Molecular and phenotypic characterisation of extended spectrum ß-lactamase CTX-M Escherichia coli from farm animals in Great Britain.

The aim of this study was to characterise CTX-M Escherichia coli isolates from cattle, chickens and turkeys in Great Britain with respect to CTX-M sequence type, replicon type, ability to transfer plasmids, and for the presence of antibiotic resistance, fitness and virulence genes as determined by micro-arrays. The main CTX-M enzymes identified in E. coli from cattle, chicken and turkeys were 14 and 15, 1 and 15, and 1 and 14 respectively. Most isolates from different animal species transferred their plasmids with similar frequencies. The plasmid replicon type I1-λ was most common and seen in 23%, 95% and 50% of the isolates tested from cattle, chickens and turkeys respectively, whilst types F, FIA, FIB and K were common to isolates from cattle and turkeys only. Thirty-eight different antibiotic resistance genes were detected by micro-array including aad genes, blaCTX-M, blaTEM, cat genes dfrA, floR, strA, strB, sul, sul2 tetA and tetB. Thirty-nine different fitness and virulence genes were also detected by-micro-array, including espP, ireA, lpfA, mchF, prfB and tsh. Fisher exact test and hierarchical clustering of the antibiotic resistance and virulence gene results showed some genes were more commonly associated with isolates from chickens or cattle. This study provides a baseline of the characteristics of CTX-M E. coli isolates from animals in Great Britain and suggests that chicken and cattle CTX-M E. coli represent different populations.

Epidemiology of extended spectrum beta-lactamase E. coli (CTX-M-15) on a commercial dairy farm.

The epidemiology of an extended spectrum beta-lactamase Escherichia coli (CTX-M-15) was observed and described on a commercial dairy farm located in the United Kingdom. During 2008 longitudinal sampling of faecal pat samples from different cattle groups comprising milking and non-milking cows, calving cows, calves, and the environment was carried out. The proportion of CTX-M-15 E. coli positive samples was significantly (p<0.0.01) higher in milking cows (30.3%, CI(95%) 26.8; 33.8) than in the herd as a whole (17.0%, CI(95%) 14.9; 19.0). In 2008 95.6% of sampled calves tested positive for CTX-M-15 E. coli at two days of age. A more detailed investigation in 2009 revealed that cows and heifers were approximately eight times more likely to test positive in the 10 days after calving than the 9 days before (OR 7.6, CI(95%) 2.32; 24.9). The CTX-M15 E. coli was also readily isolated from the immediate calving pen environment, including the water troughs. A cyclic pattern was apparent where cows immediately after calving and as high yielders were highly positive, but where the prevalence decreased during the dry period. The increased prevalence of the CTX-M-15 E. coli in certain cattle groups and farm environments including calving pens suggested that husbandry, antimicrobial usage and hygiene may play a significant role on a farm with regards to the epidemiology of CTX-M-15. This may offer a practical opportunity to reduce further dissemination through good practice and hygiene around calving.

Genomic characterization of Campylobacter jejuni strain M1.

Campylobacter jejuni strain M1 (laboratory designation 99/308) is a rarely documented case of direct transmission of C. jejuni from chicken to a person, resulting in enteritis. We have sequenced the genome of C. jejuni strain M1, and compared this to 12 other C. jejuni sequenced genomes currently publicly available. Compared to these, M1 is closest to strain 81116. Based on the 13 genome sequences, we have identified the C. jejuni pan-genome, as well as the core genome, the auxiliary genes, and genes unique between strains M1 and 81116. The pan-genome contains 2,427 gene families, whilst the core genome comprised 1,295 gene families, or about two-thirds of the gene content of the average of the sequenced C. jejuni genomes. Various comparison and visualization tools were applied to the 13 C. jejuni genome sequences, including a species pan- and core genome plot, a BLAST Matrix and a BLAST Atlas. Trees based on 16S rRNA sequences and on the total gene families in each genome are presented. The findings are discussed in the background of the proven virulence potential of M1.