Controlling antibiotic usage-A national analysis of General Practitioner/Family Doctor practices links overall antibiotic levels to demography, geography, comorbidity factors with local discretionary prescribing choices.

INTRODUCTION: Ecological studies show association between antimicrobial resistance (AMR), and inappropriate oral antibiotics use. Moderating antibiotic prescribing requires an understanding of all drivers of local prescribing. The aim was to quantify how much is determined by external factors compared with discretionary clinical choices. METHODS: Oral antibiotic usage taken from England General Practitioner/Family Doctor practice prescribing data was aggregated using WHO/ATC defined daily doses (DDDs). The average annual antibiotic daily prescribing rate (AAADPR) in each practice was the total DDD of oral antibiotics divided by registered population and 365. The AAADPR of English practices in 2017_18 was linked by regression to factors including demographics, geography, medical comorbidities, clinical performance, patient satisfaction, medical workforce characteristics and prescribing selection. The regression coefficients for modifiable prescribing selection factors were applied to the difference between the median and top decile practice values to establish overall reduction opportunities through changing prescribing behaviour. RESULTS: Twenty five factors accounted for 58% of the AAADPR variation in 5889 practices supporting 49.8 million patients. Non-modifiable factors linked increased AAADPR to more northerly location, higher prevalence of diabetes, COPD, CHD, and asthma; higher white ethnicity; higher patient satisfaction and lower population density. Modifiable behaviour accounted for 11% of the variation in AAADPR, with increases associated with a wider range of antibiotics, higher proportion taken as liquids, higher doses in each prescription, lower guideline compliance, lower targeted antibiotics, lower spend/dose, and less seasonal variation. If all practices achieved the level of modifiable factors of the top decile, this model suggests that overall AAADPR could reduce by 31%. CONCLUSION: Such analysis is associative and does not infer causation. However, demographics, location, medical condition of the population, and prescribing selection are drivers of overall antibiotic prescribing. This analysis provides benchmarks for both non-modifiable and modifiable factors against which practices could evaluate their opportunities to reduce antibiotic prescribing.

Structure and function of cytidine monophosphate kinase from Yersinia pseudotuberculosis, essential for virulence but not for survival.

The need for new antibiotics has become pressing in light of the emergence of antibiotic-resistant strains of human pathogens. Yersinia pestis, the causative agent of plague, is a public health threat and also an agent of concern in biodefence. It is a recently emerged clonal derivative of the enteric pathogen Yersinia pseudotuberculosis. Previously, we developed a bioinformatic approach to identify proteins that may be suitable targets for antimicrobial therapy and in particular for the treatment of plague. One such target was cytidine monophosphate (CMP) kinase, which is an essential gene in some organisms. Previously, we had thought CMP kinase was essential for Y. pseudotuberculosis, but by modification of the mutagenesis approach, we report here the production and characterization of a Δcmk mutant. The isogenic mutant had a growth defect relative to the parental strain, and was highly attenuated in mice. We have also elucidated the structure of the CMP kinase to 2.32 Å, and identified three key residues in the active site that are essential for activity of the enzyme. These findings will have implications for the development of novel CMP kinase inhibitors for therapeutic use.

The VC1777-VC1779 proteins are members of a sialic acid-specific subfamily of TRAP transporters (SiaPQM) and constitute the sole route of sialic acid uptake in the human pathogen Vibrio cholerae.

Sialic acids are nine-carbon amino sugars that are present on all mucous membranes and are often used by bacteria as nutrients. In pathogenic Vibrio the genes for sialic acid catabolism (SAC) are known to be important for host colonization, yet the route for sialic acid uptake is not proven. Vibrio cholerae contains a tripartite ATP-independent periplasmic (TRAP) transporter, SiaPQM (VC1777-VC1779), encoded by genes within the Vibrio pathogenicity island-2 (VPI-2), which are adjacent to the SAC genes nanA, nanE and nanK. We demonstrate a correlation of the occurrence of VPI-2 and the ability of Vibrio to grow on the common sialic acid N-acetylneuraminic acid (Neu5Ac), and that a V. cholerae N16961 mutant defective in vc1777, encoding the large membrane protein component of the TRAP transporter, SiaM, is unable to grow on Neu5Ac as the sole carbon source. Using the genome context and known structures of the SiaP protein component of the TRAP transporter, we define a subfamily of Neu5Ac-specific TRAP transporters, of which the vc1777-vc1779 genes are the only representatives in V. cholerae. A recent report has suggested that an entirely different TRAP transporter (VC1927-VC1929) is the Neu5Ac transporter in V. cholerae. Bioinformatics and genomic analysis suggest strongly that this is a C(4)-dicarboxylate-specific TRAP transporter, and indeed disruption of vc1929 results in a defect in growth on C(4)-dicarboxylates but not Neu5Ac. Together these data demonstrate unequivocally that the siaPQM-encoded TRAP transporter within VPI-2 is the sole sialic acid transporter in V. cholerae.

Predicting conserved essential genes in bacteria: in silico identification of putative drug targets.

Many genes have been listed as putatively essential for bacterial viability in the Database of Essential Genomes (DEG), although few have been experimentally validated. By prioritising targets according to the criteria suggested by the Research and Training in Tropical Diseases (TDR) Targets database, we have developed a modified down-selection tool to identify essential genes conserved across diverse genera. Using this approach we identified 52 proteins conserved to 7 or more of the 14 genomes in DEG. We confirmed the validity of the down-selection by attempting to make mutants of 8 of these targets in a model organism, Yersinia pseudotuberculosis, which is not closely related to any of the bacteria in DEG. Mutants were recovered for only one of the 8 targets, suggesting that the other 7 were essential in Y. pseudotuberculosis, an impressive success rate compared to other approaches of identification for such targets. Identification of essential proteins common in diverse bacterial genera can then be used to facilitate the selection of effective targets for novel broad-spectrum antibiotics.