Infection Genetics and Evolution最新文献

{"title":"Application of targeted next-generation sequencing for detecting respiratory pathogens in the sputum of patients with pulmonary infections","authors":"Hongting Da ,&nbsp;Tao Meng ,&nbsp;Yuanhong Xu","doi":"10.1016/j.meegid.2025.105722","DOIUrl":"10.1016/j.meegid.2025.105722","url":null,"abstract":"<div><div>Targeted next-generation sequencing (tNGS) might be valuable for identifying disease-causing pathogens. Herein, we assessed the utility of tNGS in diagnosing pulmonary infections using sputum samples. We gathered complete clinical information and tested the specimens using both conventional microbiological tests (CMTs) and tNGS. The goal was to compare the effectiveness of these two methods in detecting viral, bacterial, and fungal pathogens. Notably, tNGS demonstrated a higher pathogen detection rate compared to CMTs (80.26 % [122/152] vs. 33.55 % [51/152], <em>P</em> = 0.029). Specifically, tNGS was more effective in detecting viruses than CMTs (90.00 % vs. 28.07 %, <em>P</em> = 0.003). Moreover, tNGS detected certain fungi, such as <em>Candida albicans</em> and <em>Cryptococcus neoformans</em>, although the difference between the two assays was not statistically significant (<em>P</em> &gt; 0.05). Our findings reveal that tNGS offers significant advantages in detecting pathogens in patients with lung infections, particularly for bacteria and viruses, providing valuable information that complements CMTs.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"128 ","pages":"Article 105722"},"PeriodicalIF":2.6,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143226890","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 σNS protein of NDRV antagonizes TRIM59-mediated antiviral innate immune response of Cherry Valley duck","authors":"Xiuyuan Wang ,&nbsp;Tingting Zhang ,&nbsp;Xiaoyu Lu ,&nbsp;Yirui Zhang ,&nbsp;Mingzhuo Tian ,&nbsp;Yujing Chen ,&nbsp;Yikun Wang ,&nbsp;Nan Liu ,&nbsp;Shuhan Li ,&nbsp;Jie Zhang ,&nbsp;Liangmeng Wei","doi":"10.1016/j.meegid.2025.105724","DOIUrl":"10.1016/j.meegid.2025.105724","url":null,"abstract":"<div><div>In recent years, outbreak of the novel duck reovirus (NDRV) disease has occurred frequently in duck populations. Due to its rapid spreading, absence of effective control methods, and high treatment costs, the NDRV disease has caused huge losses to waterfowl breeding in China. As reported, four non-structural (NS) proteins are encoded by the NDRV genome, among which the σNS protein is an RNA-binding protein that can improve the stability of bound RNA by forming oligomers (<span><span>Adams and Cory, 1998</span></span>). Nevertheless, the mechanism by which it facilitates reovirus replication remains ambiguous. According to previous studies, the NS protein 11 of the porcine reproductive and respiratory syndrome virus (PRRSV) can interact with tripartite motif-containing 59 (TRIM59) to regulate viral infection. However, the specific role of TRIM59 in NDRV infection remains unclear. This study focused on full-length amplification of duTRIM59, the mRNA distribution of duTRIM59 in Cherry Valley duck and successive biological examinations. The homology with <em>Anas platyrhynchos</em> TRIM59 was 98.6 %. The mRNA distribution level of duTRIM59 showed that duTRIM59 was widely expressed in bursae and thymus of the immune organs. Nevertheless, TRIM59 comprises three domains, including the transmembrane (TM), B-box (B), and RING-finger (R) domains. It also has the activity of ubiquitin-protein ligase (E3). It has been demonstrated that NDRV replication is inhibited by TRIM59 overexpression in duck embryonic fibroblasts (DEF) cells, particularly when the R domain is intact, suggesting that the R domain plays a key role in the spreading of the NDRV virus. In contrast, NDRV infection in DEF cells increased when TRIM59 was depleted by using small interfering RNA. Moreover, the σNS protein can be co-localized with duTRIM59 and stimulate NDRV replication in DEF cells in cases of NDRV infection. This study clarifies the correlation of NDRV infection and TRIM59-mediated antiviral innate immunity, and provides a sound theoretical basis for further understanding this disease.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"128 ","pages":"Article 105724"},"PeriodicalIF":2.6,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143082318","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":"Some novel field isolates belonging to lineage-1 of the genotype GI-avian infectious bronchitis virus (AIBV) show strong evidence of recombination with field/vaccinal strains","authors":"Abid Ullah Shah ,&nbsp;Lalitha Peddireddi ,&nbsp;Beverly Wood ,&nbsp;Maged Gomaa Hemida","doi":"10.1016/j.meegid.2025.105723","DOIUrl":"10.1016/j.meegid.2025.105723","url":null,"abstract":"<div><div>Avian infectious bronchitis virus (AIBV) infection remains one of the significant challenges for the poultry industry due to the high rates of morbidity, mortality, and poor production performance. The AIBV genome is prone to frequent changes due to the possibility of drift and recombination between various genotypes. Despite the massive administration of several types of vaccines, many outbreaks of AIBV continue to be reported worldwide. One of the major goals of this study was to monitor genetic changes in the viral genomes of some recent field isolates of the AIBV from broiler chickens. To achieve these goals, we tested several pools of tissue specimens (trachea and kidneys) from some suspected AIBV outbreaks in broiler chickens by quantitative real-time PCR (q-RT-PCR). We selected two samples, one from the trachea (IBV-4) and one from the kidney (AIBV-6), for the next-generation sequencing (NGS). The full-length genomes of these two isolates were deposited in the GenBank (Accession Numbers: PQ468962 and PQ468963). The viral genome size of AIBV-4 and AIBV-6 was 27,475 and 27,469 nucleotides in length. AIBV-4 have typical AIBV genome organization (5’UTR, ORF1a, ORF1b, S, 3a, 3b, E, M, 4b, 5a, 5b, N, and 3’UTR), while AIBV-6 lack 5b. These two AIBV isolates belong to sublineage-1 of the genotype GI-1 based on the phylogenetic using the full-length, the S, and the N protein sequences. The S1/S2 cleavage sites show polybasic amino acid sequences (RR-F-RR) as direct evidence of virulence of these isolates. The analysis shows multiple recombination events of these isolates with some natural and vaccine strains. The potential major parent for both AIBV-4 and AIBV-6 was AIBV Beaudette. Active and vigilant monitoring of the AIBV sequences of the currently circulating strains in chickens is highly encouraged to help develop novel vaccines and diagnostic assays that match the field circulating strains.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"129 ","pages":"Article 105723"},"PeriodicalIF":2.6,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143076393","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":"Genome based characterization of Yersinia enterocolitica from different food matrices in Switzerland in 2024","authors":"Marc J.A. Stevens,&nbsp;Karen Barmettler,&nbsp;Lucien Kelbert,&nbsp;Roger Stephan,&nbsp;Magdalena Nüesch-Inderbinen","doi":"10.1016/j.meegid.2025.105719","DOIUrl":"10.1016/j.meegid.2025.105719","url":null,"abstract":"<div><div><em>Yersinia enterocolitica</em> causes food-borne gastroenteritis. However, little is known about the genetic diversity and pathogenic potential of <em>Y. enterocolitica</em> in different food commodities.</div><div>In this study, presumptive <em>Y. enterocolitica</em> strains were isolated from 32 of 100 pork samples, from 25 of 100 chicken meat samples, and from 22 of 97 produce samples (fresh herbs and salads), all collected at retail level in Switzerland in 2024. All isolates underwent whole-genome sequencing (WGS). One isolate was re-classified as <em>Y. hibernica</em>. Three strains belonged to biotype (BT) 4, all from pork, and 86 strains to BT 1A. The isolates belonged to 45 sequence types (STs). A total of 76 putative plasmids were detected. Each BT 4 isolate carried a pYV-like plasmid harbouring 44 virulence factors (VFs). Plasmids from the same type were identified in different ST, showing that genetic exchange between ST occurs. Twelve isolates from poultry meat carried plasmids harbouring the <em>msrAB</em> operon which is linked to oxidative stress tolerance. Nine isolates from pork and poultry meat contained plasmids carrying the <em>cag</em> pathogenicity island associated with cytotoxicity, and four isolates from produce carried plasmids harbouring a heat labile enterotoxin. None of the isolates harboured plasmid-mediated antimicrobial resistance (AMR) genes. <em>Y. enterocolitica</em> BT 4 (<em>n</em> = 3) and BT 1A (n = 3) were clonal to <em>Y. enterocolitica</em> previously isolated from Swiss human cases.</div><div>Our data provide valuable insights into the occurrence and genomic characteristics of <em>Y. enterocolitica</em> in food, their relatedness to human strains, and their adaptation to food matrices.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"128 ","pages":"Article 105719"},"PeriodicalIF":2.6,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143069742","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":"Assessing the potential role of deer in the dissemination of Mycobacterium bovis infection to cattle in Northern Ireland","authors":"Adrian Allen ,&nbsp;Siobhán Porter ,&nbsp;David McCleery ,&nbsp;Purnika Damindi Ranasinghe ,&nbsp;Ryan Devaney ,&nbsp;Tara Ardis ,&nbsp;Maggie Lyons ,&nbsp;Donald Whiteside ,&nbsp;Christopher Corrigan ,&nbsp;Carl McCormick ,&nbsp;Eleanor Presho ,&nbsp;Clare Holmes ,&nbsp;Jim McCarthy ,&nbsp;Dale Decena ,&nbsp;Michael Doyle ,&nbsp;Josh Montgomery ,&nbsp;Sophie Redpath ,&nbsp;Suzan Thompson ,&nbsp;Lorraine Wright ,&nbsp;Kerri Jones ,&nbsp;Robin Skuce","doi":"10.1016/j.meegid.2025.105721","DOIUrl":"10.1016/j.meegid.2025.105721","url":null,"abstract":"<div><div><em>Mycobacterium bovis</em>, the causative agent of animal tuberculosis, exhibits a broad host range - infecting, inducing pathology and transmitting from both bovine and wildlife hosts. Considerable effort has been extended to understanding the role wildlife may play in persistence and spread of infection.</div><div>Infected cervids can spread infection to conspecifics and sympatric livestock as observed in the white-tailed deer (<em>Odocoileus virginanus</em>) population of Michigan, USA. However, in other territories, there is debate about whether cervids act as maintenance or spillover hosts, with ecological contexts such as deer density and proximity to livestock likely to be key determinants. In Ireland, sika deer (<em>Cervus nippon</em>) populations in County Wicklow have been proposed to act as maintenance hosts, an observation at odds with the view that elsewhere on the island they are primarily spillover hosts.</div><div>In Northern Ireland, policy makers sought to understand the role cervids may be playing in the epidemiology of animal TB. A province wide cull of 522 deer, undertaken from 2019 to 2023, yielded 13 culture confirmed <em>M. bovis</em> isolates (animal prevalence 2.5 %). These were subjected to whole genome sequencing, alongside a further four archived isolates from deer and 190 from cattle to undertake a genome epidemiology study. Bayesian phylogenetic methods of birth death skyline and structured coalescent analyses were applied to track epidemic progression and estimate raw counts and rates of <em>M. bovis</em> transmission withing and between cattle and deer. Findings were consistent with the main driver of disease transmission detected being infected cattle, with deer playing a smaller role.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"128 ","pages":"Article 105721"},"PeriodicalIF":2.6,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143069737","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 variations underlying aminoglycoside resistance in antibiotic-induced Mycobacterium intracellulare mutants","authors":"Hyun-Eui Park ,&nbsp;Jeong-Ih Shin ,&nbsp;Kyu-Min Kim ,&nbsp;Jeong-Gyu Choi ,&nbsp;Won Jun Anh ,&nbsp;Minh Phuong Trinh ,&nbsp;Kyeong-Min Kang ,&nbsp;Jung-Hyun Byun ,&nbsp;Jung-Wan Yoo ,&nbsp;Hyung-Lyun Kang ,&nbsp;Seung-Chul Baik ,&nbsp;Woo-Kon Lee ,&nbsp;Myunghwan Jung ,&nbsp;Min-Kyoung Shin","doi":"10.1016/j.meegid.2025.105716","DOIUrl":"10.1016/j.meegid.2025.105716","url":null,"abstract":"<div><div><em>Mycobacterium avium</em> complex (MAC) is an emerging pathogen leading to public health concerns in developing and developed countries, particularly among immunocompromised individuals and patients with structural lung diseases. Current clinical guidelines recommend combination antibiotic therapy for treating MAC pulmonary disease (MAC-PD). However, the rising prevalence of antibiotic resistance poses significant challenges, including treatment failure and clinical recurrence. A deeper understanding of the mechanisms underlying MAC antibiotic resistance is essential to improve treatment outcomes. This study investigates the genetic variations associated with aminoglycoside resistance in an antibiotic-induced <em>Mycobacterium intracellulare</em> mutant derived from a clinical strain. Whole-genome analysis identified seven mutations in the aminoglycoside-resistant mutant, including single nucleotide polymorphisms (SNPs) and insertions/deletions (InDels). Key genetic alterations included a frameshift variant in a gene encoding a secreted protein antigen, missense mutations in <em>rpsL</em> and <em>rsmG</em>, and synonymous and in-frame deletion variants in <em>srfAB</em> and <em>mtrB</em>, respectively. These findings highlight the complex genetic landscape of aminoglycoside resistance in <em>M. intracellulare</em>. Understanding these resistance determinants provides valuable insights for developing diagnostic tools to detect drug-resistant MAC strains and optimizing therapeutic strategies for managing MAC infections in clinical practice.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"128 ","pages":"Article 105716"},"PeriodicalIF":2.6,"publicationDate":"2025-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143016193","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":"Revealing a novel GI-19 lineage infectious bronchitis virus sub-genotype with multiple recombinations in South Korea using whole-genome sequencing","authors":"Ji-Ye Kim ,&nbsp;Hoang Duc Le ,&nbsp;Tuyet Ngan Thai ,&nbsp;Jae-Kyeom Kim ,&nbsp;Hye-Soon Song ,&nbsp;Moon Her ,&nbsp;Hye-Ryoung Kim","doi":"10.1016/j.meegid.2025.105717","DOIUrl":"10.1016/j.meegid.2025.105717","url":null,"abstract":"<div><div>Infectious bronchitis (IB), caused by the infectious bronchitis virus (IBV), is a highly contagious chicken disease, causing economic losses worldwide. New IBV strains and variants continue to emerge despite using inactivated and live-attenuated vaccines to prevent or control IB. In this study, the S1 genes of 46 IBV strains, isolated from commercial chicken flocks between 2003 and 2024 in Korea were sequenced and genetically characterized. The IBV isolates belonged to Korean group II (K-II), which was included in the GI-19 lineage. The K-II was divided into five sub-genogroups (a–e) based on phylogenetic tree analysis results and nucleotide identification of the S1 gene. Of these, K-IId was the most common genotype in Korea; however, eight novel isolates belonging to the K-IIe sub-genotype were discovered. The nucleotide and amino acid identities of the other four K-II sub-genotypes and the eight isolates were 84.42–95.89 % and 84.02–95.86 %, respectively. The complete genomes of the eight K-IIe isolates were obtained using next-generation sequencing. Various recombination patterns were observed despite the high homology of the S1 gene among the eight IBV strains. Among the eight K-IIe isolates, six were recombinants, exhibiting recombinations between K-IIe and K-IIc, K-IIe and K-IIa, and with the live vaccine strain. Most recombination breakpoints were detected in the nsp2 region of the ORF1a, S2, and M genes. The present study proposed new classification criteria for the K-II belonged to the GI-19 lineage prevalent in South Korea and revealed the recombination patterns of recently identified novel isolates, providing important information on novel viral sub-genotype strains and IBV evolution.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"128 ","pages":"Article 105717"},"PeriodicalIF":2.6,"publicationDate":"2025-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143016195","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":"Considerable genetic diversity within Paragonimus heterotremus in Luang Prabang, northern Lao People's Democratic Republic","authors":"Alongkorn Nonthapa ,&nbsp;Rutchanee Rodpai ,&nbsp;Tongjit Thanchomnang ,&nbsp;Patcharaporn Boonroumkaew ,&nbsp;Lakkhana Sadaow ,&nbsp;David Blair ,&nbsp;Pewpan M. Intapan ,&nbsp;Wanchai Maleewong ,&nbsp;Virasack Banouvong ,&nbsp;Sakhone Laymanivong ,&nbsp;Oranuch Sanpool","doi":"10.1016/j.meegid.2025.105718","DOIUrl":"10.1016/j.meegid.2025.105718","url":null,"abstract":"<div><div>Paragonimiasis, caused by infection with lung flukes of the genus <em>Paragonimus</em>, remains a significant public health concern in Southeast Asia. In Lao People's Democratic Republic (Lao PDR), information on the distribution and genetic diversity of <em>Paragonimus</em> species is limited. This study investigated <em>Paragonimus</em> metacercariae in freshwater (mountain) crabs and analyzed their genetic diversity and phylogenetic relationships. Thirty-six crabs (<em>Indochinamon</em> sp.) were received from Xiang Ngeun and Pak Ou in Luang Prabang Province, northern Lao PDR. Partial mitochondrial 16S rRNA sequences obtained from four crabs indicated a moderately close relationship with <em>Indochinamon ou.</em> A total of 81 metacercariae identified morphologically as <em>Paragonimus heterotremus</em> were found among 13 out of the 32 crabs dissected (40.6 %). Molecular analyses targeting the ribosomal ITS2 region and mitochondrial cytochrome <em>c</em> oxidase subunit 1 (<em>cox1</em>) gene were conducted on these metacercariae. Phylogenetic analyses revealed that <em>P. heterotremus</em> sequences from Lao PDR clustered with those from neighboring countries—China, Myanmar, Vietnam and Thailand—suggesting potential genetic connectivity among eastern Asian populations. Haplotype-network analysis demonstrated significant genetic diversity within <em>P. heterotremus</em> populations from Lao PDR, separating into two distinct haplotype groups, one of which was unique to this study. This is the first report that <em>Indochinamon</em> sp. crabs serve as key intermediate host for a member of the <em>P. heterotremus</em> complex in Luang Prabang Province and highlights the parasite's genetic diversity in this region.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"128 ","pages":"Article 105718"},"PeriodicalIF":2.6,"publicationDate":"2025-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143016035","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":"Molecular ecology of novel amdoparvoviruses and old protoparvoviruses in Spanish wild carnivorans","authors":"Marta Canuti ,&nbsp;Francesco Mira ,&nbsp;Diego Villanúa ,&nbsp;Ruth Rodríguez-Pastor ,&nbsp;Annalisa Guercio ,&nbsp;Fermín Urra ,&nbsp;Javier Millán","doi":"10.1016/j.meegid.2025.105714","DOIUrl":"10.1016/j.meegid.2025.105714","url":null,"abstract":"<div><div>Wild carnivorans are key hosts of parvoviruses of relevance for animal health and wildlife conservation. However, the distribution and diversity of parvoviruses among wild carnivorans are under-investigated, particularly in Southern Europe. We evaluated the presence, spread, and diversity of multi-host protoparvoviruses (canine parvovirus type 2 (CPV-2), feline panleukopenia virus (FPV)), and amdoparvoviruses in 12 carnivoran species from Northern Spain to explore viral ecology. Broad-range PCRs were used to screen spleens (<em>N</em> = 157) and intestines (<em>N</em> = 116) from 171 road-killed mustelids, viverrids, and felids; identified viruses were molecularly characterized. We detected an Asian-like CPV-2c strain in the spleen of one wildcat (<em>Felis silvestris</em>, 1/40, 2.5 %), a globally distributed FPV strain in the spleen of one Eurasian badger (<em>Meles meles</em>, 1/35, 2.9 %), a novel amdoparvovirus (European mustelid amdoparvovirus 1), in the intestine and spleen of one stone marten (<em>Martes foina</em>, 1/16, 6.3 %) and in the spleen of one Eurasian badger (1/35, 2.9 %), the red fox fecal amdovirus (RFFAV) in the intestine and spleen of three wildcats (3/40, 7.5 %), and a novel amdoparvovirus closely related to RFFAV (European felid amdoparvovirus 1) in one wildcat (1/40, 2.5 %). We observed a correlation between the phylogeny of carnivorans and the one of amdoparvoviruses, possibly indicating virus-host co-evolution. Species originating from North America and Eurasia formed different clades, indicating local segregation in the absence of man-linked transboundary movements. In contrast, CPV-2 and FPV strains were internationally dispersed. Different parvovirus species co-occur in sympatric host populations, and higher viral diversity and additional hosts will likely be identified in future studies.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"128 ","pages":"Article 105714"},"PeriodicalIF":2.6,"publicationDate":"2025-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142985511","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":"Genotypic and phenotypic diversity of Mycobacterium tuberculosis strains from eastern India","authors":"Arup Ghosh ,&nbsp;Viplov Kumar Biswas ,&nbsp;Himadri Bhusan Bal ,&nbsp;Dasarathi Das ,&nbsp;Sanghmitra Pati ,&nbsp;Bhawna Gupta ,&nbsp;Sunil Kumar Raghav","doi":"10.1016/j.meegid.2025.105713","DOIUrl":"10.1016/j.meegid.2025.105713","url":null,"abstract":"<div><div>Whole genome sequencing has been used to investigate the genomic diversity of <em>M. tuberculosis</em> in the northern and southern states of India, but information about the eastern part of the country is still limited. Through a sequencing-based strategy, this study seeks to comprehend the diversity and drug resistance pattern in the eastern region. A total of 102 <em>M. tuberculosis</em> isolates from North East (<em>n</em> = 54), and Odisha (<em>n</em> = 48) were sequenced along with 7 follow up isolates from Sikkim. The pre-XDR and XDR isolates diagnosed as per the NTEP diagnostic algorithm were subjected for phenotypic second-line liquid culture drug susceptibility testing in MGIT-960 system. After filtering out low quality isolates based on taxonomic classification and depth of coverage, variant calling was performed. We observed a high prevalence of multi-drug resistant TB (MDR-TB) lineage 2 (52/54) isolates in northeast whereas there was a mixed representation of lineage 1 (30/48) &amp; lineage 3 (11/48) in Odisha. The MDR-TB isolates from Sikkim posed a high rate (51/53) of fluoroquinolone resistance and pairwise SNV distances (≤10) indicating possible local transmission events in the region. We observed occurrence of genetic variations in genes associated with bedaquiline and delamanid resistance. Our findings show the diversity of <em>M. tuberculosis</em> vary across the eastern regions, in north eastern states lineage 2 has a dominant presence while lineage 1 and 3 has mixed representation in Odisha. The high prevalence of fluoroquinolone resistance in north eastern region associated with variations in <em>gyrA</em> gene and may have been caused by local transmission events based on genomic similarities.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"128 ","pages":"Article 105713"},"PeriodicalIF":2.6,"publicationDate":"2025-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142973323","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}