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Katie L Hopkins

Publications and source records attributed to Katie L Hopkins.

12 recordsLinked to original sources
PubMed2026

The role of microbial genomics in delivering the UK's national action plan for confronting antimicrobial resistance 2024-29.

Antimicrobial resistance (AMR) is a major threat to human and animal health, in addition to environmental resilience. Countries set the agenda on their national action against AMR in the form of National Action Plans (NAPs), with the UK's latest NAP released in May, 2024. Advances in genomics have strengthened our ability to work towards NAP priorities; however, to date, no mapping of the role genomics plays in contributing to specific goals within the NAP has been undertaken. The UK Research and Innovation-funded Transdisciplinary Antimicrobial Resistance Genomics Network brought together a range of stakeholders to discuss the role of genomics for action on AMR and to deliver policy priority-led research, as outlined in the UK NAP 2024-29. We report our discussions in this Personal View, with key roles for genomics, including informing targeted stewardship in health-care settings, supporting AMR literacy, and supporting effective antimicrobial innovation. However, changes in infrastructure, communication, and cross-sector coordination are needed to support implementation.

United Kingdom↗
PubMed2006

Wide geographic spread of diverse acquired AmpC beta-lactamases among Escherichia coli and Klebsiella spp. in the UK and Ireland.

OBJECTIVES: To determine the distribution of acquired AmpC beta-lactamases in 173 isolates of Escherichia coli and Klebsiella spp. submitted to the UK's national reference laboratory for antibiotic resistance. METHODS: MICs were determined and interpreted according to BSAC guidelines. Candidate isolates were those resistant to cefotaxime and/or ceftazidime, irrespective of addition of clavulanic acid. Genes encoding six phylogenetic groups of acquired AmpC enzymes were sought by PCR. Selected isolates were compared by pulsed-field gel electrophoresis (PFGE), and one bla(AmpC) amplicon was sequenced. RESULTS: Genes encoding acquired AmpC enzymes were detected in 67 (49%) candidate E. coli and 21 (55%) Klebsiella spp. Sixty isolates produced CIT-type enzymes, 14 had ACC types, 11 had FOX types and 3 had DHA enzymes. The low-level cephalosporin resistance of the remaining isolates (n = 85; 49%) was inferred to result from reduced permeability or, in E. coli, from hyperexpression of chromosomal ampC. Twenty-four E. coli isolates from one hospital produced a CIT-type enzyme, with 20 of these additionally producing a group 1 CTX-M extended-spectrum beta-lactamase. PFGE indicated that these isolates belonged to UK epidemic strain A, which normally produces CTX-M-15, but no acquired AmpC. Sequencing a representative bla(AmpC) amplicon indicated that in one centre this strain had acquired a novel CMY-2 variant, designated CMY-23. CONCLUSIONS: Diverse acquired AmpC enzymes occur in E. coli and Klebsiella spp. isolates in the UK and Ireland, with CIT types the most common. Producers are geographically scattered, but with some local outbreaks. Acquisition of a CMY-2-like enzyme by E. coli epidemic strain A suggests that these enzymes may be poised to become an important public health issue.

Bacterial Proteins↗
PubMed2006

Rapid detection of gyrA and parC mutations in quinolone-resistant Salmonella enterica using Pyrosequencing technology.

Fluoroquinolones are broad-spectrum antimicrobials highly effective in the treatment of a wide variety of clinical infections. Salmonella gastroenteritis is usually only treated with fluoroquinolones when the patient is elderly or immunocompromised. Fluoroquinolones are also used for the treatment of systemic Salmonella infection or for long-term salmonella carriage. Resistance to quinolones is commonly mediated by point mutations within the topoisomerase genes gyrA and parC. Pyrosequencing technology is a DNA sequencing method using 'sequencing by synthesis' and is suitable for the rapid detection of single nucleotide polymorphisms (SNPs). One hundred and ten Salmonella enterica isolates, representing 18 different serotypes, were used in this study. One hundred and four isolates had ciprofloxacin MICs of 0.25-32 microg/mL; the remaining six were ciprofloxacin-sensitive (ciprofloxacin MIC<or=0.125 microg/mL). PCR amplification of the quinolone resistance-determining regions of gyrA and parC was performed and the resulting amplicons subjected to a Pyrosequencing protocol using cyclic dispensation of nucleotides. Amino acid substitutions at S83 and D87 were detected in gyrA and at T57 and S80 in parC. Silent mutations were also identified at G81 of gyrA and at V67, H75 and H77 of parC. This is the first report of a Pyrosequencing assay being used to detect mutations in genes conferring quinolone resistance. The Pyrosequencing technology is a rapid and reliable alternative to current methods for identification of gyrA and parC mutations in S. enterica.

Amino Acid Sequence↗
PubMed2006

Replicon typing of plasmids carrying CTX-M or CMY beta-lactamases circulating among Salmonella and Escherichia coli isolates.

Replicon typing of plasmids carrying bla(CTX-M) or bla(CMY) beta-lactamase genes indicates a predominance of I1 and A/C replicons among bla(CMY)-carrying plasmids and five different plasmid scaffolds associated with the different types of bla(CTX-M) genes (I1, FII, HI2, K, and N). These results demonstrate the association of certain beta-lactamase genes with specific plasmid backbones.

Cephalosporin Resistance↗
PubMed2005

Identification of plasmids by PCR-based replicon typing.

The epidemiological importance of tracing plasmids conferring drug resistance prompted us to develop a PCR method based on replicons (inc/rep PCR) of the major plasmid incompatibility groups among Enterobacteriaceae. Eighteen pairs of primers were designed to perform 5 multiplex- and 3 simplex-PCRs, recognizing FIA, FIB, FIC, HI1, HI2, I1-Igamma, L/M, N, P, W, T, A/C, K, B/O, X, Y, F, and FIIA. The specificity of the method was tested on a collection of 61 reference plasmids and on 20 Salmonella enterica strains of different serotypes isolated in Italy. Results indicated that the inc/rep PCR method demonstrates high specificity and sensitivity in detecting replicons on reference plasmids and also revealed the presence of recurrent and common plasmids in epidemiologically unrelated Salmonella isolates of different serotypes. These results suggest that the method is potentially applicable to a large number of strains to trace the diffusion of specific multi-drug resistance plasmids in different environments.

Bacterial Typing Techniques↗
PubMed2005

Mechanisms of quinolone resistance in Escherichia coli and Salmonella: recent developments.

Fluoroquinolones are broad-spectrum antimicrobials highly effective for treatment of a variety of clinical and veterinary infections. Their antibacterial activity is due to inhibition of DNA replication. Usually resistance arises spontaneously due to point mutations that result in amino acid substitutions within the topoisomerase subunits GyrA, GyrB, ParC or ParE, decreased expression of outer membrane porins, or overexpression of multidrug efflux pumps. In addition, the recent discovery of plasmid-mediated quinolone resistance could result in horizontal transfer of fluoroquinolone resistance between strains. Acquisition of high-level resistance appears to be a multifactorial process. Care needs to taken to avoid overuse of this important class of antimicrobial in both human and veterinary medicine to prevent an increase in the occurrence of resistant zoonotic and non-zoonotic bacterial pathogens that could subsequently cause human or animal infections.

Animals↗
PubMed2004

Frequency and polymorphism of sopE in isolates of Salmonella enterica belonging to the ten most prevalent serotypes in England and Wales.

Translocated effector protein, SopE, leads to actin cytoskeletal rearrangements and membrane ruffling. Only a subset of Salmonella enterica serotypes possess sopE, with the majority of sopE-carrying S. enterica serotype Typhimurium associated with epidemics. Using real-time PCR and sequencing, sopE was investigated in the ten most prevalent serotypes of S. enterica in England and Wales in 2001. sopE was identified in S. Typhimurium definitive phage types 29, 44, 49, 204b and 204c, all of which either have been involved in major epidemics or are precursors of epidemic strains. The presence of sopE varied in the remaining nine serotypes, but was more common in the top four (Enteritidis, Virchow, Hadar and Newport). Nucleotide changes were detected throughout sopE and may result in altered specificity for certain signal transduction pathways. Since acquisition of sopE may play a key role in emergence of epidemic strains, detection of sopE could aid identification of those Salmonella strains with the potential for epidemic spread.

Bacterial Proteins↗
PubMed2004

Fluorescent amplified fragment length polymorphism genotyping of Campylobacter jejuni and Campylobacter coli strains and its relationship with host specificity, serotyping, and phage typing.

Fluorescent amplified fragment length polymorphism (FAFLP) analysis was applied to 276 Campylobacter jejuni strains and 87 Campylobacter coli strains isolated from humans, pigs, cattle, poultry, and retail meats to investigate whether certain FAFLP genotypes of C. jejuni and C. coli are associated with a particular host and to determine the degree of association between FAFLP-defined genotypes and heat-stable serotypes and/or phage types. Within C. coli, the poultry strains clustered separately from those of porcine origin. In contrast, no evidence of host specificity was detected among C. jejuni strains. While C. coli strains show host specificity by FAFLP genotyping, C. jejuni strains that are genotypically similar appear to colonize a range of hosts, rather than being host adapted. Some serotypes and/or phage types (C. jejuni serotype HS18, phage type PT6, and serophage type HS19/PT2 and C. coli HS66, PT2, and HS56/PT2) were the most homogeneous by FAFLP genotyping, while others were more heterogeneous (C. jejuni HS5 and PT39, and C. coli HS24 and PT44) and therefore poor indicators of genetic relatedness between strains. The lack of host specificity in C. jejuni suggests that tracing the source of infection during epidemiological investigations will continue to be difficult. The lack of congruence between some serotypes and/or phage types and FAFLP genotype underlines the need for phenotypic testing to be supplemented by genotyping. This study also demonstrates how, in general, FAFLP generates "anonymous" genetic markers for strain characterization and epidemiological investigation of Campylobacter in the food chain.

Animals↗
PubMed2001

Restriction endonuclease analysis of RAPD-PCR amplicons derived from Shiga-like toxin-producing Escherichia coli O157 isolates.

Shiga-like toxin-producing Escherichia coli O157 isolates were characterised by random amplification of polymorphic DNA by PCR (RAPD-PCR) analysis developed to allow robust epidemiological typing of E. coli. Amplification with primer 1247 or 1290 generated a reproducible profile, but was not capable of distinguishing sufficiently between epidemiologically unrelated strains. Subsequent digestion of the amplicons with selected restriction endonucleases improved the discriminatory ability of this method for strains showing limited differentiation following RAPD-PCR analysis alone. Restriction endonuclease analysis of RAPD-PCR fragments generated from closely related strains has the potential to provide additional discriminatory information without loss of specificity.

Bacterial Typing Techniques↗