Microbiology Research Articles

To study the isolation and identification of fungi from oral cancer after radiotherapy

Background: Cancer, known medically as a malignant neoplasm, is a broad group of diseases involving unregulated cell growth. In oral cavity infection, the oral microflora may be subsequently replaced by potentially pathogenic microorganisms such as candela species (from 72% to 92%). Hence, because of a weakened line of defense in oral cancer patients, the present prospective cohort study was carried out with the aim of isolation and identification of fungal colonization from oral cavity from radiotherapy. Radiotherapy and both radio-chemotheray treated patients. Methods: The proposed study was carried out on clinical samples in the Department of Microbiology in S. P. Medical College, Bikaner, Rajasthan. Isolates from clinical samples were collected from Acharya Tulsi Regional Cancer Hospital, Bikaner, Rajasthan. Samples of the lesion from the tongue and mouth were obtained with a sterile cotton swab. The sample was cultured on Sabouraud's dextrose agar and typical yeast colonies were determined after 72 h. After, staining isolates were subjected to biochemical identification. Results: A total of fifty isolates were taken for the study. Out of these fifty isolates, 45 (90%) were male, whereas 5 (10%) were female. In this study, about 90% of oral and pharyngeal cancer in men and around 10% in women can be estimated. Out of fifty, the highest isolates obtained were Candida albicans (15, 30%), followed by Candida glabrata (11, 22%) and Candida tropicalis (8, 16%), and the lowest number was of Candida krusei (6, 12%). In this purposed study, out of fifty patients, C. albicans can be isolated in 15 patients that is a higher value. Conclusion: C. albicans is the most commonly implicated organism in the mouth after radiotherapy and radio chemotherapy. It is clear that C. albicans is the most commonly found fungi to cause secondary infection.

Tamoxifen from chemotherapy to antiviral drug: Possible activity against COVID-19

Tamoxifen (TAM) is the oldest and the most-prescribed selective estrogen receptor modulator (SERM). It is a member of the triphenylethylene group. TAM has been used to treat breast cancer that spreads to other parts of the human body; it is also utilized to decreasing the chances of breast cancer developing in high-risk patients. Recently, some studies focused on the potential antimicrobial action of TAM. Coronaviruses are enveloped positive-sense RNA nucleic acid viruses that have club-like spikes, characterized by a distinctive replication strategy; they are round and sometimes pleomorphic in shape. Coronavirus disease 2019 (COVID-19) is regarding the new genera of coronaviredia that appeared for the first time in Wuhan, China, in early December 2019. Due to the continuous spread of the novel COVID-19 with the exponential rise in death numbers, new therapeutic development is urgent; in general, there are no specific antiviral drugs or vaccines for 2019-nCoV. Hence, this review will discuss the most recent information about the antiviral action of TAM against COVID-19 infection by trying to give a deep understanding of major properties, mechanisms of action, immune system responses, and antimicrobial efficiency of TAM that is regarding the promising way to treat COVID-19 novel infection. The current review may serve as an impetus for researchers working in the field of medical microbiology, vaccination, and antiviral drug design. The review also rationally reports and critically analyzes the available knowledge by focusing and mentioning future steps and strategies trying to find appropriate solutions regarding challenges in COVID-19 management by TAM utilization.

REVIEW OF USE OF NANO MATERIAL IN MODIFYING THE PROPERTIES OF CONCRETE

Modern technologies have affected all fields of human activities. Traditionally nanotechnologies deal with material having a dimension in the range of one billionth of a meter or 100 Nano meter in size. It has been widely used in natural sciences and biomedical sciences in the fields like microbiology, medicine, electronic, chemical, and materials sciences. The application of nontechnology and Nano material in Civil Engineering is still under active research in the areas of Concrete Technology, Construction management, water purification systems, Properties of Concrete at early ages and use of modern polymers in producing High Performance Concrete (HPC). The use of Nano material to produce relatively sustainable concrete represents a promising area of research in Nano material. In this paper the State of the Art of application of Nanotechnologies to Civil Engineering and its future prospects with special reference to sustainability in construction.

Outcome-based education combined with inquiry-based teaching model in experimental teaching of medical microbiology

In this study, a new medical microbiology experiment teaching system, which was based on outcome-based education combined with inquiry-based teaching model, was developed and evaluated. According to the professional requirements of doctors, the objectives of emotion and comprehensive experimental ability were added, and the requirement for experimental operation skills was raised. In accordance with the concept of inquiry-based teaching, experimental contents were reorganized, and practical operation contents and comprehensive analytical experiments were increased to facilitate students' abilities of independent thinking and innovation. In addition, the proportion of microbiology laboratory examination was increased, experimental skill examination was focused, the assessment method was reformed, and extracurricular interest groups were established to deepen the learning. The teaching effect was evaluated by questionnaire, performance and follow-up survey. The result showed that the new model increased the students' course scores, improved their capability in innovation, academic writing and clinical working, and strengthened the weakness of traditional teaching in application and exploration, providing a new idea for the reform in medical microbiology experiment teaching. Key words: Outcome-based education; Inquiry-based learning; Medical microbiology; Experimental teaching

Аctual Problems and Tasks of Microbiology

Аctual Problems and Tasks of Microbiology

Molecular epidemiological characteristics of Streptococcus pyogenes causing scarlet fever and angina in children

Objective To investigate the antimicrobial resistance, macrolide-resistance genes, virulence genes and emm types in Streptococcus pyogenes isolates. Methods A total of 247 oropharyngeal swab specimens were collected from pediatric outpatients (aged 2-11 years) who were clinically diagnosed as scarlet fever in Children′s Hospital of Fudan University from January to December, 2018. These specimens were timely sent to the Microbiology Laboratory for isolation and identification of Streptococcus pyogenes strains were isolate after culturing and identified with bacitracin susceptibility test. Moreover, the diameter of bacitracin inhibition zone was measured by vernier caliper. Their susceptibility to seven antibiotics, including erythromycin, clarithromycin, clindamycin, ampicillin, ceftriaxone, norfloxacin and chloramphenicol, were measured using KB method. Macrolide-resistance genes (mefA, ermA, ermB and Tn916 transposon) and virulence genes (speA, speB, speC, speG, speH, speI, speJ and speK) were detected by PCR. Amplification and sequencing of emm gene were conducted according to the protocol in the website of Centre for Disease Control and Prevention (CDC). Results A total of 86 strains of Streptococcus pyogenes were isolated from the 247 specimens. Their resistance rates to erythromycin, clarithromycin and clindamycin were 89.5%, 95.3% and 96.5%, respectively. However, these isolates showed high susceptibility to ampicillin (100.0%), ceftriaxone (100.0%), norfloxacin (90.7%) and chloramphenicol (95.3%). The positive rates of mefA, ermA, ermB and Tn916 genes were 20.9%, 24.4%, 98.8% and 97.7%. There was significant difference in the mefA-carrying rates between patients with scarlet fever and angina. The positive rates of virulence genes of speA, speB, speC, speG, speH, speI, speJ, speK, speL and speM were 8.1%, 100.0%, 95.3%, 100.0%, 80.2%, 90.7%, 10.5%, 100.0%, 5.8% and 5.8%. Seven emm types were identified and the predominant types were emm12.0 (75.6%), emm12.19 (9.3%) and emm1.0 (8.1%). The diameter of bacitracin inhibition zone was smaller in isolates of emm1.0 type than in emm12.0 type strains. The profile of virulence genes varied in the strains of different emm types. All types of strains carried speB, speG and speK genes. The isolates of emm1.0 type carried speA virulence gene, while speB, speC, speG, speH, speI and speK genes were more often identified in emm12.0 type isolates. Conclusions This study showed that emm types were associated with the profile of virulence genes and the diameter of bacitracin inhibition zone. It was recommended that the diameter of bacitracin inhibition zone should be measured in bacitracin inhibition susceptibility test apart from only observing the formation of inhibition zone. Key words: Streptococcus pyogenes; Antimicrobial resistance; Virulence gene; emm type; Bacitracin susceptibility test

Only vaccines can eradicate parasitic worms.

Microbiologist Jeffrey Bethony details progress in efforts to protect people from hookworms and schistosomiasis. Microbiologist Jeffrey Bethony details progress in efforts to protect people from hookworms and schistosomiasis.

Towards 21st century microbiology in Africa.

Towards 21st century microbiology in Africa.

2441. Automated, Rapid Detection of Potential Healthcare-Acquired Infection Clusters Based on Microbiology And Patient Geotemporal Data

BackgroundWhole-genome sequencing (WGS) has shown promise in identifying transmissions of healthcare-associated infections (HAIs), but it may be costly to sequence all potential HAIs. By automatically identifying samples likely to be HAIs, WGS can be focused on specific samples. We describe an algorithm that quickly identifies potential HAI clusters by analyzing patient geotemporal and pathogen microbiology data. This approach systematically triages potential HAI investigations to aid infection control professionals (ICPs) in their workflow.MethodsThis novel algorithm within Philips IntelliSpace Epidemiology scores the potential of transmission for pairs of infections. Inputs include microbiology (MB) data (genus- or species-level identification and antimicrobial susceptibility test results) and geotemporal (GT) data (timing of sample collection and shared location stays). From the resulting pairwise scores, clusters of potential HAIs are identified. Leveraging 9 months (June, 2018 – March, 2019) of data from a 900-bed US hospital (i.e., 2825 samples, 1814 patients and 13 organisms—of which a subset of 404 samples had WGS performed concomitantly with MB studies), we evaluated the extent to which this algorithm captures genetically similar sample pairs.ResultsPairwise scores enrich for genetically similar samples when considering MB data only (odds ratio: 17.3), GT only (odds ratio: 6.1) and a combination of both (odds ratio: 19.8), with highly significant P-values for all (P < 10−16). Considering MB only, 91% of samples group together in potential transmission clusters. With MB and GT data, this fraction drops to 24.6% (694 samples) forming 178 possible clusters, 173 of which contain fewer than ten samples each. The 5 larger clusters contain 40–64 samples each and span multiple units in the hospital.ConclusionThe proposed system automatically suggests potential HAI clusters. By combining MB and GT data, the number of samples to review is reduced, enabling ICPs to focus their attention and sequencing efforts. By focusing on a targeted group of higher probability clusters, ICPs may be able to increase their efficiency and effectiveness in controlling the spread of HAIs—thus boosting potential for patient safety and amelioration of cost of care.Disclosures All authors: No reported disclosures.

Flower Microbiology: Old concept but new approach

Flower Microbiology: Old concept but new approach

Isolasi dan Identifikasi Cendawan Mikoriza Arbuskular Pada Tiga Pusat Lokasi Tanaman Jagung di Kabupaten Jember

Penelitian ini bertujuan untuk Mengisolasi dan Mendapatkan Isolat Cendawan Mikoriza Arbuskular Pada Tiga Pusat Lokasi Tanaman Jagung Di Kabupaten Jember. Penelitian dilakukan selama 6 bulan dari bulan Agustus 2018 sampai dengan bulan Januari 2019. Kegiatan Penelitian dilakukan di Laboratorium Mikrobiologi Universitas Jember dan Laboratorium Jurusan Hama Penyakit Univeristas Brawijaya Malang. Penelitian ini menggunakan 3 lokasi dan 3 kedalaman untuk pengambilan sampel yaitu Kecamatan Arjasa, Kecamatan Bangsalsari, dan Kecamatan Kencong dengan kedalaman 10 cm, 20 cm dan 30 cm dari permukaan tanah. Data dianalisis secara deskriptif kualitatif dengan mengidentifikasi jenis Cendawan Mikoriza Arbuskular yang sudah di isolasi. Hasil penelitian ini menunjukan bahwa Cendawan Mikoriza Arbuskular dari rhizosfer tanaman jagung dapat di identifikasi sebagai jenis Cendawan Mikoriza dari genus Glomus sp dan Acaulospora delicata yang memiliki karakteristik warna coklat dan memiliki bentuk bulan sampai dengan lonjong. Genus Glomus sp memiliki tingkat adaptasi yang lebih dominan di Kecamatan Arjasa pada kedalaman tanah 10 cm dengan jumlah spora 75. Genus Acaulospora delicata memiliki adaptasi lebih dominan di Kecamatan Arjasa pada Kedalaman 20 cm dengan jumlah spora 111.

Proyectos interuniversitarios y multidisciplinarios relacionados con el patógeno zoonótico Brucella abortus realizados en el CIB

Desde el año 2009, el Centro de Investigación en Biotecnología (CIB) del TEC ha venido desarrollando varios proyectos de investigación interuniversitarios y multidisciplinarios relacionados con la bacteria Brucella abortus. Estos proyectos se hicieron en conjunto con el Programa de Investigación en Enfermedades Tropicales (PIET) de la Escuela de Medicina Veterinaria de la Universidad Nacional (UNA) y el Centro de Investigación en Enfermedades Tropicales (CIET) de la Facultad de Microbiología de la Universidad de Costa Rica (UCR). La mayoría de estos proyectos contaron principalmente con financiamiento de los Fondos Especiales para la Educación Superior (FEES) del Consejo Nacional de Rectores (CONARE). Durante la última década, el financiamiento recibido del FEES, permitió crear y equipar el Laboratorio de Bacteriología en el CIB; realizar trabajos finales de graduación y tesis de licenciatura, maestría y doctorado, en las áreas de biotecnología, microbiología, medicina veterinaria y ciencias biomédicas. También se han publicado artículos científicos en revistas indexadas y se están elaborando manuscritos, como resultado de las tesis doctorales en ejecución.

Augmenting Analytics Software for Clinical Microbiology by Man-Machine Interaction.

In the present study, we intended to solve identification problems in analyzing the results of microbiology by proactive man-machine interaction. We modified the analytics software MOMO so that it flags laboratory results containing textual elements unknown to the thesaurus, and a human expert assigns the elements to the respective existing thesaurus elements or creates new ones. In 773,309 laboratory results, roughly 2.6% contained unassigned elements and would have been ignored in thesaurus-based analyses for purposes other than simply reporting microbiological findings to physicians. In current use, the thesaurus is kept up to date with synonyms, syntactic deviations, misspellings, and entries not contained earlier, with man-machine interaction of 2-3 hours per week. This approach helps to accommodate both up-to-date clinical reporting for immediate patient care as well as up-to-date queries for infection surveillance and epidemiology, outbreak management, quality control and benchmarking, and antimicrobial stewardship.

A Decision Support System for Pathology Test Result Reviews in an Emergency Department to Support Patient Safety and Increase Efficiency.

The review of pathology test results for missed diagnoses in Emergency Departments is time-consuming, laborious, and can be inaccurate. An automated solution, with text mining and clinical terminology semantic capabilities, was developed to provide clinical decision support. The system focused on the review of microbiology test results that contained information on culture strains and their antibiotic sensitivities, both of which can have a significant impact on ongoing patient safety and clinical care. The system was highly effective at identifying abnormal test results, reducing the number of test results for review by 92%. Furthermore, the system reconciled antibiotic sensitivities with documented antibiotic prescriptions in discharge summaries to identify patient follow-ups with a 91% F-measure - allowing for the accurate prioritization of cases for review. The system dramatically increases accuracy, efficiency, and supports patient safety by ensuring important diagnoses are recognized and correct antibiotics are prescribed.

Adaptation of wild strain of duck plague virus in cell culture systems

Duck virus enteritis (DVE) is an acute, contagious herpes viral disease of ducks, geese and swans and members of the family Anatidae under the order Anseriformes. As per the recent taxonomic classification by ICTV, DEV has been classified into the genus Mardivirus, subfamily Alpha-herpesvirinae of the family Herpesviridae. Vaccination is the only option for the prevention and control of Duck plague. In India vaccination is done with chicken embryo adapted live virus which has many shortcomings. So, in this present situation a safe and potent vaccine development is the need of the hour. The use of chicken embryo fibroblast and a certified cell line may, probably, be the best option to achieve this. Therefore, the present study was undertaken for adaptation and propagation of local strain of duck plague virus in various cell culture systems. During the study a wild strain of DPV (DP/As-Km/0019) which was isolated in Duck Embryo Fibroblast, available in the Department of Microbiology was selected. The selected wild strain was used for adaptation in various cell culture systems viz. Chicken embryo fibroblast cell culture (CEF), Vero cell line and QT-35 cell line. The virus was passaged up to 12th passage levels and the presence of viral antigen was demonstrated by appearance of cytopathic effect (CPE), by Polymerase Chain Reaction (PCR) and by Sandwich ELISA. PCR was able to detect virus from all the cell cultures from 5th passage onwards and virus titre was detected at 10th and 12th passage level by S-ELISA. It was observed that various cell culture systems can be a good candidate for propagation of DPV and further study is required to study its immunogenicity and its feasibility as a vaccine candidate.

Standardization of Antimicrobial Sensitivity testing in Clinical Microbiology Laboratory: Bangladesh Perspective

Abstract not available&#x0D; Bangladesh Journal of Infectious Diseases, December 2018;5(2):39-40

Using Microbiological Data Analysis to Tackle Antibiotic Resistance of Klebsiella Pneumoniae.

Optimal antibiotic use for the treatment of nosocomial infections plays a central role in the effort to control the rapidly increasing prevalence of multidrug-resistant bacteria. Antibiotic selection should be based on accurate knowledge of local susceptibility rates. Traditional methods of resistance reporting, which are in routine use by microbiology laboratories could be enhanced by using statistically significant results. We present a method of reporting based on antibiotic susceptibility data analysis which offers an accurate tool that reduces clinician uncertainty and enables optimization of the antibiotic selection process.

The clinical characteristics and risk factors of mixed Candida/bacterial bloodstream infections

Objective To investigate the clinical characteristics and associated risk factors for patients with mixed Candida/bacterial bloodstream infections (BSIs). Methods A retrospective study was conducted in the Second Affiliated hHospital of Zhejiang University School of Medicine from February 2012 to June 2015. The clinical data of cases was collected, and the clinical characteristics, the microbiology data and outcomes in patients with mixed Candida/bacterial BSIs confirmed by blood culture were compared with those with candidaemia. A Logistic regression analysis was performed to investigate the independent risk factors. Results A total of 136 candidaemia cases were analyzed including 40 cases (29.4%) of mixed Candida/bacterial BSIs and 96 cases of candidaemia. Among the 136 candidas strains, the proportion of non-albicans exceeded the albicans (50.7% vs 49.3%), although the later was still the predominant one. There was no significant difference in the distribution of candidas strains between patients with mixed Candida/bacterial BSIs and patients with candidaemia. In patients with mixed Candida/bacterial BSIs, 25 strains (61.0%) of gram-positive cocci and 16 strains (39.0%) of gram-negative bacilli were isolated. Compared with patients with candidaemia, patients with mixed Candida/bacterial BSIs needed longer period of antifungal therapy [12.0 (4.0-25.0)days vs 7.0 (3.0-13.5) days, P=0.027], but the crude 30-day and 90-day mortality did not differ between the two groups (40.0% vs 32.3%; 45.0% vs 36.5%; both P>0.05). Univariate analysis revealed that the prior hospital stay, ICU admission at the onset of candidaemia, blood transfusion, human albumin infusion, mechanical ventilation, linezolid use and high SOFA score were related with the occurrence of mixed Candida/bacterial BSIs (all P<0.05). Multivariate analysis showed that only high SOFA score was the independent risk factor (P=0.003). Conclusions Gram-positive cocci were the predominant species in mixed Candida/bacterial BSIs. Compared with candidaemia, mixed Candida/bacterial BSIs needs a longer ICU stay, a longer hospital stay, and a prolonged antifungal therapy. High SOFA score is the independent risk factor for mixed Candida/bacterial BSIs. Key words: Candidaemia; Bacterial bloodstream; Mixed infection; Clinical characteristics; Strains distribution; Antifungal susceptibility; Risk factors; Clinical outcome

Detection of mecA gene and drug-resistance analysis

Objective To determine whether coagulase-negative non-epidermal staphylococcus is methicillin-resistant coagulase-negative staphylococcus by mecA gene test, when the minimal inhibitory concentration(MIC)of oxacillin is between 0.5-2.0 mg/L. Methods The mecA gene was detected and analyzed by the cefoxitin disk diffusion, E-test, VITEK-2 Compact and polymerase chain reaction(PCR)purification. Results A total of 300 strains of coagulase-negative staphylococci were screened from 4032 patients(7.4%), of which 45 strains of Staphylococcus saprophyticus and 80 strains of Staphylococcus hemolyticus were identified by Compact VITEK-2.There was a statistically significant difference in the positive rate of mecA gene detection between Staphylococcus saprophyticus and Staphylococcus hemolyticus(P<0.05). The results of detection of cefoxitin disk diffusion(inhibitory zone diameter ≥25 mm), E-test(MIC of oxacillin between 0.5-2.0 mg/L)and Compact VITEK-2(MIC of oxacillin between 0.5-2.0 mg/L)showed that there were 81 strains of coagulase-negative non-Staphylococci, of which 10 strains with positive mecA gene were confirmed by PCR. Conclusions When the minimal inhibitory concentration(MIC)of oxacillin against coagulase-negative non-Staphylococci stains is between 0.5-2.0 mg/L, the guidelines of the American clinical laboratory standardization institute(CLSI)should be strictly implemented in clinical microbiology laboratory and the mecA gene must be tested.Based on the wide dissemination of the mecA gene in Staphylococcus aureus population, if the mecA gene test is negative, it is reported as methicillin-susceptible coagulase-negative Staphylococcus(MSCNS), and the reverse result is reported as methicillin-resistant coagulase-negative staphylococcus(MRCNS). Key words: Coagulase; Methicillin resistant; Staphylococcus; mecA gene

Progress in lactic acid-mediated maintenance of healthy vaginal microecology

Lactic acid is the main substance produced by Lactobacillus and plays an important role in maintaining a healthy vaginal microecology. Recent studies indicates that both L- and D-chiral isomers of lactic acid can be protonated and destroy the cell membranes of pathogens, thereby inhibiting bacterial vaginosis- and aerobic vaginitis-related pathogens. Lactic acid also can inhibit the pathogens of sexually transmitted diseases such as Chlamydia trachomatis and human immunodeficiency virus. Moreover, lactic acid acts as an immunomodulator to inhibit the inflammatory responses caused by pathogenic microorganisms and as an epigenetic regulator regulating gene expression in vaginal epithelial cells. In this paper, we reviewed the progress in lactic acid-mediated maintenance of a healthy vaginal microbiology in recent years for providing reference for further research. Key words: Lactobacillus; Lactic acid; Pathogen; Immunomodulator; Vaginal microecology