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Yadav JP, Kaur S, Dhaka P, Vijay D, Bedi JS. Prevalence, molecular characterization, and antimicrobial resistance profile of Clostridium perfringens from India: A scoping review. Anaerobe 2022; 77:102639. [PMID: 36108893 DOI: 10.1016/j.anaerobe.2022.102639] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 04/27/2022] [Accepted: 09/07/2022] [Indexed: 11/01/2022]
Abstract
Clostridium perfringens is one of the most important foodborne pathogens that causes histotoxic diseases and intestinal infections in both humans and animals. The present scoping review has been designed to analyze the literature published during 2000-2021 from India on the prevalence, molecular characterization, and antimicrobial resistance profile of C. perfringens isolates recovered from humans, animals, animal-based foods, and associated environmental samples. The peer-reviewed articles retrieved from four electronic databases (Google Scholar, PubMed, Science Direct, and Web of Science) were assessed using PRISMA-ScR guidelines. A total of 32 studies from India were selected on the basis of their relevance and inclusion criteria. The overall prevalence of C. perfringens among domestic animals having history of clinical symptoms and among healthy animals was found to be 65.8% (508/772) and 42.8% (493/1152), respectively. The pathogen was also detected in clinically affected wild animals (75%), healthy wild animals (35.4%), and captive birds (24.5%). The detection of C. perfringens among poultry having necrotic enteritis and among healthy birds was found to be 66.8% (321/480) and 25.6% (80/312), respectively. The detection of pathogen among animal-based foods (i.e., meat, milk, and fish and their products) and environmental samples depicted a prevalence of 20.8% (325/1562) and 30.2% (23/76), respectively. However, the prevalence of C. perfringens among humans having history of diarrhea and among healthy humans was found to be 25% (70/280) and 23.2% (36/155), respectively. The genotyping of C. perfringens isolates revealed that toxin type A was found to be the most prevalent genotype. Along with the alpha toxin gene (cpa), beta (cpb), epsilon (etx), iota (itx), enterotoxin (cpe), beta-2 toxin (cpb2), and NetB (netB) toxins were also detected in different combinations. Antimicrobial resistance profile of C. perfringens isolates recovered from different sources demonstrated that the highest resistance was detected against sulphonamides (76.8%) and tetracycline (41.3%) by phenotypic and genotypic detection methods, respectively. Comprehensive scientific studies covering different geographical areas at the human-animal-environment interface are crucial to generalize the real magnitude of C. perfringens-associated problem in India and for establishing a reliable database.
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Affiliation(s)
- Jay Prakash Yadav
- Department of Veterinary Public Health and Epidemiology, College of Veterinary Science, Guru Angad Dev Veterinary and Animal Sciences University, Rampura Phul, Bathinda, 151103, India.
| | - Simranpreet Kaur
- Centre for One Health, College of Veterinary Science, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, 141004, India
| | - Pankaj Dhaka
- Centre for One Health, College of Veterinary Science, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, 141004, India
| | - Deepthi Vijay
- Department of Veterinary Public Health, College of Veterinary and Animal Sciences, Mannuthy, Thrissur, 680651, India
| | - Jasbir Singh Bedi
- Centre for One Health, College of Veterinary Science, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, 141004, India
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Han X, Zou G, Liu J, Yang C, Du X, Chen G, Sun Z, Zhang X, Sun Y, Zhang W, Jiang X. Mechanisms of linezolid resistance in Staphylococcus capitis with the novel mutation C2128T in the 23S rRNA gene in China. BMC Microbiol 2022; 22:203. [PMID: 35987607 PMCID: PMC9392311 DOI: 10.1186/s12866-022-02616-9] [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: 04/16/2022] [Accepted: 08/10/2022] [Indexed: 11/10/2022] Open
Abstract
Purpose The objective of this study was to investigate the molecular characteristics and potential resistance mechanisms of linezolid-resistant (LZR) Staphylococcus capitis isolates from a tertiary hospital in China. Methods S. capitis isolates were obtained from clinical patient specimens; three of the isolates came from blood cultures and one from the hydrothorax. The agar dilution and E-test methods were used to identify antibiotic resistance. The chloramphenicol-florfenicol resistance (cfr) gene carrier status of the strains was determined by PCR. Whole-genome sequencing (WGS) was used to identify point mutations and L3, L4, and L22 mutations and to study the genetic environment of the cfr gene and the relationships between strains. Results The 4 isolates obtained in this study were all linezolid-resistant Staphylococcus strains. A similar of susceptibility profile pattern was observed in all four S. capitis strains, each of which exhibited a multidrug-resistant phenotype. A potentially novel mutation, C2128T, was identified, and the cfr genes of S. capitis strains were all positive. Additionally, the same mutations (C2128T and G2600T) were identified in all 23S rRNA sequences of the isolates, whereas mutations were lacking in the L3, L4, and L22 ribosomal proteins. The genetic environments surrounding cfr were identical in all four isolates. A schematic diagram of the phylogenetic tree showed that they were closely related to AYP1020, CR01, and TW2795, and a total of seven drug resistance genes were identified in these strains. Conclusions The study indicated that the resistance of the Staphylococcus capitis strains to linezolid was caused by multiple mechanisms, and a potential novel mutation, C2128T, that may have an impact on bacterial resistance was identified. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02616-9.
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A study on fungal defensin against multidrug-resistant Clostridium perfringens and its treatment on infected poultry. Appl Microbiol Biotechnol 2021; 105:7265-7282. [PMID: 34491399 DOI: 10.1007/s00253-021-11500-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 07/29/2021] [Accepted: 08/05/2021] [Indexed: 12/25/2022]
Abstract
In the present study, we aimed to investigate the antibacterial activity and mechanisms of plectasin-derived peptide NZ2114 in vitro and its therapeutic effects in vivo on broilers challenged with Clostridium perfringens. In vitro assay showed that NZ2114 had potent (minimal inhibitory concentration, 0.91 μM) and rapid antibacterial activity (99.9% reduction within 2 h), and the dual antibacterial mechanisms (including interfering with the cell membrane and intracellular DNA) against C. perfringens CVCC 2030. In vivo study, NZ2114 tended to increase linearly and quadratically the average daily gain as NZ2114 level increased and was the highest at 20 mg/L. NZ2114 at 10 ~ 40 mg/L dramatically reduced jejunal lesion score. Besides, the levels of IL-6, TNF-α, and IL-1β tended to downregulate linearly and quadratically as the NZ2114 level increased and were all the lowest at the dose of 20 mg/L. NZ2114 significantly upregulated those levels of IgA, IgG, IgM, and sIgA with a linear and quadratic dose effect, with the highest IgA, IgG, IgM, and sIgA at 20 mg/L. Finally, NZ2114 tended to linearly and quadratically increase the numerical value of crypt depth, with the lowest value at 40 mg/L. Lincomycin only dramatically reduced the jejunal lesion score and increased the numerical value of crypt depth. These results indicate that NZ2114 has the potential as a new alternative to antibiotics for the treatment of C. perfringens-induced necrotic enteritis infection.Key points• NZ2114 could kill C. perfringens by dual antibacterial mechanisms• Broiler necrotic enteritis model induced by C. perfringens was established• NZ2114 treatment could ameliorate C. perfringens-induced necrotic enteritis.
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Zhou Y, Li J, Schwarz S, Zhang S, Tao J, Fan R, Walsh TR, Wu C, Wang Y. Mobile oxazolidinone/phenicol resistance gene optrA in chicken Clostridium perfringens. J Antimicrob Chemother 2021; 75:3067-3069. [PMID: 32562540 DOI: 10.1093/jac/dkaa236] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Yuqing Zhou
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China.,Department of Medical Microbiology and Infectious Disease, Division of Infection and Immunity, Cardiff University, Cardiff, UK
| | - Jiyun Li
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China.,College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan, China
| | - Stefan Schwarz
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China.,Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Shan Zhang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Jin Tao
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Run Fan
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Timothy R Walsh
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China.,Department of Medical Microbiology and Infectious Disease, Division of Infection and Immunity, Cardiff University, Cardiff, UK
| | - Congming Wu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yang Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China.,Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
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Mobile Oxazolidinone Resistance Genes in Gram-Positive and Gram-Negative Bacteria. Clin Microbiol Rev 2021; 34:e0018820. [PMID: 34076490 DOI: 10.1128/cmr.00188-20] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Seven mobile oxazolidinone resistance genes, including cfr, cfr(B), cfr(C), cfr(D), cfr(E), optrA, and poxtA, have been identified to date. The cfr genes code for 23S rRNA methylases, which confer a multiresistance phenotype that includes resistance to phenicols, lincosamides, oxazolidinones, pleuromutilins, and streptogramin A compounds. The optrA and poxtA genes code for ABC-F proteins that protect the bacterial ribosomes from the inhibitory effects of oxazolidinones. The optrA gene confers resistance to oxazolidinones and phenicols, while the poxtA gene confers elevated MICs or resistance to oxazolidinones, phenicols, and tetracycline. These oxazolidinone resistance genes are most frequently found on plasmids, but they are also located on transposons, integrative and conjugative elements (ICEs), genomic islands, and prophages. In these mobile genetic elements (MGEs), insertion sequences (IS) most often flanked the cfr, optrA, and poxtA genes and were able to generate translocatable units (TUs) that comprise the oxazolidinone resistance genes and occasionally also other genes. MGEs and TUs play an important role in the dissemination of oxazolidinone resistance genes across strain, species, and genus boundaries. Most frequently, these MGEs also harbor genes that mediate resistance not only to antimicrobial agents of other classes, but also to metals and biocides. Direct selection pressure by the use of antimicrobial agents to which the oxazolidinone resistance genes confer resistance, but also indirect selection pressure by the use of antimicrobial agents, metals, or biocides (the respective resistance genes against which are colocated on cfr-, optrA-, or poxtA-carrying MGEs) may play a role in the coselection and persistence of oxazolidinone resistance genes.
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Ledger L, Eidt J, Cai HY. Identification of Antimicrobial Resistance-Associated Genes through Whole Genome Sequencing of Mycoplasma bovis Isolates with Different Antimicrobial Resistances. Pathogens 2020; 9:pathogens9070588. [PMID: 32707642 PMCID: PMC7400188 DOI: 10.3390/pathogens9070588] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/15/2020] [Accepted: 07/16/2020] [Indexed: 01/08/2023] Open
Abstract
Antimicrobial resistance (AMR) in Mycoplasma bovis has been previously associated with topoisomerase and ribosomal gene mutations rather than specific resistance-conferring genes. Using whole genome sequencing (WGS) to identify potential new AMR mechanisms for M. bovis, it was found that a 2019 clinical isolate with high MIC (2019-043682) for fluoroquinolones, macrolides, lincosamides, pleuromutilins and tetracyclines had a new core genome multilocus sequencing (cgMLST) type (ST10-like) and 91% sequence similarity to the published genome of M. bovis PG45. Closely related to PG45, a 1982 isolate (1982-M6152) shared the same cgMLST type (ST17), 97.2% sequence similarity and low MIC results. Known and potential AMR- associated genetic events were identified through multiple sequence alignment of the three genomes. Isolate 2019-043682 had 507 genes with non-synonymous mutations (NSMs) and 67 genes disrupted. Isolate 1982-M6152 had 81 NSMs and 20 disruptions. Using functional roles and known mechanisms of antimicrobials, a 55 gene subset was assessed for AMR potential. Seventeen were previously identified from other bacteria as sites of AMR mutation, 38 shared similar functions to them, and 11 contained gene-disrupting mutations. This study indicated that M. bovis may obtain high AMR characteristics by mutating or disrupting other functional genes, in addition to topoisomerases and ribosomal genes.
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Archambault M, Rubin JE. Antimicrobial Resistance in Clostridium and Brachyspira spp. and Other Anaerobes. Microbiol Spectr 2020; 8:10.1128/microbiolspec.arba-0020-2017. [PMID: 31971162 PMCID: PMC10773235 DOI: 10.1128/microbiolspec.arba-0020-2017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Indexed: 01/26/2023] Open
Abstract
This article describes the antimicrobial resistance to date of the most frequently encountered anaerobic bacterial pathogens of animals. The different sections show that antimicrobial resistance can vary depending on the antimicrobial, the anaerobe, and the resistance mechanism. The variability in antimicrobial resistance patterns is also associated with other factors such as geographic region and local antimicrobial usage. On occasion, the same resistance gene was observed in many anaerobes, whereas some were limited to certain anaerobes. This article focuses on antimicrobial resistance data of veterinary origin.
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Affiliation(s)
- Marie Archambault
- Département de Pathologie et Microbiologie, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, Québec J2S 2M2, Canada
| | - Joseph E Rubin
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatchewan S7N 5B4, Canada
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Exploring bacterial resistome and resistance dessemination: an approach of whole genome sequencing. Future Med Chem 2019; 11:247-260. [PMID: 30801197 DOI: 10.4155/fmc-2018-0201] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
For several decades antibiotics are used to combat against pathogenic bacteria, but their misuse and overuse have caused the emergence of resistant bacteria. The scarcities of effective antibiotics along with unavailability of alternative solutions have exacerbated bacterial infections and mortality rate. This review provides the concept of bacterial resistome and mechanisms of resistance. It has also described the utility of whole genome sequencing in identifying resistance and its dissemination in association with available bioinformatics tools and databases. Moreover, the whole genome sequencing methodology described in this review will help to select effective antibiotics, maintain unparalleled surveillance of resistance and provide early diagnosis during resistance outbreaks. The provided information could be used to control infection caused by resistant microorganisms.
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Zhou W, Gao S, Xu H, Zhang Z, Chen F, Shen H, Zhang C. Distribution of the optrA gene in Enterococcus isolates at a tertiary care hospital in China. J Glob Antimicrob Resist 2019; 17:180-186. [PMID: 30641287 DOI: 10.1016/j.jgar.2019.01.001] [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] [Received: 08/14/2018] [Revised: 01/02/2019] [Accepted: 01/03/2019] [Indexed: 10/27/2022] Open
Abstract
OBJECTIVES Linezolid-resistant Enterococcus have spread worldwide. This study investigated the prevalence of linezolid-non-susceptible Enterococcus (LNSE) and the potential mechanism and molecular epidemiology of LNSE isolates from Nanjing, China. METHODS Linezolid susceptibility of 2555 Enterococcus was retrospectively determined by Etest. Vancomycin and teicoplanin MICs were determined for LNSE by Etest. PCR and DNA sequencing were used to investigate the potential molecular mechanism. Clonal relatedness between LNSE isolates was analysed by MLST. WGS was also performed. RESULTS A total of 27 Enterococcus isolates (24 Enterococcus faecalis, 3 Enterococcus faecium) with linezolid MICs of 4-48μg/mL were identified, among which 20 E. faecalis and 3 E. faecium were positive for optrA. No mutations were found in genes encoding domain V of 23S rRNA or ribosomal proteins L3/L4; the cfr gene was not found. The 24 linezolid-non-susceptible E. faecalis were classified into eight STs (ST16, ST480, ST476, ST631, ST585, ST428, ST25 and ST689). The three linezolid-non-susceptible E. faecium were classified as ST17, ST400 and ST195. Comparison of the deduced OptrA amino acid sequences of the 23 optrA-positive isolates by PCR-based sequencing and WGS with that of the original OptrA from E. faecalis E349 revealed seven variants (KD, EDP, EDM, D, EDD, RDK and DP) in 16 isolates, with no mutations in the remaining 7 isolates. optrA was found downstream of fexA by searching the pE349 sequence based on WGS data. CONCLUSIONS Emergence of LNSE with optrA-mediated resistance and clonal dissemination of ST16 E. faecalis in our hospital may pose a potential public-health threat.
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Affiliation(s)
- Wanqing Zhou
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, 321# Zhongshan Road, Gulou District, Nanjing, Jiangsu Province 210008, PR China
| | - Shuo Gao
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, 321# Zhongshan Road, Gulou District, Nanjing, Jiangsu Province 210008, PR China
| | - Hongjing Xu
- Department of Laboratory Medicine, Jiangning District Hospital of Traditional Chinese Medicine, 657# Tianyin Avenue, Jiangning District, Nanjing, Jiangsu Province 211100, PR China
| | - Zhifeng Zhang
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, 321# Zhongshan Road, Gulou District, Nanjing, Jiangsu Province 210008, PR China
| | - Fei Chen
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, 321# Zhongshan Road, Gulou District, Nanjing, Jiangsu Province 210008, PR China
| | - Han Shen
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, 321# Zhongshan Road, Gulou District, Nanjing, Jiangsu Province 210008, PR China.
| | - Chunni Zhang
- Department of Clinical Laboratory, Jinling Hospital, Nanjing University School of Medicine, Nanjing University, 305# East Zhongshan Road, Qinhuai District, Nanjing, Jiangsu Province 210008, PR China.
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Navarro-Gonzalez N, Castillo-Contreras R, Casas-Díaz E, Morellet N, Concepción Porrero M, Molina-Vacas G, Torres RT, Fonseca C, Mentaberre G, Domínguez L, Lavín S, Serrano E. Carriage of antibiotic-resistant bacteria in urban versus rural wild boars. EUR J WILDLIFE RES 2018. [DOI: 10.1007/s10344-018-1221-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Ma YH, Ye GS. Determination of multidrug resistance mechanisms in Clostridium perfringens type A isolates using RNA sequencing and 2D-electrophoresis. ACTA ACUST UNITED AC 2018; 51:e7044. [PMID: 29898034 PMCID: PMC6002133 DOI: 10.1590/1414-431x20187044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 03/16/2018] [Indexed: 11/22/2022]
Abstract
In this study, we screened differentially expressed genes in a
multidrug-resistant isolate strain of Clostridium perfringens
by RNA sequencing. We also separated and identified differentially expressed
proteins (DEPs) in the isolate strain by two-dimensional electrophoresis (2-DE)
and mass spectrometry (MS). The RNA sequencing results showed that, compared
with the control strain, 1128 genes were differentially expressed in the isolate
strain, and these included 227 up-regulated genes and 901 down-regulated genes.
Bioinformatics analysis identified the following genes and gene categories that
are potentially involved in multidrug resistance (MDR) in the isolate strain:
drug transport, drug response, hydrolase activity, transmembrane transporter,
transferase activity, amidase transmembrane transporter, efflux transmembrane
transporter, bacterial chemotaxis, ABC transporter, and others. The results of
the 2-DE showed that 70 proteins were differentially expressed in the isolate
strain, 45 of which were up-regulated and 25 down-regulated. Twenty-seven DEPs
were identified by MS and these included the following protein categories:
ribosome, antimicrobial peptide resistance, and ABC transporter, all of which
may be involved in MDR in the isolate strain of C. perfringens. The results
provide reference data for further investigations on the drug resistant
molecular mechanisms of C. perfringens.
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Affiliation(s)
- Yu-Hua Ma
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China.,College of Agriculture and Animal Husbandry, Qinghai University, Xining, China
| | - Gui-Sheng Ye
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China.,College of Agriculture and Animal Husbandry, Qinghai University, Xining, China
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Different Resistance Mechanisms for Cadazolid and Linezolid in Clostridium difficile Found by Whole-Genome Sequencing Analysis. Antimicrob Agents Chemother 2017; 61:AAC.00384-17. [PMID: 28584149 DOI: 10.1128/aac.00384-17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 05/27/2017] [Indexed: 12/16/2022] Open
Abstract
Cadazolid (CDZ) is a new antibiotic currently in clinical development for the treatment of Clostridium difficile infections. CDZ interferes with the bacterial protein synthesis machinery. The aim of the present study was to identify resistance mechanisms for CDZ and compare the results to those obtained for linezolid (LZD) in C. difficile by whole-genome sequencing (WGS) of strains generated by in vitro passages and to those obtained for LZD-resistant clinical isolates. Clones of C. difficile 630 selected with CDZ during 46 passages had a maximally 4-fold increase in CDZ MIC, while the LZD MIC for clones selected with LZD increased up to 16-fold. CDZ cross-resistance with LZD was maximally 4-fold, and no cross-resistance with other antibiotics tested was observed. Our data suggest that there are different resistance mechanisms for CDZ and LZD in C. difficile Mutations after passages with CDZ were found in rplD (ribosomal protein L4) as well as in tra and rmt, whereas similar experiments with LZD showed mutations in rplC (ribosomal protein L3), reg, and tpr, indicating different resistance mechanisms. Although high degrees of variation between the sequenced genomes of the clinical isolates were observed, the same mutation in rplC was found in two clinical isolates with high LZD MICs. No mutations were found in the 23S rRNA genes, and attempts to isolate the cfr gene from resistant clinical isolates were unsuccessful. Analysis of 50% inhibitory concentrations (IC50s) determined in in vitro transcription/translation assays performed with C. difficile cell extracts from passaged clones correlated well with the MIC values for all antibiotics tested, indicating that the ribosomal mutations are causing the resistant phenotype.
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Li Z, Pérez-Osorio A, Wang Y, Eckmann K, Glover WA, Allard MW, Brown EW, Chen Y. Whole genome sequencing analyses of Listeria monocytogenes that persisted in a milkshake machine for a year and caused illnesses in Washington State. BMC Microbiol 2017; 17:134. [PMID: 28619007 PMCID: PMC5472956 DOI: 10.1186/s12866-017-1043-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 06/03/2017] [Indexed: 11/25/2022] Open
Abstract
Background In 2015, in addition to a United States multistate outbreak linked to contaminated ice cream, another outbreak linked to ice cream was reported in the Pacific Northwest of the United States. It was a hospital-acquired outbreak linked to milkshakes, made from contaminated ice cream mixes and milkshake maker, served to patients. Here we performed multiple analyses on isolates associated with this outbreak: pulsed-field gel electrophoresis (PFGE), whole genome single nucleotide polymorphism (SNP) analysis, species-specific core genome multilocus sequence typing (cgMLST), lineage-specific cgMLST and whole genome-specific MLST (wgsMLST)/outbreak-specific cgMLST. We also analyzed the prophages and virulence genes. Results The outbreak isolates belonged to sequence type 1038, clonal complex 101, genetic lineage II. There were no pre-mature stop codons in inlA. Isolates contained Listeria Pathogenicity Island 1 and multiple internalins. PFGE and multiple whole genome sequencing (WGS) analyses all clustered together food, environmental and clinical isolates when compared to outgroup from the same clonal complex, which supported the finding that L. monocytogenes likely persisted in the soft serve ice cream/milkshake maker from November 2014 to November 2015 and caused 3 illnesses, and that the outbreak strain was transmitted between two ice cream production facilities. The whole genome SNP analysis, one of the two species-specific cgMLST, the lineage II-specific cgMLST and the wgsMLST/outbreak-specific cgMLST showed that L. monocytogenes cells persistent in the milkshake maker for a year formed a unique clade inside the outbreak cluster. This clustering was consistent with the cleaning practice after the outbreak was initially recognized in late 2014 and early 2015. Putative prophages were conserved among prophage-containing isolates. The loss of a putative prophage in two isolates resulted in the loss of the AscI restriction site in the prophage, which contributed to their AscI-PFGE banding pattern differences from other isolates. Conclusions The high resolution of WGS analyses allowed the differentiation of epidemiologically unrelated isolates, as well as the elucidation of the microevolution and persistence of isolates within the scope of one outbreak. We applied a wgsMLST scheme which is essentially the outbreak-specific cgMLST. This scheme can be combined with lineage-specific cgMLST and species-specific cgMLST to maximize the resolution of WGS.
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Affiliation(s)
- Zhen Li
- Washington State Department of Health, Public Health Laboratories, Shoreline, Washington, USA
| | - Ailyn Pérez-Osorio
- Washington State Department of Health, Public Health Laboratories, Shoreline, Washington, USA
| | - Yu Wang
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, USA
| | - Kaye Eckmann
- Washington State Department of Health, Public Health Laboratories, Shoreline, Washington, USA
| | - William A Glover
- Washington State Department of Health, Public Health Laboratories, Shoreline, Washington, USA
| | - Marc W Allard
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, USA
| | - Eric W Brown
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, USA
| | - Yi Chen
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, USA.
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Islam MM, Hameed HMA, Mugweru J, Chhotaray C, Wang C, Tan Y, Liu J, Li X, Tan S, Ojima I, Yew WW, Nuermberger E, Lamichhane G, Zhang T. Drug resistance mechanisms and novel drug targets for tuberculosis therapy. J Genet Genomics 2016; 44:21-37. [PMID: 28117224 DOI: 10.1016/j.jgg.2016.10.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 09/26/2016] [Accepted: 10/10/2016] [Indexed: 10/20/2022]
Abstract
Drug-resistant tuberculosis (TB) poses a significant challenge to the successful treatment and control of TB worldwide. Resistance to anti-TB drugs has existed since the beginning of the chemotherapy era. New insights into the resistant mechanisms of anti-TB drugs have been provided. Better understanding of drug resistance mechanisms helps in the development of new tools for the rapid diagnosis of drug-resistant TB. There is also a pressing need in the development of new drugs with novel targets to improve the current treatment of TB and to prevent the emergence of drug resistance in Mycobacterium tuberculosis. This review summarizes the anti-TB drug resistance mechanisms, furnishes some possible novel drug targets in the development of new agents for TB therapy and discusses the usefulness using known targets to develop new anti-TB drugs. Whole genome sequencing is currently an advanced technology to uncover drug resistance mechanisms in M. tuberculosis. However, further research is required to unravel the significance of some newly discovered gene mutations in their contribution to drug resistance.
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Affiliation(s)
- Md Mahmudul Islam
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - H M Adnan Hameed
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Julius Mugweru
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chiranjibi Chhotaray
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Changwei Wang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; Institute of Chemical Biology and Drug Discovery, Stony Brook University-State University of New York, Stony Brook, NY 11794-3400, USA
| | - Yaoju Tan
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, The Guangzhou Chest Hospital, Guangzhou 510095, China
| | - Jianxiong Liu
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, The Guangzhou Chest Hospital, Guangzhou 510095, China
| | - Xinjie Li
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, The Guangzhou Chest Hospital, Guangzhou 510095, China
| | - Shouyong Tan
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, The Guangzhou Chest Hospital, Guangzhou 510095, China
| | - Iwao Ojima
- Institute of Chemical Biology and Drug Discovery, Stony Brook University-State University of New York, Stony Brook, NY 11794-3400, USA
| | - Wing Wai Yew
- Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Eric Nuermberger
- Center for Tuberculosis Research, Department of Medicine, Johns Hopkins University, Baltimore, MD 21231-1002, USA
| | - Gyanu Lamichhane
- Center for Tuberculosis Research, Department of Medicine, Johns Hopkins University, Baltimore, MD 21231-1002, USA
| | - Tianyu Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Mechanism of action of a novel recombinant peptide, MP1102, against Clostridium perfringens type C. Appl Microbiol Biotechnol 2016; 100:5045-57. [DOI: 10.1007/s00253-016-7387-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 02/03/2016] [Accepted: 02/05/2016] [Indexed: 01/25/2023]
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Akhi MT, Bidar Asl S, Pirzadeh T, Naghili B, Yeganeh F, Memar Y, Mohammadzadeh Y. Antibiotic Sensitivity of Clostridium perfringens Isolated From Faeces in Tabriz, Iran. Jundishapur J Microbiol 2015; 8:e20863. [PMID: 26421135 PMCID: PMC4584078 DOI: 10.5812/jjm.20863v2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2014] [Revised: 08/12/2014] [Accepted: 08/28/2014] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Clostridium perfringens, a Gram-positive, anaerobic bacterium that produces at least 16 virulence factors including 12 toxins (α-ν), enterotoxin, hemolysin and neuraminidase, can create variable pathogenic condition, ranging from a food poisoning to life-threatening myonecrosis. Among C. perfringens strains, resistance to the drug choices such as penicillin as well as to alternatives of penicillin like metronidazole and clindamycin has also been observed. OBJECTIVES The aim of this study was to determine the resistance of isolated toxigenic and non-toxigenic C. perfringens strains against common antimicrobial agents. MATERIALS AND METHODS In this descriptive study, a total of 136 stool specimens were collected. At first, cooked meat medium enrichment method was performed on samples at 45°C. Thereafter, a loopful of the enriched culture was transferred to blood agar and incubated anaerobically at 37°C for 24-72 hours. Colonies with double zone of hemolysis were identified by different biochemical tests such as phospholipase C (lecithinase) test, indole and urease production. The Minimum Inhibitory Concentration (MIC) for common antibiotics was determined by Etests (Epsilometer) and duplex Polymerase Chain Reaction (PCR) reaction was performed with specific primers for amplification of cpe (426 bp) and plc (283 bp) Genes. RESULTS Of 136 stool samples including diarrhea [48] and non-diarrhea [88] ones, 83 (61.02%) C. perfringens were cultured. Of these 83, 79 C. perfringens isolates showed the alpha-toxin (phospholipase C) production gene by PCR. Respectively, 3 (9.09%) and 2 (4.34%) cpe genes were present in diarrhea and non-diarrhea samples. Of 79 isolates of C. perfringens, 34 (43.03%) cases showed no resistance, 18 (22.78%) had one resistance and 27 (34.17%) isolates had multiple resistance to imipenem, metronidazole, ceftriaxone, clindamycin, chloramphenicol, and penicillin. CONCLUSIONS Periodic evaluation of antimicrobial susceptibility for C. perfringens should be performed. Harboring of enterotoxigenic C. perfringens in individuals not necessarily results in diarrhea.
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Affiliation(s)
- Mohammad Taghi Akhi
- Research Center of Infectious and Tropical Diseases, Tabriz University of Medical Sciences, Tabriz, IR Iran
- Department of Bacteriology and Virology, School of Medicine, Tabriz University of Medical Sciences, Tabriz IR Iran
| | - Saeid Bidar Asl
- Department of Bacteriology and Virology, School of Medicine, Tabriz University of Medical Sciences, Tabriz IR Iran
| | - Tahereh Pirzadeh
- Department of Bacteriology and Virology, School of Medicine, Tabriz University of Medical Sciences, Tabriz IR Iran
| | - Behruz Naghili
- Department of Infectious Disease, Medical Faculty, Tabriz University of Medical Science, Tabriz, IR Iran
| | - Fatemeh Yeganeh
- Department of Bacteriology and Virology, School of Medicine, Tabriz University of Medical Sciences, Tabriz IR Iran
| | - Yousef Memar
- Department of Bacteriology and Virology, School of Medicine, Tabriz University of Medical Sciences, Tabriz IR Iran
| | - Yalda Mohammadzadeh
- Department of Bacteriology and Virology, School of Medicine, Tabriz University of Medical Sciences, Tabriz IR Iran
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Zhou W, Niu D, Cao X, Ning M, Zhang Z, Shen H, Zhang K. Clonal dissemination of linezolid-resistant Staphylococcus capitis with G2603T mutation in domain V of the 23S rRNA and the cfr gene at a tertiary care hospital in China. BMC Infect Dis 2015; 15:97. [PMID: 25888130 PMCID: PMC4352562 DOI: 10.1186/s12879-015-0841-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 02/18/2015] [Indexed: 11/22/2022] Open
Abstract
Background The present study aims to investigate the potential mechanism of linezolid-resistant Staphylococcus capitis (LRSC) isolates collected from our hospital. Methods The susceptibilities of 5 Staphylococcus capitis isolates displaying resistance towards linezolid were determined by E-test. Polymerase chain reactions (PCRs) and DNA sequencing were used to investigate the potential molecular mechanism. Clonal relatedness between these strains was analyzed by pulsed-field gel electrophoresis (PFGE). Results The MICs of linezolid on these 5 isolates were >256 μg/mL. The G2603T mutation was observed in the domain V of the 23S rRNA with cfr gene being also widely detected among these 5 strains. PFGE analysis displayed close genetic relatedness between these linezolid-resistant isolates. Conclusions The emergence of LRSC isolates carrying G2603T mutation in the domain V of the 23S rRNA and harboring cfr gene in our hospital may pose a potential challenge to the public health.
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Affiliation(s)
- Wanqing Zhou
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, the affiliated Hospital of Nanjing University Medical School, 321# Zhongshan Road, Gulou District, Nanjing, Jiangsu Province, 210008, PR China.
| | - Dongmei Niu
- Department of Laboratory Medicine, Nanjing Jinling Hospital, the affiliated Hospital of Nanjing University Medical School, 305# East Zhongshan Road, Baixia District, Nanjing, Jiangsu Province, 210002, PR China.
| | - Xiaoli Cao
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, the affiliated Hospital of Nanjing University Medical School, 321# Zhongshan Road, Gulou District, Nanjing, Jiangsu Province, 210008, PR China.
| | - Mingzhe Ning
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, the affiliated Hospital of Nanjing University Medical School, 321# Zhongshan Road, Gulou District, Nanjing, Jiangsu Province, 210008, PR China.
| | - Zhifeng Zhang
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, the affiliated Hospital of Nanjing University Medical School, 321# Zhongshan Road, Gulou District, Nanjing, Jiangsu Province, 210008, PR China.
| | - Han Shen
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, the affiliated Hospital of Nanjing University Medical School, 321# Zhongshan Road, Gulou District, Nanjing, Jiangsu Province, 210008, PR China.
| | - Kui Zhang
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, the affiliated Hospital of Nanjing University Medical School, 321# Zhongshan Road, Gulou District, Nanjing, Jiangsu Province, 210008, PR China.
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Jahne MA, Rogers SW, Ramler IP, Holder E, Hayes G. Hierarchal clustering yields insight into multidrug-resistant bacteria isolated from a cattle feedlot wastewater treatment system. ENVIRONMENTAL MONITORING AND ASSESSMENT 2015; 187:4168. [PMID: 25504186 DOI: 10.1007/s10661-014-4168-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 11/17/2014] [Indexed: 06/04/2023]
Abstract
Forty-two percent of Escherichia coli and 58% of Enterococcus spp. isolated from cattle feedlot runoff and associated infiltration basin and constructed wetland treatment system were resistant to at least one antibiotic of clinical importance; a high level of multidrug resistance (22% of E. coli and 37% of Enterococcus spp.) was observed. Hierarchical clustering revealed a closely associated resistance cluster among drug-resistant E. coli isolates that included cephalosporins (ceftiofur, cefoxitin, and ceftriaxone), aminoglycosides (gentamycin, kanamycin, and amikacin), and quinolone nalidixic acid; antibiotics from these classes were used at the study site, and cross-resistance may be associated with transferrable multiple-resistance elements. For Enterococcus spp., co-resistance among vancomycin, linezolid, and daptomycin was common; these antibiotics are reserved for complicated clinical infections and have not been approved for animal use. Vancomycin resistance (n = 49) only occurred when isolates were resistant to linezolid, daptomycin, and all four of the MLSB (macrolide-lincosamide-streptogramin B) antibiotics tested (tylosin, erythromycin, lincomycin, and quinipristin/dalfopristin). This suggests that developing co-resistance to MLSB antibiotics along with cyclic lipopeptides and oxazolidinones may result in resistance to vancomycin as well. Effects of the treatment system on antibiotic resistance were pronounced during periods of no rainfall and low flow (long residence time). Increased hydraulic loading (short residence time) under the influence of rain caused antibiotic-resistant bacteria to be flushed through the treatment system. This presents concern for environmental discharge of multidrug-resistant organisms relevant to public health.
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Affiliation(s)
- Michael A Jahne
- Institute for a Sustainable Environment, Clarkson University, Potsdam, NY, 13699, USA
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Investigations of the mode of action and resistance development of cadazolid, a new antibiotic for treatment of Clostridium difficile infections. Antimicrob Agents Chemother 2013; 58:901-8. [PMID: 24277035 DOI: 10.1128/aac.01831-13] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Cadazolid is a new oxazolidinone-type antibiotic currently in clinical development for the treatment of Clostridium difficile-associated diarrhea. Here, we report investigations on the mode of action and the propensity for spontaneous resistance development in C. difficile strains. Macromolecular labeling experiments indicated that cadazolid acts as a potent inhibitor of protein synthesis, while inhibition of DNA synthesis was also observed, albeit only at substantially higher concentrations of the drug. Strong inhibition of protein synthesis was also obtained in strains resistant to linezolid, in agreement with low MICs against such strains. Inhibition of protein synthesis was confirmed in coupled transcription/translation assays using extracts from different C. difficile strains, including strains resistant to linezolid, while inhibitory effects in DNA topoisomerase assays were weak or not detectable under the assay conditions. Spontaneous resistance frequencies of cadazolid were low in all strains tested (generally <10(-10) at 2× to 4× the MIC), and in multiple-passage experiments (up to 13 passages) MICs did not significantly increase. Furthermore, no cross-resistance was observed, as cadazolid retained potent activity against strains resistant or nonsusceptible to linezolid, fluoroquinolones, and the new antibiotic fidaxomicin. In conclusion, the data presented here indicate that cadazolid acts primarily by inhibition of protein synthesis, with weak inhibition of DNA synthesis as a potential second mode of action, and suggest a low potential for spontaneous resistance development.
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Campanile F, Mongelli G, Bongiorno D, Adembri C, Ballardini M, Falcone M, Menichetti F, Repetto A, Sabia C, Sartor A, Scarparo C, Tascini C, Venditti M, Zoppi F, Stefani S. Worrisome trend of new multiple mechanisms of linezolid resistance in staphylococcal clones diffused in Italy. J Clin Microbiol 2013; 51:1256-9. [PMID: 23345292 PMCID: PMC3666802 DOI: 10.1128/jcm.00098-13] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2013] [Accepted: 01/14/2013] [Indexed: 01/03/2023] Open
Abstract
In order to assess the frequency of clinically relevant linezolid-resistant staphylococcal isolates, and the role of linezolid in maintaining and coselecting multiple resistance mechanisms (cfr, 23S rRNA, L3/L4 mutations), a prospective Italian study was performed from 2010 to 2011 to confirm the diffusion of three major multidrug-resistant clones (ST2, ST5, ST23).
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Affiliation(s)
| | | | | | - Chiara Adembri
- Azienda Ospedaliera Universitaria Careggi, Firenze, Italy
| | | | | | | | | | - Carla Sabia
- University of Modena and Reggio, Modena, Italy
| | - Assunta Sartor
- Santa Maria della Misericordia University Hospital, Udine, Italy
| | - Claudio Scarparo
- Santa Maria della Misericordia University Hospital, Udine, Italy
| | | | | | - Federica Zoppi
- Azienda Ospedaliera Universitaria Careggi, Firenze, Italy
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Brown-Elliott BA, Nash KA, Wallace RJ. Antimicrobial susceptibility testing, drug resistance mechanisms, and therapy of infections with nontuberculous mycobacteria. Clin Microbiol Rev 2012; 25:545-82. [PMID: 22763637 PMCID: PMC3416486 DOI: 10.1128/cmr.05030-11] [Citation(s) in RCA: 335] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Within the past 10 years, treatment and diagnostic guidelines for nontuberculous mycobacteria have been recommended by the American Thoracic Society (ATS) and the Infectious Diseases Society of America (IDSA). Moreover, the Clinical and Laboratory Standards Institute (CLSI) has published and recently (in 2011) updated recommendations including suggested antimicrobial and susceptibility breakpoints. The CLSI has also recommended the broth microdilution method as the gold standard for laboratories performing antimicrobial susceptibility testing of nontuberculous mycobacteria. This article reviews the laboratory, diagnostic, and treatment guidelines together with established and probable drug resistance mechanisms of the nontuberculous mycobacteria.
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rplC T460C identified as a dominant mutation in linezolid-resistant Mycobacterium tuberculosis strains. Antimicrob Agents Chemother 2012; 56:2743-5. [PMID: 22371899 DOI: 10.1128/aac.06227-11] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The ribosomal L3 protein was identified as a novel target in linezolid (LZD)-resistant Mycobacterium tuberculosis strains. Next-generation sequencing confirmed rplC T460C as the sole mutation in an LZD-resistant M. tuberculosis H37Rv strain selected in vitro. Sequencing analysis revealed the rplC T460C mutation in eight further LZD-resistant isolates (three in vitro-selected mutants and five patient isolates, including isolates from three different patients that developed LZD resistance during treatment) but in none of the susceptible control strains (n = 84).
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Long KS, Vester B. Resistance to linezolid caused by modifications at its binding site on the ribosome. Antimicrob Agents Chemother 2012; 56:603-12. [PMID: 22143525 PMCID: PMC3264260 DOI: 10.1128/aac.05702-11] [Citation(s) in RCA: 245] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Linezolid is an oxazolidinone antibiotic in clinical use for the treatment of serious infections of resistant Gram-positive bacteria. It inhibits protein synthesis by binding to the peptidyl transferase center on the ribosome. Almost all known resistance mechanisms involve small alterations to the linezolid binding site, so this review will therefore focus on the various changes that can adversely affect drug binding and confer resistance. High-resolution structures of linezolid bound to the 50S ribosomal subunit show that it binds in a deep cleft that is surrounded by 23S rRNA nucleotides. Mutation of 23S rRNA has for some time been established as a linezolid resistance mechanism. Although ribosomal proteins L3 and L4 are located further away from the bound drug, mutations in specific regions of these proteins are increasingly being associated with linezolid resistance. However, very little evidence has been presented to confirm this. Furthermore, recent findings on the Cfr methyltransferase underscore the modification of 23S rRNA as a highly effective and transferable form of linezolid resistance. On a positive note, detailed knowledge of the linezolid binding site has facilitated the design of a new generation of oxazolidinones that show improved properties against the known resistance mechanisms.
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Affiliation(s)
- Katherine S. Long
- Department of Systems Biology and Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Birte Vester
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
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Billal DS, Feng J, Leprohon P, Légaré D, Ouellette M. Whole genome analysis of linezolid resistance in Streptococcus pneumoniae reveals resistance and compensatory mutations. BMC Genomics 2011; 12:512. [PMID: 22004526 PMCID: PMC3212830 DOI: 10.1186/1471-2164-12-512] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Accepted: 10/17/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Several mutations were present in the genome of Streptococcus pneumoniae linezolid-resistant strains but the role of several of these mutations had not been experimentally tested. To analyze the role of these mutations, we reconstituted resistance by serial whole genome transformation of a novel resistant isolate into two strains with sensitive background. We sequenced the parent mutant and two independent transformants exhibiting similar minimum inhibitory concentration to linezolid. RESULTS Comparative genomic analyses revealed that transformants acquired G2576T transversions in every gene copy of 23S rRNA and that the number of altered copies correlated with the level of linezolid resistance and cross-resistance to florfenicol and chloramphenicol. One of the transformants also acquired a mutation present in the parent mutant leading to the overexpression of an ABC transporter (spr1021). The acquisition of these mutations conferred a fitness cost however, which was further enhanced by the acquisition of a mutation in a RNA methyltransferase implicated in resistance. Interestingly, the fitness of the transformants could be restored in part by the acquisition of altered copies of the L3 and L16 ribosomal proteins and by mutations leading to the overexpression of the spr1887 ABC transporter that were present in the original linezolid-resistant mutant. CONCLUSIONS Our results demonstrate the usefulness of whole genome approaches at detecting major determinants of resistance as well as compensatory mutations that alleviate the fitness cost associated with resistance.
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Affiliation(s)
- Dewan S Billal
- Centre de recherche en Infectiologie du Centre de recherche du CHUL, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec, Canada
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Feng J, Billal DS, Lupien A, Racine G, Winstall E, Légaré D, Leprohon P, Ouellette M. Proteomic and transcriptomic analysis of linezolid resistance in Streptococcus pneumoniae. J Proteome Res 2011; 10:4439-52. [PMID: 21875071 DOI: 10.1021/pr200221s] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Linezolid is an oxazolidinone antibiotic that inhibits the initiation of translation. Although resistance to linezolid is an uncommon event, it has been reported in clinical isolates. The genome sequence of Streptococcus pneumoniae linezolid-resistant mutants recently revealed mutations associated with resistance. A proteomic and transcriptomic screen now reveals a possible increase in the metabolism and transport of carbohydrates in these linezolid-resistant S. pneumoniae mutants. Several glycolytic proteins were shown to be overexpressed in the resistant strains, along with other enzymes and transporters involved in the metabolism of sugars. An increase in energy needs appears to be required to sustain extended levels of resistance to linezolid as the disruption of two ABC transporters putatively involved in the import of carbohydrates leads to a 2-fold sensitization to linezolid. Furthermore, the disruption of the catabolite control protein A, a regulator of the metabolism of sugars whose expression is highly increased in one linezolid-resistant mutant, resulted in a 2-fold increase in linezolid susceptibility. This global scale analysis of gene and protein expression profiling highlights metabolism alterations associated with linezolid resistance in S. pneumoniae.
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Affiliation(s)
- Jie Feng
- Centre de Recherche en Infectiologie and Plate-forme §Protéomique du Centre de génomique de Québec, Université Laval, CHUQ, Pavillon CHUL, 2705 boulevard Laurier, Quebec, QC, Canada, G1V 4G2
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Bryant AE, Stevens DL. Clostridial myonecrosis: new insights in pathogenesis and management. Curr Infect Dis Rep 2011; 12:383-91. [PMID: 21308521 DOI: 10.1007/s11908-010-0127-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Clostridial myonecrosis remains an important cause of human morbidity and mortality worldwide. Although traumatic gas gangrene can be readily diagnosed from clinical findings and widely available technologies, spontaneous gas gangrene is more insidious, and gynecologic infections due to Clostridium sordellii progress so rapidly that death often precedes diagnosis. In each case, extensive tissue destruction and the subsequent systemic manifestations are mediated directly and indirectly by potent bacterial exotoxins. The management triumvirate of timely diagnosis, thorough surgical removal of necrotic tissue, and treatment with antibiotics that inhibit toxin synthesis remains the gold standard of care. Yet, despite these measures, mortality remains 30% to 100% and survivors often must cope with life-altering amputations. Recent insights regarding the genetic regulation of toxin production, the molecular mechanisms of toxin-induced host cell dysfunction, and the roles of newly described toxins in pathogenesis suggest that novel prevention, diagnostic, and treatment modalities may be on the horizon for these devastating infections.
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Affiliation(s)
- Amy E Bryant
- Infectious Diseases Section, Veterans Affairs Medical Center, 500 West Fort Street (Bldg 45), Boise, ID, 83702, USA,
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Mendes RE, Deshpande LM, Farrell DJ, Spanu T, Fadda G, Jones RN. Assessment of linezolid resistance mechanisms among Staphylococcus epidermidis causing bacteraemia in Rome, Italy. J Antimicrob Chemother 2010; 65:2329-35. [PMID: 20841419 DOI: 10.1093/jac/dkq331] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES To characterize linezolid resistance among blood cultured Staphylococcus epidermidis from patients at the Polyclinic Agostino Gemelli (2006-08). Isolates also showed elevated MICs of macrolide, lincosamide and streptogramin (MLS) compounds, which were investigated. METHODS Ten S. epidermidis exhibiting linezolid MICs ≥ 4 mg/L were included. Isolates were screened for cfr mutations in 23S rRNA, L3, L4 and L22, and MLS genes by PCR/sequencing. Ribosomal proteins were compared with those from a linezolid-susceptible (MIC, 1 mg/L) clinical strain and ATCC 12228. cfr location was determined by Southern blot/hybridization. The cfr strain was submitted to plasmid curing. Epidemiology was assessed by PFGE and multilocus sequence typing (MLST). RESULTS S. epidermidis displayed linezolid MICs of 4 or 8 mg/L, except for strain 4303A (MIC, 64 mg/L). These organisms and a linezolid-susceptible strain exhibited L3 Leu101Val compared with ATCC 12228. Isolates also showed L3 Phe147Leu and Ala157Arg, and L4 Asn158Ser. Strain 12375A possessed L4 Lys68Arg. Isolates were wild-type for 23S rRNA and L22. cfr was plasmid located in strain 4303A and the plasmid-cured strain exhibited a linezolid MIC (4 mg/L) similar to that for cfr-negative strains (4-8 mg/L). All organisms harboured erm(A) and msr(A), while vga(A) was detected in several isolates. All isolates were clonally related and ST-23. CONCLUSIONS L3 Phe147Leu and/or Ala157Arg appeared responsible for the elevated linezolid MIC, since adjacent alterations have been associated with resistance. L4 Asn158Ser has been reported in a linezolid-susceptible isolate and Lys68Arg detected here did not seem to provide an additive effect. Acquisition of cfr markedly increased (8- to 16-fold) the linezolid MICs. vga(A) was associated with higher MICs of quinupristin/dalfopristin and retapamulin.
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Structure-activity relationships of diverse oxazolidinones for linezolid-resistant Staphylococcus aureus strains possessing the cfr methyltransferase gene or ribosomal mutations. Antimicrob Agents Chemother 2010; 54:5337-43. [PMID: 20837751 DOI: 10.1128/aac.00663-10] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Staphylococcal resistance to linezolid (LZD) is mediated through ribosomal mutations (23S rRNA or ribosomal proteins L3 and L4) or through methylation of 23S rRNA by the horizontally transferred Cfr methyltransferase. To investigate the structural basis for oxazolidinone activity against LZD-resistant (LZD(r)) strains, we compared structurally diverse, clinically relevant oxazolidinones, including LZD, radezolid (RX-1741), TR-700 (torezolid), and a set of TR-700 analogs (including novel CD-rings and various A-ring C-5 substituents), against a panel of laboratory-derived and clinical LZD(r) Staphylococcus aureus strains possessing a variety of resistance mechanisms. Potency against all strains was correlated with optimization of C- and D-rings, which interact with more highly conserved regions of the peptidyl transferase center binding site. Activity against cfr strains was retained with either hydroxymethyl or 1,2,3-triazole C-5 groups but was reduced by 2- to 8-fold in compounds with acetamide substituents. LZD, which possesses a C-5 acetamide group and lacks a D-ring substituent, demonstrated the lowest potency against all strains tested, particularly against cfr strains. These data reveal key features contributing to oxazolidinone activity and highlight structural tradeoffs between potency against susceptible strains and potency against strains with various resistance mechanisms.
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Elevated linezolid resistance in clinical cfr-positive Staphylococcus aureus isolates is associated with co-occurring mutations in ribosomal protein L3. Antimicrob Agents Chemother 2010; 54:5352-5. [PMID: 20837755 DOI: 10.1128/aac.00714-10] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Resistance to linezolid (LZD) occurs through mutations in 23S rRNA and ribosomal proteins L3 and L4 or through methylation of 23S rRNA by Cfr. Here we report novel L3 mutations, ΔSer145/His146Tyr and ΔMet169-Gly174, co-occurring with cfr in LZD-resistant Staphylococcus aureus isolates recovered from a hospital outbreak in Madrid, Spain. LZD MIC values (16, 32, or 64 μg/ml) correlated with the presence and severity of the L3 mutation. All isolates had TR-700 (torezolid) MIC values of ≤ 2 μg/ml.
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