Genetic diversity of Escherichia coli isolates of animal and environmental origins from an integrated poultry production chain Frédérique Pasquali a, *, Alex Lucchi a , Simonetta Braggio a , Davide Giovanardi b , Achille Franchini a , Maurizio Stonfer c , Gerardo Manfreda a a Department of Agricultural and Food Sciences, Alma Mater Studiorum—University of Bologna, Via del Florio 2, 40064 Ozzano dell’Emilia, Italy b TRE VALLI Laboratory, Viale Apollinare Veronesi 5, 37132 San Michele Extra (VR), Italy c Bayer Health Care, Animal Health Division, Viale Certosa 130, 20156 Milan, Italy A R T I C L E I N F O Article history: Received 26 January 2015 Received in revised form 8 May 2015 Accepted 11 May 2015 Keywords: Lincospectin Colibacillosis Broiler Breeder A B S T R A C T Escherichia coli is a normal inhabitant of the intestinal tract of chickens, but when an imbalance in the gut microbiota occurs, E. coli may overgrow and cause extraintestinal infections. The aims of this study were to assess the distribution and spread of E. coli isolates with specific phylogenetic groups and antimicrobial resistance characters among asymptomatic breeder flocks and their broiler progenies with early symptoms of colibacillosis. Broiler flocks were treated with lincospectin during the first week of life and sampled at one, 21 and 42 days. The majority of the 363 E. coli isolates belonged to phylogenetic group A (53.17%), followed by groups D (23.14%), B1 (19.28%) and B2 (4.41%). In broilers, group A was the most represented in birds of 21 and 42 days of age whereas group B1 was the most represented phylogroup in one-day old chicks. More than 90.00% of the isolates were resistant to one or more antimicrobials. Along the life-time of broilers, no differences were found on the occurrence of resistant isolates except for the number of E. coli with elevated MIC to spectinomycin, which increased significantly after the lincospectin treatment. According to XbaI-macrorestriction analysis, a high genetic diversity among E. coli isolates was underlined. Four antimicrobial resistant E. coli isolates of phylogroups A, B1 and D collected from breeders showed similar PFGE patterns to five isolates collected from the respective broiler progenies suggesting a potential spread of these isolates from breeders to broilers. ã2015 Elsevier B.V. All rights reserved. 1. Introduction Escherichia coli is a normal inhabitant of the intestinal tract of chickens and is harmless as long as its growth and colonization is inhibited by other commensal intestinal microbial populations. When an imbalance in the gut microbiota occurs, E. coli may overgrow and cause extraintestinal infections. Avian pathogenic E. coli strains (APEC) might cause colibacillosis often associated to extraintestinal diseases such as omphalitis, yolk sac infections, respiratory tract infections as well as pericarditis and aerosaccu- litis (Barnes et al., 2003). E. coli strains might be categorised into one of four phylogenetic groups A, B1, B2 and D. In Humans, these groups apparently differ from some characteristics including site of infection, pathogenicity and antimicrobial resistance. It is believed that most commensal strains belong to phylogenetic groups A or B1, although a comprehensive review examining published data on distribution of phylogenetic groups among commensal E. coli isolates from all over the world revealed large geographic and temporal variations with overall groups A and B2 more abundant than B1 or D in human feces (Duriez et al., 2001; Bailey et al., 2010). Among pathogenic strains, extraintestinal strains of phylogenetic group B2 showed to kill mice at the highest frequency and carried the highest number of virulence determinants (Picard et al., 1999). Moreover, the phylogenetic group B2 was the most abundant group within pathogenic E. coli implicated in urinary tract infections, neonatal meningitis and inflammatory bowel disease (Bingen et al., 1998; Petersen et al., 2009; Basu et al., 2013). In poultry, this association is still under debate. APEC E. coli strains belonging to serogroups O1, O2, O18 were mostly assigned to group B2, whereas APEC strains of O78 serogroup clustered within phylogenetic groups B1 and D (Moulin-Schouleur et al., 2007). However in another study, APEC E. coli strains clustered within group A, B1 and D and only in less than 20% of cases to B2 (Rodriguez-Siek et al., 2005; Johnson et al., 2008; Graziani et al., 2009). As far as commensal E. coli strains are concerned, only few * Corresponding author. Tel.: +39 051 209 7862; fax: +39 051 209 7852. E-mail address: frederique.pasquali@unibo.it (F. Pasquali). http://dx.doi.org/10.1016/j.vetmic.2015.05.007 0378-1135/ ã 2015 Elsevier B.V. All rights reserved. Veterinary Microbiology 178 (2015) 230–237 Contents lists available at ScienceDirect Veterinary Microbiology journa l homepage: www.e lsevier.com/loca te/vetmic