Xanthomonas rydalmerensis sp. nov., a non-pathogenic member of Group 1 Xanthomonas

Five bacterial isolates were isolated from Fragaria × ananassa in 1976 in Rydalmere, Australia, during routine biosecurity surveillance. Initially, the results of biochemical characterisation indicated that these isolates represented members of the genus Xanthomonas. To determine their species, further analysis was conducted using both phenotypic and genotypic approaches. Phenotypic analysis involved using MALDI-TOF MS and BIOLOG GEN III microplates, which confirmed that the isolates represented members of the genus Xanthomonas but did not allow them to be classified with respect to species. Genome relatedness indices and the results of extensive phylogenetic analysis confirmed that the isolates were members of the genus Xanthomonas and represented a novel species. On the basis the minimal presence of virulence-associated factors typically found in genomes of members of the genus Xanthomonas, we suggest that these isolates are non-pathogenic. This conclusion was supported by the results of a pathogenicity assay. On the basis of these findings, we propose the name Xanthomonas rydalmerensis, with DAR 34855T = ICMP 24941 as the type strain.

Mycorrhiza-induced mycocypins of Laccaria bicolor are potent protease inhibitors with nematotoxic and collembola antifeedant activity

Fungivory of mycorrhizal hyphae has a significant impact on fungal fitness and, by extension, on nutrient transfer between fungi and host plants in natural ecosystems. Mycorrhizal fungi have therefore evolved an arsenal of chemical compounds that are hypothesized to protect the hyphal tissues from being eaten, such as the protease inhibitors mycocypins. The genome of the ectomycorrhizal fungus Laccaria bicolor has an unusually high number of mycocypin-encoding genes. We have characterized the evolution of this class of proteins, identified those induced by symbiosis with a host plant and characterized the biochemical properties of two upregulated L. bicolor mycocypins. More than half of L. bicolor mycocypin-encoding genes are differentially expressed during symbiosis or fruiting body formation. We show that two L. bicolor mycocypins that are strongly induced during symbiosis are cysteine protease inhibitors and exhibit similar but distinct localization in fungal tissues at different developmental stages and during interaction with a host plant. Moreover, we show that these L. bicolor mycocypins have toxic and feeding deterrent effect on nematodes and collembolans, respectively. Therefore, L. bicolor mycocypins may be part of a mechanism by which this species deters grazing by different members of the soil food web.

Nitrogen fertilization differentially affects the symbiotic capacity of two co-occurring ectomycorrhizal species

Forest trees rely on ectomycorrhizal (ECM) fungi to obtain growth-limiting nutrients. While addition of nitrogen (N) has the potential to disrupt these critical relationships, there is conflicting evidence as to the mechanism by which ECM:host mutualism may be affected. We evaluated how N fertilization altered host interactions and gene transcription between Eucalyptus grandis and Pisolithus microcarpus or Pisolithus albus, two closely related ECM species that typically co-occur within the same ecosystem. Our investigation demonstrated species-specific responses to elevated N: P. microcarpus maintained its ability to transport microbially sourced N to its host but had a reduced ability to penetrate into root tissues, while P. albus maintained its colonization ability but reduced delivery of N to its host. Transcriptomic analysis suggests that regulation of different suites of N-transporters may be responsible for these species-specific differences. In addition to N-dependent responses, we were also able to define a conserved 'core' transcriptomic response of Eucalyptus grandis to mycorrhization that was independent of abiotic conditions. Our results demonstrate that even between closely related ECM species, responses to N fertilization can vary considerably, suggesting that a better understanding of the breadth and mechanisms of their responses is needed to support forest ecosystems into the future.

Order of microbial succession affects rhizobia-mediated biocontrol efforts against Phytophthora root rot

The management of soilborne root diseases in pulse crops is challenged by a limited range of resistance sources and often a complete absence of in-crop management options. Therefore, alternative management strategies need to be developed. We evaluated disease limiting interactions between the rhizobia species Mesorhizobium ciceri, and the oomycete pathogen Phytophthora medicaginis, which causes Phytophthora root rot (PRR) of chickpea (Cicer arietinum). For the PRR susceptible var. Sonali plants, post-pathogen M. ciceri inoculation significantly improved probability of plant survival when compared to P. medicaginis infected plants only pre-inoculated with M. ciceri (75 % versus 35 %, respectively). Potential mechanisms for these effects were investigated: rhizobia inoculation benefits to plant nodulation were not demonstrated, but the highest nodule N-fixation activity of P. medicaginis inoculated plants occurred for the post-pathogen M. ciceri treatment; rhizobia inoculation treatment did not reduce lesion development but certain combinations of microbial inoculation led to significant reduction in root growth. Microcosm studies, however, showed that the presence of M. ciceri reduced growth of P. medicaginis isolates. Putative chickpea disease resistance gene expression was evaluated using qPCR in var. Sonali roots. When var. Sonali plants were treated with M. ciceri post-P. medicaginis inoculation, the gene regulation in the plant host became more similar to PRR moderately resistant var. PBA HatTrick. These results suggest that M. ciceri application post P. medicaginis inoculation may improve plant survival by inducing defense responses similar to a PRR moderately resistant chickpea variety. Altogether, these results indicate that order of microbial succession can significantly affect PRR plant survial in susceptible chickpea under controlled conditions and improved plant survival effects are due to a number of different mechanisms including improved host nutrition, through direct inhibiton of pathogen growth, as well as host defense priming.

Perspectives on the preventability of emergency department visits by older patients

BACKGROUND

Older people increasingly demand emergency department (ED) care. ED visits have a profound impact on older patients, including high risk of adverse outcomes and loss of independency. In this study, we evaluated the opinions of patients, caregivers, general practitioners, and ED physicians on the preventability of ED visits.

METHODS

Prospective, mixed-method observational and qualitative study of 200 patients aged ≥ 70 years visiting a teaching hospital ED in the Netherlands. Semi-structured interviews were performed with patients, caregivers, and general practitioners. ED physicians were provided with written surveys. Patient data were extracted to determine vulnerability.

RESULTS

The mean age of the patients was 79.6 years; 49.5% were male. Ninety-five percent lived independently before the ED visit. Most patients reported domiciliary care (23%), a caregiver (21.5%), or both (29.5%). Patients considered 12.2% of visits potentially preventable, caregivers 9%, general practitioners 20.7%, and ED physicians 31.2%. Consensus on preventability was poor, especially among patients and professionals. While patients most frequently blamed themselves, healthcare providers predominantly mentioned lack of communication and organisational issues as contributing factors.

CONCLUSION

Patients and caregivers consider an ED visit preventable less frequently than professionals do. Little consensus was found among patients and healthcare providers, and the perspectives on contributing factors to a preventable visit differ between groups. To help improve geriatric emergency care, future studies should focus on why these perspectives are so different and aim to align them.

Impact of diarrhoea and faecal incontinence on the daily life of HIV-infected patients

Diarrhoea in HIV-1 infected persons is an important clinical problem. To improve care and counselling, information about the way, and the extent to which, diarrhoea influences the daily life of these patients can be useful. A cross-sectional descriptive study was performed at the HIV infection clinic of three major hospitals in Amsterdam. A diary, the Coates card system (to determine the relative severity of the symptoms) and an interview were used as outcome measures. Sixty-two patients participated and were classified into four groups: group 1 (minor diarrhoea, n = 26), group 2 (mild diarrhoea, n = 18), group 3 (moderate diarrhoea, n = 7) and group 4 (severe diarrhoea, n = 11). Diarrhoea was considered a very severe symptom in groups 2, 3 and 4. Even mild diarrhoea may have a debilitating impact on the day-to-day life of HIV-infected patients. Faecal incontinence occurs frequently. Patients can worry about their diarrhoea because of lack of information. Patients who do not have diarrhoea according to current definitions of it, consider diarrhoea to be equally problematic as those with (moderate) diarrhoea. More information on prognosis and practical solutions for patients are recommended.

A geographic information system on the potential distribution and abundance of Fasciola hepatica and F. gigantica in east Africa based on Food and Agriculture Organization databases

An adaptation of a previously developed climate forecast computer model and digital agroecologic database resources available from FAO for developing countries were used to develop a geographic information system risk assessment model for fasciolosis in East Africa, a region where both F. hepatica and F. gigantica occur as a cause of major economic losses in livestock. Regional F. hepatica and F. gigantica forecast index maps were created. Results were compared to environmental data parameters, known life cycle micro-environment requirements and to available Fasciola prevalence survey data and distribution patterns reported in the literature for each species (F. hepatica above 1200 m elevation, F. gigantica below 1800 m, both at 1200-1800 m). The greatest risk, for both species, occurred in areas of extended high annual rainfall associated with high soil moisture and surplus water, with risk diminishing in areas of shorter wet season and/or lower temperatures. Arid areas were generally unsuitable (except where irrigation, water bodies or floods occur) due to soil moisture deficit and/or, in the case of F. hepatica, high average annual mean temperature >23 degrees C. Regions in the highlands of Ethiopia and Kenya were identified as unsuitable for F. gigantica due to inadequate thermal regime, below the 600 growing degree days required for completion of the life cycle in a single year. The combined forecast index (F. hepatica+F. gigantica) was significantly correlated to prevalence data available for 260 of the 1220 agroecologic crop production system zones (CPSZ) and to average monthly normalized difference vegetation index (NDVI) values derived from the advanced very high resolution radiometer (AVHRR) sensor on board the NOAA polar-orbiting satellites. For use in Fasciola control programs, results indicate that monthly forecast parameters, developed in a GIS with digital agroecologic zone databases and monthly climate databases, can be used to define the distribution range of the two Fasciola species, regional variations in intensity and seasonal transmission patterns at different sites. Results further indicate that many of the methods used for crop productivity models can also be used to define the potential distribution and abundance of parasites.

Prevalence of Campylobacter-associated diarrhea among patients infected with human immunodeficiency virus

We performed a cross-sectional study at an outpatient AIDS clinic to assess the prevalence of Campylobacter species in stool specimens from 201 consecutive patients infected with human immunodeficiency virus (HIV). We characterized campylobacters phenotypically and genetically by using primers for the group of common species (i.e., C. jejuni, C. coli, C. lari, and C. upsaliensis) and for most individual uncommon species. We performed cultures with use of a membrane filter technique on nonselective blood agar and found that Campylobacter species were the most frequent enteropathogenic bacteria: the organisms were recovered from 7 (16%) of 43 patients with diarrhea and 5 (3%) of 158 patients without diarrhea (P = .001). We isolated only one campylobacter with use of conventional culture techniques on selective media. Phenotypic characterization of 10 campylobacter strains resulted in the misidentification of four isolates. C. upsaliensis was the most frequently isolated species, followed by C. jejuni and C. coli. Two strains could not be identified with the available primers. Two of 12 Campylobacter strains were resistant to erythromycin, and two were resistant to ciprofloxacin. We conclude that Campylobacter species other than C. jejuni can frequently be detected in the stools of HIV-infected patients and that these organisms could be associated with diarrhea.

Duodenal intraepithelial and lamina propria T lymphocytes in human immunodeficiency virus-infected patients with and without diarrhoea

BACKGROUND

Diarrhoea is an important problem in human immunodeficiency virus (HIV)-infected patients. Intestinal pathologic conditions may arise from changes in local immunocyte populations. The aims of our study were to establish the histologic features of the duodenal mucosa of HIV-infected patients and to determine a) the phenotype of small-intestinal-intraepithelial (IELs) and lamina propria (LPLs)-lymphocytes; b) their degree of activation and differentiation within the lamina propria; and c) their relation to the presence of diarrhoea.

METHODS

Distal duodenal biopsy specimens were obtained prospectively from 29 HIV-infected patients-11 patients with diarrhoea (group 1) and 18 patients without diarrhoea (group 2)- and from 42 patients who had neither any risk factor for HIV nor diarrhoea (group 3). Histopathologic and immunohistochemical studies were combined with flow cytometric analysis, after separation of the mucosal intraepithelial compartment from the lamina propria.

RESULTS

The median number of IELs and the percentage of gamma delta IELs were both unchanged in HIV-infected patients as compared with controls. In HIV-infected patients LP CD4 cells were decreased, and LP CD8 cells increased. No significant difference was found in the expression of CD25 or CD27 within the LP CD8 populations of HIV-infected patients in groups 1 and 2.

CONCLUSIONS

These findings suggest that the occurrence of diarrhoea in HIV-infected patients is unrelated to IEL and LPL phenotype.

Human immunodeficiency virus type 1 RNA populations in faeces with higher homology to intestinal populations than to blood populations

To determine whether human immunodeficiency virus type 1 (HIV-1) in faeces is representative of the HIV-1 population in intestinal tissue, we studied HIV-1 V3 variation in faeces, intestinal biopsies and serum from two individuals. Phylogenic analysis of HIV-1 V3-coding RNA in faeces from one individual showed three distinct genotypes. Viruses belonging to all three genotypes were also present in sigmoidal tissue and in serum. Jejunal tissue contained two of these three genotypes. Analysis of the V3-coding RNA in faeces of the other individual showed five distinct genotypes. One of these genotypes was present in all specimens from this individual. Besides this shared genotype, jejunal tissue and serum contained sequences belonging to one other genotype. In addition, one of the other three V3 variants was detected in sigmoidal tissue. For both persons the shared HIV-1 RNA genotypes in faeces and serum displayed a distinctly different frequency distribution. In one individual, the genotype which was detected in a majority of the clones in faeces (59%) and as a minority in serum (11%), was the most abundant genotype in jejunal and sigmoidal tissue (61% and 80%, respectively). For the other individual the genotype that was present in faeces in a significant number of clones (43%) was detected in serum as a minority (8%), whereas this genotype composed 47% of the clones isolated from jejunal tissue. Taken together these data suggest that faeces contain HIV-1 sequences that are derived from local HIV-1 replication in intestinal tissue.

Increased numbers of granzyme-B-expressing cytotoxic T-lymphocytes in the small intestine of HIV-infected patients

The objective of this study was to determine whether granzyme B-expressing cells, which identify activated cytotoxic lymphocytes, are present in the small intestinal mucosa of human immunodeficiency virus (HIV)-infected patients with and without diarrhea. Therefore, duodenal biopsy specimens from 29 HIV-infected patients (11 with diarrhea and 18 without diarrhea) and 15 control patients were stained for the presence of granzyme B expressing cells. In HIV-infected patients, a significantly increased expression of granzyme B in the lamina propria was observed (p = 0.00001): In 22 of 29 patients, at least 5-10 cells per high-power field were counted. In contrast, in 13 of 15 control patients, granzyme B was not expressed or minimally so, and in two others a maximum of five granzyme-B-expressing cells could be detected per high-power field. No significant difference was found between the HIV-infected patients with and without diarrhea. Double staining revealed that the granzyme-B-expressing cells were mainly CD3 positive. These data show that activated cytotoxic T lymphocytes (CTLs) are present in the duodenal mucosa of HIV-infected patients. No relation between the number of CTLs and the presence of diarrhea was demonstrated. CTLs are known to be involved in the pathogenesis of HIV infection and in the production of tissue injury, but their functional role in intestinal HIV-related pathology has yet to be elucidated.

Diarrhoea in HIV-infected patients: no evidence of cytokine-mediated inflammation in jejunal mucosa

OBJECTIVE

To determine whether a mucosal cytokine-mediated inflammatory response is involved in cryptosporidial or microsporidial diarrhoea, as well as in diarrhoea of unknown origin in HIV-infected patients.

DESIGN

Prospective study.

METHODS

Jejunal biopsies were obtained from HIV-infected patients with diarrhoea. Controls were HIV-infected and HIV-seronegative patients without diarrhoea. Two biopsies were homogenized immediately and two other biopsies were first cultured for 20 h. Cytokines [tumour necrosis factor (TNF), interleukin (IL)-1 beta, IL-6, IL-8, IL-10], soluble TNF receptors (sTNFR) p55 and p75, and soluble IL-2 receptor (sIL-2R) were assessed in the homogenates and in the supernatants by sandwich enzyme-linked immunosorbent or enzyme-linked binding assays. The cytokine receptors were also measured in serum.

RESULTS

Six HIV-infected patients with cryptosporidiosis, six with microsporidiosis, seven with diarrhoea of unknown origin, seven without diarrhoea, and seven HIV-seronegative patients were eligible. Four patients were excluded because of the presence of other pathogens. No cytokines were detected in immediately homogenized jejunal tissue. Following culture, IL-6 and IL-8 levels were higher in HIV-infected patients with diarrhoea of unknown origin than in HIV-seronegative controls without diarrhoea, although this was not statistically significant. No differences in serum or post-culture supernatant sTNFR p55 and p75 levels existed between the HIV-infected patients with or without diarrhoea. sTNFR, IL-1 beta, IL-10 and the sIL-2R were only detected in low amounts or not at all, and were equally distributed among all patient groups.

CONCLUSIONS

This study indicates that mucosal cytokine-mediated inflammatory responses do not play an important role in the pathogenesis of different types of diarrhoea in HIV-infected patients. These results do not support the use of immunomodulatory therapy in these patients.

Isolation of human immunodeficiency virus type 1 (HIV-1) RNA from feces by a simple method and difference between HIV-1 subpopulations in feces and serum

A simple method for the isolation and subsequent detection of human immunodeficiency virus type 1 (HIV-1) RNA from feces is described. Viral RNA was isolated by the method developed by Boom et al. (R. Boom, C.J.A. Sol, M.M.M. Salimans, C.L. Jansen, P.M.E. Wertheim-van Dillen, and J. van der Noordaa, J. Clin. Microbiol. 28:495-503, 1990), which was adapted for feces. HIV-1 RNA was detected by reverse transcription (RT) followed by a nested PCR encompassing the V3 region. Reconstruction experiments revealed that the efficiencies of the extraction technique and the subsequent RT-PCR were not considerably affected by the varied composition of feces. The method was applied on fecal specimens from 18 HIV-1-infected individuals, among which were samples that had been stored for 9 years. It appeared that HIV-1 RNA was detectable in the feces of 12 persons (67%). Viral RNA was present in the feces of persons who fulfilled the criteria for CDC class II and CDC class III HIV infection as well as in patients who were diagnosed with AIDS (CDC class IV). Direct sequencing of amplimers obtained from paired fecal and serum specimens showed that differences in sequence heterogeneity existed. In one patient a remarkable difference in the HIV-1 sequences between isolates from feces and serum was observed. In conclusion, HIV-1 RNA is frequently present in the feces of HIV-1-infected individuals, and in some cases the HIV-1 subpopulation in feces differs from the HIV-1 subpopulation in serum.

Diagnosis of intestinal and disseminated microsporidial infections in patients with HIV by a new rapid fluorescence technique

AIMS

To assess the value of a new rapid fluorescence method for the diagnosis of microsporidiosis in HIV seropositive patients.

METHODS

Microsporidian spores in stools were demonstrated by using the fluorochrome stain Uvitex 2B. The new technique was evaluated in three groups of HIV seropositive patients with diarrhoea. Group 1: 19 patients with biopsy confirmed E bieneusi infection (186 stool samples); group 2: 143 consecutive patients from whom faeces were submitted for routine investigation of diarrhoea (318 samples); group 3: 16 patients with small intestinal biopsy specimens negative for microsporidia (55 samples). The new method was used to monitor spore shedding during experimental treatment with paromomycin and albendazole in four patients.

RESULTS

Brightly fluorescent spores were detected in all stool samples of patients in group 1. In group 2 16 (11%) patients had spores in their stool samples. E bieneusi was found in 11 patients; in the other five another genus of microsporidia, Encephalitozoon, was recognised. Encephalitozoon spores were also found in the urine of three of these patients and in the maxillary sinus aspirate of two of them, suggesting disseminated infection. The results were confirmed by electron microscopic examination. In group 3 negative biopsy specimens were confirmed by negative stool samples in all cases. Treatment with albendazole and paromomycin did not affect the spore shedding in three patients with E bieneusi infection. By contrast, in a patient with Encephalitozoon sp infection albendazole treatment resulted in clinical improvement together with complete cessation of spore excretion in the stool.

CONCLUSION

The Uvitex 2B fluorescence method combines speed, sensitivity, and specificity for the diagnosis and treatment evaluation of intestinal and disseminated microsporidiosis.