scholarly journals Complete genome sequence of Enterobacter cloacae R11 reveals multiple genes potentially associated with high-level polymyxin E resistance

2018 ◽  
Vol 64 (1) ◽  
pp. 87-90 ◽  
Author(s):  
Chuanqing Zhong ◽  
Chao Zhang ◽  
Jiafang Fu ◽  
Wenbing Chen ◽  
Tianyi Jiang ◽  
...  
Keyword(s):  
Multidrug Resistance ◽  
Genome Sequence ◽  
Resistance Genes ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Antibiotic Resistance Genes ◽  
Enterobacter Cloacae ◽  
Coli Strain ◽  
Circular Chromosome ◽  
Polymyxin E

Enterobacter cloacae strain R11 is a multidrug-resistant bacterium isolated from sewage water near a swine feedlot in China. Strain R11 can survive in medium containing up to 192 μg/mL polymyxin E, indicating a tolerance for this antibiotic that is significantly higher than that reported for other gram-negative bacteria. In this study, conjugation experiments showed that partial polymyxin E resistance could be transferred from strain R11 to Escherichia coli strain 25922, revealing that some genes related to polymyxin E resistance are plasmid-based. The complete genome sequence of this strain was determined, yielding a total of 4 993 008 bp (G+C content, 53.15%) and 4908 genes for the circular chromosome and 4 circular plasmids. Genome analysis revealed a total of 73 putative antibiotic resistance genes, including several polymyxin E resistance genes and genes potentially involved in multidrug resistance. These data provide insights into the genetic basis of the polymyxin E resistance and multidrug resistance of E. cloacae.

scholarly journals Complete genome sequence of Arthrobacter sp. PAMC25564 and its comparative genome analysis for elucidating the role of CAZymes in cold adaptation

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
So-Ra Han ◽  
Byeollee Kim ◽  
Jong Hwa Jang ◽  
Hyun Park ◽  
Tae-Jin Oh
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Cold Adaptation ◽  
Gc Content ◽  
Glycogen Metabolism ◽  
Extreme Environment ◽  
Circular Chromosome ◽  
Cold Regions ◽  
Insight Into

Abstract Background The Arthrobacter group is a known set of bacteria from cold regions, the species of which are highly likely to play diverse roles at low temperatures. However, their survival mechanisms in cold regions such as Antarctica are not yet fully understood. In this study, we compared the genomes of 16 strains within the Arthrobacter group, including strain PAMC25564, to identify genomic features that help it to survive in the cold environment. Results Using 16 S rRNA sequence analysis, we found and identified a species of Arthrobacter isolated from cryoconite. We designated it as strain PAMC25564 and elucidated its complete genome sequence. The genome of PAMC25564 is composed of a circular chromosome of 4,170,970 bp with a GC content of 66.74 % and is predicted to include 3,829 genes of which 3,613 are protein coding, 147 are pseudogenes, 15 are rRNA coding, and 51 are tRNA coding. In addition, we provide insight into the redundancy of the genes using comparative genomics and suggest that PAMC25564 has glycogen and trehalose metabolism pathways (biosynthesis and degradation) associated with carbohydrate active enzyme (CAZymes). We also explain how the PAMC26654 produces energy in an extreme environment, wherein it utilizes polysaccharide or carbohydrate degradation as a source of energy. The genetic pattern analysis of CAZymes in cold-adapted bacteria can help to determine how they adapt and survive in such environments. Conclusions We have characterized the complete Arthrobacter sp. PAMC25564 genome and used comparative analysis to provide insight into the redundancy of its CAZymes for potential cold adaptation. This provides a foundation to understanding how the Arthrobacter strain produces energy in an extreme environment, which is by way of CAZymes, consistent with reports on the use of these specialized enzymes in cold environments. Knowledge of glycogen metabolism and cold adaptation mechanisms in Arthrobacter species may promote in-depth research and subsequent application in low-temperature biotechnology.

scholarly journals Complete Genome Sequence of Lanthionine-Producing Lactobacillus brevis Strain 100D8, Generated by PacBio Sequencing

2018 ◽  
Vol 7 (14) ◽  
Author(s):  
Min-Jung Kim ◽  
Hye Sun Kim ◽  
Sam Churl Kim ◽  
Youn-Sig Kwak
Keyword(s):  
Antifungal Activity ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Lactobacillus Brevis ◽  
Pacbio Sequencing ◽  
Circular Chromosome ◽  
Coding Sequences ◽  
Content Type

Lactobacillus brevis strain 100D8 was isolated from rye silage and showed rapid acidification ability in vitro and antifungal activity against mycotoxin-producing fungi. We report here the complete genome sequence of L. brevis strain 100D8, which has a circular chromosome (2,351,988 bp, 2,304 coding sequences [CDSs]) and three plasmids (45,061 bp, 57 CDSs; 40,740 bp, 40 CDSs; and 39,943 bp, 57 CDSs).

scholarly journals Extreme genome selection towards complete antimicrobial resistance in a nosocomial strain of Stenotrophomonas maltophilia complex

2019 ◽  
Author(s):  
Sanjeet Kumar ◽  
Kanika Bansal ◽  
Prashant P. Patil ◽  
Amandeep Kaur ◽  
Satinder Kaur ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Antibiotic Resistance ◽  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Stenotrophomonas Maltophilia ◽  
Antibiotic Resistance Genes ◽  
Chromosomal Origin ◽  
Extreme Drug Resistance

ABSTRACTWe report first complete genome sequence and analysis of an extreme drug resistance (XDR) nosocomial Stenotrophomonas maltophilia that is resistant to the mainstream drugs i.e. trimethoprim/sulfamethoxazole (TMP/SXT) and levofloxacin. Taxonogenomic analysis revealed it to be a novel genomospecies of the Stenotrophomonas maltophilia complex (Smc). Comprehensive genomic investigation revealed fourteen dynamic regions (DRs) exclusive to SM866, consisting of diverse antibiotic resistance genes, efflux pumps, heavy metal resistance, various transcriptional regulators etc. Further, resistome analysis of Smc clearly depicted SM866 to be an enriched strain, having diversified resistome consisting of sul1 and sul2 genes. Interestingly, SM866 does not have any plasmid but it harbors two diverse super-integrons of chromosomal origin. Apart from genes for sulfonamide resistance (sul1 and sul2), both of these integrons harbor an array of antibiotic resistance genes linked to ISCR (IS91-like elements common regions) elements. These integrons also harbor genes encoding resistance to commonly used disinfectants like quaternary ammonium compounds and heavy metals like mercury. Hence, isolation of a novel strain belonging to a novel sequence type (ST) and genomospecies with diverse array of resistance from a tertiary care unit of India indicates extent and nature of selection pressure driving XDRs in hospital settings. There is an urgent need to employ complete genome based investigation using emerging technologies for tracking emergence of XDR at the global level and designing strategies of sanitization and antibiotic regime.Impact StatementThe hospital settings in India have one of the highest usage of antimicrobials and heavy patient load. Our finding of a novel clinical isolate of S. maltophilia complex with two super-integrons harbouring array of antibiotic resistance genes along with antimicrobials resistance genes indicates the extent and the nature of selection pressures in action. Further, the presence of ISCR type of transposable elements on both integrons not only indicates its propensity to transfer resistome but also their chromosomal origin suggests possibilities for further genomic/phenotypic complexities. Such complex cassettes and strain are potential threat to global health care. Hence, there is an urgent need to employ cost-effective long read technologies to keep vigilance on novel and extreme antimicrobial resistance pathogens in populous countries. There is also need for surveillance for usage of antimicrobials for hygiene and linked/rapid co-evolution of extreme drug resistance in nosocomial pathogens. Our finding of the chromosomal encoding XDR will shed a light on the need of hour to understand the evolution of an opportunistic nosocomial pathogen belonging to S. maltophilia.RepositoriesComplete genome sequence of Stenotrophomonas maltophilia SM866: CP031058

scholarly journals Complete Genome Sequence of Streptococcus pneumoniae Strain Rx1, a Hex Mismatch Repair-Deficient Standard Transformation Recipient

2021 ◽  
Vol 10 (41) ◽  
Author(s):  
Anna Maria Cuppone ◽  
Lorenzo Colombini ◽  
Valeria Fox ◽  
David Pinzauti ◽  
Francesco Santoro ◽  
...  
Keyword(s):  
Streptococcus Pneumoniae ◽  
Mismatch Repair ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Gc Content ◽  
Open Reading Frames ◽  
Circular Chromosome ◽  
Content Type ◽  
Sequencing Technologies

The complete genome sequence of Streptococcus pneumoniae strain Rx1, a Hex mismatch repair-deficient standard transformation recipient, was obtained by combining Nanopore and Illumina sequencing technologies. The genome consists of a 2.03-Mb circular chromosome, with 2,054 open reading frames and a GC content of 39.72%.

scholarly journals Complete Genome Sequence of Thiohalobacter sp. Strain COW1, Isolated from Activated Sludge Treating Coke Oven Wastewater

2021 ◽  
Vol 10 (7) ◽  
Author(s):  
Kentaro Miyazaki ◽  
Hikaru Suenaga ◽  
Mamoru Oshiki ◽  
Shuichi Kawano ◽  
Toshikazu Fukushima
Keyword(s):  
Activated Sludge ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Coke Oven ◽  
Rrna Genes ◽  
Trna Genes ◽  
Circular Chromosome ◽  
Protein Coding ◽  
Degrading Bacterium

ABSTRACT A thiocyanate-degrading bacterium, Thiohalobacter sp. strain COW1, was isolated from activated sludge treating coke oven wastewater, and the complete genome sequence was determined. COW1 contained a single circular chromosome (3.23 Mb; G+C content, 63.4%) in which 2,788 protein-coding genes, 39 tRNA genes, and 3 rRNA genes were identified.

scholarly journals Complete High-Quality Genome Sequence of Clostridium limosum (Hathewaya limosa) Isolate 14S0207, Recovered from a Cow with Suspected Blackleg in Germany

2020 ◽  
Vol 9 (2) ◽  
Author(s):  
Prasad Thomas ◽  
Mostafa Y. Abdel-Glil ◽  
Anne Busch ◽  
Lothar H. Wieler ◽  
Inga Eichhorn ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Intestinal Tract ◽  
High Quality ◽  
Circular Chromosome ◽  
Content Type ◽  
High Quality Genome

Clostridium limosum can be found in soil and the intestinal tract of animals. In 2014, C. limosum was isolated from a suspected blackleg outbreak in cattle in Schleswig-Holstein, Germany. We present a complete genome sequence of a C. limosum strain represented by a circular chromosome and three plasmids.

scholarly journals Complete Genome Sequence of Stenotrophomonas maltophilia Myophage Moby

2020 ◽  
Vol 9 (1) ◽  
Author(s):  
Alison Vicary ◽  
Heather Newkirk ◽  
Russell Moreland ◽  
Carlos F. Gonzalez ◽  
Mei Liu ◽  
...  
Keyword(s):  
Multidrug Resistance ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Stenotrophomonas Maltophilia ◽  
Nosocomial Pathogen ◽  
Protein Coding ◽  
Content Type ◽  
Protein Coding Genes ◽  
Phage T4

Stenotrophomonas maltophilia is a prevalent nosocomial pathogen with multidrug resistance. Here, we describe the complete genome of S. maltophilia myophage Moby, which shares characteristics with Enterobacteria phage T4 and is closely related to Stenotrophomonas phage IME-SM1. Moby has a 159,365-bp genome with 271 predicted protein-coding genes and 24 predicted tRNAs.

scholarly journals Complete Genome Sequence of the Carotenoid-Producing Deinococcus sp. Strain AJ005

2019 ◽  
Vol 8 (48) ◽  
Author(s):  
Jun Young Choi ◽  
Kunjoong Lee ◽  
Pyung Cheon Lee
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Novel Species ◽  
The Novel ◽  
King George Island ◽  
Circular Chromosome ◽  
Single Circular Chromosome

The novel species Deinococcus sp. strain AJ005, isolated from King George Island, synthesizes a red carotenoid. Its complete genome is made up of a single circular chromosome (3,380,712 bp, 64.2% G+C content) and four circular plasmids.

scholarly journals Complete Genome Sequence of the Neonatal Meningitis-Causing Escherichia coli Strain NMEC O18

2016 ◽  
Vol 4 (6) ◽  
Author(s):  
Bryon A. Nicholson ◽  
Yvonne M. Wannemuehler ◽  
Catherine M. Logue ◽  
Ganwu Li ◽  
Lisa K. Nolan
Keyword(s):  
Escherichia Coli ◽  
Bacterial Meningitis ◽  
Neonatal Mortality ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Coli Strain ◽  
Neonatal Meningitis ◽  
Neurologic Sequelae ◽  
Highly Virulent

Neonatal meningitis Escherichia coli (NMEC) is a common agent of neonatal bacterial meningitis, causing high neonatal mortality and neurologic sequelae in its victims. Here, we present the complete genome sequence of NMEC O18 (also known as NMEC 58), a highly virulent (O18ac:K1, ST416) strain.

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