Strategies for the identification of disease-related patterns of volatile organic compounds: prediction of paratuberculosis in an animal model using random forests

Modern statistical methods which were developed for pattern recognition are increasingly being used for data analysis in studies on emissions of volatile organic compounds (VOCs). With the detection of disease-related VOC profiles, novel non-invasive diagnostic tools could be developed for clinical applications. However, it is important to bear in mind that not all statistical methods are equally suitable for the investigation of VOC profiles. In particular, univariate methods are not able to discover VOC patterns as they consider each compound separately. The present study demonstrates this fact in practice. Using VOC samples from a controlled animal study on paratuberculosis, the random forest classification method was applied for pattern recognition and disease prediction. This strategy was compared with a prediction approach based on single compounds. Both methods were framed within a cross-validation procedure. A comparison of both strategies based on these VOC data reveals that random forests achieves higher sensitivities and specificities than predictions based on single compounds. Therefore, it will most likely be more fruitful to further investigate VOC patterns instead of single biomarkers for paratuberculosis. All methods used are thoroughly explained to aid the transfer to other data analyses.

Progressive glycosylation of the haemagglutinin of avian influenza H5N1 modulates virus replication, virulence and chicken-to-chicken transmission without significant impact on antigenic drift

Highly pathogenic H5N1 avian influenza virus (A/H5N1) devastated the poultry industry and continues to pose a pandemic threat. Studying the progressive genetic changes in A/H5N1 after long-term circulation in poultry may help us to better understand A/H5N1 biology in birds. A/H5N1 clade 2.2.1.1 antigenic drift viruses have been isolated from vaccinated commercial poultry in Egypt. They exhibit a peculiar stepwise accumulation of glycosylation sites (GS) in the haemagglutinin (HA) with viruses carrying, beyond the conserved 5 GS, additional GS at amino acid residues 72, 154, 236 and 273 resulting in 6, 7, 8 or 9 GS in the HA. Available information about the impact of glycosylation on virus fitness and pathobiology is mostly derived from mammalian models. Here, we generated recombinant viruses imitating the progressive acquisition of GS in HA and investigated their biological relevance in vitro and in vivo. Our in vitro results indicated that the accumulation of GS correlated with increased glycosylation, increased virus replication, neuraminidase activity, cell-to-cell spread and thermostability, however, strikingly, without significant impact on virus escape from neutralizing antibodies. In vivo, glycosylation modulated virus virulence, tissue tropism, replication and chicken-to-chicken transmission. Predominance in the field was towards viruses with hyperglycosylated HA. Together, progressive glycosylation of the HA may foster persistence of A/H5N1 by increasing replication, stability and bird-to-bird transmission without significant impact on antigenic drift.

Prevalence of the C-terminal truncations of NS1 in avian influenza A viruses and effect on virulence and replication of a highly pathogenic H7N1 virus in chickens

Highly pathogenic (HP) avian influenza viruses (AIV) evolve from low pathogenic (LP) precursors after circulation in poultry by reassortment and/or single mutations in different gene segments including that encoding NS1. The carboxyl terminal end (CTE) of NS1 exhibits deletions between amino acid 202 and 230 with still unknown impact on virulence of AIV in chickens. In this study, NS1 protein sequences of all AIV subtypes in birds from 1902 to 2015 were analyzed to study the prevalence and distribution of CTE truncation (ΔCTE). Thirteen different ΔCTE forms were observed in NS1 proteins from 11 HA and 8 NA subtypes with high prevalences in H9, H7, H6 and H10 and N9, N2, N6 and N1 subtypes particularly in chickens and minor poultry species. With 88% NS217 lacking amino acids 218-230 was the most common ΔCTE form followed by NS224 (3.6%). NS217 was found in 10 and 8 different HA and NA subtypes, respectively, whereas NS224 was detected exclusively in the Italian HPAIV H7N1 suggesting relevance for virulence. To test this assumption, 3 recombinant HPAIV H7N1 were constructed carrying wild-type HP NS1 (Hp-NS224), NS1 with extended CTE (Hp-NS230) or NS1 from LPAIV H7N1 (Hp-NSLp), and tested in-vitro and in-vivo. Extension of CTE in Hp NS1 significantly decreased virus replication in chicken embryo kidney cells. Truncation in the NS1 decreased the tropism of Hp-NS224 to the endothelium, central nervous system and respiratory tract epithelium without significant difference in virulence in chickens. This study described the variable forms of ΔCTE in NS1 and indicated that CTE is not an essential virulence determinant particularly for the Italian HPAIV H7N1 but may be a host-adaptation marker required for efficient virus replication.

Impact of food intake on in vivo VOC concentrations in exhaled breath assessed in a caprine animal model

Physiological processes within the body may change emitted volatile organic compound (VOC) composition, and may therefore cause confounding biological background variability in breath gas analyses. To evaluate the effect of food intake on VOC concentration patterns in exhaled breath, this study assessed the variability of VOC concentrations due to food intake in a standardized caprine animal model. VOCs in (i) alveolar breath gas samples of nine clinically healthy goats and (ii) room air samples were collected and pre-concentrated before morning feeding and repeatedly after (+60 min, +150 min, +240 min) using needle trap microextraction (NTME). Analysis of VOCs was performed by gas chromatography and mass spectrometry (GC-MS). Only VOCs with significantly higher concentrations in breath gas samples compared to room air samples were taken into consideration. Six VOCs that belonged to the chemical classes of hydrocarbons and alcohols were identified presenting significantly different concentrations before and after feeding. Selected hydrocarbons showed a concentration pattern that was characterized by an initial increase 60 min after food intake, and a subsequent gradual decrease. Results emphasize consideration of physiological effects on exhaled VOC concentrations due to food intake with respect to standardized protocols of sample collection and critical evaluation of results.

Culicoides vector species on three South American camelid farms seropositive for bluetongue virus serotype 8 in Germany 2008/2009

Palearctic species of Culicoides (Diptera, Ceratopogonidae), in particular of the Obsoletus and Pulicaris complexes, were identified as putative vectors of bluetongue virus serotype 8 (BTV-8) on ruminant farms during the epizootic in Germany from 2006 to 2009. BTV may cause severe morbidity and mortality in ruminants and sporadically in South American camelids (SAC). However, the fauna of Culicoides spp. on SAC farms has not been investigated. Therefore, the ceratopogonid fauna was monitored on three farms with BTV-seropositive SAC in Germany. Black-light traps were set up on pastures and in stables from summer 2008 to autumn 2009. Additionally, ceratopogonids were caught in emergence traps mounted on llama dung and dung-free pasture from spring to autumn 2009. After morphological identification, selected Culicoides samples were analysed for BTV-RNA by real-time RT-PCR. The effects of the variables 'location', 'temperature' and 'humidity' on the number of Culicoides caught in black-light traps were modelled using multivariable Poisson regression. In total, 26 species of Culicoides and six other genera of biting midges were identified. The most abundant Culicoides spp. collected both outdoors and indoors with black-light traps belonged to the Obsoletus (77.4%) and Pulicaris (16.0%) complexes. The number of Culicoides peaked in summer, while no biting midges were caught during the winter months. Daily collections of Culicoides were mainly influenced by the location and depended on the interaction of temperature and humidity. In the emergence traps, species of the Obsoletus complex predominated the collections. In summary, the absence of BTV-RNA in any of the analysed Culicoides midges and in the BTV-seropositive SAC on the three farms together with the differences in the pathogenesis of BTV-8 in SAC compared to ruminants suggests a negligible role of SAC in the spread of the virus. Although SAC farms may provide similar suitable habitats for putative Culicoides vectors than ruminant farms, the results suggest that geographic and meteorological factors had a stronger influence on Culicoides abundance than the animal species.

A multi prototype classification algorithm and its application to multi class diagnostics.. [DOI: 10.7287/peerj.preprints.1180v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

This paper introduces a novel, universal distance-based classification procedure. It is based on a simple geometric model. Considering all objects as points in a metric space, a class is imagined as covered by potentially differentsized hyperspheres, the centres of which are referred to as prototypes. The radii of the hyperspheres are individually optimised by a generalised ROC-analysis. For the approximate solution of the entire discrete optimisation problem, a greedy algorithm was developed and implemented in R. It runs in O(k2∙n2∙log(n)) time where k is the number of prototypes to be selected and n the number of training objects. For application to multi class problems, one against all approach is performed. The diagnostic decision is finalised for that class of maximum positive predictive value when in doubt. Objects not recognised as a member of any of the classes are assigned to an additional residual class. The performance of the classification system presented is demonstrated on various data examples, and in comparison with other methods.

Physiological variability in volatile organic compounds (VOCs) in exhaled breath and released from faeces due to nutrition and somatic growth in a standardized caprine animal model

Physiological effects may change volatile organic compound (VOC) concentrations and may therefore act as confounding factors in the definition of VOCs as disease biomarkers. To evaluate the extent of physiological background variability, this study assessed the effects of feed composition and somatic growth on VOC patterns in a standardized large animal model. Fifteen clinically healthy goats were followed during their first year of life. VOCs present in the headspace over faeces, exhaled breath and ambient air inside the stable were repeatedly assessed in parallel with the concentrations of glucose, protein, and albumin in venous blood. VOCs were collected and analysed using solid-phase or needle-trap microextraction and gas chromatograpy together with mass spectroscopy. The concentrations of VOCs in exhaled breath and above faeces varied significantly with increasing age of the animals. The largest variations in volatiles detected in the headspace over faeces occurred with the change from milk feeding to plant-based diet. VOCs above faeces and in exhaled breath correlated significantly with blood components. Among VOCs exhaled, the strongest correlations were found between exhaled nonanal concentrations and blood concentrations of glucose and albumin. Results stress the importance of a profound knowledge of the physiological backgrounds of VOC composition before defining reliable and accurate marker sets for diagnostic purposes.

Sample preparation for avian and porcine influenza virus cDNA amplification simplified: Boiling vs. conventional RNA extraction

RNA extraction and purification is a fundamental step that allows for highly sensitive amplification of specific RNA targets in PCR applications. However, commercial extraction kits that are broadly used because of their robustness and high yield of purified RNA are expensive and labor-intensive. In this study, boiling in distilled water or a commercial lysis buffer of different sample matrices containing avian or porcine influenza viruses was tested as an alternative. Real-time PCR (RTqPCR) for nucleoprotein gene fragment was used as read out. Results were compared with freshly extracted RNA by use of a commercial extraction kit. Different batches of virus containing materials, including diluted virus positive allantoic fluid or cell culture supernatant, and avian faecal, cloacal or oropharyngeal swab samples were used in this study. Simple boiling of samples without any additional purification steps can be used as an alternative RNA preparation method to detect influenza A virus nucleoprotein RNA in oropharyngeal swab samples, allantoic fluid or cell-culture supernatant. The boiling method is not applicable for sample matrices containing faecal material.

In Vivo Volatile Organic Compound Signatures of Mycobacterium avium subsp. paratuberculosis

Mycobacterium avium ssp. paratuberculosis (MAP) is the causative agent of a chronic enteric disease of ruminants. Available diagnostic tests are complex and slow. In vitro, volatile organic compound (VOC) patterns emitted from MAP cultures mirrored bacterial growth and enabled distinction of different strains. This study was intended to determine VOCs in vivo in the controlled setting of an animal model. VOCs were pre-concentrated from breath and feces of 42 goats (16 controls and 26 MAP-inoculated animals) by means of needle trap microextraction (breath) and solid phase microextraction (feces) and analyzed by gas chromatography/ mass spectrometry. Analyses were performed 18, 29, 33, 41 and 48 weeks after inoculation. MAP-specific antibodies and MAP-specific interferon-γ-response were determined from blood. Identities of all marker-VOCs were confirmed through analysis of pure reference substances. Based on detection limits in the high pptV and linear ranges of two orders of magnitude more than 100 VOCs could be detected in breath and in headspace over feces. Twenty eight substances differed between inoculated and non-inoculated animals. Although patterns of most prominent substances such as furans, oxygenated substances and hydrocarbons changed in the course of infection, differences between inoculated and non-inoculated animals remained detectable at any time for 16 substances in feces and 3 VOCs in breath. Differences of VOC concentrations over feces reflected presence of MAP bacteria. Differences in VOC profiles from breath were linked to the host response in terms of interferon-γ-response. In a perspective in vivo analysis of VOCs may help to overcome limitations of established tests.

Effects of zoledronic acid on bone mineral density in premenopausal women receiving neoadjuvant or adjuvant therapies for HR+ breast cancer: the ProBONE II study

The effects of bisphosphonates on altered bone turnover marker (BTM) levels associated with adjuvant endocrine or chemotherapy in early breast cancer have not been systematically investigated. In ProBONE II, zoledronic acid decreased these elevated BTM levels and increased bone mineral density (BMD) during adjuvant therapy, consistent with its antiresorptive effects.

INTRODUCTION

Adjuvant chemotherapy or endocrine therapy for early hormone receptor-positive breast cancer (HR(+) BC) is associated with rapid BMD loss and altered BTM levels. Adjuvant bisphosphonate studies demonstrated BMD increases, but did not investigate BTM effects. The randomized, double-blind, ProBONE II study investigated the effect of adjuvant zoledronic acid (ZOL) on BMD and BTM in premenopausal women with early HR(+) BC.

METHODS

Seventy premenopausal women with early HR(+) BC received adjuvant chemotherapy and/or endocrine therapy plus ZOL (4 mg IV every 3 months) or placebo for 24 months. Primary endpoint was change in lumbar spine BMD at 24 months versus baseline. Secondary endpoints included femoral neck and total femoral BMD changes, changes in BTM, and safety.

RESULTS

Lumbar spine BMD increased 3.14% from baseline to 24 months in ZOL-treated participants versus a 6.43% decrease in placebo-treated participants (P < 0.0001). Mean changes in T- and Z-scores, and femoral neck and total femoral BMD, showed similar results. Bone resorption marker levels decreased ∼ 55% in ZOL-treated participants versus increases up to 65% in placebo-treated participants (P < 0.0001 for between-group differences). Bone formation marker (procollagen I N-terminal propeptide) levels decreased ∼ 57% in ZOL-treated participants versus increases up to 45% in placebo-treated participants (P < 0.0001 for between-group differences). Adverse events were consistent with the established ZOL safety profile and included one case of osteonecrosis of the jaw after a tooth extraction.

CONCLUSIONS

Adding ZOL to adjuvant therapy improved BMD, reduced BTM levels, and was well tolerated in premenopausal women with early HR(+) BC receiving adjuvant chemotherapy and/or endocrine therapy.

ClassyFlu: classification of influenza A viruses with Discriminatively trained profile-HMMs

Accurate and rapid characterization of influenza A virus (IAV) hemagglutinin (HA) and neuraminidase (NA) sequences with respect to subtype and clade is at the basis of extended diagnostic services and implicit to molecular epidemiologic studies. ClassyFlu is a new tool and web service for the classification of IAV sequences of the HA and NA gene into subtypes and phylogenetic clades using discriminatively trained profile hidden Markov models (HMMs), one for each subtype or clade. ClassyFlu merely requires as input unaligned, full-length or partial HA or NA DNA sequences. It enables rapid and highly accurate assignment of HA sequences to subtypes H1-H17 but particularly focusses on the finer grained assignment of sequences of highly pathogenic avian influenza viruses of subtype H5N1 according to the cladistics proposed by the H5N1 Evolution Working Group. NA sequences are classified into subtypes N1-N10. ClassyFlu was compared to semiautomatic classification approaches using BLAST and phylogenetics and additionally for H5 sequences to the new "Highly Pathogenic H5N1 Clade Classification Tool" (IRD-CT) proposed by the Influenza Research Database. Our results show that both web tools (ClassyFlu and IRD-CT), although based on different methods, are nearly equivalent in performance and both are more accurate and faster than semiautomatic classification. A retraining of ClassyFlu to altered cladistics as well as an extension of ClassyFlu to other IAV genome segments or fragments thereof is undemanding. This is exemplified by unambiguous assignment to a distinct cluster within subtype H7 of sequences of H7N9 viruses which emerged in China early in 2013 and caused more than 130 human infections. http://bioinf.uni-greifswald.de/ClassyFlu is a free web service. For local execution, the ClassyFlu source code in PERL is freely available.

Avian influenza virus h3 hemagglutinin may enable high fitness of novel human virus reassortants

Reassortment of influenza A virus genes enables antigenic shift resulting in the emergence of pandemic viruses with novel hemagglutinins (HA) acquired from avian strains. Here, we investigated whether historic and contemporary avian strains with different replication capacity in human cells can donate their hemagglutinin to a pandemic human virus. We performed double-infections with two avian H3 strains as HA donors and a human acceptor strain, and determined gene compositions and replication of HA reassortants in mammalian cells. To enforce selection for the avian virus HA, we generated a strictly elastase-dependent HA cleavage site mutant from A/Hong Kong/1/68 (H3N2) (Hk68-Ela). This mutant was used for co-infections of human cells with A/Duck/Ukraine/1/63 (H3N8) (DkUkr63) or the more recent A/Mallard/Germany/Wv64-67/05 (H3N2) (MallGer05) in the absence of elastase but presence of trypsin. Among 21 plaques analyzed from each assay, we found 12 HA reassortants with DkUkr63 (4 genotypes) and 14 with MallGer05 (10 genotypes) that replicated in human cells comparable to the parental human virus. Although DkUkr63 replicated in mammalian cells at a reduced level compared to MallGer05 and Hk68, it transmitted its HA to the human virus, indicating that lower replication efficiency of an avian virus in a mammalian host may not constrain the emergence of viable HA reassortants. The finding that HA and HA/NA reassortants replicated efficiently like the human virus suggests that further HA adaptation remains a relevant barrier for emergence of novel HA reassortants.

Serotyping of Toxoplasma gondii in cats (Felis domesticus) reveals predominance of type II infections in Germany

Background

Cats are definitive hosts of Toxoplasma gondii and play an essential role in the epidemiology of this parasite. The study aims at clarifying whether cats are able to develop specific antibodies against different clonal types of T. gondii and to determine by serotyping the T. gondii clonal types prevailing in cats as intermediate hosts in Germany.

Methodology

To establish a peptide-microarray serotyping test, we identified 24 suitable peptides using serological T. gondii positive (n=21) and negative cat sera (n=52). To determine the clonal type-specific antibody response of cats in Germany, 86 field sera from T. gondii seropositive naturally infected cats were tested. In addition, we analyzed the antibody response in cats experimentally infected with non-canonical T. gondii types (n=7).

Findings

Positive cat reference sera reacted predominantly with peptides harbouring amino acid sequences specific for the clonal T. gondii type the cats were infected with. When the array was applied to field sera from Germany, 98.8% (85/86) of naturally-infected cats recognized similar peptide patterns as T. gondii type II reference sera and showed the strongest reaction intensities with clonal type II-specific peptides. In addition, naturally infected cats recognized type II-specific peptides significantly more frequently than peptides of other type-specificities. Cats infected with non-canonical types showed the strongest reactivity with peptides presenting amino-acid sequences specific for both, type I and type III.

Conclusions

Cats are able to mount a clonal type-specific antibody response against T. gondii. Serotyping revealed for most seropositive field sera patterns resembling those observed after clonal type II-T. gondii infection. This finding is in accord with our previous results on the occurrence of T. gondii clonal types in oocysts shed by cats in Germany.

The prescribing of contraceptives for adolescents in German gynecologic practices in 2007 and 2011: a retrospective database analysis

OBJECTIVE

To investigate the prescribing trend of contraceptives in adolescent girls aged 12-18 years and to compare prescribing patterns of the most frequently used contraceptives among this population in Germany in 2007 and 2011.

METHODS

A retrospective cohort study was conducted to analyze contraceptive prescriptions written by gynecologists in 2007 and 2011 in Germany by using the IMS Disease Analyzer database (IMS HEALTH). All adolescent girls aged 12-18 years with at least 1 prescription of a contraceptive drug in 2007 or 2011 were identified. The prevalence of contraceptive prescriptions was calculated and the types of contraceptive substances prescribed were examined.

RESULTS

A total of 21,026 teenage girls in 2007 and 18,969 in 2011 received contraceptive prescriptions. The prevalence of contraceptive prescribing rose significantly between 2007 and 2011 (P < .001). The percentage of teen girls who received prescriptions of levonorgestrel and chlormadinone pills was significantly higher in 2011 compared to 2007 (P < .001). However, the portion of contraceptive pills containing drospirenone or desogestrel significantly decreased in 2011 compared to 2007 (P < .01).

CONCLUSION

There was a significant increase in contraceptive prescription usage among adolescent girls between 2007 and 2011 in Germany. However, the prescription behavior of doctors also changed; they consequently prescribed contraceptives with more evidence. Further research is needed to better understand the various factors associated with contraceptive use among this population.

Prevalence of female subfertility in German gynecological practices

INTRODUCTION

The aim of this study was to calculate the number of women with a subfertility diagnosis in gynecological practices in Germany between 2006 and 2010 based on the data from a large epidemiological database.

METHODS

All calculations are based on a representative, epidemiological database called "disease analyzer". Women with a confirmed diagnosis of female infertility (ICD 10: N97) or/and with documentation of procreative management (ICD 10: Z31) were identified. They were summarized under the term "subfertility".

RESULTS

In total, data on 1,975,253 female patients with between 2006 and 2010 were included. Estimates for patients with "subfertility" compared to number of women lived in Germany (aged 18-45) was 2.44% (CI: 2.43-2.45) in 2006, 2.52% (CI: 2.51-2.53) in 2007, 2.56% (CI: 2.55-2.57) in 2008, 2.68% (CI: 2.67-2.69) in 2009 and 2.69% (CI: 2.68-2.70) in 2010. The difference was significant (p < 0.01). In total, between 2006 and 2010 an estimated 8.91% of all German women had been diagnosed "subfertile".

CONCLUSION

When calculated for 5 years almost 1 out of 10 women aged 18 to 45 was counseled, investigated or treated by her gynecologist for "subfertility". This study provides reliable, representative data on a major healthcare issue in Germany.

Hepatitis E virus seroprevalence of domestic pigs in Germany determined by a novel in-house and two reference ELISAs

Autochthonous hepatitis E virus (HEV) infections by zoonotic transmission of genotype 3 (GT3) have been reported increasingly from industrialized countries. In this paper the development and validation of an IgG ELISA for the detection of HEV-specific antibodies in domestic pigs is described. Comparison of the diagnostic value of Escherichia coli-expressed HEV-GT3 capsid protein (CP) derivatives revealed a carboxy-terminal derivative as most suitable. Validation of the in-house assay using a commercially available IgG ELISA revealed a high diagnostic specificity and sensitivity. The average HEV seroprevalence of domestic pigs from Germany and the federal state Baden-Wuerttemberg determined by the in-house test was 42.7% and 50.3%, respectively. The seroprevalence in different districts of Baden-Wuerttemberg ranged from 34.9% to 60%, but from 0% to 100% between different herds. These data were compared to those achieved by two commercially available ELISA kits and an in-house ratHEV-based ELISA. In conclusion, the CP-based in-house test proved sensitive and specific, indicating that the ORF3-encoded protein might be dispensable for diagnostics. The novel assay also allowed a parallel analysis by a homologous ratHEV-derived antigen. Thus, the novel IgG ELISA represents a useful tool for future standardized seroprevalence studies in domestic pigs from Germany and other regions of Europe.

Rapid identification of Burkholderia mallei and Burkholderia pseudomallei by intact cell Matrix-assisted Laser Desorption/Ionisation mass spectrometric typing

Background

Burkholderia (B.) pseudomallei and B. mallei are genetically closely related species. B. pseudomallei causes melioidosis in humans and animals, whereas B. mallei is the causative agent of glanders in equines and rarely also in humans. Both agents have been classified by the CDC as priority category B biological agents. Rapid identification is crucial, because both agents are intrinsically resistant to many antibiotics. Matrix-assisted laser desorption/ionisation mass spectrometry (MALDI-TOF MS) has the potential of rapid and reliable identification of pathogens, but is limited by the availability of a database containing validated reference spectra. The aim of this study was to evaluate the use of MALDI-TOF MS for the rapid and reliable identification and differentiation of B. pseudomallei and B. mallei and to build up a reliable reference database for both organisms.

Results

A collection of ten B. pseudomallei and seventeen B. mallei strains was used to generate a library of reference spectra. Samples of both species could be identified by MALDI-TOF MS, if a dedicated subset of the reference spectra library was used. In comparison with samples representing B. mallei, higher genetic diversity among B. pseudomallei was reflected in the higher average Eucledian distances between the mass spectra and a broader range of identification score values obtained with commercial software for the identification of microorganisms. The type strain of B. pseudomallei (ATCC 23343) was isolated decades ago and is outstanding in the spectrum-based dendrograms probably due to massive methylations as indicated by two intensive series of mass increments of 14 Da specifically and reproducibly found in the spectra of this strain.

Conclusions

Handling of pathogens under BSL 3 conditions is dangerous and cumbersome but can be minimized by inactivation of bacteria with ethanol, subsequent protein extraction under BSL 1 conditions and MALDI-TOF MS analysis being faster than nucleic amplification methods. Our spectra demonstrated a higher homogeneity in B. mallei than in B. pseudomallei isolates. As expected for closely related species, the identification process with MALDI Biotyper software (Bruker Daltonik GmbH, Bremen, Germany) requires the careful selection of spectra from reference strains. When a dedicated reference set is used and spectra of high quality are acquired, it is possible to distinguish both species unambiguously. The need for a careful curation of reference spectra databases is stressed.

Saving resources: avian influenza surveillance using pooled swab samples and reduced reaction volumes in real-time RT-PCR

The occurrence of highly pathogenic (HP) avian influenza (AI) H5N1 in Asia and its spread to Africa and Europe prompted costly monitoring programs of wild birds and domestic poultry. AI virus excretion is tested by examining avian swab samples by real-time reverse transcription PCR (RT-qPCR). In this study, pools of swab samples and a reagents volume reduction per RT-qPCR were evaluated as measures of economization. Viral transport medium and faecal matrices were spiked with different low pathogenic AI virus strains and tested for loss of target RNA during all processing steps as individual rayon swabs or in sample pools of 5, 10 and 15 swabs. Fresh faeces from Mallard ducks and other aquatic bird species as sample matrix resulted in loss of AIV RNA of about 90% compared to transport medium. Due to sample RNA dilution in pools the likelihood of detection of single positive samples is decreasing with increasing size of sample pools. However, pools of five samples containing only one positive sample consistently gave positive results. Similarly, no differences in detection rates were obtained when analyzing 1030 wild bird swab samples either individually or in pools of five. Reducing the reaction volume of influenza A virus generic as well as of subtype-specific RT-qPCRs to 12.5 μl (2.5 μl template) instead of 25 μl did not adversely affect the limit of detection of these RT-qPCRs. A significant economic benefit without impeding detection efficacy can be achieved when sample pools of five samples are analyzed by RT-qPCR using a reduction of the reaction mix to the half of the original volume.

Pathogenicity and immunogenicity of different recombinant Newcastle disease virus clone 30 variants after in ovo vaccination

Even though Newcastle disease virus (NDV) live vaccine strains can be applied to 1-day-old chickens, they are pathogenic to chicken embryos when given in ovo 3 days before hatch. Based on the reverse genetics system, we modified recombinant NDV (rNDV) established from lentogenic vaccine strain Clone 30 by introducing specific mutations within the fusion (F) and hemagglutinin-neuraminidase (HN) proteins, which have recently been suggested as being responsible for attenuation of selected vaccine variants (Mast et al. Vaccine 24:1756-1765, 2006) resulting in rNDV49. Another recombinant (rNDVGu) was generated to correct sequence differences between rNDV and vaccine strain NDV Clone 30. Recombinant viruses rNDV, rNDV49, and rNDVGu have reduced virulence compared with NDV Clone 30, represented by lower intracerebral pathogenicity indices and elevated mean death time. After in ovo inoculation, hatchability was comparable for all infected groups. However, only one chicken from the NDV Clone 30 group survived a 21-day observation period; whereas, the survival rate of hatched chicks from groups receiving recombinant NDV was between 40% and 80%, with rNDVGu being the most pathogenic virus. Furthermore, recombinant viruses induced protection against challenge infection with virulent NDV 21 days post hatch. Differences in antibody response of recombinant viruses indicate that immunogenicity is correlated to virulence. In summary, our data show that point mutations can reduce virulence of NDV. However, alteration of specific amino acids in F and HN proteins of rNDV did not lead to further attenuation as indicated by their pathogenicity for chicken after in ovo inoculation.

Seroprevalence study in forestry workers from eastern Germany using novel genotype 3- and rat hepatitis E virus-specific immunoglobulin G ELISAs

Hepatitis E virus (HEV) is the causative agent of an acute self-limiting hepatitis in humans. In industrialized countries, autochthonous cases are linked to zoonotic transmission from domestic pigs, wild boar and red deer. The main route of human infection presumably is consumption of contaminated meat. Farmers, slaughterers and veterinarians are expected to be risk groups as they work close to potentially infected animals. In this study, we tested four Escherichia coli-expressed segments of the capsid protein (CP) of a German wild boar-derived HEV genotype 3 strain for their diagnostic value in an indirect immunoglobulin G (IgG) ELISA. In an initial validation experiment, a carboxy-terminal CP segment spanning amino acid (aa) residues 326-608 outperformed the other segments harbouring aa residues 112-608, 326-660 and 112-335. Based on this segment, an indirect ELISA for detection of anti-HEV IgG antibodies in human sera was established and validated using a commercial line immunoassay as reference assay. A total of 563 sera from forestry workers of all forestry offices of Brandenburg, eastern Germany and 301 sera of blood donors from eastern Germany were surveyed using these assays. The commercial test revealed seroprevalence rates of 11% for blood donors and 18% for forestry workers. These rates are in line with data obtained by the in-house test (12 and 21%). Hence, the in-house test performed strikingly similar to the commercial test (sensitivity 0.9318, specificity 0.9542). An initial screening of forestry worker and blood donor sera with a corresponding CP segment of the recently discovered Norway rat-associated HEV revealed several strong positive sera exclusively in the forestry worker panel. Future investigations have to prove the performance of this novel IgG ELISA in large-scale seroepidemiological studies. In addition, the observed elevated seroprevalence in a forestry worker group has to be confirmed by studies on groups of forestry workers from other regions. The epidemiological role of ratHEV in human disease should be assessed in a large-scale study of risk and non-risk groups.

P2-17-02: Increased Progression Free and Overall Survival in Breast Cancer Patients with Menopausal Symptoms or Arthralgia/Myalgia during Adjuvant Treatment with Exemestane or Tamoxifen – Results of the German TEAM Trial

Background

Previous studies have suggested a correlation between the occurrence of vasomotor or joint symptoms during tamoxifen or aromatase inhibitor treatment and improved clinical response. We assessed if there was any correlation between treatment-emergent adverse events during exemestane or tamoxifen treatment and clinical response.

Methods: A retrospective analysis of the German cohort of the TEAM trial was performed to assess progression-free survival and overall survival in patients with and without menopausal symptoms or arthralgia/myalgia during adjuvant treatment with exemestane or tamoxifen.

Results: A total of 1502 patients were included in this analysis; 739 patients received tamoxifen and 763 received exemestane. Patients reporting menopausal symptoms and patients reporting arthralgia/myalgia during tamoxifen or exemestane treatment had significantly longer overall survival and progression-free survival. The effect on overall survival was irrespective of treatment. Progression-free survival was significantly improved in exemestane-treated patients reporting menopausal symptoms or those reporting arthralgia/myalgia versus those not reporting these adverse events. There was no significant difference in progression-free survival between tamoxifen-treated patients reporting these symptoms versus those who did not. A combined analysis of patients reporting either menopausal symptoms or arthralgia/myalgia showed that overall survival and progressionfree survival was significantly improved in patients reporting one of these symptoms versus those not reporting either symptom. In this analysis, the effect on overall survival and progression-free survival was irrespective of treatment.

Conclusions: Our results suggest that the occurrence of menopausal symptoms or arthralgia/myalgia during treatment with tamoxifen or exemestane is associated with significantly improved overall survival.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P2-17-02.

P2-19-03: Influence of Zoledronic Acid on BMD in Premenopausal Women with Breast Cancer and Neoadjuvant or Adjuvant Chemotherapy and/or Endocrine Treatment – The ProBone Studies

Background: Based on baseline bone mineral density (BMD), adjuvant chemotherapy or endocrine therapy for early breast cancer patients can lead to substantially increased fracture risk. A significant decrease of BMD &gt;10% after 2 years of chemotherapy (CT) and/or endocrine therapy (ET) has been reported. In recent studies, zoledronic acid (ZOL) produced an increase in BMD in premenopausal and postmenopausal patients with breast cancer (ABCSG-12, Z-FAST, ZO-FAST, etc). In addition, a significant increase in disease-free survival (DFS) with ZOL vs no ZOL was observed in most of these studies.

Methods: The aim of 2 single-center, placebo-controlled, randomized studies—Probone I and Probone II—was to investigate the effect of adjuvant treatment with ZOL on BMD in premenopausal women with early breast cancer treated with CT and/or ET. Patients with hormone-receptor-negative (HR−) breast cancer (Probone I) were treated with (neo)adjuvant CT; patients with hormone-receptor-positive (HR+) breast cancer (Probone II) were treated with ET alone or in combination with (neo)adjuvant CT. Randomized patients received ZOL 4 mg or placebo IV every 3 months for 24 months. The primary objective was the change in BMD at the lumbar spine between baseline and month 24 (measured by dual-energy X-ray absorptiometry [DXA]). Secondary objectives included DFS; BMD at total hip, femur, and os calcis; quantitative ultrasonometry (QUS) at os calcis and phalanges; markers of bone turnover (C-telopeptide of type I collagen [CTX] and N-terminal propeptide of type I procollagen [P1NP]); endocrine hormones (follicle-stimulating hormone [FSH], estradiol, testosterone, sex hormone-binding globulin [SHBG], parathyroid hormone [PTH], vitamin D, anti-Müllerian hormone [AMH], inhibin A/B, etc); pathologic fractures; and safety and tolerability.

Results: 70 HR+ and 11 HR− breast cancer patients have been enrolled into the studies. The last patient will have been treated for 24 months by the end of June 2011.

Conclusions: The effects of ZOL on lumbar spine BMD at 24 months and secondary endpoints will be presented at the meeting.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P2-19-03.

Priority areas for surveillance and prevention of avian influenza during the water-bird migration season in Pakistan

Avian influenza viruses may be introduced into domestic poultry through migratory wild birds, particularly from Pakistan, which is situated across the migratory Indus flyway and holds more than 225 wetlands. To answer the question which areas should be given priority in surveillance and prevention with respect to notifiable avian influenza during the migratory season, a subset of Asian waterbird census data was reviewed. The dataset contains 535 local sites and available counts of waterbirds reported from 1987 to 2007. However, as the majority of the sites are not counted regularly gaps in data matrix appeared. The coordinates of 270 known sites completely fitted the administrative boundaries of the country. These coordinates were geo-processed with polygons of water-bodies and a raster map of predicted poultry density. Pixels representing the estimated number of poultry per km2 were found within a 3 to 9 km range of the census sites (or water-bodies) in their proximity. The coordinates were also used to map the maximum reported counts of waterbirds and local clusters of under-sampled sites. A retrospective case-series analysis of previous outbreaks (2006-2008) of influenza A virus, subtype H5N1 was performed, which revealed that 64% of outbreaks, reported to Office International des Epizooties, the World Organization for Animal Health, occurred during the migratory period. This paper highlights the potential use and limitations of the Asian waterbirds census data in the context of avian influenza. The proposed methodology may be used to prioritize districts for surveillance and economize prevention measures provided better data are generated in future.

Seroprevalence study in forestry workers of a non-endemic region in eastern Germany reveals infections by Tula and Dobrava-Belgrade hantaviruses

Highly endemic and outbreak regions for human hantavirus infections are located in the southern, southeastern, and western parts of Germany. The dominant hantavirus is the bank vole transmitted Puumala virus (PUUV). In the eastern part of Germany, previous investigations revealed Tula virus (TULV) and Dobrava-Belgrade virus (DOBV) infections in the respective rodent reservoirs. Here, we describe a seroprevalence study in forestry workers from Brandenburg, eastern Germany, using IgG ELISA and immunoblot tests based on recombinant TULV, DOBV, and PUUV antigens. Out of the 563 sera tested, 499 from male and 64 from female workers, we found 41 out of the 499 (8.2%) sera from men (mean age 47 years) and 10 out of 64 (15.6%) from the women (mean age 48 years) anti-hantavirus-positive. The majority of the 51 seropositive samples reacted exclusively in the TULV (n=22) and DOBV tests (n=17). Focus reduction neutralization assay investigations on selected sera confirmed the presence of TULV- and DOBV-specific antibodies in the forestry workers. These investigations demonstrated a potential health threat for forestry workers and also the average population in non-endemic geographical regions where TULV and DOBV are circulating in the corresponding reservoir hosts. The infections in this region might be frequently overlooked due to their unspecific and mild symptoms.

Highly pathogenic avian influenza virus H5N1 from Egypt escapes vaccine-induced immunity but confers clinical protection against a heterologous clade 2.2.1 Egyptian isolate

The poultry populations of Egypt are endemically infected by highly pathogenic avian influenza viruses (HPAIV) of subtype H5N1. Vaccination was chosen as an auxiliary tool to control HPAIV in poultry. Potency of commercial vaccines regarding emerging variants is under discussion. In the current study efficacy of four different inactivated whole H5 virus vaccines representing different sublineages of HPAIV H5N1 were tested in chickens against challenge viruses currently co-circulating in Egypt and representing two antigenically widely distinct HPAIV H5N1 lineages, i.e., "variant" (clade 2.2.1var) and "proper" (clade 2.2.1pro) viruses. All vaccines induced clinical protection against challenge with 2.2.1pro Egyptian strains. In contrast, when challenged with a variant strain, only chickens vaccinated with the homologous Egyptian clade 2.2.1var virus or an inactivated re-assorted H5N1 strain (Re-5, clade 2.3) were protected. However, only the homologous virus induced sterile immunity whereas chickens clinically protected after Re-5 vaccination shed virus at day two after infection indistinguishable to H5N2 vaccines. In conclusion, monitoring vaccine-driven evolution of HPAIV H5N1 by surveillance, antigenic characterization, and challenge studies is essential to assess efficacy of AIV vaccination campaigns.

Broad spectrum reactivity versus subtype specificity-trade-offs in serodiagnosis of influenza A virus infections by competitive ELISA

Avian influenza viruses (AIVs) of the H5 and H7 subtypes can cause substantial economic losses in the poultry industry and are a potential threat to public health. Serosurveillance of poultry populations is an important monitoring tool and can also be used for control of vaccination campaigns. The purpose of this study was to develop broadly reactive, yet subtype-specific competitive ELISAs (cELISAs) for the specific detection of antibodies to the notifiable AIV subtypes H5 and H7 as an alternative to the gold standard haemagglutination inhibition assay (HI). Broadly reacting monoclonal competitor antibodies (mAbs) and genetically engineered subtype H5 or H7 haemagglutinin antigen, expressed and in vivo biotinylated in insect cells, were used to develop the cELISAs. Sera from galliform species and water fowl (n=793) were used to evaluate the performance characteristics of the cELISAs. For the H5 specific cELISA, 98.1% test sensitivity and 91.5% test specificity (97.7% and 90.2% for galliforms; 98.9% and 92.6% for waterfowl), and for the H7 cELISA 97.3% sensitivity and 91.8% specificity (95.3% and 98.9% for galliforms; 100% and 82.7% for waterfowl) were reached when compared to HI. The use of competitor mAbs with broad spectrum reactivity within an AIV haemagglutinin subtype allowed for homogenous detection with high sensitivity of subtype-specific antibodies induced by antigenically widely distinct isolates including antigenic drift variants. However, a trade-off regarding sensitivity versus nonspecific detection of interfering antibodies induced by phylo- and antigenically closely related subtypes, e.g., H5 versus H2 and H7 versus H15, must be considered. The observed intersubtype antibody cross-reactivity remains a disturbance variable in AIV subtype-specific serodiagnosis which negatively affects specificity.

Abstract P5-11-08: Effects of Exemestane or Tamoxifen on Bone Health within the Tamoxifen Exemestane Adjuvant Multinational (TEAM) Trial: A Meta-Analysis

Background: TEAM is the largest AI phase III trial comparing exemestane with tamoxifen followed by exemestane as adjuvant breast cancer therapy in postmenopausal women. We performed a meta-analysis of three randomized sub-studies of the TEAM trial conducted in Germany, the Netherlands/Belgium and the United States to determine the effects on bone health.

Methods: Patients were randomised to exemestane or tamoxifen as adjuvant therapy for hormone receptor-positive breast cancer. Bone mineral density (BMD) was assessed by dual-energy X-ray absorptiometry at baseline and after 6, 12 and 24 months’ treatment. Bone turnover markers were also measured.

Results: 412 patients were evaluable. Patients in the tamoxifen group showed a mean increase in lumbar spine BMD of 1.2% from baseline to month 12 and 0.2% to month 24. Patients in the exemestane group showed a mean decrease from baseline of 2.6% after 12 months and 3.5% after 24 months. There were significant differences in the changes in BMD at the lumbar spine between treatment groups (P&lt;0.0001 at both timepoints). In the tamoxifen group, a mean increase in total hip BMD of 0.8% from baseline to month 12 and a mean decrease from baseline of 0.4% after 24 months was observed, compared with a mean decrease of 1.3% after 12 months and 3.3% after 24 months in the exemestane group. Changes in BMD from baseline at the total hip were also significantly different between exemestane and tamoxifen (P&lt;0.05 at both timepoints). Bone turnover markers decreased from baseline with tamoxifen and increased with exemestane.

Conclusions: After 24 months, exemestane treatment resulted in decreases in BMD and increases in bone turnover markers. In contrast, BMD was increased and bone turnover markers were decreased with tamoxifen. BMD and bone turnover changes appeared to stabilise after initial treatment.

Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P5-11-08.

Simultaneous detection and differentiation by multiplex real time RT-PCR of highly pathogenic avian influenza subtype H5N1 classic (clade 2.2.1 proper) and escape mutant (clade 2.2.1 variant) lineages in Egypt

Background

The endemic status of highly pathogenic avian influenza virus (HPAIV) of subtype H5N1 in Egypt continues to devastate the local poultry industry and poses a permanent threat for human health. Several genetically and antigenically distinct H5N1 lineages co-circulate in Egypt: Strains of clade 2.2.1 proper replicate mainly in backyard birds causing the bulk of human infections, while a variant lineage within 2.2.1 (2.2.1v) appears to be perpetuated mainly in commercial poultry farms in Egypt. Viruses of the 2.2.1v lineage represent drift variants escaping from conventional vaccine-induced immunity and some of these strains also escaped detection by commercial real time reverse transcriptase PCR (RT-qPCR) protocols due to mismatches in the primers/probe binding sites.

Results

We developed therefore a versatile, sensitive and lineage-specific multiplex RT-qPCR for detection and typing of H5N1 viruses in Egypt. Analytical characterization was carried out using 50 Egyptian HPAIV H5N1 strains isolated since 2006 and 45 other avian influenza viruses (AIV). A detection limit of 400 cRNA copies per ml sample matrix was found. Higher diagnostic sensitivity of the multiplex assay in comparison to other generic H5 or M-gene based RT-qPCR assays were found by examination of 63 swab samples from experimentally infected chickens and 50 AIV-positive swab samples from different host species in the field in Egypt.

Conclusions

The new multiplex RT-qPCR assay could be useful for rapid high-throughput monitoring for the presence of HPAIV H5N1 in commercial poultry in Egypt. It may also aid in prospective epidemiological studies to further delineate and better control spread of HPAIV H5N1 in Egypt.

Adherence and persistence in patients with severe osteoporosis treated with teriparatide

INTRODUCTION

Medical intervention plays a key role in the treatment of postmenopausal osteoporosis and patients' adherence to therapy is essential for optimal clinical outcomes. While adherence in RCTs is usually around 70-90%, a previous study showed that in clinical practice only 27.8% and 46.5% of the women on oral daily vs. weekly alendronate were still on treatment after 12 months. Data on adherence to teriparatide (TPTD) treatment of severe postmenopausal osteoporosis are available from only few countries. This study assessed adherence and persistence with TPTD in Germany.

MATERIAL AND METHODS

A sample of 50 women with severe postmenopausal osteoporosis treated with TPTD in accordance to the German osteoporosis guidelines was included. Treatment was initiated 12-24 months before recruitment. Patient self report was assessed using a validated questionnaire. In addition medication possession ratio (MPR) was calculated by counting prescription refills, and therefore all physicians who were treating the patients for any disease were contacted. Patients were classified adherent at 12 months of therapy if self-reported adherence and an MPR of > or =80% were achieved. Persistence was calculated in months and analysed with a Kaplan-Meier estimate.

RESULTS

Apart from a significantly lower age at menopause in the adherent group (46.1 vs. 50.0; p < 0.006) there were no significant differences in baseline demographics between adherent and non-adherent patients. After 12 months, 80% of the patients treated with TPTD were adherent, while 20% were non-adherent. A significant correlation with treatment adherence was found for self-reported medication tolerability (p < 0.001). Furthermore 79% of patients were persistent after 12 months.

CONCLUSION

These results indicate that more patients seem to be adherent and persistent with TPTD than with oral treatments of postmenopausal osteoporosis. As these patients suffered from severe osteoporosis and sustained several fragility fractures, the generalisability of our retrospective study analysing a small sample is limited. The major factor that reduced adherence and persistence was tolerability. These findings are of practical relevance as numerous studies on antiresorptive therapies have shown that high adherence and persistence were needed to ensure an optimal therapeutic outcome.

Assessment of fracture risk in women with breast cancer using current vs emerging guidelines

Background:

Breast cancer (BC) therapies can have negative effects on bone. Current guidelines recommend antiresorptive therapy based on bone mineral density (BMD), and emerging guidelines include both clinical risk factors and BMD to assess the overall fracture risk. A retrospective, case–controlled study based on current and emerging guidelines was conducted in women with newly diagnosed BC to identify those who were at increased fracture risk based on current and emerging guidelines.

Methods:

Baseline characteristics, fracture risk factors, and lumbar–spine (LS) and total-hip BMD in women with BC (88 premenopausal and 402 postmenopausal) were assessed to determine who would receive bisphosphonate therapy based on current and emerging guidelines.

Results:

Among patients with estrogen-receptor-positive (ER⁺) BC, 18.8% of premenopausal and 36.9% of postmenopausal women were osteopenic at LS. In the postmenopausal cohort, osteoporosis was more prevalent in patients with ER⁺vs ER^– BC. Current guidelines identified 8.9% of patients as eligible for antiresorptive therapy, clinical risk factors alone identified 6.5%, and BMD plus clinical risk factors identified 28.6%.

Conclusions:

In addition to fracture risk factors present at BC diagnosis, cancer therapies leading to BMD loss further increase fracture risk. Evaluating both BMD and clinical risk factors may allow more effective identification of BC patients with elevated fracture risk.

The effect of exemestane or tamoxifen on markers of bone turnover: results of a German sub-study of the Tamoxifen Exemestane Adjuvant Multicentre (TEAM) trial

Adjuvant treatment of breast cancer with aromatase inhibitors has been associated with increased bone loss. In this study, postmenopausal patients with oestrogen receptor positive breast cancer were randomised to exemestane for 5 years or tamoxifen for 2-2.5 years, followed by exemestane for 2-2.5 years. Levels of bone formation markers (bone specific alkaline phosphatase, amino terminal propeptide of type I procollagen, osteocalcin), and the bone resorption marker (carboxyterminal crosslinked telopeptide of type I collagen), were assessed at baseline and after 3, 6 and 12 months of treatment. Exemestane (n=78) resulted in increases from baseline in all bone turnover marker levels at all timepoints. In contrast, levels of all bone marker turnovers decreased with tamoxifen (n=83). Differences between tamoxifen and exemestane were statistically significant for all bone turnover markers at all timepoints. In conclusion, exemestane results in increases in markers of bone formation and resorption, while decreases are observed with tamoxifen.