Consenso latinoamericano sobre la importancia de un sistema de gestión de datos microbiológicos para apoyar el programa de optimización de uso de antimicrobianos (PROA): Recomendaciones basadas en la evidencia. Parte 1 / Latin American consensus on the importance of a microbiological data management system to support antimicrobial use optimization program (PROA): Evidence-based recommendations. Part 1

La resistencia antimicrobiana es una amenaza para los logros de la medicina moderna y una de las medidas más efectivas para contrarrestarla son los programas de optimización del uso de antimicrobianos (PROA), en el cual el laboratorio de microbiología es uno de los principales componentes. La aplicación efectiva de tecnología de la información en los procesos es fundamental, pero existe poca información en Latinoamérica sobre el desarrollo y la articulación de las herramientas tecnológicas para apoyar los PROA. Este consenso hace recomendaciones sobre la gestión de los datos microbiológicos para la toma de decisiones. En la Parte I, se presentan las recomendaciones en cuanto al uso de un sistema informatizado de gestión de datos microbiológicos en la práctica clínica, los requerimientos de datos y de reporte en el laboratorio de microbiología, y los contenidos del sistema de gestión de calidad avanzado en el laboratorio. En la Parte II, se discuten los requerimientos de información para la gestión de PROA en estadios intermedios, iniciales y avanzados por el laboratorio y la farmacia; así como la integración del equipo de PROA con el Comité de Prevención y Control de Infecciones y la información para la gestión de PROA a nivel gerencial.

Antimicrobial resistance is a threat to the achievements of modern medicine and one of the most effective measures to counteract it is antimicrobial use optimization programs (AMS), in which the microbiology laboratory is one of the main components. The effective application of information technology in the processes is fundamental, but there is little information in Latin America on the development and articulation of technological tools to support AMSs. This consensus makes recommendations on the management of microbiological data for decision making. In Part I, recommendations on the use of a computerized microbiological data management system in clinical practice, data and reporting requirements in the microbiology laboratory, as well as the contents of the advanced quality management system in the laboratory are presented. In Part II, the information requirements for AMS management in intermediate, initial, and advanced stages by the laboratory and pharmacy are discussed; as well as the integration of the AMS team with the Infection Prevention and Control Committee and the information for AMS management at the management level.

Corynebacterium guaraldiae sp. nov.: a new species of Corynebacterium from human infections.

Non-diphtheria Corynebacterium species (NDC) belonging to the human skin and mucosa microbiota are frequently neglected as contaminants. However, reports of human infections by Corynebacterium spp. have increased considerably in recent years. In this study, a group of six NDC isolates of urine (n = 5) and sebaceous cyst (n = 1) from two South American countries were identified at genus level or misidentified based on API® Coryne and genetic/molecular analyses. The 16S rRNA (99.09-99.56%) and rpoB (96.18-97.14%) gene sequence similarities of the isolates were higher when compared with Corynebacterium aurimucosum DSM 44532 T. Multilocus sequence analysis (MLSA) indicated that these six NDC isolates compose a distinctive phylogenetic clade. Genome-based taxonomic analysis with the whole-genome sequences was able to separate these six isolates from other known Corynebacterium type strains. Average nucleotide identity (ANI), average amino acid identity (AAI), and digital DNA-DNA hybridization (dDDH) values between closely related type strains and the six isolates were considerably lower than the currently recommended threshold values for species circumscription. Phylogenetic and genomic taxonomy analyses indicated these microorganisms as a novel Corynebacterium species, for which we formally propose the name Corynebacterium guaraldiae sp. nov. with isolate 13T (= CBAS 827T = CCBH 35012T) as type strain.

Low microbiome diversity in threatened amphibians from two biodiversity hotspots.

Microbial diversity positively influences community resilience of the host microbiome. However, extinction risk factors such as habitat specialization, narrow environmental tolerances, and exposure to anthropogenic disturbance may homogenize host-associated microbial communities critical for stress responses including disease defense. In a dataset containing 43 threatened and 90 non-threatened amphibian species across two biodiversity hotspots (Brazil's Atlantic Forest and Madagascar), we found that threatened host species carried lower skin bacterial diversity, after accounting for key environmental and host factors. The consistency of our findings across continents suggests the broad scale at which low bacteriome diversity may compromise pathogen defenses in species already burdened with the threat of extinction.

A new Chiasmocleis (Anura: Microhylidae) from the eastern Guiana Shield with an amended definition of C. haddadi Peloso, Sturaro, Forlani, Gaucher, Motta, & Wheeler, 2014.

The existence of an unnamed (candidate) species from French Guiana and the state of Amapá (Brazil) closely related to Chiasmocleis haddadi has been hypothesized in previous DNA-based studies. With an integrative use of genetic, morphological and acoustic data we confirm that these populations are indeed distinct from C. haddadi and all other known congeners. We herein describe and name this new species, and amend the definition of C. haddadi since the type-series and its original diagnosis included specimens of the new species. Geographically, the new species occurs eastward of its sister species C. haddadi from which it can be distinguished by having a larger body, a proportionally smaller eye and a distinct dorsal colouration. We suspect that the new species breeds in the leaf litter and that tadpoles undergo endotrophic development whereas co-occurring C. haddadi and C. hudsoni lay clutches in the leaf litter nearby standing water of temporary ponds where exotrophic tadpoles complete their development. This new species is a new addition to the already long list of animals being endemic to the easternmost part of the Guiana Shield, a region identified as a singular bioregion within Amazonia by previous research.

The phylogeny of Dendropsophini (Anura: Hylidae: Hylinae).

The relationships of the hyline tribe Dendropsophini remain poorly studied, with most published analyses dealing with few of the species groups of Dendropsophus. In order to test the monophyly of Dendropsophini, its genera, and the species groups currently recognized in Dendropsophus, we performed a total evidence phylogenetic analysis. The molecular dataset included sequences of three mitochondrial and five nuclear genes from 210 terminals, including 12 outgroup species, the two species of Xenohyla, and 93 of the 108 recognized species of Dendropsophus. The phenomic dataset includes 46 terminals, one per species (34 Dendropsophus, one Xenohyla, and 11 outgroup species). Our results corroborate the monophyly of Dendropsophini and the reciprocal monophyly of Dendropsophus and Xenohyla. Some species groups of Dendropsophus are paraphyletic (the D. microcephalus, D. minimus, and D. parviceps groups, and the D. rubicundulus clade). On the basis of our results, we recognize nine species groups; for three of them (D. leucophyllatus, D. microcephalus, and D. parviceps groups) we recognize some nominal clades to highlight specific morphology or relationships and facilitate species taxonomy. We further discuss the evolution of oviposition site selection, where our results show multiple instances of independent evolution of terrestrial egg clutches during the evolutionary history of Dendropsophus.

Phylogenomics Reveals Ancient Gene Tree Discordance in the Amphibian Tree of Life.

Molecular phylogenies have yielded strong support for many parts of the amphibian Tree of Life, but poor support for the resolution of deeper nodes, including relationships among families and orders. To clarify these relationships, we provide a phylogenomic perspective on amphibian relationships by developing a taxon-specific Anchored Hybrid Enrichment protocol targeting hundreds of conserved exons which are effective across the class. After obtaining data from 220 loci for 286 species (representing 94% of the families and 44% of the genera), we estimate a phylogeny for extant amphibians and identify gene tree-species tree conflict across the deepest branches of the amphibian phylogeny. We perform locus-by-locus genealogical interrogation of alternative topological hypotheses for amphibian monophyly, focusing on interordinal relationships. We find that phylogenetic signal deep in the amphibian phylogeny varies greatly across loci in a manner that is consistent with incomplete lineage sorting in the ancestral lineage of extant amphibians. Our results overwhelmingly support amphibian monophyly and a sister relationship between frogs and salamanders, consistent with the Batrachia hypothesis. Species tree analyses converge on a small set of topological hypotheses for the relationships among extant amphibian families. These results clarify several contentious portions of the amphibian Tree of Life, which in conjunction with a set of vetted fossil calibrations, support a surprisingly younger timescale for crown and ordinal amphibian diversification than previously reported. More broadly, our study provides insight into the sources, magnitudes, and heterogeneity of support across loci in phylogenomic data sets.[AIC; Amphibia; Batrachia; Phylogeny; gene tree-species tree discordance; genomics; information theory.].

Description and phylogenetic relationships of a new trans-Andean species of Elachistocleis Parker 1927 (Amphibia, Anura, Microhylidae).

Elachistocleis is a Neotropical genus of microhylid frogs with 18 species, most of which occur east of the Andes in South America. Here, we present a new phylogeny of Gastrophryninae and describe and name a new species of Elachistocleis from southern Ecuador-the first to be found west of the Andes and also the first from Ecuador. Our phylogeny is based on DNA sequences of the mitochondrial genes 12S rRNA, 16S rRNA, COI, and the nuclear genes BDNF, cmyc2, H3A, 28S, SIA1, and Tyr. Elachistocleis araios sp. n., is the sister species of all other Elachistocleis. The finding of this taxon highlights the probability of the existence of more Elachistocleis species west of the Andes.

Ciprofloxacin-Resistant Kerstersia gyiorum Isolated From a Chronic Wound in Brazil: A Case Report.

The presence of Kerstersia gyiorum in lower leg wounds has been reported in case studies from several countries. OBJECTIVE: This study evaluated the antimicrobial susceptibility profile of K gyiorum isolated from a chronic wound. METHODS: An 85-year-old woman with chronic venous insufficiency presented to an intermediate care unit in Niteroi City, Rio de Janeiro, Brazil, with an instep chronic wound of 14 cm² with wound duration of 6 months. K gyiorum was identified by matrix-assisted laser desorption ionization-time of flight, confirmed by 16S rRNA partial sequence analysis, and classified as resistant for ciprofloxacin by reagent strips(minimum inhibitory concentration [MIC] = 32 µg/mL) and the broth macrodilution method (MIC = 8 µg/mL). Intermediate resistance for ciprofloxacin was verified by microscan (MIC = 2 µg/mL). CONCLUSION: The authors identified the first, to their knowledge, lower leg wound with K gyiorum in Brazil and verified that it was ciprofloxacin resistant.

Diversification history of clown tree frogs in Neotropical rainforests (Anura, Hylidae, Dendropsophus leucophyllatus group).

General consensus emphasizes that no single biological process can explain the patterns of species' distributions and diversification in the Neotropics. Instead, the interplay of several processes across space and time must be taken into account. Here we investigated the phylogenetic relationships and biogeographic history of tree frogs in the Dendropsophus leucophyllatus species group (Amphibia: Hylidae), which is distributed across Amazonia and the Atlantic rainforests. Using Next Generation Sequencing (NGS) and double digest restriction-site associated DNA (ddRADseq), we inferred phylogenetic relationships, species limits, and temporal and geographic patterns of diversification relative to the history of these biomes. Our results indicate that the D. leucophyllatus species group includes at least 14 independent lineages, which are currently arranged into ten described species. Therefore, a significant portion of species in the group are still unnamed. Different processes were associated to the group diversification history. For instance, the Andes uplift likely caused allopatric speciation for Cis-Andean species, whereas it may also be responsible for changes in the Amazonian landscape triggering parapatric speciation by local adaptation to ecological factors. Meanwhile, Atlantic Forest ancestors unable to cross the dry diagonal biomes after rainforest's retraction, evolved in isolation into different species. Diversification in the group began in the early Miocene, when connections between Atlantic Forest and the Andes (Pacific Dominion) by way of a south corridor were possible. The historical scenario in Amazonia, characterized by several speciation events and habitat heterogeneity, helped promoting diversification, resulting in the highest species diversity for the group. This marked species diversification did not happen in Atlantic Forest, where speciation is very recent (late Pliocene and Pleistocene), despite its remarkable climatic heterogeneity.

Resolving the taxonomic puzzle of Boana cinerascens (Spix, 1824), with resurrection of Hyla granosa gracilis Melin, 1941 (Anura: Hylidae).

Expeditions to unexplored or little explored places are important for discovering new species and also for collecting new samples (including specimens and tissues for DNA sequencing ) that may help resolve a plethora of taxonomic problems. In the 19th century, several naturalists explored a number of localities in Amazonia, describing species for which type material was deposited, mostly, in European museums of natural history. Some of these types were lost or destroyed in World War II and recent expeditions have focused on sampling new material from the type localities. material from Boana cinerascens, which allowed us to infer phylogenetic relationships of the Boana punctata group (i.e., green Boana), based on DNA sequence data, and to revaluate the status of B. cinerascens and its synonyms. We designate, redescribe and illustrate a neotype for B. cinerascens, which was described by Spix in 1824, from the Municipality of Tefé, State of Amazonas, Brazil. We revalidate, redescribe, and illustrate Hyla granosa gracilis Melin, 1941(= Boana gracilis). Corroborating previous studies, the green Boana were not recovered as a monophyletic group. Boana cinerascens is sister of B. gracilis plus a clade containing B. atlantica + B. punctata (both species not recovered as monophyletic).

A species-level total evidence phylogeny of the microteiid lizard family Alopoglossidae (Squamata: Gymnophthalmoidea).

Alopoglossidae is a family of Neotropical lizards composed of 23 species allocated in two genera (Alopoglossus and Ptychoglossus). There is a lack of knowledge about the phylogenetic relationships and systematics of this family. Published phylogenies that include alopoglossid species have very low taxon coverage within the family, and are usually based on limited character sampling. Considering these shortcomings, we infer the phylogenetic relationships of Alopoglossidae-including all but one species in the family-based on the combined analyses of DNA sequences and morphological characters. We use four loci (the mitochondrial 12S, 16S and ND4; the nuclear C-mos) and a matrix of 143 phenotypic characters from scutellation, tongue morphology, hemipenis morphology, and osteology. The dataset is analyzed with Maximum Parsimony, with four alternative weighting schemes: three under Extended Implied Weighting, and one with equal weighting. The respective resulting topologies are compared in a sensitivity analysis framework. Our analyses support the paraphyly of Ptychoglossus, with Alopoglossus nested within it. We provide an updated classification for the family, where Ptychoglossus Boulenger, 1890 is considered a junior synonym of Alopoglossus Boulenger, 1885.

Skull Morphology of the Lizard Ptychoglossus vallensis (Squamata: Alopoglossidae) With Comments on the Variation Within Gymnophthalmoidea.

In recent years, major changes have been proposed for the phylogenetic relationships within the Gymnophthalmoidea, including the description of Alopoglossidae. Recent studies relied primarily on molecular data and have not accounted for evidence from alternative sources, such as morphology. In this study, we provide a detailed bone-by-bone description of the skull of Ptychoglossus vallensis and compare this species with other gymnophthalmoideans. The description was based on 10 cleared-and-stained specimens, four disarticulated skulls, and computed microtomography data of P. vallensis. Most recent phylogenetic hypothesis for the Gymnophthalmoidea was used as a framework to compare the skull of P. vallensis with other species of the Alopoglossidae, Gymnophthalmidae, and Teiidae. Marked similarities between alopoglossids and gymnophthalmids were observed in contrast to teiids, probably due to convergence generated by miniaturization. We also qualitatively analyzed the kinesis of the skull of P. vallensis concluding that is highly akinetic, a trait commonly evolved in fossorial, primarily burrowing squamates. We also describe one unique osteological feature for Alopoglossidae that is not known in any other squamate group. Anat Rec, 302:1074-1092, 2019. © 2018 Wiley Periodicals, Inc.

Multiple connections between Amazonia and Atlantic Forest shaped the phylogenetic and morphological diversity of Chiasmocleis Mehely, 1904 (Anura: Microhylidae: Gastrophryninae).

Chiasmocleis is the most species-rich genus of Neotropical microhylids. Herein, we provide the first comprehensive multilocus phylogeny for the genus, including all but 3 of the 34 recognized species and multiple individuals per species. We discuss cryptic speciation, species discovery, patterns of morphological evolution, and provide a historical biogeographic analysis to account for the current distribution of the genus. Diversification of Chiasmocleis from other New World microhylids began during the Eocene, app. 40 mya, in forested areas, and current diversity seems to be a product of recurrent connections between the Atlantic Forest and Amazonia. Small-sized species evolved independently three times in Chiasmocleis. Furthermore, the extremely small-bodied (i.e. miniaturized) species with associated loss of digits, phalanges, and pectoral girdle cartilages evolved only once and are restricted to Amazonia. Using the phylogeny, we recognized three subgenera within Chiasmocleis: Chiasmocleis Méhely, 1904, Relictus subg. nov., and Syncope Walker, 1973. The recognition of the subgenus Syncope informs future research on patterns of miniaturization in the genus, and the subgenus Relictus highlights isolation of an endemic and species-poor lineage to the Atlantic Forest, early (about 40 mya) in the history of Chiasmocleis.

Comparative analyses of species delimitation methods with molecular data in snappers (Perciformes: Lutjaninae).

The integration of approaches that allow the incorporation of stochasticity of gene histories with phylogenetic methods resulted in new approaches for the old issue of species delimitation. Nevertheless, coalescent methods seem problematic for taxa with large effective population size and shallow temporal diversification (like marine fishes). Here, we investigate the performance of single-locus (cytochrome oxidase 1, commonly used in DNA barcoding initiatives) methods for molecular species delimitation in snappers of Lutjaninae from the Western Atlantic and Pacific Eastern. Our results show incongruences among methods. ABGD, PTP and mPTP trend towards a lower number of estimated species. Phylogenetic-coalescent methods with single threshold were majority congruent for a same number of lineages. On the other hand, algorithms with multiple thresholds tend to estimate a higher number of potential species. We do not endorse the use of single-locus for species delimitation, but we do reinforce that single-locus data is sufficient to flag many problems.

A new species of Phyzelaphryne Heyer, 1977 (Anura: Eleutherodactylidae) from the Japurá River basin, with a discussion of the diversity and distribution of the genus.

We describe and name the second species of Phyzelaphryne (Brachycephaloidea, Eleutherodactylidae), from northwestern Brazilian Amazonia. Phyzelaphryne nimio sp. nov. is distinguished from its only congener, Phyzelaphryne miriamae, by its smaller body size and the anatomy of the carpal and metacarpal regions, with relatively larger (sometimes fused) supernumerary carpal and metacarpal tubercles. Molecular phylogenetic analyses based on fragments of the mitochondrial genes 16S rRNA and COI suggest that the currently known distribution of the species is restricted to its type locality and other areas within Estação Ecológica Juami-Japurá, state of Amazonas, Brazil. Based on molecular, morphological and bioacoustic evidence, we assigned other specimens recently collected in Parque Nacional do Jaú, state of Amazonas, Brazil, to P. miriamae, extending the species' known geographic distribution north of the Amazon River.

Amphibians and reptiles from Floresta Nacional de Pau-Rosa, Amazonas, Brazil: an important protected area at the heart of Amazonia / Anfíbios e répteis da Floresta Nacional de Pau-Rosa, Amazonas, Brasil: uma importante área protegida no coração da Amazônia

ABSTRACT Amazonia harbors the largest and most diverse tropical forest in the world, but knowledge about the species diversity of the region is still far from ideal. Given this low level of faunal and floral knowledge, we present an annotated list of the species of amphibians and reptiles found in Floresta Nacional do Pau-Rosa (FNPR), along the Rio Paraconi, municipality of Maués, state of Amazonas, Brazil. Herpetofauna of the FNPR was sampled with pitfall traps, active search and occasional encounters from February 18 to March 28, 2009. A total of 270 specimens were collected, representing 39 species of amphibians and 24 species of reptiles. At least seven of the species collected at FNPR represented, at the time, unnamed taxa (four of which have now been named). The number of taxa collected and the high number of unnamed taxa highlight the importance of this area in terms of biodiversity and as a priority for conservation. We also discuss about the amphibian diversity in Amazonia.

RESUMO A Amazônia engloba a maior e mais diversa floresta tropical do mundo, mas o conhecimento sobre a diversidade de espécies da região ainda está longe do ideal. Apresentamos aqui uma lista comentada das espécies de anfíbios e répteis encontradas na Floresta Nacional de Pau-Rosa (FNPR), ao longo do Rio Paraconi, município de Maués, estado do Amazonas, Brasil. Espécimes da FNPR foram coletados com armadilhas de queda, busca ativa e encontros ocasionais de 18 fevereiro a 28 março de 2009. Um total de 270 espécimes foram coletados, o que representou 39 espécies de anfíbios e 24 espécies de répteis. Pelo menos sete das espécies coletadas na FNPR representaram, na época, táxons sem nome (quatro dos quais já foram nomeados). O número de exemplares recolhidos e o elevado número de táxons destaca a importância desta área em termos de biodiversidade e como uma área prioritária para a conservação. Nós também discutimos a diversidade de anfíbios na Amazônia.

Nomenclatural stability does not justify recognition of paraphyletic taxa: A response to Scherz et al. (2016).

Peloso et al. (2015: PELOSO) published a comprehensive phylogenetic study of the frog family Microhylidae, which resulted in the discovery that several taxa were not monophyletic. To remedy this, a series of nomenclatural changes were proposed (several generic synonymies and two new subfamilies named). A recent study published in this journal by Scherz et al. (2016: SCHERZ), provided a novel phylogeny for the Malagasy subfamily Cophylinae. SCHERZ dispute the analyses and taxonomic conclusions of PELOSO. Their study is, however, based on substantial reduction of data from the PELOSO study, limited addition of new data, and different analytical methods. In spite of the fact that their own results are consistent with the taxonomy of PELOSO, SCHERZ reject that conservative taxonomy and suggest the revalidation of Platypelis (from the synonymy of Cophyla), the revalidation of Stumpffia (from the synonymies of Rhombophryne), and the creation of at least two new genera (only one named therein). In doing so, SCHERZ accept the recognition of likely paraphyletic taxa, with Stumpffia paraphyletic in their parsimony analysis. Herein, we provide a response to several points raised in SCHERZ: (1) we discuss issues with their interpretation (and selective use) of available phylogenetic and phenotypic evidence; (2) and provide a new phylogenetic analysis of all the data in PELOSO and SCHERZ combined. In the new analysis Stumpffia is paraphyletic with respect to Rhombophryne, whereas Cophyla and Platypelis are both monophyletic and sister taxa. We provide a case for the use of the taxonomy suggested in PELOSO.