Infection Genetics and Evolution最新文献

{"title":"The impact of infections and genetics on secondary sex ratio","authors":"Iasonas Dermitzakis ,&nbsp;Paschalis Theotokis ,&nbsp;Efthymia Delilampou ,&nbsp;Evangelos Axarloglou ,&nbsp;Chrysoula Gouta ,&nbsp;Maria Eleni Manthou ,&nbsp;Soultana Meditskou ,&nbsp;Dimosthenis Miliaras","doi":"10.1016/j.meegid.2025.105770","DOIUrl":"10.1016/j.meegid.2025.105770","url":null,"abstract":"<div><div>The secondary sex ratio (SSR), which reflects the proportion of male to female offspring at birth, is influenced by a complex interplay of multiple factors. This review delves into the current understanding of how infections and genetics contribute to variations in the SSR. The effects of infections on the SSR represent an intriguing intersection of biology and epidemiology. Research indicates that several infectious diseases, such as toxoplasmosis, coronavirus disease 2019, Spanish flu, acquired immunodeficiency syndrome and tuberculosis, can impact the SSR through mechanisms that are only partially understood. Genetics are also scrutinized in this review. Although their involvement in determining the SSR is debatable, various genetic factors have been studied. The influences of the Rhesus D heterozygous phenotype, major histocompatibility complex, corticosteroid-binding globulin deficiency, ethnicity, and consanguinity on SSR have been delineated. By amalgamating findings from diverse disciplines, this review aims to offer a comprehensive overview of the multifaceted impact of infections and genetics on SSR, pinpointing potential implications for reproductive biology and public health.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"132 ","pages":"Article 105770"},"PeriodicalIF":2.6,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144123994","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular characterization and genetic diversity of mumps virus genotype G in Pakistan during the 2023 outbreaks","authors":"Hina Fatima ,&nbsp;Muhammad Salman ,&nbsp;Zunera Jamal ,&nbsp;Rabia Hakim ,&nbsp;Massab Umair ,&nbsp;Javaria Qazi","doi":"10.1016/j.meegid.2025.105766","DOIUrl":"10.1016/j.meegid.2025.105766","url":null,"abstract":"<div><div>Mumps, despite being a vaccine-preventable disease, poses a significant public health challenge globally. In Pakistan, the absence of mumps vaccination in the national immunization program, coupled with limited epidemiological and surveillance data, presents a concerning scenario. This study investigates the molecular epidemiology of the Mumps virus (MuV) during the 2023 outbreaks, focusing on the genetic variability of the small hydrophobic (SH) gene, a key determinant for viral evolution and genotyping. Buccal swabs were collected from suspected patients presenting swollen parotid glands during the outbreak periods. Out of 62 mumps suspects, 40 (64.5 %) samples tested positive for MuV through RT-PCR. The incidence rate of positive cases was higher in males (70 %) than in females (30 %), with the highest incidence observed in early childhood (0–5 year-old) infants. Phylogenetic analysis revealed that all the specimens belonged to genotype G, with 97.4 % homology with genotype G of MuV isolates from Spain and up to 98.73 % with Japan, and UK. This research study underscores Pakistan's vulnerability to mumps outbreaks due to the absence of mumps vaccine in the national immunization program and highlights the need for effective surveillance systems for Mumps in the country.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"132 ","pages":"Article 105766"},"PeriodicalIF":2.6,"publicationDate":"2025-05-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144112980","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effect of large-scale population-based dietary change to vegetarianism on antimicrobial resistance and bacterial composition of sewage in Thailand","authors":"Pimlapas Leekitcharoenphon ,&nbsp;Valeria Bortolaia ,&nbsp;Viktor Karl Wilhelm Tornblom ,&nbsp;Achiraya Siriphap ,&nbsp;Orasa Suthienkul ,&nbsp;Jednipit Borthong ,&nbsp;Kaknokrat Chonsin ,&nbsp;Frederik Duus Møller ,&nbsp;Baptiste Avot ,&nbsp;Saria Otani ,&nbsp;Frank M. Aarestrup","doi":"10.1016/j.meegid.2025.105765","DOIUrl":"10.1016/j.meegid.2025.105765","url":null,"abstract":"<div><div>Antimicrobial resistance (AMR) is on one of the global priority challenges. This study explored the impact of diet alteration on AMR bacteria through metagenomic analysis during the annual vegetarian festival in Thailand in October 2019. The study investigated the effects of a 10-day shift from a regular to a vegetarian diet by collecting urban sewage from Nakhon Sawan, Surat Thani, and Bangkok before, during, and after the festival. Additionally, faecal samples from individuals in the northern city were analyzed. Using shotgun metagenomic sequencing, the samples were mapped against bacterial, AMR genes, and carbohydrate-active enzymes databases.</div><div>The results revealed significant changes in AMR gene abundance and increased carbohydrate metabolism genes in sewage samples from all three cities during the festival. There was also a notable shift in the composition and diversity of bacterial species, particularly in the northern city. The total abundance of AMR genes increased during the vegetarian festival across all locations. This study highlights the correlation between a population's vegetarian diet and increased AMR in Thailand. It also demonstrates that metagenomic analysis of sewage can effectively assess the impact of dietary changes on bacterial communities and AMR at a population level, providing valuable insights for public health strategies.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"132 ","pages":"Article 105765"},"PeriodicalIF":2.6,"publicationDate":"2025-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144103210","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-based alert on a clinical Plesiomonas shigelloides PSU59 from Thailand: Resistance and virulence features","authors":"Thunchanok Yaikhan ,&nbsp;Kamonnut Singkhamanan ,&nbsp;Thitaporn Dechathai ,&nbsp;Arnon Chukamnerd ,&nbsp;Sarunyou Chusri ,&nbsp;Rattanaruji Pomwised ,&nbsp;Monwadee Wonglapsuwan ,&nbsp;Komwit Surachat","doi":"10.1016/j.meegid.2025.105764","DOIUrl":"10.1016/j.meegid.2025.105764","url":null,"abstract":"<div><div><em>Plesiomonas shigelloides</em>, an aquatic Gram-negative bacterium, is increasingly recognized as an emerging pathogen with antimicrobial resistance (AMR) potential. This study provides a genome-based alert on <em>P. shigelloides</em> PSU59, isolated from a patient in Thailand. Whole-genome sequencing (WGS) revealed a 3.6 Mb draft genome (38 contigs, 51.9 % GC) encoding 3265 coding sequences and 129 RNA genes. Thirteen AMR genes were identified, including efflux pumps (<em>adeF</em>, <em>tet(A)</em>), target modifiers (<em>dfrA1</em>, <em>sul2</em>), and aminoglycoside-inactivating enzymes. Mobile genetic elements (MGEs) flanking resistance genes suggest horizontal gene transfer (HGT). Virulence analysis revealed 48 factors, notably flagellar genes (<em>fliM</em>, <em>fliN</em>, <em>flhA</em>) linked to motility. Phylogenetic comparison placed PSU59 in Clade 3, closely related to a food-derived strain. These results highlight the pathogenic and drug-resistant potential of <em>P. shigelloides</em> PSU59 and underscore the importance of genomic surveillance in tracking emerging threats among under-recognized pathogens.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"132 ","pages":"Article 105764"},"PeriodicalIF":2.6,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144089364","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Corrigendum to “Pathogens and drug resistance or virulence genes from animals and surrounding environment in Shenzhen, 2023 using targeted next-generation sequencing” [Infection, Genetics and Evolution, volume 131, 105755].","authors":"Dandan Niu ,&nbsp;Yankun Ke ,&nbsp;Qiuying Lv ,&nbsp;Zhen Zhang ,&nbsp;Tengyingzi Liu ,&nbsp;Zhongyao Xu ,&nbsp;Tong Li ,&nbsp;Yingluan Zhang ,&nbsp;Renli Zhang ,&nbsp;Xiaomin Zhang ,&nbsp;Shunping Cai ,&nbsp;Xiaonan You ,&nbsp;Yuqing Chen ,&nbsp;Hanguang Wu ,&nbsp;Yingxin Li ,&nbsp;Chan Yin ,&nbsp;Danzhu Wang ,&nbsp;Xinhua Duan ,&nbsp;Yongchao Guo ,&nbsp;Rongqi Liu ,&nbsp;Tiejian Feng","doi":"10.1016/j.meegid.2025.105759","DOIUrl":"10.1016/j.meegid.2025.105759","url":null,"abstract":"","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"131 ","pages":"Article 105759"},"PeriodicalIF":2.6,"publicationDate":"2025-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144071219","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characterisation of M. tuberculosis isolates obtained from Tamil Nadu prevalence survey by whole genome sequencing analysis","authors":"Priya Rajendran ,&nbsp;Prathiksha Giridaran ,&nbsp;Silla Varghese Thomas ,&nbsp;Navinkumar Nagaraj ,&nbsp;Kannan Thiruvengadam ,&nbsp;Golla Radhika ,&nbsp;Roja Samyuktha ,&nbsp;Sriram Selvaraju ,&nbsp;Asha Frederick ,&nbsp;Chandrasekaran Padmapriyadarsini ,&nbsp;Sivakumar Shanmugam","doi":"10.1016/j.meegid.2025.105763","DOIUrl":"10.1016/j.meegid.2025.105763","url":null,"abstract":"<div><div>Recent advances in whole genome sequencing have facilitated the understanding of drug resistance patterns and lineage distribution of <em>M. tuberculosis</em> worldwide. In this study, we aimed to determine the genetic diversity of MTB isolates from presumptive pulmonary TB patients obtained from a state prevalence survey. A total of 124 isolates were available for further characterisation, out of which 71 (57.2 %) and 47 (37.9 %) were subjected to sequencing and phenotypic DST, respectively. The phenotypic resistance profile revealed 3 isolates with multidrug resistance and 3 with mono-INH resistance. Out of 71 isolates, sequencing data were available for 61 (85.9 %), where the lineage distribution and drug resistance profile were analysed in comparison with phenotypic DST results. All the mutations were significant, accounting for one or the other resistance pattern. The concordance between pDST and gDST for the drugs was above 90 % except for ETH (77 %) and INH (87 %). The phylogenetic analysis of the lineage distribution revealed three clusters with MDR isolates belonging to lineage 1 and lineage 3. While lineage 2 is more frequently associated with MDR distribution both in India and worldwide, we did not find any lineage 2 MDR-TB isolates in our study. The use of WGS analysis improved our understanding of the genetic characteristics of MTB and its correlation with DR-TB transmission.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"132 ","pages":"Article 105763"},"PeriodicalIF":2.6,"publicationDate":"2025-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143947249","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular sequence typing of carbapenem-resistant Acinetobacter baumannii clinical isolates: A comprehensive global update","authors":"Kamonwan Taesoongnern ,&nbsp;Krit Thirapanmethee ,&nbsp;Mullika Traidej Chomnawang","doi":"10.1016/j.meegid.2025.105762","DOIUrl":"10.1016/j.meegid.2025.105762","url":null,"abstract":"<div><div>The emergence and spread of antimicrobial resistance (AMR) pose significant challenges to public health worldwide. Understanding the dynamics of AMR within bacterial populations is crucial for devising effective strategies to mitigate its impact. Clonal lineages, representing genetically related group of bacteria, play a vital role in shaping the landscape of AMR dissemination. This review endeavors to provide a comprehensive update on the molecular sequence typing of carbapenem-resistant <em>Acinetobacter baumannii</em> (CRAB) clinical isolates across various geographical regions, with particular emphasis on the application of multilocus sequence typing (MLST). CRAB poses a silent threat in healthcare settings, emerging as a public health concern globally corporate with limited treatment options due to the resistance to carbapenems, the last-line antibiotics, leading to increased mortality rates. This review will serve as invaluable resources, offering in-depth analysis and interpretation of epidemiological data related to CRAB. Through meticulous examination of this data, healthcare professionals will be equipped with a nuanced understanding of the spread and prevalence of this pathogen across diverse geographic regions. Additionally, by incorporating evidence-based strategies informed by epidemiological insights, stakeholders can enhance their ability to effectively combat this formidable pathogen, thereby safeguarding public health and promoting optimal patient outcomes.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"131 ","pages":"Article 105762"},"PeriodicalIF":2.6,"publicationDate":"2025-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143937503","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Emerging genetic diversity of Mycoplasma gallisepticum in Mexican house finches: Evidence of possible independent spillover events","authors":"María Teresa Reinoso-Pérez ,&nbsp;Luz Elena Díaz Ávila ,&nbsp;Santiago García Jacobo ,&nbsp;Víctor Manuel Rodríguez-García ,&nbsp;André A. Dhondt","doi":"10.1016/j.meegid.2025.105761","DOIUrl":"10.1016/j.meegid.2025.105761","url":null,"abstract":"<div><div>In a previous study, we reported for the first time the detection of <em>Mycoplasma gallisepticum</em> (MG) in Mexican house finches (<em>Haemorhous mexicanus</em>). Building on this finding, we explored the genetic diversity of MG, addressing the potential independent spillover events. Samples from 247 wild finches across Mexico revealed MG infection in 72 % of choanal swabs and 24 % of conjunctival swabs, with no clinical signs observed. Phylogenetic analysis identified two novel MG clades distinct from U.S. house finch-associated and poultry-associated MG strains, suggesting independent evolution within Mexico. Coinfections with diverse haplotypes were common, raising concerns about recombination and shifts in virulence. This research highlights the asymptomatic carrier state of Mexican house finches, their potential as reservoirs, and the ecological implications of pathogen spread and adaptation. These findings underscore the need for enhanced surveillance and further study on MG's dynamics in Mexican avifauna.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"132 ","pages":"Article 105761"},"PeriodicalIF":2.6,"publicationDate":"2025-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144040804","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A highly virulent BA-producing Burkholderia gladioli strain linked to a fatal foodborne outbreak in China, 2020","authors":"Jinrui Hu ,&nbsp;Yucheng Xue ,&nbsp;Jinhui Zhang ,&nbsp;Jinyue Liu ,&nbsp;Xiaohua Zheng ,&nbsp;Jing Bai ,&nbsp;Zhigang Cui ,&nbsp;Weiqi Zhong ,&nbsp;Haijian Zhou","doi":"10.1016/j.meegid.2025.105760","DOIUrl":"10.1016/j.meegid.2025.105760","url":null,"abstract":"<div><h3>Background</h3><div><em>Burkholderia gladioli,</em> particularly its pathovar <em>cocovenenans</em>, poses a significant public health threat through the production of bongkrekic acid (BA), a lethal tricarboxylic fatty acid encoded by the <em>bon</em> gene cluster. Despite the rarity of BA-associated outbreaks, historical cases in Asia and Mozambique demonstrate mortality rates exceeding 30 %.</div></div><div><h3>Methods</h3><div>In October 2020, a foodborne outbreak occurred in Heilongjiang, China, linked to homemade fermented corn. Nine symptomatic patients developed acute gastroenteritis within 3 h and died within 14 days. Routine pathogen screening, aflatoxin quantification, and toxicological analyses were performed. <em>B. gladioli</em> was isolated from contaminated corn flour, identified via VITEK 2 Compact and genomic sequencing. Antimicrobial susceptibility testing was conducted using the BD Phoenix system. Genomic analysis characterized the <em>bon</em> cluster, resistance genes, and phylogeny.</div></div><div><h3>Results</h3><div>BA concentrations reached 330.16 mg/kg in corn flour and 3.16 mg/L in gastric fluid. One strain YD01, was isolated from the corn flour sample. The isolate exhibited elevated MIC values for β-lactams (e.g., ceftazidime, aztreonam), nitrofurantoin, and colistin, but susceptibility to tetracycline and meropenem using 2024 CLSI breakpoints. Whole-genome sequencing confirmed a 67.5-kbp <em>bon</em> cluster homologous to BA-producing strains and identified antibiotic resistance genes (<em>smeR</em>, <em>smeE</em>, <em>mexB</em>, <em>LRA-1</em>, and <em>B. pseudomallei</em> omp38) associated with efflux pumps and β-lactamases. Phylogenetically, YD01 clustered with clinical <em>B. gladioli</em> strains from the United States (ANI 99.21 %).</div></div><div><h3>Conclusions</h3><div>This outbreak highlights the dual threat of hypervirulent BA production and intrinsic multidrug resistance in <em>B. gladioli</em>. The absence of CLSI breakpoints for this pathogen complicates clinical susceptibility interpretations, yet YD01's resistance profile suggests limited therapeutic options in empirical treatment. Enhanced surveillance, species-specific antimicrobial guidelines, and rapid diagnostics targeting both <em>bon</em> and resistance genes are urgently needed to mitigate future risks.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"131 ","pages":"Article 105760"},"PeriodicalIF":2.6,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143929166","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Emerging threat of Human Metapneumovirus (HMPV) and strategies for its containment and control","authors":"Sridevi Gnanasekaran ,&nbsp;MD. Abu Bashar ,&nbsp;Abin K. Rajan ,&nbsp;Prabhat Prabhat","doi":"10.1016/j.meegid.2025.105758","DOIUrl":"10.1016/j.meegid.2025.105758","url":null,"abstract":"<div><div>Human Metapneumovirus (HMPV) has emerged as a significant respiratory pathogen, particularly affecting children, the elderly, and immunocompromised individuals. Although HMPV is commonly associated with mild to moderate respiratory illness, its potential to cause severe disease has raised concerns and has alarmed the global public health. This review aims to provide an overview of the current understanding of HMPV epidemiology, pathogenesis, clinical manifestations, diagnostic approaches, and available therapeutic options. Furthermore, we discuss strategies for the containment of HMPV, including preventive measures, surveillance programs, and the development of vaccines and antiviral therapies, with a focus on the International Health Regulations (IHR) and pandemic preparedness activities.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"131 ","pages":"Article 105758"},"PeriodicalIF":2.6,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143922074","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}