Genomics and Systems Biology Perspectives in Bacterial Pathogenesis and Antimicrobial Resistance

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

Deadline for manuscript submissions: closed (31 August 2022) | Viewed by 7926

Special Issue Editors


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Guest Editor
Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
Interests: emerging infectious diseases; bacterial pathogenesis; antimicrobial resistance

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Guest Editor
Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, China
Interests: host specificity; metagenomics; microbial genomics; molecular epidemiology; strain typing
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Special Issue Information

Dear Colleagues,

Given the increasing prevalence of antimicrobial resistance, bacterial infectious disease remains a severe threat to human health. Combat against bacterial infectious disease requires extensive knowledge of bacterial pathogenicity and antimicrobial resistance. The last decade has witnessed advances in genome sequencing, accompanied by the development of the related fields of genomics and systems biology, which has greatly facilitated bacterial research.

This Special Issue encourages the submission of original research, perspectives, and (mini)reviews that focus on the exploration of the mechanisms of bacterial pathogenesis and antimicrobial resistance at the whole genome level. Topics related to genome-based pathogen surveillance and epidemiological studies are also welcome.

Prof. Dr. Cheng-Hsun Chiu
Dr. Ye Feng
Guest Editors

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Keywords

  • bacterial pathogenesis
  • antimicrobial resistance
  • genomics

Published Papers (4 papers)

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Research

12 pages, 4127 KiB  
Article
Genomic Characteristics and Phylogenetic Analyses of a Multiple Drug-Resistant Klebsiella pneumoniae Harboring Plasmid-Mediated MCR-1 Isolated from Tai’an City, China
by Qinqin Liu, Zhiyun Guo, Gang Zhu, Ning Li, Guanchen Bai and Meijie Jiang
Pathogens 2023, 12(2), 221; https://doi.org/10.3390/pathogens12020221 - 31 Jan 2023
Cited by 1 | Viewed by 1653
Abstract
Klebsiella pneumoniae is a clinically common opportunistic pathogen that causes pneumonia and upper respiratory tract infection in humans as well as community-and hospital-acquired infections, posing significant threats to public health. Moreover, the insertion of a plasmid carrying the mobile colistin resistance (MCR) genes [...] Read more.
Klebsiella pneumoniae is a clinically common opportunistic pathogen that causes pneumonia and upper respiratory tract infection in humans as well as community-and hospital-acquired infections, posing significant threats to public health. Moreover, the insertion of a plasmid carrying the mobile colistin resistance (MCR) genes brings obstacles to the clinical treatment of K. pneumoniae infection. In this study, a strain of colistin-resistant K. pneumoniae (CRKP) was isolated from sputum samples of a patient who was admitted to a tertiary hospital in Tai’an city, China, and tested for drug sensitivity. The results showed that KPTA-2108 was multidrug-resistant (MDR), being resistant to 21 of 26 selected antibiotics, such as cefazolin, amikacin, tigecycline and colistin but sensitive to carbapenems via antibiotic resistance assays. The chromosome and plasmid sequences of the isolated strain KPTA-2108 were obtained using whole-genome sequencing technology and then were analyzed deeply using bioinformatics methods. The whole-genome sequencing analysis showed that the length of KPTA-2108 was 5,306,347 bp and carried four plasmids, pMJ4-1, pMJ4-2, pMJ4-3, and pMJ4-4-MCR. The plasmid pMJ4-4-MCR contained 30,124 bp and was found to be an IncX4 type. It was the smallest plasmid in the KPTA-2108 strain and carried only one resistance gene MCR-1. Successful conjugation tests demonstrated that pMJ4-4-MCR carrying MCR-1 could be horizontally transmitted through conjugation between bacteria. In conclusion, the acquisition and genome-wide characterization of a clinical MDR strain of CRKP may provide a scientific basis for the treatment of K. pneumoniae infection and epidemiological data for the surveillance of CRKP. Full article
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9 pages, 685 KiB  
Article
Molecular Characterization of Methicillin-Sensitive Staphylococcus aureus from the Intestinal Tracts of Adult Patients in China
by Yang Li, Yuanyue Tang, Zhongyi Jiang, Zhenyu Wang, Qiuchun Li and Xinan Jiao
Pathogens 2022, 11(9), 978; https://doi.org/10.3390/pathogens11090978 - 26 Aug 2022
Cited by 4 | Viewed by 1386
Abstract
Intestinal infections caused by methicillin-sensitive Staphylococcus aureus (MSSA) have posed a great challenge for clinical treatments. In recent years, the intestinal carriage rates of MSSA have risen steadily in hospital settings in China. However, the epidemiology and molecular characteristics of MSSA from the [...] Read more.
Intestinal infections caused by methicillin-sensitive Staphylococcus aureus (MSSA) have posed a great challenge for clinical treatments. In recent years, the intestinal carriage rates of MSSA have risen steadily in hospital settings in China. However, the epidemiology and molecular characteristics of MSSA from the intestinal tracts of Chinese adult patients remain unknown. In the present study, a total of 80 S. aureus isolates, including 64 MSSA and 16 methicillin-resistant Staphylococcus aureus (MRSA), were recovered from 466 fecal swabs in adult patients between 2019 and 2021 in China. The MSSA isolates exhibited high resistance to penicillin (92.2%) and erythromycin (45.3%). In addition, a higher proportion of MSSA isolates (14.1%) were multidrug-resistant (MDR) strains than that of MRSA isolates (1.3%). Among the 64 MSSA isolates, we identified 17 MLST types, of which ST398 and ST15 were the most predominant types. The most frequently detected resistance genes were blaZ (87.5%) and erm(C) (21.9%). The hemolysin genes (hla, hld, hlgA, hlgB, hlgC) were detected in all the MSSA isolates, but the Panton–Valentine leucocidin (pvl) gene was identified in 1.7% of the MSSA isolates. Our findings indicated that the prevalence and antimicrobial resistance of intestinal MSSA was a serious concern among adult patients in China. Full article
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14 pages, 2104 KiB  
Article
Metagenomic Insights into Pathogenic Characterization of ST410 Acinetobacter nosocomialis Prevalent in China
by Liang Jing, Zhuofei Xu, Youping Zhang, Dayong Li, Yaqin Song, Hongjie Hu, Yuan Fang and Wei Zhu
Pathogens 2022, 11(8), 838; https://doi.org/10.3390/pathogens11080838 - 27 Jul 2022
Cited by 2 | Viewed by 1846
Abstract
Acinetobacter nosocomialis is a prevalent opportunistic pathogen that causes hospital-acquired infections. The increasing threats from A. nosocomialis infections have led to attention from the scientific and medical communities. Metagenomic next-generation sequencing (mNGS) was performed for an exudate specimen collected from an ICU patient [...] Read more.
Acinetobacter nosocomialis is a prevalent opportunistic pathogen that causes hospital-acquired infections. The increasing threats from A. nosocomialis infections have led to attention from the scientific and medical communities. Metagenomic next-generation sequencing (mNGS) was performed for an exudate specimen collected from an ICU patient with wound infection, followed by sepsis, in Tongji Hospital. Three assembly strategies were employed to recover the genome of A. nosocomialis in the metagenomic sample. Together with publicly available genomes of A. nosocomialis, the features of population genetics and molecular epidemiology were deeply analyzed. A draft genome was reconstructed for the metagenomic strain WHM01, derived from the ST410 A. nosocomialis dominating the microbial community, thereby prompting its highly pathogenic risk, which is associated with infection and persistence. The structure of the bacterial pangenome was characterized, including the 1862 core and 11,815 accessory genes present in the 157 strains. The genetic diversity of the genes coding for the 128 virulence factors assigned to 14 functional categories was uncovered in this nosocomial pathogen, such as the lipooligosaccharide, capsule, type IV pilus, and outer membrane proteins. Our work revealed genomic properties of ST410 A. nosocomialis, which is prevalent in China, and further highlighted that metagenomic surveillance may be a prospective application for evaluating the pathogenic characteristics of the nosocomial opportunistic pathogens. Full article
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9 pages, 439 KiB  
Article
Prevalence, Serotypes, and Antimicrobial Resistance Patterns of Non-Typhoid Salmonella in Food in Northern Taiwan
by Yi-Jung Chang, Chyi-Liang Chen, Hsin-Ping Yang and Cheng-Hsun Chiu
Pathogens 2022, 11(6), 705; https://doi.org/10.3390/pathogens11060705 - 18 Jun 2022
Cited by 10 | Viewed by 2189
Abstract
Salmonella is one of the most common bacteria causing food poisoning worldwide. We evaluated the prevalence, the serotypes, and the antimicrobial resistance (AMR) of Salmonella isolates from many kinds of food, particularly pork and chicken in retail, in Taiwan between January 2017 and [...] Read more.
Salmonella is one of the most common bacteria causing food poisoning worldwide. We evaluated the prevalence, the serotypes, and the antimicrobial resistance (AMR) of Salmonella isolates from many kinds of food, particularly pork and chicken in retail, in Taiwan between January 2017 and December 2019. The E-test was used to assess antimicrobial susceptibility and a polymerase chain reaction was performed for serotyping. A total of 459 different foods were investigated, and 117 Salmonella strains were isolated. Retail pork and chicken were the most common Salmonella-contaminated foods (64.1% and 29.1%, respectively). Of the 117 isolates, 23 serotypes were identified. The serotypes Derby (16.2%), Anatum (13.7%), and Agona (8.5%) were the most prevalent. The resistance rates to ciprofloxacin, ceftriaxone, and carbapenem were 41.9%, 11.1%, and 1.7%, respectively. The Derby and Anatum serotypes were prevalent in chicken and pork; the Anatum serotype had significantly higher ciprofloxacin and ceftriaxone resistance rates and was highly prevalent in 2017 and 2018. Multi-locus sequence typing analysis revealed that the 58 randomly chosen Salmonella isolates belonged to 18 sequence types (STs). ST64 (Anatum, 16 out of 58, 27.6%) was the most common, followed by ST321 (Muenster, 6/58, 10.3%), ST831 (Give, 5/58, 8.6%), ST155 (London, 4/58, 6.9%) and ST314 (Kentucky, 4/58, 6.9%). Multidrug-resistant Salmonella strains were remarkably observed in the serotypes Anatum (ST64) and Goldcoast (ST358). This study revealed that retail pork was commonly contaminated with antimicrobial-resistant Salmonella. Thus, periodic investigations of Salmonella serotypes and AMR are needed. Full article
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