Infection Genetics and Evolution最新文献

{"title":"First report of the emergence of novel sub-genotype XIII.2.3 of Newcastle disease virus in chickens from selected regions of Bangladesh","authors":"Farah Zereen ,&nbsp;Md. Abdur Rahman ,&nbsp;Md. Golzar Hossain ,&nbsp;Jahangir Alam ,&nbsp;Masaru Shimada ,&nbsp;Md. Tanvir Rahman ,&nbsp;Sukumar Saha","doi":"10.1016/j.meegid.2025.105742","DOIUrl":"10.1016/j.meegid.2025.105742","url":null,"abstract":"<div><div>Newcastle disease (ND) is one of the most economically devastating infectious diseases impacting the poultry industry in Bangladesh. This study aimed to characterize the pathotype, genotype, evolutionary divergence, and mutations of circulating virulent Newcastle disease virus (NDV) in chickens from the Gazipur, Tangail, and Mymensingh districts of Bangladesh between October 2023 and December 2024. ND-suspected samples, including lung, trachea, and caecal tonsil tissues, were collected, processed, and inoculated into 10–12-day-old embryonated chicken eggs (ECEs) via the allantoic cavity. Allantoic fluids were harvested after 24 h of incubation, and virulent NDV was identified through RT-PCR targeting the fusion (F) gene using specific primers. Pathogenicity was assessed using the mean death time (MDT), intracerebral pathogenicity index (ICPI), and intravenous pathogenicity index (IVPI). The pathotype and genotype were confirmed by complete sequencing of the F gene and phylogenetic analysis. Further evolutionary divergence and mutations were analyzed using MEGA-11 software. RT-PCR yielded specific amplification of a 254-bp product indicative of virulent NDV. Pathogenicity indices—MDT (&lt;60 h), ICPI (&gt;1.5), and IVPI (&gt;1.70)—confirmed a velogenic strain. Complete F gene sequencing revealed an F-protein cleavage site motif of “RRQKRF,” while phylogenetic analysis classified the isolates as belonging to sub-genotype XIII.2.3 under genotype XIII. Evolutionary divergence (0.00–0.06) and mutations at neutralizing epitopes 1 and 2 (at the 74th and 170th amino acids, respectively) suggested moderate genetic diversity. This study represents the first report in Bangladesh identifying the emergence of the novel sub-genotype XIII.2.3 of genotype XIII NDV associated with chicken mortality in selected regions.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"130 ","pages":"Article 105742"},"PeriodicalIF":2.6,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143694416","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":"ListPred: A predictive ML tool for virulence potential and disinfectant tolerance in Listeria monocytogenes","authors":"Alexander Gmeiner ,&nbsp;Mirena Ivanova ,&nbsp;Rolf Sommer Kaas ,&nbsp;Yinghua Xiao ,&nbsp;Saria Otani ,&nbsp;Pimlapas Leekitcharoenphon","doi":"10.1016/j.meegid.2025.105739","DOIUrl":"10.1016/j.meegid.2025.105739","url":null,"abstract":"<div><div>Despite current surveillance and sanitation strategies, foodborne pathogens continue to threaten the food industry and public health. Whole genome sequencing (WGS) has reached an unprecedented resolution to analyse and compare pathogenic bacterial isolates. The increased resolution significantly enhances the possibility of tracing transmission routes and contamination sources of foodborne pathogens. In addition, machine learning (ML) on WGS data has shown promising applications for predicting important microbial traits such as virulence, growth potential, and resistance to antimicrobials. Many regulatory agencies have already adapted WGS and ML methods. However, the food industry hasn't followed a similarly enthusiastic implementation. Some possible reasons for this might be the lack of computational resources and limited expertise to analyse WGS and ML data and interpret the results. Here, we present ListPred, a ML tool to analyse WGS data of <em>Listeria monocytogenes,</em> a very concerning foodborne pathogen. ListPred relies on genomic markers and pre-trained ML models from two previous studies, and it is able to predict two important bacterial traits, namely virulence potential and disinfectant tolerance. ListPred only requires limited computational resources and practically no bioinformatic expertise, which is essential for a broad application in the food industry.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"130 ","pages":"Article 105739"},"PeriodicalIF":2.6,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143671865","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":"First report of blaVEB-3 and blaKPC-2 coexistence with a novel blaKPC-2 transposon in Klebsiella michiganensis","authors":"Yuxia Zhong ,&nbsp;Peibo Yuan ,&nbsp;Liting Dai ,&nbsp;Ling Yang ,&nbsp;Zhenbo Xu ,&nbsp;Dingqiang Chen","doi":"10.1016/j.meegid.2025.105740","DOIUrl":"10.1016/j.meegid.2025.105740","url":null,"abstract":"<div><h3>Background</h3><div><em>Klebsiella michiganensis</em>, an emerging opportunistic pathogen, poses public health risks due to its increasing multidrug resistance (MDR), especially to carbapenems.</div></div><div><h3>Case and method</h3><div>A 46-year-old man with pulmonary fibrosis was hospitalized in Guangzhou, China, for worsening pneumonia. A multidrug-resistant <em>K. michiganensis</em> strain (YK6) was isolated from his sputum before treatment. The strain was characterized using MALDI-TOF mass spectrometry, antimicrobial susceptibility testing (AST), and whole genome sequencing (WGS). Targeted therapy guided by AST successfully resolved the infection.</div></div><div><h3>Results</h3><div>The YK6 strain exhibited resistance to carbapenems, β-lactam/β-lactamase inhibitors, cephalosporins, aminoglycosides, and quinolones, except colistin and tigecycline. Genomic analysis revealed a 41.9-kb MDR island and an intact I-E CRISPR-Cas system on the chromosome, along with two plasmids: IncFIA/IncFII plasmid pYK6–1 carrying <em>bla</em>_KPC-2 and IncC plasmid pYK6–2 harboring <em>bla</em>_VEB-3. A novel <em>bla</em>_KPC-2-transposon in pYK6–1 was identified, consisting of a non-Tn<em>4401</em> element (NTE)-like structure (Tn<em>3</em>-IS<em>Kpn27</em>-<em>bla</em>_KPC-2-ΔIS<em>Kpn6</em>-<em>korC</em>) flanked by inversely oriented IS<em>Kpn19</em>-<em>tnpM-tnpR</em> elements and 31-bp inverted repeats never reported, a configuration did not reported previously. Furthermore, the <em>bla</em>_VEB-3 genetic environment in pYK6–2 featured a unique cassette: IS<em>26</em>-IS<em>6100</em>-<em>bla</em>_VEB-3-<em>tnp</em>-IS<em>As1</em>-<em>qacEΔ1</em>-<em>sul1</em>-IS<em>CR1</em>. An additional IS<em>As1</em> insertion between the <em>tnpF</em>-like integrase and <em>qacEΔ1</em> distinguishes it from similar <em>bla</em>_VEB-3-harboring cassettes. The <em>bla</em>_VEB-3 resistance region in pYK6–2 likely originated from homologous recombination mediated by IS<em>26</em> and <em>Tn5403</em>, which flank the gene cassette.</div></div><div><h3>Conclusions</h3><div>To our knowledge, this is the first report of concurrent <em>bla</em>_VEB-3 and <em>bla</em>_KPC-2 in <em>K. michiganensis</em>, along with a novel <em>bla</em>_KPC-2 transposon structure. These findings highlight the urgent need for enhanced surveillance of MDR <em>K. michiganensis</em> to prevent treatment failures.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"130 ","pages":"Article 105740"},"PeriodicalIF":2.6,"publicationDate":"2025-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143652072","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-based characterization of Listeria monocytogenes isolated from cattle and pig slaughterhouses","authors":"Serim Hong ,&nbsp;Jin-San Moon ,&nbsp;Young Ju Lee ,&nbsp;Ha-Young Kim","doi":"10.1016/j.meegid.2025.105737","DOIUrl":"10.1016/j.meegid.2025.105737","url":null,"abstract":"<div><div><em>Listeria monocytogenes</em> is a foodborne pathogen that causes human listeriosis and may be transmitted to humans via the food chain, beginning at slaughter and extending through food production and consumption. In this study, we performed whole-genome sequencing (WGS) analysis to determine the genetic characteristics of <em>L</em>. <em>monocytogenes</em> from the carcasses and environments of cattle and pig slaughterhouses in Korea. In total, 50 <em>L. monocytogenes</em> isolates were collected from 46 cattle and 47 pig slaughterhouses nationwide from 2014 to 2022. They were classified into two lineages, 12 sublineages, 12 sequence types, 11 clonal complexes (CCs), and 15 core-genome multilocus sequence types. <em>L. monocytogenes</em> isolates were divided into two lineages: lineage I (serotypes 1/2b and 4b) and lineage II (serotypes 1/2a and 1/2c). The most frequent CCs were CC9 (46.0 %), followed by CC224 (16.0 %) and CC155 (14.0 %). Although all isolates exhibited highly conserved LIPI-1, 20.0 % and 2.0 % contained LIPI-3 or LIPI-4, respectively. Moreover, 96.0 % of the isolates had full-length <em>inlA</em>. Interestingly, 21 of the 23 CC9 isolates contained mutations in <em>inlA</em> resulting from premature stop codon (PMSC). The <em>mdrL</em> and <em>Listeria</em> genomic island-2 (LGI-2) were identified in all <em>L</em>. <em>monocytogenes</em> isolates, whereas LGI-3 was identified in 32.0 % of the isolates. The <em>L</em>. <em>monocytogenes</em> isolates contained various antimicrobial resistance genes, moreover, the plasmid-borne resistance genes <em>tetM</em> and <em>mprF</em> were also identified in 34.0 % and 100 % of the isolates, respectively. Twenty-four isolates (48.0 %) harbored one or two plasmids (pLM33, DOp1, pLGUG1, and pLM5578), and 29 isolates (58.0 %) harbored at least one insertion sequence, composite transposon, and integrative conjugative element. Four isolates showed two CRISPR-Cas types I<img>B and II-A. In addition, phage sequences associated with the spacer constituting the CRISPR array were identified in 26 <em>Listeria</em> phages from 14 <em>L. monocytogenes</em> isolates. The genetic composition of <em>L</em>. <em>monocytogenes</em> was conserved in a collinearity relationship between each of the five <em>L</em>. <em>monocytogenes</em> isolates from the cattle and pig slaughterhouses. These findings suggest that <em>L</em>. <em>monocytogenes</em> isolated from cattle and pig slaughterhouses have the ability to cause human disease and exhibit virulent characteristics.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"130 ","pages":"Article 105737"},"PeriodicalIF":2.6,"publicationDate":"2025-03-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143606755","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":"First report of third-generation cephalosporin-resistant clinical isolate of Salmonella Bareilly ST203 harbouring plasmid-mediated AmpC β-lactamase CMY6 from India: Genome characteristics and transmissibility","authors":"Subhasree Roy ,&nbsp;Agniva Majumdar ,&nbsp;Souvik Nandy ,&nbsp;Juhi Pal ,&nbsp;Balaji Veeraraghavan ,&nbsp;Kamini Walia ,&nbsp;Shanta Dutta","doi":"10.1016/j.meegid.2025.105736","DOIUrl":"10.1016/j.meegid.2025.105736","url":null,"abstract":"<div><div>Non-typhoidal Salmonella (NTS) infections are a major public health concern in India because of inadequate knowledge of antimicrobial resistance, limiting therapeutic options. The study aimed to characterize and analyse the genome of a 3rd-generation cephalosporins (3GCs)-resistant clinical isolate of <em>Salmonella</em> Bareilly-harbouring plasmid-mediated AmpC (pAmpC) CMY-6. Identification, antibiotic susceptibility and Whole Genome Sequencing (WGS)-based analysis were performed. Transmissibility, replicon types of <em>bla</em>_CMY-6-harbouring plasmid were evaluated. <em>S.</em> Bareilly ST203 (Clonal-Complex 206.2) was isolated from clinical specimen of a paediatric patient and was found to be multidrug-resistant with resistance to 3rd generation cephalosporins, fluoroquinolone and aminoglycosides. WGS revealed pAmpC <em>bla</em>_CMY-6 on conjugative IncC plasmid (158,385 kb) which successfully transferred into the transconjugant with other resistance determinants (<em>bla</em>_TEM-1A, <em>armA, aac(6′)-Ib-cr, sul1</em>), showed higher MICs for 3GCs. Downstream regions of <em>bla</em>_CMY-6 include <em>blc</em> (lipocalin), <em>sugE</em> (efflux protein) and truncated <em>ecnR</em> (entericidin R) followed by other resistance genes. Presence of IS<em>Ecp1</em> in the genome facilitated the transfer of <em>bla</em>_CMY-6. Several efflux pump genes, two complete CRISPR arrays and intact phage sequences were also detected. Virulence factors associated with Salmonella Pathogenicity Islands SPI-1/SPI-2/SP-3 and their effectors indicated the virulence potential of this strain. To the best of our knowledge, genome of a 3GCs-resistant clinical isolate of <em>S.</em> Bareilly-harbouring pAmpC <em>bla</em>_CMY-6 was reported and analysed for the first time in this study. <em>S.</em> Bareilly was found to cause outbreaks in earlier reports but lower resistance was reported in this serovar compared to other NTS. As infections by NTS are concerning, early detection of such strains is of utmost importance.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"130 ","pages":"Article 105736"},"PeriodicalIF":2.6,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143588316","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":"Unraveling the role of IL-17A variants in pulmonary tuberculosis: Insights from a case-control study","authors":"Mahdi Majidpour ,&nbsp;Mahboobeh Sabeti Akbar-Abad ,&nbsp;Hossein Shahriari ,&nbsp;Sajad Barakzaee ,&nbsp;Khashayar Zafarmohammadi ,&nbsp;Zahra Mohammadghasemipour","doi":"10.1016/j.meegid.2025.105735","DOIUrl":"10.1016/j.meegid.2025.105735","url":null,"abstract":"<div><h3>Objectives</h3><div>The present study aimed to investigate the association between certain interleukin-17 A (<em>IL-17 A</em>) polymorphisms, specifically rs2275913 and rs8193036, and the susceptibility to pulmonary tuberculosis (PTB). Considering the function of <em>IL-17 A</em> in regulating immunological responses, especially regarding bacterial infections, we sought to determine if variations in the <em>IL-17 A</em> gene effect on PTB in the examined group.</div></div><div><h3>Methods</h3><div>We performed a case-control study with 100 individuals who were confirmed to have PTB and 100 control subjects. Genotyping for the <em>IL-17 A</em> SNPs rs2275913 and rs8193036 was performed using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and Tetra-primer Amplification Refractory Mutation System (Tetra-ARMS PCR) methodologies. A statistical analysis encompassing odds ratios (OR) and 95 % confidence intervals (CI) was conducted to assess the association between the polymorphisms and the risk of PTB.</div></div><div><h3>Results</h3><div>Our data indicated a significant connection between the rs2275913 polymorphism and elevated susceptibility to PTB (OR = 1.69, 95 % CI: 1.09–2.61; <em>p</em> = 0.031). Also, a significant association between the rs8193036 polymorphism and increased susceptibility to PTB (OR = 2.18, 95 % CI: 1.46–3.27; <em>p</em> &lt; 0.001).</div></div><div><h3>Conclusion</h3><div>The <em>IL-17 A</em> polymorphisms rs2275913 and rs8193036 strongly correlate with increased susceptibility to PTB, according to this study. This suggests a potential genetic risk factor in the progression of the disease.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"130 ","pages":"Article 105735"},"PeriodicalIF":2.6,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143588318","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":"In silico comparative analysis of genetic diversity and natural selection of Plasmodium knowlesi and Plasmodium vivax etramp11.2 gene","authors":"Ahmed Saif ,&nbsp;Pratisthita Baruah ,&nbsp;Syeda Wasfeea Wazid ,&nbsp;Ashish Panigrahi ,&nbsp;Jin-hee Han ,&nbsp;Md Atique Ahmed ,&nbsp;Fu-Shi Quan","doi":"10.1016/j.meegid.2025.105733","DOIUrl":"10.1016/j.meegid.2025.105733","url":null,"abstract":"<div><div>A comprehensive analysis of genetic diversity in field samples is essential for developing an effective strain-transcending malaria vaccine and antigens capable of producing cross-protective immunity can be crucial in combatting malaria. We explored the genetic diversity, natural selection, epitope prediction, and haplotype network analysis of <em>etramp11.2</em>, a potential antigen recently shown to exhibit cross-species reactivity in clinical samples of <em>Plasmodium knowlesi</em> and <em>Plasmodium vivax</em>. We retrieved gene sequences of <em>etramp11.2</em> from <em>P. knowlesi</em> (<em>n</em> = 42) and <em>P. vivax</em> (<em>n</em> = 112) from public databases and studied the genetic diversity, natural selection, haplotype diversity, and epitope prediction analyses. Both species exhibited low worldwide nucleotide diversity within the cross-reactive domain. Purifying selection was stronger in <em>P. knowlesi</em> compared to <em>P. vivax</em>. Regional analysis in <em>Pvetramp11.2</em> revealed higher genetic diversity in Africa, followed by North and South America, compared to low nucleotide diversity observed in Asia and Oceania. Haplotype network analysis showed shared clusters and with no geographical clustering of samples. In silico epitope prediction identified six potential epitopes in <em>P. knowlesi</em> and two in <em>P. vivax</em>, including a fully conserved epitope (AERKKRN) in both species. This study provides a preliminary snapshot of ETRAMP11.2 diversity in field samples and its potential for future studies towards a cross-protective vaccine target against both species. Further studies with higher numbers of sequences and functional antibody analyses are needed to validate these findings.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"129 ","pages":"Article 105733"},"PeriodicalIF":2.6,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143538184","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":"Phylodynamics and phylogeography of watermelon mosaic virus: Multiple local invasion routes in southern France and recombination-driven limits to global analysis","authors":"Patrick Hoscheit ,&nbsp;Cécile Desbiez","doi":"10.1016/j.meegid.2025.105732","DOIUrl":"10.1016/j.meegid.2025.105732","url":null,"abstract":"<div><div>Watermelon mosaic virus (WMV) is a major plant pathogen, infecting over 170 plant species, including cucurbits and legumes. Though mostly propagated locally by aphids in a non-persistent manner, long-range dispersal can occur through human-induced plant or vector movements. Understanding patterns of local and global spread of WMV is crucial to help formulate adequate control strategies. We used phylodynamic methods based on partial and whole-genome sequences collected in France between 2000 and 2017 to reconstruct the introduction of new lineages in the past 30 years and their subsequent diffusion in the country. We identified at least 11 different introduction events, hailing from different parts of the global diversity of WMV, highlighting the critical role international exchanges play in the spread of plant pathogens. For three of these lineages, we estimated the time and location of their introduction in the mid-1990s in the south of France and the speed at which they spread in this specific landscape. We also showed that the highly recombinogenic nature of WMV, as with most potyviruses, makes the use of whole genomes necessary to classify these viruses on a global scale and must be taken into consideration to reconstruct viral evolutionary history. Our results demonstrate how genomic sequencing of plant viruses can help reconstruct specific viral outbreaks and understand global circulation patterns of plant pathogens.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"129 ","pages":"Article 105732"},"PeriodicalIF":2.6,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143531088","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":"Reassessing the dengue virus type 4 in Brazil: Genomic sequencing and dispersion dynamics, 2011–2017","authors":"Priscila Fonseca Ferreira ,&nbsp;Luiz Fernando Almeida Machado ,&nbsp;Jedson F. Cardoso ,&nbsp;Luciano C. Franco Filho ,&nbsp;Alex Ranieri Jerônimo Lima ,&nbsp;Marcelo Adriano Mendes dos Santos ,&nbsp;James Siqueira Pereira ,&nbsp;Márcio R.T. Nunes","doi":"10.1016/j.meegid.2025.105731","DOIUrl":"10.1016/j.meegid.2025.105731","url":null,"abstract":"<div><div><em>Orthoflavivirus denguei</em> (Dengue virus) type 4; (DENV-4) has emerged as a significant public health concern in Brazil, particularly following its reintroduction in the early 21st century. This study provides a comprehensive analysis of DENV-4's genetic characterization and its spatiotemporal dynamics reassessment within Brazil, with a focus on the period between 2010 and 2017. We performed direct genomic sequencing on 24 human samples obtained from various Brazilian states using a multiplex sequencing approach on the Ion Torrent platform. Phylogenetic analysis revealed that the new isolates belong exclusively to the genotype 4II, lineage 4II_B.1.1, with no detection of genotype 4I, which was previously identified in Brazil. This absence of genotype 4I in our findings suggests a potential decline, not adaptation to mosquito host, sub endemic circulation or displacement of this genotype in the country. The phylogeographic analysis indicates multiple introduction events of genotype 4II into Brazil, with significant dispersion across different regions, including the North, Northeast, Midwest, and Southeast. The temporal analysis confirmed a robust evolutionary signal, supporting the observed phylogenetic clustering. Eighteen of the 24 genomes in this study had unique nonsynonymous mutations across the entire coding sequences and seven genomes showed mutations that altered the biochemical property of the amino acids at E, NS1, NS2B, NS3,and NS5 genes compared with genotype 4I. Our findings underscore the ongoing spread of DENV-4 within Brazil, and in the Americas driven by complex networks of viral dispersion, and highlight the dynamic nature of DENV-4 genotype distribution. This study emphasizes the importance of advanced direct genomic sequencing tools in understanding the DENV-4 dynamics and spreading, providing critical insights for public health strategies on genomic surveillance to control further dengue outbreaks.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"129 ","pages":"Article 105731"},"PeriodicalIF":2.6,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143519519","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":"Unraveling the genome of Proteus mirabilis strain representing the O78 serogroup: Insights into the unique features of the O-antigen biosynthesis gene cluster","authors":"Katarzyna Zegadło ,&nbsp;Dominika Drzewiecka ,&nbsp;Grzegorz Czerwonka","doi":"10.1016/j.meegid.2025.105730","DOIUrl":"10.1016/j.meegid.2025.105730","url":null,"abstract":"<div><div>Lipopolysaccharide (LPS), the outermost component of Gram-negative bacterial cells, is critical to bacterial pathogenicity, functioning as an endotoxin that activates the human immune system and induces an inflammatory response during infection. LPS comprises three primary components: lipid A, the oligosaccharide core, and the O-antigen. The O-antigen, in particular, is highly variable and strain-specific, playing a pivotal role in how the host immune system recognizes bacterial cells. This study focuses on the <em>Proteus mirabilis</em> 1B-m strain, belonging to serogroup O78, the most prevalent serogroup in hospitals in Lodz, Poland. Given the increasing hospitalization rates, particularly among the elderly and catheterized patients, understanding the common strains and their virulence factors is crucial. This work presents bioinformatics analyses based on next-generation sequencing data (both short and long reads), aimed at elucidating the structure of the gene cluster responsible for O-antigen biosynthesis in the 1B-m strain. Our results suggest the presence of a unique <em>wzx</em> flippase in the strain, alongside the characterization of role of the <em>licD</em> gene, which was most often assigned a role in the phosphocholine decoration process of LPS. The function of <em>licD</em> in this strain appears to be linked to the <em>ispD</em> gene, potentially involved in the biosynthesis of CDP-ribitol. Additionally, we explored other genomic features, including the strain's genetic similarity to closely related microorganisms, the presence of antimicrobial resistance genes, and prophage elements. This study provides valuable insights into the genetic factors underlying the pathogenicity of the <em>P. mirabilis</em> 1B-m strain and its potential implications for hospital-acquired infections.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"129 ","pages":"Article 105730"},"PeriodicalIF":2.6,"publicationDate":"2025-02-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143506152","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}