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Franz E, Rotariu O, Lopes BS, MacRae M, Bono JL, Laing C, Gannon V, Söderlund R, van Hoek AHAM, Friesema I, French NP, George T, Biggs PJ, Jaros P, Rivas M, Chinen I, Campos J, Jernberg C, Gobius K, Mellor GE, Chandry PS, Perez-Reche F, Forbes KJ, Strachan NJC. Phylogeographic Analysis Reveals Multiple International transmission Events Have Driven the Global Emergence of Escherichia coli O157:H7. Clin Infect Dis 2020; 69:428-437. [PMID: 30371758 DOI: 10.1093/cid/ciy919] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 10/28/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Shiga toxin-producing Escherchia coli (STEC) O157:H7 is a zoonotic pathogen that causes numerous food and waterborne disease outbreaks. It is globally distributed, but its origin and the temporal sequence of its geographical spread are unknown. METHODS We analyzed whole-genome sequencing data of 757 isolates from 4 continents, and performed a pan-genome analysis to identify the core genome and, from this, extracted single-nucleotide polymorphisms. A timed phylogeographic analysis was performed on a subset of the isolates to investigate its worldwide spread. RESULTS The common ancestor of this set of isolates occurred around 1890 (1845-1925) and originated from the Netherlands. Phylogeographic analysis identified 34 major transmission events. The earliest were predominantly intercontinental, moving from Europe to Australia around 1937 (1909-1958), to the United States in 1941 (1921-1962), to Canada in 1960 (1943-1979), and from Australia to New Zealand in 1966 (1943-1982). This pre-dates the first reported human case of E. coli O157:H7, which was in 1975 from the United States. CONCLUSIONS Inter- and intra-continental transmission events have resulted in the current international distribution of E. coli O157:H7, and it is likely that these events were facilitated by animal movements (eg, Holstein Friesian cattle). These findings will inform policy on action that is crucial to reduce the further spread of E. coli O157:H7 and other (emerging) STEC strains globally.
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Affiliation(s)
- Eelco Franz
- National Institute for Public Health and the Environment, Centre for Infectious Disease Control, Bilthoven, The Netherlands
| | - Ovidiu Rotariu
- School of Biological Sciences, The University of Aberdeen, United Kingdom
| | - Bruno S Lopes
- School of Medicine, Medical Sciences & Nutrition, The University of Aberdeen, United Kingdom
| | - Marion MacRae
- School of Medicine, Medical Sciences & Nutrition, The University of Aberdeen, United Kingdom
| | - James L Bono
- United States Department of Agriculture, Agricultural Research Service, US Meat Animal Research Center, Clay Center, Nebraska
| | - Chad Laing
- National Microbiology Laboratory, Public Health Agency of Canada, Lethbridge, Alberta
| | - Victor Gannon
- National Microbiology Laboratory, Public Health Agency of Canada, Lethbridge, Alberta
| | | | - Angela H A M van Hoek
- National Institute for Public Health and the Environment, Centre for Infectious Disease Control, Bilthoven, The Netherlands
| | - Ingrid Friesema
- National Institute for Public Health and the Environment, Centre for Infectious Disease Control, Bilthoven, The Netherlands
| | - Nigel P French
- Molecular EpiLab, Infectious Disease Research Centre, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Tessy George
- Molecular EpiLab, Infectious Disease Research Centre, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Patrick J Biggs
- Molecular EpiLab, Infectious Disease Research Centre, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Patricia Jaros
- Molecular EpiLab, Infectious Disease Research Centre, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Marta Rivas
- Instituto Nacional de Enfermedades Infecciosas, Administracion Nacional del Laboratorios et Institutos de Salud "Dr Carlos G. Malbrán," Buenos Aires, Argentina
| | - Isabel Chinen
- Instituto Nacional de Enfermedades Infecciosas, Administracion Nacional del Laboratorios et Institutos de Salud "Dr Carlos G. Malbrán," Buenos Aires, Argentina
| | - Josefina Campos
- Instituto Nacional de Enfermedades Infecciosas, Administracion Nacional del Laboratorios et Institutos de Salud "Dr Carlos G. Malbrán," Buenos Aires, Argentina
| | - Cecilia Jernberg
- Department of Microbiology, The Public Health Agency of Sweden, Stockholm
| | - Kari Gobius
- The Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Werribee, Victoria, Australia
| | - Glen E Mellor
- The Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Werribee, Victoria, Australia
| | - P Scott Chandry
- The Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Werribee, Victoria, Australia
| | - Francisco Perez-Reche
- Institute of Complex Systems and Mathematical Biology, SUPA, School of Natural and Computing Sciences, University of Aberdeen, United Kingdom
| | - Ken J Forbes
- School of Medicine, Medical Sciences & Nutrition, The University of Aberdeen, United Kingdom
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Loiseau C, Menardo F, Aseffa A, Hailu E, Gumi B, Ameni G, Berg S, Rigouts L, Robbe-Austerman S, Zinsstag J, Gagneux S, Brites D. An African origin for Mycobacterium bovis. Evol Med Public Health 2020; 2020:49-59. [PMID: 32211193 PMCID: PMC7081938 DOI: 10.1093/emph/eoaa005] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 12/24/2019] [Accepted: 01/24/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND AND OBJECTIVES Mycobacterium bovis and Mycobacterium caprae are two of the most important agents of tuberculosis in livestock and the most important causes of zoonotic tuberculosis in humans. However, little is known about the global population structure, phylogeography and evolutionary history of these pathogens. METHODOLOGY We compiled a global collection of 3364 whole-genome sequences from M.bovis and M.caprae originating from 35 countries and inferred their phylogenetic relationships, geographic origins and age. RESULTS Our results resolved the phylogenetic relationship among the four previously defined clonal complexes of M.bovis, and another eight newly described here. Our phylogeographic analysis showed that M.bovis likely originated in East Africa. While some groups remained restricted to East and West Africa, others have subsequently dispersed to different parts of the world. CONCLUSIONS AND IMPLICATIONS Our results allow a better understanding of the global population structure of M.bovis and its evolutionary history. This knowledge can be used to define better molecular markers for epidemiological investigations of M.bovis in settings where whole-genome sequencing cannot easily be implemented. LAY SUMMARY During the last few years, analyses of large globally representative collections of whole-genome sequences (WGS) from the human-adapted Mycobacterium tuberculosis complex (MTBC) lineages have enhanced our understanding of the global population structure, phylogeography and evolutionary history of these pathogens. In contrast, little corresponding data exists for M. bovis, the most important agent of tuberculosis in livestock. Using whole-genome sequences of globally distributed M. bovis isolates, we inferred the genetic relationships among different M. bovis genotypes distributed around the world. The most likely origin of M. bovis is East Africa according to our inferences. While some M. bovis groups remained restricted to East and West Africa, others have subsequently dispersed to different parts of the world driven by cattle movements.
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Affiliation(s)
- Chloé Loiseau
- Molecular Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Fabrizio Menardo
- Molecular Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Abraham Aseffa
- Mycobacterial Diseases Directorate, Armauer Hansen Research Centre, Addis Ababa, Ethiopia
| | - Elena Hailu
- Mycobacterial Diseases Directorate, Armauer Hansen Research Centre, Addis Ababa, Ethiopia
| | - Balako Gumi
- Department of Animal Science and Range Management, Bule Hora University, Bule Hora Town, Ethiopia
| | - Gobena Ameni
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Stefan Berg
- Bacteriology Department, Animal & Plant Health Agency (APHA), Weybridge, Surrey, UK
| | - Leen Rigouts
- Mycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Collection of Mycobacterial Cultures (BCCM/ITM), Institute of Tropical Medicine, Antwerp, Belgium
- Department of Biomedical Sciences, Antwerp University, Antwerp, Belgium
| | - Suelee Robbe-Austerman
- Diagnostic Bacteriology and Pathology Laboratory, National Veterinary Services Laboratories, United States Department of Agriculture, Ames, IA, USA
| | - Jakob Zinsstag
- Molecular Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Sebastien Gagneux
- Molecular Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Daniela Brites
- Molecular Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
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Browne AS, Biggs PJ, Wilkinson DA, Cookson AL, Midwinter AC, Bloomfield SJ, Hranac CR, Rogers LE, Marshall JC, Benschop J, Withers H, Hathaway S, George T, Jaros P, Irshad H, Fong Y, Dufour M, Karki N, Winkleman T, French NP. Use of Genomics to Investigate Historical Importation of Shiga Toxin-Producing Escherichia coli Serogroup O26 and Nontoxigenic Variants into New Zealand. Emerg Infect Dis 2019; 25:489-500. [PMID: 30789138 PMCID: PMC6390770 DOI: 10.3201/eid2503.180899] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Shiga toxin-producing Escherichia coli serogroup O26 is an important public health pathogen. Phylogenetic bacterial lineages in a country can be associated with the level and timing of international imports of live cattle, the main reservoir. We sequenced the genomes of 152 E. coli O26 isolates from New Zealand and compared them with 252 E. coli O26 genomes from 14 other countries. Gene variation among isolates from humans, animals, and food was strongly associated with country of origin and stx toxin profile but not isolation source. Time of origin estimates indicate serogroup O26 sequence type 21 was introduced at least 3 times into New Zealand from the 1920s to the 1980s, whereas nonvirulent O26 sequence type 29 strains were introduced during the early 2000s. New Zealand's remarkably fewer introductions of Shiga toxin-producing Escherichia coli O26 compared with other countries (such as Japan) might be related to patterns of trade in live cattle.
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Price-Carter M, Brauning R, de Lisle GW, Livingstone P, Neill M, Sinclair J, Paterson B, Atkinson G, Knowles G, Crews K, Crispell J, Kao R, Robbe-Austerman S, Stuber T, Parkhill J, Wood J, Harris S, Collins DM. Whole Genome Sequencing for Determining the Source of Mycobacterium bovis Infections in Livestock Herds and Wildlife in New Zealand. Front Vet Sci 2018; 5:272. [PMID: 30425997 PMCID: PMC6218598 DOI: 10.3389/fvets.2018.00272] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 10/11/2018] [Indexed: 01/18/2023] Open
Abstract
The ability to DNA fingerprint Mycobacterium bovis isolates helped to define the role of wildlife in the persistence of bovine tuberculosis in New Zealand. DNA fingerprinting results currently help to guide wildlife control measures and also aid in tracing the source of infections that result from movement of livestock. During the last 5 years we have developed the ability to distinguish New Zealand (NZ) M. bovis isolates by comparing the sequences of whole genome sequenced (WGS) M. bovis samples. WGS provides much higher resolution than our other established typing methods and greatly improves the definition of the regional localization of NZ M. bovis types. Three outbreak investigations are described and results demonstrate how WGS analysis has led to the confirmation of epidemiological sourcing of infection, to better definition of new sources of infection by ruling out other possible sources, and has revealed probable wildlife infection in an area considered to be free of infected wildlife. The routine use of WGS analyses for sourcing new M. bovis infections will be an important component of the strategy employed to eradicate bovine TB from NZ livestock and wildlife.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Garry Knowles
- Aquaculture Veterinary Services Ltd., Clyde, New Zealand
| | | | - Joseph Crispell
- University College Dublin School of Veterinary Medicine, Dublin, Ireland
| | - Rowland Kao
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Suelee Robbe-Austerman
- Diagnostic Bacteriology Laboratory, National Veterinary Services Laboratories, U.S. Department of Agriculture, Animal and Plant Health Inspection Service, Veterinary Service, Ames, IA, United States
| | - Tod Stuber
- Diagnostic Bacteriology Laboratory, National Veterinary Services Laboratories, U.S. Department of Agriculture, Animal and Plant Health Inspection Service, Veterinary Service, Ames, IA, United States
| | - Julian Parkhill
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - James Wood
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Simon Harris
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Desmond M Collins
- AgResearch, Hopkirk Research Institute, Palmerston North, New Zealand
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Local and global genetic diversity of protozoan parasites: Spatial distribution of Cryptosporidium and Giardia genotypes. PLoS Negl Trop Dis 2017; 11:e0005736. [PMID: 28704362 PMCID: PMC5526614 DOI: 10.1371/journal.pntd.0005736] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 07/25/2017] [Accepted: 06/21/2017] [Indexed: 01/09/2023] Open
Abstract
Cryptosporidiosis and giardiasis are recognized as significant enteric diseases due to their long-term health effects in humans and their economic impact in agriculture and medical care. Molecular analysis is essential to identify species and genotypes causing these infectious diseases and provides a potential tool for monitoring. This study uses information on species and genetic variants to gain insights into the geographical distribution and spatial patterns of Cryptosporidium and Giardia parasites. Here, we describe the population heterogeneity of genotypic groups within Cryptosporidium and Giardia present in New Zealand using gp60 and gdh markers to compare the observed variation with other countries around the globe. Four species of Cryptosporidium (C. hominis, C. parvum, C. cuniculus and C. erinacei) and one species of Giardia (G. intestinalis) were identified. These species have been reported worldwide and there are not unique Cryptosporidium gp60 subtype families and Giardiagdh assemblages in New Zealand, most likely due to high gene flow of historical and current human activity (travel and trade) and persistence of large host population sizes. The global analysis revealed that genetic variants of these pathogens are widely distributed. However, genetic variation is underestimated by data biases (e.g. neglected submission of sequences to genetic databases) and low sampling. New genotypes are likely to be discovered as sampling efforts increase according to accumulation prediction analyses, especially for C. parvum. Our study highlights the need for greater sampling and archiving of genotypes globally to allow comparative analyses that help understand the population dynamics of these protozoan parasites. Overall our study represents a comprehensive overview for exploring local and global protozoan genotype diversity and advances our understanding of the importance for surveillance and potential risk associated with these infectious diseases. Infectious diseases threaten the health and well-being of wildlife, livestock and human populations and contribute to significant economic impact in agriculture and medical care. Cryptosporidium and Giardia are enteric protozoan pathogens that cause diarrhea and nutritional disorders on a global level. Using molecular analysis and a review framework we showed that species and genetic variants within genera Cryptosporidium and Giardia (including two species recently infecting humans) found in an island system are not different from other parts of the world. This similarity is likely due to high gene flow of historical and current human activity (travel and trade) and persistence of large host population sizes, such as cattle and people. We also show that, although species and genotypes are widely distributed, new variants will arise when sampling effort increase and their dispersal will be facilitated by human activity. These findings suggest that geographical distribution of species and genotypes within Cryptosporidium and Giardia parasites may yield important clues for designing effective surveillance strategies and identification of factors driving within and cross species transmission.
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Crispell J, Zadoks RN, Harris SR, Paterson B, Collins DM, de-Lisle GW, Livingstone P, Neill MA, Biek R, Lycett SJ, Kao RR, Price-Carter M. Using whole genome sequencing to investigate transmission in a multi-host system: bovine tuberculosis in New Zealand. BMC Genomics 2017; 18:180. [PMID: 28209138 PMCID: PMC5314462 DOI: 10.1186/s12864-017-3569-x] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 02/09/2017] [Indexed: 12/13/2022] Open
Abstract
Background Bovine tuberculosis (bTB), caused by Mycobacterium bovis, is an important livestock disease raising public health and economic concerns around the world. In New Zealand, a number of wildlife species are implicated in the spread and persistence of bTB in cattle populations, most notably the brushtail possum (Trichosurus vulpecula). Whole Genome Sequenced (WGS) M. bovis isolates sourced from infected cattle and wildlife across New Zealand were analysed. Bayesian phylogenetic analyses were conducted to estimate the substitution rate of the sampled population and investigate the role of wildlife. In addition, the utility of WGS was examined with a view to these methods being incorporated into routine bTB surveillance. Results A high rate of exchange was evident between the sampled wildlife and cattle populations but directional estimates of inter-species transmission were sensitive to the sampling strategy employed. A relatively high substitution rate was estimated, this, in combination with a strong spatial signature and a good agreement to previous typing methods, acts to endorse WGS as a typing tool. Conclusions In agreement with the current knowledge of bTB in New Zealand, transmission of M. bovis between cattle and wildlife was evident. Without direction, these estimates are less informative but taken in conjunction with the low prevalence of bTB in New Zealand’s cattle population it is likely that, currently, wildlife populations are acting as the main bTB reservoir. Wildlife should therefore continue to be targeted if bTB is to be eradicated from New Zealand. WGS will be a considerable aid to bTB eradication by greatly improving the discriminatory power of molecular typing data. The substitution rates estimated here will be an important part of epidemiological investigations using WGS data. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3569-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Joseph Crispell
- Institute of Biodiversity, Animal Health, and Comparative Medicine, University of Glasgow, Glasgow, Scotland, G61 1QH, UK
| | - Ruth N Zadoks
- Institute of Biodiversity, Animal Health, and Comparative Medicine, University of Glasgow, Glasgow, Scotland, G61 1QH, UK
| | - Simon R Harris
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Brent Paterson
- TBfree New Zealand, PO Box 3412, Wellington, 6140, New Zealand
| | | | | | | | - Mark A Neill
- TBfree New Zealand, PO Box 3412, Wellington, 6140, New Zealand
| | - Roman Biek
- Institute of Biodiversity, Animal Health, and Comparative Medicine, University of Glasgow, Glasgow, Scotland, G61 1QH, UK
| | - Samantha J Lycett
- Infection and Immunity Division, The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, Scotland, UK
| | - Rowland R Kao
- Institute of Biodiversity, Animal Health, and Comparative Medicine, University of Glasgow, Glasgow, Scotland, G61 1QH, UK.
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Whole Genome Sequencing demonstrates that Geographic Variation of Escherichia coli O157 Genotypes Dominates Host Association. Sci Rep 2015; 5:14145. [PMID: 26442781 PMCID: PMC4595763 DOI: 10.1038/srep14145] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 08/19/2015] [Indexed: 02/04/2023] Open
Abstract
Genetic variation in an infectious disease pathogen can be driven by ecological niche dissimilarities arising from different host species and different geographical locations. Whole genome sequencing was used to compare E. coli O157 isolates from host reservoirs (cattle and sheep) from Scotland and to compare genetic variation of isolates (human, animal, environmental/food) obtained from Scotland, New Zealand, Netherlands, Canada and the USA. Nei’s genetic distance calculated from core genome single nucleotide polymorphisms (SNPs) demonstrated that the animal isolates were from the same population. Investigation of the Shiga toxin bacteriophage and their insertion sites (SBI typing) revealed that cattle and sheep isolates had statistically indistinguishable rarefaction profiles, diversity and genotypes. In contrast, isolates from different countries exhibited significant differences in Nei’s genetic distance and SBI typing. Hence, after successful international transmission, which has occurred on multiple occasions, local genetic variation occurs, resulting in a global patchwork of continental and trans-continental phylogeographic clades. These findings are important for three reasons: first, understanding transmission and evolution of infectious diseases associated with multiple host reservoirs and multi-geographic locations; second, highlighting the relevance of the sheep reservoir when considering farm based interventions; and third, improving our understanding of why human disease incidence varies across the world.
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Jaros P, Cookson AL, Campbell DM, Duncan GE, Prattley D, Carter P, Besser TE, Shringi S, Hathaway S, Marshall JC, French NP. Geographic divergence of bovine and human Shiga toxin–producing Escherichia coli O157:H7 genotypes, New Zealand. Emerg Infect Dis 2014; 20:1980-9. [PMID: 25568924 PMCID: PMC4257794 DOI: 10.3201/eid2012.140281] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC)O157:H7 is a zoonotic pathogen of public health concern worldwide. To compare the local and large-scale geographic distributions of genotypes of STEC O157:H7 isolates obtained from various bovine and human sources during 2008–2011, we used pulsed-field gel electrophoresis and Shiga toxin–encoding bacteriophage insertion (SBI) typing. Using multivariate methods, we compared isolates from the North and South Islands of New Zealand with isolates from Australia and the United States. The STEC O157:H7 population structure differed substantially between the 2 islands and showed evidence of finer scale spatial structuring, which is consistent with highly localized transmission rather than disseminated foodborne outbreaks. The distribution of SBI types differed markedly among isolates from New Zealand, Australia, and the United States. Our findings also provide evidence for the historic introduction into New Zealand of a subset of globally circulating STEC O157:H7 strains that have continued to evolve and be transmitted locally between cattle and humans.
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