Personal digital assistants to collect tuberculosis bacteriology data in Peru reduce delays, errors, and workload, and are acceptable to users: cluster randomized controlled trial

SummaryObjectivesTo evaluate the effectiveness of a personal digital assistant (PDA)-based system for collecting tuberculosis test results and to compare this new system to the previous paper-based system. The PDA- and paper-based systems were evaluated based on processing times, frequency of errors, and number of work-hours expended by data collectors.MethodsWe conducted a cluster randomized controlled trial in 93 health establishments in Peru. Baseline data were collected for 19 months. Districts (n=4) were then randomly assigned to intervention (PDA) or control (paper) groups, and further data were collected for 6 months. Comparisons were made between intervention and control districts and within-districts before and after the introduction of the intervention.ResultsThe PDA-based system had a significant effect on processing times (p<0.001) and errors (p=0.005). In the between-districts comparison, the median processing time for cultures was reduced from 23 to 8 days and for smears was reduced from 25 to 12 days. In that comparison, the proportion of cultures with delays >90 days was reduced from 9.2% to 0.1% and the number of errors was decreased by 57.1%. The intervention reduced the work-hours necessary to process results by 70% and was preferred by all users.ConclusionsA well-designed PDA-based system to collect data from institutions over a large, resource-poor area can significantly reduce delays, errors, and person-hours spent processing data

Tuberculosis laboratory information systems for resource-poor settings

Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, February 2009.Includes bibliographical references (p. 132-143).Multi-drug resistant tuberculosis (MDR-TB) patients in resource-poor settings experience large delays in starting appropriate drug regimens and are often not monitored appropriately due to an overburdened health care system, communication delays, and missing or error-prone data. Medical information systems can be used to alleviate these problems by increasing the timeliness and quality of laboratory information available. The research reported in this thesis developed, implemented, and evaluated two such systems in the urban, resource-poor setting of Lima, Peru in institutions with and without internet. The first part addresses the electronic collection of tuberculosis (TB) laboratory information from multiple institutions without internet. A handheld computer-based system was developed and implemented. A cluster randomized controlled trial and before-and-after comparison showed that this system had a significant effect in reducing processing times from 23 to 8 days, the proportion of cultures with delays >90 days from 9.2% to 0.1%, the number of errors by 57.1%, and the work-hours necessary to process results by 60%. A cost and timeline framework was developed to allow other organizations in resource-poor settings to implement this technology. The second part addresses a web-based system, e-Chasqui, developed to provide electronic communication and reporting of TB laboratory information to health care personnel within institutions with internet. A cluster randomized controlled trial showed that access to e-Chasqui resulted in significantly less time to receipt of test results, a 56% reduction in tests taking over 60 days to arrive and a 98% reduction of results that never arrived, as well as a significantly faster time to culture conversion among patients in intervention versus control centers.(cont.) These two parts describe verified medical informatics tools and an implementation methodology for settings both with and without internet connectivity.by Joaquin Andres Blaya.Ph.D

Streptomyces venezuelae: a source of ECF-sigma factors for genetic switches and a model for antibiotic resistance studies

The soil is a challenging habitat where microorganisms are exposed to adverse environmental conditions and where they compete for space and resources. Surviving in such situations requires bacteria to permanently monitor their environment and initiate the appropriate responses to counteract the deleterious effects of a given adverse condition. For this, bacteria have sophisticated systems to sense environmental changes and elaborate specialized responses in order to overcome conditions that could cause harm. These systems are i) one-component system (1CS), ii) two-component systems, and iii) extracytoplasmic function (ECF) σ factors. Streptomycetes are gram-positive soil bacteria with a complex life cycle, being antibiotic producers and also antibiotic resistant. Additionally, these bacteria present one of the highest repertoires of ECF σ factors making them the ideal model organism for this study. The aims of this study were to i) use of ECF σ factors of S. venezuelae to design and implement orthogonal switches in B. subtilis and ii) elucidate the mechanisms of resistance against antimicrobial peptides in S. venezuelae. The performance of the ECF19-based switch was tested in the presence of its anti-σ factor, upon variation in copy number of each constituent transcriptional unit, type of inducible promoter, ECF σ factor stability and under the effects of antisense transcription. This systematic characterization of the ECF19 switch has shown it is the best performing heterologous ECF-based switch so far described for B. subtilis. Its activity is nonetheless compromised by genetic perturbations caused by changes in the copy number, protein stability and antisense transcription. This study also demonstrates that S. venezuelae is highly resistant to the antimicrobial peptide bacitracin. By performing random mutagenesis followed by genome sequencing and RNAseq analysis, it was possible to identify the genes that might be involved in bacitracin resistance in S. venezuelae.Der Erdboden ist ein herausforderndes Habitat, in dem Mikroorganismen widrigen Umwelteinflüssen ausgesetzt sind und zusätzlich um Raum und Ressourcen konkurrieren müssen. Um in solchen Situationen überleben zu können, sind die Bakterien permanent darauf angewiesen, ihre Umgebung zu überwachen. Bei gegebenen ungünstigen Bedingungen müssen entsprechende angemessene Reaktionen initiiert werden, damit sie diesen schädlichen Effekten entgegen wirken zu können. Für diese Aufgabe stellen Bakterien komplexe Systeme bereit, die die Umweltveränderungen wahrnehmen und spezialisierte Antworten auslösen, um Bedingungen zu überwinden, die Schäden verursachen können. Diese Systeme sind i) Einkomponentensysteme (1CS), ii) Zweikomponentensysteme (2CS) und iii) extracytoplasmic function (ECF)-Sigmafaktoren. Streptomyceten sind grampositive Bodenbakterien mit komplexen Lebenszyklen, die Antibiotika produzieren aber auch selbst antibiotische Resistenzen aufweisen. Zusätzlich stellen diese Bakterien ein sehr breites Repertoire an ECF-Sigmafaktoren bereit, was sie zu einem optimalen Modellorganismus für diese Arbeit macht. Das Ziel dieser Arbeit bestand darin, i) die Nutzung von ECF-Sigmafaktoren in S. venezuelae zu erläutern, darauf aufbauend orthogonale Schalter in B. subtilis zu konzipieren und zu implementieren. ii) Des Weiteren sollten die Mechanismen der Resistenz gegen antimikrobielle Peptide in S. venezuelae aufgeklärt werden. Die Leistungsfähigkeit des, auf ECF19 basierenden, Schalters wurde unter verschiedenen Bedingungen getestet: in der Anwesenheit seines anti-Sigmafaktors, nach Veränderung der Kopiezahl jeder einzelnen Transkriptionseinheit, unter der Kontrolle unterschiedlicher Typen des induzierenden Promoters, auf Stabilität des ECF-Sigmafaktors und auf den Effekt der antisense-Transkription. Diese systematische Charakterisierung des ECF19-Schalters hat gezeigt, dass es sich dabei um einen heterologen ECF-Schalter mit der besten Leistung in B. subtilis handelt, die bisher beschrieben wurde. Die Aktivität des Schalters wird allerdings beeinträchtigt durch genetische Störungen, die durch Änderungen der Kopiezahl, der Proteinstabilität und antisense-Transkription hervorgerufen werden. Diese Arbeit hat weiterhin demonstriert, dass S. venezuelae hochresistent gegen das antimikrobielle Peptid, Bacitracin, ist. Aufgrund der Durchführung von zufälliger Mutagenese, gefolgt von Genomsequenzierung und RNAseq war es möglich, Gene zu identifizieren, die höchstwahrscheinlich in der Bacitracin-Resistenz in S. venezuelae eine wichtige Rolle spielen

Streptomyces venezuelae: a source of ECF-sigma factors for genetic switches and a model for antibiotic resistance studies

The soil is a challenging habitat where microorganisms are exposed to adverse environmental conditions and where they compete for space and resources. Surviving in such situations requires bacteria to permanently monitor their environment and initiate the appropriate responses to counteract the deleterious effects of a given adverse condition. For this, bacteria have sophisticated systems to sense environmental changes and elaborate specialized responses in order to overcome conditions that could cause harm. These systems are i) one-component system (1CS), ii) two-component systems, and iii) extracytoplasmic function (ECF) σ factors. Streptomycetes are gram-positive soil bacteria with a complex life cycle, being antibiotic producers and also antibiotic resistant. Additionally, these bacteria present one of the highest repertoires of ECF σ factors making them the ideal model organism for this study. The aims of this study were to i) use of ECF σ factors of S. venezuelae to design and implement orthogonal switches in B. subtilis and ii) elucidate the mechanisms of resistance against antimicrobial peptides in S. venezuelae. The performance of the ECF19-based switch was tested in the presence of its anti-σ factor, upon variation in copy number of each constituent transcriptional unit, type of inducible promoter, ECF σ factor stability and under the effects of antisense transcription. This systematic characterization of the ECF19 switch has shown it is the best performing heterologous ECF-based switch so far described for B. subtilis. Its activity is nonetheless compromised by genetic perturbations caused by changes in the copy number, protein stability and antisense transcription. This study also demonstrates that S. venezuelae is highly resistant to the antimicrobial peptide bacitracin. By performing random mutagenesis followed by genome sequencing and RNAseq analysis, it was possible to identify the genes that might be involved in bacitracin resistance in S. venezuelae.Der Erdboden ist ein herausforderndes Habitat, in dem Mikroorganismen widrigen Umwelteinflüssen ausgesetzt sind und zusätzlich um Raum und Ressourcen konkurrieren müssen. Um in solchen Situationen überleben zu können, sind die Bakterien permanent darauf angewiesen, ihre Umgebung zu überwachen. Bei gegebenen ungünstigen Bedingungen müssen entsprechende angemessene Reaktionen initiiert werden, damit sie diesen schädlichen Effekten entgegen wirken zu können. Für diese Aufgabe stellen Bakterien komplexe Systeme bereit, die die Umweltveränderungen wahrnehmen und spezialisierte Antworten auslösen, um Bedingungen zu überwinden, die Schäden verursachen können. Diese Systeme sind i) Einkomponentensysteme (1CS), ii) Zweikomponentensysteme (2CS) und iii) extracytoplasmic function (ECF)-Sigmafaktoren. Streptomyceten sind grampositive Bodenbakterien mit komplexen Lebenszyklen, die Antibiotika produzieren aber auch selbst antibiotische Resistenzen aufweisen. Zusätzlich stellen diese Bakterien ein sehr breites Repertoire an ECF-Sigmafaktoren bereit, was sie zu einem optimalen Modellorganismus für diese Arbeit macht. Das Ziel dieser Arbeit bestand darin, i) die Nutzung von ECF-Sigmafaktoren in S. venezuelae zu erläutern, darauf aufbauend orthogonale Schalter in B. subtilis zu konzipieren und zu implementieren. ii) Des Weiteren sollten die Mechanismen der Resistenz gegen antimikrobielle Peptide in S. venezuelae aufgeklärt werden. Die Leistungsfähigkeit des, auf ECF19 basierenden, Schalters wurde unter verschiedenen Bedingungen getestet: in der Anwesenheit seines anti-Sigmafaktors, nach Veränderung der Kopiezahl jeder einzelnen Transkriptionseinheit, unter der Kontrolle unterschiedlicher Typen des induzierenden Promoters, auf Stabilität des ECF-Sigmafaktors und auf den Effekt der antisense-Transkription. Diese systematische Charakterisierung des ECF19-Schalters hat gezeigt, dass es sich dabei um einen heterologen ECF-Schalter mit der besten Leistung in B. subtilis handelt, die bisher beschrieben wurde. Die Aktivität des Schalters wird allerdings beeinträchtigt durch genetische Störungen, die durch Änderungen der Kopiezahl, der Proteinstabilität und antisense-Transkription hervorgerufen werden. Diese Arbeit hat weiterhin demonstriert, dass S. venezuelae hochresistent gegen das antimikrobielle Peptid, Bacitracin, ist. Aufgrund der Durchführung von zufälliger Mutagenese, gefolgt von Genomsequenzierung und RNAseq war es möglich, Gene zu identifizieren, die höchstwahrscheinlich in der Bacitracin-Resistenz in S. venezuelae eine wichtige Rolle spielen

Potential biological control pseudomonas sp. PCI2 against damping-off of tomato caused by Sclerotium Rolfsii

Fluorescent Pseudomonas spp. isolated from the roots of healthy tomato plants were screened for their antagonistic activities against Sclerotium rolfsii, Alternaria alternata and Fusarium solani, three phytopathogenic fungi of tomato and pepper. They were tested for phosphate solubilization ability and production of siderophores, hydrolytic enzymes, indole 3-acetic acid and hydrogen cyanid. The isolates were also characterized based on biochemical (API 20NE test) and genotypic (ERIC-PCR fingerprinting) features. A Pseudomonas sp. strain denoted PCI2 was chosen as a potential candidate for controlling tomato damping-off caused by Sclerotium rolfsii. PCI2 was identified at the genus level with a 16S rDNA partial sequence analysis and its phylogenetic relationship with previously characterized Pseudomonas species was determined. PCI2 clustered with the P. putida species. Growth chamber studies resulted in statistically significant increases in plant stand (29%) as well as in root dry weight (58%). PCI2 was able to establish itself and survive in tomato rhizosphere after 40 days, following planting of bacterized seeds. PCI2 is a potential biological control agent that may contribute to the protection of tomato plants against damping-off caused by S. rolfsii.Fil: Pastor, Nicolás Alejandro. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas Fisicoquímicas y Naturales. Departamento de Biología Molecular; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba; ArgentinaFil: Reynoso, Maria Marta. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas, Fisicoquímicas y Naturales. Departamento de Microbiología e Inmunología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba; ArgentinaFil: Tonelli, Maria Laura. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas Fisicoquímicas y Naturales; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba; ArgentinaFil: Masciarelli, Oscar Alberto. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas Fisicoquímicas y Naturales; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba; ArgentinaFil: Rosas, Susana Beatriz. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas Fisicoquímicas y Naturales. Departamento de Biología Molecular; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba; ArgentinaFil: Rovera, Marisa. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas, Fisicoquímicas y Naturales. Departamento de Microbiología e Inmunología; Argentin

BIOLOGICAL CONTROL OF SUDDEN DECLINE DISEASE OF DATE PALM (PHOENIX DACTYLIFERA L.) IN THE UNITED ARAB EMIRATES

Date palm orchards suffer from serious diseases, including sudden decline syndrome (SDS). The fungal pathogen Fusarium solani was associated with SDS on date palm in the United Arab Emirates (UAE). Application of Cidely® Top (difenoconazole and cyflufenamid) significantly inhibited the fungal mycelial growth In vitro and reduced SDS development on date palm seedlings pre-inoculated with F. solani under greenhouse conditions. This is the first report confirming that the chemical fungicide Cidely® Top is strongly effective against SDS on date palm. Fungal pathogens not only inhibit plant growth directly but also induce the plant to synthesize stress ethylene. Much of the damage sustained by plants infected with fungal phytopathogens occurs as a result of the response of the plant to the increased levels of ethylene. The aim of the present study was to compare the effectiveness of antagonistic actinobacteria capable of producing 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase, with those incapables of producing ACC deaminase, on suppression and severity of SDS on date palm. To achieve this, actinobacteria-producing ACC deaminase isolated from the rhizosphere of date palm in the UAE were evaluated for their potential to produce antifungal metabolites and cell-wall degrading enzymes that can inhibit the growth of the pathogen In vitro. The most inhibitory isolates produced chitinase, diffusible antifungal metabolites, and siderophores, and were able to lyse the hyphae of the three pathogens In vitro. Under greenhouse conditions, the ACC deaminase-producing isolates were significantly more effective in reducing the incidence and severity of SDS compared to ACC deaminase-non-producing isolates. This study demonstrated for the first time the superiority of antagonistic rhizosphere actinobacteria to enhance their effectiveness as biocontrol agents by their abilities to produce ACC deaminase in addition to their abilities to produce antifungal metabolites and cell-wall degrading enzymes. The results clearly showed the potential to enhance most if not all of the biocontrol agent’s performance by including the ACC deaminase ability in the strains

FIELD IMPLEMENTATION OF \u3cem\u3ePHANEROCHAETE CHRYSOSPORIUM\u3c/em\u3e BIOMASS PRETREATMENT: FUNGAL IDENTIFICATION AND INOCULATION TECHNIQUES

Scaling biological pretreatment from the bench scale to the production scale may be more economical if unsterilized feedstock are used, however these allow for microbial competition from contaminates. An accurate and rapid method for identifying the desired biological pretreatment organism is necessary to confirm the presence of the desired organism when contaminates are morphologically similar to the target organism. Traditional methods, such as visual identification, sequencing, and selective plating can be time consuming and are sometimes still inconclusive. Based on methods described in the literature, plasmid DNA containing the marker genes gus (�-glucuronidase), LacZ, and gfp (green fluorescence protein) incorporated into the lignin-degrading basidiomycete Phanerochaete chrysosporium would result in a rapid genetic test for the desired organism. The presence of these genes can be confirmed either through an X-Gluc (cyclohexylammonia salt), X-Gal histochemical assay or observing the gfp’s fluorescence by a specially equipped confocal microscope. Each reporter systems will allow for rapid, reliable identification of the target species. This study will report on the success of the transformation methods in creating a transformed fungus to be used in the context of a large-scale fermentation operation. Additionally, a novel in-harvest lignocellulose feedstock biological pretreatment inoculation trial was performed comparing lignolytic performance between fungal inoculum application techniques. Optimization of carbohydrate availability for enhanced saccharification was determined by analyzing glucose release by treated and non-treated unsterilized switchgrass. This study also focused on identifying parameters to enhance saccharification efficacy at the farm-scale

Evaluation morphométrique des chevaux pur-sang Arabe en Algérie: mensurations corporelles et proposition d’équations barymétriques

Cette étude vise à la caractérisation morphobiométrique des chevaux de course pur-sang arabe et à l’estimation d’équations barymétriques adaptées à cette race. La caractérisation a concerné 98 chevaux, dont 44 femelles et 54 mâles, tous âgés de trois ans et plus, auprès de 77 propriétaires-éleveurs dans 3 hippodromes d’Algérie (Zemmouri, Tiaret et Caroubier). Dix-neuf mensurations étaient relevées ainsi que le poids vif (PV). Le poids moyen est de 456,2 +/- 43,0 kg, variant de 335 kg à 545 kg. La sélection des variables à inclure dans les équations barymétriques a été réalisée à l’aide de la procédure stepwise du SAS. Quatre mensurations parmi les 19 réalisées ont été retenues pour la proposition d’équations d’estimation du poids vif des chevaux : le périmètre thoracique (PT), la hauteur à la croupe (HC), la longueur de l’encolure (LE) et le tour de l’encolure (TE). Ainsi, les équations proposées pour les mâles et pour les femelles sont respectivement de : PV= 7,024*PT - 787,119 (R²=0,99); PV=6,207*PT + 0,633*HC + 0,668*TE - 0,878*LE - 746,370 (R²=0,96). Les résultats de cette étude devraient permettre aux propriétaires-éleveurs et entraineurs de suivre aisément le poids de leurs chevaux. Ce suivi est nécessaire pour adapter l’activité et l’alimentation des chevaux et favoriser leur performance en course

Airborne microbiota and related environmental parameters associated with a typical dairy farm plant

Thesis (M. Tech. (Environmental health: Food safety )) - Central university of Technology, Free State, 2013Food processing plants and agricultural environments have a long-standing history of being known to provide a conducive environment for the prevalence and distribution of microorganisms which emanate as a consequence of activities undertaken in such premises. Microorganisms in the aforementioned environments may be found in the atmosphere (airborne), and/or on food contact surfaces. Airborne microorganisms from food handlers and in food products and raw materials (as part of bioaerosols) have in the past been implicated as having a potential to cause adverse health effects (especially in indoor environments) and therefore also to have economic implications. Recently their effect on food safety has received increased interest. The recent international interest in bioaerosols in the food industry has played a role in rapidly providing increased understanding of bioaerosols and their effects in different food processing environments. However, there is still a lack of research on the actual impact of bioaerosols over time in most of the food premises especially in Southern Africa and other developing countries. The overall purpose of this dissertation was to assess possible microbial contaminants and the role of selected environmental parameters on these microbes at a dairy farm plant in central South Africa. In relation to the purpose of the study, the objectives of this dissertation were to investigate and establish the food handler’s food safety knowledge, attitude, behaviour and practices. The sub-objective was to investigate the prevalence and distribution of microbial contaminants (both airborne and food contact surface populations), and concomitant environmental parameters. The microbe isolates from both investigations (i.e. air samples and food contact surfaces) were identified to strain level using matrix-assisted laser desorption ionization – time of flight mass spectrometry (MALDI-TOF MS). The findings of this study in relation to food handlers’ food safety knowledge, attitude, behaviour and practices indicated a dire need for training of employees as well as improved health and hygiene measures as emphasised by some of the identified strains. The environmental parameters (both indoor and outdoor) were similar, with no relationship established between airborne microbes’ prevalence and environmental parameters. The samples of the airborne microbial populations in both indoor and outdoor environments were similar. Airborne microbial counts at the dairy farm plant over the entire duration of the study ranged between 1.50 x 101cfu.m-3and 1.62 x 102cfu.m-3. Microbial counts on food contact surfaces ranged between 2.50 x 102 cfu.cm-2 and 1.10 x 105 cfu.cm-2 over the entire duration of the study. A wide variety of microorganisms (from air and food contact surfaces) such as the Gram-positive bacteria, Gram-negative bacteria, as well as fungi were present at the dairy farm plant. A number of the isolated genera have previously been associated with agricultural environments whilst others are associated with hospital environments. The positively identified strains were from genera such as Aeromonas, Arthrobacter, Candida, Pseudomonas, Pantoea, Citrobacter, Staphylococcus, Bacillus, Escherichia, Rhodococcus and Rhodotorula, amongst others. The isolation of microorganisms associated with food spoilage and foodborne disease outbreaks, which are known as indicator organisms such as Escherichia coli, Staphylococcus and Bacillus from both air and surface samples, signified possible faecal contamination and could be attributed to poor health and hygiene practices at the dairy farm plant. Despite the isolation of microorganisms associated with food spoilage and foodborne disease outbreaks, the isolation of microorganisms not usually associated with the food processing industry (usually associated with hospital environments) was an enormous and serious concern which suggested a need for further investigations at dairy farm plants as the implications of these pathogenic microorganisms in food is not known. The isolation of similar microorganisms from both the air samples and surface swabs suggests that airborne microbes have a potential of settling on food contact surfaces, therefore having a potential to contaminate dairy products which are known to be more prone to contamination and which, because of their nutritional status, serve as a good substrate for the growth of microorganisms

Seed tuber treatments with Pseudomonas spp. to reduce potato common scab incidence and severity

Potato common scab is a tuber- or soil-borne disease caused by several species in the genus Streptomyces. The objective of this study was to study the treatment of seed tubers with Pseudomonas spp. as a means to reduce common scab incidence and severity, and improve seed tuber quality and marketability. All four Pseudomonas spp. tested inhibited Streptomyces SS-1; PEI-1 and AL-1 in vitro. In laboratory trials, treatments of seed tubers with Pseudomonas strains A25, A145, and A153, significantly reduced in the number of pathogenic Streptomyces in comparison to untreated tubers within five weeks (P\u3c0.05). Seed tuber treatments with A25 and A153 significantly reduced scab incidence and severity in Russets Burbank and Prospect, respectively. This study also demonstrated the use of TaqMan qPCR detecting the txtAB gene analysis as a novel and practical method to quantify pathogenic Streptomyces in tissues of scabby and apparently clean potato seed tubers