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

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.

[1]  Brian H. Raphael,et al.  Genomic heterogeneity differentiates clinical and environmental subgroups of Legionella pneumophila sequence type 1 , 2018, PloS one.

[2]  Jeffrey L. Parks,et al.  Evaluating Water Lead Levels During the Flint Water Crisis. , 2018, Environmental science & technology.

[3]  Brian H. Raphael,et al.  Comparative genome analysis reveals a complex population structure of Legionella pneumophila subspecies. , 2018, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

[4]  N. Love,et al.  Prevalence of Infection-Competent Serogroup 6 Legionella pneumophila within Premise Plumbing in Southeast Michigan , 2018, mBio.

[5]  N. Love,et al.  Assessment of the Legionnaires’ disease outbreak in Flint, Michigan , 2018, Proceedings of the National Academy of Sciences.

[6]  A. Pruden,et al.  Prevention of Legionnaires’ Disease in the 21st Century by Advancing Science and Public Health Practice , 2017, Emerging Infectious Diseases.

[7]  Jeffrey L. Parks,et al.  Distribution System Operational Deficiencies Coincide with Reported Legionnaires' Disease Clusters in Flint, Michigan. , 2017, Environmental science & technology.

[8]  J Moran-Gilad,et al.  A bioinformatics tool for ensuring the backwards compatibility of Legionella pneumophila typing in the genomic era. , 2017, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.

[9]  Amy Pruden,et al.  Legionella DNA Markers in Tap Water Coincident with a Spike in Legionnaires’ Disease in Flint, MI , 2016 .

[10]  M. L. Ricci,et al.  A multicenter study of viable PCR using propidium monoazide to detect Legionella in water samples. , 2016, Diagnostic microbiology and infectious disease.

[11]  Brian H. Raphael,et al.  Genomic Resolution of Outbreak-Associated Legionella pneumophila Serogroup 1 Isolates from New York State , 2016, Applied and Environmental Microbiology.

[12]  R. Lan,et al.  Population structure and minimum core genome typing of Legionella pneumophila , 2016, Scientific Reports.

[13]  Amy Pruden,et al.  Water heater temperature set point and water use patterns influence Legionella pneumophila and associated microorganisms at the tap , 2015, Microbiome.

[14]  A. Thomas,et al.  Active Bacterial Core Surveillance for Legionellosis - United States, 2011-2013. , 2015, MMWR. Morbidity and mortality weekly report.

[15]  Tom Slezak,et al.  kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference genome , 2015, Bioinform..

[16]  Alimuddin Zumla,et al.  Epidemiology and clinical management of Legionnaires' disease. , 2014, The Lancet. Infectious diseases.

[17]  Björn Usadel,et al.  Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..

[18]  S. Vesper,et al.  Widespread molecular detection of Legionella pneumophila Serogroup 1 in cold water taps across the United States. , 2014, Environmental science & technology.

[19]  K. Konstantinidis,et al.  Bypassing Cultivation To Identify Bacterial Species: Culture-independent genomic approaches identify credibly distinct clusters, avoid cultivation bias, and provide true insights into microbial species , 2014 .

[20]  Holly M. Bik,et al.  PhyloSift: phylogenetic analysis of genomes and metagenomes , 2014, PeerJ.

[21]  Sergey I. Nikolenko,et al.  SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing , 2012, J. Comput. Biol..

[22]  L. Hampton,et al.  Legionellosis—United States, 2000–2009 , 2012, American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons.

[23]  F. Vandenesch,et al.  Legionella pneumophila Sequence Type 1/Paris Pulsotype Subtyping by Spoligotyping , 2011, Journal of Clinical Microbiology.

[24]  C. Buchrieser,et al.  Specific Real-Time PCR for Simultaneous Detection and Identification of Legionella pneumophila Serogroup 1 in Water and Clinical Samples , 2010, Applied and Environmental Microbiology.

[25]  Paramvir S. Dehal,et al.  FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments , 2010, PloS one.

[26]  K. Bernard,et al.  Legionella pneumophila monoclonal antibody subgroups and DNA sequence types isolated in Canada between 1981 and 2009: Laboratory Component of National Surveillance , 2010, European Journal of Clinical Microbiology & Infectious Diseases.

[27]  Rick L. Stevens,et al.  The RAST Server: Rapid Annotations using Subsystems Technology , 2008, BMC Genomics.

[28]  J. Helbig,et al.  Occurrence and distribution of sequence types among Legionella pneumophila strains isolated from patients in Germany: common features and differences to other regions of the world , 2007, European Journal of Clinical Microbiology & Infectious Diseases.

[29]  P. Vandamme,et al.  DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. , 2007, International journal of systematic and evolutionary microbiology.

[30]  J. Etienne,et al.  Consensus Sequence-Based Scheme for Epidemiological Typing of Clinical and Environmental Isolates of Legionella pneumophila , 2005, Journal of Clinical Microbiology.

[31]  J. Kusnetsov,et al.  Persistent Legionella pneumophila colonization of a hospital water supply: efficacy of control methods and a molecular epidemiological analysis , 2005, APMIS : acta pathologica, microbiologica, et immunologica Scandinavica.

[32]  V. Yu,et al.  Hospital-acquired legionellosis: solutions for a preventable infection. , 2002, The Lancet. Infectious diseases.

[33]  C. Helms,et al.  Persistence of Legionella Pneumophila in a Hospital's Water System: A 13-Year Survey , 1999, Infection Control & Hospital Epidemiology.

[34]  Lisa Scheinkopf.  The Full Analysis , 1999 .

[35]  B. Marston,et al.  Surveillance for Legionnaires' disease. Risk factors for morbidity and mortality. , 1994, Archives of internal medicine.

[36]  R. Wadowsky,et al.  Effect of temperature, pH, and oxygen level on the multiplication of naturally occurring Legionella pneumophila in potable water , 1985, Applied and environmental microbiology.