Design of an Enterobacteriaceae Pan-Genome Microarray Chip

Microarrays are a common method for evaluating genomic content of bacterial species and comparing unsequenced bacterial genomes. This technology allows for quick scans of characteristic genes and chromosomal regions, and to search for indications of horizontal transfer. A high-density microarray chip has been designed, using 116 Enterobacteriaceae genome sequences, taking into account the enteric pan-genome. Probes for the microarray were checked in silico and performance of the chip, based on experimental strains from four different genera, demonstrate a relatively high ability to distinguish those strains on genus, species, and pathotype/serovar levels. Additionally, the microarray performed well when investigating which genes were found in a given strain of interest. The Enterobacteriaceae pan-genome microarray, based on 116 genomes, provides a valuable tool for determination of the genetic makeup of unknown strains within this bacterial family and can introduce insights into phylogenetic relationships.

[1]  Peter Gerner-Smidt,et al.  Submitting articles to the BMJ , 2003, BMJ : British Medical Journal.

[2]  B. Pettersson,et al.  DNA based classification of food associated Enterobacteriaceae previously identified by Biolog GN Microplates. , 2004, Systematic and applied microbiology.

[3]  David W Ussery,et al.  Characterization of probiotic Escherichia coli isolates with a novel pan-genome microarray , 2007, Genome Biology.

[4]  Adam M. Phillippy,et al.  Efficient oligonucleotide probe selection for pan-genomic tiling arrays , 2009, BMC Bioinformatics.

[5]  Jane Fridlyand,et al.  Bioinformatics Original Paper a Comparison Study: Applying Segmentation to Array Cgh Data for Downstream Analyses , 2022 .

[6]  C. Nusbaum,et al.  Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. , 1998, Science.

[7]  Henrik Bjørn Nielsen,et al.  OligoWiz 2.0—integrating sequence feature annotation into the design of microarray probes , 2005, Nucleic Acids Res..

[8]  D. Botstein,et al.  DNA microarray analysis of gene expression in response to physiological and genetic changes that affect tryptophan metabolism in Escherichia coli. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[9]  P. Andersen,et al.  Genetic and environmental influences on premature death in adult adoptees. , 1988, The New England journal of medicine.

[10]  S. Ahrné,et al.  Enterobacteriaceae found in high numbers in fish, minced meat and pasteurised milk or cream and the presence of toxin encoding genes. , 1998, International journal of food microbiology.

[11]  Li Sun,et al.  Analysis of the vaccine potential of a natural avirulent Edwardsiella tarda isolate. , 2010, Vaccine.

[12]  Jaideep P. Sundaram,et al.  Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome". , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[13]  R. Yee,et al.  Enterobacteriaceae and Pseudomonas aeruginosa Recovered from Vegetable Salads , 1976, Applied and environmental microbiology.

[14]  J. Do,et al.  Normalization of microarray data: single-labeled and dual-labeled arrays. , 2006, Molecules and cells.

[15]  L. McCaig,et al.  Food-related illness and death in the United States. , 1999, Emerging infectious diseases.

[16]  J. Giesecke,et al.  Short- and Long-term Effects of Bacterial Gastrointestinal Infections , 2008, Emerging infectious diseases.

[17]  Pascale Cossart,et al.  Bacterial Invasion: The Paradigms of Enteroinvasive Pathogens , 2004, Science.

[18]  W. Kuo,et al.  High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays , 1998, Nature Genetics.

[19]  Deana R. Jones,et al.  Enterobacteriaceae and related organisms isolated from shell eggs collected during commercial processing. , 2008, Poultry science.

[20]  Jean YH Yang,et al.  Bioconductor: open software development for computational biology and bioinformatics , 2004, Genome Biology.

[21]  Frederick R. Blattner,et al.  High-Density Microarray-Mediated Gene Expression Profiling of Escherichia coli , 2001, Journal of bacteriology.

[22]  E. Nielsen,et al.  DNA microarray analysis of Salmonella serotype Typhimurium strains causing different symptoms of disease , 2010, BMC Microbiology.

[23]  Trygve Almøy,et al.  Microbial comparative pan-genomics using binomial mixture models , 2009, BMC Genomics.

[24]  Rasmus Wernersson,et al.  Probe selection for DNA microarrays using OligoWiz , 2007, Nature Protocols.

[25]  L. Durso,et al.  Escherichia coli O157:H7 and Other E. coli Strains Share Physiological Properties Associated with Intestinal Colonization , 2009, Applied and Environmental Microbiology.

[26]  M. Stanhope,et al.  Evolution of the core and pan-genome of Streptococcus: positive selection, recombination, and genome composition , 2007, Genome Biology.

[27]  Garth D. Ehrlich,et al.  Pan-genome analysis provides much higher strain typing resolution than multi-locus sequence typing. , 2010, Microbiology.

[28]  Miriam L. Land,et al.  Trace: Tennessee Research and Creative Exchange Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification Recommended Citation Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification , 2022 .

[29]  D. Ussery,et al.  Design of a Seven-Genome Escherichia coli Microarray for Comparative Genomic Profiling , 2006, Journal of bacteriology.

[30]  Bryan S. Biehl,et al.  Niche-specificity and the variable fraction of the Pectobacterium pan-genome. , 2008, Molecular plant-microbe interactions : MPMI.

[31]  L. Ng,et al.  Enterobacteriaceae associated with meats and meat handling , 1981, Applied and environmental microbiology.

[32]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[33]  M. Hornef,et al.  Bacterial strategies for overcoming host innate and adaptive immune responses , 2002, Nature Immunology.

[34]  K. Laupland,et al.  Salmonella enterica bacteraemia: a multi-national population-based cohort study , 2010, BMC infectious diseases.

[35]  L. Gram,et al.  Anti‐adhesive properties of fish tropomyosins , 2008, Journal of applied microbiology.