The MocR family transcriptional regulator DnfR has multiple binding sites and regulates Dirammox gene transcription in Alcaligenes faecalis JQ135.

Microbial ammonia oxidation is vital to the nitrogen cycle. A biological process, called Dirammox (direct ammonia oxidation, NH3 →NH2 OH→N2 ), has been recently identified in Alcaligenes ammonioxydans and Alcaligenes faecalis. However, its transcriptional regulatory mechanism has not yet been fully elucidated. The present study characterized a new MocR-like transcription factor DnfR that is involved in the Dirammox process in A. faecalis strain JQ135. The entire dnf cluster was composed of 10 genes and transcribed as five transcriptional units, that is, dnfIH, dnfR, dnfG, dnfABCDE and dnfF. DnfR activates the transcription of dnfIH, dnfG and dnfABCDE genes, and represses its own transcription. The intact 1506-bp dnfR gene was required for activation of Dirammox. Electrophoretic mobility shift assays and DNase I footprinting analyses showed that DnfR has one binding site in the dnfH-dnfR intergenic region and two binding sites in the dnfG-dnfA intergenic region. Three binding sites of DnfR shared a 6-bp repeated conserved sequence 5'-GGTCTG-N17 -GGTCTG-3' which was essential for the transcription of downstream target genes. Cysteine and glutamate act as possible effectors of DnfR to activate the transcription of transcriptional units of dnfG and dnfABCDE, respectively. This study provided new insights in the transcriptional regulation mechanism of Dirammox by DnfR in A. faecalis JQ135.

Complete genome sequence and analysis of Alcaligenes faecalis strain Mc250, a new potential plant bioinoculant.

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.

Extensively drug-resistant Alcaligenes faecalis infection.

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.

Endophthalmitis caused by Alcaligenes faecalis: a case series.

PURPOSE: To profile the etiology, clinical outcomes and drug sensitivity patterns in endophthalmitis caused by Alcaligenes faecalis. METHODS: Retrospective analysis of all the cases of A. faecalis endophthalmitis presenting to tertiary referral care ophthalmic hospital in Eastern India from January 2009 to December 2012 was done. RESULTS: A total of five cases were included in the study. Out of the five cases, one was of endogenous origin and the rest were post cataract surgery. All but one case underwent vitreo-retinal surgical intervention followed by intravitreal antibiotics. Alcaligenes faecalis was isolated in all the cases. Sensitivity to ceftazidime, aminoglycosides and ciprofloxacin was 20%, 60% and 80%, respectively. Two patients attained a final visual acuity of 6/24. One eye became phthisical in due course. CONCLUSION: Alcaligenes faecalis is a very rare cause of endophthalmitis. Aminoglycosides and fluroquinolones can be considered as main line of treatment.

Isolation and characterization of a heterotrophic nitrifier from coke plant wastewater.

This study investigated some factors affecting ammonium removal and nitrite accumulation by Alcaligenes faecalis C16, which was isolated from the activated sludge of a coking wastewater treatment plant. Nitrite was produced from ammonium only in the presence of citrate, acetate, meat extract, peptone or ethanol. The highest amount of nitrite was found with citrate as carbon source. A. faecalis C16 could not use glucose, fructose, sucrose and methanol. Under the optimum conditions of initial pH 6.0, C/N 14, 30 °C and 120 rpm, a maximum nitrite accumulation of 28.29 mg/L NO(2)(-)-N was achieved when the organism grew with citrate in four days. Nitrite accumulation increased with the increase of NH(4)(+)-N. Furthermore, A. faecalis C16 was shown to have phenol-degrading capacity during ammonium removal. Metabolism of phenol resulted in acidification of the media, which is not favorable for nitrification, whereas many other carbon sources made the medium more alkaline. However, no inhibitory effect by phenol was observed when phenol and acetate were used as mixed carbon source at different phenol/sodium acetate (P/S) ratios and their pH values were all controlled above 9.2 or P/S ratios below 5:5. These results suggested that A. faecalis C16 has some potential application in industrial wastewater treatment systems.

Fluorescence in situ hybridization for rapid identification of Achromobacter xylosoxidans and Alcaligenes faecalis recovered from cystic fibrosis patients.

Achromobacter xylosoxidans is frequently isolated from the respiratory secretions of cystic fibrosis (CF) patients, but identification with biochemical tests is unreliable. We describe fluorescence in situ hybridization assays for the rapid identification of Achromobacter xylosoxidans and Alcaligenes faecalis. Both assays showed high sensitivities and high specificities with a collection of 155 nonfermenters from CF patients.

Structure-based stabilization of an enzyme: the case of penicillin acylase from Alcaligenes faecalis.

The modeled structure of penicillin acylase from Alcaligenes faecali (AFPGA) was constructed by comparative modeling with the Modeller program. Candidate positions that could be replaced with cysteine were estimated by scanning the modeled structure of AFPGA with the program MODIP (modeling disulfide bond in protein). The mutant Q3C/P751C had a higher optimum temperature by three degrees than that of the wild type AFPGA. The half life of the double mutant Q3C/P751C at 55 degrees C was increased by 50%. To our knowledge, this was the first structure-based genetic modification of AFPGA.