First Report on the Draft Genome Sequences of Corynebacterium diphtheriae Isolates from India

Veeraraghavan, Balaji; Anandan, Shalini; Sekar, Suresh Kumar Rajamani; Gopi, Radha; Ragupathi, Naveen Kumar Devanga; Ramesh, Srilekha; Verghese, Valsan Philip; Korulla, Sophy; Mathai, Sarah; Sangal, Lucky; Joshi, Sudhir

doi:10.1128/genomea.01316-16

Cited by 5 publications

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“…The toxigenic strains sequenced in this study were characterized using traditional phenotypic and whole genome-based MLST typing methods. Seven of the toxigenic C. diphtheriae isolates (WD37, WD45, WD 46, WD57, WD71, WD76, and WD138) sequenced in this study represents the novel ST, ST-405, which was reported in our previous study isolates from Kadapa region of Andhra Pradesh ( 8 ). This implicates that same ST is circulating in two different states of South India (Andhra Pradesh and Kerala).…”

Section: Discussionsupporting

confidence: 54%

“…Twenty-one lab confirmed isolates were subjected to whole genome sequencing by Ion torrent next generation sequencing technology as described in our previous study ( 8 ). Briefly, the whole genomic DNA was extracted as described before, and the purified DNA was used for the preparation of library fragments using the Ion Plus fragment library kit (Ion Torrent; Life Technologies, USA).…”

Section: Methodsmentioning

confidence: 99%

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Resurgence of Diphtheria in North Kerala, India, 2016: Laboratory Supported Case-Based Surveillance Outcomes

Sangal

Joshi

Anandan

et al. 2017

Front. Public Health

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introduction: As part of national program, laboratory supported vaccine preventable diseases surveillance was initiated in Kerala in 2015. Mechanisms have been strengthened for case investigation, reporting, and data management. Specimens collected and sent to state and reference laboratories for confirmation and molecular surveillance. The major objective of this study is to understand the epidemiological information generated through surveillance system and its utilization for action.Methods: Surveillance data captured from reporting register, case investigation forms, and laboratory reports was analyzed. Cases were allotted unique ID and no personal identifying information was used for analysis. Throat swabs were collected from investigated cases as part of surveillance system. All Corynebacterium diphtheriae isolates were confirmed with standard biochemical tests, ELEK's test, and real-time PCR. Isolates were characterized using whole genome-based multi locus sequence typing method. Case investigation forms and laboratory results were recorded electronically. Public health response by government was also reviewed.results: A total of 533 cases were identified in 11 districts of Kerala in 2016, of which 92% occurred in 3 districts of north Kerala; Malappuram, Kozhikode, and Kannur. Almost 79% cases occurred in >10 years age group. In <18 years age group, 62% were male while in ≥18 years, 69% were females. In <10 years age group, 31% children had received three doses of diphtheria vaccine, whereas in ≥10 years, 3% cases had received all doses. Fifteen toxigenic C. diphtheriae isolates represented 6 novel sequence types (STs) . Other STs observed are ST-50, ST-295, and ST-377.conclusion: Diphtheria being an emerging pathogen, establishing quality surveillance for providing real-time information on disease occurrence and mortality is imperative. The epidemiological data thus generated was used for targeted interventions and to 2 Sangal et al.

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Section: Discussionsupporting

confidence: 54%

Section: Methodsmentioning

confidence: 99%

Resurgence of Diphtheria in North Kerala, India, 2016: Laboratory Supported Case-Based Surveillance Outcomes

Sangal

Joshi

Anandan

et al. 2017

Front. Public Health

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“…DNA was extracted using Qiasymphony (Qiagen) as per manufacturer’s instructions. The whole genome sequencing was done with Ion Torrent PGM platform using 400 bp read chemistry as described in our previous report [ 12 ]. Raw reads were assembled de novo using Assembler SPAdes software v5.0 in Torrent suite server version 4.4.3.…”

Section: Methodsmentioning

confidence: 99%

Whole genome analysis of hypervirulent Klebsiella pneumoniae isolates from community and hospital acquired bloodstream infection

et al. 2018

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BackgroundHypervirulent K. pneumoniae (hvKp) causes severe community acquired infections, predominantly in Asia. Though initially isolated from liver abscesses, they are now prevalent among invasive infections such as bacteraemia. There have been no studies reported till date on the prevalence and characterisation of hvKp in India. The objective of this study is to characterise the hypervirulent strains isolated from bacteraemic patients for determination of various virulence genes and resistance genes and also to investigate the difference between healthcare associated and community acquired hvKp with respect to clinical profile, antibiogram, clinical outcome and molecular epidemiology.ResultsSeven isolates that were susceptible to all of the first and second line antimicrobials and phenotypically identified by positive string test were included in the study. They were then confirmed genotypically by presence of rmpA and rmpA2 by PCR. Among the study isolates, four were from patients with healthcare associated infections; none were fatal. All patients with community acquired infection possessed chronic liver disease with fatal outcome. Genes encoding for siderophores such as aerobactin, enterobactin, yersiniabactin, allantoin metabolism and iron uptake were identified by whole genome sequencing. Five isolates belonged to K1 capsular type including one K. quasipneumoniae. None belonged to K2 capsular type. Four isolates belonged to the international clone ST23 among which three were health-care associated and possessed increased virulence genes. Two novel sequence types were identified in the study; K. pneumoniae belonging to ST2319 and K. quasipneumoniae belonging to ST2320. Seventh isolate belonged to ST420.ConclusionThis is the first report on whole genome analysis of hypervirulent K. pneumoniae from India. The novel sequence types described in this study indicate that these strains are evolving and hvKp is now spread across various clonal types. Studies to monitor the prevalence of hvKp is needed since there is a potential for the community acquired isolates to develop multidrug resistance in hospital environment and may pose a major challenge for clinical management.

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“…We generated a maximum-likelihood phylogenetic tree by using RaxML version 8 ( 21 ). To contextualize the South Africa isolates, we included C. diphtheriae genomes from ATCC and NCTC control strains ( Table 1 ) together with publicly available genomes from Brazil (n = 3) ( 5 ), India (n = 2) ( 22 ), and Malaysia (n = 2) ( 23 ) (selected from GenBank). We identified CRISPR-Cas systems in silico with the online CRISPRFinder program ( 24 ) and determined CRISPR-Cas cassettes by using the classification and nomenclature described by Makarova et al ( 25 ).…”

Section: Methodsmentioning

confidence: 99%

Molecular Characterization ofCorynebacterium diphtheriaeOutbreak Isolates, South Africa, March–June 2015

Plessis¹,

Wolter²,

Allam³

et al. 2017

Emerg. Infect. Dis.

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In 2015, a cluster of respiratory diphtheria cases was reported from KwaZulu-Natal Province in South Africa. By using whole-genome analysis, we characterized 21 Corynebacterium diphtheriae isolates collected from 20 patients and contacts during the outbreak (1 patient was infected with 2 variants of C. diphtheriae). In addition, we included 1 cutaneous isolate, 2 endocarditis isolates, and 2 archived clinical isolates (ca. 1980) for comparison. Two novel lineages were identified, namely, toxigenic sequence type (ST) ST-378 (n = 17) and nontoxigenic ST-395 (n = 3). One archived isolate and the cutaneous isolate were ST-395, suggesting ongoing circulation of this lineage for >30 years. The absence of preexisting molecular sequence data limits drawing conclusions pertaining to the origin of these strains; however, these findings provide baseline genotypic data for future cases and outbreaks. Neither ST has been reported in any other country; this ST appears to be endemic only in South Africa.

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First Report on the Draft Genome Sequences of Corynebacterium diphtheriae Isolates from India

Abstract: We report here the draft genome sequences of five Corynebacterium diphtheriae isolates of Indian origin. The C. diphtheriae isolates TH1141, TH510, TH1526, TH1337, and TH2031 belong to sequence type ST-50, ST-295, ST-377, ST-405, and ST-405, with an average genome size of 2.5 Mbp.

Cited by 5 publications

References 5 publications

Resurgence of Diphtheria in North Kerala, India, 2016: Laboratory Supported Case-Based Surveillance Outcomes

Resurgence of Diphtheria in North Kerala, India, 2016: Laboratory Supported Case-Based Surveillance Outcomes

Whole genome analysis of hypervirulent Klebsiella pneumoniae isolates from community and hospital acquired bloodstream infection

Molecular Characterization ofCorynebacterium diphtheriaeOutbreak Isolates, South Africa, March–June 2015

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