# | Rank | Similarity | Title + Abs. | Year | PMID |
|---|---|---|---|---|---|
| 0 | 1 | 2 | 3 | 4 | 5 |
| 106 | 0 | 0.9198 | Genomic evidence of the illumination response mechanism and evolutionary history of magnetotactic bacteria within the Rhodospirillaceae family. BACKGROUND: Magnetotactic bacteria (MTB) are ubiquitous in natural aquatic environments. MTB can produce intracellular magnetic particles, navigate along geomagnetic field, and respond to light. However, the potential mechanism by which MTB respond to illumination and their evolutionary relationship with photosynthetic bacteria remain elusive. RESULTS: We utilized genomes of the well-sequenced genus Magnetospirillum, including the newly sequenced MTB strain Magnetospirillum sp. XM-1 to perform a comprehensive genomic comparison with phototrophic bacteria within the family Rhodospirillaceae regarding the illumination response mechanism. First, photoreceptor genes were identified in the genomes of both MTB and phototrophic bacteria in the Rhodospirillaceae family, but no photosynthesis genes were found in the MTB genomes. Most of the photoreceptor genes in the MTB genomes from this family encode phytochrome-domain photoreceptors that likely induce red/far-red light phototaxis. Second, illumination also causes damage within the cell, and in Rhodospirillaceae, both MTB and phototrophic bacteria possess complex but similar sets of response and repair genes, such as oxidative stress response, iron homeostasis and DNA repair system genes. Lastly, phylogenomic analysis showed that MTB cluster closely with phototrophic bacteria in this family. One photoheterotrophic genus, Phaeospirillum, clustered within and displays high genomic similarity with Magnetospirillum. Moreover, the phylogenetic tree topologies of magnetosome synthesis genes in MTB and photosynthesis genes in phototrophic bacteria from the Rhodospirillaceae family were reasonably congruent with the phylogenomic tree, suggesting that these two traits were most likely vertically transferred during the evolution of their lineages. CONCLUSION: Our new genomic data indicate that MTB and phototrophic bacteria within the family Rhodospirillaceae possess diversified photoreceptors that may be responsible for phototaxis. Their genomes also contain comprehensive stress response genes to mediate the negative effects caused by illumination. Based on phylogenetic studies, most of MTB and phototrophic bacteria in the Rhodospirillaceae family evolved vertically with magnetosome synthesis and photosynthesis genes. The ancestor of Rhodospirillaceae was likely a magnetotactic phototrophic bacteria, however, gain or loss of magnetotaxis and phototrophic abilities might have occurred during the evolution of ancestral Rhodospirillaceae lineages. | 2019 | 31117953 |
| 4514 | 1 | 0.9193 | Phenotypic and resistome analysis of antibiotic and heavy metal resistance in the Antarctic bacterium Pseudomonas sp. AU10. Resistance to antibiotics and heavy metals in Antarctic bacteria has been investigated due to anthropogenic impact on the continent. However, there is still much to learn about the genetic determinants of resistance in native bacteria. In this study, we investigated antibiotic, heavy metal, and metalloid resistance in Pseudomonas sp. AU10, isolated from King George Island (Antarctica), and analyzed its genome to look for all the associated genetic determinants (resistome). We found that AU10 displayed resistance to Cr(VI), Cu(II), Mn(II), Fe(II), and As(V), and produced an exopolysaccharide with high Cr(VI)-biosorption capacity. Additionaly, the strain showed resistance to aminopenicillins, cefotaxime, aztreonam, azithromycin, and intermediate resistance to chloramphenicol. Regarding the resistome, we did not find resistance genes in AU10's natural plasmid or in a prophage context. Only a copper resistance cluster indicated possible horizontal acquisition. The mechanisms of resistance found were mostly efflux systems, several sequestering proteins, and a few enzymes, such as an AmpC β-lactamase or a chromate reductase, which would account for the observed phenotypic profile. In contrast, the presence of a few gene clusters, including the terZABCDE operon for tellurite resistance, did not correlate with the expected phenotype. Despite the observed resistance to multiple antibiotics and heavy metals, the lack of resistance genes within evident mobile genetic elements is suggestive of the preserved nature of AU10's Antarctic habitat. As Pseudomonas species are good bioindicators of human impact in Antarctic environments, we consider that our results could help refine surveillance studies based on monitoring resistances and associated resistomes in these populations. | 2023 | 37783937 |
| 5050 | 2 | 0.9187 | Genomic Insights into Drug Resistance Determinants in Cedecea neteri, A Rare Opportunistic Pathogen. Cedecea, a genus in the Enterobacteriaceae family, includes several opportunistic pathogens reported to cause an array of sporadic acute infections, most notably of the lung and bloodstream. One species, Cedecea neteri, is associated with cases of bacteremia in immunocompromised hosts and has documented resistance to different antibiotics, including β-lactams and colistin. Despite the potential to inflict serious infections, knowledge about drug resistance determinants in Cedecea is limited. In this study, we utilized whole-genome sequence data available for three environmental strains (SSMD04, M006, ND14a) of C. neteri and various bioinformatics tools to analyze drug resistance genes in this bacterium. All three genomes harbor multiple chromosome-encoded β-lactamase genes. A deeper analysis of β-lactamase genes in SSMD04 revealed four metallo-β-lactamases, a novel variant, and a CMY/ACT-type AmpC putatively regulated by a divergently transcribed AmpR. Homologs of known resistance-nodulation-cell division (RND)-type multidrug efflux pumps such as OqxB, AcrB, AcrD, and MdtBC were also identified. Genomic island prediction for SSMD04 indicated that tolC, involved in drug and toxin export across the outer membrane of Gram-negative bacteria, was acquired by a transposase-mediated genetic transfer mechanism. Our study provides new insights into drug resistance mechanisms of an environmental microorganism capable of behaving as a clinically relevant opportunistic pathogen. | 2021 | 34442820 |
| 6386 | 3 | 0.9187 | Distribution of antibiotic and metal resistance genes in two glaciers of North Sikkim, India. Glacier studies as of late have ruffled many eyeballs, exploring this frigid ecology to understand the impact of climate change. Mapquesting the glaciers led to the discovery of concealed world of "psychrophiles" harboring in it. In the present study, the antibiotic resistance genes (ARGs) and heavy metal resistance genes (MRGs) were evaluated through both the culture-dependent and culture-independent methods. Samples were collected from two different glaciers, i.e., debris-covered glacier (Changme Khangpu) and debris-free glacier (Changme Khang). Functional metagenomics of both the glacier samples, provided evidence of presence of resistant genes against various antibiotic groups. Bacitracin resistant gene (bacA) was the predominant ARG in both the glaciers. MRGs in both the glacier samples were diversified as the genes detected were resistant against various heavy metals such as arsenic, tungsten, mercury, zinc, chromium, copper, cobalt, and iron. Unique MRGs identified from Changme Khangpu glacier were resistant to copper (cutA, cutE, cutC, cutF, cueR, copC, and copB) and chromium (yelf, ruvB, nfsA, chrR, and chrA) whereas, from Changme Khang glacier they showed resistance against cobalt (mgtA, dmef, corD, corC, corB, and cnrA), and iron (yefD, yefC, yefB, and yefA) heavy metals. ARGs aligned maximum identity with Gram-negative psychrotolerant bacteria. The cultured bacterial isolates showed tolerance to high concentrations of tested heavy metal solutions. Interestingly, some of the antibiotic resistant bacterial isolates also showed tolerance towards the higher concentrations of heavy metals. Thus, an introspection of the hypothesis of co-occurrence and/co-selection of ARGs and MRGs in such environments has been highlighted here. | 2020 | 32888596 |
| 3069 | 4 | 0.9181 | The hospital sink drain biofilm resistome is independent of the corresponding microbiota, the environment and disinfection measures. In hospitals, the transmission of antibiotic-resistant bacteria (ARB) may occur via biofilms present in sink drains, which can lead to infections. Despite the potential role of sink drains in the transmission of ARB in nosocomial infections, routine surveillance of these drains is lacking in most hospitals. As a result, there is currently no comprehensive understanding of the transmission of ARB and the dissemination of antimicrobial resistance genes (ARGs) and associated mobile genetic elements (MGEs) via sink drains. This study employed a multifaceted approach to monitor the total aerobic bacteria as well as the presence of carbapenemase-producing Enterobacterales (CPEs), the microbiota and the resistome of sink drain biofilms (SDBs) and hospital wastewater (WW) of two separate intensive care units (ICUs) in the same healthcare facility in France. Samples of SDB and WW were collected on a monthly basis, from January to April 2023, in the neonatal (NICU) and the adult (AICU) ICUs of Grenoble Alpes University Hospital. In the NICU, sink drain disinfection with surfactants was performed routinely. In the AICU, routine disinfection is not carried out. Culturable aerobic bacteria were quantified on non-selective media, and CPEs were screened using two selective agars. Isolates were identified by MALDI-TOF MS, and antibiotic susceptibility testing (AST) was performed on Enterobacterales and P. aeruginosa. The resistome was analyzed by high-throughput qPCR targeting >80 ARGs and MGEs. The overall bacterial microbiota was assessed via full-length 16S rRNA sequencing. No CPEs were isolated from SDBs in either ICU by bacterial culture. Culture-independent approaches revealed an overall distinct microbiota composition of the SDBs in the two ICUs. The AICU SDBs were dominated by pathogens containing Gram-negative bacterial genera including Pseudomonas, Stenotrophomona, Klebsiella, and Gram-positive Staphylococcus, while the NICU SDBs were dominated by the Gram-negative genera Achromobacter, Serratia, and Acidovorax, as well as the Gram-positive genera Weisella and Lactiplantibacillus. In contrast, the resistome of the SDBs exhibited no significant differences between the two ICUs, indicating that the abundance of ARGs and MGEs is independent of microbiota composition and disinfection practices. The AICU WW exhibited more distinct aerobic bacteria than the NICU WW. In addition, the AICU WW yielded 15 CPEs, whereas the NICU WW yielded a single CPE. All the CPEs were characterized at the species level. The microbiota of the NICU and AICU WW samples differed from their respective SDBs and exhibited distinct variations over the four-month period:the AICU WW contained a greater number of genes conferring resistance to quinolones and integron integrase genes, whereas the NICU WW exhibited a higher abundance of streptogramin resistance genes. Our study demonstrated that the resistome of the hospital SDBs in the two ICUs of the investigated healthcare institute is independent of the microbiota, the environment, and the local disinfection measures. However, the prevalence of CPEs in the WW pipes collecting the waste from the investigated drains differed. These findings offer valuable insights into the resilience of resistance genes in SDBs in ICUs, underscoring the necessity for innovative strategies to combat antimicrobial resistance in clinical environments. | 2025 | 40483807 |
| 2994 | 5 | 0.9174 | Molecular Characterization of Salmonella spp. Isolates from Wild Colombian Babilla (Caiman crocodilus fuscus) Isolated In Situ. Salmonella enterica is a pathogen capable of colonizing various environments, including the intestinal tract of different animals such as mammals, birds, and reptiles, which can act as carriers. S. enterica infection induces different clinical diseases, gastroenteritis being the most common, which in some cases, can evolve to septicemia and meningitis. Reptiles and amphibians have been reported as a reservoir of Salmonella, and transmission of the pathogen to humans has been documented. This study aimed to determine the presence of virulence genes and characterize the genotypic antibiotic resistance profile in Salmonella strains isolated from Caiman crocodilus fuscus obtained in situ (natural habitat) in Prado, Tolima, Colombia in a previous study and stored in a strain bank in our laboratory. Fifteen Salmonella strains were evaluated through endpoint PCR to determine the presence of resistance genes and virulence genes. The genes bla(TEM), strB, and sul1 were detected in all the strains that confer resistance to ampicillin, streptomycin, and sulfamethoxazole, as well as the virulence genes invA, pefA, prgH, spaN, tolC, sipB, sitC, pagC, msgA, spiA, sopB, sifA, lpfA, csgA, hilA, orgA, iroN, avrA, and sivH, indicating the possible role of babilla (Caiman crocodilus fuscus) as a carrier of multidrug-resistant bacteria. | 2022 | 36496880 |
| 5138 | 6 | 0.9174 | Diversity and role of plasmids in adaptation of bacteria inhabiting the Lubin copper mine in Poland, an environment rich in heavy metals. The Lubin underground mine, is one of three mining divisions in the Lubin-Glogow Copper District in Lower Silesia province (Poland). It is the source of polymetallic ore that is rich in copper, silver and several heavy metals. Black shale is also significantly enriched in fossil organic matter in the form of long-chain hydrocarbons, polycyclic aromatic hydrocarbons, organic acids, esters, thiophenes and metalloporphyrins. Biological analyses have revealed that this environment is inhabited by extremophilic bacteria and fungi. Kupfershiefer black shale and samples of water, bottom and mineral sediments from the underground (below 600 m) Lubin mine were taken and 20 bacterial strains were isolated and characterized. All exhibited multi-resistant and hypertolerant phenotypes to heavy metals. We analyzed the plasmidome of these strains in order to evaluate the diversity and role of mobile DNA in adaptation to the harsh conditions of the mine environment. Experimental and bioinformatic analyses of 11 extrachromosomal replicons were performed. Three plasmids, including a broad-host-range replicon containing a Tn3 family transposon, carried genes conferring resistance to arsenic, cadmium, cobalt, mercury and zinc. Functional analysis revealed that the resistance modules exhibit host specificity, i.e., they may increase or decrease tolerance to toxic ions depending on the host strain. The other identified replicons showed diverse features. Among them we identified a catabolic plasmid encoding enzymes involved in the utilization of histidine and vanillate, a putative plasmid-like prophage carrying genes responsible for NAD biosynthesis, and two repABC-type plasmids containing virulence-associated genes. These findings provide an unique molecular insight into the pool of extrachromosomal replicons and highlight their role in the biology and adaptation of extremophilic bacteria inhabiting terrestrial deep subsurface. | 2015 | 26074880 |
| 107 | 7 | 0.9172 | Common ancestry of iron oxide- and iron-sulfide-based biomineralization in magnetotactic bacteria. Magnetosomes are prokaryotic organelles produced by magnetotactic bacteria that consist of nanometer-sized magnetite (Fe(3)O(4)) or/and greigite (Fe(3)S(4)) magnetic crystals enveloped by a lipid bilayer membrane. In magnetite-producing magnetotactic bacteria, proteins present in the magnetosome membrane modulate biomineralization of the magnetite crystal. In these microorganisms, genes that encode for magnetosome membrane proteins as well as genes involved in the construction of the magnetite magnetosome chain, the mam and mms genes, are organized within a genomic island. However, partially because there are presently no greigite-producing magnetotactic bacteria in pure culture, little is known regarding the greigite biomineralization process in these organisms including whether similar genes are involved in the process. Here using culture-independent techniques, we now show that mam genes involved in the production of magnetite magnetosomes are also present in greigite-producing magnetotactic bacteria. This finding suggest that the biomineralization of magnetite and greigite did not have evolve independently (that is, magnetotaxis is polyphyletic) as once suggested. Instead, results presented here are consistent with a model in which the ability to biomineralize magnetosomes and the possession of the mam genes was acquired by bacteria from a common ancestor, that is, the magnetotactic trait is monophyletic. | 2011 | 21509043 |
| 4691 | 8 | 0.9172 | HME, NFE, and HAE-1 efflux pumps in Gram-negative bacteria: a comprehensive phylogenetic and ecological approach. The three primary resistance-nodulation-cell division (RND) efflux pump families (heavy metal efflux [HME], nodulation factor exporter [NFE], and hydrophobe/amphiphile efflux-1 [HAE-1]) are almost exclusively found in Gram-negative bacteria and play a major role in resistance against metals and bacterial biocides, including antibiotics. Despite their significant societal interest, their evolutionary history and environmental functions are poorly understood. Here, we conducted a comprehensive phylogenetic and ecological study of the RND permease, the subunit responsible for the substrate specificity of these efflux pumps. From 920 representative genomes of Gram-negative bacteria, we identified 6205 genes encoding RND permeases with an average of 6.7 genes per genome. The HME family, which is involved in metal resistance, corresponds to a single clade (21.8% of all RND pumps), but the HAE-1 and NFE families had overlapping distributions among clades. We propose to restrict the HAE-1 family to two phylogenetic sister clades, representing 41.8% of all RND pumps and grouping most of the RND pumps involved in multidrug resistance. Metadata associated with genomes, analyses of previously published metagenomes, and quantitative Polymerase Chain Reaction (qPCR) analyses confirmed a significant increase in genes encoding HME permeases in metal-contaminated environments. Interestingly, and possibly related to their role in root colonization, genes encoding HAE-1 permeases were particularly abundant in the rhizosphere. In addition, we found that the genes encoding these HAE-1 permeases are significantly less abundant in marine environments, whereas permeases of a new proposed HAE-4 family are predominant in the genomes of marine strains. These findings emphasize the critical role of the RND pumps in bacterial resistance and adaptation to diverse ecological niches. | 2024 | 38371394 |
| 8708 | 9 | 0.9169 | Genome-Driven Discovery of Enzymes with Industrial Implications from the Genus Aneurinibacillus. Bacteria belonging to the genus Aneurinibacillus within the family Paenibacillaceae are Gram-positive, endospore-forming, and rod-shaped bacteria inhabiting diverse environments. Currently, there are eight validly described species of Aneurinibacillus; however, several unclassified species have also been reported. Aneurinibacillus spp. have shown the potential for producing secondary metabolites (SMs) and demonstrated diverse types of enzyme activities. These features make them promising candidates with industrial implications. At present, genomes of 9 unique species from the genus Aneurinibacillus are available, which can be utilized to decipher invaluable information on their biosynthetic potential as well as enzyme activities. In this work, we performed the comparative genome analyses of nine Aneurinibacillus species representing the first such comprehensive study of this genus at the genome level. We focused on discovering the biosynthetic, biodegradation, and heavy metal resistance potential of this under-investigated genus. The results indicate that the genomes of Aneurinibacillus contain SM-producing regions with diverse bioactivities, including antimicrobial and antiviral activities. Several carbohydrate-active enzymes (CAZymes) and genes involved in heavy metal resistance were also identified. Additionally, a broad range of enzyme classes were also identified in the Aneurinibacillus pan-genomes, making this group of bacteria potential candidates for future investigations with industrial applications. | 2021 | 33652876 |
| 5141 | 10 | 0.9168 | Flavobacterium flabelliforme sp. nov. and Flavobacterium geliluteum sp. nov., Two Multidrug-Resistant Psychrotrophic Species Isolated From Antarctica. Despite unfavorable Antarctic conditions, such as cold temperatures, freeze-thaw cycles, high ultraviolet radiation, dryness and lack of nutrients, microorganisms were able to adapt and surprisingly thrive in this environment. In this study, eight cold-adapted Flavobacterium strains isolated from a remote Antarctic island, James Ross Island, were studied using a polyphasic taxonomic approach to determine their taxonomic position. Phylogenetic analyses based on the 16S rRNA gene and 92 core genes clearly showed that these strains formed two distinct phylogenetic clusters comprising three and five strains, with average nucleotide identities significantly below 90% between both proposed species as well as between their closest phylogenetic relatives. Phenotyping revealed a unique pattern of biochemical and physiological characteristics enabling differentiation from the closest phylogenetically related Flavobacterium spp. Chemotaxonomic analyses showed that type strains P4023(T) and P7388(T) were characterized by the major polyamine sym-homospermidine and a quinone system containing predominantly menaquinone MK-6. In the polar lipid profile phosphatidylethanolamine, an ornithine lipid and two unidentified lipids lacking a functional group were detected as major lipids. These characteristics along with fatty acid profiles confirmed that these species belong to the genus Flavobacterium. Thorough genomic analysis revealed the presence of numerous cold-inducible or cold-adaptation associated genes, such as cold-shock proteins, proteorhodopsin, carotenoid biosynthetic genes or oxidative-stress response genes. Genomes of type strains surprisingly harbored multiple prophages, with many of them predicted to be active. Genome-mining identified biosynthetic gene clusters in type strain genomes with a majority not matching any known clusters which supports further exploratory research possibilities involving these psychrotrophic bacteria. Antibiotic susceptibility testing revealed a pattern of multidrug-resistant phenotypes that were correlated with in silico antibiotic resistance prediction. Interestingly, while typical resistance finder tools failed to detect genes responsible for antibiotic resistance, genomic prediction confirmed a multidrug-resistant profile and suggested even broader resistance than tested. Results of this study confirmed and thoroughly characterized two novel psychrotrophic Flavobacterium species, for which the names Flavobacterium flabelliforme sp. nov. and Flavobacterium geliluteum sp. nov. are proposed. | 2021 | 34745033 |
| 5235 | 11 | 0.9164 | Draft genome sequences of rare Lelliottia nimipressuralis strain MEZLN61 and two Enterobacter kobei strains MEZEK193 and MEZEK194 carrying mobile colistin resistance gene mcr-9 isolated from wastewater in South Africa. OBJECTIVES: Antimicrobial-resistant bacteria of the order Enterobacterales are emerging threats to global public and animal health, leading to morbidity and mortality. The emergence of antimicrobial-resistant, livestock-associated pathogens is a great public health concern. The genera Enterobacter and Lelliottia are ubiquitous, facultatively anaerobic, motile, non-spore-forming, rod-shaped Gram-negative bacteria belonging to the Enterobacteriaceae family and include pathogens of public health importance. Here, we report the first draft genome sequences of a rare Lelliottia nimipressuralis strain MEZLN61 and two Enterobacter kobei strains MEZEK193 and MEZEK194 in Africa. METHODS: The bacteria were isolated from environmental wastewater samples. Bacteria were cultured on nutrient agar, and the pure cultures were subjected to whole-genome sequencing. Genomic DNA was sequenced using an Illumina MiSeq platform. Generated reads were trimmed and subjected to de novo assembly. The assembled contigs were analysed for virulence genes, antimicrobial resistance genes, and extra-chromosomal plasmids, and multilocus sequence typing was performed. To compare the sequenced strains with other, previously sequenced E. kobei and L. nimipressuralis strains, available raw read sequences were downloaded, and all sequence files were treated identically to generate core genome bootstrapped maximum likelihood phylogenetic trees. RESULTS: Whole-genome sequencing analyses identified strain MEZLN61 as L. nimipressuralis and strains MEZEK193 and MEZEK194 as E. kobei. MEZEK193 and MEZEK194 carried genes encoding resistance to fosfomycin (fosA), beta-lactam antibiotics (bla(ACT-9)), and colistin (mcr-9). Additionally, MEZEK193 harboured nine different virulence genes, while MEZEK194 harboured eleven different virulence genes. The phenotypic analysis showed that L. nimipressuralis strain MEZLN61 was susceptible to colistin (2 μg/mL), while E. kobei MEZEK193 (64 μg/mL) and MEZEK194 (32 μg/mL) were resistant to colistin. CONCLUSION: The genome sequences of strains L. nimipressuralis MEZLN6, E. kobei MEZEK193, and E. kobei MEZEK194 will serve as a reference point for molecular epidemiological studies of L. nimipressuralis and E. kobei in Africa. In addition, this study provides an in-depth analysis of the genomic structure and offers important information that helps clarify the pathogenesis and antimicrobial resistance of L. nimipressuralis and E. kobei. The detection of mcr-9, which is associated with very low-level colistin resistance in Enterobacter species, is alarming and may indicate the undetected dissemination of mcr genes in bacteria of the order Enterobacterales. Continuous monitoring and surveillance of the prevalence of mcr genes and their associated phenotypic changes in clinically important pathogens and environmentally associated bacteria is necessary to control and prevent the spread of colistin resistance. | 2023 | 36948496 |
| 124 | 12 | 0.9163 | A bacterial view of the periodic table: genes and proteins for toxic inorganic ions. Essentially all bacteria have genes for toxic metal ion resistances and these include those for Ag+, AsO2-, AsO4(3-), Cd2+ Co2+, CrO4(2-), Cu2+, Hg2+, Ni2+, Pb2+, TeO3(2-), Tl+ and Zn2+. The largest group of resistance systems functions by energy-dependent efflux of toxic ions. Fewer involve enzymatic transformations (oxidation, reduction, methylation, and demethylation) or metal-binding proteins (for example, metallothionein SmtA, chaperone CopZ and periplasmic silver binding protein SilE). Some of the efflux resistance systems are ATPases and others are chemiosmotic ion/proton exchangers. For example, Cd2+-efflux pumps of bacteria are either inner membrane P-type ATPases or three polypeptide RND chemiosmotic complexes consisting of an inner membrane pump, a periplasmic-bridging protein and an outer membrane channel. In addition to the best studied three-polypeptide chemiosmotic system, Czc (Cd2+, Zn2+, and Co2), others are known that efflux Ag+, Cu+, Ni2+, and Zn2+. Resistance to inorganic mercury, Hg2+ (and to organomercurials, such as CH3Hg+ and phenylmercury) involve a series of metal-binding and membrane transport proteins as well as the enzymes mercuric reductase and organomercurial lyase, which overall convert more toxic to less toxic forms. Arsenic resistance and metabolizing systems occur in three patterns, the widely-found ars operon that is present in most bacterial genomes and many plasmids, the more recently recognized arr genes for the periplasmic arsenate reductase that functions in anaerobic respiration as a terminal electron acceptor, and the aso genes for the periplasmic arsenite oxidase that functions as an initial electron donor in aerobic resistance to arsenite. | 2005 | 16133099 |
| 123 | 13 | 0.9163 | Genes for all metals--a bacterial view of the periodic table. The 1996 Thom Award Lecture. Bacterial chromosomes have genes for transport proteins for inorganic nutrient cations and oxyanions, such as NH4+, K+, Mg2+, Co2+, Fe3+, Mn2+, Zn2+ and other trace cations, and PO4(3-), SO4(2-) and less abundant oxyanions. Together these account for perhaps a few hundred genes in many bacteria. Bacterial plasmids encode resistance systems for toxic metal and metalloid ions including Ag+, AsO2-, AsO4(3-), Cd2+, Co2+, CrO4(2-), Cu2+, Hg2+, Ni2+, Pb2+, TeO3(2-), Tl+ and Zn2+. Most resistance systems function by energy-dependent efflux of toxic ions. A few involve enzymatic (mostly redox) transformations. Some of the efflux resistance systems are ATPases and others are chemiosmotic ion/proton exchangers. The Cd(2+)-resistance cation pump of Gram-positive bacteria is membrane P-type ATPase, which has been labeled with 32P from [gamma-32P]ATP and drives ATP-dependent Cd2+ (and Zn2+) transport by membrane vesicles. The genes defective in the human hereditary diseases of copper metabolism, Menkes syndrome and Wilson's disease, encode P-type ATPases that are similar to bacterial cadmium ATPases. The arsenic resistance system transports arsenite [As(III)], alternatively with the ArsB polypeptide functioning as a chemiosmotic efflux transporter or with two polypeptides, ArsB and ArsA, functioning as an ATPase. The third protein of the arsenic resistance system is an enzyme that reduces intracellular arsenate [As(V)] to arsenite [As(III)], the substrate of the efflux system. In Gram-negative cells, a three polypeptide complex functions as a chemiosmotic cation/protein exchanger to efflux Cd2+, Zn2+ and Co2+. This pump consists of an inner membrane (CzcA), an outer membrane (CzcC) and a membrane-spanning (CzcB) protein that function together. | 1998 | 9523453 |
| 166 | 14 | 0.9160 | Cupriavidus metallidurans: evolution of a metal-resistant bacterium. Cupriavidus metallidurans CH34 has gained increasing interest as a model organism for heavy metal detoxification and for biotechnological purposes. Resistance of this bacterium to transition metal cations is predominantly based on metal resistance determinants that contain genes for RND (resistance, nodulation, and cell division protein family) proteins. These are part of transenvelope protein complexes, which seem to detoxify the periplasm by export of toxic metal cations from the periplasm to the outside. Strain CH34 contains 12 predicted RND proteins belonging to a protein family of heavy metal exporters. Together with many efflux systems that detoxify the cytoplasm, regulators and possible metal-binding proteins, RND proteins mediate an efficient defense against transition metal cations. To shed some light into the origin of genes encoding these proteins, the genomes of C. metallidurans CH34 and six related proteobacteria were investigated for occurrence of orthologous and paralogous proteins involved in metal resistance. Strain CH34 was not much different from the other six bacteria when the total content of transport proteins was compared but CH34 had significantly more putative transition metal transport systems than the other bacteria. The genes for these systems are located on its chromosome 2 but especially on plasmids pMOL28 and pMOL30. Cobalt-nickel and chromate resistance determinants located on plasmid pMOL28 evolved by gene duplication and horizontal gene transfer events, leading to a better adaptation of strain CH34 to serpentine-like soils. The czc cobalt-zinc-cadmium resistance determinant, located on plasmid pMOL30 in addition copper, lead and mercury resistance determinants, arose by duplication of a czcICAB core determinant on chromosome 2, plus addition of the czcN gene upstream and the genes czcD, czcRS, czcE downstream of czcICBA. C. metallidurans apparently evolved metal resistance by horizontal acquisition and by duplication of genes for transition metal efflux, mostly on the two plasmids, and decreased the number of uptake systems for those metals. | 2009 | 18830684 |
| 3863 | 15 | 0.9160 | Antibiotic resistance in mucosal bacteria from high Arctic migratory salmonids. Two related salmonids, Arctic char (Salvelinus alpinus) and lake whitefish (Coregonus clupeaformis) sampled from the high Arctic region of Nunavut, Canada are anadromous fish, migrating annually from the same ice-covered freshwater waterbodies to spend summers in the marine waters of the Arctic Ocean. Microbiota associated with the skin-associated mucus undergo community change coincident with migration, and irrespective of this turnover, antibiotic resistance was detected in mixed bacterial cultures initiated with mucus samples. Although as expected most bacteria were unculturable, however, 5/7 isolates showed susceptibility to a panel of five common antibiotics. The fish were sampled under severe conditions and at remote locations far from human habitation. Regardless, two isolates, 'Carnobacterium maltaromaticum sm-2' and 'Arthrobacter citreus sm', showed multi-resistance to two or more antibiotics including ampicillin and streptomycin indicating multiple resistance genes. It is unknown if these fish bacteria have 'natural' resistance phenotypes or if resistance has been acquired. As result of these observations, we urge long-term monitoring of drug-resistant bacteria in the region and caution the assumption of a lack of drug-resistant organisms even in such extreme environments. | 2022 | 34109745 |
| 6387 | 16 | 0.9159 | Insights into the Evolutionary and Ecological Roles of Bathyarchaeia in Arsenic Detoxification. Arsenic (As) is a prevalent toxic element, posing significant risks to organisms, including microbes. While microbial arsenic detoxification has been extensively studied in bacteria, archaeal mechanisms remain understudied. Here, we investigated arsenic resistance genes in Bathyarchaeia, one of the most abundant archaeal lineages on Earth. Comprehensive genomic analysis of 318 Bathyarchaeia representatives revealed a widespread distribution of arsenic resistance genes, with 60% of genomes harboring genes for arsenate reduction (arsR1 and arsC2), arsenite methylation (arsM), and arsenic transport (acr3, arsP, and arsB). Phylogenetic analysis revealed that these genes are widely distributed across 14 archaeal phyla, including Asgardarchaeota, Thermoproteota, and Thermoplasmatota, with close evolutionary relationships among these archaeal lineages. In situ investigation of sediment columns and laboratory microcosm experiments demonstrated a strong positive correlation between Bathyarchaeia abundance and arsenic concentrations, suggesting their adaptation to arsenic-rich environments. Molecular dating analysis placed the emergence of Bathyarchaeia at approximately 3.01 billion years ago, with the evolution of their arsenic resistance mechanisms closely tracking major geological events, including the Great Oxidation Event (2.4-2.1 Gya), Huronian Glaciation (2.29-2.25 Gya), and Cryogenian Glaciation (∼700 Mya). Our findings highlight the critical role of Archaea in the arsenic cycle and provide insights into the evolutionary history of arsenic resistance associated with paleogeochemical changes in Bathyarchaeia. | 2025 | 40921195 |
| 6084 | 17 | 0.9157 | Characterization and identification of Pseudomonas sp. AW4, an arsenic-resistant and plant growth-promoting bacteria isolated from the soybean (Glycine max L.) rhizosphere. Pseudomonas sp. AW4 is a highly arsenic (As) resistant bacterium with plant growth promoting properties, originally isolated from the soybean (Glycine max L.) rhizosphere. In order to safely use this isolate in diverse bioformulations, its characterization needs to be completed and a reliable identification must be provided. In the present work, we analyzed the morpho-physiological, biochemical and genomic characteristics of Pseudomonas sp. AW4. Identification of the isolate varied according to the parameters analyzed, mainly biochemical and physiological tests or individual genes and phylogenetic analyses. In this regard, we performed massive sequencing of its genome, in order to consistently complete its characterization and identification. Pseudomonas sp. AW4 formed a monophyletic clade with P. urmiensis SWRI10, presenting 3.08 % of unique genes against this reference isolate. More than 70 % of AW4 genes were also shared with P. oryziphila strain 1257 NZ and with P. reidholzensis strain CCOS 865. The search for genes related to As resistance evidenced the presence of the operon arsHRBC. Taken together, results of the present work allow identification of this bacterium as Pseudomonas urmiensis AW4 and open up a number of opportunities to study this strain and understand the mechanisms of arsenic resistance and plant growth promotion. | 2025 | 39647648 |
| 3739 | 18 | 0.9157 | Survey of drug resistance associated gene mutations in Mycobacterium tuberculosis, ESKAPE and other bacterial species. Tuberculosis treatment includes broad-spectrum antibiotics such as rifampicin, streptomycin and fluoroquinolones, which are also used against other pathogenic bacteria. We developed Drug Resistance Associated Genes database (DRAGdb), a manually curated repository of mutational data of drug resistance associated genes (DRAGs) across ESKAPE (i.e. Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.) pathogens, and other bacteria with a special focus on Mycobacterium tuberculosis (MTB). Analysis of mutations in drug-resistant genes listed in DRAGdb suggested both homoplasy and pleiotropy to be associated with resistance. Homoplasy was observed in six genes namely gidB, gyrA, gyrB, rpoB, rpsL and rrs. For these genes, drug resistance-associated mutations at codon level were conserved in MTB, ESKAPE and many other bacteria. Pleiotropy was exemplified by a single nucleotide mutation that was associated with resistance to amikacin, gentamycin, rifampicin and vancomycin in Staphylococcus aureus. DRAGdb data also revealed that mutations in some genes such as pncA, inhA, katG and embA,B,C were specific to Mycobacterium species. For inhA and pncA, the mutations in the promoter region along with those in coding regions were associated with resistance to isoniazid and pyrazinamide respectively. In summary, the DRAGdb database is a compilation of all the major MTB drug resistance genes across bacterial species, which allows identification of homoplasy and pleiotropy phenomena of DRAGs. | 2020 | 32488120 |
| 5135 | 19 | 0.9156 | Arsenotrophic Achromobacter aegrifaciens strains isolated from arsenic contaminated tubewell water and soil sources shared similar genomic potentials. BACKGROUND: Arsenic (As), found in diverse ecosystems, poses major public health risks in various parts of the world. Arsenotrophic bacteria in contaminated environments help reduce toxicity by converting arsenite (AsIII) to less harmful arsenate (AsV). We assumed that Achromobacter aegrifaciens strains from As-contaminated tubewell water and soil would share similar genomic characteristics associated with arsenic detoxification and bioremediation. To investigate this, we employed both culture-dependent and culture-independent viz. whole genome sequencing (WGS) methods to thoroughly elucidate the phenotypic and genotypic features of two A. aegrifaciens strains isolated from As-contaminated tubewell water (BAW48) and soil (BAS32) samples collected in the Bogura district of Bangladesh. RESULTS: Both BAW48 and BAS32 isolates demonstrated As(III) oxidation in the KMNO4 test, which was corroborated by molecular analysis confirming the presence of aioA and arsB genes in both strains. These strains were found to be phylogenetically related to many strains of Achromobacter spp., isolated from biological inorganic reactors, environmental soils, sediments and human clinical samples across diverse geographical regions. Moreover, both strains possessed distinct heavy metal resistance genes conferring resistance to Co, Zn, Cu, Cd, Hg, As, and Cr. Three As gene clusters such as As(III) oxidizing aioBA, As(III) reducing arsRCDAB and the MMA(III) oxidizing ars resistance gene (arsHCsO) cluster were predicted in both genomes of A. aegrifaciens. Further genomic analyses revealed similar profiles in both strains, with mobile genetic elements, antimicrobials and heavy metal resistance genes, virulence genes, and metabolic features. Pangenome and synteny analysis showed that the two genomes are evolutionary distinct from other strains, but closely related to one another. CONCLUSION: The genomic data confirmed that A. aegrifaciens strains can oxidize As(III) and detoxify heavy metals like As, suggesting their potential for As detoxification and bioremediation. These findings align with our assumption and provide a basis for developing sustainable solutions for bioremediation efforts in As-contaminated environments. | 2024 | 39627700 |