First isolation of Clostridium difficile PCR ribotype 027 from a patient with severe persistent diarrhoea in Hungary

A recent Supplement to Clinical Microbiology and Infection entitled ‘Infection control measures to limit the spread of C. difficile’ pointed out that the incidence of C. difficile-associated diarrhoea (CDAD) has been increasing worldwide, and stressed the importance of research in the fields of epidemiology and infection control [1]. Since 2003, one of the main causes of the increasing prevalence of CDAD has been claimed to be the emergence of PCR ribotype 027/NAP1, which has caused epidemics in North America, the UK, the Netherlands, Belgium and France. The presence of PCR ribotype 027 in Austria, Japan, Ireland, Germany and Switzerland has also been reported recently [2,3]. The majority of publications have emphasized that the presence of this strain is usually associated with more severe symptoms and signs than those associated with the other more common toxinpositive strains [4,5]. Whereas PCR ribotype 027 was present in the population earlier, the majority of the historic strains were fluoroquinolone sensitive [6]. The overuse of antibiotics such as fluoroquinolones may lead to the selection and emergence of resistant strains, and may contribute to the spread of PCR ribotype 027, which is usually resistant to erythromycin. Here, the Eastern European spread of C. difficile PCR ribotype 027 is reported

Molecular, microbiological and clinical characterization of Clostridium difficile isolates from tertiary care hospitals in Colombia

In Colombia, the epidemiology and circulating genotypes of Clostridium difficile have not yet been described. Therefore, we molecularly characterized clinical isolates of C.difficile from patients with suspicion of C.difficile infection (CDI) in three tertiary care hospitals. C.difficile was isolated from stool samples by culture, the presence of A/B toxins were detected by enzyme immunoassay, cytotoxicity was tested by cell culture and the antimicrobial susceptibility determined. After DNA extraction, tcdA, tcdB and binary toxin (CDTa/CDTb) genes were detected by PCR, and PCR-ribotyping performed. From a total of 913 stool samples collected during 2013–2014, 775 were included in the study. The frequency of A/B toxins-positive samples was 9.7% (75/775). A total of 143 isolates of C.difficile were recovered from culture, 110 (76.9%) produced cytotoxic effect in cell culture, 100 (69.9%) were tcdA+/tcdB+, 11 (7.7%) tcdA-/tcdB+, 32 (22.4%) tcdA-/tcdB- and 25 (17.5%) CDTa+/CDTb+. From 37 ribotypes identified, ribotypes 591 (20%), 106 (9%) and 002 (7.9%) were the most prevalent; only one isolate corresponded to ribotype 027, four to ribotype 078 and four were new ribotypes (794,795, 804,805). All isolates were susceptible to vancomycin and metronidazole, while 85% and 7.7% were resistant to clindamycin and moxifloxacin, respectively. By multivariate analysis, significant risk factors associated to CDI were, staying in orthopedic service, exposure to third-generation cephalosporins and staying in an ICU before CDI symptoms; moreover, steroids showed to be a protector factor. These results revealed new C. difficile ribotypes and a high diversity profile circulating in Colombia different from those reported in America and European countries

Ungulate browsing shapes climate change impacts on forest biodiversity in Hungary

Climate change can result in a slow disappearance of forests dominated by less drought-tolerant native European beech (Fagus sylvatica) and oak species (Quercus spp.) and further area expansion of more drought-tolerant non-native black locust (Robinia pseudoacacia) against those species in Hungary. We assumed that the shift in plant species composition was modified by selective ungulate browsing. Thus, we investigated which woody species are selected by browsing game. We have collected data on the species composition of the understory and the browsing impact on it in five different Hungarian even-aged forests between 2003 and 2005. Based on these investigations the non-native Robinia pseudoacacialiving under more favourable climatic conditions was generally preferred (Jacobs’ selectivity index: D=0.04±0.77), while the nativeFagus sylvatica and Quercus spp. (Q. petraea, Q. robur), both more vulnerable to increasing aridity, were avoided (D=-0.37±0.11;-0.79±0.56;-0.9±0.16; respectively) among target tree species. However, economically less or not relevant species, e.g. elderberry (Sambucus spp.), blackberry (Rubus spp.) or common dogwood (Cornus sanguinea) were the most preferred species (D=0.01±0.71; -0.12±0.58; -0.2±0.78, respectively). Our results imply that biodiversity conservation, i.e. maintaining or establishing a multi-species understory layer, can be a good solution to reduce the additional negative game impact on native target tree species suffering from drought. Due to preference for Robinia pseudoacaciaselective browsing can decelerate the penetration of this species into native forest habitats. We have to consider the herbivorous pressure of ungulates and their feeding preferences in planning our future multifunctional forests in the light of climate change impacts

Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020

We show the distribution of SARS-CoV-2 genetic clades over time and between countries and outline potential genomic surveillance objectives. We applied three available genomic nomenclature systems for SARS-CoV-2 to all sequence data from the WHO European Region available during the COVID-19 pandemic until 10 July 2020. We highlight the importance of real-time sequencing and data dissemination in a pandemic situation. We provide a comparison of the nomenclatures and lay a foundation for future European genomic surveillance of SARS-CoV-2.Peer reviewe

Modified Multiple-Locus Variable-Number Tandem-Repeat Analysis for Rapid Identification and Typing of Clostridium difficile during Institutional Outbreaks▿

A modified multiple-locus variable-number tandem-repeat analysis (MMLVA) method was validated on Clostridium difficile-infected stool specimens from institutional outbreaks. The method allows simultaneous detection of toxin genes, deletions, and tandem repeats from cultured isolates or stool specimens. Results were used to aid institutional outbreak investigation by identifying clusters of NAP1/027

Species identification of clinical isolates of Bacteroides by matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry

Bacteroides fragilis and related species are important human pathogens involved in mixed infections of different origins. The B. fragilis group isolates are phenotypically very similar, grow more slowly than aerobic bacteria and, accordingly, are frequently misidentifed with classical or automated phenotypical identification methods. Recent taxonomic changes and new species accepted as members of the Bacteroides genus are not included in the different databases of commercially available identification kits. The use of matrix-assisted laser-desorption/ ionization time-of-flight mass spectrometry (MALDI-TOF MS) was therefore evaluated for the species identification of 277 clinical isolates of the Bacteroides genus. Species identification was carried out with MALDI Bruker Daltonik Biotyper software (Bruker Daltonik GmbH, Bremen, Germany) by comparing the mass spectrum of each strain with the mass spectra of the 3260 reference strains currently available. The results of conventional phenotypical identification of the isolates were used as a reference. 16S rRNA gene sequencing was performed for a selection of the strains that gave discrepant results and for all those inconclusively identified by MALDI-TOF MS; 270 isolates (97.5%) were unequivocally identified [log(score) =2.0] by comparison with the reference strains present in the MALDI Biotyper database. Of the 23 isolates for which the MALDI-TOF MS species identification differed from the conventional phenotypical identification, 11 were sequenced. The sequencing data confirmed the MALDI-TOF MS result in ten cases and, for the remaining isolate, the sequencing data did not lead to the determination of the species, but only to that of the genus (Bacteroides sp.). The discriminating power and identification accuracy of MALDI-TOF MS proved to be superior to that of biochemical testing for Bacteroides thetaiotaomicron , Bacteroides ovatus and Bacteroides uniformis. © 2009 The Authors Journal compilation © 2009 European Society of Clinical Microbiology and Infectious Diseases

Antimicrobial susceptibility of Bacteroides fragilis group isolates in Europe: 20 years of experience

The susceptibilities of 824 Bacteroides fragilis group isolates against nine antibiotics were evaluated in a Europe-wide study involving 13 countries. Species determination, by different methods, was carried out on all but one isolate. Resistance rates were evaluated according to species and geographical areas via CLSI and the European Committee on Antimicrobial Susceptibility Testing (EUCAST) breakpoints. The present data were compared with those obtained 10 and 20 years ago at a European level. High-level resistance (MIC 6564 mg/L) to ampicillin was observed in 44.5% of the strains, which is a significant increase relative to 20 years ago (16%). Piperacillin/tazobactam was more active than amoxicillin/clavulanic acid (3.1% and 10.4% resistance, respectively), again with a resistance increase relative to earlier studies. Dramatic increases in resistance were observed for cefoxitin, clindamycin and moxifloxacin, with rates of 17.2%, 32.4% and 13.6%, respectively. The lowest resistances were found for imipenem, metronidazole and tigecycline (1.2%, <1% and 1.7%). Nonsusceptible strains to imipenem and metronidazole were more resistant to other anti-anaerobic drugs. Differences were detected between geographical areas, with higher resistance rates for moxifloxacin in Scandinavian countries (21.4%) than in Mediterranean countries (5.4%), whereas, for clindamycin, the resistance rates were higher in Mediterranean (41.8%) and lower in Scandinavian countries (22.5%). Piperacillin/tazobactam resistance was also higher in Scandinavian countries