Impaired STING Activation Due to a Variant in the E3 Ubiquitin Ligase AMFR in a Patient with Severe VZV Infection and Hemophagocytic Lymphohistiocytosis.

Varicella zoster virus (VZV) is a neurotropic alphaherpesvirus exclusively infecting humans, causing two distinct pathologies: varicella (chickenpox) upon primary infection and herpes zoster (shingles) following reactivation. In susceptible individuals, VZV can give rise to more severe clinical manifestations, including disseminated infection, pneumonitis, encephalitis, and vasculopathy with stroke. Here, we describe a 3-year-old boy in whom varicella followed a complicated course with thrombocytopenia, hemorrhagic and necrotic lesions, pneumonitis, and intermittent encephalopathy. Hemophagocytic lymphohistiocytosis (HLH) was strongly suspected and as the condition deteriorated, HLH therapy was initiated. Although the clinical condition improved, longstanding hemophagocytosis followed despite therapy. We found that the patient carries a rare monoallelic variant in autocrine motility factor receptor (AMFR), encoding a ubiquitin ligase involved in innate cytosolic DNA sensing and interferon (IFN) production through the cyclic GMP-AMP synthase-stimulator of IFN genes (cGAS-STING) pathway. Peripheral blood mononuclear cells (PBMCs) from the patient exhibited impaired signaling downstream of STING in response dsDNA and 2'3'-cGAMP, agonists of cGAS and STING, respectively, and fibroblasts from the patient showed impaired type I IFN responses and significantly increased VZV replication. Overexpression of the variant AMFR R594C resulted in decreased K27-linked STING ubiquitination compared to WT AMFR. Moreover, ImageStream technology revealed reduced STING trafficking from ER to Golgi in cells expressing the patient AMFR R594C variant. This was supported by a dose-dependent dominant negative effect of expression of the patient AMFR variant as measured by IFN-ß reporter gene assay. Finally, lentiviral transduction with WT AMFR partially reconstituted 2'3'-cGAMP-induced STING-mediated signaling and ISG expression in patient PBMCs. This work links defective AMFR-STING signaling to severe VZV disease and hyperinflammation and suggests a direct role for cGAS-STING in the control of viral infections in humans. In conclusion, we describe a novel genetic etiology of severe VZV disease in childhood, also representing the first inborn error of immunity related to a defect in the cGAS-STING pathway.

Core genome multilocus sequence typing (cgMLST) applicable to the monophyletic Klebsiella oxytoca species complex.

The environmental bacterium Klebsiella oxytoca displays an alarming increase of antibiotic-resistant strains that frequently cause outbreaks in intensive care units. Due to its prevalence in the environment and opportunistic presence in humans, molecular surveillance (including resistance marker screening) and high-resolution cluster analysis are of high relevance. Furthermore, K. oxytoca previously described in studies is rather a species complex (KoSC) than a single species comprising at least six closely related species that are not easily differentiated by standard typing methods. To reach a discriminatory power high enough to identify and resolve clusters within these species, whole genome sequencing is necessary. The resolution is achievable with core genome multilocus sequence typing (cgMLST) extending typing of a few housekeeping genes to thousands of core genome genes. CgMLST is highly standardized and provides a nomenclature enabling cross laboratory reproducibility and data exchange for routine diagnostics. Here, we established a cgMLST scheme not only capable of resolving the KoSC species but also producing reliable and consistent results for published outbreaks. Our cgMLST scheme consists of 2,536 core genome and 2,693 accessory genome targets, with a percentage of good cgMLST targets of 98.31% in 880 KoSC genomes downloaded from the National Center for Biotechnology Information (NCBI). We also validated resistance markers against known resistance gene patterns and successfully linked genetic results to phenotypically confirmed toxic strains carrying the til gene cluster. In conclusion, our novel cgMLST enables highly reproducible typing of four different clinically relevant species of the KoSC and thus facilitates molecular surveillance and cluster investigations.

Varicella zoster virus-induced autophagy in human neuronal and hematopoietic cells exerts antiviral activity.

Autophagy is a degradational pathway with pivotal roles in cellular homeostasis and survival, including protection of neurons in the central nervous system (CNS). The significance of autophagy as antiviral defense mechanism is recognized and some viruses hijack and modulate this process to their advantage in certain cell types. Here, we present data demonstrating that the human neurotropic herpesvirus varicella zoster virus (VZV) induces autophagy in human SH-SY5Y neuronal cells, in which the pathway exerts antiviral activity. Productively VZV-infected SH-SY5Y cells showed increased LC3-I-LC3-II conversion as well as co-localization of the viral glycoprotein E and the autophagy receptor p62. The activation of autophagy was dependent on a functional viral genome. Interestingly, inducers of autophagy reduced viral transcription, whereas inhibition of autophagy increased viral transcript expression. Finally, the genotype of patients with severe ocular and brain VZV infection were analyzed to identify potential autophagy-associated inborn errors of immunity. Two patients expressing genetic variants in the autophagy genes ULK1 and MAP1LC3B2, respectively, were identified. Notably, cells of both patients showed reduced autophagy, alongside enhanced viral replication and death of VZV-infected cells. In conclusion, these results demonstrate a neuro-protective role for autophagy in the context of VZV infection and suggest that failure to mount an autophagy response is a potential predisposing factor for development of severe VZV disease.

Real-Time Nanopore Q20+ Sequencing Enables Extremely Fast and Accurate Core Genome MLST Typing and Democratizes Access to High-Resolution Bacterial Pathogen Surveillance.

Next-generation whole-genome sequencing is essential for high-resolution surveillance of bacterial pathogens, for example, during outbreak investigations or for source tracking and escape variant analysis. However, current global sequencing and bioinformatic bottlenecks and a long time to result with standard technologies demand new approaches. In this study, we investigated whether novel nanopore Q20+ long-read chemistry enables standardized and easily accessible high-resolution typing combined with core genome multilocus sequence typing (cgMLST). We set high requirements for discriminatory power by using the slowly evolving bacterium Bordetella pertussis as a model pathogen. Our results show that the increased raw read accuracy enables the description of epidemiological scenarios and phylogenetic linkages at the level of gold-standard short reads. The same was true for our variant analysis of vaccine antigens, resistance genes, and virulence factors, demonstrating that nanopore sequencing is a legitimate competitor in the area of next-generation sequencing (NGS)-based high-resolution bacterial typing. Furthermore, we evaluated the parameters for the fastest possible analysis of the data. By combining the optimized processing pipeline with real-time basecalling, we established a workflow that allows for highly accurate and extremely fast high-resolution typing of bacterial pathogens while sequencing is still in progress. Along with advantages such as low costs and portability, the approach suggested here might democratize modern bacterial typing, enabling more efficient infection control globally.

Parentage analysis across age cohorts reveals sex differences in reproductive skew in a group-living cichlid fish, Neolamprologus multifasciatus.

Group-living animals are often faced with complex reproductive decisions, namely how to partition within-group reproduction, how to obtain extra-group reproduction and how these two means of reproduction should be balanced. The solutions to these questions can be difficult to predict because ecological conditions can affect the scopes for within-group and extra-group reproduction in complex ways. For example, individuals that are restricted from moving freely around their habitats may have limited extra-group reproductive opportunities, but at the same time, groups may live in close proximity to one another, which could potentially have the opposite effect. The group-living cichlid fish Neolamprologus multifasciatus experiences such ecological conditions, and we conducted an intensive genetic parentage analysis to investigate how reproduction is distributed within and among groups for both males and females. We found that cohabiting males live in "high-skew" societies, where dominant males monopolize the majority of within-group reproduction, while females live in "low-skew" societies, where multiple females can produce offspring concurrently. Despite extremely short distances separating groups, we inferred only very low levels of extra-group reproduction, suggesting that subordinate males have very limited reproductive opportunities. A strength of our parentage analysis lies in its inclusion of individuals that spanned a wide age range, from young fry to adults. We outline the logistical circumstances when very young offspring may not always be accessible to parentage researchers, and present strategies to overcome the challenges of inferring mating patterns from a wide age range of offspring.

Supplementation with conjugated linoleic acids extends the adiponectin deficit during early lactation in dairy cows.

Decreasing insulin sensitivity (IS) in peripheral tissues allows for partitioning nutrients towards the mammary gland. In dairy cows, extensive lipid mobilization and continued insulin resistance (IR) are typical for early lactation. Adiponectin, an adipokine, promotes IS. Supplementation with conjugated linoleic acids (CLA) in rodents and humans reduces fat mass whereby IR and hyperinsulinemia may occur. In dairy cows, CLA reduce milk fat, whereas body fat, serum free fatty acids and leptin are not affected. We aimed to investigate the effects of CLA supplementation on serum and adipose tissue (AT) adiponectin concentrations in dairy cows during the lactation driven and parity modulated changes of metabolism. High yielding cows (n=33) were allocated on day 1 post partum to either 100 g/day of a CLA mixture or a control fat supplement (CON) until day 182 post partum. Blood and subcutaneous (sc) AT (AT) biopsy samples were collected until day 252 post partum to measure adiponectin. Serum adiponectin decreased from day 21 pre partum reaching a nadir at calving and thereafter increased gradually. The distribution of adiponectin molecular weight forms was neither affected by time, parity nor treatment. Cows receiving CLA had decreased serum adiponectin concentrations whereby primiparous cows responded about 4 weeks earlier than multiparous cows. The time course of adiponectin concentrations in sc AT (corrected for residual blood) was similar to serum concentrations, without differences between CLA and CON. CLA supplementation attenuated the post partum increase of circulating adiponectin thus acting towards prolongation of peripartal IR and drain of nutrients towards the mammary gland.

Aggression and spatial positioning of kin and non-kin fish in social groups.

Group-living animals are faced with the challenge of sharing space and local resources amongst group members who may be either relatives or non-relatives. Individuals may reduce the inclusive fitness costs they incur from competing with relatives by either reducing their levels of aggression toward kin, or by maintaining physical separation between kin. In this field study, we used the group-living cichlid Neolamprologus multifasciatus to examine whether within-group aggression is reduced among group members that are kin, and whether kin occupy different regions of their group's territory to reduce kin competition over space and local resources. We determined the kinship relationships among cohabiting adults via microsatellite genotyping and then combined these with spatial and behavioral analyses of groups in the wild. We found that aggressive contests between group members declined in frequency with spatial separation between their shelters. Female kin did not engage in aggressive contests with one another, whereas non-kin females did, despite the fact these females lived at similar distances from one another on their groups' territories. Contests within male-male and male-female dyads did not clearly correlate with kinship. Non-kin male-male and male-female dyads lived at more variable distances from one another on their territories than their corresponding kin dyads. Together, our study indicates that contests among group members can be mediated by relatedness in a sex-dependent manner. We also suggest that spatial relationships can play an important role in determining the extent to which group members compete with one another.

Complete Genome Sequence of Klebsiella oxytoca Strain AHC-6, Isolated from a Patient during Acute Antibiotic-Associated Hemorrhagic Colitis.

Klebsiella oxytoca is a ubiquitous bacterium that is increasingly associated with inflammatory diseases. Here, we report the hybrid assembled genome for cytotoxic K. oxytoca strain AHC-6. The genome comprises a total of 5.7 Mbp, with a GC content of 55.2% and 5,258 coding sequences after assembly and annotation.

Whole exome sequencing of patients with varicella-zoster virus and herpes simplex virus induced acute retinal necrosis reveals rare disease-associated genetic variants.

Purpose: Herpes simplex virus (HSV) and varicella-zoster virus (VZV) are neurotropic human alphaherpesviruses endemic worldwide. Upon primary infection, both viruses establish lifelong latency in neurons and reactivate intermittently to cause a variety of mild to severe diseases. Acute retinal necrosis (ARN) is a rare, sight-threatening eye disease induced by ocular VZV or HSV infection. The virus and host factors involved in ARN pathogenesis remain incompletely described. We hypothesize an underlying genetic defect in at least part of ARN cases. Methods: We collected blood from 17 patients with HSV-or VZV-induced ARN, isolated DNA and performed Whole Exome Sequencing by Illumina followed by analysis in Varseq with criteria of CADD score > 15 and frequency in GnomAD < 0.1% combined with biological filters. Gene modifications relative to healthy control genomes were filtered according to high quality and read-depth, low frequency, high deleteriousness predictions and biological relevance. Results: We identified a total of 50 potentially disease-causing genetic variants, including missense, frameshift and splice site variants and on in-frame deletion in 16 of the 17 patients. The vast majority of these genes are involved in innate immunity, followed by adaptive immunity, autophagy, and apoptosis; in several instances variants within a given gene or pathway was identified in several patients. Discussion: We propose that the identified variants may contribute to insufficient viral control and increased necrosis ocular disease presentation in the patients and serve as a knowledge base and starting point for the development of improved diagnostic, prophylactic, and therapeutic applications.

Patterns of sex-biased dispersal are consistent with social and ecological constraints in a group-living cichlid fish.

BACKGROUND: Sex-biased dispersal is a common and widespread phenomenon that can fundamentally shape the genetic structure of the social environments in which animals live. For animals that live in and move between social groups, sex-biased dispersal can result in an asymmetry in the degree of relatedness among cohabiting males and females, which can have strong implications for their social evolution. In this study, we measured the relatedness structure within and across groups of a wild population of Neolamprologus multifasciatus, a highly-social, shell-dwelling cichlid fish endemic to Lake Tanganyika, East Africa. In total, we genotyped 812 fish from 128 social groups at 20 microsatellite loci. Neolamprologus multifasciatus live at high densities, and also experience strong ecological constraints on free movement throughout their habitat. At the same time, they exhibit sex differences in the degree of reproductive competition within their groups and this makes them an excellent model system for studying the factors associated with sex-biased dispersal. RESULTS: Social groups of N. multifasciatus consist of multiple males and females living together. We found that cohabiting females were unrelated to one another (Lynch-Ritland estimates of relatedness = 0.045 ± 0.15, average ± SD), while males shared much higher, albeit variable, levels of relatedness to other males in their groups (0.23 ± 0.27). We uncovered a pronounced decline in relatedness between males living in separate groups as the spatial separation between them increased, a pattern that was not evident in females. Female dispersal was also markedly constrained by the distribution and availability of nearby territories to which they could emigrate. CONCLUSIONS: Our results indicate female-biased dispersal in N. multifasciatus. Our study also highlights how the spatial distribution of suitable dispersal destinations can influence the movement decisions of animals. We also emphasize how sex-biased dispersal can influence the relatedness structure of the social environment in which individuals interact and compete with one another.

The Role of Autophagy in Varicella Zoster Virus Infection.

Autophagy is an evolutionary conserved cellular process serving to degrade cytosolic organelles or foreign material to maintain cellular homeostasis. Autophagy has also emerged as an important process involved in complex interactions with viral pathogens during infection. It has become apparent that autophagy may have either proviral or antiviral roles, depending on the cellular context and the specific virus. While evidence supports an antiviral role of autophagy during certain herpesvirus infections, numerous examples illustrate how herpesviruses may also evade autophagy pathways or even utilize this process to their own advantage. Here, we review the literature on varicella zoster virus (VZV) and autophagy and describe the mechanisms by which VZV may stimulate autophagy pathways and utilize these to promote cell survival or to support viral egress from cells. We also discuss recent evidence supporting an overall antiviral role of autophagy, particularly in relation to viral infection in neurons. Collectively, these studies suggest complex and sometimes opposing effects of autophagy in the context of VZV infection. Much remains to be understood concerning these virus-host interactions and the impact of autophagy on infections caused by VZV.

Essential role of autophagy in restricting poliovirus infection revealed by identification of an ATG7 defect in a poliomyelitis patient.

Paralytic poliomyelitis is a rare disease manifestation following poliovirus (PV) infection. The disease determinants remain largely unknown. We used whole exome sequencing to uncover possible contributions of host genetics to the development of disease outcome in humans with poliomyelitis. We identified a patient with a variant in ATG7, an important regulatory gene in the macroautophagy/autophagy pathway. PV infection did not induce a prominent type I interferon response, but rather activated autophagy in neuronal-like cells, and this was essential for viral control. Importantly, virus-induced autophagy was impaired in patient fibroblasts and associated with increased viral burden and enhanced cell death following infection. Lack of ATG7 prevented control of infection in neuronal-like cells, and reconstitution of patient cells with wild-type ATG7 reestablished autophagy-mediated control of infection. Collectively, these data suggest that ATG7 defect contributes to host susceptibility to PV infection and propose autophagy as an unappreciated antiviral effector in viral infection in humans.

Characterization of adiponectin concentrations and molecular weight forms in serum, seminal plasma, and ovarian follicular fluid from cattle.

Adiponectin (AdipoQ), an adipocyte-derived hormone, is one of the most abundant adipokines in the blood circulation. Adiponectin has various metabolic functions, such as improving insulin sensitivity in humans and rodents. The role of AdipoQ in reproduction is not yet fully understood, but the expression of AdipoQ in reproductive tissues has been observed in various animals and humans, including chicken testis, bovine ovary, and human placenta. The objective of this study was to characterize AdipoQ in the bovine body fluids related to reproduction. Therefore, we evaluated the seminal plasma (SP) from breeding bulls (n = 29) and follicular fluid (FF) from heifers (n = 14), and we also collected blood samples from these animals. In addition, blood samples from other bulls (n = 30) and heifers (n = 14) were assayed for AdipoQ. The concentrations were assessed using a bovine-specific ELISA, and the molecular weight (MW) pattern of the AdipoQ protein was estimated by the Western blot analysis. The SP AdipoQ concentrations were approximately 180-fold lower compared with that in the serum concentrations. Furthermore, the AdipoQ concentrations in the serum and SP were positively correlated. The MW patterns of AdipoQ in the serum and SP were different such that the high MW form of AdipoQ was more abundant in the SP than serum. The AdipoQ concentrations in the serum and SP also increased with age: old bulls (>6 years) had higher AdipoQ concentrations in the serum and SP than bulls aged 24 months or lesser (P < 0.05). In the FF, the AdipoQ concentrations were 1.6-fold lower than those in the corresponding serum samples, and the concentrations in the serum and FF were not correlated (P > 0.1). In the FF, only the middle MW forms of AdipoQ were detectable by Western blotting. The MW pattern in the serum did not differ between the sexes. Our data provide both the AdipoQ concentration and the MW patterns for bovine body fluids related to reproduction.