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Phydbac (phylogenomic display of bacterial genes): an interactive resource for the annotation of bacterial genomes

F. Enault
2003 Nucleic Acids Research  
An extension of Phydbac, including precomputed profiles for all available bacterial genomes (including major pathogens) will soon be available. Phydbac can be accessed at:  ...  Phydbac is a web interactive resource based on phylogenomic profiling, designed to help microbiologists to annotate bacterial proteins.  ...  The phylogenomic profile is computed on line, using an ORF database derived from 71 bacterial and archaeal (non-redundant) species.  ... 
doi:10.1093/nar/gkg603 pmid:12824402 pmcid:PMC169009 fatcat:f4jpkzqamfaylglyjh7xhczrua

Comparative phylogenomics of pathogenic bacteria by microarray analysis

Nick Dorrell, Stewart J Hinchliffe, Brendan W Wren
2005 Current Opinion in Microbiology  
and evolution of bacterial pathogens.  ...  This, coupled with new methods to model DNA microarray data, is facilitating the development of robust comparative phylogenomics analyses.  ...  Acknowledgements We wish to acknowledge the Biotechnology and Biological Sciences Research Council (BBSRC), the Medical Research Council (MRC), the Defence Science Technology Laboratory (DSTL) and the  ... 
doi:10.1016/j.mib.2005.08.012 pmid:16125441 pmcid:PMC7108221 fatcat:hrnwrtjfvzfhhj76xotqrgaocy

Large scale automated phylogenomic analysis of bacterial isolates and the Evergreen Online platform

Judit Szarvas, Johanne Ahrenfeldt, Jose Luis Bellod Cisneros, Martin Christen Frølund Thomsen, Frank M. Aarestrup, Ole Lund
2020 Communications Biology  
We have therefore created a bioinformatics pipeline for rapid subtyping and continuous phylogenomic analysis of bacterial samples, suited for large-scale surveillance.  ...  Public health authorities whole-genome sequence thousands of isolates each month for microbial diagnostics and surveillance of pathogenic bacteria.  ...  Acknowledgements The authors would like to thank every public health institute, that releases their sequencing data to the public in a prompt manner.  ... 
doi:10.1038/s42003-020-0869-5 pmid:32198478 fatcat:726wct4vpbfd7fxgtl76ksmer4

Phylogenomic pipeline validation for foodborne pathogen disease surveillance

Ruth E. Timme, Errol Strain, Joseph Baugher, Steven Davis, Narjol Gonzalez-Escalona, Maria Sanchez-Leon, Marc W. Allard, Eric W. Brown, Sandra Tallent, Hugh Rand
2019 Journal of Clinical Microbiology  
This review provides a historical perspective on the use of WGS for pathogen tracking and summarizes the efforts underway to ensure the major steps in phylogenomic pipelines used for pathogen disease surveillance  ...  WGS requires a new suite of analysis tools, some of which have long histories in academia, but are new to the field of public health and regulatory decision making.  ...  Both SNP-362 based and wgMLST-based phylogenomic analysis approaches have been widely adopted for 363 foodborne pathogen surveillance; it is crucial that these approaches are validated in context.  ... 
doi:10.1128/jcm.01816-18 pmid:30728194 pmcid:PMC6498022 fatcat:7upwdqmk4zg23ksgh7jpqjhvn4

Large scale automated phylogenomical analysis of bacterial whole-genome isolates and the Evergreen platform [article]

Judit Szarvas, Johanne Ahrenfeldt, Jose L. Bellod Cisneros, Martin C. F. Thomsen, Frank M. Aarestrup, Ole Lund
2019 bioRxiv   pre-print
We have therefore created a bioinformatics pipeline for rapid subtyping and continuous phylogenomic analysis of bacterial samples, suited for large-scale surveillance.  ...  Public health authorities whole-genome sequence thousands of pathogenic isolates each month for microbial diagnostics and surveillance of pathogenic bacteria.  ...  and continuous phylogenomical analysis 275 on a growing number of bacterial samples.  ... 
doi:10.1101/540138 fatcat:or6rvy57gjdqjd6qtugulmduze

The Entomopathogenic Bacterial Endosymbionts Xenorhabdus and Photorhabdus: Convergent Lifestyles from Divergent Genomes

John M. Chaston, Garret Suen, Sarah L. Tucker, Aaron W. Andersen, Archna Bhasin, Edna Bode, Helge B. Bode, Alexander O. Brachmann, Charles E. Cowles, Kimberly N. Cowles, Creg Darby, Limaris de Léon (+45 others)
2011 PLoS ONE  
Members of the bacterial genus Photorhabdus also associate with nematodes to kill insects, and both genera of bacteria provide similar services to their different nematode hosts through unique physiological  ...  To test this, we sequenced to completion the genomes of Xenorhabdus nematophila ATCC 19061 and Xenorhabdus bovienii SS-2004.  ...  Acknowledgments We would like to thank Joanne McAndrews for editing the manuscript. This paper is dedicated to the late Nancy Leimgruber.  ... 
doi:10.1371/journal.pone.0027909 pmid:22125637 pmcid:PMC3220699 fatcat:vstusooztzbadntwdurann3f6u

Phydbac2: improved inference of gene function using interactive phylogenomic profiling and chromosomal location analysis

F. Enault, K. Suhre, O. Poirot, C. Abergel, J.-M. Claverie
2004 Nucleic Acids Research  
This method was able to increase the predictive power of phylogenomic profiling by about 25% when compared to the classical approach based on Hamming distances.  ...  The expanded functionality of Phydbac2 now allows the user to query more than 50 different genomes, including at least one member of each major bacterial group, most major pathogens and potential bio-terrorism  ...  This approach was shown to improve the predictive power of phylogenomic profiling by about 25% with respect to the classical approach (11) .  ... 
doi:10.1093/nar/gkh365 pmid:15215406 pmcid:PMC441503 fatcat:esgg2bu4ijeg5k7e37xxbd26ky

Comparative genomics confirms a rare melioidosis human-to-human transmission event and reveals incorrect phylogenomic reconstruction due to polyclonality [article]

Ammar Aziz, Bart J. Currie, Mark Mayo, Derek S. Sarovich, Erin P. Price
2019 bioRxiv   pre-print
Next, phylogenomic analysis of all isolates, including the mother's mixed ST-259/261 sputum sample was performed to investigate the effects of mixtures on phylogenetic inference.  ...  Although phylogenomics can provide clues about the presence of mixtures within WGS datasets, our results demonstrate that this methodology can lead to phylogenetic misinterpretation if mixed genomes are  ...  Such an approach 245 is only suited for parsing apart mixtures of two strains.  ... 
doi:10.1101/804344 fatcat:lrecpnopibddbbs4g3p7uz66p4

Future perspectives, applications and challenges of genomic epidemiology studies for food-borne pathogens: A case study of EnterohemorrhagicEscherichia coli(EHEC) of the O157:H7 serotype

Mark Eppinger, Thomas A Cebula
2014 Gut microbes  
enabling deep sampling and phylogenomic analysis of ever-larger bacterial pathogen populations and metagenomic samples.  ...  SNP discovery approaches have yielded thousands of high-quality SNPs as critical bases for the development of a refined phylogenomic framework. 9, 21, 57 anonical SNPs can be implemented in an efficient  ...  Addendum to: Eppinger M, Mammel MK, LeClerc JE, Ravel J, Cebula TA. Genomic anatomy of Escherichia coli O157:H7 outbreaks. Proceedings of the National Academy of Sciences 2011; 108:20142-20147.  ... 
doi:10.4161/19490976.2014.969979 pmid:25483335 pmcid:PMC4615391 fatcat:2b7cn7lr7rd77nxsddohy2ljmu

Machine Learning Approaches for Epidemiological Investigations of Food-Borne Disease Outbreaks

Baiba Vilne, Irēna Meistere, Lelde Grantiņa-Ieviņa, Juris Ķibilds
2019 Frontiers in Microbiology  
genomics, and inference of phylogeny or phylogenomics.  ...  As genotyping using whole-genome sequencing (WGS) is becoming more accessible and affordable, it is increasingly used as a routine tool for the detection of pathogens, and has the potential to differentiate  ...  FIGURE 1 | 1 An overview of an example bacterial sequence data analysis workflow. TABLE 1 | 1 An non-exhaustive list of the mechanistic model-based vs. ML tools for microbial genome analysis.  ... 
doi:10.3389/fmicb.2019.01722 pmid:31447800 pmcid:PMC6691741 fatcat:3kuz7hgocrepjemyb5gb7mg7my

Comparative genomics confirms a rare melioidosis human-to-human transmission event and reveals incorrect phylogenomic reconstruction due to polyclonality

Ammar Aziz, Bart J. Currie, Mark Mayo, Derek S. Sarovich, Erin P. Price
2020 Microbial Genomics  
Next, phylogenomic analysis of all isolates, including the mother's mixed ST-259/ST-261 sputum sample, was performed to investigate the effects of mixtures on phylogenetic inference.  ...  Analysis of purified ST-259 isolates showed no genetic variation between mother and baby isolates, providing the strongest possible evidence of B. pseudomallei human-to-human transmission, probably via  ...  Acknowledgements We thank Vanessa Rigas (Menzies School of Health Research, Australia) for laboratory assistance.  ... 
doi:10.1099/mgen.0.000326 pmid:31958055 pmcid:PMC7067207 fatcat:qemkwgx4qzf65atqsze42xzczi

Application of Comparative Phylogenomics To Study the Evolution of Yersinia enterocolitica and To Identify Genetic Differences Relating to Pathogenicity

S. L. Howard, M. W. Gaunt, J. Hinds, A. A. Witney, R. Stabler, B. W. Wren
2006 Journal of Bacteriology  
Yersinia enterocolitica, an important cause of human gastroenteritis generally caused by the consumption of livestock, has traditionally been categorized into three groups with respect to pathogenicity  ...  In this study, we applied comparative phylogenomics (whole-genome comparisons of microbes with DNA microarrays combined with Bayesian phylogenies) to investigate a diverse collection of 94 strains of Y  ...  The approach described in this study provides a methodological prototype of robust phylogenomics that should be applicable to the study of other microbes.  ... 
doi:10.1128/jb.188.10.3645-3653.2006 pmid:16672618 pmcid:PMC1482848 fatcat:fkyb6jyvsnbp3ij7wg2q22bshe

Benchmark datasets for phylogenomic pipeline validation, applications for foodborne pathogen surveillance

Ruth E. Timme, Hugh Rand, Martin Shumway, Eija K. Trees, Mustafa Simmons, Richa Agarwala, Steven Davis, Glenn E. Tillman, Stephanie Defibaugh-Chavez, Heather A. Carleton, William A. Klimke, Lee S. Katz
2017 PeerJ  
Here we propose a set of benchmark datasets to be used for comparison and validation of phylogenomic pipelines.  ...  Methods We identified four well-documented foodborne pathogen events in which the epidemiology was concordant with routine phylogenomic analyses (reference-based SNP and wgMLST approaches).  ...  ACKNOWLEDGEMENTS We would like to thank Chris Tillman at CFSAN and Cheryl Tarr at CDC for sequencing work on L. monocytogenes. We would also like to thank Collette Fitzgerald, Vikrant Dutta,  ... 
doi:10.7717/peerj.3893 pmid:29372115 pmcid:PMC5782805 fatcat:kip2pjj6lzcrzbd43qlefo6bo4

Comparative phylogenomics of the food-borne pathogen Campylobacter jejuni reveals genetic markers predictive of infection source

O. L. Champion, M. W. Gaunt, O. Gundogdu, A. Elmi, A. A. Witney, J. Hinds, N. Dorrell, B. W. Wren
2005 Proceedings of the National Academy of Sciences of the United States of America  
The comparative phylogenomics approach described provides a robust methodological prototype that should be applicable to other microbes. microarray analysis ͉ gastrointestinal pathogen ͉ Bayesian-based  ...  We report the use of genomotyping (whole-genome comparisons of microbes using DNA microarrays) combined with Bayesian-based algorithms to model the phylogeny of this major food-borne pathogen.  ...  Recently, we applied the comparative phlyogenomics approach to other gastrointestinal bacterial pathogens, including Yersinia enterocolitica and Clostridium difficile, where distinct clades relating to  ... 
doi:10.1073/pnas.0503252102 pmid:16230626 pmcid:PMC1276044 fatcat:qohklcmnbratzhkfaye2bvljfq

Epidemiological and Genomic Characterization of Campylobacter jejuni Isolates from a Foodborne Outbreak at Hangzhou, China

Hua Yu, Mohammed Elbediwi, Xiaohong Zhou, Huiqun Shuai, Xiuqin Lou, Haoqiu Wang, Yan Li, Min Yue
2020 International Journal of Molecular Sciences  
Routine real-time fluorescent PCR assays were used for scanning the potential infectious agents, including viral pathogens (norovirus, rotavirus, adenovirus, and astrovirus), and bacterial pathogens (Salmonella  ...  The examined fourteen strains of ST2988 from CC354 clone group have very minimal genetic difference (3~66 SNPs), demonstrated by the phylogenomic investigation.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/ijms21083001 pmid:32344510 fatcat:7bsqrxaa5zaa5kfzmyou5qhkzq
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