Diagnostic Microbiology and Infectious Disease

Pre-exposure prophylaxis (PrEP) is crucial to prevent severe COVID-19 in immunocompromised patients. A reliable method is needed to quantify anti-SARS-CoV-2 antibody levels for personalized monitoring during PrEP. We measured the binding antibody concentrations of 63 immunocompromised patients receiving 300mg or 600mg tixagevimab/cilgavimab on PrEP day and twice during the following 3 months. All blood samples were tested using the Abbott anti-SARS-CoV-2 IgG II Quant assay, the Roche Elecsys anti-SARS-CoV-2 S assay, and live virus-based neutralization assays...

Three years into the coronavirus disease (COVID)-19 pandemic and the world is still struggling with the aftermath of this global health crisis. In Brazil, we are witnessing serious economic, health, social, and political problems. The rapid spread of the virus in our country was the result of a shortage of vaccines and the lack of an effective national campaign to identify and report cases. This health crisis also intensified social inequalities, hitting Indigenous peoples hard due to the lack of access to health services...

The aim of the study was to evaluate the frequency and characteristics of mixed (multiple-genotype) Helicobacter pylori infections (MGIs) in 155 Bulgarian symptomatic patients (21 children and 134 adults). MGIs were common (36.1%), including double-strain (34.8%) and triple-strain infections (1.3%). None of the 8 ulcer patients harbored multiple subtypes. We detected 18 multiple allelic combinations, of which the most frequent subtypes (17.4%) were vacA s1as2 and vacA s1cs2. The 2 patients with triple-strain infections had vacA s1bs1cs2i1i2/iceA1A2 and vacA s1as1cs2 subtypes...

Since the beginning of the pandemic, SARS-CoV-2 has shown genetic variability. All the variants that have sustained pandemic waves have shown several mutations, especially in the Spike protein that could affect viral pathogenesis. A total of 15,729 respiratory samples, collected between December 2020 and August 2022, have been included in this study. We report the circulation of SARS-CoV-2 variants in the Lombardy region, Italy, in a 2-year study period. Alpha, Delta, and Omicron variants became predominant causing the majority of cases whereas Beta or Gamma variants mostly caused local outbreaks...

Among people living with HIV (PLHIV), progressive disseminated histoplasmosis (PDH) represents an important cause of mortality. Since antigen detection allows a rapid diagnosis and the instauration of a specific treatment this study aimed to evaluate the analytical performance of the Hcp100 dot blot, an in-house assay that detects the Histoplasma capsulatum 100-kilodalton antigen in urine and compare it with 2 commercially available assays the Histoplasma Urine Antigen Lateral Flow Assay (MVD-LFA) (MiraVista® Diagnostics) and the Clarus Histoplasma Galactomannan EIA (Clarus HGM) (IMMY)...

Trichosporon asahii is an emerging opportunistic fungus that mainly causes fatal disseminated trichosporonosis, especially in immunocompromised patients. T. asahii infection has been reported in Thailand, but few studies of this fungus have been published. Therefore, this study investigated the genetic diversity of 51 clinical strains of T. asahii from urine samples in Thailand. We sequenced and characterized the beta-1-tubulin (TUB1), copper-exporting ATPase (ATP), phosphate carrier protein (PHCP), and topoisomerase-1 (TOP1) genes...

A rapid, easy-to-handle, cost-effective and universal culture-based test was developed for the identification of linezolid resistance among the most clinically relevant enterococcal and staphylococcal species. Our technique was tested using linezolid-resistant (n = 50) and linezolid-susceptible (n = 67) Gram-positive isolates: 34 Enterococcus faecium, 20 Enterococcus faecalis, 20 Staphylococcus aureus, 38 Staphylococcus epidermidis, and 5 Staphylococcus capitis. The susceptibility/resistance phenotype of E...

A member of the Enterobacteriaceae family, Providencia alcalifaciens is typically recognized as a source of gastrointestinal illness. Although its pathogenicity is not well known, many studies have suggested its mechanism of action involves the invasion of the intestinal mucosal layer. Although P. alcalifaciens is a urease producing microorganism, it has not been associated with the formation of a staghorn calculus in the setting of a urinary tract infection. This organism is neither commonly pursued in research or investigation nor is it commonly tested for in the clinical setting...

Human adenoviruses (HAdV) of species F are commonly involved in pediatric acute gastroenteritis (AGE). The real impact on Venezuelan health is unknown. To investigate the prevalence and molecular diversity of HAdV in Venezuela, 630 fecal samples collected from children with AGE in 3 cities, from 2001 to 2013, were tested by PCR. Species F and types F40/41 were identified by REA. HAdV was detected in 123 cases (19.5%), most from outpatient females under 24 months old. A progressive and substantial increase in the detection rate was observed over time, significantly higher in rotavirus vaccinated than unvaccinated children (28...

The study aimed to assess the diagnostic and prognostic value of 3 specific microRNAs (miRNAs) in early-onset neonatal sepsis (NS). We examined miR-1, miR-124, and miR-34a in 70 NS patients upon admission and compared them to 70 healthy controls by RT-PCR. The main finding of the study was the difference in miRNA expression levels between NS patients and controls. Higher expression levels of miR-1 and miR-124 were significantly associated with NS, while miR-34a expression was reduced. Among the studied miRNAs, miR-34a exhibited the highest specificity (97%) as a confirmatory test for NS...

The Resist Acineto from Coris Bioconcept is a novel immunochromatographic test for detection of the major acquired carbapenemases (OXA-23, OXA-40, OXA-58, and NDM) identified in Acinetobacter spp. This rapid and easy-to-perform test showed an excellent specificity and sensitivity, with positive and negatives predictive values of 100% in both cases.

We compared the performance of the STANDARD F and SD BIOLINE stool antigen tests in 335 patients. The performance of STANDARD F (sensitivity: 95.6%; specificity: 94%) was highly comparable to that of SD BIOLINE (sensitivity: 92.6%; specificity: 93.5%), suggesting that STANDARD F is useful for the detection of Helicobacter pylori infection.

Infectious diseases are commonly demonstrated to be caused by polymicrobial infections, which correlate with increased infection severity and poorer clinical outcomes. In this study, we report a rare intestinal coinfection case of non-O1/O139 Vibrio cholerae and Salmonella typhimurium, along with V. cholerae septicemia. The data of quantitative real-time PCR and competition assay showed that V. cholerae may present enhanced virulence in the presence of S. typhimurium, and exerted an inhibitory growth effect over S...

Current study aims to explore the correlation between the administered dose and efficacy of voriconazole in the treatment of invasive fungal infection (IFI). The correlation between different doses of Voriconazole and plasma concentrations as well as clinical efficacy was counted. Consequently, 40 strains of pathogenic micro-organisms were isoninelated and cultured from etiological samples. A total of 66 patients with steady-state trough serum concentrations ranging from 1.0 to 5.5 μg/mL were measured, with a compliance rate of 79...

Identification of mycobacteria is crucial for clinical management of patients. The new MBT Mycobacteria kit from the Easy MycoEx protocol (Bruker) is used for the identification of mycobacteria by MALDI Biotyper. The Easy MycoEx protocol was compared to the MycoEx protocol (1) for identification of various mycobacterial isolates collected from samples in 2021, (2) for prospective identification on primary culture during 2 periods. For 44 isolates in MGIT broth, identification rates were high and similar for both protocols (98% vs 95% at cut-off 1...

Enteroaggregative Escherichia coli (EAEC), a biofilm forming pathogen, causes acute and persistent diarrhea worldwide, requiring antimicrobial therapy in severe or persistent cases. To determine the susceptibility of EAEC biofilm to antimicrobials, as single-agent or combined therapy, biofilm formation was investigated using EAEC clinical strains via peg lid. Of the 78 initially analyzed strains, 35 could form biofilms, 15 (42.9%; 15/35) were resistant to at least 1 tested antimicrobial and 20 (57.1%) were susceptible to all of them in the planktonic form...

Rickettsioses, a category of zoonosis primarily caused by Rickettsia and Orientia, is a huge cause of public health concern worldwide. Diseases like murine typhus, scrub typhus, Mediterranean spotted fever and rocky mountain spotted fever are major contributors of Rickettsioses globally, with peculiar distributions in south-east Asia, Africa, Arabia and the Americas. With the innovations in molecular diagnostics, Isothermal Amplification Technology is gaining popularity for its fidelity, rapidity and cost-effectiveness...

Acute respiratory infections represent the leading cause of morbimortality in children and viruses are the main etiological agents. Here we describe the clinical characteristics and evolution of infants admitted to intensive care unit with severe acute respiratory infection (SARI) due to Human Bocavirus 1 mono-infection in patients without previous comorbidity. We also compared them with respiratory syncytial virus (RSV) cases. Of 141 cases included (age 5.43 ± 4.54 months, 52% male), 80% had at least 1 virus detected...

OBJECTIVES: To develop an in-house matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) library for improved identification of species and subspecies of the Streptococcus bovis/Streptococcus equinus-complex (SBSEC). METHODS: A total of 236 SBSEC isolates from blood stream infections and culture collections, determined by whole genome sequencing to subspecies level, were grown in brain heart infusion broth. Mass spectra were collected using the Bruker MALDI Biotyper system after ethanol-formic acid extraction...

Brain abscess is medically challenging. In this study, we applied nanopore sequencing for 16S rRNA analysis and investigated its efficacy and diagnostic value for patients with brain abscesses. Genomic DNA was extracted from the pus samples (n = 27) of brain abscess, and 16S rRNA genes were amplified by PCR. Sequencing libraries were generated using a rapid barcoding kit, and the generated reads were analyzed using the EPI2ME16S workflow. A conventional culture study was performed. More sensitive identification of pathogens was made by 16S sequencing, faster than the culture study...