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1 - 6 of 6 for "Sara A. Burgess"
Genomic epidemiology of extended-spectrum beta-lactamase-producing Escherichia coli from humans and a river in Aotearoa New Zealand
In Aotearoa New Zealand urinary tract infections in humans are commonly caused by extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli. This group of antimicrobial-resistant bacteria are often multidrug resistant. However there is limited information on ESBL-producing E. coli found in the environment and their link with human clinical isolates. In this study we examined the genetic relationship between environmental and human clinical ESBL-producing E. coli and isolates collected in parallel within the same area over 14 months. Environmental samples were collected from treated effluent stormwater and multiple locations along an Aotearoa New Zealand river. Treated effluent stormwater and river water sourced downstream of the treated effluent outlet were the main samples that were positive for ESBL-producing E. coli (7/14 samples 50.0%; 3/6 samples 50%; and 15/28 samples 54% respectively). Whole-genome sequence comparison was carried out on 307 human clinical and 45 environmental ESBL-producing E. coli isolates. Sequence type 131 was dominant for both clinical (147/307 47.9%) and environmental isolates (11/45 24.4%). Only one ESBL gene was detected in each isolate. Among the clinical isolates the most prevalent ESBL genes were bla CTX-M-27 (134/307 43.6%) and bla CTX-M-15 (134/307 43.6%). Among the environmental isolates bla CTX-M-15 (28/45 62.2%) was the most prevalent gene. A core SNP analysis of these isolates suggested that some strains were shared between humans and the local river. These results highlight the importance of understanding different transmission pathways for the spread of ESBL-producing E. coli.
Corrigendum: The characterisation of antimicrobial resistant Escherichia coli from dairy calves
The characterisation of antimicrobial resistant Escherichia coli from dairy calves
Introduction. Dairy calves particularly pre-weaned calves have been identified as a common source of multidrug resistant (MDR) Escherichia coli .
Gap statement. E. coli strains isolated from dairy calves and the location of their resistance genes (plasmid or chromosomal) have not been well characterised.
Aim. To characterise the phenotypic and genotypic features as well as the population structure of antimicrobial-resistant E. coli isolated from calves located on dairy farms that feed waste-milk to their replacement calves.
Methodology. Recto-anal swab enrichments from 40 dairy calves (≤ 14 days old) located on four dairy farms were examined for tetracycline streptomycin ciprofloxacin and third-generation cephalosporin resistant E. coli . Whole genome sequencing was performed using both short- and long-read technologies on selected antimicrobial resistant E. coli .
Results. Fifty-eight percent (23/40) of calves harboured antimicrobial resistant E. coli : 43 % (17/40) harboured tetracycline resistant and 23 % (9/40) harboured chromosomal mediated AmpC producing E. coli . Whole genome sequencing of 27 isolates revealed five sequence types with ST88 being the dominant ST (17/27 63 % of the sequenced isolates) followed by ST1308 (3/27 11 %) along with the extraintestinal pathogenic E. coli lineages ST69 (3/27 11 %) ST10 (2/27 7 %) and ST58 (2/27 7 %). Additionally 16 isolates were MDR harbouring additional resistance genes that were not tested phenotypically. Oxford Nanopore long-read sequencing technologies enabled the location of multiple resistant gene cassettes in IncF plasmids to be determined.
Conclusion. Our study identified a high incidence of tetracycline and streptomycin-resistant E. coli in dairy calves and highlighted the presence of multidrug-resistant strains emphasising the need for further investigation into potential associations with farm management practices.
Whole genome sequence analysis of ESBL-producing Escherichia coli recovered from New Zealand freshwater sites
Extended-spectrum beta lactamase (ESBL)-producing Escherichia coli are often isolated from humans with urinary tract infections and may display a multidrug-resistant phenotype. These pathogens represent a target for a One Health surveillance approach to investigate transmission between humans animals and the environment. This study examines the multidrug-resistant phenotype and whole genome sequence data of four ESBL-producing E . coli isolated from freshwater in New Zealand. All four isolates were obtained from a catchment with a mixed urban and pastoral farming land-use. Three isolates were sequence type (ST) 131 (CTX-M-27-positive) and the other ST69 (CTX-M-15-positive); a phylogenetic comparison with other locally isolated strains demonstrated a close relationship with New Zealand clinical isolates. Genes associated with resistance to antifolates tetracyclines aminoglycosides and macrolides were identified in all four isolates together with fluoroquinolone resistance in two isolates. The ST69 isolate harboured the bla CTX-M-15 gene on a IncHI2A plasmid and two of the three ST131 isolates harboured the bla CTX-M-27 genes on IncF plasmids. The last ST131 isolate harboured bla CTX-M-27 on the chromosome in a unique site between gspC and gspD. These data highlight a probable human origin of the isolates with subsequent transmission from urban centres through wastewater to the wider environment.
Occurrence of genes encoding spore germination in Clostridium species that cause meat spoilage
Members of the genus Clostridium are frequently associated with meat spoilage. The ability for low numbers of spores of certain Clostridium species to germinate in cold-stored vacuum-packed meat can result in blown pack spoilage. However little is known about the germination process of these clostridia despite this characteristic being important for their ability to cause spoilage. This study sought to determine the genomic conditions for germination of 37 representative Clostridium strains from seven species ( C. estertheticum C. tagluense C. frigoris C. gasigenes C. putrefaciens C. aligidicarnis and C. frigdicarnis) by comparison with previously characterized germination genes from C. perfringens C. sporogenes and C. botulinum . All the genomes analysed contained at least one gerX operon. Seven different gerX operon configuration types were identified across genomes from C. estertheticum C. tagluense and C. gasigenes . Differences arose between the C. gasigenes genomes and those belonging to C. tagluense / C. estertheticum in the number and type of genes coding for cortex lytic enzymes suggesting the germination pathway of C. gasigenes is different. However the core components of the germination pathway were conserved in all the Clostridium genomes analysed suggesting that these species undergo the same major steps as Bacillus subtilis for germination to occur.
The epidemiology of AmpC-producing Escherichia coli isolated from dairy cattle faeces on pasture-fed farms
Introduction. Antibiotic use particularly amoxicillin-clavulanic acid in dairy farming has been associated with an increased incidence of AmpC-hyperproducing Escherichia coli .
Gap statement. There is limited information on the incidence of AmpC-hyperproducing E. coli from seasonal pasture-fed dairy farms.
Aim. We undertook a New Zealand wide cross-sectional study to determine the prevalence of AmpC-producing E. coli carried by dairy cattle.
Methodology. Paddock faeces were sampled from twenty-six dairy farms and were processed for the selective growth of both extended-spectrum beta-lactamase (ESBL)- and AmpC-producing E. coli . Whole genome sequence analysis was carried out on 35 AmpC-producing E. coli .
Results. No ESBL- or plasmid mediated AmpC-producing E. coli were detected but seven farms were positive for chromosomal mediated AmpC-hyperproducing E. coli . These seven farms were associated with a higher usage of injectable amoxicillin antibiotics. Whole genome sequence analysis of the AmpC-producing E. coli demonstrated that the same strain (<3 SNPs difference) of E. coli ST5729 was shared between cows on a single farm. Similarly the same strain (≤15 SNPs difference) of E. coli ST8977 was shared across two farms (separated by approximately 425 km).
Conclusion. These results infer that both cow-to-cow and farm-to-farm transmission of AmpC-producing E. coli has occurred.