Infection Genetics and Evolution最新文献

{"title":"Characteristics and comparative genome analysis of Yersinia enterocolitica and related species associated with human infections in Switzerland 2019–2023","authors":"Marc J.A. Stevens ,&nbsp;Jule Anna Horlbog ,&nbsp;Andrea Diethelm ,&nbsp;Roger Stephan ,&nbsp;Magdalena Nüesch-Inderbinen","doi":"10.1016/j.meegid.2024.105652","DOIUrl":"10.1016/j.meegid.2024.105652","url":null,"abstract":"<div><h3>Purpose</h3><p>We aimed to characterise <em>Yersinia enterocolitica</em> from human clinical specimens in Switzerland using epidemiological, microbiological and whole-genome sequencing (WGS) data.</p></div><div><h3>Methods</h3><p>Isolates (<em>n</em> = 149) were collected between January 2019 and December 2023. Epidemiological data was noted and strains were characterized by biochemical and serological typing, antimicrobial susceptibility testing (AST), and WGS-based analysis.</p></div><div><h3>Results</h3><p>Most of the isolates (86%) were from stool specimens and 52% were from male patients. The patients' median age was 28 years (range &lt; 1–94 years). Typing assigned the isolates to bioserotype 4/O:3 (44%), biotype 1A (34%), bioserotype 2/O:9 (21%), and bioserotype 3/O:3 (1%). WGS identified <em>Y. enterocolitica</em> (<em>n</em> = 147), <em>Y. alsatica</em> (n = 1) and <em>Y. proxima</em> (n = 1). Seven isolates were multidrug resistant (MDR) and harboured plasmid pAB829 carrying <em>aph(3″)-Ib, aph(6)-Id,</em> and <em>tet</em>(Y) (<em>n</em> = 1), pAC120 carrying <em>aph(6)-Id</em> and <em>tet</em>(A) (<em>n</em> = 2), or a 12.6 kb Tn<em>2670</em>-like transposon containing <em>catA1</em>, <em>aadA12, sul1,</em> and <em>qacE</em>Δ1 (<em>n</em> = 4). Virulence factors (VFs) included <em>ail</em> (<em>n</em> = 99), <em>invB</em>, (<em>n</em> = 145), <em>ystA</em> (n = 99), <em>ystB</em> (<em>n</em> = 48) and pYV-associated VFs (<em>n</em> = 93). MLST and cgMLST analysis showed that BT 1A strains consisted of several STs and were highly diverse, whereas BT 2/O:9 strains were all ST12 and clustered closely, and BT 4/O:3 strains mostly belonged to ST18 but were more diverse. SNP analysis revealed two highly clonal BT 4/O:3 subpopulations with wide spatio-temporal distribution.</p></div><div><h3>Conclusions</h3><p><em>Y. enterocolitica</em> BT 1A, BT 2/O:9 and BT 4/O:3 are frequently associated with human yersiniosis in Switzerland. WGS-based subtyping of <em>Y. enterocolitica</em> is a powerful tool to explore the genetic diversity and the pathogenic potential of human isolates.</p></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"123 ","pages":"Article 105652"},"PeriodicalIF":2.6,"publicationDate":"2024-08-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1567134824001035/pdfft?md5=c63b00a2a4f2385706bde74f612d48a0&pid=1-s2.0-S1567134824001035-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141894912","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":"Sequence and phylogenetic analysis of FMD virus isolated from two outbreaks in Egypt","authors":"Emad Al-Ebshahy ,&nbsp;Ramy E. El-Ansary ,&nbsp;Jie Zhang ,&nbsp;Yassien Badr ,&nbsp;Alaa Rady ,&nbsp;Saeed El-Ashram ,&nbsp;Yabin Ma ,&nbsp;Ming Yuan ,&nbsp;Emad Elgendy","doi":"10.1016/j.meegid.2024.105651","DOIUrl":"10.1016/j.meegid.2024.105651","url":null,"abstract":"<div><p>Despite intensive control efforts, Foot and mouth disease (FMD) outbreaks continue to occur regularly in Egypt and resulting in dramatic economic losses to the livestock industry. During 2018 and 2022, FMD was clinically suspected among previously vaccinated cattle in Beheira and Kafr El-Sheikh provinces, Egypt. FMDV RNA was detected in 18 (45%) out of 40 epithelial tissue samples using real-time RT-PCR based on a pan-FMDV primers set. The 2018 outbreak isolates (<em>n</em> = 8) included the FMDV serotypes A and SAT2, whereas all isolates (<em>n</em> = 10) from the 2022 outbreak belonged to the FMDV serotype A. Four selected isolates, designated FMDV/SAT2/EGY/Beheira/2018, FMDV/A/EGY/Kafr El-Sheikh/2018, FMDV/A/EGY/Kafr El-Sheikh/2022 and FMDV/A/EGY/Behiera/2022, were characterized on the basis of partial VP1 gene sequence analysis. The FMDV/SAT2/EGY/Beheira/2018 strain was clustered within the Lib-12 lineage of the topotype VII and shared 79.2–98.4% nucleotide identity with other Egyptian SAT2 strains available in Genbank database. On the other hand, the three FMDV serotype A sequences shared 74.4–99.1% nucleotide identity with each other. Also, they were phylogenetically classified within two distinct topotypes. The FMDV/A/Egy/Kafr El-Sheikh/2018 strain was grouped within the Asian topotype, meanwhile the FMDV/A/EGY/Kafr El-Sheikh/2022 and FMDV/A/EGY/Behiera/2022 strains were grouped together within the genotype IV of the African topotype. Interestingly, the deduced amino acid sequences of the four strains displayed numerous variations in comparison to the vaccine strains currently used in Egypt. In addition, most of these variations were present in prominent antigenic positions in the VP1 protein. These findings raise a crucial need to validate the protective potential of the vaccine strains against the newly emerging FMDV field strains and to update the vaccination strategy accordingly.</p></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"123 ","pages":"Article 105651"},"PeriodicalIF":2.6,"publicationDate":"2024-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1567134824001023/pdfft?md5=bcfffbf2f34adcf18738b2a6190d086e&pid=1-s2.0-S1567134824001023-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141876696","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":"Gene expression analysis of Anopheles Meigen, 1818 (Diptera: Culicidae) innate immunity after Plasmodium Marchiafava & Celli, 1885 (Apicomplexa) infection: Toward developing new malaria control strategies","authors":"Zahra Sadat Mousavi Shafi ,&nbsp;Zeinab Mohammadi Firouz ,&nbsp;Sakineh Pirahmadi","doi":"10.1016/j.meegid.2024.105650","DOIUrl":"10.1016/j.meegid.2024.105650","url":null,"abstract":"<div><p>Despite the critical role of the <em>Anopheles</em> innate immune system in defending against <em>Plasmodium</em> infection, there is still limited information about the key immune mechanisms in <em>Anopheles</em>. This review assesses recent findings on the expression characteristics of immune-related genes in <em>Anopheles</em> following exposure to <em>Plasmodium</em>. A literature review, unrestricted by publication date, was conducted to evaluate immune-related gene expression in different organs of <em>Anopheles</em> after <em>Plasmodium</em> infection. Mosquito immune responses in the midgut are essential for reducing parasite populations. Additionally, innate immune responses in the salivary glands and hemocytes circulating in the hemocoel play key roles in defense against the parasite. Transcriptomic analysis of the mosquito's innate immune response to <em>Plasmodium</em> infection provides valuable insights into key immune mechanisms in mosquito defense. A deeper understanding of immune mechanisms in different organs of <em>Anopheles</em> following <em>Plasmodium</em> infection will aid in discovering critical targets for designing novel control strategies.</p></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"123 ","pages":"Article 105650"},"PeriodicalIF":2.6,"publicationDate":"2024-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1567134824001011/pdfft?md5=601cc29ff3da10d7e73401a439790719&pid=1-s2.0-S1567134824001011-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141876695","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":"Resolution of cryptic mosquito species through wing morphometrics","authors":"Huiqing Yeo ,&nbsp;Jiawei Lin ,&nbsp;Tze Xuan Yeoh,&nbsp;Nalini Puniamoorthy","doi":"10.1016/j.meegid.2024.105647","DOIUrl":"10.1016/j.meegid.2024.105647","url":null,"abstract":"<div><p>Mosquitoes are medically important insects, and accurate species identification is crucial to understanding vector biology, forming the cornerstone of successful vector control programs. Identification is difficult owing to morphologically similar species. Wing morphometrics can provide a simple, fast, and accurate way to classify species, and using it as a method to differentiate vector species among its cryptic congeners has been underexplored. Using a total of 227 mosquitoes and 20 landmarks per specimen, we demonstrated the utility of wing morphometrics in differentiating species two groups occurring in sympatry – <em>Culex</em> (<em>Culex</em>) <em>vishnui</em> group and <em>Culex</em> (<em>Lophoceraomyia</em>) subgenus, as well as explored population-level variation in the wing shape of <em>Aedes albopictus</em> across habitats. Cytochrome oxidase subunit I (COI) gene region was sequenced to validate the morphological and morphometric identification. Procrustes ANOVA regression and CVA based on wing shape reflected that the wing landmarks across all species differed significantly, and leave-one-out cross validation revealed an overall high accuracy of &gt;97% for the two <em>Culex</em> groups. Wing morphometrics uncovered population-level variation within <em>Aedes albopictus</em>, but cross validation accuracy was low. Overall, we show that wing geomorphometric analysis is able to resolve cryptic <em>Culex</em> species (including vectors) occurring sympatrically, and is a robust tool for identifying mosquitoes reliably.</p></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"123 ","pages":"Article 105647"},"PeriodicalIF":2.6,"publicationDate":"2024-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1567134824000984/pdfft?md5=859b2dea97c584477df4a374015e3d76&pid=1-s2.0-S1567134824000984-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141789946","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":"A comparative analysis of mycobacterial ribonucleases: Towards a therapeutic novel drug target","authors":"Lav Kumar Jaiswal ,&nbsp;Rakesh Kumar Singh ,&nbsp;Tanmayee Nayak ,&nbsp;Anuja Kakkar ,&nbsp;Garima Kandwal ,&nbsp;Vijay Shankar Singh ,&nbsp;Ankush Gupta","doi":"10.1016/j.meegid.2024.105645","DOIUrl":"10.1016/j.meegid.2024.105645","url":null,"abstract":"<div><p>Bacterial responses to continuously changing environments are addressed through modulation of gene expression at the level of transcription initiation, RNA processing and/or decay. Ribonucleases (RNases) are hydrolytic or phosphorolytic enzymes involved in a majority of RNA metabolism reactions. RNases play a crucial role in RNA degradation, either independently or in collaboration with various trans-acting regulatory factors. The genus <em>Mycobacterium</em> consists of five subgenera: <em>Mycobacteroides</em>, <em>Mycolicibacterium</em>, <em>Mycobacterium</em>, <em>Mycolicibacter</em> and <em>Mycolicibacillus</em>, which include 63 fully sequenced species (pathogenic/non-pathogenic) to date. These include 13 different RNases, among which 5 are exonucleases (RNase PH, PNPase, RNase D, nano-RNases and RNase AS) and 8 are endonucleases (RNase J, RNase H, RNase P, RNase III, RNase BN, RNase Z, RNase G and RNase E), although RNase J and RNase BN were later identified to have exoribonuclease functions also. Here, we provide a detailed comparative insight into the <em>Escherichia coli</em> and mycobacterial RNases with respect to their types, phylogeny, structure, function, regulation and mechanism of action, with the main emphasis on RNase E. Among these 13 different mycobacterial RNases, 10 are essential for cell survival and have diverse structures hence, they are promising drug targets. RNase E is also an essential endonuclease that is abundant in many bacteria, forms an RNA degradosome complex that controls central RNA processing/degradation and has a conserved 5′ sensor domain/DNase-I like region in its RNase domain. The essential mycobacterial RNases especially RNase E provide a potential repertoire of drug targets that can be exploited for inhibitor/modulator screening against many deadly mycobacterial diseases.</p></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"123 ","pages":"Article 105645"},"PeriodicalIF":2.6,"publicationDate":"2024-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1567134824000960/pdfft?md5=75164ee5ed33661464ae05df60994f95&pid=1-s2.0-S1567134824000960-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141789945","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":"A genome-based investigation of the Priestia species isolated from anthrax endemic regions in Kruger National Park","authors":"Thuto Gomolemo Magome ,&nbsp;Sunday Ochonu Ochai ,&nbsp;Ayesha Hassim ,&nbsp;Cornelius Carlos Bezuidenhout ,&nbsp;Henriette van Heerden ,&nbsp;Kgaugelo Edward Lekota","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":"123 ","pages":"Article 105649"},"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":"Michael Asare-Baah ,&nbsp;Marie Nancy Séraphin ,&nbsp;LaTweika A.T. Salmon-Trejo ,&nbsp;Lori Johnston ,&nbsp;Lina Dominique ,&nbsp;David Ashkin ,&nbsp;Krishna Vaddiparti ,&nbsp;Awewura Kwara ,&nbsp;Anthony T. Maurelli ,&nbsp;Michael Lauzardo","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":"123 ","pages":"Article 105648"},"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":"Zhongcheng Han,&nbsp;Ayixiamuguli Aizezi,&nbsp;Lili Ma,&nbsp;Ying Su,&nbsp;Lijuan Fan,&nbsp;Jiang Liu","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":"123 ","pages":"Article 105646"},"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":"Musab M. Ali Albsheer ,&nbsp;Alfred Hubbard ,&nbsp;Cheikh Cambel Dieng ,&nbsp;Eyoab Iyasu Gebremeskel ,&nbsp;Safaa Ahmed ,&nbsp;Virginie Rougeron ,&nbsp;Muntaser E. Ibrahim ,&nbsp;Eugenia Lo ,&nbsp;Muzamil M. Abdel Hamid","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":"123 ","pages":"Article 105643"},"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":"Danieli Conte ,&nbsp;Dany Mesa ,&nbsp;Damaris Krul ,&nbsp;Larissa Bail ,&nbsp;Carmen Antônia Sanches Ito ,&nbsp;Jussara Kasuko Palmeiro ,&nbsp;Libera Maria Dalla-Costa","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":"123 ","pages":"Article 105644"},"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}