Evolution of Extensively Drug-Resistant Tuberculosis over Four Decades: Whole Genome Sequencing and Dating Analysis of Mycobacterium tuberculosis Isolates from KwaZulu-Natal.

BACKGROUND: The continued advance of antibiotic resistance threatens the treatment and control of many infectious diseases. This is exemplified by the largest global outbreak of extensively drug-resistant (XDR) tuberculosis (TB) identified in Tugela Ferry, KwaZulu-Natal, South Africa, in 2005 that continues today. It is unclear whether the emergence of XDR-TB in KwaZulu-Natal was due to recent inadequacies in TB control in conjunction with HIV or other factors. Understanding the origins of drug resistance in this fatal outbreak of XDR will inform the control and prevention of drug-resistant TB in other settings. In this study, we used whole genome sequencing and dating analysis to determine if XDR-TB had emerged recently or had ancient antecedents. METHODS AND FINDINGS: We performed whole genome sequencing and drug susceptibility testing on 337 clinical isolates of Mycobacterium tuberculosis collected in KwaZulu-Natal from 2008 to 2013, in addition to three historical isolates, collected from patients in the same province and including an isolate from the 2005 Tugela Ferry XDR outbreak, a multidrug-resistant (MDR) isolate from 1994, and a pansusceptible isolate from 1995. We utilized an array of whole genome comparative techniques to assess the relatedness among strains, to establish the order of acquisition of drug resistance mutations, including the timing of acquisitions leading to XDR-TB in the LAM4 spoligotype, and to calculate the number of independent evolutionary emergences of MDR and XDR. Our sequencing and analysis revealed a 50-member clone of XDR M. tuberculosis that was highly related to the Tugela Ferry XDR outbreak strain. We estimated that mutations conferring isoniazid and streptomycin resistance in this clone were acquired 50 y prior to the Tugela Ferry outbreak (katG S315T [isoniazid]; gidB 130 bp deletion [streptomycin]; 1957 [95% highest posterior density (HPD): 1937-1971]), with the subsequent emergence of MDR and XDR occurring 20 y (rpoB L452P [rifampicin]; pncA 1 bp insertion [pyrazinamide]; 1984 [95% HPD: 1974-1992]) and 10 y (rpoB D435G [rifampicin]; rrs 1400 [kanamycin]; gyrA A90V [ofloxacin]; 1995 [95% HPD: 1988-1999]) prior to the outbreak, respectively. We observed frequent de novo evolution of MDR and XDR, with 56 and nine independent evolutionary events, respectively. Isoniazid resistance evolved before rifampicin resistance 46 times, whereas rifampicin resistance evolved prior to isoniazid only twice. We identified additional putative compensatory mutations to rifampicin in this dataset. One major limitation of this study is that the conclusions with respect to ordering and timing of acquisition of mutations may not represent universal patterns of drug resistance emergence in other areas of the globe. CONCLUSIONS: In the first whole genome-based analysis of the emergence of drug resistance among clinical isolates of M. tuberculosis, we show that the ancestral precursor of the LAM4 XDR outbreak strain in Tugela Ferry gained mutations to first-line drugs at the beginning of the antibiotic era. Subsequent accumulation of stepwise resistance mutations, occurring over decades and prior to the explosion of HIV in this region, yielded MDR and XDR, permitting the emergence of compensatory mutations. Our results suggest that drug-resistant strains circulating today reflect not only vulnerabilities of current TB control efforts but also those that date back 50 y. In drug-resistant TB, isoniazid resistance was overwhelmingly the initial resistance mutation to be acquired, which would not be detected by current rapid molecular diagnostics employed in South Africa that assess only rifampicin resistance.

Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans.

Phytophthora infestans is the most destructive pathogen of potato and a model organism for the oomycetes, a distinct lineage of fungus-like eukaryotes that are related to organisms such as brown algae and diatoms. As the agent of the Irish potato famine in the mid-nineteenth century, P. infestans has had a tremendous effect on human history, resulting in famine and population displacement. To this day, it affects world agriculture by causing the most destructive disease of potato, the fourth largest food crop and a critical alternative to the major cereal crops for feeding the world's population. Current annual worldwide potato crop losses due to late blight are conservatively estimated at $6.7 billion. Management of this devastating pathogen is challenged by its remarkable speed of adaptation to control strategies such as genetically resistant cultivars. Here we report the sequence of the P. infestans genome, which at approximately 240 megabases (Mb) is by far the largest and most complex genome sequenced so far in the chromalveolates. Its expansion results from a proliferation of repetitive DNA accounting for approximately 74% of the genome. Comparison with two other Phytophthora genomes showed rapid turnover and extensive expansion of specific families of secreted disease effector proteins, including many genes that are induced during infection or are predicted to have activities that alter host physiology. These fast-evolving effector genes are localized to highly dynamic and expanded regions of the P. infestans genome. This probably plays a crucial part in the rapid adaptability of the pathogen to host plants and underpins its evolutionary potential.

Study the Effect of Relative Energy Deficiency on Physiological and Physical Variables in Professional Women Athletes: A Randomized Controlled Trial.

Energy deficits are often observed in athletes, especially in female athletes, due to the high expenditure of sport and strict diets. Low energy availability can cause serious health problems and affect sport performance. The aim of this study was to evaluate the effects of different personalized dietary plans on physiological and physical factors related to energy deficit syndrome in female professional handball players. Twenty-one professional female handball players, aged 22 ± 4 years, 172.0 ± 5.4 cm and 68.4 ± 6.7 kg, divided into three groups (FD: free diet; MD: Mediterranean diet; and AD: high antioxidant diet), participated in this 12-week randomized controlled trial. Energy expenditure through indirect calorimetry, energy availability, 7 day dietary intake analysis, blood pressure, cholesterol, menstrual function, body composition by both anthropometry and bioelectrical impedance, and strength performance were assessed. All participants showed low energy availability (<30 kcal/lean mass per day); despite this, all had eumenorrhea. Significant improvements were found after the intervention in all components of body composition (p < 0.05). In the remaining variables, despite slight improvements, none were significant neither over time nor between the different groups. Low energy availability has been observed in all professional female handball players, which may lead to serious consequences. A longer period of intervention is required to assess the differences between diets and improvements in other parameters.

Study of Different Personalised Dietary Plans on Eating Behaviour, Body Image and Mood in Young Female Professional Handball Players: A Randomised Controlled Trial.

Low energy availability may precede or be caused by cognitive disturbances in professional athletes. Related psychological problems include disordered eating patterns, body shape preoccupation, depression or anxiety. The objective of this research was to evaluate the effects of different personalised dietary plans on psychological factors in young professional female handball players with low energy availability. This 12-week randomised clinical trial involved 21 female players aged 22 ± 4 years, 172.0 ± 5.4 cm and 68.4 ± 6.7 kg divided into three groups (FD: free diet; MD: Mediterranean diet; HAD: high antioxidant diet). Eating behaviour (Eating Attitude Test, EAT-26: diet, bulimia and oral control subscales), body image (Body Shape Questionnaire, BSQ) and mood state (Profile of Mode State, POMS: tension, vigour, anger, depression, fatigue) were assessed. All participants showed low energy availability (<30 kcal/lean mass per day). The different plans showed no significant differences between them but significant differences over time within groups for the variables: body image, Tension, Vigour and Depression (p < 0.05). Eating behaviour improved slightly but did not show statistically significant changes. Following an adequate nutritional planning for athletes seems to improve the mood and body perception of young female handball players. A longer intervention period is required to assess the differences between diets and improvement of other parameters.

Quantitative Diet, Body Composition and Sprint Performance in Female Professional Beach Handball Players.

Women's elite sports have experienced an exponential increase in the last decade, as has beach handball (BH). The high demands of this sport mean that athletes need to be in superior physical condition, so nutrition and body composition are determining factors in their sporting performance. For this reason, the aim of this study was to analyze, compare and correlate the most relevant variables of food intake (quantitative), body composition (focus on the bone mass characteristics) and sprint performance in female professional BH players. Thirty-three women from the National Spanish Team participated in this study. Dietary assessment, anthropometric measurements and sprint tests were performed. In general, the players had a low carbohydrate intake and adequate protein intake, with no significant differences depending on the category and playing position. For senior players, positive correlations were found between protein intake and bone mass (r = 0.584, p = 0.022), polyunsaturated fatty acid intake and muscle mass (r = 0.387, p = 0.026) and finally between fat mass and animal protein intake (r = 0.569, p = 0.027). Body composition was similar in both categories; however, goalkeepers had the highest fat (22.6 ± 3.86%, 16.2 ± 4.84 kg) component (vs. wings: 17.4 ± 3.53%, p = 0.031/vs. specialists: 11.1 ± 1.91 kg, p = 0.034), and senior players had higher muscle mass (kilograms). It is worth noting the finding that players with a greater trochanter height had significantly lower sprint times (p = 0.014 and p = 0.048 for 5 and 10 m, respectively). Certain bone characteristics, such as iliospinale height, biacromial and bimalleolar diameters, mesosternal perimeter and biceps skinfold, differ depending on the position. In addition, the greater speed of the senior players may be due to the greater specialization, number of training sessions performed and specific bone characteristics, such as trochanter height. In this regard, the data provided in this study will assist with establishing criteria for the selection of talent for this sporting discipline.

Comparative genomic characterization of Francisella tularensis strains belonging to low and high virulence subspecies.

Tularemia is a geographically widespread, severely debilitating, and occasionally lethal disease in humans. It is caused by infection by a gram-negative bacterium, Francisella tularensis. In order to better understand its potency as an etiological agent as well as its potential as a biological weapon, we have completed draft assemblies and report the first complete genomic characterization of five strains belonging to the following different Francisella subspecies (subsp.): the F. tularensis subsp. tularensis FSC033, F. tularensis subsp. holarctica FSC257 and FSC022, and F. tularensis subsp. novicida GA99-3548 and GA99-3549 strains. Here, we report the sequencing of these strains and comparative genomic analysis with recently available public Francisella sequences, including the rare F. tularensis subsp. mediasiatica FSC147 strain isolate from the Central Asian Region. We report evidence for the occurrence of large-scale rearrangement events in strains of the holarctica subspecies, supporting previous proposals that further phylogenetic subdivisions of the Type B clade are likely. We also find a significant enrichment of disrupted or absent ORFs proximal to predicted breakpoints in the FSC022 strain, including a genetic component of the Type I restriction-modification defense system. Many of the pseudogenes identified are also disrupted in the closely related rarely human pathogenic F. tularensis subsp. mediasiatica FSC147 strain, including modulator of drug activity B (mdaB) (FTT0961), which encodes a known NADPH quinone reductase involved in oxidative stress resistance. We have also identified genes exhibiting sequence similarity to effectors of the Type III (T3SS) and components of the Type IV secretion systems (T4SS). One of the genes, msrA2 (FTT1797c), is disrupted in F. tularensis subsp. mediasiatica and has recently been shown to mediate bacterial pathogen survival in host organisms. Our findings suggest that in addition to the duplication of the Francisella Pathogenicity Island, and acquisition of individual loci, adaptation by gene loss in the more recently emerged tularensis, holarctica, and mediasiatica subspecies occurred and was distinct from evolutionary events that differentiated these subspecies, and the novicida subspecies, from a common ancestor. Our findings are applicable to future studies focused on variations in Francisella subspecies pathogenesis, and of broader interest to studies of genomic pathoadaptation in bacteria.

Prevalencia de caídas en adultos mayores y factores asociados en la parroquia Sidcay, Cuenca, 2013 / Prevalence of falls in older adults and associated factors in the Sidcay parish. Cuenca, 2013

INTRODUCCIÓN: Un problema de salud derivado de los cambios del adulto mayor son las caídas, la prevalen-cia de caídas en adultos mayores sanos varía de 15 a 30%. Su etiología es multifactorial, identificándose fac-tores condicionantes y precipitantes. OBJETIVO: Determinar la prevalencia de caídas en adultos mayores y factores asociados intrínsecos: en-fermedades crónicas, estado mental, deambulación; extrínsecos: fármacos, alcohol, calzado, actividades diarias, lugar, condición del suelo, intervalo del día, y no clasificables: caídas previas, temor a caer, tipos de caídas; en la Parroquia Sidcay, Cantón Cuenca. METODOLOGÍA: Se trató de un estudio transversal; en 489 adultos mayores de la Parroquia Sidcay. Para el le-vantamiento de datos se utilizó un cuestionario basado en la OMS y "Escala de Riesgo de Caídas de Dowton", los datos fueron tabulados y analizados en el programa SPSS 15.0, para variables demográficas se usaron por-centaje, frecuencia, y medidas de tendencia central, para buscar asociación razón de prevalencia con in-tervalo de confianza de 95% y significancia estadística Chi cuadrado. RESULTADOS: La prevalencia de caídas fue 33.9%, mayor prevalencia en >74 años (43.1%), de sexo femenino (40.9%), sin pareja (45.1%), y con alteraciones nutricionales (64.8%). El riesgo de caída según la escala de Dawton fue: riesgo alto 32.1% y riesgo bajo 67.9%. Estuvo asociada a: >74 años RP1,84(1.4-2.42), sexo femenino RP1.65 (1.25-2.17), vivir sin pareja RP1.73 (1.35-2.22), en-fermedades crónicas RP1.62 (1.23-2.13), estado mental confuso RP2.10 (1.37-3.22), deambulación insegura con o sin ayuda RP2.31 (1.8-2.9), consumo de medicamen-tos RP1.29 (1.01-2.15), deambulación con pies descalzos RP 3(2.5-3.5) y caídas previas, en todos los casos p < 0.05 . CONCLUSIONES: Existe una población de adultos mayo-res en riesgo ya sea alto o bajo de caídas, esto supone la necesidad de integrar al cuidado de esta población ambientes seguros como los domicilios, que se adapten a las necesidades del usuario en el aspecto físico y así contribuir a disminuir las caídas.

INTRODUCTION: Health problems derived from the changes in seniors are falls, the prevalence of falls in healthy seniors oscillate from 15-30%. The etiology is mul-tifactorial; there have been identified conditions and precipitating factors. OBJECTIVE : To determine the prevalence of falls in se-niors and associated factors intrinsic: chronic diseases, mental status, ambulation; extrinsic: drugs, alcohol, shoes, daily activities, location, condition of the floor , day interval, and not classifiable: previous falls, fear of falling , types of falls, in the Parish Sidcay, Canton Cuen-ca. METHODOLOGY: This was a cross-sectional study, the population was established in the seniors of the Parish Sidcay. We worked with 489 seniors. For the recollection of data we used a questionnaire based on the WHO and the "Risk Scale Dowton Falls", the data were tabu-lated and analyzed using SPSS 15.0, for demographic variables we used the percentage, frequency, and measures of central tendency, to find association pre-valence ratio with confidence interval of 95% and for statistical significance with the chi-square p value. RESULTS: The prevalence of falls was 33.9%. Had a higher prevalence of falls patients > 74 years (43.1 %), female (40.9%), without partner (45.1 %) and the patients with nutritional disorders (64.8%). The risk of falling according to the Dawton scale was: high risk 32.1% and low risk 67.9%. It was associated with:> 74 years RP1.84 (1.4 to 2.42), female RP1.65 (1.25 to 2.17), living without partner RP1.73 (1.35 to 2.22) , chronic diseases RP1.62 (1.23 to 2.13), confused mental state RP2.10 (1.37 to 3.22), unsa-fe ambulation with or without help RP2.31 (1.8-2.9), drug consumption RP 1.29 (1.01 to 2.15), walking barefoot RP3 (2.5-3.5) and previous falls in all cases p <0.05. CONCLUSIONS: As reviewed there is a population of ol-der adults at risk either high or low falls, this implies the need to integrate the care of this population safe.