RESUMEN
The high-consequence pathogen Bacillus anthracis causes human anthrax and often results in lethal infections without the rapid administration of effective antimicrobial treatment. Antimicrobial resistance profiling is therefore critical to inform post-exposure prophylaxis and treatment decisions, especially during emergencies such as outbreaks or where intentional release is suspected. Whole-genome sequencing using a rapid long-read sequencer can uncover antimicrobial resistance patterns if genetic markers of resistance are known. To identify genomic markers associated with antimicrobial resistance, we isolated B. anthracis derived from the avirulent Sterne strain with elevated minimal inhibitory concentrations to clarithromycin. Mutants were characterized both phenotypically through broth microdilution susceptibility testing and observations during culturing, as well as genotypically with whole-genome sequencing. We identified two different in-frame insertions in the L22 ribosomal protein-encoding gene rplV, which were subsequently confirmed to be involved in clarithromycin resistance through the reversion of the mutant gene to the parent (drug-susceptible) sequence. Detection of the rplV insertions was possible with rapid long-read sequencing, with a time-to-answer within 3 h. The mutations associated with clarithromycin resistance described here will be used in conjunction with known genetic markers of resistance for other antimicrobials to strengthen the prediction of antimicrobial resistance in B. anthracis.IMPORTANCEThe disease anthrax, caused by the pathogen Bacillus anthracis, is extremely deadly if not treated quickly and appropriately. Clarithromycin is an antibiotic recommended for the treatment and post-exposure prophylaxis of anthrax by the Centers for Disease Control and Prevention; however, little is known about the ability of B. anthracis to develop resistance to clarithromycin or the mechanism of that resistance. The characterization of clarithromycin-resistant isolates presented here provides valuable information for researchers and clinicians in the event of a release of the resistant strain. Additionally, knowledge of the genetic basis of resistance provides a foundation for susceptibility prediction through rapid genome sequencing to inform timely treatment decisions.
Asunto(s)
Carbunco , Antibacterianos , Bacillus anthracis , Claritromicina , Farmacorresistencia Bacteriana , Pruebas de Sensibilidad Microbiana , Secuenciación Completa del Genoma , Bacillus anthracis/genética , Bacillus anthracis/efectos de los fármacos , Claritromicina/farmacología , Antibacterianos/farmacología , Farmacorresistencia Bacteriana/genética , Carbunco/microbiología , Humanos , Mutación , Proteínas Bacterianas/genética , Proteínas Ribosómicas/genética , Genoma Bacteriano/genéticaRESUMEN
Previous studies have shown the sugarcane microbiome harbors diverse plant growth promoting microorganisms, including nitrogen-fixing bacteria (diazotrophs), which can serve as biofertilizers. The genomes of 22 diazotrophs from Colombian sugarcane fields were sequenced to investigate potential biofertilizers. A genome-enabled computational phenotyping approach was developed to prioritize sugarcane associated diazotrophs according to their potential as biofertilizers. This method selects isolates that have potential for nitrogen fixation and other plant growth promoting (PGP) phenotypes while showing low risk for virulence and antibiotic resistance. Intact nitrogenase (nif) genes and operons were found in 18 of the isolates. Isolates also encode phosphate solubilization and siderophore production operons, and other PGP genes. The majority of sugarcane isolates showed uniformly low predicted virulence and antibiotic resistance compared to clinical isolates. Six strains with the highest overall genotype scores were experimentally evaluated for nitrogen fixation, phosphate solubilization, and the production of siderophores, gibberellic acid, and indole acetic acid. Results from the biochemical assays were consistent and validated computational phenotype predictions. A genotypic and phenotypic threshold was observed that separated strains by their potential for PGP versus predicted pathogenicity. Our results indicate that computational phenotyping is a promising tool for the assessment of bacteria detected in agricultural ecosystems.
Asunto(s)
Proteínas Bacterianas/genética , Genoma Bacteriano , Bacterias Fijadoras de Nitrógeno/fisiología , Saccharum/microbiología , Agricultura , Farmacorresistencia Bacteriana/efectos de los fármacos , Farmacorresistencia Bacteriana/genética , Genómica/métodos , Klebsiella/genética , Klebsiella/aislamiento & purificación , Bacterias Fijadoras de Nitrógeno/efectos de los fármacos , Bacterias Fijadoras de Nitrógeno/genética , Bacterias Fijadoras de Nitrógeno/aislamiento & purificación , Oxidorreductasas/genética , Rizosfera , Microbiología del Suelo , Factores de Virulencia/genéticaRESUMEN
Members of the Klebsiella genus promote plant growth. We report here draft whole-genome sequences for 15 Klebsiella sp. isolates from sugarcane fields in the Cauca Valley of Colombia. The genomes of these isolates were characterized as part of a broader effort to evaluate their utility as endemic plant growth-promoting biofertilizers.