{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,29]],"date-time":"2026-08-29T00:22:04Z","timestamp":1787962924179,"version":"build-2784847793"},"reference-count":62,"publisher":"MDPI AG","issue":"6","license":[{"start":{"date-parts":[[2024,3,9]],"date-time":"2024-03-09T00:00:00Z","timestamp":1709942400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"DURABLE","award":["101102733"],"award-info":[{"award-number":["101102733"]}]},{"name":"DURABLE","award":["EU4H-2022-DGA-MS-IBA-1"],"award-info":[{"award-number":["EU4H-2022-DGA-MS-IBA-1"]}]},{"name":"European Union","award":["101102733"],"award-info":[{"award-number":["101102733"]}]},{"name":"European Union","award":["EU4H-2022-DGA-MS-IBA-1"],"award-info":[{"award-number":["EU4H-2022-DGA-MS-IBA-1"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>In response to the pressing need for continuous monitoring of emergence and circulation of pathogens through genomics, it is imperative to keep developing bioinformatics tools that can help in their rapid characterization and classification. Here, we introduce ReporType, a versatile bioinformatics pipeline designed for targeted loci screening and typing of infectious agents. Developed using the snakemake workflow manager, ReporType integrates multiple software for read quality control and de novo assembly, and then applies ABRicate for locus screening, culminating in the production of easily interpretable reports for the identification of pathogen genotypes and\/or screening of specific genomic loci. The pipeline accommodates a range of input formats, from Illumina or Oxford Nanopore Technology (ONT) reads (FASTQ) to Sanger sequencing files (AB1), or FASTA files, making it flexible for application in multiple pathogens and with different purposes. ReporType is released with pre-prepared databases for some viruses and bacteria, yet it remains easily configurable to handle custom databases. ReporType performance and functionality were validated through proof-of-concept exercises, encompassing diverse pathogenic species, including viruses such as measles, Newcastle disease virus (NDV), Dengue virus (DENV), influenza, hepatitis C virus (HCV) and Human T-Cell Lymphotropic virus type 1 (HTLV-1), as well as bacteria like Chlamydia trachomatis and Legionella pneumophila. In summary, ReporType emerges as a simple, dynamic and pan-pathogen tool, poised to evolve in tandem with the ever-changing needs of the fields of pathogen genomics, infectious disease epidemiology, and one health bioinformatics. ReporType is freely available at GitHub.<\/jats:p>","DOI":"10.3390\/ijms25063172","type":"journal-article","created":{"date-parts":[[2024,3,11]],"date-time":"2024-03-11T06:05:30Z","timestamp":1710137130000},"page":"3172","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["ReporType: A Flexible Bioinformatics Tool for Targeted Loci Screening and Typing of Infectious Agents"],"prefix":"10.3390","volume":"25","author":[{"ORCID":"https:\/\/orcid.org\/0009-0004-3716-6503","authenticated-orcid":false,"given":"Helena","family":"Cruz","sequence":"first","affiliation":[{"name":"Institute of Biomedicine-iBiMED, Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Miguel","family":"Pinheiro","sequence":"additional","affiliation":[{"name":"Institute of Biomedicine-iBiMED, Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3767-2209","authenticated-orcid":false,"given":"V\u00edtor","family":"Borges","sequence":"additional","affiliation":[{"name":"Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), 1649-016 Lisbon, Portugal"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2024,3,9]]},"reference":[{"key":"ref_1","unstructured":"World Health Organization (2022). Global Genomic Surveillance Strategy for Pathogens with Pandemic and Epidemic Potential, 2022\u20132032, World Health Organization."},{"key":"ref_2","unstructured":"World Health Organization (2022). WHO Guiding Principles for Pathogen Genome Data Sharing, World Health Organization."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1038\/nrg.2017.88","article-title":"Towards a genomics-informed, real-time, global pathogen surveillance system","volume":"19","author":"Gardy","year":"2018","journal-title":"Nat. Rev. Genet."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"861","DOI":"10.1016\/j.chom.2023.03.003","article-title":"Toward a global virus genomic surveillance network","volume":"31","author":"Hill","year":"2023","journal-title":"Cell Host Microbe"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"499","DOI":"10.1038\/s41588-022-01033-y","article-title":"Global landscape of SARS-CoV-2 genomic surveillance and data sharing","volume":"54","author":"Chen","year":"2022","journal-title":"Nat. Genet."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"eabq5358","DOI":"10.1126\/science.abq5358","article-title":"The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance","volume":"378","author":"Tegally","year":"2022","journal-title":"Science"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"20386","DOI":"10.2807\/ese.18.04.20386-en","article-title":"From molecular to genomic epidemiology: Transforming surveillance and control of infectious diseases","volume":"18","author":"Struelens","year":"2013","journal-title":"Eurosurveillance"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"3773","DOI":"10.21105\/joss.03773","article-title":"Nextclade: Clade assignment, mutation calling and quality control for viral genomes","volume":"6","author":"Aksamentov","year":"2021","journal-title":"J. Open Source Softw."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"veab064","DOI":"10.1093\/ve\/veab064","article-title":"Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool","volume":"7","author":"Scher","year":"2021","journal-title":"Virus Evol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1735","DOI":"10.1093\/bioinformatics\/btab856","article-title":"CoV-Spectrum: Analysis of globally shared SARS-CoV-2 data to identify and characterize new variants","volume":"38","author":"Chen","year":"2022","journal-title":"Bioinformatics"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1186\/s13073-018-0555-0","article-title":"INSaFLU: An automated open web-based bioinformatics suite \u201cfrom-reads\u201d for influenza whole-genome-sequencing-based surveillance","volume":"10","author":"Borges","year":"2018","journal-title":"Genome Med."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"4121","DOI":"10.1093\/bioinformatics\/bty407","article-title":"Nextstrain: Real-time tracking of pathogen evolution","volume":"34","author":"Hadfield","year":"2018","journal-title":"Bioinformatics"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"871","DOI":"10.1093\/bioinformatics\/bty695","article-title":"Genome Detective: An automated system for virus identification from high-throughput sequencing data","volume":"35","author":"Vilsker","year":"2019","journal-title":"Bioinformatics"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1186\/s42522-020-0010-1","article-title":"Typing methods based on whole genome sequencing data","volume":"2","author":"Uelze","year":"2020","journal-title":"One Health Outlook"},{"key":"ref_15","unstructured":"Seemann, T. (2024, January 22). mlst. Available online: https:\/\/github.com\/tseemann\/mlst."},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Jolley, K.A., and Maiden, M.C. (2010). BIGSdb: Scalable analysis of bacterial genome variation at the population level. BMC Bioinform., 11.","DOI":"10.1186\/1471-2105-11-595"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"e00197-18","DOI":"10.1128\/JCM.00197-18","article-title":"Kaptive Web: User-Friendly Capsule and Lipopolysaccharide Serotype Prediction for Klebsiella Genomes","volume":"56","author":"Wick","year":"2018","journal-title":"J. Clin. Microbiol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"e01746-19","DOI":"10.1128\/AEM.01746-19","article-title":"SeqSero2: Rapid and Improved Salmonella Serotype Determination Using Whole-Genome Sequencing Data","volume":"85","author":"Zhang","year":"2019","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_19","first-page":"000748","article-title":"ResFinder\u2014An open online resource for identification of antimicrobial resistance genes in next-generation sequencing data and prediction of phenotypes from genotypes","volume":"8","author":"Florensa","year":"2022","journal-title":"Microb. Genom."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"e27943","DOI":"10.4161\/bact.27943","article-title":"Applying the ResFinder and VirulenceFinder web-services for easy identification of acquired antibiotic resistance and E. coli virulence genes in bacteriophage and prophage nucleotide sequences","volume":"4","author":"Kleinheinz","year":"2014","journal-title":"Bacteriophage"},{"key":"ref_21","unstructured":"Seemann, T. (2023, December 20). ABRicate. Available online: https:\/\/github.com\/tseemann\/abricate."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"2520","DOI":"10.1093\/bioinformatics\/bts480","article-title":"Snakemake\u2014A scalable bioinformatics workflow engine","volume":"28","author":"Rahmann","year":"2012","journal-title":"Bioinformatics"},{"key":"ref_23","unstructured":"(2023, December 20). ABIView. Available online: https:\/\/emboss.sourceforge.net\/apps\/cvs\/emboss\/apps\/abiview.html."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: A flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing","volume":"19","author":"Bankevich","year":"2012","journal-title":"J. Comput. Biol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"2666","DOI":"10.1093\/bioinformatics\/bty149","article-title":"NanoPack: Visualizing and processing long-read sequencing data","volume":"34","author":"Schultz","year":"2018","journal-title":"Bioinformatics"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"332","DOI":"10.1038\/s43588-021-00073-4","article-title":"Time- and memory-efficient genome assembly with Raven","volume":"1","author":"Vaser","year":"2021","journal-title":"Nat. Comput. Sci."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The Sequence Alignment\/Map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"ref_29","unstructured":"(2024, February 27). ReporType. Available online: https:\/\/github.com\/insapathogenomics\/reportype."},{"key":"ref_30","unstructured":"(2024, February 27). Chapter 7: Manual for the Laboratory-based Surveillance of Measles, Rubella, and Congenital Rubella Syndrome. Available online: https:\/\/www.who.int\/publications\/m\/item\/chapter-7-manual-for-the-laboratory-based-surveillance-of-measles-rubella-and-congenital-rubella-syndrome."},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Schoch, C.L., Ciufo, S., Domrachev, M., Hotton, C.L., Kannan, S., Khovanskaya, R., Leipe, D., Mcveigh, R., O\u2019Neill, K., and Robbertse, B. (2023, December 20). NCBI Taxonomy: A Comprehensive Update on Curation, Resources and Tools\u2014Measles. Database (Oxford), 2020, Available online: https:\/\/www.ncbi.nlm.nih.gov\/Taxonomy\/Browser\/wwwtax.cgi?name=Measles+morbillivirus.","DOI":"10.1093\/database\/baaa062"},{"key":"ref_32","unstructured":"(2023, December 20). Manual for the Laboratory-Based Surveillance of Measles, Rubella, and Congenital Rubella Syndrome. Available online: https:\/\/www.who.int\/publications\/m\/item\/chapter-1-manual-for-the-laboratory-based-surveillance-of-measles-rubella-and-congenital-rubella-syndrome."},{"key":"ref_33","unstructured":"(2023, June 13). NCBI Virus Database\u2014Taxid: 11234, Available online: https:\/\/www.ncbi.nlm.nih.gov\/labs\/virus\/vssi\/#\/."},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"Namuwulya, P., Bukenya, H., Tushabe, P., Tweyongyere, R., Bwogi, J., Cotten, M., and Phan, M.V.T. (2022). Near-Complete Genome Sequences of Measles Virus Strains from 10 Years of Uganda Country-wide Surveillance. Microbiol. Resour. Announc., 11.","DOI":"10.1128\/mra.00606-22"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"329","DOI":"10.1080\/03079457.2012.697991","article-title":"The long view: A selective review of 40 years of Newcastle disease research","volume":"41","author":"Alexander","year":"2012","journal-title":"Avian Pathol."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"103917","DOI":"10.1016\/j.meegid.2019.103917","article-title":"Updated unified phylogenetic classification system and revised nomenclature for Newcastle disease virus","volume":"74","author":"Dimitrov","year":"2019","journal-title":"Infect. Genet. Evol."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"e0024122","DOI":"10.1128\/jvi.00241-22","article-title":"Surveillance of Class I Newcastle Disease Virus at Live Bird Markets in China and Identification of Variants with Increased Virulence and Replication Capacity","volume":"96","author":"Sun","year":"2022","journal-title":"J. Virol."},{"key":"ref_38","first-page":"217","article-title":"Genomics, proteomics and evolution of dengue virus","volume":"16","author":"Dwivedi","year":"2017","journal-title":"Brief. Funct. Genom."},{"key":"ref_39","first-page":"e000328","article-title":"DEN-IM: Dengue virus genotyping from amplicon and shotgun metagenomic sequencing","volume":"6","author":"Mendes","year":"2020","journal-title":"Microb. Genom."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"e21","DOI":"10.5808\/gi.21077","article-title":"Genome characterization and mutation analysis of human influenza A virus in Thailand","volume":"20","author":"Rattanaburi","year":"2022","journal-title":"Genom. Inform."},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"King, J., Harder, T., Beer, M., and Pohlmann, A. (2020). Rapid multiplex MinION nanopore sequencing workflow for Influenza A viruses. BMC Infect. Dis., 20.","DOI":"10.1186\/s12879-020-05367-y"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1186\/s12985-019-1214-9","article-title":"Hepatitis C virus genotyping based on Core and NS5B regions in Cameroonian patients","volume":"16","author":"Ngoufack","year":"2019","journal-title":"Virol. J."},{"key":"ref_43","doi-asserted-by":"crossref","unstructured":"Ramos, D., Pinto, M., Sousa Coutinho, R., Silva, C., Quina, M., Gomes, J.P., and P\u00e1dua, E. (2023). Looking at the Molecular Target of NS5A Inhibitors throughout a Population Highly Affected with Hepatitis C Virus. Pathogens, 12.","DOI":"10.3390\/pathogens12060754"},{"key":"ref_44","doi-asserted-by":"crossref","unstructured":"Schoch, C.L., Ciufo, S., Domrachev, M., Hotton, C.L., Kannan, S., Khovanskaya, R., Leipe, D., Mcveigh, R., O\u2019Neill, K., and Robbertse, B. (2023, December 20). NCBI Taxonomy: A Comprehensive Update on Curation, Resources and Tools\u2014HTLV-1. Database (Oxford), 2020, Available online: https:\/\/www.ncbi.nlm.nih.gov\/Taxonomy\/Browser\/wwwtax.cgi?name=HTLV-1.","DOI":"10.1093\/database\/baaa062"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"317","DOI":"10.1089\/aid.2010.0195","article-title":"Molecular characterization of human T cell leukemia virus type 1 subtypes in a group of infected individuals diagnosed in Portugal and Spain","volume":"27","author":"Silva","year":"2011","journal-title":"AIDS Res. Hum. Retroviruses"},{"key":"ref_46","doi-asserted-by":"crossref","unstructured":"Quina, M., Ramos, D., Silva, C., and P\u00e1dua, E. (2023). Diversity of Human T-Lymphotropic Virus Type 1 Cosmopolitan Subtype (HTLV-1a) Circulating in Infected Residents in Portugal. AIDS Res. Hum. Retroviruses.","DOI":"10.1089\/aid.2023.0026"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"7182","DOI":"10.1128\/JB.00895-09","article-title":"Evolutionary dynamics of ompA, the gene encoding the Chlamydia trachomatis key antigen","volume":"191","author":"Nunes","year":"2009","journal-title":"J. Bacteriol."},{"key":"ref_48","first-page":"e000313","article-title":"Chlamydia trachomatis: When the virulence-associated genome backbone imports a prevalence-associated major antigen signature","volume":"5","author":"Borges","year":"2019","journal-title":"Microb. Genom."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"413","DOI":"10.1038\/ng.2214","article-title":"Whole-genome analysis of diverse Chlamydia trachomatis strains identifies phylogenetic relationships masked by current clinical typing","volume":"44","author":"Harris","year":"2012","journal-title":"Nat. Genet."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"312","DOI":"10.12688\/wellcomeopenres.16068.1","article-title":"An inducible transposon mutagenesis approach for the intracellular human pathogen Chlamydia trachomatis","volume":"6","author":"Skilton","year":"2021","journal-title":"Wellcome Open Res."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"855","DOI":"10.1101\/gr.150037.112","article-title":"Whole-genome sequences of Chlamydia trachomatis directly from clinical samples without culture","volume":"23","author":"Harris","year":"2013","journal-title":"Genome Res."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"1220","DOI":"10.1101\/gr.212647.116","article-title":"Comprehensive global genome dynamics of Chlamydia trachomatis show ancient diversification followed by contemporary mixing and recent lineage expansion","volume":"27","author":"Hadfield","year":"2017","journal-title":"Genome Res."},{"key":"ref_53","doi-asserted-by":"crossref","unstructured":"Underwood, A.P., Jones, G., Mentasti, M., Fry, N.K., and Harrison, T.G. (2013). Comparison of the Legionella pneumophila population structure as determined by sequence-based typing and whole genome sequencing. BMC Microbiol., 13.","DOI":"10.1186\/1471-2180-13-302"},{"key":"ref_54","first-page":"21186","article-title":"Design and application of a core genome multilocus sequence typing scheme for investigation of Legionnaires\u2019 disease incidents","volume":"20","author":"Prior","year":"2015","journal-title":"Euro Surveill."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"2047","DOI":"10.1128\/JCM.43.5.2047-2052.2005","article-title":"Consensus sequence-based scheme for epidemiological typing of clinical and environmental isolates of Legionella pneumophila","volume":"43","author":"Gaia","year":"2005","journal-title":"J. Clin. Microbiol."},{"key":"ref_56","unstructured":"Seemann, T. (2023, December 20). Legsta. Available online: https:\/\/github.com\/tseemann\/legsta."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1101\/gr.7229808","article-title":"Multigenome analysis identifies a worldwide distributed epidemic Legionella pneumophila clone that emerged within a highly diverse species","volume":"18","author":"Cazalet","year":"2008","journal-title":"Genome Res."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"6647","DOI":"10.1128\/AEM.01957-13","article-title":"Development of a DNA microarray method for detection and identification of all 15 distinct O-antigen forms of Legionella pneumophila","volume":"79","author":"Cao","year":"2013","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"26261","DOI":"10.1038\/srep26261","article-title":"Legionella pneumophila strain associated with the first evidence of person-to-person transmission of Legionnaires\u2019 disease: A unique mosaic genetic backbone","volume":"6","author":"Borges","year":"2016","journal-title":"Sci. Rep."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"172","DOI":"10.1016\/j.meegid.2018.02.008","article-title":"Comparative genome analysis reveals a complex population structure of Legionella pneumophila subspecies","volume":"59","author":"Morrison","year":"2018","journal-title":"Infect. Genet. Evol."},{"key":"ref_61","doi-asserted-by":"crossref","unstructured":"Khan, M.A., Knox, N., Prashar, A., Alexander, D., Abdel-Nour, M., Duncan, C., Tang, P., Amatullah, H., Dos Santos, C.C., and Tijet, N. (2013). Comparative Genomics Reveal that Host-Innate Immune Responses Influence the Clinical Prevalence of Legionella pneumophila Serogroups. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0067298"},{"key":"ref_62","doi-asserted-by":"crossref","unstructured":"David, S., S\u00e1nchez-Bus\u00f3, L., Harris, S.R., Marttinen, P., Rusniok, C., Buchrieser, C., Harrison, T.G., and Parkhill, J. (2017). Dynamics and impact of homologous recombination on the evolution of Legionella pneumophila. PLoS Genet., 13.","DOI":"10.1371\/journal.pgen.1007116"}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/25\/6\/3172\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T14:11:23Z","timestamp":1760105483000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/25\/6\/3172"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,3,9]]},"references-count":62,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2024,3]]}},"alternative-id":["ijms25063172"],"URL":"https:\/\/doi.org\/10.3390\/ijms25063172","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,3,9]]}}}