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Detection and Analysis of Clinical Microbial Infections

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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 (15 March 2024) | Viewed by 12785

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Special Issue Editor

Dr. Stefano Ravaioli

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Guest Editor

Laboratorio di Patologia delle Infezioni Associate all’Impianto, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano 1/10, 40136 Bologna, Italy
Interests: implant-associated infections; anti-infective substances and strategies; virulence factors; bacterial biofilm; bacterial molecular epidemiology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Microbiological infections and diseases can be caused by bacteria, viruses, parasites, and fungi. This issue has caused worldwide concern and requires rapid detection and identification of the pathogens responsible for microbial infections. The first crucial and complex phase of the diagnostic process is the definition of the methods for collecting microbiological samples. In fact, depending on the heterogeneous diffusion and probable low number of pathogenic microorganisms, as well as on the chosen diagnostic method that will be used, sampling can be considered a difficult step, especially in chronic infections. The identification methods can be grouped into different clinical–diagnostic categories, namely methods of isolation and culture with the determination of phenotypic and biochemical characteristics; morphological observation under microscope, particularly used for mixed microbial populations and non-culturable pathogens; antigenic tests, commonly used for their rapidity and simplicity; serological assays, with high specificity and sensitivity; and molecular biology techniques, for a definite microorganism recognition. "-Omics" technologies, in particular genomics (PCR, PFGE, ribotyping, RFLP, RAPD-PCR, DNA sequencing, WGS) and transcriptomics (qPCR, RNA sequencing), but also proteomics (MALDI-TOF MS) and metabolomics (mass spectrometry-based methods), with an improved advancement of their limit of detection, are considered the firestones of clinical microbial analysis.

In addition to the demand for a rapid and accurate diagnosis, due to new emerging microbial pathogens, there is a need for greater standardization of testing and centralized laboratories with the ability to collect and analyze large quantities of samples and perform various identification techniques.

Research articles and systematic reviews are both welcome.

Manuscript topics may include the following:

Identification of unculturable pathogens and mixed microbial populations.
Sampling, culture, and isolation of the pathogen responsible for infectious diseases.
Advantages and limits of clinical microbial identification techniques.
New molecular biology techniques for microbial identification.
Standardization of techniques and sample data centralization.

Dr. Stefano Ravaioli
Guest Editor

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

microorganisms’ detection and analysis
clinical microbiology
identification technologies
new identification methods
heterogeneous dissemination
unculturable pathogens
mixed microbial populations
new emerging pathogens
genomics, transcriptomics, proteomics, metabolomics
standardization of testing
sample data centralization

Published Papers (9 papers)

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Research

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14 pages, 1057 KiB

Open AccessArticle

Herpesviridae and Atypical Bacteria Co-Detections in Lower Respiratory Tract Samples of SARS-CoV-2-Positive Patients Admitted to an Intensive Care Unit

by Gašper Grubelnik, Miša Korva, Rok Kogoj, Tina Polanc, Matej Mavrič, Monika Jevšnik Virant, Tina Uršič, Darja Keše, Katja Seme, Miroslav Petrovec, Matjaž Jereb and Tatjana Avšič-Županc

Microorganisms 2024, 12(4), 714; https://doi.org/10.3390/microorganisms12040714 - 31 Mar 2024

Viewed by 821

Abstract

Shortly after the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), cases of viral, bacterial, and fungal coinfections in hospitalized patients became evident. This retrospective study investigates the prevalence of multiple pathogen co-detections in 1472 lower respiratory tract (LRT) samples from 229 SARS-CoV-2-positive patients treated in the largest intensive care unit (ICU) in Slovenia. In addition to SARS-CoV-2, (rt)RT-PCR tests were used to detect cytomegalovirus (CMV), Epstein–Barr virus (EBV), herpes simplex virus 1 (HSV-1), herpes simplex virus 2 (HSV-2), varicella zoster virus (VZV), and atypical bacteria: Chlamydia pneumoniae, Mycoplasma pneumoniae and Legionella pneumophila/spp. At least one co-detection was observed in 89.1% of patients. EBV, HSV-1, and CMV were the most common, with 74.7%, 58.1%, and 38.0% of positive patients, respectively. The median detection time of EBV, HSV-1, and CMV after initial SARS-CoV-2 confirmation was 11 to 20 days. Bronchoalveolar lavage (BAL) and tracheal aspirate (TA) samples showed equivalent performance for the detection of EBV, CMV, and HSV-1 in patients with both available samples. Our results indicate that SARS-CoV-2 infection could be a risk factor for latent herpesvirus reactivation, especially HSV-1, EBV, and CMV. However, additional studies are needed to elucidate the clinical importance of these findings. Full article

(This article belongs to the Special Issue Detection and Analysis of Clinical Microbial Infections)

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12 pages, 310 KiB

Open AccessArticle

Impact of COVID-19 Pandemic on the Trends of Trichomonas vaginalis Infection in a Tertiary Hospital of Madrid, Spain

by Celia Bolumburu, Vega Zamora, María Muñoz-Algarra, Maria Luisa de la Cruz Conty, José Antonio Escario and Alexandra Ibáñez-Escribano

Microorganisms 2024, 12(3), 620; https://doi.org/10.3390/microorganisms12030620 - 20 Mar 2024

Viewed by 692

Abstract

More than one million sexually transmitted infections (STIs) occur every day, and Trichomonas vaginalis is responsible for more than 156 million cases each year worldwide. Nevertheless, epidemiological studies of this parasite in Europe are scarce. The aim of this study was to evaluate the impact that the COVID-19 pandemic may have had in the diagnosis and epidemiology of trichomoniasis. All available data from January 2018 to December 2021 for T. vaginalis isolation on gynecologic patients attending a Spanish Tertiary Hospital were analyzed. Pre-pandemic results (2018–2019) were compared to pandemic results (2020–2021). The pre-pandemic T. vaginalis prevalence in women was 1.15% (95% Confidence Interval, CI: 0.94–1.41), and significantly decreased in 2020–2021 (0.77%, 95% CI: 0.57–1.03; p = 0.025). Demographic nor clinical characteristics of women diagnosed with trichomoniasis did not statistically differ between the periods, although an increase in chlamydia co-infected patients was observed in the latest (from 8% in 2018–2019 to 19% in 2020–2021). This study has detected a decrease in the diagnosis of trichomoniasis; however, this is probably due to the increase in the healthcare pressure triggered by the pandemic. More than 75% of the cases diagnosed in 2021 occurred in the second half, which suggests that special attention should be given to the evolution in the coming years once normality has been restored in hospitals. Moreover, these results warn of the lack of routine diagnosis of trichomoniasis during pregnancy and the absence of specific protocols for possible co-infections, which could become a strategy to reduce the growing trend of STIs, including T. vaginalis detection, as an interesting marker of sexual risk behaviors. Full article

(This article belongs to the Special Issue Detection and Analysis of Clinical Microbial Infections)

13 pages, 1073 KiB

Open AccessArticle

Comparison of Neutralizing Activity between Vaccinated and Unvaccinated Hospitalized COVID-19 Patients Infected with Delta, Omicron BA.1, or Omicron BA.2 Variant

by Keun Ju Kim, Seo-Jin Park, Seung Gyu Yun, Sang Wook Kim, Myung-Hyun Nam, Eun Kyong Shin, Eun-Ah Chang, Dae Won Park, Chang Kyu Lee, Young Kyung Yoon and Yunjung Cho

Microorganisms 2024, 12(3), 509; https://doi.org/10.3390/microorganisms12030509 - 2 Mar 2024

Viewed by 989

Abstract

Background: Understanding the immune response to evolving viral strains is crucial for evidence-informed public health strategies. The main objective of this study is to assess the influence of vaccination on the neutralizing activity of SARS-CoV-2 delta and omicron infection against various SARS-CoV-2 variants. Methods: A total of 97 laboratory-confirmed COVID-19 cases were included. To assess the influence of vaccination on neutralizing activity, we measured the neutralizing activity of SARS-CoV-2 delta or omicron (BA.1 or BA.2) infection against wild-type (WT), delta, BA.1, and BA.2, with the results stratified based on vaccination status. Results: The neutralizing activity against the WT, delta, and omicron variants (BA.1 and BA.2) was significantly higher in the vaccinated patients than those in the unvaccinated patients. In the unvaccinated individuals infected with the delta variant, the decrease in binding to BA.1 and BA.2 was statistically significant (3.9- and 2.7-fold, respectively) compared to the binding to delta. In contrast, vaccination followed by delta breakthrough infection improved the cross-neutralizing activity against omicron variants, with only 1.3- and 1.2-fold decreases in BA.1 and BA.2, respectively. Vaccination followed by infection improved cross-neutralizing activity against WT, delta, and BA.2 variants in patients infected with the BA.1 variant, compared to that in unvaccinated patients. Conclusions: Vaccination followed by delta or BA.1 infection is associated with improved cross-neutralizing activity against different SARS-CoV-2 variants. The enhanced protection provided by breakthrough infections could have practical implications for optimizing vaccination strategies. Full article

(This article belongs to the Special Issue Detection and Analysis of Clinical Microbial Infections)

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14 pages, 3339 KiB

Open AccessArticle

Epidemiology of Pneumococcal Pneumonia in Louisville, Kentucky, and Its Estimated Burden of Disease in the United States

by Julio Ramirez, Stephen Furmanek, Thomas R. Chandler, Timothy Wiemken, Paula Peyrani, Forest Arnold, William Mattingly, Ashley Wilde, Jose Bordon, Rafael Fernandez-Botran, Ruth Carrico, Rodrigo Cavallazzi and The University of Louisville Pneumonia Study Group

Microorganisms 2023, 11(11), 2813; https://doi.org/10.3390/microorganisms11112813 - 20 Nov 2023

Cited by 1 | Viewed by 849

Abstract

Streptococcus pneumoniae remains a primary pathogen in hospitalized patients with community-acquired pneumonia (CAP). The objective of this study was to define the epidemiology of pneumococcal pneumonia in Louisville, Kentucky, and to estimate the burden of pneumococcal pneumonia in the United States (US). This study was nested in a prospective population-based cohort study of all adult residents in Louisville, Kentucky, who were hospitalized with CAP from 1 June 2014 to 31 May 2016. In hospitalized patients with CAP, urinary antigen detection of 24 S. pneumoniae serotypes (UAD-24) was performed. The annual population-based pneumococcal pneumonia incidence was calculated. The distribution of S. pneumoniae serotypes was characterized. Ecological associations between pneumococcal pneumonia and income level, race, and age were defined. Mortality was evaluated during hospitalization and at 30 days, 6 months, and 1 year after hospitalization. Among the 5402 CAP patients with a UAD-24 test performed, 708 (13%) patients had pneumococcal pneumonia. The annual cumulative incidence was 93 pneumococcal pneumonia hospitalizations per 100,000 adults (95% CI = 91–95), corresponding to an estimated 226,696 annual pneumococcal pneumonia hospitalizations in the US. The most frequent serotypes were 19A (12%), 3 (11%), and 22F (11%). Clusters of cases were found in areas with low incomes and a higher proportion of Black or African American population. Pneumococcal pneumonia mortality was 3.7% during hospitalization, 8.2% at 30 days, 17.6% at 6 months, and 25.4% at 1 year after hospitalization. The burden of pneumococcal pneumonia in the US remains significant, with an estimate of more than 225,000 adults hospitalized annually, and approximately 1 out of 4 hospitalized adult patients dies within 1 year after hospitalization. Full article

(This article belongs to the Special Issue Detection and Analysis of Clinical Microbial Infections)

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10 pages, 666 KiB

Open AccessCommunication

Diagnostic Testing Accuracy for Helicobacter pylori Infection among Adult Patients with Dyspepsia in Cuba’s Primary Care Setting

by Amílcar Duquesne, Rosabel Falcón, Belkys Galindo, Onelkis Feliciano, Oderay Gutiérrez, Waldemar Baldoquín, Magile C. Fonseca, Rafael Llanes and Luis Sarmiento

Microorganisms 2023, 11(4), 997; https://doi.org/10.3390/microorganisms11040997 - 11 Apr 2023

Cited by 1 | Viewed by 2460

Abstract

Evidence of the effectiveness of the tests used to diagnose Helicobacter pylori (H. pylori) in primary healthcare is limited. This cross-sectional study aims to assess the accuracy of tests used for to diagnose H. pylori infection in primary care patients and its relationship with gastroduodenal pathologies. Over 12 months, 173 primary care patients with dyspeptic symptoms were referred for upper gastrointestinal endoscopy to obtain gastric biopsies, and venous blood was extracted from them. H. pylori infection was detected using a rapid urease test (RUT), real-time polymerase chain reaction (RT-PCR), H. pylori-IgG ELISA, and Western blot (WB). The culture and histological findings were used as the reference standard for H. pylori infection. H. pylori prevalence was 50%. There were no significant differences between men and women overall or by age group. The presence of H. pylori was associated with chronic moderate gastritis and its absence with chronic inactive gastritis, as well as the combination of gastritis and gastric lesions (p < 0.05). RUT and ELISA H. pylori -IgG tests showed the highest overall performance (accuracy 98.9% and 84.4%), followed by WB and RT-PCR (accuracy 79.3% and 73.9%). These findings support the notion that combined invasive and noninvasive methods, such as RUT and H. pylori-IgG ELISA, can be a primary diagnostic screening tool for detecting H. pylori among adult dyspeptic patients in Cuba’s primary care setting. Full article

(This article belongs to the Special Issue Detection and Analysis of Clinical Microbial Infections)

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10 pages, 6838 KiB

Open AccessArticle

Transphyseal Hematogenous Osteomyelitis: An Epidemiological, Bacteriological, and Radiological Retrospective Cohort Analysis

by Blaise Cochard, Céline Habre, Nastassia Pralong-Guanziroli, Nathaly Gavira, Giorgio Di Laura Frattura, Giacomo Di Marco, Christina N. Steiger, Geraldo De Coulon, Romain Dayer and Dimitri Ceroni

Microorganisms 2023, 11(4), 894; https://doi.org/10.3390/microorganisms11040894 - 30 Mar 2023

Cited by 2 | Viewed by 1307

Abstract

Transphyseal hematogenous osteomyelitis (THO) is a serious condition that can affect the growing physis, yet it is insufficiently recognized in children. The aim of this study was to explore the prevalence and epidemiology of pediatric THO, and to discuss the underlying pathophysiology. All consecutive cases of acute and subacute osteomyelitis admitted to our institution over 17 years were retrospectively studied. Medical records were examined for patient characteristics, bacteriological etiology, and medical and surgical management. Magnetic resonance imaging was reviewed for all patients to identify those with transphyseal spread of infection. For positive cases, the surface area of the transphyseal lesion was estimated relative to the total physeal cross-sectional area. Fifty-four (25.7%) of the 210 patients admitted for acute or subacute osteomyelitis were diagnosed with THO. The study population’s ages ranged from 1 month to 14 years old (median age 5.8 years, interquartile range 1–167 months). Fourteen (25.9%) patients were younger than 18 months old; the remaining 40 (74.1%) had a mean age of 8.5 years old. The most common sites of THO were the distal tibia (29.1%), the proximal tibia (16.4%), and the distal fibula (14.5%). Transphyseal lesions were due to acute infection in 41 cases and to subacute osteomyelitis in 14 cases. The two most frequently identified pathogens were Staphylococcus aureus (49.1%) and Kingella kingae (20.0%). An average transphyseal lesion represented 8.9% of the total physeal surface, and lesions comprised more than 7% of the physeal cross-sectional area in 51% of cases. Our study revealed that pediatric THO was more frequent than commonly thought. Transphyseal lesions were frequently above this 7% cut-off, which is of paramount importance since subsequent growth is more likely to be disturbed when more than 7% of the physeal cross-sectional area is injured. THO also affected children older than 18 months, an age at which transphyseal arterial blood supply to the epiphysis is believed to have disconnected. This finding suggests another pathophysiological reason for the transphyseal diffusion of infection, a topic deserving further studies and greater understanding. Full article

(This article belongs to the Special Issue Detection and Analysis of Clinical Microbial Infections)

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18 pages, 3208 KiB

Open AccessArticle

Nasal Bacteriomes of Patients with Asthma and Allergic Rhinitis Show Unique Composition, Structure, Function and Interactions

by Marcos Pérez-Losada, Eduardo Castro-Nallar, José Laerte Boechat, Luis Delgado, Tiago Azenha Rama, Valentín Berrios-Farías and Manuela Oliveira

Microorganisms 2023, 11(3), 683; https://doi.org/10.3390/microorganisms11030683 - 7 Mar 2023

Cited by 6 | Viewed by 1947

Abstract

Allergic rhinitis and asthma are major public health concerns and economic burdens worldwide. However, little is known about nasal bacteriome dysbiosis during allergic rhinitis, alone or associated with asthma comorbidity. To address this knowledge gap we applied 16S rRNA high-throughput sequencing to 347 nasal samples from participants with asthma (AS = 12), allergic rhinitis (AR = 53), allergic rhinitis with asthma (ARAS = 183) and healthy controls (CT = 99). One to three of the most abundant phyla, and five to seven of the dominant genera differed significantly (p < 0.021) between AS, AR or ARAS and CT groups. All alpha-diversity indices of microbial richness and evenness changed significantly (p < 0.01) between AR or ARAS and CT, while all beta-diversity indices of microbial structure differed significantly (p < 0.011) between each of the respiratory disease groups and controls. Bacteriomes of rhinitic and healthy participants showed 72 differentially expressed (p < 0.05) metabolic pathways each related mainly to degradation and biosynthesis processes. A network analysis of the AR and ARAS bacteriomes depicted more complex webs of interactions among their members than among those of healthy controls. This study demonstrates that the nose harbors distinct bacteriotas during health and respiratory disease and identifies potential taxonomic and functional biomarkers for diagnostics and therapeutics in asthma and rhinitis. Full article

(This article belongs to the Special Issue Detection and Analysis of Clinical Microbial Infections)

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11 pages, 2011 KiB

Open AccessCommunication

Detection of Oxacillin/Cefoxitin Resistance in Staphylococcus aureus Present in Recurrent Tonsillitis

by Aline Cristine Magalhães Costa Messias, Aline Rodrigues Gama, Letícia Suriano de Almeida Prado, Paulo Alex Neves da Silva, Arlindo Rodrigues Galvão Filho, Clarimar José Coelho, Melissa Ameloti Gomes Avelino, José Daniel Gonçalves Vieira and Lilian Carla Carneiro

Microorganisms 2023, 11(3), 615; https://doi.org/10.3390/microorganisms11030615 - 28 Feb 2023

Viewed by 1711

Abstract

Background: Recurrent tonsillitis is one of the most common diseases in childhood, caused many times by ß-lactam-resistant S. aureus. The objective of this study was to investigate an alternative method to identify resistance to oxacillin/cefoxitin in S. aureus from hospitalized children with recurrent tonsillitis. Methods: The samples of S. aureus came from patients with recurrent tonsillitis and were used in 16S rRNA sequencing and an antibiogram test for identification and verifying resistance, after which HSI methodology were applied for separation of S. aureus resistances. Results: The S. aureus isolated showed sensitivity to oxacillin/cefoxitin and the diagnostic images show a visual description of the resistance different groups formed, that may be related to sensitivity and resistance to oxacillin/cefoxitin, characterizing the MRSA S. aureus. Conclusions: Samples that showed phenotypic resistance to oxacillin/cefoxitin were clearly separated from samples that did not show this resistance. A PLS-DA model predicted the presence of resistance to oxacillin/cefoxitin in S. aureus samples and it was possible to observe the pixels classified as MRSA. The HSI was able to successfully discriminate samples in replicas that were sensitive and resistant, based on the calibration model it received. Full article

(This article belongs to the Special Issue Detection and Analysis of Clinical Microbial Infections)

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11 pages, 4016 KiB

Open AccessCase Report

Diagnostic and Management of Emphysematous Hepatitis with Emphasis on Biopathology

by Déborah Porez, Hatem Kallel, Succes Dobian, Timotée Gerbert-Ferrendier, Mathieu Nacher, Félix Djossou, Magalie Demar, Hakim Amroun, Magaly Zappa and Kinan Drak Alsibai

Microorganisms 2023, 11(9), 2137; https://doi.org/10.3390/microorganisms11092137 - 23 Aug 2023

Viewed by 785

Abstract

Emphysematous hepatitis is a rare infectious disease, which corresponds to the presence of gas in the liver, without collection and after exclusion of vascular origin. This entity belongs to the group of emphysematous infections, whose physiopathology seems to be linked to the presence of unbalanced diabetes and to bacterial fermentation, leading to the production of gas within the liver parenchyma. Very few cases of emphysematous hepatitis have been described in the literature, and most of them had a rapidly fatal course. In this manuscript, we report the case of a 59-year-old man with emphysematous hepatitis due to wild-type Klebsiella pneumoniae that was successfully managed by surgery, and we perform a review of the literature to describe the clinical and biopathological aspects of this rare hepatic disease. Our manuscript underlines the need to perform biological and histopathological sampling to better understand the pathophysiology of this rare entity. The causes and mechanisms of emphysematous hepatitis, which seem to be multiple, lead us to believe that it is a syndrome rather than a simple infectious disease. Full article

(This article belongs to the Special Issue Detection and Analysis of Clinical Microbial Infections)

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