Self-Collected Samples to Detect SARS-CoV-2: Direct Comparison of Saliva, Tongue Swab, Nasal Swab, Chewed Cotton Pads and Gargle Lavage

Testing for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) by RT-PCR is a vital public health tool in the pandemic. Self-collected samples are increasingly used as an alternative to nasopharyngeal swabs. Several studies suggested that they are sufficiently sensitive to be a useful alternative. However, there are limited data directly comparing several different types of self-collected materials to determine which material is preferable. A total of 102 predominantly symptomatic adults with a confirmed SARS-CoV-2 infection self-collected native saliva, a tongue swab, a mid-turbinate nasal swab, saliva obtained by chewing a cotton pad and gargle lavage, within 48 h of initial diagnosis. Sample collection was unsupervised. Both native saliva and gargling with tap water had high diagnostic sensitivity of 92.8% and 89.1%, respectively. Nasal swabs had a sensitivity of 85.1%, which was not significantly inferior to saliva (p = 0.092), but 16.6% of participants reported they had difficult in self-collection of this sample. A tongue swab and saliva obtained by chewing a cotton pad had a significantly lower sensitivity of 74.2% and 70.2%, respectively. Diagnostic sensitivity was not related to the presence of clinical symptoms or to age. When comparing self-collected specimens from different material, saliva, gargle lavage or mid-turbinate nasal swabs may be considered for most symptomatic patients. However, complementary experiments are required to verify that differences in performance observed among the five sampling modes were not attributed to collection impairment.

Continued vigilance - development of an online evaluation tool for assessing preparedness of medical facilities for biological events

OBJECTIVE

Effective response to biological events necessitates ongoing evaluation of preparedness. This study was a bilateral German-Israeli collaboration aimed at developing an evaluation tool for assessing preparedness of medical facilities for biological events.

METHODS

Measurable parameters were identified through a literature review for inclusion in the evaluation tool and disseminated to 228 content experts in two modified Delphi cycles. Focus groups were conducted to identify psychosocial needs of the medical teams. Table-top and functional exercises were implemented to review applicability of the tool.

RESULTS

One hundred seventeen experts from Germany and Israel participated in the modified Delphi. Out of 188 parameters that were identified, 183 achieved a consensus of >75% of the content experts. Following comments recommended in the Delphi cycles, and feedback from focus groups and hospital exercises, the final tool consisted of 172 parameters. Median level of importance of each parameter was calculated based on ranking recommended in the Delphi process. Computerized web-based software was developed to calculate scores of preparedness for biological events.

CONCLUSION

Ongoing evaluation means, such as the tool developed in the study, can facilitate the need for a valid and reliable mechanism that may be widely adopted and implemented as quality assurance measures. The tool is based on measurable parameters and indicators that can effectively present strengths and weaknesses in managing a response to a public health threat, and accordingly, steps can be implemented to improve readiness. Adoption of such a tool is an important component of assuring public health and effective emergency management.

[Management of the influenza pandemic on a local health authority level]

In most cities and districts, the influenza pandemic of 2009 could be handled without any restrictions in providing medical care or any disturbance in public life. Despite its relatively mild course, the local public health services reached their limits of capacity. Based on nationwide regulations, the local management determines the success of the measures. Evaluating the experience on the community level offers the chance of facing future pandemics more efficiently. Press conferences, press releases, and the internet are the most reliable tools to inform the public even in terms of personnel expenses. Telephone conferences and internet platforms help to reduce time-consuming meetings. An electronic database and logbook provide up-to-date information for all parties involved and allow quick, rational, coordinated, and transparent decision-making. Local evaluation of registration data, reports on cases of illness, and the availability of hospital beds on a daily basis allow intervention at an early stage to cope with the pandemic efficiently and helps save resources. Recruitment of external personnel, e.g., for the call center and the vaccination campaign, relieves the public health employees in charge with respect to their main tasks of directing and management functions.

Multiplex real-time PCR and blood culture for identification of bloodstream pathogens in patients with suspected sepsis

Severe sepsis is increasingly a cause of death. Rapid and correct initial antimicrobial treatment reduces mortality. The aetiological agent(s) cannot always be found in blood cultures (BCs). A novel multiplex PCR test (SeptiFast (alpha version)) that allows identification of 20 bacterial and fungal species directly from blood was used, comparatively with BC, in a multicentre trial of patients with suspected bacterial or fungal sepsis. Five hundred and fifty-eight paired samples from 359 patients were evaluated. The rate of positivity was 17% for BC and 26% for SeptiFast. Ninety-six microorganisms were isolated with BC, and 186 microorganisms were identified with SeptiFast; 231 microorganisms were found by combining the two tests. Of the 96 isolates identified with BC, 22 isolates were considered to be contaminants. Of the remaining 74 non-contaminant BC isolates available for comparison with SeptiFast, 50 were identified as a species identical to the species identified with SeptiFast in the paired sample. Of the remaining 24 BC isolates for which the species, identified in the BC, could not be detected in the paired SeptiFast sample, 18 BC isolates were identified as a species included in the SeptiFast master list, and six BC isolates were identified as a species not included in the SeptiFast master list. With SeptiFast, 186 microorganisms were identified, 12 of which were considered to be contaminants. Of the 174 clinically relevant microorganisms identified with SeptiFast, 50 (29%) were detected by BC. More than half of the remaining microorganisms identified with SeptiFast (but not isolated after BC) were also found in routine cultures of other relevant samples taken from the patients. Future clinical studies should assess whether the use of SeptiFast is of significant advantage in the detection of bloodstream pathogens.

16S rRNA gene sequencing versus the API 20 NE system and the VITEK 2 ID-GNB card for identification of nonfermenting Gram-negative bacteria in the clinical laboratory

Over a period of 26 months, we have evaluated in a prospective fashion the use of 16S rRNA gene sequencing as a means of identifying clinically relevant isolates of nonfermenting gram-negative bacilli (non-Pseudomonas aeruginosa) in the microbiology laboratory. The study was designed to compare phenotypic with molecular identification. Results of molecular analyses were compared with two commercially available identification systems (API 20 NE, VITEK 2 fluorescent card; bioMérieux, Marcy l'Etoile, France). By 16S rRNA gene sequence analyses, 92% of the isolates were assigned to species level and 8% to genus level. Using API 20 NE, 54% of the isolates were assigned to species and 7% to genus level, and 39% of the isolates could not be discriminated at any taxonomic level. The respective numbers for VITEK 2 were 53%, 1%, and 46%, respectively. Fifteen percent and 43% of the isolates corresponded to species not included in the API 20 NE and VITEK 2 databases, respectively. We conclude that 16S rRNA gene sequencing is an effective means for the identification of clinically relevant nonfermenting gram-negative bacilli. Based on our experience, we propose an algorithm for proper identification of nonfermenting gram-negative bacilli in the diagnostic laboratory.

[Pneumonia induced by nocardia -- a case report]

We describe a case of lung manifestation of nocardiosis with upper lobe shrinking of the right lung in a 45 year old patient without evident signs of an immuno-compromising illness. The patient came to the hospital in a reduced general state of health with severe cough, red and brown sputum and exertional dyspnoea. X-ray pictures of the thorax showed inflammatory infiltration and shrinking of the upper left lobe of the right lung. Gram-positive, branching rods were detected in the patient's bronchial secretion with the microscope and in cultures. Nocoardia transvalensis was identified via polymerase chain reaction (PCR). The antibiotic therapy was planned according to the bacterial resistance pattern. Imipenem was administered for 5 weeks and Amikacin was added for 3 weeks in the 3 (rd) week of therapy. The patient left the hospital in a good general state of health. There was no relapse.

Non-Surgical Periodontal Therapy With Adjunctive Topical Doxycycline: A Double-Masked, Randomized, Controlled Multicenter Study. II. Microbiological Results

BACKGROUND

Topical application of active substances offers an additional option in periodontal therapy. The aim of this study was to examine the influence of the administration of a novel, biodegradable 14% doxycycline gel on microbiological findings, in connection with scaling and root planing.

METHODS

One hundred ten patients in three centers (Frankfurt and Heidelberg, Germany; Nijmegen, The Netherlands) with moderate to advanced periodontitis were evaluated in this randomized, double-masked, split-mouth clinical trial. In each patient, three test teeth were randomly assigned to one of three treatment modalities: 1) scaling and root planing (SRP) alone; 2) SRP with subgingival placebo gel (VEH); or 3) SRP and 14% doxycycline gel (DOX). Subgingival plaque samples were analyzed at baseline and 3 and 6 months after therapy for Actinobacillus actinomycetemcomitans (A.a.), Tannerella forsythensis (T.f.), Porphyromonas gingivalis (P.g.), and Treponema denticola (T.d.) using a RNA probe. Samples from 10 patients were tested for resistance against doxycycline, amoxicillin/clavulanic acid, cefoxitin, clindamycin, and metronidazole using agar diffusion testing.

RESULTS

The largest decrease in pathogens was found after 3 months, with the most pronounced differences between DOX and SRP (P <0.05). At 6 months, pathogens were still reduced markedly in all groups. Treatment results were consolidated for VEH and DOX, with a slight deterioration for SRP (DOX versus SRP: P <0.001). Resistance was observed to amoxycillin/clavulanic acid, cefoxitin, clindamycin, and metronidazole (four isolates) but not to doxycycline.

CONCLUSION

The addition of subgingival instillation of a 14% doxycycline gel resulted in pronounced reduction of periodontal pathogens after 3 months and stabilizing results up to 6 months after therapy. Resistance to doxycycline was not induced.

Biological cost of rifampin resistance from the perspective of Staphylococcus aureus

Resistance determinants that interfere with normal physiological processes in the bacterial cell usually cause a reduction in biological fitness. Fitness assays revealed that 17 of 18 in vitro-selected chromosomal mutations within the rpoB gene accounting for rifampin resistance in Staphylococcus aureus were associated with a reduction in the level of fitness. There was no obvious correlation between the level of resistance to rifampin and the level of fitness loss caused by rpoB mutations. Among 23 clinical rifampin-resistant S. aureus isolates from six countries, only seven different rpoB genotypes could be identified, whereby the mutation 481His-->Asn was present in 21 (91%) of these 23 isolates. The mutation 481His-->Asn, in turn, which confers low-level rifampin resistance on its own, was not shown to be associated with a cost of resistance in vitro. The restriction to distinct mutations that confer rifampin resistance in vivo, as demonstrated here, appears to be determined by the Darwinian fitness of the organisms.

Cross-talk between nitric oxide and superoxide determines ceramide formation and apoptosis in glomerular cells

BACKGROUND

The modulation of cell signaling by nitric oxide (NO) and superoxide (O(-)(2)) is associated with apoptotic cell death in inflammatory kidney diseases. Recently, we have shown that NO induces ceramide production in glomerular mesangial and endothelial cells and the ratio of NO and O(-)(2) determines whether cells live or die.

METHODS

Glomerular endothelial and mesangial cells were labeled with [(14)C]serine, the precursor of all sphingolipids, then stimulated with reactive oxygen species- or reactive nitrogen species-generating substances and subjected to lipid extraction. Radioactive lipids were separated and analyzed by thin-layer chromatography. DNA fragmentation, as a characteristic feature of apoptosis, was measured by a nucleosome/DNA-ELISA, which quantitatively recorded the histone-associated DNA fragments.

RESULTS

Exposure of glomerular endothelial and mesangial cells to either NO donors or superoxide-generating substances led to a delayed and sustained ceramide formation that paralleled the induction of apoptosis in both cell types. Coincubation of endothelial cells with NO and superoxide, which led to the generation of peroxynitrite, caused a synergistic enhancement of ceramide generation and apoptosis when compared to either stimulus alone. By contrast, in glomerular mesangial cells costimulation with superoxide neutralized not only NO-induced apoptosis but also NO-induced ceramide formation, although O(-)(2) alone triggered ceramide formation in mesangial cells and caused cell death. Moreover, SIN-1, a substance that simultaneously releases NO and O(-)(2) and thereby generates peroxynitrite, also stimulated a delayed ceramide formation in endothelial cells but not in mesangial cells. Furthermore, exposure of endothelial cells to glucose oxidase, which generates hydrogen peroxide, or to exogenous hydrogen peroxide, also showed a dose-dependent increase in ceramide formation and apoptosis, although to a lesser extent than did superoxide.

CONCLUSIONS

These data suggest that ceramide represents an important mediator of reactive oxygen and nitrogen species-triggered cell responses, like apoptosis. There seem to be cell type-specific protective mechanisms that critically depend on a fine-tuned redox balance between reactive nitrogen and oxygen species to determine whether a cell undergoes apoptosis or survives when exposed to oxidative and/or nitrosative stress conditions.

Removal of PCR inhibitors by silica membranes: evaluating the Amplicor Mycobacterium tuberculosis kit

The effectiveness of PCR inhibitor removal by silica membranes in combination with the Amplicor Mycobacterium tuberculosis kit was analyzed for 655 respiratory and nonrespiratory specimens. The overall inhibition rate was reduced from 12.5%, when applying the Amplicor kit alone, to 1.1% with the addition of silica membrane DNA purification.

Superoxide potently induces ceramide formation in glomerular endothelial cells

Recent evidence suggests that the sphingolipid-derived second messenger ceramide and oxidative stress are intimately involved in apoptosis induction. Here we report that exposure of microcapillary glomerular endothelial cells to superoxide-generating substances, including hypoxanthine/xanthine oxidase and the redox cyclers DMNQ and menadione results in a dose-dependent and delayed increase in the lipid signaling molecule ceramide. Long-term incubation of endothelial cells for 2-30 h with either DMNQ or hypoxanthine/xanthine oxidase leads to a continuous increase in ceramide levels. In contrast, short-term stimulation for 1 min up to 1 h had no effect on ceramide formation. The DMNQ-induced delayed ceramide formation is dose-dependently inhibited by reduced glutathione, whereas oxidized glutathione was without effect. Furthermore, N-acetylcysteine completely blocks DMNQ-induced ceramide formation. All superoxide-generating substances were found to dose-dependently trigger endothelial cell apoptosis. In addition, glutathione and N-acetylcysteine also prevented superoxide-induced apoptosis and implied that ceramide represents an important mediator of superoxide-triggered cell responses like apoptosis.

Rapid molecular typing of methicillin-resistant Staphylococcus aureus by PCR-RFLP

OBJECTIVE

To establish a new, rapid, and reliable genotypic fingerprinting technique for methicillin-resistant Staphylococcus aureus (MRSA) typing in routine epidemiological surveillance.

DESIGN

The method is based on polymerase chain reaction (PCR) restriction fragment-length polymorphism (RFLP) following HaeII digestion of simultaneously amplified parts of the protein A gene, the coagulase gene, and the hypervariable region adjacent to mecA. A total of 46 MRSA initial isolates were analyzed, including 14 isolates from five countries; the six German epidemic strains; 16 isolates from the Frankfurt metropolitan area, which were known to be heterogeneous by pulsed-field gel electrophoresis (PFGE); and 10 isolates obtained during three epidemics, all of which displayed an identical genotype.

RESULTS

Restriction analysis by PCR-RFLP permitted discrimination of 10 of 14 international isolates, all six German epidemic strains, and 15 of 16 national isolates. It also confirmed the homogeneous character of the 10 outbreak isolates.

CONCLUSIONS

This new and rapid PCR-RFLP typing method is an attractive tool in routine epidemiological surveillance. Its impressive characteristics are ease of performance and interpretation, while at the same time guaranteeing good discriminatory power, reproducibility, and typeability.

Differential effect of rpoB mutations on antibacterial activities of rifampicin and KRM-1648 against Staphylococcus aureus

The in vitro antibacterial activities of the rifamycin derivatives rifampicin and KRM-1648 against 150 Staphylococcus aureus isolates were determined. The MICs of rifampicin and KRM-1648 for 90% of rifampicin-susceptible S. aureus isolates (n = 100) were 0.016 and 0.001 mg/L, respectively. In rifampicin-resistant S. aureus isolates (n = 50), different levels of resistance to rifamycins were associated with mutations at different sites in rpoB. Mutations at some sites were associated with high-level resistance to both rifamycins, while certain mutations were associated with the activity of KRM-1648 being < or = 100-fold better than that of rifampicin.

Contribution of the multidrug efflux pump LfrA to innate mycobacterial drug resistance

Multidrug resistance (MDR) in bacteria has been associated with efflux pumps that export structurally unrelated compounds and decrease cytoplasmic drug accumulation. To investigate MDR in mycobacteria, we studied the Mycobacterium smegmatis mutant mc(2)11, which is resistant to doxorubicin, tetracycline, rhodamine, ethidium bromide and the hydrophilic fluoroquinolones. A genomic library constructed from this mutant was used to select clones conferring resistance to doxorubicin. Surprisingly, the clone selected encodes the efflux pump LfrA, which has been reported to confer resistance to hydrophilic fluoroquinolones, ethidium bromide, rhodamine, and acriflavine. To define the contribution of LfrA to the innate mycobacterial drug resistance and to the MDR phenotype in mc(2)11, the lfrA gene was disrupted in both the mc(2)11 mutant and the mc(2)155 wild-type parent. LfrA disruption of the wild-type strain decreased resistance to ethidium bromide and acriflavine, and increased accumulation of ethidium bromide. However, disruption of lfrA gene results only in a 2-fold decrease in minimal inhibitory concentrations (MICs) for ciprofloxacin, doxorubicin, rhodamine, and accumulation of [(14)C]ciprofloxacin was unchanged. LfrA disruption of the MDR strain mc(2)11 produced a similar phenotype. Thus, LfrA contributes significantly to the intrinsic MICs of M. smegmatis for ethidium bromide and acriflavine, but not for ciprofloxacin, doxorubicin or rhodamine.

Molecular characterization of rpoB mutations conferring cross-resistance to rifamycins on methicillin-resistant Staphylococcus aureus

Mutations of the rpoB gene conferring resistance to rifampin were analyzed in 40 methicillin-resistant Staphylococcus aureus isolates obtained from six countries. Interestingly, the majority of clinical isolates showed multiple mutations within rpoB. The amino acid substitution 481His-->Asn was the most prevalent one, capable of conferring low-level resistance on its own. Cross-resistance to rifampin, rifabutin, and rifapentine was demonstrated for all mutants identified. The level of resistance to rifamycins correlated with both the mutation position and type of amino acid substitution.

Mycobacterium malmoense infections in immunocompetent patients

While Mycobacterium malmoense infections were originally restricted to northern Europe, there has been an increasing number of reports of cases of infection in other countries. Two cases of infections due to Mycobacterium malmoense in immunocompetent patients in Germany are presented. In both cases a presumptive diagnosis of tuberculosis was established initially. Mycobacterium malmoense was cultured after a long incubation period (6-8 weeks). The patients were successfully treated with a triple regimen consisting of rifampicin, ethambutol and clarithromycin. The epidemiology and difficulties in diagnosis of Mycobacterium malmoense infection are discussed.

Detection and identification of mycobacteria by amplification of rRNA

Oligonucleotides specific at a genus, group, or species level were defined by a systematic comparison of small-subunit rRNA sequences from Mycobacterium tuberculosis, M. bovis, M. africanum, M. bovis BCG, M. avium, M. kansasii, M. marinum, M. gastri, M. chelonae, M. smegmatis, M. terrae, M. nonchromogenicum, M. xenopi, M. malmoense, M. szulgai, M. scrofulaceum, M. fortuitum, M. gordonae, M. intracellulare, M. simiae, M. flavescens, M. paratuberculosis, M. sphagni, M. cookii, M. komossense, M. phlei, and M. farcinica. On the basis of the defined oligonucleotides, the polymerase chain reaction technique was explored to develop a sensitive taxon-specific detection system for mycobacteria. By using M. tuberculosis as a model system, fewer than 10 bacteria could be reliably detected by this kind of assay. These results suggest that amplification of rRNA sequences by the polymerase chain reaction may provide a highly sensitive and specific tool for the direct detection of microorganisms without the need for prior cultivation.

Phylogenetic analysis and identification of different serovars of Mycobacterium intracellulare at the molecular level

Comparative 16S rRNA sequencing was used to infer the phylogenetic relationship among different serovars of the Mycobacterium avium-M. intracellulare complex as well as to define signature nucleotides characteristic for different serovars. In general, the groups defined by rRNA sequencing reflect the classification obtained with sensitin tests and pathogenicity examinations in chickens. Unique 16S rRNA sequence patterns could be defined for (1) M. avium, (2) M. intracellulare serovars 4, 5, 6, 8, 9, 10 and 11, (3) M. intracellulare serovars 12, 13, 14, 15, 17, 19 and 20, (4) M. intracellulare serovar 7 and (5) M. intracellulare serovar 18. Phylogenetically, groups 1 and 2 on one hand and groups 3, 4 and 5 on the other hand each share a common ancestor. M. paratuberculosis was indistinguishable from M. intracellulare serovars 4, 5, 6, 8, 9, 10 and 11 by this kind of analysis.