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[(D)-6.2(a)-.7(t)-5.4(a)-392.4(e)-6.5(n).4(t)-5.4(r)-5.3(y,)-393.5(t)-5.4(a)-6.5(bu)-5.3(la)-6.5(ti)-5.4(on)-5.3(,)-393.5(a)-6.5(nd)-397(an)-5.3(al)-5.4(y)-5.3(s).6(i)-5.4(s)-396.8(we)-6.5(re)-398.1(co)-5.3(mp)-5.3(le)-6.5(te)-6.5(d)-397(i).3(n)]TJ
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[(M)-6.2(i)-5.4(cr)-5.3(os)-5.1(of)-5.3(t)-374.1(E)-6.5(xc)-6.5(el)-5.4(.)-376.3(T)-.8(a)-6.5(b).4(l)-5.4(e)-6.5(s)-373.7(w)-.4(e)-6.5(r)]TJ
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[(e)-372.9(c)1.5(onstructed)-377.5(to)-377.5(compare)-372.9(t)-3.2(he)]TJ
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[(exp)5(o)-.7(s)5.2(e)-1.9(d)-329(t)-.8(o)-329(e)-1.9(ach)-329(f)-.7(o)5(o)-.7(d)-329(i)-.8(t)4.9(e)-1.9(m,)-331.3(fo)5(ll)4.9(owed)-329(by)-329(th)5(e)-335.9(c)3.9(al)4.9(cu)5(latio)5(n)-334.8(o)5(f)]TJ
T*
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[(\(CI)5.2(s)-.4(\))-294.3(f)5.2(or)-294.3(i)5(n)-.6(d)5.1(i)-.7(vi)5(du)5.1(al)-294.5(exp)5.1(o)-.6(su)5.1(res)-294.2(t)-.7(o)-294.4(i)5(ll)5(ness.)-290.9(The)-295.5(p)5.1(ub)5.1(lic)-289.8(healt)5(h)]TJ
0 -1.1116 TD
[(uni)4.9(t)-185.2(w)4.2(here)-186.2(t)4.9(h)-.7(e)-180.4(o)-.7(u)5(t)-.8(br)5.1(eak)-185(o)5(ccurr)5.1(ed)-179.3(led)-185(t)-.8(h)5(e)-186.2(i)4.9(n)-.7(d)5(i)-.8(v)5(i)-.8(du)5(al)-179.4(ou)5(tbr)5.1(e)-1.9(ak)]TJ
T*
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[(inv)6(e)-.9(s)6.2(tig)6(at)5.9(io)6(ns.)]TJ
/F2 1 Tf
8.9663 0 0 8.9663 313.0582 560.7495 Tm
0 Tc
[(Food)-335(and)-335.7(environmental)-335.2(investigations)]TJ
/F6 1 Tf
9.843 0 0 9.843 323.0361 544.3085 Tm
[(Food)-298(safety)-296.8(authorities)-302.7(in)-296.1(the)-298.3(affected)-301.5(states)-302.5(and)-292.4(territory)]TJ
-1.0137 -1.1174 TD
[(inspected)-531.8(the)-528.7(implicated)-534.6(food)-528.5(premises.)-528.1(Where)-534.2(possible,)]TJ
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[(food)-419.1(or)-416.9(environmental)-422.6(samples)-419.9(were)-416.5(collected)-423.9(for)-417.9(testing.)]TJ
T*
[(The)-443.4(inspections)-440.7(and)-436.4(sampling)-443.3(at)-435.5(these)-439.7(premises)-444.1(aimed)-435.4(to)]TJ
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[(identify)-258(any)-257.9(food)-257.8(safety)-256.5(hazards)-258.6(and)-257.9(detect)-258(contamination)-255.7(in)]TJ
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[(food)-257.8(or)-261.4(the)-258(environment)-257.8(of)-255.6(the)-258(premises.)-263.2(We)-259.1(also)-258.9(conducted)]TJ
T*
[(egg)-286.7(trace-back)-287.6(at)-280(the)-281.1(implicated)-287(food)-280.8(premises)-282.8(to)-284.5(identify)-281(if)]TJ
0 -1.1174 TD
[(they)-201.5(were)-203.4(using)-195.5(a)-198.1(common)-200.3(egg)-200.3(supplier.)-197.8(We)-201.5(inspected)-203.5(an)-199.2(egg)]TJ
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T*
[(farm)-225.6(next)-224.6(to)-227(the)-223.5(grading)-222.1(facility,)-228.2(where)-227.5(we)-223.1(collected)-228.1(samples)]TJ
T*
[(of)-284.4(chicken)-282(feces,)-282.9(feed,)-286.6(egg,)-278.6(and)-280.9(environmental)-284.4(swabs.)]TJ
/F2 1 Tf
8.9663 0 0 8.9663 313.0582 412.7243 Tm
[(Microbiological)-343(investigation)]TJ
/F6 1 Tf
9.843 0 0 9.843 323.0361 396.2834 Tm
[(The)-374.3(food)-367.2(and)-373.1(environmental)-376.5(samples)-373.9(collected)-372.1(from)-374.2(the)]TJ
-1.0137 -1.1116 TD
[(implicated)-436.7(food)-430.6(premises)-432.5(in)-428.5(each)-434.1(outbreak)-431.7(were)-433.8(tested)-429.5(in)]TJ
T*
[(the)-355.9(state)-347.7(or)-353.5(territory)-351.2(in)-347.9(which)-353.3(the)-350.2(outbreak)-351.1(occurred.)-355.5(Swab)]TJ
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[(sampl)-7.8(es)-400.6(from)-403(the)-402(egg)-401.9(grading)-400.6(facility)-409(were)-405(tested)-400.7(using)-402.9(a)]TJ
0 -1.1116 TD
[(modied)-309.6(Australian)-313.9(Standard)-304.8(5013.10)-309.6(\(Standards)-306.8(Australia,)]TJ
T*
[(2009\).)-371.8(This)-368.4(method)-372(incorporates)-368.1(nonselective)-375.2(liquid)-369.9(resus-)]TJ
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[(citation)-380.3(and)-378.8(then)-374.3(screening)-376.2(for)-377.6(the)-373.2(presence)-381.9(of)]TJ
/F5 1 Tf
19.7846 0 TD
(Salmonella)Tj
/F6 1 Tf
-19.7846 -1.1116 TD
[(using)-414.4(a)-417(commercial)-421.5(polymerase)-413.1(chain)-416.9(reaction)-415.7(kit.)-415.9(Liquid)]TJ
T*
[(resuscitatio)-11(n)-427.3(broths)-427(positive)-430.6(for)]TJ
/F5 1 Tf
13.6332 0 TD
(Salmonella)Tj
/F6 1 Tf
4.9418 0 TD
[(are)-431.8(conrmed)]TJ
-18.5751 -1.1116 TD
[(culturally)-313.3(using)-304.9(liquid)-306.5(selective)-314.3(enrichment)-309.7(and)-309.7(solid)-305.1(selec-)]TJ
0 -1.1174 TD
[(tive)-311.1(media)-308.7(for)-308.5(the)-309.9(isolation)-310.9(of)]TJ
/F5 1 Tf
12.5043 0 TD
(Salmonella)Tj
/F6 1 Tf
4.5098 0 TD
[(.)-302.9(Typical)-311(colonies)]TJ
-17.0142 -1.1116 TD
[(were)-203.4(inoculated)-205(onto)-200.4(plate)-198.2(count)-202.6(agar)-202.5(and)-200.3(individual)-197(colonies)]TJ
T*
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0 -1.1174 TD
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[(of)-259.4()5.7(i)-.3(gh)5.5(t)-259.5(m)4.3(as)5.7(s)-259.2(s)0(p)5.5(e)-1.4(ctro)5.5(metr)5.6(y.)-256(Co)5.5(n)5.7(rmed)]TJ
/F5 1 Tf
16.3403 0 TD
.0123 Tc
[(Sal)5.3(mo)5.4(nell)5.3(a)]TJ
/F6 1 Tf
4.8727 0 TD
.0116 Tc
[(is)4.9(ol)4.6(ates)]TJ
-21.213 -1.1116 TD
.0123 Tc
[(fro)5.4(m)-329.8(t)-.4(he)-329.8(g)5.4(r)-.3(ad)5.4(in)5.4(g)-334.4(f)5.5(acil)5.3(ity)-328.6(were)-329.8(sent)-328.7(to)-328.6(th)5.4(e)-329.8(M)-1.2(i)5.3(c)-1.5(ro)5.4(bi)5.3(ol)5.3(ogi)5.3(cal)]TJ
T*
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[(Diagn)5(o)-.7(s)5.2(tic)-266.8(Uni)4.9(t)-271.6(P)5.2(u)-.7(b)5(lic)-266.8(Healt)4.9(h)-271.4(Lab)5(o)-.7(r)5.1(a)-1.9(t)4.9(ory)-265.7(\()-81.3(M)4.1(DU)-266.5(PHL\))-265.6(fo)5(r)]TJ
0 -1.1174 TD
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[(ser)5.9(o).1(t)5.7(ypi)5.7(ng)5.8(.)]TJ
1.0137 -1.1116 TD
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-1.0137 -1.1116 TD
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[(wer)4.9(e)-388(s)5(e)-2.1(q)4.8(u)-.9(enced)-386.8(a)3.7(s)-386.6(p)4.8(art)-381.2(o)-.9(f)-381(a)-388(s)5(t)-1(ud)4.8(y)-386.8(t)4.7(o)-386.8(p)4.8(ros)5(pect)4.7(ively)-381(W)-3.2(GS)]TJ
/F5 1 Tf
0 -1.1174 TD
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[(Sal)5.4(mo)5.5(nella)]TJ
/F6 1 Tf
5.0052 0 TD
0 Tc
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[(tory)-206.1(\(Ford)]TJ
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4.2391 0 TD
[(et)-199.3(al.)]TJ
/F6 1 Tf
1.9583 0 TD
[(,)-205(2018\).)-199(Serotyping)-202.3(and)-200.3(MLVA)-204.1(of)-203.8(the)-200.4(isolates)]TJ
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[(were)-364.7(completed)-360.5(at)-354.8(MDU)-357.3(PHL)-356.6(in)-359.4(Victoria,)-361.4(the)-355.9(Institute)-357(for)]TJ
T*
[(Clinical)-318(Pathology)-316.4(and)-309.7(Medical)-317.6(Research)-319.5(\(ICPMR\))-315.7(in)-313.3(New)]TJ
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[(South)-264.7(W)-14.9(a)-8(l)-12.7(e)-8(s)-12.4(,)-274.1(o)-6.9(r)-271.8(Q)-13.5(u)-6.9(e)-13.8(e)-8(n)-12.6(s)-12.4(l)-7(a)-13.8(n)-6.9(d)-271.8(H)-13.5(e)-13.8(a)-8(l)-12.7(t)-7(h)-271.8(F)-12.5(o)-6.9(r)-12.6(e)-13.8(n)-6.9(s)-12.4(i)-7(c)-278.7(a)-8(n)-12.6(d)-271.8(S)-6.7(c)-13.8(i)-7(e)-13.8(n)-6.9(t)-12.7(i)-12.7()-6.7(c)]TJ
0 -1.1116 TD
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T*
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[(det)5(e)-1.8(r)5.2(m)-1.8(i)5(n)-.6(ed)-219.5(usi)5(n)-.6(g)-219.5(a)4(nt)5(is)5.3(era)-220.7(a)4(nd)-219.5(s)5.3(e)-1.8(r)5.2(o)-.6(ty)5.1(ped)-219.5(i)-.7(n)-219.5(a)4(ccor)5.2(dance)-214.9(w)-1.5(it)5(h)]TJ
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[(the)-209(W)3(hit)5.1(e)-1.7(-)5.3(K)-1.4(auf)5.3(f)-.5(man-)5.3(Le)-209(Mi)5.1(no)5.2(r)-213.6(s)5.4(ch)5.2(eme)-214.8(\()5.3(Iss)5.4(e)-1.7(n)5.2(hut)5.1(h-)5.3(Jeanj)5.1(e)-1.7(an)]TJ
/F5 1 Tf
0 -1.1116 TD
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[(et)-454(a)6.9(l)6.8(.)]TJ
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2.3212 0 TD
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-2.3212 -1.1116 TD
0 Tc
[(descri)-8.8(bed)-280.9(\(Lindstedt)]TJ
/F5 1 Tf
8.5301 0 TD
[(et)-285.7(al.)]TJ
/F6 1 Tf
2.0447 0 TD
[(,)-279.9(2004\).)]TJ
-9.5611 -1.1174 TD
[(Sequenced)-233.3(isolates)-235.8(were)-226.4(then)-230.3(subcultured)-233.3(for)-227.9(purity)-6.8(,)-228.1(DNA)]TJ
-1.0137 -1.1116 TD
[(extracted)-348.9(using)-339.5(Presto)-341.6(Mini)-345.4(gDNA)-341.1(Bacteria)-348.8(kit)-337.6(\(GeneAid\),)]TJ
T*
[(and)-327(DNA)-322.7(libraries)-323.4(prepared)-329(using)-322.2(the)-321.4(Illumina)-322.6(Nextera)-323.2(XT)]TJ
/F4 1 Tf
8.9663 0 0 8.9663 62.022 749.6502 Tm
(286)Tj
48.2754 0 TD
[(FORD)-330.5(ET)-338.7(AL.)]TJ
ET
endstream
endobj
40 0 obj
<>stream
/GS1 gs
BT
/F6 1 Tf
9.843 0 0 9.843 59.7543 725.1588 Tm
0 0 0 rg
0 Tc
0 Tw
[(kit)-297.3(\(Illumina,)-304(Inc.\).)-294.6(WGS)-300(was)-298.9(performed)-301.4(using)-293.4(the)-298.3(Illumina)]TJ
0 -1.1174 TD
[(NextSeq)-321.9(500)-320.1(platform)-322.4(with)-322.3(2)]TJ
/F9 1 Tf
12.1357 0 TD
()Tj
/F6 1 Tf
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[(150)-170.3(bp)-319(pairedend)-321(chemis-)]TJ
-12.8499 -1.1116 TD
[(try.)-369.7(The)-368.5()45(Nullarbor)49.1()-369.7(pipeline)-368.6(\(https://github.com/tseeman/)]TJ
T*
[(nullarbor\))-196.7(was)-195.2(used)-189.7(to)-192.4(trim)-195.9(the)-188.9(reads,)-195.4(check)-193.3(the)-194.7(sequence)-197.6(data)]TJ
T*
[(quality,)-444.7(and)-436.4(perform)-442(core)-444.4(genome)-436.4(single-nucleotide)-450(poly-)]TJ
0 -1.1174 TD
[(morphisms)-415.3(\(SNPs\))-410.1(by)-411.1(aligning)-407.8(short-read)-410.6(data)-415.8(against)-407.5(the)]TJ
/F5 1 Tf
0 -1.1116 TD
(Salmonella)Tj
/F6 1 Tf
4.89 0 TD
[(Typhimurium)-373.1(LT2)-380.1(reference)-378.5(genome.)-376.5(The)-374.3(sig-)]TJ
-4.89 -1.1116 TD
[(nicant)-321.2(thresholds)-323(for)-314.3(SNP)-320.6(calling)-315.7(were)-324.4(set)-315.4(for)-320(a)-319(minimum)]TJ
0 -1.1174 TD
[(coverage)-255.3(at)-245.4(30.)-247.5(The)-247.6(phylogenetic)-253.3(analysis)-252.9(was)-247(performed)-249.5(on)]TJ
0 -1.1116 TD
[(the)-304.1(generated)-302.6(SNP)-297.6(alignment)-301.9(le)-298.2(to)-301.8(infer)-300.5(core)-300.4(SNP)-297.6(phylog-)]TJ
T*
[(eny)-246.4(using)-241.6(the)-246.5(maximum)-248.8(likelihood)-243.1(method)-245.3(at)-245.4(100)-239.5(bootstraps)]TJ
0 -1.1174 TD
[(by)-198(MEGA)-198.3(7)-191.2(\(Kumar)]TJ
/F5 1 Tf
8.3343 0 TD
[(et)-193.6(al.)]TJ
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1.9525 0 TD
[(,)-193.5(2016\).)-199(We)-195.7(describe)-196.5(these)-197.8(methods)]TJ
-10.2868 -1.1116 TD
[(in)-284.6(more)-277.5(detail)-285.8(elsewhere)-286(\(Ford)]TJ
/F5 1 Tf
12.7174 0 TD
[(et)-280(al.)]TJ
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2.0389 0 TD
[(,)-279.9(2018\).)]TJ
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[(While)-314.5(this)-315.5(study)-310.7(aimed)-314.5(to)-313.4(prospectively)-317.5(WGS)-311.5(all)]TJ
/F5 1 Tf
20.447 0 TD
(Salmo-)Tj
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(nella)Tj
/F6 1 Tf
2.3039 0 TD
[(Typhimurium)-292.5(03-26-13-08-523)-292.9(isolates)-299.1(from)-287.8(the)-292.6(Aus-)]TJ
-2.3039 -1.1174 TD
[(tralian)-379(Capital)-380.1(Territory,)-384.5(sequencing)-377.3(was)-379.5(not)-377.8(performed)-376.2(in)]TJ
0 -1.1116 TD
[(real)-404.2(time.)-402.1(Isolates)-408.4(from)-397.2(outbreaks)-409.6(in)-399.7(Queensland)-401.2(were)-405(se-)]TJ
T*
[(quenced)-310.7(at)-308.8(MDU)-311.2(PHL)-310.5(and)-304(added)-313.1(into)-304.2(the)-309.9(analysis)-310.5(after)-307.4(the)]TJ
0 -1.1174 TD
[(outbreaks)-409.6(had)-401.9(been)-404.1(identied)-404.1(and)-401.9(invest)-7.8(igated.)-404.3(Additional)]TJ
0 -1.1116 TD
[(isolates)-230(from)-224.4(outbreaks)-231(in)-227(New)-225.1(South)-224.3(Wales)-228.9(were)-232.2(sequenced)]TJ
T*
[(just)-442.2(for)-435.2(this)-436.4(study)-437.4(at)-435.5(ICPMR)-440.3(and)-436.4(added)-439.8(into)-436.6(the)-436.6(analysis)]TJ
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(retrospectively.)Tj
/F4 1 Tf
8.9663 0 0 8.9663 59.7543 466.5826 Tm
(Results)Tj
/F2 1 Tf
0 -1.8336 TD
[(Epidemiological)-337.4(investigations)]TJ
/F6 1 Tf
9.843 0 0 9.843 69.7323 433.7007 Tm
[(Between)-353.1(October)-345.1(2015)-350(and)-344.3(March)-348.5(2016,)-347.7(there)-347.7(were)-347.4(272)]TJ
-1.0137 -1.1116 TD
[(cases)-279.3(of)]TJ
/F5 1 Tf
3.4961 0 TD
(Salmonella)Tj
/F6 1 Tf
4.7806 0 TD
[(Typhimurium)-275.2(03-26-13-08-523)-275.6(notied)]TJ
-8.2767 -1.1174 TD
[(in)-365.2(the)-361.7(Australian)-365.7(Capital)-368.6(Territory,)-361.5(New)-363.3(South)-362.6(Wales,)-364.8(and)]TJ
0 -1.1116 TD
[(Queensland)-193.9(\(Fig.)-180.6(1\).)-184.2(Of)-187.3(these,)-189.8(115)-181.9(\(42%\))-185.1(cases)-187.2(were)-186.1(linked)-186.6(to)]TJ
T*
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T*
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T*
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T*
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T*
[(three)-278.6(outbreaks)-288.6(\(Table)-280.9(1)-277.6(and)-286.7(Supplementary)-284.1(Table)-279.9(S2\).)]TJ
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T*
[(outbreaks)-248.3(to)-244.2(the)-246.5(same)-249.7(grading)-250.9(facility.)-245.4(During)-249.5(the)-246.5(inspection)]TJ
T*
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17.0948 0 TD
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[(barn,)-325.8(and)-327(free-range)-332.3(eggs)-322.2(per)-327(day,)-330.4(including)-322.5(about)-329.3(120,000)]TJ
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[(FIG.)-313.7(1.)]TJ
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(Salmonella)Tj
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[(Typhimurium)-314.2(03-26-13-08-523)-308.5(case)-312.5(notications)-314(by)-307.2(week)]TJ
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