scholarly journals Multiple Genetic Elements Carry the Tetracycline Resistance Gene tet(W) in the Animal Pathogen Arcanobacterium pyogenes

2006 ◽  
Vol 50 (11) ◽  
pp. 3580-3587 ◽  
Author(s):  
Stephen J. Billington ◽  
B. Helen Jost
Keyword(s):  
Resistance Gene ◽  
Bacterial Species ◽  
Tetracycline Resistance ◽  
Opportunistic Pathogen ◽  
Human Gut ◽  
Low Frequencies ◽  
Genetic Elements ◽  
Wide Range ◽  
Show Evidence ◽  
Arcanobacterium Pyogenes

ABSTRACT The tet(W) gene is associated with tetracycline resistance in a wide range of bacterial species, including obligately anaerobic rumen bacteria and isolates from the human gut and oral mucosa. However, little is known about how this gene is disseminated and the types of genetic elements it is carried on. We examined tetracycline-resistant isolates of the animal commensal and opportunistic pathogen Arcanobacterium pyogenes, all of which carried tet(W), and identified three genetic elements designated ATE-1, ATE-2, and ATE-3. These elements were found in 25%, 35%, and 60% of tetracycline-resistant isolates, respectively, with some strains carrying both ATE-2 and ATE-3. ATE-1 shows characteristics of a mobilizable transposon, and the tet(W) genes from strains carrying this element can be transferred at low frequencies between A. pyogenes strains. ATE-2 has characteristics of a simple transposon, carrying only the resistance gene and a transposase, while in ATE-3, the tet(W) gene is associated with a streptomycin resistance gene that is 100% identical at the DNA level with the aadE gene from the Campylobacter jejuni plasmid pCG8245. Both ATE-2 and ATE-3 show evidence of being carried on larger genetic elements, but conjugation to other strains was not observed under the conditions tested. ATE-1 was preferentially associated with A. pyogenes strains of bovine origin, while ATE-2 and ATE-3 elements were primarily found in porcine isolates, suggesting that these elements may circulate in different environments. In addition, four alleles of the tet(W) gene, primarily associated with different elements, were detected among A. pyogenes isolates.

scholarly journals SCAPP: an algorithm for improved plasmid assembly in metagenomes

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
David Pellow ◽  
Alvah Zorea ◽  
Maraike Probst ◽  
Ori Furman ◽  
Arik Segal ◽  
...  
Keyword(s):  
Bacterial Species ◽  
Bacterial Genome ◽  
Biological Knowledge ◽  
Assessment Procedure ◽  
Metagenomic Sequencing ◽  
Sequencing Data ◽  
Human Gut ◽  
Double Stranded Dna ◽  
Wide Range ◽  
Python Package

Abstract Background Metagenomic sequencing has led to the identification and assembly of many new bacterial genome sequences. These bacteria often contain plasmids: usually small, circular double-stranded DNA molecules that may transfer across bacterial species and confer antibiotic resistance. These plasmids are generally less studied and understood than their bacterial hosts. Part of the reason for this is insufficient computational tools enabling the analysis of plasmids in metagenomic samples. Results We developed SCAPP (Sequence Contents-Aware Plasmid Peeler)—an algorithm and tool to assemble plasmid sequences from metagenomic sequencing. SCAPP builds on some key ideas from the Recycler algorithm while improving plasmid assemblies by integrating biological knowledge about plasmids. We compared the performance of SCAPP to Recycler and metaplasmidSPAdes on simulated metagenomes, real human gut microbiome samples, and a human gut plasmidome dataset that we generated. We also created plasmidome and metagenome data from the same cow rumen sample and used the parallel sequencing data to create a novel assessment procedure. Overall, SCAPP outperformed Recycler and metaplasmidSPAdes across this wide range of datasets. Conclusions SCAPP is an easy to use Python package that enables the assembly of full plasmid sequences from metagenomic samples. It outperformed existing metagenomic plasmid assemblers in most cases and assembled novel and clinically relevant plasmids in samples we generated such as a human gut plasmidome. SCAPP is open-source software available from: https://github.com/Shamir-Lab/SCAPP.

scholarly journals Bifidobacterium adolescentis shows potential to strengthen host defence against gastrointestinal infection via inhibition of the opportunistic pathogen Candida albicans and stimulation of human-isolated macrophages killing capacity in vitro

2020 ◽  
Vol 2 (7A) ◽  
Author(s):  
Liviana Ricci ◽  
Joanna Mackie ◽  
Megan D. Lenardon ◽  
Caitlin Jukes ◽  
Ahmed N. Hegazy ◽  
...  
Keyword(s):  
Candida Albicans ◽  
Bacterial Species ◽  
Opportunistic Pathogen ◽  
Limited Information ◽  
Human Gut ◽  
Bifidobacterium Adolescentis ◽  
Host Immune Responses ◽  
Opportunistic Fungal Pathogen ◽  
Antimicrobial Metabolites

The human gut microbiota enhances the host’s resistance to enteric pathogens via colonisation resistance, a phenomenon that is driven by multiple mechanisms, such as production of antimicrobial metabolites and activation of host immune responses. However, there is limited information on how individual gut bacterial species, particularly many of the dominant anaerobes, might impact the host’s defence. This study investigated the potential of specific human gut isolates to bolster the host’s resistance to infection. First, by antagonising the opportunistic fungal pathogen Candida albicans, and secondly, by modulating the killing capacity of human-isolated macrophages in vitro. Co-culturing C. albicans with faecal microbiota from different healthy individuals revealed varying levels of fungal inhibition. In vitro assays with a panel of representative human gut anaerobes confirmed that culture supernatants from certain bacterial isolates, in particular of Bifidobacterium adolescentis, significantly inhibited C. albicans growth. Mechanistic studies revealed that microbial fermentation acids including acetate and lactate, in combination with the associated decrease in pH, were strong drivers of this inhibitory activity. In the second in vitro assay, human-isolated macrophages were exposed to bacterial supernatants, and subsequently tested for their capacity to eliminate adherent-invasive Escherichia coli. Among the gut anaerobes tested, B. adolescentis was revealed to exert the strongest immunostimulatory and killing effect when compared to the unstimulated macrophages control. B. adolescentis is known to be stimulated by dietary consumption of resistant starch andmay therefore represent an attractive target for the development of probiotic and prebiotic interventions tailored to enhancethe host’s natural defences against infection.

scholarly journals Occurrence of the New Tetracycline Resistance Gene tet(W) in Bacteria from the Human Gut

2000 ◽  
Vol 44 (3) ◽  
pp. 775-777 ◽  
Author(s):  
Karen P. Scott ◽  
Claire M. Melville ◽  
Teresa M. Barbosa ◽  
Harry J. Flint
Keyword(s):  
Resistance Gene ◽  
Bifidobacterium Longum ◽  
Tetracycline Resistance ◽  
Human Feces ◽  
Human Gut ◽  
Tetracycline Resistance Gene ◽  
Butyrivibrio Fibrisolvens

ABSTRACT Members of our group recently identified a new tetracycline resistance gene, tet(W), in three genera of rumen obligate anaerobes. Here, we show that tet(W) is also present in bacteria isolated from human feces. The tet(W) genes found in human Fusobacterium prausnitzii andBifidobacterium longum isolates were more than 99.9% identical to those from a rumen isolate of Butyrivibrio fibrisolvens.

scholarly journals Tetracycline Resistance in Chlamydia suis Mediated by Genomic Islands Inserted into the Chlamydial inv-Like Gene

2004 ◽  
Vol 48 (10) ◽  
pp. 3989-3995 ◽  
Author(s):  
Jae Dugan ◽  
Daniel D. Rockey ◽  
Loren Jones ◽  
Arthur A. Andersen
Keyword(s):  
Resistance Gene ◽  
Bacterial Species ◽  
Tetracycline Resistance ◽  
Genomic Islands ◽  
Resistance Pattern ◽  
Obligate Intracellular ◽  
Associated Sequences ◽  
Identical Position ◽  
Chlamydia Suis ◽  
Tetracycline Repressor

ABSTRACT Many strains of Chlamydia suis, a pathogen of pigs, express a stable tetracycline resistance phenotype. We demonstrate that this resistance pattern is associated with a resistance gene, tet(C), in the chlamydial chromosome. Four related genomic islands were identified in seven tetracycline-resistant C. suis strains. All resistant isolates carry the structural gene tet(C) and the tetracycline repressor gene tetR(C). The islands share significant nucleotide sequence identity with resistance plasmids carried by a variety of different bacterial species. Three of the four tet(C) islands also carry a novel insertion sequence that is homologous to the IS605 family of insertion sequences. In each strain, the resistance gene and associated sequences are recombined into an identical position in a gene homologous to the inv gene of the yersiniae. These genomic islands represent the first examples of horizontally acquired DNA integrated into a natural isolate of chlamydiae or within any other obligate intracellular bacterium.

scholarly journals SCAPP: An algorithm for improved plasmid assembly in metagenomes

2020 ◽  
Author(s):  
David Pellow ◽  
Alvah Zorea ◽  
Maraike Probst ◽  
Ori Furman ◽  
Arik Segal ◽  
...  
Keyword(s):  
Bacterial Species ◽  
Bacterial Genome ◽  
Biological Knowledge ◽  
Assessment Procedure ◽  
Metagenomic Sequencing ◽  
Sequencing Data ◽  
Human Gut ◽  
Double Stranded Dna ◽  
Wide Range ◽  
Python Package

Background: Metagenomic sequencing has led to the identification and assembly of many new bacterial genome sequences. These bacteria often contain plasmids: usually small, circular double-stranded DNA molecules that may transfer across bacterial species and confer antibiotic resistance. These plasmids are generally less studied and understood than their bacterial hosts. Part of the reason for this is insufficient computational tools enabling the analysis of plasmids in metagenomic samples. Results: We developed SCAPP (Sequence Contents-Aware Plasmid Peeler) - an algorithm and tool to assemble plasmid sequences from metagenomic sequencing. SCAPP builds on some key ideas from the Recycler algorithm while improving plasmid assemblies by integrating biological knowledge about plasmids. We compared the performance of SCAPP to Recycler and metaplasmidSPAdes on simulated metagenomes, real human gut microbiome samples, and a human gut plasmidome dataset that we generated. We also created plasmidome and metagenome data from the same cow rumen sample and used the parallel sequencing data to create a novel assessment procedure. Overall, SCAPP outperformed Recycler and metaplasmidSPAdes across this wide range of datasets. Conclusions: SCAPP is an easy to use Python package that enables the assembly of full plasmid sequences from metagenomic samples. It outperformed existing metagenomic plasmid assemblers in most cases, and assembled novel and clinically relevant plasmids in samples we generated such as a human gut plasmidome. SCAPP is open-source software available from: https://github.com/Shamir-Lab/SCAPP.

scholarly journals Resistance Genes and Genetic Elements Associated with Antibiotic Resistance in Clinical and Commensal Isolates of Streptococcus salivarius

2015 ◽  
Vol 81 (12) ◽  
pp. 4155-4163 ◽  
Author(s):  
Fanny Chaffanel ◽  
Florence Charron-Bourgoin ◽  
Virginie Libante ◽  
Nathalie Leblond-Bourget ◽  
Sophie Payot
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Gene ◽  
Resistance Genes ◽  
Genetic Linkage ◽  
Antibiotic Resistance Genes ◽  
Tetracycline Resistance ◽  
Streptococcus Salivarius ◽  
Content Type ◽  
Clinical Strains ◽  
Genetic Elements

ABSTRACTThe diversity of clinical (n= 92) and oral and digestive commensal (n= 120) isolates ofStreptococcus salivariuswas analyzed by multilocus sequence typing (MLST). No clustering of clinical or commensal strains can be observed in the phylogenetic tree. Selected strains (92 clinical and 46 commensal strains) were then examined for their susceptibilities to tetracyclines, macrolides, lincosamides, aminoglycosides, and phenicol antibiotics. The presence of resistance genestet(M),tet(O),erm(A),erm(B),mef(A/E), andcatQand associated genetic elements was investigated by PCR, as was the genetic linkage of resistance genes. High rates of erythromycin and tetracycline resistance were observed among the strains. Clinical strains displayed either theerm(B) (macrolide-lincosamide-streptogramin B [MLSB] phenotype) ormef(A/E) (M phenotype) resistance determinant, whereas almost all the commensal strains harbored themef(A/E) resistance gene, carried by a macrolide efflux genetic assembly (MEGA) element. A genetic linkage between a macrolide resistance gene and genes of Tn916was detected in 23 clinical strains and 5 commensal strains, with a predominance of Tn3872elements (n= 13), followed by Tn6002(n= 11) and Tn2009(n= 4) elements. Four strains harboring amef(A/E) gene were also resistant to chloramphenicol and carried acatQgene. Sequencing of the genome of one of these strains revealed that these genes colocalized on an IQ-like element, as already described for other viridans group streptococci. ICESt3-related elements were also detected in half of the isolates. This work highlights the potential role ofS. salivariusin the spread of antibiotic resistance genes both in the oral sphere and in the gut.

scholarly journals Widespread Distribution of a Tet W Determinant among Tetracycline-Resistant Isolates of the Animal Pathogen Arcanobacterium pyogenes

2002 ◽  
Vol 46 (5) ◽  
pp. 1281-1287 ◽  
Author(s):  
Stephen J. Billington ◽  
J. Glenn Songer ◽  
B. Helen Jost
Keyword(s):  
Low Frequency ◽  
Tetracycline Resistance ◽  
Opportunistic Pathogen ◽  
Rumen Bacterium ◽  
Gene Encoding ◽  
Butyrivibrio Fibrisolvens ◽  
Widespread Distribution ◽  
Resistance Protein ◽  
Arcanobacterium Pyogenes ◽  
Mobilization Protein

ABSTRACT Tetracycline resistance is common among isolates of the animal commensal and opportunistic pathogen Arcanobacterium pyogenes. The tetracycline resistance determinant cloned from two bovine isolates of A. pyogenes was highly similar at the DNA level (92% identity) to the tet(W) gene, encoding a ribosomal protection tetracycline resistance protein, from the rumen bacterium Butyrivibrio fibrisolvens. The tet(W) gene was found in all 20 tetracycline-resistant isolates tested, indicating that it is a widely distributed determinant of tetracycline resistance in this organism. In 25% of tetracycline-resistant isolates, the tet(W) gene was associated with a mob gene, encoding a functional mobilization protein, and an origin of transfer, suggesting that the determinant may be transferable to other bacteria. In fact, low-frequency transfer of tet(W) was detected from mob+ A. pyogenes isolates to a tetracycline-sensitive A. pyogenes recipient. The mobile nature of this determinant and the presence of A. pyogenes in the gastrointestinal tract of cattle and pigs suggest that A. pyogenes may have inherited this determinant within the gastrointestinal tracts of these animals.

scholarly journals A heme-binding protein produced byHaemophilus haemolyticusinhibits non-typeableHaemophilus influenzae

2019 ◽  
Author(s):  
Roger D. Latham ◽  
Mario Torrado ◽  
Brianna Atto ◽  
James L. Walshe ◽  
Richard Wilson ◽  
...  
Keyword(s):  
Pathogenic Bacteria ◽  
Biochemical Characterization ◽  
Binding Protein ◽  
Bacterial Species ◽  
Opportunistic Pathogen ◽  
Heme Iron ◽  
Heme Binding ◽  
Therapeutic Uses ◽  
Wide Range ◽  
Heme Binding Protein

AbstractMany commensal bacteria and opportunistic pathogens scavenge heme from their environment. Pathogens and host are engaged in an arms race to control access to heme, but similar conflicts between bacterial species that might regulate pathogen colonisation are largely unknown. We show here that a commensal bacterium,Haemophilus haemolyticus, makes hemophilin, a heme-binding protein that not only allows the bacterium to effectively scavenge heme for its own growth, but also inhibits co-culture of the opportunistic pathogen, non-typeableHaemophilus influenzae(NTHi), by heme starvation. Knockout of the hemophilin gene abrogates the ability ofH. haemolyticusto inhibit NTHi and an x-ray crystal structure shows that hemophilin has a previously unreported heme-binding structure. The bound heme molecule is deeply buried and the heme iron atom is coordinated through a single histidine side chain. Biochemical characterization shows that this arrangement allows heme to be captured in the ferrous or ferric state, and with small ferrous or ferric heme-ligands bound, suggesting hemophilin could function over in a wide range of physiological conditions. Our data raise the possibility that competition for heme between commensal and pathogenic bacteria can influence bacterial colonisation, and therefore disease likelihood, and suggest that strains ofH. haemolyticusthat overproduce hemophilin might have therapeutic uses in reducing colonisation and subsequent opportunistic infection by NTHi.

scholarly journals The unforeseen intracellular lifestyle of Enterococcus faecalis in hepatocytes

2021 ◽  
Author(s):  
Natalia Nunez ◽  
Aurelie Derre-Bobillot ◽  
Goran Lakisic ◽  
Alexandre Lecomte ◽  
Francoise Mercier-Nome ◽  
...  
Keyword(s):  
Enterococcus Faecalis ◽  
Bacterial Species ◽  
Opportunistic Pathogen ◽  
Kidney Cells ◽  
Cell Type ◽  
Human Gut ◽  
Primary Mouse Hepatocytes ◽  
Primary Mouse ◽  
Mouse Hepatocytes

Enterococcus faecalis is a bacterial species present at a sub-dominant level in the human gut microbiota. This commensal turns into an opportunistic pathogen under specific conditions involving dysbiosis and host immune deficiency. E. faecalis is also the only intestinal pathobiont identified to date as contributing to liver damage in alcoholic liver disease. We have previously observed that E. faecalis is internalized in hepatocytes. Here, the survival and fate of E. faecalis was examined in hepatocytes, the main epithelial cell type in the liver. Although referred to as an extracellular pathogen, we demonstrate that E. faecalis is able to survive and divide in hepatocytes, and form intracellular clusters in two distinct hepatocyte cell lines, in primary mouse hepatocytes, as well as in vivo. This novel process extends to kidney cells. Unravelling the intracellular lifestyle of E. faecalis, our findings contribute to the understanding of pathobiont-driven diseases.

scholarly journals Isolation, Detection, and Characterization of Enterotoxigenic Bacteroides fragilis in Clinical Samples

2016 ◽  
Vol 10 (1) ◽  
pp. 57-63 ◽  
Author(s):  
Payam Fathi ◽  
Shaoguang Wu
Keyword(s):  
Bacteroides Fragilis ◽  
Opportunistic Pathogen ◽  
Clinical Samples ◽  
Normal Flora ◽  
Human Gut ◽  
Wide Range ◽  
Inflammatory Bowel ◽  
Generation Sequencing ◽  
Isolated Species

Bacteroides fragilisis an extensively studied anaerobic bacterium comprising the normal flora of the human gut.B. fragilisis known to be one of the most commonly isolated species from clinical samples and has been shown to cause a wide range of pathologies in humans [1, 2]. As an opportunistic pathogenB. fragiliscan cause abscess formation and bacteremia [2]. Additionally in its enterotoxigenic form,B. fragilisis a known cause of diarrheal illness, is associated with inflammatory bowel disease, and has been recently characterized in patients with colon cancer [3 - 5]. As research in the field of the gut microbiome continues to expand at an ever increasing rate due to advances in the availability of next generation sequencing and analysis tools it is important to outline various molecular methods that can be employed in quickly detecting and isolating relevant strains ofB. fragilis. This review outlines methods that are routinely employed in the isolation and detection ofB. fragilis, with an emphasis on characterizing enterotoxigenicB. fragilis(ETBF) strains.

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