Antimicrobial Resistance and Multidrug-Resistant Bacteria in Infectious Patients

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

Deadline for manuscript submissions: closed (15 June 2024) | Viewed by 13008

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Department of Odontostomatology and surgery, University Aldo Moro of Bari, 70010 Bari, Italy
Interests: preventive medicine; infectious diseases; public health; applied microbiology; sexual infectious diseases; pandemic COVID-19; antibiotic-resistance
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Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, 71100 Foggia, Italy
Interests: preventive medicine; infectious diseases; public health; applied microbiology; sexual infectious diseases; pandemic COVID-19; antibiotic-resistance
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IRCCS Istituto Tumori Giovanni Paolo II, Bari, Italy
Interests: preventive medicine; infectious diseases; public health; applied microbiology; sexual infectious diseases; pandemic COVID-19; antibiotic -resistance
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IRCCS Cancer Institute "Giovanni Paolo II", Bari, Italy
Interests: preventive medicine; infectious diseases; public health; applied microbiology; sexual infectious diseases; pandemic COVID-19; antibiotic-resistance
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Special Issue Information

Dear Colleagues,

Antimicrobial resistance is considered a worldwide burden, affecting the patients of critical hospital wards, such as intensive care units (ICUs). Hospitalized patients have been demonstrated to have an increased risk of developing infections due to exposure to several invasive devices (mechanical ventilation, urinary tract catheters) and to other related conditions. Careful clinical surveillance, together with the monitoring of the well-known bacterial strains responsible for inducing HAI, may help clinicians to choose the appropriate antibiotic therapies.

Bacterial infections have impacted humans throughout the centuries, and were particularly harmful until the discovery of antibiotics, which revolutionized the treatment of infectious diseases. Because of their ability to survive in different environments, bacteria are increasingly able to face antibacterial treatments over time by means of different adaptative strategies. They can modify the quaternary structure of specific target proteins, substitute metabolic pathways by synthesizing alternative biomolecules, and produce enzymes able to inactivate antibiotics; this is also possible through the camouflage of their structure, for example, behind a proteoglycan capsule.

A common bacterial weapon against penicillin is the beta-lactamase enzyme, which alters the beta-lactamic structure, thus maintaining the building of the bacterial wall and creating the local conditions to promote several diseases. Bacteria are also able to synthesize effective isoforms of the beta-lactamase enzyme; the extended-spectrum beta lactamase (ESBL) and the ESBL carbapenemase give bacteria resistance to third-generation cephalosporins and carbapenamase-class antibiotics, respectively. These antibiotics are widely used in several nosocomial infections.

Recently, several strategies have been proposed to face this challenge, such as strong prevention or the support of computer-based analyses. The EU’s call for projects has also promoted the development of innovative artificial intelligence (AI) solutions to prevent infections inside clinical departments. In particular, an interesting ongoing project (LAOCOONTE, by Energent S.p.A.) has the objective of developing specific use cases, where data can be used by machine- and deep-learning models to evaluate the likelihood of infection in clinical departments, in an Italian clinical setting. This approach is very promising; in fact, AI currently plays an important role in different fields, from smart manufacturing to the Internet of things, human–computer interaction and medicine.

The attention paid by the scientific community and industry to the AI field is related to the excellent performance achieved in recent years by the so-called artificial neural networks, in particular the deep architectures, in various fields such as text, images and audio.

Nosocomial infections (NIs) are even more preventable, as they represent a biological and social cost for hospitalized patients. The growing availability of computerized patient records in hospitals allows for the improvement of data storage with traditional machine-learning methods, which have been shown to outperform deep learning’s performance when applied to tabular data.

Additionally, nanoparticles associated to antibiotics are used as an effective therapeutic method to combat multi-drug-resistant bacteria, and gold nanoparticles are used against viruses such as HIV and Ebola.

Prof. Dr. Danila De Vito
Dr. Antonio Parisi
Dr. Patrizia Nardulli
Dr. Maria Rita Laforgia
Guest Editors

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Keywords

  • diffusion multi-drug resistant bacteria
  • outbreak by ESKAPE bacteria
  • hospital infections
  • care-related infections
  • anti-microbial nano-particles
  • role of antimicrobial nanomaterials in medicine
  • mechanism of action of antimicrobial nanomaterials
  • antimicrobial food packaging

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Published Papers (8 papers)

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Research

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19 pages, 536 KiB  
Article
Antimicrobial Resistance of Staphylococcus spp. from Human Specimens Submitted to Diagnostic Laboratories in South Africa, 2012–2017
by Themba Titus Sigudu, James Wabwire Oguttu and Daniel Nenene Qekwana
Microorganisms 2024, 12(9), 1862; https://doi.org/10.3390/microorganisms12091862 - 9 Sep 2024
Viewed by 778
Abstract
Antimicrobial resistance (AMR) poses a significant worldwide health challenge associated with prolonged illnesses, increased healthcare costs, and high mortality rates. The present study examined the patterns and predictors of AMR among human Staphylococcus isolates obtained from diagnostic laboratories in South Africa between 2012 [...] Read more.
Antimicrobial resistance (AMR) poses a significant worldwide health challenge associated with prolonged illnesses, increased healthcare costs, and high mortality rates. The present study examined the patterns and predictors of AMR among human Staphylococcus isolates obtained from diagnostic laboratories in South Africa between 2012 and 2017. This study examined data from 404 217 isolates, assessing resistance rates across different characteristics such as age, sample origin, Staphylococcus species, and study period. The highest resistance was observed against cloxacillin (70.3%), while the lowest resistance was against Colistin (0.1%). A significant (p < 0.05) decreasing trend in AMR was observed over the study period, while a significant increasing temporal trend (p < 0.05) was observed for multidrug resistance (MDR) over the same period. A significant (p < 0.05) association was observed between specimen type, species of organism, and year of isolation with AMR outcome. Significant (p < 0.05) associations were observed between specimen type and season with MDR. The observed high levels of AMR and a growing trend in MDR are concerning for public health. Clinicians should take these findings into account when deciding on therapeutic options. Continued monitoring of AMR among Staphylococcus spp. and judicious use of antimicrobials in human medicine should be promoted. Full article
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20 pages, 8997 KiB  
Article
Potential Convergence to Accommodate Pathogenicity Determinants and Antibiotic Resistance Revealed in Salmonella Mbandaka
by Na Lv, Jinjing Ni, Shiqi Fang, Yue Liu, Shuang Wan, Chao Sun, Jun Li and Aiping Zhou
Microorganisms 2024, 12(8), 1667; https://doi.org/10.3390/microorganisms12081667 - 13 Aug 2024
Viewed by 1141
Abstract
Salmonella species are causal pathogens instrumental in human food-borne diseases. The pandemic survey related to multidrug resistant (MDR) Salmonella genomics enables the prevention and control of their dissemination. Currently, serotype Mbandaka is notorious as a multiple host-adapted non-typhoid Salmonella. However, its epidemic [...] Read more.
Salmonella species are causal pathogens instrumental in human food-borne diseases. The pandemic survey related to multidrug resistant (MDR) Salmonella genomics enables the prevention and control of their dissemination. Currently, serotype Mbandaka is notorious as a multiple host-adapted non-typhoid Salmonella. However, its epidemic and MDR properties are still obscure, especially its genetic determinants accounting for virulence and MD resistance. Here, we aim to characterize the genetic features of a strain SMEH pertaining to Salmonella Mbandaka (S. Mbandaka), isolated from the patient’s hydropericardium, using cell infections, a mouse model, antibiotic susceptibility test and comparative genomics. The antibiotic susceptibility testing showed that it could tolerate four antibiotics, including chloramphenicol, tetracycline, fisiopen and doxycycline by Kirby–Bauer (K-B) testing interpreted according to the Clinical and Laboratory Standards Institute (CLSI). Both the reproducibility in RAW 264.7 macrophages and invasion ability to infect HeLa cells with strain SMEH were higher than those of S. Typhimurium strain 14028S. In contrast, its attenuated virulence was determined in the survival assay using a mouse model. As a result, the candidate genetic determinants responsible for antimicrobial resistance, colonization/adaptability and their transferability were comparatively investigated, such as bacterial secretion systems and pathogenicity islands (SPI-1, SPI-2 and SPI-6). Moreover, collective efforts were made to reveal a potential role of the plasmid architectures in S. Mbandaka as the genetic reservoir to transfer or accommodate drug-resistance genes. Our findings highlight the essentiality of antibiotic resistance and risk assessment in S. Mbandaka. In addition, genomic surveillance is an efficient method to detect pathogens and monitor drug resistance. The genetic determinants accounting for virulence and antimicrobial resistance underscore the increasing clinical challenge of emerging MDR Mbandaka isolates, and provide insights into their prevention and treatment. Full article
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11 pages, 1098 KiB  
Article
Enteropathogenic Providencia alcalifaciens: A Subgroup of P. alcalifaciens That Causes Diarrhea
by Dieter Bulach, Glen P. Carter and M. John Albert
Microorganisms 2024, 12(7), 1479; https://doi.org/10.3390/microorganisms12071479 - 19 Jul 2024
Cited by 1 | Viewed by 1167
Abstract
Despite being considered a normal flora, Providencia alcalifaciens can cause diarrhea. In a previous study, strain 2939/90, obtained from a diarrheal patient, caused invasion and actin condensation in mammalian cells, and diarrhea in a rabbit model. Four TnphoA mutants of 2939/90 produced [...] Read more.
Despite being considered a normal flora, Providencia alcalifaciens can cause diarrhea. In a previous study, strain 2939/90, obtained from a diarrheal patient, caused invasion and actin condensation in mammalian cells, and diarrhea in a rabbit model. Four TnphoA mutants of 2939/90 produced negligible invasion and actin condensation in mammalian cells. Now, the parent strain and the mutants have been sequenced to locate TnphoA insertion sites and determine the effect on virulence. A TnphoA insertion was detected in the type three secretion system (T3SS) locus on a large plasmid and not in a T3SS locus on the chromosome. In 52 genomes of P. alcalifaciens surveyed, the chromosomal T3SS locus was present in all strains, including both P. alcalifaciens genomic clades, which we classified as group A and group B. Plasmid T3SS was present in 21 of 52 genomes, mostly in group A genomes, which included isolates from an outbreak of hemorrhagic diarrhea in dogs. The TnphoA insertion only in the plasmid T3SS locus affected the invasion phenotype, suggested that this locus is critical for causation of diarrhea. We conclude that a subgroup of P. alcalifaciens that possesses this plasmid-mediated T3SS is an enteric pathogen that can cause diarrheal disease. Full article
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12 pages, 1374 KiB  
Article
High Prevalence of Novel Sequence Types in Streptococcus pneumoniae That Caused Invasive Diseases in Kuwait in 2018
by Eiman Mokaddas, Mohammad Asadzadeh, Shabeera Syed and M. John Albert
Microorganisms 2024, 12(1), 225; https://doi.org/10.3390/microorganisms12010225 - 22 Jan 2024
Viewed by 1554
Abstract
Background: Multilocus sequence typing (MLST) is used to gain insight into the population genetics of bacteria in the form of sequence type (ST). MLST has been used to study the evolution and spread of virulent clones of Streptococcus pneumoniae in many parts of [...] Read more.
Background: Multilocus sequence typing (MLST) is used to gain insight into the population genetics of bacteria in the form of sequence type (ST). MLST has been used to study the evolution and spread of virulent clones of Streptococcus pneumoniae in many parts of the world. Such data for S. pneumoniae are lacking for the countries of the Arabian Peninsula, including Kuwait. Methods: We determined the STs of all 31 strains of S. pneumoniae from invasive diseases received at a reference laboratory from various health centers in Kuwait during 2018 by MLST. The relationship among the isolates was determined by phylogenetic analysis. We also determined the serotypes by Quellung reaction, and antimicrobial susceptibility by Etest, against 15 antibiotics belonging to 10 classes. Results: There were 28 STs among the 31 isolates, of which 14 were new STs (45.2%) and 5 were rare STs (16.1%). Phylogenetic analysis revealed that 26 isolates (83.9%) were unrelated singletons, and the Kuwaiti isolates were related to those from neighboring countries whose information was gleaned from unpublished data available at the PubMLST website. Many of our isolates were resistant to penicillin, erythromycin, and azithromycin, and some were multidrug-resistant. Virulent serotype 8-ST53, and serotype 19A with new STs, were detected. Conclusions: Our study detected an unusually large number of novel STs, which may indicate that Kuwait provides a milieu for the evolution of novel STs. Novel STs may arise due to recombination and can result in capsular switching. This can impact the effect of vaccination programs on the burden of invasive pneumococcal disease. This first report from the Arabian Peninsula justifies the continuous monitoring of S. pneumoniae STs for the possible evolution of new virulent clones and capsular switching. Full article
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10 pages, 1493 KiB  
Article
Mycobacterium chimaera Infections in a Unit of Cardio Surgery: Study at a General Hospital in Padua, Italy
by Silvia Cocchio, Michele Nicoletti, Fabio Zanella, Dania Gaburro, Roberto Bianco, Gino Gerosa, Cristina Contessa, Margherita Boschetto, Paola Stano, Valentina Militello, Claudia Cozzolino, Tiziano Martello and Vincenzo Baldo
Microorganisms 2024, 12(1), 29; https://doi.org/10.3390/microorganisms12010029 - 23 Dec 2023
Cited by 2 | Viewed by 1571
Abstract
Mycobacterium chimaera is a slow-growing non-tuberculous mycobacterium already known for being able to colonize cardio surgery heater–cooler units (HCUs). This study aims to describe the real magnitude of the phenomenon, providing a methodological protocol and the results of a longitudinal survey. In the [...] Read more.
Mycobacterium chimaera is a slow-growing non-tuberculous mycobacterium already known for being able to colonize cardio surgery heater–cooler units (HCUs). This study aims to describe the real magnitude of the phenomenon, providing a methodological protocol and the results of a longitudinal survey. In the period 1 January 2017–23 May 2022, over 1191 samples were collected on 35 HCUs of two different manufacturers. Among them, we identified 118 (10.3%) positive results for M. chimaera. We propose our 4-year biosurveillance experience as a practical model to minimize microbiological patients’ risk, suggesting the need for new procedures and interventions for a safer and more ecological cardio surgery. Full article
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12 pages, 313 KiB  
Article
Multidrug-Resistant and Extensively Drug-Resistant Escherichia coli in Sewage in Kuwait: Their Implications
by Mahdi A. Redha, Noura Al Sweih and M. John Albert
Microorganisms 2023, 11(10), 2610; https://doi.org/10.3390/microorganisms11102610 - 23 Oct 2023
Cited by 1 | Viewed by 1664
Abstract
In Kuwait, some sewage is discharged into the sea untreated, causing a health risk. Previously, we investigated the presence of pathogenic E. coli among the 140 isolates of E. coli cultured from the raw sewage from three sites in Kuwait. The aim of [...] Read more.
In Kuwait, some sewage is discharged into the sea untreated, causing a health risk. Previously, we investigated the presence of pathogenic E. coli among the 140 isolates of E. coli cultured from the raw sewage from three sites in Kuwait. The aim of the current study was to characterize the antimicrobial resistance of these isolates and the implications of resistance. Susceptibility to 15 antibiotic classes was tested. Selected genes mediating resistance to cephalosporins and carbapenems were sought. ESBL and carbapenemase production were also determined. Two virulent global clones, ST131 and ST648, were sought. A total of 136 (97.1%), 14 (10.0%), 128 (91.4%), and 2 (1.4%) isolates were cephalosporin-resistant, carbapenem-resistant, multidrug-resistant (MDR), and extensively drug-resistant (XDR), respectively. Among the cephalosporin-resistant isolates, ampC, blaTEM, blaCTX-M, blaOXA-1, and blaCMY-2 were found. Eighteen (12.9%) samples were ESBL producers. All carbapenem-resistant isolates were negative for carbapenemase genes (blaOXA-48, blaIMP, blaGES, blaVIM, blaNDM, and blaKPC), and for carbapenemase production. Resistance rates in carbapenem-resistant isolates to many other antibiotics were significantly higher than in susceptible isolates. A total of four ST131 and ST648 isolates were detected. The presence of MDR and XDR E. coli and global clones in sewage poses a threat in treating E. coli infections. Full article

Review

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14 pages, 443 KiB  
Review
Infective Endocarditis Due to Corynebacterium jeikeium: Four Case Reports and Narrative Review of the Literature
by Daniel Arnés-García, Laura Lucena-Torres, Antonio Bustos-Merlo, Antonio Rosales-Castillo and Carmen Hidalgo-Tenorio
Microorganisms 2024, 12(7), 1337; https://doi.org/10.3390/microorganisms12071337 - 29 Jun 2024
Viewed by 1282
Abstract
Corynebacterium jeikeium, a pleomorphic Gram-positive bacillus, is a common component of the cutaneous microbiota, usually considered as a contaminant, with little pathogenic potential. However, its role in various types of infections, such as bacteremia, sepsis, endocarditis (IE) and infection of prosthetic material [...] Read more.
Corynebacterium jeikeium, a pleomorphic Gram-positive bacillus, is a common component of the cutaneous microbiota, usually considered as a contaminant, with little pathogenic potential. However, its role in various types of infections, such as bacteremia, sepsis, endocarditis (IE) and infection of prosthetic material is gradually being proven. Few cases of IE due to Corynebacterium jeikeium have been described in the literature. The aim of this article was to describe four cases of IE due to Corynebacterium jeikeium diagnosed in our hospital between May 2021 and April 2022, as well as to conduct a narrative review of the literature on this entity. After analysis, we highlight that 65.6% were men, 81.3% were valve or intravascular device carriers, and IE cases presented early, before one year after surgery. The most affected valve was the aortic valve (68.8%), followed by the mitral valve (21.1%). Valve replacement was performed in 65.6% of cases, and the most commonly used antibiotic was vancomycin (68.8%) at a dose of 15 mg/kg/12 h. With respect to prognosis, the overall mortality rate was 21.9%. The comparative results between our series and the literature review were similar except for a higher mortality rate (50%) and the use of dalbavancin in the treatment. We go on to review previously reported cases, along with four cases described in our hospital, of C. jeikeium endocarditis and will discuss various aspects of C. jeikeium infection, focusing on microbiology, pathophysiology, and treatment. Full article
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16 pages, 375 KiB  
Review
The Role of Stakeholders’ Understandings in Emerging Antimicrobial Resistance: A One Health Approach
by Patrizia Nardulli, Andrea Ballini, Maria Zamparella and Danila De Vito
Microorganisms 2023, 11(11), 2797; https://doi.org/10.3390/microorganisms11112797 - 17 Nov 2023
Cited by 6 | Viewed by 2113
Abstract
The increasing misuse of antibiotics in human and veterinary medicine and in agroecosystems and the consequent selective pressure of resistant strains lead to multidrug resistance (AMR), an expanding global phenomenon. Indeed, this phenomenon represents a major public health target with significant clinical implications [...] Read more.
The increasing misuse of antibiotics in human and veterinary medicine and in agroecosystems and the consequent selective pressure of resistant strains lead to multidrug resistance (AMR), an expanding global phenomenon. Indeed, this phenomenon represents a major public health target with significant clinical implications related to increased morbidity and mortality and prolonged hospital stays. The current presence of microorganisms multi-resistant to antibiotics isolated in patients is a problem because of the additional burden of disease it places on the most fragile patients and the difficulty of finding effective therapies. In recent decades, international organizations like the World Health Organization (WHO) and the European Centre for Disease Prevention and Control (ECDC) have played significant roles in addressing the issue of AMR. The ECDC estimates that in the European Union alone, antibiotic resistance causes 33,000 deaths and approximately 880,000 cases of disability each year. The epidemiological impact of AMR inevitably also has direct economic consequences related not only to the loss of life but also to a reduction in the number of days worked, increased use of healthcare resources for diagnostic procedures and the use of second-line antibiotics when available. In 2015, the WHO, recognising AMR as a complex problem that can only be addressed by coordinated multi-sectoral interventions, promoted the One Health approach that considers human, animal, and environmental health in an integrated manner. In this review, the authors try to address why a collaboration of all stakeholders involved in AMR growth and management is necessary in order to achieve optimal health for people, animals, plants, and the environment, highlighting that AMR is a growing threat to human and animal health, food safety and security, economic prosperity, and ecosystems worldwide. Full article
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