A bioinformatics tool for ensuring the backwards compatibility of Legionella pneumophila typing in the genomic era

Gordon, Michal; Yakunin, Eugenia; Valinsky, Lea; Chalifa‐Caspi, Vered; Moran-Gilad, Jacob

doi:10.1016/j.cmi.2017.01.002

Cited by 21 publications

(24 citation statements)

References 14 publications

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“…1.2.10) (17). In addition, seven genetic loci ( flaA - pilE - asd - mip - mompS - proA - neuA ) associated with a sequence-based typing (SBT) scheme were extracted from genomic sequence data (18). The allelic profile of these loci determines a sequence type (ST).…”

Section: Methodsmentioning

confidence: 99%

Culture of Clinical Specimens Reveals Extensive Diversity of Legionella pneumophila Strains in Arizona

Raphael

Huynh

Brown

et al. 2019

mSphere

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Between 2000 and 2017, a total of 236 Legionella species isolates from Arizona were submitted to the CDC for reference testing. Most of these isolates were recovered from bronchoalveolar lavage specimens. Although the incidence of legionellosis in Arizona is less than the overall U.S. incidence, Arizona submits the largest number of isolates to the CDC for testing compared to those from other states. In addition to a higher proportion of culture confirmation of legionellosis cases in Arizona than in other states, all Legionellapneumophila isolates are forwarded to the CDC for confirmatory testing. Compared to that from other states, a higher proportion of isolates from Arizona were identified as belonging to L. pneumophila serogroups 6 (28.2%) and 8 (8.9%). Genome sequencing was conducted on 113 L. pneumophila clinical isolates not known to be associated with outbreaks in order to understand the genomic diversity of strains causing legionellosis in Arizona. Whole-genome multilocus sequence typing (wgMLST) revealed 17 clusters of isolates sharing at least 99% identical allele content. Only two of these clusters contained isolates from more than one individual with exposure at the same facility. Additionally, wgMLST analysis revealed a group of 31 isolates predominantly belonging to serogroup 6 and containing isolates from three separate clusters. Single nucleotide polymorphism (SNP) and pangenome analysis were used to further resolve genome sequences belonging to a subset of isolates. This study demonstrates that culture of clinical specimens for Legionella spp. reveals a highly diverse population of strains causing legionellosis in Arizona which could be underappreciated using other diagnostic approaches. IMPORTANCE Culture of clinical specimens from patients with Legionnaires’ disease is rarely performed, restricting our understanding of the diversity and ecology of Legionella. Culture of Legionella from patient specimens in Arizona revealed a greater proportion of non-serogroup 1 Legionellapneumophila isolates than in other U.S. isolates examined. Disease caused by such isolates may go undetected using other diagnostic methods. Moreover, genome sequence analysis revealed that these isolates were genetically diverse, and understanding these populations may help in future environmental source attribution studies.

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Section: Methodsmentioning

confidence: 99%

Culture of Clinical Specimens Reveals Extensive Diversity of Legionella pneumophila Strains in Arizona

Raphael

Huynh

Brown

et al. 2019

mSphere

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“…We also included 9 L. pneumophila reference strains (Appendix 1 Table 2). We performed sequence-based typing targeting the flaA , pilE , asd , mip , mompS , proA , and neuA alleles ( 18 ) by using the mompS tool ( 19 ).…”

Section: Methodsmentioning

confidence: 99%

Comparison of Whole-Genome Sequences ofLegionella pneumophilain Tap Water and in Clinical Strains, Flint, Michigan, USA, 2016

Garner¹,

Brown²,

Schwake³

et al. 2019

Emerg. Infect. Dis.

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During the water crisis in Flint, Michigan, USA (2014–2015), 2 outbreaks of Legionnaires’ disease occurred in Genesee County, Michigan. We compared whole-genome sequences of 10 clinical Legionella pneumophila isolates submitted to a laboratory in Genesee County during the second outbreak with 103 water isolates collected the following year. We documented a genetically diverse range of L. pneumophila strains across clinical and water isolates. Isolates belonging to 1 clade (3 clinical isolates, 3 water isolates from a Flint hospital, 1 water isolate from a Flint residence, and the reference Paris strain) had a high degree of similarity (2–1,062 single-nucleotide polymorphisms), all L. pneumophila sequence type 1, serogroup 1. Serogroup 6 isolates belonging to sequence type 2518 were widespread in Flint hospital water samples but bore no resemblance to available clinical isolates. L. pneumophila strains in Flint tap water after the outbreaks were diverse and similar to some disease-causing strains.

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“…Contrary to that, an example for backwards compatibility challenges is the difficulty in calling the 7-loci sequence-based type in L. pneumophila from WGS data. The creation of an in silico solution for this required much bioinformatics development work but was considered mandatory to facilitate the introduction of WGS for the global network of Legionnaires' disease surveillance [23].…”

Section: Maintaining Backwards Compatibility With Wgsmentioning

confidence: 99%

Practical issues in implementing whole-genome-sequencing in routine diagnostic microbiology

Rossen

Friedrich

Moran-Gilad

2018

Clinical Microbiology and Infection

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211

161

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Background: Next generation sequencing (NGS) is increasingly being used in clinical microbiology. Like every new technology adopted in microbiology, the integration of NGS into clinical and routine workflows must be carefully managed. Aim: To review the practical aspects of implementing bacterial whole genome sequencing (WGS) in routine diagnostic laboratories. Sources: Review of the literature and expert opinion. Content: In this review, we discuss when and how to integrate whole genome sequencing (WGS) in the routine workflow of the clinical laboratory. In addition, as the microbiology laboratories have to adhere to various national and international regulations and criteria for their accreditation, we deliberate on quality control issues for using WGS in microbiology, including the importance of proficiency testing. Furthermore, the current and future place of this technology in the diagnostic hierarchy of microbiology is described as well as the necessity of maintaining backwards compatibility with already established methods. Finally, we speculate on the question of whether WGS can entirely replace routine microbiology in the future and the tension between the fact that most sequencers are designed to process multiple samples in parallel whereas for optimal diagnosis a one-by-one processing of the samples is preferred. Special reference is made to the cost and turnaround time of WGS in diagnostic laboratories. Implications: Further development is required to improve the workflow for WGS, in particular to shorten the turnaround time, reduce costs, and streamline downstream data analyses. Only when these processes reach maturity will reliance on WGS for routine patient management and infection control management become feasible, enabling the transformation of clinical microbiology into a genome-based and personalized diagnostic field.

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A bioinformatics tool for ensuring the backwards compatibility of Legionella pneumophila typing in the genomic era

Abstract: As WGS becomes more accessible, technical difficulties in routine clinical and surveillance work will arise. The case of mompS in L. pneumophila serves as an example for such limitations that necessitate the development of novel computational solutions that meet end-user demands.

Cited by 21 publications

References 14 publications

Culture of Clinical Specimens Reveals Extensive Diversity of Legionella pneumophila Strains in Arizona

Culture of Clinical Specimens Reveals Extensive Diversity of Legionella pneumophila Strains in Arizona

Comparison of Whole-Genome Sequences ofLegionella pneumophilain Tap Water and in Clinical Strains, Flint, Michigan, USA, 2016

Practical issues in implementing whole-genome-sequencing in routine diagnostic microbiology

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