Bacterial coinfections in coronavirus disease 2019

Synthesis and evolution of 16-membered macrolide carrimycin derivatives as a novel class of anti-HCoV-OC43 agents targeting viral FSE RNA

We first demonstrate that carrimycin, as an antibiotic, shows broad-spectrum anti-coronavirus activity by targeting frameshifting element (FSE) RNA. Herein, taking carrimycin as the lead, 26 new 16-membered macrolides were synthesized and evaluated for antiviral activity against coronavirus strains. Compound 2d exhibited the elevated antiviral efficacy against HCoV-OC43 and HCoV-229E with EC50 values of 0.85 μM and 1.45 μM by directly targeting coronaviral FSE RNA pseudoknot. Molecular simulations revealed that the introduction of a 4″-substituent transforms the macrocyclic core into U-shaped conformation, enabling the higher binding with FSE. Meanwhile, using thermal proteome profiling (TPP) technology, we identified DIS3L2 as a potential host target, which probably assisted 2d to exert the antiviral effect. Therefore, the 16-membered macrolides constituted a new class of RNA inhibitors against coronaviruses, and 2d owns a dual-target mechanism that acts on both viral FSE RNA and host DIS3L2.

Zhike Erfang Alleviates MRSA-Induced Pneumonia by Inhibiting TRAF6 and Activating NLRP3 Inflammatory Body

Purpose

The therapeutic effects of Zhike Erfang in modulating the cellular responses and immune microenvironment associated with MRSA-induced acute lung injury remain unclear. This study aims to elucidate the potential mechanisms by which Zhike Erfang mitigate the cellular and molecular effects of MRSA in a laboratory model.

Patients and Methods

A mouse model of acute lung injury was established using heat-inactivated MRSA. Lung tissue and bronchoalveolar lavage fluid were collected for analysis. Macrophages were pretreated with Zhike Erfang for 30 minutes before exposure to heat-inactivated MRSA for 24 hours. Protein expressions of TRAF6, iNOS, TNF-α, IL-1β, NLRP3, and caspase-1 in lung tissues were quantified using Western blot. The content of LDH was detected by the lactate dehydrogenase cytotoxicity test kit.

Results

Zhike Erfang significantly reduced the expression of iNOS, LDH, TNF-α, IL-1β, NLRP3, and caspase-1 in a dose-dependent manner in lung tissues from the MRSA model. Zhike Erfang inhibited the expression of TRAF6.

Conclusion

Zhike Erfang can alleviate pneumonia caused by MRSA by inhibiting TRAF6 and inducing NLRP3 inflammatory body activation.

Efficacy of Three Kayviruses Against Staphylococcus aureus Strains Isolated from COVID-19 Patients

Background/Objectives: The viral pandemic caused by the SARS-CoV-2 virus has affected millions of people. However, it was noticed that high mortality was often a result of bacterial co-infections. One of the main pathogens responsible for secondary infections in patients with viral respiratory tract infections, including COVID-19, is Staphylococcus aureus. In recent years, the number of infections caused by drug-resistant strains of S. aureus has been growing rapidly, often exceeding the number of infections caused by antibiotic-sensitive strains. In addition, biofilm-related infections are more difficult to treat due to the lower sensitivity of biofilm structure to antibiotics. Bacteriophages are seen as alternative treatment of bacterial infections. Therefore, in our work, we have analyzed the efficacy of three Kayviruses against S. aureus strains isolated from COVID-19 patients. Methods: We analyzed the ability of tested phages to remove S. aureus biofilm both from polystyrene plates as well as from the surface of pulmonary epithelial cells. Results: We have observed that tested Kayviruses had a broad host range. Furthermore, phages were able to effectively reduce biofilm biomass and number of viable cells in pure culture. During our research, none of the tested phages was shown to have a negative effect on cell viability and were able to inhibit the negative effect S. aureus had on cell condition. Conclusions: Our results show tested phages were effective in reducing the biofilm of S. aureus strains isolated from COVID-19 patients, had no adverse effect on lung epithelial cell viability. Therefore, it should be recognized that the properties of three studied Kayviruses give them an advantage in the selection of phages for treatment of staphylococcal infections.

Biofilm Formation and Plasmid-Mediated Quinolone Resistance Genes at Varying Quinolone Inhibitory Concentrations in Quinolone-Resistant Bacteria Superinfecting COVID-19 Inpatients

The likelihood of antimicrobial failure in COVID-19 patients with bacterial superinfection arises from both phenotypic (biofilms) and genotypic mechanisms. This cross-sectional study aimed to determine the inhibitory concentrations of quinolones-nalidixic acid, norfloxacin, ciprofloxacin, ofloxacin, and levofloxacin-in biofilm formers (minimum biofilm inhibitory concentration [MBIC]) and nonformers (minimum inhibitory concentration [MIC]) and correlate inhibitory concentrations with plasmid-mediated quinolone resistance (PMQR) genes in quinolone-resistant bacteria isolated from COVID-19 inpatients. Quinolone-resistant bacteria (n = 193), verified through disc diffusion, were tested for quinolone inhibitory concentrations using broth microdilution and biofilm formation using microtiter plate methods. The polymerase chain reaction was used to detect PMQR genes. Study variables were analyzed using SPSS v.17.0, with a significance level set at P <0.05. MIC-to-MBIC median fold increases for ciprofloxacin, ofloxacin, and levofloxacin were 128 (2-8,192), 64 (4-1,024), and 32 (4-512) in gram-positive cocci (GPC, n = 43), respectively, whereas they were 32 (4-8,192), 32 (4-2,048), and 16 (2-1,024) in fermentative gram-negative bacilli (F-GNB, n = 126) and 16 (4-4,096), 64 (2-64), and 16 (8-512) in nonfermentative gram-negative bacilli (NF-GNB, n = 24). In biofilm-forming F-GNB and NF-GNB, qnrB (10/32 versus 3/10), aac(6')-Ib-cr (10/32 versus 4/10), and qnrS (9/32 versus 0/10) genes were detected. A 32-fold median increase in the MIC-to-MBIC of ciprofloxacin was significantly (P <0.05) associated with qnrA in F-GNB and qnrS in NF-GNB. Biofilms formed by F-GNB and NF-GNB were significantly associated with the aac(6')-Ib-cr and qnrS genes, respectively. Nearly one-third of the superinfecting bacteria in COVID-19 patients formed biofilms and had at least one PMQR gene, thus increasing the need for quinolones at higher inhibitory concentrations.

Impact of healthcare-associated infections on mortality of hospitalized patients with COVID-19: a systematic review

Although most cases of COVID-19 are mild cases, severe cases requiring hospitalization and mechanical ventilation were sufficient to overwhelm healthcare systems worldwide, leading to more than 6 million deaths and the increase in healthcare associated infections (HAIs). The incidence of HAIs in COVID-19 hospitalized patients has been addressed in systematic reviews, but in these there was no description of mortality related to these infections. Therefore, the aim of this review was to evaluate the impact of HAIs on mortality of hospitalized patients with COVID-19, specially by multidrug resistant bacteria as Acinetobacter baumannii. A systematic review was carried out in the PubMed database on July 2022 using the keywords "healthcare-associated infection" OR "nosocomial infection" AND "COVID-19" AND "Acinetobacter baumannii". The incidence of HAIs in COVID-19 patients was 18.85%, with 42.17% of mortality rate and relative risk (RR) 2.08 (95%CI 1.61-2.68). Considering that the risk of death was twice greater in co-infection COVID-19/HAI, it is essential the broad vaccination against COVID-19 and the adoption of measures to reduce HAI incidence in hospitalized patients and mortality by superinfections.

The evolving landscape of COVID-19: factors associated with in-hospital COVID-19 related mortality during the 2023-2024 phase of JN.1 subvariant dominance

BACKGROUND

COVID-19 remains a complex health challenge. We analysed the characteristics and outcomes of COVID-19-related hospitalisations during JN.1 variant dominance.

METHODS

Conducted in a hospital serving a socioeconomically deprived population, this study included all adults hospitalised with COVID-19 from 1st November 2023 to 31st August 2024. The primary outcome was in-hospital mortality, analysed in relation to demographic, clinical, and laboratory parameters.

RESULTS

Among 122 individuals (median age 76 years, 58.2% males, median comorbidity index 5), 114/122 (93.4%) had received ≥ 1 SARS-CoV-2 vaccination, with a median of 23 months elapsed since the last dose. Fever (67/122, 54.9%) and dyspnoea (49/122, 40.2%) were common presenting symptoms, with 78/122 (64%) showing CT evidence of SARS-CoV-2 pneumonia; 25/122 (20%) had purely neurological presentations. Treatment included remdesivir (115/122, 94.3%) and/or nirmatrelvir/ritonavir (9/122, 7.4%), sotrovimab (15/122, 12.3%), corticosteroids (61/122, 50.0%), and oxygen supplementation (76/122, 62.3%). Whereas 107/122 (87.7%) were discharged after a median of seven days, in-hospital mortality was 15/122 (12.3%) after a median of 16 days. Baseline factors associated with mortality were neutrophil-lymphocyte ratio > 8, D-dimer ≥ 1800 ng/mL, procalcitonin ≥ 1.0 ng/mL, and albumin < 3.2 g/dL; during admission, nasopharyngeal SARS-CoV-2 antigen positivity persisting for > 12 days, hospitalisation for ≥ 10 days, higher oxygen requirements with the resulting corticosteroid use, and healthcare-associated bacteraemia were associated with increased odds of mortality.

CONCLUSIONS

Baseline laboratory parameters and persistent SARS-CoV-2 antigen positivity despite antiviral therapy offer readily available prognostic insights for patients hospitalised with COVID-19. It is imperative to advocate for up-to-date COVID-19 vaccination among older people and other vulnerable groups.

Diosmetin-7-O-β-D-glucopyranoside from Pogostemonis Herba alleviated SARS-CoV-2-induced pneumonia by reshaping macrophage polarization and limiting viral replication

ETHNOPHARMACOLOGICAL RELEVANCE

Viral pneumonia is the leading cause of death after SARS-CoV-2 infection. Despite effective at early stage, long-term treatment with glucocorticoids can lead to a variety of adverse effects and limited benefits. The Chinese traditional herb Pogostemonis Herba is the aerial part of Pogostemon Cablin (Blanco) Benth., which has potent antiviral, antibacterial, anti-inflammatory, and anticancer effects. It was used widely for treating various throat and respiratory diseases, including COVID-19, viral infection, cough, allergic asthma, acute lung injury and lung cancer.

AIM OF THE STUDY

To investigate the antiviral and anti-inflammatory effects of chemical compounds from Pogostemonis Herba in SARS-CoV-2-infected hACE2-overexpressing mouse macrophage RAW264.7 cells and hACE2 transgenic mice.

MATERIALS AND METHODS

The hACE2-overexpressing RAW264.7 cells were exposed with SARS-CoV-2. The cell viability was detected by CCK8 assay and cell apoptotic rate was by flow cytometric assay. The expressions of macrophage M1 phenotype markers (TNF-α and IL-6) and M2 markers (IL-10 and Arg-1) as well as the viral loads were detected by qPCR. The mice were inoculated intranasally with SARS-CoV-2 omicron variant to induce viral pneumonia. The levels of macrophages, neutrophils, and T cells in the lung tissues of infected mice were analyzed by full spectrum flow cytometry. The expressions of key proteins were detected by Western blot assay.

RESULTS

Diosmetin-7-O-β-D-glucopyranoside (DG) presented the strongest anti-SARS-CoV-2 activity. Intervention with DG at the concentrations of 0.625-2.5 μM not only reduced the viral replication, cell apoptosis, and the productions of inflammatory cytokines (IL-6 and TNF-α) in SARS-CoV-2-infected RAW264.7 cells, but also reversed macrophage polarity from M1 to M2 phenotype. Furthermore, treatment with DG (25-100 mg/kg) alleviated acute lung injury, and reduced macrophage infiltration in SARS-COV-2-infected mice. Mechanistically, DG inhibited SARS-COV-2 gene expression and HK3 translation via targeting YTHDF1, resulting in the inactivation of glycolysis-mediated NF-κB pathway.

CONCLUSIONS

DG exerted the potent antiviral and anti-inflammatory activities. It reduced pneumonia in SARS-COV-2-infected mice via inhibiting the viral replication and accelerating M2 macrophage polarization via targeting YTHDF1, indicating its potential for COVID-19 treatment.

Epidemiological and molecular study of Providencia rettgeri outbreak at a university hospital during the COVID-19 reference center

In 2014, Brazil detected New Delhi metallo-β-lactamase (NDM)-producing Enterobacterales from a Providencia rettgeri isolate obtained through surveillance swabs in the Southern region. Subsequently, various species have reported several NDM enzymes. However, comprehensive data on the current epidemiology of NDM-producing P. rettgeri in Brazil remains limited. This study, aimed to provide a detailed characterization of the phenotypic, genotypic, and epidemiological profile of clinical isolates of P. rettgeri NDM. From April 2020 to December 2022, 18 carbapenem-resistant P. rettgeri strains, previously identified using Vitek2®, were isolated at the University Hospital of Londrina. Resistance and virulence genes were assessed through genetic analysis using ERIC PCR and NextSeq (Illumina) sequencing. Statistical analysis was conducted using SPSS version 2.0. Genomic analysis confirmed the presence of β-lactamase blaNDM-1 and blaOXA-1. All isolates showed the presence of the NDM encoding gene and genetic similarity above 90% between isolates. Clinical parameters of patients infected with P. rettgeri exhibited significant association with mechanical ventilation, prior use of carbapenems, and polymyxins. We also report a significant association between P. rettgeri infection and death outcome. This study characterizes NDM-1 metallo-β-lactmases isolates, among P. rettgeri isolates from patients at the University Hospital (HU), during the COVID-19 pandemic. The emergence of this novel resistance mechanism among P. rettgeri poses a significant challenge, limiting the therapeutic options for infections in our hospital.

Molecular pathogen profiling of COVID-19 coinfections

OBJECTIVE

This study aims to investigate the prevalence, pathogen spectrum, clinical characteristics, and prognosis-related factors of other respiratory pathogens in COVID-19-infected patients, and to explore the application of molecular detection methods in the epidemiological investigation of multiple pathogen infections.

METHODS

Respiratory samples and clinical data from 384 patients with outpatient and inpatient respiratory infections were collected and analyzed. Multiplex PCR and capillary electrophoresis were conducted to detect the distribution characteristics of 26 pathogen species, comprising 13 viruses, 13 bacteria. Statistical analysis explored the relationship between pathogen distribution with COVID-19 development.

RESULTS

There was no statistical difference in prognosis between the 230 COVID-19-positive patients and the 154 COVID-19-positive patients. COVID-19 cases co-infected with other pathogens do not correlate with patient's age and gender. The main distribution of pathogens was mainly mecA (n = 62, 26.96%), followed by SPN(n = 61; 26.52%) and KP(n = 22; 9.57%). Compared with non-COVID-19 cases, COVID-19 infected patients showed a significantly higher mecA carrying rate (26.96% vs. 15.58%, P < 0.01), while there was no statistical difference for other pathogens. Regression analysis found that mecA and KP were independent risk factors for severe illnesses (mechanical ventilation, endotracheal intubation, ECOMO, etc.) or death in COVID-19 patients had 2.391 times and 3.722 times risk of severe disease or death compared with COVID-19 patients without mecA and KP.

CONCLUSION

COVID-19 patients show a higher mecA carrier rate than non-COVID-19 patients, and mecA and KP may increase the risk of severe disease or death in COVID-19 patients, which requires close attention.

Respiratory Pathogen Coinfection During Intersecting COVID-19 and Influenza Epidemics

Respiratory pathogen coinfections pose significant challenges to global public health, particularly regarding the intersecting epidemics of COVID-19 and influenza. This study investigated the incidences of respiratory infectious pathogens in this unique context. We collected throat swab samples from 308 patients with a fever from outpatient and emergency departments at sentinel surveillance hospitals in Xiamen, southeast of China, between April and May 2023, testing for SARS-CoV-2 and 26 other respiratory pathogens. The coinfection rate of the XBB SARS-CoV-2 variant with other respiratory pathogens was higher than that observed during the Alpha and Delta phases. Among patients with influenza, bacterial coinfections were more prevalent. Only 0.65% (2/308) of the patients were concurrently infected with both COVID-19 and influenza. Age-stratified analysis showed a clear pattern, with a higher incidence of coinfections in children under 18 years of age. These findings highlight the need for the timely detection of respiratory pathogen coinfections and for the implementation of appropriate interventions, crucial for reducing disease burden during intersecting respiratory epidemics.

Antibiotics daptomycin interacts with S protein of SARS-CoV-2 to promote cell invasion of Omicron (B1.1.529) pseudovirus

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has posed enormous challenges to global public health. The use of antibiotics has greatly increased during the SARS-CoV-2 epidemic owing to the presence of bacterial co-infection and secondary bacterial infections. The antibiotics daptomycin (DAP) is widely used in the treatment of infectious diseases caused by gram-positive bacteria owing to its highly efficient antibacterial activity. It is pivotal to study the antibiotics usage options for patients of coronavirus infectious disease (COVID-19) with pneumonia those need admission to receive antibiotics treatment for bacterial co-infection in managing COVID-19 disease. Herein, we have revealed the interactions of DAP with the S protein of SARS-CoV-2 and the variant Omicron (B1.1.529) using the molecular docking approach and Omicron (B1.1.529) pseudovirus (PsV) mimic invasion. Molecular docking analysis shows that DAP has a certain degree of binding ability to the S protein of SARS-CoV-2 and several derived virus variants, and co-incubation of 1-100 μM DAP with cells promotes the entry of the PsV into human angiotensin-converting enzyme 2 (hACE2)-expressing HEK-293T cells (HEK-293T-hACE2), and this effect is related to the concentration of extracellular calcium ions (Ca2+). The PsV invasion rate in the HEK-293T-hACE2 cells concurrently with DAP incubation was 1.7 times of PsV infection alone. In general, our findings demonstrate that DAP promotes the infection of PsV into cells, which provides certain reference of antibiotics selection and usage optimization for clinicians to treat bacterial coinfection or secondary infection during SARS-CoV-2 infection.

Amphiphilic Janus Nanoparticles for Effective Treatment of Bacterial Pneumonia by Attenuating Inflammation and Targeted Bactericidal Capability

Introduction

Pseudomonas aeruginosa (P. aeruginosa)-induced pneumonia is marked by considerable infiltration of inflammatory cells and biofilm formation, which causes acute and transient lung inflammation and infection. Nevertheless, the discovery of alternative preventative and therapeutic methods is essential due to the high mortality rates in clinical settings and the resistance of P. aeruginosa infection to multiple medications.

Purpose

In this research, we constructed amphiphilic Janus nanoparticles (JNPs, denoted as SSK1@PDA/CaP@CIP), loaded with hydrophobic SSK1, a β-galactosidase (β-gal)-activated prodrug for reducing macrophages, and hydrophilic ciprofloxacin (CIP), a classic antibiotic for treating infection. SSK1@PDA/CaP@CIP was designed to effectively attenuate inflammation, eradicate biofilms, and combat planktonic P. aeruginosa.

Results

As expected, SSK1@PDA/CaP@CIP was able to target the infection site and demonstrated outstanding efficacy in treating P. aeruginosa strain PAO1-induced pneumonia by regulating macrophage infiltration to reduce inflammation and removing planktonic bacteria and biofilms to control infection. Additionally, the primary organs did not exhibit any discernible pathological changes following treatment with SSK1@PDA/CaP@CIP, which indicates superior biocompatibility throughout the treatment course.

Discussion

In conclusion, our investigation introduced a promising approach to the treatment of pneumonia associated with PAO1.

Lung infection with classical Klebsiella pneumoniae strains establishes robust macrophage-dependent protection against heterologous reinfection

At present, there is no approved vaccine for prevention of infection by the opportunistic bacterium Klebsiella pneumoniae (Kp); success in treating these infections is increasingly challenged by the spread of antibiotic resistance. Preclinical investigation of adaptive immunity elicited by lung infection with live classical Kp may reveal host mechanisms of protection against this pathogen. Here, we utilize multiple virulent classical Kp strains to demonstrate that following lung infection, surviving wild-type mice develop protective immunity against both homologous and heterologous (heterotypic) reinfection. For Kp strains with low capacity to disseminate from the lung, this immunity is B-cell-independent. We further demonstrate that this immune protection is also effective against subsequent challenge with hypervirulent Kp if the strains share the same capsule type. Systemic inoculation fails to elicit the same protective effect as lung inoculation, revealing a lung-specific immune effector function is responsible for this protection. We therefore utilized clodronate-loaded liposomes to substantially deplete both alveolar macrophages and lung interstitial macrophages, finding that simultaneous depletion of both subsets entirely ablates protection. These findings indicate that following initial lung infection with Kp, lung macrophages mediate protection against ensuing Kp challenge.

An increased prevalence of carbapenem-resistant hypervirulent Klebsiella pneumoniae associated with the COVID-19 pandemic

BACKGROUND

Klebsiella pneumoniae (Kp) is a common community-acquired and nosocomial pathogen. Carbapenem-resistant and hypervirulent (CR-hvKp) variants can emerge rapidly within healthcare facilities and impacted by other infectious agents such as COVID-19 virus.

METHODS

To understand the impact of COVID-19 virus on the prevalence of CR-hvKp, we accessed Kp genomes with corresponding metadata from GenBank. Sequence types (STs), antimicrobial resistance genes, and virulence genes, and those scores and CR-hvKp were identified. We analyzed population diversity and phylogenetic characteristics of five most common STs, measured the prevalence of CR-hvKp, identified CR-hvKp subtypes, and determined associations between carbapenem resistance gene subtypes with STs and plasmid types. These variables were compared pre- and during the COVID-19 pandemic.

FINDINGS

The proportion of CR-hvKp isolates increased within multiple STs in different continents during the COVID-19 pandemic and persistent CR-hvKp subtypes were found in common STs. blaKPC was dominant in CG258, blaKPC-2 was detected in 97 % of the ST11 CR-hvKp, blaNDM subtypes were prominent in ST147 (87.4 %) and ST307 (70.8 %); blaOXA-48 and its subtypes were prevalent in ST15 (80.5 %). The possession of carbapenemase genes was different among subclades from different origins in different periods of time within each ST. IncFIB/IncHI1B hybrid plasmids contained virulence genes and carbapenemase genes and were predominant in ST147 (67.37 %) and ST307 (56.25 %).

INTERPRETATION

The prevalence of CR-hvKp increased during the COVID-19 pandemic, which was evident by an increase in local endemic clones. This process was facilitated by the convergence of plasmids containing carbapenemase genes and virulence genes. These findings have implications for the appropriate use of antimicrobials and infection prevention and control during outbreaks of respiratory viruses and pandemic management.

Trends of coinfections among healthy blood donors: COVID-19 pandemic repercussion

Background

Human immunodeficiency virus (HIV), hepatitis B virus (HBV), and hepatitis C virus (HCV) coinfection has emerged as a leading cause of morbidity throughout the world in the last two decades. The coronavirus disease 2019 (COVID-19) pandemic has escalated the disease burden further by increasing the number of intravenous (IV) drug abusers and unemployment.

Aim

The present study was done to analyse the impact of COVID-19 on seroprevalence as well as trends during pre, post and pandemic years of coinfection and mono-infections in the Malwa region of Punjab.

Setting and Design

This descriptive cross-sectional study was done in the department of immunohematology and blood transfusion at a tertiary care hospital.

Materials and Methods

The data on transfusion-transmitted infections (TTIs) was collected for a period of four years from 2019 to 2022, that is, pre, post and during the pandemic period. All the blood samples were screened for viral markers, HIV I and II, HCV, and hepatitis B surface antigen (HBsAg) using the enzyme-linked immunosorbent assay (ELISA) technique. Malarial antigen and syphilis infection testing was done using a rapid diagnostic card test. The total number of sero-reactive cases and their distribution were noted.

Results

A total of 58,953 donors were screened and included during the study period. Each blood donor was identified by a donor registration number. The overall TTI seroprevalence in blood donors was 2.83% (n = 1670). The seroprevalence of TTIs in blood donors showed an increasing trend for HIV, HCV, and HBsAg in 2019-2021, whereas there was a decrease in reactivity status in the 2022 (back to pre-pandemic year). There was a significant increase in the coinfection rate from 0.1% to 0.25%.

Conclusion

The COVID-19 pandemic impact on the coinfection rate of TTI was significant. To curb these TTIs and coinfections, education and public awareness are the key factors. India is a developing country, so transfusion medicine specialists need to work day and night to practice safe blood services.

The emergence of transposon-driven multidrug resistance in invasive nontypeable Haemophilus influenzae over the last decade

Nontypeable Haemophilus influenzae (NTHi), once considered a harmless commensal, has emerged as a significant concern due to the increased prevalence of multidrug-resistant (MDR) strains and their association with invasive infections. This study aimed to explore the epidemiology and molecular resistance mechanisms of 51 NTHi isolates collected from patients with invasive infections in northern Taiwan between 2011 and 2020. This investigation revealed substantial genetic diversity, encompassing 29 distinct sequence types and 18 clonal complexes. Notably, 68.6% of the isolates exhibited ampicillin resistance, with 28 categorised as MDR and four isolates were even resistant to up to six antibiotic classes. Among the MDR isolates, 18 pulsotypes were identified, indicating diverse genetic lineages. Elucidation of their resistance mechanisms revealed 18 β-lactamase-producing amoxicillin-clavulanate-resistant (BLPACR) isolates, 12 β-lactamase-producing ampicillin-resistant (BLPAR) isolates, and 5 β-lactamase-nonproducing ampicillin-resistant (BLNAR) isolates. PBP3 analysis revealed 22 unique substitutions in BLPACR and BLNAR, potentially contributing to cephem resistance. Notably, novel transposons, Tn7736-Tn7739, which contain critical resistance genes, were discovered. Three strains harboured Tn7739, containing seven resistance genes [aph(3')-Ia, blaTEM-1, catA, sul2, strA, strB, and tet(B)], while four other strains carried Tn7736, Tn7737, and Tn7738, each containing three resistance genes [blaTEM-1, catA, and tet(B)]. The emergence of these novel transposons underscores the alarming threat posed by highly resistant NTHi strains. Our findings indicated that robust surveillance and comprehensive genomic studies are needed to address this growing public health challenge.

Mortality in hospitalized SARS-CoV-2 patients with contemporaneous bacterial and fungal infections

Background

The interplay between SARS-CoV-2 and contemporaneous bacterial or fungal culture growth may have crucial implications for clinical outcomes of hospitalized patients. This study aimed to quantify the effect of microbiological culture positivity on mortality among hospitalized patients with SARS-CoV-2.

Methods

In this retrospective cohort study, we included adult hospitalized patients from OPTUM COVID-19 specific data set, who tested positive for SARS-CoV-2 within 14 days of hospitalization between 01/20/2020 and 01/20/2022. We examined outcomes of individuals with organisms growing on cultures from the bloodstream infections (BSIs), urinary tract, and respiratory tract, and a composite of the three sites. We used propensity score matching on covariates included demographics, comorbidities, and hospitalization clinical parameters. In a sensitivity analysis, we included same covariates but excluded critical care variables such as length of stay, intensive care unit stays, mechanical ventilation, and extracorporeal membrane oxygenation.

Results

The cohort included 104,560 SARS-CoV-2 positive adult hospitalized patients across the United States. The unadjusted mortality odds increased significantly with BSIs (98.7%) and with growth on respiratory cultures (RC) (176.6%), but not with growth on urinary cultures (UC). Adjusted analyses showed that BSIs and positive RC independently contribute to mortality, even after accounting for critical care variables.

Conclusions

In SARS-CoV-2-positive hospitalized patients, positive bacterial and fungal microbiological cultures, especially BSIs and RC, are associated with an increased risk of mortality even after accounting for critical care variables associated with disease severity. These findings underscore the importance of stringent infection control and the effective management of secondary infections to improve patient outcomes.

Bacterial co-infection in COVID-19: a call to stay vigilant

Co-infection with diverse bacteria is commonly seen in patients infected with the novel coronavirus, SARS-CoV-2. This type of co-infection significantly impacts the occurrence and development of novel coronavirus infection. Bacterial co-pathogens are typically identified in the respiratory system and blood culture, which complicates the diagnosis, treatment, and prognosis of COVID-19, and even exacerbates the severity of disease symptoms and increases mortality rates. However, the status and impact of bacterial co-infections during the COVID-19 pandemic have not been properly studied. Recently, the amount of literature on the co-infection of SARS-CoV-2 and bacteria has gradually increased, enabling a comprehensive discussion on this type of co-infection. In this study, we focus on bacterial infections in the respiratory system and blood of patients with COVID-19 because these infection types significantly affect the severity and mortality of COVID-19. Furthermore, the progression of COVID-19 has markedly elevated the antimicrobial resistance among specific bacteria, such as Klebsiella pneumoniae, in clinical settings including intensive care units (ICUs). Grasping these resistance patterns is pivotal for the optimal utilization and stewardship of antibiotics, including fluoroquinolones. Our study offers insights into these aspects and serves as a fundamental basis for devising effective therapeutic strategies. We primarily sourced our articles from PubMed, ScienceDirect, Scopus, and Google Scholar. We queried these databases using specific search terms related to COVID-19 and its co-infections with bacteria or fungi, and selectively chose relevant articles for inclusion in our review.

Staphylococcus aureus Co-Infection in COVID-19 Patients: Virulence Genes and Their Influence on Respiratory Epithelial Cells in Light of Risk of Severe Secondary Infection

Pandemics from viral respiratory tract infections in the 20th and early 21st centuries were associated with high mortality, which was not always caused by a primary viral infection. It has been observed that severe course of infection, complications and mortality were often the result of co-infection with other pathogens, especially Staphylococcus aureus. During the COVID-19 pandemic, it was also noticed that patients infected with S. aureus had a significantly higher mortality rate (61.7%) compared to patients infected with SARS-CoV-2 alone. Our previous studies have shown that S. aureus strains isolated from patients with COVID-19 had a different protein profile than the strains in non-COVID-19 patients. Therefore, this study aims to analyze S. aureus strains isolated from COVID-19 patients in terms of their pathogenicity by analyzing their virulence genes, adhesion, cytotoxicity and penetration to the human pulmonary epithelial cell line A549. We have observed that half of the tested S. aureus strains isolated from patients with COVID-19 had a necrotizing effect on the A549 cells. The strains also showed greater variability in terms of their adhesion to the human cells than their non-COVID-19 counterparts.

To prescribe or not: a two-center retrospective observational study of antibiotics usage and outcomes of COVID-19 in Turkey

This retrospective cohort study conducted in Turkey between December 2020 and June 2022 aimed to assess antibiotic use, bacterial co-infections, and the associated factors on mortality in hospitalized patients with mild-to-severe COVID-19. Among the 445 patients, 80% received antibiotics, with fluoroquinolones being the most common choice, followed by beta-lactams and combinations. Various clinical and laboratory parameters, including symptoms, comorbidities, CCI, oxygen requirements, and CRP levels were observed to be elevated in the antibiotic group. Non-survivors had more ICU admissions and longer hospital stays compared to survivors. We conducted a multivariate Cox regression analysis to evaluate factors related to mortality. However, we did not find an association between antibiotic use and mortality [HR 2.7 (95% CI 0.4-20)]. The study identified significant factors associated with an antibiotic prescription, such as CCI (OR 1.6), CRP (OR 2.3), and ICU admission (OR 8.8), (p < 0.05). The findings suggest re-evaluating the necessity of antibiotics in COVID-19 cases based on clinical assessments, focusing on the presence of bacterial infections rather than empirical treatment. Further research is necessary to more accurately identify patients with bacterial co-infections who would benefit from antibiotic treatment.

Bacterial pneumonia patients with elevated globulin levels did not get infected with SARS-CoV-2: two case reports

Background

COVID-19 began in December 2019, rapidly spreading worldwide. China implemented a dynamic zero-COVID strategy and strict control measures after the outbreak. However, Guangzhou city ended closed-off management by the end of November 2022, leading to exposure to SARS-CoV-2. Despite most hospitalized patients being infected or co-infected with SARS-CoV-2, some remained uninfected. We report two cases of bacterial pneumonia with elevated globulin levels not infected with SARS-CoV-2, aiming to identify protection factors of SARS-CoV-2 infection and provide a scientific basis for SARS-CoV-2 prevention.

Case presentation

Case 1, a 92-year-old male, admitted on October 21, 2022, developed worsening cough and sputum after aspiration, diagnosed with bacterial pneumonia with Pseudomonas aeruginosa, Escherichia coli (CRE) and carbapenem-resistant Acinetobacter baumannii (CRAB) infections. He was treated with imipenem anti-infective therapy and mechanical ventilation, then switched to a combination of meropenem, voriconazole and amikacin anti-infective therapy due to recurrent infections and septic shock, and died of sepsis on 8 January 2023. Case 2 is an 82-year-old male admitted on 30 September 2022, with recurrent cough, sputum, and shortness of breath, diagnosed with bacterial pneumonia with carbapenem-resistant Klebsiella pneumoniae (CRKP) and Mycobacterium pneumoniae infections. He was treated with ventilator-assisted ventilation, meropenem, amikacin, tigecycline and mucomycin nebulization and discharged with improvement on 26 October. He was readmitted on 21 November 2022 and diagnosed with bacterial pneumonia. He was treated with cefoperazone sulbactam, amikacin, meropenem and fluconazole and discharged on 31 December. Neither patient was infected with SARS-CoV-2 during hospitalization. Notably, their globulin levels were elevated before SARS-CoV-2 exposure, gradually decreasing afterward.

Conclusions

Patients with bacterial pneumonia with high globulin levels likely have large amounts of immunoglobulin, and that immunoglobulin cross-reactivity causes this protein to be involved in clearing SARS-CoV-2 and preventing infection. Therefore, bacterial pneumonia patients with high globulin levels included in this study were not infected with SARS-CoV-2. After exposure to SARS-CoV-2, the amount of globulin in the patient's body was reduced because it was used to clear SARS-CoV-2. The results of this study are expected to provide a theoretical basis for the study of the mechanism of prevention and treatment of SARS-CoV-2 infection.

Outcomes in COVID-19 Patients with Acute Cholangitis: A Single-Center Retrospective Analysis

Background and Objectives: This study aimed to assess the impact of coronavirus disease 2019 (COVID-19) on patients with acute cholangitis (AC) by comparing outcomes, complications, and hospital stays in a tertiary Gastroenterology department. Materials and Methods: This retrospective observational cohort study was conducted in a tertiary gastroenterology department, collecting data from all AC and AC + COVID-19 patients between April 2020 and February 2022. Data included clinical and demographic information, COVID-19-specific details, acute cholangitis presentation, medical records, laboratory results, and interventions. AC was diagnosed using Tokyo Guidelines 2018 (TG18) criteria, with all patients undergoing bile culture sampling. Results: The study included 241 patients, 30 in the COVID group and 211 in the non-COVID group. The COVID group's mean age was significantly higher (74.3 vs. 67.3 years, p < 0.009). Abdominal pain was more common in the COVID group (90% vs. 70.6%, p < 0.025). Length of hospital stay was longer for COVID patients (13.5 vs. 7.9 days, p < 0.001). COVID patients had higher incidences of malignant causes of AC, with pancreatic cancer being the most common (30%). Pseudomonas spp. was significantly more prevalent in COVID patients (16.7% vs. 5.7%, p = 0.028). Conclusions: Our study results show that COVID-19 affected the duration of hospitalization for patients with AC. Furthermore, this study presents observations regarding the impact of COVID-19 on AC, revealing differences in microbial profiles.

John A, Tierce R, Zheng X, Zhou C, Noval MG, O'Keeffe A, Podkowik M, Gonzales S, Inglima K, Desvignes L, Hochman SE, Stapleford KA, Thorpe LE, Pironti A, Shopsin B, Cadwell K, Dittmann M, Torres VJ. SARS-CoV-2 infection predisposes patients to coinfection with Staphylococcus aureus

Severe COVID-19 has been associated with coinfections with bacterial and fungal pathogens. Notably, patients with COVID-19 who develop Staphylococcus aureus bacteremia exhibit higher rates of mortality than those infected with either pathogen alone. To understand this clinical scenario, we collected and examined S. aureus blood and respiratory isolates from a hospital in New York City during the early phase of the pandemic from both SARS-CoV-2+ and SARS-CoV-2- patients. Whole genome sequencing of these S. aureus isolates revealed broad phylogenetic diversity in both patient groups, suggesting that SARS-CoV-2 coinfection was not associated with a particular S. aureus lineage. Phenotypic characterization of the contemporary collection of S. aureus isolates from SARS-CoV-2+ and SARS-CoV-2- patients revealed no notable differences in several virulence traits examined. However, we noted a trend toward overrepresentation of S. aureus bloodstream strains with low cytotoxicity in the SARS-CoV-2+ group. We observed that patients coinfected with SARS-CoV-2 and S. aureus were more likely to die during the acute phase of infection when the coinfecting S. aureus strain exhibited high or low cytotoxicity. To further investigate the relationship between SARS-CoV-2 and S. aureus infections, we developed a murine coinfection model. These studies revealed that infection with SARS-CoV-2 renders mice susceptible to subsequent superinfection with low cytotoxicity S. aureus. Thus, SARS-CoV-2 infection sensitizes the host to coinfections, including S. aureus isolates with low intrinsic virulence.

IMPORTANCE

The COVID-19 pandemic has had an enormous impact on healthcare across the globe. Patients who were severely infected with SARS-CoV-2, the virus causing COVID-19, sometimes became infected with other pathogens, which is termed coinfection. If the coinfecting pathogen is the bacterium Staphylococcus aureus, there is an increased risk of patient death. We collected S. aureus strains that coinfected patients with SARS-CoV-2 to study the disease outcome caused by the interaction of these two important pathogens. We found that both in patients and in mice, coinfection with an S. aureus strain lacking toxicity resulted in more severe disease during the early phase of infection, compared with infection with either pathogen alone. Thus, SARS-CoV-2 infection can directly increase the severity of S. aureus infection.

The Impact of Early Antibiotic Use on Clinical Outcomes of Patients Hospitalized with COVID-19: A Propensity Score-Matched Analysis

Purpose

Early empiric antibiotics were prescribed to numerous patients during the Coronavirus disease 2019 (COVID-19) pandemic. However, the potential impact of empiric antibiotic therapy on the clinical outcomes of patients hospitalized with COVID-19 is yet unknown.

Methods

In this retrospective cohort study, early antibiotics use cohort was defined as control group, which was compared with no antibiotic use and delayed antibiotic use cohorts for all-cause mortality during hospitalization. The 1:2 propensity score matched patient populations were further developed to adjust confounding factors. Survival curves were compared between different cohorts using a Log rank test to assess the early antibiotic effectiveness.

Results

We included a total of 1472 COVID-19 hospitalized patients, of whom 87.4% (1287 patients) received early antibiotic prescriptions. In propensity-score-matched datasets, our analysis comprised 139 patients with non-antibiotic use (with 278 matched controls) and 27 patients with deferred-antibiotic use (with 54 matched controls). Patients with older ages, multiple comorbidities, severe and critical COVID-19 subtypes, higher serum infection indicators, and inflammatory indicators at admission were more likely to receive early antibiotic prescriptions. After adjusting confounding factors likely to influence the prognosis, there is no significant difference in all-cause mortality (HR=1.000(0.246-4.060), p = 1.000) and ICU admission (HR=0.436(0.093-2.04), p = 0.293), need for mechanical ventilation (HR=0.723(0.296-1.763), p = 0.476) and tracheal intubation (HR=1.338(0.221-8.103), p = 0.751) were observed between early antibiotics use cohort and non-antibiotic use cohort.

Conclusion

Early antibiotics were frequently prescribed to patients in more severe disease condition at admission. However, early antibiotic treatment failed to demonstrate better clinical outcomes in hospitalized patients with COVID-19 in the propensity-score-matched cohorts.

Intracellular Streptococcus pneumoniae develops enhanced fluoroquinolone persistence during influenza A coinfection

Streptococcus pneumoniae is a major pathogen responsible for severe complications in patients with prior influenza A virus (IAV) infection. We have previously demonstrated that S. pneumoniae exhibits increased intracellular survival within IAV-infected cells. Fluoroquinolones (FQs) are widely used to treat pneumococcal infections. However, our prior work has shown that S. pneumoniae can develop intracellular FQ persistence, a phenomenon triggered by oxidative stress within host cells. This persistence allows the bacteria to withstand high FQ concentrations. In this study, we show that IAV infection enhances pneumococcal FQ persistence during intracellular survival within pneumocytes, macrophages, and neutrophils. This enhancement is partly due to increased oxidative stress induced by the viral infection. We find that this phenotype is particularly pronounced in autophagy-proficient host cells, potentially resulting from IAV-induced blockage of autophagosome-lysosome fusion. Moreover, we identified several S. pneumoniae genes involved in oxidative stress response that contribute to FQ persistence, including sodA (superoxide dismutase), clpL (chaperone), nrdH (glutaredoxin), and psaB (Mn+2 transporter component). Our findings reveal a novel mechanism of antibiotic persistence promoted by viral infection within host cells. This underscores the importance of considering this phenomenon when using FQs to treat pneumococcal infections, especially in patients with concurrent influenza A infection.

Role and significance of virus-bacteria interactions in disease progression

Understanding disease pathogenesis caused by bacteria/virus, from the perspective of individual pathogen has provided meaningful insights. However, as viral and bacterial counterparts might inhabit the same infection site, it becomes crucial to consider their interactions and contributions in disease onset and progression. The objective of the review is to highlight the importance of considering both viral and bacterial agents during the course of coinfection. The review provides a unique perspective on the general theme of virus-bacteria interactions, which either lead to colocalized infections that are restricted to one anatomical niche, or systemic infections that have a systemic effect on the human host. The sequence, nature, and underlying mechanisms of certain virus-bacteria interactions have been elaborated with relevant examples from literature. It also attempts to address the various applied aspects, including diagnostic and therapeutic strategies for individual infections as well as virus-bacteria coinfections. The review aims to aid researchers in comprehending the intricate interplay between virus and bacteria in disease progression, thereby enhancing understanding of current methodologies and empowering the development of novel health care strategies to tackle coinfections.

Clinical and microbiological profile of health care-associated infections in a tertiary hospital: Comparison between a cohort of hospitalized patients during prepandemic and COVID-19 pandemic periods

BACKGROUND

During the COVID-19 pandemic, health service practices underwent significant changes, impacting the occurrence of health care-associated infections (HAIs). This study presents the epidemiology of bacterial infections and compares clinical data on nosocomial infections in hospitalized patients before and during the pandemic.

METHODS

A unicentric, observational, retrospective cohort study was conducted with descriptive analyses on the microorganism identification and resistance profile. Patient's clinical data who had hospital-acquired infection (HAI), during their hospitalization in a tertiary hospital before and during the COVID-19 pandemic was compared by descriptive and inferential analyses.

RESULTS

A total of 1,581 bacteria were isolated from 1,183 hospitalized patients. Among patients coinfected with COVID-19, there was a statistically significant increase in HAI-related deaths (P < .001) and HAI caused by multidrug-resistant organisms (P < .001), mainly by Acinetobacter baumannii and Staphylococcus aureus. A higher odds ratio of HAI-related deaths compared to the prepandemic period was observed (odds ratio 6.98 [95% confidence interval 3.97-12.64]).

CONCLUSIONS

The higher incidence of multidrug-resistant bacteria and increased deaths due to HAI, especially in patients with COVID-19 coinfection, might be related to various factors such as increased workload, broad-spectrum antibiotic use, and limited resources. The pandemic has changed the profile of circulating bacteria and antimicrobial resistance. Prevention strategies should be considered to reduce the impact of these infections.

COVID-19 PBMCs are doubly harmful, through LDN-mediated lung epithelial damage and monocytic impaired responsiveness to live Pseudomonas aeruginosa exposure

Introduction

Although many studies have underscored the importance of T cells, phenotypically and functionally, fewer have studied the functions of myeloid cells in COVID disease. In particular, the potential role of myeloid cells such as monocytes and low-density neutrophils (LDNs) in innate responses and particular in the defense against secondary bacterial infections has been much less documented.

Methods

Here, we compared, in a longitudinal study, healthy subjects, idiopathic fibrosis patients, COVID patients who were either hospitalized/moderate (M-) or admitted to ICU (COV-ICU) and patients in ICU hospitalized for other reasons (non-COV-ICU).

Results

We show that COVID patients have an increased proportion of low-density neutrophils (LDNs), which produce high levels of proteases (particularly, NE, MMP-8 and MMP-9) (unlike non-COV-ICU patients), which are partly responsible for causing type II alveolar cell damage in co-culture experiments. In addition, we showed that M- and ICU-COVID monocytes had reduced responsiveness towards further live Pseudomonas aeruginosa (PAO1 strain) infection, an important pathogen colonizing COVID patients in ICU, as assessed by an impaired secretion of myeloid cytokines (IL-1, TNF, IL-8,…). By contrast, lymphoid cytokines (in particular type 2/type 3) levels remained high, both basally and post PAO1 infection, as reflected by the unimpaired capacity of T cells to proliferate, when stimulated with anti-CD3/CD28 beads.

Discussion

Overall, our results demonstrate that COVID circulatory T cells have a biased type 2/3 phenotype, unconducive to proper anti-viral responses and that myeloid cells have a dual deleterious phenotype, through their LDN-mediated damaging effect on alveolar cells and their impaired responsiveness (monocyte-mediated) towards bacterial pathogens such as P. aeruginosa.

The characteristics of microbiome in the upper respiratory tract of COVID-19 patients

BACKGROUND

Co-infection with other pathogens in coronavirus disease 2019 (COVID-19) patients exacerbates disease severity and impacts patient prognosis. Clarifying the exact pathogens co-infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is premise of the precise treatment for COVID-19 patients.

METHODS

Sputum samples were collected from 17 patients in the COVID-19 positive group and 18 patients in the COVID-19 negative group. DNA extraction was performed to obtain the total DNA. Sequencing analysis using 16S and ITS rRNA gene was carried out to analyze the composition of bacterial and fungal communities. Meanwhile, all the samples were inoculated for culture.

RESULTS

We did not observe significant differences in bacterial composition between the COVID-19 positive and negative groups. However, a significantly higher abundance of Candida albicans was observed in the upper respiratory tract samples from the COVID-19 positive group compared to the COVID-19 negative group. Moreover, the Candida albicans strains isolated from COVID-19 positive group exhibited impaired secretion of aspartyl proteinases.

CONCLUSION

COVID-19 positive patients demonstrate a notable increase in the abundance of Candida albicans, along with a decrease in the levels of aspartyl proteinases, indicating the alteration of microbiota composition of upper respiratory tract.

Interactions among microorganisms open up a new world for anti-infectious therapy

The human microbiome, containing bacteria, fungi, and viruses, is a community that coexists peacefully with humans most of the time, but with the potential to cause disease under certain conditions. When the environment changes or certain stimuli are received, microbes may interact with each other, causing or increasing the severity of disease in a host. With the appropriate methods, we can make these microbiota work for us, creating new applications for human health. This review discusses the wide range of interactions between microorganisms that result in an increase in susceptibility to, severity of, and mortality of diseases, and also briefly introduces how microorganisms interact with each other directly or indirectly. The study of microbial interactions and their mechanisms has revealed a new world of treatments for infectious disease. The regulation of the balance between intestinal flora, the correct application of probiotics, and the development of effective drugs by symbiosis all demonstrate the great contributions of the microbiota to human health and its powerful potential value. Consequently, the study of interactions between microorganisms plays an essential role in identifying the causes of diseases and the development of treatments.

Herpesviridae and Atypical Bacteria Co-Detections in Lower Respiratory Tract Samples of SARS-CoV-2-Positive Patients Admitted to an Intensive Care Unit

Shortly after the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), cases of viral, bacterial, and fungal coinfections in hospitalized patients became evident. This retrospective study investigates the prevalence of multiple pathogen co-detections in 1472 lower respiratory tract (LRT) samples from 229 SARS-CoV-2-positive patients treated in the largest intensive care unit (ICU) in Slovenia. In addition to SARS-CoV-2, (rt)RT-PCR tests were used to detect cytomegalovirus (CMV), Epstein-Barr virus (EBV), herpes simplex virus 1 (HSV-1), herpes simplex virus 2 (HSV-2), varicella zoster virus (VZV), and atypical bacteria: Chlamydia pneumoniae, Mycoplasma pneumoniae and Legionella pneumophila/spp. At least one co-detection was observed in 89.1% of patients. EBV, HSV-1, and CMV were the most common, with 74.7%, 58.1%, and 38.0% of positive patients, respectively. The median detection time of EBV, HSV-1, and CMV after initial SARS-CoV-2 confirmation was 11 to 20 days. Bronchoalveolar lavage (BAL) and tracheal aspirate (TA) samples showed equivalent performance for the detection of EBV, CMV, and HSV-1 in patients with both available samples. Our results indicate that SARS-CoV-2 infection could be a risk factor for latent herpesvirus reactivation, especially HSV-1, EBV, and CMV. However, additional studies are needed to elucidate the clinical importance of these findings.

Phage-layer interferometry: a companion diagnostic for phage therapy and a bacterial testing platform

The continuing and rapid emergence of antibiotic resistance (AMR) calls for innovations in antimicrobial therapies. A promising, 're-emerging' approach is the application of bacteriophage viruses to selectively infect and kill pathogenic bacteria, referred to as phage therapy. In practice, phage therapy is personalized and requires companion diagnostics to identify efficacious phages, which are then formulated into a therapeutic cocktail. The predominant means for phage screening involves optical-based assays, but these methods cannot be carried out in complex media, such as colored solutions, inhomogeneous mixtures, or high-viscosity samples, which are often conditions encountered in vivo. Moreover, these assays cannot distinguish phage binding and lysis parameters, which are important for standardizing phage cocktail formulation. To address these challenges, we developed Phage-layer Interferometry (PLI) as a companion diagnostic. Herein, PLI is assessed as a quantitative phage screening method and prototyped as a bacterial detection platform. Importantly, PLI is amenable to automation and is functional in complex, opaque media, such as baby formula. Due to these newfound capabilities, we foresee immediate and broad impact of PLI for combating AMR and protecting against foodborne illnesses.

Phenotypes of a Pseudomonas aeruginosa hypermutator lineage that emerged during prolonged mechanical ventilation in a patient without cystic fibrosis

Hypermutator lineages of Pseudomonas aeruginosa arise frequently during the years of airway infection experienced by patients with cystic fibrosis and bronchiectasis but are rare in the absence of chronic infection and structural lung disease. Since the onset of the COVID-19 pandemic, large numbers of patients have remained mechanically ventilated for extended periods of time. These patients are prone to acquire bacterial pathogens that persist for many weeks and have the opportunity to evolve within the pulmonary environment. However, little is known about what types of adaptations occur in these bacteria and whether these adaptations mimic those observed in chronic infections. We describe a COVID-19 patient with a secondary P. aeruginosa lung infection in whom the causative bacterium persisted for >50 days. Over the course of this infection, a hypermutator lineage of P. aeruginosa emerged and co-existed with a non-hypermutator lineage. Compared to the parental lineage, the hypermutator lineage evolved to be less cytotoxic and less virulent. Genomic analyses of the hypermutator lineage identified numerous mutations, including in the mismatch repair gene mutL and other genes frequently mutated in individuals with cystic fibrosis. Together, these findings demonstrate that hypermutator lineages can emerge when P. aeruginosa persists following acute infections such as ventilator-associated pneumonia and that these lineages have the potential to affect patient outcomes.IMPORTANCEPseudomonas aeruginosa may evolve to accumulate large numbers of mutations in the context of chronic infections such as those that occur in individuals with cystic fibrosis. However, these "hypermutator" lineages are rare following acute infections. Here, we describe a non-cystic fibrosis patient with COVID-19 pneumonia who remained mechanically ventilated for months. The patient became infected with a strain of P. aeruginosa that evolved to become a hypermutator. We demonstrate that hypermutation led to changes in cytotoxicity and virulence. These findings are important because they demonstrate that P. aeruginosa hypermutators can emerge following acute infections and that they have the potential to affect patient outcomes in this setting.

Bacterial infections in patients with COVID-19: the impact of procalcitonin testing on antibiotics prescription in the real world

BACKGROUND

Bacterial infections are not prevalent among patients hospitalized with COVID-19, while unnecessary prescription of antibiotics was commonly observed. This study aimed to determine the impact of procalcitonin testing on antibiotics prescription in the real-world setting.

METHODS

We performed a territory-wide retrospective cohort study involving all laboratory-confirmed patients hospitalized in public hospitals in Hong Kong in 2020 with COVID-19. We determined the prevalence of bacterial co-infections (documented infections within 72 h of admission) and secondary bacterial infections (infections after 72 h of admission) and antibiotics consumption, and the correlation between procalcitonin testing and antibiotics prescription.

RESULTS

The cohort included 8666 patients, with mean age 45.3 ± 19.9 years, 48.5% male, and comorbidities in 26.9%. Among 2688 patients with bacterial cultures performed, 147 (5.5%) had bacterial co-infections, and 222 (8.3%) had secondary bacterial infections. Antibiotics were prescribed for 2773 (32.0%) patients during the hospital admission. Procalcitonin tests were performed for 2543 (29.3%) patients. More patients with procalcitonin testing received antibiotics (65.9% vs. 17.9%, p < 0.001). Procalcitonin testing was associated with 5-fold increased risk of antibiotics prescription after adjusting for confounding variables. At hospital level, procalcitonin testing correlated with antibiotics prescription. Patients with procalcitonin level < 0.5 ng/mL had a lower probability of antibiotics initiation and shorter duration of antibiotics therapy.

CONCLUSIONS

Procalcitonin testing was not associated with lower prescription of antibiotics. Patients with low procalcitonin level had lower antibiotics exposure, supporting the use of procalcitonin to exclude bacterial infections aiding early stopping of antibiotics among patients hospitalized with COVID-19.

Fabrication of Oleophilic Polypeptide Nanoparticle from Complexing of Cross-Linked Epsilon-poly-l-lysine with Docusate Sodium for Preparation of Bactericidal Thermoplastic Polyurethanes

Thermoplastic polyurethanes (TPUs) are extensively utilized in the biomedical field due to their exceptional mechanical properties and biocompatibility. However, the lack of antibacterial activity limits their application ranges. Nanoscopic particle-based additives with inherent antibacterial characteristics are regarded as promising strategies to prevent biomaterials-associated infection. Herein, a novel polymeric nanoparticle is prepared, which integrates chemically cross-linked epsilon-poly-l-lysine (CPL) and anionic surfactant-docusate sodium (DS). The cross-linked epsilon-poly-l-lysine/docusate sodium (CPL/DS) nanoparticle can be well dispersed in organic solvent and a polymer matrix, which is beneficial to endowing TPUs with synergistic miscibility and antibacterial properties. An antibacterial test showed that the CPL/DS nanoparticles have strong antibacterial activity against S. aureus. Moreover, the results of antibacterial experiments in vitro revealed that almost 100% of S. aureus could be killed by CPL/DS nanoparticle-embedded TPU film with a content of 0.5 wt %. In addition, all of the CPL/DS modified TPU films showed good cytocompatibility in vitro. Consequently, this kind of CPL/DS nanoplatform has great potential to serve as a safe and high-efficient bactericidal agent for endowing biomedical devices with bactericidal property.

Potential co-infection of influenza A, influenza B, respiratory syncytial virus, and Chlamydia pneumoniae: a case report with literature review

The occurrence of a co-infection involving four distinct respiratory pathogens could be underestimated. Here, we report the case of a 72-year-old woman who presented to a community hospital with a cough productive of sputum as her main clinical manifestation. Antibody detection of common respiratory pathogens revealed potential co-infection with influenza A, influenza B, respiratory syncytial virus, and Chlamydia pneumoniae. We treated her with 75 mg oseltamivir phosphate administered orally twice daily for 5 days, 0.5 g azithromycin administered orally for 5 days, and 0.3 g acetylcysteine aerosol inhaled twice daily for 3 days. The patient showed a favorable outcome on the eighth day after early diagnosis and treatment. Since co-infection with these four pathogens is rare, we performed an extensive PubMed search of similar cases and carried out a systematic review to analyze the epidemiology, clinical manifestations, transmission route, susceptible population, and outcomes of these four different pathogens. Our report highlights the importance for general practitioners to be vigilant about the possibility of mixed infections when a patient presents with respiratory symptoms. Although these symptoms may be mild, early diagnosis and timely treatment could improve outcomes. Additionally, further research is warranted to explore the potential influence of SARS-CoV-2 infection on the co-occurrence of multiple respiratory pathogens.

Clinical characteristics, bacterial coinfections and outcomes in COVID-19-associated pulmonary aspergillosis in a third-level Mexican hospital during the COVID-19 pre-vaccination era

BACKGROUND

Damage due to respiratory viruses increases the risk of bacterial and fungal coinfections and superinfections. High rates of invasive aspergillosis are seen in severe influenza and COVID-19. This report describes CAPA cases diagnosed during the first wave in the biggest reference centre for severe COVID-19 in Mexico.

OBJECTIVES

To describe the clinical, microbiological and radiological characteristics of patients with invasive pulmonary aspergillosis associated with critical COVID-19, as well as to describe the variables associated with mortality.

METHODS

This retrospective study identified CAPA cases among individuals with COVID-19 and ARDS, hospitalised from 1 March 2020 to 31 March 2021. CAPA was defined according to ECMM/ISHAM consensus criteria. Prevalence was estimated. Clinical and microbiological characteristics including bacterial superinfections, antifungal susceptibility testing and outcomes were documented.

RESULTS

Possible CAPA was diagnosed in 86 patients among 2080 individuals with severe COVID-19, representing 4.13% prevalence. All CAPA cases had a positive respiratory culture for Aspergillus species. Aspergillus fumigatus was the most frequent isolate (64%, n = 55/86). Seven isolates (9%, n = 7/80) were resistant to amphotericin B (A. fumigatus n = 5/55, 9%; A. niger, n = 2/7, 28%), two A. fumigatus isolates were resistant to itraconazole (3.6%, n = 2/55). Tracheal galactomannan values ranged between 1.2 and 4.05, while serum galactomannan was positive only in 11% (n = 3/26). Bacterial coinfection were documented in 46% (n = 40/86). Gram negatives were the most frequent cause (77%, n = 31/40 isolates), from which 13% (n = 4/31) were reported as multidrug-resistant bacteria. Mortality rate was 60% and worse prognosis was seen in older persons, high tracheal galactomannan index and high HbA1c level.

CONCLUSIONS

One in 10 individuals with CAPA carry a resistant Aspergillus isolate and/or will be affected by a MDR bacteria. High mortality rates are seen in this population.

Blood microbial analyses reveal long-term effects of SARS-CoV-2 infection on patients who recovered from COVID-19

OBJECTIVE

Few symptoms persist for a long time after patients recover from COVID-19, called "long COVID". We explored the potential microbial risk factors for COVID-19 for a deeper understanding and assistance in the follow-up treatment of these sequelae.

METHODS

Microbiome re-annotation was performed using whole blood RNA-Seq data collected from recovered COVID-19 patients and healthy controls at multiple time points. Subsequently, a series of downstream analyses were conducted to reveal the microbial characteristics of patients who recovered from SARS-CoV-2 infection.

RESULTS

The blood microbiome at 12 weeks post-infection was most evidently disturbed, including an increasing ratio of Bacillota/Bacteroidota and a higher microbial alpha diversity. In addition, a group of pathogenic microbes at 12 weeks post-infection were identified, including Staphylococcus aureus, Klebsiella pneumoniae, Streptococcus pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa, which were positively associated with host genes involved in immune regulatory and olfactory transduction pathways. Several microbes, such as Streptococcus pneumoniae were associated with infiltrating immune cells, such as M2 macrophages.

CONCLUSION

This study provides insights into the relationship between the blood microbiome and COVID-19 sequelae. Several pathogenic microbes were enriched in recovered COVID-19 patients and thus affected host genes participating in the immune and olfactory transduction pathways, which play critical roles in COVID-19 sequelae.

Antibiotic resistance profiles and associated factors of Pseudomonas Infections among patients admitted to large tertiary care hospital from a developing country

BACKGROUND

Pseudomonas infections are among the most common infections encountered in hospitalized patients, especially those with chronic illnesses or an immunocompromised state. Management of these infections has become challenging due to increased antibiotic resistance. Therefore, this study examines the antibiotic resistance profiles of Pseudomonas spp. and the associated factors among patients admitted to a large tertiary hospital in a developing country.

METHODS

This retrospective observational chart review study assessed patients admitted to a large tertiary hospital in a developing country with a positive culture growth of Pseudomonas from anybody site. Antibiotic susceptibility of the isolated Pseudomonas and patient characteristics were studied from the start of 2021 to the end of 2022. The study ground consisted of 185 patients.

RESULTS

The study included 185 patients with positive Pseudomonas isolates. Males constituted 54.6% of the sample, while 45.4% were females. The median age of the patients was 53 years. Patient comorbidities and risk factors for Pseudomonas infection and multidrug resistance were assessed. Antibiotic resistance to the Pseudomonas regimens showed the highest resistance to meropenem and ciprofloxacin (23.4%, similarly) among isolates of Pseudomonas aeruginosa. Multidrug resistance (MDR) was found in 108 (58.4%) isolates. The most commonly used antibiotic for treatment was piperacillin-tazobactam, accounting for 33.3% of cases, followed by aminoglycosides at 26.6%.

CONCLUSIONS

Pseudomonas aeruginosa isolates were resistant to meropenem and ciprofloxacin. Over half of the isolates were multidrug-resistant, which was worrying. Piperacillin-tazobactam and aminoglycosides were the most often utilized antibiotics, highlighting the significance of susceptibility testing. Implementing antimicrobial stewardship programs and infection control measures can help reduce drug resistance and improve outcomes in Pseudomonas infections.

Healthcare‑associated infections in intensive care unit patients with and without COVID-19: a single center prospective surveillance study

BACKGROUND

The coronavirus disease 2019 (COVID-19) pandemic led to a global increase in healthcare-associated infections (HAI) among intensive care unit (ICU) patients. Whether this increase is directly attributable to COVID-19 or whether the pandemic indirectly (via staff shortages or breaches in infection prevention measures) led to this increase, remains unclear. The objectives of this study were to assess HAI incidence and to identify independent risk factors for HAI in COVID-19 and non-COVID-19 ICU patients.

METHODS

We established a monocentric prospective HAI surveillance in the medical ICU of our tertiary care center from September 1st 2021 until August 31st 2022, during circulation of the SARS-CoV-2 delta and omicron variants. We consecutively included patients ≥ 18 years of age with an ICU length of stay of > 2 calendar days. HAI were defined according to the European Centre for Disease Prevention and Control definitions. HAI rate was calculated per 1,000 patient-days or device-days; risk ratios (RR) and corresponding 95% confidence intervals (CI) for COVID-19 versus non-COVID-19 patients were calculated. We used multivariable Cox regression to identify independent risk factors for HAI. As a proxy for institutional COVID-19 burden, weekly COVID-19 density (i.e. percentage of COVID-19 patients among all ICU patients) was included in the model as time-dependent co-variable.

RESULTS

We included 254 patients, 64 (25.1%) COVID-19 and 190 (74.9%) non-COVID-19 patients; 83 HAI in 72 patients were recorded, thereof 45 ventilator-associated lower respiratory tract infections (VA-LRTI) (54.2%) and 18 blood stream infections (BSI) (21.6%). HAI incidence rate was 49.1/1,000 patient-days in COVID-19 and 22.5/1,000 patient-days in non-COVID-19 patients (RR 2.2, 95%-CI 1.4-3.4). This result was mainly due to different VA-LRTI rates (40.3 vs. 11.7/1,000 ventilator days, p < 0.001), whereas BSI rates were not statistically different (9.4 vs. 5.6/1,000 patient days, p = 0.27). Multivariable analysis identified COVID-19 as main risk factor for HAI development, whereas age, mechanical ventilation and COVID-19 density were not significant.

CONCLUSIONS

These data from the fourth and fifth wave of the pandemic show a higher HAI incidence in COVID-19 than in non-COVID-19 ICU patients, mainly due to an increase in pulmonary infections. A diagnosis of COVID-19 was independently associated with HAI development, whereas institutional COVID-19 burden was not.

Bacterial respiratory infections in patients with COVID-19: A retrospective study from a tertiary care center in Lebanon

BACKGROUND

Despite multiple reports of increased incidence of bacterial respiratory tract infections following COVID-19 globally, the microbiology is not yet fully elucidated. In this study, we describe the microbiology of bacterial infections and the prevalence of multidrug resistant organisms (MDROs) in hospitalized COVID-19 patients with community-acquired pneumonia (CAP), and hospital-acquired pneumonia (HAP) which includes both non-ventilated hospital acquired pneumonia (NVHAP) and ventilator-associated pneumonia (VAP). To our knowledge, this is the first study that compares the microbiology of VAP and NVHAP in COVID-19 patients.

METHODS

This is a longitudinal retrospective cohort study conducted at the American University of Beirut Medical Center (AUBMC), a tertiary-care centre in Lebanon. Adult patients with confirmed COVID-19 and concurrent bacterial respiratory infections with an identifiable causative organism who were hospitalized between March 2020 and September 2021 were included. Bacterial isolates identified in hospital-acquired pneumonia (HAP) were divided into 3 groups based on the time of acquisition of pneumonia after admission: hospital day 3-14, 15-28 and 29-42.

RESULTS

Out of 1674 patients admitted with COVID-19, 159 (9.5%) developed one or more respiratory infections with an identifiable causative organism. Overall, Gram-negative bacteria were predominant (84%) and Stenotrophomonas maltophilia was the most common pathogen, particularly in HAP. Among 231 obtained isolates, 59 (26%) were MDROs, seen in higher proportion in HAP, especially among patients with prolonged hospital stay (> 4 weeks). Non-fermenter Gram-negative bacilli (NFGNB) (OR = 3.52, p-value<0.001), particularly S. maltophilia (OR = 3.24, p-value = 0.02), were significantly more implicated in VAP compared to NVHAP.

CONCLUSIONS

NFGNB particularly S. maltophilia were significantly associated with COVID-19 VAP. A high rate of bacterial resistance (25%), especially among Gram-negative bacteria, was found which may compromise patients' outcomes and has important implications in guiding therapeutic decisions in COVID-19 patients who acquire bacterial respiratory infections.

Impact of the COVID-19 pandemic on prevalence of highly resistant microorganisms in hospitalised patients in the Netherlands, March 2020 to August 2022

BackgroundThe COVID-19 pandemic resulted in adaptation in infection control measures, increased patient transfer, high occupancy of intensive cares, downscaling of non-urgent medical procedures and decreased travelling.AimTo gain insight in the influence of these changes on antimicrobial resistance (AMR) prevalence in the Netherlands, a country with a low AMR prevalence, we estimated changes in demographics and prevalence of six highly resistant microorganisms (HRMO) in hospitalised patients in the Netherlands during COVID-19 waves (March-June 2020, October 2020-June 2021, October 2021-May 2022 and June-August 2022) and interwaves (July-September 2020 and July-September 2021) compared with pre-COVID-19 (March 2019-February 2020).MethodsWe investigated data on routine bacteriology cultures of hospitalised patients, obtained from 37 clinical microbiological laboratories participating in the national AMR surveillance. Demographic characteristics and HRMO prevalence were calculated as proportions and rates per 10,000 hospital admissions.ResultsAlthough no significant persistent changes in HRMO prevalence were detected, some relevant non-significant patterns were recognised in intensive care units. Compared with pre-COVID-19 we found a tendency towards higher prevalence of meticillin-resistant Staphylococcus aureus during waves and lower prevalence of multidrug-resistant Pseudomonas aeruginosa during interwaves. Additionally, during the first three waves, we observed significantly higher proportions and rates of cultures with Enterococcus faecium (pooled 10% vs 6% and 240 vs 120 per 10,000 admissions) and coagulase-negative Staphylococci (pooled 21% vs 14% and 500 vs 252 per 10,000 admissions) compared with pre-COVID-19.ConclusionWe observed no substantial changes in HRMO prevalence in hospitalised patients during the COVID-19 pandemic.

Demethyleneberberine alleviates Pseudomonas aeruginosa-induced acute pneumonia by inhibiting the AIM2 inflammasome and oxidative stress

BACKGROUND

Acute pneumonia induced by Pseudomonas aeruginosa is characterized by massive infiltration of inflammatory cell and the production of reactive oxygen species (ROS), which lead to severe and transient pulmonary inflammation and acute lung injury. However, P.aeruginosa infection is resistant to multiple antibiotics and causes high mortality in clinic, the search for alternative prophylactic and therapeutic strategies is imperative.

PURPOSE

This study was aimed to investigate the anti-inflammatory and antioxidant effects of DMB, a novel derivative of berberine, and explore the role of AIM2 inflammasome in P. aeruginosa-induced acute pneumonia.

METHODS

Acute pneumonia mice were established by tracheal injection of P. aeruginosa suspension. Pathological changes of lung tissue were observed by its appearance and H&E staining. The lung coefficient ratio was measured to evaluate pulmonary edema. Inflammatory factors were detected by qRT-PCR, western blotting and immunohistochemistry. ROS and other indicators of oxidative damage were analyzed by flow cytometry and specific kit. Proteins related to AIM2 inflammasome were detected by western blotting.

RESULTS

Compared with the P. aeruginosa-induced group, DMB ameliorated pulmonary edema, hyperemia, and pathological damage based on its appearance and H&E staining in DMB groups. First, DMB attenuated the inflammatory response induced by P.aeruginosa. Compared with the P. aeruginosa-induced group, the lung coefficient ratio was decreased by 31.5%, the MPO activity of lung tissue was decreased by 44.0%, the mRNA expression levels of TNF-α, IL-1β and IL-6 were decreased by 64.8%, 51.2% and 64.0% respectively, and those protein expression levels were decreased by 40.1%, 42.8% and 47.8% respectively, and the number of white blood cells, neutrophils and monocytes were decreased by 53.5%, 29.4% and 13.7% in high dose (200 mg/kg) DMB group. Second, DMB alleviates oxidative stress in the lung tissue during P. aeruginosa-induced acute pneumonia. Compared with the P. aeruginosa-induced group, the level of GSH was increased by 42.5% and MDA was decreased by 49.5% in high dose DMB group. Moreover, the western blotting results showed that DMB markedly suppressed the expression of AIM2, ASC, Cleaved caspase1 and decreased the secretion of IL-1β. Additionally, these results were also confirmed by in vitro experiments using MH-S and BEAS-2B cell lines.

CONCLUSIONS

Taken together, these results indicated that DMB ameliorates P. aeruginosa-induced acute pneumonia through anti-inflammatory, antioxidant effects, and inhibition of AIM2 inflammasome activation.

Bacterial Biomarkers of the Oropharyngeal and Oral Cavity during SARS-CoV-2 Infection

(1) Background: Individuals with COVID-19 display different forms of disease severity and the upper respiratory tract microbiome has been suggested to play a crucial role in the development of its symptoms. (2) Methods: The present study analyzed the microbial profiles of the oral cavity and oropharynx of 182 COVID-19 patients compared to 75 unaffected individuals. The samples were obtained from gargle screening samples. 16S rRNA amplicon sequencing was applied to analyze the samples. (3) Results: The present study shows that SARS-CoV-2 infection induced significant differences in bacterial community assemblages, with Prevotella and Veillonella as biomarkers for positive-tested people and Streptococcus and Actinomyces for negative-tested people. It also suggests a state of dysbiosis on the part of the infected individuals due to significant differences in the bacterial community in favor of a microbiome richer in opportunistic pathogens. (4) Conclusions: SARS-CoV-2 infection induces dysbiosis in the upper respiratory tract. The identification of these opportunistic pathogenic biomarkers could be a new screening and prevention tool for people with prior dysbiosis.

Coinfection of SARS-CoV-2 with other respiratory pathogens in outpatients from Ecuador

Worldwide, the COVID-19 pandemic caused by SARS-CoV-2 has enormously impacted healthcare systems, especially in low and middle-income countries. Coinfections with respiratory pathogens in COVID-19 patients may contribute to worse outcomes. This study identified the presence of 12 viral coinfections and pneumococcal carriers among individuals with SARS-CoV-2 infection in outpatient and community settings in Ecuador. From January 2020 to November 2021, 215 nasopharyngeal and nasal swabs were taken from individuals who reported symptoms of COVID-19 or had known exposure to someone with confirmed or suspected COVID-19. One hundred fifty-eight tested positive for SARS-CoV-2 by RT-qPCR and coinfections were detected in 12% (19/158) of SARS-CoV-2-positive patients; the most frequent coinfection was with influenza A virus at 4.4% (7/158; 95% CI: 1.2-7.6), followed by respiratory syncytial virus with 3.1% (5/158; 95% CI: 0.4-5.8), and finally rhinovirus and human coronavirus NL63 with 1.2% (2/158). Pneumococcal carriage was detected in 3.7% (6/158; 95% CI: 0.76-6.64) of SARS-CoV-2 cases. Influenza B, adenovirus, human metapneumovirus (HMPV), parainfluenza virus types 1, 2, and 3, and human coronavirus HKU1 were undetected. To our knowledge, this is the first study of coinfection of SARS-CoV-2 and respiratory pathogens performed on outpatients in Latin America. The high proportion of outpatients with viral coinfections reported in our cohort allows us to suggest that testing for SARS-CoV-2 and other common respiratory pathogens should be carried out to ensure accurate diagnoses, prompt patient treatment, and appropriate isolation.

Associated Bacterial Coinfections in COVID-19-Positive Patients

Background and Objectives: The aim of this study was to identify specific rhino- and oropharyngeal microbiological pathogens as well as associated comorbidities that favor SARS-CoV-2 infection and corelate them. Materials and Methods: This prospective clinical study enrolled 61 patients (28 COVID-19-positive and 33 controls) who were tested for other comorbidities and co-existence of associated oral pathogenic microbiota. Results: A total of 247 bacterial isolates were identified in the bacterial cultures in both groups. Viral hepatitis type A was more prevalent in the COVID-19-positive group (p = 0.026), as was the presence of oral candidiasis (p = 0.006). In the control group, a moderate direct relationship was observed between the Beta hemolytic streptococcus group G and dermatitis, and strong direct relationships were observed between the Beta hemolytic streptococcus group G and external otitis, Streptococcus pyogenes and dental alveolitis, and Streptococcus pyogenes and chronic lymphocytic leukemia. In the test group, strong direct relationships were observed between Hemophilus influenzae and pulmonary thromboembolism; Staphylococcus aureus and autoimmune thyroiditis; post-viral immunosuppression, chronic coronary syndrome, and hypernatremia; Beta hemolytic streptococcus group C and rheumatoid polyneuropathy; Beta hemolytic streptococcus group G and hyperkalemia, hypothyroidism, secondary anemia, and splenomegaly; and active oral candidiasis and SARS-CoV-2 viral pneumonia. The following relationships were strong, but inverse: Beta hemolytic streptococcus group G and acute respiratory failure, and active oral candidiasis and SARS-CoV-2 viral bronchopneumonia. Conclusions: Briefly, COVID-19-positive patients have the predisposition to build up associated comorbidities and coinfections, which can be the expression of the immune burden that this virus generates to the host.

A Comparison between SARS-CoV-2 and Gram-Negative Bacteria-Induced Hyperinflammation and Sepsis

Sepsis is a life-threatening condition caused by the body's overwhelming response to an infection, such as pneumonia or urinary tract infection. It occurs when the immune system releases cytokines into the bloodstream, triggering widespread inflammation. If not treated, it can lead to organ failure and death. Unfortunately, sepsis has a high mortality rate, with studies reporting rates ranging from 20% to over 50%, depending on the severity and promptness of treatment. According to the World Health Organization (WHO), the annual death toll in the world is about 11 million. One of the main toxins responsible for inflammation induction are lipopolysaccharides (LPS, endotoxin) from Gram-negative bacteria, which rank among the most potent immunostimulants found in nature. Antibiotics are consistently prescribed as a part of anti-sepsis-therapy. However, antibiotic therapy (i) is increasingly ineffective due to resistance development and (ii) most antibiotics are unable to bind and neutralize LPS, a prerequisite to inhibit the interaction of endotoxin with its cellular receptor complex, namely Toll-like receptor 4 (TLR4)/MD-2, responsible for the intracellular cascade leading to pro-inflammatory cytokine secretion. The pandemic virus SARS-CoV-2 has infected hundreds of millions of humans worldwide since its emergence in 2019. The COVID-19 (Coronavirus disease-19) caused by this virus is associated with high lethality, particularly for elderly and immunocompromised people. As of August 2023, nearly 7 million deaths were reported worldwide due to this disease. According to some reported studies, upregulation of TLR4 and the subsequent inflammatory signaling detected in COVID-19 patients "mimics bacterial sepsis". Furthermore, the immune response to SARS-CoV-2 was described by others as "mirror image of sepsis". Similarly, the cytokine profile in sera from severe COVID-19 patients was very similar to those suffering from the acute respiratory distress syndrome (ARDS) and sepsis. Finally, the severe COVID-19 infection is frequently accompanied by bacterial co-infections, as well as by the presence of significant LPS concentrations. In the present review, we will analyze similarities and differences between COVID-19 and sepsis at the pathophysiological, epidemiological, and molecular levels.

The Impact of Antibiotic Prophylaxis on a Retrospective Cohort of Hospitalized Patients with COVID-19 Treated with a Combination of Steroids and Tocilizumab

OBJECTIVES

In the context of COVID-19, patients with a severe or critical illness may be more susceptible to developing secondary bacterial infections. This study aims to investigate the relationship between the use of prophylactic antibiotic therapy and the occurrence of bacterial or fungal isolates following the administration of tocilizumab in hospitalized COVID-19 patients who had previously received steroids during the first and second waves of the pandemic in Spain.

METHODS

This retrospective observational study included 70 patients hospitalized with COVID-19 who received tocilizumab and steroids between January and December 2020. Data on demographics, comorbidities, laboratory tests, microbiologic results, treatment, and outcomes were collected from electronic health records. The patients were divided into two groups based on the use of antibiotic prophylaxis, and the incidence of bacterial and fungal colonizations/infections was analyzed.

RESULTS

Among the included patients, 45 patients received antibiotic prophylaxis. No significant clinical differences were observed between the patients based on prophylaxis use regarding the number of clinically diagnosed infections, ICU admissions, or mortality rates. However, the patients who received antibiotic prophylaxis showed a higher incidence of colonization by multidrug-resistant bacteria compared to that of the subgroup that did not receive prophylaxis. The most commonly isolated microorganisms were Candida albicans, Enterococcus faecalis, Staphylococcus aureus, and Staphylococcus epidermidis. Conclusions: In this cohort of hospitalized COVID-19 patients treated with tocilizumab and steroids, the use of antibiotic prophylaxis did not reduce the incidence of secondary bacterial infections. However, it was associated with an increased incidence of colonization by multidrug-resistant bacteria.

Impact of COVID-19 pandemic on profiles of antibiotic-resistant genes and bacteria in hospital wastewater

The COVID-19 pandemic has severely affected healthcare worldwide and has led to the excessive use of disinfectants and antimicrobial agents. However, the impact of excessive disinfection measures and specific medication prescriptions on the development and dissemination of bacterial drug resistance during the pandemic remains unclear. This study investigated the influence of the pandemic on the composition of antibiotics, antibiotic resistance genes (ARGs), and pathogenic communities in hospital wastewater using ultra-performance liquid chromatography-tandem mass spectrometry and metagenome sequencing. The overall level of antibiotics decreased after the COVID-19 outbreak, whereas the abundance of various ARGs increased in hospital wastewater. After COVID-19 outbreak, blaOXA, sul2, tetX, and qnrS had higher concentrations in winter than in summer. Seasonal factors and the COVID-19 pandemic have affected the microbial structure in wastewater, especially of Klebsiella, Escherichia, Aeromonas, and Acinetobacter. Further analysis revealed the co-existence of qnrS, blaNDM, and blaKPC during the pandemic. Various ARGs significantly correlated with mobile genetic elements, implying their potential mobility. A network analysis revealed that many pathogenic bacteria (Klebsiella, Escherichia, and Vibrio) were correlated with ARGs, indicating the existence of multi-drug resistant pathogens. Although the calculated resistome risk score did not change significantly, our results suggest that the COVID-19 pandemic shifted the composition of residual antibiotics and ARGs in hospital wastewater and contributed to the dissemination of bacterial drug resistance.

Fluoride-activated photothermal system for promoting bacteria-infected wound healing

Although photothermal therapy (PTT) employing nanozymes has shown excellent antibacterial potential, excessive heating generally harms host cells and hinders recovery. Herein, we report an innovative technique for acquiring the programmed temperature by managing the catalytic activity of nanozymes. The photothermal system of CeO2 + F- + TMB can obtain precise photothermal temperature by adjusting the concentration of fluoride ions under near-infrared irradiation. At the optimized photothermal temperature, the photothermal system affords fine photothermal antibacterial treatment with high-efficiency antibacterial effects against Staphylococcus aureus and Escherichia coli in vitro. In vivo wound healing experiments confirm that the system can effectively promote fibroblast proliferation, angiogenesis and collagen deposition with remarkable wound healing efficiency. This strategy offers a novel design concept for creating a new generation of PTT and opens the way for the creation of alternative antibiotics.