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 Mycobacterium tuberculosis Beijing-like strains revealed specific genetic variations associated with virulence and drug resistance

2017 ◽  
Vol 54 ◽  
pp. 314-323 ◽  
Author(s):  
Juan Germán Rodríguez-Castillo ◽  
Camilo Pino ◽  
Luis Fernando Niño ◽  
Juan Carlos Rozo ◽  
Claudia Llerena-Polo ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Mycobacterium Tuberculosis ◽  
Genomic Analysis ◽  
Genetic Variations ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic

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 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.

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.

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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