1
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Dang Z, Yang B, Xia P, Huang J, Liao J, Li Y, Tang S, Han Q, Luo S, Xia Y. Antimicrobial susceptibilities, resistance mechanisms and molecular characteristics of toxigenic Clostridioides difficile isolates in a large teaching hospital in Chongqing, China. J Glob Antimicrob Resist 2024; 38:198-204. [PMID: 39048055 DOI: 10.1016/j.jgar.2024.07.006] [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: 08/21/2023] [Revised: 07/05/2024] [Accepted: 07/12/2024] [Indexed: 07/27/2024] Open
Abstract
OBJECTIVES Clostridioides difficile ranks among the primary sources of healthcare-related infections and diarrhoea in numerous nations. We evaluated the drug susceptibility and resistance mechanisms of C. difficile isolates from a hospital in Chongqing, China, and identified resistance rates and resistance mechanisms that differed from previous findings. METHODS The toxin genes and drug resistance genes of clinical strains were detected using Polymerase Chain Reaction (PCR), and these strains were subjected to Multilocus Sequence Typing (MLST). The agar dilution technique was employed for assessing susceptibility of antibiotics. Clinical data collection was completed through a review of electronic medical records. RESULTS A total of 67 strains of toxin-producing C. difficile were detected. All C. difficile isolates demonstrated susceptibility to both metronidazole and vancomycin. However, resistance was observed in 8.95%, 16.42%, 56.72%, 56.72%, 31.34% and 5.97% of the isolates for tigecycline, tetracycline, clindamycin, erythromycin, moxifloxacin and rifampin, respectively. Among the strains with toxin genotypes A + B + CDT - and belonging to the ST3, six strains exhibited reduced susceptibility to tigecycline (MIC=0.5mg/L) and tetracycline (MIC=8mg/L). The tetA(P) and tetB(P) genes were present in these six strains, but were absent in tetracycline-resistant strains. Resistance genes (ermB, tetM, tetA(P) and tetB(P)) and mutations (in gyrA, gyrB, and rpoB) were identified in resistant strains. CONCLUSIONS In contrast to prior studies, we found higher proportions of ST3 isolates with decreased tigecycline sensitivity, sharing similar resistance patterns and resistance genes. In the resistance process of tigecycline and tetracycline, the tetA(P) and tetB(P) genes may play a weak role.
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Affiliation(s)
- Zijun Dang
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Bingxue Yang
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Peiwen Xia
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jinzhu Huang
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jiajia Liao
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yuqiong Li
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Shiyu Tang
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Qi Han
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Shengli Luo
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yun Xia
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
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Di Bella S, Sanson G, Monticelli J, Zerbato V, Principe L, Giuffrè M, Pipitone G, Luzzati R. Clostridioides difficile infection: history, epidemiology, risk factors, prevention, clinical manifestations, treatment, and future options. Clin Microbiol Rev 2024; 37:e0013523. [PMID: 38421181 PMCID: PMC11324037 DOI: 10.1128/cmr.00135-23] [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] [Indexed: 03/02/2024] Open
Abstract
SUMMARYClostridioides difficile infection (CDI) is one of the major issues in nosocomial infections. This bacterium is constantly evolving and poses complex challenges for clinicians, often encountered in real-life scenarios. In the face of CDI, we are increasingly equipped with new therapeutic strategies, such as monoclonal antibodies and live biotherapeutic products, which need to be thoroughly understood to fully harness their benefits. Moreover, interesting options are currently under study for the future, including bacteriophages, vaccines, and antibiotic inhibitors. Surveillance and prevention strategies continue to play a pivotal role in limiting the spread of the infection. In this review, we aim to provide the reader with a comprehensive overview of epidemiological aspects, predisposing factors, clinical manifestations, diagnostic tools, and current and future prophylactic and therapeutic options for C. difficile infection.
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Affiliation(s)
- Stefano Di Bella
- Clinical Department of
Medical, Surgical and Health Sciences, Trieste
University, Trieste,
Italy
| | - Gianfranco Sanson
- Clinical Department of
Medical, Surgical and Health Sciences, Trieste
University, Trieste,
Italy
| | - Jacopo Monticelli
- Infectious Diseases
Unit, Trieste University Hospital
(ASUGI), Trieste,
Italy
| | - Verena Zerbato
- Infectious Diseases
Unit, Trieste University Hospital
(ASUGI), Trieste,
Italy
| | - Luigi Principe
- Microbiology and
Virology Unit, Great Metropolitan Hospital
“Bianchi-Melacrino-Morelli”,
Reggio Calabria, Italy
| | - Mauro Giuffrè
- Clinical Department of
Medical, Surgical and Health Sciences, Trieste
University, Trieste,
Italy
- Department of Internal
Medicine (Digestive Diseases), Yale School of Medicine, Yale
University, New Haven,
Connecticut, USA
| | - Giuseppe Pipitone
- Infectious Diseases
Unit, ARNAS Civico-Di Cristina
Hospital, Palermo,
Italy
| | - Roberto Luzzati
- Clinical Department of
Medical, Surgical and Health Sciences, Trieste
University, Trieste,
Italy
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3
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Markantonis JE, Fallon JT, Madan R, Alam MZ. Clostridioides difficile Infection: Diagnosis and Treatment Challenges. Pathogens 2024; 13:118. [PMID: 38392856 PMCID: PMC10891949 DOI: 10.3390/pathogens13020118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 02/25/2024] Open
Abstract
Clostridioides difficile is the most important cause of healthcare-associated diarrhea in the United States. The high incidence and recurrence rates of C. difficile infection (CDI), associated with high morbidity and mortality, pose a public health challenge. Although antibiotics targeting C. difficile bacteria are the first treatment choice, antibiotics also disrupt the indigenous gut flora and, therefore, create an environment that is favorable for recurrent CDI. The challenge of treating CDI is further exacerbated by the rise of antibiotic-resistant strains of C. difficile, placing it among the top five most urgent antibiotic resistance threats in the USA. The evolution of antibiotic resistance in C. difficile involves the acquisition of new resistance mechanisms, which can be shared among various bacterial species and different C. difficile strains within clinical and community settings. This review provides a summary of commonly used diagnostic tests and antibiotic treatment strategies for CDI. In addition, it discusses antibiotic treatment and its resistance mechanisms. This review aims to enhance our current understanding and pinpoint knowledge gaps in antimicrobial resistance mechanisms in C. difficile, with an emphasis on CDI therapies.
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Affiliation(s)
- John E. Markantonis
- Department of Pathology and Laboratory Medicine, Brody School of Medicine, East Carolina University, 600 Moye Boulevard, Greenville, NC 27834, USA; (J.E.M.); (J.T.F.)
| | - John T. Fallon
- Department of Pathology and Laboratory Medicine, Brody School of Medicine, East Carolina University, 600 Moye Boulevard, Greenville, NC 27834, USA; (J.E.M.); (J.T.F.)
| | - Rajat Madan
- Division of Infectious Diseases, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA;
- Veterans Affairs Medical Center, Cincinnati, OH 45220, USA
| | - Md Zahidul Alam
- Department of Pathology and Laboratory Medicine, Brody School of Medicine, East Carolina University, 600 Moye Boulevard, Greenville, NC 27834, USA; (J.E.M.); (J.T.F.)
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4
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Wickramage I, Peng Z, Chakraborty S, Harmanus C, Kuijper EJ, Alrabaa S, Smits WK, Sun X. The vanRCd Mutation 343A>G, Resulting in a Thr115Ala Substitution, Is Associated with an Elevated Minimum Inhibitory Concentration (MIC) of Vancomycin in Clostridioides difficile Clinical Isolates from Florida. Microbiol Spectr 2023; 11:e0377722. [PMID: 37125917 PMCID: PMC10269549 DOI: 10.1128/spectrum.03777-22] [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: 09/16/2022] [Accepted: 04/07/2023] [Indexed: 05/02/2023] Open
Abstract
Clostridioides difficile, the primary cause of nosocomial antibiotic-associated diarrhea, has a complex relationship with antibiotics. While the use of broad-spectrum antibiotics disrupts the gut microbiota and increases the risk of C. difficile infection (CDI), antibiotics are also the primary treatment for CDI. However, only a few antibiotics, including vancomycin, fidaxomicin, and rifaximin, are effective against CDI, and resistance to these antibiotics has emerged recently. In this study, we report the identification of two RT027 C. difficile clinical isolates (TGH35 and TGH64) obtained from symptomatic CDI-diagnosed patients in Tampa, Florida in 2016. These two strains showed an elevated minimum inhibitory concentration (MIC) of vancomycin (MIC = 4 μg/mL, compared to the EUCAST breakpoint of 2 μg/mL) and contained a vanRCd 343A>G mutation resulting in a Thr115Ala substitution in the VanRCd response regulator. This mutation was absent in the vancomycin-sensitive control epidemic strain RT027/R20291. TGH64 was also resistant to rifaximin (MIC ≥ 128 μg/mL) and carried the previously reported Arg505Lys and Ile548Met mutations in RpoB. Furthermore, we report on the antimicrobial resistance (AMR) and genomic characterization of additional C. difficile isolates, including RT106/TGH120, RT017/TGH33, and RT017/TGH51, obtained from the same patient sample cohort representing the highly prevalent and regionally distributed C. difficile ribotypes worldwide. Considering that the VanRCd Thr115Ala mutation was also independently reported in seven C. difficile clinical isolates from Texas and Israel in 2019, we recommend epidemiological surveillance to better understand the impact of this mutation on vancomycin resistance. IMPORTANCE The perpetually evolving antimicrobial resistance (AMR) of C. difficile is an important contributor to its epidemiology and is a grave concern to global public health. This exacerbates the challenge of treating the infections caused by this multidrug-resistant causative organism of potentially life-threatening diarrhea. Further, the novel resistance-determining factors can be transferred between different strains and species of bacteria and cause the spread of AMR in clinical, environmental, and community settings. In this study, we have identified a mutation (vanRCd 343A>G) that causes a Thr115Ala substitution and is linked to an increased MIC of vancomycin in clinical isolates of C. difficile obtained from Florida in 2016. Understanding the mechanisms of AMR, especially those of newly evolving strains, is essential to effectively guide antibiotic stewardship policies to combat antibiotic resistance as well as to discover novel therapeutic targets.
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Affiliation(s)
- Ishani Wickramage
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Zhong Peng
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Soumyadeep Chakraborty
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Céline Harmanus
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Ed J. Kuijper
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
- National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Sally Alrabaa
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Wiep Klaas Smits
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Xingmin Sun
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
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5
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Marcos P, Whyte P, Burgess C, Ekhlas D, Bolton D. Detection and Genomic Characterisation of Clostridioides difficile from Spinach Fields. Pathogens 2022; 11:1310. [PMID: 36365061 PMCID: PMC9695345 DOI: 10.3390/pathogens11111310] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/27/2022] [Accepted: 11/02/2022] [Indexed: 10/29/2023] Open
Abstract
Despite an increased incidence of Clostridioides difficile infections, data on the reservoirs and dissemination routes of this bacterium are limited. This study examined the prevalence and characteristics of C. difficile isolates in spinach fields. C. difficile was detected in 2/60 (3.3%) of spinach and 6/60 (10%) of soil samples using culture-based techniques. Whole genome sequencing (WGS) analysis identified the spinach isolates as belonging to the hypervirulent clade 5, sequence type (ST) 11, ribotypes (RT) 078 and 126 and carried the genes encoding toxins A, B and CDT. The soil isolates belonged to clade 1 with different toxigenic ST/RT (ST19/RT614, ST12/RT003, ST46/RT087, ST16/RT050, ST49/RT014/0) strains and one non-toxigenic ST79/RT511 strain. Antimicrobial resistance to erythromycin (one spinach isolate), rifampicin (two soil isolates), clindamycin (one soil isolate), both moxifloxacin and rifampicin (one soil isolate), and multi-drug resistance to erythromycin, vancomycin and rifampicin (two soil isolates) were observed using the E test, although a broader range of resistance genes were detected using WGS. Although the sample size was limited, our results demonstrate the presence of C. difficile in horticulture and provide further evidence that there are multiple sources and dissemination routes for these bacteria.
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Affiliation(s)
- Pilar Marcos
- Teagasc Food Research Centre, Ashtown, 15 Dublin, D15 DY05 Dublin, Ireland
- School of Veterinary Medicine, University College Dublin, Belfield, 4 Dublin, D04 V1W8 Dublin, Ireland
| | - Paul Whyte
- School of Veterinary Medicine, University College Dublin, Belfield, 4 Dublin, D04 V1W8 Dublin, Ireland
| | - Catherine Burgess
- Teagasc Food Research Centre, Ashtown, 15 Dublin, D15 DY05 Dublin, Ireland
| | - Daniel Ekhlas
- Teagasc Food Research Centre, Ashtown, 15 Dublin, D15 DY05 Dublin, Ireland
- School of Veterinary Medicine, University College Dublin, Belfield, 4 Dublin, D04 V1W8 Dublin, Ireland
| | - Declan Bolton
- Teagasc Food Research Centre, Ashtown, 15 Dublin, D15 DY05 Dublin, Ireland
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6
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Kullin B, Abratt VR, Reid SJ, Riley TV. Clostridioides difficile infection in Africa: A narrative review. Anaerobe 2022; 74:102549. [PMID: 35337974 DOI: 10.1016/j.anaerobe.2022.102549] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 03/13/2022] [Accepted: 03/17/2022] [Indexed: 12/12/2022]
Abstract
Clostridioides (Clostridium) difficile infection (CDI) places a burden on healthcare facilities worldwide. Most research studies have been concentrated in high-income countries in North America, Europe, Asia and Australia, where C. difficile is the leading cause of diarrhoea associated with antimicrobial use. This narrative review summarises African CDI studies, focussing on reports published in the last 20 years. Although relatively sparse, the data suggest that CDI is an important cause of diarrhoea on the continent. African CDI patient populations are often younger than in European and North American settings, probably due to the high prevalence of co-morbid conditions such as tuberculosis, particularly in sub-Saharan Africa. Strain typing data are rare and where reported generally limited to single sites and institutions. Despite challenges, including a lack of facilities and awareness, there is a need for further investigation to more accurately determine the true burden of disease caused by C. difficile in Africa.
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Affiliation(s)
- Brian Kullin
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Valerie R Abratt
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Sharon J Reid
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Thomas V Riley
- Medical, Molecular and Forensic Sciences, Murdoch University, Murdoch, Western Australia WA, Australia; School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia; Department of Microbiology, PathWest Laboratory Medicine, Nedlands, WA, Australia; School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia.
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7
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Dureja C, Olaitan AO, Hurdle JG. Mechanisms and impact of antimicrobial resistance in Clostridioides difficile. Curr Opin Microbiol 2022; 66:63-72. [PMID: 35077947 PMCID: PMC9064893 DOI: 10.1016/j.mib.2022.01.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 12/10/2021] [Accepted: 01/07/2022] [Indexed: 11/03/2022]
Abstract
The evolution of antimicrobial resistance in Clostridioides difficile has markedly shaped its epidemiology and detrimentally impacted patient care. C. difficile exhibits resistance to multiple classes of antimicrobials, due to accumulation of horizontally acquired resistance genes and de novo mutations to drug targets. Particularly worrying is that declines in clinical success of firstline CDI antimicrobials coincide with the spread of strains that are more resistant to these drugs. Yet, there is still much to learn regarding the prevalence of genetic elements in clinical isolates, their molecular mechanisms, and the extent to which this information can be translated to develop molecular diagnostics that improve antimicrobial prescribing and antimicrobial stewardship approaches for CDI. Thus, this perspective discusses current understanding and knowledge gaps of antimicrobial resistance mechanisms in C. difficile, emphasizing on CDI therapies.
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Affiliation(s)
- Chetna Dureja
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Department of Translational Medical Sciences, Texas A&M Health Science Center, 2121 West Holcombe Blvd, Houston, TX 77030, USA
| | - Abiola O Olaitan
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Department of Translational Medical Sciences, Texas A&M Health Science Center, 2121 West Holcombe Blvd, Houston, TX 77030, USA
| | - Julian G Hurdle
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Department of Translational Medical Sciences, Texas A&M Health Science Center, 2121 West Holcombe Blvd, Houston, TX 77030, USA.
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8
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Imwattana K, Rodríguez C, Riley TV, Knight DR. A species-wide genetic atlas of antimicrobial resistance in Clostridioides difficile. Microb Genom 2021; 7:000696. [PMID: 34793295 PMCID: PMC8743556 DOI: 10.1099/mgen.0.000696] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 09/23/2021] [Indexed: 12/27/2022] Open
Abstract
Antimicrobial resistance (AMR) plays an important role in the pathogenesis and spread of Clostridioides difficile infection (CDI), the leading healthcare-related gastrointestinal infection in the world. An association between AMR and CDI outbreaks is well documented, however, data is limited to a few ‘epidemic’ strains in specific geographical regions. Here, through detailed analysis of 10 330 publicly-available C. difficile genomes from strains isolated worldwide (spanning 270 multilocus sequence types (STs) across all known evolutionary clades), this study provides the first species-wide snapshot of AMR genomic epidemiology in C. difficile . Of the 10 330 C . difficile genomes, 4532 (43.9 %) in 89 STs across clades 1–5 carried at least one genotypic AMR determinant, with 901 genomes (8.7 %) carrying AMR determinants for three or more antimicrobial classes (multidrug-resistant, MDR). No AMR genotype was identified in any strains belonging to the cryptic clades. C. difficile from Australia/New Zealand had the lowest AMR prevalence compared to strains from Asia, Europe and North America (P <0.0001). Based on the phylogenetic clade, AMR prevalence was higher in clades 2 (84.3 %), 4 (81.5 %) and 5 (64.8 %) compared to other clades (collectively 26.9 %) (P <0.0001). MDR prevalence was highest in clade 4 (61.6 %) which was over three times higher than in clade 2, the clade with the second-highest MDR prevalence (18.3 %). There was a strong association between specific AMR determinants and three major epidemic C. difficile STs: ST1 (clade 2) with fluoroquinolone resistance (mainly T82I substitution in GyrA) (P <0.0001), ST11 (clade 5) with tetracycline resistance (various tet -family genes) (P <0.0001) and ST37 (clade 4) with macrolide-lincosamide-streptogramin B (MLSB) resistance (mainly ermB ) (P <0.0001) and MDR (P <0.0001). A novel and previously overlooked tetM -positive transposon designated Tn6944 was identified, predominantly among clade 2 strains. This study provides a comprehensive review of AMR in the global C. difficile population which may aid in the early detection of drug-resistant C. difficile strains, and prevention of their dissemination worldwide.
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Affiliation(s)
- Korakrit Imwattana
- School of Biomedical Sciences, University of Western Australia, Nedlands, Western Australia, Australia
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Nakhon Pathom, Thailand
| | - César Rodríguez
- Facultad de Microbiología & Centro de Investigación en Enfermedades Tropicales (CIET), Universidad de Costa Rica, San José, Costa Rica
| | - Thomas V. Riley
- School of Biomedical Sciences, University of Western Australia, Nedlands, Western Australia, Australia
- Medical, Molecular and Forensic Sciences, Murdoch University, Murdoch, Western Australia, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
- Department of Microbiology, PathWest Laboratory Medicine, Queen Elizabeth II Medical Centre, Nedlands, Western Australia, Australia
| | - Daniel R. Knight
- School of Biomedical Sciences, University of Western Australia, Nedlands, Western Australia, Australia
- Medical, Molecular and Forensic Sciences, Murdoch University, Murdoch, Western Australia, Australia
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9
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Wickramage I, Spigaglia P, Sun X. Mechanisms of antibiotic resistance of Clostridioides difficile. J Antimicrob Chemother 2021; 76:3077-3090. [PMID: 34297842 DOI: 10.1093/jac/dkab231] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Clostridioides difficile (CD) is one of the top five urgent antibiotic resistance threats in USA. There is a worldwide increase in MDR of CD, with emergence of novel strains which are often more virulent and MDR. Antibiotic resistance in CD is constantly evolving with acquisition of novel resistance mechanisms, which can be transferred between different species of bacteria and among different CD strains present in the clinical setting, community, and environment. Therefore, understanding the antibiotic resistance mechanisms of CD is important to guide optimal antibiotic stewardship policies and to identify novel therapeutic targets to combat CD as well as other bacteria. Epidemiology of CD is driven by the evolution of antibiotic resistance. Prevalence of different CD strains and their characteristic resistomes show distinct global geographical patterns. Understanding epidemiologically driven and strain-specific characteristics of antibiotic resistance is important for effective epidemiological surveillance of antibiotic resistance and to curb the inter-strain and -species spread of the CD resistome. CD has developed resistance to antibiotics with diverse mechanisms such as drug alteration, modification of the antibiotic target site and extrusion of drugs via efflux pumps. In this review, we summarized the most recent advancements in the understanding of mechanisms of antibiotic resistance in CD and analysed the antibiotic resistance factors present in genomes of a few representative well known, epidemic and MDR CD strains found predominantly in different regions of the world.
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Affiliation(s)
- Ishani Wickramage
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Down Blvd, Tampa, FL 33612, USA
| | - Patrizia Spigaglia
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Xingmin Sun
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Down Blvd, Tampa, FL 33612, USA
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10
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Imwattana K, Knight DR, Kullin B, Collins DA, Putsathit P, Kiratisin P, Riley TV. Antimicrobial resistance in Clostridium difficile ribotype 017. Expert Rev Anti Infect Ther 2019; 18:17-25. [PMID: 31800331 DOI: 10.1080/14787210.2020.1701436] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Introduction: Antimicrobial resistance (AMR) played an important role in the initial outbreaks of Clostridium difficile infection (CDI) in the 1970s. C. difficile ribotype (RT) 017 has emerged as the major strain of C. difficile in Asia, where antimicrobial use is poorly regulated. This strain has also caused CDI outbreaks around the world for almost 30 years. Many of these outbreaks were associated with clindamycin and fluoroquinolone resistance. AMR and selective pressure is likely to be responsible for the success of this RT and may drive future outbreaks.Areas covered: This narrative review summarizes the prevalence and mechanisms of AMR in C. difficile RT 017 and transmission of these AMR mechanisms. To address these topics, reports of outbreaks due to C. difficile RT 017, epidemiologic studies with antimicrobial susceptibility results, studies on resistance mechanisms found in C. difficile and related publications available through Pubmed until September 2019 were collated and the findings discussed.Expert opinion: Primary prevention is the key to control CDI. This should be achieved by developing antimicrobial stewardship in medical, veterinary and agricultural practices. AMR is the key factor that drives CDI outbreaks, and methods for the early detection of AMR can facilitate the control of outbreaks.
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Affiliation(s)
- Korakrit Imwattana
- School of Biomedical Sciences, The University of Western Australia, Crawley, Australia.,Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Daniel R Knight
- Medical, Molecular and Forensic Sciences, Murdoch University, Murdoch, Australia
| | - Brian Kullin
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Deirdre A Collins
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Australia
| | - Papanin Putsathit
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Australia
| | - Pattarachai Kiratisin
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Thomas V Riley
- School of Biomedical Sciences, The University of Western Australia, Crawley, Australia.,Medical, Molecular and Forensic Sciences, Murdoch University, Murdoch, Australia.,School of Medical and Health Sciences, Edith Cowan University, Joondalup, Australia.,PathWest Laboratory Medicine, Queen Elizabeth II Medical Centre, Nedlands, Australia
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11
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Kuehne SA, Dempster AW, Collery MM, Joshi N, Jowett J, Kelly ML, Cave R, Longshaw CM, Minton NP. Characterization of the impact of rpoB mutations on the in vitro and in vivo competitive fitness of Clostridium difficile and susceptibility to fidaxomicin. J Antimicrob Chemother 2019; 73:973-980. [PMID: 29253242 PMCID: PMC5890677 DOI: 10.1093/jac/dkx486] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 11/25/2017] [Indexed: 01/05/2023] Open
Abstract
Objectives To establish the role of specific, non-synonymous SNPs in the RNA polymerase β subunit (rpoB) gene in reducing the susceptibility of Clostridium difficile to fidaxomicin and to explore the potential in vivo significance of rpoB mutant strains. Methods Allelic exchange was used to introduce three different SNPs into the rpoB gene of an erythromycin-resistant derivative (CRG20291) of C. difficile R20291. The genome sequences of the created mutants were determined and each mutant analysed with respect to growth and sporulation rates, toxin A/B production and cytotoxicity against Vero cells, and in competition assays. Their comparative virulence and colonization ability was also assessed in a hamster infection model. Results The MIC of fidaxomicin displayed by three mutants CRG20291-TA, CRG20291-TG and CRG20291-GT was substantially increased (>32, 8 and 2 mg/L, respectively) relative to that of the parent strain (0.25 mg/L). Genome sequencing established that the intended mutagenic substitutions in rpoB were the only changes present. Relative to CRG20291, all mutants had attenuated growth, were outcompeted by the parental strain, had lower sporulation and toxin A/B production capacities, and displayed diminished cytotoxicity. In a hamster model, virulence of all three mutants was significantly reduced compared with the progenitor strain, whereas the degree of caecum colonization was unaltered. Conclusions Our study demonstrates that particular SNPs in rpoB lead to reduced fidaxomicin susceptibility. These mutations were associated with a fitness cost in vitro and reduced virulence in vivo.
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Affiliation(s)
- Sarah A Kuehne
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University of Nottingham, Nottingham, UK.,Gastrointestinal and Liver Disorders Theme of the NIHR Nottingham Biomedical Research Centre (BRC), Nottingham University Hospitals NHS Trust and University of Nottingham, Nottingham, UK.,School of Dentistry, Institute of Clinical Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Andrew W Dempster
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Mark M Collery
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Nimitray Joshi
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Jamie Jowett
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Michelle L Kelly
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Rory Cave
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University of Nottingham, Nottingham, UK
| | | | - Nigel P Minton
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University of Nottingham, Nottingham, UK.,Gastrointestinal and Liver Disorders Theme of the NIHR Nottingham Biomedical Research Centre (BRC), Nottingham University Hospitals NHS Trust and University of Nottingham, Nottingham, UK
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12
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Pyta K, Janas A, Szukowska M, Pecyna P, Jaworska M, Gajecka M, Bartl F, Przybylski P. Synthesis, docking and antibacterial studies of more potent amine and hydrazone rifamycin congeners than rifampicin. Eur J Med Chem 2019; 167:96-104. [PMID: 30769243 DOI: 10.1016/j.ejmech.2019.02.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Revised: 01/18/2019] [Accepted: 02/03/2019] [Indexed: 12/24/2022]
Abstract
New rifamycin congeners (1-33) with incorporated amine and hydrazone substituents leading to lipophilic and/or basic nature and altered rigidity of modified C(3) arm were synthesized and structurally characterized in detail. NMR spectroscopic studies at different temperatures indicate two types of structures of rifamycin congeners that are realized in solution: zwitterionic and non-ionic forms in dependence of the basicity of modified C(3) arm. The presence of rifamycin congeners in these two possible forms has a significant impact on the physico-chemical parameters such as lipophilicity (clogP) and water solubility and different binding mode of the C(3) arm of antibiotic at RNAP binding pocket (molecular target) leading to different antibacterial potency. The highest antibacterial potency against S. aureus (including MRSA and MLSB strains) and S. epidermidis strains, even higher than reference rifampicin (Rif) and rifaximin (Rifx) antibiotics, was found for rifamycin congeners bearing at the C(3) arm relatively rigid and basic substituents (bipiperidine and guanidine groups). These modifications provide favorable docking mode and excellent water solubility resulting in high potency (MICs 0.0078 μg/mL what gives ∼ 8.5 nM), irrespective whether rifamycin congener is a tertiary amine (15) or hydrazone (29). In turn, for a higher antibacterial potency of rifamycin congeners against E. faecalis strain (MICs 0.5 μg/mL that is 0.6 μM) as compared to Rif and Rifx, the most crucial factors are: bulkiness and the lipophilic character of the end of the C(3) rebuilt arm.
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Affiliation(s)
- Krystian Pyta
- Faculty of Chemistry, A. Mickiewicz University, Umultowska 89b, 61-614, Poznan, Poland
| | - Anna Janas
- Faculty of Chemistry, A. Mickiewicz University, Umultowska 89b, 61-614, Poznan, Poland
| | - Monika Szukowska
- Faculty of Chemistry, A. Mickiewicz University, Umultowska 89b, 61-614, Poznan, Poland
| | - Paulina Pecyna
- Department of Genetics and Pharmaceutical Microbiology, University of Medical Sciences, Swiecickiego 4, 60-781, Poznan, Poland
| | - Marcelina Jaworska
- Department of Genetics and Pharmaceutical Microbiology, University of Medical Sciences, Swiecickiego 4, 60-781, Poznan, Poland
| | - Marzena Gajecka
- Department of Genetics and Pharmaceutical Microbiology, University of Medical Sciences, Swiecickiego 4, 60-781, Poznan, Poland; Institute of Human Genetics, Polish Academy of Sciences, Strzeszynska 32, 60-479, Poznan, Poland
| | - Franz Bartl
- Humboldt-Universität zu Berlin, Lebenswissenschaftliche Fakultät, Institut für Biologie, Biophysikalische Chemie, Invalidenstr. 42, 10099, Berlin, Germany
| | - Piotr Przybylski
- Faculty of Chemistry, A. Mickiewicz University, Umultowska 89b, 61-614, Poznan, Poland.
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13
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Vernon JJ, Wilcox MH, Freeman J. Effect of fluoroquinolone resistance mutation Thr-82→Ile on Clostridioides difficile fitness. J Antimicrob Chemother 2018; 74:877-884. [DOI: 10.1093/jac/dky535] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 10/31/2018] [Accepted: 11/22/2018] [Indexed: 01/19/2023] Open
Affiliation(s)
- J J Vernon
- Healthcare-Associated Infections Research Group, Molecular Gastroenterology, Leeds Institute of Medical Research, University of Leeds, Old Medical School, Leeds General Infirmary, Leeds, UK
| | - M H Wilcox
- Healthcare-Associated Infections Research Group, Molecular Gastroenterology, Leeds Institute of Medical Research, University of Leeds, Old Medical School, Leeds General Infirmary, Leeds, UK
- Microbiology, Leeds Teaching Hospitals Trust, Leeds, UK
| | - J Freeman
- Healthcare-Associated Infections Research Group, Molecular Gastroenterology, Leeds Institute of Medical Research, University of Leeds, Old Medical School, Leeds General Infirmary, Leeds, UK
- Microbiology, Leeds Teaching Hospitals Trust, Leeds, UK
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14
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Kullin BR, Reid S, Abratt V. Clostridium difficile in patients attending tuberculosis hospitals in Cape Town, South Africa, 2014-2015. Afr J Lab Med 2018; 7:846. [PMID: 30568907 PMCID: PMC6295828 DOI: 10.4102/ajlm.v7i2.846] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 09/28/2018] [Indexed: 01/05/2023] Open
Abstract
Background Diarrhoea due to Clostridium difficile infection (CDI) poses a significant burden on healthcare systems around the world. However, there are few reports on the current status of the disease in sub-Saharan Africa. Objectives This study examined the occurrence of CDI in a South African population of tuberculosis patients, as well as the molecular epidemiology and antibiotic susceptibility profiles of C. difficile strains responsible for disease. Methods Toxigenic C. difficile in patients with suspected CDI attending two specialist tuberculosis hospitals in the Cape Town area were detected using a PCR-based diagnostic assay (Xpert® C. difficile). C. difficile strains isolated from PCR-positive specimens were characterised by ribotyping, multilocus variable-number tandem-repeat analysis and antibiotic susceptibility testing. Results The period prevalence of CDI was approximately 70.07 cases per 1000 patient admissions. Strains belonging to ribotype 017 (RT017) made up over 95% of the patient isolates and all of them were multi-drug resistant. Multilocus variable-number tandem-repeat analysis revealed several clusters of highly related C. difficile RT017 strains present in tuberculosis patients in several wards at each hospital. Conclusion Tuberculosis patients represent a population that may be at an increased risk of developing CDI and, in addition, may constitute a multi-drug resistant reservoir of this bacterium. This warrants further investigation and surveillance of the disease in this patient group and other high-risk patient groups in sub-Saharan Africa.
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Affiliation(s)
- Brian R Kullin
- Department of Molecular and Cell Biology, Faculty of Science, University of Cape Town, Cape Town, South Africa
| | - Sharon Reid
- Department of Molecular and Cell Biology, Faculty of Science, University of Cape Town, Cape Town, South Africa
| | - Valerie Abratt
- Department of Molecular and Cell Biology, Faculty of Science, University of Cape Town, Cape Town, South Africa
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15
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Yurieva O, Nikiforov V, Nikiforov V, O'Donnell M, Mustaev A. Insights into RNA polymerase catalysis and adaptive evolution gained from mutational analysis of a locus conferring rifampicin resistance. Nucleic Acids Res 2017; 45:11327-11340. [PMID: 29036608 PMCID: PMC5737076 DOI: 10.1093/nar/gkx813] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 09/06/2017] [Indexed: 01/25/2023] Open
Abstract
S531 of Escherichia coli RNA polymerase (RNAP) β subunit is a part of RNA binding domain in transcription complex. While highly conserved, S531 is not involved in interactions within the transcription complex as suggested by X-ray analysis. To understand the basis for S531 conservation we performed systematic mutagenesis of this residue. We find that the most of the mutations significantly decreased initiation-to-elongation transition by RNAP. Surprisingly, some changes enhanced the production of full-size transcripts by suppressing abortive loss of short RNAs. S531-R increased transcript retention by establishing a salt bridge with RNA, thereby explaining the R substitution at the equivalent position in extremophilic organisms, in which short RNAs retention is likely to be an issue. Generally, the substitutions had the same effect on bacterial doubling time when measured at 20°. Raising growth temperature to 37° ablated the positive influence of some mutations on the growth rate in contrast to their in vitro action, reflecting secondary effects of cellular environment on transcription and complex involvement of 531 locus in the cell biology. The properties of generated RNAP variants revealed an RNA/protein interaction network that is crucial for transcription, thereby explaining the details of initiation-to-elongation transition on atomic level.
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Affiliation(s)
- Olga Yurieva
- Laboratory of DNA Replication, The Rockefeller University and Howard Hughes Medical Institute, New York, NY 10065 USA
| | - Vadim Nikiforov
- Laboratory of DNA Replication, The Rockefeller University and Howard Hughes Medical Institute, New York, NY 10065 USA
| | - Vadim Nikiforov
- Public Health Research Institute, Newark, NJ 07103, USA.,Department of Microbiology, Biochemistry & Molecular Genetics, Rutgers New Jersey Medical School, Rutgers Biomedical and Health Sciences, Newark, NJ 07103, USA.,Institute of molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| | - Michael O'Donnell
- Laboratory of DNA Replication, The Rockefeller University and Howard Hughes Medical Institute, New York, NY 10065 USA
| | - Arkady Mustaev
- Public Health Research Institute, Newark, NJ 07103, USA.,Department of Microbiology, Biochemistry & Molecular Genetics, Rutgers New Jersey Medical School, Rutgers Biomedical and Health Sciences, Newark, NJ 07103, USA
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