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Access Microbiology 2023Strain M1325/93/1 (herein referred to by our laboratory identifier, GFKo1) of was isolated from the lung of a harbour porpoise in 1993. The genome sequence and...
Strain M1325/93/1 (herein referred to by our laboratory identifier, GFKo1) of was isolated from the lung of a harbour porpoise in 1993. The genome sequence and antimicrobial resistance profile (genomic, phenotypic) of the strain were generated, with the genomic data compared with those from closely related bacteria. We demonstrate that the recently described chromosomally encoded AmpC β-lactamase is a core gene of , and suggest that new variants of this class of lactamase are encoded by other members of the genus . Although presence of is ubiquitous across the currently sequenced members of , we highlight that strain GFKo1 is sensitive to ampicillin and cephalosporins. These data suggest that may act as a useful genetic marker for identification of strains, but its presence may not correlate with expected phenotypic resistances. Further studies are required to determine the regulatory mechanisms of in .
PubMed: 38074105
DOI: 10.1099/acmi.0.000694.v3 -
BMC Genomics Mar 2023Lelliottia amnigena PTJIIT1005 is a bacterium that utilizes nitrate as the sole nitrogen source and can remediate nitrate from media. The annotation was done related to...
Lelliottia amnigena PTJIIT1005 is a bacterium that utilizes nitrate as the sole nitrogen source and can remediate nitrate from media. The annotation was done related to nitrogen metabolic genes using the PATRIC, RAST tools, and PGAP from the genome sequence of this bacterium. Multiple sequence alignments and phylogenetic analysis of respiratory nitrate reductase, assimilatory nitrate reductase, nitrite reductase, glutamine synthetase, hydroxylamine reductase, nitric oxide reductase genes from PTJIIT1005 were done to find out sequence identities with the most similar species. The identification of operon arrangement in bacteria was also identified. The PATRIC KEGG feature mapped the N-metabolic pathway to identify the chemical process, and the 3D structure of representative enzymes was also elucidated. The putative protein 3D structure was analyzed using I-TASSER software. It gave good quality protein models of all nitrogen metabolism genes and showed good sequence identity with reference templates, approximately 81-99%, except for two genes; assimilatory nitrate reductase and nitrite reductase. This study suggested that PTJIIT1005 can remove N-nitrate from water because of having N-assimilation and denitrification genes.
Topics: Nitrates; Nitrogen; Phylogeny; Nitrate Reductase; Nitrite Reductases; Bacteria
PubMed: 36894890
DOI: 10.1186/s12864-023-09207-6 -
Microorganisms Aug 2023is a Gram-negative facultative anaerobic bacillus identified from water sources and later from food (onions, cream, unpasteurized milk, and Spanish pork sausages),...
is a Gram-negative facultative anaerobic bacillus identified from water sources and later from food (onions, cream, unpasteurized milk, and Spanish pork sausages), which, under certain circumstances, can cause infections in humans, especially in immunocompromised patients. Few cases of human infections have been reported in the literature, such as endophthalmitis, urinary tract infection, pyonephrosis, and sepsis. We describe the case of a 69-year-old Caucasian male patient who lives in an urban environment and presents himself to the emergency department with chills, fever, myalgias, marked physical asthenia, dry cough, dyspnea, symptoms for which he is tested and confirmed with SARS-CoV-2 infection using real-time reverse transcriptase-polymerase chain reaction (RT-PCR) from nasal and pharyngeal swabs, after being admitted the same day (25 May 2023) to the Infectious Diseases Clinic from the County Clinical Emergency Hospital Sibiu, Romania. At the time of admission, a pulmonary computerized tomography (CT) scan was performed, which revealed a severity score of 10 out of 25. In the second week of the disease, the patient presents with hemoptysis, from which bacteriological examinations are carried out, and and are identified. The evolution was slowly favorable under antiviral treatment, corticotherapy, antibiotic therapy (in the absence of the identified etiology, initially meropenem was administered in association with linezolid, and then ceftazidime-avibactam), voriconazole, anakinra, salbutamol inhaler, inhalation corticosteroids, with slow reduction in oxygen requirement, the patient continued oxygen therapy at home after discharge with a flow rate of 5 L/minute. During the third harvesting of sputum samples, was isolated along with , both strains of low-virulence species, and maintained susceptibility to antibiotics. In the context of an immunosuppressed patient with previous pulmonary surgery for actinomycosis, chronic obstructive pulmonary disease, and bronchiectasis, all these conditions are favorable for biofilm formation. remains a pathogen rarely isolated in human pathology, but we should pay more attention, especially in the immunosuppressed patient, where it can be responsible for an extremely serious clinical picture.
PubMed: 37763987
DOI: 10.3390/microorganisms11092143 -
Frontiers in Microbiology 2022, a bacterium usually isolated from natural environments, may cause human infections and has been suggested to be naturally resistant to second- and third-generation...
INTRODUCTION
, a bacterium usually isolated from natural environments, may cause human infections and has been suggested to be naturally resistant to second- and third-generation cephalosporins.
METHODS
In this study, we determined the whole-genome sequence of an isolate, P13, isolated from animal farm sewage. On the basis of genome sequence analysis, susceptibility testing, molecular cloning, and enzyme kinetic parameter analysis, we identified a novel chromosome-encoded AmpC β-lactamase, LAQ-1.
RESULTS AND DISCUSSION
is resistant to penicillin G, ampicillin, and several first- to fourth-generation cephalosporins, such as cefazolin, cefoxitin and cefepime. The MIC levels of some β-lactams, such as cefoxitin, cefepime, aztreonam and cefazolin, for the recombinant clone (pUCP24- /DH5α) increased by approximately 4- to 64-fold compared with those of the control strain (pUCP24/DH5α). The kinetic properties of LAQ-1, with the highest catalytic activity observed toward piperacillin, were basically the same as those of typical class C β-lactamases, and avibactam had a strong inhibitory effect on its hydrolytic activity. The genetic background of was relatively conserved, and no mobile genetic element (MGE) was found around it. The plasmid pP13-67 of L. amnigena P13 harbored 12 resistance genes [ , qacEΔ1, , and ] related to different mobile genetic elements within an ~22 kb multidrug resistance region. The multidrug resistance region shared the highest nucleotide sequence similarities with those of the chromosomes or plasmids of different bacterial species, indicating the possibility of horizontal transfer of these resistance genes among different bacterial species.
PubMed: 36504772
DOI: 10.3389/fmicb.2022.990736 -
Plants (Basel, Switzerland) Mar 2023Europe's forests, particularly in Ukraine, are highly vulnerable to climate change. The maintenance and improvement of forest health are high-priority issues, and...
Europe's forests, particularly in Ukraine, are highly vulnerable to climate change. The maintenance and improvement of forest health are high-priority issues, and various stakeholders have shown an interest in understanding and utilizing ecological interactions between trees and their associated microorganisms. Endophyte microbes can influence the health of trees either by directly interacting with the damaging agents or modulating host responses to infection. In the framework of this work, ten morphotypes of endophytic bacteria from the tissues of unripe acorns of L. were isolated. Based on the results of the sequenced 16S rRNA genes, four species of endophytic bacteria were identified: , , , and . Determining the activity of pectolytic enzymes showed that the isolates and could not cause maceration of plant tissues. Screening for these isolates revealed their fungistatic effect against phytopathogenic micromycetes, namely , , and . Inoculation of , , and their complex in oak leaves, in contrast to phytopathogenic bacteria, contributed to the complete restoration of the epidermis at the sites of damage. The phytopathogenic bacteria and caused a 2.0 and 2.2 times increase in polyphenol concentration in the plants, respectively, while the ratio of antioxidant activity to total phenolic content decreased. Inoculation of and isolates into oak leaf tissue were accompanied by a decrease in the total pool of phenolic compounds. The ratio of antioxidant activity to total phenolic content increased. This indicates a qualitative improvement in the overall balance of the oak leaf antioxidant system induced by potential PGPB. Thus, endophytic bacteria of the genus isolated from the internal tissues of unripe oak acorns have the ability of growth biocontrol and spread of phytopathogens, indicating their promise for use as biopesticides.
PubMed: 36987039
DOI: 10.3390/plants12061352 -
Frontiers in Microbiology 2022The quorum-sensing (QS) cascade is responsible for the colonization and phenotypic behavior of the pathogenic organism and the regulation of diverse signal molecules....
The quorum-sensing (QS) cascade is responsible for the colonization and phenotypic behavior of the pathogenic organism and the regulation of diverse signal molecules. The disruption of the quorum-sensing system is an effective strategy to overcome the possibility of antibiotic resistance development in the pathogen. The quorum quenching does not kill the microbes. Instead, it hinders the expression of pathogenic traits. In the present experiment, RKC1 was used to extract the metabolites responsible for quorum-sensing inhibition in soft rot pathogen RCE. During the initial screening, RKC1 was found to be most promising and inhibits violacein of MTCC2656 pyocyanin, swarming-swimming motility of MTCC2297. The characterization of metabolites produced by the microbes which are responsible for quorum-sensing inhibition through GC-MS is very scarce in scientific literature. The ethyl acetate extract of RKC1 inhibits biofilm formation of RCE while inhibiting growth at higher concentrations. The GC-MS analysis suggested that Cyclic dipeptides (CDPs) such as Cyclo (L-prolyl-L-valine), Cyclo (Pro-Leu), and Cyclo(D-phenylalanyl-L-prolyl) were predominantly found in the ethyl acetate extract of the RKC1 (93.72%). This diketopiperazine (DKPs) exhibited quorum-sensing inhibition against the pathogen in liquid media during the active growth phase and regulated diverse metabolites of the pathogen. Moreover, the metabolites data from the clear zone around wells showed a higher concentration of DKSs (9.66%) compared to other metabolites. So far, very few reports indicate the role of DKPs or CDPs in inhibiting the quorum-sensing system in plant pathogenic bacteria. This is one such report that exploits metabolites of RKC1. The present investigation provided evidence to use quorum-sensing inhibitor metabolites, to suppress microbes' pathogenesis and thus develop an innovative strategy to overcome antibiotic resistance.
PubMed: 36090086
DOI: 10.3389/fmicb.2022.977669 -
Antimicrobial Resistance and Infection... Jun 2022Sepsis due to multidrug resistant (MDR) bacteria is a growing public health problem mainly in low-income countries.
BACKGROUND
Sepsis due to multidrug resistant (MDR) bacteria is a growing public health problem mainly in low-income countries.
METHODS
A multicenter study was conducted between October 2019 and September 2020 at four hospitals located in central (Tikur Anbessa and Yekatit 12), southern (Hawassa) and northern (Dessie) parts of Ethiopia. A total of 1416 patients clinically investigated for sepsis were enrolled. The number of patients from Tikur Anbessa, Yekatit 12, Dessie and Hawassa hospital was 501, 298, 301 and 316, respectively. At each study site, blood culture was performed from all patients and positive cultures were characterized by their colony characteristics, gram stain and conventional biochemical tests. Each bacterial species was confirmed using Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI TOF). Antimicrobial resistance pattern of bacteria was determined by disc diffusion. Logistic regression analysis was used to assess associations of dependent and independent variables. A p-value < 0.05 was considered as statistically significant. The data was analyzed using SPSS version 25.
RESULTS
Among 1416 blood cultures performed, 40.6% yielded growth. Among these, 27.2%, 0.3% and 13.1%, were positive for pathogenic bacteria, yeast cells and possible contaminants respectively. Klebsiella pneumoniae (26.1%), Klebsiella variicola (18.1%) and E. coli (12.4%) were the most frequent. Most K. variicola were detected at Dessie (61%) and Hawassa (36.4%). Almost all Pantoea dispersa (95.2%) were isolated at Dessie. Rare isolates (0.5% or 0.2% each) included Leclercia adecarboxylata, Raoultella ornithinolytica, Stenotrophomonas maltophilia, Achromobacter xylosoxidans, Burkholderia cepacia, Kosakonia cowanii and Lelliottia amnigena. Enterobacteriaceae most often showed resistance to ampicillin (96.2%), ceftriaxone (78.3%), cefotaxime (78%), cefuroxime (78%) and ceftazidime (76.4%). MDR frequency of Enterobacteriaceae at Hawassa, Tikur Anbessa, Yekatit 12 and Dessie hospital was 95.1%, 93.2%, 87.3% and 67.7%, respectively. Carbapenem resistance was detected in 17.1% of K. pneumoniae (n = 111), 27.7% of E. cloacae (n = 22) and 58.8% of Acinetobacter baumannii (n = 34).
CONCLUSION
Diverse and emerging gram-negative bacterial etiologies of sepsis were identified. High multidrug resistance frequency was detected. Both on sepsis etiology types and MDR frequencies, substantial variation between hospitals was determined. Strategies to control MDR should be adapted to specific hospitals. Standard bacteriological services capable of monitoring emerging drug-resistant sepsis etiologies are essential for effective antimicrobial stewardship.
Topics: Anti-Bacterial Agents; Drug Resistance, Bacterial; Escherichia coli; Ethiopia; Hospitals; Humans; Klebsiella pneumoniae; Microbial Sensitivity Tests; Referral and Consultation; Sepsis
PubMed: 35698179
DOI: 10.1186/s13756-022-01122-x -
ACS Omega Jul 2022The quorum sensing (QS) system of bacteria helps them to communicate with each other in a density-dependent manner and regulates pathogenicity. The concentrations of...
The quorum sensing (QS) system of bacteria helps them to communicate with each other in a density-dependent manner and regulates pathogenicity. The concentrations of autoinducers, peptides, and signaling factors are required for determining the expression of virulence factors in many pathogens. The QS signals of the pathogen are regulated by the signal transduction pathway. The binding of signal molecules to its cognate receptor brings changes in the structure of the receptor, makes it more accessible to the DNA, and thus regulates diverse expression patterns, including virulence factors. Degrading the autoinducer molecules or disturbing the quorum sensing network could be exploited to control the virulence of the pathogen while avoiding multidrug-resistant phenotypes. The rhizosphere is a tremendous source of beneficial microbes that has not yet been explored properly for its anti-quorum sensing potential. causes soft rot diseases in onion, potato, and other species. The present investigation was carried out with the aim of isolating the anti-quorum sensing metabolites and elucidating their role in controlling the virulence factors of the pathogen by performing a maceration assay. The ethyl acetate extracts of various bacteria are promising for violacein inhibition assay using MTCC2656 and pyocyanin inhibition of MTCC2297. Therefore, the extract was used to deduce its role in attenuation of soft rot in potato, carrot, and cucumber. The maximum reduction of macerated tissue in carrot, potato, and cucumber was given by RC1 at 91.22, 97.59, and 88.78%, respectively. The concentration-dependent inhibition of virulence traits was observed during the entire experiment. The quorum quenching potential of the bacterial extract was used to understand the regulatory metabolites. The data of the diffusible zone and gas chromatography-mass spectrometry (GC-MS) analysis showed that diketopiperazines, . Cyclo(d-phenylalanyl-l-prolyl), Cyclo Phe-Val, Cyclo(Pro-Ala), Cyclo(l-prolyl-l-valine), Cyclo (Leu-Leu), and Cyclo(-Leu-Pro), are prominent metabolites that could modulate the pathogenicity in RCE. The interaction of bacterial extracts regulates various metabolites of the pathogens during their growth in liquid culture compared to their control counterparts. This study might help in exploiting the metabolites from bacteria to control the pathogens, with concurrent reduction in the pathogenicity of the pathogens without developing antibiotic resistance.
PubMed: 35910130
DOI: 10.1021/acsomega.2c02202 -
Plants (Basel, Switzerland) Aug 2023Euphorbiaceae is a highly diverse family of plants ranging from trees to ground-dwelling minute plants. Many of these have multi-faceted attributes like ornamental,...
Euphorbiaceae is a highly diverse family of plants ranging from trees to ground-dwelling minute plants. Many of these have multi-faceted attributes like ornamental, medicinal, industrial, and food-relevant values. In addition, they have been regarded as keystone resources for investigating plant-specific resilience mechanisms that grant them the dexterity to withstand harsh climates. In the present study, we isolated two co-culturable bacterial endophytes, EP1-AS and EP1-BM, from the stem internodal segments of the prostate spurge, , a plant member of the succulent family Euphorbiaceae. We characterized them using morphological, biochemical, and molecular techniques which revealed them as novel strains of Enterobacteriaceae, . Both the isolates significantly were qualified during the assaying of their plant growth promotion potentials. BM formed fast-growing swarms while AS showed growth as rounded colonies over nutrient agar. We validated the PGP effects of AS and BM isolates through in vitro and ex vitro seed-priming treatments with wheat and tomato, both of which resulted in significantly enhanced seed germination and morphometric and physiological plant growth profiles. In extended field trials, both AS and BM could remarkably also exhibit productive yields in wheat grain and tomato fruit harvests. This is probably the first-ever study in the context of PGPB endophytes in Euphorbia prostrata. We discuss our results in the context of promising agribiotechnology translations of the endophyte community associated with the otherwise neglected ground-dwelling spurges of Euphorbiaceae.
PubMed: 37687328
DOI: 10.3390/plants12173081 -
Microbiology Resource Announcements Jun 2022Here, we report the genome sequence of PTJIIT1005, isolated from a polluted site on the Yamuna River, Delhi. The genome is complete and consists of ~4.5 Mbp with a GC...
Here, we report the genome sequence of PTJIIT1005, isolated from a polluted site on the Yamuna River, Delhi. The genome is complete and consists of ~4.5 Mbp with a GC content of 52.62%, 4,259 protein-coding genes, 76 tRNAs, and 4 rRNAs. Strain PTJIIT1005 shows 98.89% average nucleotide identity (ANI) with Lelliottia amnigena.
PubMed: 35616378
DOI: 10.1128/mra.00229-22