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Epidemiology, Clinical Microbiology and Antimicrobial Therapy: A Shared Effort against...
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Epidemiology, Clinical Microbiology and Antimicrobial Therapy: A Shared Effort against Infectious Diseases

A special issue of Antibiotics (ISSN 2079-6382). This special issue belongs to the section "Antibiotic Therapy in Infectious Diseases".

Deadline for manuscript submissions: closed (15 December 2024) | Viewed by 9397

Special Issue Editor

Dr. Francesca Pica

E-Mail Website
Guest Editor
Department of Experimental Medicine, Faculty of Medicine and Surgery, University of Rome Tor Vergata, Via Montpellier, 1, 00133 Rome, Italy
Interests: microbiology; epidemiology and control of healthcare-associated infections; immunosuppression and immunomodulators; natural and syntetic compounds with antimicrobial and antitumor activity; biofilm

Special Issue Information

Dear Colleagues,

As reported by the WHO, national, supranational and global plans are ongoing for the control and prevention of infectious diseases, which still fall among the top 10 causes of death worldwide. Particular attention in this area is paid to antimicrobial resistance (AMR). In fact, AMR microorganisms can cause severe diseases, especially in frail and hospitalized individuals, leading to a prolonged length of hospital stay and increased mortality or long-term disability, with a relevant impact on the individual quality of life and on the financial aspects of health management. The extensive and incorrect use of antimicrobials exerts a selective pressure, favouring the emergence and spread of microbial strains often resistant to multiple drugs at the same time, i.e., the multidrug-resistant (MDR) strains. The new technologies strongly support microbiological diagnostics, allowing the identification of these new microbial strains and mutations that have occurred in them; however, sometime the discordance between genotypic and phenotypic methods makes the interpretation of results difficult. In this context, it seems urgent to strengthen a synergistic interaction among epidemiologists, microbiologists, basic researchers and clinicians to successfully counteract possibly life-threating infections in our real world, actually characterized by increasing conflicts and social inequalities. The aim of this Special Issue is to collect the most recent experiences in the field by all the professionals involved in this area.

Dr. Francesca Pica
Guest Editor

Manuscript Submission Information

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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. Antibiotics is an international peer-reviewed open access monthly journal published by MDPI.

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Keywords

  • microbes and antimicrobials
  • bacteria, fungi and viruses
  • antibiotics, antifungals and antivirals
  • antimicrobial resistance
  • rapid diagnostics
  • genotypic and phenotypic resistance
  • epidemiology
  • public health
  • infectious diseases
  • hospital-acquired infections (HAIs)
  • community infections
  • natural and synthetic antimicrobial compounds

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Published Papers (7 papers)

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Research

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11 pages, 2083 KiB  
Article
Active Surveillance of Patients Colonized with CRE: A Single-Center Study Based on a Combined Molecular/Culture Protocol
by Beatrice Silvia Orena, Maria Francesca Liporace, Antonio Teri, Daniela Girelli, Federica Salari, Michela Mutti, Gabriele Giordano, Claudia Alteri, Flaminia Gentiloni Silverj, Caterina Matinato, Annapaola Callegaro and Lisa Cariani
Antibiotics 2024, 13(11), 1053; https://doi.org/10.3390/antibiotics13111053 - 6 Nov 2024
Viewed by 783
Abstract
Background/Objectives: Carbapenem-resistant Enterobacteriaceae (CRE) are types of bacteria that need urgent attention globally. Active surveillance programs at hospitals are essential for the early identification of CRE carriers and the timely adoption of infection control measures. We aimed to analyze the epidemiology of [...] Read more.
Background/Objectives: Carbapenem-resistant Enterobacteriaceae (CRE) are types of bacteria that need urgent attention globally. Active surveillance programs at hospitals are essential for the early identification of CRE carriers and the timely adoption of infection control measures. We aimed to analyze the epidemiology of CRE identified by multiplex RT-PCR in rectal swabs of patients upon admission to high-risk wards and to compare data obtained from both molecular and culture CRE screening. Methods: A total of 2861 rectal swabs, prospectively collected within 12–24 h of admission, underwent molecular screening for identification of K. pneumoniae carbapenemase (KPC), New Delhi metallo-β-lactamase (NDM), Verona integron-mediated metallo-β-lactamase (VIM), imipenemase (IMP), and OXA-48 (AllplexTM Entero-DR Assay). Only samples that tested positive or invalid underwent culture testing (Agar MacConkey and CHROMID® CARBA plates, bioMérieux, Craponne, France). Results: A total of 118 out of 2861 (about 4%) were positive for at least one carbapenem-resistant gene by a molecular approach (MA), with KPC, NDM, and VIM having the highest prevalence. Culture testing confirmed the presence of carbapenemase in 89 samples (75.4%), showing a disagreement rate of about 25% between the two methods, which, unfortunately, rises up to 60% for VIM. The dominant bacterial species were K. pneumoniae and E. coli (MALDI-TOF mass spectrometry). Conclusions: Our data underlined the need for the molecular screening of CRE carriers in order to implement active surveillance protocol in critical care settings and to improve infection control measures. Full article
(This article belongs to the Special Issue Epidemiology, Clinical Microbiology and Antimicrobial Therapy: A Shared Effort against Infectious Diseases)
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11 pages, 266 KiB  
Article
Benefits and Safety of Empiric Antibiotic Treatment Active Against KPC-Producing Klebsiella pneumoniae for Febrile Neutropenic Episodes in Colonized Children with Acute Leukemia—An 8-Year Retrospective Observational Study
by Alessandra Micozzi, Cristina Luise, Chiara Lisi, Luisa Moleti, Stefania Santilli and Giuseppe Gentile
Antibiotics 2024, 13(11), 1017; https://doi.org/10.3390/antibiotics13111017 - 29 Oct 2024
Viewed by 660
Abstract
In children with acute leukemia (AL), the mortality rate from Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae bloodstream infection (KPC-KpBSI) exceeds 50%, highest when active treatment is delayed. Neutropenic KPC-K. pneumoniae carriers are at high risk of KPC-KpBSI, and preemptive empiric antibiotic treatment [...] Read more.
In children with acute leukemia (AL), the mortality rate from Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae bloodstream infection (KPC-KpBSI) exceeds 50%, highest when active treatment is delayed. Neutropenic KPC-K. pneumoniae carriers are at high risk of KPC-KpBSI, and preemptive empiric antibiotic treatment (EAT) of febrile neutropenic episodes (FNEs) active against KPC-K. pneumoniae may reduce this mortality. We conducted an 8-year (2014–2021) retrospective observational study of 112 febrile neutropenic episodes (FNEs) in 32 children with AL who were KPC-K. pneumoniae carriers: standard EAT for 39 FNEs and active EAT for 73 FNEs (52 ceftazidime/avibactam (CAZAVI)-based and 21 colistin-based combinations, and 5 CAZAVI monotherapy). Successful outcomes (survival from FNE) were observed in 94%; seven were fatal, with four due to infectious causes. KPC-KpBSIs caused 10/112 FNEs, 10/20 g-negative BSIs, and 3 deaths. The mortality rate of KPC-KpBSI was 30%. Active EAT was successful in 97% of the FNEs, compared to 87% with standard EAT. All deaths from KPC-KpBSI occurred in patients who received standard EAT, while none occurred with active EAT. KPC-KpBSI mortality rate with initial inactive treatment was 60%. CAZAVI-based EAT was successful in all FNEs, with a higher success rate without any modification compared to colistin-based EAT, where nephrotoxicity occurred in 14%. Therefore, active EAT, mainly a CAZAVI-based combination, was effective, safe, and associated with low overall and KPC-KpBSI-related mortality. Full article
(This article belongs to the Special Issue Epidemiology, Clinical Microbiology and Antimicrobial Therapy: A Shared Effort against Infectious Diseases)
13 pages, 926 KiB  
Article
Peripheral Intravenous Therapy in Internal Medicine Department—Antibiotics and Other Drugs’ Consumption and Characteristics of Vascular Access Devices in 2-Year Observation Study
by Piotr Piekiełko, Anna Mucha, Ewa Stawowczyk and Jadwiga Wójkowska-Mach
Antibiotics 2024, 13(7), 664; https://doi.org/10.3390/antibiotics13070664 - 18 Jul 2024
Viewed by 1127
Abstract
Background: The aim of the study was to characterize the procedure of peripheral intravenous therapy (IT), including the characteristics of vascular access and related complications and qualitative and quantitative analyses of drug consumption. Materials and Methods: A two-year, retrospective, single-center observational study was [...] Read more.
Background: The aim of the study was to characterize the procedure of peripheral intravenous therapy (IT), including the characteristics of vascular access and related complications and qualitative and quantitative analyses of drug consumption. Materials and Methods: A two-year, retrospective, single-center observational study was conducted. The criterion for including a patient in the study was the use of peripheral intravenous catheters (PIVCs) upon admission or during the stay at the internal medicine department (IMD). Results: The main reasons for hospitalization were exacerbations of chronic diseases for 78% of the patients and acute infections for 22%. IT was used in 83.6% of all the patients. IT was used primarily for antibiotics (5009.9 defined daily doses (DDD)). Further, 22.6% of the PIVCs stopped functioning within 24 h, more frequently in infectious patients. The main reasons for PIVC removal were leakage (n = 880, 26.6%) and occlusion (n = 578, 17.5%). The PIVC locations were mostly suboptimal (n = 2010, 59.5%), and such locations were related to leakage and occlusion (p = 0.017). Conclusions: In the IMD, most patients require the use of a PIVC, and antibiotics dominate the group of drugs administered intravenously. Up to 1/5 of peripheral intravenous catheters are lost within the first 24 h after their insertion, with most of them placed suboptimally. A properly functioning PIVC appears to be crucial for antimicrobial treatment. Full article
(This article belongs to the Special Issue Epidemiology, Clinical Microbiology and Antimicrobial Therapy: A Shared Effort against Infectious Diseases)
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13 pages, 3645 KiB  
Article
Screening of Klebsiella pneumoniae subsp. pneumoniae Strains with Multi-Drug Resistance and Virulence Profiles Isolated from an Italian Hospital between 2020 and 2023
by Valentina Dimartino, Carolina Venditti, Francesco Messina, Silvia D’Arezzo, Marina Selleri, Ornella Butera, Carla Nisii, Alessandra Marani, Alessia Arcangeli, Roberta Gaziano, Terenzio Cosio, Pietro Scanzano and Carla Fontana
Antibiotics 2024, 13(6), 561; https://doi.org/10.3390/antibiotics13060561 - 15 Jun 2024
Cited by 2 | Viewed by 1752
Abstract
Klebsiella pneumoniae strains that are resistant to multiple drugs (KPMDRs), which are often acquired in hospital settings and lead to healthcare-associated infections, pose a serious public health threat, as does hypervirulent K. pneumoniae (hvKp), which can also cause serious infections in otherwise healthy [...] Read more.
Klebsiella pneumoniae strains that are resistant to multiple drugs (KPMDRs), which are often acquired in hospital settings and lead to healthcare-associated infections, pose a serious public health threat, as does hypervirulent K. pneumoniae (hvKp), which can also cause serious infections in otherwise healthy individuals. The widespread and often unnecessary use of antibiotics seen during the recent COVID-19 pandemic has exacerbated the challenges posed by antibiotic resistance in clinical settings. There is growing concern that hypervirulent (hvKp) strains may acquire genes that confer antimicrobial resistance, thus combining an MDR profile with their increased ability to spread to multiple body sites, causing difficult-to-treat infections. This study aimed to compare resistance and virulence profiles in KPC-3-producing K. pneumoniae isolates collected over four years (2020–2023). A genome-based surveillance of all MDR CRE-K. pneumoniae was used to identify genetic differences and to characterize the virulence and resistance profiles. Our results provide a picture of the evolution of resistance and virulence genes and contribute to avoiding the possible spread of isolates with characteristics of multi-drug resistance and increased virulence, which are thought to be one of the main global challenges to public health, within our hospital. Full article
(This article belongs to the Special Issue Epidemiology, Clinical Microbiology and Antimicrobial Therapy: A Shared Effort against Infectious Diseases)
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8 pages, 595 KiB  
Article
Whooping Cough Cases Increase in Central Italy after COVID-19 Pandemic
by Giulia Linardos, Luana Coltella, Stefania Ranno, Velia Chiara Di Maio, Luna Colagrossi, Elisabetta Pandolfi, Maria Beatrice Chiarini Testa, Leonardo Genuini, Francesca Stoppa, Matteo Di Nardo, Annalisa Grandin, Renato Cutrera, Corrado Cecchetti, Alberto Villani, Massimiliano Raponi, Paola Bernaschi, Cristina Russo, Carlo Federico Perno and Rossana Scutari
Antibiotics 2024, 13(5), 464; https://doi.org/10.3390/antibiotics13050464 - 19 May 2024
Cited by 2 | Viewed by 2094
Abstract
Pertussis continues to be a highly contagious respiratory infection, especially in children, with cyclical peaks of disease spread every three to five years. Here, we report relevant cases of B. pertussis infection between August 2023 and January 2024, and compare them with B. [...] Read more.
Pertussis continues to be a highly contagious respiratory infection, especially in children, with cyclical peaks of disease spread every three to five years. Here, we report relevant cases of B. pertussis infection between August 2023 and January 2024, and compare them with B. pertussis prevalence in pediatric patients admitted to the Reference Italian Pediatric Hospital, located in Rome, from January 2015 to July 2023. A total of 5464 tests for B. pertussis were performed during the study period, and 6.9% were positive. At the time of the COVID-19 pandemic, there was a sharp decrease in the presence of B. pertussis, which reappeared only in August 2023, recording five new cases. All five children presented with paroxysmal cough 5 to 10 days before admission. Four patients had other mild respiratory symptoms and moderate B. pertussis DNA levels (Ct mean: 26). Only one child, with very high B. pertussis DNA levels (Ct: 9), presented with severe respiratory failure. The patients with mild/moderate infection achieved clinical recovery while the patient with the severe manifestation died of cardiac arrest. These observations highlight the reemergence of pertussis even in vaccinated countries and its association with morbidity and mortality especially in young children. This emphasizes the importance of rapid diagnosis to immediately implement appropriate treatment and monitoring of immune status. Full article
(This article belongs to the Special Issue Epidemiology, Clinical Microbiology and Antimicrobial Therapy: A Shared Effort against Infectious Diseases)
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Review

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18 pages, 1954 KiB  
Review
Structural Equation Modelling as a Proof-of-Concept Tool for Mediation Mechanisms Between Topical Antibiotic Prophylaxis and Six Types of Blood Stream Infection Among ICU Patients
by James Hurley
Antibiotics 2024, 13(11), 1096; https://doi.org/10.3390/antibiotics13111096 - 18 Nov 2024
Viewed by 806
Abstract
Whether exposing the microbiome to antibiotics decreases or increases the risk of blood stream infection with Pseudomonas aeruginosa, Staphylococcus aureus, Acinetobacter, and Candida among ICU patients, and how this altered risk might be mediated, are critical research questions. Addressing these [...] Read more.
Whether exposing the microbiome to antibiotics decreases or increases the risk of blood stream infection with Pseudomonas aeruginosa, Staphylococcus aureus, Acinetobacter, and Candida among ICU patients, and how this altered risk might be mediated, are critical research questions. Addressing these questions through the direct study of specific constituents within the microbiome would be difficult. An alternative tool for addressing these research questions is structural equation modelling (SEM). SEM enables competing theoretical causation networks to be tested ‘en bloc’ by confrontation with data derived from the literature. These causation models have three conceptual steps: exposure to specific antimicrobials are the key drivers, clinically relevant infection end points are the measurable observables, and the activity of key microbiome constituents on microbial invasion serve as mediators. These mediators, whether serving to promote, to impede, or neither, are typically unobservable and appear as latent variables in each model. SEM methods enable comparisons through confronting the three competing models, each versus clinically derived data with the various exposures, such as topical or parenteral antibiotic prophylaxis, factorized in each model. Candida colonization, represented as a latent variable, and concurrency are consistent promoters of all types of blood stream infection, and emerge as harmful mediators. Full article
(This article belongs to the Special Issue Epidemiology, Clinical Microbiology and Antimicrobial Therapy: A Shared Effort against Infectious Diseases)
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13 pages, 1668 KiB  
Review
Robinsoniella peoriensis Infections in Humans—A Narrative Review
by Petros Ioannou, Stella Baliou and Diamantis Kofteridis
Antibiotics 2024, 13(6), 570; https://doi.org/10.3390/antibiotics13060570 - 20 Jun 2024
Viewed by 1335
Abstract
Robinsoniella peoriensis is a Gram-positive, strictly anaerobic, spore-forming, rod-shaped bacterium belonging to the phylum Firmicutes and the family Lachnospiraceae. Until now, R. peoriensis is the only species of its genus. It was first isolated in 2003 during a study into the flora of lagoons [...] Read more.
Robinsoniella peoriensis is a Gram-positive, strictly anaerobic, spore-forming, rod-shaped bacterium belonging to the phylum Firmicutes and the family Lachnospiraceae. Until now, R. peoriensis is the only species of its genus. It was first isolated in 2003 during a study into the flora of lagoons and manure pits. Given the rarity of this microorganism and the sparse information in the literature about its way of transmission, the way to diagnose its infections and identify it in the microbiology laboratory, and its public health relevance, the present study aimed to identify all the published cases of Robinsoniella, describe the epidemiological, clinical, and microbiological characteristics, and provide information about its antimicrobial resistance, treatment, and outcomes. A narrative review was performed based on a Pubmed/Medline and Scopus databases search. In total, 14 studies provided data on 17 patients with infections by Robinsoniella. The median age of patients was 63 years and 47% were male. The most common types of infection were bone and joint infections, bacteremia, infective endocarditis, and peritonitis. The only isolated species was R. peoriensis, and antimicrobial resistance to clindamycin was 50%, but was 0% to the combination of piperacillin with tazobactam, aminopenicillin with a beta-lactamase inhibitor, and metronidazole which were the most commonly used antimicrobials for the treatment of these infections. The overall mortality depends on the type of infection and is notable only for bacteremia, while all other infections had an optimal outcome. Future studies should better assess these infections’ clinical and epidemiological characteristics and the mechanisms of the antimicrobial resistance of this microorganism from a mechanistic and genetic perspective. Full article
(This article belongs to the Special Issue Epidemiology, Clinical Microbiology and Antimicrobial Therapy: A Shared Effort against Infectious Diseases)
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