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PubMed2024

Tomato bacterial wilt disease outbreaks are accompanied by an increase in soil antibiotic resistance.

The presence of soil-borne disease obstacles and antibiotic resistance genes (ARGs) in soil leads to serious economic losses and health risks to humans. One area in need of attention is the evolution of ARGs as pathogenic soil gradually develops, which introduces uncertainty to the dynamic ability of conventional farming models to predict ARGs. Here, we investigated variations in tomato bacterial wilt disease accompanied by the resistome by metagenomic analysis in soils over 13 seasons of monoculture. The results showed that the abundance and diversity of ARGs and mobile genetic elements (MGEs) exhibited a significant and positive correlation with R. solanacearum. Furthermore, the binning approach indicated that fluoroquinolone (qepA), tetracycline (tetA), multidrug resistance genes (MDR, mdtA, acrB, mexB, mexE), and β-lactamases (ampC, blaGOB) carried by the pathogen itself were responsible for the increase in overall soil ARGs. The relationships between pathogens and related ARGs that might underlie the breakdown of soil ARGs were further studied in R. solanacearum invasion pot experiments. This study revealed the dynamics of soil ARGs as soil-borne diseases develop, indicating that these ecological trends can be anticipated. Overall, this study enhances our understanding of the factors driving ARGs in disease-causing soils.

Soil Microbiology↗
PubMed2024

Dynamics of antibiotic resistance genes during manure composting: Reduction in herbivores manure and accumulation in carnivores.

The elevated levels of antibiotic resistance genes (ARGs) in livestock manure represent a significant threat to both the environment and human health. Composting has been recognized as an effective strategy to mitigate the abundance of ARGs in manure. However, notable rebounds in ARGs abundance have been observed during this process. This study explored the changes in ARGs abundance and the underlying influencing factors during the composting of carnivore (chicken and pig) and herbivore (sheep and cow) manures, along with mushroom residues. The findings revealed that the total relative abundance of ARGs increased by 6.96 and 10.94 folds in chicken and pig manure composts, respectively, whereas it decreased by a remarkable 91.72% and 98.37% in sheep and cow manure composts. Nitrogen content emerged as the primary physicochemical factors governing the abundance of ARGs in chicken and pig manure composts. Conversely, carbon content played a pivotal role in determining ARGs abundance in chicken and pig manure composts. Furthermore, the presence of dominant hosts, such as Corynebacterium, Bacillus, and Clostridium, along with emerging bacteria like Thermobifida, Saccharomonospora, and Actinomadura, contributed significantly to the enrichment of total ARGs, including tetG, tetO, tetX, and sul2, in chicken and pig manure composts. The coexistence of these genes with mobile genetic elements and a plethora of host bacteria, coupled with their high abundance, renders them particularly high-risk ARGs. On the other hand, the observed decrease in the abundance of total ARGs in sheep and cow manure composts can be attributed to the decline in the population of host bacteria, specifically Atopostipes, Psychrobacter, and Corynebacterium. Collectively, these results provide crucial insights into the management of ARGs risks and offer essential theoretical support for enhancing the safe utilization of organic fertilizer in agriculture.

Manure↗
PubMed2024

Filamentous bacteria-induced sludge bulking can alter antibiotic resistance gene profiles and increase potential risks in wastewater treatment systems.

Sludge bulking caused by filamentous bacteria is a prevalent issue in wastewater treatment systems. While previous studies have primarily concentrated on controlling sludge bulking, the biological risks associated with it have been overlooked. This study demonstrates that excessive growth of filamentous bacteria during sludge bulking can significantly increase the abundance of antibiotic resistance genes (ARGs) in activated sludge. Through metagenomic analysis, we identified specific ARGs carried by filamentous bacteria, such as Sphaerotilus and Thiothrix, which are responsible for bulking. Additionally, by examining over 1,000 filamentous bacterial genomes, we discovered a diverse array of ARGs across different filamentous bacteria derived from wastewater treatment systems. Our findings indicate that 74.84% of the filamentous bacteria harbor at least one ARG, with the occurrence frequency of ARGs in these bacteria being approximately 1.5 times higher than that in the overall bacterial population in activated sludge. Furthermore, genomic and metagenomic analyses have shown that the ARGs in filamentous bacteria are closely linked to mobile genetic elements and are frequently found in potentially pathogenic bacteria, highlighting potential risks posed by these filamentous bacteria. These insights enhance our understanding of ARGs in activated sludge and underscore the importance of risk management in wastewater treatment systems.

Sewage↗
PubMed2024

Metagenomic insights into ecological risk of antibiotic resistome and mobilome in riverine plastisphere under impact of urbanization.

Microplastics (MPs) are of increasing concern due to their role as reservoirs for antibiotic resistance genes (ARGs) and pathogens. To date, few studies have explored the influence of anthropogenic activities on ARGs and mobile genetic elements (MGEs) within various riverine MPs, in comparison to their natural counterparts. Here an in-situ incubation was conducted along heavily anthropogenically-impacted Houxi River to characterize the geographical pattern of antibiotic resistome, mobilome and pathogens inhabiting MPs- and leaf-biofilms. The metagenomics result showed a clear urbanization-driven profile in the distribution of ARGs, MGEs and pathogens, with their abundances sharply increasing 4.77 to 19.90 times from sparsely to densely populated regions. The significant correlation between human fecal marker crAssphage and ARG (R2 = 0.67, P=0.003) indicated the influence of anthropogenic activity on ARG proliferation in plastisphere and natural leaf surfaces. And mantel tests and random forest analysis revealed the impact of 17 socio-environmental factors, e.g., population density, antibiotic concentrations, and pore volume of materials, on the dissemination of ARGs. Partial least squares-path modeling further unveiled that intensifying human activities not only directly boosted ARGs abundance but also exerted a comparable indirect impact on ARGs propagation. Furthermore, the polyvinylchloride plastisphere created a pathogen-friendly habitat, harboring higher abundances of ARGs and MGEs, while polylactic acid are not likely to serve as vectors for pathogens in river, with a lower resistome risk score than that in leaf-biofilms. This study highlights the diverse ecological risks associated with the dissemination of ARGs and pathogens in varied MPs, offering insights for the policymaking of usage and control of plastics within urbanization.

Urbanization↗
PubMed2004

BOF: a novel family of bacterial OB-fold proteins.

Using top-of-the-line fold recognition methods, we assigned an oligonucleotide/oligosaccharide-binding (OB)-fold structure to a family of previously uncharacterized hypothetical proteins from several bacterial genomes. This novel family of bacterial OB-fold (BOF) proteins present in a number of pathogenic strains encompasses sequences of unknown function from DUF388 (in Pfam database) and COG3111. The BOF proteins can be linked evolutionarily to other members of the OB-fold nucleic acid-binding superfamily (anticodon-binding and single strand DNA-binding domains), although they probably lack nucleic acid-binding properties as implied by the analysis of the potential binding site. The presence of conserved N-terminal predicted signal peptide indicates that BOF family members localize in the periplasm where they may function to bind proteins, small molecules, or other typical OB-fold ligands. As hypothesized for the distantly related OB-fold containing bacterial enterotoxins, the loss of nucleotide-binding function and the rapid evolution of the BOF ligand-binding site may be associated with the presence of BOF proteins in mobile genetic elements and their potential role in bacterial pathogenicity.

Amino Acid Sequence↗
PubMed2004

Molecular basis of bacterial resistance to chloramphenicol and florfenicol.

Chloramphenicol (Cm) and its fluorinated derivative florfenicol (Ff) represent highly potent inhibitors of bacterial protein biosynthesis. As a consequence of the use of Cm in human and veterinary medicine, bacterial pathogens of various species and genera have developed and/or acquired Cm resistance. Ff is solely used in veterinary medicine and has been introduced into clinical use in the mid-1990s. Of the Cm resistance genes known to date, only a small number also mediates resistance to Ff. In this review, we present an overview of the different mechanisms responsible for resistance to Cm and Ff with particular focus on the two different types of chloramphenicol acetyltransferases (CATs), specific exporters and multidrug transporters. Phylogenetic trees of the different CAT proteins and exporter proteins were constructed on the basis of a multisequence alignment. Moreover, information is provided on the mobile genetic elements carrying Cm or Cm/Ff resistance genes to provide a basis for the understanding of the distribution and the spread of Cm resistance--even in the absence of a selective pressure imposed by the use of Cm or Ff.

Animals↗
PubMed2026

Genomic determinants underlying biogenic amine detoxification phenotypes in food-associated lactic acid bacteria: Mechanism, evolutionary origin, and relevance to fermented food safety.

Biogenic amines (BAs) are toxic metabolites that accumulate in fermented foods and pose significant food safety concerns. Although several lactic acid bacteria (LAB) have previously been reported to exhibit strain-specific BA-degrading phenotypes, the genetic determinants underlying these activities have remained largely uncharacterized. Here, we analyzed 8251 LAB genomes to validate BA-degrading phenotypes. We predicted five BA-associated genes, including two direct biogenic amine-degrading genes (BADGs), mco and patA, and three polyamine-modifying genes (PMGs), speG, paiA, and bltD. Among BADGs, mco was broadly distributed across LAB and strongly enriched across food-associated niches. patA, organized within a conserved potD-glnB-potABC-patA cassette, is a putative, functionally distinct BADG in LAB, revealing a nitrogen-responsive polyamine uptake-catabolism module. Phylogenomics, phylogenetic reconciliation, and synteny analysis established that all five genes entered the LAB through episodic horizontal gene transfer followed by lineage-specific fixation. GC compositional bias and mobile genetic element association further corroborated the horizontal origin of the two BADGs. Structural analysis confirmed the conservation of catalytic core residues of BADGs across LAB, indicating strong purifying selection. Phenotype-to-genotype correlation with experimentally reported LAB suggested mco as a reliable genomic predictor of degrading phenotype. Integration of degradation and biosynthetic profiles predicted multiple LAB species capable of both synthesizing and degrading BA, along with 1823 genomes with degradation potential but lacking detectable BA biosynthesis genes. This study provides the first large-scale genome framework linking BA-degrading phenotypes with their genetic determinants in LAB and offers a rational basis for selecting BA-detoxifying strains for fermented food applications.

Biogenic Amines↗
PubMed2005

For better or worse: genomic consequences of intracellular mutualism and parasitism.

Bacteria that replicate within eukaryotic host cells include a variety of pathogenic and mutualistic species. Early genome data for these intracellular associates suggested they experience continual gene loss, little if any gene acquisition, and minimal recombination in small, isolated populations. This view of reductive evolution is itself evolving as new genome sequences clarify mechanisms and outcomes of diverse intracellular associations. Recently sequenced genomes have confirmed a trajectory of gene loss and exceptional genome stability in long-term, nutritional mutualists and certain pathogens. However, new genome data for the Rickettsiales and Chlamydiales indicate more repeated DNA, a greater abundance of mobile DNA elements, and more labile genome dynamics than previously suspected for ancient intracellular lineages. Surprising discoveries of conjugation machinery in the parasite Rickettsia felis and the amoebae symbiont Parachlamydia sp. suggest that DNA transfer might play key roles in some intracellular taxa.

Adaptation, Physiological↗
PubMed2004

Genomic organization and characterization of the promoter for the E2A gene.

Although E2A gene products are ubiquitously expressed, E2A-deficient mice display selective abnormalities in lymphocyte development, suggesting a certain requirement of the E2A gene products during lymphocyte development. To gain insights into the mechanisms of E2A transcriptional regulation, we isolated the genomic clones which are composed of four exons and one noncoding exon and span approximately 16 kb. The promoter region of E2A gene lacks a TATA box, and primer extension analysis showed several transcription initiation sites, a feature that characterizes TATA-less promoters. The transient transfection assay using the 5'-flanking region (positions -2994/+62) revealed that both positive (-357/-158) and negative (-831/-358) regulatory segments control E2A transcription in B-cell (WEHI-231) and T-cell (DO11.10) lines. However, contribution of a certain segment to promoter activity was different between lymphocytes and fibroblasts (NIH-3T3). Sequential deletion analysis of the constructs spanning the positive regulatory segments showed that the segment -257/-238 played a critical role in the basal promoter activity of the E2A gene, although other segments within -337 to -158 also appeared to be involved. Mutational analysis using the -257/-238 fragment failed to demonstrate a single cis-element responsible for the basal promoter activity, suggesting that E2A promoter requires the interaction of multiple regulatory elements. Electrophoretic mobility shift assay (EMSA) demonstrated a highly specific complex comprised of a positive regulatory segment (-267/-238) and putative transcription factor(s), which might be necessary for the basal promoter activity of the E2A gene.

5' Flanking Region↗
PubMed2004

Genomic organization of the Schistosoma mansoni aspartic protease gene, a platyhelminth orthologue of mammalian lysosomal cathepsin D.

Schistosomes are considered the most important of the helminth parasites of humans in terms of morbidity and mortality. Schistosomes employ proteolytic enzymes to digest host hemoglobin from ingested human blood, including a cathepsin D-like, aspartic protease that is overexpressed in the gut of the adult female schistosome. Because of its key role in parasite nutrition, this enzyme represents a potential intervention target. To continue exploration of this potential, here we have determined the sequence, structure and genomic organization of the cathepsin D gene locus of Schistosoma mansoni. Using the cDNA encoding S. mansoni cathepsin D as a probe, we isolated several positive bacterial artificial chromosomes (BAC) from a BAC library that represents an approximately 8-fold coverage of the schistosome genome. Sequencing of BAC clone 25-J-24 revealed that the cathepsin D gene locus was approximately 13 kb in length, and included seven exons interrupted by six introns. The exons ranged in length from 49 to 294 bp, and the introns from 30 to 5025 bp. The genomic organization of schistosome cathepsin D was similar in sequence, structure and complexity to human cathepsin D, including to a greater or lesser extent the conservation of all six exon/intron boundaries of the schistosome gene. It was less similar to aspartic protease genes of the nematodes Caenorhabditis elegans and Haemonchus contortus, and dissimilar to those of plasmepsins from malarial parasites. Examination of the introns revealed the presence of endogenous mobile genetic elements including SR2, the ASL-associated retrotransposon, and the SINE-like element, SMalpha. Phylogenetically, schistosome cathepsin D appeared to be more closely related to mammalian cathepsin D than to other sub-families of eukaryotic aspartic proteases known from mammals. Taken together, these features indicated that schistosome cathepsin D is a platyhelminth orthologue of mammalian lysosomal cathepsin D.

Amino Acid Sequence↗
PubMed2006

Ty1 transposition induced by carcinogens in Saccharomyces cerevisiae yeast depends on mitochondrial function.

The transposition of the Ty mobile genetic element of Saccharomyces cerevisiae is induced by carcinogens. While the molecular background of spontaneous Ty1 transposition is well understood, the detailed mechanism of carcinogen induced Ty1 transposition is not clear. We found that mitochondrial functions participate in the Ty induced transposition induced by carcinogens. Contrary to the parental rho(+) cells rho(-) mutants (spontaneous or induced by ethidium bromide) do not increase the rate of Ty1 transposition upon treatment with carcinogens. Preliminary results strongly suggest that the absence of oxidative phosphorylation in rho(-) mutants is the reason for the inhibited Ty transposition. The lack of carcinogen induced Ty1 transposition in rho(-) cells is not specific for a particular carcinogen and represents a general feature of different carcinogenic substances inducing rho(-). It is concluded that carcinogen induced Ty1 transposition depends on the functional state of mitochondria and cannot take place in cells with compromised mitochondrial function (rho(-)).

Carcinogens↗
PubMed2006

Nosocomial infections by Staphylococcus epidermidis: how a commensal bacterium turns into a pathogen.

Staphylococcus epidermidis is a commensal bacterium of the human skin. However, S. epidermidis and other coagulase-negative staphylococci (CNS) emerge also as common nosocomial pathogens infecting immunocompromized patients carrying medical devices. Antibiotic resistance and the ability of many nosocomial S. epidermidis isolates to form biofilms on inert surfaces make these infections hard to treat. Epidemiological analyses using multilocus sequence typing (MLST) and genetic studies suggest that S. epidermidis isolates in the hospital environment differ from those obtained outside of medical facilities with respect to biofilm formation, antibiotic resistance, and the presence of mobile DNA elements. Since S. epidermidis isolates exhibit high genome flexibility, they are now regarded as reservoirs for the evolution and spread of resistance traits within nosocomial bacterial communities.

Biofilms↗
PubMed2026

Silent carriage of tigecycline- and carbapenem-resistant Klebsiella quasipneumoniae co-harbouring tetX(4) and blaNDM-1 in healthy individuals in China.

OBJECTIVES: To investigate the occurrence and genomic characteristics of tigecycline- and carbapenem-resistant Klebsiella quasipneumoniae isolated from healthy individuals in China. METHODS: During a nationwide screening programme, faecal samples from healthy community individuals were cultured for carbapenem-resistant Enterobacterales. Antimicrobial susceptibility testing, whole-genome sequencing and conjugation assays were performed for two K. quasipneumoniae isolates co-harbouring tet(X4) and blaNDM-1. RESULTS: Two K. quasipneumoniae strains carrying tet(X4) and blaNDM-1 were recovered from healthy individuals without recent hospitalisation or antibiotic exposure. Both isolates showed resistance to tigecycline (>8 μg/mL) and carbapenems (≥4 μg/mL). Genomic analysis demonstrated close clonal relatedness between the isolates (ST6460-1LV, KL151). The blaNDM-1 gene was located on an IncX3 plasmid associated with mobile genetic elements, whereas tet(X4) was carried by an IncX1 plasmid. Conjugation assays confirmed successful transfer of both resistance genes, which frequently co-transferred into recipient strains. CONCLUSIONS: To our knowledge, this is the first report of K. quasipneumoniae co-harbouring tet(X4) and blaNDM-1 in healthy individuals in China. The findings indicate that healthy community populations may serve as a hidden reservoir for last-resort antimicrobial resistance genes and underscore the importance of community-based surveillance within a One Health framework.

Klebsiella quasipneumoniae↗
PubMed2006

Characterization of Lactobacillus helveticus strains isolated from cheeses by distribution studies of insertion sequences.

A collection of 38 Lactobacillus helveticus strains, isolated from a number of different artisan Italian cheeses, and 4 reference strains were studied with respect to the presence of insertion sequences and their distribution and abundance. The mobile genetic element ISLh1, that contains one open reading frame coding for a putative transposase of the IS982 family, was used for DNA fingerprinting, together with IS1201 and ISL2, previously isolated from L. helveticus. The number of insertion sequences per strain and the size of DNA restriction fragments containing them, was variable and allowed the discrimination at the strain-level. The genomic distribution of the three unrelated insertion sequences showed significant correlations and allowed the differentiation of the strains also with regard to the specific ecological niche of origin of the isolates. Consequently, insertion sequences comparison may be useful in determining the history of a group of strains known to be related because of identity and offers a further parameter for evaluating the population polymorphism in L. helveticus.

Amino Acid Sequence↗
PubMed2025

Molecular characterization of antimicrobial resistance in Escherichia coli from dairy farm environment.

The present study was carried out to study the prevalence and genetic mechanisms of antimicrobial resistance in E. coli strains from dairy farms. A total of 60 E. coli strains were initially isolated from 192 dairy farm samples using a selective antibiotic approach and confirmed as E. coli by PCR. Among these, 48 E. coli isolates predominantly from fecal samples were further studied. These isolates were majorly classified in phylogroup A (43.75 %) and B1 (16.66 %) and showed predominant resistance against ampicillin (60.41 %) followed by piperacillin (56.25 %), tetracycline (54.16 %), and other β-lactams such as cefotaxime (47.91 %) and cefuroxime (43.75 %). A significant portion (22.9 %) of the E. coli isolates were multidrug-resistant (MDR) and 50 % were ESBL-positive. Multiple antibiotic resistance (MAR) index ≥0.4 was exhibited by three isolates. Genotypic analysis identified resistance genes associated with β-lactams (blaCTX-M-1, 64.58 %; blaTEM, 35.41 %; blaCTX-M-9, 4.16 %), tetracycline (tetA,37.58 %; tetB, 47.91 %), trimethoprim (dfrA17, 16.66 %), aminoglycosides [aac(6')-Ib-cr, 2.08 %] and fluoroquinolones [qnrB, 25 %; qnrS, 16.66 %; gyrB (S492N), 45.83 %; gyrA (S83L), 45.83 %; gyrA(S87L), 39.58 %; parC (S80I), 14.58 %]. E. coli isolates also showed a high frequency of mobile genetic elements (MGEs) such as IS26 (56.25 %), IncFIB plasmids (52.08 %), and Tn3 transposons (56.25 %). Class 1 integrons harbouring 200 and 800 bp gene cassettes were also detected in 5 E. coli isolates (10.4 %). Overall, this study highlights the high prevalence of diverse AMR genes in cattle-derived E. coli and their strong association with various MGEs. These findings emphasize the need for continuous genomic surveillance to mitigate resistance spread, particularly within and from dairy environments.

Escherichia coli↗
PubMed2004

Surface proteins of Streptococcus agalactiae and horizontal gene transfer.

Streptococcus agalactiae is responsible for serious infectious diseases in neonates, immuno-compromised adult patients and causes bovine mastitis in animal hosts. Genome sequencing projects revealed strong indications for horizontal gene transfer events leading to virulence acquisition and genetic diversity in this species. Bacterial surface proteins establish the first contact with host tissues and represent interesting targets for the exchange of virulence properties among different streptococci. This review will focus on horizontal gene transfer events in characterized S. agalactiae surface proteins, mobile genetic elements adjacent to the corresponding genes and will discuss potential mechanisms of transfer.

Adhesins, Bacterial↗
PubMed2004

Shiga toxin-encoding bacteriophages--genomes in motion.

Shiga toxins (Stx) represent a group of bacterial toxins that are involved in human and animal disease. Stx are mainly produced by Escherichia coli isolated from human and non-human sources, Shigella dysenteriae type 1, and sporadically, by Citrobacter freundii, Enterobacter cloacae and Shigella flexneri. The genes encoding Stx are encoded in the genome of heterogeneous lambdoid prophages (Stx-converting bacteriophages; Stx-phages). They are located in a similar position in the late region of the prophage genome and stx is under control of phage genes. Therefore, induction of Stx-converting prophages triggers increased production of Stx. Following induction, Stx-phages can infect other bacteria in vivo and in vitro. Stx-phages may be considered to represent highly mobile genetic elements that play an important role in the expression of Stx, in horizontal gene transfer, and hence in genome diversification.

Animals↗
PubMed2006

Complete sequence of the large virulence plasmid pSFO157 of the sorbitol-fermenting enterohemorrhagic Escherichia coli O157:H- strain 3072/96.

The large virulence plasmid pSFO157 of sorbitol-fermenting E. coli O157:H(-) strain 3072/96 has a size of 121,239bp and contains 96 open reading frames >50bp. It is therefore 29,162bp larger (ca. 32%) than plasmid pO157 of E. coli O157:H7 strain EDL933. Major differences between the plasmids are the absence of katP, espP, and toxB in pSFO157 and, instead of these, the presence of the sfp fimbriae gene cluster and a large part of an F-plasmid transfer region, the latter accounting for most of the additional DNA. The differences in the order of the genes and their composition, as well as the presence of a number of replication-associated genes and mobile genetic elements suggests that the large E. coli O157 virulence plasmids have a complex evolutionary origin.

Bacterial Proteins↗