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Your search keyword '"Phylogenomic diversity"' showing total 3 results
Start Over Descriptor "Phylogenomic diversity" Topic phylogeny
3 results on '"Phylogenomic diversity"'

1. Phylogenomic analyses of multidrug resistant Corynebacterium striatum strains isolated from patients in a tertiary care hospital in the UK.

Author

Sangal V, Marrs ECL, Nelson A, and Perry JD

Subjects
Humans, United Kingdom epidemiology, Microbial Sensitivity Tests, Cross Infection microbiology, Cross Infection epidemiology, Male, Virulence Factors genetics, Bacterial Proteins genetics, Female, Corynebacterium genetics, Corynebacterium drug effects, Corynebacterium isolation & purification, Corynebacterium classification, Drug Resistance, Multiple, Bacterial genetics, Corynebacterium Infections microbiology, Corynebacterium Infections epidemiology, Tertiary Care Centers, Phylogeny, Anti-Bacterial Agents pharmacology
Abstract

Corynebacterium striatum is an emerging nosocomial pathogen. This is the first report showing the presence of three distinct multidrug resistant lineages of C. striatum among patients in a UK hospital. The presence of ErmX, Tet(W), Bla and AmpC proteins, and mutations in gyrA gene are associated with the resistance to clindamycin, doxycycline, penicillin and moxifloxacin, respectively. These strains are equipped with several corynebacterial virulence genes including two SpaDEF-type and a novel pilus gene cluster, which needs further molecular characterisation. This study highlights a need of developing an active surveillance strategy for routine monitoring and preventing potential cross-transmission among susceptible patients., (© 2024. The Author(s).)

Published
2024
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2. Genomic diversity and molecular dynamics interaction on mutational variances among RB domains of SARS-CoV-2 interplay drug inactivation

Author

Mahmudul Hasan, Tamanna Jahan Mony, Arabinda Ghosh, Nazmul Islam Bappy, Bashir Uddin, Samuel Muhit, Emran Hossain Sajib, Syed Sayeem Uddin Ahmed, Mohammad Mahmudul Hassan, Ramachandran Chelliah, Fazle Elahi, Deog-Hwan Oh, Se Jin Park, and Syeda Farjana Hoque

Subjects
Protein Conformation, alpha-Helical, Conformational change, Gene Expression, medicine.disease_cause, Genome, Molecular dynamics, Phylogeny, media_common, Netherlands, Genetics, Mutation, Bangladesh, Likelihood Functions, Alanine, Transition (genetics), Molecular Docking Simulation, Infectious Diseases, Spike Glycoprotein, Coronavirus, Protein Binding, Research Paper, Microbiology (medical), Drug, China, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), media_common.quotation_subject, Remdesivir, Genome, Viral, Biology, Molecular Dynamics Simulation, Microbiology, Antiviral Agents, Evolution, Molecular, S protein, medicine, Humans, Protein Interaction Domains and Motifs, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Binding Sites, SARS-CoV-2, COVID-19, Phylogenomic diversity, Mutational analysis, Adenosine Monophosphate, United States, COVID-19 Drug Treatment, Amino Acid Substitution, Protein Conformation, beta-Strand, Reference genome
Abstract

The scientific community has been releasing whole genomic sequences of SARS-CoV-2 to facilitate the investigation of molecular features and evolutionary history. We retrieved 36 genomes of 18 prevalent countries of Asia, Europe and America for genomic diversity and mutational analysis. Besides, we studied mutations in the RBD regions of Spike (S) proteins to analyze the drug efficiency against these mutations. In this research, phylogenenetic analysis, evolutionary modeling, substitution pattern analysis, molecular docking, dynamics simulation, etc. were performed. The genomic sequences showed >99% similarity with the reference sequence of China.TN93 + G was predicted as a best nucleotide substitution model. It was revealed that effective transition from the co-existing SARS genome to the SARS-CoV-2 and a noticeable positive selection in the SARS-CoV-2 genomes occurred. Moreover, three mutations in RBD domain, Val/ Phe367, Val/ Leu 382 and Ala/ Val522, were discovered in the genomes from Netherland, Bangladesh and the USA, respectively. Molecular docking and dynamics study showed RBD with mutation Val/Leu382 had the lowest binding affinity with remdesivir. In conclusion, the SARS-CoV-2 genomes are similar, but multiple degrees of transitions and transversions occurred. The mutations cause a significant conformational change, which are needed to be investigated during drug and vaccine development.

Published
2021

3. Genomic diversity of

Author

Ebenezer, Foster-Nyarko, Nabil-Fareed, Alikhan, Anuradha, Ravi, Gaëtan, Thilliez, Nicholas M, Thomson, David, Baker, Gemma, Kay, Jennifer D, Cramer, Justin, O'Grady, Martin, Antonio, and Mark J, Pallen

Subjects
Primates, phylogenomic diversity, Genomic Islands, Whole Genome Sequencing, Virulence Factors, Escherichia coli Proteins, High-Throughput Nucleotide Sequencing, Microbial evolution and epidemiology: Zoonosis/anthroponosis, Feces, Extraintestinal pathogenic E. coli, Drug Resistance, Bacterial, Escherichia coli, Animals, Humans, Gambia, Phylogeny, Research Article, Non-human primates
Abstract

Increasing contact between humans and non-human primates provides an opportunity for the transfer of potential pathogens or antimicrobial resistance between host species. We have investigated genomic diversity and antimicrobial resistance in Escherichia coli isolates from four species of non-human primates in the Gambia: Papio papio (n=22), Chlorocebus sabaeus (n=14), Piliocolobus badius (n=6) and Erythrocebus patas (n=1). We performed Illumina whole-genome sequencing on 101 isolates from 43 stools, followed by nanopore long-read sequencing on 11 isolates. We identified 43 sequence types (STs) by the Achtman scheme (ten of which are novel), spanning five of the eight known phylogroups of E. coli . The majority of simian isolates belong to phylogroup B2 – characterized by strains that cause human extraintestinal infections – and encode factors associated with extraintestinal disease. A subset of the B2 strains (ST73, ST681 and ST127) carry the pks genomic island, which encodes colibactin, a genotoxin associated with colorectal cancer. We found little antimicrobial resistance and only one example of multi-drug resistance among the simian isolates. Hierarchical clustering showed that simian isolates from ST442 and ST349 are closely related to isolates recovered from human clinical cases (differences in 50 and 7 alleles, respectively), suggesting recent exchange between the two host species. Conversely, simian isolates from ST73, ST681 and ST127 were distinct from human isolates, while five simian isolates belong to unique core-genome ST complexes – indicating novel diversity specific to the primate niche. Our results are of planetary health importance, considering the increasing contact between humans and wild non-human primates.

Published
2020

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