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Ogwaro BA, O’Gara EA, Hill DJ, Gibson H. A Study of the Antimicrobial Activity of Combined Black Pepper and Cinnamon Essential Oils against Escherichia fergusonii in Traditional African Yoghurt. Foods 2021; 10:foods10112847. [PMID: 34829130 PMCID: PMC8618451 DOI: 10.3390/foods10112847] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/05/2021] [Accepted: 11/15/2021] [Indexed: 11/25/2022] Open
Abstract
The antimicrobial activity of the essential oils of black pepper (BPE) and cinnamon bark (CE) extracts against E. fergusonii was assessed in pasteurized full cream milk during and post-fermentation. The milk was fermented with 1% (v/v) of Lactobacillus delbrueckii subspecies bulgaricus (NCIMB 11778) and Streptococcus thermophilus (NCIMB 10387) (approx. 106 cfu/mL each) and incubated and stored at 25 °C for 5 days (144 h) or at 43 °C for 24 h and then stored at 25 °C for 120 h. The milk was spiked with E. fergusonii at the start of fermentation by the lactic acid bacteria (pre-fermentation contamination) for after fermentation (post fermentation contamination). BPE and CE were applied at concentrations based on their minimum inhibitory concentration of 0.5% and 0.25% respectively as follows: 0.5% BPE alone; 0.125% BPE with 0.1875% CE; 0.25% BPE with 0.125% CE; 0.375% BPE with 0.0625% CE; 0.25% CE alone. Results showed that during fermentation at 25 °C, E. fergusonii grew to a similar level (approx. 109 CFU/mL) in control samples and 108 CFU/mL when BPE or CE were added alone. Whereas, in the samples with the combined essential oils, the bacterium grew to 106–107 CFU/mL only. During the milk fermentation at 43 °C, E. fergusonii grew to approx. 109 CFU/mL in samples without treatment. However, it was not detected in samples containing mixed BPE with CE after 8, 10 and 12 h of fermentation. Subsequent storage at 25 °C resulted in undetectable levels of the bacterium in all the samples treated with BPE or CE after 24 h of storage. These results indicated that BPE in combination with CE reduced growth during fermentation and was bactericidal during storage.
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Affiliation(s)
- Betty A. Ogwaro
- Faculty of Science and Engineering, Wolverhampton School of Sciences, University of Wolverhampton, Wulfruna Street, Wolverhampton WV1 1LY, UK; (B.A.O.); (D.J.H.)
- Faculty of Science and Engineering, Research Institute for Healthcare Science, University of Wolverhampton, Wulfruna Street, Wolverhampton WV1 1LY, UK;
| | - Elizabeth A. O’Gara
- Faculty of Science and Engineering, Research Institute for Healthcare Science, University of Wolverhampton, Wulfruna Street, Wolverhampton WV1 1LY, UK;
- Faculty of Science and Engineering, School of Medicine and Clinical Practice, University of Wolverhampton, Wufruna Street, Wolverhampton WV1 1LY, UK
| | - David J. Hill
- Faculty of Science and Engineering, Wolverhampton School of Sciences, University of Wolverhampton, Wulfruna Street, Wolverhampton WV1 1LY, UK; (B.A.O.); (D.J.H.)
- Faculty of Science and Engineering, Research Institute for Healthcare Science, University of Wolverhampton, Wulfruna Street, Wolverhampton WV1 1LY, UK;
| | - Hazel Gibson
- Faculty of Science and Engineering, Wolverhampton School of Sciences, University of Wolverhampton, Wulfruna Street, Wolverhampton WV1 1LY, UK; (B.A.O.); (D.J.H.)
- Faculty of Science and Engineering, Research Institute for Healthcare Science, University of Wolverhampton, Wulfruna Street, Wolverhampton WV1 1LY, UK;
- Correspondence:
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Gracy Jenifer S, Marimuthu G, Raghuram H. Isolation and characterization of chitinolytic bacterium, Escherichia fergusonii AMC01 from insectivorous bat, Taphozous melanopogon. J Basic Microbiol 2021; 61:940-946. [PMID: 34398462 DOI: 10.1002/jobm.202100271] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/17/2021] [Accepted: 08/07/2021] [Indexed: 11/12/2022]
Abstract
Chitinases are capable of hydrolyzing insoluble chitin into its oligo and monomeric parts and have received increased consideration because of their wide scope of biotechnological applications. The commercial application of microbial chitinase is appealing due to the relative ease of enormous production and to meet the current world demands. This study aimed at isolation and characterization of chitin degrading bacteria from the gut of Indian tropical insectivorous black-bearded tomb bat, Taphozous melanopogon. The isolated bacterial strains were characterized through biochemical analysis and nucleic acid-based approaches by 16S ribosomal RNA amplification and sequencing. The BLAST (Basic Local Alignment Search Tool) and phylogenetic analysis showed that the bacterial strain exhibited a close resemblance with Escherichia fergusonii. The chitinolytic activity of the E. fergusonii AMC01 was identified using supplemented colloidal chitin with agar medium. Compiling all, these findings would facilitate in constructing a database and presumably promote the use of E. fergusonii AMC01 as an efficient strain for the chitinase production.
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Affiliation(s)
| | - Ganapathy Marimuthu
- Department of Animal Behaviour and Physiology, School of Biological Sciences, Madurai Kamaraj University, Madurai, Tamil Nadu, India
| | - Hanumanthan Raghuram
- PG and Research Department of Zoology, The American College, Madurai, Tamil Nadu, India
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Karade S, Sen S, Shergill SPS, Jani K, Shouche Y, Gupta RM. Whole genome sequence of colistin-resistant Escherichia coli from western India. Med J Armed Forces India 2020; 77:297-301. [PMID: 34305283 DOI: 10.1016/j.mjafi.2020.10.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 10/09/2020] [Indexed: 02/05/2023] Open
Abstract
Background With virtually dried out new antibiotic discovery pipeline, emergence and spread of antimicrobial resistance is a cause for global concern. Colistin, a cyclic polypeptide antibiotic, often regarded as last resort for multi drug resistance gram-negative bacteria, is also rendered ineffective by horizontal transfer of resistance genes. Surveillance of colistin resistance in GNB is essential to ascertain molecular epidemiology. Methods Whole genome sequencing (WGS) of an unusual colistin resistant urinary isolate of Escherichia coli was performed using Illumina MiSeq platform using 2x250bp V2 chemistry by following the manufactures protocol (Illumina Inc. USA). Multiple web-based bio-informatic tools were utilized to ascertain antibiotic resistant genes. Results An approximate 5.4 Mb of genome of the urinary isolate AFMC_UC19 was sequenced successfully. Mobile colistin resistance gene (mcr) on the plasmid responsible for horizontal spread was absent in the isolate. Conclusion Colistin resistance has been reported previously in Klebsiella pneumoniae and it is a rare occurrence in Escherichia coli in Indian setting. Although the isolate lack mcr mediated colistin resistance, emergence and spread of colistin resistant in gram-negative bacteria pose a threat.
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Affiliation(s)
- Santosh Karade
- Associate Professor, Department of Microbiology, Armed Forces Medical College, Pune 40, India
| | - Sourav Sen
- Professor & Head, Department of Microbiology, Armed Forces Medical College, Pune 40, India
| | - S P S Shergill
- Associate Professor, Department of Microbiology, Armed Forces Medical College, Pune 40, India
| | - Kunal Jani
- Research Associate, National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Yogesh Shouche
- Principal Investigator & Professor Emeritus, National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - R M Gupta
- Dean & Dy Commandant, Armed Forces Medical College, Pune 40, India
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Singh AK, Das S, Kumar S, Gajamer VR, Najar IN, Lepcha YD, Tiwari HK, Singh S. Distribution of Antibiotic-Resistant Enterobacteriaceae Pathogens in Potable Spring Water of Eastern Indian Himalayas: Emphasis on Virulence Gene and Antibiotic Resistance Genes in Escherichia coli. Front Microbiol 2020; 11:581072. [PMID: 33224119 PMCID: PMC7674312 DOI: 10.3389/fmicb.2020.581072] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 09/18/2020] [Indexed: 12/25/2022] Open
Abstract
Every year millions of people die due to fatal waterborne diseases around the world especially in developing countries like India. Sikkim, a northeastern state of India, greatly depends on natural water sources. About 80% of the population of Sikkim depends on natural spring water for domestic as well as agricultural use. Recent waterborne disease outbreaks in the state raises a concerning question on water quality. In this study, we analyzed water quality especially for the detection of Enterobacteriaceae members from four districts of the state. Isolation with selective culture media techniques and taxonomic characterization of Enterobacteriaceae bacteria with 16S rRNA gene showed the prevalence of Escherichia coli (37.50%), Escherichia fergusonii (29.41%), Klebsiella oxytoca (36.93%), Citrobacter freundii (37.92%), Citrobacter amalonaticus (43.82%), Enterobacter sp. (43.82%), Morganella morganii (43.82%), Hafnia alvei (32.42%), Hafnia paralvei (38.74%), and Shigella flexneri (30.47%) in the spring water of Sikkim. Antibiotic susceptibility test (AST) showed resistance of the isolates to common antibiotics like ampicillin, amoxicillin as well as to third generation antibiotics like ceftazidime and carbapenem. None of the isolates showed resistance to chloramphenicol. E. coli isolated from spring water of Sikkim showed presence of different virulence genes such as stx1 (81.81%), elt (86.66%), and eae (66.66%) along with resistance gene for ampicillin (CITM) (80%), quinolones (qnrB) (44.44%), tetracycline (tetO) (66.66%), and streptomycin (aadA1) (66.66%). The data indicates a high incidence rate of multiple antibiotic resistant enteric bacteria in the spring water of Sikkim. Additionally, the presence of enteric bacteria in the water samples indicates widespread fecal contamination of the spring water.
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Affiliation(s)
- Ashish Kumar Singh
- Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok, India
| | - Saurav Das
- Department of Agronomy and Horticulture, University of Nebraska–Lincoln, Lincoln, NE, United States
| | - Santosh Kumar
- Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok, India
| | - Varsha Rani Gajamer
- Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok, India
| | - Ishfaq Nabi Najar
- Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok, India
| | - Yangchen D. Lepcha
- State Institute of Rural Development (SIRD), Government of Sikkim, Gangtok, India
| | - Hare Krishna Tiwari
- Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok, India
| | - Samer Singh
- Centre of Experimental Medicine and Surgery (CEMS), Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
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Zhao G, Zhang L, Li C, Zhao J, Liu N, Li Y, Wang J, Liu L. Identification of enterobacteria in viscera of pigs afflicted with porcine reproductive and respiratory syndrome and other viral co-infections. Microb Pathog 2020; 147:104385. [PMID: 32659314 PMCID: PMC7352111 DOI: 10.1016/j.micpath.2020.104385] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 07/06/2020] [Accepted: 07/06/2020] [Indexed: 01/18/2023]
Abstract
In order to investigate enterobacteria presence involved in the secondary infections in Porcine Reproductive and Respiratory Syndrome (PRRS) pigs with different viral co-infections, we identified enterobacteria for guiding clinical treatment. Twenty-one diseased pigs were diagnosed with the PRRS virus (PRRSV) and other 7 virus primers by PCR/RT-PCR in the lung and spleen samples. Enterobacteria were isolated using MacConkey agar from 5 visceral samples of PRRS pigs, and identified by 16S rDNA sequencing. PRRSV was positive in 100% of the lung samples and 81.0% of the spleen samples. Seven diseased pigs were diagnosed with only PRRSV infection (33.3%), 7 pigs with PRRSV and 1 or 2 other viruses (33.3%) and 7 pigs with PRRSV and more than 2 types of other viruses (33.3%). PRRSV was more inclined to co-infect pigs with porcine group A rotavirus (PARV) with the co-infection rate of 52.4% (11/21). Approximately 13 types of bacteria were successfully isolated from lung, spleen, liver, kidney and lymph node samples of different PRRS pigs. Enterobacteria were isolated in 100% of lung, liver and lymph samples from pigs infected with PRRSV alone. However, the isolation rates were significantly decreased in the more than 3 viruses co-infection group. Escherichia coli was the most prevalent bacterium, followed by Morganella, Proteus, Shigella, Salmonella, Klebsiella and Aeromonas. Most of the isolated enterobacteria were opportunistic pathogens. Therefore, timely combination with antimicrobial agents is necessary for effective treatment of PRRS-infected pigs. PRRSV was more inclined to co-infect with PARV. Pigs co-infected with more virus, less enterobacteria were isolated from their viscera. Enterobacteria isolated from viscera of PRRS pigs were opportunistic pathogens. coli, Morganella and Proteus were the most prevalent enterobacteria. Secondary infection of enterobacteria should be considered in PRRS treatment.
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Affiliation(s)
- Ge Zhao
- Department of Pathogenic Microorganisms, China Animal Health and Epidemiology Center, Qingdao, Shandong, 266032, China
| | - Lujie Zhang
- Institute of Animal Population Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, China
| | - Charles Li
- Animal Biosciences and Biotechnology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, US Department of Agriculture, Beltsville, MD, 20705, USA
| | - Jianmei Zhao
- Department of Pathogenic Microorganisms, China Animal Health and Epidemiology Center, Qingdao, Shandong, 266032, China
| | - Na Liu
- Department of Pathogenic Microorganisms, China Animal Health and Epidemiology Center, Qingdao, Shandong, 266032, China
| | - Yuehua Li
- Department of Pathogenic Microorganisms, China Animal Health and Epidemiology Center, Qingdao, Shandong, 266032, China
| | - Junwei Wang
- Department of Pathogenic Microorganisms, China Animal Health and Epidemiology Center, Qingdao, Shandong, 266032, China.
| | - Liheng Liu
- Institute of Animal Population Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, China.
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Adesina T, Nwinyi O, De N, Akinnola O, Omonigbehin E. First Detection of Carbapenem-Resistant Escherichia fergusonii Strains Harbouring Beta-Lactamase Genes from Clinical Samples. Pathogens 2019; 8:pathogens8040164. [PMID: 31557915 PMCID: PMC6963453 DOI: 10.3390/pathogens8040164] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 07/26/2019] [Accepted: 07/26/2019] [Indexed: 01/10/2023] Open
Abstract
Recently discovered extraintestinal Escherichia fergusonii obtained from non-clinical samples has exhibited the potential for acquiring multiple beta-lactamase genes, just like many extraintestinal Escherichia coli strains. Albeit, they are often omitted or classified as E. coli. This study aimed to, therefore, identify carbapenem-resistant extended-spectrum beta-lactamase (ESBL) producing E. fergusonii isolates from clinical samples, determine their evolutionary relatedness using 16S rRNA sequencing analysis and screen for beta-lactamase genes. A total of 135 septic wound samples were obtained from patients on referral at a General Hospital in Lagos, Nigeria. For the phenotypic identification of isolates from culture-positive samples, morphological, and physiological tests were carried out. Identities of the isolates harbouring beta-lactamase genes were assigned to their genus strains using the 16S rRNA sequencing. The Kirby Bauer disc diffusion technique and double-disc synergy test were used to screen isolates for multidrug resistance and ESBL production. Carbapenem-resistant ESBL producing isolates were screened for beta-lactamase genes in a polymerase chain reaction. Three E. fergusonii isolates (CR11, CR35 and CR49) were obtained during this study. E. fergusonii strains were motile, non-lactose and non-sorbitol fermenting but positive for cellobiose and adonitol fermentation. The I6S rRNA assigned the phenotypically identified isolates to E. fergusonii species. All three isolates were multidrug-resistant, carbapenem-resistant and ESBL producers. Isolates CR11 and CR35 harboured cefotaximase (CTX-M) and temoniera (TEM) beta-lactamase genes while CR49 harboured sulfhydryl variable (SHV) beta-lactamase gene. We herein report the detection of multiple beta-lactamase genes in carbapenem-resistant ESBL producing E. fergusonii from clinical samples.
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Affiliation(s)
- Tomilola Adesina
- Department of Microbiology, College of Science and Technology, Covenant University, 112103 Ota, Nigeria.
| | - Obinna Nwinyi
- Department of Microbiology, College of Science and Technology, Covenant University, 112103 Ota, Nigeria.
| | - Nandita De
- Department of Microbiology, College of Science and Technology, Covenant University, 112103 Ota, Nigeria.
| | - Olayemi Akinnola
- Department of Microbiology, College of Science and Technology, Covenant University, 112103 Ota, Nigeria.
| | - Emmanuel Omonigbehin
- Department of Microbiology, College of Science and Technology, Covenant University, 112103 Ota, Nigeria.
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Baek SD, Chun C, Hong KS. Hemolytic uremic syndrome caused by Escherichia fergusonii infection. Kidney Res Clin Pract 2019; 38:253-255. [PMID: 30970393 PMCID: PMC6577213 DOI: 10.23876/j.krcp.19.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 03/14/2019] [Accepted: 03/18/2019] [Indexed: 12/14/2022] Open
Affiliation(s)
- Seung Don Baek
- Department of Internal Medicine, Mediplex Sejong Hospital, Incheon, Korea
| | - Chinhak Chun
- Center for Infectious Diseases, Mediplex Sejong Hospital, Incheon, Korea
| | - Kyoung Sup Hong
- Department of Internal Medicine, Mediplex Sejong Hospital, Incheon, Korea
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Li W, Zhu Y, Li Y, Shu M, Wen Y, Gao X, Wan C. The gut microbiota of hand, foot and mouth disease patients demonstrates down-regulated butyrate-producing bacteria and up-regulated inflammation-inducing bacteria. Acta Paediatr 2019; 108:1133-1139. [PMID: 30427066 DOI: 10.1111/apa.14644] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 10/08/2018] [Accepted: 11/09/2018] [Indexed: 12/15/2022]
Abstract
AIM This study explored the gut microbiota of children with hand, foot and mouth disease (HFMD). METHODS We enrolled 15 cases with HFMD admitted to the West China Second Hospital, Sichuan University, China, from July to September 2016 at a median age of three years. The controls were 15 healthy children of a similar age who underwent routine health examinations at the hospital during the same period. Gut microbiota was analysed using high throughput 16S ribosomal deoxyribonucleic acid sequencing. RESULTS The gut microbiota in the HFMD patients was distinct from the controls. Compared with the controls, the composition of gut microbiota in the HFMD cases represented a reduction of two butyrate-producing bacteria, Ruminococcus (0.73 ± 1.28 versus 7.78 ± 20.01, p = 0.026) and Roseburia (0.67 ± 1.69 versus 1.61 ± 3.27, p = 0.024) and an up-regulation of Escherichia (5.26 ± 10.50 versus 1.59 ± 5.90,p < 0.01) and Enterococcus (4.12 ± 12.49 versus 0.12 ± 0.41, p = 0.015). CONCLUSION The dysbiosis of gut microbiota of the HFMD cases included a reduction of butyrate-producing bacteria and an up-regulation of inflammation-inducing bacteria. These may have impaired the intestinal biological mucosal barrier and host immune functions, promoting the invasion of the enterovirus.
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Affiliation(s)
- Weiran Li
- Department of Paediatrics West China Second Hospital Sichuan University Chengdu China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education Chengdu China
| | - Yu Zhu
- Department of Paediatrics West China Second Hospital Sichuan University Chengdu China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education Chengdu China
| | - Yiyuan Li
- Department of Paediatrics West China Second Hospital Sichuan University Chengdu China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education Chengdu China
| | - Min Shu
- Department of Paediatrics West China Second Hospital Sichuan University Chengdu China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education Chengdu China
| | - Yang Wen
- Department of Paediatrics West China Second Hospital Sichuan University Chengdu China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education Chengdu China
| | - Xiaolin Gao
- Department of Paediatrics West China Second Hospital Sichuan University Chengdu China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education Chengdu China
| | - Chaomin Wan
- Department of Paediatrics West China Second Hospital Sichuan University Chengdu China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education Chengdu China
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Ayyal NM, Abbas ZA, Karim AJ, Abbas ZM, Al-Salihi KA, Khalaf JM, Mahmood DD, Mohammed EA, Jumaa RS, Abdul-Majeed DI. Bacterial isolation from internal organs of rats ( Rattus rattus) captured in Baghdad city of Iraq. Vet World 2019; 12:119-125. [PMID: 30936664 PMCID: PMC6431815 DOI: 10.14202/vetworld.2019.119-125] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 12/07/2018] [Indexed: 12/19/2022] Open
Abstract
Aim Rats are accused in disseminating many zoonotic diseases. This study aimed to isolate and identify bacteria from internal organs of rats captured in Baghdad City, Iraq. Materials and Methods A total of 120 black rats (R. rattus) were trapped from different areas in Baghdad city. Rats were kept in individual plastic cages for 3 h before euthanizing. Deep pharyngeal swab, intestinal content, urine, and pieces of the liver and spleen, lung, kidney, and brain were obtained aseptically. The specimens were inoculated into peptone water and incubated at 37°C for 24 h for enrichment. A loopful of each specimen was then subcultured onto MacConkey Agar, Blood Agar, and Mannitol Salt Agar. CHROMagar O157 H7 and CHROMagar Listeria were used to detect Escherichia coli 157:7 and Listeria spp., respectively. Biochemical tests on analytical profile index, microscopic examination, and commercial kit for latex agglutination test for serotyping E. coli O157:H7 were used. Results Mixed bacterial isolates were recorded as 116, 52, 36, 28, 18, 6, and 4 from intestinal contents, deep pharyngeal, liver and spleen, urine, lung, brain, and kidney, respectively. Microorganisms included E. coli, Staphylococcus aureus, Streptococcus spp., Bacillus spp., Pseudomonas aeruginosa, Citrobacter freundii, Proteus vulgaris, E. coli O157:H7, Enterobacter cloacae, Listeria spp., Klebsiella spp., Ochrobactrum anthropi, Aeromonas spp., Brucella spp., Pseudomonas fluorescens, Escherichia fergusonii, Micrococcus spp., Morganella spp., Proteus mirabilis, Pseudomonas luteola, and Streptobacillus spp. The highest bacterial prevalence (88; 73.33%) was recorded for E. coli, where 68 isolates were identified from the intestinal contents. Of these, four isolates were E. coli O157:H7. Conclusion Rats are important carriers and transmitters of a number of pathogens and can disseminate these microorganisms to humans and animals.
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Affiliation(s)
- Nagham Mohammed Ayyal
- Unit of Zoonotic Diseases, College of Veterinary Medicine, University of Baghdad, Baghdad, Iraq
| | - Zainab Abdulzahra Abbas
- Unit of Zoonotic Diseases, College of Veterinary Medicine, University of Baghdad, Baghdad, Iraq
| | - Abdulkarim Jafar Karim
- Unit of Zoonotic Diseases, College of Veterinary Medicine, University of Baghdad, Baghdad, Iraq
| | - Zainab Majid Abbas
- Department of Pathological Analysis, Babylon Technical Institute, Al-Furat Al-Awsat Technical University, Babylon, Iraq
| | - Karima Akool Al-Salihi
- Department of Internal and Preventive Medicine, College of Veterinary Medicine, Al-Muthanna University, Al-Muthanna, Iraq
| | - Jenan Mahmood Khalaf
- Department of Internal and Preventive Medicine, College of Veterinary Medicine, University of Baghdad, Baghdad, Iraq
| | - Dunya Dhafir Mahmood
- Unit of Zoonotic Diseases, College of Veterinary Medicine, University of Baghdad, Baghdad, Iraq
| | - Eman Abdullah Mohammed
- Department of Parasitology, College of Veterinary Medicine, University of Baghdad, Baghdad, Iraq
| | - Rawaa Saladdin Jumaa
- Department of Microbiology, College of Veterinary Medicine, University of Baghdad, Baghdad, Iraq
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Functional eubacteria species along with trans-domain gut inhabitants favour dysgenic diversity in oxalate stone disease. Sci Rep 2018; 8:16598. [PMID: 30413731 PMCID: PMC6226508 DOI: 10.1038/s41598-018-33773-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 09/21/2018] [Indexed: 01/09/2023] Open
Abstract
Analyses across all three domains of life are necessary to advance our understanding of taxonomic dysbiosis in human diseases. In the present study, we assessed gut microbiota (eubacteria, archaea, and eukaryotes) of recurrent oxalate kidney stone suffers to explore the extent of trans-domain and functional species dysbiosis inside the gut. Trans-domain taxonomic composition, active oxalate metabolizer and butyrate-producing diversity were explored by utilizing frc-, but-, and buk- functional gene amplicon analysis. Operational taxonomic units (OTUs) level analyses confound with the observation that dysbiosis in gut microbiota is not just limited to eubacteria species, but also to other domains like archaea and eukaryotes. We found that some of healthy eubacterial population retained together with Oxalobacter formigenes and Lactobacillus plantarum colonization in disease condition (p < 0.001 & FDR = 0.05). Interestingly, trans-domain species diversity has been less shared and dysgenic taxa augmentation was found to be higher. Oxalate metabolizing bacterial species (OMBS) and butyrate-producing eubacteria species were found to be decreased in Oxalobacter non-colonizers; and Prevotella and Ruminococcus species which may contribute to oxalate metabolism and butyrate synthesis as well. Our study underscores fact that microbial dysbiosis is not limited to eubacteria only hence suggest the necessity of the trans-domain surveillance in metabolic diseases for intervention studies.
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Banskar S, Bhute SS, Suryavanshi MV, Punekar S, Shouche YS. Microbiome analysis reveals the abundance of bacterial pathogens in Rousettus leschenaultii guano. Sci Rep 2016; 6:36948. [PMID: 27845426 PMCID: PMC5109407 DOI: 10.1038/srep36948] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 10/24/2016] [Indexed: 12/11/2022] Open
Abstract
Bats are crucial for proper functioning of an ecosystem. They provide various important services to ecosystem and environment. While, bats are well-known carrier of pathogenic viruses, their possible role as a potential carrier of pathogenic bacteria is under-explored. Here, using culture-based approach, employing multiple bacteriological media, over thousand bacteria were cultivated and identified from Rousettus leschenaultii (a frugivorous bat species), the majority of which were from the family Enterobacteriaceae and putative pathogens. Next, pathogenic potential of most frequently cultivated component of microbiome i.e. Escherichia coli was assessed to identify its known pathotypes which revealed the presence of virulent factors in many cultivated E. coli isolates. Applying in-depth bacterial community analysis using high-throughput 16 S rRNA gene sequencing, a high inter-individual variation was observed among the studied guano samples. Interestingly, a higher diversity of bacterial communities was observed in decaying guano representative. The search against human pathogenic bacteria database at 97% identity, a small proportion of sequences were found associated to well-known human pathogens. The present study thus indicates that this bat species may carry potential bacterial pathogens and advice to study the effect of these pathogens on bats itself and the probable mode of transmission to humans and other animals.
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Affiliation(s)
- Sunil Banskar
- Microbial Culture Collection, National Centre for Cell Science, Pune, India
| | - Shrikant S Bhute
- Department of Zoology, Savitribai Phule Pune University, Pune, India
| | | | - Sachin Punekar
- Biosphere, Eshwari, 52/403, Lakshminagar, Parvati, Pune-411009 (Maharashtra), India
| | - Yogesh S Shouche
- Microbial Culture Collection, National Centre for Cell Science, Pune, India
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Maheux AF, Boudreau DK, Bergeron MG, Rodriguez MJ. Characterization of Escherichia fergusonii and Escherichia albertii isolated from water. J Appl Microbiol 2014; 117:597-609. [PMID: 24849008 DOI: 10.1111/jam.12551] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 05/16/2014] [Accepted: 05/17/2014] [Indexed: 11/28/2022]
Abstract
AIMS The aim of this study was to characterize Escherichia fergusonii and Escherichia albertii isolated from water. METHODS AND RESULTS The characterization of E. fergusonii and E. albertii isolated from water was determined using an Escherichia coli-specific uidA PCR, a tuf PCR, and with phylogenetic analysis using three housekeeping genes (adk, gyrB, and recA) from the E. coli MLST scheme, selected for their ability to discriminate among all Escherichia species. Among the 527 isolates tested, 25 (4·7%) were uidA PCR negative and tuf PCR positive. Phylogenetic analysis using adk, gyrB and recA genes showed that 6, 18 and 1 of these 25 non-E. coli Escherichia spp. isolates grouped with reference strains of E. fergusonii, E. albertii, and E. coli, respectively. Finally, the 25 non-E. coli Escherichia spp. strains isolated were investigated for the presence of pathogenic factors, comprising intimin (eae gene), cytolethal distending toxin (cdtB gene) and shiga toxin (stx gene). With the PCR primers used, the presence of eae and stx genes was not detected. However, cdtB genes types I/IV were detected for 3 (16·7%) E. albertii strains, whereas 15 of 18 (83·3%) possessed the cdtB gene types II/III/V. CONCLUSIONS These results showed that MLST scheme allows a more accurate identification of non-E. coli species than phenotypic tests. We also showed that E. fergusonii and E. albertii represent, respectively, 0·8 and 2·5% of all Escherichia species isolated and the pathogenic cdtB genes were present in 83·3% of these strains. SIGNIFICANCE AND IMPACT OF THE STUDY The data presented in this study provided an efficient way to correctly identify non-E. coli species contributing to our understanding of the risks associated with Escherichia species in water consumed by humans and animals. Furthermore, the results give an insight about the natural habitats of these species.
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Affiliation(s)
- A F Maheux
- Chaire de recherche en eau potable de l'Université Laval, Québec City, QC, Canada; École supérieure d'aménagement du territoire et de développement régional, Université Laval, Québec City, QC, Canada
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Gaastra W, Kusters JG, van Duijkeren E, Lipman LJA. Escherichia fergusonii. Vet Microbiol 2014; 172:7-12. [PMID: 24861842 DOI: 10.1016/j.vetmic.2014.04.016] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 04/17/2014] [Accepted: 04/18/2014] [Indexed: 10/25/2022]
Abstract
Escherichia fergusonii was introduced in the genus Escherichia almost 65 years later than Escherichia coli after which the genus was named. From then (1985) onwards mainly case reports on E. fergusonii associated with disease in individuals of veterinary or human origin have been reported and only very few more extensive studies became available. This has resulted in very fragmented knowledge on this organism. The aim of this manuscript is to give an overview of what is known on E. fergusonii today and to stimulate more research on this organism so that better insight can be obtained in the role that E. fergusonii plays in human and animal infections.
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Affiliation(s)
- W Gaastra
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, The Netherlands
| | - J G Kusters
- Department of Medical Microbiology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - E van Duijkeren
- Centre for Infectious Disease Control Netherlands (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - L J A Lipman
- Division of Veterinary Public Health, Institute for Risk Assessment Sciences, Utrecht University, The Netherlands.
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Isolation and epidemiological characterization of heat-labile enterotoxin-producing Escherichia fergusonii from healthy chickens. Vet Microbiol 2012; 160:170-5. [PMID: 22771038 DOI: 10.1016/j.vetmic.2012.05.020] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Revised: 05/14/2012] [Accepted: 05/16/2012] [Indexed: 11/21/2022]
Abstract
Escherichia fergusonii has been associated with a wide variety of intestinal and extraintestinal infections in both humans and animals. The aim of this study was to demonstrate the presence of heat-labile enterotoxin (LT)-producing E. fergusonii in healthy chickens and its plasmid-mediated LT toxin gene transfer to other Enterobacteriaceae. We tested faecal samples from 184 chicken flocks (consisting of 109 broilers and 75 layers) of 78 commercial chicken farms for the presence of the LT gene using a polymerase chain reaction-based screening and identified samples from 43 flocks (23.4%) as positive for the LT gene. We subsequently isolated and identified E. fergusonii harboring the LT gene from all LT-positive samples and observed 21 various biochemical types. The plasmids encoding LT in 16 (37.2%) of the 43 isolates were conjugally transferred to the recipient strain Escherichia coli J53. Southern hybridization showed that all plasmids from the transconjugants carried the eltAB gene (Ent plasmid) and belonged to the narrow-host-range IncF type. In addition, all the E. fergusonii strains identified were classified into 17 pulsed-field gel electrophoresis (PFGE) types, and it is likely that there was an association between the PFGE types and geographical location or breed of flocks. In conclusion, this is the first study to demonstrate that LT-producing E. fergusonii strains were present in the faeces of healthy chickens and that plasmid-mediated virulence genes can be transferred to E. coli and may have a great potential to cause human disease.
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Forgetta V, Rempel H, Malouin F, Vaillancourt R, Topp E, Dewar K, Diarra MS. Pathogenic and multidrug-resistant Escherichia fergusonii from broiler chicken. Poult Sci 2012; 91:512-25. [PMID: 22252367 DOI: 10.3382/ps.2011-01738] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
An Escherichia spp. isolate, ECD-227, was previously identified from the broiler chicken as a phylogenetically divergent and multidrug-resistant Escherichia coli possessing numerous virulence genes. In this study, whole genome sequencing and comparative genome analysis was used to further characterize this isolate. The presence of known and putative antibiotic resistance and virulence open reading frames were determined by comparison to pathogenic (E. coli O157:H7 TW14359, APEC O1:K1:H7, and UPEC UTI89) and nonpathogenic species (E. coli K-12 MG1655 and Escherichia fergusonii ATCC 35469). The assembled genome size of 4.87 Mb was sequenced to 18-fold depth of coverage and predicted to contain 4,376 open reading frames. Phylogenetic analysis of 537 open reading frames present across 110 enteric bacterial species identifies ECD-227 to be E. fergusonii. The genome of ECD-227 contains 5 plasmids showing similarity to known E. coli and Salmonella enterica plasmids. The presence of virulence and antibiotic resistance genes were identified and localized to the chromosome and plasmids. The mutation in gyrA (S83L) involved in fluoroquinolone resistance was identified. The Salmonella-like plasmids harbor antibiotic resistance genes on a class I integron (aadA, qacEΔ-sul1, aac3-VI, and sulI) as well as numerous virulence genes (iucABCD, sitABCD, cib, traT). In addition to the genome analysis, the virulence of ECD-227 was evaluated in a 1-d-old chick model. In the virulence assay, ECD-227 was found to induce 18 to 30% mortality in 1-d-old chicks after 24 h and 48 h of infection, respectively. This study documents an avian multidrug-resistant and virulent E. fergusonii. The existence of several resistance genes to multiple classes of antibiotics indicates that infection caused by ECD-227 would be difficult to treat using antimicrobials currently available for poultry.
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Affiliation(s)
- V Forgetta
- McGill University, Department of Human Genetics, Montréal, Québec, Canada
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Sriram MI, Gayathiri S, Gnanaselvi U, Jenifer PS, Mohan Raj S, Gurunathan S. Novel lipopeptide biosurfactant produced by hydrocarbon degrading and heavy metal tolerant bacterium Escherichia fergusonii KLU01 as a potential tool for bioremediation. BIORESOURCE TECHNOLOGY 2011; 102:9291-9295. [PMID: 21802283 DOI: 10.1016/j.biortech.2011.06.094] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Revised: 06/27/2011] [Accepted: 06/28/2011] [Indexed: 05/31/2023]
Abstract
Escherichia fergusonii KLU01, a propitious bacterial strain isolated from oil contaminated soil was identified to be hydrocarbon degrading, heavy metal tolerant and a potent producer of biosurfactant using diesel oil as the sole carbon and energy source. The biosurfactant produced by the strain was characterized to be a lipopeptide. The minimum active dose and critical micelle concentration of the biosurfactant were found as 0.165±0.08 μg and 36 mg/L, respectively. In spite of being an excellent emulsifier, the biosurfactant showed an incredible stability at extremes of temperature, pH and at various concentrations of NaCl, CaCl₂ and MgCl₂. Also the bacterium manifested tolerance towards Manganese, Iron, Lead, Nickel, Copper and Zinc. The strain emerges as a new class of biosurfactant producer with potential environmental and industrial applications, especially in hydrocarbon degradation and heavy metal bioremediation.
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Affiliation(s)
- Muthu Irulappan Sriram
- Division of Molecular and Cellular Biology, Department of Biotechnology, Kalasalingam University, Anand Nagar, Krishnankoil 626126, Tamilnadu, India
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Jackson JC, Farone AL, Farone MB. Bacterial enteropathogens associated with diarrhea in a rural population of Haiti. Res Rep Trop Med 2011; 2:129-133. [PMID: 30881186 DOI: 10.2147/rrtm.s23426] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Purpose Diarrheal disease is one of the leading causes of morbidity in developing countries. To further understand the epidemiology of diarrheal disease among a rural population surrounding Robillard, Haiti, fecal swabs from patients with diarrhea were screened for the presence of enteropathogenic bacteria. Patients and methods Fecal swabs were collected from 34 patients with signs and symptoms of diarrhea and stored in BBL™ Cary-Blair transport medium (Becton, Dickinson and Company, Sparks, MD) until transit to the USA. Swab material was inoculated on to different enrichment and selective agars for incubation. Fermenting and nonfermenting bacteria that grew on the enteric selection media were identified by the BBL™ Crystal™ Enteric/Nonferementing Identification system (Becton, Dickinson and Company). Organisms identified as Escherichia coli were further screened for the presence of virulence factors by polymerase chain reaction (PCR). Results Of 34 patients, no Campylobacter, Shigella, Salmonella, or Vibrio spp. were isolated from swabs transported to the USA for culture. Of 73 E. coli isolates cultured from the swabs, one enteropathogenic strain of E. coli was identified by multiplex PCR. Escherichia fergusonii and Cronobacter sakazakii, both potential gastrointestinal pathogens, were also isolated from patient stools. Conclusion This study was undertaken to determine if bacterial enteropathogens could be detected in the stools of patients suffering from diarrhea or dysentery and, in the absence of sufficient facilities, rectal swabs could be transported to the USA for culture. Although several genera of overt enteropathogens were not detected, one enteropathogenic E. coli and other pathogenic enterobacteriaceae were successfully cultured and identified.
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Affiliation(s)
- John C Jackson
- Biology Department, Middle Tennessee State University, Murfreesboro, Tennessee, USA,
| | - Anthony L Farone
- Biology Department, Middle Tennessee State University, Murfreesboro, Tennessee, USA,
| | - Mary B Farone
- Biology Department, Middle Tennessee State University, Murfreesboro, Tennessee, USA,
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Escherichia fergusonii bacteremia in a diabetic patient with pancreatic cancer. J Clin Microbiol 2011; 49:4001-2. [PMID: 21918030 DOI: 10.1128/jcm.05355-11] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Although Escherichia fergusonii has been identified for decades, it has rarely been recovered from clinical specimens and its clinical significance remains unclear. We describe a case of E. fergusonii bacteremia in a diabetic patient with pancreatic cancer. The isolate was confirmed by three commercial identification systems and 16S rRNA gene sequence analysis. The patient's clinical condition gradually improved, and repeated blood cultures were negative after antibiotic treatment with an in vitro active agent (ceftriaxone).
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Weiss ATA, Lübke-Becker A, Krenz M, van der Grinten E. Enteritis and Septicemia in a Horse Associated With Infection by Escherichia fergusonii. J Equine Vet Sci 2011. [DOI: 10.1016/j.jevs.2011.01.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Plasmid typing and resistance profiling of Escherichia fergusonii and other Enterobacteriaceae isolates from South Korean farm animals. Appl Environ Microbiol 2011; 77:3163-6. [PMID: 21398479 DOI: 10.1128/aem.02188-10] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In this study, we focused on determining the distribution and prevalence of major plasmid replicons in β-lactam-resistant Escherichia fergusonii and Enterobacteriaceae of animal and human origin. A high degree of plasmid variability and multiple plasmid replicons were observed among the isolates. The IncF and IncI1 replicons were the most prevalent in E. fergusonii and Salmonella enterica serovar Indiana isolated from swine and poultry in South Korea, respectively. The presence of broad-host-range plasmid replicons such as IncN, IncA/C, IncHI1, and IncHI2 that are associated with important virulence genes and toxins as well as antimicrobial resistance determinants indicates that E. fergusonii has the potential to become an important pig pathogen and possible emerging opportunistic zoonotic pathogen.
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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.
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Chern EC, Siefring S, Paar J, Doolittle M, Haugland RA. Comparison of quantitative PCR assays for Escherichia coli targeting ribosomal RNA and single copy genes. Lett Appl Microbiol 2011; 52:298-306. [PMID: 21204885 DOI: 10.1111/j.1472-765x.2010.03001.x] [Citation(s) in RCA: 110] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AIMS Compare specificity and sensitivity of quantitative PCR (qPCR) assays targeting single and multi-copy gene regions of Escherichia coli. METHODS AND RESULTS A previously reported assay targeting the uidA gene (uidA405) was used as the basis for comparing the taxonomic specificity and sensitivity of qPCR assays targeting the rodA gene (rodA984) and two regions of the multi-copy 23S ribosomal RNA gene (EC23S and EC23S857). Experimental analyses of 28 culture collection strains representing E. coli and 21 related non-target species indicated that the uidA405 and rodA984 assays were both 100% specific for E. coli while the EC23S assay was only 29% specific. The EC23S857 assay was only 95% specific due to detection of E. fergusonii. The uidA405, rodA984, EC23S and EC23S857 assays were 85%, 85%, 100% and 86% sensitive, respectively, in detecting 175 presumptive E. coli culture isolates from fresh, marine and waste water samples. In analyses of DNA extracts from 32 fresh, marine and waste water samples, the rodA984, EC23S and EC23S857 assays detected mean densities of target sequences at ratios of approximately 1:1, 243:1 and 6:1 compared with the mean densities detected by the uidA405 assay. CONCLUSIONS The EC23S assay was less specific for E. coli, whereas the rodA984 and EC23S857 assay taxonomic specificities and sensitivities were similar to those of the uidA405 gene assay. SIGNIFICANCE AND IMPACT The EC23S857 assay has a lower limit of detection for E. coli cells than the uidA405 and rodA984 assays due to its multi-copy gene target and therefore provides greater analytical sensitivity in monitoring for these faecal pollution indicators in environmental waters by qPCR methods.
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Affiliation(s)
- E C Chern
- US Environmental Protection Agency, Office of Research and Development, National Exposure Research Laboratory, Cincinnati, OH 45268, USA
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Increasing resistance in community-acquired urinary tract infections in Latin America, five years after the implementation of national therapeutic guidelines. Int J Infect Dis 2010; 14:e770-4. [PMID: 20637675 DOI: 10.1016/j.ijid.2010.02.2264] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2009] [Accepted: 02/25/2010] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND The worldwide increasing resistance to antibiotics has complicated antimicrobial treatment of urinary tract infections (UTIs), especially in Latin America. This study aimed to report the present etiology and antimicrobial susceptibility of UTIs, and the effects of the national guidelines for UTIs introduced in 2003. METHODS Urine samples were collected from 304 patients with a clinical suspicion of UTI at the university hospital and primary health centers of León, Nicaragua. When bacterial growth was reported, antimicrobial susceptibility tests for nine frequently used antibiotics were performed. RESULTS Ninety-one (29.9%) patients had a positive urine culture. The most frequently isolated microorganisms were Escherichia coli (n=44), Serratia spp (n=11), and Escherichia fergusonii (n=10). High resistance rates were observed in E. coli to ampicillin (61.4%), cefalothin (45.5%), trimethoprim-sulfamethoxazole (38.6%), ciprofloxacin (31.8%), and ceftriaxone (20.5%). Amikacin and nitrofurantoin were the only drugs to which >90% of E. coli were susceptible. E. fergusonii and Serratia spp showed comparable high resistance patterns. Thirteen strains (29.5%) of E. coli were suspected to produce extended-spectrum beta-lactamase (ESBL). CONCLUSIONS Resistance rates in community-acquired UTIs in Nicaragua are increasing. The introduction of therapeutic guidelines with ceftriaxone recommended for upper UTIs and nitrofurantoin for lower UTIs, has led to increasing resistance against both antibiotics. The emergence of ESBL-producing E. coli is worrisome, along with the appearance of Serratia spp in the population.
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Husted L, Jensen TK, Olsen SN, Mølbak L. Examination of equine glandular stomach lesions for bacteria, including Helicobacter spp by fluorescence in situ hybridisation. BMC Microbiol 2010; 10:84. [PMID: 20298612 PMCID: PMC2848230 DOI: 10.1186/1471-2180-10-84] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2009] [Accepted: 03/19/2010] [Indexed: 01/22/2023] Open
Abstract
Background The equine glandular stomach is commonly affected by erosion and ulceration. The aim of this study was to assess whether bacteria, including Helicobacter, could be involved in the aetiology of gastric glandular lesions seen in horses. Results Stomach lesions, as well as normal appearing mucosa were obtained from horses slaughtered for human consumption. All samples were tested for urease activity using the Pyloritek® assay, while mucosal bacterial content was evaluated using Fluorescence In Situ Hybridisation. In selected sub samples, bacteria characterisation was pursued further by cloning and sequencing. Mucosal lesions were found in 36/63 stomachs and included hyperplastic rugae, polypoid structures and focal erosions. None of the samples were tested positive for urease activity or for FISH using the Helicobacter genus specific probe. In samples of lesions, as well as normal samples, clones with 99% similarities to Lactobacillus salivarius and Sarcina ventriculi were found. Escherichia like bacterium clones and Enterococcus clones were demonstrated in one focal erosion. Based on a phylogenetic tree these clones had 100% similarity to Escherichia fergusonii and Enterococcus faecium. The Enterococcus were found colonising the mucosal surface, while E. fergusonii organisms were also demonstrated intraepithelial. Conclusion Gastric Helicobacter spp. could not be verified as being involved in lesions of the glandular stomach of the horse. Since E. fergusonii has been described as an emerging pathogen in both humans and animals, the finding of this bacterium in gastric erosion warrants further clarification to whether gastric infection with this type bacterium is important for horses.
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Affiliation(s)
- Louise Husted
- Department of Large Animal Sciences, Faculty of Life Sciences, University of Copenhagen, Hoejbakkegaard Allé 5, 2630 Taastrup, Denmark
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Touchon M, Hoede C, Tenaillon O, Barbe V, Baeriswyl S, Bidet P, Bingen E, Bonacorsi S, Bouchier C, Bouvet O, Calteau A, Chiapello H, Clermont O, Cruveiller S, Danchin A, Diard M, Dossat C, Karoui ME, Frapy E, Garry L, Ghigo JM, Gilles AM, Johnson J, Le Bouguénec C, Lescat M, Mangenot S, Martinez-Jéhanne V, Matic I, Nassif X, Oztas S, Petit MA, Pichon C, Rouy Z, Ruf CS, Schneider D, Tourret J, Vacherie B, Vallenet D, Médigue C, Rocha EPC, Denamur E. Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS Genet 2009; 5:e1000344. [PMID: 19165319 PMCID: PMC2617782 DOI: 10.1371/journal.pgen.1000344] [Citation(s) in RCA: 775] [Impact Index Per Article: 51.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2008] [Accepted: 12/16/2008] [Indexed: 01/01/2023] Open
Abstract
The Escherichia coli species represents one of the best-studied model organisms, but also encompasses a variety of commensal and pathogenic strains that diversify by high rates of genetic change. We uniformly (re-) annotated the genomes of 20 commensal and pathogenic E. coli strains and one strain of E. fergusonii (the closest E. coli related species), including seven that we sequenced to completion. Within the ∼18,000 families of orthologous genes, we found ∼2,000 common to all strains. Although recombination rates are much higher than mutation rates, we show, both theoretically and using phylogenetic inference, that this does not obscure the phylogenetic signal, which places the B2 phylogenetic group and one group D strain at the basal position. Based on this phylogeny, we inferred past evolutionary events of gain and loss of genes, identifying functional classes under opposite selection pressures. We found an important adaptive role for metabolism diversification within group B2 and Shigella strains, but identified few or no extraintestinal virulence-specific genes, which could render difficult the development of a vaccine against extraintestinal infections. Genome flux in E. coli is confined to a small number of conserved positions in the chromosome, which most often are not associated with integrases or tRNA genes. Core genes flanking some of these regions show higher rates of recombination, suggesting that a gene, once acquired by a strain, spreads within the species by homologous recombination at the flanking genes. Finally, the genome's long-scale structure of recombination indicates lower recombination rates, but not higher mutation rates, at the terminus of replication. The ensuing effect of background selection and biased gene conversion may thus explain why this region is A+T-rich and shows high sequence divergence but low sequence polymorphism. Overall, despite a very high gene flow, genes co-exist in an organised genome. Although abundant knowledge has been accumulated regarding the E. coli laboratory strain K-12, little is known about the evolutionary trajectories that have driven the high diversity observed among natural isolates of the species, which encompass both commensal and highly virulent intestinal and extraintestinal pathogenic strains. We have annotated or re-annotated the genomes of 20 commensal and pathogenic E. coli strains and one strain of E. fergusonii (the closest E. coli related species), including seven that we sequenced to completion. Although recombination rates are much higher than mutation rates, we were able to reconstruct a robust phylogeny based on the ∼2,000 genes common to all strains. Based on this phylogeny, we established the evolutionary scenario of gains and losses of thousands of specific genes, identifying functional classes under opposite selection pressures. This genome flux is confined to very few positions in the chromosome, which are the same for every genome. Notably, we identified few or no extraintestinal virulence-specific genes. We also defined a long-scale structure of recombination in the genome with lower recombination rates at the terminus of replication. These findings demonstrate that, despite a very high gene flow, genes can co-exist in an organised genome.
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Affiliation(s)
- Marie Touchon
- Atelier de BioInformatique, Université Pierre et Marie Curie - Paris 6 (UPMC), Paris, France
- Microbial Evolutionary Genomics, Institut Pasteur, CNRS URA2171, Paris, France
| | - Claire Hoede
- Faculté de Médecine, Université Paris 7 Denis Diderot, INSERM U722, Site Xavier Bichat, Paris, France
| | - Olivier Tenaillon
- Faculté de Médecine, Université Paris 7 Denis Diderot, INSERM U722, Site Xavier Bichat, Paris, France
| | | | - Simon Baeriswyl
- Faculté de Médecine, Université Paris 5 René Descartes, INSERM U571, Paris, France
| | - Philippe Bidet
- Université Paris 7 Denis Diderot, Hôpital Robert Debré (APHP), EA 3105, Paris, France
| | - Edouard Bingen
- Université Paris 7 Denis Diderot, Hôpital Robert Debré (APHP), EA 3105, Paris, France
| | - Stéphane Bonacorsi
- Université Paris 7 Denis Diderot, Hôpital Robert Debré (APHP), EA 3105, Paris, France
| | | | - Odile Bouvet
- Faculté de Médecine, Université Paris 7 Denis Diderot, INSERM U722, Site Xavier Bichat, Paris, France
| | - Alexandra Calteau
- Laboratoire de Génomique Comparative, CNRS UMR8030, Institut de Génomique, CEA, Génoscope, Evry, France
| | - Hélène Chiapello
- UR1077 Mathématique, Informatique, et Génome, INRA, Jouy en Josas, France
| | - Olivier Clermont
- Faculté de Médecine, Université Paris 7 Denis Diderot, INSERM U722, Site Xavier Bichat, Paris, France
| | - Stéphane Cruveiller
- Laboratoire de Génomique Comparative, CNRS UMR8030, Institut de Génomique, CEA, Génoscope, Evry, France
| | - Antoine Danchin
- Unité de Génétique des Génomes Bactériens, Institut Pasteur, CNRS URA2171, Paris, France
| | - Médéric Diard
- Faculté de Médecine, Université Paris 5 René Descartes, INSERM U571, Paris, France
| | | | - Meriem El Karoui
- UR888 Unité des Bactéries Lactiques et Pathogènes Opportunistes, INRA, Jouy en Josas, France
| | - Eric Frapy
- Faculté de Médecine, Université Paris 5 René Descartes, INSERM U570, Paris, France
| | - Louis Garry
- Faculté de Médecine, Université Paris 7 Denis Diderot, INSERM U722, Site Xavier Bichat, Paris, France
| | - Jean Marc Ghigo
- Unité de Génétique des Biofilms, Institut Pasteur, CNRS URA2172, Paris, France
| | - Anne Marie Gilles
- Unité de Génétique des Génomes Bactériens, Institut Pasteur, CNRS URA2171, Paris, France
| | - James Johnson
- Veterans Affairs Medical Center, Minneapolis, Minnesota, United States of America
- Department of Medicine, University of Minnesota, Minneapolis, Minnesota, United States of America
| | | | - Mathilde Lescat
- Faculté de Médecine, Université Paris 7 Denis Diderot, INSERM U722, Site Xavier Bichat, Paris, France
| | | | | | - Ivan Matic
- Faculté de Médecine, Université Paris 5 René Descartes, INSERM U571, Paris, France
| | - Xavier Nassif
- Faculté de Médecine, Université Paris 5 René Descartes, INSERM U570, Paris, France
| | - Sophie Oztas
- Génoscope, Institut de Génomique, CEA, Evry, France
| | - Marie Agnès Petit
- UR888 Unité des Bactéries Lactiques et Pathogènes Opportunistes, INRA, Jouy en Josas, France
| | - Christophe Pichon
- Pathogénie Bactérienne des Muqueuses, Institut Pasteur, Paris, France
| | - Zoé Rouy
- Laboratoire de Génomique Comparative, CNRS UMR8030, Institut de Génomique, CEA, Génoscope, Evry, France
| | - Claude Saint Ruf
- Faculté de Médecine, Université Paris 5 René Descartes, INSERM U571, Paris, France
| | | | - Jérôme Tourret
- Faculté de Médecine, Université Paris 7 Denis Diderot, INSERM U722, Site Xavier Bichat, Paris, France
| | | | - David Vallenet
- Laboratoire de Génomique Comparative, CNRS UMR8030, Institut de Génomique, CEA, Génoscope, Evry, France
| | - Claudine Médigue
- Laboratoire de Génomique Comparative, CNRS UMR8030, Institut de Génomique, CEA, Génoscope, Evry, France
- * E-mail: (CM); (EPCR); (ED)
| | - Eduardo P. C. Rocha
- Atelier de BioInformatique, Université Pierre et Marie Curie - Paris 6 (UPMC), Paris, France
- Microbial Evolutionary Genomics, Institut Pasteur, CNRS URA2171, Paris, France
- * E-mail: (CM); (EPCR); (ED)
| | - Erick Denamur
- Faculté de Médecine, Université Paris 7 Denis Diderot, INSERM U722, Site Xavier Bichat, Paris, France
- * E-mail: (CM); (EPCR); (ED)
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Misidentification of a variant biotype of Escherichia coli O157:H7 as Escherichia fergusonii by Vitek 2 Compact. J Clin Microbiol 2008; 47:872-3. [PMID: 19116349 DOI: 10.1128/jcm.02425-08] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Wragg P, La Ragione RM, Best A, Reichel R, Anjum MF, Mafura M, Woodward MJ. Characterisation of Escherichia fergusonii isolates from farm animals using an Escherichia coli virulence gene array and tissue culture adherence assays. Res Vet Sci 2008; 86:27-35. [PMID: 18585745 DOI: 10.1016/j.rvsc.2008.05.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2007] [Revised: 04/07/2008] [Accepted: 05/14/2008] [Indexed: 11/27/2022]
Abstract
Escherichia fergusonii has been associated with a wide variety of intestinal and extra-intestinal infections in both humans and animals but, despite strong circumstantial evidence, the degree to which the organism is responsible for the pathologies identified remains uncertain. Thirty isolates of E. fergusonii collected between 2003 and 2004 were screened using an Escherichia coli virulence gene array to test for the presence of homologous virulence genes in E. fergusonii. The iss (increased serum survival) gene was present in 13/30 (43%) of the test strains and the prfB (P-related fimbriae regulatory) and ireA (siderophore receptor IreA) genes were also detected jointly in 3/30 (10%) strains. No known virulence genes were detected in 14/30 (47%) of strains. Following confirmatory PCR and sequence analysis, the E. fergusoniiprfB, iss and ireA genes shared a high degree of sequence similarity to their counterparts in E. coli, and a particular resemblance was noted with the E. coli strain APEC O1 pathogenicity island. In tissue culture adherence assays, nine E. fergusonii isolates associated with HEp-2 cells with a 'localised adherence' or 'diffuse adherence' phenotype, and they proved to be moderately invasive. The E. fergusonii isolates in this study possess both some phenotypic and genotypic features linked to known pathotypes of E. coli, and support existing evidence that strains of E. fergusonii may act as an opportunistic pathogens, although their specific virulence factors may need to be explored.
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Affiliation(s)
- P Wragg
- Veterinary Laboratories Agency-Thirsk Regional Laboratory, Thirsk, North Yorkshire YO7 1PZ, United Kingdom.
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Abstract
We report a case in which Escherichia fergusonii, an emerging pathogen in various types of infections, was associated with cystitis in a 52-year-old woman. The offending strain was found to be multidrug resistant. Despite in vitro activity, beta-lactam treatment failed because of a lack of patient compliance with therapy. The work confirms the pathogenic potential of E. fergusonii.
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