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Search Results (649)

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18 pages, 1942 KiB  
Article
Surveillance and Characterization of Vancomycin-Resistant and Vancomycin-Variable Enterococci in a Hospital Setting
by Claudia Rotondo, Valentina Antonelli, Alberto Rossi, Silvia D’Arezzo, Marina Selleri, Michele Properzi, Silvia Turco, Giovanni Chillemi, Valentina Dimartino, Carolina Venditti, Sara Guerci, Paola Gallì, Carla Nisii, Alessia Arcangeli, Emanuela Caraffa, Stefania Cicalini and Carla Fontana
Antibiotics 2025, 14(8), 795; https://doi.org/10.3390/antibiotics14080795 - 4 Aug 2025
Abstract
Background/Objectives: Enterococci, particularly Enterococcus faecalis and Enterococcus faecium, are Gram-positive cocci that can cause severe infections in hospitalized patients. The rise of vancomycin-resistant enterococci (VRE) and vancomycin-variable enterococci (VVE) poses significant challenges in healthcare settings due to their resistance to multiple [...] Read more.
Background/Objectives: Enterococci, particularly Enterococcus faecalis and Enterococcus faecium, are Gram-positive cocci that can cause severe infections in hospitalized patients. The rise of vancomycin-resistant enterococci (VRE) and vancomycin-variable enterococci (VVE) poses significant challenges in healthcare settings due to their resistance to multiple antibiotics. Methods: We conducted a point prevalence survey (PPS) to assess the prevalence of VRE and VVE colonization in hospitalized patients. Rectal swabs were collected from 160 patients and analyzed using molecular assays (MAs) and culture. Whole-genome sequencing (WGS) and core-genome multilocus sequence typing (cgMLST) were performed to identify the genetic diversity. Results: Of the 160 rectal swabs collected, 54 (33.7%) tested positive for the vanA and/or vanB genes. Culture-based methods identified 47 positive samples (29.3%); of these, 44 isolates were identified as E. faecium and 3 as E. faecalis. Based on the resistance profiles, 35 isolates (74.5%) were classified as VRE, while 12 (25.5%) were classified as VVE. WGS and cgMLST analyses identified seven clusters of E. faecium, with sequence type (ST) 80 being the most prevalent. Various resistance genes and virulence factors were identified, and this study also highlighted intra- and inter-ward transmission of VRE strains. Conclusions: Our findings underscore the potential for virulence and resistance of both the VRE and VVE strains, and they highlight the importance of effective infection control measures to prevent their spread. VVE in particular should be carefully monitored as they often escape detection. Integrating molecular data with clinical information will hopefully enhance our ability to predict and prevent future VRE infections. Full article
(This article belongs to the Special Issue Hospital-Associated Infectious Diseases and Antibiotic Therapy)
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16 pages, 1591 KiB  
Article
Molecular and Drug Resistance Characteristics of Haemophilus influenzae Carried by Pediatric Patients with Adenoid Hypertrophy
by Nan Xiao, Jia-Hao Qin, Xiu-Ying Zhao and Lin Liu
Microorganisms 2025, 13(8), 1764; https://doi.org/10.3390/microorganisms13081764 - 29 Jul 2025
Viewed by 217
Abstract
Purpose: The adenoid microbiota plays a key role in adenoid hypertrophy (AH). This study explored the molecular epidemiology and antimicrobial resistance of Haemophilus. Influenzae (H. influenzae) strains in pediatric AH patients. Methods: Retrospective analysis of pediatric AH patients undergoing endoscopic adenoidectomy. [...] Read more.
Purpose: The adenoid microbiota plays a key role in adenoid hypertrophy (AH). This study explored the molecular epidemiology and antimicrobial resistance of Haemophilus. Influenzae (H. influenzae) strains in pediatric AH patients. Methods: Retrospective analysis of pediatric AH patients undergoing endoscopic adenoidectomy. Adenoid tissue samples were cultured to screen for pathogens. H. influenzae strains were identified by 16S rRNA sequencing and serotyped via q-PCR. Multilocus sequence typing (MLST) and ftsI gene analysis were conducted using PubMLST. β-lactamase genes (blaTEM-1, blaROB-1) were detected by PCR, and antibiotic susceptibility testing (AST) was performed using the Etest method. For imipenem-resistant strains, the acrRAB efflux pump gene cluster and ompP2 porin gene were sequenced and compared with those of the wild-type strain Rd KW20. Results: Over 8 months, 56 non-duplicate H. influenzae strains were isolated from 386 patients. The detection rate was highest in children under 5 years (30.5%) compared to those aged 5–10 years (13.4%) and 10–15 years (8.7%). Of 49 sub-cultured strains, all were non-typeable H. influenzae (NTHi). MLST identified 22 sequence types (STs) and 13 clonal complexes (CCs), with CC11 (26.5%), CC3 (14.3%), and CC107 (14.3%) being predominant. Common STs included ST103 (22.4%), ST57 (10.2%), and ST107 (10.2%). Most strains belonged to the ftsI group III-like+ (57.1%). β-lactamase positivity was 98.0% (48/49), with blaTEM-1 (95.9%) and blaROB-1 (18.4%) detected. AST showed low susceptibility to ampicillin (10.2%), amoxicillin–clavulanate (34.7%), azithromycin (12.2%), and trimethoprim–sulfamethoxazole (14.3%). Among the β-lactamase-positive strains, 44/48 were β-lactamase-positive ampicillin-resistant (BLPAR); none were β-lactamase-negative ampicillin-resistant (BLNAR). Imipenem susceptibility was 91.8% (45/49). No carbapenemases were found in the imipenem-resistant strains, but mutations in acrRAB (88.12–94.94% identity) and ompP2 (77.10–82.94% identity) were observed. Conclusions: BLPAR NTHi strains of CC11 are major epidemic strains in pediatric AH. Imipenem resistance in H. influenzae likely results from porin mutations rather than carbapenemase activity. Enhanced surveillance of H. influenzae’s role in AH and its resistance patterns is warranted. Full article
(This article belongs to the Section Medical Microbiology)
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11 pages, 1598 KiB  
Article
Genomic and Antimicrobial Resistance Analysis of an ST25 Streptococcus suis Strain Isolated from a Human in Zhejiang Province, China
by Shuirong Zhu, Xiaofang Wu, Wenwu Yao, Zhuoying Wu, Lingbo Wang, Zhangnv Yang, Beibei Wu and Yanjun Zhang
Pathogens 2025, 14(8), 742; https://doi.org/10.3390/pathogens14080742 - 28 Jul 2025
Viewed by 278
Abstract
A Streptococcus suis strain isolated from the blood of a patient in Zhejiang Province, China, was analysed using whole-genome sequencing and tested for antimicrobial resistance. The isolated strain was identified as S. suis serotype 2, and classified to ST25 on multilocus sequence typing [...] Read more.
A Streptococcus suis strain isolated from the blood of a patient in Zhejiang Province, China, was analysed using whole-genome sequencing and tested for antimicrobial resistance. The isolated strain was identified as S. suis serotype 2, and classified to ST25 on multilocus sequence typing (MLST). The minimum core genome group of the strain was identified as Group 4, and multilocus variable-number tandem-repeat analysis (MLVA) assigned it as type 2, 4.4, 0, 9, 3, 2, 0, 0. An antimicrobial resistance analysis showed that the strain was resistant to clindamycin, tetracycline, azithromycin, and erythromycin but sensitive to 11 other antibiotics. In a genomic evolution analysis, this isolate clustered on the same branch as North American pig isolate, Chinese pig isolates from Tianjin, and Hubei pig isolates. Full article
(This article belongs to the Special Issue Respiratory Diseases in Swine: Epidemiology, Diagnosis and Control)
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13 pages, 1384 KiB  
Article
Molecular Epidemiology of Brucella spp. in Aborted Livestock in the Ningxia Hui Autonomous Region, China
by Cai Yin, Cong Yang, Yawen Wu, Jing Di, Taotao Bai, Yumei Wang, Yuling Zhang, Longlong Luo, Shuang Zhou, Long Ma, Xiaoliang Wang, Qiaoying Zeng and Zhixin Li
Vet. Sci. 2025, 12(8), 702; https://doi.org/10.3390/vetsci12080702 - 28 Jul 2025
Viewed by 262
Abstract
Brucellosis is caused by Brucella spp.; it can result in fetal loss and abortion, resulting in economic losses and negative effects on human health. Herein, a cross-sectional study on the epidemiology of Brucella spp. in aborted livestock in Ningxia from 2022 to 2023 [...] Read more.
Brucellosis is caused by Brucella spp.; it can result in fetal loss and abortion, resulting in economic losses and negative effects on human health. Herein, a cross-sectional study on the epidemiology of Brucella spp. in aborted livestock in Ningxia from 2022 to 2023 was conducted. A total of 749 aborted tissue samples from 215 cattle and 534 sheep were collected from farmers who reported abortions that were supported by veterinarians trained in biosecurity. The samples were analyzed using qPCR and were cultured for Brucella spp. when a positive result was obtained; the samples were speciated using AMOS-PCR. MLST and MLVA were employed for genotype identification. The results demonstrated that 8.68% of the samples were identified as being positive for Brucella spp. based on qPCR results. In total, 14 field strains of Brucella spp. were subsequently isolated, resulting in 11 B. melitensis, 2 B. abortus, and 1 B. suis. being identified via AMOS-PCR. Four sequence types were identified via MLST—ST7 and ST8 (B. melitensis), ST2 (B. abortus), and ST14 (B. suis)—with ST8 predominating. Five MLVA-8 genotypes and seven MLVA-11 genotypes were identified, with MLVA-11 GT116 predominating in livestock. Thus, at least three Brucella species are circulating in aborted livestock in Ningxia. This suggests a significant risk of transmission to other animals and humans. Therefore, disinfection and safe treatment procedures for aborted livestock and their products should be carried out to interrupt the transmission pathway; aborted livestock should be examined to determine zoonotic causes and targeted surveillance should be strengthened to improve the early detection of infectious causes, which will be of benefit to the breeding industry and public health security. Full article
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16 pages, 1234 KiB  
Article
Genomic Insights of Emerging Multidrug-Resistant OXA-48-Producing ST135 Proteus mirabilis
by Angeliki Mavroidi, Elisavet Froukala, Nick Spanakis, Aikaterini Michelaki, Maria Orfanidou, Vasiliki Koumaki and Athanasios Tsakris
Antibiotics 2025, 14(8), 750; https://doi.org/10.3390/antibiotics14080750 - 25 Jul 2025
Viewed by 293
Abstract
Background/Objectives: Among Enterobacterales, OXA-48-like-producing Proteus mirabilis strains have been scarcely detected. Herein, we characterized a blaOXA-48-harbouring P. mirabilis strain recovered from Greece (Pm GR-1), while phylogenomics and comparative genomics analyses with previously published blaOXA-48 carriers were also assessed. [...] Read more.
Background/Objectives: Among Enterobacterales, OXA-48-like-producing Proteus mirabilis strains have been scarcely detected. Herein, we characterized a blaOXA-48-harbouring P. mirabilis strain recovered from Greece (Pm GR-1), while phylogenomics and comparative genomics analyses with previously published blaOXA-48 carriers were also assessed. Methods: Characterization of Pm GR-1 was performed by the Vitek® Compact and Mass Spectrometry systems, antimicrobial susceptibility testing, detection of beta-lactamases, multilocus-sequence typing (MLST), and whole-genome sequencing (WGS). In silico prediction of mobile genetic elements (MGEs), genomic islands (GIs), antimicrobial resistance genes (ARGs) and virulence factors (VFs), and phylogenetic, core-genome SNP and comparative genomics analyses were executed using bioinformatic tools. Results: Pm GR-1 was isolated from a urine sample of an outpatient in a Greek hospital. It exhibited a multidrug-resistant phenotype, being susceptible only to amikacin and ceftazidime/avibactam. It co-carried several beta-lactamase genes on the chromosome (blaOXA-48, blaCTX-M-14, blaTEM-1) and a plasmid (blaTEM-2) and several other ARGs, but also mutations associated with quinolone resistance in the DNA gyrase and topoisomerase IV subunits. It belonged to the international clone ST135 that has also been detected among OXA-48-producing P. mirabilis strains from Germany and the USA. Pm GR-1 was genetically related to those from Germany, sharing highly similar MGEs, GIs, ARGs and VFs, including the chromosomal blaOXA-48 genetic structure, the O-antigen locus, the flagella locus, the MR/P fimbriae operon, and the urease gene cluster. Conclusions: To our knowledge, this is the first report from Greece of a blaOXA-48-possessing P. mirabilis strain. The emergence of blaOXA-48 among P. mirabilis strains of the international clone ST135 in different geographical regions is worrying. Close monitoring of these strains is required in One Health settings. Full article
(This article belongs to the Special Issue Antimicrobial Resistance Genes: Spread and Evolution)
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15 pages, 4418 KiB  
Article
Prevalence and Genomic Characterization of Vibrio parahaemolyticus Isolated from a Vast Amount of Aquatic Products in Huzhou, China
by Wei Yan, Liping Chen, Lei Ji, Rui Yuan, Fenfen Dong and Peng Zhang
Foods 2025, 14(14), 2481; https://doi.org/10.3390/foods14142481 - 15 Jul 2025
Viewed by 380
Abstract
Vibrio parahaemolyticus is the leading bacterial cause of gastroenteritis associated with aquatic food consumption globally. This study aimed to determine the prevalence of V. parahaemolyticus in aquatic foods from Huzhou and to identify the serotypes, antimicrobial resistance, virulence factors, and genetic relatedness of [...] Read more.
Vibrio parahaemolyticus is the leading bacterial cause of gastroenteritis associated with aquatic food consumption globally. This study aimed to determine the prevalence of V. parahaemolyticus in aquatic foods from Huzhou and to identify the serotypes, antimicrobial resistance, virulence factors, and genetic relatedness of the strains. A total of 306 isolates were detected from 1314 aquatic food samples from 2022 to 2024. The results indicated that the most prevalent serotypes were O1:KUT (17.0%), O2:K28 (13.7%), and O2:KUT (13.1%). Multilocus sequence typing analysis divided the 306 isolates into 175 sequence types (STs), and the predominant sequence type was ST864 (3.3%). Antimicrobial susceptibility tests showed that 2.6% of isolates were multidrug resistant. High resistance was observed to ampicillin (64.7%) and streptomycin (44.4%). A total of seven antimicrobial categories of resistance genes were identified, and the resistance gene blaCARB was detected in all isolates. The virulence genes tdh and trh were found in 16 (5.2%) and 12 (3.9%) isolates, respectively. In addition, we observed that all the 306 V. parahaemolyticus isolates encode type III secretion systems 1. The phylogenomic analysis based on the whole-genome sequence revealed that the 306 isolates were divided into four clusters. Our findings broaden perspectives on V. parahaemolyticus genetic diversity and enhance our ability to assess the potential risks of its spread. Full article
(This article belongs to the Section Food Microbiology)
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15 pages, 2742 KiB  
Article
Resistome and Phylogenomics of Escherichia coli Strains Obtained from Diverse Sources in Jimma, Ethiopia
by Mulatu Gashaw, Esayas Kebede Gudina, Guenter Froeschl, Ralph Matar, Solomon Ali, Liegl Gabriele, Amelie Hohensee, Thomas Seeholzer, Arne Kroidl and Andreas Wieser
Antibiotics 2025, 14(7), 706; https://doi.org/10.3390/antibiotics14070706 - 14 Jul 2025
Viewed by 356
Abstract
Introduction: In recent years, antimicrobial resistance (AMR) rates have increased significantly in bacterial pathogens, particularly extended beta-lactam resistance. This study aimed to investigate resistome and phylogenomics of Escherichia coli (E. coli) strains isolated from various sources in Jimma, Ethiopia. Methods [...] Read more.
Introduction: In recent years, antimicrobial resistance (AMR) rates have increased significantly in bacterial pathogens, particularly extended beta-lactam resistance. This study aimed to investigate resistome and phylogenomics of Escherichia coli (E. coli) strains isolated from various sources in Jimma, Ethiopia. Methods: Phenotypic antibiotic resistance patterns of E. coli isolates were determined using automated Kirby–Bauer disc diffusion and minimum inhibitory concentration (MIC). Isolates exhibiting phenotypic resistance to beta-lactam antibiotics were further analyzed with a DNA microarray to confirm the presence of resistance-encoding genes. Additionally, multilocus sequence typing (MLST) of seven housekeeping genes was conducted using PCR and Oxford Nanopore-Technology (ONT) to assess the phylogenetic relationships among the E. coli isolates. Results: A total of 611 E. coli isolates from human, animal, and environmental sources were analyzed. Of these, 41.6% (254) showed phenotypic resistance to at least one of the tested beta-lactams, 96.1% (244) thereof were confirmed genotypically. More than half of the isolates (53.3%) had two or more resistance genes present. The most frequent ESBL-encoding gene was CTX-M-15 (74.2%; 181), followed by TEM (59.4%; 145) and CTX-M-9 (4.1%; 10). The predominant carbapenemase gene was NDM-1, detected in 80% (12 out of 15) of carbapenem-resistant isolates. A phylogenetic analysis revealed clonality among the strains obtained from various sources, with international high-risk clones such as ST131, ST648, ST38, ST73, and ST405 identified across various niches. Conclusions: The high prevalence of CTX-M-15 and NDM-1 in multidrug-resistant E. coli isolates indicates the growing threat of AMR in Ethiopia. The discovery of these high-risk clones in various niches shows possible routes of transmission and highlights the necessity of a One Health approach to intervention and surveillance. Strengthening antimicrobial stewardship, infection prevention, and control measures are crucial to mitigate the spread of these resistant strains. Full article
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21 pages, 1308 KiB  
Article
Mechanisms of Cefiderocol Resistance in Carbapenemase-Producing Enterobacterales: Insights from Comparative Genomics
by Alexander Tristancho-Baró, Ana Isabel López-Calleja, Ana Milagro, Mónica Ariza, Víctor Viñeta, Blanca Fortuño, Concepción López, Miriam Latorre-Millán, Laura Clusa, David Badenas-Alzugaray, Rosa Martínez, Carmen Torres and Antonio Rezusta
Antibiotics 2025, 14(7), 703; https://doi.org/10.3390/antibiotics14070703 - 12 Jul 2025
Viewed by 387
Abstract
Background/Objectives: Cefiderocol is a novel siderophore cephalosporin with potent in vitro activity against a broad spectrum of Gram-negative bacteria, including carbapenemase-producing Enterobacterales (CPE). However, the recent emergence of resistance in clinical settings raises important concerns regarding its long-term effectiveness. This study aims [...] Read more.
Background/Objectives: Cefiderocol is a novel siderophore cephalosporin with potent in vitro activity against a broad spectrum of Gram-negative bacteria, including carbapenemase-producing Enterobacterales (CPE). However, the recent emergence of resistance in clinical settings raises important concerns regarding its long-term effectiveness. This study aims to investigate the genomic determinants associated with cefiderocol resistance in CPE isolates of human origin. Methods: Comparative genomic analyses were conducted between cefiderocol-susceptible and -resistant CPE isolates recovered from human clinical and epidemiological samples at a tertiary care hospital. Whole-genome sequencing, variant annotation, structural modelling, and pangenome analysis were performed to characterize resistance mechanisms. Results: A total of 59 isolates (29 resistant and 30 susceptible) were analyzed, predominantly comprising Klebsiella pneumoniae, Escherichia coli, and Enterobacter cloacae. The most frequent carbapenemase gene among the resistant isolates was blaNDM, which was also present in a subset of susceptible strains. The resistant isolates exhibited a significantly higher burden of non-synonymous mutations in their siderophore receptor genes, notably within fecR, fecA, fiu, and cirA. Structural modelling predicted deleterious effects for mutations such as fecR:G104S and fecA:A190T. Additionally, porin loss and loop 3 insertions (e.g., GD/TD) in OmpK36, as well as OmpK35 truncations, were more frequent in the resistant isolates, particularly in high-risk clones such as ST395 and ST512. Genes associated with toxin–antitoxin systems (chpB2, pemI) and a hypothetical metalloprotease (group_2577) were uniquely found in the resistant group. Conclusions: Cefiderocol resistance in CPE appears to be multifactorial. NDM-type metallo-β-lactamases and missense mutations in siderophore uptake systems—especially in those encoded by fec, fhu, and cir operons—play a central role. These may be further potentiated by alterations in membrane permeability, such as porin disruption and efflux deregulation. The integration of genomic and structural approaches provides valuable insights into emerging resistance mechanisms and may support the development of diagnostic tools and therapeutic strategies. Full article
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19 pages, 3395 KiB  
Article
Hybrid Whole Genomes of Brucella melitensis from Tunisian Animal Isolates: Virulence Factors, Antimicrobial Susceptibility, and Phylogeny
by Ibtihel Ben Abdallah, Germán Kopprio, Awatef Béjaoui, Susanne Köhler, Kaouther Guesmi, Sana Kalthoum, Jacob Gatz, Amel Arfaoui, Monia Lachtar, Haikel Hajlaoui, Mohamed Naceur Baccar, Holger Scholz and Abderrazak Maaroufi
Microorganisms 2025, 13(7), 1651; https://doi.org/10.3390/microorganisms13071651 - 12 Jul 2025
Viewed by 423
Abstract
Brucellosis remains endemic in Tunisia, causing abortions in small ruminants, and represents a public health threat through occupational exposure and the consumption of contaminated animal products. The aims of this study are to assess the antibiotic susceptibility of two Brucella melitensis isolates (TATA [...] Read more.
Brucellosis remains endemic in Tunisia, causing abortions in small ruminants, and represents a public health threat through occupational exposure and the consumption of contaminated animal products. The aims of this study are to assess the antibiotic susceptibility of two Brucella melitensis isolates (TATA and SBZ) from aborted sheep, to analyze their genomes using hybrid whole-genome sequencing, and to investigate their antimicrobial resistance (AMR), potential virulence factors (VFs), and phylogenetic relationships. Both isolates were phenotypically confirmed to be susceptible to doxycycline, gentamicin, rifampicin, streptomycin, and trimethoprim–sulfamethoxazole, and no corresponding classical AMR genes were identified. However, several potential AMR-related genes (mprF, bepCDEFG, qacG, and adeF) and a mutation in the parC gene were detected. The analysis of the genotypes revealed 74 potential virulence genes, primarily involved in lipopolysaccharide synthesis and type IV secretion systems. Genomic comparison showed over 99% nucleotide identity between the Tunisian strains, B. melitensis bv. 1 16M and B. melitensis bv. 3 Ether. Five gene clusters, including three hypothetical proteins with 100% identity, were detected exclusively in the TATA and SBZ strains. Additionally, two unique gene clusters were identified in SBZ: a rhodocoxin reductase and another hypothetical protein. Both isolates were assigned to sequence types ST11 and ST89. Core-genome-based phylogenetic analysis clustered both strains with biovar 3 and ordered the Tunisian strains into two distinct groups: TATA within Tunisian Cluster 1 is closely related to strains from Egypt and Italy, while SBZ near MST Cluster 4 is more related to isolates from Austria and two outliers from Italy and Tunisia. This study provides the first genomic characterization of B. melitensis from aborted sheep in Tunisia and offers valuable insights into AMR, virulence, and phylogenetic distribution. Full article
(This article belongs to the Special Issue Epidemiology and Control Strategies for Brucellosis)
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17 pages, 3221 KiB  
Article
An mRNA Vaccine Targeting the C-Terminal Region of P1 Protein Induces an Immune Response and Protects Against Mycoplasma pneumoniae
by Fenglian Zhang, Chengwei Li, Yanan Wu, Hongyun Chuan, Shaohui Song, Yun Xie, Qi Zhu, Qianqian Chen, Fei Tong, Runfang Zhang, Guangbo Yuan, Xiaoyan Wu, Jian Zhou and Guoyang Liao
Int. J. Mol. Sci. 2025, 26(13), 6536; https://doi.org/10.3390/ijms26136536 - 7 Jul 2025
Viewed by 526
Abstract
Mycoplasma pneumoniae, a cell wall-deficient pathogen, primarily affects children and adolescents, causing Mycoplasma pneumoniae pneumonia (MPP). Following the relaxation of non-pharmaceutical interventions (NPIs) post COVID-19, there has been a global increase in MPP cases and macrolide-resistant strains. Vaccination against M. pneumoniae is [...] Read more.
Mycoplasma pneumoniae, a cell wall-deficient pathogen, primarily affects children and adolescents, causing Mycoplasma pneumoniae pneumonia (MPP). Following the relaxation of non-pharmaceutical interventions (NPIs) post COVID-19, there has been a global increase in MPP cases and macrolide-resistant strains. Vaccination against M. pneumoniae is being explored as a promising approach to reduce infections, limit antibiotic misuse, and prevent the emergence of drug-resistant variants. We developed an mRNA vaccine, mRNA-SP+P1, incorporating a eukaryotic signal peptide (tissue-type plasminogen activator signal peptide) fused to the C-terminal region of the P1 protein. Targeting amino acids 1288 to 1518 of the P1 protein, the vaccine was administered intramuscularly to BALB/c mice in a three-dose regimen. To evaluate immunogenicity, we quantified anti-P1 IgG antibody titers using enzyme-linked immunosorbent assays (ELISAs) and assessed cellular immune responses by analyzing effector memory T cell populations using flow cytometry. We also tested the functional activity of vaccine-induced sera for their ability to inhibit adhesion of the ATCC M129 strain to KMB17 cells. The vaccine’s protective efficacy was assessed against the ATCC M129 strain and its cross-protection against the ST3-resistant strain. Transcriptomic analysis was conducted to investigate gene expression changes in peripheral blood, aiming to uncover mechanisms of immune modulation. The mRNA-SP+P1 vaccine induces P1 protein-specific IgG antibodies and an effector memory T-cell response in BALB/c mice. Adhesion inhibition assays demonstrated that serum from vaccinated mice attenuatesthe adhesion ability of ATCC M129 to KMB17 cells. Furthermore, three doses of the vaccine confer significant and long-lasting, though partial, protection against the ATCC M129 strain and partial cross-protection against the ST3 drug-resistant strain. Transcriptome analysis revealed significant gene expression changes in peripheral blood, confirming the vaccine’s capacity to elicit an immune response from the molecular level. Our results indicate that the mRNA-SP+P1 vaccine appears to be an effective vaccine candidate against the prevalence of Mycoplasma pneumoniae. Full article
(This article belongs to the Section Molecular Immunology)
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18 pages, 3219 KiB  
Article
Mobilome of Environmental Isolates of Clostridioides difficile
by Khald Blau and Claudia Gallert
Antibiotics 2025, 14(7), 678; https://doi.org/10.3390/antibiotics14070678 - 4 Jul 2025
Viewed by 432
Abstract
Background/Objectives: Clostridioides difficile is a “One Health” pathogen and a cause of antibiotics-associated diarrhea and pseudomembranous colitis. Mobile genetic elements (MGEs) have been documented in the genomes of clinical C. difficile strains; however, the presence of MGEs in environmental strains remains poorly characterized. [...] Read more.
Background/Objectives: Clostridioides difficile is a “One Health” pathogen and a cause of antibiotics-associated diarrhea and pseudomembranous colitis. Mobile genetic elements (MGEs) have been documented in the genomes of clinical C. difficile strains; however, the presence of MGEs in environmental strains remains poorly characterized. Thus, the present study was conducted with the objective of identifying the prevalence of MGEs, including mobilizable transposons (MTns), conjugative transposons (CTns), plasmids, and insertion sequences, in whole genome sequences (WGSs) of environmental C. difficile isolates. Methods: The analysis of MGEs was conducted using 166 WGSs obtained from C. difficile strains isolated from various environmental sources contaminated with feces. The MGEs were identified using bioinformatic tools. Results: A total of 48.2% (80/166) of the studied genomes were identified to harbor nine transposons, including Tn916, Tn6194-like, Tn5397, Tn6215, Tn4001, Tn6073, Tn6110, Tn6107, or Tn5801-like. The majority of MTns and CTns could be found within C. difficile sequence types ST11, ST3, and ST35. The results demonstrated close genetic relatedness among the studied genomes, the array of antimicrobial resistance (AMR) genes, such as tetM, ermB, and aac(6′)-aph(2″), and the presence of CTns. Furthermore, the analysis revealed that 24.7% (41/166) of the genome sequences of isolates were associated with various predominant plasmid groups, including pCD6, pCD-ECE4-6, pCD-WTSI1-4, pCDBI1, and pCd1_3, which belonged to 16 different sequence types. Furthermore, several plasmids were identified as harboring the prophage phiCDHM19. Conclusions: The results of the current study suggest that the identified plasmids are abundant and may encode functions that are relevant to C. difficile physiology. The genomes of C. difficile strains examined contain closely related CTns, suggesting that horizontal transfer of AMR is important in this species or other bacterial species. Further research is required to ascertain the effect of these genetic elements and their transferability on the biology of C. difficile. Full article
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16 pages, 301 KiB  
Article
Molecular Characterization of Vancomycin-Resistant Enterococcus spp. from Clinical Samples and Identification of a Novel Sequence Type in Mexico
by Raúl Alejandro Atriano Briano, Nallely S. Badillo-Larios, Perla Niño-Moreno, Luis Fernando Pérez-González and Edgar A. Turrubiartes-Martínez
Antibiotics 2025, 14(7), 663; https://doi.org/10.3390/antibiotics14070663 - 30 Jun 2025
Viewed by 459
Abstract
Background:Enterococcus spp. is the third leading cause of healthcare-associated infections in the American continent, often because of the virulence factors that protect the bacterium against host defenses and facilitate tissue attachment and genetic material exchange. In addition, vancomycin, considered a last-resort treatment, [...] Read more.
Background:Enterococcus spp. is the third leading cause of healthcare-associated infections in the American continent, often because of the virulence factors that protect the bacterium against host defenses and facilitate tissue attachment and genetic material exchange. In addition, vancomycin, considered a last-resort treatment, has shown reduced efficacy in Enterococcus spp. strains. However, the relationship between bacterial resistance and virulence factors remains unclear. This study intends to evaluate the prevalence of glycopeptide-resistant genotypes and virulence factors in Enterococcus spp. strains. Methods: Over six months, 159 Enterococcus spp. strains causing nosocomial infections were analyzed. Multiplex PCR was performed to identify species, glycopeptide-resistant genotypes, and 12 virulence factors. Results: The most abundant species identified were Enterococcus faecalis and E. faecium. Vancomycin resistance was observed in 10.7% of the isolates, and the vanA genotype was present in 47% of resistant samples. The main virulence factors detected were acm (54%), which is related to cell adhesion; gel E (66%), a metalloproteinase linked to tissue damage; and the sex pheromones cpd (64%) and ccf (84%), which are involved in horizontal gene transfer. A significant association was found between the prevalence of acm, ccf, and cpd in VRE isolates, indicating the potential dissemination of genes to emerging strains via horizontal gene transfer. In addition, a new E. faecium, which displayed five virulence factors and harbored the vanA sequence type, was identified and registered as ST2700. Conclusions:Enterococcus faecalis and E. faecium are clinically critical due to multidrug resistance and virulence factors like acm, which aids host colonization. Genes ccf and cpd promote resistance spread via horizontal transfer, while the emerging ST2700 strain requires urgent monitoring to curb its virulent, drug-resistant spread. Full article
24 pages, 4187 KiB  
Article
Biofilm Formation, Antibiotic Resistance, and Virulence Analysis of Human and Avian Origin Klebsiella pneumoniae from Jiangsu, China
by Yulu Xue, Fangyu Shi, Bangyue Zhou, Yi Shi, Wenqing Luo, Jing Zhu, Yang Yang, Sujuan Chen, Tao Qin, Daxin Peng and Yinyan Yin
Vet. Sci. 2025, 12(7), 628; https://doi.org/10.3390/vetsci12070628 - 30 Jun 2025
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Abstract
Klebsiella pneumoniae, a zoonotic pathogen of global concern, poses significant threats to both veterinary and public health. Here, a comparative study characterized 14 clinical isolates (7 avian-derived, 7 human-derived) from Jiangsu, China, through integrated genomic and phenotypic analyses. Firstly, multilocus sequence typing [...] Read more.
Klebsiella pneumoniae, a zoonotic pathogen of global concern, poses significant threats to both veterinary and public health. Here, a comparative study characterized 14 clinical isolates (7 avian-derived, 7 human-derived) from Jiangsu, China, through integrated genomic and phenotypic analyses. Firstly, multilocus sequence typing (MLST) revealed distinct epidemiological patterns: the same ST type in avian isolates was circulating between different species and different regions, whereas it was not found in human isolates. In addition, hypervirulent Klebsiella pneumoniae (hvKP) phenotypes confirmed by string test were exclusive to two human isolates (KP15, KP20). Secondly, biofilm detection demonstrated 78.6% (11/14) of isolates possessed biofilm-forming capacity, with cellulose but not curli as the predominant matrix component. Human-derived KP15 and KP20 had the strongest biofilm formation ability in all isolates. Antimicrobial susceptibility profiling identified serious multidrug resistance in both avian and human isolates. Virulence gene analysis revealed striking disparities, with human isolates harboring 10–20 virulence factors (median 15) versus 6–7 (median 6.5) in avian counterparts. Finally, functional pathogenesis assessments demonstrated human-derived strains exhibited stronger epithelial cell adhesion (2-fold higher) and invasion (1.97-fold higher) in Calu-3 cell models and paradoxically showed reduced macrophage phagocytosis (2.85-fold lower at 2 h) for immune escape. In vivo models confirmed dose-dependent mortality, with human isolates demonstrating higher lethality in both Galleria mellonella and mice. Virulence gene burden positively correlated with mortality outcomes. These findings delineate critical host adaptation differences in Klebsiella pneumoniae populations and provide empirical evidence for pathogen transmission dynamics at the human-animal interface. Full article
(This article belongs to the Special Issue Emerging Insights into Animal Pathogens and Mucosal Immunology)
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14 pages, 1152 KiB  
Article
Study of lug Operon, SCCmec Elements, Antimicrobial Resistance, MGEs, and STs of Staphylococcus lugdunensis Clinical Isolates Through Whole-Genome Sequencing
by Tein-Yao Chang, Lee-Chung Lin, Cheng-Yen Kao and Jang-Jih Lu
Int. J. Mol. Sci. 2025, 26(13), 6106; https://doi.org/10.3390/ijms26136106 - 25 Jun 2025
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Abstract
Staphylococcus lugdunensis is a coagulase-negative staphylococcus known for its significant pathogenic potential, often causing severe infections such as endocarditis and bacteremia, with virulence comparable to S. aureus. Despite general susceptibility to most antibiotics, the emergence of oxacillin-resistant strains is increasingly concerning. This [...] Read more.
Staphylococcus lugdunensis is a coagulase-negative staphylococcus known for its significant pathogenic potential, often causing severe infections such as endocarditis and bacteremia, with virulence comparable to S. aureus. Despite general susceptibility to most antibiotics, the emergence of oxacillin-resistant strains is increasingly concerning. This study conducted whole-genome sequencing on 20 S. lugdunensis isolates from Chang Gung Memorial Hospital to explore their genetic diversity, antimicrobial resistance mechanisms, and mobile genetic elements. The lugdunin biosynthetic operon, essential for antimicrobial peptide production, was present in multilocus sequence typing (MLST) types 1, 3, and 6 but absent in STs 4, 27, and 29. Additionally, IS256 insertion elements, ranging from 7 to 17 copies, were identified in four strains and linked to multidrug resistance. CRISPR-Cas systems varied across STs, with type III-A predominant in ST1 and ST6 and type IIC in ST4, ST27, and ST29; notably, ST3 lacked CRISPR systems, correlating with a higher diversity of SCCmec elements and an increased potential for horizontal gene transfer. Phage analysis revealed stable phage–host associations in ST1, ST6, and ST29, whereas ST4 displayed a varied prophage profile. Phenotypic resistance profiles generally aligned with genomic predictions, although discrepancies were observed for aminoglycosides and clindamycin. These findings highlight the complex genetic landscape and evolutionary dynamics of S. lugdunensis, emphasizing the need for genomic surveillance to inform clinical management and prevent the spread of resistant strains. Full article
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17 pages, 5896 KiB  
Article
Molecular Identification and Genotyping of Phytoplasmas Infecting Medicinal and Aromatic Plants in Northern Italy
by Camilla Barbieri, Abdelhameed Moussa, Alessandro Passera, Paola Casati, Piero Attilio Bianco and Fabio Quaglino
Microorganisms 2025, 13(7), 1444; https://doi.org/10.3390/microorganisms13071444 - 21 Jun 2025
Viewed by 370
Abstract
During field surveys carried out in 2021 at two farms in Lombardy (North Italy), leaf samples were collected from 113 plants (both symptomatic and asymptomatic) belonging to 18 medicinal and aromatic species. Amplification and nucleotide sequence analyses of the 16S rRNA gene revealed [...] Read more.
During field surveys carried out in 2021 at two farms in Lombardy (North Italy), leaf samples were collected from 113 plants (both symptomatic and asymptomatic) belonging to 18 medicinal and aromatic species. Amplification and nucleotide sequence analyses of the 16S rRNA gene revealed the presence of ‘Candidatus Phytoplasma solani’ (subgroup 16SrXII-A) in 69 plants (61% infection rate) belonging to 14 of the 18 examined species. Among the 14 infected species, only Nepeta cataria L. exhibited symptoms including leaf and stem reddening. Molecular typing analyses showed that ‘Ca. P. solani’ strains identified in this study constitute a genetically homogeneous population, carrying the stamp gene sequence variant St5 and the new vmp1 gene sequence variant Vm93. Phylogenetic analyses showed that ‘Ca. P. solani’ strain St5/Vm93 belongs to the cluster b-II, associated with the bindweed-related pathosystem. In silico-translated Vmp1 protein sequence alignment suggested that ‘Ca. P. solani’ strain St5/Vm93 could be generated by recombination events between ‘Ca. P. solani’ strains co-infecting the same host. The results suggested future research investigating the diffusion and the ecology of ‘Ca. P. solani’ strain St5/Vm93 in agroecosystems (including other crops), and its effect on the composition of biologically active compounds in aromatic and medicinal plants. Full article
(This article belongs to the Special Issue Phytoplasmas and Phytoplasma Diseases)
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