Large-scale genomic sequencing of extraintestinal pathogenic Escherichia coli strains

Large-scale bacterial genome sequencing efforts to date have provided limited information on the most prevalent category of disease: sporadically acquired infections caused by common pathogenic bacteria. Here, we performed whole-genome sequencing and de novo assembly of 312 blood- or urine-derived isolates of extraintestinal pathogenic (ExPEC) Escherichia coli, a common agent of sepsis and community-acquired urinary tract infections, obtained during the course of routine clinical care at a single institution. We find that ExPEC E. coli are highly genomically heterogeneous, consistent with pan-genome analyses encompassing the larger species. Investigation of differential virulence factor content and antibiotic resistance phenotypes reveals markedly different profiles among lineages and among strains infecting different body sites. We use high-resolution molecular epidemiology to explore the dynamics of infections at the level of individual patients, including identification of possible person-to-person transmission. Notably, a limited number of discrete lineages caused the majority of bloodstream infections, including one subclone (ST131-H30) responsible for 28% of bacteremic E. coli infections over a 3-yr period. We additionally use a microbial genome-wide-association study (GWAS) approach to identify individual genes responsible for antibiotic resistance, successfully recovering known genes but notably not identifying any novel factors. We anticipate that in the near future, whole-genome sequencing of microorganisms associated with clinical disease will become routine. Our study reveals what kind of information can be obtained from sequencing clinical isolates on a large scale, even well-characterized organisms such as E. coli, and provides insight into how this information might be utilized in a healthcare setting.With the advent of high-throughput DNA sequencing technologies, it is becoming increasingly tractable to generate whole-genome sequence data from large numbers of clinically relevant bacterial isolates. However, most comparative genome sequencing efforts to date have focused on the biology and molecular epidemiology of organisms involved in disease outbreaks (Chin et al. 2011; Lieberman et al. 2011; Koser et al. 2012; Snitkin et al. 2012; Sanjar et al. 2014). Although illuminating, these studies have shed little light on the agents of bacterial disease that infect an overwhelming majority of patients: commonplace pathogens causing sporadically acquired infections. Outbreaks represent the transmission of a single bacterial clone over a short period of time (Kennedy et al. 2010), providing a necessarily biased sampling that does not encompass the general properties of disease-causing organisms within a larger species. Relatedly, genomic studies of most bacteria are consistent with the distributed genome hypothesis, which proposes that the genetic content of a species is much larger than that of any single strain (Tettelin et al. 2005), necessitating sequencing of large numbers of unrelated clones in order to accurately catalog genetic variation (Rasko et al. 2008).Escherichia coli is among the commonest clinical pathogens and is capable of causing a spectrum of disease both within the intestinal tract (intestinal pathogenic strains) and outside of it (extraintestinal pathogenic E. coli, or ExPEC). The most potentially destructive of these illnesses is bacterial invasion of the bloodstream: E. coli is the most common Gram-negative agent of sepsis, causing ∼30% of all bacteremias and representing the tenth most common cause of death in industrialized nations (Martin et al. 2003; Jaureguy et al. 2008). Far more prevalent are E. coli urinary tract infections, which encompass ∼95% of all community-acquired cases (Lau et al. 2008; Manges et al. 2008). E. coli infections of either type incur significant morbidity and healthcare costs (Sannes et al. 2004; Lau et al. 2008; Ron 2010; Telli et al. 2010); regardless, only a handful of strains causing these diseases have been sequenced, and knowledge of ExPEC E. coli remains incomplete.Here we performed large-scale whole-genome sequencing and analysis of clinical isolates of extraintestinal pathogenic E. coli, obtained from routine diagnostic culture of peripheral blood or urine from patients within a single hospital system. These data enable a robust pan-genome analysis of ExPEC E. coli, high-resolution molecular epidemiological analysis, and genome-wide association studies for identifying antibiotic resistance genes.