Key features of pneumococcal isolates recovered in Central and Northwestern Russia in 2011-2018 determined through whole-genome sequencing.

Invasive pneumococcal disease remains one of the leading causes of morbidity and mortality worldwide. In Russia, 13- valent pneumococcal conjugate vaccine (PCV13) was introduced into the childhood immunization programme nationwide in 2014. As part of the Global Pneumococcal Sequencing Project (GPS), we used genome data to characterize 179 pneumococcal isolates collected from Russia in 2011-2018 to investigate the circulating pneumococcal strains using a standardized genomic definition of pneumococcal lineages (global pneumococcal sequence clusters, GPSCs), prevalent serotypes and antimicrobial resistance profiles.We observed high serotype and lineage diversity among the 179 isolates recovered from cerebrospinal fluid (n=77), nasopharyngeal swabs (n=99) and other non-sterile site swabs (n=3). Overall, 60 GPSCs were identified, including 48 clonal complexes (CCs) and 14 singletons, and expressed 42 serotypes (including non-typable). Among PCV13 serotypes, 19F, 6B and 23F were the top three serotypes while 11A, 15B/C and 8 were the top three among non-PCV13 serotypes in the collection. Two lineages (GPSC6 and GPSC47) expressed both PCV13 and non-PCV13 serotypes that caused invasive disease, and were penicillin- and multidrug-resistant (MDR), highlighting their potential to adapt and continue to cause infections under vaccine and antibiotic selective pressure. PCV13 serotypes comprised 92 % (11/12) of the CSF isolates from the children aged below 5 years; however, the prevalence of PCV13 serotype isolates dropped to 53 % (31/58) among the nasopharyngeal isolates. Our analysis showed that 59 % (105/179) of the isolates were predicted to be non-susceptible to at least one class of antibiotics and 26 % (46/179) were MDR. Four MDR lineages (GPSC1, GPSC6, GPSC10 and GPSC47) accounted for 65 % (30/46) of the MDR isolates and expressed PCV13 serotypes (93 %, 28/30).This study provides evidence of high genetic and serotype diversity contributed by a mix of globally spreading and regionally circulating lineages in Russia. The observations suggest that the PCV13 vaccine could be important in reducing both invasive disease and antimicrobial resistance. We also identify potential lineages (GPSC6 and GPSC47) that may evade the vaccine.

Characteristics of Stenotrophomonas maltophilia isolates from cystic fibrosis patients in Russia.

Stenotrophomonas maltophilia is a common opportunistic microorganism and an important respiratory pathogen in cystic fibrosis (CF). The aim of this study was to determine antimicrobial resistance phenotypes, sequence-types (ST) and genetic determinants of antibiotic resistance in S. maltophilia strains recovered from CF patients in Russia. S. maltophilia isolates recovered from 170 CF patients were analyzed. Minimum inhibitory concentrations of antibacterial agents were determined using Sensititre Gram Negative GNX2F plates and the results were interpreted according to Clinical and Laboratory Standards Institute (CLSI) criteria. Whole-genome sequencing (WGS) was performed on MGISEQ-2000 platform. SPAdes software, Galaxy, ResFinder, Integrall and PubMLST were used for analysis of WGS data. S. maltophilia strains were identified from 24/170 (14%) CF patients. In total, 25 isolates were detected, two strains were isolated from the same patient. The isolates belonged to 17 different STs, including 5 new STs; ST4 was the most prevalent ST. Resistance to ceftazidime was observed in 60% of strains, to ticarcillin-clavulanate - in 32%, to levofloxacin - in 24%, to trimethoprim/sulfamethoxazole - in 12% of strains. All isolates were susceptible to minocycline. All ST4 isolates were resistant or intermediate to ceftazidime and ticarcillin-clavulanate. In two isolates, the sul1 gene was detected. In one isolate, sul1 was part of a class 1 integron. The detected integron also contained the blaGES-7 and aac(6')-Ib-cr genes. The ST4 sequence-type was the most prevalent ST among S. maltophilia strains recovered from CF patients in Russia. Antibiotic resistance genes, including sul1, blaGES-7, aac(6')-Ib-cr, were detected in single strains.

Identification of bacterial antibiotic resistance genes in next-generation sequencing data (review of literature).

The spread of antibiotic-resistant human bacterial pathogens is a serious threat to modern medicine. Antibiotic susceptibility testing is essential for treatment regimens optimization and preventing dissemination of antibiotic resistance. Therefore, development of antibiotic susceptibility testing methods is a priority challenge of laboratory medicine. The aim of this review is to analyze the capabilities of the bioinformatics tools for bacterial whole genome sequence data processing. The PubMed database, Russian scientific electronic library eLIBRARY, information networks of World health organization and European Society of Clinical Microbiology and Infectious Diseases (ESCMID) were used during the analysis. In this review, the platforms for whole genome sequencing, which are suitable for detection of bacterial genetic resistance determinants, are described. The classic step of genetic resistance determinants searching is an alignment between the query nucleotide/protein sequence and the subject (database) nucleotide/protein sequence, which is performed using the nucleotide and protein sequence databases. The most commonly used databases are Resfinder, CARD, Bacterial Antimicrobial Resistance Reference Gene Database. The results of the resistance determinants searching in genome assemblies is more correct in comparison to results of the searching in contigs. The new resistance genes searching bioinformatics tools, such as neural networks and machine learning, are discussed in the review. After critical appraisal of the current antibiotic resistance databases we designed a protocol for predicting antibiotic resistance using whole genome sequence data. The designed protocol can be used as a basis of the algorithm for qualitative and quantitative antimicrobial susceptibility testing based on whole genome sequence data.

Genome features and antibiotic resistance of Pseudomonas aeruginosa strains isolated in patients with cystic fibrosis in the Russian Federation.

Cystic fibrosis (CF) is a common genetic disease, manifested by airway obstruction and chronic respiratory infection. The most prevalent infectious agent in airways of CF patients is Pseudomonas aeruginosa. This study aimed to determine sequence-types, antimicrobial resistance phenotypes and genes defining adaptive antibiotic resistance in P. aeruginosa isolates recovered from CF patients in Russia. In total, 84 P. aeruginosa strains from 64 CF patients were analyzed. Susceptibility to antibiotics was determined by disk diffusion test. Whole-genome sequencing (WGS) was performed on MGISEQ-2000 platform. SPAdes software, Galaxy, ResFinder, PubMLST were used for analysis of WGS data. Examined P. aeruginosa isolates belonged to 53 different sequence-types (STs), including 6 new STs. High-risk epidemic clone ST235 (10%) and clonal CF P. aeruginosa strains ST17, ST242, ST274 (7%) were detected. Non-susceptibility to ticarcillin-clavulanate, cefepime, imipenem was observed in 63%, 12% and 25% of isolates, respectively; to tobramycin - in 24%, to amikacin - in 35%; to ciprofloxacin, levofloxacin - in 35% and 57% of strains, respectively. Multidrug-resistant phenotype was detected in 18% of isolates. In examined strains, genes of beta-lactamases VIM-2 (5 ST235 strains), VEB-1 (two ST2592 strains), GES-1 (1 ST235 strain), PER-1 (1 ST235 strain) were found. Ciprofloxacin-modifying enzyme CrpP gene was detected in 67% of isolates, aminoglycoside-modifying enzymes AAD, ANT, AAC genes - in 7%, 4%, 12% of strains, respectively. P. aeruginosa isolates from CF patients in Russia demonstrate a high clonal diversity, which is similar to other P. aeruginosa infections. The isolates of high-risk clone and clonal CF P. aeruginosa strains are detected.

Application of the Theoretical Domains Framework to identify factors that influence hand hygiene compliance in long-term care.

BACKGROUND: Healthcare worker (HCW) hand hygiene compliance is key to patient safety; however, compliance is suboptimal. Nevertheless hand hygiene compliance is not well studied in the long-term care setting. AIM: To apply a behaviour change framework, the Theoretical Domains Framework (TDF), to identify modifiable facilitators and barriers for HCW hand hygiene compliance in long-term care settings. METHODS: HCW hand hygiene compliance facilitators and barriers were examined using a questionnaire for HCWs from long-term care homes in Ontario, Canada. The questionnaire was informed by the TDF, which is based on a synthesis of constructs from a number of relevant psychological theories of behaviour change. FINDINGS: Barriers identified from the questionnaire aligned with the TDF domain environmental context and resources (time pressure, workload, and environmental controls). Facilitators identified from questionnaire results aligned with the TDF domains social/professional role and identity (it is what is expected of HCWs), and beliefs about consequences (risk of transmission of micro-organisms to self or others). CONCLUSION: There are several barriers to hand hygiene compliance that persist in long-term care. A behaviour change theory-informed framework such as the TDF can be helpful to identify those barriers. This study identified several key behavioural constructs aligned with the TDF that can be targeted when developing novel hand hygiene interventions.

Noncontiguous finished genome sequence of Megasphaera sp. ASD88, isolated from faeces of a child with autism spectrum disorder.

We report here a draft genome sequence of Megasphaera sp. ASD88, a strain from the intestinal microbiota of a child with autism spectrum disorder, representing a previously undescribed species of the genus Megasphaera. The assembled sequence consists of 88 scaffolds, and the total size is 2.59 Mb.

[Comparative Genotyping of Staphylococcus aureus Strains Isolated from Skin Lesions, Nasal Cavities, and Feces of Children with Atopic Dermatitis].

Background: The lesion of skin of the majority atopic dermatitis patients is chronically colonized by bacteria belonging to the species Staphylococcus aureus. Topical antibacterial and anti-inflammatory therapy treatment are often ineffective due to fast recolonization by S. aureus and exacerbation of allergic process. Aims: Our aim was to determine a frequency of S. aureus colonization in skin lesions, mucous membranes of the nasal cavity and intestine of children with atopic dermatitis, to compare the genotypes of Staphylococcus aureus strains isolated from different biotopes of atopic dermatitis patients, and to clarify whether the intestinal and nasal cavities microbiota may act as a source of S. aureus recolonization of skin lesions. Materials and Methods: Bacteriological examination of fecal samples, skin, and nasal swabs was conducted in 38 atopic dermatitis patients. The pure bacterial cultures of S. aureus were identified using API Staph (Biomerieux, France) and Vitek 2 MS (Biomerieux, France). Isolates of S. aureus were subjected to genotyping by analysis of rRNA internal 16S-23S rRNA spacer regions and high resolution melting analysis (HMR) of polymorphic spa X-regions. Results: 99% S. aureus strains were successfully identified using MALDI-TOF mass-spectrometry. S. aureus cultures were isolated from all biotopes in 31,6% of children, from skin and nasal cavities ­ in 42% of cases, from skin and feces ­ in 2,6% of cases, only from skin ­ in 10,5%, from nasal cavities and feces ­ in 2,6%, and only from nasal cavities ­ in 2,6% of cases. In 8% of children, S. aureus was not detected in any of the biotopes. Genotyping of the isolates enabled the detection of 17 different genotypes. A match between the genotypes of skin and nasal strains, and skin and fecal strains was observed in 88% and 61% of the cases respectively. Conclusions: The observed a high-frequency matching genotypes suggests the possibility of migration of S. aureus strains inside biotopes in humans and the absence of specialization to colonization of any of the niches.

[Species Diversity of Bifidobacteria in the Intestinal Microbiota Studied Using MALDI-TOF Mass-Spectrometry].

BACKGROUND: The members of genus Bifidobacterium represent a significant part of intestinal microbiota in adults and predominate in infants. Species repertoire of the intestinal bifidobacteria is known to be subjected to major changes with age; however, many details of this process are still to be elucidated. OBJECTIVE: Our aim was to study the diversity of intestinal bifidobacteria and changes of their qualitative and quantitative composition characteristics during the process of growing up using MALDI-TOF mass-spectrometric analysis ofpure bacterial cultures. METHODS: A cross-sectional study of bifidobacteria in the intestinal microbiota was performed in 93 healthy people of the ages from 1 month to 57 years. Strains were identified using Microflex LT MALDI-TOF MS, the confirmation was performed by 16S rRNA gene fragment sequencing. RESULTS: 93% of isolated bifidobacterial strains were successfully identified using MALDI-TOF mass-spectrometry. At least two of the strains from each species were additionally identified by 16S rRNA gene fragment sequencing, in all of the cases the results were the same. It was shown that the total concentration of bifidobacteria decreases with age (p<0.001) as well as the frequency of isolation of Bifidobacterium bifidum (p=0.020) and Bifidobacterium breve (p<0.001), and the frequency of isolation of Bifidobacterium adolescentis, increases (p<0.001), representing the continuous process of transformation of microbiota. CONCLUSION: The method of MALDI-TOF mass spectrometry demonstrated the ability to perform rapid and reliable identification of bifidobacteria that allowed the study of changes in the quantitative and qualitative characteristics of human microbiota in the process of growing up.

Draft Genome Sequence of Lactobacillus fermentum NB-22.

We announce here a draft genome sequence of Lactobacillus fermentum NB-22, a strain isolated from human vaginal microbiota. The assembled sequence consists of 190 contigs, joined into 137 scaffolds, and the total size is 2.01 Mb.

Draft Genome Sequence of Coprobacter fastidiosus NSB1T.

Coprobacter fastidiosus is a Gram-negative obligate anaerobic bacterium belonging to the phylum Bacteroidetes. In this work, we report the draft genome sequence of C. fastidiosus strain NSB1(T) isolated from human infant feces.

Draft Genome Sequences of Two Pairs of Human Intestinal Bifidobacterium longum subsp. longum Strains, 44B and 1-6B and 35B and 2-2B, Consecutively Isolated from Two Children after a 5-Year Time Period.

We report the genome sequences of four isolates of a human gut symbiont, Bifidobacterium longum. Strains 44B and 35B were isolated from two 1-year-old infants, while 1-6B and 2-2B were isolated from the same children 5 years later. The sequences permit investigations of factors enabling long-term colonization of bifidobacteria.

Effects of clinical service reorganisation on cellular pathology workload.

AIMS: To assess changes in volume and complexity of cellular pathology workload after clinical service reorganisation and alterations in pathology reporting practices, and to identify objective measures of change applicable to all cellular pathology departments. The ear, nose, and throat (ENT), head and neck (HN) specialty was chosen for assessment. METHODS: Cellular pathology workload from the ENT-HN surgical specialty was assessed numerically and the complexity in examination of cancer resection specimens was evaluated. Medical and technical time inputs in the reporting of ENT-HN cancer resections were measured prospectively, and the histological and cytological workload arising from the management of such cases was obtained. RESULTS: The 88.83% increase in ENT-HN specimens contrasted with a 13.53% increase in total surgical workload. Substantial increases in work complexity were found when measured as blocks/slides for each case and number of histochemical/immunohistochemical requests. On average, examination of one ENT-HN cancer case consumed 55% of one pathologist's work session and over one 10th of a technician's working week. On average, each cancer generated 3.3 histological and 1.06 cytological specimens. CONCLUSIONS: Evidence is provided of the increase in cellular pathology workload and in its complexity. This study lists objective measures of complexity applicable to all pathology subspecialties. Given the workforce crisis and expanding clinical needs, realistic workload calculations should include measurement of complexity and not just volumes.

Prevalence of lower gastrointestinal symptoms and associated consultation behaviour in a British elderly population determined by face-to-face interview.

BACKGROUND: The incidence of organic lower gastrointestinal disease increases with age. However, the prevalence of lower gastrointestinal symptoms in a British elderly population is unclear, with previous epidemiological studies focusing on younger populations. Furthermore, there is little information about consultation behaviour associated with lower gastrointestinal symptoms. AIM: To determine the prevalence of lower gastrointestinal symptoms reported by randomly selected, elderly community subjects. METHODS: An age- and sex-stratified random sample of patients aged 65 years and over was drawn from a general practice register (n = 842). Those who had not refused to participate in an initial postal survey were invited to participate in a semi-structured physician interview at their own home to assess lower gastrointestinal symptomatology (n = 745). Non-participation bias and service use of all subjects were assessed from practice records. RESULTS: Five hundred and ninety-six (71%) patients were interviewed. Fifty-seven per cent of all participants had at least one lower gastrointestinal symptom. Individual symptoms and symptom complexes were common, affecting up to 32% of subjects. Only 24% of subjects with lower gastrointestinal symptoms consulted their general practitioner (GP) with such symptoms in the previous year. As few as 31% of subjects with new onset of the significant symptoms of rectal bleeding, abdominal pain, and a change in bowel habit consulted their GP. CONCLUSION: Lower gastrointestinal symptoms are common in a British elderly population and an important reason for GP consultation.

The use of histological techniques for the demonstration of ion exchange resins.

AIM: To establish the staining characteristics of certain ion exchange resins in histological material, with a view to enabling confident differential identification. METHODS: Various histological staining procedures were applied to selected pathological material and prepared agar blocks containing the cation exchange resin calcium polystyrene sulphonate and the anion exchange resin cholestyramine. RESULTS: Calcium polystyrene sulphonate uniquely stained strongly by a direct Schiff's reagent procedure without any preoxidation and by the Ziehl-Neelsen method. Cholestyramine was negative by the former method but stained strongly with a standard Congo red technique. CONCLUSIONS: These staining results are consistent with the known structure and properties of polystyrene sulphonate and cholestyramine resins. Polystyrene sulphonate resins have the virtually pathognomonic feature of direct Schiff positivity, while morphology, location, and strong non-birefringent Congo red positivity facilitate the identification of cholestyramine. It is possible that the intrinsic staining characteristics of cholestyramine may be lost once it has bound to its target.

Subcutaneous deposition of beta 2-microglobulin amyloid in a long-term haemodialysis patient.

Subcutaneous deposition of beta 2-microglobulin (beta 2-M) amyloid is an uncommon finding in uraemic patients on long-term haemodialysis. A 60-year-old female on haemodialysis for 16 years developed a subcutaneous haematoma 2 years prior to death. At necropsy the lesion contained numerous deposits of beta 2-M amyloid as well as evidence of old haemorrhage, fibrous repair, dystrophic calcification and calcium oxalate crystal deposition. Highly sulphated glycosaminoglycans were present in the amyloid deposits. beta 2-M amyloid deposits were also present in the hip joint, cervical and lumbar spine, and in small blood vessels of the heart, liver, and lung. The possible role of trauma and tissue glycosaminoglycans changes in the formation of subcutaneous amyloid tumours is discussed.

Purification and characterization of recombinant human interleukin 4. Biological activities, receptor binding and the generation of monoclonal antibodies.

A synthetic gene coding for human interleukin 4 (IL-4) was cloned and expressed in Saccharomyces cerevisiae (baker's yeast) as a C-terminal fusion protein with the yeast prepro alpha-mating factor sequence, resulting in secretion of mature IL-4 into the culture medium (0.6-0.8 micrograms/ml). A protocol was developed for purification of this protein. Crude cell-free conditioned medium was passed over a concanavalin A-Sepharose affinity column; bound proteins were eluted and further purified by S-Sepharose Fast Flow cation exchange and C18 reverse-phase h.p.l.c. Highly purified IL-4 was obtained by this method (0.3-0.4 mg per litre of culture) with a recovery of 51%. Thermospray liquid chromatography-mass spectrometry showed the C-terminal N-glycosylation site to be largely unmodified, and also showed that the N-terminus of the purified recombinant IL-4 (rIL-4) was authentic. Thiol titration revealed no free cysteine residues, implying that there are three disulphide groups, the positions of which remain to be determined. We have characterized the biological activities of the purified rIL-4. This material is active in B-cell co-stimulator assays, T-cell proliferation assays and in the induction of cell-surface expression of CD23 (the low-affinity receptor for IgE) on tonsillar B-cells. Half-maximal biological activity of the rIL-4 was achieved at a concentration of 120 pM. We have radioiodinated rIL-4 without loss of biological activity and performed equilibrium binding studies on Raji cells, a human B-cell line. The 125I-rIL-4 bound specifically to a single class of binding studies on Raji cells, a human B-cell line. The 125I-rIL-4 bound specifically to a single class of binding site with high affinity (Kd = 100 pM) and revealed 1100 receptors per cell. Receptor-ligand cross-linking studies demonstrated a single cell-surface receptor with an apparent molecular mass of 124 kDa. Two monoclonal antibodies have been raised to the human rIL-4, one of which blocks both the biological activity of rIL-4 and binding to its receptor.

Use of betapropiolactone to disinfect fresh tissue without impairing antigenicity: method applicable to human immunodeficiency virus (HIV) positive tissue.

A method for inactivating viruses in tissues is reported that does not impair the antigenicity of the Coxsackie virus or of some common tissue antigens, a common problem with standard tissue fixation methods. Tissues can be placed briefly in Betapropiolactone before cryostat sectioning without any adverse effect on preservation or antigen expression. It is suggested that use of Betapropiolactone is applicable to tissues harbouring or exposed to the human immunodeficiency virus (HIV). As betapropiolactone has been reported to be carcinogenic in rodents any potential danger can be avoided by basic simple precautions.

Chrysiasis: transmission electron microscopy, laser microprobe mass spectrometry and epipolarized light as adjuncts to diagnosis.

Two patients receiving gold therapy for rheumatoid arthritis developed skin pigmentation, chrysiasis, which in one appeared 4 months after cessation of the therapy. The diagnosis was confirmed by transmission electron microscopy and mass spectrometry laser microprobe analysis of paraffin sections and its extent demonstrated by epipolarized light. The condition is poorly reported and clinically may be confused with silver and mercury impregnation. Tissue diagnosis requires ancillary methods and of these, transmission electron microscopy and laser microprobe mass spectrometry are excellent examples. The transmission electron microscopy findings differ from previous reports and raise doubts on the hypothesis on the role of the skin in gold excretion. Because of the renewed interest in crysotherapy and the latent period that can separate this from chrysiasis, an increase in chrysiasis and the need for its diagnosis can be anticipated.