective therapy for recurrentClostridioides difficile infection (CDI), with ~15% 1-year recurrence rate. Small studies have identified variable risk factors associated with FMT failure. We, therefore, performed a systematic review and meta-analysis to evaluate the predictors of FMT failure. A systematic search of Medline, Embase, and Web of Science was performed from January 2013 up to June 2020. Meta-analyses were performed using random-effects models and pooled adjusted odds ratios for risk factors reported in ≥2 studies were calculated. Overall, 2671 patien...
Source: European Journal of Clinical Microbiology and Infectious Diseases - June 16, 2021 Category: Microbiology Source Type: research

Performance evaluation of Alfred60AST rapid susceptibility testing directly from positive blood cultures in the routine laboratory workflow
AbstractThe aim of this study was to evaluate the performance of the new automated system Alfred60AST which is based on light scattering technology for rapid susceptibility testing directly from positive blood cultures as well as its applicability in the routine laboratory workflow. We evaluated 176 significant episodes of bacteremia due to 92 Gram-negative and 84 Gram-positive bacteria. The antimicrobial agents tested were ceftriaxone, ciprofloxacin, gentamicin, meropenem, piperacillin-tazobactam, and colistin for Gram negatives and cefoxitin, vancomycin, linezolid, and daptomycin for Gram positives. Concordance assessmen...
Source: European Journal of Clinical Microbiology and Infectious Diseases - June 16, 2021 Category: Microbiology Source Type: research

Trimethoprim-sulfamethoxazole as de-escalation in ventilator-associated pneumonia: a cohort study subanalysis
ConclusionsDe-escalation to TMP-SMX for VAP treatment was not associated with higher mortality at EoT and T30 than standard treatment with β-lactam. Monotherapy with TMP-SMX as de-escalation from broad-spectrum empirical regimens is a β-lactam sparing strategy worthy to be further investigated in either multicenter cohort studies or randomized clinical trials. (Source: European Journal of Clinical Microbiology and Infectious Diseases)
Source: European Journal of Clinical Microbiology and Infectious Diseases - June 16, 2021 Category: Microbiology Source Type: research

Clinical evaluation of commercial PCR assays for antimicrobal resistance in Mycoplasma genitalium and estimation of resistance-mediated mutation prevalence in Moscow and Moscow region
AbstractMycoplasma genitalium is a widespread sexually transmitted infection (STI) with growing rate of antimicrobials resistance. In our study, 137 vaginal and 131 urethralM. genitalium–positive swabs were sequentially collected through the work of Reference Center for STI during 2019. For prevalence evaluation of macrolide-resistance mutations three commercially available kits were used: AmpliSens®M. genitalium-ML/FQ-Resist-FL (Central Research Institute of Epidemiology, Russia), ResistancePlus ® MG (SpeeDx, Australia), and S-DiaMGRes™ (Diagenode, Belgium). Macrolide resistance mutations were detected...
Source: European Journal of Clinical Microbiology and Infectious Diseases - June 16, 2021 Category: Microbiology Source Type: research

Effect of childhood pneumococcal vaccination and beta-lactam antibiotic use on the incidence of invasive pneumococcal disease in the adult population
AbstractDescribe the incidence of invasive pneumococcal disease (IPD) in serotypes with reduced antibiotic sensitivity to penicillin (RAS-Pen) in adults over 59 years of age and its association with childhood anti-pneumococcal vaccination coverage (CVC) and community consumption of beta-lactam. We selected IPD cases in adults over 59 years of age reported in the Community of Madrid between 2007 and 2016. We estimated the incidence of cases caused by serotypes included in the 13-valent pneumococcal conjugate vaccine (PCV13), those not included (non-PCV13) and the six serotypes additional to the 7-valent (PCV13-no7). We comp...
Source: European Journal of Clinical Microbiology and Infectious Diseases - June 16, 2021 Category: Microbiology Source Type: research

Human papillomavirus prevalence among men who have sex with men in China: a systematic review and meta-analysis
AbstractHuman papillomavirus (HPV) infection among men who have sex with men (MSM) in China is underreported. We performed a systematic review and meta-analysis to clarify site-specific HPV prevalence among MSM in China. We searched both English and Chinese databases for all studies published before April 1, 2020, that reported HPV prevalence among MSM in China. Random-effects meta-analysis was used to calculate summary estimates. Thirty-four articles were eligible, where 32, 5, and 2 articles reported HPV prevalence at the anus, penis, and oral cavity, respectively. The estimated prevalence of anal HPV among MSM in China ...
Source: European Journal of Clinical Microbiology and Infectious Diseases - June 16, 2021 Category: Microbiology Source Type: research

Community-acquired versus nosocomial Legionella pneumonia: factors associated with Legionella-related mortality
AbstractOver the past decade, changes in the diagnosis and management ofLegionella pneumonia occurred and risk factors for severe infection and increased mortality were identified. Previous reports found that nosocomial infection is associated with higher mortality while others showed no differences. We aimed to evaluate the differences in the clinical course and mortality rates between hospital-acquired pneumonia (HAP) and community-acquired pneumonia (CAP) caused byLegionella pneumophila. A retrospective cohort study of patients admitted due toLegionella pneumonia between January 2012 through November 2019 was conducted ...
Source: European Journal of Clinical Microbiology and Infectious Diseases - June 16, 2021 Category: Microbiology Source Type: research

Association between high vancomycin minimum inhibitory concentration and clinical outcomes in patients with methicillin-resistant Staphylococcus aureus bacteraemia  - A retrospective cohort study
AbstractThe purpose of this study is to determine the role of high ( ≥ 1.5 mg/L) vancomycin minimum inhibitory concentration (VMIC) in predicting clinical outcomes in patients with methicillin-resistantStaphylococcus aureus bacteraemia (MRSAB). A retrospective study was conducted at Mayo Clinic, Minnesota. Patients ≥ 18 years with a 3-month follow-up were included. Outcomes were defined as 30-day all-cause in-hospital mortality, median duration of bacteraemia, metastatic infectious complications, and relapse of MRSAB. A total of 475 patients with MRSAB were identified, and 93 (19.6%) of them had high VMIC is olates. ...
Source: European Journal of Clinical Microbiology and Infectious Diseases - June 16, 2021 Category: Microbiology Source Type: research

How to optimize administration of cefoxitin for the treatment of extended spectrum producing Enterobacteriaceae-related infection?
AbstractPharmacological and clinical data regarding cefoxitin for the treatment of ESBL-producingEnterobacteriaceae-related infections are limited. We performed a multicentric prospective cohort study to evaluate continuous/prolonged, or intermittent infusion of cefoxitin. We assessed the plasma concentration as a function of the duration of infusion and then performed a simulation of the percentage of patients who would reach the PK/PD targets, set at 100% ƒT> MIC or 100% ƒT>4 MIC. Eighty-one patients were included. All patients were treated with 6 gr./day. MICs to cefoxitin ranged from 0.5 to 64 mg/L. Six...
Source: European Journal of Clinical Microbiology and Infectious Diseases - June 16, 2021 Category: Microbiology Source Type: research

Melaleuca alternifolia essential oil soap: a potential alternative for hand hygiene
This study aimed to compare the antimicrobial action of three soaps for hand hygiene (HH): 2.0% Tea Tree Oil (TTO); 0.5% triclosan; 2.0% chlorhexidine, and to explore the perception of healthcare professionals about TTO. Two-step study: a quantitative, to determine the logarithmic reduction ofEscherichia coli K12 colony-forming units before and after HH of 15 volunteers and quali-quantitative, through interviews with 23 health professionals. All the three products demonstrated antimicrobial action (a log10 reduction factor of 4.18 for TTO, 4.31 for triclosan, 3.89 for chlorhexidine, and 3.17 for reference soap). Profession...
Source: European Journal of Clinical Microbiology and Infectious Diseases - June 16, 2021 Category: Microbiology Source Type: research

Methicillin-resistant Staphylococcus argenteus in the Netherlands: not a new arrival
(Source: European Journal of Clinical Microbiology and Infectious Diseases)
Source: European Journal of Clinical Microbiology and Infectious Diseases - June 16, 2021 Category: Microbiology Source Type: research

Combined selective culture and molecular methods for the detection of carbapenem-resistant organisms from fecal specimens
The objective of this work was to further develop and compare methods that combine selective culture and/or PCR to rapidly detect and recover CRO from fecal specimens. Molecularly characterized Gram-negative bacilli (n = 62) were used to spike fecal samples to establish limit of detection (LOD; n = 12), sensitivity (n = 28), and specificity (n= 21) for 3 methods to detect CP-CRO: direct MacConkey (MAC) plate and Xpert Carba-R (Cepheid) on growth, MAC broth and Carba-R testing of the broth, and direct testing by Carba-R. This was followed by a clinical study comparing methods in parallel for 286 fecal specimens. The LOD ran...
Source: European Journal of Clinical Microbiology and Infectious Diseases - June 11, 2021 Category: Microbiology Source Type: research

Diagnostic performance of four SARS-CoV-2 antibody assays in patients with COVID-19 or with bacterial and non-SARS-CoV-2 viral respiratory infections
AbstractSARS-CoV-2 antibody assays are used for epidemiological studies and for the assessment of vaccine responses in highly vulnerable patients. So far, data on cross-reactivity of SARS-CoV-2 antibody assays is limited. Here, we compared four enzyme-linked immunosorbent assays (ELISAs; Vircell SARS-CoV-2 IgM/IgA and IgG, Euroimmun SARS-CoV-2 IgA and IgG) for detection of anti-SARS-CoV-2 antibodies in 207 patients with COVID-19, 178 patients with serological evidence of different bacterial infections, 107 patients with confirmed viral respiratory disease, and 80 controls from the pre-COVID-19 era. In COVID-19 patients, th...
Source: European Journal of Clinical Microbiology and Infectious Diseases - June 9, 2021 Category: Microbiology Source Type: research

The prevalence and functional characteristics of CrpP-like in Pseudomonas aeruginosa isolates from China
This study investigated the dissemination and functional characteristics of CrpP-like inP. aeruginosa from China. The positive rate ofcrpP-like genes in 228P. aeruginosa was 25.4% (58/228), and 6 newcrpP-like genes were determined. Transformation experiments showed that CrpP-like had a low effect on CIP and LEV susceptibility. The genetic ofcrpP-positive was diverse. Furthermore, the mean expression level ofcrpP was no statistical difference between fluoroquinolone-susceptible and -resistant group (P >  0.05). CrpP-like may not play a significant role in fluoroquinolone resistance inP. aeruginosa. (Source:...
Source: European Journal of Clinical Microbiology and Infectious Diseases - June 7, 2021 Category: Microbiology Source Type: research

Prevalence of human papillomavirus detection in ovarian cancer: a meta-analysis
AbstractWe conducted a meta-analysis of published data to update and estimate the prevalence of HPV in ovarian cancer. A comprehensive literature search was performed according to the PRISMA guidelines. Eligible articles published from 1989 until 2020 by searching Web of Sciences, Pubmed, Embase, and the Cochrane Library Central databases were gathered. A pooled estimation of HPV prevalence with a 95% confidence interval (CI) was calculated based on a random effect model. Quantitative assessment of heterogeneity was explored using Cochrane test andI2. Additionally, publication bias, sensitivity, meta-regression, and subgro...
Source: European Journal of Clinical Microbiology and Infectious Diseases - June 4, 2021 Category: Microbiology Source Type: research

Performance of a SARS CoV-2 antibody ELISA based on simultaneous measurement of antibodies against the viral nucleoprotein and receptor-binding domain
AbstractSARS CoV-2 antibody assays measure antibodies against the viral nucleoprotein (NP) or spike protein. The study examined if testing of antibodies against both antigens increases the diagnostic sensitivity. Sera (N=98) from infected individuals were tested with ELISAs based on the NP, receptor-binding domain (RBD), or both proteins. The AUROCs were 0.958 (NP), 0.991 (RBD), and 0.992 (NP/RBD). The RBD- and NP/RBD-based ELISAs showed better performance than the NP-based assay. Simultaneous testing for antibodies against NP and RBD increased the number of true and false positives. If maximum diagnostic sensitivity is re...
Source: European Journal of Clinical Microbiology and Infectious Diseases - June 4, 2021 Category: Microbiology Source Type: research

Impact of 24/7 loading of blood culture bottles in a new automated incubator on the diagnosis of bloodstream infections
AbstractBlood culturing (BC) remains the gold standard for bloodstream diagnosis but its workflow is slow. We aimed reducing this time by implementing a new automated incubator with a 24/7 BC workflow. With this new strategy, time to incubation was shorter (1.52 h vs 6.82 h), positivity rates were higher (10.6% vs 8.9%,p
Source: European Journal of Clinical Microbiology and Infectious Diseases - June 1, 2021 Category: Microbiology Source Type: research

Comparison of nine different commercially available molecular assays for detection of SARS-CoV-2 RNA
We describe our laboratory experiences evaluating nine commercially available real-time RT-PCR assays. We found that assays differed considerably in performance and validation before routine use is mandatory. (Source: European Journal of Clinical Microbiology and Infectious Diseases)
Source: European Journal of Clinical Microbiology and Infectious Diseases - May 21, 2021 Category: Microbiology Source Type: research

Early and specific targeted mass spectrometry-based identification of bacteria in endotracheal aspirates of patients suspected with ventilator-associated pneumonia
AbstractRapid and reliable pathogen identification is compulsory to confirm ventilator-associated pneumonia (VAP) in order to initiate appropriate antibiotic treatment. In the present proof of concept, the effectiveness of rapid microorganism identification with a targeted bottom-up proteomics approach was investigated in endotracheal aspirate (ETA) samples of VAP patients. To do so, a prototype selected-reaction monitoring (SRM)-based assay was developed on a triple quadrupole mass spectrometer tracking proteotypic peptide surrogates of bacterial proteomes. Through the concurrent monitoring of 97 species-specific peptides...
Source: European Journal of Clinical Microbiology and Infectious Diseases - May 21, 2021 Category: Microbiology Source Type: research

Estimation of influenza-attributable burden in primary care from season 2014/2015 to 2018/2019, France
AbstractInfluenza viruses cause seasonal epidemics whose intensity varies according to the circulating virus type and subtype. We aim to estimate influenza-like illness (ILI) incidence attributable to influenza viruses in France from October 2014 to May 2019. Physicians participating in the French Sentinelles network reported the number of patients with ILI seen in consultation and performed nasopharyngeal swabs in a sample of these patients. The swabs were tested by RT-PCR for the presence of influenza viruses. These clinical and virological data were combined to estimate ILI incidence attributable to influenza viruses by...
Source: European Journal of Clinical Microbiology and Infectious Diseases - May 21, 2021 Category: Microbiology Source Type: research

Antibody response in patients admitted to the hospital with suspected SARS-CoV-2 infection: results from a multicenter study across Spain
ConclusionThe high values of sensitivity attained in the present study from a relatively early period of time after hospitalization support the use of the evaluated serological assays as supplementary diagnostic tests for the clinical management of COVID-19. (Source: European Journal of Clinical Microbiology and Infectious Diseases)
Source: European Journal of Clinical Microbiology and Infectious Diseases - May 21, 2021 Category: Microbiology Source Type: research

Comparison between Aptima ® assays (Hologic) and the CoBAS® 6800 system (Roche) for the diagnosis of sexually transmitted infections caused by Chlamydia trachomatis , Neisseria gonorrhoeae , and Mycoplasma genitalium
AbstractNowadays, it is of utmost importance to use fully validated assays for molecular-based diagnosis. In the field of sexually transmitted disease (STD), Roche and Hologic provide assays for diagnosingChlamydia trachomatis (CT),Neisseria gonorrhoeae (NG),Mycoplasma genitalium (MG), andTrichomonas vaginalis (TV). A total of 212 clinical samples were tested. Aptima ® Combo 2 (detecting CT and NG), Aptima® M. genitalium and the Aptima® T. vaginalis on the Panther® system were compared to CoBAS® CT/NG and CoBAS® TV/MG running on the CoBAS® 6800 system. To solve the discrepancies, Allplex™ ...
Source: European Journal of Clinical Microbiology and Infectious Diseases - May 21, 2021 Category: Microbiology Source Type: research

Performance of the VITEK ®2 advanced expert system™ for the validation of antimicrobial susceptibility testing results
AbstractTime to reporting antimicrobial susceptibility testing (AST) results to physicians plays an essential role in antibiotic stewardship programs. Expert software has been developed for facilitating the microbiologists ’ AST review process. The reliability of the VITEK®2 Advanced Expert™ software to effectively alert the microbiologist in detection of atypical and inconsistent AST results was assessed at the Labor Berlin—Charité Vivantes services. The results demonstrated a confidence rate of 99.3% in repo rting fully consistent AST results to physicians. (Source: European Journal of Clinic...
Source: European Journal of Clinical Microbiology and Infectious Diseases - May 21, 2021 Category: Microbiology Source Type: research

Low prevalence of tissue detection of cefepime and daptomycin used as empirical treatment during revision for periprosthetic joint infections: results of a prospective multicenter study
AbstractData demonstrating that antibiotics administered intraoperatively in patients with surgical revision for periprosthetic joint infection achieve concentrations exceeding minimal inhibitory concentrations of the identified bacteria at the surgical site when the new implant is inserted are lacking. We prospectively included patients with periprosthetic joint infection operated with one- or two-stage replacement during which cefepime (2g)-daptomycin (10mg/kg) combination was administered intravenously as intraoperative empirical antibiotic treatment. Three biopsies (two bones and one synovial membrane) were taken from ...
Source: European Journal of Clinical Microbiology and Infectious Diseases - May 20, 2021 Category: Microbiology Source Type: research

Comparative activities of sitafloxacin against recent clinical isolates in hospitals across China
AbstractSitafloxacin is one of the newer generation fluoroquinolones. Considering the ever-changing antimicrobial resistance, it is necessary to monitor the activities of sitafloxacin against recent pathogenic isolates. Therefore, we determined the minimum inhibitory concentrations (MICs) of sitafloxacin and comparators by broth microdilution or agar dilution method against 1101 clinical isolates collected from 2017 to 2019 in 31 hospitals across China. Sitafloxacin was highly active against gram-positive isolates evidenced by the MICs required to inhibit the growth of 50%/90% isolates (MIC50/90): ≤ 0.03/0.25, ≤ 0.03...
Source: European Journal of Clinical Microbiology and Infectious Diseases - May 19, 2021 Category: Microbiology Source Type: research