Within-host evolution of Staphylococcus aureus during asymptomatic carriage

Background Staphylococcus aureus is a major cause of healthcare associated mortality, but like many important bacterial pathogens, it is a common constituent of the normal human body flora. Around a third of healthy adults are carriers. Recent evidence suggests that evolution of S. aureus during nasal carriage may be associated with progression to invasive disease. However, a more detailed understanding of within-host evolution under natural conditions is required to appreciate the evolutionary and mechanistic reasons why commensal bacteria such as S. aureus cause disease. Therefore we examined in detail the evolutionary dynamics of normal, asymptomatic carriage. Sequencing a total of 131 genomes across 13 singly colonized hosts using the Illumina platform, we investigated diversity, selection, population dynamics and transmission during the short-term evolution of S. aureus. Principal Findings We characterized the processes by which the raw material for evolution is generated: micro-mutation (point mutation and small insertions/deletions), macro-mutation (large insertions/deletions) and the loss or acquisition of mobile elements (plasmids and bacteriophages). Through an analysis of synonymous, non-synonymous and intergenic mutations we discovered a fitness landscape dominated by purifying selection, with rare examples of adaptive change in genes encoding surface-anchored proteins and an enterotoxin. We found evidence for dramatic, hundred-fold fluctuations in the size of the within-host population over time, which we related to the cycle of colonization and clearance. Using a newly-developed population genetics approach to detect recent transmission among hosts, we revealed evidence for recent transmission between some of our subjects, including a husband and wife both carrying populations of methicillin-resistant S. aureus (MRSA). Significance This investigation begins to paint a picture of the within-host evolution of an important bacterial pathogen during its prevailing natural state, asymptomatic carriage. These results also have wider significance as a benchmark for future systematic studies of evolution during invasive S. aureus disease.

Targeting Staphylococcus aureus quorum sensing with non-peptidic small molecule inhibitors

A series of 3-oxo-C12-HSL, tetramic acid and tetronic acid analogues was synthesized to gain insights into the structural requirements for quorum sensing inhibition in Staphylococcus aureus. Compounds active against agr were non-competitive inhibitors of the auto-inducing peptide (AIP)-activated AgrC receptor, by altering the activation efficacy of the cognate AIP-1. They appeared to act as negative allosteric modulators and are exemplified by 3-tetradecanoyltetronic acid 17 which reduced nasal cell colonization and arthritis in a murine infection model.

Prediction of Staphylococcus aureus antimicrobial resistance by whole-genome sequencing

Whole-genome sequencing (WGS) could potentially provide a single platform for extracting all the information required to predict an organism’s phenotype. However, its ability to provide accurate predictions has not yet been demonstrated in large independent studies of specific organisms. In this study, we aimed to develop a genotypic prediction method for antimicrobial susceptibilities. The whole genomes of 501 unrelated Staphylococcus aureus isolates were sequenced, and the assembled genomes were interrogated using BLASTn for a panel of known resistance determinants (chromosomal mutations and genes carried on plasmids). Results were compared with phenotypic susceptibility testing for 12 commonly used antimicrobial agents (penicillin, methicillin, erythromycin, clindamycin, tetracycline, ciprofloxacin, vancomycin, trimethoprim, gentamicin, fusidic acid, rifampin, and mupirocin) performed by the routine clinical laboratory. We investigated discrepancies by repeat susceptibility testing and manual inspection of the sequences and used this information to optimize the resistance determinant panel and BLASTn algorithm. We then tested performance of the optimized tool in an independent validation set of 491 unrelated isolates, with phenotypic results obtained in duplicate by automated broth dilution (BD Phoenix) and disc diffusion. In the validation set, the overall sensitivity and specificity of the genomic prediction method were 0.97 (95% confidence interval [95% CI], 0.95 to 0.98) and 0.99 (95% CI, 0.99 to 1), respectively, compared to standard susceptibility testing methods. The very major error rate was 0.5%, and the major error rate was 0.7%. WGS was as sensitive and specific as routine antimicrobial susceptibility testing methods. WGS is a promising alternative to culture methods for resistance prediction in S. aureus and ultimately other major bacterial pathogens.

Mobile elements drive recombination hotspots in the core genome of Staphylococcus aureus

Horizontal gene transfer is an important driver of bacterial evolution, but genetic exchange in the core genome of clonal species, including the major pathogen Staphylococcus aureus, is incompletely understood. Here we reveal widespread homologous recombination in S. aureus at the species level, in contrast to its near-complete absence between closely related strains. We discover a patchwork of hotspots and coldspots at fine scales falling against a backdrop of broad-scale trends in rate variation. Over megabases, homoplasy rates fluctuate 1.9-fold, peaking towards the origin-of-replication. Over kilobases, we find core recombination hotspots of up to 2.5-fold enrichment situated near fault lines in the genome associated with mobile elements. The strongest hotspots include regions flanking conjugative transposon ICE6013, the staphylococcal cassette chromosome (SCC) and genomic island νSaα. Mobile element-driven core genome transfer represents an opportunity for adaptation and challenges our understanding of the recombination landscape in predominantly clonal pathogens, with important implications for genotype–phenotype mapping.

Staphylococcus aureus MnhF mediates cholate efflux and facilitates survival under human colonic conditions

Resistance to the innate defences of the intestine is crucial for the survival and carriage of Staphylococcus aureus, a common coloniser of the human gut. Bile salts produced by the liver and secreted into the intestines are one such group of molecules with potent anti-microbial activity. The mechanisms by which S. aureus is able to resist such defences in order to colonize and survive in the human gut are unknown. Here we show that mnhF confers resistance to bile salts, which can be abrogated by efflux pump inhibitors. MnhF mediates efflux of radiolabelled cholic acid in both S. aureus and when heterologously expressed in Escherichia coli, rendering them resistant. Deletion of mnhF attenuated survival of S. aureus in an anaerobic three stage continuous culture model of the human colon (gut model), which represent different anatomical areas of the large intestine.

Susceptibility of Staphylococcus aureus to porphyrin-mediated photodynamic antimicrobial chemotherapy: an in vitro study

The ability of Staphylococcus aureus to develop multidrug resistance is well documented, and the antibiotic resistance showed by an increasing number of bacteria has shown the need for alternative therapies to treat infections, photodynamic therapy (PDT) being a potential candidate. The aim of this study was to determine the effect of photodynamic therapy as a light-based bactericidal modality to eliminate Staphylococcus aureus. The study investigated a technique based on a combination of light and a photosensitizer that is capable of producing oxidative species to induce a cytotoxic effect. A Staphylococcus aureus suspension was exposed to a light emitting diode (LED) emitting at 628 nm, 14.6 mW/cm(2), and energy density of 20J/cm(2), 40J/cm(2), or 60 J/cm(2) in the presence of different porphyrin concentrations (PhotogemA (R)). Three drug concentrations were employed: 12 mu l/ml, 25 mu l/ml, and 50 mu l/ml. The treatment response was evaluated by the number of bacterial colony forming units (CFU) after light exposure. The results indicated that exposure to 60 J/cm(2) eliminated 100% (10 log(10) scales) of bacteria, on average. The best PDT response rate to eliminate Staphylococcus aureus was achieved with exposure to LED light in combination with the photosensitizer at concentrations ranging from 25 mu l/ml to 50 mu l/ml. These data suggest that PDT has the potential to eliminate Staphylococcus aureus in suspension and indicates the necessary drug concentration and light fluency.

The Physiological, Enzymatic, and Genetic Characterization of Staphylococcus sp. Chromium (VI) Reductase Function

A strain of Staphylococcus isolated by Dr. Fekete at the Sandia National Laboratory toxic metal dumping site in Sandia, New Mexico. has been found to reduce toxic Cr(VI) to the less toxic Cr(IlI) state. We have ascertained the environmental parameters for optimal bacterial growth and Cr(VI) reduction. This knowledge may be employed in a comprehensive bioremediation scheme designed to accelerate natural reparation of that Sandia ecosystem. In addition we have investigated the genetic and enzymatic basis for this Cr(VI) reducing ability. This information may allow us to create more effective bioremediation schemes based on the comprehensive knowledge of enzyme and gene function. Preliminary investigations have been carried out toward this end which may serve as the basis for a more thorough investigation.

Avaliação da estabilidade fisico-química da solução de hipoclorito de sódio a 0,5% utilizada pela FarmaUSCS, e de sua eficácia bactericida sobre Staphylococcus aureus e Escherichia coli

A FarmaUSCS é um projeto de extensão do curso de Farmácia da Universidade Municipal de São Caetano do Sul, que tem por finalidade manipular e dispensar medicamentos para a comunidade, além de servir de campo de estágio e de desenvolvimento de projetos de pesquisa. O presente trabalho teve por objetivo avaliar a estabilidade físico-química da solução aquosa de hipoclorito de sódio a 0,5%, utilizada para a desinfecção de ambientes produtivos na FarmaUSCS, bem como sua eficácia como agente bactericida sobre Staphylococcus aureus e Escherichia coli. Para a estabilidade físico-química, amostras da solução foram submetidas a diferentes condições ambientais e determinado o teor de hipoclorito por iodometria. A eficácia do desinfetante foi realizada pela técnica da diluição em tubos. Em nenhuma das condições ambientais testadas, houve degradação do teor de hipoclorito de sódio. A solução aquosa de hipoclorito de sódio a 0,5% foi eficaz diante de S. aureus e E. coli, já a partir do tempo mínimo testado de 2,5 minutos de exposição.

Sobrevivência de Escherichia coli,Staphylococcus aureus e Salmonella Enteritidis durante o armazenamento de hambúrguer de frango

Com o objetivo de avaliar a sobrevivência ao congelamento de microrganismos potencialmente patogênicos, hambúrgueres de frango foram contaminados com Escherichia coli (ECHC), Staphylococcus aureus (SAFH) e Salmonella Enteritidis (SE86) e armazenados a -18ºC. Os mesmos microrganismos e ainda E. coli ATCC 25972, S. aureus ATCC 25923, and S. Enteritidis ATCC 13076 também foram inoculados em água peptonada 0,1% e congelados a -18ºC, a fim de avaliar um possível efeito protetor dos componentes do hambúrguer sobre os microrganismos. A quantificação dos microrganismos foi realizada nos intervalos de 0, 1, 2, 3, 4, 7, 14, 21 e 28 dias de congelamento. Com o propósito de estudar as alterações nos ácidos graxos das células microbianas expostas ao congelamento, foram extraídos os ácidos graxos de cada bactéria, congelada e não congelada, e estes foram analisados por cromatografia gasosa. Os resultados demonstraram que, de modo geral, houve uma redução média de menos de 1 unidade logarítmica (log10) no número de células artificialmente inoculadas em hambúrgueres de frango. As reduções obtidas para cada microrganismo em água peptonada 0,1% foram significativamente (P0,05) maiores do que as reduções observadas em hambúrguer de frango, sugerindo a existência de um efeito crioprotetor dos componentes do hambúrguer. Em todos os experimentos, as reduções mais expressivas foram observadas nas primeiras semanas de congelamento. Ocorreram alterações expressivas na composição de ácidos graxos de S. aureus (SAFH) e S. aureus ATCC 25923, o que pode indicar que estes microrganismos alteraram a composição dos seus ácidos graxos como resposta ao estresse causado pelo congelamento.

Avaliação da redução da sensibiladade de Staphylococcus aureus à vancomicina no Hospital de Clínicas de Porto Alegres

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Detecção de bactérias no ar em ambiente hospitalar com recurso a técnicas moleculares

A Qualidade do Ar Interior (QAI) revela-se de grande importância no ambiente hospitalar devido à disseminação aérea de bactérias potenciar as infecções nosocomiais. Os estudos nesta temática são raros em Portugal e inexistentes na Madeira. Este trabalho tem como objectivos identificar com elevada precisão a flora bacteriana aerosolizada no Hospital Dr. João de Almada (HJA) utilizando técnicas moleculares, determinar a sua origem, disseminação e especificidades e analisar globalmente a QAI. O ar exterior e de 15 locais no interior do HJA foi amostrado em Abril de 2009. Foram medidas a temperatura, humidade e concentração de CO2 e NO2 e quantificadas as bactérias e fungos no ar. Utilizaram-se testes bioquímicos e técnicas moleculares para caracterização e identificação de bactérias e foram comparadas comunidades bacterianas. A biodiversidade bacteriana no ar interior do HJA é dominada pelo género Staphylococcus (68%), sendo as espécies mais frequentes S. cohnii urealyticus, S. haemolyticus, S. capitis ou S. caprae e Micrococcus luteus. A maioria das espécies encontradas é comum em ambiente hospitalar e na flora comensal humana. As Staphylococcus spp. detectadas são consideradas patogénicas oportunistas envolvidas em infecções nosocomiais. A QAI é conforme com a legislação na maioria dos locais, havendo microorganismos em excesso em 12 das 72 amostras. O excesso de fungos relacionou-se com eventos de bruma no exterior e o excesso de bactérias correlacionou-se com a actividade humana e foi potenciado pela fraca ventilação e a presença ou manipulação de materiais contaminados. O ar exterior tem boa qualidade para ventilação do HJA, excepto durante eventos de bruma. As comunidades bacterianas aerosolizadas têm maior similaridade entre locais do mesmo tipo, sendo os ocupantes o principal foco de contaminação. São propostas medidas correctivas como o aumento da ventilação dos locais com elevada actividade humana e cuidados na manipulação de roupa suja e resíduos.

Caracterização fenotípica e genotípica de Staphylococcus aureus resistentes à meticilina isolados na cidade do Natal/RN

Staphylococcus aureus resistente à meticilina (MRSA) é um dos principais agentes de infecções associadas a serviços de saúde em todo o mundo. No Brasil, há a predominância de um clone de MRSA multirresistente denominando clone epidêmico brasileiro (CEB). Entretanto, novos clones nãomultirresistentes com alta virulência têm sido descritos em infecções comunitárias e hospitalares. O objetivo desse estudo foi realizar a caracterização fenotípica e genotípica de cepas de MRSA isoladas na cidade do Natal/RN. Inicialmente avaliamos 60 amostras de S. aureus quanto a resistência à meticilina através de diferentes técnicas fenotípicas, utilizando a detecção do gene mecA por PCR como padrão. O antibiograma de todas as cepas foi realizado utilizando 12 antimicrobianos conforme descrito pelo CLSI. As cepas de MRSA foram caracterizadas geneticamente através da tipagem do cassete cromossômico estafilocócico mec (SCCmec) e da eletroforese em campo elétrico alternado (PFGE). Dos 60 S. aureus estudados, 45 foram resistentes à meticilina. Observamos que para algumas cepas de MRSA os testes de triagem em ágar com 6μg/mL de oxacilina e difusão em meio sólido com oxacilina-1μg apresentaram dificuldades na sua interpretação. No entanto, todas as 45 amostras de MRSA, foram facilmente detectadas pelos testes com o disco de cefoxitina-30μg e pesquisa da PBP2a. A análise molecular das cepas de MRSA mostrou 8 padrões distintos de PFGE (A-H), com predominância do padrão A (73%), relacionado ao CEB. Estas carreavam o SCCmec tipo IIIA, e apresentaram uma considerável variedade de subtipos (A1-A16). Cinco cepas de MRSA portando SCCmec IV também foram xiv identificadas, três delas relacionadas geneticamente ao clone USA800 (Padrão B). Destas cinco, três (2 padrão F e 1 padrão B) foram altamente susceptíveis as drogas testadas, entretanto, dois outros isolados, padrão B, apresentaram multirresistência. As amostras restantes pertenciam a padrões de PFGE distintos dos clones internacionais predominantes em nosso continente. Para realização deste projeto de pesquisa, a metodologia exigiu a interação com pesquisadores de áreas como: infectologia, microbiologia e biologia molecular. Portanto, esta dissertação apresentou um caráter de multidisciplinaridade e transdiciplinaridade no seu desenvolvimento

Fluorescent amplified fragment length polymorphism genotyping of human and animal Staphylococcus aureus isolates from dairy farms with manual milking

Fluorescence amplified fragment length polymorphism (fAFLP) was used to assess the genetic relatedness of 40 Staphylococcus aureus strains isolated from human and animal skin samples in seven dairy farms with manual milking. S. aureus was isolated from 11 out of 30 (36%) human skin samples and from 29 out of 100 (29%) teat skin samples from apparently healthy cows. Genomic DNA from each isolate was double-digested with EcoRI and MseI and complementary oligonucleotide adaptors were ligated to the restriction fragments. Pre-selective and selective, amplification reactions were performed, the amplified fragments were separated by electrophoresis in an ABI377 sequencer and analysed using GeneScan 3.1 and Genotyper 2.5. Three single isolates (a-c), a predominant cluster with 35 isolates (d) and another cluster with two isolates (e) were identified. Both clusters d and e included human and animal isolates genetically related, because the profiles had 90-100% homology. Since no cluster was comprised uniquely of human or animal isolates and given the close genetic relatedness among human and animal samples in the farms, the present findings support the. hypothesis that dairy workers can spread S. aureus through manual milking. (C) 2005 Elsevier B.V. All rights reserved.