The interplay of Escherichia coli O157:H7 and commensal E. coli: the importance of strain-level identification

Microbiota and health

The microbiome and its relationship to human health and disease has become an important topic during the past decade. For example, the gut microbiota has been shown to play a role in diabetes, obesity, and even cardiovascular disease, leading to extensive research on the relationship between microorganisms and the host [1]. While many groundbreaking studies have focused on compositional shifts in higher-order rank such as the phyla level, recent works have highlighted the role specific species play in modulating host metabolism, such as Akkermansia muciniphila as a potential treatment for obesity in a mouse model [2]. There is less appreciation for the impact of strain level differences. This issue is well recognized by the probiotic research community, which appreciates that not all strains confer the same health benefits when consumed, as highlighted in one recent review using Lactobacillus ssp. as an example [3].

Diversity of Escherichia coli

Escherichia coli provides another example where species information is not necessarily informative about the health outcomes for the host. E. coli is a natural resident of the mammalian gastrointestinal tract, colonizing to approximately 10⁸ organisms per gram of feces in healthy adults [4], and much higher levels during inflammatory responses [5]. Over 100 million years ago, E. coli and Salmonella diverged and the former subsequently evolved into a genetically diverse collection of strains ranging from beneficial to highly pathogenic. E. coli can have anti-inflammatory properties, as highlighted by the probiotic strain Nissle marked as Mutaflor [6], or can be devastatingly virulent as seen during a 2011 fenugreek sprout-associated outbreak of O104:H4, an enteroaggregative Escherichia coli, affecting over 3,000 patients with more than 800 of those developing hemolytic uremic syndrome (HUS) [7]. This diversity is reflected in the flexible genome, with strains of E. coli carrying between 4.5 and 5.5 Mbp of DNA [8], and fewer than half of all genes encoded are conserved among all members of this species.

This impressive genetic diversity is also reflected at the serotype level. E. coli can be classified into different serogroups based upon the antibodies that bind to distinct lipopolysaccharides exposed on the surface (O-antigen), by distinct flagellar types expressed (H-type), and if present, the surface antigen K (K-type). Together, the O-, H-, and K-types are referred to as the serotype. E. coli O157:H7 in particular is a well-recognized serotype and is responsible for numerous foodborne outbreaks throughout the world. Strains of E. coli O157:H7 differ in their virulence capacity, and phylogenetic methods have been proposed to distinguish isolates with a tendency to cause severe disease from those rarely causing such symptoms [9]. Therefore, this pathogen is a model system for studying how both bacteria and host factors affect disease outcomes. Interestingly, many individuals are asymptomatic carriers, yet the mechanism behind this is not well understood. Although disease is multifactorial, most E. coli O157:H7 express two signature virulence traits, called the Locus of Enterocyte Effacement, which is responsible for attachment to the intestines and for immune modulation, and Shiga toxin, which inhibits protein synthesis and damages cells in the capillary endothelium and kidneys [10].

E. coli O157:H7 interacts with commensal bacteria

Although several studies describe how expression of E. coli O157:H7 virulence factors is altered by bacteria comprising the gut microbiota and, more recently, by fungi [11], the remainder of this review will focus on cross-talk between the pathogen and other E. coli. A seminal set of experiments by Gamage et al. showed that a co-culture of E. coli O157:H7 with a laboratory strain of E. coli designated C600 resulted in amplified Shiga toxin production over that seen when the pathogen was grown in pure culture [12]. An interesting biological characteristic of E. coli O157:H7 is that the genes for Shiga toxin are encoded within a bacteriophage (phage) integrated into the genome. These phages are capable of excising, undergoing replication, and lysing the host bacteria. Since the Shiga toxin genes are co-expressed with phage replication genes, toxin production is increased whenever the phage multiplies. This model described how these phages, when released by E. coli O157:H7, can infect and replicate within susceptible commensal E. coli, ultimately increasing toxin production [12]. Our own work expanded on this model, showing that three distinct strains of E. coli O157:H7 act differently when co-cultured with non-pathogenic E. coli C600 [13]. Both PA2 and EDL933, O157:H7 strains from a Pennsylvania outbreak and the first pathogen associated with a United States outbreak, respectively, produced more toxin when grown with C600. What was particularly interesting was that strain PA2 was the lowest toxin producer when grown as a pure culture, but the highest when co-cultured. However, a similar strain, Sakai from a Japan outbreak did not increase toxin production. This phenomenon was demonstrated in vivo, showing that 80% of germ-free mice receiving the combination of O157:H7 plus non-pathogenic C600 died or showed signs of disease, while all mice receiving just O157:H7 looked visibly healthy [13]. The mice receiving both organisms also showed greater signs of kidney damage, likely from increased toxin production. Therefore, this research potentially explains the virulence differences between strains and even between individuals infected with the same strain of E. coli O157:H7. It seems that disease outcome is driven by intrinsic properties of the pathogen as well as its interactions with members of the gut microbiota.

The microbiota can be very diverse and even strains of the same species can act differently. Weiss’ work addressed this, demonstrating that 10% of commensal E. coli isolates amplified toxin production by E. coli O157:H7 [14]. The phage-mediated mechanism may not explain all observations as other toxin-amplification mechanisms have been characterized, such as the production of a colicin with DNase activity [15]. These colicins can act similar to antibiotics, particularly DNA gyrase inhibitors [16], that cause DNA damage, followed by Stx phage excision and replication, ultimately leading to greater toxin production.

If commensal E. coli strains can impact toxin production by E. coli O157:H7, it may provide one explanation for how infections can range from being asymptomatic to the development of HUS within a population. Unfortunately, very little is known about the strain diversity of commensal E. coli carried within the intestines, even though this question was first asked at least seven decades ago by the report that a single individual carried at least 10 serologically distinguishable E. coli over a 14-month period [17]. Often one strain dominated and at times up to four distinct E. coli could be isolated per fecal sample. It was later suggested [18] that humans are colonized for long periods by E. coli termed ‘resident’, and by fleeting strains termed ‘transient’, indicating that strains humans carry are undergoing continuous turn-over. These early studies have been confirmed and extended by others [19], and more recently, Gordon et al. studied 69 individuals and found that the number of E. coli strains varied from one to eight, and that there might be site specificity along the gastrointestinal tract [20].

How can this knowledge be used to treat O157:H7 infections?

Understanding the role of the shifting communities in the microbiome can lead to better treatments for E. coli O157:H7 and for infections caused by other Shiga toxin-producing E. coli. As stated above, antibiotics are counter-indicated, leaving supportive therapy as the accepted treatment for patients. Soon, microbiota analysis may allow researchers and physicians to make predictions of the likely outcome of the disease and treat appropriately. As long DNA sequence read technologies such as PacBio and the Oxford Nanopore MinION become more accurate and high-throughput, they may be useful for providing needed strain-level information on complex communities. Additionally, understanding how multiple strains of E. coli co-exist or compete for the same resources will be important in devising strategies for displacing pathogenic strains with non-pathogenic competitors. In addition to the development of such practical applications, this research demonstrates how expression of a critical virulence factor of E. coli O157:H7 may be regulated by specific members of the gut microbiota. Understanding this diverse and dynamic microbiome, at the strain level, has become essential. Therefore, E. coli is a great model organism for studying temporal and spacial shifts in strain composition, and how this affects virulence and the outcome of disease.

Financial & competing interests disclosure

The authors have no relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending, or royalties.

Additional information

Notes on contributors

Hillary M. Figler

Edward G. Dudley