Genome Research Articles

Successful control of an environmental reservoir of NDM-producing Klebsiella pneumoniae associated with nosocomial transmissions in a low-incidence setting

BackgroundThe hospital wastewater system has been reported as a source of nosocomial acquisition of carbapenemase producing Enterobacteriaceae (CPE) in various settings. Cleaning and disinfection protocols or replacement of contaminated equipment often fail to eradicate these environmental reservoirs, which can lead to long-term transmission of CPE. We report a successful multimodal approach to control a New Delhi metallo-beta-lactamase positive Klebsiella pneumoniae (NDM-KP) nosocomial outbreak implicating contamination of sink traps in a low-incidence setting.MethodsFollowing the incidental identification of NDM-KP in a urine culture of an inpatient, we performed an epidemiological investigation, including patient and environmental CPE screening, and whole genome sequencing (WGS) of strains. We also implemented multimodal infection prevention and control (IPC) measures, namely the isolation of cases, waterless patient care, replacement of contaminated P-traps and connecting pieces, and bleach and steam disinfection of sinks for 6 months, followed by patient and environmental screenings for eradication.ResultsBetween February and May 2022, five NDM-KP cases were identified in an eight-bed neurosurgical intermediate care unit. Among the eight sink traps of the unit, three were positive for NDM-KP. Patient and environmental isolates belonged to multilocus sequence typing ST-268. All isolate genomes were genetically very similar suggesting cross-transmission and a potential role of the environment as the source of transmissions. Following the introduction of combined IPC measures, no new case was subsequently detected and sink traps remained negative for NDM-KP within 6 months after the intervention.ConclusionThe implementation of multimodal IPC measures, including waterless patient care combined with the replacement and disinfection of P-traps and connecting pieces, was successful in the control of NDM-KP after eight months. In a low-incidence setting, this approach has made it possible to pursue the objective of zero transmission of carbapenemase-producing Enterobacteriaceae (CPE).

Draft genome sequence of heat-tolerant Escherichia coli strain AKS1GF CIFRI isolated from a coal power plant discharge in the river ganga.

Escherichia coli strain, AKS1GF ICAR-CIFRI, was isolated from a thermally contaminated water with average water temperatures of 45°C ± 2.5°C in river Ganga, India. The draft genome sequence is of 4.7 MB consisting of 44 contigs. The strain contains 4,314 protein coding genes and 96 RNA genes.

Complete genome sequences of nine double recombinant vaccine-derived novel oral poliovirus type 2 genomes from Nigeria 2023-2024.

We report the complete genome sequences of nine double recombinant vaccine-derived novel oral poliovirus type 2 genomes from acute flaccid paralysis (AFP) cases (n = 3), AFP case contacts (n = 4), and environmental surveillance sampling (n = 2) in Nigeria.

Genome sequences of dengue virus serotypes 2, 3, and 4 isolated from adult patients in Thailand.

Here, we present the genome sequences of dengue viruses (DENV) isolated from adult patients in Thailand during 2016-2017: DENV2 (412749), DENV3 (416384), and DENV4 (416709). These sequences provide valuable genetic and evolutionary information for dengue research and antiviral development.

Draft genome of hydrocarbon-degrader Burkholderia cepacia BCTT, isolated from soil chronically polluted with crude oil in Trinidad.

Burkholderia cepacia BCTT, isolated from chronically polluted soil in Trinidad, shows a capacity to survive in crude oil as a sole carbon source. Here, we report its high-quality draft genome sequence and highlight those pathways and genes involved in xenobiotic degradation. These data give a clearer insight into this organism's biotechnological potential.

Intraspecific diversity is critical to population-level risk assessments

Environmental risk assessment (ERA) is critical for protecting life by predicting population responses to contaminants. However, routine toxicity testing often examines only one genotype from surrogate species, potentially leading to inaccurate risk assessments, as natural populations typically consist of genetically diverse individuals. To evaluate the importance of intraspecific variation in translating toxicity testing to natural populations, we quantified the magnitude of phenotypic variation between 20 Daphnia magna clones exposed to two levels of microcystins, a cosmopolitan cyanobacterial toxin. We observed significant genetic variation in survival, growth, and reproduction, which increased under microcystins exposure. Simulations of survival showed that using a single genotype for toxicity tolerance estimates on average failed to produce accurate predictions within the 95% confidence interval over half of the time. Whole genome sequencing of the 20 clones tested for correlations between toxicological responses and genomic divergence, including candidate loci from prior gene expression studies. We found no overall correlations, indicating that clonal variation, rather than variation at candidate genes, predicts population-level responses to toxins. These results highlight the importance of incorporating broad intraspecific genetic variation, without focusing specifically on variation in candidate genes, into ERAs to more reliably predict how local populations will respond to contaminants.

Complete genome sequence of two Christensenella minuta strains CIP 112228 and CIP 112229, isolated from human fecal samples.

Christensenella minuta is one of the representative bacterial species of the human gut microbiome. We report the complete genome sequence of two strains, Christensenella minuta CIP 112228 and CIP 112229, isolated from two healthy volunteers.

Complete genome sequence of Bulleidia sp. 10714-15 isolated from human colon cancer patients.

Bulleidia sp. is a non-spore-forming, obligatory anaerobic, Gram-positive bacterium isolated from the stool samples of human colon cancer patients. We report the complete genome sequence of Bulleidia sp. 10714-15, comprising a single linear chromosome of 2,218,984 bp with a G + C content of 36.6%.

Complete genome sequence of the saprophytic actinomycete Prescottella soli DSD51WT, closely related to the multi-host pathogen Prescottella (Rhodococcus) equi.

Prescottella soli strain DSD51WT is an aerobic, non-spore-forming, non-motile actinomycete isolated previously from soil collected from Kyoto Park, Japan, using a resuscitative technique. Here, we report the complete, circular genome sequence of P. soli DSD51WT. We employed a hybrid approach using Illumina and Oxford Nanopore platforms.

Multidrug tolerance conferred by loss-of-function mutations in anti-sigma factor RshA of Mycobacterium abscessus.

Low-level drug resistance in noncanonical pathways can constitute steppingstones toward acquisition of high-level on-target resistance mutations in the clinic. To capture these intermediate steps in Mycobacterium abscessus (Mab), we performed classic mutant selection experiments with moxifloxacin at twofold its minimum inhibitory concentration (MIC) on solid medium. We found that low-level resistance emerged reproducibly as loss-of-function mutations in RshA (MAB_3542c), an anti-sigma factor that negatively regulates activity of SigH, which orchestrates a response to oxidative stress in mycobacteria. Since oxidative stress is generated in response to many antibiotics, we went on to show that deletion of rshA confers low to moderate resistance-by measure of MIC-to a dozen agents recommended or evaluated for the treatment of Mab pulmonary infections. Interestingly, this moderate resistance was associated with a wide range of drug tolerance, up to 1,000-fold increased survival of a ΔrshA Mab mutant upon exposure to several β-lactams and DNA gyrase inhibitors. Consistent with the putative involvement of the SigH regulon, we showed that addition of the transcription inhibitor rifabutin (RBT) abrogated the high-tolerance phenotype of ΔrshA to representatives of the β-lactam and DNA gyrase inhibitor classes. In a survey of 10,000 whole Mab genome sequences, we identified several loss-of-function mutations in rshA as well as non-synonymous polymorphisms in two cysteine residues critical for interactions with SigH. Thus, the multidrug multiform resistance phenotype we have uncovered may not only constitute a step toward canonical resistance acquisition during treatment but also contribute directly to treatment failure.

Complete genome of the opportunistic pathogen Nocardia vulneris strain LPB4002 and its biosynthetic potential.

The complete genome sequence of the opportunistic pathogen Nocardia vulneris is reported. The strain N. vulneris LPB4002 was isolated from a clinical sample of a patient with actinomycetoma. The reported genome comprises a single 9,489-Kb closed chromosome, with 8,584 protein-coding genes and 68% GC content.

Canker and dieback of Alnus rubra is caused by Lonsdalea quercina.

Understanding the ecology of pathogens is important for disease management. Recently a devastating canker disease was found on red alder (Alnus rubra) planted as landscape trees. Bacteria were isolated from two groups of symptomatic trees located approximately 1 kilometer apart and one strain from each group was used to complete Koch's postulates. Results showed that these bacteria can not only cause disease on red alder but also on two other alder species. Unexpectedly, analyses of genome sequences of bacterial strains identified them as Lonsdalea quercina, a pathogenic species previously known to cause dieback of oak species, but not alder. Additionally, a core genome phylogeny clustered bacterial strains isolated from red alder within a subclade of L. quercina strains isolated from symptomatic oak trees. Consistent with the close phylogenetic relationship, there was no obvious evidence for divergence in genome composition of strains isolated from red alder and oak. Altogether, findings indicate that L. quercina is a potential threat to Alnus species.

Complete genome sequences of five bacteria isolated from rice plants in a paddy field in Sekinchan, Selangor, Malaysia.

This study examines the genome sequences of five endophytic bacterial isolates from the Oryza sativa microbiome to assess their potential as plant bio-inoculants. The five complete bacterial genomes from the genera Pseudomonas, Burkholderia, Sphingobacterium, Stenotrophomonas, and Pantoea were sequenced using Nanopore long-read sequencing technology.

Complete genome sequence of Promicromonospora sp. strain Populi, an actinobacterium isolated from Populus trichocarpa rhizosphere.

Promicromonospora sp. strain Populi is an actinobacterium isolated from the rhizosphere of a black cottonwood tree, Populus trichocarpa. We completely sequenced its 5.2-Mbp chromosome using Oxford Nanopore long reads and predicted it to encode 4,685 proteins, 3 rRNA operons, and 54 tRNAs and noncoding RNAs.

Complete genome sequence of strain KD-1T, the type strain of Sulfurisphaera javensis, isolated from an Indonesian hot spring.

Sulfurisphaera javensis KD-1T, originally isolated from an Indonesian acidic hot spring, is a hyperthermophilic, acidophilic, and facultatively anaerobic archaeon. Here, we report the 2.6 Mb complete genome sequence of KD-1T. Genes related to sulfur metabolism were found in the genome, indicating that KD-1T is involved in the sulfur cycle in its habitat.

Cardiovascular Disease Pathogenicity Predictor (CVD-PP): A Tissue-Specific In Silico Tool for Discriminating Pathogenicity of Variants of Unknown Significance in Cardiovascular Disease Genes.

Interpretation of variants of uncertain significance (VUSs) remains a challenge in the care of patients with inherited cardiovascular diseases (CVDs); 56% of variants within CVD risk genes are VUS, and machine learning algorithms trained upon large data resources can stratify VUS into higher versus lower probability of contributing to a CVD phenotype. We used ClinVar pathogenic/likely pathogenic and benign/likely benign variants from 47 CVD genes to build a predictive model of variant pathogenicity utilizing measures of evolutionary constraint, deleteriousness, splicogenicity, local pathogenicity, cardiac-specific expression, and population allele frequency. Performance was validated using variants for which the ClinVar pathogenicity assignment changed. Functional validation was assessed using prior studies in >900 identified VUS. The model utility was demonstrated using the Catheterization Genetics cohort. We identified a top-ranked model that accurately prioritized variants for which ClinVar clinical significance had changed (n=663; precision-recall area under the curve, 0.97) and performed well compared with conventional in silico methods. This model (CVD pathogenicity predictor) also had high accuracy in prioritizing VUS with functional effects in vivo (precision-recall area under the curve, 0.58). In Catheterization Genetics, there was a greater burden of higher CVD pathogenicity predictor scored VUS in individuals with dilated cardiomyopathy compared with controls (P=8.2×10-15). Of individuals in Catheterization Genetics who harbored highly ranked CVD pathogenicity predictor VUS meeting clinical pathogenicity criteria, 27.6% had clinical evidence of disease. Variant prioritization using this model increased genetic diagnosis in Catheterization Genetics participants with a known clinical diagnosis of hypertrophic cardiomyopathy (7.8%-27.2%). We present a cardiac-specific model for prioritizing variants underlying CVD syndromes with high performance in discriminating the pathogenicity of VUS in CVD genes. Variant review and phenotyping of individuals carrying VUS of pathogenic interest support the clinical utility of this model. This model could also have utility in filtering variants as part of large-scale genomic sequencing studies.

The genome sequence of the Cinerous Pearl moth, Anania fuscalis (Denis & Schiffermüller) 1775

We present a genome assembly from an individual female Anania fuscalis (the cinerous pearl; Arthropoda; Insecta; Lepidoptera; Crambidae). The genome sequence spans 563.90 megabases. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.23 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,765 protein-coding genes.

Draft genome sequence of a cyanobacterium Gloeocapsa sp. BRSZ, isolated from Bo Khlueng hot spring in Ratchaburi, Thailand.

We report the draft genome sequence of Gloeocapsa sp. BRSZ isolated from Bo Khlueng hot spring in Thailand, comprising 42 contigs assembled at the scaffold level, totaling 6,084,403 bp, with 43.5% G + C content. It contains 5,456 putative protein-coding genes, including genes responsible for biosynthesis of mycosporine-like amino acids.

Investigating Transmission Patterns and Genome Sequencing of SARS-CoV-2 in University College Dublin

Abstract Background This study describes the investigation and management of multiple outbreaks of SARS-Cov2 during the second and third wave of the pandemic at University College Dublin, Ireland from September 2020 to September 2021. Methods Relevant data were gathered as part of the public health outbreak investigations led by the UCD Internal Covid Control Team (ICCT) in collaboration with the public health teams of the Health Service Executive (HSE). Results are presented for PCR (polymerase chain reaction) confirmed cases and their close contacts, reported to the UCD ICCT between September 2020 to September 2021. Results There were 214 cases notified to ICCT. Among these, 153 cases were in residence on-campus cases. 73 epidemiologically linked clusters identified, where the number of cases linked with each cluster varied between 1 to 27. Additional cases during this period had no obvious epidemiological link to the identified clusters. Of 902 close contacts with PCR test results, 31.5% (n = 284) tested positive. 77% (n = 219) self-reported with mild to moderately symptoms while 23% (n = 65) self-reported as asymptomatic. Retrospective Whole Genome Sequence (WGS) analysis was undertaken after the outbreaks had subsided. The test positive cases were grouped into 6 clusters, and it was shown that many of the apparent sporadic cases were included in these clusters. Conclusions The proportion of close contacts testing positive varied significantly throughout the pandemic, with testing policy and type of exposure having the greatest impact. Whole genome sequencing can give a better understanding of webs of transmission to complement epidemiological investigations. It is now possible to undertake sequencing in real time where it can make a contribution to outbreak control and resolution. Public Health professionals should become familiar with WGS and bioinformatics as useful tools in their armory for the control of all communicable diseases not only SARS-CoV-2. Key messages • Combined epidemiological investigations and Whole Genome Sequencing (WGS) provide crucial insights into campus COVID-19 outbreaks, guiding effective control measures. • WGS integration enhances understanding of transmission patterns, identifies clusters, and equips public health professionals with data-driven approaches for outbreak management beyond SARS-CoV-2.

4.P. Round table: Advancing genomic diagnostics for rare genetic diseases: a focus on non-clinical domains of HTA

Abstract Genetic rare diseases are a burning global public health issue requiring a thorough assessment of the related burden. Unfortunately, curative therapies are oftentimes unavailable for genetic rare diseases; nevertheless, a prompt diagnosis could allow clinicians to elaborate supportive care plans for patients and their caregivers, determine the best care setting, and potentially consider enrolling them in clinical trials, if suitable. Innovative, effective, and sustainable diagnostic techniques, such as Whole genome sequencing (WGS), are needed to address this growing health concern. At global level, there is a paucity of research that specifically investigates the implementation of WGS into clinical practice which is even more constrained at the European level. Furthermore, given the current challenges impacting pediatric patients suspected of having genetic diseases without a definitive diagnosis, there is an urgent need to improve the diagnostic workflow based on genomic techniques, such as WGS. Delving into this topic could contribute valuable insights that can inform policymakers, at macro-level, and health professionals, at micro-level, on how to develop suited genomic policies and clinical guidelines for the proper adoption of WGS within the daily clinical practice. From an international standpoint, it could be argued that these considerations resonate with the United Nations Sustainable Development Goals (SDGs), particularly SDG 3 (i.e., “Good health and well-being”) and 10 (i.e., “Reduced inequalities”), as a priority for research and action. Notwithstanding, the broader implementation of WGS encounters hindrances owing to its complexity and the multifaceted social, economic, organizational, and ethical implications. In view of these challenges, Health Technology Assessment (HTA), as an integrated and multidisciplinary process, provides a comprehensive framework for the evaluation of these dimensions. This round table is intended to provide attendees with insights into nonclinical domains of HTA of WGS which, unlike clinical domains, demand a nuanced approach within the framework of the HTA. The intended objective is pursued through the initial presentation of a case study on the evaluation of WGS in paediatric genetic disorders from the Italian National Health Service perspectives followed by an open discussion with experts. The discussion will delve into issues related to economics, genomics, health services organization and ethics. Key messages • For pediatric patients suspected of having a genetic disease, WGS could shorten the so-called diagnostic odyssey. • Context-depending aspects of implementing WGS should be properly taken into account through HTA.