Журнал микробиологии, эпидемиологии и иммунобиологии. 2022; 99: 465-477
Молекулярно-генетическая характеристика штаммов Vibrio cholerae nonO1/nonO139, выделенных от больных отитами на территории Российской Федерации
https://doi.org/10.36233/0372-9311-215Аннотация
Введение. В 2017–2020 гг. в России впервые за много лет от больных отитами были выделены штаммы Vibrio cholerae nonO1/nonO139 (НАГ-вибрионов).
Цель работы — биоинформационный анализ полных геномов (WGSs) и отдельных генов штаммов НАГ-вибрионов — возбудителей отитов, выделенных в России.
Материалы и методы. Анализ WGSs 8 клинических изолятов НАГ-вибрионов, полученных на платформе «MiSeq Illumina», проводили с использованием программ «BioEdit», «BLASTN», «BLASTP», «Vector NTI»; антибиотикоустойчивость определяли согласно МУК 4.2.2495-09.
Результаты. Штаммы различались по содержанию SNP, наборам детерминант факторов патогенности/ персистенции и их аллелям. Все были лишены профагов CTX, preCTX, RS1, острова патогенности VPI, гена термостабильного токсина, мобильных элементов, связанных с антибиотикорезистентностью, острова пандемичности VSP-I; 2 штамма содержали остров VSP-II. В разных сочетаниях выявлены гены ряда протеаз, cholix-токсина, кластер системы секреции 3-го типа (T3SS), дополнительные кластеры T6SS. Продукты изменённых генов сохраняли либо утрачивали характерные активные домены. В цитотоксине MARTX 6 штаммов отсутствовал ключевой домен ACD, у 4 выявлен новый домен rtxA-like. Кластеры генов биоплёнкообразования варьировали по стуктуре. Присутствие генов антибиотикорезистентности не всегда коррелировало с антибиотикограммами. Все штаммы были чувствительны к большинству антибиотиков, но некоторые проявляли резистентность к 1–4 препаратам.
Выводы. Все изученные штаммы — возбудители отитов, несмотря на выявленные различия, обладают достаточными наборами детерминант, ответственных за реализацию патогенетического и персистентного потенциала. В связи с несовпадением генотипических и фенотипических показателей антибиотикорезистентности при выборе препаратов для этиотропной терапии НАГ-инфекций следует полагаться в основном на фенотип. Выявление на территории России больных отитами, вызванными НАГ-вибрионами, указывает на целесообразность включения тестов на их присутствие в схему бактериологического анализа при внекишечных инфекциях и в случаях их выделения — оперативного определения чувствительности к антибиотикам.
Список литературы
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28. Shi L., Fujihara K., Sato T., Ito H., Garg P., Chakrabarty R., et al. Distribution and characterization of integrons in various serogroups of Vibrio cholerae strains isolated from diarrhoeal patients between 1992 and 2000 in Kolkata, India. J. Med. Microbiol. 2006; 55(Pt. 5): 575–83. https://doi.org/10.1099/jmm.0.46339-0
29. Verma J., Bag S., Saha B., Kumar P., Ghosh T.S., Dayal M., et al. Genomic plasticity associated with antimicrobial resistance in Vibrio cholerae. Proc. Natl Acad. Sci. USA. 2019; 116(13): 6226–31. https://doi.org/10.1073/pnas.1900141116
30. Das B., Verma J., Kumar P., Ghosh A., Ramamurthy T. Antibiotic resistance in Vibrio cholerae: understanding the ecology of resistance genes and mechanisms. Vaccine. 2020; 38(Suppl. 1): A83–92. https://doi.org/10.1016/j.vaccine.2019.06.031
Journal of microbiology, epidemiology and immunobiology. 2022; 99: 465-477
Molecular genetic characteristics of Vibrio cholerae nonO1/nonO139 strains isolated on the territory of Russian Federation from patients with otitis
https://doi.org/10.36233/0372-9311-215Abstract
Introduction. In 2017–2020 for the first time in many years strains of Vibrio cholerae nonO1/nonO139 (NAGs) were isolated in Russia from patients with otitis.
Aim — bioinformatic analysis of whole genome sequences (WGSs) and sequences of individual genes of NAG strains - causative agents of otitis isolated in Russia.
Materials and methods. Analysis of WGSs of eight NAG clinical isolates obtained on the MiSeq Illumina platform was carried out using BioEdit, BLASTN, BLASTP, Vector NTI programs; antibiotic resistance was determined according to MUK 4.2.2495-09.
Results. The strains differed in SNP content, sets of determinants of pathogenicity/persistence factors and their alleles. All lacked CTX, preCTX, RS1 prophages, VPI pathogenicity island, thermostable toxin gene, mobile elements associated with antibiotic resistance, pandemicity island VSP-I; two strains contained VSP-II island. Genes of a number of proteases, cholix toxin, type 3 secretion system (T3SS) cluster and additional T6SS clusters formed different combinations. Products of the altered genes retained or lost their characteristic active domains. In the cytotoxin MARTX of 6 strains, the key ACD domain was absent; in 4 strains a new rtxA-like domain was revealed. Biofilm gene clusters varied in their structure. The presence of genes for antibiotic resistance did not always correlate with antibioticograms. All strains were susceptible to most antibiotics, but some showed resistance to 1–4 drugs.
Conclusion. All the studied strains — causative agents of otitis, in spite of revealed differences, have sufficient sets of determinants responsible for realization of pathogenic and persistent potential. Due to discrepancy between the genotypic and phenotypic characteristics of antibiotic resistance, one should rely mainly on the phenotype when choosing drugs for the etiotropic therapy of NAG infections. Emergence of patients with otitis caused by NAG-vibrios in Russia indicates the advisability of the inclusion of tests for their identification in the scheme of bacteriological analysis for extraintestinal infections and, in cases of their isolation, for prompt determination of sensitivity to antibiotics.
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21. Gadwal S., Johnson T.L., Remmer H., Sandkvist M. C-terminal processing of GlyGly-CTERM containing proteins by rhombosortase in Vibrio cholerae. PLoS Pathog. 2018; 14(10): e1007341. https://doi.org/10.1371/journal.ppat.1007341
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28. Shi L., Fujihara K., Sato T., Ito H., Garg P., Chakrabarty R., et al. Distribution and characterization of integrons in various serogroups of Vibrio cholerae strains isolated from diarrhoeal patients between 1992 and 2000 in Kolkata, India. J. Med. Microbiol. 2006; 55(Pt. 5): 575–83. https://doi.org/10.1099/jmm.0.46339-0
29. Verma J., Bag S., Saha B., Kumar P., Ghosh T.S., Dayal M., et al. Genomic plasticity associated with antimicrobial resistance in Vibrio cholerae. Proc. Natl Acad. Sci. USA. 2019; 116(13): 6226–31. https://doi.org/10.1073/pnas.1900141116
30. Das B., Verma J., Kumar P., Ghosh A., Ramamurthy T. Antibiotic resistance in Vibrio cholerae: understanding the ecology of resistance genes and mechanisms. Vaccine. 2020; 38(Suppl. 1): A83–92. https://doi.org/10.1016/j.vaccine.2019.06.031
