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Transmission of Antibiotic Resistant Bacteria and Genes: Unveiling the Jigsaw...
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Transmission of Antibiotic Resistant Bacteria and Genes: Unveiling the Jigsaw Pieces of a One Health Problem

A special issue of Pathogens (ISSN 2076-0817).

Deadline for manuscript submissions: closed (31 January 2020) | Viewed by 28977

Special Issue Editors

Dr. Ana R. Freitas

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Guest Editor
1. TOXRUN—Toxicology Research Unit, University Institute of Health Sciences, CESPU, CRL, 4585-116 Gandra, Portugal
2. UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, REQUIMTE Faculty of Pharmacy, University of Porto, Porto, Portugal
Interests: antimicrobial resistance and infectious diseases; molecular and genomic epidemiology of bacterial pathogens under a one health approach; forensic microbiology
Special Issues, Collections and Topics in MDPI journals
Dr. Carla Novais

E-Mail Website
Guest Editor
UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, REQUIMTE Faculty of Pharmacy, University of Porto. Porto, Portugal
Interests: infectious diseases; bacterial molecular and genomic epidemiology; eco-evolution of antibiotic resistance and biocides/metal tolerance within a one health perspective (clones and mobile genetic elements)
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The evolution of antibiotic resistance among bacterial pathogens is a complex and multifactorial process requiring urgent concerted global efforts. A One Health approach integrating human, animal, and environmental surveillance data is crucial to counteract the spread of multidrug-resistant pathogens and develop efficient control strategies. To better understand the dynamics influencing the selection and transmission of resistance, this Special Issue aims to bring together research studies related to the transmission of antibiotic-resistant (ABR) bacterial pathogens within and between different hosts and environments; the impact of emergent clones and mobile genetic elements in ABR persistence and dissemination; or focusing on different drivers promoting ABR transmission. Papers suggesting strategies to limit the transmission of antibiotic-resistant bacteria and genes are also welcome.

This issue intends to enlarge the available literature regarding the transmission of multidrug-resistant bacterial pathogens in recent collections from both clinical and non-clinical contexts.

Dr. Ana R. Freitas
Asst. Prof. Carla Novais
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. Pathogens 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 2700 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

  • Transmission of bacterial pathogens
  • Antibiotic Resistance surveillance & epidemiology
  • Virulence & Biofilm production in antibiotic-resistant bacteria
  • Clones and mobile genetic elements promoting transmission of antibiotic resistance
  • Genomics and Bioinformatic Analysis
  • Genetics and Evolution
  • Infection prevention and control
  • One Health

Published Papers (6 papers)

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Editorial

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4 pages, 185 KiB  
Editorial
Transmission of Antibiotic Resistant Bacteria and Genes: Unveiling the Jigsaw Pieces of a One Health Problem
by Carla Novais and Ana R. Freitas
Pathogens 2020, 9(6), 497; https://doi.org/10.3390/pathogens9060497 - 22 Jun 2020
Cited by 7 | Viewed by 2205
Abstract
Antimicrobial Resistance is one of the major Global Health challenges of the twenty-first century, and one of the World Health Organization’s (WHO) top ten global health threats. The evolution of antibiotic resistance among bacterial pathogens requires urgent concerted global efforts under a One [...] Read more.
Antimicrobial Resistance is one of the major Global Health challenges of the twenty-first century, and one of the World Health Organization’s (WHO) top ten global health threats. The evolution of antibiotic resistance among bacterial pathogens requires urgent concerted global efforts under a One Health approach integrating human, animal, and environmental surveillance data. This is crucial to develop efficient control strategies and counteract the spread of multidrug-resistant pathogens. The studies in this Special Issue have evidenced the hidden role of less common species, unusual clones or unexplored niches in the dissemination of antimicrobial resistance between different hosts. They reinforce the need for large-scale surveillance studies tracing and tracking both antibiotic resistance and metal tolerance in different bacterial species. Full article
(This article belongs to the Special Issue Transmission of Antibiotic Resistant Bacteria and Genes: Unveiling the Jigsaw Pieces of a One Health Problem)

Research

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11 pages, 1516 KiB  
Article
Detection of β-Lactamase-Producing Enterococcus faecalis and Vancomycin-Resistant Enterococcus faecium Isolates in Human Invasive Infections in the Public Hospital of Tandil, Argentina
by Celia M. Schell, Ana P. Tedim, Mercedes Rodríguez-Baños, Mónica D. Sparo, Sabina Lissarrague, Juan A. Basualdo and Teresa M. Coque
Pathogens 2020, 9(2), 142; https://doi.org/10.3390/pathogens9020142 - 20 Feb 2020
Cited by 8 | Viewed by 3659
Abstract
The study’s aim was to analyze the population structure of enterococci causing human invasive infections in a medium-sized Argentinian Hospital coincidental with a 5 year-period of increased recovery of antibiotic resistant enterococci (2010–2014). Species identification (biochemical testing/MALDI-TOF-MS), antimicrobial susceptibility (disk-diffusion) and clonal relatedness [...] Read more.
The study’s aim was to analyze the population structure of enterococci causing human invasive infections in a medium-sized Argentinian Hospital coincidental with a 5 year-period of increased recovery of antibiotic resistant enterococci (2010–2014). Species identification (biochemical testing/MALDI-TOF-MS), antimicrobial susceptibility (disk-diffusion) and clonal relatedness (PFGE/MLST/BAPS) were determined according to standard guidelines. β-lactamase production was determined by a nitrocefin test and confirmed by PCR/sequencing. The isolates were identified as Enterococcus faecalis and Enterococcus faecium at a 2:1 ratio. Most of the E. faecalis isolates, grouped in 25 PFGE-types (ST9/ST179/ST236/ST281/ST388/ST604/ST720), were resistant to high-levels (HLR) of gentamicin/streptomycin. A ST9 clone (bla+/HLR-gentamicin) was detected in patients of different wards during 2014. E. faecium isolates were grouped in 10 PFGE-types (ST25/ST18/ST19/ST52/ST792), with a low rate of ampicillin resistance. Five vancomycin-resistant E. faecium, three vanA (ST792/ST25) and two vanB (ST25) were detected. The ST25 clone carried either vanA or vanB. The recovery of a bla+-ST9-E. faecalis clone similar to that described in the late 1980s in Argentina suggests the possibility of a local hidden reservoir. These results reflect the relevance of local epidemiology in understanding the population structure of enterococci as well as the emergence and spread of antimicrobial resistance in predominant enterococcal clonal lineages. Full article
(This article belongs to the Special Issue Transmission of Antibiotic Resistant Bacteria and Genes: Unveiling the Jigsaw Pieces of a One Health Problem)
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16 pages, 3184 KiB  
Article
Essential Gene Clusters Involved in Copper Tolerance Identified in Acinetobacter baumannii Clinical and Environmental Isolates
by Rapee Thummeepak, Renuka Pooalai, Christian Harrison, Lucy Gannon, Aunchalee Thanwisai, Narisara Chantratita, Andrew D. Millard and Sutthirat Sitthisak
Pathogens 2020, 9(1), 60; https://doi.org/10.3390/pathogens9010060 - 15 Jan 2020
Cited by 19 | Viewed by 4096
Abstract
Copper is widely used as antimicrobial in agriculture and medicine. Copper tolerance mechanisms of pathogenic bacteria have been proven to be required for both copper tolerance and survival during bacterial infections. Here, we determined both copper-tolerant phenotype and genotype in A. baumannii originated [...] Read more.
Copper is widely used as antimicrobial in agriculture and medicine. Copper tolerance mechanisms of pathogenic bacteria have been proven to be required for both copper tolerance and survival during bacterial infections. Here, we determined both copper-tolerant phenotype and genotype in A. baumannii originated from clinical and environmental samples. Using copper susceptibility testing, copper-tolerant A. baumannii could be found in both clinical and environmental isolates. Genotypic study revealed that representative copper-related genes of the cluster A (cueR), B (pcoAB), and D (oprC) were detected in all isolates, while copRS of cluster C was detected in only copper-tolerant A. baumannii isolates. Moreover, we found that copper-tolerant phenotype was associated with amikacin resistance, while the presence of copRS was statistically associated with blaNDM-1. We chose the A. baumannii strain AB003 as a representative of copper-tolerant isolate to characterize the effect of copper treatment on external morphology as well as on genes responsible for copper tolerance. The morphological features and survival of A. baumannii AB003 were affected by its exposure to copper, while whole-genome sequencing and analysis showed that it carried fourteen copper-related genes located on four clusters, and cluster C of AB003 was found to be embedded on genomic island G08. Transcriptional analysis of fourteen copper-related genes identified in AB003 revealed that copper treatment induced the expressions of genes of clusters A, B, and D at the micromolar level, while genes of cluster C were over-expressed at the millimolar levels of copper. This study showed that both clinical and environmental A. baumannii isolates have the ability to tolerate copper and carried numerous copper tolerance determinants including intrinsic copper tolerance (clusters A, B, and D) and acquired copper tolerance (cluster C) that could respond to copper toxicity. Our evidence suggests that we need to reconsider the use of copper in hospitals and other medical environments to prevent the selection and spread of copper-tolerant organisms. Full article
(This article belongs to the Special Issue Transmission of Antibiotic Resistant Bacteria and Genes: Unveiling the Jigsaw Pieces of a One Health Problem)
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13 pages, 692 KiB  
Article
First Detection of Carbapenem-Resistant Escherichia fergusonii Strains Harbouring Beta-Lactamase Genes from Clinical Samples
by Tomilola Adesina, Obinna Nwinyi, Nandita De, Olayemi Akinnola and Emmanuel Omonigbehin
Pathogens 2019, 8(4), 164; https://doi.org/10.3390/pathogens8040164 - 25 Sep 2019
Cited by 18 | Viewed by 5386
Abstract
Recently discovered extraintestinal Escherichia fergusonii obtained from non-clinical samples has exhibited the potential for acquiring multiple beta-lactamase genes, just like many extraintestinal Escherichia coli strains. Albeit, they are often omitted or classified as E. coli. This study aimed to, therefore, identify carbapenem-resistant [...] Read more.
Recently discovered extraintestinal Escherichia fergusonii obtained from non-clinical samples has exhibited the potential for acquiring multiple beta-lactamase genes, just like many extraintestinal Escherichia coli strains. Albeit, they are often omitted or classified as E. coli. This study aimed to, therefore, identify carbapenem-resistant extended-spectrum beta-lactamase (ESBL) producing E. fergusonii isolates from clinical samples, determine their evolutionary relatedness using 16S rRNA sequencing analysis and screen for beta-lactamase genes. A total of 135 septic wound samples were obtained from patients on referral at a General Hospital in Lagos, Nigeria. For the phenotypic identification of isolates from culture-positive samples, morphological, and physiological tests were carried out. Identities of the isolates harbouring beta-lactamase genes were assigned to their genus strains using the 16S rRNA sequencing. The Kirby Bauer disc diffusion technique and double-disc synergy test were used to screen isolates for multidrug resistance and ESBL production. Carbapenem-resistant ESBL producing isolates were screened for beta-lactamase genes in a polymerase chain reaction. Three E. fergusonii isolates (CR11, CR35 and CR49) were obtained during this study. E. fergusonii strains were motile, non-lactose and non-sorbitol fermenting but positive for cellobiose and adonitol fermentation. The I6S rRNA assigned the phenotypically identified isolates to E. fergusonii species. All three isolates were multidrug-resistant, carbapenem-resistant and ESBL producers. Isolates CR11 and CR35 harboured cefotaximase (CTX-M) and temoniera (TEM) beta-lactamase genes while CR49 harboured sulfhydryl variable (SHV) beta-lactamase gene. We herein report the detection of multiple beta-lactamase genes in carbapenem-resistant ESBL producing E. fergusonii from clinical samples. Full article
(This article belongs to the Special Issue Transmission of Antibiotic Resistant Bacteria and Genes: Unveiling the Jigsaw Pieces of a One Health Problem)
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Review

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28 pages, 970 KiB  
Review
Non-typhoidal Salmonella in the Pig Production Chain: A Comprehensive Analysis of Its Impact on Human Health
by Joana Campos, Joana Mourão, Luísa Peixe and Patrícia Antunes
Pathogens 2019, 8(1), 19; https://doi.org/10.3390/pathogens8010019 - 29 Jan 2019
Cited by 94 | Viewed by 10609
Abstract
Salmonellosis remains one of the most frequent foodborne zoonosis, constituting a worldwide major public health concern. The most frequent sources of human infections are food products of animal origin, being pork meat one of the most relevant. Currently, particular pig food production well-adapted [...] Read more.
Salmonellosis remains one of the most frequent foodborne zoonosis, constituting a worldwide major public health concern. The most frequent sources of human infections are food products of animal origin, being pork meat one of the most relevant. Currently, particular pig food production well-adapted and persistent Salmonella enterica serotypes (e.g., Salmonella Typhimurium, Salmonella 1,4,[5],12:i:-, Salmonella Derby and Salmonella Rissen) are frequently reported associated with human infections in diverse industrialized countries. The dissemination of those clinically-relevant Salmonella serotypes/clones has been related to the intensification of pig production chain and to an increase in the international trade of pigs and pork meat. Those changes that occurred over the years along the food chain may act as food chain drivers leading to new problems and challenges, compromising the successful control of Salmonella. Among those, the emergence of antibiotic resistance in non-typhoidal Salmonella associated with antimicrobials use in the pig production chain is of special concern for public health. The transmission of pig-related multidrug-resistant Salmonella serotypes, clones and/or genetic elements carrying clinically-relevant antibiotic resistance genes, frequently associated with metal tolerance genes, from pigs and pork meat to humans, has been reported and highlights the contribution of different drivers to the antibiotic resistance burden. Gathered data strengthen the need for global mandatory interventions and strategies for effective Salmonella control and surveillance across the pig production chain. The purpose of this review was to provide an overview of the role of pig and pork meat in human salmonellosis at a global scale, highlighting the main factors contributing to the persistence and dissemination of clinically-relevant pig-related Salmonella serotypes and clones. Full article
(This article belongs to the Special Issue Transmission of Antibiotic Resistant Bacteria and Genes: Unveiling the Jigsaw Pieces of a One Health Problem)
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Other

5 pages, 401 KiB  
Letter
Acquired AmpC β-Lactamases among Enterobacteriaceae from Healthy Humans and Animals, Food, Aquatic and Trout Aquaculture Environments in Portugal
by Teresa Gonçalves Ribeiro, Ângela Novais, Elisabete Machado and Luísa Peixe
Pathogens 2020, 9(4), 273; https://doi.org/10.3390/pathogens9040273 - 09 Apr 2020
Cited by 8 | Viewed by 2141
Abstract
We aimed to investigate the occurrence of acquired AmpC β-lactamases (qAmpC), and characterize qAmpC-producing Enterobacteriaceae from different non-clinical environments in Portugal. We analysed 880 Enterobacteriaceae resistant to third-generation cephalosporins recovered from 632 non-clinical samples [healthy human and healthy animal (swine, chickens) faeces; uncooked [...] Read more.
We aimed to investigate the occurrence of acquired AmpC β-lactamases (qAmpC), and characterize qAmpC-producing Enterobacteriaceae from different non-clinical environments in Portugal. We analysed 880 Enterobacteriaceae resistant to third-generation cephalosporins recovered from 632 non-clinical samples [healthy human and healthy animal (swine, chickens) faeces; uncooked chicken carcasses; aquatic and trout aquaculture samples]. Bacterial and qAmpC identification, antibiotic susceptibility, clonal (PFGE, MLST) and plasmid (S1-/I-CeuI-PFGE, replicon typing, hybridization) analysis were performed using standard methods. The occurrence of qAmpC among Enterobacteriaceae from non-clinical origins was low (0.6%; n = 4/628 samples), corresponding to CMY-2-producing Escherichia coli from three healthy humans (HH) and one uncooked chicken carcass (UCC). We highlight a slight increase in CMY-2 human faecal carriage in the two periods sampled [1.0% in 2013–2014 versus 0% in 2001–2004], which is in accordance with the trend observed in other European countries. CMY-2-producing E. coli belonged to B22-ST4953 (n = 2, HH), A0-ST665 (n = 1, HH) or A1-ST48 (n = 1, UCC) clones. blaCMY-2 was identified in non-typeable and IncA/C2 plasmids. This study is one of the few providing an integrated evaluation of the qAmpC-producing Enterobacteriaceae occurrence, which was low, from a very large collection of different non-clinical origins. Further surveillance in contemporary collections can provide an integrated epidemiological information of potential shifts in reservoirs, transmission routes and mechanisms of dissemination of blaqAmpC in non-clinical settings. Full article
(This article belongs to the Special Issue Transmission of Antibiotic Resistant Bacteria and Genes: Unveiling the Jigsaw Pieces of a One Health Problem)
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