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

Deadline for manuscript submissions: closed (30 June 2023) | Viewed by 13462

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Special Issue Editor

Dr. Benoît Pilmis

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Guest Editor

Groupe Hospitalier Paris Saint-Joseph, Paris, France
Interests: antimicrobial stewardship team; multidrug resistance; immunocompromised host

Special Issue Information

Dear Colleagues,

Currently, there is a clear increase in antibiotic resistance in bacteria, especially in Gram-negative bacilli. The fight against this antibiotic resistance is based, among other things, on rapid diagnosis and the proper use of antibiotics. For this reason, the implementation of antimicrobial stewardship programs has developed significantly. This proper use of antibiotics is based on the rapid identification of the site of infection, the mechanisms of resistance, the optimization of antibiotic use (in terms of dosage, administration methods, duration of treatment) and on the rules of escalation or de-escalation of antibiotic therapy.

The project of this Special Issue is to promote the publication of literature reviews, original studies, and communications on the topic of antimicrobial stewardship and the proper use of antibiotics.

We look forward to your contributions.

Dr. Benoît Pilmis
Guest Editor

Manuscript Submission Information

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Keywords

antibiotic resistance
mechanisms
bacteria
rapid diagnosis
antimicrobial stewardship

Published Papers (7 papers)

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Research

21 pages, 716 KiB

Open AccessArticle

Antimicrobial Resistance Patterns and Risk Factors Associated with ESBL-Producing and MDR Escherichia coli in Hospital and Environmental Settings in Lusaka, Zambia: Implications for One Health, Antimicrobial Stewardship and Surveillance Systems

by Maisa Kasanga, Geoffrey Kwenda, Jian Wu, Maika Kasanga, Mark J. Mwikisa, Raphael Chanda, Zachariah Mupila, Baron Yankonde, Mutemwa Sikazwe, Enock Mwila, Doreen M. Shempela, Benjamin B. Solochi, Christabel Phiri, Steward Mudenda and Duncan Chanda

Microorganisms 2023, 11(8), 1951; https://doi.org/10.3390/microorganisms11081951 - 31 Jul 2023

Cited by 4 | Viewed by 2098

Abstract

Antimicrobial resistance (AMR) is a public health problem threatening human, animal, and environmental safety. This study assessed the AMR profiles and risk factors associated with Escherichia coli in hospital and environmental settings in Lusaka, Zambia. This cross-sectional study was conducted from April 2022 to August 2022 using 980 samples collected from clinical and environmental settings. Antimicrobial susceptibility testing was conducted using BD Phoenix^TM 100. The data were analysed using SPSS version 26.0. Of the 980 samples, 51% were from environmental sources. Overall, 64.5% of the samples tested positive for E. coli, of which 52.5% were from clinical sources. Additionally, 31.8% were ESBL, of which 70.1% were clinical isolates. Of the 632 isolates, 48.3% were MDR. Most clinical isolates were resistant to ampicillin (83.4%), sulfamethoxazole/trimethoprim (73.8%), and ciprofloxacin (65.7%) while all environmental isolates were resistant to sulfamethoxazole/trimethoprim (100%) and some were resistant to levofloxacin (30.6%). The drivers of MDR in the tested isolates included pus (AOR = 4.6, CI: 1.9–11.3), male sex (AOR = 2.1, CI: 1.2–3.9), and water (AOR = 2.6, CI: 1.2–5.8). This study found that E. coli isolates were resistant to common antibiotics used in humans. The presence of MDR isolates is a public health concern and calls for vigorous infection prevention measures and surveillance to reduce AMR and its burdens. Full article

(This article belongs to the Special Issue Clinical Microbiology and Antimicrobial Stewardship)

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14 pages, 1605 KiB

Open AccessArticle

Application of Novel Short Tandem Repeat Typing for Wickerhamomyces anomalus Reveals Simultaneous Outbreaks within a Single Hospital

by Bram Spruijtenburg, Shivaprakash M. Rudramurthy, Eelco F. J. Meijer, Merlijn H. I. van Haren, Harsimran Kaur, Arunaloke Chakrabarti, Jacques F. Meis and Theun de Groot

Microorganisms 2023, 11(6), 1525; https://doi.org/10.3390/microorganisms11061525 - 08 Jun 2023

Cited by 2 | Viewed by 1282

Abstract

Wickerhamomyces anomalus, previously known as Candida pelliculosa, occasionally causes candidemia in humans, primarily infecting neonates, and infants. The mortality rate of these invasive infections is high, and isolates with a reduced susceptibility to fluconazole have been reported. W. anomalus outbreaks are regularly reported in healthcare facilities, especially in neonatal intensive care units (NICUs). In order to rapidly genotype isolates with a high-resolution, we developed and applied a short tandem repeat (STR) typing scheme for W. anomalus. Six STR markers were selected and amplified in two multiplex PCRs, M3 and M6, respectively. In total, 90 W. anomalus isolates were typed, leading to the identification of 38 different genotypes. Four large clusters were found, unveiling simultaneous outbreak events spread across multiple units within the same hospital. STR typing results of 11 isolates were compared to whole-genome sequencing (WGS) single nucleotide polymorphism (SNP) calling, and the identified genotypic relationships were highly concordant. We performed antifungal susceptibility testing of these isolates, and a reduced susceptibility to fluconazole was found for two (2.3%) isolates. ERG11 genes of these two isolates were examined using WGS data, which revealed a novel I469L substitution in one isolate. By constructing a homology model for W. anomalus ERG11p, the substitution was found in close proximity to the fluconazole binding site. In summary, we showed multiple W. anomalus outbreak events by applying a novel STR genotyping scheme. Full article

(This article belongs to the Special Issue Clinical Microbiology and Antimicrobial Stewardship)

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12 pages, 302 KiB

Open AccessArticle

Antibiotic Management of Uncomplicated Skin and Soft Tissue Infections in the Real World

by Luis Fernando Valladales-Restrepo, Brayan Stiven Aristizábal-Carmona, Jaime Andrés Giraldo-Correa, Luis Felipe Acevedo-Medina, Laura Valencia-Sánchez, Doménica Tatiana Acevedo-López, Andrés Gaviria-Mendoza, Manuel Enrique Machado-Duque and Jorge Enrique Machado-Alba

Microorganisms 2023, 11(6), 1369; https://doi.org/10.3390/microorganisms11061369 - 24 May 2023

Cited by 1 | Viewed by 1229

Abstract

Background: Skin and soft tissue infections are one of the main causes of consultations worldwide. The objective was to determine the treatment of a group of patients with uncomplicated skin and soft tissue infections in Colombia. Methods: Follow-up study of a cohort of patients with skin infections who were treated in the Colombian Health System. Sociodemographic, clinical and pharmacological variables were identified. Treatments were evaluated using clinical practice guidelines for skin infections. Results: A total of 400 patients were analyzed. They had a median age of 38.0 years and 52.3% were men. The most commonly used antibiotics were cephalexin (39.0%), dicloxacillin (28.0%) and clindamycin (18.0%). A total of 49.8% of the subjects received inappropriate antibiotics, especially those with purulent infections (82.0%). Being cared for in an outpatient clinic (OR: 2.09; 95% CI: 1.06–4.12), presenting pain (OR: 3.72; 95% CI: 1.41–9.78) and having a purulent infection (OR: 25.71; 95% CI: 14.52–45.52) were associated with a higher probability of receiving inappropriate antibiotics. Conclusions: Half of patients with uncomplicated skin and soft tissue infections were treated with antibiotics that were not recommended by clinical practice guidelines. This inappropriate use of antibiotics occurred in the vast majority of patients with purulent infections because the antimicrobials used had no effect on methicillin-resistant Staphylococcus aureus. Full article

(This article belongs to the Special Issue Clinical Microbiology and Antimicrobial Stewardship)

11 pages, 456 KiB

Open AccessArticle

Short Peripheral Venous Catheters Contamination and the Dangers of Bloodstream Infection in Portugal: An Analytic Study

by Nádia Osório, Vânia Oliveira, Maria Inês Costa, Paulo Santos-Costa, Beatriz Serambeque, Fernando Gama, David Adriano, João Graveto, Pedro Parreira and Anabela Salgueiro-Oliveira

Microorganisms 2023, 11(3), 709; https://doi.org/10.3390/microorganisms11030709 - 09 Mar 2023

Cited by 1 | Viewed by 2060

Abstract

Peripheral venous catheters (PVCs) are the most used vascular access devices in the world. However, failure rates remain considerably high, with complications such as PVC-related infections posing significant threats to patients’ well-being. In Portugal, studies evaluating the contamination of these vascular medical devices and characterizing the associated microorganisms are scarce and lack insight into potential virulence factors. To address this gap, we analyzed 110 PVC tips collected in a large tertiary hospital in Portugal. Experiments followed Maki et al.’s semi-quantitative method for microbiological diagnosis. Staphylococcus spp. were subsequently studied for the antimicrobial susceptibility profile by disc diffusion method and based on the cefoxitin phenotype, were further classified into strains resistant to methicillin. Screening for the mecA gene was also done by a polymerase chain reaction and minimum inhibitory concentration (MIC)-vancomycin as determined by E-test, proteolytic and hemolytic activity on skimmed milk 1% plate and blood agar, respectively. The biofilm formation was evaluated on microplate reading through iodonitrotetrazolium chloride 95% (INT). Overall, 30% of PVCs were contaminated, and the most prevalent genus was Staphylococcus spp., 48.8%. This genus presented resistance to penicillin (91%), erythromycin (82%), ciprofloxacin (64%), and cefoxitin (59%). Thus, 59% of strains were considered resistant to methicillin; however, we detected the mecA gene in 82% of the isolates tested. Regarding the virulence factors, 36.4% presented α-hemolysis and 22.7% β-hemolysis, 63.6% presented a positive result for the production of proteases, and 63.6% presented a biofilm formation capacity. Nearly 36.4% were simultaneously resistant to methicillin and showed expression of proteases and/or hemolysins, biofilm formation, and the MIC to vancomycin were greater than 2 µg/mL. Conclusion: PVCs were mainly contaminated with Staphylococcus spp., with high pathogenicity and resistance to antibiotics. The production of virulence factors strengthens the attachment and the permanence to the catheter’s lumen. Quality improvement initiatives are needed to mitigate such results and enhance the quality and safety of the care provided in this field. Full article

(This article belongs to the Special Issue Clinical Microbiology and Antimicrobial Stewardship)

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14 pages, 2696 KiB

Open AccessArticle

An In-Silico Evaluation of Anthraquinones as Potential Inhibitors of DNA Gyrase B of Mycobacterium tuberculosis

by Juliana Carolina Amorim, Andrea E. Cabrera Bermeo, Viviana E. Vásquez Urgilés, Maritza R. Martínez León and Juan M. Carpio Arévalo

Microorganisms 2022, 10(12), 2434; https://doi.org/10.3390/microorganisms10122434 - 08 Dec 2022

Cited by 10 | Viewed by 1593

Abstract

The World Health Organization reported that tuberculosis remains on the list of the top ten threats to public health worldwide. Among the main causes is the limited effectiveness of treatments due to the emergence of resistant strains of Mycobacterium tuberculosis. One of the main drug targets studied to combat M. tuberculosis is DNA gyrase, the only enzyme responsible for regulating DNA topology in this specie and considered essential in all bacteria. In this context, the present work tested the ability of 2824 anthraquinones retrieved from the PubChem database to act as competitive inhibitors through interaction with the ATP-binding pocket of DNA gyrase B of M. tuberculosis. Virtual screening results based on molecular docking identified 7122772 (N-(2-hydroxyethyl)-9,10-dioxoanthracene-2-sulfonamide) as the best-scored ligand. From this anthraquinone, a new derivative was designed harbouring an aminotriazole moiety, which exhibited higher binding energy calculated by molecular docking scoring and free energy calculation from molecular dynamics simulations. In addition, in these last analyses, this ligand showed to be stable in complex with the enzyme and further predictions indicated a low probability of cytotoxic and off-target effects, as well as an acceptable pharmacokinetic profile. Taken together, the presented results show a new synthetically accessible anthraquinone with promising potential to inhibit the GyrB of M. tuberculosis. Full article

(This article belongs to the Special Issue Clinical Microbiology and Antimicrobial Stewardship)

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23 pages, 4355 KiB

Open AccessArticle

Toxicological and Safety Pharmacological Profiling of the Anti-Infective and Anti-Inflammatory Peptide Pep19-2.5

by Clemens Möller, Lena Heinbockel, Patrick Garidel, Thomas Gutsmann, Karl Mauss, Günther Weindl, Satoshi Fukuoka, Dominik Loser, Timm Danker and Klaus Brandenburg

Microorganisms 2022, 10(12), 2412; https://doi.org/10.3390/microorganisms10122412 - 06 Dec 2022

Cited by 2 | Viewed by 1428

Abstract

Aspidasept (Pep19-2.5) and its derivative Pep19-4LF (“Aspidasept II”) are anti-infective and anti-inflammatory synthetic polypeptides currently in development for application against a variety of moderate to severe bacterial infections that could lead to systemic inflammation, as in the case of severe sepsis and septic shock, as well as application to non-systemic diseases in the case of skin and soft tissue infections (SSTI). In the present study, Aspidasept and Aspidasept II and their part structures were analysed with respect to their toxic behavior in different established models against a variety of relevant cells, and in electrophysiological experiments targeting the hERG channel according to ICH S7B. Furthermore, the effects in mouse models of neurobiological behavior and the local lymph node according to OECD test guideline 429 were investigated, as well as a rat model of repeated dose toxicology according to ICH M3. The data provide conclusive information about potential toxic effects, thus specifying a therapeutic window for the application of the peptides. Therefore, these data allow us to define Aspidasept concentrations for their use in clinical studies as parenteral application. Full article

(This article belongs to the Special Issue Clinical Microbiology and Antimicrobial Stewardship)

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17 pages, 918 KiB

Open AccessArticle

Evidence of Community-Wide Spread of Multi-Drug Resistant Escherichia coli in Young Children in Lusaka and Ndola Districts, Zambia

by Flavien Nsoni Bumbangi, Ann-Katrin Llarena, Eystein Skjerve, Bernard Mudenda Hang’ombe, Prudence Mpundu, Steward Mudenda, Paulin Beya Mutombo and John Bwalya Muma

Microorganisms 2022, 10(8), 1684; https://doi.org/10.3390/microorganisms10081684 - 21 Aug 2022

Cited by 9 | Viewed by 2181

Abstract

Increased antimicrobial resistance (AMR) has been reported for pathogenic and commensal Escherichia coli (E. coli), hampering the treatment, and increasing the burden of infectious diarrhoeal diseases in children in developing countries. This study focused on exploring the occurrence, patterns, and possible drivers of AMR E. coli isolated from children under-five years in Zambia. A hospital-based cross-sectional study was conducted in the Lusaka and Ndola districts. Rectal swabs were collected from 565 and 455 diarrhoeic and healthy children, respectively, from which 1020 E. coli were cultured and subjected to antibiotic susceptibility testing. Nearly all E. coli (96.9%) were resistant to at least one antimicrobial agent tested. Further, 700 isolates were Multi-Drug Resistant, 136 were possibly Extensively-Drug Resistant and nine were Pan-Drug-Resistant. Forty percent of the isolates were imipenem-resistant, mostly from healthy children. A questionnaire survey documented a complex pattern of associations between and within the subgroups of the levels of MDR and socio-demographic characteristics, antibiotic stewardship, and guardians’ knowledge of AMR. This study has revealed the severity of AMR in children and the need for a community-specific-risk-based approach to implementing measures to curb the problem. Full article

(This article belongs to the Special Issue Clinical Microbiology and Antimicrobial Stewardship)

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