Patchy promiscuity: machine learning applied to predict the host specificity of Salmonella enterica and Escherichia coli

TY - JOUR

T1 - Patchy promiscuity

T2 - machine learning applied to predict the host specificity of Salmonella enterica and Escherichia coli

AU - Lupolova, Nadejda

AU - Dallman, Tim J.

AU - Holden, Nicola J.

AU - Gally, David L.

N1 - N. L. received a PhD scholarship from the college of Medicine and Veterinary Medicine, University of Edinburgh. D. L. G./N. L. are supported by a Roslin Institute strategic programme funded by the BBSRC (BB/P013740/1).

PY - 2017/10/1

Y1 - 2017/10/1

N2 - Salmonella enterica and Escherichia coli are bacterial species that colonize different animal hosts with sub-types that can cause life-threatening infections in humans. Source attribution of zoonoses is an important goal for infection control as is identification of isolates in reservoir hosts that represent a threat to human health. In this study, host specificity and zoonotic potential were predicted using machine learning in which Support Vector Machine (SVM) classifiers were built based on predicted proteins from whole genome sequences. Analysis of over 1000 S.enterica genomes allowed the correct prediction (67 -90 % accuracy) of the source host for S. Typhimurium isolates and the same classifier could then differentiate the source host for alternative serovars such as S. Dublin. A key finding from both phylogeny and SVM methods was that the majority of isolates were assigned to host-specific sub-clusters and had high host-specific SVM scores. Moreover, only a minor subset of isolates had high probability scores for multiple hosts, indicating generalists with genetic content that may facilitate transition between hosts. The same approach correctly identified human versus bovine E. coli isolates (83 % accuracy) and the potential of the classifier to predict a zoonotic threat was demonstrated using E. coli O157. This research indicates marked host restriction for both S. enterica and E. coli, with only limited isolate subsets exhibiting host promiscuity by gene content. Machine learning can be successfully applied to interrogate source attribution of bacterial isolates and has the capacity to predict zoonotic potential.

AB - Salmonella enterica and Escherichia coli are bacterial species that colonize different animal hosts with sub-types that can cause life-threatening infections in humans. Source attribution of zoonoses is an important goal for infection control as is identification of isolates in reservoir hosts that represent a threat to human health. In this study, host specificity and zoonotic potential were predicted using machine learning in which Support Vector Machine (SVM) classifiers were built based on predicted proteins from whole genome sequences. Analysis of over 1000 S.enterica genomes allowed the correct prediction (67 -90 % accuracy) of the source host for S. Typhimurium isolates and the same classifier could then differentiate the source host for alternative serovars such as S. Dublin. A key finding from both phylogeny and SVM methods was that the majority of isolates were assigned to host-specific sub-clusters and had high host-specific SVM scores. Moreover, only a minor subset of isolates had high probability scores for multiple hosts, indicating generalists with genetic content that may facilitate transition between hosts. The same approach correctly identified human versus bovine E. coli isolates (83 % accuracy) and the potential of the classifier to predict a zoonotic threat was demonstrated using E. coli O157. This research indicates marked host restriction for both S. enterica and E. coli, with only limited isolate subsets exhibiting host promiscuity by gene content. Machine learning can be successfully applied to interrogate source attribution of bacterial isolates and has the capacity to predict zoonotic potential.

KW - Support Vector Machine

KW - Salmonella

KW - Zoonosis

KW - Host specificity

KW - Machine learning

KW - E. coli

U2 - 10.1099/mgen.0.000135

DO - 10.1099/mgen.0.000135

M3 - Article

C2 - 29177093

SN - 2057-5858

VL - 3

SP - 1

EP - 10

JO - Microbial Genomics

JF - Microbial Genomics

IS - 10

M1 - e000135

ER -