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Diversity of Antimicrobial Resistance Genes in Clinical Settings

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A special issue of Antibiotics (ISSN 2079-6382).

Deadline for manuscript submissions: closed (30 November 2022) | Viewed by 18756

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Dr. Linda Hadjadj

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Guest Editor

IHU-Méditerranée Infection, Faculté de Pharmacie, Aix-Marseille Université, Marseille, France
Interests: antibiotic resistance genes; epidemiology; infectious diseases; antibiotic resistance mechanisms
Special Issues, Collections and Topics in MDPI journals

Dr. Yolanda Sáenz

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Guest Editor

Área de Microbiología Molecular, Centro de Investigación Biomédica de La Rioja (CIBIR), Logroño, Spain
Interests: antimicrobial resistance; One Health; Pseudomonas aeruginosa; bacterial genomics; mobile genetic elements; biofilm; new antimicrobial agents

Special Issue Information

Dear Colleagues,

Currently, infectious diseases caused by multidrug-resistant bacteria are a major therapeutic challenge in hospitals. This environment is at high risk for the development and dissemination of antibiotic resistance. Since most antibiotic resistance genes (ARGs) are found on mobile genetic elements, horizontal gene transfer between different bacterial species must be monitored with extensive and regular screening. Therefore, the emergence of new multidrug-resistant bacterial species in healthcare settings must be identified and kept under surveillance.

This Special Issue, entitled "Diversity of Antimicrobial Resistance Genes in Clinical Settings", is focused on the occurrence and epidemiology of ARGs in all pathogens. Review and research articles on the detection, dissemination, and transfer of ARGs are encouraged. In addition, studies on the spread, transmission pathways, and mechanisms of antimicrobial resistance are also interesting.

Dr. Linda Hadjadj
Dr. Yolanda Saenz Dominguez
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.

Published Papers (10 papers)

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Research

17 pages, 915 KiB

Open AccessArticle

High Prevalence of GES-5 Variant and Co-Expression of VIM-2 and GES-45 among Clinical Pseudomonas aeruginosa Strains in Tunisia

by Meha Fethi, Beatriz Rojo-Bezares, Ameni Arfaoui, Raoudha Dziri, Gabriela Chichón, Farouk Barguellil, María López, Mohamed Selim El Asli, Paula Toledano, Hadda-Imen Ouzari, Yolanda Sáenz and Naouel Klibi

Antibiotics 2023, 12(9), 1394; https://0-doi-org.brum.beds.ac.uk/10.3390/antibiotics12091394 - 31 Aug 2023

Viewed by 977

Abstract

Carbapenem-resistant Pseudomonas aeruginosa (CRPA) are a global health concern. The antimicrobial resistance, virulence, and molecular typing of 57 CRPA isolated from 43 patients who attended a specific Tunisian hospital from September 2018 to July 2019 were analyzed. All but one were multidrug-resistant CRPA, and 77% were difficult-to-treat-resistant (DTR) isolates. The bla_VIM-2 gene was detected in four strains (6.9%), and among the 36 bla_GES-positive CRPA (62%), the bla_GES-5 gene was the predominant variant (86%). Three strains co-harbored the bla_VIM-2 and bla_GES-45 genes, and seven CRPA carried the bla_SHV-2a gene (14%). OprD alterations, including truncations by insertion sequences, were observed in 18 strains. Regarding the 46 class 1 integron-positive CRPA (81%), the bla_GES-5 gene was located in integron In717, while the bla_GES-29 and bla_GES-45 genes were found in two new integrons (In2122 and In4879), and the bla_VIM-2 gene was found in In1183 and the new integron In2142. Twenty-four PFGE patterns and thirteen sequence types (three new ones) were identified. The predominant serotype O:11 and exoU (81%) were mostly associated with ST235 and the new ST3385 clones. The seven bla_SHV-2a-CRPA from different patients belonged to ST3385 and the same PFGE pattern. The bla_GES-5- and bla_VIM-2 + bla_GES-45-positive CRPA recovered mostly from ICU patients belonged to the high-risk clone ST235. Our results highlight the alarming prevalence of bla_GES-5- and ST235-CRPA, the co-existence of bla_GES-45 and bla_VIM-2, and their location within integrons favoring their dissemination. Full article

(This article belongs to the Special Issue Diversity of Antimicrobial Resistance Genes in Clinical Settings)

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17 pages, 2336 KiB

Open AccessArticle

Comparative Genomics Identifies Novel Genetic Changes Associated with Oxacillin, Vancomycin and Daptomycin Susceptibility in ST100 Methicillin-Resistant Staphylococcus aureus

by Sabrina Di Gregorio, María Sol Haim, Ángela María Rosa Famiglietti, José Di Conza and Marta Mollerach

Antibiotics 2023, 12(2), 372; https://0-doi-org.brum.beds.ac.uk/10.3390/antibiotics12020372 - 11 Feb 2023

Cited by 2 | Viewed by 1303

Abstract

Infections due to vancomycin-intermediate S. aureus (VISA) and heterogeneous VISA (hVISA) represent a serious concern due to their association with vancomycin treatment failure. However, the underlying molecular mechanism responsible for the hVISA/VISA phenotype is complex and not yet fully understood. We have previously characterized two ST100-MRSA-hVISA clinical isolates recovered before and after 40 days of vancomycin treatment (D1 and D2, respectively) and two in vitro VISA derivatives (D23C9 and D2P11), selected independently from D2 in the presence of vancomycin. This follow-up study was aimed at further characterizing these isogenic strains and obtaining their whole genome sequences to unravel changes associated with antibiotic resistance. It is interesting to note that none of these isogenic strains carry SNPs in the regulatory operons vraUTSR, walKR and/or graXRS. Nonetheless, genetic changes including SNPs, INDELs and IS256 genomic insertions/rearrangements were found both in in vivo and in vitro vancomycin-selected strains. Some were found in the downstream target genes of the aforementioned regulatory operons, which are involved in cell wall and phosphate metabolism, staphylococcal growth and biofilm formation. Some of the genetic changes reported herein have not been previously associated with vancomycin, daptomycin and/or oxacillin resistance in S. aureus. Full article

(This article belongs to the Special Issue Diversity of Antimicrobial Resistance Genes in Clinical Settings)

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9 pages, 288 KiB

Open AccessArticle

Antibiotic Susceptibility and Clarithromycin Resistance Determinants in Helicobacter pylori in the Northeast of Spain: A One-Year Prospective Study

by Saray Mormeneo Bayo, Alba Bellés Bellés, Diego Vázquez Gómez, Montserrat Planella de Rubinat, Diana Carolina Bayas Pastor, Arturo Morales Portillo, Alfredo Jover Sáenz, Éric López González, Núria Prim and Mercè García-González

Antibiotics 2023, 12(2), 356; https://0-doi-org.brum.beds.ac.uk/10.3390/antibiotics12020356 - 08 Feb 2023

Viewed by 1659

Abstract

Helicobacter pylori is one of the most widespread infections, and it is reaching alarming resistance levels worldwide. The recommended first-line empirical treatment differs according to the local rate of clarithromycin resistance. Macrolide resistance is mainly associated with three point mutations in the 23S rRNA gene. The aim of this study was to describe the antibiotic susceptibility of H. pylori in our healthcare area and the main mechanisms involved in clarithromycin resistance. Gastric biopsies (n = 641) were collected and cultured in a one-year prospective study. Antibiotic susceptibility testing was performed by gradient diffusion. A multiplex real-time PCR test (Allplex^TMH.pylori & ClariR Assay, Seegene) was used to detect the most frequent mutations associated with clarithromycin resistance. Overall, 141 isolates were available for antibiotic susceptibility testing. The highest resistance rates were detected in metronidazole and levofloxacin. The rate of clarithromycin resistance was 12.1%, and the associated mutations were A2143G and A2142G. More than half of the clarithromycin-resistant isolates presented high MIC values (>256 mg/L). Tetracycline resistance was not detected, suggesting that therapies that contain tetracycline could be a suitable option. The low clarithromycin resistance rate coupled with the high rates of metronidazole resistance may support the recovery of the classical triple therapy in our healthcare area. Full article

(This article belongs to the Special Issue Diversity of Antimicrobial Resistance Genes in Clinical Settings)

13 pages, 5058 KiB

Open AccessArticle

Antimicrobial Resistance and Pathogenicity of Aliarcobacter butzleri Isolated from Poultry Meat

by Maria Gabriela Xavier de Oliveira, Marcos Paulo Vieira Cunha, Luisa Zanolli Moreno, André Becker Simões Saidenberg, Mônica Aparecida Midolli Vieira, Tânia Aparecida Tardelli Gomes, Andrea Micke Moreno and Terezinha Knöbl

Antibiotics 2023, 12(2), 282; https://0-doi-org.brum.beds.ac.uk/10.3390/antibiotics12020282 - 01 Feb 2023

Viewed by 1810

Abstract

Aliarcobacter butzleri (A. butzleri) is an emergent zoonotic food-related pathogen that can be transmitted through the consumption of poultry meat. Data regarding the pathogenicity and resistance of A. butzleri are still scarce, and the presence of virulent MDR strains of this zoonotic pathogen in poultry meat is an issue of particular concern to public health. This study aimed to characterize the pathogenicity and antimicrobial resistance profiles of A. butzleri strains isolated from poultry meat sold at retail markets in São Paulo, Brazil. The minimum inhibitory concentrations of 27 strains were determined using the broth microdilution method. The results showed that 77.7% of the isolates were resistant to clindamycin, 62.9% to florfenicol, 59.2% to nalidixic acid, 11.1% to azithromycin, 7.4% to ciprofloxacin and telithromycin, and 3.7% to erythromycin and tetracycline, although all were susceptible to gentamicin. Moreover, 55.5% of the virulent isolates were also multidrug-resistant (MDR). Three strains were selected for pathogenicity tests in vitro and in vivo. The tested strains expressed weak/moderate biofilm production and showed a diffuse adhesion pattern (3 h) in HeLa cells and toxicity in Vero cells (24 h). Experimental inoculation in 11-week-old chicks induced a transitory inflammatory enteritis. Intestinal hemorrhage and destruction of the intestinal crypts were observed in the rabbit ileal loop test. Considering the fact that Brazil is a major exporter of poultry meat, the data from this study point to the need of improvement of the diagnostic tools, as well as of the adoption of surveillance guidelines and more specific control strategies to ensure food safety, reducing the presence of pathogenic MDR strains in broilers. Full article

(This article belongs to the Special Issue Diversity of Antimicrobial Resistance Genes in Clinical Settings)

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10 pages, 290 KiB

Open AccessArticle

First Report of IMI-2-Producing Enterobacter bugandensis and CTX-M-55-Producing Escherichia coli isolated from Healthy Volunteers in Tunisia

by Rym Ben Sallem, Ameni Arfaoui, Afef Najjari, Isabel Carvalho, Abdelmalek Lekired, Hadda-Imen Ouzari, Karim Ben Slama, Alex Wong, Carmen Torres and Naouel Klibi

Antibiotics 2023, 12(1), 116; https://0-doi-org.brum.beds.ac.uk/10.3390/antibiotics12010116 - 08 Jan 2023

Cited by 2 | Viewed by 1693

Abstract

The aim of this study was to characterize the prevalence of fecal carriage of extended-spectrum beta-lactamases and carbapenemase-producing Gram-negative bacteria among healthy humans in Tunisia. Fifty-one rectal swabs of healthy volunteers were plated on MacConkey agar plates supplemented with cefotaxime or imipenem. The occurrences of resistance genes, integrons, and phylogroup typing were investigated using PCR and sequencing. The genetic relatedness of isolates was determined by pulsed-field-gel-electrophoresis (PFGE) and multilocus-sequence-typing (MLST). Whole-genome-sequencing (WGS) was performed for the carbapenem-resistant isolate. Sixteen ESBL-producing Escherichia coli isolates and one carbapenem-resistant Enterobacter bugandensis were detected out of the fifty-one fecal samples. The ESBL-producing E. coli strains contained genes encoding CTX-M-15 (n = 9), CTX-M-1 (n = 3), CTX-M-27 (n = 3), and CTX-M-55 (n = 1). Three CTX-M-1-producers were of lineages ST131, ST7366, and ST1158; two CTX-M-15-producers belonged to lineage ST925 and ST5100; one CTX-M-27-producer belonged to ST2887, and one CTX-M-15-producer belonged to ST744. Six isolates contained class 1 integrons with the following four gene cassette arrangements: dfrA5 (two isolates), dfrA12-orf-aadA2 (two isolates), dfrA17-aadA5 (one isolate), and aadA1 (one isolate). E. bugandensis belonged to ST1095, produced IMI-2 carbapenemase, and contained qnrE1 and fosA genes. A genome-sequence analysis of the E. bugandensis strain revealed new mutations in the bla_ACT and qnr genes. Our results reveal an alarming rate of ESBL-E. coli in healthy humans in Tunisia and the first description of IMI-2 in E. bugandensis. Full article

(This article belongs to the Special Issue Diversity of Antimicrobial Resistance Genes in Clinical Settings)

11 pages, 311 KiB

Open AccessArticle

Methicillin-Resistant Staphylococcus aureus from Diabetic Foot Infections in a Tunisian Hospital with the First Detection of MSSA CC398-t571

by Ameni Arfaoui, Rym Ben Sallem, Rosa Fernández-Fernández, Paula Eguizábal, Raoudha Dziri, Idris Nasir Abdullahi, Noureddine Sayem, Salma Ben Khelifa Melki, Hadda-Imen Ouzari, Carmen Torres and Naouel Klibi

Antibiotics 2022, 11(12), 1755; https://0-doi-org.brum.beds.ac.uk/10.3390/antibiotics11121755 - 04 Dec 2022

Cited by 4 | Viewed by 1472

Abstract

This study sought to analyze the antimicrobial resistant phenotypes and genotypes as well as the virulence content of S. aureus isolates recovered from patients with diabetic foot infections (DFIs) in a Tunisian hospital. Eighty-three clinical samples of 64 patients were analyzed, and bacterial isolates were identified by MALDI-TOF. The antimicrobial resistance phenotypes were determined by the Kirby–Bauer disk diffusion susceptibility test. Resistance and virulence genes, agr profile, spa and SCCmec types were determined by PCR and sequencing. S. aureus was detected in 14 of the 64 patients (21.9%), and 15 S. aureus isolates were recovered. Six out of the fifteen S. aureus isolates were methicillin-resistant (MRSA, mecA-positive) (40%). The isolates harbored the following resistance genes (number of isolates): blaZ (12), erm(B) (2), erm(A) (1), msrA (2), tet(M) (2), tet(K) (3), tet(L) (1), aac(6′)-aph(2″) (2), ant(4″) (1) and fexA (1). The lukS/F-PV and tst genes were detected in three isolates. Twelve different spa-types were identified and assigned to seven clonal complexes with the predominance of agr-type III. Furthermore, the SCCmec types III, IV and V were found among the MRSA isolates. Moreover, one MSSA CC398-t571-agr-III isolate was found; it was susceptible to all antimicrobial agents and lacked luk-S/F-PV, tst, eta and etb genes. This is the first report on the prevalence and molecular characterization of S. aureus from DFIs and also the first detection of the MSSA-CC398-t571 clone in human infections in Tunisia. Our findings indicated a high prevalence S. aureus in DFIs with genetic diversity among the MSSA and MRSA isolates. Full article

(This article belongs to the Special Issue Diversity of Antimicrobial Resistance Genes in Clinical Settings)

8 pages, 271 KiB

Open AccessArticle

Genomic Characterization of an Extensively Drug-Resistant Extra-Intestinal Pathogenic (ExPEC) Escherichia coli Clinical Isolate Co-Producing Two Carbapenemases and a 16S rRNA Methylase

by Mustafa Sadek, Alaaeldin Mohamed Saad, Patrice Nordmann and Laurent Poirel

Antibiotics 2022, 11(11), 1479; https://0-doi-org.brum.beds.ac.uk/10.3390/antibiotics11111479 - 26 Oct 2022

Cited by 4 | Viewed by 1853

Abstract

An extensively drug-resistant Escherichia coli clinical isolate (N1606) belonging to Sequence Type 361 was recovered from the urine of a patient hospitalized in Switzerland. The strain showed resistance to virtually all β-lactams including the latest generation antibiotics cefiderocol and aztreonam–avibactam. Whole genome sequencing revealed that it possessed two carbapenemase-encoding genes, namely bla_NDM-5 and bla_KPC-3, and a series of additional β-lactamase genes, including bla_CTX-M-15 and bla_SHV-11 encoding extended-spectrum β-lactamases (ESBLs), bla_CMY-145 encoding an AmpC-type cephalosporinase, and bla_OXA-1 encoding a narrow-spectrum class D ß-lactamase. Most of these resistance genes were located on plasmids (IncFII-FIA, IncX3, IncIγ, IncFII). That strain exhibited also a four amino-acid insertion in its penicillin-binding protein 3 (PBP3) sequence, namely corresponding to YRIN. Complete genome analysis revealed that this E. coli isolate carried virulence factors (sitA, gad, hra, terC, traT, and cia) and many other non-β-lactam resistance determinants including rmtB, tet(A), dfrA17 (two copies), aadA1, aadA5 (two copies), sul1 (two copies), qacE (two copies), qepA, mdf(A), catA1, erm(B), mph(A), and qnrS1, being susceptible only to tigecycline, colistin and fosfomycin. In conclusion, we described here the phenotypic and genome characteristics of an extensively drug-resistant (XDR) E. coli ST361 being recognized as an emerging clone worldwide. Full article

(This article belongs to the Special Issue Diversity of Antimicrobial Resistance Genes in Clinical Settings)

11 pages, 1191 KiB

Open AccessArticle

Genetic Diversity and Virulence Profile of Methicillin and Inducible Clindamycin-Resistant Staphylococcus aureus Isolates in Western Algeria

by Zahoua Mentfakh Laceb, Seydina M. Diene, Rym Lalaoui, Mabrouk Kihal, Fella Hamaidi Chergui, Jean-Marc Rolain and Linda Hadjadj

Antibiotics 2022, 11(7), 971; https://0-doi-org.brum.beds.ac.uk/10.3390/antibiotics11070971 - 19 Jul 2022

Viewed by 2274

Abstract

Staphylococcus aureus causes a wide range of life-threatening infections. In this study, we determined its prevalence in the hospital environment and investigated nasal carriage among healthcare workers and patients admitted to a hospital in western Algeria. A total of 550 specimens were collected. An antibiogram was performed and the genes encoding resistance to methicillin, inducible clindamycin and toxins were sought among the 92 S. aureus isolates. The spread of clones with a methicillin- and/or clindamycin-resistance phenotype between these ecosystems was studied using genomic analysis. A prevalence of 27%, 30% and 13% of S. aureus (including 2.7%, 5% and 1.25% of MRSA) in patients, healthcare workers and the hospital environment were observed, respectively. The presence of the mecA, erm, pvl and tsst-1 genes was detected in 10.9%, 17.4%, 7.6% and 18.5% of samples, respectively. Sequencing allowed us to identify seven sequence types, including three MRSA-IV-ST6, two MRSA-IV-ST80-PVL+, two MRSA-IV-ST22-TSST-1, two MRSA-V-ST5, and one MRSA-IV-ST398, as well as many virulence genes. Here, we reported that both the hospital environment and nasal carriage may be reservoirs contributing to the spread of the same pathogenic clone persisting over time. The circulation of different pathogenic clones of MRSA, MSSA, and iMLSB, as well as the emergence of at-risk ST398 clones should be monitored. Full article

(This article belongs to the Special Issue Diversity of Antimicrobial Resistance Genes in Clinical Settings)

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12 pages, 970 KiB

Open AccessArticle

Dissemination of OXA-48- and NDM-1-Producing Enterobacterales Isolates in an Algerian Hospital

by Amel Abderrahim, Nassima Djahmi, Lotfi Loucif, Sabrina Nedjai, Widad Chelaghma, Djamila Gameci-Kirane, Mazouz Dekhil, Jean-Philippe Lavigne and Alix Pantel

Antibiotics 2022, 11(6), 750; https://0-doi-org.brum.beds.ac.uk/10.3390/antibiotics11060750 - 31 May 2022

Cited by 4 | Viewed by 2064

Abstract

Multidrug-resistant (MDR) Enterobacterales remain an increasing problem in Algeria, notably due to the emergence of carbapenemase producers. We investigated the molecular characteristics of carbapenem-resistant Enterobacterales isolates recovered from outpatients and inpatients in Eastern Algeria. Non-repetitive Enterobacterales with reduced susceptibility to carbapenems were consecutively collected from clinical specimens in Annaba University Hospital (Algeria) between April 2016 and December 2018. Isolates were characterized with regard to antibiotic resistance, resistome and virulome content, clonality, and plasmid support. Of the 168 isolates analyzed, 29 (17.3%) were carbapenemase producers and identified as K. pneumoniae (n = 23), E. coli (n = 5), and E. cloacae (n = 1). bla_OXA-48 was the most prevalent carbapenemase-encoding gene (n = 26/29), followed by bla_NDM-1 gene (n = 3/29). K. pneumoniae isolates harbored some virulence traits (entB, ugeF, ureA, mrkD, fimH), whereas E. coli had a commensal origin (E, A, and B1). Clonality analysis revealed clonal expansions of ST101 K. pneumoniae and ST758 E. coli. Plasmid analysis showed a large diversity of incompatibility groups, with a predominance of IncM (n = 26, 89.7%). A global dissemination of OXA-48-producing Enterobacterales in the Algerian hospital but also the detection of NDM-1-producing E. coli in community settings were observed. The importance of this diffusion must be absolutely investigated and controlled. Full article

(This article belongs to the Special Issue Diversity of Antimicrobial Resistance Genes in Clinical Settings)

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16 pages, 2045 KiB

Open AccessArticle

Genetic Resistance Determinants in Clinical Acinetobacter pittii Genomes

by Itziar Chapartegui-González, María Lázaro-Díez and José Ramos-Vivas

Antibiotics 2022, 11(5), 676; https://0-doi-org.brum.beds.ac.uk/10.3390/antibiotics11050676 - 17 May 2022

Cited by 2 | Viewed by 2598

Abstract

Antimicrobial-resistant pathogenic bacteria are an increasing problem in public health, especially in the healthcare environment, where nosocomial infection microorganisms find their niche. Among these bacteria, the genus Acinetobacter which belongs to the ESKAPE pathogenic group harbors different multi-drug resistant (MDR) species that cause human nosocomial infections. Although A. baumannii has always attracted more interest, the close-related species A. pittii is the object of more study due to the increase in its isolation and MDR strains. In this work, we present the genomic analysis of five clinically isolated A. pittii strains from a Spanish hospital, with special attention to their genetic resistance determinants and plasmid structures. All the strains harbored different genes related to β-lactam resistance, as well as different MDR efflux pumps. We also found and described, for the first time in this species, point mutations that seem linked with colistin resistance, which highlights the relevance of this comparative analysis among the pathogenic species isolates. Full article

(This article belongs to the Special Issue Diversity of Antimicrobial Resistance Genes in Clinical Settings)

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