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Antibiotic Resistance in Gram-Negative Bacteria: The Threat from the Pink Corner

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A special issue of Pharmaceuticals (ISSN 1424-8247). This special issue belongs to the section "Medicinal Chemistry".

Deadline for manuscript submissions: closed (31 October 2023) | Viewed by 24752

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Special Issue Editors

Dr. Bruno Silvester Lopes

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Guest Editor

Department of Medical Microbiology, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen AB25 2ZD, UK
Interests: antibiotic resistance, molecular epidemiology of Gram negative pathogens, Acinetobacter and Pseudomonas

Dr. Alfizah Hanafiah

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Guest Editor

Dept. of Medical Microbiology & Immunology, Faculty of Medicine 16th Floor, Preclinical Block, UKM Medical Centre Jln Yaacob Latif, Bandar Tun Razak 56000 Cheras, Kuala Lumpur, Malaysia
Interests: molecular microbiology; mechanism of antibiotic resistance; gastric cancer; cancer immunology; research on infectious diseases

Special Issue Information

Dear Colleagues,

This issue will cover antibiotic resistance mechanisms and advances in modern medicine from faecal microbiota transplant to the development of novel drug therapies targeting hospital-acquired as well as foodborne Gram-negative pathogens. Original articles and reviews are particularly welcome in this field which relate to Gram-negative bacteria in the ESKAPE group as well as WHO critical and high priority pathogens.

Dr. Bruno Silvester Lopes
Dr. Alfizah Hanafiah
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. Pharmaceuticals 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

gram-negative
pseudomonas
acinetobacter
campylobacter
helicobacter
klebsiella
enterobacteriaceae
arcobacter
phages
complementary alternative medicine
antimicrobial peptides
food security
hospital acquired infections
microbiome
gram negative pathogens
antibiotic resistance
virulence and other molecular mechanisms

Published Papers (10 papers)

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Research

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22 pages, 7019 KiB

Open AccessArticle

Structure-Based Optimization of 1,2,4-Triazole-3-Thione Derivatives: Improving Inhibition of NDM-/VIM-Type Metallo-β-Lactamases and Synergistic Activity on Resistant Bacteria

by Matteo Bersani, Mariacristina Failla, Filippo Vascon, Eleonora Gianquinto, Laura Bertarini, Massimo Baroni, Gabriele Cruciani, Federica Verdirosa, Filomena Sannio, Jean-Denis Docquier, Laura Cendron, Francesca Spyrakis, Loretta Lazzarato and Donatella Tondi

Pharmaceuticals 2023, 16(12), 1682; https://0-doi-org.brum.beds.ac.uk/10.3390/ph16121682 - 02 Dec 2023

Viewed by 1183

Abstract

The worldwide emergence and dissemination of Gram-negative bacteria expressing metallo-β-lactamases (MBLs) menace the efficacy of all β-lactam antibiotics, including carbapenems, a last-line treatment usually restricted to severe pneumonia and urinary tract infections. Nonetheless, no MBL inhibitor is yet available in therapy. We previously identified a series of 1,2,4-triazole-3-thione derivatives acting as micromolar inhibitors of MBLs in vitro, but devoid of synergistic activity in microbiological assays. Here, via a multidisciplinary approach, including molecular modelling, synthesis, enzymology, microbiology, and X-ray crystallography, we optimized this series of compounds and identified low micromolar inhibitors active against clinically relevant MBLs (NDM-1- and VIM-type). The best inhibitors increased, to a certain extent, the susceptibility of NDM-1- and VIM-4-producing clinical isolates to meropenem. X-ray structures of three selected inhibitors in complex with NDM-1 elucidated molecular recognition at the base of potency improvement, confirmed in silico predicted orientation, and will guide further development steps. Full article

(This article belongs to the Special Issue Antibiotic Resistance in Gram-Negative Bacteria: The Threat from the Pink Corner)

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18 pages, 1112 KiB

Open AccessArticle

Phenotypic and Genotypic Comparison of Antimicrobial-Resistant Variants of Escherichia coli and Salmonella Typhimurium Isolated from Evolution Assays with Antibiotics or Commercial Products Based on Essential Oils

by Natalia Merino, Daniel Berdejo, Elisa Pagán, Claire Girard, Sylvain Kerros, Eleonora Spinozzi, Rafael Pagán and Diego García-Gonzalo

Pharmaceuticals 2023, 16(10), 1443; https://0-doi-org.brum.beds.ac.uk/10.3390/ph16101443 - 11 Oct 2023

Viewed by 913

Abstract

On account of the widespread development and propagation of antimicrobial-resistant (AMR) bacteria, essential oils (EOs) have emerged as potential alternatives to antibiotics. However, as already observed for antibiotics, recent studies have raised concerns regarding the potential emergence of resistant variants (RVs) to EOs. In this study, we assessed the emergence of RVs in Escherichia coli and Salmonella enterica Typhimurium after evolution assays under extended exposure to subinhibitory doses of two commercial EOs (AEN and COLIFIT) as well as to two antibiotics (amoxicillin and colistin). Phenotypic characterization of RVs from evolution assays with commercial EOs yielded no relevant increases in the minimum inhibitory concentration (MIC) of E. coli and did not even modify MIC values in S. Typhimurium. Conversely, RVs of E. coli and S. Typhimurium isolated from evolution assays with antibiotics showed increased resistance. Genotypic analysis demonstrated that resistance to commercial EOs was associated with enhanced protection against oxidative stress and redirection of cell energy toward efflux activity, while resistance to antibiotics was primarily linked to modifications in the cell binding sites of antibiotics. These findings suggest that AEN and COLIFIT could serve as safe alternatives to antibiotics in combating the emergence and dissemination of antimicrobial resistance within the agrifood system. Full article

(This article belongs to the Special Issue Antibiotic Resistance in Gram-Negative Bacteria: The Threat from the Pink Corner)

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10 pages, 837 KiB

Open AccessArticle

Heavy Metal (Arsenic) Induced Antibiotic Resistance among Extended-Spectrum β-Lactamase (ESBL) Producing Bacteria of Nosocomial Origin

by Naveed Ahmed, Kinza Tahir, Sara Aslam, Sara Masood Cheema, Ali A. Rabaan, Safaa A. Turkistani, Mohammed Garout, Muhammad A. Halwani, Mohammed Aljeldah, Basim R. Al Shammari, Amal A. Sabour, Maha A. Alshiekheid, Saleh A. Alshamrani, Reyouf Al Azmi, Ghadeer H. Al-Absi, Shah Zeb and Chan Yean Yean

Pharmaceuticals 2022, 15(11), 1426; https://0-doi-org.brum.beds.ac.uk/10.3390/ph15111426 - 17 Nov 2022

Cited by 5 | Viewed by 2793

Abstract

Antimicrobial resistance (AMR) is a leading cause of treatment failure for many infectious diseases worldwide. Improper overdosing and the misuse of antibiotics contributes significantly to the emergence of drug-resistant bacteria. The co-contamination of heavy metals and antibiotic compounds existing in the environment might also be involved in the spread of AMR. The current study was designed to test the efficacy of heavy metals (arsenic) induced AMR patterns in clinically isolated extended-spectrum β-lactamase (ESBL) producing bacteria. A total of 300 clinically isolated ESBL-producing bacteria were collected from a tertiary care hospital in Lahore, Pakistan, with the demographic characteristics of patients. After the collection of bacterial isolates, these were reinoculated on agar media for reidentification purposes. Direct antimicrobial sensitivity testing (AST) for bacterial isolates by disk diffusion methods was used to determine the AST patterns with and without heavy metal. The heavy metal was concentrated in dilutions of 1.25 g/mL. The collected bacterial isolates were isolated from wounds (n = 63, 21%), urine (n = 112, 37.3%), blood (n = 43, 14.3%), pus (n = 49, 16.3%), and aspirate (n = 33, 11%) samples. From the total 300 bacterial isolates, n = 172 were Escherichia coli (57.3%), 57 were Klebsiella spp. (19%), 32 were Pseudomonas aeruginosa (10.6%), 21 were Proteus mirabilis (7%) and 18 were Enterobacter spp. (6%). Most of the antibiotic drugs were found resistant to tested bacteria. Colistin and Polymyxin-B showed the highest sensitivity against all tested bacteria, but when tested with heavy metals, these antibiotics were also found to be significantly resistant. We found that heavy metals induced the resistance capability in bacterial isolates, which leads to higher AMR patterns as compared to without heavy metal tested isolates. The results of the current study explored the heavy metal as an inducer of AMR and may contribute to the formation and spread of AMR in settings that are contaminated with heavy metals. Full article

(This article belongs to the Special Issue Antibiotic Resistance in Gram-Negative Bacteria: The Threat from the Pink Corner)

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21 pages, 4396 KiB

Open AccessArticle

Healthcare Facilities as Potential Reservoirs of Antimicrobial Resistant Klebsiella pneumoniae: An Emerging Concern to Public Health in Bangladesh

by Zahid Hayat Mahmud, Salman Zahir Uddin, M. Moniruzzaman, Sobur Ali, Monir Hossain, Md. Tamzid Islam, Dorin Teresa D. Costa, Mohammad Rafiqul Islam, Md. Shafiqul Islam, Md. Zakiul Hassan, Li-Ann Ong, Catrin E. Moore, Katrina J. Charles, Dinesh Mondal, Bruno Silvester Lopes and Shahana Parveen

Pharmaceuticals 2022, 15(9), 1116; https://0-doi-org.brum.beds.ac.uk/10.3390/ph15091116 - 07 Sep 2022

Cited by 5 | Viewed by 3457

Abstract

The emergence of virulent extended spectrum β-lactamase producing Klebsiella pneumoniae (ESBL-KP) including carbapenem-resistant Klebsiella pneumoniae (CRKP) in hospital-acquired infections has resulted in significant morbidity and mortality worldwide. We investigated the antibiotic resistance and virulence factors associated with ESBL-KP and CRKP in tertiary care hospitals in Bangladesh and explored their ability to form biofilm. A total of 67 ESBL-KP were isolated from 285 Klebsiella pneumoniae isolates from environmental and patient samples from January 2019 to April 2019. For ESBL-KP isolates, molecular typing was carried out using enterobacterial repetitive intergenic consensus polymerase chain reaction (ERIC-PCR), antibiotic susceptibility testing, PCR for virulence and drug-resistant genes, and biofilm assays were also performed. All 67 isolates were multidrug-resistant (MDR) to different antibiotics at high levels and 42 isolates were also carbapenem-resistant. The most common β-lactam resistance gene was bla_CTX-M-1 (91%), followed by bla_TEM (76.1%), bla_SHV (68.7%), bla_OXA-1 (29.9%), bla_GES (14.9%), bla_CTX-M-9 (11.9%), and bla_CTX-M-2 (4.5%). The carbapenemase genes bla_KPC (55.2%), bla_IMP (28.4%), bla_VIM (14.9%), bla_NDM-1 (13.4%), and bla_OXA-48 (10.4%) and virulence-associated genes such as fimH (71.6%), ugeF (58.2%), wabG (56.7%), ureA (47.8%) and kfuBC (28.4%) were also detected. About 96.2% of the environmental and 100% of the patient isolates were able to form biofilms. ERIC-PCR-based genotyping and hierarchical clustering of K. pneumoniae isolates revealed an association between environmental and patient samples, indicating clonal association with possible transmission of antimicrobial resistance genes. Our findings can help in improving patient care and infection control, and the development of public health policies related to hospital-acquired infections. Full article

(This article belongs to the Special Issue Antibiotic Resistance in Gram-Negative Bacteria: The Threat from the Pink Corner)

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21 pages, 2286 KiB

Open AccessArticle

Co-Occurrence of β-Lactam and Aminoglycoside Resistance Determinants among Clinical and Environmental Isolates of Klebsiella pneumoniae and Escherichia coli: A Genomic Approach

by Hisham N. Altayb, Hana S. Elbadawi, Faisal A. Alzahrani, Othman Baothman, Imran Kazmi, Muhammad Shahid Nadeem, Salman Hosawi and Kamel Chaieb

Pharmaceuticals 2022, 15(8), 1011; https://0-doi-org.brum.beds.ac.uk/10.3390/ph15081011 - 17 Aug 2022

Cited by 8 | Viewed by 2034

Abstract

The presence of antimicrobial-resistance genes (ARGs) in mobile genetic elements (MGEs) facilitates the rapid development and dissemination of multidrug-resistant bacteria, which represents a serious problem for human health. This is a One Health study which aims to investigate the co-occurrence of antimicrobial resistance determinants among clinical and environmental isolates of K. pneumoniae and E. coli. Various bioinformatics tools were used to elucidate the bacterial strains’ ID, resistome, virulome, MGEs, and phylogeny for 42 isolates obtained from hospitalized patients (n = 20) and environmental sites (including fresh vegetables, fruits, and drinking water) (n = 22). The multilocus sequence typing (MLST) showed that K. pneumoniae belonged to ten sequence types (STs) while the E. coli belonged to seventeen STs. Multidrug-resistant isolates harbored β-lactam, aminoglycoside resistance determinants, and MGE were detected circulating in the environment (drinking water, fresh vegetables, and fruits) and in patients hospitalized with postoperative infections, neonatal sepsis, and urinary tract infection. Four K. pneumoniae environmental isolates (7E, 16EE, 1KE, and 19KE) were multidrug-resistant and were positive for different beta-lactam and aminoglycoside resistance determinants. bla_CTX-M-15 in brackets of ISEc 9 and Tn 3 transposases was detected in isolates circulating in the pediatrics unit of Soba hospital and the environment. This study documented the presence of bacterial isolates harboring a similar pattern of antimicrobial resistance determinants circulating in hospitals and environments. A rapid response is needed from stakeholders to initiate a program for infection prevention and control measures to detect such clones disseminated in the communities and hospitals. Full article

(This article belongs to the Special Issue Antibiotic Resistance in Gram-Negative Bacteria: The Threat from the Pink Corner)

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14 pages, 2620 KiB

Open AccessArticle

Synthesis of Functionalized N-(4-Bromophenyl)furan-2-carboxamides via Suzuki-Miyaura Cross-Coupling: Anti-Bacterial Activities against Clinically Isolated Drug Resistant A. baumannii, K. pneumoniae, E. cloacae and MRSA and Its Validation via a Computational Approach

by Ayesha Siddiqa, Muhammad Zubair, Muhammad Bilal, Nasir Rasool, Muhammad Usman Qamar, Aqsa Khalid, Gulraiz Ahmad, Muhammad Imran, Sajid Mahmood and Ghulam Abbas Ashraf

Pharmaceuticals 2022, 15(7), 841; https://0-doi-org.brum.beds.ac.uk/10.3390/ph15070841 - 08 Jul 2022

Cited by 2 | Viewed by 1861

Abstract

N-(4-bromophenyl)furan-2-carboxamide (3) was synthesized by the reaction furan-2-carbonyl chloride (1) and 4-bromoaniline (2) in the presence of Et₃N in excellent yields of 94%. The carboxamide (3) was arylated by employing triphenylphosphine palladium as a catalyst and K₃PO₄ as a base to afford N-(4-bromophenyl)furan-2-carboxamide analogues (5a-i) in moderate to good yields (43–83%). Furthermore, we investigated the in vitro anti-bacterial activities of the respective compounds against clinically isolated drug-resistant bacteria A. baumannii, K. pneumoniae, E. cloacae and S. aureus. The molecule (3) was found to be the most effective activity against these bacteria, particularly NDM-positive bacteria A. baumannii as compared to various commercially available drugs. Docking studies and MD simulations further validated it, expressing the active site and molecular interaction stability. Full article

(This article belongs to the Special Issue Antibiotic Resistance in Gram-Negative Bacteria: The Threat from the Pink Corner)

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9 pages, 696 KiB

Open AccessArticle

Safety of Antibiotics in Hospitalized Children in Romania: A Prospective Observational Study

by Noémi-Beátrix Bulik, Andreea Farcaș, Camelia Bucșa, Irina Iaru and Ovidiu Oniga

Pharmaceuticals 2022, 15(6), 713; https://0-doi-org.brum.beds.ac.uk/10.3390/ph15060713 - 03 Jun 2022

Cited by 1 | Viewed by 1726

Abstract

Antibiotics are among the most prescribed drugs in pediatric inpatients and are frequently associated with adverse drug reactions (ADRs) in children. This study aimed to assess the frequency and type of ADRs related to the use of antibiotics in pediatric inpatients through a prospective observational study, conducted over 6 months, covering the winter and spring seasons when the incidence of infections peaks in Romania. ADRs were evaluated for causality, avoidability and severity. Among the 266 included children, 25 (9.4%) experienced 30 ADRs. ADR frequency tended to be higher in ≤2-year-olds (13 of 25, 52.0%) than in other age categories. Gastrointestinal and hematological ADRs were most frequently observed. Diarrhea was the most common ADR associated with antibiotics (8 of 30, 26.7%). Ceftriaxone (16 of 30, 53.3%), cefuroxime, ceftazidime and azithromycin (3 of 30, 10.0% each) were most commonly responsible for ADRs. After causality assessment, 2 (6.7%) ADRs were considered definite, 12 (40.0%) probable and 16 (53.3%) possible. One ADR was classified as definitely avoidable and one as possibly avoidable. Seven children required treatment for ADRs. Antibiotic treatment was discontinued in 4 children. Antibiotics frequently caused ADRs in ≤ 2-year-olds and were commonly associated with gastrointestinal symptoms. Close monitoring of antibiotic-associated ADRs remains important in the pediatric population. Full article

(This article belongs to the Special Issue Antibiotic Resistance in Gram-Negative Bacteria: The Threat from the Pink Corner)

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18 pages, 4745 KiB

Open AccessArticle

Bacterial Community and Genomic Analysis of Carbapenem-Resistant Acinetobacter baumannii Isolates from the Environment of a Health Care Facility in the Western Region of Saudi Arabia

by Muhammad Yasir, Abdullah Mohammad Subahi, Hani A. Shukri, Fehmida Bibi, Sayed Sartaj Sohrab, Maha Alawi, Anees A. Sindi, Asif A. Jiman-Fatani and Esam I. Azhar

Pharmaceuticals 2022, 15(5), 611; https://0-doi-org.brum.beds.ac.uk/10.3390/ph15050611 - 16 May 2022

Cited by 3 | Viewed by 2735

Abstract

The escalating transmission of hospital-acquired infections, especially those due to antimicrobial-resistant bacteria, is a major health challenge worldwide. In this study, a culturomic analysis of bacterial community in a tertiary care hospital in the western region of Saudi Arabia is performed using environmental samples. The genome sequencing of four Acinetobacter baumannii was performed on isolates recovered from an intensive care unit (ICU) environment and clinical samples. A total of 361 bacterial isolates from surface and air samples were identified by MALDI-TOF technique or 16S rRNA gene sequencing. The isolates were classified into 70 distinct species, including ESKAPE pathogens. Resistance in Gram-positive isolates was mainly found to be against benzylpenicillin, azithromycin, ampicillin, and trimethoprim/sulfamethoxazole. Carbapenem- and multidrug-resistant isolates of A. baumannii and Klebsiella pneumonia were found on the ICU surfaces. Genome sequencing revealed that the carbapenem-resistant A. baumannii isolate from ICU environment was linked with those of clinical origin. The isolate Ab133-HEnv was classified as a novel sequence type (ST2528) based on a new allele of Oxf_gdhB-286. Three beta-lactam-antibiotic-resistance genes, bla_ADC-25, bla_OXA-23, and bla_OXA-66, were found in most of the analyzed genomes. Collectively, the results of this study highlight the spread of antimicrobial-resistant nosocomial pathogens in a health care facility in Saudi Arabia. Full article

(This article belongs to the Special Issue Antibiotic Resistance in Gram-Negative Bacteria: The Threat from the Pink Corner)

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Review

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14 pages, 555 KiB

Open AccessReview

The Potential of Alternative Therapies and Vaccine Candidates against Helicobacter pylori

by Asif Sukri, Alfizah Hanafiah, Sandip Patil and Bruno S. Lopes

Pharmaceuticals 2023, 16(4), 552; https://0-doi-org.brum.beds.ac.uk/10.3390/ph16040552 - 06 Apr 2023

Cited by 2 | Viewed by 2647

Abstract

Alternative therapies and vaccination are essential to combat the emergence of multidrug-resistant Helicobacter pylori and to prevent the development of gastroduodenal diseases. This review aimed to systematically review recent studies on alternative therapies, i.e., probiotics, nanoparticles, and natural products from plants, as well as recent progress in H. pylori vaccines at the preclinical stage. Articles published from January 2018 to August 2022 were systematically searched using PubMed, Scopus, Web of Science, and Medline. After the screening process, 45 articles were eligible for inclusion in this review. Probiotics (n = 9 studies) and natural products from plants (n = 28 studies) were observed to inhibit the growth of H. pylori, improve immune response, reduce inflammation, and reduce the pathogenic effects of H. pylori virulence factors. Natural products from plants also showed anti-biofilm activity against H. pylori. However, clinical trials of natural products from plants and probiotics are still lacking. A paucity of data assessing the nanoparticle activity of N-acylhomoserine lactonase-stabilized silver against H. pylori was observed. Nonetheless, one nanoparticle study showed anti-biofilm activity against H. pylori. Promising results of H. pylori vaccine candidates (n = 7) were observed at preclinical stage, including elicitation of a humoral and mucosal immune response. Furthermore, the application of new vaccine technology including multi-epitope and vector-based vaccines using bacteria was investigated at the preclinical stage. Taken together, probiotics, natural products from plants, and nanoparticles exhibited antibacterial activity against H. pylori. New vaccine technology shows promising results against H. pylori. Full article

(This article belongs to the Special Issue Antibiotic Resistance in Gram-Negative Bacteria: The Threat from the Pink Corner)

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26 pages, 1765 KiB

Open AccessReview

CRISPR-Cas System: A Tool to Eliminate Drug-Resistant Gram-Negative Bacteria

by Rajeshwari Kundar and Karuna Gokarn

Pharmaceuticals 2022, 15(12), 1498; https://0-doi-org.brum.beds.ac.uk/10.3390/ph15121498 - 30 Nov 2022

Cited by 8 | Viewed by 3973

Abstract

Rapidly emerging drug-resistant superbugs, especially Gram-negative bacteria, pose a serious threat to healthcare systems all over the globe. Newer strategies are being developed to detect and overcome the arsenal of weapons that these bacteria possess. The development of antibiotics is time-consuming and may not provide full proof of action on evolving drug-resistant pathogens. The clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas) systems are promising in curbing drug-resistant bacteria. This review focuses on the pathogenesis of Gram-negative bacteria, emergence of antimicrobial drug resistance, and their treatment failures. It also draws attention to the present status of the CRISPR-Cas system in diagnosisand treatment of Gram-negative bacterial infections. Full article

(This article belongs to the Special Issue Antibiotic Resistance in Gram-Negative Bacteria: The Threat from the Pink Corner)

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