Distribution of serotypes and virulence-associated genes in pathogenic Escherichia coli isolated from ducks

Distribution of virulence-associated genes, antibiotic resistance and phylogenetic groups in Escherichia coli isolated from domestic and racing pigeons

Despite a lot of information about virulence and resistance of Escherichia coli (E. coli) in poultry, very limited data are currently available on its occurrence in pigeon isolates, although this poses a threat to human and animal health. Therefore, this study was conducted to explore the phylogenetic classification, antibiotic sensitivity, and virulence factors in E. coli isolated from cloacal swabs of domestic pigeons bred for meat (n = 47) and racing pigeons (n = 44). The most frequent phylogroup in racing pigeons was E (36, 82.00%), unlike domestic pigeons (B2- 19, 40.00%). The most abundant iron uptake system in both groups of bird was feoB (racing = 40, 90.90%; domestic = 44, 93.61%). The presence of ibeA (52, 57.10%) and kpsMTII (46, 50.50%) genes was detected in more than half of all strains belonging exclusively to phylogroups B2, D, E, F, clade I. Antibiotic resistance was higher in racing pigeons. All racing pigeon isolates were resistant to tetracycline and trimethoprim + sulphonamide. Resistance to ciprofloxacin was determined in three isolates (6.38%) of domestic and 33 isolates (75%) of racing pigeons. Aminoglycosides and β-lactamases resistance were also recorded. One of the important detected phenotypic mechanisms of resistance occurring in isolates from racing pigeons was AGL AAC(6´)I. Our study confirms that healthy pigeons are a reservoir of antibiotic-resistant E. coli containing an arsenal of virulence factors, thus capable of potentially causing infection. Pigeons with the option to fly to multiple places can transfer virulent and resistant bacteria. Direct contact with pigeons and their faeces and the contamination of water and food pose a threat of infection to humans and other animal species.

Phenotypic and genotypic characterization of Shiga toxin-producing Escherichia coli strains recovered from bovine carcasses in Uruguay

Introduction

Shiga toxin-producing Escherichia coli (STEC) is a zoonotic pathogen that cause food-borne diseases in humans. Cattle and derived foodstuffs play a known role as reservoir and vehicles, respectively. In Uruguay, information about the characteristics of circulating STEC in meat productive chain is scarce. The aim was to characterize STEC strains recovered from 800 bovine carcasses of different slaughterhouses.

Methods

To characterize STEC strains we use classical microbiological procedures, Whole Genome Sequencing (WGS) and FAO/WHO risk criteria.

Results

We analyzed 39 STEC isolated from 20 establishments. They belonged to 21 different O-groups and 13 different H-types. Only one O157:H7 strain was characterized and the serotypes O130:H11(6), O174:H28(5), and O22:H8(5) prevailed. One strain showed resistance in vitro to tetracycline and genes for doxycycline, sulfonamide, streptomycin and fosfomycin resistance were detected. Thirty-three strains (84.6%) carried the subtypes Stx2a, Stx2c, or Stx2d. The gene eae was detected only in two strains (O157:H7, O182:H25). The most prevalent virulence genes found were lpfA (n = 38), ompA (n = 39), ompT (n = 39), iss (n = 38), and terC (n = 39). Within the set of STEC analyzed, the majority (81.5%) belonged to FAO/WHO's risk classification levels 4 and 5 (lower risk). Besides, we detected STEC serotypes O22:H8, O113:H21, O130:H11, and O174:H21 belonged to level risk 2 associate with diarrhea, hemorrhagic colitis or Hemolytic-Uremic Syndrome (HUS). The only O157:H7 strain analyzed belonged to ST11. Thirty-eight isolates belonged to the Clermont type B1, while the O157:H7 was classified as E.

Discussion

The analyzed STEC showed high genomic diversity and harbor several genetic determinants associated with virulence, underlining the important role of WGS for a complete typing. In this set we did not detect non-O157 STEC previously isolated from local HUS cases. However, when interpreting this findings, the low number of isolates analyzed and some methodological limitations must be taken into account. Obtained data suggest that cattle constitute a local reservoir of non-O157 serotypes associated with severe diseases. Other studies are needed to assess the role of the local meat chain in the spread of STEC, especially those associated with severe diseases in humans.

Antimicrobial Susceptibility and Detection of Virulence-Associated Genes in Escherichia coli Strains Isolated from Commercial Broilers

The aim of this study was to investigate the presence of iron-uptake and virulence genes, antibiotic resistance profiles, and phylogenetic relatedness in 115 Escherichia coli (E. coli) strains isolated from broilers in Slovakia and to determine their potential threat to human health. The most frequent phylogroups were B1 (37%) and A (21%), and 33.9% strains were included in pathogenic groups. The commonly observed iron-uptake genes were feoB (94%), sitA (83%), and iutA (58%). Protectins (iss, kpsMTII) were identified in 30% of samples. Four percent of B2-associated broilers carried the papC (P fimbria) gene connected with upper urinary tract infection. The dominant resistance was to tetracycline (49%), ampicillin (66%), ampicillin + sulbactam (27%), ciprofloxacin (61%), and trimethoprim + sulfonamide (34%); moreover, sporadically occurring resistance to cephalosporins, aminoglycosides, fluoroquinolones, and polypeptide colistin was observed. Genotypic analysis of resistance revealed the presence of bla_CTX-M-1 and bla_CTX-M-2 in two isolates from broilers. Commercial broilers can be reservoirs of virulent and resistant genes as well as E. coli causing (extra-)intestinal infections, which can be a potential threat to humans via direct contact and food.

Putative Riemerella anatipestifer Outer Membrane Protein H Affects Virulence

Riemerella anatipestifer causes serious contagious disease in ducks, geese, and other fowl. However, as a harmful pathogen causing significant economic losses in the poultry industry, R. anatipestifer is still poorly understood for its pathogenesis mechanisms. In a previous study, we developed an indirect ELISA method for detecting R. anatipestifer infection using B739_0832 protein, a putative outer membrane protein H (OmpH) that is conserved among different serotypes of R. anatipestifer. Although OmpH in some pathogenic bacteria, such as Pasteurella, has been reported as a virulence factor, it is still not clear whether B739_0832 protein contributes to the virulence of R. anatipestifer. In this study, we confirmed that B739_0832 protein in R. anatipestifer localizes to the outer membrane. We constructed a B739_0832 deletion mutant strain (ΔB739_0832) and assayed various effects from the deletion of B739_0832. ΔB739_0832 strain had a similar growth rate to wild-type R. anatipestifer CH-1. However, the survival rate of ducklings in 10 days after infection from ΔB739_0832 strain was 50%, whereas no ducklings survived from wild-type R. anatipestifer infection. Furthermore, the median lethal dose (LD₅₀) of the ΔB739_0832 strain was approximately 150 times higher than that of the wild-type strain. Pathology examinations on infected ducklings found that, at 36 h after infection, bacterial loads in blood, liver, and brain tissues from ΔB739_0832-infected ducklings were considerably lower than those from wild-type infected ducklings. These results demonstrate that the B739_0832 protein contributes to the virulence of R. anatipestifer CH-1.

Genetic and antimicrobial resistance profiles of non-O157 Shiga toxin-producing Escherichia coli from different sources in Egypt

BACKGROUND

The Shiga toxin-producing Escherichia coli (STEC) represented a great risk to public health. In this study, 60 STEC strains recovered from broiler and duck fecal samples, cow's milk, cattle beef, human urine, and ear discharge were screened for 12 virulence genes, phenotypic and genotypic antimicrobial resistance, and multiple-locus variable-number tandem-repeat analysis (MLVA).

RESULTS

The majority of strains harbored Shiga toxin 1 (stx₁) and stx_1d, stx₂ and stx_2e, and ehxA genes, while a minority harbored stx_2c subtype and eaeA. We identified 10 stx gene combinations; most of strains 31/60 (51.7%) exhibited four copies of stx genes, namely the stx₁, stx_1d, stx₂, and stx_2e, and the strains exhibited a high range of multiple antimicrobial resistance indices. The resistance genes blaCTX-M-1 and blaTEM were detected. For the oxytetracycline resistance genes, most of strains contained tetA, tetB, tetE, and tetG while the tetC was present at low frequency. MLVA genotyping resolved 26 unique genotypes; genotype 21 was highly prevalent. The six highly discriminatory loci DI = 0.9138 are suitable for the preliminary genotyping of STEC from animals and humans.

CONCLUSIONS

The STEC isolated from animals are virulent, resistant to antimicrobials, and genetically diverse, thus demands greater attention for the potential risk to human.

Comparative Characteristics and Zoonotic Potential of Avian Pathogenic Escherichia coli (APEC) Isolates from Chicken and Duck in South Korea

Avian pathogenic Escherichia coli (APEC) causes colibacillosis, which is an economically important disease in the poultry industry worldwide. The present study investigated O-serogroups, phylogenetic groups, antimicrobial resistance, and the existence of virulence-associated genes (VAGs) and antimicrobial resistance genes in 125 APEC isolates between 2018 and 2019 in Korea. The phylogenetic group B2 isolates were confirmed for human-related sequence types (STs) through multi-locus sequence typing (MLST). O-serogroups O2 (12.5%) and O78 (10.3%) and phylogenetic group B1 (36.5%) and A (34.5%) were predominant in chicken and duck isolates, respectively. Out of 14 VAGs, iucD, iroN, hlyF, and iss were found significantly more in chicken isolates than duck isolates (p < 0.05). The resistance to ampicillin, ceftiofur, ceftriaxone, and gentamicin was higher in chicken isolates than duck isolates (p < 0.05). The multidrug resistance (MDR) rates of chicken and duck isolates were 77.1% and 65.5%, respectively. One isolate resistant to colistin (MIC 16 μg/mL) carried mcr-1. The B2-ST95 APEC isolates possessed more than 9 VAGs, and most of them were MDR (82.4%). This report is the first to compare the characteristics of APEC isolates from chickens and ducks in Korea and to demonstrate that B2-ST95 isolates circulating in Korea have zoonotic potential and pose a public health risk.

Distribution of serotypes and molecular characterization of avian pathogenic Escherichia coli isolated from chicken died of colibacillosis

Avian pathogenic Escherichia coli (APEC), can inflicts not only severe losses to the poultry industry due to morbidity and condemnations but also can pose a serious public health and food biosafety concern by playing a key role as an acceptor and donor of transmissible antimicrobial resistance mechanisms. Our studies on 71 APEC strains isolated from chicken died of colibacillosis, in Mizoram, India, revealed 13 different serotypes with predominance of O83 (35.21%). Of the 71 serotyped APEC strains, 67 (94.37%) are characterized as multidrug resistant with antimicrobial resistance as high as against 16 antibiotics tested. These strains harboured combination of up to 8 antimicrobial resistance genes tetA (92.96%), intl (70.42%), sul1 (59.15%), sul2 (56.34%), Dfrla (53.52%), Aad A (50.70%) in more than 50% of the strains. In addition, 8 different virulence associated genes with combination up to 7 genes together and with maximum frequency of fimC (97.18%), hlyE (80.28%), tsh (61.97%), fyuA (60.56%), irp2 (59.15%) and iuCD (57.75%) were detected. This is the first report on prevalence and heterogeneity of serotypes, pattern of antibiotic resistance and virulence genes content among APEC strains from North East region of India.

RanB, a putative ABC-type multidrug efflux transporter contributes to aminoglycosides resistance and organic solvents tolerance in Riemerella anatipestifer

Riemerella anatipestifer is a Gram-negative bacterium, which is an important pathogen infecting ducks and resistant to various antibiotics. The efflux pump is an important resistance mechanism of Gram-negative bacteria, but little research has been done in R. anatipestifer. In this study, the drug resistance mediated by RIA_1614 gene of R. anatipestifer RA-GD strain was studied, because the gene was presumed to be an efflux pump component of ABC. Firstly, the deletion strain RA-GD△RIA_1614 and complemented strain RA-GD△RIA_1614 pCPRA::RIA_1614 were constructed. Then, MICs of various antimicrobial agents to parent and deletion strains and the tolerance of the strains to organic solvents were detected to screen the substrates for RIA_1614 gene. Moreover, the transcription levels of RIA_1614 gene in the parent and the complemented strains exposed to the substrates were detected by quantitative real-time RT-PCR. Furthermore, the efflux abilities of parent, deletion and complemented strains to substrates were determined by antibiotic accumulation test. In addition, in vitro competition ability and virulence of the strains were also detected. The results showed that the deletion strain was more sensitive to aminoglycosides and organic solvents than parental strain RA-GD. When RA-GD and complemented strain were exposed to sub-repression levels of aminoglycosides and organic solvents, the transcription levels of RIA_1614 gene were significantly up-regulated. Sodium o-vanadate inhibitor assay confirmed that RIA_1614 protein contributed to amikacin and streptomycin resistance and organic solvent tolerance. Streptomycin accumulation test showed that the RIA_1614 protein was able to export streptomycin, and the addition of ATPase inhibitor sodium o-vanadate increased the accumulation of streptomycin, indicating that RIA_1614 protein was an ATP-dependent efflux transporter. Growth and competition experiments revealed that RIA_1614 protein had no significant effect on growth of RA-GD, but decreased in vitro competition ability of the strain. Furthermore, pathogenicity tests showed that RIA_1614 protein involved in the virulence of the strain. Based on the results and amino acid sequence analysis, it was determined that RIA_1614 protein was a member of ABC efflux pumps, and the protein was named RanB.

Isolation and characterization of E. coli strains causing intramammary infections from dairy animals and wild birds

The study was conducted to estimate the prevalence of Escherichia coli (E. coli) in sub-clinically mastitic (SCM) animals, and in wild and migratory birds which may act as reservoir disseminating such pathogen. Farm hygiene, management and milking procedures were listed through a questionnaire. Thirty lactating cows and 15 lactating buffaloes from five small-scale dairy farms were randomly selected and screened for subclinical mastitis (SCM) using California Mastitis Test (CMT) and somatic cell count (SCC). In addition, 80 teat skin swabs, 5 drinking water samples and 38 wild and migratory bird faecal matter were also collected. All samples were processed for E. coli isolation by culturing on Levine’s Eosin Methylene Blue (L-EMB) agar, followed by purification and biochemical identification. Positive samples were subjected to molecular identification and serotyping. In addition, the presence of extended-spectrum beta-lactamase (ESBL) and carbapenemase-producing E. coli have been reported by antimicrobial sensitivity testing. Escherichia coli were isolated from 7.7%, 50% and 50% of the positive CMT cows’ quarters, cows’ composite and buffaloes’ composite milk samples, respectively. In addition, 14% of cows’ teats, 20% of water samples, 70% of faecal matter from wild bird, and 33.3% of faecal matter from migratory waterfowls were carrying E. coli. Serotyping, antibiotic-resistant pattern and phylogenetic analysis have pointed the bearable implication of milking hygiene and wild birds in disseminating E. coli strains causing intramammary infections.

Molecular characterization of avian pathogenic Escherichia coli from broiler chickens with colibacillosis

Avian pathogenic Escherichia coli (APEC) causes extensive mortality in poultry flocks, leading to extensive economic losses. The aim of this study was to investigate the phenotypic and genotypic characteristics and antimicrobial resistance of recent APEC isolates. Of the 79 APEC isolates, the most predominant serogroup was O78 (16 isolates, 20.3%), followed by O2 (7 isolates, 8.9%) and O53 (7 isolates, 8.9%). Thirty-seven (46.8%) and six (7.6%) of the isolates belonged to phylogenetic groups D and B2, respectively, and presented as virulent extraintestinal E. coli. Among 5 analyzed virulence genes, the highest frequency was observed in hlyF (74 isolates, 93.7%), followed by iutA (72 isolates, 91.9%) gene. The distribution of the iss gene was significantly different between groups A/B1 and B2/D (P < 0.05). All group B2 isolates carried all 5 virulence genes. APEC isolates showed high resistance to ampicillin (83.5%), nalidixic acid (65.8%), tetracycline (64.6%), cephalothin (46.8%), and ciprofloxacin (46.8%). The β-lactamases–encoding genes bla_TEM-1 (23 isolates, 29.1%), bla_CTX-M-1 (4 isolates, 5.1%), and bla_CTX-M-15 (3 isolates, 3.8%); the aminoglycoside-modifying enzyme gene aac(3)-II (4 isolates, 5.1%); and the plasmid-mediated quinolone genes qnrA (10 isolates, 12.7%) and qnrS (2 isolates, 2.5%) were identified in APEC isolates. The tetA (37 isolates, 46.8%) and sul2 (20 isolates, 25.3%) were the most prevalent among tetracycline and sulfonamide resistant isolates, respectively. This study indicates that APEC isolates harbor a variety of virulence and resistance genes; such genes are often associated with plasmids that facilitate their transmission between bacteria and should be continuously monitored to track APEC transmission in poultry farms.

Identical Genetic Profiles of Escherichia coli Isolates from the Gut and Systemic Organs of Chickens Indicate Systemic Bacterial Dissemination, Most Likely Due to Intestinal Destruction Caused by Histomonosis

In laying and breeding chickens, pathomorphological signs of histomonosis often coincide with colibacillosis. Thus, we investigated the systemic spread of Escherichia coli in chickens affected with histomonosis and colibacillosis by characterizing their pheno- and genotypic profiles. For this, 29 birds from 11 affected flocks were necropsied and up to three E. coli isolates each from intestine, heart, and liver of the birds were isolated. A total of 251 isolates were characterized by serotyping, phylogenetic grouping, detection of virulence-associated genes (VAGs), and pulsed-field gel electrophoresis (PFGE). All birds showed egg peritonitis, and fibrinous typhlitis was additionally recorded in 18 birds. Presence of Histomonas meleagridis in ceca was confirmed by PCR and histopathology. Escherichia coli serotype O2:K1 was found to be the most prevalent (37.4%), whereas 31.1% of strains were not typeable. The majority of isolates collected from the intestine and extraintestinal organs belonged to phylogroups B2 (54.1%), D (21.5%), or A (19.5%). Isolates from these phylogroups harbored a higher number of VAGs. Macrorestriction analysis showed that 60.6% of total isolates from all organs tested were included in eight PFGE types. Isolation of E. coli with identical genomic profiles from the intestine and extraintestinal organs of the same or different birds in the same flock indicates for systemic dissemination of the bacteria, independent of E. coli genotype. Intestinal destruction due to H. meleagridis can be considered as the most plausible cause of bacterial dissemination, ultimately leading to colibacillosis.

A recombinant multi-antigen vaccine with broad protection potential against avian pathogenic Escherichia coli

Chickens are a major source of protein worldwide, yet infectious diseases continue to threaten the poultry industry. Avian pathogenic Escherichia coli (APEC), a subgroup of extraintestinal pathogenic E. coli (ExPEC), causes colibacillosis in chickens resulting in economic loss because of treatment, condemnation of products, and death. In this study, we evaluated a recombinant antigens (rAg) vaccine combining common ExPEC surface proteins EtsC, OmpA, OmpT, and TraT for broad protective potential against APEC infections in chickens. The specific objectives were to evaluate antibody (serum) and cytokines (lymphoid organs) responses to vaccination; in vitro bactericidal ability of serum and splenocytes against multiple APEC serotypes; and in vivo protection against APEC challenge in chickens. Groups of four-day old chickens (N = 10) were vaccinated twice (two-week interval) subcutaneously with rAgs alone or in combination and CpG adjuvant or PBS (control). IgY antibody in the serum and mRNA expression of IL-1β, IL-6, IL-18, IFN-γ, IL-4, IFN-β, and IL-8 in bursa, spleen, and thymus were measured using ELISA and RT-qPCR, respectively. Serum and splenocytes were tested for their bactericidal ability in vitro against multiple APEC isolates. Vaccinated and non-vaccinated chickens were challenged with 108 CFU of APEC-O2 via air sac at 31 days post first vaccination. Vaccine protection was determined by the decrease of bacterial loads in blood and organs (lung, heart, spleen, and liver), as well as gross colibacillosis lesion scores in air sac, heart, and liver. Vaccination significantly (P < 0.05) elicited IgY against specific antigens, induced immune related mRNA expression in the spleen and bursa, reduced in vitro growth of multiple APEC serotypes, and decreased bacterial loads in the heart and spleen, and gross lesion scores of the air sac, heart and liver in chickens. The vaccine reported may be used to provide broad protection against APEC strains, increasing animal welfare and food production.

Diversity of Multi-Drug Resistant Avian Pathogenic Escherichia coli (APEC) Causing Outbreaks of Colibacillosis in Broilers during 2012 in Spain

Avian pathogenic Escherichia coli (APEC) are the major cause of colibacillosis in poultry production. In this study, a total of 22 E. coli isolated from colibacillosis field cases and 10 avian faecal E. coli (AFEC) were analysed. All strains were characterised phenotypically by susceptibility testing and molecular typing methods such as pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST). The presence of 29 virulence genes associated to APEC and human extraintestinal pathogenic E. coli (ExPEC) was also evaluated. For cephalosporin resistant isolates, cephalosporin resistance genes, plasmid location and replicon typing was assessed. Avian isolates belonged to 26 O:H serotypes and 24 sequence types. Out of 22 APEC isolates, 91% contained the virulence genes predictors of APEC; iutA, hlyF, iss, iroN and ompT. Of all strains, 34% were considered ExPEC. PFGE analysis demonstrated a high degree of genetic polymorphism. All strains were multi-resistant, including those isolated from healthy animals. Eleven strains were resistant to cephalosporins; six contained bla_CTX-M-14, two bla_SHV-12, two bla_CMY-2 and one bla_SHV-2. Two strains harboured qnrA, and two qnrA together with aac(6’)-Ib-cr. Additionally, the emergent clone O25b:H4-B2-ST131 was isolated from a healthy animal which harboured bla_CMY-2 and qnrS genes. Cephalosporin resistant genes were mainly associated to the presence of IncK replicons. This study demonstrates a very diverse population of multi-drug resistant E. coli containing a high number of virulent genes. The E. coli population among broilers is a reservoir of resistance and virulence-associated genes that could be transmitted into the community through the food chain. More epidemiological studies are necessary to identify clonal groups and resistance mechanisms with potential relevance to public health.

Development of multiplex PCR assay for rapid detection of Riemerella anatipestifer, Escherichia coli, and Salmonella enterica simultaneously from ducks

Three pathogens, Riemerella anatipestifer, Escherichia coli, and Salmonella enterica, are leading causes of bacterial fibrinous pericarditis and perihepatitis in ducks in China and worldwide. It is difficult to differentiate these pathogens when obtaining a diagnosis on clinical signs and pathological changes. The aim of this research was to develop a multiplex polymerase chain reaction (m-PCR) that could discriminate R. anatipestifer, E. coli, and S. enterica rapidly in field isolates, or detect the three bacteria in clinical samples from diseased ducks. We selected the DnaB helicase (dnaB) gene of R. anatipestifer, alkaline phosphatase (phoA) gene of E. coli and invasion protein (invA) gene of S. enterica as target genes. In optimized conditions, the limitation of detection was approximately 10(3) colony forming units (CFU) of each of these three bacterial pathogens per PCR reaction tube. The m-PCR method showed specific amplification of respective genes from R. anatipestifer, E. coli, and S. enterica. Using the m-PCR system, bacterial strains isolated from diseased ducks in our laboratory were categorized successfully, and the pathogens could also be detected in clinical samples from diseased ducks. Therefore, the m-PCR system could distinguish the three pathogens simultaneously, for identification, routine molecular diagnosis and epidemiology, in a single reaction.

Escherichia coli from animal reservoirs as a potential source of human extraintestinal pathogenic E. coli

Extraintestinal pathogenic Escherichia coli (ExPEC) are an important cause of urinary tract infections, neonatal meningitis and septicaemia in humans. Animals are recognized as a reservoir for human intestinal pathogenic E. coli, but whether animals are a source for human ExPEC is still a matter of debate. Pathologies caused by ExPEC are reported for many farm animals, especially for poultry, in which colibacillosis is responsible for huge losses within broiler chickens. Cases are also reported for companion animals. Commensal E. coli strains potentially carrying virulence factors involved in the development of human pathologies also colonize the intestinal tract of animals. This review focuses on the recent evidence of the zoonotic potential of ExPEC from animal origin and their potential direct or indirect transmission from animals to humans. As antimicrobials are commonly used for livestock production, infections due to antimicrobial-resistant ExPEC transferred from animals to humans could be even more difficult to treat. These findings, combined with the economic impact of ExPEC in the animal production industry, demonstrate the need for adapted measures to limit the prevalence of ExPEC in animal reservoirs while reducing the use of antimicrobials as much as possible.