Draft genome sequence of the Streptococcus pneumoniae Avery strain A66

We have used HiSeq 2000 technology to generate a draft genome sequence of Streptococcus pneumoniae strain A66. This is a common study strain used in investigations of pneumococcal bacterium-host interactions and was used in the seminal genetic studies of Avery et al

The emergence of mecC methicillin-resistant Staphylococcus aureus.

The report of methicillin-resistant Staphylococcus aureus (MRSA) encoding a divergent mecA gene in 2011 was highly significant. This homologue, designated mecC, poses diagnostic problems with the potential to be misdiagnosed as methicillin-sensitive S. aureus, with important potential consequences for individual patients and for the surveillance of MRSA. mecC MRSA have now been reported from 13 European countries and have been isolated from 14 different host species, with evidence of a recent increase in Denmark. The emergence of mecC MRSA is a topic of interest to human and veterinary microbiology, and we consider it timely to review here its discovery and subsequent investigation.Our work on S. aureus is supported by a Medical Research Council (MRC) Partnership Award to M.A.H and funding to G.K.P from PetPlan Charitable Trust, the British Society for Antimicrobial Chemotherapy, and the Cambridge–Africa Alborada Research Fund.This is the final published version distributed under a Creative Commons Attribution License 2.0, which can also be found on the publisher's website at: http://www.cell.com/trends/microbiology/abstract/S0966-842X(13)00226-

The first report of <i>Listeria monocytogenes</i> detected in pinnipeds

The aim of this study was to describe the pathology in seals from which Listeria monocytogenes was isolated and investigate if the lesions’ nature and severity were related to the phylogeny of isolates. L. monocytogenes was isolated from 13 of 50 (26%) dead grey seal (Halichoerus grypus) pups, six (12%) in systemic distribution, on the Isle of May, Scotland. Similar fatal L. monocytogenes-associated infections were found in a grey seal pup from Carnoustie, Scotland, and a juvenile harbour seal (Phoca vitulina) in the Netherlands. Whole genome sequencing of 15 of the L. monocytogenes isolates identified 13 multilocus sequence types belonging to the L. monocytogenes lineages I and II, but with scant phenotypic and genotypic antimicrobial resistance and limited variation in virulence factors. The phylogenetic diversity present suggests there are multiple sources of L. monocytogenes, even for seal pups born in the same colony and breeding season. This is the first description of L. monocytogenes isolated from, and detected in lesions in, pinnipeds and indicates that infection can be systemic and fatal. Therefore, listeriosis may be an emerging or overlooked disease in seals with infection originating from contamination of the marine environment.</p

The first report of Listeria monocytogenes detected in pinnipeds

The aim of this study was to describe the pathology in seals from which Listeria monocytogenes was isolated and investigate if the lesions’ nature and severity were related to the phylogeny of isolates. L. monocytogenes was isolated from 13 of 50 (26%) dead grey seal (Halichoerus grypus) pups, six (12%) in systemic distribution, on the Isle of May, Scotland. Similar fatal L. monocytogenes-associated infections were found in a grey seal pup from Carnoustie, Scotland, and a juvenile harbour seal (Phoca vitulina) in the Netherlands. Whole genome sequencing of 15 of the L. monocytogenes isolates identified 13 multilocus sequence types belonging to the L. monocytogenes lineages I and II, but with scant phenotypic and genotypic antimicrobial resistance and limited variation in virulence factors. The phylogenetic diversity present suggests there are multiple sources of L. monocytogenes, even for seal pups born in the same colony and breeding season. This is the first description of L. monocytogenes isolated from, and detected in lesions in, pinnipeds and indicates that infection can be systemic and fatal. Therefore, listeriosis may be an emerging or overlooked disease in seals with infection originating from contamination of the marine environment.</p

Genomic Analysis of Companion Rabbit Staphylococcus aureus.

In addition to being an important human pathogen, Staphylococcus aureus is able to cause a variety of infections in numerous other host species. While the S. aureus strains causing infection in several of these hosts have been well characterised, this is not the case for companion rabbits (Oryctolagus cuniculus), where little data are available on S. aureus strains from this host. To address this deficiency we have performed antimicrobial susceptibility testing and genome sequencing on a collection of S. aureus isolates from companion rabbits. The findings show a diverse S. aureus population is able to cause infection in this host, and while antimicrobial resistance was uncommon, the isolates possess a range of known and putative virulence factors consistent with a diverse clinical presentation in companion rabbits including severe abscesses. We additionally show that companion rabbit isolates carry polymorphisms within dltB as described as underlying host-adaption of S. aureus to farmed rabbits. The availability of S. aureus genome sequences from companion rabbits provides an important aid to understanding the pathogenesis of disease in this host and in the clinical management and surveillance of these infections.This project was supported by internal funding from the School of Biological, Biomedical and Environmental Sciences, University of Hull (GKP), a Medical Research Council (MRC) Partnership Grant (G1001787/1) (MAH and JP), and the Wellcome Trust, Grant number 098051 (JP).This is the final version of the article. It first appeared from PLOS via http://dx.doi.org/10.1371/journal.pone.015145

Draft Genome Sequence of a Multiresistant Bovine Isolate of Staphylococcus lentus from Tanzania.

We report here the draft genome sequence of a Staphylococcus lentus isolate, 050AP, collected in Tanzania from a swab of healthy bovine perineum. The draft genome sequence contained 2.72 Mbp and 2,750 coding sequences with a G+C content of 31.7%

Detection of mecC-Methicillin-resistant Staphylococcus aureus isolates in river water : a potential role for water in the environmental dissemination

Methicillin-resistant Staphylococcus aureus (MRSA) is a public health concern due to limited treatment options. The recent description of a mecA homologue, mecC in human and cattle, led to studies to detect this new variant in human and other animal species. Detection of mecC in wild boar and fallow deer in a Spanish game estate led us to further investigate the presence of mecC-MRSA at this location. Samples from cattle, wild animals, workers and river water were tested. A further three mecC-MRSA isolates were obtained from river water. Molecular characterization (multilocus sequence typing and spa typing) and antimicrobial susceptibility testing (broth microdilution) showed that isolates were similar to those detected in wild animals. Whole genome sequencing confirmed that the isolates from the river water and wild animals in the same geographic area were all closely related isolates of ST425 mecC-MRSA. The presence of mecC-MRSA in the river water highlights the potential role of water in the dissemination of mecC-MRSA

Predictive phage therapy for Escherichia coli urinary tract infections: cocktail selection for therapy based on machine learning models

This study supports the development of predictive bacteriophage (phage) therapy: the concept of phage cocktail selection to treat a bacterial infection based on machine learning models (MLM). For this purpose, MLM were trained on thousands of measured interactions between a panel of phage and sequenced bacterial isolates. The concept was applied to Escherichia coli (E. coli) associated with urinary tract infections. This is an important common infection in humans and companion animals from which multi-drug resistant (MDR) bloodstream infections can originate. The global threat of MDR infection has reinvigorated international efforts into alternatives to antibiotics including phage therapy. E. coli exhibit extensive genome-level variation due to horizontal gene transfer via phage and plasmids. Associated with this, phage selection for E. coli is difficult as individual isolates can exhibit considerable variation in phage susceptibility due to differences in factors important to phage infection including phage receptor profiles and resistance mechanisms. The activity of 31 phage were measured on 314 isolates with growth curves in artificial urine. Random Forest models were built for each phage from bacterial genome features and the more generalist phage, acting on over 20% of the bacterial population, exhibited F1 scores of &gt;0.6 and could be used to predict phage cocktails effective against previously untested strains. The study demonstrates the potential of predictive models which integrate bacterial genomics with phage activity datasets allowing their use on data derived from direct sequencing of clinical samples to inform rapid and effective phage therapy.Significance Statement With the growing challenge of antimicrobial resistance there is an urgency for alternative treatments for common bacterial diseases including urinary tract infections (UTIs). Escherichia coli is the main causative agent of UTIs in both humans and companion animals with multidrug resistant strains such as the globally disseminated ST131 becoming more common. Bacteriophage (phage) are natural predators of bacteria and potentially an alternative therapy. However, a major barrier for phage therapy is the specificity of phage on target bacteria and therefore difficulty efficiently selecting the appropriate phage. Here, we demonstrate a genomics driven approach using machine learning prediction models combined with phage activity clustering to select phage cocktails based only on the genome sequence of the infecting bacterial strain

Old Drugs To Treat Resistant Bugs: Methicillin-Resistant Staphylococcus aureus Isolates with mecC Are Susceptible to a Combination of Penicillin and Clavulanic Acid.

β-Lactam resistance in methicillin-resistant Staphylococcus aureus (MRSA) is mediated by the expression of an alternative penicillin-binding protein 2a (PBP2a) (encoded by mecA) with a low affinity for β-lactam antibiotics. Recently, a novel variant of mecA, known as mecC, was identified in MRSA isolates from both humans and animals. In this study, we demonstrate that mecC-encoded PBP2c does not mediate resistance to penicillin. Rather, broad-spectrum β-lactam resistance in MRSA strains carrying mecC (mecC-MRSA strains) is mediated by a combination of both PBP2c and the distinct β-lactamase encoded by the blaZ gene of strain LGA251 (blaZLGA251), which is part of mecC-encoding staphylococcal cassette chromosome mec (SCCmec) type XI. We further demonstrate that mecC-MRSA strains are susceptible to the combination of penicillin and the β-lactam inhibitor clavulanic acid in vitro and that the same combination is effective in vivo for the treatment of experimental mecC-MRSA infection in wax moth larvae. Thus, we demonstrate how the distinct biological differences between mecA- and mecC-encoded PBP2a and PBP2c have the potential to be exploited as a novel approach for the treatment of mecC-MRSA infections.This work was supported by a Medical Research Council (MRC) Partnership Grant (G1001787/1) held between the Department of Veterinary Medicine, University of Cambridge (M. A. H.), the School of Clinical Medicine, University of Cambridge (S. J. P.), the Moredun Research Institute (R. N. Z.) and the Wellcome Trust Sanger Institute (J. P. and S. J. P.).This is the author accepted manuscript. The final version is available from American Society for Microbiology via http://dx.doi.org/10.1128/AAC.01469-1