Genome Research Articles

Cardiac MRI traits linked to cardiomyopathy mutations in phenotype naive carriers

Abstract Hypertrophic cardiomyopathy (HCM) and dilated cardiomyopathy (DCM) are prevalent forms of cardiomyopathies, characterised by changes in cardiac structure and function, associated with an increased risk of atrial fibrillation (AF), heart failure (HF), and sudden cardiac death (SCD). Due to these potential life-threatening consequences close monitoring of genetic mutation carriers of HCM and DCM, is important. However, disease onset in these subjects is highly variable, with a substantial subset of people only developing disease late-in-life, or not at all, making risk stratification challenging. We set out to identify cardiac MRI (CMR) based imaging biomarkers of HCM and DCM carriership in phenotype naïve individuals, which were benchmarked against associations with AF and HF. CMR and whole genome sequencing (n: 42,723) data were sourced from a UK biobank sample free of heart failure at the time of CMR measurements. A previously validated deep learning(DL) network was used to derive 22 CMR traits(1). Adjusted cox regression models were used to determine the CMR associations with the onset of heart failure and atrial fibrillation, providing empirical validation of the DL CMR network. Univariable and multivariable generalised linear models were employed to identify associations with genetic carriership conditional on cardiac risk factors. 14 and 19 CMR measurements were associated with the time until HF (274 cases), AF (704 cases), respectively. These variables included left-ventricle (LV) ejection fraction (EF), LV end systolic volume (ESV), Right-ventricular (RV) EF and right atrial (RA) EF. Using WGS data we identified 154 people with an HCM mutation and 220 with a DCM mutation, where HCM carriership associated with five and DCM with four CMR traits. This included RA-EF (OR 1.26 95%CI 1.10; 1.45), and RV-EF (OR 1.41 95%CI 1.23;1,63) for HCM, and LV-EF (OR 0.72 95%CI 0.62; 0.84), and RV stroke volume (OR 0.75 95CI 0.62; 0.91) for DCM. By combining deep learning of CMR with large sample size WGS we were able to identify cardiac imaging biomarkers of HCM and DCM carriership in apparently healthy subjects. This could prove relevant for early identification and monitoring of phenotype naïve people.

Further evidence for strong non-neutrality of yeast synonymous mutations.

Although synonymous mutations are commonly assumed neutral or nearly so, recent years have seen reports of fitness effects of synonymous mutations detected under laboratory conditions. In a previous study, we used genome editing to construct thousands of yeast mutants each carrying a synonymous or nonsynonymous mutation in one of 21 genes and discovered that most synonymous and most nonsynonymous mutations are deleterious. A concern was raised that this observation could be caused by the fitness effects of potential CRISPR/Cas9 off-target edits and/or secondary mutations, and an experiment that would be refractory to such effects was proposed. Using genome sequencing, we here show that no CRISPR/Cas9 off-target editing occurred, although some mutants did carry secondary mutations. Analysis of mutants with negligible effects from secondary mutations and new data collected from the proposed experiment confirms the original conclusion. These findings, along with other reports of fitness effects of synonymous mutations from both case and systematic studies, necessitate a paradigm shift from assuming (near) neutrality of synonymous mutations.

Molecular surveillance of A. baumannii in intensive care units: exploration of transmission chains

Abstract Background Multidrug-resistant Acinetobacter baumannii (MDR-Ab) is one of the main causes of healthcare associated infections (HAIs). During the SARS-CoV-2 pandemic there was an increase in MDR-Ab infections, especially in intensive care units (ICUs). This study aimed to assess the potential spread or emergence of specific clusters of MDR-Ab across four different ICUs at the Umberto I teaching hospital of Rome. Methods From January 2020 to January 2022 microbiological surveillance was conducted in four ICUs: two dedicated to COVID-19 patients (ICU-1C, ICU-2C) and two to non-COVID-19 patients (ICU-1R, ICU-2R). The genetic relatedness between A. baumannii isolates was assessed using pulsed-field gel electrophoresis (PFGE). Illumina whole genome sequencing was conducted on 26 representative isolates. Results In total, 178 A. baumannii isolates were obtained from 129 COVID-19 patients and 49 non-COVID-19 patients. The isolates were classified into 17 PFGE pulsotypes, being two major (A, B) and five intermediate (C, D, E, H, Q). Clone A was present in all ICUs, while Clone B was present only in ICU-1C and ICU-2R. Overall, 117 isolates belonged to clone A and exhibited a MDR phenotype; all of them were placed within the international clonal lineage II. All isolates showed carbapenems resistance primarily attributed to the presence of the blaOXA-23 gene, while aminoglycosides resistance observed in almost all isolates was attributed to the presence of the armA gene. Small outbreaks involving intermediate pulsotypes were detected between ICU-1R and ICU-2R, ICU-1C and ICU-2R, ICU-1C and ICU-2C, ICU-1C and ICU-1R. Conclusions The observed outbreaks could be attributed to a decline in attention to normal care practices for the prevention of HAIs during the COVID-19 pandemic, favouring the spread of MDR-Ab. Therefore, it is recommended the strengthen of control measures and the implementation of long-term strategies targeting MDR microorganisms in the ICUs. Key messages • Acinetobacter baumannii was frequently found infecting patients across four different ICUs at the Umberto I teaching hospital of Rome. • Acinetobacter baumanni outbreaks and multidrug resistance were observed. Therefore, the implementation of long-term strategies targeting MDR microorganisms in the ICUs is highly recommended.

A prolonged outbreak of tuberculosis associated with an intellectual disability daycentre in Ireland

Abstract One of the factors impeding tuberculosis elimination in low burden countries is its persistence and concentration in vulnerable populations. This is a complex, prolonged Tuberculosis (TB) outbreak in a daycentre for adults with intellectual disability in Ireland. This is a particularly vulnerable population with special considerations for Public Health (PH) management. There are eight cases of active TB, 46 cases of Latent TB Infection (LTBI) and a cumulative total of 116 contacts associated with this outbreak, with diagnosis spanning 15 years. The last three cases were identical on Whole Genome Sequencing. The index case was an Irish-born, Caucasian, social care worker, with smear positive pulmonary TB, who was symptomatic in the facility for three months prior to diagnosis. Case 2 was a household contact of the index case and the other 6 cases were Service Users (SUs) at the facility. At least five of the subsequent seven cases are secondary cases of the index case. Significant to this outbreak was the change in Irish guidance, 2010, relating to the management of contacts of cases. Following the notification of the most recent case, July 2023, the Outbreak Control Team decided a retrospective review be conducted of all SU contacts of the seven cases associated with the facility. The contacts were stratified according to hierarchical risk. A total of six contacts met the criteria for review and offered screening, re-screening or treatment as appropriate. In this outbreak 21.8% of the total contacts and 16.1% of SU contacts completed treatment for LTBI. The significance of this outbreak lies in its duration, infectivity of the index case and particular vulnerabilities of the SUs. There were issues with overcrowding and difficulties in relation to symptom recognition, diagnosis and treatment. The PH team tailored their approach to meet the SU needs, demonstrating the importance of person-centred contact tracing in the disruption of transmission. Key messages • A factor impeding tuberculosis elimination in low burden countries is it’s persistence and concentration in vulnerable populations. • Adapting a patient-centred approach to contact tracing can lead to higher participation rate and the disruption of infection transmission.

Isolation and characterization of bacteriophages specific to Streptococcus equi subspecies zooepidemicus and evaluation of efficacy ex vivo

Streptococcus (S.) equi subspecies (subsp.) zooepidemicus is an important facultative pathogen in horses and can cause severe infections in other species including humans. Facing the post-antibiotic era, novel antimicrobials are needed for fighting bacterial infections. Bacteriophages (phages) are the natural predators of bacteria and discussed as a promising antimicrobial treatment option. The objective of this study was to isolate and characterize S. equi subsp. zooepidemicus-specific phages for the first time and to evaluate their efficacy in vitro and ex vivo. In total, 13 phages with lytic activity were isolated and host ranges were determined. Two phages with broad host ranges and high efficiency of plating (vB_SeqZP_LmqsRe26-2 (lytic activity: 30/37 bacterial isolates) and vB_SeqZP_LmqsRe26-3 (lytic activity: 29/37 bacterial isolates)) and one phage with relatively low efficiency of plating (vB_SeqZP_LmqsRe26-1) were selected for further characterization, including electron microscopy and whole genome sequencing. In in vitro planktonic killing assays at two tested multiplicities of infection (MOI 1 and MOI 10), significant bacterial growth reduction was observed when the phages vB_SeqZP_LmqsRe26-2 and vB_SeqZP_LmqsRe26-3 were added. These phages were subsequently co-incubated with clinical S. equi subsp. zooepidemicus isolates in an equine endometrial explant model but did not achieve bacterial growth reduction at MOI 1 and MOI 10. However, helium ion microscopy revealed presence of particles adherent to the bacteria on the explant after incubation (25 h), suggesting possible phage-bacteria interactions. In conclusion, phages against S. equi subsp. zooepidemicus were successfully isolated and characterized. Promising results were observed in in vitro but no significant reduction was detected in ex vivo experiments, requiring additional investigations. However, after further adaptations (e.g., optimization of MOIs and phage administration or use of phage-antibiotic combination), phages could be a potential antimicrobial tool for future therapeutic use in S. equi subsp. zooepidemicus infections, although the available results do not currently support the therapeutic usage.

Characterization of the viral genome of Omicron variants of SARS-CoV-2 circulating in Tripura, a remote frontier state in Northeastern India.

From 2020, with advent of COVID-19 pandemic, Tripura has experienced SARS-CoV-2 viral evolution in accordance with other parts of India. Since January 2022, the Omicron variant of SARS-CoV-2 virus became the predominant lineage circulating in India and neighboring countries. This study characterizes the viral genome of the omicron variant circulating in the state since its inception to June, 2023. The current study was performed on nasopharyngeal and oropharyngeal samples received from the various departments of AGMC, as well as eight district hospitals from Tripura. The positive samples with a cycle threshold value of 25 or less for the E and/or N gene were considered for whole genome sequencing using Illumina Miseq NGS platform. Majority of the sequences belonged to Clade 21L, with BA.5.2 being the major sub variant detected during the study period. Majority of the mutations were detected in the Spike protein region, including L24-, P25-, P26-, V213G, G339D, S371F, S373P, S375F, T376A, D405N, R408S, K417N, S477N, T478K, Q498R, Y505H, Q954H and N969K. All the sequences uniquely showed the mutations A27S and G142D in N terminal domain in Spike protein, not being reported from other Indian sequences like BA.5 variants. T9I, A63T and P13L were major substitutions in E, M and N protein regions respectively. Escape of mutants from vaccine induced immunity was mostly observed in BA.2 sub variants, majority endowed with the triplet mutation of K417N + E484K + N501Y. The current study indicates that Omicron variants circulating in the state of Tripura is comparable to other regions of India and the neighbouring country of Bangladesh. Genetic mutations increasing viral transmissibility have been identified in the circulating viral genomes.

Preferences of parents from diverse backgrounds on genomic screening of apparently healthy newborns.

Genomic sequencing has been proposed as a strategy to expand newborn screening. Perspectives on genomic newborn screening from parents of diverse racial, ethnic, and socioeconomic backgrounds are needed to shape equitable implementation of this modality. We conducted 20 semi-structured interviews (15 English, 5 Spanish) and seven focus groups (4 English, 3 Spanish) with parents from diverse backgrounds to assess their perspectives regarding which disorders and variants might be screened, data privacy, and barriers to pursuing specialized care. Parents felt that genomic newborn screening would provide them with improved understanding of their children's health and had the potential to yield health and personal benefits. Themes that became evident included: interest in childhood and family health risks, the value of emotional preparation and personal planning, understanding of uncertain and low-risk results, concerns regarding data privacy, and concerns about support following the receipt of a positive newborn screening result. The expected benefits and concerns expressed by parents of diverse backgrounds regarding genomic newborn screening should guide future policy decisions. Their preferences should be considered prior to the implementation of large-scale genomic newborn screening programs.

The genome sequence of the Common Lutestring moth, Ochropacha duplaris Linnaeus, 1761

We present a genome assembly from an individual male Ochropacha duplaris (the Common Lutestring; Arthropoda; Insecta; Lepidoptera; Drepanidae). The genome sequence has a total length of 354.70 megabases. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.22 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,322 protein-coding genes.

Autosomal recessive VWA1-related disorder: comprehensive analysis of phenotypic variability and genetic mutations

Abstract A newly identified subtype of hereditary axonal motor neuropathy, characterized by early proximal limb involvement, has been discovered in a cohort of 34 individuals with biallelic variants in von Willebrand factor A domain containing 1 (VWA1). This study further delineates the disease characteristics in a cohort of 20 individuals diagnosed through genome or exome sequencing, incorporating neurophysiological, laboratory, and imaging data, along with data from previously reported cases across three different studies. Newly reported clinical features include hypermobility/hyperlaxity, axial weakness, dysmorphic signs, asymmetric presentation, dystonic features, and, notably, upper motor neuron signs. Foot drop, foot deformities, and distal leg weakness followed by early proximal leg weakness are confirmed to be initial manifestations. Additionally, this study identified 11 novel VWA1 variants, reaffirming the 10bp insertion-induced p.Gly25ArgfsTer74 as the most prevalent disease-causing allele, with a carrier frequency of ∼1 in 441 in the UK and Western European population. Importantly, VWA1-related pathology may mimic various neuromuscular conditions, advocating for its inclusion in diverse gene panels spanning hereditary neuropathies to muscular dystrophies. The study highlights the potential of lower quality control filters in exome analysis to enhance diagnostic yield of VWA1-disease that may account for up to 1% of unexplained hereditary neuropathies.

DNMT3A CHIP-driver mutations ignite the bone marrow

Abstract Background Clonal hematopoiesis of indeterminate potential (CHIP) is an acquired, genetic cardiovascular (CV) risk factor affecting about 10% of the general population at the age of 70 years. Most CHIP-driver mutations affect the epigenetic regulator gene DNMT3A. Experimental studies suggest a causal link between CHIP and inflammation-driven atherosclerosis, but the underlying mechanisms of how few mutant clones provoke adverse clinical outcomes in patients remain obscure. Methods Single monocytes and bone marrow cells from DNMT3A-mutation carriers undergoing coronary angiography and open-heart surgery underwent RNA and genomic DNA sequencing in parallel on a single cell level. This approach enabled us to compare mutant and non-mutant cells directly within carriers, and to non-carrier cells. Atherosclerotic chimeric mice reconstituted with a mixture of Dnmt3a-deficient (CD45.2) and -competent (CD45.1) bone marrow served as an experimental model to compare mutant to non-mutant macrophages in atherosclerotic lesions. Results Surprisingly, RNA/gDNA parallel sequencing revealed that gene expression profiles of mutant monocytes resembled those of non-mutant monocytes in carriers of DNMT3A-CHIP mutations (n=4). Collectively, however, monocytes of DNMT3A mutation carriers were more inflammatory than those of matched non-carrier patients. Mutant hematopoietic stem and progenitor cells, analyzed by RNA/gDNA parallel sequencing in two carriers, expressed more activation and inflammatory markers compared to non-mutant cells within the same bone marrow, and intraindividual differences declined as cells differentiated into monocytes. Macrophages were isolated from atherosclerotic aortas of mixed bone marrow chimeric mice based on CD45.1 (non-mutant) or CD45.2 (mutant or non-mutant controls) expression and subjected to single cell RNA sequencing. Inflammation markers were higher expressed in non-mutant macrophages within carrier mice than in non-mutant macrophages of non-carrier chimeras, and showed relatively small differences compared to Dnmt3a-deficient macrophages. Conclusions Our experimental findings in humans and mice support a pathomechanistic model in which few DNMT3A-CHIP mutation-carrying hematopoietic stem cells stimulate non-mutant cells within the bone marrow, thereby augmenting inflammation downstream in all circulating monocytes and their progeny in atherosclerotic lesions.

Determinants of tuberculosis site among 1035 cases in Frankfurt, 2008-2023: does lineage matter?

Abstract Extrapulmonary tuberculosis (EPTB) presents with nonspecific symptoms which can pose a diagnostic challenge. Currently, there are no clear predictors for EPTB. We aimed to identify these factors for better diagnosis and disease control. We included tuberculosis cases reported in Frankfurt from 2008-2023, with available clinical and whole genome sequencing data. According to WHO criteria, cases with pulmonary or combined pulmonary and extrapulmonary symptoms were categorised as pulmonary tuberculosis, while exclusively extrapulmonary symptoms were categorised as extrapulmonary tuberculosis. We assessed the association between EPTB and M. tuberculosis lineage, comorbidities and demographic characteristics using logistic regression, calculating crude and adjusted odds ratios (aOR). Of the 1035 reported tuberculosis cases, 272 had exclusively extrapulmonary disease and 136 had both pulmonary and extrapulmonary disease. In the univariable analysis, lineages 1 and 3 were significantly associated with extrapulmonary disease compared to lineage 4. However, this association was not observed in the multivariable analysis. In the final regression model, females were more likely to develop EPTB than men (aOR: 1.65, CI: 1.19-2.27). The odds of developing extrapulmonary disease were higher among patients born in the South-East Asian (aOR: 6.48, CI: 3.72-11.43) and Eastern Mediterranean (aOR: 5.54, CI: 3.41-9.11) than in other regions. Among the comorbidities, diabetes was found to be negatively associated with extrapulmonary disease (aOR: 0.50, CI: 0.26-0.91). Our results indicate that host factors such as geographic origin and sex are stronger predictors for extrapulmonary presentation of tuberculosis than a specific lineage. We recommend increasing physicians’ awareness of the nonspecific presentation of EPTB and adapting screening programmes, particularly for patients from South-East Asian and Eastern Mediterranean regions to foster more effective tuberculosis control measures. Key messages • Our study highlights the importance of considering host factors in predicting extrapulmonary tuberculosis, indicating their stronger influence compared to specific M. tuberculosis lineages. • Increased physicians’ awareness of the nonspecific symptoms of EPTB and targeted screening programs for high-risk populations are crucial for enhancing tuberculosis control measures.

Symmetric, Bilateral Auricular Calcifications in Twins With Noonan Syndrome.

Noonan syndrome (NS) is a rare, genetic multisystem disorder often presenting with associated craniofacial abnormalities. The authors report an identical twin pair with classical features of NS including short stature, mild ptosis, hypertelorism, down-slanting palpebral fissures, low-set angulated ears, and giant cell tumors in the craniofacial skeleton. Interestingly, these patients also presented with bilateral, symmetric, dystrophic auricular calcifications. Genome sequencing revealed identical germline son of sevenless homolog 1 mutations and inversion of chromosome 2 (p11.2q13). Awareness of the association of auricular calcifications and NS may help guide clinical management for these patients, particularly if auricular procedures are indicated.

3.Y.1. Genomics in EU Health Systems: Navigating the Opportunities and Challenges for Personalized Health

Abstract The rapid advancements in genomics research offer significant promise for revolutionizing healthcare, potentially reshaping how we approach disease prevention, diagnosis, and treatment. However, unlocking the full potential of genomics requires more than just scientific breakthroughs-it necessitates translating these discoveries into clinical practice. This involves bridging the gap between research and healthcare implementation, addressing challenges such as technical infrastructure, ethical and legal frameworks, healthcare professional competencies, and citizen engagement. As we navigate the evolving landscape of individualized patient care, it becomes increasingly crucial to implement effective risk stratification methodologies and personalized preventive measures. Among these methodologies, polygenic risk scores are gaining prominence. However, the adoption of these innovations necessitates careful consideration of their clinical utility, including their feasibility, cost-effectiveness, and acceptability in diverse healthcare settings. Validating these approaches from multiple perspectives is essential to ensure their effectiveness in real-world clinical practice. Integrating genomic sequencing data with health records presents an invaluable resource that can enhance patient outcomes and drive further research. The creation of infrastructures and initiatives such as those carried out by projects like the European Health Data Space and Genomic Data Infrastructure are fundamental to unleash the enormous potential of data-driven innovation. To date, the implementation of genomics in medical practice varies across European countries, with discrepancies in adoption levels across different aspects of healthcare, including prevention, diagnosis, and personalized treatment. Addressing these disparities and promoting standardized approaches to genomic medicine implementation are crucial steps toward ensuring equitable access and maximizing the benefits of genomics for all individuals across Europe. This workshop aims to provide decision-makers, healthcare professionals and researchers with a comprehensive overview of the state-of-the-art for the adoption of personalized approaches, and of the maturity of genomic medicine practices within different healthcare systems as well outlining the benefits of data accessibility for research. The speakers are coordinators and partners of EU projects as B1MG (Beyond One Million Genomes), Prophet (A PeRsOnalized Prevention roadmap for the future Healthcare), EHDS (European Health Data Space), GDI (European Genomic Data Infrastructure), GoE (Genome of Europe) and CanHeal. Key messages • Genomics has the potential to improve health outcomes. • Equal access to genomic medicine critical for personalized health. Ensuring equity, while considering feasibility.

Clinical genome sequencing in patients with suspected rare genetic disease in Peru

There is limited access to molecular genetic testing in most low- and middle-income countries. The iHope program provides clinical genome sequencing (cGS) to underserved individuals with signs or symptoms of rare genetic diseases and limited or no access to molecular genetic testing. Here we describe the performance and impact of cGS in 247 patients from three clinics in Peru. Although most patients had at least one genetic test prior to cGS (70.9%), the most frequent was karyotyping (53.4%). The diagnostic yield of cGS was 54.3%, with candidate variants reported in an additional 22.3% of patients. Clinical GS results impacted clinician diagnostic evaluation in 85.0% and genetic counseling in 72.1% of cases. Changes in management were reported in 71.3%, inclusive of referrals (64.7%), therapeutics (26.3%), laboratory or physiological testing (25.5%), imaging (19%), and palliative care (17.4%), suggesting that increased availability of genomic testing in Peru would enable improved patient management.

Comprehensive Analysis of Codon Usage Bias in Human Papillomavirus Type 51.

Human papillomavirus type 51 (HPV-51) is associated with various cancers, including cervical cancer. Examining the codon usage bias of the organism can offer valuable insights into its evolutionary patterns and its relationship with the host. This study comprehensively analyzed codon usage bias in HPV-51 by examining 64 complete genome sequences sourced from the NCBI GenBank database. Our analysis revealed no noteworthy preference for codon usage in HPV-51 overall. However, there was a noticeable bias towards A/T-ending codons, accompanied by GC3s below 32%. Dinucleotide frequency analysis revealed reduced frequencies for ApA, CpG, and TpC dinucleotides, while CpA and TpG dinucleotides were more frequent than others. Relative Synonymous Codon Usage analysis revealed 30 favored codons, primarily concluding with A/T nucleotides. Further analysis using Parity Rule 2, Effective Number of Codons plot, and neutrality plot indicated a balance between mutational pressure and natural selection, with natural selection being the primary force shaping codon usage bias. The Isoacceptor tRNA Pool analysis indicates that HPV-51 has a higher translation efficiency within the human cellular translational system. Moreover, the Codon Adaptation Index and Relative Codon Deoptimization Index analyses suggested a moderate adaptation of HPV-51 to human codon preferences. Our discoveries offer valuable perspectives on how HPV-51 evolves and uses genetic codes, contributing to a deeper comprehension of its endurance and disease-causing potential.

Multiple Acquisitions of XopJ2 Effectors in Populations of Xanthomonas perforans.

Type III effectors (T3Es) are major determinants of Xanthomonas virulence and targets for resistance breeding. XopJ2 (synonym AvrBsT) is a highly conserved YopJ-family T3E acquired by X. perforans, the pathogen responsible for bacterial spot disease of tomato. In this study, we characterized a new variant (XopJ2b) of XopJ2, which is predicted to have a similar three-dimensional (3D) structure as the canonical XopJ2 (XopJ2a) despite sharing only 70% sequence identity. XopJ2b carries an acetyltransferase domain and the critical residues required for its activity, and the positions of these residues are predicted to be conserved in the 3D structure of the proteins. We demonstrated that XopJ2b is a functional T3E and triggers a hypersensitive response (HR) when translocated into pepper cells. Like XopJ2a, XopJ2b triggers HR in Arabidopsis that is suppressed by the deacetylase, SOBER1. We found xopJ2b in genome sequences of X. euvesicatoria, X. citri, X. guizotiae, and X. vasicola strains, suggesting widespread horizontal transfer. In X. perforans, xopJ2b was present in strains collected in North America, Africa, Asia, Australia, and Europe, whereas xopJ2a had a narrower geographic distribution. This study expands the Xanthomonas T3E repertoire, demonstrates functional conservation in T3E evolution, and further supports the importance of XopJ2 in X. perforans fitness on tomato. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Isolation and characterisation of novel lytic bacteriophages for therapeutic applications in biofilm-associated prosthetic joint infections

Abstract Prosthetic joint infections are devastating complications of joint arthroplasties. Without effective management, they can lead to limb amputation and even death. A significant proportion of these infections is caused by the primarily commensal Coagulase-negative Staphylococci pathogens, which form thick, antibiotic-resistant biofilms at the site of infection. Combinatorial therapy involving antibiotics and bacteriophages may represent a strategy to overcome resistance. Previous research indicates that as bacteria develop resistance to antibiotics, they often become more susceptible to bacteriophages. In this study, we produced a cocktail of novel bacteriophages and assessed their viability to eradicate nosocomial staphylococcal biofilms. Here, we used clinical isolates from prosthetic joint infections to isolate and identify four new bacteriophages from sewage effluent. These novel phages were characterized through electron microscopy and full genome sequencing. Subsequently, we combined them into a phage cocktail, which effectively re-sensitized biofilms to vancomycin and flucloxacillin. Notably, this phage cocktail demonstrated low cytotoxicity in vitro to human epithelial cells, even when used alongside antibiotic treatments. These findings highlight the potential of the phage cocktail as a tool to increase antibiotic treatment success in prosthetic joint infections.

Multiple genotypes of a quarantine plant pathogen detected in New Zealand indigenous plants located in a botanical garden overseas

AbstractXylella fastidiosa is a xylem‐limited bacterial plant pathogen transmitted by insect vectors. It infects a wide range of plant species and causes devastating diseases. Botanical gardens are global repositories of plant diversity exposed to local biotic and abiotic stresses. We used molecular diagnostic tools for the detection of X. fastidiosa in a collection of New Zealand indigenous plants grown in a X. fastidiosa‐infected Californian area to determine if any species were infected with this bacterial pathogen and to help inform biosecurity responses. To this end, 130 New Zealand indigenous plant species comprising 72 genera, growing in the University of California Botanical Garden at Berkeley, California, were screened for X. fastidiosa. Multiple PCR‐based methods were used to detect the pathogen at the subspecies and sequence‐type levels directly from plant material; nine plant species tested positive by at least two PCR‐based methods. All nine infections were identified as X. fastidiosa subsp. multiplex sequence types 6 or 7 by the amplification of seven housekeeping genes. Three strains were cultured in vitro and their whole genome sequences were obtained; these strains belonged to three distinct clades within subspecies multiplex, indicating that the infections were not transmitted among these New Zealand indigenous plant species. The information gathered in this study will help to assess the risk of X. fastidiosa to New Zealand indigenous flora and the potential spillover to crops of agricultural importance. The work also shows the applied value of botanical garden collections as sentinels for international plant pathogen biosecurity risk assessment.

Genome Sequencing Identifies 13 Novel Candidate Risk Genes for Autism Spectrum Disorder in a Qatari Cohort

Autism spectrum disorder (ASD) is a neurodevelopmental condition characterized by deficits in social communication, restricted interests, and repetitive behaviors. Despite considerable research efforts, the genetic complexity of ASD remains poorly understood, complicating diagnosis and treatment, especially in the Arab population, with its genetic diversity linked to migration, tribal structures, and high consanguinity. To address the scarcity of ASD genetic data in the Middle East, we conducted genome sequencing (GS) on 50 ASD subjects and their unaffected parents. Our analysis revealed 37 single-nucleotide variants from 36 candidate genes and over 200 CGG repeats in the FMR1 gene in one subject. The identified variants were classified as uncertain, likely pathogenic, or pathogenic based on in-silico algorithms and ACMG criteria. Notably, 52% of the identified variants were homozygous, indicating a recessive genetic architecture to ASD in this population. This finding underscores the significant impact of high consanguinity within the Qatari population, which could be utilized in genetic counseling/screening program in Qatar. We also discovered single nucleotide variants in 13 novel genes not previously associated with ASD: ARSF, BAHD1, CHST7, CUL2, FRMPD3, KCNC4, LFNG, RGS4, RNF133, SCRN2, SLC12A8, USP24, and ZNF746. Our investigation categorized the candidate genes into seven groups, highlighting their roles in cognitive development, including the ubiquitin pathway, transcription factors, solute carriers, kinases, glutamate receptors, chromatin remodelers, and ion channels.

Universal newborn screening using genome sequencing: early experience from the GUARDIAN study.

For more than 20 years there has been speculation about a future in which newborns are routinely screened at birth for genetic disorders using genome sequencing, but prospective large-scale studies assessing this vision have only recently begun. Genome sequencing may provide a means of expanding the scope of conditions included in newborn screening programs and improving the positive predictive value of traditional newborn screening. However, the use of genome sequencing for newborn screening has also raised concerns including acceptability, equity, and scalability. By reviewing the initial results of the GUARDIAN study and contrasting them with other pilot studies investigating the use of genome sequencing for large-scale newborn screening, we highlight how the lessons learned from these studies are shaping the future for the implementation of truly universal and equitable newborn genomic screening.