Comparative genomic analysis of Acinetobacter baumannii clinical isolates reveals extensive genomic variation and diverse antibiotic resistance determinants

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.

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

Pathogens ◽

10.3390/pathogens9050330 ◽

2020 ◽

Vol 9 (5) ◽

pp. 330 ◽

Cited By ~ 1

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.

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

TURKISH JOURNAL OF BIOLOGY ◽

10.3906/biy-1808-97 ◽

2019 ◽

pp. 99-112 ◽

Cited By ~ 1

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.

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