Infection Genetics and Evolution最新文献

{"title":"Genome-scale analysis of Mycobacterium avium complex isolates from Portugal reveals extensive genetic diversity","authors":"Sofia Carneiro ,&nbsp;Miguel Pinto ,&nbsp;Joana Rodrigues ,&nbsp;João Paulo Gomes ,&nbsp;Rita Macedo","doi":"10.1016/j.meegid.2024.105682","DOIUrl":"10.1016/j.meegid.2024.105682","url":null,"abstract":"<div><div>Opportunist infections caused by nontuberculous mycobacteria (NTM) have emerged as a significant public health problem. Among these, species of the <em>Mycobacterium avium</em> complex (MAC) are the main responsible for the increase in the number of human disease cases. In order to address the current needs in the detection and surveillance of MAC disease cases, we evaluated different species classification methodologies (BLASTn-based marker-gene approach, Kraken v2, rMLST and MLST databases) and their congruence with a core-SNP phylogenetic approach, based on whole genome sequencing (WGS) data. For this purpose, we used a collection of 142 MAC isolates from Portuguese patients diagnosed between 2014 and 2022. The marker-gene approach (based on the <em>rpoB</em>, <em>hsp65</em> and <em>groEL</em> genes), showed the best results, allowing the identification of the 142 MAC isolates to the species/subspecies level (<em>M. avium</em> subsp. <em>hominissuis, M. intracellulare, M. intracellulare</em> subsp. <em>chimaera, M. intracellulare</em> subsp. <em>yongonense, M. marseillence</em> and <em>M. colombiense</em>). Additionally, we performed drug susceptibility testing that confirmed clarithromycin efficacy as a first-line treatment for MAC disease, as 93 % of the Portuguese isolates were susceptible. Using a core-SNP approach we also performed an in-depth phylogenetic analysis within each identified species group, and despite the high genetic diversity within the MAC species, we were able to clearly distinguish all the species/subspecies and identify genetic clusters with epidemiological potential.</div><div>We highlight not only the need for the standardization of an appropriate genotyping approach for species identification and management of MAC disease, but also a more robust large-scale WGS data analysis, in a One Health perspective, in order to identify potential routes of transmission.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"125 ","pages":"Article 105682"},"PeriodicalIF":2.6,"publicationDate":"2024-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142513267","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":"Dynamics of SARS-CoV-2 variants in West Africa: Insights into genomic surveillance in resource-constrained settings","authors":"Josue Togo ,&nbsp;Anou Moise Somboro ,&nbsp;Oumar Dolo ,&nbsp;Fatoumata Tata Traore ,&nbsp;Ibrehima Guindo ,&nbsp;Djeneba B. Fofana ,&nbsp;Eve Todesco ,&nbsp;Anne-Geneviève Marcelin ,&nbsp;Vincent Calvez ,&nbsp;Jane Holl ,&nbsp;Robert Leo Murphy ,&nbsp;Christophe Rodriguez ,&nbsp;Mamoudou Maiga ,&nbsp;Almoustapha Issiaka Maiga","doi":"10.1016/j.meegid.2024.105681","DOIUrl":"10.1016/j.meegid.2024.105681","url":null,"abstract":"<div><div>SARS-CoV-2 geno-surveillance has been challenging in West Africa. Despite the multiple challenges encountered, particularly in West Africa during the COVID-19 pandemic, efforts were made to circumscribe the spread of the disease and to provide methods and resources for surveillance. We aim to describe the dynamic of SARS-CoV-2 variants and highlight the efforts made in genomic surveillance in West Africa. Therefore, we proceeded to retrieve West African countries' SARS-CoV-2 data from public repository (GISAID) and then ensued to a descriptive statistical analysis. From the start of the pandemic till December 2023, we found less than a million COVID-19 cases notified within the West African region. Overall, the study population was 50.21 % Males with a median age of 37. Regarding genomic data, only 3.02 % of cases were sequenced and deposited in GISAID. Of the available sequence, we noted that most of the variants have circulated in West Africa before the official notification of the variants. Nigeria, Ghana, and Senegal provided together more than half of West Africa's originating sequences when Omicron and Delta variants were the most sequenced in West Africa.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"125 ","pages":"Article 105681"},"PeriodicalIF":2.6,"publicationDate":"2024-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142513266","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":"Unveiling ancestral threads: Exploring CCR5 ∆32 mutation frequencies in Colombian populations for HIV/AIDS therapeutics","authors":"Alejandro Barrios-Navas ,&nbsp;Thanh Long Nguyen ,&nbsp;Juan Esteban Gallo ,&nbsp;Leonardo Mariño-Ramírez ,&nbsp;José María Satizabal Soto ,&nbsp;Adalberto Sánchez ,&nbsp;I. King Jordan ,&nbsp;Augusto Valderrama-Aguirre","doi":"10.1016/j.meegid.2024.105680","DOIUrl":"10.1016/j.meegid.2024.105680","url":null,"abstract":"<div><div>AIDS remains a significant global health challenge since its emergence in 1981, with millions of deaths and new cases every year. The CCR5 ∆32 genetic deletion confers immunity to HIV infection by altering a cell membrane protein crucial for viral entry. Stem cell transplants from homozygous carriers of this mutation to HIV-infected individuals have resulted in viral load reduction and disease remission, suggesting a potential therapeutic avenue. This study aims to investigate the relationship between genetic ancestry and the frequency of the CCR5 ∆32 mutation in Colombian populations, exploring the feasibility of targeted donor searches based on ancestry composition. Utilizing genomic data from the CÓDIGO-Colombia consortium, comprising 532 individuals, the study assessed the presence of the CCR5 ∆32 mutation and examined if the population was on Hardy-Weinberg equilibrium. Individuals were stratified into clusters based on African, American, and European ancestry percentages, with logistic regression analysis performed to evaluate the association between ancestry and mutation frequency. Additionally, global genomic databases were utilized to visualize the worldwide distribution of the mutation. The findings revealed a significant positive association between European ancestry and the CCR5 ∆32 mutation frequency, underscoring its relevance in donor selection. African and American ancestry showed negative but non-significant associations with CCR5 ∆32 frequency, which may be attributed to the study's limitations. These results emphasize the potential importance of considering ancestry in donor selection strategies, reveal the scarcity of potential donors in Colombia, and underscore the need to consider donors from other populations with mainly European ancestry if the CCR5 ∆32 stem cell transplant becomes a routine treatment for HIV/AIDS in Colombia.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"125 ","pages":"Article 105680"},"PeriodicalIF":2.6,"publicationDate":"2024-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142395364","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":"High HIV-1 genetic diversity and low prevalence of transmitted drug resistance among treatment-naive people living with HIV in Madagascar","authors":"Fetra Angelot Rakotomalala ,&nbsp;Christelle Butel ,&nbsp;Tahinamandranto Rasamoelina ,&nbsp;Laetitia Serrano ,&nbsp;Nicole Vidal ,&nbsp;Santatriniaina Hajanirina Dauphin Randriarimanana ,&nbsp;Luca Maharavo ,&nbsp;Hajanirina Nathanaella Randriamananjara ,&nbsp;Nicolas Fernandez-Nuñez ,&nbsp;Felana Ranaivo Rabetokotany ,&nbsp;Danielle Aurore Doll Rakoto ,&nbsp;Eric Delaporte ,&nbsp;Martine Peeters ,&nbsp;François-Xavier Babin ,&nbsp;Luc Hervé Samison ,&nbsp;Eric Nerrienet ,&nbsp;Ahidjo Ayouba","doi":"10.1016/j.meegid.2024.105679","DOIUrl":"10.1016/j.meegid.2024.105679","url":null,"abstract":"<div><h3>Background and objectives</h3><div>Data on HIV drug resistance in Madagascar are rare and outdated. In this study, we assessed the prevalence of HIV drug resistance mutations to antiretrovirals (ARVs) and genetic diversity of circulating strains in treatment-naive people living with HIV (PLHIV) in Madagascar.</div></div><div><h3>Materials and methods</h3><div>We amplified the protease (PR), fragments of the Reverse Transcriptase (RT) and Integrase (IN) genes according to the French ANRS protocol. The amplicons were sequenced using next-generation sequencing technology on an Illumina platform (MiSeq). We determined HIV-1 subtypes through phylogenetic analysis using maximum likelihood in PhyML. Resistance interpretation was performed using the Stanford algorithm (version 9.5.1).</div></div><div><h3>Results</h3><div>We included 239 HIV-infected adults and children, sampled between January 2019 and November 2023, with a median age of 30 years and a mean plasma HIV viral load of 6.3 Log copies/mL. We sequenced at least one genomic fragment (PR or RT or IN) of the 239 samples, but 9 were excluded from analysis (mean depth &lt; 10,000×). Phylogenetic analysis of 230 sequences revealed the presence of subtype C (33.91 %), A1 (11.30 %), B (11.30 %), CRF02_AG (9.56 %), subtype G (3.04 %), subtype D (0.43 %), CRF01_AE (0.43 %), and a significant proportion of unique recombinant forms (URFs) (30.30 %). The prevalence of transmitted drug resistance (TDR) was 4.95 % (10/202) among patients aged 15 years and older. When stratified by ARV class, this prevalence was 4.79 % for non-nucleoside reverse transcriptase inhibitors (NNRTIs), 0.59 % for Nucleoside Reverse Transcriptase inhibitors (NRTIs), and 0.50 % for integrase strand transfer inhibitors (INSTIs). Among children under 15 years old (<em>n</em> = 28), the prevalence of TDR was 14.28 % (4/28), with all mutations conferring resistance to NNRTIs. No mutation conferring resistance to protease inhibitors was found, neither in children nor in adults.</div></div><div><h3>Conclusion</h3><div>Our results show a low prevalence of ARV resistance mutations among adult treatment-naive PLHIV in Madagascar. In children under 15 years old, 92 % were infants under two years old, the high resistance rate is likely related to mother-to-child transmission. No resistance mutation to dolutegravir was detected. We also observed high frequencies of subtypes C, B, A1 and a high proportion of URFs, highlighting an ongoing dynamic epidemic.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"125 ","pages":"Article 105679"},"PeriodicalIF":2.6,"publicationDate":"2024-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142378635","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":"Discovery of the first sea turtle adenovirus and turtle associated circoviruses","authors":"Alexandra V. Tóth ,&nbsp;Péter Berta ,&nbsp;Balázs Harrach ,&nbsp;Krisztina Ursu ,&nbsp;Ana Paula Jejesky de Oliveira ,&nbsp;Fernando Vicentini ,&nbsp;João Luiz Rossi ,&nbsp;Tibor Papp ,&nbsp;Győző L. Kaján","doi":"10.1016/j.meegid.2024.105677","DOIUrl":"10.1016/j.meegid.2024.105677","url":null,"abstract":"<div><div>Turtles are an evolutionarily unique and morphologically distinctive order of reptiles, and many species are globally endangered. Although a high diversity of adenoviruses in scaled reptiles is well-documented, turtle adenoviruses remain largely understudied. To investigate their molecular diversity, we focused on the identification and characterisation of adenoviruses in turtle-derived organ, swab and egg samples. Since reptile circoviruses have been scarcely reported and no turtle circoviruses have been documented to date, we also screened our samples for circoviruses. Host−virus coevolution is a common feature of these viral families, so we aimed to investigate possible signs of this as well. Two screening projects were conducted: one on Brazilian samples collected from animals in their natural habitat, and the other on Hungarian pet shop samples. Nested PCR systems were used for the detection of adeno- and circoviruses and purified PCR products were Sanger sequenced. Phylogenetic trees for the viruses were reconstructed based on the adenoviral DNA polymerase and hexon genes, circoviral Rep genes, and for the turtle hosts based on mitochondrial cytochrome <em>b</em> amino acid sequences. During the screening, testadeno-, siadeno-, and circovirus strains were detected. The circovirus strains were classified into the genus <em>Circovirus</em>, exhibiting significant evolutionary divergence but forming a monophyletic clade within a group of fish circoviruses. The phylogenetic tree of turtles reflected their taxonomic relationships, showing a deep bifurcation between suborders and distinct monophyletic clades corresponding to families. A similar clustering pattern was observed among the testadenovirus strains in their phylogenetic tree. As a result, this screening of turtle samples revealed at least three new testadenoviruses, including the first sea turtle adenovirus, evidence of coevolution between testadenoviruses and their hosts, and the first turtle associated circoviruses. These findings underscore the need for further research on viruses in turtles, and more broadly in reptiles, to better understand their viral diversity and the evolutionary processes shaping host–virus interactions.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"125 ","pages":"Article 105677"},"PeriodicalIF":2.6,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142373606","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":"Genomic surveillance of dengue virus in Benin","authors":"Anges Yadouleton ,&nbsp;Odilon Nouatin ,&nbsp;Islamiath Kissira ,&nbsp;Parfait Houngbegnon ,&nbsp;Gilles Cottrell ,&nbsp;Nadine Fievet ,&nbsp;Stephane Sohou ,&nbsp;Christelle Butel ,&nbsp;Laetitia Serrano ,&nbsp;Emilande Guichet ,&nbsp;Nicole Vidal ,&nbsp;Eric Delaporte ,&nbsp;Ahidjo Ayouba ,&nbsp;Martine Peeters ,&nbsp;Achille Massougbodji","doi":"10.1016/j.meegid.2024.105674","DOIUrl":"10.1016/j.meegid.2024.105674","url":null,"abstract":"<div><h3>Objective</h3><div>Dengue is a widespread viral infection transmitted from mosquitoes to humans, mainly in tropical and subtropical climates. In Benin, only dengue virus (DENV) serotype 2 infection has been previously described in humans. This study aimed to investigate DENV infection and serotypes in suspected patients.</div></div><div><h3>Methods</h3><div>Plasma samples from 464 patients attending health centers in February 2023 with clinical symptoms and suspected for dengue infection were included, and analyzed for DENV by real time quantitative Polymerase Chain Reaction (Dengue Altona 3.0 kit). PCR positives samples were further characterized by whole genome sequencing and phylogenetic analysis to identify the circulating DENV serotype.</div></div><div><h3>Results</h3><div>The RT-qPCR results showed that four patients (D6, D23, D28, D44) were positive with the cycle threshold values less than 40 (31.3, 34.7, 14.7 and 14.3) respectively. Full-length DENV sequences were obtained for D6, D28 and D44. One patient (D6) was infected with DENV-1 serotype, and the two others (D28 and D44) were positive for DENV-3. Phylogenetic analysis shows that the new DENV-1 sequence is close to those obtained in Burkina Faso in 2022 and Nigeria in 2023, and the two DENV-3 sequences form a separate cluster with sequences obtained in Burkina Faso in 2022.</div></div><div><h3>Conclusion</h3><div>We showed for the first time, the presence of dengue serotype 1 and serotype 3 infection in Benin. These results send a strong signal to health authorities and show that arbovirus surveillance efforts must be integrated into pathogen monitoring programs.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"125 ","pages":"Article 105674"},"PeriodicalIF":2.6,"publicationDate":"2024-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142332708","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":"Feline bocaviruses found in Thailand have undergone genetic recombination for their evolutions","authors":"Pattiya Lohavicharn ,&nbsp;Tanit Kasantikul ,&nbsp;Chutchai Piewbang ,&nbsp;Somporn Techangamsuwan","doi":"10.1016/j.meegid.2024.105675","DOIUrl":"10.1016/j.meegid.2024.105675","url":null,"abstract":"<div><div>Feline bocaviruses (FBoVs) have been discovered for a decade and are often detected in feces, possibly associated with diarrhea in cats. Studies on FBoV evolution remain limited and have mainly focused on prevalence and genetic characterization. Although genetic recombination serves as a potential mechanism in bocavirus evolution, research on this process for FBoVs has been scarce. In this study, we characterized 19 complete coding sequences of FBoVs obtained from Thai cats, revealing that FBoV-1, -2, and -3 were endemic in Thailand. Genetic characterizations showed that most Thai FBoVs were closely related to previously detected strains in Thailand and China. Recombination analyses indicated intragenic, intraspecies recombination in all FBoV species, with recombination breakpoints commonly found in the NP1 and VP1/2 genes, highlighting these genes may be hotspots for FBoV recombination. However, no interspecies recombination was detected. Selective pressure analysis of various FBoV genes revealed that these viruses underwent purifying selection. Although the VP1/2 gene of all FBoV species was under the strongest negative selection pressure, positive selection sites were only found in FBoV-1 and FBoV-3. This study is the first to identify natural recombination in FBoV-2 and FBoV-3 and provides evidence that genetic recombination is a potential driver of FBoV evolutions. Additionally, this study offers up-to-date information on the genetic characteristics, evolutionary dynamics, and selective pressure status of FBoVs, which should be continuously monitored.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"125 ","pages":"Article 105675"},"PeriodicalIF":2.6,"publicationDate":"2024-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142332706","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 variation and population structure of Taenia multiceps (Coenurus cerebralis) based on mitochondrial cox1 gene: A comprehensive global analysis","authors":"Shahbaz Ul Haq ,&nbsp;Muhammad Abdullah Malik ,&nbsp;Ayed Alshammari ,&nbsp;Abu Bakar Yameen ,&nbsp;Majed H. Wakid ,&nbsp;Mughees Aizaz Alvi ,&nbsp;Abdulbaset Mohammad Kabli ,&nbsp;Muhammad Saqib ,&nbsp;Warda Qamar ,&nbsp;Muhammad Sohail Sajid ,&nbsp;Fenfei Gao ,&nbsp;Li Li ,&nbsp;Bao-Quan Fu ,&nbsp;Hong-Bin Yan ,&nbsp;Wan-Zhong Jia","doi":"10.1016/j.meegid.2024.105676","DOIUrl":"10.1016/j.meegid.2024.105676","url":null,"abstract":"<div><div><em>Taenia multiceps</em> is a neglected parasite having veterinary and public health importance. The predilection sites of the parasite larva (<em>Coenurus cerebralis</em>) are brain (cerebral coenurosis) and subcutaneous (non-cerebral coenurosis). There is a dearth of data regarding molecular characterization of <em>T</em>. <em>multiceps</em> and even fewer population structure-based studies on <em>T</em>. <em>multiceps</em>. The current study was conducted to provide epidemiological information regarding the global population structure of the parasite. The NCBI GenBank database was accessed to download the sequences of <em>cox</em>1 gene, which were further subjected to PopArt software to construct median-joining networks. The DnaSp software was used to compute neutrality and diversity indices. Host and region-wise indices of neutrality and diversity were also computed. There were 166 gene sequences found in the NCBI database. Followed by removal of short gene sequences, 143 were considered to perform bioinformatic analyses. A total of 30 haplotypes with 46 mutations and 23 parsimony informative sites were found. High diversity (Hd = 0.889, π = 0.01186) and negative but statistically insignificant neutrality indices (Tajima's D = −1.57659, Fu's Fs = −10.552) were found. Region-wise results revealed highest haplotype diversities in isolates from KSA (Hd = 1.00) followed by Greece and Italy (Hd = 0.962), and China (Hd = 0.931). Host-wise data analysis showed an overall negative Tajima's D value and there exists highest haplotype diversity in cattle (Hd = 1.00) followed by dogs (Hd = 0.833), sheep (Hd = 0.795) and goats (Hd = 0.788). The findings of the study indicate that the population diversity of <em>T</em>. <em>multiceps</em> will increase worldwide as shown by high diversity and negative neutrality indices. The findings of the study significantly add-in to the existing bank of knowledge about population structure of <em>T</em>. <em>multiceps</em>. We recommend conducting more studies employing different genetic markers to better comprehend the epidemiology of the parasite.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"125 ","pages":"Article 105676"},"PeriodicalIF":2.6,"publicationDate":"2024-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142332707","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":"Mitochondrial genome analysis across different populations reveals the intraspecific variation and phylogeography of the Caucasian soft tick relapsing fever vector, Ornithodoros (Pavlovskyella) verrucosus (Ixodida: Argasidae)","authors":"Serhii Filatov ,&nbsp;Alexander R. Kneubehl ,&nbsp;Aparna Krishnavajhala ,&nbsp;Giorgi Melashvili ,&nbsp;Ana Tsitsishvili ,&nbsp;Küşver Mamedova ,&nbsp;Perot Saelao ,&nbsp;Adalberto Á. Pérez de León ,&nbsp;Job E. Lopez","doi":"10.1016/j.meegid.2024.105673","DOIUrl":"10.1016/j.meegid.2024.105673","url":null,"abstract":"<div><div>Territories in southern parts of Eastern Europe and in the Caucasus are endemic for tick-borne relapsing fever (TBRF), caused by <em>Borrelia caucasica</em>. This spirochete is transmitted exclusively by the bites of <em>Ornithodoros verrucosus</em>; however, the distribution and genetic diversity of the tick vector have not been explored. To address this, we performed a phylogeographic study of <em>O. verrucosus</em> specimens collected across a large geographic distribution. We sequenced and analyzed complete mitochondrial genomes of 54 individual <em>O. verrucosus</em> ticks representing 23 geographically diverse populations from Ukraine, Georgia, and Azerbaijan. We detected 47 unique haplotypes, with every collection site exhibiting distinct polymorphisms. This, along with other population genetic indices, suggests little evidence of gene flow between populations. The Bayesian coalescent analysis revealed the presence of four lineages that diverged in the Middle Pleistocene (770–126 kya). Two lineages were widespread and present in all study regions, while the other two were restricted to the southern foothills of the Lesser Caucasus mountain range. The sympatry of these ancient lineages suggests that isolation by environment, in addition to geographic distance, may play a role in the intraspecific divergence of tick populations. Using a phylogeographic approach, we provide a snapshot of genetic diversity in <em>O. verrucosus</em> and discuss the evolutionary history of the tick vector.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"125 ","pages":"Article 105673"},"PeriodicalIF":2.6,"publicationDate":"2024-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142332709","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":"Pneumococcal transposon profiling associated with macrolide, tetracycline, and chloramphenicol resistance from carriage isolates of serotype 19F in Indonesia","authors":"Yustinus Maladan ,&nbsp;Endah Retnaningrum ,&nbsp;Budi Setiadi Daryono ,&nbsp;Korrie Salsabila ,&nbsp;Rosantia Sarassari ,&nbsp;Miftahuddin Majid Khoeri ,&nbsp;Ratna Fathma Sari ,&nbsp;Sarah Azhari Balqis ,&nbsp;Ghina Athyah Wahid ,&nbsp;Dodi Safari","doi":"10.1016/j.meegid.2024.105672","DOIUrl":"10.1016/j.meegid.2024.105672","url":null,"abstract":"<div><div>Genetic evolution of resistance due to mutations and transposon insertions is the primary cause of antimicrobial resistance in <em>Streptococcus pneumoniae</em>. Resistance to macrolide, tetracycline, and chloramphenicol is caused by the insertion of specific genes that carried by transposon (Tn). This study aims to analyze transposon profiling associated with macrolide, tetracycline, and chloramphenicol resistance from carriage isolates of <em>S. pneumoniae</em> serotype 19F in Indonesia. <em>S. pneumoniae</em> serotype 19F isolates were collected from nasopharyngeal swab specimens from different regions in Indonesia. Genomic DNA was extracted from sixteen isolates and whole genome sequencing was performed on Illumina platform. Raw sequence data were analyzed using de novo assembly by ASA³P and Microscope server. The presence of transposons was identified with detection of <em>int</em> and <em>xis</em> genes and visualized by pyGenomeViz. The genome size of <em>S. pneumoniae</em> ranges from 2,040,117 bp to 2,437,939 bp, with a GC content of around 39 %. ST1464 (4/16) and ST271 (3/16) were found as the predominant sequence type among isolates. Tn2010 was the most common transposon among <em>S. pneumoniae</em> serotype 19F isolates (7/16) followed by Tn2009 (4/16), and Tn5253 (3/16). We identified two deletion sites within the <em>tetM</em> gene (2 bp and 58 bp) that confer tetracycline susceptibility from one isolate. This study suggests that genomic analysis can be employed for the detection and surveillance of antimicrobial resistance genes among <em>S. pneumoniae</em> strains isolated from various regions in Indonesia.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"125 ","pages":"Article 105672"},"PeriodicalIF":2.6,"publicationDate":"2024-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1567134824001230/pdfft?md5=4a0e1d5404153d8316fb369293de5676&pid=1-s2.0-S1567134824001230-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142309165","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}