Genomics for public health and international surveillance of antimicrobial resistance

Baker, Kate S; Jauneikaite, Elita; Hopkins, Katie L; Lo, Stephanie W; Sánchez-Busó, Leonor; Getino, Maria; Howden, Benjamin P; Holt, Kathryn E; Musila, Lillian A; Hendriksen, Rene S; Amoako, Daniel G; Aanensen, David M; Okeke, Iruka N; Egyir, Beverly; Nunn, Jamie G; Midega, Janet T; Feasey, Nicholas A; Peacock, Sharon J

doi:10.1016/s2666-5247(23)00283-5

Cited by 28 publications

(6 citation statements)

References 88 publications

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“…Generating high-quality whole-genome de novo assemblies for bacterial pathogens has become an important tool supporting diagnostic, infection prevention control and public health initiatives, improving our understanding of antimicrobial resistance and pathogen epidemiology [ 1 ]. The introduction of longer sequencing reads from PacBio and Oxford Nanopore Technologies (ONT) has enabled the reconstruction of previously difficult-to-assemble genomes.…”

Section: Introductionmentioning

confidence: 99%

Evaluation of the accuracy of bacterial genome reconstruction with Oxford Nanopore R10.4.1 long-read-only sequencing

Sanderson,

Hopkins,

Colpus

et al. 2024

Microbial Genomics

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Whole-genome reconstruction of bacterial pathogens has become an important tool for tracking transmission and antimicrobial resistance gene spread, but highly accurate and complete assemblies have largely only historically been achievable using hybrid long- and short-read sequencing. We previously found the Oxford Nanopore Technologies (ONT) R10.4/kit12 flowcell/chemistry produced improved assemblies over the R9.4.1/kit10 combination, however long-read only assemblies contained more errors compared to Illumina-ONT hybrid assemblies. ONT have since released an R10.4.1/kit14 flowcell/chemistry upgrade and recommended the use of Bovine Serum Albumin (BSA) during library preparation, both of which reportedly increase accuracy and yield. They have also released updated basecallers trained using native bacterial DNA containing methylation sites intended to fix systematic basecalling errors, including common adenosine (A) to guanine (G) and cytosine (C) to thymine (T) substitutions. To evaluate these improvements, we successfully sequenced four bacterial reference strains, namely Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa and Staphylococcus aureus, and nine genetically diverse E. coli bloodstream infection-associated isolates from different phylogroups and sequence types, both with and without BSA. These sequences were de novo assembled and compared against Illumina-corrected reference genomes. In this small evaluation of 13 isolates we found that nanopore long-read-only R10.4.1/kit 14 assemblies with updated basecallers trained using bacterial methylated DNA produce accurate assemblies with ≥40×depth, sufficient to be cost-effective compared with hybrid ONT/Illumina sequencing in our setting.

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Section: Introductionmentioning

confidence: 99%

Evaluation of the accuracy of bacterial genome reconstruction with Oxford Nanopore R10.4.1 long-read-only sequencing

Sanderson,

Hopkins,

Colpus

et al. 2024

Microbial Genomics

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“…The growing antimicrobial resistance (AMR) mainly because of indiscriminate use of modern antibiotics is one of the topmost public health threats globally [1,2] . Reports suggested that due to AMR about 1.27 million deaths occurred worldwide in 2019 and because of the spread of drug‐resistant microbes, the prevention and treatment of some common infections has been hampered [3‐5] . Due to AMR development, the medications become ineffective by diminishing their efficacies towards these bacteria, fungi and other microbes [6‐7] .…”

Section: Introductionmentioning

confidence: 99%

“…[1,2] Reports suggested that due to AMR about 1.27 million deaths occurred worldwide in 2019 and because of the spread of drug-resistant microbes, the prevention and treatment of some common infections has been hampered. [3][4][5] Due to AMR development, the medications become ineffective by diminishing their efficacies towards these bacteria, fungi and other microbes. [6][7] Therefore, medicinal chemists are continuously working for the development of new antimicrobial agents with distinctive mode of action.…”

Section: Introductionmentioning

confidence: 99%

Synthesis, Characterization, Antimicrobial and In Silico Studies of Isatin Schiff Base Linked 1,2,3‐Triazole Hybrids

Kumar,

Bhukal,

Raman

et al. 2024

Chemistry & Biodiversity

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A new series of isatin‐Schiff base linked 1,2,3‐triazole hybrids has been synthesized using CuAAC approach from (E)‐3‐(phenylimino)‐1‐(prop‐2‐yn‐1‐yl)indolin‐2‐one derivatives in high yield (73‐91 %). These synthesized derivatives were characterized using FT‐IR, 1H NMR, 13C NMR, 2D‐NMR and HRMS spectral techniques. The in vitro antimicrobial activity assay proposed that most of the tested hybrids exhibited promising activity. Compound 5j displayed good significant antibacterial efficacy against P. aeruginosa and B. subtilis with MIC value of 0.0062 µmol/mL. While, 5j showed better antifungal potency against A. niger with MIC value of 0.0123 µmol/mL. The docking studies of most promising compounds were also performed with the well‐known antibacterial and antifungal targets i.e. 1KZ1, 5TZ1. Molecular modelling investigations demonstrated that hybrids 5h and 5l exhibited good interactions with 1KZN and 5TZ1, with binding energies of ‐9.6 and ‐11.0 kcal/mol, respectively. Further, molecular dynamics studies of the compounds showing promising binding interactions were also carried out to study the stability of complexes of these hybrids with both the targets.

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“…Specifically, the intersection of AI and genomics impacts different public health activities, including the identification of disease risk factors, conducting disease surveillance, modelling, and forecasting, and developing data-driven public health policy [11]. Other prominent applications of AI and genomics in the public health area include detecting and understanding emerging public health threats (including healthcareassociated infections and foodborne illness), identifying novel virus variants, and enhancing the resolution of epidemiological investigation and surveillance for bacterial antimicrobial resistance [11,12]. Furthermore, AI can drive applications related to health promotion, behavioral changes, and the adoption of healthier lifestyles [2,13].…”

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confidence: 99%

“…Exponential data growth demands corresponding improvements in data interpretation and democratization. In particular, developing and agreeing on open-access databases and policies that promote data sharing and equitable data governance frameworks can ensure that essential data is available to researchers, health professionals, and even the general public [12]. Certainly, ethical principles and the protection of fundamental rights require that proportional conditions and safeguards be implemented, including those related to privacy and data protection [22].…”

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confidence: 99%

Artificial Intelligence and Precision Public Health: A Balancing Act of Scientific Accuracy, Social Responsibility, and Community Engagement

Cordeiro

2024

Port J Public Health

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In Kazuo Ishiguro's novel "Klara and Sun" [1], Mr. Capaldi, a techno-optimist scientist, is hired by Josie's mother to create a robotic duplicate of her ill daughter, capable of harboring artificial consciousness and perpetuate her existence when she eventually dies. After reflecting on the complexities of human-AI (artificial intelligence) relationships, Mr. Capaldi talks to Klara, Josie's artificial friend, and observes: "They accept that your decisions, your recommendations, are sound and dependable, almost always correct. But they do not like not knowing how you arrive at them. That's where it comes from, this backlash, this prejudice."The subject of the human relationship with technology is anything but new, and the intersection between art, science, technology, and ethics is ancient, vast, and intricate. In fact, various "what ifs" or imaginative scenarios have found their way from paintings, sculptures, novels, and movies into real life through scientific and technological progress. Public health is no stranger to this phenomenon. More recently, the discussion surrounding AI and genomics (especially in conjunction with other data modalities) within public health constitutes a good example of the delicate balance between scientific advancement based on well-guided op-

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Genomics for public health and international surveillance of antimicrobial resistance

Cited by 28 publications

References 88 publications

Evaluation of the accuracy of bacterial genome reconstruction with Oxford Nanopore R10.4.1 long-read-only sequencing

Evaluation of the accuracy of bacterial genome reconstruction with Oxford Nanopore R10.4.1 long-read-only sequencing

Synthesis, Characterization, Antimicrobial and In Silico Studies of Isatin Schiff Base Linked 1,2,3‐Triazole Hybrids

Artificial Intelligence and Precision Public Health: A Balancing Act of Scientific Accuracy, Social Responsibility, and Community Engagement

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