Detection of causative agents of tick-borne rickettsioses in Western Siberia, Russia: identification of Rickettsia raoultii and Rickettsia sibirica DNA in clinical samples

Summary Cystic echinococcosis (CE) and alveolar echinococcosis (AE) are considered as one of the most important zoonotic diseases in Romania, where they are subject to mandatory reporting. To obtain more knowledge about the genetic diversity of Echinococcus causative agents of these diseases, 11 isolates from humans and ungulate intermediate hosts from the two regions of Romania were genotyped using mitochondrial markers. In clinical samples of five patients from north-eastern Romania (Iasi, Botosani, Vaslui counties), Echinococcus multilocularis was identified as causal agent by cox1 sequence analysis. To the best of our knowledge this finding presents the first molecular evidence of E. multilocularis in humans from Romania. Only two cases of AE in patients were previously documented in the country by serological methods. In our four patients the most widespread European variant E5 of E. multilocularis was recorded, whereas in isolate from Vaslui county three nucleotide substitutions were detected as compared to the most related E5 haplotype. One of these mutations (411T/G) matched N1 and N2 haplotypes described previously from North America. In six CE samples retrieved from western Romania (Caras-Severin and Timis counties), two human isolates were diagnosed as Echinococcus canadensis G7, one as E. granulosus s.s. G1 and one as E. granulosus s.s. G3 using atp6 and rrnS sequencing. In ungulates, the cattle isolate was allocated to E. granulosus s.s. G1 and pig isolate to E. canadensis G7. The two G7 findings in humans reinforced the recent view that G7 was underestimated as compared to the E. granulosus s.s. regarding human CE threat that can be further employed for identifying sources of infections and establishing suitable preventive measures.

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IDENTIFYING OF HUMAN METAPNEUMOVIRUS AND ITS PHENOTYPE AS A CAUSATIVE AGENTS OF PNEUMONIA IN CHILDREN

Asian Journal of Pharmaceutical and Clinical Research ◽

10.22159/ajpcr.2018.v11i4.25578 ◽

2018 ◽

Vol 11 (4) ◽

pp. 450 ◽

Cited By ~ 1

Author(s):

Abbas Mohammed Hussein Al-shebani ◽

Adnan Hamad Aubaid

Keyword(s):

Phylogenetic Tree ◽

Respiratory Illness ◽

Human Metapneumovirus ◽

Clinical Samples ◽

Phylogenetic Tree Analysis ◽

Causative Agents ◽

Respiratory Tract Illness ◽

Respiratory Syncytial Viruses ◽

Ncbi Blast ◽

Tree Method

Objectives: The present investigational study was aimed to detect and identify the genotypes of Human metapneumovirus (hMPV) and its phylogeny with respiratory syncytial viruses (RSV) that cause pulmonary inflammation.Material and Methods: A total of 250 samples of patients who were clinically diagnosed respiratory tract illness were collected from Maternity and Children Hospital in Al Diwaniyah city, Iraq. The clinical samples were nasopharyngeal, nasal and throat swabs. The current study screened the presence of hMPV and RSV (A and B) genotypes from nasopharyngeal specimens of children aged from several days to 10 years old.Results: The results revealed that 6% were infected with hMPV, 8% of respiratory syncytial viruses type A (RSV-A) and 14% of respiratory syncytial virus’s type B (RSV-B) from children who are suffering from respiratory illness. Phylogenetic tree analysis of hMPV based on the partial sequences of the fusion protein (F) gene was used for genotyping and detection. The phylogenetic tree was constructed using maximum likelihood tree method in MEGA 6.0 version. The local hMPV isolates (S1) were closely related to NCBI-Blast hMPV genotype A1 (KM408076.1), the local hMPV isolates (S2, S3, and S5) were closely related to NCBI-Blast hMPV genotype B1 (KJ196323.1), and the local hMPV isolates (S4) were closely related to NCBI-Blast hMPV genotype B2 (JQ041689.1).Conclusions: The prevalence rate of hMPV is less than RSV, and both subtypes of hMPV, A and B may exist and circulate in one season, and the predominant sublineage of hMPV shifts in progressive season.

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Diagnosis and Management of Cervicofacial Actinomycosis: Lessons from Two Distinct Clinical Cases

Antibiotics ◽

10.3390/antibiotics9040139 ◽

2020 ◽

Vol 9 (4) ◽

pp. 139 ◽

Cited By ~ 6

Author(s):

Anette Stájer ◽

Barrak Ibrahim ◽

Márió Gajdács ◽

Edit Urbán ◽

Zoltán Baráth

Keyword(s):

Clinical Course ◽

Epidemiological Data ◽

Clinical Samples ◽

Ionization Mass ◽

Tissue Destruction ◽

Isolation And Identification ◽

Gram Positive Bacteria ◽

Causative Agents ◽

Medical Histories ◽

Specific Symptoms

Members of the Actinomyces genus are non-spore-forming, anaerobic, and aerotolerant Gram-positive bacteria that are abundantly found in the oropharynx. They are the causative agents of actinomycosis, a slowly progressing (indolent) infection with non-specific symptoms in its initial phase, and a clinical course of extensive tissue destruction if left untreated. Actinomycoses are considered to be rare; however, reliable epidemiological data on their prevalence is lacking. Herein, we describe two representative and contrasting cases of cervicofacial actinomycosis, where the affected patients had distinctively different backgrounds and medical histories. Identification of the relevant isolates was carried out using matrix-assisted laser desorption/ionization mass spectrometry; antimicrobial susceptibility was performed using E-tests. Cervicofacial actinomycoses are the most frequent form of the disease; isolation and identification of these microorganisms from relevant clinical samples (with or without histological examination) is the gold standard for diagnosis. The therapy of these infections includes surgical debridement and antibiotic therapy, mainly with a penicillin-derivative or clindamycin.

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Study protocol: The clinical features, epidemiology, and causes of paediatric encephalitis in southern Vietnam

Wellcome Open Research ◽

10.12688/wellcomeopenres.16770.2 ◽

2021 ◽

Vol 6 ◽

pp. 133

Author(s):

Nguyen Hoang Thien Huong ◽

Nguyen Duc Toan ◽

Du Tuan Quy ◽

Truong Huu Khanh ◽

Le Quoc Thinh ◽

...

Keyword(s):

Autoimmune Encephalitis ◽

Indirect Costs ◽

Vaccination Strategy ◽

Altered Mental Status ◽

Clinical Syndrome ◽

Clinical Samples ◽

Southern Vietnam ◽

Causative Agents ◽

Incidence Of Hospitalization ◽

Study Participants

Encephalitis is a major cause of morbidity and mortality worldwide. The clinical syndrome of encephalitis consists of altered mental status, seizures, neurologic signs, and is often accompanied by fever, headache, nausea, and vomiting. The encephalitis in children has been known that more common than in adult, with the incidence rate of infants was 3.9 times higher than that of people 20-44 years of age. The reported incidence of hospitalization attributed to paediatric encephalitis ranged from 3 to 13 admissions per 100,000 children per year with the overall mortality ranging from 0 to 7%. There are however more than 100 pathogens that can cause encephalitis and accurate diagnosis is challenging. Over 50% of patients with encephalitis are left undiagnosed despite extensive laboratory investigations. Furthermore, recent studies in high-income settings have suggested autoimmune encephalitis has now surpassed infectious aetiologies, mainly due to increased awareness and diagnostic capacity, which further challenges routine diagnosis and clinical management, especially in developing countries. There are limited contemporary data on the causes of encephalitis in children in Vietnam. Improving our knowledge of the causative agents of encephalitis in this resource-constrained setting remains critical to informing case management, resource distribution and vaccination strategy. Therefore, we conduct a prospective observational study to characterise the clinical, microbiological, and epidemiological features of encephalitis in a major children’s hospital in southern Vietnam. Admission clinical samples will be collected alongside meta clinical data and from each study participants. A combination of classical assays (serology and PCR) and metagenomic next-generation sequencing will used to identify the causative agents. Undiagnosed patients with clinical presentations compatible with autoimmune encephalitis will then be tested for common forms of the disease. Finally, using direct- and indirect costs, we will estimate the economic burden of hospitalization and seven days post hospital discharge of paediatric encephalitis in our setting.

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Molecular characterization of ESBL gene in Citrobacter spp. and antibacterial activity of omega-3 against resistant isolates

Current Issues in Pharmacy and Medical Sciences ◽

10.1515/cipms-2017-0029 ◽

2017 ◽

Vol 30 (3) ◽

pp. 156-161

Author(s):

Mayyada F. Darweesh

Keyword(s):

Antibacterial Activity ◽

Confirmatory Test ◽

Multi Drug Resistance ◽

Clinical Samples ◽

Resistance Pattern ◽

Resistant Bacteria ◽

Omega 3 ◽

Causative Agents ◽

Esbl Producers

Abstract The study aimed to investigate the prevalence and resistance pattern of different Citrobacter spp., phenotypically and genotypically, to β-lactam antibiotics, then to evaluate the antibacterial activity of omega-3 extracted from flaxseed against isolates that harboring resistance genes. Herein, 19 Citrobacter isolates were isolated from 100 stool and urine samples taken from patients attended to AL-Sadar Hospital during June- December 2016. Clinical samples were then cultured on specific media, thereafter, isolates were identified depending on morphological, biochemical characteristics and VITK-2. The results showed that the Citrobacter spp. comprise 19/78 (24%) of positive bacterial growth on macConky agar, from which 14.1% were C. freundii, C. koseri represented 6.1% and C. farmeri were 3.8% of the total. The results of antibiotic susceptibility showed that all Citrobacter 100% isolates were resistant to ampicillin and cefoxitin, but were sensitive to imipinim. Moreover, the isolates initally showed different degrees of resistant to β-lactam antibiotics. Furthermore, by confirmatory test, the results observed that 17/19 (89.4%) of the isolated were extended-spectrum β-lactamase (ESBL - producers). Finally, using the PCR technique to detect blaGenes, the results revealed that 14/17 (82.3) of potential ESBL producing Citrobacter harbored one or more ESBL genes. These included 10 isolates of C. freundii and 4 isolates of C. koseri. In related work, extracts of essential fatty acid semicarbazide - omega3 (EFASC) from Linum usitatissium (Flaxseed) were tested to evaluate their activity against resistant isolates. The results demonstrate the broad spectrum antibacterial property of EFASC compounds against resistant bacteria. In conclusion, this study found increase prevalence of multi-drug resistance MDR Citrobacter spp. as causative agents in clinical cases. Considering the antibacterial activity of EFASC that displayed high activity against resistant pathogens, deservedly, attention must be paid to developing their use as alternative antibiotics.

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Epidemiological and clinical features of cutaneous leishmaniases in Jenin District, Palestine, including characterisation of the causative agents in clinical samples

Transactions of the Royal Society of Tropical Medicine and Hygiene ◽

10.1016/j.trstmh.2012.06.005 ◽

2012 ◽

Vol 106 (9) ◽

pp. 554-562 ◽

Cited By ~ 17

Author(s):

Kifaya Azmi ◽

Gabriele Schönian ◽

Abedelmajeed Nasereddin ◽

Lionel F. Schnur ◽

Samir Sawalha ◽

...

Keyword(s):

Clinical Features ◽

Clinical Samples ◽

Causative Agents

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Influence of biologization and chemicalization factors on the phytosanitary state of barley in the forest-steppe of Western Siberia

Bulletin of NSAU (Novosibirsk State Agrarian University) ◽

10.31677/2072-6724-2021-58-1-7-16 ◽

2021 ◽

pp. 7-16

Author(s):

L. F. Ashmarina ◽

R. F. Galeev ◽

O. N. Shashkova ◽

A. I. Ermokhina

Keyword(s):

Root Rot ◽

Western Siberia ◽

Bipolaris Sorokiniana ◽

Inhibitory Effect ◽

Mineral Fertilizers ◽

Forest Steppe ◽

Similar Data ◽

Development Index ◽

Primary Roots ◽

Causative Agents

The research was carried out to study the influence of biologization and chemicalization factors on the phytosanitary state of barley in the chain of the six-field fodder crop rotation of the second rotation in the forest-steppe of Western Siberia. The biologization factor was considered sowing peas to barley. The chemicalization factor was considered as the introduction of mineral fertilizers according to the results of agrochemical analysis at a dose of N60P20. It was found that the highest development of root rot was found in the variant with sowing barley without fertilizers, where the disease development index reached an average of 14.4% for the plant. The lowest one is in the variant “barley + peas + fertilizers’ (4.6%). In the variants “barley + peas’ and “barley + fertilizer”, the intensity of the disease was approximately the same and within the limits of the severity threshold – from 6.6 to 6.9 %. Similar data were obtained for the prevalence of the disease. Among the analyzed organs, the primary roots had the greatest damage, which was due to significant infection with Bipolaris sorokiniana Sacc. Damage by leaf-stem infections was almost 2 times lower in the variant with the use of the legume component and the application of fertilizers (16.8%) versus the control variant (31.8%). It was found that the correlation coefficient of the root rot development index on average for a plant with productive tillering was r = –0.63, and with plant height r = –0.99. Confirmation of the harmfulness of root rot is a close negative correlation between the yield and the indicators of the development of the disease on average for the plant: r = –0.74. It was found that the most favorable phytosanitary situation developed in the variant of sowing barley with the use of fertilizers and a legume component, which is associated with the healing effect of fertilizers and legumes, which is reflected, on the one hand, in increasing the endurance of the plant itself, and on the other, in an inhibitory effect on causative agents of the disease.

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Detection of Microbial Agents in Oropharyngeal and Nasopharyngeal Samples of SARS-CoV-2 Patients

Frontiers in Microbiology ◽

10.3389/fmicb.2021.637202 ◽

2021 ◽

Vol 12 ◽

Author(s):

Tyler Seckar ◽

Xiang Lin ◽

Dipayan Bose ◽

Zhi Wei ◽

Joseph Rohrbaugh ◽

...

Keyword(s):

Diagnostic Techniques ◽

Clinical Samples ◽

Respiratory Pathogens ◽

The Novel ◽

Respiratory Illnesses ◽

Viral Genomes ◽

Global Pandemic ◽

Causative Agents ◽

Novel Coronavirus ◽

Microbial Agents

The novel coronavirus outbreak started in December 2019 and rapidly spread around the globe, leading to a global pandemic. Here we reported the association of microbial agents identified in oropharyngeal and nasopharyngeal samples from patients with SARS-CoV-2 infection, using a Pan-microarray based technology referred to as PathoChIP. To validate the efficiency of PathoChIP, reference viral genomes obtained from BEI resource and 25 SARS-CoV-2 positive clinical samples were tested. This technology successfully detected femtogram levels of SARS-CoV-2 viral RNA, which demonstrated greater sensitivity and specificity than conventional diagnostic techniques. Simultaneously, a broad range of other microorganisms, including other viruses, bacteria, fungi and parasites can be detected in those samples. We identified 7 viral, 12 bacterial and 6 fungal agents common across all clinical samples suggesting an associated microbial signature in individuals who are infected with SARS-CoV-2. This technology is robust and has a flexible detection methodology that can be employed to detect the presence of all human respiratory pathogens in different sample preparations with precision. It will be important for differentiating the causative agents of respiratory illnesses, including SARS-CoV-2.

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Quantitative in vivo and in vitro characterization of co-infection by two genetically distant grass carp reoviruses

Journal of General Virology ◽

10.1099/vir.0.049965-0 ◽

2013 ◽

Vol 94 (6) ◽

pp. 1301-1309 ◽

Cited By ~ 38

Author(s):

Tu Wang ◽

Jiale Li ◽

Liqun Lu

Keyword(s):

Grass Carp ◽

Ctenopharyngodon Idella ◽

Clinical Samples ◽

Fish Farms ◽

Fish Samples ◽

Causative Agents ◽

Cellular Replication ◽

Virus Strains

Grass carp reovirus (GCRV) is one of the most serious pathogens threatening grass carp (Ctenopharyngodon idella) production in China. Through sequence analysis, the co-existence of two genetically distant grass carp reoviruses, named GCRV-JX01 and GCRV-JX02, was revealed in the same diseased grass carp sample collected in 2011. GCRV-JX01 and GCRV-JX02 shared high levels of homology with GCRV-873 and GCRV-GD108, respectively. In contrast to GCRV-JX01, GCRV-JX02 induced no cytopathic effect in infected cells. A quantitative real-time PCR assay was employed to monitor the replication efficiency of both virus strains in either Ctenopharyngodon idella kidney (CIK) cells or infected cell supernatant. The results demonstrated that, although GCRV-JX02 did reduce the cellular replication level of GCRV-JX01 up to 10-fold during co-infection, there was no significant impact on the productive virus progeny level in supernatant compared to that of cells infected by GCRV-JX01 alone. To validate the hypothesis that both viruses might co-infect grass carp without significant interference in the field, we collected clinical samples from two different fish farms in 2012 and monitored virus loads for each fish. The data showed that 55 % of the collected fish samples were co-infected by GCRV-JX01 and GCRV-JX02, and the single virus infection rate was 10 % for GCRV-JX01 and 20 % for GCRV-JX02. For both viruses, the in vivo viral loads under co-infection and single viral infection were similar. No serological cross-reaction or cross-protection occurred between GCRV-JX01 and JX02 in our immunization and challenge tests. This new information on co-infection by two genetically distant virus strains should be helpful for designing vaccines targeting the causative agents of grass carp haemorrhagic disease.

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