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Article ; Online: Strain-level resolution and pneumococcal carriage dynamics by single-molecule real-time (SMRT) sequencing of the plyNCR marker: a longitudinal study in Swiss infants.

Oyewole, Oluwaseun Rume-Abiola / Latzin, Philipp / Brugger, Silvio D / Hilty, Markus

2022 Volume 10, Issue 1, Page(s) 152

Abstract: Background: Pneumococcal carriage has often been studied from a serotype perspective; however, little is known about the strain-specific carriage and inter-strain interactions. Here, we examined the strain-level carriage and co-colonization dynamics of ... ...

Abstract	Background: Pneumococcal carriage has often been studied from a serotype perspective; however, little is known about the strain-specific carriage and inter-strain interactions. Here, we examined the strain-level carriage and co-colonization dynamics of Streptococcus pneumoniae in a Swiss birth cohort by PacBio single-molecule real-time (SMRT) sequencing of the plyNCR marker. Methods: A total of 872 nasal swab (NS) samples were included from 47 healthy infants during the first year of life. Pneumococcal carriage was determined based on the quantitative real-time polymerase chain reaction (qPCR) targeting the lytA gene. The plyNCR marker was amplified from 214 samples having lytA-based carriage for pneumococcal strain resolution. Amplicons were sequenced using SMRT technology, and sequences were analyzed with the DADA2 pipeline. In addition, pneumococcal serotypes were determined using conventional, multiplex PCR (cPCR). Results: PCR-based plyNCR amplification demonstrated a 94.2% sensitivity and 100% specificity for Streptococcus pneumoniae if compared to lytA qPCR. The overall carriage prevalence was 63.8%, and pneumococcal co-colonization (≥ 2 plyNCR amplicon sequence variants (ASVs)) was detected in 38/213 (17.8%) sequenced samples with the relative proportion of the least abundant strain(s) ranging from 1.1 to 48.8% (median, 17.2%; IQR, 5.8-33.4%). The median age to first acquisition was 147 days, and having ≥ 2 siblings increased the risk of acquisition. Conclusion: The plyNCR amplicon sequencing is species-specific and enables pneumococcal strain resolution. We therefore recommend its application for longitudinal strain-level carriage studies of Streptococcus pneumoniae. Video Abstract.
MeSH term(s)	Carrier State ; Humans ; Infant ; Longitudinal Studies ; Nasopharynx ; Pneumococcal Infections/epidemiology ; Real-Time Polymerase Chain Reaction ; Streptococcus pneumoniae/genetics ; Switzerland
Language	English
Publishing date	2022-09-22
Publishing country	England
Document type	Journal Article ; Video-Audio Media ; Research Support, Non-U.S. Gov't
ZDB-ID	2697425-3
ISSN	2049-2618 ; 2049-2618
ISSN (online)	2049-2618
ISSN	2049-2618
DOI	10.1186/s40168-022-01344-6
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Article ; Online: Bacterial contamination of air and surfaces during dental procedures-An experimental pilot study using

Franz, Jessica / Scheier, Thomas C / Aerni, Maja / Gubler, Andrea / Schreiber, Peter W / Brugger, Silvio D / Schmidlin, Patrick R

Infection control and hospital epidemiology

2024 Volume 45, Issue 5, Page(s) 658–663

Abstract: Objective: The oral cavity contains numerous microorganisms, including antimicrobial-resistant bacteria. These microorganisms can be transmitted via respiratory particles from patients to healthcare providers and vice versa during dental care. We ... ...

Abstract	Objective: The oral cavity contains numerous microorganisms, including antimicrobial-resistant bacteria. These microorganisms can be transmitted via respiratory particles from patients to healthcare providers and vice versa during dental care. We evaluated the spread of Methods: During systematic therapy for dental biofilm removal (guided biofilm therapy), using an airflow or ultrasound device to a model simulation head. Results: S. aureus Conclusions: Although our findings indicate potential airborne bacterial transmission during routine prophylactic procedures, specific treatment options during biofilm removal appear to reduce air contamination. These options include ultrasonic piezo devices or the prototype suction device. The use of chlorhexidine reduced the CFU counts of
MeSH term(s)	Humans ; Chlorhexidine ; Staphylococcus aureus ; Pilot Projects ; Staphylococcal Infections ; Dentistry ; Water
Chemical Substances	Chlorhexidine (R4KO0DY52L) ; Water (059QF0KO0R)
Language	English
Publishing date	2024-01-24
Publishing country	United States
Document type	Journal Article
ZDB-ID	639378-0
ISSN	1559-6834 ; 0195-9417 ; 0899-823X
ISSN (online)	1559-6834
ISSN	0195-9417 ; 0899-823X
DOI	10.1017/ice.2023.271
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Article: CME: Dyslipidämie und kardiovaskuläres Risiko bei HIV-infizierten Patienten CME-Fragen.

Tschumi, Fabian / Brugger, Silvio D / Braun, Dominique L

Praxis

2019 Volume 108, Issue 7, Page(s) 451–458

Abstract: CME: Dyslipidemia and Cardiovascular Risk in HIV Infected ... ...

Title translation	CME: Dyslipidemia and Cardiovascular Risk in HIV Infected Patients.
Abstract	CME: Dyslipidemia and Cardiovascular Risk in HIV Infected Patients
MeSH term(s)	Antiretroviral Therapy, Highly Active ; Cardiovascular Diseases/complications ; Dyslipidemias/complications ; HIV Infections/complications ; Humans ; Risk Factors
Language	German
Publishing date	2019-06-03
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	209026-0
ISSN	1661-8165 ; 1661-8157 ; 0369-8394
ISSN (online)	1661-8165
ISSN	1661-8157 ; 0369-8394
DOI	10.1024/1661-8157/a003247
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Article: CME-Antworten: «Dyslipidämie und kardiovaskuläres Risiko bei HIV-infizierten Patienten», Praxis Nr. 7.

Tschumi, Fabian / Brugger, Silvio D / Braun, Dominique L

Praxis

2019 Volume 108, Issue 8, Page(s) 566

Title translation	CME Answers: 'Dyslipidemia and Cardiovascular Risk in HIV Infected Patients', Praxis No. 7.
Language	German
Publishing date	2019-06-11
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	209026-0
ISSN	1661-8165 ; 1661-8157 ; 0369-8394
ISSN (online)	1661-8165
ISSN	1661-8157 ; 0369-8394
DOI	10.1024/1661-8157/a003248
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Article ; Online: Phenotypic and genotypic characterization of

Jünger, Christian / Imkamp, Frank / Balakrishna, Suraj / Gysin, Marina / Haldimann, Klara / Brugger, Silvio D / Scheier, Thomas C / Hampel, Benjamin / Hobbie, Sven N / Günthard, Huldrych F / Braun, Dominique L

International journal of STD & AIDS

2024 Volume 35, Issue 6, Page(s) 462–470

Abstract: Background: While ceftriaxone resistance remains scarce in Switzerland, global : Methods: Data of MSM enrolled in three clinical cohorts with a positive polymerase chain reaction test (PCR) for NG were analysed between January 2019 and December 2021 ... ...

Abstract	Background: While ceftriaxone resistance remains scarce in Switzerland, global Methods: Data of MSM enrolled in three clinical cohorts with a positive polymerase chain reaction test (PCR) for NG were analysed between January 2019 and December 2021 and linked with antibiotic susceptibility testing. Bacterial isolates were subjected to whole genome sequencing (WGS). Results: Of 142 participants, 141 (99%) were MSM and 118 (84%) living with HIV. Participants were treated with ceftriaxone ( Conclusion: Among the MSM diagnosed with NG mainly acquired in Switzerland, ceftriaxone MICs were low for a subset of bacterial isolates studied and no treatment failures were observed. For azithromycin, high occurrences of in vitro resistance were found. Gentamicin, cefixime, cefpodoxime, ertapenem, spectinomycin, and zoliflodacin displayed excellent in vitro activity against the 23 isolates underscoring their potential as alternative agents to ceftriaxone.
MeSH term(s)	Humans ; Neisseria gonorrhoeae/genetics ; Neisseria gonorrhoeae/drug effects ; Neisseria gonorrhoeae/isolation & purification ; Switzerland/epidemiology ; Male ; Anti-Bacterial Agents/pharmacology ; Anti-Bacterial Agents/therapeutic use ; Microbial Sensitivity Tests ; Gonorrhea/drug therapy ; Gonorrhea/microbiology ; Gonorrhea/epidemiology ; Gonorrhea/diagnosis ; Adult ; Homosexuality, Male/statistics & numerical data ; Ceftriaxone/pharmacology ; Ceftriaxone/therapeutic use ; Phenotype ; Azithromycin/therapeutic use ; Azithromycin/pharmacology ; Genotype ; Whole Genome Sequencing ; Drug Resistance, Bacterial/genetics ; Middle Aged ; Sexually Transmitted Diseases/microbiology ; Sexually Transmitted Diseases/drug therapy ; Sexually Transmitted Diseases/diagnosis ; Sexually Transmitted Diseases/epidemiology ; Cefixime/pharmacology ; Cefixime/therapeutic use
Chemical Substances	Anti-Bacterial Agents ; Ceftriaxone (75J73V1629) ; Azithromycin (83905-01-5) ; Cefixime (97I1C92E55)
Language	English
Publishing date	2024-01-31
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1018089-8
ISSN	1758-1052 ; 0956-4624
ISSN (online)	1758-1052
ISSN	0956-4624
DOI	10.1177/09564624241230266
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Article ; Online: Antibiotic resistance and persistence-Implications for human health and treatment perspectives.

Huemer, Markus / Mairpady Shambat, Srikanth / Brugger, Silvio D / Zinkernagel, Annelies S

EMBO reports

2020 Volume 21, Issue 12, Page(s) e51034

Abstract: Antimicrobial resistance (AMR) and persistence are associated with an elevated risk of treatment failure and relapsing infections. They are thus important drivers of increased morbidity and mortality rates resulting in growing healthcare costs. ... ...

Abstract	Antimicrobial resistance (AMR) and persistence are associated with an elevated risk of treatment failure and relapsing infections. They are thus important drivers of increased morbidity and mortality rates resulting in growing healthcare costs. Antibiotic resistance is readily identifiable with standard microbiological assays, and the threat imposed by antibiotic resistance has been well recognized. Measures aiming to reduce resistance development and spreading of resistant bacteria are being enforced. However, the phenomenon of bacteria surviving antibiotic exposure despite being fully susceptible, so-called antibiotic persistence, is still largely underestimated. In contrast to antibiotic resistance, antibiotic persistence is difficult to measure and therefore often missed, potentially leading to treatment failures. In this review, we focus on bacterial mechanisms allowing evasion of antibiotic killing and discuss their implications on human health. We describe the relationship between antibiotic persistence and bacterial heterogeneity and discuss recent studies that link bacterial persistence and tolerance with the evolution of antibiotic resistance. Finally, we review persister detection methods, novel strategies aiming at eradicating bacterial persisters and the latest advances in the development of new antibiotics.
MeSH term(s)	Anti-Bacterial Agents/pharmacology ; Anti-Bacterial Agents/therapeutic use ; Bacteria/genetics ; Drug Resistance, Bacterial ; Drug Resistance, Microbial/genetics ; Humans
Chemical Substances	Anti-Bacterial Agents
Language	English
Publishing date	2020-12-08
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2020896-0
ISSN	1469-3178 ; 1469-221X
ISSN (online)	1469-3178
ISSN	1469-221X
DOI	10.15252/embr.202051034
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Article ; Online: Rapid detection of

Gómez-Mejia, Alejandro / Arnold, Kim / Bär, Julian / Singh, Kapil Dev / Scheier, Thomas C / Brugger, Silvio D / Zinkernagel, Annelies S / Sinues, Pablo

iScience

2022 Volume 25, Issue 10, Page(s) 105080

Abstract: Early detection of pathogenic bacteria is needed for rapid diagnostics allowing adequate and timely treatment of infections. In this study, we show that secondary electrospray ionization-high resolution mass spectrometry (SESI-HRMS) can be used as a ... ...

Abstract	Early detection of pathogenic bacteria is needed for rapid diagnostics allowing adequate and timely treatment of infections. In this study, we show that secondary electrospray ionization-high resolution mass spectrometry (SESI-HRMS) can be used as a diagnostic tool for rapid detection of bacterial infections as a supportive system for current state-of-the-art diagnostics. Volatile organic compounds (VOCs) produced by growing
Language	English
Publishing date	2022-09-06
Publishing country	United States
Document type	Journal Article
ISSN	2589-0042
ISSN (online)	2589-0042
DOI	10.1016/j.isci.2022.105080
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Article: Bacterial microbiota of the nasal passages across the span of human life

Bomar, Lindsey / Brugger, Silvio D / Lemon, Katherine P

Current opinion in microbiology. 2018 Feb., v. 41

2018

Abstract: The human nasal passages host major human pathogens. Recent research suggests that the microbial communities inhabiting the epithelial surfaces of the nasal passages are a key factor in maintaining a healthy microenvironment by affecting both resistance ... ...

Abstract	The human nasal passages host major human pathogens. Recent research suggests that the microbial communities inhabiting the epithelial surfaces of the nasal passages are a key factor in maintaining a healthy microenvironment by affecting both resistance to pathogens and immunological responses. The nasal bacterial microbiota shows distinct changes over the span of human life and disruption by environmental factors might be associated with both short- and long-term health consequences, such as susceptibility to viral and bacterial infections and disturbances of the immunological balance. Because infants and older adults experience a high burden of morbidity and mortality from respiratory tract infections, we review recent data on the bacterial nasal microbiota composition in health and acute respiratory infection in these age groups.
Keywords	animal pathogens ; bacterial infections ; elderly ; environmental factors ; epithelium ; humans ; immune response ; infants ; microbial communities ; microorganisms ; morbidity ; mortality ; nasal cavity ; public health ; respiratory tract diseases
Language	English
Dates of publication	2018-02
Size	p. 8-14.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	1418474-6
ISSN	1879-0364 ; 1369-5274
ISSN (online)	1879-0364
ISSN	1369-5274
DOI	10.1016/j.mib.2017.10.023
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Article ; Online: Rapid antimicrobial susceptibility testing in patients with bacteraemia due to Enterobacterales: an implementation study.

Reiber, Claudine / Bodendoerfer, Elias / Brugger, Silvio D / Eberhard, Nadia / Hitz, Eva / Hofmaenner, Daniel A / Herren, Sebastian / Kolesnik-Goldmann, Natalia / Manicini, Stefano / Zbinden, Reinhard / Zinkernagel, Annelies S / Hasse, Barbara

Swiss medical weekly

2023 Volume 153, Page(s) 40066

Abstract: Aims of the study: The goal of this descriptive study was to assess the performance as well as the extent of the clinical impact of rapid automated antimicrobial susceptibility testing in patients with bacteraemia due to Enterobacterales. We also aimed ... ...

Abstract	Aims of the study: The goal of this descriptive study was to assess the performance as well as the extent of the clinical impact of rapid automated antimicrobial susceptibility testing in patients with bacteraemia due to Enterobacterales. We also aimed to analyse how rapid automated antimicrobial susceptibility testing influences clinical decision-making. Methods: This single-centre study conducted at the University Hospital of Zurich included data from all consecutive patients with Enterobacterales bacteraemia from November 2019 to October 2020. There was no control group. The primary outcome was the effect of rapid automated antimicrobial susceptibility testing on antibiotic therapy (no adjustment, escalation to a broader-spectrum antibiotic or de-escalation to a narrower-spectrum antibiotic). Rapid automated antimicrobial susceptibility testing results were further compared to susceptibility tests using European Committee on Antimicrobial Susceptibility Testing (EUCAST) standard methods and erroneous results were noted. Additionally, we investigated turnaround times for rapid automated antimicrobial susceptibility testing and routine diagnostic testing. Results: We analysed 106 patients with 116 episodes of bacteraemia due to Enterobacterales, with Escherichia coli and Klebsiella pneumoniae being the most frequent isolates. Almost 8% of pathogens were multidrug resistant. Rapid automated antimicrobial susceptibility testing showed category agreement in 98.4% of all interpretable cases. A significant reduction of more than 20 h in turnaround times could be achieved with rapid automated antimicrobial susceptibility testing compared to the routine diagnostic workflow. In the majority of cases, rapid automated antimicrobial susceptibility testing had no effect, given that the empirical therapy was already correct or circumstances did not allow for de-escalation. In 38.8% of cases, antimicrobial therapy was adjusted, whereas eight cases were de-escalated based on rapid automated antimicrobial susceptibility testing alone. Conclusions: Rapid automated antimicrobial susceptibility testing may be a valuable and safe way to accelerate diagnosis. In particular, time to suitable therapy can be shortened in cases of incorrect therapy. However, physicians are reluctant to de-escalate antibiotic therapy based on rapid automated antimicrobial susceptibility testing alone, limiting its impact in everyday clinics. To further explore the potential of rapid automated antimicrobial susceptibility testing, a stringent/compulsory antibiotic stewardship programme would be a valuable next step.
MeSH term(s)	Humans ; Anti-Bacterial Agents/pharmacology ; Anti-Bacterial Agents/therapeutic use ; Bacteremia/diagnosis ; Bacteremia/drug therapy ; Escherichia coli ; Klebsiella pneumoniae ; Hospitals, University ; Microbial Sensitivity Tests
Chemical Substances	Anti-Bacterial Agents
Language	English
Publishing date	2023-05-03
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2036179-8
ISSN	1424-3997 ; 1424-7860
ISSN (online)	1424-3997
ISSN	1424-7860
DOI	10.57187/smw.2023.40066
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Article ; Online: Limited Adaptation of

Räz, Anna K / Andreoni, Federica / Boumasmoud, Mathilde / Bergada-Pijuan, Judith / Schweizer, Tiziano A / Mairpady Shambat, Srikanth / Hasse, Barbara / Zinkernagel, Annelies S / Brugger, Silvio D

Microbiology spectrum

2023 Volume 11, Issue 4, Page(s) e0259021

Abstract: Staphylococcus aureus carriage is a risk factor for invasive infections. Unique genetic elements favoring the transition from colonizing to invasive phenotype have not yet been identified, and phenotypic adaptation traits are understudied. We therefore ... ...

Abstract	Staphylococcus aureus carriage is a risk factor for invasive infections. Unique genetic elements favoring the transition from colonizing to invasive phenotype have not yet been identified, and phenotypic adaptation traits are understudied. We therefore assessed phenotypic and genotypic profiles of 11 S. aureus isolate pairs sampled from colonized patients simultaneously suffering from invasive S. aureus infections. Ten out of 11 isolate pairs displayed the same
MeSH term(s)	Humans ; Staphylococcus aureus ; Staphylococcal Infections/microbiology ; Adaptation, Physiological ; Nasal Cavity/microbiology ; Virulence
Language	English
Publishing date	2023-06-21
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2807133-5
ISSN	2165-0497 ; 2165-0497
ISSN (online)	2165-0497
ISSN	2165-0497
DOI	10.1128/spectrum.02590-21
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