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Genetics of Antimicrobial Resistance
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Genetics of Antimicrobial Resistance

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Microbial Genetics and Genomics".

Deadline for manuscript submissions: closed (20 May 2021) | Viewed by 21350

Special Issue Editors

Dr. Avelino Álvarez-Ordoñez

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Guest Editor
Department of Food Hygiene and Technology and Institute of Food Science and Technology, University of León, León, Spain
Interests: food safety; foodborne pathogens; bacterial physiology; bacterial stress responses; ecology and biocontrol of microbial biofilms; antimicrobial resistance; food microbiome; novel technologies of food preservation
Special Issues, Collections and Topics in MDPI journals
Dr. José F. Cobo-Díaz

E-Mail Website
Guest Editor
Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, León, Spain
Interests: next generation sequencing; antimicrobial resistance; food safety; bioinformatics; foodborne pathogens
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Antimicrobial Resistance (AR) is an increased risk for human health, due to the intensive use of antimicrobial compounds on agricultural applications and livestock industries in recent decades. The spread of AR genes along the food chain is an important health risk factor that needs to be deeply studied. Moreover, recent studies on AR genes (ARGs) spread along wastewater or even coastal sea water samples have shown the prevalence of such genes in natural environments due to human activities, which can involve ecosystem disturbances.

Whole genome and metaganome sequencing technologies, including both next-generation sequencing (NGS) and software development for NGS data analysis, have notably increased the capacity to detect and study ARGs on isolated bacteria and environmental samples. These technologies also allow one to determine the genomic environment of such ARGs, including mobile element regions, favoring the execution of more accurate risk assessments. Furthermore, transcriptomic and metatranscriptomic approaches have allowed one to obtain a wider knowledge of the genetic regulation of AR on isolated bacteria. 

This Special Issue welcomes submissions on issues relating to the genetics of antimicrobial resistance in the food chain and the environment, including on topics such as comparative genomics, ARG detection on environmental samples, whole genome sequencing, whole metagenome sequencing, transcriptomics, and the characterization of genes involved in AR and its regulation.

All contributions to this Special Issue must be in line with the scope of the journal. Manuscripts discovered, during any stage of peer review process, to be outside of the scope may be transferred to a suitable section or field, or withdrawn from review.

With this background, we welcome researchers working on antimicrobial resistance across the world to contribute their high-quality original research manuscripts, critical reviews, and opinion articles covering all these aspects related to the genetics of antimicrobial resistance.

Dr. Avelino Álvarez-Ordoñez
Dr. José F. Cobo-Díaz
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. Genes 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 2600 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

  • Antimicrobial resistance
  • Whole-genome sequencing
  • Metagenomics
  • RNA-seq.

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Published Papers (5 papers)

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Research

15 pages, 755 KiB  
Article
Genomic Characterization of Fluoroquinolone-Resistant Thermophilic Campylobacter Strains Isolated from Layer Chicken Feces in Gangneung, South Korea by Whole-Genome Sequencing
by Noel Gahamanyi, Dae-Geun Song, Kye-Yoon Yoon, Leonard E. G. Mboera, Mecky I. Matee, Dieudonné Mutangana, Erick V. G. Komba, Cheol-Ho Pan and Raghavendra G. Amachawadi
Genes 2021, 12(8), 1131; https://doi.org/10.3390/genes12081131 - 25 Jul 2021
Cited by 4 | Viewed by 3779
Abstract
Thermophilic Campylobacter species of poultry origin have been associated with up to 80% of human campylobacteriosis cases. Layer chickens have received less attention as possible reservoirs of Campylobacter species. Initially, the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of two archived [...] Read more.
Thermophilic Campylobacter species of poultry origin have been associated with up to 80% of human campylobacteriosis cases. Layer chickens have received less attention as possible reservoirs of Campylobacter species. Initially, the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of two archived Campylobacter isolates (Campylobacter jejuni strain 200605 and Campylobacter coli strain 200606) from layer chickens to five antimicrobials (ciprofloxacin, nalidixic acid, erythromycin, tetracycline, and gentamicin) were determined using broth microdilution while the presence of selected antimicrobial resistance genes was performed by polymerase chain reaction (PCR) using specific primers. Whole-genome sequencing (WGS) was performed by the Illumina HiSeq X platform. The analysis involved antimicrobial resistance genes, virulome, multilocus sequence typing (MLST), and phylogeny. Both isolates were phenotypically resistant to ciprofloxacin (MIC: 32 vs. 32 µg/mL), nalidixic acid (MIC: 128 vs. 64 µg/mL), and tetracycline (MIC: 64 vs. 64 µg/mL), but sensitive to erythromycin (MIC: 1 vs. 2 µg/mL) and gentamicin (MIC: 0.25 vs. 1 µg/mL) for C. jejuni strain 200605 and C. coli strain 200606, respectively. WGS confirmed C257T mutation in the gyrA gene and the presence of cmeABC complex conferring resistance to FQs in both strains. Both strains also exhibited tet(O) genes associated with tetracycline resistance. Various virulence genes associated with motility, chemotaxis, and capsule formation were found in both isolates. However, the analysis of virulence genes showed that C. jejuni strain 200605 is more virulent than C. coli strain 200606. The MLST showed that C. jejuni strain 200605 belongs to sequence type ST-5229 while C. coli strain 200606 belongs to ST-5935, and both STs are less common. The phylogenetic analysis clustered C. jejuni strain 200605 along with other strains reported in Korea (CP028933 from chicken and CP014344 from human) while C. coli strain 200606 formed a separate cluster with C. coli (CP007181) from turkey. The WGS confirmed FQ-resistance in both strains and showed potential virulence of both strains. Further studies are recommended to understand the reasons behind the regional distribution (Korea, China, and Vietnam) of such rare STs. Full article
(This article belongs to the Special Issue Genetics of Antimicrobial Resistance)
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19 pages, 2706 KiB  
Article
Genomic Investigation of Carbapenem-Resistant Klebsiella pneumonia Colonization in an Intensive Care Unit in South Africa
by Osama Madni, Daniel G. Amoako, Akebe Luther King Abia, Joan Rout and Sabiha Yusuf Essack
Genes 2021, 12(7), 951; https://doi.org/10.3390/genes12070951 - 22 Jun 2021
Cited by 11 | Viewed by 3646
Abstract
The study investigated carbapenemase-producing Klebsiella pneumoniae (CPKP) isolates of patients in an intensive care unit (ICU) in a public hospital in the KwaZulu-Natal province, South Africa using whole-genome sequencing (WGS). Ninety-seven rectal swabs, collected from all consenting adult patients (n = [...] Read more.
The study investigated carbapenemase-producing Klebsiella pneumoniae (CPKP) isolates of patients in an intensive care unit (ICU) in a public hospital in the KwaZulu-Natal province, South Africa using whole-genome sequencing (WGS). Ninety-seven rectal swabs, collected from all consenting adult patients (n = 31) on days 1, 3, and 7 and then weekly, were screened for carbapenemase-production using Chrome-ID selective media. Antibiotic susceptibility was determined for the fourteen positive CPKP isolates obtained using the VITEK 2 automated system. All isolates (100%) were resistant to ertapenem and meropenem, and 71.4% (n = 10) were resistant to imipenem. All CPKP isolates were subjected to ERIC/PCR, and a sub-sample of isolates was selected for WGS based on their antibiograms and clonality. All sequenced isolates harbored the blaOXA-181 carbapenemase (100%) and co-carried other β-lactamase genes such as blaOXA-1, blaCTX-M-15, blaTEM-1B, and blaSHV-1. IncF, IncX3, and Col plasmid replicons groups and class I integrons (ln191 and ln27) were detected. All isolates belonged to the same sequence type ST307 and capsular serotypes (K102, O2v2). All the isolates carried the same virulence repertoire, reflecting the epidemiological relationship between isolates. blaOXA-181 was located on a multi-replicon plasmid similar to that of E. coli p010_B-OXA181, and isolates were aligned with several South African and international clades, demonstrating horizontal and vertical transboundary distribution. The findings suggest that blaOXA-181 producing K. pneumoniae is endemic in this ICU, colonizing the patients. CRE screening and enhanced infection prevention and control measures are urgently required. Full article
(This article belongs to the Special Issue Genetics of Antimicrobial Resistance)
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16 pages, 3968 KiB  
Article
In Silico Characterization of Toxin-Antitoxin Systems in Campylobacter Isolates Recovered from Food Sources and Sporadic Human Illness
by Bishoy Wadie, Mohamed A. Abdel-Fattah, Alshymaa Yousef, Shaimaa F. Mouftah, Mohamed Elhadidy and Tamer Z. Salem
Genes 2021, 12(1), 72; https://doi.org/10.3390/genes12010072 - 7 Jan 2021
Cited by 1 | Viewed by 4271
Abstract
Campylobacter spp. represents the most common cause of gastroenteritis worldwide with the potential to cause serious sequelae. The ability of Campylobacter to survive stressful environmental conditions has been directly linked with food-borne illness. Toxin-antitoxin (TA) modules play an important role as defense systems [...] Read more.
Campylobacter spp. represents the most common cause of gastroenteritis worldwide with the potential to cause serious sequelae. The ability of Campylobacter to survive stressful environmental conditions has been directly linked with food-borne illness. Toxin-antitoxin (TA) modules play an important role as defense systems against antimicrobial agents and are considered an invaluable strategy harnessed by bacterial pathogens to survive in stressful environments. Although TA modules have been extensively studied in model organisms such as Escherichia coli K12, the TA landscape in Campylobacter remains largely unexplored. Therefore, in this study, a comprehensive in silico screen of 111 Campylobacter (90 C.jejuni and 21 C.coli) isolates recovered from different food and clinical sources was performed. We identified 10 type II TA systems belonging to four TA families predicted in Campylobacter genomes. Furthermore, there was a significant association between the clonal population structure and distribution of TA modules; more specifically, most (12/13) of the Campylobacter isolates belonging to ST-21 isolates possess HicB-HicA TA modules. Finally, we observed a high degree of shared synteny among isolates bearing certain TA systems or even coexisting pairs of TA systems. Collectively, these findings provide useful insights about the distribution of TA modules in a heterogeneous pool of Campylobacter isolates from different sources, thus developing a better understanding regarding the mechanisms by which these pathogens survive stressful environmental conditions, which will further aid in the future designing of more targeted antimicrobials. Full article
(This article belongs to the Special Issue Genetics of Antimicrobial Resistance)
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13 pages, 3668 KiB  
Article
Long-Term Impact of Suppressive Antibiotic Therapy on Intestinal Microbiota
by Rosa Escudero-Sánchez, Manuel Ponce-Alonso, Hugo Barragán-Prada, María Isabel Morosini, Rafael Cantón, Javier Cobo and Rosa del Campo
Genes 2021, 12(1), 41; https://doi.org/10.3390/genes12010041 - 30 Dec 2020
Cited by 5 | Viewed by 3856
Abstract
The aim was to describe the safety of indefinite administration of antibiotics, the so-called suppressive antibiotic therapy (SAT) and to provide insight into their impact on gut microbiota. 17 patients with SAT were recruited, providing a fecal sample. Bacterial composition was determined by [...] Read more.
The aim was to describe the safety of indefinite administration of antibiotics, the so-called suppressive antibiotic therapy (SAT) and to provide insight into their impact on gut microbiota. 17 patients with SAT were recruited, providing a fecal sample. Bacterial composition was determined by 16S rDNA massive sequencing, and their viability was explored by PCR-DGGE with and without propidium monoazide. Presence of antibiotic multirresistant bacteria was explored through the culture of feces in selective media. High intra-individual variability in the genera distribution regardless of the antibiotic or antibiotic administration ingestion period, with few statistically significant differences detected by Bray-Curtis distance-based principle component analysis, permutational multivariate analysis of variance and linear discriminant analysis effect size analysis. However, the microbiota composition of patients treated with both beta-lactams and sulfonamides clustered by a heat map. Curiously, the detection of antibiotic resistant bacteria was almost anecdotic and CTX-M-15-producing E. coli were detected in two subjects. Our work demonstrates the overall clinical safety of SAT and the low rate of the selection of multidrug-resistant bacteria triggered by this therapy. We also describe the composition of intestinal microbiota under the indefinite use of antibiotics for the first time. Full article
(This article belongs to the Special Issue Genetics of Antimicrobial Resistance)
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17 pages, 1682 KiB  
Article
Genomic Characterization of Methicillin-Resistant Staphylococcus aureus (MRSA) by High-Throughput Sequencing in a Tertiary Care Hospital
by May Sherif Soliman, Noha Salah Soliman, Arwa Ramadan El-Manakhly, Shahira AbdelSalam ElBanna, Ramy Karam Aziz and Amani Ali El-Kholy
Genes 2020, 11(10), 1219; https://doi.org/10.3390/genes11101219 - 17 Oct 2020
Cited by 14 | Viewed by 4688
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) strains are associated with serious complications and poor clinical outcome. In Egypt, they contribute to more than 70% of S. aureus healthcare-associated infections. This study combined whole-genome sequencing, bioinformatics, and statistical analyses to identify the phylogeny, resistome, virulome and [...] Read more.
Methicillin-resistant Staphylococcus aureus (MRSA) strains are associated with serious complications and poor clinical outcome. In Egypt, they contribute to more than 70% of S. aureus healthcare-associated infections. This study combined whole-genome sequencing, bioinformatics, and statistical analyses to identify the phylogeny, resistome, virulome and potential genotype–phenotype–clinical correlation among 18 clinical isolates of MRSA in a tertiary hospital in Cairo, Egypt. The ST1535-V MRSA clone was the most frequently isolated (16.6%), followed by ST5-VI, ST1-V and ST239-III (11.1% each). SCCmec V, VI, IV and III types were detected at frequencies of 50%, 16.6%, 11.1% and 11.1%, respectively. None of the tested virulence genes were detected in all isolates, but they ranged in distribution from 1/18 to 17/18. The Panton–Valentine leukocidin (PVL)-encoding genes were detected in only four isolates and were enriched in isolates causing non-severe cases. Phylogenetic analysis revealed relatedness between three ST1535-Vs, two ST5-VIs, two ST239-IIIs and two ST1-Vs; however, only the two genetically related ST1-V isolates were epidemiologically linked. While disease outcome and source of infection had no correlation with a particular genotypic pattern, the sequence type was the most correlated factor with phylogeny and genotypic patterns, and a few genes were associated with non-severe cases. Full article
(This article belongs to the Special Issue Genetics of Antimicrobial Resistance)
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