March 2014 • issue 10 www.paneuropeannetworks.com

Front cover inspired by:

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etworks: SC

IENCE&

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March 2014 •

issue 10

Lauritz B Holm-Nielsen:The EuroScience President advocates aconcerted collaborative European effort,in the true spirit of the ERA

19 142 Constantijn Van Oranje-Nassau:The Head of Cabinet for Vice-PresidentNeelie Kroes on the promotion of theDigital Agenda in Europe

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Science&Technology

Ladislav Miko:DG SANCO’s Deputy Director Generalfor the Food Chain championssustainability and safety in agriculture

THE WAR ON CANCERDoes the future of cancer treatment lie in the large scale analysis of glycan binding biomolecules?

THE WAR ON CANCERDoes the future of cancer treatment lie in the large scale analysis of glycan binding biomolecules?

AT THE GENOMIC LEVELThe combination of comparative and functional genomics helps toprevent and combat bacterial infections of humans and livestock,

as Professor Ulrich Dobrindt discusses

Pan European Networks: Science & Technology 10 www.paneuropeannetworks.com278

PROFILE

The Microbial Genome Plasticity – Molecular InfectionBiology group at the Institute of Hygiene, University ofMünster, is applying next generation DNA sequencing

techniques to study genome plasticity of the bacterium Escherichiacoli and its impact on (i) pathogenicity, (ii) antibiotic resistances,and (iii) bacterial adaptation in different niches and environments.

Normally, E. coli bacteria belong to the normal gut flora ofhumans and many animals. They persist as harmless commensalsin the mucous layer of the intestinal tract. Several pathogenicvariants, however, cause intestinal or extraintestinal infections.Intestinal pathogenic E. coli include many important foodbornepathogens and cause diarrhoea, whereas E. coli causingextraintestinal diseases are one of the major sources of urinarytract infection and bacteraemia in humans. Frequentextraintestinal infections in ruminants and poultry include mastitisand colibacillosis, respectively, and cause heavy economic lossesdue to mortality and morbidity. As certain human bacteraemiaand avian pathogenic E. coli (APEC) isolates cannot always beclearly distinguished based on molecular epidemiology and theirvirulence-associated genome content, APEC are considered as areservoir of virulence and resistance-associated genes for humanpathogens and a zoonotic risk cannot be excluded.

New discoveriesE. coli is a heterogeneous species because its genome is highlydynamic and consequently, E. coli pathogens are remarkablydiverse. The ability of certain E. coli variants to accumulate andexpress multiple virulence associated determinants increases their

fitness and adaptability and determines their potential to causedisease. In addition to their role in the disease process, thesevirulence factors enable the pathogens to exploit their hosts inways unavailable to commensals, and thus to spread and topersist in the bacterial community. A variety of virulence-associatedand fitness factors have been extensively studied. However, thefunction and regulation of a large number of determinants requiresfurther analysis to better understand their contribution to virulence.

Using next generation sequencing and functional as well ascomparative genomic analyses, we characterise the virulence andfitness-associated genome content of E. coli pathogens andcommensals (Fig. 1). We study mechanisms of bacterium-hostinteraction which contribute to host colonisation. Completegenome sequence data help to identify virulence traits.Furthermore, individual differences in genome content andstructure may contribute to the development of improveddiagnostic approaches against extraintestinal pathogenic E. coli(ExPEC) infection in humans and livestock (Fig. 2).

We study differential regulation of gene expression in commensalsand pathogens by genome-wide transcriptome sequencing,metabolic analyses and interaction strategies with eukaryoteswhich may distinguish commensals from pathogens or different E.coli pathotypes (Fig. 3). Deep RNA sequencing also enables thediscovery of small, non-coding RNAs (sRNAs), some of whichseem to be key regulators that are involved in managing and finetuning of bacterial virulence gene expression. The simultaneousanalysis of the bacterial and eukaryotic transcriptomes is achallenging and recently expanding application of next generationsequencing. New insights into host-bacterium interaction orbacterial adaptability to, e.g. environmental changes or antibiotictreatment, can be achieved. The identification of new virulence orresistance-associated bacterial pathways, or differential regulationof common genes in pathogens and commensals, will enable usto design new therapies to specifically disrupt these virulence orresistance pathways. Similarly, the characterisation andmodulation of sRNAs may improve antimicrobial therapies. Ourstudies on genome content and regulation of gene expression onbovine mastitis isolates identified several virulence and fitness-associated traits which are candidate diagnostic markers ortargets for preventive and therapeutic approaches.

Studies and surveillance Next generation sequencing and comparative analysis of completegenome sequences offer a high discriminatory power for thesubtyping of bacterial isolates and allows the ability to distinguisheven closely related isolates. The combination of genomic data and

Fig. 1 Next generation sequencing and comparative genomics: powerfultools for infectious disease research. Whole genome sequence analyseshelp us to gain insight into the molecular pathogenesis and population

structure of E. coli. Data obtained from comparative genomic andtranscriptomic analyses can be used to further develop new tools for

diagnostic, preventive and therapeutic approaches

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www.paneuropeannetworks.com Pan European Networks: Science & Technology 10 279

PROFILE

Prof Dr Ulrich DobrindtInstitute of HygieneSection 'Microbial Genome Plasticity – Molecular Infection Biology'University of Münster

tel: +49 (0)251 980-2875

dobrindt@uni-muenster.dehttp://campus.uni-muenster.de/hyg_forsch_dobrindt.html?&L=1

temporal-geographic or disease or phenotype information allowsthe identification of so far unrecognised genetic relationships, andinfer the sequence of evolutionary events. The comparative andfunctional genomic analysis of closely related clinical ExPECisolates funded in the second ERA-Net Pathogenomics callallowed us to study bacterial adaptation strategies to long termcolonisation and chronic infection. Our results showed that longterm colonisation and adaptation is in part achieved by phenotypicattenuation, thus preventing activation of host mucosalinflammation as well as metabolic adaptation. These adaptationmechanisms appear to be unique for each host.

Because of the increasing number and the spread of (multi)resistant E. coli and their high genomic diversity, these strainsconstitute a serious problem regarding the treatment of thesepathogens. The major tools used for combatting E. coli infectionsare antibiotics and vaccines. ‘Traditional’ vaccines, based oninactivated bacteria, protect against infection with thehomologous strains but are less efficient against heterologousstrains. Hence, vaccination for ExPEC is not widely practisedbecause of the large pheno and genotypic variability of strainsresponsible for field outbreaks. The use of antibiotic therapy isproblematic because of the increasing resistance to antibiotics.Moreover, to meet consumer demands and regulations, antibioticuse in animal production is expected to substantially decrease inthe future. Consequently, there is an urgent need for alternativeapproaches to treat and prevent E. coli infection. One promisingapproach to control such infections is through the use of vaccines,providing that it is possible to design an efficient vaccine that isprotective against a large number of strains. In the framework onan EMIDA ERA-Net consortium, we participated in the

development of such an APEC vaccine. The population structure ofAPEC and commensal chicken isolates has been analysed, andprotective antigens preferentially expressed in pathogenic strains,as identified by comparative genomics, have been successfullytested regarding their ability to protect against heterologousinfection. The work of our EMIDA ERA-Net consortium shouldimprove vaccine development which should give a broad range ofprotection against the important APEC clones.

We anticipate that the use of next generation sequencingtechniques to study the pathogenesis, resistance or adaptation ofpathogenic E. coli causing disease in animals will continue. Thecontinuation of research on virulence and resistance mechanismsof pathogenic E. coli will contribute to improved diagnostic,preventive and therapeutic approaches and, thus, also toconsumer safety. We are well positioned to continue with nextgeneration sequencing analyses in this field, and are also verymuch interested to go beyond the analysis based on single strainsand pure cultures by analysing the role of probiotics and morecomplex bacterial populations during infection.

Fig. 2 Comparative analysis of complete genome sequence data ofpathogenic and non-pathogenic E. coli identifies virulence, resistance

and fitness associated genomic information. The comparison ofcomplete genome sequences of different E. coli isolates helps to

identify genomic regions which are specific for individual strains or forpathotypes (e.g. uropathogenic E. coli, UPEC; avian pathogenic E. coli,

APEC; bovine mastitis E. coli; enterohaemorrhagic E. coli, EHEC)

Fig. 3 Interaction of ExPEC with eukaryotic cells. Dual RNA sequencingenables the simultaneous investigation of host-pathogen interaction of

both, the pathogen and the eukaryotic host, on the transcriptional level.Infecting ExPEC strain (red), host cell actin (green), host cell nucleus (blue)

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Reproduced by kind permission of Pan European Networks Ltd, www.paneuropeannetworks.com © Pan European Networks 2016