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Article ; Online: Tracing the Origin and Transmission of Severe Acute Respiratory Syndrome-CoV-2

Thangam Menon

Journal of Clinical and Diagnostic Research, Vol 14, Iss 8, Pp DE01-DE

Does Genome Research Hold the Key?

2020 Volume 03

Abstract: The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) was first identified in December 2019 in Wuhan, China. Since then, the virus has been rapidly spreading across countries, resulting in the present Corona Virus Disease (COVID-2019) pandemic. ...

Abstract	The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) was first identified in December 2019 in Wuhan, China. Since then, the virus has been rapidly spreading across countries, resulting in the present Corona Virus Disease (COVID-2019) pandemic. Thousands of genomes of different strains of the virus have been sequenced and made available in the public domain which has helped to detect viral mutations and track movement of the virus across the globe. The whole genome sequence of SARS-CoV-2 isolated from a human strain has 96.2% similarity to a bat coronavirus. The strains of SARS-CoV-2 found in different countries are genetically diverse and infections have been shown to be caused by multiple introductions in the same country. Though there are several theories regarding the origin of this virus, genetic studies indicate that it may have appeared by natural selection in humans following zoonotic transfer. This review highlights the recent knowledge of the origin of the coronavirus, its diversity in different geographical regions and mutations, which have aided it to infect the human host.
Keywords	coronavirus 2 ; diversity ; mutation ; pandemic ; Medicine ; R
Language	English
Publishing date	2020-08-01T00:00:00Z
Publisher	JCDR Research and Publications Private Limited
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Metagenomic Characterisation of Microorganisms in the Dental Plaque- A Pilot Study

Ashok Veni Baskaran / Aishwarya Dhanalakshmi Jayaraj / Thangam Menon

Journal of Clinical and Diagnostic Research, Vol 16, Iss 8, Pp DM01-DM

2022 Volume 03

Abstract: Introduction: Progression of dental plaque gives rise to periodontal disease. The oral cavity has a diverse flora of microorganisms and caries is often caused by members of the oral microbiome. Metagenomic techniques and next-generation sequencing ... ...

Abstract	Introduction: Progression of dental plaque gives rise to periodontal disease. The oral cavity has a diverse flora of microorganisms and caries is often caused by members of the oral microbiome. Metagenomic techniques and next-generation sequencing technology have been used to analyse microbiomes. Aim: To analyse the components of the dental plaque by culture and metagenomics techniques. Materials and Methods: The present study was a pilot study in which analysis of the components of the dental plaque by bacteriological culture, 16s ribosomal Ribonucleic acid (rRNA) Polymerase Chain Reaction (PCR) with region specific primers and sequencing of V3-V4 regions, using the Illumina platform was performed. Results: Ten different phyla were identified (Firmicutes, Bacteroidetes, Proteobacteria, Fusobacteria, Actinobacteria, TM7, Spirochaetes, Tenericutes, SR1, GN02). Bacteriodetes was the most abundant phylum in the plaque samples. Firmicutes was less abundant in the plaque samples, when compared to the control. Streptococci were more abundant in the control (57.93%) when compared to plaque samples (10.7%, 19.3%). Routine culture grew only Viridans group streptococci (VGS). Conclusion: The 16S rRNA gene sequencing is a useful method for studying the bacterial composition of the dental plaque.
Keywords	bacterial composition ; oral microbiome ; sequencing ; Medicine ; R
Subject code	670
Language	English
Publishing date	2022-08-01T00:00:00Z
Publisher	JCDR Research and Publications Private Limited
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Assessment of Serum Cytokine Concentrations in Infective Endocarditis Patients

Rayvathy Balasubramanian / Thangam Menon

Journal of Clinical and Diagnostic Research, Vol 14, Iss 3, Pp DC10-DC

2020 Volume 14

Abstract: Introduction: Infective Endocarditis (IE) remains a devastating disease despite advances in diagnosis and treatment. The main stay of diagnosis is blood culture, however many cases are culture negative. Measuring levels of inflammatory markers in serum ... ...

Abstract	Introduction: Infective Endocarditis (IE) remains a devastating disease despite advances in diagnosis and treatment. The main stay of diagnosis is blood culture, however many cases are culture negative. Measuring levels of inflammatory markers in serum of these patients will aid in the diagnosis. Aim: To estimate the levels of various cytokines in the serum samples of IE patients and to compare them with two control groups- healthy individuals and patients with non-IE infections. Materials and Methods: Serum concentration of Interleukin (IL)- 1β, IL-6, IL-8, IL-10, IL-12, Tumour Necrosis Factor (TNF)-α and Interferon (IFN)-γ of 52 IE patients, 10 patients with non-IE infections and 10 healthy individuals were determined, between February 2017 and June 2018, using quantitative Enzyme Linked Immuno Sorbent Assay (ELISA). Comparison of cytokine values among the groups was done using Kruskal Wallis test, post-hoc test and ROC curve. Results: IE patients presented with high serum concentration of IFN-γ, TNF-α, IL-1β, IL-6 and IL-8 when compared to control groups. ROC curve analysis comparing IE patients with non-IE patients suggested that IL-6 (AUC-0.8) and IL-8 (AUC-0.876) may serve as reliable markers for the diagnosis of IE. Conclusion: Measurement of various serum cytokines showed that the levels of all of them except IL-10 and IL-12 were significantly higher in patients with IE and non-IE infections as compared to healthy controls. IL-6 and IL-8 levels may serve as additional biomarkers in the diagnosis of IE.
Keywords	biomarkers ; endocardium ; enzyme linked immunosorbent assay ; infection ; Medicine ; R
Subject code	610
Language	English
Publishing date	2020-03-01T00:00:00Z
Publisher	JCDR Research and Publications Private Limited
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Composition of the Oral Microbiome in Patients with Coronary Artery Disease

Thangam Menon / Supraja Kalyanaraman / Seethalakshmi Srinivasan

Journal of Clinical and Diagnostic Research, Vol 14, Iss 9, Pp DM01-DM

2020 Volume 03

Abstract: Introduction: Distinct microbial communities reside in the oral cavity and the composition of the oral microbiota has important implications for human health and disease. Identification of bacterial flora of the microbiome is done by metagenomic analysis ...

Abstract	Introduction: Distinct microbial communities reside in the oral cavity and the composition of the oral microbiota has important implications for human health and disease. Identification of bacterial flora of the microbiome is done by metagenomic analysis of 16S ribosomal RNA sequences. Aim: The aim of this study was to characterise the human microbiome in patients with Coronary Artery Disease (CAD) in comparison with the normal human microbiome. Materials and Methods: A pilot study was carried out in tertiary hospital, Chennai. Oral mouthwash samples collected from nine patients with CAD were selected, with one control group. They were studied by metagenomic analysis of V3-V4 region of 16SrRNA gene sequences. Sequencing of the variable V3 and V4 regions was done using Illumina platform. Results: The six major phyla, Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, Spirochaetes, and Fusobacteria contained 99% of the taxa in all the samples analysed. Conclusion: Diversity of the microbiome in patients with CAD was similar to the normal human microbiome.
Keywords	dysbiosis ; metagenomic analysis ; phylum ; taxa ; Medicine ; R
Subject code	610
Language	English
Publishing date	2020-09-01T00:00:00Z
Publisher	JCDR Research and Publications Private Limited
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Molecular detection of Orientia tsutsugamushi from suspected scrub typhus cases

Seethalakshmi Srinivasan / Thangam Menon

Indian Journal of Pathology and Microbiology, Vol 60, Iss 1, Pp 70-

2017 Volume 73

Abstract: Context: Scrub typhus is an acute febrile illness caused by Orientia tsutsugamushi. The disease is under-diagnosed in India, because of low index of suspicion and also due to its nonspecific presentation, and lack of confirmatory diagnostic tests. Aims: ... ...

Abstract	Context: Scrub typhus is an acute febrile illness caused by Orientia tsutsugamushi. The disease is under-diagnosed in India, because of low index of suspicion and also due to its nonspecific presentation, and lack of confirmatory diagnostic tests. Aims: This study was undertaken to diagnose scrub typhus in patients with undifferentiated fevers by serology and molecular methods. Materials and Methods: A total of 68 blood samples were collected from patients clinically suspected to have scrub typhus. After transportation to the laboratory, the serum was separated from the blood and subjected to rapid card test. The ethylenediaminetetraacetic acid blood samples were subjected to DNA extraction using QIAamp DNA Mini Kit followed by nested polymerase chain reaction (nPCR). Results: 24/68 (35.29%) cases showed the presence of antibody against scrub typhus by serology. 6/68 (8.8%) patients showed the presence of outer membrane protein antigen gene 56 kDa by nPCR. 5/24 serology positive cases showed the presence of 56 kDa outer membrane protein antigen gene by nPCR. A large number of cases positive by serology were negative by PCR which may indicate a low sensitivity of this test either due to low copy numbers or due to excess host DNA. Conclusion: Delay in treatment may increase disease severity and leads to higher mortality. Thus, molecular methods of diagnosis may aid in the early diagnosis of infection and enable prompt treatment. This is the first report on the diagnosis of scrub typhus in the suburbs of Chennai using molecular methods and reemphasizes the need for increased awareness of rickettsial infections in rural areas.
Keywords	Diagnosis ; nested polymerase chain reaction ; Orientia tsutsugamushi ; rapid test ; scrub typhus ; Pathology ; RB1-214 ; Medicine ; R ; Microbiology ; QR1-502 ; Science ; Q
Subject code	610 ; 630
Language	English
Publishing date	2017-01-01T00:00:00Z
Publisher	Medknow Publications
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Genome sequence of an invasive strain of Streptococcus gordonii

Thangam Menon / V Naveen Kumar

Indian Journal of Medical Microbiology, Vol 35, Iss 2, Pp 274-

2017 Volume 276

Abstract: We report the genome sequence of IE35, a strain of Streptococcus gordonii isolated from the blood of a patient with prosthetic valve endocarditis. Whole-genome sequencing of S. gordonii IE35 strain by the combination of Illumina HiSeq2000 paired-end, Ion ...

Abstract	We report the genome sequence of IE35, a strain of Streptococcus gordonii isolated from the blood of a patient with prosthetic valve endocarditis. Whole-genome sequencing of S. gordonii IE35 strain by the combination of Illumina HiSeq2000 paired-end, Ion Torrent single-end sequencing and gap closing by Illumina NextSeq yielded a single, circular chromosome of 2,190,105 bp. It had 2106 predicted coding sequences, of which 2014 genes encoded proteins involved in various cellular processes and 66 genes coded for RNA. The predicted RNA genes were annotated up to pathway level and genes responsible for various metabolic processes and virulence were identified.
Keywords	Endocarditis ; Genome sequence ; Streptococcus gordonii ; Science ; Q ; Microbiology ; QR1-502
Language	English
Publishing date	2017-01-01T00:00:00Z
Publisher	Wolters Kluwer Medknow Publications
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Emergence of rmtC and rmtF 16S rRNA methyltransferase in clinical isolates of Pseudomonas aeruginosa

Lavanya Mohanam / Thangam Menon

Indian Journal of Medical Microbiology, Vol 35, Iss 2, Pp 282-

2017 Volume 285

Abstract: Occurrence of aminoglycoside (AG) resistance in clinical isolates of Pseudomonas aeruginosa is investigated in this study. Antimicrobial susceptibility test and minimum inhibitory concentration (MIC) for amikacin and gentamicin were performed followed by ...

Abstract	Occurrence of aminoglycoside (AG) resistance in clinical isolates of Pseudomonas aeruginosa is investigated in this study. Antimicrobial susceptibility test and minimum inhibitory concentration (MIC) for amikacin and gentamicin were performed followed by polymerase chain reaction amplifications of AG modifying enzyme genes (aac(6´)-I, aac(6´)-II, aac(3)-II/VI, ant(2´´)-I, aph(3´)-VI) and 16S methylases (rmtA-D, rmtF and armA). MIC50and MIC90were 64, 128 and > 256, >256 for amikacin and gentamicin, respectively. Four types of genes (aac(6´)-I, aac(3)-II/VI, ant(2´´)-I and aph(3´)-VI) were found in 53 (57.6%) isolates. ant(2´´)-I was the most predominant gene (28 isolates) followed by aac(6´)-I (23 isolates). Nineteen (20.6%) isolates were positive for 16S RMTases (rmtB, rmtC, rmtF and armA) and two isolates co-harboured rmtB + rmtC + rmtF.
Keywords	16S rRNA methylase ; aminoglycoside modifying enzymes ; aminoglycosides ; ISEcp1 ; Pseudomonas aeruginosa ; Science ; Q ; Microbiology ; QR1-502
Language	English
Publishing date	2017-01-01T00:00:00Z
Publisher	Wolters Kluwer Medknow Publications
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Coexistence of metallo-beta-lactamase-encoding genes in Pseudomonas aeruginosa

Lavanya Mohanam / Thangam Menon

Indian Journal of Medical Research, Vol 146, Iss 7, Pp 46-

2017 Volume 52

Abstract: Background & objectives: The emergence and rapid spread of carbapenem resistance mediated by metallo-beta-lactamase (MBL) in Pseudomonas aeruginosa is of major concern due to limited therapeutic options. This study was aimed at detecting the presence of ... ...

Abstract	Background & objectives: The emergence and rapid spread of carbapenem resistance mediated by metallo-beta-lactamase (MBL) in Pseudomonas aeruginosa is of major concern due to limited therapeutic options. This study was aimed at detecting the presence of MBL and its association with integrons in imipenem-resistant P. aeruginosa isolates and to determine their genetic relatedness. Methods: A total of 213 P. aeruginosa isolates were collected from two tertiary care centres and tested against anti-pseudomonal antibiotics by antimicrobial susceptibility testing, followed by the detection of MBL production by combined disk method. Minimum inhibitory concentration (MIC) of meropenem was determined by E-test. Multiplex polymerase chain reaction (PCR) was performed for the detection of blaSPM, blaIMP, blaVIM, blaNDM, blaGIM and blaSIM. PCR was carried out to characterize the variable region of class 1 integron. Transcongujation assay was carried out for the confirmation of plasmid-mediated resistance. Enterobacterial repetitive intergenic consensus sequence (ERIC)-PCR was performed for determining the genetic relatedness among P. aeruginosa isolates. Results: Of the 213 P. aeruginosa isolates, 22 (10%) were found to be carbapenem resistant and these were from pus 18 (82%), urine 2 (9%), sputum 1 (5%) and tracheal wash 1 (5%). Among 22 isolates, 18 (81.8%) were found to be MBL producers by phenotypic method and MIC range of meropenem was 8 to >32 μg/ml. PCR amplification showed that 20 (91%) isolates carried any one of the MBL genes tested: blaVIM and blaNDM in seven (32%) and six (27%) isolates, respectively; blaVIM and blaNDMin three (14%); blaIMP and blaNDM in two (9%); blaVIM and blaIMP in one (5%) isolate. The blaVIM, blaIMP and blaNDM were found to co-exist in one isolate. None of the isolates were positive for blaSPM, blaSIM and blaGIM. All 22 isolates carried class I integron. Of the 20 MBL-positive isolates, transconjugants were obtained for 15 isolates. ERIC-PCR analysis showed all isolates to be clonally ...
Keywords	Class I integron - ERIC-PCR - metallo-beta-lactamase - Pseudomonas aeruginosa ; Medicine ; R
Language	English
Publishing date	2017-01-01T00:00:00Z
Publisher	Wolters Kluwer Medknow Publications
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Bartonella Endocarditis

Rayvathy Balasubramanian / Pierre Edouard Fournier / Panneer Selvam Ganesan / Thangam Menon

Journal of Clinical and Diagnostic Research, Vol 14, Iss 6, Pp DR01-DR

A Case Series from Chennai, India

2020 Volume 03

Abstract: ABSTRACT Bartonella spp. are Gram-negative haemotropic bacteria transmitted by arthropod vectors. They are considered as important aetiologic agents of Blood Culture Negative Endocarditis (BCNE). The diagnosis of Bartonella endocarditis is often ... ...

Abstract	ABSTRACT Bartonella spp. are Gram-negative haemotropic bacteria transmitted by arthropod vectors. They are considered as important aetiologic agents of Blood Culture Negative Endocarditis (BCNE). The diagnosis of Bartonella endocarditis is often challenging because of its non-specific clinical presentation and difficulty in isolating the microorganism in culture using standard microbiological techniques as it is an intracellular bacterium. A combination of serological and molecular methods will aid in a comprehensive diagnosis of this condition. This study reports a series of four Bartonella endocarditis cases diagnosed in Chennai, Tamil Nadu, India. All of them were known Rheumatic Heart Disease (RHD) patients. The common valves affected in the patients were mitral and aortic valves. Three out of four cases showed presence of valvular vegetation in echocardiogram. One patient had a history of close contact with cats. Specific real time Polymerase Chain Reaction (PCR) targeting 16S-23S rRNA spacer region of Bartonella spp. was positive in three cases. Serology using Indirect Immunofluorescence Assay (IFA) was positive in one case. Western blot test was performed on serum samples of all four cases and Bartonella henselae was identified as the aetiological agent in one case. Extra cardiac complications were observed in three cases. Antibiotic treatment was successful in three out of four cases. One patient died due to acute renal failure.
Keywords	gram-negative bacilli ; infective endocarditis ; real-time polymerase chain reaction ; Medicine ; R
Subject code	616
Language	English
Publishing date	2020-06-01T00:00:00Z
Publisher	JCDR Research and Publications Private Limited
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Molecular Basis for Erythromycin Resistance in Group A Streptococcus Isolated From Skin and Soft Tissue Infections

Sunil Shivekar / Thangam Menon

Journal of Clinical and Diagnostic Research, Vol 9, Iss 11, Pp DC21-DC

2015 Volume 23

Abstract: Background: In recent years there has been an increase in the use of erythromycin in the treatment of infections caused by bacteria other than Group A Streptococcus (GAS), which has resulted in increased resistance to this antibiotic. Erythromycin and ... ...

Abstract	Background: In recent years there has been an increase in the use of erythromycin in the treatment of infections caused by bacteria other than Group A Streptococcus (GAS), which has resulted in increased resistance to this antibiotic. Erythromycin and other macrolides are alternative agents for treating GAS infections in patients, who are allergic to penicillin and its derivatives. Aim: The main aim of this study was to identify frequency, pattern and genetic determinant of erythromycin resistance among the GAS isolated from skin and soft tissue infections. Materials and Methods: A total 100 isolates of GAS were screened for erythromycin resistance by phenotypic and genotypic method. Results: The results of the present study showed that 38% isolates were resistant to erythromycin. The iMLS (inducible macrolide-lincosamide-streptogramin) phenotype was predominant (55.26%) followed by M phenotype (26.32%) and cMLS (constitutive macrolide-lincosamide-streptogramin) (18.42%). Conclusion: Phenotypic and genotypic analysis showed that the MLSB phenotype with ermB mediated mechanism of resistance was found the most common (76.31%) followed by mefA (20.51%). The ermTR genes was absent in all the isolates.
Keywords	erythromycin resistance ; genotypes ; phenotypes ; Medicine ; R
Subject code	610
Language	English
Publishing date	2015-11-01T00:00:00Z
Publisher	JCDR Research and Publications Private Limited
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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