Correction: Kurpas et al. Genomic Analysis of SARS-CoV-2 Alpha, Beta and Delta Variants of Concern Uncovers Signatures of Neutral and Non-Neutral Evolution. Viruses 2022, 14, 2375.

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A Comprehensive Virulence and Resistance Characteristics of Listeria monocytogenes Isolated from Fish and the Fish Industry Environment.

Listeria monocytogenes is an important pathogen, often associated with fish, that can adapt and survive in products and food processing plants, where it can persist for many years. It is a species characterized by diverse genotypic and phenotypic characteristics. Therefore, in this study, a total of 17 L. monocytogenes strains from fish and fish-processing environments in Poland were characterized for their relatedness, virulence profiles, and resistance genes. The Core Genome Multilocus Sequence Typing (cgMLST) analysis revealed that the most frequent serogroups were IIa and IIb; sequence types (ST) were ST6 and ST121; and clonal complexes (CC) were CC6 and CC121. Core genome multilocus sequence typing (cgMLST) analysis was applied to compare the present isolates with the publicly available genomes of L. monocytogenes strains recovered in Europe from humans with listeriosis. Despite differential genotypic subtypes, most strains had similar antimicrobial resistance profiles; however, some of genes were located on mobile genetic elements that could be transferred to commensal or pathogenic bacteria. The results of this study showed that molecular clones of tested strains were characteristic for L. monocytogenes isolated from similar sources. Nevertheless, it is worth emphasizing that they could present a major public health risk due to their close relation with strains isolated from human listeriosis.

Genomic Analysis of SARS-CoV-2 Alpha, Beta and Delta Variants of Concern Uncovers Signatures of Neutral and Non-Neutral Evolution.

Due to the emergence of new variants of the SARS-CoV-2 coronavirus, the question of how the viral genomes evolved, leading to the formation of highly infectious strains, becomes particularly important. Three major emergent strains, Alpha, Beta and Delta, characterized by a significant number of missense mutations, provide a natural test field. We accumulated and aligned 4.7 million SARS-CoV-2 genomes from the GISAID database and carried out a comprehensive set of analyses. This collection covers the period until the end of October 2021, i.e., the beginnings of the Omicron variant. First, we explored combinatorial complexity of the genomic variants emerging and their timing, indicating very strong, albeit hidden, selection forces. Our analyses show that the mutations that define variants of concern did not arise gradually but rather co-evolved rapidly, leading to the emergence of the full variant strain. To explore in more detail the evolutionary forces at work, we developed time trajectories of mutations at all 29,903 sites of the SARS-CoV-2 genome, week by week, and stratified them into trends related to (i) point substitutions, (ii) deletions and (iii) non-sequenceable regions. We focused on classifying the genetic forces active at different ranges of the mutational spectrum. We observed the agreement of the lowest-frequency mutation spectrum with the Griffiths-Tavaré theory, under the Infinite Sites Model and neutrality. If we widen the frequency range, we observe the site frequency spectra much more consistently with the Tung-Durrett model assuming clone competition and selection. The coefficients of the fitting model indicate the possibility of selection acting to promote gradual growth slowdown, as observed in the history of the variants of concern. These results add up to a model of genomic evolution, which partly fits into the classical drift barrier ideas. Certain observations, such as mutation "bands" persistent over the epidemic history, suggest contribution of genetic forces different from mutation, drift and selection, including recombination or other genome transformations. In addition, we show that a "toy" mathematical model can qualitatively reproduce how new variants (clones) stem from rare advantageous driver mutations, and then acquire neutral or disadvantageous passenger mutations which gradually reduce their fitness so they can be then outcompeted by new variants due to other driver mutations.

Rare Occurrence of Blastocystis in Pet Animals and Their Owners in the Pomeranian Voivodeship in Poland in the Light of Literature Data.

Blastocystis is an intestinal microeukaryote with ambiguous pathogenicity, commonly detected in human feces worldwide. It comprises at least 28 genetically diverse subtypes (STs), 12 of which also occur in a wide range of animal species, giving rise to suspicion of zoonotic transmission. To investigate this, we conducted a molecular study of 145 stool samples of pet animals, and 67 of their owners, living in an urban area in Poland. Blastocystis was detected in only three (2.1%) animal samples (of two bearded agamas and a leopard gecko), while all dogs, cats, and pet rodents were Blastocystis-negative. Blastocystis was also present in three (4.5%) owners of animals, but they were cat owners, not reptile owners, and the subtypes identified in them differed significantly from those of reptiles. Additionally, the frequency of Blastocystis in different groups of dogs (depending on how they were kept) was analyzed. This work is the first to find Blastocystis in pet reptiles, and we encourage further investigation of Blastocystis in this poorly examined group of animals, as well as continued study on the transmission of this microorganism between humans and animals.

Effect of Manual Therapy Compared to Ibuprofen on Primary Dysmenorrhea in Young Women-Concentration Assessment of C-Reactive Protein, Vascular Endothelial Growth Factor, Prostaglandins and Sex Hormones.

BACKGROUND: The study aimed to assess if manual therapy, compared to ibuprofen, impacts the concentration of inflammatory factors, sex hormones, and dysmenorrhea in young women Methods: Thirty-five women, clinically diagnosed with dysmenorrhea, were included in the study. They were divided into group A-manual therapy (n = 20) and group B-ibuprofen therapy (n = 15). Inflammatory factors such as vascular endothelial growth factor (VEGF), C-reactive protein (CRP), prostaglandin F2α (PGF2α), E2 (PGE2) and sex hormones levels were measured. Dysmenorrhea assessed with the numerical pain rating scale (NPRS), myofascial trigger points, and muscle flexibility were examined before and after the interventions. RESULTS: The difference in the level of 17-ß-estradiol after manual and ibuprofen therapy was significant, as compared to baseline (p = 0.036). Progesterone levels decreased in group A (p = 0.002) and B (p = 0.028). The level of CRP was negatively correlated with sex hormones. Decrease in dysmenorrhea was significant in both groups (group A p = 0.016, group B p = 0.028). Non-significant differences were reported in prostaglandins, VEGF and CRP levels, in both groups. CONCLUSIONS: There were no significant differences in CRP, prostaglandins and VEGF factors after manual or ibuprofen therapy. It has been shown that both manual therapy and ibuprofen can decrease progesterone levels. Manual therapy had a similar effect on the severity of dysmenorrhea as ibuprofen, but after manual therapy, unlike after ibuprofen, less muscles with dysfunction were detected in patients with primary dysmenorrhea.

Environmental Factors and the Risk of Developing Type 1 Diabetes-Old Disease and New Data.

The incidence of type 1 diabetes (T1D) is increasing worldwide. The onset of T1D usually occurs in childhood and is caused by the selective destruction of insulin-producing pancreatic islet cells (ß-cells) by autoreactive T cells, leading to insulin deficiency. Despite advanced research and enormous progress in medicine, the causes of T1D are still not fully understood. Therefore, an extensive online search for scientific research on environmental factors associated with diabetes and the identification of new factors of unexplained etiology has been carried out using the PubMed, Cochrane, and Embase databases. The search results were limited to the past 11 years of research and discovered 143 manuscripts published between 2011 and 2022. Additionally, 21 manuscripts from between 2000 and 2010 and 3 manuscripts from 1974 to 2000 were referenced for historical reference as the first studies showcasing a certain phenomenon or mechanism. More and more scientists are inclined to believe that environmental factors are responsible for the increased incidence of diabetes. Research results show that higher T1D incidence is associated with vitamin D deficiency, a colder climate, and pollution of the environment, as well as the influence of viral, bacterial, and yeast-like fungi infections. The key viral infections affecting the risk of developing T1DM are rubella virus, mumps virus, Coxsackie virus, cytomegalovirus, and enterovirus. Since 2020, i.e., from the beginning of the COVID-19 pandemic, more and more studies have been looking for a link between Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and diabetes development. A better understanding of the role of viral, bacterial, and yeast-like fungi infections related to the risk of T1DM in children and adolescents and the identification of new risk factors, especially those spread by the droplet route, is of great importance for people and families with diabetes.

Modes of Selection in Tumors as Reflected by Two Mathematical Models and Site Frequency Spectra.

The tug-of-war model was developed in a series of papers of McFarland and co-authors to account for existence of mutually counteracting rare advantageous driver mutations and more frequent slightly deleterious passenger mutations in cancer. In its original version, it was a state-dependent branching process. Because of its formulation, the tug-of-war model is of importance for tackling the problem as to whether evolution of cancerous tumors is "Darwinian" or "non-Darwinian." We define two Time-Continuous Markov Chain versions of the model, including identical mutation processes but adopting different drift and selection components. In Model A, drift and selection process preserves expected fitness whereas in Model B it leads to non-decreasing expected fitness. We investigate these properties using mathematical analysis and extensive simulations, which detect the effect of the so-called drift barrier in Model B but not in Model A. These effects are reflected in different structure of clone genealogies in the two models. Our work is related to the past theoretical work in the field of evolutionary genetics, concerning the interplay among mutation, drift and selection, in absence of recombination (asexual reproduction), where epistasis plays a major role. Finally, we use the statistics of mutation frequencies known as the Site Frequency Spectra (SFS), to compare the variant frequencies in DNA of sequenced HER2+ breast cancers, to those based on Model A and B simulations. The tumor-based SFS are better reproduced by Model A, pointing out a possible selection pattern of HER2+ tumor evolution. To put our models in context, we carried out an exploratory study of how publicly accessible data from breast, prostate, skin and ovarian cancers fit a range of models found in the literature.

Mold and Yeast-Like Fungi in the Seaside Air of the Gulf of Gdansk (Southern Baltic) after an Emergency Disposal of Raw Sewage.

The aim of this study was to determine the correlation between the meteorological factors and the number of molds and yeast-like fungi in the air in the five coastal towns in the years 2014-2017, and in 2018, after emergency disposal of raw sewage to the Gdansk Gulf. In the years 2014-2018, a total number of 88 air samples were collected in duplicate in the five coastal towns of Hel, Puck, Gdynia, Sopot, and Gdansk-Brzezno. After the application of the (PCA) analysis, this demonstrated that the first principal component (PC1) had a positive correlation with the water temperature, wind speed, air temperature, and relative humidity. The second principal component (PC2) had a positive correlation with the relative humidity, wind speed, wind direction, and air temperature. In 2018, potentially pathogenic mold and yeast-like fungi (Candida albicans, Stachybotrys chartarum complex, Aspergillus section Fumigati) were detected in the seaside air. While the detected species were not observed in the years 2014-2017. We suggest that it is advisable to inform residents about the potential health risk in the event of raw sewage disposal into the water. Moreover, in wastewater treatment plants, tighter measures, including wastewater disinfection, should be introduced.

First report of the presence of Vibrio vulnificus in the Gulf of Gdansk.

BACKGROUND: Vibrio infections are becoming more frequent in the Baltic Sea region, which is caused by an increase in the sea surface temperature. Climate change creates the conditions for the emergence of new environmental niches that are beneficial for Vibrio spp., especially in the summer months. Vibrio vulnificus, which causes wound infections and septicaemia, represents a particularly dangerous species of Vibrio spp. There are numerous publications on the prevalence of V. vulnificus in various regions of the Baltic Sea, but there is a lack of such data for the Polish coast. This prompted us to conduct a pilot study into the prevalence of the bacteria in the Gulf of Gdansk. The study aimed to detect Vibrio spp. in the coastal waters and the wet sand at the beaches and bathing areas in the Gulf of Gdansk. MATERIALS AND METHODS: During the period from June 16th to September 23rd 2020, 112 samples of seawater and 105 samples of wet sand were collected at 16 locations along the coast of the Gulf of Gdansk and Hel peninsula. Isolation of Vibrio spp. was conducted by filtering method and the isolated bacteria was cultured on CHROM agar Vibrio and TCBS agar. Final genus identification was performed by the MALDI TOF technique. RESULTS: In the present study, 10 isolates of Vibrio spp. were obtained from seawater and wet sand samples collected in the Gulf of Gdansk and Hel peninsula coast. Three of the isolates were identified as V. vulnificus; the presence of the species was confirmed in the seawater samples which had been collected in Hel (1 isolate), Jastarnia (1 isolate), and Chalupy (1 isolate). One strain of Vibrio alginolyticus was isolated from the seawater sample collected in Hel. Moreover, identification was incomplete for 6 of the isolated strains, these were identified as Vibrio cholerae/mimicus These strains were collected in Jastarnia (1 isolate), Kuznica (1 isolate), Gdansk-Brzezno (1 isolate), Puck (2 isolates), Chalupy (1 isolate). CONCLUSIONS: Our preliminary research study confirmed the presence of potentially pathogenic V. vulnificus in the Gulf of Gdansk in the summer months. Therefore, further monitoring of the presence of Vibrio spp. in the Baltic coast area is necessary.

Genomic Characterization of Listeria monocytogenes Isolated From Ready-to-Eat Meat and Meat Processing Environments in Poland.

Listeria monocytogenes is one of the major foodborne pathogens. Isolates of PCR-serogroups IIb (n = 17) and IVb (n = 31) recovered from food (n = 33) and food processing environment (n = 15) in Poland were characterized using whole genome sequencing. Most isolates belonged to Multi-Locus Sequence Type (MLST) ST2 (31.3%) and ST5 (22.9%). Core genome MLST (cgMLST) analysis classified isolates into seven sublineages (SL) and 25 different cgMLST types (CT). Consistent with the MLST results, most sublineages were SL2 and SL5. Eleven isolates harbored aacA4 encoding resistance to aminoglycosides, three isolates harbored emrC (n = 3) and one brcABC (n = 1) encoding tolerance to benzalkonium chloride. Isolates belonging to SL5 CT2323 carried a so far unreported inlB allele with a deletion of 141 nucleotides encoding the ß-repeat sheet and partially the GW1 domain of InlB. Comparison with publicly available genome sequences from L. monocytogenes isolated from human listeriosis cases in Poland from 2004 to 2013 revealed five common CTs, suggesting a possible epidemiological link with these strains. The present study contributes to characterize the diversity of L. monocytogenes in ready-to-eat (RTE) meat and meat processing environments in Poland and unravels previously unnoticed links with clinical cases in Europe.

Ready-to-eat Meat Products As a Source of Listeria Monocytogenes.

In 2015 in the European Union member states listeriosis caused 270 deaths. Food is the route of transmission in 99% of all human infection cases. Several studies from different countries have shown that the presence of Listeria monocytogenes in food can be as high as 58.3%. One of the most important ways to protect food from these microorganisms is to prevent the spread of the bacteria at processing plants at different stages of food production chain. The ability of L. monocytogenes to survive in extreme conditions and to form biofilms on various surfaces is a significant challenge for food safety. Removal of these bacteria from niches in processing plants is difficult and requires the use of sanitisers and precise equipment cleaning. The presence of L. monocytogenes in processing environment at slaughterhouses, deli meat factories or in retail may be a reason of cross-contamination. Proper hygienic systems applied by workers in food preparing places and knowledge about different routes of spreading of these bacteria may effectively decrease the risk of food contamination. Standardised legal regulations and control of meat product manufacture should be a fundamental way to protect food from L. monocytogenes contamination.

A novel mathematical model of ATM/p53/NF- κB pathways points to the importance of the DDR switch-off mechanisms.

BACKGROUND: Ataxia telangiectasia mutated (ATM) is a detector of double-strand breaks (DSBs) and a crucial component of the DNA damage response (DDR) along with p53 and NF- κB transcription factors and Wip1 phosphatase. Despite the recent advances in studying the DDR, the mechanisms of cell fate determination after DNA damage induction is still poorly understood. RESULTS: To investigate the importance of various DDR elements with particular emphasis on Wip1, we developed a novel mathematical model of ATM/p53/NF- κB pathways. Our results from in silico and in vitro experiments performed on U2-OS cells with Wip1 silenced to 25 % (Wip1-RNAi) revealed a strong dependence of cellular response to DNA damages on this phosphatase. Notably, Wip1-RNAi cells exhibited lower resistance to ionizing radiation (IR) resulting in smaller clonogenicity and higher apoptotic fraction. CONCLUSIONS: In this article, we demonstrated that Wip1 plays a role as a gatekeeper of apoptosis and influences the pro-survival behaviour of cells - the level of Wip1 increases to block the apoptotic decision when DNA repair is successful. Moreover, we were able to verify the dynamics of proteins and transcripts, apoptotic fractions and cells viability obtained from stochastic simulations using in vitro approaches. Taken together, we demonstrated that the model can be successfully used in prediction of cellular behaviour after exposure to IR. Thus, our studies may provide further insights into key elements involved in the underlying mechanisms of the DDR.