Volumen 60 (2021): Edición 1 (January 2021)

The clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins are components of the adaptive immunity system, protecting against foreign DNA, which are present in many bacteria species. Recent years have brought extensive research on this system however, not all of its biological properties have been discovered so far. It was recently discovered that CRISPR-Cas can regulate the formation of biofilm and is closely associated with the DNA repair system in bacterial cells. It is also likely that some of the spacer sequences are complementary to short sequences in the bacterial genome, which may have an influence on regulation of bacterial genes, e.g. virulence factors. Besides, phages can synthesize anti-CRISPR genes, which could be of use in the future for the purpose of development of an alternative therapy against multi-drug resistant bacterial strains. Here we present an elementary characteristic of CRISPR-Cas system, including the structure and the brief mechanism of action, systematic classification and its importance for medicine and biotechnology issues. We would like to stress the huge potential of CRISPR-Cas by discussing the selected but varied aspects.

1. Introduction. 2. Structure, operation and differences. 3. Bacterial typing. 4. Correlation with bacterial pathogenicity. 5. Potential tool for medicine. 5.1. CRISPR-tool for genome editing. 5.2. Instances of CRISPR-tool strategies in medicine. 6. Phage response. 7. Conclusions

Starting from the end of 2019 the new SARs-CoV-2 virus, in the period of a few months, had spread to 210 countries and its territories. The Wuhan wild animal market, in Hubei province, China is considered the epicenter of this pandemic. WHO declared the name COVID-19 to designate the disease caused by the SARS-CoV-2 virus. It is the third coronavirus pandemic after SARS in 2002–2003 and MERS-CoV in 2012. Genome sequencing of this new COVID-19/SARS-CoV-2 virus shows slight genetic diversity when compared to other coronaviruses. Owing to its pathogenesis, and less known replication cycle, no universal antiviral treatment can be applied and vaccine preparation is still a larger challenge. The present article will highlight transmission, pandemic status, genetic diversity current antiviral therapy, and vaccine trials for COVID-19.

1. Introduction. 2. Pathogenesis of coronaviruses. 3. Genetic diversity. 4. Transmission. 5. Vaccination strategies against COVID-19. 6. In Process Vaccination strategies against COVID-19. 7. Lack of antiviral treatment and antiviral treatment studies. 8. Precautions. 9. Conclusions

Microbiological studies show that there is a possibility of PMI estimation in reference to presence of typical bacteria and fungi on cadaver or in soil beneath. Microbiome after death (thanatomicrobiome) changes and depends on time since death, temperature, seasons and environment-if human remains are covered, buried, placed in ice or left on the surface. To enlarge current knowledge, some of studies are conducted on animal models with further comparison thanatomicrobiome of different animals-pig, rats-to human cadaver thanatomicrobiome. This study collects different branches of thanatomicrobiome studies as a review to summarize current knowledge.

1. Introduction. 2. Living host microbiome and mycobiome. 3. Diseases-related differences. 4. Thanatomicrobiome – human cadavers studies. 5. Fungi presence – thanatomycobiome. 6. Thanatomicrobiome of frozen cadavers. 7. Soil microbial communities changes. 8. Seasons related microbial changes. 9. Thanatomicrobiome and entomology correlation. 10. Conclusions

Fungal diseases affect over 300 million people worldwide each year and cause over 1.6 million deaths. Even with such a high prevalence of fungal infections, relatively few fungal species are pathogens, and invasive fungal infections are rarely diagnosed in healthy subjects. Comparative analyses of mycobiomes reveal that the human organism is colonized by specific fungi soon after birth, and the quantitative and qualitative composition of the mycobiota changes throughout life. In recent years, correlations between the mycobiome structure and health status, also in disease conditions, have been analyzed at the level of fungus-mycobiome-host interactions. The relationship between the colonized area of the human body defined as anatomical location, and fungal species specific for this area, indicates a strong selective pressure that promotes the growth of species specific for a given ecological niche within the organism. Another issue is the validation and standardization of mycobiome analysis methods. In this respect, metagenomic sequencing methods are currently arousing considerable interest. The review presents the current knowledge about the mycobiome in physiological and disease states induced by the dysbiosis of the existing microbiome. The methods and diagnostic challenges in the quantitative and qualitative analysis of mycobiomes are discussed as well.

1. Introduction. 2. Mycobiome in health and disease states. 2.1. Pulmonary mycobiome. 2.2. Intestinal mycobiome. 2.3. Skin mycobiome. 2.4. Mycobiome and neurological disorders. 2.5. Environmental mycobiome. 3. Mycobiome studies in clinical practice. 4. Analysis of mycobiomes: methodologies and challenges. 4.1. Sample processing. 4.2. Amplicon sequencing. 4.3. Metagenomic sequencing. 4.4. Bioinformatics challenges. 5. Summary

The oral cavity is colonized by more than 700 bacterial species. They occur in the form of individual cells or form multispecies biofilms. The formation of biofilm, its abnormal growth combined with impaired functioning of the defense mechanisms of the body and disorders in the quantitative and qualitative composition of the oral microbiota can lead to the development of caries, gingival inflammation, parodontosis or peri-implantitis. The paper discusses the stages of biofilm formation as well as microbial interactions within this organized community. It also addresses the significance of multispecies biofilm in oral infections and, very importantly, the methods to combat it.

1. Biofilm – definition, formation stages, microbial communication within biofilm. 2. Biofilm in different parts of the human body. 3. Multispecies oral biofilm. 4. Oral infections associated with multispecies biofilm. 5. Prevention and methods of combating oral biofilm. 5.1. Prophylaxis and proper oral hygiene. 5.2. Alternative therapy of biofilm-related oral infections. 6. Summary

Modern research in food science and nutrition is transferring from classical methodologies to advanced molecular strategies in which next-generation sequencing (NGS) technology plays a crucial role. In this context, Foodomics has been recently defined as a new and global field using advanced “omics” technologies in food analysis. In recent years, “food-omics” technologies are widely applicated in food microbiology to identify, quantify and to track food microbial consortia in the food chain, as well as in the food safety and quality assessment. Metagenomics, referred to as community genomics is a sequence-based analysis of the collective genomes of microorganisms present in a given environment. This rapidly developing technique has provided new knowledge about taxonomic diversity and the dynamics of microbial communities at the genus, species and even strain level. An comprehensive metagenomic approach has proven to be a powerful tool in profiling the microbial ecology of complex ecosystems such as fermented foods. Currently, research focuses on understanding and controlling the fermentation process to ensure the consistent sensory properties of food products, increase safety and reduce food spoilage. The goal of this review is to provide an overview of the latest achievements of the “food-omics” technologies applied to biodiversity and functionality of food microflora, food safety and quality control. Furthermore, we discuss current challenges and future applications of “food-omics” technologies in the food industry.

1. Introduction. 2. Methodologies and technologies in the field of food-omics. 3. Application of “food-omics” technology in food analysis. 3.1. Metagenomics as a tool for monitoring the fermentation process. 3.2. Monitoring food storage conditions. 3.3. Food safety monitoring. 4. Summary

Sandboxes are present on almost every playground. They enjoy constant popularity among the youngest. Are we sometimes wonder who is responsible for their sanitary condition? Play in them can be a threat to children? This article will discuss the subject of monitoring the sanitary condition of sandboxes. The microbiological threat of contact with contaminated sand will also be presented. Escherichia coli and Staphylococcus aureus are bacteria that can inhabit sandboxes and pose a threat to health. Both of these microorganisms should not be found in the environment. Their presence means contamination of sand, and contact with it can be hazardous to human health. What’s more, these bacteria increasingly show resistance to antibiotics routinely used to treat infections. The problem of microorganism resistance to therapeutics is very important because the number of drug-resistant strains is growing alarmingly. The pool of effective antibiotics is contracting and new ones are not developing. In this work, antibiotics used during the treatment will be presented: aminoglycosides, ansamycins, β-lactam antibiotics, quinolones, fusidans, MLS group, sulfonamides, and tetracyclines. The paper also presents information concerning so far known mechanisms of antibiotic action. The article also presents the resistance mechanisms of Enterobacteriaceae; ESBL mechanism (extended-spectrum β-lactamases), production of MBL (metallo-β-lactamase), CRE (carbapenem-resistant Enterobacteriaceae) and resistance mechanisms of S. aureus, to penicillin, MRSA – methicillin-resistant S. aureus, and for vancomycin VRSA resistant S. aureus. Drug resistance has become a global problem. The presence of drug-resistant strains carries the risk of spreading antibiotic-resistant strains of microorganisms in natural environments like water, air, soil and sand. Infections caused by such microorganisms are very difficult to treat, because the small pool of antibiotics that can be used during treatment, and thus reduces the effectiveness of therapy.

1. Introduction. 2. Monitoring of the sandboxes sanitary condition. 3. 3. Bacteria E. coli and S. aureus as a potential health hazard factor. 4. Antibiotics characteristic. 4.1. Antibiotics grups. 4.2. Mechanism of antibiotics action. 5. Antibiotic resistance. 5.1. Resistance of Enterobacteriaceae. 5.2. Resistance of S. aureus 6. Resistance as a global problem. 7. Conclusions. 8. Bibilography

The infections caused by orthohantaviruses were already known in the Middle Ages as “English sweats.” There are two main diseases caused by these viruses – HPS (hantavirus pulmonary syndrome) and HFRS (hemorrhagic fever with renal syndrome). Rodents are the main reservoir of these microorganisms, and humans usually catch them by inhalation, as a result of contact with secretions and droppings of carriers. HPS is characterized by a sudden onset, and symptoms include primarily cough, fever and difficulty breathing, and in extreme cases – respiratory failure and cardiogenic shock. HFRS begins suddenly and the main manifestation includes fever, renal failure, hemorrhage, hematuria and proteinuria, as well as shock. At present, anti-hantavirus therapy with proven effectiveness does not exist. A key role in the treatment is resting lifestyle, electrolyte control, fluid therapy and prevention of hypotension, and in harder cases – administration of oxygen. Deviations from normal values in laboratory analyzes of people infected with this pathogen depend on the organ affected by the disease process

1. History 2. Systematics of Orthohantavirus spp. genus 3. Morphology 3.1. Genome 3.2. Structure of the virion 4. Mechanism of infection 4.1. Route of infection 4.2. Life cycle 5. Pathogenicity 6. Treatment 7. Diagnostics 8. Prevention – vaccines 9. Summary