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Opis: Clostridioides (Clostridium) difficile is the most commonly recognized cause of infectious diarrhea in healthcare settings. Currently there is no vaccine to prevent initial or recurrent C. difficile infection (CDI). Two large clostridial toxins, TcdA and TcdB, are the primary virulence factors for CDI. Immunological approaches to prevent CDI include antibody-mediated neutralization of the cytotoxicity of these toxins. An understanding of the sequence diversity of the two toxins expressed by disease causing isolates is critical for the interpretation of the immune response to the toxins. In this study, we determined the whole genome sequence (WGS) of 478 C. difficile isolates collected in 12 countries between 2004 and 2018 to probe toxin variant diversity. A total of 44 unique TcdA variants and 37 unique TcdB variants were identified. The amino acid sequence conservation among the TcdA variants (>98%) is considerably greater than among the TcdB variants (as low as 86.1%), suggesting that different selection pressures may have contributed to the evolution of the two toxins. Phylogenomic analysis of the WGS data demonstrate that isolates grouped together based on ribotype or MLST code for multiple different toxin variants. These findings illustrate the importance of determining not only the ribotype but also the toxin sequence when evaluating strain coverage using vaccine strategies that target these virulence factors. We recommend that toxin variant type and sequence type (ST), be used together with ribotype data to provide a more comprehensive strain classification scheme for C. difficile surveillance during vaccine development objectives.
Ključne besede: Clostridioides difficile, Clostridium difficile, TCDB, TcdA, vaccines, whole genome sequencing
Objavljeno v DKUM: 28.01.2025; Ogledov: 0; Prenosov: 5
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Opis: Introduction: Although the distinction between the Community-Associated-Methicillin-Resistant Staphylococcus aureus (CA-MRSA) and Hospital-Associated-Methicillin-Resistant S. aureus (HA-MRSA) has blurred in recent years, the CA-MRSA is an important group because of its potential to cause fulminant and severe infections. Its importance has further increased with the emergence of Livestock-Associated-Methicillin-Resistant S. aureus (LA-MRSA). Methods: In the present study we analysed clonal distributions and virulence factors in presumptive CA-MRSA isolated from January 2014 to December 2015 and compared the results with our previous study from 2010. Phenotypic definition for presumptive CA-MRSA was based on resistance to cefoxitin and oxacillin and susceptibility to at least two of the following four antibiotics: ciprofloxacin, erythromycin, clindamycin and gentamicin. Results:In 2014 and 2015 altogether 304 MRSA isolates fulfilled our screening phenotypic definition, 45 isolates were cultivated from clinical specimens and 259 from screening specimens. Sequence types ST398, LA-MRSA and mecC MRSA increased significantly in 2015 compared to 2010 (p-value <0.05) and were spread over Slovenia. Conclusion:The clonal distribution of presumptive CA-MRSA has changed within the study period in Slovenia. In 2015 the most frequent clone among clinical and screening specimens was a pig-associated clone, ST398, but the number of confirmed ST398 infections remains low. While previously ST398 and mecC positive MRSA strains were geographically limited, they have spread throughout the country since 2010.
Ključne besede: Slovenia, CA-MRSA, LA-MRSA, mecC, spa types, clones
Objavljeno v DKUM: 20.01.2025; Ogledov: 0; Prenosov: 403
Celotno besedilo (1,32 MB)
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Opis: The aim of the present study was to characterize human milk microbiota (HMM) with 16S rRNA gene amplicon next-generation sequencing and cultivation/matrix-assisted laser desorption/ionization (MALDI)-time of flight (TOF) mass spectrometry (MS) identification approaches. We analyzed 31 human milk samples from healthy Slovenian mothers. To check the accuracy of MALDI-TOF MS identification, several colonies representing most abundant genera and those, which could not be reliably identified by MALDI-TOF, were subjected to Sanger sequencing of their 16S rRNA gene. We showed that cultivation/MALDI-TOF MS was a suitable tool for culture-dependent determination of HMM. With both approaches, Staphylococcus and Streptococcus were found as predominant genera in HMM and the abundance of Staphylococcus was associated with decreased microbial diversity. In addition, we characterized factors that might influence HMM. The use of a breast pump was significantly associated with composition of HMM, higher microbial load, and lower abundance of cultivable staphylococci. Moreover, our study suggests that administration of probiotics to the suckling infant might influence HMM by increased abundance of lactobacilli and the presence of viable probiotic bacteria in human milk. However, since our study was observational with relatively small sample size, more targeted studies are needed to study possible transfer of probiotics to the mammary gland via an external route and the physiological relevance of these events.
Ključne besede: milk microbiota, microbiota assembly, breastfeeding, breast pump, probiotic drops
Objavljeno v DKUM: 27.12.2024; Ogledov: 0; Prenosov: 3
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Opis: Clostridioides difficile is often found in animals and their environment. However, not much has been reported on veterinary clinics environment in terms of the spore load, prevalence and PCR ribotype diversity. The aim of this study was to assess the prevalence of C. difficile on shoe soles of veterinarians, veterinary support staff and veterinary students at the Veterinary Faculty campus. Altogether, 50 shoe sole swabs were collected, and the positivity rates ranged from 86.7% in swabs from veterinarians to 100% in swabs from support staff and students. Non-toxigenic and toxigenic strains representing toxinotypes 0, IV and XIX were isolated and distributed into 17 different PCR ribotypes, most common being 010, 014/020, SLO002 and 009. PCR ribotype 010 was the most prevalent and isolated from shoe soles sampled in 6/7 areas. Students' shoes had highest ribotype diversity (15/17 PCR ribotypes) but showed a low overlap with ribotype isolated from vets and support staff shoes. Veterinary students are likely the main vectors of C. difficile spores transmissions among veterinary teaching clinics and the hospital.
Ključne besede: Clostridioides (Clostridium) difficile, environment, footwear, One Health, transmission, veterinary clinic
Objavljeno v DKUM: 22.10.2024; Ogledov: 0; Prenosov: 1
Celotno besedilo (1,33 MB)
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Opis: Microbiota analysis can provide valuable insights in various fields, including diet and nutrition, understanding health and disease, and in environmental contexts, such as understanding the role of microorganisms in different ecosystems. Based on the results, we can provide targeted therapies, personalized medicine, or detect environmental contaminants. In our research, we examined the gut microbiota of 16 animal taxa, including humans, as well as the microbiota of cattle and pig manure, where we focused on 16S rRNA V3-V4 hypervariable regions. Analyzing these regions is common in microbiome studies but can be challenging since the results are high-dimensional. Thus, we utilized machine learning techniques and demonstrated their applicability in processing microbial sequence data. Moreover, we showed that techniques commonly employed in natural language processing can be adapted for analyzing microbial text vectors. We obtained the latter through frequency analyses and utilized the proposed hierarchical clustering method over them. All steps in this study were gathered in a proposed microbial sequence data processing pipeline. The results demonstrate that we not only found similarities between samples but also sorted groups’ samples into semantically related clusters. We also tested our method against other known algorithms like the Kmeans and Spectral Clustering algorithms using clustering evaluation metrics. The results demonstrate the superiority of the proposed method over them. Moreover, the proposed microbial sequence data pipeline can be utilized for different types of microbiota, such as oral, gut, and skin, demonstrating its reusability and robustness.
Ključne besede: machine learning, NLP, hierarchical clustering, microbial data, microbiome, n-grame
Objavljeno v DKUM: 04.09.2024; Ogledov: 38; Prenosov: 9
Celotno besedilo (4,48 MB)