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When a bloodstream infection (BSI) is suspected, most of the laboratory results--biochemical and haematologic--are available within the first hours after hospital admission of the patient. This is not the case for diagnostic microbiology, which generally takes a longer time because blood culture, which is to date the reference standard for the documentation of the BSI microbial agents, relies on bacterial or fungal growth. The microbial diagnosis of BSI directly from blood has been proposed to speed the determination of the etiological agent but was limited by the very low number of circulating microbes during these paucibacterial infections. Thanks to recent advances in molecular biology, including the improvement of nucleic acid extraction and amplification, several PCR-based methods for the diagnosis of BSI directly from whole blood have emerged. In the present review, we discuss the advantages and limitations of these new molecular approaches, which at best complement the culture-based diagnosis of BSI. [ABSTRACT FROM AUTHOR]

Microbiological war and terrorist attacks are made to weaken populations by transmitting pathogenic and epidemic microorganisms. These bacteria or viruses are often difficult to diagnose. Anthrax alerts following September 2001 showed that most clinical microbiology laboratories were not adequately prepared, using obsolete diagnostic methods or being too slow to use accurate tools when facing a major threat. Following this period, most microbiology laboratories were prepared for bioterrorism alerts, in order to provide accurate and rapid results, although such events are rare and unexpected. In this review, we describe the organization and preparedness of our clinical microbiology laboratory regarding bioterrorism risk, although its main task is to perform routine diagnostic microbiology tests. To illustrate the difficulties, we briefly describe an anthrax alert. [ABSTRACT FROM AUTHOR]

Among 112 patients infected only by Plasmodium falciparum , WHO criteria of severity were compared with parasite load assessed by microscopy and quantitative PCR. Clinical severity was significantly correlated with higher parasite load as determined by microscopy (p < 0.001) and by PCR (p < 0.001). Hence, quantitative PCR might be useful to predict outcome. [ABSTRACT FROM AUTHOR]

Since routine eubacterial 16S rRNA PCR does not amplify members of the Chlamydiales order, we tested all samples received in our laboratory during a 10 months period using a pan-Chlamydiales real-time PCR. 3 of 107 samples (2.8%) revealed to be positive, suggesting a role of some Chlamydiales in the pathogenesis of chronic bronchial stenosis or bronchial stenosis superinfection and as agents of orthopaedic prosthesis infections. [ABSTRACT FROM AUTHOR]

The article presents a case study of a 48-year-old Caucasian woman who was taking chloroquine weekly for malaria chemoprophylaxis and self-medicated with aspirin. She was found dead and the prosecutor ordered medico-legal autopsy. The post-mortem identification revealed the pulmonary oedema, hepatomegaly and splenomegaly. The article discusses the challenges regarding the post-mortem identification of malaria which is aetiology of sudden death in non-endemic countries.

Abstract 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. [ABSTRACT FROM AUTHOR]

Carbapenemases should be accurately and rapidly detected, given their possible epidemiological spread and their impact on treatment options. Here, we developed a simple, easy and rapid matrix-assisted laser desorption ionization-time of flight ( MALDI- TOF)-based assay to detect carbapenemases and compared this innovative test with four other diagnostic approaches on 47 clinical isolates. Tandem mass spectrometry ( MS- MS) was also used to determine accurately the amount of antibiotic present in the supernatant after 1 h of incubation and both MALDI- TOF and MS- MS approaches exhibited a 100% sensitivity and a 100% specificity. By comparison, molecular genetic techniques (Check- MDR Carba PCR and Check- MDR CT103 microarray) showed a 90.5% sensitivity and a 100% specificity, as two strains of Aeromonas were not detected because their chromosomal carbapenemase is not targeted by probes used in both kits. Altogether, this innovative MALDI- TOF-based approach that uses a stable 10- μg disk of ertapenem was highly efficient in detecting carbapenemase, with a sensitivity higher than that of PCR and microarray. [ABSTRACT FROM AUTHOR]

To face the current COVID-19 pandemic, diagnostic tools are essential. It is recommended to use real-time RT-PCR for RNA viruses in order (a) to perform a rapid and accurate diagnostic, (b) to guide patient care and management and (c) to guide epidemiological strategies. Further studies are warranted to define the role of serological diagnosis and a possible correlation between serological response and prognosis. The aim was to guide clinical microbiologists in the use of these diagnostic tests and clinicians in the interpretation of their results. A search of literature was performed through PubMed and Google Scholar using the keywords SARS-CoV-2, SARS-CoV-2 molecular diagnosis, SARS-CoV-2 immune response, SARS-CoV-2 serology/antibody testing, coronavirus diagnosis. The present review discusses performances, limitations and use of current and future diagnostic tests for SARS-CoV-2. Real-time RT-PCR remains the reference method for diagnosis of SARS-CoV-2 infection. On the other hand, notwithstanding its varying sensitivity according to the time of infection, serology represents a valid asset (a) to try to solve possible discrepancies between a highly suggestive clinical and radiological presentation and negative RT-PCR, (b) to solve discrepancies between different PCR assays and (c) for epidemiological purposes. [ABSTRACT FROM AUTHOR]

Tuberculosis diagnosis has dramatically improved since the introduction of the rapid molecular test Xpert MTB/RIF (Xpert) detecting M. tuberculosis and rifampicin resistance directly from clinical specimens, therefore shortening the turnaround time, reducing patient's isolation period and decreasing the time to start anti-TB drugs. The new version, Xpert MTB/RIF Ultra (Ultra), displays a higher sensitivity and an improved rifampicin resistance detection. Both tests have been endorsed by the World Health Organisation. Xpert and Ultra rapidly became widespread and paved the way for new approaches and new paradigms as well as for the development of molecular point-of-care tests (POCTs). In this narrative review, we aimed to address their performance in the diagnosis of tuberculosis and to discuss the expectations of these tests as well as their limits and the unmet needs. Peer-reviewed publications addressing the diagnostic performance of Ultra and Xpert. We focused on publications that evaluated the performance of Ultra and Xpert on the same group of patients or the same set of specimens in different tuberculosis-burden settings. The studies published so far reported an increased sensitivity of Ultra when compared to Xpert, which represents a benefit for tuberculosis diagnosis. The fact that such a sensitive assay cannot distinguish between alive and dead bacilli emphasizes that caution should be exercised regarding indications and interpretation of results. Additional studies are needed to determine the true performance for the diagnosis of extrapulmonary tuberculosis because of the great diversity of the specimens. [ABSTRACT FROM AUTHOR]

Since late 2014, multiple cases of abscesses and boils due to methicillin-susceptible Staphylococcus aureus (MSSA) expressing the Panton–Valentine leucocidin (PVL) were observed in Eritrean asylum seekers in Lausanne, Switzerland. Strains isolated from infected Eritrean and non-Eritrean patients were compared by whole genome sequencing to determine whether these numerous cases result from an outbreak. The genome of S. aureus PVL-producing strains were sequenced and compared. Clinical and epidemiological characteristics of patients infected by PVL-producing strains were investigated. This work reports 15 cases of infections due to PVL-producing strains affecting mostly asylum seekers ( n = 10), people working with refugees and/or exposed to Africans ( n = 3). Most infections were due to closely related strains of CC152 ( n = 8) and CC15 ( n = 3), two distantly related (>34 000 core single nucleotide polymorphisms) clonal complexes. An epidemiological link between the 15 cases could be ruled out by whole genome sequencing (33 to 172 core single nucleotide polymorphisms between the different strains of a given complex). Altogether, these results reflect the probable high incidence of CC15 and CC152 PVL-producing strains in eastern Africa. Clinicians facing unusual skin infections in African refugees (or in any person returning from this region of high endemicity) should consider S. aureus PVL-producer before suspecting rare infections such as leishmaniasis or rickettsiosis. Clinicians should also remember that PVL are frequently expressed by MSSA in some regions of the world and that antibiotics that are efficient on toxin expression, such as clindamycin, represent the best therapeutic option. [ABSTRACT FROM AUTHOR]

Airborne precautions are required at hospital admission for patients with suspected pulmonary tuberculosis. The isolation is maintained until 3 serially collected sputum smears are acid-fast bacilli negative, a time- and labor-intensive method with limited sensitivity and specificity, which has a great impact on patient flow management. We evaluated the possibility of replacing the result of microscopy by the semiquantitative result of the molecular point-of-care test Xpert MTB/RIF to assess patients' transmission risk to quickly guide airborne isolation decisions in low-endemic countries. The performance of the Xpert MTB/RIF, used as a first-line test, was compared to the results of microscopy for specimens ( n = 242) collected from May 2010 to December 2014 in Lausanne, Switzerland. The sensitivity and specificity of Xpert MTB/RIF were 91.5% (65/71) and 99.6% (170/171), respectively, vs. 64.8% (46/71) and 94.2% (161/171) for microscopy. Samples with negative Xpert MTB/RIF were all smear negative for Mycobacterium tuberculosis (negative predictive value, 100%). The semiquantitative results of Xpert MTB/RIF—high, medium, low or very low—were found to correlate with acid-fast bacilli detection: positive predictive value of 100% (6/6), 96.5% (27/28), 52.2% (12/23) and 11.1% (1/9) respectively. Finally, when including clinical criteria, we identified 11 smear-negative but Xpert MTB/RIF–positive patients with a significant transmission potential. In conclusion, our data support the introduction of an Xpert MTB/RIF–based strategy as a replacement of smear microscopy for a faster and more accurate management of tuberculosis patients' transmission risk in a low-prevalence country. [ABSTRACT FROM AUTHOR]

Detection of cryptococcal antigen in serum or cerebrospinal fluid allows cryptococcal meningitis diagnosis within few hours with >90% sensitivity. In an HIV-positive patient with Cryptococcus neoformans meningitis, initial antigen detection by immunoagglutination was negative. We thus evaluated a new immunochromatographic detection assay that exhibited a higher sensitivity. [ABSTRACT FROM AUTHOR]

Effective empirical treatment is of paramount importance to improve the outcome of patients with Staphylococcus aureus bacteraemia. We aimed to evaluate a PCR-based rapid diagnosis of methicillin resistance (GeneXpert MRSA) after early detection of S. aureus bacteraemia using matrix-assisted laser desorption ionization time-of-flight mass spectrometry ( MALDI- TOF MS). Patients with a first episode of S. aureus bacteraemia identified using MALDI- TOF MS were randomized in a prospective interventional open study between October 2010 and August 2012. In the control group, antibiotic susceptibility testing was performed after MALDI- TOF MS identification on blood culture pellets. In the intervention group, a GeneXpert MRSA was performed after S. aureus identification. The primary outcome was the performance of GeneXpert MRSA directly on blood cultures. We then assessed the impact of early diagnosis of methicillin resistance on the empirical treatment. In all, 197 episodes of S. aureus bacteraemia were included in the study, of which 106 were included in the intervention group. Median time from MALDI- TOF MS identification to GeneXpert MRSA result was 97 min (range 25-250). Detection of methicillin resistance using GeneXpert MRSA had a sensitivity of 99% and a specificity of 100%. There was less unnecessary coverage of MRSA in the intervention group (17.1% versus 29.2%, p 0.09). GeneXpert MRSA was highly reliable in diagnosing methicillin resistance when performed directly on positive blood cultures. This could help to avoid unnecessary prescriptions of anti- MRSA agents and promote the introduction of earlier adequate coverage in unsuspected cases. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Previously limited to symptomatic patients, our hospital introduced a universal admission screening strategy for coronavirus disease 2019 on 25 April 2020. All patients were tested by RT-PCR. We observed decreased viral loads linked to increased screening of asymptomatic patients highlighting the fact that viral load values could guide infection control decisions. [ABSTRACT FROM AUTHOR]

Contact investigations following the diagnosis of active tuberculosis (TB) are paramount for the control of the disease. Epidemiological data are very powerful for contact tracing but might be delayed and/or difficult to integrate, especially in the setting of multiple contact-tracing investigations. The aim of this study was to address the added-value of whole-genome sequencing (WGS) to routine local TB surveillance systems. From November 2016 to July 2017, the local TB surveillance system identified three clusters that could constitute a unique larger outbreak. Epidemiological and clinical information were integrated with WGS genotyping data of Mycobacterium tuberculosis strains obtained using a simple DNA extraction method coupled with sequencing using an Illumina MiSeq platform and an in-house bioinformatics pipeline for single nucleotide polymorphism (SNP) analysis. Epidemiological investigations identified three putative TB clusters potentially interrelated including eight patients with active TB. Seven M. tuberculosis isolates were available and analysed by WGS. Using a 5-SNP threshold to define recent transmission, WGS-based genotyping supported the occurrence of the three clusters as well as a link between clusters 1 and 2 (SNP ≤1), constituting a larger outbreak. This outbreak was clearly delineated by refuting a potential link with the third cluster (SNP >500). Genotyping data did not support the belonging of patient 7 to any studied cluster. This study illustrates the usefulness of WGS genotyping for routine TB surveillance systems in local communities to rapidly confirm or disprove epidemiological hypotheses and delineate TB clusters, especially in the context of multiple contact-tracing investigations. [ABSTRACT FROM AUTHOR]

A letter to the editor is presented regarding two cases of Aerococcus urinae infections along with the role of matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) and 16S rDNA polymerase chain reaction (PCR).

In 2010, Jaton et al . (False-negative PCR result due to gene polymorphism: the example of Neisseria meningitidis . J Clin Microbiol 2010;48:4590–2) reported an isolate of Neisseria meningitidis serogroup B that was not detected by the ctrA quantitative real-time PCR (qRT-PCR) used in our diagnostic laboratory. Sequence analysis of ctrA revealed several single nucleotide polymorphisms responsible for the negative qRT-PCR. Therefore, we sequenced the genome of this isolate and performed comparative genomics to propose new gene targets for the specific detection of N. meningitidis from clinical specimens. We identified 11 genes as specific to N. meningitidis genomes and common to at least 177 (97%) of the 183 genomes available. Among them, three genes ( metA, tauE and shlA ) were selected to develop new qRT-PCRs for the detection of N. meningitidis DNA. The three qRT-PCRs were highly sensitive and specific, and they exhibited a good reproducibility when tested on plasmidic positive controls and genomic DNA extracted from strains of N. meningitidis and other relevant bacterial species. The clinical sensitivity and specificity of metA and tauE qRT-PCRs were both 100% based on a testing of cerebrospinal fluid samples positive for N. meningitidis or other clinically relevant bacteria. Despite a 100% specificity, the sensitivity of the shlA qRT-PCR was only 70%. We thus recommend using the metA and/or tauE qRT-PCRs developed here. To prevent PCR failure in the presence of new polymorphic strains, the detection of dual targets by duplex qRT-PCR would be more accurate and suitable for the diagnosis of N. meningitidis from clinical specimens. [ABSTRACT FROM AUTHOR]