Compassionate Use of Cefiderocol as Adjunctive Treatment of Native Aortic Valve Endocarditis Due to Extremely Drug-resistant Pseudomonas aeruginosa

Serious infections such as endocarditis due to extremely drug-resistance gram-negative bacteria are an increasing challenge. Here, we present successful adjunctive use of cefiderocol for a patient with persistently bacteremic healthcare-associated native aortic valve endocarditis due to an extended-spectrum beta-lactamase-positive Pseudomonas aeruginosa susceptible in vitro only to colistin, following failure of conventional therapeutic options.

Genetic Diversity and Antimicrobial Drug Resistance of Serotype VI Group B Streptococcus, Canada

Two genetically dissimilar sequence type 1 clades dominate the serotype VI group B Streptococcus population of strains causing invasive disease in Canada. Isolates of this rare serotype, recovered mainly from adult patients, were all susceptible to penicillin and vancomycin. However, we observed resistance to erythromycin and clindamycin.

Ultraviolet inactivation of bacteria and model viruses in coconut water using a collimated beam system

This study investigated the effect of ultraviolet-C irradiation on the inactivation of microorganisms in coconut water, a highly opaque liquid food (1.01 ± 0.018 absorption coefficient). Ultraviolet-C inactivation kinetics of two bacteriophages (MS2, T1UV) and three surrogate bacteria (Escherichia coli, Salmonella Typhimurium, Listeria monocytogenes) in 0.1% (w/v) peptone and coconut water were investigated. Ultraviolet-C irradiation at 254 nm was applied to stirred samples, using a collimated beam device. A series of known ultraviolet-C doses (0-40 mJ cm^-2) were applied for ultraviolet-C treatment except for MS2 where higher doses were delivered (100 mJ cm^-2). Inactivation levels of all organisms were proportional to ultraviolet-C dose. At the highest dose of 40 mJ cm^-2, three surrogates of pathogenic bacteria were inactivated by more than 5-log₁₀ (p < 0.05) in 0.1% (w/v) peptone and coconut water. Results showed that ultraviolet-C irradiation effectively inactivated bacteriophage and surrogate bacteria in highly opaque coconut water. The log reduction kinetics of microorganisms followed log-linear and exponential models with higher R² (>0.95) and low root mean square error values. The D₁₀ values of 3, 5.48, and 4.58 mJ cm^-2 were obtained from the inactivation of E. coli, S. Typhimurium, and L. monocytogenes, respectively. Models for predicting log reduction as a function of ultraviolet-C irradiation dose were found to be significant (p < 0.05). Fluid optics were the key controlling parameters for efficient microbial inactivation. Therefore, the ultraviolet-C dose must be calculated not only from the incident ultraviolet-C intensity but must also consider the attenuation in the samples. The results from this study imply that adequate log reduction of vegetative cells and model viruses is achievable in coconut water and suggested significant potential for ultraviolet-C treatment of other liquid foods.

Extended-spectrum β-lactamase in the rectal flora of patients undergoing transrectal prostate biopsy: a study of the prevalence in a major metropolitan hospital

OBJECTIVES

To determine the prevalence of extended-spectrum β-lactamase (ESBL) in patients undergoing transrectal prostate biopsy, to assess the incidence of postoperative sepsis, to correlate the development of sepsis with the presence of preoperative ESBL on rectal swabs, and to assess the adequacy of prophylactic antibiotic guidelines in the context of local ESBL prevalence.

METHODS

Patients undergoing transrectal ultrasonography (TRUS)-guided biopsy at the Royal Melbourne Hospital between January 2012 and July 2016 had rectal swabs taken immediately prior to TRUS with specific cultures to identify the presence of ESBL. Patients were given a prophylactic antibiotic, 500 mg oral ciprofloxacin, 1 h before the TRUS procedure. Data were collected prospectively, with retrospective review of all readmitted patient files and audit data to ensure complete capture of events.

RESULTS

A total of 387 TRUS-guided biopsy procedures were performed. Rectal swabs were correctly collected in 352 patients (91%). The median patient age was 65 years. In all, 25 (7%) ESBL-positive swabs were identified. Most ESBL were Escherichia coli. Half (50%) of ESBL were resistant to ciprofloxacin and all were sensitive to meropenem. A small increase in ESBL prevalence over time was not significant (R² = 0.35). Four patients (1.1%) were readmitted with sepsis; ESBL Pseudomonas had previously grown in one patient, but sepsis was attributable to non-ESBL E. coli. In one of the readmitted patients ESBL E. coli was present, but this patient did not have ESBL preoperatively. There were no deaths or high-dependency/intensive care unit admissions.

CONCLUSIONS

This study represents the largest Australian series to investigate ESBL prevalence, and reveals a rate lower than that of many other nations. Our sepsis rate is lower than many international series, perhaps because of our low ESBL rate and strict antibiotic prophylaxis. Preoperative swab results did not predict postoperative sepsis, and the process was therefore not useful for guiding antibiotic therapy. In this patient population, TRUS biopsy, with ciprofloxacin prophylaxis, remains a safe option for diagnostic prostate biopsy.

Egg Protein Transferrin-Derived Peptides IRW and IQW Regulate Citrobacter rodentium-Induced, Inflammation-Related Microbial and Metabolomic Profiles

Bioactive peptides that target the gastrointestinal tract can strongly affect the health of animals and humans. This study aimed to evaluate the abilities of two peptides derived from egg albumin transferrin, IRW and IQW, to treat enteritis in a mouse model of Citrobacter rodentium-induced colitis by evaluating serum metabolomics and gut microbes. Forty-eight mice were randomly assigned to six groups: basal diet (CTRL), intragastric administration Citrobacter rodentium (CR), basal diet with 0.03%IRW (IRW), CR with 0.03% IRW (IRW+CR), basal diet with 0.03%IQW (IQW) and CR with 0.03% IQW (IQW+CR). CR administration began on day 10 and continued for 7 days. After 14 days of IRW and IQW treatment, serum was collected and subjected to a metabolomics analysis. The length and weight of each colon were measured, and the colon contents were collected for 16srRNA sequencing. The colons were significantly longer in the CR group, compared to the CTRL group. A serum metabolomics analysis revealed no significant difference in microbial diversity between the six groups. Compared with the CTRL group, the proportions of Firmicutes and Actinobacteria species decreased significantly and the proportions of Bacteroidetes and Proteobacteria species increased in the CR group. There were no significant differences between the CTRL and other groups. The serum metabolomics analysis revealed that Infected by CR increased the levels of oxalic acid, homogentisic acid and prostaglandin but decreased the levels of L-glutamine, L-acetyl carnitine, 1-methylhistidine and gentisic acid. Therefore, treatment with IRW and IQW was shown to regulate the intestinal microorganisms associated with colonic inflammation and serum metabolite levels, thus improving intestinal health.

The Beneficial and Debilitating Effects of Environmental and Microbial Toxins, Drugs, Organic Solvents and Heavy Metals on the Onset and Progression of Multiple Sclerosis

Multiple sclerosis (MS), a chronic inflammatory disease of the central nervous system is common amongst young adults, leading to major personal and socioeconomic burdens. However, it is still considered complex and challenging to understand and treat, in spite of the efforts made to explain its etiopathology. Despite the discovery of many genetic and environmental factors that might be related to its etiology, no clear answer was found about the causes of the illness and neither about the detailed mechanism of these environmental triggers that make individuals susceptible to MS. In this review, we will attempt to explore the major contributors to MS autoimmunity including genetic, epigenetic and ecological factors with a particular focus on toxins, chemicals or drugs that may trigger, modify or prevent MS disease.

Mixotrophy in nanoflagellates across environmental gradients in the ocean

Mixotrophy, the combination of autotrophic and heterotrophic nutrition, is a common trophic strategy among unicellular eukaryotes in the ocean. There are a number of hypotheses about the conditions that select for mixotrophy, and field studies have documented the prevalence of mixotrophy in a range of environments. However, there is currently little evidence for how mixotrophy varies across environmental gradients, and whether empirical patterns support theoretical predictions. Here I synthesize experiments that have quantified the abundance of phototrophic, mixotrophic, and heterotrophic nanoflagellates, to ask whether there are broad patterns in the prevalence of mixotrophy (relative to pure autotrophy and heterotrophy), and to ask whether observed patterns are consistent with a trait-based model of trophic strategies. The data suggest that mixotrophs increase in abundance at lower latitudes, while autotrophs and heterotrophs do not, and that this may be driven by increased light availability. Both mixotrophs and autotrophs increase greatly in productive coastal environments, while heterotrophs increase only slightly. These patterns are consistent with a model of resource competition in which nutrients and carbon can both limit growth and mixotrophs experience a trade-off in allocating biomass to phagotrophy vs. autotrophic functions. Importantly, mixotrophy is selected for under a range of conditions even when mixotrophs experience a penalty for using a generalist trophic strategy, due to the synergy between photosynthetically derived carbon and prey-derived nutrients. For this reason mixotrophy is favored relative to specialist strategies by increased irradiance, while at the same time increased nutrient supply increases the competitive ability of mixotrophs against heterotrophs.

Innovative Seizure of Metal/Metal Oxide Nanoparticles in Water Purification: A Critical Review of Potential Risks

Water contamination is a worldwide critical issue for the present society to avoid competition and maintain an environmentally friendly scenario. Removal of various pollutants including inorganic and organic compounds from water is a big challenge nowadays. Worldwide attention to promote polluted water and technologies related to its treatment has been adversely increased. The utilization of metal/metal oxide nanoparticles (NPs) for this purpose has gained much attention due to its exceptional properties imparted by reduced size and effective surface area. Moreover, metal/metal oxide NPs-based innovation for improved expulsion productivity is an ingenious area for research and development but the use of such NPs presents some serious risks. Herein, the advanced requisition of NPs for polluted water treatment is highlighted along with the difficulties related to them and their toxic impacts when used as water purifiers. Additionally, the plausible fate of metal/metal oxide NPs incorporated in the water for purification and salient future challenges are deliberated.

Antibiotic Resistance Policy and the Stewardship Role of the Nurse

Government policy, at all levels, should reflect current scientific evidence to curb the spread of multidrug-resistant organisms (MDROs) and to promote healthier lives for citizens and the global community. The World Health Organization estimates that approximately 63,000 Americans die annually of infections from MDROs. Annual spending in the United States used to combat MDRO infections surpassed $35 billion in 2015. This article is a review of U.S. policy regarding MDROs and focuses on several means with which nurses can implement antibiotic stewardship within their practices to stall the creation and global spread of antibiotic-resistant organisms. Nurses are vital to successfully implementing methods of antibiotic stewardship as they are at the center of multidisciplinary health care teams and have the greatest direct patient contact of all members within the team. Methods of antibiotic stewardship include limiting the use of antibiotics within animal husbandry industries, promotion of health care policy in line with antibiotic stewardship standards, and adopting more stringent clinical prescribing practices of antibiotics used in human therapies. Application of these improvements to U.S. federal, state, and local facility policies is in line with current scientific evidence and will provide a framework for cohesive partnerships with nations and institutions abroad that also struggle with the spread of MDROs in their own communities.

Coconut Bio-yoghurt Phytochemical-chemical and Antimicrobial-microbial Activities

BACKGROUND AND OBJECTIVE

Coconut flour is known to be highly nutritious flour and contains high dietary fiber. The aim of this study was to make "bio-yoghurt beverage grafted with coconut flour and containing probiotic bacteria which is recommended as a functional milk product.

MATERIALS AND METHODS

Chemical, phytochemical studies and antimicrobial activity have been performed on coconut flour which was used to make the beverage. Bio-yoghurt beverages made with different ratios of coconut flour (0, 2, 4 and 6%) were chemical, microbiological and sensory tested when fresh and during storage for 15 days of cold storage.

RESULTS

Chemical composition of coconut flour showed reasonable contents of moisture, ash, fat, fatty acids, protein, crude fiber, total solids, total phenols and antioxidants. Coconut flour showed antibacterial activity against some foodborne pathogenic bacteria. The addition of coconut flour to make bio-yoghurt beverages increased its contents of total solids, protein, ash, fiber, acidity, antioxidant activity, total phenols, improved yoghurt sensory and rheological properties especially when probiotic bacteria were used. The results did not reveal any significant differences (p>0.05), between the bacterial counts of yoghurt starter culture, Lactobacillus rhamnosus, Lactobacillus casei in yoghurt control (without coconut) and bio-yoghurt treatments (with coconut), during cold storage. Moulds and yeasts were not detected in all bio-yoghurt treatments; meanwhile they appeared in yoghurt control after 15 days indicating coconut antifungal activity and subsequently a period of time to save more for this drink. All bio-yoghurt beverages with different ratios of coconut flour were sensory accepted and showed more favorable properties, particularly for the viscosity.

CONCLUSION

A new functional dairy product of bio-yoghurt beverage contain coconut flour high fiber content was prepared with probiotic bacteria and showed good chemical, microbiological and sensory/rheological properties.

Impartiality and infectious disease: Prioritizing individuals versus the collective in antibiotic prescription

BACKGROUND

Antimicrobial resistance (AMR) is a global public health disaster driven largely by antibiotic use in human health care. Doctors considering whether to prescribe antibiotics face an ethical conflict between upholding individual patient health and advancing public health aims. Existing literature mainly examines whether patients awaiting consultations desire or expect to receive antibiotic prescriptions, but does not report views of the wider public regarding conditions under which doctors should prescribe antibiotics. It also does not explore the ethical significance of public views or their sensitivity to awareness of AMR risks or the standpoint (self-interested or impartial) taken by participants.

METHODS

An online survey was conducted with a sample of the U.S. public (n = 158). Participants were asked to indicate what relative priority should be given to individual patients and society-at-large from various standpoints and in various contexts, including antibiotic prescription.

RESULTS

Of the participants, 50.3% thought that doctors should generally prioritize individual patients over society, whereas 32.0% prioritized society over individual patients. When asked in the context of AMR, 39.2% prioritized individuals whereas 45.5% prioritized society. Participants were significantly less willing to prioritize society over individuals when they themselves were the patient, both in general (p = .001) and in relation to AMR specifically (p = .006).

CONCLUSIONS

Participants' attitudes were more oriented to society and sensitive to collective responsibility when informed about the social costs of antibiotic use and when considered from a third-person rather than first-person perspective. That is, as participants came closer to taking the perspective of an informed and impartial "ideal observer," their support for prioritizing society increased. Our findings suggest that, insofar as antibiotic policies and practices should be informed by attitudes that are impartial and well-informed, there is significant support for prioritizing society.

Weak Iron Oxidation by Sulfobacillus thermosulfidooxidans Maintains a Favorable Redox Potential for Chalcopyrite Bioleaching

Bioleaching is an emerging technology, describing the microbially assisted dissolution of sulfidic ores that provides a more environmentally friendly alternative to many traditional metal extraction methods, such as roasting or smelting. Industrial interest is steadily increasing and today, circa 15-20% of the world's copper production can be traced back to this method. However, bioleaching of the world's most abundant copper mineral chalcopyrite suffers from low dissolution rates, often attributed to passivating layers, which need to be overcome to use this technology to its full potential. To prevent these passivating layers from forming, leaching needs to occur at a low oxidation/reduction potential (ORP), but chemical redox control in bioleaching heaps is difficult and costly. As an alternative, selected weak iron-oxidizers could be employed that are incapable of scavenging exceedingly low concentrations of iron and therefore, raise the ORP just above the onset of bioleaching, but not high enough to allow for the occurrence of passivation. In this study, we report that microbial iron oxidation by Sulfobacillus thermosulfidooxidans meets these specifications. Chalcopyrite concentrate bioleaching experiments with S. thermosulfidooxidans as the sole iron oxidizer exhibited significantly lower redox potentials and higher release of copper compared to communities containing the strong iron oxidizer Leptospirillum ferriphilum. Transcriptomic response to single and co-culture of these two iron oxidizers was studied and revealed a greatly decreased number of mRNA transcripts ascribed to iron oxidation in S. thermosulfidooxidans when cultured in the presence of L. ferriphilum. This allowed for the identification of genes potentially responsible for S. thermosulfidooxidans' weaker iron oxidation to be studied in the future, as well as underlined the need for new mechanisms to control the microbial population in bioleaching heaps.

Review: The application of omics to rumen microbiota function

Rumen microbiome profiling uses 16S rRNA (18S rRNA, internal transcribed spacer) gene sequencing, a method that usually sequences a small portion of a single gene and is often biased and varies between different laboratories. Functional information can be inferred from this data, but only for those that are closely related to known annotated species, and even then may not truly reflect the function performed within the environment being studied. Genome sequencing of isolates and metagenome-assembled genomes has now reached a stage where representation of the majority of rumen bacterial genera are covered, but this still only represents a portion of rumen microbial species. The creation of a microbial genome (bins) database with associated functional annotations will provide a consistent reference to allow mapping of RNA-Seq reads for functional gene analysis from within the rumen microbiome. The integration of multiple omic analytics is linking functional gene activity, metabolic pathways and rumen metabolites with the responsible microbiota, supporting our biological understanding of the rumen system. The application of these techniques has advanced our understanding of the major microbial populations and functional pathways that are used in relation to lower methane emissions, higher feed efficiencies and responses to different feeding regimes. Continued and more precise use of these tools will lead to a detailed and comprehensive understanding of compositional and functional capacity and design of techniques for the directed intervention and manipulation of the rumen microbiota towards a desired state.

The physiochemical properties and shelf-life of orange-fleshed sweet potato puree composite bread

Value addition of orange-fleshed sweet potato (OFSP) increases diversified utilization of this crop, which is rich in provitamin A carotenoids. OFSP bread, in which 30%-45% of wheat flour is replaced with OFSP puree, has been successfully commercialized in Kenya. However, the effect of this substitution on the bread's physiochemical properties and its shelf-life are currently unknown. This study was designed to determine the physiochemical properties and shelf-life of OFSP puree-wheat flour composite bread (30% puree), compared to standard, 100% wheat flour, bread. Freshly baked bread samples were stored at 7, 20, 25, and 30°C, and monitored for moisture content, water activity, color, texture, volume, carotenoids, and microbial load. The moisture content, β-carotene content, and color of bread significantly decreased with increase in storage temperature and time (p < 0.05). Bread made with OFSP puree had a longer shelf-life, showing spoilage on day six compared with the white bread, which spoiled on the fourth day. This is attributed to the significantly higher water activity in white bread than in the OFSP bread. The substitution of wheat with OFSP puree resulted in reduced extensibility of gluten, thus, specific volume of white bread was significantly (p < 0.05) higher than that in OFSP puree bread. Refrigeration increased crumb firmness, chewiness and cohesiveness in both types of bread. In conclusion, OFSP puree increases the water binding capacity of the bread, which reduces water activity and increases its shelf-life.

Urine cultures and antibiotics for urinary tract infections in Dutch general practice

BACKGROUND

Urinary tract infections (UTIs) are common in general practice, and antibiotic resistance is often seen. Urine cultures are advised by the Dutch national UTI guideline for patients at high risk of UTI complications. Prudent use of antibiotics and taking into account national guidelines and urine culture results are important to combat antibiotic resistance in general practice.

AIM

To identify subgroups of UTI patients in which the use of urine cultures and antibiotic prescriptions deviates from the national guidelines.

METHODS

We investigated associations of several characteristics with urine culture orders in patients with UTI in 2015 from seven Dutch general practices (n=1295). These included subgroups at risk for UTI complications, comorbidities, age and history of UTI recurrence. In addition, we assessed the level of adherence to the guideline for antibiotic prescriptions in subgroups at risks for UTI complications.

FINDINGS

Urine cultures were ordered in 17% (n=221) of patients, more frequently in high-risk patients (32%) than in low-risk patients (7%), for UTI complications (OR=6.4; 95% CI 4.6-9.0). In low-risk patients, 91% received antibiotics that were recommended in the guideline. For high-risk patients this percentage ranged widely, and was particularly low in the risk groups with signs of tissue invasion (29-50%). Diagnostic and therapeutic adequacy can still be improved by increasing the adherence to the guideline in UTI patients at high risk for complications. This may contribute to containing antibiotic resistance in UTI by ordering urine cultures and use the results to adjust prescriptions to antibiotic susceptibility of the uropathogen.

Releasing the "GENI": integrating authentic microbial genomics research into the classroom through GENI-ACT

The integration of genomics research into the undergraduate biology curriculum provides students with the opportunity to become familiar with bioinformatics tools and answer original research questions. Our purpose with this research project was to upscale the research experience through integration with classroom experience giving students access to authentic research projects. Students annotated 60 predicted ABC genes of Methanothermobacter thermautotrophicus and Methanobacterium sp. SWAN-1, and they were required to present a research poster to demonstrate their understanding of the project. During this research project a number of tests, assessments and surveys were conducted to assess familiarity with technical and conceptual understanding of genome annotation, satisfaction with annotation instruction, gain in bioinformatics research skills, scientific communications skills and increased student interest in research. We found that students gained significant skills in bioinformatics, specifically genome annotation skills and also gained confidence in their abilities to carry out scientific research. As a result of this authentic undergraduate research experience under-represented students were motivated to pursue future careers in STEM fields.

Emerging Opportunities for Synthetic Biology in Agriculture

Rapid expansion in the emerging field of synthetic biology has to date mainly focused on the microbial sciences and human health. However, the zeitgeist is that synthetic biology will also shortly deliver major outcomes for agriculture. The primary industries of agriculture, fisheries and forestry, face significant and global challenges; addressing them will be assisted by the sector’s strong history of early adoption of transformative innovation, such as the genetic technologies that underlie synthetic biology. The implementation of synthetic biology within agriculture may, however, be hampered given the industry is dominated by higher plants and mammals, where large and often polyploid genomes and the lack of adequate tools challenge the ability to deliver outcomes in the short term. However, synthetic biology is a rapidly growing field, new techniques in genome design and synthesis, and more efficient molecular tools such as CRISPR/Cas9 may harbor opportunities more broadly than the development of new cultivars and breeds. In particular, the ability to use synthetic biology to engineer biosensors, synthetic speciation, microbial metabolic engineering, mammalian multiplexed CRISPR, novel anti microbials, and projects such as Yeast 2.0 all have significant potential to deliver transformative changes to agriculture in the short, medium and longer term. Specifically, synthetic biology promises to deliver benefits that increase productivity and sustainability across primary industries, underpinning the industry’s prosperity in the face of global challenges.

Pathophysiology of diverticular disease

Inflammation of diverticula, or outpouchings of the colonic mucosa and submucosa through the muscularis layer, leads to diverticulitis. The development of diverticular disease, encompassing both diverticulosis and diverticulitis, is a result of genetic predisposition, lifestyle, and environmental factors, including the microbiome. Areas covered: Previous reports implicated genetic predisposition, environmental factors, and colonic dysmotility in diverticular disease. Recent studies have associated specific host immune responses and the microbiome as contributors to diverticulitis. To review pertinent literature describing pathophysiological factors associated with diverticulosis or diverticulitis, we searched the PubMed database (March 2018) for articles considering the role of colonic architecture, genetic predisposition, environment, colonic motility, immune response, and the microbiome. Expert commentary: In the recent years, research into the molecular underpinnings of diverticular disease has enhanced our understanding of diverticular disease pathogenesis. Although acute uncomplicated diverticulitis is treated with broad spectrum antibiotics, evaluation of the microbiome has been limited and requires further comprehensive studies. Evidence suggests that a deregulation of the host immune response is associated with both diverticulosis and diverticulitis. Further examining these pathways may reveal proteins that can be therapeutic targets or aid in identifying biological determinants of clinical or surgical decision making.

Deficient Phagocytosis Among HIV-1 Infected Adults Over Time Even in HAART Setting

BACKGROUND

Phagocytosis is regarded to be impaired in HIV-1 infected adults, leading to high frequency and severity of several infections in this population. Data is contradictory with regards to individual facets in HIV infection.

OBJECTIVE

Aim of this study was to assess the phagocytic activity during the natural course of HIV infection.

METHOD

It is a longitudinal study assessing natural course and impairment of neutrophil and monocyte phagocytosis in both naïve and HAART treated patients.

RESULTS

A lower neutrophil phagocytic activity was recorded in naïve patients compared to treated patients. Interestingly, a downward trend of neutrophil phagocytic activity was recorded in both groups, irrespectively of HAART intake, within 48 weeks of observation.

CONCLUSION

Defects of innate immunity appear to be present in HIV infected patients regarding phagocytic activity of monocytes and of neutrophils which seems to decline over time. These deficiencies are influenced by the levels of CD4 cell counts and viral load.

Dehalogenases: From Improved Performance to Potential Microbial Dehalogenation Applications

The variety of halogenated substances and their derivatives widely used as pesticides, herbicides and other industrial products is of great concern due to the hazardous nature of these compounds owing to their toxicity, and persistent environmental pollution. Therefore, from the viewpoint of environmental technology, the need for environmentally relevant enzymes involved in biodegradation of these pollutants has received a great boost. One result of this great deal of attention has been the identification of environmentally relevant bacteria that produce hydrolytic dehalogenases—key enzymes which are considered cost-effective and eco-friendly in the removal and detoxification of these pollutants. These group of enzymes catalyzing the cleavage of the carbon-halogen bond of organohalogen compounds have potential applications in the chemical industry and bioremediation. The dehalogenases make use of fundamentally different strategies with a common mechanism to cleave carbon-halogen bonds whereby, an active-site carboxylate group attacks the substrate C atom bound to the halogen atom to form an ester intermediate and a halide ion with subsequent hydrolysis of the intermediate. Structurally, these dehalogenases have been characterized and shown to use substitution mechanisms that proceed via a covalent aspartyl intermediate. More so, the widest dehalogenation spectrum of electron acceptors tested with bacterial strains which could dehalogenate recalcitrant organohalides has further proven the versatility of bacterial dehalogenators to be considered when determining the fate of halogenated organics at contaminated sites. In this review, the general features of most widely studied bacterial dehalogenases, their structural properties, basis of the degradation of organohalides and their derivatives and how they have been improved for various applications is discussed.

A Novel Herbal Formulation versus Chlorhexidine Mouthwash in Efficacy against Oral Microflora

Aims and Objectives:

The aim of the study was to compare and to analyze the antimicrobial efficacy of 0.12% chlorhexidine and new formulated herbal mouthwash after using for 14 days. The objective was to signify whether the noval herbal combination could be a better alternative mouthwash to Chlorhexidine (CHX).

Materials and Methods:

This is a double-blinded, random controlled research study conducted in the Department of Oral Pathology and Microbiology. A total of 200 dental students were selected randomly, comprising of two groups, 100 in each, aged between 18 and 22 years with gingival index of score II. The first group was advised to oral rinse with 0.12% chlorhexidine mouthwash and the second group with new formulated herbal mouthwash for 14 days. Saliva samples were collected on the day 0 (baseline), followed by day 7 and 14 and microbial colony count was performed. The data obtained was statistically analyzed using SPSS version 16. Student's t-test was applied for comparison of the mean microbial count between the two groups. Repeated measures analysis of variance followed by Tukey's post hoc test was applied to assess the changes from day 0 to day 7 to day 14. The statistical significance level was set at P < 0.05.

Results:

Microbial colonies were reduced better in chlorhexidine group on the day 7 whereas, on day 14, greater reduction was observed in the herbal group in both gender groups with high statistical significance (P < 0.001).

Conclusions:

Herbal mouthwash formulation performed effectively well on long-term usage, could be used as an alternative mouthwash to overcome the disadvantages of chlorhexidine.

SIPSim: A Modeling Toolkit to Predict Accuracy and Aid Design of DNA-SIP Experiments

DNA Stable isotope probing (DNA-SIP) is a powerful method that links identity to function within microbial communities. The combination of DNA-SIP with multiplexed high throughput DNA sequencing enables simultaneous mapping of in situ assimilation dynamics for thousands of microbial taxonomic units. Hence, high throughput sequencing enabled SIP has enormous potential to reveal patterns of carbon and nitrogen exchange within microbial food webs. There are several different methods for analyzing DNA-SIP data and despite the power of SIP experiments, it remains difficult to comprehensively evaluate method accuracy across a wide range of experimental parameters. We have developed a toolset (SIPSim) that simulates DNA-SIP data, and we use this toolset to systematically evaluate different methods for analyzing DNA-SIP data. Specifically, we employ SIPSim to evaluate the effects that key experimental parameters (e.g., level of isotopic enrichment, number of labeled taxa, relative abundance of labeled taxa, community richness, community evenness, and beta-diversity) have on the specificity, sensitivity, and balanced accuracy (defined as the product of specificity and sensitivity) of DNA-SIP analyses. Furthermore, SIPSim can predict analytical accuracy and power as a function of experimental design and community characteristics, and thus should be of great use in the design and interpretation of DNA-SIP experiments.

Biodiversity and Microbial Resistance of Lactobacilli Isolated From the Traditional Greek Cheese Kopanisti

Kopanisti is a Greek artisan cheese produced from raw milk in the island of Mykonos, Greece. The milk is left to rest for 12–24 h and then the rennet is added. After its formation the curd is left to drain for 2–3 days and is ready either for consumption (as tyrovolia fresh cheese), or with the addition of extra salt, the curd is left to ripen through further fermentation and surface development of Penicillium fungi, aprocess leading to the production of the traditional Greek cheese Kopanisti. From 120 samples of kopanisti, 574 Lactobacillus strains were isolated, distributed in 17 species (16 of them isolated from tyrovolia as well). Strains from 15 species were found resistant or multiresistant against 15 antimicrobial agents, representing all categories of antibiotics. Analysis revealed that the resistance was moderated during ripening of the curd from tyrovolia to Kopanisti. Resistance against penicillin G, ampicillin/sulbactam, clindamycin, chloramphenicol, streptomycin, trimethoprim, metronidazole, vancomycin, teichoplanin, and quinupristin/dalvopristin was significantly enhanced, while the resistance against ampicillin, erythromycin, oxytetracycline, gentamycin, and fucidic acid was significantly reduced. These changes during ripening suggest that resistance to antimicrobials is a dynamic process subjected to environmental factors. The biodiversity of isolated Lactobacillus strains is impressive and explains the exquisite sensorial characteristics of the cheese. However, the extent of the resistance is alarming.

Adaptive Designs for Clinical Trials: Application to Healthcare Epidemiology Research

Clinical trials with adaptive designs use data that accumulate during the course of the study to modify study elements in a prespecified manner. The goal is to provide flexibility such that a trial can serve as a definitive test of its primary hypothesis, preferably in a shorter time period, involving fewer human subjects, and at lower cost. Elements that may be modified include the sample size, end points, eligible population, randomization ratio, and interventions. Accumulating data used to drive these modifications include the outcomes, subject enrollment (including factors associated with the outcomes), and information about the application of the interventions. This review discusses the types of adaptive designs for clinical trials, emphasizing their advantages and limitations in comparison with conventional designs, and opportunities for applying these designs to healthcare epidemiology research, including studies of interventions to prevent healthcare-associated infections, combat antimicrobial resistance, and improve antimicrobial stewardship.

The 24th Annual Midwest Microbial Pathogenesis Meeting

The 24th Annual Midwest Microbial Pathogenesis Conference (MMPC) was held at the University of Notre Dame from August 25-27, 2017. The conference provided an opportunity for scientists from the Midwest to discuss new advances in microbial pathogenesis, including how pathogens promote disease, and how they interact with each other, the microbiome and the host. This commentary highlights the MMPC history, the topics presented at the conference and the reports in this issue.

Assessment of heavy metals and microbial contamination of gari from Liberia

Cassava is a staple mostly eaten in the form of gari, after rice in Liberia. The local method of gari processing often leads to product contamination, thus, a study was done to assess the heavy metals and microbial contamination of gari in eight counties of the country. A total of sixty-one gari samples were collected and packaged in an airtight polyethylene bag for analyses, using standard methods. Results depict that the mean of the heavy metals in the gari samples is iron (Fe) 43.87 ppm, copper (Cu) 0.94 ppm, zinc (Zn) 5.49 ppm and aluminum (Al) 257.45 ppm. Yellow gari had the highest Fe (64.90 ppm), Cu (1.25 ppm) and Zn (7.85 ppm) content, but with the least Al content (87.15 ppm). The Fe content was lower in groundnut-fortified gari (42.93 ppm), and the Cu (0.70 ppm) and Zn (3.50 ppm) content were lower in groundnut-moringa-fortified gari. The samples and counties have no significant statistical effect (p > .05) on the heavy metals composition of the products. No microbial growth was observed in groundnut-fortified and groundnut-moringa-fortified gari but with coconut-fortified gari having the highest total fungi count of 800 CFU/g. The major fungi identified in the gari samples are Penicillium and Aspergillus spps., but with their counts within the regulated level. Therefore, the gari consumed in Liberia are safe except for the high Fe and Al content, which needs to be addressed with the use of unpainted stainless steel materials as food contact surfaces.

Microbial Degradation Behavior in Seawater of Polyester Blends Containing Poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) (PHBHHx)

The microbial degradation behavior of poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) (PHBHHx) and its compound with several polyesters such as poly(butylene adipate-co-telephtharate) (PBAT), poly(butylene succinate) (PBS), and polylactic acid (PLA) in seawater was tested by a biological oxygen demand (BOD) method. PHBHHx showed excellent biodegradation in seawater in this study. In addition, the biodegradation rate of several blends was much influenced by the weight ratio of PHBHHx in their blends and decreased in accordance with the decrement of PHBHHX ratio. The surface morphology of the sheet was important factor for controlling the biodegradation rate of PHBHHx-containing blends in seawater.

A Haloalkane Dehalogenase from a Marine Microbial Consortium Possessing Exceptionally Broad Substrate Specificity

The haloalkane dehalogenase enzyme DmmA was identified by marine metagenomic screening. Determination of its crystal structure revealed an unusually large active site compared to those of previously characterized haloalkane dehalogenases. Here we present a biochemical characterization of this interesting enzyme with emphasis on its structure-function relationships. DmmA exhibited an exceptionally broad substrate specificity and degraded several halogenated environmental pollutants that are resistant to other members of this enzyme family. In addition to having this unique substrate specificity, the enzyme was highly tolerant to organic cosolvents such as dimethyl sulfoxide, methanol, and acetone. Its broad substrate specificity, high overexpression yield (200 mg of protein per liter of cultivation medium; 50% of total protein), good tolerance to organic cosolvents, and a broad pH range make DmmA an attractive biocatalyst for various biotechnological applications.IMPORTANCE We present a thorough biochemical characterization of the haloalkane dehalogenase DmmA from a marine metagenome. This enzyme with an unusually large active site shows remarkably broad substrate specificity, high overexpression, significant tolerance to organic cosolvents, and activity under a broad range of pH conditions. DmmA is an attractive catalyst for sustainable biotechnology applications, e.g., biocatalysis, biosensing, and biodegradation of halogenated pollutants. We also report its ability to convert multiple halogenated compounds to corresponding polyalcohols.

Demystifying Dysbiosis: Can the Gut Microbiome Promote Oral Tolerance Over IgE-mediated Food Allergy?

The growing burden of food allergy is being driven by environmental exposures and the potential role of gut micro-organisms (or 'microbiota') is hotly debated. Early culture-based studies outlined that imbalances between commensal gut constituents ('dysbiosis') early in life may raise the risk of developing allergic disease. A number of studies using animal models describe mechanisms by which specific bacterial taxa within the gut microbiota, their diversity and dietary substrates such as fibre may promote oral tolerance. Next-generation sequencing now allows the detailed characterization of the microbiota in relation to epidemiological exposures and clinical food allergy status in humans. Faecal samples from one birth cohort characterized for food allergy status have been sequenced and showed less gut microbiota richness amongst three month infants who later developed food sensitization at one year. A large cross-sectional survey of young children with milk allergy showed that greater gut microbiota diversity and enrichment of Clostridia and Firmicutes phyla during early infancy is associated with greater likelihood of out-growing milk allergy by eight years of age. Case control studies are limited to selecting participants from amongst hospital patients and have only allowed comparison of heterogeneous groups. To assess whether infants' gut microbiota may predispose towards the development of food allergy, cohort studies must be undertaken to evaluate gut microbiota development from early in infancy and prospectively characterise patterns according to whether challenge proven food allergy later develops, whilst adjusting for atopic dermatitis, dietary and antibiotic exposures.

Impacts of Irradiation Sources on Quality Attributes of Low-salt Sausage during Refrigerated Storage

This study was performed to investigate the impacts of irradiation sources on quality attributes of low-salt sausage during refrigerated storage. Control sausage was prepared with 1.5% sodium chloride (NaCl), whereas low-salt sausage was formulated with 0.75% NaCl (a 50% reduction; L-control). Sausage samples were vacuum-packaged, and low-sausages were irradiated with gamma-ray, electron-beam and X-ray at 5 kGy, respectively. The samples were stored at 4°C for 28 d to determine changes in quality attributes. The pH of low-salt sausages was unaffected by irradiation at 5 kGy (p>0.05). Higher redness values were found at irradiated low-salt sausages compared to control (p<0.05). The hardness, gumminess and chewiness of control sausage were higher than those of low-salt sausages (p<0.05). However, there were no significant differences in the textural parameters between low-salt sausage treatments. The overall sensory acceptability score of irradiated/low-salt sausages were lower than L-control due to decreased scores for cooked meat flavor but increased radiolytic off-flavor (p<0.05). The initial 2-thiobarbituric acid-reactive substances (TBARS) values of irradiated/low-salt sausages were higher than control and L-control (p<0.05). However, the TBARS values of irradiated treatments were significantly lower than control at the end of storage. Irradiation could effectively inhibit the microorganism growth (total aerobic bacteria, coliforms, Enterobacteriaceae, and Pseudomonas spp.) in low-salt sausages (p<0.05). Therefore, our findings show that irradiation could be to improve microbial safety of low-salt sausages, and suggest that further studies should be necessary to reducing radiolytic off-flavor of irradiated/low-salt sausages.

Protective roles of intestinal microbiota derived short chain fatty acids in Alzheimer's disease-type beta-amyloid neuropathological mechanisms

BACKGROUND

Dietary fibers are metabolized by gastrointestinal (GI) bacteria into short-chain fatty acids (SCFAs). We investigated the potential role of these SCFAs in β-amyloid (Aβ) mediated pathological processes that play key roles in Alzheimer's disease (AD) pathogenesis.

RESEARCH DESIGN AND METHODS

Multiple complementary assays were used to investigate individual SCFAs for their dose-responsive effects in interfering with the assembly of Aβß1-40 and Aβ1-42 peptides into soluble neurotoxic Aβ aggregates.

RESULTS

We found that several select SCFAs are capable of potently inhibiting Aβ aggregations, in vitro.

CONCLUSION

Our studies support the hypothesis that intestinal microbiota may help protect against AD, in part, by supporting the generation of select SCFAs, which interfere with the formation of toxic soluble Aβ aggregates.

Microbial acceleration of aerobic pyrite oxidation at circumneutral pH

Pyrite (FeS₂ ) is the most abundant sulfide mineral on Earth and represents a significant reservoir of reduced iron and sulfur both today and in the geologic past. In modern environments, oxidative transformations of pyrite and other metal sulfides play a key role in terrestrial element partitioning with broad impacts to contaminant mobility and the formation of acid mine drainage systems. Although the role of aerobic micro-organisms in pyrite oxidation under acidic-pH conditions is well known, to date there is very little known about the capacity for aerobic micro-organisms to oxidize pyrite at circumneutral pH. Here, we describe two enrichment cultures, obtained from pyrite-bearing subsurface sediments, that were capable of sustained cell growth linked to pyrite oxidation and sulfate generation at neutral pH. The cultures were dominated by two Rhizobiales species (Bradyrhizobium sp. and Mesorhizobium sp.) and a Ralstonia species. Shotgun metagenomic sequencing and genome reconstruction indicated the presence of Fe and S oxidation pathways in these organisms, and the presence of a complete Calvin-Benson-Bassham CO₂ fixation system in the Bradyrhizobium sp. Oxidation of pyrite resulted in thin (30-50 nm) coatings of amorphous Fe(III) oxide on the pyrite surface, with no other secondary Fe or S phases detected by electron microscopy or X-ray absorption spectroscopy. Rates of microbial pyrite oxidation were approximately one order of magnitude higher than abiotic rates. These results demonstrate the ability of aerobic microbial activity to accelerate pyrite oxidation and expand the potential contribution of micro-organisms to continental sulfide mineral weathering around the time of the Great Oxidation Event to include neutral-pH environments. In addition, our findings have direct implications for the geochemistry of modern sedimentary environments, including stimulation of the early stages of acid mine drainage formation and mobilization of pyrite-associated metals.

Estrategia de control de la resistencia bacteriana a los antimicrobianos en Argentina

La aceleración observada en las últimas décadas sobre la emergencia y diseminación de la resistencia a los antimicrobianos está vinculada al abuso y/o mal uso de los antimicrobianos. En 2014, el Ministerio de Salud de Argentina, junto a otros organismos e instituciones, implementó una estrategia nacional para el control de la resistencia a los antimicrobianos con el objetivo de retrasar o impedir la emergencia y diseminación de bacterias resistentes. Este trabajo describe las acciones propuestas y los resultados obtenidos durante el primer período de implementación en materia de fortalecimiento de la vigilancia en salud humana, creación de una red de vigilancia en salud animal, planificación de la vigilancia del consumo de antimicrobianos, fiscalización de restricciones en la venta de estos, adecuación de las formas farmacéuticas a las necesidades de tratamiento, actualización del registro de antimicrobianos y de métodos de diagnóstico, restricción de su uso como promotores de crecimiento, promoción de su uso responsable, elaboración de guías de diagnóstico y tratamiento, creación de programas de gestión de antimicrobianos, y fortalecimiento de los programas de prevención y control de infecciones en establecimientos de salud y de producción agropecuaria. Muchas de estas medidas son de implementación inmediata, particularmente en materia de regulación, fiscalización y gestión de antimicrobianos, y pueden reducir su uso innecesario y con ello el impacto sobre la resistencia a los antimicrobianos.

Regulatory requirements for genotoxicity assessment of plant protection product active ingredients, impurities, and metabolites

Active ingredients in plant protection products are subject to rigorous safety assessment during their development, including assessment of genotoxicity. Plant protection products are used for agriculture in multiple regions and for the registration of active ingredients it is necessary to satisfy the data requirements of these different regions. There are no overarching global agreements on which genotoxicity studies need to be conducted to satisfy the majority of regulatory authorities. The implementation of new OECD guidelines for the in vitro micronucleus, transgenic rodent somatic and germ cell gene mutation and in vivo comet assays, as well as the revision of a number of other OECD test guidelines has resulted in some changes to data requirements. This review describes the genotoxicity data requirements for chemical active ingredients as well as biologicals, microbials, ground water metabolites, metabolites, and impurities in a number of regions. Similarities and differences are highlighted. Environ. Mol. Mutagen. 58:325-344, 2017. © 2017 Wiley Periodicals, Inc.

Historical climate controls soil respiration responses to current soil moisture

Ecosystem carbon losses from soil microbial respiration are a key component of global carbon cycling, resulting in the transfer of 40-70 Pg carbon from soil to the atmosphere each year. Because these microbial processes can feed back to climate change, understanding respiration responses to environmental factors is necessary for improved projections. We focus on respiration responses to soil moisture, which remain unresolved in ecosystem models. A common assumption of large-scale models is that soil microorganisms respond to moisture in the same way, regardless of location or climate. Here, we show that soil respiration is constrained by historical climate. We find that historical rainfall controls both the moisture dependence and sensitivity of respiration. Moisture sensitivity, defined as the slope of respiration vs. moisture, increased fourfold across a 480-mm rainfall gradient, resulting in twofold greater carbon loss on average in historically wetter soils compared with historically drier soils. The respiration-moisture relationship was resistant to environmental change in field common gardens and field rainfall manipulations, supporting a persistent effect of historical climate on microbial respiration. Based on these results, predicting future carbon cycling with climate change will require an understanding of the spatial variation and temporal lags in microbial responses created by historical rainfall.

Experimental demonstration of an Allee effect in microbial populations

Microbial populations can be dispersal limited. However, microorganisms that successfully disperse into physiologically ideal environments are not guaranteed to establish. This observation contradicts the Baas-Becking tenet: 'Everything is everywhere, but the environment selects'. Allee effects, which manifest in the relationship between initial population density and probability of establishment, could explain this observation. Here, we experimentally demonstrate that small populations of Vibrio fischeri are subject to an intrinsic demographic Allee effect. Populations subjected to predation by the bacterivore Cafeteria roenbergensis display both intrinsic and extrinsic demographic Allee effects. The estimated critical threshold required to escape positive density-dependence is around 5, 20 or 90 cells ml(-1)under conditions of high carbon resources, low carbon resources or low carbon resources with predation, respectively. This work builds on the foundations of modern microbial ecology, demonstrating that mechanisms controlling macroorganisms apply to microorganisms, and provides a statistical method to detect Allee effects in data.

Benthic Diatom Based Indices for Water Quality Assessment in Two Subtropical Streams

Benthic diatoms have been universally used as indicators to assess water quality in lotic ecosystems. However, most diatom-based indices developed in Europe have not been widely used or tested in other continents such as Asia or Oceania. This study compared the performance of 14 widely-applied diatom indices in assessing ecological conditions in subtropical streams in South East Queensland (SEQ) in Australia and in the upper Han River in China. Most water quality variables in the upper Han River including dissolved organic carbon (DOC), total nitrogen (TN), and soluble reactive phosphorus (SRP) had strong relationships with at least one diatom index, with the exception of IDAP (Index Diatom Artois-Picardie), and TDI (Trophic Diatom Index). However, in SEQ, most of the environmental variables including DOC, ammonia nitrogen (NH₄-N), TN, SRP, and electrical conductivity (EC) showed no significant relationships with diatom indices, and the DI-CH (Swiss Diatom Index) and WAT (Watanabe's Index) were unrelated to any of the variables examined. Only pH and nitrite or nitrate nitrogen (NO_X-N) were significant predictors of several diatom indices in SEQ, especially TID (Rott trophic index). In the upper Han River, much of the spatial variation in most diatom indices was explained by proximate determinants alone, including EC, DOC, dissolved oxygen (DO) or SRP, or a combination of ultimate (canopy, forest) and proximate factors (R² in most models> 0.75). Most diatom indices performed as predicted in the upper Han River where nutrient and organic matter pollution was relatively high, and variation in pH low. However, the indices performed poorly in SEQ where the water quality gradient was low and instead most responded to spatial variation in pH. This finding serves as a caution to the application of diatom indices in river basins that fall outside of the range of water quality values of the systems in which they originally developed.

Antibiotic prescribing for acute otitis media and acute sinusitis: a cross-sectional analysis of the ReCEnT study exploring the habits of early career doctors in family practice

BACKGROUND

Antibiotic resistance is a public health concern, and is linked to over-prescribing. In self-limiting infections such as acute otitis media (AOM) and acute sinusitis, prescribing remains high despite strong guideline recommendations against the routine use of antibiotics. Early career General Practitioners may find evidence-based prescribing challenging.

AIM

To establish the prevalence and associations of antibiotic prescribing for AOM and acute sinusitis by Australian vocational trainees in General Practice.

METHOD

A cross-sectional analysis of data from the Registrar Clinical Encounters in Training (ReCEnT) study. This ongoing, multicentre prospective cohort study documents trainees' consultation-based clinical experiences. Univariate and logistic regression analyses were conducted on data recorded in consultations for AOM or acute sinusitis in nine collection periods during 2010-2014.

RESULTS

Data from 856 individual trainees (response rate 95.2%) were analysed. AOM was managed in 0.9% of encounters. Antibiotics were prescribed in 78.8% of cases. Prescribing was significantly associated with longer consultation time and first presentation for this problem. There was no significant association with patient age group. Acute sinusitis was managed in 0.9% of encounters. Antibiotics were prescribed in 71.2% of cases. Later-stage trainees and trainees who did not receive their primary medical qualification in Australia were more likely to prescribe an antibiotic for acute sinusitis.

CONCLUSION

Early career GPs are not prescribing in an evidence-based manner. The complexity of guidelines for AOM and acute sinusitis may be confusing for prescribers, especially early career doctors struggling with inexperience and diagnostic uncertainty. Educational interventions are necessary to bring prescribing rates closer to quality benchmarks.

GAMOLA2, a Comprehensive Software Package for the Annotation and Curation of Draft and Complete Microbial Genomes

Expert curated annotation remains one of the critical steps in achieving a reliable biological relevant annotation. Here we announce the release of GAMOLA2, a user friendly and comprehensive software package to process, annotate and curate draft and complete bacterial, archaeal, and viral genomes. GAMOLA2 represents a wrapping tool to combine gene model determination, functional Blast, COG, Pfam, and TIGRfam analyses with structural predictions including detection of tRNAs, rRNA genes, non-coding RNAs, signal protein cleavage sites, transmembrane helices, CRISPR repeats and vector sequence contaminations. GAMOLA2 has already been validated in a wide range of bacterial and archaeal genomes, and its modular concept allows easy addition of further functionality in future releases. A modified and adapted version of the Artemis Genome Viewer (Sanger Institute) has been developed to leverage the additional features and underlying information provided by the GAMOLA2 analysis, and is part of the software distribution. In addition to genome annotations, GAMOLA2 features, among others, supplemental modules that assist in the creation of custom Blast databases, annotation transfers between genome versions, and the preparation of Genbank files for submission via the NCBI Sequin tool. GAMOLA2 is intended to be run under a Linux environment, whereas the subsequent visualization and manual curation in Artemis is mobile and platform independent. The development of GAMOLA2 is ongoing and community driven. New functionality can easily be added upon user requests, ensuring that GAMOLA2 provides information relevant to microbiologists. The software is available free of charge for academic use.

Routine Ertapenem Prophylaxis for Transrectal Ultrasound Guided Prostate Biopsy does Not Select for Carbapenem Resistant Organisms: A Prospective Cohort Study

PURPOSE

Sepsis after transrectal ultrasound guided prostate biopsy is an increasing problem in this era of rising antibiotic resistance. Although ertapenem prophylaxis has proved effective at our institution to reduce this, it has raised local and regional antimicrobial stewardship concerns. We investigated the possible selective effect of single dose ertapenem prophylaxis on fecal colonization with carbapenem resistant Enterobacteriaceae.

MATERIALS AND METHODS

Patients underwent a rectal swab prior to receiving prebiopsy ertapenem prophylaxis. A second swab was obtained at followup 4 to 6 weeks later. Swabs were screened for carbapenem resistant Enterobacteriaceae using an enhanced CDC (Centers for Disease Control) method. Prebiopsy swabs were also screened for extended spectrum β-lactamase producing and ciprofloxacin resistant Enterobacteriaceae. Patients were monitored for post-biopsy sepsis.

RESULTS

A total of 326 patients were enrolled in the study. At baseline 6.4% and 9.0% of patients had colonization with extended spectrum β-lactamase producing and ciprofloxacin resistant Enterobacteriaceae, respectively. Carbapenem resistant Enterobacteriaceae were not detected at baseline or followup in any patients. Colonization with nonfermentative organisms with intrinsic ertapenem resistance was detected in 29.4% of patients at baseline and followup (p = 1.0). Three cases (0.9%, 95% CI 0.2-2.8) of probable post-biopsy sepsis were identified during the study period. None was bacteremic or required intensive care unit admission.

CONCLUSIONS

Single dose ertapenem prophylaxis did not appear to have a significant selective effect on fecal colonization with carbapenem resistant Enterobacteriaceae or other ertapenem resistant gram-negative organisms in this outpatient group. It is highly effective prophylaxis for transrectal ultrasound guided prostate biopsy. In the right setting ertapenem may represent a useful prophylactic option to prevent post-transrectal ultrasound guided prostate biopsy sepsis.

Ventilator-Associated Pneumonia and Its Responsible Germs; an Epidemiological Study

INTRODUCTION

Ventilator-associated pneumonia (VAP) is one of the most common hospital infections and a side effect of lengthy stay in intensive care unit (ICU). Considering the ever-changing pattern of common pathogens in infectious diseases and the raise in prevalence of hospital infections, the present study was designed aiming to determine the prevalence of VAP and its bacterial causes.

METHODS

In this cross-sectional study, the medical profiles of all the patients under mechanical ventilation, who had no symptoms of pneumonia at the time of intubation and developed new infiltration in chest radiography after 48 hours under mechanical ventilation along with at least 2 of the symptoms including fever, hypothermia, leukocytosis, leukopenia, or purulent discharge from the lungs, were evaluated. Demographic data, clinical and laboratory findings, and final outcome of the patients were extracted from the patient's clinical profile and reported using SPSS version 20 and descriptive statistics.

RESULTS

518 patients with the mean age of 62.3 ± 20.8 years were evaluated (50.9% female). Mean time interval between intubation and showing symptoms was 10.89 ± 12.27 days. Purulent discharges (100%), leukocytosis (71.9%), fever (49.1%), hypothermia (12.3%), and leukopenia (8.8%) were the most common clinical and laboratory symptoms and acinetobacter baumannii (31.58%) and klebsiella pneumoniae (29.82%) were the most common germs growing in sputum cultures. 19 (33.3%) cases of pan drug resistance (PDR) and 10 (17.5%) cases of extensive drug resistance (XDR) were seen. Mortality due to VAP was 78.9% and there was no significant correlation between age (p = 0.841), sex (p = 0.473), ICU admission (p = 0.777), duration of hospitalization (p = 0.254), leukocytosis (p = 0.790), leukopenia (p = 0.952), fever (p = 0.171), hypothermia (p = 0.639), type of culture (p = 0.282), and type of antibiotic resistance (p = 0.066) with mortality.

CONCLUSION

Prevalence of VAP and its associated mortality were 11% and 78.9%, respectively. The most common symptoms and signs were purulent discharge, leukocytosis, and fever. Acinetobacter baumannii and klebsiella pneumoniae were the most common germs in sputum cultures with 50% resistance to commonly used antibiotics.

NifH-Harboring Bacterial Community Composition across an Alaskan Permafrost Thaw Gradient

Since nitrogen (N) is often limiting in permafrost soils, we investigated the N2-fixing genetic potential and the inferred taxa harboring those genes by sequencing nifH gene fragments in samples taken along a permafrost thaw gradient in an Alaskan boreal soil. Samples from minimally, moderately and extensively thawed sites were taken to a depth of 79 cm to encompass zones above and below the depth of the water table. NifH reads were translated with frameshift correction and 112,476 sequences were clustered at 5% amino acid dissimilarity resulting in 1,631 OTUs. Sample depth in relation to water table depth was correlated to differences in the NifH sequence classes with those most closely related to group I nifH-harboring Alpha- and Beta-Proteobacteria in higher abundance above water table depth while those related to group III nifH-harboring Delta Proteobacteria more abundant below. The most dominant below water table depth NifH sequences, comprising 1/3 of the total, were distantly related to Verrucomicrobia-Opitutaceae. Overall, these results suggest that permafrost thaw alters the class-level composition of N2-fixing communities in the thawed soil layers and that this distinction corresponds to the depth of the water table. These nifH data were also compared to nifH sequences obtained from a study at an Alaskan taiga site, and to those of other geographically distant, non-permafrost sites. The two Alaska sites were differentiated largely by changes in relative abundances of the same OTUs, whereas the non-Alaska sites were differentiated by the lack of many Alaskan OTUs, and the presence of unique halophilic, sulfate- and iron-reducing taxa in the Alaska sites.

Lytic Polysaccharide Monooxygenases: The Microbial Power Tool for Lignocellulose Degradation

Lytic polysaccharide monooxygenases (LPMOs) are copper-enzymes that catalyze oxidative cleavage of glycosidic bonds. These enzymes are secreted by many microorganisms to initiate infection and degradation processes. In particular, the concept of fungal degradation of lignocellulose has been revised in the light of this recent finding. LPMOs require a source of electrons for activity, and both enzymatic and plant-derived sources have been identified. Importantly, light-induced electron delivery from light-harvesting pigments can efficiently drive LPMO activity. The possible implications of LPMOs in plant-symbiont and -pathogen interactions are discussed in the context of the very powerful oxidative capacity of these enzymes.

Recent progress and future challenges in algal biofuel production

Modern society is fueled by fossil energy produced millions of years ago by photosynthetic organisms. Cultivating contemporary photosynthetic producers to generate energy and capture carbon from the atmosphere is one potential approach to sustaining society without disrupting the climate. Algae, photosynthetic aquatic microorganisms, are the fastest growing primary producers in the world and can therefore produce more energy with less land, water, and nutrients than terrestrial plant crops. We review recent progress and challenges in developing bioenergy technology based on algae. A variety of high-value products in addition to biofuels can be harvested from algal biomass, and these may be key to developing algal biotechnology and realizing the commercial potential of these organisms. Aspects of algal biology that differentiate them from plants demand an integrative approach based on genetics, cell biology, ecology, and evolution. We call for a systems approach to research on algal biotechnology rooted in understanding their biology, from the level of genes to ecosystems, and integrating perspectives from physical, chemical, and social sciences to solve one of the most critical outstanding technological problems.