Infection Genetics and Evolution最新文献

{"title":"A genome-based investigation of the Priestia species isolated from anthrax endemic regions in Kruger National Park","authors":"","doi":"10.1016/j.meegid.2024.105649","DOIUrl":"10.1016/j.meegid.2024.105649","url":null,"abstract":"<div><p><em>Priestia</em> is a genus that was renamed from the genus <em>Bacillus</em> based on the conserved signature indels (CSIs) in protein sequences that separate <em>Priestia</em> species from <em>Bacillus</em>, with the latter only including species closely related to <em>B. subtilis</em> and <em>B. cereus</em>. Diagnosis of anthrax, a zoonotic disease, is implicated by tripartite anthrax virulence genes (<em>lef, pagA</em>, and <em>cya</em>) and poly-γ-D-glutamic acid capsular genes <em>cap-ABCDE</em> of <em>Bacillus anthracis.</em> Due to the amplification of anthrax virulence genes in <em>Priestia</em> isolates, the search for homologous anthrax virulence genes within the <em>Priestia</em> genomes (n = 9) isolated from animal blood smears was embarked upon through whole genome sequencing. In silico taxonomic identification of the isolates was conducted using genome taxonomy database (GTDB), average nucleotide identity (ANI), and multi-locus sequence typing (MLST), which identified the genomes as <em>P. aryabhattai</em> (n = 5), <em>P. endophytica</em> (n = 2) and <em>P. megaterium</em> (n = 2)<em>.</em> A pan-genome analysis was further conducted on the <em>Priestia</em> genomes, including the screening of virulence, antibiotic resistance genes and mobile genetic elements on the sequenced genomes. The oligoribonuclease NrnB protein sequences showed that <em>Priestia</em> spp. possess a unique CSI that is absent in other <em>Bacillus</em> species. Furthermore, the CSI in <em>P. endophytica</em> is unique from other <em>Priestia</em> spp. Pan-genomic analysis indicates that <em>P. endophytica</em> clusters separately from <em>P. aryabhattai</em> and <em>P. megaterium</em>. In silico BLASTn genome analysis using the SYBR primers, Taqman probes and primers that target the chromosomal marker (Ba-1), protective antigen (<em>pagA</em>), and lethal factor (<em>lef</em>) on <em>B. anthracis</em>, showed partial binding to <em>Priestia</em> regions encoding for hypothetical proteins, pyridoxine biosynthesis, hydrolase, and inhibitory proteins. The antibiotic resistance genes (ARG) profile of <em>Priestia</em> spp. showed that the genomes contained no more than two ARGs. This included genes conferring resistance to rifamycin and fosfomycin on <em>P. endophytica</em>, as well as clindamycin on <em>P. aryabhattai</em> and <em>P. megaterium</em>. <em>Priestia</em> genomes lacked <em>B. anthracis</em> plasmids and consisted of plasmid replicon types with unknown functions. Furthermore, the amplification of <em>Priestia</em> strains may result in false positives when qPCR is used to detect the virulence genes of <em>B. anthracis</em> in soil, blood smears, and/or environmental samples.</p></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S156713482400100X/pdfft?md5=8051da659314f41494278573a9829002&pid=1-s2.0-S156713482400100X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141768104","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effects of the Beijing genotype on latent tuberculosis infection, TB disease risk, and clustering of TB cases","authors":"","doi":"10.1016/j.meegid.2024.105648","DOIUrl":"10.1016/j.meegid.2024.105648","url":null,"abstract":"<div><h3>Background</h3><p>The Beijing genotype of <em>Mycobacterium tuberculosis</em> (Mtb) has sparked debate regarding its virulence and transmissibility. This study contributes to this discussion by assessing its effect on the risk of latent tuberculosis infection (LTBI), active tuberculosis (TB) disease among contacts, and clustering of known TB cases.</p></div><div><h3>Methods</h3><p>We conducted a retrospective cohort study using the records of 4457 culture-confirmed TB patients and their contacts (20,448) reported to the Florida Department of Health between 2009 and 2023. Univariate and multivariate analyses were used to evaluate the effect of the Beijing strain on LTBI, active TB risk among contacts, and case clustering.</p></div><div><h3>Results</h3><p>Our study revealed no significant difference in transmissibility between the Beijing and non-Beijing genotypes among contacts. LTBI prevalence was 19.9%, slightly higher in non-Beijing than Beijing genotypes (20.2% vs. 15.5%, <em>p</em> &lt; 0.001). The prevalence of active TB was 1.8%, with no significant difference between the Beijing and non-Beijing genotypes (1.4% vs. 1.8%, <em>p</em> = 0.296). Increased LTBI risk was associated with older age, male sex, Hispanic ethnicity, multidrug-resistant TB exposure, household exposure, and a longer exposure duration. Active TB risk was higher for males, HIV-positive individuals, and contacts with more prolonged exposure to index cases. The Beijing genotype was associated with increased TB case clustering (aOR = 1.98, 95%CI: 1.53, 2.55, <em>p</em> &lt; 0.001) as compared to the non-Beijing genotypes. US birthplace (aOR = 2.75, 95%CI: 2.37, 3.19, <em>p</em> &lt; 0.001), pulmonary disease (aOR = 1.27, 95%CI: 1.04, 1.56, <em>p</em> &lt; 0.020), cavitary TB (aOR = 1.25, 95% CI: 1.08, 1.44, <em>p</em> &lt; 0.003), previous year alcohol use (aOR = 1.68, 95%CI: 1.38, 2.04, p &lt; 0.001), and recreational drug use (aOR = 1.32, 95%CI: 1.04, 1.67, <em>p</em> &lt; 0.024) were also associated with an increased risk of TB case clustering.</p></div><div><h3>Conclusion</h3><p>While the Beijing genotype did not increase the risk of LTBI or active TB among contacts, it showed a higher tendency for case clustering. Hence, interventions should prioritize populations where this genotype is prevalent.</p></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1567134824000996/pdfft?md5=17fca684ee21c14dfa845276647ded3a&pid=1-s2.0-S1567134824000996-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141768105","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The association between human papillomavirus and lung cancer: A Mendelian randomization study","authors":"","doi":"10.1016/j.meegid.2024.105646","DOIUrl":"10.1016/j.meegid.2024.105646","url":null,"abstract":"<div><h3>Background</h3><p>To investigate the causal relationship between human papillomavirus (HPV) and lung cancer, we conducted a study using the two-sample Mendelian randomization (TSMR).</p></div><div><h3>Method</h3><p>Data from genome-wide association studies (GWAS) were analyzed with HPV E7 Type 16 and HPV E7 Type 18 as exposure factors. The outcome variables included lung cancer, small cell lung cancer, adenocarcinoma and squamous cell lung cancer. Causality was estimated using inverse variance weighted (IVW), MR-Egger and weighted median methods. Heterogeneity testing, sensitivity analysis, and multiple validity analysis were also performed..</p></div><div><h3>Results</h3><p>The results showed that HPV E7 Type 16 infection was associated with a higher risk of squamous cell lung cancer (OR = 7.69; 95% CI:1.98–29.85; <em>p</em> = 0.0149). HPV E7 Type 18 infection significantly increased the risk of lung adenocarcinoma (OR = 0.71; 95% CI: 0.38–1.31; <em>p</em> = 0.0079) and lung cancer (OR = 7.69; 95% CI:1.98–29.85; <em>p</em> = 0.0292). No significant causal relationship was found between HPV E7 Type 16 and lung adenocarcinoma, lung cancer, or small cell lung carcinoma, and between HPV E7 Type 18 and squamous cell lung cancer or small cell lung carcinoma.</p></div><div><h3>Conclusions</h3><p>This study has revealed a causal relationship between HPV and lung cancers. Our findings provide valuable insights for further mechanistic and clinical studies on HPV-mediated cancer.</p></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1567134824000972/pdfft?md5=a88d7e3f5058489725884e3096bc51fb&pid=1-s2.0-S1567134824000972-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141768106","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Extensive genetic diversity in Plasmodium vivax from Sudan and its genetic relationships with other geographical isolates","authors":"","doi":"10.1016/j.meegid.2024.105643","DOIUrl":"10.1016/j.meegid.2024.105643","url":null,"abstract":"<div><p><em>Plasmodium vivax</em>, traditionally overlooked has experienced a notable increase in cases in East Africa. This study investigated the geographical origin and genetic diversity of <em>P. vivax</em> in Sudan using 14 microsatellite markers. A total of 113 clinical <em>P. vivax</em> samples were collected from two different ecogeographical zones, New Halfa and Khartoum, in Sudan. Additionally, 841 geographical samples from the database were incorporated for a global genetic analysis to discern genetic relationships among <em>P. vivax</em> isolates on regional and worldwide scales. On the regional scale, our findings revealed 91 unique and 8 shared haplotypes among the Sudan samples, showcasing a remarkable genetic diversity compared to other geographical isolates and supporting the hypothesis that <em>P. vivax</em> originated from Africa. On a global scale, distinct genetic clustering of <em>P. vivax</em> isolates from Africa, South America, and Asia (including Papua New Guinea and Solomon Island) was observed, with limited admixture among the three clusters. Principal component analysis emphasized the substantial contribution of African isolates to the observed global genetic variation. The Sudanese populations displayed extensive genetic diversity, marked by significant multi-locus linkage disequilibrium, suggesting an ancestral source of <em>P. vivax</em> variation globally and frequent recombination among the isolates. Notably, the East African <em>P. vivax</em> exhibited similarity with some Asian isolates, indicating potential recent introductions. Overall, our results underscore the effectiveness of utilizing microsatellite markers for implementing robust control measures, given their ability to capture extensive genetic diversity and linkage disequilibrium patterns.</p></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1567134824000947/pdfft?md5=493cb4d6ded3c8232bdef783ff3f629c&pid=1-s2.0-S1567134824000947-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141762765","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative genomics of IncQ1 plasmids carrying blaGES variants from clinical and environmental sources in Brazil","authors":"","doi":"10.1016/j.meegid.2024.105644","DOIUrl":"10.1016/j.meegid.2024.105644","url":null,"abstract":"<div><p>IncQ-type plasmids have become important vectors in the dissemination of <em>bla</em>_GES among different bacterial genera and species from different environments around the world, and studies estimating the occurrence of Guiana extended-spectrum (GES)-type β-lactamases are gaining prominence. We analyzed the genetic aspects of two IncQ1 plasmids harboring different <em>bla</em>_GES variants from human and environmental sources. The <em>bla</em>_GES variants were identified using polymerase chain reaction (PCR) in <em>Aeromonas veronii</em> isolated from hospital effluent and <em>Klebsiella variicola</em> isolated from a rectal swab of a patient admitted to the cardiovascular intensive care unit in a different hospital. Antimicrobial-susceptibility testing and transformation experiments were performed for phenotypic analysis. Whole-genome sequencing was performed using Illumina and Oxford Nanopore platforms. The comparative analysis of plasmids was performed using BLASTn, and the IncQ1 plasmids showed a high identity and similar size. <em>A. veronii</em> harbored <em>bla</em>_GES-7 in a class 1 integron (In2061), recently described by our group, and <em>K. variicola</em> carried <em>bla</em>_GES-5 in the known class 1 integron. Both integrons showed a fused gene cassette that encodes resistance to aminoglycosides and fluoroquinolones, with an IS<em>6100</em> truncating the 3′-conserved segment. The fused genes are transcribed together, although the <em>attC</em> site is disrupted. These gene cassettes can no longer be mobilized. This study revealed a mobilome that may contribute to the dissemination of GES-type β-lactamases in Brazil. Class 1 integrons are hot spots for bacterial evolution, and their insertion into small IncQ-like plasmids displayed successful recombination, allowing the spread of <em>bla</em>_GES variants in various environments. Therefore, they can become prevalent across clinically relevant pathogens.</p></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1567134824000959/pdfft?md5=13fd2c4522f11cb05edf810382fbf2d8&pid=1-s2.0-S1567134824000959-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141749799","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Further evidence of low infection frequencies of Wolbachia in soil arthropod communities","authors":"","doi":"10.1016/j.meegid.2024.105641","DOIUrl":"10.1016/j.meegid.2024.105641","url":null,"abstract":"<div><p>Endosymbiotic Alphaproteobacteria of the genus <em>Wolbachia</em> are exclusively transferred maternally from mother to offspring, but horizontal transfer across species boundaries seems to be frequent as well. However, the (ecological) mechanisms of how these bacteria are transferred between distantly related arthropod hosts remain unclear. Based on the observation that species that are part of the same ecological community often also share similar <em>Wolbachia</em> strains, host ecology has been hypothesized as an important factor enabling transmission and a key factor in explaining the global distribution of <em>Wolbachia</em> lineages.</p><p>In this study, we focus on the diversity and abundance of <em>Wolbachia</em> strains in soil arthropods, a so far rather neglected community. We screened 82 arthropod morphotypes collected in the beech forest (dominated by <em>Fagus</em> sp.) soil in the area of Göttingen in central Germany for the presence of <em>Wolbachia</em>. By performing a PCR screen with <em>Wolbachia-</em>MLST markers (<em>coxA</em>, <em>dnaA</em>, <em>fbpA</em>, <em>ftsZ</em>, <em>gatB</em>, and <em>hcpA</em>), we found a rather low infection frequency of 12,2%. Additionally, we performed metagenomic screening of pooled individuals from the same sampling site and could not find evidence that this low infection frequency is an artefact due to PCR-primer bias. Phylogenetic analyses of the recovered <em>Wolbachia</em> strains grouped them in three known supergroups (A, B, and E), with the first report of <em>Wolbachia</em> in Protura (Hexapoda). Moreover, <em>Wolbachia</em> sequences from the pseudoscorpion <em>Neobisium carcinoides</em> cluster outside the currently known supergroup diversity. Our screening supports results from previous studies that the prevalence of <em>Wolbachia</em> infections seems to be lower in soil habitats than in above-ground terrestrial habitats. The reasons for this pattern are not completely understood but might stem from the low opportunity of physical contact and the prevalence of supergroups that are less suited for horizontal transfer.</p></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1567134824000923/pdfft?md5=ddd3834821a514e4d7ae9d116c968cc2&pid=1-s2.0-S1567134824000923-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141617684","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Whole genome sequencing and genomic characteristics analysis of carbapenem-resistant Acinetobacter baumannii clinical isolates in two hospitals in China","authors":"","doi":"10.1016/j.meegid.2024.105642","DOIUrl":"10.1016/j.meegid.2024.105642","url":null,"abstract":"<div><p>Nosocomial outbreaks caused by carbapenem-resistant <em>Acinetobacter baumannii</em> (CRAB) strains are rapidly emerging worldwide and are cause for concern. Herein, we aimed to describe the genomic characteristics of CRAB strains isolated from two hospitals in China in 2023. The <em>A. baumannii</em> isolates were mainly collected from the ICU and isolated from the sputum (71.43%, 15/21), followed by urine (14.29%, 3/21). Twenty-one <em>A. baumannii</em> strains possessed a multidrug-resistant (MDR) profile, and whole-genome sequencing showed that they all carried <em>bla</em>_OXA-23. Based on the Pasteur multilocus sequence typing (MLST) scheme, all strains were typed into a sequence type 2 (ST2). Based on the Oxford MLST scheme, six strains belonged to ST540, three of which were ST208, and four strains were assigned to ST784. <em>Kaptive</em> showed most of the strains (38.10%, 8/21) contained KL93. As for the lipoolygosaccharide (OC locus) type, OCL1c and OCL1d were identified, accounting for 33.33% (7/21) and 66.67% (14/21), respectively. Based on the BacWGSTdb server, we found that the strains belonging to ST540 and ST784 were all collected from China. However, the ST938 strains were isolated from Malaysia and Thailand. Comparative genomics analysis showed that the AB10 strain had a closed relationship with SXAB10-SXAB13 strains, suggesting the transmission happened in these two hospitals and other hospital in China. In addition, the 4300STDY7045869 strain, which was collected from Thailand, possessed near genetic relationship with our isolates in this study, suggesting the possible spread among various countries. Additionally, 3–237 single nucleotide polymorphisms were observed among these strains. In conclusion, this study conducted a genome-based study for <em>A. baumannii</em> strains collected from two hospitals in China and revealed their epidemiological and molecular features. Clone spreading occurred in these two hospitals. Hence, there is an urgent need for increased surveillance in hospitals and other clinical settings to prevent and control CRAB spreading.</p></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1567134824000935/pdfft?md5=5f3eaccce3ac822fb856bf2a9ad42c5c&pid=1-s2.0-S1567134824000935-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141629322","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comprehensive genomics reveals novel sequence types of multidrug resistant Klebsiella oxytoca with uncharacterized capsular polysaccharide K- and lipopolysaccharide O-antigen loci from the National Hospital of Uganda","authors":"","doi":"10.1016/j.meegid.2024.105640","DOIUrl":"10.1016/j.meegid.2024.105640","url":null,"abstract":"<div><p>The <em>Klebsiella oxytoca</em> complex comprises diverse opportunistic bacterial pathogens associated with hospital and community-acquired infections with growing alarming antimicrobial resistance. We aimed to uncover the genomic features underlying the virulence and antimicrobial resistance of isolates from Mulago National Hospital in Uganda. We coupled whole genome sequencing with Pathogenwatch multilocus sequence typing (MLST) and downstream bioinformatic analysis to delineate sequence types (STs) capsular polysaccharide K- and O-antigen loci, along with antimicrobial resistance (AMR) profiles of eight clinical isolates from the National Referral Hospital of Uganda. Our findings revealed that only two isolates (RSM6774 and RSM7756) possess a known capsular polysaccharide K-locus (KL74). The rest carry various unknown K-loci (KL115, KL128, KLI52, KL161 and KLI63). We also found that two isolates possess unknown loci for the lipopolysaccharide O-antigen (O1/O2v1 type OL104 and unknown O1). The rest possess known O1 and O3 serotypes. From MLST, we found four novel sequence types (STs), carrying novel alleles for the housekeeping genes glyceraldehyde-6-phosphate dehydrogenase A (<em>gapA</em>), glucose-6-phosphate isomerase (<em>pgi</em>), and RNA polymerase subunit beta (<em>rpoB</em>). Our AMR analysis revealed that all the isolates are resistant to ampicillin and ceftriaxone, with varied resistance to other antibiotics, but all carry genes for extended-spectrum beta-lactamases (ESBLs). Notably, one strain (RSM7756) possesses outstanding chromosomal and plasmid-encoded AMR to beta-lactams, cephalosporins, fluoroquinolones and methoprims. Conclusively, clinical samples from Mulago National Referral Hospital harbor novel STs and multidrug resistant <em>K. oxytoca</em> strains, with significant public health importance, which could have been underrated.</p></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1567134824000911/pdfft?md5=892922c7f600040e36d1bb7a348c2e5d&pid=1-s2.0-S1567134824000911-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141604573","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ecological and evolutionary dynamics of CRISPR-Cas systems in Clostridium botulinum: Insights from genome mining and comparative analysis","authors":"","doi":"10.1016/j.meegid.2024.105638","DOIUrl":"10.1016/j.meegid.2024.105638","url":null,"abstract":"<div><p>Understanding the prevalence and distribution of CRISPR-Cas systems across different strains can illuminate the ecological and evolutionary dynamics of <em>Clostridium botulinum</em> populations. In this study, we conducted genome mining to characterize the CRISPR-Cas systems of <em>C. botulinum</em> strains. Our analysis involved retrieving complete genome sequences of these strains and assessing the diversity, prevalence, and evolution of their CRISPR-Cas systems. Subsequently, we performed an analysis of homology in spacer sequences from identified CRISPR arrays to investigate and characterize the range of targeted phages and plasmids. Additionally, we investigated the evolutionary trajectory of <em>C. botulinum</em> strains under selective pressures from foreign invasive DNA. Our findings revealed that 306 strains possessed complete CRISPR-Cas structures, comprising 58% of the studied <em>C. botulinum</em> strains. Secondary structure prediction of consensus repeats indicated that subtype II-C, with longer stems compared to subtypes I<img>D and I<img>B, tended to form more stable RNA secondary structures. Moreover, protospacer motif analysis demonstrated that strains with subtype I<img>B CRISPR-Cas systems exhibited 5′-CGG-3′, 5′-CC-3′, and 5′-CAT-3′ motifs in the 3′ flanking regions of protospacers. The diversity observed in CRISPR-Cas systems indicated their classification into subtypes I<img>B, I<img>D, II-C, III-B, and III-D. Furthermore, our results showed that systems with subtype I<img>D and III-D frequently harbored similar spacer patterns. Moreover, analysis of spacer sequences homology with phage and prophage genomes highlighted the specific activities exhibited by subtype I<img>B and III-B against phages and plasmids, providing valuable insights into the functional specialization within these systems.</p></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1567134824000893/pdfft?md5=85d8f5ba2afb6494ab5dc8b9ea3fe7e0&pid=1-s2.0-S1567134824000893-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141604574","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Spatio-temporal analysis of genetic diversity of merozoite surface protein-3 alpha in Myanmar Plasmodium vivax isolates","authors":"Tuấn Cường Võ ,&nbsp;Jung-Mi Kang ,&nbsp;Hương Giang Lê ,&nbsp;Haung Naw ,&nbsp;Tong-Soo Kim ,&nbsp;Ho-Joon Shin ,&nbsp;Moe Kyaw Myint ,&nbsp;Zaw Than Htun ,&nbsp;Byoung-Kuk Na","doi":"10.1016/j.meegid.2024.105639","DOIUrl":"10.1016/j.meegid.2024.105639","url":null,"abstract":"<div><p>Myanmar aims to eliminate malaria by 2030. However, recent increase of malaria incidence is a great challenge to archive that goal. Increasing prevalence of <em>Plasmodium vivax</em> also hinders this endeavor. Monitoring genetic structure of the parasite is necessary to understand genetic nature and evolutionary aspect of <em>P. vivax</em> population in Myanmar. Partial fragment flanking blocks I and II of merozoite surface protein-3 alpha of <em>P. vivax</em> (<em>pvmsp-3α</em>) was amplified from <em>P. vivax</em> isolates collected in Pyin Oo Lwin, Mandalay Region, Myanmar in 2013–2015. Sequence analysis of <em>pvmsp-3α</em> was performed to determine genetic diversity and natural selection of this gene. Spatio-temporal genetic changes of <em>pvmsp-3α</em> in Myanmar <em>P. vivax</em> population were also investigated via comparative analysis of gene sequences obtained in this study and previously reported Myanmar <em>pvmsp-3α</em> sequences. Genetic diversity of Myanmar <em>pvmsp-3α</em> was detected in <em>P. vivax</em> isolates analyzed. Size polymorphisms in block I and amino acid changes and recombination events in block II were main factors contributing to the genetic diversity of <em>pvmsp-3α</em>. Comparative spatio-temporal analysis with previously reported Myanmar <em>pvmsp-3α</em> populations revealed the presence of genetic differences by population with moderate genetic differentiation between populations. Similar pattern of natural selection was also detected in Myanmar <em>pvmsp-3α</em> populations. These suggested that enough size of the <em>P. vivax</em> population sufficient to generate or maintain the genetic diversity remains in the population. Thus, continuous molecular surveillance of genetic structure of Myanmar <em>P. vivax</em> is necessary.</p></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S156713482400090X/pdfft?md5=dee5bb5d50f434f234a099a0450eb647&pid=1-s2.0-S156713482400090X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141602203","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}