17 November 2022

The human microbiome in the clinic

"Clinical diagnostics and personalized medicine": human microbiome in the clinic


On the first day of the conference "Clinical diagnostics and personalized Medicine", on November 16, 2022, the section "Microbiota as a tool of personalized medicine" was held.


Tatiana Mayatskaya, assistant of the Department of Pediatrics with Infectious Diseases in Children of the N.I.Pirogov RNIMU, presented the results of a study of the intestinal microbiota in children under three years old born to mothers with gestational diabetes mellitus. The composition of the microbiota was different than in the children of women without this diagnosis. Such changes adversely affect the metabolism and can be considered as a predictor of metabolic disorders.

Ekaterina Sorokina (FSBI FNCC of Resuscitation and Rehabilitation, RUDN) stressed that algorithms for normalization of intestinal microbiota in postcovid syndrome are needed and presented data on phage therapy in patients undergoing rehabilitation.

The topic of the microbiome of newborns and young children was continued by Bayr Bembeeva, a bacteriologist at the Institute of Microbiology, Antimicrobial Therapy and Epidemiology of the V.I.Kulakov NMIC AGP. Studies of newborn feces using culturomics and sequencing of bacterial 16S DNA on the first, seventh, 30th day of life, and then a year later demonstrated how the diversity of microorganisms grows over time, from practically sterile primordial feces to microcenosis similar to "adult". Interestingly, supplements with bifidobacteria do not immediately affect the composition of the gastrointestinal microbiome than supplements with lactobacilli; this is probably due to the degree of maturity of toll-like receptors of newborn enterocytes binding bacteria.

Severe complications in cardiac surgery that increase mortality are associated with infections, recalled Ekaterina Chernevskaya, PhD, Senior Researcher, FSBI FNCC of Resuscitation and Rehabilitation. In people with complications, the intestinal microbiome changes, although during hospitalization and discharge it may be similar to the microbiome of healthy people; changes appear already on the day of surgery. It is possible that an early assessment of the composition of the microbiota will reduce the percentage of complications.

Georgy Leonov (FGBUN "FITZ Nutrition and Biotechnology") cited data confirming the influence of periodontitis-associated microorganisms on the risk of developing cardiovascular diseases. Hundreds of species of microorganisms live in the human oral cavity — bacteria and archaea, fungi, protozoa, viruses. The composition of the microbiome is influenced by heredity, alcohol intake and smoking, antibiotic treatment (although to a lesser extent than the gastrointestinal microbiota), diet, socio-economic status, pregnancy. On the other hand, the microbiome of the oral cavity affects a variety of body systems. There are works that show its effect on the state of the cardiovascular system and gastrointestinal tract, even on neurodegenerative diseases such as Alzheimer's disease. The speaker's own research with colleagues showed, in particular, that young people with normal body weight have less Porphyromonas gingivalis bacteria in the oral microbiome that causes gum disease than people of the same age group with obesity, and even more of it in the elderly.

Evgeny Pronkin, Ph.D., Head of the Department of Urology, FGBI FNCC FHM FMBA of Russia, told about PCR diagnostics of antibiotic resistance in urology. Sepsis is a frequent complication of urological diseases, and it is important to determine which drugs the pathogen is sensitive to in order to prescribe treatment. PCR analysis allows you to get the result within 24-48 hours and with high accuracy. As an example, the speaker cited a clinical case in 2019: a 68-year-old woman with a right kidney abscess, a catheter-associated bloodstream infection and a clinical picture of sepsis, received meropenem and vancomycin in the intensive care unit, but there was no improvement for two days. The sowing showed that the infection was caused by klebsiella, and PCR analysis confirmed resistance to carbapenems. The appointment of amikacin and tigecycline improved the situation and may have saved the patient. This technique has been used in the urology department for about 4 years: if there are bacteria in the urine culture that are not sensitive to any drugs, it is possible to pick up an antibiotic using PCR. Evgeny Pronkin added that incorrectly prescribed antibiotic therapy is harmful in all respects. Unfortunately, PCR analysis is not yet performed by the CHI.

The report of Alina Melkumyan, Ph.D., Head of the Center for Laboratory Diagnostics of the Inozemtsev State Clinical Hospital, was called "Changes in the microbiome in bacterial infections and their relationship with the severity and outcomes of the disease." Although cultivation remains the gold standard — only it allows to obtain a pure culture, to study the bacterium phenotypically, finally, in modern conditions it can be combined with mass spectrometry. — PCR analysis has its advantages. The availability of PCR diagnostics has increased dramatically during COVID-19, and genome sequencing is also getting cheaper.

The report examined specific examples of the pathogenic effects of certain components of the microbiome. Clostridium difficile is often found in children, and in adults it can cause antibiotic-associated diarrhea or pseudomembranous colitis. Streptococcus agalactiae belongs to the normoflora, but is the causative agent of neonatal infections and the cause of infant mortality. Finally, Lactobacillus iners, despite belonging to the "good" genus Lactobacillus, is associated with a predisposition to bacterial vaginosis. In pregnant women, L.iners infection may be associated with premature birth. In addition, lactobacilli, as permanent inhabitants of the lower genital tract, can be a reservoir of resistance genes (resistome) and transmit them to transit bacteria.

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