The In Vitro Ability of Klebsiella pneumoniae to Form Biofilm and the Potential of Various Compounds to Eradicate it from Urinary Catheters

Urinary infections related to the presence of bacterial biofilm on catheters are responsible for loss of patients’ health and, due to their high frequency of occurrence, generate a significant economic burden for hospitals. Klebsiella pneumoniae is a pathogen frequently isolated from this type of infection. In this study, using a cohesive set of techniques performed under stationary and flow conditions, we assessed the ability of 120 K. pneumoniae strains to form biofilm on various surfaces, including catheters, and evaluated the usefulness of clinically applied and experimental compounds to remove biofilm. The results of our study indicate the high impact of intraspecies variability with respect to K. pneumoniae biofilm formation and its susceptibility to antimicrobials and revealed the crucial role of mechanical flushing out of the biofilm from the catheter’s surface with use of locally active antimicrobials. Therefore, our work, although of in vitro character, may be considered an important step in the direction of efficient reduction of K. pneumoniae biofilm-related hospital infections associated with the presence of urine catheters.

Subtyping Options for Microsporum canis Using Microsatellites and MLST: A Case Study from Southern Italy

Microsporum canis is considered one of the most common zoophilic dermatophyte species causing infections in animals and humans worldwide. However, molecular epidemiological studies on this dermatophyte are still rare. In this study, we aimed to analyse the population structure and relationships between M. canis strains (n = 66) collected in southern Italy and those isolated from symptomatic and asymptomatic animals (cats, dogs and rabbits) and humans. For subtyping purposes, using multilocus sequence typing (MLST) and multilocus microsatellite typing (MLMT), we first used a limited set of strains to screen for variability. No intraspecies variability was detected in six out of the eight reference genes tested and only the ITS and IGS regions showed two and three sequence genotypes, respectively, resulting in five MLST genotypes. All of eight genes were, however, useful for discrimination among M. canis, M. audouinii and M. ferrugineum. In total, eighteen microsatellite genotypes (A–R) were recognized using MLMT based on six loci, allowing a subdivision of strains into two clusters based on the Bayesian iterative algorithm. Six MLMT genotypes were from multiple host species, while 12 genotypes were found only in one host. There were no statistically significant differences between clusters in terms of host spectrum and the presence or absence of lesions. Our results confirmed that the MLST approach is not useful for detailed subtyping and examining the population structure of M. canis, while microsatellite analysis is a powerful tool for conducting surveillance studies and gaining insight into the epidemiology of infections due to this pathogen.

The Impact of Intraspecies Variability on Growth Rate and Cellular Metabolic Activity of Bacteria Exposed to Rotating Magnetic Field

Majority of research on the influence of magnetic fields on microorganisms has been carried out with the use of different species or different groups of microorganisms, but not with the use of different strains belonging to one species. The purpose of the present study was to assess the effect of rotating magnetic fields (RMF) of 5 and 50 Hz on the growth and cellular metabolic activity of eight species of bacteria: Staphylococcus aureus, Pseudomonas aeruginosa, Proteus mirabilis, Klebsiella pneumoniae, Enterococcus faecalis, Enterobacter cloacae, Moraxella catarrhalis, and Bacillus cereus. However, contrary to the research conducted so far, each species was represented by at least four different strains. Moreover, an additional group of S. aureus belonging to a single clonal type but representing different biotypes was also included in the experiment. The results showed a varied influence of RMF on growth dynamics and cellular metabolic activity, diversified to the greatest extent in dependence on the bacterial strain exposed to the RMF and to a lesser extent in dependence on the frequency of the generated magnetic field. It was found that, with regard to the exposed strain of the same species, the effect exerted by the RMF may be positive (i.e., manifests as the increase in the growth rate or/and cellular metabolic activity) or negative (i.e., manifests as a reduction of both aforementioned features) or none. Even when one clonal type of S. aureus was used, the results of RMF exposure also varied (although the degree of differentiation was lower than for strains representing different clones). Therefore, the research has proven that, apart from the previously described factors related primarily to the physical parameters of the magnetic field, one of the key parameters affecting the final result of its influence is the bacterial intraspecies variability.

Acer negundo, morphometric parameters, the level of variability

The article investigates the morphometric characteristics of the fruits of Acer negundo L. in the conditions of urbanized ecotops of the Mykolaiv region. Acer negundo an ornamental plant from South America, which was completely naturalized in the conditions of Ukraine. As the data of the literature indicate, A. negundo actively spreads not only in the green plantations of cities, but also penetrates into the natural cenoses, displacing and oppressing the local plants. Thus, this species can be considered as invasive, which requires control over its spreading. In this regard, the actual issue is the study of the peculiarities of the seed reproduction of A. negundo and the establishment of its role in distribution of this species. Morphological parameters of A. negundo fruits are pretty changeable depending on environmental conditions, that is why there is a question of current interest in studying the variability of carpological parameters and the diapason of modifiability. The purpose of the article is to establish the characteristics of intraspecific variability of the linear morphological parameters of A. negundo. The subject of the research is variability of morphological parametres of the fruits of A. negundo urbanized ecotops of the Mykolaiv region. The work materials are results of measurements of fruits of 50 A. negundo individuals on 15 test areas in urbanized biotopes. The following carpological parameters of A. negundo were investigated: 1) angle of divergence of mericarps; 2) fruit’s length and width; 3) width of winglet. The received data allowed to define criteria of variability and ecological flexibility of morphological features. Determination of the variability of morphological characters was carried out according to the technique of S.A. Mamaev. The level of variability of morphological characters (Cv) was assessed on an empirical scale: very low (<7%); low (8-12%); average (13-20%); increased (21-30%); high (31-40%); very high (> 40%). As a result of our investigations, we found the following carpological features of A. negundo. In the conditions of Mykolaiv region A. negundo shapes the fruits with the dimension of length from 3,0 to 4,8 cm (the mean is 3,5±0,02 cm) and with the dimension of width from 2,0 to 4,3 (the mean is 3,2±0,05 cm). Mericarps are located at an angle from 25º to 60º (40 ± 1º), elongated with an elongated wing, the width of which varies within 1,3 ± 0,03 cm. The established carpological features of A. negundo meets norms. On the basis of the study of linear morphological parameters of the fruits, the phenotypic variability of A. negundo individuals was revealed, which indicates the presence of intraspecies variability on these features. The most variable carpological parametrs of A. negundo are the angle of divergence of mericarps (Cv=29%) and width of winglet (Cv=34%); the most constant characteristic is the width of fruits (Cv=6%). Prospects for further research are the study of the biology of seeds reproduction of A. negundo and other representatives of the genus Acer in the territory of the Northern Black Sea region.

Improvement of Torulaspora delbrueckii Genome Annotation: Towards the Exploitation of Genomic Features of a Biotechnologically Relevant Yeast

Saccharomyces cerevisiae is the most commonly used yeast in wine, beer, and bread fermentations. However, Torulaspora delbrueckii has attracted interest in recent years due to its properties, ranging from its ability to produce flavor- and aroma-enhanced wine to its ability to survive longer in frozen dough. In this work, publicly available genomes of T. delbrueckii were explored and their annotation was improved. A total of 32 proteins were additionally annotated for the first time in the type strain CBS1146, in comparison with the previous annotation available. In addition, the annotation of the remaining three T. delbrueckii strains was performed for the first time. eggNOG-mapper was used to perform the functional annotation of the deduced T. delbrueckii coding genes, offering insights into its biological significance, and revealing 24 clusters of orthologous groups (COGs), which were gathered in three main functional categories: information storage and processing (28% of the proteins), cellular processing and signaling (27%), and metabolism (23%). Small intraspecies variability was found when considering the functional annotation of the four available T. delbrueckii genomes. A comparative study was also conducted between the T. delbrueckii genome and those from 386 fungal species, revealing a high number of homologous genes with species from the Zygotorulaspora and Zygosaccharomyces genera, but also with Lachancea and S. cerevisiae. Lastly, the phylogenetic placement of T. delbrueckii was clarified using the core homologs that were found across 204 common protein sequences of 386 fungal species and strains.

To denoise or to cluster, that is not the question: optimizing pipelines for COI metabarcoding and metaphylogeography

Background The recent blooming of metabarcoding applications to biodiversity studies comes with some relevant methodological debates. One such issue concerns the treatment of reads by denoising or by clustering methods, which have been wrongly presented as alternatives. It has also been suggested that denoised sequence variants should replace clusters as the basic unit of metabarcoding analyses, missing the fact that sequence clusters are a proxy for species-level entities, the basic unit in biodiversity studies. We argue here that methods developed and tested for ribosomal markers have been uncritically applied to highly variable markers such as cytochrome oxidase I (COI) without conceptual or operational (e.g., parameter setting) adjustment. COI has a naturally high intraspecies variability that should be assessed and reported, as it is a source of highly valuable information. We contend that denoising and clustering are not alternatives. Rather, they are complementary and both should be used together in COI metabarcoding pipelines. Results Using a COI dataset from benthic marine communities, we compared two denoising procedures (based on the UNOISE3 and the DADA2 algorithms), set suitable parameters for denoising and clustering, and applied these steps in different orders. Our results indicated that the UNOISE3 algorithm preserved a higher intra-cluster variability. We introduce the program DnoisE to implement the UNOISE3 algorithm taking into account the natural variability (measured as entropy) of each codon position in protein-coding genes. This correction increased the number of sequences retained by 88%. The order of the steps (denoising and clustering) had little influence on the final outcome. Conclusions We highlight the need for combining denoising and clustering, with adequate choice of stringency parameters, in COI metabarcoding. We present a program that uses the coding properties of this marker to improve the denoising step. We recommend researchers to report their results in terms of both denoised sequences (a proxy for haplotypes) and clusters formed (a proxy for species), and to avoid collapsing the sequences of the latter into a single representative. This will allow studies at the cluster (ideally equating species-level diversity) and at the intra-cluster level, and will ease additivity and comparability between studies.

To denoise or to cluster? That is not the question. Optimizing pipelines for COI metabarcoding and metaphylogeography

The recent blooming of metabarcoding applications to biodiversity studies comes with some relevant methodological debates. One such issue concerns the treatment of reads by denoising or by clustering methods, which have been wrongly presented as alternatives. It has also been suggested that denoised sequence variants should replace clusters as the basic unit of metabarcoding analyses, missing the fact that sequence clusters are a proxy for species-level entities, the basic unit in biodiversity studies. We argue here that methods developed and tested for ribosomal markers have been uncritically applied to highly variable markers such as cytochrome oxidase I (COI) without conceptual or operational (e.g., parameter setting) adjustment. COI has a naturally high intraspecies variability that should be assessed and reported, as it is a source of highly valuable information. We contend that denoising and clustering are not alternatives. Rather, they are complementary and both should be used together in COI metabarcoding pipelines. Using a typical dataset from benthic marine communities, we compared two denoising procedures (based on the UNOISE3 and the DADA2 algorithms), set suitable parameters for denoising and clustering COI datasets, and compared the outcome of applying these processes in different orders. Our results indicate that denoising based on the UNOISE3 algorithm preserves a higher intra-cluster variability. We suggest and test ways to improve this algorithm taking into account the natural variability of each codon position in coding genes. The order of the steps (denoising and clustering) has little influence on the final outcome. We recommend researchers to consider reporting their results in terms of both denoised sequences (a proxy for haplotypes) and clusters formed (a proxy for species), and to avoid collapsing the sequences of the latter into a single representative. This will allow studies at the cluster (ideally equating species-level diversity) and at the intra-cluster level, and will ease additivity and comparability between studies.