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

Emily Garner; Connor L. Brown; David Otto Schwake; William J. Rhoads; Gustavo Arango-Argoty; Liqing Zhang; Guillaume Jospin; David A. Coil; Jonathan A. Eisen; Marc A. Edwards; Amy Pruden


Emerging Infectious Diseases. 2019;25(11):2013-2020. 

In This Article

Abstract and Introduction


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.


Legionnaires' disease is a severe form of pneumonia caused by inhalation of virulent species of aerosolized Legionella bacteria. In January 2016, the Michigan Department of Health and Human Services (MDHHS) and the Genesee County Health Department publicly announced 2 Legionnaires' disease outbreaks in Genesee County, Michigan, USA.[1,2] The first outbreak occurred from June 2014 through March 2015 and the second from May 2015 through October 2015; a total of 90 cases and 12 deaths were documented.[1–3] From April 2014 through October 2015, the city of Flint, in Genesee County, switched its drinking water source from Detroit Water and Sewer Department (DWSD), which used corrosion control, to the corrosive Flint River, without implementing federally mandated corrosion control; this new water source led to elevated lead in tap water over a prolonged period, now called the Flint water crisis.[4] This disruption in water quality likely also stimulated the growth of L. pneumophila, the species most frequently identified as the causative agent of Legionnaires' disease,[5,6] in Flint's distribution and plumbing systems.[7]

Our prior work associated the Legionnaires' disease outbreaks with factors known to be conducive to Legionella growth: elevated iron (a consequence of corroded iron water mains), reduced free chlorine disinfectant residuals, and elevated water temperatures.[7,8] Later, Zahran and colleagues reported that the odds of Flint residents being referred for Legionnaires' disease treatment while the Flint River was the source of tap water increased 6.3-fold and confirmed our report of associations with low chlorine residuals,[9] but the odds analysis, which was based on the use of referral date rather than symptom onset date, excluded many healthcare-associated cases.[10] Furthermore, during the second outbreak, Legionella spp. and L. pneumophila genes were found to be higher in the tap water of large buildings in Flint than in other water systems in US areas not experiencing outbreaks.[8] Conversely, levels of the mip gene, which is specific to L. pneumophila, were largely below detection in Flint single-family residences, at least during the later stages of the water crisis when they were measured (2015–2016).[8] Large buildings with extensive plumbing networks, such as hospitals, are generally more susceptible to Legionella growth than are simpler plumbing systems characteristic of single-family homes;[11] however, residences are also of interest for Legionella growth, given concerns about the high rate of sporadic Legionnaires' disease[12] and potential for exposure in the home.

Our study objective was to use next-generation DNA sequencing to compare L. pneumophila isolated from Flint tap water after the second Legionnaires' disease outbreak with tap water isolates from neighboring drinking water systems outside of Flint that were never served by Flint River water and clinical strains received during the second outbreak at a regional reference laboratory in Genesee County. Within Flint, Legionella isolates were obtained from the tap water of a hospital, a large public building, and single-family residences several months after the water source was switched back to DWSD. In addition to serogroup testing, we used whole-genome sequencing to compare isolates in terms of sequence type (ST), average nucleotide identity, and single-nucleotide polymorphisms (SNPs).