Saint Petersburg Pasteur Institute ACTIVITY Saint Petersburg Pasteur Institute ACTIVITY REPORT 2017-2018 Saint Petersburg 2019 Saint Petersburg Pasteur Institute 14, Mira Street, 197101, Saint Petersburg, Russian Federation Phone: +7 (812) 233-20-92 Fax: +7 (812) 232-92-17 E-mail: [email protected] Internet: http://pasteurorg.ru Director – Areg TOTOLIAN Deputy Director for Research – Vladimir DEDKOV Deputy Director for Innovation – Alexander SEMENOV Scientific Secretary – Galina TRIFONOVA International Department – Kseniia SMIRNOVA Currently, it is one of the largest institutes of epidemiology and microbiology in Russia, especially in the northwestern region of Russia. The Institute has a modern material base and a quality scientific staff that are united in five departments: – Department of microbiology; – Department of virology; – Department of epidemiology; – Department of immunology; – Department of new technologies. At the Institute work: – Scientific and Methodological Center for the Surveillance of Pathogens of Infectious and Parasitic Diseases of II-IV Pathogenicity Groups in the North-West Federal District of Russia; – North-West District Center for AIDS Prevention and Control; – Regional Center for Epidemiological Surveillance of Poliomyelitis; – Regional Center for Epidemiological Surveillance of Measles and Rubella. The Institute has two reference centers of the Russian Federation: – Federal Center for Surveillance of Typhoid Fever; – Federal Center for Surveillance of Yersinioses. Collaboration with WHO: – WHO Global Polio Laboratory Network (WHO Polio Laboratory); – WHO Subnational Measles and Rubella Laboratory (European Measles Laboratory Network). Contents DEPARTMENT OF MICROBIOLOGY ............................................................................... 4 Laboratory of Enteric Infections ........................................................................................................................... 4 Laboratory of Medical Bacteriology ..................................................................................................................... 8 Laboratory of Zooanthroponoses ...................................................................................................................... 11 DEPARTMENT OF VIROLOGY ...................................................................................... 15 Laboratory of Etiology and Viral Infections Control ....................................................................................... 15 Laboratory of Experimental Virology ................................................................................................................ 23 DEPARTMENT OF IMMUNOLOGY ............................................................................... 41 Laboratory for Pathogen Identification ............................................................................................................. 41 Laboratory of Molecular Immunology (Resource Sharing Centre) ............................................................... 44 DEPARTMENT OF EPIDEMIOLOGY ............................................................................. 49 Laboratory of Epidemiology of Infectious and Non-Infectious Diseases ................................................... 49 Laboratory of Viral Hepatitis ............................................................................................................................... 53 Laboratory of Molecular Epidemiology and Evolutionary Genetics ............................................................ 55 NORTHWESTERN DISTRICT CENTRE FOR AIDS PREVENTION AND CONTROL .............................................................................................................. 64 Laboratory of HIV Immunology and Virology .................................................................................................. 64 DEPARTMENT OF NEW TECHNOLOGIES .................................................................... 70 THE TESTING LABORATORY CENTRE ......................................................................... 72 Activity Report 2017-2018 3 Department of Microbiology LABORATORY OF ENTERIC INFECTIONS Head of the Laboratory: Lidia Kaftyreva Researchers: Z. Matveeva, E. Voitenkova, A. Zabrovskaya, M. Makarova, S. Egorova, A. Porin, L. Suzhaeva Genetic characteristics of Escherichia coli Conclusions. The population of E. coli strains, serolo- strains, О26, О55 and О111 serological gical groups О26, О111 and О55, isolated from children groups is inhomogeneous in terms of serotypes and the presence of genes coding ЕРЕС, STEC and ЕАЕС pathogenicity fac- Acute enteric infections with signs of hemorrhagic co- tors. The obtained data show we need further research into litis (HC) and hemolytic-uremic syndrome (HUS) that are the intraspecific biodiversity of E. coli, identification of pa- caused by shiga toxin-producing Escherichia coli (STEC) thogenicity factors or their genetic determinants along are common throughout the world and are registered as with serotyping for the final identification of E. coli as cau- sporadic cases or outbreaks. Of E. coli strains, pathoge- sative agents of acute enteric infections. nic strains synthesizing verotoxins (shiga-like toxins) are of particular importance. E. coli O157:H7 is the serotype Phylogenetic structure of S. Typhi that is most often associated with disease outbreaks and population isolated in Russia in 2005–2018 severe clinical outcomes. As of today, it is believed to be the most common STEC serotype in the world. At the same The global S. Typhi population is rather young, highly time, serotypes other than О157, namely O26, О55, O103, clonal and originated from a common ancestor existed so O111, and O145, are also known for their pathogenic poten- recently that multiple mutations have not yet accumulated. tial and together they make the so called five serogroups To evaluate the phylogenetic relatedness of the high clo- of non-О157 STEC pathogenic for humans. nal pathogen population, the genotyping method, based Materials and methods. 76 strains of E. coli isolated from on the detection in the compared genomes of the whole children were examined including O26 (53 strains), О111 (17 range of core single-nucleotide variations (SNV) located strains) and О55 (7 strains). Serotype characteristics (O- and both in coding and non-coding genome regions, is com- H-antigens) and virulence factor genes, i.e. of STX produc- monly used. The principle of SNV-typing of S. Typhi isolates tion (stx1/stx1a, stx1c, stx1d; stx2/stx2a, stx2b, stx2c, stx2d, is currently widely used to evaluate the pathogen popu- stx2e, stx2f, stx2g), α-hemolysin (hlyA), enterohemolysin lation structure and to determine the relation between (ehxA), the adhesion factor intimin (еае) and pilus conjuga- single/group of isolates. tion formation factor (bfp) as well as transcriptional regula- Whole genome sequencing of S. Typhi was performed tor of enteroaggregative E. coli (EAEC) aggR were examined on MiSeq (Illumina, USA) with MiSeq Reagent Kit v3 600 using PCR. cycles. Genomic DNA was isolated by the DNeasy Blood & Results. The findings of strain examination are summa- Tissue Kit (Qiagen). Genome libraries were prepared using rized in the Tabl. 1. According to serotyping, the examined MiSeq Nextera XT (Illumina, USA). Genome assembly and strains belong to six serovars: О26:Н11 (53 strains), О55:Н6 analysis was performed using CLC Genomics Workbench (5 strains), О55:Н7 (1 strain), О55:Н21 (1 strain), О111:Н2 8.0 (QIAGEN, Germany). (12 strains), and О111:Н8 (5 strains). To reconstruct the global phylogenetic tree, we analyzed According to our data, the STEC group included a set of 1683 S. Typhi isolates, which included both Russian 19 strains of E. coli О26:Н11, five strains of E. coli О111:Н8 isolates and isolates sequenced in previous studies. Thus, and one strain of E. coli О55:Н7. They had stx1/stx1a, еае, the set of strains under our investigation was characterized and ehxA genes. 34 strains of E. coli О26:Н11, five strains by the wide isolation time period (from 1905 to 2013) and of E. coli О55:Н6 and 12 strains of E. coli О111:Н2 had еае, broad geographical origin (63 countries, 6 continents: Asia, bfp, and hlyA virulence genes and according to this factor Africa, North and South America, Europe, Australia and they were classified as enteropathogenicE. coli (ЕРЕС). Oceania). One strain of E. coli О55:Н21 had neither STEC nor EPEC The detection of orthological SNV was performed virulence genes but it had EAEC-typical genes. using the previously developed algorithm of data analysis Table 1. Molecular-genetic characteristics of E. coli O26, O55, and O111 isolated from children with the diarrheal syndrome in St. Petersburg E. coli Number Virulence genes serotype of strains stx1 stx2 еае bfp aggR hlyA ehxA О26:Н11 19 stx1a – + – – – + О26:Н11 34 – – + + – + – О55:Н6 5 – – + + – + – О55:Н7 1 stx1a – + – – – – О55:Н21 1 – – – – + – – О111:Н2 12 – – + + – + – О111:Н8 5 stx1a – + – – – + 4 Activity Report 2017-2018 Saint Petersburg Pasteur Institute Laboratory of Enteric Infections (Kuleshov K.V. et al., Infect. Genet. Evol., 2016). The nucleo- The described phylogenetic groups of Н58 haplotype tide sequence of S. Typhi CT18 strain (NCBI acc. AL513382) included S. Typhi strains isolated in different regions of Rus- was used as a reference genome for reads mapping. The re- sian during all years under study. Epidemiological data was sulting matrix of orthologous SNV was used for phyloge- agreed