GUT MICROBIOME DIVERSITY OF THREE RHINOCEROS SPECIES IN EUROPEAN ZOOS.

The wild rhinoceros populations have declined drastically in the past decades because the rhinoceros are heavily hunted for their horns. Zoological institutions aim to conserve rhinoceros populations in captivity, but one of the challenges of ex situ conservation is to provide food sources that resemble those available in the wild. Considering that the mammalian gut microbiota is a pivotal player in their host's health, the gut microbiota of rhinoceros may also play a role in the bioavailability of nutrients. Therefore, this study aims to characterize the fecal microbiome composition of grazing white rhinoceros (WR; Ceratotherium simum) and greater one-horned rhinoceros (GOHR; Rhinoceros unicornis) as well as the browsing black rhinoceros (BR; Diceros bicornis) kept in European zoos. Over the course of 1 yr, 166 fecal samples in total were collected from 9 BR (n = 39), 10 GOHR (n = 56), and 14 WR (n = 71) from 23 zoological institutions. The bacterial composition in the samples was determined using 16S rRNA gene Illumina sequencing. The fecal microbiomes of rhinoceros clustered by species, with BR clustering more distantly from GOHR and WR. Furthermore, the data report clustering of rhinoceros microbiota according to individual rhinoceros and institutional origin, showing that zoological institutions play a significant role in shaping the gut microbiome of rhinoceros species. In addition, BR exhibit a relatively higher microbial diversity than GOHR and WR. BR seem more susceptible to microbial gut changes and appear to have a more diverse microbiome composition among individuals than GOHR and WR. These data expand on the role of gut microbes and can provide baseline data for continued efforts in rhinoceros conservation and health status.

Prevalence of active tuberculosis infection in transplant recipients: A systematic review and meta-analysis.

INTRODUCTION: Tuberculosis (TB) is considered as a serious complication of organ transplant; therefore, the detection and appropriate treatment of active TB infection is highly recommended for the reduction of mortality in the future. The aim of this review was to conduct a systematic review and meta-analysis assessing the prevalence of active TB infection in transplant recipients (TRs). MATERIAL AND METHODS: Electronic databases, including MEDLINE (via PubMed), SCOPUS and Web of Science were searched up to December 24, 2017. The prevalence of active TB was estimated using the random effects meta-analysis. Heterogeneity was evaluated by subgroup analysis. Data were analyzed by STATA version 14. RESULTS: The pooled prevalence of post-transplant active TB was estimated 3% [95% CI: 2-3]. The pooled prevalence of active TB in different transplant forms was as follows: renal,3% [95% CI: 2-4]; stem cell transplant (SCT), 1% [95% CI: 0-3]; lung, 4% [95% CI: 2-6]; heart, 3% [95% CI: 2-4]; liver, 1% [95% CI: 1], and hematopoietic stem cell transplant (HSCT), 2% [95% CI: 1-3]. The prevalence of different clinical presentations of TB was as follows: pulmonary TB (59%; 95% CI: 54-65), extra pulmonary TB (27%; 95% CI: 21-33), disseminated TB (15%; 95% CI: 12-19) and miliary TB (8%; 95% CI: 4-13). The pooled prevalence of different diagnostic tests was as follows: chest X-ray, 57% [95% CI, 46-67]; culture, 56% [95% CI, 45-68]; smear, 49% [95% CI, 40-58]; PCR, 43% [95% CI, 40-58]; histology, 26% [95% CI, 20-32], and tuberculin skin test, 19% [95% CI, 10-28]. CONCLUSION: A high suspicion level for TB, the early diagnosis and the prompt initiation of therapy could increase the survival rates among SOT patients. Overall, renal and lung TRs appear to have a higher predisposition for acquiring TB than other type of recipients. Monitoring of the high-risk recipients, prompt diagnosis, and appropriate treatment are required to manage TB infection among TRs especially in endemic areas.

Integrating drone imagery with existing rangeland monitoring programs.

The recent availability of small and low-cost sensor carrying unmanned aerial systems (UAS, commonly known as drones) coupled with advances in image processing software (i.e., structure from motion photogrammetry) has made drone-collected imagery a potentially valuable tool for rangeland inventory and monitoring. Drone-imagery methods can observe larger extents to estimate indicators at landscape scales with higher confidence than traditional field sampling. They also have the potential to replace field methods in some instances and enable the development of indicators not measurable from the ground. Much research has already demonstrated that several quantitative rangeland indicators can be estimated from high-resolution imagery. Developing a suite of monitoring methods that are useful for supporting management decisions (e.g., repeatable, cost-effective, and validated against field methods) will require additional exploration to develop best practices for image acquisition and analytical workflows that can efficiently estimate multiple indicators. We embedded with a Bureau of Land Management (BLM) field monitoring crew in Northern California, USA to compare field-measured and imagery-derived indicator values and to evaluate the logistics of using small UAS within the framework of an existing monitoring program. The unified workflow we developed to measure fractional cover, canopy gaps, and vegetation height was specific for the sagebrush steppe, an ecosystem that is common in other BLM managed lands. The correspondence between imagery and field methods yielded encouraging agreement while revealing systematic differences between the methods. Workflow best practices for producing repeatable rangeland indicators is likely to vary by vegetation composition and phenology. An online space dedicated to sharing imagery-based workflows could spur collaboration among researchers and quicken the pace of integrating drone-imagery data within adaptive management of rangelands. Though drone-imagery methods are not likely to replace most field methods in large monitoring programs, they could be a valuable enhancement for pressing local management needs.

The efficacy of lyticase and ß-glucosidase enzymes on biofilm degradation of Pseudomonas aeruginosa strains with different gene profiles.

BACKGROUND: Pseudomonas aeruginosa is a nosocomial pathogen that causes severe infections in immunocompromised patients. Biofilm plays a significant role in the resistance of this bacterium and complicates the treatment of its infections. In this study, the effect of lyticase and ß-glucosidase enzymes on the degradation of biofilms of P. aeruginosa strains isolated from cystic fibrosis and burn wound infections were assessed. Moreover, the decrease of ceftazidime minimum biofilm eliminating concentrations (MBEC) after enzymatic treatment was evaluated. RESULTS: This study demonstrated the effectiveness of both enzymes in degrading the biofilms of P. aeruginosa. In contrast to the lyticase enzyme, ß-glucosidase reduced the ceftazidime MBECs significantly (P < 0.05). Both enzymes had no cytotoxic effect on the A-549 human lung carcinoma epithelial cell lines and A-431 human epidermoid carcinoma cell lines. CONCLUSION: Considering the characteristics of the ß-glucosidase enzyme, which includes the notable degradation of P. aeruginosa biofilms and a significant decrease in the ceftazidime MBECs and non-toxicity for eukaryotic cells, this enzyme can be a promising therapeutic candidate for degradation of biofilms in burn wound patients, but further studies are needed.

Convergence in relationships between leaf traits, spectra and age across diverse canopy environments and two contrasting tropical forests.

Leaf age structures the phenology and development of plants, as well as the evolution of leaf traits over life histories. However, a general method for efficiently estimating leaf age across forests and canopy environments is lacking. Here, we explored the potential for a statistical model, previously developed for Peruvian sunlit leaves, to consistently predict leaf ages from leaf reflectance spectra across two contrasting forests in Peru and Brazil and across diverse canopy environments. The model performed well for independent Brazilian sunlit and shade canopy leaves (R2  = 0.75-0.78), suggesting that canopy leaves (and their associated spectra) follow constrained developmental trajectories even in contrasting forests. The model did not perform as well for mid-canopy and understory leaves (R2  = 0.27-0.29), because leaves in different environments have distinct traits and trait developmental trajectories. When we accounted for distinct environment-trait linkages - either by explicitly including traits and environments in the model, or, even better, by re-parameterizing the spectra-only model to implicitly capture distinct trait-trajectories in different environments - we achieved a more general model that well-predicted leaf age across forests and environments (R2  = 0.79). Fundamental rules, linked to leaf environments, constrain the development of leaf traits and allow for general prediction of leaf age from spectra across species, sites and canopy environments.

Land Use and Environmental Variability Impacts on the Phenology of Arid Agro-Ecosystems.

The overexploitation of water resources in arid environments often results in abandonment of large extensions of agricultural lands, which may (1) modify phenological trends, and (2) alter the sensitivity of specific phenophases to environmental triggers. In Mexico, current governmental policies subsidize restoration efforts, to address ecological degradation caused by abandonments; however, there is a need for new approaches to assess their effectiveness. Addressing this, we explore a method to monitor and assess (1) land surface phenology trends in arid agro-ecosystems, and (2) the effect of climatic factors and restoration treatments on the phenology of abandoned agricultural fields. We used 16-day normalized difference vegetation index composites from the moderate resolution imaging spectroradiometer from 2000 to 2009 to derive seasonal phenometrics. We then derived phenoclimatic variables and land cover thematic maps, to serve as a set of independent factors that influence vegetation phenology. We conducted a multivariate analysis of variance to analyze phenological trends among land cover types, and developed multiple linear regression models to assess influential climatic factors driving phenology per land cover analyzed. Our results suggest that the start and length of the growing season had different responses to environmental factors depending on land cover type. Our analysis also suggests possible establishment of arid adapted species (from surrounding ecosystems) in abandoned fields with longer times since abandonment. Using this approach, we were able increase our understanding on how climatic factors influence phenology on degraded arid agro-ecosystems, and how this systems evolve after disturbance.

Productivity and phenological responses of natural vegetation to present and future inter-annual climate variability across semi-arid river basins in Chile.

Time series of vegetation indices and remotely sensed phenological data offer insights about the patterns in vegetation dynamics. Both are useful sources of information for analyzing and monitoring ecosystem responses to environmental variations caused by natural and anthropogenic drivers. In the semi-arid region of Chile, climate variability and recent severe droughts in addition to land-use changes pose threats to the stability of local ecosystems. Normalized difference vegetation index time series (2000-2013) data from the moderate resolution imaging spectroradiometer (MODIS) was processed to monitor the trends and patterns of vegetation productivity and phenology observed over the last decade. An analysis of the relationship between (i) vegetation productivity and (ii) precipitation and temperature data for representative natural land-use cover classes was made. Using these data and ground measurements, productivity estimates were projected for two climate change scenarios (RCP2.6 and RCP8.5) at two altitudinal levels. Results showed negative trends of vegetation productivity below 2000 m a.s.l. and positive trends for higher elevations. Phenology analysis suggested that mountainous ecosystems were starting their growing period earlier in the season, coinciding with a decreased productivity peak during the growing season. The coastal shrubland/grassland land cover class had a significant positive relation with rainfall and a significant negative relation with temperature, suggesting that these ecosystems are vulnerable to climate change. Future productivity projections indicate that under an RCP8.5 climate change scenario, productivity could decline by 12% in the period of 2060-2100, leading to a severe vegetation degradation at lower altitudes and in drier areas.

Polymerase chain reaction for Enterococcus faecalis in drain fluid: the first screening test for symptomatic colorectal anastomotic leakage. The Appeal-study: analysis of parameters predictive for evident anastomotic leakage.

PURPOSE: With current diagnostic methods, the majority of patients with symptomatic colorectal anastomotic leakage(CAL) is identified approximately 1 week after operation.The aim of this study is to determine whether real-time polymerase chain reaction (RT-PCR) for detection of Escherichia coli and Enterococcus faecalis on drain fluid can serve as a screening test for CAL in the early postoperative phase. METHODS: All patients included in this multicenter prospective observational study underwent left-sided colorectal resection for both malignant and benign diseases with construction of an anastomosis. In all patients, an intra-abdominal drain was placed during operation. During the first five postoperative days, drain fluid was processed for RT-PCR. The quantitative results of the RT-PCR on days 2 to 5 were compared to the results of day 1 in order to detect concentration changes. RESULTS: In total, 243 patients, with both benign and malignant diseases, were included of whom 19 (7.8 %) developed symptomatic CAL. An increase in E. coli concentration was found insignificantly more patients with CAL on day 4 and 5 [p =0.0004; diagnostic odds ratio (DOR) 7.9]. For E. faecalis, this result was found for days 2, 3, and 4 (p <0.003) with highest DOR on day 3 (31.6). Sensitivity and negative predictive values were 92.9 and 98.7 %, respectively, virtually ruling out CAL in case of negative test results on the third postoperative day. CONCLUSION: Quantitative PCR for E. faecalis performed on drain fluid may be an objective, affordable and fast screening tool for symptomatic colorectal anastomotic leakage.

Molecular analysis and the toxin, MSCRAMM, and biofilm genes of methicillin-resistant Staphylococcus aureus strains isolated from pemphigus wounds: A study based on SCCmec and dru typing.

INTRODUCTION: Pemphigus is a chronic autoimmune blistering disease. Pemphigus blisters can damage the natural skin barrier and increase the risk of life-threatening conditions. Colonization of pemphigus wounds with methicillin-resistant Staphylococcus aureus (MRSA) prolongs wound healing and increases mortality rate. Assessing MRSA prevalence, types, and toxin and adhesion genes can facilitate the detection of MRSA strains which cause infections, selection of appropriate treatments, and healing of pemphigus wounds. This study aimed to determine the SCCmec, the direct repeat unit (dru) types (dts), and the toxin, MSCRAMM, and biofilm genes of MRSA strains isolated from pemphigus wounds. METHODS: In this cross-sectional study, 118 S. aureus isolates were gathered from 118 patients with pemphigus. MRSA detection was performed using the mecA gene. Using the polymerase chain reaction method, all MRSA isolates were assessed for the presence of the sea, seb, sec, tst, eta, pvl, hla, hlb, MSCRAMM, and ica genes. Typing and subtyping were performed through respectively SCCmec typing and dru typing methods. The Bionumerics software was used for analyzing the data and drawing the minimum spanning tree. FINDINGS: From 118 S. aureus isolates, 51 were MRSA. SCCmec typing revealed the prevalence of SCCmec II with a prevalence of 64.7% (33 out of 51 isolates) and SCCmec III with a prevalence of 35.3% (18 out of 51 isolates). Dru typing indicated seven dts, namely dts 10a, 10g, 10m, 13i, 8h, 8i, and 9ca in two main clusters. The dt9ca was a new dru type and was registered in the dru-typing database (www.dru-typing.org). The prevalence rates of the hla, sea, and sec genes in MRSA isolates were respectively 54.9%, 27.4%, and 1.9%, while the hlb, seb, eta, and pvl genes were not detected at all. Only one MRSA with SCCmec III and dt10a carried the tst encoding gene. MSCRAMM gene analysis revealed the high prevalence of the eno (31.3%) and the fib (21.5%) genes. The prevalence rates of the icaA and icaD biofilm formation genes were 3.9% and 5.8%, respectively. There were no significant differences between the two detected SCCmec types and between the two detected dts clusters respecting the prevalence of the encoding genes of virulence factors and MSCRAMMs. CONCLUSION: The toxin genes hla and sea are prevalent among MRSA strains with SCCmec II and III isolated from pemphigus wounds. The most prevalent dts are dt10a and dt10g among MRSA with SCCmec III and dt8h and dt8i among MRSA with SCCmec II.

Combinatorial effects of antibiotics and enzymes against dual-species Staphylococcus aureus and Pseudomonas aeruginosa biofilms in the wound-like medium.

Bacterial biofilms are one of the major issues in the treatment of chronic infections such as chronic wounds, where biofilms are typically polymicrobial. The synergy between species can occur during most polymicrobial infections, where antimicrobial resistance enhances as a result. Furthermore, self-produced extracellular polymeric substance (EPS) in biofilms results in a high tolerance to antibiotics that complicates wound healing. Since most antibiotics fail to remove biofilms in chronic infections, new therapeutic modalities may be required. Disruption of EPS is one of the effective approaches for biofilm eradication. Therefore, degradation of EPS using enzymes may result in improved chronic wounds healing. In the current study, we investigated the efficacy of trypsin, ß-glucosidase, and DNase I enzymes on the degradation of dual-species biofilms of Pseudomonas aeruginosa and Staphylococcus aureus in a wound-like medium. These species are the two most common bacteria associated with biofilm formation in chronic wounds. Moreover, the reduction of minimum biofilm eradication concentration (MBEC) of meropenem and amikacin was evaluated when combined with enzymes. The minimum effective concentrations of trypsin, ß-glucosidase, and DNase I enzymes to degrade biofilms were 1 µg/ml, 8 U/ml, and 150 U/ml, respectively. Combination of 0.15 µg/ml trypsin and 50 U/ml DNase I had a significant effect on S. aureus-P. aeruginosa biofilms which resulted in the dispersal and dissolution of all biofilms. In the presence of the enzymatic mixture, MBECs of antibiotics showed a significant decrease (p < 0.05), at least 2.5 fold. We found that trypsin/DNase I mixture can be used as an anti-biofilm agent against dual-species biofilms of S. aureus-P. aeruginosa.

A new portable sampler to monitor pollen at street level in the environment of patients.

Allergic rhinitis caused by pollen exposure is one of the most common allergic diseases. Therefore monitoring pollen levels in ambient air is an important tool in research and health care. Most European monitoring stations collect airborne pollen at rooftop levels for measurements in the larger surrounding of the sampling station, and not in the direct environment of sensitized subjects. Here we present the development and evaluation of a portable pollen sampler, called "Pollensniffer", that was designed to collect pollen in the immediate environment of allergic subjects. Validation of the Pollensniffer against the standard volumetric pollen sampler showed for most pollen types high correlations between the number of pollen collected by those two devices (Spearman's Correlation Coefficient > 0.8); the Pollensniffer appeared to collect on average 5.8 times more pollen per hour than the static sampler. Pollen monitoring was performed using this Pollensniffer at street level at 3 different locations in the city of Leiden during 22 weeks in 2017 and 21 weeks in 2018, during three 15-min periods a day and at one day in the week. The results showed that the pollen levels for birch and grass pollen can significantly differ from location to location and per time of day. Furthermore, the Pollensniffer measurements at street level showed that birch and grass pollen grains were detected 1 1/2 and 2-3 weeks, respectively, before detection at rooftop level. The street measurements show that allergic subjects can encounter varying pollen levels throughout the city and that they can be exposed to grass and birch pollen and may experience hay fever symptoms, even before the sampler at rooftop level registers these pollen.

Optical fingerprinting in bacterial epidemiology: Raman spectroscopy as a real-time typing method.

Hospital-acquired infections (HAI) increase morbidity and mortality and constitute a high financial burden on health care systems. An effective weapon against HAI is early detection of potential outbreaks and sources of contamination. Such monitoring requires microbial typing with sufficient reproducibility and discriminatory power. Here, a microbial-typing method is presented, based on Raman spectroscopy. This technique provides strain-specific optical fingerprints in a few minutes instead of several hours to days, as is the case with genotyping methods. Although the method is generally applicable, we used 118 Staphylococcus aureus isolates to illustrate that the discriminatory power matches that of established genotyping techniques (numerical index of diversity [D]=0.989) and that concordance with the gold standard (pulsed-field gel electrophoresis) is high (95%). The Raman clustering of isolates was reproducible to the strain level for five independent cultures, despite the various culture times from 18 h to 24 h. Furthermore, this technique was able to classify stored (-80 degrees C) and recent isolates of a methicillin-resistant Staphylococcus aureus-colonized individual during surveillance studies and did so days earlier than established genotyping techniques did. Its high throughput and ease of use make it suitable for use in routine diagnostic laboratory settings. This will set the stage for continuous, automated, real-time epidemiological monitoring of bacterial infections in a hospital, which can then be followed by timely corrective action by infection prevention teams.

Co-evolutionary aspects of human colonisation and infection by Staphylococcus aureus.

Although Staphylococcus aureus is a bacterial species of medical significance, only approximately 30% of all humans carry staphylococcal cells persistently but asymptomatically in their nasopharynx and/or other body sites. This goes largely unnoticed by the host, which shows that in the natural situation the human ecosystem is hospitable or at least receptive to the bacteria and that by a process of co-evolution this has lead to a state of mutual acceptance or tolerance. However, upon disturbance of this balanced, neutral state, localized or disseminated invasive infection can occur. Unfortunately, the events leading to infection are still largely unknown and especially the causal events leading to the transition from colonization to infection are ill-defined in vivo. Whether certain genotypes of S. aureus are more prone to colonise and/or infect humans is still quite heavily debated. The genetic population structure of S. aureus has been largely solved by using a number of different DNA polymorphism-interrogating laboratory methods. However, even this major effort has not (yet) revealed major clues with respect to colonisation and infection potency of the clonal lineages that were thus identified, except for the fact that certain lineages are highly epidemic. The overall picture is that in principle all S. aureus strains can become invasive given the proper circumstances. What these, primarily host-defined circumstances are is still enigmatic. However, a large variety of staphylococcal virulence and colonization factors have been identified as well as a number of host' colonisation and infection susceptibility traits. How these are specifically involved in colonisation and infection has been experimentally substantiated in only a limited number of cases. The present review paper will explore the relevance of these and other, for instance environmental factors that define the colonisation or infection state in humans. When the nature of these states would be known in more detail, this knowledge could be used to design novel and empirical, knowledge-driven means of preventing colonisation from proceeding into S. aureus infection.

Methicillin-resistant and -susceptible Staphylococcus aureus sequence type 398 in pigs and humans.

Methicillin-resistant Staphylococcus aureus sequence type 398 (ST398 MRSA) was identified in Dutch pigs and pig farmers. ST398 methicillin-susceptible S. aureus circulates among humans at low frequency (0.2%) but was isolated in 3 human cases of bacteremia (2.1%; p = 0.026). Although its natural host is probably porcine, ST398 MRSA likely causes infections in humans.

Host-microbe interplay in persistent Staphylococcus aureus nasal carriage in HIV patients.

It has been shown that persistent Staphylococcus aureus nasal carriage results in increased bacterial dispersal and a higher risk of infection compared to non-or-intermittent S. aureus carriage. Although many studies investigated S. aureus nasal carriage in HIV patients, none compared persistent carriage to non-persistent carriage nor were studies performed in the HAART era. We investigated the host-microbe interplay of persistent S. aureus nasal carriage in HIV-infected patients by studying host determinants of persistent carriage as well as the genetic structure of S. aureus strains isolated. We compared this genetic structure with the previously determined population structure of S. aureus isolates obtained from healthy individuals. Between February 2004 and June 2005 all HIV patients visiting the outpatient department of Erasmus MC (Rotterdam, The Netherlands) were asked to participate in this study. Participants were interviewed and screened for persistent S. aureus carriage using two semi-quantitative nasal swab cultures. For 443 patients two cultures were available, 131 (29.6%) were persistent carriers, which is significantly higher as compared to healthy individuals from the same geographic region (17.6%; P<0.0001). Male sex (odds ratio [OR], 2.22; 95% confidence interval [CI], 1.32-3.73), current smoking (OR, 0.58; 95% CI, 0.38-0.90), Pneumocystis jiroveci pneumonia (PCP) prophylaxis (OR, 0.39; 95% CI, 0.16-0.97) and antiretroviral therapy (OR, 0.61; 95% CI, 0.38-0.98) were independent determinants of persistent carriage. Only two strains were mecA positive (1.2%) and no PVL positive strains were detected. The population structure of S. aureus strains isolated from HIV patients appeared to be strongly overlapping with that of S. aureus isolates from healthy individuals.

RespiFinder: a new multiparameter test to differentially identify fifteen respiratory viruses.

Broad-spectrum analysis for pathogens in patients with respiratory tract infections is becoming more relevant as the number of potential infectious agents is still increasing. Here we describe the new multiparameter RespiFinder assay, which is based on the multiplex ligation-dependent probe amplification (MLPA) technology. This assay detects 15 respiratory viruses in one reaction. The MLPA reaction is preceded by a preamplification step which ensures the detection of both RNA and DNA viruses with the same specificity and sensitivity as individual monoplex real-time reverse transcription-PCRs. The RespiFinder assay was validated with 144 clinical samples, and the results of the assay were compared to those of cell culture and a respiratory syncytial virus (RSV)-specific immunochromatography assay (ICA). Compared to the cell culture results, the RespiFinder assay showed specificities and sensitivities of 98.2% and 100%, respectively, for adenovirus; 96.4% and 100%, respectively, for human metapneumovirus; 98.2% and 100%, respectively, for influenza A virus (InfA); 99.1% and 100%, respectively, for parainfluenza virus type 1 (PIV-1); 99.1% and 80%, respectively, for PIV-3; 90.1% and 100%, respectively, for rhinovirus; and 94.6% and 100%, respectively, for RSV. Compared to the results of the RSV-specific ICA, the RespiFinder assay gave a specificity and a sensitivity of 82.4% and 80%, respectively. PIV-2, PIV-4, influenza B virus, InfA H5N1, and coronavirus 229E were not detected in the clinical specimens tested. The use of the RespiFinder assay resulted in an increase in the diagnostic yield compared to that obtained by cell culture (diagnostic yields, 60% and 35.5%, respectively). In conclusion, the RespiFinder assay provides a user-friendly and high-throughput tool for the simultaneous detection of 15 respiratory viruses with excellent overall performance statistics.

Detection of methicillin-resistant Staphylococcus aureus in a low-prevalence setting by polymerase chain reaction with a selective enrichment broth.

The objective of this study was to evaluate the test characteristics of a modified BD GeneOhm methicillin-resistant Staphylococcus aureus (MRSA) assay on individual and pooled samples in a setting of low MRSA prevalence. The results of the polymerase chain reaction (PCR) assay were compared with culture results from a selective phenol red mannitol broth subcultured after 48 h. Sensitivity, specificity, and positive and negative predictive values (PPV and NPV, respectively) were calculated. For individual testing, 581 samples from 201 persons were collected; 18 (3.2%) were MRSA culture positive. Five hundred ten broths from 174 persons were combined in 106 pools after overnight incubation; 8 pools (7.5%) contained 1 or more MRSA culture-positive specimens. There were no inhibited PCR tests. The combined sensitivity of individual and pooled specimens was 92% (95% confidence interval [CI], 73-99%), the specificity was 98% (95% CI, 96-99%), and the PPV and NPV were 63% and 99.7%, respectively. Our modified procedure gives satisfactory results, and the pooling of broths may reduce costs.

Monitoring the Effects of Forest Restoration Treatments on Post-Fire Vegetation Recovery with MODIS Multitemporal Data.

This study examines how satellite based time-series vegetation greenness data and phenological measurements can be used to monitor and quantify vegetation recovery after wildfire disturbances and examine how pre-fire fuel reduction restoration treatments impact fire severity and impact vegetation recovery trajectories. Pairs of wildfire affected sites and a nearby unburned reference site were chosen to measure the post-disturbance recovery in relation to climate variation. All site pairs were chosen in forested uplands in Arizona and were restricted to the area of the Rodeo-Chediski fire that occurred in 2002. Fuel reduction treatments were performed in 1999 and 2001. The inter-annual and seasonal vegetation dynamics before, during, and after wildfire events can be monitored using a time series of biweekly composited MODIS NDVI (Moderate Resolution Imaging Spectroradiometer - Normalized Difference Vegetation Index) data. Time series analysis methods included difference metrics, smoothing filters, and fitting functions that were applied to extract seasonal and inter-annual change and phenological metrics from the NDVI time series data from 2000 to 2007. Pre- and post-fire Landsat data were used to compute the Normalized Burn Ratio (NBR) and examine burn severity at the selected sites. The phenological metrics (pheno-metrics) included the timing and greenness (i.e. NDVI) for the start, peak and end of the growing season as well as proxy measures for the rate of green-up and senescence and the annual vegetation productivity. Pre-fire fuel reduction treatments resulted in lower fire severity, which reduced annual productivity much less than untreated areas within the Rodeo-Chediski fire perimeter. The seasonal metrics were shown to be useful for estimating the rate of post-fire disturbance recovery and the timing of phenological greenness phases. The use of satellite time series NDVI data and derived pheno-metrics show potential for tracking vegetation cover dynamics and successional changes in response to drought, wildfire disturbances, and forest restoration treatments in fire-suppressed forests.

Prevalence of Group B Streptococcus in Pregnant Women in Iran: A Systematic Review and Meta-analysis.

BACKGROUND: Group B Streptococcus (GBS or S. agalactiae) is a major cause of severe disease in neonates. In perinatal infections or early-onset disease, GBS is transmitted vertically to the newborn from the birth canal during labor and delivery. Limited information is available on the prevalence of GBS recto-vaginal colonization among pregnant women in Iran. METHODS: We performed a systematic search by using different electronic databases including Medline (via Pubmed), Embase, Web of Science and Iranian Database. Meta-analysis was performed by Comprehensive Meta-Analysis (Biostat V2.2) software. RESULTS: Of 250 articles published from January 2000 to September 2016, 25 studies that reported incidence of GBS colonization in pregnant women were included in this review. The meta-analyses showed that the prevalence of GBS colonization among Iranian pregnant women was 9.8% (95% confidence interval, 7.9-12). CONCLUSIONS: The results of this study indicate that GBS screening measures and chemoprophylaxis guidelines concerning GBS infections must be established for pregnant women in Iran, and these guidelines must provide guidance for obstetricians, midwives and neonatologists on the prevention of GBS infections.

High diversity in SCCmec elements among multidrug-resistant Staphylococcus haemolyticus strains originating from paediatric patients; characterization of a new composite island.

PURPOSE: Staphylococcus haemolyticus has emerged as a highly antimicrobial-resistant healthcare-associated pathogen, in particular for patients admitted to neonatal intensive care. The objective of this study was to study the nature of SCCmec types among MDR-SH strains isolated from paediatric patients. METHODOLOGY: S. haemolyticus strains (n=60) were isolated from paediatric patients. Antibiotic resistance patterns were established using the disk agar diffusion and micro-broth dilution methods. SCCmec typing was performed using whole-genome sequencing (WGS) and an additional PCR analysis. RESULTS: All S. haemolyticus isolates demonstrated multidrug resistance. Using WGS, various novel mec types and combinations of SCCmec types were found, including a new composite island [SCCmec type V (Vd)+SCC cad/ars/cop] comprising 30 % of the strains. SCCmec type V was identified in 23 % of the isolates. A combination of the mecA gene enclosed by two copies of IS431 and absence of the mecRI and ccr genes was identified in 11 strains. In total, mecA regulatory genes were absent in all SH isolates used in this study. CONCLUSION: A high diversity of SCCmec elements with the prevalence of a new composite island was determined among MRSH strains. The structure of the composite island represented by MDR-SH strains in this study, in combination with the presence of a restriction-modification system type III, is described for the first time in this study. The presence of an 8 bp direct repeat (DR) and the sequences flanking the DR may support the integration of the mecA gene complex as a composite transposon (IS431-mecA-IS431) independently from recombinase genes.