Biology subjects

Patch, C.

Publications and source records attributed to Patch, C..

2 recordsLinked to original sources

bioRxiv2025

Stress tolerance of multiple Salmonella enterica strains associated with foodborne outbreaks

Salmonella enterica is a foodborne pathogen commonly found in food processing environments. While control methods such as heat treatment and sanitizers are often used, S. enterica has evolved strategies for survival and persistence to overcome pathogen control. This study assessed 43 outbreak-associated (OA) and non-outbreak associated (NOA) S. enterica isolates from serovars Enteritidis, Heidelberg, Newport, Typhimurium, and monophasic Typhimurium (I 4,[5],12:i:-) for enhanced stress tolerance. Heat shock at 56{degrees} C, minimum inhibitory concentrations (MICs) for sanitizers sodium hypochlorite (NaOCl) and peracetic acid (PAA), and crystal violet microtiter assays were used to evaluate heat tolerance, sanitizer tolerance, and attachment capacity, respectively. Most isolates (n =34/43) carried at least one antimicrobial resistance gene, and nearly half (n =21/43) displayed genotypic and/or phenotypic resistance to ampicillin, ciprofloxacin, or ceftriaxone. Most isolates carried genes conferring resistance to gold (n =43/43) and arsenic (n= 41/43), and tolerance to mercury, copper, and silver was common among monophasic Typhimurium and Heidelberg isolates. Efflux pump qacEdelta1 was detected among eight Heidelberg isolates. We found enhanced stress tolerance (i.e. an unusually high ability to survive and adapt to various environmental stresses) to sanitizers and enhanced attachment capacity, indicating biofilm formation. Isolates evaluated for heat tolerance survived at least 15 min at 56{degrees} C and three survived >60 min. Overall, we found evidence of enhanced tolerance to individual stresses across both OA and NOA S. enterica. There were no strong patterns based upon serovar or OA/NOA status; however, we did find that specific enhanced stress tolerance profiles may have contributed to outbreak characteristics.

microbiology↗

bioRxiv2020

Whole genome sequencing for diagnosis of neurological repeat expansion disorders

BackgroundRepeat expansion (RE) disorders affect ~1 in 3000 individuals and are clinically heterogeneous diseases caused by expansions of short tandem DNA repeats. Genetic testing is often locus-specific, resulting in under diagnosis of atypical clinical presentations, especially in paediatric patients without a prior positive family history. Whole genome sequencing (WGS) is emerging as a first-line test for rare genetic disorders, but until recently REs were thought to be undetectable by this approach. MethodsWGS pipelines for RE disorder detection were deployed by the 100,000 Genomes Project and Illumina Clinical Services Laboratory. Performance was retrospectively assessed across the 13 most common neurological RE loci using 793 samples with prior orthogonal testing (182 with expanded alleles and 611 with alleles within normal size) and prospectively interrogated in 13,331 patients with suspected genetic neurological disorders. FindingsWGS RE detection showed minimum 97{middle dot}3% sensitivity and 99{middle dot}6% specificity across all 13 disease-associated loci. Applying the pipeline to patients from the 100,000 Genomes Project identified pathogenic repeat expansions which were confirmed in 69 patients, including seven paediatric patients with no reported family history of RE disorders, with a 0.09% false positive rate. InterpretationWe show here for the first time that WGS enables the detection of causative repeat expansions with high sensitivity and specificity, and that it can be used to resolve previously undiagnosed neurological disorders. This includes children with no prior suspicion of a RE disorder. These findings are leading to diagnostic implementation of this analytical pipeline in the NHS Genomic Medicine Centres in England. FundingMedical Research Council, Department of Health and Social Care, National Health Service England, National Institute for Health Research, Illumina Inc

genomics↗