Cryptosporidium genotyping in Europe: The current status and processes for a harmonised multi-locus genotyping scheme.

Due to the occurrence of genetic recombination, a reliable and discriminatory method to genotype Cryptosporidium isolates at the intra-species level requires the analysis of multiple loci, but a standardised scheme is not currently available. A workshop was held at the Robert Koch Institute, Berlin in 2016 that gathered 23 scientists with appropriate expertise (in either Cryptosporidium genotyping and/or surveillance, epidemiology or outbreaks) to discuss the processes for the development of a robust, standardised, multi-locus genotyping (MLG) scheme and propose an approach. The background evidence and main conclusions were outlined in a previously published report; the objectives of this further report are to describe 1) the current use of Cryptosporidium genotyping, 2) the elicitation and synthesis of the participants' opinions, and 3) the agreed processes and criteria for the development, evaluation and validation of a standardised MLG scheme for Cryptosporidium surveillance and outbreak investigations. Cryptosporidium was characterised to the species level in 7/12 (58%) participating European countries, mostly for human outbreak investigations. Further genotyping was mostly by sequencing the gp60 gene. A ranking exercise of performance and convenience criteria found that portability, biological robustness, typeability, and discriminatory power were considered by participants as the most important attributes in developing a multilocus scheme. The major barrier to implementation was lack of funding. A structured process for marker identification, evaluation, validation, implementation, and maintenance was proposed and outlined for application to Cryptosporidium, with prioritisation of Cryptosporidium parvum to support investigation of transmission in Europe.

New lipid-dependent Malassezia species from parrots / Nuevas especies lipodependientes del género Malassezia procedentes de loros

Background. All the currently recognized Malassezia species have been isolated from mammals. However, only a few of them have been isolated from birds. In fact, birds have been less frequently studied as carriers of Malassezia yeasts than mammals. Aim. In this study we describe two new taxa, Malassezia brasiliensis sp. nov. and Malassezia psittaci sp. nov. Methods. The isolates studied in this publication were isolated from pet parrots from Brazil. They were characterized using the current morphological and physiological identification scheme. DNA sequencing and analysis of the D1/D2 regions of the 26S rRNA gene, the ITS-5.8S rRNA gene sequences and the β-tubulin gene were also performed. Results. The strains proposed as new species did not completely fit the phenotypic profiles of any the described species. The validation of these new species was supported by analysis of the genes studied. The multilocus sequence analysis of the three loci provides robust support to delineate these species. Conclusions. These studies confirm the separation of these two new species from the other species of the genus Malassezia, as well as the presence of lipid-dependent Malassezia yeasts on parrots (AU)

Antecedentes. Todas las especies del género Malassezia actualmente identificadas se han aislado de mamíferos. Sin embargo, tan solo unas pocas de ellas se han aislado de aves. De hecho, las aves han sido estudiadas con menos frecuencia como portadoras de estas levaduras que los mamíferos. Objetivos. En este estudio describimos dos nuevas especies del género Malassezia: Malassezia brasiliensis sp. nov. y Malassezia psittaci sp. nov. Métodos. Las cepas estudiadas en esta publicación se aislaron de loros utilizados como animales de compañía en Brasil. Las cepas se caracterizaron mediante los criterios morfológicos y fisiológicos actualmente utilizados para la identificación de estas levaduras. También se llevó a cabo la secuenciación y el análisis de los fragmentos génicos D1/D2 26S e ITS-5.8S del ADN ribosómico y del gen de la β-tubulina. Resultados. Los perfiles fenotípicos de las cepas propuestas como nuevas especies no encajaron completamente con los de las especies descritas en este género. Además, el análisis de los genes estudiados respaldó la validez de las nuevas especies. El análisis multilocus de secuencias de los tres loci estudiados reforzó con mayor firmeza la definición de las nuevas especies. Conclusiones. Todos estos estudios confirman la separación de estas dos nuevas especies del resto de las especies descritas del género Malassezia, así como la existencia de especies dependientes de lípidos del género Malassezia en loros (AU)

Current application and future perspectives of molecular typing methods to study Clostridium difficile infections.

Molecular typing is an essential tool to monitor Clostridium difficile infections and outbreaks within healthcare facilities. Molecular typing also plays a key role in defining the regional and global changes in circulating C. difficile types. The patterns of C. difficile types circulating within Europe (and globally) remain poorly understood, although international efforts are under way to understand the spatial and temporal patterns of C. difficile types. A complete picture is essential to properly investigate type-specific risk factors for C. difficile infections (CDI) and track long-range transmission. Currently, conventional agarose gel-based polymerase chain reaction (PCR) ribotyping is the most common typing method used in Europe to type C. difficile. Although this method has proved to be useful to study epidemiology on local, national and European level, efforts are made to replace it with capillary electrophoresis PCR ribotyping to increase pattern recognition, reproducibility and interpretation. However, this method lacks sufficient discriminatory power to study outbreaks and therefore multilocus variable-number tandem repeat analysis (MLVA) has been developed to study transmission between humans, animals and food. Sequence-based methods are increasingly being used for C. difficile fingerprinting/typing because of their ability to discriminate between highly related strains, the ease of data interpretation and transferability of data. The first studies using whole-genome single nucleotide polymorphism typing of healthcare-associated C. difficile within a clinically relevant timeframe are very promising and, although limited to select facilities because of complex data interpretation and high costs, these approaches will likely become commonly used over the coming years.