Gut bacterial dysbiosis and instability is associated with the onset of complications and mortality in COVID-19.

There is a growing debate about the involvement of the gut microbiome in COVID-19, although it is not conclusively understood whether the microbiome has an impact on COVID-19, or vice versa, especially as analysis of amplicon data in hospitalized patients requires sophisticated cohort recruitment and integration of clinical parameters. Here, we analyzed fecal and saliva samples from SARS-CoV-2 infected and post COVID-19 patients and controls considering multiple influencing factors during hospitalization. 16S rRNA gene sequencing was performed on fecal and saliva samples from 108 COVID-19 and 22 post COVID-19 patients, 20 pneumonia controls and 26 asymptomatic controls. Patients were recruited over the first and second corona wave in Germany and detailed clinical parameters were considered. Serial samples per individual allowed intra-individual analysis. We found the gut and oral microbiota to be altered depending on number and type of COVID-19-associated complications and disease severity. The occurrence of individual complications was correlated with low-risk (e.g., Faecalibacterium prausznitzii) and high-risk bacteria (e.g., Parabacteroides ssp.). We demonstrated that a stable gut bacterial composition was associated with a favorable disease progression. Based on gut microbial profiles, we identified a model to estimate mortality in COVID-19. Gut microbiota are associated with the occurrence of complications in COVID-19 and may thereby influencing disease severity. A stable gut microbial composition may contribute to a favorable disease progression and using bacterial signatures to estimate mortality could contribute to diagnostic approaches. Importantly, we highlight challenges in the analysis of microbial data in the context of hospitalization.

SARS-CoV-2, other respiratory viruses and bacteria in aerosols: Report from Kuwait's hospitals.

The role of airborne particles in the spread of severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) is well explored. The novel coronavirus can survive in aerosol for extended periods, and its interaction with other viral communities can cause additional virulence and infectivity. This baseline study reports concentrations of SARS-CoV-2, other respiratory viruses, and pathogenic bacteria in the indoor air from three major hospitals (Sheikh Jaber, Mubarak Al-Kabeer, and Al-Amiri) in Kuwait dealing with coronavirus disease 2019 (COVID-19) patients. The indoor aerosol samples showed 12-99 copies of SARS-CoV-2 per m3 of air. Two non-SARS-coronavirus (strain HKU1 and NL63), respiratory syncytial virus (RSV), and human bocavirus, human rhinoviruses, Influenza B (FluB), and human enteroviruses were also detected in COVID-positive areas of Mubarak Al Kabeer hospital (MKH). Pathogenic bacteria such as Mycoplasma pneumonia, Streptococcus pneumonia and, Haemophilus influenza were also found in the hospital aerosols. Our results suggest that the existing interventions such as social distancing, use of masks, hand hygiene, surface sanitization, and avoidance of crowded indoor spaces are adequate to prevent the spread of SARS-CoV-2 in enclosed areas. However, increased ventilation can significantly reduce the concentration of SARS-CoV-2 in indoor aerosols. The synergistic or inhibitory effects of other respiratory pathogens in the spread, severity, and complexity of SARS-CoV-2 need further investigation.

Diversity and functional landscapes in the microbiota of animals in the wild.

Animals in the wild are able to subsist on pathogen-infected and poisonous food and show immunity to various diseases. These may be due to their microbiota, yet we have a poor understanding of animal microbial diversity and function. We used metagenomics to analyze the gut microbiota of more than 180 species in the wild, covering diverse classes, feeding behaviors, geographies, and traits. Using de novo metagenome assembly, we constructed and functionally annotated a database of more than 5000 genomes, comprising 1209 bacterial species of which 75% are unknown. The microbial composition, diversity, and functional content exhibit associations with animal taxonomy, diet, activity, social structure, and life span. We identify the gut microbiota of wild animals as a largely untapped resource for the discovery of therapeutics and biotechnology applications.

Variations in respiratory pathogen carriage among a homeless population in a shelter for men in Marseille, France, March-July 2020: cross-sectional 1-day surveys.

We aimed to compare respiratory pathogen carriage by PCR during three different time periods in 2020 in sheltered homeless people in Marseille, France. The overall prevalence of respiratory pathogen carriage in late March-early April (69.9%) was significantly higher than in late April (42.3%) and mid-July (45.1%). Bacterial carriage significantly decreased between late March-early April and late April. SARS-CoV-2 was detected only in late March-early April samples (20.6%). Measures aiming at mitigating SARS-CoV-2 transmission were effective and also impacted bacterial carriage. Seasonal variations of bacterial carriage between winter and summer in this population were not marked.

Unraveling the Interconnection Patterns Across Lung Microbiome, Respiratory Diseases, and COVID-19.

Albeit the lungs were thought to be sterile, recent scientific data reported a microbial microbiota in the lungs of healthy individuals. Apparently, new developments in technological approachesincluding genome sequencing methodologies contributed in the identification of the microbiota and shed light on the role of the gut and lung microbiomes in the development of respiratory diseases. Moreover, knowledge of the human microbiome in health may act as a tool for evaluating characteristic shifts in the case of disease. This review paper discusses the development of respiratory disease linked to the intestinal dysbiosis which influences the lung immunity and microbiome. The gastrointestinal-lung dialogue provides interesting aspects in the pathogenesis of the respiratory diseases. Lastly, we were further interested on the role of this interconnection in the progression and physiopathology of newly emergedCOVID-19.

Detection of Bacterial Coinfection in COVID-19 Patients Is a Missing Piece of the Puzzle in the COVID-19 Management in Indonesia.

Bacterial coinfection in COVID-19 patients has the potential to complicate treatments and accelerate the development of antibiotic resistance in the clinic due to the widespread use of broad-spectrum antibiotics, including in Indonesia. The surge of COVID-19 patients may worsen antibiotic overuse; therefore, information on the actual extent of bacterial coinfection in COVID-19 patients in Indonesia is crucial to inform appropriate treatment. This Viewpoint elaborates on a nascent research project focused on sequencing of swab samples to detect bacterial coinfection in COVID-19 patients in Indonesia. Supported by a L'Oréal-UNESCO For Women in Science National Fellowship, it is designed to inform better clinical management of COVID-19 in Indonesia.

Bacterial but no SARS-CoV-2 contamination after terminal disinfection of tertiary care intensive care units treating COVID-19 patients.

BACKGROUND: In intensive care units (ICUs) treating patients with Coronavirus disease 2019 (COVID-19) invasive ventilation poses a high risk for aerosol and droplet formation. Surface contamination of severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) or bacteria can result in nosocomial transmission. METHODS: Two tertiary care COVID-19 intensive care units treating 53 patients for 870 patient days were sampled after terminal cleaning and preparation for regular use to treat non-COVID-19 patients. RESULTS: A total of 176 swabs were sampled of defined locations covering both ICUs. No SARS-CoV-2 ribonucleic acid (RNA) was detected. Gram-negative bacterial contamination was mainly linked to sinks and siphons. Skin flora was isolated from most swabbed areas and Enterococcus faecium was detected on two keyboards. CONCLUSIONS: After basic cleaning with standard disinfection measures no remaining SARS-CoV-2 RNA was detected. Bacterial contamination was low and mainly localised in sinks and siphons.

Enriched Aerosol-to-Hydrosol Transfer for Rapid and Continuous Monitoring of Bioaerosols.

Bioaerosols, including infectious diseases such as COVID-19, are a continuous threat to global public safety. Despite their importance, the development of a practical, real-time means of monitoring bioaerosols has remained elusive. Here, we present a novel, simple, and highly efficient means of obtaining enriched bioaerosol samples. Aerosols are collected into a thin and stable liquid film by the unique interaction of a superhydrophilic surface and a continuous two-phase centrifugal flow. We demonstrate that this method can provide a concentration enhancement ratio of ∼2.4 × 106 with a collection efficiency of ∼99.9% and an aerosol-into-liquid transfer rate of ∼95.9% at 500 nm particle size (smaller than a single bacterium). This transfer is effective in both laboratory and external ambient environments. The system has a low limit of detection of <50 CFU/m3air using a straightforward bioluminescence-based technique and shows significant potential for air monitoring in occupational and public-health applications.

Gut microbiota composition reflects disease severity and dysfunctional immune responses in patients with COVID-19.

OBJECTIVE: Although COVID-19 is primarily a respiratory illness, there is mounting evidence suggesting that the GI tract is involved in this disease. We investigated whether the gut microbiome is linked to disease severity in patients with COVID-19, and whether perturbations in microbiome composition, if any, resolve with clearance of the SARS-CoV-2 virus. METHODS: In this two-hospital cohort study, we obtained blood, stool and patient records from 100 patients with laboratory-confirmed SARS-CoV-2 infection. Serial stool samples were collected from 27 of the 100 patients up to 30 days after clearance of SARS-CoV-2. Gut microbiome compositions were characterised by shotgun sequencing total DNA extracted from stools. Concentrations of inflammatory cytokines and blood markers were measured from plasma. RESULTS: Gut microbiome composition was significantly altered in patients with COVID-19 compared with non-COVID-19 individuals irrespective of whether patients had received medication (p<0.01). Several gut commensals with known immunomodulatory potential such as Faecalibacterium prausnitzii, Eubacterium rectale and bifidobacteria were underrepresented in patients and remained low in samples collected up to 30 days after disease resolution. Moreover, this perturbed composition exhibited stratification with disease severity concordant with elevated concentrations of inflammatory cytokines and blood markers such as C reactive protein, lactate dehydrogenase, aspartate aminotransferase and gamma-glutamyl transferase. CONCLUSION: Associations between gut microbiota composition, levels of cytokines and inflammatory markers in patients with COVID-19 suggest that the gut microbiome is involved in the magnitude of COVID-19 severity possibly via modulating host immune responses. Furthermore, the gut microbiota dysbiosis after disease resolution could contribute to persistent symptoms, highlighting a need to understand how gut microorganisms are involved in inflammation and COVID-19.

Bacterial coinfection in critically ill COVID-19 patients with severe pneumonia.

Severe 2019 novel coronavirus infectious disease (COVID-19) with pneumonia is associated with high rates of admission to the intensive care unit (ICU). Bacterial coinfection has been reported to be rare. We aimed at describing the rate of bacterial coinfection in critically ill adult patients with severe COVID-19 pneumonia. All the patients with laboratory-confirmed severe COVID-19 pneumonia admitted to the ICU of Tenon University-teaching hospital, from February 22 to May 7th, 2020 were included. Respiratory tract specimens were obtained within the first 48 h of ICU admission. During the study period, 101 patients were referred to the ICU for COVID-19 with severe pneumonia. Most patients (n = 83; 82.2%) were intubated and mechanically ventilated on ICU admission. Overall, 20 (19.8%) respiratory tract specimens obtained within the first 48 h. Staphylococcus aureus was the main pathogen identified, accounting for almost half of the early-onset bacterial etiologies. We found a high prevalence of early-onset bacterial coinfection during severe COVID-19 pneumonia, with a high proportion of S. aureus. Our data support the current WHO guidelines for the management of severe COVID-19 patients, in whom antibiotic therapy directed to respiratory pathogens is recommended.

Nosocomial infections associated to COVID-19 in the intensive care unit: clinical characteristics and outcome.

Bacterial and fungal co-infection has been reported in patients with COVID-19, but there is limited experience on these infections in critically ill patients. The objective of this study was to assess the characteristics and ouctome of ICU-acquired infections in COVID-19 patients. We conducted a retrospective single-centre, case-control study including 140 patients with severe COVID-19 admitted to the ICU between March and May 2020. We evaluated the epidemiological, clinical, and microbiological features, and outcome of ICU-acquired infections. Fifty-seven patients (40.7%) developed a bacterial or fungal nosocomial infection during ICU stay. Infection occurred after a median of 9 days (IQR 5-11) of admission and was significantly associated with the APACHE II score (p = 0.02). There were 91 episodes of infection: primary (31%) and catheter-related (25%) bloodstream infections were the most frequent, followed by pneumonia (23%), tracheobronchitis (10%), and urinary tract infection (8%) that were produced by a wide spectrum of Gram-positive (55%) and Gram-negative bacteria (30%) as well as fungi (15%). In 60% of cases, infection was associated with septic shock and a significant increase in SOFA score. Overall ICU mortality was 36% (51/140). Infection was significantly associated with death (OR 2.7, 95% CI 1.2-5.9, p = 0.015) and a longer ICU stay (p < 0.001). Bacterial and fungal nosocomial infection is a common complication of ICU admission in patients with COVID-19. It usually presents as a severe form of infection, and it is associated with a high mortality and longer course of ICU stay.

Sensors and Analytical Technologies for Air Quality: Particulate Matters and Bioaerosols.

Particulate matters (PMs), e. g. dusts, fibres, smokes, fumes, mists, liquid droplets and airborne respirable solid or liquid particles, are the major sources of air pollution concerning outdoor and indoor air quality. Among various PMs, bioaerosols are airborne particles that are either living organisms (bacteria, viruses, and fungi) or originate from living organisms (endotoxin, allergen, etc). PMs and/or bioaerosols have adverse health effects of infection, allergy, and irritation. Proper management and source identification of PMs and bioaerosols will reduce their negative health impact. In this review, we will discuss the analytical technologies and sensors for PMs and bioaerosols. We will first introduce four types of PM analysers, namely, filter-based gravimetric method (GMM), optical method, ß-ray absorption method (BAM), and tapered element oscillating microbalance (TEOM). We will provide examples of how commercial PM analyzers of different principles have been compared and calibrated for specific applications under different climate conditions of specific geographic locations. For bioaerosols, having more complex biological and biochemical identity, we will start from air sampling techniques, followed by a discussion of various detection methods (plate culture, molecular methods, immunoassays and biosensors) in association with compatible sampling technologies. Using Influenza A (H1 N1) virus and SARS-CoV-2 (COVID-19) virus as examples, we have highlighted air sampling and detection challenges for viral aerosols relative to bacterial and fungal aerosols. Finally, we provide a perspective for future trends according to the limitation of current commercial products and the key challenges in this field.

Recognition and management of respiratory co-infection and secondary bacterial pneumonia in patients with COVID-19.

In COVID-19, respiratory infection with SARS-CoV-2 plus another virus (viral co-infection) or with SARS-CoV-2 plus a bacterial pathogen (combined viral and bacterial pneumonia) has been described. Secondary bacterial pneumonia can follow the initial phase of viral respiratory infection or occur during the recovery phase. No obvious pattern or guidelines exist for viral co-infection, combined viral and bacterial pneumonia, or secondary bacterial pneumonia in COVID-19. Based on existing clinical data and experience with similar viruses such as influenza and SARS-CoV, the management approach in COVID-19 should, ideally, take into consideration the overall presentation and the trajectory of illness.

Severity of Respiratory Infections With Seasonal Coronavirus Is Associated With Viral and Bacterial Coinfections.

The clinical presentation of human coronavirus (HCoV) infections in children varies strongly. We show that children with an HCoV-associated lower respiratory tract infection more frequently had respiratory syncytial virus codetected and higher abundance of Haemophilus influenzae/haemolyticus than asymptomatic HCoV carriers as well as children with a non-HCoV-associated lower respiratory tract infection. Viral and bacterial cooccurrence may drive symptomatology of HCoV-associated infections including coronavirus disease 2019.

Novel manufacturing of simple masks in response to international shortages: Bacterial and particulate filtration efficiency testing.

Many healthcare systems have been forced to outsource simple mask production due to international shortages caused by the COVID-19 pandemic. Providence created simple masks using surgical wrap and submitted samples to an environmental lab for bacterial filtration efficiency testing. Bacterial filtration efficiency rates ranged from 83.0% to 98.1% depending on specific material and ply, and particular filtration efficiency rates ranged from 92.3% to 97.7%. Based on mask configuration, specific surgical wrap selected, and ply, the recommended filtration efficiency for isolation and surgical masks of 95% and 98%, respectively can be achieved. These alternative masks can allow for similar coverage and safety when hospital-grade isolation masks are in short supply.

Graphene biosensors for bacterial and viral pathogens.

The infection and spread of pathogens (e.g., COVID-19) pose an enormous threat to the safety of human beings and animals all over the world. The rapid and accurate monitoring and determination of pathogens are of great significance to clinical diagnosis, food safety and environmental evaluation. In recent years, with the evolution of nanotechnology, nano-sized graphene and graphene derivatives have been frequently introduced into the construction of biosensors due to their unique physicochemical properties and biocompatibility. The combination of biomolecules with specific recognition capabilities and graphene materials provides a promising strategy to construct more stable and sensitive biosensors for the detection of pathogens. This review tracks the development of graphene biosensors for the detection of bacterial and viral pathogens, mainly including the preparation of graphene biosensors and their working mechanism. The challenges involved in this field have been discussed, and the perspective for further development has been put forward, aiming to promote the development of pathogens sensing and the contribution to epidemic prevention.

Bacterial co-infection and secondary infection in patients with COVID-19: a living rapid review and meta-analysis.

BACKGROUND: Bacterial co-pathogens are commonly identified in viral respiratory infections and are important causes of morbidity and mortality. The prevalence of bacterial infection in patients infected with SARS-CoV-2 is not well understood. AIMS: To determine the prevalence of bacterial co-infection (at presentation) and secondary infection (after presentation) in patients with COVID-19. SOURCES: We performed a systematic search of MEDLINE, OVID Epub and EMBASE databases for English language literature from 2019 to April 16, 2020. Studies were included if they (a) evaluated patients with confirmed COVID-19 and (b) reported the prevalence of acute bacterial infection. CONTENT: Data were extracted by a single reviewer and cross-checked by a second reviewer. The main outcome was the proportion of COVID-19 patients with an acute bacterial infection. Any bacteria detected from non-respiratory-tract or non-bloodstream sources were excluded. Of 1308 studies screened, 24 were eligible and included in the rapid review representing 3338 patients with COVID-19 evaluated for acute bacterial infection. In the meta-analysis, bacterial co-infection (estimated on presentation) was identified in 3.5% of patients (95%CI 0.4-6.7%) and secondary bacterial infection in 14.3% of patients (95%CI 9.6-18.9%). The overall proportion of COVID-19 patients with bacterial infection was 6.9% (95%CI 4.3-9.5%). Bacterial infection was more common in critically ill patients (8.1%, 95%CI 2.3-13.8%). The majority of patients with COVID-19 received antibiotics (71.9%, 95%CI 56.1 to 87.7%). IMPLICATIONS: Bacterial co-infection is relatively infrequent in hospitalized patients with COVID-19. The majority of these patients may not require empirical antibacterial treatment.

Heparin 2.0: A New Approach to the Infection Crisis.

In April 2020, the US Food and Drug Administration granted emergency use authorization for certain medical devices to be used in patients with coronavirus disease 2019 (CO-VID-19). This included extracorporeal blood purification devices. This narrative review will give a brief overview regarding some of the extracorporeal devices that could be used to treat COVID-19 patients, including the Seraph® 100 Microbind® Affinity Blood Filter, produced by ExThera Medical (Martinez, CA, USA), first licensed in the European Economic Area in 2019. The Seraph® 100 contains ultrahigh molecular weight polyethylene beads with end point-attached heparin and is approved for the reduction of pathogens from the bloodstream either as a single agent or as an adjunct to conventional anti-infective agents. Bacteria, viruses, fungi, and toxins have been shown to bind to the immobilized heparin in a similar way to the interaction with heparan sulfate on the cell surface. This binding is nonreversible and as such, the pathogens are removed from the bloodstream. In this review, we describe the pathophysiological basis and rationale for using heparin for pathogen removal from the blood as well as exploring the technology behind the adaptation of heparin to deprive it of its systemic anticoagulant activity. In addition, we summarize the in vitro data as well as the available preclinical testing and published clinical reports. Finally, we discuss the enormous potential of this technology in an era of increasing antibiotic resistance and high mortality associated with sepsis and consider the application of this as a possible treatment option for COVID-19.