Ann Microbiol Immunol | Volume 1, Issue 1 | Review Article | Open Access

New Trends in Microbial Epidemiology: Can An Old Dog Learn New Tricks?

Manuela Oliveira^1,2,3*, Miguel Arenas^1,2,4 and António Amorim^1,2,3

¹i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal
²Ipatimup - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Portugal
³Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Portugal
⁴Department of Biochemistry, Genetics and Immunology, University of Vigo, Spain

^*Correspondance to: Manuela Oliveira 

Fulltext PDF

Abstract

In historical terms, almost 50 years ago, all the knowledge coming from clinical microbiology was provided by classical methods, mainly based on phenotypic observations and culture-dependent methods. With the advent of DNA fragment analysis, PCR-based methods and Sanger sequencing, the dawn of the Era of Molecular Diagnosis began. Significant improvements were achieved, namely improved resolution concerning the identification of etiological agents was possible in a reduced timeframe between sample collection and results. To overcome some of the difficulties presented by molecular diagnosis, almost 20 years ago, massive parallel sequencing technology was introduced into epidemiological studies. Nowadays, is possible to sequence the whole genome of a given microorganism (including information on antibiotic resistance, virulence factors, and evolutionary relationships) or to assess the complete diversity of microorganisms present in a given individual or in environmental samples (metagenomics).The present review covers the major outbreaks registered worldwide in the past 12 years and highlights the use of new technologies in source identification, outbreak detection, routes of transmission determination, pathogen evolution inference and mechanisms of pathogen adaptation to drug therapies.

Keywords:

Clinical microbiology; Epidemiology; Genetics; Massive parallel Sequencing; Microbiome

Citation:

Oliveira M, Arenas M, Amorim A. New Trends in Microbial Epidemiology: Can An Old Dog Learn New Tricks? Ann Microbiol Immunol. 2018; 1(1): 1004.