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South American Plasmodium falciparum after the Malaria Eradication Era: Clonal Population Expansion and Survival of the Fittest Hybrids  [PDF]
Sean M. Griffing, Tonya Mixson-Hayden, Sankar Sridaran, Md Tauqeer Alam, Andrea M. McCollum, César Cabezas, Wilmer Marqui?o Quezada, John W. Barnwell, Alexandre Macedo De Oliveira, Carmen Lucas, Nancy Arrospide, Ananias A. Escalante, David J. Bacon, Venkatachalam Udhayakumar
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0023486
Abstract: Malaria has reemerged in many regions where once it was nearly eliminated. Yet the source of these parasites, the process of repopulation, their population structure, and dynamics are ill defined. Peru was one of malaria eradication's successes, where Plasmodium falciparum was nearly eliminated for two decades. It reemerged in the 1990s. In the new era of malaria elimination, Peruvian P. falciparum is a model of malaria reinvasion. We investigated its population structure and drug resistance profiles. We hypothesized that only populations adapted to local ecological niches could expand and repopulate and originated as vestigial populations or recent introductions. We investigated the genetic structure (using microsatellites) and drug resistant genotypes of 220 parasites collected from patients immediately after peak epidemic expansion (1999–2000) from seven sites across the country. The majority of parasites could be grouped into five clonal lineages by networks and AMOVA. The distribution of clonal lineages and their drug sensitivity profiles suggested geographic structure. In 2001, artesunate combination therapy was introduced in Peru. We tested 62 parasites collected in 2006–2007 for changes in genetic structure. Clonal lineages had recombined under selection for the fittest parasites. Our findings illustrate that local adaptations in the post-eradication era have contributed to clonal lineage expansion. Within the shifting confluence of drug policy and malaria incidence, populations continue to evolve through genetic outcrossing influenced by antimalarial selection pressure. Understanding the population substructure of P. falciparum has implications for vaccine, drug, and epidemiologic studies, including monitoring malaria during and after the elimination phase.
The current MLVA typing scheme for Enterococcus faecium is less discriminatory than MLST and PFGE for epidemic-virulent, hospital-adapted clonal types
Guido Werner, Ingo Klare, Wolfgang Witte
BMC Microbiology , 2007, DOI: 10.1186/1471-2180-7-28
Abstract: All 51 but one hospital isolates from 1996–2006 were assigned to the clonal complex (CC) of epidemic-virulent, hospital-adapted lineages (MLST CC-17; MLVA CC-1) and differed from isolates of sporadic infections and colonizations (n = 7; 1991–1995) and other non-hospital origins (n = 27). Typing of all 58 hospital VRE revealed MLVA as the least discriminatory method (Simpson's diversity index 0.847) when compared to MLST (0.911) and PFGE (0.976). The two most common MLVA types MT-1 (n = 16) and MT-159 (n = 14) combined isolates of several MLST types including also major epidemic, hospital-adapted, clonal types (MT-1: ST-17, ST-18, ST-280, ST-282; MT-159: ST-78, ST-192, ST-203). These data clearly indicate that non-related E. faecium could possess an identical MLVA type being especially critical when MLVA is used to elucidate supposed outbreaks with E. faecium within a single or among different hospitals. Stability of a given MLVA profile MT-12 (ST-117) during an outbreak over a period of five years was also shown.MLVA is a suitable method to assign isolates of E. faecium into distinct clonal complexes. To investigate outbreaks the current MLVA typing scheme for E. faecium does not discriminate enough and cannot be recommended as a standard superior to PFGE.Effective typing of microorganisms is a prerequisite for establishing epidemiological or phylogenetic links between corresponding isolates. A plethora of different methods has been successfully applied to type and differentiate bacterial strains and clonal groups from each other [1]. A critical point to all of these methods is their applicability to answer distinct questions ranging from investigation of outbreaks to establishing rather broad phylogenetic trees of relatedness and arrangement of strains within major clonal complexes. Each method has its respective weaknesses and strengths according to the question(s) addressed and the methodology behind [2-7].Recently, a new method was introduced using small repetit
Clonal Replacement of Epidemic Methicillin-Resistant Staphylococcus aureus Strains in a German University Hospital over a Period of Eleven Years  [PDF]
Nicole Albrecht, Lutz Jatzwauk, Peter Slickers, Ralf Ehricht, Stefan Monecke
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0028189
Abstract: Worldwide, methicillin-resistant Staphylococcus aureus (MRSA) pose an increased risk for healthcare- and community-associated infections. Since the first report of MRSA in England in 1961, several distinct clones or strains have emerged. Changes within the MRSA population of whole countries, small regions or of single hospitals have been observed with some clones replacing others. In this study, the clonal replacement of MRSA isolates in a South-eastern German tertiary care hospital between 2000 and 2010 is described based on microarray analyses of 778 isolates and at least 50 MRSA per year. Within these eleven years, four common epidemic strains, CC22-MRSA-IV, CC45-MRSA-IV, CC5/ST228-MRSA-I (including a variant with a truncated SCCmec element) and CC5-MRSA-II were identified. The PVL-negative CC22-MRSA-IV strain (Barnim Epidemic Strain, UK-EMRSA-15) was detected for the first time in 2001 and its abundance increased since then to 58.6% in 2010. CC5-MRSA-II increased from 2% (2000) to about 30% (2003), and since then it fluctuates between 23 and 37% of isolates. CC5/ST228-MRSA-I decreased from about the half of tested isolates (2000) to 2.3% (2010). A similar trend was observed for CC45-MRSA-IV, which decreased drastically down to 3.4% in 2010 after reaching a maximum of 62.0% in 2002. Seventeen other PVL-negative MRSA strains were identified sporadically with no significant trend being observed. Seven PVL-positive MRSA strains were found, but they remained rare during the study period accounting together for 2.7% of isolates.
The Spread of Mycoplasma pneumoniae Is Polyclonal in Both an Endemic Setting in France and in an Epidemic Setting in Israel  [PDF]
Sabine Pereyre, Alain Charron, Carlos Hidalgo-Grass, Arabella Touati, Allon E. Moses, Ran Nir-Paz, Cécile Bébéar
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0038585
Abstract: Mycoplasma pneumoniae infections occur both endemically and epidemically, and macrolide resistance has been spreading for 10 years worldwide. A substantial increased incidence of M. pneumoniae infections has been reported in several countries since 2010. Whether this increased incidence is attributed to different or to the same M. pneumoniae genotype is unknown. We have developed a multilocus variable-number tandem-repeat (VNTR) analysis (MLVA) for the molecular typing of M. pneumoniae isolates. In this study, the MLVA typing method was modified and validated to be applicable directly to respiratory tract specimens without culture. This method was applied to 34 M. pneumoniae-positive specimens received at the Bordeaux Hospital, France, between 2007 and 2010 in an endemic setting, and to 63 M. pneumoniae-positive specimens collected during an epidemic surge of M. pneumoniae infections in 2010 in Jerusalem, Israel. The M. pneumoniae endemic spread was shown to be polyclonal in France, with 15 MLVA types identified. Strikingly, the Israeli epidemic surge was also a multi-clonal phenomenon, with 18 circulating MLVA types. The macrolide resistance-associated substitution, A2058G, was found in 22% of the Israeli patients. Macrolide-resistant M. pneumoniae belonged to four MLVA types, the MLVA type Z being the most frequent one. An association between the MLVA type Z and macrolide resistance might exist since macrolide resistance was present or generated during the course of illness in all patients infected with this MLVA type. In conclusion, the discriminatory power of the MLVA showed that the spread of M. pneumoniae strains in France in an endemic setting was polyclonal as well as the surge of M. pneumoniae infections in Israel in 2010.
Clonal Propagation of Khaya senegalensis: The Effects of Stem Length, Leaf Area, Auxins, Smoke Solution, and Stockplant Age  [PDF]
Catherine Ky-Dembele,Mulualem Tigabu,Jules Bayala,Patrice Savadogo,Issaka Joseph Boussim,Per Christer Odén
International Journal of Forestry Research , 2011, DOI: 10.1155/2011/281269
Abstract: Khaya senegalensis is a multipurpose African timber species. The development of clonal propagation could improve plantation establishment, which is currently impeded by mahogany shoot borer. To examine its potential for clonal propagation, the effects of cutting length, leaf area, stockplant maturation, auxin, and smoke solution treatments were investigated. Leafy cuttings rooted well (up to 80%) compared to leafless cuttings (0%). Cuttings taken from seedlings rooted well (at least 95%), but cuttings obtained from older trees rooted poorly (5% maximum). The rooting ability of cuttings collected from older trees was improved (16% maximum) by pollarding. Auxin application enhanced root length and the number of roots while smoke solution did not improve cuttings' rooting ability. These results indicate that juvenile K. senegalensis is amenable to clonal propagation, but further work is required to improve the rooting of cuttings from mature trees. 1. Introduction Khaya senegalensis A. Juss. (Meliaceae), commonly known as Senegal mahogany, is an evergreen tree that typically grows to a height of 15–20?m (up to 35?m on fertile soils) and has a diameter at breast height of 1.5?m, with a clean bole of 8–16?m. Its natural distribution extends from Mauritania and Senegal east to northern Uganda, within the rainfall range 650–1300?mm (and even up to 1800?mm) [1]. In Burkina Faso, the northern limit of the natural distribution of K. senegalensis is 13°55′?N within the South-Sahelian zone. It occurs in various habitat types, such as on river banks, and in fields, fallows, and protected woodlands, and its population density increases from North to South, reaching up to 17 trees per hectare [2]. K. senegalensis is a multipurpose tree with a variety of economic and environmental values [1]. It is one of the major timber species in West Africa owing to its hard and fungus- and termite-resistant red wood; it is highly valued for carpentry, joinery, furniture, ship building, and as a decorative veneer. The bark is used in traditional medicine to treat malaria, diarrhoea, dysentery, anaemia, and so forth. Recently, the stem bark has been found to contain chemicals (limonoids) that exhibit antiproliferative activity against human cancer cell lines [3]. It is also a good source of fodder for cattle, because of its high dry matter but relatively low crude protein content [4], it is also a source of edible and cosmetic oils [1]. In West Africa, the species has become an important urban amenity tree, commonly planted as a roadside or ornamental shade tree. It is also
The Western Africa Ebola virus disease epidemic exhibits both global exponential and local polynomial growth rates  [PDF]
Gerardo Chowell,Cécile Viboud,James M. Hyman,Lone Simonsen
Quantitative Biology , 2014,
Abstract: Background: While many infectious disease epidemics are initially characterized by an exponential growth in time, we show that district-level Ebola virus disease (EVD) outbreaks in West Africa follow slower polynomial-based growth kinetics over several generations of the disease. Methods: We analyzed epidemic growth patterns at three different spatial scales (regional, national, and subnational) of the Ebola virus disease epidemic in Guinea, Sierra Leone and Liberia by compiling publicly available weekly time series of reported EVD case numbers from the patient database available from the World Health Organization website for the period 05-Jan to 17-Dec 2014. Results: We found significant differences in the growth patterns of EVD cases at the scale of the country, district, and other subnational administrative divisions. The national cumulative curves of EVD cases in Guinea, Sierra Leone, and Liberia show periods of approximate exponential growth. In contrast, local epidemics are asynchronous and exhibit slow growth patterns during 3 or more EVD generations, which can be better approximated by a polynomial than an exponential. Conclusions: The slower than expected growth pattern of local EVD outbreaks could result from a variety of factors, including behavior changes, success of control interventions, or intrinsic features of the disease such as a high level of clustering. Quantifying the contribution of each of these factors could help refine estimates of final epidemic size and the relative impact of different mitigation efforts in current and future EVD outbreaks.
International response to the HIV/AIDS epidemic: planning for success
Piot,Peter; Coll Seck,Awa Marie;
Bulletin of the World Health Organization , 2001, DOI: 10.1590/S0042-96862001001200006
Abstract: more assertive political leadership in the global response to aids in both poor and rich countries culminated in june 2001 at the un general assembly special session on aids. delegates made important commitments there, and endorsed a global strategy framework for shifting the dynamics of the epidemic by simultaneously reducing risk, vulnerability and impact. this points the way to achievable progress in the fight against hiv/aids. evidence of success in tackling the spread of aids comes from diverse programme areas, including work with sex workers and clients, injecting drug users, and young people. it also comes from diverse countries, including india, the russian federation, senegal, thailand, the united republic of tanzania, and zambia. their common feature is the combination of focused approaches with attention to the societywide context within which risk occurs. similarly, building synergies between prevention and care has underpinned success in brazil and holds great potential for sub-saharan africa, where 90% reductions have been achieved in the prices at which antiretroviral drugs are available. success also involves overcoming stigma, which undermines community action and blocks access to services. work against stigma and discrimination has been effectively carried out in both health sector and occupational settings. accompanying attention to the conditions for success against hiv/aids is global consensus on the need for additional resources. the detailed estimate of required aids spending in low- and middle-income countries is us$ 9.2 billion annually, compared to the $ 2 billion currently spent. additional spending should be mobilized by the new global fund to fight aids, tuberculosis and malaria, but needs to be joined by additional government and private efforts within countries, including from debt relief. commitment and capacity to scale up hiv prevention and care have never been stronger. the moment must be seized to prevent a global catastrophe.
International response to the HIV/AIDS epidemic: planning for success  [cached]
Piot Peter,Coll Seck Awa Marie
Bulletin of the World Health Organization , 2001,
Abstract: More assertive political leadership in the global response to AIDS in both poor and rich countries culminated in June 2001 at the UN General Assembly Special Session on AIDS. Delegates made important commitments there, and endorsed a global strategy framework for shifting the dynamics of the epidemic by simultaneously reducing risk, vulnerability and impact. This points the way to achievable progress in the fight against HIV/AIDS. Evidence of success in tackling the spread of AIDS comes from diverse programme areas, including work with sex workers and clients, injecting drug users, and young people. It also comes from diverse countries, including India, the Russian Federation, Senegal, Thailand, the United Republic of Tanzania, and Zambia. Their common feature is the combination of focused approaches with attention to the societywide context within which risk occurs. Similarly, building synergies between prevention and care has underpinned success in Brazil and holds great potential for sub-Saharan Africa, where 90% reductions have been achieved in the prices at which antiretroviral drugs are available. Success also involves overcoming stigma, which undermines community action and blocks access to services. Work against stigma and discrimination has been effectively carried out in both health sector and occupational settings. Accompanying attention to the conditions for success against HIV/AIDS is global consensus on the need for additional resources. The detailed estimate of required AIDS spending in low- and middle-income countries is US$ 9.2 billion annually, compared to the $ 2 billion currently spent. Additional spending should be mobilized by the new global fund to fight AIDS, tuberculosis and malaria, but needs to be joined by additional government and private efforts within countries, including from debt relief. Commitment and capacity to scale up HIV prevention and care have never been stronger. The moment must be seized to prevent a global catastrophe.
Cholera Outbreak in Senegal in 2005: Was Climate a Factor?  [PDF]
Guillaume Constantin de Magny, Wassila Thiaw, Vadlamani Kumar, No?l M. Manga, Bernard M. Diop, Lamine Gueye, Mamina Kamara, Benjamin Roche, Raghu Murtugudde, Rita R. Colwell
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0044577
Abstract: Cholera is an acute diarrheal illness caused by Vibrio cholerae and occurs as widespread epidemics in Africa. In 2005, there were 31,719 cholera cases, with 458 deaths in the Republic of Senegal. We retrospectively investigated the climate origin of the devastating floods in mid-August 2005, in the Dakar Region of Senegal and the subsequent outbreak of cholera along with the pattern of cholera outbreaks in three other regions of that country. We compared rainfall patterns between 2002 and 2005 and the relationship between the sea surface temperature (SST) gradient in the tropical Atlantic Ocean and precipitation over Senegal for 2005. Results showed a specific pattern of rainfall throughout the Dakar region during August, 2005, and the associated rainfall anomaly coincided with an exacerbation of the cholera epidemic. Comparison of rainfall and epidemiological patterns revealed that the temporal dynamics of precipitation, which was abrupt and heavy, was presumably the determining factor. Analysis of the SST gradient showed that the Atlantic Ocean SST variability in 2005 differed from that of 2002 to 2004, a result of a prominent Atlantic meridional mode. The influence of this intense precipitation on cholera transmission over a densely populated and crowded region was detectable for both Dakar and Thiès, Senegal. Thus, high resolution rainfall forecasts at subseasonal time scales should provide a way forward for an early warning system in Africa for cholera and, thereby, trigger epidemic preparedness. Clearly, attention must be paid to both natural and human induced environmental factors to devise appropriate action to prevent cholera and other waterborne disease epidemics in the region.
Malaria hotspot areas in a highland Kenya site are consistent in epidemic and non-epidemic years and are associated with ecological factors
Kacey C Ernst, Samson O Adoka, Dickens O Kowuor, Mark L Wilson, Chandy C John
Malaria Journal , 2006, DOI: 10.1186/1475-2875-5-78
Abstract: To address this issue, spatial distribution of malaria incidence and the relationship of ecological factors to malaria incidence were assessed in the highland area of Kipsamoite, Kenya, from 2001–2004.Clustering of disease in a single geographic "hotspot" area occurred in epidemic and non-epidemic years, with a 2.6 to 3.2-fold increased risk of malaria inside the hotspot, as compared to outside the area (P < 0.001, all 4 years). Altitude and proximity to the forest were independently associated with increased malaria risk in all years, including epidemic and non-epidemic years.In this highland area, areas of high malaria risk are consistent in epidemic and non-epidemic years and are associated with specific ecological risk factors. Ongoing interventions in areas of ecological risk factors could be a cost-effective method of significantly reducing malaria incidence and blunting or preventing epidemics, even in the absence of malaria early warning systems. Further studies should be conducted to see if these findings hold true in varied highland settings.It has been estimated that 34 million individuals in highland areas of East Africa are at risk for malaria [1] and malaria in these highland areas has been responsible for numerous deaths [2]. However, the levels of variation in malaria risk within these highland areas are not well described and only a few studies have investigated risk factors for malaria there [3-5]. Previous studies have demonstrated that malaria cases aggregate from the household to the countrywide level [3,6,7]. The determinants of such clustering are likely due to shared anthropogenic and environmental variables, as well as factors related to contagion such as population density and human interactions [8,9]. Brooker et al demonstrated that there was spatial clustering of malaria cases in children during an epidemic in a single year in highland area of Kenya [3]. However, without data from multiple years, it is difficult to discern if clusters of
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