scholarly journals Comparative Genomic Analysis Provides Insights into the Phylogeny, Resistome, Virulome, and Host Adaptation in the Genus Ewingella

Pathogens ◽  
2020 ◽  
Vol 9 (5) ◽  
pp. 330 ◽  
Author(s):  
Zhenghui Liu ◽  
Hongyan Sheng ◽  
Benjamin Azu Okorley ◽  
Yu Li ◽  
Frederick Leo Sossah
Keyword(s):  
Antibiotic Resistance ◽  
Control Strategies ◽  
Bacterial Pathogen ◽  
Genomic Analysis ◽  
Defense Responses ◽  
Host Adaptation ◽  
Comparative Genomic Analysis ◽  
Effective Control ◽  
Comparative Genomic ◽  
Temperature Oxidation

Ewingella americana is a cosmopolitan bacterial pathogen that has been isolated from many hosts. Here, we sequenced a high-quality genome of E. americana B6-1 isolated from Flammulina filiformis, an important cultivated mushroom, performed a comparative genomic analysis with four other E. americana strains from various origins, and tested the susceptibility of B6-1 to antibiotics. The genome size, predicted genes, and GC (guanine-cytosine) content of B6-1 was 4.67 Mb, 4301, and 53.80%, respectively. The origin of the strains did not significantly affect the phylogeny, but mobile genetic elements shaped the evolution of the genus Ewingella. The strains encoded a set of common genes for type secretion, virulence effectors, CAZymes, and toxins required for pathogenicity in all hosts. They also had antibiotic resistance, pigments to suppress or evade host defense responses, as well as genes for adaptation to different environmental conditions, including temperature, oxidation, and nutrients. These findings provide a better understanding of the virulence, antibiotic resistance, and host adaptation strategies of Ewingella, and they also contribute to the development of effective control strategies.

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.

scholarly journals Comparative genomic analysis of Methanimicrococcus blatticola provides insights into host adaptation in archaea and the evolution of methanogenesis

2021 ◽  
Vol 1 (1) ◽  
Author(s):  
Courtney M. Thomas ◽  
Najwa Taib ◽  
Simonetta Gribaldo ◽  
Guillaume Borrel
Keyword(s):  
Gut Microbiota ◽  
Large Scale ◽  
Genomic Analysis ◽  
Host Adaptation ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Methyl Branch ◽  
Mechanisms Of Adaptation ◽  
Hydrogenotrophic Methanogens ◽  
Almost All

AbstractOther than the Methanobacteriales and Methanomassiliicoccales, the characteristics of archaea that inhabit the animal microbiome are largely unknown. Methanimicrococcus blatticola, a member of the Methanosarcinales, currently reunites two unique features within this order: it is a colonizer of the animal digestive tract and can only reduce methyl compounds with H2 for methanogenesis, a increasingly recognized metabolism in the archaea and whose origin remains debated. To understand the origin of these characteristics, we have carried out a large-scale comparative genomic analysis. We infer the loss of more than a thousand genes in M. blatticola, by far the largest genome reduction across all Methanosarcinales. These include numerous elements for sensing the environment and adapting to more stable gut conditions, as well as a significant remodeling of the cell surface components likely involved in host and gut microbiota interactions. Several of these modifications parallel those previously observed in phylogenetically distant archaea and bacteria from the animal microbiome, suggesting large-scale convergent mechanisms of adaptation to the gut. Strikingly, M. blatticola has lost almost all genes coding for the H4MPT methyl branch of the Wood–Ljungdahl pathway (to the exception of mer), a phenomenon never reported before in any member of Class I or Class II methanogens. The loss of this pathway illustrates one of the evolutionary processes that may have led to the emergence of methyl-reducing hydrogenotrophic methanogens, possibly linked to the colonization of organic-rich environments (including the animal gut) where both methyl compounds and hydrogen are abundant.

scholarly journals Genomic analysis of halophilic bacterium, Lentibacillus sp. CBA3610, derived from human feces

Gut Pathogens ◽  
2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Seung Woo Ahn ◽  
Se Hee Lee ◽  
Hong-Seok Son ◽  
Seong Woon Roh ◽  
Yoon-E Choi
Keyword(s):  
Phylogenetic Analysis ◽  
Antibiotic Resistance ◽  
Genome Sequence ◽  
Dna Sequences ◽  
Antibiotic Resistance Gene ◽  
Genomic Analysis ◽  
Halophilic Bacterium ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Genomic Analyses

Abstract Background Lentibacillus species are gram variable aerobic bacteria that live primarily in halophilic environments. Previous reports have shown that bacteria belonging to this species are primarily isolated from salty environments or food. We isolated a bacterial strain CBA3610, identified as a novel species of the genus Lentibacillus, from a human fecal sample. In this report, the whole genome sequence of Lentibacillus sp. CBA3610 is presented, and genomic analyses are performed. Results Complete genome sequence of strain CBA3610 was obtained through PacBio RSII and Illumina HiSeq platforms. The size of genome is 4,035,571 bp and genes estimated to be 4714 coding DNA sequences and 64 tRNA and 17 rRNA were identified. The phylogenetic analysis confirmed that it belongs to the genus Lentibacillus. In addition, there were genes related to antibiotic resistance and virulence, and genes predicted as CRISPR and prophage were also identified. Genes related to osmotic stress were found according to the characteristics of halophilic bacterium. Genomic differences from other Lentibacillus species were also confirmed through comparative genomic analysis. Conclusions Strain CBA3610 is predicted to be a novel candidate species of Lentibacillus through phylogenetic analysis and comparative genomic analysis with other species in the same genus. This strain has antibiotic resistance gene and pathogenic genes. In future, the information derived from the results of several genomic analyses of this strain is thought to be helpful in identifying the relationship between halophilic bacteria and human gut microbiota.

scholarly journals Complete genome sequence analysis of a lytic Shigella flexneri vB_SflS-ISF001 bacteriophage

2019 ◽  
pp. 99-112 ◽  
Author(s):  
Khashayar SHAHIN ◽  
Majid BOUZARI ◽  
Ran WANG
Keyword(s):  
Antibiotic Resistance ◽  
Genome Sequence ◽  
Shigella Flexneri ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Open Reading Frames ◽  
Whole Genome Sequence ◽  
Comparative Genomic ◽  
Shigella Spp ◽  
Enteric Infections

Shigellosis is one of the most important acute enteric infections caused by different species of Shigella, such as Shigella flexneri. Despite the use of antibiotic therapy to reduce disease duration, this approach is becoming less effective due to the emergence of antibiotic resistance among Shigella spp. Bacteriophages have been introduced as an alternative for controlling shigellosis. However, the bacteriophages must be without any lysogenic or virulence factors, toxin coding, or antibiotic-resistant genes. In this study, the whole genome sequence of vB_SflS-ISF001, a virulent Siphoviridae bacteriophage specific for Shigella flexneri, was obtained, and a comparative genomic analysis was carried out to identify its properties and safety. vB_SflS-ISF001 genomic DNA was measured at 50,552 bp with 78 deduced open reading frames (ORFs), with 24 ORFs (30.77%) sharing similarities with proteins from the genomes of homologous phages that had been reported earlier. Genetic analysis classifies it under the genus T1virus of the subfamily Tunavirinae. Moreover, comparative genomic analysis revealed no undesirable genes in the genome of vB_SflS-ISF001, such as antibiotic resistance, virulence, lysogeny, or toxin-coding genes. The results of this investigation indicate that vB_SflS-ISF001 is a new species, and confirm its safety for the biocontrol of S. flexneri.

scholarly journals Comparative Genomic Analysis of Trichinella spiralis Reveals Potential Mechanisms of Adaptive Evolution

2019 ◽  
Vol 2019 ◽  
pp. 1-12 ◽  
Author(s):  
Zigang Qu ◽  
Wenhui Li ◽  
Nianzhang Zhang ◽  
Li Li ◽  
Hongbin Yan ◽  
...  
Keyword(s):  
Adaptive Evolution ◽  
Vaccine Development ◽  
Trichinella Spiralis ◽  
Cell Formation ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Effective Control ◽  
Parasitic Nematodes ◽  
Comparative Genomic ◽  
Low Oxygen

Trichinellosis caused by parasitic nematodes of the genus Trichinella may result in human morbidity and mortality worldwide. Deciphering processes that drive species diversity and adaptation are key to understanding parasitism and developing effective control strategies. Our goal was to identify genes that are under positive selection and possible mechanisms of adaptive evolution of Trichinella spiralis genes using a comparative genomic analysis with the genomes of Brugia malayi, Trichuris suis, Ancylostoma ceylanicum, and Caenorhabditis elegans. The CODEML program derived from the PAML package was used to deduce the most probable dN/dS ratio, a measurement to detect genes/proteins undergoing adaptation. For each pair of sequences, those with a dN/dS ratio > 1 were considered positively selected genes (PSGs). Altogether, 986 genes were positively selected (p-value < 0.01). Genes involved in metabolic pathways, signaling pathways, and cytosolic DNA-sensing pathways were significantly enriched among the PSGs. Several PSGs are associated with exploitation of the host: modification of the host’s metabolism, creation of new parasite-specific morphological structures between T. spiralis and the host interface, xenobiotic metabolism to combat low oxygen concentrations and host toxicity, muscle cell transformation, cell cycle arrest, DNA repair processes during nurse cell formation, antiapoptotic factors, immunomodulation, and regulation of epigenetic processes. Some of the T. spiralis PSGs have C. elegans orthologs that confer severe or lethal RNAi phenotypes. Fifty-seven PSGs in T. spiralis were analyzed to encode differentially expressed proteins. The present study utilized an overall comparative genomic analysis to discover PSGs within T. spiralis and their relationships with biological function and organism fitness. This analysis adds to our understanding of the possible mechanism that contributes to T. spiralis parasitism and biological adaptation within the host, and thus these identified genes may be potential targets for drug and vaccine development.

scholarly journals Genomic Analysis ofAcinetobacter baumanniiA118 by Comparison of Optical Maps: Identification of Structures Related to Its Susceptibility Phenotype

2011 ◽  
Vol 55 (4) ◽  
pp. 1520-1526 ◽  
Author(s):  
Maria Soledad Ramirez ◽  
Mark D. Adams ◽  
Robert A. Bonomo ◽  
Daniela Centrón ◽  
Marcelo E. Tolmasky
Keyword(s):  
Drug Resistance ◽  
Antibiotic Resistance ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Restriction Maps ◽  
Sequence Analyses ◽  
Resistant Phenotype ◽  
Optical Map ◽  
Optical Maps

ABSTRACTAcinetobacter baumanniiA118, a naturally competent clinical isolate, is unusually susceptible to several antibiotics. Comparison of the optical map of strain A118 within silico-generated restriction maps of sequenced genomes and sequence analyses showed that the AbaR region, commonly found inserted within thecomMgene in other isolates, is missing in strain A118, which could in part explain the susceptible phenotype exhibited by this isolate. These comparative studies also showed differences in regions where genes coding for functions that may be involved in drug resistance or susceptibility are located. Further sequencing demonstrated thatcatandblaADC, namedblaADC-55, are present but that atet(A) gene usually found in other strains is not. In addition,carOandpbp2, which may play a role in susceptibility to carbapenems, are present in strain A118. These findings support the idea thatA. baumanniistrains possess multiple mechanisms that contribute to antibiotic resistance, and the presence of some of them is not sufficient for a resistant phenotype. The results shown here indicate that optical mapping is a useful tool for preliminary comparative genomic analysis.

Comparative Genomic Analysis of Extended-spectrum β-lactamase and mcr-1 Positive Escherichia coli from Gut Microbiota of Healthy Singaporeans

2021 ◽  
Author(s):  
Yichen Ding ◽  
Woei-Yuh Saw ◽  
Linda Wei Lin Tan ◽  
Don Kyin Nwe Moong ◽  
Niranjan Nagarajan ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Meat Products ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Colistin Resistance ◽  
Human Gut ◽  
Raw Meat ◽  
E Coli ◽  
Resistance Plasmids

Multidrug resistant (MDR) Escherichia coli strains that carry extended-spectrum β-lactamases (ESBLs) or colistin resistance gene mcr-1 have been identified in the human gut at an increasing incidence worldwide. In this study, we isolated and characterized MDR Enterobacteriaceae from the gut microbiota of healthy Singaporeans and show that the detection rates for ESBL-producing and mcr -positive Enterobacteriaceae are 25.7% (28/109) and 7.3% (8/109), respectively. Whole-genome sequencing analysis of the 37 E. coli isolates assigned them into 25 sequence types and six different phylogroups, suggesting that the MDR E. coli gut colonizers are highly diverse. We then analysed the genetic context of the resistance genes and found that composite transposons played important roles in the co-transfer of bla CTX-M-15/55 and qnrS1 , as well as the acquisition of mcr-1 . Furthermore, comparative genomic analysis showed that 12 of the 37 MDR E. coli isolates showed high similarity to ESBL-producing E. coli isolates from raw meat products in local markets. By analyzing the core genome SNPs shared by these isolates, we identified possible clonal transmission of a MDR E. coli clone between human and raw meat, as well as a group of highly similar IncI2 (Delta) plasmids that might be responsible for the dissemination of mcr-1 in a much wider geographic region. Together, these results suggest that antibiotic resistance may be transmitted between different environmental settings by the expansion of MDR E. coli clones, as well as by the dissemination of resistance plasmids. Importance The human gut can harbor both antibiotic resistant and virulent E. coli which may subsequently cause infections. In this study, we found that MDR E. coli isolates from the gut of healthy Singaporeans carry a diverse range of antibiotic resistance mechanisms and virulence factor genes, and are highly diverse to each other. By comparing their genomes with the ESBL-producing E. coli isolates from raw meat products that were sampled at a similar time from local markets, we detected a MDR E. coli clone that was possibly transmitted between humans and raw meat products. Furthermore, we also found that a group of resistance plasmids might be responsible for the dissemination of colistin resistance gene mcr-1 in Singapore, Malaysia and Europe. Our findings call for better countermeasures to block the transmission of antibiotic resistance.

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