within-host evolution

Most people infected with Mycobacterium tuberculosis ( Mtb ) are believed to be in a state of latent tuberculosis (TB) infection (LTBI). Although LTBI is asymptomatic and not infectious, there is a risk of developing active disease even decades after infection. Here, to characterize mutations acquired during LTBI, we collected and analyzed Mtb genomes from seven Japanese patient pairs, each pair consisting of two active TB patients whose starting dates of developing active disease were >3 years apart; one had a high suspicion of LTBI before developing active disease, whereas the other did not...

Group B Streptococcus (GBS) is a major cause of contagious bovine mastitis (CBM) in Brazil. The GBS population is composed of host-generalist and host-specialist lineages, which may differ in antimicrobial resistance (AMR) and zoonotic potential, and the surveillance of bovine GBS is crucial to developing effective CBM control and prevention measures. Here, we investigated bovine GBS isolates ( n = 156) collected in Brazil between 1987 and 2021 using phenotypic testing and whole-genome sequencing to uncover the molecular epidemiology of bovine GBS...

BACKGROUND: The emergence of multidrug-resistant (MDR) Escherichia coli strains poses significant challenges in clinical settings, particularly when these strains harbor New Delhi metallo-ß-lactamase (NDM) gene, which confer resistance to carbapenems, a critical class of last-resort antibiotics. This study investigates the genetic characteristics and implications of a novel blaNDM-5 -carrying plasmid pNDM-5-0083 isolated from an E. coli strain GZ04-0083 from clinical specimen in Zhongshan, China...

BACKGROUND: Transposable elements (TEs) are mobile DNA sequences that propagate within genomes, occupying a significant portion of eukaryotic genomes and serving as a source of genetic variation and innovation. TEs can impact genome dynamics through their repetitive nature and mobility. Nematodes are incredibly versatile organisms, capable of thriving in a wide range of environments. The plant-parasitic nematodes are able to infect nearly all vascular plants, leading to significant crop losses and management expenses worldwide...

In interactions between plants and herbivorous insects, the traits enabling phytophagous insects to overcome chemical defenses of their host plants have evolved multiple times. A prominent example of such adaptive key innovations in herbivorous insects are nitrile-specifier proteins (NSPs) that enabled Pierinae butterflies to colonize Brassicales host plants that have a glucosinolate-myrosinase defense system. Although the evolutionary aspects of NSP encoding genes have been studied in some Pierinae taxa (especially among Pieris butterflies), the ancestral evolutionary state of NSPs is unclear due to the limited genomic information available for species within Pierinae...

The expansion of forest cover and intensification of agriculture represent the main threats to the bush cricket Saga pedo , currently listed as Vulnerable globally by the IUCN and included in Annex IV of the European Union Habitats Directive. Gathering information on its ecology and population size is challenging due to its low abundance and localized distribution. Additionally, the elusive and cryptic behavior of this species reduces the likelihood of its detection, potentially resulting in population underestimations...

Pathogen diversity resulting in quasispecies can enable persistence and adaptation to host defenses and therapies. However, accurate quasispecies characterization can be impeded by errors introduced during sample handling and sequencing, which can require extensive optimizations to overcome. We present complete laboratory and bioinformatics workflows to overcome many of these hurdles. The Pacific Biosciences single molecule real-time platform was used to sequence polymerase-chain reaction (PCR) amplicons derived from cDNA templates tagged with unique molecular identifiers (SMRT-UMI)...

Guanylate-binding proteins (GBPs) are a subfamily of interferon-inducible proteins that undertake distinct roles in the the context of bacteria, virus, chlamydia and parasites infections. These proteins exert a notable influence on the progression and outcomes of infectious diseases. Within the realm of host cell-autonomous immunity against pathogens, GBPs have been identified as the regulators of pyroptosis through canonical and noncanonical inflammasome activation pathways. In this review, we summarize the structure and evolution of GBP family members, the canonical and noncanonical inflammasome activation pathways, the roles of GBPs in regulating inflammasome activation, and the mechanisms of GBPs affecting infections induced by different pathogens...

Human gut antibiotic resistome widely occur in anoxic environments characterized by high density of bacterial cells and frequent transmission of antibiotic resistance genes (ARGs). Such resistome is greatly diluted, degraded, and restrained in the aerobic habitats within most natural rivers (regarded as "terrestrial guts") connecting continents and the oceans. Here we implemented a large-scale monitoring campaign extending 5,200 km along the Yellow River, and provide the first integral biogeographic pattern for both ARGs and their hosts...

Topological Dirac nodal-line semimetals host topologically nontrivial electronic structure with nodal-line crossings around the Fermi level, which could affect the photocarrier dynamics and lead to novel relaxation mechanisms. Herein, by using time- and angle-resolved photoemission spectroscopy, we reveal the previously inaccessible linear dispersions of the bulk conduction bands above the Fermi level in a Dirac nodal-line semimetal PtSn4 , as well as the momentum and temporal evolution of the gapless nodal lines...

Parasitism is the most common lifestyle on Earth and has emerged many times independently across the eukaryotic tree of life. It is frequently found among chytrids (Chytridiomycota), which are early-branching unicellular fungi that feed osmotrophically via rhizoids as saprotrophs or parasites. Chytrids are abundant in most aquatic and terrestrial environments and fulfil important ecosystem functions. As parasites, they can have significant impacts on host populations. They cause global amphibian declines and influence the Earth's carbon cycle by terminating algal blooms...

The emergence of nosocomial infections caused by hypervirulent and carbapenem-resistant K. pneumoniae (hv-CRKP) has become a significant public health challenge. The genetic traits of virulence and resistance plasmids in hv-CRKP have been extensively studied; however, research on the adaptive evolution strategies of clinical strains inside the host was scarce. This study aimed to understand the effects of antibiotic treatment on the phenotype and genotype characteristics of hv-CRKP. We investigated the evolution of hv-CRKP strains isolated from the same patient to elucidate the transition between hospital invasion and colonization...

OBJECTIVE: The term source (or focus) control encompasses all those physical measures that can be used to reduce the inoculum and modify those factors in the infectious medium that promote microbial growth or foreign antimicrobial defenses of the host. The main objective of this systematic review (SR) is to know and compare whether early detection and control of the focus (in less than 6 hours) in adult patients treated in the ED for severe infection or sepsis, compared to not controlling the focus or delayed focus control (more than 12 hours) is more effective and safer (improves clinical evolution, mortality, complications, hospital stay or need for ICU admission)...

The Arctic fox (Vulpes lagopus) is the primary infection reservoir of Arctic rabies, the dynamics of which are poorly understood and subject to significant spatiotemporal variation. Although rabies presence has been documented in the region since the mid-19th century, there is currently no evidence of rabies impacting Arctic fox population size. Under the influence of climate change in a rapidly changing Arctic ecosystem, changes in transmission dynamics are predicted, with implications for this species. Concurrently, the World Health Organization leads the United Against Rabies collective in the aim of elimination of dog-mediated rabies by 2030, and although efforts have justifiably been directed to tropical regions, elimination will require a good understanding of rabies in the Arctic...

OBJECTIVE: This study aimed to assess the impact of colonization status on the outcomes of Acinetobacter spp. bloodstream infection (BSI) and investigate the homology and within-host evolution between colonizing and bloodstream carbapenem-resistant Acinetobacter spp. (CRA) to inform antibiotic therapeutic decisions. METHODS: We analyzed clinical outcomes of 46 hematological patients with Acinetobacter spp. BSI and performed whole-genome sequencing on the remaining CRA isolates...

BACKGROUND: Genomic regions that remain poorly understood, often referred to as the dark genome, contain a variety of functionally relevant and biologically informative features. These include endogenous viral elements (EVEs)-virus-derived sequences that can dramatically impact host biology and serve as a virus fossil record. In this study, we introduce a database-integrated genome screening (DIGS) approach to investigate the dark genome in silico, focusing on EVEs found within vertebrate genomes...

The Scutellaris Group of Aedes comprises 47 mosquito species, including Aedes albopictus. While Ae. albopictus is widely distributed, the other species are mostly found in the Asia-Pacific region. Evolutionary history researches of Aedes species within the Scutellaris Group have mainly focused on Ae. albopictus, a species that raises significant public health concerns, neglecting the other species. In this study, we aimed to assess genetic diversity and estimate speciation times of several species within the Scutellaris Group...

Temperate phages can interact with bacterial hosts through lytic and lysogenic cycles via different mechanisms. Lysogeny has been identified as the major form of bacteria-phage interaction in the coral-associated microbiome. However, the lysogenic-to-lytic switch of temperate phages in ecologically important coral-associated bacteria and its ecological impact have not been extensively investigated. By studying the prophages in coral-associated Halomonas meridiana, we found that two prophages, Phm1 and Phm3, are inducible by the DNA-damaging agent mitomycin C and that Phm3 is spontaneously activated under normal cultivation conditions...

The interaction between a host and its microbiome is an area of intense study. For the human host, it is known that the various body-site-associated microbiomes impact heavily on health and disease states. For instance, the oral microbiome is a source of various pathogens and potential antibiotic resistance gene pools. The effect of historical changes to the human host and environment to the associated microbiome, however, has been less well explored. In this review, we characterize several historical and prehistoric events which are considered to have impacted the oral environment and therefore the bacterial communities residing within it...

This study investigates the presence of mycoviruses in Antarctic fungi and elucidates their evolutionary relationships. To achieve this, we aligned mycoviral gene sequences with genomes of previously sequenced Antarctic endophytic fungi, made available by our research group and accessible via Joint Genome Institute. Our findings reveal that the most prevalent genetic regions in all endophytic fungi are homologous to Partitiviruses, Baculoviridae, and Phycodnaviridae. These regions display evidence of positive selection pressure, suggesting genetic diversity and the accumulation of nonsynonymous mutations...