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BMC Genomics Apr 2022Drug-resistant bacteria are important carriers of antibiotic-resistant genes (ARGs). This fact is crucial for the development of precise clinical drug treatment...
BACKGROUND
Drug-resistant bacteria are important carriers of antibiotic-resistant genes (ARGs). This fact is crucial for the development of precise clinical drug treatment strategies. Long-read sequencing platforms such as the Oxford Nanopore sequencer can improve genome assembly efficiency particularly when they are combined with short-read sequencing data.
RESULTS
Alcaligenes faecalis PGB1 was isolated and identified with resistance to penicillin and three other antibiotics. After being sequenced by Nanopore MinION and Illumina sequencer, its entire genome was hybrid-assembled. One chromosome and one plasmid was assembled and annotated with 4,433 genes (including 91 RNA genes). Function annotation and comparison between strains were performed. A phylogenetic analysis revealed that it was closest to A. faecalis ZD02. Resistome related sequences was explored, including ARGs, Insert sequence, phage. Two plasmid aminoglycoside genes were determined to be acquired ARGs. The main ARG category was antibiotic efflux resistance and β-lactamase (EC 3.5.2.6) of PGB1 was assigned to Class A, Subclass A1b, and Cluster LSBL3.
CONCLUSIONS
The present study identified the newly isolated bacterium A. faecalis PGB1 and systematically annotated its genome sequence and ARGs.
Topics: Alcaligenes faecalis; Anti-Bacterial Agents; High-Throughput Nucleotide Sequencing; Nanopores; Phylogeny; Prostaglandins B; Sequence Analysis, DNA
PubMed: 35443609
DOI: 10.1186/s12864-022-08507-7 -
BMC Infectious Diseases Nov 2020Alcaligenes faecalis is usually causes opportunistic infections in humans. Alcaligenes faecalis infection is often difficult to treat due to its increased resistance to...
BACKGROUND
Alcaligenes faecalis is usually causes opportunistic infections in humans. Alcaligenes faecalis infection is often difficult to treat due to its increased resistance to several antibiotics. The results from a clinical study of patients with Alcaligenes faecalis infection may help improve patients' clinical care.
METHODS
We conducted a retrospective analysis of all patients presenting with Alcaligenes faecalis infection from January 2014 to December 2019. The medical records of all patients were reviewed for demographic information, clinical symptoms and signs, comorbidities, use of intravenous antibiotics within the past three months, bacterial culture, antibiotics sensitivity test, and clinical outcomes.
RESULTS
Sixty-one cases of Alcaligenes faecalis infection were seen during the study period, including 25 cases of cystitis, nine cases of diabetic foot infection, eight cases of pneumonia, seven cases of acute pyelonephritis, three cases of bacteremia, and nine cases of infection at specific sites. Thirty-seven patients (60.7%) had a history of receiving intravenous antibiotics within three months of the diagnosis. Fifty-one (83.6%) cases were mixed with other bacterial infections. Extensively drug-resistant infections have been reported since 2018. The best sensitivity rate to Alcaligenes faecalis was 66.7% for three antibiotics (imipenem, meropenem, and ceftazidime) in 2019. Two antibiotics (ciprofloxacin and piperacillin/tazobactam) sensitivity rates to A. faecalis were less than 50%.
CONCLUSIONS
The most frequent Alcaligenes faecalis infection sites, in order, are the bloodstream, urinary tract, skin and soft tissue, and middle ear. The susceptibility rate of Alcaligenes faecalis to commonly used antibiotics is decreasing. Extensively drug-resistant Alcaligenes faecalis infections have emerged.
Topics: Adult; Aged; Aged, 80 and over; Alcaligenes faecalis; Anti-Bacterial Agents; Bacteremia; Ceftazidime; Drug Resistance, Multiple, Bacterial; Female; Gram-Negative Bacterial Infections; Humans; Imipenem; Male; Meropenem; Microbial Sensitivity Tests; Middle Aged; Retrospective Studies; Treatment Outcome
PubMed: 33176714
DOI: 10.1186/s12879-020-05557-8 -
Scientific Reports Feb 2018Bacteria within the genus Alcaligenes, exhibit diverse properties but remain largely unexplored at genome scale. To shed light on the genome structure, heterogeneity and...
Bacteria within the genus Alcaligenes, exhibit diverse properties but remain largely unexplored at genome scale. To shed light on the genome structure, heterogeneity and traits of Alcaligenes species, the genome of a tannery effluent isolated Alcaligenes faecalis subsp. phenolicus MB207 was sequenced and assembled. The genome was compared to the whole genome sequences of genus Alcaligenes present in the National Centre for Biotechnology Information database. Core, pan and species specific gene sequences i.e. singletons were identified. Members of this genus did not portray exceptional genetic heterogeneity or conservation and out of 5,166 protein coding genes from pooled genome dataset, 2429 (47.01%) contributed to the core, 1193 (23.09%) to singletons and 1544 (29.88%) to accessory genome. Secondary metabolite forming apparatus, antibiotic production and resistance was also profiled. Alcaligenes faecalis subsp. phenolicus MB207 genome consisted of a copious amount of bioremediation genes i.e. metal tolerance and xenobiotic degrading genes. This study marks this strain as a prospective eco-friendly bacterium with numerous benefits for the environment related research. Availability of the whole genome sequence heralds an opportunity for researchers to explore enzymes and apparatus for sustainable environmental clean-up as well as important compounds/substance production.
Topics: Alcaligenes faecalis; Biodegradation, Environmental; DNA, Bacterial; Sequence Analysis, DNA; Whole Genome Sequencing
PubMed: 29483539
DOI: 10.1038/s41598-018-21919-4 -
Molecules (Basel, Switzerland) Apr 2021Although the anti-tumor and anti-infective properties of β-glucans have been well-discussed, their role in bone metabolism has not been reviewed so far. This review... (Review)
Review
Although the anti-tumor and anti-infective properties of β-glucans have been well-discussed, their role in bone metabolism has not been reviewed so far. This review discusses the biological effects of β-glucans on bone metabolisms, especially on bone-resorbing osteoclasts, which are differentiated from hematopoietic precursors. Multiple immunoreceptors that can recognize β-glucans were reported to be expressed in osteoclast precursors. Coordinated co-stimulatory signals mediated by these immunoreceptors are important for the regulation of osteoclastogenesis and bone remodeling. Curdlan from the bacterium negatively regulates osteoclast differentiation in vitro by affecting both the osteoclast precursors and osteoclast-supporting cells. We also showed that laminarin, lichenan, and glucan from baker's yeast, as well as β-1,3-glucan from inhibit the osteoclast formation in bone marrow cells. Consistent with these findings, systemic and local administration of β-glucan derived from and suppressed bone resorption in vivo. However, zymosan derived from stimulated the bone resorption activity and is widely used to induce arthritis in animal models. Additional research concerning the relationship between the molecular structure of β-glucan and its effect on osteoclastic bone resorption will be beneficial for the development of novel treatment strategies for bone-related diseases.
Topics: Animals; Bone Regeneration; Bone Resorption; Bone and Bones; Cartilage; Cell Differentiation; Glucans; Humans; Immunomodulation; Osteoclasts; Osteogenesis; Receptors, Immunologic
PubMed: 33915775
DOI: 10.3390/molecules26071982 -
PloS One 2020Here we present and analyze the complete genome of Alcaligenes faecalis strain Mc250 (Mc250), a bacterium isolated from the roots of Mimosa calodendron, an endemic plant...
Here we present and analyze the complete genome of Alcaligenes faecalis strain Mc250 (Mc250), a bacterium isolated from the roots of Mimosa calodendron, an endemic plant growing in ferruginous rupestrian grasslands in Minas Gerais State, Brazil. The genome has 4,159,911 bp and 3,719 predicted protein-coding genes, in a single chromosome. Comparison of the Mc250 genome with 36 other Alcaligenes faecalis genomes revealed that there is considerable gene content variation among these strains, with the core genome representing only 39% of the protein-coding gene repertoire of Mc250. Mc250 encodes a complete denitrification pathway, a network of pathways associated with phenolic compounds degradation, and genes associated with HCN and siderophores synthesis; we also found a repertoire of genes associated with metal internalization and metabolism, sulfate/sulfonate and cysteine metabolism, oxidative stress and DNA repair. These findings reveal the genomic basis for the adaptation of this bacterium to the harsh environmental conditions from where it was isolated. Gene clusters associated with ectoine, terpene, resorcinol, and emulsan biosynthesis that can confer some competitive advantage were also found. Experimental results showed that Mc250 was able to reduce (~60%) the virulence phenotype of the plant pathogen Xanthomonas citri subsp. citri when co-inoculated in Citrus sinensis, and was able to eradicate 98% of juveniles and stabilize the hatching rate of eggs to 4% in two species of agricultural nematodes. These results reveal biotechnological potential for the Mc250 strain and warrant its further investigation as a biocontrol and plant growth-promoting bacterium.
Topics: Alcaligenes faecalis; Animals; Anti-Bacterial Agents; Base Sequence; Citrus; DNA, Circular; Drug Resistance, Microbial; Genome, Bacterial; Genomic Islands; Iron; Metals, Heavy; Mimosa; Nematoda; Phenols; Phylogeny; Whole Genome Sequencing
PubMed: 33151992
DOI: 10.1371/journal.pone.0241546 -
BioRxiv : the Preprint Server For... Jun 2023Chronic wounds are a common and costly complication of diabetes, where multifactorial defects contribute to dysregulated skin repair, inflammation, tissue damage, and...
Chronic wounds are a common and costly complication of diabetes, where multifactorial defects contribute to dysregulated skin repair, inflammation, tissue damage, and infection. We previously showed that aspects of the diabetic foot ulcer microbiota were correlated with poor healing outcomes, but many microbial species recovered remain uninvestigated with respect to wound healing. Here we focused on , a Gram-negative bacterium that is frequently recovered from chronic wounds but rarely causes infection. Treatment of diabetic wounds with accelerated healing during early stages. We investigated the underlying mechanisms and found that treatment promotes re-epithelialization of diabetic keratinocytes, a process which is necessary for healing but deficient in chronic wounds. Overexpression of matrix metalloproteinases in diabetes contributes to failed epithelialization, and we found that treatment balances this overexpression to allow proper healing. This work uncovers a mechanism of bacterial-driven wound repair and provides a foundation for the development of microbiota-based wound interventions.
PubMed: 37425836
DOI: 10.1101/2023.06.30.547263 -
Toxins Aug 2022Ochratoxin A (OTA) is one of the most prevalent mycotoxins that threatens food and feed safety. Biodegradation of OTA has gained much attention. In this study, an...
Ochratoxin A (OTA) is one of the most prevalent mycotoxins that threatens food and feed safety. Biodegradation of OTA has gained much attention. In this study, an strain named ANSA176, with a strong OTA-detoxifying ability, was isolated from donkey intestinal chyme and characterized. The strain ANSA176 could degrade 97.43% of 1 mg/mL OTA into OTα within 12 h, at 37 °C. The optimal levels for bacterial growth were 22-37 °C and pH 6.0-9.0. The effects of ANSA176 on laying hens with an OTA-contaminated diet were further investigated. A total of 36 laying hens were assigned to three dietary treatments: control group, OTA (250 µg/kg) group, and OTA + ANSA176 (6.2 × 10 CFU/kg diet) group. The results showed that OTA decreased the average daily feed intake (ADFI) and egg weight (EW); meanwhile, it increased serum alanine aminopeptidase (AAP), leucine aminopeptidase (LAP), β2-microglobulin (β2-MG), immunoglobulin G (IgG), tumor necrosis factor-α (TNF-α), and glutathione reductase (GR). However, the ANSA176 supplementation inhibited or attenuated the OTA-induced damages. Taken together, OTA-degrading strain ANSA176 was able to alleviate the immune injury and inflammation induced by OTA.
Topics: Alcaligenes faecalis; Animal Feed; Animals; Chickens; Female; Inflammation; Ochratoxins
PubMed: 36006231
DOI: 10.3390/toxins14080569 -
Applied and Environmental Microbiology Mar 2022Ammonia oxidation is an important process in both the natural nitrogen cycle and nitrogen removal from engineered ecosystems. Recently, a new ammonia oxidation pathway...
Ammonia oxidation is an important process in both the natural nitrogen cycle and nitrogen removal from engineered ecosystems. Recently, a new ammonia oxidation pathway termed Dirammox (ect onia idation, NH→NHOH→N) has been identified in . However, whether Dirammox is present in other microbes, as well as its genetic regulation, remains unknown. In this study, it was found that the metabolically versatile bacterium Alcaligenes faecalis strain JQ135 could efficiently convert ammonia into N via NHOH under aerobic conditions. Genetic deletion and complementation results suggest that is responsible for the ammonia oxidation to N in this strain. Strain JQ135 also employs aerobic denitrification, mainly producing NO and trace amounts of N, with nitrite as the sole nitrogen source. Deletion of the and genes, which are essential for denitrification, did not impair the capability of JQ135 to oxidize ammonia to N (i.e., Dirammox is independent of denitrification). Furthermore, it was also demonstrated that (which encodes pyruvic oxime dioxygenase) was not involved in Dirammox and that (which was previously annotated as ammonia monooxygenase and is widespread in heterotrophic bacteria) was not an ammonia monooxygenase. The MocR-family transcriptional regulator DnfR was characterized as an activator of the operon with the binding motif 5'-TGGTCTGT-3' in the promoter region. A bioinformatic survey showed that homologs of genes are widely distributed in heterotrophic bacteria. In conclusion, this work demonstrates that, besides A. ammonioxydans, Dirammox occurs in other bacteria and is regulated by the MocR-family transcriptional regulator DnfR. Microbial ammonia oxidation is a key and rate-limiting step of the nitrogen cycle. Three previously known ammonia oxidation pathways (i.e., nitrification, anaerobic ammonia oxidation [Anammox], and complete ammonia oxidation [Comammox]) are mediated by autotrophic microbes. However, the genetic foundations of ammonia oxidation by heterotrophic microorganisms have not been investigated in depth. Recently, a previously unknown pathway, termed direct ammonia oxidation to N (Dirammox), has been identified in the heterotrophic bacterium HO-1. This paper shows that, in the metabolically versatile bacterium Alcaligenes faecalis JQ135, the Dirammox pathway is mediated by genes, which are independent of the denitrification pathway. A bioinformatic survey suggests that homologs of genes are widely distributed in bacteria. These findings enhance the understanding of the molecular mechanisms of heterotrophic ammonia oxidation to N.
Topics: Aerobiosis; Alcaligenes faecalis; Ammonia; Denitrification; Ecosystem; Nitrification; Nitrites; Nitrogen
PubMed: 35108103
DOI: 10.1128/aem.02261-21 -
Scientific Reports Sep 2022Pectin is one of the main structural components in fruits and an indigestible fiber made of D-galacturonic acid units with α (1-4) linkage. This study investigates the...
Pectin is one of the main structural components in fruits and an indigestible fiber made of D-galacturonic acid units with α (1-4) linkage. This study investigates the microbial degradation of pectin in apple waste and the production of bioactive compounds. Firstly, pectin-degrading bacteria were isolated and identified, then pectinolytic activity was assessed by DNS. The products were evaluated by TLC and LC-MS-ESI. The antioxidative effects were investigated using DPPH and anti-cancer effects and cytotoxicity were analyzed by MTT and flow cytometry. In this study two new bacterial isolates, Alcaligenes faecalis AGS3 and Paenibacillus polymyxa S4 with the pectinolytic enzyme were introduced. Structure analysis showed that the products of enzymatic degradation include unsaturated mono, di, tri, and penta galacturonic acids with 74% and 69% RSA at 40 mg/mL for A. faecalis and P. polymyxa S4, respectively. The results of anti-tumor properties on MCF-7 cells by MTT assay, for products of AGS3 and S4 at 40 mg/mL after 48 h, showed 7% and 9% survival, respectively. In the flow cytometric assessment, the compounds of AGS3 at 40 mg/mL were 100% lethal in 48 h and regarding S4 isolate caused 98% death. Cytotoxicity evaluation on L-929 cells showed no significant toxicity on living cells.
Topics: Alcaligenes faecalis; Hexuronic Acids; Malus; Paenibacillus; Paenibacillus polymyxa; Pectins; Polygalacturonase
PubMed: 36138114
DOI: 10.1038/s41598-022-20011-2 -
Biotechnology Reports (Amsterdam,... Mar 2020A laccase producing new bacterial strain ) was isolated from green site of Chandigarh (India) by standard screening method. Nutrient broth medium containing 0.2 mM...
A laccase producing new bacterial strain ) was isolated from green site of Chandigarh (India) by standard screening method. Nutrient broth medium containing 0.2 mM CuSO was used for the production of laccase. Maximum production (110 U/ml) was achieved after four days of incubation. The extracellular laccase from the medium was purified by simple salt precipitation and ion exchange technique to get 3.8 fold purified protein with 1637.8 U/mg specific activity. Purified laccase (named as LAC1*) revealed its optimum activity at pH 8.0 and 80 °C temperature, and displayed remarkable stability in the range of 70-90 °C and in the pH range (pH 7.0-9.0). The single bands on SDS-PAGE represents the purity of LAC1* with molecular weight of ∼71 kDa. The kinetic parameters for 2,6-DMP oxidation was K, V and k were 480 μM, 110 U/mL and 1375 s. Enzyme activity of the LAC1* was significantly enhanced by Cu, Mg, Mn SDS and NaCl, and was slightly inhibited in the presence of conventional inhibitors like cysteine, EDTA and sodium azide. Extracellular nature and significant stability of LAC1* under extreme conditions of temperature, pH, heavy metals, halides and detergents confined its suitability for various biotechnological and industrial applications which required these qualities of laccase. So after recognizing all these properties the purified laccase was studied for its application in decolorization of industrial dyes.
PubMed: 31890646
DOI: 10.1016/j.btre.2019.e00413