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Sangal V, Marrs ECL, Nelson A, Perry JD. Phylogenomic analyses of multidrug resistant Corynebacterium striatum strains isolated from patients in a tertiary care hospital in the UK. Eur J Clin Microbiol Infect Dis 2024:10.1007/s10096-024-04857-0. [PMID: 38801486 DOI: 10.1007/s10096-024-04857-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 05/17/2024] [Indexed: 05/29/2024]
Abstract
Corynebacterium striatum is an emerging nosocomial pathogen. This is the first report showing the presence of three distinct multidrug resistant lineages of C. striatum among patients in a UK hospital. The presence of ErmX, Tet(W), Bla and AmpC proteins, and mutations in gyrA gene are associated with the resistance to clindamycin, doxycycline, penicillin and moxifloxacin, respectively. These strains are equipped with several corynebacterial virulence genes including two SpaDEF-type and a novel pilus gene cluster, which needs further molecular characterisation. This study highlights a need of developing an active surveillance strategy for routine monitoring and preventing potential cross-transmission among susceptible patients.
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Affiliation(s)
- Vartul Sangal
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK.
| | - Emma C L Marrs
- Microbiology Research Department, Freeman Hospital, Newcastle upon Tyne, UK
| | - Andrew Nelson
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - John D Perry
- Microbiology Research Department, Freeman Hospital, Newcastle upon Tyne, UK
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Wolf LJ, Stingu CS. Antimicrobial Susceptibility Profile of Rare Anaerobic Bacteria. Antibiotics (Basel) 2022; 12:antibiotics12010063. [PMID: 36671264 PMCID: PMC9854874 DOI: 10.3390/antibiotics12010063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/23/2022] [Accepted: 12/27/2022] [Indexed: 12/31/2022] Open
Abstract
Anaerobes play an important role in clinically relevant infections and resistance is increasing worldwide. We tested 120 rare anaerobic isolates belonging to 16 genera for antimicrobial resistance using the agar dilution method and compared those results to the time-saving E-test method. The susceptibility data for 12 antimicrobial substances (benzylpenicillin, ampicillin/sulbactam, piperacillin/tazobactam, imipenem, meropenem, cefoxitin, metronidazole, moxifloxacin, clindamycin, doxycycline, tigecycline, eravacycline) were collected. Susceptibility testing showed low resistance to β-lactam/β-lactamase inhibitor combinations and no resistance to carbapenems and tigecycline. We observed moderate to high rates of resistance to moxifloxacin and clindamycin which differed depending on the methodology used. The essential and categorical agreement was over 90% for ampicillin/sulbactam, meropenem, moxifloxacin, and tigecycline. For metronidazole and clindamycin, the essential agreement was below 90% but the categorical agreement was near or above 90%. Penicillin presented with the lowest categorical agreement of 86.7% and a very high very major error rate of 13.3%. The resistance rates reported in this study are concerning and show the importance of routine susceptibility testing. Further investigations are necessary to determine the reason for high error rates and how to improve susceptibility testing of fastidious anaerobes.
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Li XY, Yu R, Xu C, Shang Y, Li D, Du XD. A Small Multihost Plasmid Carrying erm(T) Identified in Enterococcus faecalis. Front Vet Sci 2022; 9:850466. [PMID: 35711812 PMCID: PMC9197182 DOI: 10.3389/fvets.2022.850466] [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: 01/07/2022] [Accepted: 04/20/2022] [Indexed: 11/13/2022] Open
Abstract
The aim of this study was to determine the mobile genetic elements involved in the horizontal transfer of erm(T) in Enterococcus faecalis, and its transmission ability in heterologous hosts. A total of 159 erythromycin-resistant enterococci isolates were screened for the presence of macrolide resistance genes by PCR. Whole genome sequencing for erm(T)-carrying E. faecalis E165 was performed. The transmission ability in heterologous hosts was explored by conjugation, transformation, and fitness cost. The erm(T) gene was detected only in an E. faecalis isolate E165 (1/159), which was located on a 4,244-bp small plasmid, designed pE165. Using E. faecalis OG1RF as the recipient strain, pE165 is transferable. Natural transformation experiments using Streptococcus suis P1/7 and Streptococcus mutans UA159 as the recipients indicated it is transmissible, which was also observed by electrotransformation using Staphylococcus aureus RN4220 as a recipient. The erm(T)-carrying pE165 can replicate in the heterologous host including E. faecalis OG1RF, S. suis P1/7, S. mutans UA159, and S. aureus RN4220 and conferred resistance to erythromycin and clindamycin to all hosts. Although there is no disadvantage of pE165 in the recipient strains in growth curve experiments, all the pE165-carrying recipients had a fitness cost compared to the corresponding original recipients in growth competition experiments. In brief, an erm(T)-carrying plasmid was for the first time described in E. faecalis and as transmissible to heterologous hosts.
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Li B, Chen D, Lin F, Wu C, Cao L, Chen H, Hu Y, Yin Y. Genomic Island-Mediated Horizontal Transfer of the Erythromycin Resistance Gene erm(X) among Bifidobacteria. Appl Environ Microbiol 2022; 88:e0041022. [PMID: 35477272 PMCID: PMC9128502 DOI: 10.1128/aem.00410-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 04/02/2022] [Indexed: 01/20/2023] Open
Abstract
Antibiotic resistance is a serious medical issue driven by antibiotic misuse. Bifidobacteria may serve as a reservoir for antibiotic resistance genes (ARGs) that have the potential risk of transfer to pathogens. The erythromycin resistance gene erm(X) is an ARG with high abundance in bifidobacteria, especially in Bifidobacterium longum species. However, the characteristics of the spread and integration of the gene erm(X) into the bifidobacteria genome are poorly understood. In this study, 10 tetW-positive bifidobacterial strains and 1 erm(X)-positive bifidobacterial strain were used to investigate the transfer of ARGs. Conjugation assays found that the erm(X) gene could transfer to five other bifidobacterial strains. Dimethyl sulfoxide (DMSO) and vorinostat significantly promoted the transfer of the erm(X) from strain Bifidobacterium catenulatum subsp. kashiwanohense DSM 21854 to Bifidobacterium longum subsp. suis DSM 20211. Whole-genome sequencing and comparative genomic analysis revealed that the erm(X) gene was located on the genomic island BKGI1 and that BKGI1 was conjugally mobile and transferable. To our knowledge, this is the first report that a genomic island-mediated gene erm(X) transfer in bifidobacteria. Additionally, BKGI1 is very unstable in B. catenulatum subsp. kashiwanohense DSM 21854 and transconjugant D2TC and is highly excisable and has an intermediate circular formation. In silico analysis showed that the BKGI1 homologs were also present in other bifidobacterial strains and were especially abundant in B. longum strains. Thus, our results confirmed that genomic island BKGI1 was one of the vehicles for erm(X) spread. These findings suggest that genomic islands play an important role in the dissemination of the gene erm(X) among Bifidobacterium species. IMPORTANCE Bifidobacteria are a very important group of gut microbiota, and the presence of these bacteria has many beneficial effects for the host. Thus, bifidobacteria have attracted growing interest owing to their potential probiotic properties. Bifidobacteria have been widely exploited by the food industry as probiotic microorganisms, and some species have a long history of safe use in food and feed production. However, the presence of antibiotic resistance raises the risk of its application. In this study, we analyzed the transfer of the erythromycin resistance gene erm(X) and revealed that the molecular mechanism behind the spread of the gene erm(X) was mediated by genomic island BKGI1. To the best of our knowledge this is the first report to describe the transfer of the gene erm(X) via genomic islands among bifidobacteria. This may be an important way to disseminate the gene erm(X) among bifidobacteria.
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Affiliation(s)
- Baiyuan Li
- Key Laboratory of Comprehensive Utilization of Advantage Plant Resources in Hunan South, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou, Hunan, China
| | - Dan Chen
- Key Laboratory of Comprehensive Utilization of Advantage Plant Resources in Hunan South, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou, Hunan, China
| | - Fan Lin
- Key Laboratory of Comprehensive Utilization of Advantage Plant Resources in Hunan South, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou, Hunan, China
| | - Chuanyu Wu
- Key Laboratory of Comprehensive Utilization of Advantage Plant Resources in Hunan South, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou, Hunan, China
| | - Linyan Cao
- Key Laboratory of Comprehensive Utilization of Advantage Plant Resources in Hunan South, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou, Hunan, China
| | - Huahai Chen
- Key Laboratory of Comprehensive Utilization of Advantage Plant Resources in Hunan South, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou, Hunan, China
| | - Yunfei Hu
- Key Laboratory of Comprehensive Utilization of Advantage Plant Resources in Hunan South, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou, Hunan, China
| | - Yeshi Yin
- Key Laboratory of Comprehensive Utilization of Advantage Plant Resources in Hunan South, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou, Hunan, China
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Guérin F, Dejoies L, Degand N, Guet-Revillet H, Janvier F, Corvec S, Barraud O, Guillard T, Walewski V, Gallois E, Cattoir V. In Vitro Antimicrobial Susceptibility Profiles of Gram-Positive Anaerobic Cocci Responsible for Human Invasive Infections. Microorganisms 2021; 9:microorganisms9081665. [PMID: 34442745 PMCID: PMC8398781 DOI: 10.3390/microorganisms9081665] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 07/29/2021] [Accepted: 07/30/2021] [Indexed: 12/14/2022] Open
Abstract
The aim of this multicentre study was to determine the in vitro susceptibility to anti-anaerobic antibiotics of Gram-positive anaerobic cocci (GPAC) isolates responsible for invasive infections in humans. A total of 133 GPAC isolates were collected in nine French hospitals from 2016 to 2020. All strains were identified to the species level (MALDI-TOF mass spectrometry, 16S rRNA sequencing). Minimum inhibitory concentrations (MICs) of amoxicillin, piperacillin, cefotaxime, imipenem, clindamycin, vancomycin, linezolid, moxifloxacin, rifampicin, and metronidazole were determined by the reference agar dilution method. Main erm-like genes were detected by PCR. The 133 GPAC isolates were identified as follows: 10 Anaerococcus spp., 49 Finegoldia magna, 33 Parvimonas micra, 30 Peptoniphilus spp., and 11 Peptostreptococcus anaerobius. All isolates were susceptible to imipenem, vancomycin (except 3 P. micra), linezolid and metronidazole. All isolates were susceptible to amoxicillin and piperacillin, except for P. anaerobius (54% and 45% susceptibility only, respectively). MICs of cefotaxime widely varied while activity of rifampicin, and moxifloxacin was also variable. Concerning clindamycin, 31 were categorized as resistant (22 erm(A) subclass erm(TR), 7 erm(B), 1 both genes and 1 negative for tested erm genes) with MICs from 8 to >32 mg/L. Although GPACs are usually susceptible to drugs commonly used for the treatment of anaerobic infections, antimicrobial susceptibility should be evaluated in vitro.
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Affiliation(s)
- François Guérin
- Service de Bactériologie-Hygiène Hospitalière, CHU de Rennes, F-35033 Rennes, France; (F.G.); (L.D.)
| | - Loren Dejoies
- Service de Bactériologie-Hygiène Hospitalière, CHU de Rennes, F-35033 Rennes, France; (F.G.); (L.D.)
| | - Nicolas Degand
- Laboratoire de Bactériologie, CHU de Nice, F-06202 Nice, France;
| | | | - Frédéric Janvier
- Service de Microbiologie et Hygiène Hospitalière, Hôpital d’Instruction des Armées Saint-Anne, F-83800 Toulon, France;
| | - Stéphane Corvec
- Service de Bactériologie et des Contrôles Microbiologiques, CHU de Nantes, F-44093 Nantes, France;
| | - Olivier Barraud
- Laboratoire de Bactériologie-Virologie-Hygiène, CHU Dupuytren, F-87042 Limoges, France;
| | - Thomas Guillard
- Laboratoire de Bactériologie-Virologie-Hygiène Hospitalière, Hôpital Robert Debré-CHU de Reims, F-51090 Reims, France;
| | - Violaine Walewski
- Service de Microbiologie, Hôpitaux Universitaires de Paris Seine Denis (HUPSSD), Site Avicenne, AP-HP, F-93000 Bobigny, France;
| | | | - Vincent Cattoir
- Service de Bactériologie-Hygiène Hospitalière, CHU de Rennes, F-35033 Rennes, France; (F.G.); (L.D.)
- Correspondence: ; Tel.: +33-2-99-28-42-76; Fax: +33-2-99-28-41-59
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Reissier S, Cattoir V. Streptogramins for the treatment of infections caused by Gram-positive pathogens. Expert Rev Anti Infect Ther 2020; 19:587-599. [PMID: 33030387 DOI: 10.1080/14787210.2021.1834851] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
INTRODUCTION Streptogramins (pristinamycin and quinupristin-dalfopristin) can be interesting options for the treatment of infections due to Gram-positive cocci, especially multidrug-resistant isolates. AREAS COVERED This review provides an updated overview of structural and activity characteristics, mechanisms of action and resistance, pharmacokinetic/pharmacodynamic, and clinical use of streptogramins. EXPERT OPINION The streptogramin antibiotics act by inhibition of the bacterial protein synthesis. They are composed of two chemically distinct compounds, namely type A and type B streptogramins, which exert a rapid bactericidal activity against a wide range of Gram-positive bacteria (including methicillin-resistant staphylococci and vancomycin-resistant enterococci). Several mechanisms of resistance have been identified in staphylococci and enterococci but the prevalence of streptogramin resistance among clinical isolates remains very low. Even if only a few randomized clinical trials have been conducted, the efficacy of pristinamycin has been largely demonstrated with an extensive use for 50 years in France and some African countries. Despite its effectiveness in the treatment of severe Gram-positive bacterial infections demonstrated in several studies and the low rate of reported resistance, the clinical use of quinupristin-dalfopristin has remained limited, mainly due to its poor tolerance. Altogether, streptogramins (especially pristinamycin) can be considered as potential alternatives for the treatment of Gram-positive infections.
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Affiliation(s)
| | - Vincent Cattoir
- Université De Rennes 1, Unité Inserm U1230, Rennes, France.,Service De Bactériologie-Hygiène Hospitalière, CHU De Rennes, Rennes, France.,Centre National De Référence De La Résistance Aux Antibiotiques (Laboratoire Associé 'Entérocoques'), CHU De Rennes, Rennes, France
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Guérin F, Lachaal S, Auzou M, Le Brun C, Barraud O, Decousser JW, Lienhard R, Baraduc R, Dubreuil L, Cattoir V. Molecular basis of macrolide-lincosamide-streptogramin (MLS) resistance in Finegoldia magna clinical isolates. Anaerobe 2020; 64:102220. [PMID: 32531434 DOI: 10.1016/j.anaerobe.2020.102220] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 05/25/2020] [Accepted: 06/01/2020] [Indexed: 12/21/2022]
Affiliation(s)
- François Guérin
- CHU de Caen, Service de Microbiologie, Caen, F-14033, France; Université de Caen Normandie, EA4655 (équipe "Antibio-résistance"), Caen, F-14032, France
| | - Sabrine Lachaal
- CHU de Caen, Service de Microbiologie, Caen, F-14033, France
| | - Michel Auzou
- CHU de Caen, Service de Microbiologie, Caen, F-14033, France; Université de Caen Normandie, EA4655 (équipe "Antibio-résistance"), Caen, F-14032, France
| | - Cécile Le Brun
- CHRU de Tours, Service de Bactériologie-Virologie, Hôpital Bretonneau, F-37044, Tours, France
| | - Olivier Barraud
- CHU Limoges, Laboratoire de Bactériologie-Virologie-Hygiène, Limoges, F-87042, France
| | - Jean-Winoc Decousser
- CHU Henri Mondor, Assistance Publique-Hôpitaux de Paris, Laboratoire de Microbiologie, Créteil, F-94010, France
| | - Reto Lienhard
- ADMED Microbiologie, La-Chaux-de-Fonds, CH-2303, Switzerland
| | - Régine Baraduc
- CHU de Clermont-Ferrand, Laboratoire de Microbiologie, Clermont-Ferrand, F-63003, France
| | - Luc Dubreuil
- CHRU de Lille, Laboratoire de Bactériologie-Hygiène et de Virologie, Lille, F-59 037, France
| | - Vincent Cattoir
- CHU Rennes, Service de Bactériologie et Hygiène Hospitalière, Rennes, F-35033, France; CNR de la Résistance aux Antibiotiques, Rennes, F-35033, France.
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Antimicrobial Susceptibility and Clonality of Vaginally Derived Multidrug-Resistant Mobiluncus Isolates in China. Antimicrob Agents Chemother 2020; 64:AAC.00780-20. [PMID: 32513795 DOI: 10.1128/aac.00780-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 06/02/2020] [Indexed: 12/16/2022] Open
Abstract
Here, the antimicrobial susceptibility, resistance mechanisms, and clonality of Mobiluncus sp. isolates recovered from gynecological outpatients in China were investigated. Compared to M. mulieris, M. curtisii exhibited higher antimicrobial resistance to metronidazole, clindamycin, and tetracycline. Whole-genome sequencing indicated that the clindamycin resistance gene erm(X) was located on a transposable element, Tn5432, which was composed of two IS1249 sequences. Phylogenetic analysis indicated that Mobiluncus spp. had high diversity, with isolates being grouped into several sporadic clades.
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Antibiotic resistance genes in the Actinobacteria phylum. Eur J Clin Microbiol Infect Dis 2019; 38:1599-1624. [PMID: 31250336 DOI: 10.1007/s10096-019-03580-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 05/01/2019] [Indexed: 02/07/2023]
Abstract
The Actinobacteria phylum is one of the oldest bacterial phyla that have a significant role in medicine and biotechnology. There are a lot of genera in this phylum that are causing various types of infections in humans, animals, and plants. As well as antimicrobial agents that are used in medicine for infections treatment or prevention of infections, they have been discovered of various genera in this phylum. To date, resistance to antibiotics is rising in different regions of the world and this is a global health threat. The main purpose of this review is the molecular evolution of antibiotic resistance in the Actinobacteria phylum.
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Amigo CR, Moreno LZ, Ferreira TSP, Gomes VTDM, Poor AP, de Oliveira CH, Parra BM, Silva APS, Moreno AM. Phenotypic, molecular and genomic characterization of Actinobaculum suis isolated from swine in Brazil. Anaerobe 2019; 56:27-33. [PMID: 30630038 DOI: 10.1016/j.anaerobe.2019.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 12/19/2018] [Accepted: 01/05/2019] [Indexed: 10/27/2022]
Abstract
Urinary tract infections (UTI) are considered one of the most important diseases of sows due to its close relationship with reproductive problems such as reduced litter size, increase in the rate of return to estrous, vulvar discharge, abortion, mastitis and anestrus. Actinobaculum suis is one of the main agents involved in porcine urinary tract infection and is responsible for the most severe and fatal cases in sows. In the present report, 23 A. suis strains isolated from a sow and boars in Brazil were identified by PCR and further characterized by broth microdilution, molecular typing by pulsed-field gel electrophoresis (PFGE), single-enzyme amplified fragment length polymorphism (SE-AFLP), and whole-genome sequencing. All strains were sensitive to ceftiofur, linezolid, nitrofurantoin, quinupristin-dalfopristin and vancomycin. Ciprofloxacin, daptomycin, lincomycin, erythromycin and tylosin resistance was observed in 100% of tested strains. Tetracycline and tigecycline also presented high resistance rates (87% and 30.4%, respectively). PFGE with eight different restriction enzymes and three programs did not enable strain characterization; however, all strains were typed by SE-AFLP that clustered strains according to their origin, thus proving an effective tool for A. suis genotyping. Whole-genome sequencing and comparative analysis enabled species differentiation from closely related genus. This is the first report of genomic characterization of A. suis.
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Affiliation(s)
- Cristina Román Amigo
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
| | - Luisa Zanolli Moreno
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil; Centro Universitário Max Planck (UniMax), Indaiatuba, SP, Brazil
| | - Thais Sebastiana Porfida Ferreira
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
| | - Vasco Túlio de Moura Gomes
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
| | - André Pegoraro Poor
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
| | - Carolina Helena de Oliveira
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
| | - Beatriz Martins Parra
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
| | - Ana Paula Santos Silva
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
| | - Andrea Micke Moreno
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil.
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Aoki S, Nakase K, Hayashi N, Noguchi N. Transconjugation of erm(X) conferring high-level resistance of clindamycin for Cutibacterium acnes. J Med Microbiol 2018; 68:26-30. [PMID: 30431414 DOI: 10.1099/jmm.0.000875] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cutibacterium acnes (C. acnes) can become an exacerbating factor in acne vulgaris. Clindamycin has been most frequently used for the treatment of inflammatory acne vulgaris. We studied clindamycin susceptibility and resistance determinants of C. acnes isolated from acne patients in Japan. The isolation rate of clindamycin-resistant C. acnes had significantly increased from 20.3 % in 2009-2010 to 44.1 % in 2016-2017. Strains carrying erm(X), which confers high-level resistance to clindamycin, had significantly increased from 1.4 to 11.8 %. Sequence analysis of the resistance determinant showed that erm(X) was coded on transposon Tn5432. A transconjugation experiment showed that erm(X) can be transferred between C. acnes strains with high frequency and the transconjugants harboured transposon Tn5432 encoding erm(X). Our data show the transconjugation of erm(X) in C. acnes and strongly suggest that the transmission of erm(X) between C. acnes contributes to the increase and spread of clindamycin-resistant C. acnes strains in acne patients.
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Affiliation(s)
- Sae Aoki
- 1Department of Microbiology, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Keisuke Nakase
- 1Department of Microbiology, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Nobukazu Hayashi
- 2Department of Dermatology, Toranomon Hospital, 2-2-2 Toranomon, minato-ku, Tokyo 105-8470, Japan
| | - Norihisa Noguchi
- 1Department of Microbiology, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
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Leo S, Gaïa N, Ruppé E, Emonet S, Girard M, Lazarevic V, Schrenzel J. Detection of Bacterial Pathogens from Broncho-Alveolar Lavage by Next-Generation Sequencing. Int J Mol Sci 2017; 18:ijms18092011. [PMID: 28930150 PMCID: PMC5618659 DOI: 10.3390/ijms18092011] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 09/10/2017] [Accepted: 09/13/2017] [Indexed: 11/16/2022] Open
Abstract
The applications of whole-metagenome shotgun sequencing (WMGS) in routine clinical analysis are still limited. A combination of a DNA extraction procedure, sequencing, and bioinformatics tools is essential for the removal of human DNA and for improving bacterial species identification in a timely manner. We tackled these issues with a broncho-alveolar lavage (BAL) sample from an immunocompromised patient who had developed severe chronic pneumonia. We extracted DNA from the BAL sample with protocols based either on sequential lysis of human and bacterial cells or on the mechanical disruption of all cells. Metagenomic libraries were sequenced on Illumina HiSeq platforms. Microbial community composition was determined by k-mer analysis or by mapping to taxonomic markers. Results were compared to those obtained by conventional clinical culture and molecular methods. Compared to mechanical cell disruption, a sequential lysis protocol resulted in a significantly increased proportion of bacterial DNA over human DNA and higher sequence coverage of Mycobacterium abscessus, Corynebacterium jeikeium and Rothia dentocariosa, the bacteria reported by clinical microbiology tests. In addition, we identified anaerobic bacteria not searched for by the clinical laboratory. Our results further support the implementation of WMGS in clinical routine diagnosis for bacterial identification.
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Affiliation(s)
- Stefano Leo
- Genomic Research Laboratory, Service of Infectious Diseases, Geneva University Hospitals (HUG), 1205 Geneva, Switzerland.
| | - Nadia Gaïa
- Genomic Research Laboratory, Service of Infectious Diseases, Geneva University Hospitals (HUG), 1205 Geneva, Switzerland.
| | - Etienne Ruppé
- Genomic Research Laboratory, Service of Infectious Diseases, Geneva University Hospitals (HUG), 1205 Geneva, Switzerland.
| | - Stephane Emonet
- Service of Infectious Diseases, Geneva University Hospitals and Faculty of Medicine, 1205 Geneva, Switzerland.
- Bacteriology Laboratory, Geneva University Hospitals and Faculty of Medicine, 1205 Geneva, Switzerland.
| | - Myriam Girard
- Genomic Research Laboratory, Service of Infectious Diseases, Geneva University Hospitals (HUG), 1205 Geneva, Switzerland.
| | - Vladimir Lazarevic
- Genomic Research Laboratory, Service of Infectious Diseases, Geneva University Hospitals (HUG), 1205 Geneva, Switzerland.
| | - Jacques Schrenzel
- Genomic Research Laboratory, Service of Infectious Diseases, Geneva University Hospitals (HUG), 1205 Geneva, Switzerland.
- Service of Infectious Diseases, Geneva University Hospitals and Faculty of Medicine, 1205 Geneva, Switzerland.
- Bacteriology Laboratory, Geneva University Hospitals and Faculty of Medicine, 1205 Geneva, Switzerland.
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Antimicrobial susceptibility of clinical isolates of Actinomyces and related genera reveals an unusual clindamycin resistance among Actinomyces urogenitalis strains. J Glob Antimicrob Resist 2017; 8:115-120. [DOI: 10.1016/j.jgar.2016.11.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 09/29/2016] [Accepted: 11/16/2016] [Indexed: 11/23/2022] Open
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14
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Actinotignum (formerly Actinobaculum) schaalii: a review of MALDI-TOF for identification of clinical isolates, and a proposed method for presumptive phenotypic identification. Pathology 2016; 48:367-71. [PMID: 27131934 DOI: 10.1016/j.pathol.2016.03.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 03/12/2016] [Accepted: 03/21/2016] [Indexed: 12/21/2022]
Abstract
Actinotignum schaalii is a recognised cause of urinary tract infection. Following a case of urosepsis, 20 isolates of A. schaalii were collected over an initial 18 month period from urine and blood culture. An additional 25 isolates were collected over the following 13 months. Actinotignum schaalii had likely been overlooked or dismissed as a contaminant in our laboratory prior to this study period. It grows slowly on blood agar with supplemental CO2 or anaerobically. It may not grow on MacConkey agar or chromogenic agars used for routine urine culture. Repeated attempts at identification by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) may be required as the optimal age of cultures for testing is unclear. Utilising its characteristic antibiogram may assist phenotypic identification of this organism which is otherwise difficult to distinguish from other actinomycetes.
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15
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Isnard C, Lienhard R, Reissier S, Rodriguez S, Krähenbühl J, Liassine N, Guérin F, Cattoir V. In vitro antimicrobial susceptibility of Alloscardovia omnicolens and molecular mechanisms of acquired resistance. Diagn Microbiol Infect Dis 2016; 84:227-9. [PMID: 26763712 DOI: 10.1016/j.diagmicrobio.2015.08.009] [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: 06/23/2015] [Revised: 08/09/2015] [Accepted: 08/14/2015] [Indexed: 10/23/2022]
Abstract
All the 31 isolates of Alloscardovia omnicolens exhibited low MICs for β-lactams, glycopeptides, linezolid, tetracyclines, and cotrimoxazole. One strain showed MICs ≥256μg/mL for both erythromycin and clindamycin with a single point mutation in 23S rRNA. One strain likely had acquired fluoroquinolone resistance associated with a unique mutation in ParC.
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Affiliation(s)
- Christophe Isnard
- CHU de Caen, Service de Microbiologie, F-14033 Caen, France; Université de Caen Basse-Normandie, EA4655 (équipe "Antibiorésistance"), F-14032 Caen, France
| | - Reto Lienhard
- Laboratoire ADMED, CH-2300 La-Chaux-de-Fonds, Switzerland
| | | | | | - Joanna Krähenbühl
- CH de Bienne, Service de Médecine Interne, CH-2502 Bienne, Switzerland
| | | | - François Guérin
- CHU de Caen, Service de Microbiologie, F-14033 Caen, France; Université de Caen Basse-Normandie, EA4655 (équipe "Antibiorésistance"), F-14032 Caen, France; CNR de la Résistance aux Antibiotiques, Laboratoire Associé "Entérocoques et résistances particulières des bactéries à Gram positif", F-14033 Caen, France
| | - Vincent Cattoir
- CHU de Caen, Service de Microbiologie, F-14033 Caen, France; Université de Caen Basse-Normandie, EA4655 (équipe "Antibiorésistance"), F-14032 Caen, France; CNR de la Résistance aux Antibiotiques, Laboratoire Associé "Entérocoques et résistances particulières des bactéries à Gram positif", F-14033 Caen, France.
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16
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Lotte R, Lotte L, Ruimy R. Actinotignum schaalii (formerly Actinobaculum schaalii): a newly recognized pathogen-review of the literature. Clin Microbiol Infect 2015; 22:28-36. [PMID: 26577137 DOI: 10.1016/j.cmi.2015.10.038] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Revised: 10/14/2015] [Accepted: 10/29/2015] [Indexed: 11/19/2022]
Abstract
The genus Actinotignum contains three species, Actinotignum schaalii (formerly Actinobaculum schaalii), Actinotignum urinale and Actinotignum sanguinis. A. schaalii is the species most frequently involved in human infections, with 172 cases, mostly urinary tract infections (UTIs), reported so far. Invasive infections have also been described. This facultative anaerobic Gram-positive rod is part of the urinary microbiota of healthy patients. It is responsible for UTIs, particularly in elderly men and young children. A. schaalii is an underestimated cause of UTIs because of its fastidious growth on usual media and difficulties associated with its identification using phenotypic methods. Indeed, this slow-growth bacterium requires blood-enriched media and an incubation time of 48 hours under anaerobic or 5% CO2 atmosphere. Furthermore, only matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF) or molecular-based methods allow the accurate identification of this bacteria. MALDI-TOF using Microflex LT with the Biotyper database (Bruker Daltonics, Bremen, Germany) is the most reliable technology for the routine identification of A. schaalii. The identification of this uropathogen is all the more important because it is resistant to trimethoprim/sulfamethoxazole and second-generation quinolones that are widely used in the treatment of UTIs. Antimicrobial therapy using β-lactams prolonged for up to 2 weeks is the most efficient treatment and should be recommended. Microbiologists should assess the presence of A. schaalii in urine using appropriate culture and identification methods in the case of a direct examination that is positive for small coccoid rods, a negative nitrite urinary stick associated with leukocyturia, treatment failure with trimethoprim/sulfamethoxazole or fluoroquinolones, or undocumented, repeated UTIs.
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Affiliation(s)
- R Lotte
- Department of Bacteriology at Nice Academic Hospital, Nice, France; Nice Medical University, Nice-Sophia Antipolis University, Nice, France; INSERM U1065 (C3M), Bacterial Toxins in Host Pathogen Interactions, C3M, Bâtiment Universitaire Archimed, Nice, France.
| | - L Lotte
- Department of Bacteriology at Nice Academic Hospital, Nice, France; Nice Medical University, Nice-Sophia Antipolis University, Nice, France
| | - R Ruimy
- Department of Bacteriology at Nice Academic Hospital, Nice, France; Nice Medical University, Nice-Sophia Antipolis University, Nice, France; INSERM U1065 (C3M), Bacterial Toxins in Host Pathogen Interactions, C3M, Bâtiment Universitaire Archimed, Nice, France
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17
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Lotte L, Lotte R, Durand M, Degand N, Ambrosetti D, Michiels JF, Amiel J, Cattoir V, Ruimy R. Infections related to Actinotignum schaalii (formerly Actinobaculum schaalii): a 3-year prospective observational study on 50 cases. Clin Microbiol Infect 2015; 22:388-390. [PMID: 26551841 DOI: 10.1016/j.cmi.2015.10.030] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 10/29/2015] [Indexed: 11/17/2022]
Affiliation(s)
- L Lotte
- Department of Bacteriology at Nice Academic Hospital, Nice, France
| | - R Lotte
- Department of Bacteriology at Nice Academic Hospital, Nice, France; Nice Medical University, Nice-Sophia Antipolis University, Nice, France; INSERM 1065(C3M), Team6, Bâtiment universitaire Archimed, Nice, France.
| | - M Durand
- Nice Medical University, Nice-Sophia Antipolis University, Nice, France; Department of Urology at Nice Academic Hospital, Nice, France
| | - N Degand
- Department of Bacteriology at Nice Academic Hospital, Nice, France
| | - D Ambrosetti
- Nice Medical University, Nice-Sophia Antipolis University, Nice, France; Department of Pathology at Nice Academic Hospital, Nice, France
| | - J-F Michiels
- Nice Medical University, Nice-Sophia Antipolis University, Nice, France; Department of Pathology at Nice Academic Hospital, Nice, France
| | - J Amiel
- Nice Medical University, Nice-Sophia Antipolis University, Nice, France; Department of Urology at Nice Academic Hospital, Nice, France
| | - V Cattoir
- Department of Bacteriology at Caen Academic Hospital, Caen, France; National Reference Centre for Antimicrobial Resistance (lab 'Enterococci'), Caen, France; University of Caen Basse-Normandie, EA 4655 U2RM (team 'Antibioresistance'), Caen, France
| | - R Ruimy
- Department of Bacteriology at Nice Academic Hospital, Nice, France; Nice Medical University, Nice-Sophia Antipolis University, Nice, France; INSERM 1065(C3M), Team6, Bâtiment universitaire Archimed, Nice, France
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18
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Vergne A, Guérin F, Lienhard R, Le Coustumier A, Daurel C, Isnard C, Marty N, Poyart C, Cattoir V. In vitro antimicrobial susceptibility of Helcococcus kunzii and molecular analysis of macrolide and tetracycline resistance. Eur J Clin Microbiol Infect Dis 2015; 34:2057-61. [PMID: 26194694 DOI: 10.1007/s10096-015-2451-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 07/03/2015] [Indexed: 11/25/2022]
Abstract
Thanks to the recent advent of matrix-assisted laser desorption/ionisation time-of-flight (MALDI-TOF) technology, Helcococcus kunzii is now easily identifiable and considered as an opportunistic pathogen. However, data about antimicrobial susceptibilities remain very limited. The aim of the study was, then, to assess its in vitro susceptibility to 18 antimicrobial agents and to investigate the genetic basis of macrolide and tetracycline resistance. Thirty-nine human clinical isolates of H. kunzii collected from 2008 to 2013 were studied, as well as the type strain ATCC 51366(T). Minimum inhibitory concentrations (MICs) of penicillin G, amoxicillin, cefotaxime, imipenem, gentamicin, erythromycin, clindamycin, quinupristin-dalfopristin, ciprofloxacin, levofloxacin, tetracycline, tigecycline, vancomycin, teicoplanin, linezolid, daptomycin, cotrimoxazole and rifampin were determined by the microdilution method. Screening for macrolide [erm(A) including erm(TR), erm(B), erm(C), erm(F), erm(T), erm(X), msr(A) and mef(A)] and tetracycline [tet(L), tet(M) and tet(O)] resistance genes was performed, as well as the detection of mutations in 23S rRNA. Except for one strain resistant to cefotaxime, all strains were categorised as susceptible to β-lactams, glycopeptides, linezolid, daptomycin and tigecycline. Whereas ciprofloxacin and gentamicin exhibited limited activity, 95% of strains were categorised as susceptible to levofloxacin. Concerning erythromycin, a bimodal distribution was observed, with 29 'wild-type' strains (MICs from 0.25 to 2 mg/L) and 11 'resistant' strains (MICs ≥ 256 mg/L), including ten harbouring erm(TR). Two isolates exhibited acquired tetracycline resistance (MICs of 16 mg/L) by the production of tet(M). This large study on the in vitro antimicrobial susceptibility of H. kunzii suggests that β-lactams (especially penicillins) should be preferred for the treatment.
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Affiliation(s)
- A Vergne
- Laboratoire de Biologie, CH de Cahors, Cahors, France
| | - F Guérin
- Service de Microbiologie & CNR de la Résistance aux Antibiotiques, CHU de Caen, Caen, France.,Université de Caen Basse-Normandie, EA4655 (équipe "Antibio-résistance"), Caen, France
| | - R Lienhard
- ADMED Microbiologie, La Chaux-de-Fonds, Switzerland
| | | | - C Daurel
- Service de Microbiologie & CNR de la Résistance aux Antibiotiques, CHU de Caen, Caen, France
| | - C Isnard
- Service de Microbiologie & CNR de la Résistance aux Antibiotiques, CHU de Caen, Caen, France.,Université de Caen Basse-Normandie, EA4655 (équipe "Antibio-résistance"), Caen, France
| | - N Marty
- Service de Bactériologie-Hygiène, CHU de Toulouse, Toulouse, France
| | - C Poyart
- Service de Bactériologie & CNR des Streptocoques, GH Cochin-Hôtel Dieu-Broca, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - V Cattoir
- Service de Microbiologie & CNR de la Résistance aux Antibiotiques, CHU de Caen, Caen, France. .,Université de Caen Basse-Normandie, EA4655 (équipe "Antibio-résistance"), Caen, France.
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First report of macrolide resistance gene erm(T) harbored by a novel small plasmid from Erysipelothrix rhusiopathiae. Antimicrob Agents Chemother 2015; 59:2462-5. [PMID: 25666150 DOI: 10.1128/aac.00228-15] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The macrolide resistance gene erm(T) was identified for the first time in a porcine Erysipelothrix rhusiopathiae isolate from swine in China. The novel 3,749-bp small plasmid pER29, which carries erm(T), had a G+C content of 31% and four distinct open reading frames. The presence of pER29 increased by at least 128-fold the MICs of clindamycin and erythromycin for E. rhusiopathiae. The fitness cost of pER29 could be responsible for the low frequency of erm(T) in E. rhusiopathiae.
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Complete Genome Sequence of Corynebacterium ureicelerivorans DSM 45051, a Lipophilic and Urea-Splitting Isolate from the Blood Culture of a Septicemia Patient. GENOME ANNOUNCEMENTS 2014; 2:2/6/e01211-14. [PMID: 25414509 PMCID: PMC4239364 DOI: 10.1128/genomea.01211-14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
ABSTRACT
Corynebacterium ureicelerivorans
is an opportunistic pathogen with a lipophilic lifestyle and an exceptionally high urease activity. The genome sequence of the type strain revealed that lipophilism is caused by the lack of a fatty acid synthase gene. The
ureABCEFGD
genes are similar to the urease gene region of
Corynebacterium glucuronolyticum
.
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Skin and soft-tissue infections caused by Actinobaculum schaalii: report of two cases and literature review. Anaerobe 2014; 28:95-7. [PMID: 24923266 DOI: 10.1016/j.anaerobe.2014.05.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 05/20/2014] [Accepted: 05/21/2014] [Indexed: 11/24/2022]
Abstract
Skin and soft-tissue infections (SSTIs) caused by Actinobaculum spp. are very rare. In the present study, we report two cases and review the literature. The first case was an immunocompromised patient with an extensive cellulitis secondary to an inguinal abscess, and the second case was a patient with a pilonidal abscess. Clinical outcomes of both patients were good after surgical drainage and treatment with cloxacillin. The review of the literature showed that SSTIs caused by Actinobaculum spp. are usually located on the perineal and inguinal regions and can be severe, particularly in immunocompromised patients. SSTIs caused by Actinobaculum spp. can be overlooked because identification is often difficult and they can be considered as contaminants.
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