Microorganisms

19 pages, 1021 KiB

Open AccessArticle

An Easy-to-Use Tool to Predict SARS-CoV-2 Risk of Infection in Closed Settings: Validation with the Use of an Individual-Based Monte Carlo Simulation

by Benedetta Santoro, Francesca Larese Filon and Edoardo Milotti

Microorganisms 2024, 12(12), 2401; https://doi.org/10.3390/microorganisms12122401 - 22 Nov 2024

Abstract

The dynamics of the SARS-CoV-2 pandemic showed that closed environments, such as hospitals and schools, are more likely to host infection clusters due to environmental variables like humidity, ventilation, and overcrowding. This study aimed to validate our local transmission model by reproducing the [...] Read more.

The dynamics of the SARS-CoV-2 pandemic showed that closed environments, such as hospitals and schools, are more likely to host infection clusters due to environmental variables like humidity, ventilation, and overcrowding. This study aimed to validate our local transmission model by reproducing the data on SARS-CoV-2 diffusion in a hospital ward. We implemented our model in a Monte Carlo procedure that simulates the contacts between patients and healthcare workers in Trieste’s geriatric ward and calculates the number of infected individuals. We found the median number of infected workers to be 38.98 (IQR = 7.75), while all patients were infected in most of the simulation runs. More infections occurred in rooms with lower volumes. Higher ventilation and mask-wearing contribute to reduced infections; in particular, we obtained a median value of 35.06 (IQR = 9.21) for the simulation in which we doubled room ventilation and 26.12 (IQR = 10.33) in the simulation run in which workers wore surgical masks. We managed to reproduce the data on infections in the ward; using a sensitivity analysis, we identified the parameters that had the greatest impact on the probability of transmission and the size of the outbreak. Full article

(This article belongs to the Special Issue Airborne Microbial Communities)

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17 pages, 3411 KiB

Open AccessArticle

Salmonella Phage vB_SpuM_X5: A Novel Approach to Reducing Salmonella Biofilms with Implications for Food Safety

by Xinxin Jin, Xiuxiu Sun, Qin Lu, Zui Wang, Zhenggang Zhang, Xiaochun Ling, Yunpeng Xu, Ruiqin Liang, Junjie Yang, Li Li, Tengfei Zhang, Qingping Luo and Guofu Cheng

Microorganisms 2024, 12(12), 2400; https://doi.org/10.3390/microorganisms12122400 - 22 Nov 2024

Abstract

Salmonella, a prevalent foodborne pathogen, poses a significant social and economic strain on both food safety and public health. The application of phages in the control of foodborne pathogens represents an emerging research area. In this study, Salmonella pullorum phage vB_SpuM_X5 (phage [...] Read more.

Salmonella, a prevalent foodborne pathogen, poses a significant social and economic strain on both food safety and public health. The application of phages in the control of foodborne pathogens represents an emerging research area. In this study, Salmonella pullorum phage vB_SpuM_X5 (phage X5) was isolated from chicken farm sewage samples. The results revealed that phage X5 is a novel Myoviridae phage. Phage X5 has adequate temperature tolerance (28 °C–60 °C), pH stability (4–12), and a broad host range of Salmonella bacteria (87.50% of tested strains). The addition of phage X5 (MOI of 100 and 1000) to milk inoculated with Salmonella reduced the number of Salmonella by 0.72 to 0.93 log₁₀ CFU/mL and 0.66 to 1.06 log₁₀ CFU/mL at 4 °C and 25 °C, respectively. The addition of phage X5 (MOI of 100 and 1000) to chicken breast inoculated with Salmonella reduced bacterial numbers by 1.13 to 2.42 log₁₀ CFU/mL and 0.81 to 1.25 log₁₀ CFU/mL at 4 °C and 25 °C, respectively. Phage X5 has bactericidal activity against Salmonella and can be used as a potential biological bacteriostatic agent to remove mature biofilms of Salmonella or for the prevention and control of Salmonella. Full article

(This article belongs to the Special Issue Phage-Bacteria Interplay: Phage Biology and Phage Therapy)

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12 pages, 6703 KiB

Open AccessArticle

Conservation and Dynamics of Maize Seed Endophytic Bacteria Across Progeny Transmission

by Kaihui Zhai, Yingying Zhang, Caihong Zhao, Qing Wang and Xiquan Gao

Microorganisms 2024, 12(12), 2399; https://doi.org/10.3390/microorganisms12122399 - 22 Nov 2024

Abstract

Maize (Zea mays L.) is an important cereal crop species for food, feedstock and industrial material. Maize seeds host a suitable ecosystem for endophytic bacteria, facilitating seed germination and seedling growth. However, the inheritance, diversity and potential function of seed endophytic bacteria [...] Read more.

Maize (Zea mays L.) is an important cereal crop species for food, feedstock and industrial material. Maize seeds host a suitable ecosystem for endophytic bacteria, facilitating seed germination and seedling growth. However, the inheritance, diversity and potential function of seed endophytic bacteria in maize remain largely unexplored. In this study, the endophytic bacteria in the seeds of maize inbred line WU109 collected during three consecutive seasons were identified using 16S rDNA sequencing. Core community composition was essentially consistent across three seed generations and two planting locations. In total, 212 operational taxonomic units (OTUs) belonging to 11 phyla were identified, among which proteobacteria was the dominant phylum. Fifty-six OTUs were conserved across three seed generations. Within them, 16 OTUs were core components and the dominant OTUs were Ralstonia solanacearum, Delftia tsuruhatensis, Bacillu svelezensis and Shigella boydii, accounting for 60% of the total abundance of OTUs. COG and KEGG analyses showed that the function of seed endophytic bacteria was mainly enriched in metabolic processes, especially in amino acid, carbohydrate and energy metabolism. Taken together, the results suggested that the community of maize seed endophytic bacteria was likely co-shaped by both genetic determination and the environment, while the core constitutes of seed endophytes were largely conserved due to transgenerational transmission. Establishing the mutualistic link between the maize seed and its endophytic bacteria enables the exploitation of the potential of endophytes for enhancing crop production. This finding provides a reference to better understand the inheritance and composition of seed core endophytic bacteria in maize. Full article

(This article belongs to the Special Issue Functional Genomics of Crop-Microbe Interactions)

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16 pages, 8051 KiB

Open AccessArticle

Synthesis of Super-High-Viscosity Poly-γ-Glutamic Acid by pgdS-Deficient Strain of Bacillus licheniformis and Its Application in Microalgae Harvesting

by Xiaohui Zhang, Wei Wu, Hongxiao Mou, Jun Liu, Lei Lei, Xin Li, Dongbo Cai, Yangyang Zhan, Xin Ma and Shouwen Chen

Microorganisms 2024, 12(12), 2398; https://doi.org/10.3390/microorganisms12122398 - 22 Nov 2024

Abstract

Poly-γ-glutamic acid (γ-PGA) is a natural polymer whose molecular weight and viscosity are critical for its application in various fields. However, research on super-high-molecular-weight or -viscosity γ-PGA is limited. In this study, the pgdS gene in Bacillus licheniformis WX-02 was knocked out using [...] Read more.

Poly-γ-glutamic acid (γ-PGA) is a natural polymer whose molecular weight and viscosity are critical for its application in various fields. However, research on super-high-molecular-weight or -viscosity γ-PGA is limited. In this study, the pgdS gene in Bacillus licheniformis WX-02 was knocked out using homologous recombination, and the batch fermentation performances of the recombinant strain WX-ΔpgdS were compared to those of WX-02. Nitrate accumulation was observed in the early fermentation stages of WX-ΔpgdS, and gene transcription analysis and cell morphology observations revealed that nitrite accumulation was caused by oxygen limitation due to cell aggregation. When the aeration and agitation rates were increased to 2.5 vvm and 600 r/min, respectively, and citrate was used as a precursor, nitrite accumulation was alleviated in WX-ΔpgdS fermentation broth, while γ-PGA yield and broth viscosity reached 17.3 g/L and 4988 mPa·s. Scanning electron microscopy (SEM) showed that the γ-PGA produced by WX-ΔpgdS exhibited a three-dimensional porous network structure. At a γ-PGA concentration of 5 mg/L, the fermentation broth of WX-ΔpgdS achieved a flocculation efficiency of 95.7% after 30 min of microalgae settling. These findings demonstrate that pgdS knockout results in super-high-viscosity γ-PGA, positioning it as an eco-friendly and cost-effective biocoagulant for microalgae harvesting. Full article

(This article belongs to the Special Issue Resources and Application of Industrial Microorganisms)

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17 pages, 3270 KiB

Open AccessArticle

The Small RNA MicF Represses ObgE and SeqA in Escherichia coli

by Aaron Y. Stibelman, Amy Y. Sariles and Melissa K. Takahashi

Microorganisms 2024, 12(12), 2397; https://doi.org/10.3390/microorganisms12122397 - 22 Nov 2024

Abstract

Small regulatory RNAs (sRNA) have been shown to play a large role in the management of stress responses in Escherichia coli and other bacteria. Upon fluctuations in nutrient availability and exposure to antimicrobials and superoxide-generating agents, the MicF sRNA in E. coli has [...] Read more.

Small regulatory RNAs (sRNA) have been shown to play a large role in the management of stress responses in Escherichia coli and other bacteria. Upon fluctuations in nutrient availability and exposure to antimicrobials and superoxide-generating agents, the MicF sRNA in E. coli has been shown to regulate a small set of genes involved in the management of membrane permeability. Currently, it is unknown whether MicF acts on other processes to mediate the response to these agents. Using an sRNA interaction prediction tool, we identified genes in E. coli that are potentially regulated by MicF. Through subsequent analysis using a sfGFP-based reporter–gene fusion, we have validated two novel targets of MicF regulation: ObgE, a GTPase crucial for chromosome partitioning, and SeqA, a negative modulator of DNA replication. Importantly, the interaction between MicF and these target mRNAs is contingent upon the presence of the RNA chaperone protein, Hfq. Furthermore, our findings affirm the role of MicF’s conserved 5’ seed pairing region in initiating these regulatory interactions. Our study suggests that, beyond its established role in membrane permeability management, MicF exerts control over chromosome dynamics in response to distinct environmental cues, implicating a more multifaceted regulatory function in bacterial stress adaptation. Full article

(This article belongs to the Section Molecular Microbiology and Immunology)

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16 pages, 2847 KiB

Open AccessArticle

Regulation of Isoleucine on Colonic Barrier Function in Rotavirus-Infected Weanling Piglets and Analysis of Gut Microbiota and Metabolomics

by Changsheng Jiang, Weiying Chen, Yanan Yang, Xiaojin Li, Mengmeng Jin, Ahmed H. Ghonaim, Shenghe Li and Man Ren

Microorganisms 2024, 12(12), 2396; https://doi.org/10.3390/microorganisms12122396 - 22 Nov 2024

Abstract

Rotavirus (RV) is a significant contributor to diarrhea in both young children and animals, especially in piglets, resulting in considerable economic impacts on the global pig industry. Isoleucine (Ile), a branched-chain amino acid, is crucial for regulating nutrient metabolism and has been found [...] Read more.

Rotavirus (RV) is a significant contributor to diarrhea in both young children and animals, especially in piglets, resulting in considerable economic impacts on the global pig industry. Isoleucine (Ile), a branched-chain amino acid, is crucial for regulating nutrient metabolism and has been found to help mitigate diarrhea. This study aimed to assess the impact of isoleucine supplementation in feed on colonic barrier function, colonic microbiota, and metabolism in RV-infected weanling piglets. A total of thirty-two weaned piglets, aged 21 days, were randomly assigned to two dietary groups (each further divided into two subgroups, with eight replicates in each subgroup), receiving diets with either 0% or 1% isoleucine for a duration of 14 days. One group from each treatment was then challenged with RV, and the experimental period lasted for 19 days. The results showed that dietary Ile significantly increased the secretion of IL-4, IL-10, and sIgA in the colon of RV-infected weanling piglets (p < 0.05). In addition, Ile supplementation notably increased the expression of tight junction proteins, including Claudin-3, Occludin, and ZO-1 (p < 0.01), as well as the mucin protein MUC-1 in the colon of RV-infected weanling piglets (p < 0.05). Gut microbiota analysis revealed that dietary Ile increased the relative abundance of Prevotella and decreased the relative abundance of Rikenellaceae in the colons of RV-infected weanling piglets. Compared with the RV+CON, metabolic pathways in the RV+ILE group were significantly enriched in vitamin digestion and absorption, steroid biosynthesis, purine metabolism, pantothenate and CoA biosynthesis, cutin, suberine, and wax biosynthesis, as well as fatty acid biosynthesis, and unsaturated fatty acid biosynthesis. In conclusion, dietary Ile supplementation can improve immunity, colonic barrier function, colonic microbiota, and colonic metabolism of RV-infected weaned piglets. These findings provide valuable insights into the role of isoleucine in the prevention and control of RV. Full article

(This article belongs to the Special Issue Enteric Disease-Associated Pathogens)

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18 pages, 1468 KiB

Open AccessReview

Separating Infectious Proctitis from Inflammatory Bowel Disease—A Common Clinical Conundrum

by Richard Hall, Kamal Patel, Andrew Poullis, Richard Pollok and Sailish Honap

Microorganisms 2024, 12(12), 2395; https://doi.org/10.3390/microorganisms12122395 - 22 Nov 2024

Abstract

Proctitis refers to inflammation in the rectum and may result in rectal bleeding, discharge, urgency, tenesmus, and lower abdominal pain. It is a common presentation, particularly in genitourinary medicine and gastroenterology, as the two most common causes are sexually transmitted infections and inflammatory [...] Read more.

Proctitis refers to inflammation in the rectum and may result in rectal bleeding, discharge, urgency, tenesmus, and lower abdominal pain. It is a common presentation, particularly in genitourinary medicine and gastroenterology, as the two most common causes are sexually transmitted infections and inflammatory bowel disease. The incidence of infective proctitis is rising, particularly amongst high-risk groups, including men who have sex with men, those with HIV seropositive status, and those participating in high-risk sexual behaviours. The most commonly isolated organisms are Neisseria gonorrhoeae, Chlamydia trachomatis, Treponema palladium, herpes simplex virus, and Mycoplasma genitalium. Recently, proctitis was also identified as a common feature during the Mpox outbreak. Distinguishing infective proctitis from inflammatory bowel disease remains a significant clinical challenge as there is significant overlap in the clinical presentation and their endoscopic and histological features. This review compares and highlights the distinguishing hallmarks of both inflammatory and infective causes of proctitis. It provides a practical guide to describe the key features that clinicians should focus on in both clinical and key diagnostic investigations to avoid potential misdiagnosis. Full article

(This article belongs to the Section Medical Microbiology)

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17 pages, 939 KiB

Open AccessReview

Optimizing Ultrasound Probe Disinfection for Healthcare-Associated Infection Control: A Comparative Analysis of Disinfectant Efficacy

by Gaetano Ferrara, Giovanni Cangelosi, Sara Morales Palomares, Stefano Mancin, Marianna Melina, Orejeta Diamanti, Marco Sguanci, Antonella Amendola and Fabio Petrelli

Microorganisms 2024, 12(12), 2394; https://doi.org/10.3390/microorganisms12122394 - 22 Nov 2024

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Abstract

Background/Aims: Ultrasound is a key diagnostic tool in modern medicine due to its ability to provide real-time, high-resolution images of the internal structures of the human body. Despite its undeniable advantages, there are challenges related to the contamination of ultrasound probes, with the [...] Read more.

Background/Aims: Ultrasound is a key diagnostic tool in modern medicine due to its ability to provide real-time, high-resolution images of the internal structures of the human body. Despite its undeniable advantages, there are challenges related to the contamination of ultrasound probes, with the risk of healthcare-associated infections. The aim of this review was to identify the most effective disinfectants for disinfecting ultrasound probes to prevent the transmission of pathogens between patients. Methods: A narrative review was conducted using the PubMed, CINAHL, Embase, and Cochrane Library databases, resulting in the inclusion of 16 studies from an initial 1202 records. Results: Hydrogen peroxide (H₂O₂) was the most effective disinfectant, especially in automated systems, achieving a >5-log₁₀ reduction in viral load, including that of resistant pathogens like Human Papillomavirus. Chlorhexidine gluconate (4%) demonstrated strong antibacterial efficacy, eliminating 84.62% of bacterial contamination, but was less effective against viral pathogens. Glutaraldehyde was effective in some cases, though its use carried a higher risk of probe damage. The use of sodium hypochlorite varied across guidelines; some endorsed it for COVID-19 prevention, while others cautioned against its application due to potential probe damage. Conclusions: This study highlights the importance of advanced disinfection technologies and strict adherence to protocols in improving infection control. Automated systems utilizing H₂O₂ strike an ideal balance between antimicrobial efficacy and equipment preservation. Future research should focus on developing disinfection methods that prioritize safety, cost-effectiveness, and environmental sustainability in various clinical environments. Full article

(This article belongs to the Special Issue Latest Review Papers in Medical Microbiology 2024)

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16 pages, 8810 KiB

Open AccessArticle

Streptococcus agalactiae Infection in Wild Trahira (Hoplias malabaricus) and Farmed Arapaima (Arapaima gigas) in Brazil: An Interspecies Transmission in Aquatic Environments Shared with Nile Tilapia (Oreochromis niloticus)

by Carlos Augusto Gomes Leal, Rafael Gariglio Clark Xavier, Guilherme Alves de Queiroz, Tarcísio Martins França Silva, Júnia Pacheco Teixeira, Flávia Figueira Aburjaile and Guilherme Campos Tavares

Microorganisms 2024, 12(12), 2393; https://doi.org/10.3390/microorganisms12122393 - 22 Nov 2024

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Abstract

Streptococcus agalactiae is an important pathogen responsible for cases of high mortality in farmed and wild fish worldwide. In Brazil, this bacterium has been commonly associated with outbreaks in Nile tilapia farms, but other native fish species are also susceptible. Since floating cages [...] Read more.

Streptococcus agalactiae is an important pathogen responsible for cases of high mortality in farmed and wild fish worldwide. In Brazil, this bacterium has been commonly associated with outbreaks in Nile tilapia farms, but other native fish species are also susceptible. Since floating cages are one of the most common culture systems used in the country, the close contact between farmed tilapia and native fish species presents a risk concerning the transmission of this pathogen. In this study, we characterized a mortality outbreak in free-living trahira and in farmed arapaima, as well as the genetic and antimicrobial susceptibility patterns of the isolates obtained. During the outbreaks, moribund fish were sampled and subjected to bacterial examination, after which the isolates were identified via MALDI-ToF analysis. Genotyping was evaluated using repetitive sequence-based PCR (REP-PCR) and multilocus sequence typing (MLST). Antimicrobial susceptibility was evaluated using disc diffusion assays. In addition, whole-genome analysis also was performed. S. agalactiae was identified in all diseased fish, all of which belonged to serotype Ib; however, trahira strains were classified as non-typeable lineages in the MLST assay, while arapaima strains were classified as ST260. These isolates were shown to be similar to the main genotype found in Nile tilapia in Brazil, using REP-PCR, MLST and phylogenomic analysis. The pathogenicity of the bacterium was confirmed by Koch’s postulates for both fish species. The antimicrobial susceptibility assay showed variable results to the same antibiotics among the isolates, prompting four of the isolates to be classified as multidrug-resistant. This study represents the first report of a natural outbreak of Streptococcus agalactiae infection in wild trahira and farmed arapaima inhabiting the same aquatic environment as Nile tilapia. Full article

(This article belongs to the Special Issue Infectious Diseases in Aquaculture)

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16 pages, 1450 KiB

Open AccessReview

Interkingdom Communication via Extracellular Vesicles: Unraveling Plant and Pathogen Interactions and Its Potential for Next-Generation Crop Protection

by Fei Li, Yuntong Lu, Kuanling Xi, Yuke Li, Xiaoyan Chen, Puchang Wang and Xiaolong Huang

Microorganisms 2024, 12(12), 2392; https://doi.org/10.3390/microorganisms12122392 - 22 Nov 2024

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Abstract

Recent advancements in the field of plant–pathogen interactions have spotlighted the role of extracellular vesicles (EVs) as pivotal mediators of cross-kingdom communication, offering new vistas for enhancing crop protection strategies. EVs are instrumental in the transport of small regulatory RNAs (sRNAs) and other [...] Read more.

Recent advancements in the field of plant–pathogen interactions have spotlighted the role of extracellular vesicles (EVs) as pivotal mediators of cross-kingdom communication, offering new vistas for enhancing crop protection strategies. EVs are instrumental in the transport of small regulatory RNAs (sRNAs) and other bioactive molecules across species boundaries, thus playing a critical role in the molecular warfare between plants and pathogens. This review elucidates the sophisticated mechanisms by which plants utilize EVs to dispatch sRNAs that silence pathogenic genes, fortifying defenses against microbial threats. Highlighting both eukaryotic and prokaryotic systems, this review delves into the biogenesis, isolation, and functional roles of EVs, illustrating their importance not only in fundamental biological processes but also in potential therapeutic applications. Recent studies have illuminated the significant role of EVs in facilitating communication between plants and pathogens, highlighting their potential in host-defense mechanisms. However, despite these advancements, challenges remain in the efficient isolation and characterization of plant-derived EVs. Overcoming these challenges is critical for fully harnessing their potential in developing next-generation crop protection strategies. This review proposes innovative strategies for utilizing RNA-based interventions delivered via EVs to bolster plant resilience against diseases. By integrating the latest scientific findings with practical applications in agriculture, this review aims to enhance the connection between fundamental plant biology and the development of innovative crop management technologies. Full article

(This article belongs to the Special Issue Latest Review Papers in Plant Microbe Interactions 2024)

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15 pages, 2994 KiB

Open AccessReview

Insights on the Pooled Prevalence and Global Distribution of Leptospirosis in Goats: Systematic Review and Meta-Analysis

by Roseane de Araújo Portela, Clécio Henrique Limeira, José Artur Brilhante Bezerra, Camila Marinelli Martins, Diego Figueiredo da Costa, Carolina de Sousa Américo Batista Santos, Clebert José Alves and Sérgio Santos de Azevedo

Microorganisms 2024, 12(12), 2391; https://doi.org/10.3390/microorganisms12122391 - 22 Nov 2024

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Abstract

Leptospira spp. infection in small ruminants is usually asymptomatic or presents nonspecific clinical signs and has an economic impact on goat farming and public health. The aim of this study was to carry out a systematic review with meta-analysis on the global seroprevalence [...] Read more.

Leptospira spp. infection in small ruminants is usually asymptomatic or presents nonspecific clinical signs and has an economic impact on goat farming and public health. The aim of this study was to carry out a systematic review with meta-analysis on the global seroprevalence and distribution of leptospirosis in goats. The methodology was based on the recommendations of Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA), and the review project was registered in the International Prospective Register of Systematic Reviews (PROSPERO—ID: CRD42023405693). Overall, 79 articles were included in the study. The global prevalence of leptospirosis in goats was 18.6% (CI 95% = 15.08–22.71%), with no publication bias and high heterogeneity. The records originated from South America (n = 32), Asia (n = 26), Europe (n = 8), North America (n = 7), and Africa (n = 6), and seropositivities were 17%, 19%, 12%, 34%, and 22%, respectively. It is concluded that Leptospira spp. infection is widespread in goat herds, including regions with semi-arid and arid climates, and it is suggested that the prospects for controlling the disease should focus on avoiding environmental contamination and improving management measures and sanitary practices. This important information provides guidance for actions to protect against human contamination and to control animal leptospirosis. Full article

(This article belongs to the Special Issue Epidemiology of Leptospira sp. Infection: Current Status, Insights and Future Prospects: 2nd Edition)

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14 pages, 1424 KiB

Open AccessArticle

Infections in Kidney Transplant Recipients: Perspectives in French Caribbean

by Laurène Tardieu, Gary Doppelt, Muriel Nicolas, Violaine Emal, Pascal Blanchet, Samuel Markowicz, Valérie Galantine, Pierre-Marie Roger, Joëlle Claudéon and Loïc Epelboin

Microorganisms 2024, 12(12), 2390; https://doi.org/10.3390/microorganisms12122390 - 22 Nov 2024

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Abstract

Few studies have focused on the infectious complications in kidney transplant recipients in tropical regions, particularly in the Caribbean. The primary objective of this study was to determine the incidence of bacterial, fungal, and parasitic infections in kidney transplant recipients in the French [...] Read more.

Few studies have focused on the infectious complications in kidney transplant recipients in tropical regions, particularly in the Caribbean. The primary objective of this study was to determine the incidence of bacterial, fungal, and parasitic infections in kidney transplant recipients in the French Caribbean and French Guiana. We included all patients who received a kidney transplant at the University Hospital of Guadeloupe between January 2014 and October 2016, with post-transplant follow-up in the French Caribbean. A total of 91 patients were included, of whom 57 developed an infectious event during follow-up. When infections were documented (94/111), bacterial infections were the most frequent (79/94), followed by fungal (11/94) and parasitic infections (4/94). Four cases of nocardiosis were identified (4/79). Phaeohyphomycosis was the most common fungal infection (7/11). In a multivariate analysis, the female gender and diabetes mellitus at the time of transplant were significantly associated with a higher risk of infection. This study is the first to describe the epidemiology of infections in kidney transplant recipients in the Caribbean and to analyze the potential risk factors. We reported a similar profile of bacterial infections to that which were observed in the European and American studies. However, we found a higher incidence of tropical infections, such as nocardiosis and phaeohyphomycosis, which highlights the need for heightened awareness among healthcare teams to ensure earlier and more appropriate treatment. Further studies focusing on these rare tropical infections are necessary to better understand their risk factors Full article

(This article belongs to the Special Issue Infections in Solid Organ Transplant Recipients)

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13 pages, 1237 KiB

Open AccessArticle

Nanopore Sequencing Allows Recovery of High-Quality Completely Closed Genomes of All Cronobacter Species from Powdered Infant Formula Overnight Enrichments

by Narjol Gonzalez-Escalona, Hee Jin Kwon and Yi Chen

Microorganisms 2024, 12(12), 2389; https://doi.org/10.3390/microorganisms12122389 - 22 Nov 2024

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Abstract

Precision metagenomic approaches using Oxford Nanopore Technology (ONT) sequencing has been shown to allow recovery of complete genomes of foodborne bacteria from overnight enrichments of agricultural waters. This study tests the applicability of a similar approach for Cronobacter genome recovery from powdered infant [...] Read more.

Precision metagenomic approaches using Oxford Nanopore Technology (ONT) sequencing has been shown to allow recovery of complete genomes of foodborne bacteria from overnight enrichments of agricultural waters. This study tests the applicability of a similar approach for Cronobacter genome recovery from powdered infant formula (PIF) overnight enrichments, where Cronobacter typically dominates the overall microbiome (>90%). This study aimed to test whether using ONT sequencing of overnight PIF enrichments could recover a completely closed Cronobacter genome for further genomic characterization. Ten PIF samples, each inoculated with different Cronobacter strains, covering Cronobacter sakazakii, C. muytjensii, C. dublinensis, C. turicensis, and C. universalis, were processed according to the Bacteriological Analytical Manual (BAM) protocol. Real-time quantitative PCR (qPCR) was used for initial screening (detection and quantification) of the overnight enrichments and confirmed that the inoculated PIF samples after the overnight enrichment had high levels of Cronobacter (10⁷ to 10⁹ CFU/mL). DNA from overnight PIF enrichments was extracted from the enrichment broth and sequenced using ONT. Results showed that ONT sequencing could accurately identify, characterize, and close the genomes of Cronobacter strains from overnight PIF enrichments in 3 days, much faster than the nearly 2 weeks required by the current BAM method. Complete genome recovery and species differentiation were achieved. This suggests that combining qPCR with ONT sequencing provides a rapid, cost-effective alternative for detecting and characterizing Cronobacter in PIF, enabling timely corrective actions during outbreaks. Full article

(This article belongs to the Special Issue Foodborne Pathogens: Detection Methods, Food Safety, and Public Health, 2nd Edition)

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8 pages, 563 KiB

Open AccessCommunication

Prevalence of Four Nematode Species (Mermithidae) in Adult Mosquitoes (Diptera: Culicidae): First Comments Since Infection/Parasitism in Fourth-Instar Larvae

by Rafael Pérez-Pacheco, Edward G. Platzer, Carlos Granados-Echegoyen, Sabino H. Martinez-Tomas, Baldomero H. Zárate-Nicolás, Beatriz Quiroz-González, Henry Loeza-Concha, Jorge Tucuch-Haas, Alicia Fonseca-Muñoz and Fabián Arroyo-Balán

Microorganisms 2024, 12(12), 2388; https://doi.org/10.3390/microorganisms12122388 - 21 Nov 2024

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Abstract

We examined the infective capacity of the mermithid nematodes, Romanomermis iyengari, Romanomermis culicivorax, Romanomermis wuchangensis, and Strelkovimermis spiculatus in fourth-instar mosquito larvae nearing pupation of Aedes aegypti, Aedes sierrensis, and Culex pipiens to determine their prevalence in the [...] Read more.

We examined the infective capacity of the mermithid nematodes, Romanomermis iyengari, Romanomermis culicivorax, Romanomermis wuchangensis, and Strelkovimermis spiculatus in fourth-instar mosquito larvae nearing pupation of Aedes aegypti, Aedes sierrensis, and Culex pipiens to determine their prevalence in the adults of these mosquitoes. We exposed 100 fourth-instar larvae to pre-parasitic nematodes (juvenile 2 stages) at a ratio of 10:1 (10 nematodes per mosquito larvae). Two days after the nematode applications, a sample of 20 pupae was taken and placed into transparent plastic cups with distilled water to observe the development and growth of pupae until they reached the adult phase with nematodes inside. The four species of nematodes showed the highest prevalence of infection on the Cx. pipiens mosquito, exceeding 55% parasitism, while R. wuchangensis and R. iyengari surpassed this value on Ae. sierrensis by 61.11% and 57.89%. Aedes aegypti was the least susceptible to nematodes, with parasitism values between 30% and 40%. In laboratory settings, we obtained high rates (26.32–77.78%) of parasitized adults when the three-mosquito species in fourth-instar larvae nearing pupation were exposed to infective nematodes. R. wuchangensis (1.86) and S. spiculatus (1.80) were infected Cx. pipiens with greater intensity and R. iyengari (1.33) and R. culicivorax (1.09) with less intensity. This evaluation offers valuable insights into the variability of nematode prevalence of infection and infectivity in fourth-instar larvae, which host mermithids capable of progressing through the pupal stage to adulthood. Full article

(This article belongs to the Section Public Health Microbiology)

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12 pages, 1947 KiB

Open AccessBrief Report

A Case Series Report on the Effect of Tofacitinib on Joint Inflammation and Gut Microbiota Composition in Psoriatic Arthritis Patients Naive to Biologic Agents

by Andrea Picchianti Diamanti, Concetta Panebianco, Valeria Di Gioia, Ilaria Anna Bellofatto, Simonetta Salemi, Roberta Di Rosa, Giorgio Sesti, Gabriele Nalli, Gerardo Salerno, Etta Finocchiaro and Bruno Laganà

Microorganisms 2024, 12(12), 2387; https://doi.org/10.3390/microorganisms12122387 - 21 Nov 2024

Viewed by 247

Abstract

Introduction: Psoriatic arthritis (PsA) is a complex condition within the Spondyloarthritis (SpA) group. Recent studies have focused on the important role of the intestinal microbiota in maintaining immunological homeostasis, highlighting how intestinal dysbiosis may act as a trigger for autoimmune diseases. Tofacitinib is [...] Read more.

Introduction: Psoriatic arthritis (PsA) is a complex condition within the Spondyloarthritis (SpA) group. Recent studies have focused on the important role of the intestinal microbiota in maintaining immunological homeostasis, highlighting how intestinal dysbiosis may act as a trigger for autoimmune diseases. Tofacitinib is a Janus kinase inhibitor (JAK-i) with proven efficacy for the treatment of both rheumatoid arthritis and PsA. However, there is a lack of data on its ability to reduce joint remission through ultrasonography (US) and the effects it might have on the composition of the gut microbiota. Methods: Here, we present a case series of seven bio-naïve PsA patients who received tofacitinib treatment and were followed up for 12 months. The clinical response was assessed using validated scores (DAPSA, ASDAS, and BASDAI), laboratory tests, and US assessment of the target joint and enthesis. Finally, we evaluated changes in the composition of the intestinal microbiota using next-generation sequencing analysis of fecal samples. Results: The patients in the study showed a significant improvement in all clinical scores used; this improvement was also confirmed by a significant reduction in the US synovitis scores. The data on the microbiota analysis suggested that the effectiveness of tofacitinib in ameliorating PsA activity was associated with a relevant modification of some gut bacterial lineages. No cases of severe adverse effects were reported. Conclusions: Treatment with tofacitinib proved to be effective, safe and capable of varying the composition of the gut microbiota by selecting bacterial strains considered beneficial in immune modulation. Full article

(This article belongs to the Special Issue Diet, Supplements, Lifestyle and Human Microbiota: Impacts on Health and Disease)

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18 pages, 5378 KiB

Open AccessArticle

Biological Characteristics and Fungicide Screening of Colletotrichum fructicola Causing Mulberry Anthracnose

by Ping Li, Xue Dai, Siyi Wang, Qian Luo, Qingqing Tang, Zijing Xu, Weiguo Zhao and Fuan Wu

Microorganisms 2024, 12(12), 2386; https://doi.org/10.3390/microorganisms12122386 - 21 Nov 2024

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Abstract

Mulberry is an important economic crop in China that is widely planted and has important edible and medicinal value. Anthracnose, a critical leaf disease, severely compromises the yield and quality of mulberry trees. However, there are many kinds of pathogens causing mulberry anthracnose [...] Read more.

Mulberry is an important economic crop in China that is widely planted and has important edible and medicinal value. Anthracnose, a critical leaf disease, severely compromises the yield and quality of mulberry trees. However, there are many kinds of pathogens causing mulberry anthracnose and it is difficult to control. This study was undertaken to elucidate the biological characteristics of Colletotrichum fructicola, the pathogen responsible for mulberry leaf spot in Zhejiang Province, and to screen out effective fungicides for its management. The biological characteristics of the pathogen were studied using the cross method and spore counting method, while the sensitivity of the pathogen to seven different fungicides was determined using the growth rate method. The findings indicated that potato dextrose agar (PDA) is the optimal growth medium for the pathogen. The pathogen was capable of growing across a temperature range of 5 to 40 °C, with optimum growth observed at 25 °C. Exposure to a 56 °C water bath for 10 min resulted in the death of the pathogen. It was also found to grow and sporulate within a pH range of 4 to 12, with an optimum pH of 7. Under alternating 12 h light and dark cycles, the colonies grew rapidly and produced abundant spores. Among the fungicides tested, 97% carbendazim WP exhibited the best inhibitory effect, with an EC₅₀ (concentration for 50% of maximal effect) value of 0.0242 μg/mL. This was followed by 35% propiconazole SC, which had an EC₅₀ of 0.4180 μg/mL. The fungicidal effect of 25 g/L fludioxonil SSCC was relatively poor, with an EC₅₀ value of 103.0170 μg/mL. This study clarifies the optimal conditions for the growth and sporulation of the mulberry anthracnose pathogen and identifies fungicides with effective inhibitory properties. These findings will provide valuable guidance for field applications and disease management in controlling mulberry anthracnose. Full article

(This article belongs to the Section Plant Microbe Interactions)

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17 pages, 10197 KiB

Open AccessArticle

Factors and Mechanisms Affecting Arsenic Migration in Cultivated Soils Irrigated with Contained Arsenic Brackish Groundwater

by Wenjing Dai, Rongguang Shi, Xiaodong Li, Zhiqi Zhao, Zihan Xia, Dongli Li, Yan Li, Gaoyang Cui and Shiyuan Ding

Microorganisms 2024, 12(12), 2385; https://doi.org/10.3390/microorganisms12122385 - 21 Nov 2024

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Abstract

Contained arsenic (As) and unsafe brackish groundwater irrigation can lead to serious As pollution and increase the ecological risk in cultivated soils. However, little is known about how Fe oxides and microbes affect As migration during soil irrigation processes involving arsenic-contaminated brackish groundwater. [...] Read more.

Contained arsenic (As) and unsafe brackish groundwater irrigation can lead to serious As pollution and increase the ecological risk in cultivated soils. However, little is known about how Fe oxides and microbes affect As migration during soil irrigation processes involving arsenic-contaminated brackish groundwater. In this study, the samples (porewater and soil) were collected through the dynamic soil column experiments to explore the As migration process and its effect factors during soil irrigation. The results showed that the As concentration in porewater samples from the topsoil was enriched compared to that in the subsoil, and the main solid As fractions were strongly adsorbed or bound to amorphous and crystalline Fe oxides. The aqueous As concentration and the solid As fractions indicated that reductive dissolution and desorption from amorphous Fe oxides were the primary mechanisms of As release at the topsoil and subsoil, respectively. Meanwhile, Sphingomonas_sp., Microvirga_ossetica and Acidobacteriota_bacterium were the dominant microbes affecting As biotransformation by arsenate reductase gene (arsC) expression. Accompanied by the Eh and competitive ions concentration change, amorphous Fe oxide dissolution increased to facilitate the As release, and the changes in the microbial community structure related to As reduction may have enhanced As mobilization in soils irrigated by As-containing brackish groundwater. Full article

(This article belongs to the Special Issue Role of Microbes in the Remediation of Pollutants in the Environment)

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17 pages, 3270 KiB

Open AccessArticle

Bacillus subtilis PE7-Mediated Alleviation of Phosphate Starvation and Growth Promotion of Netted Melon (Cucumis melo L. var. reticulatus Naud.)

by Seong Eun Han, Kil Yong Kim and Chaw Ei Htwe Maung

Microorganisms 2024, 12(12), 2384; https://doi.org/10.3390/microorganisms12122384 - 21 Nov 2024

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Abstract

Members of Bacillus species are able to enhance the level of available phosphorus (P) for plant absorption through mechanisms of P solubilization and mineralization. In our study, B. subtilis PE7 showed P-solubilizing activity in simple phosphate broth (SPB) medium, and acetic acid, iso-butyric [...] Read more.

Members of Bacillus species are able to enhance the level of available phosphorus (P) for plant absorption through mechanisms of P solubilization and mineralization. In our study, B. subtilis PE7 showed P-solubilizing activity in simple phosphate broth (SPB) medium, and acetic acid, iso-butyric acid, and iso-valeric acid were major organic acids responsible for the increase in soluble P and decrease in pH of SPB medium. In addition, strain PE7 released phytase on phytase-screening agar (PSA) medium, and analysis of semi-quantitative reverse transcription and polymerase chain reaction (sqRT-PCR) revealed that the phyC gene expression was the highest at 1 day after incubation. A low concentration of KH₂PO₄ in SPB medium induced more biofilm formation than a high concentration of KH₂PO₄. Strain PE7 showed swimming and swarming motilities in TY and TrA agar media. Under P starvation, inoculation with higher cell numbers of strain PE7 enhanced biomass and nutrient acquisition by melon plants, resulting in higher values of growth parameters and nutrient contents. Moreover, the persistence of bacterial cells on the root surface and in the rhizosphere of melon plants indicated colonization of the plants by strain PE7. Due to its capacity for P solubilization and mineralization, B. subtilis PE7 could be utilized as an alternative to synthetic fertilizer for P deficient-stress management in crop plantation. Full article

(This article belongs to the Special Issue Rhizosphere Microbial Community, 3rd Edition)

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14 pages, 2366 KiB

Open AccessArticle

Dual Roles of Heterotrophic Ammonia-Oxidizing Bacteria in Enhancing Compensatory Growth upon Post-Drought in Maize

by Hao Yu, Xiao-Ling Wang, Run-Hong Sun, Lin Qi, Peng Song and Tong-Chao Wang

Microorganisms 2024, 12(12), 2383; https://doi.org/10.3390/microorganisms12122383 - 21 Nov 2024

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Abstract

This study investigates the mechanisms driving maize compensatory growth upon post-drought, to reveal how the root’s original cytokinins are regulated by the two-fold roles of heterotrophic bacteria with ammonia-oxidizing (HAOB) capabilities. The HAOB’ dual roles encompass influencing root cytokinin synthesis and transport through [...] Read more.

This study investigates the mechanisms driving maize compensatory growth upon post-drought, to reveal how the root’s original cytokinins are regulated by the two-fold roles of heterotrophic bacteria with ammonia-oxidizing (HAOB) capabilities. The HAOB’ dual roles encompass influencing root cytokinin synthesis and transport through nitrification and a direct pathway. Experiment 1 involved introducing the application of varying amounts of NO₃⁻ to the roots to examine how nitrification affects cytokinin roots-to-leaves transport. Results demonstrate that the 30–40 mmol·L⁻¹ NO₃⁻ concentration had ideal effects on enhancing post-drought growth in maize by facilitating cytokinin synthesis and transport. In experiment 2, an HAOB strain, S2_8_1, was utilized and NO₃⁻ was supplemented alongside HAOB inoculation to assess the joint impacts of nitrification and the direct pathway on the production and transportation of cytokinins. Results demonstrate that the HAOB strain S2_8_1 increases nitrification rates in rhizosphere soil, thereby promoting the transport of cytokinins from roots to leaves. In addition, the HAOB strain promotes root cytokinin transport to leaves autonomously, showcasing its direct pathway. Inoculation with the HAOB strain increased leaf cytokinin content and improved water use efficiency compared to the addition of NO₃⁻; however, the combination of NO₃⁻ and HAOB strains resulted in a synergistic effect and further improvement. These findings elucidate how HAOB can enhance maize compensatory growth through its dual roles, presenting promising applications in agriculture. Full article

(This article belongs to the Section Plant Microbe Interactions)

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12 pages, 269 KiB

Open AccessReview

Importance of Lactobacilli for Human Health

by Piotr B. Heczko, Milena Giemza, Weronika Ponikiewska and Magdalena Strus

Microorganisms 2024, 12(12), 2382; https://doi.org/10.3390/microorganisms12122382 - 21 Nov 2024

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Abstract

As an extraordinarily diverse group of bacteria, lactobacilli are now classified into several genera, many of which still include “Lactobacillus” in their names. Despite their names, this group of lactic acid bacteria comprises microorganisms that are crucial for human health, especially during the [...] Read more.

As an extraordinarily diverse group of bacteria, lactobacilli are now classified into several genera, many of which still include “Lactobacillus” in their names. Despite their names, this group of lactic acid bacteria comprises microorganisms that are crucial for human health, especially during the early development of the human microbiota and immune system. The interactions between lactobacilli and components of the mucosal immunity lead to its shaping and development, which is possibly considered a prime mover in the advancement of the human immune system. Although much of the evidence backing the pivotal role of lactobacilli in maintaining human health comes from studies on probiotics aiming to elucidate the mechanisms of their functional activities and studies on mucosal immunity in germ-free mice, it is justifiable to extend observations on the properties of the individual probiotic Lactobacillus that are related to health benefits onto other strains sharing common characteristics of the species. In this review, we will discuss the acquisition, presence, and functions of lactobacilli in different human microbiota throughout their whole life, including those arising in the amnion and their interactions with mucosal and immune cells. Examples of immune system modulation by probiotic lactobacilli include their colonic competition for available nutrients, interference with colonization sites, competition for binding sites on gut epithelial cells, bacteriocin production, reduction of colonic pH, and nonspecific stimulation of the immune system. Full article

(This article belongs to the Special Issue Probiotic and Postbiotic Properties of Lactobacillus)

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