Journal Pone 0261435
Journal Pone 0261435
RESEARCH ARTICLE
2. Results
2.1. Culture, AST and real-time PCR
A total of 441 diphtheria suspected specimens [isolates (n = 204); throat swabs (n = 218); other
samples (n = 19)] were received and screened for diphtheria by both culture and real-time
PCR. These included samples collected at study participating centres. All these samples were
confirmed at the NRL for diphtheria at CMC, Vellore. Detailed breakdown of positives by cul-
ture and PCR were given in S1 Table. Out of 218 swabs received, 32 were culture positive and
43 were PCR positive for C. diphtheriae. One isolate was identified to be toxin (toxA) negative
by PCR. Of the 204 isolates received from participating centres, 180 were confirmed as C.
diphtheriae by PCR with 8.3% (n = 15) toxA negative isolates. Among the 19 other samples, 10
were found to be positive, of which 7 were toxin negative. Antimicrobial susceptibility testing
for the subset of 33 isolates (CMC) showed intermediate susceptibility to penicillin. Whereas
all tested isolates were susceptible to erythromycin and cefotaxime according to CLSI-M45
guidelines.
Table 1. SNP analysis of sequence types identified among the study isolates.
Sequence type atpA dnaE dnaK fusA leuA odhA rpoB SNPs Clonal complex
ST3 3 3 3 2 3 3 3 Known ST CC209
ST295 2 1 20 19 3 3 14 Known ST CC509
ST50 2 2 4 1 3 3 2 Known ST CC5
ST377 2 43 87 4 59 3 6 Known ST CC540
ST301 2 10 3 1 7 3 2 Known ST CC574
ST308 4 12 4 1 18 3 13 Known ST CC5
�
ST405 4 12 4 1 18 3 2 SLV of ST308 by 3 SNPs CC5
�
ST408 8 2 3 1 18 3 13 TLV of ST308 by atpA—4 dnaE—5 dnaK—11 SNPs
�
ST409 6 7 21 12 9 12 11 SLV of ST163 by 1 SNP CC42
ST422 2 2 38 58 3 3 22 TLV of ST50 by dnaK—17 fusA—6 rpoB—3 SNPs
ST443 3 1 20 19 37 3 35 TLV of ST295 by atpA—2 leuA—4 rpoB—1 SNPs
ST446 4 2 4 1 3 3 2 SLV of ST50 by 4 SNPs CC5
�
ST466 2 3 3 1 2 3 13 None CC466
�
ST468 3 2 4 19 59 3 13 DLV of ST136 by fusA—7 leuA—4 CC5
�
ST469 4 10 3 1 7 3 13 DLV of ST301 by atpA—4 rpoB—3 SNPs
�
ST470 3 2 99 1 20 3 13 TLV of ST408 by atpA—2 dnaK—7 leuA—6 SNPs
�
ST540 2 43 87 4 2 3 6 SLV of ST377 by 8 SNPs CC377
�
ST541 2 3 3 1 59 3 13 SLV of ST466 by 8 SNPs CC466
�
ST542 3 1 4 19 5 3 9 TLV of ST468 by dnaE—1 leuA—3 rpoB—3 SNPs
ST548 3 3 4 2 3 3 5 SLV of ST209 by 4 SNPs CC209
ST566 19 9 4 19 30 26 22 None
ST567 23 3 3 1 2 3 13 SLV of ST466 by 1 SNP CC466
ST568 3 1 49 19 3 3 6 TLV of ST542 by dnaK—10 leuA—1 rpoB—3 SNPs
ST569 3 2 4 19 3 3 13 SLV of ST468 by 4 SNPs CC5
ST570 3 3 3 2 41 3 3 SLV of ST3 by 2 SNPs CC209
ST573 2 3 76 1 25 3 13 DLV of ST466 by dnaK—5 leuA—3 SNPs CC466
ST574 2 10 3 1 3 3 2 SLV of ST301 by 6 SNPs CC574
ST575 3 1 4 58 5 3 22 DLV of ST542 by fusA -1 rpoB—5 SNPs
ST576 2 10 3 64 7 3 2 SLV of ST301 by 1 SNP CC574
ST587 2 3 97 1 2 3 35 DLV of ST466 dnaK—8 rpoB—1 SNPs CC466
ST588 2 3 3 1 2 16 13 SLV of ST466 by odhA—4 SNP CC466
ST590 2 10 3 1 3 57 2 DLV of ST301 by leuA—6 odhA—1 SNPs CC574
ST591 2 3 38 1 3 3 22 DLV of ST422 by dnaE—1 fusA—6 SNPs
ST592 2 12 87 4 59 3 2 DLV of ST377 by dnaE—4 rpoB—1 SNPs
ST599 2 12 4 1 18 3 2 SLV of ST405 by atpA—4 SNP CC5
https://doi.org/10.1371/journal.pone.0261435.t001
ST443, ST422, ST566, and ST568, whereas the STs identified in both toxigenic and non-toxi-
genic isolates were ST408, ST466, ST591 and ST575, respectively. The MLST sequences
obtained, and its distribution among the study isolates are given in the S2 Table. The phyloge-
netic tree showed the relatedness of the isolates based on the concatenated MLST gene
sequences (Fig 2). Individual isolate details on toxigenicity, ST, region and year of isolation
were given in S3 Table. The possible routes of transmission of STs were mapped according to
their pattern of first occurrence and their sample collection date (Fig 3).
3. Discussion
Diphtheria remains endemic in many parts of the world and continues to be a major public
health problem in India. There have been numerous reports of diphtheria from several parts of
Fig 2. Maximum likelihood phylogeny of MLST alleles from 216 C. diphtheriae isolates. The clades are highlighted based on the common ST types identified in the
study. STs associated with non-toxigenic strains are highlighted in yellow. The inner ring represents the toxigenicity results of the isolates followed by date of collection.
The outer ring represents the region of isolation.
https://doi.org/10.1371/journal.pone.0261435.g002
India for the past 10 years [8]. The occurrence of novel sequence types and their circulation in
different geographical regions has recently become a serious concern. To the best of our
knowledge, this is the first extensive study of the epidemiology of C. diphtheriae from India.
Amongst the total C. diphtheriae positive cases in this study, most of them were from Tamil
Nadu, Kerala and Uttar Pradesh (Lucknow) which indicates the burden of diphtheria in the
respective localities. Epidemiological surveillance provides significant understanding of the
clonal population of C. diphtheriae particularly in endemic region like India. The presented
MLST analysis of the C. diphtheriae isolates revealed great diversity among the isolates over
the years 2015–2020. The MLST analysis also includes isolates from the Kerala outbreak
reported in 2016 [6].
Fig 3. Illustration of the probable routes of transmission of STs identified in this study. The coloured circles represent the first occurrence of the ST and
the dotted arrow with colour indicates the possible transmission routes according to the year of isolation. The red dotted lines highlight the hotspot for novel
sequence types. Map outline was created using mapchart.net. Republished from mapchart.net under a CC BY license, with permission from MapChart,
original copyright 2021.
https://doi.org/10.1371/journal.pone.0261435.g003
The predominant sequence type in this study was ST466 (28.6%), a novel sequence type
which was first observed in the Kerala outbreak in 2016. Later in 2017, the ST was consistently
seen in Kerala and was also found in Lucknow and Chandigarh. While in 2018, it was found in
significant numbers in Lucknow, Uttar Pradesh and Madhya Pradesh which shows the ability
of this clone to disseminate rapidly. The second most common sequence type was ST405
(14.5%). This is an SLV of ST308 and was first observed in the year 2015 in Andhra Pradesh.
This clone further spread to Kerala in 2016. While in 2017, it was also seen in Tamil Nadu and
Karnataka. However, in 2018, ST405 was found endemic in Karnataka. Notably, all the identi-
fied novel sequence types evolved from established known sequence types by locus variations.
ST377 (9.2%) which was identified among isolates from Tamil Nadu in 2015, began to be
seen in Kerala after 2016. Whereas ST469 (7.8%) was first identified in Kerala in 2016 and
from 2017 it was also seen in Tamil Nadu.
Interestingly, a region-specific sequence type was identified in this study. ST301 which was
restricted to Lucknow was not found in any other region in India. ST301 was first identified in
2017 and continue to persist in Lucknow. A SLV of ST301 was identified and assigned the
novel type as ST576. This shows region specific emergence of novel clones due to SNPs in the
existing clones.
Results from this study reveal that C. diphtheriae strains are highly diverse. Till date differ-
ent STs have reported from different countries [9–11]. Such global outbreak associated clones
include, ST8, ST12, ST52, and ST66 from United Kingdom [9]. Similarly, ST378 and ST395
seems to be common in South Africa [11]. Whereas, in India ST405, ST466 and ST377 are
common as observed in this study. Moreover, the international clone, ST50 was identified in
2016 in Tamil Nadu and Andhra Pradesh. In 2017 and 2018 it was common in Karnataka
which shows the inter-state spread of the ST50 clone. Most of the STs identified in India are
diverse but the reason for this and the source of these clones is not well established. Socio-geo-
graphical approach is required to understand and identify the ancestral lineage of these clones.
It has been postulated that non-toxigenic strains occur more frequently in individuals who
have been previously immunized [12]. In this study, though the immunization status was not
known, 14% of strains were negative for toxin by PCR. Further, phylogenetic analysis revealed
that majority of the non-toxigenic strains were clustered in two different clades associated
with ST408 and ST542. These were mostly seen in isolates from Kerala. Non-toxigenic ST408
and ST542 were found to have evolved from the existing sequence types of toxigenic ST301
and ST377 respectively. This scenario could be due to the loss of genes that affect the expres-
sion of tox gene during the evolution.
MLST is a useful tool for evolutionary studies and for tracking the dissemination of clones.
However, there is a limitation in discriminating strains within the same ST due to continuing
change in their accessory genomes. Previous studies revealed that approximately one-third of
the C. diphtheriae genome encodes accessory genes that vary widely between strains. The
strains within individual STs differed by the presence or absence of up to 290 genes, which are
mostly present on the genomic islands [13]. This study clearly indicates the evolving genome
diversity of C. diphtheriae strains in India.
Clonal variation among the C. diphtheriae strains was observed in the study population.
The epidemiological analysis revealed the emergence of novel STs and the clones with better
dissemination properties. This indicates a rapid evolution of C. diphtheriae in India. In the
present study, ST466 was found to be the predominant sequence type with better adaptive and
dissemination capabilities. ST301 was identified as a region-specific toxigenic clone, from
which the non-toxigenic ST408 has evolved. This study has now revealed the pattern of circu-
lating STs of C. diphtheriae among the different regions of India.
Public Health, Trivandrum, Kerala; St. John’s Hospital, RIMS, Raichur and S. Nijalingappa
Medical College, Karnataka. The samples representing the North Indian population were col-
lected from the following centres: PGIMER, Chandigarh; KGMC, Lucknow; Bharathi Vidya
Peeth, Sangli, Maharashtra; and LTM Medical College, Mumbai.
Supporting information
S1 Table. Laboratory confirmation of C. diphtheriae cases at NRL for diphtheria, CMC,
Vellore.
(DOCX)
S2 Table. Distribution of sequence types among different states in India.
(DOCX)
S3 Table. Metadata including isolate ID, toxigenicity, STs, region and year of isolation for
C. diphtheriae isolates depicted in the MLST phylogeny Fig 2.
(XLSX)
Acknowledgments
The authors gratefully acknowledge the Institutional Review Board of the Christian Medical
College, Vellore (83-i/11/13) for approving the study and providing lab space and facilities.
Author Contributions
Conceptualization: Naveen Kumar Devanga Ragupathi, Dhiviya Prabaa Muthuirulandi
Sethuvel, Lucky Sangal, Balaji Veeraraghavan.
Data curation: Dhiviya Prabaa Muthuirulandi Sethuvel.
Formal analysis: Naveen Kumar Devanga Ragupathi, Vikas Gautam, Prashanth Gupta, Jaic-
hand Johnson, Naresh Chand Sharma, Ankur Mutreja, Arun Kumar, Pankaj Bhatnagar,
Balaji Veeraraghavan.
Funding acquisition: Pradeep Haldar, Arun Kumar, Pankaj Bhatnagar, Lucky Sangal.
Investigation: Naveen Kumar Devanga Ragupathi, Vikas Gautam, Prashanth Gupta, Jaichand
Johnson, Naresh Chand Sharma.
Methodology: Dhivya Murugan, Ranjini Ranjan.
Resources: Vikas Gautam, Prashanth Gupta, Jaichand Johnson, Naresh Chand Sharma, Pra-
deep Haldar, Arun Kumar, Pankaj Bhatnagar, Lucky Sangal.
Software: Naveen Kumar Devanga Ragupathi.
Supervision: Naveen Kumar Devanga Ragupathi, Balaji Veeraraghavan.
Validation: Naveen Kumar Devanga Ragupathi, Pradeep Haldar, Pankaj Bhatnagar, Lucky
Sangal, Balaji Veeraraghavan.
Writing – original draft: Naveen Kumar Devanga Ragupathi, Dhiviya Prabaa Muthuirulandi
Sethuvel, Lucky Sangal, Balaji Veeraraghavan.
Writing – review & editing: Ankur Mutreja, Pradeep Haldar, Arun Kumar, Pankaj Bhatnagar,
Lucky Sangal, Balaji Veeraraghavan.
References
1. Sharma NC, Efstratiou A, Mokrousov I, Mutreja A, Das B, Ramamurthy T. Diphtheria. Nat Rev Dis Prim-
ers. 2019; 5:81. https://doi.org/10.1038/s41572-019-0131-y PMID: 31804499
2. Meera M, Rajarao M. Diphtheria in Andhra Pradesh–a clinical-epidemiological study. Int J Infect Dis.
2014; 19:74–78. https://doi.org/10.1016/j.ijid.2013.10.017 PMID: 24295558
3. World Health Organization. Vaccine preventable diseases: monitoring system 2020 global summary;
2020. Available from: https://apps.who.int/immunization_monitoring/globalsummary/timeseries/
tsincidencediphtheria.html [accessed 05.05.2020].
4. Gupta A, Gujral M, Singh A, Chawla K. Diphtheria resurgence in India: A case study from south Karna-
taka. J Family Med Prim Care. 2020; 9:5776. https://doi.org/10.4103/jfmpc.jfmpc_480_20 PMID:
33532432
5. Murhekar MV. Resurgence of diphtheria in India. J Infect. 2020; 80:232–254. https://doi.org/10.1016/j.
jinf.2019.10.010 PMID: 31629864
6. Sangal L, Joshi S, Anandan S, Balaji V, Johnson J, Satapathy A, et al. Resurgence of diphtheria in
North Kerala, India, 2016: Laboratory supported case-based surveillance outcomes. Front Public
Health. 2017; 5:218. https://doi.org/10.3389/fpubh.2017.00218 PMID: 28913330
7. Veeraraghavan B, Anandan S, Rajamani Sekar SK, Gopi R, Devanga Ragupathi NK, Ramesh S, et al.
First report on the draft genome sequences of Corynebacterium diphtheriae isolates from India.
Genome Announc. 2016; 4:e01316–16. https://doi.org/10.1128/genomeA.01316-16 PMID: 27881543
8. Murhekar M. Epidemiology of diphtheria in India, 1996–2016: implications for prevention and control.
Am J Trop Med Hyg. 2017; 97:313–318. https://doi.org/10.4269/ajtmh.17-0047 PMID: 28722581
9. Bolt F, Cassiday P, Tondella ML, DeZoysa A, Efstratiou A, Sing A, et al. Multilocus sequence typing
identifies evidence for recombination and two distinct lineages of Corynebacterium diphtheriae. J Clin
Microbiol. 2010; 48:4177–4185. https://doi.org/10.1128/JCM.00274-10 PMID: 20844217
10. Farfour E, Badell E, Zasada A, Hotzel H, Tomaso H, Guillot S, et al. Characterization and comparison of
invasive Corynebacterium diphtheriae isolates from France and Poland. J Clin Microbiol. 2012; 50:173–
175. https://doi.org/10.1128/JCM.05811-11 PMID: 22090411
11. du Plessis M, Wolter N, Allam M, de Gouveia L, Moosa F, Ntshoe G, et al. Molecular Characterization of
Corynebacterium diphtheriae Outbreak Isolates, South Africa, March-June 2015. Emerg Infect Dis.
2017; 23:1308–1315. https://doi.org/10.3201/eid2308.162039 PMID: 28726616
12. Kanungo R, Vijayalakshmi N, Nalini P, Bhattacharya S. Diphtheria due to non-toxigenic Corynebacte-
rium diphtheriae: a report of two cases. Indian J Med Microbiol. 2002; 20:50. PMID: 17657027
13. Sangal V, Blom J, Sutcliffe IC, von Hunolstein C, Burkovski A, Hoskisson PA. Adherence and invasive
properties of Corynebacterium diphtheriae strains correlates with the predicted membrane-associated
and secreted proteome. BMC genomics. 2015; 16:1–5. https://doi.org/10.1186/1471-2164-16-1 PMID:
25553907
14. Clinical and Laboratory Standards Institute (CLSI 2016 Methods for antimicrobial dilution and disk sus-
ceptibility testing of infrequently isolated or fastidious bacteria. Document M45. 3rd ed. Wayne, PA:
CLSI
15. De Zoysa A, Efstratiou A, Mann G, Harrison TG, Fry NK. Development, validation and implementation
of a quadruplex real-time PCR assay for identification of potentially toxigenic corynebacteria. J Med
Microbiol. 2016; 65:1521–1527. https://doi.org/10.1099/jmm.0.000382 PMID: 27902437
16. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for big-
ger datasets. Mol Biol Evol. 2016; 33:1870–1874. https://doi.org/10.1093/molbev/msw054 PMID:
27004904
17. Letunic I, Bork P. Interactive Tree of Life (iTOL) v4: recent updates and new developments. Nucleic
Acids Res. 2019. 47:W256–W259. https://doi.org/10.1093/nar/gkz239 PMID: 30931475
18. Ribeiro-Gonçalves B, Francisco AP, Vaz C, Ramirez M, Carriço JA. PHYLOViZ Online: web-based tool
for visualization, phylogenetic inference, analysis and sharing of minimum spanning trees. Nucleic
Acids Res. 2016; 44:W246–W251. https://doi.org/10.1093/nar/gkw359 PMID: 27131357