Antimicrobial Resistance of Escherichia coli Isolates from Mastitic Milk and its Possible Relationship with Resistance and Virulence Genes

AbstractThe emergence of antimicrobial resistance (AMR) is one of the biggest health threats globally. In addition, the use of antimicrobial drugs in humans and livestock is considered an important driver of antimicrobial resistance. The commensal microbiota, and especially the intestinal microbiota, has been shown to have an important role in the emergence of AMR. Mobile genetic elements (MGEs) also play a central role in facilitating the acquisition and spread of AMR genes. We isolated Escherichia coli (n = 627) from fecal samples in respectively 25 poultry, 28 swine, and 15 veal calf herds from 6 European countries to investigate the phylogeny of E. coli at country, animal host and farm levels. Furthermore, we examine the evolution of AMR in E. coli genomes including an association with virulence genes, plasmids and MGEs. We compared the abundance metrics retrieved from metagenomic sequencing and whole genome sequenced of E. coli isolates from the same fecal samples and farms. The E. coli isolates in this study indicated no clonality or clustering based on country of origin and genetic markers; AMR, and MGEs. Nonetheless, mobile genetic elements play a role in the acquisition of AMR and virulence genes. Additionally, an abundance of AMR was agreeable between metagenomic and whole genome sequencing analysis for several AMR classes in poultry fecal samples suggesting that metagenomics could be used as an indicator for surveillance of AMR in E. coli isolates and vice versa.

Download Full-text

Molecular characterisation of antimicrobial resistance and virulence genes in Escherichia coli strains isolated from diarrhoeic and healthy rabbits in Tunisia

World Rabbit Science ◽

10.4995/wrs.2020.10879 ◽

2020 ◽

Vol 28 (2) ◽

pp. 81

Author(s):

Raouia Ben Rhouma ◽

Ahlem Jouini ◽

Amira Klibi ◽

Safa Hamrouni ◽

Aziza Boubaker ◽

...

Keyword(s):

Escherichia Coli ◽

Antimicrobial Resistance ◽

Virulence Genes ◽

Antimicrobial Agents ◽

Antibiotic Resistance Genes ◽

Virulence Gene ◽

Diffusion Method ◽

Class 1 Integron ◽

E Coli ◽

Class 1

The purpose of this study was to identify Escherichia coli isolates in diarrhoeic and healthy rabbits in Tunisia and characterise their virulence and antibiotic resistance genes. In the 2014-2015 period, 60 faecal samples from diarrhoeic and healthy rabbits were collected from different breeding farms in Tunisia. Susceptibility to 14 antimicrobial agents was tested by disc diffusion method and the mechanisms of gene resistance were evaluated using polymerase chain reaction and sequencing methods. Forty E. coli isolates were recovered in selective media. High frequency of resistance to tetracycline (95%) was detected, followed by different levels of resistance to sulphonamide (72.5%), streptomycin (62.5%), trimethoprim-sulfamethoxazole (60%), nalidixic acid (32.5%), ampicillin (37.5%) and ticarcillin (35%). E. coli strains were susceptible to cefotaxime, ceftazidime and imipenem. Different variants of blaTEM, tet, sul genes were detected in most of the strains resistant to ampicillin, tetracycline and sulphonamide, respectively. The presence of class 1 integron was studied in 29 sulphonamide-resistant E. coli strains from which 15 harboured class 1 integron with four different arrangements of gene cassettes, dfrA17+aadA5 (n=9), dfrA1 + aadA1 (n=4), dfrA12 + addA2 (n=1), dfrA12+orf+addA2 (n=1). The qnrB gene was detected in six strains out of 13 quinolone-resistant E. coli strains. Seventeen E. coli isolates from diarrhoeic rabbits harboured the enteropathogenic eae genes associated with different virulence genes tested (fimA, cnf1, aer), and affiliated to B2 (n=8) and D (n=9) phylogroups. Isolated E. coli strains from healthy rabbit were harbouring fim A and/or cnf1 genes and affiliated to A and B1 phylogroups. This study showed that E. coli strains from the intestinal tract of rabbits are resistant to the widely prescribed antibiotics in medicine. Therefore, they constitute a reservoir of antimicrobial-resistant genes, which may play a significant role in the spread of antimicrobial resistance. In addition, the eae virulence gene seemed to be implicated in diarrhoea in breeder rabbits in Tunisia.

Download Full-text

Virulence Genes of Escherichia coli Strains Isolated from Mastitic Milk

Journal of Veterinary Medicine Series B ◽

10.1111/j.1439-0450.2004.00772.x ◽

2004 ◽

Vol 51 (6) ◽

pp. 285-287 ◽

Cited By ~ 17

Author(s):

A. Bean ◽

J. Williamson ◽

R. T. Cursons

Keyword(s):

Escherichia Coli ◽

Virulence Genes ◽

Mastitic Milk

Download Full-text

Serotypes, virulence genes profiles and antimicrobial resistance patterns of Escherichia coli recovered from feces of healthy lambs in Mexico

Small Ruminant Research ◽

10.1016/j.smallrumres.2017.05.003 ◽

2017 ◽

Vol 153 ◽

pp. 41-47 ◽

Cited By ~ 1

Author(s):

Edgar Enriquez-Gómez ◽

Martín Talavera-Rojas ◽

Edgardo Soriano-Vargas ◽

Armando Navarro-Ocaña ◽

Vicente Vega-Sánchez ◽

...

Keyword(s):

Escherichia Coli ◽

Antimicrobial Resistance ◽

Virulence Genes ◽

Resistance Patterns

Download Full-text

Genome-based characterization of Escherichia coli causing bloodstream infection through next-generation sequencing

PLoS ONE ◽

10.1371/journal.pone.0244358 ◽

2020 ◽

Vol 15 (12) ◽

pp. e0244358

Author(s):

Rafika Indah Paramita ◽

Erni Juwita Nelwan ◽

Fadilah Fadilah ◽

Editha Renesteen ◽

Nelly Puspandari ◽

...

Keyword(s):

Escherichia Coli ◽

Antimicrobial Resistance ◽

Whole Genome Sequencing ◽

Bloodstream Infection ◽

Genome Sequencing ◽

Virulence Genes ◽

Sequence Type ◽

Whole Genome ◽

National Hospital ◽

Sequence Types

Escherichia coli are one of the commonest bacteria causing bloodstream infection (BSI). The aim of the research was to identify the serotypes, MLST (Multi Locus Sequence Type), virulence genes, and antimicrobial resistance of E. coli isolated from bloodstream infection hospitalized patients in Cipto Mangunkusumo National Hospital Jakarta. We used whole genome sequencing methods rather than the conventional one, to characterized the serotypes, MLST (Multi Locus Sequence Type), virulence genes, and antimicrobial resistance (AMR) of E. coli. The composition of E. coli sequence types (ST) was as follows: ST131 (n = 5), ST38 (n = 3), ST405 (n = 3), ST69 (n = 3), and other STs (ST1057, ST127, ST167, ST3033, ST349, ST40, ST58, ST6630). Enteroaggregative E. coli (EAEC) and Extra-intestinal pathogenic E. coli (ExPEC) groups were found dominant in our samples. Twenty isolates carried virulence genes for host cells adherence and 15 for genes that encourage E. coli immune evasion by enhancing survival in serum. ESBL-genes were present in 17 E. coli isolates. Other AMR genes also encoded resistance against aminoglycosides, quinolones, chloramphenicol, macrolides and trimethoprim. The phylogeny analysis showed that phylogroup D is dominated and followed by phylogroup B2. The E. coli isolated from 22 patients in Cipto Mangunkusumo National Hospital Jakarta showed high diversity in serotypes, sequence types, virulence genes, and AMR genes. Based on this finding, routinely screening all bacterial isolates in health care facilities can improve clinical significance. By using Whole Genome Sequencing for laboratory-based surveillance can be a valuable early warning system for emerging pathogens and resistance mechanisms.

Download Full-text

Virulence Characteristics and Antimicrobial Resistance Profiles of Shiga Toxin-Producing Escherichia coli Isolates from Humans in South Africa: 2006–2013

Toxins ◽

10.3390/toxins11070424 ◽

2019 ◽

Vol 11 (7) ◽

pp. 424 ◽

Cited By ~ 5

Author(s):

Karama ◽

Cenci-Goga ◽

Malahlela ◽

Smith ◽

Keddy ◽

...

Keyword(s):

Escherichia Coli ◽

South Africa ◽

Antimicrobial Resistance ◽

Shiga Toxin ◽

Human Disease ◽

Virulence Genes ◽

Pulsed Field Gel Electrophoresis ◽

Marker Genes ◽

Surveillance Programs ◽

Monitoring And Surveillance

Shiga toxin-producing Escherichia coli (STEC) isolates (N = 38) that were incriminated in human disease from 2006 to 2013 in South Africa were characterized by serotype, virulence-associated genes, antimicrobial resistance and pulsed-field gel electrophoresis (PFGE). The isolates belonged to 11 O:H serotypes. STEC O26:H11 (24%) was the most frequent serotype associated with human disease, followed by O111:H8 (16%), O157:H7 (13%) and O117:H7 (13%). The majority of isolates were positive for key virulence-associated genes including stx1 (84%), eaeA (61%), ehxA (68.4%) and espP (55%), but lacked stx2 (29%), katP (42%), etpD (16%), saa (16%) and subA (3%). stx2 positive isolates carried stx2c (26%) and/or stx2d (26%) subtypes. All pathogenicity island encoded virulence marker genes were detected in all (100%) isolates except nleA (47%), nleC (84%) and nleD (76%). Multidrug resistance was observed in 89% of isolates. PFGE revealed 34 profiles with eight distinct clusters that shared ≥80% intra-serotype similarity, regardless of the year of isolation. In conclusion, STEC isolates that were implicated in human disease between 2006 and 2013 in South Africa were mainly non-O157 strains which possessed virulence genes and markers commonly associated with STEC strains that have been incriminated in mild to severe human disease worldwide. Improved STEC monitoring and surveillance programs are needed in South Africa to control and prevent STEC disease in humans.

Download Full-text

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

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.03679-14 ◽

2014 ◽

Vol 58 (11) ◽

pp. 6886-6895 ◽

Cited By ~ 35

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.

Download Full-text

Virulence Genes and Antimicrobial Resistance Pattern in Uropathogenic Escherichia coli Isolated From Hospitalized Patients in Kashan, Iran

Jundishapur Journal of Microbiology ◽

10.5812/jjm.17514 ◽

2015 ◽

Vol 8 (2) ◽

Cited By ~ 14

Author(s):

Foroogh Neamati ◽

Farzaneh Firoozeh ◽

Mahmood Saffari ◽

Mohammad Zibaei

Keyword(s):

Escherichia Coli ◽

Antimicrobial Resistance ◽

Virulence Genes ◽

Uropathogenic Escherichia Coli ◽

Hospitalized Patients ◽

Resistance Pattern

Download Full-text

A Virulence and Antimicrobial Resistance DNA Microarray Detects a High Frequency of Virulence Genes in Escherichia coli Isolates from Great Lakes Recreational Waters

Applied and Environmental Microbiology ◽

10.1128/aem.00137-06 ◽

2006 ◽

Vol 72 (6) ◽

pp. 4200-4206 ◽

Cited By ~ 82

Author(s):

Katia Hamelin ◽

Guillaume Bruant ◽

Abdel El-Shaarawi ◽

Stephen Hill ◽

Thomas A. Edge ◽

...

Keyword(s):

Public Health ◽

Escherichia Coli ◽

Antimicrobial Resistance ◽

Great Lakes ◽

Dna Microarray ◽

Resistance Genes ◽

Virulence Genes ◽

Recreational Waters ◽

E Coli ◽

Antimicrobial Resistance Genes

ABSTRACT Escherichia coli is generally described as a commensal species with occasional pathogenic strains. Due to technological limitations, there is currently little information concerning the prevalence of pathogenic E. coli strains in the environment. For the first time, using a DNA microarray capable of detecting all currently described virulence genes and commonly found antimicrobial resistance genes, a survey of environmental E. coli isolates from recreational waters was carried out. A high proportion (29%) of 308 isolates from a beach site in the Great Lakes carried a pathotype set of virulence-related genes, and 14% carried antimicrobial resistance genes, findings consistent with a potential risk for public health. The results also showed that another 8% of the isolates had unusual virulence gene combinations that would be missed by conventional screening. This new application of a DNA microarray to environmental waters will likely have an important impact on public health, epidemiology, and microbial ecology in the future.

Download Full-text