Antimicrobial resistance in ICUs: an update in the light of the COVID-19 pandemic

Combined effect of SAR-endolysin LysKpV475 with polymyxin B and Salmonella bacteriophage phSE-5

Endolysins are bacteriophage (or phage)-encoded enzymes that catalyse the peptidoglycan breakdown in the bacterial cell wall. The exogenous action of recombinant phage endolysins against Gram-positive organisms has been extensively studied. However, the outer membrane acts as a physical barrier when considering the use of recombinant endolysins to combat Gram-negative bacteria. This study aimed to evaluate the antimicrobial activity of the SAR-endolysin LysKpV475 against Gram-negative bacteria as single or combined therapies, using an outer membrane permeabilizer (polymyxin B) and a phage, free or immobilized in a pullulan matrix. In the first step, the endolysin LysKpV475 in solution, alone and combined with polymyxin B, was tested in vitro and in vivo against ten Gram-negative bacteria, including highly virulent strains and multidrug-resistant isolates. In the second step, the lyophilized LysKpV475 endolysin was combined with the phage phSE-5 and investigated, free or immobilized in a pullulan matrix, against Salmonella enterica subsp. enterica serovar Typhimurium ATCC 13311. The bacteriostatic action of purified LysKpV475 varied between 8.125 μg ml-1 against Pseudomonas aeruginosa ATCC 27853, 16.25 μg ml-1 against S. enterica Typhimurium ATCC 13311, and 32.50 μg ml-1 against Klebsiella pneumoniae ATCC BAA-2146 and Enterobacter cloacae P2224. LysKpV475 showed bactericidal activity only for P. aeruginosa ATCC 27853 (32.50 μg ml-1) and P. aeruginosa P2307 (65.00 μg ml-1) at the tested concentrations. The effect of the LysKpV475 combined with polymyxin B increased against K. pneumoniae ATCC BAA-2146 [fractional inhibitory concentration index (FICI) 0.34; a value lower than 1.0 indicates an additive/combined effect] and S. enterica Typhimurium ATCC 13311 (FICI 0.93). A synergistic effect against S. enterica Typhimurium was also observed when the lyophilized LysKpV475 at ⅔ MIC was combined with the phage phSE-5 (m.o.i. of 100). The lyophilized LysKpV475 immobilized in a pullulan matrix maintained a significant Salmonella reduction of 2 logs after 6 h of treatment. These results demonstrate the potential of SAR-endolysins, alone or in combination with other treatments, in the free form or immobilized in solid matrices, which paves the way for their application in different areas, such as in biocontrol at the food processing stage, biosanitation of food contact surfaces and biopreservation of processed food in active food packing.

Device-Associated Infections in COVID-19 Patients: Frequency of Resistant Bacteria, Predictors and Mortality in Medellín, Colombia

INTRODUCTION

Increased antimicrobial use during the COVID-19 pandemic has raised concerns about the spread of resistant bacteria. This study analyzed the frequency of device-associated infections (DAI) caused by resistant bacteria, the predictors of these infections, and 30-day all-cause mortality in patients with and without COVID-19.

METHODS

A retrospective cohort study was conducted on DAI patients admitted to the ICU (intensive care unit) in 20 hospitals in Medellin, Colombia (2020-2021). The exposure assessed was the COVID-19 diagnosis, and outcomes analyzed were resistant bacterial infections and 30-day mortality. Clinical and microbiological information was collected from surveillance databases. Statistical analysis included generalized linear mixed-effects models.

RESULTS

Of the 1521 patients included, 1033 (67.9%) were COVID-19-positive and 1665 DAI were presented. Carbapenem-resistant Enterobacteriaceae (CRE) infections predominated during the study (n = 98; 9.9%). The patients with COVID-19 had a higher frequency of metallo-beta-lactamase-producing CRE infections (n = 15; 33.3%) compared to patients without the disease (n = 3; 13.0%). Long-stay in the ICU (RR: 2.09; 95% CI: 1.39-3.16), diabetes (RR: 1.73; 95% CI: 1.21-2.49), and mechanical ventilation (RR: 2.13; 95% CI: 1.01-4.51) were CRE infection predictors in COVID-19 patients, with a mortality rate of 60.3%.

CONCLUSION

CRE infections were predominant in COVID-19 patients. In pandemic situations, the strategies to control DAI should be maintained to avoid infections caused by resistant bacteria, such as length of stay in the ICU and duration of mechanical ventilation.

The impact of the COVID-19 pandemic on gram-negative bacteria susceptibility patterns in respiratory samples of intensive care units in the Brussels Capital Region, 2010-2021

BACKGROUND

The effect of the Coronavirus Disease 2019 (COVID-19) pandemic on gram-negative bacteria nonsusceptibility to antibiotics is unclear.

METHODS

Between January 1, 2010, and December 31, 2021, the respiratory samples of intensive care unit patients at 3 University Hospitals in Brussels were retrieved. Based on the nonsusceptibility to antimicrobial classes, drug-resistance patterns were defined as multi-drug-resistant, extensively drug-resistant, and pan-drug-resistant. The study time frame was divided into 6 periods of 2 years each, and the impact of the COVID-19 pandemic (last period: 2020-2021) was assessed.

RESULTS

During the current study, 10,577 samples were identified from 5,889 patients. While a significant augmentation of multi-drug-resistant isolates was noticed once comparing 2 prepandemic periods (2012-2013 and 2014-2015), all 3 patterns of nonsusceptibility significantly increased, comparing the years before and throughout the COVID-19 pandemic (2018-2019 and 2020-2021). Globally, the greatest increase in antimicrobial nonsusceptibility, comparing the last 2 periods, was reported for piperacillin-tazobactam (from 28% to 38%). Pseudomonas aeruginosa was the most isolated species, and the most involved in the appearance of resistance, with an augmentation of nonsusceptibility percentage to meropenem of 22% (from 25% to 47%), between the prepandemic and the pandemic periods.

CONCLUSIONS

The COVID-19 pandemic was associated with increasing trends of antimicrobial resistance in respiratory samples of patients admitted to the intensive care units in university hospitals with well-implemented antibiotic stewardship programs.

Genomic Surveillance Uncovers a 10-Year Persistence of an OXA-24/40 Acinetobacter baumannii Clone in a Tertiary Hospital in Northern Spain

Infections caused by carbapenem-resistant Acinetobacter baumannii are a global threat causing a high number of fatal infections. This microorganism can also easily acquire antibiotic resistance determinants, making the treatment of infections a big challenge, and has the ability to persist in the hospital environment under a wide range of conditions. The objective of this work was to study the molecular epidemiology and genetic characteristics of two blaOXA24/40Acinetobacter baumannii outbreaks (2009 and 2020-21) at a tertiary hospital in Northern Spain. Thirty-six isolates were investigated and genotypically screened by Whole Genome Sequencing to analyse the resistome and virulome. Isolates were resistant to carbapenems, aminoglycosides and fluoroquinolones. Multi-Locus Sequence Typing analysis identified that Outbreak 1 was mainly produced by isolates belonging to ST3Pas/ST106Oxf (IC3) containing blaOXA24/40, blaOXA71 and blaADC119. Outbreak 2 isolates were exclusively ST2Pas/ST801Oxf (IC2) blaOXA24/40, blaOXA66 and blaADC30, the same genotype seen in two isolates from 2009. Virulome analysis showed that IC2 isolates contained genes for capsular polysaccharide KL32 and lipooligosacharide OCL5. A 8.9 Kb plasmid encoding the blaOXA24/40 gene was common in all isolates. The persistance over time of a virulent IC2 clone highlights the need of active surveillance to control its spread.

Fernández-de-Bobadilla M, Serrano-Tomás MI, Sánchez-Díaz AM, Avendaño-Ortiz J, Coque TM, Ruiz-Garbajosa P, del Campo R, Cantón R. A long-term survey of Serratia spp. bloodstream infections revealed an increase of antimicrobial resistance involving adult population

Serratia spp. is a well-recognized pathogen in neonates; however, limited data are available in adults. We studied microbiological and clinical characteristics of Serratia spp. causing bloodstream infections (BSI) in our institution (January 2005-July 2020). Overall, 141 BSI episodes affecting 139 patients were identified and medical records reviewed. Antimicrobial susceptibility was recovered from our informatics system and 118 isolates from 116 patients were available for further microbiological studies. Whole genome sequencing (WGS) was completed in 107 isolates. Incidence of Serratia BSI was 0.3/1000 overall admissions (range 0.12-0.60), with maximum prevalence (27 episodes, 19.1%) during 2017-2018. Relevant patients' clinical characteristics were 71.9% ≥60 years (n = 100), with high comorbidity rates (49%, ≥2), 23 (74.2%) of them died within 1 month of the BSI episode. WGS identified all isolates as Serratia marcescens when Kraken bioinformatics taxonomic tool was used despite some which were identified as Serratia nematodiphila (32/118) or Serratia ureilytica (5/118) by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Nevertheless, when using MASH distance, Serratia nevei (63/107), S. ureilytica (38/107), and S. marcescens (6/107) were assigned. Carbapenemase (blaVIM-1) and extended-spectrum β-lactases (ESBL) (blaSHV-12) genes were found in seven and three isolates, respectively, one of them expressing both genes. The worldwide-disseminated IncL/M scaffold plasmid was identified in six VIM producers. Four genotypes were established based on their virulence factors and resistome. Serratia spp. emerged as a relevant nosocomial pathogen causing BSI in elderly patients in our hospital, particularly in recent years with a remarkable increase in antibiotic resistance. ESBL and carbapenemases production related to plasmid dissemination are particularly noteworthy.IMPORTANCESerratia spp. is the third most frequent pathogen involved in outbreaks at neonatal facilities and is primarily associated with bacteremia episodes. In this study, we characterized all causing bloodstream infection (BSI) in patients admitted to our hospital during a 16-year period (2005-2020). Despite having no neonatal intensive care unit in our hospital, this study revealed that Serratia spp. is a relevant pathogen causing BSI in elderly patients with high comorbidity rates. A significant increase of antimicrobial resistance was detected over time, particularly in 2020 and coinciding with the coronavirus disease (COVID-19) pandemic and nosocomial spread of multidrug-resistant Serratia spp. isolates. extended-spectrum β-lactases and carbapenemases genes associated with plasmid dissemination, typically detected in other Enterobacterales species, were also identified, reinforcing the role of Serratia spp. in the antimicrobial resistance landscape. Additionally, this work highlights the need to reclassify the species of Serratia, since discrepancies were observed in the identification when using different tools.

An insights into emerging trends to control the threats of antimicrobial resistance (AMR): an address to public health risks

Antimicrobial agents are used to treat microbial ailments, but increased use of antibiotics and exposure to infections in healthcare facilities and hospitals as well as the excessive and inappropriate use of antibiotics at the society level lead to the emergence of multidrug-resistant (MDR) bacteria. Antimicrobial resistance (AMR) is considered a public health concern and has rendered the treatment of different infections more challenging. The bacterial strains develop resistance against antimicrobial agents by limiting intracellular drug accumulation (increasing efflux or decreasing influx of antibiotics), modification and inactivation of drugs and its targets, enzymatic inhibition, and biofilm formation. However, the driving factors of AMR include the sociocultural and economic circumstances of a country, the use of falsified and substandard medicines, the use of antibiotics in farm animals, and food processing technologies. These factors make AMR one of the major menaces faced by mankind. In order to promote reciprocal learning, this article summarizes the current AMR situation in Pakistan and how it interacts with the health issues related to the COVID-19 pandemic. The COVID-19 pandemic aids in illuminating the possible long-term impacts of AMR, which are less immediate but not less severe since their measures and effects are equivalent. Impact on other sectors, including the health industry, the economy, and trade are also discussed. We conclude by summarizing the several approaches that could be used to address this issue.

Impact of coronavirus disease 2019 (COVID-19) on antimicrobial resistance among major pathogens causing healthcare-associated infection

BACKGROUND

Coronavirus disease 2019 (COVID-19) has caused great impact on healthcare systems, including antibiotic usage and multi-drug resistant (MDR) bacterial infections at hospitals. We aim to investigate the trends of antimicrobial resistance among the major pathogens causing healthcare-associated infection (HAI) at intensive care units (ICU).

MATERIAL AND METHODS

The demographic characteristics of hospitalization, usage of antimicrobial agents, counted by half-an-year DID (defined daily dose per 1000 patient-days), and HAI density of five major MDR bacteria, including methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant enterococci (VRE), carbapenem-resistant Acinetobacter baumannii (CRAB), carbapenem-resistant Klebsiella pneumoniae (CRKP), and carbapenem-resistant Pseudomonas aeruginosa (CRPA), of ICU patients at a medical center in Taiwan during January 2017 to December 2021 were collected and analyzed.

RESULTS

The total antibiotic usage, counted by DID, had a significant increasing trend, before COVID-19 occurrence in 2017-2019, but no further increase during the pandemic period in 2020-2021. However, comparing the two time periods, antibiotics consumption was significantly increased during pandemic period. There was no significant change of HAI density in MRSA, VRE, CRAB, CRKP, and CRPA, comparing the pandemic to the pre-pandemic period. Although, CRKP and CRPA infection rates were increasing during the pre-pandemic period, there was no further increase of CRKP and CRPA HAI rates during the pandemic period.

CONCLUSION

During COVID-19 pandemic, there was no significant increase in HAI density of five major MDR bacteria at ICU in Taiwan, despite increased antibiotic usage. Strict infection prevention measures for COVID-19 precautions and sustained antimicrobial stewardship probably bring these effects.

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

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

Update of antimicrobial resistance in level III and IV health institutions in Colombia between January 2018 and December 2021

Introduction

Antimicrobial resistance surveillance is a fundamental tool for the development, improvement, and adjustment of antimicrobial stewardship programs, therapeutic guidelines, and universal precautions to limit the cross-transmission of resistant bacteria between patients. Since the beginning of 2020, the SARS-CoV-2 pandemic profoundly challenged the health system and, according to some reports, increased the rates of antimicrobial resistance.

Objective

To describe the behavior of antimicrobial resistance of the most frequent bacterial pathogens in twenty Colombian hospitals from January 2018 to December 2021.

Materials and methods

We conducted a descriptive study based on the microbiological information recorded from January 2018 to December 2021 in twenty levels III and IV health institutions in twelve Colombian cities. We identified the species of the ten most frequent bacteria along with their resistance profile to the antibiotic markers after analyzing the data through WHONET.

Results

We found no statistically significant changes in most pathogens’ resistance profiles from January 2018 to December 2021. Only Pseudomonas aeruginosa had a statistically significant increase in its resistance profile, particularly to piperacillin/tazobactam and carbapenems.

Conclusions

The changes in antimicrobial resistance in these four years were not statistically significant except for P. aeruginosa to piperacillin/tazobactam and carbapenems.

Evaluation of Acinetobacter baumannii, Klebsiella pneumoniae, and Staphylococcus aureus respiratory tract superinfections among patients with COVID-19 at a tertiary-care hospital in Tehran, Iran

BACKGROUND

The emergence of healthcare-associated infections (HAIs) or superinfections in COVID-19 patients has resulted in poor prognosis and increased mortality.

METHODS

In a cross-sectional study, 101 respiratory samples were collected from ICU-admitted COVID-19 patients. The HAI rate, demographics, and antibiotic resistance were assessed.

RESULTS

The HAI rate was 83.16% (76.62% bacterial and 6.54% fungal). The prevalence of 3 major HAI-causing organisms included Klebsiella pneumoniae (41.5%), Acinetobacter baumannii (20.8%), and Staphylococcus aureus (4.9%). Mortality and intubation ventilation proportions of 90% (p = 0.027) and 92.2% (p = 0.02) were significant among patients with superinfection, respectively. Multiple logistic regression analysis showed SpO2 pressure (odds ratio 0.842; 95% CI 0.750-0.945; p = 0.004) as a predictive factor in the association between antibiotic usage and mortality. More than 50% of patients received carbapenems. The resistance rates to at least one antibiotic of third-generation cephalosporins, aminoglycosides, quinolones/fluoroquinolones, tetracyclines, and β-lactam inhibitors were 95.2%, 95.2%, 90%, 57.1%, and 100% among A. baumannii isolates and 71.4%, 55%, 69%, 61.9%, and 59.5% among K. pneumoniae isolates, respectively. A proportion of 60% was recorded for methicillin-resistant S. aureus isolates.

CONCLUSION

As a result, antibiotic treatment should be administered following the microbial resistance profile. Contact isolation and infection control measures should be implemented as needed.

ESKAPE and Beyond: The Burden of Coinfections in the COVID-19 Pandemic

The ESKAPE group constitute a threat to public health, since these microorganisms are associated with severe infections in hospitals and have a direct relationship with high mortality rates. The presence of these bacteria in hospitals had a direct impact on the incidence of healthcare-associated coinfections in the SARS-CoV-2 pandemic. In recent years, these pathogens have shown resistance to multiple antibiotic families. The presence of high-risk clones within this group of bacteria contributes to the spread of resistance mechanisms worldwide. In the pandemic, these pathogens were implicated in coinfections in severely ill COVID-19 patients. The aim of this review is to describe the main microorganisms of the ESKAPE group involved in coinfections in COVID-19 patients, addressing mainly antimicrobial resistance mechanisms, epidemiology, and high-risk clones.

Antibiotic resistance and consumption before and during the COVID-19 pandemic in Valle del Cauca, Colombia

Objective

To assess changes in antibiotic resistance of eight of the World Health Organization priority bug-drug combinations and consumption of six antibiotics (ceftriaxone, cefepime, piperacillin/tazobactam, meropenem, ciprofloxacin, vancomycin) before (March 2018 to July 2019) and during (March 2020 to July 2021) the COVID-19 pandemic in 31 hospitals in Valle del Cauca, Colombia.

Methods

This was a before/after study using routinely collected data. For antibiotic consumption, daily defined doses (DDD) per 100 bed-days were compared.

Results

There were 23 405 priority bacterial isolates with data on antibiotic resistance. The total number of isolates increased from 9 774 to 13 631 in the periods before and during the pandemic, respectively. While resistance significantly decreased for four selected bug-drug combinations (Klebsiella pneumoniae, extended spectrum beta lactamase [ESBL]-producing, 32% to 24%; K. pneumoniae, carbapenem-resistant, 4% to 2%; Pseudomonas aeruginosa, carbapenem-resistant, 12% to 8%; Acinetobacter baumannii, carbapenem-resistant, 23% to 9%), the level of resistance for Enterococcus faecium to vancomycin significantly increased (42% to 57%). There was no change in resistance for the remaining three combinations (Staphylococcus aureus, methicillin-resistant; Escherichia coli, ESBL-producing; E. coli, carbapenem-resistant). Consumption of all antibiotics increased. However, meropenem consumption decreased in intensive care unit settings (8.2 to 7.1 DDD per 100 bed-days).

Conclusions

While the consumption of antibiotics increased, a decrease in antibiotic resistance of four bug-drug combinations was observed during the pandemic. This was possibly due to an increase in community-acquired infections. Increasing resistance of E. faecium to vancomycin must be monitored. The findings of this study are essential to inform stewardship programs in hospital settings of Colombia and similar contexts elsewhere.

Pseudomonas aeruginosa Bloodstream Infections in SARS-CoV-2 Infected Patients: A Systematic Review

Bacterial co-infections increase the severity of respiratory viral infections and are frequent causes of mortality in COVID-19 infected subjects. During the COVID-19 period, especially at the beginning of the pandemic, an inappropriate use of broad-spectrum antibiotic treatments has been frequently described, mainly due to prolonged hospitalization, especially in intensive care unit departments, and the use of immune-suppressive treatments as steroids. This misuse has finally led to the occurrence of infections by multi-drug resistant (MDR) bacteria in hospitalized COVID-19 patients. Although different reports assessed the prevalence of Gram-negative infections in COVID-19 infected patients, scarce data are currently available on bloodstream infections caused by Pseudomonas aeruginosa in hospitalized COVID-19 patients. The aim of our systematic review is to describe data on this specific population and to discuss the possible implications that these co-infections could have in the management of COVID-19 pandemics in the future. We systematically analysed the current literature to find all the relevant articles that describe the occurrence of P. aeruginosa bloodstream infections in COVID-19 patients. We found 40 papers that described in detail P. aeruginosa HAIs-BSI in COVID-19 patients, including 756,067 patients overall. The occurrence of severe infections due to MDR bacteria had a significant impact in the management of hospitalized patients with COVID-19 infections, leading to a prolonged time of hospitalization and to a consequent increase in mortality. In the near future, the increased burden of MDR bacteria due to the COVID-19 pandemic might partially be reduced by maintaining the preventive measures of infection control implemented during the acute phase of the COVID-19 pandemic. Finally, we discuss how the COVID-19 pandemic changed the role of antimicrobial stewardship in healthcare settings, according to the isolation of MDR bacteria and how to restore on a large scale the optimization of antibiotic strategies in COVID-19 patients.

A Tale of Two Pandemics: Antimicrobial Resistance Patterns of Enterococcus spp. in COVID-19 Era

Although the COVID-19 pandemic has held the spotlight over the past years, the antimicrobial resistance (AMR) phenomenon continues to develop in an alarming manner. The lack of strict antibiotic regulation added to the overuse of antimicrobials fueled the AMR pandemic. This paper aims to analyze and identify the impact of the COVID-19 pandemic on antibiotic resistance patterns of Enterococcus spp. The study was designed as a retrospective observational study. Enterococcus spp. infections data were collected from one academic hospital in Cluj-Napoca, Romania over 18 months. A statistical analysis was performed to compare antibiotic resistance phenotypes identified. We recorded an increase in the isolation rates of Enterococcus spp. strains, from 26 isolates (26.53%) during Period A (November 2020-April 2021) to 42 strains (42.85%) during Period C (November 2021-April 2022). The number of strains with resistance to vancomycin increased from 8 during Period A to 17 during Period C. Of the total 36 strains with resistance to vancomycin, 25 were identified as E. faecium. SARS-CoV-2 patients (n = 29) proved to be at risk to develop an E. faecium co-infection (n = 18). We observed that strains with resistance to ampicillin (n = 20) and vancomycin (n = 15) are more often isolated from these patients. All changes identified in our study are to be considered in the light of COVID-19 pandemic, highlighting the threatening AMR phenomenon in Romania. Further studies should be performed to quantify the worldwide effects of these pandemics.

The Epidemiological Pattern, Resistance Characteristics and Clinical Outcome of Enterobacter cloacae: Recent Updates and Impact of COVID-19 Pandemic

OBJECTIVES

E. cloacae is an opportunistic organism that causes serious infections, particularly in immuno-compromised and hospitalized patients, along with the emergence of resistance traits. The COVID-19 pandemic has impacted the epidemiological pattern and resistance traits of E. cloacae infections as well as those of other bacteria. The study aims to assess the epidemiological patterns, resistance characteristics and clinical outcomes of E. cloacae in Saudi Arabia and the impact of the COVID-19 pandemic.

METHODS

King Fahad Medical City in Riyadh provided the data between January 2019 and December 2021 for the retrospective study of 638 isolates of E. cloacae. The clinical outcome of an E. cloacae infection was also determined by collecting and statistically analyzing the clinical records of 153 ICU patients.

RESULTS

The total percentage of resistant E. cloacae isolates decreased from 48.36% in 2019 to 38% in 2020 and 37.6% in 2021. The overall mortality rate among ICU patients was 40.5%, with an adult age group having a substantial relative risk value of 1.37.

CONCLUSION

E. cloacae is a prevalent nosocomial infection in which adult age is a significant risk factor for mortality. Moreover, this study emphasizes the importance of comparing E. cloacae resistance trends before and throughout the pandemic period in order to better understand the bacteria's behaviour.

Carbapenemase-Producing Klebsiella pneumoniae in COVID-19 Intensive Care Patients: Identification of IncL-VIM-1 Plasmid in Previously Non-Predominant Sequence Types

During the COVID-19 pandemic, intensive care units (ICUs) operated at or above capacity, and the number of ICU patients coinfected by nosocomial microorganisms increased. Here, we characterize the population structure and resistance mechanisms of carbapenemase-producing Klebsiella pneumoniae (CP-Kpn) from COVID-19 ICU patients and compare them to pre-pandemic populations of CP-Kpn. We analyzed 84 CP-Kpn isolates obtained during the pandemic and 74 CP-Kpn isolates obtained during the pre-pandemic period (2019) by whole genome sequencing, core genome multilocus sequence typing, plasmid reconstruction, and antibiotic susceptibility tests. More CP-Kpn COVID-19 isolates produced OXA-48 (60/84, 71.4%) and VIM-1 (18/84, 21.4%) than KPC (8/84, 9.5%). Fewer pre-pandemic CP-Kpn isolates produced VIM-1 (7/74, 9.5%). Cefiderocol (97.3-100%) and plazomicin (97.5-100%) had the highest antibiotic activity against pandemic and pre-pandemic isolates. Sequence type 307 (ST307) was the most widely distributed ST in both groups. VIM-1-producing isolates belonging to ST307, ST17, ST321 and ST485, (STs infrequently associated to VIM-1) were detected during the COVID-19 period. Class 1 integron Int1-bla_VIM-1-aac(6')-1b-dfrB1-aadAI-catB2-qacEΔ1/sul1, found on an IncL plasmid of approximately 70,000 bp, carried bla_VIM-1 in ST307, ST17, ST485, and ST321 isolates. Thus, CP-Kpn populations from pandemic and pre-pandemic periods have similarities. However, VIM-1 isolates associated with atypical STs increased during the pandemic, which warrants additional monitoring and surveillance.

Antibiotic Consumption and Bacterial Resistance Rates in Hospitalized COVID-19 Patients: A Retrospective Study During the 3 First Surges

In our hospital, during COVID-19 pandemic, overall consumption of antibiotics increased during the three first surges, mainly due to ICU prescription However, antibiotic consumption decreased in the Infectious Diseases Department. Rates of ESBL Enterobacterales remained stable.

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.

Les misérables: a Parallel Between Antimicrobial Resistance and COVID-19 in Underdeveloped and Developing Countries

Purpose of Review

The COVID-19 pandemic has been responsible for more than 6.3 million deaths worldwide. During the pandemic, the indiscriminate use of antibiotics has increased, contributing to the spread of multidrug-resistant bacteria. In this review, we aim to determine the spread and impact of antibiotic treatments in patients with COVID-19, focusing on underdeveloped and developing countries.

Recent Findings

Meta-analysis revealed that bacterial co-infections and secondary infections are relatively rare in COVID-19 patients, corresponding to less than 20% of hospitalized patients. Even so, most of these patients have received antibiotic treatments.

Summary

This review discusses how the COVID-19 pandemic could increase the emergence of multidrug-resistant strains to currently available antibiotics. Initially, we discussed the spread and impact of multidrug resistance of ESKAPE pathogens associated with nosocomial infections and analyzed their risk of secondary infections in patients with COVID-19. Then we highlight three factors related to the spread of resistant bacteria during the current pandemic: overprescription of antibiotics followed by self-medication. Finally, we discussed the lack of availability of diagnostic tests to discriminate the etiologic agent of a disease. All these factors lead to inappropriate use of antibiotics and, therefore, to an increase in the prevalence of resistance, which can have devastating consequences shortly. The data compiled in this study underscore the importance of epidemiological surveillance of hospital isolates to provide new strategies for preventing and controlling infections caused by multidrug-resistant bacteria. In addition, the bibliographic research also highlights the need for an improvement in antibiotic prescribing in the health system.

Modification of the immune response by bacteriophages alters methicillin-resistant Staphylococcus aureus infection

There is an urgent need to develop phage therapies for multidrug-resistant bacterial infections. However, although bacteria have been shown to be susceptible to phage therapy, phage therapy is not sufficient in some cases. PhiMR003 is a methicillin-resistant Staphylococcus aureus phage previously isolated from sewage influent, and it has demonstrated high lytic activity and a broad host range to MRSA clinical isolates in vitro. To investigate the potential of phiMR003 for the treatment of MRSA infection, the effects of phiMR003 on immune responses in vivo were analysed using phiMR003-susceptible MRSA strains in a mouse wound infection model. Additionally, we assessed whether phiMR003 could affect the immune response to infection with a nonsusceptible MRSA strain. Interestingly, wounds infected with both susceptible and nonsusceptible MRSA strains treated with phiMR003 demonstrated decreased bacterial load, reduced inflammation and accelerated wound closure. Moreover, the infiltration of inflammatory cells in infected tissue was altered by phiMR003. While the effects of phiMR003 on inflammation and bacterial load disappeared with heat inactivation of phiMR003. Transcripts of proinflammatory cytokines induced by lipopolysaccharide were reduced in mouse peritoneal macrophages. These results show that the immune modulation occurring as a response to the phage itself improves the clinical outcomes of phage therapy.

Relevance of the Consensus Principles for Appropriate Antibiotic Prescribing in 2022

Background

In the late 1990s, as a response to rising antimicrobial resistance (AMR), an independent multinational, interdisciplinary group was formed specifically targeting primary care antibiotic prescribing for community-acquired respiratory tract infections (CA-RTIs). The group comprised senior clinicians from Canada, Israel, Spain, Sweden, UK and USA. The group’s objectives were to provide recommendations for antibiotic stewardship in the community because, whilst it was widely accepted that inappropriate antibiotic use was contributing to AMR, it remained difficult to change prescribing behaviour. The group aimed to identify principles underlying appropriate antibiotic prescribing and guideline formulation to reduce morbidity from CA-RTIs, limit therapeutic failure and, importantly, curb AMR emergence. The group published a report in 2002, which has become known as the Consensus Principles.

Objectives

(i) To consider the relevance of the Consensus Principles in 2022 by reviewing current global approaches to rising AMR. A wide range of factors, such as antibiotic overuse, most recently seen in COVID-19 patients, are still driving rising AMR even though there has been a high-level international response to the AMR threat; and (ii) as an introduction to this Supplement, which reports the findings of analyses of how AMR is being addressed in nine disparate countries (Brazil, India, Kuwait, Mexico, Pakistan, Russia, Saudi Arabia, Türkiye and Vietnam). Understanding how these initiatives are being pursued in different countries helps identify areas where more information is needed.

Conclusions

Adherence to the Consensus Principles remains as important now as it was in 2002. Achieving appropriate antibiotic prescribing is a vital objective in order that the right patient receives the right antibiotics at the right time to ensure optimal clinical outcomes while at the same time helping to limit further increases in AMR.

Activity of meropenem/vaborbactam and comparators against non-carbapenemase-producing carbapenem-resistant Enterobacterales isolates from Europe

Background

Carbapenem-resistant Enterobacterales (CRE) isolates have disseminated worldwide. CREs usually produce a carbapenemase; however, some isolates are negative for known carbapenemases. In this study, we evaluated the activity of meropenem/vaborbactam and comparators against CREs without a carbapenemase (nonCP CREs) collected from European hospitals from 2016 to 2019.

Materials and methods

23 043 Enterobacterales clinical isolates were collected in 41 hospitals located in 20 countries. Susceptibility (S) testing was performed using the broth microdilution method. CLSI/EUCAST (2021) interpretive criteria were used. 978 CREs were identified with MICs >2 mg/L to meropenem or imipenem. Whole-genome sequencing was performed on each CRE isolate. 125 isolates were negative for carbapenemase genes, including blaKPC, blaNDM, blaIMP, blaVIM and blaOXA-48-like. NonCP CRE isolates were analysed for the presence of other β-lactamases, multilocus sequence types (ST) and mutations in outer membrane protein (OMP) sequences.

Results

Most nonCP CRE were Klebsiella pneumoniae (KPN; n = 97/125). 84.0% of nonCP CRE (n = 105) were from Poland, including 88 KPN. The most common β-lactamase was blaCTX-M-15 in 92/125 isolates. OMP disruptions or alterations were noted among 76 KPN. Among KPN isolates that had MLST typing, 30 belonged to ST11, 18 to ST152 and 17 to ST147, while 13 other STs were observed. Susceptibility to meropenem/vaborbactam was 96.0/97.6% (CLSI/EUCAST) while meropenem was 2.4/8.0%S.

Conclusions

Meropenem/vaborbactam had potent in vitro activity against CRE isolates that lacked known carbapenemases. Resistance mechanisms observed among nonCP CREs included acquired β-lactamases and OMP alterations. These results indicate that meropenem/vaborbactam may be a useful treatment for infections caused by nonCP CREs.

Antibacterial, Antibiofilm, and Antioxidant Activity of 15 Different Plant-Based Natural Compounds in Comparison with Ciprofloxacin and Gentamicin

Plant-based natural compounds (PBCs) are comparatively explored in this study to identify the most effective and safe antibacterial agent/s against six World Health Organization concern pathogens. Based on a contained systematic review, 11 of the most potent PBCs as antibacterial agents are included in this study. The antibacterial and antibiofilm efficacy of the included PBCs are compared with each other as well as common antibiotics (ciprofloxacin and gentamicin). The whole plants of two different strains of Cannabis sativa are extracted to compare the results with sourced ultrapure components. Out of 15 PBCs, tetrahydrocannabinol, cannabidiol, cinnamaldehyde, and carvacrol show promising antibacterial and antibiofilm efficacy. The most common antibacterial mechanisms are explored, and all of our selected PBCs utilize the same pathway for their antibacterial effects. They mostly target the bacterial cell membrane in the initial step rather than the other mechanisms. Reactive oxygen species production and targeting [Fe-S] centres in the respiratory enzymes are not found to be significant, which could be part of the explanation as to why they are not toxic to eukaryotic cells. Toxicity and antioxidant tests show that they are not only nontoxic but also have antioxidant properties in Caenorhabditis elegans as an animal model.

Characterization of blaNDM-5-and blaCTX-M-199-Producing ST167 Escherichia coli Isolated from Shared Bikes

Shared bikes as a public transport provide convenience for short-distance travel. Whilst they also act as a potential vector for antimicrobial resistant (AR) bacteria and antimicrobial resistance genes (ARGs). However, the understanding of the whole genome sequence of AR strains and ARGs-carrying plasmids collected from shared bikes is still lacking. Here, we used the HiSeq platform to sequence and analyze 24 Escherichia coli isolated from shared bikes around Metro Stations in Beijing. The isolates from shared bikes showed 14 STs and various genotypes. Two blaNDM-5 and blaCTX-M-199-producing ST167 E. coli have 16 resistance genes, four plasmid types and show >95% of similarities in core genomes compared with the ST167 E. coli strains from different origins. The blaNDM-5- or blaCTX-M-199-carrying plasmids sequencing by Nanopore were compared to plasmids with blaNDM-5- or blaCTX-M-199 originated from humans and animals. These two ST167 E. coli show high similarities in core genomes and the plasmid profiles with strains from hospital inpatients and farm animals. Our study indicated that ST167 E. coli is retained in diverse environments and carried with various plasmids. The analysis of strains such as ST167 can provide useful information for preventing or controlling the spread of AR bacteria between animals, humans and environments.

Long-Term Impact of the COVID-19 Pandemic on In-Hospital Antibiotic Consumption and Antibiotic Resistance: A Time Series Analysis (2015-2021)

The coronavirus disease 2019 (COVID-19)-pandemic-related overload of health systems has compromised the application of antimicrobial stewardship (AS) models and infection prevention and control (IPC) programs. We aimed to evaluate the impact of COVID-19 on antimicrobial consumption (AC) and antimicrobial resistance (AMR) in the University Hospital of Modena. A time series analysis with an autoregressive integrated moving average model was conducted from January 2015 to October 2021 to evaluate the AC in the whole hospital and the intensive care unit (ICU), the incidence density (ID) of bloodstream infections (BSIs) due to the main multidrug-resistant organisms, and of C. difficile infections (CDIs). After an initial peak during the COVID-19 period, a decrease in the trend of AC was observed, both at the hospital (CT: -1.104, p = 0.025) and ICU levels (CT: -4.47, p = 0.047), with no significant difference in the single classes. Among the Gram-negative isolates, we observed a significant increase only in the level of BSIs due to carbapenem-susceptible Pseudomonas aeruginosa (CL: 1.477, 95% CI 0.130 to 2.824, p = 0.032). Considering Gram-positive bacteria, an increase in the level of BSIs due to methicillin-resistant Staphylococcus aureus and in the trend of CDIs were observed, though they did not reach statistical significance (CL: 0.72, 95% CI -0.039 to 1.48, p = 0.062; CT: 1.43, 95% CI -0.002 to 2.863, p = 0.051; respectively). Our findings demonstrated that the increases in AMR and AC that appeared in the first COVID-19 wave may be later controlled by restoring IPC and AS programs to pre-epidemic levels. A coordinated healthcare effort is necessary to address the longer-term impact of COVID-19 on AC to avoid irreversible consequences on AMR.

Non-Antibiotic Drug Repositioning as an Alternative Antimicrobial Approach

The worldwide scenario of antibiotic resistance and the falling number of funds for the development of novel antibiotics have led research efforts toward the study of specific cost-effective strategies aimed at discovering drugs against microbial infections. Among the potential options, drug repositioning, which has already exhibited satisfactory results in other medical fields, came out as the most promising. It consists of finding new uses for previously approved medicines and, over the years, many “repurposed drugs” displayed some encouraging in vitro and in vivo results beyond their initial application. The principal theoretical justification for reusing already existing drugs is that they have known mechanisms of action and manageable side effects. Reuse of old drugs is now considered an interesting approach to overcome the drawbacks of conventional antibiotics. The purpose of this review is to offer the reader a panoramic view of the updated studies concerning the repositioning process of different classes of non-antibiotic drugs in the antimicrobial field. Several research works reported the ability of some non-steroidal anti-inflammatory drugs (NSAIDs), antidepressants, antipsychotics, and statins to counteract the growth of harmful microorganisms, demonstrating an interesting winning mode to fight infectious diseases caused by antimicrobial resistant bacteria.

Nosocomial Outbreak of Extensively Drug-Resistant (Polymyxin B and Carbapenem) Klebsiella pneumoniae in a Collapsed University Hospital Due to COVID-19 Pandemic

We correlated clinical, epidemiological, microbiological, and genomic data of an outbreak with polymyxin B (PB)- and carbapenem-resistant Klebsiella pneumoniae during the COVID-19 pandemic. Twenty-six PB- and carbapenem-resistant K. pneumoniae were isolated from patients in the COVID-19 ICU (Intensive Care Unit), non-COVID-19 ICU (Intensive Care Unit), clinical, or surgical ward. Bacterial identification, drug susceptibility tests, and DNA sequencing were performed, followed by in silico resistance genes identification. All isolates showed extensively drug-resistant (XDR) phenotypes. Four different sequence types (ST) were detected: ST16, ST11, ST258, and ST437. Nineteen isolates were responsible for an outbreak in the ICU in September 2020. They belong to ST258 and harbored the 42Kb IncX3plasmid (pKP98M3N42) with the same genomic pattern of two K. pneumoniae identified in 2018. Twenty-four isolates carried bla_-KPC-2 gene. No plasmid-mediated colistin (mcr) resistance genes were found. Eight isolates presented mgrB gene mutation. The clonal isolates responsible for the outbreak came from patients submitted to pronation, with high mortality rates in one month. XDR-K. pneumoniae detected during the outbreak presented chromosomal resistance to PB and plasmid-acquired carbapenem resistance due to KPC production in most isolates and 42Kb IncX3(pKP98M3N42) plasmid carrying bla_KPC-2 was associated with ST258 isolates. The outbreak followed the collapse of the local healthcare system with high mortality rates.

Part I Antimicrobial resistance: Bacterial pathogens of dermatologic significance and implications of rising resistance

Although the COVID-19 pandemic has been the defining global health crisis of our time, public health officials have been sounding the alarm of another ominous threat for years: an impending antimicrobial resistance crisis. In dermatology, antibiotics are often used for prolonged courses in the treatment of skin and soft tissue infections and common inflammatory skin conditions, increasing the risk of microbiome alteration and antibiotic-related adverse effects, all while exerting consequential selective pressures on both pathogenic and bystander bacteria. In this review, we hope to raise awareness of the crisis of antimicrobial resistance and review resistance concerns related to dermatology-relevant bacterial pathogens.

Ventilator-associated pneumonia in critically ill patients with COVID-19 infection, a narrative review

COVID pneumonitis can cause patients to become critically ill. They may require intensive care and mechanical ventilation. Ventilator-associated pneumonia is a concern. This review aims to discuss the topic of ventilator-associated pneumonia in this group. Several reasons have been proposed to explain the elevated rates of VAP in critically ill COVID patients compared to non-COVID patients. Extrinsic factors include understaffing, lack of PPE and use of immunomodulating agents. Intrinsic factors include severe parenchymal damage, immune dysregulation, along with pulmonary vascular endothelial inflammation and thrombosis. The rate of VAP has been reported at 45.4%, with an ICU mortality rate of 42.7%. Multiple challenges to diagnosis exist. Other conditions such as acute respiratory distress syndrome, pulmonary oedema and atelectasis can present with similar features. Frequent growth of gram-negative bacteria has been shown in multiple studies, with particularly high rates of pseudomonas aeruginosa. The rate of invasive pulmonary aspergillosis has been reported at 4–30%. We would recommend the use of invasive techniques when possible. This will enable de-escalation of antibiotics as soon as possible, decreasing overuse. It is also important to keep other possible causes of ventilator-associated pneumonia in mind, such as COVID-19 associated pulmonary aspergillosis, cytomegalovirus, etc. Diagnostic tests such as galactomannan and B-D-glucan should be considered. These patients may face a long treatment course, with risk of re-infection, along with prolonged weaning, which carries its own long-term consequences.

Delineating the impact of COVID-19 on antimicrobial resistance: An Indian perspective

The COVID-19 pandemic has shattered millions of lives globally and continues to be a challenge to public health due to the emergence of variants of concern. Fear of secondary infections following COVID-19 has led to an escalation in antimicrobial use during the pandemic, while some antimicrobials have been repurposed as treatments for SARS-CoV-2, further driving antimicrobial resistance. India is one of the largest producers and consumers of antimicrobials globally, hence the task of curbing antimicrobial resistance is a huge challenge. Practices like empirical antimicrobial prescription and repurposing of drugs in clinical settings, self-medication and excessive use of antimicrobial hygiene products may have negatively impacted the prevalence of antimicrobial resistance in India. However, the expanded production of antimicrobials and disinfectants during the pandemic in response to increased demand may have had an even greater impact on the threat of antimicrobial resistance through major impacts on the environment. The review provides an outline of the impact COVID-19 can have on antimicrobial resistance in clinical settings and the possible outcomes on the environment. This review calls for the upgrading of existing antimicrobial policies and emphasizes the need for research studies to understand the impact of the pandemic on antimicrobial resistance in India.

Impact of COVID-19 on Antimicrobial Consumption and Spread of Multidrug-Resistance in Bacterial Infections

The spread of COVID-19 pandemic may have affected antibiotic consumption patterns and the prevalence of colonized or infected by multidrug-resistant (MDR) bacteria. We investigated the differences in the consumption of antibiotics easily prone to resistance and the prevalence of MDR bacteria during the COVID-19 pandemic (March 2020 to September 2021) compared to in the pre-pandemic period (March 2018 to September 2019). Data on usage of antibiotics and infections caused by methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant Enterococcus (VRE), carbapenem-resistant Enterobacteriaceae (CRE), carbapenem-resistant Acinetobacter baumannii (CRAB), and carbapenem-resistant Pseudomonas aeruginosa (CRPA) were obtained from hospitalized patients in four university hospitals. The consumption of penicillin with β-lactamase inhibitors (3.4% in ward, 5.8% in intensive care unit (ICU)), and carbapenems (25.9% in ward, 12.1% in ICU) increased during the pandemic period. The prevalence of MRSA (4.7%), VRE (49.0%), CRE (22.4%), and CRPA (20.1%) isolated in clinical samples from the ward and VRE (26.7%) and CRE (36.4%) isolated in clinical samples from the ICU were significantly increased, respectively. Meanwhile, only the prevalence of CRE (38.7%) isolated in surveillance samples from the ward increased. The COVID-19 pandemic is associated with increased consumption of antibiotics and has influenced the prevalence of infections caused by MDR isolates.

High burden and diversity of carbapenemase-producing Enterobacterales observed in wastewater of a tertiary care hospital in Germany

Hospitals are one of the main reservoirs of multi-resistant Enterobacterales (MRE). As MRE are resistant to the most frequently used antibiotics, therapy for patients with MRE infections is challenging. It has been previously described that MRE from hospital wastewater can pass into municipal wastewater and even surface water. In this study, we investigated the diversity and epidemiology of MRE in the wastewater of a large tertiary care hospital. Wastewater samples were collected for a four-day period and tested for the presence of Enterobacterales resistant to 3rd gen. cephalosporins. Representative isolates were further characterized by whole genome sequencing. In 120 β-glucuronidase-producing isolates, 68 Escherichia coli and, interestingly, also 52 Citrobacter freundii were identified. In 120 β-glucosidase-producing isolates 45 Serratia marcescens, 34 Klebsiella oxytoca, 32 Enterobacter cloacae and 9 Klebsiella pneumoniae were observed. For all species various MLST sequence types and different clusters of resistance genes were determined, showing a great diversity within the different Enterobacterales, further corroborated by clonal analysis performed by cgMLST. The most prominent clone was wastewater associated E. coli ST635, which accounted for 47.1% of all E. coli isolates. Interestingly, 45.6% of E. coli, 88.5% of C. freundii, 95.6% of S. marcescens, 91.2% of K. oxytoca, 96.9% of E. cloacae and 88.9% of K. pneumoniae isolates carried a carbapenemase gene, indicating a high burden with carbapenemase-producing Enterobacterales. Comparison with clinical isolates from the same hospital displayed few clonal matches. One wastewater isolate of K. pneumoniae was identified to be closely related compared to a clone that had been introduced into the hospital during an outbreak four years earlier. One E. coli isolate was identified as identical to an isolate from a patient, with inpatient stay during the sampling period. The data obtained in this study highlight the problem of antibiotic resistance of Enterobacterales in hospital wastewater. In particular, the clustered occurrence of carbapenemase genes is of great concern and underscores the problem of increasingly scarce antibiotic options against these bacteria.

The Collateral Effects of COVID-19 Pandemic on the Status of Carbapenemase-Producing Pathogens

The serious challenge of antimicrobial resistance continues to threaten public health and lingers in the era of the coronavirus disease 2019 (COVID-19), declared pandemic by the World Health Organization. While the pandemic has triggered the importance of infection control practices and preventive measures such as physical distancing, hand hygiene, travel reduction and quarantine, the ongoing alarm of antimicrobial resistance seems to accompany the pandemic too. Antimicrobial resistance has been fostered during COVID-19, possibly due to high rate of empirical antibiotic utilization in COVID-19 patients, increased use of biocides, and the disruption of proper healthcare for other conditions. Specifically, carbapenemase-producing Gram-negative bacteria have shown to cause secondary bacterial infections in patients hospitalized for COVID-19. Clinical and microbiological evidence of such infections is accumulating in different parts of the world. With the resilient nature of carbapenemases, their association with mortality, and the limited treatment options available, concerns regarding this group of antibiotic-hydrolyzing enzymes during the pandemic are expected to upsurge. While the additional burden carbapenemases exert on healthcare is worrisome, it remains hidden or abandoned among the various health consequences of the pandemic. The purpose of this minireview is to shed a light on carbapenemase-associated infections during such unprecedented time of COVID-19. A focused insight shall be made into carbapenemases, their implications for COVID-19 patients, and the features and consequences of co-infection, with a review of available evidence from pertinent literature. The importance of increased surveillance for carbapenemase-producers and optimizing their management in relation to the pandemic, shall be addressed as well.

Connections between Orthopedic Conditions and Oxidative Stress: Current Perspective and the Possible Relevance of Other Factors, Such as Metabolic Implications, Antibiotic Resistance, and COVID-19

The general opinion in the literature is that these topics remain clearly understudied and underrated, with many unknown aspects and with controversial results in the respective areas of research. Based on the previous experience of our groups regarding such matters investigated separately, here we attempt a short overview upon their links. Thus, we summarize here the current state of knowledge regarding the connections between oxidative stress and: (a) orthopedic conditions; (b) COVID-19. We also present the reciprocal interferences among them. Oxidative stress is, of course, an interesting and continuously growing area, but what exactly is the impact of COVID-19 in orthopedic patients? In the current paper we also approached some theories on how oxidative stress, metabolism involvement, and even antibiotic resistance might be influenced by either orthopedic conditions or COVID-19. These manifestations could be relevant and of great interest in the context of this current global health threat; therefore, we summarize the current knowledge and/or the lack of sufficient evidence to support the interactions between these conditions.

Short and Concise Peer-to-Peer Teaching—Example of a Successful Antibiotic Stewardship Intervention to Increase Iv to Po Conversion

Antibiotic stewardship (ABS) programs aim to combine effective treatment with minimized antibiotic-related harms. Common ABS interventions are simple and effective, but their implementation in daily practice is often difficult. The aim of our study was to investigate if a single, short, peer-to-peer teaching intervention (junior doctor to junior doctor) during clinical routine can successfully improve antibiotic prescriptions. We performed a quasi-experimental before–after study on a regular care cardiology ward at a large academic medical center in Germany. We evaluated antibiotic use metrics retrospectively and calculated defined daily doses (DDD) with the anatomical therapeutic chemical/DDD classification system of the World Health Organization. We hypothesize that the over-representative use of intravenous administration is a potentially modifiable target, which can be proven by antibiotic use metrics analysis. After a single peer-to-peer teaching session with a focus on indications for iv to po conversion, the normalized percentage of intravenous compared to oral administration significantly decreased (from 86.5 ± 50.3% to 41.4 ± 70.3%). Moreover, after the intervention, antibiotics with high oral bioavailability were no longer administered intravenously at all during the following quarter. Our results indicate that even a single peer-to-peer training session is highly effective in improving the iv to po conversion rate in the short term.

Secondary bacterial infections in patients with coronavirus disease 2019-associated pneumonia

OBJECTIVE

The vast majority of patients who hospitalized with coronavirus disease 2019 are given empirical antibiotic therapy. However, information on the frequency, microorganism species, and resistance rates of secondary bacterial infections in coronavirus disease 2019 patients are insufficient. We aimed to show the frequency of secondary infections and resistance conditions in patients with coronavirus disease 2019 hospitalized in the intensive care unit.

METHODS

The results of tracheal aspirate culture, blood culture, and urine culture obtained from coronavirus disease 2019 patients - at least 2 days after their admission to the intensive care unit - were examined microbiologically.

RESULTS

A total of 514 patients hospitalized in intensive care unit were included in our study. Tracheal aspirate, blood, or urine cultures were collected from 369 patients (71.8%). Bacterial reproduction was detected in at least one sample in 171 (33.3%) of all patients. The rate of respiratory tract infection and/or bloodstream infection was found to be 21%. Acinetobacter baumannii, Klebsiella pneumoniae, and Pseudomonas aeruginosa in tracheal aspirate culture; Coagulase-negative staphylococci, K. pneumoniae, and A. baumannii in blood culture; and Escherichia coli, K. pneumoniae, and Enterococcus faecalis in urine culture were the most common microorganisms. A. baumannii was resistant to most antibiotics except colistin and P. aeruginosa strains were resistant to most antibiotics except amikacin, colistin, cefepime, and imipenem. In K. pneumoniae, the highest meropenem sensitivity (73%) was observed; there was a strong resistance to most of the remaining antibiotics.

CONCLUSIONS

We think that our study can be useful in choosing empirical antibiotic therapy in the coronavirus disease 2019 pandemic and reducing the mortality that may occur with secondary infection.

It is complicated: Potential short- and long-term impact of coronavirus disease 2019 (COVID-19) on antimicrobial resistance—An expert review

As of December 2021, the coronavirus disease 2019 (COVID-19) pandemic has claimed millions of deaths and caused disruptions in health systems around the world. The short- and long-term effects of COVID-19 on antimicrobial resistance (AMR), which was already a global threat before the pandemic, are manifold and complex. In this expert review, we summarize how COVID-19 might be affecting AMR in the short term (by influencing the key determinants antibiotic use, infection control practices and international/local mobility) and which additional factors might play a role in the long term. Whereas reduced outpatient antibiotic use in high-income countries, increased awareness for hand hygiene, and reduced mobility have likely mitigated the emergence and spread of AMR in the short term, factors such as overuse of antibiotics in COVID-19 patients, shortage of personal protective equipment, lack of qualified healthcare staff, and patient overcrowding have presumably facilitated its propagation. Unsurprisingly, international and national AMR surveillance data for 2020 show ambiguous trends. Although disruptions in antibiotic stewardship programs, AMR surveillance and research might promote the spread of AMR, other developments could prove beneficial to the cause in the long term. These factors include the increased public awareness for infectious diseases and infection control issues, the strengthening of the One Health perspective as outlined by the Centers for Disease Control and Prevention, and the unprecedented number of international research collaborations and platforms. These factors could even serve as leverage and provide opportunities to better combat AMR in the future.

Alternative Treatment Strategies for Secondary Bacterial and Fungal Infections Associated with COVID-19

Antimicrobials are essential for combating infectious diseases. However, an increase in resistance to them is a major cause of concern. The empirical use of drugs in managing COVID-19 and the associated secondary infections have further exacerbated the problem of antimicrobial resistance. Hence, the situation mandates exploring and developing efficient alternatives for the treatment of bacterial and fungal infections in patients suffering from COVID-19 or other viral infections. In this review, we have described the alternatives to conventional antimicrobials that have shown promising results and are at various stages of development. An acceleration of efforts to investigate their potential as therapeutics can provide more treatment options for clinical management of drug-resistant secondary bacterial and fungal infections in the current pandemic and similar potential outbreaks in the future. The alternatives include bacteriophages and their lytic enzymes, anti-fungal enzymes, antimicrobial peptides, nanoparticles and small molecule inhibitors among others. What is required at this stage is to critically examine the challenges in developing the listed compounds and biomolecules as therapeutics and to establish guidelines for their safe and effective application within a suitable time frame. In this review, we have attempted to highlight the importance of rational use of antimicrobials in patients suffering from COVID-19 and boost the deployment of alternative therapeutics.

Changes in resistance pattern of ESKAPE pathogens between 2010 and 2020 in the clinical center of University of Szeged, Hungary

The acronym ESKAPE stands for six antibiotic-resistant bacterial pathogens namely, Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp. Monitoring their resistance is an important task for clinical microbiology laboratories. Our aim was to analyze the resistance patterns of these bacteria over ten years in clinical samples of our department. We examined the sample types from which these pathogens were most frequently isolated. The incidence of tests with resistant results for each pathogen in aggregate and the most important subgroups of each was also analyzed. We have also intended to predict the local priorities amongst these pathogens. The results of 1,268,126 antibiotic susceptibility tests performed on a total of 70,099 isolates over this period were examined. Most strains were derived from urine, blood culture, trachea, vagina, wounds, and abscesses. Prevalence of ESKAPE bacteria increased between 2011 and 2020 however, the steepest intensifications were seen in the cases of K. pneumoniae and P. aeruginosa. The number of antibiotic susceptibility tests with resistant results has also increased over the decade but the most notable increase was detected in E. faecium and A. baumannii. Based on the calculation of antimicrobial resistance index for each pathogen, the most serious challenges for us at present are A. baumannii, P. aeruginosa, and E. faecium and their multi-resistant forms. The theoretical prediction of proportion of resistant tests between 2020 and 2030 in our care area draws attention to a worrying trend in the cases of vancomycin-resistant E. faecium and carbapenem-resistant A. baumannii strains.

Antimicrobial and therapeutic effect of probiotics in cases of experimental purulent wounds

Probiotics based on bacteria of the genus Bacillus with a multifactorial mechanism of action are considered as a possible alternative to antibiotics in the treatment of purulent wounds. The aim of the study was to determine the antimicrobial and therapeutic effect of the Arederma probiotic preparation containing probiotic strains of the genus Bacillus in an experimental model of a purulent wound in animals. The antimicrobial efficacy of the probiotic against test strains and clinical isolates of pathogenic and opportunistic microorganisms was studied using the method of delayed antagonism. Staphylococcus aureus ATCC 6538 and Streptococcus pyogenes K-7 were used to model a purulent wound. From the surface of the wounds, bacteria of Staphylococcus, Streptococcus, Enterobacteriaceae, Pseudomonas genera and Enterobacteriaceae family were sown on appropriate selective media for the cultivation and enumeration of different groups of microorganisms by generally accepted microbiological research methods. The formation of a purulent wound in rabbits caused by mechanical skin damage and subsequent double infection with Staphylococcus aureus ATCC 6538 and Streptococcus pyogenes K-7 strains was accompanied with a pronounced inflammatory process, necrosis, the formation of purulent exudate and general intoxication. Representatives of the genera Staphylococcus and Streptococcus, microscopic fungi and, to a lesser extent, members of the family Enterobacteriaceae and Pseudomonas were found on the surface of purulent wounds, which confirmed the development of the infectious-inflammatory process. Treatment of purulent wounds with a suspension of probiotic preparation once a day for 4 days led to their faster healing (gradual attenuation of the inflammatory process, reduction of edema and discharge, as well as their disappearance) compared with untreated purulent wounds (control). Representatives of the Staphylococcus and Streptococcus genera, as well as microscopic fungi, presented in purulent wounds treated with probiotic preparation in much smaller numbers than in the control, and bacteria of the Pseudomonas genus and the Enterobacteriaceae family were not detected at all. The effective antimicrobial effect of this probiotic preparation against opportunistic and pathogenic microorganisms was confirmed by in vitro studies. Therefore, the Arederma probiotic preparation showed an effective therapeutic and antimicrobial effect in the experimental model of a purulent wound in animals, so it can be recommended for further preclinical and clinical studies.

A saponin-polybromophenol antibiotic (CU1) from Cassia fistula Bark Against Multi-Drug Resistant Bacteria Targeting RNA polymerase

Background

Gradual increase of multidrug resistant infections is a threat to the human race as MDR plasmids have acquired.>10 mdr and drug efflux genes to inactivate antibiotics. Plants secret anti-metabolites to retard growth of soil and water bacteria and are ideal source of antibiotics.

Purpose

Purpose of the study is to discover an alternate phyto-drug from medicinal plants of India that selectively kills MDR bacteria.

Methods

MDR bacteria isolated from Ganga river water, milk, chicken meat and human hair for testing phyto-extracts. Eighty medicinal plants were searched and six phyto-extracts were selected having good antibacterial activities as demonstrated by agar-hole assays giving 15 ​mm or greater lysis zone. Phyto-extracts were made in ethanol or methanol (1:5 w/v) for overnight and were concentrated. Preparative TLC and HPLC were performed to purify phytochemical. MASS, NMR, FTIR methods were used for chemical analysis of CU1. In vitro RNA polymerase and DNA polymerase assays were performed for target identification.

Results

CU1 belongs to a saponin bromo-polyphenol compound with a large structure that purified on HPLC C₁₈ column at 3min. CU1 is bacteriocidal but three times less active than rifampicin in Agar-hole assay. While in LB medium it shows greater than fifteen times poor inhibitor due to solubility problem. CU1 inhibited transcription from Escherichia coli as well as Mycobacterium tuberculosis RNA Polymerases. Gel shift assays demonstrated that CU1 interferes at the open promoter complex formation step. On the other hand CU1 did not inhibit DNA polymerase.

Conclusion

Phyto-chemicals from Cassia fistula bark are abundant, less toxic, target specific and may be a safer low cost drug against MDR bacterial diseases.

•

A new saponin-polybromophenol antibiotic (CU1) was isolated from Cassia fistula bark ethanol extract and purified by TLC and HPLC.

•

The CU1 inhibits MDR bacteria isolated from human, animal, milk and water resources using agar-hole assay but highly refractile to in vitro assays using LB media due to poor solubility of CU1 in water.

•

The chemical structure was partially elucidated by Mass, NMR, FT-IR and UV–Vis spectroscopy. It was suggested that triterpine moiety was linked to two polyphenol derivatives with six bromine atoms.

•

The CU1 drug inhibits RNA polymerase of E. coli and M. tuberculosis as compare to conventional drug rifampicin.

•

The CU1 phyto-chemical is less water soluble and less toxic in rat and fish models and will be a low cost drug which is resistant to most mdr bacteria.

Impact of coronavirus disease 2019 on infectious disease treatment and infection control at a tertiary hospital in Japan

Introduction

Coronavirus disease 2019 (COVID-19) has greatly impacted medical care practices. Although the effects on infectious disease treatment and infection control, such as antimicrobial resistance, have been specified, very few reports exist on the specific effects of COVID-19.

Methods

We investigated the effects of COVID-19 on daily medical practices at a tertiary hospital in Japan by comparing the use of hand sanitizers, the detection of bacteria from blood cultures, and the amount dose of antibacterial drugs used for one year before (April 2019 to March 2020, fiscal year 2019.) and after COVID-19 admissions began (April 2020 to March 2021, fiscal year 2020).

Results

The use of hand sanitizers increased by 1.4–3 times during the year after COVID-19 admissions began; the incidence of methicillin-susceptible Staphylococcus aureus and all S. aureus detected in blood cultures reduced in all departments. No decrease was observed in the usage of all antibacterial drugs; rather, the usage of all antibacterial drugs tended to increase in all departments. Therefore, no significant change was observed in the detection of drug-resistant bacteria and the trends of antibacterial drug use based on the acceptance of COVID-19 patients.

Conclusions

The prevalence of drug-resistant bacteria and trends of antibacterial drug use remained unchanged despite the increased use of hand sanitizers due to the admission of patients with COVID-19.

Mapping of New Pharmacological Alternatives in the Face of the Emergence of Antibiotic Resistance in COVID-19 Patents Treated for Opportunistic Respiratory Bacterial Pathogens

BACKGROUND

The increase in bacterial resistance against antibiotics is thought to be another type of pandemic after COVID-19. Emergency treatment based on antibiotics is a major influence in increasing this resistance. Bacteria, such as Klebsiella pneumoniae, are the most affected by the indiscriminate use of antibiotics, since they are resistant to most antibiotics currently available on the market.

OBJECTIVE

This review aimed to evaluate patents of new drugs and formulations, for the treatment of infections caused by Klebsiella pneumoniae.

METHODS

The present patent review was carried out through a specialized search database Espacenet. The selection was based on the criteria of patents published from 2010 to May 2021, in any language, and containing the keywords in title or abstract. Also, a research was performed on the PubMed database, using the inclusion criteria.

RESULTS

Twenty-two patents were selected for the analysis according to the aim of the study. The advance of new patents has been mostly observed in the World Intellectual Property Organization, China, and United States. The results showed that the main approach was the drug association, followed by drug carriers, new isolated products, and vaccines.

CONCLUSION

It has been observed that few studies use new drug alternatives for the treatment, probably due to the higher cost of the development and lack of investments. The effectiveness and safety of these therapies depend on the acceptance, the correct prescription, and rational use of medicines. Therefore, this review can further develop new treatments as alternatives against Klebsiella pneumoniae and pneumonia caused by it.

COVID-19 pandemic and antimicrobial resistance in developing countries

A wide range of antimicrobial agents were touted as potential remedies during the COVID-19 pandemic. While both developed and developing countries have recorded an increase in the use of antimicrobial drugs, use and misuse have occurred to a far greater degree in developing countries. This can have deleterious consequences on antimicrobial resistance, especially when various developing countries have already reported the emergence of various drug-resistant organisms even before the pandemic. Telemedicine services, societal and cultural pressures, and bacterial co-infections can predispose to overwhelming antimicrobial prescriptions. The emergence of new multidrug resistance species is a major concern for the developing world especially since health services are already overburdened and lack the diagnostic capabilities and basic amenities for infection prevention and control. This can lead to outbreaks and the rampant spread of such microorganisms. Improper waste management and disposal from hospitals and communities establish freshwater runoffs as hubs of various microorganisms that can predispose to the rise of multidrug-resistant species. Microplastics' ability to act as vectors for antibiotic-resistant organisms is also particularly concerning for lower-middle-income countries. In this review, we aim to study the impact of antimicrobial use during the COVID-19 pandemic and antimicrobial resistance in lower middle-income countries, by understanding various determinants of resistance unique to the developing world and exploring solutions to combat the problem.

Phenotypic and genotypic characteristics of carbapenemase- and extended spectrum β-lactamase-producing Klebsiella pneumoniae ozaenae clinical isolates within a hospital in Panama City

Klebsiella pneumoniae spp ozaenae is a versatile bacterial species able to acquire antimicrobial resistance; the species presents a higher antimicrobial resistance profile compared to Klebsiella pneumoniae spp pneumoniae. Carbapenemase and extended spectrum β-lactamase (ESBL)-producing bacteria commonly arise in clinical settings where antimicrobial stewardship is limited. Our study aims to report the phenotypical and genetic characteristics of nosocomial Klebsiella pneumoniae spp ozaenae isolates associated with mortality collected from a tertiary-level hospital in Panama City. In October 2020, 11 consecutive multidrug-resistant Gram-negative isolates were recovered from secretions and blood cultures from hospitalized patients. Nearly 90% (10/11) of these patients died, and bacteria was obtained from six patients for investigation. Biochemical evaluation of the six isolates revealed the presence of multidrug-resistant Klebsiella pneumoniae spp ozaenae. Phenotypic evaluation indicated resistance to carbapenemase and EBSL. In contrast, genetic evaluation by PCR showed that only 30% (2/6) were resistant to CTX-M-1 (CTX-M group 1), whereas 60.7% (4/6) presented carbapenemase resistance genes, and 33.3% (2/6) presented New Delhi metallo-β-lactamase (NDM) resistance genes. Klebsiella pneumoniae ST258 was identified in 83.3% (5/6) of the isolates. Phylogenetic analysis using 16S revealed low homology among the six isolates. These results suggest that antibiotic resistance genes may have been incorporated into these Klebsiella pneumoniae spp ozaenae isolates within the hospital environment. We recommend strengthening the antimicrobial stewardship program and antibiotic control policy, as well as heightened infection control and prevention measures, such as ward sanitation and increased hand washing frequency.

Surging bloodstream infections and antimicrobial resistance during the first wave of COVID-19: a study in a large multihospital institution in the Paris region

Objectives

This study measured the impact of the first wave of COVID-19 pandemic (COVID-19) (March–April 2020) on the incidence of bloodstream infections (BSIs) at Assistance Publique – Hôpitaux de Paris (APHP), the largest multisite public healthcare institution in France.

Methods

The number of patient admission blood cultures (BCs) collected, number of positive BCs, and antibiotic resistance and consumption were analysed retrospectively for the first quarter of 2020, and also for the first quarter of 2019 for comparison, in 25 APHP hospitals (ca. 14 000 beds).

Results

Up to a fourth of patients admitted in March–April 2020 in these hospitals had COVID-19. The BSI rate per 100 admissions increased overall by 24% in March 2020 and 115% in April 2020, and separately for the major pathogens (Escherichia coli, Klebsiella pneumoniae, enterococci, Staphylococcus aureus, Pseudomonas aeruginosa, yeasts). A sharp increase in the rate of BSIs caused by microorganisms resistant to third-generation cephalosporins (3GC) was also observed in March–April 2020, particularly in K. pneumoniae, enterobacterial species naturally producing inducible AmpC (Enterobacter cloacae...), and P. aeruginosa. A concomitant increase in 3GC consumption occurred.

Conclusions

The COVID-19 pandemic had a strong impact on hospital management and also unfavourable effects on severe infections, antimicrobial resistance, and laboratory work diagnostics.

In vitro synergistic activity of aztreonam (AZT) plus novel and old β-lactamase inhibitor combinations against metallo-β-lactamase-producing AZT-resistant Enterobacterales

The emergence of metallo-β-lactamase (MBL)-producing Enterobacterales, mainly New Delhi metallo-β-lactamase (NDM), represents a clinical threat due to the limited therapeutic alternatives. Aztreonam (AZT) is stable to MBLs, but most MBL-producing Enterobacterales isolates usually co-harbour other β-lactamases that confer resistance to AZT and, consequently, its use is restricted in these isolates. We compared the ability of sulbactam (SUL), tazobactam (TAZ), clavulanic acid (CLA) and avibactam (AVI) to restore the AZT activity in MBL-producing AZT-resistant Enterobacterales isolates. A collection of 64 NDM-producing AZT-resistant Enterobacterales from five hospitals in Buenos Aires city, Argentina, were studied during the period July-December 2020. MICs were determined using the agar dilution method with Mueller-Hinton agar according to Clinical and Laboratory Standards Institute (CLSI) recommendations. AVI, SUL and TAZ were used at a fixed concentration of 4 mg l^-1, whereas CLA was used at a fixed concentration of 2 mg l^-1. A screening method based on disc diffusion to evaluate this synergy was also conducted. Detection of bla _KPC, bla _OXA, bla _NDM, bla _VIM, bla _CTXM-1, bla _PER-2 and bla _CIT was performed by PCR. The AZT-AVI combination restored the AZT activity in 98.4 % of AZT-resistant strains, whereas CLA, TAZ and SUL did so in 70.3, 15.6 and 12.5 %, respectively, in isolates co-harbouring extended-spectrum β-lactamases, but were inactive in isolates harbouring AmpC-type enzymes and/or KPC. The synergy screening test showed an excellent negative predictive value to confirm the absence of synergy, but positive results should be confirmed by a quantitative method. The excellent in vitro performance of the AZT-CLA combination represents a much more economical alternative to AZT-AVI, which could be of use in the treatment of MBL-producing, AZT-resistant Enterobacterales.

COVID-19: Impact on prescribing and antimicrobial resistance

The onset of the COVID-19 pandemic challenged health-care systems focusing their activity on patients infected with SARS-CoV-2. Previous experience with co-infections and superinfections in patients infected with other coronaviruses (SARS-CoV and MERS), the influenza patients admitted to hospitals and prevention of the unknown led to the increased empirical use of broad-spectrum antibiotics in hospitals. The breakdown of antimicrobial stewardship and infection control programs determine an increase in infections due to multi-drug-resistant bacteria, particularly in intensive care units. Most of these infections are related to high-risk carbapenemase-producing clones and occasionally with resistance to new β-lactamβ-lactamase inhibitor combinations. On the contrary, in the primary care, there has been a decrease in the use of antimicrobials during the first wave, although it would not have had a significant impact on pathogens associated with community-acquired infections. The accumulated experience reaffirms the need to maintain antimicrobial stewardship and infection control programs in future health crises.