Molecular typing of Y. pestis strains: practical application Elisabeth Carniel Yersinia Research Unit National Reference Laboratory WHO collaborating Center Institut Pasteur France
Y. pestis: very young bacterium (< 5,000 y) Phenotypic polymorphism very low 4 biovars: Antiqua, Medievalis,, Pestoides Molecular tools - Ribotyping - Pulsed field gel electrophoresis (PFGE) - IS fingerprinting (IS-RFLP) Achtman et al. (1999) PNAS.
MADAGASCAR - Endemic foci - Outbreaks - Re-emergence in some 'plague-free' areas
Ribotyping Ribotype B () Guiyoule et al. (1994) J. Clin. Microbiol.
Ribotype B Emergence of new ribotypes: Q, R, T Guiyoule et al. (1997) J. Clin. Microbiol.
B R Q T Ambositra Ambohimahasoa
Number of strains Evolution of the new variants 9 0 80 70 60 50 40 30 20 10 B R T Q 0 4 0-4 9 5 0-5 9 6 0-6 9 7 0-7 9 8 0-8 9 9 0-9 6 Years
Mahajanga outbreak (Resurgence in1995) Mahajanga Reservoir? Rats Fleas Humans?? Shrews
PFGE Mahajanga
Geographical origin: Mahajanga Andapa - From a Malagasy focus? - Imported? Antananarivo PFGE
Algeria - Oran, June 2003 - No plague cases for 50 years - Cases: First on June 2 in Kehailia 11 year old boy who died on June 4 Bertherat et al. (2007) Emerg. Infect. Dis.
Ain Temouchent: June 28 50 km from Kehailia
Are the human cases in Kehailia and Ain Temouchent related? Five strains isolated: 3 around Kehailia 2 from Ain Temouchent Phenotyping Typical strains Ribotyping Typical ribotype B PFGE
Hama Ali Kehailia Hamoul Ain Temouchent Ain Temouchent PFGE (NotI) M 194 145 3 pulsotypes 97 Different strains Closely related 48 23
Algeria 2003 Algeria 1944 Algeria 1945 Senegal Belgian Congo Morocco Belgian Congo Namibia Algeria 2003 Algeria 1944 Origin of this outbreak? Re-emergence of a quiescent plague focus? Imported? 2 human Y. pestis isolates: Oran 1944 Oran 1945 PFGE (SpeI)
IS Fingerprinting (IS-RFLP) IS100 IS1541 EcoRI HindIII Torrea et al. (2006) J. Clin. Microbiol.
IP577 IP578 IP523 IP524 IP685 IP696 IP610 IP695 IP528 IP529 IP1595 IP283 IP304 IP678 IP573 IP1747 IP574 IP579 IP1535 IP530 IP241 IP666 IP644 IP567 IP571 IP568 IP569 IP521 IP1867 IP532 IP940 IP989 IP513 IP772 IP820 IP507 IP612 IP613 IP1538 IP1540 IP1537 IP1541 IP1542 IP519 IP562 IP564 IP557 IP516 IP565 IP537 IP543 IP539 IP542 IP549 IP550 IP677 IP544 IP545 IP553 IP552 IP554 Morocco Morocco Senegal Senegal Germany Germany Argentina Germany Madagascar Madagascar India India Madagascar Belgian Congo USA USA USA India South Africa Madagascar Madagascar Madagascar Madagascar Brazil Brazil Brazil Brazil Turkey Algeria Vietnam Vietnam Vietnam Vietnam Vietnam Vietnam Vietnam Burma Burma Namibia Namibia Namibia Namibia Namibia Kurdistan Kurdistan Kurdistan Kurdistan Kurdistan Turkey Kenya Belgian Congo Kenya Kenya Belgian Congo Kenya Kenya Kenya Kenya Kenya Kenya Kenya 1940 1940 1944 1944 1952 1952 1946 1952 1946 1951 1994 1994 1969 1950 1948 1992 1950 1908 1982 >1939 1989 1992 1989 1967 1967 1967 1967 UN 1945 1955 1965 1964 1964 1963 1964 1955 1970 1970 1984 1985 1984 1986 1986 1951 1947 1948 1963 1948 1952 1952 1953 1952 1952 1953 UN UN UN UN UN UN UN Medievalis Medievalis Medievalis Medievalis Medievalis Medievalis Antiqua Antiqua Antiqua Antiqua Antiqua Antiqua Antiqua Antiqua Antiqua Antiqua Antiqua Antiqua Strain Country Year Biovar A M O IS-RFLP Northern Africa Germany India USA Brazil Vietnam Burma Namibia Asia Africa
Strain Country Year Ribotype IS-RFLP Algerian strains Origin from Northern Africa Medievalis Antiqua
Libya - Tobruk, June 2009 - No plague cases for 25 years - Cases: First on June 9 in Eltarsha 13 year old boy who died on June 11
Tobruk (June 9) 3 strains isolated (by IP Madagascar) 10 km Zafrana (June 18) Beer Alashahab (June 16) TUNISIA Benghazi Tobruk LIBYA EGYPT NIGER CHAD SUDAN
Cases related? Yes IS100 IS1541 M 1 2 3 1 2 3 1 2 3 194 145 97 PFGE IS-RFLP 48 23 9 Cabanel et al. (2013) Emerg. Infect. Dis.
Kurdistan Kurdistan Turkey Libya Kurdistan Kurdistan Origin? M Biovar Medievalis Ribotype O 194 PFGE 145 97 48 23
Strain Country Year Ribotype IS-RFLP Medievalis Antiqua
Oran MOROCCO Laghouat TUNISIA Benghazi Tobruk MA LI ALGERIA LIBYA EGYPT MAURITANIA MALI NIGER CHAD SUDAN No Link between the Algerian and Libyan plague outbreaks Algeria: Northern Africa focus Libya: Central Asia origin
Sequenced-based technics 923 Y. pestis strains Morelli et al. (2010) Nature Genetics
Collaborators Institut Pasteur Paris Annie Guiyoule Gabriella Torrea Nicolas Cabanel WHO Eric Bertherat University Hospital Oran, Algeria Souad Bekhoucha Institut Pasteur Madagascar Mino Rajerison NCDC Libya Badereddin Annajar