1
|
Bywater A, Dintwe G, Alexander KA, Ponder MA. Characterization of Diarrheagenic Escherichia coli and Salmonella enterica from Produce in the Chobe District of Botswana. J Food Prot 2024; 87:100351. [PMID: 39187132 DOI: 10.1016/j.jfp.2024.100351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 07/30/2024] [Accepted: 08/20/2024] [Indexed: 08/28/2024]
Abstract
Diarrheal disease is a leading cause of death in children in low- and moderate-income countries. Fresh produce, including fruits and vegetables, may harbor diarrheal disease-causing bacteria including strains of Salmonella enterica and Escherichia coli. This study aimed to determine the prevalence and antibiotic resistance profiles of S. enterica and E. coli isolated from produce samples (n = 207) obtained from retail markets in northern Botswana in Chobe District of Botswana in 2022. Samples were enriched in the appropriate selective media: Brilliant Green Bile Broth for E. coli and Rappaport Vassiliadis Broth for S. enterica. E. coli were confirmed by PCR detecting the phoA gene, and classified as potentially pathogenic through screening for the eae, stx, and stx2 and estIb genes. S. enterica isolates were confirmed using invA primers. Isolates were evaluated for resistance to ampicillin, amoxicillin-clavulanic acid, chloramphenicol, cefotaxime, doxycycline, streptomycin, sulfamethoxazole, and tetracycline antibiotic using the Kirby-Bauer Disk Diffusion method. E. coli was isolated from 15.5% of produce samples (n = 207). The gene eae was detected from 1.5% of samples, while stx1, stx2, and estIb were not detected. Resistance to one or more antibiotics was common (72%) with the majority of the resistant E. coli (n = 32) isolated from fruits (22%) and greens (18%) compared to other types of vegetables. Multidrug resistance (MDR, resistant to 3 or more antibiotics) was identified in 18% of samples. S. enterica was isolated from 3.4% of produce samples (7, n = 207). Resistance was uncommon among the S. enterica isolates (1/7). Overall prevalence of diarrheagenic S. enterica and E. coli was low; however, their presence and that of MDR E. coli in foods commonly consumed raw increases the risk to vulnerable populations. Strategies to reduce contamination of fresh produce and public education on washing and cooking some types of produce may be useful to reduce disease.
Collapse
Affiliation(s)
- Auja Bywater
- Virginia Tech, Department of Food Science and Technology, 1230 Washington St, Blacksburg, VA 24061, USA
| | - Galaletsang Dintwe
- Center for African Resources: Animals, Communities and Land Use (CARACAL), Kasane, Botswana
| | - Kathleen A Alexander
- Center for African Resources: Animals, Communities and Land Use (CARACAL), Kasane, Botswana; Virginia Tech, Department of Fisheries and Wildlife, Blacksburg, VA 24061, USA
| | - Monica A Ponder
- Virginia Tech, Department of Food Science and Technology, 1230 Washington St, Blacksburg, VA 24061, USA.
| |
Collapse
|
2
|
Garcia CR, Norfolk WA, Howard AK, Glatter AL, Beaudry MS, Mallis NA, Welton M, Glenn TC, Lipp EK, Ottesen EA. Long-term gut colonization with ESBL-producing Escherichia coli in participants without known risk factors from the southeastern United States. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.02.03.24302254. [PMID: 38370669 PMCID: PMC10871458 DOI: 10.1101/2024.02.03.24302254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
We evaluated gut carriage of extended spectrum beta lactamase producing Enterobacteriaceae (ESBL-E) in southeastern U.S. residents without recent in-patient healthcare exposure. Study enrollment was January 2021-February 2022 in Athens, Georgia, U.S. and included a diverse population of 505 adults plus 50 child participants (age 0-5). Based on culture-based screening of stool samples, 4.5% of 555 participants carried ESBL-Es. This is slightly higher than reported in studies conducted 2012-2015, which found carriage rates of 2.5-3.9% in healthy U.S. residents. All ESBL-E confirmed isolates (n=25) were identified as Escherichia coli. Isolates belonged to 11 sequence types, with 48% classified as ST131. Ninety six percent of ESBL-E isolates carried a blaCTX-M gene. Isolated ESBL-Es frequently carried virulence genes as well as multiple classes of antibiotic resistance genes. Long-term colonization was common, with 64% of ESBL-E positive participants testing positive when rescreened three months later. One participant yielded isolates belonging to two different E. coli sequence types that carried blaCTX-M-1 genes on near-identical plasmids, suggesting intra-gut plasmid transfer. Isolation of E. coli on media without antibiotics revealed that ESBL-E. coli typically made up a minor fraction of the overall gut E. coli population, although in some cases they were the dominant strain. ESBL-E carriage was not associated with a significantly different stool microbiome composition. However, some microbial taxa were differentially abundant in ESBL-E carriers. Together, these results suggest that a small subpopulation of US residents are long-term, asymptomatic carriers of ESBL-Es, and may serve as an important reservoir for community spread of these ESBL genes.
Collapse
Affiliation(s)
| | - William A. Norfolk
- Department of Environmental Health Sciences, University of Georgia, Athens, GA, USA
- Center for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Amanda K. Howard
- Department of Environmental Health Sciences, University of Georgia, Athens, GA, USA
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Amanda L. Glatter
- Department of Environmental Health Sciences, University of Georgia, Athens, GA, USA
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Megan S. Beaudry
- Department of Environmental Health Sciences, University of Georgia, Athens, GA, USA
- Daicel Arbor Biosciences, Ann Arbor, MI, USA
| | - Nicholas A. Mallis
- Department of Epidemiology and Biostatistics, University of Georgia, Athens, GA, USA
| | - Michael Welton
- Department of Epidemiology and Biostatistics, University of Georgia, Athens, GA, USA
| | - Travis C. Glenn
- Department of Environmental Health Sciences, University of Georgia, Athens, GA, USA
| | - Erin K. Lipp
- Department of Environmental Health Sciences, University of Georgia, Athens, GA, USA
| | | |
Collapse
|
3
|
Okumu NO, Ngeranwa JJN, Muloi DM, Ochien’g L, Moodley A, Mutisya C, Kiarie A, Wasonga JO, Watson J, Amon-Tanoh MA, Cumming O, Cook EAJ. Risk factors for diarrheagenic Escherichia coli infection in children aged 6-24 months in peri-urban community, Nairobi, Kenya. PLOS GLOBAL PUBLIC HEALTH 2023; 3:e0002594. [PMID: 37992040 PMCID: PMC10664883 DOI: 10.1371/journal.pgph.0002594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 10/16/2023] [Indexed: 11/24/2023]
Abstract
Escherichia coli commonly inhabits the gut of humans and animals as part of their microbiota. Though mostly innocuous, some strains have virulence markers that make them pathogenic. This paper presents results of a cross-sectional epidemiological study examining prevalence of diarrheagenic E. coli (DEC) pathotypes in stool samples of asymptomatic healthy children (n = 540) in Dagoretti South subcounty, Nairobi, Kenya. E. coli was cultured and pathotyped using PCR to target specific virulence markers associated with Shiga-toxin, enteropathogenic, enterotoxigenic, enteroaggregative, entero-invasive and diffusely adherent E. coli. Overall prevalence of DEC pathotypes was 20.9% (113/540) with enteropathogenic E. coli being the most prevalent (34.1%), followed by enteroaggregative E. coli (23.5%) and Shiga-toxin producing E. coli (22.0%) among positive samples. We found evidence of co-infection with multiple pathotypes in 15% of the positive samples. Our models indicated that at the household level, carriage of DEC pathotypes in children was associated with age group [12-18 months] (OR 1.78; 95%CI 1.03-3.07; p = 0.04), eating matoke (mashed bananas) (OR 2.32; 95%CI 1.44-3.73; p = 0.001) and pulses/legumes (OR 1.74; 95%CI 1.01-2.99; p = 0.046) while livestock ownership or contact showed no significant association with DEC carriage (p>0.05). Our findings revealed significant prevalence of pathogenic DEC circulating among presumptive healthy children in the community. Since there has been no previous evidence of an association between any food type and DEC carriage, unhygienic handling, and preparation of matoke and pulses/legumes could be the reason for significant association with DEC carriage. Children 12-18 months old are more prone to DEC infections due to exploration and hand-to-mouth behavior. A detailed understanding is required on what proportion of positive cases developed severe symptomatology as well as fatal outcomes. The co-infection of pathotypes in the rapidly urbanizing environment needs to be investigated for hybrid or hetero-pathotype circulation that have been implicated in previous infection outbreaks.
Collapse
Affiliation(s)
- Noah O. Okumu
- Animal and Human Health Department, International Livestock Research Institute, Nairobi, Kenya
- Department of Biochemistry, Biotechnology and Microbiology, Kenyatta University, Nairobi, Kenya
| | - Joseph J. N. Ngeranwa
- Department of Biochemistry, Biotechnology and Microbiology, Kenyatta University, Nairobi, Kenya
| | - Dishon M. Muloi
- Animal and Human Health Department, International Livestock Research Institute, Nairobi, Kenya
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Linnet Ochien’g
- Animal and Human Health Department, International Livestock Research Institute, Nairobi, Kenya
| | - Arshnee Moodley
- Animal and Human Health Department, International Livestock Research Institute, Nairobi, Kenya
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Christine Mutisya
- Animal and Human Health Department, International Livestock Research Institute, Nairobi, Kenya
| | - Alice Kiarie
- Animal and Human Health Department, International Livestock Research Institute, Nairobi, Kenya
| | - Joseph O. Wasonga
- Animal and Human Health Department, International Livestock Research Institute, Nairobi, Kenya
| | - Julie Watson
- Department of Disease Control, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Maud Akissi Amon-Tanoh
- Department of Disease Control, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Oliver Cumming
- Department of Disease Control, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Elizabeth A. J. Cook
- Animal and Human Health Department, International Livestock Research Institute, Nairobi, Kenya
| |
Collapse
|
4
|
Occurrence of diarrheagenic Escherichia coli pathotypes from raw milk and unpasteurized buttermilk by culture and multiplex polymerase chain reaction in southwest Iran. Mol Biol Rep 2023; 50:3661-3667. [PMID: 36808583 DOI: 10.1007/s11033-023-08261-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 01/09/2023] [Indexed: 02/23/2023]
Abstract
BACKGROUND In developing countries including Iran, there are limited data on diarrheagenic Escherichia coli (DEC) contamination in milk and unpasteurized buttermilks. This study aimed to determine the occurrence of DEC pathotypes by culture and multiplex polymerase chain reaction (M-PCR) in some dairy products from southwest Iran. METHODS AND RESULTS In this cross-sectional study (September to October 2021), 197 samples (87 unpasteurized buttermilk and 110 raw cow milk) were collected from dairy stores of Ahvaz, southwest Iran. The presumptive E. coli isolates were primarily identified using biochemical tests and then confirmed by PCR of uidA gene. The occurrence of 5 DEC pathotypes: enterotoxigenic E. coli (ETEC), enterohemorrhagic E. coli (EHEC), enteropathogenic E. coli (EPEC), enteroaggregative E. coli (EAEC), and enteroinvasive E. coli (EIEC) were investigated using M-PCR. Overall, 76 (76/197, 38.6%) presumptive E. coli isolates were identified by biochemical tests. Using uidA gene, only 50 isolates (50/76, 65.8%) were confirmed as E. coli. DEC pathotypes were detected in 27 of 50 (54.0%) E. coli isolates (74.1%, 20/27 from raw cow milk and 25.9%, 7/27 from unpasteurized buttermilk). The frequency of DEC pathotypes was as follows: 1 (3.7%) EAEC, 2 (7.4%) EHEC, 4 (14.8%) EPEC, 6 (22.2%) ETEC, and 14 (51.9%) EIEC. However, 23 (46.0%) E. coli isolates had only the uidA gene and were not considered DEC pathotypes. CONCLUSION Possible health risks for Iranian consumers can be attributed to the presence of DEC pathotypes in dairy products. Hence, serious control and prevention efforts are needed to stop the spread of these pathogens.
Collapse
|
5
|
Ohmura-Hoshino M, Miyaki Y, Yashima S. A one-step multiplex PCR-based assay for simultaneous detection and classification of virulence factors to identify five diarrheagenic E. coli pathotypes. Heliyon 2022; 8:e10231. [PMID: 36046532 PMCID: PMC9421181 DOI: 10.1016/j.heliyon.2022.e10231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 03/22/2022] [Accepted: 08/04/2022] [Indexed: 12/02/2022] Open
Abstract
Human diarrhea-causing strains of Escherichia coli are referred to as diarrheagenic E. coli (DEC). DEC can be divided into five main categories based on distinct epidemiological and clinical features, specific virulence determinants, and association with certain serotypes. In the present study, a simple and rapid one-step single reaction multiplex PCR (mPCR) assay was developed for the simultaneous identification and differentiation of five currently established DEC pathotypes causing gastrointestinal diseases. The mPCR incorporated 10 primer pairs to amplify 10 virulence genes specific to the different pathotypes (i.e., stx1 and stx2 for EHEC, elt and sth for ETEC, eaeA and bfpA for EPEC, aggR and astA for EAEC, and ipaH and invE for EIEC) and to generate DNA fragments of sufficiently different sizes to be unequivocally resolved. All strains were detected at concentrations ranging from 104 to 107 CFU/mL. To demonstrate the utility of the mPCR assay, 236 clinically isolated strains of DEC from two hospitals were successfully categorized. One-step mPCR technique reduced the cost and effort involved in the identification of various virulence factors in DEC. Thus, we demonstrated that the newly developed mPCR assay has the potential to be introduced as a diagnostic tool that can be utilized for the detection of DEC as an additional check in clinical laboratories and for confirmation in health and environment institutes, health centers, and reference laboratories. We developed a one-step single reaction mPCR to detect DEC strains. 10 prominently expressed genes characteristic to the five pathotypes were assayed. All the strains were detected at concentrations ranging from 104 to 107 CFU/mL. We show cost- and time-effective detection of DEC in clinical cultured samples.
Collapse
Affiliation(s)
- Mari Ohmura-Hoshino
- Department of Medical Technology, School of Nursing and Medical Care, Yokkaichi Nursing and Medical Care University, Yokkaichi, Japan
| | | | | |
Collapse
|
6
|
Tubón J, Barragán-Fonseca G, Lalaleo L, Calero-Cáceres W. Data on antibiograms and resistance genes of Enterobacterales isolated from ready-to-eat street food of Ambato, Ecuador. F1000Res 2022; 11:669. [PMID: 35844814 PMCID: PMC9257263 DOI: 10.12688/f1000research.117116.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/10/2022] [Indexed: 11/20/2022] Open
Abstract
Foodborne pathogens represent a significant cause of negative impacts on human health and the economy worldwide. Unfortunately, information about epidemiological insights in Latin American countries is scarce. The consumption of ready-to-eat street food in Ecuador is extensive, and information about the presence of foodborne pathogens, their virulence factors, and antimicrobial resistance is negligible. This data includes the occurrence, phenotypic antibiotic resistance profiles, and antibiotic resistance genes of Enterobacterales isolated from ready-to-eat street food in Ambato, central Ecuador during 2020 and 2021. The most common genera detected were
Escherichia coli,
Klebsiella spp., and
Cronobacter spp. Agar disk diffusion assays were performed to determine their phenotypic resistance. The presence of antibiotic resistance genes conferring resistance against colistin, β-Lactams, aminoglycosides, tetracyclines, sulfonamides, fluoroquinolones, and amphenicols was detected via polymerase chain reaction (PCR) amplification.
Collapse
Affiliation(s)
- Jessica Tubón
- UTA RAM One Health, Department of Food and Biotechnology Science and Engineering, Universidad Técnica de Ambato, Ambato, 180103, Ecuador
| | - Gabriela Barragán-Fonseca
- UTA RAM One Health, Department of Food and Biotechnology Science and Engineering, Universidad Técnica de Ambato, Ambato, 180103, Ecuador
| | - Liliana Lalaleo
- UTA RAM One Health, Department of Food and Biotechnology Science and Engineering, Universidad Técnica de Ambato, Ambato, 180103, Ecuador
| | - William Calero-Cáceres
- UTA RAM One Health, Department of Food and Biotechnology Science and Engineering, Universidad Técnica de Ambato, Ambato, 180103, Ecuador
| |
Collapse
|
7
|
Barragán-Fonseca G, Tubón J, Calero-Cáceres W. Data on antibiogram and resistance genes of Enterobacterales isolated from fresh vegetables in Ecuador. Data Brief 2022; 42:108249. [PMID: 35599824 PMCID: PMC9120250 DOI: 10.1016/j.dib.2022.108249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 04/21/2022] [Accepted: 05/02/2022] [Indexed: 11/17/2022] Open
Abstract
This article describes the occurrence, antibiograms, and detection of antibiotic resistance genes of Enterobacterales isolated from fresh vegetables commercialized in Riobamba, Ecuador. Escherichia coli isolates were screened to detect diarrheagenic pathotypes via PCR. Agar diffusion assay was performed to determine the phenotypic antibiotic resistance of the Enterobacterales strains. The presence of antibiotic resistance genes conferring resistance against beta-lactams, mobile colistin resistance, carbapenems, quinolones, tetracyclines, and sulphonamides was detected via PCR amplification.
Collapse
|
8
|
Evaluation of the BioFire Gastrointestinal Panel to Detect Diarrheal Pathogens in Pediatric Patients. Diagnostics (Basel) 2021; 12:diagnostics12010034. [PMID: 35054200 PMCID: PMC8774520 DOI: 10.3390/diagnostics12010034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 12/17/2021] [Accepted: 12/20/2021] [Indexed: 12/04/2022] Open
Abstract
Infectious diarrhea is a global pediatric health concern; therefore, rapid and accurate detection of enteropathogens is vital. We evaluated the BioFire® FilmArray® Gastrointestinal (GI) Panel with that of comparator laboratory tests. Stool samples of pediatric patients with diarrhea were prospectively collected and tested. As a comparator method for bacteria, culture, conventional PCR for diarrheagenic E. coli, and Allplex GI-Bacteria(I) Assay were tested. For discrepancy analysis, BD MAX Enteric Bacterial Panel was used. As a comparator method for virus, BD MAX Enteric Virus Panel and immunochromatography was used and Allplex GI-Virus Assay was used for discrepancy analysis. The “true positive” was defined as culture-positive and/or positive results from more than two molecular tests. Of the 184 stool samples tested, 93 (50.5%) were true positive for 128 pathogens, and 31 (16.9%) were positive for multiple pathogens. The BioFire GI Panel detected 123 pathogens in 90 of samples. The BioFire GI Panel demonstrated a sensitivity of 100% for 12 targets and a specificity of >95% for 16 targets. The overall positive rate and multiple pathogen rate among patients in the group without underlying diseases were significantly higher than those in the group with hematologic disease (57.0% vs. 28.6% (p = 0.001) and 20.4% vs. 4.8% (p = 0.02), respectively). The BioFire GI Panel provides comprehensive results within 2 h and may be useful for the rapid identification of enteropathogens.
Collapse
|
9
|
Fadare FT, Adefisoye MA, Okoh AI. Occurrence, identification, and antibiogram signatures of selected Enterobacteriaceae from Tsomo and Tyhume rivers in the Eastern Cape Province, Republic of South Africa. PLoS One 2020; 15:e0238084. [PMID: 33284819 PMCID: PMC7721149 DOI: 10.1371/journal.pone.0238084] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 11/23/2020] [Indexed: 12/19/2022] Open
Abstract
The increasing occurrence of multidrug-resistant Enterobacteriaceae in clinical and environmental settings has been seen globally as a complex public health challenge, mostly in the developing nations where they significantly impact freshwater used for a variety of domestic purposes and irrigation. This paper detail the occurrence and antibiogram signatures of the Enterobacteriaceae community in Tsomo and Tyhume rivers within the Eastern Cape Province, the Republic of South Africa, using standard methods. The average distribution of the presumptive Enterobacteriaceae in the rivers ranged from 1 × 102 CFU/100ml to 1.95 × 104 CFU/100ml. We confirmed 56 (70.8%) out of 79 presumptive Enterobacteriaceae isolated being species within the family Enterobacteriaceae through the Matrix-Assisted Laser Desorption Ionization Time of Flight technique. Citrobacter-, Enterobacter-, Klebsiella species, and Escherichia coli were selected (n = 40) due to their pathogenic potentials for antibiogram profiling. The results of the antibiotic susceptibility testing gave a revelation that all the isolates were phenotypically multidrug-resistant. The resistance against ampicillin (95%), tetracycline and doxycycline (88%), and trimethoprim-sulfamethoxazole (85%) antibiotics were most prevalent. The Multiple Antibiotic Resistance indices stretched from 0.22 to 0.94, with the highest index observed in a C. freundii isolate. Molecular characterisation using the PCR technique revealed the dominance of blaTEM (30%; 12/40) among the eight groups of β-lactams resistance determinants assayed. The prevalence of others was blaCTX-M genes including group 1, 2 and 9 (27.5%), blaSHV (20%), blaOXA-1-like (10%), blaPER (2.5%), and blaVEB (0%). The frequencies of the resistance determinants for the carbapenems were blaKPC (17.6%), blaGES (11.8%), blaIMP (11.8%), blaVIM (11.8%), and blaOXA-48-like (5.9%). Out of the six plasmid-mediated AmpC (pAmpC) genes investigated blaACC, blaEBC, blaFOX, blaCIT, blaDHA, and blaMOX, only the first four were detected. In this category, the most dominant was blaEBC, with 18.4% (7/38). The prevalence of the non-β-lactamases include tetA (33.3%), tetB (30.5%), tetC (2.8%), tetD (11.1%), tetK (0%), tetM (13.9%), catI (12%), catII (68%), sulI (14.3%), sulII (22.9%) and aadA (8.3%). Notably, a C. koseri harboured 42.8% (12/28) of the genes assayed for which includes five of the ESBL genes (including the only blaPER detected in this study), two of the pAmpC resistance genes (blaACC and blaCIT), and five of the non-β-lactamase genes. This study gives the first report on C. koseri exhibiting the co-occurrence of ESBL/AmpC β-lactamase genes from the environment to the best of our knowledge. The detection of a blaPER producing Citrobacter spp. in this study is remarkable. These findings provide evidence that freshwater serves as reservoirs of antimicrobial resistance determinants, which can then be easily transferred to human beings via the food chain and water.
Collapse
Affiliation(s)
- Folake Temitope Fadare
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, South Africa
- Applied and Environmental Microbiology Research Group, Department of Biochemistry and Microbiology, University of Fort Hare, Alice, South Africa
- * E-mail:
| | - Martins Ajibade Adefisoye
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, South Africa
- Applied and Environmental Microbiology Research Group, Department of Biochemistry and Microbiology, University of Fort Hare, Alice, South Africa
| | - Anthony Ifeanyi Okoh
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, South Africa
- Applied and Environmental Microbiology Research Group, Department of Biochemistry and Microbiology, University of Fort Hare, Alice, South Africa
| |
Collapse
|
10
|
Sun J, Shi Y, Du Y, Wang Z, Liu Z, Wang H, Zhao G, Ma Y, Zheng M. Rapid Detection of Diarrheagenic Escherichia coli by a New Multiplex Real-Time Quantitative PCR Assay. APPL BIOCHEM MICRO+ 2020. [DOI: 10.1134/s0003683820060174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
11
|
Al-Farsi HM, Camporeale A, Ininbergs K, Al-Azri S, Al-Muharrmi Z, Al-Jardani A, Giske CG. Clinical and molecular characteristics of carbapenem non-susceptible Escherichia coli: A nationwide survey from Oman. PLoS One 2020; 15:e0239924. [PMID: 33036018 PMCID: PMC7546912 DOI: 10.1371/journal.pone.0239924] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 09/15/2020] [Indexed: 01/07/2023] Open
Abstract
The prevalence of carbapenem-resistant Enterobacterales (CRE) in the Arabian Peninsula is predicted to be high, as suggested from published case reports. Of particular concern, is carbapenem-resistant E. coli (CR-EC), due to the importance of this species as a community pathogen. Herein, we conducted a comprehensive molecular characterization of putative CR-EC strains from Oman. We aim to establish a baseline for future molecular monitoring. We performed whole-genome sequencing (WGS) for 35 putative CR-EC. Isolates were obtained from patients at multiple centers in 2015. Genetic relatedness was investigated using several typing approaches such as MLST, SNP calling, phylogroup and CRISPR typing. Maxiuium likelihood SNP-tree was performed by RAxML after variant calling and removal of recombination regions with Snippy and Gubbins, respectively. Resistance genes, plasmid replicon types, virulence genes, and prophage were also characterised. The online databases CGE, CRISPRcasFinder, Phaster and EnteroBase were used for the in silico analyses. Screening for mutations in genes regulating the expression of porins and efflux pump as well as mutations lead to fluoroquinolones resistance were performed with CLC Genomics Workbench. The genetic diversity suggests a polyclonal population structure with 21 sequence types (ST), of which ST38 being the most prevalent (11%). SNPs analysis revealed possible transmission episodes. Whereas, CRISPR typing helped to spot outlier strains belonged to phylogroups other than B2 which was CRISPR-free. The virulent phylogroups B2 and D were detected in 4 and 9 isolates, respectively. In some strains bacteriophages acted as vectors for virulence genes. Regarding resistance to β-lactam, 22 were carbapenemase producers, 3 carbapenem non-susceptible but carbapenemase-negative, 9 resistant to expanded-spectrum cephalosporins, and one isolate with susceptibility to cephalosporins and carbapenems. Thirteen out of the 22 (59%) carbapenemase-producing isolates were NDM and 7 (23%) were OXA-48-like which mirrors the situation in Indian subcontinent. Two isolates co-produced NDM and OXA-48-like enzymes. In total, 80% (28/35) were CTX-M-15 producers and 23% (8/35) featured AmpC. The high-risk subclones ST131-H30Rx/C2, ST410-H24RxC and ST1193-H64RxC were detected, the latter associated with NDM. To our knowledge, this is the first report of ST1193-H64Rx subclone with NDM. In conclusion, strains showed polyclonal population structure with OXA-48 and NDM as the only carbapenemases in CR-EC from Oman. We detected the high-risk subclone ST131-H30Rx/C2, ST410-H24RxC and ST1193-H64RxC. The latter was reported with carbapenemase gene for the first time here.
Collapse
Affiliation(s)
- Hissa M. Al-Farsi
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
- Central Public Health Laboratories, Ministry of Health, Muscat, Oman
| | - Angela Camporeale
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Karolina Ininbergs
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Saleh Al-Azri
- Central Public Health Laboratories, Ministry of Health, Muscat, Oman
| | - Zakariya Al-Muharrmi
- Department of Clinical Microbiology, Sultan Qaboos University Hospital, Muscat, Oman
| | - Amina Al-Jardani
- Central Public Health Laboratories, Ministry of Health, Muscat, Oman
| | - Christian G. Giske
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| |
Collapse
|
12
|
Molecular characterization of pathogenic Escherichia coli isolated from diarrheic and in-contact cattle and buffalo calves. Trop Anim Health Prod 2020; 52:3173-3185. [PMID: 32647966 PMCID: PMC7347405 DOI: 10.1007/s11250-020-02343-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 07/02/2020] [Indexed: 11/04/2022]
Abstract
Escherichia coli field isolates from calves were characterized and categorized into the most significant diarrheagenic pathotypes using polymerase chain reaction (PCR) assays with different specific primers. The used PCR systems were designed to detect sequences representing the group-specific virulence genes encoding fimbriae f5 (K99), Shiga toxins (stx1 and stx2), heat-stable enterotoxins (st), heat-labile enterotoxins (lt), intimin (eae), hemolysin (hylA), and EAEC heat-stable enterotoxin (astA). In the present work, a total of 150 E. coli field isolates were recovered from 150 fecal swabs collected from 100 diarrheic and 50 apparently healthy in-contact cattle and buffalo calves under 3 months old. Out of these 150 isolated E. coli, 106 isolates from 77 diarrheic and 29 in-contact calves harbored one or more of the investigated virulence genes. The pathotyping of the isolates could classify them into shigatoxigenic E. coli (STEC), enteropathogenic E. coli (EPEC), enterotoxigenic E. coli (ETEC), and enteroaggregative E. coli (EAEC) with a 30.7, 2.7, 12.7, and 7.3% distribution, respectively. Meanwhile, the detection rates of f5, stx1, stx2, st, lt, eae, hylA, and astA genes were 17.3, 27.3, 6.7, 10, 37.3, 17.7, 9.3, and 20.7%, respectively. These virulence genes were found either single or in different combinations, such as stx/eae, stx/st/f5, eae/st/f5, or st/lt/f5. Four attaching-effacing shigatoxigenic E. coli isolates (AE-STEC) harboring stx/eae were retrieved from diarrheic calves. Although none of the stx-or eae-positive isolates was verified as O157:H7, STEC isolates detected in apparently healthy calves have potential pathogenicity to humans highlighting their zoonotic importance as reservoirs. Atypical combinations of ETEC/STEC and ETEC/EPEC were also detected in percentages of 14.7 and 2.7%, respectively. Most of these atypical combinations were found more in buffalo calves than in cattle calves. While STEC and EPEC isolates were detected more in cattle calves than in buffalo calves, ETEC isolates were the same in the two species. The pathogenic E. coli infection in calves was recorded to be higher in the first weeks of life with the largest numbers of virulence factor-positive isolates detected at the age of 4 weeks. Histopathological examination of five intestinal samples collected from four dead buffalo calves revealed typical attaching and effacing (AE) lesion which was correlated with the presence of intimin encoding virulence gene (eae). Other lesions characterized by hemorrhagic enteritis, shortening and fusion of intestinal villi and desquamation of the lining epithelium of intestinal mucosa had also been detected.
Collapse
|
13
|
Jin L, Li T, Wu B, Yang T, Zou D, Liang X, Hu L, Huang G, Zhang J. Rapid detection of Salmonella in milk by nuclear magnetic resonance based on membrane filtration superparamagnetic nanobiosensor. Food Control 2020. [DOI: 10.1016/j.foodcont.2019.107011] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
|
14
|
Okada K, Wongboot W, Kamjumphol W, Suebwongsa N, Wangroongsarb P, Kluabwang P, Chuenchom N, Swaddiwudhipong W, Wongchai T, Manosuthi W, Assawapatchara N, Khum-On P, Udompat P, Thanee C, Kitsaran S, Jirapong L, Jaiwong C, Nedsuwan S, Siripipattanamongkol C, Okada PA, Chantaroj S, Komukai S, Hamada S. Etiologic features of diarrheagenic microbes in stool specimens from patients with acute diarrhea in Thailand. Sci Rep 2020; 10:4009. [PMID: 32132604 PMCID: PMC7055299 DOI: 10.1038/s41598-020-60711-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 02/13/2020] [Indexed: 12/13/2022] Open
Abstract
Many microbial species have been recognized as enteropathogens for humans. Here, we predicted the causative agents of acute diarrhea using data from multiplex quantitative PCR (qPCR) assays targeting 19 enteropathogens. For this, a case-control study was conducted at eight hospitals in Thailand. Stool samples and clinical data were collected from 370 hospitalized patients with acute diarrhea and 370 non-diarrheal controls. Multiple enteropathogens were detected in 75.7% and 13.0% of diarrheal stool samples using multiplex qPCR and bacterial culture methods, respectively. Asymptomatic carriers of enteropathogens were found among 87.8% and 45.7% of individuals by qPCR and culture methods, respectively. These results suggested the complexity of identifying causative agents of diarrhea. An analysis using the quantification cut-off values for clinical relevance drastically reduced pathogen-positive stool samples in control subjects from 87.8% to 0.5%, whereas 48.9% of the diarrheal stool samples were positive for any of the 11 pathogens. Among others, rotavirus, norovirus GII, Shigella/EIEC, and Campylobacter were strongly associated with acute diarrhea (P-value < 0.001). Characteristic clinical symptoms, epidemic periods, and age-related susceptibility to infection were observed for some enteropathogens. Investigations based on qPCR approaches covering a broad array of enteropathogens might thus improve our understanding of diarrheal disease etiology and epidemiological trends.
Collapse
Affiliation(s)
- Kazuhisa Okada
- Thailand-Japan Research Collaboration Center on Emerging and Re-emerging Infections, Nonthaburi, Thailand. .,Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.
| | - Warawan Wongboot
- Thailand-Japan Research Collaboration Center on Emerging and Re-emerging Infections, Nonthaburi, Thailand.,National Institute of Health, Department of Medical Sciences, Nonthaburi, Thailand
| | - Watcharaporn Kamjumphol
- Thailand-Japan Research Collaboration Center on Emerging and Re-emerging Infections, Nonthaburi, Thailand
| | - Namfon Suebwongsa
- Thailand-Japan Research Collaboration Center on Emerging and Re-emerging Infections, Nonthaburi, Thailand
| | - Piyada Wangroongsarb
- National Institute of Health, Department of Medical Sciences, Nonthaburi, Thailand
| | - Pipat Kluabwang
- Department of Pediatrics, Maesot General Hospital, Tak, Thailand
| | | | | | - Thanee Wongchai
- Department of Clinical Laboratory, Maesot General Hospital, Tak, Thailand
| | - Weerawat Manosuthi
- Department of Medicine, Bamrasnaradura Infectious Diseases Institute, Nonthaburi, Thailand
| | | | - Patchanee Khum-On
- Department of Medical Technology, Chum Phae Hospital, Khon Kaen, Thailand
| | - Patpong Udompat
- Department of Community and Social Medicine, Prapokklao Hospital, Chanthaburi, Thailand
| | - Chareeya Thanee
- Department of Pediatrics, Sunpasitthiprasong Hospital, Ubon Ratchathani, Thailand
| | - Suwatthiya Kitsaran
- Department of Medicine, Sunpasitthiprasong Hospital, Ubon Ratchathani, Thailand
| | - Lakkana Jirapong
- Department of Radiology, Samutsakhon Hospital, Samutsakhon, Thailand
| | - Charoen Jaiwong
- Department of Pediatrics, Chiangrai Prachanukroh Hospital, Chiang Rai, Thailand
| | - Supalert Nedsuwan
- Department of Preventive and Social Medicine, Chiangrai Prachanukroh Hospital, Chiang Rai, Thailand
| | | | | | - Siriporn Chantaroj
- National Institute of Health, Department of Medical Sciences, Nonthaburi, Thailand
| | - Sho Komukai
- Department of Integrated Medicine of Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Shigeyuki Hamada
- Thailand-Japan Research Collaboration Center on Emerging and Re-emerging Infections, Nonthaburi, Thailand.,Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| |
Collapse
|
15
|
Wen W, Shi L, Chen X. Simultaneous Detection of Actinobacillus pleuropneumoniae and Haemophilus parasuis in Pig by Duplex Droplet Digital PCR. EFOOD 2020. [DOI: 10.2991/efood.k.200918.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
|
16
|
Hu J, Wang Y, Su H, Ding H, Sun X, Gao H, Geng Y, Wang Z. Rapid analysis of Escherichia coli O157:H7 using isothermal recombinase polymerase amplification combined with triple-labeled nucleotide probes. Mol Cell Probes 2019; 50:101501. [PMID: 31887422 DOI: 10.1016/j.mcp.2019.101501] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 12/04/2019] [Accepted: 12/26/2019] [Indexed: 12/21/2022]
Abstract
Rapid analytical methods are urgently needed to evaluate Escherichia coli (E. coli) O157:H7 in food. In this work, a novel recombinase polymerase amplification (RPA)-based lateral flow dipstick (LFD) method was developed to detect E. coli. Briefly, suitable primers and probes were designed and screened. Then, RPA reaction parameters, including volume, time, and temperature, were optimized. The specificity and sensitivity of RPA-LFD were analyzed, and a contaminated milk sample was used to test the detection performance of the proposed method. The optimal RPA reaction conditions included a minimum volume of 10 μL, incubation time of 10 min, temperature range of 39-42 °C, the primer pair EOF4/EOR3, and the probe EOProb. RPA-LFD was highly sensitive, it could detect as little as 1 fg of the genomic DNA of E. coli O157:H7, and 19 nontarget DNA of foodborne bacteria did not yield amplification products. Finally, the limit of detection of RPA-LFD for E. coli O157:H7 in artificially contaminated raw milk was 4.4 CFU/mL. In summary, the RPA-LFD assay developed in this study is an effective tool for the rapid investigation of E. coli O157:H7 contamination in raw milk samples.
Collapse
Affiliation(s)
- Jinqiang Hu
- School of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou, 450000, Henan Province, China; Henan International Joint Laboratory of Food Safety, Zhengzhou, 450000, Henan Province, China; Collaborative Innovation Center of Food Production and Safety, Zhengzhou, 450000, Henan Province, China; Henan Key Laboratory of Cold Chain Food Quality and Safety Control, Zhengzhou, 450000, Henan Province, China.
| | - Yi Wang
- School of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou, 450000, Henan Province, China
| | - Haijian Su
- Technology Center, China Tobacco Shandong Industrial Co., Ltd, Zhengzhou, 266000, Shandong Province, China
| | - Huimin Ding
- School of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou, 450000, Henan Province, China
| | - Xincheng Sun
- School of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou, 450000, Henan Province, China; Henan International Joint Laboratory of Food Safety, Zhengzhou, 450000, Henan Province, China; Collaborative Innovation Center of Food Production and Safety, Zhengzhou, 450000, Henan Province, China
| | - Hui Gao
- School of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou, 450000, Henan Province, China
| | - Yao Geng
- School of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou, 450000, Henan Province, China
| | - Zhangcun Wang
- School of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou, 450000, Henan Province, China; Henan International Joint Laboratory of Food Safety, Zhengzhou, 450000, Henan Province, China
| |
Collapse
|
17
|
Li X, Luo Q, Yu X, Zhang Y, Cao X, Li D. Diversity of Virulence Genes in Multidrug Resistant Escherichia coli from a Hospital in Western China. Infect Drug Resist 2019; 12:3817-3826. [PMID: 31824179 PMCID: PMC6901040 DOI: 10.2147/idr.s226072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 11/16/2019] [Indexed: 11/25/2022] Open
Abstract
Background Escherichia coli strains are the most commonly isolated bacteria in hospitals. The normally harmless commensal E. coli can become a highly adapted pathogen, capable of causing various diseases both in healthy and immunocompromised individuals, by acquiring a combination of mobile genetic elements. Our aim was to characterize E. coli strains from a hospital in western China to determine their virulence and antimicrobial resistance potential. Methods A total of 97 E. coli clinical isolates were collected from the First Affiliated Hospital of Chengdu Medical College from 2015 to 2016. Microbiological methods, PCR, and antimicrobial susceptibility tests were used in this study. Results The frequency of occurrence of the virulence genes fimC, irp2, fimH, fyuA, lpfA, hlyA, sat, and cnf1 in the E. coli isolates was 93.81, 92.78, 91.75, 84.54, 41.24, 32.99, 28.86, and 7.22%, respectively. Ninety-five (97.9%) isolates carried two or more different virulence genes. Of these, 44 (45.4%) isolates simultaneously harbored five virulence genes, 24 (24.7%) isolates harbored four virulence genes, and 17 (17.5%) isolates harbored six virulence genes. In addition, all E. coli isolates were multidrug resistant and had a high degree of antimicrobial resistance. Conclusion These results indicate a high frequency of occurrence and heterogeneity of virulence gene profiles among clinical multidrug resistant E. coli isolates. Therefore, appropriate surveillance and control measures are essential to prevent the further spread of these isolates in hospitals.
Collapse
Affiliation(s)
- Xue Li
- Non-Coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, Sichuan 610500, People's Republic of China
| | - Qi Luo
- Non-Coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, Sichuan 610500, People's Republic of China
| | - Xinyu Yu
- Non-Coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, Sichuan 610500, People's Republic of China
| | - Yanling Zhang
- Non-Coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, Sichuan 610500, People's Republic of China
| | - Xiaoyue Cao
- Non-Coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, Sichuan 610500, People's Republic of China
| | - Dan Li
- School of Medical Laboratory Science, Chengdu Medical College, Chengdu, Sichuan 610500, People's Republic of China.,Sichuan Provincial Engineering Laboratory for Prevention and Control Technology of Veterinary Drug Residue in Animal-Origin Food, Chengdu Medical College, Chengdu, Sichuan 610500, People's Republic of China
| |
Collapse
|
18
|
Barbosa CA, Conceição TA, Baliza MD, Camilo VMA, Juiz PJL, Silva IMM. Virulence genes in Escherichia coli isolates from commercialized saltwater mussels Mytella guyanensis (Lamarck, 1819). BRAZ J BIOL 2019; 79:625-628. [DOI: 10.1590/1519-6984.185930] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 02/26/2018] [Indexed: 12/13/2022] Open
Abstract
Abstract The isolation of Escherichia coli from food is a major concern. Pathogenic strains of these bacteria cause diseases which range from diarrhea to hemolytic-uremic syndrome. Therefore the virulence genes in E. coli isolates from the mussel ( Mytella guyanensis) commercialized in Cachoeira, Bahia, Brazil were investigated. Samples were purchased from four vendors: two from supermarkets and two from fair outlets. They were conditioned into isothermal boxes with reusable ice and transported to the laboratory for analysis. E. coli strains were isolated in eosin methylene blue agar, preserved in brain-heart infusion medium with 15% glycerol and stored at -20 °C, after microbiological analysis. Virulence genes in the isolated strains were identified by specific primers, with Polymerase Chain Reaction. Twenty-four isolates were obtained, with a prevalence of elt gene, typical from enterotoxigenic infection, in 75% of the isolates. The stx and bfpA genes, prevalent in enterohemorragic and enteropathogenic E. coli, respectively, were not detected. The occurrence of elt virulence-related gene in the E. coli isolates of Mytella guyanensis reveals urgent improvement in food processing, including good handling practices, adequate storage and cooking before consumption, to ensure consumer’s health.
Collapse
Affiliation(s)
- C. A. Barbosa
- Universidade Federal do Recôncavo da Bahia, Brasil; Universidade Federal do Recôncavo da Bahia, Brasil
| | | | - M. D. Baliza
- Universidade Federal do Recôncavo da Bahia, Brasil
| | | | | | | |
Collapse
|
19
|
Hu J, Huang R, Sun Y, Wei X, Wang Y, Jiang C, Geng Y, Sun X, Jing J, Gao H, Wang Z, Dong C. Sensitive and rapid visual detection of Salmonella Typhimurium in milk based on recombinase polymerase amplification with lateral flow dipsticks. J Microbiol Methods 2019; 158:25-32. [DOI: 10.1016/j.mimet.2019.01.018] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 01/25/2019] [Accepted: 01/28/2019] [Indexed: 12/20/2022]
|
20
|
Yoo J, Park J, Lee HK, Yu JK, Lee GD, Park KG, Oak HC, Park YJ. Comparative Evaluation of Seegene Allplex Gastrointestinal, Luminex xTAG Gastrointestinal Pathogen Panel, and BD MAX Enteric Assays for Detection of Gastrointestinal Pathogens in Clinical Stool Specimens. Arch Pathol Lab Med 2019; 143:999-1005. [PMID: 30763118 DOI: 10.5858/arpa.2018-0002-oa] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT.— Infectious gastroenteritis is caused by various pathogens, including bacteria, viruses, and parasites. OBJECTIVE.— To compare the performance of Seegene Allplex Gastrointestinal (24 targets: 13 bacteria, 5 viruses, and 6 parasites in 4 panels), Luminex xTAG Gastrointestinal Pathogen Panel (15 targets: 9 bacteria, 3 viruses, and 3 parasites), and BD MAX Enteric panel (5 bacteria and 3 parasites). We estimated the agreement among 3 molecular assays. DESIGN.— A total of 858 stool samples (554 bacterial/parasite and 304 viral pathogens) were included. A consensus positive/negative was defined as concordant results from at least 2 tests. To evaluate the agreement among the assays, κ value was calculated. RESULTS.— The overall positive percentage agreements of Seegene, Luminex, and BD MAX were 94% (258 of 275), 92% (254 of 275), and 78% (46 of 59), respectfully. For Salmonella, Luminex showed low negative percentage agreement because of frequent false positives (n = 31) showing low median fluorescent intensity. For viruses, positive/negative percentage agreements of Seegene and Luminex were 99%/96% and 93%/99%, respectively. Compared with routine microbiology testing, Seegene, Luminex, and BD MAX additionally identified 39, 40, and 12 pathogens, respectively. Sixty-one cases (16 cases with Seegene, 51 cases with Luminex, and 1 case with BD MAX) showed positive results for multiple pathogens, but only 3 were consensus positive. CONCLUSIONS.— These multiplex molecular assays appear to be promising tools for the detection and identification of multiple gastrointestinal pathogens simultaneously. However, careful interpretation of positive results for multiple pathogens is required.
Collapse
Affiliation(s)
- Jaeeun Yoo
- From the Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea (Drs Yoo, J. Park, H. K. Lee, and Y.-J. Park); the Department of Laboratory Medicine, Seoul St Mary's Hospital, The Catholic University of Korea, Seoul, Korea (Mss Yu and K. G. Park and Mr G. D. Lee); and the Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge (Ms Oak)
| | - Joonhong Park
- From the Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea (Drs Yoo, J. Park, H. K. Lee, and Y.-J. Park); the Department of Laboratory Medicine, Seoul St Mary's Hospital, The Catholic University of Korea, Seoul, Korea (Mss Yu and K. G. Park and Mr G. D. Lee); and the Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge (Ms Oak)
| | - Hae Kyung Lee
- From the Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea (Drs Yoo, J. Park, H. K. Lee, and Y.-J. Park); the Department of Laboratory Medicine, Seoul St Mary's Hospital, The Catholic University of Korea, Seoul, Korea (Mss Yu and K. G. Park and Mr G. D. Lee); and the Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge (Ms Oak)
| | - Jin Kyung Yu
- From the Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea (Drs Yoo, J. Park, H. K. Lee, and Y.-J. Park); the Department of Laboratory Medicine, Seoul St Mary's Hospital, The Catholic University of Korea, Seoul, Korea (Mss Yu and K. G. Park and Mr G. D. Lee); and the Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge (Ms Oak)
| | - Gun Dong Lee
- From the Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea (Drs Yoo, J. Park, H. K. Lee, and Y.-J. Park); the Department of Laboratory Medicine, Seoul St Mary's Hospital, The Catholic University of Korea, Seoul, Korea (Mss Yu and K. G. Park and Mr G. D. Lee); and the Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge (Ms Oak)
| | - Kang Gyun Park
- From the Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea (Drs Yoo, J. Park, H. K. Lee, and Y.-J. Park); the Department of Laboratory Medicine, Seoul St Mary's Hospital, The Catholic University of Korea, Seoul, Korea (Mss Yu and K. G. Park and Mr G. D. Lee); and the Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge (Ms Oak)
| | - Hayeon Caitlyn Oak
- From the Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea (Drs Yoo, J. Park, H. K. Lee, and Y.-J. Park); the Department of Laboratory Medicine, Seoul St Mary's Hospital, The Catholic University of Korea, Seoul, Korea (Mss Yu and K. G. Park and Mr G. D. Lee); and the Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge (Ms Oak)
| | - Yeon-Joon Park
- From the Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea (Drs Yoo, J. Park, H. K. Lee, and Y.-J. Park); the Department of Laboratory Medicine, Seoul St Mary's Hospital, The Catholic University of Korea, Seoul, Korea (Mss Yu and K. G. Park and Mr G. D. Lee); and the Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge (Ms Oak)
| |
Collapse
|
21
|
Khan S, Imran A, Malik A, Chaudhary AA, Rub A, Jan AT, Syed JB, Rolfo C. Bacterial imbalance and gut pathologies: Association and contribution of E. coli in inflammatory bowel disease. Crit Rev Clin Lab Sci 2018; 56:1-17. [DOI: 10.1080/10408363.2018.1517144] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Shahanavaj Khan
- Nanomedicine Research Unit, Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
- Department of Bioscience, Shri Ram Group of College (SRGC), Muzaffarnagar, India
| | - Ahamad Imran
- King Abdullah Institute for Nanotechnology, King Saud University, Riyadh, Saudi Arabia
| | - Abdul Malik
- Department of Clinical Laboratory Science, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Anis Ahmad Chaudhary
- Department of Pharmacology, College of Medicine, Al-Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia
| | - Abdur Rub
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah, Saudi Arabia
| | - Arif Tasleem Jan
- School of Biotechnology, Yeungnam University, Gyeongsan, Republic of Korea
| | - Jakeera Begum Syed
- King Abdullah Institute for Nanotechnology, King Saud University, Riyadh, Saudi Arabia
- College of Medicine and Dentistry, Dar Al Uloom University, Riyadh, Saudi Arabia
| | - Christian Rolfo
- Phase I-Early Clinical Trials Unit, Oncology Department and Multidisciplinary Oncology Center Antwerp (MOCA), Antwerp University Hospital, Edegem, Belgium
| |
Collapse
|
22
|
Hu J, Huang R, Wang Y, Wei X, Wang Z, Geng Y, Jing J, Gao H, Sun X, Dong C, Jiang C. Development of duplex PCR-ELISA for simultaneous detection of Salmonella spp. and Escherichia coli O157: H7 in food. J Microbiol Methods 2018; 154:127-133. [PMID: 30393180 DOI: 10.1016/j.mimet.2018.10.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 10/26/2018] [Indexed: 11/28/2022]
Abstract
In the current study, a duplex PCR-ELISA method was developed targeting the specific genes, invA of Salmonella spp. and rfbE of Escherichia coli O157: H7, to detect one or both bacteria in food. In brief, PCR product amplified by PCR primer labeled with digoxin at the 5'-end and a probe labeled with biotin at the 3'-end can form dimer by nucleic acid hybridization which can be captured by binding of biotin to streptomycin coated in ELISA plate before using enzyme-labeled anti-digoxin antibody and substrate to develop color. Also, evaluation of the duplex PCR-ELISA method was conducted in different food samples including milk, juice, cabbage, shrimp, chicken, pork and beef. Results indicated that the duplex PCR-ELISA developed here was specific when using 25 non-target bacteria strains as controls and was sensitive with a limit of detection (LOD) of 1 CFU/mL, 1, 000 times higher than that of the duplex PCR method and was repeatable regardless of inter- and intra-batch variations. The duplex PCR-ELISA method established in the present study has proven to be highly specific, sensitive and repeatable. It has the potential to be applied in such fields as clinical diagnosis of food-borne diseases, food hygiene monitoring and pathogen detection in food.
Collapse
Affiliation(s)
- Jinqiang Hu
- School of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450000, Henan Province, China; International Joint Laboratory of Food Safety, Zhengzhou 450000, Henan Province, China; Collaborative Innovation Center of Food Production and Safety, Zhengzhou 450000, Henan Province, China; Henan Key Laboratory of Cold Chain Food Quality and Safety Control, Zhengzhou 450000, Henan Province, China.
| | - Runna Huang
- School of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450000, Henan Province, China
| | - Yi Wang
- School of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450000, Henan Province, China
| | - Xiangke Wei
- School of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450000, Henan Province, China
| | - Zhangcun Wang
- School of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450000, Henan Province, China
| | - Yao Geng
- School of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450000, Henan Province, China; International Joint Laboratory of Food Safety, Zhengzhou 450000, Henan Province, China
| | - Jianzhou Jing
- School of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450000, Henan Province, China; International Joint Laboratory of Food Safety, Zhengzhou 450000, Henan Province, China
| | - Hui Gao
- School of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450000, Henan Province, China; International Joint Laboratory of Food Safety, Zhengzhou 450000, Henan Province, China
| | - Xincheng Sun
- School of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450000, Henan Province, China; International Joint Laboratory of Food Safety, Zhengzhou 450000, Henan Province, China
| | - Caiwen Dong
- School of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450000, Henan Province, China
| | - Chunpeng Jiang
- School of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450000, Henan Province, China
| |
Collapse
|
23
|
Li D, Shen M, Xu Y, Liu C, Wang W, Wu J, Luo X, Jia X, Ma Y. Virulence gene profiles and molecular genetic characteristics of diarrheagenic Escherichia coli from a hospital in western China. Gut Pathog 2018; 10:35. [PMID: 30127859 PMCID: PMC6097206 DOI: 10.1186/s13099-018-0262-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 08/09/2018] [Indexed: 02/05/2023] Open
Abstract
Background Diarrheagenic Escherichia coli (DEC) is one of the most important etiological agents of diarrheal diseases. In this study we investigated the prevalence, virulence gene profiles, antimicrobial resistance, and molecular genetic characteristics of DEC at a hospital in western China. Methods A total of 110 Escherichia coli clinical isolates were collected from the First Affiliated Hospital of Chengdu Medical College from 2015 to 2016. Microbiological methods, PCR, antimicrobial susceptibility test, pulsed-field gel electrophoresis and multilocus sequence typing were used in this study. Results Molecular analysis of six DEC pathotype marker genes showed that 13 of the 110 E. coli isolates (11.82%) were DEC including nine (8.18%) diffusely adherent Escherichia coli (DAEC) and four (3.64%) enteroaggregative Escherichia coli (EAEC). The adherence genes fimC and fimH were present in all DAEC and EAEC isolates. All nine DAEC isolates harbored the virulence genes fyuA and irp2 and four (44.44%) also carried the hlyA and sat genes. The virulence genes fyuA, irp2, cnf1, hlyA, and sat were found in 100%, 100%, 75%, 50%, and 50% of EAEC isolates, respectively. In addition, all DEC isolates were multidrug resistant and had high frequencies of antimicrobial resistance. Molecular genetic characterization showed that the 13 DEC isolates were divided into 11 pulsed-field gel electrophoresis patterns and 10 sequence types. Conclusions To the best of our knowledge, this study provides the first report of DEC, including DAEC and EAEC, in western China. Our analyses identified the virulence genes present in E. coli from a hospital indicating their role in the isolated DEC strains’ pathogenesis. At the same time, the analyses revealed, the antimicrobial resistance pattern of the DEC isolates. Thus, DAEC and EAEC among the DEC strains should be considered a significant risk to humans in western China due to their evolved pathogenicity and antimicrobial resistance pattern.
Collapse
Affiliation(s)
- Dan Li
- 1Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan China.,2School of Medical Laboratory Science, Chengdu Medical College, Chengdu, 610500 Sichuan China
| | - Min Shen
- 3Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, 610500 Sichuan China
| | - Ying Xu
- 4Clinical Laboratory, The First Affiliated Hospital of Chengdu Medical College, Chengdu, 610500 Sichuan China
| | - Chao Liu
- 3Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, 610500 Sichuan China
| | - Wen Wang
- 5West China School of Public Health, Sichuan University, Chengdu, 610041 Sichuan China
| | - Jinyan Wu
- 3Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, 610500 Sichuan China
| | - Xianmei Luo
- 3Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, 610500 Sichuan China
| | - Xu Jia
- 3Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, 610500 Sichuan China
| | - Yongxin Ma
- 1Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan China
| |
Collapse
|
24
|
Barbau-Piednoir E, Denayer S, Botteldoorn N, Dierick K, De Keersmaecker SCJ, Roosens NH. Detection and discrimination of five E. coli pathotypes using a combinatory SYBR® Green qPCR screening system. Appl Microbiol Biotechnol 2018; 102:3267-3285. [PMID: 29460001 PMCID: PMC5852171 DOI: 10.1007/s00253-018-8820-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 01/12/2018] [Accepted: 01/19/2018] [Indexed: 12/22/2022]
Abstract
A detection and discrimination system for five Escherichia coli pathotypes, based on a combination of 13 SYBR® Green qPCR, has been developed, i.e., combinatory SYBR® Green qPCR screening system for pathogenic E. coli (CoSYPS Path E. coli). It allows the discrimination on isolates and the screening of potential presence in food of the following pathotypes of E. coli: shigatoxigenic (STEC) (including enterohemorrhagic (EHEC)), enteropathogenic (EPEC), enteroaggregative (EAggEC), enteroaggregative shigatoxigenic (EAggSTEC), and enteroinvasive (EIEC) E. coli. The SYBR® Green qPCR assays target the uidA, ipaH, eae, aggR, aaiC, stx1, and stx2 genes. uidA controls for E. coli presence and all the other genes are specific targets of E. coli pathotypes. For each gene, two primer pairs have been designed to guarantee a sufficient detection even in case of deletion or polymorphisms in the target gene. Moreover, all the qPCR have been designed to be run together in a single analytical PCR plate. This study includes the primer pairs' design, in silico and in situ selectivity, sensitivity, repeatability, and reproducibility evaluation of the 13 SYBR® Green qPCR assays. Each target displayed a selectivity of 100%. The limit of detection of the 13 assays is between 1 and 10 genomic copies. Their repeatability and reproducibility comply with the European requirements. As a preliminary feasibility study on food, the CoSYPS Path E. coli system was subsequently evaluated on four food matrices artificially contaminated with pathogenic E. coli. It allowed the detection of an initial contamination level as low as 2 to 7 cfu of STEC/25 g of food matrix after 24 h of enrichment.
Collapse
Affiliation(s)
- Elodie Barbau-Piednoir
- Scientific Service Foodborne Pathogens, Scientific Institute of Public Health, J. Wytsmanstraat 14, B-1050, Brussels, Belgium
- Platform Biotechnology and Bioinformatics, Scientific Institute of Public Health, J. Wytsmanstraat 14, B-1050, Brussels, Belgium
| | - Sarah Denayer
- Scientific Service Foodborne Pathogens, Scientific Institute of Public Health, J. Wytsmanstraat 14, B-1050, Brussels, Belgium
| | - Nadine Botteldoorn
- Scientific Service Foodborne Pathogens, Scientific Institute of Public Health, J. Wytsmanstraat 14, B-1050, Brussels, Belgium
| | - Katelijne Dierick
- Scientific Service Foodborne Pathogens, Scientific Institute of Public Health, J. Wytsmanstraat 14, B-1050, Brussels, Belgium
| | - Sigrid C J De Keersmaecker
- Platform Biotechnology and Bioinformatics, Scientific Institute of Public Health, J. Wytsmanstraat 14, B-1050, Brussels, Belgium
| | - Nancy H Roosens
- Platform Biotechnology and Bioinformatics, Scientific Institute of Public Health, J. Wytsmanstraat 14, B-1050, Brussels, Belgium.
| |
Collapse
|
25
|
Development of Single-Walled Carbon Nanotube-Based Biosensor for the Detection of Staphylococcus aureus. J FOOD QUALITY 2017. [DOI: 10.1155/2017/5239487] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The goal of this research is to develop a single-walled carbon nanotube- (SWCNT-) based biosensor to detect Staphylococcus aureus. The specificity of 11 bacteria and polyclonal anti-Staphylococcus aureus antibodies (pAbs) was determined using an indirect ELISA. The pAbs were immobilized onto sensor platform after the hybridization of 1-pyrenebutanoic acid succinimidyl ester (PBASE). The resistance difference (ΔR) was calculated using a potentiostat. The bacteria detected by the biosensor were observed using a scanning electron microscope (SEM). The optimum concentration of SWCNTs on the platform was determined to be 0.1 mg/mL. The binding of pAbs with S. aureus resulted in a significant increase in resistance value of the biosensor (P<0.05). The SEM images confirmed the specific binding of S. aureus on the biosensor. The SWCNT-based biosensor was able to detect S. aureus with a limit of detection (LOD) of 4 logCFU/mL.
Collapse
|
26
|
Petersen AM, Halkjær SI, Gluud LL. Intestinal colonization with phylogenetic group B2 Escherichia coli related to inflammatory bowel disease: a systematic review and meta-analysis. Scand J Gastroenterol 2016; 50:1199-207. [PMID: 25910859 DOI: 10.3109/00365521.2015.1028993] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
BACKGROUND AND OBJECTIVES Increased numbers of Escherichia coli and, furthermore, specific subtypes of E. coli, such as E. coli of the phylogenetic groups B2 and D have been found in the intestine of patients with inflammatory bowel disease (IBD). In this review, we wanted to evaluate the relationship between B2 and D E. coli intestinal colonization and IBD. METHODS A systematic review with meta-analyses. We included studies comparing colonization with B2 and D E. coli in IBD patients and in controls. Random-effects and fixed-effect meta-analyses were performed. RESULTS We included 7 studies on 163 patients with IBD and 89 controls. Among IBD patients, 57 patients had ulcerative colitis (UC) and 95 Crohn's disease (CD). Random-effects meta-analysis showed that IBD patients were more likely to have B2 E. coli intestinal colonization compared with controls (odds ratio [OR]: 2.28; 95% confidence interval [CI]: 1.25-4.16). There was little between-study heterogeneity (I(2) = 0). The result was confirmed in subgroup analyses of patients with UC (OR: 3.58; 95% CI: 1.62-7.90), but not CD (OR: 1.94; 95% CI: 0.98-3.82). Intestinal colonization with phylogenetic group D E. coli was not found to be related to IBD, UC or CD. CONCLUSIONS Our study reveals that intestinal colonization with phylogenetic group B2 E. coli is associated with UC. Due to the design, we are unable to determine if the colonization with B2 E. coli leads to the development of the disease or the disease increases the risk of colonization with B2 E. coli.
Collapse
|
27
|
Iwu CJ, Iweriebor BC, Obi LC, Okoh AI. Occurrence of non-O157 Shiga toxin-producing Escherichia coli in two commercial swine farms in the Eastern Cape Province, South Africa. Comp Immunol Microbiol Infect Dis 2016; 44:48-53. [DOI: 10.1016/j.cimid.2015.12.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 12/11/2015] [Accepted: 12/17/2015] [Indexed: 12/28/2022]
|
28
|
Wong YP, Chua KH, Thong KL. One-step species-specific high resolution melting analysis for nosocomial bacteria detection. J Microbiol Methods 2015; 107:133-7. [PMID: 25307691 DOI: 10.1016/j.mimet.2014.10.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 09/09/2014] [Accepted: 10/02/2014] [Indexed: 11/25/2022]
Abstract
Nosocomial infections are a major public health concern worldwide. Early and accurate identification of nosocomial pathogens which are often multidrug resistant is crucial for prompt treatment. Hence, an alternative real-time polymerase chain reaction coupled with high resolution melting-curve analysis (HRMA) was developed for identification of five nosocomial bacteria. This assay targets species-specific regions of each nosocomial bacteria and produced five distinct melt curves with each representing a particular bacterial species. The melting curves were characterized by peaks of 78.8 ± 0.2 °C for Acinetobacter baumannii, 82.7 ± 0.2 °C for Escherichia coli, 86.3 ± 0.3 °C for Klebsiella pneumoniae, 88.8 ± 0.2 °C for Pseudomonas aeruginosa and 74.6 ± 02 °C for methicillin-resistant Staphylococcus aureus. The assay was able to specifically detect the five bacterial species with an overall detection limit of 2 × 10(-2) ng/μL. In conclusion, the HRM assay developed is a simple and rapid method for identification of the selected nosocomial pathogens.
Collapse
Affiliation(s)
- Yeng Pooi Wong
- Microbiology Unit, Institute of Biological Science, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia.
| | | | | |
Collapse
|
29
|
Gomi R, Matsuda T, Fujimori Y, Harada H, Matsui Y, Yoneda M. Characterization of Pathogenic Escherichia coli in River Water by Simultaneous Detection and Sequencing of 14 Virulence Genes. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:6800-6807. [PMID: 25919763 DOI: 10.1021/acs.est.5b00953] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The occurrence of pathogenic Escherichia coli in environmental waters increases the risk of waterborne disease. In this study, 14 virulence genes in 669 E. coli isolates (549 isolates from the Yamato River in Japan, and 30 isolates from each of the following hosts: humans, cows, pigs, and chickens) were simultaneously quantified by multiplex PCR and dual index sequencing to determine the prevalence of potentially pathogenic E. coli. Among the 549 environmental isolates, 64 (12%) were classified as extraintestinal pathogenic E. coli (ExPEC) while eight (1.5%) were classified as intestinal pathogenic E. coli (InPEC). Only ExPEC-associated genes were detected in human isolates and pig isolates, and 11 (37%) and five (17%) isolates were classified as ExPEC, respectively. A high proportion (63%) of cow isolates possessed Shiga-toxin genes (stx1 or stx2) and they were classified as Shiga toxin-producing E. coli (STEC) or enterohemorrhagic E. coli (EHEC). Among the chicken isolates, 14 (47%) possessed iutA, which is an ExPEC-associated gene. This method can determine the sequences as well as the presence/absence of virulence genes. By comparing the sequences of virulence genes, we determined that sequences of iutA were different among sources and may be useful for discriminating isolates, although further studies including larger numbers of isolates are needed. Results indicate that humans are a likely source of ExPEC strains in the river.
Collapse
Affiliation(s)
- Ryota Gomi
- †Department of Environmental Engineering, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, 615-8540, Kyoto, Japan
| | - Tomonari Matsuda
- ‡Research Center for Environmental Quality Management, Kyoto University, 1-2 Yumihama, Otsu, 520-0811, Shiga, Japan
| | - Yuji Fujimori
- §Graduate School of Global Environmental Studies, Kyoto University, Yoshida-honmachi, Sakyo-ku, 606-8501, Kyoto, Japan
| | - Hidenori Harada
- §Graduate School of Global Environmental Studies, Kyoto University, Yoshida-honmachi, Sakyo-ku, 606-8501, Kyoto, Japan
| | - Yasuto Matsui
- †Department of Environmental Engineering, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, 615-8540, Kyoto, Japan
| | - Minoru Yoneda
- †Department of Environmental Engineering, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, 615-8540, Kyoto, Japan
| |
Collapse
|
30
|
Shan S, Lai W, Xiong Y, Wei H, Xu H. Novel strategies to enhance lateral flow immunoassay sensitivity for detecting foodborne pathogens. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:745-53. [PMID: 25539027 DOI: 10.1021/jf5046415] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Food contaminated by foodborne pathogens causes diseases, affects individuals, and even kills those affected individuals. As such, rapid and sensitive detection methods should be developed to screen pathogens in food. One current detection method is lateral flow immunoassay, an efficient technique because of several advantages, including rapidity, simplicity, stability, portability, and sensitivity. This review presents the format and principle of lateral flow immunoassay strip and the development of conventional lateral flow immunoassay for detecting foodborne pathogens. Furthermore, novel strategies that can be applied to enhance the sensitivity of lateral flow immunoassay to detect foodborne pathogens are presented; these strategies include innovating new label application, designing new formats of lateral flow immunoassay, combining with other methods, and developing signal amplification systems. With these advancements, detection sensitivity and detection time can be greatly improved.
Collapse
Affiliation(s)
- Shan Shan
- State Key Laboratory of Food Science and Technology, Nanchang University , Nanchang 330047, China
| | | | | | | | | |
Collapse
|
31
|
Kim HR, Kim NH, Park HS, Kim DH, Lee JH. Survey of fecal coliform contamination in sands of educational facilities and parks in Seoul. ACTA ACUST UNITED AC 2014. [DOI: 10.7853/kjvs.2014.37.4.307] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
32
|
Chen Q, Shi X, Li Y, Jiang Y, Lin Y, Qiu Y, Li Q, Hu Q. Rapid genetic typing of diarrheagenic Escherichia coli using a two-tube modified molecular beacon based multiplex real-time PCR assay and its clinical application. Ann Clin Microbiol Antimicrob 2014; 13:30. [PMID: 25023669 PMCID: PMC4115161 DOI: 10.1186/s12941-014-0030-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 07/05/2014] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Diarrheagenic Escherichia coli (DEC), including Enterotoxigenic E.coli (ETEC), Enteroaggregative E.coli (EAEC), Enteropathogenic E.coli (EPEC), Enterohemolysin E.coli (EHEC) and Enteroinvasive E.coli (EIEC) causes diarrhea or hemolytic uremic syndromes among infants and travelers around the world. A rapid, reliable and repeatable method is urgent for identifying DEC so as to provide the reference for responding to diarrheal disease outbreak and the treatment of the diarrheal patients associated with DEC. METHODS In this study, specific primers and modified molecular beacon probes of nine specific virulence genes, whose 5'end were added with homo tail sequence, were designed; and a two-tube modified molecular beacon based multiplex real-time PCR (rtPCR) assay for the identification of five Escherichia coli pathotypes, including ETEC, EAEC, EPEC, EHEC and EIEC was developed and optimized. Totally 102 bacterial strains, including 52 reference bacterial strains and 50 clinical strains were detected to confirm whether the target genes selected were specific. Then detection limits of the assay were tested. Lastly, the assay was applied to the detection of 11860 clinical samples to evaluate the specificity and sensitivity of the developed assay compared with the conventional PCR. RESULTS The target genes were 100% specific as assessed on 102 bacterial strains since no cross-reactions were observed. The detection limits ranged from 88 CFU/mL (EHEC) to 880 CFU/mL (EPEC). Compared with the conventional PCR, the specificity and sensitivity of the multiplex rtPCR was 100% and over 99%, respectively. The coefficient of variation (CV) for each target gene ranged from 0.45% to 1.53%. 171 positive clinical samples were mostly identified as ETEC (n = 111, 64.9%) and EPEC (n = 38, 22.2%), which were the dominating pathotypes of DEC strains. CONCLUSION The developed multiplex rtPCR assay for the identification of DEC was high sensitive and specific and could be applied to the rapid identification of DEC in clinical and public health laboratories.
Collapse
|