scholarly journals Diversification of Escherichia albertii H-Antigens and Development of H-Genotyping PCR

2021 ◽  
Vol 12 ◽  
Author(s):  
Koji Nakae ◽  
Tadasuke Ooka ◽  
Koichi Murakami ◽  
Yukiko Hara-Kudo ◽  
Naoko Imuta ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Life Cycle ◽  
Multiplex Pcr ◽  
Epidemiological Studies ◽  
Strain Typing ◽  
Rare Occurrence ◽  
E Coli ◽  
Clear Sign ◽  
Natural Hosts ◽  
Sequence Types

Escherichia albertii is a recently recognized human enteropathogen that is closely related to Escherichia coli. As E. albertii sometimes causes outbreaks of gastroenteritis, rapid strain typing systems, such as the O- and H-serotyping systems widely used for E. coli, will be useful for outbreak investigation and surveillance. Although an O-genotyping system has recently been developed, the diversity of E. albertii H-antigens (flagellins) encoded by fliC genes remains to be systematically investigated, and no H-serotyping or genotyping system is currently available. Here, we analyzed the fliC genes of 243 genome-sequenced E. albertii strains and identified 73 sequence types, which were grouped into four clearly distinguishable types designated E. albertii H-genotypes 1–4 (EAHg1–EAHg4). Although there was a clear sign of intraspecies transfer of fliC genes in E. albertii, none of the four E. albertii H-genotypes (EAHgs) were closely related to any of the 53 known E. coli H-antigens, indicating the absence or rare occurrence of interspecies transfer of fliC genes between the two species. Although the analysis of more E. albertii strains will be required to confirm the low level of variation in their fliC genes, this finding suggests that E. albertii may exist in limited natural hosts or environments and/or that the flagella of E. albertii may function in a limited stage(s) in their life cycle. Based on the fliC sequences of the four EAHgs, we developed a multiplex PCR-based H-genotyping system for E. albertii (EAH-genotyping PCR), which will be useful for epidemiological studies of E. albertii infections.

scholarly journals Rapid Identification of Major Escherichia coli Sequence Types Causing Urinary Tract and Bloodstream Infections

2014 ◽  
Vol 53 (1) ◽  
pp. 160-166 ◽  
Author(s):  
M. Doumith ◽  
M. Day ◽  
H. Ciesielczuk ◽  
R. Hope ◽  
A. Underwood ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Urinary Tract ◽  
Bloodstream Infections ◽  
Epidemiological Studies ◽  
Rapid Identification ◽  
Content Type ◽  
E Coli ◽  
Genes Encoding ◽  
Signature Sequences ◽  
Sequence Types

Escherichia colisequence types (STs) 69, 73, 95, and 131 are collectively responsible for a large proportion ofE. coliurinary tract and bloodstream infections, and they differ markedly in their antibiotic susceptibilities. Here, we describe a novel PCR method to rapidly detect and distinguish these lineages. Three hundred eighteen publishedE. coligenomes were compared in order to identify signature sequences unique to each of the four major STs. The specificities of these sequences were assessedin silicoby seeking them in an additional 98 genomes. A PCR assay was designed to amplify size-distinguishable fragments unique to the four lineages and was validated using 515E. coliisolates of known STs. Genome comparisons identified 22 regions ranging in size from 335 bp to 26.5 kb that are unique to one or more of the four predominantE. coliSTs, with two to 10 specific regions per ST. These regions predominantly harbor genes encoding hypothetical proteins and are within or adjacent to prophage sequences. Most (13/22) were highly conserved (>96.5% identity) in the genomes of their respective ST. The new assay correctly identified all 142 representatives of the four major STs in the validation set (n= 515), with only two ST12 isolates misidentified as ST95. Compared with MLST, the assay has 100% sensitivity and 99.5% specificity. The rapid identification of major extraintestinalE. coliSTs will benefit future epidemiological studies and could be developed to tailor antibiotic therapy to the different susceptibilities of these dominant lineages.

Usefulness of a Multiplex PCR for Detection of Diarrheagenic Escherichia coli in a Diagnostic Microbiology Laboratory Setting

2016 ◽  
Vol 1 (2) ◽  
pp. 38-42 ◽  
Author(s):  
Khairun Nessa ◽  
Dilruba Ahmed ◽  
Johirul Islam ◽  
FM Lutful Kabir ◽  
M Anowar Hossain
Keyword(s):  
Escherichia Coli ◽  
Multiplex Pcr ◽  
Clinical Laboratory ◽  
Proteinase K ◽  
Microbiology Laboratory ◽  
Pcr Assay ◽  
E Coli ◽  
Diarrheagenic Escherichia Coli ◽  
Multiplex Pcr Assay ◽  
Diagnostic Microbiology

A multiplex PCR assay was evaluated for diagnosis of diarrheagenic Escherichia coli in stool samples of patients with diarrhoea submitted to a diagnostic microbiology laboratory. Two procedures of DNA template preparationproteinase K buffer method and the boiling method were evaluated to examine isolates of E. coli from 150 selected diarrhoeal cases. By proteinase K buffer method, 119 strains (79.3%) of E. coli were characterized to various categories by their genes that included 55.5% enteroaggregative E. coli (EAEC), 18.5% enterotoxigenic E. coli (ETEC), 1.7% enteropathogenic E. coli (EPEC), and 0.8% Shiga toxin-producing E. coli (STEC). Although boiling method was less time consuming (<24 hrs) and less costly (<8.0 US $/ per test) but was less efficient in typing E. coli compared to proteinase K method (41.3% vs. 79.3% ; p<0.001). The sensitivity and specificity of boiling method compared to proteinase K method was 48.7% and 87.1% while the positive and negative predictive value was 93.5% and 30.7%, respectively. The majority of pathogenic E. coli were detected in children (78.0%) under five years age with 53.3% under one year, and 68.7% of the children were male. Children under 5 years age were frequently infected with EAEC (71.6%) compared to ETEC (24.3%), EPEC (2.7%) and STEC (1.4%). The multiplex PCR assay could be effectively used as a rapid diagnostic tool for characterization of diarrheagenic E. coli using a single reaction tube in the clinical laboratory setting.Bangladesh J Med Microbiol 2007; 01 (02): 38-42

scholarly journals Presence of β-Lactamase-producing Enterobacterales and Salmonella Isolates in Marine Mammals

2021 ◽  
Vol 22 (11) ◽  
pp. 5905
Author(s):  
Olivia M. Grünzweil ◽  
Lauren Palmer ◽  
Adriana Cabal ◽  
Michael P. Szostak ◽  
Werner Ruppitsch ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Marine Mammals ◽  
Virulence Genes ◽  
Multidrug Resistant ◽  
Healthcare Sector ◽  
Whole Genome ◽  
E Coli ◽  
High Prevalence ◽  
Lactamase Gene ◽  
Sequence Types

Marine mammals have been described as sentinels of the health of marine ecosystems. Therefore, the aim of this study was to investigate (i) the presence of extended-spectrum β-lactamase (ESBL)- and AmpC-producing Enterobacterales, which comprise several bacterial families important to the healthcare sector, as well as (ii) the presence of Salmonella in these coastal animals. The antimicrobial resistance pheno- and genotypes, as well as biocide susceptibility of Enterobacterales isolated from stranded marine mammals, were determined prior to their rehabilitation. All E. coli isolates (n = 27) were screened for virulence genes via DNA-based microarray, and twelve selected E. coli isolates were analyzed by whole-genome sequencing. Seventy-one percent of the Enterobacterales isolates exhibited a multidrug-resistant (MDR) pheno- and genotype. The gene blaCMY (n = 51) was the predominant β-lactamase gene. In addition, blaTEM-1 (n = 38), blaSHV-33 (n = 8), blaCTX-M-15 (n = 7), blaOXA-1 (n = 7), blaSHV-11 (n = 3), and blaDHA-1 (n = 2) were detected. The most prevalent non-β-lactamase genes were sul2 (n = 38), strA (n = 34), strB (n = 34), and tet(A) (n = 34). Escherichia coli isolates belonging to the pandemic sequence types (STs) ST38, ST167, and ST648 were identified. Among Salmonella isolates (n = 18), S. Havana was the most prevalent serotype. The present study revealed a high prevalence of MDR bacteria and the presence of pandemic high-risk clones, both of which are indicators of anthropogenic antimicrobial pollution, in marine mammals.

scholarly journals Virulence Properties of mcr-1-Positive Escherichia coli Isolated from Retail Poultry Meat

2021 ◽  
Vol 9 (2) ◽  
pp. 308
Author(s):  
Michaela Kubelová ◽  
Ivana Koláčková ◽  
Tereza Gelbíčová ◽  
Martina Florianová ◽  
Alžběta Kalová ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Poultry Meat ◽  
Human Populations ◽  
E Coli ◽  
Antimicrobial Resistance Genes ◽  
Mlst Type ◽  
On Line ◽  
Sequence Types

The great plasticity and diversity of the Escherichia coli genome, together with the ubiquitous occurrence, make E. coli a bacterium of world-wide concern. Of particular interest are pathogenic strains and strains harboring antimicrobial resistance genes. Overlapping virulence-associated traits between avian-source E. coli and human extraintestinal pathogenic E. coli (ExPEC) suggest zoonotic potential and safety threat of poultry food products. We analyzed whole-genome sequencing (WGS) data of 46 mcr-1-positive E. coli strains isolated from retail raw meat purchased in the Czech Republic. The investigated strains were characterized by their phylogroup—B1 (43%), A (30%), D (11%), E (7%), F (4%), B2 (2%), C (2%), MLST type, and serotype. A total of 30 multilocus sequence types (STs), of which ST744 was the most common (11%), were identified, with O8 and O89 as the most prevalent serogroups. Using the VirulenceFinder tool, 3 to 26 virulence genes were detected in the examined strains and a total of 7 (15%) strains met the pathogenic criteria for ExPEC. Four strains were defined as UPEC (9%) and 18 (39%) E. coli strains could be classified as APEC. The WGS methods and available on-line tools for their evaluation enable a comprehensive approach to the diagnosis of virulent properties of E. coli strains and represent a suitable and comfortable platform for their detection. Our results show that poultry meat may serve as an important reservoir of strains carrying both virulence and antibiotic resistance genes for animal and human populations.

scholarly journals Multidrug Resistance Dissemination in Escherichia coli Isolated from Wild Animals: Bacterial Clones and Plasmid Complicity

2021 ◽  
Vol 12 (1) ◽  
pp. 123-137
Author(s):  
Carolina Sabença ◽  
Gilberto Igrejas ◽  
Patrícia Poeta ◽  
Frédéric Robin ◽  
Richard Bonnet ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Epidemiological Data ◽  
Generation Cephalosporin ◽  
Wild Animals ◽  
Variable Regions ◽  
E Coli ◽  
Wild Fauna ◽  
Long Read ◽  
Sequence Types ◽  
Animal Isolates

Objectives. Epidemiological data concerning third-generation cephalosporin (3GC) resistance in wild fauna are scarce. The aim of this study was to characterize the resistance genes, their genetic context, and clonal relatedness in 17 Escherichia coli resistant to 3GC isolated from wild animals. Methods. The isolates were characterized by short-read whole genome sequencing, and long-read sequencing was used for the hybrid assembly of plasmid sequences. Results. The 3GC resistance gene most identified in the isolates was the extended-spectrum β-lactamases (ESBL)-encoding gene blaCTX-M-1 (82.3%), followed by blaCTX-M-32 (5.9%), blaCTX-M-14 (5.9%), and blaSHV-12 (5.9%). E. coli isolates mainly belonged to the sequence types (STs) rarely reported from humans. The single nucleotide polymorphism (SNP)-based typing showed that most E. coli genomes from wild animals (wild boars, birds of prey, and buzzards) formed clonal clusters (<5 SNPs), showing a clonal dissemination crossing species boundaries. blaCTX-M-1-harboring IncI1-ST3 plasmid was the predominant ESBL-encoding plasmid (76.4%) in wild animal isolates. Plasmid comparison revealed a 110-kb self-transferable plasmid consisting of a conserved backbone and two variable regions involved in antimicrobial resistance and in interaction with recipient cells during conjugation. Conclusion. Our results highlighted the unexpected clonal dissemination of blaCTX-M-1-encoding clones and the complicity of IncI1-ST3 plasmid in the spread of blaCTX-M-1 within wild fauna.

scholarly journals Population genomics and antimicrobial resistance dynamics of Escherichia coli in wastewater and river environments

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Jose F. Delgado-Blas ◽  
Cristina M. Ovejero ◽  
Sophia David ◽  
Natalia Montero ◽  
William Calero-Caceres ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Population Genomics ◽  
Population Diversity ◽  
Genomic Diversity ◽  
Resistant Bacteria ◽  
Aquatic Environments ◽  
E Coli ◽  
Water Ecosystems ◽  
Sequence Types

AbstractAquatic environments are key niches for the emergence, evolution and dissemination of antimicrobial resistance. However, the population diversity and the genetic elements that drive the dynamics of resistant bacteria in different aquatic environments are still largely unknown. The aim of this study was to understand the population genomics and evolutionary events of Escherichia coli resistant to clinically important antibiotics including aminoglycosides, in anthropogenic and natural water ecosystems. Here we show that less different E. coli sequence types (STs) are identified in wastewater than in rivers, albeit more resistant to antibiotics, and with significantly more plasmids/cell (6.36 vs 3.72). However, the genomic diversity within E. coli STs in both aquatic environments is similar. Wastewater environments favor the selection of conserved chromosomal structures associated with diverse flexible plasmids, unraveling promiscuous interplasmidic resistance genes flux. On the contrary, the key driver for river E. coli adaptation is a mutable chromosome along with few plasmid types shared between diverse STs harboring a limited resistance gene content.

scholarly journals Bacterial genotypic and patient risk factors for adverse outcomes in Escherichia coli bloodstream infections: a prospective molecular-epidemiological study

2021 ◽  
Author(s):  
Elita Jauneikaite ◽  
Kate Honeyford ◽  
Oliver Blandy ◽  
Mia Mosavie ◽  
Max Pearson ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Length Of Stay ◽  
Single Agent ◽  
Bloodstream Infections ◽  
Outcome Data ◽  
Sequence Type ◽  
Adverse Outcomes ◽  
Beta Lactam ◽  
E Coli ◽  
Sequence Types

Background Escherichia coli bloodstream infections have increased rapidly in the UK, for reasons that are unclear. The relevance of highly fit, or multi-drug resistant lineages such as ST131 to overall E. coli disease burden remains to be fully determined. We set out to characterise the prevalence of E. coli multi-locus sequence types (MLST) and determine if these were associated with adverse outcomes in an urban population of E. coli bacteraemia patients. Methods We undertook whole genome sequencing of E. coli blood isolates from all patients with diagnosed E. coli bacteraemia in north-west London from July 2015 to August 2016 and assigned multi-locus sequence types to all isolates. Isolate sequence types were linked to routinely collected antimicrobial susceptibility, patient demographic, and clinical outcome data to explore relationships between the E. coli sequence types, patient factors, and outcomes. Findings A total of 551 E. coli genomes were available for analysis. More than half of these cases were caused by four E. coli sequence types: ST131 (21%), ST73 (15%), ST69 (9%) and ST95 (8%). E. coli genotype ST131-C2 was associated with non-susceptibility to quinolones and third-generation cephalosporins, and also to amoxicillin, augmentin, gentamicin and trimethoprim. An association between the ST131-C2 lineage and longer length-of-stay was detected, although multivariable regression modelling did not demonstrate an association between E. coli sequence type and mortality. However, a number of unexpected associations were identified, including gentamicin non-susceptibility, ethnicity, and sex that might influence mortality and length-of-stay, requiring further research. Interpretation Although E. coli sequence type was associated with antimicrobial non-susceptibility patterns and length-of-stay, we did not find that E. coli sequence type was associated with increased mortality. Where ST131 is prevalent, caution is required when pairing beta-lactam agents with gentamicin or using single agent aminoglycosides.

Diarrheagenic Escherichia coli pathotypes isolated from a swine farm in a region of Morelos state, Mexico

2020 ◽  
Author(s):  
Elsa María Tamayo-Legorreta ◽  
Alejandro García-Radilla ◽  
Eduardo Moreno-Vázquez ◽  
Fabián Téllez-Figueroa ◽  
Celia M Alpuche-Aranda
Keyword(s):  
Escherichia Coli ◽  
Multiplex Pcr ◽  
Potential Risk ◽  
Virulence Gene ◽  
Central Mexico ◽  
Swine Farm ◽  
Fecal Samples ◽  
E Coli ◽  
Diarrheagenic Escherichia Coli

Objective. Determine the frequency of diarrheagenic Escherichia coli pathotypes colonizing swine. Materials and Methods. E. coli strains isolated of fecal samples from 280 swine, produced for local consumption, in a semi-technical farm of Morelos state, (central Mexico) were tested to identify the diarrheagenic E. coli pathotypes by multiplex PCR. Results. Of the 521-diarrheagenic E. coli isolates examined, 50 (9.6%) were positive for at least one virulence gene in 42 different animals. Thus, 15% (42/280) of the swine in this farm were colonized with pathogenic E. coli. Among the E. coli isolates, the pathotype EPEC (6.5%) was the most frequently, followed by EHEC (2.3%), ETEC and EIEC (0.4%). Conclusions. In this study, four different E. coli pathotypes were found among swine colonized by E. coli in this farm. Thus, these swine are reservoirs for these virulent bacteria and there is potential risk of causing diarrhea in swine and in the population consuming the meat.

scholarly journals Extraintestinal pathogenic Escherichia coli in Saudi Arabia: A review of antimicrobial resistance and molecular epidemiology

2020 ◽  
Vol 19 (2) ◽  
pp. 447-453
Author(s):  
Abdulaziz Alqasim
Keyword(s):  
Escherichia Coli ◽  
Saudi Arabia ◽  
Antimicrobial Resistance ◽  
Molecular Epidemiology ◽  
Bloodstream Infections ◽  
Epidemiological Studies ◽  
Colistin Resistance ◽  
E Coli ◽  
Extended Spectrum ◽  
Pathogenic Escherichia Coli

Extra-intestinal pathogenic Escherichia coli (ExPEC) is commonly associated with causing urinary tract and bloodstream infections. Over the past two decades, the antimicrobial resistance of ExPEC has increasingly been reported [1]. Given that Saudi Arabia annually hosts mass religious events, such as Hajj, this review investigated several aspects of antimicrobial resistance of ExPEC in this country including the current prevalence of resistance and molecular epidemiology of ExPEC isolates. Generally, the overall prevalence of antibiotic resistance of ExPEC in Saudi Arabia is on increase. The current emergence of colistin resistance in ExPEC represents a major challenge to public health. Local molecular epidemiological studies have shown the dominance of E. coli sequence type 131 (E. coli ST131) over other major ExPEC STs. This is an important observation given that this clone has been associated with high multidrug resistance and extended-spectrum β-lactamases carriage. To reduce the burden of this resistance in the future, it would be crucial to avoid uncontrolled use of antibiotics in either clinical settings or animal food industry. Keywords: Extra-intestinal pathogenic Escherichia coli, Antimicrobial resistance, ST131, Saudi Arabia, Colistin resistance, Extended-spectrum β-lactamases

scholarly journals Additional Og-Typing PCR Techniques Targeting Escherichia coli-Novel and Shigella-Unique O-Antigen Biosynthesis Gene Clusters

2020 ◽  
Vol 58 (11) ◽  
Author(s):  
Atsushi Iguchi ◽  
Hironobu Nishii ◽  
Kazuko Seto ◽  
Jiro Mitobe ◽  
Kenichi Lee ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Strong Association ◽  
Gene Clusters ◽  
Epidemiological Studies ◽  
Content Type ◽  
E Coli ◽  
O Antigen ◽  
Wide Range ◽  
Biosynthesis Gene ◽  
Almost All

ABSTRACT The O-serogrouping of pathogenic Escherichia coli is a standard method for subtyping strains for epidemiological studies and controls. O-serogroup diversification shows a strong association with the genetic diversity in some O-antigen biosynthesis gene clusters. Through genomic studies, in addition to the types of O-antigen biosynthesis gene clusters (Og-types) from conventional O-serogroup strains, a number of novel Og-types have been found in E. coli isolates. To assist outbreak investigations and surveillance of pathogenic E. coli at inspection institutes, in previous studies, we developed PCR methods that could determine almost all conventional O-serogroups and some novel Og-types. However, there are still many Og-types that may not be determined by simple genetic methods such as PCR. Thus, in the present study, we aimed to develop an additional Og-typing PCR system. Based on the novel Og-types, including OgN32, OgN33, and OgN34, presented in this study, we designed an additional 24 PCR primer pairs targeting 14 novel and 2 diversified E. coli Og-types and 8 Shigella-unique Og-types. Subsequently, we developed 5 new multiplex PCR sets consisting of 33 primers, including the aforementioned 24 primers and 9 primers reported in previous studies. The accuracy and specificity of the PCR system was validated using approximately 260 E. coli and Shigella O-serogroup and Og-type reference strains. The Og-typing PCR system reported here can determine a wide range of Og-types of E. coli and may help epidemiological studies, in addition to the surveillance of pathogenic E. coli.

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