Perioperative antibiotics for preventing post-surgical site infections in solid organ transplant recipients.

BACKGROUND: Solid organ transplant recipients are at high risk for infections due to the complexity of surgical procedures combined with the impact of immunosuppression. No consensus exists on the role of antibiotics for surgical site infections in solid organ transplant recipients. OBJECTIVES: To assess the benefits and harms of prophylactic antimicrobial agents for preventing surgical site infections in solid organ transplant recipients. SEARCH METHODS: The Cochrane Kidney and Transplant Register of Studies was searched up to 21 April 2020 through contact with the Information Specialist using search terms relevant to this review. Studies in the Register are identified through searches of CENTRAL, MEDLINE, and EMBASE, conference proceedings, the International Clinical Trials Register (ICTRP) Search Portal, and ClinicalTrials.gov. SELECTION CRITERIA: All randomised controlled trials (RCTs) and quasi-RCTs in any language assessing prophylactic antibiotics in preventing surgical site infections in solid organ transplant recipients at any time point after transplantation. DATA COLLECTION AND ANALYSIS: Two authors independently determined study eligibility, assessed quality, and extracted data. Primary outcomes were surgical site infections and antimicrobial resistance. Other outcomes included urinary tract infections, pneumonias and septicaemia, death (any cause), graft loss, graft rejection, graft function, adverse reactions to antimicrobial agents, and outcomes identified by the Standardised Outcomes of Nephrology Group (SONG), specifically graft health, cardiovascular disease, cancer and life participation. Summary effect estimates were obtained using a random-effects model and results were expressed as risk ratios (RR) and 95% confidence intervals (CI). The quality of the evidence was assessed using the risk of bias and the GRADE approach. MAIN RESULTS: We identified eight eligible studies (718 randomised participants). Overall, five studies (248 randomised participants) compared antibiotics versus no antibiotics, and three studies (470 randomised participants) compared extended duration versus short duration antibiotics. Risk of bias was assessed as high for performance bias (eight studies), detection bias (eight studies) and attrition bias (two studies). It is uncertain whether antibiotics reduce the incidence of surgical site infections as the certainty of the evidence has been assessed as very low (RR 0.42, 95% CI 0.21 to 0.85; 5 studies, 226 participants; I2 = 25%). The certainty of the evidence was very low for all other reported outcomes (death, graft loss, and other infections). It is uncertain whether extended duration antibiotics reduces the incidence of surgical site infections in either solid organ transplant recipients (RR 1.19, 95% CI 0.58 to 2.48; 2 studies, 302 participants; I2 = 0%) or kidney-only transplant recipients (RR 0.50, 95% CI 0.05 to 5.48; 1 study, 205 participants) as the certainty of the evidence has been assessed as very low. The certainty of the evidence was very low for all other reported outcomes (death, graft loss, and other infections). None of the eight included studies evaluated antimicrobial agent adverse reactions, graft health, cardiovascular disease, cancer, life participation, biochemical and haematological parameters, intervention cost, hospitalisation length, or overall hospitalisation costs. AUTHORS' CONCLUSIONS: Due to methodological limitations, risk of bias and significant heterogeneity, the current evidence for the use of prophylactic perioperative antibiotics in transplantation is of very low quality. Further high quality, adequately powered RCTs would help better inform clinical practice.

Using Machine Learning to Provide Reliable Differentiated Services for IoT in SDN-Like Publish/Subscribe Middleware.

At present, most publish/subscribe middlewares suppose that there are equal Quality of Service (QoS) requirements for all users. However, in many real-world Internet of Things (IoT) service scenarios, different users may have different delay requirements. How to provide reliable differentiated services has become an urgent problem. The rise of Software-Defined Networking (SDN) provides endless possibilities to improve the QoS of publish/subscribe middlewares due to its greater programmability. We can encode event topics and priorities into flow entries of SDN switches directly to meet customized requirements. In this paper, we first propose an SDN-like publish/subscribe middleware architecture and describe how to use this architecture and priority queues supported by OpenFlow switches to realize differentiated services. Then we present a machine learning method using the eXtreme Gradient Boosting (XGBoost) model to solve the difficult issue of getting the queuing delay of switches accurately. Finally, we propose a reliable differentiated services guarantee mechanism according to the queuing delay and the programmability of SDN to improve QoS, namely, a two-layer queue management mechanism. Experimental evaluations show that the delay predicted by the XGBoost method is closer to the real value; our mechanism can save end-to-end delay, reduce packet loss rate, and allocate bandwidth more reasonably.

Endemic Mimosa species from Mexico prefer alphaproteobacterial rhizobial symbionts.

The legume genus Mimosa has > 500 species, with two major centres of diversity, Brazil (c. 350 spp.) and Mexico (c. 100 spp.). In Brazil most species are nodulated by Burkholderia. Here we asked whether this is also true of native and endemic Mexican species. We have tested this apparent affinity for betaproteobacteria by examining the symbionts of native and endemic species of Mimosa in Mexico, especially from the central highlands where Mimosa spp. have diversified. Nodules were tested for betaproteobacteria using in situ immunolocalization. Rhizobia isolated from the nodules were genetically characterized and tested for their ability to nodulate Mimosa spp. Immunological analysis of 25 host taxa suggested that most (including all the highland endemics) were not nodulated by betaproteobacteria. Phylogenetic analyses of 16S rRNA, recA, nodA, nodC and nifH genes from 87 strains isolated from 20 taxa confirmed that the endemic Mexican Mimosa species favoured alphaproteobacteria in the genera Rhizobium and Ensifer: this was confirmed by nodulation tests. Host phylogeny, geographic isolation and coevolution with symbionts derived from very different soils have potentially contributed to the striking difference in the choice of symbiotic partners by Mexican and Brazilian Mimosa species.

Environmental risk factors in the incidence of Johne's disease.

This review addresses the survival and persistence of Mycobacterium avium subsp. paratuberculosis (MAP), the causative pathogen of Johne's disease (JD), once it has left its ruminant host. JD has significant economic impact on dairy, beef and sheep industries and is difficult to control due to the long-term sub-clinical nature of the infection, intermittent or persistent MAP shedding during and after this period, inadequate test effectiveness, and the potential for MAP to exist for extended periods outside the host. The role that environmental factors play in the persistence and spread of MAP and consequent disease is assessed. Published risk factor analysis, organism survival across various environmental media and conditions, presence and spread in ruminant and non-ruminant wildlife, and the general potential for survival and multiplication of MAP ex-host both on and off-farm are discussed and knowledge gaps highlighted. An inclusive approach to disease management that takes into account the persistence and transport of the causative organism in on-farm soils and waters, land use and management, dispersal by domestic and non-domestic host species, as well as general animal husbandry is required on those farms where more traditional approaches to disease management have failed to reduce disease prevalence.

Burkholderia diazotrophica sp. nov., isolated from root nodules of Mimosa spp.

Five strains, JPY461(T), JPY359, JPY389, DPU-3 and STM4206 were isolated from nitrogen-fixing nodules on the roots of Mimosa spp. and their taxonomic positions were investigated using a polyphasic approach. All five strains grew at 15-40 °C (optimum, 30-37 °C), at pH 4.0-8.0 (optimum, pH 6.0-7.0) and with 0-1 % (w/v) NaCl [optimum, 0 % (w/v)]. On the basis of 16S rRNA gene sequence analysis, a representative strain (JPY461(T)) showed 97.2 % sequence similarity to the closest related species Burkholderia acidipaludis SA33(T), a similarity of 97.2 % to Burkholderia terrae KMY02(T), 97.1 % to Burkholderia phymatum STM815(T) and 97.1 % to Burkholderia hospita LMG 20598(T). The predominant fatty acids of the five novel strains were summed feature 2 (comprising C(16 : 1) iso I and/or C(14 : 0) 3-OH), summed feature 3 (comprising C(16 : 1)ω7c and/or C(16 : 1)ω6c), C(16 : 0) , C(16 : 0) 3-OH, C(17 : 0) cyclo, C(18 : 1)ω7c and C(19 : 0) cyclo ω8c. The major isoprenoid quinone was Q-8 and the DNA G+C content of the strains was 63.0-65.0 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an unidentified aminophospholipid, an unidentified aminolipid and several unidentified phospholipids. The DNA-DNA relatedness of the novel strain with respect to recognized species of the genus Burkholderia was less than 54 %. On the basis of 16S rRNA and recA gene sequence similarities, chemotaxonomic and phenotypic data, the five strains represent a novel species in the genus Burkholderia, for which the name Burkholderia diazotrophica sp. nov. is proposed with the type strain, JPY461(T) ( = LMG 26031(T) = BCRC 80259(T) = KCTC 23308(T)).

Burkholderia symbiotica sp. nov., isolated from root nodules of Mimosa spp. native to north-east Brazil.

Four strains, designated JPY-345(T), JPY-347, JPY-366 and JPY-581, were isolated from nitrogen-fixing nodules on the roots of two species of Mimosa, Mimosa cordistipula and Mimosa misera, that are native to North East Brazil, and their taxonomic positions were investigated by using a polyphasic approach. All four strains grew at 15-43 °C (optimum 35 °C), at pH 4-7 (optimum pH 5) and with 0-2 % (w/v) NaCl (optimum 0 % NaCl). On the basis of 16S rRNA gene sequence analysis, strain JPY-345(T) showed 97.3 % sequence similarity to the closest related species Burkholderia soli GP25-8(T), 97.3 % sequence similarity to Burkholderia caryophylli ATCC25418(T) and 97.1 % sequence similarity to Burkholderia kururiensis KP23(T). The predominant fatty acids of the strains were C(18 : 1)ω7c (36.1 %), C(16 : 0) (19.8 %) and summed feature 3, comprising C(16 : 1)ω7c and/or C(16 : 1)ω6c (11.5 %). The major isoprenoid quinone was Q-8 and the DNA G+C content of the strains was 64.2-65.7 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and several uncharacterized aminophospholipids and phospholipids. DNA-DNA hybridizations between the novel strain and recognized species of the genus Burkholderia yielded relatedness values of <51.8 %. On the basis of 16S rRNA and recA gene sequence similarities and chemotaxonomic and phenotypic data, the four strains represent a novel species in the genus Burkholderia, for which the name Burkholderia symbiotica sp. nov. is proposed. The type strain is JPY-345(T) (= LMG 26032(T) = BCRC 80258(T) = KCTC 23309(T)).

Legume-nodulating betaproteobacteria: diversity, host range, and future prospects.

Rhizobia form specialized nodules on the roots of legumes (family Fabaceae) and fix nitrogen in exchange for carbon from the host plant. Although the majority of legumes form symbioses with members of genus Rhizobium and its relatives in class Alphaproteobacteria, some legumes, such as those in the large genus Mimosa, are nodulated predominantly by betaproteobacteria in the genera Burkholderia and Cupriavidus. The principal centers of diversity of these bacteria are in central Brazil and South Africa. Molecular phylogenetic studies have shown that betaproteobacteria have existed as legume symbionts for approximately 50 million years, and that, although they have a common origin, the symbiosis genes in both subclasses have evolved separately since then. Additionally, some species of genus Burkholderia, such as B. phymatum, are highly promiscuous, effectively nodulating several important legumes, including common bean (Phaseolus vulgaris). In contrast to genus Burkholderia, only one species of genus Cupriavidus (C. taiwanensis) has so far been shown to nodulate legumes. The recent availability of the genome sequences of C. taiwanensis, B. phymatum, and B. tuberum has paved the way for a more detailed analysis of the evolutionary and mechanistic differences between nodulating strains of alpha- and betaproteobacteria. Initial analyses of genome sequences have suggested that plant-associated Burkholderia spp. have lower G+C contents than Burkholderia spp. that are opportunistic human pathogens, thus supporting previous suggestions that the plant- and human-associated groups of Burkholderia actually belong in separate genera.

Nodulation and nitrogen fixation by Mimosa spp. in the Cerrado and Caatinga biomes of Brazil.

*An extensive survey of nodulation in the legume genus Mimosa was undertaken in two major biomes in Brazil, the Cerrado and the Caatinga, in both of which there are high degrees of endemicity of the genus. *Nodules were collected from 67 of the 70 Mimosa spp. found. Thirteen of the species were newly reported as nodulating. Nodules were examined by light and electron microscopy, and all except for M. gatesiae had a structure typical of effective Mimosa nodules. The endosymbiotic bacteria in nodules from all of the Mimosa spp. were identified as Burkholderia via immunolabelling with an antibody against Burkholderia phymatum STM815. *Twenty of the 23 Mimosa nodules tested were shown to contain nitrogenase by immunolabelling with an antibody to the nitrogenase Fe- (nifH) protein, and using the delta(15)N ((15)N natural abundance) technique, contributions by biological N(2) fixation of up to 60% of total plant N were calculated for Caatinga Mimosa spp. *It is concluded that nodulation in Mimosa is a generic character, and that the preferred symbionts of Brazilian species are Burkholderia. This is the first study to demonstrate N(2) fixation by beta-rhizobial symbioses in the field.

Burkholderia species are ancient symbionts of legumes.

Burkholderia has only recently been recognized as a potential nitrogen-fixing symbiont of legumes, but we find that the origins of symbiosis in Burkholderia are much deeper than previously suspected. We sampled 143 symbionts from 47 native species of Mimosa across 1800 km in central Brazil and found that 98% were Burkholderia. Gene sequences defined seven distinct and divergent species complexes within the genus Burkholderia. The symbiosis-related genes formed deep Burkholderia-specific clades, each specific to a species complex, implying that these genes diverged over a long period within Burkholderia without substantial horizontal gene transfer between species complexes.

Prophylaxis, empirical and preemptive treatment of invasive candidiasis.

PURPOSE OF REVIEW: Invasive candidiasis remains an important infection for ICU patients, associated with poor clinical outcomes. It has been increasingly recognized that the traditional paradigm of culture-directed antifungal treatment is unsatisfactory, and that earlier antifungal intervention strategies, such as prophylaxis, preemptive therapy, and empiric therapy, are required to improve patient outcomes. The purpose of this review is to summarize the recent supportive evidence for such strategies and to highlight the current challenges in their implementation. RECENT FINDINGS: Despite new antifungal agents and classes, the mortality from invasive candidiasis remains high. Antifungal prophylaxis remains the best-studied early antifungal intervention strategy; however, unless targeted to patients at highest risk, is inefficient. Recent data suggests that although risk predictive models, using a combination of clinical risk factors and Candida colonization parameters, may be a relatively simple and practical approach to guide prophylaxis or preemptive therapy, further validation of these models is required. A single trial has demonstrated that empiric antifungal therapy is not of benefit when instituted to patients with antibiotic-refractory fever alone. SUMMARY: On the basis of current knowledge, it is difficult to universally recommend antifungal prophylaxis, apart from patient groups with a known very high risk, such as those with necrotising pancreatitis or recurrent gastrointestinal perforations. Antifungal prophylaxis may also be reasonable where local incidence rates and epidemiology are compelling. Among stable patients with multifocal Candida colonization and/or a multitude of clinical-risk factors, preemptive therapy is currently not indicated, although the development of better risk predictive models may assist with such patients. Among patients with refractory fever despite broad-spectrum antibacterial therapy, empiric antifungal therapy may be reasonable where local incidence rates are high (e.g. >10%); however, a thorough search for alternate causes must be instituted.

Safety, tolerability, pharmacokinetics, and immunogenicity of a human monoclonal antibody targeting the G glycoprotein of henipaviruses in healthy adults: a first-in-human, randomised, controlled, phase 1 study.

BACKGROUND: The monoclonal antibody m102.4 is a potent, fully human antibody that neutralises Hendra and Nipah viruses in vitro and in vivo. We aimed to investigate the safety, tolerability, pharmacokinetics, and immunogenicity of m102.4 in healthy adults. METHODS: In this double-blind, placebo-controlled, single-centre, dose-escalation, phase 1 trial of m102.4, we randomly assigned healthy adults aged 18-50 years with a body-mass index of 18·0-35·0 kg/m2 to one of five cohorts. A sentinel pair for each cohort was randomly assigned to either m102.4 or placebo. The remaining participants in each cohort were randomly assigned (5:1) to receive m102.4 or placebo. Cohorts 1-4 received a single intravenous infusion of m102.4 at doses of 1 mg/kg (cohort 1), 3 mg/kg (cohort 2), 10 mg/kg (cohort 3), and 20 mg/kg (cohort 4), and were monitored for 113 days. Cohort 5 received two infusions of 20 mg/kg 72 h apart and were monitored for 123 days. The primary outcomes were safety and tolerability. Secondary outcomes were pharmacokinetics and immunogenicity. Analyses were completed according to protocol. The study was registered on the Australian New Zealand Clinical Trials Registry, ACTRN12615000395538. FINDINGS: Between March 27, 2015, and June 16, 2016, 40 (52%) of 77 healthy screened adults were enrolled in the study. Eight participants were assigned to each cohort (six received m102.4 and two received placebo). 86 treatment-emergent adverse events were reported, with similar rates between placebo and treatment groups. The most common treatment-related event was headache (12 [40%] of 30 participants in the combined m102.4 group, and three [30%] of ten participants in the pooled placebo group). No deaths or severe adverse events leading to study discontinuation occurred. Pharmacokinetics based on those receiving m102.4 (n=30) were linear, with a median half-life of 663·3 h (range 474·3-735·1) for cohort 1, 466·3 h (382·8-522·3) for cohort 2, 397·0 h (333·9-491·8) for cohort 3, and 466·7 h (351·0-889·6) for cohort 4. The elimination kinetics of those receiving repeated dosing (cohort 5) were similar to those of single-dose recipients (median elimination half-time 472·0 [385·6-592·0]). Anti-m102.4 antibodies were not detected at any time-point during the study. INTERPRETATION: Single and repeated dosing of m102.4 were well tolerated and safe, displayed linear pharmacokinetics, and showed no evidence of an immunogenic response. This study will inform future dosing regimens for m102.4 to achieve prolonged exposure for systemic efficacy to prevent and treat henipavirus infections. FUNDING: Queensland Department of Health, the National Health and Medical Research Council, and the National Hendra Virus Research Program.

Burkholderia spp. are the most competitive symbionts of Mimosa, particularly under N-limited conditions.

Bacteria isolated from Mimosa nodules in Taiwan, Papua New Guinea, Mexico and Puerto Rico were identified as belonging to either the alpha- or beta-proteobacteria. The beta-proteobacterial Burkholderia and Cupriavidus strains formed effective symbioses with the common invasive species Mimosa diplotricha, M. pigra and M. pudica, but the alpha-proteobacterial Rhizobium etli and R. tropici strains produced a range of symbiotic phenotypes from no nodulation through ineffective to effective nodulation, depending on Mimosa species. Competition studies were performed between three of the alpha-proteobacteria (R. etli TJ167, R. tropici NGR181 and UPRM8021) and two of the beta-rhizobial symbionts (Burkholderia mimosarum PAS44 and Cupriavidus taiwanensis LMG19424) for nodulation of these invasive Mimosa species. Under flooded conditions, B. mimosarum PAS44 out-competed LMG19424 and all three alpha-proteobacteria to the point of exclusion. This advantage was not explained by initial inoculum levels, rates of bacterial growth, rhizobia-rhizobia growth inhibition or individual nodulation rate. However, the competitive domination of PAS44 over LMG19424 was reduced in the presence of nitrate for all three plant hosts. The largest significant effect was for M. pudica, in which LMG19424 formed 57% of the nodules in the presence of 0.5 mM potassium nitrate. In this host, ammonium also had a similar, but lesser, effect. Comparable results were also found using an N-containing soil mixture, and environmental N levels are therefore suggested as a factor in the competitive success of the bacterial symbiont in vivo.

Nodulation of Sesbania species by Rhizobium (Agrobacterium) strain IRBG74 and other rhizobia.

Concatenated sequence analysis with 16S rRNA, rpoB and fusA genes identified a bacterial strain (IRBG74) isolated from root nodules of the aquatic legume Sesbania cannabina as a close relative of the plant pathogen Rhizobium radiobacter (syn. Agrobacterium tumefaciens). However, DNA:DNA hybridization with R. radiobacter, R. rubi, R. vitis and R. huautlense gave only 44%, 5%, 8% and 8% similarity respectively, suggesting that IRBG74 is potentially a new species. Additionally, it contained no vir genes and lacked tumour-forming ability, but harboured a sym-plasmid containing nifH and nodA genes similar to those in other Sesbania symbionts. Indeed, IRBG74 effectively nodulated S. cannabina and seven other Sesbania spp. that nodulate with Ensifer (Sinorhizobium)/Rhizobium strains with similar nodA genes to IRBG74, but not species that nodulate with Azorhizobium or Mesorhizobium. Light and electron microscopy revealed that IRBG74 infected Sesbania spp. via lateral root junctions under flooded conditions, but via root hairs under non-flooded conditions. Thus, IRBG74 is the first confirmed legume-nodulating symbiont from the Rhizobium (Agrobacterium) clade. Cross-inoculation studies with various Sesbania symbionts showed that S. cannabina could form fully effective symbioses with strains in the genera Rhizobium and Ensifer, only ineffective ones with Azorhizobium strains, and either partially effective (Mesorhizobium huakii) or ineffective (Mesorhizobium plurifarium) symbioses with Mesorhizobium. These data are discussed in terms of the molecular phylogeny of Sesbania and its symbionts.

Antifungals in the ICU.

PURPOSE OF REVIEW: Invasive fungal infections remain a serious complication for critically ill ICU patients. The aim of this article is to review recent efficacy data of newer antifungal agents for the treatment of invasive candidiasis. The influence that recent epidemiological trends, advances in diagnostic testing, and risk prediction methods exert on the optimization of antifungal therapy for critically ill ICU patients will also be reviewed. RECENT FINDINGS: Recent clinical trials have documented the clinical efficacy of the echinocandins and the newer triazoles for the management of invasive candidiasis. Thus far, resistance to echinocandins remains rare. Changes in the epidemiology of Candida spp. causing invasive candidiasis, such as an increasing relative proportion of non-albicans Candida spp., have not been universally reported, although they have important implications for the use of fluconazole as first-line therapy for invasive candidiasis. Efforts to improve the timeliness and accuracy of laboratory diagnostic techniques and clinical prediction models to allow early and accurately targeted antifungal intervention strategies continue. SUMMARY: Echinocandins, given their clinical efficacy, spectrum of activity, and favourable pharmacological properties, are likely to replace fluconazole as initial antifungal agents of choice among critically ill ICU patients. The optimization of patient outcomes will require more accurately targeted early antifungal intervention strategies based upon sensitive and specific biological and clinical markers of risk.

Nodulation of Cyclopia spp. (Leguminosae, Papilionoideae) by Burkholderia tuberum.

BACKGROUND AND AIMS: Species of the genus Burkholderia, from the Betaproteobacteria, have been isolated from legume nodules, but so far they have only been shown to form symbioses with species of Mimosa, sub-family Mimosoideae. This work investigates whether Burkholderia tuberum strains STM678 (isolated from Aspalathus carnosa) and DUS833 (from Aspalathus callosa) can nodulate species of the South African endemic papilionoid genera Cyclopia (tribe Podalyrieae) and Aspalathus (Crotalarieae) as well as the promiscuous legume Macroptilium atropurpureum (Phaseoleae). METHODS: Bacterial strains and the phylogeny of their symbiosis-related (nod) genes were examined via 16S rRNA gene sequencing. Seedlings were grown in liquid culture and inoculated with one of the two strains of B. tuberum or with Sinorhizobium strain NGR 234 (from Lablab purpureus), Mesorhizobium strain DUS835 (from Aspalathus linearis) or Methylobacterium nodulans (from Crotalaria podocarpa). Some nodules, inoculated with green fluorescence protein (GFP)-tagged strains, were examined by light and electron microscopy coupled with immunogold labelling with a Burkholderia-specific antibody. The presence of active nitrogenase was checked by immunolabelling of nitrogenase and by the acetylene reduction assay. B. tuberum STM678 was also tested on a wide range of legumes from all three sub-families. KEY RESULTS: Nodules were not formed on any of the Aspalathus spp. Only B. tuberum nodulated Cyclopia falcata, C. galioides, C. genistoides, C. intermedia and C. pubescens. It also effectively nodulated M. atropurpureum but no other species tested. GFP-expressing inoculant strains were located inside infected cells of C. genistoides, and bacteroids in both Cyclopia spp. and M. atropurpureum were immunogold-labelled with antibodies against Burkholderia and nitrogenase. Nitrogenase activity was also shown using the acetylene reduction assay. This is the first demonstration that a beta-rhizobial strain can effectively nodulate papilioinoid legumes. CONCLUSIONS: Papilionoid legumes from widely different tribes can be nodulated by beta-rhizobia, forming both indeterminate (Cyclopia) and determinate (Macroptilium) nodules.

Multiplex T-RFLP allows for increased target number and specificity: detection of Salmonella enterica and six species of Listeria in a single test.

A multiplex T-RFLP test was developed to detect and identify Salmonella enterica and all six species of Listeria inoculated into milk at minimal levels. Extensive in silico analysis was used to design a fifteen-primer, six-amplimer methodology and in vitro application showed target organism DNA, when amplified individually, yielded the predicted terminal restriction fragments (TRFs) following digestion. Non-target organisms were either not-amplified or yielded TRFs which did not interfere with target identification. Multiple target DNA analysis gave over 86% detection of total TRFs predicted, and this was improved to over 90% detection of total TRFs predicted when only two target DNA extracts were combined analysed. Co-inoculation of milk with five strains each of the target species of S. enterica and L. monocytogenes, along with five strains of the non-target species E. coli was followed by enrichment in SEL medium for M-TRFLP analysis. This allowed for detection of both target species in all samples, with detection of one S. enterica and two Listeria TRFs in all cases, and detection of a second S. enterica TRF in 91% of cases. This was from an initial inoculum of <5 cfu per 25 ml milk with a background of competing E. coli present, and gave a result from sampling of under 20 hours. The ability to increase target species number without loss of sensitivity means that extensive screening can be performed at reduced cost due to a reduction in the number of tests required.

Assessment of clinical risk predictive rules for invasive candidiasis in a prospective multicentre cohort of ICU patients.

PURPOSE: To assess the generalisability of published clinical risk predictive models for invasive candidiasis in ICU patients. METHODS: The performance characteristics of published clinical risk factor-only and Candida colonisation-only predictive models for invasive candidiasis were assessed in a multicentre cohort of Australian ICU patients. Clinical risk factors and Candida colonisation parameters were collected prospectively from patients. RESULTS: The two clinical risk factor-only predictive models applied to an Australian patient cohort (n = 615) performed less well than in published studies involving derivation populations. Model performance characteristics improved when Candida colonisation parameters were added post-hoc. CONCLUSIONS: Risk predictive models should factor in both clinical risk factors and Candida colonisation parameters. Integrating these models into therapeutic algorithms first requires external validation in different patient populations and settings.

Burkholderia sabiae sp. nov., isolated from root nodules of Mimosa caesalpiniifolia.

Two rhizobial strains, Br3407(T) and Br3405, were isolated from nitrogen-fixing nodules on the roots of Mimosa caesalpiniifolia, a legume tree native to Brazil. On the basis of 16S rRNA gene sequence similarities, both strains were shown previously to belong to the genus Burkholderia. A polyphasic approach, including DNA-DNA hybridizations, pulsed-field gel electrophoresis of whole-genome DNA profiles, whole-cell protein analyses, fatty acid methyl ester analysis and extensive biochemical characterization, was used to clarify the taxonomic position of these strains further; the strains are here classified within a novel species, for which the name Burkholderia sabiae sp. nov. is proposed. The type strain is strain Br3407(T) (=LMG 24235(T) =BCRC 17587(T)).

Optimizing therapy for Candida infections.

The problem of invasive candidiasis among ICU patients is an increasing and evolving one. Despite advances in supportive care, increasing numbers of critically ill and vulnerable patients are susceptible to infection, and the clinical consequences for those who do develop invasive candidiasis remain poor. Evolving epidemiological trends, particularly a relative increase in the incidence of fluconazole-resistant Candida spp., have further complicated management. The recent availability of antifungal agents, such as voriconazole, the echinocandins, and lipid-associated amphotericin B preparations, with improved safety profiles, extended spectra, and proven clinical efficacies, offers new therapeutic options. However, optimizing therapy requires the consideration of numerous factors: the differing pharmacological properties of these agents, cost, the clinical status and progress of the patient, estimates of the likelihood of resistance, and microbiological data as they become available. Because early institution of antifungal therapy appears an important determinant of favorable outcome, accurate early microbiological and clinical markers of invasive candidiasis to guide early antifungal interventions are desperately needed and remain an area of active investigation.

Burkholderia nodosa sp. nov., isolated from root nodules of the woody Brazilian legumes Mimosa bimucronata and Mimosa scabrella.

Three strains, Br3437(T), Br3461 and Br3470, were isolated from nitrogen-fixing nodules on the roots of Mimosa scabrella (Br3437(T)) and Mimosa bimucronata (Br3461, Br3470), both of which are woody legumes native to Brazil. On the basis of 16S rRNA gene sequence similarities, all the strains were shown previously to belong to the genus Burkholderia. A polyphasic approach, including DNA-DNA hybridizations, PFGE of whole-genome DNA profiles, whole-cell protein analyses, fatty acid methyl ester analysis and extensive biochemical characterization, was used to clarify the taxonomic position of these strains further; the strains are here classified within a novel species, for which the name Burkholderia nodosa sp. nov. is proposed. The type strain, Br3437(T) (=LMG 23741(T)=BCRC 17575(T)), was isolated from nodules of M. scabrella.