Precision epidemiology for infectious disease control

Ladner, Jason T.; Grubaugh, Nathan D.; Pybus, Oliver G.; Andersen, Kristian G.

doi:10.1038/s41591-019-0345-2

Cited by 109 publications

(92 citation statements)

References 86 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…With further automation (e.g. in library preparation) this workflow is suitable for high-throughput analysis and amenable for wider surveillance, in line with the vision to achieve precision epidemiology for infectious diseases 63 . Future improvements in nanopore sequencing throughput, the ability to work with lower DNA input, and use in remote settings, could help accelerate time-to-answer by reducing the culturing period, or eliminating it altogether.…”

Section: Discussionmentioning

confidence: 85%

Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment

Chng

Bertrand

et al. 2019

Preprint

View full text Add to dashboard Cite

There is growing attention surrounding hospital acquired infections (HAIs) due to high associated healthcare costs, compounded by the scourge of widespread multi-antibiotic resistance. Although hospital environment disinfection is well acknowledged to be key for infection control, an understanding of colonization patterns and resistome profiles of environment-dwelling microbes is currently lacking. We report the first extensive genomic characterization of microbiomes (355), common HAI-associated microbes (891) and transmissible drug resistance cassettes (1435) in a tertiary hospital environment based on a 2-timepoint sampling of 179 sites from 45 beds. Deep shotgun metagenomic sequencing unveiled two distinct ecological niches of microbes and antibiotic resistance genes characterized by biofilm-forming and human microbiome influenced environments that display corresponding patterns of divergence over space and time. To study common nosocomial pathogens that were typically present at low abundances, a combination of culture enrichment and long-read nanopore sequencing was used to obtain thousands of high contiguity genomes (2347) and closed plasmids (5910), a significant fraction of which (>58%) are not represented in current sequence databases. These high-quality assemblies and metadata enabled a rich characterization of resistance gene combinations, plasmid architectures, and the dynamic nature of hospital environment resistomes and their reservoirs. Phylogenetic analysis identified multidrug resistant clonal strains as being more widely disseminated and stably colonizing across hospital sites. Further genomic comparisons with clinical isolates across multiple species supports the hypothesis that multidrug resistant strains can persist in the hospital environment for extended periods (>8 years) to opportunistically infect patients. These findings highlight the importance of characterizing antibiotic resistance reservoirs in the hospital environment and establishes the feasibility of systematic genomic surveys to help target resources more efficiently for preventing HAIs.

show abstract

Section: Discussionmentioning

confidence: 85%

Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment

Chng

Bertrand

et al. 2019

Preprint

View full text Add to dashboard Cite

show abstract

“…Viral genomics coupled with modern surveillance systems is transforming the way we respond to emerging infectious diseases (Gardy and Loman 2018, Ladner, Grubaugh et al 2019). Realtime genomic epidemiology data has proven to be useful to reconstruct outbreak dynamics: from virus identification to understanding the factors contributing towards global spread (Grubaugh, Ladner et al 2019). Here, we sequenced SARS-CoV-2 genomes from clinical cases sampled since the beginning of the syndromic surveillance in France.…”

Section: Introductionmentioning

confidence: 99%

Introductions and early spread of SARS-CoV-2 in France

Gámbaro

Baidaliuk

Behillil

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…Using a broad range of different molecular tests enabled the identi cation of P. falciparum as the causal pathogen and removed any suspicion of other possible etiologies, given the unusual symptoms presented by patients. Previous studies have shown that using molecular approaches during outbreaks when patients present with either unusual or non-speci c symptoms are crucial in rapidly detecting a pathogen [10]. Similar approaches were used in patients with fever and no speci c symptoms to diagnose malaria with RDT and arbovirus using RT-PCR and ELISA [12].…”

Section: Discussionmentioning

confidence: 99%

“…Different studies have shown the important use of molecular approaches for the detection of malaria and other pathogens, epidemiologic disease comprehension especially during outbreak / hotspot cluster transmission [6] , [7], and evaluation of parasite reintroduction by human movement [8], [9]. Molecular tools can also help reveal the causative agent in the context of non-speci c symptoms including fever [10].…”

Section: Introductionmentioning

confidence: 99%

Genomic investigation of atypical malaria cases in Kanel, northern Senegal

Badiane

Siddle

et al. 2020

Preprint

View full text Add to dashboard Cite

BackgroundDiagnosis of malaria cases in regions where the malaria burden has decreased significantly and prevalence is very low becomes more challenging, in part because of reduced clinical presumption of malaria. The appearance of a cluster of malaria cases with atypical symptoms in Mbounguiel, a village in northern Senegal where malaria transmission is low, in September 2018 exemplifies this scenario. The collaboration between the national malaria control program (NMCP) at the Senegal ministry of health and the laboratory of parasitology mycology at Cheikh Anta Diop University worked together to evaluate this cluster of malaria cases using molecular and serology tools.ResultsNine of the fifteen patients were evaluated, and all nine samples were found to be positive for P. falciparum only. The 24 SNP molecular barcode showed the predominance of polygenomic infections, with identifiable strains being different from one another. All patients tested positive for the P. falciparum antigens. No other pathogenic infection was detected by either the serological panel or metagenomic sequencing. ConclusionsThis work undertaken locally within Senegal as a collaboration between the NMCP and a research malaria laboratory at University of Cheikh Anta Diop (UCAD) revealed that a cluster of malaria cases were caused by different strains of P. falciparum. The public health response in real time demonstrates the value of local molecular and genomics capacity in affected countries disease control and elimination.

show abstract

Precision epidemiology for infectious disease control

Cited by 109 publications

References 86 publications

Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment

Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment

Introductions and early spread of SARS-CoV-2 in France

Genomic investigation of atypical malaria cases in Kanel, northern Senegal

Contact Info

Product

Resources

About