Host Resistance, Genomics and Population Dynamics in a Salmonella Enteritidis and Phage System.

Bacteriophages represent an alternative solution to control bacterial infections. When interacting, bacteria and phage can evolve, and this relationship is described as antagonistic coevolution, a pattern that does not fit all models. In this work, the model consisted of a microcosm of Salmonella enterica serovar Enteritidis and φSan23 phage. Samples were taken for 12 days every 48 h. Bacteria and phage samples were collected; and isolated bacteria from each time point were challenged against phages from previous, contemporary, and subsequent time points. The phage plaque tests, with the genomics analyses, showed a mutational asymmetry dynamic in favor of the bacteria instead of antagonistic coevolution. This is important for future phage-therapy applications, so we decided to explore the population dynamics of Salmonella under different conditions: pressure of one phage, a combination of phages, and phages plus an antibiotic. The data from cultures with single and multiple phages, and antibiotics, were used to create a mathematical model exploring population and resistance dynamics of Salmonella under these treatments, suggesting a nonlethal, growth-inhibiting antibiotic may decrease resistance to phage-therapy cocktails. These data provide a deep insight into bacterial dynamics under different conditions and serve as additional criteria to select phages and antibiotics for phage-therapy.

Phage ΦPan70, a Putative Temperate Phage, Controls Pseudomonas aeruginosa in Planktonic, Biofilm and Burn Mouse Model Assays.

Pseudomonas aeruginosa is one of the Multi-Drug-Resistant organisms most frequently isolated worldwide and, because of a shortage of new antibiotics, bacteriophages are considered an alternative for its treatment. Previously, P. aeruginosa phages were isolated and best candidates were chosen based on their ability to form clear plaques and their host range. This work aimed to characterize one of those phages, ΦPan70, preliminarily identified as a good candidate for phage-therapy. We performed infection curves, biofilm removal assays, transmission-electron-microscopy, pulsed-field-gel-electrophoresis, and studied the in vivo ΦPan70 biological activity in the burned mouse model. ΦPan70 was classified as a member of the Myoviridae family and, in both planktonic cells and biofilms, was responsible for a significant reduction in the bacterial population. The burned mouse model showed an animal survival between 80% and 100%, significantly different from the control animals (0%). However, analysis of the ΦPan70 genome revealed that it was 64% identical to F10, a temperate P. aeruginosa phage. Gene annotation indicated ΦPan70 as a new, but possible temperate phage, therefore not ideal for phage-therapy. Based on this, we recommend genome sequence analysis as an early step to select candidate phages for potential application in phage-therapy, before entering into a more intensive characterization.

Molecular characterization of Salmonella paratyphi B dT+ and Salmonella Heidelberg from poultry and retail chicken meat in Colombia by pulsed-field gel electrophoresis.

Salmonella Paratyphi B dT+ variant (also termed Salmonella Java) and Salmonella Heidelberg are pathogens of public health importance that are frequently isolated from poultry. As a step toward implementing the Colombian Integrated Program for Antimicrobial Resistant Surveillance, this study characterized molecular patterns of Salmonella Paratyphi B dT+ and Salmonella Heidelberg isolated from poultry farms, fecal samples, and retail chicken meat using pulsed-field gel electrophoresis (PFGE). The objective of this study was to determine the genetic relationship among isolates and to determine potential geographically predominant genotypes. Based on PFGE analysis, both serovars exhibited high heterogeneity: the chromosomal DNA fingerprints of 82 Salmonella Paratyphi B dT+ isolates revealed 42 PFGE patterns, whereas the 21 isolates of Salmonella Heidelberg revealed 10 patterns. Similar genotypes of both serovars were demonstrated to be present on farms and in retail outlets. For Salmonella Paratyphi B dT+, closely genetically related strains were found among isolates coming from different farms and different integrated poultry companies within two departments (Santander and Cundinamarca) and also from farms located in the two geographically distant departments. For Salmonella Heidelberg, there were fewer farms with genetically related isolates than for Salmonella Paratyphi B dT+. A possible dissemination of similar genotypes of both serovars along the poultry production chain is hypothesized, and some facilitating factors existing in Colombia are reviewed.

Co-evolutionary dynamics of the bacteria Vibrio sp. CV1 and phages V1G, V1P1, and V1P2: implications for phage therapy.

Bacterial infections are the second largest cause of mortality in shrimp hatcheries. Among them, bacteria from the genus Vibrio constitute a major threat. As the use of antibiotics may be ineffective and banned from the food sector, alternatives are required. Historically, phage therapy, which is the use of bacteriophages, is thought to be a promising option to fight against bacterial infections. However, as for antibiotics, resistance can be rapidly developed. Since the emergence of resistance is highly undesirable, a formal characterization of the dynamics of its acquisition is mandatory. Here, we explored the co-evolutionary dynamics of resistance between the bacteria Vibrio sp. CV1 and the phages V1G, V1P1, and V1P2. Single-phage treatments as well as a cocktail composed of the three phages were considered. We found that in the presence of a single phage, bacteria rapidly evolved resistance, and the phages decreased their infectivity, suggesting that monotherapy may be an inefficient treatment to fight against Vibrio infections in shrimp hatcheries. On the contrary, the use of a phage cocktail considerably delayed the evolution of resistance and sustained phage infectivity for periods in which shrimp larvae are most susceptible to bacterial infections, suggesting the simultaneous use of multiple phages as a serious strategy for the control of vibriosis. These findings are very promising in terms of their consequences to different industrial and medical scenarios where bacterial infections are present.

Implementing a cumulative supermatrix approach for a comprehensive phylogenetic study of the Teloschistales (Pezizomycotina, Ascomycota).

The resolution of the phylogenetic relationships within the order Teloschistales (Ascomycota, lichen-forming-fungi), with nearly 2000 known species and outstanding phenotypic diversity, has been hindered by the limitation in the resolving power that single-locus or two-locus phylogenetic studies have provided to date. In this context, an extensive taxon sampling within the Teloschistales with more loci (especially nuclear protein-coding genes) was needed to confront the current taxonomic delimitations and to understand evolutionary trends within this order. Comprehensive maximum likelihood and bayesian analyses were performed based on seven loci using a cumulative supermatrix approach, including protein-coding genes RPB1 and RPB2 in addition to nuclear and mitochondrial ribosomal RNA-coding genes. We included 167 taxa representing 12 of the 15 genera recognized within the currently accepted Teloschistineae, 22 of the 43 genera within the Physciineae, 49 genera of the closely related orders Lecanorales, Lecideales, and Peltigerales, and the dubiously placed family Brigantiaeaceae and genus Sipmaniella. Although the progressive addition of taxa (cumulative supermatrix approach) with increasing amounts of missing data did not dramatically affect the loss of support and resolution, the monophyly of the Teloschistales in the current sense was inconsistent, depending on the loci-taxa combination analyzed. Therefore, we propose a new, but provisional, classification for the re-circumscribed orders Caliciales and Teloschistales (previously referred to as Physciineae and Teloschistineae, respectively). We report here that the family Brigantiaeaceae, previously regarded as incertae sedis within the subclass Lecanoromycetidae, and Sipmaniella, are members of the Teloschistales in a strict sense. Within this order, one lineage led to the diversification of the mostly epiphytic crustose Brigantiaeaceae and Letrouitiaceae, with a circumpacific center of diversity and found mostly in the tropics. The other main lineage led to another epiphytic crustose family, mostly tropical, and with an Australasian center of diversity--the Megalosporaceae--which is sister to the mainly rock-inhabiting, cosmopolitan, and species rich Teloschistaceae, with a diversity of growth habits ranging from crustose to fruticose. Our results confirm the use of a cumulative supermatrix approach as a viable method to generate comprehensive phylogenies summarizing relationships of taxa with multi-locus to single locus data.