Implications of Foraging and Interspecies Interactions of Birds for Carriage of Escherichia coli Strains Resistant to Critically Important Antimicrobials

Abstract

Globally, gulls have been associated with carriage of high levels of Escherichia coli strains resistant to critically important antimicrobials (CIAs), a major concern, as these antimicrobials are the sole alternative or one among only a few alternatives available to treat severe life-threatening infections in humans. Previous studies of Australian silver gulls demonstrated high levels of resistance to CIAs, particularly fluoroquinolone and extended-spectrum cephalosporins, among E. coli strains (carriage at 24% and 22%, respectively). This study aimed to identify and characterize strains from four distinct bird species inhabiting a common coastal environment, determine the frequency of carriage of CIA-resistant E. coli strains, and examine if these resistant clones and their resistance-encoding mobile genetic elements (MGEs) could be transmitted between species. CIA-resistant E. coli was detected in silver gulls (53%), little penguins (11%), and feral pigeons (10%), but not in bridled terns. In total, 37 different sequence types (STs) were identified, including clinically significant human-associated lineages, such as ST131, ST95, ST648, ST69, ST540, ST93, ST450, and ST10. Five main mobile genetic elements associated with bla_CTX-M-positive E. coli strains isolated from three bird species were detected. Examination of clonal lineages and MGEs provided indirect evidence of transfer of resistance between bird species. The carriage of CIA-resistant E. coli by gulls and pigeons with proximity to humans, and in some instances food-producing animals, increases the likelihood of further bidirectional dissemination.IMPORTANCE It has been shown that 20% of Australian silver gulls carry drug-resistant Escherichia coli strains of anthropogenic origin associated with severe diseases, such as sepsis and urinary tract infections, in humans. To further characterize the dynamics of drug-resistant E. coli in wildlife populations, we investigated the carriage of critically important antimicrobial (CIA) drug-resistant E. coli in four bird species in a common environment. Our results indicated that gulls, pigeons, and penguins carried drug-resistant E. coli strains, and analysis of mobile genetic elements associated with resistance genes indicated interspecies resistance transfer. Terns, representing a bird species that forages on natural food sources at sea and distant from humans, did not test positive for drug-resistant E. coli This study demonstrates carriage of CIA-resistant bacteria in multiple bird species living in areas commonly inhabited by humans and provides further evidence for a leapfrog effect of resistance in wildlife, facilitated by feeding habits.

Keywords: Antimicrobial resistance; CTX-M; Escherichia coli; ST131; bird; gulls; mobile genetic elements; penguins; pigeons.

FIG 1

Frequency (percent) of carriage of resistant E. coli strains in fecal swabs from the four bird species. CIA, resistant to fluoroquinolones and/or extended-spectrum cephalosporins; FQ, fluoroquinolone resistant; ESC, extended-spectrum cephalosporin resistant. Resistance was measured on selective medium containing each drug and confirmed by antimicrobial susceptibility testing using disc diffusion.

FIG 2

Maximum-likelihood midpoint-rooted phylogenetic tree representing clonal diversity among 61 E. coli isolates from silver gulls, feral pigeons, and little penguins on Penguin Island, Western Australia. The colored circles represent different bird species the E. coli strain was isolated from. The scale bar corresponds to ∼2,650 SNPs. The asterisks mark clinically significant human-associated CIA-resistant E. coli lineages. Mobile genetic element designations (1 to 5) are as follows: ISEcp1-bla_CTX-M-15-ORF477Δ (2,971-bp TU), bla_CTX-M-15-Tn2, IS26-bla_CTX-M-27-IS903C, IS26-bla_CTX-M-27-IS903B, and ISEcp1-bla_CTX-M-14/ISEcp1-bla_CTX-M-14-IS903C.

FIG 3

Schematic diagram of commonly observed mobile genetic elements containing bla_CTX-M-15. (a) MGE 1. (b) MGE 2. The source animals, sequence types of origin, and numbers of isolates are indicated. IR-L, left inverted repeat; IR-R, right inverted repeat.

FIG 4

Schematic diagrams of both mobile genetic elements carrying bla_CTX-M-27, including source animals, sequence types, and total numbers of isolates. (a) MGE 3. (b) MGE 4.

FIG 5

Schematic diagram of mobile genetic element carrying bla_CTX-M-14, including sequence type information, numbers of isolates, and source animals. The region of the mobile genetic element shown in gray was present only in ST695 isolates.