Sylvain Godreuil

First Molecular Epidemiology Study of Mycobacterium tuberculosis in Burkina Faso

ABSTRACT We conducted a molecular epidemiology study on 120 Mycobacterium tuberculosis isolates from patients presenting pulmonary tuberculosis (TB) in Burkina Faso. Classical antibiogram studies and genetic characterization, using mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) typing and spoligotyping, were applied after culture. Molecular analysis of specific signatures showed that all TB cases reported in this study were caused by M. tuberculosis and identified no Mycobacterium bovis or Mycobacterium africanum isolates. This result is unexpected, as M. africanum strains were reportedly the etiologic agent in 20% of TB cases 2 decades ago. The comparison of spoligotypes from Burkina Faso with an international spoligotype database (SpolDB4) showed that the majority of isolates belong to major clades of M. tuberculosis (Haarlem, 9%; Latin American-Mediterranean, 30%; and T, 20%). The predominant group of isolates (30%) corresponds to spoligotype 61, described in Cameroon as the “Cameroon family.” In Burkina Faso, as in Cameroon, this family could be associated with recent transmission of TB, suggesting a recent expansion in West Africa. Our data suggest a low level of primary drug resistance that may be a positive result of the Directly Observed Therapy Shortcourse program. Besides, based on spoligotyping plus MIRU-VNTR, data showed a high number of clusters in our sample, suggesting a high level of recent TB transmission in Burkina Faso. Nevertheless, an important genetic polymorphism was observed in this country, reflecting an endemicity situation where the control of TB would have less impact in the main towns.

Evaluation of the enhanced bacterial detection system for screening of contaminated platelets

BACKGROUND:  The Pall third‐generation enhanced bacterial detection system (eBDS) was recently approved for detection of bacterial contamination in leukoreduced platelets (PLTs). The method is based on the measurement of the oxygen content as a marker for bacteria. eBDS incorporates major modifications including removal of the sample‐set filter, modification of the culture medium, and incubation with agitation of the sample pouch.

Extended-Spectrum β-Lactamase TEM-24 in an Aeromonas Clinical Strain: Acquisition from the Prevalent Enterobacter aerogenes Clone in France

The TEM-24 extended-spectrum β-lactamase (ESBL), initially characterized in Klebsiella pneumoniae (3), is currently the predominant ESBL in France (4). This could be related to the spread of a TEM-24-producing Enterobacter aerogenes clone present in most French hospitals (1) but also found in Belgium (5) and Spain (2). TEM-24 enzyme has been recovered from an increasing number of species of the family Enterobacteriaceae (6, 8) and in Pseudomonas aeruginosa (7). In contrast, resistance to expanded-spectrum cephalosporins mediated by ESBLs has never been described in the genus Aeromonas, for which β-lactam resistance involves three chromosomally mediated enzymes: a cephalosporinase, a penicillinase, and a carbapenemase (9). We report the first characterization of a TEM-24-producing clinical Aeromonas strain. 16S ribosomal DNA (rDNA) and gyrB sequencing (10) showed that the strain was most closely related to Aeromonas caviae. This strain was recovered together with an ESBL-producing E. aerogenes isolate from the diarrheal feces of a 76-year-old man admitted to Montpellier Hospital for intestinal ischemia. Based on the resistance phenotype observed after the disk diffusion assay, both E. aerogenes and Aeromonas sp. isolates were suspected to produce ceftazidimase-type ESBL and AAC(6′)-I enzyme. Synergy was clearly observed between expanded-spectrum cephalosporins and clavulanate. The resistance phenotype was transferred in Escherichia coli C600 by mating experiments using Mueller-Hinton agar (Sanofi Diagnostics Pasteur, Marnes-la-Coquette, France) containing ceftazidime (4 μg/ml). The MICs of β-lactams showed high levels of resistance with the E. aerogenes strain and the two transconjugants for penicillins (64 to >2,048 μg/ml), ceftazidime (512 to 1,048 μg/ml), and aztreonam (64 to 1,048 μg/ml). A low level of resistance or decrease in susceptibility was observed for cefotaxime (4 to 8 μg/ml). The Aeromonas sp. strain showed lower resistance levels (penicillins, 8 to 256 μg/ml; ceftazidime, 64 μg/ml; and aztreonam, 8 μg/ml). Clavulanate and tazobactam partially or completely restored the susceptibility to penicillins. ESBL characterization was performed for the two isolates by isoelectric focusing, ESBL-encoding gene amplification and sequencing, and plasmid content analysis (6, 7). The ESBLs were focused at a pI of 6.5. The sequence of ESBL-encoding genes shared 100% identity with the blaTEM-24 gene. Plasmids of approximately 180 kb, which displayed similar restriction patterns, were isolated from the two strains and their transconjugants. These results suggested an in vivo transfer of TEM-24-encoding plasmid from E. aerogenes to Aeromonas sp. in the intestinal tract. We have previously reported the transfer of 180-kb TEM-24-encoding plasmid from E. aerogenes to Providencia rettgeri CIP 107053 (6) and P. aeruginosa CIP 107051 (7). A comparative study of the restriction profiles obtained for the plasmids recovered from these organisms and from the strains analyzed here revealed similar restriction patterns (Fig. ​(Fig.1).1). Pulsed-field gel electrophoresis (PFGE) analysis of the E. aerogenes strains isolated in this study and previously (6, 7) revealed that they belong to the TEM-24-producing E. aerogenes clone prevalent in France. FIG. 1. EcoRI-SalI restriction patterns of 180-kb TEM-24-encoding plasmids obtained from transconjugants corresponding to the following clinical isolates: lane 2, P. rettgeri CIP 107053 (6); lane 3, P. aeruginosa CIP 107051 (7); lane 4, Aeromonas sp. (this study); ... This clone had disseminated the same TEM-24-encoding plasmid among various bacterial species for several years. The isolation of a TEM-24-producing Aeromonas sp. strain extends the list of TEM-24-harboring bacteria, and this wide host range is one of the factors responsible for the persistence and spread of the TEM-24-encoding plasmid.

Pulmonary tuberculosis due to Mycobacterium microti: a study of six recent cases in France.

Human tuberculosis caused by Mycobacterium microti is rare, but its prevalence and clinical significance may have been underestimated. To the best of our knowledge, 21 cases have been reported in the literature in the last decade. We report six recent pulmonary cases caused by M. microti over a period of 5 years detected in French clinical mycobacteriology laboratories of the hospital network. Our data confirm the potential of M. microti to cause clinical illness in immunocompetent patients. M. microti grew slowly from specimens, delaying the final microbiological diagnosis. Therefore, patients with tuberculosis caused by M. microti could benefit from the use of rapid diagnostic molecular techniques directly on clinical samples. From a review of the literature and this study, a classical antituberculous therapy seems effective in treating patients with M. microti disease.

Antimicrobial resistance in wildlife

1. The spread of antimicrobial resistance is of major concern for human health and leads to growing economic costs. While it is increasingly hypothesized that wildlife could play an important role in antimicrobial-resistant bacteria dynamics, empirical data remain scarce. 2. The present work builds on a systematic review of the available data in order to highlight the main information we have and to suggest research pathways that should be followed if we aim to fill the gaps in our current knowledge. 3. To achieve this goal, we address four questions: (i) Which resistant bacteria are the most frequently observed in wildlife? (ii) How are resistant bacteria exchanged between wildlife and the other hosts involved? (iii) In which habitats are those resistant bacteria found? (iv) Are resistances associated with certain ecological traits of the host? 4. Synthesis and applications. We highlight the strong link existing between the impact of human activities on natural habitats and the carriage of antimicrobial-resistant bacteria by wildlife. Furthermore, we underline that omnivorous, anthropophilic and carnivorous species are at high risk of being carriers and potentially spreaders of antimicrobial-resistant bacteria. Identifying among those groups key sentinel species may be of particular interest to implement ecosystem contamination surveillance. Finally, we discuss possible exchange routes for antimicrobial-resistant bacteria between humans and wildlife. Considering that water is of major importance in those exchanges, a critical way to control antimicrobial resistance spread may be to limit aquatic environment contamination by antimicrobial-resistant bacteria and antibiotics.

Identification of a Haarlem Genotype-Specific Single Nucleotide Polymorphism in the mgtC Virulence Gene of Mycobacterium tuberculosis

ABSTRACT MgtC is a virulence factor common to several intracellular pathogens, including Mycobacterium tuberculosis, that might have been acquired through horizontal gene transfer. In the present study, we investigated the polymorphism of mgtC in clinical isolates representative of the main epidemic groups of M. tuberculosis. MgtC appears to have a low polymorphism rate in M. tuberculosis that consists exclusively of nonsynonymous mutations. We identified a single nucleotide polymorphism (SNP) at mgtC codon 182 (mgtC182) specifically associated with the Haarlem genotype. A simple PCR assay, called the “on/off switch assay,” using phosphorothioate-modified primers and Pfu polymerase allowed us to distinguish Haarlem from non-Haarlem strains based on the mgtC182 SNP. The amino acid change (H182R) associated with the mgtC182 SNP in Haarlem strains does not appear to procure a selective advantage. Our results offer a simple and rapid tool to distinguish between Haarlem and non-Haarlem strains. In addition, the on/off switch assay, which allows the detection of SNPs on chromosomal DNA and M. tuberculosis cultures, provides a novel approach for the screening of known SNPs in M. tuberculosis.

Circulating Cell Free Tumor DNA Detection as a Routine Tool forLung Cancer Patient Management

Circulating tumoral DNA (ctDNA), commonly named “liquid biopsy”, has emerged as a new promising noninvasive tool to detect biomarker in several cancers including lung cancer. Applications involving molecular analysis of ctDNA in lung cancer have increased and encompass diagnosis, response to treatment, acquired resistance and prognosis prediction, while bypassing the problem of tumor heterogeneity. ctDNA may then help perform dynamic genetic surveillance in the era of precision medicine through indirect tumoral genomic information determination. The aims of this review were to examine the recent technical developments that allowed the detection of genetic alterations of ctDNA in lung cancer. Furthermore, we explored clinical applications in patients with lung cancer including treatment efficiency monitoring, acquired therapy resistance mechanisms and prognosis value.

No evidence for transmission of antibiotic-resistant Escherichia coli strains from humans to wild western lowland gorillas in Lopé National Park, Gabon.

ABSTRACT The intensification of human activities within the habitats of wild animals is increasing the risk of interspecies disease transmission. This risk is particularly important for great apes, given their close phylogenetic relationship with humans. Areas of high human density or intense research and ecotourism activities expose apes to a high risk of disease spillover from humans. Is this risk lower in areas of low human density? We determined the prevalence of Escherichia coli antibiotic-resistant isolates in a population of the critically endangered western lowland gorilla (Gorilla gorilla gorilla) and other wild mammals in Lopé National Park (LNP), Gabon, and we tested whether the observed pattern could be explained by bacterial transmission from humans and domestic animals into wildlife populations. Our results show a high prevalence of antibiotic-resistant bacterial isolates in humans and low levels in gorillas and other wildlife. The significant differences in the genetic background of the resistant bacteria isolated from humans and gorillas suggest that transmission is low or does not occur between these two species. These findings indicate that the presence of antibiotic-resistant strains in wildlife do not imply direct bacteria transmission from humans. Thus, in areas of low human density, human-wildlife E. coli transmission seems to be low. The presence of antibiotic-resistant isolates in gorillas may be better explained by other mechanisms for resistance acquisition, such as horizontal gene exchange among bacteria or naturally acquired resistance.

Nocardia veterana Isolated from Ascitic Fluid of a Patient with Human Immunodeficiency Virus Infection

ABSTRACT Nocardia veterana is a recently characterized species within the genus Nocardia, and only three human clinical isolates have been reported for this species. We describe a case of ascitic fluid infection in an immunocompromised patient due to N. veterana. To our knowledge, this is the first report of a Nocardia sp. strain from ascitic fluid and the fourth report of N. veterana isolated from human samples. Chemotaxonomic methods showed the strain to belong to the genus Nocardia, and identification to the species level was done by 16S ribosomal DNA gene sequencing. The antibiotic susceptibility profile of N. veterana is reported here for the second time. The strain was deposited in the Collection of the Pasteur Institute and in the Culture Collection of the University of Göteborg (CIP 107497 and CCUG 46576). The corresponding 16S ribosomal DNA gene sequence is available from the GenBank database under accession number AY149599 . A phylogenetic analysis was conducted and showed that N. veterana was most closely related to the recently characterized species Nocardia africana rather than to Nocardia vaccinii, as previously reported.

Mycobacterium bovis in Burkina Faso: Epidemiologic and Genetic Links between Human and Cattle Isolates

Background In sub-Saharan Africa, bovine tuberculosis (bTB) is a potential hazard for animals and humans health. The goal of this study was to improve our understanding of bTB epidemiology in Burkina Faso and especially Mycobacterium bovis transmission within and between the bovine and human populations. Methodology/principal findings Twenty six M. bovis strains were isolated from 101 cattle carcasses with suspected bTB lesions during routine meat inspections at the Bobo Dioulasso and Ouagadougou slaughterhouses. In addition, 7 M. bovis strains were isolated from 576 patients with pulmonary tuberculosis. Spoligotyping, RDAf1 deletion and MIRU-VNTR typing were used for strains genotyping. The isolation of M. bovis strains was confirmed by spoligotyping and 12 spoligotype signatures were detected. Together, the spoligotyping and MIRU-VNTR data allowed grouping the 33 M. bovis isolates in seven clusters including isolates exclusively from cattle (5) or humans (1) or from both (1). Moreover, these data (genetic analyses and phenetic tree) showed that the M. bovis isolates belonged to the African 1 (Af1) clonal complex (81.8%) and the putative African 5 (Af5) clonal complex (18.2%), in agreement with the results of RDAf1 deletion typing. Conclusions/Significance This is the first detailed molecular characterization of M. bovis strains from humans and cattle in Burkina Faso. The distribution of the two Af1 and putative Af5 clonal complexes is comparable to what has been reported in neighbouring countries. Furthermore, the strain genetic profiles suggest that M. bovis circulates across the borders and that the Burkina Faso strains originate from different countries, but have a country-specific evolution. The genetic characterization suggests that, currently, M. bovis transmission occurs mainly between cattle, occasionally between cattle and humans and potentially between humans. This study emphasizes the bTB risk in cattle but also in humans and the difficulty to set up proper disease control strategies in Burkina Faso.