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.

Outbreak of cholera caused by Vibrio cholerae O1 El Tor variant strain in Bihar, India.

An outbreak of cholera struck Bihar, an Indian state, in August 2008 following a massive flood. Here we report the phenotypic and genotypic characteristics of Vibrio cholerae strains isolated from patients with diarrhea. Rectal swabs were obtained from patients with diarrhea who were admitted to medical camps or the hospital, and the strains were biochemically and serologically characterized. V. cholerae was isolated from 21 (65.6%) of 32 rectal swabs. Serological studies revealed that all the 21 isolates belonged to V. cholerae O1 Ogawa. Mismatch amplification mutation assay (MAMA)-PCR showed that the isolates belonged to El Tor variant group, and pulsed-field gel electrophoresis (PFGE) proved that these isolates were of a different lineage than the conventional El Tor variant strains. These isolates were resistant to several drugs, including ampicillin, streptomycin, tetracycline, nalidixic acid, and furazolidone. The uniqueness of the current report arises from the fact that records of cholera in Bihar are availiable for the early 1960s but not for the next 4 decades. Moreover, the present study is the first to report a cholera outbreak in Bihar that was caused by an El Tor variant strain.

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.

Phage types of Vibrio cholerae O1 and O139 in the past decade in India.

Cholera has been a prevalent disease worldwide since the early 19th century. Vibrio cholerae O1 and O139 are the two serogroups that have been mainly implicated in causing cholera. This study reports the results of biotyping, serotyping and phage typing of V. cholerae O1 and O139 (1998-2007) strains received from different parts of India for the identification of the trends in the occurrence and spread of cholera in the country. However, there has been a notable steep decline in the occurrence of V. cholerae O139 strains over the past few years resulting in no strain of V. cholerae O139 being received from any part of India in 2007 and 2008. Of the total strains received, 79.1% were serotyped as Ogawa and the remaining 20.9% were found to be Inaba, which indicates that Ogawa was the predominant serotype. Almost 100% typeability was observed with the new scheme of V. cholerae O1, with type 27 being the dominant phage type and V. cholerae O139 strains were clustered into the predominant phage type T-1. From the phage typing and serotyping results, it can be concluded that V. cholerae O1 (T-27) and O139 (T-1) strains circulate throughout the country at any given time.

Emergence of multiple drug resistance Vibrio cholerae O1 in East Delhi.

INTRODUCTION: Considering the changing geographical and temporal occurrence of Vibrio cholerae, there is a continuing need to monitor the strain characteristics and antibiotic resistance patterns of this pathogen. The present study was conducted to document the changing biology of V. cholerae isolates in and around Delhi, India, and the development of antibiotic resistance. METHODOLOGY: A total of 1,424 stool samples or rectal swabs from patients with acute secretory diarrhoea admitted to Guru Teg Bahadur Hospital, Delhi, between January 2007 and December 2009 were processed using standard bacteriological methods. Strains identified as V. cholerae were further subjected to serogrouping, phage typing and antimicrobial susceptibility testing. Minimum inhibitory concentration (MIC) of gentamicin and tetracycline was determined. RESULTS: V. cholerae was isolated in 242/1,424 (17.0%) specimens. Of these, the majority were V. cholerae O1 serotype (98.3%) and serovar Ogawa. The drugs to which V. cholerae O1 isolates showed high levels of resistance were nalidixic acid, furazolidone, and cotrimoxazole throughout the study period, whereas strains were usually susceptible to chloramphenicol and cefotaxime. In 2007, there was a sudden increase of resistance to gentamicin and tetracycline, followed by a slow reversal to previous levels in subsequent years. The phage typing pattern (Basu and Mukherjee scheme) showed a dominance of phage type 2 throughout the study period. CONCLUSION: The importance of reporting all cases of V. cholerae, should be greatly emphasized, with the ultimate goal of understanding the constantly changing resistance patterns of this pathogen.

Genotypic characterization of Vibrio cholerae isolates using several DNA fingerprint techniques.

Serious pandemics of cholera have occurred throughout the known history of mankind, especially in India, which is a motherland for cholera disease. For the last 20 years several DNA-based typing methods have been employed to study the clonal relatedness between Vibrio cholerae isolates irrespective of their geographical locations. Traditional typing methods, such as biochemical tests, phage typing, serotyping, biotyping and antimicrobial susceptibility tests, have produced reliable and informative data regarding V. cholerae for a long time. Gradually molecular typing techniques have taken the place of traditional typing methods because they produce the same results upon repeat testing of V. cholerae strain. In this article we focus on the discriminatory power of different DNA fingerprint techniques that are generally used to know the homogeneity and heterogeneity among different V. cholerae isolates.

Multilocus variable-number tandem repeat analysis of Vibrio cholerae O1 El Tor strains harbouring classical toxin B.

Atypical Vibrio cholerae O1 strains - hybrid strains (strains that cannot be classified either as El Tor or classical biotype) and altered strains (El Tor biotype strains that produce classical cholera toxin) - are currently prevalent in Asia and Africa. A total of 74 hybrid and altered strains that harboured classical cholera toxin were investigated by multilocus variable-number tandem repeat analysis (MLVA). The results showed that the hybrid/altered strains could be categorized into three groups and that they were distant from the El Tor strain responsible for the seventh cholera pandemic. Hybrid/altered strains with a tandem repeat of the classical CTX prophage on the small chromosome were divided into two MLVA groups (group I: Mozambique/Bangladesh group; group III: Vietnam group), and altered strains with the RS1-CTX prophage containing the El Tor type rstR and classical ctxB on the large chromosome were placed in two MLVA groups (group II: India/Bangladesh group; group III: India/Vietnam group).

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.

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.

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.

Pathogenic potential of vibriophages against an experimental infection with Vibrio cholerae O1 in the RITARD model.

Cholera continues to be an important public health problem in developing countries, including India. This study concerns the feasibility of possible exploitation of bacteriophages as a biocontrol agent to eliminate the pathogen Vibrio cholerae from the gut using the removable intestinal tie-adult rabbit diarrhoea (RITARD) model. A control rabbit challenged with 10(9) colony-forming units (CFU)/mL of V. cholerae MAK 757 developed Grade II to IV diarrhoea, but the phage-treated rabbit that received 10(9)CFU/mL MAK 757 and 10(8) plaque-forming units (PFU)/mL cocktail phages produced only Grade II diarrhoea. Histological results revealed that in the control rabbit (MAK 757-treated), villi lost their normal shape and showed more inflammatory cellular infiltration in the lamina propria compared with the experimental rabbit. Our data suggest that phages could be valuable as prophylaxis against V. cholerae infection.

Classification of hybrid and altered Vibrio cholerae strains by CTX prophage and RS1 element structure.

Analysis of the CTX prophage and RS1 element in hybrid and altered Vibrio cholera O1 strains showed two classifiable groups. Group I strains contain a tandem repeat of classical CTX prophage on the small chromosome. Strains in this group either contain no element(s) or an additional CTX prophage or RS1 element(s) on the large chromosome. Group II strains harbor RS1 and CTX prophage, which has an E1 Tor type rstR and classical ctxB on the large chromosome.

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.

Phenotypic and molecular typing of Vibrio cholerae O1 and O139 isolates from India.

OBJECTIVES: To determine whether Vibrio cholerae strains with similar phage types are also genetically homogeneous or heterogeneous by molecular typing methods like PFGE and RAPD-PCR employed in this study. METHODS: A total of 26 V. cholerae O1 and O139 strains received from different parts of India were analyzed by using conventional phage typing method, antibiogram and molecular typing methods such as PFGE and RAPD-PCR. RESULTS: Both O1 and O139 strains were resistant against two antibiotics (Ampicillin and Furazolidone) were detected. All of these strains were clustered in a single phage type, i.e., Type 27 for V. cholerae O1 and Type 1 for V. cholerae O139. Extensive molecular characterization by RAPD and PFGE showed that six sets of O1 and O139 strains, each comprising two strains, had identical PFGE and RAPD profiles. Only one O139 strain (PL-4) had unique RAPD and PFGE profile among all the 26 V. cholerae strains used in this study. CONCLUSION: Apart from serology, the strains of V. cholerae can be discriminated by this conventional phage typing system that offers the basic information on identification, biotyping and discrimination of strains. But, a high level of heterogeneity was observed in RAPD and PFGE profiles indicating the clonal diversity of V. cholerae O1 and O139 strains. It was concluded that these strains were phenotypically identical through phage typing system and antibiogram but genetically dissimilar, as shown in molecular typing systems.