Evaluation of a chromogenic agar medium for the detection of extended-spectrum ß-lactamase-producing Enterobacteriaceae

Aim: To compare the performance of a new chromogenic agar medium CHROMagar ESBL (KC‐ESBL) to chromID ESBL (SB‐ESBL) for the detection and presumptive identification of extended‐spectrum β‐lactamase (ESBL)‐producing Enterobacteriaceae directly from clinical specimens. Methods and Results: A total of 256 specimens were screened for ESBL producers. Also, the genotypes of the ESBLs and plasmid‐mediated AmpC β‐lactamases (pAmpCBLs) were characterized by PCR and sequencing. Among the 256 specimens, 17 (6·6%) ESBL producers were isolated on both media. The sensitivity, specificity, positive predictive value and negative predictive value were higher for KC‐ESBL (100, 93·3, 51·5 and 100%, respectively) than for SB‐ESBL (88·2, 92·9, 46·9 and 99·1%, respectively) (P = 0·72). Enterobacteriaceae harbouring pAmpCBL genes as well as chromosomal cephalosporinase‐ and penicillinase‐hyperproducing Enterobacteriaceae and Pseudomonas aeruginosa accounted for the false‐positive results. Conclusion: KC‐ESBL can detect ESBL producers from clinical specimens with good selectivity and rapid presumptive identification by means of colony colour at 24 h. Significance and Impact of the Study: This is the first study that has evaluated the performance of KC‐ESBL that enables the detection and presumptive identification of ESBL producers from clinical specimens.     

“7-in” medium,a simple medium for the rapid presumptive identification of bothSalmonella andShigella

A one-tube method using a homogeneous medium for the rapid screening of colonies forSalmonella as well asShigella is described. The selection is based on the following properties: 1) glucose fermentation (acid, gas), 2) lactose fermentation, 3) saccharose fermentation, 4) production of H₂S, 5) urease activity, 6) motility, and 7) indole production.     

Assessment of the multi-criteria evaluation system of the Welfare Quality® protocol for growing pigs

Animal welfare has become an important subject of public and political debate, leading to the necessity of an objective evaluation system for on-farm use. As welfare is a multi-dimensional concept, it makes sense to use a multi-criteria aggregation system to obtain an overall welfare score. Such an aggregation system is provided by the Welfare Quality® Network. The present paper focusses on the assessment of the multi-criteria evaluation model included in the Welfare Quality® protocol for growing pigs in order to aggregate the animal-based indicators first to criteria, then to principles and finally to an overall welfare score. Specifically, the importance of the indicators on the overall assessment of growing pig farms is analysed in a given population which consisted of a total of 198 protocol assessments carried out on a sample of 24 farms in Germany. By means of partial least squares modelling, the influence of measures in the calculation procedure is estimated by calculation and interpretation of Variable Importance for Projection (VIP) scores. Variable Importance for Projection scores revealed some meaningful, unexpected influences as the multi-criteria evaluation model of Welfare Quality® aimed at avoiding interferences and double-counting. Some of these influences led to the assumption that some measures might have potential as iceberg indicators, whereas others showed lesser importance. Thus, feasibility can be gained by the deletion and special weighting of indicators according to their importance. Altogether, the study is an essential contribution to the further development of the Welfare Quality® protocols as well as the application of multi-criteria decision systems in the field of animal welfare science in general.     

Assessment of β-tubulin gene as a complementary molecular marker for desert truffle identification: a study case on Tunisian samples

Tunisian desert truffles have been identified on the basis of the internal transcribed spacer (ITS) locus as Tirmania nivea, Terfezia bouderii and T. arenaria. ITS and, for the first time, β-tubulin gene were employed in the phylogenetic analyses of these species to assess whether β-tubulin gene could be a complementary molecular tool for resolution of phylogenetic species. From their comparison, both markers showed to be suitable to distinguish Tirmania nivea from Terfezia bouderii and T. arenaria and, focusing on the T. boudieri complex, to assign the phylogenetic types previously described. In addition to give a first glimpse into the distribution of desert truffles from north to south of Tunisia, we then suggest to use the β-tubulin gene as a complementary marker to ITS. This indication can be useful above all for the phylogenetic reconstruction of the T. boudieri complex.     

Assessment of the relationship between signal intensities and transcript concentration for Affymetrix GeneChip®arrays

Background

The availability of both mouse and human draft genomes has marked the beginning of a new era of comparative mammalian genomics. The two available mouse genome assemblies, from the public mouse genome sequencing consortium and Celera Genomics, were obtained using different clone libraries and different assembly methods.

Results

We present here a critical comparison of the two latest mouse genome assemblies. The utility of the combined genomes is further demonstrated by comparing them with the human 'golden path' and through a subsequent analysis of a resulting conserved sequence element (CSE) database, which allows us to identify over 6,000 potential novel genes and to derive independent estimates of the number of human protein-coding genes.

Conclusion

The Celera and public mouse assemblies differ in about 10% of the mouse genome. Each assembly has advantages over the other: Celera has higher accuracy in base-pairs and overall higher coverage of the genome; the public assembly, however, has higher sequence quality in some newly finished bacterial artifical chromosome clone (BAC) regions and the data are freely accessible. Perhaps most important, by combining both assemblies, we can get a better annotation of the human genome; in particular, we can obtain the most complete set of CSEs, one third of which are related to known genes and some others are related to other functional genomic regions. More than half the CSEs are of unknown function. From the CSEs, we estimate the total number of human protein-coding genes to be about 40,000. This searchable publicly available online CSEdb will expedite new discoveries through comparative genomics.     

Assessment of Schwanniomyces occidentalis as a host for protein production using the wide-range Xplor®2 expression platform

The wide-range transformation/expression platform, Xplor®2, was employed for the assessment of Schwanniomyces occidentalis as a potential producer of the recombinant proteins human IFNα2a (IFNα2a) and S. occidentalis fructofuranosidase (SFfase), and its efficiency was compared to that of Arxula adeninivorans. ADE2 and URA3 genes from both yeast species were isolated, characterized and used as selection markers in combination with the IFNα2a and SFfase expression modules, which used the strong constitutive A. adeninivorans-derived TEF1 promoter. Yeast rDNA integrative expression cassettes and yeast integrative expression cassettes equipped with a selection marker and expression modules were transformed into auxotrophic S. occidentalis and A. adeninivorans strains and a quantitative comparison of the expression efficiency was made. Whilst IFNα2a was mainly accumulated extracellularly (>95 %) in A. adeninivorans, extracellular SFfase (>90 %) was detected in both yeast species. The DNA composition of the selection marker modules and expression modules, especially their open reading frame codon usage, affects auxotrophy recovery as well as protein expression. Auxotrophy recovery was only achieved with selection marker modules of the homologous gene donor yeast. The concentration of recombinant IFNα2a was fivefold higher in A. adeninivorans (1 mg?L^?1), whereas S. occidentalis accumulated 1.5- to 2-fold more SFfase (0.5 Units ml^?1). These results demonstrate the extension of the use of the wide-range expression platform Xplor®2 to another yeast species of biotechnological interest.     

Evaluation of two commercial methods for the susceptibility testing of Candida species: Vitek 2® and Sensititre YeastOne®

Background

An increased incidence of fungal infections caused by Candida species, especially Candida glabrata and Candida krusei, which are less susceptible to azoles, has been observed. Standardized susceptibility testing is essential for clinical management and for monitoring the epidemiology of resistance.

Usefulness of core needle biopsy for the diagnosis of thyroid Burkitt’s lymphoma: a case report and review of the literature

Background

Thyroid lymphomas are an exceptional finding in patients with thyroid nodules. Burkitt’s lymphoma is one of the rarest and most aggressive forms of thyroid lymphomas, and its prognosis depends on the earliness of medical treatment. Given the rarity of this disease, making a prompt diagnosis can be challenging. For instance, fine-needle aspiration (FNA) cytology, which is the first-line diagnostic test that is performed in patients with thyroid nodules, is often not diagnostic in cases of thyroid lymphomas, with subsequent delay of the start of therapy.

Case presentation

Here we report the case of a 52-year-old woman presenting with a rapidly enlarging thyroid mass. Thyroid ultrasonography demonstrated a solid hypoechoic nodule. FNA cytology was only suggestive of a lymphoproliferative disorder and did not provide a definitive diagnosis. It is core needle biopsy (CNB) that helped us to overcome the limitations of routine FNA cytology, showing the presence of thyroid Burkitt’s lymphoma. Subsequent staging demonstrated bone marrow involvement. The early start of an intensive multi-agent chemotherapy resulted in complete disease remission. At 60 months after the diagnosis, the patient is alive and has not had any recurrence.

Conclusions

Clinicians should be aware that thyroid Burkitt’s lymphoma is an aggressive disease that needs to be treated with multi-agent chemotherapy as soon as possible. To diagnose it promptly, they should consider to order/perform a CNB in any patient with a rapidly enlarging thyroid mass that is suspicious for lymphoma.

     

Comparison between conventional methods, ChromAgar Candida® and PCR method for the identification of Candida species in clinical isolates

The increase in the incidence of yeast species causing fungemia in susceptible immunocompromised patients in the last two decades and the low sensitivity of conventional blood culture has led to the need to develop alternative approaches for the early detection and identification of causative species. The aim of this study was to compare the usefulness of molecular testing by the polymerase chain reaction (PCR) and conventional methods to identify clinical isolates of different species, using the ID32C ATB system (bioMérieux, France), chromogenic culture Chromagar Candida? (CHROMagar, France) and morphogenesis in corn meal agar. We studied 79 isolates, in which the most prevalent species using the system ID32C and PCR was C. albicans, followed by C. tropicalis, C. glabrata and C .krusei. PCR patterns obtained for the identification of clinical isolates were stable and consistent in the various independent studies and showed good reproducibility, concluding that PCR with species-specific primers that amplify genes ITS1 and ITS2 for rRNA or topoisomerase II primers is a very specific and sensitive method for the identification of C. glabrata, C. krusei, C. albicans, and with less specificity for C. tropicalis.     

Evaluation of CHROMagar™ StrepB agar, an aerobic chromogenic medium for prepartum vaginal/rectal Group B Streptococcus screening

An aerobic chromogenic medium, CHROMagar™ StrepB agar, designed for isolation of group B Streptococci, was evaluated on 285 prepartum vaginal/rectal swabs from pregnant women. After overnight enrichment in Todd-Hewitt broth containing 15 μg/ml nalidixic acid and 10 μg/ml colistin, sensitivities were respectively 79% on day 1 and 92% on day 2, and significantly higher than those achieved by blood agar (40% and 58%) and colimycin-nalidixic-acid agar (82% on day 2).     

Carboxymethylated-κ-casein: A convenient tool for the identification of polyphenolic inhibitors of amyloid fibril formation

Reduced and carboxymethylated-κ-casein (RCM-κ-CN) is a milk-derived amyloidogenic protein that readily undergoes nucleation-dependent aggregation and amyloid fibril formation via a similar pathway to disease-specific amyloidogenic peptides like amyloid beta (Aβ), which is associated with Alzheimer’s disease. In this study, a series of flavonoids, many known to be inhibitors of Aβ fibril formation, were screened for their ability to inhibit RCM-κ-CN fibrilisation, and the results were compared with literature data on Aβ inhibition. Flavonoids that had a high degree of hydroxylation and molecular planarity gave good inhibition of RCM-κ-CN fibril formation. IC₅₀ values were between 10- and 200-fold higher with RCM-κ-CN than literature results for Aβ fibril inhibition, however, with few exceptions, they showed a similar trend in potency. The convenience and reproducibility of the RCM-κ-CN assay make it an economic alternative first screen for Aβ inhibitory activity, especially for use with large compound libraries.     

Germination ecology of two closely related taxa in the genus Oenanthe: Fine tuning for the habitat?

For two closely related amphibious plant taxa of the genus Oenanthe (Apiaceae) germination traits were examined. Habitats of the two taxa differ in hydroregime. The endemic Oenanthe conioides of the river Elbe estuary experiences daily tidal fluctuations whereas the widespread Oenanthe aquatica grows at the edge of ponds and in freshwater wetlands with rare and unpredictable fluctuations of water table.Seeds of both taxa could be characterized as non-dormant and light dependent. Under temperature fluctuations, germination percentage was higher than under constant temperatures. Salinity was tolerated to up to 3.3‰. At 10‰ there was a strong decrease in germination percentage, which did not result from ionic toxicity, as experiments with a gradient in osmolarity showed.Differences between the taxa were found concerning hydrological and temperature fluctuations. While O. aquatica showed no reduction in germination percentage under permanent 1 cm flooding, O. conioides did. On the other hand, germination under an artificial tidal hydroregime was better in O. conioides than in O. aquatica. During fluctuating temperatures of 3/22 and 6/22 °C O. conioides germinated much quicker and had a higher final germination percentage.Differences between the taxa could be correlated with differences of the hydrological regime in the specific habitat. Taking into account that O. conioides is phylogenetically a relatively young taxon, it may be hypothesized that a quick adaptation to the tidal conditions might have taken place.     

Can we use the Shiga-bacteriophage as indicator for a faecal pollution of water?

Summary and conclusions In an important percentage of stools of healthy persons Shiga bacteriophage occurs.The Shiga bacteriophage occurs during some lapse of time in water which has been polluted by human faeces. The Shiga bacteriophage could be ascertained in water by means of the enrichment method ofNyberg.The Shiga bacteriophage method for indicating the pollution of strongly polluted water is as sensitive or sometimes less so than the methods ofEijkman and ofClemesha.For the examination of water in several stages of purification in water works the Shiga bacteriophage method is as sensitive or even more so than the other methods.The Shiga bacteriophage does not act strongly in the self-purification of polluted water.The Shiga bacteriophage may be used as indicator for a faecal pollution of water and this method may be applied along with the other bacteriological methods in water control. It may be advantageous to study more closely its limits and its benefits in the practice of water control     

Assessment of the efficacy of parasiticides for the control of tick infection in dogs under field conditions: what's new?

For their biological and ecological characteristics, ticks are vectors of the widest variety of pathogens causing tick-borne diseases (TBDs). Little information is available about the ways in which time spent by ticks to feed on hosts, transmission times and TBD prevention are related and it is exclusively limited to laboratory reports on adult stages. In particular, the time required by immature stages to transmit pathogens has not been determined for most TBDs. Considering their importance for animal and human health, effective control of immature ticks is advisable to reduce the damage ticks cause. Recently, the efficacy of a combination of imidacloprid 10%/permethrin 50% was compared with that of fipronil 10%/S-methoprene 9% against ticks when administered to naturally infected dogs. A semi-quantitative method was used to assess the methodological parameters to calculate drug efficacy on immature stages. On adult ticks, the efficacy of both products was high and overall very similar, whereas for the immature stages the combination of imidacloprid 10% and permethrin 50% had a higher efficacy than fipronil 10% and methoprene 9% throughout the observation period (statistically significant difference on day + 28 only). The semi-quantitative method proposed for the evaluation of immature stages can be considered a useful tool for calculating the efficacy of a drug in the field. Due the important role of immatures in the spread of TBDs, the immature tick load should be calculated to assess the efficacy of acaricidal products both under laboratory and field conditions.     

Safety profile of Coartem®: the evidence base

Background

Dihydroartemisinin (DHA), a powerful anti-malarial drug, has been used as monotherapy and artemisinin-based combination therapy (ACT) for more than decades. So far, however, the tissue distribution and metabolic profile of DHA data are not available from animal and humans.

Methods

Pharmacokinetics, tissue distribution, mass balance, and elimination of [¹⁴C] DHA have been studieded in rats following a single intravenous administration. Protein binding was performed with rat and human plasma. Drug concentrations were obtained up to 192 hr from measurements of total radioactivity and drug concentration to determine the contribution by the parent and metabolites to the total dose of drug injected from whole blood, plasma, urine and faecal samples.

Results

Drug was widely distributed after 1 hr and rapidly declined at 24 hr in all tissues except spleen until 96 hrs. Only 0.81% of the total radioactivity was detected in rat brain tissue. DHA revealed a high binding capacity with both rat and human plasma proteins (76–82%). The concentration of total radioactivity in the plasma fraction was less than 25% of that in blood total. Metabolism of DHA was observed with high excretion via bile into intestines and approximately 89–95% dose of all conjugations were accounted for in blood, urine and faeces. However, the majority of elimination of [¹⁴C] DHA was through urinary excretion (52% dose). The mean terminal half-lives of plasma and blood radioactivity (75.57–122.13 h) were significantly prolonged compared with that of unchanged DHA (1.03 h).

Conclusion

In rat brain, the total concentration of [¹⁴C] was 2-fold higher than that in plasma, indicating the radioactivity could easily penetrate the brain-blood barrier. Total radioactivity distributed in RBC was about three- to four-fold higher than that in plasma, suggesting that the powerful anti-malarial potency of DHA in the treatment of blood stage malaria may relate to the high RBC binding. Biliary excretion and multiple concentration peaks of DHA have been demonstrated with high urinary excretion due to a most likely drug re-absorption in the intestines (enterohepatic circulation). The long lasting metabolites of DHA (> 192 hr) in the rats may be also related to the enterohepatic circulation.     

Navigating the iceberg: reducing the number of parameters within the Welfare Quality® assessment protocol for dairy cows

The Welfare Quality® protocols provide a multidimensional assessment of welfare, which is lengthy, and hence limited in terms of practicality. The aim of this study was to investigate potential ‘iceberg indicators’ which could reliably predict the overall classification as a means of reducing the length of time for an assessment and so increase the feasibility of the Welfare Quality® protocol as a multidimensional assessment of welfare. Full Welfare Quality® assessments were carried out on 92 dairy farms in England and Wales. The farms were all classified as Acceptable or Enhanced. Logistic regression models with cross validation were used to compare model fit for the overall classification on farms. ‘Absence of prolonged thirst’, on its own, was found to correctly classify farms 88% of the time. More generally, the inclusion of more measures in the models was not associated with greater predictive ability for the overall classification. Absence of prolonged thirst could thus, in theory, be considered to be an iceberg indicator for the Welfare Quality® protocol, and could reduce the length of time for a farm assessment to 15 min. Previous work has shown that the parameters within the Welfare Quality® protocol are important and relevant for welfare assessment. However, it is argued that the credibility of the published aggregation system is compromised by the finding that one resource measure (Absence of prolonged thirst) is a major driver for the overall classification. It is therefore suggested that the prominence of Absence of prolonged thirst in this role may be better understood as an unintended consequence of the published measure aggregation system rather than as reflecting a realistic iceberg indicator.