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Turco S, Russo S, Pietrucci D, Filippi A, Milanesi M, Luzzago C, Garbarino C, Palladini G, Chillemi G, Ricchi M. High clonality of Mycobacterium avium subsp. paratuberculosis field isolates from red deer revealed by two different methodological approaches of comparative genomic analysis. Front Vet Sci 2024; 11:1301667. [PMID: 38379925 PMCID: PMC10876796 DOI: 10.3389/fvets.2024.1301667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 01/10/2024] [Indexed: 02/22/2024] Open
Abstract
Mycobacterium avium subsp. paratuberculosis (MAP) is the aetiological agent of paratuberculosis (Johne's disease) in both domestic and wild ruminants. In the present study, using a whole-genome sequence (WGS) approach, we investigated the genetic diversity of 15 Mycobacterium avium field strains isolated in the last 10 years from red deer inhabiting the Stelvio National Park and affected by paratuberculosis. Combining de novo assembly and a reference-based method, followed by a pangenome analysis, we highlight a very close relationship among 13 MAP field isolates, suggesting that a single infecting event occurred in this population. Moreover, two isolates have been classified as Mycobacterium avium subsp. hominissuis, distinct from the other MAPs under comparison but close to each other. This is the first time that this subspecies has been found in Italy in samples without evident epidemiological correlations, having been isolated in two different locations of the Stelvio National Park and in different years. Our study highlights the importance of a multidisciplinary approach incorporating molecular epidemiology and ecology into traditional infectious disease knowledge in order to investigate the nature of infectious disease in wildlife populations.
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Affiliation(s)
- Silvia Turco
- Dipartimento di Scienze Agrarie e Forestali (DAFNE), Università degli Studi della Tuscia, Viterbo, Italy
| | - Simone Russo
- National Reference Centre and WOAH Reference Laboratory for Paratuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna “Bruno Ubertini”, Piacenza, Italy
| | - Daniele Pietrucci
- Dipartimento per l'Innovazione nei Sistemi Biologici, Agroalimentari e Forestali (DIBAF), Università degli Studi della Tuscia, Viterbo, Italy
| | - Anita Filippi
- National Reference Centre and WOAH Reference Laboratory for Paratuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna “Bruno Ubertini”, Piacenza, Italy
| | - Marco Milanesi
- Dipartimento per l'Innovazione nei Sistemi Biologici, Agroalimentari e Forestali (DIBAF), Università degli Studi della Tuscia, Viterbo, Italy
| | - Camilla Luzzago
- Department of Veterinary Medicine and Animal Sciences, Coordinated Research Centre "EpiSoMI", University of Milan, Lodi, Italy
| | - Chiara Garbarino
- National Reference Centre and WOAH Reference Laboratory for Paratuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna “Bruno Ubertini”, Piacenza, Italy
| | - Giorgia Palladini
- National Reference Centre and WOAH Reference Laboratory for Paratuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna “Bruno Ubertini”, Piacenza, Italy
| | - Giovanni Chillemi
- Dipartimento per l'Innovazione nei Sistemi Biologici, Agroalimentari e Forestali (DIBAF), Università degli Studi della Tuscia, Viterbo, Italy
- Institute of Translational Pharmacology, National Research Council, CNR, Rome, Italy
| | - Matteo Ricchi
- National Reference Centre and WOAH Reference Laboratory for Paratuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna “Bruno Ubertini”, Piacenza, Italy
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An Embedded Multiscale Modelling to Guide Control and Elimination of Paratuberculosis in Ruminants. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2021; 2021:9919700. [PMID: 34868347 PMCID: PMC8642023 DOI: 10.1155/2021/9919700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 11/05/2021] [Indexed: 11/18/2022]
Abstract
In recent years, multiscale modelling approach has begun to receive an overwhelming appreciation as an appropriate technique to characterize the complexity of infectious disease systems. In this study, we develop an embedded multiscale model of paratuberculosis in ruminants at host level that integrates the within-host scale and the between-host. A key feature of embedded multiscale models developed at host level of organization of an infectious disease system is that the within-host scale and the between-host scale influence each other in a reciprocal (i.e., both) way through superinfection, that is, through repeated infection before the host recovers from the initial infectious episode. This key feature is demonstrated in this study through a multiscale model of paratuberculosis in ruminants. The results of this study, through numerical analysis of the multiscale model, show that superinfection influences the dynamics of paratuberculosis only at the start of the infection, while the MAP bacteria replication continuously influences paratuberculosis dynamics throughout the infection until the host recovers from the initial infectious episode. This is largely because the replication of MAP bacteria at the within-host scale sustains the dynamics of paratuberculosis at this scale domain. We further use the embedded multiscale model developed in this study to evaluate the comparative effectiveness of paratuberculosis health interventions that influence the disease dynamics at different scales from efficacy data.
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Nigsch A, Robbe-Austerman S, Stuber TP, Pavinski Bitar PD, Gröhn YT, Schukken YH. Who infects whom?-Reconstructing infection chains of Mycobacterium avium ssp. paratuberculosis in an endemically infected dairy herd by use of genomic data. PLoS One 2021; 16:e0246983. [PMID: 33983941 PMCID: PMC8118464 DOI: 10.1371/journal.pone.0246983] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 04/30/2021] [Indexed: 12/18/2022] Open
Abstract
Recent evidence of circulation of multiple strains within herds and mixed infections of cows marks the beginning of a rethink of our knowledge on Mycobacterium avium ssp. paratuberculosis (MAP) epidemiology. Strain typing opens new ways to investigate MAP transmission. This work presents a method for reconstructing infection chains in a setting of endemic Johne’s disease on a well-managed dairy farm. By linking genomic data with demographic field data, strain-specific differences in spreading patterns could be quantified for a densely sampled dairy herd. Mixed infections of dairy cows with MAP are common, and some strains spread more successfully. Infected cows remain susceptible for co-infections with other MAP genotypes. The model suggested that cows acquired infection from 1–4 other cows and spread infection to 0–17 individuals. Reconstructed infection chains supported the hypothesis that high shedding animals that started to shed at an early age and showed a progressive infection pattern represented a greater risk for spreading MAP. Transmission of more than one genotype between animals was recorded. In this farm with a good MAP control management program, adult-to-adult contact was proposed as the most important transmission route to explain the reconstructed networks. For each isolate, at least one more likely ancestor could be inferred. Our study results help to capture underlying transmission processes and to understand the challenges of tracing MAP spread within a herd. Only the combination of precise longitudinal field data and bacterial strain type information made it possible to trace infection in such detail.
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Affiliation(s)
- Annette Nigsch
- Department of Animal Sciences, Wageningen University, Wageningen, The Netherlands
- * E-mail:
| | - Suelee Robbe-Austerman
- USDA APHIS National Veterinary Services Laboratories, Ames, Iowa, United States of America
| | - Tod P. Stuber
- USDA APHIS National Veterinary Services Laboratories, Ames, Iowa, United States of America
| | - Paulina D. Pavinski Bitar
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States of America
| | - Yrjö T. Gröhn
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States of America
| | - Ynte H. Schukken
- Department of Animal Sciences, Wageningen University, Wageningen, The Netherlands
- Royal GD, Deventer, The Netherlands
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