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At least 19 recordsLinked to original sources

PubMed2025

Unveiling the Dynamics of SARS-CoV-2 Gamma and Delta Waves in Paraná, Brazil - Delta Displacing a Persistent Gamma Through Alternative Routes of Dispersal.

The Gamma and Delta variants of concern (VOCs) of SARS-CoV-2 drove the second and third wave in Brazil and significantly intensified the number of cases and deaths. In this study, we investigate the timeline and origins of the Gamma and Delta variants using a spatiotemporal analysis based on 1508 genomes collected between March and September 2021 from health administrative regions in Paraná state, Brazil. Our findings indicate that community transmission of Gamma-P.1 began in late 2020, with substantial contributions from the Northeast and North regions. In contrast, our analysis of the Delta-AY.101 genomes underscored the crucial role of Paraná in national-level transmission dynamics beginning in late March 2021. At a local level, the movement estimates inferred from the monophyletic clades showed that the Curitiba health region was the primary source for Gamma-P.1, with a substantial contribution from Londrina. This health-region also emerged as an important hub for Delta-AY.101. Our phylogeographical GLM analysis demonstrates that air travel fluxes and population size at the origin of locations were the strongest predictors of shaping SARS-CoV-2 dispersal dynamics within Paraná. In addition, viral load analysis suggests that Gamma-P.1 and Delta-AY.101 may have maintained a similarly high transmissibility potential throughout the evaluated months, providing insights into the prolonged co-circulation dynamics. Our study underscores the relevance of understanding SARS-CoV-2 introductions and regional circulation contributions at the country level to enhance public health preparedness and strengthen local surveillance programs.

Brazil↗

PubMed2025

Global Evolution and Transmission Dynamics of Enterovirus D68.

Enterovirus D68 (EV-D68), a serotype of the enterovirus species D, has garnered significant attention due to outbreaks reported in 2014, 2016, and 2018. In this study, 36 Chinese EV-D68 strains were isolated, sequenced, and combined with all EV-D68 VP1 sequences from GenBank to form a data set of 1679 sequences. This data set served as the basis for phylogenetic, evolutionary dynamics, phylogeographic, and key amino acid site mutation analyses of EV-D68. Based on the VP1 region, EV-D68 is classified into four genotypes (A-D), and seven subgenotypes (B1-B3, D1-D4), with B3 and D3 being the predominant subgenotypes. Bayesian skyline plots indicated that genotypes B and D experienced multiple population expansions, aligning with reported EV-D68 outbreaks. Phylogeographic analyses of the B3 subgenotypes revealed sequences from Europe and North America clustering into a single evolutionary branch, suggesting significant transmission between these regions. Additionally, mutation analysis identified VP1-98 as a high-frequency mutation site, differing significantly between the previously prevalent A and C genotypes and the currently prevalent B and D genotypes. However, the functional implications of this mutation require further investigation. This study provides a solid theoretical basis for epidemiological research, disease surveillance, and prevention efforts related to EV-D68.

Enterovirus Infections↗

PubMed2025

Quaternary Glaciation Accelerates Speciation in Aquatic Snakes Through Recent Bottlenecks.

Climatic fluctuations during glacial periods have profoundly shaped the demographic history and gene flow dynamics of many taxa. This study integrated high-throughput sequencing of 67 individuals with comprehensive genomic analyses to investigate biogeographic patterns, genetic divergence and demographic trajectories in the Opisthotropis latouchii species complex, a group of mountain stream snakes distributed across Central China. Our analyses revealed substantial genetic divergence, identifying four distinct lineages, each confined to one of the four major mountain ranges in Central China, including one previously unrecognised species. These lineages exhibited distinct demographic signatures, with population bottlenecks occurring during Quaternary glaciations. Initial isolation in the glacial refugia of the southern regions of these mountains during the Late Pliocene was followed by postglacial expansions along a northward trajectory, with further divergence along a latitudinal gradient associated with mountain distribution. Notably, the mountain ranges of Central China acted as critical refugia during glacial periods, promoting rapid speciation, and as dispersal corridors during interglacial periods, facilitating range expansion and enabling recent gene flow. These findings highlight the profound impact of Quaternary climatic oscillations on genetic structure, demographic history and gene flow patterns of these endemic taxa.

Animals↗

PubMed2025

There and back again: historical biogeography of neotropical magnolias based on high-throughput sequencing.

BACKGROUND: The Neotropics are considered one of the most biodiverse areas in the world, housing at least one third of all vascular plant species. One of the genera that has diversified in the Neotropics is Magnolia, with about 174 species of three sections (Macrophylla, Magnolia and Talauma) endemic to the Americas. In this work, we study the biogeographic history of the Neotropical Magnolia species using high-throughput sequencing data. Sequences from 39 species (38 from Magnolia and one from the sister genus Liriodendron) were assembled. The dataset contained sequences from 239 nuclear targets and complete chloroplast genomes. Phylogenomic hypotheses and the ancestral distribution range of Magnolia were reconstructed. RESULTS: The results of the calibrated phylogenetic hypotheses and ancestral range construction suggest that the earliest arrival in the Neotropics were the ancestors of section Talauma (38 million years ago), which colonized the Pacific region. This early presence in South America suggests long-distance, overwater dispersal from North America, the presumed origin of the genus Magnolia. The analysis and the extant Talauma distribution indicate a south to north recolonization. The ancestors of the other two Neotropical sections, Magnolia and Macrophylla, migrated around 19 mya from Asia to North America, radiating southward to the Neotropics afterwards, around 11 mya. CONCLUSIONS: Our results suggest that Neotropical magnolias originated from a North American ancestor. The current sections arrived at the region independently influenced by climatic processes such as temperature drops or the Miocene Climatic Optimum. Additionally, geological processes, such as the movement of the South and North American land masses and the emergence of the Panama isthmus, facilitated the migration between continents.

Magnolia↗

PubMed2026

Spatiotemporal patterns of Rift Valley fever virus in Africa: a retrospective genomic epidemiology and phylodynamic modelling study.

BACKGROUND: Rift Valley fever virus (RVFV) is a mosquito-borne zoonotic pathogen causing outbreaks in humans and ruminants across Africa and the Arabian Peninsula. Originally restricted to the Great Rift Valley, RVFV has expanded geographically, prompting its classification by WHO as a pathogen of pandemic potential. We investigated the evolutionary and spatial dynamics of RVFV across Africa. METHODS: We used genomic data generated at the International Livestock Research Institute Nairobi genomic laboratory (BioProject PRJNA1106221) and combined with publicly available datasets retrieved from the National Center for Biotechnology (NCBI) GenBank nucleotide database. In retrieving RVFV genome sequences from the NCBI GenBank, we applied the search terms "Rift Valley fever virus segment L AND 6404[SLEN]", "Rift Valley fever virus segment M AND 3885[SLEN]", and "Rift Valley fever virus segment S AND 1520:1690[SLEN]" for L (Large), M (Medium), and S (Small) segments, respectively. For sequences without additional spatiotemporal information, we searched PubMed to extract the associated sequence metadata. We performed molecular clock analysis, phylogenetic inference, phylodynamic modelling (continuous phylogeographic reconstruction), and landscape phylogeography on the three RVFV genome segments (L, M, and S). We aimed to assess evolutionary rates, dispersal patterns, and environmental drivers. Focus was placed on lineage C, the most widely distributed variant. FINDINGS: The global dataset used in this study consisted of large (n=236), medium (n=237), and small (n=247), which were further filtered to exclude potential reassortants and vaccine strains. Genome sequences retrieved from NCBI GenBank database comprised large (n=180), medium (n=184), and small (n=202). The genome sequences from retrospective human and livestock isolates comprised large (n=56), medium (n=53), and small (n=45) collected in Burundi (2018), Kenya (2007, 2018, 2019, 2021, and 2022), and Rwanda (2018 and 2022). Our dataset revealed that RVFV exhibited low overall genetic diversity. Lineage C, however, showed evidence of active evolution, with substitution rates ranging from 3·58 × 10-4 to 9·76 × 10-4 substitutions per site per year. This lineage probably originated in Zimbabwe in the mid-1970s and has since expanded across eastern and southern Africa. Phylogeographic reconstructions revealed rapid spread, with diffusion coefficients exceeding 50 000 km2 per year. INTERPRETATION: Lineage C appears capable of establishing endemic transmission in new regions, with ongoing diversification observed during interepidemic periods. These observations reinforce the value of continuous genomic surveillance, particularly during cryptic transmission phases when adaptive mutations might emerge. Although further evidence is needed, observed trends in climate variability and land-use change point to the potential benefit of targeted surveillance in settings that could be at increased risk, including urban centres and wetlands. FUNDING: This work was supported by the German Federal Ministry for Economic Cooperation and Development, the Rockefeller Foundation, and the Africa Centres for Disease Control and Prevention.

Rift Valley fever virus↗

PubMed2026

From Southeast Asia to global: phylogeny, biogeography and character evolution of the thread-legged bug tribe Leistarchini (Hemiptera: Reduviidae: Emesinae).

The thread-legged bug tribe Leistarchini (Hemiptera: Reduviidae: Emesinae) is a cosmopolitan and diverse group characterized by a highly disproportionate spatial distribution across zoogeographic regions. Due to a historical lack of phylogenetic focus, the internal relationships and evolutionary history of the tribe remain poorly understood. In this study, we provide the first robust phylogenetic framework for Leistarchini by integrating molecular data from mitochondrial genomes and nuclear rDNA (88 taxa, 19 937 bp) with universal single-copy orthologs (24 taxa, 667 loci). Our results support the monophyly of Leistarchini and identify five major clades, including a newly described genus Calliemesa gen. n. Our findings further reveal that the five most species-rich genera (Nesita, Orthunga, Pleias, Ploiaria and Tinna) are either paraphyletic or polyphyletic as currently circumscribed. Molecular dating and biogeographic reconstructions suggest a Southeast Asian origin for the Leistarchini crown group during the late Palaeocene (ca. 57 Ma). Early diversification appears to have been driven by Paleogene geological and climatic shifts in Southeast Asia, while multiple intercontinental dispersals since the middle Eocene into the Afrotropics, Madagascar and the New World shaped the current global distribution. Ancestral state reconstructions indicate that the Leistarchini ancestor possessed a well-developed posterior pronotal lobe and a three-segmented protarsus. Subsequent evolutionary trajectories involved four independent transitions toward a shortened posterior pronotal lobe, and four separate reductions in protarsal segmentation.

Animals↗

PubMed2026

Genome Wide Analysis Reveals Divergence and Ancestral Origins of Min Pigs.

The Min pig, a representative northern Chinese indigenous breed, carries a unique ancestral background shaped by the historical phylogeography of Northeast Asia. This study aimed to dissect the population structure, temporal genetic divergence, and ancestral composition of Min pigs, trace their evolutionary origin, and identify trait-linked functional genes, providing information regarding their evolutionary history and conservation. We analyzed 61 Min pigs sampled across nearly 20 years and 701 reference pigs comprising other Chinese indigenous breeds, Western commercial lines, and Chinese wild boars, using PCA, NJ phylogenetic analysis, Admixture, TreeMix, D-statistic, f4-ratio, and combined selection signature scans (sliding-window FST, XP-EHH, and π-ratio). Clear genetic stratification was observed among Min pig subpopulations, reflecting long-term divergence under natural and artificial selection. PCA and Admixture (K = 2-4) separated East Asian indigenous and Western ancestral components, verifying an admixed Northeast Asian origin with a dominant ancient East Asian component and a Western component. Compared with early-2000s Min pigs, contemporary individuals are genetically closer to Western breeds and exhibit a more scattered structure due to shifted ancestral component proportions, further confirmed by D-statistic and f4-ratio values. We identified 321 differentiated SNP loci based on the Animal QTL database, corresponding to core candidate genes (AKT3, ACACA, MAP3K5, FGFR4, C3, and SERPINC1) enriched for meat quality, growth, reproduction, immunity, energy metabolism, and MAPK/PI3K-Akt/AMPK pathways. This study reveals Min pigs' admixed origin and temporal divergence, clarifying their Northeast Asian evolution and providing molecular markers for genetic monitoring and conservation.

Animals↗

PubMed2026

Emergence and phylogeography of the dengue vector Aedes aegypti in Southeastern Iran.

BACKGROUND: Aedes (Stegomyia) aegypti (Linnaeus) is the primary vector of dengue, chikungunya, Zika, and yellow fever viruses. Its recent detection in southeastern Iran raises public health concerns about arbovirus spread to new regions. This study provides the first genetic and phylogeographic analysis of Ae. aegypti populations from Sistan and Baluchistan Province (SBP), Iran, to infer their origin and invasion pathways. METHODS: Mitochondrial COI and ND4 genes were analysed in newly collected Ae. aegypti specimens from border areas, ports, and urban centres of SBP. Haplotype network analyses were constructed using the TCS method in PopART, and phylogenetic analyses were conducted using global reference sequences. RESULTS: Iranian specimens comprised 7 COI haplotypes (n = 18) and 10 ND4 haplotypes (n = 17). COI phylogeny placed Iranian specimens into two main clades, while ND4 analysis distributed them across several derived clades, mostly clustering with lineages from Latin America (Brazil, Mexico) or Africa. One Iranian specimen showed a close relationship with a Saudi Arabian sequence (bootstrap: 98%) near the basal region. Combined COI + ND4 analysis revealed a monophyletic clade of Iranian specimens with a Sri Lankan specimen, distinct from other global lineages. The global COI network (n = 47) showed a star-like topology with a dominant haplotype 1 shared among 10 Iranian specimens. The ND4 network (n = 31) revealed a complex topology with 18 haplotypes, where a Saudi Arabian and one Iranian specimen (~30 mutational steps) possibly represented the peripheral root. CONCLUSIONS: Detection of diverse Ae. aegypti clades confirm establishment of this vector in southeastern Iran. Results support multiple introductions and genetic connectivity with Latin America, Africa, and South Asia, pointing to an emerging invasion corridor. Continued genomic surveillance and integrated vector monitoring are urgently needed to guide prevention strategies.

Animals↗

PubMed2026

Phylogeography and molecular evolution of Newcastle disease virus across a century of global surveillance.

Newcastle disease virus (NDV) remains one of the most economically important avian pathogens worldwide, causing recurrent outbreaks in poultry despite decades of vaccination and disease control efforts. Since the first reported outbreak of NDV a hundred years ago, numerous molecular epidemiological studies have been conducted globally across diverse geographic and production settings. Following a century of NDV circulation and evolution, the present study aimed to compile all publicly available NDV sequence data and perform a comprehensive global analysis of the genetic diversity, phylogenetic relationship, and global spatiotemporal distribution of NDV over a 100-year timescale. All publicly available NDV complete genome and full-length fusion (F) gene sequences were retrieved from GenBank up to February 2026. Following rigorous quality control, phylogenetic analyses were performed based on complete genomes and F gene datasets. Phylogenetic analysis identified two genotypes within Class I and 20 genotypes within Class II NDVs, with extensive diversification at the sub-genotype level. Genotype XIII exhibited the greatest sub-genotypic diversity, while genotype VII represented the most globally disseminated genotype, reported across 36 countries. Chronological assessment based on the earliest available reports indicated an increasing number of recognized genotypes from the 1930s to recently described sub-genotypes such as XIII.2.3 and XXII.2.2. Regional diversity analysis revealed the highest genotype diversity in Western Africa, Eastern Asia, and Southern Asia. Comparative residue analysis demonstrated substantial genotype-specific variation within critical functional domains of the fusion protein, including cleavage sites, neutralizing epitopes, and heptad repeat regions. Overall, this study provides the first comprehensive 100-year global overview of NDV evolution and phylogeography. The findings highlight continuous viral diversification, broad geographic dissemination of multiple genotypes, and ongoing molecular variation, emphasizing the need for sustained genomic surveillance and periodic evaluation of vaccine compatibility with emerging NDV genotypes.

100-years of data↗

PubMed2026

Genomic epidemiology and ceftazidime-avibactam resistance mechanism of KPC-3-producing Pseudomonas aeruginosa: A decade retrospective study in China.

OBJECTIVES: Carbapenem-resistant Pseudomonas aeruginosa (CRPA), especially KPC-producing P. aeruginosa, is rapidly expanding and posing a serious public health threat. Here, we aim to characterise the epidemiology of KPC-3-producing P. aeruginosa in a tertiary hospital over a 10-year period and elucidate the mechanism of ceftazidime-avibactam (CZA) resistance driven by blaKPC-3 to blaKPC-267 mutations in CRPA, along with conducting a global phylogeographic analysis of KPC-3-producing P. aeruginosa. METHODS: 11 non-duplicate KPC-3-producing CRPA isolates collected over a 10-year period were characterized by antimicrobial susceptibility testing and whole-genome sequencing (WGS). The genetic context and transferability of blaKPC-3/267 and the mechanism of KPC-267-mediated CZA resistance were investigated. Global phylogenomic analysis was performed to characterize the geographic distribution and population structure of blaKPC-3-carrying P. aeruginosa. RESULTS: All 11 KPC-3-producing CRPA strains in this study belonged to ST1076 and exhibited multidrug resistance. The blaKPC-267-positive CZA-resistant strain SRMPA3523 was isolated from patient 1 after blaKPC-3-positive P. aeruginosa SRMPA1139 and SRMPA1630 were treated with CZA. WGS indicated that blaKPC-3/267 was located on the Tn6296 transposon contained in the transferable IncP-2 plasmid. KPC-267 mediates resistance to CZA by reducing the inhibitory effect of avibactam and increasing affinity for ceftazidime. Global analysis indicated that blaKPC-3-carrying P. aeruginosa were predominantly in China, America, and Colombia, with ST1076 and ST111 as dominant clones. CONCLUSIONS: This study characterised the global phylogeography of blaKPC-3-carrying P. aeruginosa and identified KPC-267 as a KPC-3-derived variant associated with CZA resistance. This finding highlighted the risk of developing CZA resistance in KPC-producing P. aeruginosa strains under therapeutic pressure.

CRPA↗

PubMed2026

Phylogeographic epidemiology of Dabie bandavirus in East Asia: divergent transmission networks and genotype‑linked clinical severity.

BACKGROUND: Severe fever with thrombocytopenia syndrome (SFTS), caused by Dabie bandavirus (SFTSV), exhibits geographically decoupled incidence and fatality patterns across East Asia. We aimed to elucidate the distinct ecological drivers and phylogeographic dynamics underlying this inland-coastal epidemiological divergence. METHODS: Integrating 1820 high-quality global genomes of SFTSV with well-characterized clinical cohorts (936 patients) and nationwide surveillance data (27,457 cases) from China, we constructed a comprehensive analytical framework. Ecological modeling, Bayesian phylogeography, and genotype-phenotype association analyses were employed to trace the evolutionary trajectories and clinical implications of the virus. RESULTS: A pronounced "inland-high-incidence vs. coastal-high-fatality" pattern of SFTS was identified. The incidence of SFTS exhibited divergent sensitivities to meteorological factors; inland transmission was sensitive to thermal fluctuations, whereas coastal dynamics were constrained by a sunshine threshold (> 200 h/month). In contrast, spatial divergence in clinical severity correlated with the distribution of regional viral genetic structures. Inland regions mainly co-circulated genotypes A, C, and D, while coastal regions were dominated by genotype B. Zhejiang province was identified as a genetic hub with significantly higher recombination frequencies than inland regions (11.0% vs. 3.5%, P < 0.001). Bayesian phylogeographic inference indicated frequent lineage exchange of Zhejiang province in China with the Republic of Korea and Japan. Clinically, genotypes B and D were associated with elevated mortality in coastal and inland regions, respectively, suggesting that the severe coastal phenotype is shaped by its genotype B-dominated structure. Additionally, the RdRp-N828S mutation emerged as a robust molecular correlate of fatal outcomes, warranting further functional validation. CONCLUSIONS: Divergent meteorological factors and plausible maritime transmission networks may underlie the geographically decoupled epidemiology of SFTS. These findings highlight that risk assessment must extend beyond incidence alone and provide a phylogeographically informed framework for targeted surveillance and genotype-specific interventions in high-risk hotspots.

Humans↗

PubMed2025

Bayesian Inference of Pathogen Phylogeography using the Structured Coalescent Model.

Over the past decade, pathogen genome sequencing has become well established as a powerful approach to study infectious disease epidemiology. In particular, when multiple genomes are available from several geographical locations, comparing them is informative about the relative size of the local pathogen populations as well as past migration rates and events between locations. The structured coalescent model has a long history of being used as the underlying process for such phylogeographic analysis. However, the computational cost of using this model does not scale well to the large number of genomes frequently analysed in pathogen genomic epidemiology studies. Several approximations of the structured coalescent model have been proposed, but their effects are difficult to predict. Here we show how the exact structured coalescent model can be used to analyse a precomputed dated phylogeny, in order to perform Bayesian inference on the past migration history, the effective population sizes in each location, and the directed migration rates from any location to another. We describe an efficient reversible jump Markov Chain Monte Carlo scheme which is implemented in a new R package StructCoalescent. We use simulations to demonstrate the scalability and correctness of our method and to compare it with existing software. We also applied our new method to several state-of-the-art datasets on the population structure of real pathogens to showcase the relevance of our method to current data scales and research questions.

Bayes Theorem↗

PubMed2024

Next-generation phylogeography reveals unanticipated population history and climate and human impacts on the endangered floodplain bitterling (Acheilognathus longipinnis).

BACKGROUND: Floodplains harbor highly biodiverse ecosystems, which have been strongly affected by both past climate change and by recent human activities, resulting in a high prevalence of many endangered species in these habitats. Understanding the history of floodplain species over a wide range of timescales can contribute to effective conservation planning. We reconstructed the population formation history of the Itasenpara bitterling Acheilognathus longipinnis, an endangered floodplain fish species in Japan, over a broad timescale based on phylogenetic analysis, demographic modeling, and historical demographic analysis using mitogenome and whole-genome sequences. A genome sequence was newly assembled as a reference for the resequencing analysis. This bitterling is distributed in three plains separated by high mountain ranges and exhibits ecological characteristics well adapted to floodplain environments. RESULTS: Our analyses revealed an unexpected population branching pattern, gene flow, and timing of the differentiation that occurred within a few hundred thousand years, i.e., long after the mountain uplift that was assumed to be the primary geological cause of the population differentiation. The analyses also showed that all local populations experienced a severe decline during the last glacial and post-glacial periods. CONCLUSIONS: Our results suggest that the floodplain bitterling was able to disperse through unknown routes after mountain uplift and that its populations were strongly influenced by climatic and geographic changes in glacial-interglacial cycles and subsequent human activities, probably related to its floodplain-dependent ecology. The genomic data highlight the unanticipated distribution process of this species and the magnitude of the impact of human activities, with important implications for its conservation.

Endangered Species↗

PubMed2026

Molecular epidemiology and phylogeographic architecture of oncogenic intracellular bacteria in cervical cancer patients across Northern China.

BACKGROUND: Oncogenic intracellular bacteria, including Chlamydia trachomatis, Mycoplasma genitalium, and Fusobacterium nucleatum, have emerged as significant contributors to cervical carcinogenesis. Despite growing interest in microbial oncology, the molecular epidemiological landscape and phylogeographic distribution of these pathogens in Northern China remain poorly characterized. This study aimed to determine the prevalence, co-infection patterns, genotypic diversity, and spatial phylogeographic clustering of oncogenic intracellular bacteria among cervical cancer patients across five provinces of Northern China. METHODS: A cross-sectional, multi-center study was conducted between March 2022 and November 2024 across Shaanxi, Heilongjiang, Beijing, Shandong, and Inner Mongolia. Cervical swab specimens were collected from 1247 confirmed cervical cancer patients. Pathogen detection was performed using multiplex real-time polymerase chain reaction, 16S rRNA gene amplicon sequencing, and whole-genome sequencing. Phylogeographic analyses employed maximum likelihood and Bayesian evolutionary inference frameworks. Statistical analyses included multivariate logistic regression and geographic information system-based spatial clustering. RESULTS: The overall prevalence of at least one oncogenic intracellular bacterium was 68.3% (n = 852). Chlamydia trachomatis was the most prevalent pathogen detected in 41.2% of participants. Co-infection with two or more bacteria was identified in 29.7% of cases and was independently associated with advanced-stage cervical cancer (adjusted odds ratio = 2.87; 95% confidence interval: 1.94 to 4.23; p < 0.001). Phylogeographic analysis revealed three distinct molecular clades with evidence of bidirectional gene flow between Shaanxi and Heilongjiang. Whole-genome sequencing identified 14 novel virulence gene variants not previously characterized in Chinese clinical isolates. CONCLUSIONS: Oncogenic intracellular bacteria are highly prevalent and genotypically diverse among cervical cancer patients in Northern China. The identified phylogeographic clustering and novel virulence variants have direct implications for regional screening programs, targeted antimicrobial strategies, and the development of region-specific molecular diagnostic panels.

Cervical cancer↗

PubMed2026

Phylogeographic analysis of Staphylococcus nepalensis reveals global occurrence of antimicrobial-resistant lineages carrying the sal(E) resistance gene.

BACKGROUND: Staphylococcus nepalensis is an emerging species first described in 2003 from the respiratory tract of goats in Nepal. We report the identification of S. nepalensis of a hypersaline lagoon in Brazil, along with in-depth phylogeographical and resistome analysis of publicly available genomes. METHODS AND RESULTS: During a local survey from hypersaline aquatic environments in Rio de Janeiro, Brazil, two staphylococcal strains were recovered, designated as COLB and AM1. These isolates were subjected to antimicrobial susceptibility testing, genomic sequencing, and comprehensive phylogenomic analyses. Genomic analysis confirmed the taxonomic identity of COLB and AM1 as S. nepalensis. Both isolates harbored the sal(E) conferring resistance to pleuromutilins and streptogramin A, whereas tet(K) conferring to tetracyclines. Additionally, AM1 carried lnu(A), consistent with the reduced susceptibility to clindamycin (MIC = 2 µg/mL) relative to COLB. Genes associated with arsenic and copper tolerance, and the replicons rep7a and rep19c, were confirmed. Phylogenomic analysis indicated that COLB and AM1 were clonally related (1 cgSNP-difference) but distinct from global isolates. Phylogeographic analysis revealed wide geographic occurrence, with some lineages carrying blaZ and mecA associated with beta-lactamase production and methicillin resistance, respectively. Strikingly, sal(E) is conserved across all S. nepalensis genomes. CONCLUSIONS: The findings confirm the presence of S. nepalensis in South America as early as 2016 and documented among available genomes from environmental, human, and animal-associated sources. Furthermore, reveal the circulation of some lineages carrying clinically relevant antimicrobial genes, underscoring the importance of accurate species identification and continuous genomic surveillance and potential One Health relevance.

Phylogeography↗

PubMed2025

Macrolide-resistant Mycoplasma pneumoniae resurgence in Chinese children in 2023: a longitudinal, cross-sectional, genomic epidemiology study.

BACKGROUND: After a prolonged period of low detection rates, Mycoplasma pneumoniae resurged in China, during September to November, 2023, raising global concern. This study aims to gain a better understanding of the genetic mechanisms underlying the 2023 increase in cases and the evolutionary dynamics of the epidemic populations, which has been previously hampered due to limited genomic data of this pathogen. METHODS: We sequenced 685 M pneumoniae isolates, including 248 isolates from 11 Chinese provinces and municipalities in 2023 and 437 isolates from Beijing (2013-22). By analysing these isolates and 436 publicly global sequences, we reconstructed the pathogen's evolutionary history using time-calibrated phylogenies and effective population size inference. We investigated potential genomic variations contributing to the 2023 resurgence through genome-wide association study and conducted phylogeographic analysis of the 2023 isolates across China. FINDINGS: Two macrolide-resistant epidemic clusters (T1-2-EC1 and T2-2-EC2) were responsible for the 2023 resurgence in China. Both clusters, having acquired the 23S ribosomal RNA A2063G mutation conferring macrolide resistance, emerged in approximately 1997 and 2014, respectively, and subsequently outcompeted their predecessor populations. This coincided with China's large-scale adoption of azithromycin for paediatric community-acquired pneumonia around the early 2000s. Aside from macrolide resistance, T1-2-EC1 independently acquired 17 clade-specific mutations and T2-2-EC2 four clade-specific mutations, which could further explain their increased competitiveness. Whole-genome analysis revealed no resurgence-specific mutations in the 2023 isolates. Phylogeographic analysis showed rapid mixing of T1-2-EC1 isolates between different sampled regions within China. INTERPRETATION: Our study provides evidence that the 2023 resurgence in China is a continuation of the pre-COVID epidemic, rather than emergence of novel variants. The high prevalence of macrolide resistance and rapid intranational spread emphasise the urgent need for enhanced global surveillance of this pathogen. FUNDING: National Key Research and Development Program of China, National Natural Science Foundation of China for Key Programs of China Grants, and Beijing High-Level Public Health Technical Talent Project.

Humans↗

PubMed2024

Expansion of Oropouche virus in non-endemic Brazilian regions: analysis of genomic characterisation and ecological drivers.

BACKGROUND: Oropouche virus (OROV) is an arbovirus endemic in the Amazon region that closely resembles other arboviruses in terms of human disease, leading to potential misdiagnoses. The virus ecology has mostly restricted its occurrence to the Amazon biome; however, after a large 2023-24 OROV epidemic in the Brazilian Amazon region, outbreaks are being reported across Brazil and in other countries in Latin America. Here, we investigate the OROV spread outside Amazonia. METHODS: In this genomic and epidemiological study, OROV cases from January, 2023, to July, 2024, provided by the General Coordination of Public Health Laboratories of Brazil on Aug 1, 2024, were compared by geographical location (Amazon vs non-Amazon) and municipal population size, and a linear mixed model was employed to assess the relationship between agricultural area size and cases. OROV-positive samples from central laboratories of five non-Amazonian Brazilian states were sequenced using an amplicon-based approach. Bayesian phylogeographical analysis was performed with near full-length viral genomes, incorporating individual travel histories when relevant. The estimated dates of viral introductions in each sampled location were then contextualised with public epidemiological data. FINDINGS: Epidemic data show that outside the Amazon region, OROV cases frequency was 3·9-times higher in small municipalities than in large municipalities. The planted areas of some agricultural products, such as banana plantations, were positively correlated (r=0·39, p<0·0001) with OROV cases. The linear mixed model revealed that, besides banana, cassava also has larger (p<0·05) planted areas in municipalities with OROV cases when compared with those with no cases. The phylogenetic analysis of 32 new OROV genomes reconstructed multiple exportation events of the newly identified reassortant lineage from the Amazon to other Brazilian regions between January and March, 2024. At least three of the previously described OROV phylogenetic clades circulating in the Amazon were the source of viral introductions. Molecular clock analysis estimated that viral introductions happened from 50 days to 100 days before detecting the outbreaks in each state. INTERPRETATION: Our results confirm that the novel OROV reassortant lineage spread from the Amazon to other regions in early 2024, successfully establishing local transmission. The fact that outbreaks were observed in small municipalities, instead of large urban centres, suggests that local ecological conditions that are ideal for OROV vector occurrence, such as the banana plantation environment, might be important factors driving its spread in Brazil. FUNDING: DECIT, CNPq, FAPEAM, and Inova-Fiocruz. TRANSLATION: For the Portuguese translation of the abstract see Supplementary Materials section.

Brazil↗

PubMed2026

Hidden Diversity in the Sands: Genomic Footprints of Pleistocene Refugia and Fragile Futures of the Turkestan Ground-Jay (Podoces panderi) in Central Asia.

The Turkestan ground-jay (Podoces panderi), a corvid endemic to Central Asia's deserts and steppes, exemplifies how extreme environments drive speciation. Our study provides the first comprehensive high-resolution genomic analysis of this species, using complete mitochondrial genomes (49 individuals) to decode its population structure and demographic past. Our analyses revealed three highly divergent genetic clusters with strong geographic structure. The P. p. iliensis population (Cluster_3) showed particularly pronounced genetic distinctiveness, with significant differentiation from P. p. panderi (Cluster_2 and Cluster_1) populations. This clear genetic separation supports the taxonomic validity of P. p. iliensis as a distinct evolutionary lineage. Demographic reconstruction indicated that Cluster_2 likely represents the ancestral group, with subsequent southward expansion into the Karakum region. The isolated P. p. iliensis population exhibited signatures of long-term isolation, including reduced genetic diversity and absence of recent gene flow with other clusters. These results provide strong evidence that P. p. iliensis represents a distinct evolutionary unit. The genetic structuring into three clusters reflects historical isolation in desert refugia during Pleistocene climatic fluctuations. Notably, we detected asymmetric gene flow among three clusters. These findings redefine P. panderi as a model for desert adaptation, where climatic extremes forged genetic fragmentation amid limited dispersal. Beyond taxonomy, our work highlights how aridification sculpted biodiversity in Asia's interior, urging conservation attention for these evolutionarily distinct lineages.

Animals↗