Phylogenetic Clustering Research Articles

Increasing Phylogenetic Clustering of Arbuscular Mycorrhizal Fungal Communities in Roots Explains Enhanced Plant Growth and Phosphorus Uptake.

Temporal variation during the assembly of arbuscular mycorrhizal (AM) fungal communities within plant roots have been posited as critical drivers of the plant-fungal symbiotic outcomes. However, functional implications of these dynamics for the host plant remain poorly understood. We conducted a controlled pot experiment with Sorghum bicolor to investigate how temporal shifts in AM fungal community composition and phylogenetic diversity influence plant growth and phosphorus responses to the symbiosis. We characterised the root-colonising AM fungal communities across three time points and explored their community assembly processes by analysing their phylogenetic diversity and employing joint species distribution modelling with the Hierarchical Modelling of Species Communities (HMSC) framework. We found strong AM fungal turnover through time with a high phylogenetic signal, indicating recruitment of phylogenetically clustered AM fungal species in the host. This temporal phylogenetic clustering of communities coincided with marked increases in plant biomass and phosphorus responses to the AM fungal symbiosis, suggesting that host selection for specific fungi may be a key determinant of these benefits.

A Phylogenetic Assessment of HIV-1 Transmission Trends among People Who Inject Drugs from Coastal and Nairobi, Kenya

ABSTRACT Background Although recent modeling suggests needle-syringe programs have reduced parenteral HIV transmission among people who inject drugs (PWID) in Kenya, the prevalence in this population remains high (~14-20%, compared to ~4% in the larger population). Reducing transmission or acquisition requires understanding historic and modern transmission trends, but the relationship between the PWID HIV-1 sub-epidemic and the general epidemic in Kenya is not well understood. Methods We incorporated 303 new (2018-2021) HIV-1 pol sequences from PWID and their sexual and injecting partners with 2,666 previously published Kenyan HIV-1 sequences to quantify relative rates and direction of HIV-1 transmissions involving PWID from the coast and Nairobi regions of Kenya. We used genetic similarity cluster analysis (thresholds: patristic distance <0.045 & <0.015) and maximum likelihood and Bayesian ancestral state reconstruction to estimate transmission histories at the population group (female sex workers, men who have sex with men, PWID, or general population) and regional (coast or Nairobi) levels. Results Of 1,081 participants living with HIV-1, 274 (25%) were not virally suppressed and 303 (28%) had sequences available. Of new sequences from PWID, 58% were in phylogenetic clusters at distance threshold <0.045. Only 21% of clusters containing sequences from PWID included a second PWID sequence. Sequences from PWID were similarly likely to cluster with sequences from female sex workers, men who have sex with men, and the general population. Ancestral state reconstruction suggested transmission to PWID from other populations was more common than from PWID to other populations. Conclusion This study expands our understanding of the HIV-1 sub-epidemic among PWID in Kenya by incorporating 4-times more HIV-1 sequences from this population than prior studies. Despite recruiting many PWID from local sexual and injecting networks, we found low levels of linked transmission in this population. This may suggest lower relative levels of parenteral transmission in recent years and supports maintaining needle-syringe programs among PWID while also strengthening interventions to reduce HIV-1 sexual acquisition and transmission for this population.

A global overview of insect-fern interactions and its ecological trends.

Historically, ferns have been described as underutilized by insects. However, studies have shown a diversity of insects interacting with ferns, although the evolutionary and ecological drivers of these interactions are still to be untangled. To fill these gaps, we compiled more than 100 yr of global data on insect-fern interactions from the literature comprising 374 fern and 649 insect species. With this database we assessed how fern trophic specialization, phylogenetic relationships and climate have shaped their interactions with insects. Our findings showed that interactions between ferns and insects can be explained by the phylogenetic relations among them. We observed that insect orders part of the Endopterygota clade tend to interact with similar fern species, which might be a result of the inheritance of Endopterygota ancestors probably due to phylogenetic niche conservationism. Under an ecological context, fern specialization increased with temperature, precipitation, and climatic stability. Our results show that climate might be one of the main factors explaining the spatial variation of insect-fern interactions, postulate also supported by the observed phylogenetic clustering of the studied ferns species. Our study highlights the intricate and multifaceted nature of insect-fern interactions, where evolutionary history and ecological factors converge to shape these relationships.

Novel genetic variants of banana streak MY virus and banana streak IM virus naturally infecting banana in Northeast India.

Divergent banana streak viruses (BSV) were characterized from banana plants exhibiting diverse symptoms in the Northeast region (NER) of India. Using rolling circle amplification (RCA), the complete genome sequences of seven episomal banana streak MY virus (BSMYV) isolates, including two novel variants, and two new banana streak IM virus (BSIMV) isolates were characterized. The novel BSMYV genetic variants were associated with conspicuous necrosis on newly emerged leaves, peduncle distortion, pseudostem internal necrosis, in addition to common streak symptoms. For complete genome nucleotide sequences, BSMYV-IN4 and IN5 shared 77-79% identity with other BSMYVs, while BSMYV-IN7 and IN8 exhibited identities of 77-97%. This study reports for the first time, the complete genomes of two banana streak IM virus (BSIMV-IN1 and -IN2) infecting triploid banana hybrids exhibiting leaf distortion, stunted rosette-like growth, and necrosis, sharing 87% sequence identity with reference BSIMV genome (GenBank accession no. HQ593112). Phylogenetic inference based on complete genomes revealed the distinct and congruent placement of BSMYV-IN4 and IN5 within the BSMYV cluster. Pairwise sequence comparisons of the conserved RT/RNase H nucleotide (nt) sequences revealed that the BSMYV-IN7 and IN4 isolates showed 85% and 97% identity to BSMYV (AY805074), respectively, which shared highest nt identity with BSMYV-IN6, IN9, and IN10, at 100%. The RT/RNase H nt sequences of BSIMV-IN1 and IN2 had 98% identity with the BSIMV (HQ593112), but were characterized as novel variants of BSIMV based on complete genomes. An analysis of relative synonymous codon usage (RSCU) pattern in the ORFIII polyprotein of BSMYV and BSIMV isolates revealed AGA and AGG (arginine) as the most frequently overrepresented codons (>1.5), evolutionary conserved in the genome of both species. A total of 14 recombination events were detected among the 36 BSV genomes, with recombination breakpoints mainly located in the ORFI, III, and IGR genomic regions. A novel phylogenetic cluster, comprised of BSMYV-IN4 and IN5 within the clade I was probably derived from heterologous recombination between parents resembling banana streak VN virus (BSVNV; AY750155) and banana streak GF virus (BSGFV; KJ013507) isolates. The present study conclusively reports the infection of genetically and symptomatically distinct variants of BSMYV and BSIMV infecting banana hybrids in NER India.

Hot node limitations and impact of taxonomic resolution on phylogenetic divergence patterns: A case study on Ecuadorian ethnomedicinal flora

SummarySocietal Impact StatementNovel phylogenetic approaches have emerged in recent years to study traditional medicinal plants, aiming to identify potential sources of new drugs. This line of research holds considerable promise yet remains in its early stages. Here, we examine the prevalent methods employed in the field, revealing the impact of methodological choices that have often been made arbitrarily. We also highlight a widespread misconception regarding ‘hot node analysis’, a tool gaining popularity for identifying plants with high bioactive potential. Our findings should advance future research aimed at guiding the selection of promising candidates for bioprospection.Summary Advances in phylogenetics offer a ground‐breaking approach to analysing ethnobotanical data. This line of research typically involves calculating the degree of phylogenetic clustering (i.e. phylogenetic divergence) of a set of medicinal plants and identifying clades with a significant overabundance of these plants, known as hot nodes, which are purportedly responsible for the clustering patterns. However, despite showing great promise, the adequacy of this procedure remains to be tested, and the results have so far been inconclusive and, at times, contradictory. Here, we examine two key elements through a case study of Ecuadorian medicinal flora: the impact of taxonomic resolution (species‐ and genus‐level data) on phylogenetic divergence metrics (Mean Pairwise Distance; MPD, and Mean Nearest Taxon Distance; MNTD), and the efficacy of the hot node analysis in identifying clades that significantly influence these metrics. To identify clades with a significant impact on MPD and MNTD, we implemented a jackknifing procedure and compared outcomes with the hot nodes. Phylogenetic divergence was strongly dependent on the taxonomic resolution, with clustering mainly revealed by MPD at the genus level. Further, the hot nodes incompletely matched those with significant influence on MPD and MNTD according to the jackknifing analysis. We highlight the impact of taxonomic resolution on commonly used phylogenetic divergence metrics and the limitations of hot nodes in identifying influential clades, stressing the potential of alternative jackknifing techniques. We recommend the use of the most resolved tree possible and combining jackknifing with hot node analyses as complementary sources to pinpoint clades for bioprospection.

Transmitted drug resistance and molecular transmission network among treatment-naive HIV-1 patients in Wenzhou, China, 2020–2023

BackgroundTransmitted drug resistance (TDR) increases the risk of antiretroviral therapy (ART) failure in HIV-1 patients. This study investigated the molecular epidemiology of TDR and its transmission networks among newly diagnosed HIV-1 patients in Wenzhou, China.MethodsWe enrolled 1878 ART-naive HIV-1 patients from January 2020 to October 2023. TDR was evaluated using the Stanford University HIV Drug Resistance Database. We performed phylogenetic analysis, genotyping, transmission clustering, and population-based TDR-related factor analysis.ResultsAmong 1782 patients with successful genotyping, TDR prevalence was 5.7%. Multivariable analysis identified CRF08_BC subtype (adjusted odds ratio [aOR] 18.59, 95% CI 3.79-336.18, p = 0.004), CD4 > 500 cells/mm³ (aOR 2.19, 95% CI 1.16–4.03, p = 0.013), and year 2023 (aOR 1.83, 95% CI 1.11–4.89, p = 0.039) as factors associated with higher TDR risk. The most prevalent NNRTI mutations were K103N, E138A, and V179E. Seven TDR transmission clusters were identified, notably one with V179D that expanded during 2020–2023.ConclusionsWhile TDR prevalence in Wenzhou remained lower than in other Chinese regions, an upward trend was observed. Most resistant individuals were in transmission clusters, predominantly middle-aged and elderly. NNRTI resistance was severe and concentrated in efavirenz, nevirapine, and rilpivirine. Enhanced HIV surveillance and wider free antiretroviral options are crucial to control drug-resistant HIV spread in Wenzhou.

Genetic analysis of drug resistance mechanisms and phylogenetic clustering in Candida auris isolates from Western India

Objectives: Candida auris is an emerging multidrug-resistant fungal pathogen that poses a significant threat to global health. Limited information is available from the Indian subcontinent regarding mutations associated with drug resistance and genetic variability among the isolates. In this study, we employed whole-genome sequencing (WGS) to investigate the genetic variations and drug resistance mechanisms within C. auris isolates from the western region of India. Materials and Methods: A total of twenty archived isolates were subjected to WGS on the Illumina NextSeq 2000 platform. A set of 18 genes was analyzed to check for the presence of drug-resistant mutations. Phylogenetic analysis was done using MEGA v6.06 software to identify the C. auris subgroup or clade and to check genetic relatedness among species. Statistical Analysis: The data related to drug resistance were presented in numbers and percentages. Results: Through manual analysis, drug-resistant mutations were detected in ERG11, CDR1, and TAC1b genes, which are known to be associated with reduced susceptibility to antifungal agents. Phylogenetic analysis revealed that all the isolates clustered within Clade I, indicating a high degree of genetic similarity among isolates. The absence of comprehensive antifungal mutation databases and automated tools for drug resistance detection necessitated the utilization of specialized computational skills of bioinformaticians for data analysis. Conclusions: The study provides valuable insights into the genetic diversity and drug resistance mechanisms of C. auris isolates in the western region of India and emphasizes the need for continued research and surveillance to combat this emerging pathogen. Our findings underscore the need for the development of user-friendly automated tools and comprehensive databases to facilitate rapid and accurate identification of drug resistance in C. auris.

Thermal Tolerance and Species Distributions: Interactions Between Latitude, Elevation and Arboreality in Ants

ABSTRACTAimGlobal warming has highlighted the importance of understanding the role of thermal tolerance as a driver of species distributions, especially for ectotherms. Here we analyse interactions between latitude, elevation and arboreality as predictors of geographic patterns of thermal tolerance in ants.LocationThe collected data are distributed globally.MethodsWe first tested the effect of latitude, elevation and its interactive effect on ant CTmax and CTmin. Second, we tested whether CTmax and CTmin are phylogenetic clustering. Finally, we tested whether CTmax and CTmin can be explained by nesting microhabitat (ground vs. tree‐nesting species) and whether the probability of occurrence of tree‐nesting species along thermal gradients helps explain the global pattern in ant CTmax.ResultsCTmax and CTmin displayed high and low phylogenetic signals respectively and therefore showed different responses to geographic gradients. Notably, we found that CTmax was higher in higher latitudes. This was explained by a lack of elevational turnover at high latitudes among tree‐nesting species, which are exposed to warmer microclimates and have higher CTmax compared with ground‐nesting species. CTmin decreased with elevation at low latitudes, but did not vary with elevation at higher latitudes.Main ConclusionsOur findings highlight the important influence of arboreality on the macroecology of thermal tolerance, substantially modifying traditional notions of variation along latitudinal and elevation gradients.

Morphometric trait normalization, cluster analysis and molecular phylogenetic analysis in delimiting sympatric Neolissochilus hexastichus and N. hexagonolepis in Umngi River, Meghalaya (India)

Aim: To assess the ability of an integrative approach comprising multivariate morphometric data analysis and mitochondrial cytochrome oxidase subunit I (CO I) sequence divergence analysis in delimiting sympatric Neolissochilus hexastichus (McClleland, 1839) and N. hexagonolepis (McClleland, 1839) mahseer populations in River Umngi, Meghalaya. Methodology: Authoritative descriptions of mahseers were referred during the sampling of 40 individuals from River Umngi, Meghalaya. Multivariate morphometric data were normalized with respect to standard length. The normalization procedure maintained the particular shape factor for each sample. Normalised data were subjected to hierarchical clustering on principal components Analysis (HCPC) for grouping samples according to morphometric features. Genetic affinities based on CO I sequence divergence were assessed by Bayesian Inference (BI) and Automatic Barcode Gap Discovery (ABGD) protocols. Results: The normalization protocols removed the variations in traits due to body size effects and facilitated the identification of allometric traits. HCPC analysis revealed morphometric features that had a significant impact on clustering. Nine N. hexagonolepis and 13 N. hexastichus individuals were identified by integrative morphological and molecular phylogenetic approach. The remaining 18 individuals had incongruence in their memberships in the morphometric and phylogenetic clusters. Interpretation: The integrative approach, apart from delineating N. hexagonolepis and N. hexastichus congeners, highlighted the need to include nuclear genetic markers in future studies for confirming the presence of natural hybrids in sympatric populations of Neolissochilus mahseers. Key words: Cluster, Morphometric, Neolissochilus, Normalization, Phylogenetics

Comparative analysis of the whole mitochondrial genomes of four species in sect. Chrysantha (Camellia L.), endemic taxa in China

BackgroundThe sect. Chrysantha Chang of plants with yellow flowers of Camellia species as the “Queen of the Tea Family”, most of these species are narrowly distributed endemics of China and are currently listed Grde-II in National Key Protected Wild Plant of China. They are commercially important plants with horticultural medicinal and scientific research value. However, the study of the sect. Chrysantha species genetics are still in its infancy, to date, the mitochondrial genome in sect. Chrysantha has been still unexplored.ResultsIn this study, we provide a comprehensive assembly and annotation of the mitochondrial genomes for four species within the sect. Chrysantha. The results showed that the mitochondrial genomes were composed of closed-loop DNA molecules with sizes ranging from 850,836 bp (C. nitidissima) to 1,098,121 bp (C. tianeensis) with GC content of 45.71–45.78% and contained 48–58 genes, including 28–37 protein-coding genes, 17–20 tRNA genes and 2 rRNA genes. We also examined codon usage, sequence repeats, RNA editing and selective pressure in the four species. Then, we performed a comprehensive comparison of their basic structures, GC contents, codon preferences, repetitive sequences, RNA editing sites, Ka/Ks ratios, haplotypes, and RNA editing sites. The results showed that these plants differ little in gene type and number. C. nitidissima has the greatest variety of genes, while C. tianeensis has the greatest loss of genes. The Ka/Ks values of the atp6 gene in all four plants were greater than 1, indicating positive selection. And the codons ending in A and T were highly used. In addition, the RNA editing sites differed greatly in number, type, location, and efficiency. Twelve, six, five, and twelve horizontal gene transfer (HGT) fragments were found in C. tianeensis, Camellia huana, Camellia liberofilamenta, and C. nitidissima, respectively. The phylogenetic tree clusters the four species of sect. Chrysantha plants into one group, and C. huana and C. liberofilamenta have closer affinities.ConclusionsIn this study, the mitochondrial genomes of four sect. Chrysantha plants were assembled and annotated, and these results contribute to the development of new genetic markers, DNA barcode databases, genetic improvement and breeding, and provide important references for scientific research, population genetics, and kinship identification of sect. Chrysantha plants.

Genomic evidence of two-staged transmission of the early seventh cholera pandemic

The seventh cholera pandemic started in 1961 in Indonesia and spread across the world in three waves in the decades that followed. Here, we utilised genomic evidence to detail the first wave of the seventh pandemic. Genomes of 22 seventh pandemic Vibrio cholerae isolates from 1961 to 1979 were completely sequenced. Together with 152 publicly available genomes from the same period, they fell into seven phylogenetic clusters (CL1–CL7). By multilevel genome typing (MGT), all were assigned to MGT2 ST1 (Wave 1) except three isolates in CL7 which were typed as MGT2 ST2 (Wave 2). The Wave 1 seventh pandemic expanded in two stages, with Stage 1 (CL1–CL5) spread across Asia and Stage 2 (CL6 and CL7) spread to the Middle East and Africa. Three non-synonymous mutations, one each, in three regulatory genes, csrD (global regulator), acfB (chemotaxis), and luxO (quorum sensing) may have critically contributed to its pandemicity. The three MGT2 ST2 isolates in CL7 were the progenitors of Wave 2 and evolved from within Wave 1 with acquisition of a novel IncA/C plasmid. Our findings provide new insight into the evolution and transmission of the early seventh pandemic, which may aid future cholera prevention and control.

Phylogenetic structure and turnover between lowland and montane subtropical forests indicate differential community assembly processes, affected by successional stage and spatial gradients

Secondary forests represent an increasing proportion of global forest cover and offer a range of ecosystem services that are integral to environmental policy targets. Highly disturbed landscapes with temporal records of forest plant community composition offer key insights into the processes that shape plant communities as forests undergo secondary succession. We investigated patterns of plant community phylogenetic structure and phylogenetic beta diversity. Mean pairwise distance (MPD) and Mean Nearest Taxon Distance (MNTD) metrics were determined between co-occurring species within plant communities, in addition to phylogenetic beta diversity metrics relative to null models of random phylogenetic assembly. MPD and MNTD were compared between elevational and successional classes and modelled as products of intercommunity distance (metres) and forest community age (years). Phylogenetic nonmetric multidimensional scaling explored phylogenetic community structure between lowland and montane forest type in Hong Kong. We found that plant communities in secondary forests in Hong Kong exhibited patterns of increased basal phylogenetic clustering with increasing community elevation, while phylogenetic turnover was influenced by spatial and successional factors in lowland and montane forest. Our findings indicate differential community assembly in lowland compared to montane forest type in Hong Kong, as well as evidence for barriers to plant dispersal in secondary forest communities due to patterns of spatial phylogenetic clustering. Plant communities in montane forests were found to be phylogenetically distinct from lowland forest plant communities. Patterns of spatial phylogenetic clustering may suggest significant dispersal or post-dispersal processes causing the clustering of related species at fine spatial scales, while phylogenetic turnover with increasing successional age may indicate compositional changes during the process of passive forest regeneration. Collectively, these results emphasize the need to investigate active pathways for rewilding dispersal limited late successional forest tree species in Hong Kong.

Construction of core genome multi-locus sequence typing schemes for population structure analyses of Nocardia species

Nocardia, a member of the Actinobacteria phylum, populates diverse habitats globally, with certain species being the cause of various clinical infections in humans. There is paucity of data regarding the population structure of this genus and of established genomic-based phylogenetic methods. We examined the whole genome sequences of 193 isolates spanning five major pathogenic Nocardia species sourced from public databases, encompassing diverse geographic regions. Using the chewBBACA pipeline, a species-specific core genome multilocus sequence typing (cgMLST) schema was created for N. cyriacigeorgica, N. farcinica, N. brasiliensis, N. wallacei, and N. abscessus. Additional genomic features that were examined included virulence factor (VF) profile, total length and open-reading frame count, the core genome length and core gene count, and GC content. Our findings indicated that: (i) N. brasiliensis diverges significantly from the other four species, underscoring its distinct evolutionary trajectory; (ii) the population structures of all species were polyclonal, with phylogenetic clustering occurring in the minority of isolates; (iii) clonal complexes were largely restricted to specific geographical locations, rather than demonstrating a global distribution, and (iv) initial evidence suggests no direct common-source transmission amongst the studied strains. Our study establishes a comprehensive genome-based phylogenetic methodology for population structure of Nocardia species.

Transmission network of Hepatitis C virus subtype 2a in Huazhou County, Shaanxi Province, China

BackgroundHuazhou County has one of the highest rates of hepatitis C virus (HCV) infection incidence and prevalence in Shaanxi Province, northwest China. Understanding the characteristics of HCV transmission patterns in this area could help guide targeted prevention strategies. This study employed phylogenetic analysis and the construction of a molecular transmission network of HCV-infected people in Huazhou County to describe the predominant strains of HCV and identify factors associated with onward transmission.MethodsWhole blood samples were obtained from HCV RNA-positive individuals for sequencing of the non-structural protein 5B region. A maximum-likelihood (ML) phylogenetic tree was constructed to determine HCV subgenotypes, and Bayesian phylogenetic analysis was employed to estimate the evolutionary history. The transmission network was constructed using the ML phylogenetic tree and pairwise distances. Logistic regression was used to identify factors associated with clustering in the transmission network.ResultsML phylogenetic analysis confirmed that the 61 sequences analyzed in the study belonged to subtype 2a. Bayesian phylogenetic analysis showed that the majority of subtype 2a sequences originated in the northwest of China and had descended approximately 8 to 20 years before sampling. Overall, 26.2% of participant sequences were grouped into phylogenetic network clusters. Multivariate logistic regression showed that individuals who had a history of blood transfusions and were living in Shi Village, Huazhou County, were more likely to form clusters within the transmission network.ConclusionHCV transmission in Huazhou County was predominantly associated with subtype 2a. Having a history of blood transfusions and living in residential Shi Village, Huazhou County, were factors associated with a high risk of HCV infection transmission. Prioritizing targeted interventions for these patient groups may help to prevent further infections.

Joint HIV and hepatitis C virus phylogenetic analyses signal network overlap among women engaged in sex work and men who purchase sex.

Transmission of HIV and hepatitis C virus (HCV) are heavily influenced by complex interactions within sexual or injecting networks where risk behaviors occur. In Ukraine, women engaged in sex work (WSW) and men who purchase sex (MWPS) are disproportionately affected by both viruses. The aim of our study was to the investigate the influence of underlying networks on transmission of HIV and HCV. A cross-sectional integrated bio-behavioural survey was implemented among 560 WSW and 370 MWPS representative of sex work hotspots in Dnipro, Ukraine (December 2017 to March 2018). A portion of the HIV reverse transcriptase gene (n = 13; 62% WSW, 38% MWPS) and HCV NS5B gene (n = 46; 70% WSW, 30% MWPS) were sequenced from dried blood spot specimens. Tip-to-tip distances on phylogenetic trees were used to infer phylogenetic clusters for identifying potential transmission clusters. Phylogenetic analyses identified two HIV clusters containing four sequences (50% WSW; 50% MWPS) and 11 HCV clusters containing 31 sequences - the majority comprising infections in WSW (83.9%). Nearly half (45.4%) of HCV clusters contained at least one WSW with a history of injecting drugs. Joint analyses of HIV and HCV signal overlap in sex work and injecting networks in Ukraine, suggesting implications for the comprehensive coverage of prevention programs for WSW including harm reduction services. Conducting phylogenetic analyses with HCV may provide a more complete appraisal of underlying transmission networks than HIV alone, particularly in the context of high HIV treatment coverage yielding viral suppression.

Widespread occurrence of dissolved oxygen anomalies, aerobic microbes, and oxygen-producing metabolic pathways in apparently anoxic environments.

Nearly all molecular oxygen (O2) on Earth is produced via oxygenic photosynthesis by plants or photosynthetically active microorganisms. Light-independent O2 production, which occurs both abiotically, e.g., through water radiolysis, or biotically, e.g., through the dismutation of nitric oxide or chlorite, has been thought to be negligible to the Earth system. However, recent work indicates that O2 is produced and consumed in dark and apparently anoxic environments at a much larger scale than assumed. Studies have shown that isotopically light O2 can accumulate in old groundwaters; that strictly aerobic microorganisms are present in many apparently anoxic habitats; and that microbes and metabolisms that can produce O2 without light are widespread and abundant in diverse ecosystems. Analysis of published metagenomic data reveals that the enzyme putatively capable of nitric oxide dismutation (NOD) forms four major phylogenetic clusters and occurs in at least 16 bacterial phyla most notably the Bacteroidota. Similarly, a re-analysis of published isotopic signatures of dissolved O2 in groundwater suggests in-situ production in up to half of the studied ecosystems. Geochemical and microbiological data supports the conclusion that "dark oxygen" production is an important and widespread yet overlooked process in apparently anoxic environments with far-reaching implications for subsurface biogeochemistry and ecology.

Profile of Persons Recently Infected with HIV-1 in Belgium: New Insights to Tailor Prevention Efforts.

Despite wide availability of prevention and treatment services, including the ongoing roll-out of pre-exposure prophylaxis (PrEP), the HIV epidemic is not under control in Belgium. Hence, there is a recognized need to improve case finding and early diagnosis to curb the further spread of HIV more effectively. The objective of the present study was to improve insight into the profiles of persons recently infected with HIV-1 and on their prevention trajectory. Between May 2018 and December 2022, we selected persons diagnosed in Belgium within three months of the presumed infection date. We then analyzed information collected using a questionnaire covering topics on HIV testing, sexually transmitted infections (STIs), PrEP use, sexual behavior, partner notification and substance use. The data obtained were analyzed alongside information derived from phylogenetic cluster analysis of the viral source of infection. A total of 93 persons with a recent HIV-1 infection completed the questionnaire, the majority (74%) being MSM, 14% were heterosexual women and 12% were heterosexual men. Nearly one-third of participants engaged in sexual activity with an average of 2 to 5 casual partners around the presumed time of infection. A significant percentage reported frequent substance use during sexual activity (65%), being previously diagnosed with STI (65%) and using condoms infrequently (44%). 63% reported a testing frequency of at least one HIV test per year before being diagnosed and 46% notified their previous sex partner(s) after being diagnosed. Over 20% of respondents (including 11 MSM, 4 heterosexual men and 5 heterosexual women) reported exclusive sexual activity with their steady partner. Eight participants (9%, all MSM, 75% born outside of Belgium) reported PrEP use in the past. No significant differences in behavioral characteristics were found between persons who were part of a local transmission cluster (48%) and persons that were not part of a cluster (47%). The study results revealed that the majority of persons diagnosed early with HIV-1 infection in Belgium exhibited characteristics corresponding to a high-at-risk population and were aware of this risk, as evidenced by a high testing frequency. However, partner notification rates were low and use and awareness of PrEP limited. A notable group of persons not corresponding to the high-risk profiles was also identified. This information may help to expose missed opportunities for prevention and contribute to enhancing the implementation of future prevention measures.

Molecular cluster, transmission characteristics, origin and dynamics analysis of HIV-1 CRF59_01B in China: A molecular epidemiology study

PurposeThis study investigated for the HIV-1 CRF59_01B epidemic's spatiotemporal dynamics and its transmission networks in China. MethodsBetween 2007 and 2020, a total of 250 partial pol gene sequences of HIV-1 CRF59_01B were collected from four regions (10 Chinese provinces). Phylogenetic tree construction and cluster identification were then performed. The Bayesian skyline and birth–death susceptible–infected–removed models were employed for the phylodynamic analyses of subtypes and large clusters, respectively. Phylogenetic analyses and trait diffusion of these sequences were performed using Bayesian phylogenetic methods (beast-classic package). Distance-based molecular network analyses were performed to identify putative relationships. ResultsUsing a genetic distance threshold of 1.3 %, We identified 45 clusters that included 62.40 % (156/250) of the sequences. Three clusters (6.67 %, 3/45) had 10 or more sequences, and were considered "large clusters". Six clusters (13.33 %) included sequences from different regions (Southeast, Northeast, Southeast, and Central China). Thirteen clusters (28.89 %) included sequences of men who had sex with men only, three clusters (6.67 %) included sequences of heterosexuals only, and 12 clusters (26.67 %) included sequences of both groups. The substitution rate of CRF59_01B was 1.91 × 10–3 substitutions per site per year [95 % highest posterior density (HPD) interval: 1.39 × 10−3–2.49 × 10−3)], the time to the most recent common ancestor of CRF59_01B was to be 1992.83 (95 % HPD: 1977.97–2002.81). A Bayesian skyline plot revealed that the effective population size of CRF59_01B increased from 2000 to 2015 and remained stable after 2015. The large clusters showed continuous growth from 2013 to 2020. Phylogeographic analysis showed that CRF59_01B B most likely originated in Southeast China, with a posterior probability of 97.44 %, and then spread to other regions. ConclusionsOur study revealed the temporal and geographical origins of HIV-1 CRF59_01B as well as the process of transmission among various regions and risk groups in China, which can help develop targeted HIV prevention strategies.

Phylogenetic Analysis Based on Whole Genome Sequences, Antibiotic Resistance, and Virulence of Salmonella enterica Clinical Isolates from South Korea.

Salmonella is a major cause of foodborne disease and frequently causes human salmonellosis in South Korea. In this study, we investigated the genome diversity, antimicrobial resistance, and virulence of clinical isolates of Salmonella enterica from South Korea. We collected 42 S. enterica subsp. enterica isolates from two hospitals in South Korea. Whole genome sequences were determined. Serovars and sequence types (STs) based on multilocus sequence typing (MLST) were identified from whole genome sequences. Phylogenetic trees based on whole genome sequences and a minimum spanning tree based on MLST were constructed. Human serum resistance assays and gentamicin protection assays were performed to assess in vitro virulence. Nineteen serovars were identified among 42 clinical isolates, including nine Salmonella Typhi isolates. There were inconsistencies between serogroups and phylogenetic clusters in the phylogenetic tree and minimum spanning tree, but high clonality of S. Typhi was observed. Salmonella Typhi isolates were divided into two clusters, corresponding to ST1 and ST2. Isolates of serovars Typhimurium and I4,[5],12:i:- clustered into a group, and a hybrid isolate between the two serovars was identified. Four ciprofloxacin-resistant isolates were identified among nine S. Typhi isolates, and all isolates of S. Enteritidis and S. Panama were resistant to colistin. The gentamicin protection assay revealed that serogroup D1 was significantly less virulent than the other serogroups. Our study suggests high diversity of S. enterica clinical isolates from South Korea and non-monophyly of serogroups. In addition, subgroups of S. Typhi isolates and a hybrid isolate between serovars Typhimurium and I4,[5],12:i:- were identified.

HEV-3 subtypes and strains detected in cases of HEV infection in central Italy from 2015 to 2023.

HEV is an emerging pathogen in Europe and was previously shown to be hyperendemic in areas of Abruzzo and Lazio, Central Italy. No systematic analysis of the HEV strains responsible for human infections over several years in Central Italy has previously been reported. Aim of the study was the molecular characterization of HEV from autochthonous hepatitis E cases occurred in Abruzzo and Lazio between 2015 and 2023. Samples from 118 cases collected as part of virological surveillance in Abruzzo and Lazio from 2015 to 2023 were subjected to HEV sequencing and phylogenetic analysis. The main observed subtype was 3f, followed by 3c and 3e. The annual subtype distribution was quite stable over the observation period, but 3f cases tended to concentrate in winter/early spring whereas 3e cases in summer. Phylogenetic clusters of highly related sequences (a) highlighted unrecognized "point source outbreaks", (b) provided molecular support to temporally and/or geographically linked cases and (c) provided evidence for transmission of identical/highly related strains up to months/years following their first detection. The data provide an overview of the HEV strains responsible for human infections over eight years in Central Italy. The observed subtype distribution appears to agree better with the subtype distribution reported in Italy in pigs rather than in geographically matched wild boars, suggesting pig and its derivate food was a more frequent source of infection than wild boar in Abruzzo and Lazio. Molecular characterization is essential to recognize "point source outbreaks" and to monitor HEV circulation.