Understanding Pathogen Behaviour

Virulence, Stress Response and Resistance

M. Griffiths

• Publisher: Woodhead Publishing
• Year: 2005
• Print ISBN: 9781855739536
• eBook ISBN: 9781845690229
• Topic: Technology & Engineering
• Subtopic: Food Science
• Index: Technology & Engineering

Pathogens respond dynamically to their environment. Understanding their behaviour is critical both because of evidence of increased resistance to established sanitation and preservation techniques, and because of the increased use of minimal processing technologies which are more vulnerable to the development of resistance. Understanding pathogen behaviour summarises the wealth of recent research and its implications for the food industry.After two introductory chapters on ways of analysing and modelling pathogens, Part one summarises current research on what determines pathogenicity, stress response, adaptation and resistance. Part two reviews the behaviour of particular pathogens, reviewing virulence, stress response and resistance mechanisms in such pathogens as Salmonella, E.coli and Campylobacter. The final part of the book assesses how pathogens react and adapt to particular stresses from heat treatment and the effects of low temperature to the use of disinfectants and sanitisers.With its distinguished editor and international team of contributors, Understanding pathogen behaviour is a standard reference for the food industry in ensuring food safety.- Summarises the wealth of recent research in pathogen behaviour- Assesses implications for microbiologists and QA staff in the food industry

Part I

Understanding virulence, stress response and resistance mechanisms

Outline

Chapter 1: Understanding the behaviour of pathogenic cells: proteome and metabolome analyses

Chapter 2: Mechanistic modelling of pathogen stress response

Chapter 3: The development of pathogenicity

Chapter 4: Host–pathogen interactions

Chapter 5: Factors affecting stress response

Chapter 6: Cross-protective effects of bacterial stress

Chapter 7: Sublethal injury, pathogen virulence and adaptation

Chapter 8: Detecting sublethally damaged cells

1

Understanding the behaviour of pathogenic cells: proteome and metabolome analyses

S. Vaidyanathan and R. Goodacre, The University of Manchester, UK

1.1 Introduction

Post-genome science and technology are defined by the need to characterize function at the level of the genes, transcripts, proteins and metabolites to explain cellular processes. The understanding of biological systems is increasingly being driven by a paradigm shift in emphasis from the traditional divisive biochemical approaches that concentrate on local cellular processes, one at a time, to global approaches of analysing cellular compositions in parallel and in its entirety, with a view to obtain a more ‘holistic’ picture. Genomic sequencing initiatives have resulted in the sequencing of over 250 organisms, which include several pathogens (http://www.genomesonline.org). However, the functions of many (typically ~40 %) open reading frames (ORFs) within the sequenced genomes are still unknown. In this regard, analysis at the level of the functional units, i.e. transcripts (transcriptome), proteins (proteome) and metabolites (metabolome) is increasingly becoming relevant. In particular, post-transcriptional regulation of cellular activities necessitates analysis at the level of the proteome and the metabolome to better understand cellular processes. Strategies for the simultaneous high-throughput measurement of several analytes at the level of the proteome and metabolome are progressively being developed, and these form the subject-matter of this chapter.

In some cases, techniques that enable differences to be delineated between different biological systems or even between different states of a system may be useful in understanding cellular processes, even when a complete knowledge of the genetic make-up of the system is not available. In this regard, fingerprinting approaches are discussed that provide proteomic and metabolomic ‘snapshots’ and offer potential for rapid assessment of biological systems at the functional level. Although deductive reasoning dictates much of scientific inference, the practice of ‘holistic’ science and the inundation of data as a result necessitate a greater participation of inductive reasoning in the cycle of knowledge (Oldroyd, 1986) (Fig. 1.1). In this regard, computational sciences have much to offer, resulting in the birth of data-driven sciences such as ‘bioinformatics’, the application of which to proteome and metabolome analyses will also be discussed. Finally, the contribution of proteome and metabolome analyses to the understanding of pathogen behaviour is discussed, with relevant examples. The topical nature of the subject and its wide scope makes it difficult for a comprehensive coverage. Instead an attempt is made at capturing the general themes and trends to help keep the readers abreast of the developments.

Fig. 1.1 The traditional deductive cycle of knowledge and the hypothesis generation cycle via holism.

1.2 Rationale behind analysing proteomes and metabolomes

The first complete genomic sequencing of a free-living organism was that of a human pathogen, Haemophilus influenzae, in 1995 (Fleischmann et al., 1995). Ever since, the genomic sequence of several pathogens have been revealed, including foodborne pathogens, with Campylobacter jejuni being the first food pathogen genome to be sequenced in 2000 (Parkhill et al., 2000). The availability of genetic information has enabled comparative genomic assessments that have contributed to the understanding of pathogen behaviour (Alm et al., 1999). However, genomic information alone is not sufficient for understanding biological processes. With the sequencing of the human genome, it is now known that we as humans have only three times as many genes as a nematode (Caenorhabditis elegans), with respect to the number of genes carried in our respective genetic make-up, and that the genetic make-up of diverse species are remarkably similar. Indeed genome sequencing projects alone have shown that we have 50 % genes in common with the fruit fly, 85 % with our canine friends and 99 % with chimpanzees; not forgetting that there is a significant portion shared with prokaryotes. This suggests that more than the genetic make-up, the contextual combination of gene products confers complexity and diversity to the functional genome. Consequently, in addition to cataloguing genomes and their function, it is necessary to generate an understanding of which gene products are expressed and how they come together to constitute a functional unit that responds to the different stimuli, be it of growth or environmentally induced. There is therefore a greater need to analyse at the level of the transcriptomes, proteomes and metabolomes (Fig. 1.2).

Fig. 1.2 Schematic of ‘omic’ expression, showing some prominent accompanying events.

Transcriptomic analysis results in monitoring gene expression. Nucleic acid arrays produced by the robotic deposition of polymerase chain reaction (PCR) products, plasmids or oligonucleotides onto a glass slide or in situ synthesis of oligonucleotides using photolithography have been used in hybridization experiments to monitor gene expression. Array-based approaches, especially those that probe tens of thousands of genes, are useful in that they enable the development of a ‘holistic’ and unbiased view, rather than a targeted view of cellular response, without a priori knowledge of which genes or mechanisms are important. These and other tools, such as sequential analysis of gene expression (SAGE), can be used for monitoring morphological and physiological/phenotypical differences and can be indicative of cellular response to environmental stimuli and perturbations. However, mRNA is only an intermediate in translating the genetic information to cellular response and function, the business end of which is enacted by proteins and metabolites. Changes in the temporal expression and accumulation patt...

Table of contents

• Cover image
• Title page
• Table of Contents
• Related titles from Woodhead’s food science, technology and nutrition list
• Copyright
• Contributor contact details
• Introduction
• Part I: Understanding virulence, stress response and resistance mechanisms
• Part II: Virulence and stress response mechanisms of particular pathogens
• Part III: Pathogen resistance and adaptation to particular stresses
• Part IV: Appendix