Статті в журналах: "Coli Genome"

1

KRÖGER, MANFRED. "E. coli genome." Nature 339, no. 6223 (June 1989): 330. http://dx.doi.org/10.1038/339330b0.

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2

Dixit, Purushottam D., Tin Yau Pang, F. William Studier, and Sergei Maslov. "Recombinant transfer in the basic genome ofEscherichia coli." Proceedings of the National Academy of Sciences 112, no. 29 (July 7, 2015): 9070–75. http://dx.doi.org/10.1073/pnas.1510839112.

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An approximation to the ∼4-Mbp basic genome shared by 32 strains ofEscherichia colirepresenting six evolutionary groups has been derived and analyzed computationally. A multiple alignment of the 32 complete genome sequences was filtered to remove mobile elements and identify the most reliable ∼90% of the aligned length of each of the resulting 496 basic-genome pairs. Patterns of single base-pair mutations (SNPs) in aligned pairs distinguish clonally inherited regions from regions where either genome has acquired DNA fragments from diverged genomes by homologous recombination since their last common ancestor. Such recombinant transfer is pervasive across the basic genome, mostly between genomes in the same evolutionary group, and generates many unique mosaic patterns. The six least-diverged genome pairs have one or two recombinant transfers of length ∼40–115 kbp (and few if any other transfers), each containing one or more gene clusters known to confer strong selective advantage in some environments. Moderately diverged genome pairs (0.4–1% SNPs) show mosaic patterns of interspersed clonal and recombinant regions of varying lengths throughout the basic genome, whereas more highly diverged pairs within an evolutionary group or pairs between evolutionary groups having >1.3% SNPs have few clonal matches longer than a few kilobase pairs. Many recombinant transfers appear to incorporate fragments of the entering DNA produced by restriction systems of the recipient cell. A simple computational model can closely fit the data. Most recombinant transfers seem likely to be due to generalized transduction by coevolving populations of phages, which could efficiently distribute variability throughout bacterial genomes.

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3

Cochrane, Ryan R., Stephanie L. Brumwell, Arina Shrestha, Daniel J. Giguere, Samir Hamadache, Gregory B. Gloor, David R. Edgell, and Bogumil J. Karas. "Cloning of Thalassiosira pseudonana’s Mitochondrial Genome in Saccharomyces cerevisiae and Escherichia coli." Biology 9, no. 11 (October 26, 2020): 358. http://dx.doi.org/10.3390/biology9110358.

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Algae are attractive organisms for biotechnology applications such as the production of biofuels, medicines, and other high-value compounds due to their genetic diversity, varied physical characteristics, and metabolic processes. As new species are being domesticated, rapid nuclear and organelle genome engineering methods need to be developed or optimized. To that end, we have previously demonstrated that the mitochondrial genome of microalgae Phaeodactylum tricornutum can be cloned and engineered in Saccharomyces cerevisiae and Escherichia coli. Here, we show that the same approach can be used to clone mitochondrial genomes of another microalga, Thalassiosira pseudonana. We have demonstrated that these genomes can be cloned in S. cerevisiae as easily as those of P. tricornutum, but they are less stable when propagated in E. coli. Specifically, after approximately 60 generations of propagation in E. coli, 17% of cloned T. pseudonana mitochondrial genomes contained deletions compared to 0% of previously cloned P. tricornutum mitochondrial genomes. This genome instability is potentially due to the lower G+C DNA content of T. pseudonana (30%) compared to P. tricornutum (35%). Consequently, the previously established method can be applied to clone T. pseudonana’s mitochondrial genome, however, more frequent analyses of genome integrity will be required following propagation in E. coli prior to use in downstream applications.

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4

Zhang, Hui, Yao Xiong, Wenhai Xiao, and Yi Wu. "Investigation of Genome Biology by Synthetic Genome Engineering." Bioengineering 10, no. 2 (February 20, 2023): 271. http://dx.doi.org/10.3390/bioengineering10020271.

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Synthetic genomes were designed based on an understanding of natural genomic information, offering an opportunity to engineer and investigate biological systems on a genome-wide scale. Currently, the designer version of the M. mycoides genome and the E. coli genome, as well as most of the S. cerevisiae genome, have been synthesized, and through the cycles of design–build–test and the following engineering of synthetic genomes, many fundamental questions of genome biology have been investigated. In this review, we summarize the use of synthetic genome engineering to explore the structure and function of genomes, and highlight the unique values of synthetic genomics.

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5

Dobrindt, Ulrich, Franziska Agerer, Kai Michaelis, Andreas Janka, Carmen Buchrieser, Martin Samuelson, Catharina Svanborg, Gerhard Gottschalk, Helge Karch, and Jörg Hacker. "Analysis of Genome Plasticity in Pathogenic and Commensal Escherichia coli Isolates by Use of DNA Arrays." Journal of Bacteriology 185, no. 6 (March 15, 2003): 1831–40. http://dx.doi.org/10.1128/jb.185.6.1831-1840.2003.

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ABSTRACT Genomes of prokaryotes differ significantly in size and DNA composition. Escherichia coli is considered a model organism to analyze the processes involved in bacterial genome evolution, as the species comprises numerous pathogenic and commensal variants. Pathogenic and nonpathogenic E. coli strains differ in the presence and absence of additional DNA elements contributing to specific virulence traits and also in the presence and absence of additional genetic information. To analyze the genetic diversity of pathogenic and commensal E. coli isolates, a whole-genome approach was applied. Using DNA arrays, the presence of all translatable open reading frames (ORFs) of nonpathogenic E. coli K-12 strain MG1655 was investigated in 26 E. coli isolates, including various extraintestinal and intestinal pathogenic E. coli isolates, 3 pathogenicity island deletion mutants, and commensal and laboratory strains. Additionally, the presence of virulence-associated genes of E. coli was determined using a DNA “pathoarray” developed in our laboratory. The frequency and distributional pattern of genomic variations vary widely in different E. coli strains. Up to 10% of the E. coli K-12-specific ORFs were not detectable in the genomes of the different strains. DNA sequences described for extraintestinal or intestinal pathogenic E. coli are more frequently detectable in isolates of the same origin than in other pathotypes. Several genes coding for virulence or fitness factors are also present in commensal E. coli isolates. Based on these results, the conserved E. coli core genome is estimated to consist of at least 3,100 translatable ORFs. The absence of K-12-specific ORFs was detectable in all chromosomal regions. These data demonstrate the great genome heterogeneity and genetic diversity among E. coli strains and underline the fact that both the acquisition and deletion of DNA elements are important processes involved in the evolution of prokaryotes.

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6

Mori, Hideo, Hiroshi Mizoguchi, and Tatsuro Fujio. "Escherichia coli minimum genome factory." Biotechnology and Applied Biochemistry 46, no. 3 (March 1, 2007): 157. http://dx.doi.org/10.1042/ba20060107.

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7

Hayashi, Tetsuya. "Genome plasticity of Escherichia coli; insights from genome analysis." Environmental Mutagen Research 27, no. 2 (2005): 117–18. http://dx.doi.org/10.3123/jems.27.117.

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8

Cui, Tailin, Naoki Moro‐oka, Katsufumi Ohsumi, Kenichi Kodama, Taku Ohshima, Naotake Ogasawara, Hirotada Mori, Barry Wanner, Hironori Niki, and Takashi Horiuchi. "Escherichia coli with a linear genome." EMBO reports 8, no. 2 (January 12, 2007): 181–87. http://dx.doi.org/10.1038/sj.embor.7400880.

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9

Kolisnychenko, V. "Engineering a Reduced Escherichia coli Genome." Genome Research 12, no. 4 (April 1, 2002): 640–47. http://dx.doi.org/10.1101/gr.217202.

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10

KOOB, MICHAEL D., ANITA J. SHAW, and DOUGLAS C. CAMERON. "Minimizing the Genome of Escherichia coli." Annals of the New York Academy of Sciences 745, no. 1 (December 17, 2006): 1–3. http://dx.doi.org/10.1111/j.1749-6632.1994.tb44359.x.

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11

Wang, Kaihang, Daniel de la Torre, Wesley E. Robertson, and Jason W. Chin. "Programmed chromosome fission and fusion enable precise large-scale genome rearrangement and assembly." Science 365, no. 6456 (August 29, 2019): 922–26. http://dx.doi.org/10.1126/science.aay0737.

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The design and creation of synthetic genomes provide a powerful approach to understanding and engineering biology. However, it is often limited by the paucity of methods for precise genome manipulation. Here, we demonstrate the programmed fission of the Escherichia coli genome into diverse pairs of synthetic chromosomes and the programmed fusion of synthetic chromosomes to generate genomes with user-defined inversions and translocations. We further combine genome fission, chromosome transplant, and chromosome fusion to assemble genomic regions from different strains into a single genome. Thus, we program the scarless assembly of new genomes with nucleotide precision, a key step in the convergent synthesis of genomes from diverse progenitors. This work provides a set of precise, rapid, large-scale (megabase) genome-engineering operations for creating diverse synthetic genomes.

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12

Rasko, David A., M. J. Rosovitz, Garry S. A. Myers, Emmanuel F. Mongodin, W. Florian Fricke, Pawel Gajer, Jonathan Crabtree, et al. "The Pangenome Structure of Escherichia coli: Comparative Genomic Analysis of E. coli Commensal and Pathogenic Isolates." Journal of Bacteriology 190, no. 20 (August 1, 2008): 6881–93. http://dx.doi.org/10.1128/jb.00619-08.

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ABSTRACT Whole-genome sequencing has been skewed toward bacterial pathogens as a consequence of the prioritization of medical and veterinary diseases. However, it is becoming clear that in order to accurately measure genetic variation within and between pathogenic groups, multiple isolates, as well as commensal species, must be sequenced. This study examined the pangenomic content of Escherichia coli. Six distinct E. coli pathovars can be distinguished using molecular or phenotypic markers, but only two of the six pathovars have been subjected to any genome sequencing previously. Thus, this report provides a seminal description of the genomic contents and unique features of three unsequenced pathovars, enterotoxigenic E. coli, enteropathogenic E. coli, and enteroaggregative E. coli. We also determined the first genome sequence of a human commensal E. coli isolate, E. coli HS, which will undoubtedly provide a new baseline from which workers can examine the evolution of pathogenic E. coli. Comparison of 17 E. coli genomes, 8 of which are new, resulted in identification of ∼2,200 genes conserved in all isolates. We were also able to identify genes that were isolate and pathovar specific. Fewer pathovar-specific genes were identified than anticipated, suggesting that each isolate may have independently developed virulence capabilities. Pangenome calculations indicate that E. coli genomic diversity represents an open pangenome model containing a reservoir of more than 13,000 genes, many of which may be uncharacterized but important virulence factors. This comparative study of the species E. coli, while descriptive, should provide the basis for future functional work on this important group of pathogens.

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13

Lagesen, Karin, Dave W. Ussery, and Trudy M. Wassenaar. "Genome update: the 1000th genome – a cautionary tale." Microbiology 156, no. 3 (March 1, 2010): 603–8. http://dx.doi.org/10.1099/mic.0.038257-0.

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There are now more than 1000 sequenced prokaryotic genomes deposited in public databases and available for analysis. Currently, although the sequence databases GenBank, DNA Database of Japan and EMBL are synchronized continually, there are slight differences in content at the genomes level for a variety of logistical reasons, including differences in format and loading errors, such as those caused by file transfer protocol interruptions. This means that the 1000th genome will be different in the various databases. Some of the data on the highly accessed web pages are inaccurate, leading to false conclusions for example about the largest bacterial genome sequenced. Biological diversity is far greater than many have thought. For example, analysis of multiple Escherichia coli genomes has led to an estimate of around 45 000 gene families — more genes than are recognized in the human genome. Moreover, of the 1000 genomes available, not a single protein is conserved across all genomes. Excluding the members of the Archaea, only a total of four genes are conserved in all bacteria: two protein genes and two RNA genes.

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14

Iguchi, Atsushi, Nicholas R. Thomson, Yoshitoshi Ogura, David Saunders, Tadasuke Ooka, Ian R. Henderson, David Harris, et al. "Complete Genome Sequence and Comparative Genome Analysis of Enteropathogenic Escherichia coli O127:H6 Strain E2348/69." Journal of Bacteriology 191, no. 1 (October 24, 2008): 347–54. http://dx.doi.org/10.1128/jb.01238-08.

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ABSTRACT Enteropathogenic Escherichia coli (EPEC) was the first pathovar of E. coli to be implicated in human disease; however, no EPEC strain has been fully sequenced until now. Strain E2348/69 (serotype O127:H6 belonging to E. coli phylogroup B2) has been used worldwide as a prototype strain to study EPEC biology, genetics, and virulence. Studies of E2348/69 led to the discovery of the locus of enterocyte effacement-encoded type III secretion system (T3SS) and its cognate effectors, which play a vital role in attaching and effacing lesion formation on gut epithelial cells. In this study, we determined the complete genomic sequence of E2348/69 and performed genomic comparisons with other important E. coli strains. We identified 424 E2348/69-specific genes, most of which are carried on mobile genetic elements, and a number of genetic traits specifically conserved in phylogroup B2 strains irrespective of their pathotypes, including the absence of the ETT2-related T3SS, which is present in E. coli strains belonging to all other phylogroups. The genome analysis revealed the entire gene repertoire related to E2348/69 virulence. Interestingly, E2348/69 contains only 21 intact T3SS effector genes, all of which are carried on prophages and integrative elements, compared to over 50 effector genes in enterohemorrhagic E. coli O157. As E2348/69 is the most-studied pathogenic E. coli strain, this study provides a genomic context for the vast amount of existing experimental data. The unexpected simplicity of the E2348/69 T3SS provides the first opportunity to fully dissect the entire virulence strategy of attaching and effacing pathogens in the genomic context.

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15

Mori, Hirotada, Masakazu Kataoka, and Xi Yang. "Past, Present, and Future of Genome Modification in Escherichia coli." Microorganisms 10, no. 9 (September 14, 2022): 1835. http://dx.doi.org/10.3390/microorganisms10091835.

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Escherichia coli K-12 is one of the most well-studied species of bacteria. This species, however, is much more difficult to modify by homologous recombination (HR) than other model microorganisms. Research on HR in E. coli has led to a better understanding of the molecular mechanisms of HR, resulting in technical improvements and rapid progress in genome research, and allowing whole-genome mutagenesis and large-scale genome modifications. Developments using λ Red (exo, bet, and gam) and CRISPR-Cas have made E. coli as amenable to genome modification as other model microorganisms, such as Saccharomyces cerevisiae and Bacillus subtilis. This review describes the history of recombination research in E. coli, as well as improvements in techniques for genome modification by HR. This review also describes the results of large-scale genome modification of E. coli using these technologies, including DNA synthesis and assembly. In addition, this article reviews recent advances in genome modification, considers future directions, and describes problems associated with the creation of cells by design.

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16

Wannier, Timothy M., Aditya M. Kunjapur, Daniel P. Rice, Michael J. McDonald, Michael M. Desai, and George M. Church. "Adaptive evolution of genomically recodedEscherichia coli." Proceedings of the National Academy of Sciences 115, no. 12 (February 13, 2018): 3090–95. http://dx.doi.org/10.1073/pnas.1715530115.

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Efforts are underway to construct several recoded genomes anticipated to exhibit multivirus resistance, enhanced nonstandard amino acid (nsAA) incorporation, and capability for synthetic biocontainment. Although our laboratory pioneered the first genomically recoded organism (Escherichia colistrain C321.∆A), its fitness is far lower than that of its nonrecoded ancestor, particularly in defined media. This fitness deficit severely limits its utility for nsAA-linked applications requiring defined media, such as live cell imaging, metabolic engineering, and industrial-scale protein production. Here, we report adaptive evolution of C321.∆A for more than 1,000 generations in independent replicate populations grown in glucose minimal media. Evolved recoded populations significantly exceeded the growth rates of both the ancestral C321.∆A and nonrecoded strains. We used next-generation sequencing to identify genes mutated in multiple independent populations, and we reconstructed individual alleles in ancestral strains via multiplex automatable genome engineering (MAGE) to quantify their effects on fitness. Several selective mutations occurred only in recoded evolved populations, some of which are associated with altering the translation apparatus in response to recoding, whereas others are not apparently associated with recoding, but instead correct for off-target mutations that occurred during initial genome engineering. This report demonstrates that laboratory evolution can be applied after engineering of recoded genomes to streamline fitness recovery compared with application of additional targeted engineering strategies that may introduce further unintended mutations. In doing so, we provide the most comprehensive insight to date into the physiology of the commonly used C321.∆A strain.

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17

Cummins, Max L., Dmitriy Li, Aeman Ahmad, Rhys Bushell, Amir H. Noormohammadi, Dinidu S. Wijesurendra, Andrew Stent, Marc S. Marenda, and Steven P. Djordjevic. "Whole Genome Sequencing of Avian Pathogenic Escherichia coli Causing Bacterial Chondronecrosis and Osteomyelitis in Australian Poultry." Microorganisms 11, no. 6 (June 6, 2023): 1513. http://dx.doi.org/10.3390/microorganisms11061513.

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Bacterial chondronecrosis with osteomyelitis (BCO) impacts animal welfare and productivity in the poultry industry worldwide, yet it has an understudied pathogenesis. While Avian Pathogenic Escherichia coli (APEC) are known to be one of the main causes, there is a lack of whole genome sequence data, with only a few BCO-associated APEC (APECBCO) genomes available in public databases. In this study, we conducted an analysis of 205 APECBCO genome sequences to generate new baseline phylogenomic knowledge regarding the diversity of E. coli sequence types and the presence of virulence associated genes (VAGs). Our findings revealed the following: (i) APECBCO are phylogenetically and genotypically similar to APEC that cause colibacillosis (APECcolibac), with globally disseminated APEC sequence types ST117, ST57, ST69, and ST95 being predominate; (ii) APECBCO are frequent carriers of ColV-like plasmids that carry a similar set of VAGs as those found in APECcolibac. Additionally, we performed genomic comparisons, including a genome-wide association study, with a complementary collection of geotemporally-matched genomes of APEC from multiple cases of colibacillosis (APECcolibac). Our genome-wide association study found no evidence of novel virulence loci unique to APECBCO. Overall, our data indicate that APECBCO and APECcolibac are not distinct subpopulations of APEC. Our publication of these genomes substantially increases the available collection of APECBCO genomes and provides insights for the management and treatment strategies of lameness in poultry.

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18

Juhas, Mario, Daniel R. Reuß, Bingyao Zhu, and Fabian M. Commichau. "Bacillus subtilis and Escherichia coli essential genes and minimal cell factories after one decade of genome engineering." Microbiology 160, no. 11 (November 1, 2014): 2341–51. http://dx.doi.org/10.1099/mic.0.079376-0.

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Investigation of essential genes, besides contributing to understanding the fundamental principles of life, has numerous practical applications. Essential genes can be exploited as building blocks of a tightly controlled cell ‘chassis’. Bacillus subtilis and Escherichia coli K-12 are both well-characterized model bacteria used as hosts for a plethora of biotechnological applications. Determination of the essential genes that constitute the B. subtilis and E. coli minimal genomes is therefore of the highest importance. Recent advances have led to the modification of the original B. subtilis and E. coli essential gene sets identified 10 years ago. Furthermore, significant progress has been made in the area of genome minimization of both model bacteria. This review provides an update, with particular emphasis on the current essential gene sets and their comparison with the original gene sets identified 10 years ago. Special attention is focused on the genome reduction analyses in B. subtilis and E. coli and the construction of minimal cell factories for industrial applications.

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19

Kang, Yisheng, Tim Durfee, Jeremy D. Glasner, Yu Qiu, David Frisch, Kelly M. Winterberg, and Frederick R. Blattner. "Systematic Mutagenesis of the Escherichia coli Genome." Journal of Bacteriology 186, no. 15 (August 1, 2004): 4921–30. http://dx.doi.org/10.1128/jb.186.15.4921-4930.2004.

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ABSTRACT A high-throughput method has been developed for the systematic mutagenesis of the Escherichia coli genome. The system is based on in vitro transposition of a modified Tn5 element, the Sce-poson, into linear fragments of each open reading frame. The transposon introduces both positive (kanamycin resistance) and negative (I-SceI recognition site) selectable markers for isolation of mutants and subsequent allele replacement, respectively. Reaction products are then introduced into the genome by homologous recombination via the λRed proteins. The method has yielded insertion alleles for 1976 genes during a first pass through the genome including, unexpectedly, a number of known and putative essential genes. Sce-poson insertions can be easily replaced by markerless mutations by using the I-SceI homing endonuclease to select against retention of the transposon as demonstrated by the substitution of amber and/or in-frame deletions in six different genes. This allows a Sce-poson-containing gene to be specifically targeted for either designed or random modifications, as well as permitting the stepwise engineering of strains with multiple mutations. The promiscuous nature of Tn5 transposition also enables a targeted gene to be dissected by using randomly inserted Sce-posons as shown by a lacZ allelic series. Finally, assessment of the insertion sites by an iterative weighted matrix algorithm reveals that these hyperactive Tn5 complexes generally recognize a highly degenerate asymmetric motif on one end of the target site helping to explain the randomness of Tn5 transposition.

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20

Kang, Yisheng, Tim Durfee, Jeremy D. Glasner, Yu Qiu, David Frisch, Kelly M. Winterberg, and Frederick R. Blattner. "Systematic Mutagenesis of the Escherichia coli Genome." Journal of Bacteriology 186, no. 24 (December 15, 2004): 8548. http://dx.doi.org/10.1128/jb.186.24.8548.2004.

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21

Pallen, Mark. "Escherichia Coli: From Genome Sequences to Consequence." Canadian Journal of Infectious Diseases and Medical Microbiology 17, no. 2 (2006): 114–16. http://dx.doi.org/10.1155/2006/345319.

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The present article summarizes a presentation given by Professor Mark Pallen of the School of Medicine at the University of Birmingham (Birmingham, United Kingdom) for the Fourth Stanier Lecture held in Regina, Saskatchewan, on November 9, 2004. Professor Pallen's lecture, entitled 'Escherichia coli: From genome sequences to consequences', provides a summary of the important discoveries of his team of research scientists in the area of genetic sequencing and variations in phenotypic expression.

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22

Xie, Ting, Liang-Yu Fu, Qing-Yong Yang, Heng Xiong, Hongrui Xu, Bin-Guang Ma, and Hong-Yu Zhang. "Spatial features for Escherichia coli genome organization." BMC Genomics 16, no. 1 (2015): 37. http://dx.doi.org/10.1186/s12864-015-1258-1.

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23

O'Brien, Claire. "Entire E. coli genome sequenced–at last." Nature 385, no. 6616 (February 1997): 472. http://dx.doi.org/10.1038/385472a0.

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24

Mellmann, Alexander, Martina Bielaszewska, and Helge Karch. "Intrahost Genome Alterations in Enterohemorrhagic Escherichia coli." Gastroenterology 136, no. 6 (May 2009): 1925–38. http://dx.doi.org/10.1053/j.gastro.2008.12.072.

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25

Posfai, G. "Emergent Properties of Reduced-Genome Escherichia coli." Science 312, no. 5776 (May 19, 2006): 1044–46. http://dx.doi.org/10.1126/science.1126439.

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26

Sheppard, Samuel K., Xavier Didelot, Keith A. Jolley, Aaron E. Darling, Ben Pascoe, Guillaume Meric, David J. Kelly, et al. "Progressive genome‐wide introgression in agriculturalCampylobacter coli." Molecular Ecology 22, no. 4 (December 20, 2012): 1051–64. http://dx.doi.org/10.1111/mec.12162.

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27

Sperandio, Vanessa. "Genome sequence of E. coli O157:H7." Trends in Microbiology 9, no. 4 (April 2001): 159. http://dx.doi.org/10.1016/s0966-842x(01)02023-6.

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28

Méric, Guillaume, Matthew D. Hitchings, Ben Pascoe, and Samuel K. Sheppard. "From Escherich to the Escherichia coli genome." Lancet Infectious Diseases 16, no. 6 (June 2016): 634–36. http://dx.doi.org/10.1016/s1473-3099(16)30066-4.

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29

Tsai, Lu, and Zhirong Sun. "Dynamic flexibility in the Escherichia coli genome." FEBS Letters 507, no. 2 (October 15, 2001): 225–30. http://dx.doi.org/10.1016/s0014-5793(01)02978-7.

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30

Butcher, James. "Geneticists sequence Escherichia coli O157:H7 genome." Lancet 357, no. 9252 (January 2001): 286. http://dx.doi.org/10.1016/s0140-6736(05)71728-1.

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31

Swinbanks, David. "Japan's E. coli genome project falling short." Nature 368, no. 6470 (March 1994): 383. http://dx.doi.org/10.1038/368383a0.

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32

Song, J. Y., R. H. Yoo, S. Y. Jang, W. K. Seong, S. Y. Kim, H. Jeong, S. G. Kang, et al. "Genome Sequence of Enterohemorrhagic Escherichia coli NCCP15658." Journal of Bacteriology 194, no. 14 (June 27, 2012): 3749–50. http://dx.doi.org/10.1128/jb.00653-12.

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33

Jeong, Jaehwan, Namjin Cho, Daehee Jung, and Duhee Bang. "Genome-scale genetic engineering in Escherichia coli." Biotechnology Advances 31, no. 6 (November 2013): 804–10. http://dx.doi.org/10.1016/j.biotechadv.2013.04.003.

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34

Fudge, Jared B. "Retrofitted E. coli genome confers phage resistance." Nature Biotechnology 41, no. 4 (April 2023): 470. http://dx.doi.org/10.1038/s41587-023-01764-1.

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35

McClelland, Michael, and Richard K. Wilson. "Comparison of Sample Sequences of the Salmonella typhiGenome to the Sequence of the Complete Escherichia coliK-12 Genome." Infection and Immunity 66, no. 9 (September 1, 1998): 4305–12. http://dx.doi.org/10.1128/iai.66.9.4305-4312.1998.

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ABSTRACT Raw sequence data representing the majority of a bacterial genome can be obtained at a tiny fraction of the cost of a completed sequence. To demonstrate the utility of such a resource, 870 single-stranded M13 clones were sequenced from a shotgun library of the Salmonella typhi Ty2 genome. The sequence reads averaged over 400 bases and sampled the genome with an average spacing of once every 5,000 bases. A total of 339,243 bases of unique sequence was generated (approximately 7% representation). The sample of 870 sequences was compared to the complete Escherichia coli K-12 genome and to the rest of the GenBank database, which can also be considered a collection of sampled sequences. Despite the incomplete S. typhidata set, interesting categories could easily be discerned. Sixteen percent of the sequences determined from S. typhi had close homologs among known Salmonella sequences (P < 1e −40 in BlastX or BlastN), reflecting the proportion of these genomes that have been sequenced previously; 277 sequences (32%) had no apparent orthologs in the complete E. coli K-12 genome (P > 1e −20), of which 155 sequences (18%) had no close similarities to any sequence in the database (P> 1e −5). Eight of the 277 sequences had similarities to genes in other strains of E. coli or plasmids, and six sequences showed evidence of novel phage lysogens or sequence remnants of phage integrations, including a member of the lambda family (P < 1e −15). Twenty-three sample sequences had a significantly closer similarity a sequence in the database from organisms other than the E. coli/Salmonella clade (which includes Shigella andCitrobacter). These sequences are new candidate lateral transfer events to the S. typhi lineage or deletions on the E. coli K-12 lineage. Eleven putative junctions of insertion/deletion events greater than 100 bp were observed in the sample, indicating that well over 150 such events may distinguishS. typhi from E. coli K-12. The need for automatic methods to more effectively exploit sample sequences is discussed.

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Abdelgader, Sheikheldin A., Donglin Shi, Mianmian Chen, Lei Zhang, Hassan M. A. Hejair, Umair Muhammad, Huochun Yao, and Wei Zhang. "Antibiotics Resistance Genes Screening and Comparative Genomics Analysis of Commensal Escherichia coli Isolated from Poultry Farms between China and Sudan." BioMed Research International 2018 (August 26, 2018): 1–9. http://dx.doi.org/10.1155/2018/5327450.

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Escherichia coli (E. coli) strains, from the gut of animals and humans, harbor wide range of drug resistance genes. A comparative study is conducted on the intestinal E. coli from fecal samples of healthy chicken from China and Sudan in order to monitor the antimicrobial sensitivity pattern. A number of 250 E. coli isolates from chicken farms, including 120 from China and 130 from Sudan, were isolated and identified. All isolates were subjected to susceptibility tests against 10 antibiotics and the distribution of antibiotic resistant genes was confirmed by PCR amplification, involving genes such as ampC, tetA, pKD13, acrA, ermA, ermB, ermC, tetB, mphA, aadA14, aadA1, aac3-1, and aac3- III. Many isolates were found to exhibit resistance against more than one antibiotic. However, the Chinese isolates showed more antibiotics resistance and resistance genes compared to the Sudanese isolates. For better understanding of the multidrug resistance factors, we conducted whole genome analyses of E. coli D107 isolated from China, which revealed that the genome possesses multiple resistance genes including tetracycline, erythromycin, and kanamycin. Furthermore, E. coli D4 isolate from Sudan was more sensitive to antibiotics such as erythromycin, tetracycline, and gentamicin. After analysis by RAST and MAUVE, the two strains showed 89% average nucleotide identity. However, the genomes mostly differed at the number of antibiotics-related genes, as the genome of D107 revealed a considerable number of antibiotics resistance genes such as ermA and mphD which were found to be absent in D4 genome. These outcomes provided confirmation that the poultry farms environment in different countries (China and Sudan) may serve as a potential reservoir of antimicrobial resistance genes and also indicated the evolutionary differences of strains in terms of resistant genes expression.

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Kim, Yong Chan, Heun Choi, Young Ah Kim, Yoon Soo Park, Young Hee Seo, Hyukmin Lee, and Kyungwon Lee. "Risk factors and microbiological features of recurrent Escherichia coli bloodstream infections." PLOS ONE 18, no. 1 (January 10, 2023): e0280196. http://dx.doi.org/10.1371/journal.pone.0280196.

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Understanding the risk factors and microbiological features in recurrent Escherichia coli BSI is helpful for clinicians. Data of patients with E. coil BSI from 2017 to 2018 were collected. Antimicrobial resistance rates of E. coli were determined. We also identified the ST131 and ESBL genotype to evaluate the molecular epidemiology of E. coli. Whole genome sequencing was conducted on the available ESBL-producing E. coli samples. Of 808 patients with E. coli BSI, 57 (6.31%) experienced recurrence; 29 developed at 4–30 days after initial BSI (early onset recurrence) and 28 at 31–270 days after initial BSI (late onset recurrence). One hundred forty-nine patients with single episode, whose samples were available for determining the molecular epidemiology, were selected for comparison. Vascular catheterization (adjusted odds ratio [aOR], 4.588; 95% confidence interval [CI], 1.049–20.068), ESBL phenotype (aOR, 2.037; 95% CI, 1.037–3.999) and SOFA score ≥9 (aOR, 3.210; 95% CI, 1.359–7.581) were independent risk factors for recurrence. The proportion of ST131 and ESBL genotype was highest in early onset recurrent BSI (41.4% and 41.4%, respectively), from which E. coil had the highest resistance rates to most antimicrobial agents. Whole genome sequencing on 27 of ESBL-producing E. coli (11 from single episode, 11 from early onset recurrence, and 5 from late onset recurrence) demonstrated that various virulence factors, resistant genes, and plasmid types existed in isolates from all types of BSI. Risk factors contributing to the recurrence and microbiological features of E. coli causing recurrent BSI may be helpful for management planning in the clinical setting.

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Korf, Imke H. E., Jan P. Meier-Kolthoff, Evelien M. Adriaenssens, Andrew M. Kropinski, Manfred Nimtz, Manfred Rohde, Mark J. van Raaij, and Johannes Wittmann. "Still Something to Discover: Novel Insights into Escherichia coli Phage Diversity and Taxonomy." Viruses 11, no. 5 (May 17, 2019): 454. http://dx.doi.org/10.3390/v11050454.

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The aim of this study was to gain further insight into the diversity of Escherichia coli phages followed by enhanced work on taxonomic issues in that field. Therefore, we present the genomic characterization and taxonomic classification of 50 bacteriophages against E. coli isolated from various sources, such as manure or sewage. All phages were examined for their host range on a set of different E. coli strains, originating, e.g., from human diagnostic laboratories or poultry farms. Transmission electron microscopy revealed a diversity of morphotypes (70% Myo-, 22% Sipho-, and 8% Podoviruses), and genome sequencing resulted in genomes sizes from ~44 to ~370 kb. Annotation and comparison with databases showed similarities in particular to T4- and T5-like phages, but also to less-known groups. Though various phages against E. coli are already described in literature and databases, we still isolated phages that showed no or only few similarities to other phages, namely phages Goslar, PTXU04, and KWBSE43-6. Genome-based phylogeny and classification of the newly isolated phages using VICTOR resulted in the proposal of new genera and led to an enhanced taxonomic classification of E. coli phages.

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Hochhauser, Dina, Adi Millman, and Rotem Sorek. "The defense island repertoire of the Escherichia coli pan-genome." PLOS Genetics 19, no. 4 (April 6, 2023): e1010694. http://dx.doi.org/10.1371/journal.pgen.1010694.

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It has become clear in recent years that anti-phage defense systems cluster non-randomly within bacterial genomes in so-called “defense islands”. Despite serving as a valuable tool for the discovery of novel defense systems, the nature and distribution of defense islands themselves remain poorly understood. In this study, we comprehensively mapped the defense system repertoire of >1,300 strains of Escherichia coli, the most widely studied organism for phage-bacteria interactions. We found that defense systems are usually carried on mobile genetic elements including prophages, integrative conjugative elements and transposons, which preferentially integrate at several dozens of dedicated hotspots in the E. coli genome. Each mobile genetic element type has a preferred integration position but can carry a diverse variety of defensive cargo. On average, an E. coli genome has 4.7 hotspots occupied by defense system-containing mobile elements, with some strains possessing up to eight defensively occupied hotspots. Defense systems frequently co-localize with other systems on the same mobile genetic element, in agreement with the observed defense island phenomenon. Our data show that the overwhelming majority of the E. coli pan-immune system is carried on mobile genetic elements, explaining why the immune repertoire varies substantially between different strains of the same species.

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Weinroth, Margaret D., and James L. Bono. "Comparative Genomics of Escherichia coli Serotype O55:H7 Using Complete Closed Genomes." Microorganisms 10, no. 8 (July 30, 2022): 1545. http://dx.doi.org/10.3390/microorganisms10081545.

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Escherichia coli O55:H7 is a human foodborne pathogen and is recognized as the progenitor strain of E. coli O157:H7. While this strain is important from a food safety and genomic evolution standpoint, much of the genomic diversity of E. coli O55:H7 has been demonstrated using draft genomes. Here, we combine the four publicly available E. coli O55:H7 closed genomes with six newly sequenced closed genomes to provide context to this strain’s genomic diversity. We found significant diversity within the 10 E. coli O55:H7 strains that belonged to three different sequence types. The prophage content was about 10% of the genome, with three prophages common to all strains and seven unique to one strain. Overall, there were 492 insertion sequences identified within the six new sequence strains, with each strain on average containing 75 insertions (range 55 to 114). A total of 31 plasmids were identified between all isolates (range 1 to 6), with one plasmid (pO55) having an identical phylogenetic tree as the chromosome. The release and comparison of these closed genomes provides new insight into E. coli O55:H7 diversity and its ability to cause disease in humans.

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Fukiya, Satoru, Hiroshi Mizoguchi, Toru Tobe, and Hideo Mori. "Extensive Genomic Diversity in Pathogenic Escherichia coli and Shigella Strains Revealed by Comparative Genomic Hybridization Microarray." Journal of Bacteriology 186, no. 12 (June 15, 2004): 3911–21. http://dx.doi.org/10.1128/jb.186.12.3911-3921.2004.

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ABSTRACT Escherichia coli, including the closely related genus Shigella, is a highly diverse species in terms of genome structure. Comparative genomic hybridization (CGH) microarray analysis was used to compare the gene content of E. coli K-12 with the gene contents of pathogenic strains. Missing genes in a pathogen were detected on a microarray slide spotted with 4,071 open reading frames (ORFs) of W3110, a commonly used wild-type K-12 strain. For 22 strains subjected to the CGH microarray analyses 1,424 ORFs were found to be absent in at least one strain. The common backbone of the E. coli genome was estimated to contain about 2,800 ORFs. The mosaic distribution of absent regions indicated that the genomes of pathogenic strains were highly diversified becasue of insertions and deletions. Prophages, cell envelope genes, transporter genes, and regulator genes in the K-12 genome often were not present in pathogens. The gene contents of the strains tested were recognized as a matrix for a neighbor-joining analysis. The phylogenic tree obtained was consistent with the results of previous studies. However, unique relationships between enteroinvasive strains and Shigella, uropathogenic, and some enteropathogenic strains were suggested by the results of this study. The data demonstrated that the CGH microarray technique is useful not only for genomic comparisons but also for phylogenic analysis of E. coli at the strain level.

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Chen, Jingchao, Yi Li, Kun Zhang та Hailei Wang. "Whole-Genome Sequence of Phage-Resistant Strain Escherichia coli DH5α". Genome Announcements 6, № 10 (8 березня 2018). http://dx.doi.org/10.1128/genomea.00097-18.

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ABSTRACT The genomes of many strains of Escherichia coli have been sequenced, as this organism is a classic model bacterium. Here, we report the genome sequence of Escherichia coli DH5α, which is resistant to a T4 bacteriophage (CCTCC AB 2015375), while its other homologous E. coli strains, such as E. coli BL21, DH10B, and MG1655, are not resistant to phage invasions. Thus, understanding of the genome of the DH5α strain, along with comparative analysis of its genome sequence along with other sequences of E. coli strains, may help to reveal the bacteriophage resistance mechanism of E. coli .

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Tantoso, Erwin, Birgit Eisenhaber, Miles Kirsch, Vladimir Shitov, Zhiya Zhao, and Frank Eisenhaber. "To kill or to be killed: pangenome analysis of Escherichia coli strains reveals a tailocin specific for pandemic ST131." BMC Biology 20, no. 1 (June 16, 2022). http://dx.doi.org/10.1186/s12915-022-01347-7.

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Abstract Background Escherichia coli (E. coli) has been one of the most studied model organisms in the history of life sciences. Initially thought just to be commensal bacteria, E. coli has shown wide phenotypic diversity including pathogenic isolates with great relevance to public health. Though pangenome analysis has been attempted several times, there is no systematic functional characterization of the E. coli subgroups according to the gene profile. Results Systematically scanning for optimal parametrization, we have built the E. coli pangenome from 1324 complete genomes. The pangenome size is estimated to be ~25,000 gene families (GFs). Whereas the core genome diminishes as more genomes are added, the softcore genome (≥95% of strains) is stable with ~3000 GFs regardless of the total number of genomes. Apparently, the softcore genome (with a 92% or 95% generation threshold) can define the genome of a bacterial species listing the critically relevant, evolutionarily most conserved or important classes of GFs. Unsupervised clustering of common E. coli sequence types using the presence/absence GF matrix reveals distinct characteristics of E. coli phylogroups B1, B2, and E. We highlight the bi-lineage nature of B1, the variation of the secretion and of the iron acquisition systems in ST11 (E), and the incorporation of a highly conserved prophage into the genome of ST131 (B2). The tail structure of the prophage is evolutionarily related to R2-pyocin (a tailocin) from Pseudomonas aeruginosa PAO1. We hypothesize that this molecular machinery is highly likely to play an important role in protecting its own colonies; thus, contributing towards the rapid rise of pandemic E. coli ST131. Conclusions This study has explored the optimized pangenome development in E. coli. We provide complete GF lists and the pangenome matrix as supplementary data for further studies. We identified biological characteristics of different E. coli subtypes, specifically for phylogroups B1, B2, and E. We found an operon-like genome region coding for a tailocin specific for ST131 strains. The latter is a potential killer weapon providing pandemic E. coli ST131 with an advantage in inter-bacterial competition and, suggestively, explains their dominance as human pathogen among E. coli strains.

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Abram, Kaleb, Zulema Udaondo, Carissa Bleker, Visanu Wanchai, Trudy M. Wassenaar, Michael S. Robeson, and David W. Ussery. "Mash-based analyses of Escherichia coli genomes reveal 14 distinct phylogroups." Communications Biology 4, no. 1 (January 26, 2021). http://dx.doi.org/10.1038/s42003-020-01626-5.

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AbstractIn this study, more than one hundred thousand Escherichia coli and Shigella genomes were examined and classified. This is, to our knowledge, the largest E. coli genome dataset analyzed to date. A Mash-based analysis of a cleaned set of 10,667 E. coli genomes from GenBank revealed 14 distinct phylogroups. A representative genome or medoid identified for each phylogroup was used as a proxy to classify 95,525 unassembled genomes from the Sequence Read Archive (SRA). We find that most of the sequenced E. coli genomes belong to four phylogroups (A, C, B1 and E2(O157)). Authenticity of the 14 phylogroups is supported by several different lines of evidence: phylogroup-specific core genes, a phylogenetic tree constructed with 2613 single copy core genes, and differences in the rates of gene gain/loss/duplication. The methodology used in this work is able to reproduce known phylogroups, as well as to identify previously uncharacterized phylogroups in E. coli species.

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Kolenda, Rafał, Katarzyna Sidorczuk, Mateusz Noszka, Adrianna Aleksandrowicz, Muhammad Moman Khan, Michał Burdukiewicz, Derek Pickard, and Peter Schierack. "Genome placement of alpha-haemolysin cluster is associated with alpha-haemolysin sequence variation, adhesin and iron acquisition factor profile of Escherichia coli." Microbial Genomics 7, no. 12 (December 23, 2021). http://dx.doi.org/10.1099/mgen.0.000743.

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Since the discovery of haemolysis, many studies focused on a deeper understanding of this phenotype in Escherichia coli and its association with other virulence genes, diseases and pathogenic attributes/functions in the host. Our virulence-associated factor profiling and genome-wide association analysis of genomes of haemolytic and nonhaemolytic E. coli unveiled high prevalence of adhesins, iron acquisition genes and toxins in haemolytic bacteria. In the case of fimbriae with high prevalence, we analysed sequence variation of FimH, EcpD and CsgA, and showed that different adhesin variants were present in the analysed groups, indicating altered adhesive capabilities of haemolytic and nonhaemolytic E. coli . Analysis of over 1000 haemolytic E. coli genomes revealed that they are pathotypically, genetically and antigenically diverse, but their adhesin and iron acquisition repertoire is associated with genome placement of hlyCABD cluster. Haemolytic E. coli with chromosome-encoded alpha-haemolysin had high frequency of P, S, Auf fimbriae and multiple iron acquisition systems such as aerobactin, yersiniabactin, salmochelin, Fec, Sit, Bfd and hemin uptake systems. Haemolytic E. coli with plasmid-encoded alpha-haemolysin had similar adhesin profile to nonpathogenic E. coli, with high prevalence of Stg, Yra, Ygi, Ycb, Ybg, Ycf, Sfm, F9 fimbriae, Paa, Lda, intimin and type 3 secretion system encoding genes. Analysis of HlyCABD sequence variation revealed presence of variants associated with genome placement and pathotype.

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Dutta, Vikrant, Eric Altermann, Jonathan Olson, Gregory Allan Wray, Robin M. Siletzky, and Sophia Kathariou. "Whole-Genome Sequences of Agricultural, Host-Associated Campylobacter coli and Campylobacter jejuni Strains." Genome Announcements 4, no. 4 (August 18, 2016). http://dx.doi.org/10.1128/genomea.00833-16.

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We report here the genome sequences of four agricultural, multidrug-resistant Campylobacter spp.: C. coli 11601 and C. jejuni 11601MD, isolated from turkey cecum and jejunum, respectively, and C. coli 6067 and C. coli 6461, isolated from turkey-house water and swine feces, respectively. The genomes provide insights on Campylobacter antimicrobial resistance and host adaptations.

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Yang, Tong, and Feng Gao. "High-quality pan-genome of Escherichia coli generated by excluding confounding and highly similar strains reveals an association between unique gene clusters and genomic islands." Briefings in Bioinformatics, July 9, 2022. http://dx.doi.org/10.1093/bib/bbac283.

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Abstract The pan-genome analysis of bacteria provides detailed insight into the diversity and evolution of a bacterial population. However, the genomes involved in the pan-genome analysis should be checked carefully, as the inclusion of confounding strains would have unfavorable effects on the identification of core genes, and the highly similar strains could bias the results of the pan-genome state (open versus closed). In this study, we found that the inclusion of highly similar strains also affects the results of unique genes in pan-genome analysis, which leads to a significant underestimation of the number of unique genes in the pan-genome. Therefore, these strains should be excluded from pan-genome analysis at the early stage of data processing. Currently, tens of thousands of genomes have been sequenced for Escherichia coli, which provides an unprecedented opportunity as well as a challenge for pan-genome analysis of this classical model organism. Using the proposed strategies, a high-quality E. coli pan-genome was obtained, and the unique genes was extracted and analyzed, revealing an association between the unique gene clusters and genomic islands from a pan-genome perspective, which may facilitate the identification of genomic islands.

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Montealegre, Maria Camila, Alba Talavera Rodríguez, Subarna Roy, Muhammed Iqbal Hossain, Mohammad Aminul Islam, Val F. Lanza, and Timothy R. Julian. "High Genomic Diversity and Heterogenous Origins of Pathogenic and Antibiotic-Resistant Escherichia coli in Household Settings Represent a Challenge to Reducing Transmission in Low-Income Settings." mSphere 5, no. 1 (January 15, 2020). http://dx.doi.org/10.1128/msphere.00704-19.

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ABSTRACT Escherichia coli is present in multiple hosts and environmental compartments as a normal inhabitant, temporary or persistent colonizer, and as a pathogen. Transmission of E. coli between hosts and with the environment is considered to occur more often in areas with poor sanitation. We performed whole-genome comparative analyses on 60 E. coli isolates from soils and fecal sources (cattle, chickens, and humans) in households in rural Bangladesh. Isolates from household soils were in multiple branches of the reconstructed phylogeny, intermixed with isolates from fecal sources. Pairwise differences between all strain pairs were large (minimum, 189 single nucleotide polymorphisms [SNPs]), suggesting high diversity and heterogeneous origins of the isolates. The presence of multiple virulence and antibiotic resistance genes is indicative of the risk that E. coli from soil and feces represent for the transmission of variants that pose potential harm to people. Analysis of the accessory genomes of the Bangladeshi E. coli relative to E. coli genomes available in NCBI identified a common pool of accessory genes shared among E. coli isolates in this geographic area. Together, these findings indicate that in rural Bangladesh, a high level of E. coli in soil is likely driven by contributions from multiple and diverse E. coli sources (human and animal) that share an accessory gene pool relatively unique to previously published E. coli genomes. Thus, interventions to reduce environmental pathogen or antimicrobial resistance transmission should adopt integrated One Health approaches that consider heterogeneous origins and high diversity to improve effectiveness and reduce prevalence and transmission. IMPORTANCE Escherichia coli is reported in high levels in household soil in low-income settings. When E. coli reaches a soil environment, different mechanisms, including survival, clonal expansion, and genetic exchange, have the potential to either maintain or generate E. coli variants with capabilities of causing harm to people. In this study, we used whole-genome sequencing to identify that E. coli isolates collected from rural Bangladeshi household soils, including pathogenic and antibiotic-resistant variants, are diverse and likely originated from multiple diverse sources. In addition, we observed specialization of the accessory genome of this Bangladeshi E. coli compared to E. coli genomes available in current sequence databases. Thus, to address the high level of pathogenic and antibiotic-resistant E. coli transmission in low-income settings, interventions should focus on addressing the heterogeneous origins and high diversity.

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Nguyen, Marcus, Zachary Elmore, Clay Ihle, Francesco S. Moen, Adam D. Slater, Benjamin N. Turner, Bruce Parrello, Aaron A. Best, and James J. Davis. "Predicting variable gene content in Escherichia coli using conserved genes." mSystems, June 14, 2023. http://dx.doi.org/10.1128/msystems.00058-23.

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ABSTRACT Having the ability to predict the protein-encoding gene content of an incomplete genome or metagenome-assembled genome is important for a variety of bioinformatic tasks. In this study, as a proof of concept, we built machine learning classifiers for predicting variable gene content in Escherichia coli genomes using only the nucleotide k-mers from a set of 100 conserved genes as features. Protein families were used to define orthologs , and a single classifier was built for predicting the presence or absence of each protein family occurring in 10%–90% of all E. coli genomes. The resulting set of 3,259 extreme gradient boosting classifiers had a per-genome average macro F1 score of 0.944 [0.943–0.945, 95% CI]. We show that the F1 scores are stable across multi-locus sequence types and that the trend can be recapitulated by sampling a smaller number of core genes or diverse input genomes. Surprisingly, the presence or absence of poorly annotated proteins, including “hypothetical proteins” was accurately predicted (F1 = 0.902 [0.898–0.906, 95% CI]). Models for proteins with horizontal gene transfer-related functions had slightly lower F1 scores but were still accurate (F1s = 0.895, 0.872, 0.824, and 0.841 for transposon, phage, plasmid, and antimicrobial resistance-related functions, respectively). Finally, using a holdout set of 419 diverse E. coli genomes that were isolated from freshwater environmental sources, we observed an average per-genome F1 score of 0.880 [0.876–0.883, 95% CI], demonstrating the extensibility of the models. Overall, this study provides a framework for predicting variable gene content using a limited amount of input sequence data. IMPORTANCE Having the ability to predict the protein-encoding gene content of a genome is important for assessing genome quality, binning genomes from shotgun metagenomic assemblies, and assessing risk due to the presence of antimicrobial resistance and other virulence genes. In this study, we built a set of binary classifiers for predicting the presence or absence of variable genes occurring in 10%–90% of all publicly available E. coli genomes. Overall, the results show that a large portion of the E. coli variable gene content can be predicted with high accuracy, including genes with functions relating to horizontal gene transfer. This study offers a strategy for predicting gene content using limited input sequence data.

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Wan, Yu, Ewurabena Mills, Rhoda C. Y. Leung, Ana Vieira, Elita Jauneikaite, Xiangyun Zhi, Nicholas Croucher, Matthew J. Ellington, and Shiranee Sriskandan. "Nitrofurantoin-resistant Escherichia coli in the UK: genetic determinants, diversity, and undetected occurrences." Access Microbiology 4, no. 5 (May 27, 2022). http://dx.doi.org/10.1099/acmi.ac2021.po0086.

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Background Antimicrobial resistance in enteric or urinary E. coli might predispose invasive E. coli infection and bacteraemia. Nitrofurantoin resistance occurs in <6% of UK urinary E. coli isolates, however, 2018 national recommendations to prescribe nitrofurantoin for uncomplicated urinary tract infection (UTI) raised concerns for increased prevalence of nitrofurantoin-resistant E. coliin the future. Therefore, we investigated mechanisms of nitrofurantoin resistance in UK E. coli isolates and assessed their occurrences in a large dataset of E. coli genomes. Methods To elucidate chromosomal and acquired genetic determinants of nitrofurantoin resistance in E. coli, we analysed whole-genome sequences of nine randomly selected nitrofurantoin-resistant UTI E. coli isolates from West London. We then performed targeted analysis of 12,412 E. coli genomes collected from across the UK and predicted nitrofurantoin susceptibility from identified genotypes. Results Using comparative genomics, we found known and novel point mutations or insertion sequences (ISs) in chromosomal genes encoding oxygen-insensitive nitroreductases NfsA and NfsB in the nine isolates. Most of these genetic alterations resulted in gene inactivation. We also identified the same kinds of mutations in NfsA, NfsB, and their associated enzyme RibE in a number of 12,412 E. coli genomes. We also observed homoplasic mutations in all these proteins. By contrast, multidrug efflux pump OqxAB, which confers resistance when horizontally transferred, was only encoded by one genome. Conclusions Chromosomal de novo mutations and ISs are main causes of nitrofurantoin resistance in UK E. coli. Prevalence of nitrofurantoin resistance should be monitored among urine, blood, and enteric isolates as nitrofurantoin exposure increases.

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