Capnocytophaga canimorsus meningitis diagnosed by 16S rRNA PCR.

Capnocytophaga canimorsus is a common Gram-negative anaerobic bacterium from the oral flora of dogs, typically transmitted to humans by dog bites. We report a case of C. canimorsus meningitis where there was (on presentation) no apparent predisposing risk factor and in whom we used 16S rRNA PCR gene sequencing to identify the pathogen quickly and to switch to appropriate antibiotic therapy. Physicians should be aware of potential C. canimorsus meningitis if conventional cerebrospinal fluid bacterial culture is negative but Gram staining identifies bacteria, especially in patients with a recent dog bite or known immunodeficiency.

High Coxiella burnetii DNA load in serum during acute Q fever is associated with progression to a serologic profile indicative of chronic Q fever.

PCR is very effective in diagnosing acute Q fever in the early stages of infection, when bacterial DNA is present in the bloodstream but antibodies have not yet developed. The objective of this study was to further analyze the diagnostic value of semiquantitative real-time PCR (qPCR) in diagnosing acute Q fever in an outbreak situation. At the Jeroen Bosch Hospital, in 2009, qPCR testing for Coxiella burnetii DNA was performed for 2,715 patients suspected of having acute Q fever (positive, n = 385; negative, n = 2,330). The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of the qPCR assay were calculated for patients with negative qPCR results with a follow-up sample obtained within 14 days (n = 305) and qPCR-positive patients with at least one follow-up sample (n = 369). The correctness of the qPCR result was based on immunofluorescence assay results for samples submitted for qPCR and follow-up testing. The sensitivity of the Q fever qPCR assay was 92.2%, specificity 98.9%, PPV 99.2%, and NPV 89.8%. Patients who later developed serologic profiles indicative of chronic Q fever infection had significantly higher C. burnetii DNA loads during the acute phase than did patients who did not (P < 0.001). qPCR testing is a valuable tool for the diagnosis of acute Q fever and should be used in outbreak situations when the onset of symptoms is <15 days earlier. Special attention is needed in the follow-up monitoring of patients with high C. burnetii DNA loads during the acute phase, as this might be an indicator for the development of a serologic profile indicative of chronic infection.

Real-time PCR to distinguish livestock-associated (ST398) from non-livestock-associated (methicillin-resistant) Staphylococcus aureus.

BACKGROUND: The Netherlands is one of the most densely populated countries in the world, with extensive livestock of pigs. In 2005, the emergence of livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) was a fact, with a relatively high MRSA colonisation among pig farmers. These MRSA isolates mostly belonged to sequence type 398 (ST398). Compared to hospital-associated MRSA (HA-MRSA), severe infections due to LA-MRSA and transmission between individuals are still relatively rare. Therefore, LA-MRSA may warrant less stringent containment measures than HA-MRSA in hospital settings. RESULTS: The aim of this study was to develop a rapid diagnostic tool to distinguish LA-MRSA from non-LA-MRSA in aid of infection control. Here, we show that ST398 strains can be readily detected with real-time polymerase chain reaction (PCR). Analysis of a large panel of related and unrelated microorganisms confirmed that the real-time ST398 PCR (ST398-qPCR) assay does not cross-react with other microorganisms or with non-LA-S. aureus strains. ST398-qPCR analysis of MRSA isolates collected in 2010, 2011 and 2012 at the Jeroen Bosch Hospital (n = 275) showed that an average of 78 % of MRSA belonged to sequence type ST398. CONCLUSION: We conclude that the ST398 real-time PCR is a reliable assay to detect LA-S. aureus and anticipate that the use of this assay can prevent the unnecessary closing of hospital wards, which may lead to substantial savings for the health care system.

Validation and implementation of the Panbio COVID-19 Ag rapid test for the diagnosis of SARS-CoV-2 infection in symptomatic hospital healthcare workers.

BACKGROUND: RT-PCR is the current recommended laboratory method to diagnose SARS-CoV-2 in healthcare workers (HCW). As RT-PCR is not widely available and is time-consuming, it limits decision making on removal from and return to work of possibly contagious HCW. AIM: In this study we evaluated the Panbio™ COVID-19 Ag rapid test (PanbioCAgRT) in 825 hospital HCW. METHODS AND FINDING: This study consisted of two phases. In the validation phase, we tested hospital HCW with mild symptoms (three days or less) in parallel using the PanbioCAgRT and the RT-qPCR test. The PanbioCAgRT demonstrated 86.7% sensitivity, 100% specificity, 100% PPV and 98.5% NPV with regard to RT-qPCR. For HCW with PanbioCAgRT-/RT-qPCR+, the median Ct value was 30.9, whereas for the HCW with PanbioCAgRT+/RT-qPCR+ the median Ct value was 19.3 (P<0.001). In the second phase, we implemented an on-site antigen test-based strategy for symptomatic hospital HCW: HCW that tested positive with the PanbioCAgRT on-site were considered SARS-CoV-2 positive and were sent home. HCW that tested negative with the PanbioCAgRT on-site were allowed to work with PPE pending RT-qPCR test results from the laboratory. Sensitivity of the antigen test-based strategy was 72.5% and NPV was 97%. For HCW with PanbioCAgRT-/RT-qPCR+ median Ct values were 27.8. CONCLUSION: The PanbioCAgRTt validated in this study showed a high sensitivity and specificity in samples obtained from HCW with high viral loads. The antigen-based testing strategy proposed in this study seems to be effective, safe and easy to implement in a wide range of occupational healthcare settings.

Legionella pneumophila DNA in serum samples during Legionnaires' disease in relation to C-reactive protein levels.

Legionella pneumophila DNA can be detected in serum from patients with Legionnaires' disease (LD). We explored this observation studying the kinetics of L. pneumophila DNA in serum samples in relation to C-reactive protein (CRP). Eleven hospitalized patients with LD were studied. Diagnosis was made by Legionella urinary antigen test in 8 patients and seroconversion in 3 patients. A macrophage infectivity potentiator (MIP) real-time PCR was performed on 31 serum samples, including 20 follow-up serum samples. Serum samples obtained on the day of admission were MIP PCR-positive in 7 (64%) and MIP PCR-negative in 4 (36%) patients. Three (75%) of the 4 patients with a MIP PCR-negative serum sample on the day of admission became positive during follow-up. Overall, L. pneumophila DNA was detected in serum samples from 10 of the 11 patients (91%). CRP levels in the 7 patients with a positive MIP PCR serum sample on day of admission (499 +/- 144 mg/l; median +/- SD) were significantly higher than those in the 4 patients with a negative MIP PCR serum sample on the day of admission (244 +/- 97 mg/l). No difference in the severity of the disease on the day of admission was found between these patients. The presence of L. pneumophila DNA in serum is a common phenomenon in hospitalized patients with LD, although in some cases it is not yet present on the day of admission. L. pneumophila DNA in serum on the day of admission correlates with high CRP levels, but not with the severity of the disease.

Investigating unexpected INRs: in search of the culprit--adherence, interactions, genetics, and superwarfarin.

Treatment with coumarin derivatives is highly individualised due to high intra- and inter-individual variation in dose response and risks of severe bleeding or thromboembolic complications. Treatment focuses on reaching and maintaining a stable target international normalised ratio (INR). However, unexpected INRs that are not explained by noncompliance or vitamin K intake may occur. Here we describe seven cases of unexpected INRs, and provide clues that clarify the underlying mechanism.

Implementation of point-of-care testing and a temporary influenza ward in a Dutch hospital.

BACKGROUND: The seasonal influenza epidemic poses a significant burden on hospitals, both in terms of capacity and costs. Beds that are occupied by isolated influenza patients result in hospitals temporary being closed to admissions and elective operations being cancelled. Improving hospital and emergency department (ED) patient flow during the influenza season could solve these problems. Microbiological point-of-care-testing (POCT) could reduce unnecessary patient isolation by providing a positive/negative result before admission, but has not yet broadly been implemented. METHODS: A clinical pathway for patients with acute respiratory tract infection presenting at the ED was implemented, including a PCR-based POCT for influenza, operated by nurses and receptionists. In parallel, a temporary ward equipped with 15 beds for influenza-positive patients was established. In this retrospective observational study, we describe the results of implementing this pathway by comparison with the previous epidemic. RESULTS: Clinical performance of the POCT within the clinical pathway was good with strongly decreased time from ED presentation to sample collection (194 vs 47 min) and time from sample collection to result (1094 vs 62 min). Hospital patient flow was improved by a decreased percentage of admitted influenza-positive patients (91% vs 73%) and shorter length of subsequent stay (median 5.86 vs 4.61 days) compared to the previous influenza epidemic. In addition, 430 patient-days of unnecessary isolation have been prevented within a time span of 18 weeks. Roughly estimated savings were almost 400,000 euros. CONCLUSION: We recommend that hospitals explore possibilities for improving patient flow during an influenza epidemic.

Kinetics of antibody response to Coxiella burnetii infection (Q fever): Estimation of the seroresponse onset from antibody levels.

BACKGROUND: From 2007 to 2009, the Netherlands experienced a major Q fever epidemic. Long-term serological follow-up of acute Q fever patients enabled the investigation of longitudinal antibody responses and estimating the onset of the seroresponse in individual patients. METHODS: All available IgG and IgM phase I and II antibody measurements determined by immunofluorescence assay at month 3, 6, 12, and 48 from 2321 acute Q fever patients were retrospectively analyzed. Characteristic features of the antibody response were calculated. To model the seroresponse onset, serological data from patients diagnosed with a positive C. burnetii PCR test (n=364), and therefore with a known time of infection, were used as reference. RESULTS: In 9083 IgG samples and 3260 IgM samples large heterogeneity in shape and magnitude of antibody responses was observed. Phase II reached higher levels than phase I, and IgG antibodies were more persistent than IgM. The estimated seroresponse latency allowed for determining the time since start of the seroresponse from the concentrations of the different antibodies against C. burnetii. CONCLUSIONS: The extraordinary large serological dataset provides new insight into the kinetics of the immunoglobulins against C. burnetii antigens. This knowledge is useful for seroprevalence studies and helps to better understand infection dynamics.

Correlations between peripheral blood Coxiella burnetii DNA load, interleukin-6 levels, and C-reactive protein levels in patients with acute Q fever.

From 2007 to 2010, the Netherlands experienced the largest reported Q fever outbreak, with >4,000 notified cases. We showed previously that C-reactive protein is the only traditional infection marker reflecting disease activity in acute Q fever. Interleukin-6 is the principal inducer of C-reactive protein. We questioned whether increased C-reactive protein levels in acute Q fever patients coincide with increased interleukin-6 levels and if these levels correlate with the Coxiella burnetii DNA load in serum. In addition, we studied their correlation with disease severity, expressed by hospital admission and the development of fatigue. Interleukin-6 and C-reactive protein levels were analyzed in sera from 102 patients diagnosed with seronegative PCR-positive acute Q fever. Significant but weak negative correlations were observed between bacterial DNA loads expressed as cycle threshold values and interleukin-6 and C-reactive protein levels, while a significant moderate-strong positive correlation was present between interleukin-6 and C-reactive protein levels. Furthermore, significantly higher interleukin-6 and C-reactive protein levels were observed in hospitalized acute Q fever patients in comparison to those in nonhospitalized patients, while bacterial DNA loads were the same in the two groups. No marker was prognostic for the development of fatigue. In conclusion, the correlation between interleukin-6 and C-reactive protein levels in acute Q fever patients points to an immune activation pathway in which interleukin-6 induces the production of C-reactive protein. Significant differences in interleukin-6 and C-reactive protein levels between hospitalized and nonhospitalized patients despite identical bacterial DNA loads suggest an important role for host factors in disease presentation. Higher interleukin-6 and C-reactive protein levels seem predictive of more severe disease.

Early diagnosis and treatment of patients with symptomatic acute Q fever do not prohibit IgG antibody responses to Coxiella burnetii.

Little is known about the effect of timing of antibiotic treatment on development of IgG antibodies following acute Q fever. We studied IgG antibody responses in symptomatic patients diagnosed either before or during development of the serologic response to Coxiella burnetii. Between 15 and 31 May 2009, 186 patients presented with acute Q fever, of which 181 were included in this retrospective study: 91 early-diagnosed (ED) acute Q fever patients, defined as negative IgM phase II enzyme-linked immunosorbent assay (ELISA) and positive PCR, and 90 late-diagnosed (LD) acute Q fever patients, defined as positive/dubious IgM phase II ELISA and positive immunofluorescence assay (IFA). Follow-up serology at 3, 6, and 12 months was performed using IFA (IgG phase I and II). High IgG antibody titers were defined as IgG phase II titers of ≥1:1,024 together with IgG phase I titers of ≥1:256. At 12 months, 28.6% of ED patients and 19.5% of LD patients had high IgG antibody titers (P = 0.17). No statistically significant differences were found in frequencies of IgG phase I and IgG phase II antibody titers at all follow-up appointments for adequately and inadequately treated patients overall, as well as for ED and LD patients analyzed separately. Additionally, no significant difference was found in frequencies of high antibody titers and between early (treatment started within 7 days after seeking medical attention) and late timing of treatment. This study indicates that early diagnosis and antibiotic treatment of acute Q fever do not prohibit development of the IgG antibody response.

Single nucleotide polymorphism profiling assay to exclude serum sample mix-up.

BACKGROUND AND OBJECTIVES: Sample mix-ups are a threat to the validity of clinical laboratory test results. To detect serum sample mix-ups we developed a single nucleotide polymorphism (SNP) profiling test. SNPs are frequent sequence variations in the human genome. Each individual has a unique combination of these nucleotide variations. MATERIALS AND METHODS: Predeveloped SNP amplification assays are commercially available. We recently discovered that these SNP assays could be applied to serological samples, which is not self-evident because a key step in serum preparation is removal of white blood cells, the major source of DNA, from blood. DNA was extracted from serum samples. Real-time polymerase chain reaction (PCR) analysis of the purified DNA using a selection of 10 SNP assays provided SNP profiles. RESULTS: The applicability of the SNP profiling test was demonstrated by means of a case where hepatitis E virus serological determinations of four serum samples of one patient seemed inconsistent. SNP profiling of the samples demonstrated that this was due to the enzyme-linked immunosorbent assay test instead of sample mix-up. CONCLUSION: We have developed an SNP profiling assay that provides a way to link human serum samples to a source, without post-PCR processing. The chance for two randomly chosen individuals to have an identical profile is 1 in 18 000. Solving potential serum sample mix-ups will secure downstream evaluations and critical decisions concerning the patients involved.

Multicenter comparison of molecular methods for detection of Legionella spp. in sputum samples.

Legionellosis can be diagnosed by PCR using sputum samples. In this report, the methods of nine laboratories for 12 sputum samples with Legionella pneumophila and Legionella longbeachae are compared. We conclude that (i) liquefaction prevents PCR inhibition, (ii) the employed mip gene PCRs detected L. pneumophila only, and (iii) the 16S rRNA gene PCR detected both Legionella species and is preferred for the diagnosis of legionellosis.

A sensitive and reliable semi-quantitative real-time PCR assay to detect JAK2 V617F in blood.

Diagnosis of the myeloproliferative disorders, polycythemia vera (PV), essential thrombocythemia (ET) and idiopathic myelofibrosis (IMF) is difficult due to lack of diagnostic markers. Recently, the acquisition of a mutation in the Janus kinase 2 (JAK2) gene by hemopoietic cells has been described as a genetic defect underlying myeloproliferative disorders. The mutation leads to constitutive activation of JAK2, a tyrosine kinase involved in cytokine receptor signalling. Because of the clinical importance of this mutation (JAK2 V617F) in diagnosing myeloproliferative disorders and its relevance for disease progression, we developed a semi-quantitative real-time PCR test to detect JAK2 V617F. With this assay, quantities down to 0.8% JAK2 V617F amongst wild-type DNA could reliably be detected. For quantification purposes, low intra- and inter-assay variabilities ensure good reproducibility of the assay. Thus the JAK2 V617F qPCR assay described here is quick, robust, simple and more sensitive than direct sequencing, RFLP, ARMS assay and other methods published so far to detect JAK2 V617F. We therefore believe that the assay will contribute to early diagnosis of myeloproliferative disorders and to disease management, especially when JAK2-specific inhibitors have become available for therapeutic use.

Specific and sensitive detection of Neisseria gonorrhoeae in clinical specimens by real-time PCR.

Early diagnosis of Neisseria gonorrhoeae infections is important with regard to patients' health and infectivity. We report the development of a specific and sensitive TaqMan assay for the detection of N. gonorrhoeae in clinical samples. The target sequence is a 76-bp fragment of the 5' untranslated region of the opa genes that encode opacity proteins. A panel of 448 well-defined N. gonorrhoeae isolates was used to evaluate and optimize the assay. The method employs two minor-groove binding probes, one of them recognizing a newly identified sequence in the opa genes. Testing a large panel of related and unrelated microorganisms revealed that other Neisseria strains and other microorganisms tested negative in the opa test. With a lower detection limit of one genome per reaction, the opa test appeared more sensitive than both the COBAS AMPLICOR (Roche Diagnostics Nederland BV, Almere, The Netherlands) and a LightCycler 16S rRNA test. Analysis of a panel of 122 COBAS AMPLICOR-positive samples revealed that 68% were negative in both the 16S rRNA test and the opa assay (confirming that the COBAS AMPLICOR test produces false positives), while 30% were positive in both assays. Three samples were opa positive and 16S rRNA negative, which may be due to the higher sensitivity of the opa assay. We conclude that the opa gene-based real-time amplification assay offers a sensitive, specific, semiquantitative, and reliable assay suitable for the detection of N. gonorrhoeae in clinical specimens and/or for confirmation of less specific tests.