Microbiol. Res., Volume 14, Issue 1 (March 2023) – 33 articles

Pekar et al. (2022) propose that SARS-CoV-2 was a zoonotic spillover that first infected humans in the Huanan Seafood Market in Wuhan, China. They propose that there were two separate spillovers of the closely related lineages A and lineage B in a short period of time. The two lineages are differentiated by two SNVs; hence, a single-SNV A-B intermediate must have occurred in an unsampled animal host if the two-spillover hypothesis is correct. Consequently, confirmation of the existence of an intermediate A-B genome from humans would falsify their hypothesis of two spillovers. Pekar et al. identified and excluded 20 A-B intermediate genomes from their analysis. A variety of exclusion criteria were applied, including low read depth and the assertion of repeated erroneous base calls at lineage-defining positions 8782 and 28144. However, data from GISAID show that most of the genomes were sequenced to high average sequencing depth, appearing inconsistent with these criteria. The decision to exclude the majority of genomes was based on personal communications, with raw data unavailable for inspection. Multiple errors, biases, and inconsistencies were observed in the exclusion process. For example, 12 intermediate genomes from one study were excluded; however, 54 other genomes from the same study were included, indicating selection bias. Puzzlingly, two intermediate genomes from Beijing were discarded despite an average sequencing depth of 2175X; however, four genomes from the same sequencing study were included in the analysis. Lastly, we discuss 14 additional possible intermediate genomes not discussed by Pekar et al. and note that genome sequence filtration is inappropriate when considering the presence or absence of a specific SNV pair in an outbreak. Consequently, we find that the exclusion of many of the intermediate genomes is unfounded, leaving the conclusion of two natural zoonoses unsupported. Full article

The prevalence of nontuberculous mycobacteria (NTM) infections and disease is rising worldwide due to increased research, diagnostics capabilities, and awareness of the disease. There is limited prevalence data for NTM from different sources in Zambia. The aim of this study was to determine the prevalence and species distribution of NTM at the human–livestock–environment interface. A cross-section study was conducted in Namwala, Chipata, and Lundazi Districts of Zambia from April 2020 to December 2021. Sputum samples were collected from tuberculosis presumptive patients from different health centers, cattle tissues were collected from different abattoirs during routine post-mortem, and water samples were collected from different drinking points for humans and animals such as taps, boreholes, wells, rivers, dams and ponds, and then cultured following standard mycobacteriology procedures. Capilia TB-Neo assay was used to identify NTM from the positive cultures. DNA was extracted and the 16S to 23S rRNA (internal transcribed spacer region) (ITS) was amplified and sequenced to identify the species. The overall prevalence of NTM from humans, cattle, and water was 9.1% (72/794, 95% CI 7.2–11.3). The prevalence in humans was 7.8% (33/421, 95% CI 5.54–10.94), in cattle it was 10.6% (15/142, 95% CI 6.2–17.1), and in water it was 10.4% (24/231, 95% CI 6.9–15.2). Our study has shown, for the first time in Zambia, simultaneous isolation of NTM at the human–livestock–environment interface; M. avium complex and M. fortuitum were the most commonly isolated species. M. fortuitum and M. gordonae were isolated from all three sources, while M. abscessus was isolated from humans and water. The isolation of similar NTM species at the interface which are potentially pathogenic is a public health problem which merits further investigation. Full article

The aim of this systematic review was to investigate new research on the antioxidant, anti-acetylcholine, antimicrobial, and antitumor activity of genus Schizophyllum, as well as to describe the mycochemical profiles. A summary was made on the published studies in the five-year period from 2017 to 2022, with the focus on the most investigated species of this genus, S. commune. Data were obtained through various scientific online databases, including Google Scholar, Semantic Scholar, PubMed, Science Direct, Elsevier, and Wiley Online Library using specific keywords. Out of 918 records published between 2017 and 2022, a total of 44 peer-reviewed studies were included in qualitative synthesis. Most examined compounds were glucans isolated from the submerged cultivation of S. commune, even though many studies reported proteins, phenolics, and some other secondary metabolites such as flavonoids, saponins, steroids, tannins, triterpenoids, etc. Schizophyllan (SPG), one of the most studied β-glucans isolated from S. commune, has been utilized in clinical trials to treat patients receiving anticancer therapy as an immunopotentiator. Considering the enormous biopotential of genus Schizophyllum, specifically S. commune and S. radiatum, additional attention should be paid to identify the biomolecules more accurately and focus on their antitumor and anti-acetylcholinesterase properties, since they proved to have great prospects in the pharmaceutical and nutraceutical industries. Full article

The human gastrointestinal tract hosts a complex and dynamic population of commensal bacterial species, which have coevolved with the host, generating a symbiotic relationship. Some compounds present in foods, such as polyols, prebiotic fibers, or phenolic compounds, are poorly metabolized and absorbed by the host before the transformation guided by the colonic microbiota. By influencing gut microbiota, diet plays a fundamental role in understanding the beneficial effects of the gut microbiota on the host, including its long-term metabolism. The idea that probiotics can act not only by influencing the colonizing microbiota opens the door to a wider range of probiotic possibilities, encouraging innovation in the field. Furthermore, it has been shown both that some probiotics increase phagocytosis or the activity of natural killer cells. Current prebiotics are mainly based on carbohydrates, but other substances, such as polyphenols and polyunsaturated fatty acids, could exert prebiotic effects. A prebiotic substance has been defined as ‘a substrate that is selectively used by host microorganisms that confer a health benefit’, and so can interact with the gut microbiota through competition for nutrients, antagonism, cross-feeding, and support for microbiota stability. Influencing its composition in terms of richness and diversity, food components have a key impact on the intestinal microbiota. Eating habits can strongly influence the composition of the intestinal microbiota. A healthy intestinal microbiota is essential for maintaining general health, and diet is one of the major modulators of this fascinating world of microorganisms. This must give us one more reason to adopt a healthy lifestyle. Full article

Plant disease outbreaks are increasingly exacerbated by climate change and the conditions of stress combinations. They are negatively affecting crop yield and driving threats to food security in many areas of the world. Although synthetic pesticides offer relative success in the control of pests and plant diseases, they are often overused, and this method faces numerous drawbacks, including environmental toxicity, soil degradation, and adverse effects on human health. Therefore, alternatives are being developed and examined, including the biocontrol of pests and pathogens and biomass pyrolysis leading to wood vinegar that has shown great promise in agriculture and organic farming. However, while wood vinegar use is expanding and allows the control of numerous pests and bacterial and fungal diseases, its application to control oomycete diseases is limited. This study aimed to test wood vinegar for the control of oomycete plant pathogens from which six wood vinegars of pistachio, pomegranate, almond, pine, cypress, and walnut were produced. The inhibitory effects of volatile metabolites (semi-VOCs) of different wood vinegars concentrations (100%, 50%, 25%, 12.5%, and 6.25%) were examined against the hyphal growth of Globisporangium ultimum and Pythium aphanidermatum isolates. An in vitro analysis unambiguously demonstrated that for Globisporangium ultimum, the wood vinegar semi-VOCs of almond, pistachio (C 100% and 50%), and walnut (C 100%) totally inhibited mycelial growth. On the other hand, Pythium aphanidermatum, pistachio (C 100%, 50%, and 25%), and cypress (C 100%) expressed their abilities to completely inhibit the mycelial growth. Other treatments, including relevant concentrations of pine and pomegranate significantly inhibited the growth of mycelia of both species compared to the control (p ≤ 0.05). Therefore, wood vinegar could be considered a natural and organic product to use in agriculture to cope not only against pests, bacterial and fungal pests but also against emerging oomycete plant diseases. Full article

Despite the use of highly active antiretroviral therapy approved by the United States Food and Drug Administration (FDA) for the treatment of human immunodeficiency virus (HIV) infection, HIV remains a public health concern due to the inability of the treatment to eradicate the virus. In this study, N-methyl-N-phenyl dithiocarbamate complexes of indium(III), bismuth(III), antimony(III), silver(I), and copper(II) were synthesized. The complexes were characterized by thermal gravimetric analysis (TGA), differential scanning calorimetry (DSC), and Fourier transform infrared spectroscopy (FTIR). The N-methyl-N-phenyl dithiocarbamate complexes were then evaluated for their antiviral effects against HIV-1 subtypes A (Q168), B (QHO.168), and C (CAP210 and ZM53). The results showed that the copper(II)-bis (N-methyl-N-phenyl dithiocarbamate) complex had a neutralization efficiency of 94% for CAP210, 54% for ZM53, 45% for Q168, and 63% for QHO.168. The silver(I)-bis (N-methyl-N-phenyl dithiocarbamate) complex showed minimal neutralization efficiency against HIV, while indium(III) and antimony(III) N-methyl-N-phenyl dithiocarbamate complexes had no antiviral activity against HIV-1. The findings revealed that copper(II)-bis (N-methyl-N-phenyl dithiocarbamate), with further improvement, could be explored as an alternative entry inhibitor for HIV. Full article

CSF is enzootic in most of pig-producing states, particularly in the NorthEastern (NE) region of India. In this study, a total of 249 sera and 190 tissue samples were collected from different parts of Meghalaya. Samples were processed by ELISA and RT-PCR for serological and molecular diagnosis. Representative positive samples from the Khasi Hills region were selected for sequencing and “close grid” phylogenetic relationship using partial genomic regions of 5′UTR and E2. High seroprevalence (74.7%) of CSFV was recorded. Detection of the CSFV genome in serologically positive serum samples and tissue samples was 61.29% and 18.94%, respectively. BLAST and phylogenetic analyses indicate the clustering of all the field samples in subgroup 2.2, with high identity with EF014334 from China. Molecular structural modelling of the E2 partial sequence using representative sequences MG563797 from Meghalaya and EF014334 from China indicate potential changes in the protein motif and its conformation, which may explain the emergence of subgroup 2.2 CSFV replacing the predominant subgroup 1.1 viruses in NorthEast India. The epidemiological information presented in this study may be helpful for determination of disease incidence in this region, whereas the virus profile may be useful for framing disease control programs. Full article

Studies of newly isolated strains of lactic acid bacteria (LAB) are a good basis for expanding the potential for their applications in functional foods, probiotic food supplements, and other probiotic products. They exhibit various functional properties, including such with antiviral activity. Probiotic strains can manifest their antiviral effects by various mechanisms, including direct interaction with viruses, production of antiviral compounds, or immune system modulation. Ten newly isolated LAB strains from traditional fermented food products have been tested for the determination of their antiviral activity. This study was performed to evaluate the effect of cell-free supernatants (CFSs) from the studied strains for the effect on viral replication of Human alphaherpesvirus—HHV-1 and HHV-2 as well as for direct virucidal activity. The CFSs of the LAB strains were used in non-toxic concentrations of 25%, 6.25%, and 1.6%. No direct virucidal activity was observed in tested CFSs, but five of the strains observed a well-defined effect of viral replication inhibition with the selective index (SI) from 4.40 to >54. For two of these five strains, Lactobacillus delbrueckii subsp. bulgaricus KZM 2-11-3 and Lactiplantibacillus plantarum KC 5-12 strong activity against HHV-2 with a selective index (SI) over 45 was detected, which is a good basis for further research. Full article

Brazil is an important peanut producer, but despite its high production, there still needs to be an inoculant for the peanut crop. In addition, the use of microorganisms that promote plant growth (PGPM) is not common, and this crop is highly dependent on chemical fertilizers. An excellent alternative to reduce the use of fertilizers and chemical inputs in peanut crops while reducing the production cost and environmental impact is the use of PGPM. The objective of this study was to evaluate the effects of Azospirillum brasilense, Bacillus subtilis, Bradyrhizobium japonicum, and Trichoderma harzianum as single inoculants and co-inoculants on the growth promotion and productivity of peanuts in greenhouse and field conditions. In the greenhouse, the experiment was conducted with 12 treatments with six repetitions. In the field conditions, the experiment was conducted with five treatments with four repetitions. Both experiments were conducted in randomized blocks. In general, all the microorganisms evaluated in the present study promoted increases in root dry mass, shoot dry mass, phosphorus concentrations, and plant height in the greenhouse and under field conditions compared with the control. Interestingly, the mixtures of microorganisms inoculated in peanut plants did not promote greater plant growth and development compared with inoculations of the microorganisms separately. Specifically, in the field, the highest productivity was found for the inoculation of B. japonicum alone. The PGPM evaluated in the present study for peanut crops generally promoted some increases in productivity in greenhouse and field conditions. Full article

The objective of this study was to create a fermentation process for the production of inulinase, an important enzyme with numerous applications in the food and pharmaceutical industries, using low-cost agricultural waste as substrates for Rhizopus oryzae NRRL 3563. High titer inulinase production in chicory roots by Rhizopus oryzae in a submerged culture was accomplished using a statistical experimental design. A two-level Plackett–Burman design followed by a three-level Box–Behnken design producing a high inulinase titer of 1085.11 U/mL, 2.83-fold the maximum level, was obtained in the screening experiment. The optimal levels were as follows: chicory root, 10 g/L; NaNO₃, 5 g/L; and KCl, 0.2 g/L. The produced inulinase enzyme was purified using 70% ammonium sulfate precipitation and ultra-filtration causing 3.63-fold purification with 60% activity recovery. The enzyme had a molecular weight of approximately 130 KDa. The purified enzyme showed optimum activity at 50 °C and pH 6.0. The pH stability range was three to six and the temperature stability was up 70 °C. The purified inulinase could hydrolyze inulin and sucrose, but not cellobiose or soluble starch. Km and Vmax for inulin were determined to be 0.8 mg/mL and 50,000 U/mg, respectively. The two-level Plackett–Burman design was applied followed by a Box–Behnken model for optimization of fermentation conditions. Accordingly, the optimal combination of fermentation was a reaction time of seven hours, a temperature of 60 °C, and an enzyme concentration of 40,000 U/mL, which resulted in a 58.07% saccharification yield. The characteristics of the enzyme and its kinetic parameters suggested that it was highly effective in the fermentation of inulin and inulin-containing substrates. Additionally, it raises the potential of using inulinase enzymes in pharmaceutical and food industries. Full article

This study assessed the association between multimorbidity and mortality from COVID-19 in the Middle East and North Africa region, where such data are scarce. We conducted a cross-sectional study using data of all cases with COVID-19 reported to the Ministry of Public Health of Qatar from March to September 2020. Data on pre-existing comorbidities were collected using a questionnaire and multimorbidity was defined as having at least two comorbidities. Proportions of deaths were compared by comorbidity and multimorbidity status and multivariable logistic regression analyses were carried out. A total of 92,426 participants with a mean age of 37.0 years (SD 11.0) were included. Mortality due to COVID-19 was associated with gastrointestinal diseases (aOR 3.1, 95% CI 1.16–8.30), respiratory diseases (aOR 2.9, 95% CI 1.57–5.26), neurological diseases (aOR 2.6, 95% CI 1.19–5.54), diabetes (aOR 1.8, 95% CI 1.24–2.61), and CVD (aOR 1.5, 95% CI 1.03–2.22). COVID-19 mortality was strongly associated with increasing multimorbidity; one comorbidity (aOR 2.0, 95% CI 1.28–3.12), two comorbidities (aOR 2.8, 95% CI 1.79–4.38), three comorbidities (aOR 6.0, 95% 3.34–10.86) and four or more comorbidities (aOR 4.15, 95% 1.3–12.88). This study demonstrates a strong association between COVID-19 mortality and multimorbidity in Qatar. Full article

This study aimed to evaluate the abilities of three bacteria, Bacillus cereus, Succinovibrio dextrinosolvens, and Lactobacillus acidophilus, to fix nitrogen, solubilize phosphorus, and produce cellulosic and amylolytic enzymes. Then, these bacteria were evaluated in potato plants under field conditions. The bacterium B. cereus showed the ability to synthesize amylase, indole acetic acid (IAA) production of 9.08 μg mL⁻¹, phosphorus solubilization of 14.93 mg P L⁻¹, and nitrogen fixation of 0.7 mg of nitrogen L⁻¹. S. dextrinosolvens showed the ability to synthesize siderophores and amylase, IAA production of 10.25 μg mL⁻¹, phosphorus solubilization of 41.38 mg P L⁻¹, and nitrogen fixation of 0.42 mg N L⁻¹. L. acidophilus showed the ability to synthesize siderophores, IAA production of 7.25 μg mL⁻¹, phosphorus solubilization of 5.58 mg P L⁻¹, and nitrogen fixation of 0.5 mg N L⁻¹. Some plant parameters were increased as shoot dry matter by B. cereus, and the mixture of bacteria increased shoot and root dry matter and increased phosphorus from the root. More studies are needed to deepen the understanding of the potential of these bacteria; however, B. cereus showed great potential to be used as a plant growth promoter in potato crops in the future. Full article

Lactic acid bacteria are widely studied microorganisms and are one of the prevalent groups of bacteria in the oral cavity microbiome. This work aimed to isolate new lactic acid bacterial strains from the human oral cavity and evaluate their characteristics and probiotic potential. Twelve strains were isolated and identified as belonging to several genera in the family Lactobacillaceae. Screening for antimicrobial activity was held, where two of the strains showed antagonistic activity against Streptococcus mutans and most of the strains expressed inhibition against Escherichia coli, Bacillus subtilis, and Bacillus cereus. The ability of the studied strains to autoaggregate and bind to mucin was assessed, showing autoaggregative properties and mucin binding at 5 logs CFU/mL. The survival ability in simulated oral and gastrointestinal conditions and growth dynamics with different gastrointestinal stress factors was studied. Most of the strains showed a good growth potential in the presence of oral and gastrointestinal stress factors. All tested strains exhibited high survival rates in the simulated oral environment, thus having the potential for colonizing the oral cavity and their beneficial properties to be applied. These results are a good basis for continuing the research into these strains so they can be included in new functional products for oral health. Full article

With the rapid development of industry, Cr has become one of the major heavy metal pollutants in soil, severely impacting soil microecology, among which rhizosphere microorganisms can improve the soil microenvironment to promote plant growth. However, how rhizosphere bacterial communities respond to Cr stress under different cultivation modes remains to be further studied. Therefore, in this study, a greenhouse pot experiment combined with 16S rRNA high-throughput sequencing technology was used to study the effects of Cr stress at 200 mg kg⁻¹ on the bacterial community structure and diversity in the rhizosphere soil of Iris tectorum under different cultivation modes. The results showed that the rhizosphere bacterial community diversity index (Shannon and Simpson) and abundance index (Ace and Chao) increased significantly with wetland plant diversity under Cr stress. Moreover, the bacterial community changed by 20.1% due to the addition of Cr, further leading to a 15.9% decrease in the common species of the bacterial community, among which Proteobacteria, Actinobacteria, Chloroflexi, and Acidobacteriota accounted for more than 74.8% of the total sequence. However, with the increase in plant diversity, the abundance of rhizosphere-dominant bacteria and plant growth-promoting bacteria communities increased significantly. Meanwhile, the symbiotic network analysis found that under the two cultivation modes, the synergistic effect between the dominant bacteria was significantly enhanced, and the soil microenvironment was improved. In addition, through redundancy analysis, it was found that C, N, and P nutrients in uncontaminated soil were the main driving factors of bacterial community succession in the rhizosphere of I. tectorum, and Cr content in contaminated soil was the main driving factor of bacterial community succession in I. tectorum rhizosphere. In summary, the results of this study will provide a basis for the response of the rhizosphere bacterial community to Cr and the interaction between wetland plants and rhizosphere bacteria in the heavy metal restoration of wetland plants under different cultivation modes. Full article

The increasing production of industrial aromatic plant residues (IAPRs) are potentially environmental risky, and composting is a promising solution to resolve the coming IAPR problems. Carbon source degradation is a basic but important field in compost research; however, we still lack a clear understanding of carbon source degradation and the corresponding relationship to microbial community variation during IAPR composting, which hampers the improvement of IAPR composting efficiency and the promotion of this technology. In this study, samples were chosen on the first day, the 10th day, the 20th day, and the last day during the composting of Cinnamomum camphora leaf IAPRs, and the microbial community composition, main carbon source composition, and several enzyme activities were measured accordingly. The results showed that during composting, the hemicellulose had the highest reduction (200 g kg⁻¹), followed by cellulose (143 g kg⁻¹), lignin (15.5 g kg⁻¹), starch (5.48 g kg⁻¹), and soluble sugar (0.56 g kg⁻¹), which supported that hemicellulose and cellulose were the main carbon source to microbes during composting. The relative abundance of the main bacterial phylum Firmicute decreased from 85.1% to 40.3% while Actinobactreia increased from 14.4% to 36.7%, and the relative abundance of main fungal class Eurotiomycetes decreased from 60.9% to 19.6% while Sordariomycetes increased from 16.9% to 69.7%. Though principal coordinates analysis found that both bacterial and fungal community composition significantly varied during composting (p < 0.05), structure equation modeling (SEM) supported that bacterial composition rather than fungal counterpart was more responsible for the change in carbon source composition, as the standard total effects offered by bacterial composition (−0.768) was about five times the fungal composition (−0.144). Enzyme2 (comprised of xylanase, laccase, cellulase and manganese peroxidase) provided −0.801 standard total effects to carbon source composition, while Enzyme1 (comprised of lignin peroxidase and polyphenol oxidase) had only 0.172. Furthermore, xylanase and laccase were the only two enzymes appeared in co-occurrence network, clustered with nearly all the carbon sources concerned (except starch) in module-II. Xylanase, hemicellulose, and cellulose were linked to higher numbers of OTUs, more than laccase and other carbon sources. In addition, there were 11 BOTUs but only 1 FOTUs directly interacted to xylanase, hemicellulose, and cellulose simultaneously, three of them were Limnochordaceae and two were Savagea, which highlighted the potential core function in lignocellulose degradation provided by bacterial members, especially Limnochordaceae and Savagea. Thus, the results supported that during composting of Cinnamomum camphora leaf IAPRs, the degradation of dominate carbon sources, hemicellulose and cellulose, was mainly driven by bacterial community rather than fungal community. In addition, the bacterial originated xylanase and laccase played potentially core roles in the functional modules. This research clearly investigated the microbial dynamics of carbon source degradation during the composting of Cinnamomum camphora leaf IAPRs, and offers valuable information about and new insight into future IAPRs waste treatment. Full article

Background: Access to safe drinking water remains a global issue with fecal indicator bacteria being major pollutants. Biochars offer low-cost adsorbents for bacterial pathogens. A fundamental understanding of how biochars interact with bacterial pathogens is essential to designing effective biofilters. Methods: Water-saturated sand columns amended with Magnesium and Nitrogen-doped biochars produced by pyrolysis at 400, 500, 600, and 700 °C were used to Quantify the transport of pathogenic Escherichia coli O157:H7 and nonpathogenic E. coli k12 strains in porous media. Measured data were modeled using DLVO theory of colloidal stability. were explored. Results: (1) Biochar is hydrophobic while sand and bacteria are hydrophilic; (2) all Gibbs free energy values quantified between E. coli O157:H7 and biochar were negative except for biochar produced at 700 °C; (3) all types of forces investigated (van der Waals, electrostatic, and acid-base interactions) played a role in governing the interactions between bacteria and biochar. Conclusions: (1) Adding doped biochar to sand at a 2% weight ratio enhanced the retention of bacterial cells in the sand/biochar columns; (2) bacterial transport is strain-dependent and mediated by various types of forces resulting from interactions between the various functional groups displayed on bacteria and biochar/sand. Our findings emphasize the importance of monitoring biochar’s functionality to eliminate bacterial pollutants from contaminated water. Full article

Hops contain a wide variety of polyphenolic compounds with diverse antimicrobial properties. This study aimed to evaluate the impact of temperature on the bioactive components of samples of aqueous extracts of hops with different characteristics. A central compound rotating design model was used in order to obtain optimal conditions of temperature and extract concentration to inhibit Fusarium oxysporum and Alternaria solani. At intermediate temperatures according to the design of experiments, significant effects on antifungal activity were observed. The optimal conditions with antifungal activity were at a concentration of 160 mg/mL and a temperature of 65 °C to obtain mycelial diameters ≤ 25 mm. The bioactive compounds were shown in the FT-IR spectrum after each heat treatment of both samples; significant changes were observed in the bands between 2786 to 3600 cm⁻¹ and 1022 to 1729 cm⁻¹. The content of total phenols and flavonoids showed a concentration increase of 4.54 to 6.24 mg GAE/g and 6.21 to 8.12 mg QE/g from an initial evaluation temperature of 25 °C to 57.5 °C, respectively, benefited by the heating temperature, enhancing antifungal activity. However, when increasing the temperature ≥90 °C, a tendency to decrease the concentration of bioactive compounds was observed, probably due to their denaturation due to the effect of temperature and exposure time, being non-thermolabile compounds at high temperatures. These aqueous extracts are an alternative to effective natural antifungals. Full article

Calcitonin (CT) and adrenomedullin (ADM) are members of the CT family. Procalcitonin (PCT) is a prohormone of CT. Elevations in serum PCT and ADM levels are associated with severe sepsis and coronavirus disease 2019 (COVID-19). PCT enhances sepsis mortality and it binds to the CGRP receptor, which is a heterodimer of CT receptor-like receptor and receptor activity-modifying protein 1. The N-terminal truncated form of PCT, PCT_3-116, is produced by the cleavage of PCT by dipeptidyl peptidase 4 (DPP-4) and is the main form of PCT in serum during sepsis, inducing microvascular permeability. Mid-regional pro-adrenomedullin (MR-proADM) is used instead of ADM as a biological indicator because ADM is rapidly degraded, and MR-proADM is released at the same rate as ADM. ADM reduces endothelial permeability and promotes endothelial stability. Endothelial dysfunction is responsible for multiple organ failure in sepsis and COVID-19 patients. Therefore, ADM may be an important molecule for improving the severity associated with sepsis and COVID-19. This review focuses on the current knowledge of PCT and ADM in sepsis and COVID-19. Full article

Introduction: Invading extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-PE), non-ESBL E. coli, and other bacteria form a complex environment in the gut. The duration and dynamics of ESBL-PE colonization varies among individuals. Understanding the factors associated with colonization may lead to decolonization strategies. In this study, we aim to identify (i) single E. coli strains and (ii) microbiome networks that correlate with retention or decline of colonization, and (iii) pan-sensitive E. coli strains that potentially could be used to displace ESBL-PE during colonization. Methods and analysis: We recruit healthy travellers to Southeast Asia for a one-year prospective observational follow-up study. We collect and biobank stool, serum, and peripheral blood mononuclear cells (PBMCs) at predefined timepoints. Additional information is collected with questionnaires. We determine the colonization status with ESBL-PE and non-ESBL E. coli and quantify cell densities in stools and ratios over time. We characterize multiple single bacterial isolates per patient and timepoint using whole genome sequencing (WGS) and 16S/ITS amplicon-based and shotgun metagenomics. We determine phylogenetic relationships between isolates, antimicrobial resistance (AMR; phenotypic and genotypic), and virulence genes. We describe the bacterial and fungal stool microbiome alpha and beta diversity on 16S/ITS metagenomic data. We describe patterns in microbiome dynamics to identify features associated with protection or risk of ESBL-PE colonization. Ethics and dissemination: The study is registered (clinicaltrials.gov; NCT04764500 on 09/02/2019) and approved by the Ethics Committee (EKNZ project ID 2019-00044). We will present anonymized results at conferences and in scientific journals. Bacterial sequencing data will be shared via publicly accessible databases according to FAIR principles. Full article

This study investigated the presence of Aeromonas spp. on a dairy farm in central Texas that employed a free-stall management system. A total of 140 samples were collected from areas of two different barns. Twenty-two presumptive Aeromonas isolates were cultured. Phenotypic analysis identified five Aeromonas spp. Twenty isolates exhibited β-lactam and one displayed tetracycline resistance. Phylogenetic analysis of the WGS data suggested only four Aeromonas spp. All isolates possessed at least one β-lactam resistance gene and one isolate possessed tet(E). No plasmids were identified from sequence alignments. Virulence genes were identified in all four Aeromonas spp. Mobility elements were identified in three of these, with the exception being A. dhakensis. Four of the transposons identified in this study have been associated with multidrug resistance in Italy, Sweden, and Singapore. There was no significant difference in the proportion of isolates from either barn. The absence of plasmids suggests mobility elements and virulence genes were localized to the chromosome. On a dairy farm of healthy cattle, these 22 Aeromonas isolates were considered normal environmental flora while illustrating the ubiquitous nature of Aeromonas spp. globally. Full article

E. coli O157:H7 is a known Shiga toxin-producing Escherichia coli (STEC), causing foodborne disease globally. Cattle are the main reservoir and consumption of beef and beef products contaminated with E. coli O157:H7 is an important source of STEC infections in humans. To emphasize the cattle-to-human transmission through the consumption of contaminated beef in Bishoftu, Ethiopia, whole-genome sequencing (WGS) was performed on E. coli O157 strains isolated from three sources (cattle, beef, and humans). Forty-four E. coli O157:H7 isolates originating from 23 cattle rectal contents, three cattle hides, five beef carcasses, seven beef cuts at retail shops, and six human stools in Bishoftu between June 2017 and May 2019 were included. This study identified six clusters of closely related E. coli O157:H7 isolates based on core genome multilocus sequence typing (cgMLST) by targeting 2513 loci. A genetic linkage was observed among the isolate genomes from the cattle rectal contents, cattle hides, beef carcasses at slaughterhouses, beef at retail shops, and human stool within a time frame of 20 months. All the strains carried practically the same repertoire of virulence genes except for the stx2 gene, which was present in all but eight of the closely related isolates. All the strains carried the mdfA gene, encoding for the MdfA multi-drug efflux pump. CgMLST analysis revealed genetically linked E. coli O157:H7 isolates circulating in the area, with a potential transmission from cattle to humans through the consumption of contaminated beef and beef products. Full article

Heterosigma akashiwo is a golden-brown unicellular phytoflagellate with a high potential to create harmful algal blooms (HABs) and kill fish in many coastal regions worldwide, resulting in significant economic losses. Climate change and global warming have been introduced as triggers that impact the frequency and severity of H. akashiwo and other bloom-forming species in the past decades. In this review paper, the author tried to briefly discuss the morphology and taxonomy of H. akashiwo and show how environmental parameters can influence the physiology and toxicity of this species. Although the toxin production and mechanisms are still a conundrum, the proposed fish-killing mechanisms will be reviewed in the next step. Full article

Vector-borne diseases spread from wild animals and their associated ectoparasites to humans and domesticated animals. Wildlife markets are recognized as important areas where this transfer can take place. We assessed the potential for spreading vector-borne diseases in two live and wet markets in Myanmar (Mong La, on the Myanmar-China border) and Indonesia (Sukahaji in Bandung on the island of Java) by making an inventory of all live and freshly killed wild mammals for sale. For eight mammal families, we quantified the number of animals on offer, and we used a heatmap cluster analysis to map vector-borne diseases that these families may carry. In Myanmar, we observed large numbers of wild pigs and deer (potentially carrying West Nile and various encephalitis viruses) whereas in Indonesia we observed Old World fruit bats (potentially carrying Chikungunya and encephalitis viruses) and squirrels (potentially carrying West Nile and encephalitis viruses). The trade in Indonesia was dominated by live mammals offered for sale as pets, and only Old World fruit bats and squirrels traded for traditional Asian medicine were killed in the markets. The trade in Myanmar was more geared towards wild meat (e.g., wild pigs, deer, primates) and traditional Asian medicine (squirrels). The combined risks of vector-borne diseases spreading from traded animals to human health highlight the need for an integrated approach protecting public health, economic interests and biodiversity. Full article

Between 2018 and 2021, several mastic trees (Pistacia lentiscus var. Chia) sampled in the field and the nursery of the Chios Mastiha Growers Association (CMGA) were analyzed to determine the cause of dominant diseases. Symptoms included defoliation, leaf, and twig blight, wilting and/or apoplexy of trees and apoplexy of young hardwood cuttings. Moreover, brown discoloration had also been observed on older woody parts of the trees such as branches and tree trunks. Several pathogens have been isolated and identified as the causing agents. Neopestalotiopsis and Alternaria species were isolated consistently from necrotic tissues of mastic trees (branches, twigs, and leaves) in the field and the nursery. All fungal isolates’ pathogenicity was confirmed by applying Koch’s postulates on young mastic trees under glasshouse conditions. Fungal pathogens were identified by sequence analyses of the ITS, β-tubulin, and histone gene regions. Alternaria species were analyzed further by sequencing the endopolygalacturonase (endoPG) and the Alternaria major allergen (Alta1) genes. More specifically, the isolates were identified as Neopestalotiopsis clavispora, Alternaria arborescens, and A. alternata based on morphological features and sequence analyses. This is the first report of N. clavispora, A. arborescens, and A. alternata on P. lentiscus var. Chia. Full article

Increasing pollution has significantly threatened the Antarctic ecosystem. The contamination of hydrocarbons has drawn a considerable amount of attention owing to their toxicity, recalcitrance, and persistence. Considering the Antarctic Treaty, only indigenous species are allowed to bioremediate the contaminated environment. However, the knowledge of the ecological role, physiology, function, and genomics of endemic hydrocarbon consumers is still limited. Here, we investigated the dynamics of phenanthrene-consuming communities derived from the Antarctic soil and found that Variovorax, Rhodocyclaceae, and Hydrogenophaga were differentiated in all the phenanthrene-consuming subcultures. We isolated a pure culture of the key hydrocarbon consumer Variovorax sp. strain N23. Moreover, the result of the polyphasic approach suggested that strain N23 represents a novel species of the genus Variovorax. In addition, the genomic characteristics of this strain revealed incomplete degradation pathways for diverse hydrocarbons. Overall, this study reveals the relatively weak hydrocarbon-degrading potential of the indigenous bacteria and suggests the need for more careful protection of the Antarctic ecosystem. Full article

The available literary data suggest the general applicability and benefits of the Matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometry (MS) in the field of microbiological identification. Due to its high reliability, MALDI-TOF might generally be the alternative to the the16s-rRNA sequence-based and serological-based methods. The essence of the technique is to map the unique protein pattern of microbes that contributes to characterizing a wide variety of microorganisms, including bacteria, fungi, and viruses. With its application, the well-known bacterial and fungal species can be quickly identified, thus saving time in clinical diagnostics. In recent years, new protocols have appeared for directly identifying pathogenic strains from patient samples (blood, urine, feces), a major milestone in healthcare applications. On the other hand, these applications only have reliable results under certain conditions (homogeneous infection, adequate cell count, appropriate separation technique). This review aims to introduce and summarize those developments that have been enabled for routine application in the field of clinical diagnosis. Full article

Background: D-dimer, generated upon the degradation of fibrin, is extensively used to detect thrombosis in various diseases. It is also explored as a marker for thrombosis in cases with COVID-19 disease. Few studies have confirmed its utility as a marker for assessing disease severity. Objectives: The current research was undertaken to determine the role of D-dimer in patients with COVID-19 and to investigate any association with the progression and severity of the disease in the Saudi population. Methods: Clinical indices in confirmed COVID-19 patients were collected from tertiary care hospitals in Aljouf and Qassim regions. The plasma D-dimer levels were quantified directly in the samples collected from COVID-19 patients (n = 148) using an immunofluorescence assay, and the data were presented in Fibrinogen Equivalent Units (mg/L). The collected data of D-dimer were analyzed based on COVID-19 severity, age, and the gender of patients. Results: The findings show that the plasma D-dimer concentrations were significantly (p = 0.0027) elevated in COVID-19 cases (n = 148), compared to in the normal healthy uninfected controls (n = 309). Moreover, the D-dimer levels were analyzed according to the severity of the disease in the patients. The data revealed that D-dimer concentrations were significantly increased in patients with mild infection to moderate disease, and the levels were the highest in patients with severe COVID-19 disease (p < 0.05). Our analysis demonstrates that the D-dimer levels have no association with the age or gender of COVID-19 patients (p > 0.05) in the study population. Conclusions: D-dimer can serve as a biomarker not only for the detection of COVID-19 infection, but also for determining the severity of infection of COVID-19 disease. Full article

Sampling animals for carriage of meticillin-resistant, coagulase-positive staphylococci (MRCoPS), considered zoonotic pathogens, can be challenging and time-consuming. Developing methods to identify mecA from non-invasive samples, e.g., faeces, would benefit AMR surveillance and management of MRS carrier animals. This study aimed to distinguish MRS carriers from non-carriers from faecal samples using quantitative polymerase chain reaction (qPCR) for mecA. Paired faecal and nasal swab samples (n = 86) were obtained from 13 dogs and 20 humans as part of a longitudinal study. Nasal MRCoPS carriage (either MR-Staphylococcus aureus or MR-Staphylococcus pseudintermedius was confirmed by identification of species (nuc) and meticillin resistance (mecA) (PCR). Faecal DNA (n = 69) was extracted and a qPCR method was optimised to provide a robust detection method. The presence of faecal mecA was compared between MRS carriers and non-carriers (Kruskal–Wallis test). Nasal swabbing identified seven canine and four human MRCoPS carriers. mecA was detected in 13/69 faecal samples, including four MRCoPS carriers and nine non-carriers. For dogs, there was no significant association (p = 1.000) between carrier status and mecA detection; for humans, mecA was more commonly detected in MRCoPS carriers (p = 0.047). mecA was detected in faeces of MRCoPS carriers and non-carriers by qPCR, but larger sample sizes are required to determine assay sensitivity. This rapid method enables passive surveillance of mecA in individuals and the environment. Full article

Ticks are amongst the important ectoparasites where livestock are concerned, as they adversely affect the animals through bloodsucking. In tropical and subtropical countries, they transmit pathogens such as babesiosis, theileriosis, ehrlichiosis, and anaplasmosis in cattle, causing a reduction in production rate and significant concomitant economic losses. Ticks affect 80% of the cattle population across the world, with an estimated economic loss of USD 20–30 billion per year. In South Africa, economic losses in the livestock industry caused by ticks and tick-borne diseases are estimated to exceed USD 33 million per year (ZAR 500 million). There are seven major genera of ixodid ticks in Southern Africa (i.e., Amblyomma, Dermacentor, Haemaphysalis, Hyalomma, Ixodes and Rhipicephalus). The environment in which a tick lives is made up of all the various biological and abiotic factors that are either necessary or unnecessary for its life. The areas where various ticks have been found have been documented in many publications. Using these data, maps of possible species’ habitats can be made. Historical records on tick distribution may be incorrect due to identification mistakes or a change in the tick’s name. All the sources used to generate the maps for this review were unpublished and came from a wide range of sources. To identify tick species and the accompanying microbial ecosystems, researchers are increasingly adopting tick identification methods including 16S and 18S rDNA gene sequencing. Indeed, little is known about the genetic alterations that give important traits, including the predilection for tick hosts, transmission, and acaricide resistance. Opportunities for exploring these changes in tick populations and subpopulations are provided by advancements in omics technologies. The literature on the variety of ixodid ticks, their direct and indirect effects, and control methods in South Africa is compiled in this review. Full article