scholarly journals ShadowCaster: Compositional Methods under the Shadow of Phylogenetic Models to Detect Horizontal Gene Transfers in Prokaryotes

Genes ◽  
2020 ◽  
Vol 11 (7) ◽  
pp. 756
Author(s):  
Daniela Sánchez-Soto ◽  
Guillermin Agüero-Chapin ◽  
Vinicio Armijos-Jaramillo ◽  
Yunierkis Perez-Castillo ◽  
Eduardo Tejera ◽  
...  
Keyword(s):  
Hybrid Approach ◽  
Phylogenetic Reconstruction ◽  
Heavy Metal Resistance ◽  
Nucleotide Composition ◽  
Metal Resistance ◽  
Support Vector ◽  
Computational Approaches ◽  
Reconstruction Methods ◽  
Genomic Scale ◽  
Phylogenetic Models

Horizontal gene transfer (HGT) plays an important role for evolutionary innovations within prokaryotic communities and is a crucial event for their survival. Several computational approaches have arisen to identify HGT events in recipient genomes. However, this has been proven to be a complex task due to the generation of a great number of false positives and the prediction disagreement among the existing methods. Phylogenetic reconstruction methods turned out to be the most reliable ones, but they are not extensible to all genes/species and are computationally demanding when dealing with large datasets. In contrast, the so-called surrogate methods that use heuristic solutions either based on nucleotide composition patterns or phyletic distribution of BLAST hits can be applied easily to the genomic scale, but they fail in identifying common HGT events. Here, we present ShadowCaster, a hybrid approach that sequentially combines nucleotide composition-based predictions by support vector machines (SVMs) under the shadow of phylogenetic models independent of tree reconstruction, to improve the detection of HGT events in prokaryotes. ShadowCaster successfully predicted close and distant HGT events in both artificial and bacterial genomes. ShadowCaster detected HGT related to heavy metal resistance in the genome of Rhodanobacter denitrificans with higher accuracy than the most popular state-of-the-art computational approaches, encompassing most of the predicted cases made by other methods. ShadowCaster is released at the GitHub platform as an open-source software under the GPLv3 license.

scholarly journals ShadowCaster: compositional methods under the shadow of phylogenetic models for the detection of horizontal gene transfer events in prokaryotes

2019 ◽  
Author(s):  
Daniela Sánchez-Soto ◽  
Guillermin Agüero-Chapin ◽  
Vinicio Armijos-Jaramillo ◽  
Yunierkis Perez-Castillo ◽  
Eduardo Tejera ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Hybrid Approach ◽  
Phylogenetic Reconstruction ◽  
Heavy Metal Resistance ◽  
Metal Resistance ◽  
Computational Approaches ◽  
Link Type ◽  
Reconstruction Methods ◽  
Phylogenetic Models

AbstractHorizontal gene transfer (HGT) plays an important role in the evolution of many organisms, especially in prokaryotes where commonly occurs. Microbial communities can improve survival due to the evolutionary innovations induced by HGT events. Thus, several computational approaches have arisen to identify such events in recipient genomes. However, this has been proven to be a complex task due to the generation of a great number of false positives and the prediction disagreement among the existing methods. Phylogenetic reconstruction methods turned out to be the most reliable but they are not extensible to all genes/species and are computationally demanding when dealing with large datasets. On the other hand, the so-called surrogate methods that use heuristic solutions either based on nucleotide composition patterns or phyletic distribution of BLAST hits can be applied easily to genomic scale, however, they fail in identifying common HGT events. Here, we present ShadowCaster, a hybrid approach that sequentially combines compositional features under the shadow of phylogenetic models independent of tree reconstruction to improve the detection of HTG events in prokaryotes. ShadowCaster predicted successfully close and distant HTG events in both artificial and bacterial genomes. It detected HGT related to heavy metal resistance in the genome of Rhodanobacter denitrificans with higher accuracy than the most popular state-of-the-art computational approaches. ShadowCaster’s predictions showed the highest agreement among those obtained with other assayed methods. ShadowCaster is released as an open-source software under the GPLv3 license. Source code is hosted at https://github.com/dani2s/ShadowCaster and documentation at https://shadowcaster.readthedocs.io/en/latest/.

scholarly journals Comparative Genomic Analysis of 450 Strains of Salmonella enterica Isolated from Diseased Animals

Genes ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 1025
Author(s):  
Shaohua Zhao ◽  
Cong Li ◽  
Chih-Hao Hsu ◽  
Gregory H. Tyson ◽  
Errol Strain ◽  
...  
Keyword(s):  
Resistance Genes ◽  
Bacterial Infections ◽  
Genomic Analysis ◽  
Heavy Metal Resistance ◽  
Metal Resistance ◽  
Comparative Genomic ◽  
Salmonella Infections ◽  
Antimicrobial Resistance Genes ◽  
Salmonella Pathogenicity Islands ◽  
Shed Light

Salmonella is a leading cause of bacterial infections in animals and humans. We sequenced a collection of 450 Salmonella strains from diseased animals to better understand the genetic makeup of their virulence and resistance features. The presence of Salmonella pathogenicity islands (SPIs) varied by serotype. S. Enteritidis carried the most SPIs (n = 15), while S. Mbandaka, S. Cerro, S. Meleagridis, and S. Havana carried the least (n = 10). S. Typhimurium, S. Choleraesuis, S. I 4,5,12:i:-, and S. Enteritidis each contained the spv operon on IncFII or IncFII-IncFIB hybrid plasmids. Two S. IIIa carried a spv operon with spvD deletion on the chromosome. Twelve plasmid types including 24 hybrid plasmids were identified. IncA/C was frequently associated with S. Newport (83%) and S. Agona (100%) from bovine, whereas IncFII (100%), IncFIB (100%), and IncQ1 (94%) were seen in S. Choleraesuis from swine. IncX (100%) was detected in all S. Kentucky from chicken. A total of 60 antimicrobial resistance genes (ARGs), four disinfectant resistances genes (DRGs) and 33 heavy metal resistance genes (HMRGs) were identified. The Salmonella strains from sick animals contained various SPIs, resistance genes and plasmid types based on the serotype and source of the isolates. Such complicated genomic structures shed light on the strain characteristics contributing to the severity of disease and treatment failures in Salmonella infections, including those causing illnesses in animals.

scholarly journals Heavy Metal Tolerance Trend in Extended-Spectrum β-Lactamase Encoding Strains Recovered from Food Samples

2021 ◽  
Vol 18 (9) ◽  
pp. 4718
Author(s):  
Kashaf Junaid ◽  
Hasan Ejaz ◽  
Iram Asim ◽  
Sonia Younas ◽  
Humaira Yasmeen ◽  
...  
Keyword(s):  
Heavy Metal ◽  
Metal Tolerance ◽  
Heavy Metal Tolerance ◽  
Heavy Metal Resistance ◽  
Metal Resistance ◽  
Food Samples ◽  
Esbl Production ◽  
Extended Spectrum ◽  
Retail Food ◽  
Esbl Producers

This study evaluates bacteriological profiles in ready-to-eat (RTE) foods and assesses antibiotic resistance, extended-spectrum β-lactamase (ESBL) production by gram-negative bacteria, and heavy metal tolerance. In total, 436 retail food samples were collected and cultured. The isolates were screened for ESBL production and molecular detection of ESBL-encoding genes. Furthermore, all isolates were evaluated for heavy metal tolerance. From 352 culture-positive samples, 406 g-negative bacteria were identified. Raw food samples were more often contaminated than refined food (84.71% vs. 76.32%). The predominant isolates were Klebsiella pneumoniae (n = 76), Enterobacter cloacae (n = 58), and Escherichia coli (n = 56). Overall, the percentage of ESBL producers was higher in raw food samples, although higher occurrences of ESBL-producing E. coli (p = 0.01) and Pseudomonas aeruginosa (p = 0.02) were observed in processed food samples. However, the prevalence of ESBL-producing Citrobacter freundii in raw food samples was high (p = 0.03). Among the isolates, 55% were blaCTX-M, 26% were blaSHV, and 19% were blaTEM. Notably, heavy metal resistance was highly prevalent in ESBL producers. These findings demonstrate that retail food samples are exposed to contaminants including antibiotics and heavy metals, endangering consumers.

scholarly journals Phylogenetic Analysis: Basic Concepts and Its Use as a Tool for Virology and Molecular Epidemiology

2018 ◽  
Vol 44 (1) ◽  
pp. 20
Author(s):  
Eloiza Teles Caldart ◽  
Helena Mata ◽  
Cláudio Wageck Canal ◽  
Ana Paula Ravazzolo
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Molecular Epidemiology ◽  
Phylogenetic Analyses ◽  
Phylogenetic Reconstruction ◽  
Evolutionary Process ◽  
Amino Acid Sequences ◽  
Evolutionary Models ◽  
Reconstruction Methods ◽  
Basic Concepts

Background: Phylogenetic analyses are an essential part in the exploratory assessment of nucleic acid and amino acid sequences. Particularly in virology, they are able to delineate the evolution and epidemiology of disease etiologic agents and/or the evolutionary path of their hosts. The objective of this review is to help researchers who want to use phylogenetic analyses as a tool in virology and molecular epidemiology studies, presenting the most commonly used methodologies, describing the importance of the different techniques, their peculiar vocabulary and some examples of their use in virology.Review: This article starts presenting basic concepts of molecular epidemiology and molecular evolution, emphasizing their relevance in the context of viral infectious diseases. It presents a session on the vocabulary relevant to the subject, bringing readers to a minimum level of knowledge needed throughout this literature review. Within its main subject, the text explains what a molecular phylogenetic analysis is, starting from a multiple alignment of nucleotide or amino acid sequences. The different software used to perform multiple alignments may apply different algorithms. To build a phylogeny based on amino acid or nucleotide sequences it is necessary to produce a data matrix based on a model for nucleotide or amino acid replacement, also called evolutionary model. There are a number of evolutionary models available, varying in complexity according to the number of parameters (transition, transversion, GC content, nucleotide position in the codon, among others). Some papers presented herein provide techniques that can be used to choose evolutionary models. After the model is chosen, the next step is to opt for a phylogenetic reconstruction method that best fits the available data and the selected model. Here we present the most common reconstruction methods currently used, describing their principles, advantages and disadvantages. Distance methods, for example, are simpler and faster, however, they do not provide reliable estimations when the sequences are highly divergent. The accuracy of the analysis with probabilistic models (neighbour joining, maximum likelihood and bayesian inference) strongly depends on the adherence of the actual data to the chosen development model. Finally, we also explore topology confidence tests, especially the most used one, the bootstrap. To assist the reader, this review presents figures to explain specific situations discussed in the text and numerous examples of previously published scientific articles in virology that demonstrate the importance of the techniques discussed herein, as well as their judicious use.Conclusion: The DNA sequence is not only a record of phylogeny and divergence times, but also keeps signs of how the evolutionary process has shaped its history and also the elapsed time in the evolutionary process of the population. Analyses of genomic sequences by molecular phylogeny have demonstrated a broad spectrum of applications. It is important to note that for the different available data and different purposes of phylogenies, reconstruction methods and evolutionary models should be wisely chosen. This review provides theoretical basis for the choice of evolutionary models and phylogenetic reconstruction methods best suited to each situation. In addition, it presents examples of diverse applications of molecular phylogeny in virology.

scholarly journals Genome-Driven Discovery of Enzymes with Industrial Implications from the Genus Aneurinibacillus

2021 ◽  
Vol 9 (3) ◽  
pp. 499
Author(s):  
Majid Rasool Kamli ◽  
Nada A. Y. Alzahrani ◽  
Nahid H. Hajrah ◽  
Jamal S. M. Sabir ◽  
Adeel Malik
Keyword(s):  
Heavy Metal ◽  
Enzyme Activities ◽  
Heavy Metal Resistance ◽  
Industrial Applications ◽  
Metal Resistance ◽  
The Family ◽  
Antiviral Activities ◽  
Genome Level ◽  
Genome Analyses ◽  
Unique Species

Bacteria belonging to the genus Aneurinibacillus within the family Paenibacillaceae are Gram-positive, endospore-forming, and rod-shaped bacteria inhabiting diverse environments. Currently, there are eight validly described species of Aneurinibacillus; however, several unclassified species have also been reported. Aneurinibacillus spp. have shown the potential for producing secondary metabolites (SMs) and demonstrated diverse types of enzyme activities. These features make them promising candidates with industrial implications. At present, genomes of 9 unique species from the genus Aneurinibacillus are available, which can be utilized to decipher invaluable information on their biosynthetic potential as well as enzyme activities. In this work, we performed the comparative genome analyses of nine Aneurinibacillus species representing the first such comprehensive study of this genus at the genome level. We focused on discovering the biosynthetic, biodegradation, and heavy metal resistance potential of this under-investigated genus. The results indicate that the genomes of Aneurinibacillus contain SM-producing regions with diverse bioactivities, including antimicrobial and antiviral activities. Several carbohydrate-active enzymes (CAZymes) and genes involved in heavy metal resistance were also identified. Additionally, a broad range of enzyme classes were also identified in the Aneurinibacillus pan-genomes, making this group of bacteria potential candidates for future investigations with industrial applications.

scholarly journals Discriminative Learning Approach Based on Flexible Mixture Model for Medical Data Categorization and Recognition

Sensors ◽  
2021 ◽  
Vol 21 (7) ◽  
pp. 2450
Author(s):  
Fahd Alharithi ◽  
Ahmed Almulihi ◽  
Sami Bourouis ◽  
Roobaea Alroobaea ◽  
Nizar Bouguila
Keyword(s):  
Mixture Model ◽  
Hybrid Approach ◽  
Medical Data ◽  
Support Vector ◽  
Discriminative Learning ◽  
Learning Approach ◽  
X Rays ◽  
Intrinsic Nature ◽  
Discriminative Models ◽  
Dirichlet Mixture

In this paper, we propose a novel hybrid discriminative learning approach based on shifted-scaled Dirichlet mixture model (SSDMM) and Support Vector Machines (SVMs) to address some challenging problems of medical data categorization and recognition. The main goal is to capture accurately the intrinsic nature of biomedical images by considering the desirable properties of both generative and discriminative models. To achieve this objective, we propose to derive new data-based SVM kernels generated from the developed mixture model SSDMM. The proposed approach includes the following steps: the extraction of robust local descriptors, the learning of the developed mixture model via the expectation–maximization (EM) algorithm, and finally the building of three SVM kernels for data categorization and classification. The potential of the implemented framework is illustrated through two challenging problems that concern the categorization of retinal images into normal or diabetic cases and the recognition of lung diseases in chest X-rays (CXR) images. The obtained results demonstrate the merits of our hybrid approach as compared to other methods.

scholarly journals Retromobilization of heavy metal resistance genes in unpolluted and heavy metal polluted soil

1995 ◽  
Vol 18 (3) ◽  
pp. 191-203 ◽  
Author(s):  
Eva M. Top ◽  
Helene Rore ◽  
Jean-Marc Collard ◽  
Veerle Gellens ◽  
Galina Slobodkina ◽  
...  
Keyword(s):  
Heavy Metal ◽  
Resistance Genes ◽  
Heavy Metal Resistance ◽  
Metal Resistance ◽  
Polluted Soil

scholarly journals Replication of Staphylococcal Multiresistance Plasmids

2000 ◽  
Vol 182 (8) ◽  
pp. 2170-2178 ◽  
Author(s):  
Neville Firth ◽  
Sumalee Apisiridej ◽  
Tracey Berg ◽  
Brendon A. O'Rourke ◽  
Steve Curnock ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Heavy Metal Resistance ◽  
Metal Resistance ◽  
Replication Initiation ◽  
Conjugative Plasmid ◽  
Rolling Circle ◽  
Segregational Stability ◽  
Structural And Functional Properties ◽  
Resistance Plasmids ◽  
Genes Encoding

ABSTRACT Based on structural and functional properties, three groups of large staphylococcal multiresistance plasmids have been recognized, viz., the pSK1 family, pSK41-like conjugative plasmids, and β-lactamase–heavy-metal resistance plasmids. Here we describe an analysis of the replication functions of a representative of each of these plasmid groups. The replication initiation genes from theStaphylococcus aureus plasmids pSK1, pSK41, and pI9789::Tn552 were found to be related to each other and to the Staphylococcus xylosus plasmid pSX267 and are also related to rep genes of several plasmids from other gram-positive genera. Nucleotide sequence similarity between pSK1 and pI9789::Tn552 extended beyond theirrep genes, encompassing upstream divergently transcribed genes, orf245 and orf256, respectively. Our analyses revealed that genes encoding proteins related to the deducedorf245 product are variously represented, in several types of organization, on plasmids possessing six seemingly evolutionarily distinct types of replication initiation genes and including both theta-mode and rolling-circle replicons. Construction of minireplicons and subsequent functional analysis demonstrated that orf245is required for the segregational stability of the pSK1 replicon. In contrast, no gene equivalent to orf245 is evident on the conjugative plasmid pSK41, and a minireplicon encoding only the pSK41 rep gene was found to exhibit a segregational stability approaching that of the parent plasmid. Significantly, the results described establish that many of the large multiresistance plasmids that have been identified in clinical staphylococci, which were formerly presumed to be unrelated, actually utilize an evolutionarily related theta-mode replication system.

Screening of heavy metal and antibiotic resistance among Proteus vulgaris isolates from hospital wastewater of Northern India

2021 ◽  
Vol 19 ◽  
Author(s):  
Manzar Alam ◽  
Mohd Imran ◽  
Syed Sayeed Ahmad
Keyword(s):  
Heavy Metals ◽  
Heavy Metal ◽  
Multiple Drug Resistance ◽  
Heavy Metal Resistance ◽  
Metal Resistance ◽  
Antibiotics Resistance ◽  
Proteus Vulgaris ◽  
Resistance To Antibiotics ◽  
Transfer Frequency ◽  
Resistance Patterns

Background: Microbial resistance to antibiotics and heavy metals is a rising problem in the world today. All the Proteus vulgaris isolates showed their MIC in between 50-1600 µg/ml. Of 70% and 46% of the isolates showed their MIC at 800-1200 µg/ml against Zn2+ and Cu2+ while 80% of the isolates showed their MIC at 100-200 µg/ml against Ni2+, respectively. All Proteus vulgaris isolates also exhibited multiple resistance patterns (2-7 heavy metals) in different combination of metals. The Multi metal resistance Index (MHMR) ranges were found (0.04-0.5). Methods: A high level of antibiotics resistance was observed against Methicillin (100%) and least to Oflaxicin (6%), Gentamycine and Neomycin (10%). All Proteus vulgaris isolates also showed multiple drug resistance patterns (2-12 antibiotics) in different combination of antibiotics. The MAR index ranges were found (0.02-0.7). Of 98%, 84% and 80% of the total isolates showed urease, gelatinase and amylase activity. Results: The Proteus vulgaris isolates contained plasmid of size ranging from 42.5 to 57.0kb and molecular weight of plasmids ranged from 27.2 to 37.0 MD. Incidences of resistance transfer, 7 pairs of isolates were assessed for the transfer of the antibiotic/ heavy metal resistance markers. The higher (4.4x10-1 and 3.4x10-1) transfer frequency was observed among antibiotic and heavy metal while lower transfer frequency were (5.0x10-2 and 1.0x10-2) showed against antibiotic and heavy metal in both the medium from the entire site tested, respectively. Conclusion: Indicating the high threat of environmental pollution and appearance of heavy metal resistance which may support the enlargement of resistance to antibiotics among the pathogens.

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