Abolishment of morphology-based taxa and change to binomial species names: 2022 taxonomy update of the ICTV bacterial viruses subcommittee.

This article summarises the activities of the Bacterial Viruses Subcommittee of the International Committee on Taxonomy of Viruses for the period of March 2021-March 2022. We provide an overview of the new taxa proposed in 2021, approved by the Executive Committee, and ratified by vote in 2022. Significant changes to the taxonomy of bacterial viruses were introduced: the paraphyletic morphological families Podoviridae, Siphoviridae, and Myoviridae as well as the order Caudovirales were abolished, and a binomial system of nomenclature for species was established. In addition, one order, 22 families, 30 subfamilies, 321 genera, and 862 species were newly created, promoted, or moved.

Bacterial Viruses Subcommittee and Archaeal Viruses Subcommittee of the ICTV: update of taxonomy changes in 2021.

In this article, we - the Bacterial Viruses Subcommittee and the Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV) - summarise the results of our activities for the period March 2020 - March 2021. We report the division of the former Bacterial and Archaeal Viruses Subcommittee in two separate Subcommittees, welcome new members, a new Subcommittee Chair and Vice Chair, and give an overview of the new taxa that were proposed in 2020, approved by the Executive Committee and ratified by vote in 2021. In particular, a new realm, three orders, 15 families, 31 subfamilies, 734 genera and 1845 species were newly created or redefined (moved/promoted).

Taxonomy of prokaryotic viruses: 2018-2019 update from the ICTV Bacterial and Archaeal Viruses Subcommittee.

This article is a summary of the activities of the ICTV's Bacterial and Archaeal Viruses Subcommittee for the years 2018 and 2019. Highlights include the creation of a new order, 10 families, 22 subfamilies, 424 genera and 964 species. Some of our concerns about the ICTV's ability to adjust to and incorporate new DNA- and protein-based taxonomic tools are discussed.

Retrospective genomic analysis of Vibrio cholerae O1 El Tor strains from different places in India reveals the presence of ctxB-7 allele found in Haitian isolates.

A total of 45 strains of Vibrio cholerae O1 isolated from 10 different places in India where they were associated with cases of cholera between the years 2007 and 2008 were examined by molecular methods. With the help of phenotypic and genotypic tests the strains were confirmed to be O1 El Tor biotype strains with classical ctxB gene. Polymerase chain reaction (PCR) analysis by double - mismatch amplification mutation assay PCR showed 16 of these strains carried the ctxB-7 allele reported in Haitian strains. Sequencing of the ctxB gene in all the 45 strains revealed that in 16 strains the histidine at the 20th amino acid position had been replaced by asparagine and this single nucleotide polymorphism did not affect cholera toxin production as revealed by beads enzyme-linked immunosorbent assay. This study shows that the new ctxB gene sequence was circulating in different places in India. Seven representatives of these 45 strains analysed by pulsed - field gel electrophoresis showed four distinct Not I digested profiles showing that multiple clones were causing cholera in 2007 and 2008.

Vibrio cholerae typing phage N4: genome sequence and its relatedness to T7 viral supergroup.

OBJECTIVES: In countries where cholera is endemic, Vibrio cholerae O1 bacteriophages have been detected in sewage water. These have been used to serve not only as strain markers, but also for the typing of V. cholerae strains. Vibriophage N4 (ATCC 51352-B1) occupies a unique position in the new phage-typing scheme and can infect a larger number of V. cholerae O1 biotype El Tor strains. Here we characterized the complete genome sequence of this typing vibriophage. METHODS: The complete DNA sequence of the N4 genome was determined by using a shotgun sequencing approach. RESULTS: Complete genome sequence explored that phage N4 is comprised of one circular, double-stranded chromosome of 38,497 bp with an overall GC content of 42.8%. A total of 47 open reading frames were identified and functions could be assigned to 30 of them. Further, a close relationship with another vibriophage, VP4, and the enterobacteriophage T7 could be established. DNA-DNA hybridization among V. cholerae O1 and O139 phages revealed homology among O1 vibriophages at their genomic level. CONCLUSIONS: This study indicates two evolutionary distinctive branches of the possible phylogenetic origin of O1 and O139 vibriophages and provides an unveiled collection of information on viral gene products of typing vibriophages.

Evaluation of VcA VNTR as a strain-typing and phylogeny study method of Vibrio cholerae strains.

This study attempted to examine the relatedness between RAPD-PCR, PFGE and VcA VNTR results with those of conventional phage typing of V. cholerae strains and to evaluate VcA VNTR as an indispensable molecular-typing tool that accomplishes the urgent need for effective epidemiological surveillance. All the O1 El Tor strains were predominantly clustered into phage type T27 with the new phage-typing scheme. Using RAPD-PCR, a total of 69 O1 El Tor strains were grouped under 16 different electrophoretic patterns. A total of 33 pulsotypes were identified in these strains by PFGE. VcA VNTR revealed high VcA polymorphism in all V. cholerae strains incorporated in this study. Our results underline the considerable potential of VcA VNTR analysis as a tool for molecular typing of V. cholerae.

Development of simple and rapid PCR-fingerprinting methods for Vibrio cholerae on the basis of genetic diversity of the superintegron.

AIMS: To develop simple and rapid PCR-fingerprinting methods for Vibrio cholerae O1 (El Tor and classical biotypes) and O139 serogroup strains which cause major cholera epidemics, on the basis of the diversity of superintegron (SI) carried by these strains. METHODS AND RESULTS: PCR-restriction fragment length polymorphism (PCR-RFLP) assay was developed targeting region between integrase gene in the SI and its nearby ORF, followed by BglI digestion. Besides, a V. cholerae repeat-amplified fragment length polymorphism (VCR-AFLP) assay was also developed. In the PCR-RFLP, 94 El Tor, 29 classical and 54 O139 strains produced nine, three and six different DNA fingerprints, respectively. On the other hand, VCR-AFLP distinguished these El Tor, classical and O139 strains into five, nine and two DNA fingerprints, respectively. Combining both assays the El Tor, classical and O139 strains could be differentiated into 11, 10 and seven different types, respectively. In a comparative study, pulsed-field gel electrophoresis (PFGE) showed similar differentiation for El Tor (11 types), but lower discrimination for O139 (two types) and classical strains (five types). CONCLUSIONS: The PCR assays based on SI diversity can be used as a useful typing tool for epidemiological studies of V. cholerae. SIGNIFICANCE AND IMPACT OF STUDY: This newly developed method is more discriminatory, simple, rapid and cost-effective in comparison with PFGE, and thus can be widely applicable.

Detection of virulence-associated and regulatory protein genes in association with phage typing of human Vibrio cholerae from several geographical regions of the world.

Vibrio cholerae O1, O139 and occasionally non-O1/non-O139 serogroups are most often responsible for epidemic and pandemic cholera. This study used genotypic patterns of PCR-based detection of virulence-associated and regulatory protein genes, along with phage typing, to characterize 86 V. cholerae strains. Thirty-eight of 53 O1 biotype El Tor strains harboured both tcpA classical and tcpA El Tor genes, and three El Tor strains lacked the V. cholerae O1-specific gene (Vc-O1); three O139 strains contained both Vc-O1 and Vc-O139 genes and seven out of ten non-O1/non-O139 strains possessed the Vc-O1 gene. The latter strains all harboured the virulence-associated genes ctxA, zot, ace, RS1, hlyA, ompU, rtxA and sxt. Two phage types, T27 and T25, were predominant in strains from different geographical regions of India, whereas more variation in phage susceptibility was observed for tetracycline-resistant strains from Kolkata. These results suggest that the pattern and distribution of virulence genes and phage types of V. cholerae are equally useful and discriminatory in tracing the origin of newly emerging strains.

Epidemiology & antibiograms of Vibrio cholerae isolates from a tertiary care hospital in Chandigarh, north India.

BACKGROUND & OBJECTIVE: Cholera is endemic in Chandigarh and its surrounding areas. This retrospective study was undertaken over a period of nine years (January 1999-December 2007) from a tertiary care hospital in north India to understand the changing epidemiology aspects and antibiotic resistance patterns in Vibrio cholerae isolates. METHODS: A total of 277 isolates of V. cholerae were included in the study. V. cholerae was identified by standard microbiological procedures. Antibiotic sensitivity testing was performed by disc diffusion method and isolates phage typed. RESULTS: All the isolates were identified as V. cholerae O1 biotype El Tor serotype Ogawa; phage 27 was the predominant type. Men were more commonly affected with maximum number in the age group 0-5 yr. Majority of the isolates were resistant to furazolidone but sensitive to gentamicin and cefotaxime. Resistance pattern to amoxycillin was variable. Three isolates were found to be resistant to ciprofloxacin. All the patients presented during June-October coinciding with the monsoon season and a majority were from suburbs. INTERPRETATION & CONCLUSION: The emergence of resistance amongst V. cholerae especially towards ciprofloxacin may significantly influence the control strategies in future outbreaks. Phage 27 remained the predominant type in all the years. Continuous surveillance with regard to drug resistance, early detection and a strong regional commitment may help contain the disease.

Occurrence, significance & molecular epidemiology of cholera outbreaks in West Bengal.

BACKGROUND & OBJECTIVE: Diarrhoeal disease outbreaks are causes of major public health emergencies in India. We carried out investigation of two cholera outbreaks, for identification, antimicrobial susceptibility testing, phage typing and molecular characterization of isolated Vibrio cholerae O1, and to suggest prevention and control measures. METHODS: A total of 22 rectal swabs and 20 stool samples were collected from the two outbreak sites. The V. cholerae isolates were serotyped and antimicrobial susceptibility determined. Pulsed- field gel electrophoresis (PFGE) was performed to identify the clonality of the V. cholerae strains which elucidated better understanding of the epidemiology of the cholera outbreaks. RESULTS: Both the outbreaks were caused by V. cholerae O1 (one was caused by serotype Ogawa and the other by serotype Inaba). Clinically the cases presented with profuse watery diarrhoea and dehydration. All the tested V. cholerae isolates were sensitive to tetracycline, gentamycin and azithromycin but resistance for ampicillin, co-trimoxazole, nalidixic acid, and furazolidone. PFGE pattern of the isolates from the two outbreaks revealed that they were clonal in origin. Stoppage of the source of water contamination and chlorination of drinking water resulted in terminating the two outbreaks. INTERPRETATION & CONCLUSION: The two diarrhoeal outbreaks were caused by V. cholerae O1 (Inaba/Ogawa). Such outbreaks are frequently seen in cholera endemic areas in many parts of the world. Vaccination is an attractive disease (cholera) prevention strategy although long-term measures like improvement of sanitation and personal hygiene, and provision of safe water supply are important, but require time and are expensive.

Epidemiological, microbiological & electron microscopic study of a cholera outbreak in a Kolkata slum community.

BACKGROUND & OBJECTIVE: Epidemics of cholera caused by Vibrio cholerae O1 or O139 have been reported from different parts of India. Factors such as unsafe water supply, poor environmental sanitation, indiscriminate defaecation and lack of personal hygiene are mainly responsible for continued transmission of this disease. We report here epidemiological and microbiological findings of a localized outbreak of cholera, which occurred during March and April 2004 in the eastern part of Kolkata city. METHODS: The affected slum area has a population of 4409, predominantly muslims. Patients suffering from acute watery diarrhoea attended the health outposts organized by National Institute of Cholera and Enteric Diseases, Kolkata and International Vaccine Institute, South Korea as part of a routine surveillance programme at the locality as well as the emergency medical camp organized by the Kolkata Municipal Corporation. Stool and water samples were collected and tested for diarrhoeagenic pathogens in the laboratory. Bacteriophages specific for V. cholerae were isolates and studied electron microscopically for morphology. RESULTS: A total of 89 diarrhoea cases were reported giving an attack rate of 2 per cent. V. cholerae O1 biotype ElTor, serotype Ogawa was isolated as a sole pathogen from 15 (15.8%) of 89 stool samples screened. Water samples (2 from tube wells, 3 from municipal taps and 1 from well) showed presence of coliform bacilli with high MPN (Most Probable Number) count. Bacteriophages specific to V. cholerae were isolated from 2 of 6 water samples examined. A leakage was detected in the main pipeline supplying drinking water to that area. INTERPRETATION & CONCLUSION: The outbreak was caused by V. cholerae O1 (Ogawa) biotype ElTor. The presence of phages in the water samples was an additional indicator for V. cholerae contamination in this community. Occurrences of such outbreaks support vaccination against cholera as an alternative strategy.

Isolation of Vibrio cholerae 0139 phages to develop a phage typing scheme.

Five V. cholerae 0139 phages isolated from different parts of India have been used for phage typing study. A strain isolated from Nagpur city (NPR-4) was used as the host for phage propagation. All but one of the 260 strains of V. cholerae 0139 were found to be typeable and could be clustered into 8 distinct phage types as revealed by lytic patterns. Phage type 1 was the predominant type (61.15%) followed by type 2 (18.46%). The strains isolated from Madras exhibited 7 out of 8 phage types. These newly isolated phages could be adopted for phage typing of V. cholerae 0139 strains as an epidemiological tool.

Bacteriological profile of cholera in Tamil Nadu (1980-2001).

BACKGROUND & OBJECTIVE: In addition to Vibrio cholerae O1, a recently emerged non-O1 serotype, V. cholerae O139 has also been found to be responsible for epidemics of cholera. In the context of the changing etiology of cholera, the occurrence of different serotypes, biotypes and phage types of V. cholerae in Tamil Nadu is presented. METHODS: Between 1980 and 2001, 26,502 stool/rectal swabs from patients suspected to have cholera were processed for the presence of V. cholerae at the King Institute of Preventive Medicine, Chennai (Madras), Tamil Nadu. Serotypes, biotypes and phage types (Basu & Mukerjee and new phage typing method) of the isolates were determined. Antimicrobial susceptibility determination was included from 1997 onwards. RESULTS: Of the 26,502 stool/rectal swabs tested, 6035 (22.8%) specimens yielded V. cholerae. 4,046 (67%) of them were O1 serotype; followed by 1529 (25.3%) O139 serotype and 448 (7.4%) non-O1 serotypes other than O139 were encountered. Twelve specimens yielded rough strains of V. cholerae. All V. cholerae O1 were the biotype ElTor and the predominant serotype was Ogawa (95.9%). After the initial explosive epidemic by O139 serotype in late 1992 and early 1993 occurrence of this serotype had declined. Resurgence of this new serotype was observed in 1997. O1 domination was observed during 1995 and 1996. The new phage typing scheme for V. cholerae O1 was able to differentiate the isolates into 22 types, type 27 (68.2%) being the predominant one followed by type 26 (12.3%). In Basu & Mukerjee scheme, the isolates were clustered between two types--type 2 (34%) and type 4 (61%). Further, about 5 per cent of them were untypeable. All but a few of the isolates irrespective of serotype, were susceptible to chloramphenicol, tetracycline, gentamicin and ciprofloxacin. 97 per cent of the O1 strains and 48.9 per cent of the O139 strains were resistant to cotrimoxazole. INTERPRETATION & CONCLUSION: V. cholerae O139 might have the ability to survive during interepidemic periods. Both V. cholerae O1 and O139--the two serotypes with epidemic potential seem to be firmly established in this region. This situation warrants constant surveillance.

Outbreak of cholera due to Vibrio cholerae 01 in Orissa state.

During May-June 1993, an outbreak of acute diarrhoea resulting in deaths primarily in adults was reported in two districts of Orissa state. Epidemiological and microbiological investigations revealed that this outbreak was caused by V. cholerae 01 biotype EITor. V. cholerae 01 strains were uniformly resistant to furazolidone.

An outbreak of acute diarrhoeal disease amongst tribal population in Tripura.

A massive outbreak of acute diarrhoeal diseases occurred during March-April, 1992 in the north district of Tripura. Investigation of the outbreak revealed Vibrio cholerae 01 biotype ElT or as the main etiologic agent in 50 per cent of patients. The outbreak which started amongst the tribal population might have spread due to prevailing illiteracy, poverty, low personal and domestic hygiene and vulnerable water sources (chhara water).

Biological activity & interaction of Vibrio cholerae bacteriophages in rabbit ileal loop.

A set of ten V. cholerae EITor phages is in routine use for phage typing of V. cholerae O1 biotype EITor strains. These phages were used in rabbit ileal loop experiment to investigate whether these phages have any prophylactic value as regards their lytic capability on V. cholerae strains. The phages were found to have no prophylactic use as they were unable to lyse the standard bacterial strain V. cholerae MAK 757.

Validity of new phage typing scheme against Vibrio cholerae 01 biotype ElTor strains.

A total of 538 strains of V. cholerae 01 biotype ElTor were phage typed by the conventional Basu and Mukerjee and also the new typing scheme developed at the National Institute of Cholera and Enteric Diseases, Calcutta. The strains could be clustered into seven types by the new scheme as against only two by the conventional method. The results provide conclusive evidence on the validity of the new scheme for phage typing of V. cholerae strains.

Distribution of phage type of Vibrio cholerae O1 biotype ElTor in Indian scenario (1991-98).

During the period 1991-98, distribution of biotype, serotype and phage type of V. cholerae O1 strains isolated from different parts of the country and referred to the National Institute of Cholera and Enteric Diseases, Calcutta were studied. Of the 8101 strains received, 5613 (69.2%) were subjected to phage typing. All these strains belonged to the biotype ElTor and Ogawa was the predominant serotype (96.08%). The strains were clustered into only two types--types 2 and 4 and around 10 per cent strains remained untypable. However, using the new scheme, all these strains were found to be typable and 8 major types were recognized of which type number 27 was the predominant type (66.12%). The distribution of a common type throughout the country suggests that a particular clone of V. cholerae O1 is probably circulating all over India. A constant monitoring through phage typing is necessary to observe the emergence of any new clone of V. cholerae O1 in India.

An el tor cholera outbreak amongst tribal population in Tripura.

An outbreak of acute diarrhoeal disease occurred in Dhalai and North Tripura district, Tripura during month of May 2004. An investigation was done to identify causative agent with anti microbial susceptibility pattern and to know the epidemiological feature. Overall attack rate and Case Fatality Rate (CFR) was 18.8%. and 6.9/1000 respectively. Vibrio cholerae O1 biotype El Tor, Ogawa was isolated as sole pathogen in 40% of hospitalized acute diarrhoea patient and from a water samples examined. The strains were sensitive to Tetracycline, Doxycycline, Norfloxacin, Ciprofloxacin, Chloramphenicol, and Azithromycin. Bad peridomestic sanitation, use of contaminated surface water along with low literacy, lack of personal hygiene, frequent movement might be the factor associated with persistence and spread of pathogen amongst tribal groups leading to outbreak of cholera.