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Antimicrobial Resistance and Virulence - 2nd Volume

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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 December 2021) | Viewed by 26789

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Dr. Manuela Oliveira

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Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, Universidade de Lisboa, Lisbon, Portugal
Interests: antimicrobial resistance; bacterial virulence; biofilms; genomics; infections pathogenesis; food safety
Special Issues, Collections and Topics in MDPI journals

Dr. Elisabete Silva

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CIISA – Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine of Lisbon, Lisboa, Portugal
Interests: animal reproduction; bacterial infections; host–bacterial interactions; molecular biology; genomics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

The worldwide dissemination of antimicrobial-resistant bacteria, particularly those resistant to last-resource antibiotics, is a common problem for which no immediate solution is foreseen. In 2017, the World Health Organization (WHO) published a list of antimicrobial-resistant “priority pathogens”, which include a group of microorganisms with high level resistance to multiple drugs, named ESKAPE pathogens, comprising vancomycin-resistant Enterococcus faecium (VRE), methicillin- and vancomycin-resistant Staphylococcus aureus (MRSA and VRSA), extended spectrum β-lactamase (ESBL) or carbapenem-resistant Klebsiella pneumoniae, carbapenem-resistant Acinetobacter baumannii, carbapenem-resistant Pseudomonas aeruginosa, and extended spectrum β-lactamase (ESBL)- or carbapenem-resistant Enterobacter spp. These bacteria also have the ability to produce several virulence factors which have a major influence on the outcome of infectious diseases. Bacterial resistance and virulence are interrelated since antibiotic pressure may influence bacterial virulence gene expression and, consequently, infection pathogenesis. In addition, some virulence factors contribute to an increased resistance ability, as observed in biofilm-producing strains. Surveillance of important resistant and virulent clones and associated mobile genetic elements is essential to decision-making in terms of mitigation measures to be applied for the prevention of such infections in both human and veterinary medicine, being also relevant to address the role of natural environments as important components of the dissemination cycle of these strains.

This Special Issue represents the second volume of “Antimicrobial Resistance and Virulence” and aims to publish manuscripts that further clarify the impact of bacterial antimicrobial resistance and virulence in the three areas of the One Health triad, i.e., animal, human, and environmental health.

Dr. Manuela Oliveira
Dr. Elisabete Silva
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

antimicrobial resistance
bacterial virulence
biofilms
epidemiology
genomics
infection pathogenesis
One Health

Published Papers (10 papers)

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Research

17 pages, 2289 KiB

Open AccessArticle

Influence of Nisin-Biogel at Subinhibitory Concentrations on Virulence Expression in Staphylococcus aureus Isolates from Diabetic Foot Infections

by Carolina Jesus, Rui Soares, Eva Cunha, Miguel Grilo, Luís Tavares and Manuela Oliveira

Antibiotics 2021, 10(12), 1501; https://doi.org/10.3390/antibiotics10121501 - 07 Dec 2021

Cited by 2 | Viewed by 2867

Abstract

A new approach to diabetic foot infections (DFIs) has been investigated, using a nisin-biogel combining the antimicrobial peptide (AMP) nisin with the natural polysaccharide guar-gum. Since in in vivo conditions bacteria may be exposed to decreased antimicrobial concentrations, known as subinhibitory concentrations (sub-MICs), effects of nisin-biogel sub-MIC values corresponding to 1/2, 1/4 and 1/8 of nisin’s minimum inhibitory concentration (MIC) on virulence expression by six Staphylococcus aureus DFI isolates was evaluated by determining bacteria growth rate; expression of genes encoding for staphylococcal protein A (spA), coagulase (coa), clumping factor A (clfA), autolysin (atl), intracellular adhesin A (icaA), intracellular adhesin D (icaD), and the accessory gene regulator I (agrI); biofilm formation; Coa production; and SpA release. Nisin-biogel sub-MICs decreased bacterial growth in a strain- and dose-dependent manner, decreased agrI, atl and clfA expression, and increased spA, coa, icaA and icaD expression. Biofilm formation increased in the presence of nisin-biogel at 1/4 and 1/8 MIC, whereas 1/2 MIC had no effect. Finally, nisin-biogel at sub-MICs did not affect coagulase production, but decreased SpA production in a dose-dependent manner. Results highlight the importance of optimizing nisin-biogel doses before proceeding to in vivo trials, to reduce the risk of virulence factor’s up-regulation due to the presence of inappropriate antimicrobial concentrations. Full article

(This article belongs to the Special Issue Antimicrobial Resistance and Virulence - 2nd Volume)

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10 pages, 1117 KiB

Open AccessArticle

Characterization of bla_KPC-2-Carrying Plasmid pR31-KPC from a Pseudomonas aeruginosa Strain Isolated in China

by Min Yuan, Hongxia Guan, Dan Sha, Wenting Cao, Xiaofeng Song, Jie Che, Biao Kan and Juan Li

Antibiotics 2021, 10(10), 1234; https://doi.org/10.3390/antibiotics10101234 - 11 Oct 2021

Cited by 8 | Viewed by 1985

Abstract

This work aimed to characterize a 29-kb bla_KPC-2-carrying plasmid, pR31-KPC, from a multidrug resistant strain of Pseudomonas aeruginosa isolated from the sputum of an elderly patient with multiple chronic conditions in China. The backbone of pR31-KPC is closely related to four other bla_KPC-2-carrying plasmids, YLH6_p3, p1011-KPC2, p14057A, and pP23-KPC, none of which have been assigned to any of the known incompatibility groups. Two accessory modules, the IS26-bla_KPC-2-IS26 unit and IS26-ΔTn6376-IS26 region, separated by a 5.9-kb backbone region, were identified in pR31-KPC, which was also shown to carry the unique resistance marker bla_KPC-2. A comparative study of the above five plasmids showed that p1011-KPC2 may be the most complete plasmid of this group to be reported, while pR31-KPC is the smallest plasmid having lost most of its conjugative region. Regions between the iterons and orf207 in the backbone may be hot spots for the acquisition of exogenous resistance entities. The accessory regions of these plasmids have all undergone several biological events when compared with Tn6296. The further transfer of bla_KPC-2 in these plasmids may be initiated by either the Tn3 family or IS26-associated transposition or homologous recombination. The data presented here will contribute to a deeper understanding of bla_KPC-2 carrying plasmids in Pseudomonas. Full article

(This article belongs to the Special Issue Antimicrobial Resistance and Virulence - 2nd Volume)

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12 pages, 311 KiB

Open AccessArticle

Virulence, Antimicrobial Resistance and Biofilm Production of Escherichia coli Isolates from Healthy Broiler Chickens in Western Algeria

by Qada Benameur, Teresa Gervasi, Filippo Giarratana, Maria Vitale, Davide Anzà, Erminia La Camera, Antonia Nostro, Nicola Cicero and Andreana Marino

Antibiotics 2021, 10(10), 1157; https://doi.org/10.3390/antibiotics10101157 - 24 Sep 2021

Cited by 6 | Viewed by 1860

Abstract

The aim of this study was to assess the virulence, antimicrobial resistance and biofilm production of Escherichia coli strains isolated from healthy broiler chickens in Western Algeria. E. coli strains (n = 18) were identified by matrix-assisted laser desorption–ionization time-of-flight mass spectrometry. Susceptibility to 10 antibiotics was determined by standard methods. Virulence and extended-spectrum β-lactamase (ESBL) genes were detected by PCR. The biofilm production was evaluated by microplate assay. All the isolates were negative for the major virulence/toxin genes tested (rfbE, fliC, eaeA, stx1), except one was stx2-positive. However, all were resistant to at least three antibiotics. Ten strains were ESBL-positive. Seven carried the β-lactamase bla_TEM gene only and two co-harbored bla_TEM and bla_CTX-M−1 genes. One carried the bla_SHV gene. Among the seven strains harboring bla_TEM only, six had putative enteroaggregative genes. Two contained irp2, two contained both irp2 and astA, one contained astA and another contained aggR, astA and irp2 genes. All isolates carrying ESBL genes were non-biofilm producers, except one weak producer. The ESBL-negative isolates were moderate biofilm producers and, among them, two harbored astA, two irp2, and one aggR, astA and irp2 genes. This study highlights the spread of antimicrobial-resistant E. coli strains from healthy broiler chickens in Western Algeria. Full article

(This article belongs to the Special Issue Antimicrobial Resistance and Virulence - 2nd Volume)

12 pages, 299 KiB

Open AccessArticle

Molecular Detection, Serotyping, and Antibiotic Resistance of Shiga Toxigenic Escherichia coli Isolated from She-Camels and In-Contact Humans in Egypt

by Mohamed Said Diab, Reda Tarabees, Yasser F. Elnaker, Ghada A. Hadad, Marwa A. Saad, Salah A. Galbat, Sarah Albogami, Aziza M. Hassan, Mahmoud A. O. Dawood and Sabah Ibrahim Shaaban

Antibiotics 2021, 10(8), 1021; https://doi.org/10.3390/antibiotics10081021 - 23 Aug 2021

Cited by 4 | Viewed by 2528

Abstract

This study aims to determine the prevalence of STEC in she-camels suffering from mastitis in semi-arid regions by using traditional culture methods and then confirming it with Serological and molecular techniques in milk samples, camel feces, as well as human stool samples for human contacts. In addition, an antibiotic susceptibility profile for these isolates was investigation. Mastitic milk samples were taken after California Mastitis Test (CMT) procedure, and fecal samples were taken from she-camels and human stool samples, then cultured using traditional methods to isolate Escherichiacoli. These isolates were initially classified serologically, then an mPCR (Multiplex PCR) was used to determine virulence genes. Finally, both camel and human isolates were tested for antibiotic susceptibility. Out of a total of 180 she-camels, 34 (18.9%) were mastitic (8.3% clinical and 10.6% sub-clinical mastitis), where it was higher in camels bred with other animals. The total presence of E. coli was 21.9, 13.9, and 33.7% in milk, camel feces, and human stool, respectively, whereas the occurrence of STEC from the total E. coli isolates were 36, 16, and 31.4% for milk, camel feces, and stool, respectively. Among the camel isolates, stx₁ was the most frequently detected virulence gene, while hlyA was not detected. The most detected virulence gene in human isolates was stx₂ (45.5%), followed by stx₁. Camel STEC showed resistance to Oxytetracycline only, while human STEC showed multiple drug resistance to Amoxicillin, Gentamycin, and Clindamycin with 81.8, 72.7, and 63.6%, respectively. Breeding camels in semi-arid areas separately from other animals may reduce the risk of infection with some bacteria, including E. coli; in contrast, mixed breeding with other animals contributes a significant risk factor for STEC emergence in camels. Full article

(This article belongs to the Special Issue Antimicrobial Resistance and Virulence - 2nd Volume)

14 pages, 668 KiB

Open AccessArticle

Antimicrobial Resistance Genes and Diversity of Clones among Faecal ESBL-Producing Escherichia coli Isolated from Healthy and Sick Dogs Living in Portugal

by Isabel Carvalho, Rita Cunha, Carla Martins, Sandra Martínez-Álvarez, Nadia Safia Chenouf, Paulo Pimenta, Ana Raquel Pereira, Sónia Ramos, Madjid Sadi, Ângela Martins, Jorge Façanha, Fazle Rabbi, Rosa Capita, Carlos Alonso-Calleja, Maria de Lurdes Nunes Enes Dapkevicius, Gilberto Igrejas, Carmen Torres and Patrícia Poeta

Antibiotics 2021, 10(8), 1013; https://doi.org/10.3390/antibiotics10081013 - 20 Aug 2021

Cited by 17 | Viewed by 3703

Abstract

The purpose of this study was to analyse the prevalence and genetic characteristics of ESBL and acquired-AmpC (qAmpC)-producing Escherichia coli isolates from healthy and sick dogs in Portugal. Three hundred and sixty-one faecal samples from sick and healthy dogs were seeded on MacConkey agar supplemented with cefotaxime (2 µg/mL) for cefotaxime-resistant (CTX^R) E. coli recovery. Antimicrobial susceptibility testing for 15 antibiotics was performed and the ESBL-phenotype of the E. coli isolates was screened. Detection of antimicrobial resistance and virulence genes, and molecular typing of the isolates (phylogroups, multilocus-sequence-typing, and specific-ST131) were performed by PCR (and sequencing when required). CTX^RE. coli isolates were obtained in 51/361 faecal samples analysed (14.1%), originating from 36/234 sick dogs and 15/127 healthy dogs. Forty-seven ESBL-producing E. coli isolates were recovered from 32 sick (13.7%) and 15 healthy animals (11.8%). Different variants of bla_CTX-M genes were detected among 45/47 ESBL-producers: bla_CTX-M-15 (n = 26), bla_CTX-M-1 (n = 10), bla_CTX-M-32 (n = 3), bla_CTX-M-55 (n = 3), bla_CTX-M-14 (n = 2), and bla_CTX-M-variant (n = 1); one ESBL-positive isolate co-produced CTX-M-15 and CMY-2 enzymes. Moreover, two additional CTX^R ESBL-negative E. coli isolates were CMY-2-producers (qAmpC). Ten different sequence types were identified (ST/phylogenetic-group/β-lactamase): ST131/B2/CTX-M-15, ST617/A/CTX-M-55, ST3078/B1/CTX-M-32, ST542/A/CTX-M-14, ST57/D/CTX-M-1, ST12/B2/CTX-M-15, ST6448/B1/CTX-M-15 + CMY-2, ST5766/A/CTX-M-32, ST115/D/CMY-2 and a new-ST/D/CMY-2. Five variants of CTX-M enzymes (CTX-M-15 and CTX-M-1 predominant) and eight different clonal complexes were detected from canine ESBL-producing E. coli isolates. Although at a lower rate, CMY-2 β-lactamase was also found. Dogs remain frequent carriers of ESBL and/or qAmpC-producing E. coli with a potential zoonotic role. Full article

(This article belongs to the Special Issue Antimicrobial Resistance and Virulence - 2nd Volume)

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14 pages, 1276 KiB

Open AccessArticle

Diversity of International High-Risk Clones of Acinetobacter baumannii Revealed in a Russian Multidisciplinary Medical Center during 2017–2019

by Andrey Shelenkov, Lyudmila Petrova, Mikhail Zamyatin, Yulia Mikhaylova and Vasiliy Akimkin

Antibiotics 2021, 10(8), 1009; https://doi.org/10.3390/antibiotics10081009 - 20 Aug 2021

Cited by 16 | Viewed by 2171

Abstract

Acinetobacter baumannii is a dangerous bacterial pathogen possessing the ability to persist on various surfaces, especially in clinical settings, and to rapidly acquire the resistance to a broad spectrum of antibiotics. Thus, the epidemiological surveillance of A. baumannii within a particular hospital, region, and across the world is an important healthcare task that currently usually includes performing whole-genome sequencing (WGS) of representative isolates. During the past years, the dissemination of A. baumannii across the world was mainly driven by the strains belonging to two major groups called the global clones or international clones (ICs) of high risk (IC1 and IC2). However, currently nine ICs are already considered. Although some clones were previously thought to spread in particular regions of the world, in recent years this is usually not the case. In this study, we determined five ICs, as well as three isolates not belonging to the major ICs, in one multidisciplinary medical center within the period 2017–2019. We performed WGS using both short- and long-read sequencing technologies of nine representative clinical A. baumannii isolates, which allowed us to determine the antibiotic resistance and virulence genomic determinants, reveal the CRISPR/Cas systems, and obtain the plasmid structures. The phenotypic and genotypic antibiotic resistance profiles are compared, and the possible ways of isolate and resistance spreading are discussed. We believe that the data obtained will provide a better understanding of the spreading and resistance acquisition of the ICs of A. baumannii and further stress the necessity for continuous genomic epidemiology surveillance of this problem-causing bacterial species. Full article

(This article belongs to the Special Issue Antimicrobial Resistance and Virulence - 2nd Volume)

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15 pages, 2418 KiB

Open AccessArticle

Climatic Alterations Influence Bacterial Growth, Biofilm Production and Antimicrobial Resistance Profiles in Aeromonas spp.

by Miguel L. Grilo, Ana Pereira, Carla Sousa-Santos, Joana I. Robalo and Manuela Oliveira

Antibiotics 2021, 10(8), 1008; https://doi.org/10.3390/antibiotics10081008 - 20 Aug 2021

Cited by 6 | Viewed by 2087

Abstract

Climate change is expected to create environmental disruptions that will impact a wide array of biota. Projections for freshwater ecosystems include severe alterations with gradients across geographical areas. Life traits in bacteria are modulated by environmental parameters, but there is still uncertainty regarding bacterial responses to changes caused by climatic alterations. In this study, we used a river water microcosm model to evaluate how Aeromonas spp., an important pathogenic and zoonotic genus ubiquitary in aquatic ecosystems, responds to environmental variations of temperature and pH as expected by future projections. Namely, we evaluated bacterial growth, biofilm production and antimicrobial resistance profiles of Aeromonas species in pure and mixed cultures. Biofilm production was significantly influenced by temperature and culture, while temperature and pH affected bacterial growth. Reversion of antimicrobial susceptibility status occurred in the majority of strains and tested antimicrobial compounds, with several combinations of temperature and pH contributing to this effect. Current results highlight the consequences that bacterial genus such as Aeromonas will experience with climatic alterations, specifically how their proliferation and virulence and phenotypic resistance expression will be modulated. Such information is fundamental to predict and prevent future outbreaks and deleterious effects that these bacterial species might have in human and animal populations. Full article

(This article belongs to the Special Issue Antimicrobial Resistance and Virulence - 2nd Volume)

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17 pages, 438 KiB

Open AccessArticle

Antibiotic Susceptibility, Virulome, and Clinical Outcomes in European Infants with Bloodstream Infections Caused by Enterobacterales

by Laura Folgori, Domenico Di Carlo, Francesco Comandatore, Aurora Piazza, Adam A. Witney, Ilia Bresesti, Yingfen Hsia, Kenneth Laing, Irene Monahan, Julia Bielicki, Alessandro Alvaro, Gian Vincenzo Zuccotti, Tim Planche, Paul T. Heath and Mike Sharland

Antibiotics 2021, 10(6), 706; https://doi.org/10.3390/antibiotics10060706 - 11 Jun 2021

Cited by 8 | Viewed by 2162

Abstract

Mortality in neonates with Gram-negative bloodstream infections has remained unacceptably high. Very few data are available on the impact of resistance profiles, virulence factors, appropriateness of empirical treatment and clinical characteristics on patients’ mortality. A survival analysis to investigate 28-day mortality probability and predictors was performed including (I) infants <90 days (II) with an available Enterobacterales blood isolate with (III) clinical, treatment and 28-day outcome data. Eighty-seven patients were included. Overall, 299 virulence genes were identified among all the pathogens. Escherichia coli had significantly more virulence genes identified compared with other species. A strong positive correlation between the number of resistance and virulence genes carried by each isolate was found. The cumulative probability of death obtained by the Kaplan-Meier survival analysis was 19.5%. In the descriptive analysis, early age at onset, gestational age at onset, culture positive for E. coli and number of classes of virulence genes carried by each isolate were significantly associated with mortality. By Cox multivariate regression, none of the investigated variables was significant. This pilot study has demonstrated the feasibility of investigating the association between neonatal sepsis mortality and the causative Enterobacterales isolates virulome. This relationship needs further exploration in larger studies, ideally including host immunopathological response, in order to develop a tailor-made therapeutic strategy. Full article

(This article belongs to the Special Issue Antimicrobial Resistance and Virulence - 2nd Volume)

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18 pages, 1312 KiB

Open AccessArticle

Virulence Factors in Staphylococcus Associated with Small Ruminant Mastitis: Biofilm Production and Antimicrobial Resistance Genes

by Nara Cavalcanti Andrade, Marta Laranjo, Mateus Matiuzzi Costa and Maria Cristina Queiroga

Antibiotics 2021, 10(6), 633; https://doi.org/10.3390/antibiotics10060633 - 25 May 2021

Cited by 18 | Viewed by 3841

Abstract

Small ruminant mastitis is a serious problem, mainly caused by Staphylococcus spp. Different virulence factors affect mastitis pathogenesis. The aim of this study was to investigate virulence factors genes for biofilm production and antimicrobial resistance to β-lactams and tetracyclines in 137 staphylococcal isolates from goats (86) and sheep (51). The presence of coa, nuc, bap, icaA, icaD, blaZ, mecA, mecC, tetK, and tetM genes was investigated. The nuc gene was detected in all S. aureus isolates and in some coagulase-negative staphylococci (CNS). None of the S. aureus isolates carried the bap gene, while 8 out of 18 CNS harbored this gene. The icaA gene was detected in S. aureus and S. warneri, while icaD only in S. aureus. None of the isolates carrying the bap gene harbored the ica genes. None of the biofilm-associated genes were detected in 14 isolates (six S. aureus and eight CNS). An association was found between Staphylococcus species and resistance to some antibiotics and between antimicrobial resistance and animal species. Nine penicillin-susceptible isolates exhibited the blaZ gene, questioning the reliability of susceptibility testing. Most S. aureus isolates were susceptible to tetracycline, and no cefazolin or gentamycin resistance was detected. These should replace other currently used antimicrobials. Full article

(This article belongs to the Special Issue Antimicrobial Resistance and Virulence - 2nd Volume)

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10 pages, 1456 KiB

Open AccessArticle

Selection of a Gentamicin-Resistant Variant Following Polyhexamethylene Biguanide (PHMB) Exposure in Escherichia coli Biofilms

by Clémence Cuzin, Paméla Houée, Pierrick Lucas, Yannick Blanchard, Christophe Soumet and Arnaud Bridier

Antibiotics 2021, 10(5), 553; https://doi.org/10.3390/antibiotics10050553 - 10 May 2021

Cited by 5 | Viewed by 2183

Abstract

Antibiotic resistance is one of the most important issues facing modern medicine. Some biocides have demonstrated the potential of selecting resistance to antibiotics in bacteria, but data are still very scarce and it is important to better identify the molecules concerned and the underlying mechanisms. This study aimed to assess the potential of polyhexamethylene biguanide (PHMB), a widely used biocide in a variety of sectors, to select antibiotic resistance in Escherichia coli grown in biofilms. Biofilms were grown on inox coupons and then exposed daily to sublethal concentrations of PHMB over 10 days. Antibiotic-resistant variants were then isolated and characterized phenotypically and genotypically to identify the mechanisms of resistance. Repeated exposure to PHMB led to the selection of an E. coli variant (Ec04m1) with stable resistance to gentamycin (8-fold increase in minimum inhibitory concentration (MIC) compared to the parental strain. This was also associated with a significant decrease in the growth rate in the variant. Sequencing and comparison of the parental strain and Ec04m1 whole genomes revealed a nonsense mutation in the aceE gene in the variant. This gene encodes the pyruvate dehydrogenase E1 component of the pyruvate dehydrogenase (PDH) complex, which catalyzes the conversion of pyruvate to acetyl-CoA and CO₂. A growth experiment in the presence of acetate confirmed the role of this mutation in a decreased susceptibility to both PHMB and gentamicin (GEN) in the variant. This work highlights the potential of PHMB to select resistance to antibiotics in bacteria, and that enzymes of central metabolic pathways should be considered as a potential target in adaptation strategies, leading to cross-resistance toward biocides and antibiotics in bacteria. Full article

(This article belongs to the Special Issue Antimicrobial Resistance and Virulence - 2nd Volume)

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