The EGD Murray collection consists of approximately 500 clinical bacterial isolates, mainly Enterobacteriaceae, isolated from around the world between 1917 and 1949. A number of these "Murray" isolates have subsequently been identified as Klebsiella pneumoniae. Antimicrobial susceptibility testing of these isolates showed that over 30% were resistant to penicillins due to the presence of diverse bla SHV ␤-lactamase genes. Analysis of susceptibility to skin antiseptics and triclosan showed that while the Murray isolates displayed a range of MIC/minimal bactericidal concentration (MBC) values, the mean MIC value was lower than that for more modern K. pneumoniae isolates tested. All Murray isolates contained the cation efflux gene cepA, which is involved in disinfectant resistance, but those that were more susceptible to chlorhexidine were found to have a 9-or 18-bp insertion in this gene. Susceptibility to other disinfectants, e.g., H 2 O 2 , in the Murray isolates was comparable to that in modern K. pneumoniae isolates. The Murray isolates were also less virulent in Galleria and had a different complement of putative virulence factors than the modern isolates, with the exception of an isolate related to the modern lineage CC23. More of the modern isolates (41% compared to 8%) are classified as good/very good biofilm formers, but there was overlap in the two populations. This study demonstrated that a significant proportion of the Murray Klebsiella isolates were resistant to penicillins before their routine use. This collection of pre-antibiotic era isolates may provide significant insights into adaptation in K. pneumoniae in relation to biocide susceptibility.

SummaryBackgroundShigellosis (previously bacillary dysentery) was the primary diarrhoeal disease of World War 1, but outbreaks still occur in military operations, and shigellosis causes hundreds of thousands of deaths per year in developing nations. We aimed to generate a high-quality reference genome of the historical Shigella flexneri isolate NCTC1 and to examine the isolate for resistance to antimicrobials.MethodsIn this genomic analysis, we sequenced the oldest extant Shigella flexneri serotype 2a isolate using single-molecule real-time (SMRT) sequencing technology. Isolated from a soldier with dysentery from the British forces fighting on the Western Front in World War 1, this bacterium, NCTC1, was the first isolate accessioned into the National Collection of Type Cultures. We created a reference sequence for NCTC1, investigated the isolate for antimicrobial resistance, and undertook comparative genetics with S flexneri reference strains isolated during the 100 years since World War 1.FindingsWe discovered that NCTC1 belonged to a 2a lineage of S flexneri, with which it shares common characteristics and a large core genome. NCTC1 was resistant to penicillin and erythromycin, and contained a complement of chromosomal antimicrobial resistance genes similar to that of more recent isolates. Genomic islands gained in the S flexneri 2a lineage over time were predominately associated with additional antimicrobial resistances, virulence, and serotype conversion.InterpretationThis S flexneri 2a lineage is a well adapted pathogen that has continued to respond to selective pressures. We have created a valuable historical benchmark for shigellae in the form of a high-quality reference sequence for a publicly available isolate.FundingThe Wellcome Trust.

Studies of historical isolates inform on the evolution and emergence of important pathogens and phenotypes, including antimicrobial resistance. Crucial to studying antimicrobial resistance are isolates that predate the widespread clinical use of antimicrobials. The Murray collection of several hundred bacterial strains of pre-antibiotic era Enterobacteriaceae is an invaluable resource of historical strains from important pathogen groups. Studies performed on the Collection to date merely exemplify its potential, which will only be realised through the continued effort of many scientific groups. To enable that aim, we announce the public availability of the Murray collection through the National Collection of Type Cultures, and present associated metadata with whole genome sequence data for over half of the strains. Using this information we verify the metadata for the collection with regard to subgroup designations, equivalence groupings and plasmid content. We also present genomic analyses of population structure and determinants of mobilisable antimicrobial resistance to aid strain selection in future studies. This represents an invaluable public resource for the study of these important pathogen groups and the emergence and evolution of antimicrobial resistance.Electronic supplementary materialThe online version of this article (doi:10.1186/s13073-015-0222-7) contains supplementary material, which is available to authorized users.

No abstract

The National Collection of Type Cultures (NCTC) is the world’s oldest repository of medically-relevant bacteria. NCTC contains 5,500 bacterial strains, 500 of which are anaerobes, with the collection regularly receiving new Type strains and recent clinical isolates. Fastidious anaerobes pose a unique challenge during the authentication process. NCTC must ensure that the strains are free from contamination and that the organism survives the lyophilisation process. Species-level identification of anaerobic bacterial strains is achieved using a combination of the both MALDI-TOF MS and VITEK2 instruments. This study evaluates the use of MALDI-TOF MS (Bruker) and VITEK2 (BioMerieux) to identify the anaerobic strains in the NCTC collection. 176 NCTC strains were tested on the MALDI-TOF platform and 60 strains were identified using VITEK2. MALDI-TOF was able to identify 79% anaerobes to genus-level and 64% to species-level. In comparison the VITEK2 identified 68% to genus and 46% to species-level. The main limiting factor for both these platforms is the database. This may be due to novel anaerobe species NCTC receives not being present on the databases. In the event of no identification, 16S ribosomal RNA sequencing is employed. Furthermore, detection of specific characteristics is carried out by specialist reference laboratories in Cardiff and Colindale, ensuring a robust collection of anaerobic bacteria for use in research and as control strains.