Journal Article

Machine learning to predict the source of campylobacteriosis using whole genome data

Bayliss, Sion, Arning, Nicolas, Clifton, David A., Wilson, Daniel J., Sheppard, Samuel K.

2021

Overview

Campylobacteriosis is among the world’s most common foodborne illnesses, caused predominantly by the bacterium Campylobacter jejuni . Effective interventions require determination of the infection source which is challenging as transmission occurs via multiple sources such as contaminated meat, poultry, and drinking water. Strain variation has allowed source tracking based upon allelic variation in multi-locus sequence typing (MLST) genes allowing isolates from infected individuals to be attributed to specific animal or environmental reservoirs. However, the accuracy of probabilistic attribution models has been limited by the ability to differentiate isolates based upon just 7 MLST genes. Here, we broaden the input data spectrum to include core genome MLST (cgMLST) and whole genome sequences (WGS), and implement multiple machine learning algorithms, allowing more accurate source attribution. We increase attribution accuracy from 64% using the standard iSource population genetic approach to 71% for MLST, 85% for cgMLST and 78% for kmerized WGS data using the classifier we named aiSource. To gain insight beyond the source model prediction, we use Bayesian inference to analyse the relative affinity of C . jejuni strains to infect humans and identified potential differences, in source-human transmission ability among clonally related isolates in the most common disease causing lineage (ST-21 clonal complex). Providing generalizable computationally efficient methods, based upon machine learning and population genetics, we provide a scalable approach to global disease surveillance that can continuously incorporate novel samples for source attribution and identify fine-scale variation in transmission potential.

• Publisher: Public Library of Science,Public Library of Science (PLoS)
• Subject: Algorithms / Animals / Bayes Theorem / Bayesian analysis / Biology and Life Sciences / Birds / Campylobacter / Campylobacter infections / Campylobacter Infections - microbiology / Campylobacter jejuni - genetics / Campylobacteriosis / Chickens - microbiology / Computer and Information Sciences / Datasets / Deep learning / Drinking water / Feature selection / Food contamination / Foodborne diseases / Gastroenteritis / Gastroenteritis - microbiology / Genes / Genetic aspects / Genetic research / Genetics, Population - methods / Genomes / Genotype & phenotype / Humans / Infections / Learning algorithms / Machine Learning / Mathematical models / Meat / Meat - microbiology / Multilocus sequence typing / Multilocus Sequence Typing - methods / Physical Sciences / Population / Population genetics / Poultry / Research and Analysis Methods / Sheep / Technology application / Whole Genome Sequencing - methods