bluuebunny/crossref_metadata_2025 huggingface dataset:
Managing scientific and technical experts in R&D: beyond tensions, conflicting logics and orders of worth
Authors: Bobadilla Natalia , Gilbert Patrick
Published: December 2015

Practices for managing scientific and technical experts today require a critical re‐evaluation. This paper takes a sociological perspective (convention theory) to examine the tensions and conflicts that arise in the implementation of practices for managing knowledge workers. Drawing on six case studies of knowledge‐intensive organizations and participant observation, we elucidate three different coexisting logics – technical, market and managerial – that together create tensions. We go beyond the analysis of practices in R&D to unveil the nature of those tensions and to show how and under what circumstances arrangements are made between the different logics. Our study demonstrates that knowledge‐intensive organizations have relied on reward and dual ladder systems to solve the tensions between logics. Dual ladders often fail because they are the representation of the problem rather than the solution. We argue that the way for the issue of managing knowledge workers to evolve lies in the enrichment of arrangements, the deepening of compromises and logic hybridization. We discuss the implications of these findings for R&D management practices.
Pseudomonas aeruginosa antibiotic resistance in Australian cystic fibrosis centres
Authors: Smith Daniel J. , Ramsay Kay A. , Yerkovich Stephanie T. , Reid David W. , Wainwright Claire E. , Grimwood Keith , Bell Scott C. , Kidd Timothy J.
Published: December 2015

Background and objective

In cystic fibrosis (CF), chronic Pseudomonas aeruginosa infection is associated with increased morbidity, antibiotic treatments and mortality. By linking Australian CF registry data with a national microbiological data set, we examined the association between where treatment was delivered, its intensity and P. aeruginosa antibiotic resistance.

Methods

Sputa were collected from paediatric and adult CF patients attending 18 Australian CF centres. P. aeruginosa antibiotic susceptibilities determined by local laboratories were correlated with clinical characteristics, treatment intensity and infection with strains commonly shared among Australian CF patients. Between‐centre differences in treatment and antibiotic resistance were also compared.

Results

Large variations in antibiotic usage, maintenance treatment practices and multi‐antibiotic resistant P. aeruginosa (MARPA) prevalence exist between Australian CF centres, although the overall proportions of MARPA isolates were similar in paediatric and adult centres (31% vs 35%, P = 0.29). Among paediatric centres, MARPA correlated with intravenous antibiotic usage and the Australian state where treatment was delivered, while azithromycin, reduced lung function and treating state predicted intravenous antibiotic usage. In adult centres, body mass index (BMI) and treating state were associated with MARPA, while intravenous antibiotic use was predicted by gender, BMI, dornase‐alpha, azithromycin, lung function and treating state. In adults, P. aeruginosa strains AUST‐01 and AUST‐02 independently predicted intravenous antibiotic usage.

Conclusion

Increased treatment intensity in paediatric centres and the Australian state where treatment was received are both associated with greater risk of MARPA, but not worse clinical outcomes.
Hermeneutic application research – finding a common understanding and consensus on care and caring
Authors: Koskinen Camilla , Nyström Lisbet
Published: December 2015

To clinically and contextually implement the theoretical and factual knowledge of care and caring that has been developed in the last 30 years is seen as a great challenge in caring science research. Emphasis has been put on problem‐solving research methodologies and action research in hopes of narrowing the divide between caring theory and clinical practice. Thus, the intention is now to further action research towards a hermeneutic approach and to put emphasis on hermeneutic application where theory and praxis become one through human dialogue. This article highlights hermeneutic application research as an alternative methodology within participatory‐oriented research which presents a new opportunity to unite clinical practice and caring theory. The aim is to contribute to the development of the hermeneutical application research design in its epistemological, ontological and ethical perspective, by articulating and clarifying the central foundations in the application. On the basis of Gadamer's hermeneutical thinking and Levinas ethical thinking, the central foundations in the application research are ethics, creation of a hermeneutical room, dialogue and common understanding and appropriation and action. When theoretical understanding turns into praxis, knowledge also becomes activity and theory and practice become one. Application thus realises the basic idea that praxis and theory are one, and thus, theory of caring can only become evident and implemented in a clinical practice through moments when the participants find a common understanding and consensus on the knowledge of care and caring.
Beyond Racism: Response to Embrick, Hughey, Miller, Rosenfeld, and Ross
Authors: Hirschfield Paul J.
Published: December 2015

This essay serves as a response to Embrick (2016), Hughey (2016), Miller (2016), Rosenfeld (2016), and Ross (2016), all of whom reflected on my article “Lethal Policing: Making Sense of American Exceptionalism,” published in the December 2015 issue of this journal.
Analysis of Thermal-Hydraulic Fluctuations in Trillo NPP With CTF/PARCS v. 2.7 Coupled Code
Authors: Abarca A. , Miró R. , Verdú G. , Bermejo J. A.
Published: December 2015

The low-frequency noises are fluctuations in the neutron flux density, in the low-frequency range up to 4 Hz, which generate noise in the neutron instrumentation and could affect the limitation and protection system of the reactor core. Some European pressurized water reactors (PWRs) experienced the effect of low-frequency noise, opening a new research line for the verification of the neutron-kinetics/thermal-hydraulic coupled codes. A CTF/PARCS v. 2.7 simulation study to verify whether periodical fluctuations in the core inlet temperature could activate the core protection system has been done, obtaining the frequency spectrum of the power oscillation amplitudes.
Magine Snowboards
Authors: Lam Jose , Walsh Jacqueline
Published: December 2015

This case illustrates the challenges entrepreneurs experience as they try to guide a new venture to the commercialization stage in the entrepreneurial process. Steve Wheeler, Mike Maddock, and Marcel Savidon are three young entrepreneurs and friends who founded Magine Snowboards, a company focused on the manufacturing of snowboards. This case is set in January of 2012 as Steve Wheeler debates the next strategic step for the company. Magine has developed an innovative product—a snowboard that uses environmentally friendly and sustainable materials. The entrepreneurs have been able to start the business through bootstrapping. However, they now need to develop a strategy that can guide the company forward.
Case Study: Competition Nutrition Intakes During the Open Water Swimming Grand Prix Races in Elite Female Swimmer
Authors: Kumstát Michal , Rybářová Silvie , Thomas Andy , Novotný Jan
Published: December 2015

The nutritional intake of elite open water swimmers during competition is not well established, and therefore this case study aims to provide new insights by describing the feeding strategies adopted by an elite female swimmer (28 yrs; height; 1.71 m; body mass: 60 kg; body fat: 16.0%) in the FINA open water Grand Prix 2014.Seven events of varying distances (15–88 km) and durations (3–12 hrs) were included. In all events, except one, feeds were provided from support boats. Swimmer and support staff were instructed to track in detail all foods and beverages consumed during the events. Nutritional information was gathered from the packaging and dietary supplements labels and analyzed by nutrition software. Mean carbohydrate (CHO) and protein intake reached 83 ± 5 g·h-1 and 12 ± 8 g·h-1, respectively. Fat intake was neglected (~1 g·h-1). Mean in-race energy intake reached 394 ± 26 kcal·h-1. Dietary supplements in the form of sport beverages and gels, containing multitransportable CHO, provided 40 ± 4 and 49 ± 6% of all CHO energy, respectively. Caffeine (3.6 ± 1.8 mg·kg-1 per event) and sodium (423 ± 16 mg·h-1) were additionally supplemented in all events. It was established that continuous intake of high doses of CHO and sodium and moderate dose of caffeine were an essential part of the feeding strategy for elite-level high intensity ultra-endurance open-water swimming races. A well scheduled and well-prepared nutrition strategy is believed to have ensured optimal individual performance during Grand Prix events.
Designing a Pediatric Study for an Antimalarial Drug by Using Information from Adults
Authors: Petit Caroline , Jullien Vincent , Samson Adeline , Guedj Jérémie , Kiechel Jean-René , Zohar Sarah , Comets Emmanuelle
Published: December 2015

The objectives of this study were to design a pharmacokinetic (PK) study by using information about adults and evaluate the robustness of the recommended design through a case study of mefloquine. PK data about adults and children were available from two different randomized studies of the treatment of malaria with the same artesunate-mefloquine combination regimen. A recommended design for pediatric studies of mefloquine was optimized on the basis of an extrapolated model built from adult data through the following approach. (i) An adult PK model was built, and parameters were estimated by using the stochastic approximation expectation-maximization algorithm. (ii) Pediatric PK parameters were then obtained by adding allometry and maturation to the adult model. (iii) A D-optimal design for children was obtained with PFIM by assuming the extrapolated design. Finally, the robustness of the recommended design was evaluated in terms of the relative bias and relative standard errors (RSE) of the parameters in a simulation study with four different models and was compared to the empirical design used for the pediatric study. Combining PK modeling, extrapolation, and design optimization led to a design for children with five sampling times. PK parameters were well estimated by this design with few RSE. Although the extrapolated model did not predict the observed mefloquine concentrations in children very accurately, it allowed precise and unbiased estimates across various model assumptions, contrary to the empirical design. Using information from adult studies combined with allometry and maturation can help provide robust designs for pediatric studies.
Key Roles of Human Polymorphonuclear Cells and Ciprofloxacin in Lactobacillus Species Infection Control
Authors: Mandras Narcisa , Tullio Vivian , Furneri Pio Maria , Roana Janira , Allizond Valeria , Scalas Daniela , Petronio Petronio Giulio , Fuochi Virginia , Banche Giuliana , Cuffini Anna Maria
Published: December 2015

Lactobacilli have the potential to act as reservoirs of antibiotic resistance genes similar to those found in human pathogens, with the risk of transferring these genes to many pathogenic bacteria. In this study, we investigated the role of human polymorphonuclear cells (PMNs) against
Lactobacillus
spp. both resistant and susceptible to ciprofloxacin (a fluoroquinolone) and the effect of ciprofloxacin on the interaction between PMNs and three
Lactobacillus
spp. with different patterns of susceptibility to this drug. Hence, the primary functions of PMNs, such as phagocytosis and bacterial intracellular killing, against lactobacilli were investigated. The rate of PMN phagocytosis was high for ciprofloxacin-sensitive and ciprofloxacin-resistant strains. The patterns of intracellular killing of ciprofloxacin-sensitive and ciprofloxacin-resistant strains by PMNs underline that PMNs alone were able to kill lactobacilli. The addition of ciprofloxacin to PMNs did not result in a significant increase in the bacterial uptake by phagocytes. On the contrary, ciprofloxacin had a marked effect on PMN intracellular killing, resulting in increased numbers of killed ciprofloxacin-sensitive bacteria in comparison with antibiotic-free controls. Our data show that by itself, the profile of antibiotic resistance does not constitute an intrinsic factor of greater or lesser pathogenicity toward the host. The ability of PMNs to kill a diverse array of bacterial pathogens is essential for human innate host defense, primarily in immunocompromised patients.
Efficacy and Safety of AFN-1252, the First Staphylococcus-Specific Antibacterial Agent, in the Treatment of Acute Bacterial Skin and Skin Structure Infections, Including Those in Patients with Significant Comorbidities
Authors: Hafkin B. , Kaplan N. , Murphy B.
Published: December 2015

This open-label noncontrolled, phase II multicenter trial was designed to evaluate the safety, tolerability, and efficacy of 200 mg of AFN-1252, a selective inhibitor of
Staphylococcus aureus
enoyl-acyl carrier protein reductase (FabI), given by mouth twice daily in the treatment of acute bacterial skin and skin structure infections (ABSSSI) due to staphylococci. Important aspects of the current study included a comparison of early response efficacy endpoints with end-of-treatment and follow-up endpoints. Many patients in the intent-to-treat population (
n
= 103) had significant comorbidities. The overall early response rate at day 3 was 97.3% (wound, 100%; abscess, 96.6%; cellulitis, 94.4%) in the microbiologically evaluable (ME) population. Within the ME population, 82.9% of patients had a ≥20% decrease in the area of erythema, and 77.9% of patients had a ≥20% decrease in the area of induration, on day 3.
S. aureus
was detected in 97.7% of patients (
n
= 37 patients with methicillin-resistant
S. aureus
[MRSA], and
n
= 39 with methicillin-sensitive
S. aureus
[MSSA]). No isolates had increased AFN-1252 MICs posttreatment. Microbiologic eradication rates for
S. aureus
were 93.2% at short-term follow-up (STFU) and 91.9% at long-term follow-up (LTFU) in the ME population. Eradication rates for MRSA and MSSA were 91.9% and 92.3%, respectively, at STFU and 91.9% and 89.7%, respectively, at LTFU. The most frequently reported drug-related adverse events, which were mostly mild or moderate, were headache (26.2%) and nausea (21.4%). These studies demonstrate that AFN-1252 is generally well tolerated and effective in the treatment of ABSSSI due to
S. aureus
, including MRSA. (This study has been registered at ClinicalTrials.gov under registration no. NCT01519492.)
Posttreatment Antifungal Resistance among Colonizing Candida Isolates in Candidemia Patients: Results from a Systematic Multicenter Study
Authors: Jensen R. H. , Johansen H. K. , Søes L. M. , Lemming L. E. , Rosenvinge F. S. , Nielsen L. , Olesen B. , Kristensen L. , Dzajic E. , Astvad K. M. T. , Arendrup M. C.
Published: December 2015

The prevalence of intrinsic and acquired resistance among colonizing
Candida
isolates from patients after candidemia was investigated systematically in a 1-year nationwide study. Patients were treated at the discretion of the treating physician. Oral swabs were obtained after treatment. Species distributions and MIC data were investigated for blood and posttreatment oral isolates from patients exposed to either azoles or echinocandins for <7 or ≥7 days. Species identification was confirmed using matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) and internal transcribed spacer (ITS) sequencing, susceptibility was examined by EUCAST EDef 7.2 methodology, echinocandin resistance was examined by
FKS
sequencing, and genetic relatedness was examined by multilocus sequence typing (MLST). One hundred ninety-three episodes provided 205 blood and 220 oral isolates. MLST analysis demonstrated a genetic relationship for 90% of all paired blood and oral isolates. Patients exposed to azoles for ≥7 days (
n
= 93) had a significantly larger proportion of species intrinsically less susceptible to azoles (particularly
Candida glabrata
) among oral isolates than among initial blood isolates (36.6% versus 12.9%;
P
< 0.001). A similar shift toward species less susceptible to echinocandins among 85 patients exposed to echinocandins for ≥7 days was not observed (4.8% of oral isolates versus 3.2% of blood isolates;
P
> 0.5). Acquired resistance in
Candida albicans
was rare (<5%). However, acquired resistance to fluconazole (29.4%;
P
< 0.05) and anidulafungin (21.6%;
P
< 0.05) was common in
C. glabrata
isolates from patients exposed to either azoles or echinocandins. Our findings suggest that the colonizing mucosal microbiota may be an unrecognized reservoir of resistant
Candida
species, especially
C. glabrata
, following treatment for candidemia. The resistance rates were high, raising concern in general for patients exposed to antifungal drugs.
C646, a Novel p300/CREB-Binding Protein-Specific Inhibitor of Histone Acetyltransferase, Attenuates Influenza A Virus Infection
Authors: Zhao Dongming , Fukuyama Satoshi , Sakai-Tagawa Yuko , Takashita Emi , Shoemaker Jason E. , Kawaoka Yoshihiro
Published: December 2015

New strategies to develop novel broad-spectrum antiviral drugs against influenza virus infections are needed due to the emergence of antigenic variants and drug-resistant viruses. Here, we evaluated C646, a novel p300/CREB-binding protein-specific inhibitor of histone acetyltransferase (HAT), as an anti-influenza virus agent
in vitro
and
in vivo
and explored how C646 affects the viral life cycle and host response. Our studies highlight the value of targeting HAT activity for anti-influenza drug development.
Suppression of Emergence of Resistance in Pathogenic Bacteria: Keeping Our Powder Dry, Part 1
Authors: Drusano G. L. , Louie Arnold , MacGowan Alasdair , Hope William
Published: December 2015

We are in a crisis of bacterial resistance. For economic reasons, most pharmaceutical companies are abandoning antimicrobial discovery efforts, while, in health care itself, infection control and antibiotic stewardship programs have generally failed to prevent the spread of drug-resistant bacteria. At this point, what can be done? The first step has been taken. Governments and international bodies have declared there is a worldwide crisis in antibiotic drug resistance. As discovery efforts begin anew, what more can be done to protect newly developing agents and improve the use of new drugs to suppress resistance emergence? A neglected path has been the use of recent knowledge regarding antibiotic dosing as single agents and in combination to minimize resistance emergence, while also providing sufficient early bacterial kill. In this review, we look at the data for resistance suppression. Approaches include increasing the intensity of therapy to suppress resistant subpopulations; developing concepts of clinical breakpoints to include issues surrounding suppression of resistance; and paying attention to the duration of therapy, which is another important issue for resistance suppression. New understanding of optimizing combination therapy is of interest for difficult-to-treat pathogens like
Pseudomonas aeruginosa
,
Acinetobacter
spp., and multidrug-resistant (MDR)
Enterobacteriaceae
. These lessons need to be applied to our old drugs to preserve them as well and need to be put into national and international antibiotic resistance strategies. As importantly, from a regulatory perspective, new chemical entities should have a corresponding resistance suppression plan at the time of regulatory review. In this way, we can make the best of our current situation and improve future prospects.
Treatment with a Nucleoside Polymerase Inhibitor Reduces Shedding of Murine Norovirus in Stool to Undetectable Levels without Emergence of Drug-Resistant Variants
Authors: Rocha-Pereira Joana , Van Dycke Jana , Neyts Johan
Published: December 2015

Prolonged norovirus shedding may occur in certain patients, such as organ transplant recipients. We established a mouse model for persistent norovirus infection (using the mouse norovirus MNV.CR6 strain). The nucleoside viral polymerase inhibitor 2′-
C
-methylcytidine (2CMC), but not favipiravir (T-705), reduced viral shedding to undetectable levels. Viral rebound was observed after stopping treatment, which was again effectively controlled by treatment with 2CMC. No drug-resistant variants emerged.
The Staphylococcus aureus Chaperone PrsA Is a New Auxiliary Factor of Oxacillin Resistance Affecting Penicillin-Binding Protein 2A
Authors: Jousselin Ambre , Manzano Caroline , Biette Alexandra , Reed Patricia , Pinho Mariana G. , Rosato Adriana E. , Kelley William L. , Renzoni Adriana
Published: December 2015

Expression of the methicillin-resistant
S. aureus
(MRSA) phenotype results from the expression of the extra penicillin-binding protein 2A (PBP2A), which is encoded by
mecA
and acquired horizontally on part of the SCC
mec
cassette. PBP2A can catalyze
dd
-transpeptidation of peptidoglycan (PG) because of its low affinity for β-lactam antibiotics and can functionally cooperate with the PBP2 transglycosylase in the biosynthesis of PG. Here, we focus upon the role of the membrane-bound PrsA foldase protein as a regulator of β-lactam resistance expression. Deletion of
prsA
altered oxacillin resistance in three different SCC
mec
backgrounds and, more importantly, caused a decrease in PBP2A membrane amounts without affecting
mecA
mRNA levels. The N- and C-terminal domains of PrsA were found to be critical features for PBP2A protein membrane levels and oxacillin resistance. We propose that PrsA has a role in posttranscriptional maturation of PBP2A, possibly in the export and/or folding of newly synthesized PBP2A. This additional level of control in the expression of the
mecA
-dependent MRSA phenotype constitutes an opportunity to expand the strategies to design anti-infective agents.
Impairment of Pseudomonas aeruginosa Biofilm Resistance to Antibiotics by Combining the Drugs with a New Quorum-Sensing Inhibitor
Authors: Furiga Aurelie , Lajoie Barbora , El Hage Salome , Baziard Genevieve , Roques Christine
Published: December 2015

Pseudomonas aeruginosa
plays an important role in chronic lung infections among patients with cystic fibrosis (CF) through its ability to form antibiotic-resistant biofilms. In
P. aeruginosa
, biofilm development and the production of several virulence factors are mainly regulated by the
rhl
and
las
quorum-sensing (QS) systems, which are controlled by two
N
-acyl-homoserine lactone signal molecules. In a previous study, we discovered an original QS inhibitor,
N
-(2-pyrimidyl)butanamide, called C11, based on the structure of C
4
-homoserine lactone, and found that it is able to significantly inhibit
P. aeruginosa
biofilm formation. However, recent data indicate that
P. aeruginosa
grows under anaerobic conditions and forms biofilms in the lungs of CF patients that are denser and more robust than those formed under aerobic conditions. Our confocal microscopy observations of
P. aeruginosa
biofilms developed under aerobic and anaerobic conditions confirmed that the biofilms formed under these two conditions have radically different architectures. C11 showed significant dose-dependent antibiofilm activity on biofilms grown under both aerobic and anaerobic conditions, with a greater inhibitory effect being seen under conditions of anaerobiosis. Gene expression analyses performed by quantitative reverse transcriptase PCR showed that C11 led to the significant downregulation of
rhl
QS regulatory genes but also to the downregulation of both
las
QS regulatory genes and QS system-regulated virulence genes,
rhlA
and
lasB
. Furthermore, the activity of C11 in combination with antibiotics against
P. aeruginosa
biofilms was tested, and synergistic antibiofilm activity between C11 and ciprofloxacin, tobramycin, and colistin was obtained under both aerobic and anaerobic conditions. This study demonstrates that C11 may increase the efficacy of treatments for
P. aeruginosa
infections by increasing the susceptibility of biofilms to antibiotics and by attenuating the pathogenicity of the bacterium.
Discovery of Structurally Diverse Small-Molecule Compounds with Broad Antiviral Activity against Enteroviruses
Authors: Zuo Jun , Kye Steve , Quinn Kevin K. , Cooper Paige , Damoiseaux Robert , Krogstad Paul
Published: December 2015

Antiviral drugs do not currently exist for the treatment of enterovirus infections, which are often severe and potentially life-threatening. We conducted high-throughput molecular screening and identified a structurally diverse set of compounds that inhibit the replication of coxsackievirus B3, a commonly encountered enterovirus. These compounds did not interfere with the function of the viral internal ribosome entry site or with the activity of the viral proteases, but they did drastically reduce the synthesis of viral RNA and viral proteins in infected cells. Sequence analysis of compound-resistant mutants suggests that the viral 2C protein is targeted by most of these compounds. These compounds demonstrated antiviral activity against a panel of the most commonly encountered enteroviruses and thus represent potential leads for the development of broad-spectrum anti-enteroviral drugs.
Pharmacokinetics of Transfer of Azithromycin into the Breast Milk of African Mothers
Authors: Salman Sam , Davis Timothy M. E. , Page-Sharp Madhu , Camara Bully , Oluwalana Claire , Bojang Abdoulie , D'Alessandro Umberto , Roca Anna
Published: December 2015

Azithromycin (AZI) is used for its antibiotic and antimalarial properties in pregnancy. Reported estimates of AZI breast milk transfer, based on concentrations in mostly single samples from small numbers of women, have suggested that infant intake is safe. To better characterize infant intake and the associated potential benefits and risks, AZI was measured by liquid chromatography-mass spectrometry in four breast milk samples taken over 28 days postpartum from each of 20 Gambian women given 2 g AZI during labor. A population pharmacokinetic model utilizing published parameters for AZI disposition in pregnancy, the present breast milk concentrations, and increasing/decreasing sigmoid maximum-effect (Emax) functions adequately described temporal changes in the milk/plasma ratio. The median estimated absolute and relative cumulative infant doses were 4.5 mg/kg of body weight (95% prediction interval, 0.6 to 7.0 mg/kg) and 15.7% (95% prediction interval, 2.0 to 27.8%) of the maternal dose, respectively; the latter exceeded the recommended 10% safety limit. Although some infants with bacterial infections may benefit from AZI in breast milk, there is a risk of hypertrophic pyloric stenosis with a worst-case number needed to harm of 60 based on the present and available epidemiologic data. (This study has been registered at ClinicalTrials.gov under registration no. NCT01800942.)
Bacteriophage Can Prevent Encrustation and Blockage of Urinary Catheters by Proteus mirabilis
Authors: Nzakizwanayo Jonathan , Hanin Aurélie , Alves Diana R. , McCutcheon Benjamin , Dedi Cinzia , Salvage Jonathan , Knox Karen , Stewart Bruce , Metcalfe Anthony , Clark Jason , Gilmore Brendan F. , Gahan Cormac G. M. , Jenkins A. Toby A. , Jones Brian V.
Published: December 2015

Proteus mirabilis
forms dense crystalline biofilms on catheter surfaces that occlude urine flow, leading to serious clinical complications in long-term catheterized patients, but there are presently no truly effective approaches to control catheter blockage by this organism. This study evaluated the potential for bacteriophage therapy to control
P. mirabilis
infection and prevent catheter blockage. Representative
in vitro
models of the catheterized urinary tract, simulating a complete closed drainage system as used in clinical practice, were employed to evaluate the performance of phage therapy in preventing blockage. Models mimicking either an established infection or early colonization of the catheterized urinary tract were treated with a single dose of a 3-phage cocktail, and the impact on time taken for catheters to block, as well as levels of crystalline biofilm formation, was measured. In models of established infection, phage treatment significantly increased time taken for catheters to block (∼3-fold) compared to untreated controls. However, in models simulating early-stage infection, phage treatment eradicated
P. mirabilis
and prevented blockage entirely. Analysis of catheters from models of established infection 10 h after phage application demonstrated that phage significantly reduced crystalline biofilm formation but did not significantly reduce the level of planktonic cells in the residual bladder urine. Taken together, these results show that bacteriophage constitute a promising strategy for the prevention of catheter blockage but that methods to deliver phage in sufficient numbers and within a key therapeutic window (early infection) will also be important to the successful application of phage to this problem.
Identification of Specialists and Abundance-Occupancy Relationships among Intestinal Bacteria of
Aves
, Mammalia, and Actinopterygii
Authors: Green Hyatt C. , Fisher Jenny C. , McLellan Sandra L. , Sogin Mitchell L. , Shanks Orin C.
Published: December 2015

The coalescence of next-generation DNA sequencing methods, ecological perspectives, and bioinformatics analysis tools is rapidly advancing our understanding of the evolution and function of vertebrate-associated bacterial communities. Delineation of host-microbe associations has applied benefits ranging from clinical treatments to protecting our natural waters. Microbial communities follow some broad-scale patterns observed for macroorganisms, but it remains unclear how the specialization of intestinal vertebrate-associated communities to a particular host environment influences broad-scale patterns in microbial abundance and distribution. We analyzed the V6 region of 16S rRNA genes amplified from 106 fecal samples spanning
Aves
,
Mammalia
, and
Actinopterygii
(ray-finned fish). We investigated the interspecific abundance-occupancy relationship, where widespread taxa tend to be more abundant than narrowly distributed taxa, among operational taxonomic units (OTUs) within and among host species. In a separate analysis, we identified specialist OTUs that were highly abundant in a single host and rare in all other hosts by using a multinomial model without excluding undersampled OTUs
a priori
. We show that intestinal microbes in humans and other vertebrates display abundance-occupancy relationships, but because intestinal host-associated communities have undergone intense specialization, this trend is violated by a disproportionately large number of specialist taxa. Although it is difficult to distinguish the effects of dispersal limitations, host selection, historical contingency, and stochastic processes on community assembly, results suggest that intestinal bacteria can be shared among diverse hosts in ways that resemble the distribution of “free-living” bacteria in the extraintestinal environment.
Biofilm-Forming Abilities of Shiga Toxin-Producing Escherichia coli Isolates Associated with Human Infections
Authors: Vogeleer Philippe , Tremblay Yannick D. N. , Jubelin Grégory , Jacques Mario , Harel Josée
Published: December 2015

Forming biofilms may be a survival strategy of Shiga toxin-producing
Escherichia coli
to enable it to persist in the environment and the food industry. Here, we evaluate and characterize the biofilm-forming ability of 39 isolates of Shiga toxin-producing
Escherichia coli
isolates recovered from human infection and belonging to seropathotypes A, B, or C. The presence and/or production of biofilm factors such as curli, cellulose, autotransporter, and fimbriae were investigated. The polymeric matrix of these biofilms was analyzed by confocal microscopy and by enzymatic digestion. Cell viability and matrix integrity were examined after sanitizer treatments. Isolates of the seropathotype A (O157:H7 and O157:NM), which have the highest relative incidence of human infection, had a greater ability to form biofilms than isolates of seropathotype B or C. Seropathotype A isolates were unique in their ability to produce cellulose and poly-
N
-acetylglucosamine. The integrity of the biofilms was dependent on proteins. Two autotransporter genes,
ehaB
and
espP
, and two fimbrial genes,
z1538
and
lpf2
, were identified as potential genetic determinants for biofilm formation. Interestingly, the ability of several isolates from seropathotype A to form biofilms was associated with their ability to agglutinate yeast in a mannose-independent manner. We consider this an unidentified biofilm-associated factor produced by those isolates. Treatment with sanitizers reduced the viability of Shiga toxin-producing
Escherichia coli
but did not completely remove the biofilm matrix. Overall, our data indicate that biofilm formation could contribute to the persistence of Shiga toxin-producing
Escherichia coli
and specifically seropathotype A isolates in the environment.
Long-Term Enrichment on Cellulose or Xylan Causes Functional and Taxonomic Convergence of Microbial Communities from Anaerobic Digesters
Authors: Jia Yangyang , Wilkins David , Lu Hongyuan , Cai Mingwei , Lee Patrick K. H.
Published: December 2015

Cellulose and xylan are two major components of lignocellulosic biomass, which represents a potentially important energy source, as it is abundant and can be converted to methane by microbial action. However, it is recalcitrant to hydrolysis, and the establishment of a complete anaerobic digestion system requires a specific repertoire of microbial functions. In this study, we maintained 2-year enrichment cultures of anaerobic digestion sludge amended with cellulose or xylan to investigate whether a cellulose- or xylan-digesting microbial system could be assembled from sludge previously used to treat neither of them. While efficient methane-producing communities developed under mesophilic (35°C) incubation, they did not under thermophilic (55°C) conditions. Illumina amplicon sequencing results of the archaeal and bacterial 16S rRNA genes revealed that the mature cultures were much lower in richness than the inocula and were dominated by single archaeal (genus
Methanobacterium
) and bacterial (order
Clostridiales
) groups, although at finer taxonomic levels the bacteria were differentiated by substrates. Methanogenesis was primarily via the hydrogenotrophic pathway under all conditions, although the identity and growth requirements of syntrophic acetate-oxidizing bacteria were unclear. Incubation conditions (substrate and temperature) had a much greater effect than inoculum source in shaping the mature microbial community, although analysis based on unweighted UniFrac distance found that the inoculum still determined the pool from which microbes could be enriched. Overall, this study confirmed that anaerobic digestion sludge treating nonlignocellulosic material is a potential source of microbial cellulose- and xylan-digesting functions given appropriate enrichment conditions.
Curing the Megaplasmid pTT27 from Thermus thermophilus HB27 and Maintaining Exogenous Plasmids in the Plasmid-Free Strain
Authors: Ohtani Naoto , Tomita Masaru , Itaya Mitsuhiro
Published: December 2015

Stepwise deletions in the only plasmid in
Thermus thermophilus
HB27, megaplasmid pTT27, showed that two distantly located loci were important for maintenance of the plasmid. One is a minimum replicon including one gene,
repT
, coding a replication initiator, and the other encodes subunits of class I ribonucleotide reductase (RNR) for deoxynucleoside triphosphate (dNTP) synthesis. Since the initiator protein, RepT, bound to direct repeats downstream from its own gene, it was speculated that a more-downstream A+T-rich region, which was critical for replication ability, could be unwound for replication initiation. On the other hand, the class I RNR is not necessarily essential for cell growth, as evidenced by the generation of the plasmid-free strain by the loss of pTT27. However, the plasmid-free strain culture has fewer viable cells than the wild-type culture, probably due to a dNTP pool imbalance in the cell. This is because of the introduction of the class I RNR genes or the supplementation of 5′-deoxyadenosylcobalamin, which stimulated class II RNR encoded in the chromosome, resolved the decrease in the number of viable cells in the plasmid-free strain. Likewise, these treatments dramatically enhanced the efficiency of transformation by exogenous plasmids and the stability of the plasmids in the strain. Therefore, the class I RNR would enable the stable maintenance of plasmids, including pTT27, as a result of genome replication normalized by reversing the dNTP pool imbalance. The generation of this plasmid-free strain with great natural competence and its analysis in regard to exogenous plasmid maintenance will expand the availability of HB27 for thermophilic cell factories.
Marker Exchange Mutagenesis of
mxaF
, Encoding the Large Subunit of the Mxa Methanol Dehydrogenase, in Methylosinus trichosporium OB3b
Authors: Farhan Ul Haque Muhammad , Gu Wenyu , DiSpirito Alan A. , Semrau Jeremy D.
Published: December 2015

Methanotrophs have remarkable redundancy in multiple steps of the central pathway of methane oxidation to carbon dioxide. For example, it has been known for over 30 years that two forms of methane monooxygenase, responsible for oxidizing methane to methanol, exist in methanotrophs, i.e., soluble methane monooxygenase (sMMO) and particulate methane monooxygenase (pMMO), and that expression of these two forms is controlled by the availability of copper. Specifically, sMMO expression occurs in the absence of copper, while pMMO expression increases with increasing copper concentrations. More recently, it was discovered that multiple forms of methanol dehydrogenase (MeDH), Mxa MeDH and Xox MeDH, also exist in methanotrophs and that the expression of these alternative forms is regulated by the availability of cerium. That is, expression of Xox MeDH increases in the presence of cerium, while Mxa MeDH expression decreases in the presence of cerium. As it had been earlier concluded that pMMO and Mxa MeDH form a supercomplex in which electrons from Mxa MeDH are back donated to pMMO to drive the initial oxidation of methane, we speculated that Mxa MeDH could be rendered inactive through marker-exchange mutagenesis but growth on methane could still be possible if cerium was added to increase the expression of Xox MeDH under sMMO-expressing conditions. Here we report that
mxaF
, encoding the large subunit of Mxa MeDH, could indeed be knocked out in
Methylosinus trichosporium
OB3b, yet growth on methane was still possible, so long as cerium was added. Interestingly, growth of this mutant occurred in both the presence and the absence of copper, suggesting that Xox MeDH can replace Mxa MeDH regardless of the form of MMO expressed.
Escherichia coli Population Structure and Antibiotic Resistance at a Buffalo/Cattle Interface in Southern Africa
Authors: Mercat Mathilde , Clermont Olivier , Massot Méril , Ruppe Etienne , de Garine-Wichatitsky Michel , Miguel Eve , Valls Fox Hugo , Cornelis Daniel , Andremont Antoine , Denamur Erick , Caron Alexandre
Published: December 2015

At a human/livestock/wildlife interface,
Escherichia coli
populations were used to assess the risk of bacterial and antibiotic resistance dissemination between hosts. We used phenotypic and genotypic characterization techniques to describe the structure and the level of antibiotic resistance of
E. coli
commensal populations and the resistant
Enterobacteriaceae
carriage of sympatric African buffalo (
Syncerus caffer caffer
) and cattle populations characterized by their contact patterns in the southern part of Hwange ecosystem in Zimbabwe. Our results (i) confirmed our assumption that buffalo and cattle share similar phylogroup profiles, dominated by B1 (44.5%) and E (29.0%) phylogroups, with some variability in A phylogroup presence (from 1.9 to 12%); (ii) identified a significant gradient of antibiotic resistance from isolated buffalo to buffalo in contact with cattle and cattle populations expressed as the Murray score among
Enterobacteriaceae
(0.146, 0.258, and 0.340, respectively) and as the presence of tetracycline-, trimethoprim-, and amoxicillin-resistant subdominant
E. coli
strains (0, 5.7, and 38%, respectively); (iii) evidenced the dissemination of tetracycline, trimethoprim, and amoxicillin resistance genes (
tet
,
dfrA
, and
bla
TEM-1
) in 26 isolated subdominant
E. coli
strains between nearby buffalo and cattle populations, that led us (iv) to hypothesize the role of the human/animal interface in the dissemination of genetic material from human to cattle and toward wildlife. The study of antibiotic resistance dissemination in multihost systems and at anthropized/natural interface is necessary to better understand and mitigate its multiple threats. These results also contribute to attempts aiming at using
E. coli
as a tool for the identification of pathogen transmission pathway in multihost systems.
The Polymorphic Aggregative Phenotype of Shiga Toxin-Producing Escherichia coli O111 Depends on RpoS and Curli
Authors: Diodati M. E. , Bates A. H. , Miller W. G. , Carter M. Q. , Zhou Y. , Brandl M. T.
Published: December 2015

Escherichia coli
O111 is an emerging non-O157:H7 serotype of Shiga toxin-producing
E. coli
(STEC). We previously reported that outbreak and environmental, but not sporadic-case, strains of STEC O111 share a distinct aggregation phenotype (M. E. Diodati, A. H. Bates, M. B. Cooley, S. Walker, R. E. Mandrell, and M. T. Brandl, Foodborne Pathog Dis 12:235−243, 2015,
http://dx.doi.org/10.1089/fpd.2014.1887
). We show here the natural occurrence of nonaggregative variants in single STEC O111 strains. These variants do not produce curli fimbriae and lack RpoS function but synthesize cellulose. The deletion of
csgBAC
or
rpoS
in an aggregative outbreak strain abolished aggregate formation, which was rescued when curli biogenesis or RpoS function, respectively, was restored. Complementation of a nonaggregative variant with RpoS also conferred curli production and aggregation. These observations were supported by Western blotting with an anti-CsgA antibody. Immunomicroscopy revealed that curli were undetectable on the cells of the nonaggregative variant and the RpoS mutant but were present in large quantities in the intercellular matrix of the assemblages formed by aggregative strains. Sequence analysis of
rpoS
in the aggregative strain and its variant showed a single substitution of threonine for asparagine at amino acid 124. Our results indicate that the multicellular behavior of STEC O111 is RpoS dependent via positive regulation of curli production. Aggregation may confer a fitness advantage in O111 outbreak strains under stressful conditions in hydrodynamic environments along the food production chain and in the host, while the occurrence of nonaggregative variants may allow the cell population to adapt to conditions benefiting a planktonic lifestyle.
Mycobacterium tuberculosis Resists Stress by Regulating PE19 Expression
Authors: Ramakrishnan Pavithra , Aagesen Alisha M. , McKinney John D. , Tischler Anna D.
Published: December 2015

Mycobacterium tuberculosisrequires the phosphate-sensing signal transduction system Pst/SenX3-RegX3 to resist host immune responses. A ΔpstA1mutant lacking a Pst phosphate uptake system component is hypersensitive to diverse stress conditionsin vitroand is attenuatedin vivodue to constitutive expression of the phosphate starvation-responsive RegX3 regulon. Transcriptional profiling of the ΔpstA1mutant revealed aberrant expression of certainpeandppegenes. PE and PPE proteins, defined by conserved N-terminal domains containing Pro-Glu (PE) or Pro-Pro-Glu (PPE) motifs, account for a substantial fraction of theM. tuberculosisgenome coding capacity, but their functions are largely uncharacterized. Because some PE and PPE proteins localize to the cell wall, we hypothesized that overexpression of these proteins sensitizesM. tuberculosisto stress by altering cell wall integrity. To test this idea, we deletedpeandppegenes that were overexpressed by ΔpstA1bacteria. Deletion of a singlepegene,pe19, suppressed hypersensitivity of the ΔpstA1mutant to both detergent and reactive oxygen species. Ethidium bromide uptake assays revealed increased envelope permeability of the ΔpstA1mutant that was dependent on PE19. The replication defect of the ΔpstA1mutant in NOS2−/−mice was partially reversed by deletion ofpe19, suggesting that increased membrane permeability due to PE19 overexpression sensitizesM. tuberculosisto host immunity. Our data indicate that PE19, which comprises only a 99-amino-acid PE domain, has a unique role in the permeability of theM. tuberculosisenvelope that is regulated to resist stresses encountered in the host.
Kinetics of Genetic Variation of the Mycoplasma genitalium MG192 Gene in Experimentally Infected Chimpanzees
Authors: Ma Liang , Jensen Jørgen S. , Mancuso Miriam , Myers Leann , Martin David H.
Published: December 2015

Mycoplasma genitalium
, a human pathogen associated with sexually transmitted diseases, is capable of causing chronic infections, though mechanisms for persistence remain unclear. Previous studies have found that variation of the MgPa operon occurs by recombination of repetitive chromosomal sequences (known as MgPars) into the MG191 and MG192 genes carried on this operon, which may lead to antigenic variation and immune evasion. In this study, we determined the kinetics of MG192 sequence variation during the course of experimental infection using archived specimens from two chimpanzees infected with
M. genitalium
strain G37. The highly variable region of MG192 was amplified by PCR from
M. genitalium
isolates obtained at various time points postinfection (p.i.). Sequence analysis revealed that MG192 sequence variation began at 5 weeks p.i. With the progression of infection, sequence changes accumulated throughout the MG192 variable region. The presence of MG192 variants at specific time points was confirmed by variant-specific PCR assays and sequence analysis of single-colony cloned
M. genitalium
organisms. MG192 nucleotide sequence variation correlated with estimated recombination events, predicted amino acid changes, and time of seroconversion, a finding consistent with immune selection of MG192 variants. In addition, we provided evidence that MG192 sequence variation occurred during the process of
M. genitalium
single-colony cloning. Such spontaneous variation suggests that some MG192 variation is independent of immune selection but may form the basis for subsequent immune selection.