Strengthening the Reporting of Molecular Epidemiology for Infectious Diseases (STROME-ID): an extension of the STROBE statement

Abstract

Molecular data are now widely used in epidemiological studies to investigate the transmission, distribution, biology, and diversity of pathogens. Our objective was to establish recommendations to support good scientific reporting of molecular epidemiological studies to encourage authors to consider specific threats to valid inference. The statement Strengthening the Reporting of Molecular Epidemiology for Infectious Diseases (STROME-ID) builds upon the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) initiative. The STROME-ID statement was developed by a working group of epidemiologists, statisticians, bioinformaticians, virologists, and microbiologists with expertise in control of infection and communicable diseases. The statement focuses on issues relating to the reporting of epidemiological studies of infectious diseases using molecular data that were not addressed by STROBE. STROME-ID addresses terminology, measures of genetic diversity within pathogen populations, laboratory methods, sample collection, use of molecular markers, molecular clocks, timeframe, multiple-strain infections, non-independence of infectious-disease data, missing data, ascertainment bias, consistency between molecular and epidemiological data, and ethical considerations with respect to infectious-disease research. In total, 20 items were added to the 22 item STROBE checklist. When used, the STROME-ID recommendations should advance the quality and transparency of scientific reporting, with clear benefits for evidence reviews and health-policy decision making.

Application of Whole-Genome Sequencing for Bacterial Strain Typing in Molecular Epidemiology

“…In addition to preventative measures (2), effective infection control is achieved through active surveillance of infection and recognition of burgeoning disease outbreaks that can be interrupted through health care interventions (1). Molecular epidemiological investigations have become increasingly integral to these functions and rely on methods that can rapidly and effectively assess genetic relatedness among strains (1,4,5).…”

Molecular epidemiology study of swine influenza virus revealing a reassorted virus H1N1 in swine farms in Cuba

“…This finding was possible by the application of a molecular epidemiology approach using complete genome sequence information obtained from the A/swine/Pinar del Río/3/2010 (H1N1) isolate. In fact, the use of molecular epidemiology studies of infectious diseases has become, in the current day, a powerful method to investigate the transmission, distribution, biology and diversity of pathogens (reviewed in Field et al, 2014). This scientific discipline together with the development of sequencing technologies have allowed to gain insight into the origin, emergence and spread of viral agents (Pérez et al, 2011;Alfonso-Morales et al, 2013), support vaccination programs established for control of viral endemic diseases (Pérez et al, 2012) and others.…”

A Primer on Infectious Disease Bacterial Genomics

“…Open data also provide researchers with data to develop, enhance, and benchmark analytical methods. Consequently, there is increasing pressure to provide open data through initiatives such as the STROME-ID (Strengthening the Reporting of Molecular Epidemiology for Infectious Diseases) statement (235). Many journals have adopted mandatory open data policies, meaning that all supporting data must be submitted to a relevant publicly accessible depository.…”