Low specificity of Aspergillus spp. ELITe MGB assay, and potential risks in management of invasive aspergillosis.

Objectives: In recent years, commercial molecular tools for diagnosis of invasive aspergillosis have emerged, requiring evaluation to ensure quality. Here we assessed the specificity of Aspergillus spp.-ELITe MGB Assay a commercial assay tergeting 18S gene of Aspergillus spp. Design and methods: As part of a method validation, we evaluate the specificity of the Aspergillus spp.-ELITe MGB Assay by testing fourteen culture based samples of sequenced non-Aspergillus fungal species. The benefits of a pre-lysis treatment was evaluated in parallel on serial dilutions of an Aspergillus fumigatus strain. Results: Our findings revealed cross-reactivity in five strains using the 50 copies/mL cut-off recommended by the manufacturer, suggesting potential diagnostic errors and inappropriate management of patients. Pre-lysis treatment does not affect the limit of detection at serial dilution. Conclusions: In conclusion, the Aspergillus spp. ELITe MGB Assay exhibits limited specificity in culture-based samples, underscoring the importance of careful utilization in laboratories. Further studies are warranted to better comprehend of the impact of this cross-reactivity on clinical samples.

Antibiotic consumption history of patients in a referred laboratory in Yaounde.

Background: Regulation of antibiotic prescription and consumption remains a major public health burden in low- and middle- income countries. Objective: This study aimed to describe the antibiotic consumption of patients who had a positive antibiotic culture in a reference laboratory. Methods: A retrospective descriptive study was conducted among 113 participants with positive antibiograms with a documented history of antibiotics intake at the Yaoundé University Teaching Hospital in Cameroon between January 2016 and June 2021. Data were stored and analyzed using the Census and Survey Processing System version 7.3 and Statistical Package for Social Science version 25.0. Descriptive statistics were used to estimate the indicators. Results: Of the 113 patients enrolled, 105 had a history of drug use; 56 participants (53.3%) had taken at least 2 antibiotics prior to sampling. Cephalosporins were the most consumed antibiotics (41%), followed by nitroimidazols (28.6%) and penicillins (28.6%). According to the World Health Organization classification, 55 (52.4%) took major priority antibiotics. Conclusion: We are on the alert and there is an urgent need to raise awareness among clinicians and patients alike by providing them with good clinical practice guidelines.

Antibiotic consumption history of patients in a referred laboratory in Yaounde

Background. Regulation of antibiotic prescription and consumption remain a major public health burden in low- and middle-income country. This study aimed to describe the antibiotic consumption of patients who had a positive antibiotic culture in a reference laboratory. Methods. A retrospective descriptive study was conducted among 113 participants with positive antibiogram with a documented history of antibiotics intake at the Yaoundé University Teaching Hospital (YUTH) in Cameroon between January 2016 to June 2021. Data were stored and analyzed using the Census and Survey Processing System (CSPro) version 7.3 and Statistical Package for Social Science (SPSS) version 25.0. Descriptive statistic was used to estimate the indicators. Results. Of the 113 patients enrolled, 105 had a history of drug use; 56 participants (53, 3%) had taken at least 2 antibiotics prior to sampling. Cephalosporins were the most consumed antibiotics (41, 0%), followed by nitroimidazols (28, 6%) and penicillins (28,6%). According to the WHO classification, 55 (52, 4%) took the major priority antibiotics. Conclusion. We are on the alert and there is an urging need to raise awareness among clinicians and patients alike by providing them with good clinical practice guidelines.

How to choose the right real-time RT-PCR primer sets for the SARS-CoV-2 genome detection?

OBJECTIVES: The SARS-CoV-2 pandemic has created an unprecedented need for rapid large-scale diagnostic testing to prompt clinical and public health interventions. Currently, several quantitative reverse-transcription polymerase chain reaction (RT-qPCR) assays recommended by the World Health Organization are being used by clinical and public health laboratories and typically target regions of the RNA-dependent RNA polymerase (RdRp), envelope (E) and nucleocapsid (N) coding region. However, it is currently unclear if results from different tests are comparable. This study aimed to clarify the clinical performances of the primer/probe sets designed by US CDC and Charité/Berlin to help clinical laboratories in assay selection for SARS-CoV-2 routine detection. METHODS: We compared the clinical performances of the recommended primer/probe sets using one hundred nasopharyngeal swab specimens from patients who were clinically diagnosed with COVID-19. An additional 30 "pre-intervention screening" samples from patients who were not suspected of COVID-19 were also included in this study. We also performed sequence alignment between 31064 European SARS-CoV-2 and variants of concern genomes and the recommended primer/probe sets. RESULTS: The present study demonstrates substantial differences in SARS-CoV-2 RNA detection sensitivity among the primer/probe sets recommended by the World Health Organization especially for low-level viral loads. The alignment of thousands of SARS-CoV-2 sequences reveals that the genetic diversity remains relatively low at the primer/probe binding sites. However, multiple nucleotide mismatches might contribute to false negatives. CONCLUSION: An understanding of the limitations depending on the targeted genes and primer/probe sets may influence the selection of molecular detection assays by clinical laboratories.

Performance Evaluation of the MBT STAR®-Carba IVD Assay for the Detection of Carbapenemases With MALDI-TOF MS.

Objectives: The increasing rate of carbapenem resistance in Gram-negative bacteria is a major public health problem and rapid detection is essential for infection management. We evaluated the performances of the MBT STAR®-Carba IVD assay (Bruker Daltonics) to detect carbapenemase-producing organisms (CPO) from bacterial colonies and directly from positive blood culture bottles with MALDI-TOF MS. Methods: We analyzed 130 strains with a reduced susceptibility to at least one carbapenem including 109 CPO (6 KPC, 27 NDM, 21 VIM, 1 IMP, 41 OXA-48-like, 8 OXA-23, 2 OXA-24/-40, and 2 OXA-58) and 21 non-CPO. The assay on colonies was performed with all 130 strains while the assay on spiked blood cultures was performed with 45 strains. Samples were prepared with the MBT STAR®-CARBA IVD kit and imipenem hydrolysis by the potential carbapenemase was analyzed with the MBT STAR®-BL module (Bruker Daltonics) on MALDI-TOF MS. Results: Performed on colonies, the assay detected all carbapenemase-producing Enterobacteriaceae (n = 78), Pseudomonas spp. (n = 19) and Acinetobacter spp. (n = 12). All 21 tested non-CPO remained negative resulting in sensitivity and specificity of 100%. Performed on positive blood cultures, the assay detected all carbapenemase-producing Enterobacteriaceae (n = 23) and Pseudomonas spp. (n = 4) but missed 9/12 carbapenemase-producing Acinetobacter spp. However, a prolonged imipenem-incubation time of the strain pellet improved carbapenemase detection. Non-CPO from positive blood culture bottles remained negative (n = 5) with the assay with the exception of one Klebsiella pneumoniae isolate. Conclusion: The MBT STAR®-Carba IVD assay is a highly reliable method for the detection of carbapenemase activity in Gram-negative bacteria. However, time-consuming sample preparation steps and reagent costs need to be considered before implementation in a routine clinical microbiology laboratory.

Study of genotypes and virB4 secretion gene of Bartonella henselae strains from patients with clinically defined cat scratch disease.

Bartonella henselae is the causative agent of cat scratch disease (CSD), which usually presents as a self-limiting lymphadenopathy. Occasionally, the bacteria will spread and be responsible for tissue and visceral involvement. Two B. henselae genotypes (genotypes I and II) have been described to be responsible for uncomplicated CSD on the basis of 16S rRNA sequence analysis. A type IV secretion system (T4SS) similar to the virulence-associated VirB system of Agrobacterium tumefaciens was recently identified in the B. henselae Houston-1 genotype I strain. We studied the correlations of the B. henselae genotypes with the clinical presentations and with the presence of T4SS. Isolates originated from CSD patients whose lymph nodes were prospectively analyzed. B. henselae genotype I was identified in 13 of 42 patients (30%). Among these, two teenage twins presented with hepatosplenic CSD and one immunocompetent adult presented with osteomyelitis. Genotype II was detected in 28 of 42 patients (67%), all of whom presented with uncomplicated CSD. The last patient was infected with both genotypes. T4SS was studied by PCR amplification of the virB4 gene. Amplification of virB4 codons 146 to 256, 273 to 357, and 480 to 537 enabled us to detect 66, 90, and 100% of the B. henselae isolates, respectively. Sequence analysis revealed sequence variations that correlated with genotype distribution. Our studies suggest that B. henselae genotype I strains harbor virB4 genes that are different from those harbored by genotype II strains and that genotype I strains might be more pathogenic.