Molecular microbiological testing of lower respiratory tract samples during COVID-19 pandemic / Alsó légúti minták molekuláris mikrobiológiai vizsgálata a koronavírus-járvány idoszakában

Introduction: BioFire FilmArray Pneumonia plus Panel (bioMerieux) is a PCR method for microbiological diagnostics of lower respiratory infections. It can detect 18 bacteria, 9 viruses and 7 antibiotic resistance genes in real time. It can help the differential diagnosis and the choice of therapy of pneumonia, by giving results in two hours. Objective: Reviewing the results of pneumonia PCR tests performed in our laboratory, and comparing them with the results of conventional culturing. Method: From October 2020 to September 2021, 820 lower respiratory tract samples were analyzed from inpatients with suspected pneumonia. Beside the PCR test, culturing was also performed. Oropharyngeal swabs were used for supplementary SARS-CoV-2 PCR. Results: 40% of samples were collected from SARS-CoV-2-positive patients. In 60% of the samples, the PCR test detected pathogens or resistance genes. The most commonly detected pathogens were Pseudomonas aeruginosa, Staphylococcus aureus and Acinetobacter baumannii. 44% of the bacteria detected by PCR were not verified by culturing, whereas by culturing, several other bacteria, fungi and antibiotic resistance mechanisms were detected, which were not shown in the results of the multiplex PCR tests. In SARS-CoV-2-positive inpatients, 25.8% of the detected bacteria was S. aureus. The most common resistance gene was mecA/C (MRSA). In this group, other respiratory virus genes were detected in 2% of SARS-CoV-2-positive patients, whereas in 13% in samples of SARS-CoV-2-negative patients. Conclusions: Because of the importance of pathogens excluded from the PCR targets and multifactorial mechanisms of antibiotic resistance, culturing is recommended to perform beside pneumonia-specific multiplex PCR tests.

Occurrence of Escherichia coli producing extended spectrum ß-lactamases in food-producing animals.

Multidrug resistance due to the production of extended-spectrum beta-lactamases (ESBLs) is a major problem in human as well as in veterinary medicine. These strains appear in animal and human microbiomes and can be the source of infection both in animal and in human healthcare, in accordance with the One Health theorem. In this study we examined the prevalence of ESBL-producing bacteria in food-producing animals. We collected 100 porcine and 114 poultry samples to examine the prevalence of ESBL producers. Isolates were identified using the MALDI-TOF system and their antibiotic susceptibility was tested using the disk diffusion method. ESBL gene families and phylogroups were detected by polymerase chain reactions. The prevalence of ESBL producers was relatively high in both sample groups: 72 (72.0%) porcine and 39 (34.2%) poultry isolates were ESBL producers. Escherichia coli isolates were chosen for further investigations. The most common ESBL gene was CTX-M-1 (79.3%). Most of the isolates belong to the commensal E. coli phylogroups. The porcine isolates could be divided into three phylogroups, while the distribution of the poultry isolates was more varied. In summary, ESBL-producing bacteria are prevalent in the faecal samples of the examined food-producing animals, with a dominance of the CTX-M-1 group enzymes and commensal E. coli phylogroups.