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Antibiotics
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Pathogenic Bacteria: Genomics, Virulence Factors, and Antibiotic Resistance
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Pathogenic Bacteria: Genomics, Virulence Factors, and Antibiotic Resistance

A special issue of Antibiotics (ISSN 2079-6382). This special issue belongs to the section "Mechanism and Evolution of Antibiotic Resistance".

Deadline for manuscript submissions: closed (31 January 2023) | Viewed by 10261

Special Issue Editor

Prof. Dr. Yunsong Yu

E-Mail Website
Guest Editor
Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310052, China
Interests: resistant mechanism of multi-drug resistant bacteria; molecular epidemiology of multi-drug resistance; diagnosis of infectious diseases

Special Issue Information

Dear Colleagues,

Pathogenic bacteria induce various diseases, such as intestinal infection, urinary tract infection, pneumonia, and even systemic infection, which cause significant harm to human health. Without effective control, bacterial infection will become the most important cause of death worldwide. Effective treatment and prevention of bacterial infections are essential to human health, and scientific research is the foundation of our defense against bacterial infection. In recent years, research on pathogenic bacteria has mainly included investigating bacterial drug resistance, bacterial virulence, and bacterial genomics in various circumstances. Clinical treatment and drug development depend on the mechanism studies of bacterial drug resistance and the function of their virulence factors. Along with developing the whole-genome sequencing technique, bacterial genomics studies significantly benefit pathogenic bacteria investigations. Overall, this Special Issue of Antibiotics aims to highlight recent findings in our knowledge of pathogenic bacteria studies, including genomics, virulence factors, and antibiotic resistance, and contributors are encouraged to provide original research papers or reviews in the related fields.

Prof. Dr. Yunsong Yu
Guest Editor

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Keywords

  • pathogenic bacteria
  • drug resistance
  • virulence
  • genomics

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Published Papers (4 papers)

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Research

13 pages, 1982 KiB  
Article
Emergence and Evolution of OXA-23-Producing ST46Pas-ST462Oxf-KL28-OCL1 Carbapenem-Resistant Acinetobacter baumannii Mediated by a Novel ISAba1-Based Tn7534 Transposon
by Haiyang Liu, Xiaochen Liu, Jintao He, Linghong Zhang, Feng Zhao, Zhihui Zhou, Xiaoting Hua and Yunsong Yu
Antibiotics 2023, 12(2), 396; https://doi.org/10.3390/antibiotics12020396 - 16 Feb 2023
Cited by 2 | Viewed by 1998
Abstract
Carbapenem-resistant Acinetobacter baumannii (CRAB) isolates of global clone 1 (GC1) and global clone 2 (GC2) have been widely reported. Nevertheless, non-GC1 and non-GC2 CRAB strains have been studied less. In particular, no reports concerning sequence type 46 (ST46Pas) CRAB strains have [...] Read more.
Carbapenem-resistant Acinetobacter baumannii (CRAB) isolates of global clone 1 (GC1) and global clone 2 (GC2) have been widely reported. Nevertheless, non-GC1 and non-GC2 CRAB strains have been studied less. In particular, no reports concerning sequence type 46 (ST46Pas) CRAB strains have been described thus far. In this work, the genomic features and possible evolution mechanism of ST46Pas OXA-23-producing CRAB isolates from clinical specimens are reported for the first time. Antimicrobial susceptibility testing of three ST46Pas strains revealed identical resistance profiles (resistance to imipenem, meropenem, ciprofloxacin and the combination of cefoperazone/sulbactam at a 2:1 ratio). They were found to belong to ST46Pas and ST462Oxf with capsular polysaccharide 28 (KL28) and lipooligosaccharide 1 (OCL1), respectively. Whole-genome sequencing (WGS) revealed that all contained one copy of chromosomal blaOXA-23, which was located in a novel ISAba1-based Tn7534 composite transposon. In particular, another copy of the Tn7534 composite transposon was identified in an Hgz_103-type plasmid with 9 bp target site duplications (TSDs, ACAACATGC) in the A. baumannii ZHOU strain. As the strains originated from two neighboring intensive care units (ICUs), ST46Pas OXA-23-producing CRAB strains may have evolved via transposition events or a pdif module. Based on the GenBank database, ST46Pas strains were collected from various sources; however, most were collected in Hangzhou (China) from 2014 to 2021. Pan-genome analysis revealed 3276 core genes, 0 soft-core genes, 768 shell genes and 443 cloud genes shared among all ST46Pas strains. In conclusion, the emergence of ST46Pas CRAB strains might present a new threat to healthcare settings; therefore, effective surveillance is required to prevent further dissemination. Full article
(This article belongs to the Special Issue Pathogenic Bacteria: Genomics, Virulence Factors, and Antibiotic Resistance)
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16 pages, 4191 KiB  
Article
Pathogenicity Islands in Uropathogenic Escherichia coli Clinical Isolate of the Globally Disseminated O25:H4-ST131 Pandemic Clonal Lineage: First Report from Egypt
by Azza S. Zakaria, Eva A. Edward and Nelly M. Mohamed
Antibiotics 2022, 11(11), 1620; https://doi.org/10.3390/antibiotics11111620 - 13 Nov 2022
Cited by 5 | Viewed by 2207
Abstract
Uropathogenic Escherichia coli (UPEC) is the main etiological agent of urinary tract infections (UTIs). The pathogenesis of UTIs relies upon UPEC’s acquisition of virulence determinants that are commonly inserted into large chromosomal blocks which are termed ‘pathogenicity islands’ (PAIs). In this study, we [...] Read more.
Uropathogenic Escherichia coli (UPEC) is the main etiological agent of urinary tract infections (UTIs). The pathogenesis of UTIs relies upon UPEC’s acquisition of virulence determinants that are commonly inserted into large chromosomal blocks which are termed ‘pathogenicity islands’ (PAIs). In this study, we investigated the virulence-associated genes embedded in the chromosome of a UPEC Egyptian strain, EC14142. Additionally, we present a detailed characterization of the PAIs in the EGY_EC14142 chromosome. The isolate displayed a multidrug-resistant phenotype, and whole genome sequencing indicated that it belonged to the globally disseminated O25:H4-ST131 pandemic lineage and the H30-Rx clade. EGY_EC14142 carried genes that are responsible for resistance to aminoglycosides, fluoroquinolones, extended-spectrum β-lactams, macrolides, folate pathway antagonists, and tetracyclines. It encoded five PAIs with a high similarity to PAI II536, PAI IV536, PAI V536, PAI-536-icd, and PAIusp. The genome analysis of EGY_EC14142 with other closely related UPEC strains revealed that they have a high nucleotide sequence identity. The constructed maximum-likelihood phylogenetic tree showed the close clonality of EGY_EC14142 with the previously published ST131 UPEC international isolates, thus endorsing the broad geographical distribution of this clone. This is the first report characterizing PAIs in a UPEC Egyptian strain belonging to the globally disseminated pandemic clone O25:H4-ST131. Full article
(This article belongs to the Special Issue Pathogenic Bacteria: Genomics, Virulence Factors, and Antibiotic Resistance)
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9 pages, 1244 KiB  
Article
The Genetic Characteristics and Carbapenem Resistance Mechanism of ST307 Klebsiella pneumoniae Coharbouring blaCMY-6, blaOXA-48, and a Truncated blaNDM-1
by Qiucheng Shi, Xinhong Han, Qin Huang, Yan Meng, Ping Zhang, Zhengan Wang, Huangdu Hu, Yan Jiang, Xiaoxing Du and Yunsong Yu
Antibiotics 2022, 11(11), 1616; https://doi.org/10.3390/antibiotics11111616 - 13 Nov 2022
Cited by 2 | Viewed by 2076
Abstract
Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a common nosocomial pathogen causing severe infectious diseases, and ST307 CRKP is an emerging clone. In this study, we collected five ST307 CRKP isolates, evaluated their antimicrobial susceptibility using microbroth dilution, and their clonality and population structure by [...] Read more.
Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a common nosocomial pathogen causing severe infectious diseases, and ST307 CRKP is an emerging clone. In this study, we collected five ST307 CRKP isolates, evaluated their antimicrobial susceptibility using microbroth dilution, and their clonality and population structure by PFGE, cgMLST, and SNP-based phylogenetic analysis. Then, the genome characteristics, such as antimicrobial resistance genes and plasmid profiles, were studied by subsequent genomic analysis. The plasmid transfer ability was evaluated by conjugation, and the carbapenem resistance mechanism was elucidated by gene cloning. The results showed that all five ST307 CRKP isolates harboured blaCMY-6, blaOXA-48, and blaNDM-1; however, the end of the blaNDM-1 signal peptide was interrupted and truncated by an IS10 element, resulting in the deactivation of carbapenemase. The ST307 isolates were closely related, and belonged to the globally disseminated clade. blaOXA-48 and blaNDM-1 were located on the different mobilisable IncL/M- and IncA/C2-type plasmids, respectively, and either the pOXA-48 or pNDM-1 transconjugants were ertapenem resistant. Gene cloning showed that blaCMY-6 could elevate the MICs of carbapenems up to 64-fold and was located on the same plasmid as blaNDM-1. In summary, ST307 is a high-risk clone type, and its prevalence should be given additional attention. Full article
(This article belongs to the Special Issue Pathogenic Bacteria: Genomics, Virulence Factors, and Antibiotic Resistance)
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13 pages, 2206 KiB  
Article
New Insights into Listeria monocytogenes Antimicrobial Resistance, Virulence Attributes and Their Prospective Correlation
by Mahmoud E. Elsayed, Marwa I. Abd El-Hamid, Attia El-Gedawy, Mahmoud M. Bendary, Reham M. ELTarabili, Majid Alhomrani, Abdulhakeem S. Alamri, Saleh A. Alghamdi, Marwa Arnout, Dalal N. Binjawhar, Mohammad M. Al-Sanea and Amira I. Abousaty
Antibiotics 2022, 11(10), 1447; https://doi.org/10.3390/antibiotics11101447 - 21 Oct 2022
Cited by 9 | Viewed by 3220
Abstract
Listeriosis is one of the most common foodborne diseases caused by Listeria monocytogenes (L. monocytogenes). A poor prognosis has been recorded for the invasive listeriosis, especially neurolisteriosis. In several countries throughout the world, foodborne infections with L. monocytogenes exceeded the legal [...] Read more.
Listeriosis is one of the most common foodborne diseases caused by Listeria monocytogenes (L. monocytogenes). A poor prognosis has been recorded for the invasive listeriosis, especially neurolisteriosis. In several countries throughout the world, foodborne infections with L. monocytogenes exceeded the legal safety limits in animal sourced foods. Therefore, we decided to investigate the variability, virulence and antimicrobial resistance profiles of this pathogen. Both phenotypic and genotypic methods were used for identifying L. monocytogenes isolates and confirming their virulence profiles. The antimicrobial resistances and their correlation analysis with the existence of virulence genes were detected. Additionally, sequencing and phylogenetic analysis based on L. monocytogenes inlA and inlB genes were undertaken. The prevalence rate (11.9%) and the resistance profiles of L. monocytogenes were shocking. The multi-drug resistance (MDR) phenotypes were common among our isolates (64.9%). Fortunately, the resistance phenotypes were always associated with low virulence arrays and the MDR strains possessed low virulence fitness. Herein, the high genotypic and phenotypic diversity of L. monocytogenes isolates and their weak clonality and adaptability highlighted the difficulty in controlling and managing this pathogen. Therefore, it is important to add more restriction guidelines from national authorities on the consumption of ready to eat foods. Full article
(This article belongs to the Special Issue Pathogenic Bacteria: Genomics, Virulence Factors, and Antibiotic Resistance)
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