scholarly journals Insights into Mobile Genetic Elements of the Biocide-Degrading Bacterium Pseudomonas nitroreducens HBP-1

Genes ◽  
2020 ◽  
Vol 11 (8) ◽  
pp. 930
Author(s):  
Nicolas Carraro ◽  
Vladimir Sentchilo ◽  
Lenka Polák ◽  
Claire Bertelli ◽  
Jan Roelof van der Meer
Keyword(s):  
Heavy Metal ◽  
Heavy Metal Resistance ◽  
Metal Resistance ◽  
Genomic Islands ◽  
Bacterial Strains ◽  
Variable Regions ◽  
Integrative And Conjugative Elements ◽  
Degrading Bacterium ◽  
Pseudomonas Nitroreducens ◽  
Chromosomal Genes

The sewage sludge isolate Pseudomonas nitroreducens HBP-1 was the first bacterium known to completely degrade the fungicide 2-hydroxybiphenyl. PacBio and Illumina whole-genome sequencing revealed three circular DNA replicons: a chromosome and two plasmids. Plasmids were shown to code for putative adaptive functions such as heavy metal resistance, but with unclarified ability for self-transfer. About one-tenth of strain HBP-1′s chromosomal genes are likely of recent horizontal influx, being part of genomic islands, prophages and integrative and conjugative elements (ICEs). P. nitroreducens carries two large ICEs with different functional specialization, but with homologous core structures to the well-known ICEclc of Pseudomonas knackmussii B13. The variable regions of ICEPni1 (96 kb) code for, among others, heavy metal resistances and formaldehyde detoxification, whereas those of ICEPni2 (171 kb) encodes complete meta-cleavage pathways for catabolism of 2-hydroxybiphenyl and salicylate, a protocatechuate pathway and peripheral enzymes for 4-hydroxybenzoate, ferulate, vanillin and vanillate transformation. Both ICEs transferred at frequencies of 10−6–10−8 per P. nitroreducens HBP-1 donor into Pseudomonas putida, where they integrated site specifically into tRNAGly-gene targets, as expected. Our study highlights the underlying determinants and mechanisms driving dissemination of adaptive properties allowing bacterial strains to cope with polluted environments.

scholarly journals Draft Genome Sequence of Stenotrophomonas maltophilia CBF10-1, an Organophosphate-Degrading Bacterium Isolated from Ranch Soil in Fairchilds, Texas

2016 ◽  
Vol 4 (3) ◽  
Author(s):  
Rupa Iyer ◽  
Ashish Damania
Keyword(s):  
Heavy Metal ◽  
Resistance Genes ◽  
Stenotrophomonas Maltophilia ◽  
Draft Genome ◽  
Heavy Metal Resistance ◽  
Metal Resistance ◽  
Degradation Pathways ◽  
Multidrug Transporters ◽  
Degrading Bacterium ◽  
Xenobiotic Degradation

Stenotrophomonas maltophilia CBF10-1 was isolated from a ranch in Fairchilds, Texas, USA. Its genome reveals a highly adaptable microorganism with a large complement of antibiotic and heavy metal resistance genes, efflux pumps, multidrug transporters, and xenobiotic degradation pathways.

scholarly journals Integrase-Controlled Excision of Metal-Resistance Genomic Islands in Acinetobacter baumannii

Genes ◽  
2018 ◽  
Vol 9 (7) ◽  
pp. 366 ◽  
Author(s):  
Zaaima AL-Jabri ◽  
Roxana Zamudio ◽  
Eva Horvath-Papp ◽  
Joseph Ralph ◽  
Zakariya AL-Muharrami ◽  
...  
Keyword(s):  
Heavy Metal ◽  
Acinetobacter Baumannii ◽  
Core Genome ◽  
Susceptibility Testing ◽  
Gene Clusters ◽  
Heavy Metal Resistance ◽  
Metal Resistance ◽  
Genomic Islands ◽  
Genome Plasticity ◽  
E Coli

Genomic islands (GIs) are discrete gene clusters encoding for a variety of functions including antibiotic and heavy metal resistance, some of which are tightly associated to lineages of the core genome phylogenetic tree. We have investigated the functions of two distinct integrase genes in the mobilization of two metal resistant GIs, G08 and G62, of Acinetobacter baumannii. Real-time PCR demonstrated integrase-dependent GI excision, utilizing isopropyl β-d-1-thiogalactopyranoside IPTG-inducible integrase genes in plasmid-based mini-GIs in Escherichia coli. In A. baumannii, integrase-dependent excision of the original chromosomal GIs could be observed after mitomycin C induction. In both E. coli plasmids and A. baumannii chromosome, the rate of excision and circularization was found to be dependent on the expression level of the integrases. Susceptibility testing in A. baumannii strain ATCC 17978, A424, and their respective ΔG62 and ΔG08 mutants confirmed the contribution of the GI-encoded efflux transporters to heavy metal decreased susceptibility. In summary, the data evidenced the functionality of two integrases in the excision and circularization of the two Acinetobacter heavy-metal resistance GIs, G08 and G62, in E. coli, as well as when chromosomally located in their natural host. These recombination events occur at different frequencies resulting in genome plasticity and may participate in the spread of resistance determinants in A. baumannii.

scholarly journals Complete Genome Sequence of Cycloclasticus sp. Strain PY97N, Which Includes Two Heavy Metal Resistance Genomic Islands

2019 ◽  
Vol 8 (40) ◽  
Author(s):  
Zhisong Cui ◽  
Veronika Kivenson ◽  
Na Liu ◽  
Angela Xu ◽  
Xiao Luan ◽  
...  
Keyword(s):  
Heavy Metal ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Heavy Metal Resistance ◽  
Metal Resistance ◽  
Genomic Islands ◽  
Circular Chromosome ◽  
Content Type

We present the complete genome sequence of fluoranthene-consuming Cycloclasticus sp. strain PY97N. This strain has one circular chromosome with a G+C content of 42.06%. Moreover, two genomic islands were identified as putative conjugative elements. These genomic details are expected to inform our understanding of the remarkable catabolic capacities of organisms of the Cycloclasticus lineage.

scholarly journals Plasmids pMOL28 and pMOL30 of Cupriavidus metallidurans Are Specialized in the Maximal Viable Response to Heavy Metals

2007 ◽  
Vol 189 (20) ◽  
pp. 7417-7425 ◽  
Author(s):  
Sébastien Monchy ◽  
Mohammed A. Benotmane ◽  
Paul Janssen ◽  
Tatiana Vallaeys ◽  
Safiyh Taghavi ◽  
...  
Keyword(s):  
Heavy Metals ◽  
Heavy Metal ◽  
Heavy Metal Stress ◽  
Heavy Metal Resistance ◽  
Metal Resistance ◽  
Genomic Islands ◽  
Specific Response ◽  
Resistance Proteins ◽  
Cupriavidus Metallidurans ◽  
General Response

ABSTRACT We fully annotated two large plasmids, pMOL28 (164 open reading frames [ORFs]; 171,459 bp) and pMOL30 (247 ORFs; 233,720 bp), in the genome of Cupriavidus metallidurans CH34. pMOL28 contains a backbone of maintenance and transfer genes resembling those found in plasmid pSym of C. taiwanensis and plasmid pHG1 of C. eutrophus, suggesting that they belong to a new class of plasmids. Genes involved in resistance to the heavy metals Co(II), Cr(VI), Hg(II), and Ni(II) are concentrated in a 34-kb region on pMOL28, and genes involved in resistance to Ag(I), Cd(II), Co(II), Cu(II), Hg(II), Pb(II), and Zn(II) occur in a 132-kb region on pMOL30. We identified three putative genomic islands containing metal resistance operons flanked by mobile genetic elements, one on pMOL28 and two on pMOL30. Transcriptomic analysis using quantitative PCR and microarrays revealed metal-mediated up-regulation of 83 genes on pMOL28 and 143 genes on pMOL30 that coded for all known heavy metal resistance proteins, some new heavy metal resistance proteins (czcJ, mmrQ, and pbrU), membrane proteins, truncated transposases, conjugative transfer proteins, and many unknown proteins. Five genes on each plasmid were down-regulated; for one of them, chrI localized on pMOL28, the down-regulation occurred in the presence of five cations. We observed multiple cross-responses (induction of specific metal resistance by other metals), suggesting that the cellular defense of C. metallidurans against heavy metal stress involves various regulons and probably has multiple stages, including a more general response and a more metal-specific response.

scholarly journals Genomic Islands Confer Heavy Metal Resistance in Mucilaginibacter kameinonensis and Mucilaginibacter rubeus Isolated from a Gold/Copper Mine

Genes ◽  
2018 ◽  
Vol 9 (12) ◽  
pp. 573 ◽  
Author(s):  
Yuan Li ◽  
Nicolas Carraro ◽  
Nan Yang ◽  
Bixiu Liu ◽  
Xian Xia ◽  
...  
Keyword(s):  
Heavy Metals ◽  
Heavy Metal ◽  
Metal Binding ◽  
Heavy Metal Resistance ◽  
Metal Resistance ◽  
Genomic Islands ◽  
High Abundance ◽  
Metal Transporter ◽  
Genes Encoding ◽  
Living Organisms

Heavy metals (HMs) are compounds that can be hazardous and impair growth of living organisms. Bacteria have evolved the capability not only to cope with heavy metals but also to detoxify polluted environments. Three heavy metal-resistant strains of Mucilaginibacer rubeus and one of Mucilaginibacter kameinonensis were isolated from the gold/copper Zijin mining site, Longyan, Fujian, China. These strains were shown to exhibit high resistance to heavy metals with minimal inhibitory concentration reaching up to 3.5 mM Cu(II), 21 mM Zn(II), 1.2 mM Cd(II), and 10.0 mM As(III). Genomes of the four strains were sequenced by Illumina. Sequence analyses revealed the presence of a high abundance of heavy metal resistance (HMR) determinants. One of the strain, M. rubeus P2, carried genes encoding 6 putative PIB-1-ATPase, 5 putative PIB-3-ATPase, 4 putative Zn(II)/Cd(II) PIB-4 type ATPase, and 16 putative resistance-nodulation-division (RND)-type metal transporter systems. Moreover, the four genomes contained a high abundance of genes coding for putative metal binding chaperones. Analysis of the close vicinity of these HMR determinants uncovered the presence of clusters of genes potentially associated with mobile genetic elements. These loci included genes coding for tyrosine recombinases (integrases) and subunits of mating pore (type 4 secretion system), respectively allowing integration/excision and conjugative transfer of numerous genomic islands. Further in silico analyses revealed that their genetic organization and gene products resemble the Bacteroides integrative and conjugative element CTnDOT. These results highlight the pivotal role of genomic islands in the acquisition and dissemination of adaptive traits, allowing for rapid adaption of bacteria and colonization of hostile environments.

scholarly journals Plasmid-Mediated Ampicillin, Quinolone, and Heavy Metal Co-Resistance among ESBL-Producing Isolates from the Yamuna River, New Delhi, India

Antibiotics ◽  
2020 ◽  
Vol 9 (11) ◽  
pp. 826
Author(s):  
Mohammad Tahir Siddiqui ◽  
Aftab Hossain Mondal ◽  
Firdoos Ahmad Gogry ◽  
Fohad Mabood Husain ◽  
Ali Alsalme ◽  
...  
Keyword(s):  
Heavy Metals ◽  
Heavy Metal ◽  
Resistance Genes ◽  
Aquatic Environment ◽  
Heavy Metal Resistance ◽  
Metal Resistance ◽  
New Delhi ◽  
Bacterial Strains ◽  
Genetic Determinants ◽  
Yamuna River

Antibiotic resistance is one of the major current global health crises. Because of increasing contamination with antimicrobials, pesticides, and heavy metals, the aquatic environment has become a hotspot for emergence, maintenance, and dissemination of antibiotic and heavy metal resistance genes among bacteria. The aim of the present study was to determine the co-resistance to quinolones, ampicillin, and heavy metals among the bacterial isolates harboring extended-spectrum β-lactamases (ESBLs) genes. Among 73 bacterial strains isolated from a highly polluted stretch of the Yamuna River in Delhi, those carrying blaCTX-M, blaTEM, or blaSHV genes were analyzed to detect the genetic determinants of resistance to quinolones, ampicillin, mercury, and arsenic. The plasmid-mediated quinolone resistance (PMQR) gene qnrS was found in 22 isolates; however, the qnrA, B, C, and qnrD genes could not be detected in any of the bacteria. Two variants of CMY, blaCMY-2 and blaCMY-42, were identified among eight and seven strains, respectively. Furthermore, merB, merP, merT, and arsC genes were detected in 40, 40, 44, and 24 bacterial strains, respectively. Co-transfer of different resistance genes was also investigated in a transconjugation experiment. Successful transconjugants had antibiotic and heavy metal resistance genes with similar tolerance toward antibiotics and heavy metals as did their donors. This study indicates that the aquatic environment is a major reservoir of bacteria harboring resistance genes to antibiotics and heavy metals and emphasizes the need to study the genetic basis of resistant microorganisms and their public health implications.

scholarly journals Genomic Islands Confer Heavy Metal Resistance in Mucilaginibacter Kameinonensis and Mucilaginibacter Rubeus Isolated from a Gold/Copper Mine

2018 ◽  
Author(s):  
Yuan Ping Li ◽  
Nicolas Carraro ◽  
Nan Yang ◽  
Bixiu Liu ◽  
Xian Xia ◽  
...  
Keyword(s):  
Heavy Metals ◽  
Heavy Metal ◽  
Metal Binding ◽  
Heavy Metal Resistance ◽  
Metal Resistance ◽  
Genomic Islands ◽  
High Abundance ◽  
Metal Transporter ◽  
Genes Encoding ◽  
Living Organisms

Heavy metals are compounds that can be hazardous and impair growth of living organisms. Bacteria have evolved the capability not only to cope with heavy metals but also to detoxify polluted environments. Three heavy metal-resistant strains of Mucilaginibacer rubeus and one of Mucilaginibacter kameinonensis were isolated from the gold/copper Zijin mining site, Longyan, Fujian, China. These strains were shown to exhibit high resistance to heavy metals with minimal inhibitory concentration reaching up to 3.5 mM Cu(II), 21 mM Zn(II), 1.2 mM Cd(II), and 10.0 mM As(III). Genomes of the four strains were sequenced by Illumina. Sequence analyses revealed the presence of a high abundance of heavy metal resistance (HMR) determinants. One of the strain, M. rubeus P2, carried genes encoding 6 putative P1B-1-ATPase, 5 putative P1B-3-ATPase and 4 putative Zn(II)/Cd(II) P1B-4 type ATPase, and 16 putative RND-type metal transporter systems. Moreover, the four genomes carry a high abundance of genes coding for putative metal binding chaperones. Analysis of the close vicinity of these HMR determinants uncovered the presence of clusters of genes potentially associated with mobile genetic elements. These loci include genes coding for tyrosine recombinases (integrases) and subunits of mating pore (type 4 secretion system) respectively allowing integration/excision and conjugative transfer of numerous genomic islands. Further in silico analyses revealed that their genetic organization and gene products resemble the Bacteroides integrative and conjugative element CTnDOT. These results highlight the pivotal role of genomic islands in the acquisition and dissemination of adaptive traits, allowing for rapid adaption of bacteria and colonization of hostile environments.

scholarly journals Redefinition and Unification of the SXT/R391 Family of Integrative and Conjugative Elements

2018 ◽  
Vol 84 (13) ◽  
pp. e00485-18 ◽  
Author(s):  
Audrey Bioteau ◽  
Romain Durand ◽  
Vincent Burrus
Keyword(s):  
Heavy Metal ◽  
Antibiotic Resistance ◽  
Vibrio Cholerae ◽  
Pathogenic Bacteria ◽  
Heavy Metal Resistance ◽  
Metal Resistance ◽  
Integrase Gene ◽  
Content Type ◽  
Integrative And Conjugative Elements ◽  
Epidemiological Surveys

ABSTRACT Integrative and conjugative elements (ICEs) of the SXT/R391 family are key drivers of the spread of antibiotic resistance in Vibrio cholerae, the infectious agent of cholera, and other pathogenic bacteria. The SXT/R391 family of ICEs was defined based on the conservation of a core set of 52 genes and site-specific integration into the 5′ end of the chromosomal gene prfC. Hence, the integrase gene int has been intensively used as a marker to detect SXT/R391 ICEs in clinical isolates. ICEs sharing most core genes but differing by their integration site and integrase gene have been recently reported and excluded from the SXT/R391 family. Here we explored the prevalence and diversity of atypical ICEs in GenBank databases and their relationship with typical SXT/R391 ICEs. We found atypical ICEs in V. cholerae isolates that predate the emergence and expansion of typical SXT/R391 ICEs in the mid-1980s in seventh-pandemic toxigenic V. cholerae strains O1 and O139. Our analyses revealed that while atypical ICEs are not associated with antibiotic resistance genes, they often carry cation efflux pumps, suggesting heavy metal resistance. Atypical ICEs constitute a polyphyletic group likely because of occasional recombination events with typical ICEs. Furthermore, we show that the alternative integration and excision genes of atypical ICEs remain under the control of SetCD, the main activator of the conjugative functions of SXT/R391 ICEs. Together, these observations indicate that substitution of the integration/excision module and change of specificity of integration do not preclude atypical ICEs from inclusion into the SXT/R391 family. IMPORTANCE Vibrio cholerae is the causative agent of cholera, an acute intestinal infection that remains to this day a world public health threat. Integrative and conjugative elements (ICEs) of the SXT/R391 family have played a major role in spreading antimicrobial resistance in seventh-pandemic V. cholerae but also in several species of Enterobacteriaceae. Most epidemiological surveys use the integrase gene as a marker to screen for SXT/R391 ICEs in clinical or environmental strains. With the recent reports of closely related elements that carry an alternative integrase gene, it became urgent to investigate whether ICEs that have been left out of the family are a liability for the accuracy of such screenings. In this study, based on comparative genomics, we broaden the SXT/R391 family of ICEs to include atypical ICEs that are often associated with heavy metal resistance.

scholarly journals Heavy Metal Tolerance Trend in Extended-Spectrum β-Lactamase Encoding Strains Recovered from Food Samples

2021 ◽  
Vol 18 (9) ◽  
pp. 4718
Author(s):  
Kashaf Junaid ◽  
Hasan Ejaz ◽  
Iram Asim ◽  
Sonia Younas ◽  
Humaira Yasmeen ◽  
...  
Keyword(s):  
Heavy Metal ◽  
Metal Tolerance ◽  
Heavy Metal Tolerance ◽  
Heavy Metal Resistance ◽  
Metal Resistance ◽  
Food Samples ◽  
Esbl Production ◽  
Extended Spectrum ◽  
Retail Food ◽  
Esbl Producers

This study evaluates bacteriological profiles in ready-to-eat (RTE) foods and assesses antibiotic resistance, extended-spectrum β-lactamase (ESBL) production by gram-negative bacteria, and heavy metal tolerance. In total, 436 retail food samples were collected and cultured. The isolates were screened for ESBL production and molecular detection of ESBL-encoding genes. Furthermore, all isolates were evaluated for heavy metal tolerance. From 352 culture-positive samples, 406 g-negative bacteria were identified. Raw food samples were more often contaminated than refined food (84.71% vs. 76.32%). The predominant isolates were Klebsiella pneumoniae (n = 76), Enterobacter cloacae (n = 58), and Escherichia coli (n = 56). Overall, the percentage of ESBL producers was higher in raw food samples, although higher occurrences of ESBL-producing E. coli (p = 0.01) and Pseudomonas aeruginosa (p = 0.02) were observed in processed food samples. However, the prevalence of ESBL-producing Citrobacter freundii in raw food samples was high (p = 0.03). Among the isolates, 55% were blaCTX-M, 26% were blaSHV, and 19% were blaTEM. Notably, heavy metal resistance was highly prevalent in ESBL producers. These findings demonstrate that retail food samples are exposed to contaminants including antibiotics and heavy metals, endangering consumers.

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