Pub Date : 2024-07-05DOI: 10.1016/j.meegid.2024.105636
Mobile colistin resistance (mcr) genes are pivotal contributors to last-line of antimicrobial resistance in human infections. Shewanella, 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 Shewanella 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 mcr-4 genes and a complete metal-reduction pathways gene cluster. Remarkably, a novel Arctic Shewanella strain in L3, exhibits similar genetic characteristics with CG strains that carried both mcr-4 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.
{"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":null,"pages":null},"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}
Pub Date : 2024-07-03DOI: 10.1016/j.meegid.2024.105635
Cong Yang , Jianwei Gao , Ran Xian , Xiang Liu , Wenhe Kuai , Cai Yin , Haohao Fan , Jinhua Tian , Xueping Ma , Jiangtao Ma
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 Brucella melitensis, studies on the molecular epidemiology of Brucella abortus are notably scarce. Consequently, this study aims to undertake pathogenic isolation and molecular epidemiological research on Brucella abortus 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 Brucella abortus from various geographical origins. The results indicate that four Brucella abortus 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 Brucella abortus in certain environmental sectors of Ningxia indicates a risk of transmission from the environment to animals and subsequently to humans. In conclusion, the Brucella abortus 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.
{"title":"Molecular epidemiology of Brucella abortus isolated from the environment in Ningxia Hui autonomous region, China","authors":"Cong Yang , Jianwei Gao , Ran Xian , Xiang Liu , Wenhe Kuai , Cai Yin , Haohao Fan , Jinhua Tian , Xueping Ma , 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":null,"pages":null},"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}
Pub Date : 2024-07-03DOI: 10.1016/j.meegid.2024.105633
Sofía Grecco , Emma Condon , Danilo Bucafusco , Ana Cristina Bratanich , Yanina Panzera , Ruben Pérez
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.
犬细小病毒(CPV)是全球家犬的一种重要病原体,可导致严重的疾病,而且往往是致命的。CPV 包括三种抗原变体(2a、2b 和 2c),在几个系统发育群中分布不均。本研究比较了南美洲 CPV 群体的遗传变异和进化模式。我们从邻近的阿根廷和乌拉圭收集了疑似感染 CPV 的幼犬样本。利用 PCR-RFLP 和部分 vp2 测序初步确定了抗原变异的特征。2008-2018 年期间在阿根廷采集的样本主要是 2c 变异株。在乌拉圭的菌株中(2012-2019 年),2a 变种从 2014 年起完全取代了 2c。全长编码基因组和 vp2 序列与全球菌株进行了比较。通过系统发育分析,2c 和 2a 菌株分为两个系统群(欧洲 I 和亚洲 I)。来自阿根廷和乌拉圭的 2c 菌株与来自美洲、欧洲、亚洲和大洋洲的菌株归入欧洲 I 组。欧洲 I 型广泛分布于南美洲的狗群中,在野生动物群中也有发现。乌拉圭的 2a 株系与来自亚洲、非洲、美洲和大洋洲的株系组成了独特的亚洲 I 组。这个亚洲 I 组在南美洲和全球的分布日益扩大。我们的研究揭示了南美 CPV 相邻同步样本的高遗传变异性和不同的进化模式。我们还强调了祖先迁徙和局部多样化在全球 CPV 株系进化中的重要性。
{"title":"Comparative genomics of canine parvovirus in South America: Diversification patterns in local populations","authors":"Sofía Grecco , Emma Condon , Danilo Bucafusco , Ana Cristina Bratanich , Yanina Panzera , 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":null,"pages":null},"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}
Pub Date : 2024-07-02DOI: 10.1016/j.meegid.2024.105632
Urooj Afreen Abro , Shaista Bano , Sarfraz Ali Tunio , Shah Muhammad Abassi
Objectives
The aim of this study was to understand the status of extensively drug-resistance (XDR) genotype in Salmonella enterica serotype Typhi (S. Typhi) recovered during the pre to post COVID-19 pandemic period using Multiplex PCR.
Methods
A longitudinal descriptive study was carried out during five years. Antibiotic susceptibility testing was performed according to the Clinical Laboratory Standards Institute antimicrobial susceptibility testing guidelines. The identification of S. Typhi, the detection of their high-risk lineages and XDR genotype was done using single nucleotide polymorphism-based multiplex PCR.
Results
A total of four hundred nine (n = 409) S. 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 S. Typhi isolates with high prevalence of XDR-S. Typhi were observed. However, there was comparatively different frequency of their occurrence among the S. Typhi isolates recovered during pre to post COVID-19 pandemic period. Multiplex PCR showed that the majority of S. Typhi isolates were the H58 haplotype or genotype 4.3.1 which contained XDR genotype.
Conclusions
The increasing episodes of XDR-S. 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.
{"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 , Shaista Bano , Sarfraz Ali Tunio , 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":null,"pages":null},"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}
Pub Date : 2024-06-29DOI: 10.1016/j.meegid.2024.105634
Zu Ma, Qing Liu, Ming Wang, Yu-tong Du, Jing-wen Xie, Zi-ge Yi, Jing-hong Cai, Tong-yan Zhao, Heng-duan Zhang
Background
Aedes albopictus is an important vector of chikungunya, dengue, yellow fever and Zika viruses. Insecticides are often the most effective tools for rapidly decreasing the density of vector populations, especially during arbovirus disease outbreaks. However, the intense use of insecticides, particularly pyrethroids, has led to the selection of resistant mosquito populations worldwide. Mutations in the voltage-gated sodium channel (VGSC) gene are one of the main drivers of insecticide resistance in Ae. albopictus and are also known as “knockdown resistance” (kdr) mutations. Knowledge about genetic mutations associated with insecticide resistance is a prerequisite for developing techniques for rapid resistance diagnosis. Here, we report studies on the origin and dispersion of kdr haplotypes in samples of Ae. albopictus from the Yangtze River Basin, China;
Methods
Here, we report the results of PCR genotyping of kdr mutations in 541 Ae. albopictus specimens from 22 sampling sites in 7 provinces and municipalities in the Yangtze River Basin. Partial DNA sequences of domain II and domain III of the VGSC gene were amplified. These DNA fragments were subsequently sequenced to discover the possible genetic mutations mediating knockdown resistance (kdr) to pyrethroids. The frequency and distribution of kdr mutations were assessed in 22 Ae. albopictus populations. Phylogenetic relationships among the haplotypes were used to infer whether the kdr mutations had a single or multiple origins;
Results
The kdr mutation at the 1016 locus had 2 alleles with 3 genotypes: V/V (73.38%), V/G (26.43%) and G/G (0.18%). The 1016G homozygous mutation was found in only one case in the CQSL strain in Chongqing, and no 1016G mutations were detected in the SHJD (Shanghai), NJDX (Jiangsu) or HBQN (Hubei) strains. A total of 1532 locus had two alleles and three genotypes, I/I (88.35%), I/T (8.50%) and T/T (3.14%). A total of 1534 locus had four alleles and six genotypes: F/F (49.35%), F/S (19.96%), F/C (1.48%) and F/L (0.18%); S/S (23.66%); and C/C (5.36%). Haplotypes with the F1534C mutation were found only in Ae. albopictus populations in Chongqing and Hubei, and C1534C was found only in three geographic strains in Chongqing. Haplotypes with the 1534S mutation were found only in Ae. albopictus populations in Sichuan and Shanghai. F1534L was found only in HBYC. The Ae. albopictus populations in Shanghai were more genetically differentiated from those in the other regions (except Sichuan), and the genetic differentiation between the populations in Chongqing and those in the middle-lower reaches of the Yangtze River (Huber, Jiangsu, Jiangxi, and Anhui) was lower. Shanghai and Sichuan displayed low haplotype diversity and low nucleotide diversity. Phylogenetic anal
{"title":"Detection and population genetic analysis of Aedes albopictus (Diptera: Culicidae) based on knockdown resistance (kdr) mutations in the Yangtze River basin of China","authors":"Zu Ma, Qing Liu, Ming Wang, Yu-tong Du, Jing-wen Xie, Zi-ge Yi, Jing-hong Cai, Tong-yan Zhao, Heng-duan Zhang","doi":"10.1016/j.meegid.2024.105634","DOIUrl":"10.1016/j.meegid.2024.105634","url":null,"abstract":"<div><h3>Background</h3><p><em>Aedes albopictus</em> is an important vector of chikungunya, dengue, yellow fever and Zika viruses. Insecticides are often the most effective tools for rapidly decreasing the density of vector populations, especially during arbovirus disease outbreaks. However, the intense use of insecticides, particularly pyrethroids, has led to the selection of resistant mosquito populations worldwide. Mutations in the voltage-gated sodium channel (VGSC) gene are one of the main drivers of insecticide resistance in <em>Ae. albopictus</em> and are also known as “knockdown resistance” (<em>kdr</em>) mutations. Knowledge about genetic mutations associated with insecticide resistance is a prerequisite for developing techniques for rapid resistance diagnosis. Here, we report studies on the origin and dispersion of <em>kdr</em> haplotypes in samples of <em>Ae. albopictus</em> from the Yangtze River Basin, China;</p></div><div><h3>Methods</h3><p>Here, we report the results of PCR genotyping of <em>kdr</em> mutations in 541 <em>Ae. albopictus</em> specimens from 22 sampling sites in 7 provinces and municipalities in the Yangtze River Basin. Partial DNA sequences of domain II and domain III of the VGSC gene were amplified. These DNA fragments were subsequently sequenced to discover the possible genetic mutations mediating knockdown resistance (<em>kdr</em>) to pyrethroids. The frequency and distribution of <em>kdr</em> mutations were assessed in 22 <em>Ae. albopictus</em> populations. Phylogenetic relationships among the haplotypes were used to infer whether the <em>kdr</em> mutations had a single or multiple origins;</p></div><div><h3>Results</h3><p>The <em>kdr</em> mutation at the 1016 locus had 2 alleles with 3 genotypes: <em>V</em>/V (73.38%), V/G (26.43%) and G/G (0.18%). The 1016G homozygous mutation was found in only one case in the CQSL strain in Chongqing, and no 1016G mutations were detected in the SHJD (Shanghai), NJDX (Jiangsu) or HBQN (Hubei) strains. A total of 1532 locus had two alleles and three genotypes, I/I (88.35%), I/T (8.50%) and T/T (3.14%). A total of 1534 locus had four alleles and six genotypes: F/F (49.35%), F/S (19.96%), F/C (1.48%) and F/L (0.18%); S/S (23.66%); and C/C (5.36%). Haplotypes with the F1534C mutation were found only in <em>Ae. albopictus</em> populations in Chongqing and Hubei, and C1534C was found only in three geographic strains in Chongqing. Haplotypes with the 1534S mutation were found only in <em>Ae. albopictus</em> populations in Sichuan and Shanghai. F1534L was found only in HBYC. The <em>Ae. albopictus</em> populations in Shanghai were more genetically differentiated from those in the other regions (except Sichuan), and the genetic differentiation between the populations in Chongqing and those in the middle-lower reaches of the Yangtze River (Huber, Jiangsu, Jiangxi, and Anhui) was lower. Shanghai and Sichuan displayed low haplotype diversity and low nucleotide diversity. Phylogenetic anal","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-06-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1567134824000856/pdfft?md5=ad8bcdece9464d502683742101bf5609&pid=1-s2.0-S1567134824000856-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141478012","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}
Pub Date : 2024-06-28DOI: 10.1016/j.meegid.2024.105631
Background
Chronic leg ulcers are hard to treat and can be a burden, particularly in resource-limited settings where diagnosis is a challenge. Staphylococcus aureus is among the common bacteria isolated from chronic wounds with a great impact on wound healing, particularly in patients with co-morbidities. Antimicrobial resistance genes and virulence factors in Staphylococcus aureus isolates were assessed to support healthcare professionals to make better therapeutic choices, and importantly to curb the development and spread of antibiotic resistance.
Methods
A cross-sectional study involved both inpatients and outpatients with chronic leg ulcers was conducted from August 2022 to April 2023 in 2 health facilities in Kilimanjaro region in Tanzania. Antimicrobial susceptibility testing was done using the disk diffusion method. Further, whole genome sequencing was performed to study the genotypic characteristics of the isolates.
Results
A total of 92 participants were recruited in which 9 participants were only positive for 10 Staphylococcus aureus isolates upon culture. Five STs among 9 isolates were identified. Most of them belonged to ST8 (44%), with 1 isolate does not belong to any ST. Additionally, 50% of the isolates were methicillin-resistant Staphylococcus aureus (MRSA). All S. aureus isolates had almost similar virulence factors such as hemolysin, proteases and evasions that promote toxin production, protease production and host immune evasion respectively. Moreover, all mecA positive S. aureus isolates were phenotypically susceptible to cefoxitin.
Conclusion
Presence of mecA positive S. aureus isolates which are also phenotypically susceptible to cefoxitin implies the possibility of classifying MRSA as MSSA. This may result in the possible emergence of highly cefoxitin - resistant strains in health care and community settings when subsequently exposed to beta-lactam agents. Therefore, combination of whole genome sequencing and conventional methods is important in assessing bacterial resistance and virulence to improve management of patients.
{"title":"Whole genome-based antimicrobial resistance and virulence profiling of Staphylococcus aureus isolates from chronic leg ulcer patients in Kilimanjaro, Tanzania","authors":"","doi":"10.1016/j.meegid.2024.105631","DOIUrl":"10.1016/j.meegid.2024.105631","url":null,"abstract":"<div><h3>Background</h3><p>Chronic leg ulcers are hard to treat and can be a burden, particularly in resource-limited settings where diagnosis is a challenge. <em>Staphylococcus aureus</em> is among the common bacteria isolated from chronic wounds with a great impact on wound healing, particularly in patients with co-morbidities. Antimicrobial resistance genes and virulence factors in <em>Staphylococcus aureus</em> isolates were assessed to support healthcare professionals to make better therapeutic choices, and importantly to curb the development and spread of antibiotic resistance.</p></div><div><h3>Methods</h3><p>A cross-sectional study involved both inpatients and outpatients with chronic leg ulcers was conducted from August 2022 to April 2023 in 2 health facilities in Kilimanjaro region in Tanzania. Antimicrobial susceptibility testing was done using the disk diffusion method. Further, whole genome sequencing was performed to study the genotypic characteristics of the isolates.</p></div><div><h3>Results</h3><p>A total of 92 participants were recruited in which 9 participants were only positive for 10 <em>Staphylococcus aureus</em> isolates upon culture. Five STs among 9 isolates were identified. Most of them belonged to ST8 (44%), with 1 isolate does not belong to any ST. Additionally, 50% of the isolates were methicillin-resistant <em>Staphylococcus aureus</em> (MRSA). All <em>S. aureus</em> isolates had almost similar virulence factors such as hemolysin, proteases and evasions that promote toxin production, protease production and host immune evasion respectively. Moreover, all <em>mecA</em> positive <em>S. aureus</em> isolates were phenotypically susceptible to cefoxitin.</p></div><div><h3>Conclusion</h3><p>Presence of <em>mecA</em> positive <em>S. aureus</em> isolates which are also phenotypically susceptible to cefoxitin implies the possibility of classifying MRSA as MSSA. This may result in the possible emergence of highly cefoxitin - resistant strains in health care and community settings when subsequently exposed to beta-lactam agents. Therefore, combination of whole genome sequencing and conventional methods is important in assessing bacterial resistance and virulence to improve management of patients.</p></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1567134824000820/pdfft?md5=372cbf0c2316d46e0b151760ee4fee21&pid=1-s2.0-S1567134824000820-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141472808","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}
Pub Date : 2024-06-25DOI: 10.1016/j.meegid.2024.105630
Wesley Arruda Gimenes Nantes , Sany Caroline Liberal , Filipe Martins Santos , Maria Augusta Dario , Lincoln Takashi Hota Mukoyama , Katrine Berres Woidella , Paula Helena Santa Rita , André Luiz Rodrigues Roque , Carina Elisei de Oliveira , Heitor Miraglia Herrera , Ana Maria Jansen
Trypanosomatids have achieved significant evolutionary success in parasitizing various groups, yet reptiles remain relatively unexplored. The utilization of advanced molecular tools has revealed an increased richness of trypanosomatids in vertebrate hosts. The aim of this study was to identify the trypanosomatid species infecting Bothrops moojeni and Crotalus durissus kept in captivity from 2000 to 2022. Blood samples were obtained from 106 snakes: 73C. durissus and 33 B. moojeni. Whole blood was collected for hemoculture, blood smears and centrifugated to obtain the blood clot that had its DNA extracted and submitted to Nested PCR (18S rDNA gene) to detect Trypanosomatidae. Positive samples were quantified and submitted to both conventional (Sanger) and next generation sequencing (NGS). Cloning of the amplified PCR product was performed for only one individual of C. durissus. To exclude the possibility of local vector transmission, attempts to capture sandflies were conducted using six CDC-LT type light traps. Molecular diagnosis revealed that 34% of the snakes presented trypanosomatid DNA, 47.94% in C. durissus and 3.9% in B. moojeni. The cloning process generated four colonies identified as a new MOTU named Trypanosomatidae sp. CROT. The presence of DNA of five trypanosomatids (Trypanosoma cruzi TcII/VI, Trypanosoma sp. DID, Trypanosoma cascavelli, Trypanosomatidae sp. CROT, Leishmania infantum and Leishmania sp.) and one free-living kinetoplastid (Neobodo sp.) was revealed through NGS and confirmed by phylogenetic analysis. The haplotypic network divided the T. cascavelli sequences into two groups, 1) marsupials and snakes and 2) exclusive to marsupials. Therefore, the diversity of Kinetoplastea is still underestimated. Snakes have the ability to maintain infection with T. cruzi and L. infantum for up to 20 years and the DNA finding of Neobodo sp. in the blood of a C. durissus suggests that this genus can infect vertebrates.
锥虫在寄生于不同类群方面取得了巨大的进化成功,但爬行动物相对而言仍未被探索。利用先进的分子工具发现,脊椎动物宿主中的锥虫种类越来越丰富。本研究旨在鉴定 2000 年至 2022 年期间人工饲养的 Bothrops moojeni 和 Crotalus durissus 所感染的锥虫种类。研究人员采集了 106 条蛇的血液样本:其中,73 条为杜氏蝮蛇,33 条为莫氏蝮蛇。采集全血进行血液培养、血液涂片和离心,以获得血凝块,提取其 DNA 并提交巢式 PCR(18S rDNA 基因)以检测锥虫。对阳性样本进行量化,并提交给传统(桑格)和新一代测序(NGS)。仅对 C. durissus 的一个个体进行了 PCR 扩增产物的克隆。为了排除本地病媒传播的可能性,我们尝试使用 6 个 CDC-LT 型灯光诱捕器捕捉沙蝇。分子诊断结果显示,34%的蛇携带锥虫 DNA,其中 47.94% 为 C. durissus,3.9% 为 B. moojeni。克隆过程中产生的四个菌落被鉴定为一种新的 MOTU,命名为 Trypanosomatidae sp.CROT。克隆过程中产生的四个菌落被鉴定为新的 MOTU,命名为 Trypanosomatidae sp.)和一种自由生活的奇异变形虫(Neobodo sp.),并通过系统发育分析得到证实。单倍型网络将 T. cascavelli 序列分为两组:1)有袋类动物和蛇类;2)有袋类动物独有。因此,Kinetoplastea 的多样性仍被低估。蛇类有能力维持感染 T. cruzi 和 L. infantum 长达 20 年的时间,而在 C. durissus 的血液中发现 Neobodo sp.的 DNA 表明该属可以感染脊椎动物。
{"title":"Viperidae snakes infected by mammalian-associated trypanosomatids and a free-living kinetoplastid","authors":"Wesley Arruda Gimenes Nantes , Sany Caroline Liberal , Filipe Martins Santos , Maria Augusta Dario , Lincoln Takashi Hota Mukoyama , Katrine Berres Woidella , Paula Helena Santa Rita , André Luiz Rodrigues Roque , Carina Elisei de Oliveira , Heitor Miraglia Herrera , Ana Maria Jansen","doi":"10.1016/j.meegid.2024.105630","DOIUrl":"10.1016/j.meegid.2024.105630","url":null,"abstract":"<div><p>Trypanosomatids have achieved significant evolutionary success in parasitizing various groups, yet reptiles remain relatively unexplored. The utilization of advanced molecular tools has revealed an increased richness of trypanosomatids in vertebrate hosts. The aim of this study was to identify the trypanosomatid species infecting <em>Bothrops moojeni</em> and <em>Crotalus durissus</em> kept in captivity from 2000 to 2022. Blood samples were obtained from 106 snakes: 73<em>C. durissus</em> and 33 <em>B. moojeni</em>. Whole blood was collected for hemoculture, blood smears and centrifugated to obtain the blood clot that had its DNA extracted and submitted to Nested PCR (18S rDNA gene) to detect Trypanosomatidae. Positive samples were quantified and submitted to both conventional (Sanger) and next generation sequencing (NGS). Cloning of the amplified PCR product was performed for only one individual of <em>C. durissus</em>. To exclude the possibility of local vector transmission, attempts to capture sandflies were conducted using six CDC-LT type light traps. Molecular diagnosis revealed that 34% of the snakes presented trypanosomatid DNA, 47.94% in <em>C. durissus</em> and 3.9% in <em>B. moojeni</em>. The cloning process generated four colonies identified as a new MOTU named Trypanosomatidae sp. CROT. The presence of DNA of five trypanosomatids (<em>Trypanosoma cruzi</em> TcII/VI, <em>Trypanosoma</em> sp. DID, <em>Trypanosoma cascavelli</em>, Trypanosomatidae sp. CROT, <em>Leishmania infantum</em> and <em>Leishmania</em> sp.) and one free-living kinetoplastid (<em>Neobodo</em> sp.) was revealed through NGS and confirmed by phylogenetic analysis. The haplotypic network divided the <em>T. cascavelli</em> sequences into two groups, 1) marsupials and snakes and 2) exclusive to marsupials. Therefore, the diversity of Kinetoplastea is still underestimated. Snakes have the ability to maintain infection with <em>T. cruzi</em> and <em>L. infantum</em> for up to 20 years and the DNA finding of <em>Neobodo</em> sp. in the blood of a <em>C. durissus</em> suggests that this genus can infect vertebrates.</p></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1567134824000819/pdfft?md5=0bbcd3a4eaff2f818b7f5a5180ce944b&pid=1-s2.0-S1567134824000819-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141472810","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}
Pub Date : 2024-06-25DOI: 10.1016/j.meegid.2024.105629
Guoyan Zhou , Haining Zhang , Wangkai Chen , Zhi Li , Xueyong Zhang , Yong Fu
Hydatigera kamiyai (H. kamiyai) is a new species within Hydatigera that has recently been resurrected. Voles and cats are hosts of H. kamiyai and have a certain impact on its health and economy. Moreover, the Qinghai-Tibetan plateau (QTP) is a research hotspot representing Earth's biodiversity, as its unique geographical environment and climatic conditions support the growth of a variety of mammals and provide favorable conditions for various parasites to complete their life history. The aim of this study was to reveal the phylogenetic relationships and divergence times of H. kamiyai strains isolated from Neodon fuscus on the QTP using morphological and molecular methods. In this study, we morphologically observed H. kamiyai and sequenced the whole mitochondrial genome. Then, we constructed phylogenetic trees with the maximum likelihood (ML) and Bayesian inference (BI) methods. The GTR alternative model was selected for divergence time analysis. These data demonstrated that the results were consistent with the general morphological characteristics of Hydatigera. The whole genome of H. kamiyai was 13,822 bp in size, and the A + T content (73%) was greater than the G + C content (27%). The Ka/Ks values were all <1, indicating that all 13 protein-coding genes (13 PCGs) underwent purifying selection during the process of evolution. The phylogenetic tree generated based on the 13 PCGs, cytochrom oxidase subunit I (COI), 18S rRNA and 28S rRNA revealed close phylogenetic relationships between H. kamiyai and Hydatigera, with high node support for the relationship. The divergence time based on 13 PCGs indicated that H. kamiyai diverged approximately 11.3 million years ago (Mya) in the Miocene. Interestingly, it diverged later than the period of rapid uplift in the QTP. We also speculated that H. kamiyai differentiation was caused by host differentiation due to the favorable living conditions brought about by the uplift of the QTP. As there have been relatively few investigations on the mitochondrial genome of H. kamiyai, our study could provide factual support for further studies of H. kamiyai on the QTP. We also emphasized the importance of further studies of its hosts, Neodon fuscus and cats, which will be important for further understanding the life cycle of H. kamiyai.
Hydatigera kamiyai(H. kamiyai)是最近复活的 Hydatigera 中的一个新物种。田鼠和猫是 H. kamiyai 的寄主,对其健康和经济有一定影响。此外,青藏高原是代表地球生物多样性的研究热点,因为其独特的地理环境和气候条件支持多种哺乳动物的生长,并为各种寄生虫完成其生活史提供了有利条件。本研究的目的是利用形态学和分子学方法揭示从QTP上的Neodon fuscus分离到的H. kamiyai菌株的系统发育关系和分化时间。在本研究中,我们对 H. kamiyai 进行了形态学观察,并对其线粒体基因组进行了测序。然后,我们用最大似然法(ML)和贝叶斯推断法(BI)构建了系统发生树。分歧时间分析选择了 GTR 替代模型。这些数据表明,研究结果符合水螅的一般形态特征。H. kamiyai的全基因组大小为13,822 bp,A+T含量(73%)大于G+C含量(27%)。Ka/Ks 值均为
{"title":"Morphological observation, molecular identification and evolutionary analysis of Hydatigera kamiyai found in Neodon fuscus from the Qinghai-Tibetan plateau","authors":"Guoyan Zhou , Haining Zhang , Wangkai Chen , Zhi Li , Xueyong Zhang , Yong Fu","doi":"10.1016/j.meegid.2024.105629","DOIUrl":"10.1016/j.meegid.2024.105629","url":null,"abstract":"<div><p><em>Hydatigera kamiyai</em> (<em>H. kamiyai</em>) is a new species within <em>Hydatigera</em> that has recently been resurrected. Voles and cats are hosts of <em>H. kamiyai</em> and have a certain impact on its health and economy. Moreover, the Qinghai-Tibetan plateau (QTP) is a research hotspot representing Earth's biodiversity, as its unique geographical environment and climatic conditions support the growth of a variety of mammals and provide favorable conditions for various parasites to complete their life history. The aim of this study was to reveal the phylogenetic relationships and divergence times of <em>H. kamiyai</em> strains isolated from <em>Neodon fuscus</em> on the QTP using morphological and molecular methods. In this study, we morphologically observed <em>H. kamiyai</em> and sequenced the whole mitochondrial genome. Then, we constructed phylogenetic trees with the maximum likelihood (ML) and Bayesian inference (BI) methods. The GTR alternative model was selected for divergence time analysis. These data demonstrated that the results were consistent with the general morphological characteristics of <em>Hydatigera</em>. The whole genome of <em>H. kamiyai</em> was 13,822 bp in size, and the A + T content (73%) was greater than the G + C content (27%). The Ka/Ks values were all <1, indicating that all 13 protein-coding genes (13 PCGs) underwent purifying selection during the process of evolution. The phylogenetic tree generated based on the 13 PCGs, cytochrom oxidase subunit I (COI), 18S rRNA and 28S rRNA revealed close phylogenetic relationships between <em>H. kamiyai</em> and <em>Hydatigera</em>, with high node support for the relationship. The divergence time based on 13 PCGs indicated that <em>H. kamiyai</em> diverged approximately 11.3 million years ago (Mya) in the Miocene. Interestingly, it diverged later than the period of rapid uplift in the QTP. We also speculated that <em>H. kamiyai</em> differentiation was caused by host differentiation due to the favorable living conditions brought about by the uplift of the QTP. As there have been relatively few investigations on the mitochondrial genome of <em>H. kamiyai</em>, our study could provide factual support for further studies of <em>H. kamiyai</em> on the QTP. We also emphasized the importance of further studies of its hosts, <em>Neodon fuscus</em> and cats, which will be important for further understanding the life cycle of <em>H. kamiyai</em>.</p></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1567134824000807/pdfft?md5=16744eef47359b338b7815e5d189d99f&pid=1-s2.0-S1567134824000807-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141472807","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}
Pub Date : 2024-06-25DOI: 10.1016/j.meegid.2024.105628
Gabriela M. Fernandes , Guilherme H. Rodrigues-Mattos , Letícia M. Torres , Karla S. Guedes , Cor J.F. Fontes , Francis B. Ntumngia , John H. Adams , Cristiana F.A. Brito , Flora S. Kano , Taís N. de Sousa , Luzia H. Carvalho
In malaria parasites, the erythrocyte binding-like proteins (EBL) are a family of invasion proteins that are attractive vaccine targets. In the case of Plasmodium vivax, the widespread malaria parasite, blood-stage vaccines have been largely focused on a single EBL candidate, the Duffy binding-like domain (DBL) of the Duffy binding protein (DBPII), due to its well-characterized role in the reticulocyte invasion. A novel P. vivax EBL family member, the Erythrocyte binding protein (EBP2, also named EBP or DBP2), binds preferentially to reticulocytes and may mediate an alternative P. vivax invasion pathway. To gain insight into the natural genetic diversity of the DBL domain of EBP2 (region II; EBP2-II), we analyzed ebp2-II gene sequences of 71 P. vivax isolates collected in different endemic settings of the Brazilian Amazon rainforest, where P. vivax is the predominant malaria-associated species. Although most of the substitutions in the ebp2-II gene were non-synonymous and suggested positive selection, the results showed that the DBL domain of the EBP2 was much less polymorphic than that of DBPII. The predominant EBP2 haplotype in the Amazon region corresponded to the C127 reference sequence first described in Cambodia (25% C127-like haplotype). An overview of ebp2-II gene sequences available at GenBank (n = 352) from seven countries (Cambodia, Madagascar, Myanmar, PNG, South Korea, Thailand, Vietnam) confirmed the C127-like haplotype as highly prevalent worldwide. Two out of 43 haplotypes (5 to 20 inferred per country) showed a global frequency of 60%. The results presented here open new avenues of research pursuit while suggesting that a vaccine based on the DBL domain of EBP2 should target a few haplotypes for broad coverage.
{"title":"Natural genetic diversity of the DBL domain of a novel member of the Plasmodium vivax erythrocyte binding-like proteins (EBP2) in the Amazon rainforest","authors":"Gabriela M. Fernandes , Guilherme H. Rodrigues-Mattos , Letícia M. Torres , Karla S. Guedes , Cor J.F. Fontes , Francis B. Ntumngia , John H. Adams , Cristiana F.A. Brito , Flora S. Kano , Taís N. de Sousa , Luzia H. Carvalho","doi":"10.1016/j.meegid.2024.105628","DOIUrl":"10.1016/j.meegid.2024.105628","url":null,"abstract":"<div><p>In malaria parasites, the erythrocyte binding-like proteins (EBL) are a family of invasion proteins that are attractive vaccine targets. In the case of <em>Plasmodium vivax,</em> the widespread malaria parasite, blood-stage vaccines have been largely focused on a single EBL candidate, the Duffy binding-like domain (DBL) of the Duffy binding protein (DBPII), due to its well-characterized role in the reticulocyte invasion. A novel <em>P. vivax</em> EBL family member, the Erythrocyte binding protein (EBP2, also named EBP or DBP2), binds preferentially to reticulocytes and may mediate an alternative <em>P. vivax</em> invasion pathway. To gain insight into the natural genetic diversity of the DBL domain of EBP2 (region II; EBP2-II), we analyzed <em>ebp2-II</em> gene sequences of 71 <em>P. vivax</em> isolates collected in different endemic settings of the Brazilian Amazon rainforest, where <em>P. vivax</em> is the predominant malaria-associated species. Although most of the substitutions in the <em>ebp2-II</em> gene were non-synonymous and suggested positive selection, the results showed that the DBL domain of the EBP2 was much less polymorphic than that of DBPII. The predominant EBP2 haplotype in the Amazon region corresponded to the C127 reference sequence first described in Cambodia (25% C127-like haplotype). An overview of <em>ebp2-II</em> gene sequences available at GenBank (<em>n</em> = 352) from seven countries (Cambodia, Madagascar, Myanmar, PNG, South Korea, Thailand, Vietnam) confirmed the C127-like haplotype as highly prevalent worldwide. Two out of 43 haplotypes (5 to 20 inferred per country) showed a global frequency of 60%. The results presented here open new avenues of research pursuit while suggesting that a vaccine based on the DBL domain of EBP2 should target a few haplotypes for broad coverage.</p></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1567134824000790/pdfft?md5=cb327ed3110dd5ab37f73f0bea89e755&pid=1-s2.0-S1567134824000790-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141472809","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}
Hainan Island and the Leizhou Peninsula, the southernmost part of mainland China, are areas where Aedes aegypti and Ae. albopictus are sympatric and are also high-incidence areas of dengue outbreaks in China. Many studies have suggested that Aedes endogenous viral components (EVEs) are enriched in piRNA clusters which can silence incoming viral genomes. Investigation the EVEs present in the piRNA clusters associated with viral infection of Aedes mosquitoes in these regions may provide a theoretical basis for novel transmission-blocking vector control strategies.
Methods
In this study, specific primers for endogenous Flaviviridae elements (EFVEs) and endogenous Rhabdoviridae elements (ERVEs) were used to detect the distribution of Zika virus infection associated EVEs in the genomes of individuals of the two Aedes mosquitoes. Genetic diversity of EVEs with a high detection rate was also analyzed.
Results
The results showed that many EVEs associated with Zika virus infection were detected in both Aedes species, with the detection rates were 47.68% to 100% in Ae. aegypti and 36.15% to 92.31% in sympatric Ae. albopictus populations. EVEs detection rates in another 17 Ae. albopictus populations ranged from 29.39% to 89.85%. Genetic diversity analyses of the four EVEs (AaFlavi53, AaRha61, AaRha91 and AaRha100) of Ae. aegypti showed that each had high haplotype diversity and low nucleotide diversity. The number of haplotypes in AaFlavi53 was 8, with the dominant haplotype being Hap_1 and the other 7 haplotypes being further mutated from Hap_1 in a lineage direction. In contrast, the haplotype diversity of the other three ERVEs (AaRha61, AaRha91 and AaRha100) was more diverse and richer, with the haplotype numbers were 9, 15 and 19 respectively. In addition, these EVEs all showed inconsistent patterns of both population differentiation and dispersal compared to neutral evolutionary genes such as the Mitochondrial COI gene.
Conclusion
The EFVEs and ERVEs tested were present at high frequencies in the field Aedes mosquito populations. The haplotype diversity of the EFVE AaFlavi53 was relatively lower and the three ERVEs (AaRha61, AaRha91, AaRha100) were higher. None of the four EVEs could be indicative of the genetic diversity of the Ae. aegypti population. This study provided theoretical support for the use of EVEs to block arbovirus transmission, but further research is needed into the mechanisms by which these EVEs are antiviral to Aedes mosquitoes.
{"title":"Genetic diversity of Flaviviridae and Rhabdoviridae EVEs in Aedes aegypti and Aedes albopictus on Hainan Island and the Leizhou Peninsula, China","authors":"Minghui Zhao , Xin Ran , Qiang Zhang , Jian Gao , Mingyu Wu , Dan Xing , Hengduan Zhang , Tongyan Zhao","doi":"10.1016/j.meegid.2024.105627","DOIUrl":"10.1016/j.meegid.2024.105627","url":null,"abstract":"<div><h3>Background</h3><p>Hainan Island and the Leizhou Peninsula, the southernmost part of mainland China, are areas where <em>Aedes aegypti</em> and <em>Ae. albopictus</em> are sympatric and are also high-incidence areas of dengue outbreaks in China. Many studies have suggested that <em>Aedes</em> endogenous viral components (EVEs) are enriched in piRNA clusters which can silence incoming viral genomes. Investigation the EVEs present in the piRNA clusters associated with viral infection of <em>Aedes</em> mosquitoes in these regions may provide a theoretical basis for novel transmission-blocking vector control strategies.</p></div><div><h3>Methods</h3><p>In this study, specific primers for endogenous <em>Flaviviridae</em> elements (EFVEs) and endogenous <em>Rhabdoviridae</em> elements (ERVEs) were used to detect the distribution of Zika virus infection associated EVEs in the genomes of individuals of the two <em>Aedes</em> mosquitoes. Genetic diversity of EVEs with a high detection rate was also analyzed.</p></div><div><h3>Results</h3><p>The results showed that many EVEs associated with Zika virus infection were detected in both <em>Aedes</em> species, with the detection rates were 47.68% to 100% in <em>Ae. aegypti</em> and 36.15% to 92.31% in sympatric <em>Ae. albopictus</em> populations. EVEs detection rates in another 17 <em>Ae. albopictus</em> populations ranged from 29.39% to 89.85%. Genetic diversity analyses of the four EVEs (AaFlavi53, AaRha61, AaRha91 and AaRha100) of <em>Ae. aegypti</em> showed that each had high haplotype diversity and low nucleotide diversity. The number of haplotypes in AaFlavi53 was 8, with the dominant haplotype being Hap_1 and the other 7 haplotypes being further mutated from Hap_1 in a lineage direction. In contrast, the haplotype diversity of the other three ERVEs (AaRha61, AaRha91 and AaRha100) was more diverse and richer, with the haplotype numbers were 9, 15 and 19 respectively. In addition, these EVEs all showed inconsistent patterns of both population differentiation and dispersal compared to neutral evolutionary genes such as the Mitochondrial COI gene.</p></div><div><h3>Conclusion</h3><p>The EFVEs and ERVEs tested were present at high frequencies in the field <em>Aedes</em> mosquito populations. The haplotype diversity of the EFVE AaFlavi53 was relatively lower and the three ERVEs (AaRha61, AaRha91, AaRha100) were higher. None of the four EVEs could be indicative of the genetic diversity of the <em>Ae. aegypti</em> population. This study provided theoretical support for the use of EVEs to block arbovirus transmission, but further research is needed into the mechanisms by which these EVEs are antiviral to <em>Aedes</em> mosquitoes.</p></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1567134824000789/pdfft?md5=1322f40547c2d22eb7c376a1d2eddea3&pid=1-s2.0-S1567134824000789-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141443779","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}