Last data update: Jul 01, 2024. (Total: 47134 publications since 2009)
Records 1-10 (of 10 Records) |
Query Trace: Sylvain D [original query] |
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Global phylogeography and evolutionary history of Shigella dysenteriae type 1.
Njamkepo E , Fawal N , Tran-Dien A , Hawkey J , Strockbine N , Jenkins C , Talukder KA , Bercion R , Kuleshov K , Kolínská R , Russell JE , Kaftyreva L , Accou-Demartin M , Karas A , Vandenberg O , Mather AE , Mason CJ , Page AJ , Ramamurthy T , Bizet C , Gamian A , Carle I , Sow AG , Bouchier C , Wester AL , Lejay-Collin M , Fonkoua MC , Le Hello S , Blaser MJ , Jernberg C , Ruckly C , Mérens A , Page AL , Aslett M , Roggentin P , Fruth A , Denamur E , Venkatesan M , Bercovier H , Bodhidatta L , Chiou CS , Clermont D , Colonna B , Egorova S , Pazhani GP , Ezernitchi AV , Guigon G , Harris SR , Izumiya H , Korzeniowska-Kowal A , Lutyńska A , Gouali M , Grimont F , Langendorf C , Marejková M , Peterson LA , Perez-Perez G , Ngandjio A , Podkolzin A , Souche E , Makarova M , Shipulin GA , Ye C , Žemličková H , Herpay M , Grimont PA , Parkhill J , Sansonetti P , Holt KE , Brisse S , Thomson NR , Weill FX . Nat Microbiol 2016 1 16027 ![]() Together with plague, smallpox and typhus, epidemics of dysentery have been a major scourge of human populations for centuries(1). A previous genomic study concluded that Shigella dysenteriae type 1 (Sd1), the epidemic dysentery bacillus, emerged and spread worldwide after the First World War, with no clear pattern of transmission(2). This is not consistent with the massive cyclic dysentery epidemics reported in Europe during the eighteenth and nineteenth centuries(1,3,4) and the first isolation of Sd1 in Japan in 1897(5). Here, we report a whole-genome analysis of 331 Sd1 isolates from around the world, collected between 1915 and 2011, providing us with unprecedented insight into the historical spread of this pathogen. We show here that Sd1 has existed since at least the eighteenth century and that it swept the globe at the end of the nineteenth century, diversifying into distinct lineages associated with the First World War, Second World War and various conflicts or natural disasters across Africa, Asia and Central America. We also provide a unique historical perspective on the evolution of antibiotic resistance over a 100-year period, beginning decades before the antibiotic era, and identify a prevalent multiple antibiotic-resistant lineage in South Asia that was transmitted in several waves to Africa, where it caused severe outbreaks of disease. |
The Global Meningitis Genome Partnership.
Rodgers E , Bentley SD , Borrow R , Bratcher HB , Brisse S , Brueggemann AB , Caugant DA , Findlow J , Fox L , Glennie L , Harrison LH , Harrison OB , Heyderman RS , van Rensburg MJ , Jolley KA , Kwambana-Adams B , Ladhani S , LaForce M , Levin M , Lucidarme J , MacAlasdair N , Maclennan J , Maiden MCJ , Maynard-Smith L , Muzzi A , Oster P , Rodrigues CMC , Serino ORL , Smith V , van der Ende A , Vazquez J , Wang X , Yezli S , Stuart JM . J Infect 2020 81 (4) 510-520 ![]() ![]() Genomic surveillance of bacterial meningitis pathogens is essential for effective disease control globally, enabling identification of emerging and expanding strains and consequent public health interventions. While there has been a rise in the use of whole genome sequencing, this has been driven predominately by a subset of countries with adequate capacity and resources. Global capacity to participate in surveillance needs to be expanded, particularly in low and middle-income countries with high disease burdens. In light of this, the WHO-led collaboration, Defeating Meningitis by 2030 Global Roadmap, has called for the establishment of a Global Meningitis Genome Partnership that links resources for: N. meningitidis (Nm), S. pneumoniae (Sp), H. influenzae (Hi) and S. agalactiae (Sa) to improve worldwide co-ordination of strain identification and tracking. Existing platforms containing relevant genomes include: PubMLST: Nm (31,622), Sp (15,132), Hi (1,935), Sa (9,026); The Wellcome Sanger Institute: Nm (13,711), Sp (>24,000), Sa (6,200), Hi (1738); and BMGAP: Nm (8,785), Hi (2,030). A steering group is being established to coordinate the initiative and encourage high-quality data curation. Next steps include: developing guidelines on open-access sharing of genomic data; defining a core set of metadata; and facilitating development of user-friendly interfaces that represent publicly available data. |
Revisiting the taxonomy of the genus Elizabethkingia using whole-genome sequencing, optical mapping, and MALDI-TOF, along with proposal of three novel Elizabethkingia species: Elizabethkingia bruuniana sp. nov., Elizabethkingia ursingii sp. nov., and Elizabethkingia occulta sp. nov.
Nicholson AC , Gulvik CA , Whitney AM , Humrighouse BW , Graziano J , Emery B , Bell M , Loparev V , Juieng P , Gartin J , Bizet C , Clermont D , Criscuolo A , Brisse S , McQuiston JR . Antonie Van Leeuwenhoek 2017 111 (1) 55-72 ![]() ![]() The genus Elizabethkingia is genetically heterogeneous, and the phenotypic similarities between recognized species pose challenges in correct identification of clinically derived isolates. In addition to the type species Elizabethkingia meningoseptica, and more recently proposed Elizabethkingia miricola, Elizabethkingia anophelis and Elizabethkingia endophytica, four genomospecies have long been recognized. By comparing historic DNA-DNA hybridization results with whole genome sequences, optical maps, and MALDI-TOF mass spectra on a large and diverse set of strains, we propose a comprehensive taxonomic revision of this genus. Genomospecies 1 and 2 contain the type strains E. anophelis and E. miricola, respectively. Genomospecies 3 and 4 are herein proposed as novel species named as Elizabethkingia bruuniana sp. nov. (type strain, G0146T = DSM 2975T = CCUG 69503T = CIP 111191T) and Elizabethkingia ursingii sp. nov. (type strain, G4122T = DSM 2974T = CCUG 69496T = CIP 111192T), respectively. Finally, the new species Elizabethkingia occulta sp. nov. (type strain G4070T = DSM 2976T = CCUG 69505T = CIP 111193T), is proposed. |
Evolutionary dynamics and genomic features of the Elizabethkingia anophelis 2015 to 2016 Wisconsin outbreak strain.
Perrin A , Larsonneur E , Nicholson AC , Edwards DJ , Gundlach KM , Whitney AM , Gulvik CA , Bell ME , Rendueles O , Cury J , Hugon P , Clermont D , Enouf V , Loparev V , Juieng P , Monson T , Warshauer D , Elbadawi LI , Walters MS , Crist MB , Noble-Wang J , Borlaug G , Rocha EPC , Criscuolo A , Touchon M , Davis JP , Holt KE , McQuiston JR , Brisse S . Nat Commun 2017 8 15483 ![]() ![]() An atypically large outbreak of Elizabethkingia anophelis infections occurred in Wisconsin. Here we show that it was caused by a single strain with thirteen characteristic genomic regions. Strikingly, the outbreak isolates show an accelerated evolutionary rate and an atypical mutational spectrum. Six phylogenetic sub-clusters with distinctive temporal and geographic dynamics are revealed, and their last common ancestor existed approximately one year before the first recognized human infection. Unlike other E. anophelis, the outbreak strain had a disrupted DNA repair mutY gene caused by insertion of an integrative and conjugative element. This genomic change probably contributed to the high evolutionary rate of the outbreak strain and may have increased its adaptability, as many mutations in protein-coding genes occurred during the outbreak. This unique discovery of an outbreak caused by a naturally occurring mutator bacterial pathogen provides a dramatic example of the potential impact of pathogen evolutionary dynamics on infectious disease epidemiology. |
Whole genome-based population biology and epidemiological surveillance of Listeria monocytogenes.
Moura A , Criscuolo A , Pouseele H , Maury MM , Leclercq A , Tarr C , Bjorkman JT , Dallman T , Reimer A , Enouf V , Larsonneur E , Carleton H , Bracq-Dieye H , Katz LS , Jones L , Touchon M , Tourdjman M , Walker M , Stroika S , Cantinelli T , Chenal-Francisque V , Kucerova Z , Rocha EP , Nadon C , Grant K , Nielsen EM , Pot B , Gerner-Smidt P , Lecuit M , Brisse S . Nat Microbiol 2016 2 16185 ![]() Listeria monocytogenes (Lm) is a major human foodborne pathogen. Numerous Lm outbreaks have been reported worldwide and associated with a high case fatality rate, reinforcing the need for strongly coordinated surveillance and outbreak control. We developed a universally applicable genome-wide strain genotyping approach and investigated the population diversity of Lm using 1,696 isolates from diverse sources and geographical locations. We define, with unprecedented precision, the population structure of Lm, demonstrate the occurrence of international circulation of strains and reveal the extent of heterogeneity in virulence and stress resistance genomic features among clinical and food isolates. Using historical isolates, we show that the evolutionary rate of Lm from lineage I and lineage II is low ( approximately 2.5 x 10-7 substitutions per site per year, as inferred from the core genome) and that major sublineages (corresponding to so-called 'epidemic clones') are estimated to be at least 50-150 years old. This work demonstrates the urgent need to monitor Lm strains at the global level and provides the unified approach needed for global harmonization of Lm genome-based typing and population biology. |
Need for certification of household water treatment products: examples from Haiti
Murray A , Pierre-Louis J , Joseph F , Sylvain G , Patrick M , Lantagne D . Trop Med Int Health 2014 20 (4) 462-70 OBJECTIVE: To evaluate four household water treatment (HWT) products currently seeking approval for distribution in Haiti, through the application of a recently-developed national HWT product certification process. METHODS: Four chemical treatment products were evaluated against the certification process validation stage by verifying international product certifications confirming treatment efficacy and reviewing laboratory efficacy data against WHO HWT microbiological performance targets; and against the approval stage by confirming product composition, evaluating treated water chemical content against national and international drinking water quality guidelines and reviewing packaging for dosing ability and usage directions in Creole. RESULTS: None of the four evaluated products fulfilled validation or approval stage requirements. None was certified by an international agency as efficacious for drinking water treatment, and none had data demonstrating its ability to meet WHO HWT performance targets. All product sample compositions differed from labelled composition by >20%, and no packaging included complete usage directions in Creole. CONCLUSIONS: Product manufacturers provided information that was inapplicable, did not demonstrate product efficacy, and was insufficient to ensure safe product use. Capacity building is needed with country regulatory agencies to objectively evaluate HWT products. Products should be internationally assessed against WHO performance targets and also locally approved, considering language, culture and usability, to ensure effective HWT. |
Skin and respiratory symptoms in peanut inspectors with peanut dust and endotoxin exposure
Tapp L , Sylvain D . J Occup Environ Hyg 2012 10 (2) D19-24 The National Institute for Occupational Safety and Health (NIOSH) provided technical assistance at a peanut grading room in response to a request from a state health department for an evaluation of respiratory and skin symptoms among peanut inspectors. Reported symptoms included dermal (skin rash, burning/itching skin); respiratory (cough, shortness of breath, respiratory tract irritation, nosebleeds); and flu-like symptoms after being exposed to “bad” peanuts. We evaluated the workplace during two site visits 10 months apart. |
Evaluation of air sampling methods for abrasive blasting
Ceballos D , Sylvain D , Kiefer M . J Occup Environ Hyg 2012 10 (3) D34-9 The National Institute for Occupational Safety and Health (NIOSH) investigators compared methods for collecting personal breathing zone (PBZ) air samples for particulates during abrasive blasting at a shipyard. Abrasive blasting is the cleaning or finishing of surfaces by the use of an abrasive carried in a strong current of air. The U.S. government has provided regulatory requirements and guidelines for ventilation, enclosures, and personal protective equipment during abrasive blasting [NIOSH 1987; OSHA 2012a]. However, current Occupational Safety and Health Administration (OSHA) sampling and analytical methods can overestimate worker exposures to airborne metals and other particulate contaminants during abrasive blasting [NIOSH 1994; NIOSH 1998; OSHA 2012b]. | Shielding the 37-mm filter cassette inlet to exclude non-inhalable particles, mounting the PBZ air sampler behind the employee's head to protect the sampler from rebounding abrasive materials, and using the Institute of Medicine inhalable dust sampler, have been proposed as alternatives to assess exposure. All were found to be impractical or ineffective in abrasive blasting environments [NIOSH 1994, 1998]. Sampling simultaneously inside and outside the employees' abrasive blast hood has shown that the lower air concentrations inside the abrasive blast hood produce less overloading of the 37-mm cassettes [NIOSH 1998]; however, sampling inside PPE is not accepted by OSHA for compliance purposes [OSHA 2012a, b]. | Aizenberg et al. [2000] used a Button Aerosol Sampler® (BAS) (part number 225–360, SKC Inc., Eighty Four, Pennsylvania) with a prototype shield to evaluate PBZ exposures during abrasive blasting operations. The investigators reported that the protective shield prevented non-inhalable particles from overloading the filter and did not interfere with sampling smaller particles; however, the researchers did not determine whether the prototype protective shield altered the collection efficiency of the BAS. Following the Aizenberg et al. [2000] study, SKC Inc. designed a snap-on dome-shaped stainless steel protective secondary shield for use with the BAS when sampling during abrasive blasting (Abrasive Blasting Sampler for Heavy Metals kit, part number 225–367, SKC Inc., Eighty Four, Pennsylvania). This shield differed in size, shape, and screen opening from the prototype screen tested by Aizenberg et al. [2000]. Due to uncertainty about possible effects that shielding may have on the performance characteristics of the BAS, the objectives of this evaluation were to: (1) compare the commercially available BAS (with and without the shield) with the conventional 37-mm cassette sampler in an abrasive blasting environment and (2) evaluate whether the protective shield designed for the BAS prevented inertia-driven particles from entering and possibly overloading the sampler [NIOSH 2012a]. |
Characterization of two virulent phages of Lactobacillus plantarum.
Briggiler Marcó Mariángeles, Garneau Josiane E, Tremblay Denise, Quiberoni Andrea, Moineau Sylvain. Applied and environmental microbiology 2012 Dec 78(24) 8719-34 . Applied and environmental microbiology 2012 Dec 78(24) 8719-34 ![]() Briggiler Marcó Mariángeles, Garneau Josiane E, Tremblay Denise, Quiberoni Andrea, Moineau Sylvain. Applied and environmental microbiology 2012 Dec 78(24) 8719-34 |
Deepwater Horizon response workers exposure assessment at the source: MC252 well no. 1
Ahrenholz SH , Sylvain DC . J Occup Environ Hyg 2011 8 (6) 43-50 The National Institute for Occupational Safety and Health (NIOSH) conducted a health hazard evaluation (HHE) of Deepwater Horizon Response workers in response to a request submitted by BP management on May 28, 2010. The NIOSH HHE addressed numerous potential worker exposures on land; at the land-water interface; and with a variety of vessels carrying out oil release response activities on, in, and beneath the waters of the Gulf of Mexico.( Citation1 ) This case study reports the NIOSH worker exposure assessment completed for workers aboard two main vessels working to contain, control, and ultimately stop the release of oil into the Gulf of Mexico from the damaged blow out preventer (BOP) at the site of the Deepwater Horizon Mississippi Canyon (MC) 252 Well No. 1 oil release. This assessment was part of a series of requests from BP concerning workers involved in the response. NIOSH evaluated exposures of workers closest to the oil release, at the source, on June 21–23, 2010. |
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