Infection Genetics and Evolution最新文献

{"title":"Further evidence of low infection frequencies of Wolbachia in soil arthropod communities","authors":"Marta Tischer,&nbsp;Christoph Bleidorn","doi":"10.1016/j.meegid.2024.105641","DOIUrl":"10.1016/j.meegid.2024.105641","url":null,"abstract":"<div><p>Endosymbiotic Alphaproteobacteria of the genus <em>Wolbachia</em> are exclusively transferred maternally from mother to offspring, but horizontal transfer across species boundaries seems to be frequent as well. However, the (ecological) mechanisms of how these bacteria are transferred between distantly related arthropod hosts remain unclear. Based on the observation that species that are part of the same ecological community often also share similar <em>Wolbachia</em> strains, host ecology has been hypothesized as an important factor enabling transmission and a key factor in explaining the global distribution of <em>Wolbachia</em> lineages.</p><p>In this study, we focus on the diversity and abundance of <em>Wolbachia</em> strains in soil arthropods, a so far rather neglected community. We screened 82 arthropod morphotypes collected in the beech forest (dominated by <em>Fagus</em> sp.) soil in the area of Göttingen in central Germany for the presence of <em>Wolbachia</em>. By performing a PCR screen with <em>Wolbachia-</em>MLST markers (<em>coxA</em>, <em>dnaA</em>, <em>fbpA</em>, <em>ftsZ</em>, <em>gatB</em>, and <em>hcpA</em>), we found a rather low infection frequency of 12,2%. Additionally, we performed metagenomic screening of pooled individuals from the same sampling site and could not find evidence that this low infection frequency is an artefact due to PCR-primer bias. Phylogenetic analyses of the recovered <em>Wolbachia</em> strains grouped them in three known supergroups (A, B, and E), with the first report of <em>Wolbachia</em> in Protura (Hexapoda). Moreover, <em>Wolbachia</em> sequences from the pseudoscorpion <em>Neobisium carcinoides</em> cluster outside the currently known supergroup diversity. Our screening supports results from previous studies that the prevalence of <em>Wolbachia</em> infections seems to be lower in soil habitats than in above-ground terrestrial habitats. The reasons for this pattern are not completely understood but might stem from the low opportunity of physical contact and the prevalence of supergroups that are less suited for horizontal transfer.</p></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"123 ","pages":"Article 105641"},"PeriodicalIF":2.6,"publicationDate":"2024-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1567134824000923/pdfft?md5=ddd3834821a514e4d7ae9d116c968cc2&pid=1-s2.0-S1567134824000923-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141617684","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":"Whole genome sequencing and genomic characteristics analysis of carbapenem-resistant Acinetobacter baumannii clinical isolates in two hospitals in China","authors":"Chongmei Tian ,&nbsp;Lingfang Di ,&nbsp;Su Dong ,&nbsp;Xuebin Tian ,&nbsp;Delian Huang ,&nbsp;Yaping Zhao ,&nbsp;Jingbai Chen ,&nbsp;Daozong Xia ,&nbsp;Siwei Wang","doi":"10.1016/j.meegid.2024.105642","DOIUrl":"10.1016/j.meegid.2024.105642","url":null,"abstract":"<div><p>Nosocomial outbreaks caused by carbapenem-resistant <em>Acinetobacter baumannii</em> (CRAB) strains are rapidly emerging worldwide and are cause for concern. Herein, we aimed to describe the genomic characteristics of CRAB strains isolated from two hospitals in China in 2023. The <em>A. baumannii</em> isolates were mainly collected from the ICU and isolated from the sputum (71.43%, 15/21), followed by urine (14.29%, 3/21). Twenty-one <em>A. baumannii</em> strains possessed a multidrug-resistant (MDR) profile, and whole-genome sequencing showed that they all carried <em>bla</em>_OXA-23. Based on the Pasteur multilocus sequence typing (MLST) scheme, all strains were typed into a sequence type 2 (ST2). Based on the Oxford MLST scheme, six strains belonged to ST540, three of which were ST208, and four strains were assigned to ST784. <em>Kaptive</em> showed most of the strains (38.10%, 8/21) contained KL93. As for the lipoolygosaccharide (OC locus) type, OCL1c and OCL1d were identified, accounting for 33.33% (7/21) and 66.67% (14/21), respectively. Based on the BacWGSTdb server, we found that the strains belonging to ST540 and ST784 were all collected from China. However, the ST938 strains were isolated from Malaysia and Thailand. Comparative genomics analysis showed that the AB10 strain had a closed relationship with SXAB10-SXAB13 strains, suggesting the transmission happened in these two hospitals and other hospital in China. In addition, the 4300STDY7045869 strain, which was collected from Thailand, possessed near genetic relationship with our isolates in this study, suggesting the possible spread among various countries. Additionally, 3–237 single nucleotide polymorphisms were observed among these strains. In conclusion, this study conducted a genome-based study for <em>A. baumannii</em> strains collected from two hospitals in China and revealed their epidemiological and molecular features. Clone spreading occurred in these two hospitals. Hence, there is an urgent need for increased surveillance in hospitals and other clinical settings to prevent and control CRAB spreading.</p></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"123 ","pages":"Article 105642"},"PeriodicalIF":2.6,"publicationDate":"2024-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1567134824000935/pdfft?md5=5f3eaccce3ac822fb856bf2a9ad42c5c&pid=1-s2.0-S1567134824000935-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141629322","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":"Comprehensive genomics reveals novel sequence types of multidrug resistant Klebsiella oxytoca with uncharacterized capsular polysaccharide K- and lipopolysaccharide O-antigen loci from the National Hospital of Uganda","authors":"Reuben S. Maghembe ,&nbsp;Maximilian A.K. Magulye ,&nbsp;Abdalah Makaranga ,&nbsp;Edward Moto ,&nbsp;Simon Sekyanzi ,&nbsp;Savannah Mwesigwa ,&nbsp;Eric Katagirya","doi":"10.1016/j.meegid.2024.105640","DOIUrl":"10.1016/j.meegid.2024.105640","url":null,"abstract":"<div><p>The <em>Klebsiella oxytoca</em> complex comprises diverse opportunistic bacterial pathogens associated with hospital and community-acquired infections with growing alarming antimicrobial resistance. We aimed to uncover the genomic features underlying the virulence and antimicrobial resistance of isolates from Mulago National Hospital in Uganda. We coupled whole genome sequencing with Pathogenwatch multilocus sequence typing (MLST) and downstream bioinformatic analysis to delineate sequence types (STs) capsular polysaccharide K- and O-antigen loci, along with antimicrobial resistance (AMR) profiles of eight clinical isolates from the National Referral Hospital of Uganda. Our findings revealed that only two isolates (RSM6774 and RSM7756) possess a known capsular polysaccharide K-locus (KL74). The rest carry various unknown K-loci (KL115, KL128, KLI52, KL161 and KLI63). We also found that two isolates possess unknown loci for the lipopolysaccharide O-antigen (O1/O2v1 type OL104 and unknown O1). The rest possess known O1 and O3 serotypes. From MLST, we found four novel sequence types (STs), carrying novel alleles for the housekeeping genes glyceraldehyde-6-phosphate dehydrogenase A (<em>gapA</em>), glucose-6-phosphate isomerase (<em>pgi</em>), and RNA polymerase subunit beta (<em>rpoB</em>). Our AMR analysis revealed that all the isolates are resistant to ampicillin and ceftriaxone, with varied resistance to other antibiotics, but all carry genes for extended-spectrum beta-lactamases (ESBLs). Notably, one strain (RSM7756) possesses outstanding chromosomal and plasmid-encoded AMR to beta-lactams, cephalosporins, fluoroquinolones and methoprims. Conclusively, clinical samples from Mulago National Referral Hospital harbor novel STs and multidrug resistant <em>K. oxytoca</em> strains, with significant public health importance, which could have been underrated.</p></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"123 ","pages":"Article 105640"},"PeriodicalIF":2.6,"publicationDate":"2024-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1567134824000911/pdfft?md5=892922c7f600040e36d1bb7a348c2e5d&pid=1-s2.0-S1567134824000911-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141604573","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":"Ecological and evolutionary dynamics of CRISPR-Cas systems in Clostridium botulinum: Insights from genome mining and comparative analysis","authors":"Naiymeh Sheykholeslami ,&nbsp;Hamid Mirzaei ,&nbsp;Yousef Nami ,&nbsp;Jalil Khandaghi ,&nbsp;Afshin Javadi","doi":"10.1016/j.meegid.2024.105638","DOIUrl":"10.1016/j.meegid.2024.105638","url":null,"abstract":"<div><p>Understanding the prevalence and distribution of CRISPR-Cas systems across different strains can illuminate the ecological and evolutionary dynamics of <em>Clostridium botulinum</em> populations. In this study, we conducted genome mining to characterize the CRISPR-Cas systems of <em>C. botulinum</em> strains. Our analysis involved retrieving complete genome sequences of these strains and assessing the diversity, prevalence, and evolution of their CRISPR-Cas systems. Subsequently, we performed an analysis of homology in spacer sequences from identified CRISPR arrays to investigate and characterize the range of targeted phages and plasmids. Additionally, we investigated the evolutionary trajectory of <em>C. botulinum</em> strains under selective pressures from foreign invasive DNA. Our findings revealed that 306 strains possessed complete CRISPR-Cas structures, comprising 58% of the studied <em>C. botulinum</em> strains. Secondary structure prediction of consensus repeats indicated that subtype II-C, with longer stems compared to subtypes I<img>D and I<img>B, tended to form more stable RNA secondary structures. Moreover, protospacer motif analysis demonstrated that strains with subtype I<img>B CRISPR-Cas systems exhibited 5′-CGG-3′, 5′-CC-3′, and 5′-CAT-3′ motifs in the 3′ flanking regions of protospacers. The diversity observed in CRISPR-Cas systems indicated their classification into subtypes I<img>B, I<img>D, II-C, III-B, and III-D. Furthermore, our results showed that systems with subtype I<img>D and III-D frequently harbored similar spacer patterns. Moreover, analysis of spacer sequences homology with phage and prophage genomes highlighted the specific activities exhibited by subtype I<img>B and III-B against phages and plasmids, providing valuable insights into the functional specialization within these systems.</p></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"123 ","pages":"Article 105638"},"PeriodicalIF":2.6,"publicationDate":"2024-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1567134824000893/pdfft?md5=85d8f5ba2afb6494ab5dc8b9ea3fe7e0&pid=1-s2.0-S1567134824000893-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141604574","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":"Spatio-temporal analysis of genetic diversity of merozoite surface protein-3 alpha in Myanmar Plasmodium vivax isolates","authors":"Tuấn Cường Võ ,&nbsp;Jung-Mi Kang ,&nbsp;Hương Giang Lê ,&nbsp;Haung Naw ,&nbsp;Tong-Soo Kim ,&nbsp;Ho-Joon Shin ,&nbsp;Moe Kyaw Myint ,&nbsp;Zaw Than Htun ,&nbsp;Byoung-Kuk Na","doi":"10.1016/j.meegid.2024.105639","DOIUrl":"10.1016/j.meegid.2024.105639","url":null,"abstract":"<div><p>Myanmar aims to eliminate malaria by 2030. However, recent increase of malaria incidence is a great challenge to archive that goal. Increasing prevalence of <em>Plasmodium vivax</em> also hinders this endeavor. Monitoring genetic structure of the parasite is necessary to understand genetic nature and evolutionary aspect of <em>P. vivax</em> population in Myanmar. Partial fragment flanking blocks I and II of merozoite surface protein-3 alpha of <em>P. vivax</em> (<em>pvmsp-3α</em>) was amplified from <em>P. vivax</em> isolates collected in Pyin Oo Lwin, Mandalay Region, Myanmar in 2013–2015. Sequence analysis of <em>pvmsp-3α</em> was performed to determine genetic diversity and natural selection of this gene. Spatio-temporal genetic changes of <em>pvmsp-3α</em> in Myanmar <em>P. vivax</em> population were also investigated via comparative analysis of gene sequences obtained in this study and previously reported Myanmar <em>pvmsp-3α</em> sequences. Genetic diversity of Myanmar <em>pvmsp-3α</em> was detected in <em>P. vivax</em> isolates analyzed. Size polymorphisms in block I and amino acid changes and recombination events in block II were main factors contributing to the genetic diversity of <em>pvmsp-3α</em>. Comparative spatio-temporal analysis with previously reported Myanmar <em>pvmsp-3α</em> populations revealed the presence of genetic differences by population with moderate genetic differentiation between populations. Similar pattern of natural selection was also detected in Myanmar <em>pvmsp-3α</em> populations. These suggested that enough size of the <em>P. vivax</em> population sufficient to generate or maintain the genetic diversity remains in the population. Thus, continuous molecular surveillance of genetic structure of Myanmar <em>P. vivax</em> is necessary.</p></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"123 ","pages":"Article 105639"},"PeriodicalIF":2.6,"publicationDate":"2024-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S156713482400090X/pdfft?md5=dee5bb5d50f434f234a099a0450eb647&pid=1-s2.0-S156713482400090X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141602203","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":"Analysis of viral diversity in dogs with acute gastroenteritis from Brazilian Amazon","authors":"Danielle Rodrigues de Deus ,&nbsp;Jones Anderson Monteiro Siqueira ,&nbsp;Marcelino Antonio Costa Maués ,&nbsp;Márcia Janete de Fátima Mesquita de Figueiredo ,&nbsp;Edivaldo Costa Sousa Júnior ,&nbsp;Renato da Silva Bandeira ,&nbsp;Kenny da Costa Pinheiro ,&nbsp;Dielle Monteiro Teixeira ,&nbsp;Luciana Damascena da Silva ,&nbsp;Sylvia de Fátima dos Santos Guerra ,&nbsp;Luana da Silva Soares ,&nbsp;Yvone Benchimol Gabbay","doi":"10.1016/j.meegid.2024.105637","DOIUrl":"10.1016/j.meegid.2024.105637","url":null,"abstract":"<div><p>Viral gastroenteritis is commonly reported in dogs and involves a great diversity of enteric viruses. In this research, viral diversity was investigated in dogs with diarrhea in Northern Brazil using shotgun metagenomics. Furthermore, the presence of norovirus (NoV) was investigated in 282 stool/rectal swabs of young/adult dogs with or without diarrhea from two public kennels, based on one-step reverse transcription polymerase chain reaction (RT-PCR) for genogroup VI and VII (GVI and GVII) and real-time RT-PCR for GI, GII, and GIV. Thirty-one viral families were identified, including bacteriophages. Phylogenetic analyses showed twelve complete or nearly complete genomes belonging to the species of <em>Protoparvovirus carnivoran1</em>, <em>Mamastrovirus 5</em>, <em>Aichivirus A2</em>, <em>Alphacoronavirus 1,</em> and <em>Chipapillomavirus 1</em>. This is the first description of the intestinal virome of dogs in Northern Brazil and the first detection of canine norovirus GVII in the country. These results are important for helping to understand the viral groups that circulate in the canine population.</p></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"123 ","pages":"Article 105637"},"PeriodicalIF":2.6,"publicationDate":"2024-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1567134824000881/pdfft?md5=56d78ea07ebdf750299f44ba4c9b02bb&pid=1-s2.0-S1567134824000881-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141581563","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":"Emergence of mcr-4.3 genes in a novel Shewanella specie isolated from the Arctic environment","authors":"","doi":"10.1016/j.meegid.2024.105636","DOIUrl":"10.1016/j.meegid.2024.105636","url":null,"abstract":"<div><p>Mobile colistin resistance (<em>mcr</em>) genes are pivotal contributors to last-line of antimicrobial resistance in human infections. <em>Shewanella</em>, historically recognized as a natural environmental bacterium with metal reduction capabilities, recently has been observed in clinical settings. However, limited knowledge has been explored on genetic differences between strains from non-clinical and clinical strains. In this study, we conducted the whole genome sequencing on six Arctic strains, illustrated the phylogenetic relationships on published 393 <em>Shewanella</em> strains that categorized the genus into four lineages (L1 to L4). Over 86.4% of clinical strain group (CG) strains belonged to L1 and L4, carrying <em>mcr-4</em> genes and a complete metal-reduction pathways gene cluster. Remarkably, a novel Arctic <em>Shewanella</em> strain in L3, exhibits similar genetic characteristics with CG strains that carried both <em>mcr-4</em> genes and a complete metal reduction pathway gene cluster. It raised concerns about the transmission ability from environment to clinic setting causing in the potential infections, and emphasized the need for monitoring the emerging strains with human infections.</p></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"123 ","pages":"Article 105636"},"PeriodicalIF":2.6,"publicationDate":"2024-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S156713482400087X/pdfft?md5=c9a88ec8d86edeccffb3931b3a49ed19&pid=1-s2.0-S156713482400087X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141555998","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 epidemiology of Brucella abortus isolated from the environment in Ningxia Hui autonomous region, China","authors":"Cong Yang ,&nbsp;Jianwei Gao ,&nbsp;Ran Xian ,&nbsp;Xiang Liu ,&nbsp;Wenhe Kuai ,&nbsp;Cai Yin ,&nbsp;Haohao Fan ,&nbsp;Jinhua Tian ,&nbsp;Xueping Ma ,&nbsp;Jiangtao Ma","doi":"10.1016/j.meegid.2024.105635","DOIUrl":"10.1016/j.meegid.2024.105635","url":null,"abstract":"<div><p>Brucellosis is among the key zoonotic infectious diseases in China, and The Ningxia Hui Autonomous Region represents a major endemic area, and it is one of the main causes of poverty in the region due to illness. In Ningxia, there is substantial research on <em>Brucella melitensis,</em> studies on the molecular epidemiology of <em>Brucella abortus</em> are notably scarce. Consequently, this study aims to undertake pathogenic isolation and molecular epidemiological research on <em>Brucella abortus</em> isolated from the environment in Ningxia, providing insights and evidence to advance the prevention and control measures for brucellosis in the region. Building on traditional pathogenic detection methods, this research employs whole-genome sequencing(WGS) techniques and bioinformatics software to conduct a phylogenetic comparison of Ningxia strains and strains of <em>Brucella abortus</em> from various geographical origins. The results indicate that four <em>Brucella abortus</em> strains are classified as biovar 3 and MLST type ST2. It is shown that the local strains were closer phylogenetic relationships with strains from Asian and European countries. The presence of <em>Brucella abortus</em> in certain environmental sectors of Ningxia indicates a risk of transmission from the environment to animals and subsequently to humans. In conclusion, the <em>Brucella abortus</em> exists in some farming environments in Ningxia, and exists for a long time. Therefore, it is necessary to strengthen the monitoring of the disinfection effect of the farming environment to provide a basis for the forward movement of the gate of brucellosis prevention and control.</p></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"123 ","pages":"Article 105635"},"PeriodicalIF":2.6,"publicationDate":"2024-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1567134824000868/pdfft?md5=1d8db51af56db073a8715d8d0d6d1858&pid=1-s2.0-S1567134824000868-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141538987","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative genomics of canine parvovirus in South America: Diversification patterns in local populations","authors":"Sofía Grecco ,&nbsp;Emma Condon ,&nbsp;Danilo Bucafusco ,&nbsp;Ana Cristina Bratanich ,&nbsp;Yanina Panzera ,&nbsp;Ruben Pérez","doi":"10.1016/j.meegid.2024.105633","DOIUrl":"10.1016/j.meegid.2024.105633","url":null,"abstract":"<div><p>Canine parvovirus (CPV) is a significant pathogen in domestic dogs worldwide, causing a severe and often fatal disease. CPV comprises three antigenic variants (2a, 2b, and 2c) distributed unevenly among several phylogenetic groups. The present study compared genetic variability and evolutionary patterns in South American CPV populations. We collected samples from puppies suspected of CPV infection in the neighboring Argentina and Uruguay. Antigenic variants were preliminarily characterized using PCR-RFLP and partial vp2 sequencing. Samples collected in Argentina during 2008–2018 were mainly of the 2c variant. In the Uruguayan strains (2012–2019), the 2a variant wholly replaced the 2c from 2014. Full-length coding genome and vp2 sequences were compared with global strains. The 2c and 2a strains fell by phylogenetic analysis into two phylogroups (Europe I and Asia I). The 2c strains from Argentina and Uruguay clustered in the Europe I group, with strains from America, Europe, Asia, and Oceania. Europe I is widely distributed in South America in the dog population and is also being detected in the wildlife population. The 2a strains from Uruguay formed the distinct Asia I group with strains from Asia, Africa, America, and Oceania. This Asia I group is increasing its distribution in South America and worldwide. Our research reveals high genetic variability in adjacent synchronic samples and different evolutionary patterns in South American CPV. We also highlight the importance of ancestral migrations and local diversification in the evolution of global CPV strains.</p></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"123 ","pages":"Article 105633"},"PeriodicalIF":2.6,"publicationDate":"2024-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1567134824000844/pdfft?md5=5f31cd0ad7631c16311a2fca010edc55&pid=1-s2.0-S1567134824000844-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141538986","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":"Antibiotic resistance trends in high-risk lineages of Salmonella enterica serovar Typhi: A study spanning pre to post COVID-19 pandemic","authors":"Urooj Afreen Abro ,&nbsp;Shaista Bano ,&nbsp;Sarfraz Ali Tunio ,&nbsp;Shah Muhammad Abassi","doi":"10.1016/j.meegid.2024.105632","DOIUrl":"10.1016/j.meegid.2024.105632","url":null,"abstract":"<div><h3>Objectives</h3><p>The aim of this study was to understand the status of extensively drug-resistance (XDR) genotype in <em>Salmonella enterica</em> serotype Typhi (<em>S.</em> Typhi) recovered during the pre to post COVID-19 pandemic period using Multiplex PCR.</p></div><div><h3>Methods</h3><p>A longitudinal descriptive study was carried out during five years<em>.</em> Antibiotic susceptibility testing was performed according to the Clinical Laboratory Standards Institute antimicrobial susceptibility testing guidelines<em>.</em> The identification of <em>S.</em> T<em>yphi</em>, the detection of their high-risk lineages and XDR genotype was done using single nucleotide polymorphism-based multiplex PCR.</p></div><div><h3>Results</h3><p>A total of four hundred nine (<em>n</em> = 409) <em>S.</em> Typhi isolates were recovered during pre to post COVID-19 pandemic period. Among them, 30.81% belonged to the pre COVID-19 period while 69.19% to the post COVID-19 period. Different trends in antibiotic resistance in <em>S.</em> Typhi isolates with high prevalence of XDR-<em>S.</em> Typhi were observed. However, there was comparatively different frequency of their occurrence among the <em>S.</em> Typhi isolates recovered during pre to post COVID-19 pandemic period. Multiplex PCR showed that the majority of <em>S.</em> Typhi isolates were the H58 haplotype or genotype 4.3.1 which contained XDR genotype.</p></div><div><h3>Conclusions</h3><p>The increasing episodes of XDR-<em>S.</em> Typhi causing typhoid fever in endemic areas is alarming. The antibiotic resistance in food and water borne pathogens greatly contribute to the dissemination of the antimicrobial resistance in pathogenic bacteria, which has now been considered as a global concern.</p></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"123 ","pages":"Article 105632"},"PeriodicalIF":2.6,"publicationDate":"2024-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1567134824000832/pdfft?md5=406090682bb8c16a80969151cbf69895&pid=1-s2.0-S1567134824000832-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141535987","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}