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In this study we used spoligotyping and 15-loci MIRU-VNTRs for a finer characterization of Mycobacterium tuberculosis strains isolated from patients residing in Guyana (n = 74) and Suriname (n = 80). The mean age of the patients was 38.5 years (36.5 and 40.2 years for Guyana vs. Suriname), with a male-to-female sex-ratio of 2.25 for Guyana vs. 4.27 in Suriname. Spoligotyping and 15-loci MIRU-VNTRs led to a total of 41 and 65 different patterns respectively, with an overall clustering rate of 83.8% vs. 68.8%. Combined spoligotyping and VNTR analysis led to the detection of 18 clusters of 2–41 isolates, with an overall clustering of 67.5% and a recent “n − 1” transmission rate of 55.8%. Importantly, Guyana was characterized by a significantly higher percentage of clustered isolates than Suriname (79.7% vs. 56.3%; p = 0.0019). Three big spoligo/MIRU (SIT/MIT) clusters containing >10 isolates each were shared between the 2 countries, and concerned: T1 sublineage cluster 53/861 (n = 41, 37 in Guyana vs. 4 in Suriname); EAI6-BGD1 sublineage cluster 1340/860 (n = 16, 3 in Guyana vs. 13 in Suriname); and T1 sublineage cluster 131/146 (n = 11, 6 in Guyana vs. 5 in Suriname); as well as 2 smaller clusters of 2 and 3 isolates respectively. However, the relative phylogeographical specificities of strains in circulation as well as a lack of drug-resistance observed among strains from Suriname suggested that trans-border transmission of drug-resistant isolates occurred less frequently than thought. Tracing and interrupting transmission channels of a specific clone (SIT53/15-MIT861) should become a priority in Guyana, not only because it is by far most abundant but also because it accounts for almost half of the drug resistant isolates (n = 8/17, 47.1%) in our study, and clustered 5/12 (41.7%) MDR isolates.

The scientific programme of the 9th International Congress “Flour-Bread ’17” and the 11th Croatian Congress of Cereal Technologists “Brašno-Kruh ’17” held from 25 to 27 October in Grand Hotel Adriatic, Opatija, Croatia, included 39 oral and 38 poster presentations. Three plenary lectures, 11 invited lectures, 19 oral presentations, three sponsor advertisement presentations, 3 interactive workshop lectures and 38 poster presentations were within one of five different Congress topics: Cereals and Cereal Product Quality, Cereal Processing Technologies, Cereals and Health, Cereal Food Safety, and Cereal Waste Management.

Il s’agit du premier etat des lieux concernant la circulation d’isolats de Mycobacterium tuberculosis resistants et multiresistants aux antituberculeux dans les departements francais d’Amerique (DFA — Guadeloupe, Martinique Guyane francaise) sur une periode de 17 ans (janvier 1995-decembre 2011). Un total de 1 239 cas de tuberculose a ete etudie: 1 199 nouveaux cas (resistances et multiresistances primaires de 11,8 et 1,6 %) et 40 persistants (definis comme des cas avec antecedent de culture positive a plus de six mois d’intervalle et dont les spoligotypes restent identiques) pour lesquels des proportions significativement plus importantes de resistance a au moins l’isoniazide (22,5 %; p = 0,002), a la rifampicine (20,0 %; p < 0,001) et de multiresistances (17,5 %; p < 0,001) ont ete observees par comparaison aux nouveaux cas. Les 281 profils de spoligotypage obtenus montrent la presence de cinq lignees principales, T (29,9 %), LAM (23,9 %), Haarlem (22,1 %), EAI (7,1 %) et X (6,7 %). Deux de ces lignees, lignee X et LAM, predominent parmi les isolats resistants et multiresistants respectivement (X: 10,5 % des isolats resistants, p = 0,04; LAM: 42,3 % des isolats multiresistants, p = 0,02). Quatre des 19 profils de spoligotypage majoritaires, correspondant aux SIT 20, 64, 45 et 46, etaient significativement associes a la resistance aux antituberculeux. Parmi eux, le genotype SIT 20, associe a une monoresistance a l’isoniazide et a une multiresistance aux antituberculeux, serait en circulation active et persistante depuis 1999, en Guyane francaise, departement dans lequel il a par ailleurs ete observe la presence de souches de M. tuberculosis phylogeographiquement associees au Guyana et au Suriname (SIT 131 et SIT 1340).

During an 8-year period, 17 316 samples of feed and feed raw materials from all over the world were analysed for contamination with aflatoxins, ochratoxin A, zearalenone, deoxynivalenol and fumonisins. Overall, 72% of the samples tested positive for at least one mycotoxin and 38% were found to be co-contaminated. Mycotoxin concentrations were generally low and the majority of the samples were compliant with the most stringent EU guidance values or maximum levels for mycotoxins in feed. However, in their present state these regulations do not address co-contamination and associated risks. Long-term trends are difficult to establish as strong yearly variations were observed regarding mycotoxin prevalence and contamination levels. In some cases unusual weather conditions can be linked with high observed mycotoxin loads. An exception to this rule is South-East Asia, where a steady increase of aflatoxin prevalence has been observed. The percentage of aflatoxin-positive samples in this region rose from 32% in 2005 to 71% in 2011.

The development of liquid chromatography-mass spectrometry (LC-MS)/mass spectrometry (MS) methods for the simultaneous detection and quantification of a broad spectrum of mycotoxins has facilitated the screening of a larger number of samples for contamination with a wide array of less well-known "emerging" mycotoxins and other metabolites. In this study, 83 samples of feed and feed raw materials were analysed. All of them were found to contain seven to 69 metabolites. The total number of detected metabolites amounts to 139. Fusarium mycotoxins were most common, but a number of Alternaria toxins also occurred very often. Furthermore, two so-called masked mycotoxins (i.e., mycotoxin conjugates), namely deoxynivalenol-3-glucoside (75% positives) and zearalenone-4-sulfate (49% positives), were frequently detected. Although the observed median concentrations of the individual analytes were generally in the low μg/kg range, evaluating the toxicological potential of a given sample is difficult. Toxicity data on less well-known mycotoxins and other detected metabolites are notoriously scarce, as an overview on the available information on the most commonly detected metabolites shows. Besides, the possible synergistic effects of co-occurring substances have to be considered.

International audience; Mycotoxins are secondary metabolites produced by fungi especially those belonging to the genus Aspergillus, Penicillum and Fusarium. Mycotoxin contamination can occur in all agricultural commodities in the field and/or during storage, if conditions are favourable to fungal growth. Regarding animal feed, five mycotoxins (aflatoxins, deoxynivalenol, zearalenone, fumonisins and ochratoxin A) are covered by EU legislation (regulation or recommendation). Transgressions of these limits are rarely observed in official monitoring programs. However, low level contamination by Fusarium toxins is very common (e.g., deoxynivalenol (DON) is typically found in more than 50% of the samples) and co-contamination is frequently observed. Multi-mycotoxin studies reported 75%-100% of the samples to contain more than one mycotoxin which could impact animal health at already low doses. Co-occurrence of mycotoxins is likely to arise for at least three different reasons (i) most fungi are able to simultaneously produce a number of mycotoxins, (ii) commodities can be contaminated by several fungi, and (iii) completed feed is made from various commodities. In the present paper, we reviewed the data published since 2004 concerning the contamination of animal feed with single or combinations of mycotoxins and highlighted the occurrence of these co-contaminations.

With the exception of some French-speaking islands, data on tuberculosis (TB) in the Caribbean are scarce. In this study, we report a first assessment of genetic diversity of a convenience sample ofMycobacterium tuberculosisstrains received from twelve Caribbean territories by spoligotyping and describe their drug-resistance patterns. Of the 480 isolates, 40 (8.3%) isolates showed resistance to at least one anti-TB drug. The proportion of drug-resistant strains was significantly higher in The Bahamas (21.4%;P=0.02), and Guyana (27.5%;P<0.0001), while it was significantly lower in Jamaica (2.4%;P=0.03) than in other countries of the present study. Regarding genetic diversity, 104 distinct spoligotype patterns were observed: 49 corresponded to clustered strains (2 to 93 strains per cluster), while 55 remained unclustered among which 16 patterns were not reported previously. Combining the study results with regional data retrieved from the international SITVIT2 database underlined a connection between frequency of certainM. tuberculosisphylogenetic lineages and the language spoken, suggesting historical (colonial) and ongoing links (trade, tourism, and migratory flows) with European countries with which they shared a common past.

The population of the French Departments of the Americas (FDA) is highly influenced by the intense migratory flows with mainland France and surrounding countries of the Caribbean and Latin America, some of which have high incidence rates of tuberculosis (Haiti: 230/100,000; Guyana: 111/100,000; and Suriname: 145/100,000) and drug resistance. Since the development of drug resistance to conventional antituberculous drugs has a major impact on the treatment success of tuberculosis, we therefore decided to review carefullyMycobacterium tuberculosisdrug resistance and associated genotypic lineages in the FDA over a seventeen-year period (January 1995–December 2011). A total of 1239 cases were studied, including 153 drug-resistant and 26 multidrug-resistant- (MDR-) TB cases, representing 12.3% and 2.1% of the TB cases in our study setting. A significantly higher proportion ofM. tuberculosisisolates among relapse cases showed drug resistance to isoniazid (22.5%,P=0.002), rifampicin (20.0%,P<0.001), or both (MDR-TB, 17.5%;P<0.001). Determination of spoligotyping based phylogenetic clades showed that among the five major lineages observed—T family (30.1%); Latin-American and Mediterranean (LAM, 23.7%); Haarlem (H, 22.2%); East-African Indian (EAI, 7.2%); and X family (6.5%)—two lineages, X and LAM, were overrepresented in drug-resistant and MDR-TB cases, respectively. Finally, 19 predominant spoligotypes were identified for the 1239 isolates ofM. tuberculosisin our study among which 4 were significantly associated with drug resistance corresponding to SIT20/LAM1, SIT64/LAM6, SIT45/H1, and SIT46/undefined lineage.

During an 8-year period, 17 316 samples of feed and feed raw materials from all over the world were analysed for contamination with aflatoxins, ochratoxin A, zearalenone, deoxynivalenol and fumonisins. Overall, 72% of the samples tested positive for at least one mycotoxin and 38% were found to be co-contaminated. Mycotoxin concentrations were generally low and the majority of the samples were compliant with the most stringent EU guidance values or maximum levels for mycotoxins in feed. However, in their present state these regulations do not address co-contamination and associated risks. Long-term trends are difficult to establish as strong yearly variations were observed regarding mycotoxin prevalence and contamination levels. In some cases unusual weather conditions can be linked with high observed mycotoxin loads. An exception to this rule is South-East Asia, where a steady increase of aflatoxin prevalence has been observed. The percentage of aflatoxin-positive samples in this region rose from 32% in 2005 to 71% in 2011.

Multiple-locus variable-number tandem repeat analysis (MLVA) is useful to establish transmission routes and sources of infections for various microorganisms including Mycobacterium tuberculosis complex (MTC). The recently released SITVITWEB database contains 12-loci Mycobacterial Interspersed Repetitive Units – Variable Number of Tandem DNA Repeats (MIRU-VNTR) profiles and spoligotype patterns for thousands of MTC strains; it uses MIRU International Types (MIT) and Spoligotype International Types (SIT) to designate clustered patterns worldwide. Considering existing doubts on the ability of spoligotyping alone to reveal exact phylogenetic relationships between MTC strains, we developed a MLVA based classification for MTC genotypic lineages. We studied 6 different subsets of MTC isolates encompassing 7793 strains worldwide. Minimum spanning trees (MST) were constructed to identify major lineages, and the most common representative located as a central node was taken as the prototype defining different phylogenetic groups. A total of 7 major lineages with their respective prototypes were identified: Indo-Oceanic/MIT57, East Asian and African Indian/MIT17, Euro American/MIT116, West African-I/MIT934, West African-II/MIT664, M. bovis/MIT49, M.canettii/MIT60. Further MST subdivision identified an additional 34 sublineage MIT prototypes. The phylogenetic relationships among the 37 newly defined MIRU-VNTR lineages were inferred using a classification algorithm based on a bayesian approach. This information was used to construct an updated phylogenetic and phylogeographic snapshot of worldwide MTC diversity studied both at the regional, sub-regional, and country level according to the United Nations specifications. We also looked for IS6110 insertional events that are known to modify the results of the spoligotyping in specific circumstances, and showed that a fair portion of convergence leading to the currently observed bias in phylogenetic classification of strains may be traced back to the presence of IS6110. These results shed new light on the evolutionary history of the pathogen in relation to the history of peopling and human migration.

L'article est également disponible en français à l'adresse suivante:https://pro.anses.fr/euroreference/Documents/ER12-RESEAUX-Mycobacterium.pdf; International audience; In this paper we will briefly review various Mycobacterium tuberculosis complex (MTBC) genotyping databases developed over last fifteen years at the Institut Pasteur de la Guadeloupe, which represent a great concerted initiative and effort to control the tuberculosis epidemic. Starting from the initial excel-based version in 1999 (SpolDB1; n=610 clinical isolates) to the fourth MySQL-based version in 2006 (SpolDB4; n=39,295 clinical isolates), these databases permitted to have a first phylogeographical snapshot of circulating MTBC genotypic lineages based on spacer oligonucleotide typing (spoligotyping) which allows to study the polymorphism of the Direct Repeat (DR) locus. The two most recent MySQL-based multimarker versions concern the 5th version SITVITWEB released in 2012 (n=62,582 clinical isolates) with both spoligotyping and 12-loci Mycobacterial Interspersed Repetitive Units - Variable Number of Tandem Repeats (MIRU-VNTRs); and the 6th version named SITVIT2 that will be released in 2014 (n= 111,635 clinical isolates) with spoligotyping and 12-, 15- or 24-loci MIRUVNTR data. In these recent versions, a web-based interface allows the user to search for strains through the database by criteria, such as the year, the isolation country, the country of origin, the investigator’s name. It further facilitates to perform combined searches in SITVIT2, making it possible to get the genotyping data on selected strains in conjunction with their geographical distribution, as well as available data on drug resistance, demographic and epidemiologic characteristics. Our research initiative is thus focused to further improve in depth phylogenetic characterization of MTBC lineages in conjunction with epidemiological analysis of circulating clones to generate evidence-based geographical mapping of predominant clinical isolates of tubercle bacilli causing the bulk of the disease both at country and regional level. Further superimposition of these maps with socio-political, economical, and demographical characteristics available through Geographic Information Systems (GIS) allows to have a precise view of prevailing disparities as seen at the level of United Nation’s sub-regional stratification. An in-depth comprehension of these disparities and drawbacks is important to take appropriate actions by decision-makers and public health authorities alike, in order to better monitor, understand and control the tuberculosis epidemic worldwide.; Dans cet article, nous présenterons rapidement plusieurs bases de données de génotypage du complexe Mycobacterium tuberculosis (MTBC), élaborées au cours des quinze dernières années à l’Institut Pasteur de la Guadeloupe (IPG), dans le cadre d’une grande initiative concertée visant à lutter contre l’épidémie mondiale de la tuberculose. De la toute première version au format Excel en 1999 (SpolDB1 ; n = 610 isolats cliniques) à la quatrième au format MySQL en 2006 (SpolDB4 ; n = 39 295 isolats cliniques), ces bases de données ont brossé un premier tableau de la phylogéographie des lignées génotypiques de MTBC en circulation, en utilisant le typage oligonucléotidique des espaceurs (spoligotypage) qui permet d’étudier le polymorphisme du locus DR (Direct Repeat). Les deux dernières versions multimarqueurs sous MySQL constituent respectivement la 5e version de SITVITWEB, publiée en 2012 (n = 62 582 isolats cliniques), qui repose sur le spoligotypage et le typage MIRU-VNTR (Mycobacterial Interspersed Repetitive Units/Variable Number of Tandem Repeats) 12 loci, et la 6e version, dénommée SITVIT2, qui sera publiée en 2014 (n = 111 635 isolats cliniques) et qui contient des données de spoligotypage et de MIRU-VNTR 12, 15 ou 24 loci. Sur ces dernières versions, une interface en ligne permet à l’utilisateur de rechercher des souches dans la base de données au moyen de critères tels que l’année, le pays d’isolement, le pays d’origine ou le nom du chercheur. Cette interface permet en outre d’effectuer des recherches mixtes dans SITVIT2, permettant d’obtenir les données de génotypage de certaines souches, conjointement avec leur répartition géographique, ainsi que les données disponibles sur la résistance aux antibiotiques ou les caractéristiques démographiques et épidémiologiques. Notre initiative de recherche a ainsi pour but d’améliorer la caractérisation phylogénétique détaillée des lignées du MTBC, ainsi que l’épidémiologie des clones en circulation, afin d’élaborer une cartographie géographique factuelle des isolats cliniques prédominants pour les bacilles tuberculeux principalement impliqués dans la maladie, à l’échelle nationale et régionale. La superposition ultérieure de ces cartes avec des données sociopolitiques, économiques et démographiques obtenues auprès de Systèmes d’information géographique (SIG) dressera un portrait précis des disparités actuelles par sous-région, selon la classification des Nations Unies. Il est important de comprendre le détail de ces disparités et faiblesses pour que les décideurs politiques et les autorités de santé publique puissent prendre les mesures qui s’imposent pour mieux surveiller, comprendre et contrôler l’épidémie mondiale de la tuberculose.

L'article est également disponible en français à l'adresse suivante:https://pro.anses.fr/euroreference/Documents/ER12-RESEAUX-Mycobacterium.pdf; International audience; In this paper we will briefly review various Mycobacterium tuberculosis complex (MTBC) genotyping databases developed over last fifteen years at the Institut Pasteur de la Guadeloupe, which represent a great concerted initiative and effort to control the tuberculosis epidemic. Starting from the initial excel-based version in 1999 (SpolDB1; n=610 clinical isolates) to the fourth MySQL-based version in 2006 (SpolDB4; n=39,295 clinical isolates), these databases permitted to have a first phylogeographical snapshot of circulating MTBC genotypic lineages based on spacer oligonucleotide typing (spoligotyping) which allows to study the polymorphism of the Direct Repeat (DR) locus. The two most recent MySQL-based multimarker versions concern the 5th version SITVITWEB released in 2012 (n=62,582 clinical isolates) with both spoligotyping and 12-loci Mycobacterial Interspersed Repetitive Units - Variable Number of Tandem Repeats (MIRU-VNTRs); and the 6th version named SITVIT2 that will be released in 2014 (n= 111,635 clinical isolates) with spoligotyping and 12-, 15- or 24-loci MIRUVNTR data. In these recent versions, a web-based interface allows the user to search for strains through the database by criteria, such as the year, the isolation country, the country of origin, the investigator’s name. It further facilitates to perform combined searches in SITVIT2, making it possible to get the genotyping data on selected strains in conjunction with their geographical distribution, as well as available data on drug resistance, demographic and epidemiologic characteristics. Our research initiative is thus focused to further improve in depth phylogenetic characterization of MTBC lineages in conjunction with epidemiological analysis of circulating clones to generate evidence-based geographical mapping of predominant clinical isolates of tubercle bacilli causing the bulk of the disease both at country and regional level. Further superimposition of these maps with socio-political, economical, and demographical characteristics available through Geographic Information Systems (GIS) allows to have a precise view of prevailing disparities as seen at the level of United Nation’s sub-regional stratification. An in-depth comprehension of these disparities and drawbacks is important to take appropriate actions by decision-makers and public health authorities alike, in order to better monitor, understand and control the tuberculosis epidemic worldwide.; Dans cet article, nous présenterons rapidement plusieurs bases de données de génotypage du complexe Mycobacterium tuberculosis (MTBC), élaborées au cours des quinze dernières années à l’Institut Pasteur de la Guadeloupe (IPG), dans le cadre d’une grande initiative concertée visant à lutter contre l’épidémie mondiale de la tuberculose. De la toute première version au format Excel en 1999 (SpolDB1 ; n = 610 isolats cliniques) à la quatrième au format MySQL en 2006 (SpolDB4 ; n = 39 295 isolats cliniques), ces bases de données ont brossé un premier tableau de la phylogéographie des lignées génotypiques de MTBC en circulation, en utilisant le typage oligonucléotidique des espaceurs (spoligotypage) qui permet d’étudier le polymorphisme du locus DR (Direct Repeat). Les deux dernières versions multimarqueurs sous MySQL constituent respectivement la 5e version de SITVITWEB, publiée en 2012 (n = 62 582 isolats cliniques), qui repose sur le spoligotypage et le typage MIRU-VNTR (Mycobacterial Interspersed Repetitive Units/Variable Number of Tandem Repeats) 12 loci, et la 6e version, dénommée SITVIT2, qui sera publiée en 2014 (n = 111 635 isolats cliniques) et qui contient des données de spoligotypage et de MIRU-VNTR 12, 15 ou 24 loci. Sur ces dernières versions, une interface en ligne permet à l’utilisateur de rechercher des souches dans la base de données au moyen de critères tels que l’année, le pays d’isolement, le pays d’origine ou le nom du chercheur. Cette interface permet en outre d’effectuer des recherches mixtes dans SITVIT2, permettant d’obtenir les données de génotypage de certaines souches, conjointement avec leur répartition géographique, ainsi que les données disponibles sur la résistance aux antibiotiques ou les caractéristiques démographiques et épidémiologiques. Notre initiative de recherche a ainsi pour but d’améliorer la caractérisation phylogénétique détaillée des lignées du MTBC, ainsi que l’épidémiologie des clones en circulation, afin d’élaborer une cartographie géographique factuelle des isolats cliniques prédominants pour les bacilles tuberculeux principalement impliqués dans la maladie, à l’échelle nationale et régionale. La superposition ultérieure de ces cartes avec des données sociopolitiques, économiques et démographiques obtenues auprès de Systèmes d’information géographique (SIG) dressera un portrait précis des disparités actuelles par sous-région, selon la classification des Nations Unies. Il est important de comprendre le détail de ces disparités et faiblesses pour que les décideurs politiques et les autorités de santé publique puissent prendre les mesures qui s’imposent pour mieux surveiller, comprendre et contrôler l’épidémie mondiale de la tuberculose.