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Bianco CM, Moustafa AM, O’Brien K, Martin MA, Read TD, Kreiswirth BN, Planet PJ. Pre-epidemic evolution of the MRSA USA300 clade and a molecular key for classification. Front Cell Infect Microbiol 2023; 13:1081070. [PMID: 36761897 PMCID: PMC9902376 DOI: 10.3389/fcimb.2023.1081070] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 01/04/2023] [Indexed: 01/26/2023] Open
Abstract
Introduction USA300 has remained the dominant community and healthcare associated methicillin-resistant Staphylococcus aureus (MRSA) clone in the United States and in northern South America for at least the past 20 years. In this time, it has experienced epidemic spread in both of these locations. However, its pre-epidemic evolutionary history and origins are incompletely understood. Large sequencing databases, such as NCBI, PATRIC, and Staphopia, contain clues to the early evolution of USA300 in the form of sequenced genomes of USA300 isolates that are representative of lineages that diverged prior to the establishment of the South American epidemic (SAE) clade and North American epidemic (NAE) clade. In addition, historical isolates collected prior to the emergence of epidemics can help reconstruct early events in the history of this lineage. Methods Here, we take advantage of the accrued, publicly available data, as well as two newly sequenced pre-epidemic historical isolates from 1996, and a very early diverging ACME-negative NAE genome, to understand the pre-epidemic evolution of USA300. We use database mining techniques to emphasize genomes similar to pre-epidemic isolates, with the goal of reconstructing the early molecular evolution of the USA300 lineage. Results Phylogenetic analysis with these genomes confirms that the NAE and SAE USA300 lineages diverged from a most recent common ancestor around 1970 with high confidence, and it also pinpoints the independent acquisition events of the of the ACME and COMER loci with greater precision than in previous studies. We provide evidence for a North American origin of the USA300 lineage and identify multiple introductions of USA300 into South and North America. Notably, we describe a third major USA300 clade (the pre-epidemic branching clade; PEB1) consisting of both MSSA and MRSA isolates circulating around the world that diverged from the USA300 lineage prior to the establishment of the South and North American epidemics. We present a detailed analysis of specific sequence characteristics of each of the major clades, and present diagnostic positions that can be used to classify new genomes.
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Affiliation(s)
- Colleen M. Bianco
- Division of Pediatric Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Ahmed M. Moustafa
- Division of Pediatric Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, PA, United States,Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Kelsey O’Brien
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Michael A. Martin
- Division of Infectious Diseases & Department of Human Genetics Emory University School of Medicine, Atlanta, GA, United States
| | - Timothy D. Read
- Division of Infectious Diseases & Department of Human Genetics Emory University School of Medicine, Atlanta, GA, United States
| | - Barry N. Kreiswirth
- Center for Discovery & Innovation, Hackensack Meridian Health, Nutley, NJ, United States
| | - Paul J. Planet
- Division of Pediatric Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, PA, United States,Department of Pediatrics, Perelman College of Medicine, University of Pennsylvania, Philadelphia, PA, United States,American Museum of Natural History, New York, NY, United States,*Correspondence: Paul J. Planet,
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Thompson AT, Dominguez K, Cleveland CA, Dergousoff SJ, Doi K, Falco RC, Greay T, Irwin P, Lindsay LR, Liu J, Mather TN, Oskam CL, Rodriguez-Vivas RI, Ruder MG, Shaw D, Vigil SL, White S, Yabsley MJ. Molecular Characterization of Haemaphysalis Species and a Molecular Genetic Key for the Identification of Haemaphysalis of North America. Front Vet Sci 2020; 7:141. [PMID: 32232062 PMCID: PMC7082797 DOI: 10.3389/fvets.2020.00141] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 02/25/2020] [Indexed: 11/16/2022] Open
Abstract
Haemaphysalis longicornis (Acari: Ixodidae), the Asian longhorned tick, is native to East Asia, but has become established in Australia and New Zealand, and more recently in the United States. In North America, there are other native Haemaphysalis species that share similar morphological characteristics and can be difficult to identify if the specimen is damaged. The goal of this study was to develop a cost-effective and rapid molecular diagnostic assay to differentiate between exotic and native Haemaphysalis species to aid in ongoing surveillance of H. longicornis within the United States and help prevent misidentification. We demonstrated that restriction fragment length polymorphisms (RFLPs) targeting the 16S ribosomal RNA and the cytochrome c oxidase subunit I (COI) can be used to differentiate H. longicornis from the other Haemaphysalis species found in North America. Furthermore, we show that this RFLP assay can be applied to Haemaphysalis species endemic to other regions of the world for the rapid identification of damaged specimens. The work presented in this study can serve as the foundation for region specific PCR-RFLP keys for Haemaphysalis and other tick species and can be further applied to other morphometrically challenging taxa.
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Affiliation(s)
- Alec T. Thompson
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
- Center for the Ecology of Infectious Diseases, Odum School of Ecology, University of Georgia, Athens, GA, United States
| | - Kristen Dominguez
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Christopher A. Cleveland
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Shaun J. Dergousoff
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB, Canada
| | - Kandai Doi
- Laboratory of Wildlife Medicine, Nippon Veterinary and Life Science University, Musashino, Japan
| | - Richard C. Falco
- New York State Department of Health, Louis Calder Center, Fordham University, Armonk, NY, United States
| | - Telleasha Greay
- Vector and Waterborne Pathogens Research Group, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
| | - Peter Irwin
- Vector and Waterborne Pathogens Research Group, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
| | - L. Robbin Lindsay
- Public Health Agency of Canada, National Microbiology Laboratory, Winnipeg, MB, Canada
| | - Jingze Liu
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Thomas N. Mather
- Center for Vector-Borne Diseases, University of Rhode Island, Kingston, RI, United States
| | - Charlotte L. Oskam
- Vector and Waterborne Pathogens Research Group, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
| | - Roger I. Rodriguez-Vivas
- Campus of Biology and Agricultural Sciences, Department of Veterinary Medicine and Animal Husbandry, National Autonomous University of Yucatan, Merida, Mexico
| | - Mark G. Ruder
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - David Shaw
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Stacey L. Vigil
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Seth White
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA, United States
| | - Michael J. Yabsley
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
- Center for the Ecology of Infectious Diseases, Odum School of Ecology, University of Georgia, Athens, GA, United States
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA, United States
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Planet PJ, Kachlany SC, DeSalle R, Figurski DH. Phylogeny of genes for secretion NTPases: identification of the widespread tadA subfamily and development of a diagnostic key for gene classification. Proc Natl Acad Sci U S A 2001; 98:2503-8. [PMID: 11226268 PMCID: PMC30167 DOI: 10.1073/pnas.051436598] [Citation(s) in RCA: 169] [Impact Index Per Article: 7.3] [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] [Indexed: 11/18/2022] Open
Abstract
Macromolecular transport systems in bacteria currently are classified by function and sequence comparisons into five basic types. In this classification system, type II and type IV secretion systems both possess members of a superfamily of genes for putative NTP hydrolase (NTPase) proteins that are strikingly similar in structure, function, and sequence. These include VirB11, TrbB, TraG, GspE, PilB, PilT, and ComG1. The predicted protein product of tadA, a recently discovered gene required for tenacious adherence of Actinobacillus actinomycetemcomitans, also has significant sequence similarity to members of this superfamily and to several unclassified and uncharacterized gene products of both Archaea and Bacteria. To understand the relationship of tadA and tadA-like genes to those encoding the putative NTPases of type II/IV secretion, we used a phylogenetic approach to obtain a genealogy of 148 NTPase genes and reconstruct a scenario of gene superfamily evolution. In this phylogeny, clear distinctions can be made between type II and type IV families and their constituent subfamilies. In addition, the subgroup containing tadA constitutes a novel and extremely widespread subfamily of the family encompassing all putative NTPases of type IV secretion systems. We report diagnostic amino acid residue positions for each major monophyletic family and subfamily in the phylogenetic tree, and we propose an easy method for precisely classifying and naming putative NTPase genes based on phylogeny. This molecular key-based method can be applied to other gene superfamilies and represents a valuable tool for genome analysis.
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Affiliation(s)
- P J Planet
- Department of Microbiology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
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