1
|
Dhivahar J, Parthasarathy A, Krishnan K, Kovi BS, Pandian GN. Bat-associated microbes: Opportunities and perils, an overview. Heliyon 2023; 9:e22351. [PMID: 38125540 PMCID: PMC10730444 DOI: 10.1016/j.heliyon.2023.e22351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/21/2023] [Accepted: 11/09/2023] [Indexed: 12/23/2023] Open
Abstract
The potential biotechnological uses of bat-associated bacteria are discussed briefly, indicating avenues for biotechnological applications of bat-associated microbes. The uniqueness of bats in terms of their lifestyle, genomes and molecular immunology may predispose bats to act as disease reservoirs. Molecular phylogenetic analysis has shown several instances of bats harbouring the ancestral lineages of bacterial (Bartonella), protozoal (Plasmodium, Trypanosoma cruzi) and viral (SARS-CoV2) pathogens infecting humans. Along with the transmission of viruses from bats, we also discuss the potential roles of bat-associated bacteria, fungi, and protozoan parasites in emerging diseases. Current evidence suggests that environmental changes and interactions between wildlife, livestock, and humans contribute to the spill-over of infectious agents from bats to other hosts. Domestic animals including livestock may act as intermediate amplifying hosts for bat-origin pathogens to transmit to humans. An increasing number of studies investigating bat pathogen diversity and infection dynamics have been published. However, whether or how these infectious agents are transmitted both within bat populations and to other hosts, including humans, often remains unknown. Metagenomic approaches are uncovering the dynamics and distribution of potential pathogens in bat microbiomes, which might improve the understanding of disease emergence and transmission. Here, we summarize the current knowledge on bat zoonoses of public health concern and flag the gaps in the knowledge to enable further research and allocation of resources for tackling future outbreaks.
Collapse
Affiliation(s)
- J. Dhivahar
- Research Department of Zoology, St. Johns College, Palayamkottai, 627002, India
- Department of Plant Biology and Biotechnology, Laboratory of Microbial Ecology, Loyola College, Chennai, 600034, India
- Department of Biotechnology, Laboratory of Virology, University of Madras, Chennai, 600025, India
| | - Anutthaman Parthasarathy
- Department of Chemistry and Biosciences, Richmond Building, University of Bradford, Bradford, West Yorkshire, BD7 1DP, United Kingdom
| | - Kathiravan Krishnan
- Department of Biotechnology, Laboratory of Virology, University of Madras, Chennai, 600025, India
| | - Basavaraj S. Kovi
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Yoshida Ushinomiyacho, 69, Sakyo Ward, 606-8501, Kyoto, Japan
| | - Ganesh N. Pandian
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Yoshida Ushinomiyacho, 69, Sakyo Ward, 606-8501, Kyoto, Japan
| |
Collapse
|
2
|
McDougall F, Gordon D, Robins-Browne R, Bennett-Wood V, Boardman WSJ, Graham PL, Power M. Characterisation of typical enteropathogenic Escherichia coli (tEPEC) lineages and novel bfpA variants detected in Australian fruit bats (Pteropus poliocephalus). THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 902:166336. [PMID: 37591385 DOI: 10.1016/j.scitotenv.2023.166336] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 08/09/2023] [Accepted: 08/14/2023] [Indexed: 08/19/2023]
Abstract
Enteropathogenic Escherichia coli (EPEC) is an important cause of diarrhoeal disease in human infants. EPEC strains are defined by the presence of specific virulence factors including intimin (encoded by the eae gene) and bundle forming pili (Bfp). Bfp is encoded by the bfp operon and includes the bfpA gene for the major pilus subunit. By definition, Bfp are only present in typical EPEC (tEPEC), for which, humans are considered to be the only known natural host. This study detected tEPEC in faecal samples from a wild Australian fruit bat species, the grey-headed flying-fox (Pteropus poliocephalus). Whole genome sequencing of 61 E. coli isolates from flying-foxes revealed that 21.3 % (95%CI: 13 %-33 %) were tEPEC. Phylogenetic analyses showed flying-fox tEPEC shared evolutionary lineages with human EPEC, but were predominantly novel sequence types (9 of 13) and typically harboured novel bfpA variants (11 of 13). HEp-2 cell adhesion assays showed adherence to human-derived epithelial cells by all 13 flying-fox tEPEC, indicating that they all carried functional Bfp. Using an EPEC-specific duplex PCR, it was determined that tEPEC comprised 17.4 % (95%CI: 13 %-22 %) of 270 flying-fox E. coli isolates. Furthermore, a tEPEC-specific multiplex PCR detected the eae and bfpA virulence genes in 18.0 % (95%CI: 8.0 %-33.7 %) of 506 flying-fox faecal DNA samples, with occurrences ranging from 1.3 % to 87.0 % across five geographic areas sampled over a four-year period. The identification of six novel tEPEC sequence types and five novel bfpA variants suggests flying-foxes carry bat-specific tEPEC lineages. However, their close relationship with human EPEC and functional Bfp, indicates that flying-fox tEPEC have zoonotic potential and that dissemination of flying-fox tEPEC into urban environments may pose a public health risk. The consistent detection of tEPEC in flying-foxes over extensive geographical and temporal scales indicates that both wild grey-headed flying-foxes and humans should be regarded as natural tEPEC hosts.
Collapse
Affiliation(s)
- Fiona McDougall
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, NSW 2109, Australia.
| | - David Gordon
- Research School of Biology, Australian National University, ACT 2601, Australia.
| | - Roy Robins-Browne
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, VIC 3010, Australia; Murdoch Children's Research Institute, Royal Children's Hospital, VIC 3052, Australia.
| | - Vicki Bennett-Wood
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, VIC 3010, Australia; Murdoch Children's Research Institute, Royal Children's Hospital, VIC 3052, Australia.
| | - Wayne S J Boardman
- School of Animal and Veterinary Sciences, University of Adelaide, SA 5371, Australia.
| | - Petra L Graham
- School of Mathematical and Physical Sciences, Faculty of Science and Engineering, Macquarie University, NSW 2109, Australia.
| | - Michelle Power
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, NSW 2109, Australia.
| |
Collapse
|
3
|
Déchelotte P, Breton J, Trotin-Picolo C, Grube B, Erlenbeck C, Bothe G, Fetissov SO, Lambert G. The Probiotic Strain H. alvei HA4597 ® Improves Weight Loss in Overweight Subjects under Moderate Hypocaloric Diet: A Proof-of-Concept, Multicenter Randomized, Double-Blind Placebo-Controlled Study. Nutrients 2021; 13:nu13061902. [PMID: 34205871 PMCID: PMC8227740 DOI: 10.3390/nu13061902] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/27/2021] [Accepted: 05/30/2021] [Indexed: 12/20/2022] Open
Abstract
Background: Increasing evidence supports the role of the gut microbiota in the control of body weight and feeding behavior. Moreover, recent studies have reported that the probiotic strain Hafnia alvei HA4597® (HA), which produces the satietogenic peptide ClpB mimicking the effect of alpha-MSH, reduced weight gain and adiposity in rodent models of obesity. Methods: To investigate the clinical efficacy of HA, 236 overweight subjects were included, after written informed consent, in a 12-week prospective, double-blind, randomized study. All subjects received standardized counselling for a −20% hypocaloric diet and were asked to maintain their usual physical activity. Subjects of the HA group received two capsules per day providing 100 billion bacteria per day and subjects in the Placebo (P) group received two placebo capsules. The primary endpoint was the percentage of subjects achieving a weight loss of at least 3% after 12 weeks. Intention-to-treat statistical analysis was performed using exact-Fischer, Mann-Whitney and paired-Wilcoxon tests as appropriate. Results: In the HA group, significantly more subjects (+33%) met the primary endpoint than in the P group (54.9 vs. 41.4%, p = 0.048). In the HA group, an increased feeling of fullness (p = 0.009) and a greater loss of hip circumference (p < 0.001) at 12 weeks were also observed. Fasting glycemia at 12 weeks was significantly lower (p < 0.05) in the HA compared to P group. Clinical and biological tolerance was good in both groups. Conclusions: A 12-week treatment with the probiotic strain H. alvei HA4597® significantly improves weight loss, feeling of fullness and reduction of hip circumference in overweight subjects following moderate hypocaloric diet. These data support the use of H. alvei HA4597® in the global management of excess weight.
Collapse
Affiliation(s)
- Pierre Déchelotte
- Inserm UMR 1073, 76000 Rouen, France;
- Nutrition Department, University Hospital, 76000 Rouen, France
- Department of Biology, Rouen Normandy University, 76130 Mont-Saint-Aignan, France;
- Correspondence:
| | - Jonathan Breton
- Inserm UMR 1073, 76000 Rouen, France;
- Nutrition Department, University Hospital, 76000 Rouen, France
- Department of Biology, Rouen Normandy University, 76130 Mont-Saint-Aignan, France;
| | | | - Barbara Grube
- Practice for General Medicine, 12169 Berlin, Germany;
| | | | - Gordana Bothe
- Analyze & Realize GmbH, 13467 Berlin, Germany; (C.E.); (G.B.)
| | - Sergueï O. Fetissov
- Department of Biology, Rouen Normandy University, 76130 Mont-Saint-Aignan, France;
- Inserm UMR 1239, 76130 Mont-Saint-Aignan, France
| | | |
Collapse
|
4
|
The Changing Face of the Family Enterobacteriaceae (Order: " Enterobacterales"): New Members, Taxonomic Issues, Geographic Expansion, and New Diseases and Disease Syndromes. Clin Microbiol Rev 2021; 34:34/2/e00174-20. [PMID: 33627443 DOI: 10.1128/cmr.00174-20] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The family Enterobacteriaceae has undergone significant morphogenetic changes in its more than 85-year history, particularly during the past 2 decades (2000 to 2020). The development and introduction of new and novel molecular methods coupled with innovative laboratory techniques have led to many advances. We now know that the global range of enterobacteria is much more expansive than previously recognized, as they play important roles in the environment in vegetative processes and through widespread environmental distribution through insect vectors. In humans, many new species have been described, some associated with specific disease processes. Some established species are now observed in new infectious disease settings and syndromes. The results of molecular taxonomic and phylogenetics studies suggest that the current family Enterobacteriaceae should possibly be divided into seven or more separate families. The logarithmic explosion in the number of enterobacterial species described brings into question the relevancy, need, and mechanisms to potentially identify these taxa. This review covers the progression, transformation, and morphogenesis of the family from the seminal Centers for Disease Control and Prevention publication (J. J. Farmer III, B. R. Davis, F. W. Hickman-Brenner, A. McWhorter, et al., J Clin Microbiol 21:46-76, 1985, https://doi.org/10.1128/JCM.21.1.46-76.1985) to the present.
Collapse
|
5
|
Sanyal SK, Reith F, Shuster J. A genomic perspective of metal-resistant bacteria from gold particles: Possible survival mechanisms during gold biogeochemical cycling. FEMS Microbiol Ecol 2020; 96:5851273. [DOI: 10.1093/femsec/fiaa111] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 06/02/2020] [Indexed: 11/13/2022] Open
Abstract
ABSTRACT
A bacterial consortium was enriched from gold particles that ‘experienced’ ca. 80 years of biotransformation within waste-rock piles (Australia). This bacterial consortium was exposed to 10 µM AuCl3 to obtain Au-tolerant bacteria. From these isolates, Serratia sp. and Stenotrophomonas sp. were the most Au-tolerant and reduced soluble Au as pure gold nanoparticles, indicating that passive mineralisation is a mechanism for mediating the toxic effect of soluble Au produced during particle dissolution. Genome-wide analysis demonstrated that these isolates also possessed various genes that could provide cellular defence enabling survival under heavy-metal stressed condition by mediating the toxicity of heavy metals through active efflux/reduction. Diverse metal-resistant genes or genes clusters (cop, cus, czc, zntand ars) were detected, which could confer resistance to soluble Au. Comparative genome analysis revealed that the majority of detected heavy-metal resistant genes were similar (i.e. orthologous) to those genes of Cupriavidus metallidurans CH34. The detection of heavy-metal resistance, nutrient cycling and biofilm formation genes (pgaABCD, bsmAandhmpS) may have indirect yet important roles when dealing with soluble Au during particle dissolution. In conclusion, the physiological and genomic results suggest that bacteria living on gold particles would likely use various genes to ensure survival during Au-biogeochemical cycling.
Collapse
Affiliation(s)
- Santonu Kumar Sanyal
- School of Biological Sciences, The University of Adelaide, North Terrace, Adelaide, South Australia 5005, Australia
- CSIRO Land & Water, Environmental Contaminant Mitigation and Technologies, Gate 4 Waite Road, Glen Osmond, South Australia 5064, Australia
| | - Frank Reith
- School of Biological Sciences, The University of Adelaide, North Terrace, Adelaide, South Australia 5005, Australia
- CSIRO Land & Water, Environmental Contaminant Mitigation and Technologies, Gate 4 Waite Road, Glen Osmond, South Australia 5064, Australia
| | - Jeremiah Shuster
- School of Biological Sciences, The University of Adelaide, North Terrace, Adelaide, South Australia 5005, Australia
- CSIRO Land & Water, Environmental Contaminant Mitigation and Technologies, Gate 4 Waite Road, Glen Osmond, South Australia 5064, Australia
| |
Collapse
|
6
|
Baquero F, Coque TM, Martínez JL, Aracil-Gisbert S, Lanza VF. Gene Transmission in the One Health Microbiosphere and the Channels of Antimicrobial Resistance. Front Microbiol 2019; 10:2892. [PMID: 31921068 PMCID: PMC6927996 DOI: 10.3389/fmicb.2019.02892] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 12/02/2019] [Indexed: 12/12/2022] Open
Abstract
Antibiotic resistance is a field in which the concept of One Health can best be illustrated. One Health is based on the definition of communication spaces among diverse environments. Antibiotic resistance is encoded by genes, however, these genes are propagated in mobile genetic elements (MGEs), circulating among bacterial species and clones that are integrated into the multiple microbiotas of humans, animals, food, sewage, soil, and water environments, the One Health microbiosphere. The dynamics and evolution of antibiotic resistance depend on the communication networks linking all these ecological, biological, and genetic entities. These communications occur by environmental overlapping and merging, a critical issue in countries with poor sanitation, but also favored by the homogenizing power of globalization. The overwhelming increase in the population of highly uniform food animals has contributed to the parallel increase in the absolute size of their microbiotas, consequently enhancing the possibility of microbiome merging between humans and animals. Microbial communities coalescence might lead to shared microbiomes in which the spread of antibiotic resistance (of human, animal, or environmental origin) is facilitated. Intermicrobiome communication is exerted by shuttle bacterial species (or clones within species) belonging to generalist taxa, able to multiply in the microbiomes of various hosts, including humans, animals, and plants. Their integration into local genetic exchange communities fosters antibiotic resistance gene flow, following the channels of accessory genome exchange among bacterial species. These channels delineate a topology of gene circulation, including dense clusters of species with frequent historical and recent exchanges. The ecological compatibility of these species, sharing the same niches and environments, determines the exchange possibilities. In summary, the fertility of the One Health approach to antibiotic resistance depends on the progress of understanding multihierarchical systems, encompassing communications among environments (macro/microaggregates), among microbiotas (communities), among bacterial species (clones), and communications among MGEs.
Collapse
Affiliation(s)
- Fernando Baquero
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
| | - Teresa M. Coque
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
| | - José-Luis Martínez
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Sonia Aracil-Gisbert
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
| | - Val F. Lanza
- Bioinformatics Unit, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
- CIBER in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| |
Collapse
|
7
|
Gu W, Tong P, Liu C, Wang W, Lu C, Han Y, Sun X, Kuang DX, Li N, Dai J. The characteristics of gut microbiota and commensal Enterobacteriaceae isolates in tree shrew (Tupaia belangeri). BMC Microbiol 2019; 19:203. [PMID: 31477004 PMCID: PMC6721287 DOI: 10.1186/s12866-019-1581-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 08/27/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Tree shrew is a novel laboratory animal with specific characters for human disease researches in recent years. However, little is known about its characteristics of gut microbial community and intestinal commensal bacteria. In this study, 16S rRNA sequencing method was used to illustrate the gut microbiota structure and commensal Enterobacteriaceae bacteria were isolated to demonstrate their features. RESULTS The results showed Epsilonbacteraeota (30%), Proteobacteria (25%), Firmicutes (19%), Fusobacteria (13%), and Bacteroidetes (8%) were the most abundant phyla in the gut of tree shrew. Campylobacteria, Campylobacterales, Helicobacteraceae and Helicobacter were the predominant abundance for class, order, family and genus levels respectively. The alpha diversity analysis showed statistical significance (P < 0.05) for operational taxonomic units (OTUs), the richness estimates, and diversity indices for age groups of tree shrew. Beta diversity revealed the significant difference (P < 0.05) between age groups, which showed high abundance of Epsilonbacteraeota and Spirochaetes in infant group, Proteobacteria in young group, Fusobacteria in middle group, and Firmicutes in senile group. The diversity of microbial community was increased followed by the aging process of this animal. 16S rRNA gene functional prediction indicated that highly hot spots for infectious diseases, and neurodegenerative diseases in low age group of tree shrew (infant and young). The most isolated commensal Enterobacteriaceae bacteria from tree shrew were Proteus spp. (67%) and Escherichia coli (25%). Among these strains, the antibiotic resistant isolates were commonly found, and pulsed-field gel electrophoresis (PFGE) results of Proteus spp. indicated a high degree of similarity between isolates in the same age group, which was not observed for other bacteria. CONCLUSIONS In general, this study made understandings of the gut community structure and diversity of tree shrew.
Collapse
Affiliation(s)
- Wenpeng Gu
- Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Yunnan Innovation Team of Standardization and Application Research in Tree Shrew, Zhao zong Road 66, Kunming, 650118, China.,Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Centre for Disease Control and Prevention, Kunming, 650022, China
| | - Pinfen Tong
- Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Yunnan Innovation Team of Standardization and Application Research in Tree Shrew, Zhao zong Road 66, Kunming, 650118, China
| | - Chenxiu Liu
- Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Yunnan Innovation Team of Standardization and Application Research in Tree Shrew, Zhao zong Road 66, Kunming, 650118, China
| | - Wenguang Wang
- Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Yunnan Innovation Team of Standardization and Application Research in Tree Shrew, Zhao zong Road 66, Kunming, 650118, China
| | - Caixia Lu
- Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Yunnan Innovation Team of Standardization and Application Research in Tree Shrew, Zhao zong Road 66, Kunming, 650118, China
| | - Yuanyuan Han
- Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Yunnan Innovation Team of Standardization and Application Research in Tree Shrew, Zhao zong Road 66, Kunming, 650118, China
| | - Xiaomei Sun
- Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Yunnan Innovation Team of Standardization and Application Research in Tree Shrew, Zhao zong Road 66, Kunming, 650118, China
| | - De Xuan Kuang
- Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Yunnan Innovation Team of Standardization and Application Research in Tree Shrew, Zhao zong Road 66, Kunming, 650118, China
| | - Na Li
- Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Yunnan Innovation Team of Standardization and Application Research in Tree Shrew, Zhao zong Road 66, Kunming, 650118, China
| | - Jiejie Dai
- Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Yunnan Innovation Team of Standardization and Application Research in Tree Shrew, Zhao zong Road 66, Kunming, 650118, China.
| |
Collapse
|
8
|
Clermont O, Dixit OVA, Vangchhia B, Condamine B, Dion S, Bridier-Nahmias A, Denamur E, Gordon D. Characterization and rapid identification of phylogroup G in Escherichia coli, a lineage with high virulence and antibiotic resistance potential. Environ Microbiol 2019; 21:3107-3117. [PMID: 31188527 DOI: 10.1111/1462-2920.14713] [Citation(s) in RCA: 124] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/31/2019] [Accepted: 06/09/2019] [Indexed: 12/22/2022]
Abstract
The phylogeny of the Escherichia coli species, with the identification of seven phylogroups (A, B1, B2, C, D, E and F), is linked to the lifestyle of the strains. With the accumulation of whole genome sequence data, it became clear that some strains belong to a group intermediate between the F and B2 phylogroups, designated as phylogroup G. Here, we studied the complete sequences of 112 strains representative of the G phylogroup diversity and showed that it is composed of one main sequence type complex (STc)117 and four other STcs (STc657, STc454, STc738 and STc174). STc117, which phylogeny is characterized by very short internal branches, exhibits extensive O diversity, but little H-type and fimH allele diversity, whereas the other STcs are characterized by a main O, H and fimH type. STc117 strains possess many traits associated with extra-intestinal virulence, are virulent in a mouse sepsis model and exhibit multi-drug resistance such as CTX-M production. Epidemiologic data on 4,524 Australian and French strains suggest that STc117 is a poultry-associated lineage that can also establish in humans and cause extra-intestinal diseases. We propose an easy identification method that will help to trace this potentially virulent and resistant phylogroup in epidemiologic studies.
Collapse
Affiliation(s)
- Olivier Clermont
- IAME, UMR 1137, INSERM, Université de Paris, Paris, 75018, France
| | - Ojas V A Dixit
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Belinda Vangchhia
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia.,Department of Veterinary Microbiology, College of Veterinary Sciences & Animal Husbandry, Central Agricultural University, Aizawl, 796014, India
| | | | - Sara Dion
- IAME, UMR 1137, INSERM, Université de Paris, Paris, 75018, France
| | | | - Erick Denamur
- IAME, UMR 1137, INSERM, Université de Paris, Paris, 75018, France.,Laboratoire de Génétique Moléculaire, Hôpital Bichat, Paris, 75018, France
| | - David Gordon
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| |
Collapse
|
9
|
Horváthová T, Babik W, Kozłowski J, Bauchinger U. Vanishing benefits - The loss of actinobacterial symbionts at elevated temperatures. J Therm Biol 2019; 82:222-228. [PMID: 31128651 DOI: 10.1016/j.jtherbio.2019.04.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 04/15/2019] [Accepted: 04/20/2019] [Indexed: 12/11/2022]
Abstract
Only a few insect species are known to engage in symbiotic associations with antibiotic-producing Actinobacteria and profit from this kind of protection against pathogens. However, it still remains elusive how widespread the symbiotic interactions with Actinobacteria in other organisms are and how these partnerships benefit the hosts in terms of the growth and survival. We characterized a drastic temperature-induced change in the occurrence of Actinobacteria in the gut of the terrestrial isopod Porcellio scaber reared under two different temperature (15 °C and 22 °C) and oxygen conditions (10% and 22% O2) using 16S rRNA gene sequencing. We show that the relative abundance of actinobacterial gut symbionts correlates with increased host growth at lower temperature. Actinobacterial symbionts were almost completely absent at 22 °C under both high and low oxygen conditions. In addition, we identified members of nearly half of the known actinobacterial families in the isopod microbiome, and most of these include members that are known to produce antibiotics. Our study suggests that hosting diverse actinobacterial symbionts may provide conditions favorable for host growth. These findings show how a temperature-driven decline in microbiome diversity may cause a loss of beneficial functions with negative effects on ectotherms.
Collapse
Affiliation(s)
- Terézia Horváthová
- Institute of Environmental Sciences, Jagiellonian University, ul. Gronostajowa 7, 30-387 Kraków, Poland; Institute of Soil Biology, Biology Centre, Czech Academy of Sciences, Na Sádkách 7, České Budějovice, Czech Republic.
| | - Wiesław Babik
- Institute of Environmental Sciences, Jagiellonian University, ul. Gronostajowa 7, 30-387 Kraków, Poland
| | - Jan Kozłowski
- Institute of Environmental Sciences, Jagiellonian University, ul. Gronostajowa 7, 30-387 Kraków, Poland
| | - Ulf Bauchinger
- Institute of Environmental Sciences, Jagiellonian University, ul. Gronostajowa 7, 30-387 Kraków, Poland
| |
Collapse
|
10
|
Nanayakkara BS, O'Brien CL, Gordon DM. Diversity and distribution of Klebsiella capsules in Escherichia coli. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:107-117. [PMID: 30411512 DOI: 10.1111/1758-2229.12710] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 10/31/2018] [Accepted: 11/03/2018] [Indexed: 06/08/2023]
Abstract
E. coli strains responsible for elevated counts (blooms) in freshwater reservoirs in Australia carry a capsule originating from Klebsiella. The occurrence of Klebsiella capsules in E. coli was about 7% overall and 23 different capsule types were detected. Capsules were observed in strains from phylogroups A, B1 and C, but were absent from phylogroup B2, D, E and F strains. In general, few A, B1 or C lineages were capsule-positive, but when a lineage was encapsulated multiple different capsule types were present. All Klebsiella capsule-positive strains were of serogroups O8, O9 and O89. Regardless of the phylogroup, O9 strains were more likely to be capsule-positive than O8 strains. Given the sequence similarity, it appears that both the capsule region and the O-antigen gene region are transferred to E. coli from Klebsiella as a single block via horizontal gene transfer events. Pan genome analysis indicated that there were only modest differences between encapsulated and non-encapsulated strains belonging to phylogroup A. The possession of a Klebsiella capsule, but not the type of capsule, is likely a key determinant of the bloom status of a strain.
Collapse
Affiliation(s)
- Buddhie S Nanayakkara
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
- Department of Botany, Faculty of Science, University of Peradeniya, Peradeniya, 20400, Sri Lanka
| | - Claire L O'Brien
- Medical School, The Australian National University, Canberra, ACT 2601, Australia
- Gastroenterology and Hepatology Unit, Canberra Hospital, Canberra, ACT, Australia
| | - David M Gordon
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| |
Collapse
|
11
|
Blin C, Passet V, Touchon M, Rocha EPC, Brisse S. Metabolic diversity of the emerging pathogenic lineages of Klebsiella pneumoniae. Environ Microbiol 2017; 19:1881-1898. [PMID: 28181409 DOI: 10.1111/1462-2920.13689] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 02/01/2017] [Accepted: 02/01/2017] [Indexed: 11/30/2022]
Abstract
Multidrug resistant and hypervirulent clones of Klebsiella pneumoniae are emerging pathogens. To understand the association between genotypic and phenotypic diversity in this process, we combined genomic, phylogenomic and phenotypic analysis of a diverse set of K. pneumoniae and closely related species. These species were able to use an unusually large panel of metabolic substrates for growth, many of which were shared between all strains. We analysed the substrates used by only a fraction of the strains, identified some of their genetic basis, and found that many could not be explained by the phylogeny of the strains. Puzzlingly, few traits were associated with the ecological origin of the strains. One noticeable exception was the ability to use D-arabinose, which was much more frequent in hypervirulent strains. The broad carbon and nitrogen core metabolism of K. pneumoniae might contribute to its ability to thrive in diverse environments. Accordingly, even the hypervirulent and multidrug resistant clones have the metabolic signature of ubiquitous bacteria. The apparent few metabolic differences between hypervirulent, multi-resistant and environmental strains may favour the emergence of dual-risk strains that combine resistance and hypervirulence.
Collapse
Affiliation(s)
- Camille Blin
- UPMC Univ Paris06, IFD, 4 Place Jussieu, Sorbonne Universités, 75252 PARIS cedex 05, France.,Institut Pasteur, Microbial Evolutionary Genomics, Paris, France.,UMR3525, Paris, CNRS, France
| | - Virginie Passet
- Institut Pasteur, Microbial Evolutionary Genomics, Paris, France.,UMR3525, Paris, CNRS, France
| | - Marie Touchon
- Institut Pasteur, Microbial Evolutionary Genomics, Paris, France.,UMR3525, Paris, CNRS, France
| | - Eduardo P C Rocha
- Institut Pasteur, Microbial Evolutionary Genomics, Paris, France.,UMR3525, Paris, CNRS, France
| | - Sylvain Brisse
- Institut Pasteur, Microbial Evolutionary Genomics, Paris, France.,UMR3525, Paris, CNRS, France.,Institut Pasteur, Molecular Prevention and Therapy of Human Diseases, Paris, France
| |
Collapse
|
12
|
Atzinger A, Butela K, Lawrence JG. The O-antigen mediates differential survival of Salmonella against communities of natural predators. MICROBIOLOGY-SGM 2016; 162:610-621. [PMID: 26888189 DOI: 10.1099/mic.0.000259] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Antigenically distinct members of bacterial species can be differentially distributed in the environment. Predators known to consume antigenically distinct prey with different efficiencies are also differentially distributed. Here we show that antigenically distinct, but otherwise isogenic and physiologically indistinct, strains of Salmonella enterica show differential survival in natural soil, sediment and intestinal environments, where they would face a community of predators. Decline in overall cell numbers is attenuated by factors that inhibit the action of predators, including heat and antiprotozoal and antihelminthic drugs. Moreover, the fitness of strains facing these predators - calculated by comparing survival with and without treatments attenuating predator activity - varies between environments. These results suggest that relative survival in natural environments is arbitrated by communities of natural predators whose feeding preferences, if not species composition, vary between environments. These data support the hypothesis that survival against natural predators may drive the differential distribution of bacteria among microenvironments.
Collapse
Affiliation(s)
- Aletheia Atzinger
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Kristen Butela
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Jeffrey G Lawrence
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| |
Collapse
|
13
|
Spatial Variation and Survival of Salmonella enterica Subspecies in a Population of Australian Sleepy Lizards (Tiliqua rugosa). Appl Environ Microbiol 2015; 81:5804-11. [PMID: 26092451 DOI: 10.1128/aem.00997-15] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2015] [Accepted: 06/11/2015] [Indexed: 01/09/2023] Open
Abstract
The life cycles of many enteric bacterial species require a transition between two very distinct environments. Their primary habitat is the gastrointestinal tract of the host, while their secondary habitat, during transmission from one host to another, consists of environments external to the host, such as soil, water, and sediments. Consequently, both host and environmental factors shape the genetic structure of enteric bacterial populations. This study examined the distribution of four Salmonella enterica subspecies in a population of sleepy lizards, Tiliqua rugosa, in a semiarid region of South Australia. The lizards living within the 1,920-m by 720-m study site were radio tracked, and their enteric bacteria were sampled at regular intervals throughout their active seasons in the years 2001, 2002, and 2006. Four of the six subspecies of S. enterica were present in this population and were nonrandomly distributed among the lizards. In particular, S. enterica subsp. diarizonae was restricted to lizards living in the most shaded parts of the study site with an overstorey of Casuarina trees. Experiments undertaken to investigate the survival of S. enterica cells under seminatural conditions revealed that cell survival decreased with increased exposure to elevated temperatures and UV light. Among the three S. enterica subspecies tested, S. enterica subsp. diarizonae consistently had an average expected life span that was shorter than that observed for the other two subspecies. There was no indication in the data that there was any competitive dominance hierarchy among the S. enterica subspecies within individual hosts. Thus, the nonrandom distribution of S. enterica subspecies in this population of lizards appears to be driven by their different survival characteristics in the external environment.
Collapse
|
14
|
Murugaiyan J, Krueger K, Roesler U, Weinreich J, Schierack P. Assessment of species and antimicrobial resistance among Enterobacteriaceae isolated from mallard duck faeces. ENVIRONMENTAL MONITORING AND ASSESSMENT 2015; 187:127. [PMID: 25697309 DOI: 10.1007/s10661-015-4346-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 02/09/2015] [Indexed: 06/04/2023]
Abstract
Mallard ducks have demonstrated to be a likely reservoir for zoonotic E. coli strains; thus, it is possible that these ducks could also act as a reservoir for other Enterobacteriaceae members. The present study was initiated to evaluate the species distribution of Enterobacteriaceae other than E. coli in 175 fresh faecal samples collected from a population of mallard ducks. Sixty-four samples displayed detectable colonies of Enterobacteriaceae (excluding E. coli), which resulted in 75 pulsed-field gel electrophoresis (PFGE) types. Seventy-five single representatives of each PFGE type were subjected to identification with API 32NE and MALDI TOF MS systems due to the practical difficulties in species differentiation of Enterobacteriaceae. Those isolated were found to be from nine genera: Buttiauxella (15 %), Citrobacter (5 %), Enterobacter (32 %), Hafnia (1 %), Leclercia (1 %), Pantoea (7 %), Raoultella (21 %), Rahnella (7 %) and Serratia (11 %). Evaluation of antimicrobial resistance phenotypes using the disc method and detection of resistance genes using the microarray method revealed that these microbes possess resistance to β-lactams, aminoglycosides, macrolides, quinolones, rifamycine, sulphonamides, streptogramins and diaminopyrimidines. In conclusion, mallard ducks harbour a variety of non-pathogenic and pathogenic Enterobacteriaceae species like Enterobacter cloacae and Enterobacter amnigenus in their intestine and could act as a reservoir of resistant Enterobacteriaceae.
Collapse
Affiliation(s)
- Jayaseelan Murugaiyan
- Institute of Animal Hygiene and Environmental Health, Center for Infectious Medicine, Freie Universitaet Berlin, Robert-von-Ostertag Str. 7-13, 14163, Berlin, Germany,
| | | | | | | | | |
Collapse
|
15
|
Escherichia coli isolate for studying colonization of the mouse intestine and its application to two-component signaling knockouts. J Bacteriol 2014; 196:1723-32. [PMID: 24563035 DOI: 10.1128/jb.01296-13] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The biology of Escherichia coli in its primary niche, the animal intestinal tract, is remarkably unexplored. Studies with the streptomycin-treated mouse model have produced important insights into the metabolic requirements for Escherichia coli to colonize mice. However, we still know relatively little about the physiology of this bacterium growing in the complex environment of an intestine that is permissive for the growth of competing flora. We have developed a system for studying colonization using an E. coli strain, MP1, isolated from a mouse. MP1 is genetically tractable and does not require continuous antibiotic treatment for stable colonization. As an application of this system, we separately knocked out each two-component system response regulator in MP1 and performed competitions against the wild-type strain. We found that only three response regulators, ArcA, CpxR, and RcsB, produce strong colonization defects, suggesting that in addition to anaerobiosis, adaptation to cell envelope stress is a critical requirement for E. coli colonization of the mouse intestine. We also show that the response regulator OmpR, which had previously been hypothesized to be important for adaptation between in vivo and ex vivo environments, is not required for MP1 colonization due to the presence of a third major porin.
Collapse
|
16
|
The evolutionary histories of clinical and environmental SHV β-lactamases are intertwined. J Mol Evol 2013; 76:388-93. [PMID: 23860538 DOI: 10.1007/s00239-013-9574-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 07/05/2013] [Indexed: 10/26/2022]
Abstract
The rise of antibiotic-resistant pathogens focuses our attention on the source of antibiotic resistance genes, on the existence of these genes in environments exposed to little or no antibiotics, and on the relationship between resistance genes found in the clinic and those encountered in non-clinical settings. Here, we address the evolutionary history of a class of resistance genes, the SHV β-lactamases. We focus on bla SHV genes isolated both from clinical and non-clinical sources and show that clinically important resistance determinants arise repeatedly from within a diverse pool of bla SHV genes present in the environment. While our results argue against the notion of a single common origin for all clinically derived bla SHV genes, we detect a characteristic selective signature shaping this protein in clinical environments. This clinical signature reveals the joint action of purifying and positive selection on specific residues, including those known to confer extended-spectrum activity. Surprisingly, antibiotic resistance genes isolated from non-clinical-and presumably antibiotic-free-settings also experience the joint action of purifying and positive selection. The picture that emerges undercuts the notion of a separate reservoir of antibiotic resistance genes confined only to clinical settings. Instead, we argue for the presence of a single extensive and variable pool of antibiotic resistance genes present in the environment.
Collapse
|
17
|
Escherichia coli lacking RpoS are rare in natural populations of non-pathogens. G3-GENES GENOMES GENETICS 2012; 2:1341-4. [PMID: 23173085 PMCID: PMC3484664 DOI: 10.1534/g3.112.003855] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Accepted: 08/31/2012] [Indexed: 11/18/2022]
Abstract
The alternative sigma factor RpoS controls a large regulon that allows E. coli to respond to a variety of stresses. Mutations in rpoS can increase rates of nutrient acquisition at the cost of a decrease in stress resistance. These kinds of mutations evolve rapidly under certain laboratory conditions where nutrient acquisition is especially challenging. The frequency of strains lacking RpoS in natural populations of E. coli is less clear. Such strains have been found at frequencies over 20% in some collections of wild isolates. However, laboratory handling can select for RpoS-null strains and may have affected some of these strain collections. Other studies have included an unknown diversity of strains or only used a phenotypic proxy as a measure of RpoS levels. We directly measured RpoS levels in a collection of E. coli that includes the full diversity of the species and that was handled in a manner to minimize the potential for laboratory evolution. We found that only 2% of strains produce no functional RpoS. Comparison of these strains in multiple labs shows that these rpoS mutations occurred in the laboratory. Earlier studies reporting much higher levels of RpoS polymorphism may reflect the storage history of the strains in laboratories rather than true frequency of such strains in natural populations.
Collapse
|
18
|
Abstract
The occurrence of emerging infectious diseases and their relevance to human health has increased the interest in bats as potential reservoir hosts and vectors of zoonotic pathogens. But while previous and ongoing research activities predominantly focused on viral agents, the prevalence of pathogenic bacteria in bats and their impact on bat mortality have largely neglected. Enteric pathogens found in bats are often considered to originate from the bats' diet and foraging habitats, despite the fact that little is known about the actual ecological context or even transmission cycles involving bats, humans and other animals like pets and livestock. For some bacterial pathogens common in human and animal diseases (e.g. Pasteurella, Salmonella, Escherichia and Yersinia spp.), the pathogenic potential has been confirmed for bats. Other bacterial pathogens (e.g. Bartonella, Borrelia and Leptospira spp.) provide evidence for novel species that seem to be specific for bat hosts but might also be of disease importance in humans and other animals. The purpose of this review is to summarize the current knowledge of bacterial pathogens identified in bats and to consider factors that might influence the exposure and susceptibility of bats to bacterial infection but could also affect bacterial transmission rates between bats, humans and other animals.
Collapse
Affiliation(s)
- K Mühldorfer
- Research Group of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany.
| |
Collapse
|
19
|
Clermont O, Gordon DM, Brisse S, Walk ST, Denamur E. Characterization of the cryptic Escherichia lineages: rapid identification and prevalence. Environ Microbiol 2011; 13:2468-77. [PMID: 21651689 DOI: 10.1111/j.1462-2920.2011.02519.x] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Strains phenotypically indistinguishable from Escherichia coli and belonging to at least five distinct cryptic lineages, named Escherichia clades I to V, that are genetically divergent from E. coli yet members of the genus have been recently found using multi-locus sequence typing (MLST). Very few epidemiological data are available on these strains as their detection by MLST is not suitable for large-scale studies. In this work, we developed a rapid PCR method based on aes and chuA allele-specific amplifications that assigns a strain a cryptic lineage membership. By screening more than 3500 strains with this approach, we show that the cryptic lineages of Escherichia are unlikely to be detected in human faecal samples (2-3% frequency) and even less likely to be isolated from extra-intestinal body sites (< 1% frequency). They are more abundant in animal faeces ranging from 3-8% in non-human mammals to 8-28% in birds. Overall, the strains from the clade V are the most abundant and from the clade II very rare. These results suggest that members of the cryptic clades are unlikely to be of significance to human and health but may influence the use of 'E. coli' as an indicator of water quality.
Collapse
|
20
|
Substructure within Salmonella enterica subsp. enterica isolates from Australian wildlife. Appl Environ Microbiol 2011; 77:3151-3. [PMID: 21378038 DOI: 10.1128/aem.02764-10] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Multilocus sequence typing of 56 Salmonella enterica subsp. enterica strains isolated from Australian wildlife hosts was performed. The results of population assignment algorithms revealed that the 56 strains could be subdivided into two distinct clades. Strains belonging to the two clades were further distinguished phenotypically, genotypically, and with respect to host distribution.
Collapse
|
21
|
Biofilm formation by and thermal niche and virulence characteristics of Escherichia spp. Appl Environ Microbiol 2011; 77:2695-700. [PMID: 21335385 DOI: 10.1128/aem.02401-10] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
In order to better understand the ecological and virulence characteristics of the various clades of Escherichia, in vitro and in vivo experiments were undertaken. Members of the recently described cryptic clades of Escherichia (clades III, IV, and V) were found to have an enhanced ability to form biofilms compared to strains of Escherichia coli, E. fergusonii, or E. albertii. Members of the cryptic clades were also able to replicate at a lower temperature (5°C versus 11°C) than strains of the named species of Escherichia. Neither a strain's maximal growth rate nor its optimal temperature for growth varied with respect to the strain's phylogenetic affiliation. Escherichia strains not belonging to the species E. coli were positive for a mix of traits thought to enhance a strain's ability to cause either intestinal or extraintestinal disease. However, no non-E. coli Escherichia strain was virulent in a mouse model of extraintestinal infection. The frequency of resistance to antibiotics was low, and none of the strains tested harbored class 1, 2, or 3 integrons. The results of these experiments support the hypothesis that members of the cryptic Escherichia clades may be better able to persist in the external environment compared to E. coli, E. fergusonii, or E. albertii, isolates.
Collapse
|
22
|
Stressmann FA, Rogers GB, Klem ER, Lilley AK, Donaldson SH, Daniels TW, Carroll MP, Patel N, Forbes B, Boucher RC, Wolfgang MC, Bruce KD. Analysis of the bacterial communities present in lungs of patients with cystic fibrosis from American and British centers. J Clin Microbiol 2011; 49:281-91. [PMID: 21068277 PMCID: PMC3020463 DOI: 10.1128/jcm.01650-10] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2010] [Revised: 09/24/2010] [Accepted: 11/01/2010] [Indexed: 12/24/2022] Open
Abstract
The aim of this study was to determine whether geographical differences impact the composition of bacterial communities present in the airways of cystic fibrosis (CF) patients attending CF centers in the United States or United Kingdom. Thirty-eight patients were matched on the basis of clinical parameters into 19 pairs comprised of one U.S. and one United Kingdom patient. Analysis was performed to determine what, if any, bacterial correlates could be identified. Two culture-independent strategies were used: terminal restriction fragment length polymorphism (T-RFLP) profiling and 16S rRNA clone sequencing. Overall, 73 different terminal restriction fragment lengths were detected, ranging from 2 to 10 for U.S. and 2 to 15 for United Kingdom patients. The statistical analysis of T-RFLP data indicated that patient pairing was successful and revealed substantial transatlantic similarities in the bacterial communities. A small number of bands was present in the vast majority of patients in both locations, indicating that these are species common to the CF lung. Clone sequence analysis also revealed that a number of species not traditionally associated with the CF lung were present in both sample groups. The species number per sample was similar, but differences in species presence were observed between sample groups. Cluster analysis revealed geographical differences in bacterial presence and relative species abundance. Overall, the U.S. samples showed tighter clustering with each other compared to that of United Kingdom samples, which may reflect the lower diversity detected in the U.S. sample group. The impact of cross-infection and biogeography is considered, and the implications for treating CF lung infections also are discussed.
Collapse
Affiliation(s)
- Franziska A. Stressmann
- Molecular Microbiology Research Laboratory, Pharmaceutical Science Research Division, King's College London, 150 Stamford Street, Franklin-Wilkins Building, London, SE1 9NH, United Kingdom, Cystic Fibrosis/Pulmonary Research and Treatment Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, Cystic Fibrosis Unit, Southampton University Hospitals NHS Trust, Tremona Road, Southampton, SO16 6YD, United Kingdom, Pharmaceutical Science Division, King's College London, 150 Stamford Street, Franklin-Wilkins Building, London, SE1 9NH, United Kingdom, Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Geraint B. Rogers
- Molecular Microbiology Research Laboratory, Pharmaceutical Science Research Division, King's College London, 150 Stamford Street, Franklin-Wilkins Building, London, SE1 9NH, United Kingdom, Cystic Fibrosis/Pulmonary Research and Treatment Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, Cystic Fibrosis Unit, Southampton University Hospitals NHS Trust, Tremona Road, Southampton, SO16 6YD, United Kingdom, Pharmaceutical Science Division, King's College London, 150 Stamford Street, Franklin-Wilkins Building, London, SE1 9NH, United Kingdom, Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Erich R. Klem
- Molecular Microbiology Research Laboratory, Pharmaceutical Science Research Division, King's College London, 150 Stamford Street, Franklin-Wilkins Building, London, SE1 9NH, United Kingdom, Cystic Fibrosis/Pulmonary Research and Treatment Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, Cystic Fibrosis Unit, Southampton University Hospitals NHS Trust, Tremona Road, Southampton, SO16 6YD, United Kingdom, Pharmaceutical Science Division, King's College London, 150 Stamford Street, Franklin-Wilkins Building, London, SE1 9NH, United Kingdom, Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Andrew K. Lilley
- Molecular Microbiology Research Laboratory, Pharmaceutical Science Research Division, King's College London, 150 Stamford Street, Franklin-Wilkins Building, London, SE1 9NH, United Kingdom, Cystic Fibrosis/Pulmonary Research and Treatment Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, Cystic Fibrosis Unit, Southampton University Hospitals NHS Trust, Tremona Road, Southampton, SO16 6YD, United Kingdom, Pharmaceutical Science Division, King's College London, 150 Stamford Street, Franklin-Wilkins Building, London, SE1 9NH, United Kingdom, Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Scott H. Donaldson
- Molecular Microbiology Research Laboratory, Pharmaceutical Science Research Division, King's College London, 150 Stamford Street, Franklin-Wilkins Building, London, SE1 9NH, United Kingdom, Cystic Fibrosis/Pulmonary Research and Treatment Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, Cystic Fibrosis Unit, Southampton University Hospitals NHS Trust, Tremona Road, Southampton, SO16 6YD, United Kingdom, Pharmaceutical Science Division, King's College London, 150 Stamford Street, Franklin-Wilkins Building, London, SE1 9NH, United Kingdom, Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Thomas W. Daniels
- Molecular Microbiology Research Laboratory, Pharmaceutical Science Research Division, King's College London, 150 Stamford Street, Franklin-Wilkins Building, London, SE1 9NH, United Kingdom, Cystic Fibrosis/Pulmonary Research and Treatment Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, Cystic Fibrosis Unit, Southampton University Hospitals NHS Trust, Tremona Road, Southampton, SO16 6YD, United Kingdom, Pharmaceutical Science Division, King's College London, 150 Stamford Street, Franklin-Wilkins Building, London, SE1 9NH, United Kingdom, Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Mary P. Carroll
- Molecular Microbiology Research Laboratory, Pharmaceutical Science Research Division, King's College London, 150 Stamford Street, Franklin-Wilkins Building, London, SE1 9NH, United Kingdom, Cystic Fibrosis/Pulmonary Research and Treatment Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, Cystic Fibrosis Unit, Southampton University Hospitals NHS Trust, Tremona Road, Southampton, SO16 6YD, United Kingdom, Pharmaceutical Science Division, King's College London, 150 Stamford Street, Franklin-Wilkins Building, London, SE1 9NH, United Kingdom, Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Nilesh Patel
- Molecular Microbiology Research Laboratory, Pharmaceutical Science Research Division, King's College London, 150 Stamford Street, Franklin-Wilkins Building, London, SE1 9NH, United Kingdom, Cystic Fibrosis/Pulmonary Research and Treatment Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, Cystic Fibrosis Unit, Southampton University Hospitals NHS Trust, Tremona Road, Southampton, SO16 6YD, United Kingdom, Pharmaceutical Science Division, King's College London, 150 Stamford Street, Franklin-Wilkins Building, London, SE1 9NH, United Kingdom, Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Benjamin Forbes
- Molecular Microbiology Research Laboratory, Pharmaceutical Science Research Division, King's College London, 150 Stamford Street, Franklin-Wilkins Building, London, SE1 9NH, United Kingdom, Cystic Fibrosis/Pulmonary Research and Treatment Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, Cystic Fibrosis Unit, Southampton University Hospitals NHS Trust, Tremona Road, Southampton, SO16 6YD, United Kingdom, Pharmaceutical Science Division, King's College London, 150 Stamford Street, Franklin-Wilkins Building, London, SE1 9NH, United Kingdom, Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Richard C. Boucher
- Molecular Microbiology Research Laboratory, Pharmaceutical Science Research Division, King's College London, 150 Stamford Street, Franklin-Wilkins Building, London, SE1 9NH, United Kingdom, Cystic Fibrosis/Pulmonary Research and Treatment Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, Cystic Fibrosis Unit, Southampton University Hospitals NHS Trust, Tremona Road, Southampton, SO16 6YD, United Kingdom, Pharmaceutical Science Division, King's College London, 150 Stamford Street, Franklin-Wilkins Building, London, SE1 9NH, United Kingdom, Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Matthew C. Wolfgang
- Molecular Microbiology Research Laboratory, Pharmaceutical Science Research Division, King's College London, 150 Stamford Street, Franklin-Wilkins Building, London, SE1 9NH, United Kingdom, Cystic Fibrosis/Pulmonary Research and Treatment Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, Cystic Fibrosis Unit, Southampton University Hospitals NHS Trust, Tremona Road, Southampton, SO16 6YD, United Kingdom, Pharmaceutical Science Division, King's College London, 150 Stamford Street, Franklin-Wilkins Building, London, SE1 9NH, United Kingdom, Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Kenneth D. Bruce
- Molecular Microbiology Research Laboratory, Pharmaceutical Science Research Division, King's College London, 150 Stamford Street, Franklin-Wilkins Building, London, SE1 9NH, United Kingdom, Cystic Fibrosis/Pulmonary Research and Treatment Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, Cystic Fibrosis Unit, Southampton University Hospitals NHS Trust, Tremona Road, Southampton, SO16 6YD, United Kingdom, Pharmaceutical Science Division, King's College London, 150 Stamford Street, Franklin-Wilkins Building, London, SE1 9NH, United Kingdom, Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| |
Collapse
|
23
|
Cabral JPS. Water microbiology. Bacterial pathogens and water. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2010; 7:3657-703. [PMID: 21139855 PMCID: PMC2996186 DOI: 10.3390/ijerph7103657] [Citation(s) in RCA: 415] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/19/2010] [Revised: 09/07/2010] [Accepted: 09/28/2010] [Indexed: 02/07/2023]
Abstract
Water is essential to life, but many people do not have access to clean and safe drinking water and many die of waterborne bacterial infections. In this review a general characterization of the most important bacterial diseases transmitted through water—cholera, typhoid fever and bacillary dysentery—is presented, focusing on the biology and ecology of the causal agents and on the diseases’ characteristics and their life cycles in the environment. The importance of pathogenic Escherichia coli strains and emerging pathogens in drinking water-transmitted diseases is also briefly discussed. Microbiological water analysis is mainly based on the concept of fecal indicator bacteria. The main bacteria present in human and animal feces (focusing on their behavior in their hosts and in the environment) and the most important fecal indicator bacteria are presented and discussed (focusing on the advantages and limitations of their use as markers). Important sources of bacterial fecal pollution of environmental waters are also briefly indicated. In the last topic it is discussed which indicators of fecal pollution should be used in current drinking water microbiological analysis. It was concluded that safe drinking water for all is one of the major challenges of the 21st century and that microbiological control of drinking water should be the norm everywhere. Routine basic microbiological analysis of drinking water should be carried out by assaying the presence of Escherichia coli by culture methods. Whenever financial resources are available, fecal coliform determinations should be complemented with the quantification of enterococci. More studies are needed in order to check if ammonia is reliable for a preliminary screening for emergency fecal pollution outbreaks. Financial resources should be devoted to a better understanding of the ecology and behavior of human and animal fecal bacteria in environmental waters.
Collapse
Affiliation(s)
- João P S Cabral
- Center for Interdisciplinary Marine and Environmental Research (C. I. I. M. A. R.), Faculty of Sciences, Oporto University, Rua do Campo Alegre, 4169-007 Oporto, Portugal.
| |
Collapse
|
24
|
Parsons SK, Bull CM, Gordon DM. Low prevalence of Salmonella enterica in Australian wildlife. ENVIRONMENTAL MICROBIOLOGY REPORTS 2010; 2:657-659. [PMID: 23766252 DOI: 10.1111/j.1758-2229.2010.00152.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
A total of 2489 wildlife hosts from Australia were sampled in order to determine the fraction of hosts that harboured Salmonella enterica as a dominant member of the host's enteric community. Hosts sampled included fish, frogs, reptiles, birds and mammals from the four main climatic regions of Australia: desert, grassland, temperate and tropical. Salmonella enterica was predominately isolated from reptiles, in particular, lizards. It was also isolated from mammals, though not from any fish, frog or bird host. Salmonella enterica was more likely to be isolated from lizards living in desert or grassland regions of Australia compared with lizards inhabiting tropical or temperate regions. The low prevalence of S. enterica isolated from wildlife hosts in Australia indicates that Australian wildlife are unlikely to play a large role in disseminating S. enterica to humans and livestock.
Collapse
Affiliation(s)
- Sandra K Parsons
- Research School of Biology, Australian National University, Canberra, ACT 0200, Australia. School of Biological Sciences, Flinders University, Adelaide, SA 5001, Australia
| | | | | |
Collapse
|
25
|
Dick LK, Stelzer EA, Bertke EE, Fong DL, Stoeckel DM. Relative decay of Bacteroidales microbial source tracking markers and cultivated Escherichia coli in freshwater microcosms. Appl Environ Microbiol 2010; 76:3255-62. [PMID: 20348289 PMCID: PMC2869114 DOI: 10.1128/aem.02636-09] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2009] [Accepted: 03/20/2010] [Indexed: 11/20/2022] Open
Abstract
Fecal indicator bacteria (FIB), commonly used to regulate sanitary water quality, cannot discriminate among sources of contamination. The use of alternative quantitative PCR (qPCR) methods for monitoring fecal contamination or microbial source tracking requires an understanding of relationships with cultivated FIB, as contamination ages under various conditions in the environment. In this study, the decay rates of three Bacteroidales 16S rRNA gene markers (AllBac for general contamination and qHF183 and BacHum for human-associated contamination) were compared with the decay rate of cultivated Escherichia coli in river water microcosms spiked with human wastewater. The following five sets of microcosms were monitored over 11 days: control, artificial sunlight, sediment exposure, reduced temperature, and no autochthonous predation. Decay was characterized by estimation of the time needed to produce a 2-log reduction (t(99)). No treatment-associated differences in the decay of the 4 targets were evident except with reduced predation, where E. coli, qHF183, and BacHum markers had lower levels of decay by day 3. However, there were substantial target-associated differences. Decay curves for the AllBac marker indicated a larger persistent population than those of the other targets. Exposure to sunlight, sediment, and reduced predation resulted in more rapid decay of the human-associated markers relative to cultivable E. coli, but there were no differences in t(99) values among the 4 targets under control conditions or at reduced temperatures. Further evaluation of epidemiological relationships will be needed in order to relate the markers directly to health risk. These findings suggest that the tested human-associated markers can complement E. coli as indicators of the human impact on sanitary water quality under the constrained conditions described in this paper.
Collapse
Affiliation(s)
- Linda K. Dick
- School of Environment and Natural Resources, The Ohio State University, Columbus, Ohio 43210, U.S. Geological Survey, Ohio Water Science Center, Columbus, Ohio 43229
| | - Erin A. Stelzer
- School of Environment and Natural Resources, The Ohio State University, Columbus, Ohio 43210, U.S. Geological Survey, Ohio Water Science Center, Columbus, Ohio 43229
| | - Erin E. Bertke
- School of Environment and Natural Resources, The Ohio State University, Columbus, Ohio 43210, U.S. Geological Survey, Ohio Water Science Center, Columbus, Ohio 43229
| | - Denise L. Fong
- School of Environment and Natural Resources, The Ohio State University, Columbus, Ohio 43210, U.S. Geological Survey, Ohio Water Science Center, Columbus, Ohio 43229
| | - Donald M. Stoeckel
- School of Environment and Natural Resources, The Ohio State University, Columbus, Ohio 43210, U.S. Geological Survey, Ohio Water Science Center, Columbus, Ohio 43229
| |
Collapse
|
26
|
Derivation of Escherichia coli O157:H7 from its O55:H7 precursor. PLoS One 2010; 5:e8700. [PMID: 20090843 PMCID: PMC2806823 DOI: 10.1371/journal.pone.0008700] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2009] [Accepted: 12/14/2009] [Indexed: 11/25/2022] Open
Abstract
There are 29 E. coli genome sequences available, mostly related to studies of species diversity or mode of pathogenicity, including two genomes of the well-known O157:H7 clone. However, there have been no genome studies of closely related clones aimed at exposing the details of evolutionary change. Here we sequenced the genome of an O55:H7 strain, closely related to the major pathogenic O157:H7 clone, with published genome sequences, and undertook comparative genomic and proteomic analysis. We were able to allocate most differences between the genomes to individual mutations, recombination events, or lateral gene transfer events, in specific lineages. Major differences include a type II secretion system present only in the O55:H7 chromosome, fewer type III secretion system effectors in O55:H7, and 19 phage genomes or phagelike elements in O55:H7 compared to 23 in O157:H7, with only three common to both. Many other changes were found in both O55:H7 and O157:H7 lineages, but in general there has been more change in the O157:H7 lineages. For example, we found 50% more synonymous mutational substitutions in O157:H7 compared to O55:H7. The two strains also diverged at the proteomic level. Mutational synonymous SNPs were used to estimate a divergence time of 400 years using a new clock rate, in contrast to 14,000 to 70,000 years using the traditional clock rates. The same approaches were applied to three closely related extraintestinal pathogenic E. coli genomes, and similar levels of mutation and recombination were found. This study revealed for the first time the full range of events involved in the evolution of the O157:H7 clone from its O55:H7 ancestor, and suggested that O157:H7 arose quite recently. Our findings also suggest that E. coli has a much lower frequency of recombination relative to mutation than was observed in a comparable study of a Vibrio cholerae lineage.
Collapse
|
27
|
Lawrence JG, Retchless AC. The interplay of homologous recombination and horizontal gene transfer in bacterial speciation. Methods Mol Biol 2009; 532:29-53. [PMID: 19271178 DOI: 10.1007/978-1-60327-853-9_3] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Bacteria experience recombination in two ways. In the context of the Biological Species concept, allelic exchange purges genic variability within bacterial populations as gene exchange mediates selective sweeps. In contrast, horizontal gene transfer (HGT) increases the size of the population's pan-genome by providing an influx of novel genetic material. Here we discuss the interplay of these two processes, with an emphasis on how they allow for the maintenance of genotypically cohesive bacterial populations, yet allow for the separation of these populations upon bacterial speciation. In populations that maintain genotypic similarity by frequent allelic exchange, horizontally transferred genes may initiate ecological barriers to genetic exchange. The resulting recombination interference allows for the accumulation of neutral mutations and, consequently, the imposition of a pre-mating barrier to gene transfer.
Collapse
Affiliation(s)
- Jeffrey G Lawrence
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | | |
Collapse
|
28
|
Abstract
In recent years, the importance of horizontal gene transfer (HGT) in bacterial evolution has been elevated to such a degree that many bacteriologists now question the very existence of bacterial species. If gene transfer is as rampant as comparative genomic studies have suggested, how could bacterial species survive such genomic fluidity? And yet, most bacteriologists recognize, and name, as species, clusters of bacterial isolates that share complex phenotypic properties. The Core Genome Hypothesis (CGH) has been proposed to explain this apparent paradox of fluid bacterial genomes associated with stable phenotypic clusters. It posits that there is a core of genes responsible for maintaining the species-specific phenotypic clusters observed throughout bacterial diversity and argues that, even in the face of substantial genomic fluidity, bacterial species can be rationally identified and named.
Collapse
Affiliation(s)
- Margaret A Riley
- Department of Biology, University of Massachusetts, Amherst, MA, USA
| | | |
Collapse
|
29
|
Tominaga T, Sekine M, Oyaizu H. Tracing the contamination origin of coliform bacteria in two small food-processing factories. J Food Prot 2008; 71:1910-4. [PMID: 18810877 DOI: 10.4315/0362-028x-71.9.1910] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The objective of this study was to trace contamination sources of coliform bacteria by comparing the types of coliforms between food samples and the processing environments in two small food-processing factories (factories A and B). Fermentation tests of five sugars enabled the successful classification of 16 representative type strains into eight distinct groups. The grouping procedure was then applied to comparison of the coliform flora between food products and various locations in their processing environments. The consistency between each food and the tested locations was evaluated using the Jaccard index. The air conditioner and refrigeration room floor in factory A showed an index of 1.00, while the shaping machine in factory B showed an index of 0.98, indicating that these locations could be contamination sources. The validity of our results was confirmed by randomly amplified polymorphic DNA, which showed 100% matched profiles between the air conditioner and the food in factory A, and highly matched profiles between the machine and the food in factory B. This method for comparing the coliform flora between food and environments has the potential to be a reliable tracing tool for various food industries.
Collapse
Affiliation(s)
- Tatsuya Tominaga
- Saitama Industrial Technology Center North Institute, 2-133 Suehiro, Kumagaya-shi, Saitama 360-0031, Japan.
| | | | | |
Collapse
|
30
|
Kim JM, Linton RH. Identification of a non-pathogenic surrogate organism for chlorine dioxide (ClO2) gas treatment. Food Microbiol 2008; 25:597-606. [PMID: 18456115 DOI: 10.1016/j.fm.2008.02.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2007] [Revised: 02/07/2008] [Accepted: 02/12/2008] [Indexed: 10/22/2022]
Abstract
The identification of non-pathogenic surrogate microorganisms is beneficial for determining and validating the efficacy of antimicrobial treatments in food manufacturing environments. A surrogate organism was identified to aid in the decontamination process of fresh produce when treated with chlorine dioxide (ClO(2)) gas. Thirty-two known strains of pathogenic and non-pathogenic microorganisms and seven unknown microbial isolates from mushroom, tomatoes, and strawberries were evaluated. The primary goal was to find alternative non-pathogenic organisms that had an equal or higher resistance compared to Escherichia coli O157:H7, Salmonella spp., and Listeria monocytogenes. Among the strains tested, MR1 (mushroom isolate), E. coli O157:H7 C7927, E. coli O157:H7 204P, STB2 (strawberry isolate), and vegetative cells of Bacillus cereus 232 in wet inoculum were found to be the most resistant to gaseous ClO(2) treatment at 0.3 mg/l for 1 min and D-values at 0.3 mg/l ClO(2) were 3.53, 1.95, 1.72, 1.68, and 1.57 min, respectively. For identification, the MR1 and STB2 strains were identified using a Ribotyper with the EcoRI restriction enzyme of 16S rDNA sequence. MR1 was identified as Hafnia alvei with a similarity value of 94% using the ribotype pattern and with a 93.6% similarity using an API 20E strip, and with a 99% similarity using 16S rDNA analysis. The Ped-2E9-based cytotoxicity assay was conducted for the MRI strain extracellular toxin and whole cell toxicity and did not show cytotoxicity. Analysis, using multiplex PCR, was performed to verify absence of the eaeA gene. H. alvei is a suitable non-pathogenic surrogate, with higher resistance to ClO(2) gas compared to pathogens studied, that may be useful to establish optimum conditions of ClO(2) gas decontamination systems.
Collapse
Affiliation(s)
- Jeong-Mok Kim
- Department of Food Science, Mokpo National University, Jeonnam 534-729, Republic of Korea
| | | |
Collapse
|
31
|
Schierack P, Walk N, Reiter K, Weyrauch KD, Wieler LH. Composition of intestinal Enterobacteriaceae populations of healthy domestic pigs. MICROBIOLOGY-SGM 2008; 153:3830-3837. [PMID: 17975092 DOI: 10.1099/mic.0.2007/010173-0] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
In this study, the Enterobacteriaceae microbiota, including their diversity as well as the distribution of haemolytic and virulence gene-harbouring Escherichia coli of 56-day-old healthy piglets, was characterized. Both the composition and the diversity of Enterobacteriaceae populations varied considerably between individual pigs and intestinal sections. E. coli, Enterobacter cloacae, Citrobacter freundii and Klebsiella pneumoniae dominated the Enterobacteriaceae microbiota. However, mucosa-associated Enterobacteriaceae were scarce or in some cases undetectable. The majority of E. coli clones from the jejunum were also found in the colon, with up to 10 different E. coli clones in one intestinal section. Other Enterobacteriaceae species were represented by only one clone localized to one intestinal section. While several piglets did not harbour virulence gene-positive or haemolytic E. coli, such strains dominated intestinal sections of other animals. This study reveals that the diversity of intestinal Enterobacteriaceae is clearly individual. In general, Enterobacteriaceae do not appear to be a consistent fraction of the microbiota of the jejunum. High numbers of adherent bacteria do not appear to be essential for successful intestinal colonization, and E. coli clones do not necessarily colonize distinct intestinal sections based on the particular phylogenetic affiliation. Furthermore, dominance of haemolytic or virulence gene-positive E. coli does not correlate with disease. Finally, probiotic Enterococcus faecium feed supplementation does not affect the Enterobacteriaceae microbiota.
Collapse
Affiliation(s)
- Peter Schierack
- Institut für Mikrobiologie und Tierseuchen, Freie Universität Berlin, Philippstr. 13, 10115 Berlin, Germany
| | - Nicole Walk
- Institut für Mikrobiologie und Tierseuchen, Freie Universität Berlin, Philippstr. 13, 10115 Berlin, Germany
| | - Katja Reiter
- Institut für Veterinär-Anatomie, Freie Universität Berlin, Koserstr. 20, 14195 Berlin, Germany
| | - Karl D Weyrauch
- Institut für Veterinär-Anatomie, Freie Universität Berlin, Koserstr. 20, 14195 Berlin, Germany
| | - Lothar H Wieler
- Institut für Mikrobiologie und Tierseuchen, Freie Universität Berlin, Philippstr. 13, 10115 Berlin, Germany
| |
Collapse
|
32
|
Wildschutte H, Lawrence JG. Differential Salmonella survival against communities of intestinal amoebae. MICROBIOLOGY-SGM 2007; 153:1781-1789. [PMID: 17526835 DOI: 10.1099/mic.0.2006/003616-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Predation from intestinal amoebae may provide selective pressure for the maintenance of high genetic diversity at the Salmonella enterica rfb locus, whereby serovars better escape predators in particular environments depending on the O-antigens they express. Here, the hypothesis that amoebae from a particular intestinal environment collectively prefer one serovar over another is tested. Collections of Acanthamoeba, Tetramitus, Naegleria and Hartmannella were isolated from the intestinal tracts of several vertebrate hosts, including bullfrog tadpoles, goldfish, turtles and bearded dragons, and their feeding preferences were determined. Congeneric amoebae from the same environment had significantly similar feeding preferences. Strikingly, even unrelated amoebae - such as Naegleria and Tetramitus from goldfish - also had significantly similar feeding preferences. Yet amoebae isolated from different environments showed no similarity in prey choice. Thus, feeding preferences of amoebae appear to reflect their environment, not their taxonomic relationships. A mechanism mediating this phenotypic convergence is discussed.
Collapse
Affiliation(s)
- Hans Wildschutte
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15235, USA
| | - Jeffrey G Lawrence
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15235, USA
| |
Collapse
|
33
|
Kreiss A, Fox N, Bergfeld J, Quinn SJ, Pyecroft S, Woods GM. Assessment of cellular immune responses of healthy and diseased Tasmanian devils (Sarcophilus harrisii). DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2007; 32:544-553. [PMID: 17988737 DOI: 10.1016/j.dci.2007.09.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2007] [Revised: 09/13/2007] [Accepted: 09/14/2007] [Indexed: 05/25/2023]
Abstract
The Tasmanian devil (TD) (Sarcophilus harrisii) is under threat from devil facial tumour disease (DFTD), a cancer that is transmitted between devils by direct cell implantation. As no devil is known to have rejected the tumour allograft, an understanding of the immune status of this species is essential to help explain the unique infectious nature of this cancer. We analysed differential white blood cell counts, the phagocytic response of neutrophils as well as mitogen-induced lymphocyte proliferation. Devils analysed included healthy TDs kept in captivity, healthy devils from disease-free and diseased areas as well as diseased devils. Neutrophils isolated from the peripheral blood of healthy devils showed competent phagocytosis and peripheral blood mononuclear cells from healthy and diseased devils proliferated in response to Con A, PHA and PWM stimulation. Although a wide range of responses was observed and relatively high doses of mitogens were required, there was no significant difference between males and females, adults and juveniles or between normal and diseased animals, suggesting that transmission of DFTD is not a consequence of a severely impaired immune system. As lymphocytes from all TDs appear to require strong stimulation for activation, this threshold may contribute to all devils being susceptible to DFTD.
Collapse
Affiliation(s)
- Alexandre Kreiss
- Menzies Research Institute, University of Tasmania, Private Bag 29, Hobart, Tasmania 7001, Australia
| | | | | | | | | | | |
Collapse
|
34
|
Cabral JP, Marques C. Faecal coliform bacteria in Febros river (northwest Portugal): temporal variation, correlation with water parameters, and species identification. ENVIRONMENTAL MONITORING AND ASSESSMENT 2006; 118:21-36. [PMID: 16897531 DOI: 10.1007/s10661-006-0771-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2005] [Accepted: 07/05/2005] [Indexed: 05/11/2023]
Abstract
Febros river water was sampled weekly, during 35 successive weeks, and analyzed for microbiological (total coliforms, faecal coliforms, faecal streptococci and enterococci) and chemical-physical (ammonia and temperature) parameters. All microbiological parameters were highly correlated with each other and with ammonia, suggesting that the simultaneous determination of all variables currently in use in the evaluation of the microbiological quality of waters is probably redundant, and could be simplified, and that ammonia should be tested as a sentinel parameter of the microbiological pollution load of Febros river. From the strains isolated from positive tubes of the faecal coliforms test (multiple tube fermentation technique) and retested in this assay, Escherichia coli, Klebsiella oxytoca and Klebsiella pneumoniae subsp. pneumoniae strains were positive, indicating that the faecal coliforms test is not totally specific for Escherichia coli, and can detect other bacteria. Considering that these Klebsiella spp. are not necessarily of faecal origin, it was concluded that the faecal coliforms test can overestimate true faecal pollution. From the strains isolated from positive tubes of the faecal coliforms procedure, only Escherichia coli strains were clearly positive in the beta-D-glucuronidase test. All other species were negative or very weakly positive, suggesting that the assay of the beta-D-glucuronidase activity is less prone to false positives than the faecal coliforms test in the quantification of Escherichia coli in environmental waters.
Collapse
Affiliation(s)
- João Paulo Cabral
- Faculty of Sciences, Department of Botany, University of Oporto, Portugal.
| | | |
Collapse
|
35
|
Abstract
The genus Hafnia, a member of the family Enterobacteriaceae, consists of gram-negative bacteria that are occasionally implicated in both intestinal and extraintestinal infections in humans. Despite the fact that the genus currently contains only a single species (H. alvei), more extensive phylogenetic depth (two or more species) is apparent based upon DNA relatedness and 16S rRNA gene sequencing studies. Hafnia causes a variety of systemic infections, including septicemia and pneumonia; however, its role as a gastrointestinal pathogen is controversial. Many of the data supporting a role for hafniae as enteric pathogens were incorrectly attributed to this genus rather than to the actual pathogen, Escherichia albertii. There are numerous gaps in our understanding of this genus, including ecologic habitats and population genetics, disease-producing role in animals, phenetic and genetic methods useful in distinguishing genomospecies within the H. alvei complex, and bona fide pathogenicity factors.
Collapse
Affiliation(s)
- J Michael Janda
- Microbial Diseases Laboratory, 850 Marina Bay Parkway, Room E164, Richmond, CA 94804, USA.
| | | |
Collapse
|
36
|
Chavan M, Rafi H, Wertz J, Goldstone C, Riley MA. Phage associated bacteriocins reveal a novel mechanism for bacteriocin diversification in Klebsiella. J Mol Evol 2005; 60:546-56. [PMID: 15883889 DOI: 10.1007/s00239-004-0263-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2004] [Accepted: 10/11/2004] [Indexed: 10/25/2022]
Abstract
Ninety-six isolates of Klebsiella pneumoniae and K. oxytoca were recovered from wild mammals in Australia. 14.6% of these bacteria produce killing phenotypes that suggest the production of bacteriocin toxins. Cloning and sequencing of the gene clusters encoding two of these killing phenotypes revealed two instances of a bacteriocin associated with a bacteriophage gene, the first such genetic organization described. The newly identified klebicin C gene cluster was discovered in both K. pneumoniae and K. oxytoca. The newly identified klebicin D gene cluster was detected in K. oxytoca. Protein sequence comparisons and phylogenetic inference suggest that klebicin C is most closely related to the rRNase group of colicins (such as colicin E4), while klebicin D is most closely related to the tRNase group of colicins (such as colicin D). The klebicin C and D gene clusters have similar genetic and regulatory organizations. In both cases, an operon structure is inferred consisting of a phage-associated open reading frame and klebicin activity and associated immunity genes. This novel bacteriophage/bacteriocin organization may provide a novel mechanism for the generation of bacteriocin diversity in Klebsiella.
Collapse
Affiliation(s)
- Milind Chavan
- Department of Biology, University of Massachusetts Amherst, 611 North Pleasant Street, Amherst, MA, 01003, USA
| | | | | | | | | |
Collapse
|
37
|
Power ML, Littlefield-Wyer J, Gordon DM, Veal DA, Slade MB. Phenotypic and genotypic characterization of encapsulated Escherichia coli isolated from blooms in two Australian lakes. Environ Microbiol 2005; 7:631-40. [PMID: 15819845 DOI: 10.1111/j.1462-2920.2005.00729.x] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Escherichia coli has long been used as an indicator organism for water quality assessment. Recently there has been an accumulation of evidence that suggests some strains of this organism are able to proliferate in the environment, a characteristic that would detract from its utility as an indicator of faecal pollution. Phenotypic and genotypic characterization of E. coli isolated from blooms in two Australian lakes, separated by a distance of approximately 200 km, identified that the blooms were dominated by three E. coli strains. A major phenotypic similarity among the three bloom strains was the presence of a group 1 capsule. Genetic characterization of a conserved region of the cps gene cluster, which encodes group 1 capsules, identified a high degree of genetic variation within the bloom isolates. This differs from previously described encapsulated E. coli strains which are highly conserved at the cps locus. The phenotypic or genotypic profiles of the bloom strains were not identified in 435 E. coli strains isolated from vertebrates. The occurrence of these encapsulated strains suggests that some E. coli have evolved a free-living lifestyle and do not require a host in order to proliferate. The presence of the same three strains in bloom events in different geographical regions of a temperate climate, and at different times, indicates that free-living E. coli strains are able to persist in these water reservoirs. This study provides further evidence of circumstances where caution is required in using E. coli as an indicator organism for water quality.
Collapse
Affiliation(s)
- Michelle L Power
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia.
| | | | | | | | | |
Collapse
|
38
|
Brisse S, Duijkeren EV. Identification and antimicrobial susceptibility of 100 Klebsiella animal clinical isolates. Vet Microbiol 2005; 105:307-12. [PMID: 15708829 DOI: 10.1016/j.vetmic.2004.11.010] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2004] [Revised: 11/10/2004] [Accepted: 11/17/2004] [Indexed: 11/23/2022]
Abstract
The objectives of this study were to determine the distribution of Klebsiella species and phylogenetic groups in animal clinical samples and to determine the levels of antimicrobial resistance of animal Klebsiella clinical isolates. One hundred Klebsiella veterinary clinical isolates were identified using gyrA PCR-RFLP and rpoB gene sequencing as a confirmatory method. Klebsiella pneumoniae phylogenetic group KpI was dominant (78 isolates), but KpII, KpIII (K. variicola), K. oxytoca, K. planticola and K. terrigena were also represented. The relative frequencies in animal infections of Klebsiella species and phylogenetic groups were similar to those observed in human nosocomial infections, suggesting that similar ecological and molecular factors cause Klebsiella infections in both situations. Resistance was common against ampicillin (99%) and cephalexin (43%) but not against ceftazidime, ceftiofur, tetracycline, enrofloxacin, gentamicin and trimethoprim-sulfamethoxazole. Thirteen isolates resistant to three or more antimicrobials or combinations thereof were found, but acquired antimicrobial resistance remains lower among animal isolates than among human nosocomial isolates.
Collapse
Affiliation(s)
- Sylvain Brisse
- Unité Biodiversité des Bactéries Pathogènes Emergentes (U389 INSERM), Institut Pasteur, 25-28 rue du Docteur Roux, F-75724 Paris Cedex 15, France.
| | | |
Collapse
|
39
|
Gordon DM. The Influence of Ecological Factors on the Distribution and the Genetic Structure of Escherichia coli. EcoSal Plus 2004; 1. [PMID: 26443349 DOI: 10.1128/ecosalplus.6.4.1] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2003] [Indexed: 06/05/2023]
Abstract
This review focuses on recent data concerning the ecological factors that determine the distribution of Escherichia coli and the genetic structures of naturally occurring E. coli populations. It summarizes some of the older literature concerning the dynamics of E. coli populations within a host and poses some questions that arise from our more recently acquired understanding of the factors affecting the genetic structures of E. coli populations. Multilocus enzyme electrophoresis (MLEE) studies indicate that E. coli, relative to other members of the family Enterobacteriaceae, exhibits a moderate degree of genetic diversity. The existence of subspecific structure in E. coli has for the most part been determined by largely neutral in its effects on the fitness of a strain. The consequences for E. coli of the transition between its primary and secondary habitats are of considerable practical significance for water quality assessment and disease transmission. E. coli causes a significant fraction of human bacterial disease and is responsible for two main types of disease in humans and domestic animals: diarrheal disease and extraintestinal infections. The observed distribution of strains from the different E. coli genetic groups indicates that they have different life history tactics and ecological niches. A and B1 strains appear to be generalists, as they can be recovered from any vertebrate group. Group B2 and D strains appear to be more specialized, as they are largely restricted to endothermic vertebrates.
Collapse
|
40
|
Wertz JE, Riley MA. Chimeric nature of two plasmids of Hafnia alvei encoding the bacteriocins alveicins A and B. J Bacteriol 2004; 186:1598-605. [PMID: 14996789 PMCID: PMC355955 DOI: 10.1128/jb.186.6.1598-1605.2004] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The complete nucleotide sequences of two bacteriocin-encoding plasmids isolated from Hafnia alvei (pAlvA and pAlvB) were determined. Both plasmids resemble ColE1-type replicons and carry mobilization genes, as well as colicin-like bacteriocin operons. These bacteriocins appear to be chimeras consisting of translocation domains from Tol-dependent colicins, unique binding domains, and killing and immunity domains similar to those of the pore-forming colicin Ia. Just as is found for colicin Ia, these H. alvei bacteriocins (alveicins) lack lysis genes. The alveicins are unusually small at 408 and 358 amino acids for alveicin A and B, respectively, which would make alveicin B the smallest pore-forming bacteriocin yet discovered. The pattern of nucleotide substitution in the alveicins suggests that the dominant forces in the evolution of their killing domains and immunity genes are neutral mutation and random genetic drift rather than diversifying selection, which has been implicated in the evolution of other colicins. Five of six bacteriocinogenic isolates of H. alvei were found to carry plasmids identical to pAlvA. Comparisons of the levels of nucleotide divergence in five housekeeping genes to the levels of divergence in their respective plasmids led us to conclude that pAlvA is transferring laterally through the H. alvei population relatively rapidly.
Collapse
Affiliation(s)
- John E Wertz
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520, USA.
| | | |
Collapse
|
41
|
McLoughlin SY, Jackson C, Liu JW, Ollis DL. Growth of Escherichia coli coexpressing phosphotriesterase and glycerophosphodiester phosphodiesterase, using paraoxon as the sole phosphorus source. Appl Environ Microbiol 2004; 70:404-12. [PMID: 14711669 PMCID: PMC321290 DOI: 10.1128/aem.70.1.404-412.2004] [Citation(s) in RCA: 62] [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
Phosphotriesterases catalyze the hydrolytic detoxification of phosphotriester pesticides and chemical warfare nerve agents with various efficiencies. The directed evolution of phosphotriesterases to enhance the breakdown of poor substrates is desirable for the purposes of bioremediation. A limiting factor in the identification of phosphotriesterase mutants with increased activity is the ability to effectively screen large mutant libraries. To this end, we have investigated the possibility of coupling phosphotriesterase activity to cell growth by using methyl paraoxon as the sole phosphorus source. The catabolism of paraoxon to phosphate would occur via the stepwise enzymatic hydrolysis of paraoxon to dimethyl phosphate, methyl phosphate, and then phosphate. The Escherichia coli strain DH10B expressing the phosphotriesterase from Agrobacterium radiobacter P230 (OpdA) is unable to grow when paraoxon is used as the sole phosphorus source. Enterobacter aerogenes is an organism capable of growing when dimethyl phosphate is the sole phosphorus source. The enzyme responsible for hydrolyzing dimethyl phosphate has been previously characterized as a nonspecific phosphohydrolase. We isolated and characterized the genes encoding the phosphohydrolase operon. The operon was identified from a shotgun clone that enabled E. coli to grow when dimethyl phosphate is the sole phosphorus source. E. coli coexpressing the phosphohydrolase and OpdA grew when paraoxon was the sole phosphorus source. By constructing a short degradative pathway, we have enabled E. coli to use phosphotriesters as a sole source of phosphorus.
Collapse
Affiliation(s)
- Sean Yu McLoughlin
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 0200, Australia
| | | | | | | |
Collapse
|
42
|
Yang HH, Vinopal RT, Grasso D, Smets BF. High diversity among environmental Escherichia coli isolates from a bovine feedlot. Appl Environ Microbiol 2004; 70:1528-36. [PMID: 15006775 PMCID: PMC368336 DOI: 10.1128/aem.70.3.1528-1536.2004] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2003] [Accepted: 11/27/2003] [Indexed: 11/20/2022] Open
Abstract
Approximately 280 Escherichia coli isolates were isolated from a bovine feedlot at the University of Connecticut campus via enrichment in lauryl tryptose broth and random selection from MacConkey plates. The E. coli subspecies diversity was estimated by employing whole-cell BOX-PCR genomic fingerprints. A total of 89 distinct operational taxonomic units (OTUs) were identified by employing a criterion of 85% fingerprint similarity as a surrogate for an OTU, while the Chao1 index estimated the E. coli population richness at 128 OTUs. One genotype (at a similarity level of 60%) dominated the population at 66% regardless of sampling depth or location, while no significant vertical distribution pattern was observed in terms of genotype, mobility, antibiotic resistance profile, or biofilm-forming ability. Motility, measured by a soft agar assay, had a very broad range among the E. coli population and was positively correlated with biofilm-forming ability in minimal medium (Spearman's rank correlation coefficient r = 0.619, P < 10(-4)) but not in Luria broth. Only an estimated 48% of the population possessed gene agn43, which encodes Ag43, a phase-variable outer membrane protein that has been implicated in biofilm formation in minimal medium. We observed significantly more biofilm formation in both minimal medium and Luria broth for agn43(+) strains, with a larger effect in minimal medium. This study represents an exhaustive inventory of extant E. coli population diversity at a bovine feedlot and reveals significant subspecies heterogeneity in interfacial behavior.
Collapse
Affiliation(s)
- Hsiao-Hui Yang
- Microbiology Program, Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269, USA
| | | | | | | |
Collapse
|
43
|
Abstract
Multilocus enzyme electrophoresis of 161 Hafnia alvei isolates from 158 hosts and 3 water column samples collected in Australia revealed that this species consists of two genetically distinct groups. The two groups of H. alvei differed significantly in their genetic structure and host distribution. The taxonomic class of the host but not geographic locality explained a significant proportion of the observed genetic and biochemical variation among strains within each genetic group.
Collapse
Affiliation(s)
- Shoko Okada
- School of Botany and Zoology, Australian National University, Canberra, ACT, Australia.
| | | |
Collapse
|
44
|
Wertz JE, Goldstone C, Gordon DM, Riley MA. A molecular phylogeny of enteric bacteria and implications for a bacterial species concept. J Evol Biol 2003; 16:1236-48. [PMID: 14640415 DOI: 10.1046/j.1420-9101.2003.00612.x] [Citation(s) in RCA: 99] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A molecular phylogeny for seven taxa of enteric bacteria (Citrobacter freundii, Enterobacter cloacae, Escherichia coli, Hafnia alvei, Klebsiella oxytoca, Klebsiella pneumoniae, and Serratia plymuthica) was made from multiple isolates per taxa taken from a collection of environmental enteric bacteria. Sequences from five housekeeping genes (gapA, groEL, gyrA, ompA, and pgi) and the 16S rRNA gene were used to infer individual gene trees and were concatenated to infer a composite molecular phylogeny for the species. The isolates from each taxa formed tight species clusters in the individual gene trees, suggesting the existence of 'genotypic' clusters that correspond to traditional species designations. These sequence data and the resulting gene trees and consensus tree provide the first data set with which to assess the utility of the recently proposed core genome hypothesis (CGH). The CGH provides a genetically based approach to applying the biological species concept to bacteria.
Collapse
Affiliation(s)
- J E Wertz
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA.
| | | | | | | |
Collapse
|
45
|
Gordon DM, Cowling A. The distribution and genetic structure of Escherichia coli in Australian vertebrates: host and geographic effects. Microbiology (Reading) 2003; 149:3575-3586. [PMID: 14663089 DOI: 10.1099/mic.0.26486-0] [Citation(s) in RCA: 237] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Escherichia coliwas isolated from more than 2300 non-domesticated vertebrate hosts living in Australia.E. coliwas most prevalent in mammals, less prevalent in birds and uncommon in fish, frogs and reptiles. Mammals were unlikely to harbourE. coliif they lived in regions with a desert climate and less likely to haveE. coliif they lived in the tropics than if they lived in semi-arid or temperate regions. In mammals, the likelihood of isolatingE. colifrom an individual depended on the diet of the host andE. coliwas less prevalent in carnivores than in herbivores or omnivores. In both birds and mammals, the probability of isolatingE. coliincreased with the body mass of the host. Hosts living in close proximity to human habitation were more likely to harbourE. colithan hosts living away from people. The relative abundance ofE. coligroups A, B1, B2 and D strains in mammals depended on climate, host diet and body mass. Group A strains were uncommon, but were isolated from both ectothermic and endothermic vertebrates. Group B1 strains could also be isolated from any vertebrate group, but were predominant in ectothermic vertebrates, birds and carnivorous mammals. Group B2 strains were unlikely to be isolated from ectotherms and were most abundant in omnivorous and herbivorous mammals. Group D strains were rare in ectotherms and uncommon in endotherms, but were equally abundant in birds and mammals. The results of this study suggest that, at the species level, the ecological niche ofE. coliis mammals with hindgut modifications to enable microbial fermentation, or in the absence of a modified hindgut,E. colican only establish a population in ‘large-bodied’ hosts. The non-random distribution ofE. coligenotypes among the different host groups indicates that strains of the fourE. coligroups may differ in their ecological niches and life-history characteristics.
Collapse
Affiliation(s)
- David M Gordon
- School of Botany and Zoology, Australian National University, Canberra, ACT 0200, Australia
| | - Ann Cowling
- Statistical Consulting Unit, Australian National University, Canberra, ACT 0200, Australia
| |
Collapse
|
46
|
Riley MA, Goldstone CM, Wertz JE, Gordon D. A phylogenetic approach to assessing the targets of microbial warfare. J Evol Biol 2003; 16:690-7. [PMID: 14632232 DOI: 10.1046/j.1420-9101.2003.00575.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Bacteriocins are the most abundant and diverse defense systems in bacteria. As a result of the specific mechanisms of bacteriocin recognition and translocation into the target cell it is assumed that these toxins mediate intra-specific or population-level interactions. However, no published studies specifically address this question. We present here a survey of bacteriocin production in a collection of enteric bacteria isolated from wild mammals in Australia. A subset of the bacteriocin-producing strains was assayed for the ability to kill a broad range of enteric bacteria from the same bacterial collection. A novel method of estimating killing breadth was developed and used to compare the surveyed bacteriocins in terms of the phylogenetic range over which they kill. The most striking result is that although bacteriocin-producers kill members of their own species most frequently, some kill phylogenetically distant taxa more frequently than they kill closer relatives. This study calls into question the role these toxins play in natural populations. A significant number of bacteriocins are highly effective in killing inter-specific strains and thus bacteriocins may serve to mediate bacterial community interactions.
Collapse
Affiliation(s)
- M A Riley
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520-8106, USA.
| | | | | | | |
Collapse
|
47
|
Carson CA, Shear BL, Ellersieck MR, Schnell JD. Comparison of ribotyping and repetitive extragenic palindromic-PCR for identification of fecal Escherichia coli from humans and animals. Appl Environ Microbiol 2003; 69:1836-9. [PMID: 12620878 PMCID: PMC150071 DOI: 10.1128/aem.69.3.1836-1839.2003] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This report compares the performances of two popular genotypic methods used for tracking the sources of fecal pollution in water, ribotyping and repetitive extragenic palindromic-PCR (rep-PCR). The rep-PCR was more accurate, reproducible, and efficient in associating DNA fingerprints of fecal Escherichia coli with human and animal hosts of origin.
Collapse
Affiliation(s)
- C Andrew Carson
- Department of Veterinary Pathobiology, 201 Connaway Hall, University of Missouri, Columbia, MO 65211, USA.
| | | | | | | |
Collapse
|
48
|
Abstract
Modern concerns about the spread of antibiotic resistance raise questions about the effect of bacterial species on plasmid evolution and maintenance. We studied 223 Enterobacteriaceae isolated from wild mammals and determined the number of plasmids per isolate, the size of those plasmids, and the distribution of plasmid incompatibility groups N, P, W, FII, and A/C. All of these variables were non-randomly distributed with respect to bacterial species, suggesting that host-cell factors constrain the plasmids that a strain will carry. The implication for the evolution of multiple-resistance plasmids in a clinical setting is that although inter-generic plasmid transfer may introduce a novel resistance plasmid into a bacterial genus, it is likely to be modified to suit the requirements of the new host cell. This then further suggests that resistance plasmids will evolve independent lineages within bacterial species although the genes incorporated in them may have come from the same original source.
Collapse
Affiliation(s)
- Miranda Sherley
- Division of Botany and Zoology, Australian National University, Acton, ACT 0200, Australia.
| | | | | |
Collapse
|
49
|
Okada S, Gordon DM. Host and geographical factors influence the thermal niche of enteric bacteria isolated from native Australian mammals. Mol Ecol 2001; 10:2499-513. [PMID: 11742550 DOI: 10.1046/j.0962-1083.2001.01384.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The thermal profiles of 118 bacterial strains, representing six species of the family Enterobacteriaceae, isolated from a variety of native Australian mammals were determined under in vitro conditions. Each of the bacterial species had a unique thermal profile and differed in their minimum or maximum temperature for growth and in their response to changing temperatures. The taxonomic classification of the host from which the bacterial strains were isolated explained a significant amount of the variation in thermal profile among strains of a species. Host effects were detected at all taxonomic levels: order, family, genus, and species. The locality (State or Territory) or climate zone from which the strain was collected explained a significant amount of the variation in the thermal profile of Citrobacter freundii, Enterobacter cloacae and Klebsiella pneumoniae strains. Genetically similar strains, as determined by allozyme profiles, had similar thermal profiles for the bacterial species Hafnia alvei and Escherichia coli. The results of this study indicate that there are potentially many aspects of host biology that may determine the thermal profile of these bacteria.
Collapse
Affiliation(s)
- S Okada
- School of Botany & Zoology, Australian National University, Canberra, ACT 0200, Australia
| | | |
Collapse
|
50
|
Gordon DM. Geographical structure and host specificity in bacteria and the implications for tracing the source of coliform contamination. MICROBIOLOGY (READING, ENGLAND) 2001; 147:1079-1085. [PMID: 11320111 DOI: 10.1099/00221287-147-5-1079] [Citation(s) in RCA: 111] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- David M Gordon
- Division of Botany & Zoology, Australian National University, Canberra, ACT 0200, Australia1
| |
Collapse
|