Transcript - Amazon Web Services

Non-travel associated Salmonella Typhimurium
ST 313 in the UK
Philip Ashton, Satheesh Nair, Chris Lane, Elizabeth de Pinna, Tansy Peters, Kathie Grant, Tim Dallman
Gastrointestainal Bacteria Reference Unit, Public Health England, 61 Colindale Avenue, NW9 5DZ
INTRODUCTION
PHE strains
Salmonella enterica serovar Typhimurium typically causes
self-limiting gastroenteritis. However, invasive non-typhoidal
Salmonella disease has been recently documented in many
sub-Saharan African countries, causing significant morbidity
and mortality. The majority of these invasive isolates belong
to one of two monomorphic lineages within a single MultiLocus-Sequence-Type, ST313. There is also evidence that
ST313 is more invasive than other closely related S.
Typhiumrium in both humans (clinical reports) and chickens
(in vivo experiments).
Here, we present an analysis of ST313 isolates received by
the PHE Salmonella Reference Service.
Patient
Year of
isolation
Phage type
Travel
Sample type
R-type
Patient 1
2012
RDNC
None reported
Faeces
SUL/NAL/CIP0.125
Patient 2
2012
RDNC
None reported
Faeces
Sensitive
Patient 3
2012
DT 56
Ghana
Blood isolate
AMP/CHL/STR/SUL/T
MP/NAL/CIP0.125
Patient 4
2012
DT 2
None reported
Faeces
Sensitive
Patient 5
2012
RDNC
None reported
Faeces
Sensitive
Patient 6
2012
DT 143
None reported
Faeces
Sensitive
Patient 7
2012
DT 75
None reported
Faeces
Sensitive
Blood/bronchial
isolates
AMP/CHL/SUL/STR/T
MP
Patient 8
2014
DT 56
None reported
- not on NHS
system
Patient 9
2014
DT 143
None reported
Faeces
Sensitive
Patient 10
2014
ND
None reported
Faeces
-
Patient 11
2014
DT 132
None reported
ND
Sensitive
Patient 12
2014
DT 132
None reported
Faeces
Sensitive
Patient 13
2014
DT 103
None reported
Faeces
Sensitive
Patient 14
2014
DT 15a
None reported
ND
Sensitive
Patient 15
2014
DT 56
Nigeria
Blood isolate
AMP/CHL/SUL/STR/T
MP
Patient 16
2014
DT 2
None reported
Blood isolate
Sensitive
Lineage
II
II
II
Table 1: S. Typhimurium ST313 isolates received by the PHE
Salmonella Reference Service.
RESULTS
 Within the wider phylogenetic context of S. Typhimurium, ST313 isolates submitted to
PHE formed a monophyletic group with the African ST313 isolates described previously.
 The most recent common ancestor (MRCA) of all ST313 dates to 1810 (95% highest
posterior distribution, 1742-1869). Descending from this ancestor are 6 lineages of
ST313, 5 of which had representatives referred to SRS between 2012 and 2014.
 ST313 isolated from Africa are
typically multi-drug resistant
(MDR), with resistance driven by
a plasmid borne MDR locus. This
entire set of loci was missing
from the non-lineage I/II isolates.
 The BTP-1 phage, which is
identical between lineage I and II,
is a site of signficicant variability
among non-lineage I/II isolates.
 All ST313 have a disrupted BTP1 insertion site, even those where
the BTP-1 phage is not present.
 This is the first description of a
BTP-1 like phage in ST19. The
ST19 strain in which it was
identified is the closest ST19
ancestor of ST313 among our
sequenced strains.
Figure 1: BEAST tree of ST313 from PHE and Okoro et al., 2012. Previously identified
lineages I & II are annotated. Node labels are posterior probabilities and node bars are
95% higher probability distributions of the node height.
Methods cont.
Discussion
Twenty three representative ST313 sequenced by Okoro
et al., were downloaded from the NCBI Short Read
Archive.
 The data we present here indicates that ST313 in the
UK is epidemiologically, clinically and genomically,
heterogenous
All sequencing data (PHE & Sanger Centre) was quality
trimmed using Trimmomatic, mapped against the LT2
reference genome (AE006468) using BWA mem. SNPs
were then called using GATK2 Core genome positions
that had a high quality SNP (>90% consensus, minimum
depth 10x, GQ >= 30, MQ >=30) in at least one strain
were extracted and RAxML v7.2.8 with the gamma model
of rate heterogeneity and 100 bootstraps carried out
To examine the evolutionary history of ST313, a number
of timed phylogenies were constructed using BEAST
v1.8.0, with varying clock rate models and tree priors.
The resulting models were compared and the one that
best fit the data was a log normal relaxed clock rate with
an exponential growth tree prior.
 There are the travel associated ST313 (3/16 patients),
which fall within the previously described lineage II.
These isolates are invasive (3/3 patients bacteraemic)
and are multi-drug resistant, encoding the same
antibiotic resistance determinants as previously
described lineage II isolates (Okoro et al. 2012).
 There are also non-travel associated ST313 (13/16, 5
of whom were subjected to extended questionnaires).
Of these 13 isolates, only one was associated with
invasive disease and one isolate was phenotypically
resistant to any of the antibiotics tested
 There are accessory genome differences between the
lineage I/II ST313 and the non-lineage I/II ST313. Long
read sequencing would help to clarify this picture.
Figure. The presence of BTP-1 in ST313
ACKNOWLEDGEMENTS
We would like to acknowledge PHE’s Genome
Sequencing and Development Unit and Infectious
Disease Informatics, Martin Day for antimicrobial
resistance typing. We would also like to thank Jay
Hinton and Sian Owen for helpful discussions and
comments.
REFERENCES
Okoro, C.K. et al., 2012. Intracontinental spread of human invasive
Salmonella Typhimurium pathovariants in sub-Saharan Africa. Nature
genetics, (September), pp.1–9.
Feasey, N. a et al., 2012. Invasive non-typhoidal salmonella disease: an
emerging and neglected tropical disease in Africa. Lancet, 379(9835),
pp.2489–99.
Kingsley, R. a et al., 2009. Epidemic multiple drug resistant Salmonella
Typhimurium causing invasive disease in sub-Saharan Africa have a
distinct genotype. Genome research, 19(12), pp.2279–87.
Parsons, B.N. et al., 2013. Invasive non-typhoidal Salmonella typhimurium
ST313 are not host-restricted and have an invasive phenotype in
experimentally infected chickens. PLoS neglected tropical diseases,
7(10), p.e2487