Overview of molecular typing methods for outbreak detection and epidemiological surveillance

Abstract

Typing methods for discriminating different bacterial isolates of the same species are essential epidemiological tools in infection prevention and control. Traditional typing systems based on phenotypes, such as serotype, biotype, phage-type, or antibiogram, have been used for many years. However, more recent methods that examine the relatedness of isolates at a molecular level have revolutionised our ability to differentiate among bacterial types and subtypes. Importantly, the development of molecular methods has provided new tools for enhanced surveillance and outbreak detection. This has resulted in better implementation of rational infection control programmes and efficient allocation of resources across Europe. The emergence of benchtop sequencers using next generation sequencing technology makes bacterial whole genome sequencing (WGS) feasible even in small research and clinical laboratories. WGS has already been used for the characterisation of bacterial isolates in several large outbreaks in Europe and, in the near future, is likely to replace currently used typing methodologies due to its ultimate resolution. However, WGS is still too laborious and time-consuming to obtain useful data in routine surveillance. Also, a largely unresolved question is how genome sequences must be examined for epidemiological characterisation. In the coming years, the lessons learnt from currently used molecular methods will allow us to condense the WGS data into epidemiologically useful information. On this basis, we have reviewed current and new molecular typing methods for outbreak detection and epidemiological surveillance of bacterial pathogens in clinical practice, aiming to give an overview of their specific advantages and disadvantages.

The whole genome sequencing of Acinetobacter-calcoaceticus-baumannii complex strains involved in suspected outbreak in an Intensive Care Unit of a pediatric hospital

“…[41] Regarding the analysis of polymixins, all the strains analyzed had a phenotypic susceptibility that correlate with the absence of a specific genetic determinant except PmrB-P170L [26,28] in ST195 strain, that in a single report was indicated as responsible for a possible resistant mechanism. [16] In general, our genetic data confirmed the phenotypic susceptibility test objectively supporting the antibiotic therapies adopted by clinicians.…”

“…[15] Therefore, hospital acquired infection (HAI) investigations are often triggered by laboratory-based surveillance programs to identify an increase of Acinetobacter baumannii infections, a cluster of infected patients, or a new strain with an atypical susceptibility profile. [16] To trace HAI it is necessary to use the best high resolution typing approach that unequivocally identifies Acinetobacter species and their clonality, in order to search for the index case and to define the strains relatedness to avoid nosocomial cross transmission. [17][18][19] This study described the use of whole genome sequencing (WGS) by Ion Torrent Personal Genome Machine to analyze Acinetobacter-calcoaceticusbaumannii complex strains isolated in a possible outbreak occurring in a Intensive Care Unit of a pediatric hospital.…”

Recent and the Latest Developments in Rapid and Efficient Detection of Salmonella in Food and Water

“…WGS provides the greatest resolution for microbial subtyping to examine the bacterial evolution and to identify the source and transmission pathways of Salmonella. WGS is becoming popular as the costs continue to drop with the improvement of the next generation sequencing technique [91,92].…”

MLST revisited: the gene-by-gene approach to bacterial genomics

“…For these applications, 16S rRNA gene sequences provide an inordinate quantity of information in relation to their small size, and they were seminal in establishing that 'prokaryotes' are not a monophyletic group, but contain two of the three domains of life: Bacteria and Archaea 12 . Despite these successes, 16S rRNA sequences provide only limited resolution among closely related bacteria: many bacterial species exhibit identical 16S rRNA sequences among diverse isolates, and even species groups within genera are often poorly resolved, if at all.The need for higher-resolution characterization of isolates has led to the development of a wide range of strain-typing methods 16 , including multilocus sequence typing (MLST) 17 , which has become the method of choice for typing many organisms 18 . MLST was designed to accommodate the conflicting signals of vertical and horizontal genetic transfer (BOX 1) that are present in bacterial populations 19 by examining the genome at multiple 'housekeeping' gene loci 17,20 .…”

“…The need for higher-resolution characterization of isolates has led to the development of a wide range of strain-typing methods 16 , including multilocus sequence typing (MLST) 17 , which has become the method of choice for typing many organisms 18 . MLST was designed to accommodate the conflicting signals of vertical and horizontal genetic transfer (BOX 1) that are present in bacterial populations 19 by examining the genome at multiple 'housekeeping' gene loci 17,20 .…”