scholarly journals Origins of the current seventh cholera pandemic

2016 ◽  
Vol 113 (48) ◽  
pp. E7730-E7739 ◽  
Author(s):  
Dalong Hu ◽  
Bin Liu ◽  
Lu Feng ◽  
Peng Ding ◽  
Xi Guo ◽  
...  
Keyword(s):  
Middle East ◽  
Driving Forces ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Bacterial Strains ◽  
Pandemic Strain ◽  
Nonpathogenic Strain ◽  
Rapid Diversification ◽  
El Tor ◽  
Key Events

Vibrio choleraehas caused seven cholera pandemics since 1817, imposing terror on much of the world, but bacterial strains are currently only available for the sixth and seventh pandemics. The El Tor biotype seventh pandemic began in 1961 in Indonesia, but did not originate directly from the classical biotype sixth-pandemic strain. Previous studies focused mainly on the spread of the seventh pandemic after 1970. Here, we analyze in unprecedented detail the origin, evolution, and transition to pandemicity of the seventh-pandemic strain. We used high-resolution comparative genomic analysis of strains collected from 1930 to 1964, covering the evolution from the first available El Tor biotype strain to the start of the seventh pandemic. We define six stages leading to the pandemic strain and reveal all key events. The seventh pandemic originated from a nonpathogenic strain in the Middle East, first observed in 1897. It subsequently underwent explosive diversification, including the spawning of the pandemic lineage. This rapid diversification suggests that, when first observed, the strain had only recently arrived in the Middle East, possibly from the Asian homeland of cholera. The lineage migrated to Makassar, Indonesia, where it gained the important virulence-associated elementsVibrioseventh pandemic island I (VSP-I), VSP-II, and El Tor type cholera toxin prophage by 1954, and it then became pandemic in 1961 after only 12 additional mutations. Our data indicate that specific niches in the Middle East and Makassar were important in generating the pandemic strain by providing gene sources and the driving forces for genetic events.

Characterization, Pathogenicity, Phylogeny, and Comparative Genomic Analysis of Pseudomonas tolaasii Strains Isolated from Various Mushrooms in China

2021 ◽  
Author(s):  
Zhenghui Liu ◽  
Yitong Zhao ◽  
Frederick Leo Sossah ◽  
Benjamin Azu Okorley ◽  
Daniel G. Amoako ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Genomic Analysis ◽  
Gene Families ◽  
Effective Control ◽  
Economic Losses ◽  
Comparative Genomic ◽  
Bacterial Strains ◽  
Secretion Systems ◽  
Pseudomonas Tolaasii ◽  
Antimicrobial Resistance Genes

Since 2016, devastating bacterial blotch affecting the fruiting bodies of Agaricus bisporus, Cordyceps militaris, Flammulina filiformis, and Pleurotus ostreatus in China has caused severe economic losses. We isolated 102 bacterial strains and characterized them polyphasically. We identified the causal agent as Pseudomonas tolaasii and confirmed the pathogenicity of the strains. A host range test further confirmed the pathogen’s ability to infect multiple hosts. This is the first report in China of bacterial blotch in C. militaris caused by P. tolaasii. Whole-genome sequences were generated for three strains: Pt11 (6.48 Mb), Pt51 (6.63 Mb), and Pt53 (6.80 Mb), and pangenome analysis was performed with 13 other publicly accessible P. tolaasii genomes to determine their genetic diversity, virulence, antibiotic resistance, and mobile genetic elements. The pangenome of P. tolaasii is open, and many more gene families are likely to emerge with further genome sequencing. Multilocus sequence analysis using the sequences of four common housekeeping genes (glns, gyrB, rpoB, and rpoD) showed high genetic variability among the P. tolaasii strains, with 115 strains clustered into a monophyletic group. The P. tolaasii strains possess various genes for secretion systems, virulence factors, carbohydrate-active enzymes, toxins, secondary metabolites, and antimicrobial resistance genes that are associated with pathogenesis and adapted to different environments. The myriad of insertion sequences, integrons, prophages, and genome islands encoded in the strains may contribute to genome plasticity, virulence, and antibiotic resistance. These findings advance understanding of the determinants of virulence, which can be targeted for the effective control of bacterial blotch disease.

Comparative genomic analysis of two isolates of Vibrio cholerae O1 Ogawa El Tor isolated during outbreak in Mariupol in 2011

2016 ◽  
Vol 44 ◽  
pp. 471-478 ◽  
Author(s):  
Konstantin V. Kuleshov ◽  
Anna Kostikova ◽  
Sergey V. Pisarenko ◽  
Dmitry A. Kovalev ◽  
Sergey N. Tikhonov ◽  
...  
Keyword(s):  
Vibrio Cholerae ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Vibrio Cholerae O1 ◽  
El Tor

scholarly journals Complete Genome Sequencing and Comparative Genomics of Three Potential Probiotic Strains, Lacticaseibacillus casei FBL6, Lacticaseibacillus chiayiensis FBL7, and Lacticaseibacillus zeae FBL8

2022 ◽  
Vol 12 ◽  
Author(s):  
Eiseul Kim ◽  
Seung-Min Yang ◽  
Dayoung Kim ◽  
Hae-Yeong Kim
Keyword(s):  
Complete Genome ◽  
Functional Characterization ◽  
Genomic Analysis ◽  
Raw Milk ◽  
Phenotypic Characterization ◽  
Comparative Genomic ◽  
Probiotic Properties ◽  
Bacterial Strains ◽  
Physiological Control ◽  
Wide Range

Lacticaseibacillus casei, Lacticaseibacillus chiayiensis, and Lacticaseibacillus zeae are very closely related Lacticaseibacillus species. L. casei has long been proposed as a probiotic, whereas studies on functional characterization for L. chiayiensis and L. zeae are some compared to L. casei. In this study, L. casei FBL6, L. chiayiensis FBL7, and L. zeae FBL8 were isolated from raw milk, and their probiotic properties were investigated. Genomic analysis demonstrated the role of L. chiayiensis and L. zeae as probiotic candidates. The three strains were tolerant to acid and bile salt, with inhibitory action against pathogenic bacterial strains and capacity of antioxidants. Complete genome sequences of the three strains were analyzed to highlight the probiotic properties at the genetic level, which results in the discovery of genes corresponding to phenotypic characterization. Moreover, genes known to confer probiotic characteristics were identified, including genes related to biosynthesis, defense machinery, adhesion, and stress adaptation. The comparative genomic analysis with other available genomes revealed 256, 214, and 32 unique genes for FBL6, FBL7, and FBL8, respectively. These genomes contained individual genes encoding proteins that are putatively involved in carbohydrate transport and metabolism, prokaryotic immune system for antiviral defense, and physiological control processes. In particular, L. casei FBL6 had a bacteriocin gene cluster that was not present in other genomes of L. casei, resulting in this strain may exhibit a wide range of antimicrobial activity compared to other L. casei strains. Our data can help us understand the probiotic functionalities of the three strains and suggest that L. chiayiensis and L. zeae species, which are closely related to L. casei, can also be considered as novel potential probiotic candidate strains.

scholarly journals Genomic characteristics of recently recognized Vibrio cholerae El Tor lineages associated with cholera in Bangladesh, 1991-2017

2021 ◽  
Author(s):  
Md Mamun Monir ◽  
Talal Hossain ◽  
Masatomo Morita ◽  
Makoto Ohnishi ◽  
Fatema-tuj Johura ◽  
...  
Keyword(s):  
Vibrio Cholerae ◽  
Genome Wide Association Study ◽  
Sequence Data ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Nucleotide Polymorphisms ◽  
Fitness Advantage ◽  
Genome Phylogeny ◽  
El Tor ◽  
Endemic Cholera

Comparative genomic analysis of Vibrio cholerae El Tor associated with endemic cholera in Asia revealed two distinct lineages, one dominant in Bangladesh and the other in India. An in depth whole genome study of V. cholerae El Tor clinical strains isolated during endemic cholera in Bangladesh (1991 – 2017) included reference genome sequence data obtained online. Core genome phylogeny established using single nucleotide polymorphisms (SNPs) showed V. choleraeEl Tor strains comprised two lineages, BD-1 and BD-2, which, according to Bayesian phylodynamic analysis, originated from paraphyletic group BD-0 around 1981. BD-1 and BD-2 lineages overlapped temporally but were negatively associated as causative agents of cholera 2004-2017. Genome wide association study (GWAS) revealed 140 SNPs and 31 indels, resulting in gene alleles unique to BD-1 and BD-2. Regression analysis of root to tip distance and year of isolation indicated early BD-0 strains at the base, whereas BD-1 and BD-2 subsequently emerged and progressed by accumulating SNPs. Pangenome analysis provided evidence of gene acquisition by both BD-1 and BD-2, of which six crucial proteins of known function were predominant in BD-2. BD-1 and BD-2 diverged and have distinctively different genomic traits, namely heterogeneity in VSP-2, VPI-1, mobile elements, toxin encoding elements, and total gene abundance. In addition, the observed phage-inducible chromosomal island-like element (PLE1), and SXT ICE elements (ICETET) in BD-2 presumably provided a fitness advantage for the lineage to outcompete BD-1 as the etiological agent of the endemic cholera in Bangladesh, with implications for global cholera epidemiology.

scholarly journals Complete Nucleotide Sequences ofblaKPC-4- andblaKPC-5-Harboring IncN and IncX Plasmids from Klebsiella pneumoniae Strains Isolated in New Jersey

2012 ◽  
Vol 57 (1) ◽  
pp. 269-276 ◽  
Author(s):  
Liang Chen ◽  
Kalyan D. Chavda ◽  
Henry S. Fraimow ◽  
José R. Mediavilla ◽  
Roberto G. Melano ◽  
...  
Keyword(s):  
New Jersey ◽  
Klebsiella Pneumoniae ◽  
Sequence Similarity ◽  
Genomic Analysis ◽  
Multidrug Resistant ◽  
Comparative Genomic ◽  
Bacterial Strains ◽  
Gene Encoding ◽  
Content Type ◽  
Plasmid Backbone

ABSTRACTKlebsiella pneumoniaecarbapenemase (KPC)-producingEnterobacteriaceaehave emerged as major nosocomial pathogens.blaKPC, commonly located on Tn4401, is found in Gram-negative bacterial strains, with the two most common variants,blaKPC-2andblaKPC-3, identified in plasmids with diverse genetic backgrounds. In this study, we examinedblaKPC-4- andblaKPC-5-bearing plasmids recovered from twoK. pneumoniaestrains, which were isolated from a single New Jersey hospital in 2005 and 2006, respectively. IncN plasmid pBK31551 is 84 kb in length and harborsblaKPC-4,blaTEM-1,qnrB2,aac(3)-Ib,aph(3′)-I,qacF,qacEΔ1,sul1, anddfrA14, which confer resistance to β-lactams, quinolones, aminoglycosides, quaternary ammonium compounds, and co-trimoxazole. The conserved regions within pBK31551 are similar to those of other IncN plasmids. Surprisingly, analysis of the Tn4401sequence revealed a large IS110- and Tn6901-carrying element (8.3 kb) inserted into theistAgene, encoding glyoxalase/bleomycin resistance, alcohol dehydrogenase, andS-formylglutathione hydrolase. Plasmid pBK31567 is 47 kb in length and harborsblaKPC-5,dfrA5,qacEΔ1, andsul1. pBK31567 belongs to a novel IncX subgroup (IncX5) and possesses a highly syntenic plasmid backbone like other IncX plasmids; however, sequence similarity at the nucleotide level is divergent. TheblaKPC-5gene is carried on a Tn4401element and differs from the genetic environment ofblaKPC-5described inPseudomonas aeruginosastrain P28 from Puerto Rico. This study underscores the genetic diversity of multidrug-resistant plasmids involved in the spread ofblaKPCgenes and highlights the mobility and plasticity of Tn4401. Comparative genomic analysis provides new insights into the evolution and dissemination of KPC plasmids belonging to different incompatibility groups.

scholarly journals Biosynthetic gene cluster profiling predicts the positive association between antagonism and phylogeny in Bacillus

2021 ◽  
Author(s):  
Liming Xia ◽  
Youzhi Miao ◽  
A'li Cao ◽  
Yan Liu ◽  
Zihao Liu ◽  
...  
Keyword(s):  
Driving Forces ◽  
Interference Competition ◽  
Genomic Analysis ◽  
Positive Association ◽  
Gene Clusters ◽  
Microbial Interactions ◽  
Comparative Genomic ◽  
Phylogenetic Distance ◽  
Biosynthetic Gene ◽  
Exploitation Competition

Understanding the driving forces and intrinsic mechanisms of microbial competition is a fundamental question in microbial ecology. Despite the well-established negative correlation between exploitation competition and phylogenetic distance, the process of interference competition that is exemplified by antagonism remains controversial. Here, we studied the genus Bacillus, a commonly recognized producer of multifarious antibiotics, to explore the role of phylogenetic patterns of biosynthetic gene clusters (BGCs) in mediating the relationship between antagonism and phylogeny. Comparative genomic analysis revealed a positive association between BGC distance and phylogenetic distance. Antagonistic tests demonstrated that the inhibition phenotype positively correlated with both phylogenetic and predicted BGC distance, especially for antagonistic strains possessing abundant BGCs. Mutant-based verification showed that the antagonism was dependent on the BGCs that specifically harbored by the antagonistic strain. These findings highlight that BGC-phylogeny coherence regulates the positive correlation between congeneric antagonism and phylogenetic distance, which deepens our understanding of the driving force and intrinsic mechanism of microbial interactions.

scholarly journals The hidden pangenome: comparative genomics reveals pervasive diversity in symbiotic and free-living sulfur-oxidizing bacteria

2020 ◽  
Author(s):  
Rebecca Ansorge ◽  
Stefano Romano ◽  
Lizbeth Sayavedra ◽  
Maxim Rubin-Blum ◽  
Harald Gruber-Vodicka ◽  
...  
Keyword(s):  
Defense Mechanisms ◽  
Hydrothermal Vents ◽  
Driving Forces ◽  
Genetic Material ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Free Living ◽  
Bacterial Populations ◽  
Genomic Studies ◽  
Sulfur Oxidizing

AbstractSulfur-oxidizing Thioglobaceae, often referred to as SUP05 and Arctic96BD clades, are widespread and common to hydrothermal vents and oxygen minimum zones. They impact global biogeochemical cycles and exhibit a variety of host-associated and free-living lifestyles. The evolutionary driving forces that led to the versatility, adoption of multiple lifestyles and global success of this family are largely unknown. Here, we perform an in-depth comparative genomic analysis using all available and newly generated Thioglobaceae genomes. Gene content variation was common, throughout taxonomic ranks and lifestyles. We uncovered a pool of variable genes within most Thioglobaceae populations in single environmental samples and we referred to this as the ‘hidden pangenome’. The ‘hidden pangenome’ is often overlooked in comparative genomic studies and our results indicate a much higher intra-specific diversity within environmental bacterial populations than previously thought. Our results show that core-community functions are different from species core genomes suggesting that core functions across populations are divided among the intra-specific members within a population. Defense mechanisms against foreign DNA and phages were enriched in symbiotic lineages, indicating an increased exchange of genetic material in symbioses. Our study suggests that genomic plasticity and frequent exchange of genetic material drives the global success of this family by increasing its evolvability in a heterogeneous environment.

scholarly journals Comparative Genomic Analysis of Labrenzia aggregata (Alphaproteobacteria) Strains Isolated From the Mariana Trench: Insights Into the Metabolic Potentials and Biogeochemical Functions

2021 ◽  
Vol 12 ◽  
Author(s):  
Haohui Zhong ◽  
Hao Sun ◽  
Ronghua Liu ◽  
Yuanchao Zhan ◽  
Xinyu Huang ◽  
...  
Keyword(s):  
Deep Sea ◽  
Sea Water ◽  
Extreme Environments ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Surface Seawater ◽  
Bacterial Strains ◽  
The East China Sea ◽  
Mariana Trench ◽  
Secondary Metabolite Biosynthesis

Hadal zones are marine environments deeper than 6,000 m, most of which comprise oceanic trenches. Microbes thriving at such depth experience high hydrostatic pressure and low temperature. The genomic potentials of these microbes to such extreme environments are largely unknown. Here, we compare five complete genomes of bacterial strains belonging to Labrenzia aggregata (Alphaproteobacteria), including four from the Mariana Trench at depths up to 9,600 m and one reference from surface seawater of the East China Sea, to uncover the genomic potentials of this species. Genomic investigation suggests all the five strains of L. aggregata as participants in nitrogen and sulfur cycles, including denitrification, dissimilatory nitrate reduction to ammonium (DNRA), thiosulfate oxidation, and dimethylsulfoniopropionate (DMSP) biosynthesis and degradation. Further comparisons show that, among the five strains, 85% gene functions are similar with 96.7% of them encoded on the chromosomes, whereas the numbers of functional specific genes related to osmoregulation, antibiotic resistance, viral infection, and secondary metabolite biosynthesis are majorly contributed by the differential plasmids. A following analysis suggests the plasmidic gene numbers increase along with isolation depth and most plasmids are dissimilar among the five strains. These findings provide a better understanding of genomic potentials in the same species throughout a deep-sea water column and address the importance of externally originated plasmidic genes putatively shaped by deep-sea environment.

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