Biochemical and structural analysis of the Streptomyces coelicolor Dps proteins.

The three DNA protection proteins from starved cells (Dps) of Streptomyces coelicolor are members of the min-ferritin super family. Considered to be of major importance to stress response systems in microorganisms. Dps proteins can aid microbial survival in extreme conditions. The S. coelicolor Dps proteins are not only induced in response to stress in a stimulus-dependent manner, but dual regulation allows these proteins to play a role in bacterial cell division; influencing condensation of nucleoids during spore formation. This study investigates the structural and functional properties of the ScDps proteins and finds multiple ways in which the homologs differ. (Abstract shortened.

Antibacterial and anti-virulence activity of manuka honey against genetically diverse Staphylococcus pseudintermedius strains

Staphylococcus pseudintermedius causes opportunistic infections in dogs. It also has significant zoonotic potential, with the emergence of multidrug-resistance leading to difficulty treating both animal and human infections. Manuka honey has previously been reported to inhibit many bacterial pathogens including methicillin resistant Staphylococcus aureus and is successfully utilised in both clinical and veterinary practice. Here we evaluated the ability of manuka honey to inhibit strains of S. pseudintermedius growth alone and in combination with antibiotics, and its capacity to modulate virulence within multiple S. pseudintermedius. All 18 of the genetically diverse S. pseudintermedius strains sequenced and tested were inhibited by ≤ 12% (w/v) medical grade manuka honey, although tolerance to five clinically relevant antibiotics was observed. The susceptibility of the isolates to four of these antibiotics was significantly increased (p ≤0.05) when combined with sub lethal concentrations of honey, although sensitivity to oxacillin was decreased. Virulence (DNase, protease and haemolysin) activity was also significantly reduced (p ≤ 0.05) in over half of isolates when cultured with sub lethal concentrations of honey (13, 9 and 10 isolates respectively). These findings highlight the potential for manuka honey to be utilised against S. pseudintermedius infections. Importance: Staphylococcus pseudintermedius is an important member of the skin microbial community in animals and can cause opportunistic infections in both pets and their owners. The high incidence of antimicrobial resistance in S. pseudintermedius highlights that this opportunistic zoonotic pathogen can cause infections which require prolonged and intensive treatment to resolve. Manuka honey has proven efficacy against many bacterial pathogens and is an accepted topical treatment for infections in both veterinary and clinical practice so is a particularly appropriate antimicrobial for use with zoonotic pathogens such as S. pseudintermedius. Here we demonstrate that manuka honey is not only highly potent against novel multi-drug resistant S. pseudintermedius isolates, but also acts synergistically with clinically relevant antibiotics. In addition, manuka honey modulates S. pseudintermedius virulence activity, even at subinhibitory concentrations. In a clinical setting these attributes may assist in controlling infection, allowing a more rapid resolution and reducing antibiotic use

Bayesian identification of bacterial strains from sequencing data

Rapidly assaying the diversity of a bacterial species present in a sample obtained from a hospital patient or an environmental source has become possible after recent technological advances in DNA sequencing. For several applications it is important to accurately identify the presence and estimate relative abundances of the target organisms from short sequence reads obtained from a sample. This task is particularly challenging when the set of interest includes very closely related organisms, such as different strains of pathogenic bacteria, which can vary considerably in terms of virulence, resistance and spread. Using advanced Bayesian statistical modelling and computation techniques we introduce a novel pipeline for bacterial identification that is shown to outperform the currently leading pipeline for this purpose. Our approach enables fast and accurate sequence-based identification of bacterial strains while using only modest computational resources. Hence it provides a useful tool for a wide spectrum of applications, including rapid clinical diagnostics to distinguish among closely related strains causing nosocomial infections. The software implementation is available at https://github.com/PROBIC/BIB.</p

Prospectus, September 9, 1991

https://spark.parkland.edu/prospectus_1991/1012/thumbnail.jp

Prevalence of faecal carriage of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli in veterinary hospital staff and students

This study is the first to investigate prevalence of antimicrobial-resistant (AMR) and ESBL-producing faecal Escherichia coli within 84 veterinary hospital staff and student members across three UK veterinary hospitals. Longitudinal carriage was followed for six weeks in 27 of the participants. MDR E. coli was detection was common (32.1 per cent; 95per cent CI 22.2 to 42.1 per cent) with a notably high prevalence of resistance to ciprofloxacin (11.9 per cent; 95 per cent CI 4.98 to 18.8 per cent). Extended-spectrum β-lactamase (ESBL) producing E coli were isolated from five samples (5.95 per cent: 95 per cent CI 0.89 to 11.0 per cent); two of these samples (E38 and S57) contained MDR ESBL-producing E coli, resistant to all antimicrobials tested. Two participants carried ESBL-producing E coli for the entire study period. Twenty-six participants (96.3 per cent; 95 per cent CI 89.2 to 100) carried ≥1 MDR E coli isolate during the six-week period, with seven participants (25.9 per cent) carrying ≥1 MDR isolate for at least five out of six weeks highlighting that whilst prevalence of ESBL-producing E coli is similar to asymptomatic in general populations, higher levels of carriage were observed longitudinally in our participants. This study highlights that veterinary hospital workers represent a high-risk population for carriage of MDR and ESBL-producing bacteria and that healthcare providers should be made aware of this

Bayesian identification of bacterial strains from sequencing data

Rapidly assaying the diversity of a bacterial species present in a sample obtained from a hospital patient or an environmental source has become possible after recent technological advances in DNA sequencing. For several applications it is important to accurately identify the presence and estimate relative abundances of the target organisms from short sequence reads obtained from a sample. This task is particularly challenging when the set of interest includes very closely related organisms, such as different strains of pathogenic bacteria, which can vary considerably in terms of virulence, resistance and spread. Using advanced Bayesian statistical modelling and computation techniques we introduce a novel pipeline for bacterial identification that is shown to outperform the currently leading pipeline for this purpose. Our approach enables fast and accurate sequence-based identification of bacterial strains while using only modest computational resources. Hence it provides a useful tool for a wide spectrum of applications, including rapid clinical diagnostics to distinguish among closely related strains causing nosocomial infections. The software implementation is available at https://github.com/PROBIC/BIB.Peer reviewe

Quantifying bacterial evolution in the wild : A birthday problem for Campylobacter lineages

Measuring molecular evolution in bacteria typically requires estimation of the rate at which nucleotide changes accumulate in strains sampled at different times that share a common ancestor. This approach has been useful for dating ecological and evolutionary events that coincide with the emergence of important lineages, such as outbreak strains and obligate human pathogens. However, in multi-host (niche) transmission scenarios, where the pathogen is essentially an opportunistic environmental organism, sampling is often sporadic and rarely reflects the overall population, particularly when concentrated on clinical isolates. This means that approaches that assume recent common ancestry are not applicable. Here we present a new approach to estimate the molecular clock rate in Campylobacter that draws on the popular probability conundrum known as the 'birthday problem'. Using large genomic datasets and comparative genomic approaches, we use isolate pairs that share recent common ancestry to estimate the rate of nucleotide change for the population. Identifying synonymous and non-synonymous nucleotide changes, both within and outside of recombined regions of the genome, we quantify clock-like diversification to estimate synonymous rates of nucleotide change for the common pathogenic bacteria Campylobacter colt (2.4 x 10(-6) s/s/y) and Campylobacter jejuni (3.4 x 10(-6) s/s/y). Finally, using estimated total rates of nucleotide change, we infer the number of effective lineages within the sample time frame-analogous to a shared birthday-and assess the rate of turnover of lineages in our sample set over short evolutionary timescales. This provides a generalizable approach to calibrating rates in populations of environmental bacteria and shows that multiple lineages are maintained, implying that large-scale clonal sweeps may take hundreds of years or more in these species.Peer reviewe

Draft Genomes, Phylogenetic Reconstruction, and Comparative Genomics of Two Novel Cohabiting Bacterial Symbionts Isolated from Frankliniella occidentalis

Obligate bacterial symbionts are widespread in many invertebrates, where they are often confined to specialized host cells and are transmitted directly from mother to progeny. Increasing numbers of these bacteria are being characterized but questions remain about their population structure and evolution. Here we take a comparative genomics approach to investigate two prominent bacterial symbionts (BFo1 and BFo2) isolated from geographically separated populations of western flower thrips, Frankliniella occidentalis. Our multifaceted approach to classifying these symbionts includes concatenated multilocus sequence analysis (MLSA) phylogenies, ribosomal multilocus sequence typing (rMLST), construction of whole-genome phylogenies, and in-depth genomic comparisons. We showed that the BFo1 genome clusters more closely to species in the genus Erwinia, and is a putative close relative to Erwinia aphidicola. BFo1 is also likely to have shared a common ancestor with Erwinia pyrifoliae/Erwinia amylovora and the nonpathogenic Erwinia tasmaniensis and genetic traits similar to Erwinia billingiae. The BFo1 genome contained virulence factors found in the genus Erwinia but represented a divergent lineage. In contrast, we showed that BFo2 belongs within the Enterobacteriales but does not group closely with any currently known bacterial species. Concatenated MLSA phylogenies indicate that it may have shared a common ancestor to the Erwinia and Pantoea genera, and based on the clustering of rMLST genes, it was most closely related to Pantoea ananatis but represented a divergent lineage. We reconstructed a core genome of a putative common ancestor of Erwinia and Pantoea and compared this with the genomes of BFo bacteria. BFo2 possessed none of the virulence determinants that were omnipresent in the Erwinia and Pantoea genera. Taken together, these data are consistent with BFo2 representing a highly novel species that maybe related to known Pantoea

Gene pool transmission of multidrug resistance among Campylobacter from livestock, sewage and human disease

The use of antimicrobials in human and veterinary medicine has coincided with a rise in antimicrobial resistance (AMR) in the food-borne pathogens Campylobacter jejuni and Campylobacter coli. Faecal contamination from the main reservoir hosts (livestock, especially poultry) is the principal route of human infection but little is known about the spread of AMR among source and sink populations. In particular, questions remain about how Campylobacter resistomes interact between species and hosts, and the potential role of sewage as a conduit for the spread of AMR. Here, we investigate the genomic variation associated with AMR in 168 C. jejuni and 92 C. coli strains isolated from humans, livestock and urban effluents in Spain. AMR was tested in vitro and isolate genomes were sequenced and screened for putative AMR genes and alleles. Genes associated with resistance to multiple drug classes were observed in both species and were commonly present in multidrug-resistant genomic islands (GIs), often located on plasmids or mobile elements. In many cases, these loci had alleles that were shared among C. jejuni and C. coli consistent with horizontal transfer. Our results suggest that specific antibiotic resistance genes have spread among Campylobacter isolated from humans, animals and the environment.S.K.S., B.P. and S.C.B. were supported by grants from the Medical Research Council (MR/L015080/1), the Wellcome Trust (088786/C/09/Z), the Food Standards Agency (FS246004) and the Biotechnology and Biological Sciences Research Council (BB/I02464X/1). E.M. received a University of Bath Faculty of Science URSA studentship. D.F.C. is supported by the FPI program (BES-2013-065003) from the Spanish Ministry of Economy and Competitiveness. J.K.C. is supported by a BBSRC KTN PhD studentship (BB/P504750/1)

Genomic tailoring of autogenous poultry vaccines to reduce Campylobacter from farm to fork

Campylobacter is a leading cause of food-borne gastroenteritis worldwide, linked to the consumption of contaminated poultry meat. Targeting this pathogen at source, vaccines for poultry can provide short-term caecal reductions in Campylobacter numbers in the chicken intestine. However, this approach is unlikely to reduce Campylobacter in the food chain or human incidence. This is likely as vaccines typically target only a subset of the high genomic strain diversity circulating among chicken flocks, and rapid evolution diminishes vaccine efficacy over time. To address this, we used a genomic approach to develop a whole-cell autogenous vaccine targeting isolates harbouring genes linked to survival outside of the host. We hyper-immunised a whole major UK breeder farm to passively target offspring colonisation using maternally-derived antibody. Monitoring progeny, broiler flocks revealed a near-complete shift in the post-vaccination Campylobacter population with an ~50% reduction in isolates harbouring extra-intestinal survival genes and a significant reduction of Campylobacter cells surviving on the surface of meat. Based on these findings, we developed a logistic regression model that predicted that vaccine efficacy could be extended to target 65% of a population of clinically relevant strains. Immuno-manipulation of poultry microbiomes towards less harmful commensal isolates by competitive exclusion, has major potential for reducing pathogens in the food production chain