Divergent evolution of Corynebacterium diphtheriae in India: An update from National Diphtheria Surveillance network.

Diphtheria is caused by a toxigenic bacterium Corynebacterium diphtheria which is being an emerging pathogen in India. Since diphtheria morbidity and mortality continues to be high in the country, the present study aimed to study the molecular epidemiology of C. diphtheriae strains from India. A total of 441 diphtheria suspected specimens collected as part of the surveillance programme between 2015 and 2020 were studied. All the isolates were confirmed as C. diphtheriae with standard biochemical tests, ELEK's test, and real-time PCR. Antimicrobial susceptibility testing for the subset of isolates showed intermediate susceptibility to penicillin and complete susceptible to erythromycin and cefotaxime. Isolates were characterized using multi locus sequence typing method. MLST analysis for the 216 C. diphtheriae isolates revealed major diversity among the sequence types. A total of 34 STs were assigned with majority of the isolates belonged to ST466 (30%). The second most common ST identified was ST405 that was present in 14% of the isolates. The international clone ST50 was also seen. The identified STs were grouped into 8 different clonal complexes (CC). The majority belongs to CC5 followed by CC466, CC574 and CC209, however a single non-toxigenic strain belongs to CC42. This epidemiological analysis revealed the emergence of novel STs and the clones with better dissemination properties. This study has also provided information on the circulating strains of C. diphtheriae among the different regions of India. The molecular data generated through surveillance system can be utilized for further actions in concern.

Genetic Diversity of Clinical Bordetella Pertussis ST2 Strains in comparison with Vaccine Reference Strains of India.

Objectives: Pertussis is a highly contagious disease of the respiratory tract caused by Bordetella pertussis, a bacterium that lives in the mouth, nose, and throat. Current study reports the highly accurate complete genomes of two clinical B. pertussis strains from India for the first time. Methods: Complete genome sequencing was performed for two B. pertussis strains using Ion Torrent PGM and Oxford nanopore sequencing method. Data was assembled de novo and the sequence annotation was performed through PATRIC and NCBI server. Downstream analyses of the isolates were performed using CGE server databases for antimicrobial resistance genes, plasmids, and sequence types. The phylogenetic analysis was performed using Roary. Results: The analysis revealed insertional elements flanked by IS481, which has been previously regarded as the important component for bacterial evolution. The two B. pertussis clinical strains exhibited diversity through genome degradation when compared to whole-cell vaccine reference strains of India. These isolates harboured multiple genetic virulence traits and toxin subunits, which belonged to sequence type ST2. Conclusion: The genome information of Indian clinical B. pertussis strains will serve as a baseline data to decipher more information on the genome evolution, virulence factors and their role in pathogenesis for effective vaccine strategies.

Spatiotemporal persistence of multiple, diverse clades and toxins of Corynebacterium diphtheriae.

Diphtheria is a respiratory disease caused by the bacterium Corynebacterium diphtheriae. Although the development of a toxin-based vaccine in the 1930s has allowed a high level of control over the disease, cases have increased in recent years. Here, we describe the genomic variation of 502 C. diphtheriae isolates across 16 countries and territories over 122 years. We generate a core gene phylogeny and determine the presence of antimicrobial resistance genes and variation within the tox gene of 291 tox+ isolates. Numerous, highly diverse clusters of C. diphtheriae are observed across the phylogeny, each containing isolates from multiple countries, regions and time of isolation. The number of antimicrobial resistance genes, as well as the breadth of antibiotic resistance, is substantially greater in the last decade than ever before. We identified and analysed 18 tox gene variants, with mutations estimated to be of medium to high structural impact.

Cholera outbreak investigation, Bhadola, Delhi, India, April-May 2018.

BACKGROUND: In the Gangetic plains of India, including Delhi, cholera is endemic. On 10 May 2018, staff at the north Delhi district surveillance unit identified a laboratory-confirmed cholera outbreak when five people tested positive for Vibrio cholerae O1 Ogawa serotype in Bhadola. We investigated to identify risk factors and recommend prevention measures. METHODS: We defined a case as ≥3 loose stools within 24 h in a Bhadola resident during 1 April-29 May 2018. We searched for cases house-to-house. In a 1 : 1 unmatched case control study, a control was defined as an absence of loose stools in a Bhadola resident during 1 April-29 May 2018. We selected cases and controls randomly. We tested stool samples for Vibrio cholerae by culture. We tested drinking water for fecal contamination. Using multivariable logistic regression we calculated adjusted ORs (aORs) with 95% CIs. RESULTS: We identified 129 cases; the median age was 14.5 y, 52% were females, 27% were hospitalized and there were no deaths. Symptoms were abdominal pain (54%), vomiting (44%) and fever (29%). Among 90 cases and controls, the odds of illness were higher for drinking untreated municipal water (aOR=2.3; 95% CI 1.0 to 6.2) and not knowing about diarrhea transmission (aOR=4.9; 95% CI 1.0 to 21.1). Of 12 stool samples, 6 (50%) tested positive for Vibrio cholerae O1 Ogawa serotype. Of 15 water samples, 8 (53%) showed growth of fecal coliforms. CONCLUSIONS: This laboratory-confirmed cholera outbreak associated with drinking untreated municipal water and lack of knowledge of diarrhea transmission triggered public health action in Bhadola, Delhi.

Prevalence of Multidrug Resistant Salmonellae with Increasing Frequency of Salmonella enterica Serovars Kentucky and Virchow among Hospitalized Diarrheal Cases in and around Delhi, India.

Non-typhoidal salmonellae (NTS) are a major cause of acute diarrhea with characteristic multidrug resistance (MDR). In a hospital-based study, 81 NTS were isolated and tested for serotypes and antimicrobial resistance (AMR). Salmonella enterica isolates were classified into 7 different typable serovars, however, 19 (23%) isolates remained untypable. The most common serovars were S. Kentucky (48%), and S. Virchow (22%). Most of the NTS isolates displayed resistance to nalidixic acid (NA) (73%), ciprofloxacin (CIP) (48%), ampicillin (AM) and norfloxacin (NOR) (36% each), and gentamicin (CN) (31%). The AMR profiles for CN and NA; and AM, CIP, NA and NOR, were found to be high in S. Virchow (83%) and S. Kentucky (43%), respectively. Analysis of the pulsed-field gel electrophoresis patterns of S. Kentucky revealed 3 clusters. S. Kentucky has clones closely related to become prominent in recent years in Delhi. The AMR appears to be consistent with the change in MDR patterns during 2014-2017. The observed prevalence of S. Kentucky and S. Virchow in large numbers of diarrheal cases is novel. The NTS are mostly resistant to fluoroquinolones, which is the current drug of choice for treating diarrheal cases. MDR is very common among clonally related S. Kentucky.

Diphtheria.

Diphtheria is a potentially fatal infection mostly caused by toxigenic Corynebacterium diphtheriae strains and occasionally by toxigenic C. ulcerans and C. pseudotuberculosis strains. Diphtheria is generally an acute respiratory infection, characterized by the formation of a pseudomembrane in the throat, but cutaneous infections are possible. Systemic effects, such as myocarditis and neuropathy, which are associated with increased fatality risk, are due to diphtheria toxin, an exotoxin produced by the pathogen that inhibits protein synthesis and causes cell death. Clinical diagnosis is confirmed by the isolation and identification of the causative Corynebacterium spp., usually by bacterial culture followed by enzymatic and toxin detection tests. Diphtheria can be treated with the timely administration of diphtheria antitoxin and antimicrobial therapy. Although effective vaccines are available, this disease has the potential to re-emerge in countries where the recommended vaccination programmes are not sustained, and increasing proportions of adults are becoming susceptible to diphtheria. Thousands of diphtheria cases are still reported annually from several countries in Asia and Africa, along with many outbreaks. Changes in the epidemiology of diphtheria have been reported worldwide. The prevalence of toxigenic Corynebacterium spp. highlights the need for proper clinical and epidemiological investigations to quickly identify and treat affected individuals, along with public health measures to prevent and contain the spread of this disease.

Publisher Correction: Genomic insights into the 2016-2017 cholera epidemic in Yemen.

In the HTML version of this Letter, the affiliations for authors Andrew S. Azman, Dhirendra Kumar and Thandavarayan Ramamurthy were inverted (the PDF and print versions of the Letter were correct); the affiliations have been corrected online.

Genomic insights into the 2016-2017 cholera epidemic in Yemen.

Yemen is currently experiencing, to our knowledge, the largest cholera epidemic in recent history. The first cases were declared in September 2016, and over 1.1 million cases and 2,300 deaths have since been reported1. Here we investigate the phylogenetic relationships, pathogenesis and determinants of antimicrobial resistance by sequencing the genomes of Vibrio cholerae isolates from the epidemic in Yemen and recent isolates from neighbouring regions. These 116 genomic sequences were placed within the phylogenetic context of a global collection of 1,087 isolates of the seventh pandemic V. cholerae serogroups O1 and O139 biotype El Tor2-4. We show that the isolates from Yemen that were collected during the two epidemiological waves of the epidemic1-the first between 28 September 2016 and 23 April 2017 (25,839 suspected cases) and the second beginning on 24 April 2017 (more than 1 million suspected cases)-are V. cholerae serotype Ogawa isolates from a single sublineage of the seventh pandemic V. cholerae O1 El Tor (7PET) lineage. Using genomic approaches, we link the epidemic in Yemen to global radiations of pandemic V. cholerae and show that this sublineage originated from South Asia and that it caused outbreaks in East Africa before appearing in Yemen. Furthermore, we show that the isolates from Yemen are susceptible to several antibiotics that are commonly used to treat cholera and to polymyxin B, resistance to which is used as a marker of the El Tor biotype.

Insights to the diphtheria toxin encoding prophages amongst clinical isolates of Corynebacterium diphtheriae from India.

Diphtheria is a dreadful disease caused by Corynebacterium diphtheriae. Lysogenised bacteriophages carrying toxin gene in C. diphtheriae can make the strain toxigenic. However, such phage disseminates the toxin genes to other strains when it undergoes lytic phase. As little is known about the phage diversity in C. diphtheriae in India, the present study was undertaken to investigate the prophages integrated into the genome of 29 clinical isolates of C. diphtheriae using whole-genome shotgun sequencing. Amongst these isolates, 27 were toxigenic, while 2 were non-toxigenic strains. Of the 27 toxigenic strains, all harbored known phages carrying toxin gene and two other phages with unknown function. However, the two non-toxin strains did not harbour any of the phages in the genome. It is imperative to devise prevention strategies that hinder the dissemination of toxin by prophages, as it may increase the complications of diphtheria post-immunisation.