A spatial approach for the epidemiology of antibiotic use and resistance in community-based studies: the emergence of urban clusters of Escherichia coli quinolone resistance in Sao Paulo, Brasil

Background: Population antimicrobial use may influence resistance emergence. Resistance is an ecological phenomenon due to potential transmissibility. We investigated spatial and temporal patterns of ciprofloxacin (CIP) population consumption related to E. coli resistance emergence and dissemination in a major Brazilian city. A total of 4,372 urinary tract infection E. coli cases, with 723 CIP resistant, were identified in 2002 from two outpatient centres. Cases were address geocoded in a digital map. Raw CIP consumption data was transformed into usage density in DDDs by CIP selling points influence zones determination. A stochastic model coupled with a Geographical Information System was applied for relating resistance and usage density and for detecting city areas of high/low resistance risk. Results: E. coli CIP resistant cluster emergence was detected and significantly related to usage density at a level of 5 to 9 CIP DDDs. There were clustered hot-spots and a significant global spatial variation in the residual resistance risk after allowing for usage density. Conclusions: There were clustered hot-spots and a significant global spatial variation in the residual resistance risk after allowing for usage density. The usage density of 5-9 CIP DDDs per 1,000 inhabitants within the same influence zone was the resistance triggering level. This level led to E. coli resistance clustering, proving that individual resistance emergence and dissemination was affected by antimicrobial population consumption.

Critical behavior of the susceptible-infected-recovered model on a square lattice

By means of numerical simulations and epidemic analysis, the transition point of the stochastic asynchronous susceptible-infected-recovered model on a square lattice is found to be c(0)=0.176 500 5(10), where c is the probability a chosen infected site spontaneously recovers rather than tries to infect one neighbor. This point corresponds to an infection/recovery rate of lambda(c)=(1-c(0))/c(0)=4.665 71(3) and a net transmissibility of (1-c(0))/(1+3c(0))=0.538 410(2), which falls between the rigorous bounds of the site and bond thresholds. The critical behavior of the model is consistent with the two-dimensional percolation universality class, but local growth probabilities differ from those of dynamic percolation cluster growth, as is demonstrated explicitly.

Strain origin drives virulence and persistence of Xylella fastidiosa in alfalfa

Generalist pathogens frequently exist as a complex of genetically differentiated strains, which can differ in virulence and transmissibility. A description of the extent to which strain variability mediates host species competence is needed to understand disease dynamics for systems with both host and pathogen strain diversity. This study tested the hypothesis that strain-specific variation of a generalist vector-borne plant pathogen, Xylella fastidiosa, affects disease severity in alfalfa (Medicago sativa) and competence of this crop as a reservoir host. Alfalfa seedlings were inoculated with one of 23 X. fastidiosa isolates collected from different hosts, eight identified as belonging to an almond strain, and the remainder from a grape strain. Pathogen population, symptom severity and infection incidence were compared over five successive harvests. Infected plant size, measured mainly by plant height, internode length and above ground biomass, was reduced up to 50% compared to buffer-inoculated controls, and more severe symptoms were observed at later harvests and for higher pathogen populations. Grape isolates had higher bacterial populations within alfalfa than almond isolates. In addition, infection with grape isolates resulted in more severe alfalfa stunting than that caused by almond isolates. Moreover, there was a strong positive relationship between isolate multiplication rate and both symptom severity and infection persistence (i.e. maintenance of chronic infection within host). Isolates with low initial populations had low incidence at the final harvest, with one isolate dying out altogether. The results showed that X. fastidiosa-genetic diversity contributed to variation in alfalfa disease severity. The results also suggest that pathogen strain may mediate host competence via differences in bacterial population density and persistence.

Liberibacters associated with orange jasmine in Brazil: incidence in urban areas and relatedness to citrus liberibacters

Two surveys (2005/2006 and 2009) were conducted in the state of Sao Paulo, Brazil, to investigate the incidence of `Candidatus Liberibacter asiaticus` and `Ca. L. americanus`, two liberibacters associated with citrus huanglongbing (HLB) disease and both transmitted by Diaphorina citri, in orange jasmine (Murraya exotica), a widespread ornamental tree in cities and villages. The graft-transmissibility of the two species, and their DNA relatedness to citrus-associated liberibacters, were also investigated. Quantitative PCR was applied to PCR-positive orange jasmine and HLB-positive citrus growing in backyards and orchards to assess their inoculum source potentials. Liberibacters were detected in 91 of 786 sampled orange jasmine plants in 10 of 76 sampled locations. PCR-positive trees exhibited yellow shoots and/or dieback symptoms indistinguishable from those on PCR-negative trees. `Candidatus Liberibacter americanus` was more common in 2005/2006 (96 center dot 6%) and `Ca. L. asiaticus` in 2009 (84 center dot 8%). rplJ nucleotide sequences were identical within all populations of either species. Graft transmission succeeded only in homologous host combinations, including `Ca. L. americanus` (2/10) from/to orange jasmine and `Ca. L. americanus` (5/18) and `Ca. L. asiaticus` (5/9) from/to citrus. Symptoms were mild and developed less rapidly in orange jasmine than in citrus, probably as a result of lower liberibacter multiplication rates. Respective titres of `Ca. L. americanus` and `Ca. L. asiaticus` in orange jasmine averaged 4 center dot 3 and 3 center dot 0 log cells g-1 tissue, compared with 5 center dot 5 and 7 center dot 3 in citrus. The results indicate that orange jasmine does not favour liberibacter multiplication as much as citrus. However, its importance in HLB epidemics should not be underestimated as it is a preferred host of D. citri and is not under any strict tree-eradication programme or measures for insect control.

Integrating infection control into the dental curriculum

The dental profession has possessed traditional standards of cross-infection control but the recent expression of real concerns by both the public and the profession over the transmissibility of infectious diseases in the dental surgery has demanded a formalized and extended approach to teaching cross-infection control in the dental curriculum. Clear curriculum content must be formulated within contemporary Workplace Health and Safety Guidelines and the Strategic Plan of the Dental School or academic health centre. The full integration demands that the area is taught as a discrete entity but recognized as an intrinsic part of each clinical encounter. This paper discusses the structure and integration of cross-infection control into the curriculum at the University of Queensland Dental School.

Conceção e construção de um simulador de controlo de vibrações

Trabalho Final de Mestrado para obtenção do grau de Mestre em Engenharia Mecânica

High prevalence and association of HIV-1 non-B subtype with specific sexual transmission risk among antiretroviral naïve patients in Porto Alegre, RS, Brazil

In South Brazil the circulation of two HIV-1 subtypes with different characteristics represents an important scenario for the study of the impact of HIV-1 diversity on the evolution of the HIV-1 epidemic and AIDS disease. HIV-1 B, the predominant variant in industrialized countries and HIV-1 C, the most prevalent subtype in areas with rapid epidemic growth, are implicated in most infections. We evaluated blood samples from 128 antiretroviral (ARV) naïve patients recruited at entry to the largest HIV outpatient service in Porto Alegre. Based on partial pol region sequencing, HIV-1 C was observed in 29%, HIV-1 B in 22.6% and, the recently identified CRF31_BC, in 23.4% of 128 volunteers. Other variants were HIV-1 F in 10% and other mosaics in 5.5%. In order to evaluate the association of socio-behavioral characteristics and HIV-1 subtypes, interviews and laboratory evaluation were performed at entry. Our data suggest an established epidemic of the three major variants, without any evidence of partitioning in either of the subgroups analyzed. However, anal sex practices were associated with subtype B, which could indicate a greater transmissibility of non-B variants by vaginal intercourse. This study provides baseline information for epidemiologic surveillance of the changes of the molecular characteristics of HIV-1 epidemics in this region.

Transmission and progression to disease of Mycobacterium tuberculosis phylogenetic lineages in The Netherlands

The aim of this study was to determine if mycobacterial lineages affect infection risk, clustering, and disease progression among Mycobacterium tuberculosis cases in The Netherlands. Multivariate negative binomial regression models adjusted for patient-related factors and stratified by patient ethnicity were used to determine the association between phylogenetic lineages and infectivity (mean number of positive contacts around each patient) and clustering (as defined by number of secondary cases within 2 years after diagnosis of an index case sharing the same fingerprint) indices. An estimate of progression to disease by each risk factor was calculated as a bootstrapped risk ratio of the clustering index by the infectivity index. Compared to the Euro-American reference, Mycobacterium africanum showed significantly lower infectivity and clustering indices in the foreign-born population, while Mycobacterium bovis showed significantly lower infectivity and clustering indices in the native population. Significantly lower infectivity was also observed for the East African Indian lineage in the foreign-born population. Smear positivity was a significant risk factor for increased infectivity and increased clustering. Estimates of progression to disease were significantly associated with age, sputum-smear status, and behavioral risk factors, such as alcohol and intravenous drug abuse, but not with phylogenetic lineages. In conclusion, we found evidence of a bacteriological factor influencing indicators of a strain's transmissibility, namely, a decreased ability to infect and a lower clustering index in ancient phylogenetic lineages compared to their modern counterparts. Confirmation of these findings via follow-up studies using tuberculin skin test conversion data should have important implications on M. tuberculosis control efforts.

A closer look at multiple-clone Plasmodium vivax infections: detection methods, prevalence and consequences

The naturally occurring clonal diversity among field isolates of the major human malaria parasite Plasmodium vivax remained unexplored until the early 1990s, when improved molecular methods allowed the use of blood samples obtained directly from patients, without prior in vitro culture, for genotyping purposes. Here we briefly review the molecular strategies currently used to detect genetically distinct clones in patient-derived P. vivax samples, present evidence that multiple-clone P. vivax infections are commonly detected in areas with different levels of malaria transmission and discuss possible evolutionary and epidemiological consequences of the competition between genetically distinct clones in natural human infections. We suggest that, when two or more genetically distinct clones are present in the same host, intra-host competition for limited resources may select for P. vivax traits that represent major public health challenges, such as increased virulence, increased transmissibility and antimalarial drug resistance.

Integration of Bridge Damage Detection Concepts and Components (3 volumes), TR-636, 2013

This work is divided into three volumes: Volume I: Strain-Based Damage Detection; Volume II: Acceleration-Based Damage Detection; Volume III: Wireless Bridge Monitoring Hardware. Volume I: In this work, a previously-developed structural health monitoring (SHM) system was advanced toward a ready-for-implementation system. Improvements were made with respect to automated data reduction/analysis, data acquisition hardware, sensor types, and communication network architecture. The statistical damage-detection tool, control-chart-based damage-detection methodologies, were further investigated and advanced. For the validation of the damage-detection approaches, strain data were obtained from a sacrificial specimen attached to the previously-utilized US 30 Bridge over the South Skunk River (in Ames, Iowa), which had simulated damage,. To provide for an enhanced ability to detect changes in the behavior of the structural system, various control chart rules were evaluated. False indications and true indications were studied to compare the damage detection ability in regard to each methodology and each control chart rule. An autonomous software program called Bridge Engineering Center Assessment Software (BECAS) was developed to control all aspects of the damage detection processes. BECAS requires no user intervention after initial configuration and training. Volume II: In this work, a previously developed structural health monitoring (SHM) system was advanced toward a ready-for-implementation system. Improvements were made with respect to automated data reduction/analysis, data acquisition hardware, sensor types, and communication network architecture. The objective of this part of the project was to validate/integrate a vibration-based damage-detection algorithm with the strain-based methodology formulated by the Iowa State University Bridge Engineering Center. This report volume (Volume II) presents the use of vibration-based damage-detection approaches as local methods to quantify damage at critical areas in structures. Acceleration data were collected and analyzed to evaluate the relationships between sensors and with changes in environmental conditions. A sacrificial specimen was investigated to verify the damage-detection capabilities and this volume presents a transmissibility concept and damage-detection algorithm that show potential to sense local changes in the dynamic stiffness between points across a joint of a real structure. The validation and integration of the vibration-based and strain-based damage-detection methodologies will add significant value to Iowa’s current and future bridge maintenance, planning, and management Volume III: In this work, a previously developed structural health monitoring (SHM) system was advanced toward a ready-for-implementation system. Improvements were made with respect to automated data reduction/analysis, data acquisition hardware, sensor types, and communication network architecture. This report volume (Volume III) summarizes the energy harvesting techniques and prototype development for a bridge monitoring system that uses wireless sensors. The wireless sensor nodes are used to collect strain measurements at critical locations on a bridge. The bridge monitoring hardware system consists of a base station and multiple self-powered wireless sensor nodes. The base station is responsible for the synchronization of data sampling on all nodes and data aggregation. Each wireless sensor node include a sensing element, a processing and wireless communication module, and an energy harvesting module. The hardware prototype for a wireless bridge monitoring system was developed and tested on the US 30 Bridge over the South Skunk River in Ames, Iowa. The functions and performance of the developed system, including strain data, energy harvesting capacity, and wireless transmission quality, were studied and are covered in this volume.

Detection of PrPres in genetically susceptible fetuses from sheep with natural scrapie

Scrapie is a transmissible spongiform encephalopathy with a wide PrPres dissemination in many non-neural tissues and with high levels of transmissibility within susceptible populations. Mechanisms of transmission are incompletely understood. It is generally assumed that it is horizontally transmitted by direct contact between animals or indirectly through the environment, where scrapie can remain infectious for years. In contrast, in utero vertical transmission has never been demonstrated and has rarely been studied. Recently, the use of the protein misfolding cyclic amplification technique (PMCA) has allowed prion detection in various tissues and excretions in which PrPres levels have been undetectable by traditional assays. The main goal of this study was to detect PrPres in fetal tissues and the amniotic fluid from natural scrapie infected ewes using the PMCA technique. Six fetuses from three infected pregnant ewes in an advanced clinical stage of the disease were included in the study. From each fetus, amniotic fluid, brain, spleen, ileo-cecal valve and retropharyngeal lymph node samples were collected and analyzed using Western blotting and PMCA. Although all samples were negative using Western blotting, PrPres was detected after in vitro amplification. Our results represent the first time the biochemical detection of prions in fetal tissues, suggesting that the in utero transmission of scrapie in natural infected sheep might be possible.

The Stealthy Superbug: the Role of Asymptomatic Enteric Carriage in Maintaining a Long-Term Hospital Outbreak of ST228 Methicillin-Resistant Staphylococcus aureus.

UNLABELLED: Whole-genome sequencing (WGS) of 228 isolates was used to elucidate the origin and dynamics of a long-term outbreak of methicillin-resistant Staphylococcus aureus (MRSA) sequence type 228 (ST228) SCCmec I that involved 1,600 patients in a tertiary care hospital between 2008 and 2012. Combining of the sequence data with detailed metadata on patient admission and movement confirmed that the outbreak was due to the transmission of a single clonal variant of ST228, rather than repeated introductions of this clone into the hospital. We note that this clone is significantly more frequently recovered from groin and rectal swabs than other clones (P < 0.0001) and is also significantly more transmissible between roommates (P < 0.01). Unrecognized MRSA carriers, together with movements of patients within the hospital, also seem to have played a major role. These atypical colonization and transmission dynamics can help explain how the outbreak was maintained over the long term. This "stealthy" asymptomatic colonization of the gut, combined with heightened transmissibility (potentially reflecting a role for environmental reservoirs), means the dynamics of this outbreak share some properties with enteric pathogens such as vancomycin-resistant enterococci or Clostridium difficile. IMPORTANCE: Using whole-genome sequencing, we showed that a large and prolonged outbreak of methicillin-resistant Staphylococcus aureus was due to the clonal spread of a specific strain with genetic elements adapted to the hospital environment. Unrecognized MRSA carriers, the movement of patients within the hospital, and the low detection with clinical specimens were also factors that played a role in this occurrence. The atypical colonization of the gut means the dynamics of this outbreak may share some properties with enteric pathogens.

Detection, transmission, pathogenicity and chemical treatment of fungi in Ceiba speciosa seeds

The aim of this work was to evaluate fungus association, transmission and pathogenicity, besides chemical seed treatment in Ceiba speciosa seeds from different regions of southern Brazil. Seven seed samples were used to do the germination test, fungus detection by blotter test and potato-dextrose-agar (PDA), fungus transmission and pathogenicity tests; besides, chemical seed treatments were tested. Germination ranged from 0 to 59,5%. The following fungi were associated in the seeds: Fusarium sp., Alternaria sp., Colletotrichum sp., Curvularia sp. and Pestalotia sp.; in addition, Fusarium sp. was found in all the samples. Alternaria sp. and Fusarium sp. were transmitted by seeds. The isolates of Alternaria sp., Colletotrichum sp. and Fusarium sp., were pathogenic to seedlings and seeds. The seed treatment with methyl tiophanate and the combination captan + methyl tiophanate reduced Fusarium sp. incidence.

Chaos in a Two-Degree of Freedom Duffing Oscillator

High dimensional dynamical systems has intricate behavior either on temporal or on spatial evolution properties. Nevertheless, most of the work on chaotic dynamics has been concentrated on temporal behavior of low-dimensional systems. This contribution is concerned with the chaotic response of a two-degree of freedom Duffing oscillator. Since the equations of motion are associated with a five-dimensional system, the analysis is performed by considering two Duffing oscillators, both with single-degree of freedom, coupled by a spring-dashpot system. With this assumption, it is possible to analyze the transmissibility of motion between the two oscillators.

The use of non-human primates as animal models for the study of hepatitis viruses

Hepatitis viruses belong to different families and have in common a striking hepatotropism and restrictions for propagation in cell culture. The transmissibility of hepatitis is in great part limited to non-human primates. Enterically transmitted hepatitis viruses (hepatitis A virus and hepatitis E virus) can induce hepatitis in a number of Old World and New World monkey species, while the host range of non-human primates susceptible to hepatitis viruses transmitted by the parenteral route (hepatitis B virus, hepatitis C virus and hepatitis delta virus) is restricted to few species of Old World monkeys, especially the chimpanzee. Experimental studies on non-human primates have provided an invaluable source of information regarding the biology and pathogenesis of these viruses, and represent a still indispensable tool for vaccine and drug testing.