Highly multiplexed targeted sequencing strategy for infectious disease surveillance

Author:

Hernández-Neuta Iván,Magoulopoulou Anastasia,Pineiro Flor,Lisby Jan Gorm,Gulberg Mats,Nilsson Mats

Abstract

Abstract Background Global efforts to characterize diseases of poverty are hampered by lack of affordable and comprehensive detection platforms, resulting in suboptimal allocation of health care resources and inefficient disease control. Next generation sequencing (NGS) can provide accurate data and high throughput. However, shotgun and metagenome-based NGS approaches are limited by low concentrations of microbial DNA in clinical samples, requirements for tailored sample and library preparations plus extensive bioinformatics analysis. Here, we adapted molecular inversion probes (MIPs) as a cost-effective target enrichment approach to characterize microbial infections from blood samples using short-read sequencing. We designed a probe panel targeting 2 bacterial genera, 21 bacterial and 6 fungi species and 7 antimicrobial resistance markers (AMRs). Results Our approach proved to be highly specific to detect down to 1 in a 1000 pathogen DNA targets contained in host DNA. Additionally, we were able to accurately survey pathogens and AMRs in 20 out of 24 samples previously profiled with routine blood culture for sepsis. Conclusions Overall, our targeted assay identifies microbial pathogens and AMRs with high specificity at high throughput, without the need for extensive sample preparation or bioinformatics analysis, simplifying its application for characterization and surveillance of infectious diseases in medium- to low- resource settings.

Funder

Stockholm University

Publisher

Springer Science and Business Media LLC

Subject

Biotechnology

Reference34 articles.

1. Sharrow D, Hug L, You D, Alkema L, Black R, Cousens S, et al. Global, regional, and national trends in under-5 mortality between 1990 and 2019 with scenario-based projections until 2030: a systematic analysis by the UN Inter-agency Group for Child Mortality Estimation. Lancet Glob Health. 2022;10:e195–206.

2. Saugstad OD. Reducing global neonatal mortality is possible. Neonatology. 2011;99:250–7.

3. Lozano R, Freeman MK, James SL, Campbell B, Lopez AD, Flaxman AD, et al. Performance of InterVA for assigning causes of death to verbal autopsies: multisite validation study using clinical diagnostic gold standards. Popul Health Metr. 2011;9:50.

4. Nsubuga P, White ME, Thacker SB, Anderson MA, Blount SB, Broome CV et al. Public Health Surveillance: A Tool for Targeting and Monitoring Interventions. In: Jamison DT, Breman JG, Measham AR, Alleyne G, Claeson M, Evans DB, editors. Disease Control Priorities in Developing Countries. 2nd edition. Washington (DC): World Bank; 2006.

5. Maljkovic Berry I, Melendrez MC, Bishop-Lilly KA, Rutvisuttinunt W, Pollett S, Talundzic E, et al. Next generation sequencing and Bioinformatics Methodologies for Infectious Disease Research and Public Health: approaches, applications, and considerations for development of Laboratory Capacity. J Infect Dis. 2020;221 Supplement3:292–307.

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