NEW MICROBIOLOGICA, 36, 385-394, 2013 Phylogenetic analysis of multidrug-resistant Escherichia coli clones isolated from humans and poultry Massimo Ciccozzi 1 , Maria Giufrè 1 , Marisa Accogli 1 , Alessandra Lo Presti 1 , Caterina Graziani 2 , Eleonora Cella 1 , Marina Cerquetti 1 1 Department of Infectious, Parasitic and Immune-mediated Diseases; 2 Department of Veterinary Public Health and Food Safety, Istituto Superiore di Sanità, Rome, Italy INTRODUCTION Escherichia coli extraintestinal infections (uri- nary tract infections and bloodstream infec- tions) represent a significant public health bur- den worldwide (Johnson and Russo, 2002; Russo and Johnson, 2003). Since the 2000s, an- timicrobial resistance among E. coli isolates has increased contributing to the complexity in management of such infections (Karlowsky et al., 2006; Pallett and Hand, 2010). Prevention and control of the spread of E. coli-causing in- Corresponding author Dr. Marina Cerquetti Department of Infectious Parasitic and Immune-mediated Diseases Istituto Superiore di Sanità Viale Regina Elena, 299 - 00161 Roma, Italy E-mail: marina.cerquetti@iss.it fections in humans requires an understanding of the population genetics of this pathogen. In the past, multilocus enzyme electrophoresis (MLEE) demonstrated that the E. coli popula- tion is largely clonal and strains fall into four major phylogenetic groups (A, B1, B2 and D) (Selander et al., 1987; Goullet and Picard, 1989; Clermont et al., 2000). At present, in the genomic era, multilocus sequence typing (MLST) has been increasingly used to investigate E. coli pop- ulation genetics (Tartof et al., 2005; Wirth et al., 2006; Lau et al., 2008; Köhler and Dobrindt, 2011). However, the majority of the studies in the literature used MLST data to identify allel- ic profiles that define distinct sequence types (STs), but no in-depth phylogenetic reconstruc- tion was carried out from the sequences. Moreover, a few investigations only compared the phylogeny of E. coli isolates from different hosts (Gordon and Cowling, 2003; Escobar- Chicken products represent a source for multidrug-resistant Escherichia coli causing extraintestinal infections (ExPEC) in humans. We applied phylogenetic analysis to a collection of E. coli strains from both hosts (poultry/humans) to improve our understanding of the origin and spread of ExPEC in humans. The dataset consisted of 58 sequences among 172 E. coli strains from human extraintestinal infections and avian species. Human phylogenetic tree analysis showed a major clade, within which ST clones belonging to groups A and B1 were largely intermixed, and two clusters, each exclusively including B2 or D clones. The avian tree exhibited greater heterogeneity between and within clades/clusters. In the Bayesian tree, con- sisting of sequences from both human and avian E. coli, the B2 and D human ST clones were clustered together separate from the avian strains, whereas B1 and A ST clones (frequently associated with multidrug resistance) were intermixed with avian strains. This study suggests that a subgroup of E. coli clones, A and B1, associated with multidrug resistance, is po- tentially exchangeable between poultry and humans. Such a subgroup may be of public health concern. On the contrary, E. coli clones included in B2 and D appeared clearly separate between human and avian sources, suggesting a minor zoonot- ic potential of these phylotypes. KEY WORDS: Escherichia coli, Phylogeny, Zoonosis, Multidrug resistance. SUMMARY Received May 31, 2013 Accepted August 11, 2013