Strain Typing Research Articles

Elaborating the microbial mechanism of humic substance formation during lignocellulosic biomass composting by inoculation with different functional microbes

This study explored the microbial mechanism of humic substance (HS) formation in the lignocellulosic biomass composting by inoculation with different functional microbes. Typical types of functional bacterial and fungal strains with higher lignocellulose degradation characteristics were inoculated into compost. Three treatment groups were set up: uninoculated microbes (CK treatment), inoculation of Bacillus subtilis (B4 treatment) and Aspergillus fumigatus (Z1 treatment). Results showed that the HS concentration for inoculation B. subtilis and A. fumigatus increased by 15.42% and 56.31%, respectively. B. subtilis could produce phenolic metabolites, cellobiose and maltose, and then enter the tricarboxylic acid cycle, thereby releasing CO2, while A. fumigatus could promote HS formation by producing phenolic metabolites, 2,4-Di-tert-butylphenol, cellobiose, maltose, glucose, galactose, xylose, arabinose, mannose, ribose and deoxyribose. In addition, inoculating A. fumigatus enhanced the correlation among lignocellulose-degrading metabolites and HS, and increased the relative abundance and numbers of microbial hosts of lignocellulose-degrading genes, promoting the HS formation. In addition, cellulose-degrading genes and lignin-degrading genes differences were the main drivers of HS formation in the inoculated treatment groups. Soluble sugar, organic matter, lignin and pH were key drivers in influencing the lignocellulose-degrading genes. This study was important for analyzing microbial biological mechanisms of HS formation during composting.

Global research trends of Mycoplasma pneumoniae pneumonia in children: a bibliometric analysis

BackgroundMycoplasma pneumoniae pneumonia (MPP), attributable to Mycoplasma pneumoniae (MP), represents a predominant form of community-acquired pneumonia in pediatric populations, thereby posing a significant threat to pediatric health. Given the burgeoning volume of research literature associated with pediatric MPP in recent years, it becomes imperative to undertake a bibliometric analysis aimed at delineating the current research landscape and emerging trends, thereby furnishing a framework for subsequent investigations.MethodsA comprehensive literature search targeting pediatric MPP was conducted in the Web of Science Core Collection. After the removal of duplicate entries through Endnote software, the remaining articles were subject to scientometric analysis via Citespace software, VOSviewer software and R language, focusing on variables such as publication volume, contributing nations, institutions and authors, references and keywords.ResultsA total of 1,729 articles pertinent to pediatric MPP were included in the analysis. China and the United States emerged as the nations with the highest publication output. Italian scholar Susanna Esposito and Japanese scholar Kazunobu Ouchi were the most influential authors in the domain of pediatric MPP. Highly-cited articles primarily focused on the epidemiological investigation of pediatric MPP, the clinical characteristics and treatment of macrolide-resistant MPP, and biomarkers for refractory Mycoplasma pneumoniae pneumonia (RMPP). From the corpus of 1,729 articles, 636 keywords were extracted and categorized into ten clusters: Cluster #0 centered on molecular-level typing of macrolide-resistant strains; Cluster #1 focused on lower respiratory tract co-infections; Clusters #2 and #6 emphasized other respiratory ailments caused by MP; Cluster #3 involved biomarkers and treatment of RMPP; Clusters #4 and #9 pertained to extrapulmonary complications of MPP, Clusters #5 and #7 addressed etiological diagnosis of MPP, and Cluster #8 explored pathogenic mechanisms.ConclusionsThe past few years have witnessed extensive attention directed towards pediatric MPP. Research in pediatric MPP principally revolves around diagnostic techniques for MP, macrolide resistance, complications of MPP, treatment and diagnosis of RMPP, and elucidation of pathogenic mechanisms. The present study provides pediatric clinicians and researchers with the research status and focal points in this field, thereby guiding the orientation of future research endeavors.

A Managerial Approach towards Modeling the Different Strains of the COVID-19 Virus Based on the Spatial GeoCity Model.

This study proposes a modification of the GeoCity model previously developed by the authors, detailing the age structure of the population, personal schedule on weekdays and working days, and individual health characteristics of the agents. This made it possible to build a more realistic model of the functioning of the city and its residents. The developed model made it possible to simulate the spread of three types of strain of the COVID-19 virus, and to analyze the adequacy of this model in the case of unhindered spread of the virus among city residents. Calculations based on the proposed model show that SARS-CoV 2 spreads mainly from contacts in workplaces and transport, and schoolchildren and preschool children are the recipients, not the initiators of the epidemic. The simulations showed that fluctuations in the dynamics of various indicators of the spread of SARS-CoV 2 were associated with the difference in the daily schedule on weekdays and weekends. The results of the calculations showed that the daily schedules of people strongly influence the spread of SARS-CoV 2. Under assumptions of the model, the results show that for the more contagious "rapid" strains of SARS-CoV 2 (omicron), immunocompetent people become a significant source of infection. For the less contagious "slow strains" (alpha) of SARS-CoV 2, the most active source of infection is immunocompromised individuals (pregnant women). The more contagious, or "fast" strain of the SARS-CoV 2 virus (omicron), spreads faster in public transport. For less contagious, or "slow" strains of the virus (alpha), the greatest infection occurs due to work and educational contacts.

First principles study on strain effect of hydrogen diffusion and dissolution behavior in Ruthenium

In this work, the role of three kinds of strain, such as volumetric, biaxial and shear strain, in the dissolution and diffusion of Hydrogen (H) in Ruthenium (Ru) were studied by using first-principles simulation method. It was found that under volumetric or biaxial strains, the dissolution energy of H in Ru increases with the increase of compressive strain and decreases with the increase of tensile strain. For shear strain, the effect of strain on the dissolution energy of H in Ru relies on the crystal plane to which the strain is applied. The diffusion coefficients of H in Ru are different along the c and a direction and strongly dependent on the type and value of strain. All above results indicate that, in comparison to strain-free Ru film, H aggregation and even H bubbles are more difficult to form in Ru film under compressive strain.

Comparison of hen performance and mortality of commercial layer flocks by Strain and cage type

This study compared the egg production, defective egg rate, and mortality of commercial laying hens based on strain and cage type under commercial farm conditions. Two commercial white egg-laying strains (Hy-line and Super Nick) and two brown egg-laying strains( Nick Brown) were housed in conventional (32409 cm2) and enrichable (7200 cm2) cage systems. These layer flocks were visited weekly from 18 to 56 weeks of age, and data were collected on daily egg production, mortality, and the number of dirty and cracked eggs. Both the strain and cage type significantly affected hen-day and hen-housed egg production. Egg production was higher in conventional cages and for brown egg strains. The strain's impact on weekly mortality became insignificant after 32 weeks, while the highest mortality rates were observed in the enrichable cages. Significant differences were in the weekly dirty and cracked egg rates between layer strains and cage types. For enrichable cages and white-laying strains, the rate of dirty and cracked eggs was higher. The interaction of strain and cage type affected egg production, the rate of cracked and dirty eggs, and mortality. As a result, the brown egg-laying strain hens exhibited higher egg production than the white strain hens, and in overcrowded and enrichable that is non-enriched cages, lower egg production, higher mortality rates, and a higher rate of dirty and cracked eggs were observed.

A Review on Ecoli 0157: H7 (EHEC)

Escherichia coli O157:H7 is an important food borne and water borne pathogen is first isolated in 1982, shiga toxin. producing Ecoli O157:H7 which causes diarrhea, hemorrhagic colitis and haemolytic uremic Syndrome in humans. Haemolytic uremic. Syndrome (Hus) is a Serious condition and upto 50% of Hus patients can develop renal acute dysfunction or blood pressure. Ecoli 0157:H7 infects the alimentary tract and induces abdominal cramps with hemorrhagic diarrhea and it can be transmitted by person to person through fecal shedding and 11%. of infection are estimated. Enterotoxigenic Escherichia coli(ETEC) strain are the main cause of the diarrheal disease problems. ETEC strains are the bacteria which cause the acute watery diarrhea in chinldren. Diarrheagenic Ecoli infection are more common in Africa countries. The occurance of antimicrobial resistance depends upon the type of antimicrobialagent,bacterial strain,dose,time and mode of ministration. some of Ecoli 0517:H7 occurs after taking the undercooked meat or deficiency pasteurized dairy products. And some of Ecoli 0157:H7 occurs due ro exposal to contaminated water from potable drinking sources,pools and lakes and foods such as inappropriate washed leafy green vegetables and fruits,apple juice and direct contact with contaminated animals. Ecoli 0157:H7 shiga toxin causes leukocyte aggregation,platelet aggregation,microthrombin formation, apoptosis of affected cells ,renal dysfunction. shiga toxin not only effect kidney but it can also effect in diffuse vasculitic injuries which cause the effect on multiple organ system and organ failure.

Transcriptome analysis of the hepatopancreas from the Litopenaeus vannamei infected with different flagellum types of Vibrio alginolyticus strains.

Vibrio alginolyticus, one of the prevalently harmful Vibrio species found in the ocean, causes significant economic damage in the shrimp farming industry. Its flagellum serves as a crucial virulence factor in the invasion of host organisms. However, the processes of bacteria flagella recognition and activation of the downstream immune system in shrimp remain unclear. To enhance comprehension of this, a ΔflhG strain was created by in-frame deletion of the flhG gene in V. alginolyticus strain HN08155. Then we utilized the transcriptome analysis to examine the different immune responses in Litopenaeus vannamei hepatopancreas after being infected with the wild type and the mutant strains. The results showed that the ΔflhG strain, unlike the wild type, lost its ability to regulate flagella numbers negatively and displayed multiple flagella. When infected with the hyperflagella-type strain, the RNA-seq revealed the upregulation of several immune-related genes in the shrimp hepatopancreas. Notably, two C-type lectins (CTLs), namely galactose-specific lectin nattectin and macrophage mannose receptor 1, and the TNF receptor-associated factor (TRAF) 6 gene were upregulated significantly. These findings suggested that C-type lectins were potentially involved in flagella recognition in shrimp and the immune system was activated through the TRAF6 pathway after flagella detection by CTLs.

Differential occurrence and strain composition of potato viruses between two major seed potato production zones in China suggest the need for different management strategies for the zones

Viral disease is one of the major reasons leading to yield and quality reduction of potato production. To gain better knowledge about seed potato quality in China, the occurrences of six common viruses, including potato leafroll virus (PLRV) and potato viruses A (PVA), M (PVM), S (PVS), X (PVX) and Y (PVY), were investigated in two of China’s four potato production zones (specifically, Zone I and Zone IV) from 2013 to 2016. A total of 1231 random tuber samples (Zone I, n = 571; Zone IV, n = 660) and 532 symptomatic leaf samples (Zone I, n = 375; Zone IV, n = 157) were collected in seed potato and commercial potato fields and tested for the viruses by reverse transcription (RT)-PCR (tuber samples) and/or enzyme-linked immunosorbent assay (ELISA; leaf samples). The results showed that virus-free tubers accounted for 79.7% and 52.0% in seed tuber samples from zones I and IV, respectively. All of the six viruses analysed were present in both zones I and IV, but occurred at different frequencies, with PVY and PVS being the predominant viruses in zones I and IV, respectively. Moreover, 44.0% and 39.8% of the virus-positive samples in zones I and IV, respectively, were found to be infected with more than one virus. Strain typing of PVS and PVY demonstrated the existence of similar strains of PVY (i.e. PVYO, PVYNTNb, PVYN:O, PVYN- Wi, PVY – (SYR-I and -II) and of PVS (i.e. PVSO and PVSA) in both zones. For PVY, recombinant strains were predominant, with SYR-II (27.7%) being the most abundant strain in Zone I and SYR-I (53.3%) being the predominant strain in Zone IV. PVSO was the predominant strain in Zone I whereas PVSA was the dominant strain in Zone IV. This study revealed not only the high incidence of viruses in both seed and commercial potatoes in China, but also the differential occurrence and strain composition of the viruses between two major production zones in China for the first time. In addition, the study suggests the need for different management strategies for different production zones to enhance the quality of seed potatoes in China.

Screening of pathogenic molecular markers of Staphylococcus aureus in children based on whole genome sequencing technology

To explore the molecular characteristics of Staphylococcus aureus (S. aureus) in children, and to compare the molecular characteristics of different types of strains (infection and colonization strains) so as to reveal pathogenic molecular markers of S. aureus. A cross-sectional study design was used to conduct nasopharyngeal swab sampling from healthy children in the community and clinical samples from infected children in the hospital. Whole genome sequencing was used to detect antibiotic resistance genes and virulence genes. A random forest method to used to screen pathogenic markers. A total of 512 S. aureus strains were detected, including 272 infection strains and 240 colonization strains. For virulence genes, the carrying rates of enterotoxin genes (seb and sep), extracellular enzyme coding genes (splA, splB, splE and edinC), leukocytotoxin genes (lukD, lukE, lukF-PV and lukS-PV) and epidermal exfoliating genes (eta and etb) in infection strains were higher than those in colonization strains. But the carrying rates of enterotoxin genes (sec, sec3, seg, seh, sei, sel, sem, sen, seo and seu) were lower in infection strains than in colonization strains (P<0.05). For antibiotic resistance genes, the carrying rates of lnuA, lnuG, aadD, tetK and dfrG were significantly higher in infection strains than in colonization strains (P<0.05). The accuracy of cross-validation of the random forest model for screening pathogenic markers of S. aureus before and after screening was 69% and 68%, respectively, and the area under the curve was 0.75 and 0.70, respectively. The random forest model finally screened out 16 pathogenic markers (sem, etb, splE, sep, ser, mecA, lnuA, sea, blaZ, cat(pC233), blaTEm-1A, aph(3')-III, ermB, ermA, ant(9)-Ia and ant(6)-Ia). The top five variables in the variable importance ranking were sem (OR=0.40), etb (OR=3.95), splE (OR=1.68), sep (OR=3.97), and ser (OR=1.68). The random forest model can screen out pathogenic markers of S. aureus and exhibits a superior predictive performance, providing genetic evidence for tracing highly pathogenic S. aureus and conducting precise targeted interventions.

Wide reference databases for typing Trypanosoma cruzi based on amplicon sequencing of the minicircle hypervariable region.

Trypanosoma cruzi, the etiological agent of Chagas Disease, exhibits remarkable genetic diversity and is classified into different Discrete Typing Units (DTUs). Strain typing techniques are crucial for studying T. cruzi, because their DTUs have significant biological differences from one another. However, there is currently no methodological strategy for the direct typing of biological materials that has sufficient sensitivity, specificity, and reproducibility. The high diversity and copy number of the minicircle hypervariable regions (mHVRs) makes it a viable target for typing. Approximately 24 million reads obtained by amplicon sequencing of the mHVR were analyzed for 62 strains belonging to the six main T. cruzi DTUs. To build reference databases of mHVR diversity for each DTU and to evaluate this target as a typing tool. Strains of the same DTU shared more mHVR clusters than strains of different DTUs, and clustered together. Different identity thresholds were used to build the reference sets of the mHVR sequences (85% and 95%, respectively). The 95% set had a higher specificity and was more suited for detecting co-infections, whereas the 85% set was excellent for identifying the primary DTU of a sample. The workflow's capacity for typing samples obtained from cultures, a set of whole-genome data, under various simulated PCR settings, in the presence of co-infecting lineages and for blood samples was also assessed. We present reference databases of mHVR sequences and an optimized typing workflow for T. cruzi including a simple online tool for deep amplicon sequencing analysis (https://ntomasini.github.io/cruzityping/). The results show that the workflow displays an equivalent resolution to that of the other typing methods. Owing to its specificity, sensitivity, relatively low cost, and simplicity, the proposed workflow could be an alternative for screening different types of samples.

Understanding the potential of ultrasound as an innovative tool for microbial inactivation, functionalization of plant-based foods, and improvements of functional food potential

This review covers the application and brings perspectives of ultrasound as a tool for microbial inactivation, plant-based foods functionalization, and improvements in their functional food potential. Fruit juices, fruit and vegetable-based products, and dairy alternatives were the main plant-based foods evaluated. Ultrasound could inactivate spoilage and pathogenic micro-organisms when used alone or associated with temperature (thermosonication). Furthermore, it promoted functionalization of plant-based products by increasing the bioactive compounds content (phenolics, flavonoids, carotenoids, anthocyanins, condensed tannins, flavonols, ascorbic acid, minerals, lycopene, oligosaccharides, organic acids, chlorophyll, amino acids, glucoraphanin, and sulforaphane) and their bioaccessibility, and improving the antioxidant and antidiabetic (α-amylase and α-glucosidase inhibitions) properties of the products. Finally, it could increase the functional food potential of plant-based products by improving probiotic growth and promoting the biotransformation of compounds to more bioactive ones. The technological (natural color, increased cloudiness, decreased sedimentation index) and sensory characteristics could also be improved. The ultrasound device, process parameters (processing times, amplitudes, intensity, temperature, nominal power), food matrix, and probiotic characteristics (strain type and growth phase) are factors to be considered for achieving results. Our review summarizes for the first time the potential of ultrasound to functionalize and improve functional food potential of plant-based foods by improving probiotic growth and metabolic activity, increasing bioactive compounds content, bioaccessibility, and functional properties, and improving technological and sensory properties. We highlight opportunities for ultrasound on postbiotic production and the need for more in vitro and in vivo studies. This review is important for the plant-based functional foods area.

Comparative Genomic Analysis of Shrimp-Pathogenic Vibrio parahaemolyticus LC and Intraspecific Strains with Emphasis on Virulent Factors of Mobile Genetic Elements.

Vibrio parahaemolyticus exhibits severe pathogenicity in humans and animals worldwide. In this study, genome sequencing and comparative analyses were conducted for in-depth characterization of the virulence factor (VF) repertoire of V. parahaemolyticus strain LC, which presented significant virulence to shrimp Litopenaeus vannamei. Strain LC, harboring two circular chromosomes and three linear plasmids, demonstrated ≥98.14% average nucleotide identities with 31 publicly available V. parahaemolyticus genomes, including 13, 11, and 7 shrimp-, human-, and non-pathogenic strains, respectively. Phylogeny analysis based on dispensable genes of pan-genome clustered 11 out of 14 shrimp-pathogenic strains and 7 out of 11 clinical strains into two distinct clades, indicating the close association between host-specific pathogenicity and accessory genes. The VFDB database revealed that 150 VFs of LC were mainly associated with the secretion system, adherence, antiphagocytosis, chemotaxis, motility, and iron uptake, whereas no homologs of the typical pathogenic genes pirA, pirB, tdh, and trh were detected. Four genes, mshB, wbfT, wbfU, and wbtI, were identified in both types of pathogenic strains but were absent in non-pathogens. Notably, a unique cluster similar to Yen-Tc, which encodes an insecticidal toxin complex, and diverse toxin-antitoxin (TA) systems, were identified on the mobile genetic elements (MGEs) of LC. Conclusively, in addition to the common VFs, various unique MGE-borne VFs, including the Yen-Tc cluster, TA components, and multiple chromosome-encoded chitinase genes, may contribute to the full spectrum of LC virulence. Moreover, V. parahaemolyticus demonstrates host-specific virulence, which potentially drives the origin and spread of pathogenic factors.

Strain Variation Can Significantly Modulate the miRNA Response to Zika Virus Infection.

Zika virus (ZIKV) is a mosquito-transmitted virus that has emerged as a major public health concern due to its association with neurological disorders in humans, including microcephaly in fetuses. ZIKV infection has been shown to alter the miRNA profile in host cells, and these changes can contain elements that are proviral, while others can be antiviral in action. In this study, the expression of 22 miRNAs in human A549 cells infected with two different ZIKV isolates was investigated. All of the investigated miRNAs showed significant changes in expression at at least one time point examined. Markedly, 18 of the miRNAs examined showed statistically significant differences in expression between the two strains examined. Four miRNAs (miR-21, miR-34a, miR-128 and miR-155) were subsequently selected for further investigation. These four miRNAs were shown to modulate antiviral effects against ZIKV, as downregulation of their expression through anti-miRNA oligonucleotides resulted in increased virus production, whereas their overexpression through miRNA mimics reduced virus production. However, statistically significant changes were again seen when comparing the two strains investigated. Lastly, candidate targets of the miRNAs miR-34a and miR-128 were examined at the level of the mRNA and protein. HSP70 was identified as a target of miR-34a, but, again, the effects were strain type-specific. The two ZIKV strains used in this study differ by only nine amino acids, and the results highlight that consideration must be given to strain type variation when examining the roles of miRNAs in ZIKV, and probably other virus infections.

Egg-associated Salmonella enterica serovar Enteritidis: comparative genomics unveils phylogenetic links, virulence potential, and antimicrobial resistance traits.

Salmonella enterica serovar Enteritidis (SE) remains a frequent cause of foodborne illnesses associated with the consumption of contaminated hen eggs. Such a food-pathogen association has been demonstrated epidemiologically, but the molecular basis for this association has not been explored. Comparative genomic analysis was implemented to decipher the phylogenomic characteristics, antimicrobial resistance, and virulence potential of eggs-associated SE. Analyzing 1,002 genomes belonging to 841 sequence types of food-isolated SE strains suggests a high genomic similarity within the egg-related lineage, which is phylogenetically close to SE strains isolated from poultry but is different from those isolated from beef. Core genome- and single nucleotide polymorphism (SNP)-based phylogeny of 74 SE strains of egg origin showcased two distinct sublineages. Time-scaled phylogeny supported the possibility of a common ancestor of egg-related SE lineages. Additionally, genome mining revealed frequent antibiotic resistance due to the presence of aac(6')-Iaa and mdsAB encoded on the genomes of egg-associated SE strains. For virulence gene profiling, 103-113 virulence determinants were identified in the egg-associated SE, which were comparable to 112 determinants found in human-associated SE, emphasizing the capacity of egg-associated strains to infect humans and cause diseases. The findings of this study proved the genomic similarity of egg-associated SE strains, and these were closely related to poultry strains. The egg-associated strains also harbor virulence genes equivalent to those found in human-associated SE strains. The analysis provided critical insights into the genetic structure, phylogenomics, dynamics of virulence, and antibiotic resistance of Salmonella Enteritidis, circulating in eggs and emphasizing the necessity of implementing anti-Salmonella intervention strategies, starting at the production stage of the poultry supply chain.

Nanocrystalline Co/Ga substituted CuFe2O4 magnetic nanoferrites for green hydrogen generation

The research study on the design of cobalt and gallium substituted copper nanoferrites through sol-gel auto-combustion were testify to check the photocatalytic/electrocatalytic water splitting efficiency of prepared nanoferrites for hydrogen generation. XRD study confirms the formation tetragonal phase for all fabricated nanoferrites with no additional phases of impurities. The tetragonal shaped grains with definite grain boundaries were observed from the FESEM study. The magnetic measurements show large hysteresis loop area with high magnetization of 58.45 emu/g for undoped copper nanoferrite. The catalytic behaviors of the fabricated nanocatalysts for the photo-catalytic H2 production was determined by using 0.079 M Na2SO3 and 0.128 M Na2S as the sacrificial agents, that give electron donor site during photo-catalysis under UV–visible irradiation. As compared to other compositions, Cu0.99Co0.01Ga0.01Fe1.99O4 (x = y = 0.01) nano photocatalyst attained the highest photocatalytic activity of 18.11 mmol gcat−1. Also, the as-synthesized photocatalysts repeatability and stability were evaluated throughout repeated runs of 4 h reaction period conducted under identical circumstances. However, all electrocatalytic analysis for hydrogen evolution reaction (HER) activity were performed using three electrode arrangements (reference, counter, and working electrodes) in 0.5 M H2SO4 electrolyte mixture. There was a rise in overpotential at 10 mA/cm−2 cathode current density as concentrations of Co/Ga for the synthesized nanoferrites were increased. It has been showed that CuFe2O4 had a high electrocatalytic HER activity. In addition, the produced nanoferrites were also examined against different type of bacterial strains, where Cu0.99Co0.01Ga0.01Fe1.99O4 indicated maximum zone of inhibition (ZOI) against Bacillus subtilis (20 ± 0.55 mm), Salmonella typhi (12 ± 0.52 mm), Escherichia coli (16 ± 0.49 mm), and Staphylococcus aureus (12 ± 0.54 mm), respectively. Hence, with these efficient overall photocatalytic and electrocatalytic water splitting traits, the prepared nanoferrites are highly useful for the green hydrogen production applications.

VBCG: 20 validated bacterial core genes for phylogenomic analysis with high fidelity and resolution

BackgroundPhylogenomic analysis has become an inseparable part of studies of bacterial diversity and evolution, and many different bacterial core genes have been collated and used for phylogenomic tree reconstruction. However, these genes have been selected based on their presence and single-copy ratio in all bacterial genomes, leaving out the gene's 'phylogenetic fidelity' unexamined.ResultsFrom 30,522 complete genomes covering 11,262 species, we examined 148 bacterial core genes that have been previously used for phylogenomic analysis. In addition to the gene presence and single-copy rations, we evaluated the gene's phylogenetic fidelity by comparing each gene's phylogeny with its corresponding 16S rRNA gene tree. Out of the 148 bacterial genes, 20 validated bacterial core genes (VBCG) were selected as the core gene set with the highest bacterial phylogenetic fidelity. Compared to the larger gene set, the 20-gene core set resulted in more species having all genes present and fewer species with missing data, thereby enhancing the accuracy of phylogenomic analysis. Using Escherichia coli strains as examples of prominent bacterial foodborne pathogens, we demonstrated that the 20 VBCG produced phylogenies with higher fidelity and resolution at species and strain levels while 16S rRNA gene tree alone could not.ConclusionThe 20 validated core gene set improves the fidelity and speed of phylogenomic analysis. Among other uses, this tool improves our ability to explore the evolution, typing and tracking of bacterial strains, such as human pathogens. We have developed a Python pipeline and a desktop graphic app (available on GitHub) for users to perform phylogenomic analysis with high fidelity and resolution.EM9SnsSGDMq_dsePyH_5KQVideo

Differences in Biofilm Formation by Methicillin-Resistant and Methicillin-Susceptible Staphylococcus aureus Strains.

Staphylococcus aureus (S. aureus) is a common pathogen involved in community- and hospital-acquired infections. Its biofilm formation ability predisposes it to device-related infections. Methicillin-resistant S. aureus (MRSA) strains are associated with more serious infections and higher mortality rates and are more complex in terms of antibiotic resistance. It is still controversial whether MRSA are indeed more virulent than methicillin-susceptible S. aureus (MSSA) strains. A difference in biofilm formation by both types of bacteria has been suggested, but how only the presence of the SCCmec cassette or mecA influences this phenotype remains unclear. In this review, we have searched for literature studying the difference in biofilm formation by MRSA and MSSA. We highlighted the relevance of the icaADBC operon in the PIA-dependent biofilms generated by MSSA under osmotic stress conditions, and the role of extracellular DNA and surface proteins in the PIA-independent biofilms generated by MRSA. We described the prominent role of surface proteins with the LPXTG motif and hydrolases for the release of extracellular DNA in the MRSA biofilm formation. Finally, we explained the main regulatory systems in S. aureus involved in virulence and biofilm formation, such as the SarA and Agr systems. As most of the studies were in vitro using inert surfaces, it will be necessary in the future to focus on biofilm formation on extracellular matrix components and its relevance in the pathogenesis of infection by both types of strains using in vivo animal models.

Pastern dermatitis outbreak associated with toxigenic and non-toxigenic Corynebacterium diphtheriae and non-toxigenic Corynebacterium ulcerans at a horse stable in Finland, 2021.

Corynebacterium diphtheriae and Corynebacterium ulcerans, when producing toxin, are the cause of diphtheria, a potentially life-threatening illness in humans. Horses (Equus ferus caballus) are known to be susceptible to infection that may manifest clinically on rare occasions. In late 2021 and early 2022, specimens from five horses suffering from pastern dermatitis were cultured at the Laboratory of Clinical Microbiology at the Faculty of Veterinary Medicine, University of Helsinki, Finland. C. diphtheriae and/or C. ulcerans were recovered from all of these. This study aimed to (1) analyse the bacterial isolates and (2) describe the outbreak and identify possible sources of the infection and infection routes in the stable. Susceptibility testing, PCR for the tox gene, and Elek test for toxin production in PCR-positive isolates were performed. Whole genome sequencing was also conducted to achieve high-resolution strain typing. An epidemiological survey was done by means of a semi-structured interview of horses' caretaker, and contact tracing was done among people at the stable. Two tox gene-positive, toxin-producing C. diphtheriae belonged to sequence type (ST) 822. Other C. diphtheriae (n = 2, ST828) and C. ulcerans (n = 2, ST325 and ST838) isolates did not carry the tox gene. The epidemiological investigation explored numerous possible routes of transmission, but the definite source of infection was not identified. All established human contacts tested negative for diphtheriae. All horses recovered after antimicrobial treatment. Our study shows that C. diphtheriae and C. ulcerans may readily spread among horses at the same stable and complicate pastern dermatitis infections. These potentially zoonotic bacteria can cause outbreaks even in a country with a very low prevalence. Caretakers should be encouraged to wear gloves and practice good hand hygiene when treating infected skin lesions in horses.

Curvature analysis and its correlation with faults and fractures in presalt carbonates, Santos Basin, Brazil

Presalt lacustrine carbonate reservoirs in the Santos Basin, Brazil, can have a high degree of fracturing. Properly characterizing such properties is important due to their influence on the porosity–permeability system. It may play a key role in the so-called excess permeability features and the flow behaviour, especially in the Aptian Alagoas Stage. Therefore, 3D characterization of the fracture system improves the reservoir model. For this purpose, correctly identifying the fault and fracture zones in seismic data is crucial. This task is generally performed manually and guided by amplitude interpretation or geometric seismic attributes. However, due to the seismic resolution of the pre-salt seismic datasets, many faults and fractured zones are not identified in the seismic amplitude domain or by standard geometric attributes such as coherence. Improving the resolution of seismic data and its geometric attributes can positively impact the delineation of fractured zones, structural lineaments, and their connectivity. Curvature (k) attributes have a high potential to reveal vertical to subvertical subseismic-scale structures, which is the main type of strain generated from the tectonic style in the Pre-salt rocks. Among the curvature attributes, the most-positive (k1) and the most-negative (k2) attributes are some of the most commonly used. The present study evaluates the use of seismic inverse Q-filter and three different dip estimation techniques based on Fast Fourier Transform (FFT), Principal Component Analysis (PCA), and Phase Gradient (PG). It also adds two postfiltering techniques (median and recursive Gaussian filters) to obtain a consistent most-positive curvature. We then analyse two analytical models that correlate the volumetric fracture intensity, measured on Borehole Image Logs (BHI), with the curvature. Then, we perform a comprehensive study to understand the role of seismic-scale strain (translated into curvature) and mechanical stratigraphy in the development of fractures in the presalt, where we address that in addition to seismic-scale deformation, the contents of silica, clay, and organic matter are also relevant variables. These results can help to guide future studies of fracture characterization to prospect naturally fractured reservoirs or to estimate fracture intensity for dual-porosity reservoir modelling on the Santos presalt carbonates.

Whole genome structure and resistance genes in carbapenemase-producing multidrug resistant ST378 Klebsiella pneumoniae

Background Carbapenemase-producing Klebsiella pneumoniae (CPKP) is one of the most dangerous multidrug-resistant (MDR) pathogens in human health due to its widespread circulation in the nosocomial environment. CPKP carried by companion dogs, which are close to human beings, should be considered a common threat to public health. However, CPKP dissemination through companion animals is still under consideration of major diagnosis and surveillance systems.MethodsTwo CPKP isolates which were genotyped to harbor blaNDM-5-encoding IncX3 plasmids, were subjected to the whole-genome study. Whole bacterial DNA was isolated, sequenced, and assembled with Oxford Nanopore long reads and corrected with short reads from the Illumina NovaSeq 6000 platform. The whole-genome structure and positions of antimicrobial resistance (AMR) genes were identified and visualized using CGView. Worldwide datasets were downloaded from the NCBI GenBank database for whole-genome comparative analysis. The whole-genome phylogenetic analysis was constructed using the identified whole-chromosome SNP sites from K. pneumoniae HS11286.ResultsAs a result of the whole-genome identification, 4 heterogenous plasmids and a single chromosome were identified, each carrying various AMR genes. Multiple novel structures were identified from the AMR genes, coupled with mobile gene elements (MGE). The comparative whole-genome epidemiology revealed that ST378 K. pneumoniae is a novel type of CPKP, carrying a higher prevalence of AMR genes.ConclusionsThe characterized whole-genome analysis of this study shows the emergence of a novel type of CPKP strain carrying various AMR genes with variated genomic structures. The presented data in this study show the necessity to develop additional surveillance programs and control measures for a novel type of CPKP strain.