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2.
BMC Genomics ; 25(1): 508, 2024 May 22.
Article in English | MEDLINE | ID: mdl-38778284

ABSTRACT

BACKGROUND: Enzymatic degradation mediated by beta-lactamases constitutes one of the primary mechanisms of resistance to beta-lactam antibiotics in gram-negative bacteria. This enzyme family comprises four molecular classes, categorized into serine beta-lactamases (Classes A, C, and D) and zinc-dependent metallo-beta-lactamases (Class B). Gram-negative bacteria producing beta-lactamase are of significant concern, particularly due to their prevalence in nosocomial infections. A comprehensive understanding of the evolution and dissemination of this enzyme family is essential for effective control of these pathogens. In this study, we conducted the prospecting, phylogenetic analysis, and in silico analysis of beta-lactamases and homologous proteins identified in 1827 bacterial genomes with phenotypic data on beta-lactam resistance. These genomes were distributed among Klebsiella pneumoniae (45%), Acinetobacter baumannii (31%), Pseudomonas aeruginosa (14%), Escherichia coli (6%), and Enterobacter spp. (4%). Using an HMM profile and searching for conserved domains, we mined 2514, 8733, 5424, and 2957 proteins for molecular classes A, B, C, and D, respectively. This set of proteins encompasses canonical subfamilies of beta-lactamases as well as hypothetical proteins and other functional groups. Canonical beta-lactamases were found to be phylogenetically distant from hypothetical proteins, which, in turn, are closer to other representatives of the penicillin-binding-protein (PBP-like) and metallo-beta-lactamase (MBL) families. The catalytic amino acid residues characteristic of beta-lactamases were identified from the sequence alignment and revealed that motifs are less conserved in homologous groups than in beta-lactamases. After comparing the frequency of protein groups in genomes of resistant strains with those of sensitive ones applying Fisher's exact test and relative risk, it was observed that some groups of homologous proteins to classes B and C are more common in the genomes of resistant strains, particularly to carbapenems. We identified the beta-lactamase-like domain widely distributed in gram-negative species of the ESKAPEE group, which highlights its importance in the context of beta-lactam resistance. Some hypothetical homologous proteins have been shown to potentially possess promiscuous activity against beta-lactam antibiotics, however, they do not appear to expressly determine the resistance phenotype. The selective pressure due to the widespread use of antibiotics may favor the optimization of these functions for specialized resistance enzymes.


Subject(s)
Gram-Negative Bacteria , Phylogeny , beta-Lactamases , beta-Lactamases/metabolism , beta-Lactamases/genetics , beta-Lactamases/chemistry , Gram-Negative Bacteria/drug effects , Gram-Negative Bacteria/genetics , Gram-Negative Bacteria/enzymology , Bacterial Proteins/metabolism , Bacterial Proteins/genetics , Bacterial Proteins/chemistry , beta-Lactams/pharmacology , beta-Lactams/metabolism , Anti-Bacterial Agents/pharmacology , Genome, Bacterial , beta-Lactam Resistance/genetics , beta Lactam Antibiotics
3.
J Microbiol Methods ; 221: 106940, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38702032

ABSTRACT

Bloodstream infections (BSI) caused by carbapenem-resistant Gram-negative bacilli (CR-GNB) are a subject of major clinical concern, mainly those associated with carbapenemase-producing isolates. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been proposed to detect specific ß-lactamases, including KPC. We aimed to detect KPC enzyme directly from positive blood cultures using MALDI-TOF MS. Overall, 146 clinical Gram-negative bacilli (46 CR-GNB) recovered from consecutive blood cultures were evaluated. Proteins were extracted using formic acid, isopropyl alcohol, and water and spotted onto a steel target plate using the double-layer sinapinic acid method. The relative ions intensity ≥120 arbitrary units (a.u.) of a peak close to 28,700 m/z indicated the presence of KPC. The results were compared to HRM-qPCR methodology. This specific peak was observed in 11/14 blood bottles with blaKPC positive isolates (78.6% sensitivity), with 3 false-positive results (97.7% specificity). Analysis from colonies reached identical sensitivity (78.6%), but higher specificity (100%). The detection of KPC peaks directly from positive blood cultures using MALDI-TOF MS is feasible and rapid. It's excellent specificity indicates that positive results are consistently associated with the presence of a KPC producer in positive blood culture.


Subject(s)
Bacterial Proteins , Blood Culture , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization , beta-Lactamases , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods , Humans , beta-Lactamases/genetics , Blood Culture/methods , Bacterial Proteins/genetics , Sensitivity and Specificity , Gram-Negative Bacteria/isolation & purification , Gram-Negative Bacteria/enzymology , Gram-Negative Bacteria/classification , Gram-Negative Bacteria/genetics , Bacteremia/microbiology , Bacteremia/diagnosis , Gram-Negative Bacterial Infections/microbiology , Gram-Negative Bacterial Infections/diagnosis , Gram-Negative Bacterial Infections/blood , Anti-Bacterial Agents/pharmacology , Carbapenems/pharmacology
4.
Arch Microbiol ; 206(6): 255, 2024 May 11.
Article in English | MEDLINE | ID: mdl-38734793

ABSTRACT

Cystic fibrosis (CF) is an inherited disease that results from mutations in the gene responsible for the cystic fibrosis transmembrane conductance regulator (CFTR). The airways become clogged with thick, viscous mucus that traps microbes in respiratory tracts, facilitating colonization, inflammation and infection. CF is recognized as a biofilm-associated disease, it is commonly polymicrobial and can develop in biofilms. This review discusses Candida spp. and both Gram-positive and Gram-negative bacterial biofilms that affect the airways and cause pulmonary infections in the CF context, with a particular focus on mixed-species biofilms. In addition, the review explores the intricate interactions between fungal and bacterial species within these biofilms and elucidates the underlying molecular mechanisms that govern their dynamics. Moreover, the review addresses the multifaceted issue of antimicrobial resistance in the context of CF-associated biofilms. By synthesizing current knowledge and research findings, this review aims to provide insights into the pathogenesis of CF-related infections and identify potential therapeutic approaches to manage and combat these complex biofilm-mediated infections.


Subject(s)
Biofilms , Candida , Cystic Fibrosis , Biofilms/growth & development , Cystic Fibrosis/microbiology , Humans , Candida/physiology , Candida/genetics , Candidiasis/microbiology , Gram-Negative Bacteria/physiology , Gram-Negative Bacteria/genetics , Anti-Bacterial Agents/pharmacology
5.
Nat Commun ; 15(1): 3947, 2024 May 10.
Article in English | MEDLINE | ID: mdl-38729951

ABSTRACT

Gram-negative bacteria (GNB) are a major cause of neonatal sepsis in low- and middle-income countries (LMICs). Although the World Health Organization (WHO) reports that over 80% of these sepsis deaths could be prevented through improved treatment, the efficacy of the currently recommended first- and second-line treatment regimens for this condition is increasingly affected by high rates of drug resistance. Here we assess three well known antibiotics, fosfomycin, flomoxef and amikacin, in combination as potential antibiotic treatment regimens by investigating the drug resistance and genetic profiles of commonly isolated GNB causing neonatal sepsis in LMICs. The five most prevalent bacterial isolates in the NeoOBS study (NCT03721302) are Klebsiella pneumoniae, Acinetobacter baumannii, E. coli, Serratia marcescens and Enterobacter cloacae complex. Among these isolates, high levels of ESBL and carbapenemase encoding genes are detected along with resistance to ampicillin, gentamicin and cefotaxime, the current WHO recommended empiric regimens. The three new combinations show excellent in vitro activity against ESBL-producing K. pneumoniae and E. coli isolates. Our data should further inform and support the clinical evaluation of these three antibiotic combinations for the treatment of neonatal sepsis in areas with high rates of multidrug-resistant Gram-negative bacteria.


Subject(s)
Acinetobacter baumannii , Anti-Bacterial Agents , Gram-Negative Bacteria , Gram-Negative Bacterial Infections , Klebsiella pneumoniae , Microbial Sensitivity Tests , Neonatal Sepsis , Humans , Anti-Bacterial Agents/therapeutic use , Anti-Bacterial Agents/pharmacology , Neonatal Sepsis/microbiology , Neonatal Sepsis/drug therapy , Infant, Newborn , Gram-Negative Bacteria/drug effects , Gram-Negative Bacteria/genetics , Gram-Negative Bacteria/isolation & purification , Gram-Negative Bacterial Infections/drug therapy , Gram-Negative Bacterial Infections/microbiology , Acinetobacter baumannii/drug effects , Acinetobacter baumannii/isolation & purification , Acinetobacter baumannii/genetics , Klebsiella pneumoniae/drug effects , Klebsiella pneumoniae/isolation & purification , Klebsiella pneumoniae/genetics , Amikacin/pharmacology , Amikacin/therapeutic use , Fosfomycin/pharmacology , Fosfomycin/therapeutic use , beta-Lactamases/genetics , beta-Lactamases/metabolism , Escherichia coli/drug effects , Escherichia coli/genetics , Escherichia coli/isolation & purification , Developing Countries , Drug Resistance, Multiple, Bacterial/genetics , Drug Therapy, Combination , Serratia marcescens/drug effects , Serratia marcescens/genetics , Serratia marcescens/isolation & purification , Enterobacter cloacae/drug effects , Enterobacter cloacae/genetics , Enterobacter cloacae/isolation & purification , Bacterial Proteins/genetics , Bacterial Proteins/metabolism
6.
Front Public Health ; 12: 1376513, 2024.
Article in English | MEDLINE | ID: mdl-38601497

ABSTRACT

Intensive care units (ICUs) are specialized environments dedicated to the management of critically ill patients, who are particularly susceptible to drug-resistant bacteria. Among these, carbapenem-resistant Gram-negative bacteria (CR-GNB) pose a significant threat endangering the lives of ICU patients. Carbapenemase production is a key resistance mechanism in CR-GNB, with the transfer of resistance genes contributing to the extensive emergence of antimicrobial resistance (AMR). CR-GNB infections are widespread in ICUs, highlighting an urgent need for prevention and control measures to reduce mortality rates associated with CR-GNB transmission or infection. This review provides an overview of key aspects surrounding CR-GNB within ICUs. We examine the mechanisms of bacterial drug resistance, the resistance genes that frequently occur with CR-GNB infections in ICU, and the therapeutic options against carbapenemase genotypes. Additionally, we highlight crucial preventive measures to impede the transmission and spread of CR-GNB within ICUs, along with reviewing the advances made in the field of clinical predictive modeling research, which hold excellent potential for practical application.


Subject(s)
Carbapenems , Gram-Negative Bacterial Infections , Humans , Carbapenems/pharmacology , Carbapenems/therapeutic use , Anti-Bacterial Agents/pharmacology , Anti-Bacterial Agents/therapeutic use , Gram-Negative Bacteria/genetics , Gram-Negative Bacterial Infections/drug therapy , Gram-Negative Bacterial Infections/prevention & control , Gram-Negative Bacterial Infections/microbiology , Intensive Care Units
7.
Commun Biol ; 7(1): 499, 2024 Apr 25.
Article in English | MEDLINE | ID: mdl-38664513

ABSTRACT

Bacterial cooperation and antagonism mediated by secretion systems are among the ways in which bacteria interact with one another. Here we report the discovery of an antagonistic property of a type IV secretion system (T4SS) sourced from a conjugative plasmid, RP4, using engineering approaches. We scrutinized the genetic determinants and suggested that this antagonistic activity is independent of molecular cargos, while we also elucidated the resistance genes. We further showed that a range of Gram-negative bacteria and a mixed bacterial population can be eliminated by this T4SS-dependent antagonism. Finally, we showed that such an antagonistic property is not limited to T4SS sourced from RP4, rather it can also be observed in a T4SS originated from another conjugative plasmid, namely R388. Our results are the first demonstration of conjugative T4SS-dependent antagonism between Gram-negative bacteria on the genetic level and provide the foundation for future mechanistic studies.


Subject(s)
Conjugation, Genetic , Plasmids , Type IV Secretion Systems , Plasmids/genetics , Type IV Secretion Systems/genetics , Type IV Secretion Systems/metabolism , Gram-Negative Bacteria/genetics , Gram-Negative Bacteria/metabolism , Escherichia coli/genetics , Escherichia coli/metabolism
8.
BMC Infect Dis ; 24(1): 378, 2024 Apr 06.
Article in English | MEDLINE | ID: mdl-38582858

ABSTRACT

INTRODUCTION: Carbapenem-resistant gram-negative bacilli are a worldwide concern because of high morbidity and mortality rates. Additionally, the increasing prevalence of these bacteria is dangerous. To investigate the extent of antimicrobial resistance and prioritize the utility of novel drugs, we evaluated the molecular characteristics and antimicrobial susceptibility profiles of carbapenem-resistant Enterobacterales, Pseudomonas aeruginosa and Acinetobacter baumannii in Ecuador in 2022. METHODS: Ninety-five clinical isolates of carbapenem non-susceptible gram-negative bacilli were collected from six hospitals in Ecuador. Carbapenem resistance was confirmed with meropenem disk diffusion assays following Clinical Laboratory Standard Institute guidelines. Carbapenemase production was tested using a modified carbapenemase inactivation method. Antimicrobial susceptibility was tested with a disk diffusion assay, the Vitek 2 System, and gradient diffusion strips. Broth microdilution assays were used to assess colistin susceptibility. All the isolates were screened for the blaKPC, blaNDM, blaOXA-48, blaVIM and blaIMP genes. In addition, A. baumannii isolates were screened for the blaOXA-23, blaOXA-58 and blaOXA-24/40 genes. RESULTS: Carbapenemase production was observed in 96.84% of the isolates. The blaKPC, blaNDM and blaOXA-48 genes were detected in Enterobacterales, with blaKPC being predominant. The blaVIM gene was detected in P. aeruginosa, and blaOXA-24/40 predominated in A. baumannii. Most of the isolates showed co-resistance to aminoglycosides, fluoroquinolones, and trimethoprim/sulfamethoxazole. Both ceftazidime/avibactam and meropenem/vaborbactam were active against carbapenem-resistant gram-negative bacilli that produce serin-carbapenemases. CONCLUSION: The epidemiology of carbapenem resistance in Ecuador is dominated by carbapenemase-producing K. pneumoniae harbouring blaKPC. Extensively drug resistant (XDR) P. aeruginosa and A. baumannii were identified, and their identification revealed the urgent need to implement strategies to reduce the dissemination of these strains.


Subject(s)
Carbapenems , beta-Lactamases , Humans , Carbapenems/pharmacology , Meropenem , Molecular Epidemiology , Ecuador/epidemiology , Microbial Sensitivity Tests , beta-Lactamases/genetics , Bacterial Proteins/genetics , Anti-Bacterial Agents/pharmacology , Gram-Negative Bacteria/genetics , Klebsiella pneumoniae/genetics , Pseudomonas aeruginosa/genetics
9.
ACS Synth Biol ; 13(4): 1093-1099, 2024 Apr 19.
Article in English | MEDLINE | ID: mdl-38593047

ABSTRACT

RNA synthetic biology tools have primarily been applied in E. coli; however, many other bacteria are of industrial and clinical significance. Thus, the multicolor fluorogenic aptamer Pepper was evaluated in both Gram-positive and Gram-negative bacteria. Suitable HBC-Pepper dye pairs were identified that give blue, green, or red fluorescence signals in the E. coli, Bacillus subtilis, and Salmonella enterica serovar Typhimurium (S. Typhimurium). Furthermore, we found that different RNA scaffolds have a drastic effect on in vivo fluorescence, which did not correlate with the in vitro folding efficiency. One such scaffold termed DF30-tRNA displays 199-fold greater fluorescence than the Pepper aptamer alone and permits simultaneous dual color imaging in live cells.


Subject(s)
Aptamers, Nucleotide , RNA , Escherichia coli/genetics , Anti-Bacterial Agents , Gram-Negative Bacteria/genetics , Gram-Positive Bacteria , Salmonella typhimurium/genetics , Aptamers, Nucleotide/genetics
10.
Methods Mol Biol ; 2778: 367-381, 2024.
Article in English | MEDLINE | ID: mdl-38478289

ABSTRACT

Biogenesis of the outer membrane (OM) of Gram-negative bacteria involves two processes essential for growth, that is, the insertion of ß-barrel outer membrane proteins (OMPs) by the Bam complex and the assembly of the LPS-containing outer leaflet of the OM by the LptD/E complex from the Lpt pathway. These processes have only recently gained attention as targets for antimicrobial drugs. Our laboratory has developed a simple screening tool to identify compounds that target processes that disrupt the biogenesis of the cell envelope, among which the activity of the Bam complex. The tool is based on the observation that such a disruption triggers cell envelope stress response systems, such as the σE, Rcs, and Cpx responses. In essence, specific stress-responsive promoters are fused to a gene encoding a bright fluorescent protein to serve as a panel of easy-to-monitor stress reporter plasmids. Using these plasmids, compounds triggering these stress systems and, therefore, putatively disrupting the biogenesis of the cell envelope can be identified by the nature and kinetics of the induced stress responses. We describe here the use of the stress reporter plasmids in high-throughput phenotypic screening using multi-well plates.


Subject(s)
Escherichia coli Proteins , Escherichia coli Proteins/metabolism , Escherichia coli/genetics , Escherichia coli/metabolism , Bacterial Outer Membrane Proteins/genetics , Bacterial Outer Membrane Proteins/metabolism , Cell Membrane/metabolism , Gram-Negative Bacteria/genetics , Gram-Negative Bacteria/metabolism
11.
Mol Genet Genomics ; 299(1): 26, 2024 Mar 07.
Article in English | MEDLINE | ID: mdl-38453747

ABSTRACT

Currently, there are several protocols to extract bacterial DNA based on different principles. However, the quantity and the quality of the DNA obtained by each method are highly variable and microorganism dependent. In most of these classical crude methods, highly toxic and hazardous organic solvents such as phenol and chloroform are used for deproteinization, whereas in certain protocols, expensive enzymes including RNases and Proteinases are used. This study was designed to introduce a simple, rapid, inexpensive and effective genomic DNA isolation procedure for Gram-negative bacteria, without the usage of toxic chemicals and costly enzymes. This novel method was compared with another classical method known as the salting-out method, which uses proteinase-K. Concentration and yield of the extracted DNA were determined by gel electrophoresis by comparing the gel band intensity of the sample DNA to that of a DNA quantitation standard and by the Quantus™ fluorometer. According to the results, the yield of extracted DNA was higher in the novel method compared to the salting-out method. Moreover, the entire process was accomplished in less than 2 h with the novel method. Purity and integrity of extracted genomic DNA by both methods were similar. In addition, the quality of DNA was determined using Multicopy Associated Filamentation (MAF) gene amplification by polymerase chain reaction (PCR). Thus, the described technique is non-toxic, less time and fund consuming, efficient and a well-suited method for routine DNA isolation from Gram negative bacteria.


Subject(s)
DNA , Gram-Negative Bacteria , DNA, Bacterial/genetics , Gram-Negative Bacteria/genetics , Polymerase Chain Reaction , Sodium Chloride , Genomics
12.
Diagn Microbiol Infect Dis ; 109(2): 116250, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38479092

ABSTRACT

In ICU settings, screening patients upon admission for potential multiresistant bacteria (BMR) carriers is crucial. Traditionally, clinical decisions relied on delayed culture results, but a rapid PCR molecular test called RealCycler-Rezero-U/G (Progenie-molecular©), emerged as an alternative. This study aimed to validate its effectiveness in detecting gram-negative BMR in rectal swabs at ICU admission. Over 24 months, an observational study was conducted on 1,234 admitted patients, with 217 meeting isolation criteria and undergoing both PCR and culture tests. Results showed a 17.5 % positive rate for screening. The PCR test exhibited impressive accuracy at 98.6 % and a strong negative predictive value of 99.4 %. The area under the ROC curve (AUC) was 0.98, indicating high reliability. Notably, PCR results were available 44.5 h earlier than culture. In conclusion, PCR-based molecular testing for gram-negative BMR offers excellent diagnostic performance and a valuable negative predictive value, making it a suitable screening tool for ICU admissions.


Subject(s)
Drug Resistance, Multiple, Bacterial , Gram-Negative Bacteria , Gram-Negative Bacterial Infections , Intensive Care Units , Molecular Diagnostic Techniques , Rectum , Humans , Gram-Negative Bacteria/genetics , Gram-Negative Bacteria/isolation & purification , Rectum/microbiology , Gram-Negative Bacterial Infections/diagnosis , Gram-Negative Bacterial Infections/microbiology , Drug Resistance, Multiple, Bacterial/genetics , Female , Male , Middle Aged , Molecular Diagnostic Techniques/methods , Molecular Diagnostic Techniques/standards , Aged , Polymerase Chain Reaction/methods , Sensitivity and Specificity , Adult , Reproducibility of Results , Predictive Value of Tests
13.
Appl Environ Microbiol ; 90(4): e0235123, 2024 Apr 17.
Article in English | MEDLINE | ID: mdl-38517167

ABSTRACT

In rice paddies, soil and plant-derived organic matter are degraded anaerobically to methane (CH4), a powerful greenhouse gas. The highest rate of methane emission occurs during the reproductive stage of the plant when mostly dicarboxylic acids are exudated by the roots. The emission of methane at this stage depends largely on the cooperative interaction between dicarboxylic acid-fermenting bacteria and methanogenic archaea in the rhizosphere. The fermentation of tartrate, one of the major acids exudated, has been scarcely explored in rice paddy soils. In this work, we characterized an anaerobic consortium from rice paddy soil composed of four bacterial strains, whose principal member (LT8) can ferment tartrate, producing H2 and acetate. Tartrate fermentation was accelerated by co-inoculation with a hydrogenotrophic methanogen. The assembled genome of LT8 possesses a Na+-dependent oxaloacetate decarboxylase and shows that this bacterium likely invests part of the H2 produced to reduce NAD(P)+ to assimilate C from tartrate. The phylogenetic analysis of the 16S rRNA gene, the genome-based classification as well as the average amino acid identity (AAI) indicated that LT8 belongs to a new genus within the Sporomusaceae family. LT8 shares a few common features with its closest relatives, for which tartrate degradation has not been described. LT8 is limited to a few environments but is more common in rice paddy soils, where it might contribute to methane emissions from root exudates.IMPORTANCEThis is the first report of the metabolic characterization of a new anaerobic bacterium able to degrade tartrate, a compound frequently associated with plants, but rare as a microbial metabolite. Tartrate fermentation by this bacterium can be coupled to methanogenesis in the rice rhizosphere where tartrate is mainly produced at the reproductive stage of the plant, when the maximum methane rate emission occurs. The interaction between secondary fermentative bacteria, such as LT8, and methanogens could represent a fundamental step in exploring mitigation strategies for methane emissions from rice fields. Possible strategies could include controlling the activity of these secondary fermentative bacteria or selecting plants whose exudates are more difficult to ferment.


Subject(s)
Euryarchaeota , Oryza , Soil/chemistry , Oryza/microbiology , Fermentation , Tartrates/metabolism , RNA, Ribosomal, 16S/genetics , RNA, Ribosomal, 16S/metabolism , Phylogeny , Base Composition , Sequence Analysis, DNA , Bacteria , Bacteria, Anaerobic/metabolism , Euryarchaeota/metabolism , Firmicutes/metabolism , Gram-Negative Bacteria/genetics , Methane/metabolism
14.
Nat Commun ; 15(1): 2758, 2024 Mar 29.
Article in English | MEDLINE | ID: mdl-38553439

ABSTRACT

Hospital surfaces can harbour bacterial pathogens, which may disseminate and cause nosocomial infections, contributing towards mortality in low- and middle-income countries (LMICs). During the BARNARDS study, hospital surfaces from neonatal wards were sampled to assess the degree of environmental surface and patient care equipment colonisation by Gram-negative bacteria (GNB) carrying antibiotic resistance genes (ARGs). Here, we perform PCR screening for extended-spectrum ß-lactamases (blaCTX-M-15) and carbapenemases (blaNDM, blaOXA-48-like and blaKPC), MALDI-TOF MS identification of GNB carrying ARGs, and further analysis by whole genome sequencing of bacterial isolates. We determine presence of consistently dominant clones and their relatedness to strains causing neonatal sepsis. Higher prevalence of carbapenemases is observed in Pakistan, Bangladesh, and Ethiopia, compared to other countries, and are mostly found in surfaces near the sink drain. Klebsiella pneumoniae, Enterobacter hormaechei, Acinetobacter baumannii, Serratia marcescens and Leclercia adecarboxylata are dominant; ST15 K. pneumoniae is identified from the same ward on multiple occasions suggesting clonal persistence within the same environment, and is found to be identical to isolates causing neonatal sepsis in Pakistan over similar time periods. Our data suggests persistence of dominant clones across multiple time points, highlighting the need for assessment of Infection Prevention and Control guidelines.


Subject(s)
Developing Countries , Neonatal Sepsis , Infant, Newborn , Humans , beta-Lactamases/genetics , Bacterial Proteins/genetics , Hospitals , Anti-Bacterial Agents/pharmacology , Klebsiella pneumoniae/genetics , Gram-Negative Bacteria/genetics , Microbial Sensitivity Tests
15.
Microbiology (Reading) ; 170(3)2024 03.
Article in English | MEDLINE | ID: mdl-38450586

ABSTRACT

Lipopolysaccharide (LPS) is a fundamental tripartite glycolipid found on the surface of nearly all Gram-negative bacteria. It acts as a protective shield for the bacterial cell and is a potent agonist of the innate immune system. This primer serves to introduce the basic properties of LPS, its function in bacterial physiology and pathogenicity, and its use as a therapeutic target.


Subject(s)
Gram-Negative Bacteria , Lipopolysaccharides , Gram-Negative Bacteria/genetics
16.
Ann Clin Microbiol Antimicrob ; 23(1): 10, 2024 Feb 01.
Article in English | MEDLINE | ID: mdl-38302964

ABSTRACT

OBJECTIVE: This study aims to identify the most effective diagnostic method for distinguishing pathogenic and non-pathogenic Gram-negative bacteria (GNB) in suspected pneumonia cases using metagenomic next-generation sequencing (mNGS) on bronchoalveolar lavage fluid (BALF) samples. METHODS: The effectiveness of mNGS was assessed on BALF samples collected from 583 patients, and the results were compared with those from microbiological culture and final clinical diagnosis. Three interpretational approaches were evaluated for diagnostic accuracy. RESULTS: mNGS outperformed culture significantly. Among the interpretational approaches, Clinical Interpretation (CI) demonstrated the best diagnostic performance with a sensitivity of 87.3%, specificity of 100%, positive predictive value of 100%, and negative predictive value of 98.3%. CI's specificity was significantly higher than Simple Interpretation (SI) at 37.9%. Additionally, CI excluded some microorganisms identified as putative pathogens by SI, including Haemophilus parainfluenzae, Haemophilus parahaemolyticus, and Klebsiella aerogenes. CONCLUSION: Proper interpretation of mNGS data is crucial for accurately diagnosing respiratory infections caused by GNB. CI is recommended for this purpose.


Subject(s)
Respiratory Tract Infections , Humans , Respiratory Tract Infections/diagnosis , High-Throughput Nucleotide Sequencing , Gram-Negative Bacteria/genetics , Metagenomics , Sensitivity and Specificity , Bronchoalveolar Lavage Fluid
17.
Appl Microbiol Biotechnol ; 108(1): 191, 2024 Feb 02.
Article in English | MEDLINE | ID: mdl-38305904

ABSTRACT

Bacterial degradation of natural rubber (NR) in an oxic environment is initiated by oxidative cleavage of double bonds in the NR-carbon backbone and is catalyzed by extracellular haem-containing rubber oxygenases. NR-cleavage products of sufficiently low molecular mass are taken up by the cells and metabolized for energy and biomass formation. Gram-negative and Gram-positive NR-degrading bacteria (usually) employ different types of rubber oxygenases such as RoxA and/or RoxB (most Gram-negative NR-degraders) or latex clearing protein Lcp (most Gram-positive NR-degraders). In order to find novel orthologues of Rox proteins, we have revisited databases and provide an update of Rox-like proteins. We describe the putative evolution of rubber oxygenases and confirm the presence of a third subgroup of Rox-related proteins (RoxCs), the biological function of which remains, however, unclear. We summarize the knowledge on the taxonomic position of Steroidobacter cummioxidans 35Y and related species. Comparison of genomic and biochemical features of strain 35Y with other species of the genus Steroidobacter suggests that strain 35Y represents a species of a novel genus for which the designation Aurantibaculum gen. nov. is proposed. A short summary on the capabilities of NR-degrading consortia, that could be superior in biotechnological applications compared to pure cultures, is also provided. KEY POINTS: • Three types of rubber oxygenases exist predominantly in Gram-negative microbes • S. cummioxidans 35Y contains RoxA and RoxB which are superior in activity • S. cummioxidans 35Y represents a species of a novel genus.


Subject(s)
Oxygenases , Rubber , Rubber/metabolism , Oxygenases/metabolism , Bacterial Proteins/metabolism , Latex/metabolism , Gram-Negative Bacteria/genetics , Gram-Negative Bacteria/metabolism
18.
Environ Microbiol Rep ; 16(1): e13232, 2024 Feb.
Article in English | MEDLINE | ID: mdl-38308519

ABSTRACT

Temperature significantly impacts bacterial physiology, metabolism and cell chemistry. In this study, we analysed lipids and the total cellular biochemical profile of 74 fast-growing Antarctic bacteria grown at different temperatures. Fatty acid diversity and temperature-induced alterations aligned with bacterial classification-Gram-groups, phylum, genus and species. Total lipid content, varied from 4% to 19% of cell dry weight, was genus- and species-specific. Most bacteria increased lipid content at lower temperatures. The effect of temperature on the profile was complex and more species-specific, while some common for all bacteria responses were recorded. Gram-negative bacteria adjusted unsaturation and acyl chain length. Gram-positive bacteria adjusted methyl branching (anteiso-/iso-), chain length and unsaturation. Fourier transform infrared spectroscopy analysis revealed Gram-, genus- and species-specific changes in the total cellular biochemical profile triggered by temperature fluctuations. The most significant temperature-related alterations detected on all taxonomy levels were recorded for mixed region 1500-900 cm-1 , specifically the band at 1083 cm-1 related to phosphodiester groups mainly from phospholipids (for Gram-negative bacteria) and teichoic/lipoteichoic acids (for Gram-positive bacteria). Some changes in protein region were detected for a few genera, while the lipid region remained relatively stable despite the temperature fluctuations.


Subject(s)
Fatty Acids , Membrane Lipids , Temperature , Membrane Lipids/analysis , Membrane Lipids/chemistry , Membrane Lipids/metabolism , Antarctic Regions , Fatty Acids/metabolism , Bacteria/genetics , Bacteria/metabolism , Gram-Negative Bacteria/genetics
19.
BMC Microbiol ; 24(1): 64, 2024 Feb 19.
Article in English | MEDLINE | ID: mdl-38373913

ABSTRACT

BACKGROUND: Multi-drug-resistant organisms (MDROs) in gram-negative bacteria have caused a global epidemic, especially the bacterial resistance to carbapenem agents. Plasmid is the common vehicle for carrying antimicrobial resistance genes (ARGs), and the transmission of plasmids is also one of the important reasons for the emergence of MDROs. Different incompatibility group plasmid replicons are highly correlated with the acquisition, dissemination, and evolution of resistance genes. Based on this, the study aims to identify relevant characteristics of various plasmids and provide a theoretical foundation for clinical anti-infection treatment. METHODS: 330 gram-negative strains with different antimicrobial phenotypes from a tertiary hospital in Henan Province were included in this study to clarify the difference in incompatibility group plasmid replicons. Additionally, we combined the information from the PLSDB database to elaborate on the potential association between different plasmid replicons and ARGs. The VITEK mass spectrometer was used for species identification, and the VITEK-compact 2 automatic microbial system was used for the antimicrobial susceptibility test (AST). PCR-based replicon typing (PBRT) detected the plasmid profiles, and thirty-three different plasmid replicons were determined. All the carbapenem-resistant organisms (CROs) were tested for the carbapenemase genes. RESULTS: 21 plasmid replicon types were detected in this experiment, with the highest prevalence of IncFII, IncFIB, IncR, and IncFIA. Notably, the detection rate of IncX3 plasmids in CROs is higher, which is different in strains with other antimicrobial phenotypes. The number of plasmid replicons they carried increased with the strain resistance increase. Enterobacterales took a higher number of plasmid replicons than other gram-negative bacteria. The same strain tends to have more than one plasmid replicon type. IncF-type plasmids tend to be associated with MDROs. Combined with PLSDB database analysis, IncFII and IncX3 are critical platforms for taking blaKPC-2 and blaNDM. CONCLUSIONS: MDROs tend to carry more complex plasmid replicons compared with non-MDROs. The plasmid replicons that are predominantly prevalent and associated with ARGs differ in various species. The wide distribution of IncF-type plasmids and their close association with MDROs should deserve our attention. Further investigation into the critical role of plasmids in the carriage, evolution, and transmission of ARGs is needed.


Subject(s)
Anti-Bacterial Agents , Anti-Infective Agents , Anti-Bacterial Agents/pharmacology , Anti-Bacterial Agents/therapeutic use , Plasmids/genetics , beta-Lactamases/genetics , Gram-Negative Bacteria/genetics , Carbapenems/pharmacology , Phenotype , Replicon , Microbial Sensitivity Tests , Klebsiella pneumoniae/genetics
20.
mSphere ; 9(2): e0063123, 2024 Feb 28.
Article in English | MEDLINE | ID: mdl-38299856

ABSTRACT

Gregory Harrison is a bacteriologist researching essential pathways in bacteria as potential therapeutic targets. In this mSphere of Influence article, he reflects on a series of studies that employ complementary genetic approaches to define the crucial role of AsmA-family proteins in transporting phospholipids between the inner and outer membranes of Gram-negative bacteria. The authors of these three studies identify this family of lipid transporters through the means of bacterial genetics, answering a long-standing question in bacterial physiology, and serving as a reminder that a well-designed genetic strategy can go a long way in uncovering new biology.


Subject(s)
Gram-Negative Bacteria , Membrane Transport Proteins , Biological Transport , Membrane Transport Proteins/genetics , Membrane Transport Proteins/metabolism , Gram-Negative Bacteria/genetics
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