Multicentric evaluation of a specific intrathecal anti-Treponema pallidum IgG index as a diagnostic biomarker of neurosyphilis: results from a retro-prospective case-control study

BACKGROUND AND OBJECTIVES

The diagnosis of neurosyphilis (NS) lacks a true 'gold standard', making the diagnosis challenging while consequences of a misdiagnosis are potentially severe. The aim of this study was to evaluate the diagnostic performance of measuring an antibody index (AI) for the intrathecal synthesis of specific anti-Treponema pallidum (T. pallidum) IgG for the diagnosis of NS.

METHODS

Specific anti-T. pallidum IgG were measured simultaneously in paired cerebrospinal fluid (CSF)-serum samples collected retrospectively and prospectively between 2007 and 2022, from patients suspected of NS, in Switzerland. An AI was calculated to account for blood-brain barrier integrity. Area under the receiver operating characteristic curve, sensitivity/specificity and positive/negative predictive values of AI test were estimated. Two NS definitions were used: NS1 included patients with NS suspicion presenting with neurological symptoms and/or acute neurosensory signs, and positive T. Pallidum Hemagglutinations Assay (TPHA)/T. pallidum particle agglutination assay (TPPA) serology and CSF-TPHA/TPPA ≥320, and either CSF-leucocytes >5 cells/mm3 and/or CSF-protein >0.45 g/L and/or a reactive CSF-venereal disease research laboratory (VDRL)/rapid plasma reagin (RPR) test. NS2 included patients with suspected NS presenting with acute ocular and/or otologic symptoms, and positive TPHA/TPPA serology, and a favourable response to NS treatment. Controls were patients diagnosed with any other central nervous system (CNS) pathologies and with positive TPHA/TPPA serology.

RESULTS

The study included 71 NS (43 NS1 and 28 NS2) and 110 controls. With a threshold of ≥1.7, sensitivity and specificity of the specific AI test were 90.7% (CI 77.7 to 97.4) and 100% (CI 96.7 to 100.0), respectively, for NS1 and 14.3% (CI 4 to 32.7) and 100% (CI 96.7 to 100.0) for NS2. In patients suspected of NS with a CNS involvement (NS1 group), NS could be confirmed by the positivity of this specific AI.

CONCLUSIONS

Measurement of an intrathecal synthesis index of specific anti-T. pallidum IgG in patients with CSF inflammatory signs appears to be a valuable diagnostic test. However, in otic or ocular syphilis, presenting few CSF abnormalities, AI is not sufficient alone to confirm NS diagnosis.

TRIAL REGISTRATION

Swiss Association of Research Ethics Committees number 2019-00232.

Vaccination against tick-borne encephalitis elicits a detectable NS1 IgG antibody response

Vaccine-induced protection against tick-borne encephalitis virus (TBEV) is mediated by antibodies to the viral particle/envelope protein. The detection of non-structural protein 1 (NS1) specific antibodies has been suggested as a marker indicative of natural infections. However, recent work has shown that TBEV vaccines contain traces of NS1, and immunization of mice induced low amounts of NS1-specific antibodies. In this study, we investigated if vaccination induces TBEV NS1-specific antibodies in humans. Healthy army members (n = 898) were asked to fill in a questionnaire relating to flavivirus vaccination or infection, and blood samples were collected. In addition, samples of 71 suspected acute TBE cases were included. All samples were screened for the presence of TBEV NS1-specific IgG antibodies using an in-house developed ELISA. Antibodies were quantified as percent positivity in reference to a positive control. For qualitative evaluation, cut-off for positivity was defined based on the mean OD of the lower 95% of the vaccinated individuals + 3 SD. We found significantly higher NS1-specific IgG antibody titers (i.e., quantitative evaluation) in individuals having received 2, 3, or 4 or more vaccine doses than in non-vaccinated individuals. Similarly, the percentage of individuals with a positive test result (i.e., qualitative evaluation) was higher in individuals vaccinated against tick-borne encephalitis than in unvaccinated study participants. Although NS1-specific IgG titers remained at a relatively low level when compared to TBE patients, a clear distinction was not always possible. Establishing a clear cut-off point in detection systems is critical for NS1-specific antibodies to serve as a marker for distinguishing the immune response after vaccination and infection.

Anti-Treponema pallidum IgA response as a potential diagnostic marker of syphilis

OBJECTIVES

Serological tests for syphilis detect mainly total Ig, IgM or IgG antibodies. We aimed to evaluate the specific IgA response in syphilis patients according to disease stage.

METHODS

A serum IgA-enzyme immunoassay was developed using commercially available microplates coated with recombinant treponemal antigens and an anti-IgA-conjugate. To define a cut-off, we used 91 syphilis positive and 136 negative sera previously defined by the rapid plasma reagin and the Treponema pallidum particle agglutination results. Then we determined the intra- and inter-assay precisions, diagnostic sensitivity according to the clinical stage (in 66, 55 and 42 sera from primary, secondary and latent syphilis patients, respectively) and specificity (in 211 sera from people with conditions different to syphilis). IgA values were further measured in 71 sera from patients with previously treated syphilis.

RESULTS

The newly developed IgA-enzyme immunoassay showed a good discrimination between negative and positive samples with intra- and inter-assay variation coefficients <20%. The sensitivity was 80.3% (95% CI, 70.0-90.6), 100.0% (95% CI, 99.1-100.0) and 95.2% (95% CI, 87.6-100.0) in primary, secondary and latent syphilis, respectively, and the specificity was 98.1% (95% CI, 96.0-100.0). Further, IgA values were negative in 61.3% (38/62) of patients with previously treated syphilis.

DISCUSSION

Our findings suggest serum IgA as a sensitive and specific marker of syphilis and its detection could be used as a screening assay for active infection. Further evaluation is needed in prospective longitudinal field studies.

IVDR: Analysis of the Social, Economic, and Practical Consequences of the Application of an Ordinance of the In Vitro Diagnostic Ordinance in Switzerland

IVDR regulation represents a major challenge for diagnostic microbiology laboratories. IVDR complicates a broad range of aspects and poses a risk given the high diversity of pathogens (including rare but highly virulent microbes) and the large variety of samples submitted for analysis. The regular emergence of new pathogens (including Echovirus E-11, Adenovirus 41, Monkeypox virus, Alongshan virus, and Enterovirus D68, as recent examples in Europe in the post SARS-CoV-2 era) is another factor that makes IVDR regulation risky, because its detrimental effect on production of in-house tests will negatively impact knowledge and expertise in the development of new diagnostic tests. Moreover, such regulations negatively impact the availability of diagnostic tests, especially for neglected pathogens, and has a detrimental effect on the overall costs of the tests. The increased regulatory burden of IVDR may thereby pose an important risk for public health. Taken together, it will have a negative impact on the financial balance of diagnostic microbiology laboratories (especially small ones). The already-high standards of quality management of all ISO-accredited and Swissmedic-authorized laboratories render IVDR law of little value, at least in Switzerland, while tremendously increasing the regulatory burden and associated costs. Eventually, patients will need to pay for diagnostic assays outside of the framework of their insurance in order to obtain a proper diagnostic assessment, which may result in social inequity. Thus, based on the risk assessment outlined above, the coordinated commission for clinical microbiology proposes adjusting the IvDO ordinance by (i) introducing an obligation to be ISO 15189 accredited and (ii) not implementing the IvDO 2028 milestone.

Quality of MALDI-TOF mass spectra in routine diagnostics: results from an international external quality assessment including 36 laboratories from 12 countries using 47 challenging bacterial strains

OBJECTIVES

Matrix assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) is a widely used method for bacterial species identification. Incomplete databases and mass spectral quality (MSQ) still represent major challenges. Important proxies for MSQ are the number of detected marker masses, reproducibility, and measurement precision. We aimed to assess MSQs across diagnostic laboratories and the potential of simple workflow adaptations to improve it.

METHODS

For baseline MSQ assessment, 47 diverse bacterial strains, which are challenging to identify by MALDI-TOF MS, were routinely measured in 36 laboratories from 12 countries, and well-defined MSQ features were used. After an intervention consisting of detailed reported feedback and instructions on how to acquire MALDI-TOF mass spectra, measurements were repeated and MSQs were compared.

RESULTS

At baseline, we observed heterogeneous MSQ between the devices, considering the median number of marker masses detected (range = [2-25]), reproducibility between technical replicates (range = [55%-86%]), and measurement error (range = [147 parts per million (ppm)-588 ppm]). As a general trend, the spectral quality was improved after the intervention for devices, which yielded low MSQs in the baseline assessment as follows: for four out of five devices with a high measurement error, the measurement precision was improved (p-values <0.001, paired Wilcoxon test); for six out of ten devices, which detected a low number of marker masses, the number of detected marker masses increased (p-values <0.001, paired Wilcoxon test).

DISCUSSION

We have identified simple workflow adaptations, which, to some extent, improve MSQ of poorly performing devices and should be considered by laboratories yielding a low MSQ. Improving MALDI-TOF MSQ in routine diagnostics is essential for increasing the resolution of bacterial identification by MALDI-TOF MS, which is dependent on the reproducible detection of marker masses. The heterogeneity identified in this external quality assessment (EQA) requires further study.

[Methicillin-resistant Staphylococcus aureus: 15 years of molecular epidemiology in Western Switzerland]

Since the introduction of antibiotics, successive waves of Staphylococcus aureus clones occurred, each one having characteristic susceptibility pattern to antibiotics and virulence factors. We report here the results of a molecular epidemiological surveillance of methicillin-resistant S. aureus (MRSA) in French-speaking Switzerland between 2006 and 2020 showing the emergence and disappearance of clones known for their international dissemination, and the sporadic appearance of other international clones. Since 2012, a marked decrease in the incidence of cases attributable to the biology of the clones and to the control measures taken in the hospitals has been observed. These results highlight the importance of continuous surveillance in order to better assess the burden of this multi-resistant pathogen in our region.

Multicenter Technical Validation of 30 Rapid Antigen Tests for the Detection of SARS-CoV-2 (VALIDATE)

During COVID19 pandemic, SARS-CoV-2 rapid antigen tests (RATs) were marketed with minimal or no performance data. We aimed at closing this gap by determining technical sensitivities and specificities of 30 RATs prior to market release. We developed a standardized technical validation protocol and assessed 30 RATs across four diagnostic laboratories. RATs were tested in parallel using the Standard Q® (SD Biosensor/Roche) assay as internal reference. We used left-over universal transport/optimum media from nasopharyngeal swabs of 200 SARS-CoV-2 PCR-negative and 100 PCR-positive tested patients. Transport media was mixed with assay buffer and applied to RATs according to manufacturer instructions. Sensitivities were determined according to viral loads. Specificity of at least 99% and sensitivity of 95%, 90%, and 80% had to be reached for 107, 106, 105 virus copies/mL, respectively. Sensitivities ranged from 43.5% to 98.6%, 62.3% to 100%, and 66.7% to 100% at 105, 106, 107 copies/mL, respectively. Automated assay readers such as ExDia or LumiraDx showed higher performances. Specificities ranged from 88.8% to 100%. Only 15 of 30 (50%) RATs passed our technical validation. Due to the high failure rate of 50%, mainly caused by lack of sensitivity, we recommend a thorough validation of RATs prior to market release.

PCR performance in the SARS-CoV-2 Omicron variant of concern?

The new SARS-CoV-2 Omicron variant (B.1.1.529) has been recently declared a Variant of Concern due to a series of important mutations in the viral spike protein and especially in the receptor-binding domain. While investigations into the spread of this new variant are ongoing, the first cases have been detected in Switzerland. Important questions have been raised: (1) Will the PCR assays commonly used to detect SARS-CoV-2 still work for the Omicron variant? (2) Can specific PCR features, e.g. S-gene dropout, be used to identify potential Omicron samples? In this minireview we provide current knowledge on the Omicron variant and guidance on its PCR validation.

A Comparative Study of Real-Time RT-PCR-Based SARS-CoV-2 Detection Methods and Its Application to Human-Derived and Surface Swabbed Material

Real-time RT-PCR remains a gold standard in the detection of various viral diseases. In the coronavirus 2019 pandemic, multiple RT-PCR-based tests were developed to screen for viral infection. As an emergency response to increasing testing demand, we established a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) PCR diagnostics platform for which we compared different commercial and in-house RT-PCR protocols. Four commercial, one customized, and one in-house RT-PCR protocols were evaluated with 92 SARS-CoV-2-positive and 92 SARS-CoV-2-negative samples. Furthermore, economical and practical characteristics of these protocols were compared. In addition, a highly sensitive digital droplet PCR (ddPCR) method was developed, and application of RT-PCR and ddPCR methods on SARS-CoV-2 environmental samples was examined. Very low limits of detection (1 or 2 viral copies/μL), high sensitivities (93.6% to 97.8%), and high specificities (98.7% to 100%) for the tested RT-PCR protocols were found. Furthermore, the feasibility of downscaling two of the commercial protocols, which could optimize testing capacity, was demonstrated. Tested commercial and customized RT-PCR detection kits show very good and comparable sensitivity and specificity, and the kits could be further optimized for use on SARS-CoV-2 viral samples derived from human and surface swabbed samples.

Implementing SARS-CoV-2 Rapid Antigen Testing in the Emergency Ward of a Swiss University Hospital: The INCREASE Study

Following the Swiss Federal Office of Public Health (FOPH) authorization of the rapid antigen test (RAT), we implemented the use of the RAT in the emergency ward of our university hospital for patients' cohorting. RAT triaging in association with RT-PCR allowed us to promptly isolate positive patients and save resources. Among 532 patients, overall sensitivities were 48.3% for Exdia and 41.2% for Standard Q®, PanbioTM and BD Veritor™. All RATs exhibited specificity above 99%. Sensitivity increased to 74.6%, 66.2%, 66.2% and 64.8% for Exdia, Standard Q®, PanbioTM and BD Veritor™, respectively, for viral loads above 105 copies/mL, to 100%, 97.8%, 96.6% and 95.6% for viral loads above 106 copies/mL and 100% for viral loads above 107 copies/mL. Sensitivity was significantly higher for patients with symptoms onset within four days (74.3%, 69.2%, 69.2% and 64%, respectively) versus patients with the evolution of symptoms longer than four days (36.8%, 21.1%, 21.1% and 23.7%, respectively). Among COVID-19 asymptomatic patients, sensitivity was 33%. All Immunoglobulin-A-positive patients resulted negative for RAT. The RAT might represent a useful resource in selected clinical settings as a complementary tool in RT-PCR for rapid patient triaging, but the lower sensitivity, especially in late presenters and COVID-19 asymptomatic subjects, must be taken into account.

SARS-CoV-2 N501Y Introductions and Transmissions in Switzerland from Beginning of October 2020 to February 2021-Implementation of Swiss-Wide Diagnostic Screening and Whole Genome Sequencing

The rapid spread of the SARS-CoV-2 lineages B.1.1.7 (N501Y.V1) throughout the UK, B.1.351 (N501Y.V2) in South Africa, and P.1 (B.1.1.28.1; N501Y.V3) in Brazil has led to the definition of variants of concern (VoCs) and recommendations for lineage specific surveillance. In Switzerland, during the last weeks of December 2020, we established a nationwide screening protocol across multiple laboratories, focusing first on epidemiological and microbiological definitions. In January 2021, we validated and implemented an N501Y-specific PCR to rapidly screen for VoCs, which are then confirmed using amplicon sequencing or whole genome sequencing (WGS). A total of 13,387 VoCs have been identified since the detection of the first Swiss case in October 2020, with 4194 being B.1.1.7, 172 B.1.351, and 7 P.1. The remaining 9014 cases of VoCs have been described without further lineage specification. Overall, all diagnostic centers reported a rapid increase of the percentage of detected VOCs, with a range of 6 to 46% between 25 to 31 of January 2021 increasing towards 41 to 82% between 22 to 28 of February. A total of 739 N501Y positive genomes were analysed and show a broad range of introduction events to Switzerland. In this paper, we describe the nationwide coordination and implementation process across laboratories, public health institutions, and researchers, the first results of our N501Y-specific variant screening, and the phylogenetic analysis of all available WGS data in Switzerland, that together identified the early introduction events and subsequent community spreading of the VoCs.

Rejection of the name Borreliella and all proposed species comb. nov. placed therein

Rejection (nomen rejiciendum) of the name Borreliella and all new combinations therein is being requested on grounds of risk to human health and patient safety (Principle 1, subprinciple 2 and Rule 56a) and violation to aim for stability of names, to avoid useless creation of names (Principle 1, subprinciple 1 and 3) and that names should not be changed without sufficient reason (Principle 9 of the International Code of Nomenclature of Prokaryotes).

[Lyme Borreliosis in 2020 practice, from a dermatological point of view]

Lyme borreliosis is a frequent disease in Switzerland. Due to the increasing number of symptoms attributed to this infection, the diagnostic is often controversy between different specialists and is often a subject of discussion. The diagnostic of Lyme disease lays particularly on the knowledge of cutaneous signs which are the only specific. Despite recent scientific progress, microbiological diagnostic is still delicate and serological tests currently used do not differentiate between an active infection versus a serological marker. Here we describe the different clinical presentations of Lyme disease diagnosis and management procedures according to stages of evolution.

A first insight into the genomic diversity of Leptospira strains isolated from patients in Cuba

Leptospirosis is a neglected disease causing severe infections in humans and animals. Due in part to misdiagnosis, this infectious disease results in nearly 60,000 deaths per year around the globe. This study represents the first effort to describe the diversity of pathogenic Leptospira in Cuba based on whole-genome sequencing. We have collected nineteen whole-blood samples from patients that were diagnosed as having leptospirosis between 2008 and 2012 in Cuba. In addition, we have enhanced our sample set by three historical strains that were used for the development of a human vaccine in 1990s. The Leptospira strains were grown and serotyped by the microscopic agglutination test, and the draft genomes were generated by NGS (Illumina). Subsequently, the core genomes were analyzed and compared to the genetic data available from other Caribbean islands and countries in Central America. Core genome Multi-locus Sequence Typing (cgMLST) revealed four different core genome clonal groups (cgCGs), with the highest number of samples belonging to L. interrogans, followed by L. borgpetersenii and L. kirschneri. All cgCGs that were found in Cuba have been also identified from multiple origins across the globe, except in neighbor countries and Central America. Serotyping divided the samples into the serogroups Canicola, Ballum and Pomona. The most frequent cgCGs, cgCG28, associated with serogroup Canicola, and cgCG15, associated with serogroup Ballum, have also been identified from samples isolated from dogs, rodents, and pigs; suggesting that these hosts represent the major source of human infection in Cuba. The vaccine strains did not significantly differ from the recent patient isolates. However, the increasing prevalence of samples belonging to the serogroup Ballum combined with the fact that the available vaccine in Cuba represents inactivated Leptospira belonging to serogroups other than Ballum, should be a valuable information for the National and Regional Leptospirosis Control Programs.

Multilocus Sequence Typing of Treponema pallidum subsp. pallidum in Cuba From 2012 to 2017

BACKGROUND

The increased prevalence of syphilis in Cuba prompted us to map the circulating Treponema pallidum subsp. pallidum allelic profiles in this geographic region.

METHODS

Samples were collected from 2012 to 2017, from 83 male patients with ulcers or skin lesions, and were examined using multilocus sequence typing. Additionally, we analyzed the 23S rDNA and 16S rDNA regions for the presence of possible mutations leading to macrolide and tetracycline resistance.

RESULTS

Among 94% of fully typed strains, we found 7 different allelic profiles, of which 4 had not been previously described. More than 87% of patients were infected with the T. pallidum SS14-like group and only 8.2% with T. pallidum Nichols-like group. As in other countries, the 1.3.1 allelic profile (ie, SS14-like) was the most common. In addition, 1 of the newly described allelic profiles represents T. pallidum strains that arose by recombination events between members of different T. pallidum subgroups. More than 90% of patients were infected with treponemes harboring the A2058G mutation. However, we found no potential tetracycline-resistant T. pallidum mutations.

CONCLUSIONS

Our results suggest that, in Cuba, tetracycline antibiotics could be used to treat syphilis in penicillin-allergic patients instead of macrolides.

Phenotypic and Genomic Analyses of Burkholderia stabilis Clinical Contamination, Switzerland

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.

Antimicrobial susceptibility profiles of anaerobic bacteria, isolated from human clinical specimens, within different European and surrounding countries. A joint ESGAI study

OBJECTIVES

Studies on the antimicrobial susceptibility profile of anaerobic bacteria are underrepresented in the literature. Within this study we aim to give an extensive overview of the differences in antimicrobial susceptibility profiles between different European and surrounding countries.

METHODS

Minimal inhibitory concentration (MIC) data of different antibiotics were collected from 10 participating laboratories, representing an equal number of countries. All MIC's were determined using Etest, according to the protocol used by the participating laboratory. Anaerobic genera represented by at least 10 clinical isolates were included in the study.

RESULTS

Each country tested different antibiotics, sometimes depending on the kind of infection and/or the anaerobic species isolated. All countries tested clindamycin and metronidazole. Resistance rates differed remarkably between the different countries. Especially in Kuwait, resistance was high for all tested antibiotics. Unexpected metronidazole resistance was observed for Finegoldia magna isolates, Peptoniphilus isolates and Eggerthella lenta isolates.

CONCLUSIONS

Due to the extensive differences in antimicrobial susceptibility profile of anaerobic bacteria isolated within different countries, we strongly recommend to perform this kind of study on a regular basis.

Accuracy of PCR and serological testing for the diagnosis of primary syphilis: Both tests are necessary

Syphilis, caused by the spirochete Treponema pallidum subspecies pallidum, is a rising global public health concern and laboratory diagnostics remain challenging. Especially during early disease, rapid and accurate diagnosis is crucial to ensure patients and their contacts receive timely treatment to eradicate infection and prevent further transmission. In this prospective observational study, we evaluated the performance of polymerase chain reaction (PCR) and serological testing for the diagnosis of primary syphilis by evaluating anogenital swabs and sera from 178 Cuban patients presenting with ulcers. Three different PCR assays were evaluated targeting polA, tpp47 and 16S rDNA loci. Sera were evaluated with venereal disease research laboratory (VDRL) and T. pallidum hemagglutination (TPHA) assays. Assuming both methods were confirmatory, our data showed that PCR and serology did not correlate well (agreement = 52.3%, kappa 0.0512, 95% CI −0.0928–0.1951, p = 0.496). The sensitivities, specificities, positive and negative predictive values of the PCR assays were 76.1%, 100%, 100% and 57.9%, respectively, while the values for serology were 62.5%, 100%, 100% and 45.2%, respectively. The combination of PCR and serology can offer valuable information for the diagnosis of syphilis in patients presenting with anogenital ulceration avoiding further clinical complications and disease transmission.

Adaptive Strategies in a Poly-Extreme Environment: Differentiation of Vegetative Cells in Serratia ureilytica and Resistance to Extreme Conditions

Poly-extreme terrestrial habitats are often used as analogs to extra-terrestrial environments. Understanding the adaptive strategies allowing bacteria to thrive and survive under these conditions could help in our quest for extra-terrestrial planets suitable for life and understanding how life evolved in the harsh early earth conditions. A prime example of such a survival strategy is the modification of vegetative cells into resistant resting structures. These differentiated cells are often observed in response to harsh environmental conditions. The environmental strain (strain Lr5/4) belonging to Serratia ureilytica was isolated from a geothermal spring in Lirima, Atacama Desert, Chile. The Atacama Desert is the driest habitat on Earth and furthermore, due to its high altitude, it is exposed to an increased amount of UV radiation. The geothermal spring from which the strain was isolated is oligotrophic and the temperature of 54°C exceeds mesophilic conditions (15 to 45°C). Although the vegetative cells were tolerant to various environmental insults (desiccation, extreme pH, glycerol), a modified cell type was formed in response to nutrient deprivation, UV radiation and thermal shock. Scanning (SEM) and Transmission Electron Microscopy (TEM) analyses of vegetative cells and the modified cell structures were performed. In SEM, a change toward a circular shape with reduced size was observed. These circular cells possessed what appears as extra coating layers under TEM. The resistance of the modified cells was also investigated, they were resistant to wet heat, UV radiation and desiccation, while vegetative cells did not withstand any of those conditions. A phylogenomic analysis was undertaken to investigate the presence of known genes involved in dormancy in other bacterial clades. Genes related to spore-formation in Myxococcus and Firmicutes were found in S. ureilytica Lr5/4 genome; however, these genes were not enough for a full sporulation pathway that resembles either group. Although, the molecular pathway of cell differentiation in S. ureilytica Lr5/4 is not fully defined, the identified genes may contribute to the modified phenotype in the Serratia genus. Here, we show that a modified cell structure can occur as a response to extremity in a species that was previously not known to deploy this strategy. This strategy may be widely spread in bacteria, but only expressed under poly-extreme environmental conditions.

Prevalence of Anaplasma phagocytophilum and Coxiella burnetii in Ixodes ricinus ticks in Switzerland: an underestimated epidemiologic risk

Ticks are vectors of several microorganisms responsible for infectious diseases in human and animals, such as Anaplasma phagocytophilum and Coxiella burnetii. In this study, we investigated the prevalence of these two bacteria in 62 889 Ixodes ricinus ticks in selected regions covering all Switzerland. A high prevalence of 11.9% of A. phagocytophilum DNA was observed by real-time PCR on 8534 pools of ticks. This pool prevalence corresponds to an estimated prevalence of 1.71% in individual tick. A total of 144 of the 171 collection sites (84.2%) were positive for the presence of A. phagocytophilum, and these sites were homogenously distributed throughout Switzerland. Such prevalence and geographical distribution underline the risk of human and animal exposure to A. phagocytophilum and highlight the need to assess the epidemiology and clinical diagnosis of human and animal anaplasmosis in Switzerland. However, DNA of C. burnetii was never found in any tick pool. This absence suggests a very low role of I. ricinus ticks as vector and reservoir of C. burnetii in Switzerland, and it supports previous reports demonstrating the role of sheep and goats in the epidemiology of Q fever. However, considering its pathogenic potential, it is necessary to keep monitoring for the possible reemergence of this bacterium in ticks in the future.

Aerococcus urinae and Aerococcus sanguinicola: Susceptibility Testing of 120 Isolates to Six Antimicrobial Agents Using Disk Diffusion (EUCAST), Etest, and Broth Microdilution Techniques

BACKGROUND

Aerococcus urinae and Aerococcus sanguinicola are relatively newcomers and emerging organisms in clinical and microbiological practice. Both species have worldwide been associated with urinary tract infections. More rarely cases of bacteremia/septicemia and infective endocarditis have been reported. Treatment options are therefore important. Just recently, European recommendations on susceptibility testing and interpretive criteria have been released.

OBJECTIVE

In this investigation 120 A. urinae and A. sanguinicola isolates were tested for susceptibility to six antimicrobial agents: Penicillin, cefotaxime, meropenem, vancomycin, linezolid, and rifampicin.

METHODS

Three susceptibility testing methods were used; disk diffusion according to The European Committee on Antimicrobial Susceptibility Testing (EUCAST) standardized disk diffusion methodology and MIC determination with Etest and broth microdilution (BMD). All testing was performed with EUCAST media for fastidious organisms.

RESULTS

Data obtained in this study were part of the background data for establishing EUCAST breakpoints. MIC values obtained by Etest and BMD were well correlated with disk diffusion results.

CONCLUSION

All isolates were found susceptible to all six antimicrobial agents: penicillin, cefotaxime, meropenem, vancomycin, linezolid, and rifampicin.

Very-late-onset cytomegalovirus disease: a case-report and review of the literature

Background

Cytomegalovirus (CMV) infection remains one of the most common and feared complications of transplantation, justifying prophylaxis or preemptive strategies guided by donor and recipient CMV serostatus. In case of seronegative donor and recipient (D−/R−), no prophylaxis is recommended. Late-onset CMV disease is usually defined as occurring after prophylaxis discontinuation in D+/R− transplant patients.

Case presentation

We are reporting the case of a D−/R− kidney Caucasian transplant recipient presenting with CMV primoinfection 12 years after renal transplant, and discuss the role of a secondary prophylaxis so late after transplantation.

Conclusions

Primary infections leading to late-onset CMV disease in transplant patients remain rare. Recurrent disease has been described in as many as one-third of these patients. A systematic secondary prophylaxis in this particular group of patients is questionable.

In vitro antimicrobial susceptibility of Alloscardovia omnicolens and molecular mechanisms of acquired resistance

All the 31 isolates of Alloscardovia omnicolens exhibited low MICs for β-lactams, glycopeptides, linezolid, tetracyclines, and cotrimoxazole. One strain showed MICs ≥256μg/mL for both erythromycin and clindamycin with a single point mutation in 23S rRNA. One strain likely had acquired fluoroquinolone resistance associated with a unique mutation in ParC.

[Lyme serology: what's the deal?]

Lyme serology is too commonly prescribed in absence of a well established differential diagnosis. Its low positive predictive value is very often unusable. IgG and IgM positive results are tricky to interpret and often lead to clinically unjustified antibiotherapy. Clinical and epidemiological approaches must integrate the serological results. The microbiologist should have all available information to be able to communicate an appropriate interpretation with the results. This way can propose adequate analysis leading to higher predictive values. We present essentials and pitfalls of the Lyme serology, suggesting new possibilities and reminding physicians as to which tests have not yet brought any proof of benefit to the patient.

Serological signature of tick-borne pathogens in Scandinavian brown bears over two decades

BACKGROUND

Anthropogenic disturbances are changing the geographic distribution of ticks and tick-borne diseases. Over the last few decades, the tick Ixodes ricinus has expanded its range and abundance considerably in northern Europe. Concurrently, the incidence of tick-borne diseases, such as Lyme borreliosis and tick-borne encephalitis, has increased in the human populations of the Scandinavian countries.

METHODS

Wildlife populations can serve as sentinels for changes in the distribution of tick-borne diseases. We used serum samples from a long-term study on the Scandinavian brown bear, Ursus arctos, and standard immunological methods to test whether exposure to Borrelia burgdorferi sensu lato, the causative agent of Lyme borreliosis, and tick-borne encephalitis virus (TBEV) had increased over time. Bears had been sampled over a period of 18 years (1995-2012) from a southern area, where Ixodes ricinus ticks are present, and a northern area where ticks are uncommon or absent.

RESULTS

Bears had high levels of IgG antibodies against B. burgdorferi sensu lato but not TBEV. Bears at the southern area had higher values of anti-Borrelia IgG antibodies than bears at the northern area. Over the duration of the study, the value of anti-Borrelia IgG antibodies increased in the southern area but not the northern area. Anti-Borrelia IgG antibodies increased with the age of the bear but declined in the oldest age classes.

CONCLUSIONS

Our study is consistent with the view that ticks and tick-borne pathogens are expanding their abundance and prevalence in Scandinavia. Long-term serological monitoring of large mammals can provide insight into how anthropogenic disturbances are changing the distribution of ticks and tick-borne diseases.

In vitro antimicrobial susceptibility of Helcococcus kunzii and molecular analysis of macrolide and tetracycline resistance

Thanks to the recent advent of matrix-assisted laser desorption/ionisation time-of-flight (MALDI-TOF) technology, Helcococcus kunzii is now easily identifiable and considered as an opportunistic pathogen. However, data about antimicrobial susceptibilities remain very limited. The aim of the study was, then, to assess its in vitro susceptibility to 18 antimicrobial agents and to investigate the genetic basis of macrolide and tetracycline resistance. Thirty-nine human clinical isolates of H. kunzii collected from 2008 to 2013 were studied, as well as the type strain ATCC 51366(T). Minimum inhibitory concentrations (MICs) of penicillin G, amoxicillin, cefotaxime, imipenem, gentamicin, erythromycin, clindamycin, quinupristin-dalfopristin, ciprofloxacin, levofloxacin, tetracycline, tigecycline, vancomycin, teicoplanin, linezolid, daptomycin, cotrimoxazole and rifampin were determined by the microdilution method. Screening for macrolide [erm(A) including erm(TR), erm(B), erm(C), erm(F), erm(T), erm(X), msr(A) and mef(A)] and tetracycline [tet(L), tet(M) and tet(O)] resistance genes was performed, as well as the detection of mutations in 23S rRNA. Except for one strain resistant to cefotaxime, all strains were categorised as susceptible to β-lactams, glycopeptides, linezolid, daptomycin and tigecycline. Whereas ciprofloxacin and gentamicin exhibited limited activity, 95% of strains were categorised as susceptible to levofloxacin. Concerning erythromycin, a bimodal distribution was observed, with 29 'wild-type' strains (MICs from 0.25 to 2 mg/L) and 11 'resistant' strains (MICs ≥ 256 mg/L), including ten harbouring erm(TR). Two isolates exhibited acquired tetracycline resistance (MICs of 16 mg/L) by the production of tet(M). This large study on the in vitro antimicrobial susceptibility of H. kunzii suggests that β-lactams (especially penicillins) should be preferred for the treatment.

Post liposuction infections by rapidly growing mycobacteria

Rapidly growing mycobacteria (RGM) are recognized agents of surgical site infections. Recently, RGM skin and soft tissue infections have been increasingly reported. As symptoms, clinical signs and disease latency remain non-specific and microbiological detection requires targeted growth media, RGM diagnosis remains challenging for clinicians. Appropriate management is often delayed due to lack of awareness of these infections. RGM infections after plastic surgery have also been described in the setting of interventions performed in developing countries, a growing phenomenon commonly known as medical tourism. We describe a case of Mycobacterium chelonae/abscessus infection following liposuction and liposculpture procedures performed in the Dominican Republic and review the literature on this subject.

Erm(X)-mediated resistance to macrolides, lincosamides and streptogramins in Actinobaculum schaalii

OBJECTIVES

Actinobaculum schaalii is a Gram-positive bacillus increasingly reported as a causative agent of urinary tract infections as well as invasive infections, mainly in the elderly and patients with underlying urological conditions. Since little is known about the molecular basis of antimicrobial resistance in A. schaalii, the aim of this study was to investigate resistance to macrolides, lincosamides and streptogramins (MLS) in this emerging pathogen.

METHODS

A total of 32 A. schaalii clinical isolates from France and Switzerland were studied. MICs of erythromycin, spiramycin, lincomycin, clindamycin and quinupristin/dalfopristin were determined by the agar dilution method. Resistance genes erm(A), erm(B), erm(C), erm(F), erm(G), erm(X), msr(A) and mef(A) were screened by PCR. The genetic environment was determined by random cloning and PCR mapping.

RESULTS

Out of 32 isolates tested, 21 were highly resistant to erythromycin, spiramycin, lincomycin and clindamycin (MICs >256 mg/L), whereas 11 exhibited low MICs (MICs < 0.12 mg/L). On the other hand, quinupristin/dalfopristin remained active against all the isolates. An inducible MLSB resistance phenotype was noted in all cases. The erm(X) gene was detected among all resistant strains, whereas none was detected in susceptible strains. Analysis of genetic support and environment revealed that erm(X) was probably part of the chromosome of A. schaalii.

CONCLUSIONS

This study is the first molecular characterization of MLS resistance in A. schaalii. In all cases, it was due to the presence of erm(X), a methylase gene previously identified in other clinically relevant Gram-positive bacilli.

Prevalence of antibodies to Borrelia burgdorferi sensu stricto in humans from a Cuban village

Lyme disease has not been officially reported in Cuba. However, clinical cases have been serologically reported. Seroprevalence survey of Borrelia burgdorferi sensu stricto antibodies in humans in the country has not been conducted.

OBJECTIVE

To estimate the prevalence of borrelial antibodies in inhabitants of a village with historically high level of tick infestation.

METHODS

Serum specimens from 247 persons randomly selected from the population of the village were examined by IgG Western blot using B31 strain for estimating the prevalence of antibodies profile.

RESULTS

A seroprevalence value interval (95% CI) of 0.6%-7.2% was estimated for the studied population. The prevalent borrelial protein bands on immunoblots were 41, 72, 90/93, 34, 47, 60, 58, 56, 65/66 and 31 kDa in a decreasing order of significance.

CONCLUSION

These results support the previous serological findings, suggesting the presence of this borreliosis in Cuba.

[Traps in infectious serology]

The role of serology in infectious disease diagnosis is highlighted by HIV and viral hepatitis diagnosis developed since the 80's. However, long before these recent developments serum reactivity played its role in diagnosing, active or previous severe bacterial infection in diseases such as typhoid fever (Widal), brucellosis (Wright test), syphilis (VDRL, Wassermann test), typhus (Weil-Felix test) etc. From early infection to immunity, serology analyzes the patient's immunological memory enabling the fight against infections. The resulting information depends on the type of pathogen, the site of infection, the host and the stage of disease. Together with the direct tests for the detection of pathogens, serological tests form the basis of microbiological diagnosis. To better understand the utility of serology, we will provide an overview and show its pitfalls.

Actinobaculum schaalii: clinical observation of 20 cases

Actinobaculum schaalii is a new species that has so far been isolated from human blood, urine and pus. Its importance has probably been underestimated and other Actinobaculum spp. may also have been underdiagnosed. This retrospective study comprises all known cases of A. schaalii infections identified since 2004 in the canton of Neuchâtel (170,000 inhabitants), Switzerland. Strains were cultivated and isolated in the bacteriology laboratory using its routine procedure. Identification included a Rapid ID 32 A strip (bioMérieux) and 16S rRNA gene sequencing. Twenty-one positive samples were found in 19 patients (11 male, 8 female) of all ages (range 16-91 years): 10 from urine (50%), six from blood (30%), one from both blood and urine (5%), and three from pus (15%). Thirteen out of 17 (76%) cases with either blood or urine specimens had underlying genitourinary tract pathologies. When urine cultures were positive for A. schaalii, leucocytes were found in all samples (10/10, 100%) but all nitrite tests were negative (10/10, 100%). The onset of appropriate treatment was delayed due to the diminished sensitivity of A. schaalii to the antibiotics commonly used for UTIs (i.e. ciprofloxacin and trimethoprim/sulfamethoxazole) and to the delay in microbiological diagnosis. A. schaalii should specifically be searched in all cases of leukocyturia with a negative nitrite test but with Gram-positive rods in the Gram stain, in patients with underlying genitourinary tract pathology, instead of dismissing these findings as clinically irrelevant colonization by coryneform bacteria. This infection may be much more common than previously thought.

In vitro susceptibility of Actinobaculum schaalii to 12 antimicrobial agents and molecular analysis of fluoroquinolone resistance

OBJECTIVES

To assess the in vitro susceptibility of Actinobaculum schaalii to 12 antimicrobial agents as well as to dissect the genetic basis of fluoroquinolone resistance.

METHODS

Forty-eight human clinical isolates of A. schaalii collected in Switzerland and France were studied. Each isolate was identified by 16S rRNA sequencing. MICs of amoxicillin, ceftriaxone, gentamicin, vancomycin, clindamycin, linezolid, ciprofloxacin, levofloxacin, moxifloxacin, co-trimoxazole, nitrofurantoin and metronidazole were determined using the Etest method. Interpretation of results was made according to EUCAST clinical breakpoints. The quinolone-resistance-determining regions (QRDRs) of gyrA and parC genes were also identified and sequence analysis was performed for all 48 strains.

RESULTS

All isolates were susceptible to amoxicillin, ceftriaxone, gentamicin, clindamycin (except three), vancomycin, linezolid and nitrofurantoin, whereas 100% and 85% were resistant to ciprofloxacin/metronidazole and co-trimoxazole, respectively. Greater than or equal to 90% of isolates were susceptible to the other tested fluoroquinolones, and only one strain was highly resistant to levofloxacin (MIC ≥32 mg/L) and moxifloxacin (MIC 8 mg/L). All isolates that were susceptible or low-level resistant to levofloxacin/moxifloxacin (n = 47) showed identical GyrA and ParC amino acid QRDR sequences. In contrast, the isolate exhibiting high-level resistance to levofloxacin and moxifloxacin possessed a unique mutation in GyrA, Ala83Val (Escherichia coli numbering), whereas no mutation was present in ParC.

CONCLUSIONS

When an infection caused by A. schaalii is suspected, there is a risk of clinical failure by treating with ciprofloxacin or co-trimoxazole, and β-lactams should be preferred. In addition, acquired resistance to fluoroquinolones more active against Gram-positive bacteria is possible.

[Diseases and pathogenic agents transmitted by ticks in Switzerland]

Among the 20 tick species described in Switzerland, Ixodes ricinus, the most frequent one, is implicated in the transmission of pathogenic agents. Lyme borreliosis and tick-borne encephalitis (TBE) are the major tick-borne diseases transmitted to human. Presently 5 Borrelia species, belonging to the group Borrelia burgdorferi, are recognized as human pathogens. The risks of infection depend on the stage of the vector, the multiple hosts, the pathogenic agent, as well as human behavior in nature. The detection of other pathogenic agents in ticks: Anaplasma, Babesia and Rickettsia predispose to infections or co-infections. Results of sero-epidemiologic studies suggest human infections. Active surveillance by physicians is necessary and clinical studies are required to evaluate the importance of these infections in Switzerland.