Evolutionary Biology by Pierre Pontarotti

Author:Pierre Pontarotti
Language: eng
Format: epub
Publisher: Springer International Publishing, Cham

13.5 High-throughput Investigation of Legionella Pneumophila Outbreaks

High-throughput sequencing can also be used to study organisms with higher level of polymorphism and strictly environmental, contrary to Mycobacterium tuberculosis . This is the case of L. pneumophila, causative agent of Legionellosis , and for which there is only one report of a possible person-to-person transmission (Correia et al. 2016) up to date. This opportunistic pathogen can produce pneumonia after inhalation of aerosols with enough bacterial load, with the highest burden in warm water-related environments. The first reported outbreak dates from 1976 when more than hundred legionnaires were infected in a convention in Philadelphia (Fraser et al. 1977). A legionellosis outbreak is defined as a cluster of more than three cases occurring at the same place and time, and the epidemiological investigation is crucial to find the environmental sources.

The investigation of legionellosis outbreaks has traditionally been conducted by using biochemical or molecular methods that allows comparing the clinical isolates with the strains obtained from the environment (Fields et al. 2002). Broad techniques such as serogrouping benefited from genetic methods that provided improved resolution in the so-called sequence-based typing (SBT) (Gaia et al. 2003, 2005), based on MLST approach (Urwin and Maiden 2003) but incorporating virulence genes in the scheme to increase the discrimination power among strains.

However, although SBT provided researchers with a tool that allowed the classification of strains into groups (sequence types, STs), the introduction of high-throughput sequencing techniques for microbial analysis and outbreak investigations in other species derived in its application to legionellosis outbreaks because of its increased discrimination power. The first published work was indeed a pilot study to test the potential of whole-genome sequencing (WGS) on the discrimination between isolates from an outbreak produced in the UK in 2003 and non-outbreak-related strains (Reuter et al. 2013b). From this point, a number of other outbreaks have been analyzed using WGS, as for example an outbreak of ST62 associated with a cooling tower in Quebec City in 2012 (Lévesque et al. 2014) or a massive outbreak that occurred in Edinburgh (UK 2012) related to multiple STs and including mixed infections (McAdam et al. 2014). WGS has also been used to investigate the persistent infection history of ST23 in a hotel in Spain in 2012 (Sánchez-Busó et al. 2016) and the eradication of L. pneumophila associated with a hospital in Australia that have been responsible of nosocomial cases (Bartley et al. 2016).

The environmental source of legionellosis cases has been historically difficult to trace, and because of the high social and economic impact of this kind of outbreaks on the affected populations, public health interventions are obliged to be rapid and accurate. WGS has shown further variability within many STs (Underwood et al. 2013a; Sánchez-Busó et al. 2014), showing evidence that at least some of them are not clonal. This observation complicates the study of legionellosis outbreaks and was the leading aim in the study by Sánchez-Busó et al. (2014). In this work, 69 isolates including strains associated with 13 different outbreaks and

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