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Microorganisms
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Molecular Epidemiology of Antimicrobial Resistance, 2nd Edition
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Molecular Epidemiology of Antimicrobial Resistance, 2nd Edition

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Antimicrobial Agents and Resistance".

Deadline for manuscript submissions: closed (31 October 2024) | Viewed by 13212

Special Issue Editors

Prof. Dr. Raffaele Zarrilli

E-Mail Website
Guest Editor
Department of Public Health, University of Naples Federico II, Naples, Italy
Interests: genotyping; horizontal gene transfer of antimicrobial resistance; MDR Acinetobacter baumannii; MDR Klebsiella pneumoniae; molecular epidemiology of healthcare-associated infections
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Asad U. Khan

E-Mail Website
Guest Editor
Medical Microbiology and Molecular Biology Lab, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
Interests: antimicrobial resistance; CRISPR; biofilm; quorum sensing

Special Issue Information

Dear Colleagues,

Antimicrobial resistance and multidrug-resistant organisms currently constitute a severe public health problem. Multidrug-resistant (MDR) organisms are resistant to multiple antibiotic classes, resulting in limited therapeutic options and difficult-to-treat health-care-associated and community infections, with high morbidity and mortality rates. In particular, carbapenem-resistant (CR) Acinetobacter baumannii, CR Pseudomonas aeruginosa, CR Enterobacterales, methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus spp. are recognized by the World Health Organization as global priority pathogens of critical or high priority (doi:10.1590/S0100-15742013000100018). In the A. baumannii group, other MDR species such as A. nosocomialis, A. pittii, A. seifertii, and A. lactucae are emerging. The spread of MDR organisms is contributed to by tolerance to biocides, used as antiseptics or disinfectants. It is therefore evident that infections by MDR organisms entail challenges in their detection, control, and management. This Special Issue is dedicated to updates on the “Molecular Epidemiology of Antimicrobial Resistance”. We invite contributors to submit original research papers, reviews, short notes, or commentaries in the following primary areas:

  • new or changing patterns in the epidemiology of MDR organisms and antimicrobial resistances;
  • molecular determinants, genetic and genomic elements of antimicrobial resistance and tolerance to biocides;
  • diagnostics and detection methods of antimicrobial resistances;
  • description of new mechanisms of resistance and/or tolerance to antimicrobial compounds of clinical interest; and
  • management, therapeutics, and strategies for the prevention and control of infections caused by MDR organisms.

Prof. Dr. Raffaele Zarrilli
Prof. Dr. Asad U. Khan
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 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

  • molecular epidemiology of antimicrobial resistance
  • CR Enterobacterales
  • CR Acinetobacter baumannii
  • methicillin-resistant Staphylococcus aureus
  • diagnostics
  • mobile genetic elements
  • antimicrobial therapy

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Published Papers (5 papers)

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Research

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15 pages, 4046 KiB  
Article
Healthcare Equipment and Personnel Reservoirs of Carbapenem-Resistant Acinetobacter baumannii Epidemic Clones in Intensive Care Units in a Tunisian Hospital
by Sana Azaiez, Marisa Haenni, Asma Ben Cheikh, Mohamed Sahbi Chalbi, Aziza Messaoudi, Lamia Tilouch, Sana Bahri, Antoine Drapeau, Estelle Saras, Mariem Mtibâa, Rania Zouaoui, Houyem Said, Jean-Yves Madec, Agnese Lupo and Wejdene Mansour
Microorganisms 2023, 11(11), 2637; https://doi.org/10.3390/microorganisms11112637 - 26 Oct 2023
Cited by 1 | Viewed by 1890
Abstract
Carbapenem-resistant Acinetobacter baumannii (CRAB) strains can cause severe and difficult-to-treat infections in patients with compromised general health. CRAB strains disseminate rapidly in nosocomial settings by patient-to-patient contact, through medical devices and inanimate reservoirs. The occurrence of CRAB in patients residing in the intensive [...] Read more.
Carbapenem-resistant Acinetobacter baumannii (CRAB) strains can cause severe and difficult-to-treat infections in patients with compromised general health. CRAB strains disseminate rapidly in nosocomial settings by patient-to-patient contact, through medical devices and inanimate reservoirs. The occurrence of CRAB in patients residing in the intensive care units (ICUs) of the Sahloul University hospital in Sousse, Tunisia is high. The objective of the current study was to determine whether the surfaces of items present in five ICU wards and the medical personnel there operating could serve as reservoirs for CRAB strains. Furthermore, CRAB isolates from patients residing in the ICUs during the sampling campaign were analyzed for genome comparison with isolates from the ICUs environment. Overall, 206 items were screened for CRAB presence and 27 (14%) were contaminated with a CRAB isolate. The items were located in several areas of three ICUs. Eight of the 54 (15%) screened people working in the wards were colonized by CRAB on the hands. Patients residing in the ICUs were infected with CRAB strains sharing extensive genomic similarity with strains recovered in the nosocomial environment. The strains belonged to three sub-clades of the internationally disseminated clone (ST2). A clone emerging in the Mediterranean basin (ST85) was detected as well. The strains were OXA-23 or NDM-1 producers and were also pan-aminoglycoside resistant due to the presence of the armA gene. Hygiene measures are urgent to be implemented in the Sahloul hospital to avoid further spread of difficult-to-treat CRAB strains and preserve health of patients and personnel operating in the ICU wards. Full article
(This article belongs to the Special Issue Molecular Epidemiology of Antimicrobial Resistance, 2nd Edition)
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8 pages, 403 KiB  
Communication
The Molecular Genetic Epidemiology and Antimicrobial Resistance of Neisseria gonorrhoeae Strains Obtained from Clinical Isolates in Central Panama
by Virginia Núñez-Samudio, Mellissa Herrera, Genarino Herrera, Gumercindo Pimentel-Peralta and Iván Landires
Microorganisms 2023, 11(10), 2572; https://doi.org/10.3390/microorganisms11102572 - 16 Oct 2023
Viewed by 1772
Abstract
We aim to analyze Neisseria gonorrhoeae isolates in central Panama, characterize the associated gonococcal antimicrobial resistance (AMR) and conduct molecular epidemiology and genetic typing. We conducted a retrospective study based on N. gonorrhoeae hospital isolates collected between 2013 and 2018. AMR was determined using [...] Read more.
We aim to analyze Neisseria gonorrhoeae isolates in central Panama, characterize the associated gonococcal antimicrobial resistance (AMR) and conduct molecular epidemiology and genetic typing. We conducted a retrospective study based on N. gonorrhoeae hospital isolates collected between 2013 and 2018. AMR was determined using dilution agar and Etest®. Molecular typing was conducted using the Multilocus Sequence Typing (ST) scheme. The isolates analyzed (n = 30) showed resistance to penicillin (38%), tetracycline (40%), and ciprofloxacin (30%), and sensitivity to extended-spectrum cephalosporins and azithromycin. We identified 11 STs, the most frequent of which was ST1901 among the strains with decreased sensitivity and resistance to three types of antibiotics. We identified eight variations for the penA gene, all non-mosaic, with type II LVG as the most frequent (50%). To the best of our knowledge, we conducted the first Central American genomic study that analyzes a collection of gonococcal isolates, which represents a benchmark for future epidemiological and molecular genetic studies. The high prevalence of ciprofloxacin, tetracycline, and penicillin resistance, in addition to the identification of the worldwide spread of multidrug-resistant clone ST1901, should prompt the continuous and reinforced surveillance of AMR, including the molecular epidemiology of N. gonorrhoeae in Panama. Full article
(This article belongs to the Special Issue Molecular Epidemiology of Antimicrobial Resistance, 2nd Edition)
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14 pages, 1012 KiB  
Article
Acinetobacter baumannii IC2 and IC5 Isolates with Co-Existing blaOXA-143-like and blaOXA-72 and Exhibiting Strong Biofilm Formation in a Mexican Hospital
by Julia Moreno-Manjón, Santiago Castillo-Ramírez, Keith A. Jolley, Martin C. J. Maiden, Catalina Gayosso-Vázquez, José Luis Fernández-Vázquez, Valeria Mateo-Estrada, Silvia Giono-Cerezo and María Dolores Alcántar-Curiel
Microorganisms 2023, 11(9), 2316; https://doi.org/10.3390/microorganisms11092316 - 14 Sep 2023
Cited by 3 | Viewed by 1632
Abstract
Acinetobacter baumannii is an opportunistic pathogen responsible for healthcare-associated infections (HAIs) and outbreaks. Antimicrobial resistance mechanisms and virulence factors allow it to survive and spread in the hospital environment. However, the molecular mechanisms of these traits and their association with international clones are [...] Read more.
Acinetobacter baumannii is an opportunistic pathogen responsible for healthcare-associated infections (HAIs) and outbreaks. Antimicrobial resistance mechanisms and virulence factors allow it to survive and spread in the hospital environment. However, the molecular mechanisms of these traits and their association with international clones are frequently unknown in low- and middle-income countries. Here, we analyze the phenotype and genotype of seventy-six HAIs and outbreak-causing A. baumannii isolates from a Mexican hospital over ten years, with special attention to the carbapenem resistome and biofilm formation. The isolates belonged to the global international clone (IC) 2 and the Latin America endemic IC5 and were predominantly extensively drug-resistant (XDR). Oxacillinases were identified as a common source of carbapenem resistance. We noted the presence of the blaOXA-143-like family (not previously described in Mexico), the blaOXA-72 and the blaOXA-398 found in both ICs. A low prevalence of efflux pump overexpression activity associated with carbapenem resistance was observed. Finally, strong biofilm formation was found, and significant biofilm-related genes were identified, including bfmRS, csuA/BABCDE, pgaABCD and ompA. This study provides a comprehensive profile of the carbapenem resistome of A. baumannii isolates belonging to the same pulse type, along with their significant biofilm formation capacity. Furthermore, it contributes to a better understanding of their role in the recurrence of infection and the endemicity of these isolates in a Mexican hospital. Full article
(This article belongs to the Special Issue Molecular Epidemiology of Antimicrobial Resistance, 2nd Edition)
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20 pages, 1782 KiB  
Article
Study of Antimicrobial Resistance, Biofilm Formation, and Motility of Pseudomonas aeruginosa Derived from Urine Samples
by Telma de Sousa, Michel Hébraud, Olimpia Alves, Eliana Costa, Luís Maltez, José Eduardo Pereira, Ângela Martins, Gilberto Igrejas and Patricia Poeta
Microorganisms 2023, 11(5), 1345; https://doi.org/10.3390/microorganisms11051345 - 19 May 2023
Cited by 13 | Viewed by 3818
Abstract
Pseudomonas aeruginosa causes urinary tract infections associated with catheters by forming biofilms on the surface of indwelling catheters. Therefore, controlling the spread of the bacteria is crucial to preventing its transmission in hospitals and the environment. Thus, our objective was to determine the [...] Read more.
Pseudomonas aeruginosa causes urinary tract infections associated with catheters by forming biofilms on the surface of indwelling catheters. Therefore, controlling the spread of the bacteria is crucial to preventing its transmission in hospitals and the environment. Thus, our objective was to determine the antibiotic susceptibility profiles of twenty-five P. aeruginosa isolates from UTIs at the Medical Center of Trás-os-Montes and Alto Douro (CHTMAD). Biofilm formation and motility are also virulence factors studied in this work. Out of the twenty-five P. aeruginosa isolates, 16% exhibited multidrug resistance, being resistant to at least three classes of antibiotics. However, the isolates showed a high prevalence of susceptibility to amikacin and tobramycin. Resistance to carbapenem antibiotics, essential for treating infections when other antibiotics fail, was low in this study, Notably, 92% of the isolates demonstrated intermediate sensitivity to ciprofloxacin, raising concerns about its efficacy in controlling the disease. Genotypic analysis revealed the presence of various β-lactamase genes, with class B metallo-β-lactamases (MBLs) being the most common. The blaNDM, blaSPM, and blaVIM-VIM2 genes were detected in 16%, 60%, and 12% of the strains, respectively. The presence of these genes highlights the emerging threat of MBL-mediated resistance. Additionally, virulence gene analysis showed varying prevalence rates among the strains. The exoU gene, associated with cytotoxicity, was found in only one isolate, while other genes such as exoS, exoA, exoY, and exoT had a high prevalence. The toxA and lasB genes were present in all isolates, whereas the lasA gene was absent. The presence of various virulence genes suggests the potential of these strains to cause severe infections. This pathogen demonstrated proficiency in producing biofilms, as 92% of the isolates were found to be capable of doing so. Currently, antibiotic resistance is one of the most serious public health problems, as options become inadequate with the continued emergence and spread of multidrug-resistant strains, combined with the high rate of biofilm production and the ease of dissemination. In conclusion, this study provides insights into the antibiotic resistance and virulence profiles of P. aeruginosa strains isolated from human urine infections, highlighting the need for continued surveillance and appropriate therapeutic approaches. Full article
(This article belongs to the Special Issue Molecular Epidemiology of Antimicrobial Resistance, 2nd Edition)
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Review

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19 pages, 1242 KiB  
Review
Updates on the Virulence Factors Produced by Multidrug-Resistant Enterobacterales and Strategies to Control Their Infections
by Mohd W. Azam, Raffaele Zarrilli and Asad U. Khan
Microorganisms 2023, 11(8), 1901; https://doi.org/10.3390/microorganisms11081901 - 27 Jul 2023
Cited by 4 | Viewed by 2658
Abstract
The Enterobacterales order is a massive group of Gram-negative bacteria comprised of pathogenic and nonpathogenic members, including beneficial commensal gut microbiota. The pathogenic members produce several pathogenic or virulence factors that enhance their pathogenic properties and increase the severity of the infection. The [...] Read more.
The Enterobacterales order is a massive group of Gram-negative bacteria comprised of pathogenic and nonpathogenic members, including beneficial commensal gut microbiota. The pathogenic members produce several pathogenic or virulence factors that enhance their pathogenic properties and increase the severity of the infection. The members of Enterobacterales can also develop resistance against the common antimicrobial agents, a phenomenon called antimicrobial resistance (AMR). Many pathogenic Enterobacterales members are known to possess antimicrobial resistance. This review discusses the virulence factors, pathogenicity, and infections caused by multidrug-resistant Enterobacterales, especially E. coli and some other bacterial species sharing similarities with the Enterobacterales members. We also discuss both conventional and modern approaches used to combat the infections caused by them. Understanding the virulence factors produced by the pathogenic bacteria will help develop novel strategies and methods to treat infections caused by them. Full article
(This article belongs to the Special Issue Molecular Epidemiology of Antimicrobial Resistance, 2nd Edition)
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