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Martínez JRW, Planet PJ, Spencer-Sandino M, Rivas L, Díaz L, Moustafa AM, Quesille-Villalobos A, Riquelme-Neira R, Alcalde-Rico M, Hanson B, Carvajal LP, Rincón S, Reyes J, Lam M, Calderon JF, Araos R, García P, Arias CA, Munita JM. Dynamics of the MRSA Population in a Chilean Hospital: a Phylogenomic Analysis (2000-2016). Microbiol Spectr 2023; 11:e0535122. [PMID: 37338398 PMCID: PMC10433796 DOI: 10.1128/spectrum.05351-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 05/29/2023] [Indexed: 06/21/2023] Open
Abstract
The global dissemination of methicillin-resistant Staphylococcus aureus (MRSA) is associated with the emergence and establishment of clones in specific geographic areas. The Chilean-Cordobes clone (ChC) (ST5-SCCmecI) has been the predominant MRSA clone in Chile since its first description in 1998, despite the report of other emerging MRSA clones in recent years. Here, we characterize the evolutionary history of MRSA from 2000 to 2016 in a Chilean tertiary health care center using phylogenomic analyses. We sequenced 469 MRSA isolates collected between 2000 and 2016. We evaluated the temporal trends of the circulating clones and performed a phylogenomic reconstruction to characterize the clonal dynamics. We found a significant increase in the diversity and richness of sequence types (STs; Spearman r = 0.8748, P < 0.0001) with a Shannon diversity index increasing from 0.221 in the year 2000 to 1.33 in 2016, and an effective diversity (Hill number; q = 2) increasing from 1.12 to 2.71. The temporal trend analysis revealed that in the period 2000 to 2003 most of the isolates (94.2%; n = 98) belonged to the ChC clone. However, since then, the frequency of the ChC clone has decreased over time, accounting for 52% of the collection in the 2013 to 2016 period. This decline was accompanied by the rise of two emerging MRSA lineages, ST105-SCCmecII and ST72-SCCmecVI. In conclusion, the ChC clone remains the most frequent MRSA lineage, but this lineage is gradually being replaced by several emerging clones, the most important of which is clone ST105-SCCmecII. To the best of our knowledge, this is the largest study of MRSA clonal dynamics performed in South America. IMPORTANCE Methicillin-resistant Staphylococcus aureus (MRSA) is a major public health pathogen that disseminates through the emergence of successful dominant clones in specific geographic regions. Knowledge of the dissemination and molecular epidemiology of MRSA in Latin America is scarce and is largely based on small studies or more limited typing techniques that lack the resolution to represent an accurate description of the genomic landscape. We used whole-genome sequencing to study 469 MRSA isolates collected between 2000 and 2016 in Chile providing the largest and most detailed study of clonal dynamics of MRSA in South America to date. We found a significant increase in the diversity of MRSA clones circulating over the 17-year study period. Additionally, we describe the emergence of two novel clones (ST105-SCCmecII and ST72-SCCmecVI), which have been gradually increasing in frequency over time. Our results drastically improve our understanding of the dissemination and update our knowledge about MRSA in Latin America.
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Affiliation(s)
- José R. W. Martínez
- Genomics & Resistant Microbes (GeRM), ICIM, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
- Multidisciplinary Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Santiago, Chile
| | - Paul J. Planet
- Division of Pediatric Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- American Museum of Natural History, New York, New York, USA
| | - Maria Spencer-Sandino
- Genomics & Resistant Microbes (GeRM), ICIM, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
- Multidisciplinary Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Santiago, Chile
| | - Lina Rivas
- Genomics & Resistant Microbes (GeRM), ICIM, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
- Multidisciplinary Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Santiago, Chile
| | - Lorena Díaz
- Genomics & Resistant Microbes (GeRM), ICIM, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
- Multidisciplinary Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Santiago, Chile
- Molecular Genetics and Antimicrobial Resistance Unit, Universidad El Bosque, Bogotá, Colombia
| | - Ahmed M. Moustafa
- Division of Pediatric Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Ana Quesille-Villalobos
- Genomics & Resistant Microbes (GeRM), ICIM, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
- Multidisciplinary Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Santiago, Chile
| | - Roberto Riquelme-Neira
- Genomics & Resistant Microbes (GeRM), ICIM, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
- Multidisciplinary Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Santiago, Chile
- Núcleo de Investigaciones Aplicadas en Ciencias Veterinarias y Agronómicas, Facultad de Medicina Veterinaria y Agronomía, Universidad de Las Américas, Santiago, Chile
| | - Manuel Alcalde-Rico
- Genomics & Resistant Microbes (GeRM), ICIM, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
- Multidisciplinary Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Santiago, Chile
- Grupo de Resistencia a los Antibióticos en Bacterias Patógenas y Ambientales (GRABPA), Pontificia Univ. Católica de Valparaíso, Valparaiso, Chile
| | - Blake Hanson
- Center for Antimicrobial Resistance and Microbial Genomics, Univ. of Texas Health Science Center, McGovern Medical School, Houston, Texas, USA
| | - Lina P. Carvajal
- Molecular Genetics and Antimicrobial Resistance Unit, Universidad El Bosque, Bogotá, Colombia
| | - Sandra Rincón
- Molecular Genetics and Antimicrobial Resistance Unit, Universidad El Bosque, Bogotá, Colombia
| | - Jinnethe Reyes
- Molecular Genetics and Antimicrobial Resistance Unit, Universidad El Bosque, Bogotá, Colombia
| | - Marusella Lam
- Departamento de Laboratorios Clínicos, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Juan F. Calderon
- Centro de Genética y Genómica Instituto de Ciencias e Innovación en Medicina Facultad de Medicina Clínica Alemana Universidad Del Desarrollo, Santiago, Chile
- Research Center for the Development of Novel Therapeutic Alternatives for Alcohol Use Disorders, Santiago, Chile
| | - Rafael Araos
- Genomics & Resistant Microbes (GeRM), ICIM, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
- Multidisciplinary Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Santiago, Chile
| | - Patricia García
- Multidisciplinary Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Santiago, Chile
- Departamento de Laboratorios Clínicos, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - César A. Arias
- Division of Infectious Diseases, Houston Methodist Hospital, Houston, Texas, USA
- Center for Infectious Diseases, Houston Methodist Research Institution, Houston, Texas, USA
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - José M. Munita
- Genomics & Resistant Microbes (GeRM), ICIM, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
- Multidisciplinary Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Santiago, Chile
- Hospital Padre Hurtado, Santiago, Chile
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Martínez JRW, Planet PJ, Maria SS, Lina R, Lorena D, Ana QV, Roberto RN, Manuel AR, Blake H, Carvajal LP, Sandra R, Jinnethe R, Marusella L, Rafael A, Patricia G, Arias CA, Munita JM. Dynamics of the MRSA Population in A Chilean Hospital: A Phylogenomic Analysis (2000-2016). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.06.526811. [PMID: 36798318 PMCID: PMC9934535 DOI: 10.1101/2023.02.06.526811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
The global dissemination of methicillin-resistant Staphylococcus aureus (MRSA) is associated with the emergence and establishment of clones in specific geographic areas. The Chilean-Cordobes clone (ChC) (ST5-SCC mec I) has been the predominant MRSA clone in Chile since its first description in 1998, despite the report of other emerging MRSA clones in the last years. Here, we characterize the evolutionary history of MRSA from 2000 to 2016 in a Chilean tertiary healthcare center using phylogenomic analyses. We sequenced 469 MRSA isolates collected between 2000-2016 in a tertiary healthcare center in Chile. We evaluated the temporal trends of the circulating clones and performed a phylogenomic reconstruction to characterize the clonal dynamics. We found a significant increase in the diversity and richness of sequence types (STs; Spearman r=0.8748, p<0.0001) with a Shannon diversity index increasing from 0.221 in the year 2000 to 1.33 in 2016. The temporal trend analysis revealed that in the period 2000-2003 most of the isolates (94.2%; n=98) belonged to the ChC clone. However, since then, the frequency of the ChC clone has decreased over time, accounting for 52% of the collection in the 2013-2016 period. This decline was accompanied by the rise of two emerging MRSA lineages, ST105-SCC mec II and ST72-SCC mec VI. In conclusion, the ChC clone remains the most frequent MRSA lineage in Chile. However, this lineage is gradually being replaced by several emerging clones, the most important of which is clone ST105-SCC mec II. To the best of our knowledge, this is the largest study of MRSA clonal dynamics performed in South America. Importance Methicillin-resistant Staphylococcus aureus (MRSA) is a major public health pathogen that disseminates through the emergence of successful dominant clones in specific geographic regions. Knowledge of the dissemination and molecular epidemiology of MRSA in Latin America is scarce and is largely based on small studies or classical typing techniques with several limitations to depict an accurate description of their genomic landscape. We used whole-genome sequencing to study 469 MRSA isolates collected between 2000-2016 in Chile to provide the largest and most detailed study of clonal dynamics of MRSA carried out in South America to date. We found a significant increase in the diversity of MRSA clones circulating over the 17-year study period. Additionally, we describe the emergence of two novel clones (ST105-SCCmecII and ST72-SCCmecVI), which have been gradually increasing their frequency over time. Our results drastically improve our understanding of the dissemination and update our knowledge about MRSA in Latin America.
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Drug Resistance of Mycobacterium tuberculosis Based on Whole-Genome Sequencing in the Yi Ethnic Group, Sichuan Province, China. J Immunol Res 2023; 2023:4431209. [PMID: 36726492 PMCID: PMC9886460 DOI: 10.1155/2023/4431209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 11/11/2022] [Accepted: 11/24/2022] [Indexed: 01/25/2023] Open
Abstract
This study investigated drug-resistant tuberculosis (DR-TB) in the Yi ethnic group. The study was designed to identify risk factors for DR-TB and its relationship with HIV/AIDS. To establish the resistance to antituberculosis drugs, whole-genome sequencing (WGS) was performed using culture-positive Mycobacterium tuberculosis samples collected from people of the Yi ethnic group from March 2019 to March 2021. Baseline characteristics were obtained from China's tuberculosis surveillance system. A total of 116 M. tuberculosis strains were included in the final analysis. Lineage 2.2 (75.86%) was the dominant sublineage, followed by lineage 4.5 (18.97%) and lineage 4.4 (5.17%). The rates of rifampicin-resistant (RR-TB), multidrug-resistant (MDR-TB), and preextensively drug-resistant TB (pre-XDR-TB) were 18.97%, 10.34%, and 6.03%, respectively. Drug-resistant strains were not found in the elderly (age ≥ 65 years). The proportions of RR/MDR-TB and pre-XDR-TB cases among re-treatment patients were higher than those among new patients (χ 2 = 12.155, P = 0.003; χ 2 = 22.495, P = 0.001, respectively). The pre-XDR-TB case proportions were higher among female patients than among males and higher among referred patients (χ 2 = 5.456, P = 0.032; χ 2 = 15.134, P = 0.002, respectively). The rates of RR/MDR-TB and pre-XDR-TB did not differ appreciably among groups with different HIV infection statuses nor lineage populations. DR-TB poses a serious challenge to the Yi ethnic group. Re-treatment patients, women, and referred patients were at high risk of MDR/RR-TB or pre-XDR-TB while HIV and lineage 2 had negligible association with drug resistance. Whole-genome sequencing should be used to guide the design of treatment regimens and to tailor public interventions.
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Mehta K, Narayanan N, Heysell SK, Bisson GP, Subbian S, Kurepina N, Kreiswirth BN, Vinnard C. Pharmacogenetic variability and the probability of site of action target attainment during tuberculosis meningitis treatment: A physiologically based pharmacokinetic modeling and simulations study. Tuberculosis (Edinb) 2022; 137:102271. [PMID: 36375279 DOI: 10.1016/j.tube.2022.102271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 09/01/2022] [Accepted: 10/12/2022] [Indexed: 11/22/2022]
Abstract
OBJECTIVE AND METHODS Our objective was to investigate the role of patient pharmacogenetic variability in determining site of action target attainment during tuberculous meningitis (TBM) treatment. Rifampin and isoniazid PBPK model that included SLCO1B1 and NAT2 effects on exposures respectively were obtained from literature, modified, and validated using available cerebrospinal-fluid (CSF) concentrations. Population simulations of isoniazid and rifampin concentrations in brain interstitial fluid and probability of target attainment according to genotypes and M. tuberculosis MIC levels, under standard and intensified dosing, were conducted. RESULTS The rifampin and isoniazid model predicted steady-state drug concentration within brain interstitial fluid matched with the observed CSF concentrations. At MIC level of 0.25 mg/L, 57% and 23% of the patients with wild type and heterozygous SLCO1B1 genotype respectively attained the target in CNS with rifampin standard dosing, improving to 98% and 91% respectively with 35 mg/kg dosing. At MIC level of 0.25 mg/L, 33% of fast acetylators attained the target in CNS with isoniazid standard dosing, improving to 90% with 7.5 mg/kg dosing. CONCLUSION In this study, the combined effects of pharmacogenetic and M. tuberculosis MIC variability were potent determinants of target attainment in CNS. The potential for genotype-guided dosing during TBM treatment should be further explored in prospective clinical studies.
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Affiliation(s)
| | | | - Scott K Heysell
- University of Virginia, Division of Infectious Diseases and International Health, Charlottesville, VA, USA
| | - Gregory P Bisson
- University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Selvakumar Subbian
- Public Health Research Institute, New Jersey Medical School, Newark, NJ, USA
| | - Natalia Kurepina
- Center for Discovery & Innovation, Hackensack Meridian Health, Nutley, NJ, USA
| | - Barry N Kreiswirth
- Center for Discovery & Innovation, Hackensack Meridian Health, Nutley, NJ, USA
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Brown TS, Robinson DA, Buckee CO, Mathema B. Connecting the dots: understanding how human mobility shapes TB epidemics. Trends Microbiol 2022; 30:1036-1044. [PMID: 35597716 PMCID: PMC10068677 DOI: 10.1016/j.tim.2022.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 04/18/2022] [Accepted: 04/19/2022] [Indexed: 01/13/2023]
Abstract
Tuberculosis (TB) remains a leading infectious cause of death worldwide. Reducing TB infections and TB-related deaths rests ultimately on stopping forward transmission from infectious to susceptible individuals. Critical to this effort is understanding how human host mobility shapes the transmission and dispersal of new or existing strains of Mycobacterium tuberculosis (Mtb). Important questions remain unanswered. What kinds of mobility, over what temporal and spatial scales, facilitate TB transmission? How do human mobility patterns influence the dispersal of novel Mtb strains, including emergent drug-resistant strains? This review summarizes the current state of knowledge on mobility and TB epidemic dynamics, using examples from three topic areas, including inference of genetic and spatial clustering of infections, delineating source-sink dynamics, and mapping the dispersal of novel TB strains, to examine scientific questions and methodological issues within this topic. We also review new data sources for measuring human mobility, including mobile phone-associated movement data, and discuss important limitations on their use in TB epidemiology.
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Affiliation(s)
- Tyler S Brown
- Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Infectious Diseases Division, Massachusetts General Hospital, Boston, MA, USA
| | - D Ashley Robinson
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, MS, USA
| | - Caroline O Buckee
- Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Barun Mathema
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA.
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Chmel M, Bartoš O, Kabíčková H, Pajer P, Kubíčková P, Novotná I, Bartovská Z, Zlámal M, Burantová A, Holub M, Jiřincová H, Nagy A, Černíková L, Zákoucká H, Dresler J. Retrospective Analysis Revealed an April Occurrence of Monkeypox in the Czech Republic. Viruses 2022; 14:v14081773. [PMID: 36016395 PMCID: PMC9412638 DOI: 10.3390/v14081773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/09/2022] [Accepted: 08/12/2022] [Indexed: 11/16/2022] Open
Abstract
Herein, we present our findings of an early appearance of the Monkeypox virus in Prague, Czech Republic. A retrospective analysis of biological samples, carried out on the 28th of April, revealed a previously unrecognized case of Monkeypox virus (MPxV) infection. Subsequent data analysis confirmed that the virus strain belongs to the ongoing outbreak. Combined with clinical and epidemiological investigations, we extended the roots of the current outbreak at least back to 16th of April, 2022.
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Affiliation(s)
- Martin Chmel
- Military Health Institute, Military Medical Agency, 16200 Prague, Czech Republic
- Department of Infectious Diseases, First Faculty of Medicine, Charles University and Military University Hospital Prague, 12108 Prague, Czech Republic
- Correspondence: ; Tel.: +420-722712999
| | - Oldřich Bartoš
- Military Health Institute, Military Medical Agency, 16200 Prague, Czech Republic
| | - Hana Kabíčková
- Military Health Institute, Military Medical Agency, 16200 Prague, Czech Republic
| | - Petr Pajer
- Military Health Institute, Military Medical Agency, 16200 Prague, Czech Republic
| | - Pavla Kubíčková
- Military Health Institute, Military Medical Agency, 16200 Prague, Czech Republic
| | - Iva Novotná
- Military Health Institute, Military Medical Agency, 16200 Prague, Czech Republic
| | - Zofia Bartovská
- Department of Infectious Diseases, First Faculty of Medicine, Charles University and Military University Hospital Prague, 12108 Prague, Czech Republic
| | - Milan Zlámal
- Department of Infectious Diseases, First Faculty of Medicine, Charles University and Military University Hospital Prague, 12108 Prague, Czech Republic
| | - Anna Burantová
- Department of Infectious Diseases, First Faculty of Medicine, Charles University and Military University Hospital Prague, 12108 Prague, Czech Republic
| | - Michal Holub
- Department of Infectious Diseases, First Faculty of Medicine, Charles University and Military University Hospital Prague, 12108 Prague, Czech Republic
| | - Helena Jiřincová
- National Reference Laboratory for Influenza and Respiratory Viruses, National Institute for Public Health, 10042 Prague, Czech Republic
| | - Alexander Nagy
- National Reference Laboratory for Influenza and Respiratory Viruses, National Institute for Public Health, 10042 Prague, Czech Republic
- State Veterinary Institute, 16503 Prague, Czech Republic
| | | | - Hana Zákoucká
- Department of Sexually Transmitted Infections, National Institute for Public Health, 10042 Prague, Czech Republic
| | - Jiří Dresler
- Military Health Institute, Military Medical Agency, 16200 Prague, Czech Republic
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Sabin S, Morales-Arce AY, Pfeifer SP, Jensen JD. The impact of frequently neglected model violations on bacterial recombination rate estimation: a case study in Mycobacterium canettii and Mycobacterium tuberculosis. G3 (BETHESDA, MD.) 2022; 12:jkac055. [PMID: 35253851 PMCID: PMC9073693 DOI: 10.1093/g3journal/jkac055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 02/28/2022] [Indexed: 12/04/2022]
Abstract
Mycobacterium canettii is a causative agent of tuberculosis in humans, along with the members of the Mycobacterium tuberculosis complex. Frequently used as an outgroup to the M. tuberculosis complex in phylogenetic analyses, M. canettii is thought to offer the best proxy for the progenitor species that gave rise to the complex. Here, we leverage whole-genome sequencing data and biologically relevant population genomic models to compare the evolutionary dynamics driving variation in the recombining M. canettii with that in the nonrecombining M. tuberculosis complex, and discuss differences in observed genomic diversity in the light of expected levels of Hill-Robertson interference. In doing so, we highlight the methodological challenges of estimating recombination rates through traditional population genetic approaches using sequences called from populations of microorganisms and evaluate the likely mis-inference that arises owing to a neglect of common model violations including purifying selection, background selection, progeny skew, and population size change. In addition, we compare performance when full within-host polymorphism data are utilized, versus the more common approach of basing analyses on within-host consensus sequences.
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Affiliation(s)
- Susanna Sabin
- Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Ana Y Morales-Arce
- Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Susanne P Pfeifer
- Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Jeffrey D Jensen
- Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
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Santos-Lazaro D, Gavilan RG, Solari L, Vigo AN, Puyen ZM. Whole genome analysis of extensively drug resistant Mycobacterium tuberculosis strains in Peru. Sci Rep 2021; 11:9493. [PMID: 33947918 PMCID: PMC8097007 DOI: 10.1038/s41598-021-88603-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 04/14/2021] [Indexed: 02/02/2023] Open
Abstract
Peru has the highest burden of multidrug-resistant tuberculosis in the Americas region. Since 1999, the annual number of extensively drug-resistant tuberculosis (XDR-TB) Peruvian cases has been increasing, becoming a public health challenge. The objective of this study was to perform genomic characterization of Mycobacterium tuberculosis strains obtained from Peruvian patients with XDR-TB diagnosed from 2011 to 2015 in Peru. Whole genome sequencing (WGS) was performed on 68 XDR-TB strains from different regions of Peru. 58 (85.3%) strains came from the most populated districts of Lima and Callao. Concerning the lineages, 62 (91.2%) strains belonged to the Euro-American Lineage, while the remaining 6 (8.8%) strains belonged to the East-Asian Lineage. Most strains (90%) had high-confidence resistance mutations according to pre-established WHO-confident grading system. Discordant results between microbiological and molecular methodologies were caused by mutations outside the hotspot regions analysed by commercial molecular assays (rpoB I491F and inhA S94A). Cluster analysis using a cut-off ≤ 10 SNPs revealed that only 23 (34%) strains evidenced recent transmission links. This study highlights the relevance and utility of WGS as a high-resolution approach to predict drug resistance, analyse transmission of strains between groups, and determine evolutionary patterns of circulating XDR-TB strains in the country.
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Affiliation(s)
| | - Ronnie G. Gavilan
- grid.419228.40000 0004 0636 549XInstituto Nacional de Salud, Lima, Peru ,grid.441740.20000 0004 0542 2122Escuela Profesional de Medicina Humana, Universidad Privada San Juan Bautista, Lima, Peru
| | - Lely Solari
- grid.419228.40000 0004 0636 549XInstituto Nacional de Salud, Lima, Peru
| | - Aiko N. Vigo
- grid.419228.40000 0004 0636 549XInstituto Nacional de Salud, Lima, Peru
| | - Zully M. Puyen
- grid.419228.40000 0004 0636 549XInstituto Nacional de Salud, Lima, Peru ,grid.441917.e0000 0001 2196 144XEscuela de Medicina, Universidad Peruana de Ciencias Aplicadas, Lima, Peru
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Cheng B, Behr MA, Howden BP, Cohen T, Lee RS. Reporting practices for genomic epidemiology of tuberculosis: a systematic review of the literature using STROME-ID guidelines as a benchmark. THE LANCET. MICROBE 2021; 2:e115-e129. [PMID: 33842904 PMCID: PMC8034592 DOI: 10.1016/s2666-5247(20)30201-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND Pathogen genomics have become increasingly important in infectious disease epidemiology and public health. The Strengthening the Reporting of Molecular Epidemiology for Infectious Diseases (STROME-ID) guidelines were developed to outline a minimum set of criteria that should be reported in genomic epidemiology studies to facilitate assessment of study quality. We evaluate such reporting practices, using tuberculosis as an example. METHODS For this systematic review, we initially searched MEDLINE, Embase Classic, and Embase on May 3, 2017, using the search terms "tuberculosis" and "genom* sequencing". We updated this initial search on April 23, 2019, and also included a search of bioRxiv at this time. We included studies in English, French, or Spanish that recruited patients with microbiologically confirmed tuberculosis and used whole genome sequencing for typing of strains. Non-human studies, conference abstracts, and literature reviews were excluded. For each included study, the number and proportion of fulfilled STROME-ID criteria were recorded by two reviewers. A comparison of the mean proportion of fulfilled STROME-ID criteria before and after publication of the STROME-ID guidelines (in 2014) was done using a two-tailed t test. Quasi-Poisson regression and tobit regression were used to examine associations between study characteristics and the number and proportion of fulfilled STROME-ID criteria. This study was registered with PROSPERO, CRD42017064395. FINDINGS 976 titles and abstracts were identified by our primary search, with an additional 16 studies identified in bioRxiv. 114 full texts (published between 2009 and 2019) were eligible for inclusion. The mean proportion of STROME-ID criteria fulfilled was 50% (SD 12; range 16-75). The proportion of criteria fulfilled was similar before and after STROME-ID publication (51% [SD 11] vs 46% [14], p=0·26). The number of criteria reported (among those applicable to all studies) was not associated with impact factor, h-index, country of affiliation of senior author, or sample size of isolates. Similarly, the proportion of criteria fulfilled was not associated with these characteristics, with the exception of a sample size of isolates of 277 or more (the highest quartile). In terms of reproducibility, 100 (88%) studies reported which bioinformatic tools were used, but only 33 (33%) reported corresponding version numbers. Sequencing data were available for 86 (75%) studies. INTERPRETATION The reporting of STROME-ID criteria in genomic epidemiology studies of tuberculosis between 2009 and 2019 was low, with implications for assessment of study quality. The considerable proportion of studies without bioinformatics version numbers or sequencing data available highlights a key concern for reproducibility.
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Affiliation(s)
- Brianna Cheng
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
| | - Marcel A Behr
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
| | - Benjamin P Howden
- The Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | | | - Robyn S Lee
- Epidemiology Division, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
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10
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Morales-Arce AY, Harris RB, Stone AC, Jensen JD. Evaluating the contributions of purifying selection and progeny-skew in dictating within-host Mycobacterium tuberculosis evolution. Evolution 2020; 74:992-1001. [PMID: 32233086 DOI: 10.1111/evo.13954] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/08/2020] [Indexed: 12/28/2022]
Abstract
The within-host evolutionary dynamics of tuberculosis (TB) remain unclear, and underlying biological characteristics render standard population genetic approaches based upon the Wright-Fisher model largely inappropriate. In addition, the compact genome combined with an absence of recombination is expected to result in strong purifying selection effects. Thus, it is imperative to establish a biologically relevant evolutionary framework incorporating these factors in order to enable an accurate study of this important human pathogen. Further, such a model is critical for inferring fundamental evolutionary parameters related to patient treatment, including mutation rates and the severity of infection bottlenecks. We here implement such a model and infer the underlying evolutionary parameters governing within-patient evolutionary dynamics. Results demonstrate that the progeny skew associated with the clonal nature of TB severely reduces genetic diversity and that the neglect of this parameter in previous studies has led to significant mis-inference of mutation rates. As such, our results suggest an underlying de novo mutation rate that is considerably faster than previously inferred, and a progeny distribution differing significantly from Wright-Fisher assumptions. This inference represents a more appropriate evolutionary null model, against which the periodic effects of positive selection, associated with drug-resistance for example, may be better assessed.
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Affiliation(s)
- Ana Y Morales-Arce
- Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, USA
| | - Rebecca B Harris
- Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, USA
| | - Anne C Stone
- Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, USA.,School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, USA
| | - Jeffrey D Jensen
- Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, USA.,School of Life Sciences, Arizona State University, Tempe, Arizona, USA
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11
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Van Goethem N, Descamps T, Devleesschauwer B, Roosens NHC, Boon NAM, Van Oyen H, Robert A. Status and potential of bacterial genomics for public health practice: a scoping review. Implement Sci 2019; 14:79. [PMID: 31409417 PMCID: PMC6692930 DOI: 10.1186/s13012-019-0930-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 07/26/2019] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Next-generation sequencing (NGS) is increasingly being translated into routine public health practice, affecting the surveillance and control of many pathogens. The purpose of this scoping review is to identify and characterize the recent literature concerning the application of bacterial pathogen genomics for public health practice and to assess the added value, challenges, and needs related to its implementation from an epidemiologist's perspective. METHODS In this scoping review, a systematic PubMed search with forward and backward snowballing was performed to identify manuscripts in English published between January 2015 and September 2018. Included studies had to describe the application of NGS on bacterial isolates within a public health setting. The studied pathogen, year of publication, country, number of isolates, sampling fraction, setting, public health application, study aim, level of implementation, time orientation of the NGS analyses, and key findings were extracted from each study. Due to a large heterogeneity of settings, applications, pathogens, and study measurements, a descriptive narrative synthesis of the eligible studies was performed. RESULTS Out of the 275 included articles, 164 were outbreak investigations, 70 focused on strategy-oriented surveillance, and 41 on control-oriented surveillance. Main applications included the use of whole-genome sequencing (WGS) data for (1) source tracing, (2) early outbreak detection, (3) unraveling transmission dynamics, (4) monitoring drug resistance, (5) detecting cross-border transmission events, (6) identifying the emergence of strains with enhanced virulence or zoonotic potential, and (7) assessing the impact of prevention and control programs. The superior resolution over conventional typing methods to infer transmission routes was reported as an added value, as well as the ability to simultaneously characterize the resistome and virulome of the studied pathogen. However, the full potential of pathogen genomics can only be reached through its integration with high-quality contextual data. CONCLUSIONS For several pathogens, it is time for a shift from proof-of-concept studies to routine use of WGS during outbreak investigations and surveillance activities. However, some implementation challenges from the epidemiologist's perspective remain, such as data integration, quality of contextual data, sampling strategies, and meaningful interpretations. Interdisciplinary, inter-sectoral, and international collaborations are key for an appropriate genomics-informed surveillance.
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Affiliation(s)
- Nina Van Goethem
- Department of Epidemiology and public health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium
- Department of Epidemiology and Biostatistics, Institut de recherche expérimentale et clinique, Faculty of Public Health, Université catholique de Louvain, Clos Chapelle-aux-champs 30, 1200 Woluwe-Saint-Lambert, Belgium
| | - Tine Descamps
- Department of Epidemiology and public health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium
| | - Brecht Devleesschauwer
- Department of Epidemiology and public health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium
- Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Nancy H. C. Roosens
- Transversal Activities in Applied Genomics, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium
| | - Nele A. M. Boon
- Department of Epidemiology and public health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium
| | - Herman Van Oyen
- Department of Epidemiology and public health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium
- Department of Public Health and Primary Care, Faculty of Medicine, Ghent University, De Pintelaan 185, 9000 Ghent, Belgium
| | - Annie Robert
- Department of Epidemiology and Biostatistics, Institut de recherche expérimentale et clinique, Faculty of Public Health, Université catholique de Louvain, Clos Chapelle-aux-champs 30, 1200 Woluwe-Saint-Lambert, Belgium
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12
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Nelson KN, Shah NS, Mathema B, Ismail N, Brust JCM, Brown TS, Auld SC, Omar SV, Morris N, Campbell A, Allana S, Moodley P, Mlisana K, Gandhi NR. Spatial Patterns of Extensively Drug-Resistant Tuberculosis Transmission in KwaZulu-Natal, South Africa. J Infect Dis 2018; 218:1964-1973. [PMID: 29961879 PMCID: PMC6217717 DOI: 10.1093/infdis/jiy394] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Accepted: 06/26/2018] [Indexed: 12/29/2022] Open
Abstract
Background Transmission is driving the global drug-resistant tuberculosis (TB) epidemic; nearly three-quarters of drug-resistant TB cases are attributable to transmission. Geographic patterns of disease incidence, combined with information on probable transmission links, can define the spatial scale of transmission and generate hypotheses about factors driving transmission patterns. Methods We combined whole-genome sequencing data with home Global Positioning System coordinates from 344 participants with extensively drug-resistant (XDR) TB in KwaZulu-Natal, South Africa, diagnosed from 2011 to 2014. We aimed to determine if genomically linked (difference of ≤5 single-nucleotide polymorphisms) cases lived close to one another, which would suggest a role for local community settings in transmission. Results One hundred eighty-two study participants were genomically linked, comprising 1084 case-pairs. The median distance between case-pairs' homes was 108 km (interquartile range, 64-162 km). Between-district, as compared to within-district, links accounted for the majority (912/1084 [84%]) of genomic links. Half (526 [49%]) of genomic links involved a case from Durban, the urban center of KwaZulu-Natal. Conclusions The high proportions of between-district links with Durban provide insight into possible drivers of province-wide XDR-TB transmission, including urban-rural migration. Further research should focus on characterizing the contribution of these drivers to overall XDR-TB transmission in KwaZulu-Natal to inform design of targeted strategies to curb the drug-resistant TB epidemic.
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Affiliation(s)
- Kristin N Nelson
- Rollins School of Public Health, Emory University, Atlanta, Georgia
| | - N Sarita Shah
- Rollins School of Public Health, Emory University, Atlanta, Georgia
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Barun Mathema
- Mailman School of Public Health, Columbia University, New York, New York
| | - Nazir Ismail
- National Institute for Communicable Diseases, Johannesburg
- University of Pretoria, South Africa
| | - James C M Brust
- Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, New York
| | - Tyler S Brown
- Infectious Diseases Division, Massachusetts General Hospital, Boston
| | - Sara C Auld
- Rollins School of Public Health, Emory University, Atlanta, Georgia
- Emory University School of Medicine, Atlanta, Georgia
| | | | - Natashia Morris
- Environment and Health Research Unit, South African Medical Research Council, Johannesburg
| | - Angie Campbell
- Rollins School of Public Health, Emory University, Atlanta, Georgia
| | - Salim Allana
- Rollins School of Public Health, Emory University, Atlanta, Georgia
| | - Pravi Moodley
- National Health Laboratory Service, University of KwaZulu-Natal, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Koleka Mlisana
- National Health Laboratory Service, University of KwaZulu-Natal, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Neel R Gandhi
- Rollins School of Public Health, Emory University, Atlanta, Georgia
- Emory University School of Medicine, Atlanta, Georgia
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13
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Brynildsrud OB, Pepperell CS, Suffys P, Grandjean L, Monteserin J, Debech N, Bohlin J, Alfsnes K, Pettersson JOH, Kirkeleite I, Fandinho F, da Silva MA, Perdigao J, Portugal I, Viveiros M, Clark T, Caws M, Dunstan S, Thai PVK, Lopez B, Ritacco V, Kitchen A, Brown TS, van Soolingen D, O’Neill MB, Holt KE, Feil EJ, Mathema B, Balloux F, Eldholm V. Global expansion of Mycobacterium tuberculosis lineage 4 shaped by colonial migration and local adaptation. SCIENCE ADVANCES 2018; 4:eaat5869. [PMID: 30345355 PMCID: PMC6192687 DOI: 10.1126/sciadv.aat5869] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 09/11/2018] [Indexed: 05/23/2023]
Abstract
On the basis of population genomic and phylogeographic analyses of 1669 Mycobacterium tuberculosis lineage 4 (L4) genomes, we find that dispersal of L4 has been completely dominated by historical migrations out of Europe. We demonstrate an intimate temporal relationship between European colonial expansion into Africa and the Americas and the spread of L4 tuberculosis (TB). Markedly, in the age of antibiotics, mutations conferring antimicrobial resistance overwhelmingly emerged locally (at the level of nations), with minimal cross-border transmission of resistance. The latter finding was found to reflect the relatively recent emergence of these mutations, as a similar degree of local restriction was observed for susceptible variants emerging on comparable time scales. The restricted international transmission of drug-resistant TB suggests that containment efforts at the level of individual countries could be successful.
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Affiliation(s)
- Ola B. Brynildsrud
- Division of Infectious Diseases and Environmental Health, Norwegian Institute of Public Health, Lovisenberggata 8, 0456 Oslo, Norway
| | - Caitlin S. Pepperell
- Division of Infectious Disease, Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53726, USA
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Philip Suffys
- Laboratory of Molecular Biology Applied to Mycobacteria, Oswaldo Cruz Institute, Avenida Brasil 4365, C.P. 926, Manguinhos 21040-360, Rio de Janeiro, Brazil
| | - Louis Grandjean
- Department of Paediatric Infectious Diseases, Imperial College London, W2 1NY, London, UK
| | - Johana Monteserin
- Instituto Nacional de Enfermedades Infecciosas, ANLIS Carlos Malbran, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Buenos Aires, Argentina
| | - Nadia Debech
- Division of Infectious Diseases and Environmental Health, Norwegian Institute of Public Health, Lovisenberggata 8, 0456 Oslo, Norway
| | - Jon Bohlin
- Division of Infectious Diseases and Environmental Health, Norwegian Institute of Public Health, Lovisenberggata 8, 0456 Oslo, Norway
| | - Kristian Alfsnes
- Division of Infectious Diseases and Environmental Health, Norwegian Institute of Public Health, Lovisenberggata 8, 0456 Oslo, Norway
| | - John O.-H. Pettersson
- Division of Infectious Diseases and Environmental Health, Norwegian Institute of Public Health, Lovisenberggata 8, 0456 Oslo, Norway
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, Uppsala University, Uppsala, Sweden
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales 2006, Australia
- Public Health Agency of Sweden, Nobels vg 18, SE-171 82 Solna, Sweden
| | - Ingerid Kirkeleite
- Division of Infectious Diseases and Environmental Health, Norwegian Institute of Public Health, Lovisenberggata 8, 0456 Oslo, Norway
| | - Fatima Fandinho
- Laboratorio de Bacteriologia da Tuberculose, Centro de Referłncia Professor Helio Fraga-Jacarepagu, Estrada de Curicica 2000, Brazil
| | - Marcia Aparecida da Silva
- Laboratorio de Bacteriologia da Tuberculose, Centro de Referłncia Professor Helio Fraga-Jacarepagu, Estrada de Curicica 2000, Brazil
| | - Joao Perdigao
- Instituto de Investigao do Medicamento, Faculdade de Farmcia, Universidade de Lisboa, Lisboa, Portugal
| | - Isabel Portugal
- Instituto de Investigao do Medicamento, Faculdade de Farmcia, Universidade de Lisboa, Lisboa, Portugal
| | - Miguel Viveiros
- Unidade de Microbiologia Medica, Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Taane Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Maxine Caws
- Liverpool School of Tropical medicine, Department of Clinical Sciences, Liverpool, UK
- Birat-Nepal Medical Trust, Lazimpat, Kathmandu, Nepal
| | - Sarah Dunstan
- Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | | | - Beatriz Lopez
- Instituto Nacional de Enfermedades Infecciosas, ANLIS Carlos Malbran, Buenos Aires, Argentina
| | - Viviana Ritacco
- Instituto Nacional de Enfermedades Infecciosas, ANLIS Carlos Malbran, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Buenos Aires, Argentina
| | - Andrew Kitchen
- Department of Anthropology, University of Iowa, Iowa City, IA 52242, USA
| | - Tyler S. Brown
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Dick van Soolingen
- Center for Infectious Disease Research, Diagnostics and Perinatal Screening, National Institute for Public Health and the Environment, P.O. Box 1, 3720 BA Bilthoven, Netherlands
| | - Mary B. O’Neill
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53726, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Kathryn E. Holt
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
- Department of Biochemistry and Molecular Biology and Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Edward J. Feil
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
| | - Barun Mathema
- Mailman School of Public Health, Columbia University, 722 West 168th Street, New York, NY 10032, USA
| | - Francois Balloux
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Vegard Eldholm
- Division of Infectious Diseases and Environmental Health, Norwegian Institute of Public Health, Lovisenberggata 8, 0456 Oslo, Norway
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