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Pathogens
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Antimicrobial Resistance Trends in the COVID-19 Pandemic
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Antimicrobial Resistance Trends in the COVID-19 Pandemic

A special issue of Pathogens (ISSN 2076-0817). This special issue belongs to the section "Bacterial Pathogens".

Deadline for manuscript submissions: closed (31 August 2023) | Viewed by 12771

Special Issue Editor

Dr. Branka Bedenic

E-Mail Website
Guest Editor
Department of Microbiology, School of Medicine, University of Zagreb, Šalata 2, Zagreb, Croatia
Interests: beta-lactamases; carbapenemases; extended-spectrum beta-lactamases; Acinetobacter baumannii; Enterobacteriacae
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The current worldwide pandemic of SARS-CoV-2, the causative agent of COVID-19, highlights the need to analyze the bacterial causative agents of ventilator-associated pneumonia (VAP) and other bacteria coinfections which often complicate pneumonia associated with the coronavirus. Secondary bacterial infections, particularly with resistant bacteria, seem to complicate clinical presentation of COVID-19 and cause increased mortality and length of hospital stay. Increased antibiotic consumption in COVID units favors proliferation of resistant Gram-negative bacteria. There are different species of multidrug-resistant (MDR) or extensively drug-resistant (XDR) organisms which cause bacterial superinfections in COVID-19 patients, such as ventilator-associated pneumonia (VAP) and bloodstream infections (BSI). ESKAPE pathogens are the most frequent isolates associated with VAP. Infections due to MDR bacteria are difficult to treat due to limited therapeutic options. Colistin was considered a last-resort antibiotic for the treatment of infections due to carbapenemase-producing Gram-negative bacteria, but resistance to this antibiotic has recently increased.

The aim of this Special Issue is to analyze the new trends of antimicrobial resistance in the era of the COVID-19 pandemic, war, and other disasters, new resistance traits, laboratory methods in the identification and analysis of resistance determinants, and new therapeutic approaches to treat infections associated with them. 

Topics:

  • multidrug-resistant bacteria in COVID-19 intensive care units
  • mechanisms of antibiotic resistance
  • extended-spectrum beta-lactamases
  • carbapenemases
  • plasmid-mediated Amp-C beta-lactamases
  • colistin resistance
  • vancomycin resistance in enterococci
  • linezolid resistance Gram-positive bacteria
  • laboratory identification and characterization of multidrug-resistant bacteria
  • new therapeutic options

Prof. Dr. Branka Bedenic
Guest Editor

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Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2200 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • extended-spectrum beta-lactamases
  • carbapanemases
  • methicillin-resistant Staphylococcus aureus (MRSA)
  • vancomycin-resistant Enterococcus faecalis (VRE)
  • carbapenem-resistant Acinetobacter baumannii (CRAB)

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Published Papers (5 papers)

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12 pages, 277 KiB  
Article
Emergence and Spread of Enterobacterales with Multiple Carbapenemases after COVID-19 Pandemic
by Branka Bedenić, Josefa Luxner, Haris Car, Sanda Sardelić, Maja Bogdan, Dijana Varda-Brkić, Sandra Šuto, Andrea Grisold, Nataša Beader and Gernot Zarfel
Pathogens 2023, 12(5), 677; https://doi.org/10.3390/pathogens12050677 - 3 May 2023
Cited by 11 | Viewed by 2069
Abstract
Resistance to carbapenems in Enterobacterales has become a matter of the highest concern in the last decade. Recently, Enterobacterales harboring multiple carbapenemases were detected in three hospital centers in Croatia and in the outpatient setting, posing a serious therapeutic challenge for clinicians. In [...] Read more.
Resistance to carbapenems in Enterobacterales has become a matter of the highest concern in the last decade. Recently, Enterobacterales harboring multiple carbapenemases were detected in three hospital centers in Croatia and in the outpatient setting, posing a serious therapeutic challenge for clinicians. In this study, we analyzed eight Klebsiella pneumoniae and two Enterobacter cloacae complex isolates with multiple carbapenemases, with regard to antibiotic susceptibility, β-lactamase production and plasmid content. The isolates demonstrated uniform resistance to amoxicillin/clavulanate, piperacillin/tazobactam, cefuroxime, ceftazidime, cefotaxime, ceftriaxone and ertapenem. Among novel β-lactam/inhibitor combinations, ceftazidime/avibactam exhibited moderate activity, with 50% of isolates susceptible. All isolates demonstrated resistance to imipenem/cilastatin/relebactam, and all but one to ceftolozane/tazobactam. Four isolates exhibited a multidrug-resistant phenotype (MDR), whereas six were allocated to an extensively drug-resistant phenotype (XDR). OKNV detected three combinations of carbapenemases: OXA-48+NDM (five isolates), OXA-48+VIM (three isolates) and OXA-48+KPC (two isolates). Inter-array testing identified a wide variety of resistance genes for β-lactam antibiotics: blaCTX-M-15, blaTEM, blaSHV, blaOXA-1, blaOXA-2, blaOXA-9, aminoglycosides: aac6, aad, rmt, arm and aph, fluoroquinolones: qnrA, qnrB and qnrS, sulphonamides: sul1 and sul2 and trimethoprim: dfrA5, dfrA7, dfrA14, dfrA17 and dfrA19. mcr genes were reported for the first time in Croatia. This study demonstrated the ability of K. pneumoniae and E. cloacae to acquire various resistance determinants under the selection pressure of antibiotics widely used during the COVID-19 pandemic. The novel inter-array method showed good correlation with OKNV and PCR, although some discrepancies were found. Full article
(This article belongs to the Special Issue Antimicrobial Resistance Trends in the COVID-19 Pandemic)
9 pages, 509 KiB  
Article
Bacterial Co-Infections and Antimicrobial Resistance in Patients Hospitalized with Suspected or Confirmed COVID-19 Pneumonia in Kazakhstan
by Alyona Lavrinenko, Svetlana Kolesnichenko, Irina Kadyrova, Anar Turmukhambetova, Lyudmila Akhmaltdinova and Dmitriy Klyuyev
Pathogens 2023, 12(3), 370; https://doi.org/10.3390/pathogens12030370 - 23 Feb 2023
Cited by 6 | Viewed by 2570
Abstract
Our study was carried out to characterize respiratory tract microbiota in patients with “COVID-like pneumonia” in Kazakhstan and analyze differences between COVID-19 positive and negative groups. Sputum samples were collected from hospitalized patients, ≥18 years old, in the three cities in Kazakhstan with [...] Read more.
Our study was carried out to characterize respiratory tract microbiota in patients with “COVID-like pneumonia” in Kazakhstan and analyze differences between COVID-19 positive and negative groups. Sputum samples were collected from hospitalized patients, ≥18 years old, in the three cities in Kazakhstan with the highest COVID-19 burden in July 2020. Isolates were identified by MALDI-TOF MS. Susceptibility testing was performed by disk diffusion. We used SPSS 26 and MedCalc 19 for statistical analysis. Among 209 patients with pneumonia, the median age was 62 years and 55% were male. RT-PCR-confirmed SARS-CoV-2 cases were found in 40% of patients, and 46% had a bacterial co-infection. Co-infection was not associated with SARS-CoV-2 RT-PCR test results, but antibiotic use was. The most frequent bacteria were Klebsiella pneumoniae (23%), Escherichia coli (12%), and Acinetobacter baumannii (11%). Notably, 68% of Klebsiella pneumoniae had phenotypic evidence of extended-spectrum beta-lactamases in disk diffusion assays, 87% of Acinetobacter baumannii exhibited resistance to beta-lactams, and >50% of E. coli strains had evidence of ESBL production and 64% were resistant to fluoroquinolones. Patients with a bacterial co-infection had a higher proportion of severe disease than those without a co-infection. The results reinforce the importance of using appropriate targeted antibiotics and effective infection control practices to prevent the spread of resistant nosocomial infections. Full article
(This article belongs to the Special Issue Antimicrobial Resistance Trends in the COVID-19 Pandemic)
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15 pages, 299 KiB  
Article
Multidrug-Resistant Bacteria in a COVID-19 Hospital in Zagreb
by Branka Bedenić, Vesna Bratić, Slobodan Mihaljević, Anita Lukić, Karlo Vidović, Krešimir Reiner, Silvia Schöenthaler, Ivan Barišić, Gernot Zarfel and Andrea Grisold
Pathogens 2023, 12(1), 117; https://doi.org/10.3390/pathogens12010117 - 10 Jan 2023
Cited by 8 | Viewed by 2475
Abstract
During November to December 2020, a high rate of COVID-19-associated pneumonia with bacterial superinfections due to multidrug-resistant (MDR) pathogens was recorded in a COVID-19 hospital in Zagreb. This study analyzed the causative agents of bacterial superinfections among patients with serious forms of COVID-19. [...] Read more.
During November to December 2020, a high rate of COVID-19-associated pneumonia with bacterial superinfections due to multidrug-resistant (MDR) pathogens was recorded in a COVID-19 hospital in Zagreb. This study analyzed the causative agents of bacterial superinfections among patients with serious forms of COVID-19. In total, 118 patients were hospitalized in the intensive care unit (ICU) of the COVID-19 hospital. Forty-six out of 118 patients (39%) developed serious bacterial infection (VAP or BSI or both) during their stay in ICU. The total mortality rate was 83/118 (70%). The mortality rate due to bacterial infection or a combination of ARDS with bacterial superinfection was 33% (40/118). Six patients had MDR organisms and 34 had XDR (extensively drug-resistant). The dominant species was Acinetobacter baumannii with all isolates (34) being carbapenem-resistant (CRAB) and positive for carbapenem-hydrolyzing oxacillinases (CHDL). One Escherichia coli causing pneumonia harboured the blaCTX-M-15 gene. It appears that the dominant resistance determinants of causative agents depend on the local epidemiology in the particular COVID center. Acinetobacter baumannii seems to easily spread in overcrowded ICUs. Croatia belongs to the 15 countries in the world with the highest mortality rate among COVID-19 patients, which could be in part attributable to the high prevalence of bacterial infections in local ICUs. Full article
(This article belongs to the Special Issue Antimicrobial Resistance Trends in the COVID-19 Pandemic)

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7 pages, 903 KiB  
Brief Report
No Changes in the Occurrence of Methicillin-Resistant Staphylococcus aureus (MRSA) in South-East Austria during the COVID-19 Pandemic
by Gernot Zarfel, Julia Schmidt, Josefa Luxner and Andrea J. Grisold
Pathogens 2023, 12(11), 1308; https://doi.org/10.3390/pathogens12111308 - 2 Nov 2023
Cited by 2 | Viewed by 1759
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is a universal threat. Once being well established in the healthcare setting, MRSA has undergone various epidemiological changes. This includes the emergence of more aggressive community-acquired MRSA (CA-MRSA) and the occurrence of MRSA which have their origin in animal [...] Read more.
Methicillin-resistant Staphylococcus aureus (MRSA) is a universal threat. Once being well established in the healthcare setting, MRSA has undergone various epidemiological changes. This includes the emergence of more aggressive community-acquired MRSA (CA-MRSA) and the occurrence of MRSA which have their origin in animal breeding, called livestock-associated MRSA (LA-MRSA). Emergence of new clones as well as changes in the occurrence of some clonal lineages also describes the fluctuating dynamic within the MRSA family. There is paucity of data describing the possible impact of the COVID-19 pandemic on the MRSA dynamics. The aim of the study was the analysis of MRSA isolates in a three-year time period, including the pre-COVID-19 years 2018 and 2019 and the first year of the pandemic 2020. The analysis includes prevalence determination, antibiotic susceptibility testing, spa typing, and detection of genes encoding the PVL toxin. The MRSA rate remained constant throughout the study period. In terms of a dynamic within the MRSA family, only a few significant changes could be observed, but all except one occurred before the start of the COVID-19 pandemic. In summary, there was no significant impact of the COVID-19 pandemic on MRSA in Austria. Full article
(This article belongs to the Special Issue Antimicrobial Resistance Trends in the COVID-19 Pandemic)
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7 pages, 254 KiB  
Brief Report
Dissemination of Clinical Acinetobacter baumannii Isolate to Hospital Environment during the COVID-19 Pandemic
by Emina Pustijanac, Jasna Hrenović, Mirna Vranić-Ladavac, Martina Močenić, Natalie Karčić, Lorena Lazarić Stefanović, Irena Hrstić, Jasenka Lončarić, Martina Šeruga Musić, Marina Drčelić, Dijana Majstorović and Ines Kovačić
Pathogens 2023, 12(3), 410; https://doi.org/10.3390/pathogens12030410 - 3 Mar 2023
Cited by 7 | Viewed by 3180
Abstract
The aim of this study was to find the source of Acinetobacter baumannii in the intensive care unit (ICU) after an outbreak during the coronavirus disease 2019 (COVID-19) pandemic, as there was no A. baumannii detected on usually screened susceptible surfaces. The screening [...] Read more.
The aim of this study was to find the source of Acinetobacter baumannii in the intensive care unit (ICU) after an outbreak during the coronavirus disease 2019 (COVID-19) pandemic, as there was no A. baumannii detected on usually screened susceptible surfaces. The screening of the ICU environment was done in April 2021 when eleven different samples were taken. One A. baumannii isolate was recovered from the air conditioner and was compared with four clinical A. baumannii isolates obtained from patients hospitalized in January 2021. Isolates were confirmed by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), minimum inhibitory concentrations (MICs) were determined, and the multilocus sequence typing (MLST) was performed. The molecular identification of A. baumannii isolates as ST208, the presence of the same blaOXA-23 carbapenemase gene, and the same antibiotic susceptibility profile suggest that the isolate recovered from the air conditioner is the same as the isolates recovered from hospitalized patients. The environmental isolate was recovered three months later than the clinical isolates, emphasizing the ability of A. baumannii to survive on dry abiotic surfaces. The air conditioner in the clinical environment is an important but undoubtedly neglected source of A. baumannii outbreaks, hence, frequent disinfection of hospital air conditioners with appropriate disinfectants is mandatory to mitigate the circulation of A. baumannii between patients and the hospital environment. Full article
(This article belongs to the Special Issue Antimicrobial Resistance Trends in the COVID-19 Pandemic)
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