1
|
Akinlabi OC, Dada RA, Nwoko ESQA, Okeke IN. PCR diagnostics are insufficient for the detection of Diarrhoeagenic Escherichia coli in Ibadan, Nigeria. PLOS GLOBAL PUBLIC HEALTH 2023; 3:e0001539. [PMID: 37549136 PMCID: PMC10406320 DOI: 10.1371/journal.pgph.0001539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 07/10/2023] [Indexed: 08/09/2023]
Abstract
Understanding the contribution of different diarrhoeagenic Escherichia coli pathotypes to disease burden is critical to mapping risk and informing vaccine development. Targeting select virulence genes by PCR is the diagnostic approach of choice in high-burden, least-resourced African settings. We compared the performance of a commonly-used multiplex protocol to whole genome sequencing (WGS). PCR was applied to 3,815 E. coli isolates from 120 children with diarrhoea and 357 healthy controls. Three or more isolates per specimen were also Illumina-sequenced. Following quality assurance, ARIBA and Virulencefinder database were used to identify virulence targets. Root cause analysis of deviant PCR results was performed by examining target sensitivity using BLAST, Sanger sequencing false-positive amplicons, and identifying lineages prone to false-positivity using in-silico multilocus sequence typing and a Single Nucleotide Polymorphism phylogeny constructed using IQTree. The sensitivity and positive predictive value of PCR compared to WGS ranged from 0-77.8% while specificity ranged from 74.5-94.7% for different pathotypes. WGS identified more enteroaggregative E. coli (EAEC), fewer enterotoxigenic E. coli (ETEC) and none of the Shiga toxin-producing E. coli detected by PCR, painting a considerably different epidemiological picture. Use of the CVD432 target resulted in EAEC under-detection, and enteropathogenic E. coli eae primers mismatched more recently described intimin alleles common in our setting. False positive ETEC were over-represented among West Africa-predominant ST8746 complex strains. PCR precision varies with pathogen genome so primers optimized for use in one part of the world may have noticeably lower sensitivity and specificity in settings where different pathogen lineages predominate.
Collapse
Affiliation(s)
- Olabisi C. Akinlabi
- Faculty of Pharmacy, Department of Pharmaceutical Microbiology, University of Ibadan, Oyo, Nigeria
| | - Rotimi A. Dada
- Faculty of Pharmacy, Bowen University Iwo and Department of Pharmaceutical Microbiology, College of Health Sciences, Medical Laboratory Science Programme, Ahmadu Bello University, Zaria, Nigeria
| | - El-shama Q. A. Nwoko
- Faculty of Pharmacy, Department of Pharmaceutical Microbiology, University of Ibadan, Oyo, Nigeria
| | - Iruka N. Okeke
- Faculty of Pharmacy, Department of Pharmaceutical Microbiology, University of Ibadan, Oyo, Nigeria
| |
Collapse
|
2
|
Whole-Genome Analysis of blaNDM-Bearing Proteus mirabilis Isolates and mcr-1-Positive Escherichia coli Isolates Carrying blaNDM from the Same Fresh Vegetables in China. Foods 2023; 12:foods12030492. [PMID: 36766021 PMCID: PMC9913981 DOI: 10.3390/foods12030492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/12/2023] [Accepted: 01/16/2023] [Indexed: 01/24/2023] Open
Abstract
The global spread of colistin or carbapenem-resistant Enterobacteriaceae (CRE) has been a pressing threat to public health. Members of Enterobacteriaceae, especially Proteus mirabilis and Escherichia coli, have been prevalent foodborne pathogens and such pathogens from fresh vegetables have triggered foodborne illness in China. However, reports about CRE, especially P. mirabilis from fresh vegetables, are still lacking. In this study, we identified five blaNDM-positive P. mirabilis and five blaNDM-positive generic E. coli concurrently from five fresh vegetables in two markets from China, and four of the five E. coli also carried mcr-1. The 10 isolates were characterized with methods including antimicrobial susceptibility testing, conjugation, whole-genome sequencing and phylogenetic analysis. All 10 isolates were multidrug-resistant (MDR). blaNDM-5 in five E. coli isolates and one P. mirabilis carrying blaNDM-5 was located on similarly transferable IncX3 plasmids, while transferably untypable plasmids were the carriers of blaNDM-1 in four P. mirabilis isolates from different types of vegetables/markets. mcr-1 in the four blaNDM-5-positive E. coli was located on similarly non-conjugative IncHI2 MDR plasmids lacking transfer region. Notably, ISCR1 complex class 1 integron capable of capturing blaNDM-1 was found on all untypable plasmids from P. mirabilis, and five copies of ISCR1 complex class 1 integron containing blaNDM-1 even occurred in one P. mirabilis, which showed high-level carbapenem resistance. Plasmid and phylogenetic analysis revealed that the blaNDM-positive P. mirabilis and E. coli from fresh vegetables might be derived from animals and transmitted to humans via the food chain. The concurrence of blaNDM-positive P. mirabilis and E. coli carrying both mcr-1 and blaNDM in different types of fresh vegetables eaten raw is alarming and threatens food safety. Sustained surveillance of these foodborne pathogens among fresh vegetables is urgent to ensure the health of food consumers. We report for the first time the concurrence of blaNDM-positive P. mirabilis and mcr-1-bearing E. coli carrying blaNDM from the same fresh vegetables.
Collapse
|
3
|
Yoneda I, Rozanah UN, Nishiyama M, Mith H, Watanabe T. Detection and genetic analysis of Escherichia coli from Tonle Sap Lake and its tributaries in Cambodia: Spatial distribution, seasonal variation, pathogenicity, and antimicrobial resistance. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 315:120406. [PMID: 36252883 DOI: 10.1016/j.envpol.2022.120406] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 09/08/2022] [Accepted: 10/06/2022] [Indexed: 06/16/2023]
Abstract
As an indicator of fecal contamination, Escherichia coli was monitored in Tonle Sap Lake, Cambodia, and its tributaries during low- and high-water seasons, focusing on the impacts on floating villagers inhabiting boathouses. E. coli concentrations in the floating villages (3.6 × 103 and 5.7 × 103 CFU/100 mL during the low- and high-water seasons, respectively) were significantly higher than those in other lake sites (4.0 × 101 and 7.0 × 100 CFU/100 mL during the low- and high-water seasons, respectively) and rivers (3.3 × 102 and 8.9 × 102 CFU/100 mL during the low- and high-water seasons, respectively), most likely because fecal materials from the boathouses were discharged without treatment. At most of the lake sampling sites remote from the boathouses, the E. coli concentration was lower during the high-water season than that during the low-water season, due to dilution by lake water. E. coli colonies detected during monitoring were isolated for pathotyping, antimicrobial susceptibility testing, beta-lactamase gene detection, and multilocus sequencing typing (MLST). Of the 659 E. coli isolates, 101 (15.3%) were diarrheagenic E. coli (DEC). The prevalence of DEC (52.2%) in the floating villages during the low-water season was higher than that during the high-water season (4.2%) and that in other sites during both seasons (10.6-21.3%). The DEC isolates from the floating villages during the low-water season showed high antimicrobial resistance, including ampicillin (83.4%) and ciprofloxacin (83.4%), and frequently possessed a beta-lactamase gene (blaTEM) (83.4%). MLST analysis indicated that the predominant sequence type (ST) of DEC isolates from the floating villages possibly originated from humans, whereas more diverse STs were detected in isolates from other sites. We revealed the wide presence of diarrheagenic and antimicrobial-resistant E. coli in Tonle Sap Lake and identified a considerable infection risk in floating villages, especially during the low-water season.
Collapse
Affiliation(s)
- Ichiro Yoneda
- Department of Regional Environment Creation, United Graduate School of Agricultural Sciences, Iwate University, 18-8 Ueda 3-Chome, Morioka, 020-8850, Japan.
| | - Ulya Nur Rozanah
- Department of Agricultural Microbiology, Faculty of Agriculture, Gadjah Mada University, Bulaksumur, Yogyakarta, 55281, Indonesia
| | - Masateru Nishiyama
- Department of Food, Life and Environmental Sciences, Faculty of Agriculture, Yamagata University, 1-23 Wakaba-Machi, Tsuruoka, 997-8555, Japan
| | - Hasika Mith
- Faculty of Chemical and Food Engineering, Institute of Technology of Cambodia, Russian Federation Blvd., P.O. Box 86, Phnom Penh, 12156, Cambodia
| | - Toru Watanabe
- Department of Food, Life and Environmental Sciences, Faculty of Agriculture, Yamagata University, 1-23 Wakaba-Machi, Tsuruoka, 997-8555, Japan
| |
Collapse
|
4
|
Khawaskar D, Anbazhagan S, Balusamy D, Inbaraj S, Verma A, Vinodh Kumar OR, Nagaleekar VK, Sinha DK, Chaudhuri P, Singh BR, Chaturvedi VK, Thomas P. A comparative genomics approach for identifying genetic factors in Escherichia coli isolates associated with bovine diseases. J Appl Microbiol 2022; 133:3490-3501. [PMID: 36648155 DOI: 10.1111/jam.15781] [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: 06/09/2022] [Revised: 07/29/2022] [Accepted: 08/10/2022] [Indexed: 01/20/2023]
Abstract
AIMS Escherichia coli are ubiquitously present bacterial pathogens that cause septicaemia, diarrhoea and other clinical illness in farm animals. Many pathogen factors can be associated with disease conditions. Currently, studies inferring E. coli genetic factors associated with infection in bovines are limited. Hence, the present study envisaged to determine the pathogen genetic factors associated with bovine disease conditions. METHOD AND RESULTS The comparative genomic analysis involved genome sequence data of 135 diseased and 145 healthy bovine origin E. coli strains. Phylogroups A and C, as well as pathotypes ExPEC and EPEC, were found to have a strong connection with bovine disease strains. STEC strains, including EHEC, seem to play a less important role in bovine disease. Sequence types (STs) predominant among strains from diarrhoeal origin were ST 301 (CC 165) and ST 342. Correlation of core genome phylogeny with accessory gene based clustering, phylogroups and pathotypes indicated lineage specific virulence factors mostly associated with disease conditions. CONCLUSIONS Comparative genomic analysis was applied to infer genetic factors significant in bovine disease origin E. coli strains. Isolates from bovine disease origin were enriched for the phylogroups A and C, and for the pathotypes ExPEC and EPEC. However, there was minimal evidence of STEC involvement. The study also indicated predominant genetic lineages and virulence genes (pap, sfa and afa) associated with disease origin strains. SIGNIFICANCE AND IMPACT OF STUDY;: The study revealed significant pathotypes, phylgroups, serotypes and sequence types associated with bovine disease conditions. These identified genetic factors can be applied for disease diagnosis, implementing vaccine and therapeutic measures. In addition, E. coli isolates from the bovine species revealed a complex pattern of disease epidemiology.
Collapse
Affiliation(s)
- Damini Khawaskar
- Division of Epidemiology, ICAR- Indian Veterinary Research Institute, Bareilly - 243122, Uttar Pradesh
| | - Subbaiyan Anbazhagan
- Division of Bacteriology and Mycology, ICAR- Indian Veterinary Research Institute, Bareilly - 243122, Uttar Pradesh.,ICMR-National Animal Resource Facility for Biomedical Research, Hyderabad
| | - Dhayanath Balusamy
- Division of Epidemiology, ICAR- Indian Veterinary Research Institute, Bareilly - 243122, Uttar Pradesh
| | - Sophia Inbaraj
- Division of Bacteriology and Mycology, ICAR- Indian Veterinary Research Institute, Bareilly - 243122, Uttar Pradesh
| | - Abhishek Verma
- Division of Bacteriology and Mycology, ICAR- Indian Veterinary Research Institute, Bareilly - 243122, Uttar Pradesh
| | | | - Viswas Konasagara Nagaleekar
- Division of Bacteriology and Mycology, ICAR- Indian Veterinary Research Institute, Bareilly - 243122, Uttar Pradesh
| | - Dharmendra K Sinha
- Division of Epidemiology, ICAR- Indian Veterinary Research Institute, Bareilly - 243122, Uttar Pradesh
| | - Pallab Chaudhuri
- Division of Epidemiology, ICAR- Indian Veterinary Research Institute, Bareilly - 243122, Uttar Pradesh
| | - Bhoj R Singh
- Division of Epidemiology, ICAR- Indian Veterinary Research Institute, Bareilly - 243122, Uttar Pradesh
| | - V K Chaturvedi
- Division of Bacteriology and Mycology, ICAR- Indian Veterinary Research Institute, Bareilly - 243122, Uttar Pradesh
| | - Prasad Thomas
- Division of Bacteriology and Mycology, ICAR- Indian Veterinary Research Institute, Bareilly - 243122, Uttar Pradesh
| |
Collapse
|
5
|
Yamamura F, Sugiura T, Munby M, Shiokura Y, Murata R, Nakamura T, Fujiki J, Iwano H. Relationship between Escherichia coli virulence factors, notably kpsMTII, and symptoms of clinical metritis and endometritis in dairy cows. J Vet Med Sci 2022; 84:420-428. [PMID: 35082195 PMCID: PMC8983293 DOI: 10.1292/jvms.21-0586] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Although Escherichia coli is a commensal bacterium of the bovine vaginal microbiota, it is an important pathogenic bacterium that causes diseases of the reproductive tract and sub-fertility. Recent studies have focused on virulence factors (VFs) of intrauterine E. coli; however, actual endometrial VFs have not been clearly identified. The purpose of this study was to identify the VFs of E. coli associated with clinical metritis and endometritis. Thirty-two strains of E. coli and four mixed Trueperella pyogenes (TP) strains were detected in the uterus of 19 Holstein dairy cows with obvious clinical signs (between 8 and 66 days postpartum). The presence of six E. coli VFs (fimH, fyuA, kpsMTII, hra1, csgA, and astA) was examined by PCR, and clinical signs and reproductive performance (mixed TP, the percentage of polymorphonuclear neutrophils [PMN%], days to uterine involution, etc.) were evaluated. Four VFs (fimH, hra1, csgA, and astA) were detected in all E. coli strains, whereas fyuA and kpsMTII were detected in 94% and 50% of strains, respectively. Cows with E. coli strains harboring kpsMTII exhibited significantly severe clinical scores (vaginal discharge score, PMN%, uterine involution), suggesting that kpsMTII is a key VF for progression of clinical metritis and endometritis. In the present study, we clearly identified six VFs associated with clinical metritis and endometritis. In addition, E. coli strains with kpsMTII probably play a crucial role in the progression of clinical metritis and endometritis.
Collapse
Affiliation(s)
- Fuminosuke Yamamura
- Laboratory of Veterinary Biochemistry, School of Veterinary Medicine, Rakuno Gakuen University
| | - Tomochika Sugiura
- Laboratory of Theriogenology, School of Veterinary Medicine, Rakuno Gakuen University
| | - Montgomery Munby
- Laboratory of Veterinary Biochemistry, School of Veterinary Medicine, Rakuno Gakuen University
| | - Yusei Shiokura
- Laboratory of Veterinary Biochemistry, School of Veterinary Medicine, Rakuno Gakuen University
| | - Ryo Murata
- Laboratory of Food Microbiology and Food Safety, School of Veterinary Medicine, Rakuno Gakuen University
| | - Tomohiro Nakamura
- Laboratory of Veterinary Biochemistry, School of Veterinary Medicine, Rakuno Gakuen University
| | - Jumpei Fujiki
- Laboratory of Veterinary Biochemistry, School of Veterinary Medicine, Rakuno Gakuen University
| | - Hidetomo Iwano
- Laboratory of Veterinary Biochemistry, School of Veterinary Medicine, Rakuno Gakuen University
| |
Collapse
|
6
|
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
|
7
|
Pathotyping and antimicrobial susceptibility testing of Escherichia coli isolates from neonatal calves. Vet Res Commun 2021; 46:353-362. [PMID: 34796436 PMCID: PMC8601779 DOI: 10.1007/s11259-021-09857-5] [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: 06/03/2021] [Accepted: 11/01/2021] [Indexed: 10/25/2022]
Abstract
Neonatal calf mortality is a major concern to livestock sector worldwide. Neonatal calf diarrhoea (NCD), an acute severe condition causes morbidity and mortality in calves. Amongst various pathogens involved in NCD, E. coli is considered as one of the major causes. The study was targeted to characterize E. coli isolates from neonatal calves for diarrhoeagenic Escherichia coli (DEC) types (pathotyping), antimicrobial resistance (AMR) profiling and to correlate with epidemiological parameters. From neonates, a total of 113 faecal samples were collected, out of that 308, lactose fermenting colonies were confirmed as E. coli. Pathotypable isolates (12.3%) were represented by STEC (6.1%), EPEC (2.9%), ETEC (1.9%), EAEC (0.9%) and EHEC (0.3%). Occurrence of STEC was more in non-diarrhoeic calves, whereas ETEC was observed more in diarrhoeic calves. EPEC occurrence was observed in both diarrhoeic and non-diarrhoeic calves. Fishers extract test showed no significant association for occurrence of DEC types to type of dairies, health status, species, breed, age and sex of neonatal calves. Two hundred and eighty isolates were tested for antimicrobial susceptibility. The isolates showed maximum resistance towards ampicillin (55.4%) followed by tetracycline (54.3%), while minimum resistance was observed towards meropenem (2.5%). Multidrug resistant E. coli isolates were found to be 139 (49.6%), and Extended-spectrum beta-lactamase (ESBL) producers were 120 (42.9%). DEC pathotypes like STEC, ETEC, EHEC and EAEC that are also multidrug resistant present in neonatal calves have zoonotic potential and hence are of public health significance.
Collapse
|
8
|
Alfinete N, Bolukaoto JY, Heine L, Potgieter N, Barnard TG. Virulence and phylogenetic analysis of enteric pathogenic Escherichia coli isolated from children with diarrhoea in South Africa. Int J Infect Dis 2021; 114:226-232. [PMID: 34775113 DOI: 10.1016/j.ijid.2021.11.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 10/22/2021] [Accepted: 11/06/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Diarrhoeagenic E. coli pose a significant risk to human health. As such, determining the source(s) of these bacteria when isolated from patients with diarrhoea is an important step in disease prevention. OBJECTIVES This study aimed to identify the presence of genes coding for virulence and phylogroups among E. coli isolated from children hospitalised due to diarrhoea in Limpopo, South Africa. METHODS E. coli isolates were identified by VITEK®-2 automated system. An 11-gene multiplex PCR was used to differentiate five pathogenic types of E. coli: enteroaggregative (EAEC), enteroinvasive (EIEC), enterohaemorrhagic (EHEC), enteropathogenic (EPEC) and enterotoxigenic (ETEC). Clermont quadruplex PCR method was used to identify phylogroups of isolates. RESULTS From the 133 isolates tested, 79 were confirmed as E. coli of which (19.0%, 15/79) were commensals and 81.0% (64/79) isolates were positive for at least one pathotype of which ETEC was predominant (16.5%, 13/79), followed by EAEC (10.1%, 8/79), EPEC (7.6%, 6/79) and EHEC (2.5%, 2/79). Hybrid pathotypes were also detected and EAEC/ETEC was predominant (25.3%, 20/79). Phylogroup B2 was predominant (30.4%, 24/79), followed by group B1 (22.8%, 18/79), phylogroup C and E both had (12.7%, 10/79) each. Just over six percent (5/79) of isolates were non-typable. CONCLUSION There was a high distribution of diarrhoeagenic E. coli associated with different phylogroups among children living in Limpopo province, South Africa. This emphasises the importance of future monitoring of virulence and phylogroup distribution of E. coli isolates in this province in particular and South Africa as a whole.
Collapse
Affiliation(s)
- Ntando Alfinete
- Water and Health Research Centre, University of Johannesburg, Doornfontein, South Africa
| | - John Y Bolukaoto
- Water and Health Research Centre, University of Johannesburg, Doornfontein, South Africa
| | - Lee Heine
- Water and Health Research Centre, University of Johannesburg, Doornfontein, South Africa
| | - Natasha Potgieter
- School of Mathematical and Natural Sciences, University of Venda, Limpopo Province, South Africa
| | - Tobias G Barnard
- Water and Health Research Centre, University of Johannesburg, Doornfontein, South Africa.
| |
Collapse
|
9
|
Bolukaoto JY, Singh A, Alfinete N, Barnard TG. Occurrence of Hybrid Diarrhoeagenic Escherichia coli Associated with Multidrug Resistance in Environmental Water, Johannesburg, South Africa. Microorganisms 2021; 9:2163. [PMID: 34683484 PMCID: PMC8538365 DOI: 10.3390/microorganisms9102163] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/25/2021] [Accepted: 09/27/2021] [Indexed: 12/20/2022] Open
Abstract
This study was undertaken to determine the virulence and antibiotic resistance profiles of diarrhoeagenic Escherichia coli (DEC) in environmental waters of Johannesburg, South Africa. Samples were collected and cultured on selective media. An 11-plex PCR assay was used to differentiate five DEC, namely: enteroaggregative (EAEC), enterohaemorrhagic (EHEC), enteroinvasive (EIEC), enteropathogenic (EPEC) and enterotoxigenic (ETEC). The antibiotic resistance profile of isolates was determined using the VITEK®-2 automated system. The virulence profiles of 170 E. coli tested showed that 40% (68/170) were commensals and 60% (102/170) were pathogenic. EPEC had a prevalence of 19.2% (32/170), followed by ETEC 11.4% (19/170), EAEC 6% (10/170) and EHEC 3% (5/170). Hybrid DEC carrying a combination of simultaneously two and three pathogenic types was detected in twenty-eight and nine isolates, respectively. The antibiotic susceptibility testing showed isolates with multidrug resistance, including cefuroxime (100%), ceftazidime (86%), cefotaxime (81%) and cefepime (79%). This study highlighted the widespread occurrence of DEC and antibiotic resistance strains in the aquatic ecosystem of Johannesburg. The presence of hybrid pathotypes detected in this study is alarming and might lead to more severe diseases. There is a necessity to enhance surveillance in reducing the propagation of pathogenic and antibiotic-resistant strains in this area.
Collapse
Affiliation(s)
| | | | | | - Tobias G. Barnard
- Water and Health Research Centre, University of Johannesburg, Doornfontein 2092, South Africa; (J.Y.B.); (A.S.); (N.A.)
| |
Collapse
|
10
|
Nowaczek A, Dec M, Stępień-Pyśniak D, Urban-Chmiel R, Marek A, Różański P. Antibiotic Resistance and Virulence Profiles of Escherichia coli Strains Isolated from Wild Birds in Poland. Pathogens 2021; 10:1059. [PMID: 34451523 PMCID: PMC8400592 DOI: 10.3390/pathogens10081059] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/09/2021] [Accepted: 08/17/2021] [Indexed: 11/16/2022] Open
Abstract
Wild animals are increasingly reported as carriers of antibiotic-resistant and pathogenic bacteria including Enterobacteriaceae. However, the role of free-living birds as reservoirs for potentially dangerous microbes is not yet thoroughly understood. In our work, we examined Escherichia coli strains from wild birds in Poland in relation to their antimicrobial agents susceptibility, virulence and phylogenetic affiliation. Identification of E. coli was performed using MALDI-TOF mass spectrometry. The antibiotic susceptibility of the isolates was determined by the broth microdilution method, and resistance and virulence genes were detected by PCR. E. coli bacteria were isolated from 32 of 34 samples. The strains were most often classified into phylogenetic groups B1 (50%) and A (25%). Resistance to tetracycline (50%), ciprofloxacin (46.8%), gentamicin (34.3%) and ampicillin (28.1%) was most frequently reported, and as many as 31.2% of E. coli isolates exhibited a multidrug resistance phenotype. Among resistance genes, sul2 (31.2% of isolates) and blaTEM (28.1%) were identified most frequently, while irp-2 (31.2%) and ompT (28.1%) were the most common virulence-associated genes. Five strains were included in the APEC group. The study indicates that wild birds can be carriers of potentially dangerous E. coli strains and vectors for the spread of resistant bacteria and resistance determinants in the environment.
Collapse
Affiliation(s)
- Anna Nowaczek
- Department of Veterinary Prevention and Avian Diseases, Faculty of Veterinary Medicine, University of Life Sciences in Lublin, Akademicka 12, 20-033 Lublin, Poland; (A.N.); (D.S.-P.); (R.U.-C.); (A.M.)
| | - Marta Dec
- Department of Veterinary Prevention and Avian Diseases, Faculty of Veterinary Medicine, University of Life Sciences in Lublin, Akademicka 12, 20-033 Lublin, Poland; (A.N.); (D.S.-P.); (R.U.-C.); (A.M.)
| | - Dagmara Stępień-Pyśniak
- Department of Veterinary Prevention and Avian Diseases, Faculty of Veterinary Medicine, University of Life Sciences in Lublin, Akademicka 12, 20-033 Lublin, Poland; (A.N.); (D.S.-P.); (R.U.-C.); (A.M.)
| | - Renata Urban-Chmiel
- Department of Veterinary Prevention and Avian Diseases, Faculty of Veterinary Medicine, University of Life Sciences in Lublin, Akademicka 12, 20-033 Lublin, Poland; (A.N.); (D.S.-P.); (R.U.-C.); (A.M.)
| | - Agnieszka Marek
- Department of Veterinary Prevention and Avian Diseases, Faculty of Veterinary Medicine, University of Life Sciences in Lublin, Akademicka 12, 20-033 Lublin, Poland; (A.N.); (D.S.-P.); (R.U.-C.); (A.M.)
| | - Paweł Różański
- Department of Animal Hygiene and Environmental Hazards, Faculty of Animal Sciences and Bioeconomy, University of Life Sciences in Lublin, Akademicka 13, 20-950 Lublin, Poland;
| |
Collapse
|
11
|
Yoo IH, Kang HM, Suh W, Cho H, Yoo IY, Jo SJ, Park YJ, Jeong DC. Quality Improvements in Management of Children with Acute Diarrhea Using a Multiplex-PCR-Based Gastrointestinal Pathogen Panel. Diagnostics (Basel) 2021; 11:diagnostics11071175. [PMID: 34203426 PMCID: PMC8303787 DOI: 10.3390/diagnostics11071175] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 11/16/2022] Open
Abstract
Conventional methods for etiologic diagnoses of acute gastroenteritis (AGE) are time consuming and have low positive yield leading to limited clinical value. This study aimed to investigate quality improvements in patient management, antibiotic stewardship, and in-hospital infection transmission prevention using BioFire® FilmArray® Gastrointestinal Panel (GI Panel) in children with acute diarrhea. This was a prospective study recruiting children < 19 years old with new onset diarrhea during the study period, and a matched historical cohort study of children diagnosed with AGE during the 4 years prior. Patients in the prospective cohort underwent stool testing with GI Panel and conventional methods. A total of 182 patients were included in the prospective cohort, of which 85.7% (n = 156) had community-onset and 14.3% (n = 26) had hospital-onset diarrhea. A higher pathogen positivity rate for community-onset diarrhea was observed by the GI Panel (58.3%, n = 91) compared to conventional studies (42.3%, n = 66) (p = 0.005) and historical cohort (31.4%, n = 49) (p < 0.001). The stool tests reporting time after admission was 25 (interquartile range, IQR 17-46) hours for the GI Panel, and 72 (IQR 48-96) hours for the historical cohort (p < 0.001). A significant reduction in antibiotic use was observed in the prospective cohort compared to historical cohort, 35.3% vs. 71.8%; p < 0.001), respectively. Compared to the GI Panel, norovirus ICT was only able to detect 4/11 (36.4%) patients with hospital-onset and 14/27 (51.8%) patients with community-onset diarrhea. The high positivity rate and rapid reporting time of the GI Panel had clinical benefits for children admitted for acute diarrhea, especially by reducing antibiotic use and enabling early adequate infection precaution and isolation.
Collapse
Affiliation(s)
- In Hyuk Yoo
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea;
| | - Hyun Mi Kang
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea;
- Correspondence: (H.M.K.); (D.C.J.); Tel.: +82-2-2258-6273 (H.M.K.); +82-2-2258-6180 (D.C.J.); Fax: +82-2-537-4544 (H.M.K. & D.C.J.)
| | - Woosuk Suh
- Uijeongbu Eulji Medical Center, Department of Pediatrics, Eulji University School of Medicine, Seongnam 11759, Korea;
| | - Hanwool Cho
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea; (H.C.); (I.Y.Y.); (S.J.J.); (Y.J.P.)
| | - In Young Yoo
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea; (H.C.); (I.Y.Y.); (S.J.J.); (Y.J.P.)
| | - Sung Jin Jo
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea; (H.C.); (I.Y.Y.); (S.J.J.); (Y.J.P.)
| | - Yeon Joon Park
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea; (H.C.); (I.Y.Y.); (S.J.J.); (Y.J.P.)
| | - Dae Chul Jeong
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea;
- Correspondence: (H.M.K.); (D.C.J.); Tel.: +82-2-2258-6273 (H.M.K.); +82-2-2258-6180 (D.C.J.); Fax: +82-2-537-4544 (H.M.K. & D.C.J.)
| |
Collapse
|
12
|
Priyanka, Meena PR, Meghwanshi KK, Rana A, Singh AP. Leafy greens as a potential source of multidrug-resistant diarrhoeagenic Escherichia coli and Salmonella. MICROBIOLOGY-SGM 2021; 167. [PMID: 34061018 DOI: 10.1099/mic.0.001059] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A continued rise in leafy green-linked outbreaks of disease caused by pathogenic Escherichia coli or Salmonella, particularly strains exhibiting multidrug resistance (MDR), has emerged as a major threat to human health and food safety worldwide. Thus, the present study was conducted to examine antimicrobial resistance, including MDR, in diarrhoeagenic E. coli (DEC) and Salmonella isolates obtained from leafy greens from rural and urban areas of India. Of the collected samples (830), 14.1 and 6.5% yielded 117 E. coli (40 DEC and 77 non-DEC) and 54 Salmonella isolates, respectively. Among the DEC pathotypes, enteroaggregative E. coli was the most prevalent (10.2 %), followed by enteropathogenic E. coli (9.4 %), enteroinvasive E. coli (7.6 %) and enterohemorrhagic E. coli (6.8 %). Antimicrobial susceptibility testing of all bacterial isolates with respect to drugs categorized as critically or highly important in both human and veterinary medicine revealed moderate to high (30-90%) resistance for amoxicillin/clavulanic acid, ampicillin, gentamycin and colistin, but relatively low resistance (>30 %) for ciprofloxacin, trimethoprim/sulfamethoxazole and fosfomycin. Notably, all DEC and more than 90% non-DEC or Salmonella isolates were found to be multidrug-resistant to drugs of both human and animal importance. Overall, the results of the present study suggest that leafy greens are potential reservoirs or sources of multidrug-resistant DEC and Salmonella strains in the rural or urban areas of India.
Collapse
Affiliation(s)
- Priyanka
- Department of Microbiology, School of Life Sciences, Central University of Rajasthan, Rajasthan, India
| | - Prem Raj Meena
- Department of Microbiology, School of Life Sciences, Central University of Rajasthan, Rajasthan, India
| | - Keshav Kumar Meghwanshi
- Department of Biotechnology, School of Life Sciences, Central University of Rajasthan, Rajasthan, India
| | - Anuj Rana
- Department of Microbiology, College of Basic Sciences & Humanities, Chaudhary Charan Singh Haryana Agricultural University, Haryana, India
| | - Arvind Pratap Singh
- Department of Microbiology, School of Life Sciences, Central University of Rajasthan, Rajasthan, India
| |
Collapse
|
13
|
Bacterial, viral and parasitic pathogens analysed by qPCR: Findings from a prospective study of travellers' diarrhoea. Travel Med Infect Dis 2020; 40:101957. [PMID: 33359433 DOI: 10.1016/j.tmaid.2020.101957] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 12/19/2020] [Accepted: 12/21/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND The diagnostics of travellers' diarrhoea (TD) has been revolutionised by multiplex qPCR assays. While mostly of bacterial aetiology, viruses and parasites account for the disease among 10-20% of travellers. Despite this, prospective studies applying qPCR assays remain scarce that cover not only bacteria, such as the various diarrhoeagenic Escherichia coli (DEC), but also viral and parasitic pathogens. METHOD We analysed by qPCR pre- and post-travel stool samples of 146 Finnish travellers for bacterial, viral and parasitic pathogens: enteropathogenic (EPEC), enteroaggregative (EAEC), enterotoxigenic (ETEC), enterohaemorrhagic (EHEC), and enteroinvasive (EIEC) E. coli; Shigella, Campylobacter, Salmonella, Yersinia and Vibrio cholerae; norovirus G1 and G2, rotavirus, enteroviruses, and sapovirus; and Giardia lamblia, Entamoeba histolytica, and Cryptosporidium. Symptoms and medication data during travel were collected by questionnaires. RESULTS We detected bacterial pathogens in 102/146 samples (69.9%; EAEC, EPEC, ETEC most common), viral ones in 13 (8.9%; norovirus most common), and parasitic ones in one (0.7%; Giardia). Noroviruses were associated with severe symptoms (23.5% versus non-severe 4.9%). In the TD group, 41.7% (5/12) of those with viral pathogens (vs. 13.3%; 11/83 without) took antibiotics. CONCLUSION Viral pathogens, particularly noroviruses, prevail in severe TD. The symptoms of viral disease are often severe and lead to unwarranted use of antibiotics.
Collapse
|
14
|
Bonkoungou IJO, Somda NS, Traoré O, Zoma BS, Garba Z, Drabo KM, Barro N. DETECTION OF DIARRHEAGENIC ESCHERICHIA COLI IN HUMAN DIARRHEIC STOOL AND DRINKING WATER SAMPLES IN OUAGADOUGOU, BURKINA FASO. Afr J Infect Dis 2020; 15:53-58. [PMID: 33884359 PMCID: PMC8047281 DOI: 10.21010/ajid.v15i1.7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 11/30/2020] [Accepted: 12/01/2020] [Indexed: 12/27/2022] Open
Abstract
Background: The presence of diarrheagenic Escherichia coli (DEC) in drinking water, is a grave public health problem. This study was aimed at characterization of diarrheagenic Escherichia coli isolated from drinking water and faecal samples from diarrheic patients in Ouagadougou, Burkina Faso. Materials and Methods: A total of 242 water samples consisting of 182 potable sachets and 60 from boreholes were collected in the period between October 2018 and April 2019 in the city of Ouagadougou. Faecal samples were also collected from 201 diarrheic patients visiting National Public Health Laboratory for a biological diagnosis by coproculture. The presence of virulence genes associated with DEC was determined by 16-plex polymerase chain reaction from bacteria culture. Results: From drinking water, we found 17% (42/242) Escherichia coli isolates in which 1% (2/242) DEC were detected. Among analyzed samples (182 sachet water versus 60 borehole water), the two DEC (01 ETEC and 01 EPEC) were detected in sachet water. DEC were detected in 20% (40/201) of patients. Enteroaggregative Escherichia coli (EAEC) were mostly detected in 10% followed by Enteropathogenic Escherichia coli (EPEC) in 4%, Enteroinvasive Escherichia coli (EIEC) in 2%, and Shiga toxin-producing Escherichia coli (STEC) 0.5%. However, Enterotoxigenic Escherichia coli (ETEC) was not detected alone, but in co-infections with EAEC. Conclusion: The present study documented the prevalence of Escherichia coli pathovars associated in patients with diarrhea, and shows that drinking water might be a source of DEC transmission in human.
Collapse
Affiliation(s)
- Isidore Juste Ouindgueta Bonkoungou
- Département de Biochimie-Microbiologie. UFR- Sciences de la vie et de la terre. Université Joseph Ki-Zerbo, 03 BP 7021 Ouagadougou 03, Burkina Faso
| | - Namwin Siourimè Somda
- Département Technologie Alimentaire (DTA) / IRSAT / CNRST, Burkina Faso, 03 BP 7047 Ouagadougou 03
| | - Oumar Traoré
- Département de Biochimie-Microbiologie. UFR- Sciences de la vie et de la terre. Université Joseph Ki-Zerbo, 03 BP 7021 Ouagadougou 03, Burkina Faso.,Unité de Formation et de Recherche en Sciences Appliquées à la Technologie (UFR/SAT). Université de Dédougou, BP 176 Dédougou
| | - Barthelemy Sibiri Zoma
- Laboratoire National de Santé Publique (LNSP), 09 BP 24 Ouagadougou 09, Burkina Faso.,Polygon Bio Services SARL,09 BP 969 Ouagadougou 09, Ouagadougou, Burkina Faso 969
| | - Zakaria Garba
- Département de Biochimie-Microbiologie. UFR- Sciences de la vie et de la terre. Université Joseph Ki-Zerbo, 03 BP 7021 Ouagadougou 03, Burkina Faso.,Unité de Recherche Clinique de NANORO, IRSS-CNRST, BP: 218 Ouaga 11 Burkina Faso
| | - Koine Maxime Drabo
- Institut de Recherche en Sciences de la santé, CNRST, 03 B.P. 7192 Ouagadougou 03 Burkina Faso
| | - Nicolas Barro
- Département de Biochimie-Microbiologie. UFR- Sciences de la vie et de la terre. Université Joseph Ki-Zerbo, 03 BP 7021 Ouagadougou 03, Burkina Faso
| |
Collapse
|
15
|
Dembélé R, Konaté A, Traoré O, Kaboré WAD, Soulama I, Kagambèga A, Traoré AS, Guessennd NK, Aidara-Kane A, Gassama-Sow A, Barro N. Extended spectrum beta-lactamase and fluoroquinolone resistance genes among Escherichia coli and Salmonella isolates from children with diarrhea, Burkina Faso. BMC Pediatr 2020; 20:459. [PMID: 33010801 PMCID: PMC7532561 DOI: 10.1186/s12887-020-02342-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 09/13/2020] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND The emergence and spread of multidrug-resistant gram-negative bacteria (MDR) has become a major public health concern worldwide. This resistance is caused by enzymes-mediated genes (i.e., extended spectrum beta-lactamases) that are common in certain Enterobacterioceae species. However, the distribution of these genes is poorly documented in Burkina Faso. This study aims to determine the prevalence and distribution of the resistant genes coding for broad spectrum beta-lactamases and quinolones in rural Burkina Faso. METHODS Multiplex PCR assays were carried out to detect ESBL-encoding genes, including blaOXA, blaTEM, blaCTX-M, blaSHV. The assays also assessed the presence of quinolone resistance gene namely qnrA, qnrB and qnrS in the quinolone-resistance DEC and Salmonella strains. RESULTS The Extended-Spectrum Beta-Lactamases (ESBL) resistance phenotype was reported in all the E. coli isolates (5/5). Cross-resistance phenotype to quinolones (CRQ) was shown by one Salmonella strain (1/9) and three E. coli (3/5). Cross-resistance phenotypes to fluoroquinolones (CRFQ) were harboured by one Salmonella (1/9) and carbapenemase phenotypes were detected in two E. coli strains (2/5). Whilst the blaOXA genes were detected in 100% (5/5) of E. coli isolates and in 33.33% (3/9) Salmonella isolates. One strain of E. coli (1/5) harbored the blaCTX-M gene and the qnrB gene simultaneously. CONCLUSIONS This study identified β-lactam (bla) and quinolone resistance (qnr) genes in multidrug-resistant E. coli and Salmonella spp. in rural Burkina Faso. Our finding which highlighted the enterobacteriaceae strains resistance to β-lactams and quinolones are of high interest for adequate management of antimicrobial resistant genes outbreak in Burkina Faso.
Collapse
Affiliation(s)
- René Dembélé
- Laboratory of Molecular Biology, Epidemiology and Surveillance of Bacteria and Viruses Transmitted by Food, Centre for Research in Biological, Food and Nutritional Sciences, Graduate School of Science and Technology, University Joseph KI-ZERBO, 03, BP 7021, Ouagadougou 03, Burkina Faso.
- Training and Research Unit in Applied Sciences and Technologies, University of Dedougou, BP 176, Dedougou, Burkina Faso.
| | - Ali Konaté
- Laboratory of Molecular Biology, Epidemiology and Surveillance of Bacteria and Viruses Transmitted by Food, Centre for Research in Biological, Food and Nutritional Sciences, Graduate School of Science and Technology, University Joseph KI-ZERBO, 03, BP 7021, Ouagadougou 03, Burkina Faso
| | - Oumar Traoré
- Laboratory of Molecular Biology, Epidemiology and Surveillance of Bacteria and Viruses Transmitted by Food, Centre for Research in Biological, Food and Nutritional Sciences, Graduate School of Science and Technology, University Joseph KI-ZERBO, 03, BP 7021, Ouagadougou 03, Burkina Faso
- Training and Research Unit in Applied Sciences and Technologies, University of Dedougou, BP 176, Dedougou, Burkina Faso
| | - Wendpoulomdé A D Kaboré
- Laboratory of Molecular Biology, Epidemiology and Surveillance of Bacteria and Viruses Transmitted by Food, Centre for Research in Biological, Food and Nutritional Sciences, Graduate School of Science and Technology, University Joseph KI-ZERBO, 03, BP 7021, Ouagadougou 03, Burkina Faso
| | - Issiaka Soulama
- National Centre for Research and Training on Malaria, 01, BP 2208, Ouagadougou 01, Burkina Faso
| | - Assèta Kagambèga
- Laboratory of Molecular Biology, Epidemiology and Surveillance of Bacteria and Viruses Transmitted by Food, Centre for Research in Biological, Food and Nutritional Sciences, Graduate School of Science and Technology, University Joseph KI-ZERBO, 03, BP 7021, Ouagadougou 03, Burkina Faso
- Institute of Sciences, 01, BP 1757, Ouagadougou 01, Burkina Faso
| | - Alfred S Traoré
- Laboratory of Molecular Biology, Epidemiology and Surveillance of Bacteria and Viruses Transmitted by Food, Centre for Research in Biological, Food and Nutritional Sciences, Graduate School of Science and Technology, University Joseph KI-ZERBO, 03, BP 7021, Ouagadougou 03, Burkina Faso
| | - Nathalie K Guessennd
- Laboratory of Bacteriology-Virology, Unit of Antibiotics, Natural Substances and Surveillance of Resistance of Microorganisms to Antimicrobials, Pasteur Institute of Abidjan, 01, BP 490, Abidjan 01, Ivory Coast
- Laboratory of Bacteriology-Virology, Unit of Training and Research of Medical Sciences, University Felix Houphouet BOIGNY, 01, BP V34, Abidjan 01, Ivory Coast
| | - Awa Aidara-Kane
- Unit of Experimental Bacteriology, Pasteur Institute of Dakar, 36 Avenue Pasteur, BP 220, Dakar, Senegal
| | - Amy Gassama-Sow
- Unit of Experimental Bacteriology, Pasteur Institute of Dakar, 36 Avenue Pasteur, BP 220, Dakar, Senegal
| | - Nicolas Barro
- Laboratory of Molecular Biology, Epidemiology and Surveillance of Bacteria and Viruses Transmitted by Food, Centre for Research in Biological, Food and Nutritional Sciences, Graduate School of Science and Technology, University Joseph KI-ZERBO, 03, BP 7021, Ouagadougou 03, Burkina Faso
| |
Collapse
|
16
|
Houattongkham S, Yamamoto E, Sithivong N, Inthaphatha S, Kariya T, Saw YM, Vongduangchanh A, Keosavanh O, Hamajima N. Etiologic agents of acute diarrhea in sentinel surveillance sites in Vientiane Capital, Lao People's Democratic Republic, 2012-2015. Eur J Clin Microbiol Infect Dis 2020; 39:1115-1122. [PMID: 31993879 DOI: 10.1007/s10096-020-03827-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 01/21/2020] [Indexed: 10/23/2022]
Abstract
This study aims to identify the pathogens of diarrhea in Vientiane Capital, Lao People's Democratic Republic (Lao PDR). The data of 2482 patients who visited eight health facilities due to diarrhea in 2012-2015 were retrospectively reviewed. Stool or rectal swabs collected from all patients were tested for bacteria. Children who were under 5 years old were additionally tested for rotavirus. Of 2482 cases, 1566 cases were under 5 years old, and at least one enteropathogen was detected in 475 cases (19.1%). Salmonella species was the most commonly detected bacterial pathogen. Enteropathogenic Escherichia coli (EPEC) and Salmonella species was the major pathogen in the dry season and the wet season, respectively. Eighty-seven patients tested positive for multiple bacteria. Rotavirus was detected in 291 children under 5 years old (32.4%), mostly from October to April. The major bacteria of coinfection with rotavirus were EPEC followed by Salmonella species. Salmonella species was the predominant bacterial pathogen of diarrhea of all ages, and rotavirus was the predominant pathogen among children under 5 years old. Further studies examining other types of pathogens for diarrhea and the introduction of a rotavirus vaccine for children are needed in Lao PDR.
Collapse
Affiliation(s)
- Souphatsone Houattongkham
- Department of Healthcare Administration, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan.,Epidemiology Section, Bacteriology Unit, National Center for Laboratory and Epidemiology, Km 3 Thadeau Road, Ban Thaphalarnxay, Sisathanack district, Vientiane Capital, Lao PDR
| | - Eiko Yamamoto
- Department of Healthcare Administration, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan.
| | - Noikaseumsy Sithivong
- Laboratory Section, Bacteriology Unit, National Center for Laboratory and Epidemiology, Km 3 Thadeau Road, Ban Thaphalarnxay, Sisathanack district, Vientiane Capital, Lao PDR
| | - Souphalak Inthaphatha
- Department of Healthcare Administration, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Tetsuyoshi Kariya
- Department of Healthcare Administration, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Yu Mon Saw
- Department of Healthcare Administration, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Arounnapha Vongduangchanh
- Laboratory Section, Bacteriology Unit, National Center for Laboratory and Epidemiology, Km 3 Thadeau Road, Ban Thaphalarnxay, Sisathanack district, Vientiane Capital, Lao PDR
| | - Onechanh Keosavanh
- Epidemiology Section, Bacteriology Unit, National Center for Laboratory and Epidemiology, Km 3 Thadeau Road, Ban Thaphalarnxay, Sisathanack district, Vientiane Capital, Lao PDR.,Laboratory Section, Bacteriology Unit, National Center for Laboratory and Epidemiology, Km 3 Thadeau Road, Ban Thaphalarnxay, Sisathanack district, Vientiane Capital, Lao PDR
| | - Nobuyuki Hamajima
- Department of Healthcare Administration, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| |
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
|
Bolukaoto JY, Kock MM, Strydom KA, Mbelle NM, Ehlers MM. Molecular characteristics and genotypic diversity of enterohaemorrhagic Escherichia coli O157:H7 isolates in Gauteng region, South Africa. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 692:297-304. [PMID: 31351277 DOI: 10.1016/j.scitotenv.2019.07.119] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 07/04/2019] [Accepted: 07/08/2019] [Indexed: 06/10/2023]
Abstract
Enterohaemorrhagic Escherichia coli (EHEC) O157:H7 is one of the major foodborne and waterborne pathogens causing severe diseases and outbreaks worldwide. There is scarcity of EHEC O157:H7 data in South Africa. This study was carried out to determine the molecular characteristics and genotypic diversity of EHEC O157:H7 isolates in the Gauteng region, South Africa. Samples were cultured on selective chromogenic media. Antibiotic susceptibility profile of isolates was determined using the VITEK®-2 automated system. Isolates were characterised using multiplex PCR assays and the genetic diversity was determined using pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). A total of 520 samples of which 270 environmental water samples and 250 stool specimens were collected and analysed. Overall, EHEC O157:H7 was recovered from 2.3% (12/520) of samples collected. Environmental water samples and clinical stool specimens showed a prevalence of 4.07% (11/270) and 0.4% (1/250) respectively. Antibiotic susceptibility profile varied from isolates with full susceptibility to isolates with resistance to multiple antibiotics. Most resistance was detected to the penicillins, specifically ampicillin (7/12), amoxicillin (3/12) and piperacillin/Tazobactam (3/12) followed by one of the folate inhibitors, trimethoprim (3/12) and the carbapenems, imipenem and meropenem (2/12) each. Three isolates harboured a combination of Shiga-toxins (Stx)-2, intimin (eae) and enterohaemolysin (hlyA) genes, while two isolates harboured the Stx-1, Stx-2 and hlyA genes. The PFGE performed showed that EHEC O157:H7 isolates were genetically diverse, with two minor pulsotypes and eight singletons. The MLST analysis identified three sequence types (STs) (ST10, ST11 and ST1204) that have been previously reported associated with outbreaks. The STs identified in this study pose a potential public health risk to consumers of untreated environmental water and closed human contacts. There is necessity to enhance surveillance in reducing the propagation of this bacterium which is a public health problem.
Collapse
Affiliation(s)
- John Y Bolukaoto
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, South Africa
| | - Marleen M Kock
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, South Africa; National Health Laboratory Service, Tshwane Academic Division, Pretoria, South Africa
| | - Kathy-Anne Strydom
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, South Africa; Ampath National Laboratory Service, Pretoria, South Africa
| | - Nontombi M Mbelle
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, South Africa; National Health Laboratory Service, Tshwane Academic Division, Pretoria, South Africa
| | - Marthie M Ehlers
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, South Africa; National Health Laboratory Service, Tshwane Academic Division, Pretoria, South Africa.
| |
Collapse
|
19
|
Molecular Diagnosis of Diarrheagenic E. coli Infections Among the Pediatric Patients in Wasit Province, Iraq. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2018. [DOI: 10.22207/jpam.12.4.62] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
|
20
|
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
|
21
|
Mahfouz N, Caucci S, Achatz E, Semmler T, Guenther S, Berendonk TU, Schroeder M. High genomic diversity of multi-drug resistant wastewater Escherichia coli. Sci Rep 2018; 8:8928. [PMID: 29895899 PMCID: PMC5997705 DOI: 10.1038/s41598-018-27292-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 05/18/2018] [Indexed: 12/13/2022] Open
Abstract
Wastewater treatment plants play an important role in the emergence of antibiotic resistance. They provide a hot spot for exchange of resistance within and between species. Here, we analyse and quantify the genomic diversity of the indicator Escherichia coli in a German wastewater treatment plant and we relate it to isolates’ antibiotic resistance. Our results show a surprisingly large pan-genome, which mirrors how rich an environment a treatment plant is. We link the genomic analysis to a phenotypic resistance screen and pinpoint genomic hot spots, which correlate with a resistance phenotype. Besides well-known resistance genes, this forward genomics approach generates many novel genes, which correlated with resistance and which are partly completely unknown. A surprising overall finding of our analyses is that we do not see any difference in resistance and pan genome size between isolates taken from the inflow of the treatment plant and from the outflow. This means that while treatment plants reduce the amount of bacteria released into the environment, they do not reduce the potential for antibiotic resistance of these bacteria.
Collapse
Affiliation(s)
| | - Serena Caucci
- Institute for Hydrobiology, TU Dresden, Dresden, Germany.,United Nations University Institute for Integrated Management of Material Fluxes and of Resources, Dresden, Germany
| | | | - Torsten Semmler
- Institute of Microbiology und Epizootics, FU, Berlin, Germany
| | - Sebastian Guenther
- Institute of Microbiology und Epizootics, FU, Berlin, Germany.,Institut für Pharmazie Pharmazeutische Biologie, Ernst-Moritz-Arndt-Universität Greifswald, Greifswald, Germany
| | | | | |
Collapse
|
22
|
lei L, Rehman MU, Huang S, Zhang L, Wang L, Mehmood K, Zhang H, Tong X, Wang M, Li J. Antimicrobial resistance and prevalence of diarrheagenic Escherichia coli (DEC), in diarrheic yaks of Tibetan Plateau, China. Acta Trop 2018; 182:111-114. [PMID: 29470944 DOI: 10.1016/j.actatropica.2018.02.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Revised: 02/12/2018] [Accepted: 02/17/2018] [Indexed: 11/25/2022]
Abstract
This study was conducted to test the distribution of diarrheagenic Escherichia coli (DEC) associated genes in fecal isolates from diarrheic yaks of a high remote region of China. Briefly, we obtained 203 fecal samples from diarrheic adult yaks and E. coli strains were isolated and identified via standard methods The antibiotic sensitivity of isolates was determined via disk diffusion method and polymerase chain reaction (PCR) was used to detect the DEC virulence associated genes. Results of the current study showed a high rate of resistance to tetracycline (93.6%) and low rate of resistance to ofloxacin (16.7%) antibiotics. Meanwhile, five different diarrheagenic associated virulence traits were detected including; EAEC (11.80%), EHEC (25.62%), EIEC (17.18%), EPEC (36.92%) and ETEC (11.36%). Moreover, E. coli isolates were positive for all tested DEC associated virulence genes ranging from 1.48% to 33%. Additionally, four isolates were positive for more than one virulence genes. In conclusion, our investigation showed a relatively low number of E. coli virulence genes isolated from diarrheic Tibetan yaks, which could be attributed to the high altitude induced harsh environmental conditions that may not help in the growth and survival of pathogenic organisms. In addition, this study highlights the high level of antibiotic resistance in yaks, therefore; preventive measures should be taken to monitor the antibiotic usage in Tibet region of China.
Collapse
|
23
|
Abstract
BACKGROUND Globally, diarrhea kills almost 1500 children daily. In diagnostics, molecular methods are replacing traditional assays. We aimed to investigate enteropathogens in children with and without diarrhea in Luanda, the capital of Angola. METHODS One hundred and ninety-four stool samples from 98 children with acute diarrhea and 96 children without diarrhea were investigated for 17 enteropathogens with multiplex real-time polymerase chain reaction. RESULTS The median age of children was 10.5 months. Enteropathogens, bacteria, viruses and parasites were detected in 91%, 78%, 50% and 25%, respectively. A positive finding was significantly (P = 0.003) more common in diarrhea when testing for all pathogens combined, for bacteria alone and for viruses alone. More than one pathogen was found more frequently in diarrhea than in non-diarrhea stool samples, in 87% and in 59% (P < 0.0001), respectively. The median number (interquartile range) of pathogens detected was 3 (2) versus 1.5 (2; P < 0.0001), respectively. When age was taken into account, diarrhea was found to be associated with enterotoxigenic and enteroaggregative Escherichia coli, Shigella, Campylobacter, rotavirus, sapovirus and Cryptosporidium. CONCLUSIONS Multiplex polymerase chain reaction detected enteropathogens in almost all stool samples of children in Luanda, albeit this occurred more often in diarrhea. Children with diarrhea showed more mixed infections than children without diarrhea.
Collapse
|
24
|
Somda NS, Bonkoungou OJI, Zongo C, Kagambèga A, Bassolé IHN, Traoré Y, Mahillon J, Scippo ML, Hounhouigan JD, Savadogo A. Safety of ready-to-eat chicken in Burkina Faso: Microbiological quality, antibiotic resistance, and virulence genes in Escherichia coli isolated from chicken samples of Ouagadougou. Food Sci Nutr 2018; 6:1077-1084. [PMID: 29983972 PMCID: PMC6021723 DOI: 10.1002/fsn3.650] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 02/28/2018] [Accepted: 03/15/2018] [Indexed: 11/24/2022] Open
Abstract
In Burkina Faso, flamed/grilled chickens are very popular and well known to consumers. The aim of this study was to evaluate the microbiological quality, the antibiotic resistance, and the virulence gene from Escherichia coli isolated from these chickens in Ouagadougou. A total of 102 grilled, flamed, and fumed chickens were collected in Ouagadougou and analyzed, using standard microbiological methods. All E. coli isolates were checked with the antimicrobial test and also typed by 16‐plex PCR. The mean of aerobic mesophilic bacteria (AMB) and thermo‐tolerant coliforms (TTC) was found respectively between 6.90 ± 0.12 × 107CFU/g to 2.76 ± 0.44 × 108CFU/g and 2.4 ± 0.82 × 107CFU/g to 1.27 ± 0.9 × 108CFU/g. E. coli strains were found to 27.45%. Forty samples (38.24%) were unacceptable based on the AMB load. Fifty‐nine samples (57.85%) were contaminated with TTCs. Low resistance was observed with antibiotics of betalactamin family. Diarrheagenic E. coli strains were detected in 21.43% of all samples. This study showed that flamed/grilled chickens sold in Ouagadougou could pose health risks for the consumers. Need of hygienic practices or system and good manufacturing practices is necessary to improve the hygienic quality of flamed/grilled chickens. Our results highlight the need of control of good hygiene and production practices to contribute to the improvement of the safety of the products and also to avoid antibiotic resistance. Slaughter, scalding, evisceration, plucking, bleeding, washing, rinsing, preserving, grilling, and selling may be the ways of contamination.
Collapse
Affiliation(s)
- Namwin S Somda
- Laboratoire de Biochimie et d'Immunologie Appliquée (LABIA) Unité de Formation et de la Recherche en Sciences de la Vie et de la Terre Ecole Doctorale Sciences et Technologies Université Ouaga I Pr Joseph Ki-Zerbo Ouagadougou Burkina Faso.,Laboratoire National de Santé Publique (LNSP) Ouagadougou Burkina Faso
| | - Ouindgueta J I Bonkoungou
- Laboratoire National de Santé Publique (LNSP) Ouagadougou Burkina Faso.,Laboratoire de Biologie Moléculaire d'Epidémiologie et de Surveillance des agents Transmissibles par les Aliments (LABESTA) Unité de Formation et de la Recherche en Sciences de la Vie et de la Terre Ecole Doctorale Sciences et Technologies Université Ouaga I Pr Joseph Ki-Zerbo Ouagadougou Burkina Faso
| | - Cheikna Zongo
- Laboratoire de Biochimie et d'Immunologie Appliquée (LABIA) Unité de Formation et de la Recherche en Sciences de la Vie et de la Terre Ecole Doctorale Sciences et Technologies Université Ouaga I Pr Joseph Ki-Zerbo Ouagadougou Burkina Faso
| | - Assèta Kagambèga
- Laboratoire de Biologie Moléculaire d'Epidémiologie et de Surveillance des agents Transmissibles par les Aliments (LABESTA) Unité de Formation et de la Recherche en Sciences de la Vie et de la Terre Ecole Doctorale Sciences et Technologies Université Ouaga I Pr Joseph Ki-Zerbo Ouagadougou Burkina Faso
| | - Imael H N Bassolé
- Laboratoire de Biologie Moléculaire d'Epidémiologie et de Surveillance des agents Transmissibles par les Aliments (LABESTA) Unité de Formation et de la Recherche en Sciences de la Vie et de la Terre Ecole Doctorale Sciences et Technologies Université Ouaga I Pr Joseph Ki-Zerbo Ouagadougou Burkina Faso
| | - Yves Traoré
- Laboratoire de Biochimie et d'Immunologie Appliquée (LABIA) Unité de Formation et de la Recherche en Sciences de la Vie et de la Terre Ecole Doctorale Sciences et Technologies Université Ouaga I Pr Joseph Ki-Zerbo Ouagadougou Burkina Faso
| | - Jacques Mahillon
- Faculté d'ingénierie Biologique Agronomique et Environnementale Université catholique de Louvain Louvain-la-Neuve Belgium
| | - Marie-Louise Scippo
- Département des Sciences des Denrées alimentaires Centre de recherche FARAH-Secteur Santé Publique Vétérinaire Université de Liège Liège Belgium
| | - Joseph D Hounhouigan
- Laboratoire de Biochimie Microbienne et de Biotechnologie Alimentaires Université d'Abomey Calavi Abomey Calavi Benin
| | - Aly Savadogo
- Laboratoire de Biochimie et d'Immunologie Appliquée (LABIA) Unité de Formation et de la Recherche en Sciences de la Vie et de la Terre Ecole Doctorale Sciences et Technologies Université Ouaga I Pr Joseph Ki-Zerbo Ouagadougou Burkina Faso
| |
Collapse
|
25
|
Qi M, Wang Q, Tong S, Zhao G, Hu C, Chen Y, Li X, Yang W, Zhao Y, Platto S, Duncan RI, Chen J, Chen H, Guo A. Identification of Atypical Enteropathogenic Escherichia coli O98 from Golden Snub-Nosed Monkeys with Diarrhea in China. Front Vet Sci 2018; 4:217. [PMID: 29326951 PMCID: PMC5733351 DOI: 10.3389/fvets.2017.00217] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Accepted: 11/30/2017] [Indexed: 12/03/2022] Open
Abstract
Fecal samples (n = 76) were collected from 38 snub-nosed monkeys (Rhinopithecus roxellana) in Shennongjia National Nature Reserve (China) and examined for the presence of enteropathogenic Escherichia coli (EPEC). The 56 samples originated from 30 free-ranging monkeys on the reserve and 20 samples from 8 captive monkeys that were previously rescued and kept at the research center. Eight diarrhea samples were collected from four of the eight captive monkeys (two samples from each monkey), and two EPEC strains (2.6%) (95% confidence interval 0.3–9.2%) were isolated from two fecal samples from two diarrheic monkeys. Both strains belonged to serotype O98 and phylogenetic group D (TspE4C2+, ChuA+). The virulence gene detection identified these strains as an atypical EPEC (aEPEC) (bfpB–, stx1–, and stx2–) with the subtype eae+, escV+, and intiminβ+. These strains were highly sensitive to all the antibiotics tested. The lethal dose 50% of the two isolates in Kunming mice was 7.40 × 108 CFU/0.2 mL and 2.40 × 108 CFU/0.2 mL, respectively, indicating low virulence. Based on the report that this serotype had been isolated from some other non-human animals and humans with diarrhea, the first identification of aEPEC O98 strains and their drug resistance profile in R. roxellana is of ecological significance for disease control in this endangered species.
Collapse
Affiliation(s)
- Mingpu Qi
- State Key Laboratory of Agricultural Microbiology, Wuhan, China.,College of Veterinary Medicine, Wuhan, China
| | - Qiankun Wang
- State Key Laboratory of Agricultural Microbiology, Wuhan, China.,College of Veterinary Medicine, Wuhan, China
| | | | - Gang Zhao
- State Key Laboratory of Agricultural Microbiology, Wuhan, China.,College of Veterinary Medicine, Wuhan, China
| | - Changmin Hu
- College of Veterinary Medicine, Wuhan, China
| | - Yingyu Chen
- College of Veterinary Medicine, Wuhan, China
| | - Xiang Li
- College of Animal Science, Wuhan, China
| | - Wanji Yang
- Hubei Conservation and Research Center for the Golden Monkey, Shennongjia, China.,Hubei Province Key Laboratory of Conservation Biology of Shennongjia Golden Monkey, Shennongjia, China
| | - Yuchen Zhao
- Hubei Conservation and Research Center for the Golden Monkey, Shennongjia, China.,Hubei Province Key Laboratory of Conservation Biology of Shennongjia Golden Monkey, Shennongjia, China
| | - Sara Platto
- College of Veterinary Medicine, Wuhan, China
| | - Robertson Ian Duncan
- State Key Laboratory of Agricultural Microbiology, Wuhan, China.,College of Veterinary Medicine, Wuhan, China.,China-Australia International Joint Research and Training Centre for Veterinary Epidemiology, Huazhong Agricultural University, Wuhan, China
| | | | - Huanchun Chen
- State Key Laboratory of Agricultural Microbiology, Wuhan, China.,College of Veterinary Medicine, Wuhan, China
| | - Aizhen Guo
- State Key Laboratory of Agricultural Microbiology, Wuhan, China.,College of Veterinary Medicine, Wuhan, China.,China-Australia International Joint Research and Training Centre for Veterinary Epidemiology, Huazhong Agricultural University, Wuhan, China
| |
Collapse
|
26
|
Bako E, Kagambèga A, Traore KA, Bagre TS, Ibrahim HB, Bouda SC, Bonkoungou IJO, Kaboré S, Zongo C, Traore AS, Barro N. Characterization of Diarrheagenic Escherichia coli Isolated in Organic Waste Products (Cattle Fecal Matter, Manure and, Slurry) from Cattle's Markets in Ouagadougou, Burkina Faso. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2017; 14:ijerph14101100. [PMID: 28937656 PMCID: PMC5664601 DOI: 10.3390/ijerph14101100] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 09/13/2017] [Accepted: 09/14/2017] [Indexed: 11/16/2022]
Abstract
Cattle farming can promote diarrheal disease transmission through waste, effluents or cattle fecal matter. The study aims to characterize the diarrheagenic Escherichia coli (DEC) isolated from cattle feces, manure in the composting process and slurry, collected from four cattle markets in Ouagadougou. A total of 585 samples (340 cattle feces, 200 slurries and 45 manures in the composting process) were collected from the four cattle markets between May 2015 and May 2016. A multiplex Polymerase Chain Reaction (PCR), namely 16-plex PCR, was used to screen simultaneously the virulence genes specific for shiga toxin-producing E. coli (STEC), enteropathogenic E. coli (EPEC), enterotoxigenic E. coli (ETEC), enteroinvasive E. coli (EIEC) and enteroaggregative E. coli (EAEC). DEC was detected in 10.76% of samples. ETEC was the most prevalent (9.91%). STEC and EAEC have been observed with the same rate (0.51%). ETEC were detected in 12.64% of cattle feces, in 6.66% of manure in the composting process and in 5% of slurry. STEC were detected in 0.58% of cattle feces and in 2.22% of manure in the composting process. EAEC was detected only in 1% of slurry and in 2.22% of manure in the composting process. ETEC strains were identified based on estIa gene and/or estIb gene and/or elt gene amplification. Of the 58 ETEC, 10.34% contained astA, 17.24% contained elt, 3.44% contained estIa and 79.31% contained estIb. The two positive EAEC strains contained only the aggR gene, and the third was positive only for the pic gene. The results show that effluent from cattle markets could contribute to the spreading of DEC in the environment in Burkina Faso.
Collapse
Affiliation(s)
- Evariste Bako
- Laboratoire de Biologie Moléculaire d'Epidémiologie et de Surveillance des Bactéries et Virus Transmis par les Aliments (LaBESTA), Centre de Recherche en Sciences Biologiques, Alimentaires et Nutritionnelles (CRSBAN), Université Ouaga I Prof Joseph KI-ZERBO, 03 BP 7021 Ouagadougou 03, Burkina Faso.
| | - Assèta Kagambèga
- Laboratoire de Biologie Moléculaire d'Epidémiologie et de Surveillance des Bactéries et Virus Transmis par les Aliments (LaBESTA), Centre de Recherche en Sciences Biologiques, Alimentaires et Nutritionnelles (CRSBAN), Université Ouaga I Prof Joseph KI-ZERBO, 03 BP 7021 Ouagadougou 03, Burkina Faso.
- Institut de Sciences, 01 BP 1757 Ouagadougou 01, Burkina Faso.
| | - Kuan Abdoulaye Traore
- Laboratoire de Biologie Moléculaire d'Epidémiologie et de Surveillance des Bactéries et Virus Transmis par les Aliments (LaBESTA), Centre de Recherche en Sciences Biologiques, Alimentaires et Nutritionnelles (CRSBAN), Université Ouaga I Prof Joseph KI-ZERBO, 03 BP 7021 Ouagadougou 03, Burkina Faso.
| | - Touwendsida Serge Bagre
- Laboratoire de Biologie Moléculaire d'Epidémiologie et de Surveillance des Bactéries et Virus Transmis par les Aliments (LaBESTA), Centre de Recherche en Sciences Biologiques, Alimentaires et Nutritionnelles (CRSBAN), Université Ouaga I Prof Joseph KI-ZERBO, 03 BP 7021 Ouagadougou 03, Burkina Faso.
| | - Hadiza Bawa Ibrahim
- Laboratoire de Biologie Moléculaire d'Epidémiologie et de Surveillance des Bactéries et Virus Transmis par les Aliments (LaBESTA), Centre de Recherche en Sciences Biologiques, Alimentaires et Nutritionnelles (CRSBAN), Université Ouaga I Prof Joseph KI-ZERBO, 03 BP 7021 Ouagadougou 03, Burkina Faso.
| | - Soutongnooma Caroline Bouda
- Laboratoire de Biologie Moléculaire d'Epidémiologie et de Surveillance des Bactéries et Virus Transmis par les Aliments (LaBESTA), Centre de Recherche en Sciences Biologiques, Alimentaires et Nutritionnelles (CRSBAN), Université Ouaga I Prof Joseph KI-ZERBO, 03 BP 7021 Ouagadougou 03, Burkina Faso.
| | - Isidore Juste Ouindgueta Bonkoungou
- Laboratoire de Biologie Moléculaire d'Epidémiologie et de Surveillance des Bactéries et Virus Transmis par les Aliments (LaBESTA), Centre de Recherche en Sciences Biologiques, Alimentaires et Nutritionnelles (CRSBAN), Université Ouaga I Prof Joseph KI-ZERBO, 03 BP 7021 Ouagadougou 03, Burkina Faso.
| | - Saidou Kaboré
- Laboratoire de Biologie Moléculaire d'Epidémiologie et de Surveillance des Bactéries et Virus Transmis par les Aliments (LaBESTA), Centre de Recherche en Sciences Biologiques, Alimentaires et Nutritionnelles (CRSBAN), Université Ouaga I Prof Joseph KI-ZERBO, 03 BP 7021 Ouagadougou 03, Burkina Faso.
- Direction de la Nutrition, Ministère de la Santé, 03 BP 7068 Ouagadougou 03, Burkina Faso.
| | - Cheikna Zongo
- Laboratoire de Biochimie et d'Immunologie Appliquée (LABIA), Centre de Recherche en Sciences Biologiques Alimentaires et Nutritionnelles (CRSBAN), Université Ouaga I Professeur Joseph KI-ZERBO, 03 BP 7131 Ouagadougou 03, Burkina Faso.
| | - Alfred Sababenejo Traore
- Centre de Recherche en Sciences Biologiques Alimentaires et Nutritionnelles (CRSBAN), Université Ouaga I Professeur Joseph KI-ZERBO, 03 BP 7131 Ouagadougou 03, Burkina Faso.
| | - Nicolas Barro
- Laboratoire de Biologie Moléculaire d'Epidémiologie et de Surveillance des Bactéries et Virus Transmis par les Aliments (LaBESTA), Centre de Recherche en Sciences Biologiques, Alimentaires et Nutritionnelles (CRSBAN), Université Ouaga I Prof Joseph KI-ZERBO, 03 BP 7021 Ouagadougou 03, Burkina Faso.
| |
Collapse
|
27
|
Konaté A, Dembélé R, Guessennd NK, Kouadio FK, Kouadio IK, Ouattara MB, Kaboré WAD, Kagambèga A, Cissé H, Ibrahim HB, Bagré TS, Traoré AS, Barro N. Epidemiology and Antibiotic Resistance Phenotypes of Diarrheagenic Escherichia Coli Responsible for Infantile Gastroenteritis in Ouagadougou, Burkina Faso. Eur J Microbiol Immunol (Bp) 2017; 7:168-175. [PMID: 29034106 PMCID: PMC5632744 DOI: 10.1556/1886.2017.00014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 08/08/2017] [Indexed: 01/22/2023] Open
Abstract
The emergence and persistence of multidrug-resistant (MDR) diarrheagenic Escherichia coli (DEC) causing acute diarrhea is a major public health challenge in developing countries. The aim of this study was to evaluate the resistance phenotypes of DEC isolated from stool samples collected from children less than 5 years of age with acute diarrhea living in Ouagadougou/Burkina Faso. From August 2013 to October 2015, this study was carried out on 31 DEC strains of our study conducted in "Centre Médical avec Antenne Chirurgicale (CMA)" Paul VI and CMA of Schiphra. DEC were isolated and identified by standard microbiological methods and polymerase chain reaction (PCR) method was used to further characterize them. Antimicrobial susceptibility testing was done based on the disk diffusion method. DEC isolates were high resistant to tetracycline (83.9%), amoxicillin (77.4%), amoxicillin clavulanic acid (77.4%), piperacillin (64.5%), and colistin sulfate (61.3%). The most resistant phenotype represented was the extended spectrum β-lactamase (ESBL) phenotype (67.7%). Aminoglycosides were 100% active on enteroinvasive E. coli (EIEC) and enterohemorrhagic E. coli (EHEC). All the DEC isolates exhibited absolute (100%) sensitivity to ciprofloxacin. Monitoring and studying the resistance profile of DEC to antibiotics are necessary to guide probabilistic antibiotic therapy, especially in pediatric patients.
Collapse
Affiliation(s)
- Ali Konaté
- Laboratoire de Biologie Moléculaire, d’Épidémiologie et de Surveillance des Bactéries et Virus Transmissibles par les Aliments (LaBESTA)/Centre de Recherche en Sciences Biologiques, Alimentaires et Nutritionnelles (CRSBAN)/Ecole Doctorale Sciences et Technologies (EDST)/Université Ouaga I Professeur Joseph KI-ZERBO, 03 BP 7021 Ouagadougou 03, Burkina Faso, Africa
| | - René Dembélé
- Laboratoire de Biologie Moléculaire, d’Épidémiologie et de Surveillance des Bactéries et Virus Transmissibles par les Aliments (LaBESTA)/Centre de Recherche en Sciences Biologiques, Alimentaires et Nutritionnelles (CRSBAN)/Ecole Doctorale Sciences et Technologies (EDST)/Université Ouaga I Professeur Joseph KI-ZERBO, 03 BP 7021 Ouagadougou 03, Burkina Faso, Africa
| | - Nathalie K. Guessennd
- Laboratoire de Bactériologie-Virologie/Unité des Antibiotiques, des Substances Naturelles et de la Surveillance des Résistances des Micro-Organismes aux Anti-Infectieux (ASSURMI)/Institut Pasteur de Côte d’Ivoire, 01 BP 490 Abidjan 01
- Laboratoire de Bactériologie-Virologie/Unité de Formation et de Recherches des Sciences Médicales/Université Félix Houphouët Boigny, 01 BP V34 Abidjan 01, Côte d’Ivoire, Africa
| | - Fernique Konan Kouadio
- Laboratoire de Bactériologie-Virologie/Unité des Antibiotiques, des Substances Naturelles et de la Surveillance des Résistances des Micro-Organismes aux Anti-Infectieux (ASSURMI)/Institut Pasteur de Côte d’Ivoire, 01 BP 490 Abidjan 01
| | - Innocent Kouamé Kouadio
- Laboratoire de Bactériologie-Virologie/Unité des Antibiotiques, des Substances Naturelles et de la Surveillance des Résistances des Micro-Organismes aux Anti-Infectieux (ASSURMI)/Institut Pasteur de Côte d’Ivoire, 01 BP 490 Abidjan 01
| | - Mohamed Baguy Ouattara
- Laboratoire de Bactériologie-Virologie/Unité des Antibiotiques, des Substances Naturelles et de la Surveillance des Résistances des Micro-Organismes aux Anti-Infectieux (ASSURMI)/Institut Pasteur de Côte d’Ivoire, 01 BP 490 Abidjan 01
| | - Wendpoulomdé A. D. Kaboré
- Laboratoire de Biologie Moléculaire, d’Épidémiologie et de Surveillance des Bactéries et Virus Transmissibles par les Aliments (LaBESTA)/Centre de Recherche en Sciences Biologiques, Alimentaires et Nutritionnelles (CRSBAN)/Ecole Doctorale Sciences et Technologies (EDST)/Université Ouaga I Professeur Joseph KI-ZERBO, 03 BP 7021 Ouagadougou 03, Burkina Faso, Africa
| | - Assèta Kagambèga
- Laboratoire de Biologie Moléculaire, d’Épidémiologie et de Surveillance des Bactéries et Virus Transmissibles par les Aliments (LaBESTA)/Centre de Recherche en Sciences Biologiques, Alimentaires et Nutritionnelles (CRSBAN)/Ecole Doctorale Sciences et Technologies (EDST)/Université Ouaga I Professeur Joseph KI-ZERBO, 03 BP 7021 Ouagadougou 03, Burkina Faso, Africa
| | - Haoua Cissé
- Laboratoire de Biologie Moléculaire, d’Épidémiologie et de Surveillance des Bactéries et Virus Transmissibles par les Aliments (LaBESTA)/Centre de Recherche en Sciences Biologiques, Alimentaires et Nutritionnelles (CRSBAN)/Ecole Doctorale Sciences et Technologies (EDST)/Université Ouaga I Professeur Joseph KI-ZERBO, 03 BP 7021 Ouagadougou 03, Burkina Faso, Africa
| | - Hadiza Bawa Ibrahim
- Laboratoire de Biologie Moléculaire, d’Épidémiologie et de Surveillance des Bactéries et Virus Transmissibles par les Aliments (LaBESTA)/Centre de Recherche en Sciences Biologiques, Alimentaires et Nutritionnelles (CRSBAN)/Ecole Doctorale Sciences et Technologies (EDST)/Université Ouaga I Professeur Joseph KI-ZERBO, 03 BP 7021 Ouagadougou 03, Burkina Faso, Africa
| | - Touwendsida Serge Bagré
- Laboratoire de Biologie Moléculaire, d’Épidémiologie et de Surveillance des Bactéries et Virus Transmissibles par les Aliments (LaBESTA)/Centre de Recherche en Sciences Biologiques, Alimentaires et Nutritionnelles (CRSBAN)/Ecole Doctorale Sciences et Technologies (EDST)/Université Ouaga I Professeur Joseph KI-ZERBO, 03 BP 7021 Ouagadougou 03, Burkina Faso, Africa
| | - Alfred S. Traoré
- Laboratoire de Biologie Moléculaire, d’Épidémiologie et de Surveillance des Bactéries et Virus Transmissibles par les Aliments (LaBESTA)/Centre de Recherche en Sciences Biologiques, Alimentaires et Nutritionnelles (CRSBAN)/Ecole Doctorale Sciences et Technologies (EDST)/Université Ouaga I Professeur Joseph KI-ZERBO, 03 BP 7021 Ouagadougou 03, Burkina Faso, Africa
| | - Nicolas Barro
- Laboratoire de Biologie Moléculaire, d’Épidémiologie et de Surveillance des Bactéries et Virus Transmissibles par les Aliments (LaBESTA)/Centre de Recherche en Sciences Biologiques, Alimentaires et Nutritionnelles (CRSBAN)/Ecole Doctorale Sciences et Technologies (EDST)/Université Ouaga I Professeur Joseph KI-ZERBO, 03 BP 7021 Ouagadougou 03, Burkina Faso, Africa
| |
Collapse
|
28
|
Konaté A, Dembélé R, Kagambèga A, Soulama I, Kaboré WAD, Sampo E, Cissé H, Sanou A, Serme S, Zongo S, Zongo C, Fody AM, Guessennd NK, Traoré AS, Gassama-Sow A, Barro N. Molecular Characterization of Diarrheagenic Escherichia Coli in Children Less Than 5 Years of Age with Diarrhea in Ouagadougou, Burkina Faso. Eur J Microbiol Immunol (Bp) 2017; 7:220-228. [PMID: 29034111 PMCID: PMC5632749 DOI: 10.1556/1886.2017.00011] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 06/08/2017] [Indexed: 12/19/2022] Open
Abstract
Diarrheagenic Escherichia coli (DEC) is important bacteria of children’s endemic and epidemic diarrhea worldwide. The aim of this study was to determine the prevalence of DEC isolated from stool samples collected from children with acute diarrhea living in Ouagadougou, Burkina Faso. From August 2013 to October 2015, stool samples were collected from 315 children under 5 years of age suffering from diarrhea in the “Centre Médical avec Antenne Chirurgicale (CMA)” Paul VI and the CMA of Schiphra. E. coli were isolated and identified by standard microbiological methods, and the 16-plex PCR method was used to further characterize them. Four hundred and nineteen (419) E. coli strains were characterized, of which 31 (7.4%) DEC pathotypes were identified and classified in five E. coli pathotypes: 15 enteroaggregative E. coli (EAEC) (48.4%), 8 enteropathogenic E. coli (EPEC) (25.8%) with 4 typical EPEC and 4 atypical EPEC, 4 enteroinvasive E. coli (EIEC) (12.9%), 3 enterohemorrhagic E. coli (EHEC) 9.67%, and 1 enterotoxigenic E. coli (ETEC) 3.2%. The use of multiplex PCR as a routine in clinical laboratory for the detection of DEC would be a useful mean for a rapid management of an acute diarrhea in children.
Collapse
Affiliation(s)
- Ali Konaté
- Laboratoire de Biologie Moléculaire, d'Épidémiologie et de Surveillance des Bactéries et virus Transmissibles par les Aliments (LaBESTA)/Centre de Recherche en Sciences Biologiques, Alimentaires et Nutritionnelles (CRSBAN)/Ecole Doctorale Sciences et Technologies (EDST)/Université Ouaga I Professeur Joseph KI-ZERBO, 03 BP 7021 Ouagadougou 03, Burkina Faso
| | - René Dembélé
- Laboratoire de Biologie Moléculaire, d'Épidémiologie et de Surveillance des Bactéries et virus Transmissibles par les Aliments (LaBESTA)/Centre de Recherche en Sciences Biologiques, Alimentaires et Nutritionnelles (CRSBAN)/Ecole Doctorale Sciences et Technologies (EDST)/Université Ouaga I Professeur Joseph KI-ZERBO, 03 BP 7021 Ouagadougou 03, Burkina Faso
| | - Assèta Kagambèga
- Laboratoire de Biologie Moléculaire, d'Épidémiologie et de Surveillance des Bactéries et virus Transmissibles par les Aliments (LaBESTA)/Centre de Recherche en Sciences Biologiques, Alimentaires et Nutritionnelles (CRSBAN)/Ecole Doctorale Sciences et Technologies (EDST)/Université Ouaga I Professeur Joseph KI-ZERBO, 03 BP 7021 Ouagadougou 03, Burkina Faso
| | - Issiaka Soulama
- Centre National de Recherche et de Formation sur le Paludisme (CNRFP), 01 BP 2208 Ouagadougou 01, Burkina Faso
| | - Wendpoulomdé A D Kaboré
- Laboratoire de Biologie Moléculaire, d'Épidémiologie et de Surveillance des Bactéries et virus Transmissibles par les Aliments (LaBESTA)/Centre de Recherche en Sciences Biologiques, Alimentaires et Nutritionnelles (CRSBAN)/Ecole Doctorale Sciences et Technologies (EDST)/Université Ouaga I Professeur Joseph KI-ZERBO, 03 BP 7021 Ouagadougou 03, Burkina Faso
| | - Emmanuel Sampo
- Centre Médical avec Antenne Chirurgicale (CMA) de Schiphra, 07 BP 5246 Ouagadougou 07, Burkina Faso
| | - Haoua Cissé
- Laboratoire de Biologie Moléculaire, d'Épidémiologie et de Surveillance des Bactéries et virus Transmissibles par les Aliments (LaBESTA)/Centre de Recherche en Sciences Biologiques, Alimentaires et Nutritionnelles (CRSBAN)/Ecole Doctorale Sciences et Technologies (EDST)/Université Ouaga I Professeur Joseph KI-ZERBO, 03 BP 7021 Ouagadougou 03, Burkina Faso
| | - Antoine Sanou
- Centre National de Recherche et de Formation sur le Paludisme (CNRFP), 01 BP 2208 Ouagadougou 01, Burkina Faso
| | - Samuel Serme
- Centre National de Recherche et de Formation sur le Paludisme (CNRFP), 01 BP 2208 Ouagadougou 01, Burkina Faso
| | - Soumanaba Zongo
- Centre National de Recherche et de Formation sur le Paludisme (CNRFP), 01 BP 2208 Ouagadougou 01, Burkina Faso
| | - Cheikna Zongo
- Laboratoire de Biologie Moléculaire, d'Épidémiologie et de Surveillance des Bactéries et virus Transmissibles par les Aliments (LaBESTA)/Centre de Recherche en Sciences Biologiques, Alimentaires et Nutritionnelles (CRSBAN)/Ecole Doctorale Sciences et Technologies (EDST)/Université Ouaga I Professeur Joseph KI-ZERBO, 03 BP 7021 Ouagadougou 03, Burkina Faso
| | - Alio Mahamadou Fody
- Laboratoire de Biologie Moléculaire, d'Épidémiologie et de Surveillance des Bactéries et virus Transmissibles par les Aliments (LaBESTA)/Centre de Recherche en Sciences Biologiques, Alimentaires et Nutritionnelles (CRSBAN)/Ecole Doctorale Sciences et Technologies (EDST)/Université Ouaga I Professeur Joseph KI-ZERBO, 03 BP 7021 Ouagadougou 03, Burkina Faso.,Laboratoire de Biochimie Hôpital National de Niamey (HNN) BP 238, Niamey, Niger
| | - Nathalie K Guessennd
- Département de bactériologie et de virologie, Institut Pasteur de Côte d'Ivoire (IPCI), 01 BP 490, Abidjan 01, Côte d'Ivoire
| | - Alfred S Traoré
- Laboratoire de Biologie Moléculaire, d'Épidémiologie et de Surveillance des Bactéries et virus Transmissibles par les Aliments (LaBESTA)/Centre de Recherche en Sciences Biologiques, Alimentaires et Nutritionnelles (CRSBAN)/Ecole Doctorale Sciences et Technologies (EDST)/Université Ouaga I Professeur Joseph KI-ZERBO, 03 BP 7021 Ouagadougou 03, Burkina Faso
| | - Amy Gassama-Sow
- Unité de Bactériologie Expérimentale/Institut Pasteur de Dakar, BP 220 Dakar, Senegal
| | - Nicolas Barro
- Laboratoire de Biologie Moléculaire, d'Épidémiologie et de Surveillance des Bactéries et virus Transmissibles par les Aliments (LaBESTA)/Centre de Recherche en Sciences Biologiques, Alimentaires et Nutritionnelles (CRSBAN)/Ecole Doctorale Sciences et Technologies (EDST)/Université Ouaga I Professeur Joseph KI-ZERBO, 03 BP 7021 Ouagadougou 03, Burkina Faso
| |
Collapse
|
29
|
Touwendsida SB, Bissoume SB, Hadiza BI, Gertrude BT, Rene D, Abdoul AW, Evariste B, Alfred ST, Nicolas B, Amy GS. Isolation and characterization of enteropathogenic and enterotoxinogenic Escherichia coli from dairy products consumed in Burkina Faso. ACTA ACUST UNITED AC 2017. [DOI: 10.5897/ajmr2017.8485] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
|
30
|
Chau ML, Aung KT, Hapuarachchi HC, Lee PSV, Lim PY, Kang JSL, Ng Y, Yap HM, Yuk HG, Gutiérrez RA, Ng LC. Microbial survey of ready-to-eat salad ingredients sold at retail reveals the occurrence and the persistence of Listeria monocytogenes Sequence Types 2 and 87 in pre-packed smoked salmon. BMC Microbiol 2017; 17:46. [PMID: 28245788 PMCID: PMC5331722 DOI: 10.1186/s12866-017-0956-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 02/14/2017] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND As the preparation of salads involves extensive handling and the use of uncooked ingredients, they are particularly vulnerable to microbial contamination. This study aimed to determine the microbial safety and quality of pre-packed salads and salad bar ingredients sold in Singapore, so as to identify public health risks that could arise from consuming salads and to determine areas for improvement in the management of food safety. RESULTS The most frequently encountered organism in pre-packed salad samples was B. cereus, particularly in pasta salads (33.3%, 10/30). The most commonly detected organism in salad bar ingredients was L. monocytogenes, in particular seafood ingredients (44.1%, 15/34), largely due to contaminated smoked salmon. Further investigation showed that 21.6% (37/171) of the pre-packed smoked salmon sold in supermarkets contained L. monocytogenes. Significantly higher prevalence of L. monocytogenes and higher Standard Plate Count were detected in smoked salmon at salad bars compared to pre-packed smoked salmon in supermarkets, which suggested multiplication of the organism as the products move down the supply chain. Further molecular analysis revealed that L. monocytogenes Sequence Type (ST) 2 and ST87 were present in a particular brand of pre-packed salmon products over a 4-year period, implying a potential persistent contamination problem at the manufacturing level. CONCLUSIONS Our findings highlighted a need to improve manufacturing and retail hygiene processes as well as to educate vulnerable populations to avoid consuming food prone to L. monocytogenes contamination.
Collapse
Affiliation(s)
- Man Ling Chau
- Environmental Health Institute, National Environment Agency, 11 Biopolis Way, #04-03/04, Helios Block, Singapore, 138667 Singapore
| | - Kyaw Thu Aung
- Environmental Health Institute, National Environment Agency, 11 Biopolis Way, #04-03/04, Helios Block, Singapore, 138667 Singapore
| | | | - Pei Sze Valarie Lee
- Department of Chemistry, Food Science and Technology Programme, National University of Singapore, 3 Science Drive 3, Singapore, 117543 Singapore
| | - Pei Ying Lim
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551 Singapore
| | - Joanne Su Lin Kang
- Environmental Health Institute, National Environment Agency, 11 Biopolis Way, #04-03/04, Helios Block, Singapore, 138667 Singapore
| | - Youming Ng
- Environmental Health Institute, National Environment Agency, 11 Biopolis Way, #04-03/04, Helios Block, Singapore, 138667 Singapore
| | - Hooi Ming Yap
- Environmental Health Institute, National Environment Agency, 11 Biopolis Way, #04-03/04, Helios Block, Singapore, 138667 Singapore
| | - Hyun-Gyun Yuk
- Department of Chemistry, Food Science and Technology Programme, National University of Singapore, 3 Science Drive 3, Singapore, 117543 Singapore
| | - Ramona Alikiiteaga Gutiérrez
- Environmental Health Institute, National Environment Agency, 11 Biopolis Way, #04-03/04, Helios Block, Singapore, 138667 Singapore
| | - Lee Ching Ng
- Environmental Health Institute, National Environment Agency, 11 Biopolis Way, #04-03/04, Helios Block, Singapore, 138667 Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551 Singapore
| |
Collapse
|
31
|
Kim Y, Kim HJ, Lim S, Bae KS, Han SB, Jeong DC, Kang JH, Shin GJ, Lee GD, Park YJ. Community-acquired Escherichia coli Enteritis in Korean Children: The Clinical Application of a Stool Polymerase Chain Reaction Assay. Infect Chemother 2017; 49:275-281. [PMID: 29299895 PMCID: PMC5754338 DOI: 10.3947/ic.2017.49.4.275] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 11/28/2017] [Indexed: 01/31/2023] Open
Abstract
Background Although Escherichia coli is a common cause of bacterial enteritis in Korea, reports on community-acquired E. coli enteritis in Korean children are scarce. This study aimed to determine the clinical characteristics and pathotype distribution of community-acquired E. coli enteritis diagnosed by a multiplex polymerase chain reaction (PCR) assay in Korean children. Materials and Methods The medical records of children aged 18 years or less who were diagnosed with acute gastroenteritis by the attending physician between 2013 and 2016 were retrospectively reviewed. The clinical characteristics of children diagnosed with E. coli enteritis were investigated and compared with those diagnosed with Salmonella enteritis. E. coli and Salmonella infections were diagnosed by a stool PCR assay. Results Among 279 children, in whom PCR assays for E. coli and Salmonella spp. were performed, Salmonella enteritis and E. coli enteritis were diagnosed in 43 (15.4%) and 39 (14.0%) children, respectively. Among the 39 children with E. coli enteritis, enteropathogenic E. coli (n=21, 53.8%) and enteroaggregative E. coli (n=15, 38.4%) were the most common causative agents. Empirical antibiotics were administered to 33 (84.6%) children. A total of 31 (79.5%) children developed fever, and 25 (80.6%) of them had the fever for 3 days or less, which resolved a median of 1 day (range 0-3 days) after hospitalization. The most frequent gastrointestinal symptom was diarrhea (n=36, 92.3%). Significantly more children with E. coli enteritis were aged 2 years or less as compared with those with Salmonella enteritis (41.0% vs. 21.9%, P = 0.021). Children with Salmonella enteritis more frequently complained of fever (97.7% vs. 79.5%, P = 0.012), abdominal pain (90.7% vs. 64.1%, P = 0.004), and hematochezia (46.5% vs. 10.3%, P <0.001) than those with E. coli enteritis. Erythrocyte sedimentation rate and C-reactive protein levels were significantly higher in children with Salmonella enteritis than those with E. coli enteritis (P <0.001). Conclusion Enteropathogenic E. coli was the most frequent pathotype in Korean children with E. coli enteritis that caused mild clinical symptoms. A stool PCR assay for E. coli may be useful for epidemiological purpose and for an early diagnosis of E. coli enteritis.
Collapse
Affiliation(s)
- Youie Kim
- Department of Pediatrics, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Hyo Jin Kim
- Department of Pediatrics, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Sooyeon Lim
- Department of Pediatrics, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Kil Seong Bae
- Department of Pediatrics, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea.,The Vaccine Bio Research Institute, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Seung Beom Han
- Department of Pediatrics, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea.,The Vaccine Bio Research Institute, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea.
| | - Dae Chul Jeong
- Department of Pediatrics, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea.,The Vaccine Bio Research Institute, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jin Han Kang
- Department of Pediatrics, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea.,The Vaccine Bio Research Institute, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Gook Jae Shin
- Department of Laboratory Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Gun Dong Lee
- Department of Laboratory Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Yeon Joon Park
- Department of Laboratory Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| |
Collapse
|
32
|
Gomes TAT, Elias WP, Scaletsky ICA, Guth BEC, Rodrigues JF, Piazza RMF, Ferreira LCS, Martinez MB. Diarrheagenic Escherichia coli. Braz J Microbiol 2016; 47 Suppl 1:3-30. [PMID: 27866935 PMCID: PMC5156508 DOI: 10.1016/j.bjm.2016.10.015] [Citation(s) in RCA: 247] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Accepted: 10/27/2016] [Indexed: 12/22/2022] Open
Abstract
Most Escherichia coli strains live harmlessly in the intestines and rarely cause disease in healthy individuals. Nonetheless, a number of pathogenic strains can cause diarrhea or extraintestinal diseases both in healthy and immunocompromised individuals. Diarrheal illnesses are a severe public health problem and a major cause of morbidity and mortality in infants and young children, especially in developing countries. E. coli strains that cause diarrhea have evolved by acquiring, through horizontal gene transfer, a particular set of characteristics that have successfully persisted in the host. According to the group of virulence determinants acquired, specific combinations were formed determining the currently known E. coli pathotypes, which are collectively known as diarrheagenic E. coli. In this review, we have gathered information on current definitions, serotypes, lineages, virulence mechanisms, epidemiology, and diagnosis of the major diarrheagenic E. coli pathotypes.
Collapse
Affiliation(s)
- Tânia A T Gomes
- Universidade Federal de São Paulo, Escola Paulista de Medicina, Departamento de Microbiologia, Imunologia e Parasitologia, São Paulo, SP, Brazil.
| | - Waldir P Elias
- Instituto Butantan, Laboratório de Bacterologia, São Paulo, SP, Brazil
| | - Isabel C A Scaletsky
- Universidade Federal de São Paulo, Escola Paulista de Medicina, Departamento de Microbiologia, Imunologia e Parasitologia, São Paulo, SP, Brazil
| | - Beatriz E C Guth
- Universidade Federal de São Paulo, Escola Paulista de Medicina, Departamento de Microbiologia, Imunologia e Parasitologia, São Paulo, SP, Brazil
| | - Juliana F Rodrigues
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brazil
| | - Roxane M F Piazza
- Instituto Butantan, Laboratório de Bacterologia, São Paulo, SP, Brazil
| | - Luís C S Ferreira
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brazil
| | - Marina B Martinez
- Universidade de São Paulo, Faculdade de Ciências Farmacêuticas, Departamento de Análises Clínicas e Toxicológicas, São Paulo, SP, Brazil
| |
Collapse
|
33
|
Rintala A, Munukka E, Weintraub A, Ullberg M, Eerola E. Evaluation of a multiplex real-time PCR kit Amplidiag® Bacterial GE in the detection of bacterial pathogens from stool samples. J Microbiol Methods 2016; 128:61-65. [DOI: 10.1016/j.mimet.2016.07.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 07/13/2016] [Accepted: 07/14/2016] [Indexed: 02/04/2023]
|
34
|
Trainor E, Iturriza-Gómara M, Ngwira B, Cunliffe N. Detection of enterotoxigenic E. coli in hospitalised children with and without diarrhoea in Blantyre, Malawi. Paediatr Int Child Health 2016; 36:102-5. [PMID: 25940596 DOI: 10.1179/2046905515y.0000000014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
BACKGROUND Enterotoxigenic E. coli (ETEC) is an important cause of diarrhoea among children in developing countries. The burden of ETEC infection was investigated for the first time in children in Malawi. METHODS Faecal samples obtained from children < 5 years of age hospitalised with diarrhoea in Blantyre, Malawi over a 10-year period (1997-2007) before introduction of the rotavirus vaccine were examined by PCR for ETEC heat-labile (LT) and heat-stable (STh and STp) enterotoxins. Children hospitalised without diarrhoea were enrolled over a 2-year period as a comparison group. RESULTS ETEC was detected in 205 (10.6%) of 1941 children with diarrhoea. The most prevalent toxin type was STh (6·6%), followed by LT (2·1%) and STp (0·9%). ETEC infection was most prevalent in infants aged 6-11 months. Co-infection with rotavirus was common. ETEC was detected in 37 (7·3%) of 507 children without diarrhoea. CONCLUSION The burden of ETEC infection in young Malawian children is substantial and should become a focus of diarrhoea prevention efforts in the post-rotavirus vaccine era.
Collapse
Affiliation(s)
- Eamonn Trainor
- a Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health , University of Liverpool , UK
| | - Miren Iturriza-Gómara
- a Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health , University of Liverpool , UK
| | - Bagrey Ngwira
- b Department of Community Health, College of Medicine , University of Malawi, Blantyre , Malawi
| | - Nigel Cunliffe
- a Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health , University of Liverpool , UK
| |
Collapse
|
35
|
Franz E, Veenman C, van Hoek AHAM, de Roda Husman A, Blaak H. Pathogenic Escherichia coli producing Extended-Spectrum β-Lactamases isolated from surface water and wastewater. Sci Rep 2015; 5:14372. [PMID: 26399418 PMCID: PMC4585870 DOI: 10.1038/srep14372] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 08/17/2015] [Indexed: 11/10/2022] Open
Abstract
To assess public health risks from environmental exposure to Extended-Spectrum β-Lactamases (ESBL)-producing bacteria, it is necessary to have insight in the proportion of relative harmless commensal variants and potentially pathogenic ones (which may directly cause disease). In the current study, 170 ESBL-producing E. coli from Dutch wastewater (n = 82) and surface water (n = 88) were characterized with respect to ESBL-genotype, phylogenetic group, resistance phenotype and virulence markers associated with enteroaggregative E. coli (EAEC), enteroinvasive E. coli (EIEC), enteropathogenic E. coli (EPEC), enterotoxigenic E. coli (ETEC), extraintesinal E. coli (ExPEC), and Shiga toxin-producing E. coli (STEC). Overall, 17.1% of all ESBL-producing E. coli were suspected pathogenic variants. Suspected ExPECs constituted 8.8% of all ESBL-producing variants and 8.3% were potential gastrointestinal pathogens (4.1% EAEC, 1.8% EPEC, 1.2% EIEC, 1.2% ETEC, no STEC). Suspected pathogens were significantly associated with ESBL-genotype CTX-M-15 (X2 = 14.7, P < 0.001) and phylogenetic group B2 (X2 = 23.5, P < 0.001). Finally, 84% of the pathogenic ESBL-producing E. coli isolates were resistant to three or more different classes of antibiotics. In conclusion, this study demonstrates that the aquatic environment is a potential reservoir of E. coli variants that combine ESBL-genes, a high level of multi-drug resistance and virulence factors, and therewith pose a health risk to humans upon exposure.
Collapse
Affiliation(s)
- Eelco Franz
- National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, Bilthoven, The Netherlands
| | - Christiaan Veenman
- National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, Bilthoven, The Netherlands
| | - Angela H A M van Hoek
- National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, Bilthoven, The Netherlands
| | - Ana de Roda Husman
- National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, Bilthoven, The Netherlands
| | - Hetty Blaak
- National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, Bilthoven, The Netherlands
| |
Collapse
|
36
|
Pankhurst L, Macfarlane-Smith L, Buchanan J, Anson L, Davies K, O'Connor L, Ashwin H, Pike G, Dingle KE, Peto TE, Wordsworth S, Walker AS, Wilcox MH, Crook DW. Can rapid integrated polymerase chain reaction-based diagnostics for gastrointestinal pathogens improve routine hospital infection control practice? A diagnostic study. Health Technol Assess 2015; 18:1-167. [PMID: 25146932 DOI: 10.3310/hta18530] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Every year approximately 5000-9000 patients are admitted to a hospital with diarrhoea, which in up to 90% of cases has a non-infectious cause. As a result, single rooms are 'blocked' by patients with non-infectious diarrhoea, while patients with infectious diarrhoea are still in open bays because of a lack of free side rooms. A rapid test for differentiating infectious from non-infectious diarrhoea could be very beneficial for patients. OBJECTIVE To evaluate MassCode multiplex polymerase chain reaction (PCR) for the simultaneous diagnosis of multiple enteropathogens directly from stool, in terms of sensitivity/specificity to detect four common important enteropathogens: Clostridium difficile, Campylobacter spp., Salmonella spp. and norovirus. DESIGN A retrospective study of fixed numbers of samples positive for C. difficile (n = 200), Campylobacter spp. (n = 200), Salmonella spp. (n = 100) and norovirus (n = 200) plus samples negative for all these pathogens (n = 300). Samples were sourced from NHS microbiology laboratories in Oxford and Leeds where initial diagnostic testing was performed according to Public Health England methodology. Researchers carrying out MassCode assays were blind to this information. A questionnaire survey, examining current practice for infection control teams and microbiology laboratories managing infectious diarrhoea, was also carried out. SETTING MassCode assays were carried out at Oxford University Hospitals NHS Trust. Further multiplex assays, carried out using Luminex, were run on the same set of samples at Leeds Teaching Hospitals NHS Trust. The questionnaire was completed by various NHS trusts. MAIN OUTCOME MEASURES Sensitivity and specificity to detect C. difficile, Campylobacter spp., Salmonella spp., and norovirus. RESULTS Nucleic acids were extracted from 948 clinical samples using an optimised protocol (200 Campylobacter spp., 199 C. difficile, 60 S. enterica, 199 norovirus and 295 negative samples; some samples contained more than one pathogen). Using the MassCode assay, sensitivities for each organism compared with standard microbiological testing ranged from 43% to 94% and specificities from 95% to 98%, with particularly poor performance for S. enterica. Relatively large numbers of unexpected positives not confirmed with quantitative PCR were also observed, particularly for S. enterica, Giardia lamblia and Cryptosporidium spp. As the results indicated that S. enterica detection might provide generic challenges to other multiplex assays for gastrointestinal pathogens, the Luminex xTag(®) gastrointestinal assay was also run blinded on the same extracts (937/948 remaining) and on re-extracted samples (839/948 with sufficient material). For Campylobacter spp., C. difficile and norovirus, high sensitivities (> 92%) and specificities (> 96%) were observed. For S. enterica, on the original MassCode/Oxford extracts, Luminex sensitivity compared with standard microbiological testing was 84% [95% confidence interval (CI) 73% to 93%], but this dropped to 46% on a fresh extract, very similar to MassCode, with a corresponding increase in specificity from 92% to 99%. Overall agreement on the per-sample diagnosis compared with combined microbiology plus PCR for the main four/all pathogens was 85.6%/64.7%, 87.0%/82.9% and 89.8%/86.8% for the MassCode assay, Luminex assay/MassCode extract and Luminex assay/fresh extract, respectively. Luminex assay results from fresh extracts implied that 5% of samples did not represent infectious diarrhoea, even though enteropathogens were genuinely present. Managing infectious diarrhoea was a significant burden for infection control teams (taking 21% of their time) and better diagnostics were identified as having major potential benefits for patients. CONCLUSIONS Overall, the Luminex xTag gastrointestinal panel showed similar or superior sensitivity and specificity to the MassCode assay. However, on fresh extracts, this test had low sensitivity to detect a key enteric pathogen, S. enterica; making it an unrealistic option for most microbiology laboratories. Extraction efficiency appears to be a major obstacle for nucleic acid-based tests for this organism, and possibly the whole Enterobacteriaceae family. To improve workflows in service microbiology laboratories, to reduce workload for infection control practitioners, and to improve outcomes for NHS patients, further research on deoxyribonucleic acid-based multiplex gastrointestinal diagnostics is urgently needed. FUNDING The Health Technology Assessment programme of the National Institute for Health Research.
Collapse
Affiliation(s)
- Louise Pankhurst
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | | | - James Buchanan
- Health Economics Research Centre, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Luke Anson
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Kerrie Davies
- Leeds Teaching Hospitals NHS Trust, Leeds General Infirmary, Leeds, UK
| | - Lily O'Connor
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - Helen Ashwin
- University of Leeds, Microbiology, Leeds General Infirmary Old Medical School, Leeds, UK
| | - Graham Pike
- Oxford University Hospitals NHS Trust, Oxford, UK
| | - Kate E Dingle
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Timothy Ea Peto
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Sarah Wordsworth
- Health Economics Research Centre, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - A Sarah Walker
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Mark H Wilcox
- Leeds Teaching Hospitals NHS Trust, Leeds General Infirmary, Leeds, UK
| | - Derrick W Crook
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| |
Collapse
|
37
|
Ud-Din A, Wahid S. Relationship among Shigella spp. and enteroinvasive Escherichia coli (EIEC) and their differentiation. Braz J Microbiol 2015; 45:1131-8. [PMID: 25763015 PMCID: PMC4323284 DOI: 10.1590/s1517-83822014000400002] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 12/13/2013] [Indexed: 11/30/2022] Open
Abstract
Shigellosis produces inflammatory reactions and ulceration on the intestinal epithelium followed by bloody or mucoid diarrhea. It is caused by enteroinvasive E. coli (EIEC) as well as any species of the genus Shigella, namely, S. dysenteriae, S. flexneri, S. boydii, and S. sonnei. This current species designation of Shigella does not specify genetic similarity. Shigella spp. could be easily differentiated from E. coli, but difficulties observed for the EIEC-Shigella differentiation as both show similar biochemical traits and can cause dysentery using the same mode of invasion. Sequencing of multiple housekeeping genes indicates that Shigella has derived on several different occasions via acquisition of the transferable forms of ancestral virulence plasmids within commensal E. coli and form a Shigella-EIEC pathovar. EIEC showed lower expression of virulence genes compared to Shigella, hence EIEC produce less severe disease than Shigella spp. Conventional microbiological techniques often lead to confusing results concerning the discrimination between EIEC and Shigella spp. The lactose permease gene (lacY) is present in all E. coli strains but absent in Shigella spp., whereas β-glucuronidase gene (uidA) is present in both E. coli and Shigella spp. Thus uidA gene and lacY gene based duplex real-time PCR assay could be used for easy identification and differentiation of Shigella spp. from E. coli and in particular EIEC.
Collapse
Affiliation(s)
- Abu Ud-Din
- Identification and Subtyping of Enteric Pathogens International Centre for Diarrhoeal Disease Research in Bangladesh Dhaka Bangladesh Identification and Subtyping of Enteric Pathogens, International Centre for Diarrhoeal Disease Research in Bangladesh, Dhaka, Bangladesh
| | - Syeda Wahid
- Center for Food and Water Borne Disease International Centre for Diarrhoeal Disease Research in Bangladesh Dhaka Bangladesh Center for Food and Water Borne Disease, International Centre for Diarrhoeal Disease Research in Bangladesh, Dhaka, Bangladesh
| |
Collapse
|
38
|
Nyholm O, Heinikainen S, Pelkonen S, Hallanvuo S, Haukka K, Siitonen A. Hybrids of Shigatoxigenic and Enterotoxigenic Escherichia coli (STEC/ETEC) Among Human and Animal Isolates in Finland. Zoonoses Public Health 2015; 62:518-24. [PMID: 25571907 DOI: 10.1111/zph.12177] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Indexed: 11/28/2022]
Abstract
Diarrhoeagenic Escherichia coli (DEC) cause serious foodborne infections in humans. Total of 450 Shigatoxigenic E. coli (STEC) strains isolated from humans, animals and environment in Finland were examined by multiplex PCR targeting the virulence genes of various DEC pathogroups simultaneously. One per cent (3/291) of the human STEC and 14% (22/159) of the animal and environmental STEC had genes typically present in enterotoxigenic E. coli (ETEC). The strains possessed genes encoding both Shiga toxin 1 and/or 2 (stx1 and/or stx2 ) and ETEC-specific heat-stable (ST) enterotoxin Ia (estIa). The identified stx subtypes were stx1a, stx1c, stx2a, stx2d and stx2g. The three human STEC/ETEC strains were isolated from the patients with haemolytic uraemic syndrome and diarrhoea and from an asymptomatic carrier. The animal STEC/ETEC strains were isolated from cattle and moose. The human and animal STEC/ETEC strains belonged to 11 serotypes, of which O2:H27, O15:H16, O101:H-, O128:H8 and O141:H8 have previously been described to be associated with human disease. Identification of multiple virulence genes offers further information for assessing the virulence potential of STEC and other DEC. The emergence of novel hybrid pathogens should be taken into account in the patient care and epidemiological surveillance.
Collapse
Affiliation(s)
- O Nyholm
- Bacteriology Unit, National Institute for Health and Welfare (THL), Helsinki, Finland
| | - S Heinikainen
- Veterinary Bacteriology Research Unit, Finnish Food Safety Authority Evira, Kuopio, Finland
| | - S Pelkonen
- Veterinary Bacteriology Research Unit, Finnish Food Safety Authority Evira, Kuopio, Finland
| | - S Hallanvuo
- Food and Feed Microbiology Research Unit, Finnish Food Safety Authority Evira, Helsinki, Finland
| | - K Haukka
- Bacteriology Unit, National Institute for Health and Welfare (THL), Helsinki, Finland.,Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - A Siitonen
- Bacteriology Unit, National Institute for Health and Welfare (THL), Helsinki, Finland
| |
Collapse
|
39
|
Novel microbiological and spatial statistical methods to improve strength of epidemiological evidence in a community-wide waterborne outbreak. PLoS One 2014; 9:e104713. [PMID: 25147923 PMCID: PMC4141750 DOI: 10.1371/journal.pone.0104713] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 07/16/2014] [Indexed: 12/14/2022] Open
Abstract
Failures in the drinking water distribution system cause gastrointestinal outbreaks with multiple pathogens. A water distribution pipe breakage caused a community-wide waterborne outbreak in Vuorela, Finland, July 2012. We investigated this outbreak with advanced epidemiological and microbiological methods. A total of 473/2931 inhabitants (16%) responded to a web-based questionnaire. Water and patient samples were subjected to analysis of multiple microbial targets, molecular typing and microbial community analysis. Spatial analysis on the water distribution network was done and we applied a spatial logistic regression model. The course of the illness was mild. Drinking untreated tap water from the defined outbreak area was significantly associated with illness (RR 5.6, 95% CI 1.9–16.4) increasing in a dose response manner. The closer a person lived to the water distribution breakage point, the higher the risk of becoming ill. Sapovirus, enterovirus, single Campylobacter jejuni and EHEC O157:H7 findings as well as virulence genes for EPEC, EAEC and EHEC pathogroups were detected by molecular or culture methods from the faecal samples of the patients. EPEC, EAEC and EHEC virulence genes and faecal indicator bacteria were also detected in water samples. Microbial community sequencing of contaminated tap water revealed abundance of Arcobacter species. The polyphasic approach improved the understanding of the source of the infections, and aided to define the extent and magnitude of this outbreak.
Collapse
|
40
|
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
|
41
|
Pasanen T, Koskela S, Mero S, Tarkka E, Tissari P, Vaara M, Kirveskari J. Rapid molecular characterization of Acinetobacter baumannii clones with rep-PCR and evaluation of carbapenemase genes by new multiplex PCR in Hospital District of Helsinki and Uusimaa. PLoS One 2014; 9:e85854. [PMID: 24465749 PMCID: PMC3897539 DOI: 10.1371/journal.pone.0085854] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2013] [Accepted: 12/02/2013] [Indexed: 12/25/2022] Open
Abstract
Multidrug-resistant Acinetobacter baumannii (MDRAB) is an increasing problem worldwide. Prevalence of carbapenem resistance in Acinetobacter spp. due to acquired carbapenemase genes is not known in Finland. The purpose of this study was to examine prevalence and clonal spread of multiresistant A. baumannii group species, and their carbapenemase genes. A total of 55 Acinetobacter isolates were evaluated with repetitive PCR (DiversiLab) to analyse clonality of isolates, in conjunction with antimicrobial susceptibility profile for ampicillin/sulbactam, colistin, imipenem, meropenem, rifampicin and tigecycline. In addition, a new real-time PCR assay, detecting most clinically important carbapenemase genes just in two multiplex reactions, was developed. The assay detects genes for KPC, VIM, IMP, GES-1/-10, OXA-48, NDM, GIM-1, SPM-1, IMI/NMC-A, SME, CMY-10, SFC-1, SIM-1, OXA-23-like, OXA-24/40-like, OXA-58 and ISAbaI-OXA-51-like junction, and allows confident detection of isolates harbouring acquired carbapenemase genes. There was a time-dependent, clonal spread of multiresistant A. baumannii strongly correlating with carbapenamase gene profile, at least in this geographically restricted study material. The new carbapenemase screening assay was able to detect all the genes correctly suggesting it might be suitable for epidemiologic screening purposes in clinical laboratories.
Collapse
Affiliation(s)
- Tanja Pasanen
- Division of Clinical Microbiology, Helsinki University Hospital, Helsinki, Finland
- * E-mail:
| | - Suvi Koskela
- Division of Clinical Microbiology, Helsinki University Hospital, Helsinki, Finland
| | - Sointu Mero
- Division of Clinical Microbiology, Helsinki University Hospital, Helsinki, Finland
| | - Eveliina Tarkka
- Division of Clinical Microbiology, Helsinki University Hospital, Helsinki, Finland
| | - Päivi Tissari
- Division of Clinical Microbiology, Helsinki University Hospital, Helsinki, Finland
| | - Martti Vaara
- Division of Clinical Microbiology, Helsinki University Hospital, Helsinki, Finland
| | - Juha Kirveskari
- Division of Clinical Microbiology, Helsinki University Hospital, Helsinki, Finland
| |
Collapse
|
42
|
A quantitative polymerase chain reaction assay for rapid detection of 9 pathogens directly from stools of travelers with diarrhea. Clin Gastroenterol Hepatol 2013; 11:1300-1307.e3. [PMID: 23639597 DOI: 10.1016/j.cgh.2013.03.037] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Revised: 03/27/2013] [Accepted: 03/30/2013] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Every year, 80 million tourists traveling to tropical and subtropical areas contract traveler's diarrhea (TD). Forty percent to 80% of cases are caused by bacteria, yet clinical diagnostic tests are available to identify only a few of the strains that cause TD. We aimed to develop a quantitative polymerase chain reaction (qPCR) assay to identify all major pathogens in stool samples. METHODS We developed a low-cost, high-throughput, multiplex qPCR assay for simultaneous detection of 9 bacterial pathogens in stool samples: Salmonella, Yersinia, Campylobacter, and Vibrio cholerae, as well as Shigella or enteroinvasive Escherichia coli, enterohemorrhagic E coli, enterotoxigenic E coli (ETEC), enteroaggregative E coli (EAEC), and enteropathogenic E coli (EPEC). The assay was validated using positive (n = 245) and negative (n = 243) control strains, as well as preselected positive and negative stool samples. In addition, stool samples were collected from 96 returning travelers with TD. The findings were compared with those from routine diagnostic tests. RESULTS The assay detected the bacterial strains with 100% sensitivity and specificity, compared with results from the reference tests. Of all stool samples collected from travelers with TD, EPEC was found in 47%, EAEC in 46%, ETEC in 22%, enterohemorrhagic E coli in 7%, Campylobacter in 6%, Shigella or enteroinvasive E coli in 2%, and Salmonella in 2%. Multiple pathogens were found in 37% of all samples. CONCLUSIONS We developed a low-cost, high-throughput qPCR assay for use in routine diagnostic analysis and research. It detects the pathogenic bacteria most commonly associated with TD in stool samples with 100% sensitivity and specificity, compared with reference methods. The assay requires 4 hours, whereas current detection methods require 1 to 7 days. At least 1 TD pathogen was identified in stool samples from 76% of returning travelers, whereas conventional methods found a pathogen in only 17%. The most commonly detected bacteria were EPEC, EAEC, and ETEC.
Collapse
|
43
|
Chattaway MA, Harris R, Jenkins C, Tam C, Coia JE, Gray J, Iturriza-Gomara M, Wain J. Investigating the link between the presence of enteroaggregative Escherichia coli and infectious intestinal disease in the United Kingdom, 1993 to 1996 and 2008 to 2009. ACTA ACUST UNITED AC 2013; 18. [PMID: 24079400 DOI: 10.2807/1560-7917.es2013.18.37.20582] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
There are an estimated 17 million human diarrhoea cases annually in the United Kingdom. In 2008 and 2009, enteroaggregative E. coli (EAEC) were identified in 1.9% of stools. However, it remains unclear whether there is a causal link between presence of EAEC and disease. This study used bacterial load, the presence of co-infections and demographic data to assess if EAEC was independently associated with intestinal infectious disease. Quantitative real-time PCR data (Ct values) generated directly from stool specimens for several pathogen targets were analysed to identify multiple pathogens, including EAEC, in the stools of cases and healthy controls. Sensitivity and specificity using Ct value (60% and 60%) was not useful for identifying cases or controls, but an independent association between disease and EAEC presence was demonstrated: multivariate logistic regression for EAEC presence (odds ratio: 2.41; 95% confidence interval: 1.78–3.26; p<0.001). The population-attributable fraction was 3.3%. The group of bacteria known as EAEC are associated with gastrointestinal disease in at least half of the cases with EAEC positive stools. We conclude that the current definition of EAEC, by plasmid gene detection, includes true pathogens as well as non-pathogenic variants.
Collapse
Affiliation(s)
- M A Chattaway
- Gastrointestinal Bacteria Reference Unit, Public Health England, Colindale, London, United Kingdom
| | | | | | | | | | | | | | | |
Collapse
|
44
|
Huys G, Botteldoorn N, Delvigne F, De Vuyst L, Heyndrickx M, Pot B, Dubois JJ, Daube G. Microbial characterization of probiotics--advisory report of the Working Group "8651 Probiotics" of the Belgian Superior Health Council (SHC). Mol Nutr Food Res 2013; 57:1479-504. [PMID: 23801655 PMCID: PMC3910143 DOI: 10.1002/mnfr.201300065] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 01/22/2013] [Accepted: 02/20/2013] [Indexed: 12/17/2022]
Abstract
When ingested in sufficient numbers, probiotics are expected to confer one or more proven health benefits on the consumer. Theoretically, the effectiveness of a probiotic food product is the sum of its microbial quality and its functional potential. Whereas the latter may vary much with the body (target) site, delivery mode, human target population, and health benefit envisaged microbial assessment of the probiotic product quality is more straightforward. The range of stakeholders that need to be informed on probiotic quality assessments is extremely broad, including academics, food and biotherapeutic industries, healthcare professionals, competent authorities, consumers, and professional press. In view of the rapidly expanding knowledge on this subject, the Belgian Superior Health Council installed Working Group "8651 Probiotics" to review the state of knowledge regarding the methodologies that make it possible to characterize strains and products with purported probiotic activity. This advisory report covers three main steps in the microbial quality assessment process, i.e. (i) correct species identification and strain-specific typing of bacterial and yeast strains used in probiotic applications, (ii) safety assessment of probiotic strains used for human consumption, and (iii) quality of the final probiotic product in terms of its microbial composition, concentration, stability, authenticity, and labeling.
Collapse
Affiliation(s)
- Geert Huys
- Laboratory for Microbiology & BCCM/LMG Bacteria Collection, Faculty of Sciences, Ghent University, Ghent, Belgium.
| | | | | | | | | | | | | | | |
Collapse
|
45
|
Sensitive detection of enteropathogenic E. coli using a bfpA gene-based electrochemical sensor. Mikrochim Acta 2013. [DOI: 10.1007/s00604-013-1061-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
|
46
|
Lukinmaa-Åberg S, Horsma J, Pasanen T, Mero S, Aulu L, Vaara M, Siitonen A, Antikainen J. Applicability of DiversiLab repetitive sequence-based PCR method in epidemiological typing of enterohemorrhagic Escherichia coli (EHEC). Foodborne Pathog Dis 2013; 10:632-8. [PMID: 23692078 DOI: 10.1089/fpd.2012.1411] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Enterohemorrhagic Escherichia coli (EHEC) causes diarrhea, often with severe complications. Rapid and discriminatory typing of EHEC using advanced molecular methods is needed for determination of the genetic relatedness of clones responsible for foodborne outbreaks and for finding out the transmission sources of the outbreaks. This study evaluated the potential of DiversiLab, a semiautomated repetitive sequence-based polymerase chain reaction method for the genotyping of EHEC strains. A set of 52 EHEC strains belonging to 15 O:H serotypes was clustered into 10 DiversiLab groups. All of the O157 strains and one O55 strain were classified into the same group based on a 90% similarity threshold. The other serotypes were classified to their own DiversiLab group, with the exception of one R:H(-) strain that was grouped with O5:H(-) strains. In addition, O26 and O111 strains were grouped together but ultimately subdivided according to their O-serotypes based on a 95% similarity threshold. The O104 strain, which was associated with a major outbreak of hemolytic uremic syndrome in Germany in May 2011, was also classified independently. The DiversiLab performed well in identifying isolates, but the discriminatory power of the repetitive sequence-based polymerase chain reaction method was lower than that of pulsed-field gel electrophoresis. Analysis of 15 enteropathogenic E. coli (EPEC) strains revealed that some EPEC strains clustered together with EHEC strains. Therefore, the DiversiLab system cannot be used to discriminate between these pathogroups. In conclusion, DiversiLab is a rapid and easy system for the primary exclusion of unrelated EHEC strains based on their serotypes, but more discriminatory methods, such as pulsed-field gel electrophoresis, are needed for accurate typing of the EHEC strains.
Collapse
Affiliation(s)
- Susanna Lukinmaa-Åberg
- Bacteriology Unit, Department of Infectious Disease Surveillance and Control, National Institute for Health and Welfare THL, Helsinki, Finland
| | | | | | | | | | | | | | | |
Collapse
|
47
|
Fialho OB, de Souza EM, de Borba Dallagassa C, de Oliveira Pedrosa F, Klassen G, Irino K, Paludo KS, de Assis FEA, Surek M, de Souza Santos Farah SM, Fadel-Picheth CMT. Detection of diarrheagenic Escherichia coli using a two-system multiplex-PCR protocol. J Clin Lab Anal 2013; 27:155-61. [PMID: 23424166 DOI: 10.1002/jcla.21578] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2012] [Accepted: 01/04/2013] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Diarrheagenic Escherichia coli (DEC) strains are important causes of diarrhea. However, they cannot be distinguished from E. coli of the intestinal microbiota by conventional microbiological tests. METHODS This work presents a two-system multiplex PCR for detection of DEC. Primers for 16S rRNA gene were added as internal amplification control to validate negative reactions. The multiplex-PCR system 1 contains primers for detection of Shiga toxin producing E. coli (STEC; stx1, stx2), enteropathogenic E. coli (EPEC; eae, bfpA), atypical enteropathogenic E. coli (aEPEc; eae), enteroinvasive E. coli (ETEC; lt, st), enteroinvasive E. coli (EIEC; ial), and the internal amplification control 16S rRNA. The system 2 contains primers for EIEC (ipaH), enteroaggregative E. coli (CVD432), diffusely adherent E. coli (daaE), and 16S rRNA. The protocol was tested with E. coli reference strains, and also with cultures of fecal specimens of people with diarrhea and healthy controls. RESULTS The protocol correctly identified the DEC reference strains. No DEC marker was amplified for negative controls; these results were validated by the amplification of a fragment of the 16S rRNA gene. The frequency of DEC was 7.6% for both patients and healthy controls; two Shigella sonnei strains were detected in the group with diarrhea. The identity of the amplicons was confirmed by DNA sequencing. CONCLUSION The protocol is specific for DEC Shigella and is suitable for clinical laboratories.
Collapse
|
48
|
Lee S, Park YJ, Lee HK, Kim SY, Kim JY, Lee SY, Yoo JK. Detection of 13 Enteric Bacteria and 5 Viruses Causing Acute Infectious Diarrhea Using Multiplex PCR from Direct Stool Specimens. ANNALS OF CLINICAL MICROBIOLOGY 2013. [DOI: 10.5145/acm.2013.16.1.33] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Seungok Lee
- Department of Laboratory Medicine, Incehon St. Mary's Hospital, The Catholic University School of Medicine, Incheon, Korea
| | - Yeon-Joon Park
- Department of Laboratory Medicine, Seoul St. Mary's Hospital, The Catholic University School of Medicine, Seoul, Korea
| | - Hae Kyung Lee
- Department of Laboratory Medicine, Uijeongbu St. Mary's Hospital, The Catholic University School of Medicine, Uijeongbu, Korea
| | - Soo-Young Kim
- Department of Laboratory Medicine, St. Vincent's Hospital, The Catholic University School of Medicine, Suwon, Korea
| | - Ja-Young Kim
- Department of Laboratory Medicine, Daejeon St. Mary's Hospital, The Catholic University School of Medicine, Daejeon, Korea
| | - So-Young Lee
- Department of Laboratory Medicine, Yeouido St. Mary's Hospital, The Catholic University School of Medicine, Seoul, Korea
| | - Jin-Kyung Yoo
- Department of Laboratory Medicine, Seoul St. Mary's Hospital, The Catholic University School of Medicine, Seoul, Korea
| |
Collapse
|
49
|
Martikainen O, Kagambèga A, Bonkoungou IJ, Barro N, Siitonen A, Haukka K. Characterization of ShigatoxigenicEscherichia coliStrains from Burkina Faso. Foodborne Pathog Dis 2012; 9:1015-21. [DOI: 10.1089/fpd.2012.1228] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Outi Martikainen
- Bacteriology Unit, Department of Infectious Disease Surveillance and Control, National Institute for Health and Welfare, Helsinki, Finland
| | - Assèta Kagambèga
- Bacteriology Unit, Department of Infectious Disease Surveillance and Control, National Institute for Health and Welfare, Helsinki, Finland
- Laboratoire de Biologie Moléculaire et d'Epidémiologie et de Surveillance Bactéries et Virus Transmis par les Aliments, CRSBAN, Département de Biochimie-Microbiologie, UFR-SVT, Université de Ouagadougou, Ouagadougou, Burkina Faso
| | - Isidore Juste Bonkoungou
- Bacteriology Unit, Department of Infectious Disease Surveillance and Control, National Institute for Health and Welfare, Helsinki, Finland
- Laboratoire de Biologie Moléculaire et d'Epidémiologie et de Surveillance Bactéries et Virus Transmis par les Aliments, CRSBAN, Département de Biochimie-Microbiologie, UFR-SVT, Université de Ouagadougou, Ouagadougou, Burkina Faso
- Laboratoire National de Santé Publique, Ouagadougou, Burkina Faso
| | - Nicolas Barro
- Laboratoire de Biologie Moléculaire et d'Epidémiologie et de Surveillance Bactéries et Virus Transmis par les Aliments, CRSBAN, Département de Biochimie-Microbiologie, UFR-SVT, Université de Ouagadougou, Ouagadougou, Burkina Faso
| | - Anja Siitonen
- Bacteriology Unit, Department of Infectious Disease Surveillance and Control, National Institute for Health and Welfare, Helsinki, Finland
| | - Kaisa Haukka
- Bacteriology Unit, Department of Infectious Disease Surveillance and Control, National Institute for Health and Welfare, Helsinki, Finland
| |
Collapse
|
50
|
Usability and performance of CHROMagar STEC medium in detection of Shiga toxin-producing Escherichia coli strains. J Clin Microbiol 2012; 50:3586-90. [PMID: 22933601 DOI: 10.1128/jcm.01754-12] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The performance and usability of CHROMagar STEC medium (CHROMagar Microbiology, Paris, France) for routine detection of Shiga toxin-producing Escherichia coli (STEC) strains were examined. The ability of the medium to selectively propagate STEC strains differing by their serotypes and virulence genes was studied with a collection of diarrheagenic E. coli isolates (n = 365) consisting of 49 different serotypes and with non-STEC and other bacterial isolates (n = 264). A total of 272 diarrheagenic E. coli (75.0%) isolates covering 24 different serotypes grew on CHROMagar STEC. The highest detection sensitivities were observed within the STEC serogroups O26 (90.0%), O111 (100.0%), O121 (100.0%), O145 (100.0%), and O157 (84.9%), and growth on CHROMagar STEC was highly associated with the presence of the tellurite resistance gene (terD). The specificity of the medium was 98.9%. In addition, CHROMagar STEC was used in parallel with a Shiga toxin-detecting immunoassay (Ridaquick Verotoxin/O157 Combi; R-biopharm, Darmstadt, Germany) to screen fecal specimens (n = 47) collected from patients suffering from hemorrhagic diarrhea. Positive growth on CHROMagar STEC was confirmed by the Premier EHEC enzyme immunoassay (Meridian Bioscience, Inc., Cincinnati, OH), and discrepant results between the two screening methods were confirmed by stx gene-detecting PCR. All 16 of the 47 stool samples that showed positive growth on CHROMagar STEC were also positive in the confirmatory tests. CHROMagar STEC proved to be an interesting option for STEC screening, allowing good detection sensitivity and specificity and permitting strain isolation for further outbreak investigations when required.
Collapse
|