scholarly journals Genome sequencing and analysis of the first complete genome ofLactobacillus kunkeeistrain MP2, anApis melliferagut isolate

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1950 ◽  
Author(s):  
Freddy Asenjo ◽  
Alejandro Olmos ◽  
Patricia Henríquez-Piskulich ◽  
Victor Polanco ◽  
Patricia Aldea ◽  
...  
Keyword(s):  
Honey Bee ◽  
Genome Sequencing ◽  
Honey Bees ◽  
Complete Genome ◽  
Mobile Genetic Elements ◽  
Ecological Niches ◽  
Circular Chromosome ◽  
Unique Region ◽  
Genetic Elements ◽  
Unique Genes

Background.The honey bee (Apis mellifera) is the most important pollinator in agriculture worldwide. However, the number of honey bees has fallen significantly since 2006, becoming a huge ecological problem nowadays. The principal cause is CCD, or Colony Collapse Disorder, characterized by the seemingly spontaneous abandonment of hives by their workers. One of the characteristics of CCD in honey bees is the alteration of the bacterial communities in their gastrointestinal tract, mainly due to the decrease ofFirmicutespopulations, such as theLactobacilli. At this time, the causes of these alterations remain unknown. We recently isolated a strain ofLactobacillus kunkeei(L. kunkeeistrain MP2) from the gut of Chilean honey bees.L. kunkeei, is one of the most commonly isolated bacterium from the honey bee gut and is highly versatile in different ecological niches. In this study, we aimed to elucidate in detail, theL. kunkeeigenetic background and perform a comparative genome analysis with otherLactobacillusspecies.Methods.L. kunkeeiMP2 was originally isolated from the guts of ChileanA. melliferaindividuals. Genome sequencing was done using Pacific Biosciences single-molecule real-time sequencing technology.De novoassembly was performed using Celera assembler. The genome was annotated using Prokka, and functional information was added using the EggNOG 3.1 database. In addition, genomic islands were predicted using IslandViewer, and pro-phage sequences using PHAST. Comparisons betweenL. kunkeeiMP2 with otherL. kunkeei, andLactobacillusstrains were done using Roary.Results.The complete genome ofL. kunkeeiMP2 comprises one circular chromosome of 1,614,522 nt. with a GC content of 36,9%. Pangenome analysis with 16L. kunkeeistrains, identified 113 unique genes, most of them related to phage insertions. A large and unique region ofL. kunkeeiMP2 genome contains several genes that encode for phage structural protein and replication components. Comparative analysis of MP2 with otherLactobacillusspecies, identified several unique genes ofL. kunkeeiMP2 related with metabolism, biofilm generation, survival under stress conditions, and mobile genetic elements (MGEs).Discussion.The presence of multiple mobile genetic elements, including phage sequences, suggest a high degree of genetic variability inL. kunkeei. Its versatility and ability to survive in different ecological niches (bee guts, flowers, fruits among others) could be given by its genetic capacity to change and adapt to different environments.L. kunkeeicould be a new source ofLactobacilluswith beneficial properties. Indeed,L. kunkeeiMP2 could play an important role in honey bee nutrition through the synthesis of components as isoprenoids.

scholarly journals Transmission of ESBL-producing Enterobacteriaceae and their mobile genetic elements—identification of sources by whole genome sequencing: study protocol for an observational study in Switzerland

BMJ Open ◽  
2018 ◽  
Vol 8 (2) ◽  
pp. e021823 ◽  
Author(s):  
Tanja Stadler ◽  
Dominik Meinel ◽  
Lisandra Aguilar-Bultet ◽  
Jana S Huisman ◽  
Ruth Schindler ◽  
...  
Keyword(s):  
Observational Study ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Bacterial Species ◽  
Mobile Genetic Elements ◽  
University Hospital ◽  
Whole Genome ◽  
Hospital Acquired Infections ◽  
Genetic Elements ◽  
Hospital Acquired

IntroductionExtended-spectrum beta-lactamases (ESBL)-producing Enterobacteriaceae were first described in relation with hospital-acquired infections. In the 2000s, the epidemiology of ESBL-producing organisms changed as especially ESBL-producingEscherichia coliwas increasingly described as an important cause of community-acquired infections, supporting the hypothesis that in more recent years ESBL-producing Enterobacteriaceae have probably been imported into hospitals rather than vice versa. Transmission of ESBL-producing Enterobacteriaceae is complicated by ESBL genes being encoded on self-transmissible plasmids, which can be exchanged among the same and different bacterial species. The aim of this research project is to quantify hospital-wide transmission of ESBL-producing Enterobacteriaceae on both the level of bacterial species and the mobile genetic elements and to determine if hospital-acquired infections caused by ESBL producers are related to strains and mobile genetic elements predominantly circulating in the community or in the healthcare setting. This distinction is critical in prevention since the former emphasises the urgent need to establish or reinforce antibiotic stewardship programmes, and the latter would call for more rigorous infection control.Methods and analysisThis protocol presents an observational study that will be performed at the University Hospital Basel and in the city of Basel, Switzerland. ESBL-producing Enterobacteriaceae will be collected from any specimens obtained by routine clinical practice or by active screening in both inpatient and outpatient settings, as well as from wastewater samples and foodstuffs, both collected monthly over a 12-month period for analyses by whole genome sequencing. Bacterial chromosomal, plasmid and ESBL-gene sequences will be compared within the cohort to determine genetic relatedness and migration between humans and their environment.Ethics and disseminationThis study has been approved by the local ethics committee (Ethikkommission Nordwest-und Zentralschweiz) as a quality control project (Project-ID 2017–00100). The results of this study will be published in peer-reviewed medical journals, communicated to participants, the general public and all relevant stakeholders.

First Complete Genome of Lake Sinai Virus Lineage 3 and Genetic Diversity of Lake Sinai Virus Strains From Honey Bees and Bumble Bees

2020 ◽  
Vol 113 (3) ◽  
pp. 1055-1061 ◽  
Author(s):  
Laura Šimenc ◽  
Urška Kuhar ◽  
Urška Jamnikar-Ciglenečki ◽  
Ivan Toplak
Keyword(s):  
Honey Bee ◽  
Honey Bees ◽  
Complete Genome ◽  
Bumble Bees ◽  
Bumble Bee ◽  
Rt Pcr ◽  
Genome Region ◽  
Pcr Method ◽  
Next Generation Sequencing Ngs ◽  
First Time

Abstract The complete genome of Lake Sinai virus 3 (LSV3) was sequenced by the Ion Torrent next-generation sequencing (NGS) technology from an archive sample of honey bees collected in 2010. This strain M92/2010 is the first complete genome sequence of LSV lineage 3. From October 2016 to December 2017, 56 honey bee samples from 32 different locations and 41 bumble bee samples from five different locations were collected. These samples were tested using a specific reverse transcriptase-polymerase chain reaction (RT-PCR) method; 75.92% of honey bee samples and 17.07% of bumble bee samples were LSV-positive with the RT-PCR method. Phylogenetic comparison of 557-base pair-long RNA-dependent RNA polymerase (RdRp) genome region of selected 23 positive samples of honey bees and three positive bumble bee samples identified three different LSV lineages: LSV1, LSV2, and LSV3. The LSV3 lineage was confirmed for the first time in Slovenia in 2010, and the same strain was later detected in several locations within the country. The LSV strains detected in bumble bees are from 98.6 to 99.4% identical to LSV strains detected among honey bees in the same territory.

scholarly journals Independent Microevolution Mediated by Mobile Genetic Elements of IndividualClostridium difficileIsolates from Clade 4 Revealed by Whole-Genome Sequencing

mSystems ◽  
2019 ◽  
Vol 4 (2) ◽  
Author(s):  
Yuan Wu ◽  
Chen Liu ◽  
Wen-Ge Li ◽  
Jun-Li Xu ◽  
Wen-Zhu Zhang ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Clostridium Difficile ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Mobile Genetic Elements ◽  
High Rate ◽  
Whole Genome ◽  
Content Type ◽  
Genetic Elements ◽  
Sequence Types

ABSTRACTHorizontal gene transfer of mobile genetic elements (MGEs) accounts for the mosaic genome ofClostridium difficile, leading to acquisition of new phenotypes, including drug resistance and reconstruction of the genomes. MGEs were analyzed according to the whole-genome sequences of 37C. difficileisolates with a variety of sequence types (STs) within clade 4 from China. Great diversity was found in each transposon even within isolates with the same ST. Two novel transposons were identified in isolates ZR9 and ZR18, of which approximately one third to half of the genes showed heterogenous origins compared with the usual intestinal bacterial genes. Most importantly,catD, known to be harbored by Tn4453a/b, was replaced byaac(6′) aph(2′′)in isolates 2, 7, and 28. This phenomenon illustrated the frequent occurrence of gene exchanges betweenC. difficileand other enterobacteria with individual heterogeneity. Numerous prophages and CRISPR arrays were identified inC. difficileisolates of clade 4. Approximately 20% of spacers were located in prophage-carried CRISPR arrays, providing a new method for typing and tracing the origins of closely related isolates, as well as in-depth studies of the mechanism underlying genome remodeling. The rates of drug resistance were obviously higher than those reported previously around the world, although all isolates retained high sensitivity to vancomycin and metronidazole. The increasing number ofC. difficileisolates resistant to all antibiotics tested here suggests the ease with which resistance is acquiredin vivo. This study gives insights into the genetic mechanism of microevolution within clade 4.IMPORTANCEMobile genetic elements play a key role in the continuing evolution ofClostridium difficile, resulting in the emergence of new phenotypes for individual isolates. On the basis of whole-genome sequencing analysis, we comprehensively explored transposons, CRISPR, prophage, and genetic sites for drug resistance within clade 4C. difficileisolates with different sequence types. Great diversity in MGEs and a high rate of multidrug resistance were found within this clade, including new transposons, Tn4453a/bwithaac(6′) aph(2′′)instead ofcatD, and a relatively high rate of prophage-carried CRISPR arrays. These findings provide important new insights into the mechanism of genome remodeling within clade 4 and offer a new method for typing and tracing the origins of closely related isolates.

scholarly journals Complete Genome Sequence ofStreptococcus anginosusJ4211, a Clinical Isolate

2015 ◽  
Vol 3 (6) ◽  
Author(s):  
Maliha Rahman ◽  
Scott V. Nguyen ◽  
Kimberly A. McCullor ◽  
Catherine J. King ◽  
James H. Jorgensen ◽  
...  
Keyword(s):  
Clinical Isolate ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Mobile Genetic Elements ◽  
Human Pathogen ◽  
Genetic Elements ◽  
Streptococcus Anginosus ◽  
Opportunistic Human Pathogen ◽  
The Brain

Streptococcus anginosusis an opportunistic human pathogen that causes abscesses of the brain, liver, and other organs. Here, we announce the complete genome sequence of a clinically isolated strain ofS. anginosusJ4211. The genome sequence contains two prophages and multiple mobile genetic elements.

scholarly journals Complete Genome Sequences of Two Staphylococcus aureus Sequence Type 5 Isolates from California, USA

2017 ◽  
Vol 5 (13) ◽  
Author(s):  
Samantha J. Hau ◽  
Darrell O. Bayles ◽  
David P. Alt ◽  
Tracy L. Nicholson
Keyword(s):  
Staphylococcus Aureus ◽  
Complete Genome ◽  
Mobile Genetic Elements ◽  
Sequence Type ◽  
Human Diseases ◽  
Genome Sequences ◽  
Content Type ◽  
Genetic Elements

ABSTRACT Staphylococcus aureus causes a variety of human diseases ranging in severity. The pathogenicity of S. aureus can be partially attributed to the acquisition of mobile genetic elements. In this report, we provide two complete genome sequences from human clinical S. aureus isolates.

scholarly journals Comparative Genome Analysis of ‘Candidatus Phytoplasma luffae’ Reveals the Influential Roles of Potential Mobile Units in Phytoplasma Evolution

2021 ◽  
Author(s):  
Ching-Ting Huang ◽  
Shu-Ting Cho ◽  
Choon-Meng Tan ◽  
Yi-Ching Chiu ◽  
Jun-Yi Yang ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Plant Pathogens ◽  
Axenic Culture ◽  
Mobile Genetic Elements ◽  
Nucleotide Composition ◽  
Gene Organization ◽  
Circular Chromosome ◽  
Genetic Elements ◽  
Genome Variability ◽  
Sequencing Technologies

AbstractPhytoplasmas are insect-transmitted plant pathogens that cause substantial losses in agriculture. In addition to economic impact, phytoplasmas induce distinct disease symptoms in infected plants, thus attracting attention for research on molecular plant-microbe interactions and plant developmental processes. Due to the difficulty of establishing an axenic culture of these bacteria, culture-independent genome characterization is a crucial tool for phytoplasma research. However, phytoplasma genomes have strong nucleotide composition biases and are repetitive, which make it challenging to produce complete assemblies. In this study, we utilized Illumina and Oxford Nanopore sequencing technologies to obtain the complete genome sequence of ‘Candidatus Phytoplasma luffae’ strain NCHU2019 that is associated with witches’ broom disease of loofah (Luffa aegyptiaca) in Taiwan. The fully assembled circular chromosome is 769 kb in size and is the first representative genome sequence of group 16SrVIII phytoplasmas. Comparative analysis with other phytoplasmas revealed that NCHU2019 has an exceptionally repetitive genome, possessing a pair of 75 kb repeats and at least 13 potential mobile units (PMUs) that account for ∼25% of its chromosome. This level of genome repetitiveness is exceptional for bacteria, particularly among obligate pathogens with reduced genomes. Our genus-level analysis of PMUs demonstrated that these phytoplasma-specific mobile genetic elements can be classified into three major types that differ in gene organization and phylogenetic distribution. Notably, PMU abundance explains nearly 80% of the variance in phytoplasma genome sizes, a finding that provides a quantitative estimate for the importance of PMUs in phytoplasma genome variability. Finally, our investigation found that in addition to horizontal gene transfer, PMUs also contribute to intra-genomic duplications of effector genes, which may provide redundancy for neofunctionalization or subfunctionalization. Taken together, this work improves the taxon sampling for phytoplasma genome research and provides novel information regarding the roles of mobile genetic elements in phytoplasma evolution.

scholarly journals First Complete Genome Sequence of Chronic Bee Paralysis Virus Isolated from Honey Bees ( Apis mellifera ) in China

2016 ◽  
Vol 4 (4) ◽  
Author(s):  
Beibei Li ◽  
Chunsheng Hou ◽  
Shuai Deng ◽  
Xuefeng Zhang ◽  
Yanna Chu ◽  
...  
Keyword(s):  
Apis Mellifera ◽  
Honey Bee ◽  
Genome Sequence ◽  
Honey Bees ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Viral Disease ◽  
Bee Colony ◽  
Honey Bee Colony ◽  
Paralysis Virus

Chronic bee paralysis virus (CBPV) is a serious viral disease affecting adult bees. We report here the complete genome sequence of CBPV, which was isolated from a honey bee colony with the symptom of severe crawling. The genome of CBPV consists of two segments, RNA 1 and RNA 2, containing respective overlapping fragments.

scholarly journals Methicillin-Resistant and Methicillin-Susceptible Staphylococcus from Vervet Monkeys (Chlorocebus sabaeus) in Saint Kitts

Antibiotics ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 290
Author(s):  
Andreas Hoefer ◽  
Filip Boyen ◽  
Amy Beierschmitt ◽  
Arshnee Moodley ◽  
Marilyn C. Roberts ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Mobile Genetic Elements ◽  
Pcr Analysis ◽  
Whole Genome ◽  
Vervet Monkeys ◽  
Methicillin Resistant ◽  
Genetic Elements ◽  
Maldi Tof ◽  
Staphylococcus Spp

Antimicrobial resistance has been described in all ecosystems, including wildlife. Here we investigated the presence of methicillin-resistant and susceptible staphylococci in both colony-born and wild vervet monkeys (Chlorocebus sabaeus). Through selective isolation, PCR, MALDI-TOF, and whole-genome sequencing, methicillin-resistant and susceptible Staphylococcus spp. isolated from vervet monkeys were characterized. We obtained putatively methicillin-resistant staphylococci from 29 of the 34 nasal samples collected. Strains were identified by MALDI-TOF analysis. Staphylococcus cohnii (n = 15) was the most commonly isolated species, while nine other species were isolated one or two times. PCR analysis indicated that eight [28%] strains were mecA positive. The whole-genome sequencing [WGS] included eight methicillin-resistant strains (S. epidermidis (n = 2), S. cohnii (n = 3), S. arlettae (n = 2) and S. hominis (n = 1)), nine additional S. cohnii strains and two strains that could not be identified by MALDI-TOF, but genetically characterized as one S. cohnii and one S. warneri. Different resistance genes carried by different mobile genetic elements, mainly blaZ (n = 10) and tet(K) (n = 5) were found, while msr(A), cat, fosB, dfrG, erm(C), mph(C) and str were identified in one to three strains. Phylogenetic analysis of the S. cohnii strains based on SNPs indicated four clusters associated with colony born or wild. In addition, one singleton S. cohnii isolated did not form a separate group and clustered within other S. cohnii strains submitted to the NCBI. In this study, we demonstrated the presence of AMR and mobile genetic elements to both colony-born and wild vervet monkeys. We also identified a previously undescribed prevalence of S. cohnii in the nasal flora of these monkeys, which merits further investigation.

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