Recent Emergence of Clonal Group O25b:K1:H4-B2-ST131 ibeA Strains among Escherichia coli Poultry Isolates, Including CTX-M-9-Producing Strains, and Comparison with Clinical Human Isolates

ABSTRACT To discern the possible spread of the Escherichia coli O25b:H4-ST131 clonal group in poultry and the zoonotic potential of avian strains, we made a retrospective search of our strain collection and compared the findings for those strains with the findings for current strains. Thus, we have characterized a collection of 19 avian O25b:H4-ST131 E. coli strains isolated from 1995 to 2010 which, interestingly, harbored the ibeA gene. Using this virulence gene as a criterion for selection, we compared those 19 avian strains with 33 human O25b:H4-ST131 ibeA-positive E. coli strains obtained from patients with extraintestinal infections (1993 to 2009). All 52 O25b:H4-ST131 ibeA-positive E. coli strains shared the fimH, kpsMII, malX, and usp genes but showed statistically significant differences in nine virulence factors, namely, papGIII, cdtB, sat, and kpsMII K5, which were associated with human strains, and iroN, kpsMII K1, cvaC, iss, and tsh, which were associated with strains of avian origin. The XbaI macrorestriction profiles of the 52 E. coli O25b:H4-ST131 ibeA-positive strains revealed 11 clusters (clusters I to XI) of >85% similarity, with four clusters including strains of human and avian origin. Cluster VII (90.9% similarity) grouped 10 strains (7 avian and 3 human strains) that mostly produced CTX-M-9 and that also shared the same virulence profile. Finally, we compared the macrorestriction profiles of the 12 CTX-M-9-producing O25b:H4-ST131 ibeA strains (7 avian and 5 human strains) identified among the 52 strains with those of 15 human O25b:H4-ST131 CTX-M-14-, CTX-M-15-, and CTX-M-32-producing strains that proved to be negative for ibeA and showed that they clearly differed in the level of similarity from the CTX-M-9-producing strains. In conclusion, E. coli clonal group O25b:H4-ST131 ibeA has recently emerged among avian isolates with the new acquisition of the K1 capsule antigen and includes CTX-M-9-producing strains. This clonal group represents a real zoonotic risk that has crossed the barrier between human and avian hosts.

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Intestine and Environment of the Chicken as Reservoirs for Extraintestinal Pathogenic Escherichia coli Strains with Zoonotic Potential

Applied and Environmental Microbiology ◽

10.1128/aem.01324-08 ◽

2008 ◽

Vol 75 (1) ◽

pp. 184-192 ◽

Cited By ~ 133

Author(s):

Christa Ewers ◽

Esther-Maria Antï¿½o ◽

Ines Diehl ◽

Hans-C. Philipp ◽

Lothar H. Wieler

Keyword(s):

Escherichia Coli ◽

Virulence Gene ◽

Infection Model ◽

E Coli ◽

Gene Profiles ◽

Pathogenic Escherichia Coli ◽

Zoonotic Risk ◽

Resistant Strains ◽

Genetic Pool

ABSTRACT Although research has increasingly focused on the pathogenesis of avian pathogenic Escherichia coli (APEC) infections and the “APEC pathotype” itself, little is known about the reservoirs of these bacteria. We therefore compared outbreak strains isolated from diseased chickens (n = 121) with nonoutbreak strains, including fecal E. coli strains from clinically healthy chickens (n = 211) and strains from their environment (n = 35) by determining their virulence gene profiles, phylogenetic backgrounds, responses to chicken serum, and in vivo pathogenicities in a chicken infection model. In general, by examining 46 different virulence-associated genes we were able to distinguish the three groups of avian strains, but some specific fecal and environmental isolates had a virulence gene profile that was indistinguishable from that determined for outbreak strains. In addition, a substantial number of phylogenetic EcoR group B2 strains, which are known to include potent human and animal extraintestinal pathogenic E. coli (ExPEC) strains, were identified among the APEC strains (44.5%) as well as among the fecal E. coli strains from clinically healthy chickens (23.2%). Comparably high percentages (79.2 to 89.3%) of serum-resistant strains were identified for all three groups of strains tested, bringing into question the usefulness of this phenotype as a principal marker for extraintestinal virulence. Intratracheal infection of 5-week-old chickens corroborated the pathogenicity of a number of nonoutbreak strains. Multilocus sequence typing data revealed that most strains that were virulent in chicken infection experiments belonged to sequence types that are almost exclusively associated with extraintestinal diseases not only in birds but also in humans, like septicemia, urinary tract infection, and newborn meningitis, supporting the hypothesis that not the ecohabitat but the phylogeny of E. coli strains determines virulence. These data provide strong evidence for an avian intestinal reservoir hypothesis which could be used to develop intestinal intervention strategies. These strains pose a zoonotic risk because either they could be transferred directly from birds to humans or they could serve as a genetic pool for ExPEC strains.

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Isolation and Characterization of Potentially Pathogenic Antimicrobial-Resistant Escherichia coli Strains from Chicken and Pig Farms in Spain

Applied and Environmental Microbiology ◽

10.1128/aem.02421-09 ◽

2010 ◽

Vol 76 (9) ◽

pp. 2799-2805 ◽

Cited By ~ 147

Author(s):

Pilar Cortés ◽

Vanessa Blanc ◽

Azucena Mora ◽

Ghizlane Dahbi ◽

Jesús E. Blanco ◽

...

Keyword(s):

Escherichia Coli ◽

Virulence Genes ◽

Phylogenetic Analyses ◽

Virulence Gene ◽

E Coli ◽

Isolation And Characterization ◽

Zoonotic Risk ◽

Poultry Farms ◽

Pig Farms ◽

Genes Encoding

ABSTRACT To ascertain whether on animal farms there reside extended-spectrum β-lactamase (ESBL) and plasmidic class C β-lactamase-producing Escherichia coli isolates potentially pathogenic for humans, phylogenetic analyses, pulsed-field gel electrophoresis (PFGE) typing, serotyping, and virulence genotyping were performed for 86 isolates from poultry (57 isolates) and pig (29 isolates) farms. E. coli isolates from poultry farms carried genes encoding enzymes of the CTX-M-9 group as well as CMY-2, whereas those from pig farms mainly carried genes encoding CTX-M-1 enzymes. Poultry and pig isolates differed significantly in their phylogenetic group assignments, with phylogroup A predominating in pig isolates and phylogroup D predominating in avian isolates. Among the 86 farm isolates, 23 (26.7%) carried two or more virulence genes typical of extraintestinal pathogenic E. coli (ExPEC). Of these, 20 were isolated from poultry farms and only 3 from pig farms. Ten of the 23 isolates belonged to the classic human ExPEC serotypes O2:H6, O2:HNM, O2:H7, O15:H1, and O25:H4. Despite the high diversity of serotypes and pulsotypes detected among the 86 farm isolates, 13 PFGE clusters were identified. Four of these clusters contained isolates with two or more virulence genes, and two clusters exhibited the classic human ExPEC serotypes O2:HNM (ST10) and O2:H6 (ST115). Although O2:HNM and O2:H6 isolates of human and animal origins differed with respect to their virulence genes and PFGE pulsotypes, the O2:HNM isolates from pigs showed the same sequence type (ST10) as those from humans. The single avian O15:H1 isolate was compared with human clinical isolates of this serotype. Although all were found to belong to phylogroup D and shared the same virulence gene profile, they differed in their sequence types (ST362-avian and ST393-human) and PFGE pulsotypes. Noteworthy was the detection, for the first time, in poultry farms of the clonal groups O25b:H4-ST131-B2, producing CTX-M-9, and O25a-ST648-D, producing CTX-M-32. The virulence genes and PFGE profiles of these two groups were very similar to those of clinical human isolates. While further studies are required to determine the true zoonotic potential of these clonal groups, our results emphasize the zoonotic risk posed especially by poultry farms, but also by pig farms, as reservoirs of ESBL- and CMY-2-encoding E. coli.

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Epidemic Emergence in the United States of Escherichia coli Sequence Type 131-H30 (ST131-H30), 2000 to 2009

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00732-17 ◽

2017 ◽

Vol 61 (8) ◽

Cited By ~ 24

Author(s):

James R. Johnson ◽

Stephen Porter ◽

Paul Thuras ◽

Mariana Castanheira

Keyword(s):

United States ◽

Escherichia Coli ◽

Single Agent ◽

Temporal Trends ◽

Virulence Gene ◽

The United States ◽

Sequence Type ◽

Content Type ◽

E Coli ◽

Recent Emergence

ABSTRACT The H30 subclone of Escherichia coli sequence type 131 (ST131-H30) has become the leading antimicrobial resistance E. coli lineage in the United States and often exhibits resistance to one or both of the two key antimicrobial classes for treating Gram-negative infections, extended-spectrum cephalosporins (ESCs) and fluoroquinolones (FQs). However, the timing of and reasons for its recent emergence are inadequately defined. Accordingly, from E. coli clinical isolates collected systematically across the United States by the SENTRY Antimicrobial Surveillance Program in 2000, 2003, 2006, and 2009, 234 isolates were selected randomly, stratified by year, within three resistance categories: (i) ESC-reduced susceptibility, regardless of FQ phenotype (ESC-RS); (ii) FQ resistance, ESC susceptible (FQ-R); and (iii) FQ susceptible, ESC susceptible (FQ-S). Susceptibility profiles, phylogroup, ST, ST131 subclone, and virulence genotypes were determined, and temporal trends and between-variable associations were assessed statistically. From 2000 to 2006, concurrently with the emergence of ESC-RS and FQ-R strains, the prevalence of (virulence-associated) phylogroup B2 among such strains also rose dramatically, due entirely to rapid emergence of ST131, especially H30. By 2009, H30 was the dominant E. coli lineage overall (22%), accounting for a median of 43% of all single-agent and multidrug resistance (68% for ciprofloxacin). H30's emergence increased the net virulence gene content of resistant (especially FQ-R) isolates, giving stable overall virulence gene scores despite an approximately 4-fold expansion of the historically less virulent resistant population. These findings define more precisely the timing and tempo of H30's emergence in the United States, identify possible reasons for it, and suggest potential consequences, including more frequent and/or aggressive antimicrobial-resistant infections.

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Epidemic Clonal Groups of Escherichia coli as a Cause of Antimicrobial-Resistant Urinary Tract Infections in Canada, 2002 to 2004

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00297-09 ◽

2009 ◽

Vol 53 (7) ◽

pp. 2733-2739 ◽

Cited By ~ 192

Author(s):

James R. Johnson ◽

Megan Menard ◽

Brian Johnston ◽

Michael A. Kuskowski ◽

Kim Nichol ◽

...

Keyword(s):

Escherichia Coli ◽

Sequence Type ◽

Drug Resistant ◽

Clonal Group ◽

E Coli ◽

Strain Collection ◽

Group A ◽

Nationally Representative ◽

Clonal Spread ◽

Tract Infections

ABSTRACT The extent to which clonal spread contributes to emerging antimicrobial resistance in Escherichia coli is incompletely defined. To address this question within a recent, nationally representative strain collection, three established drug-resistant E. coli clonal groups (i.e., clonal group A, E. coli O15:K52:H1, and sequence type 131 [ST131]) were sought among 199 E. coli urine isolates recovered from across Canada from 2002 to 2004, with stratification by resistance to trimethoprim-sulfamethoxazole (TS) and fluoroquinolones (FQs). The isolates' clonal backgrounds, virulence genotypes, and macrorestriction profiles were assessed. The three clonal groups were found to account for 37.2% of isolates overall, but accounted for 0% of TS-susceptible (TS-S) and FQ-susceptible (FQ-S) isolates, 20% of TS-resistant (TS-R) and FQ-S isolates, 60% of TS-S and FQ-R isolates, and 68% of TS-R and FQ-R isolates (P < 0.001). E. coli ST131, the most prevalent clonal group, accounted for 23.1% of isolates overall and for 44% of the FQ-R isolates. Nearly all ST131 isolates were FQ-R (96%) but, notably, cephalosporin susceptible (98%). Although the distinctive virulence profiles of the FQ-R clonal group isolates were less extensive than those of the susceptible isolates, they were significantly more extensive than those of the other FQ-R isolates. These findings indicate that among the E. coli urine isolates studied, resistance to TS and FQs has a prominent clonal component, with the O15:K52:H1 clonal group and especially E. coli ST131 being the major contributors. These clonal groups appear to be more virulent than comparably resistant isolates, possibly contributing to their success as emerging multi-drug-resistant pathogens.

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Complete Assembly ofEscherichia coliSequence Type 131 Genomes Using Long Reads Demonstrates Antibiotic Resistance Gene Variation within Diverse Plasmid and Chromosomal Contexts

mSphere ◽

10.1128/msphere.00130-19 ◽

2019 ◽

Vol 4 (3) ◽

Cited By ~ 10

Author(s):

Arun Gonzales Decano ◽

Catherine Ludden ◽

Theresa Feltwell ◽

Kim Judge ◽

Julian Parkhill ◽

...

Keyword(s):

Escherichia Coli ◽

Dna Sequencing ◽

Health Concern ◽

Resistant Bacteria ◽

Content Type ◽

Clonal Group ◽

E Coli ◽

Two Samples ◽

Long Read ◽

M 14

ABSTRACTThe incidence of infections caused by extraintestinalEscherichia coli(ExPEC) is rising globally, which is a major public health concern. ExPEC strains that are resistant to antimicrobials have been associated with excess mortality, prolonged hospital stays, and higher health care costs.E. colisequence type 131 (ST131) is a major ExPEC clonal group worldwide, with variable plasmid composition, and has an array of genes enabling antimicrobial resistance (AMR). ST131 isolates frequently encode the AMR genesblaCTX-M-14,blaCTX-M-15, andblaCTX-M-27, which are often rearranged, amplified, and translocated by mobile genetic elements (MGEs). Short DNA reads do not fully resolve the architecture of repetitive elements on plasmids to allow MGE structures encodingblaCTX-Mgenes to be fully determined. Here, we performed long-read sequencing to decipher the genome structures of sixE. coliST131 isolates from six patients. Most long-read assemblies generated entire chromosomes and plasmids as single contigs, in contrast to more fragmented assemblies created with short reads alone. The long-read assemblies highlighted diverse accessory genomes withblaCTX-M-15,blaCTX-M-14, andblaCTX-M-27genes identified in three, one, and one isolates, respectively. One sample had noblaCTX-Mgene. Two samples had chromosomalblaCTX-M-14andblaCTX-M-15genes, and the latter was at three distinct locations, likely transposed by the adjacent MGEs: ISEcp1, IS903B,and Tn2. This study showed that AMR genes exist in multiple different chromosomal and plasmid contexts, even between closely related isolates within a clonal group such asE. coliST131.IMPORTANCEDrug-resistant bacteria are a major cause of illness worldwide, and a specific subtype calledEscherichia coliST131 causes a significant number of these infections. ST131 bacteria become resistant to treatments by modifying their DNA and by transferring genes among one another via large packages of genes called plasmids, like a game of pass-the-parcel. Tackling infections more effectively requires a better understanding of what plasmids are being exchanged and their exact contents. To achieve this, we applied new high-resolution DNA sequencing technology to six ST131 samples from infected patients and compared the output to that of an existing approach. A combination of methods shows that drug resistance genes on plasmids are highly mobile because they can jump into ST131’s chromosomes. We found that the plasmids are very elastic and undergo extensive rearrangements even in closely related samples. This application of DNA sequencing technologies illustrates at a new level the highly dynamic nature of ST131 genomes.

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Complete assembly ofEscherichia coliST131 genomes using long reads demonstrates antibiotic resistance gene variation within diverse plasmid and chromosomal contexts

10.1101/558635 ◽

2019 ◽

Cited By ~ 1

Author(s):

Arun Decano ◽

Catherine Ludden ◽

Theresa Feltwell ◽

Kim Judge ◽

Julian Parkhill ◽

...

Keyword(s):

Escherichia Coli ◽

Dna Sequencing ◽

Antibiotic Resistance Gene ◽

Health Concern ◽

Resistant Bacteria ◽

Clonal Group ◽

E Coli ◽

Two Samples ◽

Long Read ◽

M 14

AbstractThe incidence of infections caused by extraintestinalEscherichia coli(ExPEC) is rising globally, which is a major public health concern. ExPEC strains that are resistant to antimicrobials have been associated with excess mortality, prolonged hospital stays and higher healthcare costs.E. coliST131 is a major ExPEC clonal group worldwide with variable plasmid composition, and has an array of genes enabling antimicrobial resistance (AMR). ST131 isolates frequently encode the AMR genesblaCTX-M-14/15/27, which are often rearranged, amplified and translocated by mobile genetic elements (MGEs). Short DNA reads do not fully resolve the architecture of repetitive elements on plasmids to allow MGE structures encodingblaCTX-Mgenes to be fully determined. Here, we performed long read sequencing to decipher the genome structures of sixE. coliST131 isolated from six patients. Most long read assemblies generated entire chromosomes and plasmids as single contigs, contrasting with more fragmented assemblies created with short reads alone. The long read assemblies highlighted diverse accessory genomes withblaCTX-M-15,blaCTX-M-14andblaCTX-M-27genes identified in three, one and one isolates, respectively. One sample had noblaCTX-Mgene. Two samples had chromosomalblaCTX-M-14andblaCTX-M-15genes, and the latter was at three distinct locations, likely transposed by the adjacent MGEs: ISEcp1, IS903Band Tn2. This study showed that AMR genes exist in multiple different chromosomal and plasmid contexts even between closely-related isolates within a clonal group such asE. coliST131.ImportanceDrug-resistant bacteria are a major cause of illness worldwide and a specific subtype calledEscherichia coliST131 cause a significant amount of these infections. ST131 become resistant to treatment by modifying their DNA and by transferring genes among one another via large packages of genes called plasmids, like a game of pass-the-parcel. Tackling infections more effectively requires a better understanding of what plasmids are being exchanged and their exact contents. To achieve this, we applied new high-resolution DNA sequencing technology to six ST131 samples from infected patients and compared the output to an existing approach. A combination of methods shows that drug-resistance genes on plasmids are highly mobile because they can jump into ST131’s chromosomes. We found that the plasmids are very elastic and undergo extensive rearrangements even in closely related samples. This application of DNA sequencing technologies illustrates at a new level the highly dynamic nature of ST131 genomes.

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Occurrence of virulence-related sequences and phylogenetic analysis of commensal and pathogenic avian Escherichia coli strains (APEC)

Pesquisa Veterinária Brasileira ◽

10.1590/s0100-736x2008001000015 ◽

2008 ◽

Vol 28 (10) ◽

pp. 533-540 ◽

Cited By ~ 7

Author(s):

Tatiana Amabile de Campos ◽

Juliana Carvalhães Lago ◽

Gerson Nakazato ◽

Eliana Guedes Stehling ◽

Marcelo Brocchi ◽

...

Keyword(s):

Escherichia Coli ◽

Dna Sequences ◽

Pathogenic Bacteria ◽

Clinical Signs ◽

Phylogenetic Group ◽

Phylogenetic Groups ◽

Clonal Group ◽

E Coli ◽

Zoonotic Risk ◽

Group A

The presence of iron uptake (irp-2, fyuA, sitA, fepC, iucA), adhesion (iha, lpfA O157/O141, lpfA O157/O154, efa, toxB) and invasion (inv, ial-related DNA sequences and assignment to the four main Escherichia coli phylogenetic groups (A, B1, B2 e D) were determined in 30 commensal E. coli strains isolated from healthy chickens and in 49 APEC strains isolated from chickens presenting clinical signs of septicemia (n=24) swollen head syndrome (n=14) and omphalitis (n=11) by PCR. None of the strains presented DNA sequences related to the inv, ial, efa, and toxB genes. DNA sequences related to lpfA O157/O154, iucA, fepC, and irp-2 genes were significantly found among pathogenic strains, where iucA gene was associated with septicemia and swollen head syndrome and fepC and irp-2 genes were associated with swollen head syndrome strains. Phylogenetic typing showed that commensal and omphalitis strains belonged mainly to phylogenetic Group A and swollen head syndrome to phylogenetic Group D. Septicemic strains were assigned in phylogenetic Groups A and D. These data could suggest that clonal lineage of septicemic APEC strains have a multiple ancestor origin; one from a pathogenic bacteria ancestor and other from a non-pathogenic ancestor that evolved by the acquisition of virulence related sequences through horizontal gene transfer. Swollen head syndrome may constitute a pathogenic clonal group. By the other side, omphalitis strains probably constitute a non-pathogenic clonal group, and could cause omphalitis as an opportunistic infection. The sharing of virulence related sequences by human pathogenic E. coli and APEC strains could indicate that APEC strains could be a source of virulence genes to human strains and could represent a zoonotic risk.

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Phylogenetic and Molecular Analysis of Food-Borne Shiga Toxin-Producing Escherichia coli

Applied and Environmental Microbiology ◽

10.1128/aem.03552-12 ◽

2013 ◽

Vol 79 (8) ◽

pp. 2731-2740 ◽

Cited By ~ 27

Author(s):

Elisabeth Hauser ◽

Alexander Mellmann ◽

Torsten Semmler ◽

Helen Stoeber ◽

Lothar H. Wieler ◽

...

Keyword(s):

Escherichia Coli ◽

Shiga Toxin ◽

Virulence Gene ◽

Human Infection ◽

Pathogenic Potential ◽

Content Type ◽

E Coli ◽

Food Borne ◽

Strain Collection ◽

Integration Sites

ABSTRACTSeventy-five food-associated Shiga toxin-producingEscherichia coli(STEC) strains were analyzed by molecular and phylogenetic methods to describe their pathogenic potential. The presence of the locus of proteolysis activity (LPA), the chromosomal pathogenicity island (PAI) PAI ICL3, and the autotransporter-encoding genesabAwas examined by PCR. Furthermore, the occupation of the chromosomal integration sites of the locus of enterocyte effacement (LEE),selC,pheU, andpheV, as well as the Stx phage integration sitesyehV,yecE,wrbA,z2577, andssrA, was analyzed. Moreover, the antibiotic resistance phenotypes of all STEC strains were determined. Multilocus sequence typing (MLST) was performed, and sequence types (STs) and sequence type complexes (STCs) were compared with those of 42 hemolytic-uremic syndrome (HUS)-associated enterohemorrhagicE. coli(HUSEC) strains. Besides 59 STs and 4 STCs, three larger clusters were defined in this strain collection. Clusters A and C consist mostly of highly pathogeniceae-positive HUSEC strains and some related food-borne STEC strains. A member of a new O26 HUS-associated clone and the 2011 outbreak strainE. coliO104:H4 were found in cluster A. Cluster B comprises onlyeae-negative food-borne STEC strains as well as mainlyeae-negative HUSEC strains. Although food-borne strains of cluster B were not clearly associated with disease, serotypes of important pathogens, such as O91:H21 and O113:H21, were in this cluster and closely related to the food-borne strains. Clonal analysis demonstrated eight closely related genetic groups of food-borne STEC and HUSEC strains that shared the same ST and were similar in their virulence gene composition. These groups should be considered with respect to their potential for human infection.

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Lineages and Virulence Gene Content among Extended-Spectrum β-Lactamase–Producing Escherichia coli Strains of Food Origin in Tunisia

Journal of Food Protection ◽

10.4315/0362-028x.jfp-12-251 ◽

2013 ◽

Vol 76 (2) ◽

pp. 323-327 ◽

Cited By ~ 18

Author(s):

AHLEM JOUINI ◽

KARIM BEN SLAMA ◽

NAOUEL KLIBI ◽

RYM BEN SALLEM ◽

VANESA ESTEPA ◽

...

Keyword(s):

Escherichia Coli ◽

Virulence Genes ◽

Virulence Gene ◽

Food Samples ◽

Phylogenetic Groups ◽

E Coli ◽

Extended Spectrum ◽

Sequence Types ◽

M 14 ◽

High Diversity

Nineteen extended-spectrum β-lactamase (ESBL)–positive Escherichia coli strains recovered from food samples in Tunisia were characterized by multilocus sequence typing and phylogenetic typing, and the virulence gene and plasmid content were also determined. These strains presented unrelated pulsed-field gel electrophoresis patterns and contained genes coding for the following ESBLs (the number of strains is in parentheses): CTX-M-1 (15), CTX-M-14 (2), CTX-M-8 (1), and SHV-5 (1). Twelve different sequence types (STs) were identified among the 19 ESBL-positive strains, which included two new STs (ST2022 in 2 blaCTX-M-14–containing strains and ST1970 in 2 blaCTX-M-1–containing strains). ST155 and ST602 were detected in four and three blaCTX-M-1–containing strains, respectively, and ST405 was detected in one blaCTX-M-8–producing strain. All ESBL-positive strains were ascribed to the phylogenetic groups A and B1. Most of the blaCTX-M-1–containing strains harbored an IncI1 plasmid, except for the four blaCTX-M-1–positive strains of beef origin and ST155, which harbored an IncN plasmid. The two blaCTX-M-14–containing strains contained an IncI1 plasmid. The virulence gene fimA was detected in all strains. Most strains also carried the aer gene, and six strains carried the eae gene. All strains were negative for the virulence genes sxt, papG-III, papC, hly, cnf1, and bfp. We conclude that ESBL-producing E. coli strains of food origin in Tunisia show high diversity and that plasmids harboring ESBL genes could be implicated in the dissemination of this resistance phenotype.

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Genome evolution and the emergence of pathogenicity in avian Escherichia coli

Nature Communications ◽

10.1038/s41467-021-20988-w ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Leonardos Mageiros ◽

Guillaume Méric ◽

Sion C. Bayliss ◽

Johan Pensar ◽

Ben Pascoe ◽

...

Keyword(s):

Escherichia Coli ◽

Association Studies ◽

Virulence Gene ◽

Systemic Infection ◽

Disease Status ◽

Evolutionary Mechanisms ◽

Sustainable Food ◽

E Coli ◽

Common Birds ◽

Systemic Infections

AbstractChickens are the most common birds on Earth and colibacillosis is among the most common diseases affecting them. This major threat to animal welfare and safe sustainable food production is difficult to combat because the etiological agent, avian pathogenic Escherichia coli (APEC), emerges from ubiquitous commensal gut bacteria, with no single virulence gene present in all disease-causing isolates. Here, we address the underlying evolutionary mechanisms of extraintestinal spread and systemic infection in poultry. Combining population scale comparative genomics and pangenome-wide association studies, we compare E. coli from commensal carriage and systemic infections. We identify phylogroup-specific and species-wide genetic elements that are enriched in APEC, including pathogenicity-associated variation in 143 genes that have diverse functions, including genes involved in metabolism, lipopolysaccharide synthesis, heat shock response, antimicrobial resistance and toxicity. We find that horizontal gene transfer spreads pathogenicity elements, allowing divergent clones to cause infection. Finally, a Random Forest model prediction of disease status (carriage vs. disease) identifies pathogenic strains in the emergent ST-117 poultry-associated lineage with 73% accuracy, demonstrating the potential for early identification of emergent APEC in healthy flocks.

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