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Microbiol. Res., Volume 12, Issue 4 (December 2021) – 18 articles

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11 pages, 1024 KiB  
Article
Potential Associations of Mutations within the HIV-1 Env and Gag Genes Conferring Protease Inhibitor (PI) Drug Resistance
by Ntombikhona F. Maphumulo and Michelle L. Gordon
Microbiol. Res. 2021, 12(4), 967-977; https://doi.org/10.3390/microbiolres12040071 - 15 Dec 2021
Cited by 1 | Viewed by 2335
Abstract
An increasing number of patients in Africa are experiencing virological failure on a second-line antiretroviral protease inhibitor (PI)-containing regimen, even without resistance-associated mutations in the protease region, suggesting a potential role of other genes in PI resistance. Here, we investigated the prevalence of [...] Read more.
An increasing number of patients in Africa are experiencing virological failure on a second-line antiretroviral protease inhibitor (PI)-containing regimen, even without resistance-associated mutations in the protease region, suggesting a potential role of other genes in PI resistance. Here, we investigated the prevalence of mutations associated with Lopinavir/Ritonavir (LPV/r) failure in the Envelope gene and the possible coevolution with mutations within the Gag-protease (gag-PR) region. Env and Gag-PR sequences generated from 24 HIV-1 subtype C infected patients failing an LPV/r inclusive treatment regimen and 344 subtype C drug-naïve isolates downloaded from the Los Alamos Database were analyzed. Fisher’s exact test was used to determine the differences in mutation frequency. Bayesian network probability was applied to determine the relationship between mutations occurring within the env and gag-PR regions and LPV/r treatment. Thirty-five mutations in the env region had significantly higher frequencies in LPV/r-treated patients. A combination of Env and Gag-PR mutations was associated with a potential pathway to LPV/r resistance. While Env mutations were not directly associated with LPV/r resistance, they may exert pressure through the Gag and minor PR mutation pathways. Further investigations using site-directed mutagenesis are needed to determine the impact of Env mutations alone and in combination with Gag-PR mutations on viral fitness and LPV/r efficacy. Full article
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17 pages, 2029 KiB  
Article
Isolation and Optimization of Culture Conditions of a Bioflocculant-Producing Fungi from Kombucha Tea SCOBY
by Phakamani H. Tsilo, Albertus K. Basson, Zuzingcebo G. Ntombela, Tsolanku S. Maliehe and Rajasekhar V. S. R. Pullabhotla
Microbiol. Res. 2021, 12(4), 950-966; https://doi.org/10.3390/microbiolres12040070 - 14 Dec 2021
Cited by 11 | Viewed by 3743
Abstract
Biolocculants are gaining attention in research due to their environmental friendliness and innocuousness to human in comparison to the conventional flocculants. The present study aimed to investigate the ability of fungi from Kombucha tea SCOBY to produce effective bioflocculant in bulk. A 16S [...] Read more.
Biolocculants are gaining attention in research due to their environmental friendliness and innocuousness to human in comparison to the conventional flocculants. The present study aimed to investigate the ability of fungi from Kombucha tea SCOBY to produce effective bioflocculant in bulk. A 16S rRNA gene sequence analysis was utilized to identify the isolate. The medium composition (carbon and nitrogen sources) and culture conditions (inoculum size, temperature, shaking speed, pH, and time) were optimized using one-factor-at-a-time method. The functional groups, morphology, and crystallinity of the bioflocculant were evaluated using Fourier transform infrared (FT-IR), scan electron microscope (SEM) and X-ray diffractometry (XRD). The fungus was found to be Pichia kudriavzevii MH545928.1. It produced a bioflocculant with flocculating activity of 99.1% under optimum conditions; 1% (v/v) inoculum size, glucose and peptone as nutrient sources, 35 °C, pH 7 and the shaking speed of 140 rpm for 60 h. A cumulus-like structure was revealed by SEM; FT-IR displayed the presence of hydroxyl, carboxyl, amine, and thiocynates. The XRD analysis demonstrated the bioflocculant to have big particles with diffraction peaks at 10° and 40° indicating its crystallinity. Based on the obtained results, P. kudriavzevii MH545928.1 has potential industrial applicability as a bioflocculant producer. Full article
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12 pages, 6487 KiB  
Case Report
Infections in a Tertiary Care Pediatric Center in Southern Poland during the SARS-CoV-2 Pandemic
by Joanna Klepacka, Zuzanna Zakrzewska, Małgorzata Czogała, Adriana Chromy-Czoniszwili, Szymon Skoczeń and Krzysztof Fyderek
Microbiol. Res. 2021, 12(4), 938-949; https://doi.org/10.3390/microbiolres12040069 - 09 Dec 2021
Viewed by 2081
Abstract
The worldwide surge of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic and led governments to control spread of the virus and provide care for the population affected by the infection. Although, in children, COVID-19 is usually asymptomatic or [...] Read more.
The worldwide surge of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic and led governments to control spread of the virus and provide care for the population affected by the infection. Although, in children, COVID-19 is usually asymptomatic or mild (except PIMS), the pandemic affected the whole socioeconomic system and led to the overwhelming of healthcare facilities. We report retrospective observations of the prevalence of various infectious diseases during the SARS-CoV-2 pandemic in a tertiary multidisciplinary pediatric center in Southern Poland. We retrospectively evaluated the impact of the SARS-CoV-2 pandemic on the number of other infections diagnosed in a pediatric tertiary care referral center. Our analysis included the period from the beginning of February to the end of April 2020 (spring pandemic wave), and from the beginning of September to the end of November 2020 (autumn pandemic wave). We compared them to the appropriate periods of 2019. The evaluation included blood, urine, stool and lover respiratory tract cultures as well as virological investigations. Additionally, the costs of antibiotics and antifungal drugs in selected departments were assessed. Our analysis showed considerable reduction in the majority of common infections except for influenza A and B. The microbiological data correspond with economical summary of antibiotic costs, which were significantly lower during the pandemic. One exception was the number of positive blood cultures, which increased even though the overall number of tests was lower. A general reduction of the number of infections diagnosed in children could result from the implemented preventative measures associated with the pandemic and the generally increased awareness of the risk of infection among parents and guardians. The treatment of the most serious diseases continued as it did before the pandemic. To our knowledge, this study is the first attempt to assess the impact of the COVID-19 pandemic on the prevalence of infections in a large pediatric center. Further research on the impact of the COVID-19 pandemic on the healthcare systems is necessary. Full article
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22 pages, 869 KiB  
Review
Probiotics as Therapeutic Tools against Pathogenic Biofilms: Have We Found the Perfect Weapon?
by Gabriele Meroni, Simona Panelli, Gianvincenzo Zuccotti, Claudio Bandi, Lorenzo Drago and Dario Pistone
Microbiol. Res. 2021, 12(4), 916-937; https://doi.org/10.3390/microbiolres12040068 - 06 Dec 2021
Cited by 9 | Viewed by 12620
Abstract
Bacterial populations inhabiting a variety of natural and human-associated niches have the ability to grow in the form of biofilms. A large part of pathological chronic conditions, and essentially all the bacterial infections associated with implanted medical devices or prosthetics, are caused by [...] Read more.
Bacterial populations inhabiting a variety of natural and human-associated niches have the ability to grow in the form of biofilms. A large part of pathological chronic conditions, and essentially all the bacterial infections associated with implanted medical devices or prosthetics, are caused by microorganisms embedded in a matrix made of polysaccharides, proteins, and nucleic acids. Biofilm infections are generally characterized by a slow onset, mild symptoms, tendency to chronicity, and refractory response to antibiotic therapy. Even though the molecular mechanisms responsible for resistance to antimicrobial agents and host defenses have been deeply clarified, effective means to fight biofilms are still required. Lactic acid bacteria (LAB), used as probiotics, are emerging as powerful weapons to prevent adhesion, biofilm formation, and control overgrowth of pathogens. Hence, using probiotics or their metabolites to quench and interrupt bacterial communication and aggregation, and to interfere with biofilm formation and stability, might represent a new frontier in clinical microbiology and a valid alternative to antibiotic therapies. This review summarizes the current knowledge on the experimental and therapeutic applications of LAB to interfere with biofilm formation or disrupt the stability of pathogenic biofilms. Full article
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9 pages, 301 KiB  
Article
ESBL/AmpC-Producing Enterobacteriaceae Fecal Colonization in Dogs after Elective Surgery
by Adriana Belas, Joana Correia, Cátia Marques, Luís Telo da Gama and Constança Pomba
Microbiol. Res. 2021, 12(4), 907-915; https://doi.org/10.3390/microbiolres12040067 - 24 Nov 2021
Viewed by 2600
Abstract
The purpose of this study was to evaluate the presence and load of ESBL/AmpC-producing Enterobacteriaceae fecal carriage in healthy dogs. Fecal samples were collected from dogs submitted to surgical procedures (n = 25). Fecal samples were collected before surgery (BS) and after [...] Read more.
The purpose of this study was to evaluate the presence and load of ESBL/AmpC-producing Enterobacteriaceae fecal carriage in healthy dogs. Fecal samples were collected from dogs submitted to surgical procedures (n = 25). Fecal samples were collected before surgery (BS) and after surgery (AS). β-lactamases were detected by PCR. Statistical analyses were performed with SAS software (v.9.4); a p value ≤ 0.05 was considered statistically significant. The ESBL/AmpC-producing Enterobacteriaceae bacteria species detected in this study were E. coli, K. pneumoniae and E. cloacae. TEM, and CTX-M-1 group genes were the most frequent β-lactamases detected. The number of dogs colonized with 3GC-resistant Enterobacteriaceae bacteria was significantly higher in the AS (63.6%, n = 14/22) group compared to in the BS group (20.0%, n = 5/25, p = 0.0033). The ESBL/AmpC-producing bacteria fecal load was significantly higher in the AS group compared to in the BS (p = 0.025) group. This study shows that 3GC-resistant Enterobacteriaceae and ESBLs/AmpC producers in the veterinary clinical practice are a concern and highlights the need to implement preventive measures to minimize their spread. Full article
8 pages, 282 KiB  
Review
Eumycetoma Medical Treatment: Past, Current Practice, Latest Advances and Perspectives
by Emmanuel Edwar Siddig, Ayman Ahmed, Yousif Ali, Sahar Mubarak Bakhiet, Nouh Saad Mohamed, Eiman Siddig Ahmed and Ahmed Hassan Fahal
Microbiol. Res. 2021, 12(4), 899-906; https://doi.org/10.3390/microbiolres12040066 - 15 Nov 2021
Cited by 10 | Viewed by 3589
Abstract
Mycetoma is a neglected tropical disease that is associated with poor communities and socioeconomically impaired individuals in the tropical and sub-tropical areas. Interestingly, the disease is caused by either bacteria (actinomycetoma) or fungus (eumycetoma). The latter form of the disease, eumycetoma, is the [...] Read more.
Mycetoma is a neglected tropical disease that is associated with poor communities and socioeconomically impaired individuals in the tropical and sub-tropical areas. Interestingly, the disease is caused by either bacteria (actinomycetoma) or fungus (eumycetoma). The latter form of the disease, eumycetoma, is the most common type in Africa. Eumycetoma is characterized by a prolonged disease duration and low cure rate. The effective case management of eumycetoma largely depends on the accurate diagnosis and identification of the causative agent to the species level and evaluating its susceptibility to the available drugs. This review summarizes the currently available and used antifungal agents for the treatment of eumycetoma and discusses optimizing the newly developed antifungals as a potential second line for eumycetoma treatment. Full article
11 pages, 1139 KiB  
Article
Dynamics of Microbial Shedding in Market Pigs during Fasting and the Influence of Alginate Hydrogel Bead Supplementation during Transportation
by Mariana Fernandez, Arlene Garcia, David A. Vargas and Alexandra Calle
Microbiol. Res. 2021, 12(4), 888-898; https://doi.org/10.3390/microbiolres12040065 - 13 Nov 2021
Cited by 1 | Viewed by 2419
Abstract
The shedding of foodborne pathogenic bacteria by food-animals can be affected by multiple factors, such as animal health, diet, stress, and environmental conditions. The practices that come with transport involve fasting, handling, mixing with unfamiliar pigs, and fluctuating temperatures. These practices, especially fasting [...] Read more.
The shedding of foodborne pathogenic bacteria by food-animals can be affected by multiple factors, such as animal health, diet, stress, and environmental conditions. The practices that come with transport involve fasting, handling, mixing with unfamiliar pigs, and fluctuating temperatures. These practices, especially fasting and transport, can increase the microbial load in the feces of animals. The use of alginate hydrogels is a novel delivery system that can be a potential food safety intervention during transport to induce satiety and provide electrolytes to the animal’s system. This study sought to observe microbial shedding as affected by fasting and hydrogel bead supplementation during transport. Sixty market pigs were subjected to a 12 h fasting period and an additional 4 h transport period, in which a treatment group was fed hydrogel beads and a control group was not. Sampling points were before fast (BF), before transport (BT), and after transport (AT). Fecal samples were collected from every animal at each sampling point. Results from this study showed a significant increase in the concentrations of both Enterobacteriaceae and Escherichia coli between the before fast (BF) and after transport (AT) sampling points. However, no difference (p > 0.05) was found between the treatment (hydrogel) and control (no hydrogel) during transport. Moreover, no significant difference was found in the prevalence of Salmonella and E. coli O157:H7 at the three different sampling points, or between the treatment and control groups. Full article
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10 pages, 2618 KiB  
Article
Prevalence and Diversity of Hepatitis Virus Markers among Patients with Acute Febrile Jaundice in Chad
by Fissou Henry Yandai, Kuan Abdoulaye Traore, Ali Mahamat Moussa, Bruno Lalidia Ouoba, Jean Bienvenue Ouoba, Mahamat Ali Bolti, Mahamat Fayiz Abakar, Mathieu Hota, Kadidja Gamougam, Bessimbaye Nadlao, Jean-Claude Uwimbabazi, Nadji Emmanuel Tao, Bongo Nare Ngandolo, Pierre Roques and Nicolas Barro
Microbiol. Res. 2021, 12(4), 878-887; https://doi.org/10.3390/microbiolres12040064 - 12 Nov 2021
Cited by 1 | Viewed by 2792
Abstract
Only a minority of the patients with acute febrile jaundice evaluated through the Yellow Fever surveillance program were found positive for antibodies against Yellow Fever Virus (YFV). In order to characterize patients with acute febrile jaundice negative for YFV, we collected 255 sera [...] Read more.
Only a minority of the patients with acute febrile jaundice evaluated through the Yellow Fever surveillance program were found positive for antibodies against Yellow Fever Virus (YFV). In order to characterize patients with acute febrile jaundice negative for YFV, we collected 255 sera between January to December 2019. We screened for HBV antigens, and antibodies against HCV and HEV. The seroprevalences observed were 10.6% (27/255) for HBV, 2% (5/255) for HCV, 17.3% (44/255) for HEV IgG, 4.3% (11/255) for HEV IgM, and 12.5% (32/255) for both IgG and IgM HEV. Prevalence of HEV was significantly higher in females than males (p < 0.01). HEV IgG prevalence was highest in those 20–29 years old, but the highest incidence rate (IgM positive) was in children 0–9 years old. Exposure to HEV was higher in the Sahelian zone (55.8%, 95% CI: 40.97–70.66) than in the Sudanese zone (30.2%, 95% CI: 24.01–36.37, p = 0.003). The high prevalence rates and hepatitis virus diversity underline the challenge of routine clinical diagnosis in Chad’s Yellow Fever surveillance program. Full article
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16 pages, 12728 KiB  
Article
Biodiversity of Soil Bacterial Communities from the Sasso Fratino Integral Nature Reserve
by Lara Mitia Castronovo, Sara Del Duca, Sofia Chioccioli, Alberto Vassallo, Donatella Fibbi, Ester Coppini, Piero Chioccioli, Giacomo Santini, Marco Zaccaroni and Renato Fani
Microbiol. Res. 2021, 12(4), 862-877; https://doi.org/10.3390/microbiolres12040063 - 12 Nov 2021
Cited by 4 | Viewed by 2501
Abstract
The Sasso Fratino Integral Nature Reserve (Italy) aims to protect nature and territory. Since no anthropic activities are allowed, it represents a good model to study the bacterial community of a wild environment. The aim of this work was to characterise the cultivable [...] Read more.
The Sasso Fratino Integral Nature Reserve (Italy) aims to protect nature and territory. Since no anthropic activities are allowed, it represents a good model to study the bacterial community of a wild environment. The aim of this work was to characterise the cultivable and the total bacterial community of soil samples from the reserve in terms of taxonomy, composition, and structure. Seven soil samples were collected at different altitudes, and the chemical composition, the total and the cultivable microbiota, and the antibiotic resistance profiles of isolates were investigated. Total bacterial communities, studied through Next Generation Sequences analysis, included 390 genera. Samples differed in terms of microbial composition basing on the different altitude/vegetation of collection points. Random Amplified Polymorphic DNA Analysis (RAPD) allowed to identify 82 haplotypes out of 158 bacterial isolates. The taxonomic identification through 16S rDNA sequencing revealed that the strains were affiliated to 21 genera. Antibiotic resistance profiles of bacteria were also investigated, highlighting a high resistance against streptomycin and kanamycin. This work represents the first description of the soil bacterial community from the Natural Reserve of Sasso Fratino, and it is the first study considering the soil microbiota of an Italian integral nature reserve. Full article
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15 pages, 1424 KiB  
Article
Development of HIV Drug Resistance in a Cohort of Adults on First-Line Antiretroviral Therapy in Tanzania during the Stavudine Era
by Raphael Z. Sangeda, Perpétua Gómes, Soo-Yon Rhee, Fausta Mosha, Ricardo J. Camacho, Eric Van Wijngaerden, Eligius F. Lyamuya and Anne-Mieke Vandamme
Microbiol. Res. 2021, 12(4), 847-861; https://doi.org/10.3390/microbiolres12040062 - 12 Nov 2021
Cited by 5 | Viewed by 2730
Abstract
As more HIV patients start combination antiretroviral therapy (cART), the emergence of HIV drug resistance (HIVDR) is inevitable. This will have consequences for the transmission of HIVDR, the success of ART, and the nature and trend of the epidemic. We recruited a cohort [...] Read more.
As more HIV patients start combination antiretroviral therapy (cART), the emergence of HIV drug resistance (HIVDR) is inevitable. This will have consequences for the transmission of HIVDR, the success of ART, and the nature and trend of the epidemic. We recruited a cohort of 223 patients starting or continuing their first-line cART in Tanzania towards the end of the stavudine era in 2010. Patients were then followed for one year. Of those with a viral load test at baseline and follow-up time, 34% had a detectable viral load at the one-year endpoint. For 41 patients, protease and reverse transcriptase genotyping were successful. Eighteen samples were from cART-naïve patients, and 23 samples were taken under therapy either at baseline for cART-experienced patients or from follow-up samples for both cART–naïve and cART–experienced patients. The isolates were subtype A, followed by C and D in 41.5%, 22%, and 12.2% of the patients, respectively. No transmitted HIVDR was detected, as scored using the surveillance drug resistance mutations (DRMs) list. However, in 3 of the 18 samples from cART-naïve patients, the clinical Rega interpretation algorithm scored 44D or 138A as non-nucleoside reverse transcriptase inhibitor (NNRTI) resistance-associated polymorphisms. The most observed nucleoside reverse transcriptase inhibitor (NRTI) mutation was 184V. The mutation was found in 16 patients, causing resistance to lamivudine and emtricitabine. Nineteen patients had NNRTI resistance mutations, the most common of which was 103N, observed in eight patients. These high levels of resistance call for regular drug resistance surveillance in Tanzania to inform the control of the emergence and transmission of HIVDR. Full article
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7 pages, 208 KiB  
Review
Streptomyces, Greek Habitats and Novel Pharmaceuticals: A Promising Challenge
by Paris Laskaris and Amalia D. Karagouni
Microbiol. Res. 2021, 12(4), 840-846; https://doi.org/10.3390/microbiolres12040061 - 06 Nov 2021
Cited by 3 | Viewed by 2874
Abstract
Bacteria of the genus Streptomyces produce a very large number of secondary metabolites, many of which are of vital importance to modern medicine. There is great interest in the discovery of novel pharmaceutical compounds derived from strepomycetes, since novel antibiotics, anticancer and compounds [...] Read more.
Bacteria of the genus Streptomyces produce a very large number of secondary metabolites, many of which are of vital importance to modern medicine. There is great interest in the discovery of novel pharmaceutical compounds derived from strepomycetes, since novel antibiotics, anticancer and compounds for treating other conditions are urgently needed. Greece, as proven by recent research, possesses microbial reservoirs with a high diversity of Streptomyces populations, which provide a rich pool of strains with potential pharmaceutical value. This review examines the compounds of pharmaceutical interest that have been derived from Greek Streptomyces isolates. The compounds reported in the literature include antibiotics, antitumor compounds, biofilm inhibitors, antiparasitics, bacterial toxin production inhibitors and antioxidants. The streptomycete biodiversity of Greek environments remains relatively unexamined and is therefore a very promising resource for potential novel pharmaceuticals. Full article
11 pages, 1164 KiB  
Article
Culturable Endophytic Fungi from Glycyrrhiza inflata Distributed in Xinjiang, China with Antifungal Activity
by Gan Gu, Xiaowei Jia, Weixuan Wang, Peng Li, Siji Zhao, Zhiyao Zhou, Ruya Yin, Daowan Lai, Suqin Song and Ligang Zhou
Microbiol. Res. 2021, 12(4), 829-839; https://doi.org/10.3390/microbiolres12040060 - 04 Nov 2021
Cited by 2 | Viewed by 2414
Abstract
A total of 99 endophytic fungal isolates were obtained from the roots of Glycyrrhiza inflata, which was a traditional medicinal plant mainly distributed in Xinjiang, China. Twenty-two distinct isolates were selected for further taxonomical identification by morphological traits and internal transcribed spacer [...] Read more.
A total of 99 endophytic fungal isolates were obtained from the roots of Glycyrrhiza inflata, which was a traditional medicinal plant mainly distributed in Xinjiang, China. Twenty-two distinct isolates were selected for further taxonomical identification by morphological traits and internal transcribed spacer (ITS) rRNA gene sequence analysis. Eleven genera were identified, among which Aspergillus, Alternaria and Fusarium were dominant. The crude extracts of 22 distinct identified fungi were successively evaluated for their antifungal activities on three rice fungal pathogens using the method of hyphal radial growth rate. Among them, the crude extract of Alternaria an-gustiovoidea Glinf007 showed the significantly mycelial growth inhibitory activity. The results demonstrated that G. inflata contained a diversity of culturable endophytic fungi, which could produce natural antimicrobial compounds that might be of great value to the agriculture and pharmaceutical industries. Full article
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17 pages, 2890 KiB  
Article
Secondary Metabolite Production and Terpenoid Biosynthesis in Endophytic Fungi Cladosporium cladosporioides Isolated from Wild Cymbopogon martinii (Roxb.) Wats
by Hemalatha Jayaram, Vinutha Marigowda and Kunigal Jagadishchandra Thara Saraswathi
Microbiol. Res. 2021, 12(4), 812-828; https://doi.org/10.3390/microbiolres12040059 - 01 Nov 2021
Cited by 6 | Viewed by 3242
Abstract
Endophytic fungi Cladosporium cladosporioides (F1-MH810309) and Cladosporium tenuissimum (F2-MN715834) from the leaf of wild Cymbopogon martinii (MT90507) were isolated and selected based on the persistent occurrence during different seasons of the year. They were identified [...] Read more.
Endophytic fungi Cladosporium cladosporioides (F1-MH810309) and Cladosporium tenuissimum (F2-MN715834) from the leaf of wild Cymbopogon martinii (MT90507) were isolated and selected based on the persistent occurrence during different seasons of the year. They were identified based on the morphological features and molecular characterization (ITS sequence), and later deposited at NCBI. Phytochemical studies on F1, F2 and host extracts showed the presence of alkaloids, flavonoids, phenols, terpenoids and tannins. The GC-MS of F1 extract (control) under the axenic condition revealed compounds like hexadecane, heptadecane,2,4-Ditert-butylphenol, E-14 hexadecenal, geraniol, geranyl acetate and cubenol similar to the host. The GC-MS of F2 extract (control) revealed metabolites that were unique. Further, both F1 and F2 were cultured in the supplementation of different concentrations (5%, 10%, 15% and 20%) of the host plant extract (an-axenic condition). The GC-MS of F1 extracts (test) exhibited good growth and showed the gradual increased production of terpenoid compounds whereas the F2 (test) did not show any growth. These compounds such as hyrdoxymenthol, nor-borneol, cedralacetate, α-cyclogeraniol, campesterol, β-cyclogeraniol, linalool oxide,2,3-boranediol, citronellyltiglate and 2,3-pinanediol were produced in a minor quantity and were known as biotransformed forms of the precursor compounds present in the host extract. In comparison, only F1 was able to produce terpenoids similar to the host species both in axenic and an-axenic conditions. Hence from the current study, the endophytic fungus F1 isolated from wild C. martinii for the first time can serve as a better resource for the bioprospection of an important terpenoid and its metabolites. Full article
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19 pages, 1238 KiB  
Article
Retrospective Observational Study on Microbial Contamination of Ulcerative Foot Lesions in Diabetic Patients
by Federica Petrone, Anna Maria Giribono, Laura Massini, Laura Pietrangelo, Irene Magnifico, Umberto Marcello Bracale, Roberto Di Marco, Renata Bracale and Giulio Petronio Petronio
Microbiol. Res. 2021, 12(4), 793-811; https://doi.org/10.3390/microbiolres12040058 - 01 Nov 2021
Viewed by 2257
Abstract
According to recent studies, there are almost 435 million people worldwide with diabetes mellitus. It is estimated that of these 148 million will develop Diabetic foot ulcers (DFUs) during their lifetime, of which 35 to 50% will be infected. In this scenario, the [...] Read more.
According to recent studies, there are almost 435 million people worldwide with diabetes mellitus. It is estimated that of these 148 million will develop Diabetic foot ulcers (DFUs) during their lifetime, of which 35 to 50% will be infected. In this scenario, the presence and frequency of pathogenic microorganisms and their level of susceptibility to the most frequent classes of antibiotics used to treat this pathological condition from patients with DFUs admitted to the outpatient clinic of vascular surgery of the Federico II University Hospital of Naples from January 2019 to March 2021 were investigated. Furthermore, the diabetic population characteristics under study (i.e., general, clinical, and comorbidities) and the pathogenic bacteria isolated from lesions were also considered. Bacterial strains poorly susceptible to antibiotics were more frequent in polymicrobial infections than in monomicrobial infections. β-Lactams showed the highest levels of resistance, followed by fluoroquinolones, aminoglycosides, and finally macrolides. The main findings of the study demonstrated that the occurrence of resistant microorganisms is the dominant factor in ulcer healing; thus it is essential to investigate the antibiotics’ susceptibility before setting antibiotic therapy to avoid inappropriate prescriptions that would affect the treatment and increase the development and spread of antibiotic resistance. Full article
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14 pages, 2350 KiB  
Article
Diversity Profiling of Seed Associated Endophytic Microbiome in Important Species of Caricaceae Family
by Basavaprabhu L. Patil, Karthik S. Narayan and Amulya M. Gopalkrishna
Microbiol. Res. 2021, 12(4), 779-792; https://doi.org/10.3390/microbiolres12040057 - 28 Oct 2021
Cited by 2 | Viewed by 3105
Abstract
Background: Plant associated endophytic microbes play an important role in plant’s growth and development. After seed germination, the seed associated endophytes rapidly colonize the seedlings and help in their growth and protection against pathogens. This study was aimed to understand the diversity in [...] Read more.
Background: Plant associated endophytic microbes play an important role in plant’s growth and development. After seed germination, the seed associated endophytes rapidly colonize the seedlings and help in their growth and protection against pathogens. This study was aimed to understand the diversity in the endophytic microbial population associated with the seeds of papaya (Carica papaya) and its wild relatives from Vasconcellea genus (family: Caricaceae). The species of Vasconcellea genus are widely used to introgress virus resistance in cultivated varieties of papaya. Hence, the diversity of seed associated endophytic microbes and their gene functional analysis was carried out through next generation sequencing of the microbial 16S rRNA and ITS sequences. Results: The 16S rRNA amplicon analysis revealed that the number of operational taxonomic units (OTUs) was higher for the endophytic bacteria, ranging between 144–204 when compared to 41–69 OTUs for the endophytic fungi. The bacterial phylum Proteobacteria was the most abundant seed associated phylum, with 64.7–72.8% abundance, across all four species of Caricaceae family, followed by Firmicutes (13.6–26.1%), Patescibacteria (1.1–2%) and Actinobacteria (0.7–2.7%). With respect to the diversity of bacteria by abundance indices, Vasconcellea goudotiana had the highest OTUs of 204, followed by 177 in V. cauliflora, 156 in V. cundinamarcensis, and 144 in C. papaya. The alpha diversity indices and functional analysis revealed the differences in the OTUs and the functional annotations among the above four plant species. The fungal OTUs were in the range of 41–69; however, only a small fraction of them could be taxonomically classified. Conclusion: Our microbiome studies reveal the differences in the seed associated endophytic microbial community across the four plant species of Caricaceae family. This study also unravels the composition of endophytic microbial population associated with the seeds of different plant species of Caricaceae family and their gene functions. It also provides an insight into both culturable and nonculturable endophytic microbes. Further this study reveals that domestication of Carica papaya might have resulted into reduced microbial diversity when compared to their wild relatives from Vasconcellea genus. Full article
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14 pages, 2451 KiB  
Article
Keratinocytes and Activation of TREM-1 Pathway in Cutaneous Leishmaniasis Lesions
by Sara Nunes, Mariana Rosa Ampuero, Ícaro Bonyek-Silva, Reinan Lima, Filipe Rocha Lima, Sérgio Marcos Arruda, Ricardo Khouri, Pablo Rafael Silveira Oliveira, Aldina Barral, Viviane Sampaio Boaventura, Cláudia Ida Brodskyn and Natalia Machado Tavares
Microbiol. Res. 2021, 12(4), 765-778; https://doi.org/10.3390/microbiolres12040056 - 07 Oct 2021
Cited by 2 | Viewed by 2804
Abstract
Triggering Receptor Expressed on Myeloid Cells 1 (TREM-1) amplifies the immune response, operating synergistically with Toll-Like Receptors (TLRs) in the production of inflammatory mediators. TREM-1 signaling depends on the adapter protein DAP12, which results in the activation of NFkB, the expression of inflammatory [...] Read more.
Triggering Receptor Expressed on Myeloid Cells 1 (TREM-1) amplifies the immune response, operating synergistically with Toll-Like Receptors (TLRs) in the production of inflammatory mediators. TREM-1 signaling depends on the adapter protein DAP12, which results in the activation of NFkB, the expression of inflammatory genes, and the release of antimicrobial peptides, such as Beta-defensin 2. We evaluated the activation of the TREM-1 signaling pathways in Cutaneous Leishmaniasis (CL) caused by Leishmania braziliensis and linage human keratinocytes exposed to these parasites since the host immune response against Leishmania plays a critical role in promoting parasite killing but also participates in inflammation and tissue damage. We analyzed publicly available transcriptome data from the lesions of CL patients. In the CL biopsies, we found increased expression of the molecules involved in the TREM-1 pathway. We then validated these findings with RT-qPCR and immunohistochemistry in newly obtained biopsies. Surprisingly, we found a strong labeling of TREM-1 in keratinocytes, prompting the hypothesis that increased TREM-1 activation may be the result of tissue damage. However, increased TREM-1 expression was only seen in human lineage keratinocytes following parasite stimulation. Moreover, no up-regulation of TREM-1 expression was observed in the skin lesions caused by other non-infectious inflammatory diseases. Together, these findings indicate that L. braziliensis (Lb) induces the expression of the TREM-1 receptor in tissue keratinocytes regardless of tissue damage, suggesting that non-immune skin cells may play a role in the inflammatory response of CL. Full article
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12 pages, 2157 KiB  
Communication
Bioinformatics Analysis Identifies a Small ORF in the Genome of Fish Nidoviruses of Genus Oncotshavirus Predicted to Encode a Novel Integral Protein
by Frederick Kibenge, Ashley McKibbon, Molly Kibenge and Yingwei Wang
Microbiol. Res. 2021, 12(4), 753-764; https://doi.org/10.3390/microbiolres12040055 - 06 Oct 2021
Cited by 1 | Viewed by 2493
Abstract
Genome sequence analysis of Atlantic salmon bafinivirus (ASBV) revealed a small open reading frame (ORF) predicted to encode a Type I membrane protein with an N-terminal cleaved signal sequence (110 aa), likely an envelope (E) protein. Bioinformatic analyses showed that the predicted protein [...] Read more.
Genome sequence analysis of Atlantic salmon bafinivirus (ASBV) revealed a small open reading frame (ORF) predicted to encode a Type I membrane protein with an N-terminal cleaved signal sequence (110 aa), likely an envelope (E) protein. Bioinformatic analyses showed that the predicted protein is strikingly similar to the coronavirus E protein in structure. This is the first report to identify a putative E protein ORF in the genome of members of the Oncotshavirus genus (subfamily Piscavirinae, family Tobaniviridae, order Nidovirales) and, if expressed would be the third family (after Coronaviridae and Arteriviridae) within the order to have the E protein as a major structural protein. Full article
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9 pages, 272 KiB  
Article
Medicinal Plant Feed Additives Enhanced Survivability and Growth Performance of Clarias gariepinus (African Catfish) against Bacterial Infection
by Adebisi Musefiu Tiamiyu, Isaac Olufemi Olatoye, Okunlade Akinsola Olayemi, Temitope Cyrus Ekundayo, Olufemi Bolarinwa Adedeji and Reuben Chukwuka Okocha
Microbiol. Res. 2021, 12(4), 744-752; https://doi.org/10.3390/microbiolres12040054 - 29 Sep 2021
Cited by 6 | Viewed by 3260
Abstract
The growth performance and survivability enhancement potential of some medicinal plant feed additives for combatting Pseudomonad infections in Clarias gariepinus were evaluated. Three medicinal plants (5 g/kg Allium sativum, 10 g/kg Chromolaena odorata and 10 g/kg Talinum triangulare) were incorporated [...] Read more.
The growth performance and survivability enhancement potential of some medicinal plant feed additives for combatting Pseudomonad infections in Clarias gariepinus were evaluated. Three medicinal plants (5 g/kg Allium sativum, 10 g/kg Chromolaena odorata and 10 g/kg Talinum triangulare) were incorporated separately into a basic diet. Juvenile Clarias gariepinus (n = 150, 53.05 ± 0.23 g), randomised into four groups, were fed for 42 days. The control group was fed with a non-supplemented diet. Growth parameters were determined and thereafter ten fish from each group, randomly selected, were inoculated intraperitoneally with pathogenic Pseudomonas aeruginosa (0.2 mL culture containing 1.4 × 106 cfu/mL). Their survivability was observed for 7 days based on mortality rate and relative level of protection (RLP). Mean weight gains were higher in all treated groups and significantly higher (p < 0.05) in the group of fish fed with 5 g/kg Allium sativum diet compared with the control. The lowest mortality rate (20%) and highest RLP (75) was recorded in the group fed with10 g/kg Chromolaena odorata. The results suggest that medicinal plant feed additives enhanced growth and survival of the cultured Clarias gariepinus. The study recommends 5 g/kg Allium sativum and 10 g/kg Chromolaena odorata diet supplementations as an effective growth promoter and anti-Pseudomonas aeruginosa agent, respectively, for Clarias gariepinus production. Full article
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