Exploring the Knowledge Landscape of <em>Escherichia coli</em> Research: A Scientometric Overview

Escherichia coli (E. coli) has the hallmark of being the most extensively studied organism. This is shown by the thousands of articles published since its discovery by T. Escherich in 1885. On the other hand, very little is known about the intellectual landscape in E. coli research. For example, how the trend of publications on E. coli has evolved over time and which scientific topics have been the focus of interest for researchers. In this chapter, we present the results of a large-scale scientometric analysis of about 100,000 bibliographic records from PubMed over the period 1981–2021. To examine the evolution of research topics over time, we divided the dataset into four intervals of equal width. We created co-occurrence networks from keywords indexed in the Medical Subject Headings vocabulary and systematically examined the structure and evolution of scientific knowledge about E. coli. The extracted research topics were visualized in strategic diagrams and qualitatively characterized in terms of their maturity and cohesion

The Universe of Escherichia coli

The title of the book ""The Universe of Escherichia coli"" aims to present and emphasize the huge diversity of this bacterial species and our efforts to prevent the E. coli infections. As it is part of the gut microbiota, E. coli is a well-known commensal species, and probiotic E. coli strains are successfully used for improving host's health. Also many ""workhorse"" E. coli strain exist that are employed in laboratory and biotechnology settings. But certain E. coli strains can cause intestinal and also extraintestinal infections at many anatomical sites. Therefore many efforts are undertaken to prevent E. coli infections, among them food safety, vaccines, but also new antimicrobial agents are searched for

Molekularna opredelitev bakterij Escherichia coli z gumijastih tesnil pomivalnih strojev

In this study 35 Escherichia coli isolates obtained from sampled dishwashers rubber seals were analysed with polymerase chain reactions (PCR) using specific primers for phylogenetic group, multilocus sequence type (MLST) determination the presence of 43 virulence-associated genes (VAGs) linked with intestinal and extraintestinal E. coli infections and the presence of some typical E. coli virulence plasmids’ sequences in order to assess their virulence potential and/or specific genes, associated with the adaption to a specific environment. It was found that all of the 35 E. coli isolates belonged to the commensal non-pathogenic phylogenetic group A and that the diversity of these E. coli isolates, according to MLST analysis, was relatively low. Further, the prevalence of virulence-associated genes among the dishwasher rubber seal E. coli isolates was also low. Only the following VAGs were detected: fimH, crl, fluA, picU, irp, fyuA, sitA, aslA. Of the five plasmid replication regions tested only RepFIA and RepFIIA were detected. The two sequences associated with conjugative plasmids namely traJ and traT, were detected in only one isolate. Based on the obtained results the studied isolates can be designated as commensal E. coli with low pathogenic potential. Due to the low diversity of sequence types, even among isolates obtained from dishwashers from different locations, there is a possibility that strains from certain clonal groups are more adapted to specific habitats outside warm-blooded hosts than strains of other sequence types.V tej raziskavi smo analizirali 35 izolatov bakterije Escherichia coli, pridobljenih iz vzorčenih gumijastih tesnil kuhinjskih pomivalnih strojev, da bi ocenili njihovo potencialno patogenost in/ali prisotnost genov povezanih z adaptacijo na specifično okolje. Z verižno reakcijo s polimerazo (PCR), ob uporabi ustreznih oligo-nukleotidov, smo vse izolate uvrstili v filogenetske skupine, določili njihov sekvenčni tip na podlagi analize multilokusnega zaporedja (MLST), ugotavljali prisotnost 43 genov, povezanih z virulenco (VAG), ki so pomembni v črevesnih in zunaj črevesnih okužbah z E. coli ter ugotavljali prisotnost nekaterih značilnih zaporedij plazmidov, povezanih z virulenco E. coli. Ugotovili smo, da je vseh 35 izolatov E. coli pripadalo komenzalni nepatogeni filogenetski skupini A in da je bila raznolikost teh izolatov, glede na analizo MLST, relativno majhna. Poleg tega je bila razširjenost genov, povezanih z virulenco, med preučevanimi izolati E. coli nizka. Ugotovili smo le naslednje VAG: fimH, crl, fluA, picU, irp, fyuA, sitA, aslA. Od petih testiranih plazmidnih replikacijskih regij sta bili potrjeni samo RepFIA in RepFIIA. Zaporedji traJ in traT, povezani s konjugativnimi plazmidi, smo zasledili samo v enem izolatu. Na podlagi dobljenih rezultatov lahko preučevane izolate označimo kot komenzalne E. coli z nizkim patogenim potencialom. Glede na majhno diverziteto sekvenčnih tipov, tudi med izolati pridobljenimi iz pomivalnih strojev iz različnih krajev, pa obstaja možnost, da so sevi iz določenih klonalnih skupin bolj prilagojeni na specifične habitate izven toplokrvnih gostiteljev, kot sevi drugih sekvenčnih tipov

Molecular characterization of Escherichia coli from dishwasher rubber seals

In this study 35 Escherichia coli isolates obtained from sampled dishwashers rubber seals were analysed with polymerase chain reactions (PCR) using specific primers for phylogenetic group, multilocus sequence type (MLST) determination the presence of 43 virulence-associated genes (VAGs) linked with intestinal and extraintestinal E. coli infections and the presence of some typical E. coli virulence plasmids’ sequences in order to assess their virulence potential and/or specific genes, associated with the adaption to a specific environment. It was found that all of the 35 E. coli isolates belonged to the commensal non-pathogenic phylogenetic group A and that the diversity of these E. coli isolates, according to MLST analysis, was relatively low. Further, the prevalence of virulence-associated genes among the dishwasher rubber seal E. coli isolates was also low. Only the following VAGs were detected: fimH, crl, fluA, picU, irp, fyuA, sitA, aslA. Of the five plasmid replication regions tested only RepFIA and RepFIIA were detected. The two sequences associated with conjugative plasmids namely traJ and traT, were detected in only one isolate. Based on the obtained results the studied isolates can be designated as commensal E. coli with low pathogenic potential. Due to the low diversity of sequence types, even among isolates obtained from dishwashers from different locations, there is a possibility that strains from certain clonal groups are more adapted to specific habitats outside warm-blooded hosts than strains of other sequence types

The RepFIIA replicon of the natural Escherichia coli plasmid pRK100

The aim of the presented study was to identify the similarity of the plasmid pRK100 RepFIIA replicon (replication region) with similar replicons of other known plasmids of Enterobacteriaceae. For this purpose, within the determined nucleotide sequence of pRK100, theRepFIIA replicon rep genes/regions were identified. The nucleotide sequences of the pRK100 determined rep genes/regions were subsequently compared with the nucleotide sequences of other RepFIIA replicon rep genes/regions deposited in GenBank. Further, the nucleotide divergence between them was calculated. The obtained results clearly demonstrated, that the individual pRK100 rep regions are the same/most similar to rep regions from different plasmids. RepA2 of pRK100 is most similar to repA2 of pCP301, pINV_F6_M1382, pWR501 and R1, copA is the same as copA of plasmids pC15-1a and R100, repA6 of pRK100 is the same as repA6 in plasmids pC15-1a, pCP301, pINV_F6_M1382, pWR501, R1 and R100, repA1 is most similar to repA1 of the plasmid p1658/79, and repA4 of pRK100 is most similar to repA4 of pC15-1a. Hence, the composition of the pRK100 RepFIIA replicon is mosaic and unique among the plasmids