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Antibiotics
Special Issues
Genomic Analysis and AMR Detection in Pathogenic Bacteria
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Genomic Analysis and AMR Detection in Pathogenic Bacteria

A special issue of Antibiotics (ISSN 2079-6382). This special issue belongs to the section "Genetic and Biochemical Studies of Antibiotic Activity and Resistance".

Deadline for manuscript submissions: closed (31 December 2021) | Viewed by 10386

Special Issue Editors

Dr. Massimiliano Orsini

E-Mail Website
Guest Editor
Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Italy
Interests: Salmonella; genomics; bioinformatics
Dr. Carmen Losasso

E-Mail Website
Guest Editor
Laboratory of Microbial Ecology and Genomics, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Italy
Interests: microbial ecology; genomics; metagenomics

Special Issue Information

Dear Colleagues,

The investigation of bacterial genomes is challenging. This is particularly true for mechanisms behind antibiotic resistance mechanisms. Multidrug-resistant bacteria are an emergent global disease and a major public health problem. The increasing availability of NGS data has been providing new tools for the detection and typing of pathogens, including the investigation of the molecular basis of antibiotic resistance. This data availability opens up to new “in-silico” methods of analysis as functional genomics, GWAS, machine learning. These techniques have proven to be powerful methods to characterize bacterial features and to predict anti-microbial combinations. However, the performance of any in silico model depends on the quality of the input data. This Special Issue invites articles including, but not limited to, the following topics: functional genomics, methods and algorithms for genome analysis, including machine learning and systems biology approaches; characterization of mobile genetic elements, prophages, pseudogenes, and features conferring resistance to antimicrobials, disinfectants, biocides, chemical and physical stresses.

We are witnessing a dramatic increase in the number of bacterial pathogens resistant to multiple antibacterial agents. The availability of large collections of genome scale data, together with new data analysis methods, has proven to be a powerful method to predict anti-microbial combinations

Dr. Massimiliano Orsini
Dr. Carmen Losasso
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Antibiotics is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2900 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • functional genomics
  • antibiotics resistance
  • virulence factors
  • machine learning
  • GWAS

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Published Papers (3 papers)

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Research

16 pages, 1725 KiB  
Article
High Carriage Rate of the Multiple Resistant Plasmids Harboring Quinolone Resistance Genes in Enterobacter spp. Isolated from Healthy Individuals
by Yongyan Long, Xin Lu, Xiansheng Ni, Jiaqi Liu, Mengyu Wang, Xu Li, Zhe Li, Haijian Zhou, Zhenpeng Li, Kui Wu, Wei Wang, Liya Yang, Jialiang Xu, Haiying Chen and Biao Kan
Antibiotics 2022, 11(1), 15; https://doi.org/10.3390/antibiotics11010015 - 23 Dec 2021
Cited by 5 | Viewed by 3074
Abstract
Antimicrobial-resistant bacteria causing intractable and even fatal infections are a major health concern. Resistant bacteria residing in the intestinal tract of healthy individuals present a silent threat because of frequent transmission via conjugation and transposition. Plasmids harboring quinolone resistance genes are increasingly detected [...] Read more.
Antimicrobial-resistant bacteria causing intractable and even fatal infections are a major health concern. Resistant bacteria residing in the intestinal tract of healthy individuals present a silent threat because of frequent transmission via conjugation and transposition. Plasmids harboring quinolone resistance genes are increasingly detected in clinical isolates worldwide. Here, we investigated the molecular epidemiology of plasmid-mediated quinolone resistance (PMQR) in Gram-negative bacteria from healthy service trade workers. From 157 rectal swab samples, 125 ciprofloxacin-resistant strains, including 112 Escherichia coli, 10 Klebsiella pneumoniae, two Proteus mirabilis, and one Citrobacter braakii, were isolated. Multiplex PCR screening identified 39 strains harboring the PMQR genes (including 17 qnr,19 aac(6′)-Ib-cr, and 22 oqxA/oqxB). The genome and plasmid sequences of 39 and 31 strains, respectively, were obtained by short- and long-read sequencing. PMQR genes mainly resided in the IncFIB, IncFII, and IncR plasmids, and coexisted with 3–11 other resistance genes. The high PMQR gene carriage rate among Gram-negative bacteria isolated from healthy individuals suggests the high-frequency transmission of these genes via plasmids, along with other resistance genes. Thus, healthy individuals may spread antibiotic-resistant bacterial, highlighting the need for improved monitoring and control of the spread of antibiotic-resistant bacteria and genes in healthy individuals. Full article
(This article belongs to the Special Issue Genomic Analysis and AMR Detection in Pathogenic Bacteria)
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18 pages, 1265 KiB  
Article
Genetic Comparison of ESBL-Producing Escherichia coli from Workers and Pigs at Vietnamese Pig Farms
by Duong Thi Quy Truong, Yaovi Mahuton Gildas Hounmanou, Son Thi Thanh Dang, John Elmerdahl Olsen, Giang Thi Huong Truong, Nhat Thi Tran, Flemming Scheutz and Anders Dalsgaard
Antibiotics 2021, 10(10), 1165; https://doi.org/10.3390/antibiotics10101165 - 25 Sep 2021
Cited by 14 | Viewed by 3906
Abstract
We analyzed and compared genomes of Extended Spectrum Beta-Lactamase (ESBL)-producing Escherichia coli from pigs and pig farm workers at 116 farms in Vietnam. Analyses revealed the presence of blaCTX-M-55, blaCTX-M-27, blaCTX-M-15, blaCTX-M-14, blaCTX-M-3,  [...] Read more.
We analyzed and compared genomes of Extended Spectrum Beta-Lactamase (ESBL)-producing Escherichia coli from pigs and pig farm workers at 116 farms in Vietnam. Analyses revealed the presence of blaCTX-M-55, blaCTX-M-27, blaCTX-M-15, blaCTX-M-14, blaCTX-M-3, blaCTX-M-65, blaCTX-M-24, blaDHA-1, and blaCMY2 in both hosts. Most strains from pigs contained quinolones (qnr) and colistin resistance genes (mcr-1 and mcr-3). Isolates predominantly harbored more than one plasmid replicon and some harbored plasmid replicons on the same contigs as the ESBL genes. Five strains from farm workers of ST38 (2), ST69 (1), and ST1722 (2) were classified as either uropathogenic E. coli (UPECHM)/extraintestinal pathogenic E. coli (ExPECJJ) or UPECHM, and the remaining were genetically distinct commensals. A high heterogeneity was found among the ESBL-producing E. coli from pigs and workers, with most isolates belonging to unrelated phylogroups, serogroups, and sequence types with >4046 Single-Nucleotide Polymorphisms-(SNPs). In comparing the genomes of pig isolates to those from humans, it appeared that ESBL-producing E. coli in workers did not predominantly originate from pigs but were rather host-specific. Nevertheless, the occurrence of ESBL-producing E. coli carrying plasmid-mediated colistin and quinolone resistance genes in pigs could represent a potential source for horizontal transmission to humans through food rather than direct contact. Full article
(This article belongs to the Special Issue Genomic Analysis and AMR Detection in Pathogenic Bacteria)
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15 pages, 11327 KiB  
Article
Prevalence of Antibiotic-Resistant Escherichia coli Isolated from Swine Faeces and Lagoons in Bulgaria
by Lyudmila Dimitrova, Mila Kaleva, Maya M. Zaharieva, Christina Stoykova, Iva Tsvetkova, Maya Angelovska, Yana Ilieva, Vesselin Kussovski, Sevda Naydenska and Hristo Najdenski
Antibiotics 2021, 10(8), 940; https://doi.org/10.3390/antibiotics10080940 - 4 Aug 2021
Cited by 8 | Viewed by 2612
Abstract
Antimicrobial resistance (AMR) is a worldwide health problem affecting humans, animals, and the environment within the framework of the “One Health” concept. The aim of our study was to evaluate the prevalence of pathogenic strains of the species Escherichia coli (E. coli [...] Read more.
Antimicrobial resistance (AMR) is a worldwide health problem affecting humans, animals, and the environment within the framework of the “One Health” concept. The aim of our study was to evaluate the prevalence of pathogenic strains of the species Escherichia coli (E. coli), their AMR profile, and biofilm-forming potential. The isolated strains from three swine faeces and free lagoons (ISO 16654:2001/Amd 1:2017) were confirmed using Phoenix M50 and 16S rDNA PCR. The antibiotic sensitivity to 34 clinically applied antibiotics was determined by Phoenix M50 and the disc diffusion method, according to the protocols of the CLSI and EUCAST. We confirmed the presence of 16 E. coli isolates, of which 87.5% were multi-drug-resistant and 31.25% performed strong biofilms. The possibility for the carrying and transmission of antibiotic-resistance genes to quinolones (qnr), aminoglycosides (aac(3)), β-lactamase-producing plasmid genes ampC, and blaSHV/blaTEM was investigated. We confirmed the carrying of blaSHV/blaTEM in one and ampC in seven isolates. The strains were negative for the virulence genes (ETEC (LT, STa, and F4), EPEC (eae), and STEC/VTEC (stx and stx2all)). The results should contribute to the development of effective measures for limitation and control on the use of antibiotics, which is a key point in the WHO action plan. Full article
(This article belongs to the Special Issue Genomic Analysis and AMR Detection in Pathogenic Bacteria)
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