RESUMEN
Cystic fibrosis (CF) lungs harbor a complex community of interacting microbes, including pathogens like Pseudomonas aeruginosa. Meta-taxogenomic analysis based on V5-V6 rrs PCR products of 52 P. aeruginosa-positive (Pp) and 52 P. aeruginosa-negative (Pn) pooled DNA extracts from CF sputa suggested positive associations between P. aeruginosa and Stenotrophomonas and Prevotella, but negative ones with Haemophilus, Neisseria and Burkholderia. Internal Transcribed Spacer analyses (RISA) from individual DNA extracts identified three significant genetic structures within the CF cohorts, and indicated an impact of P. aeruginosa. RISA clusters Ip and IIIp contained CF sputa with a P. aeruginosa prevalence above 93%, and of 24.2% in cluster IIp. Clusters Ip and IIIp showed lower RISA genetic diversity and richness than IIp. Highly similar cluster IIp RISA profiles were obtained from two patients harboring isolates of a same P. aeruginosa clone, suggesting convergent evolution in the structure of their microbiota. CF patients of cluster IIp had received significantly less antibiotics than patients of clusters Ip and IIIp but harbored the most resistant P. aeruginosa strains. Patients of cluster IIIp were older than those of Ip. The effects of P. aeruginosa on the RISA structures could not be fully dissociated from the above two confounding factors but several trends in these datasets support the conclusion of a strong incidence of P. aeruginosa on the genetic structure of CF lung microbiota.
Asunto(s)
Bacterias/genética , Fibrosis Quística/complicaciones , ADN Bacteriano/metabolismo , Infecciones por Pseudomonas/complicaciones , Esputo/microbiología , Antibacterianos/farmacología , Bacterias/efectos de los fármacos , Bacterias/aislamiento & purificación , Análisis por Conglomerados , Fibrosis Quística/diagnóstico , ADN Bacteriano/genética , Electroforesis en Gel de Campo Pulsado , Variación Genética , Humanos , Incidencia , Metagenómica , Pruebas de Sensibilidad Microbiana , Microbiota , Reacción en Cadena de la Polimerasa , Infecciones por Pseudomonas/epidemiología , Infecciones por Pseudomonas/microbiología , Pseudomonas aeruginosa/efectos de los fármacos , Pseudomonas aeruginosa/genética , Pseudomonas aeruginosa/aislamiento & purificación , ARN Ribosómico/genética , ARN Ribosómico/metabolismo , ARN Ribosómico 16S/genética , ARN Ribosómico 16S/metabolismoRESUMEN
The occurrence of Stenotrophomonas maltophilia was monitored in organic amendments and agricultural soils from various sites in France and Tunisia. S. maltophilia was detected in horse and bovine manures, and its abundance ranged from 0.294 (±0.509) × 10(3) to 880 (±33.4) × 10(3) CFU (g drywt)(-1) of sample. S. maltophilia was recovered from most tested soil samples (104/124). Its abundance varied from 0.33 (±0.52) to 414 (±50) × 10(3) CFU (g drywt)(-1) of soil and was not related to soil characteristics. Antibiotic resistance properties of a set of environmental strains were compared to a clinical set, and revealed a high diversity of antibiotic resistance profiles, given both the numbers of resistance and the phenotypes. Manure strains showed resistance phenotypes, with most of the strains resisting between 7 and 9 antibiotics. While French soil strains were sensitive to most antibiotics tested, some Tunisian strains displayed resistance phenotypes close to those of clinical French strains. Screening for metal resistance among 66 soil strains showed a positive relationship between antibiotic and metal resistance. However, the prevalence of antibiotic resistance phenotypes in the studied sites was not related to the metal content in soil samples.
Asunto(s)
Antibacterianos/farmacología , Farmacorresistencia Bacteriana , Microbiología del Suelo , Stenotrophomonas maltophilia/efectos de los fármacos , Stenotrophomonas maltophilia/aislamiento & purificación , Animales , Carga Bacteriana , Bovinos , Recuento de Colonia Microbiana , Francia , Caballos , Estiércol/microbiología , Metales/análisis , Metales/farmacología , Pruebas de Sensibilidad Microbiana , Suelo/química , TúnezRESUMEN
The efficacy of a wastewater treatment lagoon (WWTL) at preventing the spread of Pseudomonas aeruginosa into natural aquatic habitats was investigated. A WWTL and its connected combined sewer and brook were exhaustively sampled. Physico-chemical analyses showed a stratification of the first pond according to pH, temperature and oxygen content. The P. aeruginosa counts partially matched this stratification with higher values among the bottom anaerobic waters of the first half of this pond. Genotyping of 494 WWTL P. aeruginosa strains was performed and led to the definition of 85 lineages. Dominant lineages were observed, with some being found all over the WWTL including the connected brook. IS5 was used as an indicator of genomic changes, and 1 to 12 elements were detected among 16 % of the strains. IS-driven lasR (genetic regulator) disruptions were detected among nine strains that were not part of the dominant lineages. These insertional mutants did not show significant elastase activities but showed better growth than the PAO1 reference strain in WWTL waters. Differences in growth patterns were related to a better survival of these mutants at an alkaline pH and a better ability at using some C-sources such as alanine. The opportunistic colonization of a WWTL by P. aeruginosa can involve several metabolic strategies which appeared lineage specific. Some clones appeared more successful than others at disseminating from a combined sewer toward the overflow of a WWTL.