Streptococcus pneumoniae coinfection in hospitalised patients with COVID-19

Cardiovascular events after invasive pneumococcal disease: a retrospective cohort study

OBJECTIVES

This study aims to understand the magnitude of and mechanisms underlying the development of cardiovascular events (CVEs) in patients with invasive pneumococcal disease (IPD). We aimed to identify factors that contribute to the occurrence of CVEs within 1 year after admission and discuss implications for patient care.

METHODS

A multicentered cohort study included adult patients from four Dutch hospitals who had a positive blood culture for Streptococcus pneumoniae and any type of clinical manifestation between 2012 and 2020. Disease characteristics and microbiological data were systematically collected from electronic patient files. The main outcome measures were the occurrence of stroke and acute coronary syndromes (ACS).

RESULTS

Of 914 eligible patients, 4.2% experienced a CVE within 1 year after admission for IPD. ACS mainly occurred in the first 2 weeks, whereas stroke developed throughout follow-up. Although ACS was positively associated with disease severity, the sole independent predictor was alcohol abuse (odds ratio [OR] 3.840, 95% confidence interval [CI] 1.108-13.303). Although stroke occurred in 6.3% of meningitis cases, the best clinical predictor of stroke was a body temperature >39.5 °C at admission (OR 3.117 [1.154-8.423]). In the adult IPD population aged <70 years, pneumococcal serotypes were the primary predictors of ACS (7F; OR 15.733 [1.812-136.632]) and stroke (22F; OR 7.320 [1.193-44.903]).

CONCLUSIONS

Adverse CVEs were not uncommon after IPD diagnosis and deserve attention, especially in the high-risk groups we identified in our study population. Whether specific serotypes play a role in the development of CVE requires substantiation in further research.

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

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

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

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

Recommendations and guidelines for the diagnosis and management of Coronavirus Disease-19 (COVID-19) associated bacterial and fungal infections in Taiwan

Coronavirus disease-19 (COVID-19) is an emerging infectious disease caused by SARS-CoV-2 that has rapidly evolved into a pandemic to cause over 600 million infections and more than 6.6 million deaths up to Nov 25, 2022. COVID-19 carries a high mortality rate in severe cases. Co-infections and secondary infections with other micro-organisms, such as bacterial and fungus, further increases the mortality and complicates the diagnosis and management of COVID-19. The current guideline provides guidance to physicians for the management and treatment of patients with COVID-19 associated bacterial and fungal infections, including COVID-19 associated bacterial infections (CABI), pulmonary aspergillosis (CAPA), candidiasis (CAC) and mucormycosis (CAM). Recommendations were drafted by the 7th Guidelines Recommendations for Evidence-based Antimicrobial agents use Taiwan (GREAT) working group after review of the current evidence, using the grading of recommendations assessment, development, and evaluation (GRADE) methodology. A nationwide expert panel reviewed the recommendations in March 2022, and the guideline was endorsed by the Infectious Diseases Society of Taiwan (IDST). This guideline includes the epidemiology, diagnostic methods and treatment recommendations for COVID-19 associated infections. The aim of this guideline is to provide guidance to physicians who are involved in the medical care for patients with COVID-19 during the ongoing COVID-19 pandemic.

Protecting adults at risk of pneumococcal infection and influenza from exposure to SARS-CoV-2

There is a paucity of evidence linking pneumococcal infection and influenza with SARS-CoV-2 and COVID-19. There is circumstantial evidence of the possibility of an association between S. pneumoniae and SARS-CoV-2 such as the increased binding of S. pneumoniae to coronavirus-infected human airway epithelium, the frequent use of broad-spectrum antibiotics in the management of COVID-19 which could mask secondary bacterial infection, and the observation that pneumococcal vaccination is associated with decreased SARS-CoV-2 nasopharyngeal swab positivity. We performed a targeted literature review for the year 2020, using search terms S. pneumoniae, influenza, SARS-CoV-2, and found 25 relevant articles of a total of 291. Pneumococcal and influenza vaccinations have the potential to contribute toward efforts aimed at reducing the health burden of SARS-CoV-2, especially by reducing preventable admissions to hospital for pneumonia and the consequent risk of nosocomial SARS-CoV-2 transmission.

Detection of pneumococcus during hospitalization for SARS-CoV-2

Background

Infections with respiratory viruses [e.g. influenza and respiratory syncytial virus (RSV)] can increase the risk of severe pneumococcal infections. Likewise, pneumococcal coinfection is associated with poorer outcomes in viral respiratory infection. However, there are limited data describing the frequency of pneumococcus and SARS-CoV-2 coinfection and the role of coinfection in influencing COVID-19 severity. We, therefore, investigated the detection of pneumococcus in COVID-19 inpatients during the early pandemic period.

Methods

The study included patients aged 18 years and older, admitted to the Yale-New Haven Hospital who were symptomatic for respiratory infection and tested positive for SARS-CoV-2 during March-August 2020. Patients were tested for pneumococcus through culture-enrichment of saliva followed by RT-qPCR (to identify carriage) and serotype-specific urine antigen detection (UAD) assays (to identify presumed lower respiratory tract pneumococcal disease).

Results

Among 148 subjects, the median age was 65 years; 54.7% were male; 50.7% had an ICU stay; 64.9% received antibiotics; and 14.9% died while admitted. Pneumococcal carriage was detected in 3/96 (3.1%) individuals tested by saliva RT-qPCR. Additionally, pneumococcus was detected in 14/127 (11.0%) individuals tested by UAD, and more commonly in severe than moderate COVID-19 [OR: 2.20; 95% CI: (0.72, 7.48)]; however, the numbers were small with a high degree of uncertainty. None of the UAD-positive individuals died.

Conclusions

Pneumococcal lower respiratory tract infection (LRTI), as detected by positive UAD, occurred in patients hospitalized with COVID-19. Moreover, pneumococcal LRTI was more common in those with more serious COVID-19 outcomes. Future studies should assess how pneumococcus and SARS-CoV-2 interact to influence COVID-19 severity in hospitalized patients.

Microflora of sputum and autopsy material of patients with COVID-19

The rapid spread of a new coronavirus infection in the country actualizes the conduct of bacteriological studies of clinical material obtained from the respiratory tract of patients with COVID-19. During the experiments, 230 sputum samples and 260 autopsy lung samples from patients with COVID-19 were analyzed. 946 high-risk strains were isolated and identified by MALDI-ToF mass spectrometry on a Microflex LT instrument (Bruker®). According to the results of bacteriological cultures of sputum, a predominance of gram-positive ones was revealed, amounting to 50.5% (222 strains) of the total number of isolated pathogens. However, falling into this group is manifested by natural representatives of the microflora of the human mucous membranes from the genera Streptococcus, Rothia and Lactobacillus (109 strains in total), which can be manifested by the detection of improper sputum collection, causing contamination by the substance of intense salivation and nasopharyngeal discharge. In turn, the "classic" gram-positive causative agents of pneumonia were detected much less frequently: S. aureus in 5 cases, S. pneumoniae in 6 patients. The causative agents in the order Enterobacterales are represented by 42 strains, among which the most likely species are K.pneumoniae (27 strains). In the group of non-fermenting gram-negative bacteria, A. baumanii (29 strains) prevailed, and P. aeruginosa was also identified in 2 cases. When analyzing the results of a microbiological study of autopsy material (lungs) of patients with COVID-19, significant differences in the qualitative and quantitative composition of the microflora were revealed, compared with sputum. In the group of gram-positive bacteria, 15 strains of the natural microflora of the mucous membranes were identified, while sensitive species dominated among gram-negative pathogens: K. pneumoniae (102 strains), A. baumanii (75 strains), P. aeruginosa (11 strains). Regular microbiological monitoring is essential for antibiotic therapy and prevention of secondary bacterial infection. In the event of a fatal outcome, the results of microbiological analysis of autopsy material can determine the cause of death of the patient.

Coinfections with Other Respiratory Pathogens among Patients with COVID-19

Emerging evidence indicates that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected individuals are at an increased risk for coinfections; therefore, physicians need to be cognizant about excluding other treatable respiratory pathogens. Here, we report coinfection with SARS-CoV-2 and other respiratory pathogens in patients admitted to the coronavirus disease (COVID) care facilities of an Indian tertiary care hospital. From June 2020 through January 2021, we tested 191 patients with SARS-CoV-2 for 33 other respiratory pathogens using an fast track diagnostics respiratory pathogen 33 (FTD-33) assay. Additionally, information regarding other relevant respiratory pathogens was collected by reviewing their laboratory data. Overall, 13 pathogens were identified among patients infected with SARS-CoV-2, and 46.6% (89/191) of patients had coinfection with one or more additional pathogens. Bacterial coinfections (41.4% [79/191]) were frequent, with Staphylococcus aureus being the most common, followed by Klebsiella pneumoniae. Coinfections with SARS-CoV-2 and Pneumocystis jirovecii or Legionella pneumophila were also identified. The viral coinfection rate was 7.3%, with human adenovirus and human rhinovirus being the most common. Five patients in our cohort had positive cultures for Acinetobacter baumannii and K. pneumoniae, and two patients had active Mycobacterium tuberculosis infection. In total, 47.1% (90/191) of patients with coinfections were identified. The higher proportion of patients with coinfections in our cohort supports the systemic use of antibiotics in patients with severe SARS-CoV-2 pneumonia with rapid de-escalation based on respiratory PCR/culture results. The timely and simultaneous identification of coinfections can contribute to improved health of COVID-19 patients and enhanced antibiotic stewardship during the pandemic. IMPORTANCE Coinfections in COVID-19 patients may worsen disease outcomes and need further investigation. We found that a higher proportion of patients with COVID-19 were coinfected with one or more additional pathogens. A better understanding of the prevalence of coinfection with other respiratory pathogens in COVID-19 patients and the profile of pathogens can contribute to effective patient management and antibiotic stewardship during the current pandemic.

Coinfections with Bacteria, Fungi, and Respiratory Viruses in Patients with SARS-CoV-2: A Systematic Review and Meta-Analysis

Background: Coinfection with bacteria, fungi, and respiratory viruses in SARS-CoV-2 is of particular importance due to the possibility of increased morbidity and mortality. In this meta-analysis, we calculated the prevalence of such coinfections. Methods: Electronic databases were searched from 1 December 2019 to 31 March 2021. Effect sizes of prevalence were pooled with 95% confidence intervals (CIs). To minimize heterogeneity, we performed sub-group analyses. Results: Of the 6189 papers that were identified, 72 articles were included in the systematic review (40 case series and 32 cohort studies) and 68 articles (38 case series and 30 cohort studies) were included in the meta-analysis. Of the 31,953 SARS-CoV-2 patients included in the meta-analysis, the overall pooled proportion who had a laboratory-confirmed bacterial infection was 15.9% (95% CI 13.6–18.2, n = 1940, 49 studies, I² = 99%, p < 0.00001), while 3.7% (95% CI 2.6–4.8, n = 177, 16 studies, I² = 93%, p < 0.00001) had fungal infections and 6.6% (95% CI 5.5–7.6, n = 737, 44 studies, I² = 96%, p < 0.00001) had other respiratory viruses. SARS-CoV-2 patients in the ICU had higher co-infections compared to ICU and non-ICU patients as follows: bacterial (22.2%, 95% CI 16.1–28.4, I² = 88% versus 14.8%, 95% CI 12.4–17.3, I² = 99%), and fungal (9.6%, 95% CI 6.8–12.4, I² = 74% versus 2.7%, 95% CI 0.0–3.8, I² = 95%); however, there was an identical other respiratory viral co-infection proportion between all SARS-CoV-2 patients [(ICU and non-ICU) and the ICU only] (6.6%, 95% CI 0.0–11.3, I² = 58% versus 6.6%, 95% CI 5.5–7.7, I² = 96%). Funnel plots for possible publication bias for the pooled effect sizes of the prevalence of coinfections was asymmetrical on visual inspection, and Egger’s tests confirmed asymmetry (p values < 0.05). Conclusion: Bacterial co-infection is relatively high in hospitalized patients with SARS-CoV-2, with little evidence of S. aureus playing a major role. Knowledge of the prevalence and type of co-infections in SARS-CoV-2 patients may have diagnostic and management implications.