Predictors and microbiology of respiratory and bloodstream bacterial infection in patients with COVID-19: living rapid review update and meta-regression

Polymicrobial Bloodstream Infections: A Retrospective Cohort Study on Clinical Manifestations, Co-infection Patterns, and Survival Outcomes

BACKGROUND

Polymicrobial bloodstream infections (BSI) pose a considerable diagnostic and therapeutic challenge in clinical practice due to their complex pathogenesis and wide-ranging clinical manifestations.

METHODS

We conducted a retrospective cohort study of patients with polymicrobial BSI at a tertiary hospital between 1 January 2018 and 31 May 2023 and reviewed detailed clinical data, identified infectious foci and assessed survival rates among these patients.

RESULTS

Out of 3,226 positive blood cultures, 514 (15.9%) indicated co-infections of bacterial species. Co-infections of gram-positive cocci (GPC) and gram-negative bacilli (GNB) constituted 44.7% (96/215) of cases, while GNB-GNB co-infections accounted for 42.3% (91/215). The most frequent co-infection was observed between Klebsiella pneumoniae and Escherichia coli, representing 8.8% (19/215) of cases. Notably, co-infections involving Enterococci spp. and Acinetobacter baumannii exhibited a mortality rate of 62.5% (5/8), as did those involving Enterococci spp. and K. pneumoniae, with a mortality rate of 66.7% (4/6). The study revealed that patients with GNB-GPC co-infections exhibited a significantly higher 15-day mortality compared to those with GNB-GNB co-infections (HR 1.8 (1.0-3.2, P=.046; log rank test, P=.037). Elevated levels of Procalcitonin (PCT) and C-reactive protein (CRP), MDR-MDR bacteria co-infections, and carbapenem-resistant Enterobacteriaceae (CRE) involvement were significantly associated with higher mortality rates of polymicrobial BSI.

CONCLUSION

The study reveals that patients presenting with hypoproteinemia and co-infections of GNB and GPC are at a higher risk of mortality. Furthermore, a significant correlation exists between survival rates and infection indices, which carries important implications for clinical diagnosis and treatment strategies.

The burden of nosocomial superinfections in a retrospective cohort study of critically ill COVID-19 patients

OBJECTIVES

Viral respiratory infections can be complicated by bacterial superinfections. SARS-CoV-2 patients may suffer from superinfections, and negative effects of additional infections have been identified. When analysing hospital data, patients typically leave the facility of observation, due to discharge or death, which leads to changes in the study cohort over time. This may distort the estimate of the impact of superinfection. Therefore, it is essential for the statistical analysis of hospital data to acknowledge this change of the risk set over time. We analysed superinfections in a retrospective cohort study with 268 critically ill patients, taking into account discharge and death as competing risks in the statistical analysis.

METHODS

We evaluated bacterial respiratory infections and bloodstream infections and used multi-state statistical modelling to account for the different patient states. We calculated risks of superinfection, probability of discharge or death over time and analysed subgroups according to age and sex.

RESULTS

The observed pathogen spectrum was mainly composed of Enterobacterales, Nonfermenters but also Staphylococcus aureus. We identified an elevated mortality due to bacterial infection of the respiratory tract or bloodstream infection (adj. cause-specific HR 1.7, CI 1.15-2.52) as well as a reduced discharge rate (adj. cause-specific HR 0.51, CI 0.36-0.73). Female patients showed a tendency to have a reduced risk of acquiring a superinfection (adj. subdistribution HR 0.71, CI 0.48-1.04), and in case of infection a higher mortality compared to male patients (interaction effect HR 1.49, CI 0.67-3.30).

CONCLUSIONS

The study accounts for competing risks and quantifies the risk of death associated with bacterial superinfection in critically ill COVID-19 patients. We observed an increased risk of death for patients who developed a superinfection, with Enterobacterales being the predominant agent. The results emphasize the need for microbiological sampling in SARS-CoV-2-infected patients.

CLINICAL TRIAL NUMBER

German Clinical Trials Register number: DRKS00031367, registration date: 01.03.2023 ( https://drks.de/search/de/trial/DRKS00031367 ).

Antibiotic Treatment in Patients Hospitalized for Nonsevere COVID-19

Importance

Patients hospitalized with nonsevere COVID-19 continue to receive community-acquired pneumonia (CAP) antibiotic treatment despite a low risk of bacterial coinfection. Unnecessary antibiotic prescribing contributes to global antibiotic resistance and also poses a threat to individual patients.

Objective

To examine the association of CAP antibiotic treatment started on admission with clinical outcomes among a large sample of patients hospitalized for nonsevere COVID-19 in hospitals across the US.

Design, Setting, and Participants

This retrospective cohort study used a target trial emulation design. Participants were adult, immunocompetent patients admitted to general care for COVID-19 from April 2020 to December 2023 at 1053 US-based acute-care hospitals that contribute data to the Premier Healthcare Database. Patients with nonpneumonia bacterial infections present on admission were excluded. Data were analyzed from April to October 2024.

Exposure

Receipt of a CAP antibiotic regimen on the day of admission.

Main Outcomes and Measures

The primary outcome was a composite measure of deterioration (vasopressor, high-flow oxygen, noninvasive ventilation, invasive mechanical ventilation, intermediate care, intensive care unit admission) and in-hospital mortality occurring on day 2 or later. The association between receipt of antibiotic therapy and the primary outcome was assessed using propensity methods while adjusting for a broad set of potential confounders, including cotreatments.

Results

The cohort included 520 405 patients with COVID-19 (median [IQR] age, 66 [53-78] years; 266 186 [51.2%] male), including 92 708 Black patients (17.8%), 63 619 Hispanic patients (12.2%), and 304 649 White patients (58.5%); 279 656 patients (53.7%) had Medicare insurance. A total of 160 482 patients (30.8%) were treated with a CAP antibiotic regimen on day 1 of admission. The primary composite outcome was higher in the CAP group (20.8%) compared with the unexposed (no antibiotic) group (18.4%), but the difference did not meet the predefined criteria for clinical significance (ASD, 4.1%). Patients who received CAP antibiotics had higher odds of poor clinical outcomes (propensity matched-odds ratio [OR], 1.03 [95% CI, 1.01-1.05]; P = .003; inverse probability treatment weighted-OR, 1.03 [95% CI, 1.02-1.05]; P < .001; standardized mortality ratio weighted-OR, 1.10 [95% CI, 1.08-1.12]; P < .001).

Conclusions and Relevance

In this large cohort study of patients hospitalized with nonsevere COVID-19, there was no clinically meaningful difference in outcomes with early antibiotic treatment. Given the risks associated with unnecessary antibiotic treatment, these results argue against routine antibiotic use in this population.

Kinetic Patterns of Antibiotic Consumption in German Acute Care Hospitals from 2017 to 2023

Background: Antimicrobial consumption (AMC) patterns, besides prescribing behaviors, reflect the changing epidemiology of infectious diseases. Routine surveillance data have been used to investigate the development of AMC from 2017 to 2023 and the impact of COVID-19 within the context of the framing time periods. Methods: Data from 112 hospitals, continuously participating from 2017 to 2023 in the national surveillance system of hospital antimicrobial consumption based at the Robert Koch Institute, were analyzed according to the WHO ATC (Anatomical Therapeutic Chemical)/DDD (Defined Daily Dose) method and categorized according to the WHO AWaRe-classification. AMC was quantified by consumption density (CD) expressed in DDD/100 patient days (PD) and DDD/100 admissions (AD). The time period was subdivided into three phases: pre-pandemic phase (2017-2019), main pandemic phase (2020-2021) and transition phase (2022-2023). Linear regression models have been used to determine the presence of an overall trend, the change in intra-phasic trends and phase-specific mean consumption levels over time. Results: From 2017 to 2023 total antibiotic consumption decreased by 7% from 57.1 to 52.9 DDD/100 PD. Four main kinetic patterns emerged across different antibiotic classes: Pattern 1 displays a decreasing pre-pandemic trend, which slowed down throughout the pandemic and transition phase and was exhibited by second-generation cephalosporins and fluoroquinolones. Pattern 2 reveals a rising pre-pandemic trend, which decelerated in the pandemic phase and accelerated again in the transition phase and was expressed by aminopenicillins/beta-lactamase inhibitors, beta-lactamase sensitive pencillins, azithromycin and first-generation cephalosporins. Pattern 3 shows elevated mean consumption levels in the pandemic phase exhibited by carbapenems, glycopeptides, linezolid and third-generation cephalosporins. Pattern 4 reveals a rising trend throughout the pre-pandemic and pandemic phase, which reversed in the transition phase without achieving pre-pandemic levels and was expressed by beta-lactamase resistant penicillins, daptomycin, fosfomycin (parenteral) and ceftazidime/avibactam. Conclusions: Kinetic consumption patterns across different antibiotic classes might reflect COVID-19-related effects and associated changes in the epidemiology of co-circulating pathogens and health care supply. Broad-spectrum antibiotics with persisting elevated consumption levels throughout the transition phase require special attention and focused antimicrobial stewardship activities.

Early bacterial co-infections and ventilator-associated lower respiratory tract infections among intubated patients during the first and second COVID-19 waves: a European comparative cohort study

BACKGROUND

The management of severe SARS-CoV-2 pneumonia, alongside logistical constraints, evolved between the first and subsequent COVID-19 waves. This study aimed to compare the prevalence of early bacterial pulmonary co-infections and the incidence of ventilator-associated lower respiratory tract infections (VA-LRTI) across the first and second waves of the pandemic, and to characterize their microbiology.

METHODS

Latter part of a multicenter retrospective European cohort analysis conducted in 35 ICUs. Adult patients admitted for SARS-CoV-2 pneumonia and requiring invasive mechanical ventilation ≥ 48 h were consecutively included from both waves (February-May 2020 for period 1, October 2020-April 2021 for period 2). Co-infections were defined by bacterial isolation in respiratory secretions or blood cultures, or a positive pneumococcal urinary antigen test, within 48 h after intubation. VA-LRTI, including ventilator-associated tracheobronchitis (VAT) and ventilator-associated pneumonia (VAP), were diagnosed using clinical, radiological and quantitative microbiological criteria. The 28-day cumulative incidence of first VA-LRTI episodes was estimated using the Kalbfleisch and Prentice method, with co-infection prevalence and VA-LRTI incidence compared using multivariable logistic regression and Fine-and-Gray models, respectively.

RESULTS

The study included 1,154 patients (558 in period 1 and 596 in period 2). Co-infection prevalence significantly rose from 9.7% in period 1 to 14.9% in period 2 (adjusted odds ratio (95% confidence interval) 1.52 (1.04-2.22), p = 0.03). Gram-positive cocci dropped from 59 to 48% of co-infections between periods 1 and 2. The overall incidence of VA-LRTI was similar across periods (50.4% and 53.9%, adjusted sub distribution hazard ratio (sHR) 1.14 (0.96-1.35), p = 0.11), with a significant increase in VAP incidence in period 2 (36% to 44.8%, adjusted sHR 1.37 (1.12-1.66), p = 0.001), predominantly occurring within the initial 14 days after intubation, and a concurrent significant decrease in VAT incidence (14.3% to 9.1%, adjusted sHR 0.61 (0.42-0.88), p = 0.007). Gram-negative bacilli, led by Pseudomonas aeruginosa, Enterobacter spp., and Klebsiella spp., were responsible for 89% and 84% of VA-LRTI in periods 1 and 2, respectively.

CONCLUSIONS

Between the first and second COVID-19 waves, the prevalence of early bacterial pulmonary co-infections significantly increased among intubated patients. Although the overall incidence of VA-LRTI remained stable, there was a significant shift from VAT to VAP episodes.

National Trends in Antibiotic Prescribing for Adults Hospitalized With Coronavirus Disease 2019 and Other Viral Respiratory Infections

Background

Significant concerns have been raised regarding the overuse of antibiotics among patients hospitalized for coronavirus disease 2019 (COVID-19) and the broad impact of the pandemic on antimicrobial stewardship in acute care. We sought to compare potentially unnecessary antibiotic prescribing over time among patients admitted with symptomatic COVID-19 and non-COVID-19 viral acute respiratory tract infections (ARTIs).

Methods

We conducted a repeated cross-sectional analysis of the monthly antibiotic prescribing rate from March 2020 to December 2023 for COVID-19 admissions and from January 2019 to December 2023 for other viral ARTI admissions to 803 acute care hospitals in the United States that contributed data to the Premier Healthcare Database. Our primary outcome was the receipt of ≥1 dose of an antibiotic during the first 5 days of the admission. Secondary outcomes included days and duration of antibiotic therapy.

Results

This study included 513 698 COVID-19 and 106 932 non-COVID-19 viral ARTI admissions from March 2020 to December 2023. At the onset of the pandemic, >80% of patients admitted for COVID-19 received antibiotics, and antibiotic prescribing for other viral ARTIs increased to nearly 70%. Antibiotic prescribing for these viral infections declined over time, with prescribing for COVID-19 stabilizing around 35% in 2022-2023 and prescribing for other viral ARTIs returning to 2019 seasonal patterns in 2023, with average monthly prescribing around 50%.

Conclusions

Despite improvements since the early part of the COVID-19 pandemic, potentially unnecessary antibiotic prescribing for inpatients with COVID-19 and non-COVID-19 viral ARTIs remains an important antibiotic stewardship target.

Impact of Multidrug-Resistant Bacteria in a Cohort of COVID-19 Critically Ill Patients: Data from a Prospective Observational Study Conducted in a High-Antimicrobial-Resistance-Prevalence Center

Background: Bacterial superinfections are common complications during viral infections, but the impact of multidrug-resistant (MDR) pathogens in critically ill patients affected by coronavirus disease 2019 (COVID-19) is still debated. Methods: This is an observational, monocentric, and prospective study designed to investigate the incidence, risk factors, and outcomes of MDR bacterial superinfections in COVID-19 patients admitted to the intensive care unit (ICU). Results: A high incidence of superinfections (66%, 159/241) was observed: ventilator-associated pneumonia (VAP) (65%, 104/159) and bloodstream infection (BSI, 32%, 51/159) were the most common. Superinfections, Extra-Corporeal Membrane Oxygenation (ECMO) support, and prone positioning increased the risk of death five, four, and more-than-two times, respectively (OR = 5.431, IC 95%: 1.637-18.014; 4.462, IC 95%: 1.616-12.324 and 2.346, IC 95%: 1.127-4.883). MDR bacteria were identified in 61% of patients with superinfection, with a cumulative incidence of 37.2% at day 14. Carbapenem-resistant Acinetobacter baumannii (CR-AB) and CR-Klebsiella pneumoniae (CR-KP) were the most common causative agents (24.3% and 13.7%). CR-AB was found to significantly increase both ICU and in-hospital mortality (76.4% and 78.2%), whereas CR-KP had no direct impact on mortality. Prior rectal colonization (p < 0.0001), mechanical ventilation (p = 0.0017), a prolonged ICU stay (p < 0.0001), the use of iNO (p = 0.0082), vasopressors (p = 0.0025), curarization (p = 0.0004), and prone positioning (p = 0.0084) were found to be risk factors for CR-AB. Conclusions: Critically ill COVID-19 patients are at high risk of developing MDR superinfection. While CR-KP had no direct impact on mortality, CR-AB appeared to increase ICU and in-hospital mortality.

Bacterial Infections, Trends, and Resistance Patterns in the Time of the COVID-19 Pandemic in Romania-A Systematic Review

Background: The COVID-19 pandemic has intensified concerns over bacterial infections and antimicrobial resistance, particularly in Romania. This systematic review explores bacterial infection patterns and resistance during the pandemic to address critical gaps in knowledge. Methods: A systematic review, following PRISMA guidelines, was conducted using databases such as PubMed and Scopus, focusing on studies of bacterial infections from 2020 to 2022. Articles on bacterial infections in Romanian patients during the pandemic were analyzed for demographic data, bacterial trends, and resistance profiles. Results: A total of 87 studies were included, detailing over 20,000 cases of bacterial infections. The review found that Gram-negative bacteria, particularly Escherichia coli and Klebsiella pneumoniae, were the most frequently identified pathogens, alongside Gram-positive Staphylococcus aureus and Enterococcus spp. Multidrug resistance (MDR) was noted in 24% of the reported strains, with common resistance to carbapenems and cephalosporins. Conclusions: The pandemic has amplified the complexity of managing bacterial infections, particularly in critically ill patients. The rise in MDR bacteria underscores the need for stringent antimicrobial stewardship and infection control measures. Continuous monitoring of bacterial trends and resistance profiles will be essential to improve treatment strategies in post-pandemic healthcare settings.

Prevalence and Predictors of Concomitant Bacterial Infections in Patients With Respiratory Viruses in Ontario: A Cohort Study

Background

To investigate the prevalence of concomitant bacterial infection across common viral infections.

Methods

This population-based cohort study included patients infected with influenza A and B (FLUA, FLUB) and respiratory syncytial virus (RSV) in Ontario between 2017 and 2019 and patients with SARS-CoV-2 between 2020 and 2021. Specific bacteria present in concomitant infections were identified. Concomitant infections were further classified into different categories (eg, coinfection -2 to +2 days from viral infection and secondary infection >2 days after viral infection). We used logistic regression models to estimate the odds of bacterial infections for FLUA, FLUB, and RSV relative to SARS-CoV-2 while adjusting for confounders.

Results

A total of 4230 (0.5%, 885 004) viral cases had concomitant bacterial infections, encompassing 422 of FLUB (4.7%, 8891), 861 of FLUA (3.9%, 22 313), 428 of RSV (3.4%, 12 774), and 2519 of COVID-19 (0.3%, 841 026). The most prevalent species causing concomitant bacterial infection were Staphylococcus aureus, Streptococcus pyogenes, and Pseudomonas aeruginosa. When compared with SARS-CoV-2, the adjusted odds ratio for bacterial infection was 1.69 (95% CI, 1.48-1.93) for FLUA, 2.30 (95% CI, 1.97-2.69) for FLUB, and 1.56 (95% CI, 1.33-1.82) for RSV. The adjusted odds of coinfection in patients with SARS-CoV-2 were lower but higher for secondary infection as compared with the other viruses.

Conclusions

A higher prevalence and risk of concomitant bacterial infection were found in FLUA, FLUB, and RSV as compared with SARS-CoV-2, although this is largely driven by coinfections. Ongoing surveillance efforts are needed to compare the risk of concomitant infections during periods when these viruses are cocirculating.

A scoping review of bacterial resistance among inpatients amidst the COVID-19 pandemic

OBJECTIVES

The COVID-19 pandemic disrupted antimicrobial stewardship and infection prevention operations worldwide, raising concerns for an acceleration of antimicrobial resistance (AMR). Therefore, we aimed to define the scope of peer reviewed research comparing AMR in inpatient bacterial clinical cultures before and after the start of the COVID-19 pandemic.

METHODS

We conducted a scoping review and searched PubMed, Scopus, and Web of Science through 15 June 2023. Our inclusion criteria were: (1) English language, (2) primary evidence, (3) peer-reviewed, (4) clinical culture data from humans, (5) AMR data for at least one bacterial order/species, (6) inpatient setting, (7) use of statistical testing to evaluate AMR data before and during the COVID-19 pandemic. Reviewers extracted country, study design, type of analysis, study period, setting and population, number of positive cultures or isolates, culture type(s), method of AMR analysis, organisms, and AMR results. Study results were organised by organism and antibiotic class or resistance mechanism. AMR results are also summarised by individual study and across all studies.

RESULTS

In total, 4805 articles were identified with 55 papers meeting inclusion criteria. Acinetobacter baumannii, Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Staphylococcus aureus were the most commonly studied organisms. There were 464 bacterial AMR results across all studies with 82 (18%) increase, 71 (15%) decrease, and 311 (67%) no change results.

CONCLUSIONS

The literature examining the impact of COVID-19 on AMR among inpatients is diverse with most results reflecting no change pre/post pandemic. Ongoing inquiry is needed into evolving patterns in AMR post COVID-19.

Antimicrobial use before and during COVID-19: data from 108 Veterans Affairs medical centers

Objective

Inpatient antibiotic use increased during the early phases of the COVID-19 pandemic. We sought to determine whether these changes persisted in persons with and without COVID-19 infection.

Design

Retrospective cohort analysis.

Setting

108 Veterans Affairs (VA) facilities.

Patients

Persons receiving acute inpatient care from January 2016 to October 2022.

Methods

Data on antibacterial use, patient days present, and COVID-19 care were extracted from the VA Corporate Data Warehouse. Days of therapy (DOT) per 1000 days present (DP) were calculated and stratified by Centers for Disease Control and Prevention-defined antibiotic classes.

Results

Antibiotic use increased from 534 DOT/1000 DP in 11/2019-2/2020 to 588 DOT/1000 DP in 3/2020-4/2020. Subsequently, antibiotic use decreased such that total DOT/1000 DP was 2% less in 2020 as a whole than in 2019. Driven by treatment for community acquired pneumonia, antibiotic use was 30% higher in persons with COVID-19 than in uninfected persons in 3/2020-4/2020, but only 4% higher for the remainder of 2020. In 2022 system-wide antibiotic use was 9% less in persons with COVID-19; however, antibiotic use remained higher in persons with COVID-19 in 25% of facilities.

Discussion

Although antibiotic use increased during the early phases of the COVID-19 pandemic, overall use subsequently decreased to below previous baseline levels and, in 2022, was less in persons with COVID-19 than in persons without COVID-19. However, further work needs to be done to address variances across facilities and to determine whether current levels of antibiotic use in persons with COVID-19 are justified.

Bloodstream infections in the era of the COVID-19 pandemic: Changing epidemiology of antimicrobial resistance in the intensive care unit

The Coronavirus disease 2019 (COVID-19) pandemic increased the burden of critically ill patients who required hospitalization in the intensive care unit (ICU). Bacterial and fungal co-infections, including bloodstream infections (BSIs), increased significantly in ICU patients with COVID-19; this had a significant negative impact on patient outcomes. Reported data pertaining to BSI episodes from the ICU setting during the COVID-19 pandemic were collected and analyzed for this narrative review. We searched the PubMed database for articles published between March 2020 and October 2023; the terms "COVID-19" AND "bloodstream infections" AND "ICU" were used for the search. A total of 778 articles were retrieved; however, only 27 were exclusively related to BSIs in ICU patients with COVID-19. Data pertaining to the epidemiological characteristics, risk factors, characteristics of bacterial and fungal BSIs, patterns of antimicrobial resistance, and comparisons between ICU and non-ICU patients during and before the COVID-19 pandemic were obtained. Data on antimicrobial stewardship and infection-control policies were also included. The rates of BSI were found to have increased among ICU patients with COVID-19 than in non-COVID-19 patients and those admitted during the pre-pandemic period. Male gender, 60-70 years of age, increased body mass index, high Sequential Organ Failure Assessment scores at admission, prolonged hospital and ICU stay, use of central lines, invasive ventilation, and receipt of extracorporeal membrane oxygenation were all defined as risk factors for BSI. The use of immune modulators for COVID-19 appeared to increase the risk of BSI; however, the available data are conflicting. Overall, Enterococci, Acinetobacter baumannii, and Candida spp. emerged as prominent infecting organisms during the pandemic; along with Enterobacterales and Pseudomonas aeruginosa they had a significant impact on mortality. Multidrug-resistant organisms prevailed in the ICU, especially if antimicrobial resistance was established before the COVID-19 pandemic and were significantly associated with increased mortality rates. The unnecessary and widespread use of antibiotics further increased the prevalence of multidrug-resistant organisms during COVID-19. Notably, the data indicated a significant increase in contaminants in blood cultures; this highlighted the decline in compliance with infection-control measures, especially during the initial waves of the pandemic. The implementation of infection-control policies along with antibiotic stewardship succeeded in significantly reducing the rates of blood contamination and BSI pathogens. BSIs considerably worsened outcomes in patients with COVID-19 who were admitted to ICUs. Further studies are needed to evaluate adequate preventive and control measures that may increase preparedness for the future.

Nasal carriage of virulent and multidrug resistant Staphylococcus aureus: a possible comorbidity of COVID-19

BACKGROUND

Staphylococcus aureus (S. aureus) associated with COVID-19 has not been well documented. This cross-sectional study evaluated the association between nasal S. aureus carriage and COVID-19.

METHODS AND RESULTS

Nasopharyngeal samples were collected from 391 participants presenting for COVID-19 test in Lagos, Nigeria, and S. aureus was isolated from the samples. Antimicrobial susceptibility test was done by disc diffusion method. All S. aureus isolates were screened for the presence of mecA, panton-valentine leucocidin (PVL) and toxic shock syndrome toxin (TSST) virulence genes by polymerase chain reaction. Staphylococcal protein A (spa) typing was conducted for all the isolates. Participants with COVID-19 had double the prevalence of S. aureus (42.86%) compared to those who tested negative (20.54%). A significant association was seen between S. aureus nasal carriage and COVID-19 (p = 0.004). Antimicrobial sensitivity results showed resistance to oxacillin (100%), cefoxitin (53%), and vancomycin (98.7%). However, only 41% of the isolates harbored the mecA gene, with SCCmecV being the most common SCCmec type. There was no association between the carriage of virulence genes and COVID-19. A total of 23 Spa types were detected, with t13249 and t095 being the two most common spa types.

CONCLUSION

This study examined the association between nasal S. aureus carriage and SARS-COV-2 infection. Further research is required to fully explore the implications of S. aureus co-infection with COVID-19.

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

BACKGROUND

As 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.

METHODS

In 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.

RESULTS

The 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.

CONCLUSIONS

Bacterial 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.

Burden of infectious diseases and bacterial antimicrobial resistance in China: a systematic analysis for the global burden of disease study 2019

BACKGROUND

Infectious diseases and antimicrobial resistance (AMR) has become pressing concerns in China. We aimed to comprehensively investigate the burden of them.

METHODS

Data on infectious diseases and AMR were collected by the Global Antimicrobial Resistance Burden study 2019. Multinomial network meta-regression, logistic regression, and ensemble Spatiotemporal Gaussian process regression were used to fit the number and rate in DisMod-MR 2.1 modelling framework. We reported the number and rates of the disease burdens of 12 infectious syndromes by age and sex; described the burden caused by 43 pathogens; estimated the AMR burden of 22 bacteria and bacteria-antibiotics combinations.

FINDINGS

There were an estimated 1.3 million (95% uncertainty intervals, UI 0.8-1.9) infection-related deaths, accounting for 12.1% of the total deaths in China 2019. Males were 1.5 times more affected than females. Bloodstream infections (BSIs) were most lethal infectious syndrome, associating with 521,392 deaths (286,307-870,583), followed by lower respiratory infections (373,175), and peritoneal and intra-abdominal infections (152,087). These five leading pathogens were S aureus, A baumannii, E coli, S pneumoniae, and E spp., which were associated with 41.2% (502,658/1,218,693) of all infection-related deaths. The pathogens of different infectious syndromes exhibited significant heterogeneity. In 2019, more than 600 thousand deaths were associated with AMR, including 145 thousand deaths attributable to AMR. The top 3 AMR attributable to death were carbapenems-resistance A baumannii (18,143), methicillin-resistance S aureus (16,933) and third-generation cephalosporins-resistance E coli (8032).

INTERPRETATION

Infectious diseases and bacterial antimicrobial resistance were serious threat to public health in China, related to 1.3 million and more than 600 thousand deaths per-year, respectively. Antimicrobial stewardship was urgent.

FUNDING

This work was supported by National Natural Science Foundation of China (82270626); China Mega-Project for Infectious Diseases (2017ZX10203202, 2013ZX10002005); the Project of Beijing Science and Technology Committee (Z191100007619037).

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.

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.

Prevalence of antibiotic prescribing in COVID-19 patients in China and other low- and middle-income countries during the pandemic (December 2019-March 2021): a systematic review and meta-analysis

OBJECTIVES

Low- and middle-income countries (LMICs) are particularly vulnerable to the threat of antimicrobial resistance (AMR). Use of antibiotics to treat COVID-19 patients during the pandemic may have contributed to increasing the AMR burden, but systematic evidence is lacking.

METHODS

We searched Web of Science, EMBASE, PubMed, China National Knowledge Infrastructure (CNKI) and VIP databases from 1 December 2019 to 31 March 2021. Interventional and observation studies across all settings that reported antibiotic use in at least 10 COVID-19 patients were included. We restricted publications to English and Chinese languages. Screening and data extraction were undertaken by at least two independent reviewers. Results were synthesized using random-effects meta-analyses. Subgroup analyses and meta-regression were used to explore heterogeneities. This review was registered with PROSPERO (CRD42021288291).

RESULTS

We included 284 studies involving 210 611 participants in 19 countries. The antibiotic prescribing rates (APRs) in COVID-19 inpatients were 71.7% (95% CI 66.7%-76.5%) in China and 86.5% (77.1%-93.9%) in other LMICs, respectively. APR was lower in mild/moderate cases in China [66.9% (57.9%-75.4%) compared with 91.8% (71.4%-100%) in other LMICs]. High APRs were found among pregnant women and the elderly in China. Disparities in APRs of other patient groups were identified. In studies reporting bacterial infections, the prevalence was 17.3% (10.0%-25.9%) in China and 24.9% (0.1%-68.8%) in other LMICs. Several antibiotics on the WHO 'Watch' and 'Reserve' lists were prescribed frequently in LMICs.

CONCLUSIONS

Inappropriate antibiotic use and high prevalence of antibiotic prescribing were found in COVID-19 inpatients in many LMICs.

The impact of immunosuppressive therapy on secondary infections and antimicrobial use in COVID-19 inpatients: a retrospective cohort study

BACKGROUND

Immunosuppressive therapies have become a cornerstone of the management of severe COVID-19. The impact of these therapies on secondary infections and antimicrobial prescribing remains unclear. We sought to assess antimicrobial use and the incidence of bacterial and fungal infections in patients with severe COVID-19, and to explore their associations with receipt of immunosuppressive therapies.

METHODS

Our retrospective cohort study included 715 hospitalised, adult patients with severe COVID-19 admitted to St George's Hospital, London, UK, during the first UK pandemic wave (1st March-10th June 2020). Co-infections (occurring within 48 h of admission) and secondary infections (≥ 48 h) were defined as a positive microbiological culture with supporting clinical, radiological or laboratory data to suggest true infection. Cox regression models with time-dependent covariates were used to explore the association between immunosuppressant use and secondary infection.

RESULTS

Microbiologically confirmed co-infection occurred in 4.2% (n = 30) and secondary infection in 9.3% (n = 66) of the cohort (n = 715) and were associated with in-hospital mortality (48% vs 35%, OR 1.8, 95%CI 1.1-2.7, p = 0.01). Respiratory (n = 41, 39%) and bloodstream infections (n = 38, 36%) predominated, with primarily Gram-negative pathogens. 606 (84.7%) patients received an antimicrobial, amounting to 742 days of therapy per 1000 patient-days (DOTs). In multivariable models, receipt of high-dose steroids (≥ 30 mg prednisolone or equivalent) or tocilizumab was significantly associated with increased antimicrobial consumption (+ 5.5 DOTs, 95%CI 3.4-7.7 days) but not secondary infection (HR 0.56, 95%CI 0.26-1.18).

CONCLUSIONS

Bacterial and fungal infections in severe COVID-19 were uncommon. Receipt of steroids or tocilizumab was independently associated with antimicrobial consumption despite its lack of association with secondary infection. These findings should galvanise efforts to promote antimicrobial stewardship in patients with COVID-19.

Antibiotic Use Among Hospitalized Patients With COVID-19 in the United States, March 2020-June 2022

We conducted a retrospective study to describe antibiotic use among US adults hospitalized with a COVID-19 diagnosis. Despite a decrease in overall antibiotic use, most patients hospitalized with COVID-19 received antibiotics on admission (88.1%) regardless of critical care status, highlighting that more efforts are needed to optimize antibiotic therapy.

Secondary and Co-Infections in Hospitalized COVID-19 Patients: A Multicenter Cross-Sectional Study in Malaysia

Bacterial and fungal secondary and co-infections are commonly identified with viral respiratory infections. This study was undertaken to determine the incidence and factors associated with bacterial and fungal infections in patients with COVID-19 as well as antibiotics prescription patterns within the first and second waves of the outbreak in Malaysia. Clinical records of 3532 COVID-19 patients admitted to hospitals in Malaysia between 4 February and 4 August 2020 were analyzed. Co-morbidities, clinical features, investigations, treatment, and complications were captured using the REDCap database. Culture and sensitivity test results were retrieved from the WHONET database. Univariate and multivariate regression analyses were used to identify associated determinants. A total of 161 types of bacterial and fungal infections were found in 81 patients, i.e., 2.3%. The most common bacterial cultures were Gram-negative, i.e., Pseudomonas aeruginosa (15.3%) and Klebsiella pneumoniae (13.9%). The most common fungal isolate was Candida albicans (41.2%). Augmentin, ceftriaxone, tazocin, meropenem, and azithromycin were the five most frequently prescribed antibiotics. The latter four were classified under the "Watch" category in the WHO AwaRe list. Our data showed that bacterial and fungal secondary and co-infections were frequently found in severely ill COVID-19 patients and were associated with a higher mortality rate.

Prevalence and Impact on Mortality of Colonization and Super-Infection by Carbapenem-Resistant Gram-Negative Organisms in COVID-19 Hospitalized Patients

BACKGROUND

The relationship between superinfection by multidrug-resistant Gram-negative bacteria and mortality among SARS-CoV-2 hospitalized patients is still unclear. Carbapenem-resistant Acinetobacter baumannii and carbapenemase-producing Enterobacterales are among the most frequently isolated species when it comes to hospital-acquired superinfections among SARS-CoV-2 patients.

METHODS

Herein, a retrospective study was carried out using data from adult patients hospitalized for COVID-19. The interaction between in-hospital mortality and rectal carriage and superinfection by carbapenemase-producing Enterobacterales and/or carbapenem-resistant Acinetobacter baumannii was assessed.

RESULTS

The incidence of KPC-producing Klebsiella pneumoniae and/or carbapenem-resistant Acinetobacter baumannii rectal carriage was 30%. Bloodstream infection and/or pneumonia due to KPC-producing Klebsiella pneumoniae and/or carbapenem-resistant Acinetobacter baumannii occurred in 20% of patients. A higher Charlson comorbidity index (OR 1.41, 95% CI 1.24-1.59), being submitted to invasive mechanical ventilation/ECMO ≥ 96 h (OR 6.34, 95% CI 3.18-12.62), being treated with systemic corticosteroids (OR 4.67, 95% CI 2.43-9.05) and having lymphopenia at the time of admission (OR 0.54, 95% CI 0.40-0.72) were the features most strongly associated with in-hospital mortality.

CONCLUSIONS

Although KPC-producing Klebsiella pneumoniae and/or carbapenem-resistant Acinetobacter baumannii rectal carriage, and/or bloodstream infection/pneumonia were diagnosed in a remarkable percentage of COVID-19 patients, their impact on in-hospital mortality was not significant. Further studies are needed to assess the burden of antimicrobial resistance as a legacy of COVID-19 in order to identify future prevention opportunities.

Protocol for studying co-infection between SARS-CoV-2 and Staphylococcus aureus in vitro

Bacterial co-infection is one of the most common complications of SARS CoV-2 infection. Here, we present a protocol for the in vitro study of co-infection between SARS CoV-2 and Staphylococcus aureus. We describe steps for quantifying viral and bacterial replication kinetics in the same sample, with the optional extraction of host RNA and proteins. This protocol is applicable to many viral and bacterial strains and can be performed in different cell types. For complete details on the use and execution of this protocol, please refer to Goncheva et al.1.

Bloodstream Infections in Intensive Care Unit during Four Consecutive SARS-CoV-2 Pandemic Waves

Critically ill COVID-19 patients are at an increased risk of bloodstream infections (BSIs). We performed a retrospective observational single-center study on COVID-19 patients admitted to intensive care unit (ICU) to assess the incidence of BSIs in four consecutive periods: 21 February-31 July 2020 (W1), 1 August 2020-31 January 2021 (W2), 1 February-30 September 2021 (W3) and 1 October 2021 and 30 April 2022 (W4). BSIs that occurred 48 h after ICU admission were included. The crude incidence of BSIs was estimated by means of Poisson distribution normalized to 1000 patient-days. A total of 404 critically ill COVID-19 patients were admitted to ICU, of whom 284 (61%) developed at least one episode of BSI with an overall crude incidence of 87 events every 1000 patient-days (95% CI 77-98) without a significant difference in consecutive epidemic periods (p = 0.357). Gram-positive bacteria were the most frequent etiological agents of BSIs, contributing to 74.6% episodes. A progressive decrease in BSIs due to Enterococcus spp. was observed (W1 57.4%, W2 43.7%, W3 35.7% and W4 32.7%; p = 0.004). The incidence of BSIs remained stable during different epidemic periods. Enterococcus spp. prevalence was significantly reduced, although still accounted for one third of BSIs in more recent epidemic periods.

Characteristics and risk factors of secondary bacterial infections in COVID-19 patients

Objective

To describe the characteristics and find out risk factors of COVID-19 patients infected with different categories of bacteria.

Design

Case-control.

Methods

We conducted a retrospective study including 129 COVID-19 patients admitted to a tertiary hospital between October 13, 2022 and December 31, 2022. Patients' data were collected from the hospital information system. Patients were classified as having or not having confirmed secondary bacterial infections, or gram-positive and gram-negative bacterial infections for analysis. Categories and sources of isolated bacteria, characteristics of the patients, and the risk factors for developing secondary bacterial infections were analyzed.

Results

Gram-negative bacteria accounted for the majority of secondary bacterial infections of the included patients. Critical type of COVID-19 (OR = 12.98, 95%CI 3.43∼49.18, p < 0.001), invasive therapy (OR = 9.96, 95%CI 3.01∼32.95, p < 0.001), and previous antibiotics use (OR = 17.23, 95%CI 1.38∼215.69, p = 0.027) were independent risk factors of secondary bacterial infections in COVID-19 patients. Ceftriaxone/cefotaxime use (OR = 15.45, 95%CI 2.72∼87.79, p = 0.002) was associated with gram-positive bacterial infections while age over 70 (OR = 3.30, 95%CI 1.06∼10.26, p = 0.039), invasive therapy (OR = 4.68, 95%CI 1.22∼17.93, p = 0.024), and carbapenems use (OR = 8.48, 95%CI 2.17∼33.15, p = 0.002) were associated with gram-negative bacterial infections.

Conclusions

Critical patients with invasive therapy and previous antibiotics use should be cautious with secondary bacterial infections. Third-generation cephalosporins and carbapenems should be used carefully because both are risk factors for gram-positive or gram-negative bacterial infections.

Xuanfei Baidu decoction in the treatment of coronavirus disease 2019 (COVID-19): Efficacy and potential mechanisms

Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has spread worldwide and become a major global public health concern. Although novel investigational COVID-19 antiviral candidates such as the Pfizer agent PAXLOVID™, molnupiravir, baricitinib, remdesivir, and favipiravir are currently used to treat patients with COVID-19, there is still a critical need for the development of additional treatments, as the recommended therapeutic options are frequently ineffective against SARS-CoV-2. The efficacy and safety of vaccines remain uncertain, particularly with the emergence of several variants. All 10 versions of the National Health Commission's diagnosis and treatment guidelines for COVID-19 recommend using traditional Chinese medicine. Xuanfei Baidu Decoction (XFBD) is one of the "three Chinese medicines and three Chinese prescriptions" recommended for COVID-19. This review summarizes the clinical evidence and potential mechanisms of action of XFBD for COVID-19 treatment. With XFBD, patients with COVID-19 experience improved clinical symptoms, shorter hospital stay, prevention of the progression of their symptoms from mild to moderate and severe symptoms, and reduced mortality in critically ill patients. The mechanisms of action may be associated with its direct antiviral, anti-inflammatory, immunomodulatory, antioxidative, and antimicrobial properties. High-quality clinical and experimental studies are needed to further explore the clinical efficacy and underlying mechanisms of XFBD in COVID-19 treatment.

Antibiotic-Resistant ESKAPE Pathogens and COVID-19: The Pandemic beyond the Pandemic

Antibacterial resistance is a renewed public health plague in modern times, and the COVID-19 pandemic has rekindled this problem. Changes in antibiotic prescribing behavior, misinformation, financial hardship, environmental impact, and governance gaps have generally enhanced the misuse and improper access to antibiotics during the COVID-19 pandemic. These determinants, intersected with antibacterial resistance in the current pandemic, may amplify the potential for a future antibacterial resistance pandemic. The occurrence of infections with multidrug-resistant (MDR), extensively drug-resistant (XDR), difficult-to-treat drug-resistant (DTR), carbapenem-resistant (CR), and pan-drug-resistant (PDR) bacteria is still increasing. The aim of this review is to highlight the state of the art of antibacterial resistance worldwide, focusing on the most important pathogens, namely Enterobacterales, Acinetobacter baumannii, and Klebsiella pneumoniae, and their resistance to the most common antibiotics.

Diagnostic accuracy of the BioFire® FilmArray® pneumonia panel in COVID-19 patients with ventilator-associated pneumonia

BACKGROUND

Ventilator-Associated pneumonia (VAP) is one of the leading causes of morbidity and mortality in critically ill COVID-19 patients in lower-and-middle-income settings, where timely access to emergency care and accurate diagnostic testing is not widely available. Therefore, rapid microbiological diagnosis is essential to improve effective therapy delivery to affected individuals, preventing adverse outcomes and reducing antimicrobial resistance.

METHODS

We conducted a cross-sectional study of patients with suspected VAP and COVID-19, evaluating the diagnostic performance of the BioFire® FilmArray® Pneumonia Panel (FA-PP). Respiratory secretion samples underwent standard microbiological culture and FA-PP assays, and the results were compared.

RESULTS

We included 252 samples. The traditional culture method detected 141 microorganisms, and FA-PP detected 277, resulting in a sensitivity of 95% and specificity of 60%, with a positive predictive value of 68% and negative predictive value of 93%. In samples with high levels of genetic material (> 10^5 copies/mL), the panel had a sensitivity of 94% and specificity of 86%. In addition, 40% of the culture-negative samples had positive FA-PP® results, of which 35% had > 10^5 copies/mL of genetic material. The most prevalent bacteria were Gram-negative bacilli, followed by Gram-positive cocci. The panel identified 98 genes associated with antimicrobial resistance, predominantly extended-spectrum beta-lactamases (28%).

CONCLUSION

The FA-PP is a sensitive assay for identifying bacteria causing VAP in patients with COVID-19, with a greater capacity to detect bacteria than the conventional method. The timely microbiological recognition offered by this panel could lead to optimized decision-making processes, earlier tailored treatment initiation, and improved antibiotic stewardship practices.

Prevalence and Epidemiological and Clinical Features of Bacterial Infections in a Large Cohort of Patients Hospitalized for COVID-19 in Southern Italy: A Multicenter Study

BACKGROUND

The aim of this study was to evaluate the prevalence of bacterial infections and antimicrobial prescriptions in a large cohort of COVID-19 patients and to identify the independent predictors of infection and antibiotic prescription.

METHODS

All consecutive patients hospitalized for COVID-19 from March 2020 to May 2021 at 1 of the 17 centers participating in the study were included. All subjects showing a clinical presentation consistent with a bacterial infection with microbiological confirmation (documented infection), and/or a procalcitonin value >1 ng/mL (suspected infection) were considered as having a coinfection (if present at admission) or a superinfection (if acquired after at least 48 h of hospital stay).

RESULTS

During the study period, of the 1993 patients, 42 (2.1%) presented with a microbiologically documented infection, including 17 coinfections and 25 superinfections, and 267 (13.2%) a suspected infection. A total of 478 subjects (24.5%) received an antibacterial treatment other than macrolides. No independent predictors of confirmed or suspected bacterial infection were identified. On the contrary, being hospitalized during the second wave of the pandemic (OR 1.35, 95% CI 1.18-1.97, p = 0.001), having a SOFA score ≥3 (OR 2.05, 95% CI 1.53-2.75, p < 0.001), a severe or critical disease (OR 1.66, 95% CI 1.24-2.23, p < 0.001), and a high white blood cell count (OR 1.03, 95% CI 1.004-1.06, p = 0.023) were all independently related to having received an antimicrobial prescription.

CONCLUSIONS

Our study reported a high rate of antimicrobial prescriptions despite a limited number of documented or suspected bacterial infections among the large cohort of hospitalized COVID-19 patients.

Exploring novel aryl/heteroaryl-isosteres of phenylthiazole against multidrug-resistant bacteria

Antimicrobial resistance has become a concern as a worldwide threat. A novel scaffold of phenylthiazoles was recently evaluated against multidrug-resistant Staphylococci to control the emergence and spread of antimicrobial resistance, showing good results. Several structural modifications are needed based on the structure-activity relationships (SARs) of this new antibiotic class. Previous studies revealed the existence of two key structural features essential for the antibacterial activity, the guanidine head and lipophilic tail. In this study, a new series of twenty-three phenylthiazole derivatives were synthesized utilizing the Suzuki coupling reaction to explore the lipophilic part. The in vitro antibacterial activity was evaluated against a range of clinical isolates. The three most promising compounds, 7d, 15d and 17d, with potent MIC values against MRSA USA300 were selected for further antimicrobial evaluation. The tested compounds exhibited potent results against the tested MSSA, MRSA, and VRSA strains (concentration: 0.5 to 4 μg mL-1). Compound 15d inhibited MRSA USA400 at a concentration of 0.5 μg mL-1 (one-fold more potent than vancomycin) and showed low MIC values against ten clinical isolates, including linezolid-resistant strain MRSA NRS119 and three vancomycin-resistant isolates VRSA 9/10/12. Moreover, compound 15d retained its potent antibacterial activity using the in vivo model by the burden reduction of MRSA USA300 in skin-infected mice. The tested compounds also showed good toxicity profiles and were found to be highly tolerable to Caco-2 cells at concentrations of up to 16 μg mL-1, with 100% of the cells remaining viable.

Impact of COVID-19 pandemic on blood culture practices and bacteremia epidemiology

The COVID-19 pandemic has strongly impacted healthcare settings. We assess changes in blood culture practices and results during the COVID-19 era. All blood culture vials processed between January 1, 2017, and December 31, 2020, by 3 clinical laboratories were included. A baseline period from January 1, 2017 to December 31, 2019, was compared to the year 2020. COVID-19 "waves" were defined as follows: "wave 1" from March 16 to May 10, 2020, and "wave 2" from October 29 to December 14, 2020. A mean of 143.5 and 158.6 vials per day were processed in 2019 and 2020 respectively. Up to 300 and 220 vials per day were processed during waves 1 and 2. Among positive vials, a higher rate of contaminant was noticed during wave 1 (55.9% vs 45.0%; P < 0.0001) and interwave (46.0% vs 38.6%; P < 0.0001) in comparison to previous years. The prevalence of contaminants returned to the baseline level during wave 2. Streptococcus pneumonia prevalence fell in 2020 in comparison to the baseline (0.4% vs 1.4%; P < 0.0001). The COVID-19 pandemic was associated with an increase in the number of blood culture vials processed, the rate of contaminants, and a fall in the number of pneumococcal bloodstream infections.

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.

Incidence of bloodstream infections due to multidrug-resistant pathogens in ordinary wards and intensive care units before and during the COVID-19 pandemic: a real-life, retrospective observational study

PURPOSE

SARS-COV-2 pandemic led to antibiotic overprescription and unprecedented stress on healthcare systems worldwide. Knowing the comparative incident risk of bloodstream infection due to multidrug-resistant pathogens in COVID ordinary wards and intensive care-units may give insights into the impact of COVID-19 on antimicrobial resistance.

METHODS

Single-center observational data extracted from a computerized dataset were used to identify all patients who underwent blood cultures from January 1, 2018 to May 15, 2021. Pathogen-specific incidence rates were compared according to the time of admission, patient's COVID status and ward type.

RESULTS

Among 14,884 patients for whom at least one blood culture was obtained, a total of 2534 were diagnosed with HA-BSI. Compared to both pre-pandemic and COVID-negative wards, HA-BSI due to S. aureus and Acinetobacter spp. (respectively 0.3 [95% CI 0.21-0.32] and 0.11 [0.08-0.16] new infections per 100 patient-days) showed significantly higher incidence rates, peaking in the COVID-ICU setting. Conversely, E. coli incident risk was 48% lower in COVID-positive vs COVID-negative settings (IRR 0.53 [0.34-0.77]). Among COVID + patients, 48% (n = 38/79) of S. aureus isolates were resistant to methicillin and 40% (n = 10/25) of K. pneumoniae isolates were resistant to carbapenems.

CONCLUSIONS

The data presented here indicate that the spectrum of pathogens causing BSI in ordinary wards and intensive care units varied during the pandemic, with the greatest shift experienced by COVID-ICUs. Antimicrobial resistance of selected high-priority bacteria was high in COVID positive settings.

The Staphylococcus aureus protein IsdA increases SARS CoV-2 replication by modulating JAK-STAT signaling

The Severe Acute Respiratory Syndrome Coronavirus 2 (CoV-2) pandemic has affected millions globally. A significant complication of CoV-2 infection is secondary bacterial co-infection, as seen in approximately 25% of severe cases. The most common organism isolated during co-infection is Staphylococcus aureus. Here, we describe the development of an in vitro co-infection model where both viral and bacterial replication kinetics may be examined. We demonstrate CoV-2 infection does not alter bacterial interactions with host epithelial cells. In contrast, S. aureus enhances CoV-2 replication by 10- to 15-fold. We identify this pro-viral activity is due to the S. aureus iron-regulated surface determinant A (IsdA) protein and demonstrate IsdA modifies host transcription. We find that IsdA alters Janus Kinase - Signal Transducer and Activator of Transcription (JAK-STAT) signaling, by affecting JAK2-STAT3 levels, ultimately leading to increased viral replication. These findings provide key insight into the molecular interactions between host cells, CoV-2 and S. aureus during co-infection.

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

Background

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

Methods

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

Results

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

Conclusion

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

Epidemiology of Gram-negative bacteria during coronavirus disease 2019. What is the real pandemic?

PURPOSE OF REVIEW

Bacterial infections play a key role in hospital outcomes during the coronavirus disease 2019 (COVID-19) pandemic. Nonetheless, the global impact on the epidemiology of Gram-negative bacteria (GNB) and antibiotic resistance has not been clearly established.

RECENT FINDINGS

Multiple limitations exist in the current literature, in that substantial variability was observed with regard to methodology. Notwithstanding the heterogeneity, the evidence suggests that the COVID-19 pandemic had a substantial negative impact on global epidemiology with an increase in hospital-onset infections, associated with GNB. Similarly, an alarming increase in resistant GNB compared to prepandemic rates, was apparent. This was most evident for carbapenemase-producing Klebsiella pneumoniae (bloodstream infections), carbapenem-resistant Pseudomonas aeruginosa (ventilator-associated pneumonia), and carbapenem-resistant Acinetobacter baumannii (all infections). Significant variations were most apparent in the large, system-wide regional or national comparative assessments, vs. single-centre studies. Categorizing concurrent bacteria as co- or secondary-infections may be paramount to optimize standard of care.

SUMMARY

The data from most studies signal the probability that COVID-19 accelerated resistance. However, multiple limitations intrinsic to interpretation of current COVID-19 data, prevents accurately quantifying collateral damage on the global epidemiology and antibiotic resistance amongst GNB. It is likely to be substantial and renewed efforts to limit further increases is warranted.

Coronavirus disease 2019 (COVID-19) associated bacterial coinfection: Incidence, diagnosis and treatment

Coronavirus disease 2019 (COVID-19) emerged as a pandemic that spread rapidly around the world, causing nearly 500 billion infections and more than 6 million deaths to date. During the first wave of the pandemic, empirical antibiotics was prescribed in over 70% of hospitalized COVID-19 patients. However, research now shows a low incidence rate of bacterial coinfection in hospitalized COVID-19 patients, between 2.5% and 5.1%. The rate of secondary infections was 3.7% in overall, but can be as high as 41.9% in the intensive care units. Over-prescription of antibiotics to treat COVID-19 patients fueled the ongoing antimicrobial resistance globally. Diagnosis of bacterial coinfection is challenging due to indistinguishable clinical presentations with overlapping lower respiratory tract symptoms such as fever, cough and dyspnea. Other diagnostic methods include conventional culture, diagnostic syndromic testing, serology test and biomarkers. COVID-19 patients with bacterial coinfection or secondary infection have a higher in-hospital mortality and longer length of stay, timely and appropriate antibiotic use aided by accurate diagnosis is crucial to improve patient outcome and prevent antimicrobial resistance.

Different epidemiology of bloodstream infections in COVID-19 compared to non-COVID-19 critically ill patients: a descriptive analysis of the Eurobact II study

BACKGROUND

The study aimed to describe the epidemiology and outcomes of hospital-acquired bloodstream infections (HABSIs) between COVID-19 and non-COVID-19 critically ill patients.

METHODS

We used data from the Eurobact II study, a prospective observational multicontinental cohort study on HABSI treated in ICU. For the current analysis, we selected centers that included both COVID-19 and non-COVID-19 critically ill patients. We performed descriptive statistics between COVID-19 and non-COVID-19 in terms of patients' characteristics, source of infection and microorganism distribution. We studied the association between COVID-19 status and mortality using multivariable fragility Cox models.

RESULTS

A total of 53 centers from 19 countries over the 5 continents were eligible. Overall, 829 patients (median age 65 years [IQR 55; 74]; male, n = 538 [64.9%]) were treated for a HABSI. Included patients comprised 252 (30.4%) COVID-19 and 577 (69.6%) non-COVID-19 patients. The time interval between hospital admission and HABSI was similar between both groups. Respiratory sources (40.1 vs. 26.0%, p < 0.0001) and primary HABSI (25.4% vs. 17.2%, p = 0.006) were more frequent in COVID-19 patients. COVID-19 patients had more often enterococcal (20.5% vs. 9%) and Acinetobacter spp. (18.8% vs. 13.6%) HABSIs. Bacteremic COVID-19 patients had an increased mortality hazard ratio (HR) versus non-COVID-19 patients (HR 1.91, 95% CI 1.49-2.45).

CONCLUSIONS

We showed that the epidemiology of HABSI differed between COVID-19 and non-COVID-19 patients. Enterococcal HABSI predominated in COVID-19 patients. COVID-19 patients with HABSI had elevated risk of mortality. Trial registration ClinicalTrials.org number NCT03937245 . Registered 3 May 2019.

Update on Staphylococcus aureus bacteraemia

PURPOSE OF REVIEW

To review recently published evidence relevant to Staphylococcus aureus bacteremia (SAB).

RECENT FINDINGS

Staphylococcus aureus is the most common pathogen causing co-infections and superinfections in patients with COVID-19. Methicillin-resistant Staphylococcus aureus (MRSA) bacteremia ratios have sharply risen during the pandemic. SAB mortality is 18% at 1 month and 27% at 3 months but has gradually decreased over the last 30 years. Recurrences and reinfections are common (9%). Standardised items to define complicated SAB, and a new cut-off defining persisting bacteremia after 2 days with positive blood cultures have been proposed. Multiple antibiotic combinations have been trialled including vancomycin or daptomycin with β-lactams, fosfomycin, or clindamycin, without significant results. In the recently published guidelines, vancomycin remains the first line of treatment for MRSA bacteremia. For the management of methicillin-susceptible Staphylococcus aureus , cefazolin less frequently causes acute kidney injury than flucloxacillin, and when susceptibility is demonstrated, de-escalation to penicillin G is suggested.

SUMMARY

Our review confirms that Staphylococcus aureus represents a special aetiology among all causes of bloodstream infections. Pending results of platform and larger trials, its distinct epidemiology and determinants mandate careful integration of clinical variables and best available evidence to optimize patient outcomes.

Invasiveness of Ventilation Therapy Is Associated to Prevalence of Secondary Bacterial and Fungal Infections in Critically Ill COVID-19 Patients

Superinfections are a fundamental critical care problem, and their significance in severe COVID-19 cases needs to be determined. This study analyzed data from the Lean European Open Survey on SARS-CoV-2-Infected Patients (LEOSS) cohort focusing on intensive care patients. A retrospective analysis of patient data from 840 cases of COVID-19 with critical courses demonstrated that co-infections were frequently present and were primarily of nosocomial origin. Furthermore, our analysis showed that invasive therapy procedures accompanied an increased risk for healthcare-associated infections. Non-ventilated ICU patients were rarely affected by secondary infections. The risk of infection, however, increased even when non-invasive ventilation was used. A further, significant increase in infection rates was seen with the use of invasive ventilation and even more so with extracorporeal membrane oxygenation (ECMO) therapy. The marked differences among ICU techniques used for the treatment of COVID-19-induced respiratory failure in terms of secondary infection risk profile should be taken into account for the optimal management of critically ill COVID-19 patients, as well as for adequate antimicrobial therapy.

Diagnostic concordance between BioFire® FilmArray® Pneumonia Panel and culture in patients with COVID-19 pneumonia admitted to intensive care units: the experience of the third wave in eight hospitals in Colombia

Background

The detection of coinfections is important to initiate appropriate antimicrobial therapy. Molecular diagnostic testing identifies pathogens at a greater rate than conventional microbiology. We assessed both bacterial coinfections identified via culture or the BioFire® FilmArray® Pneumonia Panel (FA-PNEU) in patients infected with SARS-CoV-2 in the ICU and the concordance between these techniques.

Methods

This was a prospective study of patients with SARS-CoV-2 who were hospitalized for no more than 48 h and on mechanical ventilation for no longer than 24 h in 8 ICUs in Medellín, Colombia. We studied mini-bronchoalveolar lavage or endotracheal aspirate samples processed via conventional culture and the FA-PNEU. Coinfection was defined as the identification of a respiratory pathogen using the FA-PNEU or cultures. Serum samples of leukocytes, C-reactive protein, and procalcitonin were taken on the first day of intubation. We analyzed the empirical antibiotics and the changes in antibiotic management according to the results of the FA-PNEUM and cultures.

Results

Of 110 patients whose samples underwent both methods, FA-PNEU- and culture-positive samples comprised 24.54% versus 17.27%, respectively. Eighteen samples were positive in both techniques, 82 were negative, 1 was culture-positive with a negative FA-PNEU result, and 9 were FA-PNEU-positive with negative culture. The two bacteria most frequently detected by the FA-PNEU were Staphylococcus aureus (37.5%) and Streptococcus agalactiae (20%), and those detected by culture were Staphylococcus aureus (34.78%) and Klebsiella pneumoniae (26.08%). The overall concordance was 90.1%, and when stratified by microorganism, it was between 92.7 and 100%. The positive predictive value (PPV) was between 50 and 100% and were lower for Enterobacter cloacae and Staphylococcus aureus. The negative predictive value (NPV) was high (between 99.1 and 100%); MecA/C/MREJ had a specificity of 94.55% and an NPV of 100%. The inflammatory response tests showed no significant differences between patients whose samples were positive and negative for both techniques. Sixty-one patients (55.45%) received at least one dose of empirical antibiotics.

Conclusions

The overall concordance was 90.1%, and it was between 92.7% and 100% when stratified by microorganisms. The positive predictive value was between 50 and 100%, with a very high NPV.

Challenges of Antimicrobial Resistance and Stewardship in Solid Organ Transplant Patients

Purpose of Review

Without effective antimicrobials, patients cannot undergo transplant surgery safely or sustain immunosuppressive therapy. This review examines the burden of antimicrobial resistance in solid organ transplant recipients and identifies opportunities for antimicrobial stewardship.

Recent Findings

Antimicrobial resistance has been identified to be the leading cause of death globally. Multidrug-resistant pathogens are associated with significant morbidity and mortality in transplant recipients. Methicillin-resistant S. aureus affects liver and lung recipients, causing bacteremia, pneumonia, and surgical site infections. Vancomycin-resistant enterococci is a nosocomial pathogen primarily causing bacteremia in liver recipients. Multidrug-resistant Gram-negative pathogens present urgent and serious threats to transplant recipients. Extended-spectrum beta-lactamase-producing E. coli and K. pneumoniae commonly cause bacteremia and intra-abdominal infections in liver and kidney recipients. Carbapenemase-producing Enterobacterales, mainly K. pneumoniae, are responsible for infections early-post transplant in liver, lung, kidney, and heart recipients. P. aeruginosa and A. baumannii continue to be critical threats. While there are new antimicrobial agents targeting resistant pathogens, judicious prescribing is crucial to minimize emerging resistance. The full implications of the COVID-19 global pandemic on antimicrobial resistance in transplant recipients remain to be understood. Currently, there are no established standards on the implementation of antimicrobial stewardship interventions, but strategies that leverage existing antimicrobial stewardship program structure while tailoring to the needs of transplant recipients may help to optimize antimicrobial use.

Summary

Clinicians caring for transplant recipients face unique challenges tackling emerging antimcirobial resistance. Coordinated antimicrobial stewardship interventions in collaboration with appropriate expertise in transplant and infectious diseases may mitigate against such threats.

Clinical Analysis of Bloodstream Infection of Escherichia coli in Patients with Pancreatic Cancer from 2011 to 2019

Background

Pancreatic cancer patients were particularly predisposed to develop Escherichia coli (E. coli) bloodstream infection (BSI); however, little information is currently available. We set out to find E. coli BSI's risk factors in pancreatic cancer to provide valuable experience.

Methods

We retrospectively analyzed the clinical data of pancreatic cancer patients (31 cases with E. coli BSI and 93 cases without BSI) by a case-control study. SPSS 17.0 was adopted to perform univariate and multivariate analyses. Bacterial resistance analysis was performed by Whonet 5.6.

Results

Hospitalization days ≥7 days, number of admissions ≥2 times, surgery, chemotherapy, the type of antibiotics used ≥2 species, albumin<40.0 g/L, and prealbumin < 0.2 g/L were the potential risk factors for pancreatic cancer patients with E. coli BSI (P < 0.1). Multivariate logistic regression showed hospitalization days ≥7 days (OR = 11.196, 95% CI = 0.024–0.333, P < 0.001), surgery (OR = 32.053, 95% CI = 0.007–0.137, P < 0.001), and chemotherapy (OR = 6.174, 95% CI = 0.038–0.688, P=0.014) were the independent risk factors for E. coli BSI of pancreatic cancer patients. E. coli resistant to carbapenems was rare; they were susceptible to cephamycin and piperacillin/tazobactam. The 90-day mortality rate of the infected group was significantly higher than the control group (41.9% versus 8.6%, P < 0.001).

Conclusions

Hospitalization days ≥7 days, surgery, and chemotherapy are the independent risk factors for E. coli BSI of pancreatic cancer patients, which allows us to identify patients at potential risk and perform preventive treatment in time.

Does dengue and COVID-19 co-infection have worse outcomes? A systematic review of current evidence

In dengue-endemic regions, the co-infection with SARS-CoV-2 and dengue is a significant health concern. Therefore, we performed a literature search for relevant papers in seven databases on 26 Spetember 2021. Out of 24 articles, the mortality rate and intensive care unit (ICU) admission were 19.1% and 7.8%, respectively. The mean hospital stay was 11.4 days. In addition, we identified two pregnancies with dengue and COVID-19 co-infection; one ended with premature rupture of membrane and intrauterine growth restriction fetus, while the other one ended with maternal mortality and intrauterine fetal death. COVID-19 and dengue co-infection had worse outcomes regarding mortality rates, ICU admission, and prolonged hospital stay. Thus, wise-decision management approaches should be adequately offered to these patients to enhance their outcomes. Establishing an early diagnosis might be the answer to reducing the estimated significant burden of these conditions.