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Microorganisms
Volume 9
Issue 10
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Microorganisms, Volume 9, Issue 10 (October 2021) – 176 articles

Cover Story (view full-size image): Myxobacteria are abundant and virtually ubiquitous environmental organisms. They have large genomes and engage in complicated behaviours, including communal predation and multicellular fruiting body formation. Myxobacterial fruiting bodies were first described and pictured by Roland Thaxter in 1892, and in 2006, the first myxobacterial genome was sequenced. Fifteen years later, more than 160 myxobacterial sequences are publicly available, and our understanding of myxobacterial biology and evolution has been transformed as a consequence. View this paper.
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18 pages, 12090 KiB  
Article
Recovery of Mycobacteria from Heavily Contaminated Environmental Matrices
by Vit Ulmann, Helena Modrá, Vladimir Babak, Ross Tim Weston and Ivo Pavlik
Microorganisms 2021, 9(10), 2178; https://doi.org/10.3390/microorganisms9102178 - 19 Oct 2021
Cited by 12 | Viewed by 2344
Abstract
For epidemiology studies, a decontamination method using a solution containing 4.0% NaOH and 0.5% tetradecyltrimethylammonium bromide (TDAB) represents a relatively simple and universal procedure for processing heavily microbially contaminated matrices together with increase of mycobacteria yield and elimination of gross contamination. A contamination [...] Read more.
For epidemiology studies, a decontamination method using a solution containing 4.0% NaOH and 0.5% tetradecyltrimethylammonium bromide (TDAB) represents a relatively simple and universal procedure for processing heavily microbially contaminated matrices together with increase of mycobacteria yield and elimination of gross contamination. A contamination rate only averaging 7.3% (2.4% in Cluster S; 6.9% in Cluster R and 12.6% in Cluster E) was found in 787 examined environmental samples. Mycobacteria were cultured from 28.5% of 274 soil and water sediments samples (Cluster S), 60.2% of 251 samples of raw and processed peat and other horticultural substrates (Cluster R), and 29.4% of 262 faecal samples along with other samples of animal origin (Cluster E). A total of 38 species of slow and rapidly growing mycobacteria were isolated. M. avium ssp. hominissuis, M. fortuitum and M. malmoense were the species most often isolated. The parameters for the quantitative detection of mycobacteria by PCR can be significantly refined by treating the sample suspension before DNA isolation with PMA (propidium monoazide) solution. This effectively eliminates DNA residue from both dead mycobacterial cells and potentially interfering DNA segments present from other microbial flora. In terms of human exposure risk assessment, the potential exposure to live non-tuberculous mycobacteria can be more accurately determined. Full article
(This article belongs to the Special Issue Nontuberculous Mycobacteria: Ecology and Impact on Animal and Human Health)
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20 pages, 1004 KiB  
Review
What Do We Know about Candida auris? State of the Art, Knowledge Gaps, and Future Directions
by Victor Garcia-Bustos, Marta D. Cabanero-Navalon, Amparo Ruiz-Saurí, Alba C. Ruiz-Gaitán, Miguel Salavert, María Á. Tormo and Javier Pemán
Microorganisms 2021, 9(10), 2177; https://doi.org/10.3390/microorganisms9102177 - 19 Oct 2021
Cited by 34 | Viewed by 9139
Abstract
Candida auris has unprecedently emerged as a multidrug resistant fungal pathogen, considered a serious global threat due to its potential to cause nosocomial outbreaks and deep-seated infections with staggering transmissibility and mortality, that has put health authorities and institutions worldwide in check for [...] Read more.
Candida auris has unprecedently emerged as a multidrug resistant fungal pathogen, considered a serious global threat due to its potential to cause nosocomial outbreaks and deep-seated infections with staggering transmissibility and mortality, that has put health authorities and institutions worldwide in check for more than a decade now. Due to its unique features not observed in other yeasts, it has been categorised as an urgent threat by the Centers for Disease Control and Prevention and other international agencies. Moreover, epidemiological alerts have been released in view of the increase of healthcare-associated C. auris outbreaks in the context of the COVID-19 pandemic. This review summarises the current evidence on C. auris since its first description, from virulence to treatment and outbreak control, and highlights the knowledge gaps and future directions for research efforts. Full article
(This article belongs to the Special Issue Diagnosis, Resistance and Treatment of Infections by Candida Species)
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10 pages, 2755 KiB  
Article
Immobilization of Polyethyleneimine (PEI) on Flat Surfaces and Nanoparticles Affects Its Ability to Disrupt Bacterial Membranes
by Nesha May Octavio Andoy, Meera Patel, Ching Lam Jane Lui and Ruby May Arana Sullan
Microorganisms 2021, 9(10), 2176; https://doi.org/10.3390/microorganisms9102176 - 19 Oct 2021
Cited by 5 | Viewed by 3595
Abstract
Interactions between a widely used polycationic polymer, polyethyleneimine (PEI), and a Gram-negative bacteria, E. coli, are investigated using atomic force microscopy (AFM) quantitative imaging. The effect of PEI, a known membrane permeabilizer, is characterized by probing both the structure and elasticity of [...] Read more.
Interactions between a widely used polycationic polymer, polyethyleneimine (PEI), and a Gram-negative bacteria, E. coli, are investigated using atomic force microscopy (AFM) quantitative imaging. The effect of PEI, a known membrane permeabilizer, is characterized by probing both the structure and elasticity of the bacterial cell envelope. At low concentrations, PEI induced nanoscale membrane perturbations all over the bacterial surface. Despite these structural changes, no change in cellular mechanics (Young’s modulus) was detected and the growth of E. coli is barely affected. However, at high PEI concentrations, dramatic changes in both structure and cell mechanics are observed. When immobilized on a flat surface, the ability of PEI to alter the membrane structure and reduce bacterial elasticity is diminished. We further probe this immobilization-induced effect by covalently attaching the polymer to the surface of polydopamine nanoparticles (PDNP). The nanoparticle-immobilized PEI (PDNP-PEI), though not able to induce major structural changes on the outer membrane of E. coli (in contrast to the flat surface), was able to bind to and reduce the Young’s modulus of the bacteria. Taken together, our data demonstrate that the state of polycationic polymers, whether bound or free—which greatly dictates their overall configuration—plays a major role on how they interact with and disrupt bacterial membranes. Full article
(This article belongs to the Special Issue The Role of Atomic Force Microscopy in Microbiology: Sensing the Cell Surface)
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10 pages, 243 KiB  
Communication
Longevity of Plant Pathogens in Dry Agricultural Seeds during 30 Years of Storage
by Guro Brodal and Åsmund Asdal
Microorganisms 2021, 9(10), 2175; https://doi.org/10.3390/microorganisms9102175 - 19 Oct 2021
Cited by 6 | Viewed by 2896
Abstract
Plant diseases may survive and be spread by infected seeds. In this study we monitored the longevity of 14 seed-borne pathogens in 9 crop species commonly grown in the Nordic countries, in addition to a sample of sclerotia of Sclerotinia sclerotiorum. The [...] Read more.
Plant diseases may survive and be spread by infected seeds. In this study we monitored the longevity of 14 seed-borne pathogens in 9 crop species commonly grown in the Nordic countries, in addition to a sample of sclerotia of Sclerotinia sclerotiorum. The data from the first 30 years of a 100-year seed storage experiment located in a natural −3.5 °C environment (permafrost) in Svalbard, Norway, are presented. To date, the pathogens, tested by traditional seed health testing methods (freezing blotter, agar plates, growing on tests), have survived. Linear regression analyses showed that the seed infection percentages of Drechslera dictyoides in meadow fescue, Drechslera phlei in timothy, and Septoria nodorum in wheat were significantly reduced compared to the percentages at the start of the experiment (from 63% to 34%, from 70% to 65%, and from 15% to 1%, respectively), and that Phoma betae in beet had increased significantly (from 43% to 56%). No trends in the infection percentage were observed over the years in Drechslera spp. in barley (fluctuating between 30% and 64%) or in Alternaria brassicicola in cabbage (fluctuating between 82% and 99%), nor in pathogens with low seed infection percentages at the start of the experiment. A major part of the stored sclerotia was viable after 30 years. To avoid the spread of seed-borne diseases, it is recommended that gene banks implement routines that avoid the use of infected seeds. Full article
(This article belongs to the Section Plant Microbe Interactions)
14 pages, 4305 KiB  
Article
Effect of 17β-Estradiol, Progesterone, and Tamoxifen on Neurons Infected with Toxoplasma gondii In Vitro
by María de la Luz Galván Ramírez, Judith Marcela Dueñas-Jiménez, Adrián Fernando Gutiérrez-Maldonado and Laura Rocío Rodríguez Pérez
Microorganisms 2021, 9(10), 2174; https://doi.org/10.3390/microorganisms9102174 - 19 Oct 2021
Cited by 1 | Viewed by 2192
Abstract
Toxoplasma gondii (T. gondii) is the causal agent of toxoplasmosis, which produces damage in the central nervous system (CNS). Toxoplasma–CNS interaction is critical for the development of disease symptoms. T. gondii can form cysts in the CNS; however, neurons are [...] Read more.
Toxoplasma gondii (T. gondii) is the causal agent of toxoplasmosis, which produces damage in the central nervous system (CNS). Toxoplasma–CNS interaction is critical for the development of disease symptoms. T. gondii can form cysts in the CNS; however, neurons are more resistant to this infection than astrocytes. The probable mechanism for neuron resistance is a permanent state of neurons in the interface, avoiding the replication of intracellular parasites. Steroids regulate the formation of Toxoplasma cysts in mice brains. 17β-estradiol and progesterone also participate in the control of Toxoplasma infection in glial cells in vitro. The aim of this study was to evaluate the effects of 17β-estradiol, progesterone, and their specific agonists–antagonists on Toxoplasma infection in neurons in vitro. Neurons cultured were pretreated for 48 h with 17β-estradiol or progesterone at 10, 20, 40, 80, or 160 nM/mL or tamoxifen 1 μM/mL plus 17β-estradiol at 10, 20, 40, 80, and 160 nM/mL. In other conditions, the neurons were pretreated during 48 h with 4,4′,4″-(4-propyl-[1H] pyrozole-1,3,5-triyl) trisphenol or 23-bis(4-hydroxyphenyl) propionitrile at 1 nM/mL, and mifepristone 1 µM/mL plus progesterone at 10, 20, 40, 80, and 160 nM/mL. Neurons were infected with 5000 tachyzoites of the T. gondii strain RH. The effect of 17β estradiol, progesterone, their agonists, or antagonists on Toxoplasma infection in neurons was evaluated at 24 and 48 h by immunocytochemistry. T. gondii replication was measured with the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide reduction assay. 17β-Estradiol alone or plus tamoxifen reduced infected neurons (50%) compared to the control at 48 h. Progesterone plus estradiol decreased the number of intracellular parasites at 48 h of treatment compared to the control (p < 0.001). 4,4′,4″-(4-propyl-[1H] pyrozole-1,3,5-triyl) trisphenol and 23-bis(4-hydroxyphenyl) propionitrile reduced infected neurons at 48 h of treatment significantly compared to the control (p < 0.05 and p < 0.001, respectively). The Toxoplasma infection process was decreased by the effect of 17β-estradiol alone or combined with tamoxifen or progesterone in neurons in vitro. These results suggest the essential participation of progesterone and estradiol and their classical receptors in the regulation of T. gondii neuron infection. Full article
(This article belongs to the Special Issue Advances in the Diagnosis, Detection, Epidemiology, and Control of Toxoplasma gondii)
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10 pages, 2166 KiB  
Article
Antimicrobial Efficacy of Contact Lens Solutions Assessed by ISO Standards
by Cindy McAnally, Rhonda Walters, Allison Campolo, Valerie Harris, Jamie King, Megan Thomas, Manal M Gabriel, Paul Shannon and Monica Crary
Microorganisms 2021, 9(10), 2173; https://doi.org/10.3390/microorganisms9102173 - 19 Oct 2021
Cited by 8 | Viewed by 3135
Abstract
Microbial keratitis (MK) is an eye infection caused by opportunistic bacteria or fungi, which may lead to sight-threatening corneal ulcers. These microorganisms can be introduced to the eye via improper contact lens usage or hygiene, or ineffective multipurpose solutions (MPSs) to disinfect daily [...] Read more.
Microbial keratitis (MK) is an eye infection caused by opportunistic bacteria or fungi, which may lead to sight-threatening corneal ulcers. These microorganisms can be introduced to the eye via improper contact lens usage or hygiene, or ineffective multipurpose solutions (MPSs) to disinfect daily wear contact lenses. Thus, the patient’s choice and use of these MPSs is a known risk factor for the development of MK. It is then critical to determine the efficacy of popular MPSs against ubiquitous ocular microorganisms. Therefore, we compare the efficacy of nine major MPSs on the global market against four different microorganism species, and with four different common contact lenses. In accordance with International Standards Organization protocol 14729 and 18259, the microorganisms were inoculated into each MPS with and without contact lenses, and held for the manufacturer’s disinfection time, 24 h, and 7 days after challenge with Serratia marcescens or Fusarium spp. Plates were incubated for 2–7 days and plate counts were conducted to determine the number of surviving microorganisms. The majority of MPSs demonstrated significantly higher disinfection efficacies without contact lenses. Broadly, among the microorganisms tested, the OPTI-FREE products (Puremoist, Express, and Replenish) maintained the highest disinfection efficacies at the manufacturer’s stated disinfection time when paired with any contact lens, compared with other MPSs. These were followed closely by RevitaLens and renu Advanced. MPSs containing dual biocides polyquaternium-1 and myristamidopropyl dimethylamine possessed the highest disinfection efficacy against multiple ocular pathogens. Full article
(This article belongs to the Special Issue Ocular Infections and Microbiota in Health and Disease)
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20 pages, 2950 KiB  
Article
Novel Phage-Derived Depolymerase with Activity against Proteus mirabilis Biofilms
by Cormac J. Rice, Stephen A. Kelly, Seamus C. O’Brien, Erinn M. Melaugh, Jan C. B. Ganacias, Zheng Hua Chai, Brendan F. Gilmore and Timofey Skvortsov
Microorganisms 2021, 9(10), 2172; https://doi.org/10.3390/microorganisms9102172 - 19 Oct 2021
Cited by 17 | Viewed by 6377
Abstract
The adherence of Proteus mirabilis to the surface of urinary catheters leads to colonization and eventual blockage of the catheter lumen by unique crystalline biofilms produced by these opportunistic pathogens, making P. mirabilis one of the leading causes of catheter-associated urinary tract infections. [...] Read more.
The adherence of Proteus mirabilis to the surface of urinary catheters leads to colonization and eventual blockage of the catheter lumen by unique crystalline biofilms produced by these opportunistic pathogens, making P. mirabilis one of the leading causes of catheter-associated urinary tract infections. The Proteus biofilms reduce efficiency of antibiotic-based treatment, which in turn increases the risk of antibiotic resistance development. Bacteriophages and their enzymes have recently become investigated as alternative treatment options. In this study, a novel Proteus bacteriophage (vB_PmiS_PM-CJR) was isolated from an environmental sample and fully characterized. The phage displayed depolymerase activity and the subsequent genome analysis revealed the presence of a pectate lyase domain in its tail spike protein. The protein was heterologously expressed and purified; the ability of the purified tail spike to degrade Proteus biofilms was tested. We showed that the application of the tail spike protein was able to reduce the adherence of bacterial biofilm to plastic pegs in a MBEC (minimum biofilm eradication concentration) assay and improve the survival of Galleria mellonella larvae infected with Proteus mirabilis. Our study is the first to successfully isolate and characterize a biofilm depolymerase from a Proteus phage, demonstrating the potential of this group of enzymes in treatment of Proteus infections. Full article
(This article belongs to the Special Issue Bacteriophages-Based Technologies for a One Health Society: Applications in Clinical, Veterinary, and Industrial Settings)
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12 pages, 2838 KiB  
Article
Detection of Clinical and Subclinical Lumpy Skin Disease Using Ear Notch Testing and Skin Biopsies
by Laetitia Aerts, Andy Haegeman, Ilse De Leeuw, Wannes Philips, Willem Van Campe, Isabelle Behaeghel, Laurent Mostin and Kris De Clercq
Microorganisms 2021, 9(10), 2171; https://doi.org/10.3390/microorganisms9102171 - 19 Oct 2021
Cited by 15 | Viewed by 2521
Abstract
Lumpy skin disease (LSD) diagnosis is primarily based on clinical surveillance complemented by PCR of lesion crusts or nodule biopsies. Since LSD can be subclinical, the sensitivity of clinical surveillance could be lower than expected. Furthermore, real-time PCR for the detection of LSD [...] Read more.
Lumpy skin disease (LSD) diagnosis is primarily based on clinical surveillance complemented by PCR of lesion crusts or nodule biopsies. Since LSD can be subclinical, the sensitivity of clinical surveillance could be lower than expected. Furthermore, real-time PCR for the detection of LSD viral DNA in blood samples from subclinical animals is only intermittently positive. Therefore, this study aimed to investigate an acceptable, easily applicable and more sensitive testing method for the detection of clinical and subclinical LSD. An animal experiment was conducted to investigate ear notches and biopsies from unaffected skin taken from the neck and dorsal back as alternatives to blood samples. It was concluded that for early LSD confirmation, normal skin biopsies and ear notches are less fit for purpose, as LSDV DNA is only detectable in these samples several days after it is detectable in blood samples. On the other hand, blood samples are less advisable for the detection of subclinical animals, while ear notches and biopsies were positive for LSD viral DNA in all subclinically infected animals by 16 days post infection. In conclusion, ear notches could be used for surveillance to detect subclinical animals after removing the clinical animals from a herd, to regain trade by substantiating the freedom of disease or to support research on LSDV transmission from subclinical animals. Full article
(This article belongs to the Special Issue Capripoxviruses: A Continuing Worldwide Threat to Sheep, Goats and Cattle)
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10 pages, 1249 KiB  
Article
Catalysis of Chlorovirus Production by the Foraging of Bursaria truncatella on Paramecia bursaria Containing Endosymbiotic Algae
by Zeina T. Al-Ameeli, Maitham A. Al-Sammak, John P. DeLong, David D. Dunigan and James L. Van Etten
Microorganisms 2021, 9(10), 2170; https://doi.org/10.3390/microorganisms9102170 - 18 Oct 2021
Cited by 5 | Viewed by 2541
Abstract
Chloroviruses are large viruses that replicate in chlorella-like green algae and normally exist as mutualistic endosymbionts (referred to as zoochlorellae) in protists such as Paramecium bursaria. Chlorovirus populations rise and fall in indigenous waters through time; however, the factors involved in these [...] Read more.
Chloroviruses are large viruses that replicate in chlorella-like green algae and normally exist as mutualistic endosymbionts (referred to as zoochlorellae) in protists such as Paramecium bursaria. Chlorovirus populations rise and fall in indigenous waters through time; however, the factors involved in these virus fluctuations are still under investigation. Chloroviruses attach to the surface of P. bursaria but cannot infect their zoochlorellae hosts because the viruses cannot reach the zoochlorellae as long as they are in the symbiotic phase. Predators of P. bursaria, such as copepods and didinia, can bring chloroviruses into contact with zoochlorellae by disrupting the paramecia, which results in an increase in virus titers in microcosm experiments. Here, we report that another predator of P. bursaria, Bursaria truncatella, can also increase chlorovirus titers. After two days of foraging on P. bursaria, B. truncatella increased infectious chlorovirus abundance about 20 times above the controls. Shorter term foraging (3 h) resulted in a small increase of chlorovirus titers over the controls and more foraging generated more chloroviruses. Considering that B. truncatella does not release viable zoochlorellae either during foraging or through fecal pellets, where zoochlorellae could be infected by chlorovirus, we suggest a third pathway of predator virus catalysis. By engulfing the entire protist and digesting it slowly, virus replication can occur within the predator and some of the virus is passed out through a waste vacuole. These results provide additional support for the hypothesis that predators of P. bursaria are important drivers of chlorovirus population sizes and dynamics. Full article
(This article belongs to the Special Issue Viruses of Plankton)
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12 pages, 2437 KiB  
Article
Identification of Potential Citrate Metabolism Pathways in Carnobacterium maltaromaticum
by Heng Li, Nancy E. Ramia, Frédéric Borges, Anne-Marie Revol-Junelles, Finn Kvist Vogensen and Jørgen J. Leisner
Microorganisms 2021, 9(10), 2169; https://doi.org/10.3390/microorganisms9102169 - 18 Oct 2021
Cited by 6 | Viewed by 3057
Abstract
In the present study, we describe the identification of potential citrate metabolism pathways for the lactic acid bacterium (LAB) Carnobacterium maltaromaticum. A phenotypic assay indicated that four of six C. maltaromaticum strains showed weak (Cm 6-1 and ATCC 35586) or even delayed [...] Read more.
In the present study, we describe the identification of potential citrate metabolism pathways for the lactic acid bacterium (LAB) Carnobacterium maltaromaticum. A phenotypic assay indicated that four of six C. maltaromaticum strains showed weak (Cm 6-1 and ATCC 35586) or even delayed (Cm 3-1 and Cm 5-1) citrate utilization activity. The remaining two strains, Cm 4-1 and Cm 1-2 gave negative results. Additional analysis showed no or very limited utilization of citrate in media containing 1% glucose and 22 or 30 mM citrate and inoculated with Cm 6-1 or ATCC 35586. Two potential pathways of citrate metabolism were identified by bioinformatics analyses in C. maltaromaticum including either oxaloacetate (pathway 1) or tricarboxylic compounds such as isocitrate and α-ketoglutarate (pathway 2) as intermediates. Genes encoding pathway 1 were present in two out of six strains while pathway 2 included genes present in all six strains. The two potential citrate metabolism pathways in C. maltaromaticum may potentially affect the sensory profiles of milk and soft cheeses subjected to growth with this species. Full article
(This article belongs to the Special Issue Functional Characterization of Lactic Acid Bacteria)
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16 pages, 3021 KiB  
Article
New Insights into the Relationships between Bacterial Dynamics and Water Quality of Aquaculture Systems Supplemented with Carbon Source and Biofilm Substratum
by Er-Meng Yu, Zhen-Chi Li, Zhi-Fei Li, Guang-Jun Wang, Yun Xia, Kai Zhang, Jing-Jing Tian, Wang-Bao Gong and Jun Xie
Microorganisms 2021, 9(10), 2168; https://doi.org/10.3390/microorganisms9102168 - 18 Oct 2021
Cited by 1 | Viewed by 2615
Abstract
Aquaculture is crucial for achieving the FAO’s goal of a world without hunger and malnutrition. Recently, biofilm substratum has been proposed as an effective means to control waste pollution caused by excessive nutrient inputs from aquaculture, but key bacterial communities involved in the [...] Read more.
Aquaculture is crucial for achieving the FAO’s goal of a world without hunger and malnutrition. Recently, biofilm substratum has been proposed as an effective means to control waste pollution caused by excessive nutrient inputs from aquaculture, but key bacterial communities involved in the remediation remain unclear. Here we reported a freshwater mesocosm study where the addition of biofilm substrata with external carbon effectively controlled the total ammonia nitrogen and improved fish growth. 16S rRNA study and Weighted UniFrac analysis revealed that bacterial compositions were significantly different (999 permutations, p-value < 0.01) between the biofilm-substrata-added and biofilm-substrata-free systems. Planctomycetes were found, as key bacteria benefited from the biofilm substrata addition and exerted the major function of ammonia nitrogen control. Our study demonstrated that the addition of biofilm substrata and an external carbon source favored fish growth and improved the aquaculture environment by the formation of a unique bacteria community. Full article
(This article belongs to the Section Environmental Microbiology)
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13 pages, 1179 KiB  
Review
Severity, Pathogenicity and Transmissibility of Delta and Lambda Variants of SARS-CoV-2, Toxicity of Spike Protein and Possibilities for Future Prevention of COVID-19
by Mehrnoosh Moghaddar, Ramtin Radman and Ian Macreadie
Microorganisms 2021, 9(10), 2167; https://doi.org/10.3390/microorganisms9102167 - 18 Oct 2021
Cited by 34 | Viewed by 7250
Abstract
The World Health Organization reports that SARS-CoV-2 has infected over 220 million people and claimed over 4.7 million lives globally. While there are new effective vaccines, the differences in behavior of variants are causing challenges in vaccine development or treatment. Here, we discuss [...] Read more.
The World Health Organization reports that SARS-CoV-2 has infected over 220 million people and claimed over 4.7 million lives globally. While there are new effective vaccines, the differences in behavior of variants are causing challenges in vaccine development or treatment. Here, we discuss Delta, a variant of concern, and Lambda, a variant of interest. They demonstrate high infectivity and are less responsive to the immune response in vaccinated individuals. In this review, we briefly summarize the reason for infectivity and the severity of the novel variants. Delta and Lambda variants exhibit more changes in NSPs proteins and the S protein, compared to the original Wuhan strain. Lambda also has numerous amino acid substitutions in NSPs and S proteins, plus a deletion in the NTD of S protein, leading to partial escape from neutralizing antibodies (NAbs) in vaccinated individuals. We discuss the role of furin protease and the ACE2 receptor in virus infection, hotspot mutations in the S protein, the toxicity of the S protein and the increased pathogenicity of Delta and Lambda variants. We discuss future therapeutic strategies, including those based on high stability of epitopes, conservation of the N protein and the novel intracellular antibody receptor, tripartite-motif protein 21 (TRIM21) recognized by antibodies against the N protein. Full article
(This article belongs to the Special Issue SARS-CoV-2: Epidemiology and Pathogenesis)
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8 pages, 1277 KiB  
Communication
Novel RNA Extraction Method for Dual RNA-seq Analysis of Pathogen and Host in the Early Stages of Yersinia pestis Pulmonary Infection
by Ofir Israeli, Inbar Cohen-Gihon, Moshe Aftalion, David Gur, Yaron Vagima, Ayelet Zauberman, Yinon Levy, Anat Zvi, Theodor Chitlaru, Emanuelle Mamroud and Avital Tidhar
Microorganisms 2021, 9(10), 2166; https://doi.org/10.3390/microorganisms9102166 - 18 Oct 2021
Cited by 1 | Viewed by 2374
Abstract
Pneumonic plague, caused by Yersinia pestis, is a rapidly progressing lethal infection. The various phases of pneumonic plague are yet to be fully understood. A well-established way to address the pathology of infectious diseases in general, and pneumonic plague in particular, is to [...] Read more.
Pneumonic plague, caused by Yersinia pestis, is a rapidly progressing lethal infection. The various phases of pneumonic plague are yet to be fully understood. A well-established way to address the pathology of infectious diseases in general, and pneumonic plague in particular, is to conduct concomitant transcriptomic analysis of the bacteria and the host. The analysis of dual RNA by RNA sequencing technology is challenging, due the difficulties of extracting bacterial RNA, which is overwhelmingly outnumbered by the host RNA, especially at the critical early time points post-infection (prior to 48 h). Here, we describe a novel technique that employed the infusion of an RNA preserving reagent (RNAlater) into the lungs of the animals, through the trachea, under deep anesthesia. This method enabled the isolation of stable dual mRNA from the lungs of mice infected with Y. pestis, as early as 24 h post-infection. The RNA was used for transcriptomic analysis, which provided a comprehensive gene expression profile of both the host and the pathogen. Full article
(This article belongs to the Special Issue Advances in RNA Biology in Pathogenic Microorganisms)
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11 pages, 1985 KiB  
Article
Characterization of “Candidatus Ehrlichia Pampeana” in Haemaphysalis juxtakochi Ticks and Gray Brocket Deer (Mazama gouazoubira) from Uruguay
by María Laura Félix, Sebastián Muñoz-Leal, Luis Andrés Carvalho, Diego Queirolo, Susana Remesar, María Teresa Armúa-Fernández and José Manuel Venzal
Microorganisms 2021, 9(10), 2165; https://doi.org/10.3390/microorganisms9102165 - 17 Oct 2021
Cited by 7 | Viewed by 2192
Abstract
Human ehrlichiosis are scantily documented in Uruguay. The aim of this study was to investigate the presence of Ehrlichia spp. in Haemaphysalis juxtakochi and in a gray brocket deer (Mazama gouazoubira) from Uruguay. The presence of Ehrlichia DNA was investigated in [...] Read more.
Human ehrlichiosis are scantily documented in Uruguay. The aim of this study was to investigate the presence of Ehrlichia spp. in Haemaphysalis juxtakochi and in a gray brocket deer (Mazama gouazoubira) from Uruguay. The presence of Ehrlichia DNA was investigated in free-living H. juxtakochi in five localities of southeast and northeast Uruguay, as well as blood, spleen, and ticks retrieved from a M. gouazoubira. Ehrlichia spp. DNA was detected in six out of 99 tick pools from vegetation, in the spleen of M. gouazoubira, and in one out of five pools of ticks feeding on this cervid. Bayesian inference analyses for three loci (16S rRNA, dsb, and groEL) revealed the presence of a new rickettsial organism, named herein as “Candidatus Ehrlichia pampeana”. This new detected Ehrlichia is phylogenetically related to those found in ticks from Asia, as well as Ehrlichia ewingii from USA and Cameroon. Although the potential pathogenicity of “Ca. E. pampeana” for humans is currently unknown, some eco-epidemiological factors may be relevant to its possible pathogenic role, namely: (i) the phylogenetic closeness with the zoonotic agent E. ewingii, (ii) the evidence of H. juxtakochi parasitizing humans, and (iii) the importance of cervids as reservoirs for zoonotic Ehrlichia spp. The molecular detection of “Ca. E. pampeana” represents the third Ehrlichia genotype described in Uruguay. Full article
(This article belongs to the Section Veterinary Microbiology)
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12 pages, 1104 KiB  
Article
Evidence of HIV-1 Genital Shedding after One Year of Antiretroviral Therapy in Females Recently Diagnosed in Bamako, Mali
by Abdelaye Keita, Josselin Rigaill, Sylvie Pillet, Youssouf Sereme, Souleymane Coulibaly, Fodé Diallo, Paul Verhoeven, Bruno Pozzetto, Tenin Aoua Thiero and Thomas Bourlet
Microorganisms 2021, 9(10), 2164; https://doi.org/10.3390/microorganisms9102164 - 17 Oct 2021
Cited by 1 | Viewed by 1793
Abstract
Little is known about the dynamic of HIV-1 shedding and resistance profiles in the female genital reservoir after antiretroviral therapy (ART) initiation in resource-limited countries (RLCs), which is critical for evaluating the residual sexual HIV-1 transmission risk. The present study aimed to evaluate [...] Read more.
Little is known about the dynamic of HIV-1 shedding and resistance profiles in the female genital reservoir after antiretroviral therapy (ART) initiation in resource-limited countries (RLCs), which is critical for evaluating the residual sexual HIV-1 transmission risk. The present study aimed to evaluate the efficacy of 1 year duration ART at blood and genital levels in females newly diagnosed for HIV-1 from three centers in Bamako, Mali. Seventy-eight consenting females were enrolled at the time of their HIV-1 infection diagnosis. HIV-1 RNA loads (Abbott Real-Time HIV-1 assay) were tested in blood and cervicovaginal fluids (CVF) before and 12 months after ART initiation. Primary and acquired resistances to ART were evaluated by ViroseqTM HIV-1 genotyping assay. The vaginal microbiota was analyzed using IonTorrentTM NGS technology (Thermo Fisher Scientific). Proportions of primary drug resistance mutations in blood and CVF were 13.4% and 25%, respectively. Discrepant profiles were observed in 25% of paired blood/CVF samples. The acquired resistance rate was 3.1% in blood. At month 12, undetectable HIV-1 RNA load was reached in 84.6% and 75% of blood and CVF samples, respectively. A vaginal dysbiosis was associated with HIV RNA shedding. Our findings emphasize the need of reinforcing education to improve retention in care system, as well as the necessity of regular virological monitoring before and during ART and of implementing vaginal dysbiosis diagnosis and treatment in RLCs. Full article
(This article belongs to the Special Issue Management and Antiretroviral Treatment of HIV Infection)
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13 pages, 1383 KiB  
Article
Occurrence of Hybrid Diarrhoeagenic Escherichia coli Associated with Multidrug Resistance in Environmental Water, Johannesburg, South Africa
by John Y. Bolukaoto, Atheesha Singh, Ntando Alfinete and Tobias G. Barnard
Microorganisms 2021, 9(10), 2163; https://doi.org/10.3390/microorganisms9102163 - 17 Oct 2021
Cited by 17 | Viewed by 2877
Abstract
This study was undertaken to determine the virulence and antibiotic resistance profiles of diarrhoeagenic Escherichia coli (DEC) in environmental waters of Johannesburg, South Africa. Samples were collected and cultured on selective media. An 11-plex PCR assay was used to differentiate five DEC, namely: [...] Read more.
This study was undertaken to determine the virulence and antibiotic resistance profiles of diarrhoeagenic Escherichia coli (DEC) in environmental waters of Johannesburg, South Africa. Samples were collected and cultured on selective media. An 11-plex PCR assay was used to differentiate five DEC, namely: enteroaggregative (EAEC), enterohaemorrhagic (EHEC), enteroinvasive (EIEC), enteropathogenic (EPEC) and enterotoxigenic (ETEC). The antibiotic resistance profile of isolates was determined using the VITEK®-2 automated system. The virulence profiles of 170 E. coli tested showed that 40% (68/170) were commensals and 60% (102/170) were pathogenic. EPEC had a prevalence of 19.2% (32/170), followed by ETEC 11.4% (19/170), EAEC 6% (10/170) and EHEC 3% (5/170). Hybrid DEC carrying a combination of simultaneously two and three pathogenic types was detected in twenty-eight and nine isolates, respectively. The antibiotic susceptibility testing showed isolates with multidrug resistance, including cefuroxime (100%), ceftazidime (86%), cefotaxime (81%) and cefepime (79%). This study highlighted the widespread occurrence of DEC and antibiotic resistance strains in the aquatic ecosystem of Johannesburg. The presence of hybrid pathotypes detected in this study is alarming and might lead to more severe diseases. There is a necessity to enhance surveillance in reducing the propagation of pathogenic and antibiotic-resistant strains in this area. Full article
(This article belongs to the Special Issue Bacterial Responses to Environmental Stress and Their Specific Contribution to Escherichia coli and Vibrio spp. Survival and Virulence 2.0)
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22 pages, 2946 KiB  
Article
Enrofloxacin Alters Fecal Microbiota and Resistome Irrespective of Its Dose in Calves
by Ashenafi Feyisa Beyi, Debora Brito-Goulart, Tyler Hawbecker, Brandon Ruddell, Alan Hassall, Renee Dewell, Grant Dewell, Orhan Sahin, Qijing Zhang and Paul J. Plummer
Microorganisms 2021, 9(10), 2162; https://doi.org/10.3390/microorganisms9102162 - 17 Oct 2021
Cited by 8 | Viewed by 2603
Abstract
Enrofloxacin is a fluoroquinolone drug used to prevent and control bovine respiratory disease (BRD) complex in multiple or single doses, ranging from 7.5 to 12.5 mg/kg body weight. Here, we examined the effects of high and low doses of a single subcutaneously injected [...] Read more.
Enrofloxacin is a fluoroquinolone drug used to prevent and control bovine respiratory disease (BRD) complex in multiple or single doses, ranging from 7.5 to 12.5 mg/kg body weight. Here, we examined the effects of high and low doses of a single subcutaneously injected enrofloxacin on gut microbiota and resistome in calves. Thirty-five calves sourced for this study were divided into five groups: control (n = 7), two low dose groups (n = 14, 7.5 mg/kg), and two high dose groups (n = 14, 12.5 mg/kg). One group in the low and high dose groups was challenged with Mannheimia haemolytica to induce BRD. Both alpha and beta diversities were significantly different between pre- and post-treatment microbial communities (q < 0.05). The high dose caused a shift in a larger number of genera than the low dose. Using metagenomic ProxiMeta Hi-C, 32 unique antimicrobial resistance genes (ARGs) conferring resistance to six antibiotic classes were detected with their reservoirs, and the high dose favored clonal expansion of ARG-carrying bacterial hosts. In conclusion, enrofloxacin treatment can alter fecal microbiota and resistome irrespective of its dose. Hi-C sequencing provides significant benefits for unlocking new insights into the ARG ecology of complex samples; however, limitations in sample size and sequencing depth suggest that further work is required to validate the findings. Full article
(This article belongs to the Special Issue Antimicrobial Stewardship in Food-Producing Animals)
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17 pages, 3913 KiB  
Article
Isolation and Characterization of Vibrio kanaloae as a Major Pathogen Associated with Mass Mortalities of Ark Clam, Scapharca broughtonii, in Cold Season
by Bowen Huang, Xiang Zhang, Chongming Wang, Changming Bai, Chen Li, Chenghua Li and Lusheng Xin
Microorganisms 2021, 9(10), 2161; https://doi.org/10.3390/microorganisms9102161 - 16 Oct 2021
Cited by 9 | Viewed by 2928
Abstract
High temperature is a risk factor for vibriosis outbreaks. Most vibrios are opportunistic pathogens that cause the mortality of aquatic animals at the vibrio optimal growth temperature (~25 °C), whereas a dominant Vibrio kanaloae strain SbA1-1 is isolated from natural diseased ark clams [...] Read more.
High temperature is a risk factor for vibriosis outbreaks. Most vibrios are opportunistic pathogens that cause the mortality of aquatic animals at the vibrio optimal growth temperature (~25 °C), whereas a dominant Vibrio kanaloae strain SbA1-1 is isolated from natural diseased ark clams (Scapharca broughtonii) during cold seasons in this study. Consistent symptoms and histopathological features reappeared under an immersion infection with SbA1-1 performed at 15 °C. The pathogenicity difference of SbA1-1 was assessed under different temperatures (15 °C and 25 °C). The cumulative mortality rates of ark clams were significantly higher at the low temperature (15 °C) than at the high temperature (25 °C); up to 98% on 16th day post SbA1-1 infection. While the growth ratio of SbA1-1 was retarded at the low temperature, the hemolytic activity and siderophores productivity of SbA1-1 were increased. This study constitutes the first isolation of V. kanaloae from the natural diseased ark clams (S. broughtonii) in cold seasons and the exposition of the dissimilar pathogenicity of SbA1-1 at a different temperature. All the above indicates that V. kanaloae constitutes a threat to ark clam culture, especially in cold seasons. Full article
(This article belongs to the Special Issue Advances in Bacterial Fish and Shellfish Diseases in Aquaculture)
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20 pages, 1163 KiB  
Review
Airport Malaria in Non-Endemic Areas: New Insights into Mosquito Vectors, Case Management and Major Challenges
by Leo Dilane Alenou and Josiane Etang
Microorganisms 2021, 9(10), 2160; https://doi.org/10.3390/microorganisms9102160 - 16 Oct 2021
Cited by 14 | Viewed by 4530
Abstract
Despite the implementation of preventive measures in airports and aircrafts, the risk of importing Plasmodium spp. infected mosquitoes is still present in malaria-free countries. Evidence suggests that mosquitoes have found a new alliance with the globalization of trade and climate change, leading to [...] Read more.
Despite the implementation of preventive measures in airports and aircrafts, the risk of importing Plasmodium spp. infected mosquitoes is still present in malaria-free countries. Evidence suggests that mosquitoes have found a new alliance with the globalization of trade and climate change, leading to an upsurge of malaria parasite transmission around airports. The resulting locally acquired form of malaria is called Airport malaria. However, piecemeal information is available, regarding its epidemiological and entomological patterns, as well as the challenges in the diagnosis, treatment, and prevention. Understanding these issues is a critical step towards a better implementation of control strategies. To cross reference this information, we conducted a systematic review on 135 research articles published between 1969 (when the first cases of malaria in airports were reported) and 2020 (i.e., 51 years later). It appears that the risk of malaria transmission by local mosquito vectors in so called malaria-free countries is not zero; this risk is more likely to be fostered by infected vectors coming from endemic countries by air or by sea. Furthermore, there is ample evidence that airport malaria is increasing in these countries. From 2010 to 2020, the number of cases in Europe was 7.4 times higher than that recorded during the 2000–2009 decade. This increase may be associated with climate change, increased international trade, the decline of aircraft disinsection, as well as delays in case diagnosis and treatment. More critically, current interventions are weakened by biological and operational challenges, such as drug resistance in malaria parasites and vector resistance to insecticides, and logistic constraints. Therefore, there is a need to strengthen malaria prevention and treatment for people at risk of airport malaria, and implement a rigorous routine entomological and epidemiological surveillance in and around airports. Full article
(This article belongs to the Special Issue Malaria in Non-Endemic Areas: Diagnosis, Therapy and Epidemiology)
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11 pages, 1544 KiB  
Article
The Combined Use of Cytokine Serum Values with Laboratory Parameters Improves Mortality Prediction of COVID-19 Patients: The Interleukin-15-to-Albumin Ratio
by Salma A. Rizo-Téllez, Lucia A. Méndez-García, Ana C. Rivera-Rugeles, Marcela Miranda-García, Aarón N. Manjarrez-Reyna, Rebeca Viurcos-Sanabria, Helena Solleiro-Villavicencio, Enrique Becerril-Villanueva, José D. Carrillo-Ruíz, Julian M. Cota-Arce, Angélica Álvarez-Lee, Marco A. De León-Nava and Galileo Escobedo
Microorganisms 2021, 9(10), 2159; https://doi.org/10.3390/microorganisms9102159 - 16 Oct 2021
Cited by 5 | Viewed by 2976
Abstract
Laboratory parameters display limited accuracy in predicting mortality in coronavirus disease 2019 (COVID-19) patients, as with serum albumin. Emerging evidence suggests that cytokine serum values may enhance the predictive capacity of albumin, especially interleukin (IL)-15. We thus investigated whether the use of the [...] Read more.
Laboratory parameters display limited accuracy in predicting mortality in coronavirus disease 2019 (COVID-19) patients, as with serum albumin. Emerging evidence suggests that cytokine serum values may enhance the predictive capacity of albumin, especially interleukin (IL)-15. We thus investigated whether the use of the IL-15-to-albumin ratio enables improving mortality prediction at hospital admission in a large group of COVID-19 patients. In this prospective cross-sectional study, we enrolled and followed up three hundred and seventy-eight patients with a COVID-19 diagnosis until hospital discharge or death. Two hundred and fifty-five patients survived, whereas one hundred and twenty-three died. Student’s T-test revealed that non-survivors had a significant two-fold increase in the IL-15-to-albumin ratio compared to survivors (167.3 ± 63.8 versus 74.2 ± 28.5), a difference that was more evident than that found for IL-15 or albumin separately. Likewise, mortality prediction considerably improved when using the IL-15-to-albumin ratio with a cut-off point > 105.4, exhibiting an area under the receiver operating characteristic curve of 0.841 (95% Confidence Interval, 0.725–0.922, p < 0.001). As we outlined here, this is the first study showing that combining IL-15 serum values with albumin improves mortality prediction in COVID-19 patients. Full article
(This article belongs to the Special Issue COVID-19: Focusing on Epidemiologic, Virologic, and Clinical Studies)
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27 pages, 2013 KiB  
Review
Lactobacillus kefiranofaciens: From Isolation and Taxonomy to Probiotic Properties and Applications
by Marina Georgalaki, Georgia Zoumpopoulou, Rania Anastasiou, Maria Kazou and Effie Tsakalidou
Microorganisms 2021, 9(10), 2158; https://doi.org/10.3390/microorganisms9102158 - 16 Oct 2021
Cited by 19 | Viewed by 5836
Abstract
One of the main lactic acid bacterial species found in the kefir grain ecosystem worldwide is Lactobacillus kefiranofaciens, exhibiting strong auto-aggregation capacity and, therefore, being involved in the mechanism of grain formation. Its occurrence and dominance in kefir grains of various types [...] Read more.
One of the main lactic acid bacterial species found in the kefir grain ecosystem worldwide is Lactobacillus kefiranofaciens, exhibiting strong auto-aggregation capacity and, therefore, being involved in the mechanism of grain formation. Its occurrence and dominance in kefir grains of various types of milk and geographical origins have been verified by culture-dependent and independent approaches using multiple growth media and regions of the 16S rRNA gene, respectively, highlighting the importance of their combination for its taxonomic identification. L. kefiranofaciens comprises two subspecies, namely kefiranofaciens and kefirgranum, but only the first one is responsible for the production of kefiran, the water-soluble polysaccharide, which is a basic component of the kefir grain and famous for its technological as well as health-promoting properties. L. kefiranofaciens, although very demanding concerning its growth conditions, can be involved in mechanisms affecting intestinal health, immunomodulation, control of blood lipid levels, hypertension, antimicrobial action, and protection against diabetes and tumors. These valuable bio-functional properties place it among the most exquisite candidates for probiotic use as a starter culture in the production of health-beneficial dairy foods, such as the kefir beverage. Full article
(This article belongs to the Special Issue Probiotics and Prebiotics in Animal Health and Food Safety)
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13 pages, 2777 KiB  
Article
The Shiga Toxin Receptor Globotriaosylceramide as Therapeutic Target in Shiga Toxin E. coli Mediated HUS
by Wouter J. C. Feitz, Romy Bouwmeester, Thea J. A. M. van der Velden, Susan Goorden, Christoph Licht, Lambert P. J. W. van den Heuvel and Nicole C. A. J. van de Kar
Microorganisms 2021, 9(10), 2157; https://doi.org/10.3390/microorganisms9102157 - 16 Oct 2021
Cited by 7 | Viewed by 3129
Abstract
In 90% of the cases, childhood hemolytic uremic syndrome (HUS) is caused by an infection with the Shiga toxin (Stx) producing E. coli bacteria (STEC-HUS). Stx preferentially binds to its receptor, the glycosphingolipid, globotriaosylceramide (Gb3), present on the surface of human kidney cells [...] Read more.
In 90% of the cases, childhood hemolytic uremic syndrome (HUS) is caused by an infection with the Shiga toxin (Stx) producing E. coli bacteria (STEC-HUS). Stx preferentially binds to its receptor, the glycosphingolipid, globotriaosylceramide (Gb3), present on the surface of human kidney cells and various organs. In this study, the glycosphingolipid pathway in endothelial cells was explored as therapeutic target for STEC-HUS. Primary human glomerular microvascular endothelial cells (HGMVECs) and human blood outgrowth endothelial cells (BOECs) in quiescent and activated state were pre-incubated with Eliglustat (Cerdelga®; glucosylceramide synthase inhibitor) or Agalsidase alpha (Replagal®; human cell derived alpha-galactosidase) in combination with various concentrations of Stx2a. Preincubation of endothelial cells with Agalsidase resulted in an increase of α-galactosidase activity in the cell, but had no effect on the binding of Stx to the cell surface when compared to control cells. However, the incubation of both types of endothelial cells incubated with or without the pro-inflammatory cytokine TNFα in combination with Eliglustat resulted in significant decrease of Stx binding to the cell surface, a decrease in protein synthesis by Stx2a, and diminished cellular Gb3 levels as compared to control cells. In conclusion, inhibition of the synthesis of Gb3 may be a potential future therapeutic target to protect against (further) endothelial damage caused by Stx. 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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24 pages, 4691 KiB  
Article
Diversity of the Tryptophanase Gene and Its Evolutionary Implications in Living Organisms
by Bharath Reddy Boya, Prasun Kumar, Jin-Hyung Lee and Jintae Lee
Microorganisms 2021, 9(10), 2156; https://doi.org/10.3390/microorganisms9102156 - 15 Oct 2021
Cited by 11 | Viewed by 3177
Abstract
Tryptophanase encoded by the gene tnaA is a pyridoxal phosphate-dependent enzyme that catalyses the conversion of tryptophan to indole, which is commonly used as an intra- and interspecies signalling molecule, particularly by microbes. However, the production of indole is rare in eukaryotic organisms. [...] Read more.
Tryptophanase encoded by the gene tnaA is a pyridoxal phosphate-dependent enzyme that catalyses the conversion of tryptophan to indole, which is commonly used as an intra- and interspecies signalling molecule, particularly by microbes. However, the production of indole is rare in eukaryotic organisms. A nucleotide and protein database search revealed tnaA is commonly reported in various Gram-negative bacteria, but that only a few Gram-positive bacteria and archaea possess the gene. The presence of tnaA in eukaryotes, particularly protozoans and marine organisms, demonstrates the importance of this gene in the animal kingdom. Here, we document the distribution of tnaA and its acquisition and expansion among different taxonomic groups, many of which are usually categorized as non-indole producers. This study provides an opportunity to understand the intriguing role played by tnaA, and its distribution among various types of organisms. Full article
(This article belongs to the Section Systems Microbiology)
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15 pages, 1106 KiB  
Review
Whole Genome Sequencing Analysis of Salmonella enterica Serovar Typhi: History and Current Approaches
by Wan Ratmaazila Wan Wan Makhtar, Izwan Bharudin, Nurul Hidayah Samsulrizal and Nik Yusnoraini Yusof
Microorganisms 2021, 9(10), 2155; https://doi.org/10.3390/microorganisms9102155 - 15 Oct 2021
Cited by 9 | Viewed by 5813
Abstract
In recent years, the advance in whole-genome sequencing technology has changed the study of infectious diseases. The emergence of genome sequencing has improved the understanding of infectious diseases, which has revamped many fields, such as molecular microbiology, epidemiology, infection control, and vaccine production. [...] Read more.
In recent years, the advance in whole-genome sequencing technology has changed the study of infectious diseases. The emergence of genome sequencing has improved the understanding of infectious diseases, which has revamped many fields, such as molecular microbiology, epidemiology, infection control, and vaccine production. In this review we discuss the findings of Salmonella enterica serovar Typhi genomes, publicly accessible from the initial complete genome to the recent update of Salmonella enterica serovar Typhi genomes, which has greatly improved Salmonella enterica serovar Typhi and other pathogen genomic research. Significant information on genetic changes, evolution, antimicrobial resistance, virulence, pathogenesis, and investigation from the genome sequencing of S. Typhi is also addressed. This review will gather information on the variation of the Salmonella enterica serovar Typhi genomes and hopefully facilitate our understanding of their genome evolution, dynamics of adaptation, and pathogenesis for the development of the typhoid point-of-care diagnostics, medications, and vaccines. Full article
(This article belongs to the Special Issue Salmonella and Salmonellosis)
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18 pages, 50409 KiB  
Article
Microbial Adhesion and Biofilm Formation on Bioactive Surfaces of Ti-35Nb-7Zr-5Ta Alloy Created by Anodization
by Laiza Maria Grassi Fais, Luana de Sales Leite, Bárbara Araújo dos Reis, Ana Lúcia Roselino Ribeiro, Luis Geraldo Vaz and Marlise Inêz Klein
Microorganisms 2021, 9(10), 2154; https://doi.org/10.3390/microorganisms9102154 - 15 Oct 2021
Cited by 1 | Viewed by 1720
Abstract
This study evaluated the microbial colonization (adhesion and biofilm) on modified surfaces of a titanium alloy, Ti-35Nb-7Zr-5Ta, anodized with Ca and P or F ions, with and without silver deposition. The chemical composition, surface topography, roughness (Ra), and surface free energy were evaluated [...] Read more.
This study evaluated the microbial colonization (adhesion and biofilm) on modified surfaces of a titanium alloy, Ti-35Nb-7Zr-5Ta, anodized with Ca and P or F ions, with and without silver deposition. The chemical composition, surface topography, roughness (Ra), and surface free energy were evaluated before and after the surface modifications (anodizing). Adhesion and biofilm formation on saliva-coated discs by primary colonizing species (Streptococcus sanguinis, Streptococcus gordonii, Actinomyces naeslundii) and a periodontal pathogen (Porphyromonasgingivalis) were assessed. The surfaces of titanium alloys were modified after anodizing with volcano-shaped micropores with Ca and P or nanosized with F, both with further silver deposition. There was an increase in the Ra values after micropores formation; CaP surfaces became more hydrophilic than other surfaces, showing the highest polar component. For adhesion, no difference was detected for S. gordonii on all surfaces, and some differences were observed for the other three species. No differences were found for biofilm formation per species on all surfaces. However, S. gordonii biofilm counts on distinct surfaces were lower than S. sanguinis, A. naeslundii, and P. gingivalis on some surfaces. Therefore, anodized Ti-35Nb-7Zr-5Ta affected microbial adhesion and subsequent biofilm, but silver deposition did not hinder the colonization of these microorganisms. Full article
(This article belongs to the Special Issue Anti-biofouling Coating Application-Promising Strategy to Prevent Infection)
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18 pages, 1072 KiB  
Article
Serologic Evidence of Occupational Exposure to Avian Influenza Viruses at the Wildfowl/Poultry/Human Interface
by Maria Alessandra De Marco, Mauro Delogu, Marzia Facchini, Livia Di Trani, Arianna Boni, Claudia Cotti, Giulia Graziosi, Diana Venturini, Denise Regazzi, Valentina Ravaioli, Fausto Marzadori, Matteo Frasnelli, Maria Rita Castrucci and Elisabetta Raffini
Microorganisms 2021, 9(10), 2153; https://doi.org/10.3390/microorganisms9102153 - 15 Oct 2021
Cited by 11 | Viewed by 2794
Abstract
Ecological interactions between wild aquatic birds and outdoor-housed poultry can enhance spillover events of avian influenza viruses (AIVs) from wild reservoirs to domestic birds, thus increasing the related zoonotic risk to occupationally exposed workers. To assess serological evidence of AIV infection in workers [...] Read more.
Ecological interactions between wild aquatic birds and outdoor-housed poultry can enhance spillover events of avian influenza viruses (AIVs) from wild reservoirs to domestic birds, thus increasing the related zoonotic risk to occupationally exposed workers. To assess serological evidence of AIV infection in workers operating in Northern Italy at the wildfowl/poultry interface or directly exposed to wildfowl, serum samples were collected between April 2005 and November 2006 from 57 bird-exposed workers (BEWs) and from 7 unexposed controls (Cs), planning three sample collections from each individual. Concurrently, AIV surveillance of 3587 reared birds identified 4 AIVs belonging to H10N7, H4N6 and H2N2 subtypes while serological analysis by hemagglutination inhibition (HI) assay showed recent infections caused by H1, H2, H4, H6, H10, H11, H12, and H13 subtypes. Human sera were analyzed for specific antibodies against AIVs belonging to antigenic subtypes from H1 to H14 by using HI and virus microneutralization (MN) assays as a screening and a confirmatory test, respectively. Overall, antibodies specific to AIV-H3, AIV-H6, AIV-H8, and AIV-H9 were found in three poultry workers (PWs) and seropositivity to AIV-11, AIV-H13—still detectable in October 2017—in one wildlife professional (WP). Furthermore, seropositivity to AIV-H2, accounting for previous exposure to the “extinct” H2N2 human influenza viruses, was found in both BEWs and Cs groups. These data further emphasize the occupational risk posed by zoonotic AIV strains and show the possible occurrence of long-lived antibody-based immunity following AIV infections in humans. Full article
(This article belongs to the Special Issue Ecology of Influenza A Viruses)
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24 pages, 2244 KiB  
Review
Cdk8 Kinase Module: A Mediator of Life and Death Decisions in Times of Stress
by Brittany Friedson and Katrina F. Cooper
Microorganisms 2021, 9(10), 2152; https://doi.org/10.3390/microorganisms9102152 - 15 Oct 2021
Cited by 10 | Viewed by 5978
Abstract
The Cdk8 kinase module (CKM) of the multi-subunit mediator complex plays an essential role in cell fate decisions in response to different environmental cues. In the budding yeast S. cerevisiae, the CKM consists of four conserved subunits (cyclin C and its cognate [...] Read more.
The Cdk8 kinase module (CKM) of the multi-subunit mediator complex plays an essential role in cell fate decisions in response to different environmental cues. In the budding yeast S. cerevisiae, the CKM consists of four conserved subunits (cyclin C and its cognate cyclin-dependent kinase Cdk8, Med13, and Med12) and predominantly negatively regulates a subset of stress responsive genes (SRG’s). Derepression of these SRG’s is accomplished by disassociating the CKM from the mediator, thus allowing RNA polymerase II-directed transcription. In response to cell death stimuli, cyclin C translocates to the mitochondria where it induces mitochondrial hyper-fission and promotes regulated cell death (RCD). The nuclear release of cyclin C requires Med13 destruction by the ubiquitin-proteasome system (UPS). In contrast, to protect the cell from RCD following SRG induction induced by nutrient deprivation, cyclin C is rapidly destroyed by the UPS before it reaches the cytoplasm. This enables a survival response by two mechanisms: increased ATP production by retaining reticular mitochondrial morphology and relieving CKM-mediated repression on autophagy genes. Intriguingly, nitrogen starvation also stimulates Med13 destruction but through a different mechanism. Rather than destruction via the UPS, Med13 proteolysis occurs in the vacuole (yeast lysosome) via a newly identified Snx4-assisted autophagy pathway. Taken together, these findings reveal that the CKM regulates cell fate decisions by both transcriptional and non-transcriptional mechanisms, placing it at a convergence point between cell death and cell survival pathways. Full article
(This article belongs to the Special Issue Adaptation, Aging, and Cell Death in Yeast Stress Response: Models, Mechanisms and Applications)
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13 pages, 27008 KiB  
Article
Structure and Topology Prediction of Phage Adhesion Devices Using AlphaFold2: The Case of Two Oenococcus oeni Phages
by Adeline Goulet and Christian Cambillau
Microorganisms 2021, 9(10), 2151; https://doi.org/10.3390/microorganisms9102151 - 14 Oct 2021
Cited by 21 | Viewed by 3263
Abstract
Lactic acid bacteria (LAB) are important microorganisms in food fermentation. In the food industry, bacteriophages (phages or bacterial viruses) may cause the disruption of LAB-dependent processes with product inconsistencies and economic losses. LAB phages use diverse adhesion devices to infect their host, yet [...] Read more.
Lactic acid bacteria (LAB) are important microorganisms in food fermentation. In the food industry, bacteriophages (phages or bacterial viruses) may cause the disruption of LAB-dependent processes with product inconsistencies and economic losses. LAB phages use diverse adhesion devices to infect their host, yet the overall picture of host-binding mechanisms remains incomplete. Here, we aimed to determine the structure and topology of the adhesion devices of two lytic siphophages, OE33PA and Vinitor162, infecting the wine bacteria Oenococcus oeni. These phages possess adhesion devices with a distinct composition and morphology and likely use different infection mechanisms. We primarily used AlphaFold2, an algorithm that can predict protein structure with unprecedented accuracy, to obtain a 3D model of the adhesion devices’ components. Using our prior knowledge of the architecture of the LAB phage host-binding machineries, we also reconstituted the topology of OE33PA and Vinitor162 adhesion devices. While OE33PA exhibits original structures in the assembly of its bulky adhesion device, Vinitor162 harbors several carbohydrate-binding modules throughout its long and extended adhesion device. Overall, these results highlight the ability of AlphaFold2 to predict protein structures and illustrate its great potential in the study of phage structures and host-binding mechanisms. Full article
(This article belongs to the Special Issue Siphophages Infecting Food Processing Bacteria)
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8 pages, 253 KiB  
Article
In Vitro Synergism of Penicillin and Ceftriaxone against Enterococcus faecalis
by Lara Thieme, Simon Briggs, Eamon Duffy, Oliwia Makarewicz and Mathias W. Pletz
Microorganisms 2021, 9(10), 2150; https://doi.org/10.3390/microorganisms9102150 - 14 Oct 2021
Cited by 3 | Viewed by 3528
Abstract
Enterococcus faecalis infective endocarditis is commonly treated with intravenous ampicillin/ceftriaxone combination therapy. Ampicillin, however, is unsuitable for outpatient parenteral antibiotic therapy (OPAT) regimens due to its instability in 24 h continuous infusors, and has been successfully replaced by benzylpenicillin used together with ceftriaxone [...] Read more.
Enterococcus faecalis infective endocarditis is commonly treated with intravenous ampicillin/ceftriaxone combination therapy. Ampicillin, however, is unsuitable for outpatient parenteral antibiotic therapy (OPAT) regimens due to its instability in 24 h continuous infusors, and has been successfully replaced by benzylpenicillin used together with ceftriaxone in a few small case series. Since in vitro synergy data of penicillin/ceftriaxone against E. faecalis are still lacking, checkerboard assays were performed for 28 clinical E. faecalis isolates and one laboratory standard strain. Synergistic effects (both lowest and median FICI) were observed for penicillin/ceftriaxone in 15/29 isolates, while ampicillin/ceftriaxone exhibited synergism in 22/29 isolates. For isolates with ceftriaxone MICs ≤ 256 mg/L, the addition of free ceftriaxone trough concentrations to penicillin or ampicillin resulted in comparable synergistic effects for both combinations. In contrast, for isolates with ceftriaxone MICs ≥ 512 mg/L free ceftriaxone trough concentrations were only sufficient to exhibit synergistic effects in combination with ampicillin, but not penicillin. This study suggests that benzylpenicillin/ceftriaxone would be expected to be suitable for the OPAT treatment of enterococcal endocarditis for E. faecalis isolates with ceftriaxone MICs ≤ 256 mg/L. However, combination therapy would be expected to provide no advantage over benzylpenicillin monotherapy for isolates with ceftriaxone MICs ≥ 512 mg/L. Further investigation is required to analyse the relationship between ceftriaxone susceptibility and penicillin/ceftriaxone synergy, especially for isolates with ceftriaxone MICs of 64 to 512 mg/L. Full article
(This article belongs to the Special Issue Antimicrobial Testing (AMT))
15 pages, 38950 KiB  
Article
Predicting the Role of the Human Gut Microbiome in Constipation Using Machine-Learning Methods: A Meta-Analysis
by Yutao Chen, Tong Wu, Wenwei Lu, Weiwei Yuan, Mingluo Pan, Yuan-Kun Lee, Jianxin Zhao, Hao Zhang, Wei Chen, Jinlin Zhu and Hongchao Wang
Microorganisms 2021, 9(10), 2149; https://doi.org/10.3390/microorganisms9102149 - 14 Oct 2021
Cited by 8 | Viewed by 4330
Abstract
(1) Background: Constipation is a common condition that affects the health and the quality of life of patients. Recent studies have suggested that the gut microbiome is associated with constipation, but these studies were mainly focused on a single research cohort. Thus, we [...] Read more.
(1) Background: Constipation is a common condition that affects the health and the quality of life of patients. Recent studies have suggested that the gut microbiome is associated with constipation, but these studies were mainly focused on a single research cohort. Thus, we aimed to construct a classification model based on fecal bacterial and identify the potential gut microbes’ biomarkers. (2) Methods: We collected 3056 fecal amplicon sequence data from five research cohorts. The data were subjected to a series of analyses, including alpha- and beta-diversity analyses, phylogenetic profiling analyses, and systematic machine learning to obtain a comprehensive understanding of the association between constipation and the gut microbiome. (3) Results: The alpha diversity of the bacterial community composition was higher in patients with constipation. Beta diversity analysis evidenced significant partitions between the two groups on the base of gut microbiota composition. Further, machine learning based on feature selection was performed to evaluate the utility of the gut microbiome as the potential biomarker for constipation. The Gradient Boosted Regression Trees after chi2 feature selection was the best model, exhibiting a validation performance of 70.7%. (4) Conclusions: We constructed an accurate constipation discriminant model and identified 15 key genera, including Serratia, Dorea, and Aeromonas, as possible biomarkers for constipation. Full article
(This article belongs to the Section Gut Microbiota)
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