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Alvaro A, Piazza A, Papaleo S, Perini M, Pasala AR, Panelli S, Nardi T, Nodari R, Sterzi L, Pagani C, Merla C, Castelli D, Olivieri E, Bracco S, Ferrando ML, Saluzzo F, Rimoldi SG, Corbella M, Cavallero A, Prati P, Farina C, Cirillo DM, Zuccotti G, Comandatore F. Cultivation and sequencing-free protocol for Serratia marcescens detection and typing. iScience 2024; 27:109402. [PMID: 38510115 PMCID: PMC10952028 DOI: 10.1016/j.isci.2024.109402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 01/08/2024] [Accepted: 02/28/2024] [Indexed: 03/22/2024] Open
Abstract
Serratia marcescens is an opportunistic pathogen that survives in inhospitable environments causing large outbreaks, particularly in neonatal intensive care units (NICUs). Genomic studies revealed that most S. marcescens nosocomial infections are caused by a specific clone (here "Infectious clone"). Whole genome sequencing (WGS) is the only portable method able to identify this clone, but it requires days to obtain results. We present a cultivation-free hypervariable-locus melting typing (HLMT) protocol for the fast detection and typing of S. marcescens, with 100% detection capability on mixed samples and a limit of detection that can reach the 10 genome copies. The protocol was able to identify the S. marcescens infectious clone with 97% specificity and 96% sensitivity when compared to WGS, yielding typing results portable among laboratories. The protocol is a cost and time saving method for S. marcescens detection and typing for large environmental/clinical surveillance screenings, also in low-middle income countries.
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Affiliation(s)
- Alessandro Alvaro
- Department of Biomedical and Clinical Sciences, Pediatric Clinical Research Center “Romeo and Enrica Invernizzi”, University of Milan, 20157 Milan, Italy
- Department of Biosciences and Pediatric Clinical Research Center "Romeo Ed Enrica Invernizzi", University of Milan, 20133 Milan, Italy
| | - Aurora Piazza
- Unit of Microbiology and Clinical Microbiology, Department of Clinical-Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia 27100, Italy
| | - Stella Papaleo
- Department of Biomedical and Clinical Sciences, Pediatric Clinical Research Center “Romeo and Enrica Invernizzi”, University of Milan, 20157 Milan, Italy
| | - Matteo Perini
- Department of Biomedical and Clinical Sciences, Pediatric Clinical Research Center “Romeo and Enrica Invernizzi”, University of Milan, 20157 Milan, Italy
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Ajay Ratan Pasala
- Department of Biomedical and Clinical Sciences, Pediatric Clinical Research Center “Romeo and Enrica Invernizzi”, University of Milan, 20157 Milan, Italy
- Biochemistry, Microbiology and Immunology Department, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Centre for Innovation, Canadian Blood Services, Ottawa, ON K1G 4J5, Canada
| | - Simona Panelli
- Department of Biomedical and Clinical Sciences, Pediatric Clinical Research Center “Romeo and Enrica Invernizzi”, University of Milan, 20157 Milan, Italy
| | - Tiago Nardi
- Department of Biomedical and Clinical Sciences, Pediatric Clinical Research Center “Romeo and Enrica Invernizzi”, University of Milan, 20157 Milan, Italy
- Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy
| | - Riccardo Nodari
- Department of Biomedical and Clinical Sciences, Pediatric Clinical Research Center “Romeo and Enrica Invernizzi”, University of Milan, 20157 Milan, Italy
| | - Lodovico Sterzi
- Department of Biomedical and Clinical Sciences, Pediatric Clinical Research Center “Romeo and Enrica Invernizzi”, University of Milan, 20157 Milan, Italy
| | - Cristina Pagani
- Laboratorio di Microbiologia Clinica, Virologia e Diagnostica delle Bioemergenze, ASST Fatebenefratelli Sacco, 20157 Milan, Italy
| | - Cristina Merla
- Department of Microbiology & Virology, Fondazione IRCCS Policlinico San Matteo, Viale Camillo Golgi 19, 27100 Pavia, Italy
| | - Daniele Castelli
- Microbiology Unit, Fondazione IRCCS San Gerardo, 20900 Monza, Italy
| | - Emanuela Olivieri
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna (IZSLER), 27100 Pavia, Italy
| | - Silvia Bracco
- Laboratory of Microbiology and Virology, Azienda Socio-Sanitaria Territoriale (ASST) Papa Giovanni XXIII, 24127 Bergamo, Italy
| | - Maria Laura Ferrando
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Francesca Saluzzo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Sara Giordana Rimoldi
- Laboratorio di Microbiologia Clinica, Virologia e Diagnostica delle Bioemergenze, ASST Fatebenefratelli Sacco, 20157 Milan, Italy
| | - Marta Corbella
- Department of Microbiology & Virology, Fondazione IRCCS Policlinico San Matteo, Viale Camillo Golgi 19, 27100 Pavia, Italy
| | | | - Paola Prati
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna (IZSLER), 27100 Pavia, Italy
| | - Claudio Farina
- Laboratory of Microbiology and Virology, Azienda Socio-Sanitaria Territoriale (ASST) Papa Giovanni XXIII, 24127 Bergamo, Italy
| | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Gianvincenzo Zuccotti
- Department of Biomedical and Clinical Sciences, Pediatric Clinical Research Center “Romeo and Enrica Invernizzi”, University of Milan, 20157 Milan, Italy
- Department of Paediatrics, Children’s Hospital "V. Buzzi", 20154 Milano, Italy
| | - Francesco Comandatore
- Department of Biomedical and Clinical Sciences, Pediatric Clinical Research Center “Romeo and Enrica Invernizzi”, University of Milan, 20157 Milan, Italy
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Sterzi L, Nodari R, Di Marco F, Ferrando ML, Saluzzo F, Spitaleri A, Allahverdi H, Papaleo S, Panelli S, Rimoldi SG, Batisti Biffignandi G, Corbella M, Cavallero A, Prati P, Farina C, Cirillo DM, Zuccotti G, Bandi C, Comandatore F. Genetic barriers more than environmental associations explain Serratia marcescens population structure. Commun Biol 2024; 7:468. [PMID: 38632370 PMCID: PMC11023947 DOI: 10.1038/s42003-024-06069-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 03/19/2024] [Indexed: 04/19/2024] Open
Abstract
Bacterial species often comprise well-separated lineages, likely emerged and maintained by genetic isolation and/or ecological divergence. How these two evolutionary actors interact in the shaping of bacterial population structure is currently not fully understood. In this study, we investigate the genetic and ecological drivers underlying the evolution of Serratia marcescens, an opportunistic pathogen with high genomic flexibility and able to colonise diverse environments. Comparative genomic analyses reveal a population structure composed of five deeply-demarcated genetic clusters with open pan-genome but limited inter-cluster gene flow, partially explained by Restriction-Modification (R-M) systems incompatibility. Furthermore, a large-scale research on hundred-thousands metagenomic datasets reveals only a partial habitat separation of the clusters. Globally, two clusters only show a separate gene composition coherent with ecological adaptations. These results suggest that genetic isolation has preceded ecological adaptations in the shaping of the species diversity, an evolutionary scenario coherent with the Evolutionary Extended Synthesis.
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Affiliation(s)
- Lodovico Sterzi
- Department of Biomedical and Clinical Sciences, Pediatric Clinical Research Center "Romeo and Enrica Invernizzi", Università Di Milano, 20157, Milan, Italy
| | - Riccardo Nodari
- Department of Biomedical and Clinical Sciences, Pediatric Clinical Research Center "Romeo and Enrica Invernizzi", Università Di Milano, 20157, Milan, Italy
| | - Federico Di Marco
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Maria Laura Ferrando
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Francesca Saluzzo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | - Hamed Allahverdi
- Department of Biomedical and Clinical Sciences, Pediatric Clinical Research Center "Romeo and Enrica Invernizzi", Università Di Milano, 20157, Milan, Italy
| | - Stella Papaleo
- Department of Biomedical and Clinical Sciences, Pediatric Clinical Research Center "Romeo and Enrica Invernizzi", Università Di Milano, 20157, Milan, Italy
| | - Simona Panelli
- Department of Biomedical and Clinical Sciences, Pediatric Clinical Research Center "Romeo and Enrica Invernizzi", Università Di Milano, 20157, Milan, Italy
| | - Sara Giordana Rimoldi
- Laboratorio di Microbiologia Clinica, Virologia e Diagnostica delle Bioemergenze, ASST Fatebenefratelli Sacco, Milan, Italy
| | | | - Marta Corbella
- Department of Microbiology & Virology, Fondazione IRCCS Policlinico San Matteo, Viale Camillo Golgi 19, 27100, Pavia, Italy
| | | | - Paola Prati
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna (IZSLER), Pavia, Italy
| | - Claudio Farina
- Laboratory of Microbiology and Virology, Azienda Socio-Sanitaria Territoriale (ASST) Papa Giovanni XXIII, Bergamo, Italy
| | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Gianvincenzo Zuccotti
- Department of Biomedical and Clinical Sciences, Pediatric Clinical Research Center "Romeo and Enrica Invernizzi", Università Di Milano, 20157, Milan, Italy
- Department of Paediatrics, Children's Hospital "V. Buzzi", Milano, Italy
| | - Claudio Bandi
- Department of Biosciences and Pediatric Clinical Research Center "Romeo Ed Enrica Invernizzi", University of Milan, 20133, Milan, Italy
| | - Francesco Comandatore
- Department of Biomedical and Clinical Sciences, Pediatric Clinical Research Center "Romeo and Enrica Invernizzi", Università Di Milano, 20157, Milan, Italy.
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Nodari R, Perini M, Fois L, Sterzi L, Luconi E, Vaglienti F, Bandi C, Biganzoli E, Galli M, Comandatore F. Computational protocol to perform a spatiotemporal reconstruction of an epidemic. STAR Protoc 2023; 4:102548. [PMID: 37717214 PMCID: PMC10514217 DOI: 10.1016/j.xpro.2023.102548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/21/2023] [Accepted: 08/09/2023] [Indexed: 09/19/2023] Open
Abstract
Here, we present a computational protocol to perform a spatiotemporal reconstruction of an epidemic. We describe steps for using epidemiological data to depict how the epidemic changes over time and for employing clustering analysis to group geographical units that exhibit similar temporal epidemic progression. We then detail procedures for analyzing the temporal and spatial dynamics of the epidemic within each cluster. This protocol has been developed to be used on historical data but could also be applied to modern epidemiological data. For complete details on the use and execution of this protocol, please refer to Galli et al. (2023).1.
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Affiliation(s)
- Riccardo Nodari
- Romeo ed Enrica Invernizzi Paediatric Research Centre, Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy.
| | - Matteo Perini
- Romeo ed Enrica Invernizzi Paediatric Research Centre, Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy; Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Luca Fois
- Department of Humanities, Section of Historical and Geographical Science, University of Pavia, Pavia, Italy
| | - Lodovico Sterzi
- Romeo ed Enrica Invernizzi Paediatric Research Centre, Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy
| | - Ester Luconi
- Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy
| | - Folco Vaglienti
- Department of Historical Studies, University of Milan, Milan, Italy
| | - Claudio Bandi
- Romeo ed Enrica Invernizzi Paediatric Research Centre, Department of Biosciences, University of Milan, Milan, Italy
| | - Elia Biganzoli
- Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy
| | - Massimo Galli
- Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy
| | - Francesco Comandatore
- Romeo ed Enrica Invernizzi Paediatric Research Centre, Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy.
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