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Microorganisms, Volume 9, Issue 4 (April 2021) – 212 articles

Cover Story (view full-size image): The aim of this work was to search for new strains of microbes. A number of microorganisms have been isolated from arable soil near Belgorod, Russia. Isolated strains of the genera Bacillus and Pseudomonas were characterized by high activity against fungal phytopathogens. Notably, one of the bacterial strains, identified as Priestia aryabhattai, had an unusual cell morphology and developmental cycle that was significantly different from all previously described bacterial Bacillus and Priestia genera. View this paper
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Article
Antimicrobial Use in Brazilian Swine Herds: Assessment of Use and Reduction Examples
Microorganisms 2021, 9(4), 881; https://doi.org/10.3390/microorganisms9040881 - 20 Apr 2021
Cited by 4 | Viewed by 969
Abstract
Brazil, as a major pig producer, is currently experiencing the widespread use of antimicrobials as a serious issue to be addressed. For measures to be taken in this direction, the extent of the problem must be known. The goal of this study was [...] Read more.
Brazil, as a major pig producer, is currently experiencing the widespread use of antimicrobials as a serious issue to be addressed. For measures to be taken in this direction, the extent of the problem must be known. The goal of this study was to evaluate the use of antimicrobials in 25 Brazilian swine herds. Antimicrobial use from birth to slaughter was correlated with biosecurity and productivity. After the first assessment (2016; M0), 13 herds implemented good practices to reduce antimicrobial use. Four years after the implementation of these measures (2020; M1), data about antimicrobial usage from these herds were collected. The results of the first assessment (M0) demonstrated a troublesome scenario: the mean value of antimicrobials used was 358.4 mg/kg of pig produced; the median of the pig’s lifetime exposure to antimicrobials was 73.7%, and the median number of drugs used was seven. A positive correlation between the antimicrobials consumed and the pig’s antimicrobial exposure time was detected. Nevertheless, these data did not correlate with biosecurity score or productivity. A significant difference was detected in M1, where a median 30% reduction in antimicrobials consumed was detected. There was also a 44.3% reduction of the pig’s lifetime exposure to antimicrobials. The median number of drugs used was reduced from seven to five. Antimicrobial use did not always reflect the sanitary condition or the real therapeutic needs, easily leading to overuse. Full article
(This article belongs to the Special Issue Farm Animal and Wildlife Zoonotic Microorganisms)
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Article
Ambroxol Treatment Suppresses the Proliferation of Chlamydia pneumoniae in Murine Lungs
Microorganisms 2021, 9(4), 880; https://doi.org/10.3390/microorganisms9040880 - 20 Apr 2021
Viewed by 1029
Abstract
Ambroxol (Ax) is used as a mucolytics in the treatment of respiratory tract infections. Ax, at a general dose for humans, does not alter Chlamydia pneumoniae growth in mice. Therefore, we aimed to investigate the potential anti-chlamydial effect of Ax at a concentration [...] Read more.
Ambroxol (Ax) is used as a mucolytics in the treatment of respiratory tract infections. Ax, at a general dose for humans, does not alter Chlamydia pneumoniae growth in mice. Therefore, we aimed to investigate the potential anti-chlamydial effect of Ax at a concentration four timed higher than that used in human medicine. Mice were infected with C. pneumoniae and 5-mg/kg Ax was administered orally. The number of recoverable C. pneumoniae inclusion-forming units (IFUs) in Ax-treated mice was significantly lower than that in untreated mice. mRNA expression levels of several cytokines, including interleukin 12 (IL-12), IL-23, IL-17F, interferon gamma (IFN-γ), and surfactant protein (SP)-A, increased in infected mice treated with Ax. The IFN-γ protein expression levels were also significantly higher in infected and Ax-treated mice. Furthermore, the in vitro results suggested that the ERK 1/2 activity was decreased, which is essential for the C. pneumoniae replication. SP-A and SP-D treatments significantly decreased the number of viable C. pneumoniae IFUs and significantly increased the attachment of C. pneumoniae to macrophage cells. Based on our results, a dose of 5 mg/kg of Ax exhibited an anti-chlamydial effect in mice, probably an immunomodulating effect, and may be used as supporting drug in respiratory infections caused by C. pneumoniae. Full article
(This article belongs to the Section Medical Microbiology)
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Communication
Activation of the JNK/MAPK Signaling Pathway by TGF-β1 Enhances Neonatal Fc Receptor Expression and IgG Transcytosis
Microorganisms 2021, 9(4), 879; https://doi.org/10.3390/microorganisms9040879 - 20 Apr 2021
Cited by 2 | Viewed by 820
Abstract
The neonatal Fc receptor (FcRn) transports maternal immunoglobulin G (IgG) to the foetus or newborn and protects the IgG from degradation. FcRn is expressed in several porcine tissues and cell types and its expression levels are regulated by immune and inflammatory events. IPEC-J2 [...] Read more.
The neonatal Fc receptor (FcRn) transports maternal immunoglobulin G (IgG) to the foetus or newborn and protects the IgG from degradation. FcRn is expressed in several porcine tissues and cell types and its expression levels are regulated by immune and inflammatory events. IPEC-J2 cells are porcine intestinal columnar epithelial cells that were isolated from neonatal piglet mid-jejunum. We hypothesized that transforming growth factor β1 (TGF-β1) upregulated pFcRn expression in IPEC-J2 cells. To test this hypothesis, we treated IPEC-J2 cells with TGF-β1 and demonstrated that porcine FcRn (pFcRn) expression was significantly increased. SP600125, a specific mitogen-activated protein kinase (MAPK) inhibitor, reduced TGF-β1-induced pFcRn expression in IPEC-J2 cells. We performed luciferase reporter assays and showed that the c-JUN sensitive region of the pFcRn promoter gene was located between positions −1215 and −140. The c-JUN sequence, in combination with the pFcRn promoter, regulated luciferase reporter activity in response to TGF-β1 stimulation. Chromatin immunoprecipitation confirmed that there were three c-JUN binding sites in the pFcRn promoter. Furthermore, in addition to increased pFcRn expression, TGF-β1 also enhanced IgG transcytosis in IPEC-J2 cells. In summary, our data showed that the modulation of JNK/MAPK signaling by TGF-β1 was sufficient to upregulate pFcRn expression. Full article
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Article
Bacterial Microbiota of Field-Collected Helicoverpa zea (Lepidoptera: Noctuidae) from Transgenic Bt and Non-Bt Cotton
Microorganisms 2021, 9(4), 878; https://doi.org/10.3390/microorganisms9040878 - 20 Apr 2021
Cited by 1 | Viewed by 973
Abstract
The bollworm, Helicoverpa zea (Boddie) (Lepidoptera: Noctuidae), is an important agricultural pest in U.S. cotton and is managed using transgenic hybrids that produce insecticidal proteins from the bacterium, Bacillus thuringiensis (Bt). The reduced efficacy against H. zea caterpillars of Bt plants expressing Cry [...] Read more.
The bollworm, Helicoverpa zea (Boddie) (Lepidoptera: Noctuidae), is an important agricultural pest in U.S. cotton and is managed using transgenic hybrids that produce insecticidal proteins from the bacterium, Bacillus thuringiensis (Bt). The reduced efficacy against H. zea caterpillars of Bt plants expressing Cry toxins is increasing in the field. In a first step towards understanding Bt cotton–bollworm–microbiota interactions, we investigated the internal bacterial microbiota of second–third stadium H. zea collected in the field from non-Bt versus Bt (WideStrike) cotton in close proximity (in North Carolina, USA). The bacterial populations were analyzed using culture-dependent and -independent molecular approaches. We found that WideStrike samples had a higher bacterial density and diversity per larva than insects collected from non-Bt cotton over two field seasons: 8.42 ± 0.23 and 5.36 ± 0.75 (log10 colony forming units per insect) for WideStrike compared to 6.82 ± 0.20 and 4.30 ± 0.56 for non-Bt cotton for seasons 1 and 2, respectively. Fifteen phyla, 103 families, and 229 genera were identified after performing Illumina sequencing of the 16S rRNA. At the family level, Enterobacteriaceae and Enterococcaceae were the most abundant taxa. The Enterococcaceae family was comprised mostly of Enterococcus species (E. casseliflavus and another Enterococcus sp.). Members of the Enterococcus genus can acidify their environment and can potentially reduce the alkaline activation of some Bt toxins. These findings argue for more research to better understand the role of cotton–bollworm–bacteria interactions and the impact on Bt toxin caterpillar susceptibility. Full article
(This article belongs to the Special Issue Microbiota in Insects)
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Article
Comparing Sediment Microbiomes in Contaminated and Pristine Wetlands along the Coast of Yucatan
Microorganisms 2021, 9(4), 877; https://doi.org/10.3390/microorganisms9040877 - 20 Apr 2021
Cited by 2 | Viewed by 1294
Abstract
Microbial communities are important players in coastal sediments for the functioning of the ecosystem and the regulation of biogeochemical cycles. They also have great potential as indicators of environmental perturbations. To assess how microbial communities can change their composition and abundance along coastal [...] Read more.
Microbial communities are important players in coastal sediments for the functioning of the ecosystem and the regulation of biogeochemical cycles. They also have great potential as indicators of environmental perturbations. To assess how microbial communities can change their composition and abundance along coastal areas, we analyzed the composition of the microbiome of four locations of the Yucatan Peninsula using 16S rRNA gene amplicon sequencing. To this end, sediment from two conserved (El Palmar and Bocas de Dzilam) and two contaminated locations (Sisal and Progreso) from the coast northwest of the Yucatan Peninsula in three different years, 2017, 2018 and 2019, were sampled and sequenced. Microbial communities were found to be significantly different between the locations. The most noticeable difference was the greater relative abundance of Planctomycetes present at the conserved locations, versus FBP group found with greater abundance in contaminated locations. In addition to the difference in taxonomic groups composition, there is a variation in evenness, which results in the samples of Bocas de Dzilam and Progreso being grouped separately from those obtained in El Palmar and Sisal. We also carry out the functional prediction of the metabolic capacities of the microbial communities analyzed, identifying differences in their functional profiles. Our results indicate that landscape of the coastal microbiome of Yucatan sediment shows changes along the coastline, reflecting the constant dynamics of coastal environments and their impact on microbial diversity. Full article
(This article belongs to the Special Issue Microbial Evolution of Extremophiles)
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Article
Immune Transcriptome of Cells Infected with Enterovirus Strains Obtained from Cases of Autoimmune Thyroid Disease
Microorganisms 2021, 9(4), 876; https://doi.org/10.3390/microorganisms9040876 - 19 Apr 2021
Cited by 2 | Viewed by 987
Abstract
Background: Hashimoto’s thyroiditis and Graves’ disease are autoimmune thyroid disorders (AITD) of unknown origin. Enterovirus (EV) infection of thyroid cells has been implicated as a possible initiator of cell damage and of organ-specific autoimmunity. We asked whether persistent infection of human epithelial cells [...] Read more.
Background: Hashimoto’s thyroiditis and Graves’ disease are autoimmune thyroid disorders (AITD) of unknown origin. Enterovirus (EV) infection of thyroid cells has been implicated as a possible initiator of cell damage and of organ-specific autoimmunity. We asked whether persistent infection of human epithelial cells with EV strains obtained from thyroid tissue of AITD patients could be associated with transcriptional changes capable of fostering immunopathology. Methods: EV isolates obtained from thyroid tissue of AITD cases were used to infect the AV3 epithelial cell line. AV3 cells incubated with a virus-free medium from thyroid tissue of subjects without evidence of thyroid autoimmunity were used as uninfected controls. Transcripts of immune-related genes were compared in infected vs. uninfected cells. Results: The EV genome and antigens were detected only in the cells exposed to AITD-derived virus isolates, not in control cells. Persistent EV infection, while suppressing transcription of several type I IFN and cytokine determinants, was associated with enhanced transcription of NFKB1/RELA, IFNAR1, JAK1/STAT1, i.e., the determinants that play key immunologic roles. Infection also led to upregulation of the CCL2 chemokine and the IL-18 pro-inflammatory interleukin. Conclusion: As in the case of EV strains obtained from autoimmune diabetes, results show that the EV strains that are present in the thyroid of AITD cases do repress IFN and cytokine pathways. JAK1/STAT1 upregulation supports activation of TLR pathways and aberrant T cell signaling. In the early phases of AITD, our results highlight the potential benefit of interventions aimed at blocking the viral infection and easing the inflammatory response. Full article
(This article belongs to the Special Issue Enterovirus Infections and Chronic Disorders)
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Article
Enteric Ganglioneuritis, a Common Feature in a Subcutaneous TBEV Murine Infection Model
Microorganisms 2021, 9(4), 875; https://doi.org/10.3390/microorganisms9040875 - 18 Apr 2021
Viewed by 1146
Abstract
Tick-borne encephalitis (TBE) is a severe neurologic disease in Europe and Asia. Disease expression ranges from asymptomatic to severe neurological clinical pictures, involving meningitis, encephalitis, meningoencephalitis and potentially fatal outcome. Humans mostly become infected with TBE virus (TBEV) by the bite of an [...] Read more.
Tick-borne encephalitis (TBE) is a severe neurologic disease in Europe and Asia. Disease expression ranges from asymptomatic to severe neurological clinical pictures, involving meningitis, encephalitis, meningoencephalitis and potentially fatal outcome. Humans mostly become infected with TBE virus (TBEV) by the bite of an infected tick. Gastrointestinal (GI) symptoms in humans are mainly attributed to the first viremic phase of TBEV infection with unspecific symptoms and/or resulting from severe neurological impairment of the central nervous system (CNS). We used the subcutaneous TBEV-infection of C57BL/6 mice as a model to analyze GI complications of TBE. We observed the acute distension and segmental dilation of the intestinal tract in 10 of 22 subcutaneously infected mice. Histological analysis revealed an intramural enteric ganglioneuritis in the myenteric and submucosal plexus of the small and large intestine. The numbers of infiltrating macrophages and CD3+ T lymphocytes correlated with the severity of ganglioneuritis, indicating an immune-mediated pathogenesis due to TBEV-infection of the enteric plexus. Our study demonstrates that the inflammation of enteric intramural ganglia presents to be a common feature in TBEV-infected mice. Accordingly, the results of this mouse model emphasize that GI disease manifestation and consequences for long-term sequelae should not be neglected for TBEV-infections in humans and require further investigation. Full article
(This article belongs to the Special Issue Tick-Borne Encephalitis)
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Article
Mitigating the Spread and Translocation of Salmonella Enteritidis in Experimentally Infected Broilers under the Influence of Different Flooring Housing Systems and Feed Particle Sizes
Microorganisms 2021, 9(4), 874; https://doi.org/10.3390/microorganisms9040874 - 18 Apr 2021
Viewed by 804
Abstract
This study aimed to evaluate the influences of different flooring designs and feed particle sizes on the spread of Salmonella (S.) in broiler chickens. Birds (n = 480) were allocated to four different housing systems (fully littered with and without [...] Read more.
This study aimed to evaluate the influences of different flooring designs and feed particle sizes on the spread of Salmonella (S.) in broiler chickens. Birds (n = 480) were allocated to four different housing systems (fully littered with and without floor heating, partially and fully slatted flooring with sand bath) and two dietary treatments (finely and coarsely ground diets) in 24 boxes. Two broilers per box were experimentally infected with S. Enteritidis (8.00 log10 CFU/bird) at d 17. Salmonella prevalence in caecal contents and the liver was highest in broilers housed on fully slatted floor until d 36/37 (88.1% and 91.5%, respectively), and lowest in litter flooring (caecal content 64.4%) and litter flooring with floor heating (liver 61.7%). In turn, broilers on littered flooring expressed the lowest Salmonella counts in caecal content at d 36/37 (2.21 ± 1.75 log10 CFU/g), partial slatted flooring the highest (3.76 ± 1.46 log10 CFU/g). The mean Salmonella count in the caecal content was significantly lower for birds fed a coarsely ground diet (0.96 and 1.94 log10 CFU/g) than a finely ground diet (5.07 and 3.34 log10 CFU/g) at d 23 and d 36/37, respectively (p < 0.0001). Slatted flooring with a sand bath did not show advantages in terms of Salmonella reduction, whereas the coarsely ground diet markedly reduced the spread of Salmonella. Full article
(This article belongs to the Special Issue Salmonella and Salmonellosis)
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Article
Encystation of Entamoeba histolytica in Axenic Culture
Microorganisms 2021, 9(4), 873; https://doi.org/10.3390/microorganisms9040873 - 18 Apr 2021
Cited by 2 | Viewed by 1330
Abstract
Entamoeba histolytica is a parasitic protozoan that causes amoebic dysentery, which affects approximately 90 million people each year worldwide. E. histolytica is transmitted through ingestion of food and water contaminated with the cyst form, which undergoes excystation in the small intestine to the [...] Read more.
Entamoeba histolytica is a parasitic protozoan that causes amoebic dysentery, which affects approximately 90 million people each year worldwide. E. histolytica is transmitted through ingestion of food and water contaminated with the cyst form, which undergoes excystation in the small intestine to the trophozoite form that colonizes the large intestine. The reptile pathogen Entamoeba invadens has served as a model for studying stage conversion between the trophozoite and cyst form due to lack of reproducible encystation of E. histolytica in the laboratory. Although much has been learned about encystation and excystation using E. invadens, the findings do not fully translate to E. histolytica due to the extensive genetic and host differences between these species. Here, we present the first reproducible encystation of E. histolytica in vitro. The cysts produced were viable and displayed the four characteristic hallmarks: round shape, chitinous cell wall, tetranucleation, and detergent resistance. Using flow cytometry analysis, glucose limitation and high cell density were key for encystation, as for E. invadens. Entry into encystation was enhanced by the short-chain fatty acids acetate and propionate, unlike for E. invadens. This new model will now allow the further study of E. histolytica stage conversion, transmission, and treatment. Full article
(This article belongs to the Section Parasitology)
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Article
Occurrence of Salmonella in the Cattle Production in France
Microorganisms 2021, 9(4), 872; https://doi.org/10.3390/microorganisms9040872 - 17 Apr 2021
Cited by 2 | Viewed by 1087
Abstract
Salmonella is among the most common foodborne pathogens worldwide, and can lead to acute gastroenteritis. Along with poultry, cattle production is recognized as an important source of human infection. Salmonella transmission from cattle to humans can occur through the environment, or through close [...] Read more.
Salmonella is among the most common foodborne pathogens worldwide, and can lead to acute gastroenteritis. Along with poultry, cattle production is recognized as an important source of human infection. Salmonella transmission from cattle to humans can occur through the environment, or through close contact with sick animals or their derived products. This study aimed to investigate the intestinal carriage of Salmonella spp. within French cattle production. A total of 959 cattle intestinal samples, from one of the largest French slaughterhouses, were analyzed. Isolated strains were genotyped by pulsed field gel electrophoresis (PFGE), and a sub-selection was taken by whole genome sequencing (WGS). Twenty-nine samples were positive for Salmonella spp., yielding an estimated prevalence of 3% in cattle production. Eight different Salmonella serotypes were found: Montevideo was the most prevalent (34%), followed by Mbandaka (24%) and Anatum (14%). PFGE genotyping allowed the clustering of Salmonella isolates according to their serotype. Within the clusters, some isolates presented 100% similarity. To investigate potential epidemiological links between them, WGS and core genome multilocus sequence typing (cgMLST) were used, revealing identical profiles between isolates originating from different areas and/or different animal breeds. This investigation provides new insights on Salmonella serotype epidemiology in cattle production in France. Full article
(This article belongs to the Special Issue Salmonella and Salmonellosis)
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Article
The Gut Microbiota Can Provide Viral Tolerance in the Honey Bee
Microorganisms 2021, 9(4), 871; https://doi.org/10.3390/microorganisms9040871 - 17 Apr 2021
Cited by 12 | Viewed by 1768
Abstract
Adult honey bees host a remarkably consistent gut microbial community that is thought to benefit host health and provide protection against parasites and pathogens. Currently, however, we lack experimental evidence for the causal role of the gut microbiota in protecting the Western honey [...] Read more.
Adult honey bees host a remarkably consistent gut microbial community that is thought to benefit host health and provide protection against parasites and pathogens. Currently, however, we lack experimental evidence for the causal role of the gut microbiota in protecting the Western honey bees (Apis mellifera) against their viral pathogens. Here we set out to fill this knowledge gap by investigating how the gut microbiota modulates the virulence of a major honey bee viral pathogen, deformed wing virus (DWV). We found that, upon oral virus exposure, honey bee survival was significantly increased in bees with an experimentally established normal gut microbiota compared to control bees with a perturbed (dysbiotic) gut microbiota. Interestingly, viral titers were similar in bees with normal gut microbiota and dysbiotic bees, pointing to higher viral tolerance in bees with normal gut microbiota. Taken together, our results provide evidence for a positive role of the gut microbiota for honey bee fitness upon viral infection. We hypothesize that environmental stressors altering honey bee gut microbiota composition, e.g., antibiotics in beekeeping or pesticides in modern agriculture, could interact synergistically with pathogens, leading to negative effects on honey bee health and the epidemiology and impact of their viruses. Full article
(This article belongs to the Special Issue Microorganisms in Pollinators: Interactions with Other Factors)
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Article
Gluconacetobacter diazotrophicus Pal5 Enhances Plant Robustness Status under the Combination of Moderate Drought and Low Nitrogen Stress in Zea mays L.
Microorganisms 2021, 9(4), 870; https://doi.org/10.3390/microorganisms9040870 - 17 Apr 2021
Cited by 2 | Viewed by 1682
Abstract
Plant growth promoting endophytic bacteria, which can fix nitrogen, plays a vital role in plant growth promotion. Previous authors have evaluated the effect of Gluconacetobacter diazotrophicus Pal5 inoculation on plants subjected to different sources of abiotic stress on an individual basis. The present [...] Read more.
Plant growth promoting endophytic bacteria, which can fix nitrogen, plays a vital role in plant growth promotion. Previous authors have evaluated the effect of Gluconacetobacter diazotrophicus Pal5 inoculation on plants subjected to different sources of abiotic stress on an individual basis. The present study aimed to appraise the effect of G. diazotrophicus inoculation on the amelioration of the individual and combined effects of drought and nitrogen stress in maize plants (Zea mays L.). A pot experiment was conducted whereby treatments consisted of maize plants cultivated under drought stress, in soil with a low nitrogen concentration and these two stress sources combined, with and without G. diazotrophicus seed inoculation. The inoculated plants showed increased plant biomass, chlorophyll content, plant nitrogen uptake, and water use efficiency. A general increase in copy numbers of G. diazotrophicus, based on 16S rRNA gene quantification, was detected under combined moderate stress, in addition to an increase in the abundance of genes involved in N fixation (nifH). Endophytic colonization of bacteria was negatively affected by severe stress treatments. Overall, G. diazotrophicus Pal5 can be considered as an effective tool to increase maize crop production under drought conditions with low application of nitrogen fertilizer. Full article
(This article belongs to the Special Issue Endophytes for Managing Biotic and Abiotic Stress in Plants)
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Communication
Escherichia coli Affects Expression of Circadian Clock Genes in Human Hepatoma Cells
Microorganisms 2021, 9(4), 869; https://doi.org/10.3390/microorganisms9040869 - 17 Apr 2021
Cited by 2 | Viewed by 900
Abstract
Recent research has indicated that dysbiosis of the gut microbiota can lead to an altered circadian clock of the mammalian host. Herein we developed an original system that allows real-time circadian studies of human HepG2 hepatoma cells co-cultured with bacteria. The HepG2 cells [...] Read more.
Recent research has indicated that dysbiosis of the gut microbiota can lead to an altered circadian clock of the mammalian host. Herein we developed an original system that allows real-time circadian studies of human HepG2 hepatoma cells co-cultured with bacteria. The HepG2 cells with stably integrated firefly luciferase reporter under the control of PERIOD2 promoter were co-cultured with E. coli strains isolated from human fecal samples from healthy individuals. The two E. coli strains differ in the phylogenetic group and the number of ExPEC virulence-associated genes: BJ17 has only two, and BJ23 has 15 of 23 tested. In the first 24 h, the E. coli BJ17 affected the HepG2 circadian clock more than BJ23. Cosinor analysis shows a statistically significant change in the amplitude of PER1 and 2 and the phase advance of PER3. A high percentage of necrotic and apoptotic cells occurred at 72 h, while a correlation between the number of ExPEC genes and the influence on the HepG2 core clock gene expression was observed. Our study reveals that the E. coli genetic background is important for the effect on the mammalian circadian clock genes, indicating possible future use of probiotic E. coli strains to influence the host circadian clock. Full article
(This article belongs to the Section Gut Microbiota)
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Review
Current Status of Putative Animal Sources of SARS-CoV-2 Infection in Humans: Wildlife, Domestic Animals and Pets
Microorganisms 2021, 9(4), 868; https://doi.org/10.3390/microorganisms9040868 - 17 Apr 2021
Cited by 18 | Viewed by 2246
Abstract
SARS-CoV-2 is currently considered to have emerged from a bat coronavirus reservoir. However, the real natural cycle of this virus remains to be elucidated. Moreover, the COVID-19 pandemic has led to novel opportunities for SARS-CoV-2 transmission between humans and susceptible animal species. In [...] Read more.
SARS-CoV-2 is currently considered to have emerged from a bat coronavirus reservoir. However, the real natural cycle of this virus remains to be elucidated. Moreover, the COVID-19 pandemic has led to novel opportunities for SARS-CoV-2 transmission between humans and susceptible animal species. In silico and in vitro evaluation of the interactions between the SARS-CoV-2 spike protein and eucaryotic angiotensin-converting enzyme 2 (ACE2) receptor have tentatively predicted susceptibility to SARS-CoV-2 infection of several animal species. Although useful, these data do not always correlate with in vivo data obtained in experimental models or during natural infections. Other host biological properties may intervene such as the body temperature, level of receptor expression, co-receptor, restriction factors, and genetic background. The spread of SARS-CoV-2 also depends on the extent and duration of viral shedding in the infected host as well as population density and behaviour (group living and grooming). Overall, current data indicate that the most at-risk interactions between humans and animals for COVID-19 infection are those involving certain mustelids (such as minks and ferrets), rodents (such as hamsters), lagomorphs (especially rabbits), and felines (including cats). Therefore, special attention should be paid to the risk of SARS-CoV-2 infection associated with pets. Full article
(This article belongs to the Section Medical Microbiology)
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Article
Diverse Genotypes and Species of Cryptosporidium in Wild Rodent Species from the West Coast of the USA and Implications for Raw Produce Safety and Microbial Water Quality
Microorganisms 2021, 9(4), 867; https://doi.org/10.3390/microorganisms9040867 - 17 Apr 2021
Cited by 2 | Viewed by 665
Abstract
Cryptosporidium spp. are protozoan parasites that infect perhaps all vertebrate animals, with a subset of species and genotypes that function as food- and waterborne pathogens. The objective of this work was to collate the Cryptosporidium species and genotypes from common wild rodents on [...] Read more.
Cryptosporidium spp. are protozoan parasites that infect perhaps all vertebrate animals, with a subset of species and genotypes that function as food- and waterborne pathogens. The objective of this work was to collate the Cryptosporidium species and genotypes from common wild rodents on the west coast of the USA and update the information regarding the zoonotic potential of Cryptosporidium from these ubiquitous wild species. Representative sequences of the 18S rRNA gene for a unique set of Cryptosporidium isolates obtained from deer mice, house mice, mountain beavers, yellow-bellied marmot, long-tailed vole, California ground squirrels, Belding’s ground squirrels, and a golden-mantled ground squirrel in GenBank were selected for phylogenetic analysis. Phylogenetic and BLAST analysis indicated that 4 (18%) of the 22 unique Cryptosporidium sequences from these wild rodent species were 99.75% to 100% identical to known zoonotic species (C. parvum, C. ubiquitum, C. xiaoi), suggesting that a minority of these representative Cryptosporidium isolates could have a public health impact through food and waterborne routes of human exposure. These zoonotic isolates were shed by deer mice and a yellow-bellied marmot from California, and from a mountain beaver trapped in Oregon. In addition, the group of unique Cryptosporidium isolates from deer mice and ground dwelling squirrels exhibited considerable DNA diversity, with multiple isolates appearing to be either host-limited or distributed throughout the various clades within the phylogenetic tree representing the various Cryptosporidium species from host mammals. These results indicate that only a subset of the unique Cryptosporidium genotypes and species obtained from wild rodents on the US west coast are of public health concern; nevertheless, given the geographic ubiquity of many of these host species and often high density at critical locations like municipal watersheds or produce production fields, prudent pest control practices are warranted to minimize the risks of water- and foodborne transmission to humans. Full article
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Article
Multi-Drug Resistant Plasmids with ESBL/AmpC and mcr-5.1 in Paraguayan Poultry Farms: The Linkage of Antibiotic Resistance and Hatcheries
Microorganisms 2021, 9(4), 866; https://doi.org/10.3390/microorganisms9040866 - 17 Apr 2021
Cited by 2 | Viewed by 914
Abstract
Poultry represents a common source of bacteria with resistance to antibiotics including the critically important ones. Selective cultivation using colistin, cefotaxime and meropenem was performed for 66 chicken samples coming from 12 farms in Paraguay while two breeding companies supplied the farms. A [...] Read more.
Poultry represents a common source of bacteria with resistance to antibiotics including the critically important ones. Selective cultivation using colistin, cefotaxime and meropenem was performed for 66 chicken samples coming from 12 farms in Paraguay while two breeding companies supplied the farms. A total of 62 Escherichia coli and 22 Klebsiella pneumoniae isolates were obtained and representative isolates were subjected to whole-genome sequencing. Relatively high prevalence of phylogenetic group D and F was observed in E. coli isolates and several zoonotic sequence types (STs) including ST457 (14 isolates), ST38 (5), ST10 (2), ST117 (2) or ST93 (4) were detected. Isolates from three farms, which purchased chicken from a Paraguayan hatchery showed higher prevalence of mcr-5.1 and blaCTX-M-8 compared to the other nine farms, which purchased chickens from a Brazilian hatchery. Moreover, none of the K. pneumoniae isolates were linked to the Paraguayan hatchery. ESBL/AmpC and mcr-5-carrying multi-drug resistant (MDR) plasmids were characterized, and complete sequences were obtained for eight plasmids. The study shed light on Paraguayan poultry farms as a reservoir of antibiotic resistance commonly conferred via MDR plasmids and showed linkage between resistance and origin of the chickens at the hatcheries level. Full article
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Article
Characterisation of Phage Susceptibility Variation in Salmonellaenterica Serovar Typhimurium DT104 and DT104b
Microorganisms 2021, 9(4), 865; https://doi.org/10.3390/microorganisms9040865 - 17 Apr 2021
Cited by 1 | Viewed by 1234
Abstract
The surge in mortality and morbidity rates caused by multidrug-resistant (MDR) bacteria prompted a renewal of interest in bacteriophages (phages) as clinical therapeutics and natural biocontrol agents. Nevertheless, bacteria and phages are continually under the pressure of the evolutionary phage–host arms race for [...] Read more.
The surge in mortality and morbidity rates caused by multidrug-resistant (MDR) bacteria prompted a renewal of interest in bacteriophages (phages) as clinical therapeutics and natural biocontrol agents. Nevertheless, bacteria and phages are continually under the pressure of the evolutionary phage–host arms race for survival, which is mediated by co-evolving resistance mechanisms. In Anderson phage typing scheme of Salmonella Typhimurium, the epidemiologically related definitive phage types, DT104 and DT104b, display significantly different phage susceptibility profiles. This study aimed to characterise phage resistance mechanisms and genomic differences that may be responsible for the divergent phage reaction patterns in S. Typhimurium DT104 and DT104b using whole genome sequencing (WGS). The analysis of intact prophages, restriction–modification systems (RMS), plasmids and clustered regularly interspaced short palindromic repeats (CRISPRs), as well as CRISPR-associated proteins, revealed no unique genetic determinants that might explain the variation in phage susceptibility among the two phage types. Moreover, analysis of genes coding for potential phage receptors revealed no differences among DT104 and DT104b strains. However, the findings propose the need for experimental assessment of phage-specific receptors on the bacterial cell surface and analysis of bacterial transcriptome using RNA sequencing which will explain the differences in bacterial susceptibility to phages. Using Anderson phage typing scheme of Salmonella Typhimurium for the study of bacteria-phage interaction will help improving our understanding of host–phage interactions which will ultimately lead to the development of phage-based technologies, enabling effective infection control. Full article
(This article belongs to the Special Issue Salmonella and Salmonellosis)
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Communication
Biological Properties and Genetic Characterization of Novel Low Pathogenic H7N3 Avian Influenza Viruses Isolated from Mallard Ducks in the Caspian Region, Dagestan, Russia
Microorganisms 2021, 9(4), 864; https://doi.org/10.3390/microorganisms9040864 - 17 Apr 2021
Viewed by 1058
Abstract
Avian influenza viruses (AIVs) are maintained in wild bird reservoirs, particularly in mallard ducks and other waterfowl. Novel evolutionary lineages of AIV that arise through genetic drift or reassortment can spread with wild bird migrations to new regions, infect a wide variety of [...] Read more.
Avian influenza viruses (AIVs) are maintained in wild bird reservoirs, particularly in mallard ducks and other waterfowl. Novel evolutionary lineages of AIV that arise through genetic drift or reassortment can spread with wild bird migrations to new regions, infect a wide variety of resident bird species, and spillover to domestic poultry. The vast continental reservoir of AIVs in Eurasia harbors a wide diversity of influenza subtypes, including both highly pathogenic (HP) and low pathogenic (LP) H7 AIV. The Caspian Sea region is positioned at the intersection of major migratory flyways connecting Central Asia, Europe, the Black and Mediterranean Sea regions and Africa and holds a rich wetland and avian ecology. To understand genetic reservoirs present in the Caspian Sea region, we collected 559 cloacal swabs from Anseriformes and other species during the annual autumn migration periods in 2017 and 2018. We isolated two novel H7N3 LPAIV from mallard ducks whose H7 hemagglutinin (HA) gene was phylogenetically related to contemporaneous strains from distant Mongolia, and more closely Georgia and Ukraine, and predated the spread of this H7 LPAIV sublineage into East Asia in 2019. The N3 neuraminidase gene and internal genes were prototypical of AIV widely dispersed in wild bird reservoirs sampled along flyways connected to the Caspian region. The polymerase and nucleoprotein segments clustered with contemporaneous H5 HPAI (clade 2.3.4.4b) isolates, suggesting the wide dispersal of H7 LPAIV and the potential of this subtype for reassortment. These findings highlight the need for deeper surveillance of AIV in wild birds to better understand the extent of infection spread and evolution along spatial and temporal flyways in Eurasia. Full article
(This article belongs to the Special Issue Ecology of Influenza A Viruses)
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Article
Comparison of In Vitro Killing Activity of Rezafungin, Anidulafungin, Caspofungin, and Micafungin against Four Candida auris Clades in RPMI-1640 in the Absence and Presence of Human Serum
Microorganisms 2021, 9(4), 863; https://doi.org/10.3390/microorganisms9040863 - 16 Apr 2021
Cited by 7 | Viewed by 1040
Abstract
Candida auris is an emerging and frequently multidrug-resistant pathogen against which the echinocandins are the preferred therapeutic option. We compared killing activities of anidulafungin, caspofungin, micafungin, and rezafungin against 13 isolates representing four C. auris clades (South Asian n = 3; East Asian [...] Read more.
Candida auris is an emerging and frequently multidrug-resistant pathogen against which the echinocandins are the preferred therapeutic option. We compared killing activities of anidulafungin, caspofungin, micafungin, and rezafungin against 13 isolates representing four C. auris clades (South Asian n = 3; East Asian n = 3; South African n = 3; South American n = 4, of which two were of environmental origin). Minimum inhibitory concentration MICs and killing kinetics in RPMI-1640 and RPMI-1640 plus 50% serum (50% serum) were determined. The four echinocandins were never fungicidal and induced large aggregates in RPMI-1640 and, less markedly, in 50% serum. Colony forming unit CFU decreases were found more consistently in 50% serum than in RPMI-1640. Isolates from the East Asian clade were killed at ≥1–≥ 4 mg/L with all echinocandins regardless of media. Anidulafungin and micafungin produced killing at peak drug serum concentration (8 mg/L) against environmental but not clinical isolates from the South American and the South African clades. Micafungin at ≥8 mg/L but not anidulafungin produced CFU decreases against the South Asian clade as well. In 50% serum, rezafungin at ≥1–≥ 8 mg/L produced killing against all four clades. The next generation echinocandin, rezafungin, showed the same or better activity at clinically attainable trough concentration regardless of media, compared with anidulafungin, caspofungin, and micafungin against all four tested C. auris clades. Full article
(This article belongs to the Special Issue Diagnosis, Resistance and Treatment of Infections by Candida Species)
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Review
Trends in Molecular Diagnosis and Diversity Studies for Phytosanitary Regulated Xanthomonas
Microorganisms 2021, 9(4), 862; https://doi.org/10.3390/microorganisms9040862 - 16 Apr 2021
Cited by 4 | Viewed by 2092
Abstract
Bacteria in the genus Xanthomonas infect a wide range of crops and wild plants, with most species responsible for plant diseases that have a global economic and environmental impact on the seed, plant, and food trade. Infections by Xanthomonas spp. cause a wide [...] Read more.
Bacteria in the genus Xanthomonas infect a wide range of crops and wild plants, with most species responsible for plant diseases that have a global economic and environmental impact on the seed, plant, and food trade. Infections by Xanthomonas spp. cause a wide variety of non-specific symptoms, making their identification difficult. The coexistence of phylogenetically close strains, but drastically different in their phenotype, poses an added challenge to diagnosis. Data on future climate change scenarios predict an increase in the severity of epidemics and a geographical expansion of pathogens, increasing pressure on plant health services. In this context, the effectiveness of integrated disease management strategies strongly depends on the availability of rapid, sensitive, and specific diagnostic methods. The accumulation of genomic information in recent years has facilitated the identification of new DNA markers, a cornerstone for the development of more sensitive and specific methods. Nevertheless, the challenges that the taxonomic complexity of this genus represents in terms of diagnosis together with the fact that within the same bacterial species, groups of strains may interact with distinct host species demonstrate that there is still a long way to go. In this review, we describe and discuss the current molecular-based methods for the diagnosis and detection of regulated Xanthomonas, taxonomic and diversity studies in Xanthomonas and genomic approaches for molecular diagnosis. Full article
Article
Comparative Study of Two Insulinlike Proteases in Cryptosporidium parvum
Microorganisms 2021, 9(4), 861; https://doi.org/10.3390/microorganisms9040861 - 16 Apr 2021
Cited by 1 | Viewed by 771
Abstract
Cryptosporidiumparvum is a common protozoan pathogen responsible for moderate-to-severe diarrhea in humans and animals. The small genome of C. parvum has 22 genes encoding insulinlike proteases (INS) with diverse sequences, suggesting that members of the protein family may have different biological functions [...] Read more.
Cryptosporidiumparvum is a common protozoan pathogen responsible for moderate-to-severe diarrhea in humans and animals. The small genome of C. parvum has 22 genes encoding insulinlike proteases (INS) with diverse sequences, suggesting that members of the protein family may have different biological functions in the life cycle. In this study, two members of the INS family, CpINS-4 and CpINS-6 with the Zn2+-binding motif “HXXEH” but different numbers of function domains, were expressed in Escherichia coli and used in the generation of polyclonal antibodies. In both recombinant and native proteins, CpINS-4 and CpINS-6 were spliced into multiple fragments. The antibodies generated recognized their respective recombinant and native proteins and the spliced products, but had minimum cross-reactivity with each other. Anti-CpINS-4 antibodies reacted with the middle region of sporozoites and merozoites, while CpINS-6 had the highest reactivity to the apical region. Polyclonal anti-CpINS-4 antibodies produced 36% reduction in parasite load in HCT-8 cultures at 24 h, while those against CpINS-6, which has one of the function domains missing, failed in doing so. The genes encoding both CpINS-4 and CpINS-6 had the highest expression in the invasion phase of in vitro C. parvum culture. These data suggest that CpINS-4 and CpINS-6 might be expressed in different organelles and play different biological functions in the life cycle of C. parvum. Full article
(This article belongs to the Special Issue Zoonotic Pathogens: A One Health Approach)
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Article
Evaluation of Thymol-β-d-Glucopyranoside as a Potential Prebiotic Intervention to Reduce Carriage of Zoonotic Pathogens in Weaned and Feeder Pigs
Microorganisms 2021, 9(4), 860; https://doi.org/10.3390/microorganisms9040860 - 16 Apr 2021
Cited by 1 | Viewed by 748
Abstract
The gut of food-producing animals is a reservoir for foodborne pathogens. Thymol is bactericidal against foodborne pathogens but rapid absorption of thymol from the proximal gut precludes the delivery of effective concentrations to the lower gut where pathogens mainly colonize. Thymol-β-d-glucopyranoside [...] Read more.
The gut of food-producing animals is a reservoir for foodborne pathogens. Thymol is bactericidal against foodborne pathogens but rapid absorption of thymol from the proximal gut precludes the delivery of effective concentrations to the lower gut where pathogens mainly colonize. Thymol-β-d-glucopyranoside is reported to be more resistant to absorption than thymol in everted jejunal segments and could potentially function as a prebiotic by resisting degradation and absorption in the proximal gut but being hydrolysable by microbial β-glycosidase in the distal gut. Previous in vitro studies showed bactericidal effects of thymol-β-d-glucopyranoside against Campylobacter, Escherichia coli, and Salmonella enterica serovar Typhimurium in the presence but not absence of intestinal microbes expressing β-glycosidase activity, indicating that hydrolysis was required to obtain antimicrobial activity. Presently, the oral administration of thymol-β-d-glucopyranoside was studied to examine the effects on intestinal carriage of Campylobacter, E. coli, and S. Typhimurium in swine. The effects of thymol-β-d-glucopyranoside or thymol on antimicrobial sensitivity of representative E. coli isolates and characterized Salmonella strains were also explored. Results from two in vivo studies revealed little antimicrobial effects of thymol-β-d-glucopyranoside on Campylobacter, E. coli, or S. Typhimurium in swine gut. These findings add credence to current thinking that hydrolysis and absorption of thymol-β-d-glucopyranoside and thymol may be sufficiently rapid within the proximal gut to preclude delivery to the distal gut. Antibiotic susceptibilities of selected bacterial isolates and strains were mainly unaffected by thymol. Further research is warranted to overcome obstacles, preventing the delivery of efficacious amounts of thymol-β-d-glucopyranoside to the lower gut. Full article
Article
Unraveling the Metabolic Potential of Asgardarchaeota in a Sediment from the Mediterranean Hydrocarbon-Contaminated Water Basin Mar Piccolo (Taranto, Italy)
Microorganisms 2021, 9(4), 859; https://doi.org/10.3390/microorganisms9040859 - 16 Apr 2021
Viewed by 894
Abstract
Increasing number of metagenome sequencing studies have proposed a central metabolic role of still understudied Archaeal members in natural and artificial ecosystems. However, their role in hydrocarbon cycling, particularly in the anaerobic biodegradation of aliphatic and aromatic hydrocarbons, is still mostly unknown in [...] Read more.
Increasing number of metagenome sequencing studies have proposed a central metabolic role of still understudied Archaeal members in natural and artificial ecosystems. However, their role in hydrocarbon cycling, particularly in the anaerobic biodegradation of aliphatic and aromatic hydrocarbons, is still mostly unknown in both marine and terrestrial environments. In this work, we focused our study on the metagenomic characterization of the archaeal community inhabiting the Mar Piccolo (Taranto, Italy, central Mediterranean) sediments heavily contaminated by petroleum hydrocarbons and polychlorinated biphenyls (PCB). Among metagenomic bins reconstructed from Mar Piccolo microbial community, we have identified members of the Asgardarchaeota superphylum that has been recently proposed to play a central role in hydrocarbon cycling in natural ecosystems under anoxic conditions. In particular, we found members affiliated with Thorarchaeota, Heimdallarchaeota, and Lokiarchaeota phyla and analyzed their genomic potential involved in central metabolism and hydrocarbon biodegradation. Metabolic prediction based on metagenomic analysis identified the malonyl-CoA and benzoyl-CoA routes as the pathways involved in aliphatic and aromatic biodegradation in these Asgardarchaeota members. This is the first study to give insight into the archaeal community functionality and connection to hydrocarbon degradation in marine sediment historically contaminated by hydrocarbons. Full article
(This article belongs to the Special Issue The Microbiology of Natural and Artificial Aquatic Ecosystems)
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Review
Brazilian Coffee Production and the Future Microbiome and Mycotoxin Profile Considering the Climate Change Scenario
Microorganisms 2021, 9(4), 858; https://doi.org/10.3390/microorganisms9040858 - 16 Apr 2021
Cited by 1 | Viewed by 1183
Abstract
Brazil holds a series of favorable climatic conditions for agricultural production including the hours and intensity of sunlight, the availability of agricultural land and water resources, as well as diverse climates, soils and biomes. Amidst such diversity, Brazilian coffee producers have obtained various [...] Read more.
Brazil holds a series of favorable climatic conditions for agricultural production including the hours and intensity of sunlight, the availability of agricultural land and water resources, as well as diverse climates, soils and biomes. Amidst such diversity, Brazilian coffee producers have obtained various standards of qualities and aromas, between the arabica and robusta species, which each present a wide variety of lineages. However, temperatures in coffee producing municipalities in Brazil have increased by about 0.25 °C per decade and annual precipitation has decreased. Therefore, the agricultural sector may face serious challenges in the upcoming decades due to crop sensitivity to water shortages and thermal stress. Furthermore, higher temperatures may reduce the quality of the culture and increase pressure from pests and diseases, reducing worldwide agricultural production. The impacts of climate change directly affect the coffee microbiota. Within the climate change scenario, aflatoxins, which are more toxic than OTA, may become dominant, promoting greater food insecurity surrounding coffee production. Thus, closer attention on the part of authorities is fundamental to stimulate replacement of areas that are apt for coffee production, in line with changes in climate zoning, in order to avoid scarcity of coffee in the world market. Full article
(This article belongs to the Special Issue Coffee, Fungi, Mycotoxins, and Climate Change)
Review
Defeating Paediatric Tuberculous Meningitis: Applying the WHO “Defeating Meningitis by 2030: Global Roadmap”
Microorganisms 2021, 9(4), 857; https://doi.org/10.3390/microorganisms9040857 - 16 Apr 2021
Cited by 6 | Viewed by 1163
Abstract
Children affected by tuberculous meningitis (TBM), as well as their families, have needs that lie at the intersections between the tuberculosis and meningitis clinical, research, and policy spheres. There is therefore a substantial risk that these needs are not fully met by either [...] Read more.
Children affected by tuberculous meningitis (TBM), as well as their families, have needs that lie at the intersections between the tuberculosis and meningitis clinical, research, and policy spheres. There is therefore a substantial risk that these needs are not fully met by either programme. In this narrative review article, we use the World Health Organization (WHO) “Defeating Meningitis by 2030: global roadmap” as a starting point to consider key goals and activities to specifically defeat TBM in children. We apply the five pillars outlined in the roadmap to describe how this approach can be adapted to serve children affected by TBM. The pillars are (i) prevention; (ii) diagnosis and treatment; (iii) surveillance; (iv) support and care for people affected by meningitis; and (v) advocacy and engagement. We conclude by calling for greater integration between meningitis and TB programmes at WHO and at national levels. Full article
(This article belongs to the Special Issue Bacterial Meningitis: Epidemiology and Vaccination)
Article
Distribution of Prophages in the Oenococcus oeni Species
Microorganisms 2021, 9(4), 856; https://doi.org/10.3390/microorganisms9040856 - 16 Apr 2021
Cited by 3 | Viewed by 946
Abstract
Oenococcus oeni is the most exploited lactic acid bacterium in the wine industry and drives the malolactic fermentation of wines. Although prophage-like sequences have been identified in the species, many are not characterized, and a global view of their integration and distribution amongst [...] Read more.
Oenococcus oeni is the most exploited lactic acid bacterium in the wine industry and drives the malolactic fermentation of wines. Although prophage-like sequences have been identified in the species, many are not characterized, and a global view of their integration and distribution amongst strains is currently lacking. In this work, we analyzed the complete genomes of 231 strains for the occurrence of prophages, and analyzed their size and positions of insertion. Our data show the limited variation in the number of prophages in O. oeni genomes, and that six sites of insertion within the bacterial genome are being used for site-specific recombination. Prophage diversity patterns varied significantly for different host lineages, and environmental niches. Overall, the findings highlight the pervasive presence of prophages in the O. oeni species, their role as a major source of within-species bacterial diversity and drivers of horizontal gene transfer. Our data also have implications for enhanced understanding of the prophage recombination events which occurred during evolution of O. oeni, as well as the potential of prophages in influencing the fitness of these bacteria in their distinct niches. Full article
(This article belongs to the Special Issue Siphophages Infecting Food Processing Bacteria)
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Communication
Use of an Alignment-Free Method for the Geographical Discrimination of GTPVs Based on the GPCR Sequences
Microorganisms 2021, 9(4), 855; https://doi.org/10.3390/microorganisms9040855 - 16 Apr 2021
Viewed by 675
Abstract
Goatpox virus (GTPV) belongs to the genus Capripoxvirus, together with sheeppox virus (SPPV) and lumpy skin disease virus (LSDV). GTPV primarily affects sheep, goats and some wild ruminants. Although GTPV is only present in Africa and Asia, the recent spread of LSDV in [...] Read more.
Goatpox virus (GTPV) belongs to the genus Capripoxvirus, together with sheeppox virus (SPPV) and lumpy skin disease virus (LSDV). GTPV primarily affects sheep, goats and some wild ruminants. Although GTPV is only present in Africa and Asia, the recent spread of LSDV in Europe and Asia shows capripoxviruses could escape their traditional geographical regions to cause severe outbreaks in new areas. Therefore, it is crucial to develop effective source tracing of capripoxvirus infections. Earlier, conventional phylogenetic methods, based on limited samples, identified three different nucleotide sequence profiles in the G-protein-coupled chemokine receptor (GPCR) gene of GTPVs. However, this method did not differentiate GTPV strains by their geographical origins. We have sequenced the GPCR gene of additional GTPVs and analyzed them with publicly available sequences, using conventional alignment-based methods and an alignment-free approach exploiting k-mer frequencies. Using the alignment-free method, we can now classify GTPVs based on their geographical origin: African GTPVs and Asian GTPVs, which further split into Western and Central Asian (WCA) GTPVs and Eastern and Southern Asian (ESA) GTPVs. This approach will help determine the source of introduction in GTPV emergence in disease-free regions and detect the importation of additional strains in disease-endemic areas. Full article
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Article
Changes in Gut Microbiota Correlates with Response to Treatment with Probiotics in Patients with Atopic Dermatitis. A Post Hoc Analysis of a Clinical Trial
Microorganisms 2021, 9(4), 854; https://doi.org/10.3390/microorganisms9040854 - 15 Apr 2021
Cited by 3 | Viewed by 1767
Abstract
Atopic dermatitis (AD) is a chronic recurrent inflammatory skin disease with a high impact on the comfort of those who are affected and long-term treated with corticosteroids with limited efficacy and a high prevalence of relapses. Because of the limited effectiveness of these [...] Read more.
Atopic dermatitis (AD) is a chronic recurrent inflammatory skin disease with a high impact on the comfort of those who are affected and long-term treated with corticosteroids with limited efficacy and a high prevalence of relapses. Because of the limited effectiveness of these treatments, new strategies for recovery from AD lesions are continually being explored. In this article, we describe the gut microbiome changes achieved in a recently published clinical trial with the probiotic formulation Bifidobacterium animalis subsp. lactis CECT 8145, Bifidobacterium longum CECT 7347, and Lacticaseibacillus casei CECT 9104 (formerly Lactobacillus casei CECT 9104), showing a significant improvement in SCORAD (scoring atopic dermatitis) index in children (4–17 years) with AD (Clinicaltrials.gov identifier: NCT02585986). The present gut microbiome post hoc study showed no significant changes in diversity (Shannon and Simpson indexes) after probiotic consumption. In the probiotic group, genera Bacteroides, Ruminococcus, and Bifidobacterium significantly increased their levels while Faecalibacterium decreased, compared to the placebo group. Faecalibacterium showed the highest presence and significant positive correlation with AD severity (SCORAD index), whereas Abyssivirga, Bifidobacterium, and Lactococcus were inversely correlated. The results suggest that the consumption of the probiotic formulation here assayed modulates the gut microbiome with significant changes in genera Bacteroides and Faecalibacterium. In turn, the improvement in SCORAD correlates with a decrease in Faecalibacterium and an increase in Bifidobacterium, among others. Full article
(This article belongs to the Special Issue The Gut Microbiota in Infants: Focus on Bifidobacterium)
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Article
Classification of Salmonella enterica of the (Para-)Typhoid Fever Group by Fourier-Transform Infrared (FTIR) Spectroscopy
Microorganisms 2021, 9(4), 853; https://doi.org/10.3390/microorganisms9040853 - 15 Apr 2021
Cited by 2 | Viewed by 1386
Abstract
Typhoidal and para-typhoidal Salmonella are major causes of bacteraemia in resource-limited countries. Diagnostic alternatives to laborious and resource-demanding serotyping are essential. Fourier transform infrared spectroscopy (FTIRS) is a rapidly developing and simple bacterial typing technology. In this study, we assessed the discriminatory power [...] Read more.
Typhoidal and para-typhoidal Salmonella are major causes of bacteraemia in resource-limited countries. Diagnostic alternatives to laborious and resource-demanding serotyping are essential. Fourier transform infrared spectroscopy (FTIRS) is a rapidly developing and simple bacterial typing technology. In this study, we assessed the discriminatory power of the FTIRS-based IR Biotyper (Bruker Daltonik GmbH, Bremen, Germany), for the rapid and reliable identification of biochemically confirmed typhoid and paratyphoid fever-associated Salmonella isolates. In total, 359 isolates, comprising 30 S. Typhi, 23 S. Paratyphi A, 23 S. Paratyphi B, and 7 S. Paratyphi C, respectively and other phylogenetically closely related Salmonella serovars belonging to the serogroups O:2, O:4, O:7 and O:9 were tested. The strains were derived from clinical, environmental and food samples collected at different European sites. Applying artificial neural networks, specific automated classifiers were built to discriminate typhoidal serovars from non-typhoidal serovars within each of the four serogroups. The accuracy of the classifiers was 99.9%, 87.0%, 99.5% and 99.0% for Salmonella Typhi, Salmonella Paratyphi A, B and Salmonella Paratyphi C, respectively. The IR Biotyper is a promising tool for fast and reliable detection of typhoidal Salmonella. Hence, IR biotyping may serve as a suitable alternative to conventional approaches for surveillance and diagnostic purposes. Full article
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Communication
Growth of Staphylococcus epidermidis on the Surface of Teatcups from Milking Parlours
Microorganisms 2021, 9(4), 852; https://doi.org/10.3390/microorganisms9040852 - 15 Apr 2021
Cited by 1 | Viewed by 671
Abstract
The growth of two Staphylococcus epidermidis isolates (one biofilm-forming and one not) on teatcups for cattle (made of rubber) or sheep (made of silicone) were assessed in nine multiplicates for 24 h post-smearing on the teatcup surface. Staphylococci were smeared on an area [...] Read more.
The growth of two Staphylococcus epidermidis isolates (one biofilm-forming and one not) on teatcups for cattle (made of rubber) or sheep (made of silicone) were assessed in nine multiplicates for 24 h post-smearing on the teatcup surface. Staphylococci were smeared on an area of 0.0003142 m2 on the material and their growth and expansion further on were monitored for 24 h. There were no differences in the frequency of recoveries between the two isolates (p > 0.82 for all comparisons). There were more recoveries from sheep teatcups than from cattle teatcups: 1280/1728 (74.1%) versus 942/1728 (54.5%), for both isolates (p < 0.0001). Significance was observed only 6 h to 15 h after smearing (p < 0.0001 for all comparisons). The median speed of linear dissemination of the isolates was 0.00000021 m s−1 on cattle teatcups and 0.00000033 m s−1 on sheep teatcups (p < 0.0001). The increased growth and faster expansion of staphylococci on silicone teatcups raise important points from a clinical viewpoint. The model could be used in the testing of staphylococcal growth in the material of milking parlours in various conditions. Full article
(This article belongs to the Special Issue Biopathology of Microbial Infections)
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