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Park HE, Kim KM, Trinh MP, Yoo JW, Shin SJ, Shin MK. Bigger problems from smaller colonies: emergence of antibiotic-tolerant small colony variants of Mycobacterium avium complex in MAC-pulmonary disease patients. Ann Clin Microbiol Antimicrob 2024; 23:25. [PMID: 38500139 PMCID: PMC10949641 DOI: 10.1186/s12941-024-00683-6] [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: 10/18/2023] [Accepted: 03/03/2024] [Indexed: 03/20/2024] Open
Abstract
BACKGROUND Mycobacterium avium complex (MAC) is a group of slow-growing mycobacteria that includes Mycobacterium avium and Mycobacterium intracellulare. MAC pulmonary disease (MAC-PD) poses a threat to immunocompromised individuals and those with structural pulmonary diseases worldwide. The standard treatment regimen for MAC-PD includes a macrolide in combination with rifampicin and ethambutol. However, the treatment failure and disease recurrence rates after successful treatment remain high. RESULTS In the present study, we investigated the unique characteristics of small colony variants (SCVs) isolated from patients with MAC-PD. Furthermore, revertant (RVT) phenotype, emerged from the SCVs after prolonged incubation on 7H10 agar. We observed that SCVs exhibited slower growth rates than wild-type (WT) strains but had higher minimum inhibitory concentrations (MICs) against multiple antibiotics. However, some antibiotics showed low MICs for the WT, SCVs, and RVT phenotypes. Additionally, the genotypes were identical among SCVs, WT, and RVT. Based on the MIC data, we conducted time-kill kinetic experiments using various antibiotic combinations. The response to antibiotics varied among the phenotypes, with RVT being the most susceptible, WT showing intermediate susceptibility, and SCVs displaying the lowest susceptibility. CONCLUSIONS In conclusion, the emergence of the SCVs phenotype represents a survival strategy adopted by MAC to adapt to hostile environments and persist during infection within the host. Additionally, combining the current drugs in the treatment regimen with additional drugs that promote the conversion of SCVs to RVT may offer a promising strategy to improve the clinical outcomes of patients with refractory MAC-PD.
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Affiliation(s)
- Hyun-Eui Park
- Department of Microbiology and Convergence of Medical Science, College of Medicine, Gyeongsang National University, Jinju, 52727, Republic of Korea
| | - Kyu-Min Kim
- Department of Microbiology and Convergence of Medical Science, College of Medicine, Gyeongsang National University, Jinju, 52727, Republic of Korea
| | - Minh Phuong Trinh
- Department of Microbiology and Convergence of Medical Science, College of Medicine, Gyeongsang National University, Jinju, 52727, Republic of Korea
| | - Jung-Wan Yoo
- Department of Internal Medicine, Gyeongsang National University Hospital, Jinju, 52727, Republic of Korea
| | - Sung Jae Shin
- Department of Microbiology, Institute for Immunology and Immunological Diseases, Brain Korea 21 Program for Leading Universities and Students (PLUS) Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea.
| | - Min-Kyoung Shin
- Department of Microbiology and Convergence of Medical Science, College of Medicine, Gyeongsang National University, Jinju, 52727, Republic of Korea.
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Noaman KA, Alharbi NS, Khaled JM, Kadaikunnan S, Alobaidi AS, Almazyed AO, Aldosary MS, Al Rashedi S. The transmutation of Escherichia coli ATCC 25922 to small colony variants (SCVs) E. coli strain as a result of exposure to gentamicin. J Infect Public Health 2023; 16:1821-1829. [PMID: 37742446 DOI: 10.1016/j.jiph.2023.08.024] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 07/28/2023] [Accepted: 08/29/2023] [Indexed: 09/26/2023] Open
Abstract
BACKGROUND Small colony variants (SCVs) are biotypes of bacteria that have a size of approximately one-tenth or less of the wild types and has distinct characteristics comparing to the wild type strains. Clinical SCVs are usually associated with persistent infection and require a long-term treatment program with antibiotics. In Saudi Arabia, there are few studies about SCVs Escherichia coli for this reason, this study is aimed to investigate the ability of gentamicin to mutate E. coli ATCC 25922 to produce small SCVs and investigate the genotypes and phenotypes changes and stress tolerance comparing to clinical SCVs E. coli and normal clinical E. coli Isolated from blood samples. METHODS In this investigation, four clinical blood samples were collected ted from patients and the cultivation and isolation were carried out in KFMC between December 2019 and February 2021. The identification of positive blood culture samples was done using phoenix MD. Non-SCV E. coli ATCC25922 were mutated to SCV using exposure to increasing gradual concentrations of gentamicin at 100-generation intervals. Biochemical features and susceptibility to standard antibiotics using automated Phoenix MD 50 and. The survival assays were done using several stresses including heat shock, low pH, high osmotic pressure, and oxidative pressure. Virulence genes screening included the detection of genes that encoded to α-haemolysin, CS12 fimbriae, F17-like fimbrial adhesion, P-related fimbriae, yersiniabactin siderophore system, P-fimbriae, aerobactin, iron-regulated genes using PCR and gel electrophoresis. RESULTS The data from the mutating E. coli ATCC 25922 small colony test with gentamicin revealed that the first emergence of the multidrug resistance (MDR) SCV E. coli strain occurred at generation number 250, corresponding to a gentamicin concentration of 57 g/ml. Pathogenicity islands detection revealed that all tested E. coli strains have PAI IV 536 genes on their chromosomes furthermore, mutated SCV E. coli ATCC 25922 acquired PAII CFT073 and PAI IV 536. Survival tests showed no significant differences changes in tolerance of mutated SCVs comparing to parental strain. CONCLUSION The present work concluded that gentamicin sub-MIC concentration gradual exposure can induce mutation responsible for SCV formation and evolving of MDR E. coli strains. The mutated SCVs evolved high-level aminoglycoside resistance for gentamicin and resistance to amikacin, it also developed resistance to 2 cephalosporin antibiotics cefuroxime, and cephalothin and a resistance to aztreonam.
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Affiliation(s)
- Khaled A Noaman
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Naiyf S Alharbi
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Jamal M Khaled
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia.
| | - Shine Kadaikunnan
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Ahmed S Alobaidi
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Abeer O Almazyed
- Microbiology Department, King Fahd Medical City, Riyadh, Saudi Arabia
| | | | - Saeed Al Rashedi
- Microbiology Department, King Fahd Medical City, Riyadh, Saudi Arabia
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Gil-Gil T, Berryhill BA, Manuel JA, Smith AP, McCall IC, Baquero F, Levin BR. The Evolution of Heteroresistance via Small Colony Variants in Escherichia coli Following Long Term Exposure to Bacteriostatic Antibiotics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.30.564761. [PMID: 37961139 PMCID: PMC10634941 DOI: 10.1101/2023.10.30.564761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Traditionally, bacteriostatic antibiotics are agents able to arrest bacterial growth. Despite being unable to kill bacterial cells, when they are used clinically the outcome of these drugs is frequently as effective as when a bactericidal drug is used. We explore the dynamics of Escherichia coli after exposure to two ribosome-targeting bacteriostatic antibiotics, chloramphenicol and azithromycin, for thirty days. The results of our experiments provide evidence that bacteria exposed to these drugs replicate, evolve, and generate a sub-population of small colony variants (SCVs) which are resistant to multiple drugs. These SCVs contribute to the evolution of heteroresistance and rapidly revert to a susceptible state once the antibiotic is removed. Stated another way, exposure to bacteriostatic drugs selects for the evolution of heteroresistance in populations previously lacking this trait. More generally, our results question the definition of bacteriostasis as populations exposed to bacteriostatic drugs are replicating despite the lack of net growth.
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Affiliation(s)
- Teresa Gil-Gil
- Department of Biology, Emory University; Atlanta, Georgia, 30322, USA
| | - Brandon A. Berryhill
- Department of Biology, Emory University; Atlanta, Georgia, 30322, USA
- Program in Microbiology and Molecular Genetics, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University; Atlanta, GA, 30322, USA
| | - Joshua A. Manuel
- Department of Biology, Emory University; Atlanta, Georgia, 30322, USA
| | - Andrew P. Smith
- Department of Biology, Emory University; Atlanta, Georgia, 30322, USA
| | - Ingrid C. McCall
- Department of Biology, Emory University; Atlanta, Georgia, 30322, USA
| | - Fernando Baquero
- Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria, and Centro de Investigación Médica en Red, Epidemiologíy Salud Pública (CIBERESP) Madrid, Spain
| | - Bruce R. Levin
- Department of Biology, Emory University; Atlanta, Georgia, 30322, USA
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Kocer K, Boudour-Halil D, Chanthalangsy Q, Sähr A, Heeg K, Boutin S, Nurjadi D. Genomic Modification of TonB and Emergence of Small-Colony Phenotype in VIM- and NDM-Producing Escherichia coli following Cefiderocol Exposure In Vitro. Antimicrob Agents Chemother 2023; 67:e0011823. [PMID: 37022155 PMCID: PMC10190670 DOI: 10.1128/aac.00118-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 03/07/2023] [Indexed: 04/07/2023] Open
Abstract
Knowledge on resistance mechanisms toward cefiderocol, a novel siderophore-conjugated cephalosporin antibiotic, is still limited. Although the presence of New-Delhi metallo-β-lactamase has been demonstrated to facilitate the resistance development toward cefiderocol via siderophore receptor mutations in Enterobacter cloacae and Klebsiella pneumoniae, the impact of metallo-β-lactamases on facilitating such mutations in Escherichia coli is not yet elucidated. Our study aimed to study the effect of the presence of various β-lactamases, such as NDM-5, VIM-1, KPC-2, and OXA-48, on the development of cefiderocol resistance in E. coli. To this end, we performed liquid mating to transfer these β-lactamases onto a defined K-12 E. coli background (J53) and exposed these transconjugants to increasing cefiderocol concentrations in a serial passage experiment. Cefiderocol-resistant isolates were genotyped by whole-genome sequencing to investigate the underlying resistance mechanism. Cefiderocol-resistant isolates emerged only in isolates producing VIM-1 and NDM-5 metallo-β-lactamase, but not in those producing the serine β-lactamases KPC-2 and OXA-48. We observed two distinct morphological changes of the J53 E. coli strain exhibiting reduced colony size after insertions of transposable elements in the tonB gene leading to alterations in the TonB binding site and morphological changes consistent with the small-colony variant (SCV) phenotype due to mutations in the hemB and hemH genes. Passaging experiments suggested that these phenotypes were highly plastic. The SCV phenotype is attributed to immune evasion and decreased susceptibility toward antibiotics. The emergence of SCV following cefiderocol exposure may have clinical implications for bacterial clearance and warrants further investigation.
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Affiliation(s)
- Kaan Kocer
- Department of Infectious Diseases, Medical Microbiology and Hospital Hygiene, University Hospital Heidelberg, Heidelberg, Germany
| | - Deniz Boudour-Halil
- Department of Infectious Diseases, Medical Microbiology and Hospital Hygiene, University Hospital Heidelberg, Heidelberg, Germany
| | - Quan Chanthalangsy
- Department of Infectious Diseases, Medical Microbiology and Hospital Hygiene, University Hospital Heidelberg, Heidelberg, Germany
| | - Aline Sähr
- Department of Infectious Diseases, Medical Microbiology and Hospital Hygiene, University Hospital Heidelberg, Heidelberg, Germany
| | - Klaus Heeg
- Department of Infectious Diseases, Medical Microbiology and Hospital Hygiene, University Hospital Heidelberg, Heidelberg, Germany
| | - Sébastien Boutin
- Translational Lung Research Center (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Dennis Nurjadi
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg-Lübeck-Borstel-Riems, Germany
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5
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Mura T, Matsumoto T, Aso M, Kawamura K, Kanaya K, Iinuma Y. First reported isolation of hemin-requiring Proteus vulgaris small-colony variant from urine culture. J Infect Chemother 2023; 29:631-633. [PMID: 36996937 DOI: 10.1016/j.jiac.2023.03.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 03/10/2023] [Accepted: 03/22/2023] [Indexed: 03/30/2023]
Abstract
A hemin-requiring Proteus vulgaris small-colony variant (SCV) was isolated from a urine culture. This isolate was grown on 5% sheep blood agar but not on modified Drigalski agar. The single nucleotide substitution was found in the SCV of the hemC gene (c.55C > T), and this substitution caused a nonsense mutation (p.Gln19Ter). Porphyrin test results showed that the biosynthesis of δ-aminolevulinic acid stopped up to porphobilinogen and not pre-uroporphyrinogen due to a mutation in the hemC gene. To our knowledge, this is the first report of hemin-requiring P. vulgaris.
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Affiliation(s)
- Tatsuki Mura
- Department of Clinical Laboratory, Kanazawa Medical University Hospital, 1-1 Daigaku, Uchinada, Kahoku, Ishikawa, 920-0293, Japan
| | - Takehisa Matsumoto
- Department of Laboratory Sciences, Gunma University Graduate School of Health Sciences, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8514, Japan
| | - Miyako Aso
- Department of Clinical Laboratory, Kanazawa Medical University Hospital, 1-1 Daigaku, Uchinada, Kahoku, Ishikawa, 920-0293, Japan
| | - Kae Kawamura
- Department of Clinical Laboratory, Kanazawa Medical University Hospital, 1-1 Daigaku, Uchinada, Kahoku, Ishikawa, 920-0293, Japan
| | - Kazumi Kanaya
- Department of Clinical Laboratory, Kanazawa Medical University Hospital, 1-1 Daigaku, Uchinada, Kahoku, Ishikawa, 920-0293, Japan
| | - Yoshitsugu Iinuma
- Department of Clinical Laboratory, Kanazawa Medical University Hospital, 1-1 Daigaku, Uchinada, Kahoku, Ishikawa, 920-0293, Japan; Department of Infectious Diseases, Kanazawa Medical University, 1-1 Daigaku, Uchinada, Kahoku, Ishikawa, 920-0293, Japan.
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Endres BT, Basseres E, Citron DM, Tyrrell KL, Begum K, Lancaster C, Warren YA, Alam MJ, Garey KW, Goldstein EJC. Fusobacteria behaving badly: Masquerading strains of strictly anaerobic Escherichiacoli misidentified due to the deletion of the hemB gene. Anaerobe 2023; 79:102682. [PMID: 36580991 DOI: 10.1016/j.anaerobe.2022.102682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 12/01/2022] [Accepted: 12/05/2022] [Indexed: 12/28/2022]
Abstract
Three strictly anaerobic strains of Escherichia coli were misidentified as Fusobacterium mortiferum, due to a deletion of the hemB gene which is involved in anaerobic respiration. An unusual antimicrobial susceptibility pattern sparked the further diagnostic strategies that eventually identified these strains as true anaerobic E. coli This phenomenon is more common than appreciated and can have an impact on clinical practice including persistent and relapsing infections.
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Affiliation(s)
- Bradley T Endres
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, TX, USA
| | - Eugenie Basseres
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, TX, USA
| | - Diane M Citron
- R. M. Alden Research Laboratory, Santa Monica, CA, 90404, USA
| | - Kerin L Tyrrell
- R. M. Alden Research Laboratory, Santa Monica, CA, 90404, USA
| | - Khurshida Begum
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, TX, USA
| | - Chris Lancaster
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, TX, USA
| | - Yumi A Warren
- R. M. Alden Research Laboratory, Santa Monica, CA, 90404, USA
| | - M Jahangir Alam
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, TX, USA
| | - Kevin W Garey
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, TX, USA
| | - Ellie J C Goldstein
- R. M. Alden Research Laboratory, Santa Monica, CA, 90404, USA; David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA.
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7
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Matsumoto T, Hiramoto S, Niwa T, Machida H, Suto C, Takahashi M. First description of a clinical glutamine-dependent Escherichia coli with a missense mutation in the glnA. J Infect Chemother 2022; 28:1513-1518. [DOI: 10.1016/j.jiac.2022.07.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 07/13/2022] [Accepted: 07/28/2022] [Indexed: 10/31/2022]
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8
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Jakovljev A, Afset JE, Haugum K, Steinum HO, Gresdal Rønning T, Samuelsen Ø, Ås CG. Phenotypic and genotypic characterisation of thymine auxotrophy in Escherichia coli isolated from a patient with recurrent bloodstream infection. PLoS One 2022; 17:e0270256. [PMID: 35802671 PMCID: PMC9269972 DOI: 10.1371/journal.pone.0270256] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 06/08/2022] [Indexed: 01/05/2023] Open
Abstract
INTRODUCTION Thymine auxotrophic in vitro mutants of Escherichia coli were first reported in the mid-20th century. Later, thymine-dependent clinical strains of E. coli as well as other Enterobacterales, Enterococcus faecalis and Staphylococcus aureus have been recognized as the cause of persistent and recurrent infections. OBJECTIVES The aim of this study was to characterize the phenotype and investigate the molecular basis of thymine auxotrophy in ten E. coli isolates obtained at different time points from a patient with recurrent bloodstream infection (BSI) due to a chronic aortic graft infection treated with Trimethoprim/sulfamethoxazole (TMP-SMX). METHODS Clinical data was obtained from hospital records. Growth characterization and antimicrobial susceptibility testing to TMP-SMX was performed on M9 agar and in MH broth with different thymine concentrations (0.5, 2, 5, 10 and 20 μg/mL), on Mueller-Hinton (MH) and blood agar. Whole genome sequencing (WGS) was performed on all E. coli isolates. RESULTS E. coli were isolated from ten consecutive BSI episodes from a patient with chronic aortic graft infection. Six of these isolates were resistant to TMP-SMX when assayed on blood agar. Growth experiments with added thymine confirmed that these isolates were thymine-dependent (thy-), and revealed growth defects (slower growth rate and smaller colony size) in these isolates relative to thy+ isolates (n = 4). WGS indicated that all isolates were of the same clonal lineage of sequence type 7358. Genomic analysis revealed a G172C substitution in thyA in all TMP-SMX resistant isolates, while mutations affecting genes involved in the deoxyribose salvage pathway (deoB and deoC) were identified in eight isolates. CONCLUSION This case highlights the risk of resistance development to TMP-SMX, especially for long-term treatment, and the possible pitfalls in detection of growth-deficient subpopulations from chronic infections, which could lead to treatment failure.
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Affiliation(s)
- Aleksandra Jakovljev
- Department of Medical Microbiology, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Jan Egil Afset
- Department of Medical Microbiology, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Kjersti Haugum
- Department of Medical Microbiology, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Harald Otto Steinum
- Department of Infectious Diseases, Clinic of Internal Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Torunn Gresdal Rønning
- Department of Medical Microbiology, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Ørjan Samuelsen
- Department of Microbiology and Infection Control, Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, University Hospital of North Norway, Tromsø, Norway
- Department of Pharmacy, UiT The Arctic University of Norway, Tromsø, Norway
| | - Christina Gabrielsen Ås
- Department of Medical Microbiology, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
- * E-mail:
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Gao S, Zhang Z, Xu X, Zhou H, Zhu H, Zhang Y, Cao X, Zhou W, Shen H. Characteristics of a capnophilic small colony variant of Escherichia coli co-isolated with two other strains from a patient with bacteremia in China. Arch Microbiol 2022; 204:333. [PMID: 35585303 DOI: 10.1007/s00203-022-02932-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 04/16/2022] [Accepted: 04/19/2022] [Indexed: 11/29/2022]
Abstract
Small colony variants (SCVs) are a slow-growing subpopulation of bacteria characterized by their atypical colony morphology and distinct biochemical properties, which are known to cause chronic persistent infections. Here, we investigated the characteristics of three phenotypes of Escherichia coli, including a capnophilic SCV, co-isolated from a 64-year-old patient with bacteremia in China. The three strains were identified as a capnophilic strain (EC1), a capnophilic SCV (EC2), and a normal colony strain (EC3). The EC1 and EC2 strains did not grow in the absence of CO2, while the EC2 colonies were pinpoint in appearance and had the ability to revert to the normal colony phenotype. The growth of the SCV was slow and not enhanced in the presence of thymidine, hemin, thiamine, and menadione. The results of antimicrobial susceptibility among the three strains showed similar sensitivity to cefoxitin and imipenem, but resistant to most of the other antimicrobials tested. Whole-genome sequencing showed that no genetic mutational variations associated with SCVs were observed, while EC1, EC2 and the revertible strains of EC2 lacked the can gene. Multi-locus sequence typing showed that all strains belonged to ST457 and nucleotide similarity analysis indicated that they had high homology. In conclusion, we report rarely described co-isolated forms of three phenotypes of E. coli that included a capnophilic SCV in a patient with bacteremia. The capnophilic SCV strain had atypical morphology and biochemical characteristics in the absence of can gene. Based on our findings, we have discussed the laboratory identification, characterization, mechanisms, and clinical treatment of capnophilic SCV strains.
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Affiliation(s)
- Shuo Gao
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, Jiangsu, China
| | - Zhifeng Zhang
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, Jiangsu, China
| | - Xuejing Xu
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, Jiangsu, China
| | - Hui Zhou
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, Jiangsu, China
| | - Hong Zhu
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, Jiangsu, China
| | - Yan Zhang
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, Jiangsu, China
| | - Xiaoli Cao
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, Jiangsu, China
| | - Wanqing Zhou
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, Jiangsu, China.
| | - Han Shen
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, Jiangsu, China.
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10
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Nandy P. The role of sigma factor competition in bacterial adaptation under prolonged starvation. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35594140 DOI: 10.1099/mic.0.001195] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The study of adaptive microbial evolution in the laboratory can illuminate the genetic mechanisms of gaining fitness under a pre-defined set of selection factors. Laboratory evolution of bacteria under long-term starvation has gained importance in recent years because of its ability to uncover adaptive strategies that overcome prolonged nutrient limitation, a condition often encountered by natural microbes. In this evolutionary paradigm, bacteria are maintained in an energy-restricted environment in a growth phase called long-term stationary phase (LTSP). This phase is characterized by a stable, viable population size and highly dynamic genetic changes. Multiple independent iterations of LTSP evolution experiments have given rise to mutants that are slow-growing compared to the ancestor. Although the antagonistic regulation between rapid growth and the stress response is well-known in bacteria (especially Escherichia coli), the growth deficit of many LTSP-adapted mutants has not been explored in detail. In this review, I pinpoint the trade-off between growth and stress response as a dominant driver of evolutionary strategies under prolonged starvation. Focusing on mainly E. coli-based research, I discuss the various affectors and regulators of the competition between sigma factors to occupy their targets on the genome, and assess its effect on growth advantage in stationary phase (GASP). Finally, I comment on some crucial issues that hinder the progress of the field, including identification of novel metabolites in nutrient-depleted media, and the importance of using multidisciplinary research to resolve them.
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Affiliation(s)
- Pabitra Nandy
- National Centre for Biological Sciences (NCBS-TIFR), Bangalore, India.,Max Planck Institute for Evolutionary Biology, Plӧn, Germany
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11
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Greninger AL, Addetia A, Tao Y, Adler A, Qin X. Inactivation of genes in oxidative respiration and iron acquisition pathways in pediatric clinical isolates of Small colony variant Enterobacteriaceae. Sci Rep 2021; 11:7457. [PMID: 33811225 PMCID: PMC8018945 DOI: 10.1038/s41598-021-86764-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 03/11/2021] [Indexed: 02/01/2023] Open
Abstract
Isolation of bacterial small colony variants (SCVs) from clinical specimens is not uncommon and can fundamentally change the outcome of the associated infections. Bacterial SCVs often emerge with their normal colony phenotype (NCV) co-isolates in the same sample. The basis of SCV emergence in vivo is not well understood in Gram-negative bacteria. In this study, we interrogated the causal genetic lesions of SCV growth in three pairs of NCV and SCV co-isolates of Escherichia coli, Citrobacter freundii, and Enterobacter hormaechei. We confirmed SCV emergence was attributed to limited genomic mutations: 4 single nucleotide variants in the E. coli SCV, 5 in C. freundii, and 8 in E. hormaechei. In addition, a 10.2 kb chromosomal segment containing 11 genes was deleted in the E. hormaechei SCV isolate. Each SCV had at least one coding change in a gene associated with bacterial oxidative respiration and another involved in iron capture. Chemical and genetic rescue confirmed defects in heme biosynthesis for E. coli and C. freundii and lipoic acid biosynthesis in E. hormaachei were responsible for the SCV phenotype. Prototrophic growth in all 3 SCV Enterobacteriaceae species was unaffected under anaerobic culture conditions in vitro, illustrating how SCVs may persist in vivo.
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Affiliation(s)
- Alexander L. Greninger
- grid.34477.330000000122986657Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA USA ,grid.240741.40000 0000 9026 4165Seattle Children’s Hospital, Seattle, WA USA
| | - Amin Addetia
- grid.34477.330000000122986657Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA USA ,grid.240741.40000 0000 9026 4165Seattle Children’s Hospital, Seattle, WA USA
| | - Yue Tao
- grid.16821.3c0000 0004 0368 8293Shanghai Children’s Medical Center, Translational Research Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127 China
| | - Amanda Adler
- grid.240741.40000 0000 9026 4165Seattle Children’s Hospital, Seattle, WA USA
| | - Xuan Qin
- grid.34477.330000000122986657Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA USA ,grid.240741.40000 0000 9026 4165Seattle Children’s Hospital, Seattle, WA USA
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Thomas GH. Microbial Musings - November 2020. MICROBIOLOGY (READING, ENGLAND) 2020; 166:1004-1006. [PMID: 33252324 PMCID: PMC7723258 DOI: 10.1099/mic.0.001005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Gavin H Thomas
- Department of Biology, University of York, PO Box 373, York, UK
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Hubbard ATM, Bulgasim I, Roberts AP. A novel hemA mutation is responsible for a small-colony-variant phenotype in Escherichia coli. MICROBIOLOGY-SGM 2020; 167. [PMID: 32762803 DOI: 10.1099/mic.0.000962] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We identified a small colony variant (SCV) of an amoxicillin/clavulanic acid-resistant derivative of a clinical isolate of Escherichia coli from Malawi, which was selected for in vitro in a subinhibitory concentration of gentamicin. The SCV was auxotrophic for hemin and had impaired biofilm formation compared to the ancestral isolates. A single novel nucleotide polymorphism (SNP) in hemA, which encodes a glutamyl-tRNA reductase that catalyses the initial step of porphyrin biosynthesis leading to the production of haem, was responsible for the SCV phenotype. We showed the SNP in hemA resulted in a significant fitness cost to the isolate, which persisted even in the presence of hemin. However, the phenotype quickly reverted during sequential sub-culturing in liquid growth media. As hemA is not found in mammalian cells, and disruption of the gene results in a significant fitness cost, it represents a potential target for novel drug development specifically for the treatment of catheter-associated urinary tract infections caused by E. coli.
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Affiliation(s)
- Alasdair T M Hubbard
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Issra Bulgasim
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Adam P Roberts
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
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Proteomic Study of the Survival and Resuscitation Mechanisms of Filamentous Persisters in an Evolved Escherichia coli Population from Cyclic Ampicillin Treatment. mSystems 2020; 5:5/4/e00462-20. [PMID: 32723793 PMCID: PMC7394356 DOI: 10.1128/msystems.00462-20] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Through adaptive laboratory evolution (ALE) experiments, it was recently found that when a bacterial population was repetitively treated with antibiotics, they will adapt to the treatment conditions and become tolerant to the drug. In this study, we utilized an ampicillin-tolerant Escherichia coli population isolated from an ALE experiment to study the mechanisms of persistence during ampicillin treatment and resuscitation. Interestingly, the persisters of this population exhibit filamentous morphology upon ampicillin treatment, and the filaments are getting longer over time. Proteomics analysis showed that proteins involved in carbohydrate metabolism are upregulated during antibiotic treatment, in addition to those involved in the oxidative stress response. Bacterial SOS response, which is associated with filamentation, was found to be induced on account of the increasing expression of RecA. Measurement of endogenous reactive oxygen species (ROS) revealed that the population have ∼100-fold less ROS generation under ampicillin treatment than the wild type, leading to a lower mutagenesis rate. Single-cell observations through time-lapse microscopy show that resuscitation of the filaments is stochastic. During resuscitation, proteins involved in the tricarboxylic acid (TCA) cycle, glyoxylate cycle and glycolytic processes, and ATP generation are downregulated, while ribosomal proteins and porins are upregulated in the filaments. One particular protein, ElaB, was upregulated by over 7-fold in the filaments after 3 h of resuspension in fresh medium, but its expression went down after the filaments divided. Knockout of elaB increased persistence on wild-type E. coli, and upon resumption of growth, mutants lacking elaB have a higher fraction of small colony variants (SCVs) than the wild type.IMPORTANCE Persisters are a subpopulation of cells with enhanced survival toward antibiotic treatment and have the ability to resume normal growth when the antibiotic stress is lifted. Although proteomics is the most suitable tool to study them from a system-level perspective, the number of persisters that present naturally is too few for proteomics analysis, and thus the complex mechanisms through which they are able to survive antibiotic stresses and resuscitate in fresh medium remain poorly understood. To overcome that challenge, we studied an evolved Escherichia coli population with elevated persister fraction under ampicillin treatment and obtained its proteome profiles during antibiotic treatment and resuscitation. We discovered that during treatment with ampicillin, this tolerant population employs an active oxidative stress response and exhibits lower ROS levels than the wild type. Moreover, an inner membrane protein which has implications in various stress responses, ElaB, was found to be highly upregulated in the persisters during resuscitation, and its knockout caused increased formation of small colony variants after ampicillin treatment, suggesting that ElaB is important for persisters to resume normal growth.
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A Mutant RNA Polymerase Activates the General Stress Response, Enabling Escherichia coli Adaptation to Late Prolonged Stationary Phase. mSphere 2020; 5:5/2/e00092-20. [PMID: 32295870 PMCID: PMC7160681 DOI: 10.1128/msphere.00092-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
An important general mechanism of a bacterium’s adaptation to its environment involves adjusting the balance between growing fast and tolerating stresses. One paradigm where this plays out is in prolonged stationary phase: early studies showed that attenuation, but not complete elimination, of the general stress response enables early adaptation of the bacterium E. coli to the conditions established about 10 days into stationary phase. We show here that this balance is not static and that it is tilted back in favor of the general stress response about 2 weeks later. This can be established by direct mutations in the master regulator of the general stress response or by mutations in the core RNA polymerase enzyme itself. These conditions can support the development of antibiotic tolerance although the bacterium is not exposed to the antibiotic. Further exploration of the growth-stress balance over the course of stationary phase will necessarily require a deeper understanding of the events in the extracellular milieu. Escherichia coli populations undergo repeated replacement of parental genotypes with fitter variants deep in stationary phase. We isolated one such variant, which emerged after 3 weeks of maintaining an E. coli K-12 population in stationary phase. This variant displayed a small colony phenotype and slow growth and was able to outcompete its ancestor over a narrow time window in stationary phase. The variant also shows tolerance to beta-lactam antibiotics, though not previously exposed to the antibiotic. We show that an RpoC(A494V) mutation confers the slow growth and small colony phenotype on this variant. The ability of this mutation to confer a growth advantage in stationary phase depends on the availability of the stationary-phase sigma factor σS. The RpoC(A494V) mutation upregulates the σS regulon. As shown over 20 years ago, early in prolonged stationary phase, σS attenuation, but not complete loss of activity, confers a fitness advantage. Our study shows that later mutations enhance σS activity, either by mutating the gene for σS directly or via mutations such as RpoC(A494V). The balance between the activities of the housekeeping major sigma factor and σS sets up a trade-off between growth and stress tolerance, which is tuned repeatedly during prolonged stationary phase. IMPORTANCE An important general mechanism of a bacterium’s adaptation to its environment involves adjusting the balance between growing fast and tolerating stresses. One paradigm where this plays out is in prolonged stationary phase: early studies showed that attenuation, but not complete elimination, of the general stress response enables early adaptation of the bacterium E. coli to the conditions established about 10 days into stationary phase. We show here that this balance is not static and that it is tilted back in favor of the general stress response about 2 weeks later. This can be established by direct mutations in the master regulator of the general stress response or by mutations in the core RNA polymerase enzyme itself. These conditions can support the development of antibiotic tolerance although the bacterium is not exposed to the antibiotic. Further exploration of the growth-stress balance over the course of stationary phase will necessarily require a deeper understanding of the events in the extracellular milieu.
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Abstract
Respiratory mutants, both naturally occurring and genetically constructed, have taught us about the importance of metabolism in influencing virulence factor production, persistence, and antibiotic resistance. As we learn more about small colony variants, we find that Staphylococcus aureus has many pathways to produce small colony variants, although the respiratory variants are the best described clinically and in the laboratory.
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Höring S, Sobotta K, Schneider S, Löffler B, Rödel J. Dwarfs in disguise: multiple spinal abscesses and spondylodiscitis caused by an Enterococcus faecium small-colony variant. Access Microbiol 2019; 1:e000012. [PMID: 32974494 PMCID: PMC7470356 DOI: 10.1099/acmi.0.000012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 02/07/2019] [Indexed: 11/18/2022] Open
Abstract
Small-colony variants are slow-growing subpopulations of bacteria known to be involved in latent or recurrent infections, especially in deep-seated foci. Their atypical growth in small colonies can hamper prompt and correct identification in clinical specimens. Here, we present the first case of multiple spinal abscesses and spondylodiscitis associated with an Enterococcus faecium small-colony-variant in an immunocompetent patient. This case demonstrates the diagnostic challenges when encountering this phenotype in the diagnostic laboratory.
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Affiliation(s)
- Steffen Höring
- Institute of Medical Microbiology, Jena University Hospital, Am Klinikum1, D-07747 Jena, Germany
| | - Katharina Sobotta
- Institute of Medical Microbiology, Jena University Hospital, Am Klinikum1, D-07747 Jena, Germany
| | - Sylke Schneider
- Clinic for Internal Medicine, Waldkrankenhaus ‘Rudolf Elle’, Klosterlausnitzer Straße 81, D-07607 Eisenberg, Germany
| | - Bettina Löffler
- Institute of Medical Microbiology, Jena University Hospital, Am Klinikum1, D-07747 Jena, Germany
| | - Jürgen Rödel
- Institute of Medical Microbiology, Jena University Hospital, Am Klinikum1, D-07747 Jena, Germany
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Park YJ, Le Phuong N, Pinto NA, Kwon MJ, D'Souza R, Byun JH, Sung H, Yong D. Urinary tract infection caused by a small colony variant form of capnophilic Escherichia coli leading to misidentification and non-reactions in antimicrobial susceptibility tests. Antimicrob Resist Infect Control 2018; 7:139. [PMID: 30479752 PMCID: PMC6245536 DOI: 10.1186/s13756-018-0438-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 11/12/2018] [Indexed: 11/10/2022] Open
Abstract
Background Small colony and capnophilic variant cases have been separately reported, but there has been no reports of their simultaneous presence in one isolate. We report a case of Escherichia coli with coexpressed small colony and capnophilic phenotypes causing misidentification in automated biochemical kits and non-reactions in antimicrobial susceptibility test cards. Case presentation An 86-year-old woman developed urinary tract infection from a strain of Escherichia coli with SCV and capnophilic phenotypes in co-existence. This strain did not grow without the presence of CO2, and therefore proper identification from automated system was not possible. 16 s rRNA sequencing and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry was able to identify the bacteria. Conclusion As these strains do not grow on culture parameters defined by CLSI or on automated systems, proper identification using alternative methods are necessary.
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Affiliation(s)
- Yu Jin Park
- 1Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Severance Hospital, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722 Republic of Korea
| | - Nguyen Le Phuong
- 1Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Severance Hospital, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722 Republic of Korea
| | - Naina Adren Pinto
- 1Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Severance Hospital, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722 Republic of Korea
| | - Mi Jeong Kwon
- 1Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Severance Hospital, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722 Republic of Korea
| | - Roshan D'Souza
- 1Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Severance Hospital, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722 Republic of Korea.,J.Craig Venter Institute (JCVI), 9605 Medical Center Dr #150, Rockville, MD 20850 USA
| | - Jung-Hyun Byun
- 1Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Severance Hospital, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722 Republic of Korea
| | - Heungsup Sung
- 3Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympic-ro 43-gil, Songpa-gu, Seoul 05505 Republic of Korea
| | - Dongeun Yong
- 1Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Severance Hospital, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722 Republic of Korea
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Negishi T, Matsumoto T, Horiuchi K, Kasuga E, Natori T, Matsuoka M, Ogiwara N, Sugano M, Uehara T, Nagano N, Honda T. Characterization of clinically isolated thymidine-dependent small-colony variants of Escherichia coli producing extended-spectrum β-lactamase. J Med Microbiol 2017; 67:33-39. [PMID: 29143727 DOI: 10.1099/jmm.0.000634] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
PURPOSE Thymidine-dependent small-colony variants (TD-SCVs) are difficult to detect or test for antimicrobial susceptibility. We investigated the characteristics of clonal TD-SCVs of Escherichia coli, both with and without blaCTX-M-3, isolated from a patient. METHODOLOGY Mutation in the thyA gene was analysed by sequencing, and morphological abnormalities in the colonies and cells of the isolates were examined. Additionally, conjugational transfer experiments were performed to prove the horizontal transferability of plasmids harbouring resistance genes. RESULTS The TD-SCVs contained a single nucleotide substitution in the thyA gene, c.62G>A, corresponding to p.Arg21His. Morphologically, their colonies were more translucent and flattened than those of the wild-type strain. In addition, cells of the TD-SCVs were swollen and elongated, sometimes with abnormal and incomplete divisions; a large amount of cell debris was also observed. Changing c.62G>A back to the wild-type sequence reversed these abnormalities. Conjugational transfer experiments showed that the TD-SCV of E. coli with blaCTX-M-3 failed to transfer blaCTX-M-3 to E. coli CSH2. However, the TD-SCV of E. coli without blaCTX-M-3 experimentally received the plasmid encoding blaSHV-18 from Klebsiella pneumoniae ATCC 700603 and transferred it to E. coli CSH2. CONCLUSION Mutation in the thyA gene causes morphological abnormalities in the colonies and cells of E. coli, as well as inducing thymidine auxotrophy. In addition, TD-SCVs horizontally transmit plasmids encoding resistance genes. It is important to detect TD-SCVs based on their characteristics because they serve as reservoirs of transferable antibiotic resistance plasmids.
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Affiliation(s)
- Tatsuya Negishi
- Department of Laboratory Medicine, Shinshu University Hospital, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan.,Department of Health and Medical Sciences, Shinshu University Graduate School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan
| | - Takehisa Matsumoto
- Department of Laboratory Sciences, Gunma University Graduate School of Health Sciences, 3-39-22 Showa-machi, Maebashi, Gunma 371-8514, Japan
| | - Kazuki Horiuchi
- Department of Laboratory Medicine, Shinshu University Hospital, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan
| | - Eriko Kasuga
- Department of Laboratory Medicine, Shinshu University Hospital, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan
| | - Tatsuya Natori
- Department of Laboratory Medicine, Shinshu University Hospital, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan
| | - Mina Matsuoka
- Department of Laboratory Medicine, Shinshu University Hospital, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan
| | - Naoko Ogiwara
- Department of Laboratory Medicine, Shinshu University Hospital, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan
| | - Mitsutoshi Sugano
- Department of Laboratory Medicine, Shinshu University Hospital, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan
| | - Takeshi Uehara
- Department of Laboratory Medicine, Shinshu University Hospital, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan
| | - Noriyuki Nagano
- Department of Health and Medical Sciences, Shinshu University Graduate School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan
| | - Takayuki Honda
- Department of Laboratory Medicine, Shinshu University Hospital, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan
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Nagano N, Nakaya H, Nagata M, Nishizawa T, Kawahara R, Matsumoto T, Oana K, Kawakami Y. Characterization of first hemin-requiring Pseudomonas aeruginosa small-colony variants from the blood of an octogenarian male-patient with double pneumonitis. J Infect Chemother 2017; 23:852-855. [PMID: 28673558 DOI: 10.1016/j.jiac.2017.06.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 05/26/2017] [Accepted: 06/02/2017] [Indexed: 10/19/2022]
Abstract
A hemin-requiring Pseudomonas aeruginosa small-colony variant (SCV) was isolated from the blood of an octogenarian male-patient with double pneumonitis. The isolate was capable of growing on both sheep blood and chocolate agars but not on MacConkey agars without blood ingredient. Furthermore, the isolate revealed to grow only around the X-factor impregnated discs when examined using the X and V disc strips. However, not only RapID-NH system but also the VITEK2 system failed to identify the isolate. The isolate was finally identified as P. aeruginosa by the sequence of the 16S rRNA genes and the MALDI-TOF MS analysis. Interestingly, the isolate represented positive reaction for δ-aminolaevulinic acid (ALA)-test despite the requirement of hemin. Detailed analysis indicated that the isolate produced protoporphyrin IX from ALA. Therefore, the reason for the hemin dependence was deduced the dysfunction of hemH-encoded ferrochelatase behaving at the end of biosynthetic pathway of heme. However, the genetic analysis of hemH gene demonstrated no variations of both the DNA and the amino-acid sequences. To the best of our knowledge, this is the first clinical isolation of a hemin-dependent P. aeruginosa SCV from blood.
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Affiliation(s)
- Natsumi Nagano
- Department of Clinical Laboratory, Kansai Medical University Medical Center, Moriguchi 570-8507, Japan
| | - Hideo Nakaya
- Department of Clinical Laboratory, Kansai Medical University Medical Center, Moriguchi 570-8507, Japan
| | - Megumi Nagata
- Department of Clinical Laboratory, Kansai Medical University Medical Center, Moriguchi 570-8507, Japan
| | - Toru Nishizawa
- Instructor of Rheumatology and Clinical Immunology, Kansai Medical University Medical Center, Moriguchi 570-8507, Japan
| | - Ryuji Kawahara
- Division of Microbiology, Osaka Institute of Public Health, Osaka 537-0025, Japan
| | - Takehisa Matsumoto
- Department of Laboratory Sciences, Gunma University Graduate School of Health Sciences, Maebashi 371-8543, Japan
| | - Kozue Oana
- Division of Infection Control and Microbiological Regulation, Department of Health and Medical Sciences, Shinshu University Graduate School of Medicine, Matsumoto 390-8621, Japan; Division of Clinical Microbiology, Department of Biomedical Laboratory Sciences, School of Health Sciences, Shinshu University School of Medicine, Matsumoto 390-8621, Japan
| | - Yoshiyuki Kawakami
- Division of Infection Control and Microbiological Regulation, Department of Health and Medical Sciences, Shinshu University Graduate School of Medicine, Matsumoto 390-8621, Japan; Division of Clinical Microbiology, Department of Biomedical Laboratory Sciences, School of Health Sciences, Shinshu University School of Medicine, Matsumoto 390-8621, Japan.
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Tashiro Y, Eida H, Ishii S, Futamata H, Okabe S. Generation of Small Colony Variants in Biofilms by Escherichia coli Harboring a Conjugative F Plasmid. Microbes Environ 2017; 32:40-46. [PMID: 28302951 PMCID: PMC5371073 DOI: 10.1264/jsme2.me16121] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A conjugative F plasmid induces mature biofilm formation by Escherichia coli by promoting F-pili-mediated cell-cell interactions and increasing the expression of biofilm-related genes. We herein demonstrated another function for the F plasmid in E. coli biofilms; it contributes to the emergence of genetic and phenotypic variations by spontaneous mutations. Small colony variants (SCVs) were more frequently generated in a continuous flow-cell biofilm than in the planktonic state of E. coli harboring the F plasmid. E. coli SCVs represented typical phenotypic changes such as slower growth, less biofilm formation, and greater resistance to aminoglycoside antibiotics than the parent strain. Genomic and complementation analyses indicated that the small colony phenotype was caused by the insertion of Tn1000, which was originally localized in the F plasmid, into the hemB gene. Furthermore, the Tn1000 insertion was removed from hemB in the revertant, which showed a normal colony phenotype. This study revealed that the F plasmid has the potential to increase genetic variations not only by horizontal gene transfer via F pili, but also by site-specific recombination within a single cell.
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Affiliation(s)
- Yosuke Tashiro
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University
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23
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Ramiro RS, Costa H, Gordo I. Macrophage adaptation leads to parallel evolution of genetically diverse Escherichia coli small-colony variants with increased fitness in vivo and antibiotic collateral sensitivity. Evol Appl 2016; 9:994-1004. [PMID: 27606007 PMCID: PMC4999529 DOI: 10.1111/eva.12397] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 05/18/2016] [Indexed: 12/20/2022] Open
Abstract
Small-colony variants (SCVs) are commonly observed in evolution experiments and clinical isolates, being associated with antibiotic resistance and persistent infections. We recently observed the repeated emergence of Escherichia coli SCVs during adaptation to the interaction with macrophages. To identify the genetic targets underlying the emergence of this clinically relevant morphotype, we performed whole-genome sequencing of independently evolved SCV clones. We uncovered novel mutational targets, not previously associated with SCVs (e.g. cydA, pepP) and observed widespread functional parallelism. All SCV clones had mutations in genes related to the electron-transport chain. As SCVs emerged during adaptation to macrophages, and often show increased antibiotic resistance, we measured SCV fitness inside macrophages and measured their antibiotic resistance profiles. SCVs had a fitness advantage inside macrophages and showed increased aminoglycoside resistance in vitro, but had collateral sensitivity to other antibiotics (e.g. tetracycline). Importantly, we observed similar results in vivo. SCVs had a fitness advantage upon colonization of the mouse gut, which could be tuned by antibiotic treatment: kanamycin (aminoglycoside) increased SCV fitness, but tetracycline strongly reduced it. Our results highlight the power of using experimental evolution as the basis for identifying the causes and consequences of adaptation during host-microbe interactions.
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Curtis TD, Gram L, Knudsen GM. The Small Colony Variant of Listeria monocytogenes Is More Tolerant to Antibiotics and Has Altered Survival in RAW 264.7 Murine Macrophages. Front Microbiol 2016; 7:1056. [PMID: 27458449 PMCID: PMC4932272 DOI: 10.3389/fmicb.2016.01056] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 06/23/2016] [Indexed: 12/11/2022] Open
Abstract
Small Colony Variant (SCV) cells of bacteria are a slow-growing phenotype that result from specific defects in the electron transport chain. They form pinpoint colonies on agar plates and have a variety of phenotypic characteristics, such as altered carbon metabolism, decreased toxin and lytic enzyme production, aminoglycoside resistance, and increased intracellular persistence. They are clinically relevant in Staphylococcus aureus and Pseudomonas aeruginosa, serving as a reservoir for recurrent or prolonged infections. Here, we found that a SCV mutant in the foodborne pathogen Listeria monocytogenes (strain SCV E18), similar to the high persister mutant phenotype, survived significantly better than the wild type when exposed over a 48-h period to concentrations above Minimal Inhibitory Concentration for most tested antibiotics. SCV E18 survived more poorly than the wildtype in unactivated RAW264.7 macrophage cells, presumably because of its reduced listeriolysin O expression, however, it survived better in reactive oxygen species producing, phorbol 12-myristate 13-acetate-activated macrophages. Although SCV E18 was sensitive to oxygen as it entered the stationary phase, it was significantly more tolerant to H2O2 than the wild type, which may result from a shift in metabolism, however, further investigation is needed to resolve this. SCV E18 is a spontaneous mutant with a point mutation in the hemA gene. A wild type copy of hemA was complemented on plasmid pSOG30222, which restored the wild type phenotype. The results reported here suggest that the SCV of L. monocytogenes could be of clinical importance and highlight a need for adequate clinical screening for this phenotype, as it could affect antibiotic treatment outcomes.
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Affiliation(s)
- Thomas D Curtis
- Gram Lab, Department of Systems Biology, Technical University of Denmark Kongens Lyngby, Denmark
| | - Lone Gram
- Gram Lab, Department of Systems Biology, Technical University of Denmark Kongens Lyngby, Denmark
| | - Gitte M Knudsen
- Gram Lab, Department of Systems Biology, Technical University of Denmark Kongens Lyngby, Denmark
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25
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Santos V, Hirshfield I. The Physiological and Molecular Characterization of a Small Colony Variant of Escherichia coli and Its Phenotypic Rescue. PLoS One 2016; 11:e0157578. [PMID: 27310825 PMCID: PMC4910995 DOI: 10.1371/journal.pone.0157578] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 06/01/2016] [Indexed: 11/18/2022] Open
Abstract
Small colony variants (SCVs) can be defined as a naturally occurring sub-population of bacteria characterized by their reduced colony size and distinct biochemical properties. SCVs of Staphylococcus aureus have been studied extensively over the past two decades due to their role in recurrent human infections. However, little work has been done on SCVs of Escherichia coli, and this work has focused on the physiology and morphology that define these colonies of E. coli, such as small size and slow growth. E. coli strain JW0623, has a null lipA mutation in the lipoic acid synthase gene (lipA), and is a lipoic acid auxotroph. When the mutant was grown in LB medium to log phase, it showed remarkable resistance to acid (pH 3), hydrogen peroxide, heat and osmotic stress compared to its parent BW25113. Using RT-PCR and real time RT-PCR, the expression of certain genes was compared in the two strains in an attempt to create a molecular profile of Escherichia coli SCVs. These include genes involved in glycolysis, TCA cycle, electron transport, iron acquisition, biofilm formation and cyclopropane fatty acid synthesis. It was also demonstrated that the addition of 5 μg/ml of lipoic acid to LB medium allows for the phenotypic rescue of the mutant; reversing its slow growth, its resistance characteristics, and elevated gene expression. These results indicate that the mutation in lipA leads to an E. coli SCV that resembles an electron transport defective SCV of S. aureus These strains are typically auxotrophs, and are phenotypically rescued by adding the missing metabolite to rich medium. There are global shifts in gene expression which are reversible and depend on whether the auxotrophic molecule is absent or present. Looking at the E. coli SCV from an evolutionary point of view, it becomes evident that its path to survival is to express genes that confer stress resistance.
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Affiliation(s)
- Victor Santos
- Department of Biological Sciences, St. John’s University, Queens, New York, United States of America
- * E-mail:
| | - Irvin Hirshfield
- Department of Biological Sciences, St. John’s University, Queens, New York, United States of America
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Johns BE, Purdy KJ, Tucker NP, Maddocks SE. Phenotypic and Genotypic Characteristics of Small Colony Variants and Their Role in Chronic Infection. Microbiol Insights 2015; 8:15-23. [PMID: 26448688 PMCID: PMC4581789 DOI: 10.4137/mbi.s25800] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 08/09/2015] [Accepted: 08/13/2015] [Indexed: 01/02/2023] Open
Abstract
Small colony variant (SCV) bacteria arise spontaneously within apparently homogeneous microbial populations, largely in response to environmental stresses, such as antimicrobial treatment. They display unique phenotypic characteristics conferred in part by heritable genetic changes. Characteristically slow growing, SCVs comprise a minor proportion of the population from which they arise but persist by virtue of their inherent resilience and host adaptability. Consequently, SCVs are problematic in chronic infection, where antimicrobial treatment is administered during the acute phase of infection but fails to eradicate SCVs, which remain within the host causing recurrent or chronic infection. This review discusses some of the phenotypic and genotypic changes that enable SCVs to successfully proliferate within the host environment as potential pathogens and strategies that could ameliorate the resolution of infection where SCVs are present.
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Affiliation(s)
- Benjamin E Johns
- Department of Biomedical Science, Cardiff School of Health Sciences, Cardiff Metropolitan University, Cardiff, UK
| | - Kevin J Purdy
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Nicholas P Tucker
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
| | - Sarah E Maddocks
- Department of Biomedical Science, Cardiff School of Health Sciences, Cardiff Metropolitan University, Cardiff, UK
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Tsuru A, Setoguchi T, Kawabata N, Hirotsu M, Yamamoto T, Nagano S, Yokouchi M, Kakoi H, Kawamura H, Ishidou Y, Tanimoto A, Komiya S. Enrichment of bacteria samples by centrifugation improves the diagnosis of orthopaedics-related infections via real-time PCR amplification of the bacterial methicillin-resistance gene. BMC Res Notes 2015; 8:288. [PMID: 26138214 PMCID: PMC4490765 DOI: 10.1186/s13104-015-1180-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2013] [Accepted: 05/20/2015] [Indexed: 11/26/2022] Open
Abstract
Background To effectively treat orthopaedic infections by methicillin-resistant strains, an early diagnosis is necessary. Bacterial cultures and real-time polymerase chain reaction (PCR) have been used to define methicillin-resistant staphylococci. However, even when patients display clinical signs of infections, bacterial culture and real-time PCR often cannot confirm infection. The aim of this study was to prospectively compare the utility of real-time PCR for the mecA gene detection following centrifugation of human samples with suspected orthopaedic infections. Results In addition to the conventional real-time PCR method, we performed real-time PCR following centrifugation of the sample at 4,830×g for 10 min in a modified real-time PCR (M-PCR) method. We suspended cultured methicillin-resistant Staphylococcus aureus and generated standard dilution series for in vitro experiments. The in vitro detection sensitivity of the M-PCR method was approximately 5.06 times higher than that of the conventional real-time PCR method. We performed bacterial culture, pathological examination, real-time PCR, and M-PCR to examine the infectious fluids and tissues obtained from 36 surgical patients at our hospital. Of these, 20 patients who had undergone primary total hip arthroplasty were enrolled as negative controls. In addition, 15 patients were examined who were clinically confirmed to have an infection, including periprosthetic joint infection (eight patients), pyogenic spondylitis (two patients), infectious pseudoarthrosis (two patients), and after spine surgery (three patients). In one sample from a patient who developed infectious pseudoarthrosis and two samples from surgical site infections after spine surgery, the mecA gene was detected only by the M-PCR method. In one patient with infectious pseudoarthrosis, one patient with infection after arthroplasty, and two patients with purulent spondylitis, the detection sensitivity of the M-PCR method was increased compared with PCR (clinical sample average: 411.6 times). Conclusions These findings suggest that the M-PCR method is useful to detect methicillin-resistant strains infections. In addition, the centrifugation process only takes 10 min longer than conventional real-time PCR methods. We believe that the M-PCR method could be clinically useful to detect orthopaedic infections caused by methicillin-resistant strains. Electronic supplementary material The online version of this article (doi:10.1186/s13104-015-1180-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Arisa Tsuru
- Department of Orthopaedic Surgery, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan.
| | - Takao Setoguchi
- The Near-Future Locomotor Organ Medicine Creation Course (Kusunoki Kai), Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima, 890-8520, Japan.
| | - Naoya Kawabata
- Department of Orthopaedic Surgery, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan.
| | - Masataka Hirotsu
- Department of Orthopaedic Surgery, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan.
| | - Takuya Yamamoto
- Department of Orthopaedic Surgery, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan.
| | - Satoshi Nagano
- Department of Orthopaedic Surgery, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan.
| | - Masahiro Yokouchi
- Department of Orthopaedic Surgery, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan.
| | - Hironori Kakoi
- Department of Orthopaedic Surgery, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan.
| | - Hideki Kawamura
- Infection Control Team, Kagoshima University Hospital, Kagoshima, Japan.
| | - Yasuhiro Ishidou
- Department of Medical Joint Materials, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan.
| | - Akihide Tanimoto
- Molecular and Cellular Pathology, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan.
| | - Setsuro Komiya
- Department of Orthopaedic Surgery, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan.
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Al-Maleki AR, Mariappan V, Vellasamy KM, Tay ST, Vadivelu J. Altered Proteome of Burkholderia pseudomallei Colony Variants Induced by Exposure to Human Lung Epithelial Cells. PLoS One 2015; 10:e0127398. [PMID: 25996927 PMCID: PMC4440636 DOI: 10.1371/journal.pone.0127398] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 04/14/2015] [Indexed: 12/19/2022] Open
Abstract
Burkholderia pseudomallei primary diagnostic cultures demonstrate colony morphology variation associated with expression of virulence and adaptation proteins. This study aims to examine the ability of B. pseudomallei colony variants (wild type [WT] and small colony variant [SCV]) to survive and replicate intracellularly in A549 cells and to identify the alterations in the protein expression of these variants, post-exposure to the A549 cells. Intracellular survival and cytotoxicity assays were performed followed by proteomics analysis using two-dimensional gel electrophoresis. B. pseudomallei SCV survive longer than the WT. During post-exposure, among 259 and 260 protein spots of SCV and WT, respectively, 19 were differentially expressed. Among SCV post-exposure up-regulated proteins, glyceraldehyde 3-phosphate dehydrogenase, fructose-bisphosphate aldolase (CbbA) and betaine aldehyde dehydrogenase were associated with adhesion and virulence. Among the down-regulated proteins, enolase (Eno) is implicated in adhesion and virulence. Additionally, post-exposure expression profiles of both variants were compared with pre-exposure. In WT pre- vs post-exposure, 36 proteins were differentially expressed. Of the up-regulated proteins, translocator protein, Eno, nucleoside diphosphate kinase (Ndk), ferritin Dps-family DNA binding protein and peptidyl-prolyl cis-trans isomerase B were implicated in invasion and virulence. In SCV pre- vs post-exposure, 27 proteins were differentially expressed. Among the up-regulated proteins, flagellin, Eno, CbbA, Ndk and phenylacetate-coenzyme A ligase have similarly been implicated in adhesion, invasion. Protein profiles differences post-exposure provide insights into association between morphotypic and phenotypic characteristics of colony variants, strengthening the role of B. pseudomallei morphotypes in pathogenesis of melioidosis.
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Affiliation(s)
- Anis Rageh Al-Maleki
- Tropical Infectious Disease Research and Education Center (TIDREC), Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Vanitha Mariappan
- Tropical Infectious Disease Research and Education Center (TIDREC), Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Kumutha Malar Vellasamy
- Tropical Infectious Disease Research and Education Center (TIDREC), Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Sun Tee Tay
- Tropical Infectious Disease Research and Education Center (TIDREC), Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Jamuna Vadivelu
- Tropical Infectious Disease Research and Education Center (TIDREC), Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
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Percival SL, Suleman L, Vuotto C, Donelli G. Healthcare-associated infections, medical devices and biofilms: risk, tolerance and control. J Med Microbiol 2015; 64:323-334. [PMID: 25670813 DOI: 10.1099/jmm.0.000032] [Citation(s) in RCA: 416] [Impact Index Per Article: 46.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 01/23/2015] [Indexed: 01/30/2023] Open
Abstract
Biofilms are of great importance in infection control and healthcare-associated infections owing to their inherent tolerance and 'resistance' to antimicrobial therapies. Biofilms have been shown to develop on medical device surfaces, and dispersal of single and clustered cells implies a significant risk of microbial dissemination within the host and increased risk of infection. Although routine microbiological testing assists with the diagnosis of a clinical infection, there is no 'gold standard' available to reveal the presence of microbial biofilm from samples collected within clinical settings. Furthermore, such limiting factors as viable but non-culturable micro-organisms and small-colony variants often prevent successful detection. In order to increase the chances of detection and provide a more accurate diagnosis, a combination of microbiological culture techniques and molecular methods should be employed. Measures such as antimicrobial coating and surface alterations of medical devices provide promising opportunities in the prevention of biofilm formation on medical devices.
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Affiliation(s)
- Steven L Percival
- Scapa Healthcare, Manchester, UK.,Surface Science Research Centre, University of Liverpool, Liverpool, UK.,Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, UK
| | - Louise Suleman
- Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, UK
| | - Claudia Vuotto
- Microbial Biofilm Laboratory, IRCCS Fondazione Santa Lucia, Rome, Italy
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Miskinyte M, Sousa A, Ramiro RS, de Sousa JAM, Kotlinowski J, Caramalho I, Magalhães S, Soares MP, Gordo I. The genetic basis of Escherichia coli pathoadaptation to macrophages. PLoS Pathog 2013; 9:e1003802. [PMID: 24348252 PMCID: PMC3861542 DOI: 10.1371/journal.ppat.1003802] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Accepted: 10/14/2013] [Indexed: 12/25/2022] Open
Abstract
Antagonistic interactions are likely important driving forces of the evolutionary process underlying bacterial genome complexity and diversity. We hypothesized that the ability of evolved bacteria to escape specific components of host innate immunity, such as phagocytosis and killing by macrophages (MΦ), is a critical trait relevant in the acquisition of bacterial virulence. Here, we used a combination of experimental evolution, phenotypic characterization, genome sequencing and mathematical modeling to address how fast, and through how many adaptive steps, a commensal Escherichia coli (E. coli) acquire this virulence trait. We show that when maintained in vitro under the selective pressure of host MΦ commensal E. coli can evolve, in less than 500 generations, virulent clones that escape phagocytosis and MΦ killing in vitro, while increasing their pathogenicity in vivo, as assessed in mice. This pathoadaptive process is driven by a mechanism involving the insertion of a single transposable element into the promoter region of the E. coli yrfF gene. Moreover, transposition of the IS186 element into the promoter of Lon gene, encoding an ATP-dependent serine protease, is likely to accelerate this pathoadaptive process. Competition between clones carrying distinct beneficial mutations dominates the dynamics of the pathoadaptive process, as suggested from a mathematical model, which reproduces the observed experimental dynamics of E. coli evolution towards virulence. In conclusion, we reveal a molecular mechanism explaining how a specific component of host innate immunity can modulate microbial evolution towards pathogenicity.
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Affiliation(s)
| | - Ana Sousa
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | | | | | | | - Iris Caramalho
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- Unidade de Imunologia Clínica, Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
| | - Sara Magalhães
- Centro Biologia Ambiental, Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| | | | - Isabel Gordo
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- * E-mail:
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Bogut A, Niedźwiadek J, Kozioł-Montewka M, Strzelec-Nowak D, Blacha J, Mazurkiewicz T, Marczyński W, Plewik D. Characterization of Staphylococcus epidermidis and Staphyloccocus warneri small-colony variants associated with prosthetic-joint infections. J Med Microbiol 2013; 63:176-185. [PMID: 24257683 DOI: 10.1099/jmm.0.066068-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
We determined the frequency of isolation of staphylococcal small-colony variants (SCVs) from 31 culture-positive patients undergoing revision of total hip prosthesis for aseptic loosening or presumed prosthetic-joint infection (PJI). We analysed auxotrophy of cultured SCVs, their antimicrobial susceptibility profiles and their biofilm-forming capacity. Eight SCV strains were cultivated from six (19 %) patients. All SCVs were coagulase-negative staphylococci (CNS) with Staphylococcus epidermidis as the predominant species; there was also one Staphylococcus warneri SCV. The SCVs were auxotrophic for haemin, with one strain additionally auxotrophic for menadione. We noted the presence of two phenotypically (differences concerning antimicrobial susceptibility) and genetically distinct SCV strains in one patient, as well as the growth of two genetically related SCVs that differed in terms of their morphology and the type of auxotrophy in another. Seven out of eight SCVs were resistant to meticillin and gentamicin. In addition, antibiotic sensitivity testing revealed three multidrug-resistant SCV-normal-morphology isolate pairs. One S. epidermidis SCV harboured icaADBC genes and was found to be a proficient biofilm producer. This paper highlights the involvement of CNS SCVs in the aetiology of PJIs, including what is believed to be the first report of a S. warneri SCV. These subpopulations must be actively sought in the routine diagnosis of implant-associated infections. Moreover, in view of the phenotypic and genetic diversity of some SCV pairs, particular attention should be paid to the investigation of all types of observed colony morphologies, and isolates should be subjected to antimicrobial susceptibility testing.
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Affiliation(s)
- Agnieszka Bogut
- Department of Medical Microbiology, Medical University of Lublin, Chodźki 1 Street, 20-093 Lublin, Poland
| | - Justyna Niedźwiadek
- Department of Medical Microbiology, Medical University of Lublin, Chodźki 1 Street, 20-093 Lublin, Poland
| | - Maria Kozioł-Montewka
- Department of Medical Microbiology, Medical University of Lublin, Chodźki 1 Street, 20-093 Lublin, Poland
| | - Dagmara Strzelec-Nowak
- Department of Medical Microbiology, Medical University of Lublin, Chodźki 1 Street, 20-093 Lublin, Poland
| | - Jan Blacha
- Orthopaedics and Traumatology Ward, Clinical Hospital No. 4, Jaczewskiego 8 Street, 20-954 Lublin, Poland
| | - Tomasz Mazurkiewicz
- Orthopaedics and Traumatology Ward, Clinical Hospital No. 4, Jaczewskiego 8 Street, 20-954 Lublin, Poland
| | - Wojciech Marczyński
- Orthopaedics Ward, Public Clinical Hospital of Prof. Adam Gruca, Konarskiego 13 Street, 05-400 Otwock, Poland
| | - Dorota Plewik
- Research Centre for Innovation, Pope John Paul II State School of Higher Education in Biała Podlaska, Sidorska 105 Street, 21-500 Biała Podlaska, Poland
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Small colony variants (SCVs) of Staphylococcus aureus--a bacterial survival strategy. INFECTION GENETICS AND EVOLUTION 2013; 21:515-22. [PMID: 23722021 DOI: 10.1016/j.meegid.2013.05.016] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2013] [Revised: 05/11/2013] [Accepted: 05/18/2013] [Indexed: 01/28/2023]
Abstract
Small colony variants (SCVs) of Staphylococcus aureus have been implicated in chronic recurrent infections and have therefore gained renewed interest during the last decade. Moreover, SCVs have been shown to be part of the regular growth cycle, are highly dynamic or stable and can be selected during various harsh conditions. As such, the emergence of SCVs has been described not only in human, but also in veterinary medicine as well as in food microbiology. SCVs are characterized by impaired growth, down-regulation of genes for metabolism and virulence, while sigB and genes important for persistence and biofilm formation are up-regulated. Furthermore, SCVs are resistant to various antibiotics such as aminoglycosides, trimethoprim-sulfamethoxazole, fluorquinolones, fusidic acid or even to antiseptics such as triclosan. An underlying mechanism has been determined for hemin-, menadione- and thymidine-dependent SCVs as well as for SCVs which are impaired in their stress response. SCVs are optimized for persistence in the host. They are able to reverse and thereby constitute a highly dynamic subpopulation of S. aureus. Such phenotype switching constitutes an integral part of the infection process enabling the bacteria to hide inside the host cell without eliciting a strong host response.
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Gruss A, Borezée-Durant E, Lechardeur D. Environmental heme utilization by heme-auxotrophic bacteria. Adv Microb Physiol 2013; 61:69-124. [PMID: 23046952 DOI: 10.1016/b978-0-12-394423-8.00003-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Heme, an iron-containing porphyrin, is the prosthetic group for numerous key cellular enzymatic and regulatory processes. Many bacteria encode the biosynthetic enzymes needed for autonomous heme production. Remarkably, however, numerous other bacteria lack a complete heme biosynthesis pathway, yet encode heme-requiring functions. For such heme-auxotrophic bacteria (HAB), heme or porphyrins must be captured from the environment. Functional studies, aided by genomic analyses, provide insight into the HAB lifestyle, how they acquire and manage heme, and the uses of heme that make it worthwhile, and sometimes necessary, to capture this bioactive molecule.
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Affiliation(s)
- Alexandra Gruss
- INRA, UMR1319 Micalis and AgroParisTech, UMR Micalis, Jouy-en-Josas, France
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Matsumoto T, Kawakami Y, Sueki A, Kasuga E, Oana K, Horiuchi K, Kato M, Honda T. Isolation of an X-factor-dependent but porphyrin-positive Escherichia coli from urine of a patient with hemorrhagic cystitis. J Infect Chemother 2012; 19:764-6. [PMID: 23108428 DOI: 10.1007/s10156-012-0503-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 10/04/2012] [Indexed: 11/30/2022]
Abstract
An Escherichia coli isolate was recovered from a 92-year-old female patient with urinary tract infection. Gram-stained preparation of the urine sediment manifested some gram-negative rod-shaped cells, and the urine specimen culture yielded nonhemolytic colonies on sheep blood agar plate. However, no visible colonies appeared on modified Drigalski agar plate. The isolate was finally identified as an X-factor-dependent E. coli. The interesting finding was that the isolate revealed a positive reaction for porphyrin test despite the requirement of hemin. This finding suggested that some pyrrol-ring-containing porphyrin compounds or fluorescent porphyrins had been produced as chemical intermediates in the synthetic pathway from δ-amino-levulinic acid (ALA), although the isolate should be devoid of synthesizing hems from ALA. This was the first clinical isolation of such a strain, indicating that the E. coli isolate should possess incomplete synthetic pathways of hems from ALA.
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Affiliation(s)
- Takehisa Matsumoto
- Department of Laboratory Medicine, Shinshu University Hospital, Matsumoto, 390-8621, Japan
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Ambrosch A, Haefner S, Jude E, Lobmann R. Diabetic foot infections: microbiological aspects, current and future antibiotic therapy focusing on methicillin-resistant Staphylococcus aureus. Int Wound J 2011; 8:567-77. [PMID: 21883937 DOI: 10.1111/j.1742-481x.2011.00849.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Diabetic patients are at increased risk of complicated skin, skin structure and bone infections including infections of diabetic foot ulcerations (DFU). Analyses of epidemiology and microbial pathogenicity show that staphylococci seem to be predestined to induce such infections. In addition, multidrug resistance particularly due to an increasing prevalence of methicillin-resistant Staphylococcus aureus (MRSA) seems to be the challenge for effective antibiotic therapy. With regard to infections with MRSA, classical agents like vancomycin, linezolid, fosfomycin or trimethroprim-sulphametoxazol might be agents of choice in DFU. New-generation drugs including broad-spectrum tetracyclines like tigecycline, first and second generation of cyclic lipopeptides, anti-MRSA β-lactams including ceftobiprole and anti-MRSA antibodies are developed or in progress and the hope for the future.
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Affiliation(s)
- Andreas Ambrosch
- Institute of Laboratory Medicine and Microbiology, St Joseph Hospital, Bremerhaven, Germany
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Pränting M, Andersson DI. Escape from growth restriction in small colony variants of Salmonella typhimurium by gene amplification and mutation. Mol Microbiol 2010; 79:305-15. [PMID: 21219453 DOI: 10.1111/j.1365-2958.2010.07458.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Antibiotic resistance in bacteria is generally associated with fitness costs that often can be reduced by second-site compensatory mutations. Here, we examined how a protamine-resistant small colony variant of Salmonella typhimurium adapts to the growth reduction conferred by a resistance mutation in hemC (encoding a haem-biosynthesis enzyme). We show that adaptation occurs in a multi-step process where fitness is successively increased. Thus, the initial adaptive response was selection for an unstable gene amplification of the mutant hemC gene that provided a small fitness increase. Fitness was increased further by a mutation that restored HemC function in one gene copy, relaxing selection for the amplification. Subsequently, the amplification segregated back to the haploid state and even higher fitness. The end result was in most cases mutant strains with a hemC sequence different from that of the wild-type strain. These findings suggest that gene amplification facilitates adaptive evolution. A higher gene dosage increases the target size for compensatory mutations and improves fitness of the cell, thereby allowing an increase in the population size, further increasing the probability of a subsequent stable mutation. Our results provide a novel genetic basis for growth compensation in small colony variants.
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Affiliation(s)
- Maria Pränting
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23 Uppsala, Sweden
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Temperature-dependent requirement for catalase in aerobic growth of Listeria monocytogenes F2365. Appl Environ Microbiol 2010; 76:6998-7003. [PMID: 20817809 DOI: 10.1128/aem.01223-10] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Listeria monocytogenes is a Gram-positive, psychrotrophic, facultative intracellular food-borne pathogen responsible for severe illness (listeriosis). The bacteria can grow in a wide range of temperatures (1 to 45°C), and low-temperature growth contributes to the food safety hazards associated with contamination of ready-to-eat foods with this pathogen. To assess the impact of oxidative stress responses on the ability of L. monocytogenes to grow at low temperatures and to tolerate repeated freeze-thaw stress (cryotolerance), we generated and characterized a catalase-deficient mutant of L. monocytogenes F2365 harboring a mariner-based transposon insertion in the catalase gene (kat). When grown aerobically on blood-free solid medium, the kat mutant exhibited impaired growth, with the extent of impairment increasing with decreasing temperature, and no growth was detected at 4°C. Aerobic growth in liquid was impaired at 4°C, especially under aeration, but not at higher temperatures (10, 25, or 37°C). Genetic complementation of the mutant with the intact kat restored normal growth, confirming that inactivation of this gene was responsible for the growth impairment. In spite of the expected impact of oxidative stress responses on cryotolerance, cryotolerance of the kat mutant was not affected.
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Escherichia coli variants in periprosthetic joint infection: diagnostic challenges with sessile bacteria and sonication. J Clin Microbiol 2010; 48:1720-5. [PMID: 20335421 DOI: 10.1128/jcm.01562-09] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The diagnostic yield of prosthetic joint-associated infection is hampered by the phenotypic change of bacteria into a sessile and resistant form, also called biofilm. With sonication, adherent bacteria can be dislodged from the prosthesis. Species identification may be difficult because of their variations in phenotypic appearance and biochemical reaction. We have studied the phenotypic, genotypic, and biochemical properties of Escherichia coli variants isolated from a periprosthetic joint infection. The strains were collected from synovial fluid, periprosthetic tissue, and fluid from the explanted and sonicated prosthesis. Isolates from synovial fluid revealed a normal phenotype, whereas a few variants from periprosthetic tissue and all isolates from sonication fluid showed different morphological features (including small-colony variants). All isolates from sonication fluid were beta-galactosidase negative and nonmotile; most were indole negative. Because of further variations in biochemical properties, species identification was false or not possible in 50% of the isolates included in this study. In contrast to normal phenotypes, variants were resistant to aminoglycosides. Typing of the isolates using pulsed-field gel electrophoresis yielded nonidentical banding patterns, but all strains were assigned to the same clonal origin when compared with 207 unrelated E. coli isolates. The bacteria were repeatedly passaged on culture media and reanalyzed. Thereafter, most variants reverted to normal phenotype and regained their motility and certain biochemical properties. In addition, some variants displayed aminoglycoside susceptibility after reversion. Sonication of an explanted prosthesis allows insight into the lifestyle of bacteria in biofilms. Since sonication fluid also reveals dislodged sessile forms, species identification of such variants may be misleading.
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To KKW, Cheng VCC, Tang BSF, Fan YW, Yuen KY. False-negative cerebrospinal fluid cryptococcal antigen test due to small-colony variants of Cryptococcus neoformans meningitis in a patient with cystopleural shunt. ACTA ACUST UNITED AC 2009; 38:1110-4. [PMID: 17148090 DOI: 10.1080/00365540600664118] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
This is the first report of a small-colony variant Cryptococcus neoformans isolated from the cerebrospinal fluid of a patient with cystopleural shunt associated chronic meningitis. Cryptococcal antigen testing of the cerebrospinal fluid and the serum were both negative. The atypical morphology and the false-negative test may lead to delay of diagnosis and treatment.
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Affiliation(s)
- Kelvin K W To
- Research Centre of Infection and Immunology, Queen Mary Hospital, The University of Hong Kong, China
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Specific distribution within the Enterobacter cloacae complex of strains isolated from infected orthopedic implants. J Clin Microbiol 2009; 47:2489-95. [PMID: 19515837 DOI: 10.1128/jcm.00290-09] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Bacteria belonging to the Enterobacter genus are frequently isolated from clinical samples but are unusual causative agents of orthopedic implant infections. Twelve genetic clusters (clusters I to XII) and one sequence crowd (sequence crowd xiii) can be distinguished within the Enterobacter cloacae nomenspecies on the basis of hsp60 sequence analysis, and until now, none of these clusters could be specifically associated with a disease. In order to investigate if specific genetic clusters would be involved in infections of orthopedic material, two series of bacterial clinical isolates identified as E. cloacae by routine phenotypic identification methods were collected either from infected orthopedic implants (n = 21) or from randomly selected samples of diverse anatomical origins (control; n = 52). Analysis of the hsp60 gene showed that genetic clusters III, VI, and VIII were the most frequent genetic clusters detected in the control group, whereas cluster III was poorly represented among the orthopedic implant isolates (P = 0.006). On the other hand, E. hormaechei (clusters VI and VIII), but not cluster III, is predominantly associated with infections of orthopedic implants and, more specifically, with infected material in the hip (P = 0.019). These results support the hypothesis that, among the isolates within the E. cloacae complex, E. hormaechei and hsp60 gene sequencing-based cluster III are involved in pathogenesis in different ways and highlight the need for more accurate routine Enterobacter identification methods.
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Vandercam B, Jeumont S, Cornu O, Yombi JC, Lecouvet F, Lefèvre P, Irenge LM, Gala JL. Amplification-based DNA analysis in the diagnosis of prosthetic joint infection. J Mol Diagn 2008; 10:537-43. [PMID: 18832459 DOI: 10.2353/jmoldx.2008.070137] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Microbiological cultures are moderately sensitive for diagnosing prosthetic joint infection (PJI). This study was conducted to determine whether amplification-based DNA methods applied on intraoperative samples could enhance PJI diagnosis compared with culture alone in routine surgical practice. Revision arthroplasty was performed for suspected PJI (n = 41) and osteoarthrosis control (n = 28) patients, and a diagnosis of PJI was confirmed in 34 patients. Amplification by polymerase chain reaction was performed on both 16S ribosomal DNA universal target genes and femA Staphylococcus-specific target genes. Species identification was achieved through amplicon sequencing. Amplification of the femA gene led to subsequent testing for methicillin resistance by amplification of the mecA gene. Microbiological and molecular assays identified a causative organism in 22 of 34 patients (64.7%) and in 31 of 34 patients (91.2%), respectively. In 18 of the 22 culture-positive patients, molecular and microbiological results were concordant for bacterial genus, species, and/or methicillin resistance. Bacterial agents were identified only by molecular methods in nine PJI patients, including seven who were receiving antibiotics at the time of surgery and one with recent but not concomitant antibiotherapy. DNA-based methods were found to effectively complement microbiological methods, without interfering with existing procedures for sample collection, for the identification of causative pathogens from intraoperative PJI samples, especially in patients with recent or concomitant antibiotherapy.
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Affiliation(s)
- Bernard Vandercam
- Division of Infectious Diseases, St-Luc's University Hospital, Université catholique de Louvain, Brussels, Belgium
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Abstract
Biofilms are communal structures of microorganisms encased in an exopolymeric coat that form on both natural and abiotic surfaces and have been associated with a variety of persistent infections that respond poorly to conventional antibiotic chemotherapy. Biofilm infections of certain indwelling medical devices by common pathogens such as staphylococci are not only associated with increased morbidity and mortality but are also significant contributors to the emergence and dissemination of antibiotic resistance traits in the nosocomial setting. Current treatment paradigms for biofilm-associated infections of semipermanent indwelling devices typically involve surgical replacement of the device combined with long-term antibiotic therapy and incur high health care costs. This review summarizes the existing data relating to the nature, prevalence, and treatment of biofilm-associated infections and highlights experimental approaches and therapies that are being pursued toward more effective treatments.
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Affiliation(s)
- A Simon Lynch
- Cumbre Pharmaceuticals Inc., Dallas, Texas 75235-2304, USA.
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Genetic and phenotypic identification of fusidic acid-resistant mutants with the small-colony-variant phenotype in Staphylococcus aureus. Antimicrob Agents Chemother 2007; 51:4438-46. [PMID: 17923494 DOI: 10.1128/aac.00328-07] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Small-colony variants (SCVs) of Staphylococcus aureus are a slow-growing subpopulation whose phenotypes can include resistance to aminoglycosides, defects in electron transport, and enhanced persistence in mammalian cells. Here we show that a subset of mutants selected as SCVs by reduced susceptibility to aminoglycosides are resistant to the antibiotic fusidic acid (FA) and conversely that a subset of mutants selected for resistance to FA are SCVs. Mutation analysis reveals different genetic classes of FA-resistant SCVs. One class, FusA-SCVs, have amino acid substitution mutations in the ribosomal translocase EF-G different from those found in classic FusA mutants. Most of these mutations are located in structural domain V of EF-G, but some are in domain I or III. FusA-SCVs are auxotrophic for hemin. A second class of FA-resistant SCVs carry mutations in rplF, coding for ribosomal protein L6, and are designated as FusE mutants. FusE mutants fall into two phenotypic groups: one auxotrophic for hemin and the other auxotrophic for menadione. Accordingly, we have identified new genetic and phenotypic classes of FA-resistant mutants and clarified the genetic basis of a subset of S. aureus SCV mutants. A clinical implication of these data is that FA resistance could be selected by antimicrobial agents other than FA.
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Abstract
Recent advances have defined risk factors for orthopaedic implant infections that suggest modifications in the clinical care of certain patients. For diagnosis, new work shows the importance of obtaining multiple specimens for culture, and the enlarging spectrum of causative organisms. The potential for the polymerase chain reaction is demonstrated. In treatment, the value of rifampicin is shown in controlled and open trials.
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Affiliation(s)
- P J Sanderson
- Barnet and Chase Farm Hospitals NHS Trust, Barnet General Hospital, Wellhouse Lane, Barnet, Herts EN5 3DJ, UK
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Neut D, van der Mei HC, Bulstra SK, Busscher HJ. The role of small-colony variants in failure to diagnose and treat biofilm infections in orthopedics. Acta Orthop 2007; 78:299-308. [PMID: 17611841 DOI: 10.1080/17453670710013843] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Biomaterial-related infection of joint replacements is the second most common cause of implant failure, with serious consequences. Chronically infected replacements cannot be treated without removal of the implant, as the biofilm mode of growth protects the bacteria against antibiotics. This review discusses biofilm formation on joint replacements and the important clinical phenomenon of small-colony variants (SCVs). These slow-growing phenotypic variants often remain undetected or are misdiagnosed using hospital microbiological analyses due to their unusual morphological appearance and biochemical reactions. In addition, SCVs make the infection difficult to eradicate. They often lead to recurrence since they respond poorly to standard antibiotic treatment and can sometimes survive intracellularly.
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Affiliation(s)
- Daniëlle Neut
- Department of Biomedical Engineering, University Medical Center Groningen, and University of Groningen, Groningen, the Netherlands.
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Tappe D, Claus H, Kern J, Marzinzig A, Frosch M, Abele-Horn M. First case of febrile bacteremia due to a wild type and small-colony variant of Escherichia coli. Eur J Clin Microbiol Infect Dis 2007; 25:31-4. [PMID: 16418831 DOI: 10.1007/s10096-005-0072-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Reported here is a case of a febrile illness caused by a wild type and small-colony variant of Escherichia coli in an anorectic patient. A review of the literature revealed that the formation of small-colony variants in E. coli has been recognized since 1931. In recent years, an association has been established between those variants and chronic recurrent infections. This report describes for the first time the isolation of an E. coli small-colony variant from a blood culture of a patient who had suffered from chronic urinary tract infections in the past.
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Affiliation(s)
- D Tappe
- Institute of Hygiene and Microbiology, Josef-Schneider-Strasse 2, 97080 Würzburg, Germany.
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Seggewiss J, Becker K, Kotte O, Eisenacher M, Yazdi MRK, Fischer A, McNamara P, Al Laham N, Proctor R, Peters G, Heinemann M, von Eiff C. Reporter metabolite analysis of transcriptional profiles of a Staphylococcus aureus strain with normal phenotype and its isogenic hemB mutant displaying the small-colony-variant phenotype. J Bacteriol 2006; 188:7765-77. [PMID: 16980462 PMCID: PMC1636313 DOI: 10.1128/jb.00774-06] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
In this study, full-genome DNA microarrays based on the sequence of Staphylococcus aureus N315 were used to compare the transcriptome of a clinical S. aureus strain with a normal phenotype to that of its isogenic mutant with a stable small-colony-variant (SCV) phenotype (hemB::ermB). In addition to standard statistical analyses, systems biology advances were applied to identify reporter metabolites and to achieve a more detailed survey of genome-wide expression differences between the hemB mutant and its parental strain. Genes of enzymes involved in glycolytic and fermentative pathways were found to be up-regulated in the hemB mutant. Furthermore, our analyses allowed identification of additional differences between the normal-phenotype S. aureus and the SCV, most of which were related to metabolism. Profound differences were identified especially in purine biosynthesis as well as in arginine and proline metabolism. Of particular interest, a hypothetical gene of the Crp/Fnr family (SA2424) that is part of the arginine-deiminase (AD) pathway, whose homologue in Streptococcus suis is assumed to be involved in intracellular persistence, showed significantly increased transcription in the hemB mutant. The hemB mutant potentially uses the up-regulated AD pathway to produce ATP or (through ammonia production) to counteract the acidic environment that prevails intracellularly. Moreover, genes involved in capsular polysaccharide and cell wall synthesis were found to be significantly up-regulated in the hemB mutant and therefore potentially responsible for the changed cell morphology of SCVs. In conclusion, the identified differences may be responsible for the SCV phenotype and its association with chronic and persistent infections.
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Affiliation(s)
- Jochen Seggewiss
- Institute of Medical Microbiology, University Hospital of Münster, Domagkstrasse 10, 48149 Münster, Germany
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Proctor RA, von Eiff C, Kahl BC, Becker K, McNamara P, Herrmann M, Peters G. Small colony variants: a pathogenic form of bacteria that facilitates persistent and recurrent infections. Nat Rev Microbiol 2006; 4:295-305. [PMID: 16541137 DOI: 10.1038/nrmicro1384] [Citation(s) in RCA: 791] [Impact Index Per Article: 43.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Small colony variants constitute a slow-growing subpopulation of bacteria with distinctive phenotypic and pathogenic traits. Phenotypically, small colony variants have a slow growth rate, atypical colony morphology and unusual biochemical characteristics, making them a challenge for clinical microbiologists to identify. Clinically, small colony variants are better able to persist in mammalian cells and are less susceptible to antibiotics than their wild-type counterparts, and can cause latent or recurrent infections on emergence from the protective environment of the host cell. This Review covers the phenotypic, genetic and clinical picture associated with small colony variants, with an emphasis on staphylococci, for which the greatest amount of information is available.
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Affiliation(s)
- Richard A Proctor
- University of Wisconsin Medical School, 436 SMI, 1300 University Avenue, Madison, Wisconsin 53706, USA.
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Rea R, Hill C, Gahan CGM. Listeria monocytogenes PerR mutants display a small-colony phenotype, increased sensitivity to hydrogen peroxide, and significantly reduced murine virulence. Appl Environ Microbiol 2006; 71:8314-22. [PMID: 16332818 PMCID: PMC1317367 DOI: 10.1128/aem.71.12.8314-8322.2005] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Deletion of perR in Listeria monocytogenes results in a small-colony phenotype (DeltaperRsm) that is slow growing and exhibits increased sensitivity to H2O2. At a relatively high frequency, large-colony variants (DeltaperRlg) arise, which are more resistant to H2O2 than the wild-type and ultimately dominate the culture. Transcriptional analysis revealed that the kat gene (catalase) is up-regulated in both types of mutants and that the highest level is apparent in DeltaperRsm mutants, demonstrating PerR regulation of this gene. Overexpression of the catalase gene in the wild-type background resulted in a slower-growing strain with a smaller colony size similar to that of DeltaperRsm. By combining a bioinformatic approach with experimental evidence, other PerR-regulated genes were identified, including fur, lmo0641, fri, lmo1604, hemA, and trxB. The transcriptional profile of these genes in both mutant backgrounds was similar to that of catalase in that a higher level of expression was observed in DeltaperRsm than in the wild type or DeltaperRlg. Murine studies revealed that the virulence potential of the DeltaperRsm mutant is substantially reduced compared to that of the wild-type and DeltaperRlg strains. Collectively, the data demonstrate that the DeltaperRsm mutant represents the true phenotype associated with the absence of PerR, which is linked to overexpression of regulated genes that negatively affect bacterial homeostasis both in vitro and in vivo. A subsequent secondary mutation occurred at a high frequency, which resulted in phenotypic reversion to a large-colony phenotype with increased fitness that may have obstructed the analysis of the role of PerR in the physiology of the bacterial cell.
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Affiliation(s)
- Rosemarie Rea
- Department of Microbiology, University College Cork, Cork, Ireland
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Neut D, Hendriks JGE, van Horn JR, van der Mei HC, Busscher HJ. Pseudomonas aeruginosa biofilm formation and slime excretion on antibiotic-loaded bone cement. Acta Orthop 2005; 76:109-14. [PMID: 15788318 DOI: 10.1080/00016470510030427] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Infection is an infrequent but serious complication of prosthetic joint surgery. These infections will usually not clear until the implant is removed and re-implantation has a high failure rate, especially when Pseudomonas aeruginosa is involved. MATERIAL AND METHODS We examined Pseudomonas aeruginosa biofilm formation on plain and gentamicin-loaded bone cement with confocal scanning laser microscopy (CSLM). Two different stains were applied in order to visualize and quantify the distribution of bacterial cells and extracellular polymeric substances (slime) from the bone cement surface to the top of the biofilm. Staining with LIVE/DEAD viability stain differentiated between live and dead bacteria within the biofilm, and slime production was evaluated after staining with Calcofluor white. RESULTS CSLM showed that the biofilm was a nonuniform structure of variable thickness, with differences in local bacterial cell and slime densities. Incorporation of gentamicin in bone cement resulted in a 44% reduction in bacterial viability, while the slime density increased significantly. In addition, conventional plate counting showed the development of small-colony variants on gentamicin-loaded bone cement with a decreased sensitivity for gentamicin (MIC: 8 m/L), as compared with normal-sized colonies taken from plain and gentamicin-loaded bone cement (MIC: 3 m/L). The enhanced slime production on antibiotic-loaded bone cement, together with the formation of small-colony variants, resulted in decreased susceptibility to antibiotics--probably concomitant with the onset of persistent and relapsing infections. INTERPRETATION In the clinical situation, our findings help to explain the frequent re-implantation failure of joint replacements infected with P. aeruginosa when the procedure has been performed using antibiotic-loaded bone cement.
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Affiliation(s)
- Daniëlle Neut
- Department of Biomedical Engineering, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
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