-
Cureus Jul 2023Introduction Non-fermenting Gram-negative bacilli (NFGNB) are emerging superbugs of bloodstream infections (BSI), causing increased mortality in hospitalized patients....
Introduction Non-fermenting Gram-negative bacilli (NFGNB) are emerging superbugs of bloodstream infections (BSI), causing increased mortality in hospitalized patients. NFGNB are challenging to identify using conventional identification techniques. Hence, automation is beneficial for accurate and fast diagnosis; it also facilitates rapid treatment and recovery of patients. This study aims to isolate/identify NFGNB from BSI and determine its antimicrobial susceptibility pattern. Material and methods This study was conducted in the Department of Microbiology, LLRMMC, Meerut, for a period of six months (June to November 2022). The samples were processed using automated blood culture (BD BACTEC) and an identification/sensitivity testing system (BD Phoenix). Results Out of 1340 blood cultures, 347 (25.7%) were flagged positive for microbial growth. A total of 103 (7.6%) NFGNB were isolated, showing their strong association with BSI. The NFGNB isolates were 23 (22.3%), 19 (18.4%), spp. 19 (18.4%), 17 (16.5%), 5 (4.8%), sp. 4 (3.8%), 3 (2.9%), 3 (2.9%), 2 (1.9%), 2 (1.9%), 2 (1.9%), 2 (1.9%), 1 (0.9%), and 1 (0.9%). Conclusions Automation helps in the prompt reporting of NFGNB and their antibiogram pattern by microbiology laboratories, facilitating the early and accurate management of patients with BSI.
PubMed: 37551224
DOI: 10.7759/cureus.41484 -
Antibiotics (Basel, Switzerland) Apr 2021(1) Background: The rise of multi-antibiotic resistant bacteria represents an emergent threat to human health. Here, we investigate antibiotic resistance mechanisms in...
(1) Background: The rise of multi-antibiotic resistant bacteria represents an emergent threat to human health. Here, we investigate antibiotic resistance mechanisms in bacteria of several species isolated from an intensive care unit in Brazil. (2) Methods: We used whole-genome analysis to identify antibiotic resistance genes (ARGs) and plasmids in 34 strains of Gram-negative and Gram-positive bacteria, providing the first genomic description of and clinical isolates from South America. (3) Results: We identified a high abundance of beta-lactamase genes in resistant organisms, including seven extended-spectrum beta-lactamases (OXA-1, OXA-10, CTX-M-1, KPC, TEM, HYDRO, BLP) shared between organisms from different species. Additionally, we identified several ARG-carrying plasmids indicating the potential for a fast transmission of resistance mechanism between bacterial strains. Furthermore, we uncovered two pairs of (near) identical plasmids exhibiting multi-drug resistance. Finally, since many highly resistant strains carry several different ARGs, we used functional genomics to investigate which of them were indeed functional. In this sense, for three bacterial strains (, , and ), we identified six beta-lactamase genes out of 15 predicted in silico as those mainly responsible for the resistance mechanisms observed, corroborating the existence of redundant resistance mechanisms in these organisms. (4) Conclusions: Systematic studies similar to the one presented here should help to prevent outbreaks of novel multidrug-resistant bacteria in healthcare facilities.
PubMed: 33920372
DOI: 10.3390/antibiotics10040419 -
The New Microbiologica Oct 2012Ralstonia mannitolilytica constitutes a rare isolate in clinical specimens and to date very few infections with this Gramnegative bacillus have been reported. The first...
Ralstonia mannitolilytica constitutes a rare isolate in clinical specimens and to date very few infections with this Gramnegative bacillus have been reported. The first case of peritonitis in a pediatric patient due to R. mannitolilytica in the setting of peritoneal dialysis is described. It is very important to view this organism as a pathogen rather than contaminant when isolated in children with peritonitis.
Topics: Anti-Bacterial Agents; Child; Female; Humans; Peritoneal Dialysis; Peritonitis; Ralstonia
PubMed: 23109020
DOI: No ID Found -
Frontiers in Microbiology 2016Microbial biofilm represents a major virulence factor associated with chronic and recurrent infections. Pathogenic bacteria embedded in biofilms are highly resistant to...
Microbial biofilm represents a major virulence factor associated with chronic and recurrent infections. Pathogenic bacteria embedded in biofilms are highly resistant to environmental and chemical agents, including antibiotics and therefore difficult to eradicate. Thus, reliable tests to assess biofilm formation by bacterial strains as well as the impact of chemicals or antibiotics on biofilm formation represent desirable tools for a most effective therapeutic management and microbiological risk control. Current methods to evaluate biofilm formation are usually time-consuming, costly, and hardly applicable in the clinical setting. The aim of the present study was to develop and assess a simple and reliable procedure for the characterization of biofilm-producing bacterial strains for future clinical applications based on the BioFilm Ring Test® (BRT) technology. The procedure developed for clinical testing (cBRT) can provide an accurate and timely (5 h) measurement of biofilm formation for the most common pathogenic bacteria seen in clinical practice. The results gathered by the cBRT assay were in agreement with the traditional crystal violet (CV) staining test, according to the κ coefficient test (κ = 0.623). However, the cBRT assay showed higher levels of specificity (92.2%) and accuracy (88.1%) as compared to CV. The results indicate that this procedure offers an easy, rapid and robust assay to test microbial biofilm and a promising tool for clinical microbiology.
PubMed: 27708625
DOI: 10.3389/fmicb.2016.01429 -
Clinical Microbiology and Infection :... May 2011DNA sequence-based identification of pathogens from ocular samples of patients with clinically suspected eye infections was accomplished using 16S and internal...
DNA sequence-based identification of pathogens from ocular samples of patients with clinically suspected eye infections was accomplished using 16S and internal transcribed spacer (ITS) ribosomal RNA gene sequence analysis. PCR was positive for 24 of 99 samples tested. Both culture and 16S rDNA sequence analysis identified Pseudomonas aeruginosa, streptococci and Enterobacteriaceae. Isolates misidentified as Burkholderia cepacia by biochemical tests were identified as Ralstonia mannitolilytica by 16S rDNA sequence analysis. Sequence analysis identified the following microorganisms from 19 culture-negative samples: Haemophilus influenzae, Sphingomonas sp., Klebsiella pneumoniae, Staphylococcus haemolyticus, Morganella morganii, Mycobacterium sp., Chryseobacterium sp., Pseudomonas saccharophila (Xanthomonas) and the fungus, Phaeoacremonium inflatipes.
Topics: DNA, Ribosomal Spacer; Eye Infections, Bacterial; Eye Infections, Fungal; Humans; In Vitro Techniques; Male; Middle Aged; Polymerase Chain Reaction; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 21521414
DOI: 10.1111/j.1469-0691.2010.03369.x -
Journal of Clinical Microbiology Jul 2005Two new PCR assays (for Ralstonia species and Ralstonia respiraculi), together with previously published PCR assays, were used to assess Ralstonia isolates recovered...
Two new PCR assays (for Ralstonia species and Ralstonia respiraculi), together with previously published PCR assays, were used to assess Ralstonia isolates recovered from 111 cystic fibrosis patients. Ralstonia mannitolilytica accounted for 46% of isolates, while R. respiraculi and Ralstonia pickettii accounted for 19% and 18%, respectively. Ralstonia basilensis and Ralstonia metallidurans, species not previously recovered from human samples, were also identified.
Topics: Bacterial Typing Techniques; Cystic Fibrosis; DNA, Bacterial; DNA, Ribosomal; Gram-Negative Bacterial Infections; Humans; Molecular Sequence Data; Polymerase Chain Reaction; RNA, Ribosomal, 16S; Ralstonia; Sensitivity and Specificity; Sequence Analysis, DNA
PubMed: 16000479
DOI: 10.1128/JCM.43.7.3463-3466.2005 -
Journal of Clinical Microbiology Jul 2003The recovery of Ralstonia and Pandoraea species from respiratory tract cultures of patients with cystic fibrosis has recently been reported. These species are difficult...
Use of amplified ribosomal DNA restriction analysis for identification of Ralstonia and Pandoraea species: interest in determination of the respiratory bacterial flora in patients with cystic fibrosis.
The recovery of Ralstonia and Pandoraea species from respiratory tract cultures of patients with cystic fibrosis has recently been reported. These species are difficult to identify, and especially to differentiate from Burkholderia cepacia complex organisms, with classical methods. The discriminatory power of amplified ribosomal DNA restriction analysis (ARDRA) within the two genera was assessed by comparing the restriction profiles of reference strains of each species by using a panel of six enzymes already proven suitable for the identification of Burkholderia species. ARDRA provided differentiation of all the Ralstonia species tested and of Pandoraea norimbergensis. Pandoraea species P. pnomenusa, P. sputorum, P. pulmonicola, and P. apista were not discriminated to the species level. This method allowed the identification of five clinical isolates recovered from French cystic fibrosis patients as Ralstonia mannitolilytica.
Topics: Bacterial Typing Techniques; Betaproteobacteria; Cystic Fibrosis; DNA, Bacterial; DNA, Ribosomal; Gram-Negative Bacterial Infections; Humans; Polymorphism, Restriction Fragment Length; RNA, Ribosomal, 16S; Respiratory System; Restriction Mapping; Species Specificity
PubMed: 12843108
DOI: 10.1128/JCM.41.7.3415-3418.2003 -
Journal of Clinical Microbiology Oct 2008The identification of nonfermenting gram-negative bacilli isolated from cystic fibrosis (CF) patients is usually achieved by using phenotype-based techniques and...
Matrix-assisted laser desorption ionization-time of flight mass spectrometry for identification of nonfermenting gram-negative bacilli isolated from cystic fibrosis patients.
The identification of nonfermenting gram-negative bacilli isolated from cystic fibrosis (CF) patients is usually achieved by using phenotype-based techniques and eventually molecular tools. These techniques remain time-consuming, expensive, and technically demanding. We used a method based on matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF-MS) for the identification of these bacteria. A set of reference strains belonging to 58 species of clinically relevant nonfermenting gram-negative bacilli was used. To identify peaks discriminating between these various species, the profile of 10 isolated colonies obtained from 10 different passages was analyzed for each referenced strain. Conserved peaks with a relative intensity greater than 0.1 were retained. The spectra of 559 clinical isolates were then compared to that of each of the 58 reference strains as follows: 400 Pseudomonas aeruginosa, 54 Achromobacter xylosoxidans, 32 Stenotrophomonas maltophilia, 52 Burkholderia cepacia complex (BCC), 1 Burkholderia gladioli, 14 Ralstonia mannitolilytica, 2 Ralstonia pickettii, 1 Bordetella hinzii, 1 Inquilinus limosus, 1 Cupriavidus respiraculi, and 1 Burkholderia thailandensis. Using this database, 549 strains were correctly identified. Nine BCC strains and one R. mannnitolilytica strain were identified as belonging to the appropriate genus but not the correct species. We subsequently engineered BCC- and Ralstonia-specific databases using additional reference strains. Using these databases, correct identification for these species increased from 83 to 98% and from 94 to 100% of cases, respectively. Altogether, these data demonstrate that, in CF patients, MALDI-TOF-MS is a powerful tool for rapid identification of nonfermenting gram-negative bacilli.
Topics: Cystic Fibrosis; Fermentation; Gram-Negative Bacteria; Gram-Negative Bacterial Infections; Humans; Sensitivity and Specificity; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
PubMed: 18685005
DOI: 10.1128/JCM.00569-08 -
Journal of Clinical Microbiology Oct 2002During 1999, we used partial 16S rRNA gene sequencing for the prospective identification of atypical nonfermenting gram-negative bacilli isolated from patients attending...
During 1999, we used partial 16S rRNA gene sequencing for the prospective identification of atypical nonfermenting gram-negative bacilli isolated from patients attending our cystic fibrosis center. Of 1,093 isolates of nonfermenting gram-negative bacilli recovered from 148 patients, 46 (4.2%) gave problematic results with conventional phenotypic tests. These 46 isolates were genotypically identified as Pseudomonas aeruginosa (19 isolates, 12 patients), Achromobacter xylosoxidans (10 isolates, 8 patients), Stenotrophomonas maltophilia (9 isolates, 9 patients), Burkholderia cepacia genomovar I/III (3 isolates, 3 patients), Burkholderia vietnamiensis (1 isolate), Burkholderia gladioli (1 isolate), and Ralstonia mannitolilytica (3 isolates, 2 patients), a recently recognized species.
Topics: Alcaligenes; Burkholderia; Cystic Fibrosis; Gram-Negative Bacteria; Humans; Pseudomonas; RNA, Ribosomal, 16S
PubMed: 12354883
DOI: 10.1128/JCM.40.10.3793-3797.2002 -
Journal of Clinical Microbiology Jun 2002Using a polyphasic approach (including cellular protein and fatty acid analysis, biochemical characterization, 16S ribosomal DNA sequencing, and DNA-DNA hybridizations),...
Using a polyphasic approach (including cellular protein and fatty acid analysis, biochemical characterization, 16S ribosomal DNA sequencing, and DNA-DNA hybridizations), we characterized 51 bacterial isolates recovered from respiratory secretions of cystic fibrosis (CF) patients. Our analyses showed that 24 isolates belong to taxa that have so far not (or only rarely) been reported from CF patients. These taxa include Acinetobacter sp., Bordetella hinzii, Burkholderia fungorum, Comamonas testosteroni, Chryseobacterium sp., Herbaspirillum sp., Moraxella osloensis, Pandoraea genomospecies 4, Ralstonia gilardii, Ralstonia mannitolilytica, Rhizobium radiobacter, and Xanthomonas sp. In addition, one isolate most likely represents a novel Ralstonia species, whereas nine isolates belong to novel taxa within the alpha-PROTEOBACTERIA: Eight of these latter isolates are classified into the novel genus Inquilinus gen. nov. as Inquilinus limosus gen. nov., sp. nov., or as Inquilinus sp. The remaining 17 isolates are characterized as members of the family ENTEROBACTERIACEAE: The recovery of these species suggests that the CF lung is an ecological niche capable of supporting the growth of a wide variety of bacteria rarely seen in clinical samples. Elucidation of the factors that account for the association between these unusual species and the respiratory tract of CF patients may provide important insights into the pathophysiology of CF infection. Because accurate identification of these organisms in the clinical microbiology laboratory may be problematic, the present study highlights the utility of reference laboratories capable of identifying unusual species recovered from CF sputum.
Topics: Alphaproteobacteria; Bacterial Proteins; Bacterial Typing Techniques; Cystic Fibrosis; DNA, Ribosomal; Enterobacteriaceae; Fatty Acids; Humans; Molecular Sequence Data; Nucleic Acid Hybridization; Phylogeny; RNA, Ribosomal, 16S; Respiratory System; Sequence Analysis, DNA; Sputum
PubMed: 12037065
DOI: 10.1128/JCM.40.6.2062-2069.2002