Epidemiology, microbiology, and treatment considerations for bacterial pneumonia complicating influenza

IL-10 Counteracts IFN-γ to Alleviate Acute Lung Injury in a Viral-Bacterial Superinfection Model

Immune activation is essential for lung control of viral and bacterial infection, but an overwhelming inflammatory response often leads to the onset of acute respiratory distress syndrome. IL-10 plays a crucial role in regulating the balance between antimicrobial immunity and immunopathology. In the present study, we investigated the role of IL-10 in acute lung injury induced by influenza A virus and methicillin-resistant Staphylococcus aureus coinfection. This unique coinfection model resembles patients with acute pneumonia undergoing appropriate antibiotic therapies. Using global IL-10 and IL-10 receptor gene-deficient mice, as well as in vivo neutralizing antibodies, we show that IL-10 deficiency promotes IFN-γ-dominant cytokine responses and triggers acute animal death. Interestingly, this extreme susceptibility is fully preventable by IFN-γ neutralization during coinfection. Further studies using mice with Il10ra deletion in selective myeloid subsets reveal that IL-10 primarily acts on mononuclear phagocytes to prevent IFN-γ/TNF-α hyperproduction and acute mortality. Importantly, this antiinflammatory IL-10 signaling is independent of its inhibitory effect on antiviral and antibacterial defense. Collectively, our results demonstrate a key mechanism of IL-10 in preventing hypercytokinemia and acute respiratory distress syndrome pathogenesis by counteracting the IFN-γ response.

Protective Effects from Prior Pneumococcal Vaccination in Patients with Chronic Airway Diseases during Hospitalization for Influenza-A Territory-Wide Study

Influenza is an important respiratory viral pathogen in adults, with secondary bacterial pneumonia being a common complication. While pneumococcal vaccines can prevent pneumococcal pneumonia and invasive pneumococcal disease, whether they can also prevent the severe in-hospital outcomes among patients hospitalized for influenza has not been examined. A territory-wide retrospective study was conducted in Hong Kong, which included all adult patients having chronic airway diseases (asthma, bronchiectasis, and chronic obstructive pulmonary disease) hospitalized for influenza and who had received seasonal influenza vaccine. The occurrence of secondary bacterial pneumonia, mortality, and other severe in-hospital outcomes were compared among subjects with or without pneumococcal vaccination. There was a total of 3066 eligible patients who were hospitalized for influenza in public hospitals in Hong Kong from 1 January 2016 to 30 June 2023. Completed pneumococcal vaccination with PSV23/PCV13 conferred protection against secondary bacterial pneumonia, all-cause mortality, and respiratory cause of mortality with adjusted odds ratios of 0.74 (95% CI = 0.57-0.95, p = 0.019), 0.12 (95% CI = 0.03-0.53, p = 0.005), and 0.04 (95% CI = 0.00-0.527, p = 0.0038), respectively.

Analysis of viral pneumonia and risk factors associated with severity of influenza virus infection in hospitalized patients from 2012 to 2016

BACKGROUND

Influenza viruses cause pneumonia in approximately one-third of cases, and pneumonia is an important cause of death. The aim was to identify risk factors associated with severity and those that could predict the development of pneumonia.

METHODS

This retrospective, observational study included all adult patients with confirmed influenza virus infection admitted to Son Espases University Hospital during four influenza seasons in Spain (October to May) from to 2012-2016.

RESULTS

Overall, 666 patients with laboratory-confirmed influenza were included, 93 (14%) of which were severe; 73 (10.9%) were admitted to Intensive Care Unit (ICU), 39 (5.8%) died, and 185 (27.7%) developed pneumonia. Compared to less severe cases, patients with severe disease: were less vaccinated (40% vs. 28%, p = 0.021); presented with more confusion (26.9% vs. 6.8%), were more hypoxemic (Horowitz index (PaO2/FiO2) 261 vs. 280), had higher C-reactive protein (CRP) (12.3 vs. 4.0), had more coinfections (26.8% vs. 6.3%) and had more pleural effusion (14% vs. 2.6%) (last six all p < 0.001). Risk factors significantly associated with severity were pneumonia [OR (95% CI) = 4.14 (2.4-7.16)], history of heart disease (1.84, 1.03-3.28), and confusion at admission (4.99, 2.55-9.74). Influenza vaccination was protective (0.53, 0.28-0.98). Compared to those without pneumonia, the pneumonia group had higher CRP (11.3 vs. 4.0, p < 0.001), lower oxygen saturation (92% vs. 94%, p < 0.001), were more hypoxic (PaO2/FiO2 266 vs. 281, p < 0.001), and incurred more mechanical ventilation, septic shock, admission to the ICU, and deaths (all four p < 0.001). Higher CRP and lower oxygen saturation were independent variables for predicting the development of pneumonia.

CONCLUSIONS

Pneumonia, history of heart disease, confusion and no influenza vaccination were independent variables to present complications in patients admitted with influenza infection.

Temporally Associated Invasive Pneumococcal Disease and SARS-CoV-2 Infection, Alaska, USA, 2020-2021

Streptococcus pneumoniae can co-infect persons who have viral respiratory tract infections. However, research on S. pneumoniae infections that are temporally associated with SARS-CoV-2 infections is limited. We described the epidemiology and clinical course of patients who had invasive pneumococcal disease (IPD) and temporally associated SARS-CoV-2 infections in Alaska, USA, during January 1, 2020-December 23, 2021. Of 271 patients who had laboratory-confirmed IPD, 55 (20%) had a positive SARS-CoV-2 test result. We observed no major differences in age, race, sex, or underlying medical conditions among IPD patients with and without SARS-CoV-2. However, a larger proportion of IPD patients with SARS-CoV-2 died (16%, n = 9) than for those with IPD alone (4%, n = 9) (p<0.01). IPD patients with SARS-CoV-2 were also more likely to be experiencing homelessness (adjusted OR 3.5; 95% CI 1.7-7.5). Our study highlights the risk for dual infection and ongoing benefits of pneumococcal and COVID-19 vaccination, especially among vulnerable populations.

Role of toll-like receptors and nod-like receptors in acute lung infection

The respiratory system exposed to microorganisms continuously, and the pathogenicity of these microbes not only contingent on their virulence factors, but also the host's immunity. A multifaceted innate immune mechanism exists in the respiratory tract to cope with microbial infections and to decrease tissue damage. The key cell types of the innate immune response are macrophages, neutrophils, dendritic cells, epithelial cells, and endothelial cells. Both the myeloid and structural cells of the respiratory system sense invading microorganisms through binding or activation of pathogen-associated molecular patterns (PAMPs) to pattern recognition receptors (PRRs), including Toll-like receptors (TLRs) and NOD-like receptors (NLRs). The recognition of microbes and subsequent activation of PRRs triggers a signaling cascade that leads to the activation of transcription factors, induction of cytokines/5chemokines, upregulation of cell adhesion molecules, recruitment of immune cells, and subsequent microbe clearance. Since numerous microbes resist antimicrobial agents and escape innate immune defenses, in the future, a comprehensive strategy consisting of newer vaccines and novel antimicrobials will be required to control microbial infections. This review summarizes key findings in the area of innate immune defense in response to acute microbial infections in the lung. Understanding the innate immune mechanisms is critical to design host-targeted immunotherapies to mitigate excessive inflammation while controlling microbial burden in tissues following lung infection.

Association of Influenza Vaccination With Risk of Bell Palsy Among Older Adults in Taiwan

Importance

Annual administration of the influenza vaccine (fluVc) is currently the most effective method of preventing the influenza virus in older adults. However, half of adults older than 65 years remain unvaccinated in Taiwan, possibly because of concern about adverse events, such as Bell palsy (BP). Currently, studies on the association between fluVc and risk of BP are inconsistent.

Objective

To determine whether the incidence of BP increases following fluVc in older adults.

Design, Setting, and Participants

A self-controlled case series study design was used. Days 1 through 7, days 8 through 14, days 15 through 30, and days 31 through 60 following fluVc were identified as risk intervals, and days 61 through 180 were considered the control interval. A total of 4367 vaccinated individuals aged 65 years or older who developed BP within 6 months following fluVc were enrolled. Population-based retrospective claims data were obtained between 2010 and 2017; data were analyzed from April 2022 through September 2022.

Exposure

Government-funded seasonal fluVc.

Main Outcomes and Measures

The outcome of interest was BP onset in risk intervals compared with control intervals. Three or more consecutive diagnoses of BP within 60 days following fluVc were used as the definition of a patient with BP. Poisson regression was used to analyze the incidence rate ratio (IRR) of risk intervals compared with control intervals.

Results

In total, 13 261 521 patients who received the fluVc were extracted from the National Health Insurance Research Database in Taiwan from January 1, 2010, to December 31, 2017. Of those, 7 581 205 patients older than 65 years old met the inclusion criteria. The number of patients with BP diagnosed within 6 months following fluVc enrolled for risk analysis was 4367 (mean [SD] age, 74.19 [5.97] years; 2349 [53.79%] female patients). The incidence rate of BP among all observed fluVc older adults was 57.87 per 100 000 person-years. The IRRs for BP on days 1 through 7, days 8 through 14, and days 15 through 30 were 4.18 (95% CI, 3.82-4.59), 2.73 (95% CI, 2.45-3.05), and 1.67 (95% CI, 1.52-1.84), respectively. However, there was no increase during days 31 through 60 (IRR, 1.06; 95% CI, 0.97-1.16). The postvaccination risk of BP was consistent across all subgroups stratified by sex, age group, and baseline conditions.

Conclusions and Relevance

The present self-controlled case series indicated that the risk of BP in individuals older than 65 years increased within the first month, especially within the first week, following fluVc. But overall, the adverse event rate of BP was low, and considering the morbidity and mortality of influenza infection, the benefits of fluVc still outweigh the risks.

Expression of TMPRSS2 is up-regulated by bacterial flagellin, LPS, and Pam3Cys in human airway cells

Many viruses require proteolytic activation of their envelope proteins for infectivity, and relevant host proteases provide promising drug targets. The transmembrane serine protease 2 (TMPRSS2) has been identified as a major activating protease of influenza A virus (IAV) and various coronaviruses (CoV). Increased TMPRSS2 expression has been associated with a higher risk of severe influenza infection and enhanced susceptibility to SARS-CoV-2. Here, we found that Legionella pneumophila stimulates the increased expression of TMPRSS2-mRNA in Calu-3 human airway cells. We identified flagellin as the dominant structural component inducing TMPRSS2 expression. The flagellin-induced increase was not observed at this magnitude for other virus-activating host proteases. TMPRSS2-mRNA expression was also significantly increased by LPS, Pam3Cys, and Streptococcus pneumoniae, although less pronounced. Multicycle replication of H1N1pdm and H3N2 IAV but not SARS-CoV-2 and SARS-CoV was enhanced by flagellin treatment. Our data suggest that bacteria, particularly flagellated bacteria, up-regulate the expression of TMPRSS2 in human airway cells and, thereby, may support enhanced activation and replication of IAV upon co-infections. In addition, our data indicate a physiological role of TMPRSS2 in antimicrobial host response.

Staphylococcus aureus bacteremia in patients with SARS-CoV-2 infection

Objectives

The aim was to compare the incidence of Staphylococcus aureus bacteremia in COVID-19 and non-COVID-19 adult patients during the pandemic period versus the previous two years. Also, we described the characteristics of both cohorts of patients in pandemic period to find differences.

Material and methods

Retrospective study in our tertiary-care centre reviewing S. aureus bacteremia episodes in COVID-19 and non-COVID-19 patients through clinical records and the Microbiology Department database.

Results

In 2018 and 2019, the incidence of S. aureus bacteremia episodes was 1.95 and 1.63 per 1000 admissions respectively. In the pandemic period, global incidence was 1.96 episodes per 1000 non-COVID-19 admissions and 10.59 episodes per 1000 COVID-19 admissions. A total of 241 bacteremia was registered during this pandemic period in 74 COVID-19 patients and in 167 non-COVID-19 patients. Methicillin resistance was detected in 32.4% and 13.8% of isolates from COVID-19 and non-COVID-19 patients respectively. In COVID-19 patients, mortality rates were significantly higher.

Conclusions

We showed a significantly high rates of S. aureus bacteremia incidence in COVID-19 patients and higher methicillin resistance and 15-day mortality rates than in non-COVID-19 patients.

COVID-19 association with multidrug-resistant bacteria superinfections: Lessons for future challenges

The future waves of COVID 19 infections will continue to raise serious problems in patients with severe forms of the disease. Bacterial infections associated with SARS-CoV-2 disease may complicate the progress of hospitalized patients with COVID-19. The present study aimed to evaluate the etiological spectrum of superinfection in adult patients with COVID-19 and to investigate the correlation between superinfection with multidrug-resistant (MDR) bacteria and serum procalcitonin (PCT). A total of 82 COVID-19 hospitalized patients with COVID-19 and bacterial superinfection were included. The superinfections were classified into early infections (3-7 days from admission) and late infections (>7 days from admission). Bacterial superinfection etiological spectrum, MDR bacteria profile and levels of serum PCT were studied. The most frequently isolated bacteria were Klebsiella pneumoniae, Acinetobacter baumannii and Enterococcus spp. MDR bacteria were involved in 73.17% of COVID-19 patients with bacterial superinfections. Most MDR bacteria superinfections (73.52%) occurred in the late infection period. Klebsiella pneumoniae, Enterococcus spp. and Methicillin-resistant Staphylococcus aureus were the most common MDR bacteria identified in late infections after hospitalization in 20.43, 4.30 and 4.30% of all infections, respectively. Serum PCT values were significantly higher in patients with MDR bacteria superinfection compared with patients with sensitive bacteria superinfection (P=0.009). The principal findings of the present study were the high prevalence of superinfection with MDR bacteria among the COVID-19 patients with bacterial superinfections and the presence of a statistically significant association between serum PCT levels and the presence of superinfection with MDR bacteria. The most effective way to fight against microbial resistance to antibiotics, whether it occurs independently or overlaps with viral infections, is to pursue a national policy for the rational use of antibiotics.

Diagnostic and Prognostic Roles of Procalcitonin and Other Tools in Community-Acquired Pneumonia: A Narrative Review

Community-acquired pneumonia (CAP) is among the most common causes of death and one of the leading healthcare concerns worldwide. It can evolve into sepsis and septic shock, which have a high mortality rate, especially in critical patients and comorbidities. The definitions of sepsis were revised in the last decade as "life-threatening organ dysfunction caused by a dysregulated host response to infection". Procalcitonin (PCT), C-reactive protein (CRP), and complete blood count, including white blood cells, are among the most commonly analyzed sepsis-specific biomarkers also used in pneumonia in a broad range of studies. It appears to be a reliable diagnostic tool to expedite care of these patients with severe infections in the acute setting. PCT was found to be superior to most other acute phase reactants and indicators, including CRP as a predictor of pneumonia, bacteremia, sepsis, and poor outcome, although conflicting results exist. In addition, PCT use is beneficial to judge timing for the cessation of antibiotic treatment in most severe infectious states. The clinicians should be aware of strengths and weaknesses of known and potential biomarkers in expedient recognition and management of severe infections. This manuscript is intended to present an overview of the definitions, complications, and outcomes of CAP and sepsis in adults, with special regard to PCT and other important markers.

Factors Associated With the Development of Bacterial Pneumonia Related to Seasonal Influenza Virus Infection: A Study Using a Large-scale Health Insurance Claim Database

Background

Influenza-related bacterial pneumonia is a leading complication of influenza infection. However, the differences in the incidence rates and risk factors associated with concomitant viral/bacterial pneumonia (CP) and secondary bacterial pneumonia following influenza (SP) remain unclear. This study aimed to clarify the incidence rates of CP and SP following seasonal influenza and identify factors associated with their development.

Methods

This retrospective cohort study was conducted using the JMDC Claims Database, a health insurance claims database in Japan. All patients aged <75 years who developed influenza during 2 consecutive epidemic seasons, 2017/2018 and 2018/2019, were analyzed. CP was defined as bacterial pneumonia diagnosed between 3 days before and 6 days after the date of influenza diagnosis, and SP was defined as pneumonia diagnosed 7-30 days after the date of diagnosis. Multivariable logistic regression analyses were performed to identify factors associated with the development of CP and SP.

Results

Among the 10 473 014 individuals registered in the database, 1 341 355 patients with influenza were analyzed. The average age at diagnosis (SD) was 26.6 (18.6) years. There were 2901 (0.22%) and 1262 (0.09%) patients who developed CP and SP, respectively. Age 65-74 years, asthma, chronic bronchitis/emphysema, cardiovascular disease, renal disease, malignant tumor, and immunosuppression were significant risk factors for both CP and SP, whereas cerebrovascular disease, neurological disease, liver disease, and diabetes were risk factors specific to CP development.

Conclusions

The results determined the incidence rates of CP and SP and identified their risk factors, such as older age and comorbidities.

Risk factors for in-hospital mortality and secondary bacterial pneumonia among hospitalized adult patients with community-acquired influenza: a large retrospective cohort study

BACKGROUND

Secondary bacterial pneumonia is an important complication of seasonal influenza, but little data is available about impact on death and risk factors. This study identified risk factors for all-cause in-hospital mortality and secondary bacterial pneumonia among hospitalized adult patients with community-acquired influenza.

METHODS

A retrospective cohort study was performed at a tertiary teaching hospital in southwest China. The study cohort included all adult hospitalized patients with a laboratory-confirmed, community-acquired influenza virus infection during three consecutive influenza seasons from 2017 to 2020. Cause-specific Cox regression was used to analyze risk factors for mortality and secondary bacterial pneumonia, respectively, accounting for competing events (discharge alive and discharge alive or death without secondary bacterial pneumonia, respectively).

RESULTS

Among 174 patients enrolled in this study, 14.4% developed secondary bacterial pneumonia and 11.5% died during hospitalization. For all-cause in-hospital mortality, time-varying secondary bacterial pneumonia was a direct risk factor of death (cause-specific hazard ratio [csHR] 3.38, 95% confidence interval [CI] 1.25-9.17); underlying disease indirectly increased death risk through decreasing the hazard of being discharged alive (csHR 0.55, 95% CI 0.39-0.77). For secondary bacterial pneumonia, the final model only confirmed direct risk factors: age ≥ 65 years (csHR 2.90, 95% CI 1.27-6.62), male gender (csHR 3.78, 95% CI 1.12-12.84) and mechanical ventilation on admission (csHR 2.96, 95% CI 1.32-6.64).

CONCLUSIONS

Secondary bacterial pneumonia was a major risk factor for in-hospital mortality among adult hospitalized patients with community-acquired influenza. Prevention strategies for secondary bacterial pneumonia should target elderly male patients and critically ill patients under mechanical ventilation.

Infection and co-infection patterns of community-acquired pneumonia in patients of different ages in China from 2009 to 2020: a national surveillance study

BACKGROUND

Severe community-acquired pneumonia (SCAP) is associated with a substantial number of hospitalisations and deaths worldwide. Infection or co-infection patterns, along with their age dependence and clinical effects are poorly understood. We aimed to explore the causal and epidemiological characteristics by age, to better describe patterns of community-acquired pneumonia (CAP) and their association with severe disease.

METHODS

National surveillance of CAP was conducted through a network of hospitals in 30 provinces in China from 2009-20 inclusive. Patients with CAP were included if they had evidence of acute respiratory tract, had evidence of pneumonia by chest radiography, diagnosis of pneumonia within 24 h of hospital admission, and resided in the study catchment area. For the enrolled patients with CAP, nasopharyngeal and oral swabs were taken and tested for eight viral pathogens; and blood, urine, or expectorated sputum was tested for six bacterial pathogens. Clinical outcomes, including SCAP, were investigated with respect to age and patterns of infections or co-infections by performing binary logistic regression and multivariate analysis.

FINDINGS

Between January, 2009, and December, 2020, 18 807 patients with CAP (3771 [20·05%] with SCAP) were enrolled. For both children (aged ≤5 years) and older adults (aged >60 years), a higher overall rate of viral and bacterial infections, as well as viral-bacterial co-infections were seen in patients with SCAP than in patients with non-SCAP. For adults (aged 18-60 years), however, only a higher rate of bacterial-bacterial co-infection was observed. The most frequent pathogens associated with SCAP were respiratory syncytial virus (RSV; 21·30%) and Streptococcus pneumoniae (12·61%) among children, and influenza virus (10·94%) and Pseudomonas aeruginosa (15·37%) among older adults. Positive rates of detection of most of the tested pathogens decreased during 2020 compared with the 2009-19 period, except for RSV, P aeruginosa, and Klebsiella pneumoniae. Multivariate analyses showed SCAP was significantly associated with infection with human adenovirus, human rhinovirus, K pneumoniae, or co-infection of RSV and Haemophilus influenzae or RSV and Staphylococcus aureus in children and adolescents (aged <18 years), and significantly associated with infection with P aeruginosa, K pneumoniae, or S pneumoniae, or co-infection with P aeruginosa and K pneumoniae in adults (aged ≥18 years).

INTERPRETATION

Both prevalence and infection pattern of respiratory pathogens differed between patients with SCAP and patients with non-SCAP in an age-dependent manner. These findings suggest potential advantages to age-related strategies for vaccine schedules, as well as clinical diagnosis, treatment, and therapy.

FUNDING

China Mega-Project on Infectious Disease Prevention and The National Natural Science Funds of China.

TRANSLATION

For the Chinese translation of the abstract see Supplementary Materials section.

Bacterial Coinfection and Superinfection in Respiratory Syncytial Virus-Associated Acute Respiratory Illness: Prevalence, Pathogens, Initial Antibiotic-Prescribing Patterns and Outcomes

We aimed to determine the prevalence of bacterial coinfection (CoBact) and bacterial superinfection (SuperBact), the causative pathogens, the initial antibiotic-prescribing practice, and the associated clinical outcomes of hospitalized patients with respiratory syncytial virus-associated acute respiratory illness (RSV-ARI). This retrospective study included 175 adults with RSV-ARI, virologically confirmed via RT-PCR, during the period 2014–2019. Thirty (17.1%) patients had CoBact, and 18 (10.3%) had SuperBact. The independent factors associated with CoBact were invasive mechanical ventilation (OR: 12.1, 95% CI: 4.7–31.4; p < 0.001) and neutrophilia (OR: 3.3, 95% CI: 1.3–8.5; p = 0.01). The independent factors associated with SuperBact were invasive mechanical ventilation (aHR: 7.2, 95% CI: 2.4–21.1; p < 0.001) and systemic corticosteroids (aHR: 3.1, 95% CI: 1.2–8.1; p = 0.02). CoBact was associated with higher mortality compared to patients without CoBact (16.7% vs. 5.5%, p = 0.05). Similarly, SuperBact was associated with higher mortality compared to patients without SuperBact (38.9% vs. 3.8%, p < 0.001). The most common CoBact pathogen identified was Pseudomonas aeruginosa (30%), followed by Staphylococcus aureus (23.3%). The most common SuperBact pathogen identified was Acinetobacter spp. (44.4%), followed by ESBL-positive Enterobacteriaceae (33.3%). Twenty-two (100%) pathogens were potentially drug-resistant bacteria. In patients without CoBact, there was no difference in mortality between patients who received an initial antibiotic treatment of <5 days or ≥5 days.

Neurologic Manifestations of Influenza in Children

OBJECTIVE

We assessed the neurologic manifestation of influenza among hospitalized children with influenza (neuro-flu), comparing their demographic and clinical characteristics to hospitalized children without neurologic manifestation (classic-flu).

METHODS

A retrospective, cohort study. All children with laboratory confirmed influenza (PCR), admitted to the Soroka University Medical Center (SUMC) between 2016 and 2019 were included.

RESULTS

Overall, 951 patients were identified: 201 with neuro-flu, and 750 with classic-flu. Seizures (n = 125) were the most common neurological manifestation of neuro-flu (seizure-flu): 73 simple febrile seizures, 45 atypical febrile seizures, and 7 afebrile seizures. Neurological comorbidities rates were significantly higher in neuro-flu versus classic-flu (13.0% vs. 6.0%), while respiratory and cardiac comorbidities were less common in neuro-flu (4.5% and 0.5% vs. 8.0% and 4.5%, respectively). Neuro-flu (compared with classic-flu) was associated with leukocytosis (21.0% vs. 13.0%, P < 0.001) and lower C-reactive protein (CRP) levels (2.4 ± 4.1 vs. 3.3 ± 5.4, P = 0.03). Notably, patients with classic flu had a more prominent respiratory disease, as they had more chest radiographs (CXR) performed (60.5% vs. 45.0%, P < 0.001), higher rates of pneumonia (27.0% vs. 12.0%, P < 0.001), and antibiotic (antibacterial) treatment (60.0% vs. 42.0%, P < 0.001).

CONCLUSIONS

Influenza can appear as a neurologic disease, manifested mainly with febrile seizures. Children with neuro-flu have more neurologic comorbidities, suggesting that neuro-flu is mainly driven by host-factors, rather than by pathogen-factors. The relatively lower rates of pneumonia in neuro-flu suggests that these patients are admitted in the early stage of the influenza infection, which triggers the neurologic response.

CRISPR-Cas system as a promising player against bacterial infection and antibiotic resistance

The phenomenon of antibiotic resistance (AR) and its increasing global trends and destructive waves concerns patients and the healthcare system. In order to combat AR, it is necessary to explore new strategies when the current antibiotics fail to be effective. Thus, knowing the resistance mechanisms and appropriate diagnosis of bacterial infections may help enhance the sensitivity and specificity of novel strategies. On the other hand, resistance to antimicrobial compounds can spread from resistant populations to susceptible ones. Antimicrobial resistance genes (ARGs) significantly disseminate AR via horizontal and vertical gene transfer. The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system is a member of the bacterial immune system with the ability to remove the ARGs; therefore, it can be introduced as an effective and innovative strategy in the battle against AR. Here, we reviewed CRISPR-based bacterial diagnosis technologies. Moreover, the strategies to battle AR based on targeting bacterial chromosomes and resistance plasmids using the CRISPR-Cas system have been explained. Besides, we have presented the limitations of CRISPR delivery and potential solutions to help improve the future development of CRISPR-based platforms.

Editorial on the Research Topic of the Special Issue "Current Status of Acinetobacter Infections"

Emerging bacterial infections will continue to be an important issue for public health, mostly because of the constant changes on our earth [...].

Staphylococcus aureus bacteremia in patients with SARS-CoV-2 infection

OBJECTIVES

The aim was to compare the incidence of Staphylococcus aureus bacteremia in COVID-19 and non-COVID-19 adult patients during the pandemic period versus the previous two years. Also, we described the characteristics of both cohorts of patients in pandemic period to find differences.

MATERIAL AND METHODS

Retrospective study in our tertiary-care centre reviewing S. aureus bacteremia episodes in COVID-19 and non-COVID-19 patients through clinical records and the Microbiology Department database.

RESULTS

In 2018 and 2019, the incidence of S. aureus bacteremia episodes was 1.95 and 1.63 per 1000 admissions respectively. In the pandemic period, global incidence was 1.96 episodes per 1000 non-COVID-19 admissions and 10.59 episodes per 1000 COVID-19 admissions. A total of 241 bacteremia was registered during this pandemic period in 74 COVID-19 patients and in 167 non-COVID-19 patients. Methicillin resistance was detected in 32.4% and 13.8% of isolates from COVID-19 and non-COVID-19 patients respectively. In COVID-19 patients, mortality rates were significantly higher.

CONCLUSIONS

We showed a significantly high rates of S. aureus bacteremia incidence in COVID-19 patients and higher methicillin resistance and 15-day mortality rates than in non-COVID-19 patients.

Pushing the envelope: Immune mechanism and application landscape of macrophage-activating lipopeptide-2

Mycoplasma fermentans can cause respiratory diseases, arthritis, genitourinary tract infections, and chronic fatigue syndrome and have been linked to the development of the human immunodeficiency virus. Because mycoplasma lacks a cell wall, its outer membrane lipoproteins are one of the main factors that induce inflammation in the organism and contribute to disease development. Macrophage-activating lipopeptide-2 (MALP-2) modulates the inflammatory response of monocytes/macrophages in a bidirectional fashion, indirectly enhances the cytotoxicity of NK cells, promotes oxidative bursts in neutrophils, upregulates surface markers on lymphocytes, enhances antigen presentation on dendritic cells and induces immune inflammatory responses in sebocytes and mesenchymal cells. MALP-2 is a promising vaccine adjuvant for this application. It also promotes vascular healing and regeneration, accelerates wound and bone healing, suppresses tumors and metastasis, and reduces lung infections and inflammation. MALP-2 has a simple structure, is easy to synthesize, and has promising prospects for clinical application. Therefore, this paper reviews the mechanisms of MALP-2 activation in immune cells, focusing on the application of MALP-2 in animals/humans to provide a basis for the study of pathogenesis in Mycoplasma fermentans and the translation of MALP-2 into clinical applications.

NLRP6 Induces Lung Injury and Inflammation Early in Brucella and Influenza Coinfection

(1) Background: With the resurgence of brucellosis epidemics in China in recent years, the chances of a brucella coinfection with other common respiratory pathogens, such as the influenza virus, have increased dramatically. However, little is known about the pathogenicity or the mechanisms of brucella and influenza coinfections. (2) Methods: To clarify the interventions in the early stages of lung damage due to brucella and influenza coinfections, we evaluated the effect of the coinfection on disease progression and mortality using a coinfection model in WT mice and NLRP6^-/- mice, and we verified the function of NLRP6 in infection and proinflammation. (3) Results: The coinfection induced significant respiratory symptoms, weight loss, and a high mortality rate in WT mice. Influenza in the coinfection group significantly increased brucella proliferation in a synergistic manner. Meanwhile, a histological examination showed severe lung tissue destruction and excessive inflammatory responses in coinfected WT animals, and the expression of NLRP6 and IL-18 was dramatically increased in the lung tissues. Furthermore, NLRP6 deletion attenuated lung injuries and inflammation, a reduced bacterial load, and decreased IL-18 protein expression. (4) Conclusions: Our findings indicated that NLRP6 plays a critical role and might be a promising potential therapeutic target for brucella-influenza coinfections.

Oral mitis group streptococci reduce infectivity of influenza A virus via acidification and H2O2 production

Members of the mitis group streptococci are the most abundant inhabitants of the oral cavity and dental plaque. Influenza A virus (IAV), the causative agent of influenza, infects the upper respiratory tract, and co-infection with Streptococcus pneumoniae is a major cause of morbidity during influenza epidemics. S. pneumoniae is a member of mitis group streptococci and shares many features with oral mitis group streptococci. In this study, we investigated the effect of viable Streptococcus oralis, a representative member of oral mitis group, on the infectivity of H1N1 IAV. The infectivity of IAV was measured by a plaque assay using Madin-Darby canine kidney cells. When IAV was incubated in growing culture of S. oralis, the IAV titer decreased in a time- and dose-dependent manner and became less than 100-fold, whereas heat-inactivated S. oralis had no effect. Other oral streptococci such as Streptococcus mutans and Streptococcus salivarius also reduced the viral infectivity to a lesser extent compared to S. oralis and Streptococcus gordonii, another member of the oral mitis group. S. oralis produces hydrogen peroxide (H2O2) at a concentration of 1–2 mM, and its mutant deficient in H2O2 production showed a weaker effect on the inactivation of IAV, suggesting that H2O2 contributes to viral inactivation. The contribution of H2O2 was confirmed by an inhibition assay using catalase, an H2O2-decomposing enzyme. These oral streptococci produce short chain fatty acids (SCFA) such as acetic acid as a by-product of sugar metabolism, and we also found that the inactivation of IAV was dependent on the mildly acidic pH (around pH 5.0) of these streptococcal cultures. Although inactivation of IAV in buffers of pH 5.0 was limited, incubation in the same buffer containing 2 mM H2O2 resulted in marked inactivation of IAV, which was similar to the effect of growing S. oralis culture. Taken together, these results reveal that viable S. oralis can inactivate IAV via the production of SCFAs and H2O2. This finding also suggests that the combination of mildly acidic pH and H2O2 at low concentrations could be an effective method to inactivate IAV.

Roles for Pathogen Interference in Influenza Vaccination, with Implications to Vaccine Effectiveness (VE) and Attribution of Influenza Deaths

Pathogen interference is the ability of one pathogen to alter the course and clinical outcomes of infection by another. With up to 3000 species of human pathogens the potential combinations are vast. These combinations operate within further immune complexity induced by infection with multiple persistent pathogens, and by the role which the human microbiome plays in maintaining health, immune function, and resistance to infection. All the above are further complicated by malnutrition in children and the elderly. Influenza vaccination offers a measure of protection for elderly individuals subsequently infected with influenza. However, all vaccines induce both specific and non-specific effects. The specific effects involve stimulation of humoral and cellular immunity, while the nonspecific effects are far more nuanced including changes in gene expression patterns and production of small RNAs which contribute to pathogen interference. Little is known about the outcomes of vaccinated elderly not subsequently infected with influenza but infected with multiple other non-influenza winter pathogens. In this review we propose that in certain years the specific antigen mix in the seasonal influenza vaccine inadvertently increases the risk of infection from other non-influenza pathogens. The possibility that vaccination could upset the pathogen balance, and that the timing of vaccination relative to the pathogen balance was critical to success, was proposed in 2010 but was seemingly ignored. Persons vaccinated early in the winter are more likely to experience higher pathogen interference. Implications to the estimation of vaccine effectiveness and influenza deaths are discussed.

IFN-γ transforms the transcriptomic landscape and triggers myeloid cell hyperresponsiveness to cause lethal lung injury

Acute Respiratory Distress Syndrome (ARDS) is an inflammatory disease that is associated with high mortality but no specific treatment. Our understanding of initial events that trigger ARDS pathogenesis is limited. We have developed a mouse model of inflammatory lung injury by influenza and methicillin-resistant Staphylococcus aureus (MRSA) coinfection plus daily antibiotic therapy. Using this pneumonic ARDS model, here we show that IFN-γ receptor signaling drives inflammatory cytokine storm and lung tissue damage. By single-cell RNA sequencing (scRNA-seq) analysis, we demonstrate that IFN-γ signaling induces a transcriptional shift in airway immune cells, particularly by upregulating macrophage and monocyte expression of genes associated with inflammatory diseases. Further evidence from conditional knockout mouse models reveals that IFN-γ receptor signaling in myeloid cells, particularly CD11c+ mononuclear phagocytes, directly promotes TNF-α hyperproduction and inflammatory lung damage. Collectively, the findings from this study, ranging from cell-intrinsic gene expression to overall disease outcome, demonstrate that influenza-induced IFN-γ triggers myeloid cell hyperresponsiveness to MRSA, thereby leading to excessive inflammatory response and lethal lung damage during coinfection.

Risk factors associated with development of coinfection in critically Ill patients with COVID-19

Background

At outset of the coronavirus disease 2019 (COVID-19) pandemic, the significance of bacterial and fungal coinfections in individuals with COVID-19 was unknown. Initial reports indicated that the prevalence of coinfection in the general population was low, but there was uncertainty regarding the risk of coinfection in critically ill patients.

Methods

Nine hundred critically ill adult patients with COVID-19 infection were enrolled in this observational case-control study. Patients with a coinfection (case) and patients without a coinfection (control) were compared using univariate and multivariable analyses. A subgroup analysis was performed on patients with coinfection, dividing them into early (infection within 7 days) and late (infection after 7 days) infection groups.

Results

Two hundred and thirty-three patients (25.9%) had a bacterial or fungal coinfection. Vasopressor use (P<0.001) and severity of illness (higher Acute Physiology and Chronic Health Evaluation III score, P=0.009) were risk factors for the development of a coinfection. Patients with coinfection had higher mortality and length of stay. Vasopressor and corticosteroid use and central line and foley catheter placement were risk factors for late infection (>7 days). There were high rates of drug-resistant infections.

Conclusions

Critically ill patients with COVID-19 are at risk for both community-acquired and hospital-acquired infections throughout their hospitalization for COVID-19. It is important to consider the development of a coinfection in clinically worsening critically ill patients with COVID-19 and consider the likelihood of drug-resistance when choosing an empiric regimen.

Host respiratory transcriptome signature associated with poor outcome in children with influenza-Staphylococcus aureus pneumonia

Respiratory coinfection of influenza with Staphylococcus aureus often causes severe disease; methicillin resistant S. aureus (MRSA) coinfection is frequently fatal. Understanding disease pathogenesis may inform therapies. We aimed to identify host and pathogen transcriptomic (mRNA) signatures from the respiratory compartment of patients with influenza-S. aureus coinfection (ISAC) critical illness that predict worse outcomes. mRNA extracted from endotracheal aspirates was evaluated for S. aureus and host transcriptomic biosignatures. Influenza-MRSA outcomes were worse, but of 190 S. aureus virulence-associated genes, 6 were differentially expressed between MRSA- versus methicillin-susceptible S. aureus coinfected patients and none discriminated outcome. Host gene expression in ISAC patients was compared to influenza infection alone. Patients with poor clinical outcomes (death or prolonged multi-organ dysfunction) had relatively reduced expression of interferons and down-regulation of interferon gamma-induced immune cell chemoattractants CXCL10 and CXCL11. In influenza-S. aureus respiratory coinfection, airway host but not pathogen gene expression profiles predicted worse clinical outcomes.

A profile of delafloxacin in the treatment of adults with community-acquired bacterial pneumonia

INTRODUCTION

Community-acquired bacterial pneumonia (CABP) is the most common infectious cause of hospital admission in adults, and poses a significant clinical and economic burden. At the same time, antimicrobial resistance is increasing worldwide with only a few new antibiotics developed in recent years. Delafloxacin is an anionic fluoroquinolone available in intravenous and oral formulations and with a broad spectrum of activity targeting Gram-positives, including methicillin-resistant Staphylococcus aureus (MRSA), gram-negative organisms, and atypical and anaerobic organisms. It also has a better adverse event profile compared to other fluoroquinolones.

AREAS COVERED

This article reviews the current epidemiology of CABP, etiologic agents and current resistance rates, current treatment guidelines, characteristics of delafloxacin (chemistry, microbiology, PK/PD), clinical efficacy and safety in pneumonia and other indications, and regulatory affairs.

EXPERT OPINION

: Delafloxacin's susceptibility profile against respiratory pathogens, bioequivalent intravenous and oral formulations and favorable safety profile, support its use for the treatment of CABP. It could be useful as empirical treatment in countries with high rates of penicillin-resistant S. pneumoniae and in patients with suspected or documented pneumonia due to MRSA. In post-influenza staphylococcal bacterial pneumonia, MRSA could be also considered an important pathogen.

Optimal use of procalcitonin to rule out bacteremia in patients with possible viral infections

Objective

During the winter, many patients present with suspected infection that could be a viral or a bacterial (co)infection. The aim of this study is to investigate whether the optimal use of procalcitonin (PCT) is different in patients with and without proven viral infections for the purpose of excluding bacteremia. We hypothesize that when a viral infection is confirmed, this lowers the probability of bacteremia and, therefore, influences the appropriate cutoff of procalcitonin.

Methods

This study was conducted in the emergency department of an academic medical center in The Netherlands in the winter seasons of 2019 and 2020. Adults (>18 years) with suspected infection, in whom a blood culture and a rapid polymerase chain reaction test for influenza was performed were included.

Results

A total of 546 patients were included of whom 47 (8.6%) had a positive blood culture. PCT had an area under the curve of 0.85, 95% confidence interval (95% CI) 0.80-0.91, for prediction of bacteremia. In patients with a proven viral infection (N = 212) PCT < 0.5 μg/L had a sensitivity of 100% (95% CI 63.1-100) and specificity of 81.2% (95% CI 75.1-86.3) to exclude bacteremia. In patients without a viral infection, the procalcitonin cutoff point of < 0.25 μg/L showed a sensitivity of 87.2% (95% CI 72.6-95.7) and specificity of 64.1 % (95% CI 58.3-69.6).

Conclusion

In patients with a viral infection, our findings suggest that a PCT concentration of <0.50 μg/L makes bacteremia unlikely. However, this finding needs to be confirmed in a larger population of patients with viral infections, especially because the rate of coinfection in our cohort was low.

The Contribution of Viral Proteins to the Synergy of Influenza and Bacterial Co-Infection

A severe course of acute respiratory disease caused by influenza A virus (IAV) infection is often linked with subsequent bacterial superinfection, which is difficult to cure. Thus, synergistic influenza-bacterial co-infection represents a serious medical problem. The pathogenic changes in the infected host are accelerated as a consequence of IAV infection, reflecting its impact on the host immune response. IAV infection triggers a complex process linked with the blocking of innate and adaptive immune mechanisms required for effective antiviral defense. Such disbalance of the immune system allows for easier initiation of bacterial superinfection. Therefore, many new studies have emerged that aim to explain why viral-bacterial co-infection can lead to severe respiratory disease with possible fatal outcomes. In this review, we discuss the key role of several IAV proteins-namely, PB1-F2, hemagglutinin (HA), neuraminidase (NA), and NS1-known to play a role in modulating the immune defense of the host, which consequently escalates the development of secondary bacterial infection, most often caused by Streptococcus pneumoniae. Understanding the mechanisms leading to pathological disorders caused by bacterial superinfection after the previous viral infection is important for the development of more effective means of prevention; for example, by vaccination or through therapy using antiviral drugs targeted at critical viral proteins.

Bacterial coinfection in influenza pneumonia: Rates, pathogens, and outcomes

BACKGROUND

Evidence from pandemics suggests that influenza is often associated with bacterial coinfection. Among patients hospitalized for influenza pneumonia, we report the rate of coinfection and distribution of pathogens, and we compare outcomes of patients with and without bacterial coinfection.

METHODS

We included adults admitted with community-acquired pneumonia (CAP) and tested for influenza from 2010 to 2015 at 179 US hospitals participating in the Premier database. Pneumonia was identified using an International Classification of Disease, Ninth Revision, Clinical Modification (ICD-9-CM) algorithm. We used multiple logistic and gamma-generalized linear mixed models to assess the relationships between coinfection and inpatient mortality, intensive care unit (ICU) admission, length of stay, and cost.

RESULTS

Among 38,665 patients hospitalized with CAP and tested for influenza, 4,313 (11.2%) were positive. In the first 3 hospital days, patients with influenza were less likely than those without to have a positive culture (10.3% vs 16.2%; P < .001), and cultures were more likely to contain Staphylococcus aureus (34.2% vs 28.2%; P = .007) and less likely to contain Streptococcus pneumoniae (24.9% vs 31.0%; P = .008). Of S. aureus isolates, 42.8% were methicillin resistant among influenza patients versus 53.2% among those without influenza (P = .01). After hospital day 3, pathogens for both groups were similar. Bacterial coinfection was associated with increased odds of in-hospital mortality (aOR, 3.00; 95% CI, 2.17-4.16), late ICU transfer (aOR, 2.83; 95% CI, 1.98-4.04), and higher cost (risk-adjusted mean multiplier, 1.77; 95% CI, 1.59-1.96).

CONCLUSIONS

In a large US inpatient sample hospitalized with influenza and CAP, S. aureus was the most frequent cause of bacterial coinfection. Coinfection was associated with worse outcomes and higher costs.

Secondary streptococcal infection following influenza

Secondary bacterial infection following influenza A virus (IAV) infection is a major cause of morbidity and mortality during influenza epidemics. Streptococcus pneumoniae has been identified as a predominant pathogen in secondary pneumonia cases that develop following influenza. Although IAV has been shown to enhance susceptibility to the secondary bacterial infection, the underlying mechanism of the viral-bacterial synergy leading to disease progression is complex and remains elusive. In this review, cooperative interactions of viruses and streptococci during co- or secondary infection with IAV are described. IAV infects the upper respiratory tract, therefore, streptococci that inhabit or infect the respiratory tract are of special interest. Since many excellent reviews on the co-infection of IAV and S. pneumoniae have already been published, this review is intended to describe the unique interactions between other streptococci and IAV. Both streptococcal and IAV infections modulate the host epithelial barrier of the respiratory tract in various ways. IAV infection directly disrupts epithelial barriers, though at the same time the virus modifies the properties of infected cells to enhance streptococcal adherence and invasion. Mitis group streptococci produce neuraminidases, which promote IAV infection in a unique manner. The studies reviewed here have revealed intriguing mechanisms underlying secondary streptococcal infection following influenza. This article is protected by copyright. All rights reserved.

Antibiotic Resistance Patterns and Association with the Influenza Season in the United States: A Multicenter Evaluation Reveals Surprising Associations Between Influenza Season and Resistance in Gram-negative Pathogens

Background

Viral infections are often treated with empiric antibiotics due to suspected bacterial coinfections, leading to antibiotic overuse. We aimed to describe antibiotic resistance (ABR) trends and their association with the influenza season in ambulatory and inpatient settings in the United States.

Methods

We used the BD Insights Research Database to evaluate antibiotic susceptibility profiles in 30-day nonduplicate bacterial isolates collected from patients >17 years old at 257 US healthcare institutions from 2011 to 2019. We investigated ABR in Gram-positive (Staphylococcus aureus and Streptococcus pneumoniae) and Gram-negative (Enterobacterales [ENT], Pseudomonas aeruginosa [PSA], and Acinetobacter baumannii spp [ACB]) bacteria expressed as the proportion of isolates not susceptible ([NS], intermediate or resistant) and resistance per 100 admissions (inpatients only). Antibiotics included carbapenems (Carb), fluoroquinolones (FQ), macrolides, penicillin, extended-spectrum cephalosporins (ESC), and methicillin. Generalized estimating equations models were used to evaluate monthly trends in ABR outcomes and associations with community influenza rates.

Results

We identified 8 250 860 nonduplicate pathogens, including 154 841 Gram-negative Carb-NS, 1 502 796 Gram-negative FQ-NS, 498 012 methicillin-resistant S aureus (MRSA), and 44 131 NS S pneumoniae. All S pneumoniae rates per 100 admissions (macrolide-, penicillin-, and ESC-NS) were associated with influenza rates. Respiratory, but not nonrespiratory, MRSA was also associated with influenza. For Gram-negative pathogens, influenza rates were associated with the percentage of FQ-NS ENT, FQ-NS PSA, and Carb-NS ACB.

Conclusions

Our study showed expected increases in rates of ABR Gram-positive and identified small but surprising increases in ABR Gram-negative pathogens associated with influenza activity. These insights may help inform antimicrobial stewardship initiatives.

The impact of antimicrobial stewardship program designed to shorten antibiotics use on the incidence of resistant bacterial infections and mortality

Reassessing the continuing need for and choice of antibiotics by using an antibiotic "time out'' program may reduce unnecessary treatment. This study aimed to explore the effect of an antibiotic stewardship program (ASP) on the antibiotics consumption, incidence of resistant bacterial infections and overall hospital mortality in a tertiary medical center during the study period 2012-2014. An ASP composed of multidisciplinary strategies including pre-prescription approval and post-approval feedback and audit, and a major "time out'' intervention (shorten the default antibiotic prescription duration) usage was introduced in year 2013. Consumption of antibiotics was quantified by calculating defined daily doses (DDDs). Interrupted time series (ITS) analysis was used to explore the changes of antibiotics consumption before and after intervention, accounting for temporal trends that may be unrelated to intervention. Our results showed that following the intervention, DDDs showed a decreased trend in overall (in particular the major consumed penicillins and cephalosporins), in both intensive care unit (ICU) and non-ICU, and in non-restrictive versus restrictive antibiotics. Importantly, ITS analysis showed a significantly slope change since intervention (slope change p value 0.007), whereas the incidence of carbapenem-resistant and vancomycin-resistant pathogens did not change significantly. Moreover, annual overall mortality rates were 3.0%, 3.1% and 3.1% from 2012 to 2014, respectively. This study indicates that implementing a multi-disciplinary strategy to shorten the default duration of antibiotic prescription can be an effective manner to reduce antibiotic consumption while not compromising resistant infection incidence or mortality rates.

Associations between Multimorbidity Patterns and Subsequent Labor Market Marginalization among Refugees and Swedish-Born Young Adults-A Nationwide Registered-Based Cohort Study

Background: Young refugees are at increased risk of labor market marginalization (LMM). We sought to examine whether the association of multimorbidity patterns and LMM differs in refugee youth compared to Swedish-born youth and identify the diagnostic groups driving this association. Methodology: We analyzed 249,245 individuals between 20–25 years, on 31 December 2011, from a combined Swedish registry. Refugees were matched 1:5 to Swedish-born youth. A multimorbidity score was computed from a network of disease co-occurrences in 2009–2011. LMM was defined as disability pension (DP) or >180 days of unemployment during 2012–2016. Relative risks (RR) of LMM were calculated for 114 diagnostic groups (2009–2011). The odds of LMM as a function of multimorbidity score were estimated using logistic regression. Results: 2841 (1.1%) individuals received DP and 16,323 (6.5%) experienced >180 annual days of unemployment during follow-up. Refugee youth had a marginally higher risk of DP (OR (95% CI): 1.59 (1.52, 1.67)) depending on their multimorbidity score compared to Swedish-born youth (OR (95% CI): 1.51 (1.48, 1.54)); no differences were found for unemployment (OR (95% CI): 1.15 (1.12, 1.17), 1.12 (1.10, 1.14), respectively). Diabetes mellitus and influenza/pneumonia elevated RR of DP in refugees (RRs (95% CI) 2.4 (1.02, 5.6) and 1.75 (0.88, 3.45), respectively); most diagnostic groups were associated with a higher risk for unemployment in refugees. Conclusion: Multimorbidity related similarly to LMM in refugees and Swedish-born youth, but different diagnoses drove these associations. Targeted prevention, screening, and early intervention strategies towards specific diagnoses may effectively reduce LMM in young adult refugees.

A TLR5 mono-agonist restores inhibited immune responses to Streptococcus pneumoniae during influenza virus infection in human monocytes

Influenza A virus (IAV) predisposes individuals to often more severe secondary bacterial infections with Streptococcus pneumonia (S. pneumoniae). The outcomes of these infections may be made worse with the increase in antimicrobial resistance and a lack of new treatments to combat this. Th17 responses are crucial in clearing S. pneumoniae from the lung. We previously demonstrated that early IAV infection of human monocytes significantly reduced levels of S. pneumoniae-driven cytokines involved in the Th17 response. Here, we have further identified that IAV targets specific TLRs (TLR2, TLR4, TLR9) involved in sensing S. pneumoniae infection resulting, in a reduction in TLR agonist-induced IL-23 and TGF-β. The effect of IAV is more profound on the TLR2 and TLR9 pathways. We have established that IAV-mediated inhibition of TLR9-induction is related to a downregulation of RORC, a Th17 specific transcription factor. Other studies using mouse models demonstrated that TLR5 agonism improved the efficacy of antibiotics in the treatment of IAV/S. pneumoniae co-infections. Therefore, we investigated if TLR5 agonism could restore inhibited Th17 responses in human monocytes. Levels of pneumococcus-driven cytokines, which had previously been inhibited by IAV were not reduced in the presence of the TLR5 mono-agonist, suggesting that such treatment may overcome IAV inhibition of Th17 responses. The importance of our research is in demonstrating the IAV directly targets S. pneumoniae-associated TLR pathways. Additionally, the IAV-inhibition of Th17 responses can be restored by TLR5 agonism, which indicates that there may be a different Th17 signalling pathway which is not affected by IAV infection.

Management of hospitalized influenza A patients during the season 2018/19 : Comparison of three medical departments and the effect on outcome and antibiotic usage

BACKGROUND

Diagnosis and treatment of influenza patients are often provided across several medical specialties. We compared patient outcomes at an infectious diseases (ID), a rheumatology (Rheu) and a pulmonology (Pul) department.

MATERIAL AND METHODS

In this prospective observational multicenter study we included all influenza positive adults who were hospitalized and treated at flu isolation wards in three hospitals in Vienna during the season 2018/2019.

RESULTS

A total of 490 patients (49% female) with a median age of 73 years (interquartile range [IQR] 61-82) were included. No differences regarding age, sex and most underlying diseases were present at admission. Frequencies of the most common complications differed: acute kidney failure (ID 12.7%, Rheu 21.2%, Pulm 37.1%, p < 0.001), acute heart failure (ID 4.3%, Rheu 17.1%, Pulm 14.4%, p < 0.001) and respiratory insufficiency (ID 45.1%, Rheu 41.5%, Pulm 56.3%, p = 0.030). Oseltamivir prescription was lowest at the pulmonology flu ward (ID 79.6%, Rheu 90.5%, Pulm 61.7%, p < 0.001). In total 176 patients (35.9%) developed pneumonia. Antibiotic selection varied between the departments: amoxicillin/clavulanic acid (ID 28.9%, Rheu 63.8%, Pulm 5.9%, p < 0.001), cefuroxime (ID 28.9%, Rheu 1.3%, Pulm 0%, p < 0.001), 3rd generation cephalosporins (ID 4.4%, Rheu 5%, Pulm 72.5%, p < 0.001), doxycycline (ID 17.8%, Rheu 0%, Pulm 0%, p < 0.001). The median length of stay was significantly different between wards: ID 6 days (IQR 5-8), Rheu 6 days (IQR 5-7) and Pulm 7 days (IQR 5-9.5, p = 0.034). In-hospital mortality was 4.3% and did not differ between specialties.

CONCLUSION

We detected differences in oseltamivir usage, length of in-hospital stay and antibiotic choices for pneumonia. Influenza-associated mortality was unaffected by specialty.

Risk factors for isolation of multi-drug resistant organisms in coronavirus disease 2019 pneumonia: A multicenter study

Objectives

Superimposed multi-drug resistant organisms (MDROs) co-infection can be associated with worse outcomes in patients with severe coronavirus disease 2019 (COVID-19), even if these patients were managed with strict airborne and contact precautions. Identifying risk factors for isolation of MDROs is critical to COVID-19 treatment.

Methods

All eligible adult patients with confirmed COVID-19 pneumonia from 10 hospitals in the Republic of Korea between February 2020 and May 2020 were retrospectively enrolled. Using this cohort, epidemiology and risk factors for isolation of MDROs were evaluated.

Results

Of 152 patients, 47 with microbial culture results were included. Twenty isolates of MDROs from 13 (28%) patients were cultured. Stenotrophomonas maltophilia (5 isolates) was the most common MDRO, followed by methicillin-resistant staphylococcus aureus (4 isolates). MDROs were mostly isolated from sputum samples (80%, 16/20). The median time from hospitalization to MDRO isolation was 28 days (interquartile range, 18-38 days). In-hospital mortality was higher in patients with MDRO isolation (62% vs 15%; P = .001). Use of systemic corticosteroids after diagnosis of COVID-19 (adjusted odds ratio [aOR]: 15.07; 95% confidence interval [CI]: 2.34-97.01; P = .004) and long-term care facility (LTCF) stay before diagnosis of COVID-19 (aOR: 6.09; 95% CI: 1.02-36.49; P = .048) were associated with MDRO isolation.

Conclusions

MDROs were isolated from 28% of COVID-19 pneumonia patients with culture data and 8.6% of the entire cohort. Previous LTCF stay and adjunctive corticosteroid use were risk factors for the isolation of MDROs. Strict infection prevention strategies may be needed in these COVID-19 patients with risk factors.

Leonurine protects against influenza A virus infection-induced pneumonia in mice

Influenza A virus (H1N1), a swine-origin influenza A virus, causes seasonal epidemics that result in severe illnesses and deaths. Leonurine has been reported to function as an anti-inflammatory agent with protective effects on nervous, urinary and cardiovascular systems. However, the therapeutic effects of leonurine on the pneumonia caused by H1N1 infection remain unclear. Hematoxylin and eosin staining was performed to evaluate the lung injuries of mice infected by H1N1. The amount of immune cells was analyzed by flow cytometry. Enzyme-linked immunosorbent assay was used to evaluate the alteration of multiple cytokines in lung tissues. Real-time quantitative polymerase chain reaction assay was performed to investigate the ribonucleic acid (RNA) levels of certain genes. The protein levels in toll-like receptor 4/nuclear factor kappa-light-chain-enhancer of activated B cells (TLR4/NF-κB) signaling were estimated by western blot assay. Leonurine treatment significantly inhibited the mortality caused by H1N1 infection. Leonurine treatment (60 mg/kg) alleviated the lung injuries caused by virus infection. The inflammatory cell accumulation and cytokine expression were inhibited by the leonurine administration. Leonurine inhibited the mRNA expression of pro-inflammatory cytokines in the lung homogenates at day 5 postinfection. Leonurine regulated the TLR4/NF-κB signaling in the lung homogenates of H1N1-infected mice at day 5 postinfection. Leonurine protects against H1N1 infection-induced pneumonia in mice.

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

BACKGROUND

Endemic to the hospital environment, Staphylococcus aureus (S. aureus) is a leading bacterial pathogen that causes deadly infections such as bacteremia and endocarditis. In past viral pandemics, it has been the principal cause of secondary bacterial infections, significantly increasing patient mortality rates. Our world now combats the rapid spread of COVID-19, leading to a pandemic with a death toll greatly surpassing those of many past pandemics. However, the impact of co-infection with S. aureus remains unclear. Therefore, we aimed to perform a high-quality scoping review of the literature to synthesize the existing evidence on the clinical outcomes of COVID-19 and S. aureus co-infection.

METHODS

A scoping review of the literature was conducted in PubMed, Scopus, Ovid MEDLINE, CINAHL, ScienceDirect, medRxiv, and the WHO COVID-19 database using a combination of terms. Articles that were in English, included patients infected with both COVID-19 and S. aureus, and provided a description of clinical outcomes for patients were eligible. From these articles, the following data were extracted: type of staphylococcal species, onset of co-infection, patient sex, age, symptoms, hospital interventions, and clinical outcomes. Quality assessments of final studies were also conducted using the Joanna Briggs Institute's critical appraisal tools.

RESULTS

Searches generated a total of 1922 publications, and 28 articles were eligible for the final analysis. Of the 115 co-infected patients, there were a total of 71 deaths (61.7%) and 41 discharges (35.7%), with 62 patients (53.9%) requiring ICU admission. Patients were infected with methicillin-sensitive and methicillin-resistant strains of S. aureus, with the majority (76.5%) acquiring co-infection with S. aureus following hospital admission for COVID-19. Aside from antibiotics, the most commonly reported hospital interventions were intubation with mechanical ventilation (74.8 %), central venous catheter (19.1 %), and corticosteroids (13.0 %).

CONCLUSIONS

Given the mortality rates reported thus far for patients co-infected with S. aureus and COVID-19, COVID-19 vaccination and outpatient treatment may be key initiatives for reducing hospital admission and S. aureus co-infection risk. Physician vigilance is recommended during COVID-19 interventions that may increase the risk of bacterial co-infection with pathogens, such as S. aureus, as the medical community's understanding of these infection processes continues to evolve.

Viral and Bacterial Co-Infections in the Lungs: Dangerous Liaisons

Respiratory tract infections constitute a significant public health problem, with a therapeutic arsenal that remains relatively limited and that is threatened by the emergence of antiviral and/or antibiotic resistance. Viral–bacterial co-infections are very often associated with the severity of these respiratory infections and have been explored mainly in the context of bacterial superinfections following primary influenza infection. This review summarizes our current knowledge of the mechanisms underlying these co-infections between respiratory viruses (influenza viruses, RSV, and SARS-CoV-2) and bacteria, at both the physiological and immunological levels. This review also explores the importance of the microbiome and the pathological context in the evolution of these respiratory tract co-infections and presents the different in vitro and in vivo experimental models available. A better understanding of the complex functional interactions between viruses/bacteria and host cells will allow the development of new, specific, and more effective diagnostic and therapeutic approaches.

[Rare superinfection in a COVID-19 patient-A chronology]

Bei einem 55-jährigen Mann, der sich zur elektiven Ablation bei Vorhofflimmern in der Klinik befand, wurde nach einer Reanimationssituation auf der peripheren Station ein SARS-CoV-2-Abstrich positiv getestet. Anamnestisch gab es im Vorwege gesicherten Kontakt zu einem COVID-19-positiven Patienten. Im Verlauf entwickelte sich das Vollbild einer COVID-19-Pneumonie mit umfangreicher intensivmedizinischer Behandlung. Nach rund 2‑wöchiger Therapie musste das Weaning bei erneuter Verschlechterung abgebrochen werden, und es ergaben sich bei dem wiederholt hochseptischen Patienten mikrobiologische Nachweise einer Superinfektion mit Cryptococcus neoformans und später Leclercia adecarboxylata. Der Patient wurde erfolgreich behandelt und überlebte die Erkrankung.

Change in patterns of hospitalization for influenza during COVID-19 surges

Background

Hospitalization due to influenza has been stable in recent years. In March 2020, New York was an epicenter for coronavirus disease 2019 (COVID‐19). Because influenza and COVID‐19 present similarly, there were serious concerns that coinfection of these viruses would burden the healthcare system. We compared incidence and outcomes of patients hospitalized with influenza before and during COVID‐19 (seasons 2017–2021).

Methods

We conducted a retrospective study evaluating hospitalized patients with influenza. Four influenza seasons were evaluated, 2017–2021, pre‐ and during COVID‐19 pandemic. We compared incidence of influenza and clinical outcomes across the seasons.

Results

We found 412 patients hospitalized due to influenza in the study period; 394 had influenza, and 18 had both influenza and COVID‐19 infections. Demographics across the four influenza seasons were comparable; the cohort was predominantly female (61%) and had an average age of 60 years old. Comorbid conditions were common. No outcome differences were found for patients with influenza when comparing influenza seasons prior to and during the COVID‐19 pandemic. The mortality for the entire cohort was 6.5%. During the COVID‐19 pandemic, there were 18 (4.4%) influenza patients coinfected with COVID‐19 and 32 (7.8%) patients with bacterial super infection. Predictors of mortality in patients with influenza included presence of shock, heart failure, bacterial pneumonia, and use of mechanical ventilation. Coinfection with COVID‐19 did not increase mortality.

Conclusion

We observed a significant decrease in the incidence of hospitalization due to influenza during the COVID‐19 pandemic. Clinical presentations and outcomes for patients with influenza remain stable. Being aware of possible increased mortality for patients with both influenza and bacterial pneumonia is important. Although coinfection with COVID‐19 did not increase mortality in influenza patients, identifying the specific virus responsible for infections has major therapeutic implications.

IFN-γ Drives TNF-α Hyperproduction and Lethal Lung Inflammation during Antibiotic Treatment of Postinfluenza Staphylococcus aureus Pneumonia

Inflammatory cytokine storm is a known cause for acute respiratory distress syndrome. In this study, we have investigated the role of IFN-γ in lethal lung inflammation using a mouse model of postinfluenza methicillin-resistant Staphylococcus aureus (MRSA) pneumonia. To mimic the clinical scenario, animals were treated with antibiotics for effective bacterial control following MRSA superinfection. However, antibiotic therapy alone is not sufficient to improve survival of wild-type animals in this lethal acute respiratory distress syndrome model. In contrast, antibiotics induce effective protection in mice deficient in IFN-γ response. Mechanistically, we show that rather than inhibiting bacterial clearance, IFN-γ promotes proinflammatory cytokine response to cause lethal lung damage. Neutralization of IFN-γ after influenza prevents hyperproduction of TNF-α, and thereby protects against inflammatory lung damage and animal mortality. Taken together, the current study demonstrates that influenza-induced IFN-γ drives a stepwise propagation of inflammatory cytokine response, which ultimately results in fatal lung damage during secondary MRSA pneumonia, despite of antibiotic therapy.

Causes and Consequences of COVID-19-Associated Bacterial Infections

The COVID-19 literature highlights that bacterial infections are more common in fatal cases than recovered cases. If bacterial infections drive mortality in COVID-19, this has clear implications for patient management. However, it is possible that the enrichment of bacterial infections in COVID-19 fatalities is simply a by-product of late-stage pathology, leading to different advice for patient management. To address this question, we review current knowledge on bacterial infections in COVID-19, assess information from past viral respiratory pandemics, and simulate alternate causal models of interactions between virus, bacteria, and mortality in COVID-19. From these models, we conclude that currently available data are not sufficient to discriminate between these alternate causal pathways, and we highlight what data are required to determine the relative contribution of bacterial infection to COVID-19 morbidity and mortality. We further summarize the potential long-term consequences of SARS-CoV-2 infection.

Association between Early Antibiotic Therapy and In-Hospital Mortality among Older Patients with SARS-CoV-2 Pneumonia

Background

It is uncertain whether antibiotic therapy should be started in SARS CoV-2 pneumonia. We aimed to investigate the association between early antibiotic therapy and the risk of in-hospital mortality in older patients.

Methods

We performed a retrospective international cohort study (ANTIBIOVID) in five COVID-19 geriatric units in France and Switzerland. Among 1,357 consecutive patients aged 75 or more hospitalised and testing positive for SARS-CoV-2, 1072 had a radiologically confirmed pneumonia, of which 914 patients were still alive and hospitalized at 48 hours. To adjust for confounders, a propensity score for treatment was created, and stabilized inverse probability of treatment weighting (SIPTW) was applied. To assess the association between early antibiotic therapy and in-hospital 30-day mortality, SIPTW-adjusted Kaplan-Meier and Cox proportional hazards regression analyses were performed.

Results

Of the 914 patients with SARS-CoV-2 pneumonia, median age of 86, 428 (46.8%) received antibiotics in the first 48 hours after diagnosis. Among these patients, 147 (34.3%) died in hospital within one month vs 118 patients (24.3%) with no early antibiotic treatment. After SIPTW, early antibiotic treatment was not significantly associated with mortality (adjusted hazard ratio, 1.23; 95% CI, 0.92-1.63; P = .160). Microbiologically confirmed superinfections occurred rarely in both groups (bacterial pneumonia: 2.5% vs 1.5%, P = .220; blood stream infection: 8.2% vs 5.2%, P = .120; Clostridioides difficile colitis: 2.4% vs 1.0%, P = .222).

Conclusions

In a large multicentre cohort of older inpatients with SARS-CoV-2 pneumonia, early antibiotic treatment did not appear to be associated with an improved prognosis.

Lower Respiratory Tract Pathogens and Their Antimicrobial Susceptibility Pattern: A 5-Year Study

Lower respiratory tract infections (LRTIs) are the most common infections in humans. It is estimated that 2.74 million deaths worldwide occur each year due to LRTIs. The aim of the study was to determine the frequency and antibiotic susceptibility pattern of microorganisms isolated from respiratory samples of patients with LRTIs. Between January 2015 and December 2019, a total of 7038 sputum and bronchoaspirate samples from suspected LRTI patients were collected. Among them, 2753 samples (39.1%) showed significant microbial growth on culture media. The LRTI rate was higher in patients with male gender (67.1%) and with age between 40–59 years (48.6%). The microorganism identification and antibiotic susceptibility testing were performed with Vitek 2. Out of 4278 isolates species, 3102 (72.5%) were Gram-negative bacteria, 1048 (24.5%) were Gram-positive bacteria, and 128 (3.0%) were Candida spp. Major microorganisms isolated were Acinetobacter baumannii (18.6%), Staphylococcus aureus (15.2%), Pseudomonas aeruginosa (14.2%), and Klebsiella pneumoniae (10.9%). In antimicrobial susceptibility testing, Staphylococcus aureus isolates were mostly resistant to Penicillin G (84.1%) and Oxacillin (48.1%), whereas they demonstrated maximum sensitivity to Tigecycline (100%) and Linezolid (99.5%). Among Gram-negative isolates, Acinetobacter baumannii showed maximum sensitivity to Colistin but was resistant to other antibiotics (95–99%). Klebsiella pneumoniae isolates were mostly resistant to Cefotaxime (72.7%) and sensitive to Gentamicin (54.3%), and Pseudomonas aeruginosa was resistant to Ciprofloxacin (40.3%) and sensitive to Amikacin (85.9%). Gram-negative bacteria represented the species most commonly isolated. A high rate of antimicrobial resistance was observed in this study. In conclusion, the correct identification of causative microorganisms and their susceptibility patterns to antibiotics is crucial for choosing targeted and effective antibiotic therapy in LRTIs, and to prevent the emergence of multidrug-resistant bacteria.

Outcomes of respiratory viral-bacterial co-infection in adult hospitalized patients

BACKGROUND

Viral infections of the respiratory tract represent a major global health concern. Co-infection with bacteria may contribute to severe disease and increased mortality in patients. Nevertheless, viral-bacterial co-infection patterns and their clinical outcomes have not been well characterized to date. This study aimed to evaluate the clinical features and outcomes of patients with viral-bacterial respiratory tract co-infections.

METHODS

We included 19,361 patients with respiratory infection due to respiratory viruses [influenza A and B, respiratory syncytial virus (RSV), parainfluenza] and/or bacteria in four tertiary hospitals in Hong Kong from 2013 to 2017 using a large territory-wide healthcare database. All microbiological tests were conducted within 48 h of hospital admission. Four etiological groups were included: (1) viral infection alone; (2) bacterial infection alone; (3) laboratory-confirmed viral-bacterial co-infection and (4) clinically suspected viral-bacterial co-infection who were tested positive for respiratory virus and negative for bacteria but had received at least four days of antibiotics. Clinical features and outcomes were recorded for laboratory-confirmed viral-bacterial co-infection patients compared to other three groups as control. The primary outcome was 30-day mortality. Secondary outcomes were intensive care unit (ICU) admission and length of hospital stay. Propensity score matching estimated by binary logistic regression was used to adjust for the potential bias that may affect the association between outcomes and covariates.

FINDINGS

Among 15,906 patients with respiratory viral infection, there were 8451 (53.1%) clinically suspected and 1,087 (6.8%) laboratory-confirmed viral-bacterial co-infection. Among all the bacterial species, Haemophilus influenzae (226/1,087, 20.8%), Pseudomonas aeruginosa (180/1087, 16.6%) and Streptococcus pneumoniae (123/1087, 11.3%) were the three most common bacterial pathogens in the laboratory-confirmed co-infection group. Respiratory viruses co-infected with non-pneumococcal streptococci or methicillin-resistant Staphylococcus aureus was associated with the highest death rate [9/30 (30%) and 13/48 (27.1%), respectively] in this cohort. Compared with other infection groups, patients with laboratory-confirmed co-infection had higher ICU admission rate (p < 0.001) and mortality rate at 30 days (p = 0.028), and these results persisted after adjustment for potential confounders using propensity score matching. Furthermore, patients with laboratory-confirmed co-infection had significantly higher mortality compared to patients with bacterial infection alone.

INTERPRETATION

In our cohort, bacterial co-infection is common in hospitalized patients with viral respiratory tract infection and is associated with higher ICU admission rate and mortality. Therefore, active surveillance for bacterial co-infection and early antibiotic treatment may be required to improve outcomes in patients with respiratory viral infection.

COVID-19 is not "just another flu": a real-life comparison of severe COVID-19 and influenza in hospitalized patients in Vienna, Austria

Background

COVID-19 is regularly compared to influenza. Mortality and case-fatality rates vary widely depending on incidence of COVID-19 and the testing policy in affected countries. To date, data comparing hospitalized patients with COVID-19 and influenza is scarce.

Methods

Data from patients with COVID-19 were compared to patients infected with influenza A (InfA) and B (InfB) virus during the 2017/18 and 2018/19 seasons. All patients were ≥ 18 years old, had PCR-confirmed infection and needed hospital treatment. Demographic data, medical history, length-of-stay (LOS), complications including in-hospital mortality were analyzed.

Results

In total, 142 patients with COVID-19 were compared to 266 patients with InfA and 300 with InfB. Differences in median age (COVID-19 70.5 years vs InfA 70 years and InfB 77 years, p < 0.001) and laboratory results were observed. COVID-19 patients had fewer comorbidities, but complications (respiratory insufficiency, pneumonia, acute kidney injury, acute heart failure and death) occurred more frequently.

Median length-of-stay (LOS) was longer in COVID-19 patients (12 days vs InfA 7 days vs. InfB 7 days, p < 0.001). There was a fourfold higher in-hospital mortality in COVID-19 patients (23.2%) when compared with InfA (5.6%) or InfB (4.7%; p < 0.001).

Conclusion

In hospitalized patients, COVID-19 is associated with longer LOS, a higher number of complications and higher in-hospital mortality compared to influenza, even in a population with fewer co-morbidities. This data, a high reproduction number and limited treatment options, alongside excess mortality during the SARS-CoV-2 pandemic, support the containment strategies implemented by most authorities.