When are pathogen genome sequences informative of transmission events?
Open accessAbstract
Recent years have seen the development of numerous methodologies for reconstructing transmission trees in infectious disease outbreaks from densely sampled whole genome sequence data. However, a fundamental and as of yet poorly addressed limitation of such approaches is the requirement for genetic diversity to arise on epidemiological timescales. Specifically, the position of infected individuals in a transmission tree can only be resolved by genetic data if mutations have accumulated between the sampled pathogen genomes. To quantify and compare the useful genetic diversity expected from genetic data in different pathogen outbreaks, we introduce here the concept of 'transmission divergence', defined as the number of mutations separating whole genome sequences sampled from transmission pairs. Using parameter values obtained by literature review, we simulate outbreak scenarios alongside sequence evolution using two models described in the literature to describe transmission divergence of ten major outbreak-causing pathogens. We find that while mean values vary significantly between the pathogens considered, their transmission divergence is generally very low, with many outbreaks characterised by large numbers of genetically identical transmission pairs. We describe the impact of transmission divergence on our ability to reconstruct outbreaks using two outbreak reconstruction tools, the R packages outbreaker and phybreak, and demonstrate that, in agreement with previous observations, genetic sequence data of rapidly evolving pathogens such as RNA viruses can provide valuable information on individual transmission events. Conversely, sequence data of pathogens with lower mean transmission divergence, including Streptococcus pneumoniae, Shigella sonnei and Clostridium difficile, provide little to no information about individual transmission events. Our results highlight the informational limitations of genetic sequence data in certain outbreak scenarios, and demonstrate the need to expand the toolkit of outbreak reconstruction tools to integrate other types of epidemiological data.
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Genomic data might be of limited value in inferring transmission trends in future MVD epidemics.
“and hence genomic data might be of limited value in inferring transmission trends in future MVD epidemics (56).”
From Marburg virus disease outbreaks, mathematical models, and disease parameters: a systematic review (2024) · cites this paper as [56]
The Discussion (page unavailable) says limited genetic diversity can restrict the use of whole-genome sequences to reconstruct transmission chains, including in some outbreaks of rapidly evolving RNA viruses. But the paper does not study Marburg virus disease (MVD), and its findings concern individual transmission events rather than broader transmission trends. Applying that limitation to future MVD epidemics is an extrapolation. (LLM, conf=0.85)
Experimental — accuracy not yet measuredThe reported substitution rates for MV are substantially lower than those reported for Ebola.
“The reported substitution rates are substantially lower than those reported for Ebola (56).”
From Marburg virus disease outbreaks, mathematical models, and disease parameters: a systematic review (2024) · cites this paper as [56]
Table 1 (Results > Transmission divergence; page unavailable) reports an Ebola virus mutation rate of 0.31 × 10⁻⁵ per site per day. It gives no rate for MV, so the cited paper does not establish that MV’s reported substitution rates are substantially lower. (LLM, conf=0.85)
Experimental — accuracy not yet measured
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Percentages, sums and reported differences re-computed from the paper’s own numbers.
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Cites
R: A Language and Environment for Statistical Computing
R Core Team (2000) · doi:10.32614/r.manuals · Cited by 355,706 · see citing works
A Mathematical Theory of Communication
Shannon, C. E. (1948) · Bell System Technical Journal · doi:10.1002/j.1538-7305.1948.tb01338.x · Cited by 88,486 · see citing works
A contribution to the mathematical theory of epidemics
Kermack, W. O., & McKendrick, A. G. (1927) · Proceedings of the Royal Society of London Series A Containing Papers of a Mathematical and Physical Character · doi:10.1098/rspa.1927.0118 · Cited by 11,854 · see citing works
Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence
Cole, S. T., Brosch, R., Parkhill, J., Garnier, T., Churcher, C., Harris, D., Gordon, S. V., Eiglmeier, K., Gas, S., Barry, C. E., et al. (1998) · Nature · doi:10.1038/31159 · Cited by 7,847 · see citing works
Superspreading and the effect of individual variation on disease emergence
Lloyd-Smith, J. O., Schreiber, S. J., Kopp, P. E., & Getz, W. M. (2005) · Nature · doi:10.1038/nature04153 · Cited by 2,514 · see citing works
Characterization of a Novel Coronavirus Associated with Severe Acute Respiratory Syndrome
Rota, P. A., Oberste, M. S., Monroe, S. S., Nix, W. A., Campagnoli, R. P., Icenogle, J. P., Peñaranda, S., Bankamp, B., Maher, K., Chen, M., et al. (2003) · Science · doi:10.1126/science.1085952 · Cited by 2,477 · see citing works
Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic
Smith, G. J. D., Vijaykrishna, D., Bahl, J., Lycett, S., Worobey, M., Pybus, O. G., Ma, S. K., Cheung, C. L., Raghwani, J., Bhatt, S., et al. (2009) · Nature · doi:10.1038/nature08182 · Cited by 2,250 · see citing works
Ebola virus disease in West Africa—the first 9 months of the epidemic and forward projections
WHO Ebola Response Team (2014) · New England Journal of Medicine · doi:10.1056/nejmoa1411100 · Cited by 1,674 · see citing works
Diep, B. A., Gill, S. R., Chang, R. F., Phan, T. H., Chen, J. H., Davidson, M. G., Lin, F., Lin, J., Carleton, H. A., Mongodin, E. F., et al. (2006) · The Lancet · doi:10.1016/s0140-6736(06)68231-7 · Cited by 1,633 · see citing works
A New Framework and Software to Estimate Time-Varying Reproduction Numbers During Epidemics
Cori, A., Ferguson, N. M., Fraser, C., & Cauchemez, S. (2013) · American Journal of Epidemiology · doi:10.1093/aje/kwt133 · Cited by 1,530 · see citing works
Self-citationClark, K., Karsch‐Mizrachi, I., Lipman, D. J., Ostell, J., & Sayers, E. W. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv1276 · Cited by 1,471 · see citing works
Transmission Dynamics and Control of Severe Acute Respiratory Syndrome
Lipsitch, M., Cohen, T., Cooper, B. S., Robins, J. M., Ma, S., James, L., Gopalakrishna, G., Chew, S. K., Tan, C. C., Samore, M. H., et al. (2003) · Science · doi:10.1126/science.1086616 · Cited by 1,467 · see citing works
Emergence of Zaire Ebola Virus Disease in Guinea
Baize, S., Pannetier, D., Oestereich, L., Rieger, T., Koivogui, L., Magassouba, N., Soropogui, B., Sow, M. S., Keïta, S., De Clerck, H., et al. (2014) · New England Journal of Medicine · doi:10.1056/nejmoa1404505 · Cited by 1,366 · see citing works
Complete Genome Sequence of a Virulent Isolate of Streptococcus pneumoniae
Tettelin, H., Nelson, K. E., Paulsen, I. T., Eisen, J. A., Read, T. D., Peterson, S. N., Heidelberg, J. F., DeBoy, R. T., Haft, D. H., Dodson, R. J., et al. (2001) · Science · doi:10.1126/science.1061217 · Cited by 1,341 · see citing works
de Groot, R. J., Baker, S. C., Baric, R. S., Brown, C. S., Drosten, C., Enjuanes, L., Fouchier, R. A. M., Galiano, M., Gorbalenya, A. E., Memish, Z. A., et al. (2013) · Journal of Virology · doi:10.1128/jvi.01244-13 · Cited by 1,238 · see citing works
Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak
Gire, S., Goba, A., Andersen, K. G., Sealfon, R. S. G., Park, D. J., Kanneh, L., Jalloh, S. C., Momoh, M., Fullah, M., Dudas, G., et al. (2014) · Science · doi:10.1126/science.1259657 · Cited by 1,218 · see citing works
Wallinga, J. (2004) · American Journal of Epidemiology · doi:10.1093/aje/kwh255 · Cited by 1,208 · see citing works
Hospital outbreak of Middle East respiratory syndrome coronavirus
Assiri, A., McGeer, A., Perl, T. M., Price, C. S., Al Rabeeah, A. A., Cummings, D. A. T., Alabdullatif, Z. N., Assad, M., Almulhim, A., Makhdoom, H., et al. (2013) · New England Journal of Medicine · doi:10.1056/nejmoa1306742 · Cited by 1,196 · see citing works
Riley, S., Fraser, C., Donnelly, C. A., Ghani, A. C., Abu-Raddad, L. J., Hedley, A. J., Leung, G. M., Ho, L., Lam, T.-H., Thach, T., et al. (2003) · Science · doi:10.1126/science.1086478 · Cited by 1,152 · see citing works
Self-citationEvolution of MRSA During Hospital Transmission and Intercontinental Spread
Harris, S. R., Feil, E. J., Holden, M. T. G., Quail, M. A., Nickerson, E. K., Chantratita, N., Gardete, S., Tavares, A. F. N., Day, N., Lindsay, J. A., et al. (2010) · Science · doi:10.1126/science.1182395 · Cited by 1,092 · see citing works
The Influenza Virus Resource at the National Center for Biotechnology Information
Bào, Y., Bolotov, P., Dernovoy, D., Kiryutin, B., Zaslavsky, L. Y., Tatusova, T. A., Ostell, J., & Lipman, D. J. (2007) · Journal of Virology · doi:10.1128/jvi.02005-07 · Cited by 989 · see citing works
Walker, T. M., Ip, C. L. C., Harrell, R., Evans, J. T., Kapatai, G., Dedicoat, M. J., Eyre, D. W., Wilson, D. J., Hawkey, P. M., Crook, D. W., et al. (2012) · The Lancet Infectious Diseases · doi:10.1016/s1473-3099(12)70277-3 · Cited by 902 · see citing works
Holden, M. T. G., Feil, E. J., Lindsay, J. A., Peacock, S. J., Day, N., Enright, M. C., Foster, T. J., Moore, C. E., Hurst, L. D., Atkin, R. J., et al. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0402521101 · Cited by 885 · see citing works
The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome
Sebaihia, M., Wren, B. W., Mullany, P. P., Fairweather, N. F., Minton, N. P., Stabler, R. A., Thomson, N. R., Roberts, A. P., Cerdeño-Tárraga, A. M., Wang, H., et al. (2006) · Nature Genetics · doi:10.1038/ng1830 · Cited by 877 · see citing works
Rapid Pneumococcal Evolution in Response to Clinical Interventions
Croucher, N. J., Harris, S. R., Fraser, C., Quail, M. A., Burton, J. H., van der Linden, M., McGee, L., von Gottberg, A., Song, J. H., Ko, K. S., et al. (2011) · Science · doi:10.1126/science.1198545 · Cited by 870 · see citing works
Snitkin, E. S., Zelazny, A. M., Thomas, P. J., Stock, F., Program, N. C. S., Henderson, D. K., Palmore, T. N., & Segre, J. A. (2012) · Science Translational Medicine · doi:10.1126/scitranslmed.3004129 · Cited by 863 · see citing works
Gibbons, A. (1985) · Cited by 828 · see citing works
Rapid Whole-Genome Sequencing for Investigation of a Neonatal MRSA Outbreak
Köser, C. U., Holden, M. T. G., Ellington, M. J., Cartwright, E. J. P., Brown, N. M., Ogilvy‐Stuart, A., Hsu, L. Y., Chewapreecha, C., Croucher, N. J., Harris, S. R., et al. (2012) · New England Journal of Medicine · doi:10.1056/nejmoa1109910 · Cited by 656 · see citing works
Diverse Sources of C. difficile Infection Identified on Whole-Genome Sequencing
Eyre, D. W., Cule, M., Wilson, D. J., Griffiths, D., Vaughan, A., O’Connor, L., Ip, C. L. C., Golubchik, T., Batty, E. M., Finney, J. M., et al. (2013) · New England Journal of Medicine · doi:10.1056/nejmoa1216064 · Cited by 649 · see citing works
Evolutionary analysis of the dynamics of viral infectious disease
Pybus, O. G., & Rambaut, A. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2583 · Cited by 611 · see citing works
Re-annotation of the genome sequence of Mycobacterium tuberculosis H37Rv
Camus, J. C., Pryor, M. J., Médigue, C., & Cole, S. T. (2002) · Microbiology · doi:10.1099/00221287-148-10-2967 · Cited by 587 · see citing works
Harris, S. R., Cartwright, E. J. P., Török, M. E., Holden, M. T. G., Brown, N. M., Ogilvy‐Stuart, A., Ellington, M. J., Quail, M. A., Bentley, S. D., Parkhill, J., et al. (2012) · The Lancet Infectious Diseases · doi:10.1016/s1473-3099(12)70268-2 · Cited by 567 · see citing works
Overview of molecular typing methods for outbreak detection and epidemiological surveillance
Sabat, A., Budimir, A., Nashev, D., Sá‐Leão, R., van Dijl, J. M., Laurent, F. J., Grundmann, H., Friedrich, A. W., & on behalf of the ESCMID Study Group (2013) · Eurosurveillance · doi:10.2807/ese.18.04.20380-en · Cited by 542 · see citing works
Family Cluster of Middle East Respiratory Syndrome Coronavirus Infections
Memish, Z. A., Zumla, A. I., Alhakeem, R. F., Al-Rabeeah, A. A., & Stephens, G. M. (2013) · New England Journal of Medicine · doi:10.1056/nejmoa1303729 · Cited by 493 · see citing works
Roetzer, A., Diel, R., Kohl, T. A., Rückert, C., Nübel, U., Blom, J., Wirth, T., Jaenicke, S., Schuback, S., Rüsch–Gerdes, S., et al. (2013) · PLoS Medicine · doi:10.1371/journal.pmed.1001387 · Cited by 482 · see citing works
Household Transmission of 2009 Pandemic Influenza A (H1N1) Virus in the United States
Cauchemez, S., Donnelly, C. A., Reed, C., Ghani, A. C., Fraser, C., Kent, C. K., Finelli, L., & Ferguson, N. M. (2009) · New England Journal of Medicine · doi:10.1056/nejmoa0905498 · Cited by 472 · see citing works
Self-citationWithin-host evolution of bacterial pathogens
Didelot, X., Walker, A. S., Peto, T., Crook, D. W., & Wilson, D. J. (2016) · Nature Reviews Microbiology · doi:10.1038/nrmicro.2015.13 · Cited by 462 · see citing works
Ruan, Y., Wei, C. L., Ling, A. E., Vega, V. B., Thoreau, H., Thoe, S. Y. S., Chia, J.-M., Ng, P., Chiu, K. P., Lim, L., et al. (2003) · The Lancet · doi:10.1016/s0140-6736(03)13414-9 · Cited by 436 · see citing works
Ferguson, N. M., Donnelly, C. A., & Anderson, R. M. (2001) · Nature · doi:10.1038/35097116 · Cited by 433 · see citing works
Self-citationHolden, M. T. G., Hsu, L.-Y., Kurt, K., Weinert, L. A., Mather, A. E., Harris, S. R., Strommenger, B., Layer, F., Witte, W., Lencastre, H., et al. (2013) · Genome Research · doi:10.1101/gr.147710.112 · Cited by 432 · see citing works
Genome dynamics and diversity of Shigella species, the etiologic agents of bacillary dysentery
Yang, F. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki954 · Cited by 415 · see citing works
Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species
Donati, C., Hiller, N. L., Tettelin, H., Muzzi, A., Croucher, N. J., Angiuoli, S. V., Oggioni, M. R., Hotopp, J. C. D., Hu, F. Z., Riley, D. R. J., et al. (2010) · Genome biology · doi:10.1186/gb-2010-11-10-r107 · Cited by 398 · see citing works
Varia, M., Wilson, S., Sarwal, S., McGeer, A., Gournis, E., Galanis, E., & Henry, B. (2003) · PubMed Central · Cited by 373 · see citing works
Evolutionary dynamics of Clostridium difficile over short and long time scales
He, M., Sebaihia, M., Lawley, T. D., Stabler, R. A., Dawson, L. F., Martin, M. J., Holt, K. E., Seth-Smith, H. M. B., Quail, M. A., Rance, R., et al. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0914322107 · Cited by 359 · see citing works
Cauchemez, S., Fraser, C., Kerkhove, M. D. V., Donnelly, C. A., Riley, S., Rambaut, A., Enouf, V., van der Werf, S., & Ferguson, N. M. (2013) · The Lancet Infectious Diseases · doi:10.1016/s1473-3099(13)70304-9 · Cited by 347 · see citing works
Self-citationCotten, M. L., Watson, S. J., Kellam, P., Al-Rabeeah, A. A., Makhdoom, H. Q., Assiri, A. M., Al‐Tawfiq, J. A., Alhakeem, R. F., Madani, H., Alrabiah, F. A., et al. (2013) · The Lancet · doi:10.1016/s0140-6736(13)61887-5 · Cited by 315 · see citing works
Holt, K. E., Baker, S. G., Weill, F., Holmes, E. C., Kitchen, A., Yu, J., Sangal, V., Brown, D., Coia, J. E., Kim, D. W., et al. (2012) · Nature Genetics · doi:10.1038/ng.2369 · Cited by 288 · see citing works
Moderate mutation rate in the SARS coronavirus genome and its implications
Zhao, Z., Li, H., Wu, X., Zhong, Y., Zhang, K., Zhang, Y.-P., Boerwinkle, E., & Fu, Y.-X. (2004) · BMC Evolutionary Biology · doi:10.1186/1471-2148-4-21 · Cited by 286 · see citing works
Spread, Circulation, and Evolution of the Middle East Respiratory Syndrome Coronavirus
Cotten, M. L., Watson, S. J., Zumla, A. I., Makhdoom, H. Q., Palser, A. L., Ong, S. H., Rabeeah, A. A. A., Alhakeem, R. F., Assiri, A. M., Al‐Tawfiq, J. A., et al. (2014) · mBio · doi:10.1128/mbio.01062-13 · Cited by 267 · see citing works
Guerra‐Assunção, J. A., Crampin, A. C., Houben, R., Mzembe, T., Mallard, K., Coll, F., Khan, P. Y., Banda, L., Chiwaya, A., Pereira, R., et al. (2015) · eLife · doi:10.7554/elife.05166 · Cited by 258 · see citing works
The Interval between Successive Cases of an Infectious Disease
Fine, P. E. M. (2003) · American Journal of Epidemiology · doi:10.1093/aje/kwg251 · Cited by 253 · see citing works
Genomic infectious disease epidemiology in partially sampled and ongoing outbreaks
Didelot, X., Fraser, C., Gardy, J. L., & Colijn, C. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msw275 · Cited by 244 · see citing works
Criteria for the control of drug-resistant tuberculosis
Dye, C., & Williams, B. G. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.140102797 · Cited by 233 · see citing works
Walker, A. S., Eyre, D. W., Wyllie, D. H., Dingle, K. E., Harding, R. M., O’Connor, L., Griffiths, D., Vaughan, A., Finney, J., Wilcox, M. H., et al. (2012) · PLoS Medicine · doi:10.1371/journal.pmed.1001172 · Cited by 223 · see citing works
Walker, T. M., Lalor, M. K., Broda, A., Ortega, L. S., Morgan, M. R., Parker, L., Churchill, S., Bennett, K., Golubchik, T., Giess, A. P., et al. (2014) · The Lancet Respiratory Medicine · doi:10.1016/s2213-2600(14)70027-x · Cited by 223 · see citing works
Faye, O., Boëlle, P.-Y., Heleze, E., Faye, O., Loucoubar, C., Magassouba, N., Soropogui, B., Keita, S., Gakou, T., Bah, E. H. I., et al. (2015) · The Lancet Infectious Diseases · doi:10.1016/s1473-3099(14)71075-8 · Cited by 220 · see citing works
Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data
Jombart, T., Cori, A., Didelot, X., Cauchemez, S., Fraser, C., & Ferguson, N. M. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003457 · Cited by 219 · see citing works
Self-citationBayesian Inference of Infectious Disease Transmission from Whole-Genome Sequence Data
Didelot, X., Gardy, J. L., & Colijn, C. (2014) · Molecular Biology and Evolution · doi:10.1093/molbev/msu121 · Cited by 197 · see citing works
Microevolutionary analysis of Clostridium difficile genomes to investigate transmission
Didelot, X., Eyre, D. W., Cule, M., Ip, C. L. C., Ansari, M. A., Griffiths, D., Vaughan, A., O’Connor, L., Golubchik, T., Batty, E. M., et al. (2012) · Genome biology · doi:10.1186/gb-2012-13-12-r118 · Cited by 192 · see citing works
Liu, P., Li, P., Jiang, X., Bi, D., Xie, Y., Tai, C., Deng, Z., Rajakumar, K., & Ou, H. (2012) · Journal of Bacteriology · doi:10.1128/jb.00043-12 · Cited by 191 · see citing works
West African Ebola Epidemic after One Year — Slowing but Not Yet under Control
WHO Ebola Response Team (2014) · New England Journal of Medicine · doi:10.1056/nejmc1414992 · Cited by 190 · see citing works
Uhlemann, A., Dordel, J., Knox, J., Raven, K. E., Parkhill, J., Holden, M. T. G., Peacock, S. J., & Lowy, F. D. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1401006111 · Cited by 185 · see citing works
McAdam, P. R., Templeton, K. E., Edwards, G. F., Holden, M. T. G., Feil, E. J., Aanensen, D. M., Bargawi, H. J. A., Spratt, B. G., Bentley, S. D., Parkhill, J., et al. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1202869109 · Cited by 185 · see citing works
A Very Early-Branching Staphylococcus aureus Lineage Lacking the Carotenoid Pigment Staphyloxanthin
Holt, D. C., Holden, M. T. G., Tong, S. Y. C., Castillo‐Ramírez, S., Clarke, L., Quail, M. A., Currie, B. J., Parkhill, J., Bentley, S. D., Feil, E. J., et al. (2011) · Genome Biology and Evolution · doi:10.1093/gbe/evr078 · Cited by 173 · see citing works
Genetic diversity and evolutionary dynamics of Ebola virus in Sierra Leone
Tong, Y., Shi, W., Liu, D., Qian, J., Liang, L., Bo, X., Liu, J., Ren, H., Fan, H., Ni, M., et al. (2015) · Nature · doi:10.1038/nature14490 · Cited by 166 · see citing works
Worby, C. J., Lipsitch, M., & Hanage, W. P. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003549 · Cited by 164 · see citing works
West African Ebola epidemic after one year — slowing but not yet under control
Nouvellet, P. (2015) · Sussex Research Online (University of Sussex) · Cited by 162 · see citing works
Norén, T., Åkerlund, T., Bäck, E., Sjöberg, L., Persson, I., Alriksson, I., & BURMAN, L. G. (2004) · Journal of Clinical Microbiology · doi:10.1128/jcm.42.8.3635-3643.2004 · Cited by 161 · see citing works
Cottam, E. M., Thébaud, G., Wadsworth, J., Gloster, J., Mansley, L. M., Paton, D. J., King, D. P., & Haydon, D. T. (2008) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2007.1442 · Cited by 161 · see citing works
Transmission parameters of the A/H1N1 (2009) influenza virus pandemic: a review
Boëlle, P., Ansart, S., Cori, A., & Valleron, A. (2011) · Influenza and Other Respiratory Viruses · doi:10.1111/j.1750-2659.2011.00234.x · Cited by 158 · see citing works
Self-citationRelating Phylogenetic Trees to Transmission Trees of Infectious Disease Outbreaks
Ypma, R. J. F., van Ballegooijen, W. M., & Wallinga, J. (2013) · Genetics · doi:10.1534/genetics.113.154856 · Cited by 148 · see citing works
Mathers, A. J., Stoesser, N. E., Sheppard, A. E., Pankhurst, L. J., Giess, A. P., Yeh, A. J., Didelot, X., Turner, S., Sebra, R., Kasarskis, A., et al. (2015) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.04292-14 · Cited by 148 · see citing works
Unravelling transmission trees of infectious diseases by combining genetic and epidemiological data
Ypma, R. J. F., Bataille, A., Stegeman, A., Koch, G., Wallinga, J., & van Ballegooijen, W. M. (2011) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2011.0913 · Cited by 135 · see citing works
Wilson, B. J. (1986) · Bulletin of the London Mathematical Society · doi:10.1112/blms/18.6.630 · Cited by 133 · see citing works
The, H. C., Karkey, A., Thanh, D. P., Boinett, C. J., Cain, A. K., Ellington, M. J., Baker, K. S., Dongol, S., Thompson, C. N., Harris, S. R., et al. (2015) · EMBO Molecular Medicine · doi:10.15252/emmm.201404767 · Cited by 120 · see citing works
Self-citationSimultaneous inference of phylogenetic and transmission trees in infectious disease outbreaks
Klinkenberg, D., Backer, J. A., Didelot, X., Colijn, C., & Wallinga, J. (2017) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1005495 · Cited by 113 · see citing works
SCOTTI: Efficient Reconstruction of Transmission within Outbreaks with the Structured Coalescent
Maio, N. D., Wu, C., & Wilson, D. J. (2016) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1005130 · Cited by 112 · see citing works
Morelli, M. J., Thébaud, G., Chadœuf, J., King, D. P., Haydon, D. T., & Soubeyrand, S. (2012) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002768 · Cited by 111 · see citing works
Epidemiological Model forClostridium difficileTransmission in Healthcare Settings
Lanzas, C., Dubberke, E. R., Lu, Z., Reske, K. A., & Grohn, Y. T. (2011) · Infection Control and Hospital Epidemiology · doi:10.1086/660013 · Cited by 106 · see citing works
Hall, M. D., Woolhouse, M. E. J., & Rambaut, A. (2015) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1004613 · Cited by 104 · see citing works
Emerging Concepts of Data Integration in Pathogen Phylodynamics
Baele, G., Suchard, M. A., Rambaut, A., & Lemey, P. (2016) · Systematic Biology · doi:10.1093/sysbio/syw054 · Cited by 102 · see citing works
Macrae, M. B., Shannon, K. P., Rayner, D., Kaiser, A. M., Hoffman, P. N., & French, G. L. (2001) · Journal of Hospital Infection · doi:10.1053/jhin.2001.1066 · Cited by 95 · see citing works
Epidemiology and control of influenza A(H1N1)v in the Netherlands: the first 115 cases
Hahné, S. J. M., Donker, T., Meijer, A., Timen, A., van Steenbergen, J., Osterhaus, A. D. M. E., van der Sande, M. A. B., Koopmans, M., Wallinga, J., Coutinho, R. A., et al. (2009) · Eurosurveillance · doi:10.2807/ese.14.27.19267-en · Cited by 92 · see citing works
Henderson-Begg, S. K., Livermore, D. M., & Hall, L. M. C. (2006) · Journal of Antimicrobial Chemotherapy · doi:10.1093/jac/dkl064 · Cited by 91 · see citing works
Kassis, N., Decré, D., Gautier, V., Burghoffer, B., Saliba, F., Mathieu, D., Samuel, D., Castaing, D., Petit, J., Dussaix, É., et al. (2005) · Journal of Antimicrobial Chemotherapy · doi:10.1093/jac/dki389 · Cited by 89 · see citing works
The early molecular epidemiology of the swine-origin A/H1N1 human influenza pandemic
Rambaut, A., & Holmes, E. C. (2009) · PLoS Currents · doi:10.1371/currents.rrn1003 · Cited by 87 · see citing works
Mollentze, N., Nel, L. H., Townsend, S. E., Roux, K., Hampson, K., Haydon, D. T., & Soubeyrand, S. (2014) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2013.3251 · Cited by 82 · see citing works
Reynolds, M. G., Anh, B. H., Thu, V. H., Montgomery, J. M., Bausch, D. G., Shah, J. J., Maloney, S., Leitmeyer, K. C., Huy, V. Q., Horby, P., et al. (2006) · BMC Public Health · doi:10.1186/1471-2458-6-207 · Cited by 65 · see citing works
Mutational dynamics of the SARS coronavirus in cell culture and human populations isolated in 2003
Vega, V. B., Ruan, Y., Liu, J., Lee, W. H., Wei, C. L., Se-Thoe, S. Y., Tang, K. F., Zhang, T., Kolatkar, P. R., Ooi, E. E., et al. (2004) · BMC Infectious Diseases · doi:10.1186/1471-2334-4-32 · Cited by 65 · see citing works
Sypsa, V., Psichοgiou, M., Bouzala, G.-A., Hadjihannas, L., Hatzakis, A. E., & Daikos, G. L. (2012) · PLoS ONE · doi:10.1371/journal.pone.0041068 · Cited by 60 · see citing works
A Systematic Bayesian Integration of Epidemiological and Genetic Data
Lau, M. S. Y., Marion, G., Streftaris, G., & Gibson, G. J. (2015) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1004633 · Cited by 59 · see citing works
Spada, E., Sagliocca, L., Sourdis, J., Garbuglia, A. R., Poggi, V., Fusco, C. D., & Mele, A. (2004) · Journal of Clinical Microbiology · doi:10.1128/jcm.42.9.4230-4236.2004 · Cited by 53 · see citing works
Reconstructing transmission trees for communicable diseases using densely sampled genetic data
Worby, C. J., O’Neill, P. D., Kypraios, T., Robotham, J. V., Angelis, D. D., Cartwright, E. J. P., Peacock, S. J., & Cooper, B. S. (2016) · The Annals of Applied Statistics · doi:10.1214/15-aoas898 · Cited by 50 · see citing works
Complete genome sequence of a serotype 11A, ST62 Streptococcus pneumoniaeinvasive isolate
Camilli, R., Bonnal, R. J. P., Grosso, M. D., Iacono, M., Corti, G., Rizzi, E., Marchetti, M., Mulas, L., Iannelli, F., Superti, F., et al. (2011) · BMC Microbiology · doi:10.1186/1471-2180-11-25 · Cited by 48 · see citing works
Complete Genome Sequence of the 2,3-Butanediol-Producing Klebsiella pneumoniae Strain KCTC 2242
Shin, S., Kim, S., Kim, J. Y., Lee, S., Um, Y. S., Oh, M., Kim, Y., Lee, J., & Yang, K.-S. (2012) · Journal of Bacteriology · doi:10.1128/jb.00027-12 · Cited by 47 · see citing works
Halting a pneumococcal pneumonia outbreak among United States Marine Corps trainees
Crum, N. F., Wallace, M. R., Lamb, C., Conlin, A. M. S., Amundson, D. E., Olson, P. E., Ryan, M. A. K., Robinson, T. J., Gray, G. C., & Earhart, K. C. (2003) · American Journal of Preventive Medicine · doi:10.1016/s0749-3797(03)00114-4 · Cited by 46 · see citing works
Hoti, F. J., Erästö, P., Leino, T. M., & Auranen, K. J. (2009) · BMC Infectious Diseases · doi:10.1186/1471-2334-9-102 · Cited by 44 · see citing works
Veen, A. V. '., van der Zee, A., Nelson, J., Speelberg, B., Kluytmans, J. A. J. W., & Buiting, A. G. M. (2005) · Journal of Clinical Microbiology · doi:10.1128/jcm.43.10.4961-4967.2005 · Cited by 38 · see citing works
Shigellosis outbreak associated with swimming.
Makintubee, S., Mallonee, J., & Istre, G. R. (1987) · American Journal of Public Health · doi:10.2105/ajph.77.2.166 · Cited by 38 · see citing works
Declaring a tuberculosis outbreak over with genomic epidemiology
Hatherell, H.-A., Didelot, X., Pollock, S., Tang, P., Crisan, A., Johnston, J. C., Colijn, C., & Gardy, J. L. (2016) · Microbial Genomics · doi:10.1099/mgen.0.000060 · Cited by 36 · see citing works
Estimation of serial interval and incubation period of tuberculosis using DNA fingerprinting.
ten Asbroek, A. H. A., Borgdorff, M. W., Nagelkerke, N. J. D., Šebek, M. M. G. G., Devillé, W. L. J. M., van Embden, J. D., & van Soolingen, D. (1999) · PubMed · Cited by 36 · see citing works
The Serial Intervals of Seasonal and Pandemic Influenza Viruses in Households in Bangkok, Thailand
Levy, J., Cowling, B. J., Simmerman, J. M., Olsen, S. J., Fang, V. J., Suntarattiwong, P., Jarman, R. G., Klick, B., & Chotipitayasunondh, T. (2013) · American Journal of Epidemiology · doi:10.1093/aje/kws402 · Cited by 35 · see citing works
Frequent Beneficial Mutations during Single-Colony Serial Transfer of Streptococcus pneumoniae
Stevens, K. E., & Sebert, M. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002232 · Cited by 32 · see citing works
Risk of secondary cases of Clostridium difficile infection among household contacts of index cases
Pépin, J., Gonzales, M., & Valiquette, L. (2011) · Journal of Infection · doi:10.1016/j.jinf.2011.12.011 · Cited by 31 · see citing works
Wang, X., Panchanathan, S., & Chowell, G. (2013) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003328 · Cited by 30 · see citing works
Complete Genome Sequences of Three Ebola Virus Isolates from the 2014 Outbreak in West Africa
Hoenen, T., Groseth, A., Feldmann, F., Marzi, A., Ebihara, H., Kobinger, G., Günther, S., & Feldmann, H. (2014) · Genome Announcements · doi:10.1128/genomea.01331-14 · Cited by 29 · see citing works
Lee, H., Kim, S., Choi, C. W., Seo, H. K., Shin, M. J., Bok, J., Cho, J. E., Kim, C. J., Shin, J., Kim, T. S., et al. (2014) · Journal of Hospital Infection · doi:10.1016/j.jhin.2014.04.003 · Cited by 22 · see citing works
Genome Sequence of Klebsiella pneumoniae Ecl8, a Reference Strain for Targeted Genetic Manipulation
Fookes, M. C., Yu, J., Majumdar, S. D., Thomson, N. R., & Schneiders, T. (2013) · Genome Announcements · doi:10.1128/genomea.00027-12 · Cited by 22 · see citing works
Joh, R. I., Hoekstra, R. M., Barzilay, E. J., Bowen, A. B., Mintz, E. D., Weiss, H., & Weitz, J. S. (2013) · American Journal of Epidemiology · doi:10.1093/aje/kwt122 · Cited by 21 · see citing works
de Champs, C., Rich, C., Chandezon, P., Chanal, C., Sirot, D., & Forestier, C. (2004) · European Journal of Clinical Microbiology & Infectious Diseases · doi:10.1007/s10096-004-1144-2 · Cited by 19 · see citing works
Patel, M., Thomas, H. C., Room, J., Wilson, Y., Kearns, A., & Gray, J. W. (2013) · Journal of Hospital Infection · doi:10.1016/j.jhin.2013.04.013 · Cited by 19 · see citing works
THOMAS, H. L., Gajraj, R., Slack, M., Sheppard, C. L., Hawkey, P. M., Gossain, S., Drew, C. M., & Pebody, R. G. (2014) · Epidemiology and Infection · doi:10.1017/s0950268814002490 · Cited by 17 · see citing works
Kuroki, T., Ishida, M., Suzuki, M., Furukawa, I., Ohya, H., Watanabe, Y., Konnai, M., Aihara, Y., Chang, B., Ariyoshi, K., et al. (2014) · Journal of the American Geriatrics Society · doi:10.1111/jgs.12863 · Cited by 12 · see citing works
[The genome comparison of SARS-CoV and other coronaviruses].
Wu, S., Du, C.-J., Wan, P., Chen, T., Li, J., Li, D., Zeng, Y., Zhu, Y., & He, F. (2003) · PubMed · Cited by 4 · see citing works
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Research works printed but not linked: 2
- A Karkey, 2015, A high-resolution genomic analysis of multidrug-resistant hospital outbreaks of Klebsiella pneumoniae, EMBO Mol Med, 7, 227, 10.15252/emmm.201404767 · DOI
- European Centre for Disease Prevention and Control. Systematic review on the incubation and infectiousness/shedding period of communicable diseases in children. 2016;Stockholm.
Cited by
Sorted by citations
Tracking virus outbreaks in the twenty-first century
Grubaugh, N. D., Ladner, J. T., Lemey, P., Pybus, O. G., Rambaut, A., Holmes, E. C., & Andersen, K. G. (2018) · Nature Microbiology · doi:10.1038/s41564-018-0296-2 · Cited by 478 · see citing works
A thermostable, closed SARS-CoV-2 spike protein trimer
Xiong, X., Qu, K., Ciazynska, K. A., Hosmillo, M., Carter, A. P., Ebrahimi, S., Ke, Z., Scheres, S. H. W., Bergamaschi, L., Grice, G. L., et al. (2020) · Nature Structural & Molecular Biology · doi:10.1038/s41594-020-0478-5 · Cited by 313 · see citing works
Abbas, M., Nunes, T. R., Martischang, R., Zingg, W., Iten, A., Pittet, D., & Harbarth, S. (2021) · Antimicrobial Resistance and Infection Control · doi:10.1186/s13756-020-00875-7 · Cited by 273 · see citing works
Outbreak analytics: a developing data science for informing the response to emerging pathogens
Polonsky, J. A., Baidjoe, A. Y., Kamvar, Z. N., Cori, A., Durski, K. N., Edmunds, W. J., Eggo, R. M., Funk, S., Kaiser, L., Keating, P., et al. (2019) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2018.0276 · Cited by 173 · see citing works
Self-citationFrom Theory to Practice: Translating Whole-Genome Sequencing (WGS) into the Clinic
Balloux, F., Brynildsrud, O. B., van Dorp, L., Shaw, L. P., Chen, H., Harris, K., Wang, H., & Eldholm, V. (2018) · Trends in Microbiology · doi:10.1016/j.tim.2018.08.004 · Cited by 171 · see citing works
Beyond the SNP Threshold: Identifying Outbreak Clusters Using Inferred Transmissions
Stimson, J. A., Gardy, J. L., Mathema, B., Crudu, V., Cohen, T., & Colijn, C. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msy242 · Cited by 160 · see citing works
Patterns of within-host genetic diversity in SARS-CoV-2
Tonkin-Hill, G., Martincorena, I., Amato, R., Lawson, A. R. J., Gerstung, M., Johnston, I., Jackson, D. K., Park, N. R., Lensing, S. V., Quail, M. A., et al. (2021) · eLife · doi:10.7554/elife.66857 · Cited by 157 · see citing works
Estimation in emerging epidemics: biases and remedies
Britton, T., & Tomba, G. S. (2019) · Journal of The Royal Society Interface · doi:10.1098/rsif.2018.0670 · Cited by 139 · see citing works
Carey, M. E., Dyson, Z. A., Ingle, D. J., Amir, A., Aworh, M. K., Mm, C., Chew, K. L., Crump, J. A., Feasey, N., Howden, B. P., et al. (2023) · eLife · doi:10.7554/elife.85867 · Cited by 126 · see citing works
Global wastewater surveillance for pathogens with pandemic potential: opportunities and challenges
Grassly, N. C., Shaw, A., & Owusu, M. (2024) · The Lancet Microbe · doi:10.1016/j.lanmic.2024.07.002 · Cited by 107 · see citing works
Dingens, A. S., Arenz, D., Weight, H., Overbaugh, J. M., & Bloom, J. D. (2019) · Immunity · doi:10.1016/j.immuni.2018.12.017 · Cited by 106 · see citing works
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Dolan, P., Whitfield, Z. J., & Andino, R. (2018) · Cell Host & Microbe · doi:10.1016/j.chom.2018.03.012 · Cited by 91 · see citing works
Xu, Y., Cancino‐Muñoz, I., Torres‐Puente, M., Villamayor, L. M., Borrás, R., Borrás-Máñez, M., Bosque, M., Camarena, J. J., Colomer-Roig, E., Colomina, J., et al. (2019) · PLoS Medicine · doi:10.1371/journal.pmed.1002961 · Cited by 89 · see citing works
Żmudziński, M., Rut, W., Olech, K., Granda, J. M., Giurg, M., Burda‐Grabowska, M., Kaleta, R., Zgarbová, M., Kasprzyk, R., Zhang, L., et al. (2023) · Scientific Reports · doi:10.1038/s41598-023-35907-w · Cited by 82 · see citing works
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Goig, G. A., Blanco, S., García‐Basteiro, A. L., & Comas, I. (2020) · BMC Biology · doi:10.1186/s12915-020-0748-z · Cited by 78 · see citing works
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Castro, P. D. J., Venkatesan, A., Redman, E., Chen, R., Malatesta, A., Huff, H., Salazar, D. A. Z., Avramenko, R. W., Gilleard, J. S., & Kaplan, R. M. (2021) · International Journal for Parasitology Drugs and Drug Resistance · doi:10.1016/j.ijpddr.2021.08.005 · Cited by 69 · see citing works
Campbell, F., Cori, A., Ferguson, N. M., & Jombart, T. (2019) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1006930 · Cited by 67 · see citing works
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Tonkin‐Hill, G. Q., Ling, C. L., Chaguza, C., Salter, S. J., Hinfonthong, P., Nikolaou, E., Tate, N., Pastusiak, A., Turner, C., Chewapreecha, C., et al. (2022) · Nature Microbiology · doi:10.1038/s41564-022-01238-1 · Cited by 66 · see citing works
Rossi, G., Crispell, J., Brough, T., Lycett, S., White, P. C. L., Allen, A. R., Ellis, R. J., Gordon, S. V., Harwood, R., Palkopoulou, E., et al. (2021) · Journal of Applied Ecology · doi:10.1111/1365-2664.14046 · Cited by 64 · see citing works
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“This systematic review presents a comprehensive set of mathematical models, outbreaks, and epidemiological parameters of MVD. Historical outbreaks and case reports in the peer-reviewed literature for MVD were rare and small in size, relative to many other pathogens, including other viral hemorrhagic fevers such as Ebo…”
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Alpizar-Sosa, E. A., Ithnin, N. R., Wei, W., Pountain, A. W., Weidt, S. K., Donachie, A. M., Ritchie, R., Dickie, E. A., Burchmore, R., Denny, P. W., et al. (2022) · PLoS neglected tropical diseases · doi:10.1371/journal.pntd.0010779 · Cited by 56 · see citing works
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Verchot, J., Herath, V., Urrutia, C. D., Gayral, M., Lyle, K., Shires, M. K., Ong, K. L., & Byrne, D. (2020) · Molecular Plant-Microbe Interactions · doi:10.1094/mpmi-04-20-0094-r · Cited by 48 · see citing works
Cori, A., Nouvellet, P., Garske, T., Bourhy, H., Nakouné, E. R., & Jombart, T. (2018) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1006554 · Cited by 47 · see citing works
Self-citationQuintana, J. F., Chandrasegaran, P. R. G., Sinton, M. C., Briggs, E. M., Otto, T. D., Heslop, R., Bentley-Abbot, C., Loney, C., de Lecea, L., Mabbott, N. A., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-33542-z · Cited by 46 · see citing works
Rice, C. A., Troth, E. V., Russell, A. C., & Kyle, D. E. (2020) · Pathogens · doi:10.3390/pathogens9060476 · Cited by 45 · see citing works
Oidtman, R. J., Lai, S., Huang, Z., Yang, J., Siraj, A. S., Reiner, R. C., Tatem, A. J., Perkins, T. A., & Yu, H. (2019) · Nature Communications · doi:10.1038/s41467-019-09035-x · Cited by 43 · see citing works
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Yadav, P. D., Nyayanit, D. A., Majumdar, T., Patil, S., Kaur, H., Gupta, N., Shete, A. M., Pandit, P., Kumar, A., Aggarwal, N., et al. (2021) · Viruses · doi:10.3390/v13050925 · Cited by 38 · see citing works
Transmission of Carbapenem-Resistant Klebsiella pneumoniae in US Hospitals
Luterbach, C., Chen, L., Komarow, L., Ostrowsky, B. E., Kaye, K. S., Hanson, B., Arias, C. A., Desai, S. S., Gallagher, J. C., Novick, E., et al. (2022) · Clinical Infectious Diseases · doi:10.1093/cid/ciac791 · Cited by 37 · see citing works
Maltby, C. J., Schofield, J. P. R., Houghton, S. D., O’Kelly, I., Vargas‐Caballero, M., Deinhardt, K., & Coldwell, M. J. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa699 · Cited by 37 · see citing works
Skazina, M. A., Odintsova, N. A., Maiorova, M. A., Ivanova, A., Väinölä, R., & Strelkov, P. (2021) · Scientific Reports · doi:10.1038/s41598-021-85098-5 · Cited by 37 · see citing works
Gupta, P., Robin, V. V., & Dharmarajan, G. (2020) · Journal of Genetics · doi:10.1007/s12041-020-01225-7 · Cited by 35 · see citing works
Genomic variant-identification methods may alter Mycobacterium tuberculosis transmission inferences
Walter, K. S., Colijn, C., Cohen, T., Mathema, B., Liu, Q., Bowers, J. R., Engelthaler, D. M., Narechania, A., Lemmer, D., Croda, J., et al. (2020) · Microbial Genomics · doi:10.1099/mgen.0.000418 · Cited by 35 · see citing works
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Murphy, J. C., Harrington, E. M., Schumann, S., Vasconcelos, E. J. R., Mottram, T. J., Harper, K. L., Aspden, J. L., & Whitehouse, A. (2023) · Nature Communications · doi:10.1038/s41467-023-35914-5 · Cited by 33 · see citing works
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Lemieux, A., Colby, G. A., Poulain, A. J., & Aris‐Brosou, S. (2022) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2022.1073 · Cited by 33 · see citing works
Insights into Pasteurellaceae carriage dynamics in the nasal passages of healthy beef calves
Thomas, A. C., Bailey, M., Lee, M. R. F., Mead, A., Morales‐Aza, B. M., Reynolds, R., Vipond, B. B., Finn, A. H. R., & Eisler, M. C. (2019) · Scientific Reports · doi:10.1038/s41598-019-48007-5 · Cited by 32 · see citing works
Guitard, J. J., Chrétien, E., Bonville, J. D., Roche, D. G., Boisclair, D., & Binning, S. A. (2022) · Journal of Experimental Biology · doi:10.1242/jeb.243160 · Cited by 32 · see citing works
Within-Host Evolution of Bacterial Pathogens in Acute and Chronic Infection
Dekker, J. P. (2023) · Annual Review of Pathology Mechanisms of Disease · doi:10.1146/annurev-pathmechdis-051122-111408 · Cited by 31 · see citing works
Systemic inflammation impairs myelopoiesis and interferon type I responses in humans
Keramati, F., Leijte, G. P., Bruse, N., Grondman, I., Habibi, E., Ruiz-Moreno, C., Megchelenbrink, W., van Ton, A. M. P., Heesakkers, H., Bremmers, M. E. J., et al. (2025) · Nature Immunology · doi:10.1038/s41590-025-02136-4 · Cited by 31 · see citing works
Trucchi, E., Gratton, P., Mafessoni, F., Motta, S., Cicconardi, F., Mancia, F., Bertorelle, G., D’Annessa, I., & Marino, D. D. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa337 · Cited by 31 · see citing works
Chéneau, C., Eichholz, K., Tran, T. H., Tran, T. T. P., Paris, O., Henriquet, C., Bajramovic, J. J., Pugnière, M., & Kremer, E. J. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.685218 · Cited by 30 · see citing works
Bandoy, D. D. R., & Weimer, B. C. (2021) · Scientific Reports · doi:10.1038/s41598-021-86265-4 · Cited by 29 · see citing works
Human FcRn expression and Type I Interferon signaling control Echovirus 11 pathogenesis in mice
Wells, A. I., Grimes, K. A., Kim, K., Branche, E., Bakkenist, C. J., DePas, W. H., Shresta, S., & Coyne, C. B. (2021) · PLoS Pathogens · doi:10.1371/journal.ppat.1009252 · Cited by 28 · see citing works
Dingens, A. S., Pratap, P. P., Malone, K. D., Hilton, S. K., Ketas, T. J., Cottrell, C. A., Overbaugh, J. M., Moore, J. P., Klasse, P. J., Ward, A. B., et al. (2021) · eLife · doi:10.7554/elife.64281 · Cited by 26 · see citing works
Permana, B., Beatson, S. A., & Forde, B. M. (2023) · BMC Bioinformatics · doi:10.1186/s12859-023-05332-x · Cited by 26 · see citing works
Dyson, Z. A., Ashton, P., Khanam, F., Chirambo, A. C., Shakya, M., Meiring, J., Tonks, S., Karkey, A., Msefula, C. L., Clemens, J. D., et al. (2024) · The Lancet Microbe · doi:10.1016/s2666-5247(24)00047-8 · Cited by 25 · see citing works
Narayanan, A., Vadnala, R. N., Ganguly, P., Selvakumar, P., Rudramurthy, S. M., Prasad, R., Chakrabarti, A., Siddharthan, R., & Sanyal, K. (2021) · mBio · doi:10.1128/mbio.00905-21 · Cited by 25 · see citing works
Duault, H., Durand, B., & Canini, L. (2022) · Pathogens · doi:10.3390/pathogens11020252 · Cited by 24 · see citing works
Kan, C.-M., Tsang, H. F., Pei, X. M., Ng, S. S. M., Yim, A. K., Yu, A. C.-S., & Wong, S. C. C. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms25063333 · Cited by 24 · see citing works
Formation and three-dimensional architecture of Leishmania adhesion in the sand fly vector
Yanase, R., Moreira-Leite, F. F., Rea, E., Wilburn, L., Sádlová, J., Vojtková, B., Pružinová, K., Taniguchi, A., Nonaka, S., Volf, P., et al. (2023) · eLife · doi:10.7554/elife.84552 · Cited by 22 · see citing works
Bridgin connects the outer kinetochore to centromeric chromatin
Sridhar, S., Hori, T., Nakagawa, R., Fukagawa, T., & Sanyal, K. (2021) · Nature Communications · doi:10.1038/s41467-020-20161-9 · Cited by 22 · see citing works
Blackburn, R. M., Frampton, D., Smith, C. M., Fragaszy, E., Watson, S. J., Ferns, R. B., Binter, Š., Coen, P. G., Grant, P. R., Shallcross, L. J., et al. (2019) · Influenza and Other Respiratory Viruses · doi:10.1111/irv.12679 · Cited by 21 · see citing works
Inferring putative transmission clusters with Phydelity
Han, A. X., Parker, E., Maurer‐Stroh, S., & Russell, C. A. (2019) · Virus Evolution · doi:10.1093/ve/vez039 · Cited by 21 · see citing works
The ESX-1 Substrate PPE68 Has a Key Function in ESX-1-Mediated Secretion in Mycobacterium marinum
Damen, M. P. M., Meijers, A. S., Keizer, E., Piersma, S. R., Jiménez, C. R., Kuijl, C. P., Bitter, W., & Houben, E. N. G. (2022) · mBio · doi:10.1128/mbio.02819-22 · Cited by 20 · see citing works
Sobkowiak, B., Romanowski, K., Sekirov, I., Gardy, J. L., & Johnston, J. C. (2023) · Epidemiology and Infection · doi:10.1017/s0950268823000900 · Cited by 20 · see citing works
Kiem, C. T., & Bedford, T. (2024) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2305299121 · Cited by 20 · see citing works
RdDM pathway components differentially modulate Tobamovirus symptom development
Leone, M., Zavallo, D., Venturuzzi, A. L., & Asurmendi, S. (2020) · Plant Molecular Biology · doi:10.1007/s11103-020-01051-6 · Cited by 19 · see citing works
Tuberculosis alters immune-metabolic pathways resulting in perturbed IL-1 responses
Llibre, A., Smith, N., Rouilly, V., Musvosvi, M., Nemes, E., Posseme, C., Mabwe, S., Charbit, B., Mbandi, S. K., Filander, E., et al. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.897193 · Cited by 19 · see citing works
Assembling highly repetitive Xanthomonas TALomes using Oxford Nanopore sequencing
Erkes, A., Grove, R., Žarković, M., Krautwurst, S., Koebnik, R., Morgan, R., Wilson, G. G., Hölzer, M., Marz, M., Boch, J., et al. (2023) · BMC Genomics · doi:10.1186/s12864-023-09228-1 · Cited by 19 · see citing works
A within-host infection model to explore tolerance and resistance
Duneau, D., Lafont, P., Lauzeral, C., Parthuisot, N., Faucher, C., Jin, X., Buchon, N., & Ferdy, J. (2025) · eLife · doi:10.7554/elife.104052 · Cited by 19 · see citing works
Nigsch, A., Robbe‐Austerman, S., Stuber, T. P., Bitar, P. D. P., Grohn, Y. T., & Schukken, Y. H. (2021) · PLoS ONE · doi:10.1371/journal.pone.0246983 · Cited by 19 · see citing works
Eichholz, K., Tran, T. H., Chéneau, C., Tran, T. T. P., Paris, O., Pugnière, M., & Kremer, E. J. (2022) · Journal of Virology · doi:10.1128/jvi.01850-21 · Cited by 19 · see citing works
Castañeda, A. F., & Glaunsinger, B. A. (2018) · Journal of Virology · doi:10.1128/jvi.01488-18 · Cited by 18 · see citing works
Recurrent evolution of high virulence in isolated populations of a DNA virus
Hill, T., & Unckless, R. L. (2020) · eLife · doi:10.7554/elife.58931 · Cited by 18 · see citing works
Wang, J., Feng, Y., & Zong, Z. (2023) · mSphere · doi:10.1128/msphere.00173-23 · Cited by 17 · see citing works
Transmission Bottleneck Size Estimation from De Novo Viral Genetic Variation
Shi, Y. T., Harris, J. D., Martin, M. A., & Koelle, K. (2023) · Molecular Biology and Evolution · doi:10.1093/molbev/msad286 · Cited by 17 · see citing works
Accuracy in Near-Perfect Virus Phylogenies
Wertheim, J. O., Steel, M., & Sanderson, M. J. (2021) · Systematic Biology · doi:10.1093/sysbio/syab069 · Cited by 17 · see citing works
Padmanabhan, C., Zheng, Y., Shamimuzzaman, M., Wilson, J. R., Gilliard, A. C., Fei, Z., & Ling, K. (2022) · PLoS ONE · doi:10.1371/journal.pone.0257936 · Cited by 17 · see citing works
Statistical outbreak detection by joining medical records and pathogen similarity
Miller, J. K., Chen, J., Sundermann, A. J., Marsh, J. W., Saul, M. I., Shutt, K. A., Pacey, M. P., Mustapha, M. M., Harrison, L. H., & Dubrawski, A. W. (2019) · Journal of Biomedical Informatics · doi:10.1016/j.jbi.2019.103126 · Cited by 17 · see citing works
Disulfide stabilization reveals conserved dynamic features between SARS-CoV-1 and SARS-CoV-2 spikes
Zhang, X., Li, Z., Zhang, Y., Liu, Y., Wang, J., Liu, B., Chen, Q., Wang, Q., Fu, L., Wang, P., et al. (2023) · Life Science Alliance · doi:10.26508/lsa.202201796 · Cited by 16 · see citing works
Yanase, R., Pružinová, K., Owino, B. O., Rea, E., Moreira-Leite, F. F., Taniguchi, A., Nonaka, S., Sádlová, J., Vojtková, B., Volf, P., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-51291-z · Cited by 16 · see citing works
Rossi, G., Crispell, J., Balaz, D., Lycett, S., Benton, C. H., Delahay, R. J., & Kao, R. R. (2020) · Scientific Reports · doi:10.1038/s41598-020-78900-3 · Cited by 16 · see citing works
How adaptive immunity constrains the composition and fate of large bacterial populations
Bonsma-Fisher, M., Soutière, D., & Goyal, S. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1802887115 · Cited by 15 · see citing works
Estimating the relative probability of direct transmission between infectious disease patients
Leavitt, S. V., Lee, R. S., Sebastiani, P., Horsburgh, C. R., Jenkins, H. E., & White, L. F. (2020) · International Journal of Epidemiology · doi:10.1093/ije/dyaa031 · Cited by 15 · see citing works
Old Drugs with New Tricks: Efficacy of Fluoroquinolones to Suppress Replication of Flaviviruses
Scroggs, S. L. P., Andrade, C. C., Ramesh, C., Azar, S. R., Schirtzinger, E. E., Garcia, E. I., Arterburn, J. B., Hanley, K. A., & Rossi, S. L. (2020) · Viruses · doi:10.3390/v12091022 · Cited by 15 · see citing works
Instability of aquaglyceroporin (AQP) 2 contributes to drug resistance in Trypanosoma brucei
Quintana, J. F., Bueren‐Calabuig, J. A., Zuccotto, F., de Koning, H. P., Horn, D., & Field, M. C. (2020) · PLoS neglected tropical diseases · doi:10.1371/journal.pntd.0008458 · Cited by 15 · see citing works
Murine cytomegalovirus downregulates ERAAP and induces an unconventional T cell response to self
Geiger, K. M., Valerio, M. M., Coombs, R., Arana, K., Park, C., Lee, A. Y., Shastri, N., Robey, E. A., & Coscoy, L. (2023) · Cell Reports · doi:10.1016/j.celrep.2023.112317 · Cited by 14 · see citing works
Xu, Y., Stockdale, J. E., Naidu, V., Hatherell, H.-A., Stimson, J. A., Stagg, H. R., Abubakar, I. I., & Colijn, C. (2020) · Microbial Genomics · doi:10.1099/mgen.0.000450 · Cited by 14 · see citing works
Cellular endosomal potassium ion flux regulates arenavirus uncoating during virus entry
Shaw, A. B., Tse, H. N., Byford, O., Plahe, G., Moon-Walker, A., Hover, S. E., Saphire, E. O., Whelan, S. P. J., Mankouri, J., Fontana, J., et al. (2024) · mBio · doi:10.1128/mbio.01684-23 · Cited by 13 · see citing works
Occurrence of foamy macrophages during the innate response of zebrafish to trypanosome infections
Jacobs, S. H., Dóró, E., Hammond, F. R., Chi, M. N., Lutfalla, G., Wiegertjes, G. F., & Forlenza, M. (2021) · eLife · doi:10.7554/elife.64520 · Cited by 13 · see citing works
Zika virus persistence in the male macaque reproductive tract
Ball, E. E., Pesavento, P. A., Rompay, K. K. A. V., Keel, M. K., Singapuri, A., Gómez-Vázquez, J. P., Dudley, D. M., O’Connor, D. H., Breitbach, M. E., Maness, N. J., et al. (2022) · PLoS neglected tropical diseases · doi:10.1371/journal.pntd.0010566 · Cited by 13 · see citing works
A phylogenetic study of dengue virus in urban Vietnam shows long-term persistence of endemic strains
Ashall, J., Shah, S., Biggs, J. R., Chang, J.-N. R., Jafari, Y., Brady, O. J., Mai, H. K., Le, L. T., Do, T. H., Nguyen, H. A. T., et al. (2023) · Virus Evolution · doi:10.1093/ve/vead012 · Cited by 13 · see citing works
Within-host diversity improves phylogenetic and transmission reconstruction of SARS-CoV-2 outbreaks
Ortiz, A. T., Kendall, M., Storey, N., Hatcher, J., Dunn, H., Roy, S., Williams, R. J., Williams, C. A., Goldstein, R. A., Didelot, X., et al. (2023) · eLife · doi:10.7554/elife.84384 · Cited by 13 · see citing works
Hajra, D., Rajmani, R. S., Chaudhary, A. D., Gupta, S. K., & Chakravortty, D. (2024) · eLife · doi:10.7554/elife.93125.4 · Cited by 13 · see citing works
Yersinia remodels epigenetic histone modifications in human macrophages
Bekere, I., Huang, J., Schnapp, M., Rudolph, M., Berneking, L., Ruckdeschel, K., Grundhoff, A. T., Günther, T., Fischer, N., & Aepfelbacher, M. (2021) · PLoS Pathogens · doi:10.1371/journal.ppat.1010074 · Cited by 12 · see citing works
Carson, J., Keeling, M. J., Ribeca, P., & Didelot, X. (2025) · Molecular Biology and Evolution · doi:10.1093/molbev/msaf083 · Cited by 12 · see citing works
Lenggenhager, L., Martischang, R., Sauser, J., Perez, M., Vieux, L., Graf, C. E., Cordey, S., Laubscher, F., Nunes, T. R., Zingg, W., et al. (2022) · Antimicrobial Resistance and Infection Control · doi:10.1186/s13756-022-01092-0 · Cited by 12 · see citing works
Self-citationRossi, G., Shih, B. B.-J., Egbe, F. N., Motta, P., Duchatel, F., Kelly, R., Ndip, L. M., Sander, M., Tanya, V. N., Lycett, S., et al. (2023) · Frontiers in Veterinary Science · doi:10.3389/fvets.2023.1086001 · Cited by 12 · see citing works
Vock, I., & Tschudin‐Sutter, S. (2019) · Infection Control and Hospital Epidemiology · doi:10.1017/ice.2019.153 · Cited by 12 · see citing works
Gallego‐García, P., Varela, N., Estévez‐Gómez, N., Chiara, L. D., Fernández-Silva, I., Valverde, D., Sapoval, N., Treangen, T. J., Regueiro, B. J., Cabrera, J. J., et al. (2022) · Virus Evolution · doi:10.1093/ve/veac008 · Cited by 12 · see citing works
Strain-level transmission inference across multi-kingdom metagenomic data using TRACS
Tonkin‐Hill, G. Q., Shao, Y., Zarebski, A. E., Mallawaarachchi, S., Xie, O., Mäklin, T., Thorpe, H. A., Davies, M. R., Bentley, S. D., Lawley, T. D., et al. (2026) · Nature Microbiology · doi:10.1038/s41564-026-02339-x · Cited by 11 · see citing works
Caution is needed in interpreting HIV transmission chains by ultradeep sequencing
Todesco, È., Wirden, M., Câlin, R., Simon, A., Sayon, S., Barin, F., Katlama, C., Cálvez, V., Marcelin, A., & Hué, S. (2018) · AIDS · doi:10.1097/qad.0000000000002105 · Cited by 11 · see citing works
Interface refinement of low- to medium-resolution Cryo-EM complexes using HADDOCK2.4
Neijenhuis, T., van Keulen, S. C., & Bonvin, A. M. J. J. (2022) · Structure · doi:10.1016/j.str.2022.02.001 · Cited by 11 · see citing works
Anthonies, S., & Vargas-Muñiz, J. M. (2022) · Frontiers in Fungal Biology · doi:10.3389/ffunb.2022.941691 · Cited by 10 · see citing works
Hayashi, T., Tsukagoshi, H., Sekizuka, T., Ishikawa, D., Imai, M., Fujita, M., Kuroda, M., & Saruki, N. (2018) · Scandinavian Journal of Infectious Diseases · doi:10.1080/23744235.2018.1490813 · Cited by 10 · see citing works
Sample size calculation for phylogenetic case linkage
Wohl, S., Giles, J. R., & Lessler, J. (2021) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1009182 · Cited by 10 · see citing works
Basant, A., & Way, M. (2022) · eLife · doi:10.7554/elife.74655 · Cited by 10 · see citing works
- Authors
- Campbell, F., Strang, C., Ferguson, N., Cori, A., & Jombart, T.
- Affiliations
- Imperial College London (GB)
- Animal Health Trust (GB)
- Corresponding author
- Campbell, Finlay
- Cori, Anne
- Jombart, Thibaut
- Venue
- PLOS Pathogens
- Publisher
- Public Library of Science (PLoS)
- Published
- 2018-02-08
- Volume
- 14
- Issue
- 2
- Pages
- e1006885
- ISSN
- 1553-7366 (ISSN-L)
- 1553-7374
- PMC
- PMC5821398
- OpenAlex
- W2786722019
- Cited by
- 199
- References
- 114
- Citations by year
- 2026: 16 · 2025: 18 · 2024: 20 · 2023: 33 · 2022: 29 · 2021: 29 · 2020: 26 · 2019: 16 · 2018: 11 · 2017: 1
- FWCI
- 6.51
- Type
- journal article
- Language
- en
- Update notices
- new_version (2018-02-21)
- Open access
- gold
- doi.org
- Licence
- Locations
- PLoS Pathogens (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- LSHTM Research Online (London School of Hygiene and Tropical Medicine) (acceptedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Figshare (submittedVersion, cc-by)
- Spiral (Imperial College London) (submittedVersion, other-oa)
- Funders
- Bill and Melinda Gates Foundation
- Wellcome Trust
- National Institute for Health Research Health Protection Research Unit
- National Institute for Health and Care Research (HPRU-2012-10080)
- Medical Research Council (MR/R015600/1)
- National Institute of General Medical Sciences (U01GM110721)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Life Sciences › Agricultural and Biological Sciences › Food Science › Salmonella and Campylobacter epidemiology
- Keywords
- whole genome sequencing, transmission trees, genetic diversity, pathogen evolution, RNA viruses, Streptococcus pneumoniae, Shigella sonnei, Clostridium difficile, phylogenetic inference, infectious disease outbreaks
- MeSH terms
- Whole Genome Sequencing, Bacteria, Base Sequence, Chromosome Mapping, Communicable Diseases, Disease Outbreaks, Humans, Phylogeny, Genetic Variation, Viruses, Genome, Viral, Genome, Bacterial, Sequence Analysis, DNA, Disease Transmission, Infectious, Genetic Predisposition to Disease
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