Infection Genetics and Evolution最新文献

{"title":"Surveillance and agnostic capture sequencing of samples from individuals with rash-associated illness in Mali indicates regional transmission of measles virus from West and Central Africa","authors":"Fousseyni Kané ,&nbsp;John Collins ,&nbsp;Amadou Koné ,&nbsp;Noumou Y. Keita ,&nbsp;Issa Cisse ,&nbsp;Klèma M. Koné ,&nbsp;Dramane Diallo ,&nbsp;Issa Konate ,&nbsp;Djeneba K. Dabitao ,&nbsp;Bassirou Diarra ,&nbsp;Ibrahim Sanogo ,&nbsp;Tenin A. Coulibaly ,&nbsp;Mountaga Diallo ,&nbsp;Daouda Keita ,&nbsp;Cheick O. Tangara ,&nbsp;Mahamadou Diakité ,&nbsp;Sounkalo Dao ,&nbsp;Karine Fouth-Tchos ,&nbsp;Jamila Aboulhab ,&nbsp;Aaron Neal ,&nbsp;Seydou Doumbia","doi":"10.1016/j.meegid.2024.105691","DOIUrl":"10.1016/j.meegid.2024.105691","url":null,"abstract":"<div><div>Measles is vaccine-preventable extremely contagious disease caused by the measles virus. High vaccination coverage is needed to prevent outbreaks of disease. Although molecular surveillance of measles is critical to characterize outbreaks and track viral evolution, few whole-genome sequences of measles virus from West Africa are available despite continual outbreaks in the region. Using VirCapSeq-VERT, an enhanced and comprehensive metagenomic sequencing technique that allows for simultaneous identification of all vertebrate viruses, 23 wild-type near-complete genomes of measles virus from across Mali were obtained from samples collected between January 2012 to October 2022. Other febrile rash illnesses were also identified by VirCapSeq-VERT, demonstrating the advantage of using broad detection agnostic methods when the clinical diagnosis is unclear. Whereas one measles virus sequence was consistent with measles vaccine-associated rash illness (VARI), the remaining 38 were classified within the B3.1 genotype. Broad surveillance throughout Mali reveals regional measles virus transmission across West and Central Africa into Mali, while local clinical testing in Bamako shows stable sequence conservation within genotype B3.1 evolving from Nigerian sequences. The genomic information generated in this study is critical in addressing the lack of whole genome sequences available in West Africa and these findings show the importance of phylogenetically tracking measles outbreaks given recent increases in measles cases globally.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"126 ","pages":"Article 105691"},"PeriodicalIF":2.6,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142688531","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 reveals circulation of potentially virulent Listeria innocua strains with novel genomic features in cattle farm environments in Dhaka, Bangladesh","authors":"Supantha Rivu ,&nbsp;Abiral Hasib Shourav ,&nbsp;Sangita Ahmed","doi":"10.1016/j.meegid.2024.105692","DOIUrl":"10.1016/j.meegid.2024.105692","url":null,"abstract":"<div><div>Through the last decade, <em>Listeria</em> spp. has been detected in food and environmental samples in Bangladesh. However, the genomic information of this bacterium that prevails in the country remains scarce. This study analyzed the complete genome sequences of two <em>Listeria</em> spp. isolates obtained from cow dung and their drinking water collected from a cattle farm in Dhaka, Bangladesh. Both the isolates were identified as <em>Listeria innocua</em>, which shared almost identical genomic features. The genome sequences demonstrated the presence of 13 virulence genes associated with invasion (<em>iap/cwh</em>A, <em>gtc</em>A, and <em>lpe</em>A), surface protein anchoring (<em>lsp</em>A), adherence (<em>fbp</em>A, and <em>lap</em>), intracellular survival (<em>lpl</em>A1, and <em>prs</em>A2), peptidoglycan modification (<em>oat</em>A, and <em>pdg</em>A), and heat stress (<em>clp</em>C, <em>clp</em>E, and <em>clp</em>P). Additionally, the gene <em>fos</em>X, conferring resistance to fosfomycin, and two copper resistance-associated genes, <em>copC</em> and <em>csoR</em>, were identified in both. The genome sequences also revealed two plasmid replicons, <em>rep</em>25 and <em>rep</em>32, along with three insertion sequences [ISLmo3 (CP022021), ISLmo7 (CP006611), ISS1N (M37395)]. Notably, a composite transposon [CN_8789_ISS1N (M37395)], was detected in both <em>L. innocua</em> isolates, representing the first documented occurrence of this particular composite transposon in any reported <em>Listeria</em> species. Furthermore, the genomes contained four prophage regions [Listeria phage LP-030-2 (NC_021539), Listeria phage vB_LmoS_188 (NC_028871), Listeria phage A118 (NC_003216) and Escherichia phage RCS47 (NC_042128)]. Two CRISPR arrays were also identified, one belonging to the family type II-A. Multilocus Sequence Typing (MLST) analysis classified the L. <em>innocua</em> isolates of the same sequence type, ST-637. Single nucleotide polymorphism (SNP) analysis uncovered the presence of 231–340 SNPs between the L. <em>innocua</em> isolates and their closely related global lineage. In contrast, only 42 SNPs were identified between the two isolates, suggesting a potential transmission of L. <em>innocua</em> between cow dung and cattle farm water. The presence of L. <em>innocua</em> isolates harboring virulence genes associated with ruminant infection in the cattle farm environment of Bangladesh raises significant concerns about the potential presence of other human and animal pathogens. This poses a serious threat to the cattle farming industry. Additionally, the genomic analysis of the L. <em>innocua</em> isolates enhances our understanding of the evolutionary dynamics of <em>Listeria</em> species.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"126 ","pages":"Article 105692"},"PeriodicalIF":2.6,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142688756","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":"Genetic association of missense (rs2919643), intergenic (rs2057178) and a 3’UTR (rs1009170) variant with tuberculosis: A replication study from India","authors":"Anuradha Gautam,&nbsp;Ahana Dasgupta ,&nbsp;Suvamita Rout ,&nbsp;Samsiddhi Bhattacharjee,&nbsp;Bhaswati Pandit","doi":"10.1016/j.meegid.2024.105690","DOIUrl":"10.1016/j.meegid.2024.105690","url":null,"abstract":"<div><div>To investigate host genetic susceptibility to tuberculosis (TB), we conducted a replication study focussed on candidate SNPs, previously reported to be associated with TB. We examined nine candidate SNPs and genotyped them in an independent cohort of TB cases and household contacts from West Bengal, India. The association with TB was replicated for rs2919643 (Chr 18), rs2057178 (Chr 11) and rs1009170 (Chr 14). rs2919643-C (<em>p</em>=8.81E-5) was a risk allele and rs2057178-A (<em>p</em>=0.04188) was protective against TB in our population. Association of rs1009170; previously reported by us with TB was also replicated in the new set of samples (<em>p</em>=0.0359). rs2919643 is a missense variant present in linkage disequilibrium with a TB associated synonymous SNP rs61104666. The risk genotype rs2919643-CC was associated with higher levels of plasma RANTES and IL5 in household contacts. rs2919643 is an eQTL for an immunosuppressive gene <em>SIGLEC15</em> and autophagy related gene <em>EPG5.</em> rs2057178 is an eQTL for a pseudogene and present within weak enhancer marks in the lungs. The genomic locus around this SNP rs1009170 encompasses an active transcription factor peak in CD14⁺ monocytes and also serves as an eQTL for <em>NDUFB1, ATXN3</em> and <em>SLC24A4.</em> TB cases with rs1009170-TT genotype showed lower expression of plasma RANTES compared to the heterozygote<em>.</em> All three associated SNPs have putative regulatory role in lungs and immune associated cells and organs which may be relevant to TB pathogenesis.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"126 ","pages":"Article 105690"},"PeriodicalIF":2.6,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142640313","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 molecular detection of adenoviruses in bats from an urban Atlantic Forest in Rio de Janeiro, Brazil","authors":"Beatriz V. Dias ,&nbsp;Natália M. Lanzarini ,&nbsp;Márcia T.B. de Moraes ,&nbsp;Johan Nordgren ,&nbsp;Patrícia E.B. Moura ,&nbsp;Ricardo Moratelli ,&nbsp;Roberto L.M. Novaes ,&nbsp;Sócrates F. Costa-Neto ,&nbsp;Iuri Veríssimo ,&nbsp;Marize P. Miagostovich ,&nbsp;Maria Ogrzewalska ,&nbsp;Marina G. Bueno","doi":"10.1016/j.meegid.2024.105687","DOIUrl":"10.1016/j.meegid.2024.105687","url":null,"abstract":"<div><div>Bats comprise one of the most diverse and abundant groups of mammals in the world and host a significant viral diversity with zoonotic potential. Bat adenoviruses (bat AdVs), members of the family <em>Adenoviridae</em>, have been detected in several bat species, suggesting that bats are natural reservoirs. Here, faeces and rectal/anal-swabs were collected from 321 bats of an urban Atlantic Forest remnant from Rio de Janeiro, during 2019–2022, and screened for bat AdV nucleic acid with PCR. The positivity of bat AdVs was 3.7 % (12/321). Twelve individuals of four bat species were infected: <em>Artibeus lituratus</em> (66.7 %; 8/12), <em>Desmodus rotundus</em> (8.3 %; 1/12), <em>Platyrrhinus lineatus</em> (16.7 %; 2/12), and <em>Sturnira lilium</em> (8.3 %; 1/12). Phylogenetic analysis based on nucleotide and amino acid sequences showed that the detected bat AdVs clustered into four clades corresponding to the host species, identifying the presence of two potentially new bat adenoviruses. This is the first report of bat AdV detected in <em>Platyrrhinus lineatus</em>.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"126 ","pages":"Article 105687"},"PeriodicalIF":2.6,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142633199","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":"Spatiotemporal dynamics of rabies virus detected in rabid dogs in Cameroon, 2010–2021","authors":"Jocelyne Noel Sowe Wobessi ,&nbsp;Jean-Luc Bailly ,&nbsp;Jean-Marc Kameni Feussom ,&nbsp;Richard Njouom ,&nbsp;Serge Alain Sadeuh-Mba","doi":"10.1016/j.meegid.2024.105688","DOIUrl":"10.1016/j.meegid.2024.105688","url":null,"abstract":"<div><div>Rabies is a viral zoonosis that causes an estimated 60,000 human deaths each year, mainly in Africa and Asia. The etiological agent of rabies, the <em>Rabies Lyssavirus</em> or Rabies Virus (RABV) has been characterized in dog populations in Cameroon, in previous studies. However, the dynamics of RABV maintenance and propagation in dogs are still to be documented in Cameroon. This study thus, aimed at investigating the spatial and temporal dynamics of RABV variants in Cameroon. Long genomic sequences of about 4893 nucleotides, encompassing the N, P, M and G genes as well as part of the G-L intergenic region (Ψ), were determined from 56 RABV strains recovered from dog populations in Cameroon from 2010 to 2021. Temporal and spatial dynamics of RABV circulation in Cameroon were investigated by Bayesian analyses with the BEAST 1.10.4 package from extended RABV genomic sequences data combined with their collection dates and the geographical coordinates of their sampling areas. This revealed a genetic evolution rate of 3.14 × 10⁻⁴ substitutions/site/year among Africa-1a and Africa-2 clades of RABV from Cameroon. The most recent common ancestor (MRCA) of the studied strains of the Africa-1a lineage was estimated to have emerged between 1880 and 1906 (95 % HPD; mean 1894), while that of the strains of the Africa-2 clade had a slightly later estimated origin between 1907 and 1928 (95 % HPD, mean 1918). Overall, phylogeographic analyses suggested RABV spread in Cameroon between sub-national regions. Our data provides substantial support to previous findings from similar epidemiological settings, indicating human mediated movements of infected dogs between distant cities may be a key factor in the maintenance of the enzootic cycle of rabies among dogs in Cameroon.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"126 ","pages":"Article 105688"},"PeriodicalIF":2.6,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142633167","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":"Emergence of non-classical genotype constellations of G9P[8] rotavirus strains in diarrheic children in Sabah, Malaysia","authors":"Siat Yee Fong ,&nbsp;Yuki Akari ,&nbsp;Lia Natasha Amit ,&nbsp;Jecelyn Leaslie John ,&nbsp;Abraham Zefong Chin ,&nbsp;Satoshi Komoto ,&nbsp;Kamruddin Ahmed","doi":"10.1016/j.meegid.2024.105685","DOIUrl":"10.1016/j.meegid.2024.105685","url":null,"abstract":"<div><div>G9P[8] has been the predominant rotavirus A (RVA) genotype in Malaysia since the 2000s. However, the overall genetic makeup and evolution of Malaysian G9P[8] strains are still unknown. Therefore, this study aimed to evaluate and characterize the complete genomes of three G9P[8] RVA strains isolated from diarrheic children under five years old in Sabah. Contrary to the classical Wa-like constellation, these strains contained a DS-1-like genotype. Two strains, namely L202 and L234, were genotype G9-P[8]-I1-R1-C1-M1-A1-N1-T1-E2-H1, while one (KN102) was genotype G9-P[8]-I1-R1-C1-M1-A2-N1-T1-E1-H1. Phylogenetic analysis revealed that the NSP4 genes of L202 and L234 strains were closer to that of G9P[8]-E2 strains from Japan, suggesting they might share a common ancestor. The findings from this study provide new insights into the genetic characteristics of circulating G9P[8] strains in Sabah, which are important for rotavirus surveillance and potential vaccine development in the region.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"125 ","pages":"Article 105685"},"PeriodicalIF":2.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142513264","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":"Spatial and temporal diversity of Simulium damnosum s.l. gut microbiota and association with Onchocerca volvulus infection in Cameroon","authors":"Arnauld Efon-Ekangouo ,&nbsp;Hugues C. Nana-Djeunga ,&nbsp;Philippe B. Nwane ,&nbsp;Narcisse Nzune-Toche ,&nbsp;Jeanne C. Sondi-Dissake ,&nbsp;Guilhem Sempere ,&nbsp;André Domche ,&nbsp;Flobert Njiokou ,&nbsp;Joseph Kamgno ,&nbsp;Paul Moundipa-Fewou ,&nbsp;Anne Geiger","doi":"10.1016/j.meegid.2024.105683","DOIUrl":"10.1016/j.meegid.2024.105683","url":null,"abstract":"<div><div>Arthropod microbiota plays an important role in host physiology, and there is growing interest in using vector symbionts to modify vector competence and control parasite transmission. This study aims to characterise the blackfly <em>Simulium damnosum</em> s.l. gut microbiota and to explore possible associations with various bio-ecological determinants of the <em>Onchocerca volvulus</em> establishment and the transmission in blackfly. Adult female blackflies were caught in three Cameroonian health districts belonging to different bioecological zones endemic for onchocerciasis. Flies were dissected and qPCR screened for <em>Onchocerca volvulus</em> infection. The diversity of the blackflies gut microbiota was assessed by high-throughput sequencing of the V3-V4 hypervariable region of the bacterial 16S ribosomal RNA. Subsequent metataxo-genomic, multivariate, and association analysis were used to investigate the variables that influence the microbiota diversity.</div><div>Transmission index rates ranging from 20.7 to 6.0 % and 6.2to 2.0 % for infection and infectivity rates, respectively, indicate ongoing transmission of onchocerciasis across all surveyed health districts. The identified bacterial taxa were clustered into four phyla, five classes, and 23 genera. The <em>S. damnosum</em> s.l. gut microbiota was dominated by <em>Wolbachia</em> and by <em>Rosenbergiella</em> in <em>Wolbachia</em>-free <em>Simulium</em>. Significant differences were observed in the diversity of <em>S. damnosum</em> s.l<em>.</em> microbiota concerning parity status (<em>P</em> = 0.007), health district of origin (<em>P</em> = 0.001), and the presence of the <em>Onchocerca volvulus</em>. <em>Simulium</em> from the Bafia health district also showed increased bacterial diversity between two consecutive years (P = 0.001). Four bacterial taxa, including <em>Serratia</em>, were associated with the absence of the <em>O. volvulus</em> infection.</div><div>These results indicate that <em>S. damnosum</em> s.l<em>.</em> from different onchocerciasis foci in Cameroon, exhibit distinguishable gut microbial compositions which are dynamic over time. Some bacterial species are associated with the <em>O. volvulus</em> infection and could be further investigated as biological target/tool for vector modified-based onchocerciasis control.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"125 ","pages":"Article 105683"},"PeriodicalIF":2.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142513265","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":"Genetic diversity and molecular evolution of the internal transcribed spacer regions (ITS1–5.8S–ITS2) of Babesia vogeli","authors":"Ansu Kumari ,&nbsp;Divya Agnihotri ,&nbsp;Anil Kumar Nehra ,&nbsp;Aman Dev Moudgil ,&nbsp;Yudhbir Singh ,&nbsp;Devendra Prasad Pateer ,&nbsp;Rajat Garg","doi":"10.1016/j.meegid.2024.105686","DOIUrl":"10.1016/j.meegid.2024.105686","url":null,"abstract":"&lt;div&gt;&lt;div&gt;Canine babesiosis, a severe haemoparasitic disease caused by &lt;em&gt;Babesia&lt;/em&gt; species, has a significant global presence and can be fatal if left untreated. The current study was aimed to perform the population genetic characterization of &lt;em&gt;B. vogeli&lt;/em&gt; on the basis of the internal transcribed spacer regions (ITS1–5.8S–ITS2). A maximum likelihood tree constructed with the Hasegawa-Kishino-Yano model grouped all sequences into a single major clade (BvG1), with the exception of a Taiwanese isolate (EF186914), which branched separately. This Taiwanese isolate represented a novel genotype (BvG2) identified in the present study. Nucleotide sequences (&lt;em&gt;n&lt;/em&gt; = 62) exhibited 92.5–100 % nucleotide identity among themselves. However, the BvG1 and BvG2 genotypes shared a lower identity of 92.5–93.8 % between them. Notably, the newly generated Indian sequences (&lt;em&gt;n&lt;/em&gt; = 21) demonstrated a high degree of homology, with 98.3–100 % identity. Alignment of the nucleotide sequences revealed 58 variations across the dataset. Additionally, 32 sites exhibited variation within the BvG1 genotype, while 56 sites differed between BvG1 and BvG2 genotypes. Within different &lt;em&gt;B. vogeli&lt;/em&gt; populations, the nucleotide diversity (π) was low, but the haplotype diversity (Hd) was high. The haplotype diversity of the Indian population, BvG1 genotype, and the combined dataset was ∼0.8 suggesting a high haplotype diversity. The median-joining haplotype network displayed a total of 21 haplotypes, out of which six haplotypes consisted of more than one sequence (2–25 sequences). Haplotype distribution showed significant geographical structuring, with most haplotypes confined to a single country. Only two haplotypes (9.52 %; Hap_1 and Hap_4) were shared between countries, whereas 19 haplotypes (90.48 %) were country-specific. Hap_1, Hap_6, and Hap_4 were the most representative haplotypes, comprising 25, 10, and four sequences, respectively. India exhibited the highest number of haplotypes (h = 13) followed by China (h = 4), the United States of America (h = 3), Taiwan and Tunisia (h = 2), and Thailand (h = 1). Both location-wise and genotype-wise median joining haplotype networks clustered the haplotypes in two groups, representing two distinct genotypes (BvG1 and BvG2). The &lt;em&gt;B. vogeli&lt;/em&gt; populations between Thailand and Tunisia exhibited the highest genetic differentiation (F&lt;sub&gt;ST&lt;/sub&gt; = 0.80) with a low gene flow (Nm = 0.125) between them. Results of AMOVA revealed a higher genetic variation within populations (69.43 %) as compared to the variation between them (30.57 %). Neutrality indices and the mismatch distributions of the Indian population and the overall dataset of &lt;em&gt;B. vogeli&lt;/em&gt; indicated a constant population size to population expansion and population expansion, respectively, with the presence of two distinct genotypes. These data provide information about parasite population genetics and highlight the importance of starting a long-te","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"125 ","pages":"Article 105686"},"PeriodicalIF":2.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142570490","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":"Corrigendum to: Novel members of the order Picornavirales identified in freshwater from Guarapiranga reservoir in São Paulo (infection, Genetics and Evolution Volume 124, October 2024, 105668)","authors":"Endrya do Socorro Foro Ramos ,&nbsp;Mikaela Renata Funada Barbosa ,&nbsp;Fabiola Villanova ,&nbsp;Renan Lourenço Oliveira Silva ,&nbsp;Suzi Cristina Garcia ,&nbsp;Maria Cassiá Mendes-Correa ,&nbsp;Ramendra Pati Pandey ,&nbsp;Adriana Luchs ,&nbsp;Maria Inês Zanoli Sato ,&nbsp;Antonio Charlys da Costa ,&nbsp;Elcio Leal","doi":"10.1016/j.meegid.2024.105678","DOIUrl":"10.1016/j.meegid.2024.105678","url":null,"abstract":"","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"125 ","pages":"Article 105678"},"PeriodicalIF":2.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142481321","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":"Dynamic pharyngeal carriage of Neisseria species in healthy population","authors":"Xiaoying Shan ,&nbsp;Shuang Chen ,&nbsp;Aiying Bai ,&nbsp;Yuwen Shi ,&nbsp;Xuanli Song ,&nbsp;Xiaoyu Yin ,&nbsp;Chunhong Duan ,&nbsp;Jinglei Tang ,&nbsp;Xian Xia ,&nbsp;Lanzheng Liu ,&nbsp;Bingqing Zhu","doi":"10.1016/j.meegid.2024.105684","DOIUrl":"10.1016/j.meegid.2024.105684","url":null,"abstract":"<div><div>Considering the significant role of commensal <em>Neisseria</em> carried in the pharynx on the variation of <em>N.meningitidis</em> and the acquisition of its resistance genes, understanding the true <em>Neisseria</em> population colonizing the human pharynx is of great significance. In this study, we carried out a five-month continuous survey of oropharyngeal carriage in a certain healthy population to reveal the long-term carriage status of different <em>Neisseria</em> species. Totally, 419 <em>Neisseria</em> strains were isolated from 203 out of 205 pharyngeal swabs of 49 participants. Using combined methods (MALDI-TOF-MS, <em>rplF</em> sequencing and genome sequencing), the isolates were identified as <em>N.subflava</em> (<em>n</em> = 290), <em>N.mucosa</em> (<em>n</em> = 52), <em>N.oralis</em> (<em>n</em> = 8), <em>N.elongata</em> group (<em>n</em> = 6) and non-species-confirmed (<em>n</em> = 63). <em>N.subflava</em> was isolated from all individuals and 168 swabs (81.95 %). <em>N.mucosa</em>, <em>N.oralis, N.elongata</em> and non-species-confirmed were isolated from 25 (45), 6 (7), 4 (5) and 20 (53) individuals (swabs) respectively. It was common that multiple <em>Neisseria</em> spp. or multiple clones of one species were isolated from a single sample. An identical strain could be isolated frequently from a single person within five months. These results indicate that <em>Neisseria</em> spp. and <em>N.subflava</em> are ubiquitous in human pharynx and both have diverse population; we should pay more attention to them when studying <em>N.meningitidis</em> or other respiratory pathogens; robust and handy method for identifying <em>Neisseria</em> species remains to be developed.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"125 ","pages":"Article 105684"},"PeriodicalIF":2.6,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142513263","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}