IDENTIFICATION OF THE MECHANISM RESPONSIBLE FOR ATENNUATION OF RIFAMPICIN-PASSAGED FLAVOBACTERIUM PSYCHROPHILUM, ETIOLOGIC AGENT OF BACTERIAL COLDWATER DISEASE

Flavobacterium psychrophilum is the etiologic agent of bacterial coldwater disease (CWD) and rainbow trout fry syndrome (RTFS) in salmonids. Presently there are no licensed vaccines for this disease, but earlier work showed that a rifampicin-attenuated strain of F. psychrophilum CSF 259-93B.17 (B17) caused no disease while inducing protection against challenge with the virulent CSF 259-93 strain. Attenuation by passage with rifampicin has been described for several bacterial pathogens, but the mechanism of attenuation is unknown. We hypothesize that passage with rifampicin leads to an accumulation of genomic mutations that, by chance, decrease virulence. Consequently, we examined LPS, proteomic and single nucleotide polymorphism (SNP) differences for two pathogenic F. psychrophilum strains (CSF 259-93 and THC 02-90) that were passaged with and without rifampicin. No apparent changes in LPS and only a few proteomic differences were observed among rifampicin-passaged strains relative to the wild-type strains. Rifampicin resistance was conveyed by expected mutations in rpoB, although affecting different portions of the gene. One rifampicin-passaged CSF 259-93 strain (CR) demonstrated attenuation (4% mortality) in challenged fish, but only accumulated seven nonsynonymous SNPs compared to its parent strain. A CSF 259-93 strain passaged without rifampicin (CN) was partially attenuated (28% mortality) compared to the parent strain (54.5% mortality). In addition to a Ser492Phe rpoB mutation and a proteomic changes, the CR strain exhibited changed colony morphology and decreased gliding motility, similarly to the B17 strain. The opposite was observed among THC 02-90 wild-type and passaged strains with no significant changes in fish mortalities, despite numerous SNPs leading to nonsynonymous amino acid changes and accumulated by these strains during passage with (n= 174) and without rifampicin (n= 126). While only four SNPs leading to nonsynonymous amino acid substitution significantly attenuated the CR and CN strains, a specific Ser492Phe rpoB mutation may contribute to differential gene regulation and further attenuation of the CR strain

qPCR Estimates of trfA and 16S rRNA concentrations

The data provided are the estimates that resulted from raw qPCR fluorescence data (available upon request). The data are those used in the analyses described in the associated manuscript. See the ReadMe file for column descriptions

Evolving Microbial Communities in Cellulose-Fed Microbial Fuel Cell

The abundance of cellulosic wastes make them attractive source of energy for producing electricity in microbial fuel cells (MFCs). However, electricity production from cellulose requires obligate anaerobes that can degrade cellulose and transfer electrons to the electrode (exoelectrogens), and thus most previous MFC studies have been conducted using two-chamber systems to avoid oxygen contamination of the anode. Single-chamber, air-cathode MFCs typically produce higher power densities than aqueous catholyte MFCs and avoid energy input for the cathodic reaction. To better understand the bacterial communities that evolve in single-chamber air-cathode MFCs fed cellulose, we examined the changes in the bacterial consortium in an MFC fed cellulose over time. The most predominant bacteria shown to be capable electron generation was Firmicutes, with the fermenters decomposing cellulose Bacteroidetes. The main genera developed after extended operation of the cellulose-fed MFC were cellulolytic strains, fermenters and electrogens that included: Parabacteroides, Proteiniphilum, Catonella and Clostridium. These results demonstrate that different communities evolve in air-cathode MFCs fed cellulose than the previous two-chamber reactors

Data from: Persistence of antibiotic resistance plasmids in bacterial biofilms

The emergence and spread of antibiotic resistance is a crisis in health care today. Antibiotic resistance is often horizontally transferred to susceptible bacteria by means of multi-drug resistance plasmids that may or may not persist in the absence of antibiotics. Because bacterial pathogens often grow as biofilms, there is a need to better understand the evolution of plasmid persistence in these environments. Here we compared the evolution of plasmid persistence in the pathogen Acinetobacter baumannii when grown under antibiotic selection in biofilms versus well-mixed liquid cultures. After four weeks, clones in which the plasmid was more stably maintained in the absence of antibiotic selection were present in both populations. On average plasmid persistence increased more in liquid batch cultures, but variation in the degree of persistence was greater among biofilm-derived clones. The results of this study show for the first time that the persistence of MDR plasmids improves in biofilm

Additional file 1: Figure S1. of Potential mechanisms of attenuation for rifampicin-passaged strains of Flavobacterium psychrophilum

SDS-PAGE analysis of carbohydrate extractions from different F. psychrophilum CSF 259-93 and THC 02-90 strains. Table S1: Single nucleotide polymorphisms (SNPs) from F. psychrophilum THC 02-90 strain passaged without rifampicin (TN). Table S2: Single nucleotide polymorphisms (SNPs) from F. psychrophilum THC 02-90 strain passaged with rifampicin (TR). Table S3: DNA methylation motifs unique for the rifampicin passaged CSF 259-93 strain (CR). Table S4: DNA methylation motifs unique for the rifampicin passaged THC 02-90 strain (TR). (DOCX 637 kb

Supplemental Material, Julie_reprod_Sci_Suppl_Table_1 - Properties of Epithelial Cells and Vaginal Secretions in Pregnant Women When <i>Lactobacillus crispatus</i> or <i>Lactobacillus iners</i> Dominate the Vaginal Microbiome

<p> Supplemental Material, Julie_reprod_Sci_Suppl_Table_1 for Properties of Epithelial Cells and Vaginal Secretions in Pregnant Women When <i>Lactobacillus crispatus</i> or <i>Lactobacillus iners</i> Dominate the Vaginal Microbiome by Julie Leizer, Dimitrios Nasioudis, Larry J. Forney, G. Maria Schneider, Karol Gliniewicz, Allison Boester, and Steven S. Witkin in Reproductive Sciences </p

Additional file 1: Figure S1. of Potential mechanisms of attenuation for rifampicin-passaged strains of Flavobacterium psychrophilum

SDS-PAGE analysis of carbohydrate extractions from different F. psychrophilum CSF 259-93 and THC 02-90 strains. Table S1: Single nucleotide polymorphisms (SNPs) from F. psychrophilum THC 02-90 strain passaged without rifampicin (TN). Table S2: Single nucleotide polymorphisms (SNPs) from F. psychrophilum THC 02-90 strain passaged with rifampicin (TR). Table S3: DNA methylation motifs unique for the rifampicin passaged CSF 259-93 strain (CR). Table S4: DNA methylation motifs unique for the rifampicin passaged THC 02-90 strain (TR). (DOCX 637 kb

Supplemental Material, Julie_Reprod_SCi_Suppl_Table_2 - Properties of Epithelial Cells and Vaginal Secretions in Pregnant Women When <i>Lactobacillus crispatus</i> or <i>Lactobacillus iners</i> Dominate the Vaginal Microbiome

<p> Supplemental Material, Julie_Reprod_SCi_Suppl_Table_2 for Properties of Epithelial Cells and Vaginal Secretions in Pregnant Women When <i>Lactobacillus crispatus</i> or <i>Lactobacillus iners</i> Dominate the Vaginal Microbiome by Julie Leizer, Dimitrios Nasioudis, Larry J. Forney, G. Maria Schneider, Karol Gliniewicz, Allison Boester, and Steven S. Witkin in Reproductive Sciences </p