Mutation frequency of non-ESBL phenotype SENTRY (Asia-Pacific) isolates of Klebsiella pneumoniae conversion to an ESBL positive phenotype

Extended spectrum β-lactamases or ESBLs, which are derived from non-ESBL precursors by point mutation of β-lactamase genes (bla), are spreading rapidly all over the world and have caused considerable problems in the treatment of infections caused by bacteria which harbour them. The mechanism of this resistance is not fully understood and a better understanding of these mechanisms might significantly impact on choosing proper diagnostic and treatment strategies. Previous work on SHV β-lactamase gene, blaSHV, has shown that only Klebsiella pneumoniae strains which contain plasmid-borne blaSHV are able to mutate to phenotypically ESBL-positive strains and there was also evidence of an increase in blaSHV copy number. Therefore, it was hypothesised that although specific point mutation is essential for acquisition of ESBL activity, it is not yet enough, and blaSHV copy number amplification is also essential for an ESBL-positive phenotype, with homologous recombination being the likely mechanism of blaSHV copy number expansion. In this study, we investigated the mutation rate of non-ESBL expressing K. pneumoniae isolates to an ESBL-positive status by using the MSS-maximum likelihood method. Our data showed that blaSHV mutation rate of a non-ESBL expressing isolate is lower than the mutation rate of the other single base changes on the chromosome, even with a plasmid-borne blaSHV gene. On the other hand, mutation rate from a low MIC ESBL-positive (≤ 8 µg/mL for cefotaxime) to high MIC ESBL-positive (≥16 µg/mL for cefotaxime) is very high. This is because only gene copy number increase is needed which is probably mediated by homologous recombination that typically takes place at a much higher frequencies than point mutations. Using a subinhibitory concentration of novobiocin, as a homologous recombination inhibitor, revealed that this is the case.

Microbial risk from rainwater tanks in South East Queensland

Quantitative Microbial Risk Assessment (QMRA) analysis was used to quantify the risk of infection associated with the exposure to pathogens from potable and non-potable uses of roof-harvested rainwater in South East Queensland (SEQ). A total of 84 rainwater samples were analysed for the presence of faecal indicators (using culture based methods) and zoonotic bacterial and protozoan pathogens using binary and quantitative PCR (qPCR). The concentrations of Salmonella invA, and Giardia lamblia β-giradin genes ranged from 65-380 genomic units/1000 mL and 9-57 genomic units/1000 mL of water, respectively. After converting gene copies to cell/cyst number, the risk of infection from G. lamblia and Salmonella spp. associated with the use of rainwater for bi-weekly garden hosing was calculated to be below the threshold value of 1 extra infection per 10,000 persons per year. However, the estimated risk of infection from drinking the rainwater daily was 44-250 (for G. lamblia) and 85-520 (for Salmonella spp.) infections per 10,000 persons per year. Since this health risk seems higher than that expected from the reported incidences of gastroenteritis, the assumptions used to estimate these infection risks are critically discussed. Nevertheless, it would seem prudent to disinfect rainwater for potable use.

Signs, symptoms and comorbidities in contact lens-related microbial keratitis

Purpose: The aim of this study was to characterize the clinical signs, symptoms, and ocular and systemic comorbidities in a large case series of contact lens-related microbial keratitis. Methods: Two hundred ninety-seven cases of contact lens-related microbial keratitis, aged between 15 and 64 years were detected through surveillance of hospital and community based ophthalmic practitioners in Australia and New Zealand. Full clinical data were available for 190 cases and 90 were interviewed by telephone. Clinical data included the size, location, and degree of anterior chamber response. Symptom data were available from the practitioner and from participant self-report. Associations between symptoms and disease severity were evaluated. Data on ocular and systemic disease were collected from participants and practitioners. The frequency of comorbidities was compared between the different severities of disease and to population norms. Results: More severe disease was associated with greater symptom severity and pain was the most prevalent symptom reported. Ninety-one percent of cases showed progression of ocular symptoms after lens removal, and symptom progression was associated with all severities of disease. Twenty-five percent of cases reported prior episodes requiring emergency attention. Thyroid disease (p 0.05) and self-reported poor health (p 0.001) were more common in cases compared with age-matched population norms. Discussion: Information on the signs, symptoms, and comorbidities associated with contact lens-related microbial keratitis may be useful in patient education and for practitioners involved in the fitting of lenses and management of complications. Although pain was the most common symptom experienced, progression of symptoms despite lens removal was close to universal. Poor general health, particularly respiratory disease and thyroid disease was more common in cases than in the general population, which may prompt practitioners to recommend flexibility in wear schedules when in poor health or the selection of a lower risk wear schedule in at risk patients

Culture independent analysis of greyback canegrub-associated microflora and microbial community comparison using subtractive hybridisation

Greyback canegrubs cost the Australian sugarcane industry around $13 million per annum in damage and control. A novel and cost effective biocontrol bacterium could play an important role in the integrated pest management program currently in place to reduce damage and control associated costs. During the course of this project, terminal restriction fragment length polymorphism (TRFLP), 16-S rDNA cloning, suppressive subtractive hybridisation (SSH) and entomopathogen-specific PCR screening were used to investigate the little studied canegrub-associated microflora in an attempt to discover novel pathogens from putatively-diseased specimens. Microflora associated with these soil-dwelling insects was found to be both highly diverse and divergent between individual specimens. Dominant members detected in live specimens were predominantly from taxa of known insect symbionts while dominant sequences amplified from dead grubs were homologous to putativelysaprophytic bacteria and bacteria able to grow during refrigeration. A number of entomopathogenic bacteria were identified such as Photorhabdus luminescens and Pseudomonas fluorescens. Dead canegrubs prior to decomposition need to be analysed if these bacteria are to be isolated. Novel strategies to enrich putative pathogen-associated sequences (SSH and PCR screening) were shown to be promising approaches for pathogen discovery and the investigation of canegrubsassociated microflora. However, due to inter- and intra-grub-associated community diversity, dead grub decomposition and PCR-specific methodological limitations (PCR bias, primer specificity, BLAST database restrictions, 16-S gene copy number and heterogeneity), recommendations have been made to improve the efficiency of such techniques. Improved specimen collection procedures and utilisation of emerging high-throughput sequencing technologies may be required to examine these complex communities in more detail. This is the first study to perform a whole-grub analysis and comparison of greyback canegrub-associated microbial communities. This work also describes the development of a novel V3-PCR based SSH technique. This was the first SSH technique to use V3-PCR products as a starting material and specifically compare bacterial species present in a complex community.

Grassland management and conversion into grassland: effects on soil carbon

Grasslands are heavily relied upon for food and forage production. A key component for sustaining production in grassland ecosystems is the maintenance of soil organic matter (SOM), which can be strongly influenced by management. Many management techniques intended to increase forage production may potentially increase SOM, thus sequestering atmospheric carbon (C). Further, conversion from either cultivation or native vegetation into grassland could also sequester atmospheric carbon. We reviewed studies examining the influence of improved grassland management practices and conversion into grasslands on soil C worldwide to assess the potential for C sequestration. Results from 115 studies containing over 300 data points were analyzed. Management improvements included fertilization (39%), improved grazing management (24%), conversion from cultivation (15%) and native vegetation (15%), sowing of legumes (4%) and grasses (2%), earthworm introduction (1%), and irrigation (1%). Soil C content and concentration increased with improved management in 74% of the studies, and mean soil C increased with all types of improvement. Carbon sequestration rates were highest during the first 40 yr after treatments began and tended to be greatest in the top 10 cm of soil. Impacts were greater in woodland and grassland biomes than in forest, desert, rain forest, or shrubland biomes. Conversion from cultivation, the introduction of earthworms, and irrigation resulted in the largest increases. Rates of C sequestration by type of improvement ranged from 0.11 3.04 Mg C.ha(-1) yr(-1), with a mean of 0.54 Mg C.ha(-1).yr(-1) and were highly influenced by biome type and climate. We conclude that grasslands can act as a significant carbon sink with the implementation of improved management.

Health risk from the use of roof-harvested rainwater in Southeast Queensland, Australia, as potable or nonpotable water, determined using quantitative microbial risk assessment

A total of 214 rainwater samples from 82 tanks were collected in urban Southeast Queensland (SEQ) in Australia and analysed for the zoonotic bacterial and protozoan pathogen using real-time binary PCR and quantitative PCR (qPCR). Quantitative Microbial Risk Assessment (QMRA) analysis was used to quantify the risk of infection associated with the exposure to potential pathogens from potable and non-potable uses of roof-harvested rainwater. Of the 214 samples tested, 10.7%, 9.8%, and 5.6%, and 0.4% samples were positive for Salmonella invA, Giardia lamblia β-giardin , Legionella pneumophila mip, and Campylobacter jejuni mapA genes. Cryptosporidium parvum could not be detected. The estimated numbers of viable Salmonella spp., G. lamblia β-giradin, and L. pneumophila genes ranged from 1.6 × 101 to 9.5 × 101 cells, 1.4 × 10-1 to 9.0 × 10-1 cysts, and 1.5 × 101 to 4.3 × 101 per 1000 ml of water, respectively. Six risk scenarios were considered from exposure to Salmonella spp., G. lamblia and L. pneumophila. For Salmonella spp., and G. lamblia, these scenarios were: (1) liquid ingestion due to drinking of rainwater on a daily basis (2) accidental liquid ingestion due to garden hosing twice a week (3) aerosol ingestion due to showering on a daily basis, and (4) aerosol ingestion due to hosing twice a week. For L. pneumophila, these scenarios were: (5) aerosol inhalation due to showering on a daily basis, and (6) aerosol inhalation due to hosing twice a week. The risk of infection from Salmonella spp., G. lamblia, and L. pneumophila associated with the use of rainwater for showering and garden hosing was calculated to be well below the threshold value of one extra infection per 10,000 persons per year in urban SEQ. However, the risk of infection from ingesting Salmonella spp. and G. lamblia via drinking exceeds this threshold value, and indicates that if undisinfected rainwater were ingested by drinking, then the gastrointestinal diseases of Salmonellosis and Giardiasis is expected to range from 5.0 × 100 to 2.8 × 101 (Salmonellosis) and 1.0 × 101 to 6.4 × 101 (Giardiasis) cases per 10,000 persons per year, respectively. Since this health risk seems higher than that expected from the reported incidences of gastroenteritis, the assumptions used to estimate these infection risks are critically examined. Nonetheless, it would seem prudent to disinfect rainwater for potable use.

Networked aquatic microbial observing systems: An overview

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Ability of silver-impregnated contact lenses to control microbial growth and colonisation

Purpose: To examine the ability of silver nano-particles to prevent the growth of Pseudomonas aeruginosa and Staphylococcus aureus in solution or when adsorbed into contact lenses. To examine the ability of silver nano-particles to prevent the growth of Acanthamoeba castellanii. ----- ----- Methods: Etafilcon A lenses were soaked in various concentrations of silver nano-particles. Bacterial cells were then exposed to these lenses, and numbers of viable cells on lens surface or in solution compared to etafilcon A lenses not soaked in silver. Acanthamoeba trophozoites were exposed to silver nano-particles and their ability to form tracks was examined. ----- ----- Results: Silver nano-particle containing lenses reduced bacterial viability and adhesion. There was a dose-dependent response curve, with 10 ppm or 20 ppm silver showing > 5 log reduction in bacterial viability in solution or on the lens surface. For Acanthamoeba, 20 ppm silver reduced the ability to form tracks by approximately 1 log unit. ----- ----- Conclusions: Silver nanoparticles are effective antimicrobial agents, and can reduce the ability of viable bacterial cells to colonise contact lenses once incorporated into the lens.----- ----- Resumen: Objetivos: Examinar la capacidad de las nanopartículas de plata para prevenir el crecimiento de Pseudomonas aeruginosa y Staphylococcus aureus en soluciones para lentes de contacto o cuando éstas las adsorben. Examinar la capacidad de las nanopartículas de plata para prevenir el crecimiento de Acanthamoeba castellanii.----- ----- Métodos: Se sumergieron lentes etafilcon A en diversas concentraciones de nanopartículas de plata. Las células bacterianas fueron posteriormente expuestas a dichas lentes, y se compararon cantidades de células viables en la superficie de la lente o en la solución con las presentes en lentes etafilcon A que no habían sido sumergidas en plata. Trofozoítos de Acanthamoeba fueron expuestos a nanopartículas de plata y se examinó su capacidad para formar quistes.----- ----- Resultados: Las lentes que contienen nanopartículas de plata redujeron la viabilidad bacteriana y la adhesión. Hubo una curva de respuesta dependiente de la dosis, en la que 10 ppm o 20 ppm de plata mostró una reducción logarítmica > 5 en la viabilidad bacteriana tanto en la solución como en la superficie de la lente. Para Acanthamoeba, 20 ppm de plata redujeron la capacidad de formar quistes en aproximadamente 1 unidad logarítmica.----- ----- Conclusiones: Las nanopartículas de plata son agentes antimicrobianos eficaces y pueden reducir la capacidad de células bacterianas viables para colonizar las lentes de contacto una vez que se han incorporado en la lente.

Incorporating parameter uncertainty into quantitative microbial risk assessment (QMRA)

Modern statistical models and computational methods can now incorporate uncertainty of the parameters used in Quantitative Microbial Risk Assessments (QMRA). Many QMRAs use Monte Carlo methods, but work from fixed estimates for means, variances and other parameters. We illustrate the ease of estimating all parameters contemporaneously with the risk assessment, incorporating all the parameter uncertainty arising from the experiments from which these parameters are estimated. A Bayesian approach is adopted, using Markov Chain Monte Carlo Gibbs sampling (MCMC) via the freely available software, WinBUGS. The method and its ease of implementation are illustrated by a case study that involves incorporating three disparate datasets into an MCMC framework. The probabilities of infection when the uncertainty associated with parameter estimation is incorporated into a QMRA are shown to be considerably more variable over various dose ranges than the analogous probabilities obtained when constants from the literature are simply ‘plugged’ in as is done in most QMRAs. Neglecting these sources of uncertainty may lead to erroneous decisions for public health and risk management.

The conversion of lignocellulosics to levulinic acid

Biomass represents an abundant and relatively low cost carbon resource that can be utilized to produce platform chemicals such as levulinic acid. Current processing technology limits the cost-effective production of levulinic acid in commercial quantities from biomass. The key to improving the yield and effi ciency of levulinic acid production from biomass lies in the ability to optimize and isolate the intermediate products at each step of the reaction pathway and reduce re-polymerization and side reactions. New technologies (including the use of microwave irradiation and ionic liquids) and the development of highly selective catalysts would provide the necessary step change for the optimization of key reactions. A processing environment that allows the use of biphasic systems and/or continuous extraction of products would increase reaction rates, yields and product quality. This review outlines the chemistry of levulinic acid synthesis and discusses current and potential technologies for producing levulinic acid from lignocellulosics.