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Ramatla T, Mafokwane T, Lekota K, Monyama M, Khasapane G, Serage N, Nkhebenyane J, Bezuidenhout C, Thekisoe O. "One Health" perspective on prevalence of co-existing extended-spectrum β-lactamase (ESBL)-producing Escherichia coli and Klebsiella pneumoniae: a comprehensive systematic review and meta-analysis. Ann Clin Microbiol Antimicrob 2023; 22:88. [PMID: 37740207 PMCID: PMC10517531 DOI: 10.1186/s12941-023-00638-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 09/12/2023] [Indexed: 09/24/2023] Open
Abstract
BACKGROUND The Escherichia coli (E. coli) and Klebsiella pneumoniae (K. pneumoniae) bacterial isolates that produce extended-spectrum β-lactamases (ESBLs) contribute to global life-threatening infections. This study conducted a systematic review and meta-analysis on the global prevalence of ESBLs in co-existing E. coli and K. pneumoniae isolated from humans, animals and the environment. METHODS The systematic review protocol was registered in the International Prospective Register of Systematic Reviews (PROSPERO) [ID no: CRD42023394360]. This study was carried out following the preferred reporting items for systematic reviews and meta-analyses (PRISMA) guidelines. One hundred and twenty-six eligible studies published on co-existing antibiotic resistance in E. coli and K. pneumoniae between 1990 and 2022 were included. RESULTS The pooled prevalence of ESBL-producing E. coli and K. pneumoniae was 33.0% and 32.7% for humans, 33.5% and 19.4% for animals, 56.9% and 24.2% for environment, 26.8% and 6.7% for animals/environment, respectively. Furthermore, the three types of resistance genes that encode ESBLs, namely blaSHVblaCTX-M,blaOXA, and blaTEM, were all detected in humans, animals and the environment. CONCLUSIONS The concept of "One-Health" surveillance is critical to tracking the source of antimicrobial resistance and preventing its spread. The emerging state and national surveillance systems should include bacteria containing ESBLs. A well-planned, -implemented, and -researched alternative treatment for antimicrobial drug resistance needs to be formulated.
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Affiliation(s)
- Tsepo Ramatla
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, 2520, South Africa.
| | - Tshepo Mafokwane
- Department of Life and Consumer Sciences, University of South Africa, Florida, 1710, South Africa
| | - Kgaugelo Lekota
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, 2520, South Africa
| | - Maropeng Monyama
- Department of Life and Consumer Sciences, University of South Africa, Florida, 1710, South Africa
| | - George Khasapane
- Department of Life Sciences, Central University of Technology, Bloemfontein, 9300, South Africa
| | - Naledi Serage
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, 2520, South Africa
| | - Jane Nkhebenyane
- Department of Life Sciences, Central University of Technology, Bloemfontein, 9300, South Africa
| | - Carlos Bezuidenhout
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, 2520, South Africa
| | - Oriel Thekisoe
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, 2520, South Africa
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Bumunang EW, Zaheer R, Stanford K, Laing C, Niu D, Guan LL, Chui L, Tarr GAM, McAllister TA. Genomic Analysis of Shiga Toxin-Producing E. coli O157 Cattle and Clinical Isolates from Alberta, Canada. Toxins (Basel) 2022; 14:toxins14090603. [PMID: 36136541 PMCID: PMC9505746 DOI: 10.3390/toxins14090603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/24/2022] [Accepted: 08/24/2022] [Indexed: 12/02/2022] Open
Abstract
Shiga toxin (stx) is the principal virulence factor of the foodborne pathogen, Shiga toxin-producing Escherichia coli (STEC) O157:H7 and is associated with various lambdoid bacterio (phages). A comparative genomic analysis was performed on STEC O157 isolates from cattle (n = 125) and clinical (n = 127) samples to characterize virulence genes, stx-phage insertion sites and antimicrobial resistance genes that may segregate strains circulating in the same geographic region. In silico analyses revealed that O157 isolates harboured the toxin subtypes stx1a and stx2a. Most cattle (76.0%) and clinical (76.4%) isolates carried the virulence gene combination of stx1, stx2, eae and hlyA. Characterization of stx1 and stx2-carrying phages in assembled contigs revealed that they were associated with mlrA and wrbA insertion sites, respectively. In cattle isolates, mlrA and wrbA insertion sites were occupied more often (77% and 79% isolates respectively) than in clinical isolates (38% and 1.6% isolates, respectively). Profiling of antimicrobial resistance genes (ARGs) in the assembled contigs revealed that 8.8% of cattle (11/125) and 8.7% of clinical (11/127) isolates harboured ARGs. Eight antimicrobial resistance genes cassettes (ARCs) were identified in 14 isolates (cattle, n = 8 and clinical, n = 6) with streptomycin (aadA1, aadA2, ant(3’’)-Ia and aph(3’’)-Ib) being the most prevalent gene in ARCs. The profound disparity between the cattle and clinical strains in occupancy of the wrbA locus suggests that this trait may serve to differentiate cattle from human clinical STEC O157:H7. These findings are important for stx screening and stx-phage insertion site genotyping as well as monitoring ARGs in isolates from cattle and clinical samples.
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Affiliation(s)
- Emmanuel W. Bumunang
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Rahat Zaheer
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB T1J 4B1, Canada
| | - Kim Stanford
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 1M4, Canada
| | - Chad Laing
- National Centre for Animal Disease Canadian Food Inspection Agency, Lethbridge, AB T1J 0P3, Canada
| | - Dongyan Niu
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Le Luo Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P9, Canada
| | - Linda Chui
- Alberta Precisions Laboratory, Alberta Public Health, Edmonton, AB T6G 2J2, Canada
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB T6G 2B7, Canada
| | - Gillian A. M. Tarr
- Division of Environmental Health Sciences, School of Public Health, University of Minnesota, Minneapolis, MN 55455, USA
| | - Tim A. McAllister
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB T1J 4B1, Canada
- Correspondence:
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Reynolds C, Checkley S, Chui L, Otto S, Neumann NF. Evaluating the risks associated with Shiga-toxin-producing Escherichia coli (STEC) in private well waters in Canada. Can J Microbiol 2020; 66:337-350. [PMID: 32069070 DOI: 10.1139/cjm-2019-0329] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Shiga-toxin-producing Escherichia coli (STEC) represent a major concern for waterborne disease outbreaks associated with consumption of contaminated groundwater. Over 4 million people rely on private groundwater systems as their primary drinking water source in Canada; many of these systems do not meet current standards for water quality. This manuscript provides a scoping overview of studies examining STEC prevalence and occurrence in groundwater, and it includes a synopsis of the environmental variables affecting survival, transport, persistence, and overall occurrence of these important pathogenic microbes in private groundwater wells used for drinking purposes.
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Affiliation(s)
- Colin Reynolds
- Environmental Health Sciences, School of Public Health, University of Alberta, Edmonton, AB T6G 2G7, Canada
| | - Sylvia Checkley
- Department of Ecosystem Public Health, Faculty of Veterinary Medicine, University of Calgary
| | - Linda Chui
- Department of Laboratory Medicine and Pathology, University of Alberta
| | - Simon Otto
- Environmental Health Sciences, School of Public Health, University of Alberta, Edmonton, AB T6G 2G7, Canada
| | - Norman F Neumann
- Environmental Health Sciences, School of Public Health, University of Alberta, Edmonton, AB T6G 2G7, Canada
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CPHLN recommendations for the laboratory detection of Shiga toxin-producing Escherichia coli (O157 and non-O157). ACTA ACUST UNITED AC 2018; 44:304-307. [PMID: 30996693 DOI: 10.14745/ccdr.v44i11a06] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Shiga toxin-producing Escherichia coli (STEC) are important enteric pathogens responsible for sporadic cases and outbreaks of gastroenteritis. E.coli O157:H7/NM (STEC O157) are the most commonly known STEC serotypes but it is now increasingly apparent that non-O157 STEC serotypes have been underreported in the past because they were not part of routine screening in many front-line laboratories. The Canadian Public Health Laboratory Network (CPHLN) has identified the need for improved detection and surveillance of non-O157 STEC and has developed the following recommendations to assist in the decision-making process for clinical and reference microbiology laboratories. These recommendations should be followed to the best of a laboratory's abilities based on the availability of technology and resources. The CPHLN recommends that when screening for the agents of bacterial gastroenteritis from a stool sample, front-line laboratories use either a chromogenic agar culture or a culture-independent diagnostic test (CIDT). CIDT options include nucleic acid amplification tests (NAATs) to detect Shiga toxin genes or enzyme immunoassays (EIAs) to detect Shiga toxins. If either CIDT method is positive for possible STEC, laboratories must have a mechanism to culture and isolate STEC in order to support both provincial and national surveillance as well as outbreak investigations and response. These CPHLN recommendations should result in improved detection of STEC in patients presenting with diarrhea, especially when due to the non-O157 serotypes. These measures should enhance the overall quality of healthcare and food safety, and provide better protection of the public via improved surveillance and outbreak detection and response.
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Yamasaki T, Miyake S, Nakano S, Morimura H, Hirakawa Y, Nagao M, Iijima Y, Narita H, Ichiyama S. Development of a Surface Plasmon Resonance-Based Immunosensor for Detection of 10 Major O-Antigens on Shiga Toxin-Producing Escherichia coli, with a Gel Displacement Technique To Remove Bound Bacteria. Anal Chem 2016; 88:6711-7. [PMID: 27243947 DOI: 10.1021/acs.analchem.6b00797] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A surface plasmon resonance-based immunosensor (SPR-immunosensor) was developed for the detection of Shiga toxin-producing Escherichia coli (STEC) belonging to the O-antigen groups O26, O91, O103, O111, O115, O121, O128, O145, O157, and O159. The polyclonal antibodies (PoAbs) generated against each of the STEC O-antigen types in rabbits were purified and were immobilized on the sensor chip at 0.5 mg/mL. The limit of detection for STEC O157 by the SPR-immunosensor was found to be 6.3 × 10(4) cells for 75 s. Each of the examined 10 O-antigens on the STECs was detected by the corresponding PoAb with almost no reaction to the other PoAbs. The detected STECs were sufficiently removed from the PoAbs using gelatin or agarose gel without deactivation of the PoAbs, enabling repeatable use of the sensor chip. The developed SPR-immunosensor can be applied for the detection of multiple STEC O-antigens. Furthermore, the new antigen removal technique using the gel displacement approach can be utilized with various immunosensors to improve the detection of pathogens in clinical and public health settings.
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Affiliation(s)
- Tomomi Yamasaki
- Advanced Science, Technology & Management Research Institute of Kyoto , Shimogyo-ku, Kyoto 600-8813, Japan
| | - Shiro Miyake
- Advanced Science, Technology & Management Research Institute of Kyoto , Shimogyo-ku, Kyoto 600-8813, Japan.,Research & Development Division, HORIBA, Ltd., Minami-ku, Kyoto 601-8510, Japan
| | - Satoshi Nakano
- Department of Clinical Laboratory Medicine, Kyoto University Graduate School of Medicine , Sakyo-ku, Kyoto 606-8507, Japan
| | - Hiroyuki Morimura
- Research & Development Division, HORIBA, Ltd., Minami-ku, Kyoto 601-8510, Japan
| | - Yuki Hirakawa
- Advanced Science, Technology & Management Research Institute of Kyoto , Shimogyo-ku, Kyoto 600-8813, Japan
| | - Miki Nagao
- Department of Clinical Laboratory Medicine, Kyoto University Graduate School of Medicine , Sakyo-ku, Kyoto 606-8507, Japan
| | - Yoshio Iijima
- Department of Microbiology, Kobe Institute of Health , Chuo-ku, Kobe 650-0046, Japan
| | - Hiroshi Narita
- Department of Food and Nutrition, Kyoto Women's University , Higashiyama-ku, Kyoto 605-8501, Japan
| | - Satoshi Ichiyama
- Department of Clinical Laboratory Medicine, Kyoto University Graduate School of Medicine , Sakyo-ku, Kyoto 606-8507, Japan
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Riddle MS, DuPont HL, Connor BA. ACG Clinical Guideline: Diagnosis, Treatment, and Prevention of Acute Diarrheal Infections in Adults. Am J Gastroenterol 2016; 111:602-22. [PMID: 27068718 DOI: 10.1038/ajg.2016.126] [Citation(s) in RCA: 189] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 03/16/2016] [Indexed: 12/11/2022]
Abstract
Acute diarrheal infections are a common health problem globally and among both individuals in the United States and traveling to developing world countries. Multiple modalities including antibiotic and non-antibiotic therapies have been used to address these common infections. Information on treatment, prevention, diagnostics, and the consequences of acute diarrhea infection has emerged and helps to inform clinical management. In this ACG Clinical Guideline, the authors present an evidence-based approach to diagnosis, prevention, and treatment of acute diarrhea infection in both US-based and travel settings.
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Affiliation(s)
- Mark S Riddle
- Enteric Diseases Department, Naval Medical Research Center, Silver Spring, Maryland, USA
| | - Herbert L DuPont
- University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Bradley A Connor
- Weill Medical College of Cornell University, New York, New York, USA
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7
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Parsons BD, Zelyas N, Berenger BM, Chui L. Detection, Characterization, and Typing of Shiga Toxin-Producing Escherichia coli. Front Microbiol 2016; 7:478. [PMID: 27148176 PMCID: PMC4828450 DOI: 10.3389/fmicb.2016.00478] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Accepted: 03/22/2016] [Indexed: 02/04/2023] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) are responsible for gastrointestinal diseases reported in numerous outbreaks around the world. Given the public health importance of STEC, effective detection, characterization and typing is critical to any medical laboratory system. While non-O157 serotypes account for the majority of STEC infections, frontline microbiology laboratories may only screen for STEC using O157-specific agar-based methods. As a result, non-O157 STEC infections are significantly under-reported. This review discusses recent advances on the detection, characterization and typing of STEC with emphasis on work performed at the Alberta Provincial Laboratory for Public Health (ProvLab). Candidates for the detection of all STEC serotypes include chromogenic agars, enzyme immunoassays (EIA) and quantitative real time polymerase chain reaction (qPCR). Culture methods allow further characterization of isolates, whereas qPCR provides the greatest sensitivity and specificity, followed by EIA. The virulence gene profiles using PCR arrays and stx gene subtypes can subsequently be determined. Different non-O157 serotypes exhibit markedly different virulence gene profiles and a greater prevalence of stx1 than stx2 subtypes compared to O157:H7 isolates. Finally, recent innovations in whole genome sequencing (WGS) have allowed it to emerge as a candidate for the characterization and typing of STEC in diagnostic surveillance isolates. Methods of whole genome analysis such as single nucleotide polymorphisms and k-mer analysis are concordant with epidemiological data and standard typing methods, such as pulsed-field gel electrophoresis and multiple-locus variable number tandem repeat analysis while offering additional strain differentiation. Together these findings highlight improved strategies for STEC detection using currently available systems and the development of novel approaches for future surveillance.
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Affiliation(s)
- Brendon D. Parsons
- Laboratory Medicine and Pathology, University of AlbertaEdmonton, AB, Canada
| | - Nathan Zelyas
- Medical Microbiology and Immunology, University of AlbertaEdmonton, AB, Canada
| | - Byron M. Berenger
- Medical Microbiology and Immunology, University of AlbertaEdmonton, AB, Canada
| | - Linda Chui
- Laboratory Medicine and Pathology, University of AlbertaEdmonton, AB, Canada
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Zelyas N, Poon A, Patterson-Fortin L, Johnson RP, Lee W, Chui L. Assessment of commercial chromogenic solid media for the detection of non-O157 Shiga toxin-producing Escherichia coli (STEC). Diagn Microbiol Infect Dis 2016; 85:302-308. [PMID: 27157987 DOI: 10.1016/j.diagmicrobio.2016.03.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 03/10/2016] [Accepted: 03/13/2016] [Indexed: 11/30/2022]
Abstract
Detection of Shiga toxin-producing Escherichia coli (STEC) has evolved significantly since the introduction of sorbitol-MacConkey agar. This study compares four chromogenic media (CHROMagar™ STEC, Rainbow® O157 agar, CHROMagar™ O157, and Colorex® O157) in their identification of non-O157 STEC. When 161 non-O157 STEC were directly inoculated onto each medium, detection rates on CHROMagar™ STEC, Rainbow® O157 agar, CHROMagar™ O157 and Colorex® O157 were 90%, 70%, 3.7% and 6.8%, respectively. Tellurite minimal inhibitory concentrations (MICs) correlated with growth on CHROMagar™ STEC as 20 of 22 isolates with poor or no growth had MICs ≤1μg/mL. Stool spiking experiments revealed that CHROMagar™ STEC had the highest recovery of the six most common non-O157 STEC, ranging from 30% (in mucoid stool) to 98% (in watery stool). When using clinical stool samples, CHROMagar™ STEC had a sensitivity, specificity, positive predictive value, and negative predictive value of 84.6%, 87%, 13.9%, and 99.6%, respectively.
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Affiliation(s)
- Nathan Zelyas
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, Canada
| | - Alan Poon
- Alberta Provincial Laboratory for Public Health, Edmonton, AB, Canada
| | | | - Roger P Johnson
- Public Health Agency of Canada, National Microbiology Laboratory@Guelph, Guelph, ON, Canada
| | - Winki Lee
- Alberta Provincial Laboratory for Public Health, Edmonton, AB, Canada
| | - Linda Chui
- Alberta Provincial Laboratory for Public Health, Edmonton, AB, Canada; Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada.
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Neher S, Hazarika AK, Barkalita LM, Borah P, Bora DP, Sharma RK. Isolation and characterization of Shiga toxigenic Escherichia coli of animal and bird origin by multiplex polymerase chain reaction. Vet World 2016; 9:123-7. [PMID: 27051196 PMCID: PMC4819360 DOI: 10.14202/vetworld.2016.123-127] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 12/17/2015] [Accepted: 12/21/2015] [Indexed: 11/16/2022] Open
Abstract
AIM The purpose of this study was to determine the virulence genes and serotype of Shiga toxin producing Escherichia coli (STEC) strains isolated from animals and birds. MATERIALS AND METHODS A total of 226 different samples viz., fecal, intestinal content, rectal swab and heart blood were collected from different clinically affected/healthy animals and birds and were streaked on McConkeys' lactose agar and eosin methylene blue agar for isolation of E. coli, confirmed by staining characteristics and biochemical tests. By polymerase chain reaction (PCR) all the E. coli isolates were screened for certain virulence genes, viz., Shiga toxin 1 (stx1), stx2 and eae and enterohemolytic (Ehly) phenotype was observed in washed sheep blood agar plate. All the isolated E. coli strains were forwarded to the National Salmonella and Escherichia Centre, Central Research Institute, Kasauli (Himachal Pradesh) for serotyping. RESULTS Out of 226 samples 138 yielded E. coli. All the isolates were screened for molecular detection of different virulent genes, viz. stx1, stx2 and eae, based on which 36 (26.08%) were identified as STEC. Among those STEC isolates, 15 (41.67%), 14 (38.89%), 1 (2.78%) exhibited eae, stx2, stx1 alone, respectively, whereas 4 (11.11%) and 2 (5.56%) carried both stx1 and stx2, stx2 and eae, respectively. Among the STEC isolates 22 were belonged to 15 different sero-groups, viz., O2, O20, O22, O25, O43, O60, O69, O90, O91, O95, O106, O118, O130, O162 and O170 and others were untypable. Ehly phenotype was observed in 10 (27.78%) the STEC isolates. CONCLUSION The present study concluded that STEC could be isolated from both clinically affected as well as healthy animals and birds. Regular monitoring of more samples from animal and bird origin is important to identify natural reservoir of STEC to prevent zoonotic infection.
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Affiliation(s)
- S. Neher
- Department of Veterinary Microbiology, College of Veterinary Science, Assam Agricultural University, Guwahati, Assam, India
| | - A. K. Hazarika
- Department of Veterinary Microbiology, College of Veterinary Science, Assam Agricultural University, Guwahati, Assam, India
| | - L. M. Barkalita
- Department of Animal Biotechnology, College of Veterinary Science, Assam Agricultural University, Guwahati, Assam, India
| | - P. Borah
- Department of Animal Biotechnology, College of Veterinary Science, Assam Agricultural University, Guwahati, Assam, India
| | - D. P. Bora
- Department of Veterinary Microbiology, College of Veterinary Science, Assam Agricultural University, Guwahati, Assam, India
| | - R. K. Sharma
- Department of Veterinary Microbiology, College of Veterinary Science, Assam Agricultural University, Guwahati, Assam, India
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Tunsjø HS, Kvissel AK, Follin-Arbelet B, Brotnov BM, Ranheim TE, Leegaard TM. Suitability of stx-PCR directly from fecal samples in clinical diagnostics of STEC. APMIS 2015; 123:872-8. [PMID: 26303619 DOI: 10.1111/apm.12428] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 07/04/2015] [Indexed: 01/01/2023]
Abstract
PCR-based testing for Shiga toxin producing Escherichia coli (STEC) directly from fecal samples is increasingly being implemented in routine diagnostic laboratories. These methods aim to detect clinically relevant amounts of microbes and not stx-carrying phages or low backgrounds of STEC. We present a diagnostic procedure and results from 1 year of stx-targeted real-time PCR of fecal samples from patients with gastrointestinal symptoms in Norway. A rapid stx2 subtyping strategy is described, which aims to quickly reveal the virulence potential of the microbe. stx was detected in 22 of 3320 samples, corresponding to a PCR positive rate of 0.66%. STEC were cultured from 72% of the PCR positive samples. Four stx1 isolates, eight stx2 isolates, and four isolates with both stx1 and stx2 were identified. With the method presented, stx-carrying phages are not commonly detected. Our results support the use of molecular testing combined with classical culture techniques for routine diagnostic purposes.
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Affiliation(s)
- Hege S Tunsjø
- Unit of Gene Technology, Department of Multidisciplinary Laboratory Medicine and Medical Biochemistry, Division of Diagnostics and Technology, Akershus University Hospital, Nordbyhagen, Norway
| | - Anne K Kvissel
- Unit of Gene Technology, Department of Multidisciplinary Laboratory Medicine and Medical Biochemistry, Division of Diagnostics and Technology, Akershus University Hospital, Nordbyhagen, Norway
| | - Benoit Follin-Arbelet
- Unit of Gene Technology, Department of Multidisciplinary Laboratory Medicine and Medical Biochemistry, Division of Diagnostics and Technology, Akershus University Hospital, Nordbyhagen, Norway
| | - Beth-Marie Brotnov
- Unit of Gene Technology, Department of Multidisciplinary Laboratory Medicine and Medical Biochemistry, Division of Diagnostics and Technology, Akershus University Hospital, Nordbyhagen, Norway
| | - Trond E Ranheim
- Department of Microbiology and Infection Control, Division of Diagnostics and Technology, Akershus University Hospital, Nordbyhagen, Norway
| | - Truls M Leegaard
- Department of Microbiology and Infection Control, Division of Diagnostics and Technology, Akershus University Hospital, Nordbyhagen, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
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Lalani T, Tisdale MD, Maguire JD, Wongsrichanalai C, Riddle MS, Tribble DR. Detection of enteropathogens associated with travelers' diarrhea using a multiplex Luminex-based assay performed on stool samples smeared on Whatman FTA Elute cards. Diagn Microbiol Infect Dis 2015; 83:18-20. [PMID: 26072151 DOI: 10.1016/j.diagmicrobio.2015.05.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 04/27/2015] [Accepted: 05/19/2015] [Indexed: 01/03/2023]
Abstract
We evaluated the limits of detection (LoD) for an 11-plex PCR-Luminex assay performed on Whatman(™) FTA Elute cards smeared with stool containing pathogens associated with travelers' diarrhea. LoDs ranged from 10(2) to 10(5)CFU, PFU, or cysts/g for most pathogens except Cryptosporidium. Campylobacter and norovirus LoDs increased with prolonged storage of cards.
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Affiliation(s)
- Tahaniyat Lalani
- Infectious Disease Clinic, Naval Medical Center, Portsmouth, VA, USA; Infectious Disease Clinical Research Program, Uniformed Services University, Bethesda, MD, USA; Henry M Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA.
| | - Michele D Tisdale
- Infectious Disease Clinic, Naval Medical Center, Portsmouth, VA, USA; Infectious Disease Clinical Research Program, Uniformed Services University, Bethesda, MD, USA; Henry M Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Jason D Maguire
- Infectious Disease Clinic, Naval Medical Center, Portsmouth, VA, USA
| | | | - Mark S Riddle
- Enteric Diseases Department, Naval Medical Research Center, Silver Spring, MD, USA
| | - David R Tribble
- Infectious Disease Clinical Research Program, Uniformed Services University, Bethesda, MD, USA
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12
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Genetic Diversity of the fliC Genes Encoding the Flagellar Antigen H19 of Escherichia coli and Application to the Specific Identification of Enterohemorrhagic E. coli O121:H19. Appl Environ Microbiol 2015; 81:4224-30. [PMID: 25862232 DOI: 10.1128/aem.00591-15] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 04/09/2015] [Indexed: 11/20/2022] Open
Abstract
Enterohemorrhagic Escherichia coli (EHEC) O121:H19 belong to a specific clonal type distinct from other classical EHEC and major enteropathogenic E. coli groups and is regarded as one of the major EHEC serogroups involved in severe infections in humans. Sequencing of the fliC genes associated with the flagellar antigen H19 (fliCH19) revealed the genetic diversity of the fliCH19 gene sequences in E. coli. A cluster analysis of 12 fliCH19 sequences, 4 from O121 and 8 from non-O121 E. coli strains, revealed five different genotypes. All O121:H19 strains fell into one cluster, whereas a second cluster was formed by five non-O121:H19 strains. Cluster 1 and cluster 2 strains differ by 27 single nucleotide exchanges in their fliCH19 genes (98.5% homology). Based on allele discrimination of the fliCH19 genes, a real-time PCR test was designed for specific identification of EHEC O121:H19. The O121 fliCH19 PCR tested negative in 73 E. coli H19 strains that belonged to serogroups other than O121, including 28 different O groups, O-nontypeable H19, and O-rough:H19 strains. The O121 fliCH19 PCR reacted with all 16 tested O121:H19 strains and 1 O-rough:H19 strain which was positive for the O121 wzx gene. A cross-reaction was observed only with E. coli H32 strains which share sequence similarities in the target region of the O121 fliCH19 PCR. The combined use of O-antigen genotyping (O121 wzx) and the detection of O121 fliCH19 allele type contributes to improving the identification and molecular serotyping of EHEC O121:H19 motile and nonmotile strains and variants of these strains lacking stx genes.
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Harper SL, Edge VL, Ford J, Thomas MK, McEwen SA. Lived experience of acute gastrointestinal illness in Rigolet, Nunatsiavut: "just suffer through it". Soc Sci Med 2014; 126:86-98. [PMID: 25528558 DOI: 10.1016/j.socscimed.2014.12.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Enteric illness associated with foodborne and waterborne disease is thought to be common in some Canadian Indigenous communities. This study aimed to understand the lived experience of acute gastrointestinal illness (AGI), including symptoms and severity, perceived causes, and healthcare seeking behaviors of AGI in the small Inuit community of Rigolet, Canada. A concurrent mixed quantitative and qualitative methods design was used. Two cross-sectional retrospective surveys provided quantitative data to examine self-reported AGI symptoms and the distribution of potential risk factors in the community. Qualitative data from in-depth interviews with one-third of AGI cases were analyzed using a constant-comparative method to describe symptoms and severity, identify perceived risk factors, and explore health seeking behavior of AGI in Rigolet. Of the survey respondents reporting AGI, most reported symptoms of diarrhea without vomiting, followed by diarrhea with vomiting, and vomiting without diarrhea. The most common secondary symptoms included stomach cramps and abdominal pain, nausea, and extreme tiredness. Community members identified potential risk factors for AGI that reflect the epidemiology triad (host, agent, and environmental factors), including hygiene, retail food, tap water, boil water advisories, and personal stress. Risk aversion and healthcare seeking behaviors reflected the core constructs of the Health Belief Model (perceived susceptibility, severity, and benefits and barriers to action). Understanding community experience, perspectives, and beliefs related to AGI is useful for public health practitioners and health care providers. This information is important especially considering the relatively high estimated burden of AGI and the relatively low healthcare seeking behaviors in some Indigenous communities compared to national estimates. Moreover, the mixed-methods approach used to understand the burden of AGI could be extended to other health research in Indigenous contexts.
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Affiliation(s)
- Sherilee L Harper
- Department of Population Medicine, University of Guelph, Guelph, Ontario, Canada.
| | - Victoria L Edge
- Department of Population Medicine, University of Guelph, Guelph, Ontario, Canada; Public Health Agency of Canada, Guelph, Ontario, Canada
| | - James Ford
- Department of Geography, McGill University, Montreal, Quebec, Canada
| | - M Kate Thomas
- Centre for Food-borne, Environmental & Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, Ontario, Canada
| | | | | | - Scott A McEwen
- Department of Population Medicine, University of Guelph, Guelph, Ontario, Canada
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Kumar A, Taneja N, Bharti B, Sharma M. Characterization of Shiga-toxigenic Escherichia coli isolated from cases of diarrhoea & haemolytic uremic syndrome in north India. Indian J Med Res 2014; 140:778-84. [PMID: 25758577 PMCID: PMC4365352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
BACKGROUND & OBJECTIVES Shiga toxin producing Escherichia coli (STEC) is an important zoonotic foodborne pathogen, capable of causing haemorrhagic colitis (HC) and haemolytic uremic syndrome (HUS). As data from India on human infections caused by STEC are limited, this study was carried out for hospital based surveillance for STEC as a causative agent of diarrhoea, bloody diarrhoea and HUS at a tertiary care centre and to study the virulence gene profile and strain relatedness by multi locus variable tandem repeat analysis (MLVA). METHODS A total of 600 stool samples were studied. Stool samples of every fifth patient presenting with non-bloody diarrhoea, all cases of bloody diarrhoea and diarrhoea associated HUS (D+HUS) were collected from October 2009 to September 2011. Stool samples were cultured for STEC and characterization of STEC was done by serogrouping, virulence genes analysis, and MLVA typing. RESULTS STEC were isolated as a sole pathogen from 11 stool samples [5 of 290 (1.7%) non-blood diarrhoea and 5 of 300 (1.6%) blood diarrhoea cases]. STEC was also isolated from one fatal case of HUS who was an eight month old child. Only six of 11 isolates were positive for stx2 gene, whereas stx1 was present in all 11 isolates. Only one isolate was positive for eae. Other adhesion genes present were iha in five isolates, followed by toxB and efa1 in two each and saa gene in one, isolate. Among the plasmid encoded genes, espP, hly and etpD were each present in one isolate each. In the MLVA typing, diverse profiles were obtained except two untypeable isolates from different patients shared the same MLVA profile. Both these isolates were not epidemiologically linked. INTERPRETATION & CONCLUSIONS This study demonstrated that STEC could be a causative agent of diarrhoea, bloody diarrhoea and sporadic HUS. However, further work needs to be done to study and explore the prevalence of these organisms in the food chain in this region.
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Affiliation(s)
- Ajay Kumar
- Department of Medical Microbiology, Postgraduate Institute of Medical Education & Research, Chandigarh, India
| | - Neelam Taneja
- Department of Medical Microbiology, Postgraduate Institute of Medical Education & Research, Chandigarh, India,Reprint requests: Dr Neelam Taneja, Additional Professor, Department of Medical Microbiology, Postgraduate Institute of Medical Education & Research. Chandigarh 160 012, India e-mail:
| | - Bhavneet Bharti
- Advanced Pediatric Centre, Postgraduate Institute of Medical Education & Research, Chandigarh, India
| | - Meera Sharma
- Department of Medical Microbiology, Postgraduate Institute of Medical Education & Research, Chandigarh, India
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Perry MD, Corden SA, Howe RA. Evaluation of the Luminex xTAG Gastrointestinal Pathogen Panel and the Savyon Diagnostics Gastrointestinal Infection Panel for the detection of enteric pathogens in clinical samples. J Med Microbiol 2014; 63:1419-1426. [PMID: 25102908 DOI: 10.1099/jmm.0.074773-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Infectious gastrointestinal disease is caused by a diverse array of pathogens, and is a challenging syndrome to correctly diagnose and manage. Conventional laboratory diagnostic methods are often time-consuming and frequently suffer from low detection rates. Two commercial multiplex nucleic acid amplification tests [Luminex xTAG Gastrointestinal Pathogen Panel (GPP) and Savyon Diagnostics Gastrointestinal Infection Panel (GIP)] were applied to 1000 stored diarrhoeal clinical stool samples. The Luminex xTAG GPP and Savyon GIP detected Campylobacter in 42/44 and 44/44 culture-positive samples, Salmonella in 4/4 and 3/4 culture-positive samples, Shigella in 1/1 culture-positive sample, Clostridium difficile toxin in 32/35 ELISA-positive samples, and Giardia in 6/6 wet-preparation-microscopy-positive samples, respectively. When the Luminex GPP assay was used concurrently with conventional methods for 472 clinical samples, it detected Campylobacter in 22/22 culture-positive samples, Salmonella in 1/1 culture-positive sample, Clostridium difficile toxin in 14/14 ELISA-positive samples and Giardia in 4/4 wet-preparation-microscopy-positive samples. The pathogen/toxin detection rate for conventional methods in both sample sets was <10%. The Luminex xTAG GPP detection rate was 24.8% in the stored samples and 32.6% in the concurrently tested samples. The Savyon GIP detection rate was 22.5%. From stored samples, 2.4% of Luminex xTAG GPP detections and 3.1% of Savyon GIP detections could not be confirmed using alternative nucleic acid amplification tests. Enhanced detection rates resulted from increased detection of pathogens routinely sought using conventional methods and were also due to ascertainment of micro-organisms that current testing strategies do not diagnose. Use of multiplex nucleic acid amplification tests will allow clinical laboratories to diagnose infectious gastroenteritis in more patients with diarrhoeal disease by increasing the sensitivity of pathogen detection and by reducing the selective bias of current strategies. The clinical and economic impact of these results warrants further investigation.
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Affiliation(s)
- Michael D Perry
- Public Health Wales Microbiology Cardiff, University Hospital of Wales, Heath Park, Cardiff, UK
| | - Sally A Corden
- Public Health Wales Microbiology Cardiff, University Hospital of Wales, Heath Park, Cardiff, UK
| | - Robin A Howe
- Public Health Wales Microbiology Cardiff, University Hospital of Wales, Heath Park, Cardiff, UK
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Kumar A, Taneja N, Sharma M. An epidemiological and environmental study of Shiga toxin-producing Escherichia coli in India. Foodborne Pathog Dis 2014; 11:439-46. [PMID: 24796582 DOI: 10.1089/fpd.2013.1613] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) are foodborne pathogens of worldwide importance, but a shortage of data exists for STEC isolation from India. Therefore, an epidemiological and environmental study that covers a large geographic area in north India was conducted. Ruminant stool samples (n=650) were collected from 59 dairies. Meat samples (n=450) were collected from local abattoirs and the main slaughterhouse of the region. Additionally, 600 human cases of diarrhea and hemolytic uremic syndrome were screened for STEC. Isolates were characterized for the virulence gene profiles and for the serogroups and were submitted to molecular typing by the multilocus variable-number tandem-repeat analysis (MLVA). Overall, 12.3% of animal stool samples and 6.3% of mutton samples (n=160) were positive for STEC. Additionally, STEC were isolated from 1.7% and 1.6% of watery (n=290) and bloody (n=310) stool specimens, respectively. Animal stool isolates were significantly more prevalent in hilly areas (p<0.05) than in plain areas. Polymerase chain reaction demonstrated the presence of stx1, stx2, hly, espP, saa, toxB, and iha genes in 117 (83.5%), 94 (67.1%), 77 (55%), 33 (23%), 62 (44.2%), 29 (20.7%), and 51 (36%) of the isolates, respectively. Five new serogroups (O55, O33, O173, O165, and O136) are being reported for the first time from India. Four isolates from serogroup O103 were found in mutton and stool specimens of cattle and humans (n=160). One isolate from serogroup O104 was isolated from a mutton sample. MLVA suggested the potential transmission of STEC from contaminated meat and bovine sources. This study confirms the frequent contamination of mutton samples (24%), whereas chicken and pork samples were negative for STEC. This study demonstrates the presence of STEC that carry a large repertoire of virulence genes and the potential transmission of STEC from contaminated mutton and animal stools in north India.
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Affiliation(s)
- Ajay Kumar
- Department of Medical Microbiology, Post Graduate Institute of Medical Education and Research , Chandigarh, India
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Johnson RP, Holtslander B, Mazzocco A, Roche S, Thomas JL, Pollari F, Pintar KDM. Detection and prevalence of verotoxin-producing Escherichia coli O157 and non-O157 serotypes in a Canadian watershed. Appl Environ Microbiol 2014; 80:2166-75. [PMID: 24487525 PMCID: PMC3993149 DOI: 10.1128/aem.03391-13] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 01/17/2014] [Indexed: 11/20/2022] Open
Abstract
Verotoxin-producing Escherichia coli (VTEC) strains are the cause of food-borne and waterborne illnesses around the world. Traditionally, surveillance of the human population as well as the environment has focused on the detection of E. coli O157:H7. Recently, increasing recognition of non-O157 VTEC strains as human pathogens and the German O104:H4 food-borne outbreak have illustrated the importance of considering the broader group of VTEC organisms from a public health perspective. This study presents the results of a comparison of three methods for the detection of VTEC in surface water, highlighting the efficacy of a direct VT immunoblotting method without broth enrichment for detection and isolation of O157 and non-O157 VTEC strains. The direct immunoblot method eliminates the need for an enrichment step or the use of immunomagnetic separation. This method was developed after 4 years of detecting low frequencies (1%) of E. coli O157:H7 in surface water in a Canadian watershed, situated within one of the FoodNet Canada integrated surveillance sites. By the direct immunoblot method, VTEC prevalence estimates ranged from 11 to 35% for this watershed, and E. coli O157:H7 prevalence increased to 4% (due to improved method sensitivity). This direct testing method provides an efficient means to enhance our understanding of the prevalence and types of VTEC in the environment. This study employed a rapid evidence assessment (REA) approach to frame the watershed findings with watershed E. coli O157:H7 prevalences reported in the literature since 1990 and the knowledge gap with respect to VTEC detection in surface waters.
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Affiliation(s)
- R. P. Johnson
- Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - B. Holtslander
- Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - A. Mazzocco
- Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - S. Roche
- Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - J. L. Thomas
- Ontario Ministry of the Environment, Etobicoke, Ontario, Canada
| | - F. Pollari
- FoodNet Canada, Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Ottawa, Ontario, Canada
| | - K. D. M. Pintar
- FoodNet Canada, Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Ottawa, Ontario, Canada
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18
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Visual endpoint detection of Escherichia coli O157:H7 using isothermal Genome Exponential Amplification Reaction (GEAR) assay and malachite green. J Microbiol Methods 2014; 98:122-7. [DOI: 10.1016/j.mimet.2014.01.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 01/02/2014] [Accepted: 01/02/2014] [Indexed: 11/20/2022]
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Occurrence of potentially human-pathogenic Escherichia coli O103 in Norwegian sheep. Appl Environ Microbiol 2013; 79:7502-9. [PMID: 24077709 DOI: 10.1128/aem.01825-13] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The investigation of an outbreak of hemorrhagic-uremic syndrome in Norway in 2006 indicated that the outbreak strain Escherichia coli O103:H25 could originate from sheep. A national survey of the Norwegian sheep population was performed, with the aim of identifying and describing a possible reservoir of potentially human-pathogenic E. coli O103, in particular of the H types 2 and 25. The investigation of fecal samples from 585 sheep flocks resulted in 1,222 E. coli O103 isolates that were analyzed for the presence of eae and stx genes, while a subset of 369 isolates was further examined for flagellar antigens (H typing), stx subtypes, bfpA, astA, and molecular typing by pulsed-field gel electrophoresis (PFGE). The total ovine E. coli O103 serogroup was genetically diverse by numbers of H types, virulotypes, and PFGE banding patterns identified, although a tendency of clustering toward serotypes was seen. The flocks positive for potentially human-pathogenic E. coli O103 were geographically widely distributed, and no association could be found with county or geographical region. The survey showed that eae-negative, stx-negative E. coli O103, probably nonpathogenic to humans, is very common in sheep, with 27.5% of flocks positive. Moreover, the study documented a low prevalence (0.7%) of potentially human-pathogenic Shiga toxin-producing E. coli O103:H2, while STEC O103:H25 was not detected. However, 3.1% and 5.8% of the flocks were positive for enteropathogenic E. coli O103 belonging to H types 2 and 25, respectively. These isolates are of concern as potential human pathogens by themselves but more importantly as possible precursors for human-pathogenic STEC.
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20
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Chui L, Lee MC, Allen R, Bryks A, Haines L, Boras V. Comparison between ImmunoCard STAT!(®) and real-time PCR as screening tools for both O157:H7 and non-O157 Shiga toxin-producing Escherichia coli in Southern Alberta, Canada. Diagn Microbiol Infect Dis 2013; 77:8-13. [PMID: 23810166 DOI: 10.1016/j.diagmicrobio.2013.05.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Revised: 05/10/2013] [Accepted: 05/15/2013] [Indexed: 11/16/2022]
Abstract
An increasing number of non-O157 Shiga toxin-producing Escherichia coli (STEC) infections and outbreaks have been reported. In this study, we evaluated the performance of ImmunoCard STAT!(®) (Meridian Bioscience, Inc., Cincinnati, OH, USA) as a method to screen stool specimens for STEC (O157 and non-O157). An in-house real-time PCR method was used as the "gold standard". We also evaluated the prevalence and clinical characteristics of STEC infections in the Alberta South West Zone. From July to November 2011, 819 stool specimens submitted for routine stool culture were tested. With our in-house real-time PCR, 7 O157:H7 and 10 non-O157 STEC isolates were identified for a total of 17 STECs. In comparison, ImmunoCard STAT!(®) identified a total of 6, resulting in a sensitivity and specificity of 35% and 99%, respectively (P < 0.05). Because of the low sensitivity, ImmunoCard STAT!(®) cannot be recommended as a routine screening test for STEC from enriched stool specimens. The rate of STEC positivity as detected by PCR was 2.08%, of which 0.86% was O157:H7 and 1.22% non-O157 STEC. Five of the 7 cases of STEC O157 infection experienced bloody diarrhea, and 1 developed hemolytic uremic syndrome.
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Affiliation(s)
- Linda Chui
- Alberta Provincial Laboratory for Public Health, Edmonton, Alberta, Canada.
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21
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Clark CG, Kruczkiewicz P, Guan C, McCorrister SJ, Chong P, Wylie J, van Caeseele P, Tabor HA, Snarr P, Gilmour MW, Taboada EN, Westmacott GR. Evaluation of MALDI-TOF mass spectroscopy methods for determination of Escherichia coli pathotypes. J Microbiol Methods 2013; 94:180-91. [PMID: 23816532 DOI: 10.1016/j.mimet.2013.06.020] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Revised: 06/20/2013] [Accepted: 06/20/2013] [Indexed: 11/30/2022]
Abstract
It is rapidly becoming apparent that many E. coli pathotypes cause a considerable burden of human disease. Surveillance of these organisms is difficult because there are few or no simple, rapid methods for detecting and differentiating the different pathotypes. MALDI-TOF mass spectroscopy has recently been rapidly and enthusiastically adopted by many clinical laboratories as a diagnostic method because of its high throughput, relatively low cost, and adaptability to the laboratory workflow. To determine whether the method could be adapted for E. coli pathotype differentiation the Bruker Biotyper methodology and a second methodology adapted from the scientific literature were tested on isolates representing eight distinct pathotypes and two other groups of E. coli. A total of 136 isolates was used for this study. Results confirmed that the Bruker Biotyper methodology that included extraction of proteins from bacterial cells was capable of identifying E. coli isolates from all pathotypes to the species level and, furthermore, that the Bruker extraction and MALDI-TOF MS with the evaluation criteria developed in this work was effective for differentiating most pathotypes.
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Affiliation(s)
- Clifford G Clark
- Enteric Diseases Program, Bacteriology and Enteric Diseases Program, National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, MB R3E 3R2 Canada.
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Improved detection of bacterial pathogens in patients presenting with gastroenteritis by use of the EntericBio real-time Gastro Panel I assay. J Clin Microbiol 2013; 51:2679-85. [PMID: 23761157 DOI: 10.1128/jcm.00809-13] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In this study, we evaluated the use of EntericBio real-time Gastro Panel I (Serosep, Limerick, Ireland) for routine use in a clinical microbiology laboratory for simultaneous detection of Campylobacter jejuni, coli, and lari, Shiga toxin-producing Escherichia coli (STEC), Salmonella spp., and Shigella spp. in feces. This system differs from its predecessor (the EntericBio Panel II system, Serosep) in that it allows real-time detection of pathogens directly from feces, without pre-enrichment. It also specifically detects Campylobacter jejuni, coli, and lari rather than all Campylobacter species, as is the case with the previous system. A total of 528 samples from patients presenting with acute gastroenteritis were screened prospectively with this assay, and results were compared with those of the current method, which combines screening the samples with a molecular assay (the EntericBio Panel II assay) and retrospective culture of the specimens in which the target was detected. Discrepancy analysis was conducted using culture and molecular methods. The real-time assay produced 84 positive results, specifically, Campylobacter spp. (n=44); Stx1 and/or Stx2 (n=35); Shigella spp. (n=3); and Salmonella spp. (n=6). Of these, 4 samples represented coinfections with Campylobacter spp. and STEC. The real-time assay showed an increased detection rate for pathogens, apart from Salmonella spp. Four Campylobacter-positive and 6 Stx-positive results remained unconfirmed by any other method used. The isolation rates for PCR-positive samples were as follows: Campylobacter spp., 80%; STEC, 45.7%; Salmonella spp., 100%; and Shigella spp., 66.7%. The sensitivity, specificity, positive predictive value, negative predictive value, and efficiency were 100%, 97.8%, 88.1%, 100%, and 98.1%, respectively.
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Abstract
In recent years, quantitative real-time PCR tests have been extensively developed in clinical microbiology laboratories for routine diagnosis of infectious diseases, particularly bacterial diseases. This molecular tool is well-suited for the rapid detection of bacteria directly in clinical specimens, allowing early, sensitive and specific laboratory confirmation of related diseases. It is particularly suitable for the diagnosis of infections caused by fastidious growth species, and the number of these pathogens has increased recently. This method also allows a rapid assessment of the presence of antibiotic resistance genes or gene mutations. Although this genetic approach is not always predictive of phenotypic resistances, in specific situations it may help to optimize the therapeutic management of patients. Finally, an approach combining the detection of pathogens, their mechanisms of antibiotic resistance, their virulence factors and bacterial load in clinical samples could lead to profound changes in the care of these infected patients.
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Affiliation(s)
- Max Maurin
- Laboratoire de Bactériologie, Département des Agents Infectieux, Institut de Biologie et Pathologie, CHU de Grenoble, Université Joseph Fourier Grenoble 1, France.
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Evaluation of a new chromogenic agar medium for detection of Shiga toxin-producing Escherichia coli (STEC) and relative prevalences of O157 and non-O157 STEC in Manitoba, Canada. J Clin Microbiol 2012; 51:466-71. [PMID: 23175263 DOI: 10.1128/jcm.02329-12] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This study assesses the detection performance of CHROMagar STEC medium relative to a reference cytotoxin assay and describes the current relative prevalence of O157 and non-O157 Shiga toxin-producing Escherichia coli (STEC) serotypes within the province of Manitoba, Canada. Over a 10-month period, 205 nonfrozen routine stool submissions to Cadham Provincial Laboratory (CPL) were used to assess the performance of CHROMagar STEC. Of the 205 stools, 14 were identified as true positives by a cytotoxin assay, with resultant CHROMagar STEC sensitivity, specificity, and positive predictive and negative predictive values of 85.7%, 95.8%, 60.0%, and 98.9%, respectively. Using a separate panel of 111 STEC strains, CHROMagar STEC was shown to support the growth of 96 (86.5%) isolates. To assess relative prevalence, attempts were made to isolate by any means all STEC strains identified at CPL over a 17-month period. Of 49 isolates (representing 86.0% of all STEC infections detected), only 28.6% were O157 STEC strains. Of the 35 non-O157 STEC strains, 29 were subjected to further molecular analysis. In contrast to earlier results from our area, carriage of stx(2) appears to have increased. Overall, although CHROMagar STEC is not recommended as a primary screen, our results indicate that it is an effective supplemental medium for the isolation of probable STEC strains. Increased isolation of these serotypes is warranted to better understand their prevalence, clinical characteristics, and epidemiology and aid in the development or enhancement of food safety control programs targeting all STEC serotypes.
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Abstract
In the setting of infectious disease emergencies, rapid and accurate identification of the causative agent is critical to optimizing antimicrobial therapy in a timely manner. It is clearly evident that the age of molecular diagnostics is now upon us, with real-time PCR becoming the standard of diagnosis for many infectious disease emergencies in either monoplex or multiplex format. Other molecular techniques such as whole or partial genome sequencing, microarrays, broad-range PCR, restriction fragment length polymorphisms, and molecular typing are also being used. However, for most small clinical laboratories, implementation of these advanced molecular techniques is not feasible owing to the high cost of instrumentation and reagents. If these tests are not available in-house, samples can be sent to national reference laboratories (eg, Mayo Medical Laboratories and Quest Diagnostics) for real-time PCR assays that can be completed in 1 day. It is anticipated that over time commercial real-time PCR tests and instrumentation will become more standardized and affordable, allowing individual laboratories to conduct tests locally, thus further reducing turnaround time. Although real-time PCR has been proved to expand our diagnostic capability, it must be stressed that such molecular methodology constitutes only an additional tool in the diagnosis of infectious diseases in emergency situations. Phenotypic methodologies (staining, cultures, biochemical tests, and serology) still play a critical role in identifying, confirming, and providing antibiotic susceptibility testing for many microbial pathogens. As multiplex assays become increasingly available, there will be even greater temptation for taking a “shotgun” approach to diagnostic testing. These new technologies will not substitute for a proper history and physical examination leading to a thoughtful differential diagnosis. None the less, these new molecular tests increase the capability of the diagnostician to rapidly identify the microbiological etiology of an infection. An added advantage of rapid diagnostic tests often not emphasized is the capability to rule out certain diagnoses for which unnecessary antimicrobial therapy may otherwise be instituted and/or continued.
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Affiliation(s)
- Neel K Krishna
- Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, VA 23507, USA.
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Alexander DC, Hao W, Gilmour MW, Zittermann S, Sarabia A, Melano RG, Peralta A, Lombos M, Warren K, Amatnieks Y, Virey E, Ma JH, Jamieson FB, Low DE, Allen VG. Escherichia coli O104:H4 infections and international travel. Emerg Infect Dis 2012; 18:473-6. [PMID: 22377016 PMCID: PMC3309582 DOI: 10.3201/eid1803.111281] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
We analyzed travel-associated clinical isolates of Escherichia coli O104:H4, including 1 from the 2011 German outbreak and 1 from a patient who returned from the Philippines in 2010, by genome sequencing and optical mapping. Despite extensive genomic similarity between these strains, key differences included the distribution of toxin and antimicrobial drug–resistance determinants.
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Abstract
PURPOSE OF REVIEW Diarrheal disease causes substantial morbidity and mortality worldwide; however, defining the microbiologic causes are challenging due to the large number of potential enteropathogens that require testing, insensitivity of existing conventional methods, the frequent occurrence of mixed infections, and high rates of background carriage in many communities. RECENT FINDINGS Here we review recent detection methods for enteropathogens with a particular focus on nucleic acid amplification assays. SUMMARY Nucleic acid amplification assays with high sensitivity and throughput now allow screening for multiple enteropathogens in stool samples. Interpretation will be complicated by high rates of mixed infections and background carriage in many communities. Therefore, new detection techniques, including quantitative methods, will need to be utilized in conjunction with the clinical context and careful study design. These methods should yield new insights into the causes and epidemiology of diarrhea.
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Prevalence of shiga toxin-producing Escherichia coli as detected by enzyme-linked immunoassays and real-time PCR during the summer months in northern Alberta, Canada. J Clin Microbiol 2011; 49:4307-10. [PMID: 21940470 DOI: 10.1128/jcm.05211-11] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) in northern Alberta was detected using two enzyme immunoassays and an in-house real-time PCR. Of 2,328 stool samples, 8 were positive for O157:H7 STEC and 13 were positive for non-O157 STEC. No significant gender (P = 0.17) or age (P = 0.81) differences between groups were seen. Most positive diarrheal stool samples were nonbloody.
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Łoś JM, Łoś M, Węgrzyn G. Bacteriophages carrying Shiga toxin genes: genomic variations, detection and potential treatment of pathogenic bacteria. Future Microbiol 2011; 6:909-24. [DOI: 10.2217/fmb.11.70] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Although most Escherichia coli strains occur in the mammalian intestine as commensals, some of them, including enterohemorrhagic E. coli (EHEC), are capable of causing disease in humans. The most notorious virulence factors of EHEC are Shiga toxins, encoded by genes located on genomes of lambdoid prophages. Production and release of these toxins is strongly stimulated after the induction of these prophages. Many antibiotics used to treat bacterial infections stimulate induction of Shiga toxin-converting prophages, enhancing severity of the disease symptoms. Hence, treatment with antibiotics is not recommended if infection with EHEC is confirmed or even suspected. In this light, rapid detection of EHEC is crucial, and understanding the mechanisms of prophage induction and phage development in the human intestine is important to facilitate development of procedures preventing or alleviating Shiga toxin-caused diseases.
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Affiliation(s)
- Joanna M Łoś
- Department of Molecular Biology, University of Gdansk, Kladki 24, 80–822 Gdansk, Poland
| | - Marcin Łoś
- Department of Molecular Biology, University of Gdansk, Kladki 24, 80–822 Gdansk, Poland
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01–224 Warsaw, Poland
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