Davide Sassera
Davide Sassera
affiliation: Department of Biology and Biotechnology - UNIPV
research area(s): Genetics And Genomics, Computational Biology
Course: Genetics, Molecular and Cellular Biology
University/Istitution: Università di Pavia
Born in Cassano d'Adda (MI), il 01/06/1980

Current position
Associate Professor in Parasitology at the Department of Biology and Biotechnology, University of Pavia.

2000-2005: Master degree in Veterinary Biotechnology at the Università degli Studi di Milano, with honors, under supervisor Prof. Claudio Bandi, with the thesis '' Manipulation of the genic expression in a host-parasite system through small RNAs, an experimental approach”.
2005-2008: Ph.D. In Veterinary Hygiene and Animal Pathology, at the Università degli Studi di Milano under supervisor Prof. Claudio Genchi, with the project "Midichloria: a new genus of the order Rickettsiales associated to Ixodidae ticks".
April 2011: COST training school in Bioinformatics. Uppsala University, Sweden.

Professional experience
July - December 2007: Research grant 'Ingenio' from the Lombardia region for "Design and validation of a diagnostic Real-time PCR method for equine babesiois".
January – September 2008: Post-doctoral fellowship in the laboratory of Prof. Luciano Sacchi, University of Pavia, working on the project "Bioinformatic analyses in the research project on microbial diversity associated with the insect vectors of phytoplasms".
October - November 2008: Project collaborator at Intervet/Schering-Plough Animal Health, with the project "Biomolecular analysis on BVDV strains isolated during studies on the Bovilis BVD vaccine".
November 2008 – October 2012: 4-year Post-doctoral fellowship in the laboratory of Prof. Claudio Bandi, Università degli Studi di Milano on «Investigation on Midichloria spp, a novel bacterial genus of the order Rickettsiales: infectivity for humans and animals, culturing and biological role”.
January-February 2009: visiting scientist. Amparo Latorre lab, Cavanilles Institut, Universitat de Valencia
November 2012 – February 2014: 2-year Post-doctoral fellowship in the laboratory of Prof. Claudio Bandi, University of Milano on “Molecular strategies of the inhibition of P-glycoproteins in the hard tick Rhipicephalus sanguineus: next-gen sequencing, gene expression studies, co-treatment with acaricide-inhibitors in cell cultures”.
Ottobre 2013 - gennaio 2014: Term contract, as specialized biotechnologist and bioinformatician, at the Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna.
March 2014 – November 2016. Researcher in Parasitology (contract RTD – type A, SSD VET/06) at the Department of Biology and Biotechnology, University of Pavia.
November 2016 – November 20169. Researcher in Parasitology (contract RTD – type B, SSD VET/06) at the Department of Biology and Biotechnology, University of Pavia.

Teaching activity and other duties
Biomedical parasitology (6 CFU) Laurea magistralis in Experimental and Applied Biology (course held in Italian)
Parasitology and symbiotic associations (6 CFU) Laurea Magistralis in Experimental and Applied Biology (course held in Italian)
Bioinformatics (3 CFU) Master Course in Molecular Biology and Genetics (course held in English)
Referee for various indexed journals, such as Genome Biology and Evolution, Nature Microbiology, Environmental Microbiology. Review Editor for Frontiers in Microbiology.
Evolution of symbiotic relationships and of infectious agents

Collaborators: Prof. Luciano Sacchi (retired Full Professor), Emanuela Clementi (Technician), Emanuela Olivieri (research fellow), Anna Maria Floriano (PhD student), Romain Daveu (PhD student), Umberto Postiglione (PhD student)

External collaborators: Stefano Gaiarsa (Research fellow), Michele Castelli (research fellow), Carolina Ferrari (Research fellow)

My focus of study are the interactions between organisms. My two main research lines in this field are the study of symbiosis and the evolution of infectious agents.

Symbioses are broadly defined as interactions between different organisms, starting from the simplest interactions, such as host-parasite and host-pathogen, to the study of the more complex ones, involving several protagonists. One example is the Midichloria system, which involves various species of vertebrate hosts, a parasitic arthropod (the tick Ixodes ricinus), an intracellular organelle (the mitochondrion) and a unique intramitochondrial symbiont. The study of symbiosis is necessarily multidisciplinary, and thus requires integrated methodological approaches. Starting
from molecular, ultrastructural and serological methodologies, I specialized in the latest -omics technologies, using proteomics and above all genomics and transcriptomics approaches for the study of different symbiotic systems.

Currently the main project on which I am working is the funded project HFSP 2016, in the context of which I lead an international team (Institut Pasteur, Walter and Eliza Hall Institute, Koln University) to understand the mechanisms of interaction between Midichloria and mitochondria. In the context of this project, the collaboration of researchers with different expertise has allowed to design a research plan that mergers genomics, parasitology, cellular biology, biochemistry and bioinformatics with the final goal to understand Midichloria to understand mitochondria.
Connected to the HFSP project, a collaboration is ongoing with the ONIRIS research center in Nantes, on the effect of antibiotic treatments on the presence of the M. mitochondrii symbionts in populations of the host tick I. ricinus. The aim of the study is to obtain aposimbiotic populations and to evaluate changes in their fitness parameters. The project is funded with a doctorate scholarship from the Italian-French University.

I am also currently involved in three bioinformatics projects that use genomics and bioinformatics to study parasites and pathogens.

The SpARK project, funded by European funds, gathers researchers from 5 countries for a genomic epidemiology approach on the nosocomial pathogen Klebsiella pneumoniae. Through a capillary sampling in the Pavia area, followed by the most advanced genomic, bioinformatic and statistical analyses, SpARK aims to understand the ways and means of transmission of clones and genes in bacteria of the genus Klebsiella.

In collaboration with the San Matteo Hospital and the University of Milan, I am involved in the Skynet platform, which aims to implement continuous microbiological genomic surveillance and integrate it with metadata on patients (including their movements) in the Lombardy health system. This ambitious goal could allow monitoring, and potentially preventing, the spread of bacterial pathogens in hospitals. Currently two pilot studies focusing on Klebsiella pneumoniae and Staphylococcus aureus are ongoing.

In a research project funded by the Ministry of Health (Finalizzata 2016), I collaborate with Roman and Pavia researchers for the development of innovative diagnostic methods for cystic echinococcosis. The role of my unit is to analyze Echinococcus -omics data to develop a protein that will allow us to test the antigenic characteristics of a set of proteins and peptides of this parasite, with the aim of obtaining serological diagnostic methods with high sensitivity and specific for the different stages of the disease.
Ferrari C, Corbella M, Gaiarsa S, Comandatore F, Scaltriti E, Bandi C, Cambieri P, Marone P, Sassera D. Multiple Klebsiella pneumoniae KPC Clones Contribute to an Extended Hospital Outbreak. Front Microbiol. 2019 Nov 29;10:2767. doi: 10.3389/fmicb.2019.02767. PMID: 31849904; PMCID: PMC6896718.

Merla C, Rodrigues C, Passet V, Corbella M, Thorpe HA, Kallonen TVS, Zong Z, Marone P, Bandi C, Sassera D, Corander J, Feil EJ, Brisse S. Description of Klebsiella spallanzanii sp. nov. and of Klebsiella pasteurii sp. nov. Front Microbiol. 2019 Oct 25;10:2360. doi: 10.3389/fmicb.2019.02360. PMID: 31708881; PMCID: PMC6824210.

Comandatore F, Sassera D, Bayliss SC, Scaltriti E, Gaiarsa S, Cao X, Gales AC, Saito R, Pongolini S, Brisse S, Feil EJ, Bandi C. Gene Composition as a Potential Barrier to Large Recombinations in the Bacterial Pathogen Klebsiella pneumoniae. Genome Biol Evol. 2019 Nov 1;11(11):3240-3251.

Olivieri E, Epis S, Castelli M, Varotto Boccazzi I, Romeo C, Desirò A, Bazzocchi C, Bandi C, Sassera D. Tissue tropism and metabolic pathways of Midichloria mitochondrii suggest tissue-specific functions in the symbiosis with Ixodes ricinus. Ticks Tick Borne Dis. 2019 Aug;10(5):1070-1077.

Castelli M, Sabaneyeva E, Lanzoni O, Lebedeva N, Floriano AM, Gaiarsa S, Benken K, Modeo L, Bandi C, Potekhin A, Sassera D, Petroni G. Deianiraea, an extracellular bacterium associated with the ciliate Paramecium, suggests an alternative scenario for the evolution of Rickettsiales. ISME J. 2019 Sep;13(9):2280-2294.

Gaiarsa S, Bitar I, Comandatore F, Corbella M, Piazza A, Scaltriti E, Villa L, Postiglione U, Marone P, Nucleo E, Pongolini S, Migliavacca R, Sassera D. Can Insertion Sequences Proliferation Influence Genomic Plasticity? Comparative Analysis of Acinetobacter baumannii Sequence Type 78, a Persistent Clone
in Italian Hospitals. Front Microbiol. 2019 Sep 12;10:2080.

De Marco L, Sassera D, Epis S, Mastrantonio V, Ferrari M, Ricci I, Comandatore F, Bandi C, Porretta D, Urbanelli S. The choreography of the chemical defensome response to insecticide stress: insights into the Anopheles stephensi transcriptome using RNA-Seq. Sci Rep. 2017 Jan 23;7:41312.

De Marco L, Epis S, Comandatore F, Porretta D, Cafarchia C, Mastrantonio V, Dantas-Torres F, Otranto D, Urbanelli S, Bandi C, Sassera D. Transcriptome of larvae representing the Rhipicephalus sanguineus complex. Mol Cell Probes. 2017 Feb;31:85-90.

Comandatore F, Cordaux R, Bandi C, Blaxter M, Darby A, Makepeace BL, Montagna M, Sassera D. Supergroup C Wolbachia, mutualist symbionts of filarial nematodes, have a distinct genome structure. Open Biol. 2015 Dec;5(12):150099.

Gaiarsa S, Comandatore F, Gaibani P, Corbella M, Dalla Valle C, Epis S, Scaltriti E, Carretto E, Farina C, Labonia M, Landini MP, Pongolini S, Sambri V, Bandi C, Marone P, Sassera D. Genomic epidemiology of Klebsiella pneumoniae in Italy and novel insights into the origin and global evolution of its resistance to carbapenem antibiotics. Antimicrob Agents Chemother. 2015 Jan;59(1):389-96.

Degli Esposti M, Chouaia B, Comandatore F, Crotti E, Sassera D, Lievens PM, Daffonchio D, Bandi C. Evolution of mitochondria reconstructed from the energy metabolism of living bacteria. PLoS One. 2014 May 7;9(5):e96566. Doi: 10.1371/journal.pone.0096566.

Comandatore F, Sassera D, Montagna M, Kumar S, Koutsovoulos G, Thomas G, Repton C, Babayan SA, Gray N, Cordaux R, Darby A, Makepeace B, Blaxter M. Phylogenomics and analysis of shared genes suggest a single transition to mutualism in Wolbachia of nematodes. Genome Biol Evol. 2013;5(9):1668-74.

Montagna M, Sassera D, Epis S, Bazzocchi C, Vannini C, Lo N, Sacchi L, Fukatsu T, Petroni G, Bandi C. "Candidatus Midichloriaceae" fam. Nov. (Rickettsiales), an ecologically widespread clade of intracellular alphaproteobacteria. Appl Environ Microbiol. 2013 May;79(10):3241-8.

Sassera D, Lo N, Epis S, D'Auria G, Montagna M, Comandatore F, Horner D, Peretó J, Luciano AM, Franciosi F, Ferri E, Crotti E, Bazzocchi C, Daffonchio D, Sacchi L, Moya A, Latorre A, Bandi C. Phylogenomic evidence for the presence of a flagellum and cbb(3) oxidase in the free-living mitochondrial ancestor. Mol Biol Evol. 2011 Dec;28(12):3285-96.

Sassera D, Lo N, Bouman EA, Epis S, Mortarino M, Bandi C. "Candidatus Midichloria" endosymbionts bloom after the blood meal of the host, the hard tick Ixodes ricinus. Appl Environ Microbiol. 2008 Oct;74(19):6138-40.

Sassera D, Beninati T, Bandi C, Bouman EA, Sacchi L, Fabbi M, Lo N. 'Candidatus Midichloria mitochondrii', an endosymbiont of the tick Ixodes ricinus with a unique intramitochondrial lifestyle. Int J Syst Evol Microbiol. 2006
Project Title:
Multidisciplinary investigation on the evolution in bacterial symbionts
Intracellular bacterial symbionts live in the closest possible association with their host, inside them. This interaction deeply impacts the biology of both hosts and symbionts, often in unpredictable ways. Among intracellular symbionts, Rickettsiales are possibly the bigger and more complex group, encompassing a number of bacteria that develop unique relationships with their host, from parasites to essential mutualists, from intramitochondrial and intranuclear bacteria to manipulators of the host reproduction.
In order to understand the characteristics and mechanisms of novel symbioses, we use a multidisciplinary approach that exploit microscopy, molecular biology and genomics. The goal is to use these methods to design hypotheses on the symbiotic interactions, from the metabolic and physiological perspectives, but also from an evolutionary point of view.

Project Title:
Genomic epidemiology of bacterial pathogens
The epidemiology of bacterial pathogens is a topic of great interest for the potential clinical applications but also for a general characterization of population dynamics and evolution.
Recent improvement in genome sequencing techniques has allowed to perform complete sequencing of a growing number of bacterial isolates, developing the field of genomic epidemiology. This project is thus based on genome sequencing and the subsequent bioinformatic analyses, which allow to dissect the genetic characteristics of bacteri at an unprecedented level of detail. Genomic epidemiology techniques allow to discern the fine differences that discriminate isolates belonging to a single epidemic outbreak, reconstructing chains of infections. Genomic characterization can detect novel determinant of antibiotic resistance or gene of virulence. The study of evolution can be performed to detect recombination events, or to date with molecular clock techniques the spread of a pathogenic strain. A strong interest and attitude in bioinformatics is fundamental for this project.