Genomic analysis of the diversity,antimicrobial resistance and virulence potential of clinical Campylobacter jejuni and Campylobacter coli strains from Chile

Campylobacter jejuni and Campylobacter coli are the leading cause of human gastroenteritis in the industrialized world and an emerging threat in developing countries. The incidence of campylobacteriosis in South America is greatly underestimated, mostly due to the lack of adequate diagnostic methods. Accordingly, there is limited genomic and epidemiological data from this region. In the present study, we performed a genome-wide analysis of the genetic diversity, virulence, and antimicrobial resistance of the largest collection of clinical C. jejuni and C. coli strains from Chile available to date (n = 81), collected in 2017–2019 in Santiago, Chile. This culture collection accounts for more than one third of the available genome sequences from South American clinical strains. cgMLST analysis identified high genetic diversity as well as 13 novel STs and alleles in both C. jejuni and C. coli. Pangenome and virulome analyses showed a differential distribution of virulence factors, including both plasmid and chromosomally encoded T6SSs and T4SSs. Resistome analysis predicted widespread resistance to fluoroquinolones, but low rates of erythromycin resistance. This study provides valuable genomic and epidemiological data and highlights the need for further genomic epidemiology studies in Chile and other South American countries to better understand molecular epidemiology and antimicrobial resistance of this emerging intestinal pathogen.     

A quantitative inventory of global soniferous fish diversity

Reviews in Fish Biology and Fisheries - Sound production in fishes is vital to an array of behaviors including territorial defense, reproduction, and competitive feeding. Unfortunately, recent...     

Modular organizations of novel cetacean papillomaviruses

The phylogenetic position of cetacean papillomaviruses (PVs: Omikron-PVs and Upsilon-PVs) varies depending on the region of the genome analysed. They cluster together with Alpha-PVs when analysing early genes and with Xi-PVs and Phi-PVs when analysing late genes. We cloned and sequenced the complete genomes of five novel PVs, sampled from genital and oesophageal lesions of free-ranging cetaceans: Delphinus delphis (DdPV1), Lagenorhynchus acutus (TtPV3 variant), and Phocoena phocoena (PphPV1, PphPV2, and PphPV3). Using Maximum Likelihood and Bayesian approaches, all cetacean PVs constituted a monophyletic group with Alpha-, Omega-, and Dyodelta-PVs as inferred from E1-E2 early genes analyses, thus matching the shared phenotype of mucosal tropism. However, cetacean PVs, with the exception of PphPV3, were the closest relatives of Xi-PVs and Phi-PVs in L2-L1 late genes analyses, isolated from cow and goat, thus reflecting the close relationship between Cetacea and Artiodactyla. Our results are compatible with a recombination between ancestral PVs infecting the Cetartiodactyla lineage. Our study supports a complex evolutionary scenario with multiple driving forces for PV diversification, possibly including recombination and also interspecies transmission.     

Specific PCR primers directed to identify cryI and cryIII genes within a Bacillus thuringiensis strain collection.

In this paper we describe a PCR strategy that can be used to rapidly identify Bacillus thuringiensis strains that harbor any of the known cryI or cryIII genes. Four general PCR primers which amplify DNA fragments from the known cryI or cryIII genes were selected from conserved regions. Once a strain was identified as an organism that contains a particular type of cry gene, it could be easily characterized by performing additional PCR with specific cryI and cryIII primers selected from variable regions. The method described in this paper can be used to identify the 10 different cryI genes and the five different cryIII genes. One feature of this screening method is that each cry gene is expected to produce a PCR product having a precise molecular weight. The genes which produce PCR products having different sizes probably represent strains that harbor a potentially novel cry gene. Finally, we present evidence that novel crystal genes can be identified by the method described in this paper.     

CO2 Exchange in soil algal crusts occurring in the trachypogon savannas of the Orinoco Llanos,Venezuela

CO₂ exchange between the atmosphere and soil algal crusts of the Trachypogon savannas of the Orinoco Llanos has been analyzed using an open gas exchange system. These savannas encompass a wide range of physiognomic types, from herbaceous communities to savanna woodlands. A maximum CO₂ flux of 0.207 mg m^-2 s^-1 was measured in the crusts of the Guanipa savannas, while in the other examined crusts (0.035–0.105 mg m^-2 s^-1) the flux was similar to values reported for terrestrial algae. The CO₂ flux data were statistically fitted to the photosynthetically active radiation by a logarithmic relationship, and the photosynthetic efficiencies of the crusts were compared. The activation energy calculated for the CO₂ fixation indicates that limitations by diffusion and photochemical processes were excluded in the Guanipa crusts (above 12 kcal mole^-1), whereas they were evident in the other crust studied. An optimum CO₂ incorporation as a function of the crust water potential was established and carbon gain strategies were proposed on the basis of the results and characteristics of the habitats.