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Microorganisms
Special Issues
Diagnosing Antimicrobial Resistance and Health Care Associated Infections
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Diagnosing Antimicrobial Resistance and Health Care Associated Infections

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

Deadline for manuscript submissions: closed (31 May 2018) | Viewed by 26563

Special Issue Editors

Dr. John W.A. Rossen

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Guest Editor
Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
Interests: antimicrobial resistance; health care; diagnose; infection prevention; genomics
Dr. Silvia García Cobos

E-Mail Website
Guest Editor
Research and Reference Laboratory on Antimicrobial Resistance and Healthcare Infections, National Microbiology Center, Majadahonda, Madrid, Spain
Interests: antimicrobial resistance; pathogenicity; infectious diseases; genomics; metagenomics; epidemiology
Special Issues, Collections and Topics in MDPI journals
Dr. Natacha Couto

E-Mail Website
Guest Editor
Department of Medical Microbiology and Infection PreventionUniversity of Groningen, University Medical Center Groningen, Groningen,The Netherlands
Interests: NGS; metagenomics; antimicrobial-resistance; one health; molecular epidemiology

Special Issue Information

Dear Colleagues,

Antimicrobial resistance (AMR) and healthcare-associated infections (HAI) are a global threat to human health. On the one hand, AMR leads to treatment failure, and, on the other hand, HAI threatens patient safety during hospitalization. A large proportion of HAI are due to common pathogens acquiring AMR genes. The dissemination of these AMR pathogens associated with HAI leads to outbreaks that require additional infection prevention measures, increasing hospital costs and, more importantly, potentially causing higher mortality rates.

Over the last two decades, new diagnostic methods have experienced rapid development and have played an increasingly-important role in medical microbiology and infection prevention departments. These methods have reduced the turnaround time, from receiving a sample to final pathogen identification, especially in hospital outbreak situations. In this Special Issue, the objective is to collect studies that provide relevant information on the surveillance and response to the threats of AMR and HAI, through the use of modern diagnostic and infection control approaches. This will include studies or reviews on 1) modern cultured-based surveillance, 2) MALDI-TOF for typing and AMR detection, 3) molecular diagnostics for the detection of HAI and AMR genes (including point-of-care assays), 4) use of next-generation sequencing in infection control; and 5) methods for the identification of plasmids and the dissemination of other mobile genetic elements (MGE).

Dr. John W.A. Rossen
Dr. Silvia Garcia Cobos
Dr. Natacha Couto
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

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

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Modern cultured-based surveillance
  • MALDI-TOF
  • Molecular diagnostics
  • Point-of-care tests
  • Next-generation sequencing
  • Whole-genome sequencing
  • Tailor-made assays
  • Mobile genetic elements
  • Metagenomics
  • Lineage-specific markers
  • Epidemiological data
  • Outbreak surveillance
  • Capacity-building

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Published Papers (5 papers)

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Research

15 pages, 8621 KiB  
Article
Detection of Legionella anisa in Water from Hospital Dental Chair Units and Molecular Characterization by Whole-Genome Sequencing
by Giuseppe Fleres, Natacha Couto, Mariette Lokate, Luc W. M. Van der Sluis, Christophe Ginevra, Sophie Jarraud, Ruud H. Deurenberg, John W. Rossen, Silvia García-Cobos and Alex W. Friedrich
Microorganisms 2018, 6(3), 71; https://doi.org/10.3390/microorganisms6030071 - 18 Jul 2018
Cited by 18 | Viewed by 6266
Abstract
This study aims to assess contamination with Legionella spp. in water from dental chair units (DCUs) of a hospital dental ward and to perform its molecular characterization by whole-genome sequencing (WGS). We collect eight water samples (250 mL) from four DCUs (sink and [...] Read more.
This study aims to assess contamination with Legionella spp. in water from dental chair units (DCUs) of a hospital dental ward and to perform its molecular characterization by whole-genome sequencing (WGS). We collect eight water samples (250 mL) from four DCUs (sink and water-syringe). Samples are tested for the presence of Legionella spp. (CFUs/mL) by culturing according to the Nederland Norm (NEN) 6265. Three DCUs are found positive for Legionella anisa, and four isolates are cultured (sink n = 2, water-syringe n = 1; two isolates from the same chair) with 1 × 102 CFU/mL. Whole-genome multi-locus sequence typing (wgMLST) results indicate that all strains belong to the same cluster with two to four allele differences. Classical culture combined with WGS allows the identification of a unique clone of L. anisa in several DCUs in the same hospital dental ward. This may indicate a common contamination source in the dental unit waterlines, which was fixed by replacing the chairs and main pipeline of the unit. Our results reveal tap water contamination in direct contact with patients and the usefulness of WGS to investigate bacterial molecular epidemiology. Full article
(This article belongs to the Special Issue Diagnosing Antimicrobial Resistance and Health Care Associated Infections)
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8 pages, 564 KiB  
Article
Defining Multidrug Resistance of Gram-Negative Bacteria in the Dutch–German Border Region—Impact of National Guidelines
by Robin Köck, Philipp Siemer, Jutta Esser, Stefanie Kampmeier, Matthijs S. Berends, Corinna Glasner, Jan P. Arends, Karsten Becker and Alexander W. Friedrich
Microorganisms 2018, 6(1), 11; https://doi.org/10.3390/microorganisms6010011 - 26 Jan 2018
Cited by 14 | Viewed by 6222
Abstract
Preventing the spread of multidrug-resistant Gram-negative bacteria (MDRGNB) is a public health priority. However, the definition of MDRGNB applied for planning infection prevention measures such as barrier precautions differs depending on national guidelines. This is particularly relevant in the Dutch–German border region, where [...] Read more.
Preventing the spread of multidrug-resistant Gram-negative bacteria (MDRGNB) is a public health priority. However, the definition of MDRGNB applied for planning infection prevention measures such as barrier precautions differs depending on national guidelines. This is particularly relevant in the Dutch–German border region, where patients are transferred between healthcare facilities located in the two different countries, because clinicians and infection control personnel must understand antibiograms indicating MDRGNB from both sides of the border and using both national guidelines. This retrospective study aimed to compare antibiograms of Gram-negative bacteria and classify them using the Dutch and German national standards for MDRGNB definition. A total of 31,787 antibiograms from six Dutch and four German hospitals were classified. Overall, 73.7% were no MDRGNB according to both guidelines. According to the Dutch and German guideline, 7772/31,787 (24.5%) and 4586/31,787 (12.9%) were MDRGNB, respectively (p < 0.0001). Major divergent classifications were observed for extended-spectrum β-lactamase (ESBL) -producing Enterobacteriaceae, non-carbapenemase-producing carbapenem-resistant Enterobacteriaceae, Pseudomonas aeruginosa and Stenotrophomonas maltophilia. The observed differences show that medical staff must carefully check previous diagnostic findings when patients are transferred across the Dutch–German border, as it cannot be assumed that MDRGNB requiring special hygiene precautions are marked in the transferred antibiograms in accordance with both national guidelines. Full article
(This article belongs to the Special Issue Diagnosing Antimicrobial Resistance and Health Care Associated Infections)
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7 pages, 212 KiB  
Article
Therapeutic Management of Pseudomonas aeruginosa Bloodstream Infection Non-Susceptible to Carbapenems but Susceptible to “Old” Cephalosporins and/or to Penicillins
by Ronit Zaidenstein, Asaf Miller, Ruthy Tal-Jasper, Hadas Ofer-Friedman, Menachem Sklarz, David E. Katz, Tsillia Lazarovitch, Paul R. Lephart, Bethlehem Mengesha, Oran Tzuman, Mor Dadon, Chen Daniel, Jacob Moran-Gilad and Dror Marchaim
Microorganisms 2018, 6(1), 9; https://doi.org/10.3390/microorganisms6010009 - 16 Jan 2018
Cited by 9 | Viewed by 3857
Abstract
It is unknown as to whether other beta-lactams can be used for bloodstream infections (BSI) resulting from Pseudomonas aeruginosa (PA) which are non-susceptible to one or more carbapenem. We conducted a retrospective cohort study at the Assaf Harofeh Medical Center (AHMC) from January [...] Read more.
It is unknown as to whether other beta-lactams can be used for bloodstream infections (BSI) resulting from Pseudomonas aeruginosa (PA) which are non-susceptible to one or more carbapenem. We conducted a retrospective cohort study at the Assaf Harofeh Medical Center (AHMC) from January 2010 to August 2014. Adult patients with PA-BSI non-susceptible to a group 2 carbapenem but susceptible to ceftazidime or piperacillin (with or without tazobactam), were enrolled. We compared the outcomes of patients who received an appropriate beta-lactam antibiotic (“cases”) to those who received an appropriate non-beta-lactam antibiotic (“controls”). Whole genome sequencing was performed for one of the isolates. Twenty-six patients with PA-BSI met inclusion criteria: 18 received a beta-lactam and 8 a non-beta-lactam (three a fluoroquinolone, two colistin, one a fluoroquinolone and an aminoglycoside, one a fluoroquinolone and colistin, and one colistin and an aminoglycoside). All clinical outcomes were similar between the groups. There were large variations in the phenotypic susceptibilities of the strains. A detailed molecular investigation of one isolate revealed a strain that belonged to MLST-137, with the presence of multiple efflux pumps, OXA-50, and a chromosomally mediated Pseudomonas-derived cephalosporinase (PDC). The oprD gene was intact. Non-carbapenem-β-lactams may still be effective alternatives for short duration therapy (up to 14 days) for BSI caused by a carbapenem non-susceptible (but susceptible to ceftazidime, piperacillin, and/or piperacillin-tazobactam) PA strain. This observation requires further confirmatory analyses. Future molecular investigations should be performed, in order to further analyze additional potential mechanisms for this prevalent phenotype. Full article
(This article belongs to the Special Issue Diagnosing Antimicrobial Resistance and Health Care Associated Infections)
8 pages, 479 KiB  
Article
Evaluation of an Accelerated Workflow for Surveillance of ESBL (CTX-M)-Producing Escherichia coli Using Amplicon-Based Next-Generation Sequencing and Automated Analysis
by Nilay Peker, John W. A. Rossen, Ruud H. Deurenberg, Paula C. Langereis, Erwin G. C. Raangs, Jan A. Kluytmans, Alexander W. Friedrich, Jacobien Veenemans and Bhanu Sinha
Microorganisms 2018, 6(1), 6; https://doi.org/10.3390/microorganisms6010006 - 11 Jan 2018
Cited by 5 | Viewed by 5000
Abstract
Outbreak management of extended spectrum β-lactamase (ESBL)-producing pathogens requires rapid and accurate diagnosis. However, conventional screening is slow and labor-intensive. The vast majority of the screened samples are negative and detection of non-outbreak-related resistant micro-organisms often complicates outbreak management. In a CTX-M-15-producing [...] Read more.
Outbreak management of extended spectrum β-lactamase (ESBL)-producing pathogens requires rapid and accurate diagnosis. However, conventional screening is slow and labor-intensive. The vast majority of the screened samples are negative and detection of non-outbreak-related resistant micro-organisms often complicates outbreak management. In a CTX-M-15-producing Escherichia coli outbreak, 149 fecal samples and rectal eSwabs were collected by a cross-sectional survey in a Dutch nursing home. Samples were processed by routine diagnostic methods. Retrospectively, ESBL-producing bacteria and resistance genes were detected directly from eSwab medium by an accelerated workflow without prior enrichment cultures by an amplicon-based next-generation sequencing (NGS) method, and culture. A total of 27 (18.1%) samples were positive in either test. Sensitivity for CTX-M detection was 96.3% for the phenotypic method and 85.2% for the NGS method, and the specificity was 100% for both methods, as confirmed by micro-array. This resulted in a positive predictive value (PPV) of 100% for both methods, and a negative predictive value (NPV) of 99.2% and 96.8% for the phenotypic method and the NGS method, respectively. Time to result was four days and 14 h for the phenotypic method and the NGS method, respectively. In conclusion, the sensitivity without enrichment shows promising results for further use of amplicon-based NGS for screening during outbreaks. Full article
(This article belongs to the Special Issue Diagnosing Antimicrobial Resistance and Health Care Associated Infections)
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1319 KiB  
Communication
The Small Regulatory RNA Spot42 Inhibits Indole Biosynthesis to Negatively Regulate the Locus of Enterocyte Effacement of Enteropathogenic Escherichia coli
by Shantanu Bhatt, Valerie Jenkins, Elisabeth Mason and Sarah Muche
Microorganisms 2017, 5(4), 78; https://doi.org/10.3390/microorganisms5040078 - 1 Dec 2017
Cited by 4 | Viewed by 4577
Abstract
The locus of enterocyte effacement is necessary for enteropathogenic Escherichia coli (EPEC) to form attaching and effacing (A/E) lesions. A/E lesions are characterized by intimate bacterial adherence to intestinal cells and destruction of microvilli, which leads to diarrhea. Therefore, studies interrogating the regulation [...] Read more.
The locus of enterocyte effacement is necessary for enteropathogenic Escherichia coli (EPEC) to form attaching and effacing (A/E) lesions. A/E lesions are characterized by intimate bacterial adherence to intestinal cells and destruction of microvilli, which leads to diarrhea. Therefore, studies interrogating the regulation of the locus of enterocyte effacement (LEE) are critical for understanding the molecular epidemiology of EPEC infections and developing interventional strategies. Hitherto, most studies have centered on protein-based regulators, whereas the role of small regulatory RNAs remains underappreciated. Previously, we identified the first sRNAs—MgrR, RyhB, and McaS—that regulate the LEE of EPEC. This study was undertaken to identify additional sRNAs that impact the LEE. Our results suggest that the catabolite-responsive sRNA, Spot42, indirectly controls the LEE by inhibiting synthesis of its inducer, indole. Spot42 base-pairs with the tnaCAB mRNA and presumably destabilizes the transcript, thereby preventing expression of the regulatory and structural proteins that are involved in the import and hydrolysis of tryptophan into indole. The absence of intracellular indole leads to reduced transcription of the LEE1-encoded master transcriptional activator Ler, thereby maintaining the LEE in its silenced state and delaying A/E lesion morphogenesis. Our results highlight the importance of riboregulators that synchronize metabolic and virulence pathways in bacterial infection. Full article
(This article belongs to the Special Issue Diagnosing Antimicrobial Resistance and Health Care Associated Infections)
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