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2012	The inaugural issue was released. Pathogens was published as a quarterly journal.
2014	Pathogens was indexed in PubMed.
2015	Pathogens was indexed in Emerging Sources Citation Index (ESCI) - Web of Science (Clarivate Analytics).
2016	Pathogens was indexed in Scopus.
2017	Pathogens established the section Plant Pathogens.
2018	Pathogens was indexed in Science Citation Index Expanded (SCIE) - Web of Science (Clarivate Analytics). Pathogens announced the first edition of the Travel Awards. Pathogens established the following sections: Human Pathogens; Animal Pathogens; Waterborne/Foodborne/Airborne Pathogens; Immunological Responses and Immune Defense Mechanisms; Vaccines and Therapeutic Developments.
2019	Pathogens received its first Impact Factor (3.405).
	Pathogens announced the first edition of the Outstanding Reviewer Awards and Best Paper Awards.
	Pathogens published its 500th paper.
2020	Pathogens adopted a monthly publication schedule.
	Pathogens established the section Ticks.
	Pathogens published its 1000th paper.
2021	Pathogens has reorganized the journal sections, and has established the following sections: Bacterial Pathogens; Fungal Pathogens; Viral Pathogens; Parasitic Pathogens; Emerging Pathogens; Prions; The following sections have been discontinued: Plant Pathogens; Human Pathogens; Animal Pathogens; Waterborne/Foodborne/Airborne Pathogens.

2012-	Founding Editor-in-Chief: Prof. Lawrence S. Young.
2020	Section Editor-in-Chief: Prof. Dr. Hinh Ly for the section on Immunological Responses and Immune Defense Mechanisms. Section Editor-in-Chief: Prof. Roberto Paganelli for the section on Vaccines and Therapeutic Developments. Section Editor-in-Chief: Dr. Alejandro Cabezas-Cruz for the section on Ticks.
2021	Section Editor-in-Chief: Dr. Sébastien Besteiro for the section on Parasitic Pathogens. Section Editor-in-Chief: Dr. Anna Honko for the section on Viral Pathogens. Section Editor-in-Chief: Prof. Dr. David Rodríguez-Lázaro for the section on Bacterial Pathogens.