Genetic determinants of virulence and drug resistance of <i>Mycobacterium avium</i> subsp. <i>hominissuis</i> — a causative agent of mycobacteriosis in humans

Among the members of the large group of non-tuberculous mycobacteria (comprising more than 180 species), M. avium subsp. hominissuis (MAH) is the most significant causative agent of pulmonary infection in immunocompetent individuals as well as disseminated infection in immunocompromised hosts, e.g. human immunodeficiency virus (HIV)-positive patients. Due to increased incidence rate of mycobacteriosis, especially in HIV infection, much still need to be learnt about the MAH genetic control and virulence mechanisms. Deciphering the genome contents of the M. avium strain 104 (isolated from an AIDS patient with disseminated MAH disease) allowed to compare genome sequences of M. avium strains to gain insights into genomic diversity associated with variable hosts and environments. Comparative genome analysis of MAH strains isolated from patients with pulmonary and disseminated forms of mycobacteri-osis revealed differences in the structure of the genome, affecting the key virulence genes. This review provides current data on the genetic determinants of MAH virulence associated with the initial phase of infection. Several mycobacterial virulence-associated gene families, such as mce (mammalian cell entry), mmp (mycobacterial membrane proteins), pe/ppe and esx expressed by MAH during human infection are thought to be crucial for adhesion, entry, survival, and reproduction inside host macrophages. The genetic mechanisms of MAH survival in human macrophage cell culture as well as mice exposed to toxic effects of reactive oxygen, nitric oxide, bactericidal proteins (cathelicidin) are discussed. The MAH survival in the latency-like state is important for pathogen dissemination. Some genetic and phenotypic features of MAH (absence of a cord factor, presence of plasmids, potential to “switch” morphological types of colonies) are compared with M. tuberculosis. In addition, we summarized current state of MAH drug discovery, a role of MAH intrinsic multidrug resistance, genetic control, as well as mechanisms underlying formation of resistance to various groups of antibiotics in MAH strains

PREVALENCE OF HIGH CARCINOGENIC RISK HUMAN PAPILLOMAVIRUS IN THE REPUBLIC OF SAKHA (YAKUTIA), ST. PETERSBURG AND THE REPUBLIC OF KARELIA

Results of the study in three regions of the Russian Federation have shown widespread of high carcinogenic human papillomavirus among patients of dermatovenerological and gynecological profile. Detection of viral DNA in the material from the cervix and urethra ranged from 25,2 (Karelia) to 42,5 (Sakha Republic (Yakutia) per 100 examined patients. In all areas in 2010-2011 first place was occupied by 16-th virus genotype - from 11,5 (Sakha Republic (Yakutia) to 15,9 (St. Petersburg) per 100 patients. Prevalence of 11 other types differs. In the Sakha Republic (Yakutia) the second rank place was occupied by types 31 and. 51 (8,0 per 100 examined patients), in St. Petersburg - by 56 and 31 types (9,7 and. 7,6 per 100 patients). Age risk group contains patients of the age of 20-29 years. Information on circulating genotypes of the virus is a necessary part of surveillance to validate vaccination against human papillomavirus infection and evaluation of its efficiency

Molecular epidemiological monitoring of the tuberculosis pathogen in the Arkhangelsk region

Introduction. Against the background of improvement of the main epidemiological indicators (morbidity and mortality) for tuberculosis in the Arkhangelsk region, the proportion of newly diagnosed tuberculosis patients with multidrug-resistant pathogen (MDR-TB) increased from 18.7% in 2002 to 33.8% in 2018. The purpose of this study was the genotypic characterization of Mycobacterium tuberculosis strains obtained from newly diagnosed tuberculosis patients in the Arkhangelsk region in 2018. Materials and methods. 89 M. tuberculosis strains isolated in 2018 from newly diagnosed tuberculosis patients were studied. Beijing genotype, its clusters B0/W148 and Central Asian/Russian were determined by PCR detection of the specific markers: IS6110 insertions in the dnaA-dnaN region, mutations in codons 48 of the mutT4 gene (CGG GGG) and 58 of the mutT2 gene (GGA CGA), IS6110 insertions in the Rv2664 region-Rv2665 and Rv1359-Rv1360, substitutions G A in the sigE gene. Non-Beijing strains were spoligotyped. Results. Drug resistance was detected in 41.6% (37/89), MDR — in 33.7% of strains. In 90% (27/30) of MDR strains, resistance to rifampicin and isoniazid was due to rpoB Ser531Leu and katG Ser315Thr mutations. Following M. tuberculosis genotypes were identified: Beijing (67.4%), T (14.6%), Ural (4.5%), Haarlem (4.5%), LAM (2.3%) and CAS1-Delhi (1.1%). Among the Beijing strains, clusters Central-Asian/Russian (60%; 36/60) and B0/W148 (30%; 18/60) prevailed. The majority of MDR strains belonged to the Beijing family (93.3%; 28/30), of which 64.3% (18/28) and 21.4% (6/28) belonged to clusters B0/W148 and Central-Asian/Russian, respectively. Conclusion. In heterogeneous population of the causative agent of tuberculosis in the Arkhangelsk region, the most common strains were those of the Beijing genotype; in 2018 its share increased to 67.4% (40.4% in 1998–1999). Among MDR strains, the proportion of Beijing reached 93.3%, of which more than half (64.3%) belonged to the epidemiologically and clinically significant in Russia cluster B0/W148

Случай хромосомно-интегрированного вируса герпеса человека 6В типа у часто длительно болеющего ребенка

The five years old boy with recurrent respiratory tract infections was under observation of infectiologist due to high levels of human herpes virus type 6 (HHV-6), found in patient’s blood and saliva during a few years. The patient got the medicines against the HHV-6, without any effect. We investigated the patient’s and his mom’s nails and found the HHV-6 type B, so it was inherited chromosomal integrated HHV-6. Thus, to avoid the unnecessary treatment, in case of repeated high level of HHV-6, we need to exclude chromosomal integrated HHV-6.У часто и длительно болеющего пятилетнего мальчика при обследовании выявлена высокая концентрация вируса герпеса человека 6 (ВГЧ-6) в слюне и крови (более 1×106 копий ДНК в мл). По этому поводу он наблюдался инфекционистом и получал противовирусную терапию в течение нескольких лет без эффекта. В ногтевых пластинах пациента и его матери методом ПЦР обнаружена ДНК ВГЧ-6В в количестве 6,37 lg и 6,04 lg на 105 клеток соответственно, что свидетельствует о хромосомно-интегрированной форме ВГЧ-6. При высокой концентрации в крови или повторном выявлении ВГЧ-6 необходимо исключать хромосомно-интегрированную форму инфекции во избежание необоснованного лечения

Видовое разнообразие нетуберкулезных микобактерий у больных микобактериозом на территориях Северо-Западного федерального округа России

The objective of the study: to analyze the structure and trends in non-tuberculous mycobacteria (NTBM) population causing diseases in the North-Western Federal District of the Russian Federation.Subjects and methods. 745 clinical NTBM strains were identified. All clinical strains of NTBM were isolated by culture from clinical samples (sputum, bronchial washings, bronchoalveolar lavage fluid, pus, stool, urine, surgical and biopsy specimens, and venous blood in case of sepsis). In 23 cases, NTBM were detected post mortem. Mycobacteria were cultured on solid media or by the automated system of Bactec MGIT 960 BD USA. Species of re-cultured mycobacteria were identified using the test system of GenoType® Mycobacterium CM/AS (Hain Lifescience, Germany).Results. Analysis of the structure of the NTBM population isolated from patients with mycobacteriosis in the North-West of Russia, for the period of 2012-2018 showed overall dominance of M. avium (56.4%). However, certain NTBM species were found to be prevailing in some regions: M. lentiflavum and M. gordonae dominated in the Komi Republic and Arkhangelsk respectively. Unlike other regions of Russia, in the North-Western region, there was a consistently low level of detection of M. кansasii and M. xenopi. For the last 12 years in Saint Petersburg and Leningrad region, the variety NTBM in patients with different immune status has been growing but the portion of M. avium remains to be stably high exceeding 50%.Цель исследования: анализ структуры и тенденций популяции нетуберкулезных микобактерий (НТМБ), вызывающих заболевания, на территориях Северо-Западного федерального округа Российской Федерации.Материалы и методы. Проведена идентификация 745 клинических штаммов НТМБ. Все клинические штаммы НТМБ выделены при культивировании клинического материала (мокрота, промывные воды бронхов, жидкость бронхоальвеолярного лаважа, гной, кал, моча, операционный и биопсированный материал, венозная кровь при септических состояниях). В 23 случаях НТМБ выявлены посмертно. Культивирование микобактерий осуществляли на плотных питательных средах или в автоматизированной системе Bactec MGIT 960 BD USA. Видовую идентификацию рекультивированных штаммов микобактерий осуществляли с использованием тест-системы для идентификации НТМБ GenoType® Mycobacterium CM/AS (Hain Lifescience, Германия).Результаты исследования. Анализ структуры популяции НТМБ, выделенных от больных микобактериозом на Северо-Западе России, за период 2012-2018 гг. показал в целом доминирование вида M. avium (56,4%). Однако выявлены территориальные особенности видового разнообразия НТМБ: в Республике Коми и Архангельской области преобладали M. lentiflavum и M. gordonae соответственно. В отличие от других регионов России, на территории Северо-Запада отмечен стабильно низкий̆ уровень выявляемости M. кansasii и M. xenopi. В Санкт-Петербурге и Ленинградской области в течение последних 12 лет отмечено увеличение разнообразия НТМБ у пациентов с разным иммунным статусом, но доля M. avium остается стабильно высокой, превышая 50%

Genome-Wide Mycobacterium tuberculosis Variation (GMTV) Database: A New Tool for Integrating Sequence Variations and Epidemiology

Background Tuberculosis (TB) poses a worldwide threat due to advancing multidrug-resistant strains and deadly co-infections with Human immunodeficiency virus. Today large amounts of Mycobacterium tuberculosis whole genome sequencing data are being assessed broadly and yet there exists no comprehensive online resource that connects M. tuberculosis genome variants with geographic origin, with drug resistance or with clinical outcome. Description Here we describe a broadly inclusive unifying Genome-wide Mycobacterium tuberculosis Variation (GMTV) database, (http://mtb.dobzhanskycenter.org) that catalogues genome variations of M. tuberculosis strains collected across Russia. GMTV contains a broad spectrum of data derived from different sources and related to M. tuberculosis molecular biology, epidemiology, TB clinical outcome, year and place of isolation, drug resistance profiles and displays the variants across the genome using a dedicated genome browser. GMTV database, which includes 1084 genomes and over 69,000 SNP or Indel variants, can be queried about M. tuberculosis genome variation and putative associations with drug resistance, geographical origin, and clinical stages and outcomes. Conclusions Implementation of GMTV tracks the pattern of changes of M. tuberculosis strains in different geographical areas, facilitates disease gene discoveries associated with drug resistance or different clinical sequelae, and automates comparative genomic analyses among M. tuberculosis strains

Генетические особенности возбудителя туберкулеза в Уральском федеральном округе России

The article presents molecular genetic description of isolates of Mycobacterium tuberculosis of 178 new patients and 78 patients who had been previously treated obtained in 2009-2011 on the territory of Urals. PCR in real time and MIRU-VNTR typing of 15 loci detected prevalence of M. tuberculosis of Beijing genotype in the both groups of patients, however the part of Beijing isolates was significantly higher in the group of patients who had been previously treated compared to new patients: 80.8% versus 55.1% (p = 0.0002). IS6110-RFLP-typing showed that the majority of Beijing isolates belonged to B0 clone, clinically and epidemiologically significant in Russia. It was found out that M. tuberculosis Beijing carrying mutations rpoB Ser531→Leu and katG Ser315→Thr played the major role in MDR tuberculosis transmission in Urals. Non-Beijing group was represented by isolates of various spoligotypes and MIRU-VNTR types among which the representatives of the following globally common genetic groups prevailed: LAM (LAM9, T5_RUS), URAL (Н3), Haarlem (H1, X), Т (Т1).Представлена молекулярно-генетическая характеристика изолятов Mycobacterium tuberculosis, полученных в 2009-2011 гг. на территории Урала от 178 ранее не леченных и 78 ранее леченных больных туберкулезом. ПЦР в режиме реального времени и MIRU-VNTR-типирование по 15 локусам выявили доминирование M. tuberculosis генотипа Beijing в обеих группах пациентов, однако доля изолятов Beijing у ранее леченных больных существенно превышала таковую в группе ранее не леченных больных: 80,8% против 55,1% (p = 0,0002). IS6110-RFLP-типирование доказало принадлежность большинства изолятов Beijing к эпидемиологически и клинически значимому в России клону В0. Установлено, что M. tuberculosis Beijing, несущие мутации rpoB Ser531→Leu и katG Ser315→Thr, играют ключевую роль в распространении туберкулеза с МЛУ возбудителя на Урале. Группа non-Beijing была представлена изолятами различных сполиготипов и MIRU-VNTR-типов, среди которых преобладали представители нескольких глобально-распространенных генетических групп LAM (LAM9, T5_RUS), URAL (Н3), Haarlem (H1, X), Т (Т1)

The Beijing genotype and drug resistant tuberculosis in the Aral Sea region of Central Asia

BACKGROUND: After the collapse of the Soviet Union, dramatically increasing rates of tuberculosis and multidrug-resistant tuberculosis (MDR-TB) have been reported from several countries. This development has been mainly attributed to the widespread breakdown of TB control systems and declining socio-economic status. However, recent studies have raised concern that the Beijing genotype of Mycobacterium tuberculosis might be contributing to the epidemic through its widespread presence and potentially enhanced ability to acquire resistance. METHODS: A total of 397 M. tuberculosis strains from a cross sectional survey performed in the Aral Sea region in Uzbekistan and Turkmenistan have been analysed by drug susceptibility testing, IS6110 fingerprinting, and spoligotyping. RESULTS: Fifteen isolates showed mixed banding patterns indicating simultaneous infection with 2 strains. Among the remaining 382 strains, 152 (40%) were grouped in 42 clusters with identical fingerprint and spoligotype patterns. Overall, 50% of all isolates were Beijing genotype, with 55% of these strains appearing in clusters compared to 25% of non-Beijing strains. The percentage of Beijing strains increased with increasing drug resistance among both new and previously treated patients; 38% of fully-susceptible isolates were Beijing genotype, while 75% of MDR-TB strains were of the Beijing type. CONCLUSION: The Beijing genotype is a major cause of tuberculosis in this region, it is strongly associated with drug resistance, independent of previous tuberculosis treatment and may be strongly contributing to the transmission of MDR-TB. Further investigation around the consequences of Beijing genotype infection for both tuberculosis transmission and outcomes of standard short course chemotherapy are urgently needed