Antimicrobial-producing Pseudoalteromonas from the marine environment of Panama shows a high phylogenetic diversity and clonal structure

Pseudoalteromonas is a genus of marine bacteria often found in association with other organisms. Although several studies have examined Pseudoalteromonas diversity and their antimicrobial activity, its diversity in tropical environments is largely unexplored. We investigated the diversity of Pseudoalteromonasin marine environments of Panama using a multilocus phylogenetic approach. Furthermore we tested their antimicrobial capacity and evaluated the effect of recombination and mutation in shaping their phylogenetic relationships. The reconstruction of clonal relationships among 78 strains including 15 reference Pseudoalteromonas species revealed 43 clonal lineages, divided in pigmented and non-pigmented strains. In total, 39 strains displayed moderate to high activity against Gram-positive and Gram-negative bacteria and fungi. Linkage disequilibrium analyses showed that the Pseudoalteromonas strains of Panama have a highly clonal structure and that, although present, recombination is not frequent enough to break the association among alleles. This clonal structure is in contrast to the high rates of recombination generally reported for aquatic and marine bacteria.We propose that this structure is likely due to the symbiotic association with marine invertebrates of most strains analyzed. Our results also show that there are several putative new species of Pseudoalteromonas in Panama to be described.Pseudoalteromonas is a genus of marine bacteria often found in association with other organisms. Although several studies have examined Pseudoalteromonas diversity and their antimicrobial activity, its diversity in tropical environments is largely unexplored. We investigated the diversity of Pseudoalteromonasin marine environments of Panama using a multilocus phylogenetic approach. Furthermore we tested their antimicrobial capacity and evaluated the effect of recombination and mutation in shaping their phylogenetic relationships. The reconstruction of clonal relationships among 78 strains including 15 reference Pseudoalteromonas species revealed 43 clonal lineages, divided in pigmented and non-pigmented strains. In total, 39 strains displayed moderate to high activity against Gram-positive and Gram-negative bacteria and fungi. Linkage disequilibrium analyses showed that the Pseudoalteromonas strains of Panama have a highly clonal structure and that, although present, recombination is not frequent enough to break the association among alleles. This clonal structure is in contrast to the high rates of recombination generally reported for aquatic and marine bacteria.We propose that this structure is likely due to the symbiotic association with marine invertebrates of most strains analyzed. Our results also show that there are several putative new species of Pseudoalteromonas in Panama to be described

Multidrogorresistencia de Salmonella infantis en Perú: un estudio mediante secuenciamiento de nueva generación

Objetivos. Describir los patrones fenotípicos y genotípicos de la resistencia antimicrobiana de Salmonella Infantis en Perú. Materiales y Métodos. Se analizaron 297 cepas de Salmonella sp. remitidas al Instituto Nacional de Salud (INS) en el periodo 2014-2016. Las cepas fueron caracterizadas fenotípicamente mediante pruebas microbiológicas, serológicas y de susceptibilidad antimicrobiana. En base a los patrones de resistencia antimicrobiana se seleccionaron 46 cepas que fueron caracterizadas genéticamente mediante secuenciamiento de nueva generación. Resultados. Se identificaron 193/297 (65,0%) cepas de Salmonella Infantis, de la cuales 143 (74,1%) fueron multidrogorresistentes productoras de betalactamasas de espectro extendido (BLEE). Con el secuenciamiento genómico se evidenció un nuevo perfil para Salmonella Infantis, además, se identificó la presencia de 15 diferentes determinantes genéticos de resistencia a los antimicrobianos codificados en cromosoma bacteriano y cinco codificados en un megaplásmido. Los patrones de resistencia fenotípicos y genotípicos coincidieron, a excepción de la ceftazidima. Asimismo, las 46 cepas presentaron resistencia y/o sensibilidad disminuida a las quinolonas. Conclusiones. Salmonella Infantis se ha convertido en una de las serovariedades más frecuentemente referidas al INS, la cual incluye cepas multidrogoresistentes productoras de BLEE con resistencia a las quinolonas. Finalmente, se reafirma la relevancia del secuenciamiento de nueva generación en la caracterización de nuevas variantes de patógenos de importancia para la salud pública y su uso potencial en los sistemas de vigilancia de resistencia antimicrobiana

Microevolution of Pandemic Vibrio parahaemolyticus Assessed by the Number of Repeat Units in Short Sequence Tandem Repeat Regions

The emergence of the pandemic strain Vibrio parahaemolyticus O3:K6 in 1996 caused a large increase of diarrhea outbreaks related to seafood consumption in Southeast Asia, and later worldwide. Isolates of this strain constitutes a clonal complex, and their effectual differentiation is possible by comparison of their variable number tandem repeats (VNTRs). The differentiation of the isolates by the differences in VNTRs will allow inferring the population dynamics and microevolution of this strain but this requires knowing the rate and mechanism of VNTRs' variation. Our study of mutants obtained after serial cultivation of clones showed that mutation rates of the six VNTRs examined are on the order of 10−4 mutant per generation and that difference increases by stepwise addition of single mutations. The single stepwise mutation (SSM) was deduced because mutants with 1, 2, 3, or more repeat unit deletions or insertions follow a geometric distribution. Plausible phylogenetic trees are obtained when, according to SSM, the genetic distance between clusters with different number of repeats is assessed by the absolute differences in repeats. Using this approach, mutants originated from different isolates of pandemic V. parahaemolyticus after serial cultivation are clustered with their parental isolates. Additionally, isolates of pandemic V. parahaemolyticus from Southeast Asia, Tokyo, and northern and southern Chile are clustered according their geographical origin. The deepest split in these four populations is observed between the Tokyo and southern Chile populations. We conclude that proper phylogenetic relations and successful tracing of pandemic V. parahaemolyticus requires measuring the differences between isolates by the absolute number of repeats in the VNTRs considered

Hidden biodiversity in Neotropical streams: DNA barcoding uncovers high endemicity of freshwater macroinvertebrates at small spatial scales.

Aquatic macroinvertebrates play a crucial role in freshwater ecosystems, but their diversity remains poorly known, particularly in the tropics. This "taxonomic void" limits our understanding of biodiversity patterns and processes in freshwater ecosystems, and the scale at which they operate. We used DNA barcoding to estimate lineage diversity (and the diversity of unique haplotypes) in 224 specimens of freshwater macroinvertebrates at a small spatial scale within the Panama Canal Watershed (PCW). In addition, we compiled available barcoding data to assess macroinvertebrate diversity at a broader spatial scale spanning the Isthmus of Panama. Consistently across two species delimitation algorithms (i.e., ABGD and GMYC), we found high lineage diversity within the PCW, with ~ 100-106 molecular operational taxonomic units (MOTUs) across 168 unique haplotypes. We also found a high lineage diversity along the Isthmus of Panama, but this diversity peaked within the PCW. However, our rarefaction/extrapolation approach showed that this diversity remains under-sampled. As expected, these results indicate that the diversity of Neotropical freshwater macroinvertebrates is higher than previously thought, with the possibility of high endemicity even at narrow spatial scales. Consistent with previous work on aquatic insects and other freshwater taxa in this region, geographic isolation is likely a main factor shaping these patterns of diversity. However, other factors such as habitat variability and perhaps local adaptation might be reshaping these patterns of diversity at a local scale. Although further research is needed to better understand the processes driving diversification in freshwater macroinvertebrates, we suggest that Neotropical streams hold a high proportion of hidden biodiversity. Understanding this diversity is crucial in the face of increasing human disturbance

Frequency of observed and expected mutants according to a geometric distribution, with 1, 2, 3, or 4 repeat unit changes for each of the clones examined.

<p>The expected frequency of mutants according to geometric distribution is shown in bold italics.</p

Frequency of mutants with increasing differences in the number of repeat units.

<p>Black bars correspond to percent of predicted mutants. Combined bars correspond to percentage of observed mutants, white sections of bars correspond to deletions and gray to insertions.</p

Number of repeat units of six VNTR loci in four clones obtained from pandemic <i>Vibrio parahaemolyticus</i> strains VpKX and PMC57.5 and mutation rates after prolonged in vitro culturing.

<p>Mutat rate: Mutation rate (x 10⁴).</p

Phylogenetic tree of the mutants from the populations of the four different clones obtained after serial subculturing of pandemic <i>V. parahaemolyticus</i>.

<p>Tree was obtained by MST-Manhattan. The founder of each cluster is indicated above the clusters.</p