Molecular Epidemiology of Human Bacterial Pathogens Tolerant to Biocides and Resistant to Antibiotics

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Molecular Microbiology and Immunology".

Deadline for manuscript submissions: closed (30 September 2023) | Viewed by 5883

Special Issue Editors


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Guest Editor
UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, REQUIMTE Faculty of Pharmacy, University of Porto, Porto, Portugal
Interests: infectious diseases; bacterial molecular and genomic epidemiology; eco-evolution of antibiotic resistance and disinfectants/metal tolerance within a one health perspective (clones and mobile genetic elements)
Special Issues, Collections and Topics in MDPI journals

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Guest Editor
1. Faculty of Nutrition and Food Sciences, University of Porto, Porto, Portugal
2. UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, REQUIMTE Faculty of Pharmacy, University of Porto, Porto, Portugal
Interests: antimicrobial resistance (antibiotics and biocides/metals) and foodborne diseases; Salmonella and other Enterobacterales at the environment–animal–food–human interface; one health approach
Special Issues, Collections and Topics in MDPI journals

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Guest Editor
1. TOXRUN—Toxicology Research Unit, University Institute of Health Sciences, CESPU, CRL, 4585-116 Gandra, Portugal
2. UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, REQUIMTE Faculty of Pharmacy, University of Porto, Porto, Portugal
Interests: antimicrobial resistance and infectious diseases; molecular and genomic epidemiology of bacterial pathogens under a one health approach; forensic microbiology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Biocides (e.g., disinfectants, metals) are critical to human and animal infection prevention and control. Although they are usually used in high concentrations, sub-inhibitory ones (e.g., due to inadequate use or environmental residues) might select human pathogenic bacteria with diverse levels of biocide tolerance in several environments. Biocides have also been pointed out as a potential player in the selection of bacteria resistant to antibiotics. The application of genomics and metagenomics could be a key strategy to decipher the molecular epidemiology of biocide tolerance (clones, genetic elements) among antibiotic-resistant human pathogenic bacteria as well as the interconnection among microbiota from overlapping ecosystems contributing to this problem. This Special Issue on “Molecular Epidemiology of Human Bacterial Pathogens Tolerant to Biocides and Resistant to Antibiotics” will highlight research findings that cover topics focusing on molecular aspects of biocide tolerance and of diverse practices associated with their use in diverse clinical, food-chain, and environmental contexts contributing to the selection and persistence of biocide-tolerant and antibiotic-resistant bacteria.

Dr. Carla Novais
Dr. Patrícia Antunes
Dr. Ana R. Freitas
Guest Editors

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Keywords

  • biocides
  • disinfectants
  • metals
  • antimicrobial resistance
  • antibiotics
  • clones
  • mobile genetic elements
  • tolerance mechanisms
  • whole-genome sequence
  • metagenomics

Published Papers (4 papers)

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Research

18 pages, 5639 KiB  
Article
Exploring Peracetic Acid and Acidic pH Tolerance of Antibiotic-Resistant Non-Typhoidal Salmonella and Enterococcus faecium from Diverse Epidemiological and Genetic Backgrounds
by Andreia Rebelo, Bárbara Duarte, Ana R. Freitas, Luísa Peixe, Patrícia Antunes and Carla Novais
Microorganisms 2023, 11(9), 2330; https://doi.org/10.3390/microorganisms11092330 - 16 Sep 2023
Viewed by 1258
Abstract
Acid stress poses a common challenge for bacteria in diverse environments by the presence of inorganic (e.g., mammals’ stomach) or organic acids (e.g., feed additives; acid-based disinfectants). Limited knowledge exists regarding acid-tolerant strains of specific serotypes, clonal lineages, or sources in human/animal pathogens: [...] Read more.
Acid stress poses a common challenge for bacteria in diverse environments by the presence of inorganic (e.g., mammals’ stomach) or organic acids (e.g., feed additives; acid-based disinfectants). Limited knowledge exists regarding acid-tolerant strains of specific serotypes, clonal lineages, or sources in human/animal pathogens: namely, non-typhoidal Salmonella enterica (NTS) and Enterococcus faecium (Efm). This study evaluated the acidic pH (Mueller–Hinton acidified with HCl) and peracetic acid (PAA) susceptibility of Efm (n = 72) and NTS (n = 60) from diverse epidemiological/genetic backgrounds and with multiple antibiotic resistance profiles. Efm minimum growth/survival pH was 4.5–5.0/3.0–4.0, and for NTS it was 4.0–4.5/3.5–4.0. Efm distribution among acidic pH values showed that only isolates of clade-non-A1 (non-hospital associated) or the food chain were more tolerant to acidic pH compared to clade-A1 (hospital-associated clones) or clinical isolates (p < 0.05). In the case of NTS, multidrug-resistant (MDR) isolates survived better in acidic pH (p < 0.05). The PAA MIC/MBC for Efm was 70–120/80–150 mg/L, and for NTS, it was 50–70/60–100 mg/L. The distribution of Efm among PAA concentrations showed that clade-A1 or MDR strains exhibited higher tolerance than clade-non-A1 or non-MDR ones (p < 0.05). NTS distribution also showed higher tolerance to PAA among non-MDR and clinical isolates than food chain ones (p < 0.05) but there were no differences among different serogroups. This unique study identifies specific NTS or Efm populations more tolerant to acidic pH or PAA, emphasizing the need for further research to tailor controlled measures of public health and food safety within a One Health framework. Full article
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21 pages, 3805 KiB  
Article
Multidrug-Resistant and Extensively Drug-Resistant Acinetobacter baumannii Causing Nosocomial Meningitis in the Neurological Intensive Care Unit
by Nadezhda K. Fursova, Mikhail V. Fursov, Evgeny I. Astashkin, Anastasiia D. Fursova, Tatiana S. Novikova, Angelina A. Kislichkina, Angelika A. Sizova, Galina N. Fedyukina, Ivan A. Savin and Olga N. Ershova
Microorganisms 2023, 11(8), 2020; https://doi.org/10.3390/microorganisms11082020 - 6 Aug 2023
Cited by 4 | Viewed by 1426
Abstract
Acinetobacter baumannii is one of the significant healthcare-associated meningitis agents characterized by multidrug resistance and a high mortality risk. Thirty-seven A. baumannii strains were isolated from thirty-seven patients of Moscow neuro-ICU with meningitis in 2013–2020. The death rate was 37.8%. Strain susceptibility to [...] Read more.
Acinetobacter baumannii is one of the significant healthcare-associated meningitis agents characterized by multidrug resistance and a high mortality risk. Thirty-seven A. baumannii strains were isolated from thirty-seven patients of Moscow neuro-ICU with meningitis in 2013–2020. The death rate was 37.8%. Strain susceptibility to antimicrobials was determined on the Vitek-2 instrument. Whole-genome sequencing was conducted using Illumina technology; the sequence types (ST), capsular types (KL), lipooligosaccharide outer core locus (OCL), antimicrobial resistance genes, and virulence genes were identified. The prevalent ST was ST2, belonging to the international clone IC2, and rarer, ST1, ST19, ST45, ST78, ST106, and ST400, with prevalence of KL9 and OCL1. Twenty-nine strains belonged to multidrug-resistant (MDR) and eight extensively drug-resistant (XDR) categories. Genes conferring resistance to beta-lactams (blaPER, blaGES, blaADC, blaCARB, blaCTX-M, blaTEM, and blaOXA-types), aminoglycosides (aac, aad, ant, aph, and arm), tetracyclines (tet), macrolides (msr and mph), phenicols (cml, cat, and flo), sulfonamides (dfr and sul), rifampin (arr), and antiseptics (qac) were identified. Virulence genes of nine groups (Adherence, Biofilm formation, Enzymes, Immune evasion, Iron uptake, Regulation, Serum resistance, Stress adaptation, and Antiphagocytosis) were detected. The study highlights the heterogeneity in genetic clones, antimicrobial resistance, and virulence genes variability among the agents of A. baumannii meningitis, with the prevalence of the dominant international clone IC2. Full article
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12 pages, 2731 KiB  
Article
Hetero-Pathogenic O181:H4 EAHEC Strain of Sequence Type ST678 Associated with Hemolytic–Uremic Syndrome in Schoolchildren in Russia
by Nikolay N. Kartsev, Elena V. Detusheva, Olga V. Kalmantaeva, Olga V. Korobova, Vladimir N. Gerasimov, Tatiana I. Kombarova, Aleksander I. Borzilov, Nadezhda K. Fursova, Anatoly N. Vereshchagin and Edward A. Svetoch
Microorganisms 2023, 11(7), 1771; https://doi.org/10.3390/microorganisms11071771 - 7 Jul 2023
Viewed by 933
Abstract
Background: In the last decade, the importance of hetero-pathogenic enteroaggregative Shiga-toxin-producing E. coli for public health has increased. Recently, we described the genetic background of the EAHEC O181:H4 strain of ST678 carrying the stx2 gene in prophage and five plasmids, including the plasmid-carrying [...] Read more.
Background: In the last decade, the importance of hetero-pathogenic enteroaggregative Shiga-toxin-producing E. coli for public health has increased. Recently, we described the genetic background of the EAHEC O181:H4 strain of ST678 carrying the stx2 gene in prophage and five plasmids, including the plasmid-carrying aggR and aaiC genes. Here, we present the morphological and enzymatic characteristics of this strain, as well as susceptibility to antimicrobials, biofilm formation, etc. Methods: Bacterial morphology was studied using an electron microscope. Susceptibility to antimicrobials was determined using the microdilution method. Cytotoxicity was estimated in Vero cells. Virulence was studied on mice. Results: The morphological and enzymatic properties of the hetero-pathogenic EAHEC strain were typical for E. coli; electron microscopy revealed the specific flagella. The strain was susceptible to most antibiotics and disinfectants but resistant to ampicillin and ciprofloxacin and showed a high degree of biofilm formation. Cytotoxicity towards Vero cells was estimated as 80%. Conclusions: The emergence of a new O181:H4 EAHEC strain poses a potential threat to humans because of the virulence potential that must be taken into account in the epidemiological analysis of outbreaks and sporadic cases of foodborne infections associated with hemolytic–uremic syndrome. Full article
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11 pages, 947 KiB  
Article
Molecular Epidemiological Investigation and Management of Outbreak Caused by Carbapenem-Resistant Acinetobacter baumannii in a Neonatal Intensive Care Unit
by Jia Jie Woon, Azanna Ahmad Kamar, Cindy Shuan Ju Teh, Nuryana Idris, Rosliza Zhazali, Suzana Saaibon, Harvinderjit Kaur Basauhra Singh, Jasreena Kaur Gill Charanjeet Singh, Adeeba Kamarulzaman and Sasheela Ponnampalavanar
Microorganisms 2023, 11(4), 1073; https://doi.org/10.3390/microorganisms11041073 - 20 Apr 2023
Cited by 2 | Viewed by 1524
Abstract
The present study describes an epidemiological investigation into a carbapenem-resistant Acinetobacter baumannii (CRAB) outbreak, which had occurred in a neonatal intensive care unit (NICU), and the subsequent strengthening of infection control interventions. Upon the onset of the outbreak, existing infection control interventions were [...] Read more.
The present study describes an epidemiological investigation into a carbapenem-resistant Acinetobacter baumannii (CRAB) outbreak, which had occurred in a neonatal intensive care unit (NICU), and the subsequent strengthening of infection control interventions. Upon the onset of the outbreak, existing infection control interventions were reviewed, and a set of containment measures were instituted. All CRAB isolates were characterized in terms of antimicrobial susceptibility testing and their genetic relatedness. The investigation process identified gaps within the NICU’s existing infection control measures, which had likely resulted in the outbreak. CRAB was isolated from nine preterm infants: five colonized and four infected. All five colonized patients were discharged well. However, three out of four of the infected infants died. Outbreak investigation and genomic subtyping of environmental swabs revealed that mini syringe drivers shared between patients and a sink in the milk preparation room had served as CRAB reservoirs with possible transmission via the hands of healthcare workers. Implementation of immediate actions such as reinforcement of hand hygiene practices, intensified environmental cleaning, geographical cohorting, reviewing of milk handling practices and sink management protocol had resulted in no further CRAB isolation. The CRAB outbreak in the NICU underlines the importance of consistent compliance with infection-control interventions. Integration of epidemiological and microbiological data, together with comprehensive preventive measures, successfully brought the outbreak to a halt. Full article
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