What can the producer do about E. coli control on their farms?
By Timothy Johnson, University of Minnesota
Escherichia coli is, arguably, the best studied bacteria in the history of microbiology. It is remarkable that a bacterial species - which is found in the normal flora of nearly every warm-blooded animal – has evolved to also have a notorious cohort of very bad players. Although it depends on how you differentiate these bad players, there are around a dozen pathotypes, or groups of E. coli capable of causing distinct diseases in animals. One of those dozen pathotypes has been coined avian pathogenic E. coli, or APEC. APEC are one of the few pathotypes which is specific for one animal species, and it is the only E. coli pathotype that causes severe disease in birds. This disease is labeled colibacillosis (which actually includes a number of different disease syndromes) and has been recognized as a major bacterial disease of commercial poultry for well over 50 years (Nolan, 2020).
Colibacillosis is generally recognized as a secondary bacterial disease that follows primary insult to the bird through another pathogen or other stress. However, many factors contribute to whether or not clinical disease will actually occur. It is also important to remember that subclinical infection, in certain scenarios, will have a negative impact on production parameters. Clinical disease manifestation is dependent on overall level of stress (including environmental, viral, or vaccine stress), the load of E. coli in the barn and within the bird, and the specific E. coli strains that are present. Strains are particularly important. In the gut, non-APEC commensals dominate and, under normal conditions, pose little threat to the bird to cause disease (Figure). In the trachea, APEC strains are better suited to colonize, and higher numbers of virulent APEC equate to more opportunities to cause disease. This then is coupled with the level of bird stress. Under low stress, non-APEC are unable to cause disease and there will be relatively low flock mortality, primarily only due to APEC of high virulence. However, as stress increases, so too does disease occurrence, and some non-APEC now become opportunists. Clearly, higher numbers of E. coli, and higher proportions of APEC strains, will increase the likelihood of clinical disease and mortality.
While we have discussed the concept of APEC, we have not yet defined APEC. Historically, APEC have been defined by their possession of a key plasmid. A plasmid is a mobile genetic element capable of spreading between closely related bacteria, including between strains of E. coli. APEC have long been known to possess a plasmid historically referred to as the “ColV plasmid” or the “APEC plasmid.” This plasmid carries a large number of genes which have been shown to provide APEC with an enhanced ability to colonize the bird, survive the extraintestinal environment, and ultimately cause disease. Approximately two decades years ago, it was found that clinical E. coli harbored this plasmid more than 80% of the time, and fecal E. coli from healthy birds harbored this plasmid less than 20% of the time (Johnson, et al., 2006). Therefore, this plasmid has been used for years as a defining marker of APEC strains (Johnson, et al., 2008).
However, recent work has shown that the populations of avian gut commensal E. coli may be changing. Multiple reports in recent years have shown that high proportions of gut commensal E. coli harbor the APEC plasmid. This brought questions about the utility of the APEC plasmid markers to differentiate between APEC and non-APEC. We addressed this question in a recent large study examining thousands of clinical and non-clinical E. coli from commercial poultry production (Johnson, et al., 2022). This study concluded:
A large proportion of commensal gut E. coli harbor the APEC plasmid
However, the isolates of these gut E. coli were distinct from clinical isolates
The majority of clinical isolates belonged to five key strain types
In a virulence model, clinical strain types were virulent and commensal strain types were not virulent, irrespective of whether or not they carried the APEC plasmid
The dominant clinical strain types (also referred to as sequence types, or STs) that were virulent included ST23, ST117, ST131, ST355, and ST428. Some of these STs are well known APEC that have been previously characterized by their serogroups, which is a classical typing scheme based upon cell surface antigens. For example, ST23 and ST117 include strains belonging to the O78 serogroup, and ST355 includes strains belonging to the O2 serogroup. Other STs appear to be emergent problems for the poultry industry. For example, ST131 (O25) strains have only recently surfaced in poultry production as a major cause of colibacillosis. From our work, it appears that the APEC status should not be reserved for any strain harboring the APEC plasmid, but only for specific combinations of certain strain types carrying the APEC plasmid. A refined tool was developed that helps producers to quickly identify these high-risk APEC, relying on the combination of strain-specific traits and APEC plasmid possession.
The idea that successful APEC have evolved through acquiring the APEC plasmid within the ideal chromosomal (strain) background means that other mix-and-match combinations will surely arise in the future. In fact, there are likely other combinations existing right now which are competing for their success. This emphasizes the importance of continued surveillance of clinical E. coli causing disease in poultry flocks. The definition of APEC still needs work; for example, what are the strain-specific gene sets that combine with the APEC plasmid presence to create a successful and dominant clone? This is a currently unanswered question. Further efforts to better understand avian E. coli ecology and pathogenesis may eventually lead us to universal markers which can better identify high-risk APEC clones.
What can the producer do about E. coli control on their farms? The evolving nature of APEC suggests that a single, universal vaccine that will protect against all high-risk APEC does not currently exist. Commercial vaccination programs absolutely have their place, and can be very effective at providing some level of protection against colibacillosis. However, such efforts cannot be the only approach. There is definitely a place for autogenous vaccination, when it is clear that there is a single, problematic strain on the farm that is likely not protected against using commercial vaccines. Other products have the potential to reduce overall E. coli load, including probiotics, postbiotics, and phytogenics. Some of these same products have the potential to modulate the immune system of the bird, which would indirectly help to maintain low stress levels in the bird. Combinations of these various products likely holds the key to effective E. coli control, and we need more research to identify synergistic combinations with optimal efficacy.
References:
Johnson, T. J., E. A. Miller, C. Flores-Figueroa, J. Munoz-Aguayo, C. Cardona, K. Fransen, M. Lighty, E. Gonder, J. Nezworski, A. Haag, M. Behl, M. Kromm, B. Wileman, M. Studniski, and R. S. Singer. 2022. Refining the definition of the avian pathogenic Escherichia coli (APEC) pathotype through inclusion of high-risk clonal groups. Poult Sci 101:102009. doi 10.1016/j.psj.2022.102009
Johnson, T. J., K. E. Siek, S. J. Johnson, and L. K. Nolan. 2006. DNA sequence of a ColV plasmid and prevalence of selected plasmid-encoded virulence genes among avian Escherichia coli strains. J Bacteriol 188:745-758. doi 10.1128/JB.188.2.745-758.2006
Johnson, T. J., Y. Wannemuehler, C. Doetkott, S. J. Johnson, S. C. Rosenberger, and L. K. Nolan. 2008. Identification of minimal predictors of avian pathogenic Escherichia coli virulence for use as a rapid diagnostic tool. J Clin Microbiol 46:3987-3996. doi 10.1128/JCM.00816-08
Nolan, L., Vaillancourt, JP, Barbieri, NL, Logue, CM. 2020. Colibacillosis in Diseases of Poultry. D. E. Swayne ed. Wiley, Ames, IA, USA.
Dr. Tim Johnson is a professor of poultry science in the University of Minnesota's College of Veterinary Medicine.
