Microorganisms

10 pages, 511 KiB

Open AccessArticle

Comparative Study of Real-Time PCR (TaqMan Probe and Sybr Green), Serological Techniques (ELISA, IFA and DAT) and Clinical Signs Evaluation, for the Diagnosis of Canine Leishmaniasis in Experimentally Infected Dogs

by María Paz Peris, Adriana Esteban-Gil, Paula Ortega-Hernández, Mariano Morales, Nabil Halaihel and Juan Antonio Castillo

Microorganisms 2021, 9(12), 2627; https://doi.org/10.3390/microorganisms9122627 - 20 Dec 2021

Cited by 8 | Viewed by 3279

Abstract

Canine leishmaniasis (CanL) diagnosis is not fully resolved. Currently, two specific methodologies are in continuous development, the detection of the parasite DNA or RNA in target organs and the detection of specific antibodies against Leishmania sp. For a correct diagnosis, it has been [...] Read more.

Canine leishmaniasis (CanL) diagnosis is not fully resolved. Currently, two specific methodologies are in continuous development, the detection of the parasite DNA or RNA in target organs and the detection of specific antibodies against Leishmania sp. For a correct diagnosis, it has been shown that the joint use of this type of test is necessary. In this work, a Sybr Green and a TaqMan Probe based on real time PCRs (qPCR) was performed for the detection of Leishmania sp. in order to correlate the results with clinicopathological and serological evaluations (IFA, ELISA and DAT) to propose an optimal biological sample to be used to detect the parasite in both early and late stages of the infection. A total of four samples were processed: conjunctival swabs, popliteal lymph node aspirates, bone marrow aspirates, and peripheral blood from experimentally infected dogs belonging to a larger study. Our results indicated that a single non-invasive sample (conjunctival swab) and the application of both types of qPCR would be reliable for determining Leishmania infection as well as the disease stage in dogs, thus avoiding bone marrow, lymph node aspirate or blood samples collection. Full article

(This article belongs to the Special Issue Leishmania and Leishmaniasis)

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15 pages, 1702 KiB

Open AccessArticle

Use of Stress Signals of Their Attached Bacteria to Monitor Sympagic Algae Preservation in Canadian Arctic Sediments

by Rémi Amiraux, Bonin Patricia, Burot Christopher and Rontani Jean-François

Microorganisms 2021, 9(12), 2626; https://doi.org/10.3390/microorganisms9122626 - 20 Dec 2021

Cited by 3 | Viewed by 2485

Abstract

Based on the strong aggregation of sympagic (ice-associated) algae and the high mortality or inactivity of bacteria attached to them, it was previously hypothesized that sympagic algae should be significant contributors to the export of carbon to Arctic sediments. In the present work, [...] Read more.

Based on the strong aggregation of sympagic (ice-associated) algae and the high mortality or inactivity of bacteria attached to them, it was previously hypothesized that sympagic algae should be significant contributors to the export of carbon to Arctic sediments. In the present work, the lipid content of 30 sediment samples collected in the Canadian Arctic was investigated to test this hypothesis. The detection of high proportions of trans vaccenic fatty acid (resulting from cis-trans isomerase (CTI) activity of bacteria under hypersaline conditions) and 10S-hydroxyhexadec-8(trans)-enoic acid (resulting from 10S-DOX bacterial detoxification activity in the presence of deleterious free palmitoleic acid) confirmed: (i) the strong contribution of sympagic material to some Arctic sediments, and (ii) the impaired physiological status of its associated bacterial communities. Unlike terrestrial material, sympagic algae that had escaped zooplanktonic grazing appeared relatively preserved from biotic degradation in Arctic sediments. The expected reduction in sea ice cover resulting from global warming should cause a shift in the relative contributions of ice-associated vs. pelagic algae to the seafloor, and thus to a strong modification of the carbon cycle. Full article

(This article belongs to the Special Issue Polar Microbes)

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10 pages, 1341 KiB

Open AccessCommunication

The Impact of Pre-Slaughter Fasting on the Ruminal Microbial Population of Commercial Angus Steers

by Christina Breanne Welch, Jeferson M. Lourenco, Darren S. Seidel, Taylor Rae Krause, Michael J. Rothrock, T. Dean Pringle and Todd R. Callaway

Microorganisms 2021, 9(12), 2625; https://doi.org/10.3390/microorganisms9122625 - 19 Dec 2021

Cited by 7 | Viewed by 2652

Abstract

Diet impacts the composition of the ruminal microbiota; however, prior to slaughter, cattle are fasted, which may change the ruminal microbial ecosystem structure and lead to dysbiosis. The objective of this study was to determine changes occurring in the rumen after pre-slaughter fasting, [...] Read more.

Diet impacts the composition of the ruminal microbiota; however, prior to slaughter, cattle are fasted, which may change the ruminal microbial ecosystem structure and lead to dysbiosis. The objective of this study was to determine changes occurring in the rumen after pre-slaughter fasting, which can allow harmful pathogens an opportunity to establish in the rumen. Ruminal samples were collected before and after pre-slaughter fasting from seventeen commercial Angus steers. DNA extraction and 16S rRNA gene sequencing were performed to determine the ruminal microbiota, as well as volatile fatty acid (VFA) concentrations. Microbial richness (Chao 1 index), evenness, and Shannon diversity index all increased after fasting (p ≤ 0.040). During fasting, the two predominant families Prevotellaceae and Ruminococcaceae decreased (p ≤ 0.029), whereas the remaining minor families increased (p < 0.001). Fasting increased Blautia and Methanosphaera (p ≤ 0.003), while Campylobacter and Treponema tended to increase (p ≤ 0.086). Butyrate concentration tended to decrease (p = 0.068) after fasting. The present findings support that fasting causes ruminal nutrient depletion resulting in dysbiosis, allowing opportunistic pathogens to exploit the void in the ruminal ecological niche. Full article

(This article belongs to the Special Issue Gut Microbiome of Farm Animals in Health and Disease)

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4 pages, 174 KiB

Open AccessEditorial

Whole-Genome Sequencing of Pathogenic Bacteria—New Insights into Antibiotic Resistance Spreading

by Andrey Shelenkov

Microorganisms 2021, 9(12), 2624; https://doi.org/10.3390/microorganisms9122624 - 19 Dec 2021

Cited by 2 | Viewed by 2415

Abstract

In recent years, the acquisition of antimicrobial resistance (AMR) by both pathogenic and opportunistic bacteria has become a major problem worldwide, which was already noticed as a global healthcare threat by the World Health Organization [...] Full article

(This article belongs to the Special Issue Whole-Genome Sequencing of Pathogenic Bacteria - New Insights into Antibiotic Resistance Spreading)

16 pages, 1195 KiB

Open AccessReview

Mycobacterium avium subsp. paratuberculosis Virulence: A Review

by Judah Ssekitoleko, Lonzy Ojok, Ahmed Abd El Wahed, Joseph Erume, Ahmad Amanzada, ElSagad Eltayeb, Kamal H. Eltom and Julius Boniface Okuni

Microorganisms 2021, 9(12), 2623; https://doi.org/10.3390/microorganisms9122623 - 19 Dec 2021

Cited by 6 | Viewed by 2969

Abstract

To propose a solution for control of Mycobacterium avium subsp. paratuberculosis (MAP) infections in animals as well as in humans, and develop effective prevention, diagnostic and treatment strategies, it is essential to understand the molecular mechanisms of MAP pathogenesis. In the present [...] Read more.

To propose a solution for control of Mycobacterium avium subsp. paratuberculosis (MAP) infections in animals as well as in humans, and develop effective prevention, diagnostic and treatment strategies, it is essential to understand the molecular mechanisms of MAP pathogenesis. In the present review, we discuss the mechanisms utilised by MAP to overcome the host defense system to achieve the virulence status. Putative MAP virulence genes are mentioned and their probable roles in view of other mycobacteria are discussed. This review provides information on MAP strain diversity, putative MAP virulence factors and highlights the knowledge gaps regarding MAP virulence mechanisms that may be important in control and prevention of paratuberculosis. Full article

(This article belongs to the Section Molecular Microbiology and Immunology)

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12 pages, 736 KiB

Open AccessArticle

Immune Response to BNT162b2 in Solid Organ Transplant Recipients: Negative Impact of Mycophenolate and High Responsiveness of SARS-CoV-2 Recovered Subjects against Delta Variant

by Irene Cassaniti, Federica Bergami, Francesca Arena, Jose Camilla Sammartino, Alessandro Ferrari, Federica Zavaglio, Irene Curti, Elena Percivalle, Federica Meloni, Laura Pandolfi, Carlo Pellegrini, Annalisa Turco, Elena Seminari, Eleonora Francesca Pattonieri, Marilena Gregorini, Teresa Rampino, Antonella Sarasini, Daniele Lilleri and Fausto Baldanti

Microorganisms 2021, 9(12), 2622; https://doi.org/10.3390/microorganisms9122622 - 18 Dec 2021

Cited by 9 | Viewed by 2642

Abstract

The immunogenicity of severe acute respiratory syndrome 2 virus (SARS-CoV-2) vaccines in immunocompromised patients remains to be further explored. Here, we evaluated the immunogenicity elicited by complete vaccination with BNT162b2 vaccine in solid organ transplant recipients (SOTRs). A cohort of 110 SOTRs from [...] Read more.

The immunogenicity of severe acute respiratory syndrome 2 virus (SARS-CoV-2) vaccines in immunocompromised patients remains to be further explored. Here, we evaluated the immunogenicity elicited by complete vaccination with BNT162b2 vaccine in solid organ transplant recipients (SOTRs). A cohort of 110 SOTRs from Northern Italy were vaccinated with two doses of BNT162b2 mRNA vaccine and prospectively monitored at baseline and after 42 days. Both SARS-CoV-2 naïve and recovered subjects were included. Humoral response elicited by vaccination, including SARS-CoV-2 neutralizing antibodies (SARS-CoV-2 NT Abs), was evaluated; additionally, ex-vivo ELISpot assay was performed for the quantification of Spike-specific T-cell response. Results were compared with those obtained in a cohort of healthy subjects. In a subset of patients, humoral and T-cell responses against delta variant were also evaluated. Less than 20% of transplanted subjects developed a positive humoral and cell-mediated response after complete vaccination schedule. Overall, median levels of immune response elicited by vaccination were significantly lower with respect to controls in SARS-CoV-2 naïve transplant, but not in SARS-CoV-2 recovered transplanted patients. Additionally, a significant impairment of both humoral and cell-mediated response was observed in mycophenolate-treated patients. Positive delta-SARS-CoV-2 NT Abs levels were detected in almost all the SARS-CoV-2 recovered subjects but not in previously uninfected patients. Our study supports previous observations of a low level of seroconversion after vaccination in transplanted patients. Full article

(This article belongs to the Section Virology)

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18 pages, 2376 KiB

Open AccessArticle

Diel Protein Regulation of Marine Picoplanktonic Communities Assessed by Metaproteomics

by Augustin Géron, Johannes Werner, Philippe Lebaron, Ruddy Wattiez and Sabine Matallana-Surget

Microorganisms 2021, 9(12), 2621; https://doi.org/10.3390/microorganisms9122621 - 18 Dec 2021

Cited by 1 | Viewed by 2319

Abstract

The diel cycle is of enormous biological importance in that it imposes temporal structure on ecosystem productivity. In the world’s oceans, microorganisms form complex communities that carry out about half of photosynthesis and the bulk of life-sustaining nutrient cycling. How the functioning of [...] Read more.

The diel cycle is of enormous biological importance in that it imposes temporal structure on ecosystem productivity. In the world’s oceans, microorganisms form complex communities that carry out about half of photosynthesis and the bulk of life-sustaining nutrient cycling. How the functioning of microbial communities is impacted by day and night periods in surface seawater remains to be elucidated. In this study, we compared the day and night metaproteomes of the free-living and the particle-attached bacterial fractions from picoplanktonic communities sampled from the northwest Mediterranean Sea surface. Our results showed similar taxonomic distribution of free-living and particle-attached bacterial populations, with Alphaproteobacteria, Gammaproteobacteria and Cyanobacteria being the most active members. Comparison of the day and night metaproteomes revealed that free-living and particle-attached bacteria were more active during the day and the night, respectively. Interestingly, protein diel variations were observed in the photoautotroph Synechococcales and in (photo)-heterotrophic bacteria such as Flavobacteriales, Pelagibacterales and Rhodobacterales. Moreover, our data demonstrated that diel cycle impacts light-dependent processes such as photosynthesis and UV-stress response in Synechococcales and Rhodobacterales, respectively, while the protein regulation from the ubiquitous Pelagibacterales remained stable over time. This study unravels, for the first time, the diel variation in the protein expression of major free-living and particle-attached microbial players at the sea surface, totaling an analysis of eight metaproteomes. Full article

(This article belongs to the Section Environmental Microbiology)

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14 pages, 313 KiB

Open AccessReview

Probiotics: Should All Patients Take Them?

by Marta Katkowska, Katarzyna Garbacz and Aida Kusiak

Microorganisms 2021, 9(12), 2620; https://doi.org/10.3390/microorganisms9122620 - 18 Dec 2021

Cited by 22 | Viewed by 4470

Abstract

The usefulness of probiotics in the treatment as well as prevention of many infections and disorders has been confirmed by previous clinical studies. They can protect not only against gastrointestinal diseases such as diarrhea or enteritis but they have proven efficacy against pneumonia, [...] Read more.

The usefulness of probiotics in the treatment as well as prevention of many infections and disorders has been confirmed by previous clinical studies. They can protect not only against gastrointestinal diseases such as diarrhea or enteritis but they have proven efficacy against pneumonia, urogenital infection, depression/anxiety, cancer metastasis, obesity, and others. However, it should be mentioned that not all clinical trials have shown improvement of health in patients undergoing probiotic treatment, and very rarely have even reported that probiotic strains may be the causative agents of opportunistic infections. Studies have documented cases of sepsis/bacteremia, endocarditis, liver abscess, pneumonia, and fungemia caused by probiotic strains, mainly in high-risk groups. This review summarizes the cases of infections caused by probiotic strains and the potential hazard associated with the supplementation of probiotics in seriously ill and hospitalized patients. Full article

(This article belongs to the Section Gut Microbiota)

23 pages, 4722 KiB

Open AccessArticle

Proteomics Readjustment of the Yarrowia lipolytica Yeast in Response to Increased Temperature and Alkaline Stress

by Varvara Y. Sekova, Leonid I. Kovalyov, Marina A. Kovalyova, Natalya N. Gessler, Maria A. Danilova, Elena P. Isakova and Yulia I. Deryabina

Microorganisms 2021, 9(12), 2619; https://doi.org/10.3390/microorganisms9122619 - 18 Dec 2021

Cited by 7 | Viewed by 2662

Abstract

Yeasts cope with a wide range of environmental challenges using different adaptive mechanisms. They can prosper at extreme ambient pH and high temperatures; however, their adaptation mechanisms have not been entirely investigated. Previously, we showed the pivotal role and flexibility of the sugar [...] Read more.

Yeasts cope with a wide range of environmental challenges using different adaptive mechanisms. They can prosper at extreme ambient pH and high temperatures; however, their adaptation mechanisms have not been entirely investigated. Previously, we showed the pivotal role and flexibility of the sugar and lipid composition of Yarrowia lipolytica W 29 upon adaptation to unfavorable conditions. In this study, we showed that extreme pH provoked significant changes in the cell wall proteins expression, with an increase in both the chaperones of heat shock protein HSP60 and some other proteins with chaperone functions. The mitochondria activity changes inducing the VDAC and malate dehydrogenase played an essential role in the adaptation, as did the altered carbohydrate metabolism, promoting its shift towards the pyruvate formation rather than gluconeogenesis. The elevated temperature led to changes in the cell wall proteins and chaperones, the induced expression of the proteins involved in the cell structural organization, ribosomal proteins, and the enzymes of formaldehyde degradation. Moreover, the readjustment of the protein composition and amount under combined stress indicated the promotion of catabolic processes related to scavenging the damaged proteins and lipids. Under all of the stress conditions studied, the process of folding, stress resistance, redox adaptation, and oxidative phosphorylation were the dominant pathways. The combined chronic alkaline and heat stress (pH 9.0, 38 °C) led to cross-adaptation, which caused “switching” over the traditional metabolism to the adaptation to the most damaging stress factor, namely the increased temperature. Full article

(This article belongs to the Special Issue Advances in Microbial Biosynthesis)

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13 pages, 1774 KiB

Open AccessArticle

The Impact of Protease during Recovery from Viable but Non-Culturable (VBNC) State in Vibrio cholerae

by Anusuya Debnath and Shin-ichi Miyoshi

Microorganisms 2021, 9(12), 2618; https://doi.org/10.3390/microorganisms9122618 - 18 Dec 2021

Cited by 3 | Viewed by 2290

Abstract

Vibrio cholerae can survive cold stress by entering into a viable but non-culturable (VBNC) state, and resuscitation can be induced either by temperature upshift only or the addition of an anti-dormancy stimulant such as resuscitation-promoting factors (Rpfs) at suitable temperature. In this study, [...] Read more.

Vibrio cholerae can survive cold stress by entering into a viable but non-culturable (VBNC) state, and resuscitation can be induced either by temperature upshift only or the addition of an anti-dormancy stimulant such as resuscitation-promoting factors (Rpfs) at suitable temperature. In this study, the role of proteinase K was analyzed as an Rpf in V. cholerae. A VBNC state was induced in V. cholerae AN59 in artificial seawater (ASW) media at 4 °C, and recovery could be achieved in filtered VBNC microcosm, called spent ASW media, merely by a temperature upshift to 37 °C. The resuscitation ability of spent ASW was further enhanced by the addition of proteinase K. The mode of action of proteinase K was investigated by comparing its effect on the growth of the VBNC and culturable state of V. cholerae in ASW and spent ASW media. The presence of proteinase K allowed culturable cells to grow faster in ASW by reducing the generation time. However, this effect of proteinase K was more pronounced in stressed VBNC cells. Moreover, proteinase K-supplemented spent ASW could also accelerate the transition of VBNC into recovered cells followed by rapid growth. Additionally, we found that dead bacterial cells were the substrate on which proteinase K acts to support high growth in spent ASW. So, the conclusion is that the proteinase K could efficiently promote the recovery and growth of dormant VBNC cells at higher temperatures by decreasing the duration of the initial lag phase required for transitioning from the VBNC to recovery state and increasing the growth rate of these recovered cells. Full article

(This article belongs to the Section Environmental Microbiology)

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15 pages, 544 KiB

Open AccessArticle

Virological and Parasitological Characterization of Mini-LEWE Minipigs Using Improved Screening Methods and an Overview of Data on Various Minipig Breeds

by Sabrina Halecker, Julia Metzger, Christina Strube, Ludwig Krabben, Benedikt Kaufer and Joachim Denner

Microorganisms 2021, 9(12), 2617; https://doi.org/10.3390/microorganisms9122617 - 18 Dec 2021

Cited by 11 | Viewed by 2626

Abstract

Minipigs play an important role in biomedical research and have also been used as donor animals in xenotransplantation. To serve as a donor in xenotransplantation, the animals must be free of potential zoonotic viruses, bacteria and parasites. Porcine endogenous retroviruses (PERVs) are integrated [...] Read more.

Minipigs play an important role in biomedical research and have also been used as donor animals in xenotransplantation. To serve as a donor in xenotransplantation, the animals must be free of potential zoonotic viruses, bacteria and parasites. Porcine endogenous retroviruses (PERVs) are integrated in the genome of all pigs and cannot be eliminated as most of the other pig viruses can. PERV-A and PERV-B infect human cells in cell culture and are integrated in all pigs, whereas PERV-C infects only pig cells and it is found in many, but not all pigs. Minipigs are known for a high prevalence of recombinant PERV-A/C viruses able to infect human cells (Denner and Schuurman, Viruses, 2021;13:1869). Here, Mini-LEWE minipigs are screened for the first time for pig viruses including PERV. Peripheral blood mononuclear cells (PBMCs) from 10 animals were screened using PCR-based methods (PCR, RT-PCR, and real-time PCR). In comparison with our previous screening assays, numerous improvements were introduced, e.g., the usage of gene blocks as a PCR standard and foreign RNA to control reverse transcription in RT-PCR. Using these improved detection methods, Mini-LEWE pigs were found to be negative for porcine cytomegalovirus (PCMV), porcine lymphotropic herpesviruses (PLHV-1, -2 and -3), porcine circoviruses (PCV1, 2, 3 and 4), porcine parvovirus (PPV) and hepatitis E virus (HEV). All animals carried PERV-A, PERV-B and PERV-C in their genome. PERV-A/C was not found. In contrast to all other minipig breeds (Göttingen minipigs, Aachen minipigs, Yucatan micropig, Massachusetts General Hospital miniature pigs), Mini-LEWE minipigs have less viruses and no PERV-A/C. Parasitological screening showed that none of the Mini-LEWE minipigs harbored ecto- and gastrointestinal parasites, but at least one animal tested positive for anti-Toxoplasma gondii antibodies. Full article

(This article belongs to the Section Virology)

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12 pages, 702 KiB

Open AccessArticle

Wild Rabbit Exposure to Leishmania infantum, Toxoplasma gondii, Anaplasma phagocytophilum and Babesia caballi Evidenced by Serum and Aqueous Humor Antibody Detection

by Labrini V. Athanasiou, Eleni G. Katsogiannou, Constantina N. Tsokana, Sofia G. Boutsini, Marina G. Bisia and Vasileios G. Papatsiros

Microorganisms 2021, 9(12), 2616; https://doi.org/10.3390/microorganisms9122616 - 17 Dec 2021

Cited by 6 | Viewed by 2354

Abstract

Wild rabbits (Oryctolagus cuniculus) can be important sentinel species for the presence of zoonotic pathogens. Therefore, we collected blood samples from wild rabbits harvested by hunters during the hunting season 2019–2020 on the island of Lemnos, to determine exposure of wild [...] Read more.

Wild rabbits (Oryctolagus cuniculus) can be important sentinel species for the presence of zoonotic pathogens. Therefore, we collected blood samples from wild rabbits harvested by hunters during the hunting season 2019–2020 on the island of Lemnos, to determine exposure of wild rabbits to the zoonotic pathogens Leishmania infantum, Toxoplasma gondii, Anaplasma phagocytophilum and Babesia caballi, as well as aqueous humor to assess its diagnostic performance in terms of sensitivity, specificity, positive and negative likelihood ratios. Antibodies against these pathogens were detected by Indirect Immunofluorescence Antibody (IFA) assay. Out of the 72 wild rabbits included in the study, 4.2%, 5.5%, 18% and 9.7% were seropositive to L. infantum, T. gondii, A. phagocytophilum and B. caballi, respectively. Although less frequently, antibodies were also detected in aqueous humor of wild rabbits. The antibody detection in aqueous humor presented 100% specificity but decreased sensitivity compared to serum suggesting that aqueous humor could be successfully used in epidemiological studies to confirm exposure at the population level but has little diagnostic value at the individual level. This is the first report on the seropositivity of wild rabbits to A. phagocytophilum and B. caballi and the detection of antibodies against A. phagocytopylum, L. infantum, T. gondii and B. caballi in the aqueous humor. Full article

(This article belongs to the Special Issue Farm Animal and Wildlife Zoonotic Microorganisms)

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11 pages, 1432 KiB

Open AccessArticle

Characterization of Erysipelothrix rhusiopathiae Isolates from Diseased Pigs in 15 Chinese Provinces from 2012 to 2018

by Chao Wu, Changjie Lv, Ya Zhao, Weifeng Zhu, Liang Liu, Ting Wang, Chao Kang, Ying Yang, Xiaomei Sun, Qiang Zhang and Meilin Jin

Microorganisms 2021, 9(12), 2615; https://doi.org/10.3390/microorganisms9122615 - 17 Dec 2021

Cited by 5 | Viewed by 2217

Abstract

Erysipelothrix rhusiopathiae can cause erysipelas in animals and erysipeloid in humans. Since its recurrence in 2012, swine erysipelas has caused serious losses within the pig industry in China. The aim of this study was to perform multilocus sequence typing and understand the virulence [...] Read more.

Erysipelothrix rhusiopathiae can cause erysipelas in animals and erysipeloid in humans. Since its recurrence in 2012, swine erysipelas has caused serious losses within the pig industry in China. The aim of this study was to perform multilocus sequence typing and understand the virulence and antimicrobial susceptibility of E. rhusiopathiae isolates in China. Multilocus sequence typing (MLST) of a total of 120 strains was performed, and as a result, three different sequence types were identified, of which ST48 was the main one. Five isolates of each MLST type were randomly selected to be used to challenge mice. ST48 was associated with a higher virulence. Antimicrobial susceptibility was tested using a microdilution technique and, to analyze the resistance mechanism, six strains were selected for genome sequencing. A comparison of the six genomes indicated the presence of a suspected macrolide resistance gene, namely, Erm(A)-like, in erythromycin-resistant strains, which increased the minimum inhibitory concentration (MIC) of erythromycin against E. coli C600 at least four-fold. In addition, three mutations (gyrA86T-I, gyrA90D-N, and parC81S-I) were observed in the quinolone resistance-determining regions (QRDRs) of gyrA and parC in quinolone-resistant strains. After the gyrA gene with the 86T-I mutation or the parC gene with the 81S-I mutation was transfected into E. coli C600, the MIC of enrofloxacin against this strain increased at least two-fold. Our findings provide a theoretical basis for developing antibacterial drugs and may contribute to the clinical prevention and control of E. rhusiopathiae. Full article

(This article belongs to the Topic Infectious Diseases)

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15 pages, 11628 KiB

Open AccessArticle

Effects of Lactic Acid Bacterial Inoculants on Fermentation Quality, Bacterial Community, and Mycotoxins of Alfalfa Silage under Vacuum or Nonvacuum Treatment

by Xiaomiao Fan, Shanshan Zhao, Fengyuan Yang, Yuan Wang and Yanping Wang

Microorganisms 2021, 9(12), 2614; https://doi.org/10.3390/microorganisms9122614 - 17 Dec 2021

Cited by 9 | Viewed by 2404

Abstract

To investigate the effects of lactic acid bacterial (LAB) inoculants and vacuuming on the fermentation quality and bacterial community, alfalfas were ensiled with or without a commercial LAB YX or Lactobacillus plantarum strain ZZUA493 for 10, 30, 60, and 90 days while undergoing [...] Read more.

To investigate the effects of lactic acid bacterial (LAB) inoculants and vacuuming on the fermentation quality and bacterial community, alfalfas were ensiled with or without a commercial LAB YX or Lactobacillus plantarum strain ZZUA493 for 10, 30, 60, and 90 days while undergoing either vacuum (V) or nonvacuum (NV) treatment. At 90 days, analysis of the microbial community by high-throughput sequencing was performed, and contents of aflatoxin B1 and deoxynivalenol (DON) mycotoxins in alfalfa silage were determined. In all inoculated alfalfa silage, irrespective of V or NV treatment, lactic acid (LA) content increased, pH (p < 0.05), and ammonia nitrogen (p < 0.05) content decreased, and no butyric acid was detected. Lactobacillus or Pediococcus became the dominant genus, and the abundance of Garciella decreased in alfalfa silage with the addition of either inoculant. The LAB inoculants YX and ZZUA493 helped reduce the mycotoxin content in alfalfa silage. The abundance of Garciella in the control and DON content in all alfalfa silage groups were higher (p < 0.05) in NV than V. In summary, LAB inoculants and vacuuming had a positive influence on alfalfa silage quality, and LAB inoculants were effective in reducing mycotoxins in silage alfalfa. Full article

(This article belongs to the Topic Development of Agricultural and Food By-Product Resources and Animal Production to Achieve Food Sustainability)

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10 pages, 590 KiB

Open AccessArticle

Colonization with Multidrug-Resistant Bacteria in the First Week of Life among Hospitalized Preterm Neonates in Serbia: Risk Factors and Outcomes

by Marija Milic, Marina Siljic, Valentina Cirkovic, Milos Jovicevic, Vladimir Perovic, Milos Markovic, Jelena Martic, Maja Stanojevic and Vera Mijac

Microorganisms 2021, 9(12), 2613; https://doi.org/10.3390/microorganisms9122613 - 17 Dec 2021

Cited by 9 | Viewed by 2402

Abstract

The aim of this prospective cohort study was to determine the prevalence of gut colonization with multidrug-resistant (MDR) bacteria, risk factors for colonization, infection risk, and outcomes among preterm neonates hospitalized at a tertiary-care center in Serbia. During the period from December 2017 [...] Read more.

The aim of this prospective cohort study was to determine the prevalence of gut colonization with multidrug-resistant (MDR) bacteria, risk factors for colonization, infection risk, and outcomes among preterm neonates hospitalized at a tertiary-care center in Serbia. During the period from December 2017 to April 2018, 103 neonates were screened for rectal carriage at admission and on the seventh day of life. Characterization of MDR strains was done by conventional microbiology and molecular methods. Out of 61 (59.2%) colonized neonates, 12 (11.6%) were found colonized at admission, while 49 (47.6%) became colonized at the study site. Among a total of 72 MDR isolates, extended-spectrum beta-lactamase (ESBL)-producing enterobacteria prevailed (56/72, 77%), followed by Acinetobacter baumannii (14/72, 19%). The majority of ESBL-producing strains carried multiple genes (blaTEM/blaCTX-M-15 or blaTEM/blaSHV). Longer previous hospitalization and delivery by cesarean section were associated with MDR colonization, while mechanical ventilation was a risk factor for colonization at the study site. Infections due to MDR bacteria were more frequent among colonized than non-colonized neonates, but not significantly, and mortality was low (1%) in the studied neonates. These results indicate that hospitalized preterm neonates in Serbia are rapidly colonized with a diversity of MDR species and resistance phenotypes/genotypes. Full article

(This article belongs to the Section Medical Microbiology)

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23 pages, 3392 KiB

Open AccessEditor’s ChoiceArticle

A Transcriptomic Atlas of the Ectomycorrhizal Fungus Laccaria bicolor

by Joske Ruytinx, Shingo Miyauchi, Sebastian Hartmann-Wittulsky, Maíra de Freitas Pereira, Frédéric Guinet, Jean-Louis Churin, Carine Put, François Le Tacon, Claire Veneault-Fourrey, Francis Martin and Annegret Kohler

Microorganisms 2021, 9(12), 2612; https://doi.org/10.3390/microorganisms9122612 - 17 Dec 2021

Cited by 11 | Viewed by 5393

Abstract

Trees are able to colonize, establish and survive in a wide range of soils through associations with ectomycorrhizal (EcM) fungi. Proper functioning of EcM fungi implies the differentiation of structures within the fungal colony. A symbiotic structure is dedicated to nutrient exchange and [...] Read more.

Trees are able to colonize, establish and survive in a wide range of soils through associations with ectomycorrhizal (EcM) fungi. Proper functioning of EcM fungi implies the differentiation of structures within the fungal colony. A symbiotic structure is dedicated to nutrient exchange and the extramatricular mycelium explores soil for nutrients. Eventually, basidiocarps develop to assure last stages of sexual reproduction. The aim of this study is to understand how an EcM fungus uses its gene set to support functional differentiation and development of specialized morphological structures. We examined the transcriptomes of Laccaria bicolor under a series of experimental setups, including the growth with Populus tremula x alba at different developmental stages, basidiocarps and free-living mycelium, under various conditions of N, P and C supply. In particular, N supply induced global transcriptional changes, whereas responses to P supply seemed to be independent from it. Symbiosis development with poplar is characterized by transcriptional waves. Basidiocarp development shares transcriptional signatures with other basidiomycetes. Overlaps in transcriptional responses of L. bicolor hyphae to a host plant and N/C supply next to co-regulation of genes in basidiocarps and mature mycorrhiza were detected. Few genes are induced in a single condition only, but functional and morphological differentiation rather involves fine tuning of larger gene sets. Overall, this transcriptomic atlas builds a reference to study the function and stability of EcM symbiosis in distinct conditions using L. bicolor as a model and indicates both similarities and differences with other ectomycorrhizal fungi, allowing researchers to distinguish conserved processes such as basidiocarp development from nutrient homeostasis. Full article

(This article belongs to the Special Issue Cellular and Molecular Basis of Plant-Fungal Interactions in Mycorrhizas)

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2 pages, 161 KiB

Open AccessEditorial

The Special Issue: Transmission and Detection of Food and Environmental Pathogens

by Nigel Cook

Microorganisms 2021, 9(12), 2611; https://doi.org/10.3390/microorganisms9122611 - 17 Dec 2021

Viewed by 1437

Abstract

To progress towards a full comprehension of the risk caused by pathogenic microorganisms transmitted via food and environmental routes, extensive information on the prevalence, the mechanisms of contamination, and the survival of pathogens is required, particularly to assist with the development of effective [...] Read more.

To progress towards a full comprehension of the risk caused by pathogenic microorganisms transmitted via food and environmental routes, extensive information on the prevalence, the mechanisms of contamination, and the survival of pathogens is required, particularly to assist with the development of effective systems to reduce contamination, and to formulate procedural control measures, such as the implementation of food safety criteria [...] Full article

(This article belongs to the Special Issue Transmission and Detection of Food and Environmental Pathogens)

16 pages, 2313 KiB

Open AccessArticle

Bap-Independent Biofilm Formation in Staphylococcus xylosus

by Carolin J. Schiffer, Miriam Abele, Matthias A. Ehrmann and Rudi F. Vogel

Microorganisms 2021, 9(12), 2610; https://doi.org/10.3390/microorganisms9122610 - 17 Dec 2021

Cited by 4 | Viewed by 2473

Abstract

The biofilm associated protein (Bap) is recognised as the essential component for biofilm formation in Staphylococcus aureus V329 and has been predicted as important for other species as well. Although Bap orthologs are also present in most S. xylosus strains, their contribution to [...] Read more.

The biofilm associated protein (Bap) is recognised as the essential component for biofilm formation in Staphylococcus aureus V329 and has been predicted as important for other species as well. Although Bap orthologs are also present in most S. xylosus strains, their contribution to biofilm formation has not yet been demonstrated. In this study, different experimental approaches were used to elucidate the effect of Bap on biofilm formation in S. xylosus and the motif structure of two biofilm-forming S. xylosus strains TMW 2.1023 and TMW 2.1523 was compared to Bap of S. aureus V329. We found that despite an identical structural arrangement into four regions, Bap from S. xylosus differs in key factors to Bap of S. aureus, i.e., isoelectric point of aggregation prone Region B, protein homology and type of repeats. Disruption of bap had no effect on aggregation behavior of selected S. xylosus strains and biofilm formation was unaffected (TMW 2.1023) or at best slightly reduced under neutral conditions (TMW 2.1523). Further, we could not observe any typical characteristics of a S. aureus Bap-positive phenotype such as functional impairment by calcium addition and rough colony morphology on congo red agar (CRA). A dominating role of Bap in cell aggregation and biofilm formation as reported mainly for S. aureus V329 was not observed. In contrast, this work demonstrates that functions of S. aureus Bap cannot easily be extrapolated to S. xylosus Bap, which appears as non-essential for biofilm formation in this species. We therefore suggest that biofilm formation in S. xylosus follows different and multifactorial mechanisms. Full article

(This article belongs to the Section Biofilm)

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18 pages, 8599 KiB

Open AccessArticle

Genomic Epidemiology of SARS-CoV-2 Divulge B.1, B.1.36, and B.1.1.7 as the Most Dominant Lineages in First, Second, and Third Wave of SARS-CoV-2 Infections in Pakistan

by Atia Basheer and Imran Zahoor

Microorganisms 2021, 9(12), 2609; https://doi.org/10.3390/microorganisms9122609 - 17 Dec 2021

Cited by 15 | Viewed by 2832

Abstract

The present study aims to investigate the genomic variability and epidemiology of SARS-CoV-2 in Pakistan along with its role in the spread and severity of infection during the three waves of COVID-19. A total of 453 genomic sequences of Pakistani SARS-CoV-2 were retrieved [...] Read more.

The present study aims to investigate the genomic variability and epidemiology of SARS-CoV-2 in Pakistan along with its role in the spread and severity of infection during the three waves of COVID-19. A total of 453 genomic sequences of Pakistani SARS-CoV-2 were retrieved from GISAID and subjected to MAFFT-based alignment and QC check which resulted in removal of 53 samples. The remaining 400 samples were subjected to Pangolin-based genomic lineage identification. And to infer our SARS-CoV-2 time-scaled and divergence phylogenetic trees, 3804 selected global reference sequences plus 400 Pakistani samples were used for the Nextstrain analysis with Wuhan/Hu-1/2019, as reference genome. Finally, maximum likelihood based phylogenetic tree was built by using the Nextstrain and coverage map was created by employing Nextclade. By using the amino acid substitutions, the maximum likelihood phylogenetic trees were developed for each wave, separately. Our results reveal the circulation of 29 lineages, belonging to following seven clades G, GH, GR, GRY, L, O, and S in the three waves. From first wave, 16 genomic lineages of SARS-CoV-2 were identified with B.1(24.7%), B.1.36(18.8%), and B.1.471(18.8%) as the most prevalent lineages respectively. The second wave data showed 18 lineages, 10 of which were overlapping with the first wave suggesting that those variants could not be contained during the first wave. In this wave, a new lineage, AE.4, was reported from Pakistan for the very first time in the world. However, B.1.36 (17.8%), B.1.36.31 (11.9%), B.1.1.7 (8.5%), and B.1.1.1 (5.9%) were the major lineages in second wave. Third wave data showed the presence of nine lineages with Alpha/B.1.1.7 (72.7%), Beta/B.1.351 (12.99%), and Delta/B.1.617.2 (10.39%) as the most predominant variants. It is suggested that these VOCs should be contained at the earliest in order to prevent any devastating outbreak of SARS-CoV-2 in the country. Full article

(This article belongs to the Section Public Health Microbiology)

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20 pages, 2664 KiB

Open AccessReview

RNase III, Ribosome Biogenesis and Beyond

by Maxence Lejars, Asaki Kobayashi and Eliane Hajnsdorf

Microorganisms 2021, 9(12), 2608; https://doi.org/10.3390/microorganisms9122608 - 17 Dec 2021

Cited by 2 | Viewed by 2999

Abstract

The ribosome is the universal catalyst for protein synthesis. Despite extensive studies, the diversity of structures and functions of this ribonucleoprotein is yet to be fully understood. Deciphering the biogenesis of the ribosome in a step-by-step manner revealed that this complexity is achieved [...] Read more.

The ribosome is the universal catalyst for protein synthesis. Despite extensive studies, the diversity of structures and functions of this ribonucleoprotein is yet to be fully understood. Deciphering the biogenesis of the ribosome in a step-by-step manner revealed that this complexity is achieved through a plethora of effectors involved in the maturation and assembly of ribosomal RNAs and proteins. Conserved from bacteria to eukaryotes, double-stranded specific RNase III enzymes play a large role in the regulation of gene expression and the processing of ribosomal RNAs. In this review, we describe the canonical role of RNase III in the biogenesis of the ribosome comparing conserved and unique features from bacteria to eukaryotes. Furthermore, we report additional roles in ribosome biogenesis re-enforcing the importance of RNase III. Full article

(This article belongs to the Special Issue Analysis of Bacterial Ribosomes and Interacting Factors)

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26 pages, 1668 KiB

Open AccessReview

Novel Therapies of Hepatitis B and D

by Iman Waheed Khan, Mati Ullah Dad Ullah, Mina Choudhry, Mukarram Jamat Ali, Muhammad Ashar Ali, Sam L. K. Lam, Pir Ahmad Shah, Satinder Pal Kaur and Daryl T. Y. Lau

Microorganisms 2021, 9(12), 2607; https://doi.org/10.3390/microorganisms9122607 - 17 Dec 2021

Cited by 9 | Viewed by 4163

Abstract

Hepatitis B virus (HBV) infection is a global public health issue and is a major cause of cirrhosis and hepatocellular carcinoma (HCC). Hepatitis D virus (HDV) requires the hepatitis B surface antigen (HBsAg) to replicate. The eradication of HBV, therefore, can also cure [...] Read more.

Hepatitis B virus (HBV) infection is a global public health issue and is a major cause of cirrhosis and hepatocellular carcinoma (HCC). Hepatitis D virus (HDV) requires the hepatitis B surface antigen (HBsAg) to replicate. The eradication of HBV, therefore, can also cure HDV. The current therapies for chronic hepatitis B and D are suboptimal and cannot definitely cure the viruses. In order to achieve functional or complete cure of these infections, novel therapeutic agents that target the various sites of the viral replicative cycle are necessary. Furthermore, novel immunomodulatory agents are also essential to achieve viral clearance. Many of these new promising compounds such as entry inhibitors, covalently closed circular DNA (cccDNA) inhibitors, small interfering RNAs (siRNAs), capsid assembly modulators and nucleic acid polymers are in various stages of clinical developments. In this review article, we provided a comprehensive overview of the structure and lifecycle of HBV, the limitations of the current therapies and a summary of the novel therapeutic agents for both HDV and HBV infection. Full article

(This article belongs to the Special Issue New Methods in Microbial Research 2.0)

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4 pages, 200 KiB

Open AccessEditorial

Special Issue: From Host–Pathogen Interaction to Host-Directed Therapies

by Maria Salomé Gomes and Luisa Pereira

Microorganisms 2021, 9(12), 2606; https://doi.org/10.3390/microorganisms9122606 - 17 Dec 2021

Cited by 1 | Viewed by 1608

Abstract

Despite the enormous progress made in the last few decades, infectious diseases still represent a huge challenge to human society and health systems, as evidenced by the recent SARS-CoV-2 pandemic [...] Full article

(This article belongs to the Special Issue From Host-Pathogen Interaction to Host-Directed Therapies)

9 pages, 4013 KiB

Open AccessCase Report

Assessment of Marine Gill Disease in Farmed Atlantic Salmon (Salmo salar) in Chile Using a Novel Total Gross Gill Scoring System: A Case Study

by Sophie Fridman, Smaragda Tsairidou, Nilantha Jayasuriya, Halina Sobolewska, Alastair Hamilton, Carlos Lobos, Ross D. Houston, Hamish Rodger, James Bron and Tharangani Herath

Microorganisms 2021, 9(12), 2605; https://doi.org/10.3390/microorganisms9122605 - 16 Dec 2021

Cited by 4 | Viewed by 3967

Abstract

Gill disorders have become more prevalent and widespread in finfish aquaculture in recent years. Their aetiology is often considered to be multifactorial. Effective diagnosis, control and prevention are hindered by the lack of standardised methodologies to characterise the aetiological agents, which produce an [...] Read more.

Gill disorders have become more prevalent and widespread in finfish aquaculture in recent years. Their aetiology is often considered to be multifactorial. Effective diagnosis, control and prevention are hindered by the lack of standardised methodologies to characterise the aetiological agents, which produce an array of clinical and pathological presentations. The aim of this study was to define a novel gross pathological scoring system suitable for field-based macroscopic assessment of complex or multifactorial gill disease in farmed Atlantic salmon, using samples derived from a gill disease outbreak in Chile. Clinical assessment of gross gill morphology was performed, and gill samples were collected for qPCR and histology. A novel total gill scoring system was developed, which assesses gross pathological changes combining both the presumptive or healed amoebic gill disease (AGD) and the presence of other types of gill lesions. This scoring system offers a standardised approach to characterise the severe proliferative pathologies in affected gills. This total gill scoring system can substantially contribute to the development of robust mitigation strategies and could be used as an indicator trait for incorporating resistance to multifactorial gill disease into breeding goals. Full article

(This article belongs to the Special Issue Amoebic Gill Disease)

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9 pages, 969 KiB

Open AccessCommunication

Evaluation of Three Culture Media for Isolation of Burkholderia cepacia Complex from Respiratory Samples of Patients with Cystic Fibrosis

by Emma C. L. Marrs, Audrey Perry and John D. Perry

Microorganisms 2021, 9(12), 2604; https://doi.org/10.3390/microorganisms9122604 - 16 Dec 2021

Cited by 5 | Viewed by 2064

Abstract

Burkholderia cepacia complex (BCC) is a significant pathogen causing respiratory disease in individuals with cystic fibrosis (CF). Diagnosis is typically achieved by isolation of BCC on selective culture media following culture of sputum or other respiratory samples. The aim of this study was [...] Read more.

Burkholderia cepacia complex (BCC) is a significant pathogen causing respiratory disease in individuals with cystic fibrosis (CF). Diagnosis is typically achieved by isolation of BCC on selective culture media following culture of sputum or other respiratory samples. The aim of this study was to compare the efficacy of three commercially available selective media for the isolation of BCC. The three media comprised Burkholderia cepacia selective agar (BCSA; bioMérieux), BD Cepacia medium (BD: Becton–Dickinson) and MAST Cepacia medium (MAST laboratories). Each medium was challenged with 270 respiratory samples from individuals with CF as well as an international collection of BCC (n = 26) and 14 other isolates of Burkholderia species at a range of inocula. The international collection was also used to artificially “spike” 26 respiratory samples. From a total of 34 respiratory samples containing BCC, 97% were recovered on BD and 94% were detected on MAST and BCSA. All three media were effective for isolation of BCC. BCSA was much more selective than the other two media (p < 0.0001) meaning that fewer isolates required processing to exclude the presence of BCC. Full article

(This article belongs to the Section Medical Microbiology)

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15 pages, 3147 KiB

Open AccessArticle

Several Yeast Species Induce Iron Deficiency Responses in Cucumber Plants (Cucumis sativus L.)

by Carlos Lucena, María T. Alcalá-Jiménez, Francisco J. Romera and José Ramos

Microorganisms 2021, 9(12), 2603; https://doi.org/10.3390/microorganisms9122603 - 16 Dec 2021

Cited by 3 | Viewed by 2338

Abstract

Iron (Fe) deficiency is a first-order agronomic problem that causes a significant decrease in crop yield and quality. Paradoxically, Fe is very abundant in most soils, mainly in its oxidized form, but is poorly soluble and with low availability for plants. In order [...] Read more.

Iron (Fe) deficiency is a first-order agronomic problem that causes a significant decrease in crop yield and quality. Paradoxically, Fe is very abundant in most soils, mainly in its oxidized form, but is poorly soluble and with low availability for plants. In order to alleviate this situation, plants develop different morphological and physiological Fe-deficiency responses, mainly in their roots, to facilitate Fe mobilization and acquisition. Even so, Fe fertilizers, mainly Fe chelates, are widely used in modern agriculture, causing environmental problems and increasing the costs of production, due to the high prices of these products. One of the most sustainable and promising alternatives to the use of agrochemicals is the better management of the rhizosphere and the beneficial microbial communities presented there. The main objective of this research has been to evaluate the ability of several yeast species, such as Debaryomyces hansenii, Saccharomyces cerevisiae and Hansenula polymorpha, to induce Fe-deficiency responses in cucumber plants. To date, there are no studies on the roles played by yeasts on the Fe nutrition of plants. Experiments were carried out with cucumber plants grown in a hydroponic growth system. The effects of the three yeast species on some of the most important Fe-deficiency responses developed by dicot (Strategy I) plants, such as enhanced ferric reductase activity and Fe²⁺ transport, acidification of the rhizosphere, and proliferation of subapical root hairs, were evaluated. The results obtained show the inductive character of the three yeast species, mainly of Debaryomyces hansenii and Hansenula polymorpha, on the Fe-deficiency responses evaluated in this study. This opens a promising line of study on the use of these microorganisms as Fe biofertilizers in a more sustainable and environmentally friendly agriculture. Full article

(This article belongs to the Special Issue Exploring Fungal Diversity: Novel Bioactive Compounds and Sustainable Bioprocesses)

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24 pages, 7878 KiB

Open AccessArticle

Diverse Single-Stranded DNA Viruses Identified in Chicken Buccal Swabs

by Klaudia Chrzastek, Simona Kraberger, Kara Schmidlin, Rafaela S. Fontenele, Arun Kulkarni, Len Chappell, Louise Dufour-Zavala, Darrell R. Kapczynski and Arvind Varsani

Microorganisms 2021, 9(12), 2602; https://doi.org/10.3390/microorganisms9122602 - 16 Dec 2021

Cited by 6 | Viewed by 2467

Abstract

High-throughput sequencing approaches offer the possibility to better understand the complex microbial communities associated with animals. Viral metagenomics has facilitated the discovery and identification of many known and unknown viruses that inhabit mucosal surfaces of the body and has extended our knowledge related [...] Read more.

High-throughput sequencing approaches offer the possibility to better understand the complex microbial communities associated with animals. Viral metagenomics has facilitated the discovery and identification of many known and unknown viruses that inhabit mucosal surfaces of the body and has extended our knowledge related to virus diversity. We used metagenomics sequencing of chicken buccal swab samples and identified various small DNA viruses with circular genome organization. Out of 134 putative circular viral-like circular genome sequences, 70 are cressdnaviruses and 26 are microviruses, whilst the remaining 38 most probably represent sub-genomic molecules. The cressdnaviruses found in this study belong to the Circoviridae, Genomoviridae and Smacoviridae families as well as previously described CRESS1 and naryavirus groups. Among these, genomoviruses and smacoviruses were the most prevalent across the samples. Interestingly, we also identified 26 bacteriophages that belong to the Microviridae family, whose members are known to infect enterobacteria. Full article

(This article belongs to the Special Issue Viral Metagenomics and Metatranscriptomics: Virus Discovery, Ecology, and Evolution)

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24 pages, 1398 KiB

Open AccessReview

Nutritional Modulation of the Immune Response Mediated by Nucleotides in Canine Leishmaniosis

by Sergi Segarra

Microorganisms 2021, 9(12), 2601; https://doi.org/10.3390/microorganisms9122601 - 16 Dec 2021

Cited by 7 | Viewed by 3950

Abstract

Leishmaniasis is an emerging, uncontrolled, and neglected zoonotic disease. Climate change is contributing to its ongoing global expansion. The dog is the main reservoir; hence the importance of implementing effective treatment, prevention, and control measures in this animal species to protect public health. [...] Read more.

Leishmaniasis is an emerging, uncontrolled, and neglected zoonotic disease. Climate change is contributing to its ongoing global expansion. The dog is the main reservoir; hence the importance of implementing effective treatment, prevention, and control measures in this animal species to protect public health. However, although the standard treatment for canine leishmaniosis (CanL) is effective, it does not provide full parasitological clearance, and side effects and drug resistance have been described. The host’s immune system plays a key role in the establishment and evolution of leishmaniasis. Dietary nucleotides modulate the immune response and, given their reported efficacy and safety in sick and clinically healthy Leishmania-infected dogs and because they represent a sustainable option with no associated side effects or resistance, they could be included within the prevention, treatment, and control strategies for leishmaniasis. This article briefly summarizes the scientific literature on CanL management, including unresolved issues, and reviews the scientific evidence on immunomodulatory effects of dietary nucleotides in different animal species. It also proposes a CanL management algorithm, including nucleotides. It is concluded that nutritional modulation of the immune response with nucleotides can contribute to better management of leishmaniasis following a One Health approach, especially in the COVID-19 era. Full article

(This article belongs to the Special Issue Leishmania and Associated Diseases)

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9 pages, 2740 KiB

Open AccessCommunication

Primary Site of Coxsackievirus B Replication in the Small Intestines: No Proof of Peyer’s Patches Involvement

by Shubhada Bopegamage, Katarina Berakova, Pavol Gomocak, Renata Baksova, Jochem Galama, Heikki Hyoty and Sisko Tauriainen

Microorganisms 2021, 9(12), 2600; https://doi.org/10.3390/microorganisms9122600 - 16 Dec 2021

Cited by 3 | Viewed by 2260

Abstract

Background: Enterovirus (EV) infections are associated with a broad range of diseases. Since the first experimental infection of primates with poliovirus (PV), tonsils and the Peyer’s patches (PPs) have been believed to be the primary replication sites of EVs. Our aim was to [...] Read more.

Background: Enterovirus (EV) infections are associated with a broad range of diseases. Since the first experimental infection of primates with poliovirus (PV), tonsils and the Peyer’s patches (PPs) have been believed to be the primary replication sites of EVs. Our aim was to localize different viral markers in the small intestines (SI) of coxsackievirus B (CVB) orally and intraperitoneally (i.p.) infected mice. Methods: Transverse sections of SIs of both infected and control male outbred mice were collected at different intervals post-infection (p.i) and analyzed for presence of interferon-alpha (IFN-α) and viral protein VP1 by immunohistochemistry and in situ hybridization (ISH). Fluorescent marker, eGFP, was identified in cryosections of mice infected with eGFP-CVB3. Results: In the infected SIs, we observed enlarged germinating centers (GCs) in the PPs; IFN-α was detected in the PPs and mucosal layer of the SIs. However, VP1, viral RNA and the eGFP were absent in the GCs of PPs at all stages of infection irrespective of the virus strains used. Conclusions: Virus was present in the epithelial cells but not in GCs of the PPs of the murine SIs. Our results do not support the hypothesis of EV replication in the PP especially in the GCs. Full article

(This article belongs to the Special Issue Coxsackievirus Infection and Associated Diseases)

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18 pages, 2040 KiB

Open AccessCase Report

Assessing Gut Microbiota in an Infant with Congenital Propionic Acidemia before and after Probiotic Supplementation

by Andrea Bordugo, Elisa Salvetti, Giulia Rodella, Michele Piazza, Alice Dianin, Angela Amoruso, Giorgio Piacentini, Marco Pane, Sandra Torriani, Nicola Vitulo and Giovanna E. Felis

Microorganisms 2021, 9(12), 2599; https://doi.org/10.3390/microorganisms9122599 - 16 Dec 2021

Cited by 6 | Viewed by 2740

Abstract

Propionic Acidemia (PA) is a rare inherited metabolic disorder caused by the enzymatic block of propionyl-CoA carboxylase with the consequent accumulation of propionic acid, which is toxic for the brain and cardiac cells. Since a considerable amount of propionate is produced by intestinal [...] Read more.

Propionic Acidemia (PA) is a rare inherited metabolic disorder caused by the enzymatic block of propionyl-CoA carboxylase with the consequent accumulation of propionic acid, which is toxic for the brain and cardiac cells. Since a considerable amount of propionate is produced by intestinal bacteria, interest arose in the attempt to reduce propionate-producing bacteria through a monthly antibiotic treatment of metronidazole. In the present study, we investigated the gut microbiota structure of an infant diagnosed at 4 days of life through Expanded Newborn Screening (NBS) and treated the child following international guidelines with a special low-protein diet, specific medications and strict biochemical monitoring. Microbiota composition was assessed during the first month of life, and the presence of Bacteroides fragilis, known to be associated with propionate production, was effectively decreased by metronidazole treatment. After five antibiotic therapy cycles, at 4 months of age, the infant was supplemented with a daily mixture of three bifidobacterial strains, known not to be propionate producers. The supplementation increased the population of bifidobacteria, with Bifidobacterium breve as the dominating species; Ruminococcus gnavus, an acetate and formate producer, was also identified. Metabarcoding analysis, compared with low coverage whole metagenome sequencing, proved to capture all the microbial biodiversity and could be the elected tool for fast and cost-effective monitoring protocols to be implemented in the follow up of rare metabolic disorders such as PA. Data obtained could be a possible starting point to set up tailored microbiota modification treatment studies in the attempt to improve the quality of life of people affected by propionic acidemia. Full article

(This article belongs to the Special Issue Probiotics and Intestinal Health)

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10 pages, 2042 KiB

Open AccessProtocol

Simplified Point-of-Care Full SARS-CoV-2 Genome Sequencing Using Nanopore Technology

by Anton Pembaur, Erwan Sallard, Patrick Philipp Weil, Jennifer Ortelt, Parviz Ahmad-Nejad and Jan Postberg

Microorganisms 2021, 9(12), 2598; https://doi.org/10.3390/microorganisms9122598 - 16 Dec 2021

Cited by 14 | Viewed by 3210

Abstract

The scale of the ongoing SARS-CoV-2 pandemic warrants the urgent establishment of a global decentralized surveillance system to recognize local outbreaks and the emergence of novel variants of concern. Among available deep-sequencing technologies, nanopore-sequencing could be an important cornerstone, as it is mobile, [...] Read more.

The scale of the ongoing SARS-CoV-2 pandemic warrants the urgent establishment of a global decentralized surveillance system to recognize local outbreaks and the emergence of novel variants of concern. Among available deep-sequencing technologies, nanopore-sequencing could be an important cornerstone, as it is mobile, scalable, and cost-effective. Therefore, streamlined nanopore-sequencing protocols need to be developed and optimized for SARS-CoV-2 variants identification. We adapted and simplified existing workflows using the ‘midnight’ 1200 bp amplicon split primer sets for PCR, which produce tiled overlapping amplicons covering almost the entire SARS-CoV-2 genome. Subsequently, we applied Oxford Nanopore Rapid Barcoding and the portable MinION Mk1C sequencer combined with the interARTIC bioinformatics pipeline. We tested a simplified and less time-consuming workflow using SARS-CoV-2-positive specimens from clinical routine and identified the CT value as a useful pre-analytical parameter, which may help to decrease sequencing failures rates. Complete pipeline duration was approx. 7 h for one specimen and approx. 11 h for 12 multiplexed barcoded specimens. The adapted protocol contains fewer processing steps and can be completely conducted within one working day. Diagnostic CT values deduced from qPCR standardization experiments can act as principal criteria for specimen selection. As a guideline, SARS-CoV-2 genome copy numbers lower than 4 × 10⁶ were associated with a coverage threshold below 20-fold and incompletely assembled SARS-CoV-2 genomes. Thus, based on the described thermocycler/chemistry combination, we recommend CT values of ~26 or lower to achieve full and high-quality SARS-CoV-2 (+)RNA genome coverage. Full article

(This article belongs to the Section Medical Microbiology)

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