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Pediatric Diagnostic Microbiology
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Pediatric Diagnostic Microbiology

A special issue of Diagnostics (ISSN 2075-4418). This special issue belongs to the section "Diagnostic Microbiology and Infectious Disease".

Deadline for manuscript submissions: closed (15 September 2023) | Viewed by 17164

Special Issue Editor

Prof. Dr. Pablo Yagupsky

E-Mail Website
Guest Editor
Clinical Microbiology Laboratory, Soroka University Medical Center, Ben-Gurion University of the Negev, Beer Sheva 8410500, Israel
Interests: pediatric infectious diseases; Kingella kingae infections; human brucellosis
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Infectious diseases are the most common problems pediatricians face in their daily practice. The vast majority of these diseases are caused by viruses, follow a benign course, and do not require a precise etiological diagnosis or antibiotic therapy. However, some children may develop rapidly progressive infections that may result in severe morbidity and long-term sequelae if not promptly diagnosed and adequately treated. The detection of the etiologic agents in the young pediatric patient presents particular challenges because of the difficulties in the collection of biological specimens such as blood, exudates from small bones and joints, sputum, urine, or cerebrospinal fluid, and the need for a timely and precise result to improve management and prevent clinical deterioration and avoid complications.

Traditionally, the Clinical Microbiology Laboratory has relied on Gram stains, cultures, antigen detection assays, and serological tests to establish the etiology of the infection, followed by antibiotic susceptibility testing of the bacterial isolates. In recent years, infectious diseases have been revolutionized by developing and introducing nucleic amplification methods that combine exquisite sensitivity and specificity and biosafety. This emerging strategy enables diagnosis in patients receiving antibiotics, identifies difficult-to-culture and novel pathogens, and shortens the identification turnaround table from days to hours.

The present Special Issue of Diagnostics aims to present an update on the recent developments in the laboratory diagnosis of pediatric infections, including the use of universal and species-specific molecular methods, panels for syndromic testing, next-generation sequencing, and molecular determination of antibiotic susceptibility.

Prof. Dr. Pablo Yagupsky
Guest Editor

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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. Diagnostics is an international peer-reviewed open access semimonthly 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 2600 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

  • children
  • infectious diseases
  • diagnostics
  • specimen collection
  • culture methods
  • nucleic acid amplification tests
  • syndromic testing panels
  • next-generation sequencing
  • antibiotic susceptibility

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Published Papers (7 papers)

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Research

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15 pages, 2118 KiB  
Article
Analysis of Intestinal and Nasopharyngeal Microbiota of Children with Meningococcemia in Pediatric Intensive Care Unit: INMACS-PICU Study
by Gurkan Bozan, Vicente Pérez-Brocal, Kaan Aslan, Eylem Kiral, Esra Sevketoglu, Mutlu Uysal Yazici, Ebru Azapagasi, Tanil Kendirli, Serhat Emeksiz, Oguz Dursun, Dincer Yildizdas, Ayse Berna Anil, Nihal Akcay, Hasan Serdar Kihtir, Merve Havan, Nazan Ulgen Tekerek, Faruk Ekinci, Omer Kilic, Andres Moya and Ener Cagri Dinleyici
Diagnostics 2023, 13(12), 1984; https://doi.org/10.3390/diagnostics13121984 - 6 Jun 2023
Cited by 2 | Viewed by 2011
Abstract
Microbiota composition might play a role in the pathophysiology and course of sepsis, and understanding its dynamics is of clinical interest. Invasive meningococcal disease (IMD) is an important cause of community-acquired serious infection, and there is no information regarding microbiota composition in children [...] Read more.
Microbiota composition might play a role in the pathophysiology and course of sepsis, and understanding its dynamics is of clinical interest. Invasive meningococcal disease (IMD) is an important cause of community-acquired serious infection, and there is no information regarding microbiota composition in children with meningococcemia. In this study, we aimed to evaluate the intestinal and nasopharyngeal microbiota composition of children with IMD. Materials and Methods: In this prospective, multi-center study, 10 children with meningococcemia and 10 age-matched healthy controls were included. Nasopharyngeal and fecal samples were obtained at admission to the intensive care unit and on the tenth day of their hospital stay. The V3 and V4 regions of the 16S rRNA gene were amplified following the 16S Metagenomic Sequencing Library Preparation. Results: Regarding the alpha diversity on the day of admission and on the tenth day at the PICU, the Shannon index was significantly lower in the IMD group compared to the control group (p = 0.002 at admission and p = 0.001, on the tenth day of PICU). A statistical difference in the stool samples was found between the IMD group at Day 0 vs. the controls in the results of the Bray–Curtis and Jaccard analyses (p = 0.005 and p = 0.001, respectively). There were differences in the intestinal microbiota composition between the children with IMD at admission and Day 10 and the healthy controls. Regarding the nasopharyngeal microbiota analysis, in the children with IMD at admission, at the genus level, Neisseria was significantly more abundant compared to the healthy children (p < 0.001). In the children with IMD at Day 10, genera Moraxella and Neisseria were decreased compared to the healthy children. In the children with IMD on Day 0, for paired samples, Moraxella, Neisseria, and Haemophilus were significantly more abundant compared to the children with IMD at Day 10. In the children with IMD at Day 10, the Moraxella and Neisseria genera were decreased, and 20 different genera were more abundant compared to Day 0. Conclusions: We first found alterations in the intestinal and nasopharyngeal microbiota composition in the children with IMD. The infection itself or the other care interventions also caused changes to the microbiota composition during the follow-up period. Understanding the interaction of microbiota with pathogens, e.g., N. meningitidis, could give us the opportunity to understand the disease’s dynamics. Full article
(This article belongs to the Special Issue Pediatric Diagnostic Microbiology)
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11 pages, 1683 KiB  
Article
Salivary Biomarkers to Differentiate between Streptococcus pneumoniae and Influenza A Virus-Related Pneumonia in Children
by Kuo-Shu Tang, Chih-Min Tsai, Ming-Chou Cheng, Ying-Hsien Huang, Chih-Hao Chang and Hong-Ren Yu
Diagnostics 2023, 13(8), 1468; https://doi.org/10.3390/diagnostics13081468 - 18 Apr 2023
Cited by 4 | Viewed by 2472
Abstract
Community-acquired pneumonia (CAP) is common among children and can be fatal in certain conditions. In children, CAP can be caused by viral or bacterial infections. Identification of pathogens can help select appropriate therapeutic strategies. Salivary analysis may be a potential diagnostic tool because [...] Read more.
Community-acquired pneumonia (CAP) is common among children and can be fatal in certain conditions. In children, CAP can be caused by viral or bacterial infections. Identification of pathogens can help select appropriate therapeutic strategies. Salivary analysis may be a potential diagnostic tool because it is noninvasive, patient-friendly, and easy to perform in children. A prospective study was conducted in children with pneumonia admitted to a hospital. Salivary samples from patients with definite Streptococcus pneumoniae and influenza A strains were used for gel-free (isobaric tag for relative and absolute quantitation (iTRAQ)) proteomics. No statistically significant difference was detected in salivary CRP levels between Streptococcus pneumoniae and influenza A pneumonia in children. Several potential salivary biomarkers were identified using gel-free iTRAQ proteomics to differentiate pneumonia from Streptococcus pneumoniae or influenza A virus infections in pediatric patients. ELISA validated that Streptococcus pneumoniae group has a higher abundance of salivary alpha 1-antichymotrypsin than those in the influenza A group. Whether these salivary biomarkers can be used to distinguish other bacteria from viral pneumonia requires further verification. Full article
(This article belongs to the Special Issue Pediatric Diagnostic Microbiology)
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12 pages, 1706 KiB  
Article
Comparison of MT-PCR with Quantitative PCR for Human Bocavirus in Respiratory Samples with Multiple Respiratory Viruses Detection
by Maja Mijač, Sunčanica Ljubin-Sternak, Irena Ivković-Jureković and Jasmina Vraneš
Diagnostics 2023, 13(5), 846; https://doi.org/10.3390/diagnostics13050846 - 23 Feb 2023
Cited by 3 | Viewed by 2173
Abstract
Human bocavirus (HBoV) is an important respiratory pathogen, especially in children, but it is often found in co-detection with other respiratory viruses, which makes the diagnostic approach challenging. We compared multiplex PCR and quantitative PCR for HBoV with multiplex tandem PCR (MT-PCR) in [...] Read more.
Human bocavirus (HBoV) is an important respiratory pathogen, especially in children, but it is often found in co-detection with other respiratory viruses, which makes the diagnostic approach challenging. We compared multiplex PCR and quantitative PCR for HBoV with multiplex tandem PCR (MT-PCR) in 55 cases of co-detection of HBoV and other respiratory viruses. In addition, we investigated whether there is a connection between the severity of the disease, measured by the localization of the infection, and amount of virus detected in the respiratory secretions. No statistically significant difference was found, but children with large amount of HBoV and other respiratory virus had a longer stay in hospital. Full article
(This article belongs to the Special Issue Pediatric Diagnostic Microbiology)
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9 pages, 294 KiB  
Article
Retrospective Study for the Clinical Evaluation of a Real-Time PCR Assay with Lyophilized and Ready-to-Use Reagents for Streptococcus agalactiae Detection in Prenatal Screening Specimens
by María Paz Peris, Gloria Martín-Saco, Henar Alonso-Ezcurra, Cristina Escolar-Miñana, Antonio Rezusta, Raquel Acero and Ana Milagro-Beamonte
Diagnostics 2022, 12(9), 2189; https://doi.org/10.3390/diagnostics12092189 - 9 Sep 2022
Cited by 5 | Viewed by 2411
Abstract
Streptococcus agalactiae is a leading cause of sepsis and meningitis in newborns and young infants. Screening programs and intrapartum antibiotic prophylaxis have reduced early neonatal onset of disease. The aim of this study was to evaluate a molecular assay with lyophilized and ready-to-use [...] Read more.
Streptococcus agalactiae is a leading cause of sepsis and meningitis in newborns and young infants. Screening programs and intrapartum antibiotic prophylaxis have reduced early neonatal onset of disease. The aim of this study was to evaluate a molecular assay with lyophilized and ready-to-use reagents: VIASURE® Streptococcus B Real Time PCR detection kit (CerTest Biotec) (Viasure qPCR assay) compared to both the GBS culture and a molecular assay with separated and frozen reagents: Strep B Real-TM Quant (Sacace Biotecnologies®) (Sacace qPCR assay). A total of 413 vaginal–rectal swabs from women between the 35th and 37th weeks of pregnancy were processed. GBS culture was firstly achieved through Granada medium and Columbia CNA agar at 35 °C in aerobic conditions. Then, nucleic acid extraction was performed for subsequent molecular analysis using both commercial assays. Discordant results were resolved via bidirectional Sanger sequencing. Viasure qPCR assay clinical sensitivity was 0.97 (0.92–0.99) and specificity 1 (0.98–1). This retrospective study demonstrated the good clinical parameters and the strong overall agreement (99.3%) between the Viasure qPCR assay and both reference assays. Finally, the added value observed of the assay under study was the stabilized and ready-to-use format, reducing the number of time-consuming steps, permitting the storage at room temperature, facilitating transport, being environmentally respectful, and reducing additional costs. Full article
(This article belongs to the Special Issue Pediatric Diagnostic Microbiology)
12 pages, 303 KiB  
Article
Detection of A2143G, A2142C, and A2142G Point Mutations with Real-Time PCR in Stool Specimens from Children Infected with Helicobacter pylori
by Nesrin Gareayaghi and Bekir Kocazeybek
Diagnostics 2022, 12(9), 2119; https://doi.org/10.3390/diagnostics12092119 - 31 Aug 2022
Cited by 4 | Viewed by 2397
Abstract
Reports have indicated an increasing prevalence of clarithromycin resistance in children relative to adults. Thus, it is important to investigate primary clarithromycin resistance before therapy to avoid treatment failure. A2142G, A2143G, and A2142C point mutations in the peptidyltransferase region of the 23S ribosomal [...] Read more.
Reports have indicated an increasing prevalence of clarithromycin resistance in children relative to adults. Thus, it is important to investigate primary clarithromycin resistance before therapy to avoid treatment failure. A2142G, A2143G, and A2142C point mutations in the peptidyltransferase region of the 23S ribosomal RNA (rRNA) of Helicobacter pylori (H. pylori) strains isolated from children with gastrointestinal symptoms and asymptomatic children were evaluated via real-time polymerase chain reaction (RT-PCR) using fecal DNA samples. The presence of H. pylori was determined using a fecal H. pylori antigen enzyme-linked immunosorbent assay (ELISA) kit from the stools of children (n = 543). A2143G, A2142C, and A2142G point mutations were detected via RT-PCR and confirmed by sequencing the 23S rDNA. Fecal H. pylori antigen testing was positive in 101 symptomatic (49) and asymptomatic (52) children. A significant difference was found between the 0–5- and 5–18-year-old groups in terms of the A2143G and A2142G point mutations (p = 0.001). The A2142C mutation was not detected. There was a significant difference in the A2143G mutation between the symptomatic and asymptomatic 5–18-year-old children (p = 0.019). Macrolides are frequently used to treat upper respiratory tract infections in children due to their selective pressure effect. We suggest that H. pylori strains carrying mutations in the 23S RNA subunit conferring clarithromycin resistance may lead to an intense inflammatory response in the gastric epithelial cells, allowing them to proliferate more rapidly and causing possible diarrhea, halitosis, or abdominal pain in children. Full article
(This article belongs to the Special Issue Pediatric Diagnostic Microbiology)
10 pages, 1431 KiB  
Article
K-Means Clustering for Shock Classification in Pediatric Intensive Care Units
by María Rollán-Martínez-Herrera, Jon Kerexeta-Sarriegi, Javier Gil-Antón, Javier Pilar-Orive and Iván Macía-Oliver
Diagnostics 2022, 12(8), 1932; https://doi.org/10.3390/diagnostics12081932 - 10 Aug 2022
Cited by 2 | Viewed by 1982
Abstract
Shock is described as an inadequate oxygen supply to the tissues and can be classified in multiple ways. In clinical practice still, old methods are used to discriminate these shock types. This article proposes the application of unsupervised classification methods for the stratification [...] Read more.
Shock is described as an inadequate oxygen supply to the tissues and can be classified in multiple ways. In clinical practice still, old methods are used to discriminate these shock types. This article proposes the application of unsupervised classification methods for the stratification of these patients in order to treat them more appropriately. With a cohort of 90 patients admitted in pediatric intensive care units (PICU), the k-means algorithm was applied in the first 24 h data since admission (physiological and analytical variables and the need for devices), obtaining three main groups. Significant differences were found in variables used (e.g., mean diastolic arterial pressure p < 0.001, age p < 0.001) and not used for training (e.g., EtCO2 min p < 0.001, Troponin max p < 0.01), discharge diagnosis (p < 0.001) and outcomes (p < 0.05). Clustering classification equaled classical classification in its association with LOS (p = 0.01) and surpassed it in its association with mortality (p < 0.04 vs. p = 0.16). We have been able to classify shocked pediatric patients with higher outcome correlation than the clinical traditional method. These results support the utility of unsupervised learning algorithms for patient classification in PICU. Full article
(This article belongs to the Special Issue Pediatric Diagnostic Microbiology)
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Review

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11 pages, 293 KiB  
Review
The Past, Present, and Future of Kingella kingae Detection in Pediatric Osteoarthritis
by Pablo Yagupsky
Diagnostics 2022, 12(12), 2932; https://doi.org/10.3390/diagnostics12122932 - 24 Nov 2022
Cited by 7 | Viewed by 2581
Abstract
As a result of the increasing use of improved detection methods, Kingella kingae, a Gram-negative component of the pediatric oropharyngeal microbiota, is increasingly appreciated as the prime etiology of septic arthritis, osteomyelitis, and spondylodiscitis in children aged 6 to 48 months. The [...] Read more.
As a result of the increasing use of improved detection methods, Kingella kingae, a Gram-negative component of the pediatric oropharyngeal microbiota, is increasingly appreciated as the prime etiology of septic arthritis, osteomyelitis, and spondylodiscitis in children aged 6 to 48 months. The medical literature was reviewed to summarize the laboratory methods required for detecting the organism. Kingella kingae is notoriously fastidious, and seeding skeletal system samples onto solid culture media usually fails to isolate it. Inoculation of synovial fluid aspirates and bone exudates into blood culture vials enhances Kingella kingae recovery by diluting detrimental factors in the specimen. The detection of the species has been further improved by nucleic acid amplification tests, especially by using species-specific primers targeting Kingella kingae’s rtxA, groEL, and mdh genes in a real-time PCR platform. Although novel metagenomic next-generation technology performed in the patient’s plasma sample (liquid biopsy) has not yet reached its full potential, improvements in the sensitivity and specificity of the method will probably make this approach the primary means of diagnosing Kingella kingae infections in the future. Full article
(This article belongs to the Special Issue Pediatric Diagnostic Microbiology)
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