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Microorganisms Associated with Infectious Disease

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

Deadline for manuscript submissions: closed (31 December 2021) | Viewed by 23540

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Special Issue Editors

Dr. Edward R. B. Moore

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Guest Editor

Department of Infectious Diseases, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; and Department of Clinical Microbiology, Sahlgrenska University Hospital, Guldhedsgatan 10A, SE 41346 Gothenburg, Sweden
Interests: microbial evolution and phylogeny; bacterial systematics and taxonomy; bacterial identification; molecular bacterial diagnostics; diagnostics of infectious diseases; antimicrobial resistance
Special Issues, Collections and Topics in MDPI journals

Dr. Daniel Jaén Luchoro

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Guest Editor

Department of Infectious Diseases, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
Interests: molecular bacterial diagnostics; bacterial identification; bacterial systematics and taxonomy

Special Issue Information

Dear Colleagues,

Are you working with interesting strains of microorganisms associated with infectious disease that you think should be described and reported to the public and scientific world but are afraid that reports of descriptions of such bacteria, yeast, fungi, viruses, parasites, etc., would not be considered to be ‘‘in scope’’ of most journals? The Special Issue, “Microorganisms Associated with Infectious Disease”, provides a venue for publications of detailed characterizations of microorganisms that have been isolated from human clinical samples, veterinary samples, plant diseases, or other pathogenic interactions, and are interesting and relevant from the perspectives of features associated with infection, virulence, molecular pathology, antimicrobial resistance, pathophysiology, coinfection, outbreak, epidemic and pandemic prevalence, etiology, mechanisms of induction of host responses, and defenses against host protective mechanisms or other interesting and relevant characteristics.

Manuscripts may focus on experimental studies, demonstrating aspects associated with mechanisms of disease, or may present descriptive characterizations of microorganisms associated with disease. Such presentations ideally should include in-depth genomic, proteomic, transcriptomic, and metabolomic characterizations, with the details of analyses. Authors should discuss causal connections, considering ‘‘causal inference’’ and ‘‘inference of association’’ of microorganisms with disease.

Prof. Edward R. B. Moore
Dr. Daniel Jaén Luchoro
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

infection
virulence
molecular pathology
antimicrobial resistance
pathophysiology
coinfection
outbreak
epidemic
pandemic
etiology
host response

Published Papers (9 papers)

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Research

13 pages, 522 KiB

Open AccessCommunication

Hepatitis B Virus Integration into Transcriptionally Active Loci and HBV-Associated Hepatocellular Carcinoma

by Maria Bousali and Timokratis Karamitros

Microorganisms 2022, 10(2), 253; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10020253 - 24 Jan 2022

Cited by 3 | Viewed by 3067

Abstract

Hepatitis B Virus (HBV) DNA integrations into the human genome are considered major causative factors to HBV-associated hepatocellular carcinoma development. In the present study, we investigated whether HBV preferentially integrates parts of its genome in specific genes and evaluated the contribution of the integrations in HCC development per gene. We applied dedicated in-house developed pipelines on all of the available HBV DNA integration data and performed a statistical analysis to identify genes that could be characterized as hotspots of integrations, along with the evaluation of their association with HBV-HCC. Our results suggest that 15 genes are recurrently affected by HBV integrations and they are significantly associated with HBV-HCC. Further studies that focus on HBV integrations disrupting these genes are mandatory in order to understand the role of HBV integrations in clonal advantage gain and oncogenesis promotion, as well as to determine whether inhibition of the HBV-disrupted genes can provide a therapy strategy for HBV-HCC. Full article

(This article belongs to the Special Issue Microorganisms Associated with Infectious Disease)

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18 pages, 771 KiB

Open AccessArticle

Antibiotic Resistance and Pathogenomics of Staphylococci Circulating in Novosibirsk, Russia

by Alevtina Bardasheva, Artem Tikunov, Yuliya Kozlova, Elena Zhirakovskaia, Valeriya Fedorets, Natalya Fomenko, Tatyana Kalymbetova, Svetlana Chretien, Vitaliy Pavlov, Nina Tikunova and Vera Morozova

Microorganisms 2021, 9(12), 2487; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9122487 - 30 Nov 2021

Cited by 6 | Viewed by 1743

Abstract

A total of 394 strains of staphylococci found in humans and pets in Novosibirsk, Siberian Russia, were characterized in terms of antibiotic resistance and corresponding genes. Two coagulase-positive and 17 coagulase-negative species were identified. The majority of isolates, with the exception of S. haemolyticus and hospital S. epidermidis isolates, were sensitive to most of the tested antibiotics, and isolates from pets displayed the lowest level of resistance. Nevertheless, methicillin-resistant (MRS) and/or multidrug-resistant (MDR) isolates were found in all prevailed species, including coagulase-negative. A set of genes corresponding to the detected resistance was identified: mecA (beta-lactam resistance), aac(6′)-Ie-aph(2″)-Ia, aph(3′)-IIIa, ant(4′)-Ia (aminoglycoside-modifying enzymes), ermA/ermC, and msrA (macrolide resistance). Complete genome analysis for ten MDR S. epidermidis and five MDR S. haemolyticus isolates revealed additional antibiotic resistance genes mphC, qacA/qacB, norA, dfrC/dfrG, lnuA, BseSR, and fosB. NorA, dfrC, and fosB were present in all S. epidermidis genomes, whereas mphC and msrA were identified in all S. haemolyticus ones. All investigated MDR S. epidermidis and four of five S. haemolyticus strains were moderate or strong biofilm producers, whereas multiple genes responsible for this function and for virulence and pathogenicity were identified mostly in S. epidermidis, but were less frequently represented in S. haemolyticus. Full article

(This article belongs to the Special Issue Microorganisms Associated with Infectious Disease)

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9 pages, 1838 KiB

Open AccessArticle

Feline Coronaviruses Identified in Feline Effusions in Suspected Cases of Feline Infectious Peritonitis

by Shih-Jung Yen and Hui-Wen Chen

Microorganisms 2021, 9(9), 1801; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9091801 - 24 Aug 2021

Cited by 3 | Viewed by 2614

Abstract

Ninety-five effusion samples were collected from cats with suspected feline infectious peritonitis in northern Taiwan; these samples showed a 47.4% (45/95) feline coronavirus (FCoV) positivity rate on immunofluorescence staining and RT-PCR. Young cats (≤24 months old) were found to have a significantly higher risk than cats >24 months old (odds ratio (OR) = 6.19, 95% confidence interval (CI) 2.54–16.00). No significant association was found between the positive rates and sex or breed. The A/G ratio in positive cases was significantly lower than the A/G ratio in negative cases. Genotyping and sequencing of the positive cases revealed 71.9% single infection with type I strains and 28.1% coinfection with types I and II. No single infections with type II strains were noted. The type I sequences had high diversity, while the type II sequences had high internal sequence identity and were more similar to CoVs from other species, such as dogs, pigs, and various small mammals. This study demonstrates the latest analysis of FCoV infection cases in northern Taiwan. Full article

(This article belongs to the Special Issue Microorganisms Associated with Infectious Disease)

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21 pages, 602 KiB

Open AccessArticle

The Pheno- and Genotypic Characterization of Porcine Escherichia coli Isolates

by Tanja Bernreiter-Hofer, Lukas Schwarz, Elke Müller, Adriana Cabal-Rosel, Maciej Korus, Dusan Misic, Katrin Frankenfeld, Kerstin Abraham, Olivia Grünzweil, Astrid Weiss, Andrea T. Feßler, Franz Allerberger, Stefan Schwarz, Michael P. Szostak, Werner Ruppitsch, Andrea Ladinig, Joachim Spergser, Sascha D. Braun, Stefan Monecke, Ralf Ehricht and Igor Loncaric Show full author list Hide full author list

Microorganisms 2021, 9(8), 1676; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9081676 - 06 Aug 2021

Cited by 14 | Viewed by 3286

Abstract

Escherichia (E.) coli is the main causative pathogen of neonatal and post-weaning diarrhea and edema disease in swine production. There is a significant health concern due to an increasing number of human infections associated with food and/or environmental-borne pathogenic and multidrug-resistant E. coli worldwide. Monitoring the presence of pathogenic and antimicrobial-resistant E. coli isolates is essential for sustainable disease management in livestock and human medicine. A total of 102 E. coli isolates of diseased pigs were characterized by antimicrobial and biocide susceptibility testing. Antimicrobial resistance genes, including mobile colistin resistance genes, were analyzed by PCR and DNA sequencing. The quinolone resistance-determining regions of gyrA and parC in ciprofloxacin-resistant isolates were analyzed. Clonal relatedness was investigated by two-locus sequence typing (CH clonotyping). Phylotyping was performed by the Clermont multiplex PCR method. Virulence determinants were analyzed by customized DNA-based microarray technology developed in this study for fast and economic molecular multiplex typing. Thirty-five isolates were selected for whole-genome sequence-based analysis. Most isolates were resistant to ampicillin and tetracycline. Twenty-one isolates displayed an ESBL phenotype and one isolate an AmpC β-lactamase-producing phenotype. Three isolates had elevated colistin minimal inhibitory concentrations and carried the mcr-1 gene. Thirty-seven isolates displayed a multi-drug resistance phenotype. The most predominant β-lactamase gene classes were bla_TEM-1 (56%) and bla_CTX-M-1 (13.71%). Mutations in QRDR were observed in 14 ciprofloxacin-resistant isolates. CH clonotyping divided all isolates into 51 CH clonotypes. The majority of isolates belonged to phylogroup A. Sixty-four isolates could be assigned to defined pathotypes wherefrom UPEC was predominant. WGS revealed that the most predominant sequence type was ST100, followed by ST10. ST131 was detected twice in our analysis. This study highlights the importance of monitoring antimicrobial resistance and virulence properties of porcine E. coli isolates. This can be achieved by applying reliable, fast, economic and easy to perform technologies such as DNA-based microarray typing. The presence of high-risk pathogenic multi-drug resistant zoonotic clones, as well as those that are resistant to critically important antibiotics for humans, can pose a risk to public health. Improved protocols may be developed in swine farms for preventing infections, as well as the maintenance and distribution of the causative isolates. Full article

(This article belongs to the Special Issue Microorganisms Associated with Infectious Disease)

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13 pages, 1330 KiB

Open AccessArticle

Dual RNA-Seq Enables Full-Genome Assembly of Measles Virus and Characterization of Host–Pathogen Interactions

by Timokratis Karamitros, Vasiliki Pogka, Gethsimani Papadopoulou, Ourania Tsitsilonis, Maria Evangelidou, Styliani Sympardi and Andreas Mentis

Microorganisms 2021, 9(7), 1538; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9071538 - 20 Jul 2021

Cited by 6 | Viewed by 2751

Abstract

Measles virus (MeV) has a negative-sense 15 kb long RNA genome, which is generally conserved. Recent advances in high-throughput sequencing (HTS) and Dual RNA-seq allow the analysis of viral RNA genomes and the discovery of viral infection biomarkers, via the simultaneous characterization of the host transcriptome. However, these host–pathogen interactions remain largely unexplored in MeV infections. We performed untargeted Dual RNA-seq in 6 pharyngeal and 6 peripheral blood mononuclear cell (PBMCs) specimens from patients with MeV infection, as confirmed via routine real-time PCR testing. Following optimised DNase treatment of total nucleic acids, we used the pharyngeal samples to build poly-A-enriched NGS libraries. We reconstructed the viral genomes using the pharyngeal datasets and we further conducted differential expression, gene-ontology and pathways enrichment analysis to compare both the pharyngeal and the peripheral blood transcriptomes of the MeV-infected patients vs. control groups of healthy individuals. We obtained 6 MeV genotype-B3 full-genome sequences. We minutely analyzed the transcriptome of the MeV-infected pharyngeal epithelium, detecting all known viral infection biomarkers, but also revealing a functional cluster of local antiviral and inflammatory immune responses, which differ substantially from those observed in the PBMCs transcriptome. The application of Dual RNA-seq technologies in MeV-infected patients can potentially provide valuable information on the virus genome structure and the cellular innate immune responses and drive the discovery of new targets for antiviral therapy. Full article

(This article belongs to the Special Issue Microorganisms Associated with Infectious Disease)

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14 pages, 1910 KiB

Open AccessArticle

Comparative Genomics of Clinical Isolates of the Emerging Tick-Borne Pathogen Neoehrlichia mikurensis

by Anna Grankvist, Daniel Jaén-Luchoro, Linda Wass, Per Sikora and Christine Wennerås

Microorganisms 2021, 9(7), 1488; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9071488 - 13 Jul 2021

Cited by 9 | Viewed by 2007

Abstract

Tick-borne ‘Neoehrlichia (N.) mikurensis’ is the cause of neoehrlichiosis, an infectious vasculitis of humans. This strict intracellular pathogen is a member of the family Anaplasmataceae and has been unculturable until recently. The only available genetic data on this new pathogen are six partially sequenced housekeeping genes. The aim of this study was to advance the knowledge regarding ‘N. mikurensis’ genomic relatedness with other Anaplasmataceae members, intra-species genotypic variability and potential virulence factors explaining its tropism for vascular endothelium. Here, we present the de novo whole-genome sequences of three ‘N. mikurensis’ strains derived from Swedish patients diagnosed with neoehrlichiosis. The genomes were obtained by extraction of DNA from patient plasma, library preparation using 10× Chromium technology, and sequencing by Illumina Hiseq-4500. ‘N. mikurensis’ was found to have the next smallest genome of the Anaplasmataceae family (1.1 Mbp with 27% GC contents) consisting of 845 protein-coding genes, every third of which with unknown function. Comparative genomic analyses revealed that ‘N. mikurensis’ was more closely related to Ehrlichia chaffeensis than to Ehrlichia ruminantium, the opposite of what 16SrRNA sequence-based phylogenetic analyses determined. The genetic variability of the three whole-genome-sequenced ‘N. mikurensis’ strains was extremely low, between 0.14 and 0.22‰, a variation that was associated with geographic origin. No protein-coding genes exclusively shared by N. mikurensis and E. ruminantium were identified to explain their common tropism for vascular endothelium. Full article

(This article belongs to the Special Issue Microorganisms Associated with Infectious Disease)

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8 pages, 468 KiB

Open AccessCommunication

KI and WU Polyomavirus in Respiratory Samples of SARS-CoV-2 Infected Patients

by Carla Prezioso, Ugo Moens, Giuseppe Oliveto, Gabriele Brazzini, Francesca Piacentini, Federica Frasca, Agnese Viscido, Mirko Scordio, Giuliana Guerrizio, Donatella Maria Rodio, Alessandra Pierangeli, Gabriella d’Ettorre, Ombretta Turriziani, Guido Antonelli, Carolina Scagnolari and Valeria Pietropaolo

Microorganisms 2021, 9(6), 1259; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9061259 - 09 Jun 2021

Cited by 4 | Viewed by 2498

Abstract

Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has been declared a global pandemic. Our goal was to determine whether co-infections with respiratory polyomaviruses, such as Karolinska Institutet polyomavirus (KIPyV) and Washington University polyomavirus (WUPyV) occur in SARS-CoV-2 infected patients. Oropharyngeal swabs from 150 individuals, 112 symptomatic COVID-19 patients and 38 healthcare workers not infected by SARS-CoV-2, were collected from March 2020 through May 2020 and tested for KIPyV and WUPyV DNA presence. Of the 112 SARS-CoV-2 positive patients, 27 (24.1%) were co-infected with KIPyV, 5 (4.5%) were positive for WUPyV, and 3 (2.7%) were infected simultaneously by KIPyV and WUPyV. Neither KIPyV nor WUPyV DNA was detected in samples of healthcare workers. Significant correlations were found in patients co-infected with SARS-CoV-2 and KIPyV (p < 0.05) and between SARS-CoV-2 cycle threshold values and KIPyV, WUPyV and KIPyV and WUPyV concurrently detected (p < 0.05). These results suggest that KIPyV and WUPyV may behave as opportunistic respiratory pathogens. Additional investigations are needed to understand the epidemiology and the prevalence of respiratory polyomavirus in COVID-19 patients and whether KIPyV and WUPyV could potentially drive viral interference or influence disease outcomes by upregulating SARS-CoV-2 replicative potential. Full article

(This article belongs to the Special Issue Microorganisms Associated with Infectious Disease)

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12 pages, 1468 KiB

Open AccessArticle

Surgical Site Infection Following Caesarean Section by Acinetobacter Species: A Report from a Hyperendemic Setting in the Brazilian Amazon Region

by Blenda Gonçalves Cabral, Danielle Murici Brasiliense, Ismari Perini Furlaneto, Yan Corrêa Rodrigues and Karla Valéria Batista Lima

Microorganisms 2021, 9(4), 743; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9040743 - 02 Apr 2021

Cited by 2 | Viewed by 1965

Abstract

Surgical site infection (SSI) following caesarean section is associated with increased morbidity, mortality, and significant health care costs. This study evaluated the epidemiological, clinical, and microbiological features of Acinetobacter spp. in women with SSIs who have undergone caesarean section at a referral hospital in the Brazilian Amazon region. This study included 69 women with post-caesarean SSI by Acinetobacter spp. admitted to the hospital between January 2012 and May 2015. The 69 Acinetobacter isolates were subjected to molecular species identification, antimicrobial susceptibility testing, detection of carbapenemase-encoding genes, and genotyping. The main complications of post-caesarean SSI by Acinetobacter were inadequate and prolonged antibiotic therapy, sepsis, prolonged hospitalization, and re-suture procedures. A. baumannii, A. nosocomialis and A. colistiniresistens species were identified among the isolates. Carbapenem resistance was associated with OXA-23-producing A. baumannii isolates and IMP-1-producing A. nosocomialis isolate. Patients with multidrug-resistant A. baumannii infection showed worse clinical courses. Dissemination of persistent epidemic clones was observed, and the main clonal complexes (CC) for A. baumannii were CC231 and CC236 (Oxford scheme) and CC1 and CC15 (Pasteur scheme). This is the first report of a long-term Acinetobacter spp. outbreak in women who underwent caesarean section at a Brazilian hospital. This study demonstrates the impact of multidrug resistance on the clinical course of post-caesarean infections. Full article

(This article belongs to the Special Issue Microorganisms Associated with Infectious Disease)

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8 pages, 3207 KiB

Open AccessCommunication

Evidence for Multi-Organ Infection During Experimental Meningococcal Sepsis due to ST-11 Isolates in Human Transferrin-Transgenic Mice

by Michael Levy, Myriam Aouiti Trabelsi and Muhamed-Kheir Taha

Microorganisms 2020, 8(10), 1456; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8101456 - 23 Sep 2020

Cited by 1 | Viewed by 1659

Abstract

The description of invasive meningococcal disease that is provoked by Neisseria meningitidis (Nm) is frequently restricted to meningitis. However, a wide panel of clinical presentations can be encountered including severe forms with intense inflammatory reaction leading to multi-organ failure. Several human factors are involved in the development of invasive infections such as transferrin, factor H or CEACAM1. In this study, we used an experimental meningococcal infection in transgenic mice expressing the human transferrin to show multi-organ infection. Mice were infected by an intraperitoneal injection of bacterial suspension (1.5 × 10⁷ colony-forming unit/mouse) of a bioluminescent serogroup C strain belonging to the clonal complex ST-11. Dynamic imaging and histological analysis were performed. The results showed invasion of tissues by Nm with bacteria observed, outside blood vessels, in the kidneys, the heart and the brain as well as skin involvement. These data further support the systemic aspect of invasive meningococcal disease with involvement of several organs including skin as in humans. Thus, our model can be used to study severe forms of meningococcal invasive infections with multi-organ failure. Full article

(This article belongs to the Special Issue Microorganisms Associated with Infectious Disease)

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