scholarly journals Population Structure and Antimicrobial Resistance of Canine UropathogenicEscherichia coli

2018 ◽  
Vol 56 (9) ◽  
Author(s):  
Tessa E. LeCuyer ◽  
Barbara A. Byrne ◽  
Joshua B. Daniels ◽  
Dubraska V. Diaz-Campos ◽  
G. Kenitra Hammac ◽  
...  
Keyword(s):  
Population Structure ◽  
Antimicrobial Resistance ◽  
Companion Animals ◽  
Sequence Type ◽  
Content Type ◽  
E Coli ◽  
Extraintestinal Disease ◽  
Human Infections ◽  
Sequence Types

ABSTRACTEscherichia coliis the most common cause of human and canine urinary tract infection (UTI). Clonal groups, often with high levels of antimicrobial resistance, are a major component of theE. colipopulation that causes human UTI. While little is known about the population structure ofE. colithat causes UTI in dogs, there is evidence that dogs and humans can share fecal strains ofE. coliand that human-associated strains can cause disease in dogs. In order to better characterize theE. colistrains that cause canine UTI, we analyzed 295E. coliisolates obtained from canine urine samples from five veterinary diagnostic laboratories and analyzed their multilocus sequence types, phenotypic and genotypic antimicrobial resistance profiles, and virulence-associated gene repertoires. Sequence type 372 (ST372), an infrequent human pathogen, was the predominant sequence type in dogs at all locations. Extended-spectrum β-lactamase-producing isolates withblaCTX-Mgenes were uncommon in canine isolates but when present were often associated with sequence types that have been described in human infections. This provides support for occasional cross-host-species sharing of strains that cause extraintestinal disease and highlights the importance of understanding the role of companion animals in the overall transmission patterns of extraintestinal pathogenicE. coli.

scholarly journals Evidence of Sharing ofKlebsiella pneumoniaeStrains between Healthy Companion Animals and Cohabiting Humans

2019 ◽  
Vol 57 (6) ◽  
Author(s):  
Cátia Marques ◽  
Adriana Belas ◽  
Catarina Aboim ◽  
Patrícia Cavaco-Silva ◽  
Graça Trigueiro ◽  
...  
Keyword(s):  
Antimicrobial Susceptibility ◽  
Close Contact ◽  
Companion Animals ◽  
Multidrug Resistant ◽  
Sequence Type ◽  
Content Type ◽  
Healthy Humans ◽  
Tract Infections ◽  
Healthy Participants

ABSTRACTThis study aimed to characterize the fecal colonization and sharing ofKlebsiella pneumoniaestrains between companion animals and humans living in close contact. Fecal samples were collected from 50 healthy participants (24 humans, 18 dogs, and 8 cats) belonging to 18 households. Samples were plated onto MacConkey agar (MCK) plates with and without cefotaxime or meropenem supplementation. Up to fiveK. pneumoniaecolonies per participant were compared by pulsed-field gel electrophoresis (PFGE) after XbaI restriction.K. pneumoniaestrains with unique pulse types from each participant were characterized for antimicrobial susceptibility, virulence genes, and multilocus sequence type (MLST). FecalK. pneumoniaepulse types were compared to those of clinicalK. pneumoniaestrains from animal and human patients with urinary tract infections (n = 104).K. pneumoniaecolonization was detected in nonsupplemented MCK in around 38% of dogs (n = 7) and humans (n = 9).K. pneumoniaestrains isolated from dogs belonged to sequence type 17 (ST17), ST188, ST252, ST281, ST423, ST1093, ST1241, ST3398, and ST3399. None of theK. pneumoniaestrains were multidrug resistant or hypervirulent. Two households included multiple colonized participants. Notably, two colonized dogs within household 15 (H15) shared a strain each (ST252 and ST1241) with one coliving human. One dog from H16 shared one PFGE-undistinguishableK. pneumoniaeST17 strain with two humans from different households; however, the antimicrobial susceptibility phenotypes of these three strains differed. Two main virulence genotypes were detected, namelyfimH-1 mrkD ycfM entB kfuandfimH-1 mrkD ycfM entB kpn. These results highlight the potential role of dogs as a reservoir ofK. pneumoniaeto humans and vice versa. Furthermore, to our best knowledge, this is the first report of healthy humans and dogs sharingK. pneumoniaestrains that were undistinguishable by PFGE/MLST.

scholarly journals Escherichia coliSequence Type 410 Is Causing New International High-Risk Clones

mSphere ◽  
2018 ◽  
Vol 3 (4) ◽  
pp. e00337-18 ◽  
Author(s):  
Louise Roer ◽  
Søren Overballe-Petersen ◽  
Frank Hansen ◽  
Kristian Schønning ◽  
Mikala Wang ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
High Risk ◽  
Antimicrobial Resistance ◽  
Sequence Type ◽  
Recurrent Infections ◽  
Content Type ◽  
E Coli ◽  
The Past ◽  
Carbapenemase Gene ◽  
Globally Distributed

ABSTRACTEscherichia colisequence type 410 (ST410) has been reported worldwide as an extraintestinal pathogen associated with resistance to fluoroquinolones, third-generation cephalosporins, and carbapenems. In the present study, we investigated national epidemiology of ST410E. coliisolates from Danish patients. Furthermore,E. coliST410 was investigated in a global context to provide further insight into the acquisition of the carbapenemase genesblaOXA-181andblaNDM-5of this successful lineage. From 127 whole-genome-sequenced isolates, we reconstructed an evolutionary framework ofE. coliST410 which portrays the antimicrobial-resistant clades B2/H24R, B3/H24Rx, and B4/H24RxC. The B2/H24R and B3/H24Rx clades emerged around 1987, concurrently with the C1/H30R and C2/H30Rx clades inE. coliST131. B3/H24Rx appears to have evolved by the acquisition of the extended-spectrum β-lactamase (ESBL)-encoding geneblaCTX-M-15and an IncFII plasmid, encoding IncFIA and IncFIB. Around 2003, the carbapenem-resistant clade B4/H24RxC emerged when ST410 acquired an IncX3 plasmid carrying ablaOXA-181carbapenemase gene. Around 2014, the clade B4/H24RxC acquired a second carbapenemase gene,blaNDM-5, on a conserved IncFII plasmid. From an epidemiological investigation of 49E. coliST410 isolates from Danish patients, we identified five possible regional outbreaks, of which one outbreak involved nine patients withblaOXA-181- andblaNDM-5-carrying B4/H24RxC isolates. The accumulated multidrug resistance inE. coliST410 over the past two decades, together with its proven potential of transmission between patients, poses a high risk in clinical settings, and thus,E. coliST410 should be considered a lineage with emerging “high-risk” clones, which should be monitored closely in the future.IMPORTANCEExtraintestinal pathogenicEscherichia coli(ExPEC) is the main cause of urinary tract infections and septicemia. Significant attention has been given to the ExPEC sequence type ST131, which has been categorized as a “high-risk” clone. High-risk clones are globally distributed clones associated with various antimicrobial resistance determinants, ease of transmission, persistence in hosts, and effective transmission between hosts. The high-risk clones have enhanced pathogenicity and cause severe and/or recurrent infections. We show that clones of theE. coliST410 lineage persist and/or cause recurrent infections in humans, including bloodstream infections. We found evidence of ST410 being a highly resistant globally distributed lineage, capable of patient-to-patient transmission causing hospital outbreaks. Our analysis suggests that the ST410 lineage should be classified with the potential to cause new high-risk clones. Thus, with the clonal expansion over the past decades and increased antimicrobial resistance to last-resort treatment options, ST410 needs to be monitored prospectively.

scholarly journals Decreasing Trend of Overlapping Multilocus Sequence Types between Human and Chicken Campylobacter jejuni Isolates over a Decade in Finland

2010 ◽  
Vol 76 (15) ◽  
pp. 5228-5236 ◽  
Author(s):  
C. P. A. de Haan ◽  
R. Kivist� ◽  
M. Hakkinen ◽  
H. Rautelin ◽  
M. L. H�nninen
Keyword(s):  
Population Structure ◽  
Campylobacter Jejuni ◽  
Sequence Type ◽  
Mlst Analysis ◽  
Structure And Dynamics ◽  
Population Structure And Dynamics ◽  
Human Infections ◽  
Sequence Types

ABSTRACT We describe the long-term multilocus sequence typing (MLST) analysis of the population structure and dynamics of 454 Finnish human Campylobacter jejuni isolates, as well as 208 chicken isolates, collected during the mid-1990s to 2007. The sequence type clonal complexes (ST CC) ST-45 CC, ST-21 CC, and ST-677 CC were the most common ones found among all isolates, and they covered 73.9% of all isolates. The ST-283 CC also was found frequently among chicken isolates (8.2%). The predominant STs among all isolates were ST-45, ST-50, and ST-677. ST-137 and ST-230 were common among human isolates, and ST-267 was found more frequently among chicken isolates than human isolates. The ST-45 CC was significantly associated with chicken isolates (P < 0.01), whereas the ST-21 CC was associated with human isolates (P < 0.001). The ST-677 CC was not associated with any host (P = 0.5), and an opposite temporary trend of this complex was seen among chicken and human isolates, with an increase in the former and a decrease in the latter during the study period. Furthermore, the ST-22 and ST-48 CCs were significantly associated with human isolates (P < 0.01), but neither of the CCs was found in chicken isolates. The annual overlap between STs from human and chicken isolates decreased from 76% at the beginning of the study to 58% at the end. Our results suggest that the importance of chicken as a reservoir for strains associated with human infections has declined despite the consumption of domestic chicken meat increasing during the follow-up period by 83%.

scholarly journals Temporal Trends in Antimicrobial Resistance and Virulence-Associated Traits within the Escherichia coli Sequence Type 131 Clonal Group and ItsH30 andH30-Rx Subclones, 1968 to 2012

2014 ◽  
Vol 58 (11) ◽  
pp. 6886-6895 ◽  
Author(s):  
Bente Olesen ◽  
Jakob Frimodt-Møller ◽  
Rikke Fleron Leihof ◽  
Carsten Struve ◽  
Brian Johnston ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Multidrug Resistance ◽  
Antimicrobial Resistance ◽  
Virulence Genes ◽  
Temporal Trends ◽  
Sequence Type ◽  
Esbl Production ◽  
Content Type ◽  
E Coli ◽  
Biofilm Production

ABSTRACTTo identify possible explanations for the recent global emergence ofEscherichia colisequence type (ST) 131 (ST131), we analyzed temporal trends within ST131 O25 for antimicrobial resistance, virulence genes, biofilm formation, and theH30 andH30-Rx subclones. For this, we surveyed the WHOE. coliandKlebsiellaCentre'sE. colicollection (1957 to 2011) for ST131 isolates, characterized them extensively, and assessed them for temporal trends. Overall, antimicrobial resistance increased temporally in prevalence and extent, due mainly to the recent appearance of theH30 (1997) andH30-Rx (2005) ST131 subclones. In contrast, neither the total virulence gene content nor the prevalence of biofilm production increased temporally, although non-H30 isolates increasingly qualified as extraintestinal pathogenicE. coli(ExPEC). Whereas virotype D occurred from 1968 forward, virotypes A and C occurred only after 2000 and 2002, respectively, in association with theH30andH30-Rx subclones, which were characterized by multidrug resistance (including extended-spectrum-beta-lactamase [ESBL] production:H30-Rx) and absence of biofilm production. Capsular antigen K100 occurred exclusively amongH30-Rx isolates (55% prevalence). Pulsotypes corresponded broadly with subclones and virotypes. Thus, ST131 should be regarded not as a unitary entity but as a group of distinctive subclones, with its increasing antimicrobial resistance having a strong clonal basis, i.e., the emergence of theH30 andH30-Rx ST131 subclones, rather than representing acquisition of resistance by diverse ST131 strains. Distinctive characteristics of theH30-Rx subclone—including specific virulence genes (iutA,afaanddra,kpsII), the K100 capsule, multidrug resistance, and ESBL production—possibly contributed to epidemiologic success, and some (e.g., K100) might serve as vaccine targets.

scholarly journals High-Resolution Melting Analysis for Rapid Detection of Sequence Type 131 Escherichia coli

2017 ◽  
Vol 61 (6) ◽  
Author(s):  
Lucas B. Harrison ◽  
Nancy D. Hanson
Keyword(s):  
Escherichia Coli ◽  
Principal Component Analysis ◽  
High Resolution ◽  
High Resolution Melting ◽  
Principal Component ◽  
Cost Effective ◽  
Sequence Type ◽  
Content Type ◽  
E Coli ◽  
Sequence Types

ABSTRACT Escherichia coli isolates belonging to the sequence type 131 (ST131) clonal complex have been associated with the global distribution of fluoroquinolone and β-lactam resistance. Whole-genome sequencing and multilocus sequence typing identify sequence type but are expensive when evaluating large numbers of samples. This study was designed to develop a cost-effective screening tool using high-resolution melting (HRM) analysis to differentiate ST131 from non-ST131 E. coli in large sample populations in the absence of sequence analysis. The method was optimized using DNA from 12 E. coli isolates. Singleplex PCR was performed using 10 ng of DNA, Type-it HRM buffer, and multilocus sequence typing primers and was followed by multiplex PCR. The amplicon sizes ranged from 630 to 737 bp. Melt temperature peaks were determined by performing HRM analysis at 0.1°C resolution from 50 to 95°C on a Rotor-Gene Q 5-plex HRM system. Derivative melt curves were compared between sequence types and analyzed by principal component analysis. A blinded study of 191 E. coli isolates of ST131 and unknown sequence types validated this methodology. This methodology returned 99.2% specificity (124 true negatives and 1 false positive) and 100% sensitivity (66 true positives and 0 false negatives). This HRM methodology distinguishes ST131 from non-ST131 E. coli without sequence analysis. The analysis can be accomplished in about 3 h in any laboratory with an HRM-capable instrument and principal component analysis software. Therefore, this assay is a fast and cost-effective alternative to sequencing-based ST131 identification.

scholarly journals Salmonella Genomic Island 1B Variant Found in a Sequence Type 117 Avian Pathogenic Escherichia coli Isolate

mSphere ◽  
2019 ◽  
Vol 4 (3) ◽  
Author(s):  
Max Laurence Cummins ◽  
Piklu Roy Chowdhury ◽  
Marc Serge Marenda ◽  
Glenn Francis Browning ◽  
Steven Philip Djordjevic
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Acinetobacter Baumannii ◽  
Genome Sequencing ◽  
Genomic Island ◽  
Sequence Type ◽  
Genomic Islands ◽  
Content Type ◽  
E Coli ◽  
Antimicrobial Resistance Genes

ABSTRACT Salmonella genomic island 1 (SGI1) is an integrative genetic island first described in Salmonella enterica serovars Typhimurium DT104 and Agona in 2000. Variants of it have since been described in multiple serovars of S. enterica, as well as in Proteus mirabilis, Acinetobacter baumannii, Morganella morganii, and several other genera. The island typically confers resistance to older, first-generation antimicrobials; however, some variants carry blaNDM-1, blaVEB-6, and blaCTX-M15 genes that encode resistance to frontline, clinically important antibiotics, including third-generation cephalosporins. Genome sequencing studies of avian pathogenic Escherichia coli (APEC) identified a sequence type 117 (ST117) isolate (AVC96) with genetic features found in SGI1. The complete genome sequence of AVC96 was assembled from a combination of Illumina and single-molecule real-time (SMRT) sequence data. Analysis of the AVC96 chromosome identified a variant of SGI1-B located 18 bp from the 3′ end of trmE, also known as the attB site, a known hot spot for the integration of genomic islands. This is the first report of SGI1 in wild-type E. coli. The variant, here named SGI1-B-Ec1, was otherwise unremarkable, apart from the identification of ISEc43 in open reading frame (ORF) S023. IMPORTANCE SGI1 and variants of it carry a variety of antimicrobial resistance genes, including those conferring resistance to extended-spectrum β-lactams and carbapenems, and have been found in diverse S. enterica serovars, Acinetobacter baumannii, and other members of the Enterobacteriaceae. SGI1 integrates into Gram-negative pathogenic bacteria by targeting a conserved site 18 bp from the 3′ end of trmE. For the first time, we describe a novel variant of SGI1 in an avian pathogenic Escherichia coli isolate. The presence of SGI1 in E. coli is significant because it represents yet another lateral gene transfer mechanism to enhancing the capacity of E. coli to acquire and propagate antimicrobial resistance and putative virulence genes. This finding underscores the importance of whole-genome sequencing (WGS) to microbial genomic epidemiology, particularly within a One Health context. Further studies are needed to determine how widespread SGI1 and variants of it may be in Australia.

scholarly journals Role of Enteroaggregative Escherichia coli Virulence Factors in Uropathogenesis

2013 ◽  
Vol 81 (4) ◽  
pp. 1164-1171 ◽  
Author(s):  
Erik J. Boll ◽  
Carsten Struve ◽  
Nadia Boisen ◽  
Bente Olesen ◽  
Steen G. Stahlhut ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Virulence Factors ◽  
Outbreak Strain ◽  
Content Type ◽  
E Coli ◽  
Abiotic Surfaces ◽  
Extraintestinal Disease ◽  
First Time ◽  
Specific Virulence

ABSTRACTA multiresistant clonalEscherichia coliO78:H10 strain qualifying molecularly as enteroaggregativeEscherichia coli(EAEC) was recently shown to be the cause of a community-acquired outbreak of urinary tract infection (UTI) in greater Copenhagen, Denmark, in 1991. This marks the first time EAEC has been associated with an extraintestinal disease outbreak. Importantly, the outbreak isolates were recovered from the urine of patients with symptomatic UTI, strongly implying urovirulence. Here, we sought to determine the uropathogenic properties of the Copenhagen outbreak strain and whether these properties are conferred by the EAEC-specific virulence factors. We demonstrated that through expression of aggregative adherence fimbriae, the principal adhesins of EAEC, the outbreak strain exhibited pronouncedly increased adherence to human bladder epithelial cells compared to prototype uropathogenic strains. Moreover, the strain was able to produce distinct biofilms on abiotic surfaces, including urethral catheters. These findings suggest that EAEC-specific virulence factors increase uropathogenicity and may have played a significant role in the ability of the strain to cause a community-acquired outbreak of UTI. Thus, inclusion of EAEC-specific virulence factors is warranted in future detection and characterization of uropathogenicE. coli.

scholarly journals Population Structure of Salmonella enterica Serovar 4,[5],12:b:− Strains and Likely Sources of Human Infection

2013 ◽  
Vol 79 (17) ◽  
pp. 5121-5129 ◽  
Author(s):  
Anne Toboldt ◽  
Erhard Tietze ◽  
Reiner Helmuth ◽  
Ernst Junker ◽  
Angelika Fruth ◽  
...  
Keyword(s):  
Population Structure ◽  
Salmonella Enterica ◽  
Human Infection ◽  
Second Phase ◽  
Gene Repertoire ◽  
Fish Food ◽  
Content Type ◽  
Potential Sources ◽  
Human Infections ◽  
Sequence Types

ABSTRACTSalmonella entericaserovar 4,[5],12:b:− is a monophasic serovar not able to express the second-phase flagellar antigen (H2 antigen). In Germany, the serovar is occasionally isolated from poultry, reptiles, fish, food, and humans. In this study, a selection of 67 epidemiologically unrelatedSalmonella entericaserovar 4,[5],12:b:− strains isolated in Germany between 2000 and 2011 from the environment, animal, food, and humans was investigated by phenotypic and genotypic methods to better understand the population structure and to identify potential sources of human infections. Strains of this monophasic serovar were highly diverse. Within the 67 strains analyzed, we identified 52 different pulsed-field gel electrophoresis XbaI profiles, 12 different multilocus sequence types (STs), and 18 different pathogenicity array types. The relatedness of strains based on the pathogenicity gene repertoire (102 markers tested) was in good agreement with grouping by MLST.S. entericaserovar 4,[5],12:b:− is distributed across multiple unrelated eBurst groups and consequently is highly polyphyletic. Two sequence types (ST88 and ST127) were linked toS. entericaserovar Paratyphi B (d-tartrate positive), two single-locus variants of ST1583 were linked toS. entericaserovar Abony, and one sequence type (ST1484) was associated withS. entericaserovar Mygdal, a recently defined, new serovar. From the characterization of clinical isolates and those of nonhuman origin, it can be concluded that the potential sources of sporadic human infections withS. entericaserovar 4,[5],12:b:− most likely are mushrooms, shellfish/fish, and poultry.

scholarly journals Dispersion of Multidrug-Resistant Enterococcus faecium Isolates Belonging to Major Clonal Complexes in Different Portuguese Settings

2009 ◽  
Vol 75 (14) ◽  
pp. 4904-4908 ◽  
Author(s):  
Ana R. Freitas ◽  
Carla Novais ◽  
Patricia Ruiz-Garbajosa ◽  
Teresa M. Coque ◽  
Luísa Peixe
Keyword(s):  
Population Structure ◽  
Enterococcus Faecium ◽  
Multilocus Sequence Typing ◽  
Multidrug Resistant ◽  
Human Infections ◽  
Sequence Types

ABSTRACT The population structure of 56 Enterococcus faecium isolates selected from a collection of enterococci from humans, animals, and the environment in Portugal (1997 to 2007) was analyzed by multilocus sequence typing. We identified 41 sequence types clustering into CC17, CC5, CC9, CC22 and CC94, all clonal lineages comprising isolates from different hosts. Our findings highlight the role of community-associated hosts as reservoirs of enterococci able to cause human infections.

scholarly journals Escherichia coli Sequence Type 457 Is an Emerging Extended-Spectrum-β-Lactam-Resistant Lineage with Reservoirs in Wildlife and Food-Producing Animals

2020 ◽  
Vol 65 (1) ◽  
pp. e01118-20
Author(s):  
Kristina Nesporova ◽  
Ethan R. Wyrsch ◽  
Adam Valcek ◽  
Ibrahim Bitar ◽  
Khin Chaw ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Large Scale ◽  
Broad Host Range ◽  
Content Type ◽  
E Coli ◽  
South Wales ◽  
High Prevalence ◽  
Genes Encoding ◽  
Extraintestinal Disease ◽  
Sequence Types

ABSTRACTSilver gulls carry phylogenetically diverse Escherichia coli, including globally dominant extraintestinal pathogenic E. coli (ExPEC) sequence types and pandemic ExPEC-ST131 clades; however, our large-scale study (504 samples) on silver gulls nesting off the coast of New South Wales identified E. coli ST457 as the most prevalent. A phylogenetic analysis of whole-genome sequences (WGS) of 138 ST457 samples comprising 42 from gulls, 2 from humans (Australia), and 14 from poultry farmed in Paraguay were compared with 80 WGS deposited in public databases from diverse sources and countries. E. coli ST457 strains are phylogenetic group F, carry fimH145, and partition into five main clades in accordance to predominant flagella H-antigen carriage. Although we identified considerable phylogenetic diversity among the 138 ST457 strains, closely related subclades (<100 SNPs) suggested zoonotic or zooanthroponosis transmission between humans, wild birds, and food-producing animals. Australian human clinical and gull strains in two of the clades were closely related (≤80 SNPs). Regarding plasmid content, country, or country/source, specific connections were observed, including I1/ST23, I1/ST314, and I1/ST315 disseminating blaCMY-2 in Australia, I1/ST113 carrying blaCTX-M-8 and mcr-5 in Paraguayan poultry, and F2:A-:B1 plasmids of Dutch origin being detected across multiple ST457 clades. We identified a high prevalence of nearly identical I1/ST23 plasmids carrying blaCMY-2 among Australian gull and clinical human strains. In summary, ST457 is a broad host range, geographically diverse E. coli lineage that can cause human extraintestinal disease, including urinary tract infection, and displays a remarkable ability to capture mobile elements that carry and transmit genes encoding resistance to critically important antibiotics.

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