Secondary Bacterial Infections Associated with Influenza Pandemics

Impact of influenza virus infection on lung microbiome in adults with severe pneumonia

BACKGROUND

Bacterial and viral infections are commonly implicated in the development of pneumonia. We aimed to compare the diversity and composition of lung bacteria among severe pneumonia patients who were influenza virus positive (IFVP) and influenza virus negative (IFVN).

METHODS

Bronchoalveolar lavage fluid specimens were procured from patients diagnosed with severe pneumonia to investigate the microbiome utilizing 16S-rDNA sequencing. The alpha diversity of the microbiome was evaluated employing Chao1, Shannon, and Simpson indexes, while the beta diversity was assessed using principal component analysis and principal coordinate analysis. Linear discriminant analysis effect size (LEfSe) was employed to determine the taxonomic differences between the IFVP and IFVN groups.

RESULTS

A total of 84 patients with 42 in the IFVP group and 42 in the IFVN group were enrolled. Slightly higher indexes of Shannon and Simpson were observed in the IFVP group without statistically significant difference. The dominant bacterial genera were Streptococcus, Klebsiella, Escherichia-Shigella in the IFVN group and Acinetobacter, Streptococcus, Staphylococcus in the IFVP group. Streptococcus pneumoniae and Acinetobacter baumannii were the most abundant species in the IFVN and IFVP groups, respectively. LEfSe analysis indicated a greater abundance of Klebsiella in the IFVN group.

CONCLUSIONS

Individuals with severe pneumonia infected with IFV exhibit heightened susceptibility to certain bacteria, especially Acinetobacter baumannii, and the underlying mechanism of the interaction between IFV and Acinetobacter baumannii in the progression of pneumonia needs further investigation.

Epidemiological Impact of the Pediatric Live Attenuated Influenza Vaccine (LAIV) Program on Group A Streptococcus (GAS) Infection in England

Background

Influenza is known to predispose to secondary bacterial infections including invasive group A streptococcal (iGAS) disease. The universal pediatric live attenuated influenza vaccine (LAIV) program introduced in England from the 2013/2014 influenza season was implemented incrementally, introducing cohorts of children annually to 2-16 years of coverage. Additionally, from the beginning of the program, discrete pilot areas offered LAIV vaccination to all primary school-age children, allowing for a unique comparison of infection rates between pilot and nonpilot areas during the program rollout.

Methods

Cumulative incidence rate ratios (IRRs) of GAS infections (all), scarlet fever (SF), and iGAS infection within each season by age group were compared for pilot and nonpilot areas using Poisson regression. The overall effect of the pilot program in the pre- (2010/2011-2012/2013 seasons) and postintroduction (2013/2014-2016/2017 seasons) periods was assessed using negative binomial regression by comparing changes in incidence between pilot/nonpilot areas (ratio of IRR [rIRR]).

Results

Reductions in IRRs of GAS and SF were observed within most post-LAIV program seasons, among the age groups 2-4 and 5-10 years. Significant reductions were seen among 5-10 years (rIRR, 0.57; 95% CI, 0.45-0.71; P < .001), 2-4 years (rIRR, 0.62; 95% CI, 0.43-0.90; P = .011), and 11-16 years (rIRR, 0.63; 95% CI, 0.43-0.90; P = .018) for GAS infections when assessing the overall effect of the program.

Conclusions

Our findings suggest that vaccination with LAIV may be associated with a reduced risk of GAS infection and support attaining high uptake of childhood influenza vaccination.

Interaction Between SARS-CoV-2 and Pathogenic Bacteria

The novel human coronavirus, Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), which results in the coronavirus disease 2019 (COVID-19), has caused a serious threat to global public health. Therefore, many studies are performed on the causes and prevalence of this disease and the possible co-occurrence of the infection with other viral and bacterial pathogens is investigated. Respiratory infections predispose patients to co-infections and these lead to increased disease severity and mortality. Numerous types of antibiotics have been employed for the prevention and treatment of bacterial co-infection and secondary bacterial infections in patients with a SARS-CoV-2 infection. Although antibiotics do not directly affect SARS-CoV-2, viral respiratory infections often result in bacterial pneumonia. It is possible that some patients die from bacterial co-infection rather than virus itself. Therefore, bacterial co-infection and secondary bacterial infection are considered critical risk factors for the severity and mortality rates of COVID-19. In this review, we will summarize the bacterial co-infection and secondary bacterial infection in some featured respiratory viral infections, especially COVID-19.

Using system biology and bioinformatics to identify the influences of COVID-19 co-infection with influenza virus on COPD

Coronavirus disease 2019 (COVID-19) has speedily increased mortality globally. Although they are risk factors for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), less is known about the common molecular mechanisms behind COVID-19, influenza virus A (IAV), and chronic obstructive pulmonary disease (COPD). This research used bioinformatics and systems biology to find possible medications for treating COVID-19, IAV, and COPD via identifying differentially expressed genes (DEGs) from gene expression datasets (GSE171110, GSE76925, GSE106986, and GSE185576). A total of 78 DEGs were subjected to functional enrichment, pathway analysis, protein-protein interaction (PPI) network construct, hub gene extraction, and other potentially relevant disorders. Then, DEGs were discovered in networks including transcription factor (TF)-gene connections, protein-drug interactions, and DEG-microRNA (miRNA) coregulatory networks by using NetworkAnalyst. The top 12 hub genes were MPO, MMP9, CD8A, HP, ELANE, CD5, CR2, PLA2G7, PIK3R1, SLAMF1, PEX3, and TNFRSF17. We found that 44 TFs-genes, as well as 118 miRNAs, are directly linked to hub genes. Additionally, we searched the Drug Signatures Database (DSigDB) and identified 10 drugs that could potentially treat COVID-19, IAV, and COPD. Therefore, we evaluated the top 12 hub genes that could be promising DEGs for targeted therapy for SARS-CoV-2 and identified several prospective medications that may benefit COPD patients with COVID-19 and IAV co-infection.

Changes in the Incidence of Invasive Pneumococcal Disease in Calgary, Canada, during the SARS-CoV-2 Pandemic 2020-2022

We describe the impact of non-pharmaceutical interventions (NPIs) during the COVID-19 pandemic on invasive pneumococcal disease (IPD) in Calgary. IPD declined significantly worldwide during 2020 and 2021. This may be due to the reduced transmission of and decrease in circulating viruses that often co-infect with the opportunistic pneumococcus. Pneumococcus has not been shown to frequently co-infect or cause secondary infection with SARS-CoV-2. We examined and compared incidence rates in Calgary per quarter in the pre-vaccine, post-vaccine, 2020 and 2021 (pandemic) and 2022 (late pandemic) eras. We also conducted a time series analysis from 2000-2022 allowing for change in trend at introduction of vaccines and for initiation of NPIs during the COVID-19 pandemic. Incidence declined in 2020/2021 but by the end of 2022 had begun to rapidly recover to near pre-vaccine rates. This recovery may be related to the high rates of viral activity in the winter of 2022 along with childhood vaccines being delayed during the pandemic. However, a large proportion of the IPD caused in the last quarter of 2022 was serotype 4, which has caused outbreaks in the homeless population of Calgary in the past. Further surveillance will be important to understand IPD incidence trends in the post-pandemic landscape.

Epidemiological Impact on Use of Antibiotics in Patients Hospitalized for COVID-19: A Retrospective Cohort Study in Italy

The increased incidence of antimicrobial resistance during coronavirus disease 2019 (COVID-19) is a very important collateral damage of global concern. The cause is multifactorial and is particularly related to the high rates of antibiotic use in COVID-19 patients with a relatively low rate of secondary co-infection. To this end, we conducted a retrospective observational study of 1269 COVID-19 patients admitted during the years 2020, 2021 and 2022 in two Italian hospitals, with a focus on bacterial co-infections and antimicrobial therapy. Multivariate logistic regression was used to analyze the association between bacterial co-infection, antibiotic use and hospital death after adjustment for age and comorbidity. Bacterial co-infection was detected in 185 patients. The overall mortality rate was 25% (n = 317). Concomitant bacterial infections were associated with increased hospital mortality (β = 1.002, p < 0.001). A total of 83.7% (n = 1062) of patients received antibiotic therapy, but only 14.6% of these patients had an obvious source of bacterial infection. There was a significantly higher rate of hospital mortality in patients who received antibiotics than in those who did not (χ² = 6.22, p = 0.012). Appropriate prescribing and the rational use of antimicrobials according to the principles of antimicrobial stewardship can help prevent the emergence of antibiotic resistance.

Impact of COVID-19 Outbreak on Influenza and Pneumococcal Vaccination Uptake: A Multi-Center Retrospective Study

During the coronavirus disease 2019 (COVID-19) pandemic, global vaccination efforts declined due to the burden on health systems and community resistance to epidemic control measures. Influenza and pneumococcal vaccines have been recommended for vulnerable populations to prevent severe pneumonia. We investigated community response towards influenza and pneumococcal vaccines (pneumococcal conjugate vaccine and pneumococcal polysaccharide vaccine) after the COVID-19 outbreak in Taiwan. We retrospectively included adults who visited Chang Gung Memorial Hospital (CGMH) institutions for influenza or pneumococcal vaccination from January 2018 to December 2021. The first case of COVID-19 in Taiwan was detected in January 2020; therefore, in this study, hospitalized cases from January 2018 to December 2019 were defined as "before COVID-19 outbreak," and hospitalized cases from January 2020 to December 2021 were defined as "after COVID-19 outbreak". A total of 105,386 adults were enrolled in the study. An increase in influenza vaccination (n = 33,139 vs. n = 62,634) and pneumococcal vaccination (n = 3035 vs. n = 4260) were observed after the COVID-19 outbreak. In addition, there was an increased willingness to receive both influenza and pneumococcal vaccinations among women, adults without underlying disease and younger adults. The COVID-19 pandemic may have increased awareness of the importance of vaccination in Taiwan.

Impact of Administering Intravenous Azithromycin within 7 Days of Hospitalization for Influenza Virus Pneumonia: A Propensity Score Analysis Using a Nationwide Administrative Database

The potential antimicrobial and anti-inflammatory effectiveness of azithromycin against severe influenza is yet unclear. We retrospectively investigated the effect of intravenous azithromycin administration within 7 days of hospitalization in patients with influenza virus pneumonia and respiratory failure. Using Japan's national administrative database, we enrolled and classified 5066 patients with influenza virus pneumonia into severe, moderate, and mild groups based on their respiratory status within 7 days of hospitalization. The primary endpoints were total, 30-day, and 90-day mortality rates. The secondary endpoints were the duration of intensive-care unit management, invasive mechanical ventilation, and hospital stay. The inverse probability of the treatment weighting method with estimated propensity scores was used to minimize data collection bias. Use of intravenous azithromycin was proportional to the severity of respiratory failure (mild: 1.0%, moderate: 3.1%, severe: 14.8%). In the severe group, the 30-day mortality rate was significantly lower with azithromycin (26.49% vs. 36.65%, p = 0.038). In the moderate group, the mean duration of invasive mechanical ventilation after day 8 was shorter with azithromycin; there were no significant differences in other endpoints between the severe and moderate groups. These results suggest that intravenous azithromycin has favorable effects in patients with influenza virus pneumonia using mechanical ventilation or oxygen.

Pathogenesis of nontypeable Haemophilus influenzae infections in chronic suppurative lung disease

The respiratory tract antimicrobial defense system is a multilayered defense mechanism that relies upon mucociliary clearance and components of both the innate and adaptive immune systems to protect the lungs from inhaled or aspirated microorganisms. One of these potential pathogens, nontypeable Haemophilus influenzae (NTHi), adopts several, multifaceted redundant strategies to successfully colonize the lower airways and establish a persistent infection. NTHi can impair mucociliary clearance, express multiple multifunctional adhesins for various cell types within the respiratory tract and evade host defenses by surviving within and between cells, forming biofilms, increasing antigenic drift, secreting proteases and antioxidants, and by host-pathogen cross-talk, impair macrophage and neutrophil function. NTHi is recognized as an important pathogen in several chronic lower respiratory disorders, such as protracted bacterial bronchitis, bronchiectasis, cystic fibrosis, and primary ciliary dyskinesia. The persistence of NTHi in human airways, including its capacity to form biofilms, results in chronic infection and inflammation, which can ultimately injure airway wall structures. The complex nature of the molecular pathogenetic mechanisms employed by NTHi is incompletely understood but improved understanding of its pathobiology will be important for developing effective therapies and vaccines, especially given the marked genetic heterogeneity of NTHi and its possession of phase-variable genes. Currently, no vaccine candidates are ready for large phase III clinical trials.

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.

Epidemiology of bacterial co-infections and risk factors in COVID-19-hospitalized patients in Spain: a nationwide study

BACKGROUND

We performed a nationwide population-based retrospective study to describe the epidemiology of bacterial co-infections in coronavirus disease 2019 (COVID-19)-hospitalized patients in Spain in 2020. We also analyzed the risk factors for co-infection, the etiology and the impact in the outcome.

METHODS

Data were obtained from records in the Minimum Basic Data Set (MBDS) of the National Surveillance System for Hospital Data in Spain, provided by the Ministry of Health and annually published with 2 years lag. COVID-19 circulated in two waves in 2020: from its introduction to 31st June and from 1st July to 31st December. The risk of developing a healthcare-associated bacterial co-infection and the risk for in-hospital and intensive care unit (ICU) mortality in co-infected patients was assessed using an adjusted logistic regression model.

RESULTS

The incidence of bacterial co-infection in COVID-19 hospitalized patients was 2.3%. The main risk factors associated with bacterial co-infection were organ failure, obesity and male sex. Co-infection was associated with worse outcomes including higher in-hospital, in-ICU mortality and higher length of stay. Gram-negative bacteria caused most infections. Causative agents were similar between waves, although higher co-infections with Pseudomonas spp. were detected in the first wave and with Haemophilus influenzae and Streptococcus pneumoniae in the second.

CONCLUSIONS

Co-infections are not as common as those found in other viral respiratory infections; therefore, antibiotics should be used carefully. Screening for actual co-infection to prescribe antibiotic therapy when required should be performed.

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.

Naturally derived cytokine peptides limit virus replication and severe disease during influenza A virus infection

Objectives

Novel host‐targeted therapeutics could treat severe influenza A virus (IAV) infections, with reduced risk of drug resistance. LAT8881 is a synthetic form of the naturally occurring C‐terminal fragment of human growth hormone. Acting independently of the growth hormone receptor, it can reduce inflammation‐induced damage and promote tissue repair in an animal model of osteoarthritis. LAT8881 has been assessed in clinical trials for the treatment of obesity and neuropathy and has an excellent safety profile. We investigated the potential for LAT8881, its metabolite LAT9991F and LAT7771 derived from prolactin, a growth hormone structural homologue, to treat severe IAV infection.

Methods

LAT8881, LAT9991F and LAT7771 were evaluated for their effects on cell viability and IAV replication in vitro, as well as their potential to limit disease in a preclinical mouse model of severe IAV infection.

Results

In vitro LAT8881 treatment enhanced cell viability, particularly in the presence of cytotoxic stress, which was countered by siRNA inhibition of host lanthionine synthetase C‐like proteins. Daily intranasal treatment of mice with LAT8881 or LAT9991F, but not LAT7771, from day 1 postinfection significantly improved influenza disease resistance, which was associated with reduced infectious viral loads, reduced pro‐inflammatory cytokines and increased abundance of protective alveolar macrophages. LAT8881 treatment in combination with the antiviral oseltamivir phosphate led to more pronounced reduction in markers of disease severity than treatment with either compound alone.

Conclusion

These studies provide the first evidence identifying LAT8881 and LAT9991F as novel host‐protective therapies that improve survival, limit viral replication, reduce local inflammation and curtail tissue damage during severe IAV infection. Evaluation of LAT8881 and LAT9991F in other infectious and inflammatory conditions of the airways is warranted.

Domestication and microbiome succession may drive pathogen spillover

Emerging infectious diseases have posed growing medical, social and economic threats to humanity. The biological background of pathogen spillover or host switch, however, still has to be clarified. Disease ecology finds pathogen spillovers frequently but struggles to explain at the molecular level. Contrarily, molecular biological traits of host-pathogen relationships with specific molecular binding mechanisms predict few spillovers. Here we aim to provide a synthetic explanation by arguing that domestication, horizontal gene transfer even between superkingdoms as well as gradual exchange of microbiome (microbiome succession) are essential in the whole scenario. We present a new perspective at the molecular level which can explain the observations of frequent pathogen spillover events at the ecological level. This proposed rationale is described in detail, along with supporting evidence from the peer-reviewed literature and suggestions for testing hypothesis validity. We also highlight the importance of systematic monitoring of virulence genes across taxonomical categories and in the whole biosphere as it helps prevent future epidemics and pandemics. We conclude that that the processes of domestication, horizontal gene transfer and microbial succession might be important mechanisms behind the many spillover events driven and accelerated by climate change, biodiversity loss and globalization.

Assessment of microbiota in the gut and upper respiratory tract associated with SARS-CoV-2 infection

BACKGROUND

The human microbiome plays an important role in modulating the host metabolism and immune system. Connections and interactions have been found between the microbiome of the gut and oral pharynx in the context of SARS-CoV-2 and other viral infections; hence, to broaden our understanding of host-viral responses in general and to deepen our knowledge of COVID-19, we performed a large-scale, systematic evaluation of the effect of SARS-CoV-2 infection on human microbiota in patients with varying disease severity.

RESULTS

We processed 521 samples from 203 COVID-19 patients with varying disease severity and 94 samples from 31 healthy donors, consisting of 213 pharyngeal swabs, 250 sputa, and 152 fecal samples, and obtained meta-transcriptomes as well as SARS-CoV-2 sequences from each sample. Detailed assessment of these samples revealed altered microbial composition and function in the upper respiratory tract (URT) and gut of COVID-19 patients, and these changes are significantly associated with disease severity. Moreover, URT and gut microbiota show different patterns of alteration, where gut microbiome seems to be more variable and in direct correlation with viral load; and microbial community in the upper respiratory tract renders a high risk of antibiotic resistance. Longitudinally, the microbial composition remains relatively stable during the study period.

CONCLUSIONS

Our study has revealed different trends and the relative sensitivity of microbiome in different body sites to SARS-CoV-2 infection. Furthermore, while the use of antibiotics is often essential for the prevention and treatment of secondary infections, our results indicate a need to evaluate potential antibiotic resistance in the management of COVID-19 patients in the ongoing pandemic. Moreover, a longitudinal follow-up to monitor the restoration of the microbiome could enhance our understanding of the long-term effects of COVID-19. Video Abstract.

The interactions of SARS-CoV-2 with cocirculating pathogens: Epidemiological implications and current knowledge gaps

Despite the availability of effective vaccines, the persistence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) suggests that cocirculation with other pathogens and resulting multiepidemics (of, for example, COVID-19 and influenza) may become increasingly frequent. To better forecast and control the risk of such multiepidemics, it is essential to elucidate the potential interactions of SARS-CoV-2 with other pathogens; these interactions, however, remain poorly defined. Here, we aimed to review the current body of evidence about SARS-CoV-2 interactions. Our review is structured in four parts. To study pathogen interactions in a systematic and comprehensive way, we first developed a general framework to capture their major components: sign (either negative for antagonistic interactions or positive for synergistic interactions), strength (i.e., magnitude of the interaction), symmetry (describing whether the interaction depends on the order of infection of interacting pathogens), duration (describing whether the interaction is short-lived or long-lived), and mechanism (e.g., whether interaction modifies susceptibility to infection, transmissibility of infection, or severity of disease). Second, we reviewed the experimental evidence from animal models about SARS-CoV-2 interactions. Of the 14 studies identified, 11 focused on the outcomes of coinfection with nonattenuated influenza A viruses (IAVs), and 3 with other pathogens. The 11 studies on IAV used different designs and animal models (ferrets, hamsters, and mice) but generally demonstrated that coinfection increased disease severity compared with either monoinfection. By contrast, the effect of coinfection on the viral load of either virus was variable and inconsistent across studies. Third, we reviewed the epidemiological evidence about SARS-CoV-2 interactions in human populations. Although numerous studies were identified, only a few were specifically designed to infer interaction, and many were prone to multiple biases, including confounding. Nevertheless, their results suggested that influenza and pneumococcal conjugate vaccinations were associated with a reduced risk of SARS-CoV-2 infection. Finally, fourth, we formulated simple transmission models of SARS-CoV-2 cocirculation with an epidemic viral pathogen or an endemic bacterial pathogen, showing how they can naturally incorporate the proposed framework. More generally, we argue that such models, when designed with an integrative and multidisciplinary perspective, will be invaluable tools to resolve the substantial uncertainties that remain about SARS-CoV-2 interactions.

Comparative effectiveness of oseltamivir versus peramivir for hospitalized children (aged 0-5 years) with influenza infection

OBJECTIVES

The effectiveness of oseltamivir versus peramivir in children infected with influenza remains unclear. This study aimed to evaluate their effectiveness in young children (aged 0-5 years) infected with severe influenza A virus (IAV) or influenza B virus (IBV).

METHODS

We analyzed a cohort of 1662 young children with either IAV (N = 1095) or IBV (N = 567) who received oseltamivir or peramivir treatment from January 1, 2018 to March 31, 2022. Propensity score matching methods were applied to match children who were oseltamivir-treated versus peramivir-treated.

RESULTS

Children who were IAV-infected and IBV-infected shared similar features, such as influenza-associated symptoms and comorbidities at baseline. Among children infected with IAV with bacterial coinfection, the recovery rate was significantly greater in children treated with oseltamivir than in children treated with peramivir (15.6% vs 4.4%, P = 0.01). The median duration of hospitalization was also shorter in children treated with oseltamivir. Among children infected with IAV without bacterial coinfection, the recovery rate was greater in children treated with oseltamivir than in children treated with peramivir (21.1% vs 3.7%, P = 0.002). However, oseltamivir and peramivir offered similar recovery rates and duration of hospitalization (P >0.05 for both) among children infected with IBV.

CONCLUSION

Oseltamivir and peramivir exhibit similar effectiveness in young children with severe influenza B, whereas oseltamivir demonstrated improved recovery and shorter hospitalization in the treatment of severe influenza A in hospitalized children.

Secondary infections in critically ill patients with viral pneumonia due to COVID-19 and influenza: a historical cohort study

PURPOSE

To compare the incidence and nature of secondary infections (SI) between critically ill patients with viral pneumonia due to COVID-19 and seasonal influenza and explore the association between SI and clinical outcomes.

METHODS

We conducted a historical cohort study of patients admitted to the intensive care unit (ICU) at two tertiary care centers during the first wave of the COVID-19 pandemic and patients admitted with influenza during the 2018-2019 season. The primary outcome was the rate of SI. Secondary outcomes included rates of ICU and in-hospital mortality, organ-support-dependent disease, and length of ICU and hospital stay.

RESULTS

Secondary infections developed in 55% of 95 COVID-19 patients and 51% of 47 influenza patients (unadjusted odds ratio [OR], 1.16; 95% confidence interval [CI], 0.57 to 2.33). After adjusting for baseline differences between cohorts, there were no significant differences between the COVID-19 cohort and the influenza cohort (adjusted OR, 1.00; 95% CI, 0.41 to 2.44). COVID-19 patients with SI had longer ICU and hospital stays and duration of mechanical ventilation. The SI incidence was higher in COVID-19 patients treated with steroids than in those not treated with steroids (15/20, 75% vs 37/75, 49%).

CONCLUSION

Secondary infections were common among critically ill patients with viral pneumonia including COVID-19. We found no difference in the incidence of SI between COVID-19 and influenza in our cohort study, but SI in patients with COVID-19 were associated with worse clinical outcomes and increased healthcare resource use. The small cohort size precludes any causal inferences but may provide a basis for future research.

Vaccine-Preventable Diseases in Older Adults

Older adults are at an increased risk of vaccine-preventable diseases partly because of physiologic changes in the immune and other body systems related to age and/or accumulating comorbidities that increase the vulnerability to infections and decrease the response to vaccines. Strategies to improve the response to vaccines include using a higher antigenic dose (such as in the high-dose inactivated influenza vaccines) as well as adding adjuvants (such as MF59 in the adjuvanted inactivated influenza vaccine).

Influenza Virus Infection Increases Host Susceptibility To Secondary Infection with Pseudomonas aeruginosa, and This Is Attributed To Neutrophil Dysfunction through Reduced Myeloperoxidase Activity

Secondary bacterial infection greatly increased the morbidity and mortality of influenza virus infection. To investigate the underlying mechanism by which influenza impairs the pulmonary defense against secondary Pseudomonas aeruginosa (P. aeruginosa) infection, we established a lethal mouse model in which to study secondary P. aeruginosa infection after influenza virus infection. We found a significant increase in host susceptibility to a secondary infection with P. aeruginosa in mice after an influenza virus infection, and this was accompanied by severe immunopathology and pulmonary inflammation. Importantly, we demonstrated that neutrophils were essential for P. aeruginosa clearance in secondarily infected mice. Further, we revealed that influenza impaired the phagocytosis and digestion functions of pulmonary neutrophils for P. aeruginosa clearance. We identified that the activity of reactive oxygen species (ROS) and the myeloperoxidase (MPO) activity of neutrophils in the lungs played an important role in antibacterial host defense in influenza-infected lungs. Hereby, influenza virus infection causes deficient MPO activity in neutrophils, and this contributes to the increased susceptibility to secondary P. aeruginosa infection. Treatment with Bacillus Calmette-Guerin polysaccharide nucleic acid (BCG-PSN) prior to secondary P. aeruginosa infection may improve the function of neutrophils, resulting in significantly reduced lethality during secondary P. aeruginosa infection. We also demonstrated that treatment with anti-influenza immune serum during the early stage of an influenza virus infection could decrease the disease severity of secondary P. aeruginosa infection. Our findings suggest that improving the MPO activity of neutrophils may provide a therapeutic strategy for viral-bacterial coinfection.

IMPORTANCE A secondary bacterial infection, such as that of P. aeruginosa, often occurs after a pulmonary virus infection and contributes to severe disease. However, the underlying mechanisms responsible for viral-bacterial synergy in the lung remain largely unknown. In this study, we reported that influenza virus infection increases a host’s susceptibility to secondary infection by P. aeruginosa by reducing the MPO activity of neutrophils. We also demonstrated that treatment with BCG-PSN or anti-influenza immune serum prior to secondary P. aeruginosa infection can reduce the disease severity. Our findings suggest that improving the MPO activity of neutrophils may provide a therapeutic strategy for viral-bacterial coinfection.

Characterization of Aspergillus spp. isolated from patients with coronavirus disease 2019

INTRODUCTION

Invasive pulmonary aspergillosis (IPA) is an important complication of coronavirus disease 2019 (COVID-19), and while there are case reports and epidemiological studies, few studies have isolated Aspergillus strains from patients. Therefore, we analyzed the strains, sensitivities, and genetic homology of Aspergillus spp. Isolated from patients with COVID-19.

METHODS

We investigated the Aspergillus strains detected from patients with COVID-19 hospitalized in Osaka Metropolitan University Hospital from December 2020 to June 2021. A molecular epidemiological analysis of Aspergillus fumigatus was performed using drug susceptibility tests and TRESPERG typing, and data on patient characteristics were collected from electronic medical records.

RESULTS

Twelve strains of Aspergillus were detected in 11 of the 122 patients (9%) with COVID-19. A. fumigatus was the most common species detected, followed by one strain each of Aspergillus aureolus, Aspergillus nidulans, Aspergillus niger, and Aspergillus terreus. A. aureolus was resistant to voriconazole, and no resistance was found in other strains. All A. fumigatus strains were genetically distinct strains. Six of the 11 patients that harbored Aspergillus received antifungal drug treatment and tested positive for β-D-glucan and/or Aspergillus galactomannan antigen. The results indicated that Aspergillus infections were acquired from outside the hospital and not from nosocomial infections.

CONCLUSION

Strict surveillance of Aspergillus spp. is beneficial in patients at high-risk for IPA. When Aspergillus is detected, it is important to monitor the onset of IPA carefully and identify the strain, perform drug sensitivity tests, and facilitate early administration of therapeutic agents to patients with IPA.

Implementation of MRSA Nasal Swabs as an Antimicrobial Stewardship Intervention to Decrease Anti-MRSA Therapy in COVID-19 Infection

In the early stages of treating patients with SARS-CoV-2, limited information was available to guide antimicrobial stewardship interventions. The COVID-19 Task Force and Antimicrobial Stewardship Committee, at a 988-bed academic medical center, implemented the use of methicillin-resistant Staphylococcus aureus (MRSA) nasal swab polymerase chain reaction (PCR) testing to assist with the de-escalation of anti-MRSA therapy in patients with suspected superimposed bacterial pneumonia in COVID-19. A retrospective study was conducted to evaluate the impact of MRSA nasal swab PCR testing on the rate of anti-MRSA therapy between 13 April 2020 and 26 July 2020. A total of 122 patients were included in the analysis. Of the patients included in the final analysis, 58 (47.5%) had anti-MRSA therapy discontinued and 41 (33.6%) avoided anti-MRSA therapy completely due to a negative swab result. With the implementation of MRSA nasal swab PCR testing in COVID-19 patients, anti-MRSA therapy was reduced in 81% of patients in this study. In patients who continued with anti-MRSA therapy, nasal swabs were either positive for MRSA or an alternative indication for anti-MRSA therapy was noted. Only three patients in the cohort had MRSA identified in a sputum culture, all of whom had anti-MRSA therapy continued. MRSA nasal swab PCR testing may serve as an effective antimicrobial stewardship tool in COVID-19 pneumonia.

Risk factors and effect on mortality of superinfections in a newly established COVID-19 respiratory sub-intensive care unit at University Hospital in Rome

BACKGROUND

Little is known on the burden of co-infections and superinfections in a specific setting such as the respiratory COVID-19 sub-intensive care unit. This study aims to (i) assess the prevalence of concurrent and superinfections in a respiratory sub-intensive care unit, (ii) evaluate the risk factors for superinfections development and (iii) assess the impact of superinfections on in-hospital mortality.

METHODS

Single-center retrospective analysis of prospectively collected data including COVID-19 patients hospitalized in a newly established respiratory sub-intensive care unit managed by pneumologists which has been set up from September 2020 at a large (1200 beds) University Hospital in Rome. Inclusion criteria were: (i) COVID-19 respiratory failure and/or ARDS; (ii) hospitalization in respiratory sub-intensive care unit and (iii) age > 18 years. Survival was analyzed by Kaplan-Meier curves and the statistical significance of the differences between the two groups was assessed using the log-rank test. Multivariable logistic regression and Cox regression model were performed to tease out the independent predictors for superinfections' development and for mortality, respectively.

RESULTS

A total of 201 patients were included. The majority (106, 52%) presented severe COVID-19. Co-infections were 4 (1.9%), whereas 46 patients (22%) developed superinfections, mostly primary bloodstream infections and pneumonia. In 40.6% of cases, multi-drug resistant pathogens were detected, with carbapenem-resistant Acinetobacter baumannii (CR-Ab) isolated in 47%. Overall mortality rate was 30%. Prior (30-d) infection and exposure to antibiotic therapy were independent risk factors for superinfection development whereas the development of superinfections was an independent risk factors for in-hospital mortality. CR-Ab resulted independently associated with 14-d mortality.

CONCLUSION

In a COVID-19 respiratory sub-intensive care unit, superinfections were common and represented an independent predictor of mortality. CR-Ab infections occurred in almost half of patients and were associated with high mortality. Infection control rules and antimicrobial stewardship are crucial in this specific setting to limit the spread of multi-drug resistant organisms.

Significance of Pulmonary Endothelial Injury and the Role of Cyclooxygenase-2 and Prostanoid Signaling

The endothelium plays a key role in the dynamic balance of hemodynamic, humoral and inflammatory processes in the human body. Its central importance and the resulting therapeutic concepts are the subject of ongoing research efforts and form the basis for the treatment of numerous diseases. The pulmonary endothelium is an essential component for the gas exchange in humans. Pulmonary endothelial dysfunction has serious consequences for the oxygenation and the gas exchange in humans with the potential of consecutive multiple organ failure. Therefore, in this review, the dysfunction of the pulmonary endothel due to viral, bacterial, and fungal infections, ventilator-related injury, and aspiration is presented in a medical context. Selected aspects of the interaction of endothelial cells with primarily alveolar macrophages are reviewed in more detail. Elucidation of underlying causes and mechanisms of damage and repair may lead to new therapeutic approaches. Specific emphasis is placed on the processes leading to the induction of cyclooxygenase-2 and downstream prostanoid-based signaling pathways associated with this enzyme.

The burden of lower respiratory infections and their underlying etiologies in the Middle East and North Africa region, 1990-2019: results from the Global Burden of Disease Study 2019

BACKGROUND

Lower respiratory infections (LRIs) cause substantial mortality and morbidity. The present study reported and analysed the burden of LRIs in the Middle East and North Africa (MENA) region between 1990 and 2019, by age, sex, etiology, and socio-demographic index (SDI).

METHODS

The data used in this study were sourced from the Global Burden of Disease (GBD) study 2019. The annual incidence, deaths, and disability-adjusted life-years (DALYs) due to LRIs were presented as counts and age-standardised rates per 100,000 population, along with their 95% uncertainty intervals (UIs). The average annual percent changes (AAPC) in the age-standardised incidence, death and DALYs rates were calculated using Joinpoint software and correlations (Pearson's correlation coefficient) between the AAPCs and SDIs were calculated using Stata software.

RESULTS

In 2019, there were 34.1 million (95% UI 31.7-36.8) incident cases of LRIs in MENA, with an age-standardised rate of 6510.2 (95% UI 6063.6-6997.8) per 100,000 population. The number of regional DALYs was 4.7 million (95% UI 3.9-5.4), with an age-standardised rate of 888.5 (95% UI 761.1-1019.9) per 100,000 population, which has decreased since 1990. Furthermore, Egypt [8150.8 (95% UI 7535.8-8783.5)] and Afghanistan [61.9 (95% UI 52.1-72.6)] had the highest age-standardised incidence and death rates, respectively. In 2019, the regional incidence and DALY rates were highest in the 1-4 age group, in both females and males. In terms of deaths, pneumococcus and H. influenza type B were the most and least common types of LRIs, respectively. From 1990 to 2019, the burden of LRIs generally decreased with increasing SDI. There were significant positive correlations between SDI and the AAPCs for the age-standardised incidence, death and DALY rates (p < 0.05). Over the 1990-2019 period, the regional incidence, deaths and DALYs attributable to LRIs decreased with AAPCs of - 1.19% (- 1.25 to - 1.13), - 2.47% (- 2.65 to - 2.28) and - 4.21% (- 4.43 to - 3.99), respectively.

CONCLUSIONS

The LRI-associated burden in the MENA region decreased between 1990 and 2019. SDI had a significant positive correlation with the AAPC and pneumococcus was the most common underlying cause of LRIs. Afghanistan, Yemen and Egypt had the largest burdens in 2019. Further studies are needed to investigate the effectiveness of healthcare interventions and programs to control LRIs and their risk factors.

Should treatment of hypogammaglobulinemia with immunoglobulin replacement therapy (IgRT) become standard of care in patients with chronic lymphocytic leukemia?

Hypogammaglobulinemia (HGG) is a frequent finding in patients with hematological malignancies, and is commonly described in chronic lymphocytic leukemia (CLL) before or after treatment. We reviewed published literature available online in the last thirty years through Medline search of indexed articles focusing on the main differences and advantages of the products now available on the market, namely intravenous Ig (IVIg) and subcutaneous Ig (SCIg) preparations. IgRT is effective and safe in the prophylaxis of infections in a selected group of patients with CLL and hypogammaglobulinemia and is therefore a valuable tool for clinicians in the everyday management of infectious risk. We encourage the use of SCIg formulations as they appear to have similar efficacy but better cost-effectiveness and tolerability.

Bacterial coinfections in hospitalized children with COVID-19 during the SARS-CoV-2 Omicron BA.2 variant pandemic in Taiwan

Background

Bacterial coinfections have been widely recognized in adults with coronavirus disease 2019 (COVID-19). However, bacterial coinfections in hospitalized children with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have not been sufficiently researched. This study aimed to determine the clinical presentations and risk factors for bacterial coinfections of pediatric inpatients during the SARS-CoV-2 Omicron BA.2 variant pandemic.

Methods

This retrospective, observational study included patients younger than 18 years of age who were hospitalized for COVID-19 confirmed by polymerase chain reaction (PCR) or antigen rapid tests during the SARS-CoV-2 Omicron BA.2 variant pandemic. Data and outcomes of these patients with or without bacterial coinfections were compared.

Results

During this study period, 161 children with confirmed COVID-19 were hospitalized. Twenty-four had bacterial coinfections. The most frequently reported concurrent diagnosis was bacterial enteritis, followed by lower respiratory tract infections. Children with bacterial coinfections had higher white blood cell (WBC) counts and PCR cycle threshold values. The bacterial coinfection group comprised a relatively greater proportion of patients who required high-flow nasal cannula oxygen and remdesivir. The length of stay in the hospital and that in the intensive care unit were longer for children with COVID-19 with bacterial coinfections. Mortality was not observed in either group. Abdominal pain, diarrhea, and comorbidity with neurologic illnesses were risk factors for bacterial coinfections with COVID-19.

Conclusion

This study provides clinicians with reference points for the detection of COVID-19 in children and its possible association with bacterial infections. Children with COVID-19 and neurologic diseases who present with abdominal pain or diarrhea are at risk of bacterial coinfections. Prolonged fever duration and higher PCR test cycle threshold values, WBC levels, and high-sensitivity C-reactive protein (hsCRP) levels may indicate bacterial coinfections in children with COVID-19.

Clinical outcomes of and risk factors for secondary infection in patients with severe COVID-19: a multicenter cohort study in South Korea

BACKGROUND/AIMS

Secondary infection with influenza virus occurs in critically ill patients and is associated with substantial morbidity and mortality; however, there is limited information about it in patients with severe coronavirus disease 2019 (COVID-19). Thus, we investigated the clinical outcomes of and risk factors for secondary infections in patients with severe COVID-19.

METHODS

This study included patients with severe COVID-19 who were admitted to seven hospitals in South Korea between February 2020 to February 2021. Multivariate logistic regression analyses were performed to assess factors associated with the risk of secondary infections.

RESULTS

Of the 348 included patients, 104 (29.9%) had at least one infection. There was no statistically significant difference in the 28-day mortality (17.3% vs. 12.3%, p = 0.214), but in-hospital mortality was higher (29.8% vs. 15.2%, p = 0.002) in the infected group than in the non-infected group. The risk factors for secondary infection were a high frailty scale (odds ratio [OR], 1.314; 95% confidence interval [CI], 1.123 to 1.538; p = 0.001), steroid use (OR, 3.110; 95% CI, 1.164 to 8.309; p = 0.024), and the application of mechanical ventilation (OR, 4.653; 95% CI, 2.533 to 8.547; p < 0.001).

CONCLUSION

In-hospital mortality was more than doubled in patients with severe COVID-19 and secondary infections. A high frailty scale, the use of steroids and application of mechanical ventilation were risk factors for secondary infection.

Difference between SARS-CoV-2, seasonal coronavirus, influenza, and respiratory syncytial virus infection in solid organ transplant recipients

BACKGROUND

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has been raging since the end of 2019 and has shown worse outcomes in solid organ transplant (SOT) recipients. The clinical differences as well as outcomes between respiratory viruses have not been well defined in this population.

METHODS

This is a retrospective cohort study of adult SOT recipients with nasopharyngeal swab or bronchoalveolar lavage PCR positive for either SARS-CoV-2, seasonal coronavirus, respiratory syncytial virus (RSV) or influenza virus from January 2017 to October 2020. The follow up period was 3 months. Clinical characteristics and outcomes were evaluated.

RESULTS

A total of 377 recipients including 157 SARS-CoV-2, 70 seasonal coronavirus, 50 RSV and 100 influenza infections were identified. The most common transplanted organ was kidney 224/377 (59.4%). Lower respiratory tract infection (LRTI) was found in 210/377 (55.7%) and the risk factors identified with multivariable analysis were SARS-CoV-2 infection, steroid use, and older age. Co- and secondary infections were seen in 77/377 (20.4%) recipients with bacterial pathogens as dominant. Hospital admission was seen in 266/377 (67.7%) recipients without significant statistical difference among viruses, however, ICU admission, mechanical ventilation and mortality were higher with SARS-CoV-2 infection. In the multivariable model, the risk factors for mortality were SARS-CoV-2 infection and older age.

CONCLUSIONS

We found higher incidence of ICU admission, mechanical ventilation, and mortality among SARS-CoV-2 infected recipients. Older age was found to be the risk factor for lower respiratory tract infection and mortality for SARS-CoV-2, coronaviruses, RSV and influenza virus groups.

Development of a live biotherapeutic throat spray with lactobacilli targeting respiratory viral infections

Respiratory viruses such as influenza viruses, respiratory syncytial virus (RSV), and coronaviruses initiate infection at the mucosal surfaces of the upper respiratory tract (URT), where the resident respiratory microbiome has an important gatekeeper function. In contrast to gut-targeting administration of beneficial bacteria against respiratory viral disease, topical URT administration of probiotics is currently underexplored, especially for the prevention and/or treatment of viral infections. Here, we report the formulation of a throat spray with live lactobacilli exhibiting several in vitro mechanisms of action against respiratory viral infections, including induction of interferon regulatory pathways and direct inhibition of respiratory viruses. Rational selection of Lactobacillaceae strains was based on previously documented beneficial properties, up-scaling and industrial production characteristics, clinical safety parameters, and potential antiviral and immunostimulatory efficacy in the URT demonstrated in this study. Using a three-step selection strategy, three strains were selected and further tested in vitro antiviral assays and in formulations: Lacticaseibacillus casei AMBR2 as a promising endogenous candidate URT probiotic with previously reported barrier-enhancing and anti-pathogenic properties and the two well-studied model strains Lacticaseibacillus rhamnosus GG and Lactiplantibacillus plantarum WCFS1 that display immunomodulatory capacities. The three strains and their combination significantly reduced the cytopathogenic effects of RSV, influenza A/H1N1 and B viruses, and HCoV-229E coronavirus in co-culture models with bacteria, virus, and host cells. Subsequently, these strains were formulated in a throat spray and human monocytes were employed to confirm the formulation process did not reduce the interferon regulatory pathway-inducing capacity. Administration of the throat spray in healthy volunteers revealed that the lactobacilli were capable of temporary colonization of the throat in a metabolically active form. Thus, the developed spray with live lactobacilli will be further explored in the clinic as a potential broad-acting live biotherapeutic strategy against respiratory viral diseases.

Variant influenza: connecting the missing dots

BACKGROUND

In June 2009, the World Health Organization declared a new pandemic, the 2009 swine influenza pandemic (swine flu). The symptoms of the swine flu pandemic causing strain were comparable to most of the symptoms noted by seasonal influenza.

AREA COVERED

Zoonotic viruses that caused the swine flu pandemic and its preventive measures.

EXPERT OPINION

As per Centers for Disease Control and Prevention (CDC), the clinical manifestations in humans produced by the 2009 H1N1 'swine flu' virus were equivalent to the manifestations caused by related flu strains. The H1N1 vaccination was the most successful prophylactic measure since it prevented the virus from spreading and reduced the intensity and consequences of the pandemic. Despite the availability of therapeutics, the ongoing evolution and appearance of new strains have made it difficult to develop effective vaccines and therapies. Currently, the CDC recommends yearly flu immunization for those aged 6 months and above. The lessons learned from the A/2009/H1N1 pandemic in 2009 indicated that readiness of mankind toward new illnesses caused by mutant viral subtypes that leap from animals to people must be maintained.

Metabolic syndrome and aberrant immune responses to viral infection and vaccination: Insights from small animal models

This review outlines the propensity for metabolic syndrome (MetS) to induce elevated disease severity, higher mortality rates post-infection, and poor vaccination outcomes for viral pathogens. MetS is a cluster of conditions including high blood glucose, an increase in circulating low-density lipoproteins and triglycerides, abdominal obesity, and elevated blood pressure which often overlap in their occurrence. MetS diagnoses are on the rise, as reported cases have increased by greater than 35% since 1988, resulting in one-third of United States adults currently diagnosed as MetS patients. In the aftermath of the 2009 H1N1 pandemic, a link between MetS and disease severity was established. Since then, numerous studies have been conducted to illuminate the impact of MetS on enhancing virally induced morbidity and dysregulation of the host immune response. These correlative studies have emphasized the need for elucidating the mechanisms by which these alterations occur, and animal studies conducted as early as the 1940s have linked the conditions associated with MetS with enhanced viral disease severity and poor vaccine outcomes. In this review, we provide an overview of the importance of considering overall metabolic health in terms of cholesterolemia, glycemia, triglyceridemia, insulin and other metabolic molecules, along with blood pressure levels and obesity when studying the impact of metabolism-related malignancies on immune function. We highlight the novel insights that small animal models have provided for MetS-associated immune dysfunction following viral infection. Such animal models of aberrant metabolism have paved the way for our current understanding of MetS and its impact on viral disease severity, dysregulated immune responses to viral pathogens, poor vaccination outcomes, and contributions to the emergence of viral variants.

High Prevalence of Fungal and NDM-OXA Producing Gram-Negative Bacterial Superinfections in the Second Wave of Coronavirus Disease 2019 in India: Experience from a Dedicated Coronavirus Disease 2019 Hospital in North India

Introduction

During the second wave of coronavirus disease 2019 (COVID-19), superinfection caused by fungus and multidrug-resistant bacteria worsened the severity of illness in COVID-19 patients. Limited studies from India reported the antimicrobial resistance pattern of secondary infections. In this study, we aim to study the epidemiology of pathogens causing superinfections and genotyping of Gram-negative isolates in COVID-19 patients.

Methods

This retrospective study was conducted at a dedicated COVID-19 center, India. The identification of bacteria/fungi was done by Vitek2^® and matrix-assisted laser desorption/ionization-time of flight mass spectrometry system. Identification of beta-lactamase genes was done using thermal cycler. The diagnosis of mucormycosis was based on 10% potassium hydroxide direct microscopy. Statistical analyses were performed using STATA version 15.1 (StataCorp., College Station, TX, USA). For continuous variables, mean and standard deviation were computed. For comparing proportions of secondary infections across admission location and outcomes, the Chi-squared test of independence was used. To compare the mean and median between intensive care units and outcomes, an independent t-test and a Mann-Whitney test were used.

Results

Of all the clinical samples, 45.4% of samples were cultured positive for secondary infections. Acinetobacter baumannii (35%) was the most common Gram-negative pathogen, while among Gram positive, it was Enterococcus faecium (40%). Among fungus, Candida spp. (61%) predominates followed by molds. Colistin and tigecycline proved effective against these pathogens. bla_NDM was the most prevalent gene followed by the bla_OX among the carbapenemase genes.

Conclusions

The mortality rate among COVID-19 patients with secondary infection was significantly higher compared to the overall mortality rate in COVID-19 patients.

Lianhuaqingwen capsule inhibits non-lethal doses of influenza virus-induced secondary Staphylococcus aureus infection in mice

ETHNOPHARMACOLOGICAL RELEVANCE

Lianhuaqingwen capsule (LH-C) is a traditional Chinese medicine (TCM), consisting of two prescriptions, Ma-xing-shi-gan-tang (MXSGT) and Yinqiao San. It has been proven to have antiviral, antibacterial, and immunomodulatory effects in recent years. Clinically, it is commonly used in the treatment of respiratory tract infections.

AIM OF THE STUDY

It was demonstrated in our previous studies that LH-C has an effect of antivirus and inhibits influenza virus-induced bacterial adhesion to respiratory epithelial cells through down-regulation of cell adhesion molecules in vitro. However, LH-C's effect against influenza-induced secondary bacterial infection in animal studies remains unclear. Therefore, in the present study, we established a mouse model of infection with non-lethal doses of influenza virus(H1N1) and secondary infection of Staphylococcus aureus (S. aureus), to investigate the potential effects of LH-C.

METHODS

Experiments were carried out on BALB/c mice infecting non-lethal doses of H1N1 and non-lethal doses of S. aureus, and the viral, and bacterial doses were determined by observing and recording changes in the body weight, mortality, and pathological changes. Moreover, after LH-C treatment, the survival rate, body weight, lung index, viral titers, bacterial colonies, pathological changes, and the inflammatory cytokines in the mouse model have all been systematically determined.

RESULTS

In the superinfection models of H1N1 and S. aureus, the mortality rate was 100% in groups of mice infected with 20 PFU/50 μL of H1N1 and 10⁵ CFU/mL of S. aureus, 20 PFU/50 μL of H1N1 and 10⁶ CFU/mL of S. aureus, 4 PFU/50 μL of H1N1 and 10⁶ CFU/mL of S. aureus. The mortality rate was 50% in the group of mice infected with 4 PFU/50 μL of H1N1 and 10⁵ CFU/mL of S. aureus. The mortality rate was 37.5% in the group of mice infected with 20 PFU/50 μL of H1N1 alone and in the group of mice infected with 2 PFU/50 μL of H1N1 and 10⁶ CFU/mL of S. aureus. The mortality rate in the group of mice infected with 2 PFU/50 μL of H1N1 and 10⁶ CFU/mL of S. aureus was 30%. The infected mice of 2 PFU/50 μL of H1N1 and 10⁶ CFU/mL of S. aureus had a weight loss of nearly 10%. About the histopathological changes in the lung tissue of infection mice, severe lung lesions were found in the superinfection models. LH-C improved survival in the superinfected mice, significantly reduced lung index, lowered viral titers and bacterial loads, and alleviated lung damage. It reduced lung inflammation by down-regulating mRNA expression levels of inflammatory mediators like IL-6, IL-1β, IL-10, TNF-α, IFN-β, MCP-1, and RANTES.

CONCLUSIONS

We found that superinfection from non-lethal doses of S. aureus following non-lethal doses of H1N1 was equally fatal in mice, confirming the severity of secondary infections. The ability of LH-C to alleviate lung injury resulting from secondary S. aureus infection induced by H1N1 was confirmed. These findings provided a further assessment of LH-C, suggesting that LH-C may have good therapeutic efficacy in influenza secondary bacterial infection disease.

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.

Long COVID and the Neuroendocrinology of Microbial Translocation Outside the GI Tract: Some Treatment Strategies

Similar to previous pandemics, COVID-19 has been succeeded by well-documented post-infectious sequelae, including chronic fatigue, cough, shortness of breath, myalgia, and concentration difficulties, which may last 5 to 12 weeks or longer after the acute phase of illness. Both the psychological stress of SARS-CoV-2 infection and being diagnosed with COVID-19 can upregulate cortisol, a stress hormone that disrupts the efferocytosis effectors, macrophages, and natural killer cells, leading to the excessive accumulation of senescent cells and disruption of biological barriers. This has been well-established in cancer patients who often experience unrelenting fatigue as well as gut and blood–brain barrier dysfunction upon treatment with senescence-inducing radiation or chemotherapy. In our previous research from 2020 and 2021, we linked COVID-19 to myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) via angiotensin II upregulation, premature endothelial senescence, intestinal barrier dysfunction, and microbial translocation from the gastrointestinal tract into the systemic circulation. In 2021 and 2022, these hypotheses were validated and SARS-CoV-2-induced cellular senescence as well as microbial translocation were documented in both acute SARS-CoV-2 infection, long COVID, and ME/CFS, connecting intestinal barrier dysfunction to disabling fatigue and specific infectious events. The purpose of this narrative review is to summarize what is currently known about host immune responses to translocated gut microbes and how these responses relate to fatiguing illnesses, including long COVID. To accomplish this goal, we examine the role of intestinal and blood–brain barriers in long COVID and other illnesses typified by chronic fatigue, with a special emphasis on commensal microbes functioning as viral reservoirs. Furthermore, we discuss the role of SARS-CoV-2/Mycoplasma coinfection in dysfunctional efferocytosis, emphasizing some potential novel treatment strategies, including the use of senotherapeutic drugs, HMGB1 inhibitors, Toll-like receptor 4 (TLR4) blockers, and membrane lipid replacement.

Increased Detection of Carbapenemase-Producing Enterobacterales Bacteria in Latin America and the Caribbean during the COVID-19 Pandemic

During 2020–2021, countries in Latin America and the Caribbean reported clinical emergence of carbapenemase-producing Enterobacterales that had not been previously characterized locally, increased prevalence of carbapenemases that had previously been detected, and co-production of multiple carbapenemases in some isolates. These increases were likely fueled by changes related to the COVID-19 pandemic, including empirical antibiotic use for potential COVID-19–related bacterial infections and healthcare limitations resulting from the rapid rise in COVID-19 cases. Strengthening antimicrobial resistance surveillance, epidemiologic research, and infection prevention and control programs and antimicrobial stewardship in clinical settings can help prevent emergence and transmission of carbapenemase-producing Enterobacterales.

Glycoconjugates: Synthesis, Functional Studies, and Therapeutic Developments

Glycoconjugates are major constituents of mammalian cells that are formed via covalent conjugation of carbohydrates to other biomolecules like proteins and lipids and often expressed on the cell surfaces. Among the three major classes of glycoconjugates, proteoglycans and glycoproteins contain glycans linked to the protein backbone via amino acid residues such as Asn for N-linked glycans and Ser/Thr for O-linked glycans. In glycolipids, glycans are linked to a lipid component such as glycerol, polyisoprenyl pyrophosphate, fatty acid ester, or sphingolipid. Recently, glycoconjugates have become better structurally defined and biosynthetically understood, especially those associated with human diseases, and are accessible to new drug, diagnostic, and therapeutic developments. This review describes the status and new advances in the biological study and therapeutic applications of natural and synthetic glycoconjugates, including proteoglycans, glycoproteins, and glycolipids. The scope, limitations, and novel methodologies in the synthesis and clinical development of glycoconjugates including vaccines, glyco-remodeled antibodies, glycan-based adjuvants, glycan-specific receptor-mediated drug delivery platforms, etc., and their future prospectus are discussed.

Effect of Influenza Vaccine on Prevention of Acute Attack of Chronic Airway Disease in Elderly Population

This study investigated the effect of influenza vaccination on prevention of acute attacks in elderly patients with chronic airway disease and provides evidence for the prevention and control strategy of chronic airway disease in the elderly population. A total of 348 elderly patients in Linquan County, Anhui Province, China, who were also in stationary phases of chronic airway disease and were vaccinated with either the tetravalent or trivalent influenza vaccine were selected. The number of patients with acute attacks, the number of outpatients with acute attacks, the number of outpatients, the number of inpatients, the total cost of patients, the cost of outpatients, the cost of hospitalization, and the length of hospitalization were collected before vaccination and after a one-year follow-up. There was no significant difference in age and sex ratio among the two vaccination groups. The ratios of acute attacks, outpatient visits, and hospitalizations and number of outpatient visits, number of hospitalizations, total medical expenses, outpatient expenses, and hospitalization expenses were significantly higher before vaccination than those after vaccination in both the trivalent-vaccination group and tetravalent-vaccination group. Additionally, there was no significant difference in the length of stay between before and after vaccination in either the trivalent-vaccination group or tetravalent-vaccination group. The protection effect between the trivalent-vaccination group and tetravalent-vaccination group was not significant. Influenza vaccination can effectively prevent the acute attack of chronic airway disease and delay the progress of chronic airway disease.

A Cephalosporin-Tripodalamine Conjugate Inhibits Metallo-β-Lactamase with High Efficacy and Low Toxicity

The wide spread of metallo-β-lactamase (MBL)-expressing bacteria has greatly threatened human health, and there is an urgent need for inhibitors against MBLs. Herein, we present a cephalosporin-tripodalamine conjugate (DPASC) as a potent MBL inhibitor with a block-release design. The cephalosporin tag blocks the ligand binding site to reduce toxicity and is cleaved by MBLs to release active ligands to inhibit MBLs in situ. The screening of MBL-expressing pathogenic strains with 16 μg/mL DPASC showed a decrease of the minimum inhibitory concentration of meropenem (MEM) by 16 to 512-fold, and its toxicity was minimal to human HepG2 cells, with an IC₅₀ exceeding 512 μg/mL. An in vivo infection model with Galleria mellonella larvae showed an increased 3-day survival rate of 87% with the coadministration of DPASC and MEM, compared to 50% with MEM alone and no toxicity at a dose of 256 mg/kg of DPASC. Our findings with DPASC demonstrate that it is an effective MBL inhibitor and that the block-release strategy could be useful for the development of new MBL inhibitors.

Alterations in the respiratory tract microbiome in COVID-19: current observations and potential significance

SARS-CoV-2 infection causes COVID-19 disease, which can result in consequences ranging from undetectable to fatal, focusing attention on the modulators of outcomes. The respiratory tract microbiome is thought to modulate the outcomes of infections such as influenza as well as acute lung injury, raising the question to what degree does the airway microbiome influence COVID-19? Here, we review the results of 56 studies examining COVID-19 and the respiratory tract microbiome, summarize the main generalizations, and point to useful avenues for further research. Although the results vary among studies, a few consistent findings stand out. The diversity of bacterial communities in the oropharynx typically declined with increasing disease severity. The relative abundance of Haemophilus and Neisseria also declined with severity. Multiple microbiome measures tracked with measures of systemic immune responses and COVID outcomes. For many of the conclusions drawn in these studies, the direction of causality is unknown-did an alteration in the microbiome result in increased COVID severity, did COVID severity alter the microbiome, or was some third factor the primary driver, such as medication use. Follow-up mechanistic studies can help answer these questions. Video Abstract.

[Impact of Staphylococcus aureus bacteremia in COVID-19 patients]

OBJECTIVE

The disease caused by SARS-CoV-2 (COVID-19) has been a challenge for healthcare professionals since its appearance. Staphylococcus aureus has been described as one of the main pathogens causing bacterial infections in viral pandemics. However, co- infection with S. aureus causing bacteremia in patients with COVID-19 has yet to be well studied.

METHODS

We performed a e study of S. aureus bacteremia (SAB) at Hospital Miguel Servet (Zaragoza) from March 2020 to February 2021. The clinical characteristics, mortality and risk factors of adults hospitalized patients with BSA associated COVID-19 compared to patients without COVID-19.

RESULTS

A total of 95 patients with SAB were identified. 27.3% were positive for SARS-CoV-2. SAB represented 9.9% of bacteremia, being the second agent in frequency after E. coli. Nosocomial bacteremia was more frequent in the group of COVID-19 patients. The most frequent source of BSA in these patients was the respiratory source (26.9% vs 0%; P<0.001) followed by the skin (15.5% vs 15.9%; P=1). The development of sepsis was more frequent in COVID-19 patients (61,5% vs 7,8%; P=0,336) and among them, who received dexamethasone at doses > 6 mg/day (62.5% vs. 37.5%, P<0.05).

CONCLUSIONS

Our data suggest that BSA has a negative impact on the evolution of patients with COVID-19. However, further and preferably prospective studies are required to obtain solid data on the impact of BSA on coronavirus patients.

The trajectory of COVID-19 cardiopulmonary disease: insights from an autopsy study of community-based, pre-hospital deaths

Background

Post mortem examination of lung and heart tissue has been vital to developing an understanding of COVID-19 pathophysiology; however studies to date have almost uniformly used tissue obtained from hospital-based deaths where individuals have been exposed to major medical and pharmacological interventions.

Methods

In this study we investigated patterns of lung and heart injury from 46 community-based, pre-hospital COVID-19-attributable deaths who underwent autopsy.

Results

The cohort comprised 22 females and 24 males, median age 64 years (range 19-91) at time of death with illness duration range 0-23 days. Comorbidities associated with poor outcomes in COVID-19 included obesity (body mass index >30 kg·m-2) in 19 out of 46 cases (41.3%). Diffuse alveolar damage in its early exudative phase was the most common pattern of lung injury; however significant heterogeneity was identified with bronchopneumonia, pulmonary oedema consistent with acute cardiac failure, pulmonary thromboembolism and microthrombosis also identified and often in overlapping patterns. Review of clinical records and next of kin accounts suggested a combination of unexpectedly low symptom burden, rapidly progressive disease and psychosocial factors may have contributed to a failure of hospital presentation prior to death.

Conclusions

Identifying such advanced acute lung injury in community-based deaths is extremely unusual and raises the question why some with severe COVID-19 pneumonitis were not hospitalised. Multiple factors including low symptom burden, rapidly progressive disease trajectories and psychosocial factors provide possible explanations.

Secondary respiratory early and late infections in mechanically ventilated patients with COVID-19

Background

Patients with COVID-19 receiving mechanical ventilation may become aggravated with a secondary respiratory infection. The aim of this study was to describe secondary respiratory infections, their predictive factors, and outcomes in patients with COVID-19 requiring mechanical ventilation.

Methods

A cohort study was carried out in a single tertiary hospital in Santiago, Chile, from 1st June to 31st July 2020. All patients with COVID-19 admitted to the intensive care unit that required mechanical ventilation were included.

Results

A total of 175 patients were enrolled, of which 71 (40.6%) developed at least one secondary respiratory infection during follow-up. Early and late secondary infections were diagnosed in 1.7% and 31.4% respectively. Within late secondary infections, 88% were bacterial, 10% were fungal, and 2% were of viral origin. One-third of isolated bacteria were multidrug-resistant. Bivariate analysis showed that the history of corticosteroids used before admission and the use of dexamethasone during hospitalization were associated with a higher risk of secondary infections (p = 0.041 and p = 0.019 respectively). Multivariate analysis showed that for each additional day of mechanical ventilation, the risk of secondary infection increases 1.1 times (_adOR = 1.07; 95% CI 1.02–1.13, p = 0.008)

Conclusions

Patients with COVID-19 admitted to the intensive care unit and requiring mechanical ventilation had a high rate of secondary infections during their hospital stay. The number of days on MV was a risk factor for acquiring secondary respiratory infections.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-022-07743-2.

Microbiological findings and prescribing trends in SARS- CoV-2 positive patients in two United Kingdom Hospitals

Objective

To describe antibiotic prescribing and microbiological findings in patients admitted to two London hospitals with COVID-19.

Methods

This is a retrospective review of confirmed SARS-CoV-2 infected adults admitted between 9th February and 10th May 2020. Demographics, critical care unit (CCU) admission, antibiotic prescribing and microbiology results within 10 days of COVID-19 diagnosis were analysed.

Results

1155 patients were identified. 32.9% (380) died. 12.4% (143) had positive microbiology. After excluding likely contaminants, 6.9% (80) had clinically significant microbiology. The most common organisms isolated from blood cultures were Escherichia coli 9.5% (7), Klebsiella pneumoniae 4.0% (3), and Staphylococcus aureus 2.7% (2). A high percentage of blood cultures yielded coagulase negative staphylococci (51/74, 68.9%) and likely represented contamination. Organisms isolated from lower respiratory tract samples included Candida albicans 44.4% (12), Staphylococcus aureus 22.2% (6), Klebsiella species 11.0% (3), Pseudomonas aeruginosa 11.0% (3), and Citrobacter species 11% (3). Legionella and pneumococcal urinary antigen tests were positive in 0/117 and 2/71 (2.8%) samples. 91% (1051) of patients received antibiotics. Clarithromycin (24.2% total antibiotic use) and amoxicillin (21%) were most frequently used, followed by piperacillin-tazobactam (12.6%), gentamicin (10.6%), co-amoxiclav (9.3%) and meropenem (3.2%). Piperacillin-tazobactam or meropenem use was associated with a higher length of stay and mortality.

Conclusions

Positive microbiology in COVID-19 patients is uncommon. Antibiotic use was widespread, despite lack of microbiological evidence of co-infection. When present, positive microbiology was more likely due to gram negative bacteria. Current local clinical and antimicrobial guidelines have incorporated these findings and recommend against routine antibiotic use in COVID-19 patients.

Seroprevalence of community-acquired atypical bacterial pneumonia among adult COVID-19 patients from a single center in Al Madinah Al Munawarah, Saudi Arabia: A retrospective cohort study

OBJECTIVES

To investigate the seroprevalence of the community-acquired bacterial that causes atypical pneumonia among confirmed severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) patients.

METHODS

In this cohort study, we retrospectively investigated the seroprevalence of Chlamydia pneumoniae, Mycoplasma pneumoniae, and Legionella pneumophila among randomly selected 189 confirmed COVID-19 patients at their time of hospital presentation via commercial immunoglobulin M (IgM) antibodies against these bacteria. We also carried out quantitative measurements of procalcitonin in patients' serum.

RESULTS

The seropositivity for L. pneumophila was 12.6%, with significant distribution among patientsolder than 50 years (χ2 test, p=0.009), while those of M. pneumoniae was 6.3% and C. pneumoniae was 2.1%, indicating an overall co-infection rate of 21% among COVID-19 patients. No significant difference (χ2 test, p=0.628) in the distribution of bacterial co-infections existed between male and female patients. Procalcitonin positivity was confirmed amongst 5% of co-infected patients.

CONCLUSION

Our study documented the seroprevalence of community-acquired bacteria co-infection among COVID-19 patients. In this study, procalcitonin was an inconclusive biomarker for non-severe bacterial co-infections among COVID-19 patients. Consideration and proper detection of community-acquired bacterial co-infection may minimize misdiagnosis during the current pandemic and positively reflect disease management and prognosis.

Hospital-acquired infections in patients hospitalized with COVID-19: First report from Taiwan

BACKGROUND

Coronavirus disease 2019 (COVID-19) inpatients may acquire infections from other pathogens during hospital admission. This is the first research on this subject to be reported from Taiwan.

METHODS

Confirmed COVID-19 inpatients were enrolled in this study from January 1, 2020 to July 31, 2021. Various types of pathogens in COVID-19 inpatients, with hospital-acquired infections, were identified and analyzed. The clinical characteristics of COVID-19 patients with and without hospital-acquired infections were reviewed and compared.

RESULTS

Of the 204 patients included in the study, 32 (15.7%) patients experienced at least one infectious episode. Of 113 recorded episodes of infection, the predominant type was bacterial (88 of 113 infections, 77.9%); the most frequently isolated bacteria were Acinetobacter spp., followed by Stenotrophomonas maltophilia . With regard to viral infections (19 of 113, 16.8%), the Epstein-Barr virus ranked first place among the identified viruses. Four (3.5%) and 2 (1.8%) of 113 infectious episodes were caused by fungi and atypical pathogens. A multivariate analysis revealed that steroid use was an independent factor in hospital-acquired infections (odds ratio [OR], 6.97; 95% confidence interval [CI], 1.15-42.43; p = 0.035). Patients with hospital-acquired infections were associated with increased 28-day and in-hospital mortality (18.8% vs 5.8% and 31.3% and 5.8%; p = 0.023 and <0.01, respectively), and a longer hospital stay (34 vs 19 days; p < 0.001), compared to those without hospital-acquired infections.

CONCLUSION

Our study revealed the unique local epidemiology of hospital-acquired infections among COVID-19 inpatients in Taiwan. These patients were associated with increased mortality and prolonged hospital admissions.