Adeno-associated virus 2 infection in children with non-A-E hepatitis.

An outbreak of acute hepatitis of unknown aetiology in children was reported in Scotland1 in April 2022 and has now been identified in 35 countries2. Several recent studies have suggested an association with human adenovirus with this outbreak, a virus not commonly associated with hepatitis. Here we report a detailed case-control investigation and find an association between adeno-associated virus 2 (AAV2) infection and host genetics in disease susceptibility. Using next-generation sequencing, PCR with reverse transcription, serology and in situ hybridization, we detected recent infection with AAV2 in plasma and liver samples in 26 out of 32 (81%) cases of hepatitis compared with 5 out of 74 (7%) of samples from unaffected individuals. Furthermore, AAV2 was detected within ballooned hepatocytes alongside a prominent T cell infiltrate in liver biopsy samples. In keeping with a CD4+ T-cell-mediated immune pathology, the human leukocyte antigen (HLA) class II HLA-DRB1*04:01 allele was identified in 25 out of 27 cases (93%) compared with a background frequency of 10 out of 64 (16%; P = 5.49 × 10-12). In summary, we report an outbreak of acute paediatric hepatitis associated with AAV2 infection (most likely acquired as a co-infection with human adenovirus that is usually required as a 'helper virus' to support AAV2 replication) and disease susceptibility related to HLA class II status.

Unravelling the complex interplay between antibiotic consumption and adaptive changes in methicillin-resistant Staphylococcus aureus.

OBJECTIVES: This study aims to elucidate the genomic dynamics driving the emergence of antimicrobial resistance (AMR), with a specific focus on the interplay between AMR and antimicrobial usage. METHODS: We conducted a comprehensive analysis using a ST239 methicillin-resistant Staphylococcus aureus (MRSA) dataset over a continuous 12-year period from a single hospital. Genomic analyses were performed tracking the changes in MRSA populations, particularly the emergence of reduced vancomycin susceptibility, and assessing the impact of glycopeptide use on these emergence events. RESULTS: Our findings reveal a significant correlation between hospital glycopeptide usage and the selection of MRSA strains with reduced vancomycin susceptibility. Genomic analyses provided insights into the molecular mechanisms driving resistance emergence, including the slowing of the molecular clock rate in response to heightened antimicrobial consumption. CONCLUSIONS: In conclusion, this study the highlights the complex dynamics between AMR and antimicrobial use at the hospital level. The observed correlation between antimicrobial consumption and the development of less susceptible MRSA strains underscores the importance of antimicrobial stewardship programmes and the establishment of optimal consumption thresholds for mitigating AMR effectively.

Consideration of within-patient diversity highlights transmission pathways and antimicrobial resistance gene variability in vancomycin-resistant Enterococcus faecium.

BACKGROUND: WGS is increasingly being applied to healthcare-associated vancomycin-resistant Enterococcus faecium (VREfm) outbreaks. Within-patient diversity could complicate transmission resolution if single colonies are sequenced from identified cases. OBJECTIVES: Determine the impact of within-patient diversity on transmission resolution of VREfm. MATERIALS AND METHODS: Fourteen colonies were collected from VREfm positive rectal screens, single colonies were collected from clinical samples and Illumina WGS was performed. Two isolates were selected for Oxford Nanopore sequencing and hybrid genome assembly to generate lineage-specific reference genomes. Mapping to closely related references was used to identify genetic variations and closely related genomes. A transmission network was inferred for the entire genome set using Phyloscanner. RESULTS AND DISCUSSION: In total, 229 isolates from 11 patients were sequenced. Carriage of two or three sequence types was detected in 27% of patients. Presence of antimicrobial resistance genes and plasmids was variable within genomes from the same patient and sequence type. We identified two dominant sequence types (ST80 and ST1424), with two putative transmission clusters of two patients within ST80, and a single cluster of six patients within ST1424. We found transmission resolution was impaired using fewer than 14 colonies. CONCLUSIONS: Patients can carry multiple sequence types of VREfm, and even within related lineages the presence of mobile genetic elements and antimicrobial resistance genes can vary. VREfm within-patient diversity could be considered in future to aid accurate resolution of transmission networks.

Cost-benefit analysis of ecosystem modeling to support fisheries management.

Mathematical and statistical models underlie many of the world's most important fisheries management decisions. Since the 19th century, difficulty calibrating and fitting such models has been used to justify the selection of simple, stationary, single-species models to aid tactical fisheries management decisions. Whereas these justifications are reasonable, it is imperative that we quantify the value of different levels of model complexity for supporting fisheries management, especially given a changing climate, where old methodologies may no longer perform as well as in the past. Here we argue that cost-benefit analysis is an ideal lens to assess the value of model complexity in fisheries management. While some studies have reported the benefits of model complexity in fisheries, modeling costs are rarely considered. In the absence of cost data in the literature, we report, as a starting point, relative costs of single-species stock assessment and marine ecosystem models from two Australian organizations. We found that costs varied by two orders of magnitude, and that ecosystem model costs increased with model complexity. Using these costs, we walk through a hypothetical example of cost-benefit analysis. The demonstration is intended to catalyze the reporting of modeling costs and benefits.

Unravelling patient pathways in the context of antibacterial resistance in East Africa.

BACKGROUND: A key factor driving the development and maintenance of antibacterial resistance (ABR) is individuals' use of antibiotics (ABs) to treat illness. To better understand motivations and context for antibiotic use we use the concept of a patient treatment-seeking pathway: a treatment journey encompassing where patients go when they are unwell, what motivates their choices, and how they obtain antibiotics. This paper investigates patterns and determinants of patient treatment-seeking pathways, and how they intersect with AB use in East Africa, a region where ABR-attributable deaths are exceptionally high. METHODS: The Holistic Approach to Unravelling Antibacterial Resistance (HATUA) Consortium collected quantitative data from 6,827 adult outpatients presenting with urinary tract infection (UTI) symptoms in Kenya, Tanzania, and Uganda between February 2019- September 2020, and conducted qualitative in-depth patient interviews with a subset (n = 116). We described patterns of treatment-seeking visually using Sankey plots and explored explanations and motivations using mixed-methods. Using Bayesian hierarchical regression modelling, we investigated the associations between socio-demographic, economic, healthcare, and attitudinal factors and three factors related to ABR: self-treatment as a first step, having a multi-step treatment pathway, and consuming ABs. RESULTS: Although most patients (86%) sought help from medical facilities in the first instance, many (56%) described multi-step, repetitive treatment-seeking pathways, which further increased the likelihood of consuming ABs. Higher socio-economic status patients were more likely to consume ABs and have multi-step pathways. Reasons for choosing providers (e.g., cost, location, time) were conditioned by wider structural factors such as hybrid healthcare systems and AB availability. CONCLUSION: There is likely to be a reinforcing cycle between complex, repetitive treatment pathways, AB consumption and ABR. A focus on individual antibiotic use as the key intervention point in this cycle ignores the contextual challenges patients face when treatment seeking, which include inadequate access to diagnostics, perceived inefficient public healthcare and ease of purchasing antibiotics without prescription. Pluralistic healthcare landscapes may promote more complex treatment seeking and therefore inappropriate AB use. We recommend further attention to healthcare system factors, focussing on medical facilities (e.g., accessible diagnostics, patient-doctor interactions, information flows), and community AB access points (e.g., drug sellers).

Detecting defense mechanisms from Adult Attachment Interview (AAI) transcripts using machine learning.

OBJECTIVE: Defensive functioning (i.e., unconscious process used to manage real or perceived threats) may play a role in the development of various psychopathologies. It is typically assessed via observer rating measures, however, human coding of defensive functioning is resource-intensive and time-consuming. The purpose of this study was to develop a machine learning approach to automate coding of defense mechanisms from interview transcripts. METHOD: Participants included a clinical sample of women with binge-eating disorder (n = 92) and a community sample without binge-eating disorder (n = 66). We trained and evaluated five RoBERTa-based models to detect the presence of defenses in 16,785 interviewer-participant talk-turn pairs nested within 192 interviews. A model detected the presence of any defense, while four additional models detected the most common defenses in this sample (repression, intellectualization, reaction formation, undoing). RESULTS: The models were capable of distinguishing defenses (ROC-AUC .82-.90) but were not proficient enough to warrant replacing human coders (PR-AUC .28-.60). Follow-up analysis was performed to assess other practical uses of these models. DISCUSSION: Our machine learning models could be used to assist coders. Future research should conduct a deployment study to determine if human coding of defense mechanisms can be expedited using machine learning models.

Presence of optrA-mediated linezolid resistance in multiple lineages and plasmids of Enterococcus faecalis revealed by long read sequencing.

Transferable linezolid resistance due to optrA, poxtA, cfr and cfr-like genes is increasingly detected in enterococci associated with animals and humans globally. We aimed to characterize the genetic environment of optrA in linezolid-resistant Enterococcus faecalis isolates from Scotland. Six linezolid-resistant E. faecalis isolated from urogenital samples were confirmed to carry the optrA gene by PCR. Short read (Illumina) sequencing showed the isolates were genetically distinct (>13900 core SNPs) and belonged to different MLST sequence types. Plasmid contents were examined using hybrid assembly of short and long read (Oxford Nanopore MinION) sequencing technologies. The optrA gene was located on distinct plasmids in each isolate, suggesting that transfer of a single plasmid did not contribute to optrA dissemination in this collection. pTM6294-2, BX5936-1 and pWE0438-1 were similar to optrA-positive plasmids from China and Japan, while the remaining three plasmids had limited similarity to other published examples. We identified the novel Tn6993 transposon in pWE0254-1 carrying linezolid (optrA), macrolide (ermB) and spectinomycin [ANT(9)-Ia] resistance genes. OptrA amino acid sequences differed by 0-20 residues. We report multiple variants of optrA on distinct plasmids in diverse strains of E. faecalis. It is important to identify the selection pressures driving the emergence and maintenance of resistance against linezolid to retain the clinical utility of this antibiotic.

Unrecognized threat to global soil carbon by a widespread invasive species.

Most of Earth's terrestrial carbon is stored in the soil and can be released as carbon dioxide (CO2 ) when disturbed. Although humans are known to exacerbate soil CO2 emissions through land-use change, we know little about the global carbon footprint of invasive species. We predict the soil area disturbed and resulting CO2 emissions from wild pigs (Sus scrofa), a pervasive human-spread vertebrate that uproots soil. We do this using models of wild pig population density, soil damage, and their effect on soil carbon emissions. Our models suggest that wild pigs are uprooting a median area of 36,214 km2 (mean of 123,517 km2 ) in their non-native range, with a 95% prediction interval (PI) of 14,208 km2 -634,238 km2 . This soil disturbance results in median emissions of 4.9 million metric tonnes (MMT) CO2 per year (equivalent to 1.1 million passenger vehicles or 0.4% of annual emissions from land use, land-use change, and forestry; mean of 16.7 MMT) but that it is highly uncertain (95% PI, 0.3-94 MMT CO2 ) due to variability in wild pig density and soil dynamics. This uncertainty points to an urgent need for more research on the contribution of wild pigs to soil damage, not only for the reduction of anthropogenically related carbon emissions, but also for co-benefits to biodiversity and food security that are crucial for sustainable development.

Invasive wild pigs (Sus scrofa) as a human-mediated source of soil carbon emissions: Uncertainties and future directions.

Invasive wild pigs (Sus scrofa) have been spread by humans outside of their native range and are now established on every continent except Antarctica. Through their uprooting of soil, they affect societal and environmental values. Our recent article explored another threat from their soil disturbance: greenhouse gas emissions (O'Bryan et al., Global Change Biology, 2021). In response to our paper, Don (Global Change Biology, 2021) claims there is no threat to global soil carbon stocks by wild pigs. While we did not investigate soil carbon stocks, we examine uncertainties regarding soil carbon emissions from wild pig uprooting and their implications for management and future research.

Genomics of Natural Populations of Staphylococcus aureus.

Staphylococcus aureus is a major human pathogen and an important cause of livestock infections. The first S. aureus genomes to be published, 15 years ago, provided the first view of genome structure and gene content. Since then, thousands of genomes from a wide array of strains from different sources have been sequenced. Comparison of these sequences has resulted in broad insights into population structure, bacterial evolution, clone emergence and expansion, and the molecular basis of niche adaptation. Furthermore, this information is now being applied clinically in outbreak investigations to inform infection control measures and to determine appropriate treatment regimens. In this review, we summarize some of the broad insights into S. aureus biology gained from the analysis of genomes and discuss future directions and opportunities in this dynamic field of research.

Poacher-population dynamics when legal trade of naturally deceased organisms funds anti-poaching enforcement.

Can a regulated, legal market for wildlife products protect species threatened by poaching? It is one of the most controversial ideas in biodiversity conservation. Perhaps the most convincing reason for legalizing wildlife trade is that trade revenue could fund the protection and conservation of poached species. In this paper, we examine the possible poacher-population dynamic consequences of legal trade funding conservation. The model consists of a manager scavenging carcasses for wildlife product, who then sells the product, and directs a portion of the revenue towards funding anti-poaching law enforcement. Through a global analysis of the model, we derive the critical proportion of product the manager must scavenge, and the critical proportion of trade revenue the manager must allocate towards increased enforcement, in order for legal trade to lead to abundant long-term wildlife populations. We illustrate how the model could inform management with parameter values derived from the African elephant literature, under a hypothetical scenario where a manager scavenges elephant carcasses to sell ivory. We find that there is a large region of parameter space where populations go extinct under legal trade unless a significant portion of trade revenue is directed towards protecting populations from poaching. The model is general and therefore can be used as a starting point for exploring the consequences of funding many conservation programs using wildlife trade revenue.

Informing management decisions for ecological networks, using dynamic models calibrated to noisy time-series data.

Well-intentioned environmental management can backfire, causing unforeseen damage. To avoid this, managers and ecologists seek accurate predictions of the ecosystem-wide impacts of interventions, given small and imprecise datasets, which is an incredibly difficult task. We generated and analysed thousands of ecosystem population time series to investigate whether fitted models can aid decision-makers to select interventions. Using these time-series data (sparse and noisy datasets drawn from deterministic Lotka-Volterra systems with two to nine species, of known network structure), dynamic model forecasts of whether a species' future population will be positively or negatively affected by rapid eradication of another species were correct > 70% of the time. Although 70% correct classifications is only slightly better than an uninformative prediction (50%), this classification accuracy can be feasibly improved by increasing monitoring accuracy and frequency. Our findings suggest that models may not need to produce well-constrained predictions before they can inform decisions that improve environmental outcomes.

SpeS: A Novel Superantigen and Its Potential as a Vaccine Adjuvant against Strangles.

Bacterial superantigens (sAgs) are powerful activators of the immune response that trigger unspecific T cell responses accompanied by the release of proinflammatory cytokines. Streptococcus equi (S. equi) and Streptococcus zooepidemicus (S. zooepidemicus) produce sAgs that play an important role in their ability to cause disease. Strangles, caused by S. equi, is one of the most common infectious diseases of horses worldwide. Here, we report the identification of a new sAg of S. zooepidemicus, SpeS, and show that mutation of the putative T cell receptor (TCR)-binding motif (YAY to IAY) abrogated TCR-binding, whilst maintaining interaction with major histocompatibility complex (MHC) class II molecules. The fusion of SpeS and SpeSY39I to six S. equi surface proteins using two different peptide linkers was conducted to determine if MHC class II-binding properties were maintained. Proliferation assays, qPCR and flow cytometry analysis showed that SpeSY39I and its fusion proteins induced less mitogenic activity and interferon gamma expression when compared to SpeS, whilst retaining Antigen-Presenting Cell (APC)-binding properties. Our data suggest that SpeSY39I-surface protein fusions could be used to direct vaccine antigens towards antigen-presenting cells in vivo with the potential to enhance antigen presentation and improve immune responses.

The mesoscavenger release hypothesis and implications for ecosystem and human well-being.

Many apex scavenger species, including nearly all obligate scavengers, are in a state of rapid decline and there is growing evidence these declines can drastically alter ecological food webs. Our understanding of how apex scavengers regulate populations of mesoscavengers, those less-efficient scavengers occupying mid-trophic levels, is improving; yet, there has been no comprehensive evaluation of the evidence around the competitive release of these species by the loss of apex scavengers. Here we present current evidence that supports the mesoscavenger release hypothesis, the increase in mesoscavengers and increase in carrion in the face of declining apex scavengers. We provide two models of scavenger dynamics to demonstrate that the mesoscavenger release hypothesis is consistent with ecological theory. We further examine the ecological and human well-being implications of apex scavenger decline, including carrion removal and disease regulation services.

Forecasting species range dynamics with process-explicit models: matching methods to applications.

Knowing where species occur is fundamental to many ecological and environmental applications. Species distribution models (SDMs) are typically based on correlations between species occurrence data and environmental predictors, with ecological processes captured only implicitly. However, there is a growing interest in approaches that explicitly model processes such as physiology, dispersal, demography and biotic interactions. These models are believed to offer more robust predictions, particularly when extrapolating to novel conditions. Many process-explicit approaches are now available, but it is not clear how we can best draw on this expanded modelling toolbox to address ecological problems and inform management decisions. Here, we review a range of process-explicit models to determine their strengths and limitations, as well as their current use. Focusing on four common applications of SDMs - regulatory planning, extinction risk, climate refugia and invasive species - we then explore which models best meet management needs. We identify barriers to more widespread and effective use of process-explicit models and outline how these might be overcome. As well as technical and data challenges, there is a pressing need for more thorough evaluation of model predictions to guide investment in method development and ensure the promise of these new approaches is fully realised.

Building a genomic framework for prospective MRSA surveillance in the United Kingdom and the Republic of Ireland.

The correct interpretation of microbial sequencing data applied to surveillance and outbreak investigation depends on accessible genomic databases to provide vital genetic context. Our aim was to construct and describe a United Kingdom MRSA database containing over 1000 methicillin-resistant Staphylococcus aureus (MRSA) genomes drawn from England, Northern Ireland, Wales, Scotland, and the Republic of Ireland over a decade. We sequenced 1013 MRSA submitted to the British Society for Antimicrobial Chemotherapy by 46 laboratories between 2001 and 2010. Each isolate was assigned to a regional healthcare referral network in England and was otherwise grouped based on country of origin. Phylogenetic reconstructions were used to contextualize MRSA outbreak investigations and to detect the spread of resistance. The majority of isolates (n = 783, 77%) belonged to CC22, which contains the dominant United Kingdom epidemic clone (EMRSA-15). There was marked geographic structuring of EMRSA-15, consistent with widespread dissemination prior to the sampling decade followed by local diversification. The addition of MRSA genomes from two outbreaks and one pseudo-outbreak demonstrated the certainty with which outbreaks could be confirmed or refuted. We identified local and regional differences in antibiotic resistance profiles, with examples of local expansion, as well as widespread circulation of mobile genetic elements across the bacterial population. We have generated a resource for the future surveillance and outbreak investigation of MRSA in the United Kingdom and Ireland and have shown the value of this during outbreak investigation and tracking of antimicrobial resistance.

Naturally occurring polymorphisms in the virulence regulator Rsp modulate Staphylococcus aureus survival in blood and antibiotic susceptibility.

Nasal colonization by the pathogen Staphylococcus aureus is a risk factor for subsequent infection. Loss of function mutations in the gene encoding the virulence regulator Rsp are associated with the transition of S. aureus from a colonizing isolate to one that causes bacteraemia. Here, we report the identification of several novel activity-altering mutations in rsp detected in clinical isolates, including for the first time, mutations that enhance agr operon activity. We assessed how these mutations affected infection-relevant phenotypes and found loss and enhancement of function mutations to have contrasting effects on S. aureus survival in blood and antibiotic susceptibility. These findings add to the growing body of evidence that suggests S. aureus 'trades off' virulence for the acquisition of traits that benefit survival in the host, and indicates that infection severity and treatment options can be significantly affected by mutations in the virulence regulator rsp.

Genome specialization and decay of the strangles pathogen, Streptococcus equi, is driven by persistent infection.

Strangles, the most frequently diagnosed infectious disease of horses worldwide, is caused by Streptococcus equi. Despite its prevalence, the global diversity and mechanisms underlying the evolution of S. equi as a host-restricted pathogen remain poorly understood. Here, we define the global population structure of this important pathogen and reveal a population replacement in the late 19th or early 20th Century. Our data reveal a dynamic genome that continues to mutate and decay, but also to amplify and acquire genes despite the organism having lost its natural competence and become host-restricted. The lifestyle of S. equi within the horse is defined by short-term acute disease, strangles, followed by long-term infection. Population analysis reveals evidence of convergent evolution in isolates from post-acute disease samples as a result of niche adaptation to persistent infection within a host. Mutations that lead to metabolic streamlining and the loss of virulence determinants are more frequently found in persistent isolates, suggesting that the pathogenic potential of S. equi reduces as a consequence of long-term residency within the horse post-acute disease. An example of this is the deletion of the equibactin siderophore locus that is associated with iron acquisition, which occurs exclusively in persistent isolates, and renders S. equi significantly less able to cause acute disease in the natural host. We identify several loci that may similarly be required for the full virulence of S. equi, directing future research toward the development of new vaccines against this host-restricted pathogen.

Genome sequencing defines phylogeny and spread of methicillin-resistant Staphylococcus aureus in a high transmission setting.

Methicillin-resistant Staphylococcus aureus (MRSA) is a major cause of nosocomial infection. Whole-genome sequencing of MRSA has been used to define phylogeny and transmission in well-resourced healthcare settings, yet the greatest burden of nosocomial infection occurs in resource-restricted settings where barriers to transmission are lower. Here, we study the flux and genetic diversity of MRSA on ward and individual patient levels in a hospital where transmission was common. We repeatedly screened all patients on two intensive care units for MRSA carriage over a 3-mo period. All MRSA belonged to multilocus sequence type 239 (ST 239). We defined the population structure and charted the spread of MRSA by sequencing 79 isolates from 46 patients and five members of staff, including the first MRSA-positive screen isolates and up to two repeat isolates where available. Phylogenetic analysis identified a flux of distinct ST 239 clades over time in each intensive care unit. In total, five main clades were identified, which varied in the carriage of plasmids encoding antiseptic and antimicrobial resistance determinants. Sequence data confirmed intra- and interwards transmission events and identified individual patients who were colonized by more than one clade. One patient on each unit was the source of numerous transmission events, and deep sampling of one of these cases demonstrated colonization with a "cloud" of related MRSA variants. The application of whole-genome sequencing and analysis provides novel insights into the transmission of MRSA in under-resourced healthcare settings and has relevance to wider global health.

Burkholderia pseudomallei sequencing identifies genomic clades with distinct recombination, accessory, and epigenetic profiles.

Burkholderia pseudomallei (Bp) is the causative agent of the infectious disease melioidosis. To investigate population diversity, recombination, and horizontal gene transfer in closely related Bp isolates, we performed whole-genome sequencing (WGS) on 106 clinical, animal, and environmental strains from a restricted Asian locale. Whole-genome phylogenies resolved multiple genomic clades of Bp, largely congruent with multilocus sequence typing (MLST). We discovered widespread recombination in the Bp core genome, involving hundreds of regions associated with multiple haplotypes. Highly recombinant regions exhibited functional enrichments that may contribute to virulence. We observed clade-specific patterns of recombination and accessory gene exchange, and provide evidence that this is likely due to ongoing recombination between clade members. Reciprocally, interclade exchanges were rarely observed, suggesting mechanisms restricting gene flow between clades. Interrogation of accessory elements revealed that each clade harbored a distinct complement of restriction-modification (RM) systems, predicted to cause clade-specific patterns of DNA methylation. Using methylome sequencing, we confirmed that representative strains from separate clades indeed exhibit distinct methylation profiles. Finally, using an E. coli system, we demonstrate that Bp RM systems can inhibit uptake of non-self DNA. Our data suggest that RM systems borne on mobile elements, besides preventing foreign DNA invasion, may also contribute to limiting exchanges of genetic material between individuals of the same species. Genomic clades may thus represent functional units of genetic isolation in Bp, modulating intraspecies genetic diversity.