The Spectrum of Antibiotic Prescribing During COVID-19 Pandemic: A Systematic Literature Review

Impact of the COVID-19 pandemic on the utilisation and quality of antibiotic use in the Scottish primary care setting: a population-based segmented interrupted time-series analysis

BACKGROUND

Inappropriate use of antibiotics is expected to increase during the COVID-19 pandemic, but there are limited data on COVID-19's long-term impact. We assessed the impact of COVID-19 on the quantity and quality of antibiotic use in Scotland.

RESEARCH DESIGN AND METHODS

A segmented interrupted time series was applied to monthly dispensed antibiotics using prescription cost analysis data from March/2019 to March/2023. Antibiotic use was quantified using the number of items dispensed/1000 inhabitants (TIDs) and defined daily dose/1000 inhabitants/day (DIDs). The quality of antibiotic use was assessed using key quality indicators including the WHO AWaRe classification, proportion of broad-spectrum and "4C"-antibiotics.

RESULTS

Overall, for all antibiotics, there was a non-significant increase in TIDs and DIDs before the first lockdown (March/2020) (β1), but a decline in the level immediately after the first (β2) and second lockdowns (β4) (November/2020), albeit non-significant. However, a significant increase in the time trend after the second lockdown (β5) for all antibiotic classes was observed. COVID-19 had no negative impact on AWaRe utilisation, with the proportion of all antibiotics from the Access group increasing from 76% in March/2019 to 90% in March/2023. The proportion of "4C" antibiotic reduced significantly after the second lockdown.

CONCLUSIONS

Neither the utilisation nor the quality of total antibiotic use appeared to have been significantly affected by COVID-19.

Tracking progress on antimicrobial resistance by the quadripartite country self-assessment survey (TrACSS) in G7 countries, 2017-2023: opportunities and gaps

Antimicrobial resistance (AMR) poses serious challenges to the healthcare systems worldwide. Multiple factors and activities contribute to the development and spread of antimicrobial-resistant microorganisms. Monitoring progress in combating AMR is fundamental at both global and national levels to drive multisectoral actions, identify priorities, and coordinate strategies. Since 2017, the World Health Organization (WHO) has collected data through the Tracking AMR Country Self-Assessment Survey (TrACSS). TrACSS data are published in a publicly-available database. In 2023, 71 (59.9%) out of 177 responding countries reported the existence of a monitoring and evaluation plan for their National Action Plan (NAP) on AMR, and just 20 countries (11.3%) the allocation of funding to support NAP implementation. Countries reported challenges including limited financial and human resources, lack of technical capacity, and variable political commitment. Even across the Group of Seven (G7) countries, which represent some of the world's most advanced economies, many areas still need improvement, such as full implementation of infection prevention and control measures, adoption of WHO access/watch/reserve (AWaRe) classification of antibiotics, effective integration of laboratories in AMR surveillance in the animal health and food safety sectors, training and education, good manufacturing and hygiene practices in food processing, optimising pesticides use and environmental residues of antimicrobial drugs. Continuous and coordinated efforts are needed to strengthen multisectoral engagement to fight AMR.

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

INTRODUCTION

Previous studies in Pakistan have shown considerable over prescribing of antibiotics in patients hospitalized with COVID-19 despite very low prevalence of bacterial infections. Irrational use of antibiotics will worsen antimicrobial resistance (AMR).

METHODS

Retrospective analysis of medical records of patients in the COVID-19 wards of three tertiary care hospitals to assess antibiotic use during the sixth COVID-19 wave.

RESULTS

A total of 284 patients were included, most were male (66.9%), aged 30-50 years (50.7%) with diabetes mellitus the most common comorbidity. The most common symptoms at presentation were cough (47.9%) and arthralgia-myalgia (41.5%). Around 3% were asymptomatic, 34.9% had mild, 30.3% moderate, and 23.6% had severe disease, with 8.1% critical. Chest X-ray abnormalities were seen in 43.3% of patients and 37% had elevated white cell counts, with 35.2% having elevated C-reactive protein levels. Around 91% COVID-19 patients were prescribed antibiotics during their hospital stay, with only a few with proven bacterial co-infections or secondary bacterial infections. Most antibiotics were from the 'Watch' category (90.8%) followed by the 'Reserve' category (4.8%), similar to previous COVID-19 waves.

CONCLUSION

There continued to be excessive antibiotics use among hospitalized COVID-19 patients in Pakistan. Urgent measures are needed to address inappropriate prescribing including greater prescribing of Access antibiotics where pertinent.

Assessing the impact of COVID-19 on prescription patterns and antibiotic use: Insights from three military health facilities

BACKGROUND

The COVID-19 pandemic disrupted health systems globally and there are suggestions it impacted antibiotics prescribing patterns in clinical practice.

OBJECTIVES

This study aimed to assess the effects of the COVID-19 pandemic on the prescribing patterns in three Nigerian military health facilities and investigate the factors associated with antibiotic prescriptions.

METHODS

This was a two-year cross-sectional retrospective study. Three hospitals and a total of 11,590 prescriptions were purposively and conveniently sampled respectively. The World Health Organisation (WHO) and International Network of Rational Use of Drugs (INRUD) prescribing indicators were used to assess for polypharmacy, injection use, use of antibiotics, use of generic drugs and prescriptions from essential drug lists for the periods of the pandemic and before the pandemic. Indicators from both periods were compared for statistical significance using the independent t-test. Generalized linear modelling was applied to assess the factors associated with antibiotic prescriptions. The relationship between the receipt of antibiotics and independent variables was presented using incident risk ratios (IRR).

RESULTS

Our findings showed that all five WHO/INRUD prescribing indicators were above the reference limit for the two-year study period. The study found there was a significant statistical difference between the COVID- and non-COVID-19 periods, with polypharmacy and antibiotic use indicators elevated during the pandemic compared to the latter. COVID-19 (IRR = 1.09), comorbidity (IRR = 1.74), pregnancy (IRR = 0.93), out-of-pocket payments (IRR = 1.10) and the inpatient department (IRR = 1.51) were associated with antibiotic prescriptions.

CONCLUSIONS

This provides insight on impact of the pandemic on prescription patterns and advocates for stewardship programs in clinical settings to ensure the rational use of drugs.

Host-response transcriptional biomarkers accurately discriminate bacterial and viral infections of global relevance

Diagnostic limitations challenge management of clinically indistinguishable acute infectious illness globally. Gene expression classification models show great promise distinguishing causes of fever. We generated transcriptional data for a 294-participant (USA, Sri Lanka) discovery cohort with adjudicated viral or bacterial infections of diverse etiology or non-infectious disease mimics. We then derived and cross-validated gene expression classifiers including: 1) a single model to distinguish bacterial vs. viral (Global Fever-Bacterial/Viral [GF-B/V]) and 2) a two-model system to discriminate bacterial and viral in the context of noninfection (Global Fever-Bacterial/Viral/Non-infectious [GF-B/V/N]). We then translated to a multiplex RT-PCR assay and independent validation involved 101 participants (USA, Sri Lanka, Australia, Cambodia, Tanzania). The GF-B/V model discriminated bacterial from viral infection in the discovery cohort an area under the receiver operator curve (AUROC) of 0.93. Validation in an independent cohort demonstrated the GF-B/V model had an AUROC of 0.84 (95% CI 0.76-0.90) with overall accuracy of 81.6% (95% CI 72.7-88.5). Performance did not vary with age, demographics, or site. Host transcriptional response diagnostics distinguish bacterial and viral illness across global sites with diverse endemic pathogens.

Healthcare commissioners' experience with antibiotic resistance during the COVID-19 pandemic in Saudi Arabia: a qualitative study

Introduction

The occurrence of antibiotic resistance (AR) has become a critical issue during the Novel coronavirus disease 2019 (COVID-19) pandemic. This study explores the experiences of healthcare commissioners with AR during the COVID-19 pandemic, identifies challenges, and provides recommendations for combating AR during pandemics.

Methods

This qualitative study was multi-centered and used a phenomenological approach. Semi-structured interviews were conducted between December 2022 and January 2023 among 11 health commissioners using video calls.

Results

Seven themes emerged from the data, including knowledge of AR and its consequences, the antibiotic prescription system, the future of AR and potential contributory factors, the impact of COVID-19 on AR and their relationship, the experience of AR during the COVID-19 pandemic in healthcare facilities, barriers that prevent the misuse of antibiotics during pandemics, and recommendations regarding antibiotic resistance during pandemics.

Conclusion

The findings of this study could be used to inform policy and practice for government healthcare workers (HCWs) and the public. Furthermore, this study identified the main challenges of AR during the pandemic, and the recommendations of health commissioners were provided accordingly. Such recommendations could be beneficial on a national and international scale to reduce the impact of future pandemics on AR.

Abbreviations

COVID-19: Novel coronavirus disease 2019; AR: Antibiotic Resistance; IPC: Infection prevention and control; MDRO: multi-drug resistant organism; ASP: Antimicrobial Stewardship Program; HCW: Healthcare worker; KSA: Kingdom of Saudi Arabia; WHO: World Health Organization; MOH: Ministry of Health; MOEWA: Ministry of Environment, Water, and Agriculture; AMR: Antimicrobial Resistance; PHCC: Primary Healthcare Center.

Use of RT-PCR in conjunction with a respiratory pathogen assay to concurrently determine the prevalence of bacteria and SARS-CoV-2 from the nasopharynx of outpatients

Introduction

COVID-19 has emerged as a highly contagious and debilitating disease caused by the SARS-CoV-2 virus and has claimed the lives of over 7.7 million people worldwide. Bacterial co-infections are one of many co-morbidities that have been suggested to impact the outcome of COVID-19 in patients. The goals of this study are to elucidate the presence of bacteria in the nasopharynx of SARS-CoV-2 positive and negative patients and to describe demographic categories that may be associated with the detection of these organisms during one of the initial waves of the COVID-19 pandemic.

Methods

To this end, we investigated SARS-CoV-2 and bacterial co-detection from outpatient RT-PCR testing in Texas.

Results

The results indicate that Staphylococcus aureus, Streptococcus pneumoniae, Klebsiella pneumoniae, Moraxella catarrhalis, and Haemophilus influenzae were the most frequently detected bacteria in both SARS-CoV-2 positive and SARS-CoV-2 negative patients and that these bacteria were present in these two patient populations at similar proportions. We also detected Staphylococcus aureus in a significantly larger proportion of males relative to females and people under 65 years of age relative to those 65 and over. Finally, we observed that SARS-CoV-2 was more commonly detected in Hispanics compared to non-Hispanics; however, low disclosure rates make volunteer bias a concern when interpreting the effects of demographic variables.

Discussion

This study describes the bacteria present in the nasopharynx of SARS-CoV-2 positive and negative patients, highlights associations between patient demographics and SARS-CoV-2 as well as bacterial co-detection. In addition, this study highlights RT-PCR based molecular testing as a tool to detect bacteria simultaneously when SARS-CoV-2 tests are performed.

Overprescription of antibiotics for treating hospitalized COVID-19 patients: A systematic review & meta-analysis

Background

Empirical use of antibiotics was reported throughout the coronavirus disease of 2019 (COVID-19) pandemic; however, evidence of bacterial coinfection or secondary bacterial infection among COVID-19 patients was sparse. Antibiotic overprescription for COVID-19 patients without confirmed bacterial coinfection can increase antimicrobial resistance (AMR). The objective of this study is to assess the appropriateness of antibiotic use during COVID-19 by summarizing the frequency of antibiotic use among hospitalized COVID-19 and the frequency of antibiotic use in patients with COVID-19.

Methods

A systematic search was conducted of the Embase, Medline, Web of Science, and Cochrane Library databases by generating search terms using the concepts of "COVID-19," "Bacterial Coinfection," "Secondary bacterial infection," and "Antimicrobial resistance" to identify studies reporting antibiotic prescription for hospitalized COVID-19 patients with or without bacterial coinfection. We excluded studies on outpatients, studies informed infection due to mechanical ventilation, and randomized controlled trials. The pooled estimate of the percentage of the total and confirmed appropriate antibiotic prescriptions provided to hospitalized COVID-19 patients was generated using a random effect meta-analysis with inverse variance weighting. The study protocol registration DOI is osf.io/d3fpm.

Results

Of 157,623 participants from 29 studies (11 countries, 45 % women) included in our review, antibiotics were prescribed to 67 % of participants (CI 64 %-71 %, P < 0·001), of which 80 % (CI 76 %-83 %, P < 0·001) of prescriptions were for COVID-19 patients without confirmed bacterial coinfections. Antibiotic overprescription varied during different periods of the pandemic and between High-Income and Upper and Lower Middle-Income Countries. We found heterogeneity among the studies (I2 = 100 %). The risk of bias analysis showed that 100 % of the included studies had the proper sample framing, and we are at low risk of bias due to sampling.

Discussion

We find greater than expected use of antibiotics to treat hospitalized COVID-19 patients without bacterial coinfections, which may contribute to AMR globally. Concrete guidelines for using antibiotics to treat COVID-19 patients, strict monitoring, and administering Antimicrobial Stewardship are needed to prevent overprescription.

Endemic High-Risk Clone ST277 Is Related to the Spread of SPM-1-Producing Pseudomonas aeruginosa during the COVID-19 Pandemic Period in Northern Brazil

Pseudomonas aeruginosa is a high-priority bacterial agent that causes healthcare-acquired infections (HAIs), which often leads to serious infections and poor prognosis in vulnerable patients. Its increasing resistance to antimicrobials, associated with SPM production, is a case of public health concern. Therefore, this study aims to determine the antimicrobial resistance, virulence, and genotyping features of P. aeruginosa strains producing SPM-1 in the Northern region of Brazil. To determine the presence of virulence and resistance genes, the PCR technique was used. For the susceptibility profile of antimicrobials, the Kirby-Bauer disk diffusion method was performed on Mueller-Hinton agar. The MLST technique was used to define the ST of the isolates. The exoS+/exoU- virulotype was standard for all strains, with the aprA, lasA, toxA, exoS, exoT, and exoY genes as the most prevalent. All the isolates showed an MDR or XDR profile against the six classes of antimicrobials tested. HRC ST277 played a major role in spreading the SPM-1-producing P. aeruginosa strains.

Development of green micellar HPLC-DAD method for simultaneous determination of some sulbactam combinations used in COVID-19 regimen

In a new attempt to separate some sulbactam combinations by green chemical method we came up with this research in which an ecofriendly, green, sustainable and selective method was established for separation of four antibiotics, namely, cefoperazone (CFP), cefixime (CFX), ampicillin (AMP) and sulbactam (SLB). No organic solvents were used in the composition of the mobile phase as it was replaced by mixing two surfactants together, sodium dodecyl sulfate (SDS) and polyoxyethylene-23-lauryl ether (Brij-35). Effect of varying the concentrations of the two surfactants on chromatographic separation was studied. Optimum separation was maintained using a mobile phase consisting of 0.01 mol/L SDS, 0.03 mol/L Brij-35, 0.4% Tri-ethylamine (TEA) and pH of 2.8 adjusted by using 1 M ortho-phosphoric acid on reversed phase Isère C18 BDS column with temperature of 40 °C at flow rate 1 mL/min, wavelength 215 nm, and the total run time was 6 min. Validation of the proposed method has been made according International Conference of Harmonization (ICH) guidelines at linearity range of 10-200 µg mL-1 for all drugs under study, high accuracy results (recovery range 98.39-100.35%). and the variation coefficient (RSD) of the points on the calibration curve was ranged from (0.1-1.7%) indicating precise method. The LOQ was (6.09 μg mL-1) for CFP, (6.07 μg mL-1) for CFX, (3.85 μg mL-1) for AMP and (7.20 μg mL-1) for SLB. Successful applications were made on marketed dosage forms with recovery range of (100.16-102.25%) and RSD of (0.03-1.88%). The method was verified on the Green Analytical Procedure Index (GAPI) and Analytical Greenness metric approach (AGREE) and it was found to be an excellent green alternative method.

Perspective on the Integration of Diagnostic Algorithms for Fever Management

The AMR Diagnostics Use Accelerator Program was established to address antimicrobial resistance. Here, we bring into broad perspective the findings and missed opportunities of the first phase of the program and look toward the second phase.

Antibiotic Consumption During the Coronavirus Disease 2019 Pandemic and Emergence of Carbapenemase-Producing Klebsiella pneumoniae Lineages Among Inpatients in a Chilean Hospital: A Time-Series Study and Phylogenomic Analysis

BACKGROUND

The impact of coronavirus disease 2019 (COVID-19) on antimicrobial use (AU) and resistance has not been well evaluated in South America. These data are critical to inform national policies and clinical care.

METHODS

At a tertiary hospital in Santiago, Chile, between 2018 and 2022, subdivided into pre- (3/2018-2/2020) and post-COVID-19 onset (3/2020-2/2022), we evaluated intravenous AU and frequency of carbapenem-resistant Enterobacterales (CRE). We grouped monthly AU (defined daily doses [DDD]/1000 patient-days) into broad-spectrum β-lactams, carbapenems, and colistin and used interrupted time-series analysis to compare AU during pre- and post-pandemic onset. We studied the frequency of carbapenemase-producing (CP) CRE and performed whole-genome sequencing analyses of all carbapenem-resistant (CR) Klebsiella pneumoniae (CRKpn) isolates collected during the study period.

RESULTS

Compared with pre-pandemic, AU (DDD/1000 patient-days) significantly increased after the pandemic onset, from 78.1 to 142.5 (P < .001), 50.9 to 110.1 (P < .001), and 4.1 to 13.3 (P < .001) for broad-spectrum β-lactams, carbapenems, and colistin, respectively. The frequency of CP-CRE increased from 12.8% pre-COVID-19 to 51.9% after pandemic onset (P < .001). The most frequent CRE species in both periods was CRKpn (79.5% and 76.5%, respectively). The expansion of CP-CRE harboring blaNDM was particularly noticeable, increasing from 40% (n = 4/10) before to 73.6% (n = 39/53) after pandemic onset (P < .001). Our phylogenomic analyses revealed the emergence of two distinct genomic lineages of CP-CRKpn: ST45, harboring blaNDM, and ST1161, which carried blaKPC.

CONCLUSIONS

AU and the frequency of CP-CRE increased after COVID-19 onset. The increase in CP-CRKpn was driven by the emergence of novel genomic lineages. Our observations highlight the need to strengthen infection prevention and control and antimicrobial stewardship efforts.

Cefiderocol-Based versus Colistin-Based Regimens for Severe Carbapenem-Resistant Acinetobacter baumannii Infections: A Propensity Score-Weighted, Retrospective Cohort Study during the First Two Years of the COVID-19 Pandemic

BACKGROUND

A large increase in multi-drug-resistant Acinetobacter baumannii, especially carbapenem-resistant strains, occurred during the first two years of the COVID-19 pandemic, posing important challenges in its treatment. Cefiderocol appeared to be a good option for the treatment of Carbapenem-resistant Acinetobacter baumannii (CR-Ab), but to date, the guidelines and evidence available are conflicting.

METHODS

We retrospectively included a group of patients with CR-Ab infections (treated with colistin- or cefiderocol-based regimens) at Padua University Hospital (August 2020-July 2022) and assessed predictors of 30-day mortality, and differences in microbiological and clinical treatment. To evaluate the difference in outcomes, accounting for the imbalance in antibiotic treatment allocation, a propensity score weighting (PSW) approach was adopted.

RESULTS

We included 111 patients, 68% males, with a median age of 69 years (IQR: 59-78). The median duration of antibiotic treatment was 13 days (IQR:11-16). In total, 60 (54.1%) and 51 (45.9%) patients received cefiderocol- and colistin-based therapy, respectively. Notably, 53 (47.7%) patients had bloodstream infections, while 58 (52.3%) had pneumonia. Colistin was combined in 96.1%, 80.4%, and 5.8% of cases with tigecycline, meropenem, and fosfomycin, respectively. Cefiderocol was combined in 13.3%, 30%, and 18.3% of cases with fosfomycin, tigecycline, and meropenem, respectively. At the baseline, the two treatment groups significantly differed in age (patients treated with colistin were significantly older), the prevalence of diabetes and obesity (more frequent in the group treated with colistin), length of stay (longer in the group receiving cefiderocol), and type of infection (BSI were more frequent in the group receiving cefiderocol). The proportion of patients who developed acute kidney injury was significantly higher in the colistin group. By using PSW, no statistically significant differences emerged for mortality or clinical and microbiological cure between the two groups. No independent predictors were detected for hospital mortality or clinical cure, while for the length of stay, the only selected predictor was age, with a non-linear effect (p-value 0.025 for non-linearity) on the prolongation of hospital stay of 0.25 days (95% CI 0.10-0.39) at increasing ages (calculated over the IQR).

CONCLUSIONS

Cefiderocol treatment did not differ in terms of main outcomes and safety profile from colistin-based regimens. More prospective studies with a larger number of patients are required to confirm our results.

Antimicrobial resistance in patients with COVID-19: a systematic review and meta-analysis

BACKGROUND

Frequent use of antibiotics in patients with COVID-19 threatens to exacerbate antimicrobial resistance. We aimed to establish the prevalence and predictors of bacterial infections and antimicrobial resistance in patients with COVID-19.

METHODS

We did a systematic review and meta-analysis of studies of bacterial co-infections (identified within ≤48 h of presentation) and secondary infections (>48 h after presentation) in outpatients or hospitalised patients with COVID-19. We searched the WHO COVID-19 Research Database to identify cohort studies, case series, case-control trials, and randomised controlled trials with populations of at least 50 patients published in any language between Jan 1, 2019, and Dec 1, 2021. Reviews, editorials, letters, pre-prints, and conference proceedings were excluded, as were studies in which bacterial infection was not microbiologically confirmed (or confirmed via nasopharyngeal swab only). We screened titles and abstracts of papers identified by our search, and then assessed the full text of potentially relevant articles. We reported the pooled prevalence of bacterial infections and antimicrobial resistance by doing a random-effects meta-analysis and meta-regression. Our primary outcomes were the prevalence of bacterial co-infection and secondary infection, and the prevalence of antibiotic-resistant pathogens among patients with laboratory-confirmed COVID-19 and bacterial infections. The study protocol was registered with PROSPERO (CRD42021297344).

FINDINGS

We included 148 studies of 362  976 patients, which were done between December, 2019, and May, 2021. The prevalence of bacterial co-infection was 5·3% (95% CI 3·8-7·4), whereas the prevalence of secondary bacterial infection was 18·4% (14·0-23·7). 42 (28%) studies included comprehensive data for the prevalence of antimicrobial resistance among bacterial infections. Among people with bacterial infections, the proportion of infections that were resistant to antimicrobials was 60·8% (95% CI 38·6-79·3), and the proportion of isolates that were resistant was 37·5% (26·9-49·5). Heterogeneity in the reported prevalence of antimicrobial resistance in organisms was substantial (I2=95%).

INTERPRETATION

Although infrequently assessed, antimicrobial resistance is highly prevalent in patients with COVID-19 and bacterial infections. Future research and surveillance assessing the effect of COVID-19 on antimicrobial resistance at the patient and population level are urgently needed.

FUNDING

WHO.

Point Prevalence Survey of Antimicrobial Use during the COVID-19 Pandemic among Different Hospitals in Pakistan: Findings and Implications

The COVID-19 pandemic has significantly influenced antimicrobial use in hospitals, raising concerns regarding increased antimicrobial resistance (AMR) through their overuse. The objective of this study was to assess patterns of antimicrobial prescribing during the current COVID-19 pandemic among hospitals in Pakistan, including the prevalence of COVID-19. A point prevalence survey (PPS) was performed among 11 different hospitals from November 2020 to January 2021. The study included all hospitalized patients receiving an antibiotic on the day of the PPS. The Global-PPS web-based application was used for data entry and analysis. Out of 1024 hospitalized patients, 662 (64.64%) received antimicrobials. The top three most common indications for antimicrobial use were pneumonia (13.3%), central nervous system infections (10.4%) and gastrointestinal indications (10.4%). Ceftriaxone (26.6%), metronidazole (9.7%) and vancomycin (7.9%) were the top three most commonly prescribed antimicrobials among surveyed patients, with the majority of antibiotics administered empirically (97.9%). Most antimicrobials for surgical prophylaxis were given for more than one day, which is a concern. Overall, a high percentage of antimicrobial use, including broad-spectrums, was seen among the different hospitals in Pakistan during the current COVID-19 pandemic. Multifaceted interventions are needed to enhance rational antimicrobial prescribing including limiting their prescribing post-operatively for surgical prophylaxis.

Impact of Antibiotic Consumption on the Acquisition of Extended-Spectrum β-Lactamase Producing Enterobacterales Carriage during the COVID-19 Crisis in French Guiana

(1) Background: During the COVID-19 outbreak, several studies showed an increased prevalence of extended-spectrum β-lactamase producing Enterobacterales (ESBL-PE) carriage in intensive care units (ICUs). Our objective was to assess the impact of antibiotic prescriptions on the acquisition of ESBL-PE in ICUs during the COVID-19 crisis. (2) Methods: We conducted an observational study between 1 April 2020, and 31 December 2021, in the medical-surgical ICU of the Cayenne General Hospital. We defined two periods: Period 1 with routine, empirical antibiotic use, and Period 2 with no systematic empiric antibiotic prescription. (3) Results: ICU-acquired ESBL-PE carriage was 22.8% during Period 1 and 9.4% during Period 2 (p = 0.005). The main isolated ESBL-PE was Klebsiella pneumoniae (84.6% in Period 1 and 58.3% in Period 2). When using a generalized linear model with a Poisson family, exposure to cefotaxime was the only factor independently associated with ESBL-PE acquisition in ICU (p = 0.002, IRR 2.59 (95% IC 1.42-4.75)). The propensity scores matching estimated the increased risk for cefotaxime use to acquire ESBL-PE carriage at 0.096 (95% CI = 0.02-0.17), p = 0.01. (4) Conclusions: Exposure to cefotaxime in patients with severe COVID-19 is strongly associated with the emergence of ESBL-PE in the context of maximal infection control measures.

Ongoing Efforts to Improve Antimicrobial Utilization in Hospitals among African Countries and Implications for the Future

There are serious concerns with rising antimicrobial resistance (AMR) across countries increasing morbidity, mortality and costs. These concerns have resulted in a plethora of initiatives globally and nationally including national action plans (NAPs) to reduce AMR. Africa is no exception, especially with the highest rates of AMR globally. Key activities in NAPs include gaining a greater understanding of current antimicrobial utilization patterns through point prevalence surveys (PPS) and subsequently instigating antimicrobial stewardship programs (ASPs). Consequently, there is a need to comprehensively document current utilization patterns among hospitals across Africa coupled with ASP studies. In total, 33 PPS studies ranging from single up to 18 hospitals were documented from a narrative review with typically over 50% of in-patients prescribed antimicrobials, up to 97.6% in Nigeria. The penicillins, ceftriaxone and metronidazole, were the most prescribed antibiotics. Appreciable extended prescribing of antibiotics up to 6 days or more post-operatively was seen across Africa to prevent surgical site infections. At least 19 ASPs have been instigated across Africa in recent years to improve future prescribing utilizing a range of prescribing indicators. The various findings resulted in a range of suggested activities that key stakeholders, including governments and healthcare professionals, should undertake in the short, medium and long term to improve future antimicrobial prescribing and reduce AMR across Africa.

A Retrospective Assessment of Laboratory Findings and Cytokine Markers in Severe SARS-CoV-2 Infection among Patients of Roma Population

Growing research data suggests that the severity of COVID-19 is linked with higher levels of inflammatory mediators, such as cytokines, chemokines, tumor necrosis factor, C-reactive protein, ferritin, and D-dimers. In addition, it was evident from the existing research data that the severity of SARS-CoV-2 infection differs according to independent risk factors such as race and ethnicity. Some scarce evidence shows that the European Roma community is likely to be at an elevated risk of illness and death during the pandemic due to their lifestyle, social factors, and economics. Assuming that precautions must be taken to protect this population from coronavirus infections and from widening existing disparities in comparison with the Romanian ethnic population, the current study aimed to observe the clinical evolution of the Roma patients with severe SARS-CoV-2 infection in correlation with the laboratory findings and inflammatory markers involved. After calculating the sample size requirements, we included 83 Roma patients admitted to the hospital with severe COVID-19 and 236 patients of Romanian ethnicity with the same inclusion criteria. Patients were selected from the period stretching from March 2020 to December 2021, before COVID-19 vaccines were introduced. Compared with the general population, the Roma patients with severe SARS-CoV-2 infection had a higher unemployment rate (39.8%), and most of them were residing in rural regions (65.4%). There were significantly more overweight patients in the Roma group than in the control group (57.8% vs. 40.7%), and it was also observed that high blood pressure and diabetes mellitus were significantly more prevalent in the Roma patients. They had significantly longer mean duration of hospitalization was significantly longer in the group of Roma patients (18.1 days vs. 16.3 days). IL-6 and CRP levels were significantly more elevated during admission in the group of Roma patients (43.4% vs. 28.4%); however, IL-6 levels normalized at discharge, but ESR remained high. Although ICU admissions were significantly more frequent in this group, the mortality rate was not significantly higher than in the general population. It is necessary to plan different healthcare strategies aimed at special populations, such as the Roma ethnicity to prevent disparities in negative outcomes reflected in this study. The results imply that community-health collaborations between organizations of minority groups and healthcare professionals can mitigate the disproportionate consequences of the pandemic on Roma.

Determinants of the Empiric Use of Antibiotics by General Practitioners in South Africa: Observational, Analytic, Cross-Sectional Study

The overuse of antibiotics is the main driver of antimicrobial resistance (AMR). However, there has been limited surveillance data on AMR and antibiotic prescribing at a primary healthcare level in South Africa. An observational, analytic, cross-sectional study was undertaken to assess key factors associated with empiric antibiotic prescribing among private sector general practitioners (GPs) in the eThekwini district in South Africa, particularly for patients with acute respiratory infections (ARIs). A semi-structured web-based questionnaire was used between November 2020−March 2021. One hundred and sixteen (55.5%) responding GPs prescribed antibiotics empirically for patients with ARIs more than 70% of the time, primarily for symptom relief and the prevention of complications. GPs between the ages of 35−44 years (OR: 3.38; 95%CI: 1.15−9.88), >55 years (OR: 4.75; 95% CI 1.08−21) and in practice < 15 years (OR: 2.20; 95%CI: 1.08−4.51) were significantly more likely to prescribe antibiotics empirically. Three factors—workload/time pressures; diagnostic uncertainty, and the use of a formulary, were significantly associated with empiric prescribing. GPs with more experience and working alone were slightly less likely to prescribe antibiotics empirically. These findings indicate that a combination of environmental factors are important underlying contributors to the development of AMR. As a result, guide appropriate interventions using a health system approach, which includes pertinent prescribing indicators and targets.

Clinical Impact of Empirical Antibiotic Therapy in Patients With Coronavirus Disease 2019 Requiring Oxygen Therapy

Despite the low prevalence of secondary bacterial infection in coronavirus disease 2019 (COVID-19) patients, most of them were administered antibiotic therapy empirically. However, the prognostic impact of empirical antibiotic therapy has not been evaluated. We conducted retrospective propensity score-matched case-control study of 233 COVID-19 patients with moderate to severe illnesses who required oxygen therapy and evaluated whether empirical antibiotic therapy could improve clinical outcomes. Empirical antibiotic therapy did not improve clinical outcomes including length of stay, days with oxygen requirement, the proportion of patients with increased oxygen demand, the proportion of patients who required mechanical ventilation, and overall mortality. This finding implies that routine administration of antibiotics for the treatment of COVID-19 is not essential and should be restricted.

Altered gut microbiota patterns in COVID-19: Markers for inflammation and disease severity

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection leads to a severe respiratory illness and alters the gut microbiota, which dynamically interacts with the human immune system. Microbiota alterations include decreased levels of beneficial bacteria and augmentation of opportunistic pathogens. Here, we describe critical factors affecting the microbiota in coronavirus disease 2019 (COVID-19) patients. These include, such as gut microbiota imbalance and gastrointestinal symptoms, the pattern of altered gut microbiota composition in COVID-19 patients, and crosstalk between the microbiome and the gut-lung axis/gut-brain-lung axis. Moreover, we have illustrated the hypoxia state in COVID-19 associated gut microbiota alteration. The role of ACE2 in the digestive system, and control of its expression using the gut microbiota is discussed, highlighting the interactions between the lungs, the gut, and the brain during COVID-19 infection. Similarly, we address the gut microbiota in elderly or co-morbid patients as well as gut microbiota dysbiosis of in severe COVID-19. Several clinical trials to understand the role of probiotics in COVID-19 patients are listed in this review. Augmented inflammation is one of the major driving forces for COVID-19 symptoms and gut microbiome disruption and is associated with disease severity. However, understanding the role of the gut microbiota in immune modulation during SARS-CoV-2 infection may help improve therapeutic strategies for COVID-19 treatment.

Antibiotic (Mis)Use in COVID-19 Patients before and after Admission to a Tertiary Hospital in Serbia

Antimicrobial resistance (AMR) is a global concern, and antibiotic use has risen throughout the COVID-19 pandemic. Up to 75% of COVID-19 patients are treated with antibiotics despite little evidence for their use. A retrospective study from 6 March 2020 (the start of the pandemic in Serbia) to 31 December 2021 was conducted at the Clinic for Infectious and Tropical Diseases, University Clinical Centre of Serbia. In total, 523 patients with a microbiological diagnosis of COVID-19 were included. Patient data were analysed, including antibiotic use before and after admission. Pre-admission use of antibiotics for COVID-19 treatment was documented in more than half of patients (58.1%), of which a third (34.1%) used more than one antibiotic. Macrolides, cephalosporins, and fluoroquinolones were mainly used, most frequently among patients aged between 31−45 years (75.2%). Prior antibiotic use was associated with a longer duration of illness at admission (8.8 vs. 5.7, p < 0.001), oxygen therapy upon admission (27.6% vs. 16.0%, p = 0.002), and a lower vaccination rate (60.7% vs. 50.7%, p = 0.04). When hospitalised, 72.1% of patients received antibiotics, primarily cephalosporins (71.9%). Significant efforts are needed to reduce antibiotic use in the community and improve prescribing rates by healthcare professionals.

Is the Pendulum of Antimicrobial Drug Resistance Swinging Back after COVID-19?

The COVID-19 pandemic may have had an effect on antimicrobial resistance. We compared the prevalence of ESKAPE multidrug-resistant (MDR) bacterial infections in COVID-19 affected/unaffected patients admitted to intensive care units (ICU) or infectious disease units at the “Mater Domini” University Hospital of Catanzaro between 1 March 2020 and 31 July 2021. Moreover, an analysis of MDR rates in ICU comparing the pre-pandemic period with the pandemic period was performed, and the possible consequence on in-hospital mortality was explored. One hundred and eighty-four ESKAPE isolates were analyzed from 362 SARS-CoV-2 positive and 199 negative patients. In total, 116 out of 171 Gram-negative isolates were classified as MDR, and a higher frequency was observed in COVID-19 compared with non-COVID-19 patients (74.2% vs. 60.3%; p = 0.052). A higher rate of MDR ESKAPE bacteria was observed in COVID-19 patients admitted to the ICU compared with COVID-19 unaffected patients admitted to the same ward in 2019 (88% vs. 80.4%; p = 0.186). Acinetobacter baumannii was the main pathogen in COVID-19 patients (58.7%), where it was the most frequent cause of bloodstream infection with the highest mortality rate (68.7%). Increase in MDR appeared to be associated with COVID-19 but only in the ICU setting. Acinetobacter baumannii was associated with the risk of death, indicating the importance of implementing infection control measures urgently.

Prospective Validation of a Rapid Host Gene Expression Test to Discriminate Bacterial From Viral Respiratory Infection

Importance

Bacterial and viral causes of acute respiratory illness (ARI) are difficult to clinically distinguish, resulting in the inappropriate use of antibacterial therapy. The use of a host gene expression-based test that is able to discriminate bacterial from viral infection in less than 1 hour may improve care and antimicrobial stewardship.

Objective

To validate the host response bacterial/viral (HR-B/V) test and assess its ability to accurately differentiate bacterial from viral infection among patients with ARI.

Design, Setting, and Participants

This prospective multicenter diagnostic study enrolled 755 children and adults with febrile ARI of 7 or fewer days' duration from 10 US emergency departments. Participants were enrolled from October 3, 2014, to September 1, 2019, followed by additional enrollment of patients with COVID-19 from March 20 to December 3, 2020. Clinical adjudication of enrolled participants identified 616 individuals as having bacterial or viral infection. The primary analysis cohort included 334 participants with high-confidence reference adjudications (based on adjudicator concordance and the presence of an identified pathogen confirmed by microbiological testing). A secondary analysis of the entire cohort of 616 participants included cases with low-confidence reference adjudications (based on adjudicator discordance or the absence of an identified pathogen in microbiological testing). Thirty-three participants with COVID-19 were included post hoc.

Interventions

The HR-B/V test quantified the expression of 45 host messenger RNAs in approximately 45 minutes to derive a probability of bacterial infection.

Main Outcomes and Measures

Performance characteristics for the HR-B/V test compared with clinical adjudication were reported as either bacterial or viral infection or categorized into 4 likelihood groups (viral very likely [probability score <0.19], viral likely [probability score of 0.19-0.40], bacterial likely [probability score of 0.41-0.73], and bacterial very likely [probability score >0.73]) and compared with procalcitonin measurement.

Results

Among 755 enrolled participants, the median age was 26 years (IQR, 16-52 years); 360 participants (47.7%) were female, and 395 (52.3%) were male. A total of 13 participants (1.7%) were American Indian, 13 (1.7%) were Asian, 368 (48.7%) were Black, 131 (17.4%) were Hispanic, 3 (0.4%) were Native Hawaiian or Pacific Islander, 297 (39.3%) were White, and 60 (7.9%) were of unspecified race and/or ethnicity. In the primary analysis involving 334 participants, the HR-B/V test had sensitivity of 89.8% (95% CI, 77.8%-96.2%), specificity of 82.1% (95% CI, 77.4%-86.6%), and a negative predictive value (NPV) of 97.9% (95% CI, 95.3%-99.1%) for bacterial infection. In comparison, the sensitivity of procalcitonin measurement was 28.6% (95% CI, 16.2%-40.9%; P < .001), the specificity was 87.0% (95% CI, 82.7%-90.7%; P = .006), and the NPV was 87.6% (95% CI, 85.5%-89.5%; P < .001). When stratified into likelihood groups, the HR-B/V test had an NPV of 98.9% (95% CI, 96.1%-100%) for bacterial infection in the viral very likely group and a positive predictive value of 63.4% (95% CI, 47.2%-77.9%) for bacterial infection in the bacterial very likely group. The HR-B/V test correctly identified 30 of 33 participants (90.9%) with acute COVID-19 as having a viral infection.

Conclusions and Relevance

In this study, the HR-B/V test accurately discriminated bacterial from viral infection among patients with febrile ARI and was superior to procalcitonin measurement. The findings suggest that an accurate point-of-need host response test with high NPV may offer an opportunity to improve antibiotic stewardship and patient outcomes.

WHO Critical Priority Escherichia coli as One Health Challenge for a Post-Pandemic Scenario: Genomic Surveillance and Analysis of Current Trends in Brazil

The dissemination of carbapenem-resistant and third generation cephalosporin-resistant pathogens is a critical issue that is no longer restricted to hospital settings. The rapid spread of critical priority pathogens in Brazil is notably worrying, considering its continental dimension, the diversity of international trade, livestock production, and human travel. We conducted a nationwide genomic investigation under a One Health perspective that included Escherichia coli strains isolated from humans and nonhuman sources, over 45 years (1974–2019). One hundred sixty-seven genomes were analyzed extracting clinically relevant information (i.e., resistome, virulome, mobilome, sequence types [STs], and phylogenomic). The endemic status of extended-spectrum β-lactamase (ESBL)-positive strains carrying a wide diversity of bla_CTX-M variants, and the growing number of colistin-resistant isolates carrying mcr-type genes was associated with the successful expansion of international ST10, ST38, ST115, ST131, ST354, ST410, ST648, ST517, and ST711 clones; phylogenetically related and shared between human and nonhuman hosts, and polluted aquatic environments. Otherwise, carbapenem-resistant ST48, ST90, ST155, ST167, ST224, ST349, ST457, ST648, ST707, ST744, ST774, and ST2509 clones from human host harbored bla_KPC-2 and bla_NDM-1 genes. A broad resistome to other clinically relevant antibiotics, hazardous heavy metals, disinfectants, and pesticides was further predicted. Wide virulome associated with invasion/adherence, exotoxin and siderophore production was related to phylogroup B2. The convergence of wide resistome and virulome has contributed to the persistence and rapid spread of international high-risk clones of critical priority E. coli at the human-animal-environmental interface, which must be considered a One Health challenge for a post-pandemic scenario.

IMPORTANCE A One Health approach for antimicrobial resistance must integrate whole-genome sequencing surveillance data of critical priority pathogens from human, animal and environmental sources to track hot spots and routes of transmission and developing effective prevention and control strategies. As part of the Grand Challenges Explorations: New Approaches to Characterize the Global Burden of Antimicrobial Resistance Program, we present genomic data of WHO critical priority carbapenemase-resistant, ESBL-producing, and/or colistin-resistant Escherichia coli strains isolated from humans and nonhuman sources in Brazil, a country with continental proportions and high levels of antimicrobial resistance. The present study provided evidence of epidemiological and clinical interest, highlighting that the convergence of wide virulome and resistome has contributed to the persistence and rapid spread of international high-risk clones of E. coli at the human-animal-environmental interface, which must be considered a One Health threat that requires coordinated actions to reduce its incidence in humans and nonhuman hosts.

Interrupted Time Series Analysis of Pediatric Infectious Diseases and the Consumption of Antibiotics in an Atlantic European Region during the SARS-CoV-2 Pandemic

The increasing concern about bacterial resistance has made the rational prescription of antibiotics even more urgent. The non-pharmacological measures established to reduce the impact of the SARS-CoV-2 pandemic have modified the epidemiology of pediatric infections and, consequently, the use of antibiotics. Interrupted time series (ITS) analyses are quasi-experimental studies that allow for the estimation of causal effects with observational data in “natural experiments”, such as changes in health policies or pandemics. The effect of the SARS-CoV-2 pandemic on the incidence of infectious diseases and the use of antibiotics between 2018 and 2020 in the Health Area of Vigo (Galicia, Spain) was quantified and analyzed. This paper outlines a real-world data study with administrative records from primary care services provided for the pediatric population. The records were related to episodes classified as infectious by the International Classification of Primary Care (ICPC-2) and oral medication in the therapeutic subgroup J01, corresponding to antibiotics for systemic use, according to the World Health Organization’s Anatomical Therapeutic Chemical (ATC) classification system. The records were classified according to incident episodes, age, dose per inhabitant, and year. Segmented regression models were applied using an algorithm that automatically identifies the number and position of the change points. During the SARS-CoV-2 pandemic, the number of infectious diseases being transmitted between individuals, through the air and through the fecal–oral route, significantly decreased, and a slight decrease in infections transmitted via other mechanisms (urinary tract infections) was also found. In parallel, during the months of the pandemic, there has been a marked and significant reduction in antibacterial agent utilization, mainly of penicillins, cephalosporins, and macrolides.

Clinical presentation of pediatric patients with symptomatic SARS-CoV-2 infection during the first months of the COVID-19 pandemic in a single center in Mexico City

BACKGROUND

The clinical spectrum of COVID-19 is broad, from asymptomatic to severe cases and death. The objective of this study is to analyze the clinical course of patients attended during the first months of the SARS-CoV-2 pandemic in a third-level pediatric hospital.

METHODS

Design: prospective cohort study. Patients with viral respiratory disease or suspected cases of COVID-19 were evaluated at the Pediatric Hospital, National Medical Center XXI Century, Mexico City, from 21 March 2020 to 13 January 2021. Statistical analysis: Chi-square test and Fisher's exact test were used for comparisons; a logistic regression model was constructed to identify clinical or laboratory characteristics associated with critical disease. A p-value < 0.05 was considered statistically significant.

RESULTS

A total of 697 patients met the operational definition of viral respiratory disease or suspected cases of COVID-19 and underwent real-time reverse transcription polymerase chain reaction (rRT-PCR) SARS-CoV-2 testing. Patients with a positive result were included. Of the 181 patients (26%), 121 (66.8%) had mild disease and were treated as outpatients and 60 (33.1%) were hospitalized. A total of six patients met the criteria for multisystem inflammatory syndrome in children (MIS-C). Of the 60 inpatients, 65% were males, and 82% had one or more comorbidities. The main comorbidities were cancer (42%) and overweight (15%). The median hospital stay was 9 days. The inpatients had a higher frequency of fever, general malaise, dyspnea, chills, polypnea, and cyanosis than the outpatients (p < 0.05). Only 21.4% of the outpatients had one or more comorbidities, which were lower than in the hospitalized patients (p < 0.001). Laboratory data at admission were similar between critically ill and those with moderate and severe disease. The patients who developed pneumonia were at higher risk of critical disease, while older age was associated with a better prognosis. A total of 13 of the 60 inpatients died (mortality 7.1%). All but one had one or more comorbidities: four had cancer, four congenital heart disease, one chronic kidney disease and epilepsy, one Epstein-Barr virus-induced hemophagocytic lymphohistiocytosis, one obesity, and one diabetes mellitus.

CONCLUSION

Hospital mortality is high, especially in children with comorbidities. Despite 2 years having passed since the beginning of the COVID-19 pandemic, the epidemiological and clinical data on children are still helpful to improve their prognosis.

Antibiotics Prescribing in Intensive Care Settings during the COVID-19 Era: A Systematic Review

The prevalence of patients admitted to intensive care units (ICUs) with SARS-CoV-2 infection who were prescribed antibiotics is undetermined and might contribute to the increased global antibiotic resistance. This systematic review evaluates the prevalence of antibiotic prescribing in patients admitted to ICUs with SARS-CoV-2 infection using PRISMA guidelines. We searched and scrutinized results from PubMed and ScienceDirect databases for published literature restricted to the English language up to 11 May 2021. In addition, we included observational studies of humans with laboratory-confirmed SARS-CoV-2 infection, clinical characteristics, and antibiotics prescribed for ICU patients with SARS-CoV-2 infections. A total of 361 studies were identified, but only 38 were included in the final analysis. Antibiotic prescribing data were available from 2715 patients, of which prevalence of 71% was reported in old age patients with a mean age of 62.7 years. From the reported studies, third generation cephalosporin had the highest frequency amongst reviewed studies (36.8%) followed by azithromycin (34.2%). The estimated bacterial infection in 12 reported studies was 30.8% produced by 15 different bacterial species, and S. aureus recorded the highest bacterial infection (75%). The fundamental outcomes were the prevalence of ICU COVID-19 patients prescribed antibiotics stratified by age, type of antibiotics prescribed, and the presence of co-infections and comorbidities. In conclusion, more than half of ICU patients with SARS-CoV-2 infection received antibiotics, and prescribing is significantly higher than the estimated frequency of identified bacterial co-infection.

A Direct Rapid Phenotypic Antimicrobial Susceptibility Test Enables Early Selection of Optimal Antibiotics to Treat Bacteremia in COVID-19 Patients

Background

Co-infection with bacteria and severe acute respiratory syndrome coronavirus 2 may result in greater use of healthcare resources and a poor prognosis. Therefore, early selection and use of optimal antibiotics are essential. The direct rapid antibiotic susceptibility test (dRAST) can detect antibiotic resistance within 6 h of a Gram smear result. This study aimed to assess the effectiveness of dRAST for improving early selection of appropriate antibiotics for coronavirus disease 2019 (COVID-19) patients with bacteremia.

Materials and Methods

This retrospective study included 96 blood culture-positive COVID-19 patients. Bacterial isolates and antimicrobial resistance profiles of each case were evaluated. Cases were divided into two groups based on whether they underwent conventional antibiotic susceptibility test (AST) or dRAST. The time to optimal targeted treatment for the two groups was investigated and compared. In addition, we examined the proportion of cases for which appropriate antibiotics were selected and broad spectrum antibiotics were administered at 72 h from blood sample collection.

Results

The mean time to optimal targeted antibiotic treatment was shorter for the dRAST group [55.7; standard deviation (SD), 28.7 vs. 92.3; SD, 51.1 h; P = 0.041]. The proportion of cases receiving optimal targeted antibiotics 72 h after blood collection for culture was higher [6/10 (60.0%) vs. 10/25 (40.0%)] and the percentage receiving broad spectrum antibiotics at 72 h was lower [6/10 (60.0%) vs. 19/25 (76.0%)] in the dRAST group than in the conventional AST group. In terms of microbiology profile, the contamination rate was high (35.5%) and multidrug-resistant strains were common (63.2%) in COVID-19 patients with bacteremia.

Conclusion

Application of dRAST for selection of antibiotics to treat bacteremia in COVID-19 patients may enable earlier and optimal treatment. The high incidence of contamination and resistant organisms in blood cultures from COVID-19 patients suggest that dRAST may speed up appropriate targeted treatment.