Whole genome sequences to assess the link between antibiotic and metal resistance in three coastal marine bacteria isolated from the mummichog gastrointestinal tract

International audienceAntibiotic resistance is a global public health issue and metal exposure can co-select for antibiotic resistance. We examined genome sequences of three multi-drug and metal resistant bacteria: one Shewanella sp., and two Vibrio spp., isolated from the gut of the mummichog fish (Fundulus heteroclitus). Our primary goal was to understand the mechanisms of co-selection. Phenotypically, the strains showed elevated resistance to arsenate, mercury, and various types of β-lactams. The genomes contained genes of public health concern including one carbapenemase (bla OXA-48). Our analyses indicate that the co-selection phenotype is mediated by chromo-somal resistance genes and cross-resistance. No evidence of co-resistance was found; most resistance genes were chromosomally located. Moreover, the identification of many efflux pump gene homologs indicates that cross-resistance and/or co-regulation may further contribute to resistance. We suggest that the mummichog gut microbiota may be a source of clinically relevant antibiotic resistance genes

Genome-facilitated discovery of RND efflux pump-mediated resistance to cephalosporins in Vibrio spp. isolated from the mummichog fish gut

International audienc

Diversity among strains of Pseudomonas aeruginosa from manure and soil, evaluated by multiple locus variable number tandem repeat analysis and antibiotic resistance profiles

International audienceThe results of a multiple locus variable number of tandem repeat (VNTR) analysis (MLVA)-based study designed to understand the genetic diversity of soil and manure-borne Pseudomonas aeruginosa isolates, and the relationship between these isolates and a set of clinical and environmental isolates, are hereby reported. Fifteen described VNTR markers were first selected, and 62 isolates recovered from agricultural and industrial soils in France and Burkina Faso, and from cattle and horse manure, along with 26 snake-related isolates and 17 environmental and clinical isolates from international collections, were genotyped. Following a comparison with previously published 9-marker MLVA schemes, an optimal 13-marker MLVA scheme (MLVA 13-Lyon) was identified that was found to be the most efficient, as it showed high typability (90%) and high discriminatory power (0.987). A comparison of MLVA with PFGE for typing of the snake-related isolates confirmed the MLVA 13-Lyon scheme to be a robust method for quickly discriminating and inferring genetic relatedness among environmental isolates. The 62 isolates displayed wide diversity, since 41 MLVA types (i.e. MTs) were observed, with 26 MTs clustered in 10 MLVA clonal complexes (MCs). Three and eight MCs were found among soil and manure isolates, respectively. Only one MC contained both soil and manure-borne isolates. No common MC was observed between soil and manure-borne isolates and the snake-related or environmental and clinical isolates. Antibiotic resistance profiles were performed to determine a potential link between resistance properties and the selective pressure that might be present in the various habitats. Except for four soil and manure isolates resistant to ticarcillin and ticarcillin/clavulanic acid and one isolate from a hydrocarbon-contaminated soil resistant to imipenem, all environmental isolates showed wild-type antibiotic profiles

Draft Genome Sequences of Stenotrophomonas maltophilia Strains Sm32COP, Sm41DVV, Sm46PAILV, SmF3, SmF22, SmSOFb1, and SmCVFa1, Isolated from Different Manures in France: TABLE 1

International audienceStenotrophomonas maltophilia is a major opportunistic human pathogen responsible for nosocomial infections. Here, we report the draft genome sequences of Sm32COP, Sm41DVV, Sm46PAILV, SmF3, SmF22, SmSOFb1, and SmCVFa1, isolated from different manures in France, which provide insights into the genetic determinism of intrinsic or acquired antibiotic resistance in this species. Citation Bodilis J, Youenou B, Briolay J, Brothier E, Favre-Bonté S, Nazaret S. 2016. Draft genome sequences of Stenotrophomonas maltophilia strains Sm32COP, Sm41DVV, Sm46PAILV, SmF3, SmF22, SmSOFb1, and SmCVFa1, isolated from different manures in France

Caracterisation des souches de Frankia isolees des nodules de Casuarina. Mise au point de marqueurs genetiques

SIGLEAvailable from INIST (FR), Document Supply Service, under shelf-number : T 78111 / INIST-CNRS - Institut de l'Information Scientifique et TechniqueFRFranc

Role and prevalence of antibiosis and the related resistance genes in the environment

It becomes increasingly clear that the basis of antibiotic resistance problem among bacterial pathogens is not confined to the borders of clinical microbiology but has broader ecological and evolutionary associations. This Research Topic “Role and prevalence of antibiosis and the related resistance genes in the environment” in Frontiers in Microbiology, section Antimicrobials, Resistance and Chemotherapy, presents the examples of occurrence and diversity of antibiotic resistance genes in the wide range of environments, from the grasslands of the Colombian Andes, to the dairy farms and small animal veterinary hospitals in the United Stated, and to the various environments of Continental Europe and Indochina. Besides, various genetic mechanisms and selection/co-selection factors contributing to the dissemination and maintenance of antibiotic resistance genes are presented. The topic is finalized by the mathematical modeling approach to access the probability of rare horizontal gene transfer events in bacterial populations

Freshwater Bacteria Can Methylate Selenium through the Thiopurine Methyltransferase Pathway

Involvement of the bacterial thiopurine methyltransferase (bTPMT) in natural selenium methylation by freshwater was investigated. A freshwater environment that had no known selenium contamination but exhibited reproducible emission of dimethyl selenide (DMSe) or dimethyl diselenide (DMDSe) when it was supplemented with an organic form of selenium [(methyl)selenocysteine] or an inorganic form of selenium (sodium selenite) was used. The distribution of the bTPMT gene (tpm) in the microflora was studied. Freshwater bacteria growing on 10 μM sodium selenite and 10 μM sodium selenate were isolated, and 4.5 and 10% of the strains, respectively, were shown by colony blot hybridization to hybridize with a Pseudomonas syringae tpm DNA probe. Ribotyping showed that these strains are closely related. The complete rrs sequence of one of the strains, designated Hsa.28, was obtained and analyzed. Its closest phyletic neighbor was found to be the Pseudomonas anguilliseptica rrs sequence. The Hsa.28 strain grown with sodium selenite or (methyl)selenocysteine produced significant amounts of DMSe and DMDSe. The Hsa.28 tpm gene was isolated by genomic DNA library screening and sequencing. BLASTP comparisons of the deduced Hsa.28 bTPMT sequence with P. syringae, Pseudomonas aeruginosa, Vibrio cholerae, rat, and human thiopurine methyltransferase sequences revealed that the levels of similarity were 52 to 71%. PCR-generated Escherichia coli subclones containing the Hsa.28 tpm open reading frame were constructed. E. coli cells harboring the constructs and grown with sodium selenite or (methyl)selenocysteine produced significant levels of DMSe and DMDSe, confirming that the gene plays a role in selenium methylation. The effect of strain Hsa.28 population levels on freshwater DMSe and DMDSe emission was investigated. An increase in the size of the Hsa.28 population was found to enhance significantly the emission of methyl selenides by freshwater samples supplemented with sodium selenite or (methyl)selenocysteine. These data suggest that bTPMT can play a role in natural freshwater selenium methylation processes

Monitoring complex bacterial communities using culture-independent molecular techniques : application to soil environment

International audienc

L'impact du mercure sur les bactéries telluriques

National audienc

Sequencing bands of ribosomal intergenic spacer analysis fingerprints for characterization and microscale distribution of soil bacterium populations responding to mercury spiking

International audienc