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Microorganisms
Special Issues
Detection and Identification of Pathogenic Bacteria and Viruses
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Detection and Identification of Pathogenic Bacteria and Viruses

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

Deadline for manuscript submissions: closed (15 March 2024) | Viewed by 6109

Special Issue Editors

Dr. Mostafa Bentahir

E-Mail Website
Guest Editor
Biological Laboratory of the Belgian Defence Laboratories (DLD), Ukkle, 1180 Brussels, Belgium
Interests: biotechnology; protein biochemistry; emerging and re-emerging bacterial and viral infectious diseases; point-of-care testing; isothermal amplification techniques
Dr. Pierre Vandenberghe

E-Mail Website
Guest Editor
Biological Laboratory of the Belgian Defence Laboratories (DLD), Ukkle, 1180 Brussels, Belgium
Interests: point-of-care testing; biosafety/biosecurity; emerging and re-emerging bacterial and viral infectious diseases

Special Issue Information

Dear Colleagues,

Pathogen detection and identification is a fundamental component of the successful response and control of epidemics and pandemics caused by bacteria and viruses, both in natural outbreaks and in intentional releases of bioterrorism agents. This essential component depends on the availability of robust and well-standardised diagnostic tools, which constitute the front-line defence in the fight against epidemics/pandemics in modern laboratories and hospitals. Nevertheless, innovative diagnostics providing sample-to-answer types (e.g., point-of-care testing devices and lab-on-chip technologies) are highly required, as they enable first responders to readily analyse on-site in the field, where molecular and biochemical diagnostics are badly needed. Scientific research is therefore crucial for a better understanding of pathogenicity, anti-microbial resistance virulence factors transfer, and drug escape mechanisms through sound studies of pathogens’ close neighbours at the biochemical and genetic levels. Therefore, valuable manuscripts addressing these specific topics will have the priority and privilege of being considered for publication in this Special Issue of the journal.

Dr. Mostafa Bentahir
Dr. Pierre Vandenberghe
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • emerging and re-emerging bacterial and viral infectious diseases
  • bioterrorism
  • molecular and biochemical diagnostics
  • food safety and security
  • point-of-care testing
  • lab-on-chip technologies
  • diagnostics validation
  • climate change

Published Papers (5 papers)

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Research

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15 pages, 2423 KiB  
Article
Unveiling Hidden Risks: Intentional Molecular Screening for Sexually Transmitted Infections and Vaginosis Pathogens in Patients Who Have Been Exclusively Tested for Human Papillomavirus Genotyping
by Fabiola Hernández-Rosas, Manuel Rey-Barrera, Flavio Hernández-Barajas, Claudia Rangel-Soto, Mariana Socorro García-González, Shumeyker Susmith Franco-González and Mercedes Piedad de León-Bautista
Microorganisms 2023, 11(11), 2661; https://doi.org/10.3390/microorganisms11112661 - 30 Oct 2023
Viewed by 850
Abstract
Human papillomavirus (HPV) is the most prevalent sexually transmitted infection (STI) worldwide, with popular screening methods including the Papanicolaou test and HPV genotyping. However, in clinical practice, coinfections with other pathogens are often underestimated. Therefore, our study aims to describe the prevalence of [...] Read more.
Human papillomavirus (HPV) is the most prevalent sexually transmitted infection (STI) worldwide, with popular screening methods including the Papanicolaou test and HPV genotyping. However, in clinical practice, coinfections with other pathogens are often underestimated. Therefore, our study aims to describe the prevalence of STIs and vaginosis in urogenital samples from patients who had been tested exclusively for HPV genotyping. Methods: This analytical, prospective, cross-sectional study included 408 males and females. Eligible participants had positive and negative HPV genotyping test results and agreed to early detection or had HPV antecedents. They provided the same urogenital samples used for HPV detection and, through our multiplex in-house PCR assay, we screened for Candida spp., Ureaplasma spp., Trichomonas vaginalis, Neisseria gonorrhoeae, Chlamydia trachomatis, herpes simplex virus 1 and 2 (HSV), Mycoplasma spp., molluscum contagiosum virus (MCV), Treponema pallidum, Haemophilus spp., Staphylococcus aureus, and Klebsiella spp. The subsequent statistical analysis aimed to reveal correlations between HPV genotypes and the identified pathogens. Results: Of the participants, 72.1% (n = 294) tested positive for HPV genotypes. HR-HPV (high-risk HPV) genotypes comprised 51 (8.1%), 66 (7.1%), and 58 (6.1%). Haemophilus spp., Ureaplasma spp., Candida spp., Staphylococcus aureus, and Mycoplasma spp. frequently co-occurred with HPV infection (p < 0.05). Gender-based variations were notorious for Ureaplasma spp., Mycoplasma spp., and MCV (p < 0.05). Coinfections were prevalent (43.9%), with a positive HPV result elevating the risk for Trichomonas vaginalis, Mycoplasma spp., Staphylococcus aureus, HSV, and MCV (OR > 1, p < 0.05). HPV 16 correlated with HSV and Ureaplasma spp., while HPV 6 was linked with HSV and MCV (p < 0.05). Conclusions: This screening strategy uncovered significant coinfections and associations between HPV genotypes and pathogens, underscoring the importance of routine screening to explore clinical implications in urogenital health. Full article
(This article belongs to the Special Issue Detection and Identification of Pathogenic Bacteria and Viruses)
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12 pages, 573 KiB  
Article
Detection of Extended-Spectrum β-Lactamase (ESBL) E. coli at Different Processing Stages in Three Broiler Abattoirs
by Nina Langkabel, Janine Burgard, Sabrina Freter, Reinhard Fries, Diana Meemken and Lüppo Ellerbroek
Microorganisms 2023, 11(10), 2541; https://doi.org/10.3390/microorganisms11102541 - 12 Oct 2023
Cited by 2 | Viewed by 1116
Abstract
The European Food Safety Authority (EFSA) identified extended-spectrum β-lactamase/AmpC β-lactamase (ESBL/AmpC)-producing E. coli as one of the main priority hazards for poultry. Different studies detected ESBL-producing E. coli at broiler fattening farms and in abattoirs, concluding that poultry meat is a potential source of human [...] Read more.
The European Food Safety Authority (EFSA) identified extended-spectrum β-lactamase/AmpC β-lactamase (ESBL/AmpC)-producing E. coli as one of the main priority hazards for poultry. Different studies detected ESBL-producing E. coli at broiler fattening farms and in abattoirs, concluding that poultry meat is a potential source of human infection. Broiler breast skin samples taken in three abattoirs with different scalding techniques were examined for ESBL-producing Escherichia (E.) coli and their phylogenetic groups. A total of 307 ESBL-producing E. coli isolates were found, and the abattoir with conventional immersion scalding with thermal treatment of the water had the lowest incidence. Phylogroups D/E and B1 were mostly detected, while phylogroups C, D, and E were not detected. Phylogroup B2 was detected in low proportions. The phylogroups B2 and D are important as they have been associated with urinary tract infections in humans, but were only detected in low proportions at different processing stages in this study. Since the risk for the consumer of being infected via chicken meat with ESBL-producing E. coli and E. coli of highly pathogenic phylogroups cannot be excluded, good kitchen hygiene is of great importance. Full article
(This article belongs to the Special Issue Detection and Identification of Pathogenic Bacteria and Viruses)
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13 pages, 2059 KiB  
Article
Identifying the Microbiome of the Adenoid Surface of Children Suffering from Otitis Media with Effusion and Children without Middle Ear Effusion Using 16S rRNA Genetic Sequencing
by Oļegs Sokolovs-Karijs, Monta Brīvība, Rihards Saksis, Maija Rozenberga, Francesca Girotto, Jana Osīte, Aigars Reinis, Gunta Sumeraga and Angelika Krūmiņa
Microorganisms 2023, 11(8), 1955; https://doi.org/10.3390/microorganisms11081955 - 31 Jul 2023
Viewed by 1059
Abstract
Background: The upper respiratory tract harbors diverse communities of commensal, symbiotic, and pathogenic organisms, originating from both the oral and nasopharyngeal microbiota. Among the primary sites of microbial colonization in the upper airways are the adenoids. Alterations in the adenoid microbiota have been [...] Read more.
Background: The upper respiratory tract harbors diverse communities of commensal, symbiotic, and pathogenic organisms, originating from both the oral and nasopharyngeal microbiota. Among the primary sites of microbial colonization in the upper airways are the adenoids. Alterations in the adenoid microbiota have been implicated in the development of various conditions, including secretory otitis media. Aim: This study aims to employ 16S rRNA genetic sequencing to identify the most common bacteria present on the surface of adenoids in children with otitis media with effusion and compare them with children without pathologies in the tympanic cavity. Additionally, we seek to determine and compare the bacterial diversity in these two study groups. Materials and Methods: A total of nineteen samples from the adenoid surfaces were collected, comprising two groups: thirteen samples from children without middle ear effusion and six samples from children with secretory otitis media. The libraries of the V3–V4 hypervariable region of the bacterial 16S rRNA gene was made and sequenced using MiSeq platform. Results: The most prevalent phyla observed in both groups were Proteobacteria, Firmicutes, and Bacteroidetes. The most common bacterial genera identified in both groups were Haemophilus, Streptococcus, Moraxella, Fusobacterium, and Bordetella, with Fusobacterium and Moraxella being more prevalent in the groups that had no middle ear effusion, while Haemophulus and Streptococcus were more prevalent in the otitis media with effusion group, although not in a statistically significant way. Statistical analysis shows a trend towards bacterial composition and beta diversity being similar between the study groups; however, due to the limited sample size and unevenness between groups, we should approach this data with caution. Conclusion: The lack of prolific difference in bacterial composition between the study groups suggests that the role of the adenoid microbiome in the development of otitis media with effusion may be less significant. Full article
(This article belongs to the Special Issue Detection and Identification of Pathogenic Bacteria and Viruses)
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11 pages, 12780 KiB  
Article
Rapid and Easy-Read Porcine Circovirus Type 4 Detection with CRISPR–Cas13a-Based Lateral Flow Strip
by Jieru Wang, Xiaojie Zhu, Dongdong Yin, Chang Cai, Hailong Liu, Yuqing Yang, Zishi Guo, Lei Yin, Xuehuai Shen, Yin Dai and Xiaocheng Pan
Microorganisms 2023, 11(2), 354; https://doi.org/10.3390/microorganisms11020354 - 31 Jan 2023
Cited by 4 | Viewed by 1631
Abstract
First identified as a new circovirus in Hunan Province in China in 2019, porcine circovirus (PCV4) is now widely detected in other Chinese provinces and South Korea. In recent years, the virus has threatened pig health and operations in the pig industry. Hence, [...] Read more.
First identified as a new circovirus in Hunan Province in China in 2019, porcine circovirus (PCV4) is now widely detected in other Chinese provinces and South Korea. In recent years, the virus has threatened pig health and operations in the pig industry. Hence, early PCV4 detection and regular surveillance are required to control the spread of infection and prevent collateral damage to the industry. Due to PCV4 being difficult to isolate in vitro, molecular detection methods, such as conventional PCR and real-time PCR, and serological assays are currently the main methods used for the detection of PCV4 infection. However, they are time-consuming, labor-intensive, and complex and require professional personnel. To facilitate rapid pen-side PCV4 diagnoses, we used clustered regularly interspaced short palindromic repeats (CRISPR) and Cas13a technology to develop a quick testing kit. Five recombinase-aided amplification (RPA) primer sets were designed based on the conserved PCV4-Cap gene nucleotide region, which were used to determine several key lateral flow strip (LFD) characteristics (sensitivity, specificity, and accuracy). The results showed that the RPA-Cas13a-LFD reaction could detect PCV4 within 1.5 h in genomic DNA harboring a minimum of a single copy. Furthermore, the assay showed good specificity and absence of cross-reactivity with PCV2, PCV3, or other porcine viruses. When we tested 15 clinical samples, a high accuracy was also recorded. Therefore, we successfully developed a detection assay that was simple, fast, accurate, and suitable for on-site PCV4 testing. Full article
(This article belongs to the Special Issue Detection and Identification of Pathogenic Bacteria and Viruses)
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Review

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15 pages, 289 KiB  
Review
Non-Microbiological Mycobacterial Detection Techniques for Quality Control of Biological Products: A Comprehensive Review
by Marine Marius and Clothilde Fernandez
Microorganisms 2024, 12(4), 788; https://doi.org/10.3390/microorganisms12040788 - 12 Apr 2024
Viewed by 333
Abstract
Mycobacteria can be one of the main contaminants of biological products, and their presence can have serious consequences on patients’ health. For this reason, the European Pharmacopoeia mandates the specific testing of biological products for mycobacteria, a critical regulatory requirement aimed at ensuring [...] Read more.
Mycobacteria can be one of the main contaminants of biological products, and their presence can have serious consequences on patients’ health. For this reason, the European Pharmacopoeia mandates the specific testing of biological products for mycobacteria, a critical regulatory requirement aimed at ensuring the safety of these products before they are released to the market. The current pharmacopeial reference, i.e., microbial culture method, cannot ensure an exhaustive detection of mycobacteria due to their growth characteristics. Additionally, the method is time consuming and requires a continuous supply of culture media, posing logistical challenges. Thus, to overcome these issues, pharmaceutical industries need to consider alternative non-microbiological techniques to detect these fastidious, slow-growing contaminating agents. This review provides an overview of alternative methods, which could be applied within a quality control environment for biological products and underlines their advantages and limitations. Nucleic acid amplification techniques or direct measurement of mycobacteria stand out as the most suitable alternatives for mycobacterial testing in biological products. Full article
(This article belongs to the Special Issue Detection and Identification of Pathogenic Bacteria and Viruses)
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