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Authors are the souls of any journal, and deserve much respect. To publish a journal manuscripts are needed from authors. Authors have a great responsibility for producing facts of their work in terms of number and results truthfully and an individual honesty is expected from authors in this regards. Both ways its true "No authors-No manuscripts-No journals" and "No journals–No manuscripts–No authors". Reviewing a manuscript is also a very responsible and important task of any peer-reviewed journal and to be taken seriously. It needs knowledge on the subject, sincerity, honesty and determination. Although the process of reviewing a manuscript is a time consuming task butit is expected to give one's best remarks within the time frame of the journal.
Salient features of the JCDR: It is a biomedical, multidisciplinary (including all medical and dental specialities), e-journal, with wide scope and extensive author support. At the same time, a free text of manuscript is available in HTML and PDF format. There is fast growing authorship and readership with JCDR as this can be judged by the number of articles published in it i e; in Feb 2007 of its first issue, it contained 5 articles only, and now in its recent volume published in April 2011, it contained 67 manuscripts. This e-journal is fulfilling the commitments and objectives sincerely, (as stated by Editor-in-chief in his preface to first edition) i e; to encourage physicians through the internet, especially from the developing countries who witness a spectrum of disease and acquire a wealth of knowledge to publish their experiences to benefit the medical community in patients care. I also feel that many of us have work of substance, newer ideas, adequate clinical materials but poor in medical writing and hesitation to submit the work and need help. JCDR provides authors help in this regards.
Timely publication of journal: Publication of manuscripts and bringing out the issue in time is one of the positive aspects of JCDR and is possible with strong support team in terms of peer reviewers, proof reading, language check, computer operators, etc. This is one of the great reasons for authors to submit their work with JCDR. Another best part of JCDR is "Online first Publications" facilities available for the authors. This facility not only provides the prompt publications of the manuscripts but at the same time also early availability of the manuscripts for the readers.
Indexation and online availability: Indexation transforms the journal in some sense from its local ownership to the worldwide professional community and to the public.JCDR is indexed with Embase & EMbiology, Google Scholar, Index Copernicus, Chemical Abstracts Service, Journal seek Database, Indian Science Abstracts, to name few of them. Manuscriptspublished in JCDR are available on major search engines ie; google, yahoo, msn.
In the era of fast growing newer technologies, and in computer and internet friendly environment the manuscripts preparation, submission, review, revision, etc and all can be done and checked with a click from all corer of the world, at any time. Of course there is always a scope for improvement in every field and none is perfect. To progress, one needs to identify the areas of one's weakness and to strengthen them.
It is well said that "happy beginning is half done" and it fits perfectly with JCDR. It has grown considerably and I feel it has already grown up from its infancy to adolescence, achieving the status of standard online e-journal form Indian continent since its inception in Feb 2007. This had been made possible due to the efforts and the hard work put in it. The way the JCDR is improving with every new volume, with good quality original manuscripts, makes it a quality journal for readers. I must thank and congratulate Dr Hemant Jain, Editor-in-Chief JCDR and his team for their sincere efforts, dedication, and determination for making JCDR a fast growing journal.
Every one of us: authors, reviewers, editors, and publisher are responsible for enhancing the stature of the journal. I wish for a great success for JCDR."
Thanking you
With sincere regards
Dr. Rajendra Kumar Ghritlaharey, M.S., M. Ch., FAIS
Associate Professor,
Department of Paediatric Surgery, Gandhi Medical College & Associated
Kamla Nehru & Hamidia Hospitals Bhopal, Madhya Pradesh 462 001 (India)
E-mail: drrajendrak1@rediffmail.com
On May 11,2011
Dr. Shankar P.R.
"On looking back through my Gmail archives after being requested by the journal to write a short editorial about my experiences of publishing with the Journal of Clinical and Diagnostic Research (JCDR), I came across an e-mail from Dr. Hemant Jain, Editor, in March 2007, which introduced the new electronic journal. The main features of the journal which were outlined in the e-mail were extensive author support, cash rewards, the peer review process, and other salient features of the journal.
Over a span of over four years, we (I and my colleagues) have published around 25 articles in the journal. In this editorial, I plan to briefly discuss my experiences of publishing with JCDR and the strengths of the journal and to finally address the areas for improvement.
My experiences of publishing with JCDR: Overall, my experiences of publishing withJCDR have been positive. The best point about the journal is that it responds to queries from the author. This may seem to be simple and not too much to ask for, but unfortunately, many journals in the subcontinent and from many developing countries do not respond or they respond with a long delay to the queries from the authors 1. The reasons could be many, including lack of optimal secretarial and other support. Another problem with many journals is the slowness of the review process. Editorial processing and peer review can take anywhere between a year to two years with some journals. Also, some journals do not keep the contributors informed about the progress of the review process. Due to the long review process, the articles can lose their relevance and topicality. A major benefit with JCDR is the timeliness and promptness of its response. In Dr Jain's e-mail which was sent to me in 2007, before the introduction of the Pre-publishing system, he had stated that he had received my submission and that he would get back to me within seven days and he did!
Most of the manuscripts are published within 3 to 4 months of their submission if they are found to be suitable after the review process. JCDR is published bimonthly and the accepted articles were usually published in the next issue. Recently, due to the increased volume of the submissions, the review process has become slower and it ?? Section can take from 4 to 6 months for the articles to be reviewed. The journal has an extensive author support system and it has recently introduced a paid expedited review process. The journal also mentions the average time for processing the manuscript under different submission systems - regular submission and expedited review.
Strengths of the journal: The journal has an online first facility in which the accepted manuscripts may be published on the website before being included in a regular issue of the journal. This cuts down the time between their acceptance and the publication. The journal is indexed in many databases, though not in PubMed. The editorial board should now take steps to index the journal in PubMed. The journal has a system of notifying readers through e-mail when a new issue is released. Also, the articles are available in both the HTML and the PDF formats. I especially like the new and colorful page format of the journal. Also, the access statistics of the articles are available. The prepublication and the manuscript tracking system are also helpful for the authors.
Areas for improvement: In certain cases, I felt that the peer review process of the manuscripts was not up to international standards and that it should be strengthened. Also, the number of manuscripts in an issue is high and it may be difficult for readers to go through all of them. The journal can consider tightening of the peer review process and increasing the quality standards for the acceptance of the manuscripts. I faced occasional problems with the online manuscript submission (Pre-publishing) system, which have to be addressed.
Overall, the publishing process with JCDR has been smooth, quick and relatively hassle free and I can recommend other authors to consider the journal as an outlet for their work."
Dr. P. Ravi Shankar
KIST Medical College, P.O. Box 14142, Kathmandu, Nepal.
E-mail: ravi.dr.shankar@gmail.com
On April 2011 Anuradha
Dear team JCDR, I would like to thank you for the very professional and polite service provided by everyone at JCDR. While i have been in the field of writing and editing for sometime, this has been my first attempt in publishing a scientific paper.Thank you for hand-holding me through the process.
Dr. Anuradha
E-mail: anuradha2nittur@gmail.com
On Jan 2020
Original article / research
Full Version
Molecular Characterisation of Corynebacterium diphtheriae Isolates of Faucial Diphtheria Cases from Assam: A Cross-sectional Study
Correspondence Address :
Dr. Gargi Choudhury,
Associate Professor, Department of Microbiology, Assam Medical College and Hospital,
Dibrugarh, Assam, India.
E-mail: gargicb@gmail.com
Introduction: Diphtheria caused by toxigenic Corynebacterium diphtheriae is an acute respiratory infection characterised by pseudomembrane formation in the throat. Although diphtheria is often reported sporadically across India, molecular characterisation of C.diphtheriae strains could play a crucial role in epidemiological investigations.
Aim: The present study aimed at molecular characterisation of Corynebacterium diphtheriae isolates of faucial diphtheria cases from Assam, North-East India utilising Multi-Locus Sequence Typing (MLST).
Materials and Methods: In this cross-sectional study, three isolates were obtained from three different cluster of cases that occurred across two districts of Assam, India for a period from November 2019 to June 2020. MLST of these three C.diphtheriae isolates were performed in Multidisciplinary Research Unit of Assam Medical College and Hospital by using the 7-gene MLST alleles of C.diphtheriae to determine the Sequence Types (ST).
Results: The MLST of the three isolates of this study revealed two distinct STs, ST-588 and ST-576 with multi-clonal lineages with ST-466, reported in C.diphtheriae strains of North Kerala and ST-301 related strains of Bangladesh respectively.
Conclusion: In spite of frequent reports of diphtheria cases from Assam, molecular typing of the C.diphtheriae strains found in North-Eastern region of India has not yet been performed. This is one of the initial investigations from this region of India to use MLST for typing C.diphtheriae strains. Therefore, studies related to molecular characterisation of C.diphtheriae strains found throughout India could immensely help in determining the clonality and diversity existing among these strains.
Clonal distribution, Diphtheria, Epidemiological investigation, Multi-locus sequence typing, Phylogenetic tree
Diphtheria caused by Corynebacterium diphtheriae is an acute infectious disease ranging from mild infection to acute airway obstruction, toxaemia and sudden death (1). The disease can have a fatality rate as high as 30.8% as reported in a previous study from Assam (2). This disease is not only prevalent in Assam, a North-Eastern state of India, but also in other parts of India (3). However, due to widespread immunisation coverage in children, a shift in burden of diphtheria cases has been observed in adolescents and adults (4). However, cases are still reported in children of marginalised population (5).
Faucial diphtheria is characterised by the formation of a pseudo-membrane on one or both tonsils that extends to the tonsillar pillars, uvula, soft palate, oropharynx, and nasopharynx. Further extension of the pseudo-membrane into the larynx or trachea or dislodgement of a piece of it may even lead to fatal airway obstruction (6).
The causative agent, Corynebacterium diphtheriae, isolated from diphtheria cases needs to be monitored and characterised to know the prevailing ST, to be able to detect any evolution in the bacteria and contain any possible spread of Corynebacterium diphtheria strains. Various reports on diphtheria cases from Assam have been published (2),(7),(8),(9). However, studies on molecular typing of C.diphtheriae using techniques like RFLP, MLST, etc., have not been done from the North-East part of India. Hence, this study was done to utilise the 7-gene MLST alleles of C.diphtheriae to determine the ST and illustrate the epidemiology of the strains prevalent in this endemic region.
A laboratory based cross-sectional study was undertaken in the Multi-disciplinary Research Unit of Assam Medical College & Hospital, Dibrugarh during the period from November 2019 to June 2020.This study was approved by the Institutional Ethics Committee of Assam Medical College and Hospital, Dibrugarh (IEC No. AMC/EC/185; Reg.no. ECR/636/Inst/AS/2014).
Inclusion criteria: Corynebacterium diphtheriae isolated from index cases of diphtheria outbreaks.
Exclusion criteria: Corynebacterium diphtheriae isolated from cases other than the index cases of diphtheria outbreaks.
Study Procedure
Three C.diphtheriae isolates were isolated during the period from 2017 to 2019 from index cases of diphtheria outbreaks which occurred in Jorhat and Dibrugarh districts of Assam were subjected to MLST. Among these isolates, two isolates (AMC1 and AMC2) were isolated in the Department of Microbiology, Assam Medical College and Hospital, Dibrugarh and one isolate (JMC1) isolated in Department of Microbiology, Jorhat Medical College and Hospital, Jorhat. Further molecular characterisation of these isolates was performed in the Multi-disciplinary Research Unit of Assam Medical College and Hospital. These isolates were confirmed as C.diphtheriae by standard biochemical methods and PCR amplification of rpoB and toxA gene of C.diphtheriae.
Bacterial DNA extraction: Bacterial DNA was extracted using QIAamp DNA mini kit (Qiagen Inc., USA) following manufacturer’s instructions and the extracted DNA was quantified using the μDrop plate in Multiskan GO (Thermo Scientific, USA).
PCR identification of C.diphtheriae isolates: The PCR targets of rpoB gene of C.diphtheriae, C. ulcerans, and toxA gene fragment of C.diphtheriae were used for identification of the C.diphtheriae isolates. The PCR amplification was carried out in a 25 μL reaction volume consisting of 12.5 μL of 2X Bioline MyTaq HS Mix (Meridian Biosciences, USA) and 500 nM of each forward and reverse primers. The PCR conditions consisted of an initial denaturation of 95°C for 1 minute followed by 35 cycles of denaturation at 95°C for 15 seconds, annealing at 55°C for 15 seconds, and extension at 72°C for 10 seconds. The PCR amplicons were visualised for respective PCR bands on a 2% agarose gel stained with ethidium bromide (7).
Multi-Locus Sequence Typing (MLST): MLST for C.diphtheriae isolates were performed by PCR amplification and sequencing of the seven housekeeping genes (atpA, dnaE, dnaK, fusA, leuA, odhA and rpoB) as per the protocol described by Bolt F et al., (10). Purification of the amplified PCR products was performed by using ExoSAP-IT PCR product clean-up reagent (ThermoFisher Scientific, USA) by following manufacturer’s instructions. Cycle sequencing was performed by using BigDye Terminator v3.1 Cycle Sequencing Kit (Applied Biosystems, USA) and sequencing was performed using Genetic Analyser 3500 (Applied Biosystems, USA). Consensus FASTA sequences were generated in BioEdit sequence alignment editor (Version 7.2.5) by multiple sequence alignment of both forward and reverse reads (11).
The population snapshot analysis of the 1357 isolates available till date in the C.diphtheriae MLST database was performed by utilising goeBURST algorithm in Phyloviz (Version 2.0) (12). The phylogenetic tree was constructed using the concatenated allele sequences in MEGA (Version X) using Neighbour-Joining method and Jukes Cantor algorithm. The test of phylogeny was done with 1000 bootstrap replicates (13). The allele sequences of the isolates of this study were submitted to Corynebacterium diphtheriae and C.ulcerans MLST sequence database (http://pubmlst.org/cdiphtheriae) and STs were assigned to each of the three isolates of this study. The isolates AMC1, AMC2, and JMC1 have been submitted to Corynebacterium diphtheriae and C. ulcerans MLST isolate database with isolate ids 851, 852, and 853 respectively (14).
Statistical Analysis
As this study involves only three isolates of C. diphtheriae, statistical methods could not be applied.
Population snapshot and phylogenetic analysis: Total three Corynebacterium diphtheriae isolates from each index case of three different diphtheria outbreaks were studied for MLST. The allele sequences of these isolates of this study were submitted to the Corynebacterium diphtheriae MLST sequence database (https://bigsdb.pasteur.fr/diphtheria/) and STs were assigned to each of the three isolates of this study. The isolates AMC1, AMC2, and JMC1 have been submitted to Corynebacterium diphtheriae MLST isolate database with isolate ids 2113, 2114, and 2115, respectively.
The population snapshot analysis of the 856 isolates available till date in the Corynebacterium diphtheriae MLST database revealed that the isolates AMC1 and AMC2 bearing ST-588 was assigned to the ST-466 Clonal Complex (CC) and is a Single Locus Variant (SLV) of ST-466 (Table/Fig 1). The JMC1 isolate with ST-576 was assigned to the ST-574 CC and is a SLV of ST301 (Table/Fig 1). The phylogenetic tree constructed using the concatenated allele sequences of seven housekeeping genes of the three C.diphtheriae isolates of this study along with reference strains (NCTC 05011, HCO1, HC04, C7betatox+, NCTC 13129, and INCA402) obtained from different parts of the world (Table/Fig 2). The isolates AMC1, AMC2, and JMC1 of this study were found to be in close relation with the NCTC 05011 strain with ST-143 originating form United Kingdom. None of the three isolates of this study were related to toxigenic reference strains of C7 beta tox (ST-26) and NCTC 13129 (ST-8).
Diphtheria owing to its high mortality rate was a much-feared disease before the introduction of a mass immunisation programme in India. However, there have been resurgences of this infectious disease in many parts of the country despite the high immunisation coverage. Outbreaks and sporadic cases of diphtheria have been reported occasionally from Assam (Table/Fig 3) (2),(7),(8),(9),(15). In one of the previous studies from Assam, 33 cases were reported and 10 cases were confirmed as C.diphtheriae by culture (7). MLST plays a crucial role in epidemiological investigation of pathogens. In 2016, C.diphtheriae strains with ST-466 were isolated during a national program surveillance in North Kerala. These ST-466 strains were found to be toxigenic as confirmed by Modified Elek’s Test (3). The isolates AMC1 and AMC2 of this study with ST-588 is a SLV of ST-446 and were found to be positive for the toxA gene as confirmed by PCR. During December 2017, an outbreak among the Forcibly Displaced Myanmar Nationals (FDMN) in Bangladesh occurred, in response to which Centers for Disease Control and Prevention (CDC) provided technical aid to study and characterise the C.diphtheriae isolates. This reported outbreak included three novel STs, two of which were also closely related to ST-301 (16). The ST-576 was assigned JMC1 isolate of this study is a SLV of ST301. The Indian state of Assam shares an international border of 263 kilometres with Bangladesh which may explain this clonality existing among the C.diphtheriae isolates of Assam and Bangladesh.
The MLST database of C.diphtheriae includes a total 1357 isolate data submitted till date from various parts of the world (14). However, only thirteen isolate data including the three isolates reported in this study have been submitted to the database from India. Though sporadic cases have been reported frequently all over the country and a nationwide surveillance programme is still going on under Integrated Disease Surveillance Programme (IDSP), molecular typing of the isolates has not been performed in most of the cases (17).
Limitation(s)
This study only included three C.diphtheriae isolates from index cases from three different diphtheria outbreaks. However, a greater number of isolates are required to determine the prevalent STs in this region. Moreover, Elek’s Gel precipitation test to determine the toxigenicity of these isolates was not performed in this study.
Two distinct STs, ST-588 and ST-576 with multi-clonal lineages with ST-466, reported in C.diphtheriae strains of North Kerala and ST-301 related strains of Bangladesh respectively, were revealed. In spite of frequent reports of diphtheria cases from Assam, molecular typing of the C.diphtheriae strains found in this region has not yet been performed. This is one of the initial investigations from the North-Eastern region of India to use MLST for typing C.diphtheriae strains found in this region. More studies from entire India on ST of C.diphtheriae strains could help immensely on establishing the prevalent STs; clonality and diversity existing among the C.diphtheriae strains found in India. The MLST on a large number of isolates from various regions of North East India could be a future perspective. Also, the determination of the toxigenic potential of all outbreak isolates of the regions could be another scope for future research. Moreover, expanded diphtheria surveillance including other anatomical sites (cutaneous, mucosal) etc., could be placed for early management of the cases.
The authors sincerely acknowledge the Indian Council of Medical Research (ICMR) for providing the platform for this study in the Multidisciplinary Research Unit (MRU-ICMR), Assam Medical College, Dibrugarh. Authors are also thankful to the technical staff of MRU-ICMR.
DOI: 10.7860/JCDR/2022/52934.16379
Date of Submission: Oct 26, 2021
Date of Peer Review: Dec 30, 2021
Date of Acceptance: Feb 22, 2022
Date of Publishing: May 01, 2022
AUTHOR DECLARATION:
• Financial or Other Competing Interests: No
• Was Ethics Committee Approval obtained for this study? Yes
• Was informed consent obtained from the subjects involved in the study? NA
• For any images presented appropriate consent has been obtained from the subjects. NA
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