Infection Genetics and Evolution最新文献

{"title":"Antimicrobial resistance profiling of bacteria isolated from wastewater and samples of pharmaceutical industries in South India","authors":"Sravani Kamatham ,&nbsp;Manoharan Seeralan ,&nbsp;Uma Sekar ,&nbsp;Sujatha Kuppusamy","doi":"10.1016/j.meegid.2024.105670","DOIUrl":"10.1016/j.meegid.2024.105670","url":null,"abstract":"<div><div>The study was aimed to determine the phenotypic and genotypic antimicrobial resistance in the isolated bacteria from the influent (25), effluent (15), surface and ground water samples (15) surrounding the pharmaceutical industries located in south India. From 55 samples, 48 isolates of 10 different bacteria were obtained. The identified bacterial isolates were viz. <em>Klebsiella pneumoniae</em>, <em>Pseudomonas aeruginosa</em>, <em>Enterobacter aerogenes</em>, <em>Corynebacterium</em> sp., <em>Acinetobacter</em> sp., <em>Aeromonas punctata</em>, <em>Ralstonia picketti</em>, <em>Staphylococcus aureus, Stenotrophomonas maltophillia</em>, <em>and Citrobacter freundii.</em> The phenotypic profile of resistance through antibiotic susceptibility test was carried out against sixteen different antibiotics. Standard PCR technique was used for the detection of 12 resistance genes encoding carbapenems, quinoline, aminoglycoside, β-lactam belonging <em>blaOXA-58</em>_<em>,</em> <em>blaOXA-22</em>_<em>,</em> <em>qnrA, qnrB, aac(6)-Ib-cr, aac (3)-XI, mec A, qepA,</em> aadB, <em>blaVIM</em>, <em>blaOXA-48</em> and <em>blaNDM</em>. <em>Pseudomonas aeruginosa</em> (1: TN/I/2020) showed presence of 3 resistance genes. <em>qnrB</em> (489 bp) gene was present in maximum of 7 isolates while <em>blaVIM</em> (196 bp) gene was present in 6 isolates. The resistance genes <em>blaNDM</em> (621 bp) was present in three different isolates; <em>aac (X):6)-lb-cr</em> (482 bp), <em>qepA</em> (495 bp), <em>aadB</em> (500 bp), <em>blaOXA-58</em> (843 bp) resistant genes were present in two different isolates each among the bacterial isolates obtained in this study. In phenotypic resistance profiling by AST method, out of 16 antibiotics tested, 14 showed resistance. Similarly, in genotypic resistance profiling, among 12 resistance genes tested, a maximum of three resistance genes were noticed in <em>Pseudomonas aeruginosa.</em> There were positive and negative correlations observed between phenotypic and genotypic resistance among different antibiotics and their resistance genes indicating the variations in the resistance gene expression.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"125 ","pages":"Article 105670"},"PeriodicalIF":2.6,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142301379","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 presence of genes encoding carbapenem-hydrolyzing oxacillinase and lack of carbapenem resistance in non-baumannii Acinetobacter misidentified as Acinetobacter baumannii causing bloodstream infections in a tertiary hospital over a 3-year period","authors":"Jie Zheng ,&nbsp;Jingru Ji ,&nbsp;Wei Chen ,&nbsp;Danwei Wang ,&nbsp;Chang Liu ,&nbsp;Yan Zhang ,&nbsp;Han Shen ,&nbsp;Xiaoli Cao ,&nbsp;Chao Wu","doi":"10.1016/j.meegid.2024.105669","DOIUrl":"10.1016/j.meegid.2024.105669","url":null,"abstract":"<div><h3>Objective</h3><div>This study aims to analyze the genomic and clinical characteristics of Non-baumannii <em>Acinetobacter</em> strains misidentified as <em>A. baumannii</em>, causing bloodstream infections (BSIs) in our hospital.</div></div><div><h3>Materials and methods</h3><div>Whole genome sequencing was performed and average nucleotide identity (ANI) was analyzed. Susceptibility testing was conducted using micro-broth methods. The distribution of antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) was examined using online software tools. The prevalence of virulence factors (VFs) was investigated through nucleotide coding sequence comparisons. Genetic structures of <em>bla</em>OXA genes were analyzed by Gcluster software. Clinical information was collected from electronic medical records for patient characterization.</div></div><div><h3>Results</h3><div>ANI analysis identified five strains as <em>Acinetobacter pittii</em>, with the remaining four identified as <em>A. geminorum</em>, <em>A. nosocomialis</em>, <em>A. soli</em> and <em>A. bereziniae</em>. The GC content of all isolates was less than 38.9 % except for <em>A. soli</em> 16,294. All Non-baumannii <em>Acinetobacter</em> strains were relatively susceptible to antibiotics, except for one <em>A. pittii</em> isolate. Nine <em>bla</em>OXA variants were identified in seven isolates, with two isolates co-carrying 2 different types of <em>bla</em>OXA. Twenty-four insertion sequences (ISs) were identified, with ISAba and IS17 being the primary ISs. Five <em>A. pittii</em> isolates shared the same genetic structures around <em>bla</em>OXA. Genes related to adherence, immune modulation, and nutritional/metabolic factors were the most frequent. Few VFs were detected in <em>A. soli</em> 16,294 and <em>A.bereziniae</em> 14,325.</div></div><div><h3>Conclusions</h3><div>The presence of carbapenem hydrolyzing oxacillinase encoding genes did not confer carbapenem resistance, possibly due to the lack of ISs in the <em>bla</em>OXA flanking sequences. Different <em>bla</em>OXA variants within distinct strains shared the same genetic structures, suggesting potential for multidrug resistance development, which warrants our attention.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"125 ","pages":"Article 105669"},"PeriodicalIF":2.6,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1567134824001205/pdfft?md5=3457782c0565ca872d7f4c3ed085bf49&pid=1-s2.0-S1567134824001205-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142301381","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":"Exploring genetic diversity of hepatitis D virus full-length genome in Brazil: Discovery of a novel HDV-8 subgenotype beyond African borders","authors":"Giovana P. Angelice,&nbsp;Tairine M. Barros,&nbsp;Vanessa A. Marques,&nbsp;Livia M. Villar,&nbsp;Barbara V. Lago,&nbsp;Francisco C.A. Mello","doi":"10.1016/j.meegid.2024.105671","DOIUrl":"10.1016/j.meegid.2024.105671","url":null,"abstract":"<div><div>Hepatitis D virus (HDV) is currently classified into 8 genotypes (1 to 8) and several subgenotypes, with distinct distribution worldwide. However, due to the scarcity of complete genome sequences in databases, this classification is constantly being updated and tends to be regularly revisited in upcoming years as more sequence data becomes available. Aiming to increase knowledge about the genetic variability of HDV, this study presents the full-length genomes of 11 HDV samples collected in Brazil in endemic and non-endemic regions, including the first complete genomes of the genotypes 5 and 8 obtained outside Africa. We also determined the co-infecting HBV genotypes to investigate their prevalence among the HDV-infected individuals throughout the country. Whole genome sequencing confirmed our previous findings based on a partial fragment of the HDV genome, in which HDV subgenoypes 3c (9/11; 81.8 %), 5b (1/11; 9.1 %) and one HDV-8 sequence (1/11; 9.1 %) were detected. As previously observed, HDV-8 formed a distinct branch apart from subgenotypes 8a and 8b, a monophyletic clade representing a novel HDV-8 subgenotype, designated as 8c. Among HDV-3 samples, the main co-infecting HBV genotype found was HBV-F (4/8; 50 %), reflecting the higher incidence of this native South American genotype in the endemic Amazon Basin. Both samples infected with HDV-5 and HDV-8 were coinfected with HBV genotype E, also a genotype with African origin. Our findings based on complete genome sequence of HDV corroborated our results based on a partial region of the HDV genome of a novel HDV-8 subgenotype and reinforced the need to use full-length genomes to properly subdivide genotypes with very low intragroup genetic variability, such as HDV-3. The provision of these complete genomes is expected to contribute to the enrichment of sequence databases for future molecular and evolutionary investigations of HDV.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"125 ","pages":"Article 105671"},"PeriodicalIF":2.6,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142301380","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":"Novel members of the order Picornavirales identified in freshwater from Guarapiranga reservoir in São Paulo","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 Cássia 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.2024.105668","DOIUrl":"10.1016/j.meegid.2024.105668","url":null,"abstract":"<div><p>The global challenge of water resource availability is exacerbated by anthropogenic influences that promote the emergence of pollutants. Among these pollutants are microbiological agents, including viruses, which are ubiquitous in the biosphere and play a pivotal role in both ecological balance and the occurrence of diseases in animals and plants. Consequently, monitoring viruses in water sources becomes indispensable for the establishment of effective prevention, promotion, and control strategies. Within this context, the study focuses on the identification of novel viruses belonging to the <em>Picornavirales</em> order in freshwater from the Guarapiranga Reservoir in the state of São Paulo, Brazil. The samples were subjected to viral metagenomics. Our analysis led to the characterization of four distinct sequences (GinkV-05, AquaV_10, MarV_14, and MarV_64), which exhibited significant divergence compared to other members of the <em>Picornavirales</em> order. This remarkable diversity prompted the identification of a potential new genus within the <em>Marnaviridae</em> family, tentatively named <em>Ginkgonavirus</em>. Additionally, we characterized four sequences in a very distinct clade and propose the recognition of a novel family (named <em>Aquaviridae</em>) within the <em>Picornavirales</em> order. Our findings contribute valuable insights into the previously uncharted diversity of <em>Picornavirales</em> present in water sources, shedding light on an important facet of viral ecology and evolution in aquatic environments.</p></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"124 ","pages":"Article 105668"},"PeriodicalIF":2.6,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1567134824001199/pdfft?md5=4ec0eb4d282f3beeefe9c393f76b15dc&pid=1-s2.0-S1567134824001199-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142230794","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 2023 South Sudanese outbreak of Hepatitis E emphasizes ongoing circulation of genotype 1 in North, Central, and East Africa","authors":"Gregory S. Orf ,&nbsp;Nicholas Bbosa ,&nbsp;Michael G. Berg ,&nbsp;Robert Downing ,&nbsp;Sonja L. Weiss ,&nbsp;Deogratius Ssemwanga ,&nbsp;Alfred Ssekagiri ,&nbsp;Shirin Ashraf ,&nbsp;Ana da Silva Filipe ,&nbsp;Ronald Kiiza ,&nbsp;Joshua Buule ,&nbsp;Hamidah Suubi Namagembe ,&nbsp;Stella Esther Nabirye ,&nbsp;John Kayiwa ,&nbsp;Lul Lojok Deng ,&nbsp;Gregory Wani ,&nbsp;James A. Maror ,&nbsp;Andrew Baguma ,&nbsp;Juma J.H. Mogga ,&nbsp;Saleem Kamili ,&nbsp;Gavin A. Cloherty","doi":"10.1016/j.meegid.2024.105667","DOIUrl":"10.1016/j.meegid.2024.105667","url":null,"abstract":"<div><p>In April 2023, an outbreak of acute hepatitis was reported amongst internally displaced persons in the Nazareth community of South Sudan. IgM serology-based screening suggested the likely etiologic agent to be Hepatitis E virus (HEV). In this study, plasma specimens collected from anti-HEV IgM-positive cases were subjected to additional RT-qPCR testing and sequencing of extracted nucleic acids, resulting in the recovery of five full and eight partial HEV genomes. Maximum likelihood phylogenetic reconstruction confirmed the genomes belong to HEV genotype 1. Using distance-based methods, we show that genotype 1 is best split into three sub-genotypes instead of the previously proposed seven, and that these sub-genotypes are geographically restricted. The South Sudanese sequences confidently cluster within sub-genotype 1e, endemic to northeast, central, and east Africa. Bayesian Inference of phylogeny incorporating sampling dates shows that this new outbreak is not directly descended from other recent local outbreaks for which sequence data is available. However, the analysis suggests that sub-genotype 1e has been consistently and cryptically circulating locally for at least the past half century and that the known outbreaks are often not directly descended from one another. The ongoing presence of HEV, combined with poor sanitation and hygiene in the conflict-affected areas in the region, place vulnerable populations at risk for infection and its more serious effects, including progression to fulminant hepatitis.</p></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"124 ","pages":"Article 105667"},"PeriodicalIF":2.6,"publicationDate":"2024-09-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1567134824001187/pdfft?md5=6c323f9c6380c1ba150f88c1c01aedf4&pid=1-s2.0-S1567134824001187-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142232296","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":"Drivers of virulence and antimicrobial resistance in Gram-negative bacteria in different settings: A genomic perspective","authors":"Anuradha Singh,&nbsp;Pittu Sandhya Rani,&nbsp;Viraj Bandsode,&nbsp;Mahanga Nyambero,&nbsp;Shamsul Qumar,&nbsp;Niyaz Ahmed","doi":"10.1016/j.meegid.2024.105666","DOIUrl":"10.1016/j.meegid.2024.105666","url":null,"abstract":"<div><p>The human gut presents a complex ecosystem harboring trillions of microorganisms living in close association with each other and the host body. Any perturbation or imbalance of the normal gut microbiota may prove detrimental to human health. Enteric infections and treatment with antibiotics pose major threats to gut microbiota health. Recent genomics-driven research has provided insights into the transmission and evolutionary dynamics of major enteric pathogens such as <em>Escherichia coli</em>, <em>Klebsiella pneumoniae</em>, <em>Vibrio cholerae</em>, <em>Helicobacter pylori</em> and <em>Salmonella</em> spp<em>.</em> Studies entailing the identification of various dominant lineages of some of these organisms based on artificial intelligence and machine learning point to the possibility of a system for prediction of antimicrobial resistance (AMR) as some lineages have a higher propensity to acquire virulence and fitness advantages. This is pertinent in the light of emerging AMR being one of the immediate threats posed by pathogenic bacteria in the form of a multi-layered fitness manifesting as phenotypic drug resistance at the level of clinics and field settings. To develop a holistic or systems-level understanding of such devastating traits, present methodologies need to be advanced with the high throughput techniques integrating community and ecosystem/niche level data across different omics platforms. The next major challenge for public health epidemiologists is understanding the interactions and functioning of these pathogens at the community level, both in the gut and outside. This would provide new insights into the dimensions of enteric bacteria in different environments and niches and would have a plausible impact on infection control strategies in terms of tackling AMR. Hence, the aim of this review is to discuss virulence and AMR in Gram-negative pathogens, the spillover of AMR and methodological advancements aimed at addressing it through a unified One Health framework applicable to the farms, the environment, different clinical settings and the human gut.</p></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"124 ","pages":"Article 105666"},"PeriodicalIF":2.6,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1567134824001175/pdfft?md5=d4c6f2a9389ead430ffec29f87e735a7&pid=1-s2.0-S1567134824001175-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142146906","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 evolutionary analysis of a strain of Senecavirus A in Anhui and the establishment of its detection method","authors":"Liang Li ,&nbsp;Xuan Wang ,&nbsp;Lijun Chen ,&nbsp;Jie Li ,&nbsp;Yuting Xue ,&nbsp;Haicheng Lin ,&nbsp;HuiHui Sun ,&nbsp;Zongyi Bo ,&nbsp;Haixiao Shen ,&nbsp;Pei Sun","doi":"10.1016/j.meegid.2024.105665","DOIUrl":"10.1016/j.meegid.2024.105665","url":null,"abstract":"<div><h3>Background</h3><p>Senecavirus A (SVA) is the only member of the genus Senecavirus in the family Picornaviridae, and is one of the pathogens of porcine blistering disease. SVA has been reported in the United States, Canada, China, Thailand, and Colombia.</p></div><div><h3>Methods</h3><p>In this study, positive SVA infection was detected by RT-PCR in sick materials collected from pig farms of different sizes in Anhui Province.</p></div><div><h3>Results</h3><p>In this study, a virulent strain of SVA was successfully obtained by viral isolation on BHK21 cells and named SVA-CH-AHAU-1. Meanwhile, a simple, rapid and accurate nano-PCR method for the detection of SVA infection was established in this study, using the recombinant plasmid pClone-SVA-3D as a template.</p></div><div><h3>Conclusions</h3><p>The complete genome of SVA-CH-AHAU-1 is 7286 bp, including a 5′ non-coding region (UTR), an open reading frame (ORF) of 6546 nucleotides, encoding 2182 amino acids (aa), and a 3’ UTR with Poly(A) features, and phylogenetic analysis showed that this isolate had the highest nucleotide homology (97.9 %) with the US isolate US-15-41901SD. In this study, the virulent strain SVA-CH-AHAU-1 was found to recombine in the ORF region with isolates SVA-CH-SDGT-2017 and SVA/Canada/ON/FMA-2015-0024 T2/2015. The complete genome has been submitted to GeneBank with the accession number OM654411. In addition, our results suggest that the established nano-PCR assay can be used as an economical, reliable and sensitive method for the field diagnosis of SVA method, especially in resource-limited areas.</p></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"124 ","pages":"Article 105665"},"PeriodicalIF":2.6,"publicationDate":"2024-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1567134824001163/pdfft?md5=e7aa7fd6f131c73dabb4e404bfadb08a&pid=1-s2.0-S1567134824001163-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142134537","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":"Multiple incursions of foot-and-mouth disease virus serotype O into the Republic of Korea between 2010 and 2019","authors":"Antonello Di Nardo ,&nbsp;Da-Rae Lim ,&nbsp;Soyoon Ryoo ,&nbsp;Hyeonjeong Kang ,&nbsp;Valerie Mioulet ,&nbsp;Jemma Wadsworth ,&nbsp;Nick J. Knowles ,&nbsp;Jae-Myung Kim ,&nbsp;Donald P. King ,&nbsp;Sang-Ho Cha","doi":"10.1016/j.meegid.2024.105664","DOIUrl":"10.1016/j.meegid.2024.105664","url":null,"abstract":"<div><p>This study characterised type O foot-and-mouth disease (FMD) viruses recovered from outbreaks that were reported between 2010 and 2019 in the Republic of Korea. We used 96 newly generated whole-genome sequences (WGS) along with 131 already published WGSs from samples collected from countries in East and Southeast Asia. We identified at least eight independent introductions of O/SEA/Mya-98 and O/ME-SA/Ind-2001e FMDV strains into the Republic of Korea during the study period, which were closely related to the sequences of viruses circulating in the East and Southeast Asia neighbourhood with over 97 % nucleotide identity. Spatial-temporal transitions of O/SEA/Mya-98 lineage viruses recovered from the largest outbreak (2014–16) showed that after initial cases were detected within a 15-day period in July 2014, a single introduction of the same virus during December 2014 generated extensive forward virus transmission between farms that lasted until March 2016. We estimated that secondary transmissions were responsible for infection on 44 % FMD affected farms, over a total of 14 generations of infection. We eastimated a median evolutionry rate of 2.51 × 10⁻⁵ nt/site/day, which is similar for other FMD epidemic scenarios. These findings suggest that regular incursions of different FMDV lineages into the Republic of Korea have posed a continuous threat from endemic countries of East and Southeast Asia. These data highlight the importance of active cooperation and information exchange on FMD situation within Asian countries and assessment about the likely risk routes of virus movement is highly necessary to prevent further incursion and virus spread of FMDV in the Republic of Korea.</p></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"124 ","pages":"Article 105664"},"PeriodicalIF":2.6,"publicationDate":"2024-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1567134824001151/pdfft?md5=0905d939ca12f679dbd085b134d19054&pid=1-s2.0-S1567134824001151-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142114941","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 of tick-borne zoonotic pathogens in ixodid ticks collected from small ruminants in Northern Pakistan","authors":"Jehan Zeb ,&nbsp;Baolin Song ,&nbsp;Munsif Ali Khan ,&nbsp;Haytham Senbill ,&nbsp;Muhammad Umair Aziz ,&nbsp;Sabir Hussain ,&nbsp;Adrian Alberto Díaz Sánchez ,&nbsp;Alejandro Cabezas-Cruz ,&nbsp;Abdulrahman Alzahrani ,&nbsp;Mohammed Alshehri ,&nbsp;Rashed Mohammed Alghamdi ,&nbsp;Olivier Andre Sparagano","doi":"10.1016/j.meegid.2024.105663","DOIUrl":"10.1016/j.meegid.2024.105663","url":null,"abstract":"<div><p>Mapping tick distribution and pathogens in unexplored areas sheds light on their importance in zoonotic and veterinary contexts. In this study, we performed a comprehensive investigation of the genetic diversity of tick and tick-borne pathogens (TBPs) detection infesting/infecting small ruminants across northern Pakistan. We collected 1587 ixodid ticks from 600 goats and sheep, an overall tick infestation rate of 50.2 %. Notably, gender-based infestation rates were higher in female goats and sheep compared to their male counterparts. Age-wise analysis showed that the tick infestation rate was higher in older animals. This study identified 11 ixodid tick species within three genera: <em>Hyalomma</em>, <em>Haemaphysalis</em>, and <em>Rhipicephalus</em>, which were taxonomically classified using <em>16S rRNA</em> and cytochrome oxidase I <em>(cox1)</em> molecular markers. Sequence analysis indicated that reported ticks are similar to ixodid species found across various Asian and African countries. Tick-borne pathogens were detected by amplifying <em>16S rRNA</em> and citrate synthase (<em>gltA</em>) for bacterial pathogens and 18S rRNA for apicomplexan parasites. The present study reported a diverse array of TBPs in ticks from the study area, with <em>Rickettsia massiliae</em> (24.5 %) and <em>Theleria ovis</em> (16.4 %) as the most prevalent bacterial and apicomplexan pathogens. Phylogenetically, detected TBPs shared evolutionary relatedness with identical TBPs from old and new world countries. These findings highlight the presence of zoonotic TBPs in ixodid ticks from Pakistan. In addition, it also provides a foundation for future epidemiological research on ticks and TBPs, emphasizing their relevance in both zoonotic and veterinary contexts.</p></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"124 ","pages":"Article 105663"},"PeriodicalIF":2.6,"publicationDate":"2024-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S156713482400114X/pdfft?md5=d1d2bcbcaf74a6bb3a37e34a38fe167b&pid=1-s2.0-S156713482400114X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142114940","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":"Novel insights on unraveling dynamics of transmission clusters in outbreaks using phylogeny-based methods","authors":"Brittany Rife Magalis ,&nbsp;Alberto Riva ,&nbsp;Simone Marini ,&nbsp;Marco Salemi ,&nbsp;Mattia Prosperi","doi":"10.1016/j.meegid.2024.105661","DOIUrl":"10.1016/j.meegid.2024.105661","url":null,"abstract":"<div><p>Molecular data analysis is invaluable in understanding the overall behavior of a rapidly spreading virus population when epidemiological surveillance is problematic. It is also particularly beneficial in describing subgroups within the population, often identified as clades within a phylogenetic tree that represent individuals connected via direct transmission or transmission via differing risk factors in viral spread. However, transmission patterns or viral dynamics within these smaller groups should not be expected to exhibit homogeneous behavior over time. As such, standard phylogenetic approaches that identify clusters based on summary statistics would not be expected to capture dynamic clusters of transmission. We, therefore, sought to evaluate the performance of existing and adapted phylogeny-based cluster identification tools on simulated transmission clusters exhibiting dynamic transmission behavior over time. Despite the complementarity of the tools, we provide strong evidence that novel cluster identification methods are needed for reliable detection of epidemiologically linked individuals, particularly those exhibiting changing transmission dynamics during dynamic outbreak scenarios.</p></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"124 ","pages":"Article 105661"},"PeriodicalIF":2.6,"publicationDate":"2024-08-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1567134824001126/pdfft?md5=81a926e7c04f5e362a67bf43f9bbaae9&pid=1-s2.0-S1567134824001126-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142074624","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}