Biology subjects

Morley, K.

Publications and source records attributed to Morley, K..

6 recordsLinked to original sources

bioRxiv2026

Local Temperature and Humidity are Associated with Proportion of Antimicrobial-Resistant Escherichia coli isolates in Farm Environments: Considerations for On-Farm Surveillance

Evidence suggests that increased local temperatures are associated with higher prevalence of antimicrobial resistance (AMR) in environmental bacteria. This study investigates the association between local climate and the proportion of antimicrobial-resistant Escherichia coli isolated from 2,766 farm environment samples from 53 English dairy farms. To do this, a non-linear Bayesian model that specifically accounts for decreased test sensitivity at low E. coli abundance was developed and used to estimate the proportion of isolates resistant to four antimicrobials (amoxicillin, cephalexin, streptomycin and tetracycline) from colony count data. Mean 7-day temperature and relative humidity at the farm location was modelled using a generalised additive model formulation. A higher proportion of E. coli isolates were resistant to cephalexin and streptomycin in samples collected from adult cow collecting yards, than heifer housing sheds. In contrast, a greater proportion of E. coli isolates from heifer housing sheds were resistant to amoxicillin and tetracycline. Evidence that local temperature is associated with an increase in the proportion of E. coli isolates resistant to streptomycin (20{degrees}C increase associated with a 5.0-fold increase; 95% CI: 1.03-33.0) and tetracycline (2.6-fold increase; 90% CI: 1.1-5.2) was observed. Additionally, relative humidity was associated with an increase in the proportion of isolates resistant to amoxicillin streptomycin and tetracycline. The influence of weather on the proportion of antimicrobial-resistant E. coli varied between samples collected from adult animals in collecting yards and heifers in housing sheds. These findings highlight the importance of considering weather conditions, sample characterises and seasonality when designing on-farm AMR surveillance systems. ImportanceUnderstanding how environmental conditions are associated with variability in AMR prevalence is critical for developing robust livestock AMR surveillance and anticipating the potential effects of climate change. The non-linear Bayesian modelling approach developed here adjusts for E. coli abundance associated variability in test sensitivity, enabling the influence of risk factors associated with the proportion of antimicrobial-resistant E. coli within samples to be more accurately estimated. Applying this approach to 2,766 faecal samples from 53 dairy farms in Southwest England indicated that the proportion of antimicrobial-resistant E. coli generally increased under warmer and wetter conditions. These findings suggest that environmental conditions can influence the prevalence of AMR E. coli in dairy farm environments and demonstrate the importance of accounting for weather related variability in livestock AMR surveillance. Adjusting for these associations in livestock AMR surveillance could improve the accuracy of modelling AMR trends and strengthen the assessment of climate-associated AMR risks.

microbiology↗

bioRxiv2021

Fluoroquinolone-Resistant Escherichia coli Originating on Dairy Farms are an Infrequent Cause of Bacteriuria in Humans Living in the Same Geographical Region

SynopsisO_ST_ABSBackgroundC_ST_ABSOur primary aim was to test whether cattle-associated fluoroquinolone-resistant (FQ-R) Escherichia coli found on dairy farms were a significant cause of bacteriuria in humans living in the same 50 x 50 km geographical region located in South West England. Another aim was to identify risk factors for the presence of FQ-R E. coli on dairy farms. MethodsFQ-R E. coli were isolated during 2017-18 from 42 dairy farms and from community urine samples. Forty-two cattle and 489 human urinary isolates were subjected to WGS, allowing phylogenetic comparisons. Risk factors were identified using a Bayesian regularisation approach. ResultsOf 489 FQ-R human isolates, 255 were also 3rd generation cephalosporin-resistant (3GC-R), with strong genetic linkage between aac(6)Ib-cr and blaCTX-M-15. We identified possible farm-to-human sharing for pairs of ST744 and ST162 isolates, but core genome SNP distances (71 and 63, respectively) were smaller in pairs of ST744 and ST162 isolates from different farms (7 and 3 SNPs, respectively). Total farm fluoroquinolone use showed a positive association with the odds of isolating FQ-R E. coli while total dry cow therapy use showed a negative association. ConclusionsThis work suggests that FQ-R E. coli found on dairy farms have a limited impact on community bacteriuria within the local human population, however, this appears greater than observed for 3GC-R E. coli when studied in parallel. Reducing fluoroquinolone use may reduce the on-farm prevalence of FQ-R E. coli, and this reduction may be greater when dry cow therapy is targeted to the ecology of resistant E. coli on the farm.

microbiology↗

bioRxiv2021

Evidence that faecal carriage of resistant Escherichia coli by 16-week-old dogs in the United Kingdom is associated with raw feeding and that E. coli from these dogs are shared with humans and cause opportunistic infections.

We report a survey (August 2017 to March 2018) and risk factor analysis of faecal carriage of antibacterial-resistant (ABR) Escherichia coli in 223 sixteen-week-old dogs in the United Kingdom. Raw feeding was associated with the presence of E. coli resistant to fluoroquinolones, tetracycline, amoxicillin, and streptomycin, but not to cefalexin or cefotaxime. Whole genome sequencing of 30 fluoroquinolone-resistant (FQ-R), 22 cefotaxime-resistant (CTX-R) and seven dual FQ-R/CTX-R E. coli isolates showed a wide range of sequence types (STs), an approximately 50:50 split of CTX-M:AmpC-mediated CTX-R, and almost exclusively mutational FQ-R dominated by ST744 and ST162. Comparisons between E. coli isolates from puppies known to be located within a 50 x 50 km region with those isolated from human urinary tract and bloodstream infections (isolated in parallel in the same region) identified a clone of ST963 E. coli carrying chromosomal blaCMY.2 in two puppies and causing two urinary tract infections and one bloodstream infection. Furthermore, an ST744 FQ-R clone was carried by one puppy and caused one urinary tract infection. Accordingly, we conclude that raw feeding is associated with carriage of ABR E. coli in dogs even at sixteen weeks of age and that bacteria carried by dogs are shared with humans.

microbiology↗

bioRxiv2019

Molecular epidemiology of cefotaxime-resistant Escherichia coli from dairy farms in South West England identifies a dominant plasmid encoding CTX-M-32

Third-generation cephalosporin resistance (3GC-R) in Escherichia coli is a rising problem in human and farmed animal populations. We conducted whole genome sequencing analysis of 138 representative 3GC-R isolates previously collected from dairy farms in South West England and confirmed by PCR to carry acquired 3GC-R genes. This analysis identified blaCTX-M (131 isolates: encoding CTX-M-1, -14, -15, -32 and the novel variant, CTX-M-214), blaCMY-2 (6 isolates) and blaDHA-1 (one isolate). A highly conserved plasmid was identified in 73 isolates, representing 27 E. coli sequence types. This novel ~220 kb IncHI2 plasmid carrying blaCTX-M-32 was sequenced to closure and designated pMOO-32. It was found experimentally to be stable in cattle and human transconjugant E. coli even in the absence of selective pressure and was found by multiplex PCR to be present on 26 study farms representing a remarkable range of transmission over 1500 square kilometres. However, the plasmid was not found amongst human urinary E. coli we have recently characterised from people living in the same geographical location, collected in parallel with farm sampling. There were close relatives of two blaCTX-M plasmids circulating amongst eight human and two cattle isolates, and a closely related blaCMY-2 plasmid found in one cattle and one human isolate. However, phylogenetic evidence of recent sharing of 3GC-R strains between farms and humans in the same region was not found. ImportanceThird-generation cephalosporins (3GCs) are critically important antibacterials and 3GC-resistance (3GC-R) threatens human health, particularly in the context of opportunistic pathogens such as Escherichia coli. There is some evidence for zoonotic transmission of 3GC-R E. coli through food, but little work has been done examining possible transmission (e.g. via interaction of people with the local near-farm environment). We characterised acquired 3GC-R E. coli found on dairy farms in a geographically restricted region of the United Kingdom and compared these with E. coli from people living in the same region, collected in parallel. Whilst there is strong evidence for recent farm-to-farm transmission of 3GC-R strains and plasmids - including one epidemic plasmid that has a remarkable capacity to transmit - there was no evidence that 3GC-R found on study farms had a significant impact on circulating 3GC-R E. coli strains or plasmids in the local human population.

microbiology↗

bioRxiv2019

Evidence for reduced CTX-M carriage in cattle-associated Escherichia coli at low temperatures and on publicly accessible farmland: implications for surveillance and potential for farm-to-human transmission

Little is known about the drivers of critically important antibacterial resistance in species with zoonotic potential present on farms (e.g. CTX-M {square}-lactamase-positive Escherichia coli). Here, we collected samples, monthly over a two-year period, on 53 dairy farms in the South West of England, and data for 610 variables concerning antimicrobial usage, management practices and meteorological factors. We detected E. coli resistant to amoxicillin, ciprofloxacin streptomycin and tetracycline, respectively, in 2754/4145 (66%), 263/4145 (6%), 1475/4145 (36%) and 2874/4145 (69%) of all samples from faecally contaminated sites. E. coli positive for blaCTX-M were detected in 224/4145 (5.4%) of samples. Multilevel, multivariable logistic regression showed antibiotic dry cow therapeutic choice (including use of cefquinome or framycetin) to be associated with increased odds of blaCTX-M positivity. Low temperature was associated with reduced odds of blaCTX-M E. coli positivity in samples and to reduced odds of finding E. coli resistant to each of the four test antibacterials. This was additional to the effect of temperature on total E. coli density. Furthermore, samples collected close to calves had increased odds of having E. coli resistance to each antibacterial or positive for blaCTX-M. Samples collected on pastureland had reduced odds of having E. coli resistant to amoxicillin or tetracycline, and being positive for blaCTX-M. ImportanceAntibacterial resistance poses a significant threat to human and animal health and global food security. Surveillance for resistance on farms is important for many reasons, including to track the impacts of interventions aimed at reducing the prevalence of resistance. In this epidemiological survey of dairy farm antibacterial resistance, we show that local temperature, as it changes over the course of a year, is associated with the prevalence of antibacterial resistant E. coli. Also, that prevalence of resistant E. coli is higher in indoor environments and in environments inhabited by young animals. These findings have profound implications for routine surveillance and for surveys carried out for research. They provide important evidence that sampling at a single time-point and/or single location on a farm is unlikely to be adequate to accurately determine the status of the farm with regard to the presence or number of resistant E. coli.

microbiology↗

bioRxiv2017

SemEHR: A General-purpose Semantic Search System to Surface Semantic Data from Clinical Notes for Tailored Care, Trial Recruitment and Clinical Research

ObjectiveUnlocking the data contained within both structured and unstructured components of Electronic Health Records (EHRs) has the potential to provide a step change in data available forsecondary research use, generation of actionable medical insights, hospital management and trial recruitment. To achieve this, we implemented SemEHR - a semantic search and analytics, open source tool for EHRs.\n\nMethodsSemEHR implements a generic information extraction (IE) and retrieval infrastructure by identifying contextualised mentions of a wide range of biomedical concepts within EHRs. Natural Language Processing (NLP) annotations are further assembled at patient level and extended with EHR-specific knowledge to generate a timeline for each patient. The semantic data is serviced via ontology-based search and analytics interfaces.\n\nResultsSemEHR has been deployed to a number of UK hospitals including the Clinical Record Interactive Search (CRIS), an anonymised replica of the EHR of the UK South London and Maudsley (SLaM) NHS Foundation Trust, one of Europes largest providers of mental health services. In two CRIS-based studies, SemEHR achieved 93% (Hepatitis C case) and 99% (HIV case) F-Measure results in identifying true positive patients. At Kings College Hospital in London, as part of the CogStack programme (github.com/cogstack), SemEHR is being used to recruit patients into the UK Dept of Health 100k Genome Project (genomicsengland.co.uk). The validation study suggests that the tool can validate previously recruited cases and is very fast in searching phenotypes - time for recruitment criteria checking reduced from days to minutes. Validated on an open intensive care EHR data - MIMICIII, the vital signs extracted by SemEHR can achieve around 97% accuracy.\n\nConclusionResults from the multiple case studies demonstrate SemEHRs efficiency - weeks or months of work can be done within hours or minutes in some cases. SemEHR provides a more comprehensive view of a patient, bringing in more and unexpected insight compared to study-oriented bespoke information extraction systems.\n\nSemEHR is open source available at https://github.com/CogStack/SemEHR.

bioinformatics↗