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Article ; Online: Structural elucidation of the O-antigen polysaccharide from Escherichia coli O125ac and biosynthetic aspects thereof.

Furevi, Axel / Udekwu, Klas I / Widmalm, Göran

2022 Volume 32, Issue 12, Page(s) 1089–1100

Abstract: Enteropathogenic Escherichia coli O125, the cause of infectious diarrheal disease, is comprised of two serogroups, viz., O125ab and O125ac, which display the aggregative adherence pattern with epithelial cells. Herein, the structure of the O-antigen ... ...

Abstract	Enteropathogenic Escherichia coli O125, the cause of infectious diarrheal disease, is comprised of two serogroups, viz., O125ab and O125ac, which display the aggregative adherence pattern with epithelial cells. Herein, the structure of the O-antigen polysaccharide from E. coli O125ac:H6 has been elucidated. Sugar analysis revealed the presence of fucose, mannose, galactose and N-acetyl-galactosamine as major components. Unassigned 1H and 13C NMR data from one- and two-dimensional NMR experiments of the O125ac O-antigen in conjunction with sugar components were used as input to the CASPER program, which can determine polysaccharide structure in a fully automated way, and resulted in the following branched pentasaccharide structure of the repeating unit: →4)[β-d-Galp-(1 → 3)]-β-d-GalpNAc-(1 → 2)-α-d-Manp-(1 → 3)-α-l-Fucp-(1 → 3)-α-d-GalpNAc-(1→, where the side chain is denoted by square brackets. The proposed O-antigen structure was confirmed by 1H and 13C NMR chemical shift assignments and determination of interresidue connectivities. Based on this structure, that of the O125ab O-antigen, which consists of hexasaccharide repeating units with an additional glucosyl group, was possible to establish in a semi-automated fashion by CASPER. The putative existence of gnu and gne in the gene clusters of the O125 serogroups is manifested by N-acetyl-d-galactosamine residues as the initial sugar residue of the biological repeating unit as well as within the repeating unit. The close similarity between O-antigen structures is consistent with the presence of two subgroups in the E. coli O125 serogroup.
MeSH term(s)	O Antigens/chemistry ; Escherichia coli/genetics ; Escherichia coli/chemistry ; Magnetic Resonance Spectroscopy ; Carbohydrates ; Sugars
Chemical Substances	O Antigens ; Carbohydrates ; Sugars
Language	English
Publishing date	2022-09-09
Publishing country	England
Document type	Journal Article
ZDB-ID	1067689-2
ISSN	1460-2423 ; 0959-6658
ISSN (online)	1460-2423
ISSN	0959-6658
DOI	10.1093/glycob/cwac061
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Article ; Online: Pharmacodynamic considerations of collateral sensitivity in design of antibiotic treatment regimen.

Udekwu, Klas I / Weiss, Howard

Drug design, development and therapy

2018 Volume 12, Page(s) 2249–2257

Abstract: Introduction: Antibiotics have greatly reduced the morbidity and mortality due to infectious diseases. Although antibiotic resistance is not a new problem, its breadth now constitutes a significant threat to human health. One strategy to help combat ... ...

Abstract	Introduction: Antibiotics have greatly reduced the morbidity and mortality due to infectious diseases. Although antibiotic resistance is not a new problem, its breadth now constitutes a significant threat to human health. One strategy to help combat resistance is to find novel ways to use existing drugs, even those that display high rates of resistance. For the pathogens Materials and methods: We evaluate antibiotic cycling protocols using pairs of such antibiotics and investigate the speed of ascent of multiply resistant mutants. Results: Our analyses show that when using low concentrations of antibiotics, treatment failure will always occur due to the rapid ascent and fixation of resistant mutants. However, moderate to high concentrations of some combinations of bacteriostatic and bactericidal antibiotics with multiday cycling prevent resistance from developing and increase the likelihood of treatment success. Conclusion: Our results call for guarded optimism in application and development of such treatment protocols.
MeSH term(s)	Anti-Bacterial Agents/chemical synthesis ; Anti-Bacterial Agents/chemistry ; Anti-Bacterial Agents/pharmacology ; Drug Design ; Escherichia coli/drug effects ; Humans ; Microbial Sensitivity Tests ; Pseudomonas aeruginosa/drug effects
Chemical Substances	Anti-Bacterial Agents
Language	English
Publishing date	2018-07-23
Publishing country	New Zealand
Document type	Journal Article
ZDB-ID	2451346-5
ISSN	1177-8881 ; 1177-8881
ISSN (online)	1177-8881
ISSN	1177-8881
DOI	10.2147/DDDT.S164316
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Article ; Online: Transcriptional and post-transcriptional regulation of the Escherichia coli luxS mRNA; involvement of the sRNA MicA.

Udekwu, Klas I

PloS one

2010 Volume 5, Issue 10, Page(s) e13449

Abstract: Background: The small RNA (sRNA) MicA has been shown to post-transcriptionally regulate translation of the outer membrane protein A (OmpA) in Escherichia coli. It uses an antisense mechanism to down-regulate OmpA protein synthesis and induce mRNA ... ...

Abstract	Background: The small RNA (sRNA) MicA has been shown to post-transcriptionally regulate translation of the outer membrane protein A (OmpA) in Escherichia coli. It uses an antisense mechanism to down-regulate OmpA protein synthesis and induce mRNA degradation. MicA is genomically localized between the coding regions of the gshA and luxS genes and is divergently transcribed from its neighbours. Transcription of the luxS gene which originates within or upstream of the MicA sequence would thus be complementary to the sRNA. LuxS regulation is as yet unclear. Methodology/principal findings: In this report, I show that the luxS mRNA exists as three long (major) transcripts of sizes that suggest just such interaction. The sRNA MicA's expression affects the abundance of each of these luxS transcripts. The involvement of the ribonuclease, RNase III in the accumulation of the shortest transcript is demonstrated. When MicA accumulates during growth, or is induced to be over-expressed, the cleaved mRNA species is observed to increase in intensity. Using primer extension and 5'-RACE experiments in combination with sRNA overexpression plasmids, I identify the exact origin of two of the three luxS transcripts, one of which is seen to result from a previously unidentified σ(S) dependent promoter. Conclusions/significance: The presented data provides strong evidence that MicA functions in cis and in trans, targeting both luxS mRNA as well as the previously established ompA and phoP regulation. The proposed luxS regulation by MicA would be in tandem with another sRNA CyaR, shown recently to be involved in inhibiting translation of the luxS mRNA. Regulation of luxS expression is additionally shown to occur on a transcriptional level via σ(S) with variable transcript levels in different growth phases unlike what was previously assumed. This is the first known case of an sRNA in E. coli which targets both in cis (luxS mRNA) and in trans (ompA and phoP mRNAs).
MeSH term(s)	Bacterial Proteins/genetics ; Base Sequence ; Blotting, Northern ; Carbon-Sulfur Lyases/genetics ; DNA Primers ; Escherichia coli/genetics ; Promoter Regions, Genetic ; RNA Processing, Post-Transcriptional ; RNA, Bacterial/genetics ; RNA, Messenger/genetics ; Sequence Homology, Nucleic Acid ; Transcription, Genetic
Chemical Substances	Bacterial Proteins ; DNA Primers ; RNA, Bacterial ; RNA, Messenger ; Carbon-Sulfur Lyases (EC 4.4.-) ; LuxS protein, Bacteria (EC 4.4.1.21)
Language	English
Publishing date	2010-10-18
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0013449
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Article ; Online: Elucidation of the O-antigen structure of Escherichia coli O93 and characterization of its biosynthetic genes.

Furevi, Axel / Ståhle, Jonas / Muheim, Claudio / Gkotzis, Spyridon / Daley, Daniel O / Udekwu, Klas I / Widmalm, Göran

Glycobiology

2022 Volume 33, Issue 4, Page(s) 289–300

Abstract: The structure of the O-antigen from the international reference strain Escherichia coli O93:-:H16 has been determined. A nonrandom modal chain-length distribution was observed for the lipopolysaccharide, a pattern which is typical when long O-specific ... ...

Abstract	The structure of the O-antigen from the international reference strain Escherichia coli O93:-:H16 has been determined. A nonrandom modal chain-length distribution was observed for the lipopolysaccharide, a pattern which is typical when long O-specific polysaccharides are expressed. By a combination of (i) bioinformatics information on the gene cluster related to O-antigen synthesis including putative function on glycosyl transferases, (ii) the magnitude of NMR coupling constants of anomeric protons, and (iii) unassigned 2D 1H, 13C-HSQC, and 1H,1H-TOCSY NMR spectra it was possible to efficiently elucidate the structure of the carbohydrate polymer in an automated fashion using the computer program CASPER. The polysaccharide also carries O-acetyl groups and their locations were determined by 2D NMR experiments showing that ~½ of the population was 2,6-di-O-acetylated, ~¼ was 2-O-acetylated, whereas ~¼ did not carry O-acetyl group(s) in the 3-O-substituted mannosyl residue of the repeating unit. The structure of the tetrasaccharide repeating unit of the O-antigen is given by: →2)-β-d-Manp-(1→3)-β-d-Manp2Ac6Ac-(1→4)-β-d-GlcpA-(1→3)-α-d-GlcpNAc-(1→, which should also be the biological repeating unit and it shares structural elements with capsular polysaccharides from E. coli K84 and K50. The structure of the acidic O-specific polysaccharide from Cellulophaga baltica strain NN015840T differs to that of the O-antigen from E. coli O93 by lacking the O-acetyl group at O6 of the O-acetylated mannosyl residue.
MeSH term(s)	O Antigens/genetics ; O Antigens/chemistry ; Escherichia coli/genetics ; Escherichia coli/chemistry ; Lipopolysaccharides ; Multigene Family ; Magnetic Resonance Spectroscopy
Chemical Substances	O Antigens ; Lipopolysaccharides
Language	English
Publishing date	2022-10-14
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1067689-2
ISSN	1460-2423 ; 0959-6658
ISSN (online)	1460-2423
ISSN	0959-6658
DOI	10.1093/glycob/cwac069
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Article ; Online: Diet change affects intestinal microbiota restoration and improves vertical sleeve gastrectomy outcome in diet-induced obese rats.

Rossell, Joana / Brindefalk, Björn / Baena-Fustegueras, Juan Antonio / Peinado-Onsurbe, Julia / Udekwu, Klas I

European journal of nutrition

2020 Volume 59, Issue 8, Page(s) 3555–3564

Abstract: Purpose: Obesity, a worldwide health problem, is linked to an abnormal gut microbiota and is currently most effectively treated by bariatric surgery. Our aim was to characterize the microbiota of high-fat fed Sprague-Dawley rats when subjected to ... ...

Abstract	Purpose: Obesity, a worldwide health problem, is linked to an abnormal gut microbiota and is currently most effectively treated by bariatric surgery. Our aim was to characterize the microbiota of high-fat fed Sprague-Dawley rats when subjected to bariatric surgery (i.e., vertical sleeve gastrectomy) and posterior refeeding with either a high-fat or control diet. We hypothesized that bariatric surgery followed by the control diet was more effective in reverting the microbiota modifications caused by the high-fat diet when compared to either of the two factors alone. Methods: Using next-generation sequencing of ribosomal RNA amplicons, we analyzed and compared the composition of the cecal microbiota after vertical sleeve gastrectomy with control groups representing non-operated rats, control fed, high-fat fed, and post-operative diet-switched animals. Rats were fed either a high-fat or control low-fat diet and were separated into three comparison groups after eight weeks comprising no surgery, sham surgery, and vertical sleeve gastrectomy. Half of the rats were then moved from the HFD to the control diet. Using next-generation sequencing of ribosomal RNA amplicons, we analyzed the composition of the cecal microbiota of rats allocated to the vertical sleeve gastrectomy group and compared it to that of the non-surgical, control fed, high-fat fed, and post-operative diet-switched groups. Additionally, we correlated different biological parameters with the genera exhibiting the highest variation in abundance between the groups. Results: The high-fat diet was the strongest driver of altered taxonomic composition, relative microbial abundance, and diversity in the cecum. These effects were partially reversed in the diet-switched cohort, especially when combined with sleeve gastrectomy, resulting in increased diversity and shifting relative abundances. Several highly-affected genera were correlated with obesity-related parameters. Conclusions: The dysbiotic state caused by high-fat diet was improved by the change to the lower fat, higher fiber control diet. Bariatric surgery contributed significantly and additively to the diet in restoring microbiome diversity and complexity. These results highlight the importance of dietary intervention following bariatric surgery for improved restoration of cecal diversity, as neither surgery nor change of diet alone had the same effects as when combined.
MeSH term(s)	Animals ; Diet, High-Fat ; Gastrectomy ; Gastrointestinal Microbiome ; Obesity/surgery ; Rats ; Rats, Sprague-Dawley
Language	English
Publishing date	2020-02-14
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1466536-0
ISSN	1436-6215 ; 1436-6207
ISSN (online)	1436-6215
ISSN	1436-6207
DOI	10.1007/s00394-020-02190-8
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Article: Structural analysis of the O-antigen polysaccharide from Escherichia coli O188

Furevi, Axel / Ståhle, Jonas / Muheim, Claudio / Gkotzis, Spyridon / Udekwu, Klas I / Daley, Daniel O / Widmalm, Göran

Carbohydrate research. 2020 Dec., v. 498

2020

Abstract: The structure of the O-antigen from Escherichia coli reference strain O188 (E. coli O188:H10) has been investigated. The lipopolysaccharide shows a typical nonrandom modal chain-length distribution and the sugar and absolute configuration analysis ... ...

Abstract	The structure of the O-antigen from Escherichia coli reference strain O188 (E. coli O188:H10) has been investigated. The lipopolysaccharide shows a typical nonrandom modal chain-length distribution and the sugar and absolute configuration analysis revealed d-Man, d-Glc, d-GlcN and d-GlcA as major components. The structure of the O-specific polysaccharide was determined using one- and two-dimensional ¹H and ¹³C NMR spectroscopy experiments, where inter-residue correlations were identified by ¹H,¹³C-heteronuclear multiple-bond correlation and ¹H,¹H-NOESY experiments, which revealed that it consists of pentasaccharide repeating units with the following structure: ▪Biosynthetic aspects and NMR analysis are consistent with the presented structure as the biological repeating unit. The O-antigen of Shigella boydii type 16 differs only in that it carries O-acetyl groups to ~50% at O6 of the branch-point mannose residues. A molecular model of the E. coli O188 O-antigen containing 20 repeating units extends ~100 Å, which is similar to the height of the periplasmic portion of polysaccharide co-polymerase Wzz proteins that regulate the O-antigen chain length of lipopolysaccharides in the Wzx/Wzy biosynthetic pathway.
Keywords	Escherichia coli ; O-antigens ; Shigella boydii ; biochemical pathways ; mannose ; molecular models ; nuclear magnetic resonance spectroscopy ; research
Language	English
Dates of publication	2020-12
Publishing place	Elsevier Ltd
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	1435-7
ISSN	1873-426X ; 0008-6215
ISSN (online)	1873-426X
ISSN	0008-6215
DOI	10.1016/j.carres.2020.108051
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Staphylococcus aureus in continuous culture: a tool for the rational design of antibiotic treatment protocols.

Udekwu, Klas I / Levin, Bruce R

PloS one

2012 Volume 7, Issue 7, Page(s) e38866

Abstract: In vitro measures of the pharmacodynamics of antibiotics that account for the factors anticipated for bacteria in infected patients are central to the rational design of antibiotic treatment protocols. We consider whether or not continuous culture ... ...

Abstract	In vitro measures of the pharmacodynamics of antibiotics that account for the factors anticipated for bacteria in infected patients are central to the rational design of antibiotic treatment protocols. We consider whether or not continuous culture devices are a way to obtain these measures. Staphylococcus aureus PS80 in high-density continuous cultures were exposed to oxacillin, ciprofloxacin, vancomycin, gentamicin, daptomycin and linezolid. Contrary to results from low density retentostats as well as to predictions of traditional PK/MIC ratios, daily dosing with up to 100× MIC did not clear these cultures. The densities of S. aureus in these cultures oscillated with constant amplitude and never fell below 10(5) CFU per ml. Save for daptomycin "treated" populations, the densities of bacteria in these cultures remained significantly below that of similar antibiotic-free cultures. Although these antibiotics varied in their pharmacodynamic properties there were only modest differences in their mean densities. Mathematical models and experiments suggest that the dominant factor preventing clearance was wall-adhering subpopulations reseeding the planktonic population which can be estimated and corrected for. Continuous cultures provide a way to evaluate the potential efficacy of antibiotic treatment regimes in vitro under conditions that are more clinically realistic and comprehensive than traditional in vitro PK/PD indices.
MeSH term(s)	Anti-Bacterial Agents/pharmacology ; Anti-Bacterial Agents/therapeutic use ; Computer Simulation ; Dose-Response Relationship, Drug ; Humans ; Microbial Sensitivity Tests ; Models, Theoretical ; Staphylococcal Infections/drug therapy ; Staphylococcus aureus/drug effects ; Staphylococcus aureus/growth & development
Chemical Substances	Anti-Bacterial Agents
Language	English
Publishing date	2012-07-20
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0038866
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Article ; Online: Plaque-forming units from air samples: Letter to Editor. Re: Jefferson et al., Indoor Air, 2022.

Rufino de Sousa, Nuno / Steponaviciute, Laura / Margerie, Lucille / Nissen, Karolina / Kjellin, Midori / Reinius, Björn / Salaneck, Erik / Udekwu, Klas I / Rothfuchs, Antonio Gigliotti

Indoor air

2022 Volume 32, Issue 11, Page(s) e13169

MeSH term(s)	Air Pollution, Indoor/analysis ; Air Microbiology ; Air Pollutants/analysis
Chemical Substances	Air Pollutants
Language	English
Publishing date	2022-11-27
Publishing country	England
Document type	Letter ; Research Support, Non-U.S. Gov't ; Comment
ZDB-ID	1081722-0
ISSN	1600-0668 ; 0905-6947
ISSN (online)	1600-0668
ISSN	0905-6947
DOI	10.1111/ina.13169
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Article ; Online: Corrigendum. Re: de Sousa, N.R., et al., 2022. Detection and isolation of airborne SARS-CoV-2 in a hospital setting. Indoor air, 32(3), e13023.

Rufino de Sousa, Nuno / Steponaviciute, Laura / Margerie, Lucille / Nissen, Karolina / Kjellin, Midori / Reinius, Björn / Salaneck, Erik / Udekwu, Klas I / Rothfuchs, Antonio Gigliotti

Indoor air

2022 Volume 32, Issue 8, Page(s) e13085

MeSH term(s)	Air Pollution, Indoor ; COVID-19 ; Hospitals ; Humans ; SARS-CoV-2
Language	English
Publishing date	2022-08-28
Publishing country	England
Document type	Letter ; Published Erratum
ZDB-ID	1081722-0
ISSN	1600-0668 ; 0905-6947
ISSN (online)	1600-0668
ISSN	0905-6947
DOI	10.1111/ina.13085
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Article ; Online: Detection and isolation of airborne SARS-CoV-2 in a hospital setting.

Rufino de Sousa, Nuno / Steponaviciute, Laura / Margerie, Lucille / Nissen, Karolina / Kjellin, Midori / Reinius, Björn / Salaneck, Erik / Udekwu, Klas I / Rothfuchs, Antonio Gigliotti

Indoor air

2022 Volume 32, Issue 3, Page(s) e13023

Abstract: Transmission mechanisms for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are incompletely understood. In particular, aerosol transmission remains unclear, with viral detection in air and demonstration of its infection potential being ... ...

Abstract	Transmission mechanisms for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are incompletely understood. In particular, aerosol transmission remains unclear, with viral detection in air and demonstration of its infection potential being actively investigated. To this end, we employed a novel electrostatic collector to sample air from rooms occupied by COVID-19 patients in a major Swedish hospital. Electrostatic air sampling in conjunction with extraction-free, reverse-transcriptase polymerase chain reaction (hid-RT-PCR) enabled detection of SARS-CoV-2 in air from patient rooms (9/22; 41%) and adjoining anterooms (10/22; 45%). Detection with hid-RT-PCR was concomitant with viral RNA presence on the surface of exhaust ventilation channels in patients and anterooms more than 2 m from the COVID-19 patient. Importantly, it was possible to detect active SARS-CoV-2 particles from room air, with a total of 496 plaque-forming units (PFUs) being isolated, establishing the presence of infectious, airborne SARS-CoV-2 in rooms occupied by COVID-19 patients. Our results support circulation of SARS-CoV-2 via aerosols and urge the revision of existing infection control frameworks to include airborne transmission.
MeSH term(s)	Air Pollution, Indoor ; COVID-19 ; Hospitals ; Humans ; RNA, Viral/analysis ; SARS-CoV-2
Chemical Substances	RNA, Viral
Language	English
Publishing date	2022-03-28
Publishing country	England
Document type	Journal Article
ZDB-ID	1081722-0
ISSN	1600-0668 ; 0905-6947
ISSN (online)	1600-0668
ISSN	0905-6947
DOI	10.1111/ina.13023
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