scholarly journals ANI, Mash and Dashing equally differentiate between Klebsiella species

2021 ◽  
Author(s):  
Julie E Hernandez-Salmeron ◽  
Gabriel Moreno-Hagelsieb
Keyword(s):  
Species Delimitation ◽  
Multidrug Resistant ◽  
Species Level ◽  
Ecological Niches ◽  
Average Nucleotide Identity ◽  
Human Pathogens ◽  
Ecological Functions ◽  
Klebsiella Species ◽  
Time Required ◽  
Functional Content

Species of the genus Klebsiella are among the most important multidrug resistant human pathogens, though they have been isolated from a variety of environments. Given the need for quickly and accurately classifying newly sequenced Klebsiella genomes, we compared 982 Klebsiella genomes using different species-delimiting measures: Average Nucleotide Identity (ANI), which is becoming a standard for species delimitation, as well as Mash, Dashing, and DNA compositional signatures, which can be run in a fraction of the time required to run ANI. ROC analyses showed equal quality in species delimitation for ANI, Mash and Dashing (AUC: 0.99), followed by DNA signatures (AUC: 0.96). The groups obtained at optimal cutoffs were largely in agreement with species designation. Using optimized cutoffs, we obtained 17 species-level groups using either ANI, Mash, or Dashing, all containing the same genomes, unlike DNA signatures which broke the dataset into 38 groups. Further use of Mash to map species after adding draft genomes to the dataset also showed excellent results (AUC: 0.99), producing a total of 28 Klebsiella species in the publicly available genome collection. The ecological niches of Klebsiella strains were found to neither be related to species delimitation, nor to protein functional content, suggesting that a single Klebsiella species can have a wide repertoire of ecological functions.

scholarly journals Antimicrobial Activities of Marine Sponge-Associated Bacteria

2021 ◽  
Vol 9 (1) ◽  
pp. 171
Author(s):  
Yitayal S. Anteneh ◽  
Qi Yang ◽  
Melissa H. Brown ◽  
Christopher M. M. Franco
Keyword(s):  
Pathogenic Bacteria ◽  
South Australia ◽  
Multidrug Resistant ◽  
Antimicrobial Activities ◽  
Marine Sponges ◽  
Bioactive Metabolites ◽  
Human Pathogens ◽  
Sponge Associated Bacteria ◽  
Microbial Symbionts ◽  
Bacteria And Fungi

The misuse and overuse of antibiotics have led to the emergence of multidrug-resistant microorganisms, which decreases the chance of treating those infected with existing antibiotics. This resistance calls for the search of new antimicrobials from prolific producers of novel natural products including marine sponges. Many of the novel active compounds reported from sponges have originated from their microbial symbionts. Therefore, this study aims to screen for bioactive metabolites from bacteria isolated from sponges. Twelve sponge samples were collected from South Australian marine environments and grown on seven isolation media under four incubation conditions; a total of 1234 bacterial isolates were obtained. Of these, 169 bacteria were tested in media optimized for production of antimicrobial metabolites and screened against eleven human pathogens. Seventy bacteria were found to be active against at least one test bacterial or fungal pathogen, while 37% of the tested bacteria showed activity against Staphylococcus aureus including methicillin-resistant strains and antifungal activity was produced by 21% the isolates. A potential novel active compound was purified possessing inhibitory activity against S. aureus. Using 16S rRNA, the strain was identified as Streptomyces sp. Our study highlights that the marine sponges of South Australia are a rich source of abundant and diverse bacteria producing metabolites with antimicrobial activities against human pathogenic bacteria and fungi.

scholarly journals Highlighting the Biotechnological Potential of Deep Oceanic Crust Fungi through the Prism of Their Antimicrobial Activity

Marine Drugs ◽  
2021 ◽  
Vol 19 (8) ◽  
pp. 411
Author(s):  
Maxence Quemener ◽  
Marie Dayras ◽  
Nicolas Frotté ◽  
Stella Debaets ◽  
Christophe Le Meur ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Antimicrobial Activity ◽  
Oceanic Crust ◽  
Gene Clusters ◽  
Multidrug Resistant ◽  
Antimicrobial Activities ◽  
Antimicrobial Compounds ◽  
Human Pathogens ◽  
Biotechnological Potential ◽  
Fungal Isolates

Among the different tools to address the antibiotic resistance crisis, bioprospecting in complex uncharted habitats to detect novel microorganisms putatively producing original antimicrobial compounds can definitely increase the current therapeutic arsenal of antibiotics. Fungi from numerous habitats have been widely screened for their ability to express specific biosynthetic gene clusters (BGCs) involved in the synthesis of antimicrobial compounds. Here, a collection of unique 75 deep oceanic crust fungi was screened to evaluate their biotechnological potential through the prism of their antimicrobial activity using a polyphasic approach. After a first genetic screening to detect specific BGCs, a second step consisted of an antimicrobial screening that tested the most promising isolates against 11 microbial targets. Here, 12 fungal isolates showed at least one antibacterial and/or antifungal activity (static or lytic) against human pathogens. This analysis also revealed that Staphylococcus aureus ATCC 25923 and Enterococcus faecalis CIP A 186 were the most impacted, followed by Pseudomonas aeruginosa ATCC 27853. A specific focus on three fungal isolates allowed us to detect interesting activity of crude extracts against multidrug-resistant Staphylococcus aureus. Finally, complementary mass spectrometry (MS)-based molecular networking analyses were performed to putatively assign the fungal metabolites and raise hypotheses to link them to the observed antimicrobial activities.

scholarly journals The resistome of common human pathogens

2017 ◽  
Author(s):  
Christian Munck ◽  
Mostafa M. Hashim Ellabaan ◽  
Michael Schantz Klausen ◽  
Morten O.A. Sommer
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Bacterial Pathogens ◽  
Antibiotic Resistance Genes ◽  
Gene Clusters ◽  
Species Level ◽  
Natural Environments ◽  
Human Pathogens ◽  
Bacterial Genomes ◽  
Risk Ranking

AbstractGenes capable of conferring resistance to clinically used antibiotics have been found in many different natural environments. However, a concise overview of the resistance genes found in common human bacterial pathogens is lacking, which complicates risk ranking of environmental reservoirs. Here, we present an analysis of potential antibiotic resistance genes in the 17 most common bacterial pathogens isolated from humans. We analyzed more than 20,000 bacterial genomes and defined a clinical resistome as the set of resistance genes found across these genomes. Using this database, we uncovered the co-occurrence frequencies of the resistance gene clusters within each species enabling identification of co-dissemination and co-selection patterns. The resistance genes identified in this study represent the subset of the environmental resistome that is clinically relevant and the dataset and approach provides a baseline for further investigations into the abundance of clinically relevant resistance genes across different environments. To facilitate an easy overview the data is presented at the species level at www.resistome.biosustain.dtu.dk.

Species delimitation in the Lepraria isidiata-L. santosii group: a population study in the Mediterranean-Macaronesian region

2009 ◽  
Vol 41 (1) ◽  
pp. 1-15 ◽  
Author(s):  
Mauro Tretiach ◽  
Lucia Muggia ◽  
Laurence Baruffo
Keyword(s):  
Phylogenetic Analysis ◽  
Genetic Variability ◽  
Species Delimitation ◽  
Carbonate Rocks ◽  
Morphological Study ◽  
Species Level ◽  
Siliceous Rocks ◽  
Group A ◽  
The Mediterranean ◽  
Mineral Soils

AbstractA thorough chemical, molecular and morphological study has been carried out on a problematic group in the genus Lepraria characterized by lobed, granular thalli with a raised rim and a preference for mosses, rocks and mineral soils in exposed, xeric habitats. The material examined was collected in seven countries of the Mediterranean-Macaronesian region, from chalk, carbonate rocks and derived soils (A-thalli), and from siliceous rocks and derived soils (B-thalli). The results of a phylogenetic analysis based on 93 ITS sequences (29 of which newly obtained) support the identification and the segregation of two taxa at species level, provisionally identified as Lepraria isidiata s. lat., (most of the A-thalli), and L. santosii s. lat. (B-thalli plus the remaining A-thalli), as the observed genetic variability is quite high. Three chemotypes were detected in L. isidiata s. lat., and seven in L. santosii s. lat. The two taxa are morphologically well characterized: in L. isidiata s. lat. the thallus is thicker and the propagules larger than in L. santosii s. lat. The first stages of thallus development from single propagules are described in both species. Some critical remarks are made about the increasing use of the species rank for taxa of Lepraria, which are morphologically and genetically scarcely characterized.

​Detection of Carbapenemase Genes (bla-NDM, bla-KPC, bla-OXA-48) in Escherichia coli and Klebsiella species, Isolated from Milk Samples of Bovine in Eastern Plain Zone of Uttar Pradesh

2021 ◽  
Author(s):  
Vibha Yadav ◽  
Rajesh Kumar Joshi ◽  
Namita Joshi ◽  
Amit Kumar ◽  
Satyavrat Singh
Keyword(s):  
Bovine Milk ◽  
Uttar Pradesh ◽  
Polymyxin B ◽  
Multidrug Resistant ◽  
Pcr Analysis ◽  
Rrna Gene ◽  
Klebsiella Species ◽  
E Coli ◽  
Species Specific ◽  
Klebsiella Spp

Background: Among enterobacteria E. coli and Klebsiella spp. are of great concern in health care settings, as these bacteria sometimes may contaminate the milk due to unhygienic practices and poor udder condition which have been associated with various illnesses. Therefore, this study aimed to detect the carbapenem resistant E. coli and Klebsiella spp. of bovine milk origin with regard to the risk of human transfer via the food chain in community. Methods: Total 240 samples were collected from Ayodhya and Sultanpur districts of Eastern Plain Zone of Uttar Pradesh (India). Confirmation of E. coli and Klebsiella spp. isolates was done by using species specific uidA and 16S rRNA gene, respectively. Then, carbapenemase positive E. coli and Klebsiella spp. were confirmend by DDST, MBL E-strip test and PCR analysis by targeting (bla-NDM, bla-OXA-48 and bla-KPC). Antibiogram of all carbapenemase positive isolates was performed against 20 antibiotics of 12 different classes. Result: In the present study, total 74(30.83%) isolates were identified including 55(22.92%) E. coli and 19(7.92%) Klebsiella spp. by PCR, out of which 12(16.21%) isolates were confirmed as carbapenemase producers comprising 7(12.72%) E. coli and 5(26.31%) Klebsiella spp by DDST and E-strip. All carbapenemase positive E. coli were found 100% sensitive to polymyxin-B and chloramphenicol, while all Klebsiella spp. were 100% sensitive to amikacin and polymyxin-B. Resistance against imipenem, meropenem, cefotaxime, cefpodoxime, ceftazidime, ceftriazone, aztreonam and ampicillin ranged between 80.0%-100%. All carbapenemase positive isolates were found multidrug resistant. Carbapenemase genes bla-NDM and bla-KPC were detected in E. coli while bla-OXA-48 and bla-KPC were detected in Klebsiella spp.

scholarly journals Marine Organisms from the Yucatan Peninsula (Mexico) as a Potential Natural Source of Antibacterial Compounds

Marine Drugs ◽  
2020 ◽  
Vol 18 (7) ◽  
pp. 369 ◽  
Author(s):  
Dawrin Pech-Puch ◽  
Mar Pérez-Povedano ◽  
Patricia Gómez ◽  
Marta Martínez-Guitián ◽  
Cristina Lasarte-Monterrubio ◽  
...  
Keyword(s):  
Marine Organism ◽  
Yucatan Peninsula ◽  
Antibacterial Activities ◽  
Multidrug Resistant ◽  
Marine Sponges ◽  
Marine Organisms ◽  
Human Pathogens ◽  
Yucatán Peninsula ◽  
Bioassay Guided Fractionation ◽  
Agelasine B

A total of 51 sponges (Porifera) and 13 ascidians (Chordata) were collected on the coast of the Yucatan Peninsula (Mexico) and extracted with organic solvents. The resulting extracts were screened for antibacterial activity against four multidrug-resistant (MDR) bacterial pathogens: the Gram-negative Acinetobacter baumannii, Klebsiella pneumoniae, and Pseudomonas aeruginosa and the Gram-positive Staphylococcus aureus. The minimum inhibitory concentrations (MICs) of the organic extracts of each marine organism were determined using a broth microdilution assay. Extracts of eight of the species, in particular the Agelas citrina and Haliclona (Rhizoniera) curacaoensis, displayed activity against some of the pathogens tested. Some of the extracts showed similar MIC values to known antibiotics such as penicillins and aminoglycosides. This study is the first to carry out antimicrobial screening of extracts of marine sponges and ascidians collected from the Yucatan Peninsula. Bioassay-guided fractionation of the active extracts from the sponges Amphimedon compressa and A. citrina displayed, as a preliminary result, that an inseparable mixture of halitoxins and amphitoxins and (-)-agelasine B, respectively, are the major compounds responsible for their corresponding antibacterial activities. This is the first report of the antimicrobial activity of halitoxins and amphitoxins against major multidrug-resistant human pathogens. The promising antibacterial activities detected in this study indicate the coast of Yucatan Peninsula as a potential source of a great variety of marine organisms worthy of further research.

Assessment of the Colorimetric and Fluorometric Assays for Alkaline Phosphatase Activity in Cow's, Goat's, and Sheep's Milk

2008 ◽  
Vol 71 (9) ◽  
pp. 1884-1888 ◽  
Author(s):  
V. KLOTZ ◽  
ART HILL ◽  
K. WARRINER ◽  
M. GRIFFITHS ◽  
J. ODUMERU
Keyword(s):  
Alkaline Phosphatase ◽  
Colorimetric Assay ◽  
Residual Activity ◽  
Raw Milk ◽  
The United States ◽  
Cow’S Milk ◽  
Human Pathogens ◽  
Cow's Milk ◽  
Limit Of Quantitation ◽  
Time Required

Raw milk is a well-established vehicle for the carriage of human pathogens, and many regulatory bodies have consequently mandated compulsory pasteurization as a food safety intervention. The residual activity of alkaline phosphatase (ALP) has historically been used to verify the adequacy of pasteurization of cow's milk. However, there is uncertainty on how the current ALP standards and methods of analysis can be applied to sheep's and goat's milk, which naturally contain different levels of the enzyme than that found in cow's milk. The official ALP methods applied in Canada (colorimetric assay; MFO-3) and in the United States (Fluorophos) were assessed for their ability to detect enzyme activity in raw and pasteurized milk derived from cows, sheep, and goats. The detection limit and the limit of quantitation were 0.8 and 2.02 μg/ml phenol, respectively, for the MFO-3 method and 43 and 85 mU/liter, respectively, for the Fluorophos method. The average ALP levels in raw goat's, cow's, and sheep's milk were 165, 1,562, and 3,512 μg/ml phenol, respectively. Raw milk detection limits, which correspond to raw milk phosphatase levels, were 0.051, 0.485, and 0.023% in cow's, goat's, and sheep's milk, respectively, for the MFO-3 method and 0.007, 0.070, and 0.004%, respectively, for the Fluorophos method. Although both methods can be used for ALP determination in cow's, goat's, and sheep's milk, the Fluorophos assay was superior to the colorimetric MFO-3 method based on sensitivity and time required to complete the analysis.

scholarly journals Emergence of plasmid-mediated mcr genes from Gram-negative bacteria at the human-animal interface

Gut Pathogens ◽  
2020 ◽  
Vol 12 (1) ◽  
Author(s):  
Humera Javed ◽  
Sidrah Saleem ◽  
Aizza Zafar ◽  
Aamir Ghafoor ◽  
Ahmad Bin Shahzad ◽  
...  
Keyword(s):  
Bacterial Infections ◽  
Multidrug Resistant ◽  
Detection Methods ◽  
Human Pathogens ◽  
Bacterial Strains ◽  
Gram Negative ◽  
Polymerase Chain ◽  
Animal Isolates ◽  
Animal Strains ◽  
Microbiological Procedures

Abstract Background The global emergence of plasmid-mediated colistin resistance (Col-R) conferred by mcr genes in gram-negative rods (GNRs) has jeopardized the last treatment option for multidrug-resistant bacterial infections in humans. This study aimed to assess the emergence of mcr gene-mediated Col-R in GNRs isolated from humans and animals in Pakistan. Methods Animal and clinical specimens collected from various sources were prospectively analysed using standard microbiological procedures. Pathogens were identified using the API 20E and API 20NE systems (bioMerieux). Minimum inhibitory concentration (MIC) against colistin was determined using the MIC detection methods, and multiplex polymerase chain reaction (PCR) was used to amplify the mcr-1 to mcr-5 genes. Results We isolated 126 (88.1%) animal and 17 (11.9%) human Col-R phenotypes, among which there was a significant association (P < 0.01) of Escherichia coli and Proteus mirabilis with animals and of Acinetobacter baumannii with humans. Animal strains exhibited statistically significant (P < 0.05) resistance to co-trimoxazole, chloramphenicol, and moxifloxacin, and the human pathogens exhibited statistically significant (P < 0.05) antibiotic resistance to cephalosporins, carbapenems, and piperacillin-tazobactam. For Col-R strains, MIC50 values were > 6 µg/mL and > 12 µg/mL for human and animal isolates, respectively. mcr genes were detected in 110 (76.9%) bacterial strains, of which 108 (98.2%) were mcr-1 and 2 (1.8%) were mcr-2. Conclusions The detection of a considerable number of mcr-1 and mcr-2 genes in animals is worrisome, as they are now being detected in clinical pathogens. The acquisition of mcr genes by colistin-susceptible bacteria could leave us in a post-antibiotic era.

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