Blacklegged ticks (Ixodes scapularis) are one of the most important pathogen vectors in the United States, responsible for transmitting Lyme disease and other tick‐borne diseases. The structure of a ...host's microbial community has the potential to affect the ecology and evolution of the host. We employed high‐throughput sequencing of the 16S rRNA gene V3‐V4 hypervariable regions in the first study to investigate the tick microbiome across all developmental stages (larvae, nymphs, adults). In addition to field‐collected life stages, newly hatched laboratory‐reared larvae were studied to determine the baseline microbial community structure and to assess transovarial transmission. We also targeted midguts and salivary glands due to their importance in pathogen maintenance and transmission. Over 100 000 sequences were produced per life stage replicate. Rickettsia was the most abundant bacterial genus across all sample types matching mostly the Ixodes rickettsial endosymbionts, and its proportion decreased as developmental stage progressed, with the exception of adult females that harboured a mean relative abundance of 97.9%. Laboratory‐reared larvae displayed the lowest bacterial diversity, containing almost exclusively Rickettsia. Many of the remaining bacteria included genera associated with soil, water and plants, suggesting environmental acquisition while off‐host. Female organs exhibited significantly different β‐diversity than the whole tick from which they were derived. Our results demonstrate clear differences in both α‐ and β‐diversity among tick developmental stages and between tick organs and the tick as a whole. Furthermore, field‐acquired bacteria appear to be very important to the overall internal bacterial community of this tick species, with influence from the host bloodmeal appearing limited.
Summary
Lyme borreliosis is caused by multiple species of the spirochete bacteria Borrelia burgdorferi sensu lato. The spirochetes are transmitted by ticks to vertebrate hosts, including small‐ and ...medium‐sized mammals, birds, reptiles, and humans. Strain‐to‐strain variation in host‐specific infectivity has been documented, but the molecular basis that drives this differentiation is still unclear. Spirochetes possess the ability to evade host immune responses and colonize host tissues to establish infection in vertebrate hosts. In turn, hosts have developed distinct levels of immune responses when invaded by different species/strains of Lyme borreliae. Similarly, the ability of Lyme borreliae to colonize host tissues varies among different spirochete species/strains. One potential mechanism that drives this strain‐to‐strain variation of immune evasion and colonization is the polymorphic outer surface proteins produced by Lyme borreliae. In this review, we summarize research on strain‐to‐strain variation in host competence and discuss the evidence that supports the role of spirochete‐produced protein polymorphisms in driving this variation in host specialization. Such information will provide greater insights into the adaptive mechanisms driving host and Lyme borreliae association, which will lead to the development of interventions to block pathogen spread and eventually reduce Lyme borreliosis health burden.
Lyme disease causing bacteria species are transmitted between ticks and different vertebrate hosts, including mammals, birds, and reptiles, and different bacteria species are associated with different hosts. Potential mechanisms driving these bacteria‐host associations include: strain‐to‐strain differences in the induced innate and adaptive immune response and bacteria protein variants that display differentially binding activity to cells.
Developing‐world shark fisheries are typically not assessed or actively managed for sustainability; one fundamental obstacle is the lack of species and size‐composition catch data. We tested and ...implemented a new and potentially widely applicable approach for collecting these data: mandatory submission of low‐value secondary fins (anal fins) from landed sharks by fishers and use of the fins to reconstruct catch species and size. Visual and low‐cost genetic identification were used to determine species composition, and linear regression was applied to total length and anal fin base length for catch‐size reconstruction. We tested the feasibility of this approach in Belize, first in a local proof‐of‐concept study and then scaling it up to the national level for the 2017–2018 shark‐fishing season (1,786 fins analyzed). Sixteen species occurred in this fishery. The most common were the Caribbean reef (Carcharhinus perezi), blacktip (C. limbatus), sharpnose (Atlantic Rhizoprionodon terraenovae and Caribbean R. porosus considered as a group), and bonnethead (Sphyrna cf. tiburo). Sharpnose and bonnethead sharks were landed primarily above size at maturity, whereas Caribbean reef and blacktip sharks were primarily landed below size at maturity. Our approach proved effective in obtaining critical data for managing the shark fishery, and we suggest the tools developed as part of this program could be exported to other nations in this region and applied almost immediately if there were means to communicate with fishers and incentivize them to provide anal fins. Outside the tropical Western Atlantic, we recommend further investigation of the feasibility of sampling of secondary fins, including considerations of time, effort, and cost of species identification from these fins, what secondary fin type to use, and the means with which to communicate with fishers and incentivize participation. This program could be a model for collecting urgently needed data for developing‐world shark fisheries globally.
Article impact statement: Shark fins collected from fishers yield data critical to shark fisheries management in developing nations.
Uso de Aletas Secundarias Proporcionadas por Pescadores para Llenar Vacíos Importantes de Información sobre las Pesquerías de Tiburones
Resumen
Con frecuencia no se evalúan las pesquerías de tiburones del mundo en desarrollo ni cuentan con un manejo activo de sustentabilidad. Uno de los principales obstáculos para esto es la falta de información sobre las especies y la composición de los tamaños en las capturas. Probamos e implementamos una estrategia nueva y potencialmente aplicable en todas partes para la recolección de estos datos: la entrega obligatoria de las aletas secundarias de bajo valor económico (aletas anales) obtenidas de los tiburones desembarcados por parte de los pescadores y el uso de estas aletas para reconstruir las especies y tamaños en la captura. Usamos identificaciones genéticas de bajo costo e identificaciones visuales para determinar la composición de las especies y aplicamos una regresión lineal a la longitud total y a la de la base de la aleta anal para la reconstrucción del tamaño en captura. Probamos la viabilidad de esta estrategia en Belice, primero en un estudio de prueba de concepto y después subiendo al nivel nacional para la temporada de pesca de tiburón 2017–2018 (1,786 aletas analizadas). Se registraron 16 especies en esta pesquería. Las más comunes fueron Carcharhinus perezi, C. limbatus, Rhizoprionodon terraenovae y R. porosus (consideradas como un grupo) y Sphyrna cf. tiburo. Las últimas tres especies fueron desembarcadas principalmente por encima del tamaño maduro, mientras que con las dos primeras especies lo hacían por debajo del tamaño maduro. Nuestra estrategia demostró ser efectiva en la obtención de información crítica para el manejo de la pesquería de tiburones y sugerimos que las herramientas desarrolladas como parte de este programa puedan ser exportadas a otras naciones en esta región y aplicadas casi de manera inmediata si existen los medios para comunicarse con los pescadores e incentivarlos a proporcionar las aletas anales. Fuera del Atlántico Occidental tropical, recomendamos una mayor investigación de la viabilidad del muestreo de aletas secundarias, incluyendo la consideración del tiempo, esfuerzo y costo de la identificación de especies a partir de estas aletas; cuál tipo de aleta secundaria utilizar; y los medios mediante los cuales comunicarse con los pescadores e incentivarlos a participar. Este programa podría ser un modelo para la recolección de información de necesidad urgente para las pesquerías del mundo en desarrollo.
【摘要】
发展中国家的鲨鱼渔业通常没有得到可持续性评估或积极管理; 其中一项基本障碍是缺乏关于物种和大小组成的渔获数据。我们测试并实施了一种可能广泛适用的新方法来收集这些数据, 即强制渔民上交捕获鲨鱼的低价值次级鱼鳍 (臀鳍), 并利用这些鳍确定捕获的物种及其大小。我们采用目测和低成本遗传鉴定的方法确定了渔获中的鲨鱼物种组成, 并基于体长和臀鳍基部长度的关系用线性回归对捕获鲨鱼的大小进行重建。我们在伯利兹测试了这种方法的可行性, 首先在局部地区进行概念验证研究, 然后在 2017–2018 年的鲨鱼捕捞季将其扩大到国家水平 (共分析 1786 个鱼鳍) 。该地区的渔场中有十六种鲨鱼, 最常见的是加勒比真鲨 (Carcharhinus perezi) 、黑边鳍真鲨 (C. limbatus) 、斜锯牙鲨 (大西洋斜锯牙鲨 Rhizoprionodon terraenovae 和加勒比斜锯牙鲨 R. porosus 被认为是一个群体), 以及窄头双髻鲨 (Sphyrna cf. tiburo) 。捕获的斜锯牙鲨和窄头双髻鲨的大小多数超过成年体型, 而加勒比真鲨和黑边鳍真鲨则大多低于成年体型。结果证明, 我们的方法可以有效地获得关键数据以管理鲨鱼渔业, 我们还建议将该项目开发的工具出口到该地域的其他国家, 且如果有与渔民沟通和激励他们提供臀鳍的渠道, 则可以立刻采取应用。在热带大西洋西部以外, 我们建议进一步研究对次级鱼鳍进行采样的可行性, 包括考虑时间、工作量、用鱼鳍进行物种鉴定的成本、使用什么鳍片类型以及采取什么方式与渔民沟通和激励参与。这个项目可以为全球发展中国家鲨鱼渔业收集迫切需要的数据提供范本。【翻译: 胡怡思; 审校: 聂永刚】
Understanding the emergence of novel viruses requires an accurate and comprehensive annotation of their genomes. Overlapping genes (OLGs) are common in viruses and have been associated with pandemics ...but are still widely overlooked. We identify and characterize
, a novel OLG in SARS-CoV-2 that is also present in Guangxi pangolin-CoVs but not other closely related pangolin-CoVs or bat-CoVs. We then document evidence of
translation, characterize its protein sequence, and conduct an evolutionary analysis at three levels: between taxa (21 members of
), between human hosts (3978 SARS-CoV-2 consensus sequences), and within human hosts (401 deeply sequenced SARS-CoV-2 samples).
has been independently identified and shown to elicit a strong antibody response in COVID-19 patients. However, it has been misclassified as the unrelated gene
, leading to confusion. Our results liken
to other accessory genes in emerging viruses and highlight the importance of OLGs.
Background: The use of DNA barcodes for the identification of described species is one of the least controversial and most promising applications of barcoding. There is no consensus, however, as to ...what constitutes an appropriate identification standard and most barcoding efforts simply attempt to pair a query sequence with reference sequences and deem identification successful if it falls within the bounds of some pre-established cutoffs using genetic distance. Since the Renaissance, however, most biological classification schemes have relied on the use of diagnostic characters to identify and place species. Methodology/Principal Findings: Here we developed a cytochrome c oxidase subunit I character-based key for the identification of all tuna species of the genus Thunnus, and compared its performance with distance-based measures for identification of 68 samples of tuna sushi purchased from 31 restaurants in Manhattan (New York City) and Denver, Colorado. Both the character-based key and GenBank BLAST successfully identified 100% of the tuna samples, while the Barcode of Life Database (BOLD) as well as genetic distance thresholds, and neighbor-joining phylogenetic tree building performed poorly in terms of species identification. A piece of tuna sushi has the potential to be an endangered species, a fraud, or a health hazard. All three of these cases were uncovered in this study. Nineteen restaurant establishments were unable to clarify or misrepresented what species they sold. Five out of nine samples sold as a variant of “white tuna” were not albacore (T. alalunga), but escolar (Lepidocybium flavorunneum), a gempylid species banned for sale in Italy and Japan due to health concerns. Nineteen samples were northern bluefin tuna (T. thynnus) or the critically endangered southern bluefin tuna (T. maccoyii), though nine restaurants that sold these species did not state these species on their menus. Conclusions/Significance: The Convention on International Trade Endangered Species (CITES) requires that listed species must be identifiable in trade. This research fulfills this requirement for tuna, and supports the nomination of northern bluefin tuna for CITES listing in 2010.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Summary
Staphylococcus aureus has evolved as a pathogen that causes a range of diseases in humans. There are two dominant modes of evolution thought to explain most of the virulence differences ...between strains. First, virulence genes may be acquired from other organisms. Second, mutations may cause changes in the regulation and expression of genes. Here we describe an evolutionary event in which transposition of an IS element has a direct impact on virulence gene regulation resulting in hypervirulence. Whole‐genome analysis of a methicillin‐resistant S. aureus (MRSA) strain USA500 revealed acquisition of a transposable element (IS256) that is absent from close relatives of this strain. Of the multiple copies of IS256 found in the USA500 genome, one was inserted in the promoter sequence of repressor of toxins (Rot), a master transcriptional regulator responsible for the expression of virulence factors in S. aureus. We show that insertion into the rot promoter by IS256 results in the derepression of cytotoxin expression and increased virulence. Taken together, this work provides new insight into evolutionary strategies by which S. aureus is able to modify its virulence properties and demonstrates a novel mechanism by which horizontal gene transfer directly impacts virulence through altering toxin regulation.
In the course of infectious disease outbreaks, barriers to accessing health care can contribute to preventable mortality. According to the Ministry of Health of Haiti (Ministère de la Santé Publique ...et de la Population MSPP), the 2010 cholera epidemic caused 7,936 deaths from October 2010 to December 2012 in Haiti alone. We seek to quantify the excess mortality attributable to patients not seeking care during the cholera outbreak in the Nord Department in 2010-2012. Using data from a community-based retrospective survey conducted by Doctors Without Borders (Médecins Sans Frontières MSF) in Northern Haiti, we used logistic regression to examine the association between healthcare utilization and fatality among household members with watery diarrhea in the Communes of Borgne, Pilate, Plaisance, and Port-Margot in the Nord Department. We found that failing to seek care resulted in a 5-fold increase in the case fatality ratio among infected individuals (26%) versus those who sought care (5%). Common concerns noted for why care was not sought included travel distance to treatment centers, not attributing watery diarrhea episodes to cholera, and being unsure where to seek health care for their watery diarrhea episodes within their Communes. In conclusion, addressing transportation and information needs could increase healthcare utilization and reduce lives lost during an outbreak.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The global trade in wildlife has historically contributed to the emergence and spread of infectious diseases. The United States is the world's largest importer of wildlife and wildlife products, yet ...minimal pathogen surveillance has precluded assessment of the health risks posed by this practice. This report details the findings of a pilot project to establish surveillance methodology for zoonotic agents in confiscated wildlife products. Initial findings from samples collected at several international airports identified parts originating from nonhuman primate (NHP) and rodent species, including baboon, chimpanzee, mangabey, guenon, green monkey, cane rat and rat. Pathogen screening identified retroviruses (simian foamy virus) and/or herpesviruses (cytomegalovirus and lymphocryptovirus) in the NHP samples. These results are the first demonstration that illegal bushmeat importation into the United States could act as a conduit for pathogen spread, and suggest that implementation of disease surveillance of the wildlife trade will help facilitate prevention of disease emergence.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The Great American Biotic Interchange (GABI) was greatly influenced by the completion of the Isthmus of Panama and impacted the composition of modern faunal assemblages in the Americas. However, the ...contribution of preceding events has been comparatively less explored, even though early immigrants in the fossil records are evidence for waif dispersals. The cricetid rodents of the subfamily Sigmodontinae are a classic example of a species-rich South American radiation resulting from an early episode of North American invasion. Here, we provide a temporal and spatial framework to address key aspects of the historical biogeography and diversification of this diverse mammal group by using mitochondrial and nuclear DNA datasets coupled with methods of divergence time estimation, ancestral area reconstruction and comparative phylogenetics. Relaxed-clock time estimates indicate that divergence of the Sigmodontinae began in the middle-late Miocene (ca. 12-9 Ma). Dispersal-vicariance analyses point to the arrival of a single lineage of northern invaders with a widespread ancestral distribution and imply that the initial differentiation between Central and South America gave rise to the most basal groups within the subfamily. These two major clades diversified in the late Miocene followed by the radiation of main tribes until the early Pliocene. Within the Oryzomyalia, tribes diverged initially in eastern South America whereas multiple dispersals into the Andes promoted further diversification of the majority of modern genera. A comparatively uniform background tempo of diversification explains the species richness of sigmodontines across most nodes, except for two akodontine genera with recent increases in diversification rates. The bridging of the Central American seaway and episodes of low sea levels likely facilitated the invasion of South America long before the onset of the post-Isthmian phase of the GABI.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Little is known about the population structure of vancomycin-resistant Enterococcus faecium (VREfm) in Latin America (LATAM). Here, we provide a complete genomic characterization of 55 representative ...Latin American VREfm recovered from 1998-2015 in 5 countries. The LATAM VREfm population is structured into two main clinical clades without geographical clustering. Using the LATAM genomes, we reconstructed the global population of VREfm by including 285 genomes from 36 countries spanning from 1946 to 2017. In contrast to previous studies, our results show an early branching of animal related isolates and a further split of clinical isolates into two sub-clades within clade A. The overall phylogenomic structure of clade A was highly dependent on recombination (54% of the genome) and the split between clades A and B was estimated to have occurred more than 2,765 years ago. Furthermore, our molecular clock calculations suggest the branching of animal isolates and clinical clades occurred ~502 years ago whereas the split within the clinical clade occurred ~302 years ago (previous studies showed a more recent split between clinical an animal branches around ~74 years ago). By including isolates from Latin America, we present novel insights into the population structure of VREfm and revisit the evolution of these pathogens.
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