Caister Academic Press

Pathogenic Escherichia coli:  Evolution, Omics, Detection and Control | Book

Publisher: Caister Academic Press
Edited by: Pina M. Fratamico, Yanhong Liu and Christopher H. Sommers
Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor, USA
Pages: c. 270
Paperback:
Publication date: April 2018Buy book
ISBN: 978-1-910190-77-7
Price: GB £159 or US $319
Ebook:
Publication date: April 2018Buy ebook
ISBN: 978-1-910190-78-4
Price: GB £159 or US $319
DOI: https://doi.org/10.21775/9781910190777

Escherichia coli is an important member of the normal healthy microbiome of humans and other mammals. In addition, some strains are thought to be probiotic, and therefore beneficial to the host. However, other strains of E. coli have evolved into highly versatile, and frequently deadly, pathogens, the resultant diseases causing significant economic loss and public health burdens worldwide. Recent studies have shown that the E. coli genome has a high plasticity allowing it to adapt to new niches and survive in stressful conditions and to evolve into new hybrid strains with shared genes, including virulence genes. Omics and whole genome sequencing approaches have transformed research in this field allowing fascinating new insights into the molecular and cellular biology of the bacterium thus paving the way for the development of novel therapeutic strategies.

Under the expert guidance of the editors in this book, renowned international authors provide timely and up-to-date reviews of current cutting-edge E. coli omics, molecular- and cellular-biology research. Topics range from E. coli genome plasticity and evolution to the application of omics technologies for in silico modeling to understand stress-triggered physiological responses.

This authoritative volume is essential reading for scientists, both experts and students, working on pathogenic E. coli in academia, government, and biotechnology companies. It is also a must-read for anyone with an interest in bacterial pathogenesis and an important acquisition for all microbiology libraries.

Table of contents
1. Escherichia coli Pathotypes
James L. Smith and Pina M. Fratamico
Escherichia coli strains are important commensals of the intestinal tract of humans and animals; however, pathogenic strains, including diarrhoea-inducing E. coli and extraintestinal pathogenic E. coli, exist. Intestinal E. coli pathotypes may cause a dehydrating watery diarrhoea, or more severe diseases such as heamorrhagic colitis and heamolytic uremic syndrome. The different E. coli pathotypes can be transmitted to humans via contaminated food and water, and transmission can also occur through animal and person-to-person contact. The extraintestinal pathogenic E. coli reside in the intestinal tract but may escape to cause disease in bodily sites outside of the gut and can cause urinary tract infection, neonatal meningitis, sepsis, and other types of infections. Avian pathogenic E. coli are a cause of poultry diseases and are closely related to extraintestinal pathogenic E. coli strains that cause human infections. Poultry contaminated with extraintestinal pathogenic E. coli and avian pathogenic E. coli may be an important source of E. coli strains that cause illness in humans at non-intestinal sites; however, additional research is needed to confirm this. Furthermore, hybrid E. coli strains have emerged in recent years that harbour virulence genes from more than one pathotype, and these have caused serious outbreaks and infections.
2. Escherichia coli Genome Plasticity and Evolution
David W. Lacher, Michael L. Kotewicz, Mark K. Mammel and Christopher A. Elkins
Escherichia coli are associated with environmental, commensal, and emergent pathogenic niches. Extensive genome sequencing has expanded and refined the landscape for this microbial species beyond traditional taxonomy reliant on fragmented phenotypic and genetic data. Core genome sequences provide a new standard to investigate clonal relationships, diversity, species definition, and strain classification. Specifically, major phylogroups originally established by multilocus enzyme electrophoresis are recapitulated with greater resolution than previously reported and new environmental cryptic lineages sharpen perspectives on species definition. Shigella species are interwoven across this high resolution landscape again providing further evidence to reject their species distinction. We use E. coli O157:H7 as a paradigm for pathogen evolution and offer critical analyses of associated clade and lineage models with respect to core genome phylogenetics. This perspective is further stratified and extended to the strain level to highlight the plasticity of genome architectures in these pathogens. In aggregate, the species landscape is expectedly well-populated from a clinical perspective but is under-represented from environmental and commensal niches. Regardless, the robustness in framework and fundamental architecture of core genome analysis should be foundational for future molecular systematic applications.
3. Diarrhoeagenic Escherichia coli: Virulence Genes and Other Markers for Detection and Typing
Stefano Morabito and Rosangela Tozzoli
Escherichia coli are usually commensal bacteria, harmlessly colonizing the gastrointestinal tract of mammals, where they exert an advantageous effect on the host. Nonetheless, some strains have evolved the ability to induce disease in humans in many anatomical sites. Among these, diarrhoeagenic E. coli (DEC) cause enteric/diarrhoeal illness, sometimes with systemic complications. DEC are subdivided into pathotypes on the basis of the colonization mechanism and the toxins elaborated, which determine the clinical, pathological, and epidemiological features of the disease induced. DEC pathotypes include enterotoxigenic (ETEC), enteroinvasive (EIEC), enteropathogenic (EPEC), enteroaggregative (EAEC), and Shiga toxin producing E. coli (STEC). In order to discriminate pathogenic E. coli strains from commensal E. coli, pathotype-specific genetic markers are generally employed for the diagnosis of the infections and strain characterization. This chapter describes the different DEC pathotypes, in order to provide a general picture of their virulence mechanisms and the associated genetic determinants, with the aim of illustrating the molecular targets used for their identification and typing.
4. Extra-intestinal Pathogenic Escherichia coli (ExPEC): Characteristics, Virulence Genes, Detection, and Control
Jeroen Geurtsen and Jan T. Poolman
Extra-intestinal pathogenic Escherichia coli (ExPEC) are major human pathogens that carry combinations of genes encoding colonization factors and toxins that allow infection outside of the gastrointestinal tract, and that act to suppress host immune responses. Subgroups within the ExPEC family cause urinary tract infections, urosepsis, bacteraemia, and neonatal meningitis, and they may be associated with inflammatory bowel disease. However, clinical distinctions are blurred because ExPEC strains may cause disease in more than one site, and the genomic and phenotypic diversity amongst ExPEC has so far eluded clear-cut classification. A virulent, antibiotic-resistant clonal group called ST131 emerged and spread globally after 2000, and is now the most common cause of multi-resistant ExPEC infections worldwide. Antibiotic resistant ExPEC and the looming threat of a pan-resistant ExPEC strain represent a worldwide threat and the major challenge facing infection control in the 21st century. The availability of E. coli vaccines could reduce the prevalence of targeted strains and make positive inroads on antibiotic resistance levels. Advances in ExPEC infection control requires a better understanding of the interactions between pathogen and host and factors that drive fitness, transmissibility, and virulence.
5. Bacteriophage-based Strategies to Control Pathogenic Escherichia coli in Humans and Animals
Michca Gordon, Brigitte Cadieux and Lawrence D. Goodridge
Escherichia coli is a bacterial species with the ability to cause a wide spectrum of diseases among humans and other animals. A great deal of research has been conducted to find ways to control this diffuse group of pathogens. Such research has accelerated recently with the understanding that the overuse of antibiotics has contributed to a rapid increase in the spread of multidrug resistant bacteria. Additionally, in some cases (i.e. treatment of Shiga toxin producing E. coli infections), antibiotic treatment is contraindicated, necessitating the development of alternative treatment strategies. This review explores the use of bacteriophages (phages) as a biocontrol strategy, and their potential to treat E. coli infections in humans and food animals.
6. New Developments in Detection Technologies for Escherichia coli and Other Pathogenic Organisms
Wen Ren, Renjie Wang, Lei Ouyang and Joseph Irudayaraj
Escherichia coli O157:H7 and other Shiga-toxin-producing E. coli (STEC), among other pathogens, are a serious threat to public safety and health. A gap between the zero tolerance regulatory requirement for O157:H7 and several other STEC serogroups, the challenges related to diverse sample conditions, and the analytical methods currently being used still exists, requiring additional research efforts. Due to advances in material science, instrumentation, and bioanalytical techniques, significant progress has been made on all aspects of technology development, including sample preparation; however, challenges remain. In this chapter , we review the unique strategies proposed for pathogen detection with a primary focus on technology development, with potential implications for monitoring for STEC.
7. Understanding Pathogenic Escherichia coli Through Whole-genome Sequencing
Valeria Michelacci and Eelco Franz
Escherichia coli is a highly diverse microorganism with very different eco-evolutionary paths, ranging from commensalism to highly virulent intestinal and extra-intestinal pathovars. The recent broad access to whole-genome sequencing technology has expanded the understanding of the genomic basis of this diversity in an unprecedented way, but without undermining the prevailing views on E. coli diversity and phylogeny based on older low-resolution typing methods. Genomics indicate that in addition to recombination and mutation the acquisition and loss of genes is a major source for genetic variation in E. coli. The relatively small core-genome compared to a large pan-genome led to the recognition of continued diversification by gene acquisition. Genomics provides insights into the plasticity of the pathovars concept and led to the current viewpoint of the apparent continuum of pathogenic E. coli rather than strictly separated pathovars. The chimaeric and dynamic genome of E. coli provides a challenge to the useful application of genomics into public health (i.e. diagnostics, risk assessment, surveillance and disease-outbreak investigation). The combined study of the variation of different fractions of the genomes, which are subjected to different mutation rates such as the core and the accessory genome could eventually provide the best way forward to a consensus typing approach.
8. Use of Whole-genome Sequencing to Improve Investigations of Outbreaks of Escherichia coli
Claire Jenkins
The aim of this chapter is to evaluate the use of whole-genome sequencing (WGS) data for detecting and investigating outbreaks of Escherichia coli. The methods available for assessing the relatedness between isolates of E. coli, and their use in public health microbiology, are summarised. WGS typing methods are suitable for all pathotypes of E. coli and provide an unprecedented level of strain discrimination. WGS typing is robust and utilises stable genetic markers that can elucidate the evolutionary context of emerging pathogenic strains. The robustness of the approach ensures confidence in the microbiological identification of linked cases when epidemiological links are obscured. Long-read technology will facilitate the analysis of loss and acquisition of mobile genetic elements in the accessory genome, and improve our understanding of the impact of short-term evolutionary changes during outbreak investigations. There is increasing evidence that the geographical origin of an isolate can be inferred from the phylogeny. Expanding WGS-based typing analysis globally will improve trace-back investigations in the event of a foodborne outbreak, ensuring the rapid implementation of interventions to protect public health. The importance of publicly available WGS data linked to the clinical, epidemiological and environmental context of the sequenced strain cannot be underestimated.
9. Data Processing of Escherichia coli Genome Sequencing, Characterization, and Comparison
Gian Marco Baranzoni, Erin R. Reichenberger and David S. Needleman
Pathogenic Escherichia coli continue to raise concerns as one of the major causes of foodborne diseases, bloodstream infections, and urinary tract infections. The remarkable advances in DNA sequencing technologies offer new alternative approaches for detection, characterisation, and tracking of pathogenic E. coli strains with higher resolution and rapid analysis time. This chapter focuses on the main steps for analysing whole-genome sequencing data and includes tools and databases suitable for E. coli genome analysis by scientists with programming and non-programming backgrounds. In particular, different sequencing platforms, typical input/output file formats, and raw data inspection and quality control assessment strategies are reviewed. Also discussed are de novo genome assembly, draft assembly improvement, and assembly visualization, as well as E. coli predictive genomic tools for serotyping and detection of virulence genes, antimicrobial resistance genes, and mobile genetic elements. Examples of genetic content comparisons and pan-genome characterisation and phylogeny are provided.
10. Culture-independent Sequence-based Approaches for Diagnostics and Food Safety Testing
Susan R. Leonard and Christopher A. Elkins
Technological advances in genome sequencing have been leveraged to determine microbial compositions of sample matrices without culturing for individual bacterial species. Such metagenomics approaches have only recently been effectively utilized in pathogenic Escherichia coli research. This chapter provides an overview of current metagenomics research and applications, bioinformatic analysis tools, and considerations for detection sensitivity as it relates to E. coli pathogens in diagnostics and food safety testing. By bioinformatically mining the metagenomic dataset, E. coli serotype, virulence determinants, and antimicrobial susceptibility can be determined. Strain-level discrimination is complex and may be complicated by indigenous E. coli strains in the sample microbiota. Nevertheless, the application of metagenomics has the potential benefit of rapid diagnosis or characterisation of a contaminating E. coli pathogen in food products. This would be particularly valuable for epidemiological efforts and source attribution during outbreak investigations. Furthermore, as the entire microbial community and relative abundances are defined, the effect of perturbations in the microbial community on the growth or survival of E. coli pathogens can be elucidated. Bioinformatic analysis tools yielding reliably accurate results presented with a straightforward interpretation will enhance the practicality of metagenomics as a surveillance method in the future.
11. Use of Omic Technologies to Develop Strategies to Control Escherichia coli from Farm to Table
Teresa M. Bergholz and Manoj K. Shah
The food supply is a series of complex environments which can pose a number of stresses to microbes. These stresses include intrinsic stresses inherent to a given food, such as pH and water activity. These stresses also include extrinsic factors that can vary during each step of food harvesting and processing, including temperature and relative humidity, as well as stresses specific to food processing. Bacteria possess a wide range of strategies to adapt to changing environmental conditions in order to survive under suboptimal conditions. These stress responses can be complex, involving activation of regulatory networks and cascades of gene and protein expression. Omics technologies allowing for the measurement of global changes in gene or protein expression, or changes in the metabolome, can provide insights into the molecular mechanisms that a bacterium utilizes to adapt to different environmental stresses. The aim of this chapter is to provide an overview of the available data assessing global changes in Shiga-toxin-producing Escherichia coli (STEC) that facilitate our understanding of how this pathogen adapts to stresses presented at different stages of food production, with the goal of using these insights to develop control measures that will effectively reduce the presence of this pathogen in foods.
12. Application of Omics Technologies for in Silico Modelling to Understand Stress-Triggered Physiology of Escherichia coli and to Develop Novel Therapeutics
Zuyi Huang, Qian Jia and Thomas K. Wood
Foodborne pathogens survive under oxidative stress conditions by changing their physiology and forming persister cells; persister cells are dormant cells that can awaken to cause chronic infections. While extensive experimental research has been conducted to investigate the genes and metabolic pathways associated with persister cell formation, no systems-level modelling approach has been developed to integrate these genes and other intracellular components to accelerate the identification of novel therapeutic targets for eliminating persister pathogens. In this work, we present the first genome-scale metabolic modelling approach to evaluate the ability of Escherichia coli to form persister cells under oxidative conditions and then identify gene targets that may be implemented to suppress persister cell formation. In particular, genomics data was integrated with a genome-scale metabolic model of E. coli to identify the reactions associated with persister cell formation. The change of activity levels of these reactions was then compared with the change of expression levels of genes obtained in persister cells to quantify the ability of the pathogen to form persister cells. Since rpoS-controlled genes and reactions have been reported for their important role in regulating persister cell formation, these genes were knocked out in the developed in-silico platform to evaluate the capability of these mutants to form persister cells. The results showed that the fluxes of rpoS-controlled reactions increase under oxidative stress and that the rpoS-deletion mutant showed an increased persister cell formation. In addition, 52 single-mutants were found to have reduced ability to form persister cells, and these genes are mainly involved in cell membrane ion transport and in energy and carbon and lipid metabolism. They can be used as therapeutic targets for eliminating persister pathogens. Finally, the challenges and limitations of genome-scale modelling are also discussed.

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(EAN: 9781910190777 9781910190784 Subjects: [bacteriology] [medical microbiology] [microbiology] )