Helgenomsekvensering epidemiologisk typning

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1 Helgenomsekvensering epidemiologisk typning Ramona Groenheit Samordningsansvarig, Mikrobiolog, PhD Enheten för laborativ bakterieövervakning

Två körningar per vecka med olika agens i

BactTyper plugin (egenutvecklad mjukvara

(Singel Nucleotide Polymorphism) typning

tuberculosis H37Rv NC_000962 MSTs (Minimum

2 Helgenomsekvensering vid Folkhälsomyndigheten Ion Torrent plattform Två körningar per vecka med olika agens i samma körning. BactTyper plugin (egenutvecklad mjukvara för automatisk analys av WGS data) SNP (Singel Nucleotide Polymorphism) typning Mappas mot M. tuberculosis H37Rv NC_ MSTs (Minimum Spanning Trees) skapas för att visa släktskap Biblioteksprep Templatberedning Sekvensering Data analys Sid

3 Helgenomsekvensering vid Folkhälsomyndigheten BactTyper analyserar 23 resistensgener CLC Genomics Workbench används för konfirmering Fenotypiska resistensresultat rapporteras tillsammans med mutationer i gener kopplade till resistens Sid

4 Övergången till helgenomsekvensering våren - sommaren 2015 Sekvensering av ca 200 isolat från Vitryssland Validering av SNP-baserad typningsalgoritm januari - september 2016 Optimering av extraktion och provflöde Parallell sekvensering med MIRU-VNTR + spoligotypning Sekvensering av retrospektiva isolat (alla lung-tb fall från 2015 samt utvalda kluster och andra intressanta isolat) oktober 2016 Extern kvalitetskontroll via det europeiska referenslaboratorienätverket för tuberkulos (ERLTB-Net) Driftsättning av helgenomsekvensering Avslut av MIRU-VNTR och spoligotypning Extern kvalitetskontroll via det europeiska referenslaboratorienätverket för tuberkulos (ERLTB-Net) november 2017 Sid Swedac-granskning gällande ackreditering av SNP-analys Swedac-granskning gällande ackreditering av resistensgens-analys samt artbestämning

5 Resultat från valideringsprocessen 618 isolat analyserades med MIRU, spoligo och helgenom 317 isolat var unika enligt MIRU+spoligo 301 isolat klustrade enligt MIRU+spoligo 155 isolat var unika enligt helgenom 146 isolat klustrade enligt helgenom Med helgenomsekvensering så halveras klustringen jämfört med MIRU+spoligo! Sid

6 Hur definieras helgenomkluster? Isolat jämförs mot vår nationella typningsdatabas* och resultatet svaras ut till Smittskyddsenheterna via SmiNet Isolat definieras som tillhörande ett helgenomkluster om 5 SNPs Sid * innehållande ca 1200 svenska isolat och ca 500 utländska isolat (augusti 2017)

7 Sid Kommentar till helgenomklustret i Milou

8 Sid 8.

9 Hur väl stämmer helgenomresultaten med epidemiologiska kopplingar? Hittills identifierat 40 stycken nationella helgenomkluster: 28 kluster känd koppling (familj, bekanta, klasskamrat, arbetsplats, grannar, delat boende, geografisk närhet) 9 kluster gemensamt ursprung 3 kluster ej ännu lyckats hitta kopplingen (men eventuell koppling i Sverige) Sid

10 The role of whole genome sequencing in international outbreak investigations Sid.

11 MDR-TB outbreak among migrants from the Horn of Africa Number of WGS confirmed cases belonging to the cluster (as of April 4 th 2017) Austria 2 Finland 1 France 2 Germany 14 Sweden 1 All cases have a recent history of migration from Somalia 23 Eritrea 3 Ethiopia 1 Sudan 1 total 28 Switzerland 8 total 28 Sid.

12 Minimum spanning tree of MDR-TB cases by country of isolation including the cluster of 28 cases among migrants Solid black branches 5 SNPs Solid grey branches 12 SNPs Dashed grey branches > 12 SNPs Minimum spanning tree showing the relatedness of 57 Mycobacterium tuberculosis Cameroon genotype (lineage 4.6.2) clinical isolates from migrants with MDR-TB in 2016 and Phylogenetic inference is based on 1150 single nucleotide polymorphisms (SNPs) using Burrows- Wheeler Aligner (BWA) and Genome Analysis Toolkit (GATK) for a reference mapping approach. Solid black branches indicate a genetic distance 5 SNPs, solid grey branches 12 SNPs, and dashed grey branches > 12 SNPs. Sid 12. Matthias Merker, German National Reference Laboratory for Mycobacteria

Reported migration routes Migration route could not be documented 8 At least six migration routes in Italy: Travelled directly to Sweden 1 Entered the EU through

13 Reported migration routes Migration route could not be documented 8 At least six migration routes in Italy: Travelled directly to Sweden 1 Entered the EU through Germany 1 Entered the EU through Italy 18 total 28 Sicily Switzerland Sicily France Sicily Germany Sardinia Switzerland Sardinia Germany Bari Finland Transit through Rome Sid.

14 Conclusion of MDR-TB outbreak among migrants from the Horn of Africa Among the 20 cases with documented migrations routes, six reported onset of symptoms prior to arrival in the EU and five reported onset of symptoms during migration. Many (n=19) cases had travelled through Libya and (n=9) had long stays in Bani Walid under unsanitary condition. Transmission took place in the country of origin or along the migration route prior to entering the EU. Sid.

15 XDR-TB outbreak linked to a university in Romania In July 2015 an Israeli student (case 1) who had returned to Israel after studying at a university in Romania was diagnosed with XDR-TB in Israel. The student had a negative (0 mm) TST in July 2014 before going to Romania but converted to positive (13 mm) in July In October 2015 Israeli National IHR Focal Point notified the Romanian National Centre for Communicable Diseases Surveillance and Control. Contact tracing was then initiated in Romania and 59 contacts among students, teachers and didactic auxiliary personnel were identified from: Romania (17) Finland (12) UK (9) Germany (4) Israel (3) Nigeria (3) Sweden (3) Mauritius Islands (2) Austria (1) Italy (1) Palestine (1) Poland (1) Hungary (1) United Arab Emirates (1) Sid.

16 XDR-TB outbreak linked to a university in Romania All 59 contacts had chest X-rays (results normal except for two contacts) As TST is only performed on persons under 19 years of age in Romania, only two contacts had a TST done. One contact was negative (4 mm) and one contact was positive (20 mm) (case 2). Sid.

17 Family member contact investigations XDR-TB outbreak linked to a university in Romania case 1 Israel presented with symptoms case 2 contact investigation lived on the same floor case 3 presented with symptoms case 4 case 6 Finland presented with symptoms case 7 case 8 case 9 presented with symptoms Sid.

18 XDR-TB outbreak linked to a university in Romania The notification of case 3 triggered the resumption of the epidemiological investigations in Romania and all the contacts were re-evaluated. 38 contacts were newly identified (in total 97 contacts): 6 students from Israel 3 students from Finland 2 students from Ireland 1 student from Romania 1 student from USA 25 university employees Sid.

19 Chest X-ray examination of the 97 contacts (65 students + 32 university personnel) Screened by chest X-ray (two were identified as TB suspects, one of them became case 5) 92 Refused examination 1 Not eligible (case 2 + case 3 + case with susceptible TB + case with Hodgkins lymphoma) 4 Sputum examinations of the 97 contacts (65 students + 32 university personnel) Sputum examinations (sputum microscopy + GeneXpert + culture = all were negative) 63 No microbiological investigation (case 2 + case 3 + case with susceptible TB + 31 university personnel) 34 Tuberculin skin test (5U PPD) of the 97 contacts (65 students + 32 university personnel) TST* (51 were negative 0-9 mm and 43 were positive 10 mm) 94 No TST (case 2 + case 3 + case with susceptible TB) 3 * In Sid October no TSTs were performed on university personnel as they were 19 years old. However in October 2016 university personell were included in TSTs examinations.

20 Israel case 1, case 5 Finland case 6 case 2, case 3, case 4, case 7 Romania other (pre)xdr-tb strains from the county Strains from the MDR-TB outbreak among migrants from the Horn of Africa Sid.

Family member contact investigations XDR-TB outbreak linked to a university in Romania

floor case 3 presented with symptoms case 5 Israel contact investigation case 4 case 7

important to trace all contacts of any additional cases in order to identify and treat

21 Family member contact investigations XDR-TB outbreak linked to a university in Romania case 1 Israel presented with symptoms case 2 contact investigation lived on the same floor case 3 presented with symptoms case 5 Israel contact investigation case 4 case 7 case 8 case 6 Finland presented with symptoms case 9 presented with symptoms It is important to trace all contacts of any additional cases in order to identify and treat active cases and to provide preventive treatment or monitoring for those diagnosed with LTBI. Sid.

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