Staphylococcus aureus ventilator-associated pneumonia in patients with COVID-19: clinical features and potential inference with lung dysbiosis

Abstract

Background Hospitalized patients with COVID-19 admitted to the intensive care unit (ICU) and requiring mechanical ventilation are at risk of ventilator-associated bacterial infections secondary to SARS-CoV-2 infection. Our study aimed to investigate clinical features of Staphylococcus aureus ventilator-associated pneumonia (SA-VAP) and, if bronchoalveolar lavage samples were available, lung bacterial community features in ICU patients with or without COVID-19. Methods We prospectively included hospitalized patients with COVID-19 across two medical ICUs of the Fondazione Policlinico Universitario A. Gemelli IRCCS (Rome, Italy), who developed SA-VAP between 20 March 2020 and 30 October 2020 (thereafter referred to as cases). After 1:2 matching based on the simplified acute physiology score II (SAPS II) and the sequential organ failure assessment (SOFA) score, cases were compared with SA-VAP patients without COVID-19 (controls). Clinical, microbiological, and lung microbiota data were analyzed. Results We studied two groups of patients (40 COVID-19 and 80 non-COVID-19). COVID-19 patients had a higher rate of late-onset (87.5% versus 63.8%; p = 0.01), methicillin-resistant (65.0% vs 27.5%; p < 0.01) or bacteremic (47.5% vs 6.3%; p < 0.01) infections compared with non-COVID-19 patients. No statistically significant differences between the patient groups were observed in ICU mortality (p = 0.12), clinical cure (p = 0.20) and microbiological eradication (p = 0.31). On multivariable logistic regression analysis, SAPS II and initial inappropriate antimicrobial therapy were independently associated with ICU mortality. Then, lung microbiota characterization in 10 COVID-19 and 16 non-COVID-19 patients revealed that the overall microbial community composition was significantly different between the patient groups (unweighted UniFrac distance, R2 0.15349; p < 0.01). Species diversity was lower in COVID-19 than in non COVID-19 patients (94.4 ± 44.9 vs 152.5 ± 41.8; p < 0.01). Interestingly, we found that S. aureus (log2 fold change, 29.5), Streptococcus anginosus subspecies anginosus (log2 fold change, 24.9), and Olsenella (log2 fold change, 25.7) were significantly enriched in the COVID-19 group compared to the non–COVID-19 group of SA-VAP patients. Conclusions In our study population, COVID-19 seemed to significantly affect microbiological and clinical features of SA-VAP as well as to be associated with a peculiar lung microbiota composition.

COVID-19 and Antimicrobial Resistance: Data from the Greek Electronic System for the Surveillance of Antimicrobial Resistance—WHONET-Greece (January 2018–March 2021)

“…In Staphylococcus aureus blood isolates from patients hospitalized in the wards, significant changes in the slope of non-susceptibility to oxacillin between the two study periods was observed, which is consistent with the literature [ 27 , 65 , 74 ]. Of note, the decreasing trend for oxacillin non-susceptibility during the pre-pandemic period was followed by an increasing one.…”

Impact of SARS-CoV-2 Epidemic on Antimicrobial Resistance: A Literature Review

“…Moreover, excluding coinfections, emerging data confirmed the importance of MRSA as a potential agent of secondary infections, including ventilator-associated pneumonia (VAP) in subjects hospitalized in ICU for SARS-CoV-2 respiratory failure [29] and severe bloodstream infections [30], significantly increasing the overall risk of mortality. In fact, a dramatically high 14-day and 30-day mortality (54.8% and 66.7%, respectively) was documented in a recently published case series of S. aureus bloodstream infections [31].…”

“…In New Jersey, during a peak of COVID-19 cases in April 2020, Perez et al reported several unintentional changes in standard infection prevention and control (IPC) practices, which included a temporary discontinuation of appropriate PPE use, environmental cleaning and prolonged use of ventilator circuits and suctioning catheters [98]. Furthermore, in Italy, in a perspective case-control study conducted by De Pascale et al on mechanically ventilated patients, the proportion of ventilator associated pneumonia due to methicillin-resistant vs. methicillin susceptible S. aureus was significantly higher for COVID-19 patients (65.0% vs. 27.5%; p < 0.01) vs. non-COVID-19 patients, suggesting a higher rate of MRSA colonization/environmental contamination in COVID-19 ICUs [29].…”

Clinical outcomes in patients co-infected with COVID-19 and Staphylococcus aureus: a scoping review

“…Of these 28 included studies, 22 were case reports (describing single patients with individual data), two were case series (describing 7–42 patients with aggregate data), and four were cohort studies (describing 4–40 patients with aggregate data). Countries of study publication included the United States (n = 7) [ 7 , 9 , 21 – 25 ], Italy (n = 7) [ 26 – 32 ], Japan (n = 2) [ 33 , 34 ], Iran (n = 2) [ 35 , 36 ], the United Kingdom (n = 2) [ 37 , 38 ], Spain (n = 2) [ 39 , 40 ], Bahrain (n = 1) [ 41 ], China (n = 1) [ 42 ], France (n = 1) [ 43 ], the Philippines (n = 1) [ 44 ], Korea (n = 1) [ 45 ], and Canada (n = 1) [ 46 ], with publication dates ranging from April 15, 2020 to June 16, 2021. Table 1 describes the characteristics of these included studies and available information on their respective patient demographics in detail.…”