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Microbial Pathogenesis Mar 2022Potato (Solanum tuberosum L.) is regarded as the fourth most important food crop because of its economic and nutritional benefits. This crop suffers significant annual...
Potato (Solanum tuberosum L.) is regarded as the fourth most important food crop because of its economic and nutritional benefits. This crop suffers significant annual losses due to a variety of phytopathogens. Bacterial soft rot disease is one of the most serious diseases that cause significant losses in potato yield all over the world. Therefore, identification of a soft rot pathogen is critical for easy control, as each pathogen has distinct ways of being controlled. Lelliottia amnigena is a subgroup of the genus Enterobacter with many species associated with crop plants, making its classification difficult and complex. Therefore, this study focused on the isolation and identification of a newly L. amnigena from rotten potato tuber obtained from the field after harvest, Lanzhou City, China. Four strains designated as PC2, PC3, PC4 and PC5 were isolated from the same rotting potato tuber. Pathogenicity test showed that strain PC3 induced soft rot symptoms on healthy potato tubers. Koch's postulates were confirmed by re-isolating the strain PC3 in the inoculated tubers. Strain PC3 showed a convex, oval and smooth colony, measuring 0.9-1.3 1.8-3.6 μm under the microscopic observation. Phylogenetic analysis based on 16S rRNA, rpoB and atpD genes showed that strain PC3 species was 99.44%, 97.24%, and 100%, closely related to L. amnigena with accession numbers 240-a-etp (MN208158.1), FDAARGOS (CP023529.1) and R-6 (MN658356.1), respectively. The bacterial strain (PC3) was deposited in the Genbank with the accession number SUB10508072 PC3 OK447935. To the best of our knowledge, this is the first report of L. amnigena causing soft rot on potato tubers in China.
Topics: Enterobacteriaceae; Phylogeny; Plant Diseases; RNA, Ribosomal, 16S; Solanum tuberosum; Virulence
PubMed: 35150870
DOI: 10.1016/j.micpath.2022.105441 -
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 -
Archives of Microbiology Jul 2022A Gram-negative, aerobic, chemoheterotrophic, rod-shaped, and motile bacterium, designated as LST-1, was isolated from wild Stevia rebaudiana Bertoni and subjected to a...
A Gram-negative, aerobic, chemoheterotrophic, rod-shaped, and motile bacterium, designated as LST-1, was isolated from wild Stevia rebaudiana Bertoni and subjected to a polyphasic taxonomic analysis. The LST-1 strain grew optimally at 37 °C and pH 6.0-7.0 in the presence of 0.5% (w/v) NaCl. Phylogenetic analysis based on the 16S rDNA sequence indicated that LST-1 is closely related to Lelliottia jeotgali PFL01 (99.85%), Lelliottia nimipressuralis LMG10245 (98.82%), and Lelliottia amnigena LMG2784 (98.54%). Multi-locus sequence typing of concatenated partial atpD, infB, gyrB, and rpoB genes was performed to improve the resolution, and clear distinctions between the closest related type strains were observed. The results of average nucleotide identify analyses and DNA-DNA hybridization with four species (16S rDNA similarity > 98.65%) were less than 90 and 40%, respectively, verifying the distinct characteristics from other species of Lelliottia. The cellular fatty acid profile of the strain consisted of C16:0, Summed Feature3, and Summed Feature8 (possibly 16:1 w6c/16:1 w7c and 18:1 w6c) as major components. The major polar lipids included phosphatidylethanolamine, phosphatidylglycerol, an aminophospholipid, three non-characteristic phospholipids, and a non-characteristic lipid. The genome of LST-1 was 4,611,055 bp in size, with a G + C content of 55.02%. The unique combination of several phenotypic, chemotaxonomic, and genomic characteristics proved that strain LST-1 belongs to a novel species, for which the name Lelliottia steviae sp. nov. is proposed. The type strain is LST-1 (= CGMCC 1.19175 = JCM 34938).Repositories: The genbank accession numbers for the 16S rRNA gene and genome sequences of strain LST-1T are MZ497264 and CP063663, respectively.
Topics: Bacterial Typing Techniques; DNA, Bacterial; DNA, Ribosomal; Fatty Acids; Multilocus Sequence Typing; Nucleic Acid Hybridization; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Stevia
PubMed: 35829834
DOI: 10.1007/s00203-022-03033-2 -
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 -
Archives of Microbiology Oct 2022Bacterial pathogenesis-associated characteristics such as biofilm formation, synthesis of hydrolyzing enzymes, and toxins are regulated by Acyl Homoserine Lactones...
Bacterial pathogenesis-associated characteristics such as biofilm formation, synthesis of hydrolyzing enzymes, and toxins are regulated by Acyl Homoserine Lactones (AHLs), small peptides and diffusing signal factors (DSF). Lelliottia amnigena is gram negative bacteria and its pathogenicity is regulated by the luxR and luxI class of quorum sensing. The signaling molecules and their concentrations are essential for the virulence of the pathogenic bacterium. To suppresses the pathogenicity; the concentration of signalling molecules must be controlled or degraded. The lactonase have the ability to hydrolyze lactones of different chain length. The present study deals with a newer approach to control the pathogenesis of Lelliottia amnigena through isolation and characterization of Aiia lactonase from Bacillus cereus RC1. Aiia lactonase specific primers were used to amplify the gene, and the sequence thus obtained was submitted to the Genbank database under accession # OK643884.1. The gene was cloned in pBE-S shuttle vector and transformed in the recombinant host. The expressed and purified protein had a molecular weight of 28.00 KDa and exhibited its optimum activity at 37℃ by inhibiting the violacein pigment of the monitor strain Chromobacterium violaceum MTCC 2656. The proteinaceous nature of the purified molecule was confirmed by incubating it in the presence of proteinase K for 1 h. The activity of the pathogenesis-related protein, polygalacturonase was drastically reduced in the presence of the purified Aiia protein. The purified protein also showed a zone of inhibition when plated together with Lelliottia amnigena RCE (MZ712952.1). Searches of the Conserved Domain Database suggested that this protein belonged to the Metallo-beta-lactamase superfamily and is closely related to Aiia from B. thuringiensis serovar kurstaki. Modeling of the protein structure was done using I-TASSER; a C-score of 0.55 suggested that the model was of good quality. To be used commercially, this recombinant protein needs to be purified at an industrial scale; it can then be used to repress the growth of soft rot causing bacteria in horticultural crops during their storage period.
Topics: Acyl-Butyrolactones; Bacillus cereus; Bacterial Proteins; Carboxylic Ester Hydrolases; Cloning, Molecular; Endopeptidase K; Enterobacteriaceae; Polygalacturonase; Quorum Sensing; Recombinant Proteins; Trans-Activators; beta-Lactamases
PubMed: 36209456
DOI: 10.1007/s00203-022-03271-4 -
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 -
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 -
International Journal of Systematic and... Aug 2018Five beige-pigmented, oxidase-negative bacterial isolates, 6331-17, 6332-17, 6333-17, 6334-17 and 9827-07, isolated either from a drinking water storage reservoir or...
Five beige-pigmented, oxidase-negative bacterial isolates, 6331-17, 6332-17, 6333-17, 6334-17 and 9827-07, isolated either from a drinking water storage reservoir or drinking water in 2006 and 2017 in Germany, were examined in detail applying by a polyphasic taxonomic approach. Cells of the isolates were rod-shaped and Gram-stain-negative. Comparison of the 16S rRNA gene sequences of these five isolates showed highest sequence similarities to Lelliottia amnigena (99.98 %) and Lelliottia nimipressuralis (99.99 %). Multilocus sequence analyses based on concatenated partial rpoB, gyrB, infB and atpD sequences confirmed the clustering of these isolates with Lelliottia species, but also revealed a clear distinction to the closest related type strains. Analysis of the genome sequences of these isolates indicated >70 % in silico DNA-DNA hybridization and high average nucleotide identities between strains. Nevertheless, they showed only <70 and <95 % similarity to the type strains of these two Lelliottia species. The fatty acid profiles of these isolates were very similar and consisted of the major fatty acids C16:0, C17 : 0cyclo, C15 : 0iso 2-OH/C16 : 1ω7c and C18 : 1ω7c. In addition, physiological/biochemical tests revealed high phenotypic similarity to each other. These cumulative data indicate that these isolates represent a novel Lelliottia species, for which the name Lelliottia aquatilis sp. nov. is proposed, with strain 6331-17 (=CCM 8846=CIP 111609=LMG 30560) as the type strain.
Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Drinking Water; Enterobacteriaceae; Fatty Acids; Genes, Bacterial; Germany; Multilocus Sequence Typing; Nucleic Acid Hybridization; Phylogeny; Pigmentation; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 29932385
DOI: 10.1099/ijsem.0.002854 -
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