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Bacteria, Volume 1, Issue 4 (December 2022) – 8 articles

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8 pages, 1237 KiB  
Article
Prevalence of Escherichia coli Producing Extended Spectrum Beta-Lactamase (ESBL) Driven Septicaemia in Children Aged 0–2 Years in Two Districts Hospitals in Yaounde, Cameroon
by Cécile Ingrid Djuikoue, Paule Dana Djouela Djoulako, Rodrigue Kamga Wouambo, Suzie Titsamp Lacmago, Audrey Dayomo, Hortense Gonsu Kamga, Benjamin D. Thumamo Pokam and Teke Apalata
Bacteria 2022, 1(4), 294-301; https://doi.org/10.3390/bacteria1040022 - 7 Dec 2022
Cited by 4 | Viewed by 2768
Abstract
Septicaemia is public health problem worldwide with a high rate of mortality among children. Epidemiological data on this phenomenon in Cameroon are still scarce. This study aimed to determine the prevalence and associated factors to septicaemia due to E. coli strains producing extended [...] Read more.
Septicaemia is public health problem worldwide with a high rate of mortality among children. Epidemiological data on this phenomenon in Cameroon are still scarce. This study aimed to determine the prevalence and associated factors to septicaemia due to E. coli strains producing extended spectrum beta-lactamase (ESBL) in two hospitals in Yaoundé, Cameroon. A prospective, cross-sectional study was conducted on infants aged 0 to 2 years old at the consultation and neonatology care unit of two district hospitals of Yaoundé (UTHY and YGOPH) during a period of seven months (from August 2019 to March 2020). Each blood sample collected per infant was cultured in hemoline performance vials, and bacterial strains were identified using the Api-20 E system. In addition, an antibiotic resistant profile of isolates as well as the ESBL production were performed in accordance with the recommendations of the Antibiogram committee of the French Society of Microbiology 2019. Data were analysed in Epi-Info7.0 and for p less than 0.05, the difference was statistically significant. Of the 300 children enrolled, 130 (43.33%) were blood culture positive, and E. coli. was the most prevalent (69.23% (90/130)). Then antibiotic susceptibility test revealed that 77 over 90 E. coli strains were resistant to penicillin (with 85.55% to amoxicillin), and 34.44% were producing ESBL. Factors such as immunodeficiency, being on antibiotics, and particularly taking β-lactam were significantly associated with E. coli ESBL production ([aOR = 19.93; p = 0.0001], [aOR = 1.97; p = 0.04], and [aOR = 3.54; p = 0.01], respectively). Moreover, co-resistance to aminoglycosides, quinolones, fluoroquinolones, and cotrimoxazole were also found. This study highlighted a high prevalence of E. coli ESBL in blood samples of children aged 0–2 years in Yaoundé and prompts the development of more efficient strategies against E. coli ESBL associated mortality in infants in Cameroon. Full article
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15 pages, 5252 KiB  
Article
Isolation and Characterization of Bacillus velezensis from Lake Bogoria as a Potential Biocontrol of Fusarium solani in Phaseolus vulgaris L.
by Tofick B. Wekesa, Vitalis W. Wekesa, Justus M. Onguso, Eliud N. Wafula and Ndinda Kavesu
Bacteria 2022, 1(4), 279-293; https://doi.org/10.3390/bacteria1040021 - 17 Nov 2022
Cited by 5 | Viewed by 4185
Abstract
The common bean (Phaseolus vulgaris L.) is a significant vegetable crop, grown because it is a rich source of protein, carbohydrates, and vitamin B complex. Fusarium solani and Rhizoctonia solani are the most widely known pathogens contributing to large yield losses for [...] Read more.
The common bean (Phaseolus vulgaris L.) is a significant vegetable crop, grown because it is a rich source of protein, carbohydrates, and vitamin B complex. Fusarium solani and Rhizoctonia solani are the most widely known pathogens contributing to large yield losses for this crop. The use of cultural and chemical control practices has been ineffective. Therefore, a sustainable, affordable, and effective control method is urgently required. In this study, we aimed to isolate and characterize Bacillus velezensis from Lake Bogoria as a potential biocontrol agent for Fusarium solani. Bacteria were isolated from soil and sediments using the serial dilution technique. Molecular characterization was performed using the 16S rRNA gene. A total of 13 bacteria were isolated from soil and sediments. Based on the partial sequences, BLAST analysis showed two isolates, B20 (Bacillus velezensis strain QH03-23) and B30 (Bacillus velezensis strain JS39D), belonging to Bacillus velezensis. Other isolates were identified as Bacillus tequilensis, Brevibacillus brevis, Bacillus subtilis, Bacillus amyloliquefaciens, and Bacillus licheniformis. The effectiveness of their antifungal properties was determined via co-culturing, and we found mycelial inhibition rates of 28.17% (for B20) and 33.33% (for B30) for the Fusarium solani isolates. The characterization of the Bacillus velezensis strain revealed that they were Gram-positive and grew well at pH 7.0 and 8.5, although growth was recorded at pH 5.0 and 10.0. In terms of temperature, the optimal temperature conditions were 30−35 °C, with an optimum salinity of 0–0.5 M NaCl. When these isolates were tested for their ability to produce secondary metabolites, they were found to produce phosphate, pectinase, chitinase, protease, indole -3- acetic acid (IAA), and hydrogen cyanide (HCD), making them potential biocontrol agents. Full article
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13 pages, 3587 KiB  
Article
Distantly Related Homologue of UhpT in Pseudomonas aeruginosa
by Tommaso Orioli and Daniela Dolce
Bacteria 2022, 1(4), 266-278; https://doi.org/10.3390/bacteria1040020 - 7 Nov 2022
Viewed by 2972
Abstract
Pseudomonas aeruginosa (PA) is an opportunistic Gram-negative bacteria that affects patients in intensive care units and chronic respiratory disease patients. Compared to other bacteria, it has a wide genome (around 6.3-Mb) that supports its metabolic versatility and antimicrobial resistance. Fosfomycin (FF) is primarily [...] Read more.
Pseudomonas aeruginosa (PA) is an opportunistic Gram-negative bacteria that affects patients in intensive care units and chronic respiratory disease patients. Compared to other bacteria, it has a wide genome (around 6.3-Mb) that supports its metabolic versatility and antimicrobial resistance. Fosfomycin (FF) is primarily used as an oral treatment for urinary tract infections (UTIs). FF diffuses inside the cell via glycerol-3-phosphate transporter (GlpT) PA, as well as in other bacteria. In other bacteria, such as E. coli, glucose-6-phosphate transporter (UhpT) functions as FF transporter. Since mutant GlpT leads to FF resistant PA, it is assumed that GlpT is the only FF transporter. However, it is also assumed that PA uses glucose-6-phosphate and, thus, homologous proteins of UhpT may be present in its genome. Here, we present an attempt to find a distant related homologue of UhpT in PA. A Hidden Markov Model (HMM) was created to seek for Major facilitator family (MFS) domain in 21 PA genomes of 14 CF patients annotated with prokka and the statistical analysis was performed (MCC: 0.84, ACC: 0.99). Then, the HMM was applied to PA genomes. Besides the actual GlpT, annotated as glpt_1, one more GlpT protein was found in 21 out of 21 genomes, annotated as glpt_2. Since glpt_2 clusters closer to UhpT than GlpT, glpt_2 was selected to build a model. Computing a structural superimposition, the model and the template of UhpT have 0.6 Å of RMSD. The model of glpt_2 has some characteristics that are fundamental to UhpT functions. The binding site, consisting of 2 arginines (Arg46 and Arg275) and Lys45, is totally conserved, as well as the topology of the structure. Asp90 is also conserved in glpt_2 model. No studies aimed at searching for distant related homologous of UhpT. Since the high genetic exchange and high mutational rate in bacteria, it is likely that PA has a UhpT-like protein in the PA genome. The binding site is superimposable to UhpT protein as well as the overall topology. In fact, the 12 TMs are completely comparable, suggesting a well-defined folding of the protein across the bilayer lipid membrane. To enforce our hypothesis, in all 21 PA genomes, we also found a protein annotated as membrane sensor protein UhpC, important for expression and function of UhpT in E. coli. Since PA strains are wild-type, we can assume that most of the PA have proteins like this. The presence of a homologue of UhpT suggests that this protein is conserved in PA genome. Full article
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16 pages, 1098 KiB  
Review
Probiotic Regulation to Modulate Aging Gut and Brain Health: A Concise Review
by Mrinal Samtiya, Anil Kumar Puniya, Monica Puniya, Nagendra P. Shah, Tejpal Dhewa and Ravichandra Vemuri
Bacteria 2022, 1(4), 250-265; https://doi.org/10.3390/bacteria1040019 - 2 Nov 2022
Cited by 2 | Viewed by 6431
Abstract
The human gastrointestinal (GI) tract contains a diverse mixture of commensal and pathogenic microbes, forming the gut microbiome. These gut microbes and their potential to improve human health are a topic of great interest to the scientific community. Many intestinal and age-related complications [...] Read more.
The human gastrointestinal (GI) tract contains a diverse mixture of commensal and pathogenic microbes, forming the gut microbiome. These gut microbes and their potential to improve human health are a topic of great interest to the scientific community. Many intestinal and age-related complications are linked to dysbiosis of the gut microbiome, often associated with a weakened immune system. A decrease in beneficial microbes, generally, along with decreased microbial diversity in the gut, can, in many cases, result in disease, particularly in older individuals. Probiotics, which are ingestible beneficial microorganisms, have the potential to positively modulate the indigenous gut microbiota. There are two predominant and conventional classes of lactic acid bacterial probiotics, lactobacilli and bifidobacteria, which have been confirmed for their health benefits and role in preventing certain gut-related disorders. The proper use of probiotics and/or supplements, along with a consistently healthy lifestyle, is a promising holistic approach to maintaining or improving gut health and minimizing other age-linked disorders. There are many properties that bacterial probiotics possess, which may allow for these beneficial effects in the gut. For instance, probiotics have adhesion capacities (capability to stay in GI tract) that are effective in excluding pathogens, while other probiotics have the potential to stimulate or modulate the intestinal immune system by regulating genes that reside within and outside of the gut environment. This review discussed the possible underlying mechanics of probiotics, evidence of probiotic-based mitigation of age-related disease, and the role of probiotics in modulating gut health and, in turn, maintaining brain health. Full article
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8 pages, 726 KiB  
Article
The First Finding of Francisella tularensis subsp. mediasiatica in Krasnoyarsk Territory, Siberia, and an Update of the Subspecies Genetic Diversity
by Vitalii Timofeev, Irina Bakhteeva, Alexander Mokrievich, Galina Vakhrameeva, Elena Gritskova, Yuriy Anisimov, Evgeny Rozhdestvensky, Galina Bazarova, Rostislav Zhumakaev, Ivan Dyatlov and Gilles Vergnaud
Bacteria 2022, 1(4), 242-249; https://doi.org/10.3390/bacteria1040018 - 20 Oct 2022
Cited by 3 | Viewed by 2217
Abstract
Tularemia is a severe infectious disease caused by the Gram-negative bacteria Francisella tularensis. F. tularensis is currently divided into three subspecies, holarctica, tularensis, and mediasiatica, which differ in their virulence and geographic distribution. Subspecies mediasiatica is the least studied [...] Read more.
Tularemia is a severe infectious disease caused by the Gram-negative bacteria Francisella tularensis. F. tularensis is currently divided into three subspecies, holarctica, tularensis, and mediasiatica, which differ in their virulence and geographic distribution. Subspecies mediasiatica is the least studied because of its very low documented virulence for humans and limited geographic distribution. It was discovered in sparsely populated regions of Central Asia. Since 2011, a new subsp. mediasiatica lineage was identified in Altai (Russia). In 2021, we isolated one subsp. mediasiatica strain in Krasnoyarsk Territory. In spite of its geographic origin, 500 km east from Altai, this strain belongs to the Altai lineage and contributes surprisingly little genetic diversity to previous knowledge. Full article
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24 pages, 70923 KiB  
Article
Comparative Genomic Analysis of Phytopathogenic Xanthomonas Species Suggests High Level of Genome Plasticity Related to Virulence and Host Adaptation
by Juan Carlos Ariute, Diego Lucas Neres Rodrigues, Siomar de Castro Soares, Vasco Azevedo, Ana Maria Benko-Iseppon and Flávia Figueira Aburjaile
Bacteria 2022, 1(4), 218-241; https://doi.org/10.3390/bacteria1040017 - 8 Oct 2022
Cited by 4 | Viewed by 3503
Abstract
Xanthomonas bacteria are known phytopathogens difficult to control in the field, which cause great losses in many economically important crops. Genomic islands are fragments acquired by horizontal transference that are important for evolution and adaptation to diverse ecological niches. Virulence and pathogenicity islands [...] Read more.
Xanthomonas bacteria are known phytopathogens difficult to control in the field, which cause great losses in many economically important crops. Genomic islands are fragments acquired by horizontal transference that are important for evolution and adaptation to diverse ecological niches. Virulence and pathogenicity islands (PAIs) enhance molecular mechanisms related to host adaptation. In this work, we have analyzed 81 genomes belonging to X. campestris, and a complex group of X. citri, X. axonopodis, and X. fuscans belonging to nine different pathovars and three subspecies, to analyze and compare their genomic contents. Xanthomonas pan-genome is open and has a massive accessory genome. Each genome showed between three and 15 exclusive PAIs, well conserved through strains of the same pathovar or subspecies. X. axonopodis pv. anacardii had higher general similarity to X. citri subsp. citri and X. fuscans subsp. aurantifolii, with which a few PAIs were shared. Genomic synteny was even for almost all strains, with few rearrangements found in X. axonopodis pv. anacardii. The prophage regions identified in the genomes were mostly questionable or incomplete, and PAI13 in X. campestris pv. campestris ATCC33913 matched a prophage region of 19 transposable elements. Finally, PAIs in Xanthomonas are pathovar-specific, requiring individual strategies of combat. Full article
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11 pages, 1175 KiB  
Article
Infectivity of Viable but Non-Cultivable Cells of Pigmented and Nonpigmented Xanthomonas citri pv. anacardii Strains Demonstrate the Need to Establish Indexing Protocols for Cashew Propagules
by Lucas Pontes Lucena, Géssyka Rodrigues Albuquerque, Elineide Barbosa Souza, Ana Maria Benko-Iseppon, Rodrigo Dias Oliveira Carvalho, Flávia Figueira Aburjaile and Marco Aurélio Siqueira Gama
Bacteria 2022, 1(4), 207-217; https://doi.org/10.3390/bacteria1040016 - 6 Oct 2022
Viewed by 2112
Abstract
Angular leaf spot of cashew tree in Brazil has been attributed to pigmented and nonpigmented strains of Xanthomonas citri pv. anacardii. Due to the possibility of dissemination of the disease by propagating material, it is necessary to understand the survival mechanisms of [...] Read more.
Angular leaf spot of cashew tree in Brazil has been attributed to pigmented and nonpigmented strains of Xanthomonas citri pv. anacardii. Due to the possibility of dissemination of the disease by propagating material, it is necessary to understand the survival mechanisms of the causal agent. Thus, the present study aimed to characterize the behavior of viable but non-cultivable cells (VBNC) in two pigmented strains (CCRMTAQ13 and CCRMTAQ18) and one nonpigmented strain (IBSBF2579) of X. citri pv. anacardii, integrating in silico, in vitro, and in vivo studies. Thirteen genes associated with the VBNC phase were identified in the genomes of these strains. The log phase was observed at 24, 48, and 120 h for CCRMTAQ13, CCRMTAQ18, and IBSBF2579 strains, respectively. The death phase was observed at 96 h for both pigmented strains and 168 h for the nonpigmented strain. Using qPCR analyses, it was possible to characterize the occurrence of VBNC for the three strains. When inoculated, the strains showed 100% incidence during the VBNC phase, with the IBSBF2579 strain having the longest incubation period (IP). The strains did not differ concerning final severity (FS) in the VBNC phase. To our knowledge, this is the first report of the occurrence of the VBNC mechanism in X. citri pv. anacardii strains. Furthermore, it has been demonstrated that X. citri pv. anacardii in the VBNC state is potentially infective when they meet their host’s apoplast, which points to the need to use integrated practices to detect this bacterium in cashew seedlings. Full article
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16 pages, 1103 KiB  
Article
Potential of Pseudarthrobacter chlorophenolicus BF2P4-5 as a Biofertilizer for the Growth Promotion of Tomato Plants
by Muazu Issifu, Edinah K. Songoro, Justus Onguso, Elijah Miinda Ateka and Victoria Wambui Ngumi
Bacteria 2022, 1(4), 191-206; https://doi.org/10.3390/bacteria1040015 - 28 Sep 2022
Cited by 7 | Viewed by 3358
Abstract
BF2P4-5 was isolated from the rhizosphere soil of tomato plants, and its potential to promote plant growth was investigated in tomato plants. An in vitro test revealed that the strain could fix nitrogen, solubilize phosphate and potassium, and synthesize indole acetic acid. The [...] Read more.
BF2P4-5 was isolated from the rhizosphere soil of tomato plants, and its potential to promote plant growth was investigated in tomato plants. An in vitro test revealed that the strain could fix nitrogen, solubilize phosphate and potassium, and synthesize indole acetic acid. The bacterial strain was identified and characterized as a kind of Pseudarthrobacter chlorophenolicus based on the analysis of culture characteristics, physiological and biochemical characteristics, and 16S rRNA gene sequence (GenBank accession number OP135548.1). pH 7.0, 15% NaCl, and 35 °C temperature were ideal for optimal strain growth under culture conditions. Tomato plants grown on a cocopeat substrate were inoculated with BF2P4-5 suspension (OD600 2.0). Positive control plants were inoculated with Nitrogen Phosphorus Potassium (NPK) fertilizer. This BF2P4-5 strain and NPK treatments were complemented with a negative control, in which only tap water was applied to tomato roots, thus, establishing three distinct treatment modalities with five replications each. Two months of greenhouse trials of inoculated tomato plants improved growth parameters. Interestingly, in most of the growth metrics evaluated, tomato plants treated with strain BF2P4-5 showed little to no variation with NPK fertilizer treatment, including plant height, stem length, girth, leaf number per plant, and chlorophyll content, when compared to uninoculated plants. Furthermore, the conditions for the cocopeat plants, including pH, EC, and moisture, were within acceptable limits. Furthermore, inoculation with BF2P4-5 increased the nitrogen, phosphorus, and potassium content available in the cocopeat medium. The results showed that the strain exhibited traits for the promotion of plant growth and could be deployed as an eco-friendly microbial biofertilizer for tomatoes and probably other essential crops. Full article
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