Whole genome sequencing analysis of multidrug-resistant tuberculosis in Singapore, 2006 –2018
AbstractThere were 290 multidrug-resistant (MDR)-TB cases diagnosed in Singapore from 2006 to 2018. Eighty-one percent were foreign-born. Spoligotyping and MIRU-VNTR methods identified 108 patients in 24 clusters. The Beijing spoligotype accounted for 22 clusters. Whole genome sequencing (WGS) analysis reduced the number of clustered patients and clusters to 43 and nine respectively. One MIRU cluster was redefined into three WGS clusters. All the clusters had foreign-born source cases. Forty percent of local-born, versus 9% of foreign-born, MDR-TB cases belonged to WGS clusters. WGS more accurately elucidated potential MDR...
Source: European Journal of Clinical Microbiology and Infectious Diseases - November 15, 2020 Category: Microbiology Source Type: research

Epidemiological characteristics of severe fever with thrombocytopenia syndrome in Hefei of Anhui Province: a population-based surveillance study from 2011 to 2018
In this study, we investigated the epidemiological characteristics of SFTS patients in Hefei from 2011 to 2018. In addition, we conducted a serological survey of SFTSV-specific antibody among healthy residents of five counties. We performed a retrospective observational study of SFTS cases reported to Hefei Center for Disease Control and Prevention (CDC) during Jan 2011 to Dec 2018. Almost every patient completed a structure questionnaire including clinical examination, course of disease, and history of epidemiology. A total of 754 serum specimens were collected and tested for IgG antibody with double-antigen sandwich ELIS...
Source: European Journal of Clinical Microbiology and Infectious Diseases - November 13, 2020 Category: Microbiology Source Type: research

Characteristics of gram-negative bacteremia during febrile neutropenia among allogeneic hematopoietic stem cell transplant recipients on levofloxacin prophylaxis
In conclusion, GNB was not a significant cause of death. In LVFX breakthrough ESBL-EC bacteremia among allo-HSCT recipients, the administration of CFPM as empiric therapy did not lead to significantly poor prognosis. Empiric CFPM administration might be an acceptable strategy. (Source: European Journal of Clinical Microbiology and Infectious Diseases)
Source: European Journal of Clinical Microbiology and Infectious Diseases - November 13, 2020 Category: Microbiology Source Type: research

Development and evaluation of a serological test for diagnosis of COVID-19 with selected recombinant spike proteins
In conclusion, the eukaryotic expression spike proteins (rS1 and rS-RBD-mFc) are more suitable than the prokaryotic expression nucleocapsid proteins for serological diagnosis of SARS-CoV-2. The proposed GICA for detection of total antibodies could be a powerful complement to the current RNA tests for COVID-19. (Source: European Journal of Clinical Microbiology and Infectious Diseases)
Source: European Journal of Clinical Microbiology and Infectious Diseases - November 12, 2020 Category: Microbiology Source Type: research

Whole genome sequencing to decipher the virulence phenotype of hypervirulent Klebsiella pneumoniae responsible for liver abscess, Marseille, France
We described three clinical cases of pyogenic liver abscess caused by hypervirulentKlebsiella pneumoniae (hvKp) successfully treated by prolonged antibiotherapy, in which one case was complicated by endophthalmitis. Whole genome sequencing helped to confirm the diagnosis of these hvKp strains, which belong to clonal complexes CC86 and CC23 and carried hvKp-associated genes (magA and/orrmpA). This syndrome is increasingly reported in France and Europe and raises questions about the source of infection. (Source: European Journal of Clinical Microbiology and Infectious Diseases)
Source: European Journal of Clinical Microbiology and Infectious Diseases - November 12, 2020 Category: Microbiology Source Type: research

Evaluating the serological status of COVID-19 patients using an indirect immunofluorescent assay, France
AbstractAn indirect in-house immunofluorescent assay was developed in order to assess the serological status of COVID-19 patients in Marseille, France. Performance of IFA was compared to a commercial ELISA IgG kit. We tested 888 RT-qPCR-confirmed COVID-19 patients (1302 serum samples) and 350 controls including 200 sera collected before the pandemic, 64 sera known to be associated with nonspecific serological interference, 36 sera from non-coronavirus pneumonia and 50 sera from patient with other common coronavirus to elicit false-positive serology. Incorporating an inactivated clinical SARS-CoV-2 isolate as the antigen, t...
Source: European Journal of Clinical Microbiology and Infectious Diseases - November 11, 2020 Category: Microbiology Source Type: research

Concomitant emphysema might increase the false-negative rate of urinary antigen tests in patients with pneumococcal pneumonia: results from a retrospective study
AbstractThe urinary antigen test (UAT) is a rapid diagnostic method for pneumococcal pneumonia, but the high false-negative rate of 30% may affect its reliability. To maximize the utility of UAT, it is necessary to investigate the patient factors affecting UAT results. However, there is no report elucidating the association between its utility and pre-existing lung abnormalities. We retrospectively reviewed 388 patients with pneumococcal pneumonia confirmed by blood and/or sputum culture tests. Finally, 94 of 388 patients who had the results of UAT and computed tomography scans were enrolled to evaluate the association bet...
Source: European Journal of Clinical Microbiology and Infectious Diseases - November 4, 2020 Category: Microbiology Source Type: research

Rates of bacterial co-infections and antimicrobial use in COVID-19 patients: a retrospective cohort study in light of antibiotic stewardship
AbstractThe coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread worldwide. Bacterial co-infections are associated with unfavourable outcomes in respiratory viral infections; however, microbiological and antibiotic data related to COVID-19 are sparse. Adequate use of antibiotics in line with antibiotic stewardship (ABS) principles is warranted during the pandemic. We performed a retrospective study of clinical and microbiological characteristics of 140 COVID-19 patients admitted between February and April 2020 to a German University hospital, with a focus...
Source: European Journal of Clinical Microbiology and Infectious Diseases - November 2, 2020 Category: Microbiology Source Type: research

Hypervitaminosis A is associated with immunological non-response in HIV-1-infected adults: a case-control study
AbstractFor people living with HIV, determinants of immunological non-response (INR) to combined antiretroviral therapy (cART) have not been fully elucidated. In a case-control study, we evaluated the influence of the nutritional and antioxidant status in HIV-1 adults whose cART was initiated between January 2001 and December 2013. Cases had persistent CD4 counts  350/μL for controls, after at least 2 years of cART with persistent viral loads (VL)  2.70 μmol/L) (p = 0.030). Cases had lower erythrocyte resistance when exposed to a controlled free radical attack (p = 0.01...
Source: European Journal of Clinical Microbiology and Infectious Diseases - October 15, 2020 Category: Microbiology Source Type: research

Is Porphyromonas gingivalis involved in Parkinson ’s disease?
AbstractPorphyromonas gingivalis, a major subgingival plaque bacterium in periodontitis, has recently attracted much attention as a possible microbial driver in Alzheimer ’s disease. In the present paper, another common neuroinflammatory disease, Parkinson’s disease (PD), is discussed. A recent study found major virulence factors ofP. gingivalis such as gingipain R1 (RgpA) and lipopolysaccharide in the blood circulation of a PD population. The current review reveals how features such as systemic inflammation, hypercoagulation, presence of amyloid fibrin(ogen) in plasma, and marked ultrastructural changes in pla...
Source: European Journal of Clinical Microbiology and Infectious Diseases - October 15, 2020 Category: Microbiology Source Type: research

Multicenter evaluation of the RAPIDEC ® CARBA NP assay for the detection of carbapenemase production in clinical isolates of Enterobacterales and Pseudomonas aeruginosa
The objective was to evaluate the performance of the RAPIDEC ® CARBA NP assay (RAPIDEC), a screening assay that utilizes a pH indicator to detect carbapenem hydrolysis within 2 h. A multicenter study evaluated 306 clinical bacterial strains of Enterobacterales (n = 257) andPseudomonas aeruginosa (n = 49). The RAPIDEC was compared to a composite reference standard—the Clinical Laboratory Standards Institute (CLSI) Carba NP assay, PCR for specific carbapenemase genes (blaKPC,blaNDM,blaOXA-48-like,blaVIM andblaIMP), and phenotypic carbapenem susceptibility testing. The assay was...
Source: European Journal of Clinical Microbiology and Infectious Diseases - October 15, 2020 Category: Microbiology Source Type: research

Management and outcomes of Burkholderia cepacia complex bacteremia in patients without cystic fibrosis: a retrospective observational study
The objective was to evaluate the management and outcomes of BCC bacteremia in patients without CF. We conducted a retrospective study of non-CF adult patients with BCC bacteremia between January 1997 and December 2016 at 4 tertiary hospitals in South Korea. A total of 216 non-CF patients with BCC bacteremia were identified. Most cases were hospital-acquired (79.2%), and the most common source was a central venous catheter (CVC) (42.1%). The rates of susceptibility to trimethoprim-sulfamethoxazole and piperacillin-tazobactam of BCC isolates were high as 92.8% and 90.3%, respectively. The rates of susceptibility to ceftazid...
Source: European Journal of Clinical Microbiology and Infectious Diseases - October 15, 2020 Category: Microbiology Source Type: research

Real-time PCR-based quantitation of viable Mycobacterium leprae strain from clinical samples and environmental sources and its genotype in multi-case leprosy families of India
AbstractThe potential role of environmentalM. leprae in the transmission of leprosy remains unknown. We investigated role of environment as a possible source of viableM. leprae responsible for transmission of leprosy. The samples were collected from 10 multi-case leprosy families comprising, slit skin smear (SSS) from 9 multibacillary (MB), 16 paucibacillary cases (PB), 22 household contacts, and 38 environmental soil samples. The quantum of viableM. leprae was estimated by qRT-PCR using16S rRNA gene from soil and SSS. Genotypes ofM. leprae were determined by gene sequencing. We could observe presence of viableM. leprae in...
Source: European Journal of Clinical Microbiology and Infectious Diseases - October 15, 2020 Category: Microbiology Source Type: research

Urinary tract infection and antibiotic use around ureteral stent insertion for urolithiasis
AbstractUrolithiasis is the main indication for a ureteral JJ stent. Our aim was to determine the incidence of urinary tract infections (UTIs) after a JJ stent for urolithiasis, with an emphasis on antibiotic use. Prospective, multicenter, cohort study over a 4-month period including all of the patients with urolithiasis requiring JJ stent insertion. The clinical and microbiological data and therapeutic information were recorded until removal of the JJ stent. Two hundred twenty-three patients at five French private hospitals were included. A urine culture was performed for 187 patients (84%) prior to insertion of a JJ sten...
Source: European Journal of Clinical Microbiology and Infectious Diseases - October 15, 2020 Category: Microbiology Source Type: research

Epidemiology of skeletal tuberculosis in Beijing, China: a 10-year retrospective analysis of data
AbstractSkeletal tuberculosis (STB) is one of the most common forms of extrapulmonary tuberculosis; however, limited epidemiological data are available on this public health concern worldwide, especially in developing countries. The aims of this study were to analyze the epidemiological characteristics of STB cases and to identify risk factors associated with drug resistance among STB cases in China. We included STB inpatients at Beijing Chest Hospital from January 2009 through December 2018. The multiple demographic and clinical variables of patients were collected from the hospital ’s electronic patient record. In ...
Source: European Journal of Clinical Microbiology and Infectious Diseases - October 15, 2020 Category: Microbiology Source Type: research

Antimicrobial resistance, genetic characterization, and molecular epidemiology of Ureaplasma species in males with infertility
This study aimed to study the antimicrobial resistance, genetic characterization, and molecular epidemiology ofUreaplasma species in order to provide clinicians sufficient data to select optimal strategies of treatment for genitourinary tract infections of infertile male patients. Firstly, a total of 817 clinical semen specimens were detected forUreaplasma species by molecular detection. Secondly, culture and identification ofUreaplasma species were achieved by using Mycoplasma ICS Test, and the antimicrobial susceptibility tests were determined by using broth microdilution assay. Then, the tetracycline resistance genetic ...
Source: European Journal of Clinical Microbiology and Infectious Diseases - October 15, 2020 Category: Microbiology Source Type: research

Antibiotic modification versus withhold in febrile patients without evidence of bacterial infection, unresponsive to initial empiric regimen: a multicentre retrospective study conducted in Israel
This study compared outcomes of modifying, withholding, or continuing the same antibiotic regimen for such patients. Febrile or hypothermic stable patients with suspected infection, unresponsive to empiric antibiotic treatment, admitted to one of 15 internal medicine departments in three hospitals during a 5-year study period, were included. Patients with a definitive clinical or microbiological bacterial infection, malignancy, immunodeficiency, altered mental status, or need for mechanical ventilation were excluded. Participants were divided into groups based on treatment strategy determined 72  h after antibiotic in...
Source: European Journal of Clinical Microbiology and Infectious Diseases - October 15, 2020 Category: Microbiology Source Type: research

How is the microbial diagnosis of bacterial vertebral osteomyelitis performed? An 11-year retrospective study
AbstractVertebral osteomyelitis (VOM) is often diagnosed with delays, resulting in poorer outcomes. Microbial documentation is particularly challenging and obtained using blood cultures (BCs) and vertebral biopsies (VBs; CT-guided or surgical). We retrospectively analysed VOM cases in a tertiary reference centre between 2004 and 2015, focusing on how and how quickly microbiological diagnosis was performed. Among 220 VOM, 88.2% had documentation, including Gram-positive cocci (GPC) (70.6%), Gram-negative rods (GNR) (9.3%), anaerobes (3.6%), polybacterial infections (6.7%) and tuberculosis (9.8%). BCs were performed in 98.2%...
Source: European Journal of Clinical Microbiology and Infectious Diseases - October 15, 2020 Category: Microbiology Source Type: research

Population differentiation, antifungal susceptibility, and host range of Trichophyton mentagrophytes isolates causing recalcitrant infections in humans and animals
AbstractThe major problems in determining the causative factors of the high prevalence of dermatophytoses include the lack of a well-standardized antifungal susceptibility testing method, the low consistency of in vitro and clinical minimal inhibitory concentration values, the high genomic diversity of the population, and the unclear mechanism of pathogenicity. These factors are of particular importance when the disease is recalcitrant and relapses. Herein, we identified and characterizedTrichophyton mentagrophytes isolates obtained from therapy-resistant cases in humans and animals. We used genomic diversity analysis of 1...
Source: European Journal of Clinical Microbiology and Infectious Diseases - October 15, 2020 Category: Microbiology Source Type: research

Influenza and respiratory syncytial virus infections in the oldest-old continent
AbstractSARS-CoV-2 dramatically revealed the sudden impact of respiratory viruses in our lives. Influenza and respiratory syncytial virus (RSV) infections are associated with high rates of morbidity, mortality, and an important burden on healthcare systems worldwide, especially in elderly patients. The aim of this study was to identify severity predictors in the oldest-old admitted with influenza and/or RSV infections. This is a multicenter, retrospective study of all oldest-old patients ( ≥ 85 years old) admitted for laboratory-confirmed influenza and/or RSV infection in three tertiary hospitals in Por...
Source: European Journal of Clinical Microbiology and Infectious Diseases - October 15, 2020 Category: Microbiology Source Type: research

Laboratory evaluation of the Sigma Transwab ® transport system for the recovery of Candida species using the Clinical and Laboratory Standards Institute (CLSI) document M40-A2
This study assessed the efficiency of the Sigma Transwab ® foam and flock swab in recovering and maintaining viability of differentCandida spp. includingC. auris, in different test conditions. Both swab types recovered and maintained viability of allCandida spp. with greater CFU at room temperature after incubation (24 and 48  h) in comparison with swabs maintained at 4 °C. (Source: European Journal of Clinical Microbiology and Infectious Diseases)
Source: European Journal of Clinical Microbiology and Infectious Diseases - October 13, 2020 Category: Microbiology Source Type: research

The clinical presentation, treatment and outcome of serologically confirmed paediatric Lyme disease in the Republic of Ireland over a 5-year period: a retrospective cohort study
This study aimed to assess the incidence, clinical presentation, treatment and outcome of serologically confirmed paediatric LD in the Republic of Ireland over a 5-year period. A retrospective review of records from accredited laboratories performingBorrelia burgdorferi serological testing was undertaken. Proformas were distributed to clinicians of children and adolescents with positive Lyme serology. Data were requested regarding clinical presentation, treatment and outcome. Updated NICE guidelines were used to classify clinical cases. Serology testing forB. burgdorferi was performed on 2908 samples. Sixty-three (2.2%) ch...
Source: European Journal of Clinical Microbiology and Infectious Diseases - October 11, 2020 Category: Microbiology Source Type: research

Is recurrence possible in coronavirus disease 2019 (COVID-19)? Case series and systematic review of literature
According to this study, the phenomenon seems to be due to the prolonged detection of SARS-CoV-2 RNA traces in respiratory samples of recovered patients. The failure of the virus to replicate in vitro suggests its inability to replicate in vivo. (Source: European Journal of Clinical Microbiology and Infectious Diseases)
Source: European Journal of Clinical Microbiology and Infectious Diseases - October 10, 2020 Category: Microbiology Source Type: research

Study on risk factors, bacterial species, and drug resistance of acute pyelonephritis associated with ureteral stent after percutaneous nephrolithotomy
This study found that diabetes, postoperative stone residuals, urinary leukocytes ≧ 100 cells/HP, positive urine culture results, ureteral stent indwelling time ≧ 8 weeks, and high S.T.O.N.E. score were independent of AP associated with ureteral stent after PCNL risk factors andEscherichia coli is the main pathogenic bacteria and shows drug resistance. (Source: European Journal of Clinical Microbiology and Infectious Diseases)
Source: European Journal of Clinical Microbiology and Infectious Diseases - October 9, 2020 Category: Microbiology Source Type: research

Drug screening and development from the affinity of S protein of new coronavirus with ACE2
AbstractRecently, various studies have shown that angiotensin-converting enzyme 2 (ACE2) acts as the “doorknob” that can be bound by the spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which conduces to its entrance to the host cells, and plays an important role in corona virus disease 2019 (COVID-19). This paper aims to collect and sorts out the existing drugs, w hich exert the ability to block the binding of S protein and ACE2 so as to provide directions for the later drug development. By reviewing the existing literature, we expound the pathogenesis of SARS-CoV-2 from the persp...
Source: European Journal of Clinical Microbiology and Infectious Diseases - October 9, 2020 Category: Microbiology Source Type: research

Effect of delayed entry on performance of the BACT/ALERT FAN PLUS bottles in the BACT/ALERT VIRTUO blood culture system
AbstractDelayed entry of patient blood culture samples into a microbial detection system is unavoidable at times, due to off-shift staffing or transporting samples to centralized laboratories. Pre-incubation time and temperature of blood culture bottles are the most critical factors impacting recovery and detection of microorganisms. A total of 1377 BACT/ALERT ® (BTA) Fastidious Antimicrobial Neutralization (FAN® PLUS) bottles (FA PLUS, FN PLUS, and PF PLUS) were tested after delayed entry times of 24 and 36 h at 20–25 °C (room temperature, RT) prior to loading into the BACT/ALERT® VIRTUO&re...
Source: European Journal of Clinical Microbiology and Infectious Diseases - October 9, 2020 Category: Microbiology Source Type: research

Comparison of conventional molecular and whole-genome sequencing methods for subtyping Salmonella enterica serovar Enteritidis strains from Tunisia
AbstractWe sought to determine the relative value of conventional molecular methods and whole-genome sequencing (WGS) for subtypingSalmonella enterica serovar Enteritidis recovered from 2000 to 2015 in Tunisia and to investigate the genetic diversity of this serotype. A total of 175Salmonella Enteritidis isolates were recovered from human, animal, and foodborne outbreak samples. Pulsed-field gel electrophoresis (PFGE), multiple locus variable-number tandem repeat analysis (MLVA), and whole-genome sequencing were performed. Eight pulsotypes were detected for all isolates with PFGE (DI  = 0.518). Forty-fiveSalm...
Source: European Journal of Clinical Microbiology and Infectious Diseases - October 8, 2020 Category: Microbiology Source Type: research

Prevalence of hyposmia and hypogeusia in 390 COVID-19 hospitalized patients and outpatients: a cross-sectional study
AbstractAnecdotal evidence rapidly accumulated during March 2020 from sites around the world that sudden hyposmia and hypogeusia are significant symptoms associated with the SARS-CoV-2 pandemic. Our objective was to describe the prevalence of hyposmia and hypogeusia and compare it in hospitalized and non-hospitalized COVID-19 patients to evaluate an association of these symptoms with disease severity. We performed a cross-sectional survey during 5 consecutive days in March 2020, within a tertiary referral center, associated outpatient clinic, and two primary care outpatient facilities in Paris. All SARS-CoV-2-positive pati...
Source: European Journal of Clinical Microbiology and Infectious Diseases - October 8, 2020 Category: Microbiology Source Type: research

Chronic hepatitis B virus infection in Italy during the twenty-first century: an updated survey in 2019
AbstractThe aim of this study is to provide updates on the characteristics of chronic HBsAg carriers in Italy before the advent of new drugs eliminating or functionally inactivating the genome HBV reservoirs. HBV endemicity has greatly decreased in Italy over the past decades. A not negligible number of chronic HBsAg carriers are still alive in the country. Chronic HBsAg carriers consecutively referring to 9  units in Italy were prospectively enrolled for a 6-month period in 2019. Multiple logistic regression analysis was performed to identify independent predictors of treatment. A total of 894 cases was recruited (se...
Source: European Journal of Clinical Microbiology and Infectious Diseases - October 7, 2020 Category: Microbiology Source Type: research

The vaginal microbiota in the course of bacterial vaginosis treatment
In this study, vaginal microbiota composition was determined in twenty-one women with BV, before and after treatment with metronidazole or clindamycin. Microbiota composition varied greatly between women and defining a (un)healthy vaginal microbiota state remains elusive, challenging BV diagnosis and treatment. While relative abundance ofLactobacillus increased after antibiotic treatment in two-third of women, its abundance was not associated with treatment outcome. Instead, remaining complaints of abnormal vaginal discharge were more common after metronidazole treatment and associated with increased relative abundance ofU...
Source: European Journal of Clinical Microbiology and Infectious Diseases - October 6, 2020 Category: Microbiology Source Type: research

Clinical and microbiological characteristics of adults with hospital-acquired pneumonia: a 10-year prospective observational study in China
AbstractHospital-acquired pneumonia (HAP) is a significant nosocomial infection; data on the distribution and antimicrobial resistance profiles of HAP in China are limited. We included 2827 adult patients with HAP from the Chinese Antimicrobial Resistance Surveillance of Nosocomial Infections network admitted in 15 Chinese teaching hospitals between 2007 and 2016. Clinical data and antimicrobial susceptibility of isolated pathogens were obtained from the medical records and central laboratory, respectively. Multivariable logistic regression was performed to determine the risk factors for mortality and multidrug resistance ...
Source: European Journal of Clinical Microbiology and Infectious Diseases - October 6, 2020 Category: Microbiology Source Type: research

Prevalence of Chlamydia trachomatis , Neisseria gonorrhoeae , Mycoplasma genitalium and Trichomonas vaginalis including relevant resistance-associated mutations in a single center in the Netherlands
ConclusionCT is found most often in our population followed by MG and NG. By using molecular assays to detect RAM supplementary to pathogen identification of NG and MG, optimal therapy can be advised. (Source: European Journal of Clinical Microbiology and Infectious Diseases)
Source: European Journal of Clinical Microbiology and Infectious Diseases - October 6, 2020 Category: Microbiology Source Type: research

A rare case of cutaneous Papiliotrema ( Cryptococcus ) laurentii infection in a 23-year-old Caucasian woman affected by an autoimmune thyroid disorder with hypothyroidism
AbstractIn recent years, the frequency of infections due to saprophytic fungi has increased.Cryptococcus laurentii, recently classified asPapiliotrema laurentii, is responsible for fungemia, meningitis, and superficial infections. Here, we report the first case of cutaneousPapiliotrema (Cryptococcus)laurentii infection in a 23-year-old Caucasian woman affected by an autoimmune thyroiditis with hypothyroidism. Impairments of the immune system are often associated with unusual fungal infections, which cannot be neglected. The isolate strain was susceptible to Amphotericin B while resistant to fluconazole, itraconazole, voric...
Source: European Journal of Clinical Microbiology and Infectious Diseases - October 5, 2020 Category: Microbiology Source Type: research

Correction to: Molecular revolution in the diagnosis of microbial brain abscesses
An erratum to this paper has been published: https://doi.org/10.1007/s10096-020-04047-8. (Source: European Journal of Clinical Microbiology and Infectious Diseases)
Source: European Journal of Clinical Microbiology and Infectious Diseases - October 5, 2020 Category: Microbiology Source Type: research

Multicenter study of automated systems for colistin susceptibility testing
AbstractPurposeBroth microdilution (BMD) stays as the reference testing method for determination of antimicrobial susceptibility testing (AST) to colistin and is considered essential for patient management and for monitoring of colistin resistance. This multicenter study aimed to evaluate the performance of automated systems for colistin AST among Enterobacterales as an alternative for BMD since the majority of laboratories use automated systems as first-line method.MethodsTwenty colistin resistant (COL-R) including 10 MCR producers and 10 colistin-susceptible (COL-S) Enterobacterales isolates were blindly tested for colis...
Source: European Journal of Clinical Microbiology and Infectious Diseases - October 5, 2020 Category: Microbiology Source Type: research

Point-of-care multiplex-PCR enables germ identification in haemolytic uremic syndrome 94  h earlier than stool culture
AbstractHaemolytic uremic syndrome often affects children causing a relevant morbidity and mortality. We compared the time to diagnosis by multiplex-PCR and stool culture in 15 children from two centres. Multiplex-PCR accelerated the time to diagnosis by 94 (95% confidence interval, 80 –119;P = 0.0007) hours. Multiplex-PCR offers a time advantage of stool culture that may aid in earlier identification of outbreak clusters. (Source: European Journal of Clinical Microbiology and Infectious Diseases)
Source: European Journal of Clinical Microbiology and Infectious Diseases - October 3, 2020 Category: Microbiology Source Type: research

Frequent detection of enterovirus D68 and rhinovirus type C in children with acute respiratory infections
This study aimed to evaluate the prevalence of human rhinoviruses (HRVs) and the emergence of enterovirus D68 (EV-D68) in children. A total of 322 nasopharyngeal swab samples were provided from children with an initial diagnosis of upper and lower respiratory tract infections. A total of 34 and 70 cases were positive for EV-D68 and HRV, respectively. The phylogenetic analysis revealed that the clades A and B are the prevalent genotypes for EV-D68 and the HRV-positive samples belong to three types including HRV-A, HRV-B, and HRV-C. The results showed that EV-D68 and HRV-C are circulating in Iran especially in the winter. (S...
Source: European Journal of Clinical Microbiology and Infectious Diseases - October 2, 2020 Category: Microbiology Source Type: research

Is it time to move away from polymyxins?: evidence and alternatives
AbstractIncreasing burden of carbapenem resistance and resultant difficult-to-treat infections are of particular concern due to the lack of effective and safe treatment options. More recently, several new agents with activity against certain multidrug-resistant (MDR) and extensive drug-resistant (XDR) Gram-negative pathogens have been approved for clinical use. These include ceftazidime-avibactam, meropenem-vaborbactam, imipenem-cilastatin-relebactam, plazomicin, and cefiderocol. For the management of MBL infections, clinically used triple combination comprising ceftazidime-avibactam and aztreonam is hindered due to non-av...
Source: European Journal of Clinical Microbiology and Infectious Diseases - October 1, 2020 Category: Microbiology Source Type: research

The metabolic and immunological characteristics of pregnant women with COVID-19 and their neonates
AbstractOur aim was to investigate whether SARS-CoV-2 infection raised high risks of late pregnancy complications, and posed health problems in fetuses and neonates. We analyzed the data of COVID-19 pregnant women with COVID-19 during late pregnancy and their neonates. Eleven out of 16 (69%) pregnant women with COVID-19 had ++ or +++ of ketone body in urine. The blood uric acid of pregnant patients was 334  μmol/L (IQR, 269–452). D-dimer and FDP in pregnant patients were 3.32 mg/L (IQR, 2.18–4.21) and 9.6 mg/L (IQR, 5.9–12.4). Results of blood samples collected at birth showed that 16 ne...
Source: European Journal of Clinical Microbiology and Infectious Diseases - October 1, 2020 Category: Microbiology Source Type: research

Changing epidemiology and resistance patterns of pathogens causing neonatal bacteremia
AbstractTo conduct a survey of the local prevalent bacteria and antibiotic resistance in a referral tertiary neonatal intensive care unit (NICU), in order to assess the efficacy of local antibiotic policies. We reviewed all positive blood and cerebrospinal fluid cultures obtained between January 2007 and December 2017 in the NICU of Schneider Children ’s Medical Center of Israel. Early and late-onset bacteremia were defined as episodes occurring within or after the first 3 calendar days of life respectively. Empiric treatment included ampicillin and gentamicin or piperacillin-tazobactam and amikacin for early or late...
Source: European Journal of Clinical Microbiology and Infectious Diseases - September 12, 2020 Category: Microbiology Source Type: research

The epidemiology of invasive meningococcal disease and the utility of vaccination in Malta
We describe the population epidemiology of IMD in Malta in order to assess the potential utility of a meningococcal vaccination programme. All cases of microbiologically confirmed IMD in the Maltese population from 2000 to 2017 were analysed to quantify the overall and capsular-specific disease burden. Mean overall crude and age-specific meningococcal incidence rates were calculated to identify the target age groups that would benefit from vaccination. Over the 18-year study period, 111 out of the 245 eligible notified cases were confirmed microbiologically of which 70.3% had septicaemia, 21.6% had meningitis, and 6.3% had...
Source: European Journal of Clinical Microbiology and Infectious Diseases - September 12, 2020 Category: Microbiology Source Type: research

Children account for a small proportion of diagnoses of SARS-CoV-2 infection and do not exhibit greater viral loads than adults
AbstractPrevious reports have suggested that children are less affected than adults by SARS-CoV-2. We analyzed SARS-CoV-2 diagnoses between February 27, 2020, and March 14, 2020, and mortality among positive patients in Marseille university hospitals. Of 4050 tested individuals, 228 were positive. Deaths occurred in 2/99 documented cases (both>  85 year-old). Children were majorly asymptomatic. Incidence increased by 7.4-fold between 1–5 and 45–65 years then decreased. It was significantly lower among 0–1 year- (0%) and 1–5 (1.1%) and 5–10 (3.6%)-year-old children than...
Source: European Journal of Clinical Microbiology and Infectious Diseases - September 12, 2020 Category: Microbiology Source Type: research

The Allplex 2019-nCoV (Seegene) assay: which performances are for SARS-CoV-2 infection diagnosis?
AbstractSeveral commercial assays for SARS-CoV-2 RT-PCR are available but few of them were assessed. We evaluate the Allplex 2019-nCoV (Seegene) assay using 41 nasopharyngeal samples. The rates of agreement were 92.7% and 100% with the GeneFinder COVID-19 plus (Elitech) and the diagnosis of the infectious disease specialist respectively. Four samples display a Ct
Source: European Journal of Clinical Microbiology and Infectious Diseases - September 12, 2020 Category: Microbiology Source Type: research

Septic shock caused by Capnocytophaga canis after a cat scratch
AbstractCapnocytophaga canis is an uncommon cause of septic shock. Only three cases have been previously reported in the literature. In this article, we describe the case of a 70-year-old male admitted to the intensive care unit for septic shock of unknown origin. On day 2, one anaerobic bottle out of the two sets taken at admission turned positive with Gram-negative bacilli. The pathogen was identified by 16S rRNA gene asC.canis. The strain was characterized and compared with other clinical isolates ofCapnocytophaga spp. (Source: European Journal of Clinical Microbiology and Infectious Diseases)
Source: European Journal of Clinical Microbiology and Infectious Diseases - September 12, 2020 Category: Microbiology Source Type: research

Gastrointestinal symptoms and the acquisition of enteric pathogens in Hajj pilgrims: a 3-year prospective cohort study
AbstractThe acquisition of enteric pathogens and risk factors for Hajj-associated diarrhea in Hajj pilgrims is poorly documented. Pilgrims from Marseille participating in the Hajj in 2016 –2018 underwent successive systematic rectal swabbing before and after their travel. Carriage of the main enteric pathogens was assessed by real-time PCR. Baseline demographics, adherence to individual preventive measures, gastrointestinal symptoms, and treatments were recorded. A total of 376 pil grims were included. The median age was 62.0 years. During the Hajj, 18.6% presented at least one gastrointestinal symptom, 13.8% ha...
Source: European Journal of Clinical Microbiology and Infectious Diseases - September 10, 2020 Category: Microbiology Source Type: research

Letermovir for the compassionate therapeutic use of cytomegalovirus infection
ConclusionLetermovir may be an effective and well tolerated option in the compassionate treatment of CMV infections, although recurrence of CMV and emergence of resistance may be issues. (Source: European Journal of Clinical Microbiology and Infectious Diseases)
Source: European Journal of Clinical Microbiology and Infectious Diseases - September 10, 2020 Category: Microbiology Source Type: research

Clinical and molecular epidemiology of vancomycin-resistant Enterococcus faecium bacteremia from an Indian tertiary hospital
AbstractWe  determined the clinical and molecular epidemiology of emerging nosocomial vancomycin-resistantEnterococcus faecium (VREfm) –causing serious bloodstream infections (BSIs) and the correlations between antibiotic resistance and virulence determinants among isolates. All isolates were confirmed by molecular methods (16SrRNA andE. faecium ddl genes) and tested for disk diffusion. PCR  was used to detectaac(6 ′)-aph(2″),vanA andvanB resistance genes, andasa1,cylA,ace,esp,gelE andhyl virulence genes. VREfm and high-level gentamicin-resistant (HLGR) representative isolates were sel...
Source: European Journal of Clinical Microbiology and Infectious Diseases - September 9, 2020 Category: Microbiology Source Type: research

How are rapid diagnostic tests for infectious diseases used in clinical practice: a global survey by the International Society of Antimicrobial Chemotherapy (ISAC)
In this study, we aim to assess the current patterns of use around the world, identify issues for successful implementation and suggest best practice advice on how to introduce new tests. An electronic survey was devised by the International Society of Antimicrobial Chemotherapy (ISAC) Rapid Diagnostics and Biomarkers working group focussing on the availability, structure and impact of RDTs around the world. It was circulated to ISAC members in December 2019. Results were collated according to the UN human development index (HDI). 81 responses were gathered from 31 different countries. 84% of institutions reported the avai...
Source: European Journal of Clinical Microbiology and Infectious Diseases - September 8, 2020 Category: Microbiology Source Type: research

Microbiological diagnosis of suspected vertebral osteomyelitis with a focus on the yield of percutaneous needle biopsy: a 10-year cohort study
This study aims to evaluate in patients hospitalized for vertebral osteomyelitis (VO) the effectiveness of bacteriological diagnosis and the yield of percutaneous needle biopsy (PNB) and to identify factors associated with the result of PNB. This retrospective, two-centre study was conducted between 2000 and 2009. Data on patients with VO were retrieved from the diagnosis database and confirmed by checking medical records. A total of 300 patients with VO were identified; 31 received antibiotics without bacteriological diagnosis, and 269 patients with spondylodiscitis imaging were included. Eighty-three (30.9%) and 18 (6.7%...
Source: European Journal of Clinical Microbiology and Infectious Diseases - September 7, 2020 Category: Microbiology Source Type: research

Application and clinical impact of the RESIST-4 O.K.N.V. rapid diagnostic test for carbapenemase detection in blood cultures and clinical samples
AbstractInvasive infections caused by carbapenemase-producing bacteria are associated with excess mortality. We applied a rapid diagnostic test (RDT) on clinical samples with an elevated likelihood of carbapenemase-producing bacteria and documented its impact on antibiotic treatment decisions. Among 38 patients, twelve tested positive for infections caused by carbapenemase-producing bacteria (31.6%), mainly in blood cultures. KPC (n = 10) was more frequent than OXA-48 (n = 2). RDT-based carbapenemase detection led to a treatment modification to ceftazidime/avibactam-containing regimens in all pa...
Source: European Journal of Clinical Microbiology and Infectious Diseases - September 6, 2020 Category: Microbiology Source Type: research