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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 28965

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Dr. Ralf Matthias Hagen

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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
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

After a year 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, much 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 sucessful 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 and strategies for infectous disease epidemiology.

Dr. Ralf Matthias Hagen
Guest Editor

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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

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.

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Published Papers (9 papers)

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Research

11 pages, 2233 KiB

Open AccessArticle

Detection of Potential Zoonotic Bartonella Species in African Giant Rats (Cricetomys gambianus) and Fleas from an Urban Area in Senegal

by Jean-Paul Demoncheaux, Hacene Medkour, Meriem Louni, Laurie Laugier, Christelle Pasqualini, Florence Fenollar, Bernard Davoust and Oleg Mediannikov

Microorganisms 2022, 10(3), 489; https://doi.org/10.3390/microorganisms10030489 - 22 Feb 2022

Cited by 2 | Viewed by 2064

Abstract

Bartonellae are bacteria associated with mammals and their ectoparasites. Rodents often host different species of Bartonella. The aim of this study was to investigate the presence of Bartonella spp. in African giant pouched rats (Cricetomys gambianus) and their ectoparasites in Dakar, Senegal. In 2012, 20 rats were caught, and their fleas were identified. DNA was extracted from 170 selected fleas and qPCR was carried out to detect Bartonella spp. Subsequently, a Bartonella culture was performed from the rat blood samples and the isolated strains (16S rRNA, rpoB, ftsZ and ITS3) were genotyped. A total of 1117 fleas were collected from 19 rats and identified as Xenopsylla cheopis, the tropical rat flea. Bartonella DNA was detected in 148 of 170 selected fleas (87.1%). In addition, Bartonella strains were isolated from the blood of 17 rats (85%). According to Bartonella gene-sequence-based criteria for species definition, the isolated strains were identified as B. massiliensis (four strains) and two potential new species related to the zoonotic B. elizabethae. In this paper, these potentially new species are provisionally called Candidatus Bartonella militaris (11 strains) and Candidatus Bartonella affinis (two strains) until their description has been completed. Cricetomys gambianus and its fleas could constitute a public health risk in Dakar due to the high prevalence of Bartonella infection reported. Full article

(This article belongs to the Special Issue Infectious Diseases: Clinical Diagnosis and Molecular Epidemiology)

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15 pages, 318 KiB

Open AccessArticle

Limited Reliability of the Molecular Detection of Plasmodium spp. from Incubated Blood Culture Samples for Forensic Purposes

by Felix Weinreich, Ralf Matthias Hagen, Wibke Loag, Oumou Maïga-Ascofaré, Denise Dekker, Hagen Frickmann and Ulrike Loderstädt

Microorganisms 2022, 10(2), 406; https://doi.org/10.3390/microorganisms10020406 - 10 Feb 2022

Viewed by 1857

Abstract

The suitability of incubated blood culture material for forensic molecular malaria diagnosis was assessed for non-endemic settings for cases in which the differential diagnosis malaria was initially overlooked. For the proof-of-principle assessment, residual blood culture materials from febrile patients from tropical Ghana were investigated by real-time PCR and compared with available historic microscopic results. In 2114 samples, for which microscopical results and real-time PCR results were available, microscopical results comprised 711 P. falciparum detections, 7 P. malariae detections, 1 microscopically not-further-discriminable Plasmodium spp. detection as well as 13 detections of mixed infections comprising 12 cases of P. falciparum/P. malariae co-infections and 1 case of a P. falciparum/P. ovale complex co-infection, while real-PCR indicated 558 P. falciparum detections, 95 P. malariae detections, 10 P. ovale complex detections, 1 P. vivax detection and 4 detected P. falciparum/P. malariae co-infections. Concordance of routine microscopy and real-time PCR was imperfect. Using routine microscopy as reference was associated with a seemingly low agreement of positive real-time PCR results of 90.9%. However, if positive samples, either by routine microscopy or real-time PCR or both, were applied as a combined reference, the agreement of positive results obtained with real-time PCR was increased from 74.0% to 77.9%, while the agreement of positive results obtained with routine microscopy was decreased from 100% to 85.3%. The predictive value of routine microscopy for negative results in the reference was slightly better with 90.9% compared to real-time PCR with 86.9%; the concordance between routine microscopy and real-time PCR was imperfect. In conclusion, even suboptimal sample materials such as incubated blood culture materials can be applied for forensic malaria diagnosis, if more suitable sample materials are not available, but the molecular detection rate of positive results in routine microscopy is much lower than previously reported for non-incubated blood. Full article

(This article belongs to the Special Issue Infectious Diseases: Clinical Diagnosis and Molecular Epidemiology)

9 pages, 603 KiB

Open AccessArticle

Molecular Epidemiology of Carbapenem-Resistant Acinetobacter baumannii Strains Isolated at the German Military Field Laboratory in Mazar-e Sharif, Afghanistan

by Paul G. Higgins, Meret Kniel, Sandra Rojak, Carsten Balczun, Holger Rohde, Hagen Frickmann and Ralf Matthias Hagen

Microorganisms 2021, 9(11), 2229; https://doi.org/10.3390/microorganisms9112229 - 26 Oct 2021

Cited by 4 | Viewed by 2724

Abstract

The study was performed to provide an overview of the molecular epidemiology of carbapenem-resistant Acinetobacter baumannii in Afghanistan isolated by the German military medical service during the Afghanistan conflict. A total of 18 isolates were collected between 2012 and 2018 at the microbiological laboratory of the field hospital in Camp Marmal near Mazar-e Sharif, Afghanistan, from Afghan patients. The isolates were subjected to phenotypic and genotypic differentiation and antimicrobial susceptibility testing as well as to a core genome multi-locus sequence typing (cgMLST) approach based on whole-genome next-generation sequence (wgNGS) data. Next to several sporadic isolates, four transmission clusters comprising strains from the international clonal lineages IC1, IC2, and IC9 were identified. Acquired carbapenem resistance was due to bla_OXA-23 in 17/18 isolates, while genes mediating resistance against sulfonamides, macrolides, tetracyclines, and aminoglycosides were frequently identified as well. In conclusion, the assessment confirmed both the frequent occurrence of A. baumannii associated with outbreak events and a variety of different clones in Afghanistan. The fact that acquired carbapenem resistance was almost exclusively associated with bla_OXA-23 may facilitate molecular resistance screening based on rapid molecular assays targeting this resistance determinant. Full article

(This article belongs to the Special Issue Infectious Diseases: Clinical Diagnosis and Molecular Epidemiology)

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11 pages, 396 KiB

Open AccessArticle

Latin American Origin Is Not Associated with Worse Outcomes among Hospitalized Patients with COVID-19 in a Public Healthcare System

by Silvia Otero-Rodriguez, Oscar Moreno-Pérez, Jose Manuel Ramos, Mar García, Vicente Boix, Sergio Reus, Diego Torrus, Pablo Chico-Sánchez, José Sánchez-Payá, Fernando Aldana-Macias, Joan Gil, Joaquín Portilla, Esperanza Merino and on behalf of COVID19 ALC Research Group

Microorganisms 2021, 9(8), 1772; https://doi.org/10.3390/microorganisms9081772 - 20 Aug 2021

Cited by 2 | Viewed by 2089

Abstract

Exploring differences in clinical outcomes based on race and origin among patients hospitalized for COVID-19 is a controversial issue. The ALC COVID-19 Registry includes all confirmed COVID-19 patients admitted to hospital from 3 March 2020 to 17 December 2020. The data were obtained from electronic health records in order to evaluate the differences in the clinical features and outcomes among European and Latin American patients. The follow-ups occurred after 156 days. A propensity score weighting (PSW) logistic regression model was used to estimate the odds ratio (OR, 95% CI) for Latin American origin and outcome associations. Of the 696 patients included, 46.7% were women, with a median age of 65 (IQR 53–67) years, 614 (88.2%) were European, and 82 (11.8%) were Latin American. Latin American patients were younger, with fewer comorbidities, and a higher incidence of extensive pneumonia. After adjusting for residual confounders, Latin American origin was not associated with an increased risk of death (PSW OR 0.85 (0.23–3.14)) or with the need for invasive mechanical ventilation (PSW OR 0.35 (0.12–1.03)). Latin American origin was associated with a shorter hospital stay, but without differences in how long the patient remained on mechanical ventilation. In a public healthcare system, the rates of death or mechanical ventilation in severe COVID-19 cases were found to be comparable between patients of European and Latin American origins. Full article

(This article belongs to the Special Issue Infectious Diseases: Clinical Diagnosis and Molecular Epidemiology)

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13 pages, 919 KiB

Open AccessArticle

Culture-Free Detection of Antibiotic Resistance Markers from Native Patient Samples by Hybridization Capture Sequencing

by Ines Ferreira, Sarah Lepuschitz, Stephan Beisken, Giuseppe Fiume, Katharina Mrazek, Bernhard J. H. Frank, Silke Huber, Miriam A. Knoll, Arndt von Haeseler, Arne Materna, Jochen G. Hofstaetter, Andreas E. Posch and Johannes Weinberger

Microorganisms 2021, 9(8), 1672; https://doi.org/10.3390/microorganisms9081672 - 5 Aug 2021

Cited by 7 | Viewed by 4072

Abstract

The increasing incidence of antimicrobial resistance (AMR) is a major global challenge. Routine techniques for molecular AMR marker detection are largely based on low-plex PCR and detect dozens to hundreds of AMR markers. To allow for comprehensive and sensitive profiling of AMR markers, we developed a capture-based next generation sequencing (NGS) workflow featuring a novel AMR marker panel based on the curated AMR database ARESdb. Our primary objective was to compare the sensitivity of target enrichment-based AMR marker detection to metagenomics sequencing. Therefore, we determined the limit of detection (LOD) in synovial fluid and urine samples across four key pathogens. We further demonstrated proof-of-concept for AMR marker profiling from septic samples using a selection of urine samples with confirmed monoinfection. The results showed that the capture-based workflow is more sensitive and requires lower sequencing depth compared with metagenomics sequencing, allowing for comprehensive AMR marker detection with an LOD of 1000 CFU/mL. Combining the ARESdb AMR panel with 16S rRNA gene sequencing allowed for the culture-free detection of bacterial taxa and AMR markers directly from septic patient samples at an average sensitivity of 99%. Summarizing, the newly developed ARESdb AMR panel may serve as a valuable tool for comprehensive and sensitive AMR marker detection. Full article

(This article belongs to the Special Issue Infectious Diseases: Clinical Diagnosis and Molecular Epidemiology)

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13 pages, 4671 KiB

Open AccessArticle

Human and Animal Dirofilariasis in Southeast of France

by Younes Laidoudi, Domenico Otranto, Natacha Stolowy, Sophie Amrane, Ranju Ravindran Santhakumari Manoj, Laurine Polette, Stéphanie Watier-Grillot, Oleg Mediannikov, Bernard Davoust and Coralie L'Ollivier

Microorganisms 2021, 9(7), 1544; https://doi.org/10.3390/microorganisms9071544 - 20 Jul 2021

Cited by 11 | Viewed by 3960

Abstract

Dirofilariasis is one of the oldest known zoonotic infections of humans mainly caused by the filarial parasites of the species Dirofilaria immitis and Dirofilaria repens, which primarily infect dogs. A five-year survey (2017 to 2021) was conducted among the dog population to assess the molecular prevalence of Dirofilaria spp. in southeast France. Morphological and genetic analysis were performed on filaroids from dogs and one infected woman from the studied area. A total of 12 (13%) dogs scored molecularly positive for Dirofilaria spp. of which nine carried blood microfilariae. Ocular dirofilariasis was detected in a 79-year-old woman with no travel history. Both electron microscopy and molecular sequencing identified the worm in the human case as D. repens. Molecularly, D. repens isolates were identical in the human and dog cases, representing the only genotype reported so far in France. Despite the distribution of this genotype through all Europe, it was grouped separately with the other two European genotypes and with Asian ones. As in almost all previous human cases in France, D. repens parasites were mainly recovered from the ocular region of patients and were geographically concentrated in the southeastern regions. Data demonstrate the sympatric occurrence of D. immitis and D. repens with high risk of infection to human and dog populations in these investigated geographical areas, thereby underlining the urgent need to implement preventive chemoprophylactic strategies and vector control to reduce the risk of these filaroids in dog and human populations. Full article

(This article belongs to the Special Issue Infectious Diseases: Clinical Diagnosis and Molecular Epidemiology)

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11 pages, 537 KiB

Open AccessArticle

How to Handle CT-Guided Abscess Drainages in Microbiological Analyses? Sterile Vials vs. Blood Culture Bottles for Transport and Processing

by Romy Skusa, Christopher Skusa, Moritz Wohlfarth, Andreas Hahn, Hagen Frickmann, Marc-André Weber, Andreas Podbielski and Philipp Warnke

Microorganisms 2021, 9(7), 1510; https://doi.org/10.3390/microorganisms9071510 - 14 Jul 2021

Cited by 3 | Viewed by 2580

Abstract

The aim of this investigation was to compare microbiological analyses of 100 computed tomography-guided drainages from infectious foci (thoracic, abdominal, musculoskeletal), transported and analyzed by two widely established techniques, that are (i) sterile vials or (ii) inoculated blood culture bottles. The mean number of detected microorganisms from blood culture (aerobic/anaerobic) or conventional method (sterile vial, solid and broth media) per specimen were comparable with 1.29 and 1.41, respectively (p = 1.0). The conventional method showed a trend towards shorter time-to-result (median 28.62 h) in comparison to blood culture incubation (median 43.55 h) (p = 0.0722). Of note, detection of anaerobes (13% vs. 36%) and the number of detected microorganisms in polymicrobial infections (2.76 vs. 3.26) differed significantly with an advantage towards conventional techniques (p = 0.0015; p = 0.035), especially in abdominal aspirations. Despite substantially overlapping results from both techniques, the conventional approach includes some benefits which justify its role as standard approach. Full article

(This article belongs to the Special Issue Infectious Diseases: Clinical Diagnosis and Molecular Epidemiology)

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16 pages, 2253 KiB

Open AccessArticle

The Isolation of Aeromonas Species and Other Common Enteric Bacterial Pathogens from Patients with Gastroenteritis in an Australian Population

by Christopher Yuwono, Michael C. Wehrhahn, Fang Liu, Stephen M. Riordan and Li Zhang

Microorganisms 2021, 9(7), 1440; https://doi.org/10.3390/microorganisms9071440 - 3 Jul 2021

Cited by 18 | Viewed by 4844

Abstract

Aeromonas species are emerging human enteric pathogens. However, systematic analysis of Aeromonas species infection in human gastroenteritis in comparison with other enteric bacterial pathogens in the Australian population is lacking. Here we analysed the isolation of Aeromonas species and other bacterial pathogens in five consecutive years (2015–2019) from 375,842 stool samples of patients with gastroenteritis in a large Australian diagnostic laboratory and identified a subset (48 isolates) of Aeromonas isolates to species level, using multilocus phylogenetic analysis. Aeromonas species were the third most common bacterial pathogens, following Campylobacter and Salmonella species. Aeromonas infection rate was significantly correlated with increasing age (p < 0.001). Aeromonas species were more often isolated in warm seasons and in males than females (p < 0.001). Five Aeromonas species were identified. Most of the infections were from three species, namely Aeromonas veronii (52%), Aeromonas caviae (27%) and Aeromonas hydrophila (12.5%). The majority of patients with Aeromonas species infection did not have a documented overseas travel history. The findings from this study support the importance of Aeromonas species in human gastroenteritis and suggest that the sources of Aeromonas infection in Australian patients should be further investigated. Full article

(This article belongs to the Special Issue Infectious Diseases: Clinical Diagnosis and Molecular Epidemiology)

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9 pages, 2167 KiB

Open AccessCommunication

Diagnosis and Monitoring of Hepatitis B Virus Infection Using the Cobas^® HBV Test for Use on the Cobas^® 4800 System

by Valérie Ortonne, Mélanie Wlassow, Magali Bouvier-Alias, Giovana Melica, Jean-Dominique Poveda, Syria Laperche, Jean-Michel Pawlotsky and Stephane Chevaliez

Microorganisms 2021, 9(3), 573; https://doi.org/10.3390/microorganisms9030573 - 11 Mar 2021

Cited by 3 | Viewed by 3009

Abstract

(1) Background: Sensitive and accurate nucleic acid amplification technologies are now recommended for hepatitis B virus (HBV) DNA detection and quantification in clinical practice to diagnose and monitor hepatitis B infection. The aim of this study was to assess the analytical and clinical performance of the cobas^® HBV Test on the cobas^® 4800 System. (2) Methods: Standard panel and clinical specimens were tested in parallel with three different real-time commercial PCR assays including the cobas ^® HBV Test, the Cobas^® AmpliPrep/Cobas^® TaqMan HBV Test v2.0 and Alinity™ m HBV assay. (3) Results: The specificity of the cobas^® HBV Test was 97.9%. The limit of detection was estimated to be 2.1 IU/mL. Intra-assay and interassay coefficients of variation varied from 0.14% to 1.92% and 2.16% to 12.02%, respectively. HBV DNA levels in patients infected with different HBV genotypes strongly correlated with those measured by the two other commercial comparators assays. (4) Conclusions: The cobas^® HBV Test can be confidently used to detect and accurately quantify HBV DNA in clinical practice as well as in clinical trials with the new anti-HBV drugs currently in development. Full article

(This article belongs to the Special Issue Infectious Diseases: Clinical Diagnosis and Molecular Epidemiology)

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