Pub Date : 2025-01-01DOI: 10.1016/j.dcit.2025.100041
Hongrang Zhou , Xiaoling Wang , Shuai Han , Ning Xiao
Echinococcosis is a group of chronic zoonotic parasitic diseases caused by the larval stage of Echinococcus tapeworms, which infect both humans and animals. Due to the complex life cycle, broad geographic distribution and wide range of host species of Echinococcus, controlling and eliminating echinococcosis remains highly challenging. Source control and the interruption of transmission pathways are critical but difficult, which always impede prevention and control efforts. Therefore, accurate detection, differentiation, diagnosis, and effective treatment, along with real-time monitoring of infections across various hosts, are essential prerequisites. This paper provides a comprehensive review of the current epidemiological status of echinococcosis, research progress, prevention and control measures, and the main challenges in efforts from control toward elimination of the disease in China, with the aim of providing reference for further optimization of present control strategies and surveillance methods.
{"title":"Advances and challenges in the prevention, control and research of echinococcosis in China","authors":"Hongrang Zhou , Xiaoling Wang , Shuai Han , Ning Xiao","doi":"10.1016/j.dcit.2025.100041","DOIUrl":"10.1016/j.dcit.2025.100041","url":null,"abstract":"<div><div>Echinococcosis is a group of chronic zoonotic parasitic diseases caused by the larval stage of <em>Echinococcus</em> tapeworms, which infect both humans and animals. Due to the complex life cycle, broad geographic distribution and wide range of host species of <em>Echinococcus</em>, controlling and eliminating echinococcosis remains highly challenging. Source control and the interruption of transmission pathways are critical but difficult, which always impede prevention and control efforts. Therefore, accurate detection, differentiation, diagnosis, and effective treatment, along with real-time monitoring of infections across various hosts, are essential prerequisites. This paper provides a comprehensive review of the current epidemiological status of echinococcosis, research progress, prevention and control measures, and the main challenges in efforts from control toward elimination of the disease in China, with the aim of providing reference for further optimization of present control strategies and surveillance methods.</div></div>","PeriodicalId":100358,"journal":{"name":"Decoding Infection and Transmission","volume":"3 ","pages":"Article 100041"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143592791","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-01DOI: 10.1016/j.dcit.2025.100058
Xiaohong Zhou , Xiang Guo , Xiaoguang Chen
Chikungunya fever (CHIK) is caused by the Chikungunya virus (CHIKV), a mosquito-borne RNA virus of the Alphavirus genus (family Togaviridae). CHIK has been imported and caused several local epidemic in China in recent years. This article describes the epidemiology of CHIK, and proposes the interventions as a response to this emerging infectious disease in China.
{"title":"Response to Chikungunya fever in China: are we ready?","authors":"Xiaohong Zhou , Xiang Guo , Xiaoguang Chen","doi":"10.1016/j.dcit.2025.100058","DOIUrl":"10.1016/j.dcit.2025.100058","url":null,"abstract":"<div><div>Chikungunya fever (CHIK) is caused by the Chikungunya virus (CHIKV), a mosquito-borne RNA virus of the Alphavirus genus (family Togaviridae). CHIK has been imported and caused several local epidemic in China in recent years. This article describes the epidemiology of CHIK, and proposes the interventions as a response to this emerging infectious disease in China.</div></div>","PeriodicalId":100358,"journal":{"name":"Decoding Infection and Transmission","volume":"3 ","pages":"Article 100058"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145019029","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-01DOI: 10.1016/j.dcit.2025.100060
Xinkun Zhu , Junyang Ma , Renge Hu , Qing Yang , Lei Yang , Shu Li , Yuanhuan Kang , Zhenlin Liang , Hany M. Elsheikha , Wei Cong
Objective
Amid rising bacterial resistance, polymyxins are a critical last resort against multidrug-resistant Gram-negative infections. Understanding and predicting the emergence of novel, nonmobile colistin resistance (NMCR) genes are essential to preserving their efficacy and preventing potential resistance crises.
Methods
Following the discovery of a high-level polymyxin B-resistant Vibrio harveyi strain WHSS0915, which exhibited antimicrobial resistance, we characterized the chromosomally encoded polymyxin-resistance protein NMCR-6 (WHSS0915). Through BLASTP searches against the Pan-Vibrio protein database, we identified the chromosomal eptA in Vibrio species as a NMCR (NMCR-6). We then investigated its global epidemiology and the potential determinants contributing to the spread of NMCR-6-bearing Vibrio strains.
Results
We identified and characterized the NMCR-6 protein in the V. harveyi strain WHSS0915. BLASTP searches based on the protein sequence revealed 14 158 sequences with over 60% homology to NMCR-6. Thirteen subtypes, named NMCR-6.1 to NMCR-6.13 according to the year of their earliest publication were classified. Phylogenetic analyses showed NMCR-6 variants form a distinctive branch among other mobile colistin resistance (MCR)/NMCR proteins. Statistical analysis of pathogenic Vibrio hosts carrying NMCR-6 revealed a broad distribution across different sample sources, detecting it in 7 clinically significant Vibrio species, notably V. parahaemolyticus. A global geographical analysis of NMCR-6 Vibrio hosts suggested that coastal extent, latitude, and temperature influence the distribution of NMCR-6 harboring Vibrio hosts.
Conclusion
Our research defined and evaluated the global epidemiology of NMCR-6 in Vibrio species, revealing the dissemination of resistance genes within pathogenic Vibrio and the associated public health risks. This knowledge will aid in predicting the emergence of new mobile colistin resistance genes.
{"title":"NMCR-6, a novel nonmobile colistin resistance gene in Vibrio bacteria: full characterization and global perspective","authors":"Xinkun Zhu , Junyang Ma , Renge Hu , Qing Yang , Lei Yang , Shu Li , Yuanhuan Kang , Zhenlin Liang , Hany M. Elsheikha , Wei Cong","doi":"10.1016/j.dcit.2025.100060","DOIUrl":"10.1016/j.dcit.2025.100060","url":null,"abstract":"<div><h3>Objective</h3><div>Amid rising bacterial resistance, polymyxins are a critical last resort against multidrug-resistant Gram-negative infections. Understanding and predicting the emergence of novel, nonmobile colistin resistance (NMCR) genes are essential to preserving their efficacy and preventing potential resistance crises.</div></div><div><h3>Methods</h3><div>Following the discovery of a high-level polymyxin B-resistant <em>Vibrio harveyi</em> strain WHSS0915, which exhibited antimicrobial resistance, we characterized the chromosomally encoded polymyxin-resistance protein NMCR-6 (WHSS0915). Through BLASTP searches against the Pan-Vibrio protein database, we identified the chromosomal <em>eptA</em> in <em>Vibrio</em> species as a NMCR (NMCR-6). We then investigated its global epidemiology and the potential determinants contributing to the spread of NMCR-6-bearing <em>Vibrio</em> strains.</div></div><div><h3>Results</h3><div>We identified and characterized the NMCR-6 protein in the <em>V. harveyi</em> strain WHSS0915. BLASTP searches based on the protein sequence revealed 14 158 sequences with over 60% homology to NMCR-6. Thirteen subtypes, named NMCR-6.1 to NMCR-6.13 according to the year of their earliest publication were classified. Phylogenetic analyses showed NMCR-6 variants form a distinctive branch among other mobile colistin resistance (MCR)/NMCR proteins. Statistical analysis of pathogenic <em>Vibrio</em> hosts carrying NMCR-6 revealed a broad distribution across different sample sources, detecting it in 7 clinically significant <em>Vibrio</em> species, notably <em>V. parahaemolyticus</em>. A global geographical analysis of NMCR-6 <em>Vibrio</em> hosts suggested that coastal extent, latitude, and temperature influence the distribution of NMCR-6 harboring <em>Vibrio</em> hosts.</div></div><div><h3>Conclusion</h3><div>Our research defined and evaluated the global epidemiology of NMCR-6 in <em>Vibrio</em> species, revealing the dissemination of resistance genes within pathogenic <em>Vibrio</em> and the associated public health risks. This knowledge will aid in predicting the emergence of new mobile colistin resistance genes.</div></div>","PeriodicalId":100358,"journal":{"name":"Decoding Infection and Transmission","volume":"3 ","pages":"Article 100060"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145264831","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-01DOI: 10.1016/j.dcit.2025.100061
R. Aswini, B. Saranya, K. Gayathri, E. Karthikeyan
The integration of advanced technologies, including next-generation sequencing, multiomics approaches, and artificial intelligence (AI), has revolutionized pathogen surveillance and preparedness. Multiomics technologies provide detailed information about how pathogens work and interact with hosts. However, the integration of diverse omics data poses bioinformatics challenges related to data heterogeneity, dimensionality, and standardization. AI is crucial for solving problems, predicting outbreaks in advance, accurately forecasting how diseases spread, and identifying new pathogen changes. Using AI in conjunction with omics and epidemiological information simplifies activities that include the identification of biomarkers, the classification of individuals, and individual treatments. The use of genomic surveillance monitoring of tuberculosis (TB) and foodborne outbreaks and AI to predict the spread of COVID-19, detect variants, and develop vaccines with the help of multiomics technologies may be considered successful. Nevertheless, the current adoption of AI-based services in public health is characterized by issues of data quality, the presence of bias in the algorithmic system, the unit of explainability, and even ethical implications. Increased preparedness for pandemics at the global level requires collaboration networks, the sharing of open data, the protection of privacy, and the adoption of One Health approaches. The increasing development of multiomics approaches and AI-based techniques and their combination has great potential to transform infectious disease surveillance and response during the precision public health era.
{"title":"Revolutionizing infectious disease surveillance: Multi-omics technologies and AI-driven integration","authors":"R. Aswini, B. Saranya, K. Gayathri, E. Karthikeyan","doi":"10.1016/j.dcit.2025.100061","DOIUrl":"10.1016/j.dcit.2025.100061","url":null,"abstract":"<div><div>The integration of advanced technologies, including next-generation sequencing, multiomics approaches, and artificial intelligence (AI), has revolutionized pathogen surveillance and preparedness. Multiomics technologies provide detailed information about how pathogens work and interact with hosts. However, the integration of diverse omics data poses bioinformatics challenges related to data heterogeneity, dimensionality, and standardization. AI is crucial for solving problems, predicting outbreaks in advance, accurately forecasting how diseases spread, and identifying new pathogen changes. Using AI in conjunction with omics and epidemiological information simplifies activities that include the identification of biomarkers, the classification of individuals, and individual treatments. The use of genomic surveillance monitoring of tuberculosis (TB) and foodborne outbreaks and AI to predict the spread of COVID-19, detect variants, and develop vaccines with the help of multiomics technologies may be considered successful. Nevertheless, the current adoption of AI-based services in public health is characterized by issues of data quality, the presence of bias in the algorithmic system, the unit of explainability, and even ethical implications. Increased preparedness for pandemics at the global level requires collaboration networks, the sharing of open data, the protection of privacy, and the adoption of One Health approaches. The increasing development of multiomics approaches and AI-based techniques and their combination has great potential to transform infectious disease surveillance and response during the precision public health era.</div></div>","PeriodicalId":100358,"journal":{"name":"Decoding Infection and Transmission","volume":"3 ","pages":"Article 100061"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145464921","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-01DOI: 10.1016/j.dcit.2025.100045
Sunjie Yang , Zedong Wang , Ruixin Guo , Yong Qi
Alongshan virus (ALSV) is an emerging tick-borne segmented RNA virus belonging to the Flaviviridae family, first identified in Northeastern China in 2017. ALSV is currently classified within the Jingmenvirus group, which includes other segmented flavi-like viruses. Since its discovery, ALSV has been detected in various regions, including China, Russia, and several European countries, highlighting its expanding geographic distribution. This review summarizes the latest research progress on ALSV, focusing on its pathogenic characteristics, pathogenicity, epidemiological features, and detection methods. ALSV exhibits a segmented genome, unique structural and nonstructural proteins, and potential neurotropism, with clinical symptoms resembling other tick-borne diseases. Detection methods, including nucleic acid detection and high-throughput sequencing, have advanced ALSV research, though challenges remain in standardization and clinical application. Understanding ALSV's ecological characteristics, transmission mechanisms, and public health impact is crucial for developing effective prevention and control strategies. This review provides valuable insights for healthcare institutions and policymakers to mitigate ALSV's risks.
{"title":"The Alongshan virus: A comprehensive review of its pathogenic characteristics, epidemiology, and detection strategies","authors":"Sunjie Yang , Zedong Wang , Ruixin Guo , Yong Qi","doi":"10.1016/j.dcit.2025.100045","DOIUrl":"10.1016/j.dcit.2025.100045","url":null,"abstract":"<div><div>Alongshan virus (ALSV) is an emerging tick-borne segmented RNA virus belonging to the <em>Flaviviridae</em> family, first identified in Northeastern China in 2017. ALSV is currently classified within the Jingmenvirus group, which includes other segmented flavi-like viruses. Since its discovery, ALSV has been detected in various regions, including China, Russia, and several European countries, highlighting its expanding geographic distribution. This review summarizes the latest research progress on ALSV, focusing on its pathogenic characteristics, pathogenicity, epidemiological features, and detection methods. ALSV exhibits a segmented genome, unique structural and nonstructural proteins, and potential neurotropism, with clinical symptoms resembling other tick-borne diseases. Detection methods, including nucleic acid detection and high-throughput sequencing, have advanced ALSV research, though challenges remain in standardization and clinical application. Understanding ALSV's ecological characteristics, transmission mechanisms, and public health impact is crucial for developing effective prevention and control strategies. This review provides valuable insights for healthcare institutions and policymakers to mitigate ALSV's risks.</div></div>","PeriodicalId":100358,"journal":{"name":"Decoding Infection and Transmission","volume":"3 ","pages":"Article 100045"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143835181","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-01DOI: 10.1016/j.dcit.2025.100047
Abdullahi Tunde Aborode , Oche Joseph Otorkpa , Omobolaji Omokorede Ayeseni , Sedoten Oluwaseun Ogun , Chibuzor Stella Amadi , Sharmistha Roy , Abdulhakeem Abayomi Olorukooba , Kenechukwu Obumneme Samuel Nwosu , Oluwafunto Adepeju Aladekomo , Barakat Olajumoke Kolawole , Tolulope Tiwa Ogundipe , Seto Charles Ogunleye , Segun Olapade , Bakare-Abidola Taiwo , Isreal Ayobami Onifade
Rabies remains a significant public health threat in Africa, and disproportionately impacts vulnerable populations to cause thousands of deaths annually. Rabies is a preventable disease and control efforts include a global target of rabies elimination by 2030. But, challenges impede this goal, such as limited access to vaccines, insufficient public awareness, and weak healthcare infrastructure. This review evaluates the barriers to vaccination coverage, including logistical constraints in vaccine delivery, high costs, and the lack of sustained funding. Additionally, the review discusses innovative strategies and best practices for rabies control, such as community-based education programs, and the integration of One Health approaches. This study synthesizes current evidence, to emphasize the urgent need for coordinated efforts, increased investment, and policy reforms to achieve sustainable rabies elimination in Africa.
{"title":"Rabies in Africa: Vaccination coverage and strategies for elimination by 2030","authors":"Abdullahi Tunde Aborode , Oche Joseph Otorkpa , Omobolaji Omokorede Ayeseni , Sedoten Oluwaseun Ogun , Chibuzor Stella Amadi , Sharmistha Roy , Abdulhakeem Abayomi Olorukooba , Kenechukwu Obumneme Samuel Nwosu , Oluwafunto Adepeju Aladekomo , Barakat Olajumoke Kolawole , Tolulope Tiwa Ogundipe , Seto Charles Ogunleye , Segun Olapade , Bakare-Abidola Taiwo , Isreal Ayobami Onifade","doi":"10.1016/j.dcit.2025.100047","DOIUrl":"10.1016/j.dcit.2025.100047","url":null,"abstract":"<div><div>Rabies remains a significant public health threat in Africa, and disproportionately impacts vulnerable populations to cause thousands of deaths annually. Rabies is a preventable disease and control efforts include a global target of rabies elimination by 2030. But, challenges impede this goal, such as limited access to vaccines, insufficient public awareness, and weak healthcare infrastructure. This review evaluates the barriers to vaccination coverage, including logistical constraints in vaccine delivery, high costs, and the lack of sustained funding. Additionally, the review discusses innovative strategies and best practices for rabies control, such as community-based education programs, and the integration of One Health approaches. This study synthesizes current evidence, to emphasize the urgent need for coordinated efforts, increased investment, and policy reforms to achieve sustainable rabies elimination in Africa.</div></div>","PeriodicalId":100358,"journal":{"name":"Decoding Infection and Transmission","volume":"3 ","pages":"Article 100047"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143903719","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-01DOI: 10.1016/j.dcit.2025.100056
Jingze Liu , Xu Zhang , Shicheng Li , Xiao Ding
Objective
Influenza A viruses, members of the Orthomyxoviridae family, are major causative agents of past flu pandemics and can infect a wide range of hosts depending on their hemagglutinin (HA) and neuraminidase (NA) gene combinations. This study aimed to identify genome-wide characteristic nucleotide fragments for rapid detection and subtype typing of influenza A viruses from large-scale genomic data.
Methods
Complete influenza genome sequences were analyzed to identify candidate characteristic fragments specific to influenza A viruses. The fragments were evaluated based on conservation probability, coverage, and specificity across different viral species, subtypes, and hosts. High-coverage fragments were selected for further analysis. Multiplex PCR primers were then designed based on the selected fragments, and their predictive performance was assessed via in silico PCR.
Results
Characteristic fragments from the M gene (20–40 bp) distinguished influenza A viruses with >92 % coverage and >99 % specificity. Forty-four fragments from the HA gene were identified across 26 subtypes, indicating the HA gene's utility for subtype differentiation. Regarding host specificity, canine-derived strains contained unique 20–40 bp fragments, the avian-specific fragment was 20 bp, and no such fragments were detected in other hosts. The designed primers achieved >98 % predicted accuracy for universal detection (M gene) and for H1N1- and H3N2-specific subtypes.
Conclusion
Genome-wide screening of influenza A virus sequences identified highly conserved and subtype-specific nucleotide fragments that enable rapid detection and precise subtyping. These findings provide a valuable resource for molecular surveillance and diagnostic assay development.
{"title":"Genome-wide identification of characteristic nucleotide fragments for surveillance and subtype typing of influenza A viruses","authors":"Jingze Liu , Xu Zhang , Shicheng Li , Xiao Ding","doi":"10.1016/j.dcit.2025.100056","DOIUrl":"10.1016/j.dcit.2025.100056","url":null,"abstract":"<div><h3>Objective</h3><div>Influenza A viruses, members of the Orthomyxoviridae family, are major causative agents of past flu pandemics and can infect a wide range of hosts depending on their hemagglutinin (HA) and neuraminidase (NA) gene combinations. This study aimed to identify genome-wide characteristic nucleotide fragments for rapid detection and subtype typing of influenza A viruses from large-scale genomic data.</div></div><div><h3>Methods</h3><div>Complete influenza genome sequences were analyzed to identify candidate characteristic fragments specific to influenza A viruses. The fragments were evaluated based on conservation probability, coverage, and specificity across different viral species, subtypes, and hosts. High-coverage fragments were selected for further analysis. Multiplex PCR primers were then designed based on the selected fragments, and their predictive performance was assessed via in silico PCR.</div></div><div><h3>Results</h3><div>Characteristic fragments from the M gene (20–40 bp) distinguished influenza A viruses with >92 % coverage and >99 % specificity. Forty-four fragments from the HA gene were identified across 26 subtypes, indicating the HA gene's utility for subtype differentiation. Regarding host specificity, canine-derived strains contained unique 20–40 bp fragments, the avian-specific fragment was 20 bp, and no such fragments were detected in other hosts. The designed primers achieved >98 % predicted accuracy for universal detection (M gene) and for H1N1- and H3N2-specific subtypes.</div></div><div><h3>Conclusion</h3><div>Genome-wide screening of influenza A virus sequences identified highly conserved and subtype-specific nucleotide fragments that enable rapid detection and precise subtyping. These findings provide a valuable resource for molecular surveillance and diagnostic assay development.</div></div>","PeriodicalId":100358,"journal":{"name":"Decoding Infection and Transmission","volume":"3 ","pages":"Article 100056"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144865678","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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