Mirko Rossi

Person

Description of research and teaching

RESEARCH

In Finland, as in most countries, the true impact of foodborne and waterborne diseases (FWD) is unknown. To prioritize food safety and environmental health interventions aimed to reduce the burden of FWDs, it is necessary to improve our knowledge in the ecology of the FWD pathogens and to reveal the molecular mechanisms regulating pathogen evolution and its interaction with the hosts.

Therefore, our research is focused on the following topics.

Genomic epidemiology and applied bioinformatics. Genomic epidemiology is a novel discipline which combines next-generation sequencing (NGS) data and statistical genomics to investigate the epidemiology of infectious diseases. We apply modern genomic methodology for exploring the complex epidemiology and ecology of Campylobacter jejuniCampylobacter coli, Yersinia enterocolitica, and pathogenic E. coli. These analyses generate increasing amounts of data that require understanding of advance computational methods. Bioinformatics, data mining, and biostatistics are therefore essential disciplines for the future of our research and teaching. Nevertheless, the routine and widespread application of modern genomic analysis for public health protection is still restricted by the absence of an accessible IT framework, and by the limited skills of the personnel involved in the surveillance of food- and water-borne diseases (from laboratory technicians and public health microbiologists to epidemiologists and physicians) in handling these novel methodologies. Therefore, advances in bioinformatics and bacterial genomics must encounter the needs of public health microbiology. In close collaboration with several international institutions, we are developing and validating novel bioinformatics solutions for high throughput sequencing data analysis and visualization applied to microbial typing; to guarantee that smaller players and end-users in the field can exploit NGSfor surveillance of food-borne diseases.

Experimental evolution. Assessing the genomic diversity in Campylobacter jejuni population is critical for deducing whether genomic differences between any two isolates are sufficiently small to assume a high likelihood of epidemiological relatedness. However, the evolutionary mechanisms and ecological conditions maintaining this diversity remain obscure. A key piece towards resolving this puzzle is the accurate assessment of mutation rates and the molecular spectrum of mutational events in C. jejuni. Yet, neither long-term evolutionary studies nor studies on the evolutionary change over time in a natural population setting are currently available for this important pathogen. Moreover, recombination plays a dominant role in the evolution of this bacterial pathogen, but its dynamics remain only partly understood. By applying high throughput sequencing technology to experimentally evolved C. jejuni strains, we aim to generate an unbiased direct estimate of the spectrum and rate of spontaneous mutations accumulated in a neutral environment, and to define evolution dynamics during adaptation. In addition we are investigating chromosomal integration patterns after natural transformation by combining NGS analysis and in vitro transformation system.

Glycobiology. Glycans decorate nearly all proteins in the host body, respond rapidly and dramatically to inflammatory cues, and have been centrally implicated in regulating the immune response. In addition, glycans decorate the external surface of all bacteria and contribute substantially in the interaction with the host and predators, being therefore subjected to strong environmental selection. With the advent of new technologies, and a great interest in the intersection of glycobiology and immunology, significant advances in understanding how glycosylation may allow pathogens to subvert the immune system or to serve as targets for the immune system are currently being accomplished. We are focusing on elucidating molecular mechanisms behind the biosynthesis of glycan structures in Campylobacter coli and their role in host response during infections.

TEACHING

Veterinary Medicine. Environmental Health course discusses key environmental issues that have a direct impact on human health. Topics include: waterborne disease epidemiology; treatment and quality of drinking and bathing water; environmental impact of solid waste and waste water; indoor and outdoor air quality and their effect on human health; health impact of soil pollution; the scientific basis for policy decisions; and emerging global environmental health problems.

Postgraduate courses. We are involved intensely in the organization of courses for PhD students under the umbrella of the Doctoral school in environmental, food, and biological sciences (YEP). Our courses are mainly focusing on: molecular epidemiology, bacterial genomics, and bioinformatics.

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Curriculum Vitae

During my degree in Doctor in Veterinary Medicine (1996-2002), I specialized in Clinical Veterinary Microbiology under the supervision of Professor Valeria Sanguinetti (University of Bologna). In my PhD (2005 - 2008), I investigated diagnostics methods and taxonomy of Campylobacter and Helicobacter species, and their prevalence in several animal hosts. I published a total of 10 papers and my thesis focused on investigating the prevalence of Helicobacter pullorum in poultry. In addition, I described two novel Campylobacter species in rabbit and poultry.

During my postdoctoral fellowship (2008 - 2012) I trained in bacterial genomics and bioinformatics, which became the main tools of my recent research activities. My postdoctoral fellowship has dedicated particularly on unveiling the molecular mechanisms associated to the zoonotic transmission of animal Helicobacter species using modern comparative genomics techniques and functional genetics, resulted in 13 published papers. The main targets of these studies were: the sialylated surface structures of H. bizzozeronii and their interaction with the human host; short term evolution of non-pylori Helicobacter spp. in the human stomach; the genomic features involved in Helicobacter, evolution, host interaction and host-jump. During my postdoctoral fellowship I established international collaborations with several research groups around the words. The collaboration with University of Gent (Belgium) on comparative genome analysis, population genetics and functional genomics of animal gastric Helicobacter species is still ongoing.

Since I started my tenure track fellowship (2013) at University of Helsinki, I moved my attention to Campylobacter species by developing my own research and group. Exploiting the competences acquired during my post-doctoral fellow, I focused my recent research on the following topics: Genomic epidemiology and applied bioinformatics; experimental evolution; glycobiology.

 

Highlighted publications

  1. Large Sequence Diversity within the Biosynthesis Locus and Common Biochemical Features of Campylobacter coli Lipooligosaccharides

    Culebro, A., Revez, J., Pascoe, B., Friedmann, Y., Hitchings, M. D., Stupak, J., Sheppard, S. K., Li, J. & Rossi, M., Oct 2016, In : Journal of Bacteriology. 198, 20, p. 2829-2840 12 p.

    Research output: Contribution to journalArticleScientificpeer-review

  2. Functional genomics in Campylobacter coli identified a novel streptomycin resistance gene located in a hypervariable genomic region

    Olkkola, S., Culebro Escandon y Perez, A., Juntunen, P., Hänninen, M-L. & Rossi, M., Jul 2016, In : Microbiology. 162, p. 1157-1166 10 p.

    Research output: Contribution to journalArticleScientificpeer-review

  3. Tracing isolates from domestic human Campylobacter jejuni infections to chicken slaughter batches and swimming water using whole-genome multilocus sequence typing

    Kovanen, S., Kivisto, R., Llarena, A-K., Zhang, J., Karkkainen, U-M., Tuuminen, T., Uksila, J., Hakkinen, M., Rossi, M. & Hanninen, M-L., 2 Jun 2016, In : International Journal of Food Microbiology. 226, p. 53-60 8 p.

    Research output: Contribution to journalArticleScientificpeer-review

  4. Refinement of Whole-Genome Multilocus Sequence Typing Analysis by Addressing Gene Paralogy

    Zhang, J., Halkilahti, J., Hänninen, M-L. & Rossi, M., May 2015, In : Journal of Clinical Microbiology. 53, 5, p. 1765-1767 3 p.

    Research output: Contribution to journalArticleScientificpeer-review

  5. Multilocus Sequence Typing (MLST) and Whole-Genome MLST of Campylobacter jejuni Isolates from Human Infections in Three Districts during a Seasonal Peak in Finland

    Kovanen, S. M., Kivistö, R. I., Rossi, M., Schott, T., Kärkkäinen, U-M., Tuuminen, T., Uksila, J., Rautelin, H. & Hänninen, M-L., Dec 2014, In : Journal of Clinical Microbiology. 52, 12, p. 4147-4154 8 p.

    Research output: Contribution to journalArticleScientificpeer-review

  6. The Helicobacter heilmannii hofE and hofF Genes are Essential for Colonization of the Gastric Mucosa and Play a Role in IL-1-Induced Gastric MUC13 Expression

    Cheng, L., Rossi, M., Sara, L., Medea, P., Caroline, B., Eva, B., Myrthe, J., Bram, F., Wim, V. D. B., Richard, D., Freddy, H. & Annemieke, S., Dec 2016, In : Helicobacter (Oxford). 21, 6, p. 504-522 19 p.

    Research output: Contribution to journalArticleScientificpeer-review

  7. Genome analysis of Campylobacter jejuni strains isolated from a waterborne outbreak

    Revez, J., Llarena, A-K., Schott, T., Kuusi, M., Hakkinen, M., Kivistö, R., Hänninen, M-L. & Rossi, M., 8 Sep 2014, In : BMC Genomics. 15, 8 p., 768.

    Research output: Contribution to journalArticleScientificpeer-review

  8. Genomic variation between Campylobacter jejuni isolates associated with milk-borne-disease outbreaks

    Revez, J., Zhang, J., Schott, T., Kivistö, R., Rossi, M. & Hänninen, M-L., 2014, In : Journal of Clinical Microbiology. 52, 8, p. 2782-2786 5 p.

    Research output: Contribution to journalArticleScientificpeer-review

  9. Comparative genomics of unintrogressed Campylobacter coli clades 2 and 3

    Skarp-de Haan, C. P. A., Culebro, A., Schott, T., Revez, J., Schweda, E. K. H., Hänninen, M-L. & Rossi, M., 13 Feb 2014, In : BMC Genomics. 15, 14 p., 129.

    Research output: Contribution to journalArticleScientificpeer-review

  10. Evolution and comparative genomics of Campylobacter jejuni ST-677 clonal complex

    Kivistö, R. I., Kovanen, S., Skarp-de Haan, A., Schott, T., Rahkio, M., Rossi, M. & Hänninen, M-L., Sep 2014, In : Genome Biology and Evolution. 6, 9, p. 2424-2438

    Research output: Contribution to journalArticleScientificpeer-review

  11. Antimicrobial resistance and Campylobacter jejuni and C. coli

    Rossi, M., Olkkola, S., Roasto, M., Kivistö, R. & Hänninen, M-L., 2015, Antimicrobial Resistance and Food Safety: Methods and Techniques. Chen, C-Y., Yan, X. & Jackson, C. R. (eds.). London, UK: Elsevier Academic Press, p. 55-75 21 p.

    Research output: Chapter in Book/Report/Conference proceedingChapterScientificpeer-review

  12. Chondroitinase AC: a host-associated genetic feature of Helicobacter bizzozeronii

    Namburi, R. B., Berteau, O., Spillmann, D. & Rossi, M., 2016, In : Veterinary Microbiology. 186, p. 21-27 7 p.

    Research output: Contribution to journalArticleScientificpeer-review

  13. Divergence between the highly virulent zoonotic pathogen Helicobacter heilmannii and its closest relative, the low-virulence “Helicobacter ailurogastricus” sp. nov.

    Joosten, M., Lindén, S., Rossi, M., Chin Yen Tay, A., Skoog, E., Padra, M., Peters, F., Perkins, T., Vandamme, P., Van Nieuwerburgh, F., D'Herde, K., Van den Broeck, W., Flahou, B., Deforce, D., Ducatelle, R., Marshall, B., Haesebrouck, F. & Smet, A., Jan 2016, In : Infection and Immunity. 84, 1, p. 293-306 14 p.

    Research output: Contribution to journalArticleScientificpeer-review

  14. Sialylation of Helicobacter bizzozeronii lipopolysaccharides modulates Toll-like receptor (TLR) 2 mediated response

    Kondadi, P. K., Revez, J., Hänninen, M-L. & Rossi, M., 21 Jan 2015, In : Veterinary Research. 46, 7 p., 4.

    Research output: Contribution to journalArticleScientificpeer-review

  15. Identification and characterization of a lipopolysaccharide α,2,3-sialyltransferase from the human pathogen Helicobacter bizzozeronii

    Kondadi, P. K., Rossi, M., Twelkmeyer, B., Schur, M. J., Li, J., Schott, T., Paulin, L., Auvinen, P., Hänninen, M-L., Schweda, E. K. H. & Wakarchuk, W., 2012, In : Journal of Bacteriology. 194, 10, p. 2540-2550 11 p.

    Research output: Contribution to journalArticleScientificpeer-review

View all (59) »

Highlighted activities

  1. Subject coordination "Ympäristöhygienia" (90040)

    Mirko Rossi (Participant)
    1 Nov 2015 → …

    Activity: Other activity typesTypes for other activities - Other

  2. Working with bacterial communities and populations

    Mirko Rossi (Chair of organizing committee)
    May 2016

    Activity: Participating in or organising an event typesOrganisation and participation in conferences, workshops, courses, seminars

  3. 1st ASM Conference on 2015 Rapid NGS Bioinformatic Pipelines for Enhanced Molecular Epidemiologic Investigation of Pathogens

    Mirko Rossi (Attendee)
    24 Sep 201527 Sep 2015

    Activity: Participating in or organising an event typesOrganisation and participation in conferences, workshops, courses, seminars

  4. Applied Bioinformatics and Public Health Microbiology

    Mirko Rossi (Attendee)
    6 May 20158 May 2015

    Activity: Participating in or organising an event typesOrganisation and participation in conferences, workshops, courses, seminars

  5. Nearly Fifty Slides of Campylobacter

    Mirko Rossi (Speaker: Keynote)
    22 May 2015

    Activity: Participating in or organising an event typesOrganisation and participation in conferences, workshops, courses, seminars

  6. Working with Bacterial Genomes

    Mirko Rossi (Chair of organizing committee)
    3 Oct 201410 Oct 2014

    Activity: Participating in or organising an event typesOrganisation and participation in conferences, workshops, courses, seminars

  7. Supervisor of MSc Alejandra Culebro 's postgraduate studies

    Mirko Rossi (Supervisor)
    Nov 2013 → …

    Activity: Examination typesSupervisor or co-supervisor of doctoral thesis

  8. Supervision of Satu Olkkola's PhD postgraduate studies

    Mirko Rossi (Co-supervisor)
    1 May 2015 → …

    Activity: Examination typesSupervisor or co-supervisor of doctoral thesis

View all (97) »

Highlighted projects

  1. INNUENDO: A new cross-sectorial platform for the integration of genomics in surveillance of food-borne pathogens

    Rossi, M., Llarena, A., Nevas, M., Lundén, J., Fredriksson-Ahomaa, M., Laukkanen-Ninios, R., Caarico, J., Garaizar , J., Hilbert, F., Salmenlinna , S., Hakkinen , M., Oleastro, M., Mäesaar , M. & Bërziņš , A.

    European Food Safety Authority

    15/01/201615/07/2018

    Project: Research project

  2. Glycobiology of Campylobacter coli

    Rossi, M., Culebro Escandon y Perez, A., Wakarchuk, W. & D'Ellios, M. M.

    Unknown funder

    01/01/201431/12/2017

    Project: Research project

View all (11) »

Education

Adjunct Professor in Zoonotic Bacteriology

ID: 22338