1
|
Obaid Hasson S, Kamil Hasan H, Abdul Kadhem Salman S, Judi HK, Akrami S, Saki M, Adil Hasan M, Fares Hashem D. In vivo and in vitro efficacy of the ithmid kohl/zinc-oxide nanoparticles, ithmid kohl/Aloe vera, and zinc-oxide nanoparticles/Aloe vera for the treatment of bacterial endophthalmitis. Sci Rep 2024; 14:15746. [PMID: 38977762 PMCID: PMC11231241 DOI: 10.1038/s41598-024-66341-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 07/01/2024] [Indexed: 07/10/2024] Open
Abstract
The aim of this study was to investigate the efficacy of the ithmid kohl/zinc-oxide nanoparticles (ZnONPs), ithmid kohl/Aloe vera, and ZnONPs/Aloe vera in the treatment of bacterial endophthalmitis. The endophthalmitis model was prepared by contaminating both eyes of 24 healthy adult male albino rabbits with a clinical isolate of Klebsiella pneumoniae. The animals were randomly divided into eight groups (A-H) according to the treatment. Group A received 1 ml of ithmid kohl/ZnONPs ointment, group B received 1 ml of ithmid kohl/Aloe vera gel ointment, group C received 1 ml of ZnONPs/Aloe vera gel ointment, and groups D, E, and F were treated with 1 ml of ithmid kohl solution (0.5 g/ml in distilled water), 1 ml of ZnONPs (0.5 g/ml) colloidal dispersion, and 1 ml of Aloe vera gel, respectively. Group G received 100 μl of a tetracycline antibiotic solution (final concentration: 16 µg/ml), and group H received sterile distilled water (no treatment). In vitro antibacterial activity was evaluated against K. pneumoniae using the agar well diffusion. The combination of ithmid kohl/ZnONPs was the most effective formulation for treating endophthalmitis model in infected rabbits within 2 days. In vitro antibacterial assay confirmed the potential of the ithmid kohl/ZnONPs formulation, which had the largest zone of inhibition (31 mm) among the compounds tested. The preparation of the ithmid kohl/ZnONPs formulation and its in vivo experiment in albino rabbits for the treatment of bacterial endophthalmitis was an innovative approach that has shown promise and may potentially serve as a viable alternative in clinical practice.
Collapse
Affiliation(s)
- Shaimaa Obaid Hasson
- Medical Biotechnology Department, College of Biotechnology, Al-Qasim Green University, Babylon, 51013, Iraq
| | | | - Sumod Abdul Kadhem Salman
- Microbiology Department, College of Veterinary Medicine, Al-Qasim Green University, Babylon, 51013, Iraq
| | - Hawraa K Judi
- Department of Medical Physics, Hilla University College, Babylon, Iraq
| | - Sousan Akrami
- Students' Scientific Research Center (SSRC), Tehran University of Medical Sciences, Tehran, Iran.
- Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
| | - Morteza Saki
- Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
| | | | | |
Collapse
|
2
|
Owaid HA, Al-Ouqaili MT. Molecular and bacteriological investigations for the co-existence CRISPR/Cas system and β-lactamases of types extended-spectrum and carbapenemases in Multidrug, extensive drug and Pandrug-Resistant Klebsiella pneumoniae. Saudi J Biol Sci 2024; 31:104022. [PMID: 38817398 PMCID: PMC11137337 DOI: 10.1016/j.sjbs.2024.104022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 05/05/2024] [Accepted: 05/10/2024] [Indexed: 06/01/2024] Open
Abstract
The recent approach towards combating the antimicrobial resistance has led to the use of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and associated sequence to overcome the challenges of antimicrobial resistance. Thus, this study aimed to detect the underlying resistance mechanisms such as ESBLs and carbapenemases and whether there is a correlation between multidrug, extensive drug and pan drug resistance and the occurrence of CRISPR loci. A total of one hundred study isolates were subjected to antimicrobial susceptibility testing using the AST card of the Vitek technique to detect resistance patterns involving ESBLs and carbapenemase (CRE). An investigation of the genes encoding CRISPR/Cas systems using PCR was achieved. Out of 81 (81.0%) resistant Klebsiella pneumoniae isolates, 71 (71%) and 21 (21.0%) produced ESBLs and carbapenemases, respectively. Also, 53 (53.0%), 19 (19.0%) and 9 (9.0%) were MDR, XDR, and PDR respectively. It was noted that Cas1, Cas3, CRISPR1, CRISPR2 and CRISPR3 were positive in 38 (38.0%) of the isolates, while CRISPR1 for incomplete CRISPR1-Cas systems alone was detected in 78 (78.0%). Further, the number of intact CRISPR1, intact CRISPR2 and intact CRISPR3 types were 7 (27.0%), 34 (34%) and 18 (18.0%) respectively. It is concluded that antibiotic resistance levels were inversely correlated with the existence of CRISPR/Cas systems. The absence of the CRISPR/Cas system increases the prevalence of MDR, XDR and PDR in ESBL and carbapenem-producing Klebsiella pneumoniae. With the increase in the degree of antibiotic resistance (MDR, XDR to PDR), the occurrence ratio of the (CRISPR)/CRISPR-associated sequence decreased.
Collapse
Affiliation(s)
- Hekmat A. Owaid
- Department of Biology, College of Science, University of Anbar, Ramadi, Iraq
| | - Mushtak T.S. Al-Ouqaili
- Department of Microbiology, College of Medicine, University of Anbar, Al-Anbar Governorate, Ramadi, Iraq
| |
Collapse
|
3
|
Zhou H, Yang Y, Zhang Y, Li F, Shen Y, Qin L, Huang W. Current Status and Perspectives of Diagnosis and Treatment of Periprosthetic Joint Infection. Infect Drug Resist 2024; 17:2417-2429. [PMID: 38912221 PMCID: PMC11192293 DOI: 10.2147/idr.s457644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 06/05/2024] [Indexed: 06/25/2024] Open
Abstract
Periprosthetic joint infection (PJI) is a catastrophic complication following joint replacement surgery, posing significant challenges to orthopedic surgeons. Due to the lack of a definitive diagnostic gold standard, timely treatment initiation is problematic, resulting in substantial economic burdens on patients and society. In this review, we thoroughly analyze the complexities of PJI and emphasize the importance of accurate diagnosis and effective treatment. The article specifically focuses on the advancements in diagnostic techniques, ranging from traditional pathogen culture to advanced molecular diagnostics, and discusses their role in enhancing diagnostic accuracy. Additionally, we review the latest surgical management strategies, including everything from debridement to revision surgeries. Our summary aims to provide practical information for the diagnosis and treatment of PJI and encourages further research to improve diagnostic accuracy and treatment outcomes.
Collapse
Affiliation(s)
- Haotian Zhou
- Department of Orthopaedics, the First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, People’s Republic of China
- Orthopedic Laboratory of Chongqing Medical University, Chongqing, 400016, People’s Republic of China
| | - Yaji Yang
- Department of Orthopaedics, the First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, People’s Republic of China
- Orthopedic Laboratory of Chongqing Medical University, Chongqing, 400016, People’s Republic of China
| | - Yanhao Zhang
- College of Pharmacy, Army Military Medical University, Chongqing, 400038, People’s Republic of China
| | - Feilong Li
- Department of Orthopaedics, the First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, People’s Republic of China
- Orthopedic Laboratory of Chongqing Medical University, Chongqing, 400016, People’s Republic of China
| | - Yidong Shen
- Department of Orthopaedics, The First People’s Hospital of Yancheng, Yancheng, 224000, People’s Republic of China
| | - Leilei Qin
- Department of Orthopaedics, the First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, People’s Republic of China
- Orthopedic Laboratory of Chongqing Medical University, Chongqing, 400016, People’s Republic of China
| | - Wei Huang
- Department of Orthopaedics, the First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, People’s Republic of China
- Orthopedic Laboratory of Chongqing Medical University, Chongqing, 400016, People’s Republic of China
| |
Collapse
|
4
|
Amábile-Cuevas CF, Lund-Zaina S. Non-Canonical Aspects of Antibiotics and Antibiotic Resistance. Antibiotics (Basel) 2024; 13:565. [PMID: 38927231 PMCID: PMC11200725 DOI: 10.3390/antibiotics13060565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 05/09/2024] [Accepted: 05/29/2024] [Indexed: 06/28/2024] Open
Abstract
The understanding of antibiotic resistance, one of the major health threats of our time, is mostly based on dated and incomplete notions, especially in clinical contexts. The "canonical" mechanisms of action and pharmacodynamics of antibiotics, as well as the methods used to assess their activity upon bacteria, have not changed in decades; the same applies to the definition, acquisition, selective pressures, and drivers of resistance. As a consequence, the strategies to improve antibiotic usage and overcome resistance have ultimately failed. This review gathers most of the "non-canonical" notions on antibiotics and resistance: from the alternative mechanisms of action of antibiotics and the limitations of susceptibility testing to the wide variety of selective pressures, lateral gene transfer mechanisms, ubiquity, and societal factors maintaining resistance. Only by having a "big picture" view of the problem can adequate strategies to harness resistance be devised. These strategies must be global, addressing the many aspects that drive the increasing prevalence of resistant bacteria aside from the clinical use of antibiotics.
Collapse
Affiliation(s)
| | - Sofia Lund-Zaina
- Department of Public Health, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| |
Collapse
|
5
|
Kadkhoda H, Gholizadeh P, Ghotaslou R, Pirzadeh T, Ahangarzadeh Rezaee M, Nabizadeh E, Feizi H, Samadi Kafil H, Aghazadeh M. Prevalence of the CRISPR-cas system and its association with antibiotic resistance in clinical Klebsiella pneumoniae isolates. BMC Infect Dis 2024; 24:554. [PMID: 38831286 PMCID: PMC11149351 DOI: 10.1186/s12879-024-09451-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Accepted: 05/30/2024] [Indexed: 06/05/2024] Open
Abstract
BACKGROUND AND OBJECTIVE(S) CRISPR-Cas is a prokaryotic adaptive immune system that protects bacteria and archaea against mobile genetic elements (MGEs) such as bacteriophages plasmids, and transposons. In this study, we aimed to assess the prevalence of the CRISPR-Cas systems and their association with antibiotic resistance in one of the most challenging bacterial pathogens, Klebsiella pneumoniae. MATERIALS AND METHODS A total of 105 K. pneumoniae isolates were collected from various clinical infections. Extended-spectrum β-lactamases (ESBLs) phenotypically were detected and the presence of ESBL, aminoglycoside-modifying enzymes (AME), and CRISPR-Cas system subtype genes were identified using PCR. Moreover, the diversity of the isolates was determined by enterobacterial repetitive intergenic consensus (ERIC)-PCR. RESULTS Phenotypically, 41.9% (44/105) of the isolates were found to be ESBL producers. A significant inverse correlation existed between the subtype I-E CRISPR-Cas system's presence and ESBL production in K. pneumoniae isolates. Additionally, the frequency of the ESBL genes blaCTX-M1 (3%), blaCTX-M9 (12.1%), blaSHV (51.5%), and blaTEM (33.3%), as well as some AME genes such as aac(3)-Iva (21.2%) and ant(2'')-Ia (3%) was significantly lower in the isolates with the subtype I-E CRISPR-Cas system in comparison to CRISPR-negative isolates. There was a significant inverse correlation between the presence of ESBL and some AME genes with subtype I-E CRISPR-Cas system. CONCLUSION The presence of the subtype I-E CRISPR-Cas system was correlated with the antibiotic-resistant gene (ARGs). The isolates with subtype I-E CRISPR-Cas system had a lower frequency of ESBL genes and some AME genes than CRISPR-negative isolates.
Collapse
Affiliation(s)
- Hiva Kadkhoda
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Medical Microbiology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Pourya Gholizadeh
- Digestive Disease Research Center, Ardabil University of Medical Sciences, Ardabil, Iran
- Zoonoses Research Center, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Reza Ghotaslou
- Department of Medical Microbiology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Tahereh Pirzadeh
- Department of Medical Microbiology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Edris Nabizadeh
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Medical Microbiology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hadi Feizi
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Medical Microbiology, Aalinasab Hospital, Social Security Organization, Tabriz, Iran
| | - Hossein Samadi Kafil
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Mohammad Aghazadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| |
Collapse
|
6
|
Tadesse T, Alemayehu H, Medhin G, Akalu A, Eguale T. Antibiogram of Escherichia coli Isolated from Dairy Cattle and in-Contact Humans in Selected Areas of Central Ethiopia. VETERINARY MEDICINE (AUCKLAND, N.Z.) 2024; 15:117-127. [PMID: 38617107 PMCID: PMC11016264 DOI: 10.2147/vmrr.s456247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 04/03/2024] [Indexed: 04/16/2024]
Abstract
Background Antimicrobial resistance (AMR) is a global threat to public and animal health. Escherichia coli is considered an indicator organism for monitoring AMR among gram-negative Enterobacteriaceae in humans and animals. The current study aims to assess the antibiogram profile of E. coli isolated from dairy cattle and in-contact humans in central Ethiopia and to identify risk factors associated with multidrug resistance (MDR). Methods A cross-sectional study was conducted in which 58 farms were recruited from selected districts of central Ethiopia. E. coli was isolated using standard bacteriological techniques. A total of 200 representative isolates (140 from cattle and 60 from humans in contact) were randomly selected and tested for susceptibility to a panel of 13 antimicrobials using the Kirby-Bauer disc diffusion assay. Results The highest rate of resistance was observed for sulfamethoxazole+trimethoprim (58.6%, 82/140) and amoxicillin+clavulanic acid (70.0%, 42/60) among E. coli isolates from cattle and hmans, respectively. In contrast, resistance rates in isolates from in contact humans with the cattle were 30%, 33.3%, and 66.7%, respectively. Resistance to tetracycline (p=0.02), streptomycin (p=0.03), and sulfamethoxazole+trimethoprim (p=0.007) was significantly high in E. coli isolated from cattle on commercial dairy farms than in those isolated from cattle on smallholder farms. There was no significant difference (p>0.05) in the rate of resistance between E. coli isolated from in contact humans with smallholder and commercial dairy farms. Antimicrobial use for treatment purpose (p=0.04) and non-compliance with the drug withdrawal period (p=0.03) were significantly associated with the farm-level occurrence of MDR. Conclusion A high rate of resistance was detected in E. coli isolated from the feces of dairy cattle and in-contact humans. This necessitates an effective intervention through a one-health approach and further molecular studies are required to establish source attribution.
Collapse
Affiliation(s)
- Tekalign Tadesse
- Department of Veterinary Science, Mattu University, Mattu, Ethiopia
| | - Haile Alemayehu
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Girmay Medhin
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Aberaw Akalu
- Food, Medicine and Healthcare Administration and Control, Addis Ababa, Ethiopia
| | - Tadesse Eguale
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
- The Ohio State University, Global One Health LLC, Addis Ababa, Ethiopia
| |
Collapse
|
7
|
Allemailem KS. Recent Advances in Understanding the Molecular Mechanisms of Multidrug Resistance and Novel Approaches of CRISPR/Cas9-Based Genome-Editing to Combat This Health Emergency. Int J Nanomedicine 2024; 19:1125-1143. [PMID: 38344439 PMCID: PMC10859101 DOI: 10.2147/ijn.s453566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 01/26/2024] [Indexed: 02/15/2024] Open
Abstract
The rapid spread of multidrug resistance (MDR), due to abusive use of antibiotics has led to global health emergency, causing substantial morbidity and mortality. Bacteria attain MDR by different means such as antibiotic modification/degradation, target protection/modification/bypass, and enhanced efflux mechanisms. The classical approaches of counteracting MDR bacteria are expensive and time-consuming, thus, it is highly significant to understand the molecular mechanisms of this resistance to curb the problem from core level. The revolutionary approach of clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated sequence 9 (CRISPR/Cas9), considered as a next-generation genome-editing tool presents an innovative opportunity to precisely target and edit bacterial genome to alter their MDR strategy. Different bacteria possessing antibiotic resistance genes such as mecA, ermB, ramR, tetA, mqrB and blaKPC that have been targeted by CRISPR/Cas9 to re-sensitize these pathogens against antibiotics, such as methicillin, erythromycin, tigecycline, colistin and carbapenem, respectively. The CRISPR/Cas9 from S. pyogenes is the most widely studied genome-editing tool, consisting of a Cas9 DNA endonuclease associated with tracrRNA and crRNA, which can be systematically coupled as sgRNA. The targeting strategies of CRISPR/Cas9 to bacterial cells is mediated through phage, plasmids, vesicles and nanoparticles. However, the targeting approaches of this genome-editing tool to specific bacteria is a challenging task and still remains at a very preliminary stage due to numerous obstacles awaiting to be solved. This review elaborates some recent updates about the molecular mechanisms of antibiotic resistance and the innovative role of CRISPR/Cas9 system in modulating these resistance mechanisms. Furthermore, the delivery approaches of this genome-editing system in bacterial cells are discussed. In addition, some challenges and future prospects are also described.
Collapse
Affiliation(s)
- Khaled S Allemailem
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah51452, Saudi Arabia
| |
Collapse
|
8
|
Ahn Y, Jin S, Park G, Lee HY, Lee H, Shin E, Kim J, Yoo J, Kim Y. Epidemiological analysis and prevention strategies in response to a shigellosis cluster outbreak: a retrospective case series in an alternative school in the Republic of Korea, 2023. Osong Public Health Res Perspect 2024; 15:68-76. [PMID: 38481051 PMCID: PMC10982656 DOI: 10.24171/j.phrp.2023.0298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 12/05/2023] [Accepted: 12/07/2023] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND In March 2023, an alternative school in the Republic of Korea reported 12 cases of shigellosis. This study aims to analyze the epidemiological characteristics in order to determine the cause of the cluster outbreak of shigellosis and to develop prevention strategies. METHODS This study focused on 12 patients with confirmed Shigella infection and investigated their demographics, clinical features, epidemiology, diagnostics, and antimicrobial susceptibility. Following the identification of Shigella, we conducted follow-up rectal smear cultures to manage patients, implementing isolation and control measures. RESULTS This study investigated the emergence of multidrug-resistant Shigella following missionary activities in Cambodia, documenting a cluster infection within an alternative school in Daejeon, the Republic of Korea. The outbreak affected 56 participants, resulting in the confirmation of 12 cases. The incidence rates varied by gender and occupation, with higher rates among males and teachers. All 12 cases demonstrated multidrug resistance. Challenges included delayed pathogen confirmation and suboptimal adherence to isolation criteria. The incident prompted revisions in the criteria for isolation release, focusing on symptom resolution. The study underscores the necessity for strengthened surveillance, educational initiatives focusing on prevention in endemic areas, and improved oversight of unlicensed educational establishments. CONCLUSION Successful response strategies included swift situation assessment, collaborative efforts, effective infection control measures, and modified criteria for isolation release. Continued surveillance of multidrug-resistant strains is recommended, especially in regions with a high prevalence.
Collapse
Affiliation(s)
- Yeongseo Ahn
- Division of Infectious Disease Response, Chungcheong Reginal Center for Disease Control and Prevention, Daejeon, Republic of Korea
| | - Sunmi Jin
- Yuseong-gu Health Center, Daejeon, Republic of Korea
| | - Gemma Park
- Division of Infectious Disease Response, Chungcheong Reginal Center for Disease Control and Prevention, Daejeon, Republic of Korea
| | - Hye Young Lee
- Division of Infectious Disease Response, Chungcheong Reginal Center for Disease Control and Prevention, Daejeon, Republic of Korea
| | - Hyungyong Lee
- Division of Infectious Disease Response, Chungcheong Reginal Center for Disease Control and Prevention, Daejeon, Republic of Korea
| | - Eunkyung Shin
- Division of Bacterial Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Junyoung Kim
- Division of Bacterial Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Jaeil Yoo
- Division of Bacterial Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Yuna Kim
- Division of Infectious Disease Response, Chungcheong Reginal Center for Disease Control and Prevention, Daejeon, Republic of Korea
| |
Collapse
|
9
|
Martínez-Trejo A, Ruiz-Ruiz JM, Gonzalez-Avila LU, Saldaña-Padilla A, Hernández-Cortez C, de Jesús Colmenero-Solís R, Bello-López JM, Castro-Escarpulli G. The CRISPR-Cas system in clinical strains of Acinetobacter baumannii: an in-silico analysis. Lett Appl Microbiol 2024; 77:ovae003. [PMID: 38211976 DOI: 10.1093/lambio/ovae003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 12/29/2023] [Accepted: 01/10/2024] [Indexed: 01/13/2024]
Abstract
Acinetobacter baumannii is a relevant bacterium due to its high-resistance profile. It is well known that antimicrobial resistance is primarily linked to mutations and the acquisition of external genomic material, such as plasmids or phages, to which the Clustered Regularly Interspaced Short Palindromic Repeats associated with Cas proteins, or CRISPR-Cas, system is related. It is known that the system can influence the acquisition of foreign genetic material and play a role in various physiological pathways. In this study, we conducted an in-silico analysis using 91 fully assembled genomes of clinical strains obtained from the NCBI database. Among the analyzed genomes, the I-F1 subtype of the CRISPR-Cas system was detected showcasing variations in architecture and phylogeny. Using bioinformatic tools, we determined the presence, distribution, and specific characteristics of the CRISPR-Cas system. We found a possible association of the system with resistance genes but not with virulence determinants. Analysis of the system's components, including spacer sequences, suggests its potential role in protecting against phage infections, highlighting its protective function.
Collapse
Affiliation(s)
- Arturo Martínez-Trejo
- Laboratorio de Investigación Clínica y Ambiental, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 11340, Mexico
| | - Juan Manuel Ruiz-Ruiz
- Laboratorio Clínico, Unidad Médica de Alta Especialidad, Hospital de Pediatría Dr. Silvestre Frenk Freud, Instituto Mexicano del Seguro Social, Mexico City 06720, Mexico
| | - Luis Uriel Gonzalez-Avila
- Laboratorio de Investigación Clínica y Ambiental, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 11340, Mexico
| | - Andres Saldaña-Padilla
- Laboratorio de Investigación Clínica y Ambiental, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 11340, Mexico
- Laboratorio de Bioquímica Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 11340, Mexico
| | - Cecilia Hernández-Cortez
- Laboratorio de Bioquímica Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 11340, Mexico
| | - Raúl de Jesús Colmenero-Solís
- Laboratorio de Investigación Clínica y Ambiental, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 11340, Mexico
| | | | - Graciela Castro-Escarpulli
- Laboratorio de Investigación Clínica y Ambiental, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 11340, Mexico
| |
Collapse
|
10
|
Fang C, Dai X, Xiang L, Qiu Y, Yin M, Fu Y, Li Y, Zhang L. Isolation and characterization of three novel lytic phages against K54 serotype carbapenem-resistant hypervirulent Klebsiella pneumoniae. Front Cell Infect Microbiol 2023; 13:1265011. [PMID: 38149011 PMCID: PMC10749971 DOI: 10.3389/fcimb.2023.1265011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 11/28/2023] [Indexed: 12/28/2023] Open
Abstract
The emergence of carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKP) has driven us to explore alternative treatments for the limitation of antimicrobial agents. Lytic phages are considered a promising alternative treatment for CR-hvKP infection. In this study, we reported three novel lytic phages, vB_KpnA_SCNJ1-Z, vB_KpnS_SCNJ1-C, and vB_KpnM_SCNJ1-Y, against a CR-hvKP strain SCNJ1, and they possess genomes of double-stranded DNA with a size of 43,428 bp, 46,039 bp, and 50,360 bp, respectively. Phylogenetic analysis demonstrated that vB_KpnA_SCNJ1-Z belongs to the family Autographiviridae within the class Caudoviricetes, while vB_KpnS_SCNJ1-C and vB_KpnM_SCNJ1-Y are unclassified Caudoviricetes. The phages showed a narrow host range only lysing 1 of 50 tested clinical bacterial strains. The one-step growth curves and stability results showed that the phages displayed relatively short latency periods, with broad pH (pH 3-14) and thermal stabilities (20-60°C). The phages showed significant inhibition of the biofilm formation by SCNJ1 and strong antibacterial activity in vitro. In the mouse model, we demonstrated that administration of a single phage or phage cocktail significantly reduced bacteria loads in the lung, liver, and spleen, and effectively rescued mice from the infection of the SCNJ1 strain, with a survival rate of 70-80%. These findings suggested the three phages have great potential as an alternative therapy with favorable stability and strong antibacterial activity both in vivo and in vitro for the treatment of CR-hvKP infection.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Ying Li
- The School of Basic Medical Science and Public Center of Experimental Technology, Southwest Medical University, Luzhou, Sichuan, China
| | - Luhua Zhang
- The School of Basic Medical Science and Public Center of Experimental Technology, Southwest Medical University, Luzhou, Sichuan, China
| |
Collapse
|
11
|
Daoud L, Al-Marzooq F, Ghazawi A, Anes F, Collyns T. High efficacy and enhanced synergistic activity of the novel siderophore-cephalosporin cefiderocol against multidrug-resistant and extensively drug-resistant Klebsiella pneumoniae from inpatients attending a single hospital in the United Arab Emirates. J Infect Public Health 2023; 16 Suppl 1:33-44. [PMID: 37953111 DOI: 10.1016/j.jiph.2023.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 10/28/2023] [Accepted: 11/01/2023] [Indexed: 11/14/2023] Open
Abstract
BACKGROUND Cefiderocol (CFDC) is a novel siderophore-cephalosporin, which usually penetrates the bacteria through the iron-uptake pathways. Data is limited on the factors affecting CFDC activity and methods for overcoming resistance development. Synergistic approaches are needed to tackle antimicrobial resistance. This study aimed to determine CFDC activity on Klebsiella pneumoniae isolates from patients attending a single hospital in the United Arab Emirates (UAE), to explore the effect of β-lactamases on CFDC activity and to enhance CFDC susceptibility in both iron-depleted and iron-enriched conditions. METHODS We investigated 238 K. pneumoniae strains from diverse clinical sources. β-lactamase genes were detected by PCR. Susceptibility to CFDC and 12 comparator antibiotics were tested. Combinations of CFDC with β-lactamase inhibitors (BLIs) and/or an outer membrane (OM) permeabilizer (polymyxin B nonapeptide) were tested in iron-depleted and iron-enriched conditions. RESULTS CFDC exhibited efficacy of 97.9%, against multidrug-resistant (MDR), and extensively drug-resistant (XDR) strains, in addition to strains resistant to the last resort drugs such as colistin and tigecycline, including dual carbapenemase-producers (blaNDM and blaOXA-48-like) with MIC ≤ 0.06-8 µg/ml. It was effective in killing strains with single and multiple β-lactamases; however, it lost activity in iron-enriched conditions. Synergy was achieved with dual combination of CFDC and BLIs, especially avibactam, which caused a significant reduction in MICs even in iron-enriched conditions. A significant reduction was seen with the triple combination including an OM permeabilizer plus avibactam. Killing-kinetic studies proved that the combination therapy caused dose reduction and faster killing by CFDC than the monotherapy. CONCLUSIONS CFDC was deemed effective against MDR and XDR K. pneumoniae. Synergistic combination of CFDC with BLIs and OM permeabilizers could be effective to treat infections in iron-rich sites, but this should be investigated in vivo.
Collapse
Affiliation(s)
- Lana Daoud
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Farah Al-Marzooq
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates.
| | - Akela Ghazawi
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Febin Anes
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | | |
Collapse
|
12
|
Jafari-Sales A, Al-Khafaji NSK, Al-Dahmoshi HOM, Sadeghi Deylamdeh Z, Akrami S, Shariat A, Judi HK, Nasiri R, Bannazadeh Baghi H, Saki M. Occurrence of some common carbapenemase genes in carbapenem-resistant Klebsiella pneumoniae isolates collected from clinical samples in Tabriz, northwestern Iran. BMC Res Notes 2023; 16:311. [PMID: 37924149 PMCID: PMC10623837 DOI: 10.1186/s13104-023-06558-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 10/09/2023] [Indexed: 11/06/2023] Open
Abstract
OBJECTIVES This study aimed to evaluate the antibiotic resistance patterns and prevalence of carbapenemase genes in Klebsiella pneumoniae isolates in different clinical samples from Tabriz city, northwestern Iran. RESULTS This cross-sectional study was conducted in the Department of Microbiology, Islamic Azad University, Ahar Branch, Iran, in 2020. K. pneumoniae isolates were collected from different clinical samples, including blood, wounds, sputum, and urine. The isolates were identified using a series of standard bacteriological tests. Antibiotic resistance was determined by the disc diffusion method. The presence of blaVIM, blaNDM, blaKPC, blaOXA, and blaIMP genes were screened by polymerase chain reaction (PCR). A total of 100 non-duplicated K. pneumoniae isolates were collected from 57 urine samples, 27 blood samples, 13 wound samples, and 3 sputum samples. Overall, 70.0% of the samples were from inpatients, while 30.0% were from outpatients. The most resistance rate was related to ampicillin (94.0%), while the lowest resistance rate was related to imipenem (18.0%) and meropenem (20.0%). Overall, 25.0% of the isolates were carbapenem-resistant, of which 13.0% were resistant to both imipenem and meropenem. The PCR showed the total prevalence of 23.0% for carbapenemase genes, including 18.0% for blaKPC, 3.0% for blaVIM, 1.0% for blaIMP, and 1.0% for blaOXA gene. The blaNDM gene was not detected in any isolate. The prevalence of carbapenemase-producing K. pneumoniae isolates was relatively lower in northwestern Iran than in other regions of the country. However, special attention should be paid to the proper use of antibiotics, particularly carbapenems, to prevent further spread of antibiotic resistance and its related genes.
Collapse
Affiliation(s)
- Abolfazl Jafari-Sales
- Department of Microbiology, School of Basic Sciences, Kazerun Branch, Islamic Azad University, Kazerun, Iran
| | - Noor S K Al-Khafaji
- Department of Biology, College of Science, University of Babylon, Babylon, Hilla City, Iraq
| | | | - Zahra Sadeghi Deylamdeh
- Department of Biology, Faculty of Sciences, Malayer Branch, Islamic Azad University, Malayer, Iran
| | - Sousan Akrami
- Students' Scientific Research Center (SSRC), Tehran University of Medical Sciences, Tehran, Iran.
- Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
| | - Afsoon Shariat
- Department of Microbiology, School of Basic Sciences, Kazerun Branch, Islamic Azad University, Kazerun, Iran
| | - Hawraa K Judi
- Department of Medical Physics, Hilla University College, Babylon, Iraq
| | - Rozita Nasiri
- Iran National Elite Foundation, 93111-14578, Tehran, Iran
| | - Hossein Bannazadeh Baghi
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Morteza Saki
- Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
| |
Collapse
|
13
|
Sato T, Ito R, Kawamura M, Fujimura S. The Drug-Specific Propensity Regarding the Acquisition of Fluoroquinolone Resistance in Escherichia coli: An in vitro Challenge and DNA Mutation Analysis. Infect Drug Resist 2023; 16:6357-6366. [PMID: 37789839 PMCID: PMC10543074 DOI: 10.2147/idr.s428383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 09/21/2023] [Indexed: 10/05/2023] Open
Abstract
Objective Many fluoroquinolones, such as ciprofloxacin, are used clinically. We investigated the relationship between resistance acquisition and exposure duration in each drug through the exposure of fluoroquinolone to Escherichia coli clinical isolates in vitro. Methods Eleven E. coli clinical isolates were exposed to each fluoroquinolone, ie, ciprofloxacin, levofloxacin, sitafloxacin, garenoxacin, and lascufloxacin, with the concentration of the mutant selection window for 5 days; these procedures were repeated 5-times. In addition, the DNA sequence in the quinolone-resistance determining region (QRDR) and the expression level in the drug efflux pump acrA were analyzed to determine the resistance mechanism. Results Although resistant strains were not detected after 5 to 10 days of exposure to fluoroquinolone, after 25 days of exposure to ciprofloxacin and levofloxacin, 100% and 45% of isolates acquired resistance, respectively. Due to 25 days of exposure to sitafloxacin, garenoxacin, and lascufloxacin, MIC measurement was elevated 2- to 4096-fold for those of the parental strain, and the cross-resistance rate to levofloxacin was 72%, 54%, and 27%, respectively. In strains with high fluoroquinolone resistance, acrA overexpression was observed in addition to QRDR mutation. Conclusion In our findings, fluoroquinolone resistance was not observed in the E. coli strain after 5- to 10-days of exposure. However, resistance acquisition was detected frequently after 15- to 25-days of exposure. Among fluoroquinolones, lascufloxacn had the least impact on the resistance acquisition in E. coli.
Collapse
Affiliation(s)
- Takumi Sato
- Division of Clinical Infectious Diseases & Chemotherapy, Tohoku Medical and Pharmaceutical University, Sendai, Japan
| | - Ryota Ito
- Division of Clinical Infectious Diseases & Chemotherapy, Tohoku Medical and Pharmaceutical University, Sendai, Japan
- Department of Pharmacy, Japan Labor Health and Welfare Organization Tohoku Rosai Hospital, Sendai, Japan
| | - Masato Kawamura
- Division of Clinical Infectious Diseases & Chemotherapy, Tohoku Medical and Pharmaceutical University, Sendai, Japan
| | - Shigeru Fujimura
- Division of Clinical Infectious Diseases & Chemotherapy, Tohoku Medical and Pharmaceutical University, Sendai, Japan
| |
Collapse
|