Publications by authors named "Carlo Casanova"

19 Publications

  • Page 1 of 1

Transition From PCR-Ribotyping to Whole Genome Sequencing Based Typing of .

Front Cell Infect Microbiol 2021 1;11:681518. Epub 2021 Jun 1.

Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland.

causes nosocomial outbreaks which can lead to severe and even life-threatening colitis. Rapid molecular diagnostic tests allow the identification of toxin-producing, potentially hypervirulent strains, which is critical for patient management and infection control. PCR-ribotyping has been used for decades as the reference standard to investigate transmission in suspected outbreaks. However, the introduction of whole genome sequencing (WGS) for molecular epidemiology provides a realistic alternative to PCR-ribotyping. In this transition phase it is crucial to understand the strengths and weaknesses of the two technologies, and to assess their correlation. We aimed to investigate ribotype prediction from WGS data, and options for analysis at different levels of analytical granularity. Ribotypes cannot be directly determined from short read Illumina sequence data as the rRNA operons including the ribotype-defining ISR fragments collapse in genome assemblies, and comparison with traditional PCR-ribotyping results becomes impossible. Ribotype extraction from long read Oxford nanopore data also requires optimization. We have compared WGS-based typing with PCR-ribotyping in nearly 300 clinical and environmental isolates from Switzerland, and in addition from the Enterobase database (n=1778). Our results show that while multi-locus sequence type (MLST) often correlates with a specific ribotype, the agreement is not complete, and for some ribotypes the resolution is insufficient. Using core genome MLST (cgMLST) analysis, there is an improved resolution and ribotypes can often be predicted within clusters, using cutoffs of 30-50 allele differences. The exceptions are ribotypes within known ribotype complexes such as RT078/RT106, where the genome differences in cgMLST do not reflect the ribotype segregation. We show that different ribotype clusters display different degrees of diversity, which could be important for the definition of ribotype cluster specific cutoffs. WGS-based analysis offers the ultimate resolution to the SNP level, enabling exploration of patient-to-patient transmission. PCR-ribotyping does not sufficiently discriminate to prove nosocomial transmission with certainty. We discuss the associated challenges and opportunities in a switch to WGS from conventional ribotyping for .
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fcimb.2021.681518DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8204696PMC
July 2021

The Impact of Pneumococcal Conjugate Vaccine (PCV) Coverage Heterogeneities on the Changing Epidemiology of Invasive Pneumococcal Disease in Switzerland, 2005-2019.

Microorganisms 2021 May 18;9(5). Epub 2021 May 18.

Institute for Infectious Diseases, University of Bern, 3001 Bern, Switzerland.

Pneumococcal conjugate vaccines (PCVs) have lowered the incidence of invasive pneumococcal disease (IPD) worldwide. However, the influence of regional vaccine uptake differences on the changing epidemiology of IPD remains unclear. We aimed to examine the overall impact of both seven- and 13-valent PCVs (PCV7 and PCV13) on IPD in Switzerland. Three-year periods from 2005-2010 and 2011-2019 were considered, respectively, as (early and late) PCV7 eras and (early, mid and late) PCV13 eras. Vaccine coverage was estimated from a nationwide survey according to east (German-speaking) and west (French/Italian-speaking) regions for each period. Reported incidence rate ratios (IRRs) were compared between successive periods and regions using nationwide IPD surveillance data. Overall IPD incidence across all ages was only 16% lower in the late PCV13 era compared to the early PCV7 era (IRR 0.83, 95% CI 0.79-0.88), due to increasing incidence of non-PCV-type IPD (2.59, 2.37-2.83) in all age groups, except children <5 years. PCV uptake rates in swiss children were slightly higher in the west than the east ( < 0.001), and were accompanied by lower IPD incidences across all age groups in the former region. Post-PCV13, non-PCV serotypes 8, 22F and 9N were the major cause of IPD in adults ≥65 years. Increased PCV coverage in both areas of Switzerland resulted in a decrease in vaccine-type and overall IPD incidence across all age groups, in a regionally dependent manner. However, the rising incidence of non-vaccine-type IPD, exclusive to older adults, may undermine indirect beneficial effects.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/microorganisms9051078DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8157260PMC
May 2021

Changes in the incidence of invasive disease due to Streptococcus pneumoniae, Haemophilus influenzae, and Neisseria meningitidis during the COVID-19 pandemic in 26 countries and territories in the Invasive Respiratory Infection Surveillance Initiative: a prospective analysis of surveillance data.

Lancet Digit Health 2021 06;3(6):e360-e370

Irish Meningitis and Sepsis Reference Laboratory, Children's Health Ireland at Temple Street, Dublin, Ireland; Royal College of Surgeons in Ireland, Beaumont Hospital, Dublin, Ireland.

Background: Streptococcus pneumoniae, Haemophilus influenzae, and Neisseria meningitidis, which are typically transmitted via respiratory droplets, are leading causes of invasive diseases, including bacteraemic pneumonia and meningitis, and of secondary infections subsequent to post-viral respiratory disease. The aim of this study was to investigate the incidence of invasive disease due to these pathogens during the early months of the COVID-19 pandemic.

Methods: In this prospective analysis of surveillance data, laboratories in 26 countries and territories across six continents submitted data on cases of invasive disease due to S pneumoniae, H influenzae, and N meningitidis from Jan 1, 2018, to May, 31, 2020, as part of the Invasive Respiratory Infection Surveillance (IRIS) Initiative. Numbers of weekly cases in 2020 were compared with corresponding data for 2018 and 2019. Data for invasive disease due to Streptococcus agalactiae, a non-respiratory pathogen, were collected from nine laboratories for comparison. The stringency of COVID-19 containment measures was quantified using the Oxford COVID-19 Government Response Tracker. Changes in population movements were assessed using Google COVID-19 Community Mobility Reports. Interrupted time-series modelling quantified changes in the incidence of invasive disease due to S pneumoniae, H influenzae, and N meningitidis in 2020 relative to when containment measures were imposed.

Findings: 27 laboratories from 26 countries and territories submitted data to the IRIS Initiative for S pneumoniae (62 837 total cases), 24 laboratories from 24 countries submitted data for H influenzae (7796 total cases), and 21 laboratories from 21 countries submitted data for N meningitidis (5877 total cases). All countries and territories had experienced a significant and sustained reduction in invasive diseases due to S pneumoniae, H influenzae, and N meningitidis in early 2020 (Jan 1 to May 31, 2020), coinciding with the introduction of COVID-19 containment measures in each country. By contrast, no significant changes in the incidence of invasive S agalactiae infections were observed. Similar trends were observed across most countries and territories despite differing stringency in COVID-19 control policies. The incidence of reported S pneumoniae infections decreased by 68% at 4 weeks (incidence rate ratio 0·32 [95% CI 0·27-0·37]) and 82% at 8 weeks (0·18 [0·14-0·23]) following the week in which significant changes in population movements were recorded.

Interpretation: The introduction of COVID-19 containment policies and public information campaigns likely reduced transmission of S pneumoniae, H influenzae, and N meningitidis, leading to a significant reduction in life-threatening invasive diseases in many countries worldwide.

Funding: Wellcome Trust (UK), Robert Koch Institute (Germany), Federal Ministry of Health (Germany), Pfizer, Merck, Health Protection Surveillance Centre (Ireland), SpID-Net project (Ireland), European Centre for Disease Prevention and Control (European Union), Horizon 2020 (European Commission), Ministry of Health (Poland), National Programme of Antibiotic Protection (Poland), Ministry of Science and Higher Education (Poland), Agencia de Salut Pública de Catalunya (Spain), Sant Joan de Deu Foundation (Spain), Knut and Alice Wallenberg Foundation (Sweden), Swedish Research Council (Sweden), Region Stockholm (Sweden), Federal Office of Public Health of Switzerland (Switzerland), and French Public Health Agency (France).
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/S2589-7500(21)00077-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8166576PMC
June 2021

Group B streptococcal colonization in elderly women.

BMC Infect Dis 2021 May 3;21(1):408. Epub 2021 May 3.

Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, 3010, Bern, Switzerland.

Background: In non-pregnant adults, the incidence of invasive Group B Streptococcus (GBS) disease is continuously increasing. Elderly and immunocompromised persons are at increased risk of infection. GBS commonly colonizes the vaginal tract, though data on colonization in the elderly are scarce. It is unknown whether the prevalence of GBS colonization is increasing in parallel to the observed rise of invasive infection. We conducted a three-year (2017-2019) prospective observational cross-sectional study in two teaching hospitals in Switzerland to determine the rate of GBS vaginal colonization in women over 60 years and i) to compare the proportions of known risk factors associated with invasive GBS diseases in colonized versus non-colonized women and ii) to evaluate the presence of GBS clusters with specific phenotypic and genotypic patterns in this population.

Methods: GBS screening was performed by using vaginal swabs collected during routine examination from women willing to participate in the study and to complete a questionnaire for risk factors. Isolates were characterized for antibiotic resistance profile, serotype and sequence type (ST).

Results: The GBS positivity rate in the elderly was 17% (44/255 positive samples), and similar to the one previously reported in pregnant women (around 20%). We could not find any association between participants' characteristics, previously published risk factors and GBS colonization. All strains were susceptible to penicillin, 22% (8/36) were not susceptible to erythromycin, 14% (5/36) were not susceptible to clindamycin and 8% (3/36) showed inducible clindamycin resistance. Both M and L phenotypes were each detected in one isolate. The most prevalent serotypes were III (33%, 12/36) and V (31%, 11/36). ST1 and ST19 accounted for 11% of isolates each (4/36); ST175 for 8% (3/36); and ST23, ST249 and ST297 for 6% each (2/36). Significantly higher rates of resistance to macrolides and clindamycin were associated with the ST1 genetic background of ST1.

Conclusions: Our findings indicate a similar colonization rate for pregnant and elderly women.

Trial Registration: Current Controlled Trial ISRCTN15468519 ; 06/01/2017.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12879-021-06102-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8091692PMC
May 2021

Carbon Source-Dependent Changes of the Structure of Capsular Polysaccharide with Serotype 6F.

Int J Mol Sci 2021 Apr 27;22(9). Epub 2021 Apr 27.

Institute for Infectious Diseases, University of Bern, 3001 Bern, Switzerland.

The structure of the exopolysaccharide capsule of is defined by the genetic arrangement of the capsule operon allowing the unequivocal identification of the pneumococcal serotype. Here, we investigated the environment-dependent composition of the polysaccharide structure of serotype 6F. When grown in a chemically defined medium (CDM) with glucose versus galactose, the exopolysaccharide capsule of the serotype 6F strains reveals a ratio of 1/0.6 or 1/0.3 for galactose/glucose in the capsule by H-NMR analyses, respectively. Increased production of the capsule precursor UDP-glucose has been identified by P-NMR in CDM with glucose. Flow cytometric experiments using monoclonal antibodies showed decreased labelling of Hyp6AG4 (specific for serotype 6A) antibodies when 6F is grown in glucose as compared to galactose, which mirrors the 1H-NMR results. Whole-genome sequencing analyses of serotype 6F isolates suggested that the isolates evolved during two different events from serotype 6A during the time when the 13-valent pneumococcal conjugate vaccine (PCV-13) was introduced. In conclusion, this study shows differences in the capsular structure of serotype 6F strains using glucose as compared to galactose as the carbon source. Therefore, 6F strains may show slightly different polysaccharide composition while colonizing the human nasopharynx (galactose rich) as compared to invasive locations such as the blood (glucose rich).
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/ijms22094580DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8123889PMC
April 2021

A Sample-to-Report Solution for Taxonomic Identification of Cultured Bacteria in the Clinical Setting Based on Nanopore Sequencing.

J Clin Microbiol 2020 05 26;58(6). Epub 2020 May 26.

University of Bern, Institute for Infectious Diseases, Bern, Switzerland

Amplicon sequencing of the 16S rRNA gene is commonly used for the identification of bacterial isolates in diagnostic laboratories and mostly relies on the Sanger sequencing method. The latter, however, suffers from a number of limitations, with the most significant being the inability to resolve mixed amplicons when closely related species are coamplified from a mixed culture. This often leads to either increased turnaround time or absence of usable sequence data. Short-read next-generation sequencing (NGS) technologies could solve the mixed amplicon issue but would lack both cost efficiency at low throughput and fast turnaround times. Nanopore sequencing developed by Oxford Nanopore Technologies (ONT) could solve those issues by enabling a flexible number of samples per run and an adjustable sequencing time. Here, we report on the development of a standardized laboratory workflow combined with a fully automated analysis pipeline (long read consensus analysis), which together provide a sample-to-report solution for amplicon sequencing and taxonomic identification of the resulting consensus sequences. Validation of the approach was conducted on a panel of reference strains and on clinical samples consisting of single or mixed rRNA amplicons associated with various bacterial genera by direct comparison to the corresponding Sanger sequences. Additionally, simulated read and amplicon mixtures were used to assess 's behavior when dealing with samples with known cross-contamination levels. We demonstrate that by combining ONT amplicon sequencing results with , the accuracy of Sanger sequencing can be closely matched (>99.6% sequence identity) and that mixed samples can be resolved at the single-base resolution level. The presented approach has the potential to significantly improve the flexibility, reliability, and availability of amplicon sequencing in diagnostic settings.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/JCM.00060-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7269405PMC
May 2020

Successful Treatment of Acute Prostatitis Caused by Multidrug-Resistant With Tigecycline Monotherapy.

Open Forum Infect Dis 2020 Jan 9;7(1):ofz551. Epub 2020 Jan 9.

Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland.

We present a successful treatment, with tigecycline monotherapy, of acute prostatitis caused by multidrug-resistant harboring an NDM-1 carbapemenase along with a CMY-2 cephalosporinase and a TEM ESBL.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/ofid/ofz551DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6975247PMC
January 2020

spp. nosocomial outbreak assessment using rapid MALDI-TOF MS based typing, confirmed by whole genome sequencing.

Antimicrob Resist Infect Control 2019 4;8:171. Epub 2019 Nov 4.

Department of Infectious Diseases, Bern University Hospital, University of Bern, Freiburgstrasse, 3001 Bern, Switzerland.

Background: A number of episodes of nosocomial spp bacteremia (two cases per year) were observed at Bern University Hospital, Switzerland, from 2015 to 2017. This triggered an outbreak investigation.

Methods: Cases of spp bacteremias that occurred between August 2011 and February 2017 were investigated employing line lists, environmental sampling, rapid protein- (MALDI-TOF MS), and genome-based typing (pulsed field gel electrophoresis and whole genome sequencing) of the clinical isolates.

Results: We describe a total of eight bacteremia episodes due to ( = 2), genomovar G3 ( = 5) and ( = 1). Two tight clusters were observed by WGS typing, representing the two isolates (cluster I, isolated in 2015) and four of the genomovar G3 isolates (cluster II, isolated in 2016 and 2017), suggesting two different point sources. The epidemiological investigations revealed two computer tomography (CT) rooms as common patient locations, which correlated with the two outbreak clusters. MALDI-TOF MS permitted faster evaluation of strain relatedness than DNA-based methods. High resolution WGS-based typing confirmed the MALDI-TOF MS clustering.

Conclusions: We report clinical and epidemiological characteristics of two outbreak clusters with spp. bacteremia likely acquired during CT contrast medium injection and highlight the use of MALDI-TOF MS as a rapid tool to assess relatedness of rare gram-negative pathogens in an outbreak investigation.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13756-019-0619-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6829841PMC
July 2020

Phenotypic and Genomic Analyses of Burkholderia stabilis Clinical Contamination, Switzerland.

Emerg Infect Dis 2019 06;25(6):1084-1092

A recent hospital outbreak related to premoistened gloves used to wash patients exposed the difficulties of defining Burkholderia species in clinical settings. The outbreak strain displayed key B. stabilis phenotypes, including the inability to grow at 42°C; we used whole-genome sequencing to confirm the pathogen was B. stabilis. The outbreak strain genome comprises 3 chromosomes and a plasmid, sharing an average nucleotide identity of 98.4% with B. stabilis ATCC27515 BAA-67, but with 13% novel coding sequences. The genome lacks identifiable virulence factors and has no apparent increase in encoded antimicrobial drug resistance, few insertion sequences, and few pseudogenes, suggesting this outbreak was an opportunistic infection by an environmental strain not adapted to human pathogenicity. The diversity among outbreak isolates (22 from patients and 16 from washing gloves) is only 6 single-nucleotide polymorphisms, although the genome remains plastic, with large elements stochastically lost from outbreak isolates.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3201/eid2506.172119DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6537712PMC
June 2019

Phylogenomics reveal that Mycobacterium kansasii subtypes are species-level lineages. Description of Mycobacterium pseudokansasii sp. nov., Mycobacterium innocens sp. nov. and Mycobacterium attenuatum sp. nov.

Int J Syst Evol Microbiol 2019 Jun 4;69(6):1696-1704. Epub 2019 Apr 4.

1​Institute of Microbiology, Department of Laboratory Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland.

Among the species Mycobacterium kansasii, seven subtypes have been previously reported based on the PCR and the restriction fragment length polymorphism of the gene hsp65. Here, we used whole-genome sequencing to refine M. kansasii taxonomy and correct multiple inconsistencies. Average nucleotide identity (ANI) values between M. kansasii subtypes ranged from 88.4 to 94.2 %, lower than the accepted 95-96 % cut-off for species delineation. In addition, Mycobacterium gastri was closer to the M. kansasii subtypes 1, 2, 3, 4 and 5 than M. kansasii subtype 6. The recently described species Mycobacterium persicum shared 99.77 % ANI with M. kansasii subtype 2. Consistent with the ANI results, the digital DNA-DNA hybridization value was below the 70 % threshold for species delineation between subtypes and above it within subtypes as well as between subtype 2 and M. persicum. Furthermore, core-genome phylogeny confirmed the current M. kansasii species to be polyphyletic. Hence, we propose (i) Mycobacterium pseudokansasii sp. nov., replacing subtype 3, with the type strain MK142(=CCUG 72128=DSM 107152), (ii) Mycobacterium innocens sp. nov., replacing subtype 5, with the type strain MK13 (=CCUG 72126=DSM 107161), and (iii) Mycobacterium attenuatum sp. nov., replacing subtype 6, with the type strain MK41(=CCUG 72127=DSM 107153). Subtype 4 represents a new species-level lineage based on the genomic data but no strain was available. No genome sequence or strain was available for subtype 7. The proposed nomenclature will facilitate the identification of the most pathogenic subtype 1 as M. kansasii by clinicians while the new species names suggest the attenuated pathogenicity of the other subtypes.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1099/ijsem.0.003378DOI Listing
June 2019

Discovery and Characterization of sp. nov., a Nontuberculous Mycobacterium Isolated From Human Lungs.

Front Microbiol 2018 8;9:3184. Epub 2019 Jan 8.

Division of Clinical Microbiology, University Hospital Basel, Basel, Switzerland.

Bacteria belonging to the genus are predominantly responsible for pulmonary diseases; most notably causes granulomatous pulmonary infections. Here we describe a novel slow growing mycobacterial species isolated from respiratory samples from five patients, four with underlying pulmonary disease. The isolates were characterized by biochemical and molecular techniques, including whole genome sequencing. Biochemical characteristics generally match those of and ; however, the most striking difference of the new species is its ability to grow at 37°C. The new species was found to grow in human macrophages, but not amoebae, suggesting a pathogenic rather than an environmental lifestyle. Phylogenetic analysis reveals a deep-rooting relationship to and . A complete genome sequence was obtained through combining short and long-read sequencing, providing a genome of 5.6 Mb. The genome appears to be highly intact, syntenic with that of , with very few insertion sequences. A vast array of virulence factors includes 283 PE/PPE surface-associated proteins, making up 10% of the coding capacity, and 22 non-ribosomal peptide synthase clusters. A comparison of six clinical isolates from the five patients shows that they differ by up to two single nucleotide polymorphisms, suggesting a common source of infection. Our findings are in accordance with the recognition of a new taxonomic entity. We propose the name , as all isolates were found in patients from the Basel area of Switzerland.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fmicb.2018.03184DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6331445PMC
January 2019

Outbreak of vancomycin-resistant clone ST796, Switzerland, December 2017 to April 2018.

Euro Surveill 2018 07;23(29)

Department of Infectious Diseases, University Hospital Bern, Bern, Switzerland.

A large outbreak of vancomycin-resistant enterococci (VRE) is affecting four hospitals in the Canton of Bern, Switzerland, since December 2017. Of 89 cases identified as carriers, 77 (86.5%) VRE isolates were virtually indistinguishable using whole genome sequencing, and identified as multilocus sequence type (MLST) ST796. This clone, previously only described in Australia and New Zealand, is characterised by rapid spread and the ability to cause bloodstream infections. It requires a multifaceted infection prevention effort.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.2807/1560-7917.ES.2018.23.29.1800351DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6152203PMC
July 2018

outbreak associated with contaminated commercially-available washing gloves, Switzerland, May 2015 to August 2016.

Euro Surveill 2017 Dec;22(49)

The members of the group are listed at the end of the paper.

We describe an outbreak of associated with contaminated washing gloves, a commercially available Class I medical device. Triggered by an increase in complex (BCC) bacteremias and the detection of BCC in unopened packages of washing gloves, an ad hoc national outbreak committee comprising representatives of a public health organisation, a regulatory agency, and an expert association convened and commissioned an outbreak investigation. The investigation included retrospective case finding across Switzerland and whole genome sequencing (WGS) of isolates from cases and gloves. The investigation revealed that BCC were detected in clinical samples of 46 cases aged 17 to 91 years (33% females) from nine institutions between May 2015 and August 2016. Twenty-two isolates from case patients and 16 from washing gloves underwent WGS. All available outbreak isolates clustered within a span of < 19 differing alleles, while 13 unrelated clinical isolates differed by > 1,500 alleles. This BCC outbreak was rapidly identified, communicated, investigated and halted by an ad hoc collaboration of multiple stakeholders. WGS served as useful tool for confirming the source of the outbreak. This outbreak also highlights current regulatory limitations regarding Class I medical devices and the usefulness of a nationally coordinated outbreak response.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.2807/1560-7917.ES.2017.22.49.17-00213DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5727593PMC
December 2017

A 10-year observational study of Streptococcus dysgalactiae bacteraemia in adults: frequent occurrence among female intravenous drug users.

Swiss Med Wkly 2017 24;147:w14469. Epub 2017 Jul 24.

Institute for Infectious Diseases, University of Bern, Switzerland, Department of Infectious Diseases, Bern University Hospital, University of Bern, Switzerland.

Beta-haemolytic streptococci of groups C and G have become increasingly recognized as causes of invasive human infections. We reviewed clinical and molecular characteristics of Streptococcus dysgalactiae isolates that caused bacteraemia in adults from 2006 to 2015. Among 67 episodes, skin and soft-tissue infections (43%) and emm types stG62647.0 (26%) were the most frequent clinical manifestation and emm type, respectively. Nineteen (28%) episodes occurred in intravenous drug users (75% women). Our observational study shows similarities to but also differences from other reports. The former include the most frequent clinical presentations, and the most frequently found emm types. This report highlights a relatively high proportion of female intravenous drug users among S. dysgalactiae bacteraemia episodes.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.4414/smw.2017.14469DOI Listing
May 2018

Campylobacter concisus pseudo-outbreak caused by improved culture conditions.

J Clin Microbiol 2015 Feb 19;53(2):660-2. Epub 2014 Nov 19.

Department of Infectious Diseases, Bern University Hospital, Bern, Switzerland.

An unusual increase in the number of Campylobacter concisus isolates found in stool cultures provoked an outbreak investigation at Bern University Hospital. No epidemiological links were found between the cases, and the Campylobacter isolates were clonally unrelated. A change in culture conditions to a hydrogen-rich atmosphere enhancing growth of C. concisus was deemed responsible for this pseudo-outbreak.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/JCM.02608-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4298506PMC
February 2015

Staphylococcus hyicus bacteremia in a farmer.

J Clin Microbiol 2011 Dec 12;49(12):4377-8. Epub 2011 Oct 12.

Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, 3010 Bern, Switzerland.

Bacteria known in animal infectious diseases can cause challenges in human diagnostic laboratories. We present pitfalls in the identification and susceptibility testing of Staphylococcus hyicus, a pathogen that typically causes exudative epidermitis in pigs. In this case, the coagulase-positive staphylococcus isolated from a septic patient was misidentified as Staphylococcus aureus.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/JCM.05645-11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3233007PMC
December 2011

Expression analysis of the Theileria parva subtelomere-encoded variable secreted protein gene family.

PLoS One 2009 27;4(3):e4839. Epub 2009 Mar 27.

Molecular Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.

Background: The intracellular protozoan parasite Theileria parva transforms bovine lymphocytes inducing uncontrolled proliferation. Proteins released from the parasite are assumed to contribute to phenotypic changes of the host cell and parasite persistence. With 85 members, genes encoding subtelomeric variable secreted proteins (SVSPs) form the largest gene family in T. parva. The majority of SVSPs contain predicted signal peptides, suggesting secretion into the host cell cytoplasm.

Methodology/principal Findings: We analysed SVSP expression in T. parva-transformed cell lines established in vitro by infection of T or B lymphocytes with cloned T. parva parasites. Microarray and quantitative real-time PCR analysis revealed mRNA expression for a wide range of SVSP genes. The pattern of mRNA expression was largely defined by the parasite genotype and not by host background or cell type, and found to be relatively stable in vitro over a period of two months. Interestingly, immunofluorescence analysis carried out on cell lines established from a cloned parasite showed that expression of a single SVSP encoded by TP03_0882 is limited to only a small percentage of parasites. Epitope-tagged TP03_0882 expressed in mammalian cells was found to translocate into the nucleus, a process that could be attributed to two different nuclear localisation signals.

Conclusions: Our analysis reveals a complex pattern of Theileria SVSP mRNA expression, which depends on the parasite genotype. Whereas in cell lines established from a cloned parasite transcripts can be found corresponding to a wide range of SVSP genes, only a minority of parasites appear to express a particular SVSP protein. The fact that a number of SVSPs contain functional nuclear localisation signals suggests that proteins released from the parasite could contribute to phenotypic changes of the host cell. This initial characterisation will facilitate future studies on the regulation of SVSP gene expression and the potential biological role of these enigmatic proteins.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0004839PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2657828PMC
July 2009

AopP, a type III effector protein of Aeromonas salmonicida, inhibits the NF-kappaB signalling pathway.

Microbiology (Reading) 2006 Sep;152(Pt 9):2809-2818

Institute of Veterinary Bacteriology, Vetsuisse Faculty, Universität Bern, Länggassstrasse 122, Postfach, CH-3001 Bern, Switzerland.

Aeromonas salmonicida subsp. salmonicida contains a functional type III secretion system that is responsible for the secretion of the ADP-ribosylating toxin AexT. In this study, the authors identified AopP as a second effector protein secreted by this system. The aopP gene was detected in both typical and atypical A. salmonicida isolates and was found to be encoded on a small plasmid of approximately 6.4 kb. Sequence analysis indicates that AopP is a member of the YopJ family of effector proteins, a group of proteins that interfere with mitogen-activated protein kinase (MAPK) and/or nuclear factor kappa B (NF-kappaB) signalling pathways. AopP inhibits the NF-kappaB pathway downstream of IkappaB kinase (IKK) activation, while a catalytically inactivated mutant, AopPC177A, does not possess this inhibitory effect. Unlike other effectors of the YopJ family, such as YopJ and VopA, AopP does not inhibit the MAPK signalling pathway.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1099/mic.0.28889-0DOI Listing
September 2006

Post-translational signal peptide cleavage controls differential epitope recognition in the QP-rich domain of recombinant Theileria parva PIM.

Mol Biochem Parasitol 2006 Oct 30;149(2):144-54. Epub 2006 May 30.

Molecular Pathology, Vetsuisse Faculty, University of Bern, CH-3012 Bern, Switzerland.

The presence of the schizont stage of the obligate intracellular parasites Theileria parva or T. annulata in the cytoplasm of an infected leukocyte results in host cell transformation via a mechanism that has not yet been elucidated. Proteins, secreted by the schizont, or expressed on its surface, are of interest as they can interact with host cell molecules that regulate host cell proliferation and/or survival. The major schizont surface protein is the polymorphic immunodominant molecule, PIM, which contains a large glutamine- and proline-rich domain (QP-rd) that protrudes into the host cell cytoplasm. Analyzing QP-rd generated by in vitro transcription/translation, we found that the signal peptide was efficiently cleaved post-translationally upon addition of T cell lysate or canine pancreatic microsomes, whereas signal peptide cleavage of a control protein only occurred cotranslationally and in the presence of microsomal membranes. The QP-rd of PIM migrated anomalously in SDS-PAGE and removal of the 19 amino acids corresponding to the predicted signal peptide caused a decrease in apparent molecular mass of 24kDa. The molecule was analyzed using monoclonal antibodies that recognize a set of previously defined PIM epitopes. Depending on the presence or the absence of the signal peptide, two conformational states could be demonstrated that are differentially recognized, with N-terminal epitopes becoming readily accessible upon signal peptide removal, and C-terminal epitopes becoming masked. Similar observations were made when the QP-rd of PIM was expressed in bacteria. Our observations could also be of relevance to other schizont proteins. A recent analysis of the proteomes of T. parva and T. annulata revealed the presence of a large family of potentially secreted proteins, characterized by the presence of large stretches of amino acids that are also particularly rich in QP-residues.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.molbiopara.2006.05.005DOI Listing
October 2006