scholarly journals Genomic contextualisation of ancient DNA molecular data from an Argentinian fifth pandemic Vibrio cholerae infection

2021 ◽  
Vol 7 (6) ◽  
Author(s):  
Matthew J. Dorman ◽  
Nicholas R. Thomson ◽  
Josefina Campos
Keyword(s):  
Latin America ◽  
Vibrio Cholerae ◽  
Ancient Dna ◽  
Type Species ◽  
Molecular Data ◽  
Molecular Evidence ◽  
Genomic Context ◽  
Content Type ◽  
The Past ◽  
Link Type

Specific lineages of serogroup O1 Vibrio cholerae are notorious for causing cholera pandemics, of which there have been seven since the 1800s. Much is known about the sixth pandemic (1899–1923) and the ongoing seventh pandemic (1961–present), but we know very little about the bacteriology of pandemics 1 to 5. Moreover, although we are learning about the contribution of non-O1 non-pandemic V. cholerae to cholera dynamics during the current pandemic, we know almost nothing about their role in the past. A recent ancient DNA study has presented what may be the first molecular evidence of a V. cholerae infection from the fifth cholera pandemic period (1886–1887 AD) in Argentina. Here, we place the molecular evidence from that study into the genomic context of non-pandemic V. cholerae from Latin America and elsewhere, and show that a gene fragment amplified from ancient DNA is most similar to that of V. cholerae from the Americas, and from Argentina. Our results corroborate and reinforce the findings of the original study, and collectively suggest that even in the 1880s, non-pandemic V. cholerae local to the Americas may have caused sporadic infections in Argentina, just as we know this to have happened during the seventh pandemic in Latin America.

scholarly journals Vibrio metoecus sp. nov., a close relative of Vibrio cholerae isolated from coastal brackish ponds and clinical specimens

2014 ◽  
Vol 64 (Pt_9) ◽  
pp. 3208-3214 ◽  
Author(s):  
Paul C. Kirchberger ◽  
Maryann Turnsek ◽  
Dana E. Hunt ◽  
Bradd J. Haley ◽  
Rita R. Colwell ◽  
...  
Keyword(s):  
Vibrio Cholerae ◽  
Type Species ◽  
The United States ◽  
Nucleotide Identity ◽  
Close Relative ◽  
Average Nucleotide Identity ◽  
Content Type ◽  
The Past ◽  
Link Type ◽  
Close Resemblance

A Gram-staining-negative, curved-rod-shaped bacterium with close resemblance to Vibrio cholerae , the aetiological agent of cholera, was isolated over the course of several years from coastal brackish water (17 strains) and from clinical cases (two strains) in the United States. 16S rRNA gene identity with V. cholerae exceeded 98 % yet an average nucleotide identity based on genome data of around 86 % and multi locus sequence analysis of six housekeeping genes (mdh, adk, gyrB, recA, pgi and rpoB) clearly delineated these isolates as a distinct genotypic cluster within the V. cholerae – V. mimicus clade. Most standard identification techniques do not differentiate this cluster of isolates from V. cholerae . Only amplification of the ompW gene using V. cholerae -specific primers and a negative Voges–Proskauer test showed a difference between the two clusters. Additionally, all isolated strains differed phenotypically from V. cholerae in their ability to utilize N-acetyl-d-galactosamine and d-glucuronic acid as sole carbon sources. Furthermore, they were generally unable to infect the slime mould Dictyostelium discoideum, a widespread ability in V. cholerae . Based on these clear phenotypic differences that are not necessarily apparent in standard tests as well as average nucleotide identity and phylogeny of protein-coding genes, we propose the existence of a novel species, Vibrio metoecus sp. nov. with the type strain OP3HT ( = LMG 27764T = CIP 110643T). Due to its close resemblance to V. cholerae and the increasing number of strains isolated over the past several years, we suggest that V. metoecus sp. nov. is a relatively common species of the genus Vibrio , isolates of which have been identified as atypical isolates of V. cholerae in the past. Its isolation from clinical samples also indicates that strains of this species, like V. cholerae , are opportunistic pathogens.

Two regulatory factors of Vibrio cholerae activating the mannose-sensitive haemagglutinin pilus expression is important for biofilm formation and colonization in mice

Microbiology ◽  
2021 ◽  
Vol 167 (10) ◽  
Author(s):  
Mengting Shi ◽  
Yue Zheng ◽  
Xianghong Wang ◽  
Zhengjia Wang ◽  
Menghua Yang
Keyword(s):  
Mouse Model ◽  
Vibrio Cholerae ◽  
Biofilm Formation ◽  
Type Species ◽  
Wild Type ◽  
Expression Library ◽  
Content Type ◽  
Genomic Expression ◽  
Infant Mouse ◽  
Link Type

Vibrio cholerae the causative agent of cholera, uses a large number of coordinated transcriptional regulatory events to transition from its environmental reservoir to the host intestine, which is its preferred colonization site. Transcription of the mannose-sensitive haemagglutinin pilus (MSHA), which aids the persistence of V. cholerae in aquatic environments, but causes its clearance by host immune defenses, was found to be regulated by a yet unknown mechanism during the infection cycle of V. cholerae . In this study, genomic expression library screening revealed that two regulators, VC1371 and VcRfaH, are able to positively activate the transcription of MSHA operon. VC1371 is localized and active in the cell membrane. Deletion of vc1371 or VcrfaH genes in V. cholerae resulted in less MshA protein production and less efficiency of biofilm formation compared to that in the wild-type strain. An adult mouse model showed that the mutants with vc1371 or VcrfaH deletion colonized less efficiently than the wild-type; the VcrfaH deletion mutant showed less colonization efficiency in the infant mouse model. The findings strongly suggested that the two regulators, namely VC1371 and VcRfaH, which are involved in the regulation of MSHA expression, play an important role in V. cholerae biofilm formation and colonization in mice.

Molecular characterization of Vibrio cholerae O1 isolates obtained from outbreaks in the Philippines, 2015–2016

2021 ◽  
Vol 70 (11) ◽  
Author(s):  
Mark Philip Bugayong ◽  
Hidemasa Izumiya ◽  
Josie M. Bilar ◽  
Masatomo Morita ◽  
Eiji Arakawa ◽  
...  
Keyword(s):  
Vibrio Cholerae ◽  
Type Species ◽  
Variable Number Tandem Repeat ◽  
The Philippines ◽  
Large Chromosome ◽  
Content Type ◽  
Link Type ◽  
Mlva Type ◽  
El Tor

Introduction. The Philippines, comprising three island groups, namely, Luzon, Visayas and Mindanao, experienced an increase in cholera outbreaks in 2016. Previous studies have shown that Vibrio cholerae isolates obtained from the Philippines are novel hybrid El Tor strains that have evolved in the country and are clearly distinct from those found in Mozambique and Cameroon. Gap statement. The characterization of the strains isolated from outbreaks has been limited to phenotypic characteristics, such as biochemical and serological characteristics, in most previous studies. Aim. We performed multilocus variable-number tandem repeat (VNTR) analysis (MLVA) for V. cholerae isolates obtained from 2015 to 2016 to further characterize and understand the emergence and dissemination of the strains in the Philippines. Methodology. A total of 139 V . cholerae O1 Ogawa biotype El Tor isolates were obtained from the Philippines during diarrhoeal outbreaks in 18 provinces between 2015 and 2016. VNTR data were analysed to classify the MLVA profiles where the large-chromosome types (LCTs) were applied for grouping. Results. We identified 50 MLVA types among 139 isolates originating from 18 provinces, and 14 LCTs. The distribution of the LCTs was variable, and a few were located in specific areas or even in specific provinces. Based on eBURST analysis, 99 isolates with 7 LCTs and 32 MLVA types belonged to 1 group, suggesting that they were related to each other. LCT A was predominant (n=67) and was isolated from Luzon and Visayas. LCT A had 14 MLVA types; however, it mostly emerged during a single quarter of a year. Eight clusters were identified, each of which involved specific MLVA type(s). The largest cluster involved 23 isolates showing 3 MLVA types, 21 of which were MLVA type A-14 isolated from Negros Occidental during quarter 4 of 2016. Comparative analysis showed that almost all isolates from the Philippines were distinct from those in other countries. Conclusions. The genotypic relationship of the V. cholerae isolates obtained during outbreaks in the Philippines was studied, and their emergence and dissemination were elucidated. MLVA revealed the short-term dynamics of V. cholerae genotypes in the Philippines.

scholarly journals Robust demarcation of 17 distinct Bacillus species clades, proposed as novel Bacillaceae genera, by phylogenomics and comparative genomic analyses: description of Robertmurraya kyonggiensis sp. nov. and proposal for an emended genus Bacillus limiting it only to the members of the Subtilis and Cereus clades of species

2020 ◽  
Vol 70 (11) ◽  
pp. 5753-5798 ◽  
Author(s):  
Radhey S. Gupta ◽  
Sudip Patel ◽  
Navneet Saini ◽  
Shu Chen
Keyword(s):  
Type Species ◽  
Phylogenetic Trees ◽  
Bacillus Species ◽  
Comparative Genomic ◽  
Molecular Evidence ◽  
Content Type ◽  
Link Type ◽  
Conserved Signature Indels ◽  
Genomic Scale

To clarify the evolutionary relationships and classification of Bacillus species, comprehensive phylogenomic and comparative analyses were performed on >300 Bacillus/Bacillaceae genomes. Multiple genomic-scale phylogenetic trees were initially reconstructed to identify different monophyletic clades of Bacillus species. In parallel, detailed analyses were performed on protein sequences of genomes to identify conserved signature indels (CSIs) that are specific for each of the identified clades. We show that in different reconstructed trees, most of the Bacillus species, in addition to the Subtilis and Cereus clades, consistently formed 17 novel distinct clades. Additionally, some Bacillus species reliably grouped with the genera Alkalicoccus, Caldalkalibacillus, Caldibacillus, Salibacterium and Salisediminibacterium . The distinctness of identified Bacillus species clades is independently strongly supported by 128 identified CSIs which are unique characteristics of these clades, providing reliable means for their demarcation. Based on the strong phylogenetic and molecular evidence, we are proposing that these 17 Bacillus species clades should be recognized as novel genera, with the names Alteribacter gen. nov., Ectobacillus gen. nov., Evansella gen. nov., Ferdinandcohnia gen. nov., Gottfriedia gen. nov., Heyndrickxia gen. nov., Lederbergia gen. nov., Litchfieldia gen. nov., Margalitia gen. nov., Niallia gen. nov., Priestia gen. nov., Robertmurraya gen. nov., Rossellomorea gen. nov., Schinkia gen. nov., Siminovitchia gen. nov., Sutcliffiella gen. nov. and Weizmannia gen. nov. We also propose to transfer ‘ Bacillus kyonggiensi s’ to Robertmurraya kyonggiensis sp. nov. (type strain: NB22=JCM 17569T=DSM 26768). Additionally, we report 31 CSIs that are unique characteristics of either the members of the Subtilis clade (containing the type species B. subtilis ) or the Cereus clade (containing B. anthracis and B. cereus ). As most Bacillus species which are not part of these two clades can now be assigned to other genera, we are proposing an emended description of the genus Bacillus to restrict it to only the members of the Subtilis and Cereus clades.

scholarly journals gbpA and chiA genes are not uniformly distributed amongst diverse Vibrio cholerae

2021 ◽  
Vol 7 (6) ◽  
Author(s):  
Thea G. Fennell ◽  
Grace A. Blackwell ◽  
Nicholas R. Thomson ◽  
Matthew J. Dorman
Keyword(s):  
Vibrio Cholerae ◽  
Metabolic Pathway ◽  
Type Species ◽  
Gene Encoding ◽  
Natural Competence ◽  
Content Type ◽  
Metabolic Substrate ◽  
Link Type ◽  
Reference Strains ◽  
Present Experimental Evidence

Members of the bacterial genus Vibrio utilize chitin both as a metabolic substrate and a signal to activate natural competence. Vibrio cholerae is a bacterial enteric pathogen, sub-lineages of which can cause pandemic cholera. However, the chitin metabolic pathway in V. cholerae has been dissected using only a limited number of laboratory strains of this species. Here, we survey the complement of key chitin metabolism genes amongst 195 diverse V. cholerae . We show that the gene encoding GbpA, known to be an important colonization and virulence factor in pandemic isolates, is not ubiquitous amongst V. cholerae . We also identify a putatively novel chitinase, and present experimental evidence in support of its functionality. Our data indicate that the chitin metabolic pathway within V. cholerae is more complex than previously thought, and emphasize the importance of considering genes and functions in the context of a species in its entirety, rather than simply relying on traditional reference strains.

scholarly journals Septic polyarthritis with Mycoplasma salivarium in a patient with common variable immunodeficiency: case report and review of the literature

2021 ◽  
Vol 3 (4) ◽  
Author(s):  
Arthur H. Totten ◽  
Li Xiao ◽  
Donna M. Crabb ◽  
Amy E. Ratliff ◽  
Ken B. Waites ◽  
...  
Keyword(s):  
Type Species ◽  
Eukaryotic Cell ◽  
Content Type ◽  
The Past ◽  
Link Type ◽  
Source Of Infection ◽  
Humoral Immunodeficiency ◽  
Mycoplasmal Infection ◽  
Common Variable ◽  
Septic Polyarthritis

Mycoplasma salivarium is a common mycoplasma usually isolated from human oropharynx, particularly from individuals with periodontal disease. It is also among the more common mycoplasmal contaminants of eukaryotic cell cultures. Although M. salivarium has been isolated occasionally from abscesses and other sterile sites, to our knowledge, only three cases of septic arthritis have been documented in the past due to this organism, all in patients with humoral immunodeficiency. We now report a fourth case of septic polyarthritis in a patient with profound hypoimmunoglobulinemia who had experienced dental abscesses within the preceding 2 years. Our case highlights the importance of considering invasive mycoplasmal infection in hypogammaglobulinemic patients. It is likely of significance that the patient had suffered recurrent dental abscesses as a source of infection with M. salivarium .

scholarly journals Phylogenetic and antimicrobial drug resistance analysis of Vibrio cholerae O1 isolates from Ghana

2021 ◽  
Vol 7 (10) ◽  
Author(s):  
Japheth A. Opintan ◽  
Robert C. Will ◽  
George K. Kuma ◽  
Mary Osei ◽  
Amos Akumwena ◽  
...  
Keyword(s):  
Vibrio Cholerae ◽  
Type Species ◽  
Lag Phase ◽  
Environmental Isolates ◽  
Content Type ◽  
Antimicrobial Drug Resistance ◽  
Link Type ◽  
Pathogen Persistence ◽  
Vibrio Cholerae O1 ◽  
Vaccination Campaigns

We investigated the evolution, phylogeny and antimicrobial resistance of Vibrio cholerae O1 isolates (VCO1) from Ghana. Outbreak and environmental sources of VCO1 were characterized, whole-genome sequenced and compared to globally available seventh pandemic (7P) strains of V. cholerae at SNP resolution. Final analyses included 636 isolates. Novel Ghanaian isolates clustered into three distinct clades (clades 1, 2 and 3) in wave 3 of the 7P lineage. The closest relatives of our novel Ghanaian isolates were from Benin, Cameroon, Togo, Niger and Nigeria. All novel Ghanaian isolates were multi-drug resistant. Environmental isolates clustered into clade 2, despite being isolated years later, showing the possibility of persistence and re-emergence of older clades. A lag phase of several years from estimated introduction to reported cases suggests pathogen persistence in the absence of reported cholera cases. These results highlight the importance of deeper surveillance for understanding transmission routes between bordering countries and planning tailored vaccination campaigns in an effort to eradicate cholera.

The enigma of Pacini’s Vibrio cholerae discovery

2021 ◽  
Vol 70 (11) ◽  
Author(s):  
Gian Piero Carboni
Keyword(s):  
Vibrio Cholerae ◽  
Intestinal Mucosa ◽  
Type Species ◽  
Polluted Water ◽  
Cholera Outbreak ◽  
Histological Techniques ◽  
Content Type ◽  
Link Type ◽  
Mutual Knowledge ◽  
Worldwide Distribution

During the 1854 cholera outbreak in Florence, Italy, Filippo Pacini documented that the cause of the infection was a bacterium. This conclusion was also independently reached by John Snow during the 1854 cholera outbreak in London. By using an epidemiological method, Snow found that the infection spread through a polluted water network. Snow identified a water pump as the source of the disease. After removing the infected handle of this pump, the cases of cholera rapidly began to decrease. A microscopic examination of the water showed organic impurities but no bacteria. This discovery was ignored during Snow’s lifetime. In contrast, through microscopy during the autopsies of cholera victims, Pacini observed that the disruption of their intestinal mucosa was closely associated with millions of the bacteria that he called Vibrio cholerae . Via histological techniques, Pacini detected that intestinal mucosa reabsorption dysfunction was the cause of debilitating diarrhoea, vomiting, severe dehydration and death. Nevertheless, his discovery of Vibrio cholerae was ignored during Pacini’s lifetime. A survey of Pacini’s autographic manuscripts suggests that Pacini and Snow may have shared mutual knowledge within their respective seminal papers. This survey also facilitates, for the first time, the creation of maps that illustrate the worldwide distribution of Pacini’s cholera papers from 1854 to 1881. The consistent neglect of Pacini’s discovery remains a true enigma.

Rhodospirillum oryzae sp. nov., a phototrophic bacterium isolated from rhizosphere soil of paddy

2013 ◽  
Vol 63 (Pt_8) ◽  
pp. 3050-3055 ◽  
Author(s):  
K. V. N. S. Lakshmi ◽  
Ch. Sasikala ◽  
E. V. V. Ramaprasad ◽  
Ch. V. Ramana
Keyword(s):  
Type Species ◽  
Rhizosphere Soil ◽  
Enrichment Culture ◽  
Sequence Similarity ◽  
Molecular Evidence ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Dna Reassociation ◽  
The Family

A reddish-brown bacterium, designated strain JA318T, was purified from a photoheterotrophic enrichment culture obtained from the rhizosphere soil of paddy. Cells of strain JA318T are spiral shaped, Gram-stain-negative and motile by means of amphitrichous flagella. Strain JA318T has no NaCl requirement for growth but can tolerate up to 1.5 % (w/v) NaCl. Internal photosynthetic membranes are present as lamellar stacks. Photoorganoheterotrophy is the only growth mode observed. Strain JA318T contains bacteriochlorophyll a, lycopene and rhodopin as major carotenoids. Thiamine, niacin and para-aminobenzoic acid (PABA) are required as growth factors. Major fatty acids are C18 : 1ω7c and C16 : 0. Ubiquinone-8 and rhodoquinone-8 are the observed quinones. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified aminolipid are the major polar lipids in strain JA318T. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain JA318T clustered with species of the genus Rhodospirillum which belongs to the class Alphaproteobacteria . The highest sequence similarity of strain JA318T was found with Rhodospirillum sulfurexigens JA143T (99.9 %). The DNA–DNA reassociation values of strain JA318T with Rsp. sulfurexigens JA143T and Rhodospirillum photometricum DSM 122T were 52±2 % and 45±1 %, respectively. The genomic DNA G+C content of strain JA318T was 60.2 mol%. Based on the morphological, physiological, chemotaxonomical and molecular evidence, strain JA318T is significantly different from the type strains of species of the genus Rhodospirillum , of the family Rhodospirillaceae , and it is proposed that the strain be classified as a representative of a novel species for which the name Rhodospirillum oryzae sp. nov. is proposed. The type strain is JA318T ( = KCTC 5960T = NBRC 107573T).

scholarly journals Thiophaeococcus fuscus sp. nov., isolated from a lagoon

2014 ◽  
Vol 64 (Pt_8) ◽  
pp. 2528-2533 ◽  
Author(s):  
B. Divyasree ◽  
K. V. N. S. Lakshmi ◽  
Ch. Sasikala ◽  
Ch. V. Ramana
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Type Species ◽  
Enrichment Culture ◽  
Sequence Similarity ◽  
Molecular Evidence ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type

A brown-coloured bacterium, designated strain JA633T, was purified from a photoheterotrophic enrichment culture obtained from black sand of a lagoon. Cells of strain JA633T were coccoid–spherical, Gram-stain-negative and motile by means of polar flagella. Strain JA633T had an obligate requirement for NaCl and could tolerate up to 4 % (w/v) NaCl. Internal photosynthetic membranes were present as vesicles. Photo-organoheterotrophy was the only growth mode observed. Strain JA633T contained bacteriochlorophyll a and a major (>85 %) unidentified carotenoid of the spirilloxanthin series. Thiamine and p-aminobenzoic acid were required for growth. Major fatty acids were C18 : 1ω7c/C18 : 1ω6c, C16 : 0 and C16 : 1ω7c/C16 : 1ω6c. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphotidylcholine and an unknown aminophospholipid were the major polar lipids in strain JA633T. The DNA G+C content of strain JA633T was 64.5 mol%. Strain JA633T shared highest 16S rRNA gene sequence similarity with the type strains of Thiorhodococcus kakinadensis (96.9 %), Thiophaeococcus mangrovi (96.3 %) and Thiorhodococcus bheemlicus (96.2 %), which belonged to the class Gammaproteobacteria . However, phylogenetic analysis based on 16S rRNA gene sequences showed that strain JA633T formed a separate clade along with Thiophaeococcus mangrovi JA304T whereas the members of the genus Thiorhodococcus remained as two distinct phylogenetic lineages. Based on morphological, physiological, chemotaxonomic and molecular evidence, strain JA633T was significantly different from the type strain of Thiophaeococcus mangrovi of the family Chromatiaceae . It is thus proposed that the strain be classified as a representative of a novel species, for which the name Thiophaeococcus fuscus sp. nov. is proposed. The type strain is JA633T ( = KCTC 15337T = NBRC 109958T).

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