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Yang Y, Xie S, He F, Xu Y, Wang Z, Ihsan A, Wang X. Recent development and fighting strategies for lincosamide antibiotic resistance. Clin Microbiol Rev 2024; 37:e0016123. [PMID: 38634634 DOI: 10.1128/cmr.00161-23] [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] [Indexed: 04/19/2024] Open
Abstract
SUMMARYLincosamides constitute an important class of antibiotics used against a wide range of pathogens, including methicillin-resistant Staphylococcus aureus. However, due to the misuse of lincosamide and co-selection pressure, the resistance to lincosamide has become a serious concern. It is urgently needed to carefully understand the phenomenon and mechanism of lincosamide resistance to effectively prevent and control lincosamide resistance. To date, six mobile lincosamide resistance classes, including lnu, cfr, erm, vga, lsa, and sal, have been identified. These lincosamide resistance genes are frequently found on mobile genetic elements (MGEs), such as plasmids, transposons, integrative and conjugative elements, genomic islands, and prophages. Additionally, MGEs harbor the genes that confer resistance not only to antimicrobial agents of other classes but also to metals and biocides. The ultimate purpose of discovering and summarizing bacterial resistance is to prevent, control, and combat resistance effectively. This review highlights four promising strategies, including chemical modification of antibiotics, the development of antimicrobial peptides, the initiation of bacterial self-destruct program, and antimicrobial stewardship, to fight against resistance and safeguard global health.
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Affiliation(s)
- Yingying Yang
- National Reference Laboratory of Veterinary Drug Residues (HZAU), Huazhong Agricultural University, Wuhan, Hubei, China
- MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Shiyu Xie
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Fangjing He
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yindi Xu
- Institute of Animal Husbandry Research, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Zhifang Wang
- Institute of Animal Husbandry Research, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Awais Ihsan
- Department of Biosciences, COMSATS University Islamabad, Sahiwal campus, Islamabad, Pakistan
| | - Xu Wang
- National Reference Laboratory of Veterinary Drug Residues (HZAU), Huazhong Agricultural University, Wuhan, Hubei, China
- MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei, China
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei, China
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Adesoji TO, George UE, Sulayman TA, Uwanibe JN, Olawoye IB, Igbokwe JO, Olanipekun TG, Adeleke RA, Akindoyin AI, Famakinwa TJ, Adamu AM, Terkuma CA, Ezekiel GO, Eromon PE, Happi AN, Fadare TO, Shittu AO, Happi CT. Molecular characterization of non-aureus staphylococci and Mammaliicoccus from Hipposideros bats in Southwest Nigeria. Sci Rep 2024; 14:6899. [PMID: 38519524 PMCID: PMC10960025 DOI: 10.1038/s41598-024-57190-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 03/14/2024] [Indexed: 03/25/2024] Open
Abstract
Bats are not only ecologically valuable mammals but also reservoirs of zoonotic pathogens. Their vast population, ability to fly, and inhabit diverse ecological niches could play some role in the spread of antibiotic resistance. This study investigated non-aureus staphylococci and Mammaliicoccus colonization in the Hipposideros bats at Obafemi Awolowo University, Ile-Ife, Nigeria. Pharyngeal samples (n = 23) of the insectivorous bats were analyzed, and the presumptive non-aureus staphylococcal and Mammaliicoccus isolates were confirmed by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). The isolates were characterized based on antibiotic susceptibility testing and whole-genome sequencing (WGS). Six bacterial genomes were assembled, and three species were identified, including Mammaliicoccus sciuri (n = 4), Staphylococcus gallinarum (n = 1), and Staphylococcus nepalensis (n = 1). All the isolates were resistant to clindamycin, while the M. sciuri and S. gallinarum isolates were also resistant to fusidic acid. WGS analysis revealed that the M. sciuri and S. gallinarum isolates were mecA-positive. In addition, the M. sciuri isolates possessed some virulence (icaA, icaB, icaC, and sspA) genes. Multi-locus sequence typing identified two new M. sciuri sequence types (STs) 233 and ST234. The identification of these new STs in a migratory mammal deserves close monitoring because previously known ST57, ST60, and ST65 sharing ack (8), ftsZ (13), glpK (14), gmk (6), and tpiA (10) alleles with ST233 and ST234 have been linked to mastitis in animals. Moreover, the broad host range of M. sciuri could facilitate the dispersal of antibiotic resistance genes. This study provides evidence of the importance of including migratory animals in monitoring the development and spread of antibiotic resistance.
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Affiliation(s)
- Tomiwa O Adesoji
- Department of Microbiology, Obafemi Awolowo University, Ile-Ife, Osun State, Nigeria
| | - Uwem E George
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State, Nigeria
| | - Taofiq A Sulayman
- Department of Microbiology, Obafemi Awolowo University, Ile-Ife, Osun State, Nigeria
| | - Jessica N Uwanibe
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
| | - Idowu B Olawoye
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State, Nigeria
| | - Joseph O Igbokwe
- Department of Zoology, Obafemi Awolowo University, Ile-Ife, Osun State, Nigeria
| | - Tobi G Olanipekun
- Department of Veterinary Microbiology, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Richard A Adeleke
- Department of Veterinary Microbiology, University of Ibadan, Ibadan, Oyo State, Nigeria
- Immunology and Infectious Diseases, College of Veterinary Medicine, Cornell University, New York, NY, 14853, USA
| | | | - Temitope J Famakinwa
- Natural History Museum, Obafemi Awolowo University, Ile-Ife, Osun State, Nigeria
| | - Andrew M Adamu
- Department of Veterinary Public Health and Preventive Medicine, Faculty of Veterinary Medicine, University of Abuja, Federal Capital Territory, Abuja, 900105, Nigeria
- Australian Institute of Tropical Health and Medicine, Division of Tropical Health and Medicine, James Cook University, Townsville, QLD, 4811, Australia
- College of Public Health, Medical and Veterinary Sciences, James Cook University, 1 James Cook Drive, Bebegu Yumba Campus, Douglas, QLD, 4811, Australia
| | - Christabel A Terkuma
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State, Nigeria
| | - Grace O Ezekiel
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State, Nigeria
| | - Philomena E Eromon
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State, Nigeria
| | - Anise N Happi
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State, Nigeria
| | - Taiwo O Fadare
- Department of Microbiology, Obafemi Awolowo University, Ile-Ife, Osun State, Nigeria
| | - Adebayo O Shittu
- Department of Microbiology, Obafemi Awolowo University, Ile-Ife, Osun State, Nigeria.
| | - Christian T Happi
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria.
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State, Nigeria.
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Abdullahi IN, Lozano C, Simón C, Zarazaga M, Torres C. Within-Host Diversity of Coagulase-Negative Staphylococci Resistome from Healthy Pigs and Pig Farmers, with the Detection of cfr-Carrying Strains and MDR- S. borealis. Antibiotics (Basel) 2023; 12:1505. [PMID: 37887206 PMCID: PMC10604674 DOI: 10.3390/antibiotics12101505] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 09/25/2023] [Accepted: 09/26/2023] [Indexed: 10/28/2023] Open
Abstract
The ecology and diversity of resistome in coagulase-negative staphylococci (CoNS) from healthy pigs and pig farmers are rarely available as most studies focused on the livestock-associated methicillin-resistant S. aureus. This study aims to characterize the antimicrobial resistance (AMR) mechanisms, intra-host species diversity (more than one species in a host), and intra-species AMR diversity (same species with more than one AMR profile) in CoNS recovered from the nasal cavities of healthy pigs and pig farmers. One-hundred-and-one CoNS strains previously recovered from 40 pigs and 10 pig farmers from four Spanish pig farms were tested to determine their AMR profiles. Non-repetitive strains were selected (n = 75) and their AMR genes, SCCmec types, and genetic lineages were analyzed by PCR/sequencing. Of the non-repetitive strains, 92% showed a multidrug resistance (MDR) phenotype, and 52% were mecA-positive, which were associated with SCCmec types V (46.2%), IVb (20.5%), and IVc (5.1%). A total of 28% of the pigs and pig farmers had intra-host species diversity, while 26% had intra-species AMR diversity. High repertoires of AMR genes were detected, including unusual ones such as tetO, ermT, erm43, and cfr. Most important was the detection of cfr (in S. saprophyticus and S. epidermidis-ST16) in pigs and pig farmers; whereas MDR-S. borealis strains were identified in pig farmers. Pig-to-pig transmission of CoNS with similar AMR genes and SCCmec types was detected in 42.5% of pigs. The high level of multidrug, within-host, and intra-species resistome diversity in the nasal CoNS highlights their ability to be AMR gene reservoirs in healthy pigs and pig farmers. The detection of MDR-S. borealis and linezolid-resistant strains underscore the need for comprehensive and continuous surveillance of MDR-CoNS at the pig farm level.
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Affiliation(s)
- Idris Nasir Abdullahi
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, 26006 Logroño, Spain; (I.N.A.); (C.L.); (M.Z.)
| | - Carmen Lozano
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, 26006 Logroño, Spain; (I.N.A.); (C.L.); (M.Z.)
| | - Carmen Simón
- Faculty of Veterinary Medicine, University of Zaragoza, 50001 Zaragoza, Spain;
| | - Myriam Zarazaga
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, 26006 Logroño, Spain; (I.N.A.); (C.L.); (M.Z.)
| | - Carmen Torres
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, 26006 Logroño, Spain; (I.N.A.); (C.L.); (M.Z.)
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Douglas EJ, Laabei M. Staph wars: the antibiotic pipeline strikes back. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001387. [PMID: 37656158 PMCID: PMC10569064 DOI: 10.1099/mic.0.001387] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 08/14/2023] [Indexed: 09/02/2023]
Abstract
Antibiotic chemotherapy is widely regarded as one of the most significant medical advancements in history. However, the continued misuse of antibiotics has contributed to the rapid rise of antimicrobial resistance (AMR) globally. Staphylococcus aureus, a major human pathogen, has become synonymous with multidrug resistance and is a leading antimicrobial-resistant pathogen causing significant morbidity and mortality worldwide. This review focuses on (1) the targets of current anti-staphylococcal antibiotics and the specific mechanisms that confirm resistance; (2) an in-depth analysis of recently licensed antibiotics approved for the treatment of S. aureus infections; and (3) an examination of the pre-clinical pipeline of anti-staphylococcal compounds. In addition, we examine the molecular mechanism of action of novel antimicrobials and derivatives of existing classes of antibiotics, collate data on the emergence of resistance to new compounds and provide an overview of key data from clinical trials evaluating anti-staphylococcal compounds. We present several successful cases in the development of alternative forms of existing antibiotics that have activity against multidrug-resistant S. aureus. Pre-clinical antimicrobials show promise, but more focus and funding are required to develop novel classes of compounds that can curtail the spread of and sustainably control antimicrobial-resistant S. aureus infections.
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Affiliation(s)
| | - Maisem Laabei
- Department of Life Sciences, University of Bath, Bath BA2 7AY, UK
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Abdullahi IN, Lozano C, Höfle Ú, Cardona-Cabrera T, Zarazaga M, Torres C. Antimicrobial resistome of coagulase-negative staphylococci from nasotracheal cavities of nestlings of Ciconia ciconia in Southern Spain: Detection of mecC-SCCmec type-XI-carrying S. lentus. Comp Immunol Microbiol Infect Dis 2023; 99:102012. [PMID: 37453201 DOI: 10.1016/j.cimid.2023.102012] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/22/2023] [Accepted: 06/24/2023] [Indexed: 07/18/2023]
Abstract
The antimicrobial resistance (AMR) genes of 268 non-duplicated coagulase-negative staphylococci (CoNS) previously obtained from nasotracheal cavities of nestling storks were characterized. They included S. sciuri isolates (n = 191), and non-sciuri-CoNS isolates (NSc-CoNS, n = 77). All S. sciuri carried the intrinsic salA gene (for clindamycin-resistance) and so, clindamycin was not considered for general analysis in this species. About 71.7%/41.6% of the S. sciuri/NSc-CoNS isolates were susceptible to all antibiotics tested; moreover, 14.1%/16.9% and 3.1%/20.8% of S. sciuri/NSc-CoNS showed single antibiotic resistance and multidrug resistance (MDR) phenotype, respectively. Of the ten mecA-positive CoNS isolates, six were associated with SCCmec types-III, -IV or -V elements. Remarkably was the detection of one MDR-S. lentus isolate carrying both mecA and mecC genes, as well as the SCCmec type-XI element. MDR-CoNS was relatively higher in nestlings of parent storks foraging in landfills (21.3%) than those in natural areas (9.7%) (χ2 = 3.421, df=1, p = 0.064). AMR phenotypes (and genes detected) include penicillin (blaZ, blaARL), erythromycin-clindamycin-constitutive (ermA, ermC, ermT), clindamycin (lnuA, salA, vgaA), erythromycin (msrA, mphC), tetracycline (tetK, tetL, tetM), tobramycin (ant4'), tobramycin-gentamicin (aac6'-aph2″), sulfamethoxazole-trimethoprim (dfrA, dfrG, dfrK), chloramphenicol (fexA, fexB, catPC221), and mupirocin (mupA). Interestingly, one S. epidermidis isolate carried the ermT gene. About 29.9% of nestlings harboured more than one non-duplicated CoNS (with varied 2-5 AMR profiles). This study demonstrated that most of the CoNS isolates were susceptible to all the antibiotics tested (63.1%). However, AMR genes of public health importance were found, including the mecC-mediated methicillin resistance trait.
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Affiliation(s)
| | - Carmen Lozano
- Area Biochemistry and Molecular Biology, University of La Rioja, Logroño, Spain
| | - Úrsula Höfle
- SaBio (Health and Biotechnology Research Group, Spanish Wildlife Research Institute IREC (CSIC-UCLM-JCCM), Ciudad Real, Spain
| | - Teresa Cardona-Cabrera
- Area Biochemistry and Molecular Biology, University of La Rioja, Logroño, Spain; SaBio (Health and Biotechnology Research Group, Spanish Wildlife Research Institute IREC (CSIC-UCLM-JCCM), Ciudad Real, Spain
| | - Myriam Zarazaga
- Area Biochemistry and Molecular Biology, University of La Rioja, Logroño, Spain
| | - Carmen Torres
- Area Biochemistry and Molecular Biology, University of La Rioja, Logroño, Spain.
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Naranjo-Lucena A, Slowey R. Invited review: Antimicrobial resistance in bovine mastitis pathogens: A review of genetic determinants and prevalence of resistance in European countries. J Dairy Sci 2023; 106:1-23. [PMID: 36333144 DOI: 10.3168/jds.2022-22267] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 08/08/2022] [Indexed: 11/06/2022]
Abstract
Antimicrobial resistance is an urgent and growing problem worldwide, both for human and animal health. In the animal health sector actions have been taken as concerns grow regarding the development and spread of antimicrobial resistance. Mastitis is the most common infection in dairy cattle. We aimed to summarize the genetic determinants found in staphylococci, streptococci, and Enterobacteriaceae isolated from mastitic milk samples and provide a comparison of percentage resistance to a variety of antimicrobials in European countries.
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Affiliation(s)
- Amalia Naranjo-Lucena
- National Reference Laboratory for Antimicrobial Resistance, Department of Agriculture, Food and the Marine, Backweston Laboratory Campus, Celbridge, Ireland W23 VW2C.
| | - Rosemarie Slowey
- National Reference Laboratory for Antimicrobial Resistance, Department of Agriculture, Food and the Marine, Backweston Laboratory Campus, Celbridge, Ireland W23 VW2C
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Antimicrobial resistance and genomic analysis of staphylococci isolated from livestock and farm attendants in Northern Ghana. BMC Microbiol 2022; 22:180. [PMID: 35864456 PMCID: PMC9306040 DOI: 10.1186/s12866-022-02589-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 07/01/2022] [Indexed: 11/29/2022] Open
Abstract
Background The emergence of antimicrobial resistant bacteria in food producing animals is of growing concern to food safety and health. Staphylococci are common inhabitants of skin and mucous membranes in humans and animals. Infections involving antibiotic resistant staphylococci are associated with increased morbidity and mortality, with notable economic consequences. Livestock farms may enable cross-species transfer of antibiotic resistant staphylococci. The aim of the study was to investigate antimicrobial resistance patterns of staphylococci isolated from livestock and farm attendants in Northern Ghana using phenotypic and genotypic methods. Antimicrobial susceptibility testing was performed on staphylococci recovered from livestock and farm attendants and isolates resistant to cefoxitin were investigated using whole genome sequencing. Results One hundred and fifty-two staphylococci comprising S. sciuri (80%; n = 121), S. simulans (5%; n = 8), S. epidermidis (4%; n = 6), S. chromogens (3%; n = 4), S. aureus (2%; n = 3), S. haemolyticus (1%; n = 2), S. xylosus (1%; n = 2), S. cohnii (1%; n = 2), S. condimenti (1%; n = 2), S. hominis (1%; n = 1) and S. arlettae (1%; n = 1) were identified. The isolates showed resistance to penicillin (89%; n = 135), clindamycin (67%; n = 102), cefoxitin (19%; n = 29), tetracycline (15%; n = 22) and erythromycin (11%; n = 16) but showed high susceptibility to gentamicin (96%; n = 146), sulphamethoxazole/trimethoprim (98%; n = 149) and rifampicin (99%; n = 151). All staphylococci were susceptible to linezolid and amikacin. Carriage of multiple resistance genes was common among the staphylococcal isolates. Genome sequencing of methicillin (cefoxitin) resistant staphylococci (MRS) isolates revealed majority of S. sciuri (93%, n = 27) carrying mecA1 (which encodes for beta-lactam resistance) and the sal(A) gene, responsible for resistance to lincosamide and streptogramin. Most of the MRS isolates were recovered from livestock. Conclusion The study provides insights into the genomic content of MRS from farm attendants and livestock in Ghana and highlights the importance of using whole-genome sequencing to investigate such opportunistic pathogens. The finding of multi-drug resistant staphylococci such as S. sciuri carrying multiple resistant genes is of public health concern as they could pose a challenge for treatment of life-threatening infections that they may cause.
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Mohamad M, Nicholson D, Saha C, Hauryliuk V, Edwards T, Atkinson G, Ranson N, O’Neill A. Sal-type ABC-F proteins: intrinsic and common mediators of pleuromutilin resistance by target protection in staphylococci. Nucleic Acids Res 2022; 50:2128-2142. [PMID: 35137182 PMCID: PMC8887462 DOI: 10.1093/nar/gkac058] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 01/14/2022] [Accepted: 01/26/2022] [Indexed: 11/14/2022] Open
Abstract
The first member of the pleuromutilin (PLM) class suitable for systemic antibacterial chemotherapy in humans recently entered clinical use, underscoring the need to better understand mechanisms of PLM resistance in disease-causing bacterial genera. Of the proteins reported to mediate PLM resistance in staphylococci, the least-well studied to date is Sal(A), a putative ABC-F NTPase that-by analogy to other proteins of this type-may act to protect the ribosome from PLMs. Here, we establish the importance of Sal proteins as a common source of PLM resistance across multiple species of staphylococci. Sal(A) is revealed as but one member of a larger group of Sal-type ABC-F proteins that vary considerably in their ability to mediate resistance to PLMs and other antibiotics. We find that specific sal genes are intrinsic to particular staphylococcal species, and show that this gene family is likely ancestral to the genus Staphylococcus. Finally, we solve the cryo-EM structure of a representative Sal-type protein (Sal(B)) in complex with the staphylococcal 70S ribosome, revealing that Sal-type proteins bind into the E site to mediate target protection, likely by displacing PLMs and other antibiotics via an allosteric mechanism.
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Affiliation(s)
- Merianne Mohamad
- Astbury Centre for Structural Molecular Biology and School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - David Nicholson
- Astbury Centre for Structural Molecular Biology and School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Chayan Kumar Saha
- Department of Molecular Biology, Umeå University, 90187 Umeå, Sweden
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden
| | - Vasili Hauryliuk
- Department of Molecular Biology, Umeå University, 90187 Umeå, Sweden
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden
| | - Thomas A Edwards
- Astbury Centre for Structural Molecular Biology and School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Gemma C Atkinson
- Department of Molecular Biology, Umeå University, 90187 Umeå, Sweden
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology and School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Alex J O’Neill
- Astbury Centre for Structural Molecular Biology and School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
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Genome-based characterization of a plasmid-associated micrococcin P1 biosynthetic gene cluster and virulence factors in Mammaliicoccus sciuri IMDO-S72. Appl Environ Microbiol 2021; 88:e0208821. [PMID: 34936836 DOI: 10.1128/aem.02088-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Analysis of the de novo assembled genome of Mammaliicoccus sciuri IMDO-S72 revealed the genetically encoded machinery behind its earlier reported antibacterial phenotype and gave further insight into the repertoire of putative virulence factors of this recently reclassified species. A plasmid-encoded biosynthetic gene cluster was held responsible for the antimicrobial activity of M. sciuri IMDO-S72, comprising genes involved in thiopeptide production. The compound encoded by this gene cluster was structurally identified as micrococcin P1. Further examination of its genome highlighted the ubiquitous presence of innate virulence factors mainly involved in surface colonization. Determinants contributing to aggressive virulence were generally absent, with exception of a plasmid-associated ica cluster. The native antibiotic resistance genes sal(A) and mecA were detected within the genome, amongst others, but were not consistently linked with a resistant phenotype. While mobile genetic elements were identified within the genome, such as an untypeable SCC element, they proved to be generally free of virulence- and antibiotic-related genes. These results further suggest a commensal lifestyle of M. sciuri and indicate the association of antibiotic resistance determinants with mobile genetic elements, as an important factor in conferring antibiotic resistance, in addition to their unilateral annotation. Importance Mammaliicoccus sciuri has been put forward as an important carrier of virulence and antibiotic resistance genes, which can be transmitted to clinically important staphylococcal species such as Staphylococcus aureus. As a common inhabitant of mammal skin, this species is believed to have a predominant commensal lifestyle although it has been reported as an opportunistic pathogen in some cases. This study provides an extensive genome-wide description of its putative virulence potential taking into consideration the genomic context in which these genes appear, an aspect that is often overlooked during virulence analysis. Additional genome and biochemical analysis linked M. sciuri with the production of micrococcin P1, gaining further insight to which extent these biosynthetic gene cluster are distributed amongst different related species. The frequent plasmid-associated character hints that these traits can be horizontally transferred and might confer a competitive advantage to its recipient within its ecological niche.
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The Resistome and Mobilome of Multidrug-Resistant Staphylococcus sciuri C2865 Unveil a Transferable Trimethoprim Resistance Gene, Designated dfrE, Spread Unnoticed. mSystems 2021; 6:e0051121. [PMID: 34374564 PMCID: PMC8407400 DOI: 10.1128/msystems.00511-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Methicillin-resistant Staphylococcus sciuri (MRSS) strain C2865 from a stranded dog in Nigeria was trimethoprim (TMP) resistant but lacked formerly described staphylococcal TMP-resistant dihydrofolate reductase genes (dfr). Whole-genome sequencing, comparative genomics, and pan-genome analyses were pursued to unveil the molecular bases for TMP resistance via resistome and mobilome profiling. MRSS C2865 comprised a species subcluster and positioned just above the intraspecies boundary. Lack of species host tropism was observed. S. sciuri exhibited an open pan-genome, while MRSS C2865 harbored the highest number of unique genes (75% associated with mobilome). Within this fraction, we discovered a transferable TMP resistance gene, named dfrE, which confers high-level TMP resistance in Staphylococcus aureus and Escherichia coli. dfrE was located in a novel multidrug resistance mosaic plasmid (pUR2865-34) encompassing adaptive, mobilization, and segregational stability traits. dfrE was formerly denoted as dfr_like in Exiguobacterium spp. from fish farm sediment in China but escaped identification in one macrococcal and diverse staphylococcal genomes in different Asian countries. dfrE shares the highest identity with dfr of soil-related Paenibacillus anaericanus (68%). Data analysis discloses that dfrE has emerged from a single ancestor and places S. sciuri as a plausible donor. C2865 unique fraction additionally enclosed novel chromosomal mobile islands, including a multidrug-resistant pseudo-SCCmec cassette, three apparently functional prophages (Siphoviridae), and an SaPI4-related staphylococcal pathogenicity island. Since dfrE seems not yet common in staphylococcal clinical specimens, our data promote early surveillance and enable molecular diagnosis. We evidence the genome plasticity of S. sciuri and highlight its role as a resourceful reservoir for adaptive traits. IMPORTANCE The discovery and surveillance of antimicrobial resistance genes (AMRG) and their mobilization platforms are critical to understand the evolution of bacterial resistance and to restrain further expansion. Limited genomic data are available on Staphylococcus sciuri; regardless, it is considered a reservoir for critical AMRG and mobile elements. We uncover a transferable staphylococcal TMP resistance gene, named dfrE, in a novel mosaic plasmid harboring additional resistance, adaptive, and self-stabilization features. dfrE is present but evaded detection in diverse species from varied sources geographically distant. Our analyses evidence that the dfrE-carrying element has emerged from a single ancestor and position S. sciuri as the donor species for dfrE spread. We also identify novel mobilizable chromosomal islands encompassing AMRG and three unrelated prophages. We prove high intraspecies heterogenicity and genome plasticity for S. sciuri. This work highlights the importance of genome-wide ecological studies to facilitate identification, characterization, and evolution routes of bacteria adaptive features.
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Crowe-McAuliffe C, Murina V, Turnbull KJ, Kasari M, Mohamad M, Polte C, Takada H, Vaitkevicius K, Johansson J, Ignatova Z, Atkinson GC, O'Neill AJ, Hauryliuk V, Wilson DN. Structural basis of ABCF-mediated resistance to pleuromutilin, lincosamide, and streptogramin A antibiotics in Gram-positive pathogens. Nat Commun 2021; 12:3577. [PMID: 34117249 PMCID: PMC8196190 DOI: 10.1038/s41467-021-23753-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 05/11/2021] [Indexed: 02/05/2023] Open
Abstract
Target protection proteins confer resistance to the host organism by directly binding to the antibiotic target. One class of such proteins are the antibiotic resistance (ARE) ATP-binding cassette (ABC) proteins of the F-subtype (ARE-ABCFs), which are widely distributed throughout Gram-positive bacteria and bind the ribosome to alleviate translational inhibition from antibiotics that target the large ribosomal subunit. Here, we present single-particle cryo-EM structures of ARE-ABCF-ribosome complexes from three Gram-positive pathogens: Enterococcus faecalis LsaA, Staphylococcus haemolyticus VgaALC and Listeria monocytogenes VgaL. Supported by extensive mutagenesis analysis, these structures enable a general model for antibiotic resistance mediated by these ARE-ABCFs to be proposed. In this model, ABCF binding to the antibiotic-stalled ribosome mediates antibiotic release via mechanistically diverse long-range conformational relays that converge on a few conserved ribosomal RNA nucleotides located at the peptidyltransferase center. These insights are important for the future development of antibiotics that overcome such target protection resistance mechanisms.
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Affiliation(s)
| | - Victoriia Murina
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Kathryn Jane Turnbull
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Marje Kasari
- University of Tartu, Institute of Technology, Tartu, Estonia
| | - Merianne Mohamad
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Christine Polte
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Hiraku Takada
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Karolis Vaitkevicius
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Jörgen Johansson
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Zoya Ignatova
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | | | - Alex J O'Neill
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Vasili Hauryliuk
- Department of Molecular Biology, Umeå University, Umeå, Sweden.
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden.
- University of Tartu, Institute of Technology, Tartu, Estonia.
- Department of Experimental Medical Science, Lund University, Lund, Sweden.
| | - Daniel N Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany.
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Shi YZ, Yoshida T, Fujiwara A, Nishiki I. Characterization of lsa(D), a Novel Gene Responsible for Resistance to Lincosamides, Streptogramins A, and Pleuromutilins in Fish Pathogenic Lactococcus garvieae Serotype II. Microb Drug Resist 2021; 27:301-310. [PMID: 32706619 DOI: 10.1089/mdr.2020.0218] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Aims: Fish pathogenic Lactococcus garvieae serotype II has been isolated from cultured fish species in Japan. This study aimed to investigate the molecular mechanisms of lincomycin (LCM)-resistant L. garvieae serotype II and assess the molecular basis for lincosamides-streptogramins A-pleuromutilins (LSAP)-resistant phenotype. Results: We identified a novel lsa(D)-encoded 497-aa ATP-binding cassette F (ABC-F) protein in the LSAP-resistant strains. Amino acid identities of 41.25-54.73% were obtained between the deduced amino acids from Lsa(D) and other Lsa-type ABC-F proteins. Furthermore, comparative analysis revealed that the allele of lsa(D) with single point mutation at 233 aa position (TGG → TAG; tryptophan→premature termination codon [PTC]) in LSAP-sensitive strains. The minimum inhibitory concentrations of antimicrobials against the lsa(D) complementary strain and lsa(D)-disrupted mutant confirmed that lsa(D) conferred the LSAP-resistant phenotype. The reverse transcription-polymerase chain reaction could not detect the noncoding region of lsa(D) allelic variant in the LSAP-sensitive strains. Additionally, the PTC (TAG) in LCM-sensitive strains was replaced by TGG, CAG, or TAT in the laboratory-induced revertant mutants. Conclusions: The novel lsa(D) conferred the LSAP-resistant phenotype in clinically LCM-resistant L. garvieae serotype II strains. However, the allele of lsa(D) gene containing the PTC was found in L. garvieae serotype II, resulting in the LSAP-susceptible phenotype.
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Affiliation(s)
- Yin-Ze Shi
- Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | | | - Atushi Fujiwara
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Fisheries Research and Education Agency, Yokohama, Japan
| | - Issei Nishiki
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Fisheries Research and Education Agency, Yokohama, Japan
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Owens LA, Colitti B, Hirji I, Pizarro A, Jaffe JE, Moittié S, Bishop-Lilly KA, Estrella LA, Voegtly LJ, Kuhn JH, Suen G, Deblois CL, Dunn CD, Juan-Sallés C, Goldberg TL. A Sarcina bacterium linked to lethal disease in sanctuary chimpanzees in Sierra Leone. Nat Commun 2021; 12:763. [PMID: 33536429 PMCID: PMC7859188 DOI: 10.1038/s41467-021-21012-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 01/04/2021] [Indexed: 12/16/2022] Open
Abstract
Human and animal infections with bacteria of the genus Sarcina (family Clostridiaceae) are associated with gastric dilation and emphysematous gastritis. However, the potential roles of sarcinae as commensals or pathogens remain unclear. Here, we investigate a lethal disease of unknown etiology that affects sanctuary chimpanzees (Pan troglodytes verus) in Sierra Leone. The disease, which we have named "epizootic neurologic and gastroenteric syndrome" (ENGS), is characterized by neurologic and gastrointestinal signs and results in death of the animals, even after medical treatment. Using a case-control study design, we show that ENGS is strongly associated with Sarcina infection. The microorganism is distinct from Sarcina ventriculi and other known members of its genus, based on bacterial morphology and growth characteristics. Whole-genome sequencing confirms this distinction and reveals the presence of genetic features that may account for the unusual virulence of the bacterium. Therefore, we propose that this organism be considered the representative of a new species, named "Candidatus Sarcina troglodytae". Our results suggest that a heretofore unrecognized complex of related sarcinae likely exists, some of which may be highly virulent. However, the potential role of "Ca. S. troglodytae" in the etiology of ENGS, alone or in combination with other factors, remains a topic for future research.
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Affiliation(s)
- Leah A Owens
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Barbara Colitti
- Department of Veterinary Science, University of Torino, Torino, Italy
| | - Ismail Hirji
- Tacugama Chimpanzee Sanctuary, Freetown, Sierra Leone
| | | | - Jenny E Jaffe
- Tai Chimpanzee Project, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany
| | - Sophie Moittié
- School of Veterinary Medicine and Sciences, University of Nottingham Sutton Bonington Campus, Sutton Bonington, Leicestershire, UK
- Twycross Zoo, Atherstone, UK
| | - Kimberly A Bishop-Lilly
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, MD, USA
| | - Luis A Estrella
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, MD, USA
| | - Logan J Voegtly
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, MD, USA
- Leidos, Reston, VI, USA
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, MD, USA
| | - Garret Suen
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Courtney L Deblois
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Christopher D Dunn
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Tony L Goldberg
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA.
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Krishnan A, Burroughs AM, Iyer LM, Aravind L. Comprehensive classification of ABC ATPases and their functional radiation in nucleoprotein dynamics and biological conflict systems. Nucleic Acids Res 2020; 48:10045-10075. [PMID: 32894288 DOI: 10.1093/nar/gkaa726] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 08/17/2020] [Accepted: 08/20/2020] [Indexed: 12/13/2022] Open
Abstract
ABC ATPases form one of the largest clades of P-loop NTPase fold enzymes that catalyze ATP-hydrolysis and utilize its free energy for a staggering range of functions from transport to nucleoprotein dynamics. Using sensitive sequence and structure analysis with comparative genomics, for the first time we provide a comprehensive classification of the ABC ATPase superfamily. ABC ATPases developed structural hallmarks that unambiguously distinguish them from other P-loop NTPases such as an alternative to arginine-finger-based catalysis. At least five and up to eight distinct clades of ABC ATPases are reconstructed as being present in the last universal common ancestor. They underwent distinct phases of structural innovation with the emergence of inserts constituting conserved binding interfaces for proteins or nucleic acids and the adoption of a unique dimeric toroidal configuration for DNA-threading. Specifically, several clades have also extensively radiated in counter-invader conflict systems where they serve as nodal nucleotide-dependent sensory and energetic components regulating a diversity of effectors (including some previously unrecognized) acting independently or together with restriction-modification systems. We present a unified mechanism for ABC ATPase function across disparate systems like RNA editing, translation, metabolism, DNA repair, and biological conflicts, and some unexpected recruitments, such as MutS ATPases in secondary metabolism.
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Affiliation(s)
- Arunkumar Krishnan
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - A Maxwell Burroughs
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Lakshminarayan M Iyer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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15
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Frequency and Characterization of Antimicrobial Resistance and Virulence Genes of Coagulase-Negative Staphylococci from Wild Birds in Spain. Detection of tst-Carrying S. sciuri Isolates. Microorganisms 2020; 8:microorganisms8091317. [PMID: 32872433 PMCID: PMC7564563 DOI: 10.3390/microorganisms8091317] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 08/20/2020] [Accepted: 08/26/2020] [Indexed: 12/27/2022] Open
Abstract
The objective of this study was to determine the prevalence and diversity of coagulase-negative staphylococci (CoNS) species from wild birds in Spain, as well as to analyze the antimicrobial resistance phenotype/genotype and the virulence gene content. During 2015–2016, tracheal samples of 242 wild birds were collected in different regions of Spain for staphylococci recovery. The species identification was performed using MALDI-TOF. The antimicrobial resistance phenotype and genotype was investigated by the disk diffusion method and by PCR, respectively. The presence of the virulence genes lukF/S-PV, tst, eta, etb, etd and scn was investigated by PCR. Moreover, CoNS carrying the mecA gene were subjected to SCCmec typing. Of the tested animals, 60% were CoNS-carriers, and 173 CoNS isolates were recovered from the 146 positive animals, which belonged to 11 species, with predominance of S. sciuri (n = 118) and S. lentus (n = 25). A total of 34% of CoNS isolates showed a multidrug resistance phenotype, and 42 mecA-positive methicillin-resistant CoNS (MRCoNS) were detected. The isolates showed resistance to the following antimicrobials (percentage of resistant isolates/antimicrobial resistance genes detected): penicillin (49/ blaZ, mecA), cefoxitin (24/ mecA), erythromycin and/or clindamycin (92/ erm(B), erm(C), erm(43), msr(A), mph(C), lnu(A), lsa(B), vga(A) and sal(A)), gentamicin and/or tobramycin (5/ aac(6′)-Ie-aph(2″)-Ia, ant(4′)-Ia), streptomycin (12/str), tetracycline (17/ tet(K), tet(L), tet(M)), ciprofloxacin (4), chloramphenicol (1/ fexA), fusidic acid (86/ fusB, fusD) and trimethoprim–sulfamethoxazole (1/ dfrK). None of the isolates harbored the lukF/S-PV, eta, etb, etd and scn genes, but two S. sciuri isolates (1%) carried the tst gene. Wild birds are frequently colonized by CoNS species, especially S. sciuri. We identified scavenging on intensively produced livestock and feeding on landfills as risk factors for CoNS carriage. High proportions of MRCoNS and multidrug resistant CoNS were detected, which coupled with the presence of important virulence genes is of concern.
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16
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Paterson GK. Genomic epidemiology of methicillin-resistant Staphylococcus sciuri carrying a SCCmec-mecC hybrid element. INFECTION GENETICS AND EVOLUTION 2019; 79:104148. [PMID: 31862259 DOI: 10.1016/j.meegid.2019.104148] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 12/16/2019] [Accepted: 12/17/2019] [Indexed: 12/19/2022]
Abstract
The recognition in 2011 of the methicillin resistance determinate mecC among staphylococci has raised many questions over its evolution and epidemiology. While mecC has been best studied in Staphylococcus aureus it has also been described in at least nine other species of staphylococci. In most cases these studies are limited to single isolates. In the widespread animal commensal Staphylococcus sciuri mecC has been described in two isolates and is located within a distinct SCCmec-mecC composite element. In this study, a further 11 mecA/mecC S. sciuri isolated from dairy farms in England and Wales in 2015 and 2016 were genome sequenced and characterised. The results show that two variants of the SCCmec-mecC element are present in S. sciuri, differentiated by different ccr alleles and likely to have arisen by homologous recombination. A phylogeny of sixty genome-sequenced S. sciuri isolates was made using core genome multi-locus sequence typing and reveals a diverse population with the SCCmec-mecC element present in four distinct branches, indicative of four independent acquisitions by S. sciuri. Finally, the study identified the rapid clonal expansion of a mecA/mecC lineage of S. sciuri among dairy farms across a wide geographical area which may contribute to the future dissemination of this methicillin resistance cassette.
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Affiliation(s)
- Gavin K Paterson
- Easter Bush Pathology, Royal (Dick) School of Veterinary Studies and The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK.
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17
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Ousalem F, Singh S, Chesneau O, Hunt JF, Boël G. ABC-F proteins in mRNA translation and antibiotic resistance. Res Microbiol 2019; 170:435-447. [PMID: 31563533 DOI: 10.1016/j.resmic.2019.09.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 09/01/2019] [Accepted: 09/11/2019] [Indexed: 12/15/2022]
Abstract
The ATP binding cassette protein superfamily comprises ATPase enzymes which are, for the most part, involved in transmembrane transport. Within this superfamily however, some protein families have other functions unrelated to transport. One example is the ABC-F family, which comprises an extremely diverse set of cytoplasmic proteins. All of the proteins in the ABC-F family characterized to date act on the ribosome and are translation factors. Their common function is ATP-dependent modulation of the stereochemistry of the peptidyl transferase center (PTC) in the ribosome coupled to changes in its global conformation and P-site tRNA binding geometry. In this review, we give an overview of the function, structure, and theories for the mechanisms-of-action of microbial proteins in the ABC-F family, including those involved in mediating resistance to ribosome-binding antibiotics.
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Affiliation(s)
- Farès Ousalem
- UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, 75005, Paris, France
| | - Shikha Singh
- Department of Biological, 702A Sherman Fairchild Center, Columbia University, New York, NY, 10027, United States
| | - Olivier Chesneau
- Département de Microbiologie, Institut Pasteur, 75724, Paris Cedex 15, France.
| | - John F Hunt
- Department of Biological, 702A Sherman Fairchild Center, Columbia University, New York, NY, 10027, United States.
| | - Grégory Boël
- UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, 75005, Paris, France.
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Low Prevalence of Gram-Positive Isolates Showing Elevated Lefamulin MIC Results during the SENTRY Surveillance Program for 2015-2016 and Characterization of Resistance Mechanisms. Antimicrob Agents Chemother 2019; 63:AAC.02158-18. [PMID: 30670418 DOI: 10.1128/aac.02158-18] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 01/18/2019] [Indexed: 12/31/2022] Open
Abstract
This study investigated the molecular mechanisms possibly associated with non-wild-type MICs for lefamulin among staphylococci and streptococci included in the lefamulin surveillance program from 2015 to 2016. A total of 2,919 Staphylococcus aureus, 276 coagulase-negative staphylococci (CoNS), 3,923 Streptococcus pneumoniae, 389 β-hemolytic, and 178 viridans group streptococci isolates were included in the surveillance studies. Eleven (0.3% of all S. aureus) S. aureus isolates with lefamulin MICs above the staphylococcal epidemiological cutoff (ECOFF) value (>0.25 μg/ml) were selected for this study. Eight (72.7%) S. aureus (lefamulin MIC, 0.5 to 4 μg/ml) isolates carried vga(A or E), one isolate (MIC, 32 μg/ml) carried lsa(E), one isolate (MIC, 16 μg/ml) had an alteration in L4, and one strain (MIC, 0.5 μg/ml) did not carry any of the investigated resistance mechanisms. A total of 14 (5.1% of all CoNS) CoNS isolates had lefamulin MICs (0.5 to >32 μg/ml) above the ECOFF. Similar to S. aureus, 8 (57.1%) CoNS (lefamulin MIC, 1 to 8 μg/ml) isolates carried vga(A or B), while 2 isolates (MIC, 4 to 32 μg/ml) carried cfr High genetic diversity was observed among staphylococci, although 3 S. aureus isolates belonged to sequence type 398 (ST398). Among the 3 Streptococcus agalactiae and 3 viridans group streptococci (0.1% of all streptococci surveyed) isolates selected for additional characterization, all but 1 isolate carried lsa(E). This study documents a low occurrence of surveillance isolates exhibiting a non-wild-type MIC for lefamulin, and among these isolates, vga and lsa(E) prevailed in staphylococci and streptococci, respectively.
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Mendes RE, Jones RN, Woosley LN, Cattoir V, Castanheira M. Application of Next-Generation Sequencing for Characterization of Surveillance and Clinical Trial Isolates: Analysis of the Distribution of β-lactamase Resistance Genes and Lineage Background in the United States. Open Forum Infect Dis 2019; 6:S69-S78. [PMID: 30895217 PMCID: PMC6419912 DOI: 10.1093/ofid/ofz004] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Background Sequencing technologies and techniques have seen remarkable transformation and innovation that have significantly affected sequencing capability. Data analyses have replaced sequencing as the main challenge. This paper provides an overview on applying next-generation sequencing (NGS) and analysis and discusses the benefits and challenges. In addition, this document shows results from using NGS and bioinformatics tools to screen for β-lactamase genes and assess the epidemiological structure of Escherichia coli– and Klebsiella pneumoniae–causing bloodstream (BSIs) and urinary tract (UTIs) infections in patients hospitalized in the United States during the SENTRY Antimicrobial Surveillance Program for 2016. Methods A total of 3525 isolates (2751 E. coli and 774 K. pneumoniae) causing BSIs (n = 892) and UTIs (n = 2633) in hospitalized patients in the United States were included. Isolates were tested for susceptibility by broth microdilution, and those that met a minimum inhibitory concentration (MIC)–based screening criteria had their genomes sequenced and analyzed. Results A total of 11.6% and 16.1% of E. coli–causing UTIs and BSIs, respectively, met the MIC-based criteria, whereas 11.0% and 13.7% of K. pneumoniae isolates causing UTIs and BSIs, respectively, met the criteria. Among E. coli, blaCTX-M variants (87.6% overall) prevailed (60.5% of CTX-M group 1 and 26.9% of group 9). A total of 60.3% of K. pneumoniae isolates carried blaCTX-M variants (52.7% and 7.6% of groups 1 and 9, respectively). Two E. coli (0.6%) and 13 K. pneumoniae (12.9%) isolates harbored blaKPC. Among KPC-producing K. pneumoniae (2 from BSIs and 11 from UTIs), 84.6% (11/13) were ST258 (CC258). Seventeen and 38 unique clonal complexes (CCs) were noted in E. coli that caused BSIs and UTIs, respectively, and CC131 (or ST131) was the most common CC among BSI (53.6%) and UTI (58.2%) isolates. Twenty-three and 26 CCs were noted among K. pneumoniae–causing BSIs and UTIs, respectively. CC258 (28.3%) prevailed in UTI pathogens, whereas CC307 (15.0%) was the most common CC among BSI isolates. Conclusions This study provides a benchmark for the distribution of β-lactamase genes and the population structure information for the most common Enterobacteriaceae species responsible for BSIs and UTIs in US medical centers during the 2016 SENTRY Program.
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Affiliation(s)
| | | | | | - Vincent Cattoir
- University Hospital of Rennes, Department of Clinical Microbiology, Rennes, France.,National Reference Center for Antimicrobial Resistance, Rennes, France.,University of Rennes 1, Unit Inserm U1230, Rennes, France
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Murina V, Kasari M, Takada H, Hinnu M, Saha CK, Grimshaw JW, Seki T, Reith M, Putrinš M, Tenson T, Strahl H, Hauryliuk V, Atkinson GC. ABCF ATPases Involved in Protein Synthesis, Ribosome Assembly and Antibiotic Resistance: Structural and Functional Diversification across the Tree of Life. J Mol Biol 2018; 431:3568-3590. [PMID: 30597160 PMCID: PMC6723617 DOI: 10.1016/j.jmb.2018.12.013] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 12/11/2018] [Accepted: 12/15/2018] [Indexed: 10/27/2022]
Abstract
Within the larger ABC superfamily of ATPases, ABCF family members eEF3 in Saccharomyces cerevisiae and EttA in Escherichia coli have been found to function as ribosomal translation factors. Several other ABCFs including biochemically characterized VgaA, LsaA and MsrE confer resistance to antibiotics that target the peptidyl transferase center and exit tunnel of the ribosome. However, the diversity of ABCF subfamilies, the relationships among subfamilies and the evolution of antibiotic resistance (ARE) factors from other ABCFs have not been explored. To address this, we analyzed the presence of ABCFs and their domain architectures in 4505 genomes across the tree of life. We find 45 distinct subfamilies of ABCFs that are widespread across bacterial and eukaryotic phyla, suggesting that they were present in the last common ancestor of both. Surprisingly, currently known ARE ABCFs are not confined to a distinct lineage of the ABCF family tree, suggesting that ARE can readily evolve from other ABCF functions. Our data suggest that there are a number of previously unidentified ARE ABCFs in antibiotic producers and important human pathogens. We also find that ATPase-deficient mutants of all four E. coli ABCFs (EttA, YbiT, YheS and Uup) inhibit protein synthesis, indicative of their ribosomal function, and demonstrate a genetic interaction of ABCFs Uup and YheS with translational GTPase BipA involved in assembly of the 50S ribosome subunit. Finally, we show that the ribosome-binding resistance factor VmlR from Bacillus subtilis is localized to the cytoplasm, ruling out a role in antibiotic efflux.
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Affiliation(s)
- Victoriia Murina
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden; Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 901 87 Umeå, Sweden
| | - Marje Kasari
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden
| | - Hiraku Takada
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden; Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 901 87 Umeå, Sweden
| | - Mariliis Hinnu
- University of Tartu, Institute of Technology, Nooruse 1, 50411 Tartu, Estonia
| | - Chayan Kumar Saha
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden
| | - James W Grimshaw
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, United Kingdom
| | - Takahiro Seki
- Department of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University, 263-8522 Chiba, Japan
| | - Michael Reith
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden
| | - Marta Putrinš
- University of Tartu, Institute of Technology, Nooruse 1, 50411 Tartu, Estonia
| | - Tanel Tenson
- University of Tartu, Institute of Technology, Nooruse 1, 50411 Tartu, Estonia
| | - Henrik Strahl
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, United Kingdom
| | - Vasili Hauryliuk
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden; Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 901 87 Umeå, Sweden; University of Tartu, Institute of Technology, Nooruse 1, 50411 Tartu, Estonia
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Feßler AT, Wang Y, Wu C, Schwarz S. Mobile lincosamide resistance genes in staphylococci. Plasmid 2018; 99:22-31. [DOI: 10.1016/j.plasmid.2018.06.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 06/16/2018] [Accepted: 06/18/2018] [Indexed: 01/31/2023]
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Abstract
ABSTRACT
Antimicrobial resistance among staphylococci of animal origin is based on a wide variety of resistance genes. These genes mediate resistance to many classes of antimicrobial agents approved for use in animals, such as penicillins, cephalosporins, tetracyclines, macrolides, lincosamides, phenicols, aminoglycosides, aminocyclitols, pleuromutilins, and diaminopyrimidines. In addition, numerous mutations have been identified that confer resistance to specific antimicrobial agents, such as ansamycins and fluoroquinolones. The gene products of some of these resistance genes confer resistance to only specific members of a class of antimicrobial agents, whereas others confer resistance to the entire class or even to members of different classes of antimicrobial agents, including agents approved solely for human use. The resistance genes code for all three major resistance mechanisms: enzymatic inactivation, active efflux, and protection/modification/replacement of the cellular target sites of the antimicrobial agents. Mobile genetic elements, in particular plasmids and transposons, play a major role as carriers of antimicrobial resistance genes in animal staphylococci. They facilitate not only the exchange of resistance genes among members of the same and/or different staphylococcal species, but also between staphylococci and other Gram-positive bacteria. The observation that plasmids of staphylococci often harbor more than one resistance gene points toward coselection and persistence of resistance genes even without direct selective pressure by a specific antimicrobial agent. This chapter provides an overview of the resistance genes and resistance-mediating mutations known to occur in staphylococci of animal origin.
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Antonelli A, D’Andrea MM, Brenciani A, Galeotti CL, Morroni G, Pollini S, Varaldo PE, Rossolini GM. Characterization of poxtA, a novel phenicol–oxazolidinone–tetracycline resistance gene from an MRSA of clinical origin. J Antimicrob Chemother 2018; 73:1763-1769. [DOI: 10.1093/jac/dky088] [Citation(s) in RCA: 140] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Accepted: 02/23/2018] [Indexed: 11/13/2022] Open
Affiliation(s)
- Alberto Antonelli
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | | | - Andrea Brenciani
- Department of Biomedical Sciences and Public Health, Polytechnic University of Marche Medical School, Ancona, Italy
| | - Cesira L Galeotti
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
- Research Centre, GlaxoSmithKline Vaccines S.r.l, Siena, Italy
| | - Gianluca Morroni
- Infectious Diseases Clinic, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche Medical School, Ancona, Italy
| | - Simona Pollini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Pietro Emanuele Varaldo
- Department of Biomedical Sciences and Public Health, Polytechnic University of Marche Medical School, Ancona, Italy
| | - Gian Maria Rossolini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
- Clinical Microbiology and Virology Unit, Careggi University Hospital, Florence, Italy
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Sharkey LKR, O’Neill AJ. Antibiotic Resistance ABC-F Proteins: Bringing Target Protection into the Limelight. ACS Infect Dis 2018; 4:239-246. [PMID: 29376318 DOI: 10.1021/acsinfecdis.7b00251] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Members of the ATP-binding cassette (ABC)-F protein subfamily collectively mediate resistance to a broader range of clinically important antibiotic classes than any other group of resistance proteins and are widespread in pathogenic bacteria. Following over 25 years' of controversy regarding the mechanism by which these proteins work, it has recently been established that they provide antibiotic resistance through the previously recognized but underappreciated phenomenon of target protection; they bind to the ribosome to effect the release of ribosome-targeted antibiotics, thereby rescuing the translation apparatus from antibiotic-mediated inhibition. Here we review the ABC-F resistance proteins with an emphasis on their mechanism of action, first exploring the history of the debate about how these proteins work and outlining our current state of knowledge and then considering key questions to be addressed in understanding the molecular detail of their function.
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Affiliation(s)
- Liam K. R. Sharkey
- Antimicrobial Research Centre and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K
| | - Alex J. O’Neill
- Antimicrobial Research Centre and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K
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25
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Christo-Foroux E, Vallaeys T, Loux V, Dassa E, Deutscher J, Wandersman C, Livernois A, Hot C, Criscuolo A, Dauga C, Clermont D, Chesneau O. Manual and expert annotation of the nearly complete genome sequence of Staphylococcus sciuri strain ATCC 29059: A reference for the oxidase-positive staphylococci that supports the atypical phenotypic features of the species group. Syst Appl Microbiol 2017; 40:401-410. [PMID: 28890241 DOI: 10.1016/j.syapm.2017.07.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 06/30/2017] [Accepted: 07/03/2017] [Indexed: 11/30/2022]
Abstract
Staphylococcus sciuri is considered to be one of the most ancestral species in the natural history of the Staphylococcus genus that consists of 48 validly described species. It belongs to the basal group of oxidase-positive and novobiocin-resistant staphylococci that diverged from macrococci approximately 250 million years ago. Contrary to other groups, the S. sciuri species group has not developed host-specific colonization strategies. Genome analysis of S. sciuri ATCC 29059 provides here the first genetic basis for atypical traits that would support the switch between the free-living style and the infective state in animals and humans. From among the most remarkable features, it was noticed in this extensive study that there were a number of phosphoenolpyruvate:carbohydrate phosphotransferase systems (PTS), almost twice as many as any other staphylococci, and the co-occurrence of mevalonate and non-mevalonate pathways for isoprenoid synthesis. The sequenced strain was devoid of the main virulence factors present in Staphylococcus aureus, although it exhibited numerous heme and iron acquisition systems, as well as crt and aldH genes necessary for gold pigment synthesis. The sensing and signaling networks, exemplified by a large and typical repertoire of two-component regulatory systems and a complete panel of master regulators, such as agr, rex, mgrA, rot, sarA and sarR genes, depict the background in which S. aureus virulence genes were later acquired. An additional sigma factor, a distinct set of electron transducer elements and many gene operons similar to those found in Bacillus spp. would constitute the most visible remnant links with Bacillaceae organisms.
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Affiliation(s)
- Eugene Christo-Foroux
- Département de Microbiologie, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France.
| | - Tatiana Vallaeys
- Département de Biologie Ecologie, Université de Montpellier, CC 13002, Place Eugène Bataillon, 34095 Montpellier, France.
| | - Valentin Loux
- MaIAGE, INRA, Université Paris-Saclay, Domaine de Vilvert, 78352 Jouy-en-Josas, France.
| | - Elie Dassa
- Département de Microbiologie, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Josef Deutscher
- CNRS, UMR 8261 Expression Génétique Microbienne, Institut de Biologie Physico-Chimique, Université Paris Diderot, Sorbonne-Paris-Cité, 13 rue Pierre et Marie Curie, Paris, France.
| | - Cécile Wandersman
- Département de Microbiologie, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Aurélien Livernois
- Département de Microbiologie, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France; Département de Biologie Ecologie, Université de Montpellier, CC 13002, Place Eugène Bataillon, 34095 Montpellier, France
| | - Chloe Hot
- Département de Microbiologie, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Alexis Criscuolo
- Hub, Center for Bioinformatics, Biostatistics and Integrative Biology (C3BI), Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France.
| | - Catherine Dauga
- International Group of Data Analysis (IGDA), Center for Bioinformatics, Biostatistics and Integrative Biology (C3BI), Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France.
| | - Dominique Clermont
- Collection de l'Institut Pasteur (CIP), Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France.
| | - Olivier Chesneau
- Département de Microbiologie, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France.
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Deng F, Wang H, Liao Y, Li J, Feßler AT, Michael GB, Schwarz S, Wang Y. Detection and Genetic Environment of Pleuromutilin-Lincosamide-Streptogramin A Resistance Genes in Staphylococci Isolated from Pets. Front Microbiol 2017; 8:234. [PMID: 28261187 PMCID: PMC5306371 DOI: 10.3389/fmicb.2017.00234] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 02/02/2017] [Indexed: 11/13/2022] Open
Abstract
Increasing emergence of staphylococci resistant to pleuromutilins, lincosamides, and streptogramin A (PLSA) and isolated from humans and pets is a growing public health concern worldwide. Currently, there was only one published study regarding one of the PLSA genes, vga(A) detected in staphylococci isolated from cat. In this study, eleven pleuromutilin-resistant staphylococci from pets and two from their owners were isolated and further characterized for their antimicrobial susceptibilities, plasmid profiles, genotypes, and genetic context of the PLSA resistance genes. The gene sal(A) identified in 11 staphylococcal isolates was found for the first time in Staphylococcus haemolyticus, Staphylococcus epidermidis, and Staphylococcus xylosus. Moreover, these 11 isolates shared the identical regions flanking the sal(A) gene located in the chromosomal DNA. Two S. haemolyticus isolates from a cat and its owner carried similar vga(A)LC plasmids and displayed indistinguishable PFGE patterns. A novel chromosomal multidrug resistance genomic island (MDRGI) containing 13 resistance genes, including lsa(E), was firstly identified in S. epidermidis. In addition, vga(A)LC, sal(A), and lsa(E) were for the first time identified in staphylococcal isolates originating from pet animals. The plasmids, chromosomal DNA region, and MDRGI associated with the PLSA resistance genes vga(A), vga(A)LC, sal(A), and lsa(E) are present in staphylococci isolated from pets and humans and present significant challenges for the clinical management of infections by limiting therapeutic options.
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Affiliation(s)
- Fengru Deng
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural UniversityBeijing, China; Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural UniversityGuangzhou, China
| | - Huiwen Wang
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University Beijing, China
| | - Yifei Liao
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University Beijing, China
| | - Jun Li
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University Beijing, China
| | - Andrea T Feßler
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin Berlin, Germany
| | - Geovana B Michael
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin Berlin, Germany
| | - Stefan Schwarz
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural UniversityBeijing, China; Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität BerlinBerlin, Germany
| | - Yang Wang
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University Beijing, China
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Schwarz S, Shen J, Kadlec K, Wang Y, Brenner Michael G, Feßler AT, Vester B. Lincosamides, Streptogramins, Phenicols, and Pleuromutilins: Mode of Action and Mechanisms of Resistance. Cold Spring Harb Perspect Med 2016; 6:a027037. [PMID: 27549310 PMCID: PMC5088508 DOI: 10.1101/cshperspect.a027037] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Lincosamides, streptogramins, phenicols, and pleuromutilins (LSPPs) represent four structurally different classes of antimicrobial agents that inhibit bacterial protein synthesis by binding to particular sites on the 50S ribosomal subunit of the ribosomes. Members of all four classes are used for different purposes in human and veterinary medicine in various countries worldwide. Bacteria have developed ways and means to escape the inhibitory effects of LSPP antimicrobial agents by enzymatic inactivation, active export, or modification of the target sites of the agents. This review provides a comprehensive overview of the mode of action of LSPP antimicrobial agents as well as of the mutations and resistance genes known to confer resistance to these agents in various bacteria of human and animal origin.
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Affiliation(s)
- Stefan Schwarz
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut (FLI), 31535 Neustadt-Mariensee, Germany
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, P.R. China
| | - Jianzhong Shen
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, P.R. China
| | - Kristina Kadlec
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut (FLI), 31535 Neustadt-Mariensee, Germany
| | - Yang Wang
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, P.R. China
| | - Geovana Brenner Michael
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut (FLI), 31535 Neustadt-Mariensee, Germany
| | - Andrea T Feßler
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut (FLI), 31535 Neustadt-Mariensee, Germany
| | - Birte Vester
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
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28
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Cui Y, Liu X, Dietrich R, Märtlbauer E, Cao J, Ding S, Zhu K. Characterization ofBacillus cereusisolates from local dairy farms in China. FEMS Microbiol Lett 2016; 363:fnw096. [DOI: 10.1093/femsle/fnw096] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2016] [Indexed: 12/11/2022] Open
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Abstract
Members of the ABC-F subfamily of ATP-binding cassette proteins mediate resistance to a broad array of clinically important antibiotic classes that target the ribosome of Gram-positive pathogens. The mechanism by which these proteins act has been a subject of long-standing controversy, with two competing hypotheses each having gained considerable support: antibiotic efflux versus ribosomal protection. Here, we report on studies employing a combination of bacteriological and biochemical techniques to unravel the mechanism of resistance of these proteins, and provide several lines of evidence that together offer clear support to the ribosomal protection hypothesis. Of particular note, we show that addition of purified ABC-F proteins to an in vitro translation assay prompts dose-dependent rescue of translation, and demonstrate that such proteins are capable of displacing antibiotic from the ribosome in vitro. To our knowledge, these experiments constitute the first direct evidence that ABC-F proteins mediate antibiotic resistance through ribosomal protection. Antimicrobial resistance ranks among the greatest threats currently facing human health. Elucidation of the mechanisms by which microorganisms resist the effect of antibiotics is central to understanding the biology of this phenomenon and has the potential to inform the development of new drugs capable of blocking or circumventing resistance. Members of the ABC-F family, which include lsa(A), msr(A), optr(A), and vga(A), collectively yield resistance to a broader range of clinically significant antibiotic classes than any other family of resistance determinants, although their mechanism of action has been controversial since their discovery 25 years ago. Here we present the first direct evidence that proteins of the ABC-F family act to protect the bacterial ribosome from antibiotic-mediated inhibition.
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Discovery of Novel MLSB Resistance Methylase Genes and Their Associated Genetic Elements in Staphylococci. CURRENT CLINICAL MICROBIOLOGY REPORTS 2016. [DOI: 10.1007/s40588-016-0030-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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31
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Characterization of a Novel lsa(E)- and lnu(B)-Carrying Structure Located in the Chromosome of a Staphylococcus aureus Sequence Type 398 Strain. Antimicrob Agents Chemother 2015; 60:1164-6. [PMID: 26596938 DOI: 10.1128/aac.01178-15] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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32
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Si H, Zhang WJ, Chu S, Wang XM, Dai L, Hua X, Dong Z, Schwarz S, Liu S. Novel plasmid-borne multidrug resistance gene cluster including lsa(E) from a linezolid-resistant Enterococcus faecium isolate of swine origin. Antimicrob Agents Chemother 2015; 59:7113-6. [PMID: 26324271 PMCID: PMC4604366 DOI: 10.1128/aac.01394-15] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2015] [Accepted: 08/20/2015] [Indexed: 01/18/2023] Open
Abstract
A novel nonconjugative plasmid of 28,489 bp from a porcine linezolid-resistant Enterococcus faecium isolate was completely sequenced. This plasmid harbored a novel type of multiresistance gene cluster that comprised the resistance genes lnu(B), lsa(E), spw, aadE, aphA3, and two copies of erm(B), which account for resistance to macrolides, lincosamides, streptogramins, pleuromutilins, streptomycin, spectinomycin, and kanamycin/neomycin. Structural comparisons suggested that this plasmid might have developed from other enterococcal plasmids by insertion element (IS)-mediated interplasmid recombination processes.
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Affiliation(s)
- Hongbin Si
- College of Animal Sciences and Technology, Guangxi University, Nanning, China
| | - Wan-Jiang Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Shengbo Chu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Xiu-Mei Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Lei Dai
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Xin Hua
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Zhimin Dong
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Stefan Schwarz
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut (FLI), Neustadt-Mariensee, Germany
| | - Siguo Liu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
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Yang S, Liu L, Li D, Xia H, Su X, Peng L, Pan S. Use of active extracts of poplar buds against Penicillium italicum and possible modes of action. Food Chem 2015; 196:610-8. [PMID: 26593534 DOI: 10.1016/j.foodchem.2015.09.101] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 08/29/2015] [Accepted: 09/28/2015] [Indexed: 01/04/2023]
Abstract
Antifungal components, from poplar buds active fraction (PBAF) against Penicillium italicum, the causal agent of blue mold in citrus fruits, were identified and possible action modes were investigated. Pinocembrin, chrysin and galangin were determined as active components in PBAF, using HPLC and HPLC-MS analysis. The antifungal activity is stable at temperatures ranging from 4 °C to 100 °C and pH levels ranging from 4 to 8. In the presence of PBAF, the hyphae become shriveled, wrinkled and the cell membrane became seriously disrupted. Further investigation on cell permeability, nucleic acid content and alkaline phosphatase suggest that the cell membrane might be the target. Mycelial oxygen consumption and the respiration-related enzymatic activity of succinate dehydrogenase, malate dehydrogenase and ATPase were all inhibited by PBAF. We propose that PBAF is a potentially useful alternative for blue mold control and may act against P. italicum by interfering with respiration and disrupting the cell membrane.
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Affiliation(s)
- Shuzhen Yang
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Limei Liu
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Dongmei Li
- Georgetown University Medical Center, Washington, DC, USA
| | - Huan Xia
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Xiaojun Su
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization, Hunan Collaborative Innovation for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, 410128, China
| | - Litao Peng
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China.
| | - Siyi Pan
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
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Wendlandt S, Kadlec K, Feßler AT, Schwarz S. Identification of ABC transporter genes conferring combined pleuromutilin-lincosamide-streptogramin A resistance in bovine methicillin-resistant Staphylococcus aureus and coagulase-negative staphylococci. Vet Microbiol 2015; 177:353-8. [PMID: 25891423 DOI: 10.1016/j.vetmic.2015.03.027] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 03/25/2015] [Accepted: 03/28/2015] [Indexed: 10/23/2022]
Abstract
The aim of this study was to investigate the genetic basis of combined pleuromutilin-lincosamide-streptogramin A resistance in 26 unrelated methicillin-resistant Staphylococcus aureus (MRSA) and coagulase-negative staphylococci (CoNS) from dairy cows suffering from mastitis. The 26 pleuromutilin-resistant staphylococcal isolates were screened for the presence of the genes vga(A), vga(B), vga(C), vga(E), vga(E) variant, sal(A), vmlR, cfr, lsa(A), lsa(B), lsa(C), and lsa(E) by PCR. None of the 26 isolates carried the genes vga(B), vga(C), vga(E), vga(E) variant, vmlR, cfr, lsa(A), lsa(B), or lsa(C). Two Staphylococcus haemolyticus and single Staphylococcus xylosus, Staphylococcus lentus, and Staphylococcus hominis were vga(A)-positive. Twelve S. aureus, two Staphylococcus warneri, as well as single S. lentus and S. xylosus carried the lsa(E) gene. Moreover, single S. aureus, S. haemolyticus, S. xylosus, and Staphylococcus epidermidis were positive for both genes, vga(A) and lsa(E). The sal(A) gene was found in a single Staphylococcus sciuri. All ABC transporter genes were located in the chromosomal DNA, except for a plasmid-borne vga(A) gene in the S. epidermidis isolate. The genetic environment of the lsa(E)-positive isolates was analyzed using previously described PCR assays. Except for the S. warneri and S. xylosus, all lsa(E)-positive isolates harbored a part of the previously described enterococcal multiresistance gene cluster. This is the first report of the novel lsa(E) gene in the aforementioned bovine CoNS species. This is also the first identification of the sal(A) gene in a S. sciuri from a case of bovine mastitis. Moreover, the sal(A) gene was shown to also confer pleuromutilin resistance.
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Affiliation(s)
- Sarah Wendlandt
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut (FLI), Neustadt-Mariensee, Germany
| | - Kristina Kadlec
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut (FLI), Neustadt-Mariensee, Germany
| | - Andrea T Feßler
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut (FLI), Neustadt-Mariensee, Germany
| | - Stefan Schwarz
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut (FLI), Neustadt-Mariensee, Germany.
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