1
|
Shifflett SA, Wiedmeyer T, Kennedy A, Maestas L, Buoni M, Ciloglu A, Ellis VA. Prevalence of Borrelia burgdorferi and diversity of its outer surface protein C (ospC) alleles in blacklegged ticks (Ixodes scapularis) in Delaware. Ticks Tick Borne Dis 2023; 14:102139. [PMID: 36780839 PMCID: PMC10033352 DOI: 10.1016/j.ttbdis.2023.102139] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/27/2023] [Accepted: 02/03/2023] [Indexed: 02/13/2023]
Abstract
Characterizing the diversity of genes associated with virulence and transmission of a pathogen across the pathogen's distribution can inform our understanding of host infection risk. Borrelia burgdorferi is a vector-borne bacterium that causes Lyme disease in humans and is common in the United States. The outer surface protein C (ospC) gene of B. burgdorferi exhibits substantial genetic variation across the pathogen's distribution and plays a critical role in virulence and transmission in vertebrate hosts. In fact, B. burgdorferi infections that disseminate across host tissues in humans are associated with only a subset of ospC alleles. Delaware has a high incidence of Lyme disease, but the diversity of ospC in B. burgdorferi in the state has not been evaluated. We used PCR to amplify ospC in B. burgdorferi-infected blacklegged ticks (Ixodes scapularis) in sites statewide and used short-read sequencing to identify ospC alleles. B. burgdorferi prevalence in blacklegged ticks varied across sites, but not significantly so. We identified 15 previously characterized ospC alleles accounting for nearly all of the expected diversity of alleles across the sites as estimated using the Chao1 index. Nearly 40% of sequenced infections (23/58) had more than one ospC allele present suggesting mixed strain infections and the relative frequencies of alleles in single infections were positively correlated with their relative frequencies in mixed infections. Turnover of ospC alleles was positively related to distance between sites with closer sites having more similar allele compositions than more distant sites. This suggests a degree of B. burgdorferi dispersal limitation or habitat specialization. OspC alleles known to cause disseminated infections in humans were found at the highest frequencies across sites, corresponding to Delaware's high incidence of Lyme disease.
Collapse
Affiliation(s)
- Scarlet A Shifflett
- Department of Entomology and Wildlife Ecology, University of Delaware, Newark, DE, USA
| | - Tyler Wiedmeyer
- Department of Entomology and Wildlife Ecology, University of Delaware, Newark, DE, USA
| | - Ashley Kennedy
- Mosquito Control Section, Division of Fish & Wildlife, Delaware Department of Natural Resources and Environmental Control, DE, USA
| | - Lauren Maestas
- Mosquito Control Section, Division of Fish & Wildlife, Delaware Department of Natural Resources and Environmental Control, DE, USA; Cattle Fever Tick Research Laboratory, USDA, Agricultural Research Service, Edinburg, TX, USA
| | - Michael Buoni
- Delaware Technical Community College, Georgetown, DE, USA; Department of Medical and Molecular Sciences, University of Delaware, Newark, DE, USA
| | - Arif Ciloglu
- Department of Parasitology, Faculty of Veterinary Medicine, Erciyes University, Kayseri, Türkiye; Vectors and Vector-Borne Diseases Implementation and Research Center, Erciyes University, Kayseri, Türkiye
| | - Vincenzo A Ellis
- Department of Entomology and Wildlife Ecology, University of Delaware, Newark, DE, USA.
| |
Collapse
|
2
|
Shlaes DM, Bradford PA. Antibiotics-From There to Where?: How the antibiotic miracle is threatened by resistance and a broken market and what we can do about it. Pathog Immun 2018; 3:19-43. [PMID: 30993248 PMCID: PMC6423724 DOI: 10.20411/pai.v3i1.231] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 02/18/2018] [Indexed: 12/15/2022] Open
Abstract
To fully appreciate the importance of antibiotics to everyday life, we must step back to the edge of the pre-antibiotic era when these lifesaving drugs were first introduced into clinical use.
Collapse
Affiliation(s)
- David M. Shlaes
- Anti-infectives Consulting (retired), Stonington, Connecticut
| | | |
Collapse
|
3
|
Fleming-Davies AE, Dukic V, Andreasen V, Dwyer G. Effects of host heterogeneity on pathogen diversity and evolution. Ecol Lett 2015; 18:1252-1261. [PMID: 26365355 PMCID: PMC10425259 DOI: 10.1111/ele.12506] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 06/28/2015] [Accepted: 08/10/2015] [Indexed: 11/29/2022]
Abstract
Phenotypic variation is common in most pathogens, yet the mechanisms that maintain this diversity are still poorly understood. We asked whether continuous host variation in susceptibility helps maintain phenotypic variation, using experiments conducted with a baculovirus that infects gypsy moth (Lymantria dispar) larvae. We found that an empirically observed tradeoff between mean transmission rate and variation in transmission, which results from host heterogeneity, promotes long-term coexistence of two pathogen types in simulations of a population model. This tradeoff introduces an alternative strategy for the pathogen: a low-transmission, low-variability type can coexist with the high-transmission type favoured by classical non-heterogeneity models. In addition, this tradeoff can help explain the extensive phenotypic variation we observed in field-collected pathogen isolates, in traits affecting virus fitness including transmission and environmental persistence. Similar heterogeneity tradeoffs might be a general mechanism promoting phenotypic variation in any pathogen for which hosts vary continuously in susceptibility.
Collapse
Affiliation(s)
- Arietta E. Fleming-Davies
- Department of Ecology & Evolution, University of Chicago, 900 E 57th St, Chicago, IL 60637, USA
- Biology Department, Radford University, PO BOX 6931, Radford, VA 24141, USA
| | - Vanja Dukic
- Department of Applied Mathematics, University of Colorado, 526 UCB, Boulder, CO 80309, USA
| | - Viggo Andreasen
- Department of Science, Systems and Models, Roskilde University, Universitetsvej 1, DK-4000 Roskilde, Denmark
| | - Greg Dwyer
- Department of Ecology & Evolution, University of Chicago, 900 E 57th St, Chicago, IL 60637, USA
| |
Collapse
|
4
|
Yao X, Chen T, Shen X, Zhao Y, Wang M, Rao X, Yin S, Wang J, Gong Y, Lu S, Le S, Tan Y, Tang J, Fuquan H, Li M. The chromosomal SezAT toxin-antitoxin system promotes the maintenance of the SsPI-1 pathogenicity island in epidemic Streptococcus suis. Mol Microbiol 2015; 98:243-57. [PMID: 26138696 DOI: 10.1111/mmi.13116] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/02/2015] [Indexed: 01/15/2023]
Abstract
Streptococcus suis has emerged as a causative agent of human meningitis and streptococcal toxic shock syndrome over the last years. The high pathogenicity of S. suis may be due in part to a laterally acquired pathogenicity island (renamed SsPI-1), which can spontaneously excise and transfer to recipients. Cells harboring excised SsPI-1 can potentially lose this island if cell division occurs prior to its reintegration; however, attempts to cure SsPI-1 from the host cells have been unsuccessful. Here, we report that an SsPI-1-borne Epsilon/Zeta toxin-antitoxin system (designated SezAT) promotes SsPI-1 stability in bacterial populations. The sezAT locus consists of two closely linked sezT and sezA genes encoding a toxin and its cognate antitoxin, respectively. Overproduction of SezT induces a bactericidal effect that can be neutralized by co-expression of SezA, but not by its later action. When devoid of a functional SezAT system, large-scale deletion of SsPI-1 is straightforward. Thus, SezAT serves to ensure inheritance of SsPI-1 during cell division, which may explain the persistence of epidemic S. suis. This report presents the first functional characterization of TA loci in S. suis, and the first biochemical evidence for the adaptive significance of the Epsilon/Zeta system in the evolution of pathogen virulence.
Collapse
Affiliation(s)
- Xinyue Yao
- Department of Microbiology, Third Military Medical University, Chongqing, 400038, China
| | - Tian Chen
- Department of Microbiology, Third Military Medical University, Chongqing, 400038, China
| | - Xiaodong Shen
- Department of Biochemistry and Molecular Biology, Third Military Medical University, Chongqing, 400038, China
| | - Yan Zhao
- Department of Microbiology, Third Military Medical University, Chongqing, 400038, China
| | - Min Wang
- Department of Microbiology, Third Military Medical University, Chongqing, 400038, China
| | - Xiancai Rao
- Department of Microbiology, Third Military Medical University, Chongqing, 400038, China
| | - Supeng Yin
- Department of Microbiology, Third Military Medical University, Chongqing, 400038, China
| | - Jing Wang
- Department of Microbiology, Third Military Medical University, Chongqing, 400038, China
| | - Yali Gong
- Department of Microbiology, Third Military Medical University, Chongqing, 400038, China
| | - Shuguang Lu
- Department of Microbiology, Third Military Medical University, Chongqing, 400038, China
| | - Shuai Le
- Department of Microbiology, Third Military Medical University, Chongqing, 400038, China
| | - Yinling Tan
- Department of Microbiology, Third Military Medical University, Chongqing, 400038, China
| | - Jiaqi Tang
- PLA Research Institute of Clinical Laboratory Medicine, Nanjing General Hospital of Nanjing Military Command, Nanjing, 210002, China
| | - Hu Fuquan
- Department of Microbiology, Third Military Medical University, Chongqing, 400038, China
| | - Ming Li
- Department of Microbiology, Third Military Medical University, Chongqing, 400038, China
| |
Collapse
|
5
|
Chalmers G, McLean J, Hunter DB, Brash M, Slavic D, Pearl DL, Boerlin P. Staphylococcus spp., Streptococcus canis, and Arcanobacterium phocae of healthy Canadian farmed mink and mink with pododermatitis. CANADIAN JOURNAL OF VETERINARY RESEARCH = REVUE CANADIENNE DE RECHERCHE VETERINAIRE 2015; 79:129-135. [PMID: 25852228 PMCID: PMC4365704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 05/30/2014] [Indexed: 06/04/2023]
Abstract
Pododermatitis is a disease of concern for mink breeders in Canada and worldwide, as it causes discomfort and lowers the breeding rates on farms affected by the disease. Unfortunately, the etiology and pathogenesis of pododermatitis are still unknown. In this study, we compared Staphylococcus spp. and Streptococcus canis isolates from healthy mink with isolates from animals with pododermatitis on 2 farms in Ontario. Almost all hemolytic Staphylococcus spp. isolated were shown to be Staphylococcus delphini Group A by 16S ribosomal ribonucleic acid (rRNA) sequence analysis and polymerase chain reaction (PCR). Pulsed-field gel electrophoresis (PFGE) did not reveal any S. delphini or S. canis clonal lineages specifically associated with pododermatitis, which suggests that these bacteria do not act as primary pathogens, but does not dismiss their potential roles as opportunistic pathogens. While S. delphini and S. canis were the most prevalent bacterial pathogens in mink pododermatitis, they were also present in samples from healthy mink. Arcanobacterium phocae is occasionally isolated from pododermatitis cases, but is difficult to recover with conventional culture methods due to its slow growth. A quantitative real-time PCR was developed for the detection of A. phocae and was tested on 138 samples of footpad tissues from 14 farms. The bacterium was detected only in pododermatitis-endemic farms in Canada and was at higher concentrations in tissues from infected footpads than in healthy tissues. This finding suggests that A. phocae is involved in the pathogenesis of pododermatitis.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Patrick Boerlin
- Address all correspondence to Dr. Patrick Boerlin; telephone: (519) 824-4120, ext. 54647; fax: (519) 824-5930; e-mail:
| |
Collapse
|
6
|
Thrall PH, Oakeshott JG, Fitt G, Southerton S, Burdon JJ, Sheppard A, Russell RJ, Zalucki M, Heino M, Ford Denison R. Evolution in agriculture: the application of evolutionary approaches to the management of biotic interactions in agro-ecosystems. Evol Appl 2015; 4:200-15. [PMID: 25567968 PMCID: PMC3352559 DOI: 10.1111/j.1752-4571.2010.00179.x] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Accepted: 11/30/2010] [Indexed: 01/04/2023] Open
Abstract
Anthropogenic impacts increasingly drive ecological and evolutionary processes at many spatio-temporal scales, demanding greater capacity to predict and manage their consequences. This is particularly true for agro-ecosystems, which not only comprise a significant proportion of land use, but which also involve conflicting imperatives to expand or intensify production while simultaneously reducing environmental impacts. These imperatives reinforce the likelihood of further major changes in agriculture over the next 30–40 years. Key transformations include genetic technologies as well as changes in land use. The use of evolutionary principles is not new in agriculture (e.g. crop breeding, domestication of animals, management of selection for pest resistance), but given land-use trends and other transformative processes in production landscapes, ecological and evolutionary research in agro-ecosystems must consider such issues in a broader systems context. Here, we focus on biotic interactions involving pests and pathogens as exemplars of situations where integration of agronomic, ecological and evolutionary perspectives has practical value. Although their presence in agro-ecosystems may be new, many traits involved in these associations evolved in natural settings. We advocate the use of predictive frameworks based on evolutionary models as pre-emptive management tools and identify some specific research opportunities to facilitate this. We conclude with a brief discussion of multidisciplinary approaches in applied evolutionary problems.
Collapse
Affiliation(s)
| | | | - Gary Fitt
- CSIRO Ecosystem Sciences Indooroopilly, Qld, Australia
| | | | | | | | | | - Myron Zalucki
- The University of Queensland, School of Integrative Biology Qld, Australia
| | - Mikko Heino
- Department of Biology, University of Bergen Bergen, Norway
| | - R Ford Denison
- University of Minnesota, Ecology, Evolution, and Behavior St. Paul, MN, USA
| |
Collapse
|
7
|
Contreras A, Moreno SM, Jaramillo A, Pelaez M, Duque A, Botero JE, Slots J. Periodontal microbiology in Latin America. Periodontol 2000 2014; 67:58-86. [DOI: 10.1111/prd.12074] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/14/2014] [Indexed: 12/19/2022]
|
8
|
Insertion sequence element single nucleotide polymorphism typing provides insights into the population structure and evolution of Mycobacterium ulcerans across Africa. Appl Environ Microbiol 2013; 80:1197-209. [PMID: 24296504 DOI: 10.1128/aem.02774-13] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Buruli ulcer is an indolent, slowly progressing necrotizing disease of the skin caused by infection with Mycobacterium ulcerans. In the present study, we applied a redesigned technique to a vast panel of M. ulcerans disease isolates and clinical samples originating from multiple African disease foci in order to (i) gain fundamental insights into the population structure and evolutionary history of the pathogen and (ii) disentangle the phylogeographic relationships within the genetically conserved cluster of African M. ulcerans. Our analyses identified 23 different African insertion sequence element single nucleotide polymorphism (ISE-SNP) types that dominate in different areas where Buruli ulcer is endemic. These ISE-SNP types appear to be the initial stages of clonal diversification from a common, possibly ancestral ISE-SNP type. ISE-SNP types were found unevenly distributed over the greater West African hydrological drainage basins. Our findings suggest that geographical barriers bordering the basins to some extent prevented bacterial gene flow between basins and that this resulted in independent focal transmission clusters associated with the hydrological drainage areas. Different phylogenetic methods yielded two well-supported sister clades within the African ISE-SNP types. The ISE-SNP types from the "pan-African clade" were found to be widespread throughout Africa, while the ISE-SNP types of the "Gabonese/Cameroonian clade" were much rarer and found in a more restricted area, which suggested that the latter clade evolved more recently. Additionally, the Gabonese/Cameroonian clade was found to form a strongly supported monophyletic group with Papua New Guinean ISE-SNP type 8, which is unrelated to other Southeast Asian ISE-SNP types.
Collapse
|
9
|
Abstract
Acute apical abscess is the most common form of dental abscess and is caused by infection of the root canal of the tooth. It is usually localized intraorally, but in some cases the apical abscess may spread and result in severe complications or even mortality. The reasons why dental root canal infections can become symptomatic and evolve to severe spreading and sometimes life-threatening abscesses remain elusive. Studies using culture and advanced molecular microbiology methods for microbial identification in apical abscesses have demonstrated a multispecies community conspicuously dominated by anaerobic bacteria. Species/phylotypes commonly found in these infections belong to the genera Fusobacterium, Parvimonas, Prevotella, Porphyromonas, Dialister, Streptococcus, and Treponema. Advances in DNA sequencing technologies and computational biology have substantially enhanced the knowledge of the microbiota associated with acute apical abscesses and shed some light on the etiopathogeny of this disease. Species richness and abundance and the resulting network of interactions among community members may affect the collective pathogenicity and contribute to the development of acute infections. Disease modifiers, including transient or permanent host-related factors, may also influence the development and severity of acute abscesses. This review focuses on the current evidence about the etiology and treatment of acute apical abscesses and how the process is influenced by host-related factors and proposes future directions in research, diagnosis, and therapeutic approaches to deal with this disease.
Collapse
|
10
|
Macrophages in tuberculosis: friend or foe. Semin Immunopathol 2013; 35:563-83. [PMID: 23864058 DOI: 10.1007/s00281-013-0388-2] [Citation(s) in RCA: 186] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 06/20/2013] [Indexed: 12/14/2022]
Abstract
Tuberculosis (TB) remains one of the greatest threats to human health. The causative bacterium, Mycobacterium tuberculosis (Mtb), is acquired by the respiratory route. It is exquisitely human adapted and a prototypic intracellular pathogen of macrophages, with alveolar macrophages (AMs) being the primary conduit of infection and disease. The outcome of primary infection is most often a latently infected healthy human host, in whom the bacteria are held in check by the host immune response. Such individuals can develop active TB later in life with impairment in the immune system. In contrast, in a minority of infected individuals, the host immune response fails to control the growth of bacilli, and progressive granulomatous disease develops, facilitating spread of the bacilli via infectious aerosols coughed out into the environment and inhaled by new hosts. The molecular details of the Mtb-macrophage interaction continue to be elucidated. However, it is clear that a number of complex processes are involved at the different stages of infection that may benefit either the bacterium or the host. Macrophages demonstrate tremendous phenotypic heterogeneity and functional plasticity which, depending on the site and stage of infection, facilitate the diverse outcomes. Moreover, host responses vary depending on the specific characteristics of the infecting Mtb strain. In this chapter, we describe a contemporary view of the behavior of AMs and their interaction with various Mtb strains in generating unique immunologic lung-specific responses.
Collapse
|
11
|
Diversity of Enterococcus cecorum from chickens. Vet Microbiol 2012; 157:405-11. [DOI: 10.1016/j.vetmic.2012.01.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Revised: 11/25/2011] [Accepted: 01/02/2012] [Indexed: 11/18/2022]
|
12
|
GUPTA BHAVNA, SRIVASTAVA NALINI, DAS APARUP. Inferring the evolutionary history of IndianPlasmodium vivaxfrom population genetic analyses of multilocus nuclear DNA fragments. Mol Ecol 2012; 21:1597-616. [DOI: 10.1111/j.1365-294x.2012.05480.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
13
|
|
14
|
Bevivino A, Costa B, Cantale C, Cesarini S, Chiarini L, Tabacchioni S, Caballero-Mellado J, Dalmastri C. Genetic relationships among Italian and Mexican maize-rhizosphere Burkholderia cepacia complex (BCC) populations belonging to Burkholderia cenocepacia IIIB and BCC6 group. BMC Microbiol 2011; 11:228. [PMID: 21995705 PMCID: PMC3377929 DOI: 10.1186/1471-2180-11-228] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Accepted: 10/13/2011] [Indexed: 11/25/2022] Open
Abstract
Background A close association between maize roots and Burkholderia cepacia complex (BCC) bacteria has been observed in different locations globally. In this study we investigated by MultiLocus Restriction Typing (MLRT) the genetic diversity and relationships among Burkholderia cenocepacia IIIB and BCC6 populations associated with roots of maize plants cultivated in geographically distant countries (Italy and Mexico), in order to provide new insights into their population structure, evolution and ecology. Results The 31 B. cenocepacia IIIB and 65 BCC6 isolates gave rise to 29 and 39 different restriction types (RTs), respectively. Two pairs of isolates of B. cenocepacia IIIB and BCC6, recovered from both Italian and Mexican maize rhizospheres, were found to share the same RT. The eBURST (Based Upon Related Sequence Types) analysis of MLRT data grouped all the B. cenocepacia IIIB isolates into four clonal complexes, with the RT-4-complex including the 42% of them, while the majority of the BCC6 isolates (94%) were grouped into the RT-104-complex. These two main clonal complexes included RTs shared by both Italian and Mexican maize rhizospheres and a clear relationship between grouping and maize variety was also found. Grouping established by eBURST correlated well with the assessment using unweighted-pair group method with arithmetic mean (UPGMA). The standardized index of association values obtained in both B. cenocepacia IIIB and BCC6 suggests an epidemic population structure in which occasional clones emerge and spread. Conclusions Taken together our data demonstrate a wide dispersal of certain B. cenocepacia IIIB and BCC6 isolates in Mexican and Italian maize rhizospheres. Despite the clear relationship found between the geographic origin of isolates and grouping, identical RTs and closely related isolates were observed in geographically distant regions. Ecological factors and selective pressure may preferably promote some genotypes within each local microbial population, favouring the spread of a single clone above the rest of the recombinant population.
Collapse
Affiliation(s)
- Annamaria Bevivino
- ENEA (Italian National Agency for New Technologies, Energy and Sustainable Development) Casaccia Research Center-Technical Unit for Sustainable Development and Innovation of Agro-Industrial System, Via Anguillarese 301, 00123 S, Maria di Galeria, Rome, Italy.
| | | | | | | | | | | | | | | |
Collapse
|
15
|
Salipante SJ, Hall BG. Towards the molecular epidemiology of Mycobacterium leprae: Strategies, successes, and shortcomings. INFECTION GENETICS AND EVOLUTION 2011; 11:1505-13. [DOI: 10.1016/j.meegid.2011.06.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Revised: 06/03/2011] [Accepted: 06/07/2011] [Indexed: 12/23/2022]
|
16
|
Bisi-Johnson MA, Obi CL, Vasaikar SD, Baba KA, Hattori T. Molecular basis of virulence in clinical isolates of Escherichia coli and Salmonella species from a tertiary hospital in the Eastern Cape, South Africa. Gut Pathog 2011; 3:9. [PMID: 21663681 PMCID: PMC3125331 DOI: 10.1186/1757-4749-3-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Accepted: 06/10/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Apart from localized gastrointestinal infections, Escherichia coli and Salmonella species are major causes of systemic disease in both humans and animals. Salmonella spp. cause invasive infections such as enteric fever, septicemia, osteomyelitis and meningitis while certain types of E. coli can cause systemic infections, includingpyelonephritis, meningitis and septicemia. These characteristic requires the involvement of a myriad of virulence factors. METHODS This study investigated the virulence factors of Escherichia coli and Salmonella species in clinical specimens from patients with diarrhoea presenting to health care centres in Oliver R. Tambo District Municipality, Eastern Cape Province, Republic of South Africa. Microbiology analysis involved the use of cultural and molecular techniques. RESULTS Out of a total of 315 samples screened, Salmonella isolates were obtained in 119 (37.8%) of cases and these comprised: S. choleraesuis (6%), S. enteritidis (4%), S. eppendorf (1%), S. hadar (1%), S. isangi (8%), S. panama (1%), S. typhi (52%), S. typhimurium (25%) and untyped Salmonella spp. (2%). Among the Salmonella species 87 (73.1%) were invasive. Using molecular diagnostic methods, diarrheagenic E. coli were detected in 90 cases (28.6%): the greater proportion of this were enteroaggregative E. coli (EAEC) 37 (41.1%), enteropathogenic E. coli (EPEC) 21 (23.3%) and enterohemorrhagic E. coli (EHEC) 21 (23.3%). The predominant virulence gene among the diarrheagenic E. coli was EAEC heat-stable enterotoxin astA genes while the virulence genes identified in the Salmonella strains were 15 (12.6%) flic and 105 (88.2%) inv genes. The amino acid identity of the representative genes showed 95-100% similarity to corresponding blast searched sequence. CONCLUSIONS This study showed the diversity of virulence gene expression in two major enteric pathogens. S. typhi and enteroaggregative E. coli were the predominant enteropathogens in our study area with an indication that EAEC is endemic within our study population. It was observed among other things that some diarrheagenic E. coli isolated from apparently asymptomatic subjects expressed some virulence genes at frequency as high as seen in diarrheagenic cases. This study underlines the importance of understanding the virulence composition and diversity of pathogens for enhanced clinico-epidemiological monitoring and health care delivery.
Collapse
Affiliation(s)
- Mary A Bisi-Johnson
- Department of Medical Microbiology, Walter Sisulu University, Mthatha 5117, South Africa.
| | | | | | | | | |
Collapse
|
17
|
Phenotypic characterization and putative virulence factors of human, animal and environmental isolates of Plesiomonas shigelloides. Folia Microbiol (Praha) 2011; 55:641-7. [PMID: 21253913 DOI: 10.1007/s12223-010-0104-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2010] [Accepted: 09/18/2010] [Indexed: 10/18/2022]
Abstract
Plesiomonas shigelloides (a bacterium widely distributed in aquatic ecosystems causing both intestinal and extra-intestinal diseases) shows a host of putative virulence markers, such as hemolysins, cytotoxins, production of exoenzymes associated with pathogenicity, adhesive ability and vacuolation of cell lines in vitro. Technical difficulties in detecting some of these virulence factors together with scantiness of epidemiological information, due to the lack of routine analysis for P. shigelloides as etiological agent of gastroenteritis, lead to sporadic and occasional finding of these bacteria. All this casts doubt on the real virulence potential of P. shigelloides and fuels a debate about assignment of these bacteria to the list of human pathogens. Here we demonstrated the phenotypic diversity and the putative virulence markers by examining serotype biochemical and virulence properties of 60 strains of P. shigelloides isolated from human, animal and environmental samples in different countries, which showed the unpredictable occurrence of the above properties depending on various locations and diverse sources.
Collapse
|
18
|
Blackall PJ, Fegan N, Chew GTI, Hampson DJ. A study of the use of multilocus enzyme electrophoresis as a typing tool in fowl cholera outbreaks. Avian Pathol 2010; 28:195-8. [DOI: 10.1080/03079459994920] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
|
19
|
Mallik S, Virdi JS. Genetic relationships between clinical and non-clinical strains of Yersinia enterocolitica biovar 1A as revealed by multilocus enzyme electrophoresis and multilocus restriction typing. BMC Microbiol 2010; 10:158. [PMID: 20509911 PMCID: PMC2889952 DOI: 10.1186/1471-2180-10-158] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2009] [Accepted: 05/28/2010] [Indexed: 11/10/2022] Open
Abstract
Background Genetic relationships among 81 strains of Y. enterocolitica biovar 1A isolated from clinical and non-clinical sources were discerned by multilocus enzyme electrophoresis (MLEE) and multilocus restriction typing (MLRT) using six loci each. Such studies may reveal associations between the genotypes of the strains and their sources of isolation. Results All loci were polymorphic and generated 62 electrophoretic types (ETs) and 12 restriction types (RTs). The mean genetic diversity (H) of the strains by MLEE and MLRT was 0.566 and 0.441 respectively. MLEE (DI = 0.98) was more discriminatory and clustered Y. enterocolitica biovar 1A strains into four groups, while MLRT (DI = 0.77) identified two distinct groups. BURST (Based Upon Related Sequence Types) analysis of the MLRT data suggested aquatic serotype O:6,30-6,31 isolates to be the ancestral strains from which, clinical O:6,30-6,31 strains might have originated by host adaptation and genetic change. Conclusion MLEE revealed greater genetic diversity among strains of Y. enterocolitica biovar 1A and clustered strains in four groups, while MLRT grouped the strains into two groups. BURST analysis of MLRT data nevertheless provided newer insights into the probable evolution of clinical strains from aquatic strains.
Collapse
Affiliation(s)
- Sarita Mallik
- Microbial Pathogenicity Laboratory, Department of Microbiology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110 021, India
| | | |
Collapse
|
20
|
Didelot X, Urwin R, Maiden MCJ, Falush D. Genealogical typing of Neisseria meningitidis. MICROBIOLOGY-SGM 2009; 155:3176-3186. [PMID: 19643763 PMCID: PMC2762044 DOI: 10.1099/mic.0.031534-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Despite the increasing popularity of multilocus sequence typing (MLST), the most appropriate method for characterizing bacterial variation and facilitating epidemiological investigations remains a matter of debate. Here, we propose that different typing schemes should be compared on the basis of their power to infer clonal relationships and investigate the utility of sequence data for genealogical reconstruction by exploiting new statistical tools and data from 20 housekeeping loci for 93 isolates of the bacterial pathogen Neisseria meningitidis. Our analysis demonstrated that all but one of the hyperinvasive isolates established by multilocus enzyme electrophoresis and MLST were grouped into one of six genealogical lineages, each of which contained substantial variation. Due to the confounding effect of recombination, evolutionary relationships among these lineages remained unclear, even using 20 loci. Analyses of the seven loci in the standard MLST scheme using the same methods reproduced this classification, but were unable to support finer inferences concerning the relationships between the members within each complex.
Collapse
Affiliation(s)
| | - Rachel Urwin
- Department of Biology, Pennsylvania State University, USA
| | | | - Daniel Falush
- Environmental Research Institute, University College Cork, Ireland
| |
Collapse
|
21
|
Evolution of virulence in epidemic community-associated methicillin-resistant Staphylococcus aureus. Proc Natl Acad Sci U S A 2009; 106:5883-8. [PMID: 19293374 DOI: 10.1073/pnas.0900743106] [Citation(s) in RCA: 309] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) has recently emerged worldwide. The United States, in particular, is experiencing a serious epidemic of CA-MRSA that is almost entirely caused by an extraordinarily infectious strain named USA300. However, the molecular determinants underlying the pathogenic success of CA-MRSA are mostly unknown. To gain insight into the evolution of the exceptional potential of USA300 to cause disease, we compared the phylogeny and virulence of USA300 with that of closely related MRSA clones. We discovered that the sublineage from which USA300 evolved is characterized by a phenotype of high virulence that is clearly distinct from other MRSA strains. Namely, USA300 and its progenitor, USA500, had high virulence in animal infection models and the capacity to evade innate host defense mechanisms. Furthermore, our results indicate that increased virulence in the USA300/USA500 sublineage is attributable to differential expression of core genome-encoded virulence determinants, such as phenol-soluble modulins and alpha-toxin. Notably, the fact that the virulence phenotype of USA300 was already established in its progenitor indicates that acquisition of mobile genetic elements has played a limited role in the evolution of USA300 virulence and points to a possibly different role of those elements. Thus, our results highlight the importance of differential gene expression in the evolution of USA300 virulence. This finding calls for a profound revision of our notion about CA-MRSA pathogenesis at the molecular level and has important implications for design of therapeutics directed against CA-MRSA.
Collapse
|
22
|
Rylev M, Kilian M. Prevalence and distribution of principal periodontal pathogens worldwide. J Clin Periodontol 2009; 35:346-61. [PMID: 18724862 DOI: 10.1111/j.1600-051x.2008.01280.x] [Citation(s) in RCA: 130] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND Detailed genetic analysis of bacteria has demonstrated an unanticipated genetic diversity within species, which often reveals evolutionary lineages that are disproportionately associated with infection. There is evidence that some evolutionary lineages of bacteria have adapted to particular ethnic groups. AIM This review analyzes to what extent observed differences in periodontal disease prevalence among ethnically or geographically distinct populations may be explained by restricted host adaptation of clones of principal periodontal pathogens. RESULTS Carriage rates of several putative periodontal pathogens and particular subsets of these species vary between ethnic groups. Few of these differences can, with the limited information available, be directly related to differences in periodontal disease prevalence. Asian populations are regularly colonized with Actinobacillus actinomycetemcomitans serotype c with questionable pathogenic potential. Conversely, the JP2 clone of A. actinomycetemcomitans has enhanced virulence and causes significantly higher prevalence of aggressive periodontitis in adolescents whose descent can be traced back to the Mediterranean and Western parts of Africa. Some genetically distinct types of Porphyromonas gingivalis are more associated with disease than others, but additional work is required to relate this to clinical differences. CONCLUSIONS Studies that take into account differences linked to the genetics of both patients and potential pathogens are likely to give better insight into the aetiology of periodontal diseases.
Collapse
Affiliation(s)
- Mette Rylev
- Institute of Medical Microbiology and Immunology, University of Aarhus, Aarhus, Denmark.
| | | |
Collapse
|
23
|
Ranguelova K, Suarez J, Metlitsky L, Yu S, Brejt SZ, Brejt SZ, Zhao L, Schelvis JPM, Magliozzo RS. Impact of Distal Side Water and Residue 315 on Ligand Binding to Ferric Mycobacterium tuberculosis Catalase−Peroxidase (KatG). Biochemistry 2008; 47:12583-92. [DOI: 10.1021/bi801511u] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kalina Ranguelova
- Department of Chemistry, Brooklyn College, 2900 Bedford Avenue, Brooklyn, New York 11210, Department of Biochemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, New York 10016, and Department of Chemistry, New York University, 31 Washington Place, New York, New York 10003
| | - Javier Suarez
- Department of Chemistry, Brooklyn College, 2900 Bedford Avenue, Brooklyn, New York 11210, Department of Biochemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, New York 10016, and Department of Chemistry, New York University, 31 Washington Place, New York, New York 10003
| | - Leonid Metlitsky
- Department of Chemistry, Brooklyn College, 2900 Bedford Avenue, Brooklyn, New York 11210, Department of Biochemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, New York 10016, and Department of Chemistry, New York University, 31 Washington Place, New York, New York 10003
| | - Shengwei Yu
- Department of Chemistry, Brooklyn College, 2900 Bedford Avenue, Brooklyn, New York 11210, Department of Biochemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, New York 10016, and Department of Chemistry, New York University, 31 Washington Place, New York, New York 10003
| | - Shelly Zev Brejt
- Department of Chemistry, Brooklyn College, 2900 Bedford Avenue, Brooklyn, New York 11210, Department of Biochemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, New York 10016, and Department of Chemistry, New York University, 31 Washington Place, New York, New York 10003
| | - Sidney Zelig Brejt
- Department of Chemistry, Brooklyn College, 2900 Bedford Avenue, Brooklyn, New York 11210, Department of Biochemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, New York 10016, and Department of Chemistry, New York University, 31 Washington Place, New York, New York 10003
| | - Lin Zhao
- Department of Chemistry, Brooklyn College, 2900 Bedford Avenue, Brooklyn, New York 11210, Department of Biochemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, New York 10016, and Department of Chemistry, New York University, 31 Washington Place, New York, New York 10003
| | - Johannes P. M. Schelvis
- Department of Chemistry, Brooklyn College, 2900 Bedford Avenue, Brooklyn, New York 11210, Department of Biochemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, New York 10016, and Department of Chemistry, New York University, 31 Washington Place, New York, New York 10003
| | - Richard S. Magliozzo
- Department of Chemistry, Brooklyn College, 2900 Bedford Avenue, Brooklyn, New York 11210, Department of Biochemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, New York 10016, and Department of Chemistry, New York University, 31 Washington Place, New York, New York 10003
| |
Collapse
|
24
|
Siqueira JF, Rôças IN, Silva MG. Prevalence and clonal analysis of Porphyromonas gingivalis in primary endodontic infections. J Endod 2008; 34:1332-1336. [PMID: 18928841 DOI: 10.1016/j.joen.2008.08.021] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2008] [Revised: 08/12/2008] [Accepted: 08/13/2008] [Indexed: 11/16/2022]
Abstract
This study investigated the prevalence of Porphyromonas gingivalis in 62 teeth with primary endodontic infections by using a species-specific 16S rRNA gene-based nested polymerase chain reaction assay. P. gingivalis isolates recovered from 2 infected root canals were also analyzed for clonal diversity by using arbitrarily primed PCR. Overall, P. gingivalis was found in 48% of the samples. This species was specifically detected in 36% of canals of teeth with chronic apical periodontitis, in 46% of the cases of acute apical periodontitis, and in 67% of acute apical abscesses. P. gingivalis was significantly more frequent in abscess aspirates than in canals of teeth with chronic apical periodontitis (P < .05). Typing of colonies retrieved from 2 infected canals revealed 2 clones per individual. These findings confirmed that P. gingivalis can be an important endodontic pathogen, mostly associated with acute abscesses, and demonstrated that different clonal types of this species can colonize the root canal in the same individual.
Collapse
Affiliation(s)
- José F Siqueira
- Department of Endodontics and Molecular Microbiology, Faculty of Dentistry, Estácio de Sá University, Rio de Janeiro, RJ, Brazil.
| | - Isabela N Rôças
- Department of Endodontics and Molecular Microbiology, Faculty of Dentistry, Estácio de Sá University, Rio de Janeiro, RJ, Brazil
| | - Marlei G Silva
- Institute of Microbiology Prof. Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| |
Collapse
|
25
|
Oyarzabal O, Backert S, Williams L, Lastovica A, Miller R, Pierce S, Vieira S, Rebollo-Carrato F. Molecular typing, serotyping and cytotoxicity testing ofCampylobacter jejunistrains isolated from commercial broilers in Puerto Rico. J Appl Microbiol 2008; 105:800-12. [DOI: 10.1111/j.1365-2672.2008.03809.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
26
|
Sriramulu DD. Adaptive expression of foreign genes in the clonal variants of bacteria: from proteomics to clinical application. Proteomics 2008; 8:882-92. [PMID: 18297656 DOI: 10.1002/pmic.200700811] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Clonal variants of bacteria are able to colonize environmental niches and patients. The factors, that determine the interplay between the colonization of diverse habitats and adaptation, are acquired through horizontal gene transfer. Elucidation of mechanisms, which lead to the prevalence of dominant bacterial clones in patients and the environment, requires the knowledge of complex phenotypes. It was found in the genomes of most bacteria, that upon a conserved chromosomal backbone there were regions of plasticity achieved by insertions, deletions and rearrangements of genomic islands and islets as well as large chromosomal inversions. However, it had been shown that environmental and clinical isolates are indistinguishable in certain pathogenic and biodegradative properties. For example, clonal variants of Pseudomonas aeruginosa exhibit convergent phenotypes despite the presence of numerous DNA insertions in the genome. Apart from this feature, expression of a few genes from the acquired genetic material is important for niche-based adaptation of this organism. Protein expression patterns at the cellular and sub-cellular levels showed common virulence factors and novel drug targets among clonal variants of bacteria. This review will give a short overview on proteomics of different clonal variants of bacteria with respect to clinical applications.
Collapse
Affiliation(s)
- Dinesh D Sriramulu
- Division of Cell and Immune Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany.
| |
Collapse
|
27
|
Caugant DA. Genetics and evolution of Neisseria meningitidis: importance for the epidemiology of meningococcal disease. INFECTION GENETICS AND EVOLUTION 2008; 8:558-65. [PMID: 18479979 DOI: 10.1016/j.meegid.2008.04.002] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2008] [Revised: 04/01/2008] [Accepted: 04/02/2008] [Indexed: 11/30/2022]
Abstract
Meningococcal disease is a life-threatening illness occurring worldwide with incidence rates varying from 1 to 1000 cases per 100,000. The causative organism, Neisseria meningitidis, is a normal commensal of humans. While strains associated with asymptomatic carriage are highly diverse, a few hyper-invasive genetic clones of the species may spread rapidly through human populations, resulting in countrywide epidemics of meningococcal meningitis. N. meningitidis fitness for spread and colonization is directly linked to the capability of the bacterium to change its genome and adapt to its environment, by means of a variety of genetic mechanisms. This review addresses some of the impacts of the evolutionary potential of N. meningitidis on the occurrence of meningococcal disease.
Collapse
Affiliation(s)
- Dominique A Caugant
- WHO Collaborating Centre for Reference and Research on Meningococci, Department of Bacteriology and Immunology, Norwegian Institute of Public Health, P.O. Box 4404 Nydalen, NO-0403 Oslo, Norway.
| |
Collapse
|
28
|
Brassard P, Henry KA, Schwartzman K, Jomphe M, Olson SH. Geography and genealogy of the human host harbouring a distinctive drug-resistant strain of tuberculosis. INFECTION GENETICS AND EVOLUTION 2007; 8:247-57. [PMID: 18316250 DOI: 10.1016/j.meegid.2007.11.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2007] [Revised: 11/28/2007] [Accepted: 11/29/2007] [Indexed: 10/22/2022]
Abstract
For a strain of Mycobacterium tuberculosis mono-resistant to pyrazinamide (PZA), we report the geographic distribution within Quebec of the 77 cases diagnosed during 1990-2000. Known as the Quebec mutation (or the pncA deletion), the strain is rare in urban areas and showed an unexpected concentration in Mauricie, one of the 16 health districts of the province, with a cluster of 10 cases situated in a rural area of 35-km radius. The cases occurred among people >50 (98%), of French Canadian origins (90%), and are understood to have arisen by reactivation. The rarity in Montreal and smaller cities is explained by the youthfulness of massive postwar migrations. To reach back into the history of settlement, we examined genealogies: 92,429 ancestral marriages for 32 of the 77 PZA-resistant isolates and 226,535 for a set of 85 controls with isolates of more diverse mycobacterial strains. Genealogical analysis showed no salient common ancestor for the cases, and kinship among them was no greater than observed in control samples from the same regions. But it identified an unsuspected geographical region as the site of ancestral concentrations prior to 1840, for both resistant strains and controls. The following scenario is proposed for the resistant strain: endemic in a specific geographical region by 1800, it dispersed with families moving into regions opened to settlement in the 1840s and 1850s, among them Mauricie, where dispersion was intensified by seasonal mobility of labour in logging, milling and marketing timber. In high-incidence areas, it is difficult to distinguish cases of reactivation from recent infections, but the low-incidence context allows us to observe a 200-year trajectory of a distinctive drug-resistant strain of M. tuberculosis.
Collapse
Affiliation(s)
- Paul Brassard
- Department of Medicine, McGill University Health Center, Royal Victoria Hospital, Montréal, Québec, Canada H3A 1A1.
| | | | | | | | | |
Collapse
|
29
|
Bañuls AL, Hide M, Prugnolle F. Leishmania and the leishmaniases: a parasite genetic update and advances in taxonomy, epidemiology and pathogenicity in humans. ADVANCES IN PARASITOLOGY 2007; 64:1-109. [PMID: 17499100 DOI: 10.1016/s0065-308x(06)64001-3] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Leishmaniases remain a major public health problem today despite the vast amount of research conducted on Leishmania pathogens. The biological model is genetically and ecologically complex. This paper explores the advances in Leishmania genetics and reviews population structure, taxonomy, epidemiology and pathogenicity. Current knowledge of Leishmania genetics is placed in the context of natural populations. Various studies have described a clonal structure for Leishmania but recombination, pseudo-recombination and other genetic processes have also been reported. The impact of these different models on epidemiology and the medical aspects of leishmaniases is considered from an evolutionary point of view. The role of these parasites in the expression of pathogenicity in humans is also explored. It is important to ascertain whether genetic variability of the parasites is related to the different clinical expressions of leishmaniasis. The review aims to put current knowledge of Leishmania and the leishmaniases in perspective and to underline priority questions which 'leishmaniacs' must answer in various domains: epidemiology, population genetics, taxonomy and pathogenicity. It concludes by presenting a number of feasible ways of responding to these questions.
Collapse
Affiliation(s)
- Anne-Laure Bañuls
- Institut de Recherche pour le Développement, UMR CNRS/IRD 2724, Génétique et Evolution des Maladies Infectieuses, IRD Montpellier, 911 avenue Agropolis, 34394 Montpellier cedex 5, France
| | | | | |
Collapse
|
30
|
Davies MR, McMillan DJ, Beiko RG, Barroso V, Geffers R, Sriprakash KS, Chhatwal GS. Virulence profiling of Streptococcus dysgalactiae subspecies equisimilis isolated from infected humans reveals 2 distinct genetic lineages that do not segregate with their phenotypes or propensity to cause diseases. Clin Infect Dis 2007; 44:1442-54. [PMID: 17479940 DOI: 10.1086/516780] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2006] [Accepted: 01/15/2007] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND In spite of the emerging importance of Streptococcus dysgalactiae subspecies equisimilis (human group C streptococci [GCS] and group G streptococci [GGS]) in human health, its molecular makeup remains largely undefined. Apart from sharing a phylogenetic relationship with the human pathogen group A streptococci (GAS), GCS/GGS and GAS colonize the same ecological niche and exhibit considerable overlap in their disease profiles. Such similarities imply that the virulence factors associated with diseases may also be similar. METHODS In this study, we used a targeted microarray containing 216 GAS virulence genes to profile the virulence gene repertoires of 58 S. dysgalactiae subspecies equisimilis isolates recovered during human infections. We performed comparative analyses to investigate the relationship between GAS virulence genes in and the invasive potential of GCS/GGS. RESULTS Up to one-half of the GAS virulence genes represented in the microarray were identified in GCS/GGS. No statistical differences were observed between isolates harboring the group C versus group G carbohydrates; however, clustering algorithms revealed 2 genetically distinct clusters of S. dysgalactiae subspecies equisimilis isolates. No relationship was observed between the virulence profile of GCS/GGS and the propensity for disease or the tissue site of isolation. CONCLUSIONS This is, to our knowledge, the first comprehensive analysis of the virulence profile of S. dysgalactiae subspecies equisimilis, and it enables novel insights into the pathogen's genetic basis of disease propensity shared with GAS. Human group C and group G streptococci may not be considered to be separate species; in fact, they may constitute 2 distinct lineages. Additional incongruent relationships were observed between virulence profiles and GCS/GGS disease propensity.
Collapse
Affiliation(s)
- Mark R Davies
- Bacterial Pathogenesis Laboratory, The Queensland Institute of Medical Research, Australia
| | | | | | | | | | | | | |
Collapse
|
31
|
Ramette A, Tiedje JM. Biogeography: an emerging cornerstone for understanding prokaryotic diversity, ecology, and evolution. MICROBIAL ECOLOGY 2007; 53:197-207. [PMID: 17106806 DOI: 10.1007/s00248-005-5010-2] [Citation(s) in RCA: 156] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2005] [Accepted: 05/25/2005] [Indexed: 05/07/2023]
Abstract
New questions about microbial ecology and diversity combined with significant improvement in the resolving power of molecular tools have helped the reemergence of the field of prokaryotic biogeography. Here, we show that biogeography may constitute a cornerstone approach to study diversity patterns at different taxonomic levels in the prokaryotic world. Fundamental processes leading to the formation of biogeographic patterns are examined in an evolutionary and ecological context. Based on different evolutionary scenarios, biogeographic patterns are thus posited to consist of dramatic range expansion or regression events that would be the results of evolutionary and ecological forces at play at the genotype level. The deterministic or random nature of those underlying processes is, however, questioned in light of recent surveys. Such scenarios led us to predict the existence of particular genes whose presence or polymorphism would be associated with cosmopolitan taxa. Furthermore, several conceptual and methodological pitfalls that could hamper future developments of the field are identified, and future approaches and new lines of investigation are suggested.
Collapse
Affiliation(s)
- Alban Ramette
- Center for Microbial Ecology, Michigan State University, 540 Plant and Soil Sciences Building, East Lansing, MI 48824-1325, USA.
| | | |
Collapse
|
32
|
Ranguelova K, Girotto S, Gerfen GJ, Yu S, Suarez J, Metlitsky L, Magliozzo RS. Radical sites in Mycobacterium tuberculosis KatG identified using electron paramagnetic resonance spectroscopy, the three-dimensional crystal structure, and electron transfer couplings. J Biol Chem 2007; 282:6255-64. [PMID: 17204474 PMCID: PMC1885898 DOI: 10.1074/jbc.m607309200] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Catalase-peroxidase (KatG) from Mycobacterium tuberculosis, a Class I peroxidase, exhibits high catalase activity and peroxidase activity with various substrates and is responsible for activation of the commonly used antitubercular drug, isoniazid (INH). KatG readily forms amino acid-based radicals during turnover with alkyl peroxides, and this work focuses on extending the identification and characterization of radicals forming on the millisecond to second time scale. Rapid freeze-quench electron paramagnetic resonance spectroscopy (RFQ-EPR) reveals a change in the structure of the initially formed radical in the presence of INH. Heme pocket binding of the drug and knowledge that KatG[Y229F] lacks this signal provides evidence for radical formation on residue Tyr(229). High field RFQ-EPR spectroscopy confirmed a tryptophanyl radical signal, and new analyses of X-band RFQ-EPR spectra also established its presence. High field EPR spectroscopy also confirmed that the majority radical species is a tyrosyl radical. Site-directed mutagenesis, along with simulations of EPR spectra based on x-ray structural data for particular tyrosine and tryptophan residues, enabled assignments based on predicted hyperfine coupling parameters. KatG mutants W107F, Y229F, and the double mutant W107F/Y229F showed alteration in type and yield of radical species. Results are consistent with formation of a tyrosyl radical reasonably assigned to residue Tyr(229) within the first few milliseconds of turnover. This is followed by a mixture of tyrosyl and tryptophanyl radical species and finally to only a tyrosyl radical on residue Tyr(353), which lies more distant from the heme. The radical processing of enzyme lacking the Trp(107)-Tyr(229)-Met(255) adduct (found as a unique structural feature of catalase-peroxidases) is suggested to be a reasonable assignment of the phenomena.
Collapse
Affiliation(s)
- Kalina Ranguelova
- Department of Chemistry, Brooklyn College, Brooklyn, NY 11210 and The Graduate Center of the City University of New York, NY 10016, USA
| | - Stefania Girotto
- Department of Chemistry, Brooklyn College, Brooklyn, NY 11210 and The Graduate Center of the City University of New York, NY 10016, USA
| | - Gary J. Gerfen
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Shengwei Yu
- Department of Chemistry, Brooklyn College, Brooklyn, NY 11210 and The Graduate Center of the City University of New York, NY 10016, USA
| | - Javier Suarez
- Department of Biochemistry, The Graduate Center of the City University of New York, NY 10016, USA
| | - Leonid Metlitsky
- Department of Chemistry, Brooklyn College, Brooklyn, NY 11210 and The Graduate Center of the City University of New York, NY 10016, USA
| | - Richard S. Magliozzo
- Department of Chemistry, Brooklyn College, Brooklyn, NY 11210 and The Graduate Center of the City University of New York, NY 10016, USA
- Department of Biochemistry, The Graduate Center of the City University of New York, NY 10016, USA
| |
Collapse
|
33
|
Abstract
Multilocus sequence typing (MLST) was proposed in 1998 as a portable, universal, and definitive method for characterizing bacteria, using the human pathogen Neisseria meningitidis as an example. In addition to providing a standardized approach to data collection, by examining the nucleotide sequences of multiple loci encoding housekeeping genes, or fragments of them, MLST data are made freely available over the Internet to ensure that a uniform nomenclature is readily available to all those interested in categorizing bacteria. At the time of writing, over thirty MLST schemes have been published and made available on the Internet, mostly for pathogenic bacteria, although there are schemes for pathogenic fungi and some nonpathogenic bacteria. MLST data have been employed in epidemiological investigations of various scales and in studies of the population biology, pathogenicity, and evolution of bacteria. The increasing speed and reduced cost of nucleotide sequence determination, together with improved web-based databases and analysis tools, present the prospect of increasingly wide application of MLST.
Collapse
Affiliation(s)
- Martin C J Maiden
- Peter Medawar Building for Pathogen Research and Department of Zoology, University of Oxford, Oxford, OX1 3SY, United Kingdom.
| |
Collapse
|
34
|
Liu X, Gutacker MM, Musser JM, Fu YX. Evidence for recombination in Mycobacterium tuberculosis. J Bacteriol 2006; 188:8169-77. [PMID: 16997954 PMCID: PMC1698211 DOI: 10.1128/jb.01062-06] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2006] [Accepted: 09/14/2006] [Indexed: 11/20/2022] Open
Abstract
Due to its mostly isolated living environment, Mycobacterium tuberculosis is generally believed to be highly clonal, and thus recombination between different strains must be rare and is not critical for the survival of the species. To investigate the roles recombination could have possibly played in the evolution of M. tuberculosis, an analysis was conducted on previously determined genotypes of 36 synonymous single nucleotide polymorphisms (SNPs) in 3,320 M. tuberculosis isolates. The results confirmed the predominant clonal structure of the M. tuberculosis population. However, recombination between different strains was also suggested. To further resolve the issue, 175 intergenic SNPs and 234 synonymous SNPs were genotyped in 37 selected representative strains. A clear mosaic polymorphic pattern ahead of the MT0105 locus encoding a PPE (Pro-Pro-Glu) protein was obtained, which is most likely a result of recombination hot spot. Given that PPE proteins are thought to be critical in host-pathogen interactions, we hypothesize that recombination has been influential in the history of M. tuberculosis and possibly a major contributor to the diversity observed ahead of the MT0105 locus.
Collapse
Affiliation(s)
- Xiaoming Liu
- Human Genetics Center, University of Texas at Houston, P.O. Box 20186, Houston, TX 77225, USA
| | | | | | | |
Collapse
|
35
|
Motiwala AS, Janagama HK, Paustian ML, Zhu X, Bannantine JP, Kapur V, Sreevatsan S. Comparative transcriptional analysis of human macrophages exposed to animal and human isolates of Mycobacterium avium subspecies paratuberculosis with diverse genotypes. Infect Immun 2006; 74:6046-56. [PMID: 17057086 PMCID: PMC1695517 DOI: 10.1128/iai.00326-06] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2006] [Revised: 04/11/2006] [Accepted: 07/16/2006] [Indexed: 12/24/2022] Open
Abstract
Mycobacterium avium subsp. paratuberculosis is the causative agent of Johne's disease in animals and has been hypothesized to be associated with Crohn's disease in humans. Recently, M. avium subsp. paratuberculosis isolates recovered from Crohn's disease patients were shown to have limited diversity, implying the existence of human disease-associated genotypes and strain sharing with animals (A. H. Ghadiali et al., J. Clin. Microbiol. 42:5345-5348, 2004). To explore whether these genotypic differences or similarities among human and animal isolates translated to functionally significant attributes such as variance in host preference and/or difference in magnitude of infections, we performed a global scale analysis of M. avium subsp. paratuberculosis isolates that were representative of different genotypes and host species using DNA microarrays. Genome-wide characterization of the transcriptional changes was carried out using a human monocytic cell line (THP-1 cells) in response to different genotypes of M. avium subsp. paratuberculosis isolates recovered from various hosts. We identified several differentially expressed genes during early intracellular infection, including those involved in common canonical pathways such as NF-kappaB, interleukin-6 (IL-6), mitogen-activated protein kinase/extracellular signal-regulated kinase, and Jun N-terminal protein kinase signaling, as well as genes involved in T helper type 1 (Th1) responses (such as CCL5 ligand) and those that encode several proinflammatory cytokines and chemokine receptors. The cattle and human isolates of M. avium subsp. paratuberculosis, regardless of their short sequence repeat (SSR) genotype, induced similar global gene expression patterns in THP-1 cells. They differentially regulated genes necessary for cell survival without causing major alterations in proinflammatory genes. In contrast, the sheep isolates representing diverse SSR genotypes closely resembled the global gene expression pattern of an M. avium subsp. avium isolate, and they significantly up-regulated proinflammatory genes related to IL-6, T-cell receptor, B-cell receptor, and death receptor signaling within THP-1 cells. Additionally, we demonstrated consistency among infecting genotypes of M. avium subsp. paratuberculosis isolated from diverse hosts [cattle (n=2), human (n=3), sheep (n=2), and bison (n=1)] in quantitative reverse transcription-PCR analysis of seven differentially expressed genes. While the levels of expression induced by the bison isolate were different compared with cattle or human isolates, they followed the common anti-inflammatory, antiapoptotic trend. Our data suggest that the macrophage responses to M. avium subsp. paratuberculosis isolates from cattle and human sources, regardless of genotype, follow a common theme of anti-inflammatory responses, an attribute likely associated with successful infection and persistence. However, these expression patterns differ significantly from those in THP-1 cells infected with sheep isolates of M. avium subsp. paratuberculosis or the M. avium subsp. avium isolate. These data provide a transcriptional basis for a variety of pathophysiological changes observed during early stages of infection by different strains of M. avium subsp. paratuberculosis, a first step in understanding trait-allele association in this economically important disease.
Collapse
Affiliation(s)
- Alifiya S Motiwala
- Division of Infectious Disease, Department of Medicine and the Ruy V. Lourenço Center for the Study of Emerging and Reemerging Pathogens, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, USA
| | | | | | | | | | | | | |
Collapse
|
36
|
Kilian M, Frandsen EVG, Haubek D, Poulsen K. The etiology of periodontal disease revisited by population genetic analysis. Periodontol 2000 2006; 42:158-79. [PMID: 16930310 DOI: 10.1111/j.1600-0757.2006.00159.x] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Mogens Kilian
- Department of Bacteriology, Institute of Medical Microbiology and Immunology, University of Aarhus, Aarhus, Denmark
| | | | | | | |
Collapse
|
37
|
Mathema B, Kurepina NE, Bifani PJ, Kreiswirth BN. Molecular epidemiology of tuberculosis: current insights. Clin Microbiol Rev 2006; 19:658-85. [PMID: 17041139 PMCID: PMC1592690 DOI: 10.1128/cmr.00061-05] [Citation(s) in RCA: 236] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Molecular epidemiologic studies of tuberculosis (TB) have focused largely on utilizing molecular techniques to address short- and long-term epidemiologic questions, such as in outbreak investigations and in assessing the global dissemination of strains, respectively. This is done primarily by examining the extent of genetic diversity of clinical strains of Mycobacterium tuberculosis. When molecular methods are used in conjunction with classical epidemiology, their utility for TB control has been realized. For instance, molecular epidemiologic studies have added much-needed accuracy and precision in describing transmission dynamics, and they have facilitated investigation of previously unresolved issues, such as estimates of recent-versus-reactive disease and the extent of exogenous reinfection. In addition, there is mounting evidence to suggest that specific strains of M. tuberculosis belonging to discrete phylogenetic clusters (lineages) may differ in virulence, pathogenesis, and epidemiologic characteristics, all of which may significantly impact TB control and vaccine development strategies. Here, we review the current methods, concepts, and applications of molecular approaches used to better understand the epidemiology of TB.
Collapse
Affiliation(s)
- Barun Mathema
- Tuberculosis Center, Public Health Research Institute, Newark, NJ 07103, USA.
| | | | | | | |
Collapse
|
38
|
Parham K, Churchward CP, McAuliffe L, Nicholas RAJ, Ayling RD. A high level of strain variation within the Mycoplasma ovipneumoniae population of the UK has implications for disease diagnosis and management. Vet Microbiol 2006; 118:83-90. [PMID: 16962728 DOI: 10.1016/j.vetmic.2006.07.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2006] [Revised: 07/07/2006] [Accepted: 07/10/2006] [Indexed: 11/21/2022]
Abstract
Mycoplasma ovipneumoniae is one of only two mycoplasma species associated with small ruminant disease in Britain and has been associated with an increasing number of disease outbreaks since 2002. This investigation used well-defined techniques to assess the variability of UK M. ovipneumoniae isolates, in an attempt to identify strain clusters within the population. Strains received for routine diagnosis between 2002 and 2004 were analysed using random amplified polymorphic DNA (RAPD) and pulsed field gel electrophoresis (PFGE). Of the 43 samples screened 40 RAPD Hum-1, 41 RAPD Hum-4 and 40 PFGE profiles were observed. Composite data analysis divided strains into 10 similarity clusters with SDS-PAGE and Western blotting indicating that this DNA variability is translated into a pattern of variable protein expression. In order to assess the strains isolated within flocks two sets of samples, from diverse locations, were included in this test panel. The presence of variable isolates existing on the same farm may reflect animal movement and the introduction of asymptomatic, carrier, animals where M. ovipneumoniae is already established within a flock. These findings have significant implications regarding disease diagnosis and management.
Collapse
Affiliation(s)
- K Parham
- Department of Statutory and Exotic Bacterial Diseases, Veterinary Laboratories Agency (Weybridge), Addlestone, Surrey KT15 3NB, United Kingdom.
| | | | | | | | | |
Collapse
|
39
|
Harris S, Brookes S, Jones G, Hutson A, Racey P, Aegerter J, Smith G, McElhinney L, Fooks A. European bat lyssaviruses: Distribution, prevalence and implications for conservation. BIOLOGICAL CONSERVATION 2006; 131:193-210. [PMID: 32226078 PMCID: PMC7096730 DOI: 10.1016/j.biocon.2006.04.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Worldwide, there are more than 1100 species of the Order Chiroptera, 45 of which are present in Europe, and 16 in the UK. Bats are reservoirs of, or can be infected by, several viral diseases, including rabies virus strains (in the Lyssavirus genus). Within this genus are bat variants that have been recorded in Europe; European bat lyssavirus 1 (EBLV-1), European bat lyssavirus 2 (EBLV-2) and, four currently unclassified isolates. Since 1977, 783 cases of EBLVs (by isolation of viral RNA) have been recorded in Europe. EBLV-1 or EBLV-2 has been identified in 12 bat species, with over 95% of EBLV-1 infections identified in Eptesicus serotinus. EBLV-2 is associated with Myotis species (Myotis daubentonii and Myotis dasycneme). A programme of passive surveillance in the United Kingdom between 1987 and 2004 tested 4871 bats for lyssaviruses. Of these, four M. daubentonii (3.57% of submitted M. daubentonii) were positive for EBLV-2. Potential bias in the passive surveillance includes possible over-representation of synanthropic species and regional biases caused by varying bat submission numbers from different parts of the UK. In 2003, active surveillance in the UK began, and has detected an antibody prevalence level of 1-5% of EBLV-2 in M. daubentonii (n = 350), and one bat with antibodies to EBLV-1 in E. serotinus (n = 52). No cases of live lyssavirus infection or lyssavirus viral RNA have been detected through active surveillance. Further research and monitoring regarding prevalence, transmission, pathogenesis and immunity is required to ensure that integrated bat conservation continues throughout Europe, whilst enabling informed policy decision regarding both human and wildlife health issues.
Collapse
Affiliation(s)
- S.L. Harris
- School of Biological Sciences, University of Bristol, Woodland Road, Bristol BS8 1UG, UK
- Rabies and Wildlife Zoonoses Group, Veterinary Laboratories Agency (Weybridge), WHO Collaborating Centre for the Characterisation of Rabies and Rabies-Related Viruses, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - S.M. Brookes
- Rabies and Wildlife Zoonoses Group, Veterinary Laboratories Agency (Weybridge), WHO Collaborating Centre for the Characterisation of Rabies and Rabies-Related Viruses, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - G. Jones
- School of Biological Sciences, University of Bristol, Woodland Road, Bristol BS8 1UG, UK
| | - A.M. Hutson
- Winkfield, Station Road, Plumpton Green, East Sussex, BN7 3BU, UK
| | - P.A. Racey
- School of Biological Sciences, University of Aberdeen, Aberdeen AB24 2TZ, UK
| | - J. Aegerter
- Central Science Laboratory, Sand Hutton, York, YO41 1LZ, UK
| | - G.C. Smith
- Central Science Laboratory, Sand Hutton, York, YO41 1LZ, UK
| | - L.M. McElhinney
- Rabies and Wildlife Zoonoses Group, Veterinary Laboratories Agency (Weybridge), WHO Collaborating Centre for the Characterisation of Rabies and Rabies-Related Viruses, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - A.R. Fooks
- Rabies and Wildlife Zoonoses Group, Veterinary Laboratories Agency (Weybridge), WHO Collaborating Centre for the Characterisation of Rabies and Rabies-Related Viruses, New Haw, Addlestone, Surrey KT15 3NB, UK
| |
Collapse
|
40
|
Zhao X, Yu H, Yu S, Wang F, Sacchettini JC, Magliozzo RS. Hydrogen peroxide-mediated isoniazid activation catalyzed by Mycobacterium tuberculosis catalase-peroxidase (KatG) and its S315T mutant. Biochemistry 2006; 45:4131-40. [PMID: 16566587 DOI: 10.1021/bi051967o] [Citation(s) in RCA: 120] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Inhibition of the enzyme Mycobacterium tuberculosis InhA (enoyl-acyl carrier protein reductase) due to formation of an isonicotinoyl-NAD adduct (IN-NAD) from isoniazid (INH) and nicotinamide adenine dinucleotide cofactor is considered central to the mode of action of INH, a first-line treatment for tuberculosis infection. INH action against mycobacteria requires catalase-peroxidase (KatG) function, and IN-NAD adduct formation is catalyzed in vitro by M. tuberculosis KatG under a variety of conditions, yet a physiologically relevant approach to the process has not emerged that allows scrutiny of the mechanism and the origins of INH resistance in the most prevalent drug-resistant strain bearing KatG[S315T]. In this report, we describe how hydrogen peroxide, delivered at very low concentrations to ferric KatG, leads to efficient inhibition of InhA due to formation of the IN-NAD adduct. The rate of adduct formation mediated by wild-type KatG was about 20-fold greater than by the isoniazid-resistant KatG[S315T] mutant under optimal conditions (H2O2 supplied along with NAD+ and INH). Slow adduct formation also occurs starting with NADH and INH, in the presence of KatG even in the absence of added peroxide, due to endogenous peroxide. The poor efficiency of the KatG[S315T] mutant can be enhanced merely by increasing the concentration of INH, consistent with this enzyme's reduced affinity for INH binding to the resting enzyme and the catalytically competent enzyme intermediate (Compound I). Origins of drug resistance in the KatG[S315T] mutant enzyme are analyzed at the structural level through examination of the three-dimensional X-ray crystal structure of the mutant enzyme.
Collapse
Affiliation(s)
- Xiangbo Zhao
- Department of Chemistry, Brooklyn College, Brooklyn, New York 11210, USA
| | | | | | | | | | | |
Collapse
|
41
|
Pohl MA, Wiedmann M, Nightingale KK. Associations amongListeria monocytogenesgenotypes and distinct clinical manifestations of listeriosis in cattle. Am J Vet Res 2006; 67:616-26. [PMID: 16579754 DOI: 10.2460/ajvr.67.4.616] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
OBJECTIVE To determine whether specific strains of Listeria monocytogenes, as determined by genetic characteristics and virulence phenotypes, were associated with distinct clinical manifestations of listeriosis in cattle and thus may potentially have tissue specificity. ANIMALS 32 cattle. PROCEDURE DNA sequence data for the virulence genes actAand inlAwere used to infer the phylogeny of L. monocytogenes and to test for positive selection. Isolates were screened for the presence or absence of internalin genes and assigned an internalin profile. Plaquing assays were performed to determine the relative cytopathogenicity of each isolate. Categorical data analyses were performed to describe associations among L. monocytogenes genotypes, virulence phenotypes, and clinical manifestations of listeriosis. RESULTS Results confirmed that L. monocytogenes represents 2 deeply separated evolutionary lineages. Genes actA and inlA contained amino acid sites under positive selection, and specific residues at some sites were associated with lineage and manifestation of listeriosis. Whereas lineage I was clonal and predominantly composed of isolates from cases of encephalitis, lineage II was more genetically diverse and equally represented by isolates from cases of encephalitis versus septicemia and fetal infection. Lineage I isolates also had greater cytopathogenicity in vitro, compared with lineage II isolates. CONCLUSIONS AND CLINICAL RELEVANCE Results indicated that L. monocytogenes virulence genes underwent positive selection that is consistent with the diversification of 2 evolutionary lineages: lineage I is clonal and associated with encephalitis, and lineage II is more genetically diverse and equally likely to cause both major forms of listeriosis in cattle.
Collapse
Affiliation(s)
- Mary Ann Pohl
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | | | | |
Collapse
|
42
|
Abstract
BACKGROUND Bacteria play an essential role in the aetiology of periodontitis. Most bacterial species isolated from subgingival plaque are indigenous to the oral cavity. Actinobacillus actinomycetemcomitans and Porphyromonas gingivalis are detected infrequently in periodontal health, which makes these species prime candidates to study person-to-person transmission. The aim of the present study was to review the literature on transmission of these periodontal bacterial species. METHOD We review the literature on bacterial typing techniques and summarize the information on clonal distribution of A. actinomycetemcomitans and P. gingivalis in family units based on different typing techniques in order to establish the likelihood for person-to-person transmission of these periodontal pathogens. RESULTS Vertical transmission of A. actinomycetemcomitans is estimated to be between 30% and 60%, whereas vertical transmission of P. gingivalis has rarely been observed. Horizontal transmission between spouses ranges between 14% and 60% for A. actinomycetemcomitans and between 30% and 75% for P. gingivalis. There is some evidence to show that cohabitation with a periodontitis patient influences the periodontal status of the spouse; however, substantially more information is needed to prove this hypothesis. CONCLUSIONS Transmission of putative periodontal pathogens between family members has been shown. The clinical consequences of these events have been poorly documented. Based on the current knowledge, screening for and prevention of transmission of specific virulent clones of A. actinomycetemcomitans may be feasible and effective in preventing some forms of periodontal disease. P. gingivalis is usually recovered from diseased adult subjects, and transmission of this pathogens seems largely restricted to adult individuals. Horizontal transmission of P. gingivalis may therefore be controlled by periodontal treatment involving elimination or significant suppression of the pathogen in diseased individuals and by a high standard of oral hygiene.
Collapse
Affiliation(s)
- A J Van Winkelhoff
- Academic Centre for Dentistry Amsterdam, Department of Oral Microbiology, Amsterdam, The Netherlands.
| | | |
Collapse
|
43
|
Hanage WP, Fraser C, Spratt BG. The impact of homologous recombination on the generation of diversity in bacteria. J Theor Biol 2005; 239:210-9. [PMID: 16236325 DOI: 10.1016/j.jtbi.2005.08.035] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2005] [Revised: 05/12/2005] [Accepted: 07/23/2005] [Indexed: 11/15/2022]
Abstract
The imprint of demographic and selective processes on bacterial population structure needs to be evaluated as deviation from the expectations of an appropriate null neutral model. We explore the impact of varying the population mutation and recombination rates theta and rho on ideal populations, using a recently developed model of neutral drift at multiple loci. This model may be fitted to experimental data to provide estimates of these parameters, and we do so for seven bacterial species (Neisseria meningitidis, Streptococcus pneumoniae, Streptococcus pyogenes, Staphylococcus aureus, Helicobacter pylori, Burkholderia pseudomallei and Bacillus cereus), illustrating that bacterial species vary extensively in these fundamental parameters. Historically, the influence of recombination has often been estimated through its influence on the Index of Association I(A). We show that this may be relatively insensitive to changes in either mutation or recombination rates. It is known that biased sampling can lead to artificially high estimates of I(A). We therefore provide a method of precisely separating the effects of such bias and true linkage between alleles. We also demonstrate that by fitting the neutral model to experimental data, more informative and precise estimates of the relative roles of recombination and mutation may be obtained.
Collapse
Affiliation(s)
- William P Hanage
- Department of Infectious Disease Epidemiology, St. Mary's Hospital Campus, Imperial College London, London W2 1PG, UK.
| | | | | |
Collapse
|
44
|
Wichmann G, Ritchie D, Kousik CS, Bergelson J. Reduced genetic variation occurs among genes of the highly clonal plant pathogen Xanthomonas axonopodis pv. vesicatoria, including the effector gene avrBs2. Appl Environ Microbiol 2005; 71:2418-32. [PMID: 15870329 PMCID: PMC1087534 DOI: 10.1128/aem.71.5.2418-2432.2005] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2004] [Accepted: 11/18/2004] [Indexed: 11/20/2022] Open
Abstract
The bacterial plant pathogen Xanthomonas axonopodis pv. vesicatoria, also known as Xanthomonas campestris pv. vesicatoria group A, is the causal agent of bacterial spot in pepper and tomato. In order to test different models that may explain the coevolution of avrBs2 with its host plants, we sequenced avrBs2 and six chromosomal loci (total of 5.5 kb per strain) from a global sample of 55 X. axonopodis pv. vesicatoria strains collected from diseased peppers. We found an extreme lack of genetic variation among all X. axonopodis pv. vesicatoria genomic loci (average nucleotide diversity, pi = 9.1 x 10(-5)), including avrBs2. This lack of diversity is consistent with X. axonopodis pv. vesicatoria having undergone a recent population bottleneck and/or selective sweep followed by population expansion. Coalescent analysis determined that approximately 1.4 x 10(4) to 7.16 x 10(4) bacterial generations have passed since the most recent common ancestor (MRCA) of the current X. axonopodis pv. vesicatoria population. Assuming a range of 50 to 500 bacterial generations per year, only 28 to 1,432 years have passed since the MRCA. This time frame coincides with human intervention with the pathogen's host plants, from domestication to modern agricultural practices. Examination of 19 mutated (loss-of-function) avrBs2 alleles detected nine classes of mutations. All mutations affected protein coding, while no synonymous changes were found. The nature of at least one of the avrBs2 mutations suggests that it may be possible to observe one stage of an evolutionary arms race as X. axonopodis pv. vesicatoria responds to selection pressure to alter avrBs2 to escape host plant resistance.
Collapse
Affiliation(s)
- Gale Wichmann
- Committee on Genetics, University of Chicago, Illinois, USA.
| | | | | | | |
Collapse
|
45
|
Branger S, Rolain JM, Raoult D. Evaluation of antibiotic susceptibilities of Ehrlichia canis, Ehrlichia chaffeensis, and Anaplasma phagocytophilum by real-time PCR. Antimicrob Agents Chemother 2005; 48:4822-8. [PMID: 15561862 PMCID: PMC529244 DOI: 10.1128/aac.48.12.4822-4828.2004] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We determined MICs of antibiotics against Anaplasma phagocytophilum, Ehrlichia chaffeensis, and Ehrlichia canis by real-time quantitative PCR. The doubling times of the organisms were established: 19 h for E. chaffeensis, 26 h for A. phagocytophilum, and 28 h for E. canis. In comparison to the reference method for determining sensitivities, which uses Diff-Quick staining, our PCR assay was very sensitive and specific. We confirmed that doxycycline and rifampin are highly active against these bacteria and found variable susceptibilities to fluoroquinolones; A. phagocytophilum was susceptible, but E. canis and E. chaffeensis were only partly susceptible. Beta-lactam compounds, cotrimoxazole, macrolide compounds, and telithromycin showed no activity against any of the three organisms. Thiamphenicol was found to be more active than chloramphenicol. For the first time, we showed that these three species have numerous point mutations in their 23S RNA genes, with those at positions 754, 2057, 2058, 2059, and 2611 (Escherichia coli numbering) known to confer resistance to macrolide compounds in other bacteria. The role of each of these mutations in resistance to these drugs should be investigated in the future. Our study confirms previous reports that quantitative PCR is a reliable method for determining antibiotic susceptibility; therefore, it might be useful for screening new drugs.
Collapse
Affiliation(s)
- S Branger
- Unité des Rickettsies, CNRS UMR 6020A, Faculté de Médecine, Marseille, France
| | | | | |
Collapse
|
46
|
Fournier PE, Zhu Y, Ogata H, Raoult D. Use of highly variable intergenic spacer sequences for multispacer typing of Rickettsia conorii strains. J Clin Microbiol 2004; 42:5757-66. [PMID: 15583310 PMCID: PMC535242 DOI: 10.1128/jcm.42.12.5757-5766.2004] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2004] [Revised: 06/28/2004] [Accepted: 08/09/2004] [Indexed: 11/20/2022] Open
Abstract
By use of the nearly perfectly colinear genomes of Rickettsia conorii and Rickettsia prowazekii, we compared the usefulness of three types of sequences for typing of R. conorii isolates: (i) 5 variable coding genes comprising the 16S ribosomal DNA, gltA, ompB, and sca4 (gene D) genes, which are present in both genomes, and the ompA gene, which is degraded in R. prowazekii; (ii) 28 genes degraded in R. conorii but intact in R. prowazekii, including 23 split and 5 remnant genes; and (iii) 27 conserved and 25 variable intergenic spacers. The 4 conserved and 23 split genes as well as the 27 conserved intergenic spacers each had identical sequences in 34 human and 5 tick isolates of R. conorii. Analysis of the ompA sequences identified three genotypes of R. conorii. The variable intergenic spacers were significantly more variable than conserved genes, split genes, remnant genes, and conserved spacers (P < 10(-2) in all cases). Four of the variable intergenic spacers (dksA-xerC, mppA-purC, rpmE-tRNA(fMet), and tRNA(Gly)-tRNA(Tyr)) had highly variable sequences; when they were combined for typing, multispacer typing (MST) identified 27 different genotypes in the 39 R. conorii isolates. Two batches from the same R. conorii strain, Malish (Seven), with different culture passage histories were found to exhibit the same MST type. MST was more discriminatory for strain genotyping than multiple gene sequencing (P < 10(-2)). Phylogenetic analysis based on MST sequences was concordant with the geographic origins of R. conorii isolates. Our study supports the usefulness of MST for strain genotyping. This tool may be useful for tracing a strain and identifying its source during outbreaks, including those resulting from bioterrorism.
Collapse
Affiliation(s)
- Pierre-Edouard Fournier
- Unité des Rickettsies, IFR 48, CNRS UMR 6020, Faculté de Médecine, Université de la Mediterranée, 27 Blvd. Jean Moulin, 13385 Marseille Cedex 5, France
| | | | | | | |
Collapse
|
47
|
Beres SB, Sylva GL, Sturdevant DE, Granville CN, Liu M, Ricklefs SM, Whitney AR, Parkins LD, Hoe NP, Adams GJ, Low DE, DeLeo FR, McGeer A, Musser JM. Genome-wide molecular dissection of serotype M3 group A Streptococcus strains causing two epidemics of invasive infections. Proc Natl Acad Sci U S A 2004; 101:11833-8. [PMID: 15282372 PMCID: PMC511060 DOI: 10.1073/pnas.0404163101] [Citation(s) in RCA: 109] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2004] [Indexed: 11/18/2022] Open
Abstract
Molecular factors that contribute to the emergence of new virulent bacterial subclones and epidemics are poorly understood. We hypothesized that analysis of a population-based strain sample of serotype M3 group A Streptococcus (GAS) recovered from patients with invasive infection by using genome-wide investigative methods would provide new insight into this fundamental infectious disease problem. Serotype M3 GAS strains (n = 255) cultured from patients in Ontario, Canada, over 11 years and representing two distinct infection peaks were studied. Genetic diversity was indexed by pulsed-field gel electrophoresis, DNA-DNA microarray, whole-genome PCR scanning, prophage genotyping, targeted gene sequencing, and single-nucleotide polymorphism genotyping. All variation in gene content was attributable to acquisition or loss of prophages, a molecular process that generated unique combinations of proven or putative virulence genes. Distinct serotype M3 genotypes experienced rapid population expansion and caused infections that differed significantly in character and severity. Molecular genetic analysis, combined with immunologic studies, implicated a 4-aa duplication in the extreme N terminus of M protein as a factor contributing to an epidemic wave of serotype M3 invasive infections. This finding has implications for GAS vaccine research. Genome-wide analysis of population-based strain samples cultured from clinically well defined patients is crucial for understanding the molecular events underlying bacterial epidemics.
Collapse
Affiliation(s)
- Stephen B Beres
- Laboratory of Human Bacterial Pathogenesis, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
48
|
de Filippis I, Salles CA, Zahner V, do Nascimento CRS, Momen H. Genetic diversity of Neisseria meningitidis strains isolated in Rio de Janeiro, Brazil, evaluated by multilocus enzyme electrophoresis. Lett Appl Microbiol 2004; 39:232-9. [PMID: 15287867 DOI: 10.1111/j.1472-765x.2004.01570.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
AIMS To analyse Neisseria meningitidis isolates from meningococcal meningitis cases in Rio de Janeiro (Brazil) from 1990 to 1993 and 1999-2002, to determine the genetic and relatedness with hypervirulent and epidemic strains. METHODS AND RESULTS The isolates were analysed by multilocus enzyme electrophoresis (MEE) clustering into 83 electrophoretic types (ET). All isolates from 1999 to 2002, formed a cluster which included one strain of the ET-5 complex worldwide associated with epidemics. CONCLUSIONS The overall results suggested a panmictic structure probably because of recombination events. The observation of a separated cluster including isolates from 1999 to 2002 and an ET-5 complex strain, also suggested the introduction of strains genetically related with this hypervirulent complex in the State of Rio de Janeiro (Brazil) over the last 5 years. SIGNIFICANCE AND IMPACT OF THE STUDY The presence of strains related to the ET-5 complex in several states of Brazil was already described elsewhere, but this is the first time it was reported in the State of Rio de Janeiro. Our findings reinforce the necessity to genetically determine the clones which should be considered to produce a national vaccine against meningococcal meningitis.
Collapse
Affiliation(s)
- I de Filippis
- Depto. de Microbiologia, Instituto Nacional de Controle de Qualidade em Saúde, FIOCRUZ, Rio de Janeiro, Brazil.
| | | | | | | | | |
Collapse
|
49
|
Kudva IT, Griffin RW, Murray M, John M, Perna NT, Barrett TJ, Calderwood SB. Insertions, deletions, and single-nucleotide polymorphisms at rare restriction enzyme sites enhance discriminatory power of polymorphic amplified typing sequences, a novel strain typing system for Escherichia coli O157:H7. J Clin Microbiol 2004; 42:2388-97. [PMID: 15184409 PMCID: PMC427851 DOI: 10.1128/jcm.42.6.2388-2397.2004] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2003] [Revised: 12/10/2003] [Accepted: 03/08/2004] [Indexed: 11/20/2022] Open
Abstract
Polymorphic amplified typing sequences (PATS) for Escherichia coli O157:H7 (O157) was previously based on indels containing XbaI restriction enzyme sites occurring in O-island sequences of the O157 genome. This strain-typing system, referred to as XbaI-based PATS, typed every O157 isolate tested in a reproducible, rapid, straightforward, and easy-to-interpret manner and had technical advantages over pulsed-field gel electrophoresis (PFGE). However, the system was less discriminatory than PFGE and was unable to differentiate fully between unrelated isolates. To overcome this drawback, we enhanced PATS by using another infrequently cutting restriction enzyme, AvrII (also known as BlnI), to identify additional polymorphic regions that could increase the discriminatory ability of PATS typing. Referred to as AvrII-based PATS, the system identified seven new polymorphic regions in the O157 genome. Unlike XbaI, polymorphisms involving AvrII sites were caused by both indels and single-nucleotide polymorphisms occurring in O-island and backbone sequences of the O157 genome. AvrII-based PATS by itself provided poor discrimination of the O157 isolates tested. However, when primer pairs amplifying the seven polymorphic AvrII sites were combined with those amplifying the eight polymorphic XbaI sites (combined PATS), the discriminatory power of PATS was enhanced. Combined PATS matched related O157 isolates better than PFGE while differentiating between unrelated isolates. PATS typed every O157 isolate tested and directly targeted polymorphic sequences responsible for differences in the restriction digest patterns of O157 genomic DNA, utilizing PCR rather than relying on gel electrophoresis. This enabled PATS to resolve the ambiguity in PFGE typing, including that arising from the "more distantly related" and "untypeable" profiles.
Collapse
Affiliation(s)
- Indira T Kudva
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA.
| | | | | | | | | | | | | |
Collapse
|
50
|
van Dessel H, Dijkshoorn L, van der Reijden T, Bakker N, Paauw A, van den Broek P, Verhoef J, Brisse S. Identification of a new geographically widespread multiresistant Acinetobacter baumannii clone from European hospitals. Res Microbiol 2004; 155:105-12. [PMID: 14990262 DOI: 10.1016/j.resmic.2003.10.003] [Citation(s) in RCA: 155] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2003] [Accepted: 10/02/2003] [Indexed: 11/16/2022]
Abstract
The aim of the study was to investigate the genetic diversity of Acinetobacter baumannii clinical strains that had previously been allocated to three major groups based on automated ribotyping. Forty-seven isolates from European hospitals and one isolate from a South African hospital, geographically representative of the three ribogroups (ribogroups 1, 2 and 3 with 10, 23 and 15 isolates, respectively), were analysed using the highly discriminatory fingerprinting methods AFLP and pulsed-field gel electrophoresis (PFGE). Based on AFLP data, the isolates clustered into three main groups, each corresponding to one ribogroup. Inclusion of reference strains of the previously described clones I and II, responsible for outbreaks in northwestern European hospitals, showed that ribogroups 1 and 2 correspond to clones I and II, respectively, whereas ribogroup 3 apparently represents a new clone. This clone III was found in France, The Netherlands, Italy and Spain. Clones I and II were not limited to northwestern European countries, as they were also recovered from Spain, South Africa, Poland and Italy (clone I) and from Spain, Portugal, South Africa, France, Greece and Turkey (clone II). Combined AFLP and PFGE data showed intraclonal diversity and led to the distinction of 23 different genotypes. Three genotypes, two of them belonging to clone II and one to clone III, were found in different hospitals and may correspond to subsets of isolates with a more recent clonal relationship, which emphasizes the epidemic potential of these organisms.
Collapse
Affiliation(s)
- Helke van Dessel
- Eijkman-Winkler Center for Microbiology, Infectious Diseases and Inflammation, University Medical Center Utrecht, AZU G04.614, P.O. Box 85500, 3508 GA, Utrecht, The Netherlands
| | | | | | | | | | | | | | | |
Collapse
|