Bacterial Co-infection Research Articles

Prevalence and risk factors associated with multidrug-resistant bacteria in COVID-19 patients.

Bacterial coinfection among patients with confirmed coronavirus disease 2019 (COVID-19) is a critical medical concern that increases the disease severity and mortality rate. The current study is aimed at evaluating the effects of bacterial coinfections among COVID-19 patients, especially in relation to degree of severity and mortality. A retrospective study was conducted for patients with positive COVID-19 test, admitted to a regional COVID-19 hospital in Jeddah, Saudi Arabia, between May and August 2020. A specimen (e.g., blood, urine, or sputum) was collected from patients with confirmed COVID-19, and was cultured to determine bacterial coinfection caused by multidrug resistant (MDR) bacteria. COVID-19 patients were categorized into 2 groups based on the result of bacterial coinfection culture, as COVID-19 patients with coinfection and COVID-19 patients without coinfection. Independent sample t test or Mann-Whitney U test was used to compare age and hospitalization period between these groups. In addition, binominal logistic regression was applied to identify risk factors associated with mortality and bacterial coinfection. The study included 342 patients with laboratory confirmed COVID-19. Eighty (23.3%) patients were diagnosed with bacterial coinfection, while the remaining 262 (76.6%) patients did not test positive for bacterial coinfection. Length of hospital stay was prolonged among COVID-19 patients diagnosed with bacterial coinfection (16.01 ± 11.36 days) when compared with patients without bacterial coinfection (6.5 ± 6.12 days). Likewise, the mortality rate was significantly higher among COVID-19 patients with bacterial coinfection (90%) compared to those without bacterial coinfection (49.2%). Gram-negative bacteria were predominant compared to gram-positive, as Klebsiella pneumoniae (35 [43.8%]) and Acinetobacter baumanni (32 [40%]). On the other hand, Staphylococcus aureus (4 [5%]), Enterococcus faecalis (1 [1.3%]), and Enterococcus faecium (1 [1.3%]) were identified as gram-positive bacterial species from recruited patients. The findings of the current study showed that prolong hospitalization is the main risk factor associated with bacterial coinfection and death. Thus, health care providers should minimize hospitalization as well as following a continuous monitoring for bacterial coinfection among COVID-19 patients, to control the spread of infection and reducing the severity and mortality rate among COVID-19 patients.

Surgical procedures for the treatment of fungal periprosthetic infection following hip arthroplasty: a systematic scoping review.

There has been limited literature synthesizing the therapeutic effects of surgical procedures for fungal periprosthetic joint infection (PJI) following hip arthroplasty. The authors' current study aims to comprehensively review and analyze those relevant literature, and carefully make recommendations for future clinical practices. Our current study was carried out in accordance with the PRISMA 2020 statement. Studies regarding the surgical management of fungal PJI following hip arthroplasty were collected via a thorough search of PubMed, Embase and Google scholar databases. The search was lastly performed in March 2023. Non-English language, reviews, articles with duplicated data, and articles without clear information about the type of fungal pathogens and treatment options were excluded. The authors evaluated their systematic review compliance by using AMSTAR 2 criteria and fell in moderate quality. Clinical outcomes of different surgical procedures were evaluated, and a binary logistic regression model was used to identify the risks associated with treatment failure. Data analyses were performed using the SPSS version 19.0. A total of 33 articles encompassing 80 patients with fungal PJI following hip arthroplasty were identified. Candida albicans was the most frequently isolated fungus (56.3%, 45/80). The overall treatment success was achieved in 71.1% (54/76) of the reported cases. Univariate analysis showed that the differences of success rate were not significant between publication periods, genders, ages, specimen collection methods, and fungal pathogens. Treatment success rate was 47.4% (9/19) in fungal PJI cases with bacterial co-infection, significantly lower than those without [vs. 79.0% (45/57), P=0.017]. The pooled success rate for surgical debridement, spacer implantation, resection arthroplasty, one-stage revision, and two-stage revision was 50.0% (4/8), 42.9% (3/7), 55.0% (11/20), 86.7% (13/15), and 88.5% (23/26), respectively, with significant differences between them (P=0.009). A binary logistic regression model showed that bacterial co-infection and surgical option were the two significant risk factors associated with treatment failure for fungal PJI following hip arthroplasty. Regarding the surgical treatment of fungal PJI following hip arthroplasty, patients with bacterial co-infection, and those treated with surgical procedures such as debridement, spacer implantation, and resection arthroplasty should be aware of the higher risks of failure. Nonetheless, future multiple-centre cohort studies are required to establish the optimal treatment.

Investigation of the Optimal Immunization Dose and Protective Efficacy of an Attenuated and Marker M. bovis-Bovine Herpesvirus Type 1 Combined Vaccine in Rabbits.

Bovine respiratory disease (BRD) is one of the most common diseases in the cattle industry; it is a globally prevalent multifactorial infection primarily caused by viral and bacterial coinfections. In China, Mycoplasma bovis (M. bovis) and bovine herpesvirus type 1 (BoHV-1) are the most notable pathogens associated with BRD. Our previous study attempted to combine the two vaccines and conducted a preliminary investigation of their optimal antigenic ratios. Based on this premise, the research extended its investigation by administering varying vaccine doses in a rabbit model to identify the most effective immunization dosage. After immunization, all rabbits in other immunization dose groups had a normal rectal temperature without obvious clinical symptoms. Furthermore, assays performed on the samples collected from immunized rabbits indicated that there were increased humoral and cellular immunological reactions. Moreover, the histological analysis of the lungs showed that immunized rabbits had more intact lung tissue than their unimmunized counterparts after the challenge. Additionally, there appears to be a positive correlation between the protective efficacy and the immunization dose. In conclusion, the different immunization doses of the attenuated and marker M. bovis HB150 and BoHV-1 gG-/tk- combined vaccine were clinically safe in rabbits; the mix of 2.0 × 108 CFU of M. bovis HB150 and 2.0 × 106 TCID50 BoHV-1 gG-/tk- strain was most promising due to its highest humoral and cellular immune responses and a more complete morphology of the lung tissue compared with others. These findings determined the optimal immunization dose of the attenuated and marker M. bovis HB150 and BoHV-1 gG-/tk- combined vaccine, laying a foundation for its clinical application.

Respiratory syncytial virus subtypes in children with bronchiolitis: does it correlate with clinical severity?

BackgroundIn this retrospective study, we aimed to evaluate the factors associated with the severity of respiratory syncytial virus (RSV) bronchiolitis in children aged under 2 years who were admitted to the Children’s Hospital of Hebei between June 2018 and January 2019.MethodsSputum samples positive for RSV via multiplex PCR were subtyped using real-time PCR. Data collected included risk factors for disease severity, demographics, microbiology, and outcomes.ResultsOf the 82 children with RSV bronchiolitis, 79 were treated and discharged with improvement, while 3 died. All three patients had underlying medical conditions, including complex congenital heart disease and severe combined immunodeficiency. Further, disease severity was associated with preexisting underlying disease, fever duration, and bacterial co-infection, but not with the RSV subtype.ConclusionsOur findings suggest that an appropriate therapeutic regimen should include the detection of bacterial co-infections and the identification of underlying diseases for the effective management of severe RSV bronchiolitis.

Prevalence of bacteria, fungi, and virus coinfections with SARS-CoV-2 Omicron variant among patients with severe COVID-19 in Guangzhou, China, winter 2022

The status of coinfection during the national outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron BA.5.2 or BF.7 in China in the winter of 2022, which is suspected to contribute substantially to the overloaded severe cases, needs to be investigated. We analyzed the coinfection status of 385 severe patients infected with the Omicron variant in Guangzhou using metagenomic sequencing. We found that 317 (82.3 %) patients were coinfected with at least one additional pathogen(s), including bacteria (58.7 %), fungi (27.1 %) and viruses (73.5 %). Pseudomonas aeruginosa (P. aeruginosa) (24.2 %), Staphylococcus aureus (S. aureus) (14.0 %), and Klebsiella pneumoniae (K. pneumonia) (13.4 %) ranked as the top three coinfected bacteria. Aspergillus fumigatus (A. fumigatus) (39.5 %), Pneumocystis jirovecii (P. jirovecii) (24.4 %) and Canidia albicans (C. albicans) (22.1 %) were the top three coinfected fungi. Epstein-Barr virus (EBV) (63.1 %), Human herpesvirus 7 (HHV-7) (34.8 %), and Herpes simplex virus 1 (HSV-1) (32.6 %) were the top three coinfected viruses. Of note, the detection of multiple coinfections of potential pathogenic bacteria, fungi, and viruses, despite lacking consistent patterns, highlighted a complicated synergistic contribution to disease severity. Our study presents the most comprehensive spectrum of bacterial, fungal, and viral coinfections in Omicron-associated severe coronavirus disease 2019 (COVID-19), implying that the coinfection of conditional pathogens might synergistically deteriorate the Omicron infection outcomes.

Differentiating Viral from Bacterial Pneumonia in Children: The Diagnostic Role of Lung Ultrasound-A Prospective Observational Study.

This prospective observational study aimed to investigate the utility of lung ultrasound (LUS) in diagnosing and managing pediatric respiratory infections, specifically focusing on viral, bacterial, and SARS-CoV-2 infections. Conducted over a period of 1 year and 8 months, this research involved 85 pediatric patients (showcasing a median age of 14 months) recruited based on specific criteria, including age, confirmed infection through multiplex PCR tests, and willingness to undergo LUS imaging. This study employed a 12-area scoring system for LUS examinations, utilizing the lung ultrasound score (LUSS) to evaluate lung abnormalities. The PCR examination results reveal diverse respiratory pathogens, with SARS-CoV-2, influenza, and bacterial co-infections being prominent among the cases. As an observational study, this study was not registered in the registry. Distinct LUS patterns associated with different pathogens were identified, showcasing the discriminatory potential of LUS in differentiating between viral and bacterial etiologies. Bacterial infections demonstrated more severe lung involvement, evident in significantly higher LUSS values compared with viral cases (p < 0.0001). The specific abnormalities found in bacterial superinfection can be integrated into diagnostic and management protocols for pediatric respiratory infections. Overall, this research contributes valuable insights into optimizing LUS as a diagnostic tool in pediatric pneumonia, facilitating more informed and tailored healthcare decisions.

Frequency of Multidrug-Resistant Microorganisms Associated with Bacterial Coinfections in Hospitalized Patient with Covid-19: A Literature Review

Patients with a doença do coronavírus 2019 (COVID-19) may be at risk of associated bacterial co-infections, and the involvement of multidrug-resistant (MDR) microorganisms in these cases can lead to an increase in morbidity and mortality rates. The objective of this study was to describe the frequency of the main MDR microorganisms associated with bacterial co-infections in patients hospitalized with COVID-19. To this end, we carried out a search in the PubMed and Regional Portal of the Virtual Health Library (VHL) databases, from December 2019 to September 2023, with the keywords COVID-19, co-infection and multidrug-resistant microorganism. Of the 535 articles initially found, only 14 were selected for analysis. Gram-negative bacteria were most frequently involved in bacterial co-infections in patients with COVID-19 (70%). Among these, Klebsiella pneumoniae and Acinetobacter baumannii predominated, with 85.71% and 78.57%, respectively. Among gram-positive bacteria, Staphylococcus aureus (71.42%) was the most common. Among MDR microorganisms, the prevalent species were carbapenem-resistant gram-negative bacilli (32%) and methicillin-resistant S. aureus (85.7%). Furthermore, a higher frequency of MDR microorganisms was observed in patients with COVID-19 in intensive care units (ICU). Thus, the findings of the present study indicate the need for attention to infections caused by multidrug-resistant microorganisms in critically ill patients with COVID-19.

Evaluation of characteristics and prognosis of COVID-19 patients requiring invasive mechanical ventilation during dominance of nonvariant, alpha, delta, and omicron variants in tertiary hospitals of Japan

BackgroundIn November 2021, the B.1.1.529 (omicron) variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was detected in South Africa and subsequently rapidly spread around the world. Despite the reduced severity of the omicron variants, many patients become severely ill after infection and undergo invasive mechanical ventilation, but there are few reports on their background and prognosis throughout all variant periods. This study aimed to evaluate risk factors affecting patients requiring invasive mechanical ventilation with each variant of COVID-19 pandemic in Japan from nonvariants to omicron variants.MethodThis retrospective observational study was conducted at the Department of Emergency and Critical Care Medicine, Kansai Medical University Hospital and Kansai Medical University Medical Center, Osaka, Japan, from March 2020 to March 2023. Eligible patients were those who underwent invasive ventilation for COVID-19 pneumonia. We set the primary endpoint as in-hospital mortality. Multivariable logistic regression analysis adjusted for clinically important variables was performed to evaluate the clinical outcomes.ResultsWe included 377 patients: 118 in the Nonvariant group, 154 in the Alpha group, 42 in the Delta group, and 63 patients in the Omicron group. Mortality rates for each group were 23.7% for the Nonvariant group, 12.3% for the Alpha group, 7.1% for the Delta group, and 30.5% for the Omicron group. Patient age was significantly associated with increased mortality (adjusted odds ratio [AOR]: 1.097; 95% confidence interval [CI]: 1.057–0.138, P < 0.001). Immunodeficiency (AOR: 3.388, 95% CI: 1.377–8.333, P = 0.008), initial SOFA score (AOR: 1.190, 95% CI: 1.056–1.341, P = 0.004), dialysis prior to COVID-19 (AOR: 3.695, 95% CI: 1.117–11.663, P = 0.026), and smoking history (AOR: 2.548, 95% CI: 1.153–5.628, P = 0.021) were significantly associated with increased mortality. Differences in variants were not significant factors associated with high mortality.ConclusionWe compared the background and prognosis of patients with COVID-19 pneumonia requiring invasive mechanical ventilation between SARS-CoV-2 variants. In these patients, differences in variants did not affect prognosis. Hospital mortality in critically ill COVID-19 patients was significantly higher in the older patients with bacterial coinfection, or patients with immunodeficiency, COPD, and chronic renal failure on dialysis.

Two complete 1918 influenza A/H1N1 pandemic virus genomes characterized by next-generation sequencing using RNA isolated from formalin-fixed, paraffin-embedded autopsy lung tissue samples along with evidence of secondary bacterial co-infection.

This study applied modern molecular biotechnology and high-throughput sequencing to formalin-fixed, paraffin-embedded autopsy lung samples from two fatal cases during the fall wave of the 1918 influenza A (H1N1) pandemic in the United States. Complete influenza genomes were obtained from both cases, which increases the total number of available complete or near-complete influenza genomes of the 1918 pandemic virus from four to six. Sequence analysis confirms that the 1918 pandemic virus was highly conserved during the main wave of the pandemic with geographic separation in North America and Europe. Metagenomic analyses revealed bacterial co-infections in both cases, including the first reported evidence of Rhodococcus-influenza co-infection. Overall, this study offers a detailed view at the molecular level of the very limited samples from the most devastating influenza pandemic in modern human history.

Assessment of Bacterial Co-Infection and Antibiotic Prescribing in Patients with COVID-19

Assessment of Bacterial Co-Infection and Antibiotic Prescribing in Patients with COVID-19

Rationality of antibiotic use in COVID-19 patients in the ICU of Dr. Hasan Sadikin General Hospital, Bandung; a cohort study

Background and Objectives: Nearly three-quarters of the patients with COVID-19 received antibiotic therapy despite the bacterial coinfection being only less than 10% in many studies and ranging from 8-22% in ICU patients. The use of broad-spectrum antibiotics in COVID-19 patients has not been proven effective. Overuse of antibiotics may be associated with side effects and antibiotic resistance. The purpose of this study was to determine the antibiotic rationality in COVID-19 patients in the ICU of Dr. Hasan Sadikin Hospital, Bandung, Indonesia.&#x0D; Methodology: This descriptive, retrospective cohort study was carried out by analyzing medical records of COVID-19 patients admitted in the ICU of Dr. Hasan Sadikin Hospital from January-June 2021.&#x0D; Results: There were 138 patients who met the inclusion criteria. A total of 126 (91.3%) patients received antibiotics. A total of 12 (8.7%) severe/critical patients did not receive antibiotics and 79 (62.70%) received inappropriate antibiotic duration. Inappropriate regimen was found in 59 patients (74.68%) with COVID-19 without HAP/VAP and 15 patients (31.92%) with HAP/VAP. The primary issue identified was the inappropriate regimen of antibiotics, Gyssens category 4a.&#x0D; Conclusion: This study concludes that 23.02% patients used rational empirical antibiotics and 45.98% used rational definitive antibiotics in COVID-19 patients in the ICU at RSUP Dr. Hasan Sadikin Bandung during January-June 2021.&#x0D; Abbreviations: ACE- Angiotensin Converting Enzyme; ICU- Intensive Care Unit; HAI- Hospital-Associated Infections; HAP- Hospital-Acquired Pneumonia; IDSA- Infectious Diseases Society of America VAP- Ventilator-Associated Pneumonia&#x0D; Key words: Antibiotics; Antimicrobial Resistance; COVID-19; Intensive Care Units; Prescribing Pattern&#x0D; Citation: Indriasari, Oktaliansah E, Munazat RI. Rationality of antibiotic use in COVID-19 patients in the ICU of Dr. Hasan Sadikin General Hospital Bandung; a cohort study. Anaesth. pain intensive care 2024;28(1):115−125.&#x0D; DOI: 10.35975/apic.v28i1.2384&#x0D; Received: November 20, 2023; Reviewed: December 03, 2023; Accepted: December 26, 2023

Fever-like temperature impacts on Staphylococcus aureus and Pseudomonas aeruginosa interaction, physiology, and virulence both in vitro and in vivo

BackgroundStaphylococcus aureus (SA) and Pseudomonas aeruginosa (PA) cause a wide variety of bacterial infections and coinfections, showing a complex interaction that involves the production of different metabolites and metabolic changes. Temperature is a key factor for bacterial survival and virulence and within the host, bacteria could be exposed to an increment in temperature during fever development. We analyzed the previously unexplored effect of fever-like temperatures (39 °C) on S. aureus USA300 and P. aeruginosa PAO1 microaerobic mono- and co-cultures compared with 37 °C, by using RNAseq and physiological assays including in vivo experiments.ResultsIn general terms both temperature and co-culturing had a strong impact on both PA and SA with the exception of the temperature response of monocultured PA. We studied metabolic and virulence changes in both species. Altered metabolic features at 39 °C included arginine biosynthesis and the periplasmic glucose oxidation in S. aureus and P. aeruginosa monocultures respectively. When PA co-cultures were exposed at 39 °C, they upregulated ethanol oxidation-related genes along with an increment in organic acid accumulation. Regarding virulence factors, monocultured SA showed an increase in the mRNA expression of the agr operon and hld, pmsα, and pmsβ genes at 39 °C. Supported by mRNA data, we performed physiological experiments and detected and increment in hemolysis, staphyloxantin production, and a decrease in biofilm formation at 39 °C. On the side of PA monocultures, we observed an increase in extracellular lipase and protease and biofilm formation at 39 °C along with a decrease in the motility in correlation with changes observed at mRNA abundance. Additionally, we assessed host–pathogen interaction both in vitro and in vivo. S. aureus monocultured at 39οC showed a decrease in cellular invasion and an increase in IL-8—but not in IL-6—production by A549 cell line. PA also decreased its cellular invasion when monocultured at 39 °C and did not induce any change in IL-8 or IL-6 production. PA strongly increased cellular invasion when co-cultured at 37 and 39 °C. Finally, we observed increased lethality in mice intranasally inoculated with S. aureus monocultures pre-incubated at 39 °C and even higher levels when inoculated with co-cultures. The bacterial burden for P. aeruginosa was higher in liver when the mice were infected with co-cultures previously incubated at 39 °C comparing with 37 °C.ConclusionsOur results highlight a relevant change in the virulence of bacterial opportunistic pathogens exposed to fever-like temperatures in presence of competitors, opening new questions related to bacteria-bacteria and host–pathogen interactions and coevolution.

Microbial associations for pneumonia causative agents and level of their resistance to antimicrobial drugs during a new coronavirus infection pandemic

Introduction. Bacterial coinfection and secondary bacterial infection are considered critical risk factors for the severity and mortality of SARS-CoV-2-caused pneumonia. The aim of the study was to analyze a pattern of microbial associations between K. pneumoniae and A. baumannii isolated from the lower respiratory tract discharge and sectional material (lung tissue) of patients diagnosed with pneumonia, and to compare resistance level in monoculture and associations during new coronavirus infection pandemic. Materials and methods. A bacteriological study of 2689 sputum and bronchial washing samples from patients at infectious diseases hospitals, and 1411 lung pathological material samples was carried out. Bacterial isolates were identified by mass spectrometry. Antibiotic sensitivity for isolates was determined by the disk diffusion method. Genetic determinants of resistance to beta-lactam antibiotics were detected by PCR. Statistical data processing was performed using SPSS version 22 software. Results. K. pneumoniae and A. baumannii isolates were predominantly found in two- and three-pathogen associations. It was established that the resistance level of K. pneumoniae isolates in association with A. baumannii is significantly higher compared to that in monoculture for all antimicrobial drugs studied. At the same time, K. pneumoniae in combination with Candida spp. vs monoculture showed significantly lower level of resistance to ciprofloxacin, amikacin, cefotaxime, ceftazidime and amoxicillin/clavulanic acid. K. pneumoniae isolates carried resistance determinants to extended-spectrum beta-lactamases: OXA-48 — (22.5%), OXA-51 — (5.6%), OXA-23 — (4.2%), KPC — 70.9%, NDM — 7%. Of these, 14.1% of strains had the ability to co-produce serine carbapenemases OXA-48 and KPC. Sputum and lung tissue A. baumannii isolates exhibited extremely high multiple resistance regardless of their associations with other microorganisms. Microbiome species similarity in the lower respiratory tract and lung tissue discharge was revealed. The proportion of lung tissue vs sputum resistant strains of K. pneumoniae and A. baumannii was significantly higher. Conclusion. The detection of of multiple drug resistant K. pneumoniae and A. baumannii isolates as well as their associations may indicate aggravated pneumonia severity.

The Rapidly Changing Patterns in Bacterial Co-Infections Reveal Peaks in Limited Gram Negatives during COVID-19 and Their Sharp Drop Post-Vaccination, Implying Potential Evolution of Co-Protection during Vaccine-Virus-Bacterial Interplay.

SARS-CoV-2 has caused the most devastating pandemic of all time in recent human history. However, there is a serious paucity of high-quality data on aggravating factors and mechanisms of co-infection. This study aimed to identify the trending patterns of bacterial co-infections and types and associated outcomes in three phases of the pandemic. Using quality hospital data, we have investigated the SARS-CoV-2 fatality rates, profiles, and types of bacterial co-infections before, during, and after COVID-19 vaccination. Out of 389 isolates used in different aspects, 298 were examined before and during the pandemic (n = 149 before, n = 149 during). In this group, death rates were 32% during compared to only 7.4% before the pandemic with significant association (p-value = 0.000000075). However, the death rate was 34% in co-infected (n = 170) compared to non-co-infected patients (n = 128), indicating a highly significant value (p-value = 0.00000000000088). However, analysis of patients without other serious respiratory problems (n = 28) indicated that among the remaining 270 patients, death occurred in 30% of co-infected patients (n = 150) and only 0.8% of non-co-infected (n = 120) with a high significant p-value = 0.00000000076. The trending patterns of co-infections before, during, and after vaccination showed a significant decline in Staphylococcus aureus with concomitant peaks in Gram negatives n = 149 before/n = 149 during, including Klebsiella pneumonian = 11/49 before/during, E. coli n = 10/24, A. baumannii n = 8/25, Ps. aeruginosa n = 5/16, and S. aureus 13/1. Nevertheless, in the post-vaccination phase (n = 91), gender-specific co-infections were examined for potential differences in susceptibility. Methicillin-resistant S. aureus dominated both genders followed by E. coli in males and females, with the latter gender showing higher rates of isolations in both species. Klebsiella pneumoniae declined to third place in male patients. The drastic decline in K. pneumoniae and Gram negatives post-vaccination strongly implied a potential co-protection in vaccines. Future analysis would gain more insights into molecular mimicry.

Risk Factors for Severe Respiratory Syncytial Virus Infection in Hospitalized Children.

Respiratory syncytial virus (RSV) is a common cause of bronchiolitis and pneumonia in infants and young children. Starting in December 2010, RSV monoclonal antibody (RSV mAb) was endorsed by Taiwan National Health Insurance and given to children with prematurity and/or congenital heart diseases, which are considered high-risk factors for severe RSV diseases. Investigating other important contributing risk factors is warranted. We conducted a cohort study at National Taiwan University Hospital to determine the rate of severe outcomes among children hospitalized due to RSV infection from 2008 to 2018. Adjusted for age, sex and birth cohorts born before and after RSV mAb endorsement, we identified risk factors for severe RSV infection, defined as the requirement of invasive ventilator support. There were 1985 admissions due to RSV infections. Among them, 66 patients (3.3%) had severe RSV infection. The proportion of severe RSV infections decreased significantly after RSV mAb endorsement. Multivariable analysis revealed that age <1.5 months and cardiovascular and congenital/genetic diseases were high-risk underlying conditions. In addition, bacterial coinfections, elevated creatinine levels and initial abnormal chest radiograph findings posed warning signs for severe RSV infection. Children younger than 1.5 months of age with cardiovascular or congenital/genetic diseases were predisposed to severe RSV infection and might benefit from RSV mAb prophylaxis.

Bacterial co-infections, secondary infections and antimicrobial use among hospitalized COVID-19 patients in the sixth wave in Pakistan: findings and implications

ABSTRACT Introduction Previous studies in Pakistan have shown considerable over prescribing of antibiotics in patients hospitalized with COVID-19 despite very low prevalence of bacterial infections. Irrational use of antibiotics will worsen antimicrobial resistance (AMR). Methods Retrospective analysis of medical records of patients in the COVID-19 wards of three tertiary care hospitals to assess antibiotic use during the sixth COVID-19 wave. Results A total of 284 patients were included, most were male (66.9%), aged 30–50 years (50.7%) with diabetes mellitus the most common comorbidity. The most common symptoms at presentation were cough (47.9%) and arthralgia-myalgia (41.5%). Around 3% were asymptomatic, 34.9% had mild, 30.3% moderate, and 23.6% had severe disease, with 8.1% critical. Chest X-ray abnormalities were seen in 43.3% of patients and 37% had elevated white cell counts, with 35.2% having elevated C-reactive protein levels. Around 91% COVID-19 patients were prescribed antibiotics during their hospital stay, with only a few with proven bacterial co-infections or secondary bacterial infections. Most antibiotics were from the ‘Watch’ category (90.8%) followed by the ‘Reserve’ category (4.8%), similar to previous COVID-19 waves. Conclusion There continued to be excessive antibiotics use among hospitalized COVID-19 patients in Pakistan. Urgent measures are needed to address inappropriate prescribing including greater prescribing of Access antibiotics where pertinent.

Risk factors, outcomes, and epidemiological and etiological study of hospitalized COVID-19 patients with bacterial co-infection and secondary infections

BackgroundAs a common complication of viral respiratory tract infection, bacterial infection was associated with higher mortality and morbidity. Determining the prevalence, culprit pathogens, outcomes, and risk factors of co-infection and secondary infection occurring in hospitalized patients with coronavirus disease 2019 (COVID-19) will be beneficial for better antibiotic management.MethodsIn this retrospective cohort research, we assessed clinical characteristics, laboratory parameters, microbiologic results, and outcomes of laboratory-confirmed COVID-19 patients with bacterial co-infection and secondary infection in West China Hospital from 2022 December 2nd to 2023 March 15th.ResultsThe incidence of bacterial co-infection and secondary infection, as defined by positive culture results of clinical specimens, was 16.3% (178/1091) and 10.1% (110/1091) respectively among 1091 patients. Acinetobacter, Klebsiella, and Pseudomonas were the most commonly identified bacteria in respiratory tract samples of COVID-19 patients. In-hospital mortality of COVID-19 patients with co-infection (17.4% vs 9.5%, p = 0.003) and secondary infection (28.2% vs 9.5%, p < 0.001) greatly exceeded that of COVID-19 patients without bacterial infection. Cardiovascular disease (1.847 (1.202–2.837), p = 0.005), severe COVID-19 (1.694 (1.033–2.778), p = 0.037), and critical COVID-19 (2.220 (1.196–4.121), p = 0.012) were proved to be risk factors for bacterial co-infection, while only critical COVID-19 (1.847 (1.202–2.837), p = 0.005) was closely related to secondary infection.ConclusionsBacterial co-infection and secondary infection could aggravate the disease severity and worsen clinical outcomes of COVID-19 patients. Notably, only critical COVID-19 subtype was proved to be an independent risk factor for both co-infection and secondary infection. Therefore, standard empirical antibiotics was recommended for critically ill COVID-19 rather than all the inpatients according to our research.

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

BackgroundBacterial 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.MethodsWe 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.ResultsThe 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.ConclusionsProcalcitonin 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.

Virome Data Explorer: A web resource to longitudinally explore respiratory viral infections, their interactions with other pathogens and host transcriptomic changes in over 100 people.

Viral respiratory infections are an important public health concern due to their prevalence, transmissibility, and potential to cause serious disease. Disease severity is the product of several factors beyond the presence of the infectious agent, including specific host immune responses, host genetic makeup, and bacterial coinfections. To understand these interactions within natural infections, we designed a longitudinal cohort study actively surveilling respiratory viruses over the course of 19 months (2016 to 2018) in a diverse cohort in New York City. We integrated the molecular characterization of 800+ nasopharyngeal samples with clinical data from 104 participants. Transcriptomic data enabled the identification of respiratory pathogens in nasopharyngeal samples, the characterization of markers of immune response, the identification of signatures associated with symptom severity, individual viruses, and bacterial coinfections. Specific results include a rapid restoration of baseline conditions after infection, significant transcriptomic differences between symptomatic and asymptomatic infections, and qualitatively similar responses across different viruses. We created an interactive computational resource (Virome Data Explorer) to facilitate access to the data and visualization of analytical results.

Coinfection of channel catfish (Ictalurus punctatus) with virulent Aeromonas hydrophila and Flavobacterium covae exacerbates mortality.

Flavobacterium covae and virulent Aeromonas hydrophila are prevalent bacterial pathogens within the US catfish industry that can cause high mortality in production ponds. An assessment of invivo bacterial coinfection with virulent A. hydrophila (ML09-119) and F. covae (ALG-00-530) was conducted in juvenile channel catfish (Ictalurus punctatus). Catfish were divided into seven treatments: (1) mock control; (2) and (3) high and low doses of virulent A. hydrophila; (4) and (5) high and low doses of F. covae; (6) and (7) simultaneous challenge with high and low doses of virulent A. hydrophila and F. covae. In addition to the mortality assessment, anterior kidney and spleen were collected to evaluate immune gene expression, as well as quantify bacterial load by qPCR. At 96 h post-challenge (hpc), the high dose of virulent A. hydrophila infection (immersed in 2.3 × 107 CFU mL-1 ) resulted in cumulative percent mortality (CPM) of 28.3 ± 9.5%, while the high dose of F. covae (immersed in 5.2 × 106 CFU mL-1 ) yielded CPM of 23.3 ± 12.9%. When these pathogens were delivered in combination, CPM significantly increased for both the high- (98.3 ± 1.36%) and low-dose combinations (76.7 ± 17.05%) (p < .001). Lysozyme activity was found to be different at 24 and 48 hpc, with the high-dose vAh group demonstrating greater levels than unexposed control fish at each time point. Three proinflammatory cytokines (tnfα, il8, il1b) demonstrated increased expression levels at 48 hpc. These results demonstrate the additive effects on mortality when these two pathogens are combined. The synthesis of these mortality and health metrics advances our understanding of coinfections of these two important catfish pathogens and will aid fish health diagnosticians and channel catfish producers in developing therapeutants and prevention methods to control bacterial coinfections.