1
|
Orosz L, Burián K. The "COVID effect" in culture-based clinical microbiology: Changes induced by COVID-19 pandemic in a Hungarian tertiary care center. J Infect Public Health 2024; 17:102453. [PMID: 38820897 DOI: 10.1016/j.jiph.2024.05.041] [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: 02/03/2024] [Revised: 05/03/2024] [Accepted: 05/14/2024] [Indexed: 06/02/2024] Open
Abstract
BACKGROUND The presence of bacterial and fungal coinfections plays an important role in the mortality of patients with coronavirus 2019 (COVID-19). We compared data from the 3 years before and 3 years after the COVID-19 pandemic outbreak to evaluate its effect on the traits of bacterial and fungal diseases. METHODS We retrospectively collected and analyzed data on positive respiratory tract samples (n = 13,133 samples from 7717 patients) and blood cultures (n = 23,652 from 9653 patients) between 2017 and 2022 from the Clinical Center of the University of Szeged, Hungary. We also evaluated antimicrobial susceptibility test results derived from 169,020 respiratory samples and 549,729 blood cultures to gain insight into changes in antimicrobial resistance. RESULTS The most common respiratory pathogen in the pre-COVID era was Pseudomonas aeruginosa, whereas Candida albicans was the most frequent during the pandemic. The number of respiratory isolates of Acinetobacter baumannii was also markedly increased. In blood cultures, Staphylococcus epidermidis, Escherichia coli, and S. aureus were dominant during the study period, and A. baumannii was widespread in blood cultures during the pandemic years. Resistance to ofloxacin, penicillin, piperacillin-tazobactam, ceftazidime, cefepime, imipenem, ceftolozane-tazobactam, and itraconazole increased significantly in the COVID era. CONCLUSIONS During the COVID-19 pandemic, there were changes in the prevalence of respiratory and blood culture pathogens at the Clinical Center of the University of Szeged. C. albicans became the predominant respiratory pathogen, and the number of A. baumannii isolates increased dramatically. Additionally, antimicrobial resistance notably increased during this period.
Collapse
Affiliation(s)
- László Orosz
- Department of Medical Microbiology, University of Szeged, H-6725 Szeged Semmelweis str. 6/b., Hungary.
| | - Katalin Burián
- Department of Medical Microbiology, University of Szeged, H-6725 Szeged Semmelweis str. 6/b., Hungary
| |
Collapse
|
2
|
Wang J, Zhang M, Pei J, Yi W, Fan L, Wang C, Xiao X. Isolation and identification of a novel phage targeting clinical multidrug-resistant Corynebacterium striatum isolates. Front Cell Infect Microbiol 2024; 14:1361045. [PMID: 38572320 PMCID: PMC10987712 DOI: 10.3389/fcimb.2024.1361045] [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: 12/24/2023] [Accepted: 02/26/2024] [Indexed: 04/05/2024] Open
Abstract
Introduction Over the past decade, Corynebacterium striatum (C. striatum), an emerging multidrug-resistant (MDR) pathogen, has significantly challenged healthcare settings, especially those involving individuals with weakened immune systems. The rise of these superbugs necessitates innovative solutions. Methods This study aimed to isolate and characterize bacteriophages targeting MDR-C. striatum. Utilizing 54 MDR-C. striatum isolates from a local hospital as target strains, samples were collected from restroom puddles for phage screening. Dot Plaque and Double-layer plate Assays were employed for screening. Results A novel temperate bacteriophage, named CSP1, was identified through a series of procedures, including purification, genome extraction, sequencing, and one-step growth curves. CSP1 possesses a 39,752 base pair circular double-stranded DNA genome with HK97-like structural proteins and potential for site-specific recombination. It represents a new species within the unclassified Caudoviricetes class, as supported by transmission electron microscopy, genomic evolutionary analysis, and collinearity studies. Notably, CSP1 infected and lysed 21 clinical MDR-C. striatum isolates, demonstrating a wide host range. The phage remained stable in conditions ranging from -40 to 55°C, pH 4 to 12, and in 0.9% NaCl buffer, showing no cytotoxicity. Discussion The identification of CSP1 as the first phage targeting clinical C. striatum strains opens new possibilities in bacteriophage therapy research, and the development of diagnostic and therapeutic tools against pathogenic bacteria.
Collapse
Affiliation(s)
- Jiao Wang
- Department of Pathogen Biology, School of Basic Medicine, Hubei University of Arts and Science, Xiangyang, China
| | - Meng Zhang
- Department of Pathogen Biology, School of Basic Medicine, Hubei University of Arts and Science, Xiangyang, China
| | - Jiao Pei
- Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, China
| | - Wei Yi
- Department of Pathogen Biology, School of Basic Medicine, Hubei University of Arts and Science, Xiangyang, China
| | - Li Fan
- Department of Pathogen Biology, School of Basic Medicine, Hubei University of Arts and Science, Xiangyang, China
| | - Chunhua Wang
- Department of Clinical Laboratory, Xiangyang No.1 People’s Hospital, Hubei University of Medicine, Xiangyang, China
| | - Xiao Xiao
- Department of Pathogen Biology, School of Basic Medicine, Hubei University of Medicine, Shiyan, China
| |
Collapse
|
3
|
Galanis A, Karampitianis S, Vlamis J, Karampinas P, Vavourakis M, Vlachos C, Papagrigorakis E, Zachariou D, Sakellariou E, Varsamos I, Patilas C, Tsiplakou S, Papaioannou V, Kamariotis S. Corynebacterium striatum Periprosthetic Hip Joint Infection: An Uncommon Pathogen of Concern? Healthcare (Basel) 2024; 12:273. [PMID: 38275553 PMCID: PMC10815444 DOI: 10.3390/healthcare12020273] [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: 11/28/2023] [Revised: 01/08/2024] [Accepted: 01/19/2024] [Indexed: 01/27/2024] Open
Abstract
BACKGROUND Total hip arthroplasty is indubitably a dominant elective surgery in orthopaedics, contributing to prodigious improvement in the quality of life of patients with osteoarthritis. One of the most potentially devastating complications of this operation is periprosthetic joint infection. Immunocompromised patients might be afflicted by infrequent low-virulence organisms not typically detected with conventional procedures. Consequently, employing advanced identification methods, such as the circumstantial sonication of orthopaedic implants, could be crucial to managing such cases. CASE PRESENTATION We present a peculiar case of a 72-year-old female patient suffering from a chronic periprosthetic hip infection due to Corynebacterium striatum. The pathogen was only identified after rigorous sonication of the extracted implants. The overall management of this case was immensely exacting, primarily because of the patient's impaired immune system, and was finally treated with two-stage revision in our Institution. LITERATURE REVIEW Although copious literature exists concerning managing periprosthetic hip infections, no concrete guidelines are available for such infections in multimorbid or immunocompromised patients with rare low-virulence microorganisms. Hence, a diagnostic work-up, antibiotic treatment and appropriate revision timeline must be determined. Sonication of extracted implants could be a powerful tool in the diagnostic arsenal, as it can aid in identifying rare microbes, such as Corynebacterium spp. Pertinent antibiotic treatment based on antibiogram analysis and apposite final revision-surgery timing are the pillars for effective therapy of such infections. CLINICAL RELEVANCE Corynebacterium striatum has been increasingly recognized as an emerging cause of periprosthetic hip infection in the last decade. A conspicuous rise in such reports has been observed in multimorbid or immunocompromised patients after the COVID-19 pandemic. This case is the first report of Corynebacterium striatum periprosthetic hip infection diagnosed solely after the sonication of extracted implants. This paper aims to increase awareness surrounding Corynebacterium spp. prosthetic joint infections, while highlighting the fields for further apposite research.
Collapse
Affiliation(s)
- Athanasios Galanis
- 3rd Department of Orthopaedic Surgery, National & Kapodistrian University of Athens, KAT General Hospital, Kifisia, 14561 Athens, Greece; (A.G.); (S.K.); (J.V.); (P.K.); (C.V.); (E.P.); (D.Z.); (E.S.); (I.V.); (C.P.)
| | - Spyridon Karampitianis
- 3rd Department of Orthopaedic Surgery, National & Kapodistrian University of Athens, KAT General Hospital, Kifisia, 14561 Athens, Greece; (A.G.); (S.K.); (J.V.); (P.K.); (C.V.); (E.P.); (D.Z.); (E.S.); (I.V.); (C.P.)
| | - John Vlamis
- 3rd Department of Orthopaedic Surgery, National & Kapodistrian University of Athens, KAT General Hospital, Kifisia, 14561 Athens, Greece; (A.G.); (S.K.); (J.V.); (P.K.); (C.V.); (E.P.); (D.Z.); (E.S.); (I.V.); (C.P.)
| | - Panagiotis Karampinas
- 3rd Department of Orthopaedic Surgery, National & Kapodistrian University of Athens, KAT General Hospital, Kifisia, 14561 Athens, Greece; (A.G.); (S.K.); (J.V.); (P.K.); (C.V.); (E.P.); (D.Z.); (E.S.); (I.V.); (C.P.)
| | - Michail Vavourakis
- 3rd Department of Orthopaedic Surgery, National & Kapodistrian University of Athens, KAT General Hospital, Kifisia, 14561 Athens, Greece; (A.G.); (S.K.); (J.V.); (P.K.); (C.V.); (E.P.); (D.Z.); (E.S.); (I.V.); (C.P.)
| | - Christos Vlachos
- 3rd Department of Orthopaedic Surgery, National & Kapodistrian University of Athens, KAT General Hospital, Kifisia, 14561 Athens, Greece; (A.G.); (S.K.); (J.V.); (P.K.); (C.V.); (E.P.); (D.Z.); (E.S.); (I.V.); (C.P.)
| | - Eftychios Papagrigorakis
- 3rd Department of Orthopaedic Surgery, National & Kapodistrian University of Athens, KAT General Hospital, Kifisia, 14561 Athens, Greece; (A.G.); (S.K.); (J.V.); (P.K.); (C.V.); (E.P.); (D.Z.); (E.S.); (I.V.); (C.P.)
| | - Dimitrios Zachariou
- 3rd Department of Orthopaedic Surgery, National & Kapodistrian University of Athens, KAT General Hospital, Kifisia, 14561 Athens, Greece; (A.G.); (S.K.); (J.V.); (P.K.); (C.V.); (E.P.); (D.Z.); (E.S.); (I.V.); (C.P.)
| | - Evangelos Sakellariou
- 3rd Department of Orthopaedic Surgery, National & Kapodistrian University of Athens, KAT General Hospital, Kifisia, 14561 Athens, Greece; (A.G.); (S.K.); (J.V.); (P.K.); (C.V.); (E.P.); (D.Z.); (E.S.); (I.V.); (C.P.)
| | - Iordanis Varsamos
- 3rd Department of Orthopaedic Surgery, National & Kapodistrian University of Athens, KAT General Hospital, Kifisia, 14561 Athens, Greece; (A.G.); (S.K.); (J.V.); (P.K.); (C.V.); (E.P.); (D.Z.); (E.S.); (I.V.); (C.P.)
| | - Christos Patilas
- 3rd Department of Orthopaedic Surgery, National & Kapodistrian University of Athens, KAT General Hospital, Kifisia, 14561 Athens, Greece; (A.G.); (S.K.); (J.V.); (P.K.); (C.V.); (E.P.); (D.Z.); (E.S.); (I.V.); (C.P.)
| | - Sofia Tsiplakou
- Department of Microbiology, KAT General Hospital, Kifisia, 14561 Athens, Greece; (S.T.); (V.P.); (S.K.)
| | - Vasiliki Papaioannou
- Department of Microbiology, KAT General Hospital, Kifisia, 14561 Athens, Greece; (S.T.); (V.P.); (S.K.)
| | - Spyridon Kamariotis
- Department of Microbiology, KAT General Hospital, Kifisia, 14561 Athens, Greece; (S.T.); (V.P.); (S.K.)
| |
Collapse
|
4
|
Orosz L, Lengyel G, Makai K, Burián K. Prescription of Rifampicin for Staphylococcus aureus Infections Increased the Incidence of Corynebacterium striatum with Decreased Susceptibility to Rifampicin in a Hungarian Clinical Center. Pathogens 2023; 12:pathogens12030481. [PMID: 36986404 PMCID: PMC10058903 DOI: 10.3390/pathogens12030481] [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: 02/01/2023] [Revised: 03/14/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023] Open
Abstract
Several reports have suggested a role for Corynebacterium striatum as an opportunistic pathogen. The authors have conducted a retrospective study at the Clinical Center of the University of Szeged, Hungary, between 2012 and 2021 that revealed significantly increased rifampicin resistance in this species. This work aimed to investigate the reasons behind this phenomenon. The data were collected corresponding to the period between 1 January 2012 and 31 December 2021 at the Department of Medical Microbiology, University of Szeged. To characterize the resistance trends, the antibiotic resistance index was calculated for each antibiotic in use. Fourteen strains with different resistance patterns were further analyzed with Fourier-transform infrared spectroscopy using the IR Biotyper®. The decline in C. striatum sensitivity to rifampicin seen during the COVID-19 pandemic may have been attributable to the use of Rifadin® to treat concomitant Staphylococcus aureus infections. The fact that the IR Biotyper® typing method revealed that the rifampicin-resistant C. striatum strains were closely related supports this hypothesis. The IR Biotyper® infrared spectroscopy proved to be a modern and fast method to support effective antimicrobial stewardship programs.
Collapse
Affiliation(s)
- László Orosz
- Department of Medical Microbiology, University of Szeged, H-6725 Szeged, Hungary
| | - György Lengyel
- Infection Control Department, Semmelweis University, H-1085 Budapest, Hungary
| | - Klára Makai
- Central Pharmacy of Albert Szent-Györgyi Health Center, University of Szeged, H-6725 Szeged, Hungary
| | - Katalin Burián
- Department of Medical Microbiology, University of Szeged, H-6725 Szeged, Hungary
| |
Collapse
|
5
|
Ravichandran S, Avatapalli S, Narasimhan Y, Kaushik KS, Yennamalli RM. 'Targeting' the search: An upgraded structural and functional repository of antimicrobial peptides for biofilm studies (B-AMP v2.0) with a focus on biofilm protein targets. Front Cell Infect Microbiol 2022; 12:1020391. [PMID: 36329825 PMCID: PMC9623296 DOI: 10.3389/fcimb.2022.1020391] [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: 08/16/2022] [Accepted: 09/16/2022] [Indexed: 12/29/2022] Open
Abstract
Bacterial biofilms, often as multispecies communities, are recalcitrant to conventional antibiotics, making the treatment of biofilm infections a challenge. There is a push towards developing novel anti-biofilm approaches, such as antimicrobial peptides (AMPs), with activity against specific biofilm targets. In previous work, we developed Biofilm-AMP, a structural and functional repository of AMPs for biofilm studies (B-AMP v1.0) with more than 5000 structural models of AMPs and a vast library of AMP annotations to existing biofilm literature. In this study, we present an upgraded version of B-AMP, with a focus on existing and novel bacterial biofilm targets. B-AMP v2.0 hosts a curated collection of 2502 biofilm protein targets across 473 bacterial species, with structural protein models and functional annotations from PDB, UniProt, and PubMed databases. The biofilm targets can be searched for using the name of the source organism, and function and type of protein, and results include designated Target IDs (unique to B-AMP v2.0), UniProt IDs, 3D predicted protein structures, PDBQT files, pre-defined protein functions, and relevant scientific literature. To present an example of the combined applicability of both, the AMP and biofilm target libraries in the repository, we present two case studies. In the first case study, we expand an in silico pipeline to evaluate AMPs against a single biofilm target in the multidrug resistant, bacterial pathogen Corynebacterium striatum, using 3D protein-peptide docking models from previous work and Molecular Dynamics simulations (~1.2µs). In the second case study, we build an in silico pipeline to identify candidate AMPs (using AMPs with both anti-Gram positive and anti-Gram negative activity) against two biofilm targets with a common functional annotation in Pseudomonas aeruginosa and Staphylococcus aureus, widely-encountered bacterial co-pathogens. With its enhanced structural and functional capabilities, B-AMP v2.0 serves as a comprehensive resource for AMP investigations related to biofilm studies. B-AMP v2.0 is freely available at https://b-amp.karishmakaushiklab.com and will be regularly updated with structural models of AMPs and biofilm targets, as well as 3D protein-peptide interaction models for key biofilm-forming pathogens.
Collapse
Affiliation(s)
- Shashank Ravichandran
- Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | | | - Yatindrapravanan Narasimhan
- Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | - Karishma S. Kaushik
- Department of Biotechnology, Savitribai Phule Pune University, Pune, India,*Correspondence: Karishma S. Kaushik, ; Ragothaman M. Yennamalli,
| | - Ragothaman M. Yennamalli
- Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India,*Correspondence: Karishma S. Kaushik, ; Ragothaman M. Yennamalli,
| |
Collapse
|
6
|
Wang J, Pei J, Liu M, Huang R, Li J, Liao S, Liang J. Identification and Evolutionary Relationship of Corynebacterium striatum Clinical Isolates. Pathogens 2022; 11:pathogens11091012. [PMID: 36145444 PMCID: PMC9501166 DOI: 10.3390/pathogens11091012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 08/27/2022] [Accepted: 09/02/2022] [Indexed: 11/16/2022] Open
Abstract
Corynebacterium striatum has developed into a new community-acquired and hospital-acquired multi-drug resistance (MDR) bacterium, and is a potential target pathogen for infection control and antibacterial management projects. In this study, non-duplicate samples of inpatients were collected from a local central hospital. Mass spectrometry showed that 54 C. striatum isolates mainly appeared in secretion and sputum from 14 departments. Protein fingerprint cluster analysis showed that the isolates were divided into four groups, most of which appeared in summer. The drug resistance test showed that all strains had multi-drug resistance, with high resistance rates to lincosamides, quinolones and tetracycline detected. Further analysis of the phylogenetic tree of C. striatum was conducted by cloning the 16S rRNA gene. It was found that isolates in the same department had high homology and tended to be located in the same branch or to be crossed in the same main branch. The strains in the same evolutionary branch group had the same drug resistance. Screening of site-specific recombinant elements revealed that 18 strains had integrase genes with the same sequence. This study shows that there may be mobile genetic elements in clinical isolates that drive gene exchange among strains, thus causing the cross-infection, spread and evolution of pathogenic bacteria in the hospital.
Collapse
Affiliation(s)
- Jiao Wang
- School of Basic Medicine, Hubei University of Arts and Science, Xiangyang 441053, China
- Correspondence: (J.W.); (J.P.)
| | - Jiao Pei
- Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang 441021, China
- Correspondence: (J.W.); (J.P.)
| | - Mingming Liu
- School of Basic Medicine, Hubei University of Arts and Science, Xiangyang 441053, China
| | - Rui Huang
- School of Basic Medicine, Hubei University of Arts and Science, Xiangyang 441053, China
| | - Jiqiang Li
- School of Basic Medicine, Hubei University of Arts and Science, Xiangyang 441053, China
| | - Shiying Liao
- School of Basic Medicine, Hubei University of Arts and Science, Xiangyang 441053, China
| | - Jian Liang
- Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang 441021, China
| |
Collapse
|