The use of whole-genome phylogenetic analysis has revolutionized our understanding of the evolution and spread of many important bacterial pathogens due to the high resolution view it provides. However, the majority of such analyses do not consider the potential role of accessory genes when inferring evolutionary trajectories. Moreover, the recently discovered importance of the switching of gene regulatory elements suggests that an exhaustive analysis, combining information from core and accessory genes with regulatory elements could provide unparalleled detail of the evolution of a bacterial population. Here we demonstrate this principle by applying it to a worldwide multi-host sample of the important pathogenic E. coli lineage ST131. Our approach reveals the existence of multiple circulating subtypes of the major drug–resistant clade of ST131 and provides the first ever population level evidence of core genome substitutions in gene regulatory regions associated with the acquisition and maintenance of different accessory genome elements.
Although Black-headed Gulls do not naturally come into contact with antibiotics, these birds can be infected with resistant E. coli and potentially serve as their reservoirs, vectors and bioindicators in the environment.
Individual cloacal swabs of mallards (Anas) to isolate fluoroquinolone-resistant E. coli. PCR was used to detect specific antibiotic resistance genes. We found 9 E. coli isolates producing ESBL with bla genes: bla CTX-M-1 (6 isolates), bla CTX-M-9 plus bla TEM-1b (1 isolate), bla CTX-M-15 plus bla OXA-1 (1 isolate), and bla SHV-12 (1 isolate). In the isolate with bla CTX-M-15 , the gene aac(6)-Ib-cr was also detected. The bla genes were harbored by transferable plasmids of the IncN and IncI1 groups. Nine quinolone-resistant E. coli isolates with qnrS genes were found and characterized. There is considerable concern about antibiotic resistance in bacteria from humans and farm animals, but the spread of resistance into wider ecosystems has received much less attention (48). Usually, isolates of the common intestinal bacterium Escherichia coli are examined to detect antibiotic resistance in populations of wild animals. Wild birds are colonized with various strains of E. coli, including strains such as E. coli O157 that are pathogenic for humans (83). Fecal strains of E. coli resistant to antibiotics have been found at various prevalences in wild bird populations. In particular, bird populations sympatric to areas inhabited by people and areas with a high density of livestock were colonized with antibiotic-resistant E. coli strains possibly selected by the antibiotic practice in humans and domestic animals. Antibiotic-resistant E. coli isolates have been found in corvids (Corvus corone, C. frugilegus, C. macrorhynchos, Pica pica, and Pyrrhocorax pyrrhocorax) (3,46,48,53,74), house sparrows (Passer domesticus) (22, 61), house martins (Delichon urbica) (73), feral pigeons (Columba livia forma domestica) (68
ObjectivesThe objective of this study was to investigate the silver gull as an indicator of environmental contamination by salmonellae and carbapenemase-producing Enterobacteriaceae (CPE) in south-east Australia.MethodsA total of 504 cloacal samples were collected from gull chicks at three nesting colonies in New South Wales, Australia [White Bay (n = 144), Five Islands (n = 200) and Montague Island (n = 160)] and were examined for salmonellae and CPE. Isolates were tested for carbapenemase genes and susceptibility to 14 antibiotics. Clonality was determined by PFGE and MLST. Genetic context and conjugative transfer of the carbapenemase gene were determined.ResultsA total of 120 CPE of 10 species, mainly Escherichia coli (n = 85), carrying the gene blaIMP-4, blaIMP-38 or blaIMP-26 were obtained from 80 (40%) gulls from Five Islands. Thirty percent of birds from this colony were colonized by salmonellae. Most isolates contained the gene within a class 1 integron showing a blaIMP-4-qacG-aacA4-catB3 array. The blaIMP gene was carried by conjugative plasmids of variable sizes (80–400 kb) and diverse replicons, including HI2-N (n = 30), HI2 (11), A/C (17), A/C-Y (2), L/M (5), I1 (1) and non-typeable (6). Despite the overall high genetic variability, common clones and plasmid types were shared by different birds and bacterial isolates, respectively.ConclusionsOur data demonstrate a large-scale transmission of carbapenemase-producing bacteria into wildlife, likely as a result of the feeding habits of the birds at a local waste depot. The isolates from gulls showed significant similarities with clinical isolates from Australia, suggesting the human origin of the isolates. The sources of CPE for gulls on Five Islands should be explored and proper measures applied to stop the transmission into the environment.
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