Microorganisms

16 pages, 2458 KiB

Open AccessArticle

Selected Rhizosphere Bacteria Help Tomato Plants Cope with Combined Phosphorus and Salt Stresses

by Gylaine Vanissa Tchuisseu Tchakounté, Beatrice Berger, Sascha Patz, Matthias Becker, Henri Fankem, Victor Désiré Taffouo and Silke Ruppel

Microorganisms 2020, 8(11), 1844; https://doi.org/10.3390/microorganisms8111844 - 23 Nov 2020

Cited by 20 | Viewed by 3277

Abstract

Plants are often challenged by multiple abiotic stresses simultaneously. The inoculation of beneficial bacteria is known to enhance plant growth under these stresses, such as phosphorus starvation or salt stress. Here, for the first time, we assessed the efficiency of selected beneficial bacterial [...] Read more.

Plants are often challenged by multiple abiotic stresses simultaneously. The inoculation of beneficial bacteria is known to enhance plant growth under these stresses, such as phosphorus starvation or salt stress. Here, for the first time, we assessed the efficiency of selected beneficial bacterial strains in improving tomato plant growth to better cope with double stresses in salty and P-deficient soil conditions. Six strains of Arthrobacter and Bacillus with different reservoirs of plant growth-promoting traits were tested in vitro for their abilities to tolerate 2–16% (w/v) NaCl concentrations, and shown to retain their motility and phosphate-solubilizing capacity under salt stress conditions. Whether these selected bacteria promote tomato plant growth under combined P and salt stresses was investigated in greenhouse experiments. Bacterial isolates from Cameroonian soils mobilized P from different phosphate sources in shaking culture under both non-saline and saline conditions. They also enhanced plant growth in P-deficient and salt-affected soils by 47–115%, and their PGP effect was even increased in higher salt stress conditions. The results provide valuable information for prospective production of effective bio-fertilizers based on the combined application of local rock phosphate and halotolerant phosphate-solubilizing bacteria. This constitutes a promising strategy to improve plant growth in P-deficient and salt-affected soils. Full article

(This article belongs to the Section Plant Microbe Interactions)

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16 pages, 3648 KiB

Open AccessArticle

Accelerated Electro-Fermentation of Acetoin in Escherichia coli by Identifying Physiological Limitations of the Electron Transfer Kinetics and the Central Metabolism

by Sebastian Beblawy, Laura-Alina Philipp and Johannes Gescher

Microorganisms 2020, 8(11), 1843; https://doi.org/10.3390/microorganisms8111843 - 23 Nov 2020

Cited by 4 | Viewed by 3129

Abstract

Anode-assisted fermentations offer the benefit of an anoxic fermentation routine that can be applied to produce end-products with an oxidation state independent from the substrate. The whole cell biocatalyst transfers the surplus of electrons to an electrode that can be used as a [...] Read more.

Anode-assisted fermentations offer the benefit of an anoxic fermentation routine that can be applied to produce end-products with an oxidation state independent from the substrate. The whole cell biocatalyst transfers the surplus of electrons to an electrode that can be used as a non-depletable electron acceptor. So far, anode-assisted fermentations were shown to provide high carbon efficiencies but low space-time yields. This study aimed at increasing space-time yields of an Escherichia coli-based anode-assisted fermentation of glucose to acetoin. The experiments build on an obligate respiratory strain, that was advanced using selective adaptation and targeted strain development. Several transfers under respiratory conditions led to point mutations in the pfl, aceF and rpoC gene. These mutations increased anoxic growth by three-fold. Furthermore, overexpression of genes encoding a synthetic electron transport chain to methylene blue increased the electron transfer rate by 2.45-fold. Overall, these measures and a medium optimization increased the space-time yield in an electrode-assisted fermentation by 3.6-fold. Full article

(This article belongs to the Special Issue Microbe Electrode Electron Transfer: Understanding Interactions from the Enzyme to the Microbial Community Level)

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17 pages, 1268 KiB

Open AccessArticle

E6/E7 Sequence Diversity of High-Risk Human Papillomaviruses in Two Geographically Isolated Populations of French Guiana

by Mathieu Nacher, Gersande Godefroy, Valentin Dufit, Maylis Douine, Fatiha Najioullah, Raymond Césaire, Nadia Thomas, Kinan Drak Alsibai, Antoine Adenis and Vincent Lacoste

Microorganisms 2020, 8(11), 1842; https://doi.org/10.3390/microorganisms8111842 - 23 Nov 2020

Cited by 6 | Viewed by 2552

Abstract

Amerindian and Maroon populations of French Guiana have been living in isolation for generations and sexual networks remained mostly endogamous. The present study aimed to describe the phylogeny of E6 and E7 sequences of the most common high-risk HPV genotypes in these regions, [...] Read more.

Amerindian and Maroon populations of French Guiana have been living in isolation for generations and sexual networks remained mostly endogamous. The present study aimed to describe the phylogeny of E6 and E7 sequences of the most common high-risk HPV genotypes in these regions, to ascertain the diversity of intra-type variants and describe evolutionary relationships. There were 106 women with at least one of HPV16, 18, 31, 52, 58, and 68 genotypes. The most clear-cut phylogenetic pattern was obtained for HPV18 and HPV58 for which the major branches were crisply divided between Amerindian villages on the Oyapock and Maroon villages on the Maroni. Such clustering was less clear for HPV31 and 52. For HPV16, there was also some evidence of clustering on the Oyapock with type A European viruses and on the Maroni with type B and C African viruses among Maroon women. HPV68 showed the largest sequence heterogeneity of the six genotypes at both nucleotide and amino acid levels and was restricted to Maroon women. The present results show that there were significant geographically based differences of E6 and E7 oncogenes. These differences were compatible with different ancestral virus populations and local virus evolution in a context of prolonged population isolation. Full article

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

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22 pages, 1921 KiB

Open AccessReview

Microfluidic Microbial Bioelectrochemical Systems: An Integrated Investigation Platform for a More Fundamental Understanding of Electroactive Bacterial Biofilms

by Stéphane Pinck, Lucila Martínez Ostormujof, Sébastien Teychené and Benjamin Erable

Microorganisms 2020, 8(11), 1841; https://doi.org/10.3390/microorganisms8111841 - 23 Nov 2020

Cited by 21 | Viewed by 5936

Abstract

It is the ambition of many researchers to finally be able to close in on the fundamental, coupled phenomena that occur during the formation and expression of electrocatalytic activity in electroactive biofilms. It is because of this desire to understand that bioelectrochemical systems [...] Read more.

It is the ambition of many researchers to finally be able to close in on the fundamental, coupled phenomena that occur during the formation and expression of electrocatalytic activity in electroactive biofilms. It is because of this desire to understand that bioelectrochemical systems (BESs) have been miniaturized into microBES by taking advantage of the worldwide development of microfluidics. Microfluidics tools applied to bioelectrochemistry permit even more fundamental studies of interactions and coupled phenomena occurring at the microscale, thanks, in particular, to the concomitant combination of electroanalysis, spectroscopic analytical techniques and real-time microscopy that is now possible. The analytical microsystem is therefore much better suited to the monitoring, not only of electroactive biofilm formation but also of the expression and disentangling of extracellular electron transfer (EET) catalytic mechanisms. This article reviews the details of the configurations of microfluidic BESs designed for selected objectives and their microfabrication techniques. Because the aim is to manipulate microvolumes and due to the high modularity of the experimental systems, the interfacial conditions between electrodes and electrolytes are perfectly controlled in terms of physicochemistry (pH, nutrients, chemical effectors, etc.) and hydrodynamics (shear, material transport, etc.). Most of the theoretical advances have been obtained thanks to work carried out using models of electroactive bacteria monocultures, mainly to simplify biological investigation systems. However, a huge virgin field of investigation still remains to be explored by taking advantage of the capacities of microfluidic BESs regarding the complexity and interactions of mixed electroactive biofilms. Full article

(This article belongs to the Special Issue Microbe Electrode Electron Transfer: Understanding Interactions from the Enzyme to the Microbial Community Level)

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33 pages, 3810 KiB

Open AccessReview

Drawing Comparisons between SARS-CoV-2 and the Animal Coronaviruses

by Souvik Ghosh and Yashpal S. Malik

Microorganisms 2020, 8(11), 1840; https://doi.org/10.3390/microorganisms8111840 - 23 Nov 2020

Cited by 15 | Viewed by 6836

Abstract

The COVID-19 pandemic, caused by a novel zoonotic coronavirus (CoV), SARS-CoV-2, has infected 46,182 million people, resulting in 1,197,026 deaths (as of 1 November 2020), with devastating and far-reaching impacts on economies and societies worldwide. The complex origin, extended human-to-human transmission, pathogenesis, host [...] Read more.

The COVID-19 pandemic, caused by a novel zoonotic coronavirus (CoV), SARS-CoV-2, has infected 46,182 million people, resulting in 1,197,026 deaths (as of 1 November 2020), with devastating and far-reaching impacts on economies and societies worldwide. The complex origin, extended human-to-human transmission, pathogenesis, host immune responses, and various clinical presentations of SARS-CoV-2 have presented serious challenges in understanding and combating the pandemic situation. Human CoVs gained attention only after the SARS-CoV outbreak of 2002–2003. On the other hand, animal CoVs have been studied extensively for many decades, providing a plethora of important information on their genetic diversity, transmission, tissue tropism and pathology, host immunity, and therapeutic and prophylactic strategies, some of which have striking resemblance to those seen with SARS-CoV-2. Moreover, the evolution of human CoVs, including SARS-CoV-2, is intermingled with those of animal CoVs. In this comprehensive review, attempts have been made to compare the current knowledge on evolution, transmission, pathogenesis, immunopathology, therapeutics, and prophylaxis of SARS-CoV-2 with those of various animal CoVs. Information on animal CoVs might enhance our understanding of SARS-CoV-2, and accordingly, benefit the development of effective control and prevention strategies against COVID-19. Full article

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

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10 pages, 237 KiB

Open AccessArticle

Detection of the Phenicol–Oxazolidinone Resistance Gene poxtA in Enterococcus faecium and Enterococcus faecalis from Food-Producing Animals during 2008–2018 in Korea

by Seok-Hyeon Na, Dong-Chan Moon, Mi-Hyun Kim, Hee-Young Kang, Su-Jeong Kim, Ji-Hyun Choi, Abraham-Fikru Mechesso, Soon-Seek Yoon and Suk-Kyung Lim

Microorganisms 2020, 8(11), 1839; https://doi.org/10.3390/microorganisms8111839 - 23 Nov 2020

Cited by 18 | Viewed by 2634

Abstract

We aimed to investigate the presence of the phenicol–oxazolidinone resistance gene poxtA in linezolid-resistant enterococci from food-producing animals and analyze its molecular characteristics. We collected 3941 Enterococcus faecium and 5088 E. faecalis isolates from all provinces of South Korea from 2008 to 2018. [...] Read more.

We aimed to investigate the presence of the phenicol–oxazolidinone resistance gene poxtA in linezolid-resistant enterococci from food-producing animals and analyze its molecular characteristics. We collected 3941 Enterococcus faecium and 5088 E. faecalis isolates from all provinces of South Korea from 2008 to 2018. We found linezolid resistance in 0.79% (94/3941) of E. faecium and 1.22% (62/5088) of E. faecalis isolates. Overall, 23.1% (36/156) of the linezolid-resistant isolates had the poxtA gene, including 31 E. faecium and five E. faecalis isolates. The poxtA-positive enterococci were mainly isolated from chicken (86.1%; 26/36). Fifteen poxtA-harboring isolates co-carried another linezolid-resistance gene, optrA. Eight E. faecium isolates had an N130K mutation in the ribosomal protein L4, while no mutations were observed in E. faecalis isolates. The poxtA gene was transferred into 10 enterococci by conjugation. Multi-locus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE) analysis indicated that poxtA-carrying isolates were heterogeneous. Three E. faecium isolates belonged to CC17 (ST32, ST121, and ST491). To our knowledge, this is the first report on the poxtA gene in Korea. Prudent use of antimicrobials and active surveillance on antimicrobial resistance are urgently needed to reduce the risk of dissemination of the linezolid-resistant isolates in humans and animals. Full article

(This article belongs to the Special Issue Antimicrobial Resistance and Molecular Tracing of Foodborne Pathogens)

13 pages, 4956 KiB

Open AccessArticle

Bacteria-Derived Hemolysis-Related Genes Widely Exist in Scuticociliates

by Jing Zhang, Kai Chen, Chuanqi Jiang, Wentao Yang, Siyu Gu, Guangying Wang, Yishan Lu, Wei Miao and Jie Xiong

Microorganisms 2020, 8(11), 1838; https://doi.org/10.3390/microorganisms8111838 - 22 Nov 2020

Cited by 4 | Viewed by 2835

Abstract

Scuticociliatosis is an invasive external or systemic infection caused by ciliated protozoa, mainly those within the subclass Scuticociliatia (scuticociliates). Many scuticociliates are fish pathogens, including Miamiensis avidus, Philasterides dicentrarchi, Pseudocohnilembus persalinus, and Uronema marinum. Our previous study showed that [...] Read more.

Scuticociliatosis is an invasive external or systemic infection caused by ciliated protozoa, mainly those within the subclass Scuticociliatia (scuticociliates). Many scuticociliates are fish pathogens, including Miamiensis avidus, Philasterides dicentrarchi, Pseudocohnilembus persalinus, and Uronema marinum. Our previous study showed that hemolysis-related genes derived from bacteria through horizontal gene transfer (HGT) may contribute to virulence in P. persalinus. Hemorrhagic lesions are a common feature of scuticociliatosis, but it is not known whether other scuticociliates also have bacteria-derived hemolysis-related genes. In this study, we constructed a high-quality macronuclear genome of another typical pathogenic scuticociliate, U. marinum. A total of 105 HGT genes were identified in this species, of which 35 were homologs of hemolysis-related genes (including hemolysin-like genes) that had previously been identified in P. persalinus. Sequencing of an additional five species from four scuticociliate families showed that bacteria-derived hemolysis-related genes (especially hemolysin-like genes) are widely distributed in scuticociliates. Based on these findings, we suggest that hemolysin-like genes may have originated before the divergence of scuticociliates. Full article

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

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22 pages, 4216 KiB

Open AccessArticle

Evaluating the Effects of Disinfectants on Bacterial Biofilms Using a Microfluidics Flow Cell and Time-Lapse Fluorescence Microscopy

by Milos Legner, James Jonkman and Dean Swift

Microorganisms 2020, 8(11), 1837; https://doi.org/10.3390/microorganisms8111837 - 22 Nov 2020

Cited by 4 | Viewed by 4003

Abstract

A commercially available microfluidics flow cell was utilized together with widefield fluorescence microscopy to evaluate the effects of disinfectants on bacterial strains. The flow cell’s inner surface supports the formation of biofilms of numerous bacterial species. The modular setup of the flow cell [...] Read more.

A commercially available microfluidics flow cell was utilized together with widefield fluorescence microscopy to evaluate the effects of disinfectants on bacterial strains. The flow cell’s inner surface supports the formation of biofilms of numerous bacterial species. The modular setup of the flow cell accessories allows connection to syringes, pumps and collection vials, facilitating aseptic experiments in a controlled fluidics environment which can be documented with precisely timed microscopy imaging. The flow cell is inoculated with a suspension of bacteria in a nutrient medium and incubated for several days allowing bacterial cells to form a biofilm. Shortly before performing an assay, the biofilm is labelled with a dual-fluorescent DNA probe which distinguishes unharmed and damaged bacteria. Then a disinfectant sample (or control) is gently injected and time-lapse imaging is used for quantifying the course of bacterial biomass response. We use a simplified widefield microscopy method that allows intensive recording and quantification of time series of two-dimensional frames for tracking the course of disinfectant action on a variety of microbial strains. This procedure has potential for the rapid evaluation of novel products. Full article

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

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17 pages, 2393 KiB

Open AccessArticle

Strain-Dependent Cheese Spoilage Potential of Clostridium tyrobutyricum

by Lucija Podrzaj, Johanna Burtscher, Franziska Küller and Konrad J. Domig

Microorganisms 2020, 8(11), 1836; https://doi.org/10.3390/microorganisms8111836 - 22 Nov 2020

Cited by 21 | Viewed by 4508

Abstract

Clostridium tyrobutyricum, a Gram-positive, anaerobic, spore-forming bacterium, is considered as one of the main causative agents for spoilage of hard and semihard cheeses. Growth of C. tyrobutyricum in cheese is critically influenced by ripening temperature and time, pH, salt and lactic acid [...] Read more.

Clostridium tyrobutyricum, a Gram-positive, anaerobic, spore-forming bacterium, is considered as one of the main causative agents for spoilage of hard and semihard cheeses. Growth of C. tyrobutyricum in cheese is critically influenced by ripening temperature and time, pH, salt and lactic acid concentration, moisture and fat content, and the presence of other microorganisms. Previous studies revealed high intraspecies diversity of C. tyrobutyricum strains and variable tolerance toward pH, temperatures, and salt concentrations. These findings indicate that strain-dependent characteristics may be relevant to assess the risk for cheese spoilage if clostridial contamination occurs. In this study, we aimed to compare the phenotypes of 12 C. tyrobutyricum strains which were selected from 157 strains on the basis of genotypic and proteotypic variability. The phenotypic analysis comprised the assessment of gas production and organic acid concentrations in an experimental cheese broth incubated at different temperatures (37, 20, and 14 °C). For all tested strains, delayed gas production at lower incubation temperatures and a strong correlation between gas production and the change in organic acid concentrations were observed. However, considering the time until gas production was visible at different incubation temperatures, a high degree of heterogeneity was found among the tested strains. In addition, variation among replicates of the same strain and differences due to different inoculum levels became evident. This study shows, that, among other factors, strain-specific germination and growth characteristics should be considered to evaluate the risk of cheese spoilage by C. tyrobutyricum. Full article

(This article belongs to the Special Issue Beneficial and Detrimental Microorganisms Occurring in Fermented Foods)

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31 pages, 2285 KiB

Open AccessReview

Deciphering Streptococcal Biofilms

by Puja Yadav, Shalini Verma, Richard Bauer, Monika Kumari, Meenakshi Dua, Atul Kumar Johri, Vikas Yadav and Barbara Spellerberg

Microorganisms 2020, 8(11), 1835; https://doi.org/10.3390/microorganisms8111835 - 21 Nov 2020

Cited by 33 | Viewed by 6660

Abstract

Streptococci are a diverse group of bacteria, which are mostly commensals but also cause a considerable proportion of life-threatening infections. They colonize many different host niches such as the oral cavity, the respiratory, gastrointestinal, and urogenital tract. While these host compartments impose different [...] Read more.

Streptococci are a diverse group of bacteria, which are mostly commensals but also cause a considerable proportion of life-threatening infections. They colonize many different host niches such as the oral cavity, the respiratory, gastrointestinal, and urogenital tract. While these host compartments impose different environmental conditions, many streptococci form biofilms on mucosal membranes facilitating their prolonged survival. In response to environmental conditions or stimuli, bacteria experience profound physiologic and metabolic changes during biofilm formation. While investigating bacterial cells under planktonic and biofilm conditions, various genes have been identified that are important for the initial step of biofilm formation. Expression patterns of these genes during the transition from planktonic to biofilm growth suggest a highly regulated and complex process. Biofilms as a bacterial survival strategy allow evasion of host immunity and protection against antibiotic therapy. However, the exact mechanisms by which biofilm-associated bacteria cause disease are poorly understood. Therefore, advanced molecular techniques are employed to identify gene(s) or protein(s) as targets for the development of antibiofilm therapeutic approaches. We review our current understanding of biofilm formation in different streptococci and how biofilm production may alter virulence-associated characteristics of these species. In addition, we have summarized the role of surface proteins especially pili proteins in biofilm formation. This review will provide an overview of strategies which may be exploited for developing novel approaches against biofilm-related streptococcal infections. Full article

(This article belongs to the Section Biofilm)

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25 pages, 3952 KiB

Open AccessArticle

Screening of FDA-Approved Drugs Using a 384-Well Plate-Based Biofilm Platform: The Case of Fingolimod

by Shella Gilbert-Girard, Kirsi Savijoki, Jari Yli-Kauhaluoma and Adyary Fallarero

Microorganisms 2020, 8(11), 1834; https://doi.org/10.3390/microorganisms8111834 - 21 Nov 2020

Cited by 22 | Viewed by 3912

Abstract

In an effort to find new repurposed antibacterial compounds, we performed the screening of an FDA-approved compounds library against Staphylococcus aureus American Type Culture Collection (ATCC) 25923. Compounds were evaluated for their capacity to prevent both planktonic growth and biofilm formation as well [...] Read more.

In an effort to find new repurposed antibacterial compounds, we performed the screening of an FDA-approved compounds library against Staphylococcus aureus American Type Culture Collection (ATCC) 25923. Compounds were evaluated for their capacity to prevent both planktonic growth and biofilm formation as well as to disrupt pre-formed biofilms. One of the identified initial hits was fingolimod (FTY720), an immunomodulator approved for the treatment of multiple sclerosis, which was then selected for follow-up studies. Fingolimod displayed a potent activity against S. aureus and S. epidermidis with a minimum inhibitory concentration (MIC) within the range of 12–15 µM at which concentration killing of all the bacteria was confirmed. A time–kill kinetic study revealed that fingolimod started to drastically reduce the viable bacterial count within two hours and we showed that no resistance developed against this compound for up to 20 days. Fingolimod also displayed a high activity against Acinetobacter baumannii (MIC 25 µM) as well as a modest activity against Escherichia coli and Pseudomonas aeruginosa. In addition, fingolimod inhibited quorum sensing in Chromobacterium violaceum and might therefore target this signaling pathway in certain Gram-negative bacteria. In conclusion, we present the identification of fingolimod from a compound library and its evaluation as a potential repurposed antibacterial compound. Full article

(This article belongs to the Section Antimicrobial Agents and Resistance)

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20 pages, 951 KiB

Open AccessReview

Autochthonous Probiotics in Meat Products: Selection, Identification, and Their Use as Starter Culture

by Paulo E. S. Munekata, Mirian Pateiro, Wangang Zhang, Rubén Domínguez, Lujuan Xing, Elena Movilla Fierro and José M. Lorenzo

Microorganisms 2020, 8(11), 1833; https://doi.org/10.3390/microorganisms8111833 - 21 Nov 2020

Cited by 21 | Viewed by 4463

Abstract

The increasing demand for functional food is pushing the food industry to innovate the conventional and well-known foods. Producing functional foods, especially with probiotics in meat products, is an intricate and multistage task that involves: the selection of microorganisms with probiotic potential, the [...] Read more.

The increasing demand for functional food is pushing the food industry to innovate the conventional and well-known foods. Producing functional foods, especially with probiotics in meat products, is an intricate and multistage task that involves: the selection of microorganisms with probiotic potential, the identification at strain level, and the evaluation of probiotic strains in the processing of meat products. The resistance to digestion, followed by the successful colonization in the small intestine and the safety are the main criteria used to select and identify (at strain level) a probiotic, as reported in recent studies about the autochthonous microbiota of meat products. Further insertion (as starter culture) in a meat system for fermentation is the simplest approach to obtain a probiotic meat product. Among the innumerous microorganisms naturally found in meat products, lactic acid bacteria (LAB) play a central role by fitting in both probiotic and meat products processing criteria. Full article

(This article belongs to the Special Issue Microbiomes for the Sustainable Production of Safe and Secure Foods)

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19 pages, 4102 KiB

Open AccessArticle

Phenotypic Characterization and Transformation Attempts Reveal Peculiar Traits of Xylella fastidiosa Subspecies pauca Strain De Donno

by Giusy D’Attoma, Massimiliano Morelli, Leonardo De La Fuente, Paul A. Cobine, Maria Saponari, Alessandra Alves de Souza, Angelo De Stradis and Pasquale Saldarelli

Microorganisms 2020, 8(11), 1832; https://doi.org/10.3390/microorganisms8111832 - 20 Nov 2020

Cited by 15 | Viewed by 4278

Abstract

Xylella fastidiosa subsp. pauca strain De Donno has been recently identified as the causal agent of a severe disease affecting olive trees in a wide area of the Apulia Region (Italy). While insights on the genetics and epidemiology of this virulent strain have [...] Read more.

Xylella fastidiosa subsp. pauca strain De Donno has been recently identified as the causal agent of a severe disease affecting olive trees in a wide area of the Apulia Region (Italy). While insights on the genetics and epidemiology of this virulent strain have been gained, its phenotypic and biological traits remained to be explored. We investigated in vitro behavior of the strain and compare its relevant biological features (growth rate, biofilm formation, cell–cell aggregation, and twitching motility) with those of the type strain Temecula1. The experiments clearly showed that the strain De Donno did not show fringe on the agar plates, produced larger amounts of biofilm and had a more aggregative behavior than the strain Temecula1. Repeated attempts to transform, by natural competence, the strain De Donno failed to produce a GFP-expressing and a knockout mutant for the rpfF gene. Computational prediction allowed us to identify potentially deleterious sequence variations most likely affecting the natural competence and the lack of fringe formation. GFP and rpfF- mutants were successfully obtained by co-electroporation in the presence of an inhibitor of the type I restriction–modification system. The availability of De Donno mutant strains will open for new explorations of its interactions with hosts and insect vectors. Full article

(This article belongs to the Special Issue Integrating Science on Xanthomonas and Xylella for Integrated Plant Disease Management)

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11 pages, 529 KiB

Open AccessArticle

The Effect of Disinfectants on Quinolone Resistant E. coli (QREC) in Biofilm

by Ane Mohr Osland, Lene K. Vestby and Live L. Nesse

Microorganisms 2020, 8(11), 1831; https://doi.org/10.3390/microorganisms8111831 - 20 Nov 2020

Cited by 5 | Viewed by 2973

Abstract

The aim of disinfection is to reduce the number of microorganisms on surfaces which is a challenge due to biofilms. In the present study, six quinolone resistant Escherichia coli (QREC) strains with three different biofilm matrix compositions were included to assess the log [...] Read more.

The aim of disinfection is to reduce the number of microorganisms on surfaces which is a challenge due to biofilms. In the present study, six quinolone resistant Escherichia coli (QREC) strains with three different biofilm matrix compositions were included to assess the log₁₀ colony forming units (CFU) reduction effect of three disinfectants at various exposure times on biofilm of different ages and morphotypes. Biofilm was formed on stainless steel coupons for two and five days before transferred to tubes with Virocid 0, 25%, VirkonS 1%, and TP990 1% and left for various exposure times. The biofilms were scraped off and serial dilutions were spread on blood agar plates where colony forming units (CFU) were counted. A mean log₁₀ CFU reduction ≥4 was seen on two-day-old biofilm with VirkonS and Virocid (30 min) but not on five-day old biofilm. TP990 did not display sufficient effect under the conditions tested. The bactericidal effect was inferior to that reported on planktonic bacteria. The findings of this study should be considered when establishing both disinfectant routines and standard susceptibility tests, which further should accommodate E. coli biofilms and not only Pseudomonas as is the case today. Full article

(This article belongs to the Special Issue Antimicrobial Resistance in the Food Production Chain )

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15 pages, 2651 KiB

Open AccessArticle

Anaplasma and Theileria Pathogens in Cattle of Lambwe Valley, Kenya: A Case for Pro-Active Surveillance in the Wildlife–Livestock Interface

by Michael N. Okal, Brenda Kisia Odhiambo, Peter Otieno, Joel L. Bargul, Daniel Masiga, Jandouwe Villinger and Shewit Kalayou

Microorganisms 2020, 8(11), 1830; https://doi.org/10.3390/microorganisms8111830 - 20 Nov 2020

Cited by 18 | Viewed by 4037

Abstract

Tick-borne pathogens (TBPs) are major constraints to livestock production and a threat to public health in Africa. This cross-sectional study investigated the risk of infection with TBPs in cattle of Lambwe Valley, Kenya. Blood samples of 680 zebu cattle from 95 herds in [...] Read more.

Tick-borne pathogens (TBPs) are major constraints to livestock production and a threat to public health in Africa. This cross-sectional study investigated the risk of infection with TBPs in cattle of Lambwe Valley, Kenya. Blood samples of 680 zebu cattle from 95 herds in six geospatial clusters within 5 km of Ruma National Park were screened for bacterial and protozoan TBPs by high-resolution melting analysis and sequencing of PCR products. We detected Anaplasma bovis (17.4%), Anaplasma platys (16.9%), Anaplasma marginale (0.6%), Theileria velifera (40%), and Theileria mutans (25.7%), as well as an Anaplasma sp. (11.6%) that matched recently reported Anaplasma sp. sequences from Ethiopia. Babesia, Rickettsia, and Ehrlichia spp. were not detected. The animal and herd-level prevalences for TBPs were 78.5% (95% confidence intervals (CI): 75.3, 81.5) and 95.8% (95% CI: 91.8, 99.8), respectively. About 31.6% of cattle were co-infected with 13 combinations of TBPs. The prevalence of TBPs differed between clusters and age, but the risk of infection was not associated with sex, herd size, or the distance of homesteads from Ruma. This study adds insight into the epidemiology of TBPs around Ruma and highlights the need for proactive surveillance of TBPs in livestock–wildlife interfaces. Full article

(This article belongs to the Special Issue Advance in Tick-Borne Diseases Research)

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16 pages, 3117 KiB

Open AccessArticle

Behind Taxonomic Variability: The Functional Redundancy in the Tick Microbiome

by Agustín Estrada-Peña, Alejandro Cabezas-Cruz and Dasiel Obregón

Microorganisms 2020, 8(11), 1829; https://doi.org/10.3390/microorganisms8111829 - 20 Nov 2020

Cited by 28 | Viewed by 5086

Abstract

The taxonomic composition and diversity of tick midgut microbiota have been extensively studied in different species of the genera Rhipicephalus, Ixodes, Amblyomma, Haemaphysalis, Hyalomma, Dermacentor, Argas and Ornithodoros, while the functional significance of bacterial diversity has [...] Read more.

The taxonomic composition and diversity of tick midgut microbiota have been extensively studied in different species of the genera Rhipicephalus, Ixodes, Amblyomma, Haemaphysalis, Hyalomma, Dermacentor, Argas and Ornithodoros, while the functional significance of bacterial diversity has been proportionally less explored. In this study, we used previously published 16S amplicon sequence data sets from three Ixodes scapularis cohorts, two of uninfected nymphs, and one of larvae experimentally infected with Borrelia burgdorferi, to test the functional redundancy of the tick microbiome. We predicted the metabolic profiling of each sample using the state-of-the-art metagenomics tool PICRUSt2. The results showed that the microbiomes of all I. scapularis samples share only 80 taxa (24.6%, total 324), while out of the 342 metabolic pathways predicted, 82.7%, were shared by all the ticks. Borrelia-infected larvae lack 15.4% of pathways found in the microbiome of uninfected nymphs. Taxa contribution analysis showed that the functional microbiome of uninfected ticks was highly redundant, with, in some cases, up to 198 bacterial taxa contributing to a single pathway. However, Borrelia-infected larvae had a smaller redundancy with 6.7% of pathways provided by more than 100 genera, while 15.7–19.2% of pathways were provided by more than 100 genera in the two cohorts of uninfected ticks. In addition, we compared the functional profiles of three microbial communities from each data set, identified through a network-based approach, and we observed functional similarity between them. Based on the functional redundancy and functional similarity of the microbiome of ticks in different developmental stages and infection status, we concluded that the tick gut microbiota is a self-regulating community of very diverse bacteria contributing to a defined set of metabolic pathways and functions with yet unexplored relevance for tick fitness and/or bacterial community stability. We propose a change of focus in which the tick microbiome must be analyzed in all dimensions, highlighting their functional traits, instead of the conventional taxonomic profiling. Full article

(This article belongs to the Section Parasitology)

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18 pages, 3233 KiB

Open AccessArticle

Phosphorus Reduces Negative Effects of Nitrogen Addition on Soil Microbial Communities and Functions

by Zongwei Xia, Jingyi Yang, Changpeng Sang, Xu Wang, Lifei Sun, Ping Jiang, Chao Wang and Edith Bai

Microorganisms 2020, 8(11), 1828; https://doi.org/10.3390/microorganisms8111828 - 20 Nov 2020

Cited by 40 | Viewed by 5137

Abstract

Increased soil nitrogen (N) from atmospheric N deposition could change microbial communities and functions. However, the underlying mechanisms and whether soil phosphorus (P) status are responsible for these changes still have not been well explained. Here, we investigated the effects of N and [...] Read more.

Increased soil nitrogen (N) from atmospheric N deposition could change microbial communities and functions. However, the underlying mechanisms and whether soil phosphorus (P) status are responsible for these changes still have not been well explained. Here, we investigated the effects of N and P additions on soil bacterial and fungal communities and predicted their functional compositions in a temperate forest. We found that N addition significantly decreased soil bacterial diversity in the organic (O) horizon, but tended to increase bacterial diversity in the mineral (A) horizon soil. P addition alone did not significantly change soil bacterial diversity but mitigated the negative effect of N addition on bacterial diversity in the O horizon. Neither N addition nor P addition significantly influenced soil fungal diversity. Changes in soil microbial community composition under N and P additions were mainly due to the shifts in soil pH and NO₃⁻ contents. N addition can affect bacterial functional potentials, such as ureolysis, N fixation, respiration, decomposition of organic matter processes, and fungal guilds, such as pathogen, saprotroph, and mycorrhizal fungi, by which more C probably was lost in O horizon soil under increased N deposition. However, P addition can alleviate or switch the effects of increased N deposition on the microbial functional potentials in O horizon soil and may even be a benefit for more C sequestration in A horizon soil. Our results highlight the different responses of microorganisms to N and P additions between O and A horizons and provides an important insight for predicting the changes in forest C storage status under increasing N deposition in the future. Full article

(This article belongs to the Special Issue Microbial Community Response to Climate and Environmental Changes)

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12 pages, 452 KiB

Open AccessReview

Autoimmune Gastritis and Gastric Microbiota

by Laura Conti, Bruno Annibale and Edith Lahner

Microorganisms 2020, 8(11), 1827; https://doi.org/10.3390/microorganisms8111827 - 19 Nov 2020

Cited by 29 | Viewed by 9297

Abstract

Autoimmune atrophic gastritis is an organ-specific immune-mediated condition characterized by atrophy of the oxyntic mucosa. Autoimmune atrophic gastritis (AIG) is characterized by a progressive loss of acid-secreting parietal cells leading to hypo-achlorhydria. Due to this peculiar intra-gastric environment, gastric microbiota composition in individuals [...] Read more.

Autoimmune atrophic gastritis is an organ-specific immune-mediated condition characterized by atrophy of the oxyntic mucosa. Autoimmune atrophic gastritis (AIG) is characterized by a progressive loss of acid-secreting parietal cells leading to hypo-achlorhydria. Due to this peculiar intra-gastric environment, gastric microbiota composition in individuals with autoimmune atrophic gastritis was first supposed and then recently reported to be different from subjects with a normal acidic healthy stomach. Recent data confirm the prominent role of Helicobacter pylori as the main bacterium responsible for gastric disease and long-term complications. However, other bacteria than Helicobacter pylori, for example, Streptococci, were found in subjects who developed gastric cancer and in subjects at risk of this fearful complication, as well as those with autoimmune gastritis. Gastric microbiota composition is challenging to study due to the acidic gastric environment, the difficulty of obtaining representative samples of the entire gastric microbiota, and the possible contamination by oral or throat microorganisms, which can potentially lead to the distortion of the original gastric microbial composition, but innovative molecular approaches based on the analysis of the hyper-variable region of the 16S rRNA gene have been developed, permitting us to obtain an overall microbial composition view of the RNA gene that is present only in prokaryotic cells. Full article

(This article belongs to the Special Issue Microbial and Autoimmune Disease)

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18 pages, 3207 KiB

Open AccessArticle

Proteomic Studies of the Biofilm Matrix including Outer Membrane Vesicles of Burkholderia multivorans C1576, a Strain of Clinical Importance for Cystic Fibrosis

by Lucrecia C. Terán, Marco Distefano, Barbara Bellich, Sara Petrosino, Paolo Bertoncin, Paola Cescutti and Daniele Sblattero

Microorganisms 2020, 8(11), 1826; https://doi.org/10.3390/microorganisms8111826 - 19 Nov 2020

Cited by 11 | Viewed by 3436

Abstract

Biofilms are aggregates of microbial cells encased in a highly hydrated matrix made up of self-produced extracellular polymeric substances (EPS) which consist of polysaccharides, proteins, nucleic acids, and lipids. While biofilm matrix polysaccharides are unraveled, there is still poor knowledge about the identity [...] Read more.

Biofilms are aggregates of microbial cells encased in a highly hydrated matrix made up of self-produced extracellular polymeric substances (EPS) which consist of polysaccharides, proteins, nucleic acids, and lipids. While biofilm matrix polysaccharides are unraveled, there is still poor knowledge about the identity and function of matrix-associated proteins. With this work, we performed a comprehensive proteomic approach to disclose the identity of proteins associated with the matrix of biofilm-growing Burkholderia multivorans C1576 reference strain, a cystic fibrosis clinical isolate. Transmission electron microscopy showed that B. multivorans C1576 also releases outer membrane vesicles (OMVs) in the biofilm matrix, as already demonstrated for other Gram-negative species. The proteomic analysis revealed that cytoplasmic and membrane-bound proteins are widely represented in the matrix, while OMVs are highly enriched in outer membrane proteins and siderophores. Our data suggest that cell lysis and OMVs production are the most important sources of proteins for the B. multivorans C1576 biofilm matrix. Of note, some of the identified proteins are lytic enzymes, siderophores, and proteins involved in reactive oxygen species (ROS) scavenging. These proteins might help B. multivorans C1576 in host tissue invasion and defense towards immune system assaults. Full article

(This article belongs to the Section Biofilm)

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12 pages, 282 KiB

Open AccessArticle

Antimicrobial Susceptibility and Association with Toxin Determinants in Clostridium perfringens Isolates from Chickens

by Bai Wei, Se-Yeoun Cha, Jun-Feng Zhang, Ke Shang, Hae-Chul Park, JeongWoo Kang, Kwang-Jick Lee, Min Kang and Hyung-Kwan Jang

Microorganisms 2020, 8(11), 1825; https://doi.org/10.3390/microorganisms8111825 - 19 Nov 2020

Cited by 20 | Viewed by 2985

Abstract

The aim of the present study was to investigate variation in antimicrobial resistance in Clostridium perfringens (C. perfringens) isolated from chickens after withdrawal of antimicrobial growth promoters (AGPs); and to investigate the correlation between the presence of toxin genes (cpb2 [...] Read more.

The aim of the present study was to investigate variation in antimicrobial resistance in Clostridium perfringens (C. perfringens) isolated from chickens after withdrawal of antimicrobial growth promoters (AGPs); and to investigate the correlation between the presence of toxin genes (cpb2, netB, and tpeL) and antimicrobial resistance. Altogether, 162 isolates of C. perfringens were obtained from chickens displaying clinical signs of necrotic enteritis (n = 65) and from healthy chickens (n = 97) in Korea during 2010–2016. Compared to before AGP withdrawal, increased antimicrobial resistance or MIC₅₀/MIC₉₀ value was observed for nine antimicrobials including penicillin, tetracycline, tylosin, erythromycin, florfenicol, enrofloxacin, monensin, salinomycin, and maduramycin. Significantly (p < 0.05) higher resistance to gentamicin, clindamycin, and virginiamycin was found in isolates from chickens with necrotic enteritis compared to those from healthy chickens. tpeL gene was not detected in C. perfringens isolates from healthy chickens. A correlation between toxin gene prevalence and antibiotic resistance was found in the C. perfringens isolates. Because the usage of antimicrobials may contribute to the selection of both resistance and toxin genes, these can potentially make it challenging to control antimicrobial resistance in pathogenic colonies. Therefore, a more complete understanding of the interplay between resistance and virulence genes is required. Full article

(This article belongs to the Section Antimicrobial Agents and Resistance)

19 pages, 689 KiB

Open AccessReview

Epstein–Barr Virus: How Its Lytic Phase Contributes to Oncogenesis

by Quincy Rosemarie and Bill Sugden

Microorganisms 2020, 8(11), 1824; https://doi.org/10.3390/microorganisms8111824 - 19 Nov 2020

Cited by 83 | Viewed by 8337

Abstract

Epstein–Barr Virus (EBV) contributes to the development of lymphoid and epithelial malignancies. While EBV’s latent phase is more commonly associated with EBV-associated malignancies, there is increasing evidence that EBV’s lytic phase plays a role in EBV-mediated oncogenesis. The lytic phase contributes to oncogenesis [...] Read more.

Epstein–Barr Virus (EBV) contributes to the development of lymphoid and epithelial malignancies. While EBV’s latent phase is more commonly associated with EBV-associated malignancies, there is increasing evidence that EBV’s lytic phase plays a role in EBV-mediated oncogenesis. The lytic phase contributes to oncogenesis primarily in two ways: (1) the production of infectious particles to infect more cells, and (2) the regulation of cellular oncogenic pathways, both cell autonomously and non-cell autonomously. The production of infectious particles requires the completion of the lytic phase. However, the regulation of cellular oncogenic pathways can be mediated by an incomplete (abortive) lytic phase, in which early lytic gene products contribute substantially, whereas late lytic products are largely dispensable. In this review, we discuss the evidence of EBV’s lytic phase contributing to oncogenesis and the role it plays in tumor formation and progression, as well as summarize known mechanisms by which EBV lytic products regulate oncogenic pathways. Understanding the contribution of EBV’s lytic phase to oncogenesis will help design ways to target it to treat EBV-associated malignancies. Full article

(This article belongs to the Special Issue Epstein–Barr Virus Infection and Associated Diseases)

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15 pages, 954 KiB

Open AccessArticle

Biofilm Formation Reducing Properties of Manuka Honey and Propolis in Proteus mirabilis Rods Isolated from Chronic Wounds

by Joanna Kwiecińska-Piróg, Jana Przekwas, Michał Majkut, Krzysztof Skowron and Eugenia Gospodarek-Komkowska

Microorganisms 2020, 8(11), 1823; https://doi.org/10.3390/microorganisms8111823 - 19 Nov 2020

Cited by 19 | Viewed by 4520

Abstract

Chronic wound infections are difficult to manage because of the biofilm formation in the wound environment. New measures for eliminating infections are necessary to increase the chance of wound healing. Apitherapy may be the new solution. The aim of this study was to [...] Read more.

Chronic wound infections are difficult to manage because of the biofilm formation in the wound environment. New measures for eliminating infections are necessary to increase the chance of wound healing. Apitherapy may be the new solution. The aim of this study was to assess the prevalence of wound infection factors and to examine the impact of Manuka honey and ethanol extract of propolis on biofilm formation of Proteus mirabilis isolated from chronic wound infections. According to the findings, the most frequent factors of infection are Staphylococcus aureus (46.1%), Pseudomonas aeruginosa (35.0%), and Proteus mirabilis (10.6%). Minimal inhibitory concentration and minimal bactericidal concentration values were assigned using the microbroth dilution test according to the Clinical and Laboratory Standards Institute. Biofilm of Proteus mirabilis isolates was formed in 96-well polystyrene plates and treated with Manuka honey (concentrations from 1.88% to 30.0%) and ethanol extract of propolis (1.0% to 40.0%). After 24 h, the biofilm viability was expressed by formazan absorbance (λ = 470 nm). Manuka honey reduced the biofilm viability in all, and ethanol extract of propolis in most, of the concentrations tested. Ethanol extract of propolis at the concentrations of 20.0% and 40.0%, reduced biofilm viability stronger than ethanol itself. With these results comes the conclusion that these substances can reduce biofilm formation. Full article

(This article belongs to the Special Issue Clinical Implications of Microbial Biofilm)

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20 pages, 19684 KiB

Open AccessArticle

Intra- and Inter-Host Assessment of Bartonella Diversity with Focus on Non-Hematophagous Bats and Associated Ectoparasites from Brazil

by Priscila Ikeda, Jaire Marinho Torres, Lívia Perles, Elizabete Captivo Lourenço, Heitor Miraglia Herrera, Carina Elisei de Oliveira, Rosangela Zacarias Machado and Marcos Rogério André

Microorganisms 2020, 8(11), 1822; https://doi.org/10.3390/microorganisms8111822 - 19 Nov 2020

Cited by 23 | Viewed by 3064

Abstract

The relationship among bats, ectoparasites and associated microorganisms is important to investigate how humans can become exposed to zoonotic agents. Even though the diversity of Bartonella spp. in bats and ectoparasites has been previously reported, the occurrence of gltA genotypes within hosts has [...] Read more.

The relationship among bats, ectoparasites and associated microorganisms is important to investigate how humans can become exposed to zoonotic agents. Even though the diversity of Bartonella spp. in bats and ectoparasites has been previously reported, the occurrence of gltA genotypes within hosts has not been assessed so far. We aimed to investigate the genetic diversity of Bartonella spp. in non-hematophagous bats and associated ectoparasites by assessing cloned gltA Bartonella genotypes in intra- and inter-hosts levels, as well as by using three additional molecular markers. Overall, 13.5% (18/133) bat blood samples, 17.18% bat flies (11/64) and 23.8% (5/21) Macronyssidae mite pools showed to be positive for Bartonella spp. Seventeen positive samples were submitted to gltA-cloning and three clones were sequenced for each sample. We also obtained 11, seven and three sequences for nuoG, rpoB and ftsZ genes, respectively. None were positive for the other target genes. We found at least two genotypes among the three gltA-cloned sequences from each sample, and 13 between all the 51 sequences. Among the nuoG, rpoB and ftsZ sequences we found eight, five and three genotypes, respectively. In the phylogenetic analysis, the sequences were positioned mainly in groups related to Bartonella identified in rodents, bats and bat flies. Herein, we showed the genetic diversity of Bartonella in bat’s blood and associated ectoparasites samples at both intra- and inter-host levels. Full article

(This article belongs to the Section Parasitology)

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11 pages, 916 KiB

Open AccessArticle

The Acquisition of Multidrug-Resistant Bacteria in Patients Admitted to COVID-19 Intensive Care Units: A Monocentric Retrospective Case Control Study

by Elisa G. Bogossian, Fabio S. Taccone, Antonio Izzi, Nicolas Yin, Alessandra Garufi, Stephane Hublet, Hassane Njimi, Amedee Ego, Julie Gorham, Baudouin Byl, Alexandre Brasseur, Maya Hites, Jean-Louis Vincent, Jacques Creteur and David Grimaldi

Microorganisms 2020, 8(11), 1821; https://doi.org/10.3390/microorganisms8111821 - 19 Nov 2020

Cited by 25 | Viewed by 3577

Abstract

Whether the risk of multidrug-resistant bacteria (MDRB) acquisition in the intensive care unit (ICU) is modified by the COVID-19 crisis is unknown. In this single center case control study, we measured the rate of MDRB acquisition in patients admitted in COVID-19 ICU and [...] Read more.

Whether the risk of multidrug-resistant bacteria (MDRB) acquisition in the intensive care unit (ICU) is modified by the COVID-19 crisis is unknown. In this single center case control study, we measured the rate of MDRB acquisition in patients admitted in COVID-19 ICU and compared it with patients admitted in the same ICU for subarachnoid hemorrhage (controls) matched 1:1 on length of ICU stay and mechanical ventilation. All patients were systematically and repeatedly screened for MDRB carriage. We compared the rate of MDRB acquisition in COVID-19 patients and in control using a competing risk analysis. Of note, although we tried to match COVID-19 patients with septic shock patients, we were unable due to the longer stay of COVID-19 patients. Among 72 patients admitted to the COVID-19 ICUs, 33% acquired 31 MDRB during ICU stay. The incidence density of MDRB acquisition was 30/1000 patient days. Antimicrobial therapy and exposure time were associated with higher rate of MDRB acquisition. Among the 72 SAH patients, 21% acquired MDRB, with an incidence density was 18/1000 patient days. The septic patients had more comorbidities and a greater number of previous hospitalizations than the COVID-19 patients. The incidence density of MDRB acquisition was 30/1000 patient days. The association between COVID-19 and MDRB acquisition (compared to control) risk did not reach statistical significance in the multivariable competing risk analysis (sHR 1.71 (CI 95% 0.93–3.21)). Thus, we conclude that, despite strong physical isolation, acquisition rate of MDRB in ICU patients was at least similar during the COVID-19 first wave compared to previous period. Full article

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

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18 pages, 3684 KiB

Open AccessArticle

Phenotypic Adaptation of Pseudomonas aeruginosa in the Presence of Siderophore-Antibiotic Conjugates during Epithelial Cell Infection

by Quentin Perraud, Paola Cantero, Mathilde Munier, Françoise Hoegy, Nicolas Zill, Véronique Gasser, Gaëtan L. A. Mislin, Laurence Ehret-Sabatier and Isabelle J. Schalk

Microorganisms 2020, 8(11), 1820; https://doi.org/10.3390/microorganisms8111820 - 18 Nov 2020

Cited by 22 | Viewed by 3642

Abstract

Iron acquisition pathways have often been considered to be gateways for the uptake of antibiotics into bacteria. Bacteria excrete chelators, called siderophores, to access iron. Antibiotic molecules can be covalently attached to siderophores for their transport into pathogens during the iron-uptake process. P. [...] Read more.

Iron acquisition pathways have often been considered to be gateways for the uptake of antibiotics into bacteria. Bacteria excrete chelators, called siderophores, to access iron. Antibiotic molecules can be covalently attached to siderophores for their transport into pathogens during the iron-uptake process. P. aeruginosa produces two siderophores and is also able to use many siderophores produced by other bacteria. We investigated the phenotypic plasticity of iron-uptake pathway expression in an epithelial cell infection assay in the presence of two different siderophore–antibiotic conjugates, one with a hydroxamate siderophore and the second with a tris-catechol. Proteomic and RT-qPCR approaches showed that P. aeruginosa was able to sense the presence of both compounds in its environment and adapt the expression of its iron uptake pathways to access iron via them. Moreover, the catechol-type siderophore–antibiotic was clearly more efficient in inducing the expression of its corresponding transporter than the hydroxamate compound when both were simultaneously present. In parallel, the expression of the proteins of the two iron uptake pathways using siderophores produced by P. aeruginosa was significantly repressed in the presence of both conjugates. Altogether, the data indicate that catechol-type siderophores are more promising vectors for antibiotic vectorization using a Trojan-horse strategy. Full article

(This article belongs to the Special Issue Bacterial Stress Response Mechanisms: Signal Perception, Transduction and Adaptation)

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12 pages, 275 KiB

Open AccessArticle

Cryptic HBV Replicative Activity Is Frequently Revealed in Anti-HBc-Positive/HBsAg-Negative Patients with HIV Infection by Highly Sensitive Molecular Assays, and Can Be Predicted by Integrating Classical and Novel Serological HBV Markers

by Romina Salpini, Vincenzo Malagnino, Lorenzo Piermatteo, Tiziana Mulas, Mohammad Alkhatib, Rossana Scutari, Elisabetta Teti, Carlotta Cerva, Katia Yu La Rosa, Marta Brugneti, Ada Bertoli, Benedetta Rossi, Vera Holzmayer, Jeffrey Gersch, Mary Kuhns, Gavin Cloherty, Francesca Ceccherini-Silberstein, Carlo-Federico Perno, Marco Iannetta, Massimo Andreoni, Loredana Sarmati and Valentina Svicher Show full author list Hide full author list

Microorganisms 2020, 8(11), 1819; https://doi.org/10.3390/microorganisms8111819 - 18 Nov 2020

Cited by 11 | Viewed by 2801

Abstract

The anti-HBc-positive/HBsAg-negative status is frequent in HIV-infection and correlates with poor survival. Here, by highly-sensitive assays, we evaluate cryptic HBV replication and factors correlated with its detection in 81 anti-HBc-positive/HBsAg-negative HIV-infected patients. Patients were treated for >12 months with HBV-active modern combined antiretroviral-therapy [...] Read more.

The anti-HBc-positive/HBsAg-negative status is frequent in HIV-infection and correlates with poor survival. Here, by highly-sensitive assays, we evaluate cryptic HBV replication and factors correlated with its detection in 81 anti-HBc-positive/HBsAg-negative HIV-infected patients. Patients were treated for >12 months with HBV-active modern combined antiretroviral-therapy (cART) and had serum HBV-DNA < 20 IU/mL by commercial Real-Time PCR. Serum HBV-DNA was quantified by droplet digital PCR, serum HBV-RNA by an Abbott research assay, and anti-HBc titer (proposed to infer intrahepatic cccDNA) by Lumipulse/Fujirebio. Cryptic serum HBV-DNA was detected in 29.6% of patients (median (IQR): 4(1–15) IU/mL) and serum HBV-RNA in 3.7% of patients despite HBsAg-negativity and HBV-active cART. Notably, cryptic serum HBV-DNA correlated with an advanced CDC-stage (p = 0.01) and a lower anti-HBs titer (p = 0.05), while serum HBV-RNA correlated with lower nadir CD4+ cell-count (p = 0.01). By analyzing serological HBV-markers, the combination of anti-HBs < 50 mIU/mL (indicating lower immune response) plus anti-HBc > 15COI (reflecting higher HBV replicative activity) was predictive of cryptic serum HBV-DNA (OR: 4.7(1.1–21.7), p = 0.046, PPV = 62.5%, and NPV = 72%). In conclusion, cryptic HBV-replication (not detected by classical assays) characterizes a conspicuous set of anti-HBc-positive HIV-infected patients despite HBsAg-negativity and HBV-active combined antiretroviral therapy (cART). The integration of classical and novel markers may help identify patients with cryptic HBV-replication, thus optimizing the monitoring of anti-HBc-positive/HBsAg-negative HIV-infected patients. Full article

(This article belongs to the Special Issue Updates on HBV Infection)

13 pages, 303 KiB

Open AccessArticle

Psychological Distress in Patients with Autoimmune Arthritis during the COVID-19 Induced Lockdown in Italy

by Andrea Picchianti Diamanti, Maria Sofia Cattaruzza, Roberta Di Rosa, Flavia Del Porto, Simonetta Salemi, Maria Laura Sorgi, Luis Severino Martin Martin, Alessandra Rai, Dalila Iacono, Giorgio Sesti, Guido Alessandri and Bruno Laganà

Microorganisms 2020, 8(11), 1818; https://doi.org/10.3390/microorganisms8111818 - 18 Nov 2020

Cited by 25 | Viewed by 3047

Abstract

Lockdowns imposed by governments worldwide as a way to limit the spread of severe atypical respiratory syndrome-coronavirus-2 (SARS-CoV2) have had heavy psychological and economic consequences. Arthritis patients are a vulnerable population at an increased risk of peritraumatic stress. This could be due to [...] Read more.

Lockdowns imposed by governments worldwide as a way to limit the spread of severe atypical respiratory syndrome-coronavirus-2 (SARS-CoV2) have had heavy psychological and economic consequences. Arthritis patients are a vulnerable population at an increased risk of peritraumatic stress. This could be due to several reasons, including the fear of shortage of medicine and difficulty receiving periodical medical checks. In the present case-control study, psychological distress in patients with autoimmune arthritis during the coronavirus disease 2019 (COVID-19) pandemic were investigated. An electronic survey was conducted to gather information on the perceived change in the emotional state, general health (GH), fatigue, joint pain, and disease activity during the lockdown, in 100 patients with autoimmune arthritis and 100 controls. Mental health status was measured using the Depression, Anxiety and Stress Scale (DASS-21). The COVID-19 Peritraumatic Distress Index (CPDI) was used to assess the frequency of peritraumatic stress disorders related to COVID-19. Patients reported a significant worsening of perceived GH (36% vs. 7%; p < 0.001), a significantly higher mean CPDI score (p < 0.001) than controls. Using multivariate analysis, arthritis patients had significantly higher CPDI scores (+3.67 points; p = 0.019), independent of depression, anxiety, and stress symptoms, comorbidities, and sociodemographic and lifestyle characteristics. Logistic regression analysis showed that the risk of reporting worsened GH was 9-fold higher in patients than controls (p < 0.001). Patients with autoimmune arthritis are at higher risk of psychological distress related to COVID-19 pandemic; thus targeted intervention should be designed to strengthen coping capacity in this vulnerable population. Full article

(This article belongs to the Special Issue Microbial and Autoimmune Disease)

13 pages, 1075 KiB

Open AccessArticle

The Red Fox (Vulpes vulpes) as Sentinel for Tick-Borne Encephalitis Virus in Endemic and Non-Endemic Areas

by Maja Haut, Philipp Girl, Beate Oswald, Thomas Romig, Anna Obiegala, Gerhard Dobler and Martin Pfeffer

Microorganisms 2020, 8(11), 1817; https://doi.org/10.3390/microorganisms8111817 - 18 Nov 2020

Cited by 13 | Viewed by 3372

Abstract

Tick-borne encephalitis (TBE) is one of the most important viral zoonosis caused by a neurotropic arbovirus (TBEV). In Germany, TBE is classified as a notifiable disease with an average of 350 autochthonous human cases annually. The incidence-based risk assessment in Germany came under [...] Read more.

Tick-borne encephalitis (TBE) is one of the most important viral zoonosis caused by a neurotropic arbovirus (TBEV). In Germany, TBE is classified as a notifiable disease with an average of 350 autochthonous human cases annually. The incidence-based risk assessment in Germany came under criticism because every year, a number of autochthonous human TBE cases have been detected outside of the official risk areas. Therefore, it is necessary to find additional parameters to strengthen TBEV surveillance. The aim of this study was to examine red foxes as sentinels for TBE. Thus far, there are no published data about the sensitivity and specificity for serological methods testing fox samples. Hence, we aimed to define a system for the screening of TBEV-specific antibodies in red foxes. A total of 1233 fox sera were collected and examined by ELISA and IIFA and confirmed by micro-NT. The overall seroprevalence of antibodies against TBEV in red foxes from Germany confirmed by micro-NT was 21.1%. The seroprevalence differed significantly between risk (30.5%) and non-risk areas (13.1%), with good correlations to local TBE incidence in humans. In conclusion, serological monitoring of red foxes represents a promising surrogate marker system and may even determine unexpected TBEV foci in regions currently regarded as non-risk areas. Full article

(This article belongs to the Special Issue Tick-Borne Encephalitis)

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8 pages, 229 KiB

Open AccessCommunication

Emergence of Enterobacter cloacae Complex Co-Producing IMP-10 and CTX-M, and Klebsiella pneumoniae Producing VIM-1 in Clinical Isolates in Japan

by Satoshi Nishida, Naohisa Matsunaga, Yuta Kamimura, Shinobu Ishigaki, Taiji Furukawa and Yasuo Ono

Microorganisms 2020, 8(11), 1816; https://doi.org/10.3390/microorganisms8111816 - 18 Nov 2020

Cited by 14 | Viewed by 2778

Abstract

Background: Carbapenemase-producing Enterobacteriaceae (CPE) are an emerging threat in healthcare settings worldwide. Objectives: We evaluated the presence of carbapenemase genes in CPE in a tertiary care university hospital in Tokyo, Japan. Methods: Carbapenem-resistant clinical isolates were collected in 2018 at Teikyo University Hospital [...] Read more.

Background: Carbapenemase-producing Enterobacteriaceae (CPE) are an emerging threat in healthcare settings worldwide. Objectives: We evaluated the presence of carbapenemase genes in CPE in a tertiary care university hospital in Tokyo, Japan. Methods: Carbapenem-resistant clinical isolates were collected in 2018 at Teikyo University Hospital (Tokyo, Japan). Bacterial species were identified using MALDI-TOF MS. Carbapenemase production was evaluated using a carbapenemase inactivation method. The presence of carbapenemase genes was confirmed by multiplex PCR and DNA sequencing. Results: Four CPE isolates were identified: two Enterobacter cloacae complex strains and Klebsiella oxytoca and Klebsiella pneumoniae strains. Three of the isolates (E. cloacae complex and K. oxytoca) were IMP-1-type producers, including IMP-10 in their produced metallo-β-lactamase, and are epidemic in East Japan. The IMP-10-producing E. cloacae complex strain also produced CTX-M ESBL. The other CPE isolate (K. pneumoniae) is a VIM-1 producer. VIM-1-producing K. pneumoniae is epidemic in Europe, especially in Greece. Accordingly, the VIM-1 producer was isolated from a patient with a medical history in Greece. Conclusions: This study revealed the emergence of E. cloacae complex co-producing IMP-1-type carbapenemase and CTX-M ESBL, and K. pneumoniae producing VIM-1 carbapenemase in clinical isolates in Japan. Metallo-β-lactamase was the most prevalent type of carbapenemase at Teikyo University Hospital, especially IMP-1-type carbapenemase. The detection of VIM-1-producing K. pneumoniae suggests that epidemic CPE from overseas can spread to countries with low CPE prevalence, such as Japan, highlighting the need for active surveillance. Full article

(This article belongs to the Special Issue Carbapenemase-producing Enterobacteriaceae)

17 pages, 2251 KiB

Open AccessArticle

Nutritional Conditions Modulate C. neoformans Extracellular Vesicles’ Capacity to Elicit Host Immune Response

by Clara Luna Marina, Pedro Henrique Bürgel, Daniel Paiva Agostinho, Daniel Zamith-Miranda, Lucas de Oliveira Las-Casas, Aldo Henrique Tavares, Joshua Daniel Nosanchuk and Anamelia Lorenzetti Bocca

Microorganisms 2020, 8(11), 1815; https://doi.org/10.3390/microorganisms8111815 - 18 Nov 2020

Cited by 20 | Viewed by 3018

Abstract

Cryptococcus neoformans is a human pathogenic fungus that mainly afflicts immunocompromised patients. One of its virulence strategies is the production of extracellular vesicles (EVs), containing cargo with immunomodulatory properties. We evaluated EV’s characteristics produced by capsular and acapsular strains of C. neoformans (B3501 [...] Read more.

Cryptococcus neoformans is a human pathogenic fungus that mainly afflicts immunocompromised patients. One of its virulence strategies is the production of extracellular vesicles (EVs), containing cargo with immunomodulatory properties. We evaluated EV’s characteristics produced by capsular and acapsular strains of C. neoformans (B3501 and ΔCap67, respectively) growing in nutritionally poor or rich media and co-cultures with bone marrow-derived macrophages or dendritic cells from C57BL/6 mice. EVs produced under a poor nutritional condition displayed a larger hydrodynamic size, contained more virulence compounds, and induced a more robust inflammatory pattern than those produced in a rich nutritional medium, independently of strain. We treated infected mice with EVs produced in the rich medium, and the EVs inhibited more genes related to the inflammasome than untreated infected mice. These findings suggest that the EVs participate in the pathogenic processes that result in the dissemination of C. neoformans. Thus, these results highlight the versatility of EVs’ properties during infection by C. neoformans in different tissues and support ongoing efforts to harness EVs to prevent and treat cryptococcosis. Full article

(This article belongs to the Special Issue Current Understanding of Cryptococcus and Cryptococcosis)

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Microorganisms, Volume 8, Issue 11 (November 2020) – 217 articles

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