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Microorganisms
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Clinical Microbial Infection and Antimicrobial Resistance
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Clinical Microbial Infection and Antimicrobial Resistance

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 March 2025) | Viewed by 14215

Special Issue Editor

Dr. Louis Saravolatz

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Guest Editor
Department of Medicine at St. John Hospital, Wayne State University, Detroit, MI 48202, USA
Interests: S. aureus; COVID; HIV; infectious disease
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Clinicians are overwhelmed by the ever-changing landscape of antimicrobial resistance that is problematic in the treatment of bacterial, viral, fungal, and even protozoal infections. This ever-changing landscape has posed serious challenges for clinical microbiologists as well as infectious disease clinicians. As new organisms emerge such as Candida auris, the problem of resistance at times seems overwhelming. Even older organisms such as Staphylococcus aureus have challenged us with not only methicillin-resistant S. aureus but also vancomycin-resistant S. aureus. HIV has had the greatest clinical impact among viral pathogens that can emerge to be drug resistant while under the pressures of therapy, and then, they are transmitted to uninfected individuals, resulting in therapeutic challenges for the practicing clinician who must utilize genotypic analysis for decision making. The World Health Organization has indicated that antimicrobial resistance is a top global health threat, contributing to 4.95 million deaths (1). At the center of this controversy is how can we avoid unnecessary antimicrobial usage through strong antimicrobial stewardship programs as advocated by the Infectious Disease Society of America. The pipeline for antimicrobial therapy is limited and poses the greatest threat to dealing with this landscape of ever-changing resistance. In addition, a challenge to clinical microbiology laboratories is providing relevant clinical information and also poses to be a rate-limiting step in addressing this problem. The economic impact of these challenges cannot be underestimated as the World Bank has estimated that antimicrobial resistance could result in USD 1 trillion of additional healthcare cost by 2050 (2). All papers examining the problem of and response to antimicrobial resistance are welcome.

Dr. Louis Saravolatz
Guest Editor

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Keywords

  • antimicrobial resistance
  • antimicrobial stewardship
  • multidrug resistance
  • antibiotic development
  • resistance control

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Published Papers (9 papers)

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Research

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13 pages, 571 KiB  
Article
Outbreak of Vancomycin-Resistant Enterococcus in a NICU: Insights into Molecular Detection and Infection Control
by Francesco Peracchi, Giovanna Travi, Alice Proto, Elena Nicolini, Andrea Busni, Luca Mezzadri, Livia Tartaglione, Alessandra Bielli, Elisa Matarazzo, Giorgia Casalicchio, Cecilia Del Curto, Roberto Rossotti, Marco Merli, Chiara Vismara, Fulvio Crippa, Stefano Martinelli and Massimo Puoti
Microorganisms 2025, 13(4), 822; https://doi.org/10.3390/microorganisms13040822 - 4 Apr 2025
Viewed by 286
Abstract
Vancomycin-resistant enterococci (VRE) are a major cause of healthcare-associated infections (HAIs). However, the clinical significance of VRE colonization and the subsequent risk of VRE infection in hospitalized patients are not fully established. Prolonged hospital stays have been observed in neonates colonized by VRE. [...] Read more.
Vancomycin-resistant enterococci (VRE) are a major cause of healthcare-associated infections (HAIs). However, the clinical significance of VRE colonization and the subsequent risk of VRE infection in hospitalized patients are not fully established. Prolonged hospital stays have been observed in neonates colonized by VRE. The mortality rate in pediatric patients with VRE infections ranges from 0% to 42% in both endemic and outbreak settings, often occurring in VRE-colonized neonates. Host and bacterial factors associated with a worse outcome are not fully understood yet. We describe an outbreak of VRE colonization in 21 newborns admitted to our neonatal intensive care unit in January 2024. Microbiological analyses on rectal swabs were performed using molecular testing and culture. Results: In January, VRE was first detected in the urine culture of a 3-week-old patient, followed by a subsequent positive rectal swab result. In accordance with our infection control policy, all the NICU patients were tested, leading to the identification of another 12 colonized patients. The implementation of molecular testing led to rapid VRE identification and the subsequent isolation of colonized neonates, which promptly contained the outbreak. The median time from NICU admission to colonization was 34 (6–37) days. Only one patient developed a CVC-related bloodstream infection, which was successfully treated with linezolid and CVC removal. No VRE-related deaths occurred, even among three patients who underwent abdominal surgery (one gastroschisis, one incarcerated abdominal hernia, and one umbilical hernia) and one patient with necrotizing enterocolitis. Our data show a low infection rate (4%) among VRE-colonized patients (4%) during a NICU outbreak. The rapid identification of multidrug-resistant genes by molecular testing may be implemented in specific settings to enable timely patient identification, adopt infection control measures, and administer appropriate antimicrobial therapy. Full article
(This article belongs to the Special Issue Clinical Microbial Infection and Antimicrobial Resistance)
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18 pages, 2427 KiB  
Article
Screening for STIs: Results of a Health-Promotion Programme in a Portuguese University
by Joana M. Oliveira, Ana Helena Martins, Daniela Veiga, Célia Lavaredas, António Queirós and Ana Miguel Matos
Microorganisms 2024, 12(12), 2479; https://doi.org/10.3390/microorganisms12122479 - 2 Dec 2024
Viewed by 1048
Abstract
Sexually Transmitted Infections (STIs) are an important and growing public health concern. Implementation of screening programmes and awareness campaigns are crucial to mitigate this problem. A university in the central region of Portugal has devised a health-promotion programme, named Protection+, specifically directed [...] Read more.
Sexually Transmitted Infections (STIs) are an important and growing public health concern. Implementation of screening programmes and awareness campaigns are crucial to mitigate this problem. A university in the central region of Portugal has devised a health-promotion programme, named Protection+, specifically directed towards the sexual health of the university community. The present study aimed to evaluate the results of the different actions undertaken as part of the health-promotion programme during the 2023–2024 academic year. Chlamydia, gonorrhoea, trichomoniasis and infection with Mycoplasma genitalium were assessed through real-time polymerase chain reaction protocols. Syphilis, infection with HIV, HBV and HCV were assessed through immunological assays. The adherence to the health-promotion programme after the awareness campaigns was also evaluated. STIs have been diagnosed in 13.7% of the 475 screened participants. Chlamydia was the STI most frequently diagnosed (8.4%), followed by infection with M. genitalium (2.3%), T. pallidum (2.0%) and N. gonorrhoeae (1.1%). HIV, HBV and HCV were diagnosed in a residual number of cases, and T. vaginalis was not detected in any of the screened participants. At the time of diagnosis, more than half of the infected patients were asymptomatic. After the implementation of awareness campaigns, an increase in the adherence to STI screening was observed, with the expected simultaneous increase in STI diagnoses. The high prevalence of STIs, particularly chlamydia, in the university population, along with the asymptomatic nature of these infections, demonstrated the importance of STI screenings and the implementation of campaigns that raise awareness on the prevention and consequences of untreated STIs. Full article
(This article belongs to the Special Issue Clinical Microbial Infection and Antimicrobial Resistance)
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13 pages, 968 KiB  
Article
High-Resolution Melting PCR as a Fast and Simple Molecular Biology-Based Method for the Identification of Hypervirulent Clostridioides difficile Strains Directly in Stool Samples
by Tomasz Bogiel, Robert Górniak, Weronika Ambroziak, Szymon Zieliński, Dominika Anna Zieja and Piotr Kanarek
Microorganisms 2024, 12(11), 2228; https://doi.org/10.3390/microorganisms12112228 - 3 Nov 2024
Cited by 1 | Viewed by 1385
Abstract
Clostridioides difficile became one of the main causes of nosocomial infections in all clinical settings worldwide, especially among patients undergoing antibiotic therapy. The incidence and severity of C. difficile infections, from mild diarrhea to life-threatening pseudomembranous colitis, correlate with the spread of the [...] Read more.
Clostridioides difficile became one of the main causes of nosocomial infections in all clinical settings worldwide, especially among patients undergoing antibiotic therapy. The incidence and severity of C. difficile infections, from mild diarrhea to life-threatening pseudomembranous colitis, correlate with the spread of the hypervirulent binary toxin (CDT)-producing strains. The use of the real-time HRM-PCR method enables the identification of hypervirulent C. difficile strains directly in the diarrheal stool samples of patients suspected of being infected with this bacterium. For this purpose, the cdtA and cdtB genes encoding CDT subunits, as well as the species-specific gluD gene, were detected to identify the presence of this bacterium in the tested samples. The sensitivity, specificity, negative predictive value (NPV) and positive predictive value (PPV) of the established method were also assessed. The obtained results were compared with the results of eazyplex® C. difficile complete test (AmplexDiagnostics GmbH) based on the LAMP method, used in standard microbiological diagnostics. The values of the assessed diagnostic parameters for the detected genes ranged from 58.82% to 98.85%. The lowest value (58.82%) was obtained for the PPV of cdtB and the highest (98.85%) for the NPV of this gene. The real-time HRM-PCR method enables fast and simple detection of the investigated genes of hypervirulent C. difficile strains and, after careful optimization, may demonstrate high potential for usefulness in routine microbiological diagnostics. Full article
(This article belongs to the Special Issue Clinical Microbial Infection and Antimicrobial Resistance)
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13 pages, 543 KiB  
Article
Clinical Manifestations, Macrolide Resistance, and Treatment Utilization Trends of Mycoplasma pneumoniae Pneumonia in Children and Adolescents in South Korea
by Joon Kee Lee, Taekjin Lee, Yae-Jean Kim, Doo Ri Kim, Areum Shin, Hyun Mi Kang, Ye Ji Kim, Dong Hyun Kim, Byung Wook Eun, Young June Choe, Hyunju Lee, Young Min Cho, Eun Young Cho, Kyung Min Kim, Byung Ok Kwak, Su Eun Park, Kyo Jin Jo, Jae Hong Choi, Dayun Kang, Eun Hwa Choi and Ki Wook Yunadd Show full author list remove Hide full author list
Microorganisms 2024, 12(9), 1806; https://doi.org/10.3390/microorganisms12091806 - 31 Aug 2024
Cited by 5 | Viewed by 2886
Abstract
A resurgence of Mycoplasma pneumoniae (MP)—the leading cause of community-acquired bacterial pneumonia, particularly in children—occurred following the COVID-19 pandemic. We aimed to investigate the clinical manifestations, macrolide resistance patterns, and therapeutic approaches related to the MP pneumonia epidemic. Children and adolescents diagnosed with [...] Read more.
A resurgence of Mycoplasma pneumoniae (MP)—the leading cause of community-acquired bacterial pneumonia, particularly in children—occurred following the COVID-19 pandemic. We aimed to investigate the clinical manifestations, macrolide resistance patterns, and therapeutic approaches related to the MP pneumonia epidemic. Children and adolescents diagnosed with MP pneumonia in September–December 2023 were screened. Clinical data were retrospectively collected from 13 major hospitals using concordant microbiological criteria, including either a positive PCR result or four-fold increase in serological markers. Demographic characteristics, treatment modalities, and clinical outcomes were analyzed. Of the 474 screened patients, 374 (median age: 7.7 [IQR, 5.4–9.6] years; hospitalization rate: 88.6%) met the microbiological confirmation criteria. Most patients experienced fever (98.9%), and lobular/lobar consolidation (59.1%) was the dominant radiological finding. The macrolide resistance rate remained high at 87.0%; corticosteroids were widely used (55.6%) alongside macrolides, despite resistance. Patients with consolidation had prolonged fever (median 8 vs. 7 days, p = 0.020) and higher hospitalization rates (92.3% vs. 83.0%, p = 0.008). Macrolide resistance did not significantly influence radiological outcomes. This study highlights the ongoing challenge of macrolide resistance in MP pneumonia and need for tailored therapeutic approaches. Despite high resistance, macrolides remain commonly prescribed, often concurrently with corticosteroids. Full article
(This article belongs to the Special Issue Clinical Microbial Infection and Antimicrobial Resistance)
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12 pages, 1009 KiB  
Article
Alteration in the Morphological and Transcriptomic Profiles of Acinetobacter baumannii after Exposure to Colistin
by Eun-Jeong Yoon, Jun Won Mo, Jee-woong Kim, Min Chul Jeong and Jung Sik Yoo
Microorganisms 2024, 12(8), 1644; https://doi.org/10.3390/microorganisms12081644 - 11 Aug 2024
Viewed by 1275
Abstract
Acinetobacter baumannii is often highly resistant to multiple antimicrobials, posing a risk of treatment failure, and colistin is a “last resort” for treatment of the bacterial infection. However, colistin resistance is easily developed when the bacteria are exposed to the drug, and a [...] Read more.
Acinetobacter baumannii is often highly resistant to multiple antimicrobials, posing a risk of treatment failure, and colistin is a “last resort” for treatment of the bacterial infection. However, colistin resistance is easily developed when the bacteria are exposed to the drug, and a comprehensive analysis of colistin-mediated changes in colistin-susceptible and -resistant A. baumannii is needed. In this study, using an isogenic pair of colistin-susceptible and -resistant A. baumannii isolates, alterations in morphologic and transcriptomic characteristics associated with colistin resistance were revealed. Whole-genome sequencing showed that the resistant isolate harbored a PmrBL208F mutation conferring colistin resistance, and all other single-nucleotide alterations were located in intergenic regions. Using scanning electron microscopy, it was determined that the colistin-resistant mutant had a shorter cell length than the parental isolate, and filamented cells were found when both isolates were exposed to the inhibitory concentration of colistin. When the isolates were treated with inhibitory concentrations of colistin, more than 80% of the genes were upregulated, including genes associated with antioxidative stress response pathways. The results elucidate the morphological difference between the colistin-susceptible and -resistant isolates and different colistin-mediated responses in A. baumannii isolates depending on their susceptibility to this drug. Full article
(This article belongs to the Special Issue Clinical Microbial Infection and Antimicrobial Resistance)
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Review

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23 pages, 1248 KiB  
Review
The Role of the Hfq Protein in Bacterial Resistance to Antibiotics: A Narrative Review
by Sylwia Bloch, Grzegorz Węgrzyn and Véronique Arluison
Microorganisms 2025, 13(2), 364; https://doi.org/10.3390/microorganisms13020364 - 7 Feb 2025
Cited by 2 | Viewed by 1089
Abstract
The antibiotic resistance of pathogenic microorganisms is currently one of most major medical problems, causing a few million deaths every year worldwide due to untreatable bacterial infections. Unfortunately, the prognosis is even worse, as over 8 million deaths associated with antibiotic resistance are [...] Read more.
The antibiotic resistance of pathogenic microorganisms is currently one of most major medical problems, causing a few million deaths every year worldwide due to untreatable bacterial infections. Unfortunately, the prognosis is even worse, as over 8 million deaths associated with antibiotic resistance are expected to occur in 2050 if no new effective antibacterial treatments are discovered. The Hfq protein has been discovered as a bacterial RNA chaperone. However, subsequent studies have indicated that this small protein (composed of 102 amino acid residues in Escherichia coli) has more activities, including binding to DNA and influencing its compaction, interaction with biological membranes, formation of amyloid-like structures, and others. Although Hfq is known to participate in many cellular processes, perhaps surprisingly, only reports from recent years have demonstrated its role in bacterial antibiotic resistance. The aim of this narrative review is to discuss how can Hfq affects antibiotic resistance in bacteria and propose how this knowledge may facilitate developing new therapeutic strategies against pathogenic bacteria. We indicate that the mechanisms by which the Hfq protein modulates the response of bacterial cells to antibiotics are quite different, from the regulation of the expression of genes coding for proteins directly involved in antibiotic transportation or action, through direct effects on membranes, to controlling the replication or transposition of mobile genetic elements bearing antibiotic resistance genes. Therefore, we suggest that Hfq could be considered a potential target for novel antimicrobial compounds. We also discuss difficulties in developing such drugs, but since Hfq appears to be a promising target for drugs that may enhance the efficacy of antibiotics, we propose that works on such potential therapeutics are encouraged. Full article
(This article belongs to the Special Issue Clinical Microbial Infection and Antimicrobial Resistance)
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12 pages, 2210 KiB  
Review
Fluoroquinolone Resistance in Escherichia coli Causing Community-Acquired Urinary Tract Infections: A Systematic Review
by Ana P. Ruiz-Lievano, Fernando Cervantes-Flores, Alessandro Nava-Torres, Paulo J. Carbajal-Morales, Luisa F. Villaseñor-Garcia and Maria G. Zavala-Cerna
Microorganisms 2024, 12(11), 2320; https://doi.org/10.3390/microorganisms12112320 - 15 Nov 2024
Cited by 3 | Viewed by 2706
Abstract
Community-acquired urinary tract infections account for 15% of all outpatient use of antibiotics, and women are primarily affected; the major causative microorganism is uropathogenic Escherichia coli (E. coli). Treatment is indicated for cystitis and pyelonephritis and includes B-lactams (amoxicillin-clavulanic acid or [...] Read more.
Community-acquired urinary tract infections account for 15% of all outpatient use of antibiotics, and women are primarily affected; the major causative microorganism is uropathogenic Escherichia coli (E. coli). Treatment is indicated for cystitis and pyelonephritis and includes B-lactams (amoxicillin-clavulanic acid or third-generation cephalosporins), fluoroquinolones (ciprofloxacin or levofloxacin), nitrofurantoin, fosfomycin, and trimethoprim–sulfamethoxazole. Resistance to antibiotic treatment is of concern; several mechanisms have been associated with the acquisition of genes that confer antimicrobial resistance to fluoroquinolones, which are often associated with other patterns of resistance, especially in extended-spectrum beta-lactamase (ESBL) producers. Several studies have addressed the prevalence of uropathogens producing ESBLs, but only a few have focused on fluoroquinolone resistance, and, to our knowledge, none have addressed the prevalence of phylotypes or genes responsible for antimicrobial resistance to fluoroquinolones. The focus of the present review was to analyze recently published papers that described the E. coli phylotype causing community-acquired UTIs in association with fluoroquinolone resistance. Full article
(This article belongs to the Special Issue Clinical Microbial Infection and Antimicrobial Resistance)
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Other

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10 pages, 2321 KiB  
Case Report
Case Report: Heart Transplantation for Refractory Candida tropicalis Endocarditis: A Case Report and Literature Review
by Ricardo El Nouwar, Eva Larranaga Lapique, Frédéric Vanden Eynden, Delphine Martiny, Myriam Remmelink, Ana Roussoulières and Maya Hites
Microorganisms 2025, 13(3), 580; https://doi.org/10.3390/microorganisms13030580 - 4 Mar 2025
Viewed by 583
Abstract
Candida infective endocarditis presents therapeutic challenges with high mortality. A complex case of Candida prosthetic valve endocarditis refractory to standard antifungals (anidulafungin and fluconazole) and high-dose caspofungin was successfully treated with heart transplantation. The literature review revealed a few cases of bacterial endocarditis [...] Read more.
Candida infective endocarditis presents therapeutic challenges with high mortality. A complex case of Candida prosthetic valve endocarditis refractory to standard antifungals (anidulafungin and fluconazole) and high-dose caspofungin was successfully treated with heart transplantation. The literature review revealed a few cases of bacterial endocarditis successfully treated with heart transplantation, but with only two transplanted cases of fungal endocarditis. This report explores heart transplantation as a last resort for managing refractory infective endocarditis. The patient is still alive and free of infection, two and a half years after transplantation. Full article
(This article belongs to the Special Issue Clinical Microbial Infection and Antimicrobial Resistance)
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6 pages, 182 KiB  
Brief Report
Clinical and Drug Resistance Characteristics of Providencia Infections
by Meenal Malviya, Pramodini Kale-Pradhan, Meredith Coyle, Christopher Giuliano and Leonard B. Johnson
Microorganisms 2024, 12(10), 2085; https://doi.org/10.3390/microorganisms12102085 - 18 Oct 2024
Cited by 1 | Viewed by 2089
Abstract
Background: Providencia is a G ram-negative bacillus that most frequently colonizes the urinary tract and is often resistant to many antimicrobials. This study aimed to evaluate the resistance patterns of Providencia spp. and clinical outcomes due to the paucity of data. Methods: [...] Read more.
Background: Providencia is a G ram-negative bacillus that most frequently colonizes the urinary tract and is often resistant to many antimicrobials. This study aimed to evaluate the resistance patterns of Providencia spp. and clinical outcomes due to the paucity of data. Methods: A multi-center, descriptive, retrospective chart review of adult patients with Providencia spp. infections was conducted from 1 January 2020 to 31 May 2022. The primary outcome was to describe the drug resistance patterns of Providencia spp. isolates. This study’s secondary outcome was to evaluate the clinical outcomes of patients with Providencia spp. infections. Results: Of the 312 patients screened, 244 were excluded primarily for polymicrobial infections. The mean age was 70 years, and 39 (56.5%) were males. Of the 68 included cases, 46 (67.6%) were P. stuartii, 20 (29.4%) were P. rettgeri, and 2 (2.9%) were P. alcalifaciens. The most common infections were bacteremia 38 (55.8%), followed by 27 (39.7%) urinary tract infections and 3 (4.4%) wound infections. In this study, 45 patients (65.2%) had urinary catheters. The primary antibiotics used for treatment consisted of ceftriaxone (25 (36.2%)), cefepime (20 (29%)), and meropenem (10 (14.5%)). Only 5 of 68 (7.2%) cases were multidrug- resistant and required meropenem. In total, 19 patients (27.1%) died during their admission, but none were related to Providencia infections. A total of 10 of the 68 patients (14.5%) were readmitted within 30 days for reasons unrelated to the progression or recurrence of Providencia infections. Conclusions:Providencia bacteremia is predominantly seen in elderly patients. Third- generation cephalosporins remain an appropriate choice of antibiotics for Providencia spp. Providencia stuartii was the only species with multidrug resistance. Full article
(This article belongs to the Special Issue Clinical Microbial Infection and Antimicrobial Resistance)
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