Genomic Pipeline for Analysis of Mutational Events in Bacteria.

Unveiling the strategies of bacterial adaptation to stress constitute a challenging area of research. The understanding of mechanisms governing emergence of resistance to antimicrobials is of particular importance regarding the increasing threat of antibiotic resistance on public health worldwide. In the last decades, the fast democratization of sequencing technologies along with the development of dedicated bioinformatical tools to process data offered new opportunities to characterize genomic variations underlying bacterial adaptation. Thereby, research teams have now the possibility to dive deeper in the deciphering of bacterial adaptive mechanisms through the identification of specific genetic targets mediating survival to stress. In this chapter, we proposed a step-by-step bioinformatical pipeline enabling the identification of mutational events underlying biocidal stress adaptation associated with antimicrobial resistance development using Escherichia marmotae as an illustrative model.

First detection of influenza A virus subtypes H1N1 and H3N8 in the Antarctic region: King George Island, 2023.

RELEVANCE: Influenza A virus is characterized by a segmented single-stranded RNA genome. Such organization of the virus genome determines the possibility of reassortment, which can lead to the emergence of new virus variants. The main natural reservoir of most influenza A virus subtypes are wild waterfowl. Seasonal migrations gather waterfowl from all major migration routes to nesting areas near the northern and southern polar circles. This makes intercontinental spread of influenza A viruses possible. Objective ‒ to conduct molecular genetic monitoring and study the phylogenetic relationships of influenza A virus variants circulating in Antarctica in 2023. MATERIALS AND METHODS: We studied 84 samples of biological material obtained from birds and marine mammals in April‒May 2023 in coastal areas of Antarctica. For 3 samples, sequencing was performed on the Miseq, Illumina platform and phylogenetic analysis of the obtained nucleotide sequences of the influenza A virus genomes was performed. RESULTS: The circulation of avian influenza virus in the Antarctic region was confirmed. Heterogeneity of the pool of circulating variants of the influenza A virus (H3N8, H1N1) was revealed. Full-length genomes of the avian influenza virus were sequenced and posted in the GISAID database (EPI_ISL_19032103, 19174530, 19174467). CONCLUSION: The study of the genetic diversity of influenza A viruses circulating in the polar regions of the Earth and the identification of the conditions for the emergence of new genetic variants is a relevant task for the development of measures to prevent biological threats.

Investigating an Outbreak of Extensively Drug-Resistant Acinetobacter baumannii in a Tertiary Healthcare Center in Lebanon Using Next-Generation Sequencing.

The frequent occurrence of Acinetobacter baumannii in hospital settings and the elevated rate of antimicrobial resistance in this pathogen represent a serious clinical and public health threat worldwide and particularly in Lebanon where outbreak surveillance and control are still insufficient. Whole-genome sequencing (WGS) is currently a fast and reliable tool to study outbreaks at the molecular level and obtain actionable knowledge leading to better control measures. We collected 59 A. baumannii isolates from intensive care unit (ICU) patients and from the hospital environment between August 2022 and May 2023, performed AST and subjected their gDNA to WGS. Analysis was performed to reveal the sequence types (ST), the relatedness to strains that caused other outbreaks and the arsenal of resistance genes harbored by these bacteria. Out of 59 isolates, 81.4% were categorized as extensively drug-resistant (XDR), 13.6% as multi-drug-resistant (MDR) and 1.7% as pan-drug-resistant. All isolates belonged to international clone (IC)2, of which the majority were of ST2 (91.5%). Our isolates clustered well with those of a previous outbreak in the same hospital. In addition, isolates from Lebanese hospitals clustered well together and some clustered with those originating from different countries. The observed genetic relatedness between our current isolates with those from the previous outbreaks underscores the importance of strict surveillance to limit the threat of outbreaks. Moreover, the clustering of Lebanese isolates with others from distant countries proves the necessity of further investigations addressing the international spread of drug-resistant pathogens and resulting in the implementation of control strategies.

Oxford Nanopore's 2024 sequencing technology for Listeria monocytogenes outbreak detection and source attribution: progress and clone-specific challenges.

Whole genome sequencing is an essential cornerstone of pathogen surveillance and outbreak detection. Established sequencing technologies are currently being challenged by Oxford Nanopore Technologies (ONT), which offers an accessible and cost-effective alternative enabling gap-free assemblies of chromosomes and plasmids. Limited accuracy has hindered its use for investigating pathogen transmission, but recent technology updates have brought significant improvements. To evaluate its readiness for outbreak detection, we selected 78 Listeria monocytogenes isolates from diverse lineages or known epidemiological clusters for sequencing with ONT's V14 Rapid Barcoding Kit and R10.4.1 flow cells. The most accurate of several tested workflows generated assemblies with a median of one error (SNP or indel) per assembly. For 66 isolates, the cgMLST profiles from ONT-only assemblies were identical to those generated from Illumina data. Eight assemblies were of lower quality, with more than 20 erroneous sites each, primarily caused by methylations at the GAAGAC motif (5'-GAAG6mAC-3'/5'-GT4mCTTC-3'). This led to inaccurate clustering, failing to group isolates from a persistence-associated clone that carried the responsible restriction-modification system. Out of 50 methylation motifs detected among the 78 isolates, only the GAAGAC motif was linked to substantially increased error rates. Our study shows that most L. monocytogenes genomes assembled from ONT-only data are suitable for high-resolution genotyping, but further improvements of chemistries or basecallers are required for reliable routine use in outbreak and food safety investigations.

Genomic evidence of Escherichia coli gut population diversity translocation in leukemia patients.

Escherichia coli, a commensal species of the human gut, is an opportunistic pathogen that can reach extra-intestinal compartments, including the bloodstream and the bladder, among others. In non-immunosuppressed patients, purifying or neutral evolution of E. coli populations has been reported in the gut. Conversely, it has been suggested that when migrating to extra-intestinal compartments, E. coli genomes undergo diversifying selection as supported by strong evidence for adaptation. The level of genomic polymorphism and the size of the populations translocating from gut to extra-intestinal compartments is largely unknown. To gain insights into the pathophysiology of these translocations, we investigated the level of polymorphism and the evolutionary forces acting on the genomes of 77 E. coli isolated from various compartments in three immunosuppressed patients. Each patient had a unique strain, which was a mutator in one case. In all instances, we observed that translocation encompasses much of the genomic diversity present in the gut. The same signature of selection, whether purifying or diversifying, and as anticipated, neutral for mutator isolates, was observed in both the gut and bloodstream. Additionally, we found a limited number of non-specific mutations among compartments for non-mutator isolates. In all cases, urine isolates were dominated by neutral selection. These findings indicate that substantial proportions of populations are undergoing translocation and that they present a complex compartment-specific pattern of selection at the patient level.IMPORTANCEIt has been suggested that intra and extra-intestinal compartments differentially constrain the evolution of E. coli strains. Whether host particular conditions, such as immunosuppression, could affect the strain evolutionary trajectories remains understudied. We found that, in immunosuppressed patients, large fractions of E. coli gut populations are translocating with variable modifications of the signature of selection for commensal and pathogenic isolates according to the compartment and/or the patient. Such multiple site sampling should be performed in large cohorts of patients to gain a better understanding of E. coli extra-intestinal diseases.

First isolation of Campylobacter vicugnae sp. nov. in humans suffering from gastroenteritis.

The present study describes the first isolation of a recently described Campylobacter species, Campylobacter vicugnae, in humans. The isolates were recovered by two independent French laboratories in 2020 and 2022 from a man and a woman suffering from gastroenteritis. Biochemical and growth characteristics, and electron microscopy for these two strains indicated that they belong to Campylobacter genus. 16S rDNA and GyrA-based phylogeny, as well as average nucleotide identity and in silico DNA-DNA Hybridization analyses revealed that both strains belong to the Campylobacter vicugnae species. Both isolates possess a complete cytolethal distending toxin (CDT) locus with cdtA, cdtB, and cdtC, and features of CDT activity were demonstrated in vitro with Caco-2 intestinal epithelial cells. Our data suggest that these two isolates of C. vicugnae were associated with gastroenteritis in humans and induced major cytopathogenic effects in vitro. C. vicugnae is likely to be a novel human pathogen, with a source of foodborne infection that needs to be determined.IMPORTANCECampylobacter species that display toxicity features are a worldwide public health issue. In clinical contexts, it is crucial to identify which isolate could be an urgent threat to a patient. Actual and widely used laboratory methods such as mass spectrometry or PCR may be flawed in the field of species identification. In contrast, the present study shows that next-generation sequencing allows to precisely identify isolates to species level that may have been omitted otherwise. Moreover, it helps to identify emerging species before they become a threat to human health. Recovery of a new Campylobacter species in human sample, such as the new species "Campylobacter vicugnae," is an important step for the identification of emerging pathogens posing threat to global health.

Analysis of soft rot Pectobacteriaceae population diversity in US potato growing regions between 2015 and 2022.

Introduction: Soft rot Pectobacteriaceae (SRP) bacteria are globally dispersed pathogens that cause significant economic loss in potato and other crops. Our understanding of the SRP species diversity has expanded in recent years due to advances and adoption of whole-genome sequence technologies. There are currently 34 recognized SRP species that belong to the Dickeya and Pectobacterium genera. Methods: We used whole-genome sequencing based analysis to describe the current distribution and epidemiology of SRP isolated from diseased potato samples obtained from commercial potato cropping systems in the United States. Our primary objectives in the present study were to: (1) identify the species of these SRP isolates recovered from potato samples across 14 states in the US, (2) describe the variation among SRP isolates from various US locations and track their temporal changes, and (3) evaluate the evolutionary relationships among these SRP isolates to deduce their source. We collected 118 SRP strains from diseased potato plants and tubers in 14 states between 2015 and 2022. Results: We identified three Dickeya and eight Pectobacterium species from diseased potato samples. Dickeya dianthicola, Pectobacterium parmentieri, P. carotovorum, and P. versatile appeared to be the predominant species, constituting 83% of the isolates. Furthermore, all D. dianthicola strains studied here as well as 90% of US D. dianthicola isolates sequenced to date exhibit significant clonality. Discussion: The prevalence of this specific group of D. dianthicola, temporally and geographically, aligns with the occurrence of blackleg and soft rot outbreaks in the northeastern US after 2014. The genomic diversity observed in P. parmentieri implies multiple introductions to the US from at least four distinct sources, earlier than the arrival of the predominant group of D. dianthicola. In contrast, P. carotovorum and P. versatile appear to be widespread, long-term endemic strains in the US.

A novel high-level phenyllactic acid fungal producer, Kodamaea ohmeri w5 screened from fermented broad bean-chili-paste.

Phenyllactic acid (PLA) is a broad-spectrum and efficient antimicrobial phenolic acid with potential applications in the food industry. Previous studies have demonstrated that fungi may be ideal producers of PLA. In this study, 15 fungi screened from Doubanjiang with the ability to produce PLA were first reported, including Wickerhamomyces anomalus, Candida etchellsii, Candida parasitosis, Pichia kudriavzevii, Pichia membranifaciens and Kodamaea ohmeri. Among them, K. ohmeri w5 had the highest PLA yield, producing up to 7160 mg/L PLA in shake flask fermentation with phenylalanine as substrate, which was more than ten times higher than the PLA produced by wild-type LAB under the similar conditions. In addition, K. ohmeri w5 was able to grow under extreme hypertonic conditions of 20 % NaCl (w/v) and 50 % glucose (w/v) as well as produce 57.12 ± 0.42 and 1609.22 ± 36.26 mg/L of PLA, respectively. Furthermore, the fermentation supernatant of K. ohmeri w5 demonstrated direct inhibitory effects against foodborne pathogenic microorganisms, Aspergillus flavus and Bacillus cereus. However, the inhibitory effect was weaker than that of the PLA standard at the same concentration. Further, 12,497,932 bp of w5 genome-wide information was obtained by sequencing and assembling. And its gene model was predicted based on transcriptomic evidence, which showed that a total of 7 genes related to PLA synthesis were identified in the w5 genome. Based on qRT-PCR, structure prediction, and molecular docking, a potentially key genetic resource from K. ohmeri w5 for PLA production was uncovered. The results will provide novel producers of PLA and its potential genetic resources.

Retrospect and prospect of Nicotiana tabacum genome sequencing.

Investigating plant genomes offers crucial foundational resources for exploring various aspects of plant biology and applications, such as functional genomics and breeding practices. With the development in sequencing and assembly technology, several Nicotiana tabacum genomes have been published. In this paper, we reviewed the progress on N. tabacum genome assembly and quality, from the initial draft genomes to the recent high-quality chromosome-level assemblies. The application of long-read sequencing, optical mapping, and Hi-C technologies has significantly improved the contiguity and completeness of N. tabacum genome assemblies, with the latest assemblies having a contig N50 size over 50 Mb. Despite these advancements, further improvements are still required and possible, particularly on the development of pan-genome and telomere-to-telomere (T2T) genomes. These new genomes will capture the genomic diversity and variations among different N. tabacum cultivars and species, and provide a comprehensive view of the N. tabacum genome structure and gene content, so to deepen our understanding of the N. tabacum genome and facilitate precise breeding and functional genomics.

Investigation of in vitro susceptibility and resistance mechanisms to amikacin among diverse carbapenemase-producing Enterobacteriaceae.

OBJECTIVE: This study aims to assess the in vitro drug susceptibility of various Carbapenemase-Producing Enterobacteriaceae (CPE) genotypes and elucidate the underlying mechanisms of amikacin resistance. METHODS: A total of 72 unique CPE strains were collected from the Second Hospital of Jiaxing between 2019 and 2022, including 51 strains of Klebsiella pneumoniae, 11 strains of Escherichia coli, 6 strains of Enterobacter cloacae, 2 strains of Klebsiella aerogenes, 1 strain of Citrobacter freundii, and 1strain of Citrobacter werkmanii. Among these strains, 24 carried blaKPC gene, 20 carried blaNDM gene, 23 carried blaOXA-48-like gene, and 5 carried both blaKPC and blaNDM. We measured the in vitro activity of amikacin and other common antibiotics. Strains carrying blaOXA-48-like gene were selected for whole genome sequencing (WGS) via next-generation sequencing to identify genes related to antimicrobial resistance (AMR) and virulence factor (VF). RESULTS: Out of the 72 CPE strains tested, 41.7% exhibited resistance to amikacin. The drug resistance rates for K. pneumoniae, E. coli, and Enterobacter spp. were 51.0%, 27.3%, and 10.0%, respectively. The majority of the CPE strains (> 90%) displayed resistance to cephalosporins and carbapenems, while most of them were sensitive to polymyxin B and tigecycline (97.2% and 94.4%). The amikacin resistance rate was 100% for strains carrying blaOXA-48, 20.8% for those with blaKPC, 5.0% for those with blaNDM, and 20.0% for those with both blaKPC and blaNDM. These differences were statistically significant (P < 0.05). Through sequencing, we detected aminoglycoside resistance genes rmtF and aac(6')-Ib, VF genes iucABCD and rmpA2 in OXA-48-producing multidrug resistance and highly virulent strains. These genes were located on a IncFIB- and IncHI1B-type plasmid, respectively. Both plasmids were highly homologous to the plasmid from OXA-232 strains in Zhejiang province and Shanghai province. Integration of these resistance genes into the IncFIB plasmid, facilitated by the IS6 and/or Tn3 transposons, resulted in OXA232-producing K. pneumoniae with amikacin resistance. CONCLUSION: This study identified significant amikacin resistance in CPE strains, particularly in those carrying the blaOXA-48 gene. Resistance genes rmtF and aac(6')-Ib were identified on plasmids. These results highlight the need for careful monitoring of amikacin resistance.

De novo AHDC1 Deletions Identified by Genome Sequencing in Two Individuals with Xia-Gibbs Syndrome.

Introduction: Xia-Gibbs syndrome (XGS) is a rare syndromic disorder characterized by developmental delay with intellectual disability, muscular hypotonia, brain anomalies, and nonspecific dysmorphic features. Different heterozygous variants in AHDC1 have been reported as causal for XGS, comprising mainly de novo stop-gain and frameshift events, but also missense variants, deletions, and a duplication of the locus. Case Presentation: We hereby report 2 patients with clinical features of XGS. In the first patient, a de novo interstitial deletion in 1p36.11p35.3 encompassing the entire coding region of AHDC1 was initially suspected by trio exome sequencing and subsequently confirmed by shallow genome sequencing. In the second patient, a de novo deletion comprising most of the 5' untranslated region of AHDC1 was detected by genome sequencing. Conclusion: We identified the smallest deletion comprising AHDC1 reported so far by shallow genome sequencing as well as another small AHDC1 deletion by genome sequencing. These methods represent useful techniques for the identification and confirmation of small deletions and structural variants. Furthermore, our data provide additional evidence of AHDC1 haploinsufficiency as a disease mechanism in XGS. Clinically, foot deformity, skin and connective tissue abnormalities observed in one of the patients are consistent with other reported cases of XGS. These findings suggest that these manifestations could be considered as more prevalent characteristics, underscoring the importance of in-depth phenotyping.

The neurodevelopmental disorder Xia-Gibbs syndrome is associated with symptoms of various organ systems. It is due to changes in the AHDC1 gene. Using sophisticated genetic testing procedures, two different deletions as a particularly rare genetic cause were identified in 2 patients. Here, we provide a summary of their individual characteristics in comparison to those of other patients with similar deletions that have been reported in the literature or public databases.

Mutational Landscape of Gastric Adenocarcinoma of the Fundic Gland Type Revealed by Whole Genome Sequencing.

BACKGROUND: Gastric adenocarcinoma of the fundic gland type (GA-FG) is a newly described variant of gastric adenocarcinoma with lack of knowledges regarding its genetic features. METHODS: We performed whole-genome sequencing (WGS) in formalin-fixed paraffin-embedded (FFPE) tumor tissues and matched adjacent noncancerous specimens from 21 patients with GA-FG, and integrated published datasets from 1105 patients with traditional gastric adenocarcinoma with the purpose of dissecting genetic determinants both common to conventional gastric adenocarcinoma and unique to GA-FG disease. RESULTS: We characterized the genomic architecture of GA-FG disease, revealing the predominant proportion of C > T substitution among the six types of SNVs. GNAS was the most significantly mutated driver gene (14.29%). 42.8% of samples harbored "Kataegis." Distinct genomic alterations between GA-FG and conventional gastric cancer were identified. Specifically, low mutational burden and relatively moderate mutational frequencies of significantly mutated driver genes, coupled with the absence of non-silent alterations of formerly well-known drivers such as TP53, PIK3CA and KRAS were identified in GA-FG patients. Oncogenic signaling pathway analysis revealed mutational processes associated with focal adhesions and proteoglycans in cancer, highlighting both common and specific procedures during the development of GA-FG and conventional gastric cancer. CONCLUSION: Our study is the first to comprehensively depict the genomic landscape highlighting the multidimensional perturbations in GA-FG patients. These discoveries offered mechanistic insights for novel diagnostic and therapeutic strategies for patients with such disease.

Molecular characterization of Mumps virus genotype C detected from Dibrugarh district of Assam, India.

Background & objectives Mumps, a contagious disease caused by the mumps virus (MuV) involves parotid gland inflammation, with potential complications affecting organs other than the parotid glands and central nervous system. Despite successful vaccination, a resurgence of mumps occurred, raising concerns about vaccine effectiveness. This study aimed to examine the entire genome of a representative MuV genotype C from Dibrugarh, Assam, and compare it with references to detect genetic variations in the circulating strain. Methods Representative MuV genotype C from our published study was subjected to whole genome sequencing. MuV genome was analyzed against the reference genome and vaccine strains before being subjected to mutational profiling, N-glycosylation site determination, and phylogenetic analysis. The Immune Epitope Database was used for epitope screening, and selected epitopes were mapped against Assam MuV for conservancy studies. Results Mutational analysis of Assam MuV with WHO (World health Organization) reference, vaccine strains Jeryl Lynn (Genotype A), and L Zagreb (Genotype N) showed variations in seven genes. Phylogenetic analysis established Assam MuV as genotype C. Epitope conservancy analysis highlighted subtle variations in experimentally determined T-cell epitopes for HN and F proteins, emphasizing overall epitope stability. Interpretation & conclusions Genome sequencing has evolved into a standard and potent method for investigating and recording circulating MuV as it provides information on surveillance, mutation analysis, and transmission dynamics. Despite mumps' global effect, genomic studies are limited, particularly in north-east. Our study provides first comprehensive whole-genome report on circulating MuV genotype C in Assam. This research contributes vital genomic data, filling gaps in MuV genetic epidemiology, supporting global research, and assessing vaccine effectiveness.

Whole-genome sequencing reveals rare variants associated with gout in Taiwanese males.

To identify rare variants (RVs) of gout, we sequenced the whole genomes of 321 male gout patients and combined these with those of 64 male gout patients and 682 normal controls at Taiwan Biobank. We performed ACAT-O to identify 682 significant RVs (p < 3.8 × 10-8) clustered on chromosomes 1, 7, 10, 16, and 18. To prioritize causal variants effectively, we sifted them by Combined Annotation-Dependent Depletion score >10 or |effect size| ≥ 1.5 for those without CADD scores. In particular, to the best of our knowledge, we identified the rare variants rs559954634, rs186763678, and 13-85340782-G-A for the first time to be associated with gout in Taiwanese males. Importantly, the RV rs559954634 positively affects gout, and its neighboring gene NPHS2 is involved in serum urate and expressed in kidney tissues. The kidneys play a major role in regulating uric acid levels. This suggests that rs559954634 may be involved in gout. Furthermore, rs186763678 is in the intron of NFIA that interacts with SLC2A9, which has the most significant effect on serum urate. Note that gene-gene interaction NFIA-SLC2A9 is significantly associated with serum urate in the Italian MICROS population and a Croatian population. Moreover, 13-85340782-G-A significantly affects gout susceptibility (odds ratio 6.0; P = 0.038). The >1% carrier frequencies of these potentially pathogenic (protective) RVs in cases (controls) suggest the revealed associations may be true; these RVs deserve further studies for the mechanism. Finally, multivariate logistic regression analysis shows that the rare variants rs559954634 and 13-85340782-G-A jointly are significantly associated with gout susceptibility.

Whole genome-based characterization of extended-spectrum ß-lactamase-producing Enterobacter cloacae from orthopedic patients and environment of a tertiary referral hospital in Tanzania.

Objectives: We investigated the genomic epidemiology of extended-spectrum ß-lactamase-producing Enterobacter cloacae (ESBL-Ec) isolates from patients and hospital environment to better understand their distribution to help devising effective strategies for infection prevention and control. Methods: We screened ESBL-Ec at Bugando Medical Center (BMC) in Mwanza, Tanzania. Rectal swabs from orthopedic patients on admission and swabs from the neighboring inanimate environment were collected. Following microbial culture, DNA was extracted from pure ESBL-Ec, and whole-genome sequencing was done. Sequence typing (ST), plasmid replicons, drug resistance, and virulence genes were deciphered using the Rapid Microbial Analysis Pipeline (rMAP). Results: We obtained 209 ESBL isolates, of which 15 (7.2 %) were ESBL-Ec [8 (53.3 %) from patients and 7 (46.7 %) from the environment]. Seven isolates were novel and eight were diverse, each with a unique ST. All isolates harbored two to five ß-lactamase genes, with the predominance of bla CTX-M-15 (15/15), bla OXA-1 (14/15), bla TEM (14/15) and bla ACT (12/15). The most common non ß-lactam drug resistance genes were aac(3)-IIa (14/15), aac(6')-Ib-cr (14/15), fosA (14/15), and qnrB1 (12/15), aph(3″)-Ib (10/15) and aph(6)-Id (10/15). Eleven different types of plasmid replicons were identified in 14/15 of the isolates, harboring one to five plasmids, with the most common plasmids being IncFII (11/15) and IncFIB (10/15). All isolates harbored the outer membrane protein (ompA), and curli protein (csg) was in 14/15 isolates. Conclusion: Admitted orthopedic patients and the hospital environment act as a reservoir of ESBL-Ec with diverse STs and endowed with drug resistance and arsenals of virulence genes, calling for their routine screening on admission for mitigation of potential subsequent infections.

Alleviating arsenic stress affecting the growth of Vigna radiata through the application of Klebsiella strain ASBT-KP1 isolated from wastewater.

Arsenic contamination of soil and water is a major environmental issue. Bioremediation through plant growth-promoting bacteria is viable, cost-effective, and sustainable. Along with arsenic removal, it also improves plant productivity under stressful conditions. A crucial aspect of such a strategy is the selection of bacterial inoculum. The described study demonstrates that the indigenous wastewater isolate, ASBT-KP1, could be a promising candidate. Identified as Klebsiella pneumoniae, ASBT-KP1 harbors genes associated with heavy metal and oxidative stress resistance, production of antimicrobial compounds and growth-promotion activity. The isolate efficiently accumulated 30 µg/g bacterial dry mass of arsenic. Tolerance toward arsenate and arsenite was 120 mM and 70 mM, respectively. Plant biomass content of Vigna radiata improved by 13% when grown in arsenic-free soil under laboratory conditions in the presence of the isolate. The increase became even more significant under the same conditions in the presence of arsenic, recording a 37% increase. The phylogenetic analysis assigned ASBT-KP1 to the clade of Klebsiella strains that promote plant growth. Similar results were also observed in Oryza sativa, employed to assess the ability of the strain to promote growth, in plants other than V. radiata. This study identifies a prospective candidate in ASBT-KP1 that could be employed as a plant growth-promoting rhizoinoculant in agricultural practices.

Identification of Terrisporobacter muris isolated from human blood using whole-genome sequencing: A case report.

We describe a case of Terrisporobacter muris bacteremia in a critically ill elderly man with a sigmoid colonic perforation. Initially, MALDI-TOF MS identified the bacterium as T. glycolicus; however, 16S rRNA gene sequencing suggested the presence of T. glycolicus, T. mayombei, or T. petrolearius. Owing to the limitations of these methods in distinguishing among the Terrisporobacter species, we employed whole-genome sequencing, which revealed the involvement of T. muris in the infection. This case represents the second report of T. muris isolated from human blood culture and is the first to describe the clinical course of this infection. Our findings underscore the diagnostic utility of whole-genome sequencing in accurately identifying novel infectious agents.

A genome-wide association study of neonatal metabolites.

Genetic factors significantly influence the concentration of metabolites in adults. Nevertheless, the genetic influence on neonatal metabolites remains uncertain. To bridge this gap, we employed genotype imputation techniques on large-scale low-pass genome data obtained from non-invasive prenatal testing. Subsequently, we conducted association studies on a total of 75 metabolic components in neonates. The study identified 19 previously reported associations and 11 novel associations between single-nucleotide polymorphisms and metabolic components. These associations were initially found in the discovery cohort (8,744 participants) and subsequently confirmed in a replication cohort (19,041 participants). The average heritability of metabolic components was estimated to be 76.2%, with a range of 69%-78.8%. These findings offer valuable insights into the genetic architecture of neonatal metabolism.

Utilizing non-invasive prenatal test sequencing data for human genetic investigation.

Non-invasive prenatal testing (NIPT) employs ultra-low-pass sequencing of maternal plasma cell-free DNA to detect fetal trisomy. Its global adoption has established NIPT as a large human genetic resource for exploring genetic variations and their associations with phenotypes. Here, we present methods for analyzing large-scale, low-depth NIPT data, including customized algorithms and software for genetic variant detection, genotype imputation, family relatedness, population structure inference, and genome-wide association analysis of maternal genomes. Our results demonstrate accurate allele frequency estimation and high genotype imputation accuracy (R2>0.84) for NIPT sequencing depths from 0.1× to 0.3×. We also achieve effective classification of duplicates and first-degree relatives, along with robust principal-component analysis. Additionally, we obtain an R2>0.81 for estimating genetic effect sizes across genotyping and sequencing platforms with adequate sample sizes. These methods offer a robust theoretical and practical foundation for utilizing NIPT data in medical genetic research.

Whole genome sequencing of Lacticaseibacillus casei KACC92338 strain with strong antioxidant activity, reveals genes and gene clusters of probiotic and antimicrobial potential.

Lacticaseibacillus casei KACC92338 was originally isolated from Korean raw milk. The antioxidant activities and protective effect in vitro of this strain were evaluated extensively. The results showed that KACC92338 can tolerate hydrogen peroxide up to 2 mM and cell-free supernatant (CFS) had higher scavenging rates for DPPH, hydroxyl radical, reducing power, and iron chelating activities with 95.61 ± 1.59%, 34.10 ± 1.93%, 2.220 ± 0.82 and 81.06 ± 1.06%, respectively. Meanwhile, the CFS showed a protective effect on yeast cells against 10 mM hydrogen peroxide with a survival rate of 76.05 ± 5.65%. To explore the probiotic potential of KACC92338, whole genome assembly and gene clusters with probiotic properties were further analyzed. The genome size was 3,050,901 bp with a 47.96% GC ratio, and 63 contigs. The genome contains 3,048 genes composed of 2,981 coding sequences and 67 RNAs (including 57 tRNAs +9 rRNAs +1 tmRNA). Average Nucleotide Identity and genome-based taxonomy showed that the KACC92338 genome had close similarity with L. casei strains with 96% ANI. Functional annotation by EggNOG and KEGG revealed the presence of numerous genes putatively involved in carbohydrate- and amino acid-transport and metabolism, genetic information processing, and signaling and cellular processes. Additionally, several genes conferring probiotic characteristics such as tolerance to stress, heat, cold, acid, bile salts, oxidative stress, immunomodulation, and adhesion to intestinal epithelium were identified. Notably absent were acquired antibiotic resistance genes, virulence, and pathogenic factors, that prove KACC92338 is a safe strain. Besides, the defense mechanisms of KACC92338 include six prophage regions and three clustered regularly interspaced short palindromic repeat (CRISPR) arrays as acquired immune systems against mobile elements. Further, the BAGEL4 database determined antimicrobial bacteriocin clusters of class IIb: sakacin-P, Enterolysin_A, sactipeptides, and Enterocin X, which suggests the strain could exhibit a wide range of antimicrobial functions. Together, these findings show that the L. casei KACC92338 strain can be a potential probiotic candidate in producing functional fermented foods-, health care- and skin care products- with antioxidant properties. However, a few more mechanistic studies are necessary on the safety assurance and potential application of the strain as a probiotic agent.