The changing pattern of bacterial and fungal respiratory isolates in patients with and without COVID-19 admitted to intensive care unit.

OBJECTIVES: Severe acute respiratory syndrome 2 (SARS-CoV-2) pandemic has had a heavy impact on national health system, especially in the first wave. That impact hit principally the intensive care units (ICUs). The large number of patients requiring hospitalization in ICUs lead to a complete upheaval of intensive wards. The increase in bed, the fewer number of nurses per patient, the constant use of personal protective equipment, the new antimicrobial surveillance protocols could have had deeply effects on microbiological flora of these wards. Moreover, the overconsumption of antimicrobial therapy in COVID-19 patients, like several studies report, could have impact of this aspect. Aim of this study is to evaluate the changing pattern of microbiological respiratory isolates during and before COVID-19 pandemic in a tertiary hospital ICUs. METHODS: A retrospective, observational study was conducted in ICUs of "ASST Papa Giovanni XXIII", a large tertiary referral hospital in Northern Italy. We have retrospectively collected the microbiological data from bronchoalveolar lavage (BAL) and tracheal aspirate (TA) of patients with COVID-19, hospitalized in ICUs from 22nd February 2020 to 31st May 2020 (Period 1), and without COVID-19, from 22nd February 2019 to 31st May 2019 (Period 2). We compared the prevalence and the antibiotic profile of bacterial and fungal species in the two time periods. RESULTS: The prevalence of Pseudomonas spp. shows a statistically significant increase from patients without COVID-19 compared to COVID-19 positive as well as the prevalence of Enterococcus spp. On the contrary, the prevalence of Gram negative non fermenting bacteria (GN-NFB), Haemophilus influenzae and Streptococcus pneumoniae showed a significant reduction between two periods. There was a statistically significant increase in resistance of Pseudomonas spp. to carbapenems and piperacillin/tazobactam and Enterobacterales spp. for piperacillin/tazobactam, in COVID-19 positive patients compared to patients without COVID-19. We did not observe significant changing in fungal respiratory isolates. CONCLUSIONS: A changing pattern in prevalence and resistance profiles of bacterial and fungal species was observed during COVID-19 pandemic.

Rapid identification of non-tuberculous mycobacteria with MALDI-TOF mass spectrometry.

Rapid and accurate identification of non-tuberculous mycobacteria (NTM) is important for a prompt start to antibiotic therapy. The aim of this study was to obtain accurate identification of NTM quickly by analyzing the performance of the MALDI-TOF mass spectrometry (MS) system VITEK® MS in identifying various NTM species from solid medium and MGIT 960 liquid medium. The study was performed in two phases: preliminary and perspective. Overall, 41/42 species and 33/34 species were correctly identified from the MGIT medium in the preliminary and perspective phases, respectively. The VITEK® MS system includes in its database part of the mycobacteria from the Mycobacterium fortuitum complex but is unable to discriminate among the various species belonging to the complex. Although the VITEK® MS system does not have the protein spectrum of Mycobacterium chimaera, it is not able to distinguish between Mycobacterium chimaera and Mycobacterium intracellulare. Since the VITEK® MS includes the separate protein spectrum of both M. chelonae and M. abscessus, it can discriminate between the two microorganisms. Thanks to these studies we show that the VITEK® MS system is a reliable method for identification of NTMs directly from MGIT liquid medium, instead of the use of solid media.

Blood stream infections during the first wave of COVID-19. A short microbiological retrospective picture at Papa Giovanni XXIII Hospital, Bergamo, Italy.

This paper aims to describe the etiology of bloodstream infections in COVID-19, Papa Giovanni XXIII Hospital, Bergamo, Italy. Two periods were evaluated: February 22-May 21, 2019/2020. We considered: the number of patients and blood culture sets, species of isolates (bacteria, specifically those indicated by EARS criteria; CoNS; Candida albicans) and their antibiotic sensitivity. In 2020 Escherichia coli and Carbapenemase-producing Klebsiella pneumoniae disappeared. Candida albicans and MDR Pseudomonas aeruginosa, Enterococcus faecium and Acinetobacter baumannii were largely present. The analysis shows: 1. BSIs number was the same; 2. In the first month of the COVID-19 period, BSIs were uncommon; 3. Microbial etiologies were different; 4. MDR isolates were less common.