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Pathogens
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Diagnosis, Immunopathogenesis and Control of Bacterial Infections
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Diagnosis, Immunopathogenesis and Control of Bacterial Infections

A special issue of Pathogens (ISSN 2076-0817). This special issue belongs to the section "Bacterial Pathogens".

Deadline for manuscript submissions: closed (15 November 2025) | Viewed by 10857

Special Issue Editor

Prof. Dr. Neil Foster

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Guest Editor
Head of Veterinary and Animal Science, SRUC Aberdeen Campus, Craibstone Estate, Ferguson Building, Aberdeen AB21 9YA, UK
Interests: innate immune responses to microbial infections; inflammation and immunomodulation; development of biomarkers of disease
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Bacterial infections remain a significant challenge in both human and veterinary medicine. In a study published in 2019, it was reported that 33 bacterial pathogens were globally responsible for 7.7 million deaths out of a total of 13.7 million deaths due to infection. Antimicrobial resistance (AMR) and a dearth in the development of new antibiotics have posed a significant morbidity and mortality risk throughout the world, with an estimated 4.95 million deaths associated with AMR in 2019.

In veterinary medicine, bacterial infections in farmed animals not only seriously impact animal welfare but also cause economic loss and are a major source of zoonoses, as bacterial infections from production animals enter the human food chain. AMR being carried into the human food chain via production animals is also a major cause of AMR in human populations, and although the use of antibiotics as growth promoters is now outlawed in many major countries who consume and export meat, the prophylactic use of antibiotics is still employed in many of these countries.

A greater emphasis on the control of bacterial infections in production animals, using non-chemotherapeutic means, is, therefore, urgently required. Combined with this is a need for enhanced on-farm surveillance, early diagnosis, and a greater understanding of the immunopathogenesis of bacterial infections in farmed species. This Special Issue aims to focus on these aspects of bacterial infections, using economically important bacterial species which have global zoonotic significance as examples.

Prof. Dr. Neil Foster
Guest Editor

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Keywords

  • bacterial infection
  • bacterial diseases
  • food chain
  • antimicrobial resistance

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Published Papers (8 papers)

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Research

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26 pages, 3467 KB  
Article
Antimicrobial Effect of Oregano Essential Oil in Na-Alginate Edible Films for Shelf-Life Extension and Safety of Feta Cheese
by Angeliki Doukaki, Aikaterini Frantzi, Stamatina Xenou, Fotoula Schoina, Georgia Katsimperi, George-John Nychas and Nikos Chorianopoulos
Pathogens 2026, 15(1), 65; https://doi.org/10.3390/pathogens15010065 - 8 Jan 2026
Viewed by 377
Abstract
The use of natural antimicrobials and advanced sensor technologies is increasingly explored to improve the safety and quality of dairy products like cheese. The current work evaluated the effect of sodium alginate edible films enriched with oregano essential oil (EO) on the microbial [...] Read more.
The use of natural antimicrobials and advanced sensor technologies is increasingly explored to improve the safety and quality of dairy products like cheese. The current work evaluated the effect of sodium alginate edible films enriched with oregano essential oil (EO) on the microbial spoilage of Feta cheese and the fate of Escherichia coli O157:H7 and Listeria monocytogenes during storage. Samples were inoculated with approximately a 4 log CFU/g of pathogens and subsequently wrapped with edible films containing EO or left without, serving as controls. Samples were stored under aerobic and vacuum conditions at 4 and 12 °C. Microbiological analyses, pH, and sensory attributes were monitored during storage, while multispectral imaging (MSI) devices were used for rapid, non-invasive quality assessment. EO films moderately suppressed spoilage and pathogen survival, particularly under aerobic conditions. The MSI spectral data coupled with machine learning models provided reasonable results for the estimation of yeast and mould populations, with the best models coming from aerobic conditions, from benchtop-MSI data, with R2 = 0.726 and RMSE = 0.426 from the Neural Networks model, and R2 = 0.661 and RMSE = 0.696 from the LARS model. The results highlight the combined potential of natural antimicrobial films and MSI-based sensors for extending Feta cheese shelf life and enabling rapid, non-destructive monitoring, respectively. Full article
(This article belongs to the Special Issue Diagnosis, Immunopathogenesis and Control of Bacterial Infections)
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16 pages, 1310 KB  
Article
Occurrence of Citrobacter spp.-Associated and Non-Associated Lesions in a Stranded Loggerhead Sea Turtle (Caretta caretta) from Italy
by Filippo Fratini, Rossana Schena, Sinem Arslan, Alessandro Beneforti, Ilaria Resci, Marco Salvadori, Annunziata Romano, Luisa De Martino and Francesca Paola Nocera
Pathogens 2026, 15(1), 56; https://doi.org/10.3390/pathogens15010056 - 6 Jan 2026
Viewed by 350
Abstract
The skin of turtles, particularly aquatic species, can harbor a diverse range of bacteria, including Citrobacter species, which are recognized as causative agents of Septicemic Cutaneous Ulcerative Disease. Consequently, turtles may act as reservoirs of pathogenic and multidrug-resistant bacteria, posing a potential public [...] Read more.
The skin of turtles, particularly aquatic species, can harbor a diverse range of bacteria, including Citrobacter species, which are recognized as causative agents of Septicemic Cutaneous Ulcerative Disease. Consequently, turtles may act as reservoirs of pathogenic and multidrug-resistant bacteria, posing a potential public health concern. This case-based study investigated the presence of Citrobacter spp. in a loggerhead sea turtle (Caretta caretta) housed at the Livorno Aquarium, Italy. Nine swabs were collected from skin lesions (plastron, carapace, nuchal mass), the oral cavity, and the cloaca. The isolated strains were identified by MALDI-TOF MS and tested for their susceptibility to 12 antimicrobials, belonging to eight antimicrobial classes, by the disc diffusion method. Isolates were investigated genotypically for extended-spectrum-β-lactamase (ESBL) blaCTX−M, blaTEM, blaSHV, blaPER, and metallo-β-lactamase (MBL) blaIMP, blaOXA−48, blaVIM, blaNDM, blaGES genes. Biofilm production ability was also evaluated. Fifteen Citrobacter spp. strains were recovered from the analyzed samples. Complete resistance was recorded for ampicillin, followed by high levels of resistance to imipenem, tetracycline and piperacillin-tazobactam. Worryingly, 86.7% were classified as multidrug-resistant. The most common ESBL-genotype combination was blaSHV and blaPER genes (60%), while the most frequently detected MBL gene was blaNDM (46.7%), followed by blaGES (40%). Most isolates were classified as weak biofilm producers (80%). The findings of this study demonstrate the presence of Citrobacter spp., an opportunistic pathogen, with a notable prevalence of multidrug-resistant strains carrying beta-lactamase-encoding genes, in a loggerhead sea turtle in Italy, across both lesioned and healthy anatomical sites. Full article
(This article belongs to the Special Issue Diagnosis, Immunopathogenesis and Control of Bacterial Infections)
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12 pages, 967 KB  
Article
Evaluating the Performance of Loop-Mediated Isothermal Amplification for the Detection of Listeria monocytogenes Biofilms on Stainless Steel Surfaces
by Carmen Pilar Garrido-Pérez, Marta López-Cabo and Alejandro Garrido-Maestu
Pathogens 2026, 15(1), 49; https://doi.org/10.3390/pathogens15010049 - 1 Jan 2026
Viewed by 352
Abstract
L. monocytogenes is the causative agent of human listeriosis, a deadly disease with fatality rates up to 20%. L. monocytogenes has the ability to grow under harsh environmental conditions. It can form biofilms in food industries, making it capable of persisting in facilities. [...] Read more.
L. monocytogenes is the causative agent of human listeriosis, a deadly disease with fatality rates up to 20%. L. monocytogenes has the ability to grow under harsh environmental conditions. It can form biofilms in food industries, making it capable of persisting in facilities. Given this scenario, it is of utmost importance to rapidly detect this bacterium not only in foods but also on food-contact surfaces. For the successful outcome of any given detection technology, it is imperative to properly process the samples. In the present work, PBS, LPT, and LPT-Pronase were compared to determine which one could provide better results in DNA-based detection. Additionally, the effect of a short TSB pre-enrichment was assessed. To better mimic a real scenario, L. monocytogenes monospecies and multispecies biofilms were analyzed. It was observed that supplementing LPT with pronase, a protein-degrading enzyme, could better detach the biofilm, which achieved a 0.5 cycle reduction compared to the other broths, and the pre-enrichment reduced the real-time PCR by ~2 cycles. The samples were analyzed by real-time PCR and colorimetric LAMP, and the same results were obtained with both techniques regardless of the concentration of L. monocytogenes present in the biofilm; the initial concentration was 1.8 log CFU/cm2 15 min after the pre-enrichment. The results were confirmed by real-time PCR, which demonstrated the applicability of the methodology to be applied in decentralized setups, such as food-processing facilities, with minimal laboratory infrastructure. Full article
(This article belongs to the Special Issue Diagnosis, Immunopathogenesis and Control of Bacterial Infections)
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25 pages, 4002 KB  
Article
Genomic Insight into Vibrio Isolates from Fresh Raw Mussels and Ready-to-Eat Stuffed Mussels
by Artun Yibar, Muhammed Duman, Hilal Ay, Nihed Ajmi, Gorkem Tasci, Fatma Gurler, Sabire Guler, Danny Morick and Izzet Burcin Saticioglu
Pathogens 2025, 14(1), 52; https://doi.org/10.3390/pathogens14010052 - 10 Jan 2025
Cited by 1 | Viewed by 3566
Abstract
Consuming raw or undercooked mussels can lead to gastroenteritis and septicemia due to Vibrio contamination. This study analyzed the prevalence, density, species diversity, and molecular traits of Vibrio spp. in 48 fresh raw wild mussels (FRMs) and 48 ready-to-eat stuffed mussels (RTE-SMs) through [...] Read more.
Consuming raw or undercooked mussels can lead to gastroenteritis and septicemia due to Vibrio contamination. This study analyzed the prevalence, density, species diversity, and molecular traits of Vibrio spp. in 48 fresh raw wild mussels (FRMs) and 48 ready-to-eat stuffed mussels (RTE-SMs) through genome analysis, assessing health risks. The results showed Vibrio prevalence rates of 12.5% in FRMs and 4.2% in RTE-SMs, with V. alginolyticus as the most common species (46.7%). It was determined that the seasonal distribution of Vibrio spp. prevalence in the samples was higher in the summer months. The genome sizes of the Vibrio spp. ranged from approximately 3.9 to 6.1 Mb, with the GC contents varying between 41.9% and 50.4%. A total of 22 virulence factor (VF) classes and up to six antimicrobial resistance (AMR) genes were detected in different Vibrio species. The presence of nine different biosynthetic gene clusters (BGCs), 27 prophage regions, and eight CRISPR/Cas systems in 15 Vibrio strains provides information about their potential pathogenicity, survival strategies, and adaptation to different habitats. Overall, this study provides a comprehensive understanding of the genomic diversity of Vibrio spp. isolated from FRM and RTE-SM samples, shedding light on the prevalence, pathogenicity, and toxicity mechanisms of Vibrio-induced gastroenteritis. Full article
(This article belongs to the Special Issue Diagnosis, Immunopathogenesis and Control of Bacterial Infections)
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Review

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22 pages, 510 KB  
Review
Diagnostic Accuracy of Multiplex NAAT/PCR and Culture Against Salmonella spp.: A Comparison of Meta-Analytical Methods
by Xanthoula Rousou, Luis Furuya-Kanamori, Eleftherios Meletis, Olympia Lioupi, Nikolaos Solomakos, Polychronis Kostoulas and Suhail A. R. Doi
Pathogens 2026, 15(1), 45; https://doi.org/10.3390/pathogens15010045 - 31 Dec 2025
Viewed by 473
Abstract
Background: Non-typhoidal (NT) Salmonella spp. constitutes a major cause of foodborne illness. Culture is the gold standard, but it is time consuming, whereas multiplex nucleic acid amplification tests (NAATs)/Polymerase Chain Reaction (PCR) offer faster detection with variable reported performance. Objectives: To compare the [...] Read more.
Background: Non-typhoidal (NT) Salmonella spp. constitutes a major cause of foodborne illness. Culture is the gold standard, but it is time consuming, whereas multiplex nucleic acid amplification tests (NAATs)/Polymerase Chain Reaction (PCR) offer faster detection with variable reported performance. Objectives: To compare the diagnostic accuracy of multiplex NAAT/PCR and culture for Salmonella spp. using various statistical models with or without a gold standard assumption. Methods: A systematic search (PubMed, Web of Science, Scopus; up to April 2024) identified 44 studies (55 comparisons). Diagnostic performance was evaluated using the frequentists bivariate model (BM) and Split Component Synthesis (SCS) and the Bayesian bivariate models (BBMs) and hierarchical summary ROC (BHSROC). Results: Across models, multiplex NAAT/PCR demonstrated high specificity (>98%) but model-dependent variability in sensitivity (85.5–94.8%), consistently substantial between study heterogeneity and threshold variation. The BM and BBM yielded a higher sensitivity estimate with narrower non-overlapping confidence intervals while SCS and BHSROC models, which are more robust to threshold differences, produced more conservative estimates with wider uncertainty. In Bayesian latent class analyses, culture remained highly accurate (Se: 97.17%, 95% CrI: 70.3–99.99; Sp: 96.06%, 95% CrI: 78.9–99.99), but with wide credible intervals indicating variation between studies, perhaps due to the different protocols used. Conclusion: Model choice affects inferred diagnostic accuracy, particularly when high heterogeneity is present. Both multiplex NAAT/PCR and culture showed high accuracy; hence, a combination of the two tests could optimise rapid diagnosis and treatment. Future research should include cost effectiveness and decision analysis to update the diagnostic algorithms. Full article
(This article belongs to the Special Issue Diagnosis, Immunopathogenesis and Control of Bacterial Infections)
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21 pages, 959 KB  
Review
The Characteristics of Patients That Develop Severe Leptospirosis: A Scoping Review
by Patrick Rosengren, Liam Johnston, Ibrahim Ismail, Simon Smith and Josh Hanson
Pathogens 2025, 14(12), 1268; https://doi.org/10.3390/pathogens14121268 - 10 Dec 2025
Cited by 1 | Viewed by 693
Abstract
This scoping review of original literature published before 1 March 2025 examined the demographic and simple clinical and laboratory findings associated with the development of severe leptospirosis. The definition of severe leptospirosis varied in different studies, but for the purposes of this review [...] Read more.
This scoping review of original literature published before 1 March 2025 examined the demographic and simple clinical and laboratory findings associated with the development of severe leptospirosis. The definition of severe leptospirosis varied in different studies, but for the purposes of this review it included death or patients with a more complicated clinical course. There were 35 articles that satisfied the review’s inclusion criteria. Increasing age was associated with severe disease in 7 studies. Abnormal respiratory examination findings (18 studies), hypotension (11 studies), oliguria (8 studies), jaundice (7 studies) and altered mental status (4 studies) also helped identify high-risk patients. Abnormal laboratory tests—specifically the complete blood count (17 studies), measures of renal function (16 studies) and liver function (14 studies)—were also associated with severe disease. There was geographical heterogeneity in the clinical phenotype of severe disease, but the presence of hypotension, respiratory or renal involvement had prognostic utility in all regions. Simple bedside findings and basic laboratory tests can provide valuable clinical information in patients with leptospirosis. Integration of these indices into early risk stratification tools may facilitate recognition of the high-risk patient and expedite escalation of care in resource-limited settings where most cases of life-threatening leptospirosis are seen. Full article
(This article belongs to the Special Issue Diagnosis, Immunopathogenesis and Control of Bacterial Infections)
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28 pages, 2097 KB  
Review
The Human Archaeome: Commensals, Opportunists, or Emerging Pathogens?
by Douglas M. Ruden
Pathogens 2025, 14(11), 1111; https://doi.org/10.3390/pathogens14111111 - 31 Oct 2025
Viewed by 1160
Abstract
Archaea, one of the three domains of life, are increasingly recognized as consistent, though often underappreciated, members of the human microbiome, yet their roles in health and disease remain poorly understood. Unlike bacteria, no archaeal species have been conclusively identified as primary mammalian [...] Read more.
Archaea, one of the three domains of life, are increasingly recognized as consistent, though often underappreciated, members of the human microbiome, yet their roles in health and disease remain poorly understood. Unlike bacteria, no archaeal species have been conclusively identified as primary mammalian pathogens, but their widespread presence across diverse body sites suggests potential indirect contributions to host physiology and pathology. Current evidence is synthesized on archaeal diversity and habitat specificity across multiple human-associated sites, encompassing the gastrointestinal, aerodigestive, and urogenital tracts as well as the skin. Methanogens dominate the lower gastrointestinal tract (LGT), where they influence fermentation dynamics and methane production, while members of the class Nitrososphaeria are prevalent on the skin and upper aerodigestive tract (UAT), reflecting ecological specialization. Variability in archaeal composition across niches highlights possible links to disease processes: methanogens have been associated with irritable bowel syndrome (IBS), inflammatory bowel disease (IBD), obesity, and colorectal cancer (CRC); Methanobrevibacter oralis is enriched in periodontal disease; and archaea have been detected in the lungs of cystic fibrosis patients. Although archaea lack canonical bacterial virulence factors, they may contribute indirectly through metabolic cross-feeding, immune modulation, synergy in polymicrobial infections, and alteration of host–microbiome network dynamics. This review explores the emerging concept of the human “archaeome”, evaluates current evidence for archaeal involvement in disease, and highlights emerging technologies, such as bacteria-MERFISH and multi-omics profiling, that enable translational applications including microbiome diagnostics, therapeutic targeting, and microbiome engineering. Full article
(This article belongs to the Special Issue Diagnosis, Immunopathogenesis and Control of Bacterial Infections)
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Other

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10 pages, 1352 KB  
Case Report
Invasive Streptococcus intermedius Infections in Children: Two Cases from a Pediatric Infectious Diseases Unit in Italy
by Piero Veronese, Simone Cella, Alessandra Giacometti, Irene Lapetina, Valentina Maffini, Marco Pappalardo, Monica Rubini, Maria Beatrice Ruozi and Icilio Dodi
Pathogens 2024, 13(12), 1099; https://doi.org/10.3390/pathogens13121099 (registering DOI) - 12 Dec 2024
Viewed by 2998
Abstract
In recent years, an increasing number of reports have described invasive infections caused by bacteria from Streptococcus anginosus group (SAGs). S. intermedius seems to be more related with pleuropulmonary infections and abscess of the brain and deep soft tissues, and it is more [...] Read more.
In recent years, an increasing number of reports have described invasive infections caused by bacteria from Streptococcus anginosus group (SAGs). S. intermedius seems to be more related with pleuropulmonary infections and abscess of the brain and deep soft tissues, and it is more likely to cause suppurative and non-bacteremic infections compared to other members of the same genus. We present two clinical cases of invasive S. intermedius infections in pediatric patients: a liver abscess case and a pansinusitis case associated with bilateral otomastoiditis and parapharyngeal abscess complicated by acute mediastinitis, thrombophlebitis of the cavernous sinus, and thrombosis of the cranial tract of the ipsilateral jugular vein. In both cases, prompt broad-spectrum antibiotic therapy and operative drainage of the collections resulted in a good clinical response with full recovery. Full article
(This article belongs to the Special Issue Diagnosis, Immunopathogenesis and Control of Bacterial Infections)
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