Secondary Infections in Patients with Extremely Severe COVID-19 During ECMO Therapy.

Up to 70% of patients hospitalized for COVID-19 need respiratory support, up to 10% need high-flow oxygen therapy, non-invasive and invasive ventilation. However, standard methods of respiratory support are ineffective in 0.4-0.5% of patients. In case of potentially reversible critical refractory respiratory failure that patients may require ECMO. Management of patients with extremely severe COVID-19 associates with numerous clinical challenges, including critical illness, multiple organ dysfunction, blood coagulation disorders, requiring prolonged ICU stay and care, use of multiple pharmacotherapies including immunosuppressive drugs. Pharmacological suppression of immunity is associated with a significant increase in the risk of secondary bacterial and fungal infections. Currently, data on epidemiology of secondary infections in patients with COVID-19 undergoing ECMO is limited. Aim. To study the prevalence and etiology of secondary infections associated with positive blood cultures in patients with extremely severe COVID-19 requiring ECMO. Materials and methods. A single-center retrospective non-interventional epidemiological study including 125 patients with extremely severe COVID-19 treated with ECMO in April 2020 to December 2021. Results. Out of 700 blood culture tests performed in 125 patients during the study, 250 tests were positive confirming bacteremia/fungemia. Isolated pathogens varied depending on the duration of ECMO: gram-positive bacteria (primarily coagulase-negative staphylococci) dominated from the initiation of ECMO support;increased duration of ECMO associated with an increasing the proportion of pathogens common in ICU (Klebsiella pneumoniae and/or Acinetobacter baumannii with extensively drug resistant and pan-drug resistant phenotypes, and vancomycin-resistant Enterococcus faecium). When ECMO lasted more than 7-14 days, opportunistic pathogens (Candida species, Stenotrophomonas maltophilia, Providencia stuartii, non-diphtheria corynebacteria, Burkholderia species and others) prevailed as etiological agents. Conclusion. Longer duration of ECMO resulted in increasing the rates of infectious complications. In patients undergoing ECMO for more than 14 days, the microbiological landscape becomes extremely diverse, which hampers choosing an empirical antimicrobial therapy. Since potential pathogens causing secondary infections in patients during ECMO are difficult to predict, rapid identification of rare opportunistic pathogens and their sensitivity profile, followed by targeted administration of antimicrobials, seems most beneficial.Copyright © 2023, V.A. Negovsky Research Institute of General Reanimatology. All rights reserved.

Bloodstream Infections with Opportunistic Pathogens in COVID-19 Era: A Real Challenge Necessitates Stringent Infection Control.

Background : Bloodstream infections (BSI) due to opportunistic microbes in the coronavirus disease 2019 (COVID-19) pandemic lead to high morbidity and mortality among hospitalized patients. Thus, it is vital to find out the risk factors of BSI and to learn the ways to mitigate it. Aim : The aim of this study was to evaluate important risk factors of BSI due to opportunistic pathogens and to assess the role of the rigid infection control program to deal with this issue. Methods : A prospective, cross-sectional study was performed for 6 months on 150 patients admitted in both COVID-19 and non-COVID-19 intensive care units of our hospital. BSI was confirmed by the BACTEC and Vitek 2 compact system. Prospective surveillance and environmental sampling were carried out for source tracking along with rigorous infection control measures and the outcome was analyzed. Findings : Burkholderia cepacia, Elizabethkingia meningoseptica, Candida auris, vancomycin-resistant Enterococcus , and Achromobacter xylosoxidans were the common opportunistic pathogens isolated from a single or paired blood sample(s) in our study. Key risk factors were prolonged intensive care unit stay, central venous access, mechanical ventilation, immune-compromised condition, and use of biologics. Reverse osmosis water and used normal saline bottles were the common environmental source of infection. Following the implementation of precise infection control measures, there was a sharp decline in BSI cases, which was not attributed to the downfall of COVID-19 cases. Conclusion : Combined prospective surveillance and environmental sampling helped to find out the sources and implementation of an intensive and insistent infection control program that are needed to control opportunistic pathogens mediated BSI.

Pinpointing drivers of widespread colonization of Legionella pneumophila in a green building: Roles of water softener system, expansion tank, and reduced occupancy

Introduction: Legionella pneumophila is an opportunistic pathogen that is a key contributor to drinking water-associated disease outbreaks in the United States. Prolonged water stagnation periods in building plumbing systems due to low occupancy, especially during building shutdowns, breaks, and holidays, can lead to water quality deterioration and (re)colonization of buildings with L. pneumophila. Water monitoring in buildings typically relies on grab samples with small datasets. Methods: In this study, a larger dataset was created by sampling a Leadership in Energy and Environmental Design (LEED)-certified data-rich commercial building for L. pneumophila and physical-chemical water quality during the COVID-19 pandemic after reduced building occupancy. A proxy for human occupancy rates using WIFI logins was recorded throughout the study period. Results: L. pneumophila was observed in grab samples taken throughout the building, where concentrations generally increased with greater distances from the building point of entry to locations throughout the building. Factors conducive to microbial growth were identified in the building including fluctuations in water temperatures, lack of chlorine residual, a low water heater setpoint, colonized water-saving fixtures, prolonged stagnation throughout the building;especially in an expansion tank designed to reduce pressure issues during demand fluctuations, and the presence of oversized softener tanks with ion exchange resin that contributed to chlorine residual removal as well as colonization of the resin with L. pneumophila. Discussion: Flushing and thermal disinfection alone did not resolve the problem, and replacement of the expansion tank ultimately resolved the L. pneumophila issue. As ad-hoc approaches are logistically- and time-intensive, more proactive approaches are needed for informing preventative and corrective actions for reducing the risk of exposure to opportunistic pathogens in the building plumbing. Copyright © 2023 Joshi, Richard, Levya, Harrison, Saetta, Sharma, Crane, Mushro, Dieter, Morgan, Heida, Welco, Boyer, Westerhoff and Hamilton.

Nasopharyngeal microbiome of COVID-19 patients revealed a distinct bacterial profile in deceased and recovered individuals.

The bacterial co-infections in SARS-CoV-2 patients remained the least explored subject of clinical manifestations that may also determine the disease severity. Nasopharyngeal microbial community structure within SARS-CoV-2 infected patients could reveal interesting microbiome dynamics that may influence the disease outcomes. Here, in this research study, we analyzed distinct nasopharyngeal microbiome profile in the deceased (n = 48) and recovered (n = 29) COVID-19 patients and compared it with control SARS-CoV-2 negative individuals (control) (n = 33). The nasal microbiome composition of the three groups varies significantly (PERMANOVA, p-value <0.001), where deceased patients showed higher species richness compared to the recovered and control groups. Pathogenic genera, including Corynebacterium (LDA score 5.51), Staphylococcus, Serratia, Klebsiella and their corresponding species were determined as biomarkers (p-value <0.05, LDA cutoff 4.0) in the deceased COVID-19 patients. Ochrobactrum (LDA score 5.79), and Burkholderia (LDA 5.29), were found in the recovered group which harbors ordinal bacteria (p-value <0.05, LDA-4.0) as biomarkers. Similarly, Pseudomonas (LDA score 6.19), and several healthy nasal cavity commensals including Veillonella, and Porphyromonas, were biomarkers for the control individuals. Healthy commensal bacteria may trigger the immune response and alter the viral infection susceptibility and thus, may play important role and possible recovery that needs to be further explored. This research finding provide vital information and have significant implications for understanding the microbial diversity of COVID-19 patients. However, additional studies are needed to address the microbiome-based therapeutics and diagnostics interventions.

Targeting current and future threats: recent methodological trends in environmental antimicrobial resistance research and their relationships to risk assessment

Antimicrobial resistance (AMR) is a growing public health threat. Improved surveillance of AMR's genetic indicators in environmental reservoirs should lead to a more comprehensive understanding of the problem at a global scale, as with SARS-CoV-2 monitoring in sewage. However, the "best" monitoring approach is unclear. Some scientific works have emphasized monitoring for the abundance of already-known antimicrobial resistance genes (ARGs);others have emphasized monitoring for the potential of new ARGs to arise. The goal of this study was to examine which methods were employed by highly-cited papers studying AMR in environmental engineering and agricultural systems, thus providing insight into current and future methodological trends for monitoring ARGs. We searched recent (2018-2020) literature documenting AMR in five environmental matrices: wastewater, surface water, drinking water, stormwater, and livestock manure. We selected the most highly-cited papers across these matrices (89 papers from 17 809 initial results) and categorized them as using targeted methods (e.g., qPCR), non-targeted methods (e.g., shotgun metagenomics), or both. More than 80% of papers employed targeted methods. Only 33% employed non-targeted methods, and the use of targeted versus non-targeted methods varied by environmental matrix. We posit that improving AMR surveillance in environmental reservoirs requires assessing risk, and that different monitoring approaches imply different objectives for risk assessment. Targeted methods are appropriate for quantifying known threats, particularly in environmental matrices where direct human exposure is likely (e.g., drinking water). However, long-term studies employing non-targeted methods are needed to provide an understanding of how frequently new threats (i.e., novel ARGs) arise.

Interplay between severities of COVID-19 and the gut microbiome: implications of bacterial co-infections?

COVID-19 is an acute respiratory distress syndrome and is often accompanied by gastrointestinal symptoms. The SARS-CoV-2 has been traced not only in nasopharyngeal and mid-nasal swabs but also in stool and rectal swabs of COVID-19 patients. The gut microbiota is important for an effective immune response as it ensures that unfavorable immune reactions in lungs and other vital organs are regulated. The human gut-lung microbiota interplay provides a framework for therapies in the treatment and management of several pulmonary diseases and infections. Here, we have collated data from COVID-19 studies, which suggest that bacterial co-infections as well as the gut-lung cross talk may be important players in COVID-19 disease prognosis. Our analyses suggests a role of gut microbiome in pathogen infections as well as in an array of excessive immune reactions during and post COVID-19 infection recovery period.