A Longitudinal Study Simultaneously Exploring the Carriage of APEC Virulence Associated Genes and the Molecular Epidemiology of Faecal and Systemic E. coli in Commercial Broiler Chickens

Abstract

Colibacillosis is an economically important syndromic disease of poultry caused by extra-intestinal avian pathogenic Escherichia coli (APEC) but the pathotype remains poorly defined. Combinations of virulence-associated genes (VAGs) have aided APEC identification. The intestinal microbiota is a potential APEC reservoir. Broiler chickens are selectively bred for fast, uniform growth. Here we simultaneously investigate intestinal E. coli VAG carriage in apparently healthy birds and characterise systemic E. coli from diseased broiler chickens from the same flocks. Four flocks were sampled longitudinally from chick placement until slaughter. Phylogrouping, macro-restriction pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST) were performed on an isolate subset from one flock to investigate the population structure of faecal and systemic E. coli. Early in production, VAG carriage among chick intestinal E. coli populations was diverse (average Simpson's D value = 0.73); 24.05% of intestinal E. coli (n = 160) from 1 day old chicks were carrying ≥5 VAGs. Generalised Linear models demonstrated VAG prevalence in potential APEC populations declined with age; 1% of E. coli carrying ≥5 VAGs at slaughter and demonstrated high strain diversity. A variety of VAG profiles and high strain diversity were observed among systemic E. coli. Thirty three new MLST sequence types were identified among 50 isolates and a new sequence type representing 22.2% (ST-2999) of the systemic population was found, differing from the pre-defined pathogenic ST-117 at a single locus. For the first time, this study takes a longitudinal approach to unravelling the APEC paradigm. Our findings, supported by other studies, highlight the difficulty in defining the APEC pathotype. Here we report a high genetic diversity among systemic E. coli between and within diseased broilers, harbouring diverse VAG profiles rather than single and/or highly related pathogenic clones suggesting host susceptibility in broilers plays an important role in APEC pathogenesis.

Environmental adaptation and vertical dissemination of ESBL‐/pAmpC‐producing Escherichia coli in an integrated broiler production chain in the absence of an antibiotic treatment

“…Intestinal pathogenic E. coli (IPEC) are causing diarrhoea syndromes and seldom colonize healthy humans whereas extraintestinal pathogenic E. coli (ExPEC) often innocuously colonize the gut but have the ability to cause severe infections such as meningitis or blood stream infections (Vila et al ., 2016). Recent studies compared the occurrence of certain virulence‐associated genes (VAGs) in avian pathogenic E. coli (APEC), uropathogenic E. coli (UPEC) and commensal E. coli from humans and broiler chickens (Kemmett et al ., 2013; de Carli et al ., 2015; van Hoek et al ., 2016; Paixao et al ., 2016; Silveira et al ., 2016). It turned out that certain VAGs (e.g.…”

Studies on avian pathogenic Escherichia coli in commercial broiler chicken in South East Queensland

“…Kemmet et al (2013) reported a wide diversity and higher prevalence of APEC-associated VGs in faecal E. coli from one-day-old chicks compared to older chickens. There was a noticeable decrease in the number of APEC-associated VGs in faecal E. coli detected at slaughter (Kemmett et al, 2013). However, these variations in the prevalence among young chickens could be as a result of young birds having more diverse microbiota and negative selection in the gut for virulent strains.…”

“…A number of overseas studies identified vectors humans (farm worker and visitors), wild birds and rodents, source and type of treatment(s) applied to the drinking water and unfavourable housing conditions as major risk factors associated with avian colibacillosis (Kemmett et al, 2013;Nolan et al, 2013;Vandekerchove et al, 2004a). Low levels of APEC on overseas poultry farms, is associated with strict farm biosecurity and management practices, such as control of vectors by minimising bird interaction with other animals and hygienic cleaning protocols Vandekerchove et al, 2004a;Zanella et al, 2000).…”

“…Previous studies have also considered AFEC as potentially pathogenic because they may harbour large numbers of APECassociated VGs. This population of gut E. coli that contain APEC-associated VGs pose a risk for birds as they have the potential to cause avian colibacillosis Kemmett et al, 2013;McPeake et al, 2005). In the one Australian study, which screened 251 AFEC isolates cultured from healthy chickens for the presence of eight ExPEC-associated VGs (papAH, papC, afa/draBC, sfa/focDE, sfaS, aerJ, kpsMT II and focG), the authors reported that 10% of AFEC isolates carried two or more of the eight VGs and 68.1% harboured none of the VGs (Obeng et al, 2012).…”

“…However, no single or specific set of VGs have been systematically linked with APEC pathogenicity. It is very rare to find the same set of VGs in all APEC, in the same study and/or different studies (Kawamura-Sato et al, 2010;Kemmett et al, 2013;Paixao et al, 2016;Rodriguez-Siek et al, 2005a;Zhao et al, 2005). Nevertheless, APEC harbour several VGs that enable the bacteria to invade, colonise, evade the immune system and cause avian colibacillosis (Guastalli et al, 2013;Horn et al, 2012;Kemmett et al, 2014;Pires-dos-Santos et al, 2013).…”