Infectious Diseases: Clinical Diagnosis and Molecular Epidemiology 2.0

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

Deadline for manuscript submissions: closed (31 December 2022) | Viewed by 14528

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Department of Microbiology and Hospital Hygiene, Bundeswehr Central Hospital, Andernacher Str 100, 56070 Koblenz, Germany
Interests: clinical microbiology; molecular diagnostics; infectious disease management and epidemiology; clinical infectiology; tropical medicine; hospital hygiene; global health
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Special Issue Information

Dear Colleagues,

This Special Issue is a continuation of our previous Special Issue "Infectious Diseases: Clinical Diagnosis and Molecular Epidemiology".

After two years focused on the COVID-19 pandemic and on the effects of an emerging variant of the SARS-CoV family on global health with all the associated challenges, I would like to direct your attention in this Special Issue of Microorganisms to the impact of other microbial pathogens (i.e., bacteria, other circulating and (re-)emerging viruses, fungi, and parasites).

In clinical settings a precise result and many more time-to-result of pathogen detection is crucial for differential diagnosis and patient management. Ever since the introduction of nucleic acid amplification techniques, a great deal of effort has been made. However, the interpretation of DNA detection results still requires experience, especially when multiple pathogens are detected. Moreover, genotypic versus phenotypic antimicrobial resistance observations have to be discussed carefully. Worldwide surveillance of resistance evolution may contribute to successful presumptive therapy.

For this Special Issue of Microorganisms dedicated to “Infectious Diseases: Clinical Diagnosis and Molecular Epidemiology”, we invite you to submit contributions concerning any aspect of recent implementations of modern diagnostic assets in the clinical routine, as well as strategies for infectious disease epidemiology.

Dr. Ralf Matthias Hagen
Guest Editor

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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

  • clinical microbiology
  • molecular detection of pathogens
  • clinical diagnosis of infectious diseases
  • infectious disease management
  • infectious disease epidemiology
  • microbial resistance
  • (re-)emerging pathogens
  • outbreak investigation
  • global health

Published Papers (9 papers)

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10 pages, 462 KiB  
Article
Comparative Assessment of Two Commercial Real-Time PCR Assays for the Diagnosis of Trypanosoma cruzi DNA in Serum
by Simone Kann, Gustavo Concha, Felix Weinreich, Andreas Hahn, Christian Rückert, Jörn Kalinowski, Olfert Landt and Hagen Frickmann
Microorganisms 2023, 11(4), 901; https://doi.org/10.3390/microorganisms11040901 - 30 Mar 2023
Viewed by 1235
Abstract
This study was performed to comparably assess two commercial real-time PCR assays for the identification of Trypanosoma cruzi DNA in serum. A total of 518 Colombian serum samples with high pre-test probability for infections with either T. cruzi or apathogenic Trypanosoma rangeli were [...] Read more.
This study was performed to comparably assess two commercial real-time PCR assays for the identification of Trypanosoma cruzi DNA in serum. A total of 518 Colombian serum samples with high pre-test probability for infections with either T. cruzi or apathogenic Trypanosoma rangeli were assessed. The assessment comprised the NDO real-time PCR (TIB MOLBIOL, ref. no. 53-0755-96, referred to as the TibMolBiol assay in the following) with specificity for T. cruzi and the RealStar Chagas PCR Kit 1.0 (altona DIAGNOSTICS, order no. 611013, referred to as the RealStar assay in the following) targeting a kinetoplast sequence of both T. cruzi and T. rangeli without further discrimination. To discriminate between T. cruzi- and T. rangeli-specific real-time PCR amplicons, Sanger sequencing results were available for a minority of cases with discordant real-time PCR results, while the amplicons of the remaining discordant samples were subjected to nanopore sequencing. The study assessment indicated a proportion of 18.1% (n = 94) T. cruzi-positive samples next to 24 samples (4.6%) containing DNA of the phylogenetically related but apathogenic parasite T. rangeli. The observed diagnostic accuracy as expressed by sensitivity and specificity was 97.9% (92/94) and 99.3% (421/424) with the TibMolBiol assay and 96.8% (91/94) and 95.0% (403/424) with the RealStar assay, respectively. Reduced specificity resulted from cross-reaction with T. rangeli in all instances (3 cross-reactions with the TibMolBiol assay and 21 cross-reactions with the RealStar assay). DNA from the six discrete typing units (DTUs) of T. cruzi was successfully amplified by both real-time PCR assays. In summary, both assays showed a comparable diagnostic accuracy for the diagnosis of T. cruzi from human serum, with a slightly higher specificity seen for the TibMolBiol assay. The pronounced co-amplification of DNA from apathogenic T. rangeli according to the RealStar assay may be a disadvantage in areas of co-circulation with T. cruzi, while the test performance of the two compared assays will be quite similar in geographic settings where T. rangeli infections are unlikely. Full article
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12 pages, 609 KiB  
Article
Viral Identification Using Multiplex Polymerase Chain Reaction Testing Does Not Reduce Antibiotic Prescribing in Paediatric Intensive Care Units
by Aurélie Hayotte, Patricia Mariani-Kurkdjian, Priscilla Boizeau, Stéphane Dauger, Charline Riaud, Boris Lacarra, Aurélie Bourmaud and Michael Levy
Microorganisms 2023, 11(4), 884; https://doi.org/10.3390/microorganisms11040884 - 29 Mar 2023
Cited by 3 | Viewed by 1076
Abstract
PCR tests for viral identification, performed on nasopharyngeal secretions, have experienced a major boom in the last few years. Their use is very frequent, but their indications are still not well defined, especially in Paediatric Intensive Care Units (PICU). These tests are used [...] Read more.
PCR tests for viral identification, performed on nasopharyngeal secretions, have experienced a major boom in the last few years. Their use is very frequent, but their indications are still not well defined, especially in Paediatric Intensive Care Units (PICU). These tests are used for the microbiological diagnosis of lower respiratory infections but can be used in other situations. The aim of the study was to investigate the effect of viral identification on antibiotic therapy management. We conducted a single-centre retrospective study from 1 October 2017 to 31 December 2019. This study included all consecutive FilmArray® Respiratory Panel tests performed in patients hospitalised in a PICU. Patients were identified using the microbiology laboratory prospective database and data were extracted from the medical record. 544 tests corresponding to 408 patients were included. The main reasons for testing were pneumonia (34%) and bronchiolitis (24%). In 70% of cases, at least one virus was identified, with Human Rhinovirus (56%) and Respiratory Syncytial Virus (28%) being the two predominant. Bacterial co-infection was present in 25% of cases. Viral identification was not associated with reduced antibiotic therapy. On multivariate analysis, antibiotic management was significantly associated with clinical gravity, CRP value or radiology findings regardless of virus identification. Viral identification has an epidemiological value, but antibiotic prescription relies on other factors. Full article
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15 pages, 536 KiB  
Article
Inherited Chromosomally Integrated Human Herpesvirus 6: Laboratory and Clinical Features
by Liliana Gabrielli, Alice Balboni, Eva Caterina Borgatti, Giulio Virgili, Evangelia Petrisli, Alessia Cantiani, Matteo Pavoni, Federico Baiesi Pillastrini, Simona Venturoli, Giulia Piccirilli and Tiziana Lazzarotto
Microorganisms 2023, 11(3), 548; https://doi.org/10.3390/microorganisms11030548 - 21 Feb 2023
Cited by 2 | Viewed by 2255
Abstract
Inherited chromosomally integrated human herpesvirus 6 (iciHHV-6) is a condition in which the complete HHV-6 genome is integrated into the chromosomes of the host germ cell and is vertically transmitted. The aims of this study were to identify iciHHV-6 prevalence in hospitalized patients [...] Read more.
Inherited chromosomally integrated human herpesvirus 6 (iciHHV-6) is a condition in which the complete HHV-6 genome is integrated into the chromosomes of the host germ cell and is vertically transmitted. The aims of this study were to identify iciHHV-6 prevalence in hospitalized patients and clinical features in individuals carrying this integration. HHV-6 PCR on hair follicles was used to confirm iciHHV-6 status when the blood viral load was more than 5 Log10 copies/mL. From January 2012 to June 2022, HHV-6 DNAemia was investigated in 2019 patients. In particular, 49 had a viral load higher than 6 Log10 copies/mL and HHV-6 DNA in hair follicles was positive. A viral load between 5.0 and 5.9 Log10 copies/mL was observed in 10 patients: 6 infants with acute HHV-6 infection and 4 patients with leukopenia and HHV-6 integration. Therefore, the iciHHV-6 prevalence in our population was 2.6% (53/2019). Adult patients with integration presented hematological (24%), autoimmune (11%), autoimmune neurological (19%), not-autoimmune neurological (22%), and other diseases (19%), whereas 5% had no clinically relevant disease. Although in our study population a high percentage of iciHHV-6 adult hospitalized patients presented a specific pathology, it is still unknown whether the integration is responsible for, or contributes to, the disease development. Full article
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10 pages, 1289 KiB  
Article
Examining Different Analysis Protocols Targeting Hospital Sanitary Facility Microbiomes
by Claudio Neidhöfer, Esther Sib, Al-Harith Benhsain, Christina Mutschnik-Raab, Anna Schwabe, Alexander Wollkopf, Nina Wetzig, Martin A. Sieber, Ralf Thiele, Manuel Döhla, Steffen Engelhart, Nico T. Mutters and Marijo Parčina
Microorganisms 2023, 11(1), 185; https://doi.org/10.3390/microorganisms11010185 - 11 Jan 2023
Cited by 4 | Viewed by 1614
Abstract
Indoor spaces exhibit microbial compositions that are distinctly dissimilar from one another and from outdoor spaces. Unique in this regard, and a topic that has only recently come into focus, is the microbiome of hospitals. While the benefits of knowing exactly which microorganisms [...] Read more.
Indoor spaces exhibit microbial compositions that are distinctly dissimilar from one another and from outdoor spaces. Unique in this regard, and a topic that has only recently come into focus, is the microbiome of hospitals. While the benefits of knowing exactly which microorganisms propagate how and where in hospitals are undoubtedly beneficial for preventing hospital-acquired infections, there are, to date, no standardized procedures on how to best study the hospital microbiome. Our study aimed to investigate the microbiome of hospital sanitary facilities, outlining the extent to which hospital microbiome analyses differ according to sample-preparation protocol. For this purpose, fifty samples were collected from two separate hospitals—from three wards and one hospital laboratory—using two different storage media from which DNA was extracted using two different extraction kits and sequenced with two different primer pairs (V1–V2 and V3–V4). There were no observable differences between the sample-preservation media, small differences in detected taxa between the DNA extraction kits (mainly concerning Propionibacteriaceae), and large differences in detected taxa between the two primer pairs V1–V2 and V3–V4. This analysis also showed that microbial occurrences and compositions can vary greatly from toilets to sinks to showers and across wards and hospitals. In surgical wards, patient toilets appeared to be characterized by lower species richness and diversity than staff toilets. Which sampling sites are the best for which assessments should be analyzed in more depth. The fact that the sample processing methods we investigated (apart from the choice of primers) seem to have changed the results only slightly suggests that comparing hospital microbiome studies is a realistic option. The observed differences in species richness and diversity between patient and staff toilets should be further investigated, as these, if confirmed, could be a result of excreted antimicrobials. Full article
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23 pages, 712 KiB  
Article
Molecular Epidemiology of Escherichia coli with Resistance against Third-Generation Cephalosporines Isolated from Deployed German Soldiers—A Retrospective Assessment after Deployments to the African Sahel Region and Other Sites between 2007 and 2016
by Frederik Pankok, Frieder Fuchs, Ulrike Loderstädt, Martin Kaase, Carsten Balczun, Simone Scheithauer, Hagen Frickmann and Ralf Matthias Hagen
Microorganisms 2022, 10(12), 2448; https://doi.org/10.3390/microorganisms10122448 - 11 Dec 2022
Cited by 1 | Viewed by 1399
Abstract
Colonization and infection with bacteria with acquired antibiotic resistance are among the risks for soldiers on international deployments. Enterobacterales with resistance against third-generation cephalosporines are amongst the most frequently imported microorganisms. To contribute to the scarcely available epidemiological knowledge on deployment-associated resistance migration, [...] Read more.
Colonization and infection with bacteria with acquired antibiotic resistance are among the risks for soldiers on international deployments. Enterobacterales with resistance against third-generation cephalosporines are amongst the most frequently imported microorganisms. To contribute to the scarcely available epidemiological knowledge on deployment-associated resistance migration, we assessed the molecular epidemiology of third-generation cephalosporine-resistant Escherichia coli isolated between 2007 and 2016 from German soldiers after deployments, with a particular focus on the African Sahel region. A total of 51 third-generation cephalosporine-resistant E. coli isolated from 51 military returnees from deployment collected during the assessment period between 2007 and 2016 were subjected to short-read next-generation sequencing analysis. Returnees from the Sahel region (Djibouti, Mali, South Sudan, Sudan, Sudan, and Uganda) comprised a proportion of 52.9% (27/51). Repeatedly isolated sequence types according to the Warwick University scheme from returnees from the Sahel region were ST38, ST131, and ST648, confirming previous epidemiological assessments from various sub-Saharan African regions. Locally prevalent resistance genes in isolates from returnees from the Sahel region associated with third-generation resistance were blaCTX-M-15, blaCTX-M-27, blaCTX-M-1, blaTEM-169, blaCTX-M-14, blaCTX-M-99-like, blaCTX-M-125, blaSHV-12, and blaDHA-1, while virulence genes were east1, sat, and tsh in declining order of frequency of occurrence each. In line with phenotypically observed high resistance rates for aminoglycosides and trimethoprim/sulfamethoxazole, multiple associated resistance genes were observed. A similar, slightly more diverse situation was recorded for the other deployment sites. In summary, this assessment provides first next-generation sequencing-based epidemiological data on third-generation cephalosporine-resistant E. coli imported by deployed German soldiers with a particular focus on deployments to the Sahel region, thus serving as a small sentinel. The detected sequence types are well in line with the results from previous epidemiological assessments in sub-Saharan Africa. Full article
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16 pages, 2614 KiB  
Article
Generation and Utilization of a Monoclonal Antibody against Hepatitis B Virus Core Protein for a Comprehensive Interactome Analysis
by Yusuke Nakai, Kei Miyakawa, Yutaro Yamaoka, Yasuyoshi Hatayama, Mayuko Nishi, Hidefumi Suzuki, Hirokazu Kimura, Hidehisa Takahashi, Yayoi Kimura and Akihide Ryo
Microorganisms 2022, 10(12), 2381; https://doi.org/10.3390/microorganisms10122381 - 30 Nov 2022
Viewed by 1454
Abstract
Hepatitis B virus (HBV) core antigen (HBc) is a structural protein that forms the viral nucleocapsid and is involved in various steps of the viral replication cycle, but its role in the pathogenesis of HBV infection is still elusive. In this study, we [...] Read more.
Hepatitis B virus (HBV) core antigen (HBc) is a structural protein that forms the viral nucleocapsid and is involved in various steps of the viral replication cycle, but its role in the pathogenesis of HBV infection is still elusive. In this study, we generated a mouse monoclonal antibody (mAb) against HBc and used it in antibody-based in situ biotinylation analysis in order to identify host proteins that interact with HBc. HBc antigen was produced with a wheat germ cell-free protein synthesis system and used to immunize mice. Among the established hybridoma clones, a single clone (mAb #7) was selected and further characterized for its ability in the antibody-based in situ biotinylation analysis to collect host proteins that are in the vicinity of HBc. Using mass spectrometry, we identified 215 HBc-interacting host proteins, three of which bind HBc most significantly under hypoxic conditions. Our results indicate that mAb #7 can be used to systematically identify host proteins that interact with HBc under pathophysiological conditions, and thus may be useful to explore the molecular pathways involved in HBV-induced cytopathogenesis. Full article
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9 pages, 873 KiB  
Article
High Procalcitonin, C-Reactive Protein, and α-1 Acid Glycoprotein Levels in Whole Blood Samples Could Help Rapid Discrimination of Active Tuberculosis from Latent Tuberculosis Infection and Healthy Individuals
by Yun-Jeong Kang, Heechul Park, Sung-Bae Park, Jiyoung Lee, Hyanglan Hyun, Minju Jung, Eun Ju Lee, Min-A Je, Jungho Kim, Yong Sung Lee and Sunghyun Kim
Microorganisms 2022, 10(10), 1928; https://doi.org/10.3390/microorganisms10101928 - 28 Sep 2022
Cited by 2 | Viewed by 1456
Abstract
Tuberculosis (TB) management is important for prompt discrimination of latent TB infection (LTBI) from active TB and proper treatment. Whole blood Interferon-gamma (IFN-γ) release assay (IGRA) is used to diagnose LTBI based on the secretion of IFN-γ by T-cells in the whole blood [...] Read more.
Tuberculosis (TB) management is important for prompt discrimination of latent TB infection (LTBI) from active TB and proper treatment. Whole blood Interferon-gamma (IFN-γ) release assay (IGRA) is used to diagnose LTBI based on the secretion of IFN-γ by T-cells in the whole blood by using a specific antigen of Mycobacterium tuberculosis. However, the ability of IGRA to distinguish active TB from LTBI is considerably limited. Distinguishing active TB from LTBI is necessary to identify indicators that can be used to effectively manage TB and develop diagnostic methods. In the present study, we used a Luminex multiplex bead array (a bead-based antibody–antigen sandwich method). The whole blood level of acute phase proteins (APPs), such as endoglin (ENG), procalcitonin (PCT), C-reactive protein (CRP), and α1-acid glycoprotein (AGP), in active TB, LTBI, and healthy individuals were analyzed and quantified. The APP test results for the serum and whole blood samples showed that the levels of PCT, CRP, and AGP were significantly increased (p < 0.0500; area under curve = 0.955) in active TB. The level of these markers in the whole blood of active TB, LTBI, and healthy individuals could provide data for effective diagnosis and treatment of TB. Full article
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9 pages, 421 KiB  
Communication
Enteric Bacteria and Parasites with Pathogenic Potential in Individuals of the Colombian Indigenous Tribe Kogui
by Simone Kann, Gustavo Concha, Thomas Köller, Juliane Alker, Ulrich Schotte, Andreas Hahn, Hagen Frickmann and Philipp Warnke
Microorganisms 2022, 10(9), 1862; https://doi.org/10.3390/microorganisms10091862 - 17 Sep 2022
Cited by 3 | Viewed by 1426
Abstract
The Kogui tribe is an indigenous population living in Colombia. The prevalence values of some enteric bacteria, parasites and microsporidia in Kogui stool samples (n = 192) were assessed by real-time polymerase chain reaction (PCR). Thus, genus- or species-specifically recorded positivity rates [...] Read more.
The Kogui tribe is an indigenous population living in Colombia. The prevalence values of some enteric bacteria, parasites and microsporidia in Kogui stool samples (n = 192) were assessed by real-time polymerase chain reaction (PCR). Thus, genus- or species-specifically recorded positivity rates among the Kogui community were assessed. Protozoa were the leading microorganisms in the stool samples of the Kogui, with an average of 1.5 pathogens per sample, followed by bacteria, with 0.6 pathogens per samples and helminths, with 0.3 pathogens per sample. Microsporidia were not detected. Thereby, the majority of detected protozoa comprised species with questionable etiological relevance such as Blastocystis hominis (n = 173) and Dientamoeba fragilis (n = 44), but also a considerable proportion of Giardia duodenalis (n = 71). Cryptosporidium spp., in contrast, was found in a single instance only. The majority of recorded bacteria were Campylobacter spp., with a strikingly high proportion of 50% (n = 96), followed by Shigella spp./enteroinvasive E. coli (EIEC) (n = 14) and Aeromonas spp. (n = 4). The quantitatively most important detected helminths were Ascaris spp. (n = 15), Hymenolepis spp. (n = 14) and Trichuris trichiura (n = 12), followed by Necator americanus (n = 6), Taenia spp. (n = 3) and Strongyloides stercoralis (n = 3) in descending order of abundance. As expected, the Kogui people’s living conditions comprising poverty, lack of access to clean water and simple housing favor a high number of gastrointestinal infections. Preventive approaches are needed to reduce their risk of infection. Full article
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7 pages, 1605 KiB  
Case Report
Acute Calculous Cholecystitis Caused by Streptococcus gallolyticus subspecies pasteurianus: A Case Report
by Tsunehiko Shigemori, Atsunori Hiasa, Yasuhiro Inoue, Satoko Oka, Taro Yasuma, Ryo Nishiwaki, Natsuko Sugimasa, Tetsuya Hamaguchi, Midori Noji, Kenji Takeuchi, Yoshiyuki Ito, Toshio Katoh, Esteban C. Gabazza and Ichiro Imoto
Microorganisms 2022, 10(10), 1929; https://doi.org/10.3390/microorganisms10101929 - 28 Sep 2022
Cited by 4 | Viewed by 1637
Abstract
Acute cholecystitis is an infectious disease of the gallbladder caused mainly by Escherichia coli, Klebsiella, and Enterococcus species. Streptococcus gallolyticus subsp. pasteurianus, previously known as Streptococcus bovis biotype II/2, rarely causes endocarditis, meningitis, and septicemia, mainly in children. Biliary tract [...] Read more.
Acute cholecystitis is an infectious disease of the gallbladder caused mainly by Escherichia coli, Klebsiella, and Enterococcus species. Streptococcus gallolyticus subsp. pasteurianus, previously known as Streptococcus bovis biotype II/2, rarely causes endocarditis, meningitis, and septicemia, mainly in children. Biliary tract infections by Streptococcus gallolyticus subsp. pasteurianus are extremely rare. There have been no reports of cases in Japan. Here, we describe the first case in Japan of acute calculous cholecystitis caused by Streptococcus gallolyticus subsp. pasteurianus infection. A 63-year-old man was admitted to our hospital with epigastric pain and vomiting. He had moderate tenderness and a full sensation in the epigastrium. Abdominal imaging revealed multiple stones in the gallbladder. After admission, he had a high fever that did not improve with antibiotics. Percutaneous transhepatic gallbladder drainage was performed. The patient underwent open cholecystectomy. During surgery, several small stones in the gallbladder and an abscess were observed at the gallbladder base. Streptococcus gallolyticus subsp. pasteurianus was detected by bacterial culture of the bile juice. The gallstones were bilirubin calcium stones. The endoscopic study showed three adenomas in the colon, but the histopathological examination demonstrated no malignant cells. Although infection by this bacterium may not be rare, this is the first reported case in Japan of acute calculous cholecystitis caused by Streptococcus gallolyticus subsp. pasteurianus infection. Full article
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