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Gilbert Greub

Publications and source records attributed to Gilbert Greub.

At least 19 recordsLinked to original sources
PubMed2026

Conference report: the third Bacterial Genome Sequencing Pan-European Network conference.

The third Bacterial Genome Sequencing Pan-European Network conference, held in Engelberg, Switzerland (12-15 January 2026), brought together experts from six European countries to discuss the implementation of bacterial genome sequencing in clinical microbiology and public health. Key themes included regulatory frameworks (In Vitro Diagnostic Regulation, General Data Protection Regulation), standardization, quality control, data sharing, economic evaluation, and the integration of artificial intelligence and long-read sequencing into diagnostic workflows. Across presentations, panel discussions, and workshops, participants emphasized that successful implementation of genome sequencing requires more than technical capacity: it depends on robust validation, sustainable funding, interoperable data standards, ethical governance, and interdisciplinary collaboration. The meeting highlighted that sequencing should remain question-driven and clinically meaningful, balancing cost, turnaround time, and public health impact. Overall, the conference reinforced the need for coordinated European efforts to advance responsible, standardized, and sustainable genomic surveillance and diagnostics.

bacterial genome sequencing↗
PubMed2026

Moraxella species isolated from blood cultures in Europe (MORAXEu): a multicentre study of epidemiology and antimicrobial susceptibility with complementary phylogenomic analysis of publicly available genomes.

INTRODUCTION: Moraxella species are fastidious Gram-negative bacteria capable of causing opportunistic infections, including bloodstream infections, especially in immunocompromised patients. Data on their epidemiology, antimicrobial susceptibility, and phylogenomics in Europe remains limited. METHODS: We conducted a multicentre, retrospective, observational study across 56 European hospital centres between January 1st 2020 and December 31st 2024. All Moraxella species isolated from blood cultures (BCs) were included. Species distribution and antimicrobial susceptibility profiles were analysed. We also performed a phylogenomic analysis of Moraxella genomes deposited in GenBank. RESULTS: A total of 709 Moraxella isolates were included. Moraxella osloensis (61.1%; n = 433/709) and Moraxella catarrhalis (20.4%; n = 145/709) were the most frequently identified species, followed by Moraxella nonliquefaciens (6.5%; n = 46/709) and Moraxella atlantae (4.8%; n = 34/709). Species distribution differed by age. M. catarrhalis was predominant in paediatric patients, whereas M. atlantae was more common in adults. Most isolates showed > 90% susceptibility to amoxicillin/clavulanate, cefotaxime, fluoroquinolones, and trimethoprim/sulfamethoxazole. Cefotaxime resistance in M. osloensis was more frequent in adults than in children (49% vs. 8%, p = 0.009). Phylogenomic analysis demonstrated the distinction of a core Moraxella group from the divergent Faucicola lineage, with M. osloensis and M. atlantae clustering within the latter. CONCLUSIONS: The epidemiology of Moraxella species from BCs in Europe showed age-group-specific differences in species distribution and generally favourable antimicrobial susceptibility patterns. Phylogenomic data corroborated recent taxonomic revisions, highlighting the need for improved diagnostics, harmonized nomenclature and sustained surveillance to inform management and stewardship of Moraxella bacteraemia.

Faucicola↗
PubMed2003

Respiratory complications of gastroesophageal reflux associated with paraesophageal hiatal hernia.

BACKGROUND: Gastroesophageal reflux disease (GERD) may be associated with episodes of bronchoaspiration, sometimes leading to life-threatening respiratory complications. GERD is frequently observed in the setting of type 1 (sliding type) hiatal hernia, but only infrequently complicates the course of type 2 (paraesophageal) hernia. METHODS OF STUDY: We performed a retrospective analysis of 50 patients operated for type 2 hiatal hernia in our hospital, to determine the prevalence of respiratory complaints related to GERD in this setting. RESULTS: We found 7 cases (14%) of type 2 hiatal hernia complicated by pulmonary manifestations as the only symptoms of GERD. These ranged from dyspnea to severe bronchoconstriction and acute respiratory failure. The series is illustrated by the report of 1 patient who experienced acute bronchospasm and cardiopulmonary arrest as a complication of GERD. In all patients, surgical repair of the hiatal hernia, together with an antireflux procedure, resulted in complete resolution of the respiratory complaints for follow-up periods up to 160 months. CONCLUSIONS: Our data emphasize the particular prevalence of respiratory involvement in the case of GERD complicating type 2 hiatal hernia, and also the excellent symptomatic results obtained by surgical therapy for this condition.

Aged↗
PubMed2003

Serological hint suggesting that Parachlamydiaceae are agents of pneumonia in polytraumatized intensive care patients.

Parachlamydiaceae are potential emerging pathogens that naturally infect free-living amoebae. Intensive-care patients are highly exposed to aerosols and, consequently, exposed to free-living amoebae and to their intracellular hosts. Thus, we tested intensive-care patients for antibodies to Parachlamydia and determined if serum reactivity was associated with pneumonia. Patients who underwent intubation and were hospitalized in our intensive-care unit were eligible. Clinical data and serum were recorded prospectively. Seventy-three sera taken from 37 intensive-care patients and 100 sera from healthy blood donors were tested for reactivity against Parachlamydia by immunofluorescence. We detected an antibody titer greater than or equal to 1:100 in 5 out of 37 intensive-care unit patients (13.5%), including three seroconversions (8.1%). By contrast, no blood donors were reactive against Parachlamydia (P < 0.001). All patients with serological evidence of a recent exposure to Parachlamydia were trauma patients with head injury and aspiration pneumonia. Moreover, both patients with serological evidence of previous exposure to Parachlamydia were admitted for a cerebral hemorrhage. This serological study suggests that Parachlamydiaceae are associated with aspiration pneumonia in trauma patients admitted to intensive-care units.

Accidents↗
PubMed2003

Parachlamydia acanthamoeba is endosymbiotic or lytic for Acanthamoeba polyphaga depending on the incubation temperature.

Parachlamydiaceae are potential emerging pathogens that naturally infect free-living amoebae. We investigated the affects of incubation temperature on the growth and cytopathic effect of P. acanthamoeba in Acanthamoeba polyphaga. A. polyphaga were infected with P. acanthamoeba and incubated at different temperatures for ten days. Bacterial growth was quantified by real-time PCR. Cytopathic effects were determined by counting the number of cysts and viable amoebae (unstained with trypan blue) in Nageotte counting chambers. Uninfected amoebae cultures were used as negative control. At 32, 35, and 37 degrees C, we observed a significant decrease in the number of viable A. polyphaga that contrasted with the delayed and smaller decrease in the number of living A. polyphaga observed at 25, 28, and 30 degrees C. Higher incubation temperature, which is associated with amoebal lysis, surprisingly was not associated with increased growth rate. P. acanthamoeba is lytic for A. polyphaga at 32-37 degrees C but endosymbiotic at 25-30 degrees C. This suggests that A. polyphaga may be a reservoir of endosymbionts at the lower temperature of the nasal mucosa, which may be liberated by lysis at higher temperature, for instance, when the amoeba is inhaled and reaches the lower respiratory tract.

Acanthamoeba↗
PubMed2003

History of the ADP/ATP-translocase-encoding gene, a parasitism gene transferred from a Chlamydiales ancestor to plants 1 billion years ago.

Nonmitochondrial ADP/ATP translocase is an energy parasite enzyme. Its encoding gene, tlc, is found only in Rickettsiales, Chlamydiales, and plant and alga plastids. We demonstrate the presence of tlc in Parachlamydia acanthamoebae. This gene shares more similarity with the tlc1 gene of Chlamydiaceae and the tlc of plant and alga plastids than with the tlc2 gene of Chlamydiaceae. Phylogenetic analysis, including all other tlc homologs found in GenBank, showed that tlc was duplicated in a Chlamydiales ancestor before the appearance of multicellular eukaryotes. A time scale, calibrated with seven independent time points obtained from fossil estimates and from the 16S rRNA molecular clock, was congruent with the molecular clock provided by tlc. Plant and alga plastids acquired tlc approximately when Parachlamydiaceae and Chlamydiaceae diverged, at the eucaryotic radiation time, ca. 1 billion years ago.

Base Sequence↗
PubMed2003

Clinical implications of Mycobacterium kansasii species heterogeneity: Swiss National Survey.

Several subtypes of Mycobacterium kansasii have been described, but their respective pathogenic roles are not clear. This study investigated the distribution of subtypes and the pathogenicity of M. kansasii strains (n = 191) isolated in Switzerland between 1991 and 1997. Demographic, clinical, and microbiological information was recorded from clinical files. Patients were classified as having an infection according to the criteria of the American Thoracic Society. Subtypes were defined by PCR-restriction enzyme analysis of the hsp65 gene. Subtype 1 comprised 67% of the isolates (n = 128), while subtypes 2 and 3 comprised 21% (n = 40) and 8% (n = 15), respectively. Other subtypes (subtypes 4 and 6 and a new subtype, 7) were recovered from only 4% of patients (n = 8). M. kansasii subtype 1 was considered pathogenic in 81% of patients, while M. kansasii subtype 2 was considered pathogenic in 67% of patients and other subtypes were considered pathogenic in 6% of patients. The majority of patients with M. kansasii subtype 2 were immunocompromised due to the use of corticosteroids (21% of patients) or coinfection with HIV (62.5% of patients). Subtyping M. kansasii may improve clinical management by distinguishing pathogenic from nonpathogenic subtypes.

Adult↗
PubMed2003

Diagnosis of Bartonella endocarditis by a real-time nested PCR assay using serum.

Bartonella endocarditis is a severe disease for which blood cultures frequently remain negative. We tested three PCR assays by using specimens of serum sampled early during the disease from 43 patients diagnosed in our laboratory as having Bartonella endocarditis on the basis of serological, culture, and/or valvular molecular detection. We tested a two-step nested PCR (TSN-PCR), a one-step nested PCR (OSN-PCR) with a regular thermal cycler, and a one-step nested PCR with the LightCycler (LCN-PCR). These assays were performed with primers derived from the riboflavin synthase-encoding gene ribC, never before amplified in our laboratory. Due to contamination of negative controls, the results of the TSN-PCR were not interpretable, and this technique was no longer considered. The LCN-PCR had a specificity of 100% and a sensitivity of 58.1%, higher than those of the OSN-PCR (18.6%; P < 0.01) and prolonged blood culturing (7.1%; P < 0.01). The LCN-PCR results correlated strictly with those of other direct diagnostic tests, when available, and identified the causative species for six patients previously diagnosed on the basis of serological analysis only. The efficacy of the LCN-PCR was not influenced by antibiotics (P = 0.96) but was altered by prolonged storage of serum specimens at -20 degrees C (P = 0.04). Overall, the LCN-PCR is specific and more sensitive than traditional methods (i.e., culturing and/or PCR with EDTA-treated blood). It can easily be applied to the diagnosis of patients with suspected Bartonella endocarditis, especially when only serum is available.

Bartonella↗
PubMed2003

Amoeba-resisting bacteria and ventilator-associated pneumonia.

To evaluate the role of amoeba-associated bacteria as agents of ventilator-associated pneumonia (VAP), we tested the water from an intensive care unit (ICU) every week for 6 months for such bacteria isolates; serum samples and bronchoalveolar lavage samples (BAL) were also obtained from 30 ICU patients. BAL samples were examined for amoeba-associated bacteria DNA by suicide-polymerase chain reaction, and serum samples were tested against ICU amoeba-associated bacteria. A total of 310 amoeba-associated bacteria from 10 species were isolated. Twelve of 30 serum samples seroconverted to one amoeba-associated bacterium isolated in the ICU, mainly Legionella anisa and Bosea massiliensis, the most common isolates from water (p=0.021). Amoeba-associated bacteria DNA was detected in BAL samples from two patients whose samples later seroconverted. Seroconversion was significantly associated with VAP and systemic inflammatory response syndrome, especially in patients for whom no etiologic agent was found by usual microbiologic investigations. Amoeba-associated bacteria might be a cause of VAP in ICUs, especially when microbiologic investigations are negative.

Adult↗
PubMed2002

Spare non-occupational HIV post-exposure prophylaxis by active contacting and testing of the source person.

OBJECTIVE: HIV-1 post-exposure prophylaxis (PEP) is frequently prescribed after exposure to source persons with an undetermined HIV serostatus. To reduce unnecessary use of PEP, we implemented a policy including active contacting of source persons and the availability of free, anonymous HIV testing ('PEP policy'). METHODS: All consultations for potential non-occupational HIV exposures i.e. outside the medical environment) were prospectively recorded. The impact of the PEP policy on PEP prescription and costs was analysed and modelled. RESULTS: Among 146 putative exposures, 47 involved a source person already known to be HIV positive and 23 had no indication for PEP. The remaining 76 exposures involved a source person of unknown HIV serostatus. Of 33 (43.4%) exposures for which the source person could be contacted and tested, PEP was avoided in 24 (72.7%), initiated and discontinued in seven (21.2%), and prescribed and completed in two (6.1%). In contrast, of 43 (56.6%) exposures for which the source person could not be tested, PEP was prescribed in 35 (81.4%), P < 0.001. Upon modelling, the PEP policy allowed a 31% reduction of cost for management of exposures to source persons of unknown HIV serostatus. The policy was cost-saving for HIV prevalence of up to 70% in the source population. The availability of all the source persons for testing would have reduced cost by 64%. CONCLUSION: In the management of non-occupational HIV exposures, active contacting and free, anonymous testing of source persons proved feasible. This policy resulted in a decrease in prescription of PEP, proved to be cost-saving, and presumably helped to avoid unnecessary toxicity and psychological stress.

Anti-HIV Agents↗
PubMed2002

Crescent bodies of Parachlamydia acanthamoeba and its life cycle within Acanthamoeba polyphaga: an electron micrograph study.

Parachlamydiaceae are endosymbionts of free-living amoeba first identified in 1997. Two developmental stages, elementary and reticulate bodies, were observed; however, their localization and proportions according to culture condition and duration remain unknown. The life cycle of Parachlamydia acanthamoeba within Acanthamoeba polyphaga was studied by transmission electron microscopy of 8-, 36-, and 144-h coculture. Morphometry and quantification were performed using SAMBA software. The elementary body, the predominant stage within the amoebae, was located mainly within their vacuoles. The multiplication of Parachlamydia bacteria by binary fission of reticulate bodies was independently associated with culture in PYG broth (odds ratio [OR] = 4.4; 95% confidence interval [CI], 1.55 to 12.46) and with the presence of reticulate bodies within the amoebae (OR = 2.10; 95% CI, 1.53 to 2.89). A third developmental stage was observed, the crescent body. Its presence outside and inside the amoebae was associated mainly with prolonged incubation time (OR = 3.98; 95% CI, 1.49 to 10.68, and OR = 5.98; 95% CI, 1.75 to 20.4, respectively). Elementary and crescent bodies were released into the extracellular medium within vesicles or after amoebal lysis. For both, phagocytosis was their mode of entry. This electron micrograph study revealed another infective developmental stage, the crescent body, and provided quantitative analysis of the life cycle of P. acanthamoeba within A. polyphaga.

Acanthamoeba↗
PubMed2002

"Actinobaculum massiliae," a new species causing chronic urinary tract infection.

We report on a new Actinobaculum species, "Actinobaculum massiliae," isolated from the urine of an elderly woman with recurrent cystitis. Its phenotypic pattern was similar to those of both of the other Actinobaculum species described to date. On 16S rRNA sequencing, the Marseille isolate shared 95% homology with Actinobaculum suis, 92 to 93% homology with Actinobaculum schaalii, 91 to 92% homology with Arcanobacterium spp., and 87 to 90% homology with Actinomyces species. A bootstrap value of 99% supports the node separating the Actinobaculum sp. from its closest neighbor (A. suis). In conclusion, on the basis of phenotypic, genotypic, and phylogenetic assessments, we show that the Marseille isolate is a previously unrecognized organism within the Actinobaculum genus, and we propose placement of the organism in the taxon "Actinobaculum massiliae."

Actinomycetaceae↗
PubMed2002

Analysis of natural variants of the human immunodeficiency virus type 1 gag-pol frameshift stem-loop structure.

Human immunodeficiency virus type 1 uses ribosomal frameshifting for translation of the Gag-Pol polyprotein. Frameshift activities are thought to be tightly regulated. Analysis of gag p1 sequences from 270 plasma virions identified in 64% of the samples the occurrence of polymorphism that could lead to changes in thermodynamic stability of the stem-loop. Expression in Saccharomyces cerevisiae of p1-beta-galactosidase fusion proteins from 10 representative natural stem-loop variants and three laboratory mutant constructs (predicted the thermodynamic stability [Delta G degrees] ranging from -23.0 to -4.3 kcal/mol) identified a reduction in frameshift activity of 13 to 67% compared with constructs with the wild-type stem-loop (Delta G degrees, -23.5 kcal/mol). Viruses carrying stem-loops associated with greater than 60% reductions in frameshift activity presented profound defects in viral replication. In contrast, viruses with stem-loop structures associated with 16 to 42% reductions in frameshift efficiency displayed no significant viral replication deficit.

Base Sequence↗
PubMed2002

Parachlamydiaceae: potential emerging pathogens.

Parachlamydiaceae, which naturally infect amoebae, form a sister taxon to the Chlamydiaceae on the basis of the Chlamydia-like cycle of replication and 80% to 90% homology of ribosomal RNA genes. Because intra-amoebal growth could increase the virulence of some intracellular bacteria, Parachlamydiaceae may be pathogenic. Arguments supporting a pathogenic role are that Chlamydia pneumoniae, a well-recognized agent of pneumonia, was shown to infect free-living amoebae and that another member of the Chlamydiales, Simkania negevensis, which has 88% homology with Parachlamydia acanthamoebae, has caused pneumonia in adults and acute bronchiolitis in infants. The recent identification of a 16S rRNA gene sequence of a Parachlamydiaceae from bronchoalveolar lavage is additional evidence supporting potential for pathogenicity.

Acanthamoeba↗