The LAUsanne STAPHylococcus aureus ENdocarditis (LAUSTAPHEN) score: A prediction score to estimate initial risk for infective endocarditis in patients with S. aureus bacteremia.

Introduction: Infective endocarditis (IE) is a common complication of Staphylococcus aureus bacteremia (SAB). The study aimed to develop and validate a prediction score to determine IE risk among SAB. Methods: This retrospective study included adults with SAB (2015-2021) and divided them into derivation and validation cohorts. Using the modified 2015 European Society of Cardiology modified Duke Criteria for definite IE, the LAUSTAPHEN score was compared to previous scores. Results: Among 821 SAB episodes, 419 and 402 were divided into derivation and validation cohorts, respectively. Transthoracic and transoesophageal echocardiography (TOE) were performed in 77.5 and 42.1% of episodes, respectively. Definite IE was diagnosed in 118 episodes (14.4%). Derivation cohort established that cardiac predisposing factors, such as cardiac implantable electronic devices, prolonged bacteremia ≥48 h, and vascular phenomena were independently associated with IE. In addition to those parameters, native bone and joint infections were used to constitute the LAUSTAPHEN score. LAUSTAPHEN and VIRSTA scores misclassified <4% of IE cases as low risk. Misclassification using POSITIVE and PREDICT scores was >10%. The number of TOEs required to safely exclude IE were 66.9 and 51.6% with VIRSTA and LAUSTAPHEN, respectively. Discussion: LAUSTAPHEN and VIRSTA scores exhibited the lowest misclassification rate of IE cases to the low-risk group. However, the number of patients requiring TOE was higher for VIRSTA than for LAUSTAPHEN.

Secondary Prevention in Lower Extremity Artery Disease Patients: Lipid-Lowering Therapy and Long-Term Guideline Adherence.

Lower extremity artery disease (LEAD) affects millions of elderly patients and is associated with elevated cardiovascular morbidity and mortality. Risk factor modification, including the therapy of dyslipidaemia, is mandatory to reduce cardiovascular event rates and to improve survival rates. However, only a minority achieve the recommended low-density lipoprotein cholesterol (LDL-C) target level < 55 mg/dL, according to the current ESC/EAS guidelines on the treatment of dyslipidaemia. This study elucidated the implementation of the lipid-lowering guideline recommendations of 400 LEAD patients with LDL-C > 100 mg/dL and their adherence to treatment adjustment during follow-up. Despite a sustained statin prescription in 93% of the patients, including 77% with high-intensity statins at follow-up, only 18% achieved the target level. Ezetimibe appeared in 21% and LDL-C goals were reached significantly more often with combination therapy. Recurrent revascularization appeared more often (28%) than coronary artery or cerebrovascular disease progression (14%) and 7% died. Despite the frequent use of high-intensity statins and expandable rates of ezetimibe, the progression of cardiovascular events remained inevitable. Only 18% of the patients had received recommendations on lifestyle modification, including dietary adaptations, which is key for a holistic approach to risk factor control. Thus, efforts for both pharmacological and behavioral strategies are needed to improve clinical outcomes and survival rates.

Computer-Aided Medical Microbiology Monitoring Tool: A Strategy to Adapt to the SARS-CoV-2 Epidemic and That Highlights RT-PCR Consistency.

Since the beginning of the COVID-19 pandemic, important health and regulatory decisions relied on SARS-CoV-2 reverse transcription polymerase chain reaction (RT-PCR) results. Our diagnostic laboratory faced a rapid increase in the number of SARS-CoV-2 RT-PCR. To maintain a rapid turnaround time, we moved from a case-by-case validation of RT-PCR results to an automated validation and immediate results transmission to clinicians. A quality-monitoring tool based on a homemade algorithm coded in R was developed, to preserve high quality and to track aberrant results. We present the results of this quality-monitoring tool applied to 35,137 RT-PCR results. Patients tested several times led to 4,939 pairwise comparisons: 88% concordant and 12% discrepant. The algorithm automatically solved 428 out of 573 discrepancies. The most likely explanation for these 573 discrepancies was related for 44.9% of the situations to the clinical evolution of the disease, 27.9% to preanalytical factors, and 25.3% to stochasticity of the assay. Finally, 11 discrepant results could not be explained, including 8 for which clinical data was not available. For patients repeatedly tested on the same day, the second result confirmed a first negative or positive result in 99.2% or 88.9% of cases, respectively. The implemented quality-monitoring strategy allowed to: i) assist the investigation of discrepant results ii) focus the attention of medical microbiologists onto results requiring a specific expertise and iii) maintain an acceptable turnaround time. This work highlights the high RT-PCR consistency for the detection of SARS-CoV-2 and the necessity for automated processes to handle a huge number of microbiological results while preserving quality.

Septic arthritis of the shoulder due to Ureaplasma urealyticum after emergency caesarean section: a case report.

BACKGROUND: Ureaplasma urealyticum is an intra-cellular bacterium frequently found colonizing the genital tract. Known complications include localized infections, which can result in premature deliveries. Septic arthritis due to U. urealyticum in healthy patients is exceptionally rare, although opportunistic septic arthritis in agammaglobulinemic patients have been reported. However, there are no reports of septic arthritis due to U. urealyticum following caesarean section or in the post-partum period. CASE PRESENTATION: A 38-year-old immunocompetent woman presented with severe right shoulder pain, 1 month following emergency caesarean section at 26 weeks of gestation for pre-eclampsia and spontaneous placental disruption with an uncomplicated post-operative recovery. Our suspicion of septic arthritis was confirmed with abundant pus following arthrotomy by a delto-pectoral approach. Awaiting culture results, empirical antibiotic treatment with intravenous amoxicilline and clavulanic acid was initiated. In spite of sterile cultures, clinical evolution was unfavorable with persistent pain, inflammation and purulent drainage, requiring two additional surgical débridement and lavage procedures. The 16S ribosomal RNA PCR of the purulent liquid was positive for U. urealyticum at 2.95 × 106 copies/ml, specific cultures inoculated a posteriori were positive for U. urealyticum. Levofloxacin and azithromycine antibiotherapy was initiated. Susceptibility testing showed an intermediate sensibility to ciprofloxacin and clarithromycin. The strain was susceptible to doxycycline. Following cessation of breastfeeding, we started antibiotic treatment with doxycycline for 4 weeks. The subsequent course was favorable with an excellent functional and biological outcome. CONCLUSIONS: We report the first case of septic arthritis due to U. urealyticum after caesarean section. We hypothesize that the breach of the genital mucosal barrier during the caesarean section led to hematogenous spread resulting in purulent septic arthritis. The initial beta-lactam based antibiotic treatment, initiated for a purulent arthritis, did not provide coverage for cell wall deficient organisms. Detection of 16S rRNA allowed for a correct microbiological diagnosis in a patient with an unexpected clinical course.

ISEcp1-Mediated Transposition Leads to Fosfomycin and Broad-Spectrum Cephalosporin Resistance in Klebsiella pneumoniae.

A fosfomycin-resistant and carbapenemase (OXA-48)-producing Klebsiella pneumoniae isolate was recovered, and whole-genome sequencing revealed ISEcp1-blaCTX-M-14b tandemly inserted upstream of the chromosomally encoded lysR-fosA locus. Quantitative evaluation of the expression of lysR and fosA genes showed that this insertion brought a strong hybrid promoter leading to overexpression of the fosA gene, resulting in fosfomycin resistance. This work showed the concomitant acquisition of resistance to broad-spectrum cephalosporins and fosfomycin due to a single genetic event.

Phenotypic, biochemical and genetic analysis of KPC-41, a KPC-3 variant conferring resistance to ceftazidime-avibactam and exhibiting reduced carbapenemase activity.

A novel KPC variant, KPC-41, was identified in a Klebsiella pneumoniae clinical isolate from Switzerland. This ß-lactamase possessed a three amino-acid insertion (Pro-Asn-Lys) located between amino acids 269 and 270 compared to the KPC-3 amino acid sequence. Cloning and expression of the bla KPC-41 gene in Escherichia coli, followed by determination of MIC values and kinetic parameters, showed that KPC-41, compared to KPC-3, has an increased affinity to ceftazidime and a decreased sensitivity to avibactam, leading to resistance to ceftazidime-avibactam once produced in K. pneumoniae Furthermore, KPC-41 exhibited a drastic decrease of its carbapenemase activity. This report highlights that a diversity of KPC variants conferring resistance to ceftazidime-avibactam already circulate in Europe.

Identification of FosA8, a Plasmid-Encoded Fosfomycin Resistance Determinant from Escherichia coli, and Its Origin in Leclercia adecarboxylata.

A plasmid-located fosfomycin resistance gene, fosA8, was identified from a CTX-M-15-producing Escherichia coli isolate recovered from urine. Identification of this gene was obtained by whole-genome sequencing. It encoded FosA8, which shares 79% and 78% amino acid identity with the most closely related FosA2 and FosA1 enzymes, respectively. The fosA8 gene was located on a transferable 50-kb plasmid of IncN type encoding high-level resistance to fosfomycin. In silico analysis and cloning experiments identified fosA8 analogues (99% identity) in the genome of Leclercia decarboxylata, which is an enterobacterial species with natural resistance to fosfomycin. This finding adds L. decarboxylata to the list of enterobacterial species that are a reservoir of fosA-like genes which have been captured from the chromosome of a progenitor and are then acquired by E. coli.

Sequencing the Obligate Intracellular Rhabdochlamydia helvetica within Its Tick Host Ixodes ricinus to Investigate Their Symbiotic Relationship.

The Rhabdochlamydiaceae family is one of the most widely distributed within the phylum Chlamydiae, but most of its members remain uncultivable. Rhabdochlamydia 16S rRNA was recently reported in more than 2% of 8,534 pools of ticks from Switzerland. Shotgun metagenomics was performed on a pool of five female Ixodes ricinus ticks presenting a high concentration of chlamydial DNA, allowing the assembly of a high-quality draft genome. About 60% of sequence reads originated from a single bacterial population that was named "Candidatus Rhabdochlamydia helvetica" whereas only few thousand reads mapped to the genome of "Candidatus Midichloria mitochondrii," a symbiont normally observed in all I. ricinus females. The 1.8 Mbp genome of R. helvetica is smaller than other Chlamydia-related bacteria. Comparative analyses with other chlamydial genomes identified transposases of the PD-(D/E)XK nuclease family that are unique to this new genome. These transposases show evidence of interphylum horizontal gene transfers between multiple arthropod endosymbionts, including Cardinium spp. (Bacteroidetes) and diverse proteobacteria such as Wolbachia, Rickettsia spp. (Rickettsiales), and Caedimonas varicaedens (Holosporales). Bacterial symbionts were previously suggested to provide B-vitamins to hematophagous hosts. However, incomplete metabolic capacities including for B-vitamin biosynthesis, high bacterial density and limited prevalence suggest that R. helvetica is parasitic rather than symbiotic to its host. The identification of novel Rhabdochlamydia strains in different hosts and their sequencing will help understanding if members of this genus have become highly specialized parasites with reduced genomes, like the Chlamydiaceae, or if they could be pathogenic to humans using ticks as a transmission vector.

Prevalence of fosfomycin resistance among ESBL-producing Escherichia coli isolates in the community, Switzerland.

Our aim was to evaluate the prevalence of fosfomycin-resistant strains among ESBL-producing Escherichia coli isolates recovered from community patients in Switzerland. A total of 1225 ESBL-producing E. coli isolates were collected between 2012 and 2013 from a private and community laboratory. Fosfomycin resistance was assessed by using the novel rapid fosfomycin/E. coli NP test and agar dilution method. Resistant isolates were further investigated for acquired resistance genes fosA1-7 by PCR and sequencing. Pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) were performed to evaluate the clonal relationship among fosA3-carrying isolates. Out of the 1225 ESBL-producing E. coli isolates analyzed in this study, 1208 were fosfomycin susceptible while 17 were fosfomycin resistant. No discrepancy was observed between the rapid fosfomycin/E. coli NP test and the agar dilution method taken as the gold standard. Five out of the 17 resistant isolates carried a fosA-like gene. No clonal relationship was observed among those isolates. Here, the prevalence of fosfomycin resistance among ESBL-producing E. coli isolates in the community is reported for the first time in Switzerland, being ca. 1.4%. Among the five isolates carrying a fosA gene, four encoded the FosA3 enzyme, being the most prevalent fosfomycin-resistant determinant. An excellent correlation was observed between minimum inhibitory concentration-based susceptibility categorization and results of the rapid fosfomycin/E. coli NP test, further indicating the excellent sensitivity and specificity of this recently developed rapid test whose results are obtained in less than 2 h.

Rapid Detection of Fosfomycin Resistance in Escherichia coli.

The rapid fosfomycin/Escherichia coli NP test was developed to detect fosfomycin resistance in E. coli isolates. The test is based on glucose metabolization and the detection of bacterial growth in the presence of fosfomycin at 40 µg/ml. Bacterial growth is visually detectable by an orange-to-yellow color change of red phenol, a pH indicator. A total of 100 E. coli isolates, among which 22 were fosfomycin resistant, were used to evaluate the test performance. The sensitivity and specificity of the test were 100% and 98.7%, respectively. This new test is user friendly, sensitive and specific, and its results are obtained in 1 h 30 min.

Cedratvirus lausannensis - digging into Pithoviridae diversity.

Amoeba-infecting viruses have raised scientists' interest due to their novel particle morphologies, their large genome size and their genomic content challenging previously established dogma. We report here the discovery and the characterization of Cedratvirus lausannensis, a novel member of the Megavirales, with a 0.75-1 µm long amphora-shaped particle closed by two striped plugs. Among numerous host cell types tested, the virus replicates only in Acanthamoeba castellanii leading to host cell lysis within 24 h. C. lausannensis was resistant to ethanol, hydrogen peroxide and heating treatments. Like 30 000-year-old Pithovirus sibericum, C. lausannensis enters by phagocytosis, releases its genetic content by fusion of the internal membrane with the inclusion membrane and replicates in intracytoplasmic viral factories. The genome encodes 643 proteins that confirmed the grouping of C. lausannensis with Cedratvirus A11 as phylogenetically distant members of the family Pithoviridae. The 575,161 bp AT-rich genome is essentially devoid of the numerous repeats harbored by Pithovirus, suggesting that these non-coding repetitions might be due to a selfish element rather than particular characteristics of the Pithoviridae family. The discovery of C. lausannensis confirms the contemporary worldwide distribution of Pithoviridae members and the characterization of its genome paves the way to better understand their evolution.

One Year Genome Evolution of Lausannevirus in Allopatric versus Sympatric Conditions.

Amoeba-resisting microorganisms raised a great interest during the last decade. Among them, some large DNA viruses present huge genomes up to 2.5 Mb long, exceeding the size of small bacterial genomes. The rate of genome evolution in terms of mutation, deletion, and gene acquisition in these genomes is yet unknown. Given the suspected high plasticity of viral genomes, the microevolution of the 346 kb genome of Lausannevirus, a member of Megavirales, was studied. Hence, Lausannevirus was co-cultured within the amoeba Acanthamoeba castellanii over one year. Despite a low number of mutations, the virus showed a genome reduction of 3.7% after 12 months. Lausannevirus genome evolution in sympatric conditions was investigated by its co-culture with Estrella lausannensis, an obligate intracellular bacterium, in the amoeba A. castellanii during one year. Cultures were split every 3 months. Genome sequencing revealed that in these conditions both, Lausannevirus and E. lausannensis, show stable genome, presenting no major rearrangement. In fact, after one year they acquired from 2 to 7 and from 4 to 10 mutations per culture for Lausannevirus and E. lausannensis, respectively. Interestingly, different mutations in the endonuclease encoding genes of Lausannevirus were observed in different subcultures, highlighting the importance of this gene product in the replication of Lausannevirus. Conversely, mutations in E. lausannensis were mainly located in a gene encoding for a phosphoenolpyruvate-protein phosphotransferase (PtsI), implicated in sugar metabolism. Moreover, in our conditions and with our analyses we detected no horizontal gene transfer during one year of co-culture.

Comparative genome analysis of Pseudomonas knackmussii†B13, the first bacterium known to degrade chloroaromatic compounds.

Pseudomonas knackmussii B13 was the first strain to be isolated in 1974 that could degrade chlorinated aromatic hydrocarbons. This discovery was the prologue for subsequent characterization of numerous bacterial metabolic pathways, for genetic and biochemical studies, and which spurred ideas for pollutant bioremediation. In this study, we determined the complete genome sequence of B13 using next generation sequencing technologies and optical mapping. Genome annotation indicated that B13 has a variety of metabolic pathways for degrading monoaromatic hydrocarbons including chlorobenzoate, aminophenol, anthranilate and hydroxyquinol, but not polyaromatic compounds. Comparative genome analysis revealed that B13 is closest to Pseudomonas denitrificans and Pseudomonas aeruginosa. The B13 genome contains at least eight genomic islands [prophages and integrative conjugative elements (ICEs)], which were absent in closely related pseudomonads. We confirm that two ICEs are identical copies of the 103 kb self-transmissible element ICEclc that carries the genes for chlorocatechol metabolism. Comparison of ICEclc showed that it is composed of a variable and a 'core' region, which is very conserved among proteobacterial genomes, suggesting a widely distributed family of so far uncharacterized ICE. Resequencing of two spontaneous B13 mutants revealed a number of single nucleotide substitutions, as well as excision of a large 220 kb region and a prophage that drastically change the host metabolic capacity and survivability.

Lausannevirus seroprevalence among asymptomatic young adults.

OBJECTIVES: The giant Lausannevirus was recently identified as a parasite of amoeba that replicates rapidly in these professional phagocytes. This study aimed at assessing Lausannevirus seroprevalence among asymptomatic young men in Switzerland and hopefully identifying possible sources of contact with this giant virus. METHODS: The presence of anti-Lausannevirus antibodies was assessed in sera from 517 asymptomatic volunteers who filled a detailed questionnaire. The coreactivity between Lausannevirus and amoeba-resisting bacteria was assessed. RESULTS: Lausannevirus prevalence ranged from 1.74 to 2.51%. Sporadic condom use or multiple sexual partners, although frequent (53.97 and 60.35%, respectively), were not associated with anti-Lausannevirus antibodies. On the contrary, frequent outdoor sport practice as well as milk consumption were significantly associated with positive Lausannevirus serologies (p = 0.0066 and 0.028, respectively). Coreactivity analyses revealed an association between Criblamydia sequanensis (an amoeba-resisting bacterium present in water environments) and Lausannevirus seropositivity (p = 0.001). CONCLUSIONS: Lausannevirus seroprevalence is low in asymptomatic Swiss men. However, the association between virus seropositivity and frequent sport practice suggests that this member of the Megavirales may be transmitted by aerosols and/or exposure to specific outdoor environments. Milk intake was also associated with seropositivity. Whether the coreactivity observed for C. sequanensis and Lausannevirus reflects a common mode of acquisition or some unexpected cross-reactivity remains to be determined.