title: Proteomics boosts translational and clinical microbiology.
abstract: The application of proteomics to translational and clinical microbiology is one of the most advanced frontiers in the management and control of infectious diseases and in the understanding of complex microbial systems within human fluids and districts. This new approach aims at providing, by dedicated bioinformatic pipelines, a thorough description of pathogen proteomes and their interactions within the context of human host ecosystems, revolutionizing the vision of infectious diseases in biomedicine and approaching new viewpoints in both diagnostic and clinical management of the patient. Indeed, in the last few years, many laboratories have matured a series of advanced proteomic applications, aiming at providing individual proteome charts of pathogens, with respect to their morph and/or cell life stages, antimicrobial or antimycotic resistance profiling, epidemiological dispersion. Herein, we aim at reviewing the current state-of-the-art on proteomic protocols designed and set-up for translational and diagnostic microbiological purposes, from axenic pathogens' characterization to microbiota ecosystems' full description. The final goal is to describe applications of the most common MALDI-TOF MS platforms to advanced diagnostic issues related to emerging infections, increasing of fastidious bacteria, and generation of patient-tailored phylotypes. This article is part of a Special Issue entitled: Trends in Microbial Proteomics.
authors.affiliation: Unit of Parasitology, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy; Unit of Metagenomics, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy.
authors.forename: F
authors.initials: F
authors.lastname: Del Chierico
authors.affiliation: Unit of Parasitology, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy; Unit of Metagenomics, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy; Department of Diagnostic Science, Sant'Andrea Hospital, Via di Grottarossa 1035, 00185 Rome, Italy.
authors.forename: A
authors.initials: A
authors.lastname: Petrucca
authors.affiliation: Unit of Parasitology, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy; Unit of Metagenomics, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy; Interdipartimental Centre for Industrial Research-CIRI-AGRIFOOD, Alma Mater Studiorum, University of Bologna, Bologna, Italy.
authors.forename: P
authors.initials: P
authors.lastname: Vernocchi
authors.affiliation: Unit of Parasitology, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy; Unit of Metagenomics, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy.
authors.forename: G
authors.initials: G
authors.lastname: Bracaglia
authors.affiliation: Laboratory Medicine, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy.
authors.forename: E
authors.initials: E
authors.lastname: Fiscarelli
authors.affiliation: Unit of Microbiology, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy.
authors.forename: P
authors.initials: P
authors.lastname: Bernaschi
authors.affiliation: Laboratory Medicine, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy.
authors.forename: M
authors.initials: M
authors.lastname: Muraca
authors.affiliation: Department of Experimental Medicine and Surgery, University "Tor Vergata", Rome, Italy; IRCCS-Santa Lucia Foundation, Rome, Italy.
authors.forename: A
authors.initials: A
authors.lastname: Urbani
authors.affiliation: Unit of Parasitology, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy; Unit of Metagenomics, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy. Electronic address: l_putignani@yahoo.com.
authors.forename: L
authors.initials: L
authors.lastname: Putignani
mesh_terms: D000818:Animals; D001419:Bacteria / Q000235:genetics / Q000378:metabolism*; D021821:Communicable Diseases, Emerging / Q000188:drug therapy / Q000235:genetics / Q000378:metabolism* / Q000382:microbiology; D024881:Drug Resistance, Bacterial; D025141:Drug Resistance, Fungal; D005658:Fungi / Q000235:genetics / Q000378:metabolism*; D006801:Humans; D064307:Microbiota; D040901:Proteomics / Q000379:methods* / Q000639:trends
keywords: Clinical microbiology; Emerging pathogens; MALDI-TOF MS; Translational proteomics