Microorganisms

13 pages, 4671 KiB

Open AccessArticle

Human and Animal Dirofilariasis in Southeast of France

by Younes Laidoudi, Domenico Otranto, Natacha Stolowy, Sophie Amrane, Ranju Ravindran Santhakumari Manoj, Laurine Polette, Stéphanie Watier-Grillot, Oleg Mediannikov, Bernard Davoust and Coralie L'Ollivier

Microorganisms 2021, 9(7), 1544; https://doi.org/10.3390/microorganisms9071544 - 20 Jul 2021

Cited by 10 | Viewed by 3320

Abstract

Dirofilariasis is one of the oldest known zoonotic infections of humans mainly caused by the filarial parasites of the species Dirofilaria immitis and Dirofilaria repens, which primarily infect dogs. A five-year survey (2017 to 2021) was conducted among the dog population to [...] Read more.

Dirofilariasis is one of the oldest known zoonotic infections of humans mainly caused by the filarial parasites of the species Dirofilaria immitis and Dirofilaria repens, which primarily infect dogs. A five-year survey (2017 to 2021) was conducted among the dog population to assess the molecular prevalence of Dirofilaria spp. in southeast France. Morphological and genetic analysis were performed on filaroids from dogs and one infected woman from the studied area. A total of 12 (13%) dogs scored molecularly positive for Dirofilaria spp. of which nine carried blood microfilariae. Ocular dirofilariasis was detected in a 79-year-old woman with no travel history. Both electron microscopy and molecular sequencing identified the worm in the human case as D. repens. Molecularly, D. repens isolates were identical in the human and dog cases, representing the only genotype reported so far in France. Despite the distribution of this genotype through all Europe, it was grouped separately with the other two European genotypes and with Asian ones. As in almost all previous human cases in France, D. repens parasites were mainly recovered from the ocular region of patients and were geographically concentrated in the southeastern regions. Data demonstrate the sympatric occurrence of D. immitis and D. repens with high risk of infection to human and dog populations in these investigated geographical areas, thereby underlining the urgent need to implement preventive chemoprophylactic strategies and vector control to reduce the risk of these filaroids in dog and human populations. Full article

(This article belongs to the Special Issue Infectious Diseases: Clinical Diagnosis and Molecular Epidemiology)

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13 pages, 1223 KiB

Open AccessArticle

A Large Retrospective Assessment of Voriconazole Exposure in Patients Treated with Extracorporeal Membrane Oxygenation

by Ruth Van Daele, Britt Bekkers, Mattias Lindfors, Lars Mikael Broman, Alexander Schauwvlieghe, Bart Rijnders, Nicole G. M. Hunfeld, Nicole P. Juffermans, Fabio Silvio Taccone, Carlos Antônio Coimbra Sousa, Luc-Marie Jacquet, Pierre-François Laterre, Eric Nulens, Veerle Grootaert, Haifa Lyster, Anna Reed, Brijesh Patel, Philippe Meersseman, Yves Debaveye, Joost Wauters, Christophe Vandenbriele and Isabel Spriet Show full author list Hide full author list

Microorganisms 2021, 9(7), 1543; https://doi.org/10.3390/microorganisms9071543 - 20 Jul 2021

Cited by 23 | Viewed by 3344

Abstract

Background: Voriconazole is one of the first-line therapies for invasive pulmonary aspergillosis. Drug concentrations might be significantly influenced by the use of extracorporeal membrane oxygenation (ECMO). We aimed to assess the effect of ECMO on voriconazole exposure in a large patient population. Methods: [...] Read more.

Background: Voriconazole is one of the first-line therapies for invasive pulmonary aspergillosis. Drug concentrations might be significantly influenced by the use of extracorporeal membrane oxygenation (ECMO). We aimed to assess the effect of ECMO on voriconazole exposure in a large patient population. Methods: Critically ill patients from eight centers in four countries treated with voriconazole during ECMO support were included in this retrospective study. Voriconazole concentrations were collected in a period on ECMO and before/after ECMO treatment. Multivariate analyses were performed to evaluate the effect of ECMO on voriconazole exposure and to assess the impact of possible saturation of the circuit’s binding sites over time. Results: Sixty-nine patients and 337 samples (190 during and 147 before/after ECMO) were analyzed. Subtherapeutic concentrations (<2 mg/L) were observed in 56% of the samples during ECMO and 39% without ECMO (p = 0.80). The median trough concentration, for a similar daily dose, was 2.4 (1.2–4.7) mg/L under ECMO and 2.5 (1.4–3.9) mg/L without ECMO (p = 0.58). Extensive inter-and intrasubject variability were observed. Neither ECMO nor squared day of ECMO (saturation) were retained as significant covariates on voriconazole exposure. Conclusions: No significant ECMO-effect was observed on voriconazole exposure. A large proportion of patients had voriconazole subtherapeutic concentrations. Full article

(This article belongs to the Special Issue Complex Infectious Issues in Critically Ill Patients)

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11 pages, 2652 KiB

Open AccessArticle

SARS-CoV-2 Spike Mutations, L452R, T478K, E484Q and P681R, in the Second Wave of COVID-19 in Maharashtra, India

by Sarah Cherian, Varsha Potdar, Santosh Jadhav, Pragya Yadav, Nivedita Gupta, Mousumi Das, Partha Rakshit, Sujeet Singh, Priya Abraham, Samiran Panda and NIC Team

Microorganisms 2021, 9(7), 1542; https://doi.org/10.3390/microorganisms9071542 - 20 Jul 2021

Cited by 446 | Viewed by 13185

Abstract

As the global severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic expands, genomic epidemiology and whole genome sequencing are being used to investigate its transmission and evolution. Against the backdrop of the global emergence of “variants of concern” (VOCs) during December 2020 and [...] Read more.

As the global severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic expands, genomic epidemiology and whole genome sequencing are being used to investigate its transmission and evolution. Against the backdrop of the global emergence of “variants of concern” (VOCs) during December 2020 and an upsurge in a state in the western part of India since January 2021, whole genome sequencing and analysis of spike protein mutations using sequence and structural approaches were undertaken to identify possible new variants and gauge the fitness of the current circulating strains. Phylogenetic analysis revealed that newly identified lineages B.1.617.1 and B.1.617.2 were predominantly circulating. The signature mutations possessed by these strains were L452R, T478K, E484Q, D614G and P681R in the spike protein, including within the receptor-binding domain (RBD). Of these, the mutations at residue positions 452, 484 and 681 have been reported in other globally circulating lineages. The structural analysis of RBD mutations L452R, T478K and E484Q revealed that these may possibly result in increased ACE2 binding while P681R in the furin cleavage site could increase the rate of S1-S2 cleavage, resulting in better transmissibility. The two RBD mutations, L452R and E484Q, indicated decreased binding to select monoclonal antibodies (mAbs) and may affect their neutralization potential. Further in vitro/in vivo studies would help confirm the phenotypic changes of the mutant strains. Overall, the study revealed that the newly emerged variants were responsible for the second wave of COVID-19 in Maharashtra. Lineage B.1.617.2 has been designated as a VOC delta and B.1.617.1 as a variant of interest kappa, and they are being widely reported in the rest of the country as well as globally. Continuous monitoring of these and emerging variants in India is essential. Full article

(This article belongs to the Special Issue COVID-19: Focusing on Epidemiologic, Virologic, and Clinical Studies)

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15 pages, 332 KiB

Open AccessReview

Grapevine Powdery Mildew: Fungicides for Its Management and Advances in Molecular Detection of Markers Associated with Resistance

by Andrea Kunova, Cristina Pizzatti, Marco Saracchi, Matias Pasquali and Paolo Cortesi

Microorganisms 2021, 9(7), 1541; https://doi.org/10.3390/microorganisms9071541 - 20 Jul 2021

Cited by 24 | Viewed by 4897

Abstract

Grapevine powdery mildew is a principal fungal disease of grapevine worldwide. Even though it usually does not cause plant death directly, heavy infections can lead to extensive yield losses, and even low levels of the disease can negatively affect the quality of the [...] Read more.

Grapevine powdery mildew is a principal fungal disease of grapevine worldwide. Even though it usually does not cause plant death directly, heavy infections can lead to extensive yield losses, and even low levels of the disease can negatively affect the quality of the wine. Therefore, intensive spraying programs are commonly applied to control the disease, which often leads to the emergence and spread of powdery mildew strains resistant to different fungicides. In this review, we describe major fungicide classes used for grapevine powdery mildew management and the most common single nucleotide mutations in target genes known to confer resistance to different classes of fungicides. We searched the current literature to review the development of novel molecular methods for quick detection and monitoring of resistance to commonly used single-site fungicides against Erysiphe necator. We analyze and compare the developed methods. From our investigation it became evident that this research topic has been strongly neglected and we hope that effective molecular methods will be developed also for resistance monitoring in biotroph pathogens. Full article

(This article belongs to the Special Issue Fungicide Resistance in Plant Pathogens)

20 pages, 3784 KiB

Open AccessArticle

Genome Characterization of Nocturne116, Novel Lactococcus lactis-Infecting Phage Isolated from Moth

by Nikita Zrelovs, Andris Dislers and Andris Kazaks

Microorganisms 2021, 9(7), 1540; https://doi.org/10.3390/microorganisms9071540 - 20 Jul 2021

Cited by 6 | Viewed by 3524

Abstract

While looking for novel insect-associated phages, a unique siphophage, Nocturne116, was isolated from a deceased local moth specimen along with its host, which was identified by 16S rRNA gene sequencing as a strain of Lactococcus lactis. Next-generation sequencing and the subsequent genome [...] Read more.

While looking for novel insect-associated phages, a unique siphophage, Nocturne116, was isolated from a deceased local moth specimen along with its host, which was identified by 16S rRNA gene sequencing as a strain of Lactococcus lactis. Next-generation sequencing and the subsequent genome annotation elaborated on herein revealed that the genome of Nocturne116 is a 25,554 bp long dsDNA molecule with 10 bp long 3′ cos overhangs and a GC content of 37.99%, comprising 52 predicted open reading frames. The complete nucleotide sequence of phage Nocturne116 genome is dissimilar to any of the already sequenced phages, save for a distant link with Lactococcus phage Q54. Functions for only 15/52 of Nocturne116 gene products could be reliably predicted using contemporary comparative genomics approaches, while 22 of its gene products do not yet have any homologous entries in the public biological sequence repositories. Despite the public availability of nearly 350 elucidated Lactococcus phage complete genomes as of now, Nocturne116 firmly stands out as a sole representative of novel phage genus. Full article

(This article belongs to the Special Issue Bacteriophage Genomics)

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19 pages, 1684 KiB

Open AccessReview

Application and Perspectives of MALDI–TOF Mass Spectrometry in Clinical Microbiology Laboratories

by Eva Torres-Sangiao, Cristina Leal Rodriguez and Carlos García-Riestra

Microorganisms 2021, 9(7), 1539; https://doi.org/10.3390/microorganisms9071539 - 20 Jul 2021

Cited by 56 | Viewed by 12697

Abstract

Early diagnosis of severe infections requires of a rapid and reliable diagnosis to initiate appropriate treatment, while avoiding unnecessary antimicrobial use and reducing associated morbidities and healthcare costs. It is a fact that conventional methods usually require more than 24–48 h to culture [...] Read more.

Early diagnosis of severe infections requires of a rapid and reliable diagnosis to initiate appropriate treatment, while avoiding unnecessary antimicrobial use and reducing associated morbidities and healthcare costs. It is a fact that conventional methods usually require more than 24–48 h to culture and profile bacterial species. Mass spectrometry (MS) is an analytical technique that has emerged as a powerful tool in clinical microbiology for identifying peptides and proteins, which makes it a promising tool for microbial identification. Matrix assisted laser desorption ionization–time of flight MS (MALDI–TOF MS) offers a cost- and time-effective alternative to conventional methods, such as bacterial culture and even 16S rRNA gene sequencing, for identifying viruses, bacteria and fungi and detecting virulence factors and mechanisms of resistance. This review provides an overview of the potential applications and perspectives of MS in clinical microbiology laboratories and proposes its use as a first-line method for microbial identification and diagnosis. Full article

(This article belongs to the Special Issue Infectious Diseases, New Approaches to Old Problems)

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13 pages, 1330 KiB

Open AccessArticle

Dual RNA-Seq Enables Full-Genome Assembly of Measles Virus and Characterization of Host–Pathogen Interactions

by Timokratis Karamitros, Vasiliki Pogka, Gethsimani Papadopoulou, Ourania Tsitsilonis, Maria Evangelidou, Styliani Sympardi and Andreas Mentis

Microorganisms 2021, 9(7), 1538; https://doi.org/10.3390/microorganisms9071538 - 20 Jul 2021

Cited by 7 | Viewed by 2761

Abstract

Measles virus (MeV) has a negative-sense 15 kb long RNA genome, which is generally conserved. Recent advances in high-throughput sequencing (HTS) and Dual RNA-seq allow the analysis of viral RNA genomes and the discovery of viral infection biomarkers, via the simultaneous characterization of [...] Read more.

Measles virus (MeV) has a negative-sense 15 kb long RNA genome, which is generally conserved. Recent advances in high-throughput sequencing (HTS) and Dual RNA-seq allow the analysis of viral RNA genomes and the discovery of viral infection biomarkers, via the simultaneous characterization of the host transcriptome. However, these host–pathogen interactions remain largely unexplored in MeV infections. We performed untargeted Dual RNA-seq in 6 pharyngeal and 6 peripheral blood mononuclear cell (PBMCs) specimens from patients with MeV infection, as confirmed via routine real-time PCR testing. Following optimised DNase treatment of total nucleic acids, we used the pharyngeal samples to build poly-A-enriched NGS libraries. We reconstructed the viral genomes using the pharyngeal datasets and we further conducted differential expression, gene-ontology and pathways enrichment analysis to compare both the pharyngeal and the peripheral blood transcriptomes of the MeV-infected patients vs. control groups of healthy individuals. We obtained 6 MeV genotype-B3 full-genome sequences. We minutely analyzed the transcriptome of the MeV-infected pharyngeal epithelium, detecting all known viral infection biomarkers, but also revealing a functional cluster of local antiviral and inflammatory immune responses, which differ substantially from those observed in the PBMCs transcriptome. The application of Dual RNA-seq technologies in MeV-infected patients can potentially provide valuable information on the virus genome structure and the cellular innate immune responses and drive the discovery of new targets for antiviral therapy. Full article

(This article belongs to the Special Issue Microorganisms Associated with Infectious Disease)

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20 pages, 3830 KiB

Open AccessArticle

Coxsackievirus B4 Transplacental Infection Severely Disturbs Central Tolerogenic Mechanisms in the Fetal Thymus

by Aymen Halouani, Hélène Michaux, Habib Jmii, Charlotte Trussart, Ahlem Chahbi, Henri Martens, Chantal Renard, Mahjoub Aouni, Didier Hober, Vincent Geenen and Hela Jaïdane

Microorganisms 2021, 9(7), 1537; https://doi.org/10.3390/microorganisms9071537 - 19 Jul 2021

Cited by 3 | Viewed by 2595

Abstract

Thymus plays a fundamental role in central tolerance establishment, especially during fetal life, through the generation of self-tolerant T cells. This process consists in T cells education by presenting them tissue-restricted autoantigens promiscuously expressed by thymic epithelial cells (TECs), thus preventing autoimmunity. Thymus [...] Read more.

Thymus plays a fundamental role in central tolerance establishment, especially during fetal life, through the generation of self-tolerant T cells. This process consists in T cells education by presenting them tissue-restricted autoantigens promiscuously expressed by thymic epithelial cells (TECs), thus preventing autoimmunity. Thymus infection by Coxsackievirus B (CV-B) during fetal life is supposed to disturb thymic functions and, hence, to be an inducing or accelerating factor in the genesis of autoimmunity. To further investigate this hypothesis, in our current study, we analyzed thymic expression of autoantigens, at the transcriptional and protein level, following in utero infection by CV-B4. mRNA expression levels of Igf2 and Myo7, major autoantigens of pancreas and heart, respectively, were analyzed in whole thymus and in enriched TECs together along with both transcription factors, Aire and Fezf2, involved in autoantigens expression in the thymus. Results show that in utero infection by CV-B4 induces a significant decrease in Igf2 and Myo7 expression at both mRNA and protein level in whole thymus and in enriched TECs as well. Moreover, a correlation between viral load and autoantigens expression can be observed in the whole thymus, indicating a direct effect of in utero infection by CV-B4 on autoantigens expression. Together, these results indicate that an in utero infection of the thymus by CV-B4 may interfere with self-tolerance establishment in TECs by decreasing autoantigen expression at both mRNA and protein level and thereby increase the risk of autoimmunity onset. Full article

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

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16 pages, 342 KiB

Open AccessReview

Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS) Analysis for the Identification of Pathogenic Microorganisms: A Review

by Xin-Fei Chen, Xin Hou, Meng Xiao, Li Zhang, Jing-Wei Cheng, Meng-Lan Zhou, Jing-Jing Huang, Jing-Jia Zhang, Ying-Chun Xu and Po-Ren Hsueh

Microorganisms 2021, 9(7), 1536; https://doi.org/10.3390/microorganisms9071536 - 19 Jul 2021

Cited by 43 | Viewed by 6017

Abstract

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been used in the field of clinical microbiology since 2010. Compared with the traditional technique of biochemical identification, MALDI-TOF MS has many advantages, including convenience, speed, accuracy, and low cost. The accuracy and [...] Read more.

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been used in the field of clinical microbiology since 2010. Compared with the traditional technique of biochemical identification, MALDI-TOF MS has many advantages, including convenience, speed, accuracy, and low cost. The accuracy and speed of identification using MALDI-TOF MS have been increasing with the development of sample preparation, database enrichment, and algorithm optimization. MALDI-TOF MS has shown promising results in identifying cultured colonies and rapidly detecting samples. MALDI-TOF MS has critical research applications for the rapid detection of highly virulent and drug-resistant pathogens. Here we present a scientific review that evaluates the performance of MALDI-TOF MS in identifying clinical pathogenic microorganisms. MALDI-TOF MS is a promising tool in identifying clinical microorganisms, although some aspects still require improvement. Full article

(This article belongs to the Special Issue Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS) for the Identification of Pathogenic Microorganisms)

17 pages, 592 KiB

Open AccessReview

Beating the Bio-Terror Threat with Rapid Antimicrobial Susceptibility Testing

by Shahar Rotem, Ida Steinberger-Levy, Ofir Israeli, Eran Zahavy and Ronit Aloni-Grinstein

Microorganisms 2021, 9(7), 1535; https://doi.org/10.3390/microorganisms9071535 - 19 Jul 2021

Cited by 2 | Viewed by 2710

Abstract

A bioterror event using an infectious bacterium may lead to catastrophic outcomes involving morbidity and mortality as well as social and psychological stress. Moreover, a bioterror event using an antibiotic resistance engineered bacterial agent may raise additional concerns. Thus, preparedness is essential to [...] Read more.

A bioterror event using an infectious bacterium may lead to catastrophic outcomes involving morbidity and mortality as well as social and psychological stress. Moreover, a bioterror event using an antibiotic resistance engineered bacterial agent may raise additional concerns. Thus, preparedness is essential to preclude and control the dissemination of the bacterial agent as well as to appropriately and promptly treat potentially exposed individuals or patients. Rates of morbidity, death, and social anxiety can be drastically reduced if the rapid delivery of antimicrobial agents for post-exposure prophylaxis and treatment is initiated as soon as possible. Availability of rapid antibiotic susceptibility tests that may provide key recommendations to targeted antibiotic treatment is mandatory, yet, such tests are only at the development stage. In this review, we describe the recently published rapid antibiotic susceptibility tests implemented on bioterror bacterial agents and discuss their assimilation in clinical and environmental samples. Full article

(This article belongs to the Special Issue Antimicrobial Testing (AMT))

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17 pages, 4374 KiB

Open AccessArticle

Research on the Biofilm Formation of Staphylococcus aureus after Cold Stress

by Jiaju Qiao, Liping Zheng, Zhaoxin Lu, Fanqiang Meng and Xiaomei Bie

Microorganisms 2021, 9(7), 1534; https://doi.org/10.3390/microorganisms9071534 - 19 Jul 2021

Cited by 6 | Viewed by 2259

Abstract

Staphylococcus aureus is a common food pathogen and has a strong tolerance to environmental stress. Here, the biofilm formation of S. aureus strains after cold stress for 24 weeks were investigated. It was found that the biofilm formation of S. aureus CICC 21600, [...] Read more.

Staphylococcus aureus is a common food pathogen and has a strong tolerance to environmental stress. Here, the biofilm formation of S. aureus strains after cold stress for 24 weeks were investigated. It was found that the biofilm formation of S. aureus CICC 21600, CICC 22942, W1, W3, and C1 cells was enhanced after cold stress for 20 weeks. What is more, the mRNA levels of the clfA, icaA, icaB, icaC or icaD genes in these strains were increased for >2-fold. The increased gene transcription levels were consistent with the increase in the polysaccharide content in the biofilm matrix of these S. aureus strains after cold stress. Meanwhile, hydrophobicity and the adhesion proteins also played a role in the formation of biofilms. The biofilm of S. aureus cells can be effectively degraded by snailase and proteinase K (125 µg/mL + 20 µg/mL) mixture. In summary, S. aureus frozen at −20 °C for 12 to 20 weeks is still a potential hazard. Food factory equipment should be cleaned in a timely manner to avoid outbreaks of foodborne pathogenic bacteria due to contamination. Full article

(This article belongs to the Section Biofilm)

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18 pages, 1736 KiB

Open AccessReview

Recent Developments in the Study of Plant Microbiomes

by Bernard R. Glick and Elisa Gamalero

Microorganisms 2021, 9(7), 1533; https://doi.org/10.3390/microorganisms9071533 - 19 Jul 2021

Cited by 84 | Viewed by 8153

Abstract

To date, an understanding of how plant growth-promoting bacteria facilitate plant growth has been primarily based on studies of individual bacteria interacting with plants under different conditions. More recently, it has become clear that specific soil microorganisms interact with one another in consortia [...] Read more.

To date, an understanding of how plant growth-promoting bacteria facilitate plant growth has been primarily based on studies of individual bacteria interacting with plants under different conditions. More recently, it has become clear that specific soil microorganisms interact with one another in consortia with the collective being responsible for the positive effects on plant growth. Different plants attract different cross-sections of the bacteria and fungi in the soil, initially based on the composition of the unique root exudates from each plant. Thus, plants mostly attract those microorganisms that are beneficial to plants and exclude those that are potentially pathogenic. Beneficial bacterial consortia not only help to promote plant growth, these consortia also protect plants from a wide range of direct and indirect environmental stresses. Moreover, it is currently possible to engineer plant seeds to contain desired bacterial strains and thereby benefit the next generation of plants. In this way, it may no longer be necessary to deliver beneficial microbiota to each individual growing plant. As we develop a better understanding of beneficial bacterial microbiomes, it may become possible to develop synthetic microbiomes where compatible bacteria work together to facilitate plant growth under a wide range of natural conditions. Full article

(This article belongs to the Special Issue Microbiota: From the Environment to Humans)

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20 pages, 22519 KiB

Open AccessArticle

Spatial and Temporal Distribution of Bacterioplankton Molecular Ecological Networks in the Yuan River under Different Human Activity Intensity

by Bobo Wu, Peng Wang, Adam T. Devlin, Lu Chen, Yang Xia, Hua Zhang, Minghua Nie and Mingjun Ding

Microorganisms 2021, 9(7), 1532; https://doi.org/10.3390/microorganisms9071532 - 19 Jul 2021

Cited by 10 | Viewed by 2691

Abstract

Bacterioplankton communities play a crucial role in freshwater ecosystem functioning, but it is unknown how co-occurrence networks within these communities respond to human activity disturbances. This represents an important knowledge gap because changes in microbial networks could have implications for their functionality and [...] Read more.

Bacterioplankton communities play a crucial role in freshwater ecosystem functioning, but it is unknown how co-occurrence networks within these communities respond to human activity disturbances. This represents an important knowledge gap because changes in microbial networks could have implications for their functionality and vulnerability to future disturbances. Here, we compare the spatiotemporal and biogeographical patterns of bacterioplankton molecular ecological networks using high-throughput sequencing of Illumina HiSeq and multivariate statistical analyses from a subtropical river during wet and dry seasons. Results demonstrated that the lower reaches (high human activity intensity) network had less of an average degree (10.568/18.363), especially during the dry season, when compared with the upper reaches (low human activity intensity) network (10.685/37.552) during the wet and dry seasons, respectively. The latter formed more complexity networks with more modularity (0.622/0.556) than the lower reaches (high human activity intensity) network (0.505/0.41) during the wet and dry seasons, respectively. Bacterioplankton molecular ecological network under high human activity intensity became significantly less robust, which is mainly caused by altering of the environmental conditions and keystone species. Human activity altered the composition of modules but preserved their ecological roles in the network and environmental factors (dissolved organic carbon, temperature, arsenic, oxidation–reduction potential and Chao1 index) were the best parameters for explaining the variations in bacterioplankton molecular ecological network structure and modules. Proteobacteria, Actinobacteria and Bacteroidetes were the keystone phylum in shaping the structure and niche differentiations in the network. In addition, the lower reaches (high human activity intensity) reduce the bacterioplankton diversity and ecological niche differentiation, which deterministic processes become more important with increased farmland and constructed land area (especially farmland) with only 35% and 40% of the community variation explained by the neutral community model during the wet season and dry season, respectively. Keystone species in high human activity intensity stress habitats yield intense functional potentials and Bacterioplankton communities harbor keystone taxa in different human activity intensity stress habitats, which may exert their influence on microbiome network composition regardless of abundance. Therefore, human activity plays a crucial role in shaping the structure and function of bacterioplankton molecular ecological networks in subtropical rivers and understanding the mechanisms of this process can provide important information about human–water interaction processes, sustainable uses of freshwater as well as watershed management and conservation. Full article

(This article belongs to the Section Environmental Microbiology)

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10 pages, 661 KiB

Open AccessArticle

Invasive Species as Hosts of Zoonotic Infections: The Case of American Mink (Neovison vison) and Leishmania infantum

by Iris Azami-Conesa, Jose Sansano-Maestre, Rafael Alberto Martínez-Díaz and María Teresa Gómez-Muñoz

Microorganisms 2021, 9(7), 1531; https://doi.org/10.3390/microorganisms9071531 - 18 Jul 2021

Cited by 8 | Viewed by 2435

Abstract

Leishmania infantum produces an endemic disease in the Mediterranean Basin that affects humans and domestic and wild mammals, which can act as reservoir or minor host. In this study, we analyzed the presence of the parasite in wild American minks, an invasive species [...] Read more.

Leishmania infantum produces an endemic disease in the Mediterranean Basin that affects humans and domestic and wild mammals, which can act as reservoir or minor host. In this study, we analyzed the presence of the parasite in wild American minks, an invasive species in Spain. We screened for L. infantum DNA by PCR using five primer pairs: Two targeting kinetoplast DNA (kDNA), and the rest targeting the ITS1 region, the small subunit of ribosomal RNA (SSU) and a repetitive sequence (Repeat region). The detection limit was determined for each method using a strain of L. infantum and a bone marrow sample from an infected dog. PCR approaches employing the Repeat region and kDNA (RV1/RV2 primers) showed higher sensitivity than the other PCR methods when control samples were employed. However, only PCR of the Repeat region and nested PCR of SSU (LnSSU) detected the parasite in the samples, while the other three were unable to do so. The majority of the analyzed animals (90.1%) tested positive. American mink may act as an incidental host of the disease for other mammals and should be further investigated, not only for their negative impact on the local fauna, but also as carriers of zoonotic diseases. Full article

(This article belongs to the Special Issue Parasitic Diseases from Wild Animals with Emphasis in Zoonotic Infections)

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14 pages, 1940 KiB

Open AccessArticle

Analyses of Virulence Genes of Clavibacter michiganensis subsp. michiganensis Strains Reveal Heterogeneity and Deletions That Correlate with Pathogenicity

by Miryam Valenzuela, Marianela González, Alexis Velásquez, Fernando Dorta, Iván Montenegro, Ximena Besoain, Francisco Salvà-Serra, Daniel Jaén-Luchoro, Edward R. B. Moore and Michael Seeger

Microorganisms 2021, 9(7), 1530; https://doi.org/10.3390/microorganisms9071530 - 18 Jul 2021

Cited by 4 | Viewed by 2841

Abstract

Clavibacter michiganensis subsp. michiganensis (Cmm) is the causal agent of bacterial canker of tomato. Differences in virulence between Cmm strains have been reported. The aim of this study was the characterization of nine Cmm strains isolated in Chile to reveal the [...] Read more.

Clavibacter michiganensis subsp. michiganensis (Cmm) is the causal agent of bacterial canker of tomato. Differences in virulence between Cmm strains have been reported. The aim of this study was the characterization of nine Cmm strains isolated in Chile to reveal the causes of their differences in virulence. The virulence assays in tomato seedlings revealed different levels of severity associated with the strains, with two highly virulent strains and one causing only mild symptoms. The two most virulent showed increased cellulase activity, and no cellulase activity was observed in the strain causing mild symptoms. In three strains, including the two most virulent strains, PCR amplification of the 10 virulence genes analyzed was observed. In the strain causing mild symptoms, no amplification was observed for five genes, including celA. Sequence and cluster analyses of six virulence genes grouped the strains, as has been previously reported, except for gene pelA1. Gene sequence analysis from the genomes of five Chilean strains revealed the presence of deletions in the virulence genes, celB, xysA, pat-1, and phpA. The results of this study allow us to establish correlations between the differences observed in disease severity and the presence/absence of genes and deletions not previously reported. Full article

(This article belongs to the Special Issue Molecular Analysis of Plant Pathogenic Bacteria)

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13 pages, 3298 KiB

Open AccessArticle

Shiga Toxin-Producing Escherichia coli Outbreaks in the United States, 2010–2017

by Danielle M. Tack, Hannah M. Kisselburgh, LaTonia C. Richardson, Aimee Geissler, Patricia M. Griffin, Daniel C. Payne and Brigette L. Gleason

Microorganisms 2021, 9(7), 1529; https://doi.org/10.3390/microorganisms9071529 - 17 Jul 2021

Cited by 31 | Viewed by 4589

Abstract

Shiga toxin-producing Escherichia coli (STEC) cause illnesses ranging from mild diarrhea to ischemic colitis and hemolytic uremic syndrome (HUS); serogroup O157 is the most common cause. We describe the epidemiology and transmission routes for U.S. STEC outbreaks during 2010–2017. Health departments reported 466 [...] Read more.

Shiga toxin-producing Escherichia coli (STEC) cause illnesses ranging from mild diarrhea to ischemic colitis and hemolytic uremic syndrome (HUS); serogroup O157 is the most common cause. We describe the epidemiology and transmission routes for U.S. STEC outbreaks during 2010–2017. Health departments reported 466 STEC outbreaks affecting 4769 persons; 459 outbreaks had a serogroup identified (330 O157, 124 non-O157, 5 both). Among these, 361 (77%) had a known transmission route: 200 foodborne (44% of O157 outbreaks, 41% of non-O157 outbreaks), 87 person-to-person (16%, 24%), 49 animal contact (11%, 9%), 20 water (4%, 5%), and 5 environmental contamination (2%, 0%). The most common food category implicated was vegetable row crops. The distribution of O157 and non-O157 outbreaks varied by age, sex, and severity. A significantly higher percentage of STEC O157 than non-O157 outbreaks were transmitted by beef (p = 0.02). STEC O157 outbreaks also had significantly higher rates of hospitalization and HUS (p < 0.001). Full article

(This article belongs to the Special Issue Know Your Enemy: Improved Understanding, Detection, Control, and Therapy for Shiga Toxin-Producing Escherichia coli Infection)

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23 pages, 8578 KiB

Open AccessArticle

Changes in the Rumen Bacteriome Structure and Enzymatic Activities of Goats in Response to Dietary Supplementation with Schizochytrium spp.

by Alexandros Mavrommatis, Dimitrios Skliros, Emmanouil Flemetakis and Eleni Tsiplakou

Microorganisms 2021, 9(7), 1528; https://doi.org/10.3390/microorganisms9071528 - 17 Jul 2021

Cited by 13 | Viewed by 3312

Abstract

With the aim to produce functional dairy products enriched with polyunsaturated fatty acids (PUFA) by using feed supplements, radical changes could occur in the rumen microbiome. This work investigated the alterations of the rumen bacteriome of goats fed with PUFA-rich marine microalgae Schizochytrium [...] Read more.

With the aim to produce functional dairy products enriched with polyunsaturated fatty acids (PUFA) by using feed supplements, radical changes could occur in the rumen microbiome. This work investigated the alterations of the rumen bacteriome of goats fed with PUFA-rich marine microalgae Schizochytrium spp. For the trial, twenty-four goats were divided into four homogenous clusters (six goats/treatment) according to their fat-corrected (4%) milk yield, body weight, and age; they were individually fed with alfalfa hay and a concentrate (F/C = 50/50). The concentrate of the control group (CON) contained no microalgae, while those of the treated groups were supplemented daily with 20 (ALG20), 40 (ALG40), and 60 g (ALG60) of Schizochytrium spp./goat. Rumen fluid samples were collected using a stomach tube during the 20th and 40th days of the experiment. The microbiome analysis using a 16S rRNA sequencing platform revealed that Firmicutes were decreased in microalgae-fed goats, while Bacteroidetes showed a tendency to increase in the ALG40 group due to the enhancement of Prevotellaceae. Cellulolytic bacteria, namely Treponema bryantii, Ruminococcus gauvreauii, R. albus, and R. flavefaciens, were decreased in the ALG40 group, resulting in an overall decrease of cellulase activity. In contrast, the amylolytic potential was significantly enhanced due to an upsurge in Ruminobacter amylophilus, Succinivibrio dextrinosolvens, and Fretibacterium fastidiosum populations. In conclusion, supplementing goats’ diets with 20 g Schizochytrium spp. could be considered a sustainable and efficient nutritional strategy to modulate rumen microbiome towards the development of dairy products enriched with bioactive compounds, while higher levels induced substantial shifts in determinant microbes’ populations. Full article

(This article belongs to the Special Issue Rumen Microbial Communities)

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16 pages, 4121 KiB

Open AccessArticle

Characterization of Two New Shiga Toxin-Producing Escherichia coli O103-Infecting Phages Isolated from an Organic Farm

by Yujie Zhang, Yen-Te Liao, Alexandra Salvador, Valerie M. Lavenburg and Vivian C. H. Wu

Microorganisms 2021, 9(7), 1527; https://doi.org/10.3390/microorganisms9071527 - 17 Jul 2021

Cited by 10 | Viewed by 2986

Abstract

Shiga toxin-producing Escherichia coli (STEC) O103 strains have been recently attributed to various foodborne outbreaks in the United States. Due to the emergence of antibiotic-resistant strains, lytic phages are considered as alternative biocontrol agents. This study was to biologically and genomically characterize two [...] Read more.

Shiga toxin-producing Escherichia coli (STEC) O103 strains have been recently attributed to various foodborne outbreaks in the United States. Due to the emergence of antibiotic-resistant strains, lytic phages are considered as alternative biocontrol agents. This study was to biologically and genomically characterize two STEC O103-infecting bacteriophages, vB_EcoP-Ro103C3lw (or Ro103C3lw) and vB_EcoM-Pr103Blw (or Pr103Blw), isolated from an organic farm. Based on genomic and morphological analyses, phages Ro103C3lw and Pr103Blw belonged to Autographiviridae and Myoviridae families, respectively. Ro103C3lw contained a 39,389-bp double-stranded DNA and encoded a unique tail fiber with depolymerase activity, resulting in huge plaques. Pr103Blw had an 88,421-bp double-stranded DNA with 26 predicted tRNAs associated with the enhancement of the phage fitness. Within each phage genome, no virulence, antibiotic-resistant, and lysogenic genes were detected. Additionally, Ro103C3lw had a short latent period (2 min) and a narrow host range, infecting only STEC O103 strains. By contrast, Pr103Blw had a large burst size (152 PFU/CFU) and a broad host range against STEC O103, O26, O111, O157:H7, and Salmonella Javiana strains. Furthermore, both phages showed strong antimicrobial activities against STEC O103:H2 strains. The findings provide valuable insight into these two phages’ genomic features with the potential antimicrobial activities against STEC O103. Full article

(This article belongs to the Special Issue Bacteriophage Genomics)

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18 pages, 2120 KiB

Open AccessArticle

Exploring the Individual Bacterial Microbiota of Questing Ixodes ricinus Nymphs

by Aurélien Alafaci, Alexandre Crépin, Sabine Beaubert, Jean-Marc Berjeaud, Vincent Delafont and Julien Verdon

Microorganisms 2021, 9(7), 1526; https://doi.org/10.3390/microorganisms9071526 - 17 Jul 2021

Cited by 2 | Viewed by 2495

Abstract

Ixodes ricinus is the most common hard tick species in Europe and an important vector of pathogens of human and animal health concerns. The rise of high-throughput sequencing has facilitated the identification of many tick-borne pathogens and, more globally, of various microbiota members [...] Read more.

Ixodes ricinus is the most common hard tick species in Europe and an important vector of pathogens of human and animal health concerns. The rise of high-throughput sequencing has facilitated the identification of many tick-borne pathogens and, more globally, of various microbiota members depending on the scale of concern. In this study, we aimed to assess the bacterial diversity of individual I. ricinus questing nymphs collected in France using high-throughput 16S gene metabarcoding. From 180 dragging-collected nymphs, we identified more than 700 bacterial genera, of which about 20 are abundantly represented (>1% of total reads). Together with 136 other genera assigned, they constitute a core internal microbiota in this study. We also identified 20 individuals carrying Borreliella. The most abundant species is B. afzelii, known to be one of the bacteria responsible for Lyme disease in Europe. Co-detection of up to four Borreliella genospecies within the same individual has also been retrieved. The detection and co-detection rate of Borreliella in I. ricinus nymphs is high and raises the question of interactions between these bacteria and the communities constituting the internal microbiota. Full article

(This article belongs to the Section Environmental Microbiology)

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18 pages, 3217 KiB

Open AccessArticle

Prokaryotic Communities in the Thalassohaline Tuz Lake, Deep Zone, and Kayacik, Kaldirim and Yavsan Salterns (Turkey) Assessed by 16S rRNA Amplicon Sequencing

by Can Akpolat, Ana Beatriz Fernández, Pinar Caglayan, Baris Calli, Meral Birbir and Antonio Ventosa

Microorganisms 2021, 9(7), 1525; https://doi.org/10.3390/microorganisms9071525 - 17 Jul 2021

Cited by 9 | Viewed by 3114

Abstract

Prokaryotic communities and physico-chemical characteristics of 30 brine samples from the thalassohaline Tuz Lake (Salt Lake), Deep Zone, Kayacik, Kaldirim, and Yavsan salterns (Turkey) were analyzed using 16S rRNA amplicon sequencing and standard methods, respectively. Archaea (98.41% of reads) was found to dominate [...] Read more.

Prokaryotic communities and physico-chemical characteristics of 30 brine samples from the thalassohaline Tuz Lake (Salt Lake), Deep Zone, Kayacik, Kaldirim, and Yavsan salterns (Turkey) were analyzed using 16S rRNA amplicon sequencing and standard methods, respectively. Archaea (98.41% of reads) was found to dominate in these habitats in contrast to the domain Bacteria (1.38% of reads). Representatives of the phylum Euryarchaeota were detected as the most predominant, while 59.48% and 1.32% of reads, respectively, were assigned to 18 archaeal genera, 19 bacterial genera, 10 archaeal genera, and one bacterial genus that were determined to be present, with more than 1% sequences in the samples. They were the archaeal genera Haloquadratum, Haloarcula, Halorhabdus, Natronomonas, Halosimplex, Halomicrobium, Halorubrum, Halonotius, Halolamina, Halobacterium, and Salinibacter within the domain Bacteria. The genera Haloquadratum and Halorhabdus were found in all sampling sites. While Haloquadratum, Haloarcula, and Halorhabdus were the most abundant genera, two uncultured Tuz Lake Halobacteria (TLHs) 1 and 2 were detected in high abundance, and an additional uncultured haloarchaeal TLH-3 was found as a minor abundant uncultured taxon. Their future isolation in pure culture would permit us to expand our knowledge on hypersaline thalassohaline habitats, as well as their ecological role and biomedical and biotechnological potential applications. Full article

(This article belongs to the Special Issue Halophilic Microorganisms)

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9 pages, 1825 KiB

Open AccessArticle

Low C/N Ratios Promote Dissimilatory Nitrite Reduction to Ammonium in Pseudomonas putida Y-9 under Aerobic Conditions

by Xuejiao Huang, Wenzhou Tie, Deti Xie and Zhenlun Li

Microorganisms 2021, 9(7), 1524; https://doi.org/10.3390/microorganisms9071524 - 17 Jul 2021

Cited by 11 | Viewed by 2223

Abstract

The biogeochemical consequences of denitrification and dissimilatory nitrate reduction to ammonium (DNRA) have a significant influence on nitrogen (N) cycling in the ecosystem. Many researchers have explored these two pathways in soil and sediment ecosystems under anaerobic conditions. However, limited information is available [...] Read more.

The biogeochemical consequences of denitrification and dissimilatory nitrate reduction to ammonium (DNRA) have a significant influence on nitrogen (N) cycling in the ecosystem. Many researchers have explored these two pathways in soil and sediment ecosystems under anaerobic conditions. However, limited information is available regarding the influence of external environmental conditions on these two pathways in a well-defined experimental system under aerobic conditions. In this study, the impacts of the external environmental factors (carbon source, C/N ratio, pH, and dissolved oxygen) on nitrite reduction through the denitrification and DNRA routes in Pseudomonas putida Y-9 were studied. Results found that sodium citrate and sodium acetate favored denitrification and DNRA, respectively. Furthermore, neutral pH and aerobic conditions both facilitated DNRA and denitrification. Especially, low C/N ratios motivated the DNRA while high C/N ratios stimulated the denitrification, which was opposite to the observed phenomena under anaerobic conditions. Full article

(This article belongs to the Section Environmental Microbiology)

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17 pages, 2019 KiB

Open AccessArticle

Dynamic Immune Response to Vibriosis in Pacific Oyster Crassostrea gigas Larvae during the Infection Process as Supported by Accurate Positioning of GFP-Tagged Vibrio Strains

by Dongdong Wang, Alfredo Loor, Lobke De Bels, Gilbert Van Stappen, Wim Van den Broeck and Nancy Nevejan

Microorganisms 2021, 9(7), 1523; https://doi.org/10.3390/microorganisms9071523 - 17 Jul 2021

Cited by 7 | Viewed by 2754

Abstract

As the immune system is not fully developed during the larval stage, hatchery culture of bivalve larvae is characterized by frequent mass mortality caused by bacterial pathogens, especially Vibrio spp. However, the knowledge is limited to the pathogenesis of vibriosis in oyster larvae, [...] Read more.

As the immune system is not fully developed during the larval stage, hatchery culture of bivalve larvae is characterized by frequent mass mortality caused by bacterial pathogens, especially Vibrio spp. However, the knowledge is limited to the pathogenesis of vibriosis in oyster larvae, while the immune response to pathogenic microorganisms in this early life stage is still far from being fully elucidated. In this study, we combined green fluorescent protein (GFP)-tagging, histological and transcriptomic analyses to clarify the pathogenesis of experimental vibriosis and the mechanisms used by the host Pacific oyster Crassostrea gigas larvae to resist infection. The Vibrio strains first colonized the digestive system and rapidly proliferated, while only the transcription level of IκB kinase (IKK) and nuclear factor κB (NF-κB) associated with signaling transduction were up-regulated in oyster at 18 h post challenge (hpc). The mRNA levels for integrin β-1, peroxinectin, and heat shock protein 70 (HSP70), which are associated with phagocytosis, cell adhesion, and cytoprotection, were not upregulated until 30 hpc when the necrosis already happened in the larval digestive system. This suggested that the immunity in the early stages of C. gigas is not strong enough to prevent vibriosis and future research may focus on the strengthening of the gastrointestinal immune ability to defend vibriosis in bivalve larvae. Full article

(This article belongs to the Topic Veterinary Infectious Diseases)

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27 pages, 785 KiB

Open AccessReview

Bacteriophages of Thermophilic ‘Bacillus Group’ Bacteria—A Review

by Beata Łubkowska, Joanna Jeżewska-Frąckowiak, Ireneusz Sobolewski and Piotr M. Skowron

Microorganisms 2021, 9(7), 1522; https://doi.org/10.3390/microorganisms9071522 - 16 Jul 2021

Cited by 18 | Viewed by 4017

Abstract

Bacteriophages of thermophiles are of increasing interest owing to their important roles in many biogeochemical, ecological processes and in biotechnology applications, including emerging bionanotechnology. However, due to lack of in-depth investigation, they are underrepresented in the known prokaryotic virosphere. Therefore, there is a [...] Read more.

Bacteriophages of thermophiles are of increasing interest owing to their important roles in many biogeochemical, ecological processes and in biotechnology applications, including emerging bionanotechnology. However, due to lack of in-depth investigation, they are underrepresented in the known prokaryotic virosphere. Therefore, there is a considerable potential for the discovery of novel bacteriophage-host systems in various environments: marine and terrestrial hot springs, compost piles, soil, industrial hot waters, among others. This review aims at providing a reference compendium of thermophages characterized thus far, which infect the species of thermophilic ‘Bacillus group’ bacteria, mostly from Geobacillus sp. We have listed 56 thermophages, out of which the majority belong to the Siphoviridae family, others belong to the Myoviridae and Podoviridae families and, apparently, a few belong to the Sphaerolipoviridae, Tectiviridae or Corticoviridae families. All of their genomes are composed of dsDNA, either linear, circular or circularly permuted. Fourteen genomes have been sequenced; their sizes vary greatly from 35,055 bp to an exceptionally large genome of 160,590 bp. We have also included our unpublished data on TP-84, which infects Geobacillus stearothermophilus (G. stearothermophilus). Since the TP-84 genome sequence shows essentially no similarity to any previously characterized bacteriophage, we have defined TP-84 as a new species in the newly proposed genus Tp84virus within the Siphoviridae family. The information summary presented here may be helpful in comparative deciphering of the molecular basis of the thermophages’ biology, biotechnology and in analyzing the environmental aspects of the thermophages’ effect on the thermophile community. Full article

(This article belongs to the Special Issue Bacillus subtilis as a Model Organism to Study Basic Cell Processes)

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12 pages, 2692 KiB

Open AccessArticle

First Insight into the Diversity and Antibacterial Potential of Psychrophilic and Psychotrophic Microbial Communities of Abandoned Amber Quarry

by Margarita Shevchenko, Stanislav Sukhikh, Olga Babich, Svetlana Noskova, Svetlana Ivanova, Valery Lisun, Viktoriya Skripskaya, Andrey Lomtev and Maria Zimina

Microorganisms 2021, 9(7), 1521; https://doi.org/10.3390/microorganisms9071521 - 16 Jul 2021

Cited by 3 | Viewed by 2004

Abstract

Natural habitats, including extreme ones, are potential sources of new antimicrobial compound producers, such as bacteriocins and enzymes, capable of degrading the matrix polysaccharides of bacterial biofilms. This study aimed to investigate biodiversity and evaluate the antibacterial potential of psychrophilic and psychrotrophic microbial [...] Read more.

Natural habitats, including extreme ones, are potential sources of new antimicrobial compound producers, such as bacteriocins and enzymes, capable of degrading the matrix polysaccharides of bacterial biofilms. This study aimed to investigate biodiversity and evaluate the antibacterial potential of psychrophilic and psychrotrophic microbial communities of the flooded Walter amber quarry (Kaliningrad region, Russia). As a result of 16S rDNA high-throughput profiling, 127 genera of bacteria belonging to 12 phyla of bacteria were found in sediment samples: Acidobacteria sp., Actinobacteria sp., Armatimonadetes sp., Bacteroidetes sp., Chloroflexi sp., Cyanobacteria sp., Firmicutes sp., Gemmatimonadetes sp., Planctomycetes sp., Proteobacteria sp., Tenericutes sp., and Verrucomicrobia sp. The dominant bacteria groups were the families Ruminococcaceae and Lachnospiraceae, belonging to the order Clostridiales phylum Firmicutes. Analysis of enrichment cultures obtained from sediments showed the presence of antibacterial and cellulolytic activity. It seems likely that the bacteria of the studied communities are producers of antimicrobial compounds and have the potential for biotechnological use. Full article

(This article belongs to the Special Issue Characterization of Microbial Communities and Its Potential Towards Biotechnological Applications)

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12 pages, 1910 KiB

Open AccessArticle

Microbial Production of Bioactive Retinoic Acid Using Metabolically Engineered Escherichia coli

by Minjae Han and Pyung Cheon Lee

Microorganisms 2021, 9(7), 1520; https://doi.org/10.3390/microorganisms9071520 - 16 Jul 2021

Cited by 9 | Viewed by 3138

Abstract

Microbial production of bioactive retinoids, including retinol and retinyl esters, has been successfully reported. Previously, there are no reports on the microbial biosynthesis of retinoic acid. Two genes (blh_SR and raldh_HS) encoding retinoic acid biosynthesis enzymes [β-carotene 15,15′-oxygenase (Blh) [...] Read more.

Microbial production of bioactive retinoids, including retinol and retinyl esters, has been successfully reported. Previously, there are no reports on the microbial biosynthesis of retinoic acid. Two genes (blh_SR and raldh_HS) encoding retinoic acid biosynthesis enzymes [β-carotene 15,15′-oxygenase (Blh) and retinaldehyde dehydrogenase2 (RALDH2)] were synthetically redesigned for modular expression. Co-expression of the blh_SR and raldh_HS genes on the plasmid system in an engineered β-carotene-producing Escherichia coli strain produced 0.59 ± 0.06 mg/L of retinoic acid after flask cultivation. Deletion of the ybbO gene encoding a promiscuous aldehyde reductase induced a 2.4-fold increase in retinoic acid production to 1.43 ± 0.06 mg/L. Engineering of the 5’-UTR sequence of the blh_SR and raldh_HS genes enhanced retinoic acid production to 3.46 ± 0.16 mg/L. A batch culture operated at 37 °C, pH 7.0, and 50% DO produced up to 8.20 ± 0.05 mg/L retinoic acid in a bioreactor. As the construction and culture of retinoic acid–producing bacterial strains are still at an early stage in the development, further optimization of the expression level of the retinoic acid pathway genes, protein engineering of Blh and RALDH2, and culture optimization should synergistically increase the current titer of retinoic acid in E. coli. Full article

(This article belongs to the Special Issue Microorganisms Possibility for Future Bioproduction)

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26 pages, 1562 KiB

Open AccessReview

Viruses and Type 1 Diabetes: From Enteroviruses to the Virome

by Sonia R. Isaacs, Dylan B. Foskett, Anna J. Maxwell, Emily J. Ward, Clare L. Faulkner, Jessica Y. X. Luo, William D. Rawlinson, Maria E. Craig and Ki Wook Kim

Microorganisms 2021, 9(7), 1519; https://doi.org/10.3390/microorganisms9071519 - 16 Jul 2021

Cited by 21 | Viewed by 7533

Abstract

For over a century, viruses have left a long trail of evidence implicating them as frequent suspects in the development of type 1 diabetes. Through vigorous interrogation of viral infections in individuals with islet autoimmunity and type 1 diabetes using serological and molecular [...] Read more.

For over a century, viruses have left a long trail of evidence implicating them as frequent suspects in the development of type 1 diabetes. Through vigorous interrogation of viral infections in individuals with islet autoimmunity and type 1 diabetes using serological and molecular virus detection methods, as well as mechanistic studies of virus-infected human pancreatic β-cells, the prime suspects have been narrowed down to predominantly human enteroviruses. Here, we provide a comprehensive overview of evidence supporting the hypothesised role of enteroviruses in the development of islet autoimmunity and type 1 diabetes. We also discuss concerns over the historical focus and investigation bias toward enteroviruses and summarise current unbiased efforts aimed at characterising the complete population of viruses (the “virome”) contributing early in life to the development of islet autoimmunity and type 1 diabetes. Finally, we review the range of vaccine and antiviral drug candidates currently being evaluated in clinical trials for the prevention and potential treatment of type 1 diabetes. Full article

(This article belongs to the Special Issue Enterovirus and Type 1 Diabetes 2.0)

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16 pages, 967 KiB

Open AccessReview

Microbiological and Molecular Diagnosis of Mucormycosis: From Old to New

by Nina Lackner, Wilfried Posch and Cornelia Lass-Flörl

Microorganisms 2021, 9(7), 1518; https://doi.org/10.3390/microorganisms9071518 - 16 Jul 2021

Cited by 37 | Viewed by 4434

Abstract

Members of the order Mucorales may cause severe invasive fungal infections (mucormycosis) in immune-compromised and otherwise ill patients. Diagnosis of Mucorales infections and discrimination from other filamentous fungi are crucial for correct management. Here, we present an overview of current state-of-the-art mucormycosis diagnoses, [...] Read more.

Members of the order Mucorales may cause severe invasive fungal infections (mucormycosis) in immune-compromised and otherwise ill patients. Diagnosis of Mucorales infections and discrimination from other filamentous fungi are crucial for correct management. Here, we present an overview of current state-of-the-art mucormycosis diagnoses, with a focus on recent developments in the molecular field. Classical diagnostic methods comprise histology/microscopy as well as culture and are still the gold standard. Newer molecular methods are evolving quickly and display great potential in early diagnosis, although standardization is still missing. Among them, quantitative PCR assays with or without melt curve analysis are most widely used to detect fungal DNA in clinical samples. Depending on the respective assay, sequencing of the resulting PCR product can be necessary for genus or even species identification. Further, DNA-based methods include microarrays and PCR-ESI-MS. However, general laboratory standards are still in development, meaning that molecular methods are currently limited to add-on analytics to culture and microscopy. Full article

(This article belongs to the Special Issue Recent Advances and Future Perspectives on Mucormycoses)

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9 pages, 2617 KiB

Open AccessArticle

Emergence and Spread of B.1.1.7 Lineage in Primary Care and Clinical Impact in the Morbi-Mortality among Hospitalized Patients in Madrid, Spain

by Laura Martínez-García, Marco Antonio Espinel, Melanie Abreu, José María González-Alba, Desirèe Gijón, Amaranta McGee, Rafael Cantón, Juan Carlos Galán and Jesús Aranaz

Microorganisms 2021, 9(7), 1517; https://doi.org/10.3390/microorganisms9071517 - 15 Jul 2021

Cited by 11 | Viewed by 2517

Abstract

In December 2020, UK authorities warned of the rapid spread of a new SARS-CoV-2 variant, belonging to the B.1.1.7 lineage, known as the Alpha variant. This variant is characterized by 17 mutations and 3 deletions. The deletion 69–70 in the spike protein can [...] Read more.

In December 2020, UK authorities warned of the rapid spread of a new SARS-CoV-2 variant, belonging to the B.1.1.7 lineage, known as the Alpha variant. This variant is characterized by 17 mutations and 3 deletions. The deletion 69–70 in the spike protein can be detected by commercial platforms, allowing its real-time spread to be known. From the last days of December 2020 and over 4 months, all respiratory samples with a positive result for SARS-CoV-2 from patients treated in primary care and the emergency department were screened to detect this variant based on the strategy S gene target failure (SGTF). The first cases were detected during week 53 (2020) and reached >90% of all cases during weeks 15–16 (2021). During this period, the B.1.1.7/SGTF variant spread at a rapid and constant replacement rate of around 30–36%. The probability of intensive care unit admission was twice higher among patients infected by the B.1.1.7/SGTF variant, but there were no differences in death rate. During the peak of the third pandemic wave, this variant was not the most prevalent, and it became dominant when this wave was declining. Our results confirm that the B.1.1.7/SGTF variant displaced other SARS-CoV-2 variants in our healthcare area in 4 months. This displacement has led to an increase in the burden of disease. Full article

(This article belongs to the Section Medical Microbiology)

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19 pages, 1861 KiB

Open AccessArticle

Impact of Landscape on Host–Parasite Genetic Diversity and Distribution Using the Puumala orthohantavirus–Bank Vole System

by Maria Razzauti, Guillaume Castel and Jean-François Cosson

Microorganisms 2021, 9(7), 1516; https://doi.org/10.3390/microorganisms9071516 - 15 Jul 2021

Cited by 2 | Viewed by 1976

Abstract

In nature, host specificity has a strong impact on the parasite’s distribution, prevalence, and genetic diversity. The host’s population dynamics is expected to shape the distribution of host-specific parasites. In turn, the parasite’s genetic structure is predicted to mirror that of the host. [...] Read more.

In nature, host specificity has a strong impact on the parasite’s distribution, prevalence, and genetic diversity. The host’s population dynamics is expected to shape the distribution of host-specific parasites. In turn, the parasite’s genetic structure is predicted to mirror that of the host. Here, we study the tandem Puumala orthohantavirus (PUUV)–bank vole system. The genetic diversity of 310 bank voles and 33 PUUV isolates from 10 characterized localities of Northeast France was assessed. Our findings show that the genetic diversity of both PUUV and voles, was positively correlated with forest coverage and contiguity of habitats. While the genetic diversity of voles was weakly structured in space, that of PUUV was found to be strongly structured, suggesting that the dispersion of voles was not sufficient to ensure a broad PUUV dissemination. Genetic diversity of PUUV was mainly shaped by purifying selection. Genetic drift and extinction events were better reflected than local adaptation of PUUV. These contrasting patterns of microevolution have important consequences for the understanding of PUUV distribution and epidemiology. Full article

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12 pages, 1122 KiB

Open AccessArticle

Perceptions, Representations, and Experiences of Patients Presenting Nonspecific Symptoms in the Context of Suspected Lyme Borreliosis

by Alice Raffetin, Aude Barquin, Steve Nguala, Giulia Paoletti, Christian Rabaud, Olivier Chassany, Pauline Caraux-Paz, Sarah Covasso and Henri Partouche

Microorganisms 2021, 9(7), 1515; https://doi.org/10.3390/microorganisms9071515 - 15 Jul 2021

Cited by 4 | Viewed by 2603

Abstract

Background: Some subjective symptoms may be reported at all stages of Lyme borreliosis (LB) and may persist for several months after treatment. Nonspecific symptoms without any objective manifestation of LB are sometimes attributed by patients to a possible tick bite. The aim of [...] Read more.

Background: Some subjective symptoms may be reported at all stages of Lyme borreliosis (LB) and may persist for several months after treatment. Nonspecific symptoms without any objective manifestation of LB are sometimes attributed by patients to a possible tick bite. The aim of our study was to explore the perceptions, representations, and experiences that these patients had of their disease and care paths. Methods: We performed a qualitative study through individual interviews (October 2017–May 2018), based on grounded theory, following the COREQ checklist. A balanced sample of patients with diverse profiles was recruited at consultations with general practitioners and infectious disease physicians. Results: Twelve patients were interviewed. Data saturation was reached at the twelfth interview. For codes, 293 were identified, and classified into 5 themes: (1) the experience of disabling nonspecific symptoms, especially pain, causing confusion and fear, (2) long and difficult care paths for the majority of the patients, experienced as an obstacle course, (3) a break with the previous state of health, causing a negative impact on every sphere of the patient’s life, (4) empowerment of the patients and the self-management of their disease, and (5) the strong expression of a desire for change, with better listening, greater recognition of the symptoms, and simpler care paths. Conclusions: This study allows for the understanding of a patient’s behaviours and the obstacles encountered, the way they are perceived, and the necessary solutions. The patients’ expectations identified here could help physicians better understand the doctor–patient relationship in these complex management situations, which would reduce the burden of the disease. The current development of specialised reference centres could help meet the patients’ demands and those of family physicians. Full article

(This article belongs to the Special Issue Borrelia Ecology and Evolution: Ticks and Hosts and the Environment)

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