Pub Date : 2024-06-06DOI: 10.1016/j.meegid.2024.105615
Ran Wang , Qingjie Xue , Lingyun Guo
{"title":"Editorial introduction: Special issue on immunology, epidemiology, prevention, diagnosis, and treatment of pediatric infectious diseases and neglected tropical diseases","authors":"Ran Wang , Qingjie Xue , Lingyun Guo","doi":"10.1016/j.meegid.2024.105615","DOIUrl":"10.1016/j.meegid.2024.105615","url":null,"abstract":"","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2024-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1567134824000662/pdfft?md5=302fccff68d4056bc8abcaf6a2784a56&pid=1-s2.0-S1567134824000662-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141288967","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 : 2024-06-04DOI: 10.1016/j.meegid.2024.105614
Marianne Lebbad , Jana Grüttner , Jessica Beser , Victor Lizana , Maria Auxiliadora Dea-Ayuela , Marianne Oropeza-Moe , David Carmena , Christen Rune Stensvold
Cryptosporidiosis is an infectious enteric disease caused by species (some of them zoonotic) of the genus Cryptosporidium that in many countries are under surveillance. Typing assays critical to the surveillance of cryptosporidiosis typically involve characterization of Cryptosporidium glycoprotein 60 genes (gp60). Here, we characterized the gp60 of Cryptosporidium suis from two samples—a human and a porcine faecal sample—based on which a preliminary typing scheme was developed. A conspicuous feature of the C. suis gp60 was a novel type of tandem repeats located in the 5′ end of the gene and that took up 777/1635 bp (48%) of the gene. The C. suis gp60 lacked the classical poly-serine repeats (TCA/TCG/TCT), which is usually subject to major genetic variation, and the length of the tandem repeat made a typing assay incorporating this region based on Sanger sequencing practically unfeasible. We therefore designed a typing assay based on the post-repeat region only and applied it to C. suis-positive samples from suid hosts from Norway, Denmark, and Spain. We were able to distinguish three different subtypes; XXVa-1, XXVa-2, and XXVa-3. Subtype XXVa-1 had a wider geographic distribution than the other subtypes and was also observed in the human sample. We think that the present data will inform future strategies to develop a C. suis typing assay that could be even more informative by including a greater part of the gene, including the tandem repeat region, e.g., by the use of long-read next-generation sequencing.
{"title":"Complete sequencing of the Cryptosporidium suis gp60 gene reveals a novel type of tandem repeats—Implications for surveillance","authors":"Marianne Lebbad , Jana Grüttner , Jessica Beser , Victor Lizana , Maria Auxiliadora Dea-Ayuela , Marianne Oropeza-Moe , David Carmena , Christen Rune Stensvold","doi":"10.1016/j.meegid.2024.105614","DOIUrl":"10.1016/j.meegid.2024.105614","url":null,"abstract":"<div><p>Cryptosporidiosis is an infectious enteric disease caused by species (some of them zoonotic) of the genus <em>Cryptosporidium</em> that in many countries are under surveillance. Typing assays critical to the surveillance of cryptosporidiosis typically involve characterization of <em>Cryptosporidium</em> glycoprotein 60 genes (<em>gp60</em>). Here, we characterized the <em>gp60</em> of <em>Cryptosporidium suis</em> from two samples—a human and a porcine faecal sample—based on which a preliminary typing scheme was developed. A conspicuous feature of the <em>C. suis gp60</em> was a novel type of tandem repeats located in the 5′ end of the gene and that took up 777/1635 bp (48%) of the gene. The <em>C. suis gp60</em> lacked the classical poly-serine repeats (TCA/TCG/TCT), which is usually subject to major genetic variation, and the length of the tandem repeat made a typing assay incorporating this region based on Sanger sequencing practically unfeasible. We therefore designed a typing assay based on the post-repeat region only and applied it to <em>C. suis</em>-positive samples from suid hosts from Norway, Denmark, and Spain. We were able to distinguish three different subtypes; XXVa-1, XXVa-2, and XXVa-3. Subtype XXVa-1 had a wider geographic distribution than the other subtypes and was also observed in the human sample. We think that the present data will inform future strategies to develop a <em>C. suis</em> typing assay that could be even more informative by including a greater part of the gene, including the tandem repeat region, e.g.<em>,</em> by the use of long-read next-generation sequencing.</p></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2024-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1567134824000650/pdfft?md5=7636cd0b5e8d1b3d6aa4054431d5ff3c&pid=1-s2.0-S1567134824000650-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141285389","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 : 2024-06-04DOI: 10.1016/j.meegid.2024.105613
Mahsa Aghajani Mir
The appearance of SARS-CoV-2 in 2019 triggered a significant economic and health crisis worldwide, with heterogeneous molecular mechanisms that contribute to its development are not yet fully understood. Although substantial progress has been made in elucidating the mechanisms behind SARS-CoV-2 infection and therapy, it continues to rank among the top three global causes of mortality due to infectious illnesses. Non-coding RNAs (ncRNAs), being integral components across nearly all biological processes, demonstrate effective importance in viral pathogenesis. Regarding viral infections, ncRNAs have demonstrated their ability to modulate host reactions, viral replication, and host-pathogen interactions. However, the complex interactions of different types of ncRNAs in the progression of COVID-19 remains understudied. In recent years, a novel mechanism of post-transcriptional gene regulation known as “competing endogenous RNA (ceRNA)” has been proposed. Long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), and viral ncRNAs function as ceRNAs, influencing the expression of associated genes by sequestering shared microRNAs. Recent research on SARS-CoV-2 has revealed that disruptions in specific ceRNA regulatory networks (ceRNETs) contribute to the abnormal expression of key infection-related genes and the establishment of distinctive infection characteristics. These findings present new opportunities to delve deeper into the underlying mechanisms of SARS-CoV-2 pathogenesis, offering potential biomarkers and therapeutic targets. This progress paves the way for a more comprehensive understanding of ceRNETs, shedding light on the intricate mechanisms involved. Further exploration of these mechanisms holds promise for enhancing our ability to prevent viral infections and develop effective antiviral treatments.
{"title":"Illuminating the pathogenic role of SARS-CoV-2: Insights into competing endogenous RNAs (ceRNAs) regulatory networks","authors":"Mahsa Aghajani Mir","doi":"10.1016/j.meegid.2024.105613","DOIUrl":"10.1016/j.meegid.2024.105613","url":null,"abstract":"<div><p>The appearance of SARS-CoV-2 in 2019 triggered a significant economic and health crisis worldwide, with heterogeneous molecular mechanisms that contribute to its development are not yet fully understood. Although substantial progress has been made in elucidating the mechanisms behind SARS-CoV-2 infection and therapy, it continues to rank among the top three global causes of mortality due to infectious illnesses. Non-coding RNAs (ncRNAs), being integral components across nearly all biological processes, demonstrate effective importance in viral pathogenesis. Regarding viral infections, ncRNAs have demonstrated their ability to modulate host reactions, viral replication, and host-pathogen interactions. However, the complex interactions of different types of ncRNAs in the progression of COVID-19 remains understudied. In recent years, a novel mechanism of post-transcriptional gene regulation known as “competing endogenous RNA (ceRNA)” has been proposed. Long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), and viral ncRNAs function as ceRNAs, influencing the expression of associated genes by sequestering shared microRNAs. Recent research on SARS-CoV-2 has revealed that disruptions in specific ceRNA regulatory networks (ceRNETs) contribute to the abnormal expression of key infection-related genes and the establishment of distinctive infection characteristics. These findings present new opportunities to delve deeper into the underlying mechanisms of SARS-CoV-2 pathogenesis, offering potential biomarkers and therapeutic targets. This progress paves the way for a more comprehensive understanding of ceRNETs, shedding light on the intricate mechanisms involved. Further exploration of these mechanisms holds promise for enhancing our ability to prevent viral infections and develop effective antiviral treatments.</p></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2024-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1567134824000649/pdfft?md5=1d8e6800c2d9d3315b625c0fe05714b5&pid=1-s2.0-S1567134824000649-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141285390","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 : 2024-06-01DOI: 10.1016/j.meegid.2024.105601
Giulia Marsili , Carlo Pallotto , Claudia Fortuna , Antonello Amendola , Cristiano Fiorentini , Sara Esperti , Pierluigi Blanc , Lorenzo Roberto Suardi , Venturi Giulietta , Claudio Argentini
Toscana Virus (TosV) was firstly isolated from phlebotomine in our Institute about fifty years ago. Later, in 1984–1985, TosV infection, although asymptomatic in most cases, was shown to cause disease in humans, mainly fever and meningitis. By means of genetic analysis of part of M segment, we describe 3 new viral isolates obtained directly from cerebrospinal fluid or sera samples of patients diagnosed with TosV infection in July 2020 in Tuscany region. Phylogenesis was used to propose the clustering of TosV lineage A strains in 3 main groups, whereas deep mutational analysis based on 12 amino acid positions, allowed the identification of 9 putative strains. We discuss deep mutational analysis as a method to identify molecular signature of host adaptation and/or pathogenesis.
{"title":"Fifty years after the first identification of Toscana virus in Italy: Genomic characterization of viral isolates within lineage A and aminoacidic markers of evolution","authors":"Giulia Marsili , Carlo Pallotto , Claudia Fortuna , Antonello Amendola , Cristiano Fiorentini , Sara Esperti , Pierluigi Blanc , Lorenzo Roberto Suardi , Venturi Giulietta , Claudio Argentini","doi":"10.1016/j.meegid.2024.105601","DOIUrl":"10.1016/j.meegid.2024.105601","url":null,"abstract":"<div><p>Toscana Virus (TosV) was firstly isolated from phlebotomine in our Institute about fifty years ago. Later, in 1984–1985, TosV infection, although asymptomatic in most cases, was shown to cause disease in humans, mainly fever and meningitis. By means of genetic analysis of part of M segment, we describe 3 new viral isolates obtained directly from cerebrospinal fluid or sera samples of patients diagnosed with TosV infection in July 2020 in Tuscany region. Phylogenesis was used to propose the clustering of TosV lineage A strains in 3 main groups, whereas deep mutational analysis based on 12 amino acid positions, allowed the identification of 9 putative strains. We discuss deep mutational analysis as a method to identify molecular signature of host adaptation and/or pathogenesis.</p></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1567134824000522/pdfft?md5=b07396c628b7957211652013b82c9769&pid=1-s2.0-S1567134824000522-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141236354","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 : 2024-05-31DOI: 10.1016/j.meegid.2024.105611
Muhammad Hassan Ahmed , Kanwal Khan , Saba Tauseef , Khurshid Jalal , Urooj Haroon , Reaz Uddin , Magda H. Abdellattif , Ajmal Khan , Ahmed Al-Harrasi
Shigellosis, induced by Shigella flexneri, constitutes a significant health burden in developing nations, particularly impacting socioeconomically disadvantaged communities. Designated as the second most prevalent cause of diarrheal illness by the World Health Organization (WHO), it precipitates an estimated 212,000 fatalities annually. Within the spectrum of S. flexneri strains, serotype X is notably pervasive and resilient, yet its comprehensive characterization remains deficient. The present investigation endeavors to discern potential pharmacological targets and repurpose existing drug compounds against S. flexneri serotype X. Employing the framework of subtractive genomics, the study interrogates the reference genome of S. flexneri Serotype X (strain 2,002,017; UP000001884) to delineate its proteome into categories of non-homologous, non-paralogous, essential, virulent, and resistant constituents, thereby facilitating the identification of therapeutic targets. Subsequently, a screening of approximately 9000 compounds from the FDA library against the identified drug target aims to delineate efficacious agents for combating S. flexneri serotype X infections. The application of subtractive genomics methodology yields prognostic insights, unveiling non-paralogous proteins (n = 4122), non-homologues (n = 1803), essential (n = 1246), drug-like (n = 389), resistant (n = 167), alongside 42 virulent proteins within the reference proteome. This iterative process culminates in the identification of Serine O-acetyltransferase as a viable drug target. Subsequent virtual screening endeavors to unearth FDA-approved medicinal compounds capable of inhibiting Serine O-acetyltransferase. Noteworthy candidates such as DB12983, DB15085, DB16098, DB16185, and DB16262 emerge, exhibiting potential for mitigating S. flexneri Serotype X. Despite the auspicious findings, diligent scrutiny is imperative to ascertain the efficacy and safety profile of the proposed drug candidates vis-à-vis S. flexneri.
由弱志贺氏杆菌引起的志贺氏菌病是发展中国家的一个重大健康负担,尤其影响到社会经济条件较差的社区。世界卫生组织(WHO)将志贺氏菌病列为腹泻疾病的第二大流行病因,估计每年有 212,000 人死于该病。在 S. flexneri 菌株谱中,血清 X 型具有显著的普遍性和顽强的生命力,但其全面特征描述仍然不足。本研究采用减法基因组学框架,对 X 血清型 S. flexneri(2,002,017 株;UP000001884)的参考基因组进行分析,将其蛋白质组划分为非同源、非同类、基本、毒性和抗性等类别,从而帮助确定治疗靶点。随后,针对所确定的药物靶点,从 FDA 库中筛选出约 9000 种化合物,目的是确定抗柔性链球菌 X 血清型感染的有效药物。减法基因组学方法的应用揭示了参考蛋白质组中的非同类蛋白(n = 4122)、非同源蛋白(n = 1803)、必需蛋白(n = 1246)、类药物蛋白(n = 389)、耐药蛋白(n = 167)以及 42 种毒力蛋白,从而对预后产生了深刻的影响。这一迭代过程最终确定丝氨酸 O-乙酰转移酶为可行的药物靶点。随后的虚拟筛选努力发掘能够抑制丝氨酸 O-乙酰转移酶的 FDA 批准的药物化合物。值得注意的候选药物包括 DB12983、DB15085、DB16098、DB16185 和 DB16262,它们都具有减轻柔直杆菌血清 X 型感染的潜力。尽管研究结果良好,但仍有必要进行严格审查,以确定候选药物对柔直杆菌的疗效和安全性。
{"title":"Identification of therapeutic drug target of Shigella Flexneri serotype X through subtractive genomic approach and in-silico screening based on drug repurposing","authors":"Muhammad Hassan Ahmed , Kanwal Khan , Saba Tauseef , Khurshid Jalal , Urooj Haroon , Reaz Uddin , Magda H. Abdellattif , Ajmal Khan , Ahmed Al-Harrasi","doi":"10.1016/j.meegid.2024.105611","DOIUrl":"10.1016/j.meegid.2024.105611","url":null,"abstract":"<div><p>Shigellosis, induced by <em>Shigella flexneri</em>, constitutes a significant health burden in developing nations, particularly impacting socioeconomically disadvantaged communities. Designated as the second most prevalent cause of diarrheal illness by the World Health Organization (WHO), it precipitates an estimated 212,000 fatalities annually. Within the spectrum of <em>S. flexneri</em> strains, serotype X is notably pervasive and resilient, yet its comprehensive characterization remains deficient. The present investigation endeavors to discern potential pharmacological targets and repurpose existing drug compounds against <em>S. flexneri</em> serotype X. Employing the framework of subtractive genomics, the study interrogates the reference genome of <em>S. flexneri</em> Serotype X (strain 2,002,017; UP000001884) to delineate its proteome into categories of non-homologous, non-paralogous, essential, virulent, and resistant constituents, thereby facilitating the identification of therapeutic targets. Subsequently, a screening of approximately 9000 compounds from the FDA library against the identified drug target aims to delineate efficacious agents for combating <em>S. flexneri</em> serotype X infections. The application of subtractive genomics methodology yields prognostic insights, unveiling non-paralogous proteins (<em>n</em> = 4122), non-homologues (<em>n</em> = 1803), essential (<em>n</em> = 1246), drug-like (<em>n</em> = 389), resistant (<em>n</em> = 167), alongside 42 virulent proteins within the reference proteome. This iterative process culminates in the identification of <em>Serine O-acetyltransferase</em> as a viable drug target. Subsequent virtual screening endeavors to unearth FDA-approved medicinal compounds capable of inhibiting <em>Serine O-acetyltransferase</em>. Noteworthy candidates such as DB12983, DB15085, DB16098, DB16185, and DB16262 emerge, exhibiting potential for mitigating <em>S. flexneri</em> Serotype X. Despite the auspicious findings, diligent scrutiny is imperative to ascertain the efficacy and safety profile of the proposed drug candidates vis-à-vis <em>S. flexneri</em>.</p></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2024-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1567134824000625/pdfft?md5=7bf801d52f07e6b47e244e454a7d3c32&pid=1-s2.0-S1567134824000625-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141187186","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 : 2024-05-31DOI: 10.1016/j.meegid.2024.105612
Myeongji Cho , Xianglan Min , Nara Been , Hyeon S. Son
African swine fever (ASF) is a serious animal disease, and has spread to Africa, Europe and Asia, causing massive economic losses. African swine fever virus (ASFV) is transmitted from a reservoir host (warthog) to domestic pigs via a sylvatic cycle (transmission between warthogs and soft ticks) and a domestic cycle (transmission between domestic pigs) and survives by expressing a variety of genes related to virus–host interactions. We evaluated differences in codon usage patterns among ASFV genotypes and clades and explored the common and specific evolutionary and genetic characteristics of ASFV sequences. We analysed the evolutionary relationships, nucleotide compositions, codon usage patterns, selection pressures (mutational pressure and natural selection) and viral adaptation to host codon usage based on the coding sequences (CDS) of key functional genes of ASFV. AT bias was detected in the six genes analysed, irrespective of clade. The AT bias of genes (A224L, A179L, EP153R) encoding proteins involved in interaction with host cells after infection was high; among them, the AT bias of EP153R was the greatest at 78.3%. A large number of overrepresented codons were identified in EP153R, whereas there were no overrepresented codons with a relative synonymous codon usage (RSCU) value of ≥3 in B646L. In most genes, the pattern of selection pressure was similar for each clade, but in EP153R, diverse patterns of selection pressure were captured within the same clade and genotype. As a result of evaluating host adaptation based on the codon adaptation index (CAI), for B646L, E183L, CP204L and A179L, the codon usage patterns in all sequences were more similar to tick than domestic pig or wild boar. However, EP153R showed the lowest average CAI value of 0.52 when selecting tick as a reference set. The genes analysed in this study showed different magnitudes of selection pressure at the clade and genotype levels, which is likely to be related to the function of the encoded proteins and may determine key evolutionary traits of viruses, such as the level of genetic variation and host range. The diversity of codon adaptations at the genetic level in ASFV may account for differences in translational selection in ASFV hosts and provides insight into viral host adaptation and co-evolution.
{"title":"The evolutionary and genetic patterns of African swine fever virus","authors":"Myeongji Cho , Xianglan Min , Nara Been , Hyeon S. Son","doi":"10.1016/j.meegid.2024.105612","DOIUrl":"10.1016/j.meegid.2024.105612","url":null,"abstract":"<div><p>African swine fever (ASF) is a serious animal disease, and has spread to Africa, Europe and Asia, causing massive economic losses. African swine fever virus (ASFV) is transmitted from a reservoir host (warthog) to domestic pigs via a sylvatic cycle (transmission between warthogs and soft ticks) and a domestic cycle (transmission between domestic pigs) and survives by expressing a variety of genes related to virus–host interactions. We evaluated differences in codon usage patterns among ASFV genotypes and clades and explored the common and specific evolutionary and genetic characteristics of ASFV sequences. We analysed the evolutionary relationships, nucleotide compositions, codon usage patterns, selection pressures (mutational pressure and natural selection) and viral adaptation to host codon usage based on the coding sequences (CDS) of key functional genes of ASFV. AT bias was detected in the six genes analysed, irrespective of clade. The AT bias of genes (<em>A224L</em>, <em>A179L</em>, <em>EP153R</em>) encoding proteins involved in interaction with host cells after infection was high; among them, the AT bias of <em>EP153R</em> was the greatest at 78.3%. A large number of overrepresented codons were identified in <em>EP153R</em>, whereas there were no overrepresented codons with a relative synonymous codon usage (RSCU) value of ≥3 in <em>B646L</em>. In most genes, the pattern of selection pressure was similar for each clade, but in <em>EP153R</em>, diverse patterns of selection pressure were captured within the same clade and genotype. As a result of evaluating host adaptation based on the codon adaptation index (CAI), for <em>B646L</em>, <em>E183L</em>, <em>CP204L</em> and <em>A179L</em>, the codon usage patterns in all sequences were more similar to tick than domestic pig or wild boar. However, <em>EP153R</em> showed the lowest average CAI value of 0.52 when selecting tick as a reference set. The genes analysed in this study showed different magnitudes of selection pressure at the clade and genotype levels, which is likely to be related to the function of the encoded proteins and may determine key evolutionary traits of viruses, such as the level of genetic variation and host range. The diversity of codon adaptations at the genetic level in ASFV may account for differences in translational selection in ASFV hosts and provides insight into viral host adaptation and co-evolution.</p></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2024-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1567134824000637/pdfft?md5=6b29120335be25d4a5d8870896038621&pid=1-s2.0-S1567134824000637-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141201532","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 : 2024-05-27DOI: 10.1016/j.meegid.2024.105610
Veronika Zdarska, Milan Kolar, Patrik Mlynarcik
Our study highlights the escalating issue of beta-lactam resistance in nosocomial pathogens, driven by the broad spectrum of antibiotic-degrading enzymes and plasmid exchange. We catalogued known beta-lactamases across 230 bacterial genera, identified 2349 potential beta-lactamases across over 673 genera, and anticipate discovering many new types, underscoring the need for targeted gene analysis in combating resistance. This study also elucidates the complex relationship between the diversity and frequency of beta-lactamase genes across bacterial genera, highlighting the need for genus-specific approaches in combating antibiotic resistance and emphasizing these genes' significant global distribution and host-specific prevalence. We report many transcriptional regulators, transposases and other factors in the genomes of 20 different bacterial isolates, some of which are consistent with the ability of these species to adapt to different environments. Although we could not determine precisely which factors regulate the presence of beta-lactamases in specific bacteria, we found that the proportion of regulatory genes, the size of the genome, and other factors are not decisive. Further studies are needed to elucidate key aspects of this process.
{"title":"Occurrence of beta-lactamases in bacteria","authors":"Veronika Zdarska, Milan Kolar, Patrik Mlynarcik","doi":"10.1016/j.meegid.2024.105610","DOIUrl":"10.1016/j.meegid.2024.105610","url":null,"abstract":"<div><p>Our study highlights the escalating issue of beta-lactam resistance in nosocomial pathogens, driven by the broad spectrum of antibiotic-degrading enzymes and plasmid exchange. We catalogued known beta-lactamases across 230 bacterial genera, identified 2349 potential beta-lactamases across over 673 genera, and anticipate discovering many new types, underscoring the need for targeted gene analysis in combating resistance. This study also elucidates the complex relationship between the diversity and frequency of beta-lactamase genes across bacterial genera, highlighting the need for genus-specific approaches in combating antibiotic resistance and emphasizing these genes' significant global distribution and host-specific prevalence. We report many transcriptional regulators, transposases and other factors in the genomes of 20 different bacterial isolates, some of which are consistent with the ability of these species to adapt to different environments. Although we could not determine precisely which factors regulate the presence of beta-lactamases in specific bacteria, we found that the proportion of regulatory genes, the size of the genome, and other factors are not decisive. Further studies are needed to elucidate key aspects of this process.</p></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2024-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1567134824000613/pdfft?md5=47cd61d00cc255611725dea0a32ff7bc&pid=1-s2.0-S1567134824000613-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141177039","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 : 2024-05-26DOI: 10.1016/j.meegid.2024.105609
Zhendong Du , Danni Tong , Xueqiu Chen , Fei Wu , Shengjun Jiang , Jingju Zhang , Yi Yang , Rui Wang , Sambuu Gantuya , Tserennyam Davaajargal , Sukhbaatar Lkhagvatseren , Zayat Batsukh , Aifang Du , Guangxu Ma
Nuclear hormone receptors (NHRs) are emerging target candidates against nematode infection and resistance. However, there is a lack of comprehensive information on NHR-coding genes in parasitic nematodes. In this study, we curated the nhr gene family for 60 major parasitic nematodes from humans and animals. Compared with the free-living model organism Caenorhabditis elegans, a remarkable contraction of the nhr family was revealed in parasitic species, with genetic diversification and conservation unveiled among nematode Clades I (10–13), III (16–42), IV (33–35) and V (25–64). Using an in vitro biosystem, we demonstrated that 40 nhr genes in a blood-feeding nematode Haemonchus contortus (clade V; barber's pole worm) were responsive to host serum and one nhr gene (i.e., nhr-64) was consistently stimulated by anthelmintics (i.e., ivermectin, thiabendazole and levamisole); Using a high-throughput RNA interference platform, we knocked down 43 nhr genes of H. contortus and identified at least two genes that are required for the viability (i.e., nhr-105) and development (i.e., nhr-17) of the infective larvae of this parasitic nematode in vitro. Harnessing this preliminary functional atlas of nhr genes for H. contortus will prime the biological studies of this gene family in nematode genetics, infection, and anthelmintic metabolism within host animals, as well as the promising discovery of novel intervention targets.
{"title":"Genome-wide RNA interference of the nhr gene family in barber's pole worm identified members crucial for larval viability in vitro","authors":"Zhendong Du , Danni Tong , Xueqiu Chen , Fei Wu , Shengjun Jiang , Jingju Zhang , Yi Yang , Rui Wang , Sambuu Gantuya , Tserennyam Davaajargal , Sukhbaatar Lkhagvatseren , Zayat Batsukh , Aifang Du , Guangxu Ma","doi":"10.1016/j.meegid.2024.105609","DOIUrl":"10.1016/j.meegid.2024.105609","url":null,"abstract":"<div><p>Nuclear hormone receptors (NHRs) are emerging target candidates against nematode infection and resistance. However, there is a lack of comprehensive information on NHR-coding genes in parasitic nematodes. In this study, we curated the <em>nhr</em> gene family for 60 major parasitic nematodes from humans and animals. Compared with the free-living model organism <em>Caenorhabditis elegans</em>, a remarkable contraction of the <em>nhr</em> family was revealed in parasitic species, with genetic diversification and conservation unveiled among nematode Clades I (10–13), III (16–42), IV (33–35) and V (25–64). Using an <em>in vitro</em> biosystem, we demonstrated that 40 <em>nhr</em> genes in a blood-feeding nematode <em>Haemonchus contortus</em> (clade V; barber's pole worm) were responsive to host serum and one <em>nhr</em> gene (<em>i.e.</em>, <em>nhr-64</em>) was consistently stimulated by anthelmintics (<em>i.e.</em>, ivermectin, thiabendazole and levamisole); Using a high-throughput RNA interference platform, we knocked down 43 <em>nhr</em> genes of <em>H. contortus</em> and identified at least two genes that are required for the viability (<em>i.e.</em>, <em>nhr-105</em>) and development (<em>i.e.</em>, <em>nhr-17</em>) of the infective larvae of this parasitic nematode <em>in vitro</em>. Harnessing this preliminary functional atlas of <em>nhr</em> genes for <em>H. contortus</em> will prime the biological studies of this gene family in nematode genetics, infection, and anthelmintic metabolism within host animals, as well as the promising discovery of novel intervention targets.</p></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2024-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1567134824000601/pdfft?md5=be2180ce9b1468c271d64c55af3ff979&pid=1-s2.0-S1567134824000601-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141162930","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 : 2024-05-26DOI: 10.1016/j.meegid.2024.105607
Clark Mbou-Boutambe , Illich Manfred Mombo , Virginie Rougeron , Fanny Degrugillier , Philippe Gauthier , Boris Makanga , Barthélemy Ngoubangoye , Eric M. Leroy , Franck Prugnolle , Larson Boundenga
Caliciviruses (Caliciviridae) and astroviruses (Astroviridae) are among the leading cause of non-bacterial foodborne disease and gastroenteritis in human. These non-enveloped RNA viruses infect a wide range of vertebrate species including rodents. Rodents are among the most important hosts of infectious diseases globally and are responsible for over 80 zoonotic pathogens that affect humans. Therefore, screening pathogens in rodents will be is necessary to prevent cross-species transmission to prevent zoonotic outbreaks. In the present study, we screened caliciviruses and astroviruses in order to describe their diversity and whether they harbor strains that can infect humans. RNA was then extracted from intestine samples of 245 rodents and retrotranscribed in cDNA to screen caliciviruses and astroviruses by PCRs. All the samples tested negative for caliciviruses and while astroviruses were detected in 18 (7.3%) samples of Rattus rattus species. Phylogenetic analyses based on the RdRp gene showed that all the sequences belonged to Mamastrovirus genus in which they were genetically related to R. rattus related AstVs previously detected in Gabon or in Rattus spp. AstV from Kenya and Asia. These findings suggested that transportation such as land and railway, as well national and international trade, are likely to facilitate spread of AstVs by the dissemination of rodents.
{"title":"Investigation of caliciviruses and astroviruses in Gabonese rodents: A possible influence of national and international trade on the spread of enteric viruses","authors":"Clark Mbou-Boutambe , Illich Manfred Mombo , Virginie Rougeron , Fanny Degrugillier , Philippe Gauthier , Boris Makanga , Barthélemy Ngoubangoye , Eric M. Leroy , Franck Prugnolle , Larson Boundenga","doi":"10.1016/j.meegid.2024.105607","DOIUrl":"10.1016/j.meegid.2024.105607","url":null,"abstract":"<div><p>Caliciviruses (<em>Caliciviridae</em>) and astroviruses (<em>Astroviridae</em>) are among the leading cause of non-bacterial foodborne disease and gastroenteritis in human. These non-enveloped RNA viruses infect a wide range of vertebrate species including rodents. Rodents are among the most important hosts of infectious diseases globally and are responsible for over 80 zoonotic pathogens that affect humans. Therefore, screening pathogens in rodents will be is necessary to prevent cross-species transmission to prevent zoonotic outbreaks. In the present study, we screened caliciviruses and astroviruses in order to describe their diversity and whether they harbor strains that can infect humans. RNA was then extracted from intestine samples of 245 rodents and retrotranscribed in cDNA to screen caliciviruses and astroviruses by PCRs. All the samples tested negative for caliciviruses and while astroviruses were detected in 18 (7.3%) samples of <em>Rattus rattus</em> species. Phylogenetic analyses based on the RdRp gene showed that all the sequences belonged to <em>Mamastrovirus</em> genus in which they were genetically related to <em>R. rattus</em> related AstVs previously detected in Gabon or in <em>Rattus</em> spp. AstV from Kenya and Asia. These findings suggested that transportation such as land and railway, as well national and international trade, are likely to facilitate spread of AstVs by the dissemination of rodents.</p></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2024-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1567134824000583/pdfft?md5=f2e2ef29274bb4d8216382c774bd9f60&pid=1-s2.0-S1567134824000583-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141162933","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 : 2024-05-23DOI: 10.1016/j.meegid.2024.105608
Haiting Zhao , Lang Qin , Xiaolong Deng , Zhilei Wang , Runzhou Jiang , Stuart R. Reitz , Shengyong Wu , Zhen He
Several studies have showed that the nucleotide and dinucleotide composition of viruses possibly follows their host species or protein coding region. Nevertheless, the influence of viral segment on viral nucleotide and dinucleotide composition is still unknown. Here, we explored through tomato spotted wilt virus (TSWV), a segmented virus that seriously threatens the production of tomatoes all over the world. Through nucleotide composition analysis, we found the same over-representation of A across all viral segments at the first and second codon position, but it exhibited distinct in segments at the third codon position. Interestingly, the protein coding regions which encoded by the same or different segments exhibit obvious distinct nucleotide preference. Then, we found that the dinucleotides UpG and CpU were overrepresented and the dinucleotides UpA, CpG and GpU were underrepresented, not only in the complete genomic sequences, but also in different segments, protein coding regions and host species. Notably, 100% of the data investigated here were predicted to the correct viral segment and protein coding region, despite the fact that only 67% of the data analyzed here were predicted to the correct viral host species. In conclusion, in case study of TSWV, nucleotide composition and dinucleotide preference of segment viruses are more strongly dependent on segment and protein coding region than on host species. This research provides a novel perspective on the molecular evolutionary mechanisms of TSWV and provides reference for future research on genetic diversity of segmented viruses.
{"title":"Nucleotide and dinucleotide preference of segmented viruses are shaped more by segment: In case study of tomato spotted wilt virus","authors":"Haiting Zhao , Lang Qin , Xiaolong Deng , Zhilei Wang , Runzhou Jiang , Stuart R. Reitz , Shengyong Wu , Zhen He","doi":"10.1016/j.meegid.2024.105608","DOIUrl":"10.1016/j.meegid.2024.105608","url":null,"abstract":"<div><p>Several studies have showed that the nucleotide and dinucleotide composition of viruses possibly follows their host species or protein coding region. Nevertheless, the influence of viral segment on viral nucleotide and dinucleotide composition is still unknown. Here, we explored through tomato spotted wilt virus (TSWV), a segmented virus that seriously threatens the production of tomatoes all over the world. Through nucleotide composition analysis, we found the same over-representation of A across all viral segments at the first and second codon position, but it exhibited distinct in segments at the third codon position. Interestingly, the protein coding regions which encoded by the same or different segments exhibit obvious distinct nucleotide preference. Then, we found that the dinucleotides UpG and CpU were overrepresented and the dinucleotides UpA, CpG and GpU were underrepresented, not only in the complete genomic sequences, but also in different segments, protein coding regions and host species. Notably, 100% of the data investigated here were predicted to the correct viral segment and protein coding region, despite the fact that only 67% of the data analyzed here were predicted to the correct viral host species. In conclusion, in case study of TSWV, nucleotide composition and dinucleotide preference of segment viruses are more strongly dependent on segment and protein coding region than on host species. This research provides a novel perspective on the molecular evolutionary mechanisms of TSWV and provides reference for future research on genetic diversity of segmented viruses.</p></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2024-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1567134824000595/pdfft?md5=ea9b45052ec8191939317351a789108f&pid=1-s2.0-S1567134824000595-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141130644","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}