Rapid pathogen characterization from positive blood cultures (BC) can improve management of patients with blood stream infections (BSI). The FilmArray blood culture identification (BCID) assay is a molecular test approved for direct identification of BSI causing pathogens from positive BC. A recently updated version of the panel (BCID2) comprises improved species identification characteristics, and allows for the detection of one ESBL- and several carbapenemase-encoding genes. Here, the clinical performance of the BCID2 assay for species identification in 180 positive BCs was evaluated. BCID2 results were concordant with standard of care (SOC) in 159/180 (88.3%) BCs. 68/74 (91.9%) and 71/74 (96.0%) of all samples growing mono-bacterial, Gram-positive or Gram-negative pathogens, respectively, were identified in agreement with SOC results. Non-concordance was related to the detection of additional pathogens by the BCID2 (n= 4), discrepant species identification (n= 4), or failure of BCID2 to detect on-panel pathogens (n= 1). A number (12/31; 38.7%) of discordant results became evident in poly-microbial BC specimens. BCID2 identified presence of blaCTX-M carrying species in 12 BC specimens, but failed to predict a third-generation cephalosporin resistance in four isolates exhibiting independent cephalosporin-resistance mechanisms. Carbapenem-resistance related to the presence of blaVIM-2 or blaOxa-48-like was correctly predicted in two isolates. In conclusion, BCID2 assay is a reliable tool for rapid BC processing and species identification. Despite inclusion of common ESBL- or carbapenemase-encoding markers, the multifactorial nature of β–lactam resistance in Gram-negative organisms warrants combination of BCID2 with (rapid) phenotypic susceptibility assays.
The role of respiratory superinfections in patients with coronavirus disease 2019 (COVID-19) pneumonia remains unclear. We investigated the prevalence of earlyand late-onset superinfections in invasively ventilated patients with COVID-19 pneumonia admitted to our department of intensive care medicine between March 2020 and November 2020. Of the 102 cases, 74 (72.5%) received invasive ventilation and were tested for viral, bacterial, and fungal pathogens on Days 0-7, 8-14, and 15-21 after the initiation of mechanical ventilation. Approximately 45% developed one or more respiratory superinfections. There was a clear correlation between the duration of invasive ventilation and the prevalence of coinfecting pathogens. Male patients with obesity and those suffering from chronic obstructive pulmonary disease and/or diabetes mellitus had a significantly higher probability to develop a respiratory superinfection. The prevalence of viral coinfections was high, with a predominance of the herpes simplex virus (HSV), followed by cytomegalovirus. No respiratory viruses or intracellular bacteria were detected in our cohort.We observed a high coincidence between Aspergillus fumigatus and HSV infection.Gram-negative bacteria were the most frequent pathogen group. Klebsiella aerogenes was detected early after intubation, while Klebsiella pneumoniae and Pseudomonas aeruginosa were related to a prolonged respiratory weaning.
Background: Kosakonia cowanii, formerly known as Enterobacter cowanii, is a Gram-negative bacillus belonging to the order Enterobacterales. The species is usually recognized as a plant pathogen and has only anecdotally been encountered as a human pathogen. Here we describe the rare case of a K. cowanii infection presenting as an acute cholecystitis and provide a review of available literature. Evident difficulties in species identification by biochemical profiling suggests that potentially, K. cowanii might represent an underestimated human pathogen. Case presentation: A 61-year old immunocompromised man presented to the hospital with fever and pain in the upper right abdomen. Sonography revealed an inflamed gall bladder and several gall stones. A cholecystectomy proved diagnosis of an acute cholecystitis with a partial necrosis of the gall bladder. Surgical specimen grew pure cultures of Gram-negative rods unambiguously identified as K. cowanii by MALDI-TOF, 16S-rRNA analysis and whole genome sequencing. Conclusions: Reporting cases of Kosakonia species can shed light on the prevalence and clinical importance of this rare cause of human infection. Our case is the first to describe an infection without prior traumatic inoculation of the pathogen from its usual habitat, a plant, to the patient. This raises the question of the route of infections as well as the pathogen's ability to colonize the human gut.
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