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Bornstein K, Gryan G, Chang ES, Marchler-Bauer A, Schneider VA. The NIH Comparative Genomics Resource: addressing the promises and challenges of comparative genomics on human health. BMC Genomics 2023; 24:575. [PMID: 37759191 PMCID: PMC10523801 DOI: 10.1186/s12864-023-09643-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 08/31/2023] [Indexed: 09/29/2023] Open
Abstract
Comparative genomics is the comparison of genetic information within and across organisms to understand the evolution, structure, and function of genes, proteins, and non-coding regions (Sivashankari and Shanmughavel, Bioinformation 1:376-8, 2007). Advances in sequencing technology and assembly algorithms have resulted in the ability to sequence large genomes and provided a wealth of data that are being used in comparative genomic analyses. Comparative analysis can be leveraged to systematically explore and evaluate the biological relationships and evolution between species, aid in understanding the structure and function of genes, and gain a better understanding of disease and potential drug targets. As our knowledge of genetics expands, comparative genomics can help identify emerging model organisms among a broader span of the tree of life, positively impacting human health. This impact includes, but is not limited to, zoonotic disease research, therapeutics development, microbiome research, xenotransplantation, oncology, and toxicology. Despite advancements in comparative genomics, new challenges have arisen around the quantity, quality assurance, annotation, and interoperability of genomic data and metadata. New tools and approaches are required to meet these challenges and fulfill the needs of researchers. This paper focuses on how the National Institutes of Health (NIH) Comparative Genomics Resource (CGR) can address both the opportunities for comparative genomics to further impact human health and confront an increasingly complex set of challenges facing researchers.
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Affiliation(s)
| | - Gary Gryan
- The MITRE Corporation, 7525 Colshire Dr, McLean, VA, USA
| | - E Sally Chang
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Aron Marchler-Bauer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Valerie A Schneider
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.
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Bornstein K, Hungerford L, Hartley D, Sorkin JD, Tapia MD, Sow SO, Onwuchekwa U, Simon R, Tennant SM, Levine MM. Modeling the Potential for Vaccination to Diminish the Burden of Invasive Non-typhoidal Salmonella Disease in Young Children in Mali, West Africa. PLoS Negl Trop Dis 2017; 11:e0005283. [PMID: 28182657 PMCID: PMC5300129 DOI: 10.1371/journal.pntd.0005283] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 12/22/2016] [Indexed: 11/30/2022] Open
Abstract
Background In sub-Saharan Africa, systematic surveillance of young children with suspected invasive bacterial disease (e.g., septicemia, meningitis) has revealed non-typhoidal Salmonella (NTS) to be a major pathogen exhibiting high case fatality (~20%). Where infant vaccination against Haemophilus influenzae type b (Hib) and Streptococcus pneumoniae has been introduced to prevent invasive disease caused by these pathogens, as in Bamako, Mali, their burden has decreased markedly. In parallel, NTS has become the predominant invasive bacterial pathogen in children aged <5 years. While NTS is believed to be acquired orally via contaminated food/water, epidemiologic studies have failed to identify the reservoir of infection or vehicles of transmission. This has precluded targeting food chain interventions to diminish disease transmission but conversely has fostered the development of vaccines to prevent invasive NTS (iNTS) disease. We developed a mathematical model to estimate the potential impact of NTS vaccination programs in Bamako. Methodology/Principal Findings A Markov chain transmission model was developed utilizing age-specific Bamako demographic data and hospital surveillance data for iNTS disease in children aged <5 years and assuming vaccine coverage and efficacy similar to the existing, successfully implemented, Hib vaccine. Annual iNTS hospitalizations and deaths in children <5 years, with and without a Salmonella Enteritidis/Salmonella Typhimurium vaccine, were the model’s outcomes of interest. Per the model, high coverage/high efficacy iNTS vaccination programs would drastically diminish iNTS disease except among infants age <8 weeks. Conclusions/Significance The public health impact of NTS vaccination shifts as disease burden, vaccine coverage, and serovar distribution vary. Our model shows that implementing an iNTS vaccine through an analogous strategy to the Hib vaccination program in Bamako would markedly reduce cases and deaths due to iNTS among the pediatric population. The model can be adjusted for use elsewhere in Africa where NTS epidemiologic patterns, serovar prevalence, and immunization schedules differ from Bamako. A surveillance program at Gabriel Touré Hospital in Mali observed a high burden of invasive disease caused by non-typhoidal Salmonella (iNTS). This surveillance program was originally instituted to measure the amount of invasive disease (e.g., septicemia, meningitis) caused by two bacteria that invade the respiratory tract: Haemophilus influenzae type b (Hib) and Streptococcus pneumoniae (pneumococcus). While documenting the burden of these pathogens, the surveillance program also found that serotypes of iNTS, mainly Salmonella Typhimurium and Salmonella Enteritidis, were common causes of severe invasive disease. As the number of cases of Hib and pneumococcus markedly decreased following the introduction of relevant vaccines, the relative threat of iNTS increased. Little is known about the reservoir of iNTS, whether it resides in humans, animals, or the environment, or how it is spread to susceptible children. Without this knowledge, it is not possible to employ certain disease control methods useful in interrupting the transmission of other pathogens. Therefore, vaccination remains the one promising control strategy for this disease. Our research modeled the potential effects of introducing an iNTS vaccine. The findings are of great importance to Mali and other developing countries where young children are at a high risk of developing iNTS disease.
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Affiliation(s)
- Kristin Bornstein
- Center for Vaccine Development and Institute for Global Health, University of Maryland School of Medicine, Baltimore, MD, United States of America
- Department of Epidemiology & Public Health, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Laura Hungerford
- Department of Epidemiology & Public Health, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - David Hartley
- James M. Anderson Center for Health Systems Excellence, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States of America
| | - John D. Sorkin
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States of America
- Baltimore VA Medical Center GRECC (Geriatric Research, Education, and Clinical Center), Baltimore Maryland
| | - Milagritos D. Tapia
- Center for Vaccine Development and Institute for Global Health, University of Maryland School of Medicine, Baltimore, MD, United States of America
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Samba O. Sow
- Centre pour le Développement des Vaccins, Mali (CVD-Mali), Bamako, Mali, Africa
| | - Uma Onwuchekwa
- Centre pour le Développement des Vaccins, Mali (CVD-Mali), Bamako, Mali, Africa
| | - Raphael Simon
- Center for Vaccine Development and Institute for Global Health, University of Maryland School of Medicine, Baltimore, MD, United States of America
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Sharon M. Tennant
- Center for Vaccine Development and Institute for Global Health, University of Maryland School of Medicine, Baltimore, MD, United States of America
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Myron M. Levine
- Center for Vaccine Development and Institute for Global Health, University of Maryland School of Medicine, Baltimore, MD, United States of America
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States of America
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, MD, United States of America
- * E-mail:
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Tapia MD, Tennant SM, Bornstein K, Onwuchekwa U, Tamboura B, Maiga A, Sylla MB, Sissoko S, Kourouma N, Toure A, Malle D, Livio S, Sow SO, Levine MM. Invasive Nontyphoidal Salmonella Infections Among Children in Mali, 2002-2014: Microbiological and Epidemiologic Features Guide Vaccine Development. Clin Infect Dis 2016; 61 Suppl 4:S332-8. [PMID: 26449949 DOI: 10.1093/cid/civ729] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND In 2002, following establishment of a clinical microbiology laboratory in the government hospital that admits children with severe illnesses in Bamako, Mali, surveillance to identify pathogens causing invasive bacterial infections (septicemia, bacteremia, meningitis, etc) was initiated. METHODS Parents/guardians of children aged <16 years admitted to l'Hôpital Gabriel Touré with high fever or clinical syndromes compatible with focal invasive bacterial disease were asked for consent to culture their child's blood/body fluid. Standard bacteriologic techniques speciated isolates; Salmonella serovars were determined. RESULTS From July 2002 through June 2014, 687 nontyphoidal Salmonella (NTS) isolates were obtained from 667 children; 667 yielded a single serovar and 20 grew 2 Salmonella serovars, 1 being NTS. Four serovars accounted for 87% of the 687 NTS isolates, including Salmonella Enteritidis (n = 244 [35.5%]), Salmonella Typhimurium (n = 221 [32.2%]), I:4,[5],12:i:- (n = 42 [6.1%]), and Salmonella Dublin (n = 89 [13.0%]). Of 553 patients with invasive NTS from whom 1 of the 4 predominant serovars was isolated in pure culture, 448 (81.0%) were aged <5 years and case fatality was 20.3%; Salmonella Enteritidis case fatality (27.8%) was higher than for other serovars (P = .0009). NTS disease showed a seasonal peak following the rainy season and into the cool, dry season. Since 2010, Salmonella Enteritidis cases have risen and Salmonella Typhimurium fallen. CONCLUSIONS NTS has become the predominant invasive pathogen as Haemophilus influenzae type b and pneumococcal vaccine use in Mali has diminished invasive disease due to those pathogens. The age distribution and limited serovars involved make control of NTS disease by vaccines epidemiologically feasible, if products under development prove safe and efficacious.
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Affiliation(s)
| | | | - Kristin Bornstein
- Center for Vaccine Development Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore
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