Biological characteristics and pathogenicity of avian Escherichia coli strains

Prevalence of specific serogroups, antibiotic resistance and virulence factors of avian pathogenic Escherichia coli (APEC) isolated from clinical cases: A systematic review and meta-analysis

Pathogenic strains of Escherichia coli infecting poultry, commonly called avian pathogenic E. coli (APEC) present significant risks, to the health of both poultry and the general public. This systematic review aimed to examine the prevalence of APEC serotypes, sequence types (ST), phylogenetic groups, virulence factors and antibiotic resistance patterns based on 189 research papers sourced from PubMed, Web of Science, and ProQuest. Then, data were extracted from the selected studies and analyzed to assess the global distribution and characteristics of APEC strains. The metaprop codes in the Meta and Metafor packages of R as implemented in RStudio were then used to conduct meta-analysis. Among APEC strains identified from these different research reports serogroup O78 had the highest overall prevalence (16 %), followed by serogroups O2 (10 %), and O117 (8 %). The most common ST profiles were ST117 (20 %), ST140 (15 %), ST95 (12 %), and ST131 (9 %). ST117 and ST140 are known reservoirs for pathogenic E. coli in humans. Moreover, phylogenetic assessment highlighted the prevalence of phylogroups A, A1, F, D, and B2 among APEC strains indicating diversity in phylogenetic origin within poultry populations. The presence of antimicrobial resistance was notable among APEC strains against antibiotics such as tetracyclines, penicillins, and cephalosporins. This resistance may be linked to use of antimicrobials in poultry production in certain regions presenting challenges for both animal health management and human infection control. Analysis of sequences linked to adherence or virulence indicated that genes encoding adhesins (csg, fimC), iron/metal uptake (sitB, sitC, iroD) and cytotoxicity (estB, hlyF), and serum resistance (traT, iss) were highly prevalent. These factors have been reported to contribute to APEC host colonization and virulence in poultry. In summary, this overview of the characteristics of APEC highlights the pressing importance of monitoring and implementing management approaches to reduce antimicrobial resistance considering that a phylogenetic diversity of E. coli strains causes infections in both poultry and humans and represents a risk to both animal and public health. Further, determining the major conserved aspects and predominant mechanisms of virulence of APEC is critical for improving diagnostics and developing preventative measures to reduce the burden of infection caused by pathogenic E. coli in poultry and lower risks associated with foodborne transmission of E. coli to humans through poultry and poultry products.

Effects of pomegranate (Punica granatum L.) peel on the growth performance and intestinal microbiota of broilers challenged with Escherichia coli

The effects of pomegranate peel on the growth performance, intestinal morphology, and the cecal microbial community were investigated in broilers challenged with avian pathogenic Escherichia coli (APEC) O78. A total of 240 one-day-old chicks (120 males and 120 females) were randomly and evenly allotted into 4 treatment groups (each with 6 biological replicates each of 10 chicks), i.e., negative control (NC), positive control (PC), and 2 experimental groups treated with 0.2% fermented pomegranate peel (FP) and 0.2% unfermented pomegranate peel (UFP), respectively, with PC, FP, and UFP groups challenged with APEC O78 (5 × 108 CFU) on day 14. Results showed that the challenge of APEC O78 decreased the body weight (BW) and average daily gain (ADG) of broilers from 1 to 28 d (P < 0.01). These broilers exhibited more pathological conditions in the heart and liver and higher mortality rates in 28 d compared to the NC group. Diet supplemented with pomegranate peel (either fermented or unfermented) significantly increased BW, ADG, and the villus height/crypt depth ratio (VCR) of small intestine in 28 d compared to the NC group (P < 0.05). Results of the taxonomic structure of the gut microbiota showed that compared to the NC group, the APEC challenge significantly decreased the relative abundance of Bacteroidetes and increased the relative abundance of Firmicutes (P < 0.01). Compared to the PC group, the relative abundance of Ruminococcus_torques_group in FP group was increased, while the relative abundance of Alistipes was decreased. In summary, our study showed that the dietary supplementation of pomegranate peel could maintain the intestinal microbiota at a state favorable to the host, effectively reduce the abnormal changes in the taxonomic structure of the intestinal microbiota, and improve the growth performance in broilers treated with APEC.

Investigation of Serotype Prevalence of Escherichia coli Strains Isolated from Layer Poultry in Greece and Interactions with Other Infectious Agents

Colibacillosis is the most common bacterial disease in poultry and it is caused by avian pathogenic Escherichia coli (APEC), which is assigned to various O-serogroups. Previous studies have shown that APEC strains are more often related to certain O-serogroups such asO78, O2 and O1. E. coli has been reported to act either as a primary or secondary agent in complicating other infections. The aim of this study was to investigate the occurrence of and characterize the O-serogroups of E. coli strains isolated from commercial layer and layer breeder flocks showing macroscopic lesions of colibacillosis and increased or normal mortality in Greece. Furthermore, we attempted to assess the interaction between infectious agents such as Mycoplasma gallisepticum (MG), Mycoplasma synoviae (MS), infectious bronchitis (IBV) and infectious laryngotracheitis (ILT) with E. coli infections in layer flocks with increased mortality. Our study revealed that in addition to the common serogroups (O78, O2), many other, and less common serogroups were identified, including O111. The O78, O111 and O2 serogroups were frequently detected in flocks with lesions of colibacillosis and increased mortality whereas O2, O88 and O8 were reported more commonly in birds with colibacillosis lesions but normal mortality rates. These data provide important information for colibacillosis monitoring and define preventative measures, especially by using effective vaccination programs because E. coli vaccines are reported to mainly offer homologous protection. Finally, concerning the association of the four tested infectious agents with E. coli mortality, our study did not reveal a statistically significant effect of the above infectious agents tested with E. coli infection mortality.

Characterizing avian pathogenic Escherichia coli (APEC) from colibacillosis cases, 2018

Colibacillosis caused by avian pathogenic Escherichia coli (APEC) is a devastating disease of poultry that results in multi-million-dollar losses annually to the poultry industry. Disease syndromes associated with APEC includes colisepticemia, cellulitis, air sac disease, peritonitis, salpingitis, omphalitis, and osteomyelitis among others. A total of 61 APEC isolates collected during the Fall of 2018 (Aug-Dec) from submitted diagnostic cases of poultry diagnosed with colibacillosis were assessed for the presence of 44 virulence-associated genes, 24 antimicrobial resistance genes and 17 plasmid replicon types. Each isolate was also screened for its ability to form biofilm using the crystal violet assay and antimicrobial susceptibility to 14 antimicrobials using the NARMS panel. Overall, the prevalence of virulence genes ranged from 1.6% to >90% with almost all strains harboring genes that are associated with the ColV plasmid-the defining trait of the APEC pathotype. Overall, 58 strains were able to form biofilms and only three strains formed negligible biofilms. Forty isolates displayed resistance to antimicrobials of the NARMS panel ranging from one to nine agents. This study highlights that current APEC causing disease in poultry possess virulence and resistance traits and form biofilms which could potentially lead to challenges in colibacillosis control.

A complex approach to a complex problem: the use of whole-genome sequencing in monitoring avian-pathogenic Escherichia coli – a review

Infections associated with Escherichia coli are responsible for immense losses in poultry production; moreover, poultry products may serve as a source of pathogenic and/or resistant strains for humans. As early as during the first hours of life, commercially hatched chickens are colonized with potentially pathogenic E. coli from the environment of hatcheries. The source of contamination has not been quite elucidated and the possibility of vertical spread of several avian pathogenic E. coli (APEC) lineages has been suggested, making the hatcheries an important node where cross-contamination of chicken of different origin can take place. The recent technological progress makes the method of whole-genome sequencing (WGS) widely accessible, allowing high-throughput analysis of a large amount of isolates. Whole-genome sequencing offers an opportunity to trace APEC and extended-spectrum/plasmid-encoded AmpC beta-lactamases-producing E. coli (ESBL/pAmpC-E.coli) along the poultry processing chain and to recognize the potential pathways of “epidemicˮ sequence types. Data from WGS may be used in monitoring antimicrobial resistance, comparative pathogenomic studies describing new virulence traits and their role in pathogenesis and, above all, epidemiologic monitoring of clonal outbreaks and description of different transmission routes and their significance. This review attempts to outline the complexity of poultry-associated E. coli issues and the possibility to employ WGS in elucidating them.

Prophage phiv205-1 facilitates biofilm formation and pathogenicity of avian pathogenic Escherichia coli strain DE205B

Avian colibacillosis caused by avian pathogenic Escherichia coli (APEC) causes significant economic losses to the poultry industry worldwide and is also a leading potential threat to human health. Bacteriophages integrate into the host bacterial chromosome, and are an important source of genetic variation and have a major impact on bacterial evolution. Previously, we predicted prophage phiv205-1 in APEC strain DE205B. Here, to determine the function of prophage phiv205-1, we constructed the prophage deletion mutant DE205BΔphiv205-1. Compared with the wild-type (WT) APEC strain DE205B, the adherence and invasive abilities of DE205BΔphiv205-1 were reduced by 41.88 %(P < 0.05). Further, the mutant strain had 52.38 % reduced biofilm formation compared with the WT strain (P < 0.001). Chick challenge showed that the median lethal dose (LD₅₀) of the mutant strain and WT strain was 3.13 × 10⁵ colony-forming units (CFU) and 3.86 × 10⁴ CFU, respectively, indicating that the mutant strain had decreased virulence compared with the WT strain. Furthermore, in vivo studies showed that, compared with the WT strain, DE205BΔphiv205-1 bacterial loads were reduced by 1.6-fold (P < 0.05) and 4.8-fold (P < 0.001) in the lungs and brains, respectively, of the infected chicks. In conclusion, the prophage phiv205-1 contributes to the virulence of APEC strain DE205B by facilitating the adherence, biofilm formation, and colonization abilities of its host strain.

Frequency of iss and irp2 genes by PCR method in Escherichia coli isolated from poultry with colibacillosis in comparison with healthy chicken in poultry farms of Zabol, South East of Iran

There is no special trait for differentiation of Avian Pathogenic Escherichia coli from Avian Fecal Escherichia coli. This investigation is aimed, as a case control study, to evaluate and compare the frequency of iss and irp2 in 43 AFEC strains and also 40 and 56 E. coli strains isolated from the liver and kidney of chickens with colibacillosis, respectively, farmed in Zabol, as a border region of Iran, by PCR. 86.9% and 37.2% of isolates collected from chickens with colibacillosis and feces samples obtained from healthy chickens were positive for iss gene, respectively (P<0.05). On average, 59.3% of E. coli strains isolated from colibacillosis have irp2 gene while 27.9% of isolates from the feces of healthy birds were positive (P<0.05). 52.15% of isolates from colibacillosis and 19.62% of isolates from healthy chicken feces were positive for both genes, with statistical significant difference (p<0.05). This marked difference in the distribution of iss and irp2 genes makes these two genes good markers to differentiate AFEC and APEC strains especially in Sistan region to improve colibacillosis control measurements.

Matrix-assisted laser desorption-ionization-time-of-flight mass spectrometry as a reliable proteomic method for characterization of Escherichia coli and Salmonella isolates

Aim:

Identification of pathogenic clinical bacterial isolates is mainly dependent on phenotypic and genotypic characteristics of the microorganisms. These conventional methods are costive, time-consuming, and need special skills and training. An alternative, mass spectral (proteomics) analysis method for identification of clinical bacterial isolates has been recognized as a rapid, reliable, and economical method for identification. This study was aimed to evaluate and compare the performance, sensitivity and reliability of traditional bacteriology, phenotypic methods and matrix-assisted laser desorption-ionization-time-of-flight mass spectrometry (MALDI-TOF MS) in the identification of clinical Escherichia coli and Salmonella isolates recovered from chickens.

Materials and Methods:

A total of 110 samples (cloacal, liver, spleen, and/or gall bladder) were collected from apparently healthy and diseased chickens showing clinical signs as white chalky diarrhea, pasty vent, and decrease egg production as well as freshly dead chickens which showing postmortem lesions as enlarged liver with congestion and enlarged gall bladder from different poultry farms.

Results:

Depending on colonial characteristics and morphological characteristics, E. coli and Salmonella isolates were recovered and detected in only 42 and 35 samples, respectively. Biochemical identification using API 20E identification system revealed that the suspected E. coli isolates were 33 out of 42 of colonial and morphological identified E. coli isolates where Salmonella isolates were represented by 26 out of 35 of colonial and morphological identified Salmonella isolates. Serological identification of isolates revealed that the most predominant E. coli serotypes were O1 and O78 while the most predominant Salmonella serotype of Salmonella was Salmonella Pullorum. All E. coli and Salmonella isolates were examined using MALDI-TOF MS. In agreement with traditional identification, MADI-TOF MS identified all clinical bacterial samples with valid scores as E. coli and Salmonella isolates except two E. coli isolates recovered from apparently healthy and diseased birds, respectively, with recovery rate of 93.9% and 2 Salmonella isolates recovered from apparently healthy and dead birds, respectively, with recovery rate of 92.3%.

Conclusion:

Our study demonstrated that Bruker MALDI-TOF MS Biotyper is a reliable rapid and economic tool for the identification of Gram-negative bacteria especially E. coli and Salmonella which could be used as an alternative diagnostic tool for routine identification and differentiation of clinical isolates in the bacteriological laboratory. MALDI-TOF MS need more validation and verification and more study on the performance of direct colony and extraction methods to detect the most sensitive one and also need using more samples to detect sensitivity, reliability, and performance of this type of bacterial identification.

Phenotypic and genotypic analysis of pathogenic Escherichia coli virulence genes recovered from Riyadh, Saudi Arabia

The current study was carried out to evaluate the phenotypic and genotypic characterization of avian pathogenic Escherichia coli recovered from Riyadh, Saudi Arabia. During the period of 10th February–30th May 2015, 70 E. coli strains were isolated from chicken farms located in Riyadh, Saudi Arabia. All strains were tested phenotypically by standard microbiological techniques, serotyped and the virulence genes of such strains were detected by polymerase chain reaction (PCR). Most of the recovered strains from chickens belonged to serotype O111:K58 25 strains (35.7%), followed by serotype O157:H7 13 strains (18.57%), followed by serotype O114:K90 10 strains (14.29%), then serotype O126:K71 9 strains (12.9%), serotype O78:K80 8 strains (11.43%) and in lower percentage serotype O114:K90 and O119:K69 5 strains (7.14%). The virulence genotyping of E. coli isolates recovered from broilers revealed the presence of the uidA gene in all the field isolates (6 serovars) examined in an incidence of 100%, as well as the cvaC gene was also present in all field isolates (6 serovars), while the iutA gene and the iss gene were detected in 5 out of 6 field serovars in an incidence of 81.43% and 64.29%, respectively. Phenotypical examination of the other virulence factors revealed that 65 isolates were hemolytic (92.9%), as well as 15 isolates (21.42%) were positive for enterotoxin production. Meanwhile, 21 isolates (30%) were positive for verotoxin production, 58 isolates (82.86%) for the invasiveness and 31 isolates (44.29%) for Congo red binding activities of the examined serotypes.

Autoinducer-2 of quorum sensing is involved in cell damage caused by avian pathogenic Escherichia coli

Avian pathogenic Escherichia coli (APEC) infections are responsible for great losses in the poultry industry. Quorum sensing (QS) acts as a global regulatory system that controls genes involved in bacterial pathogenesis, metabolism and protein biosynthesis. However, whether QS of APEC is related to cell damage has not been elucidated. In the present study, we explored the correlation between the damage of chicken type II pneumocytes induced by APEC and the autoinducer-2 (AI-2) activity of APEC. The results showed that when chicken type II pneumocytes were co-cultured with 10⁸ CFU/ml of APEC-O78 for 6 h, the release of LDH reached the highest level (192.5 ± 13.4 U/L) (P < 0.01), and the percentages of dead cells followed the same trend in trypan blue exclusion assay. In addition, the AI-2 activity of cell-free culture fluid (CF) reached the maximum value after 6 h co-culture with 10⁸ CFU/ml of APEC-O78. At the same time, the mRNA expressions of eight virulence genes (papC, fimA, fimC, hlyE, ompA, luxS, pfs, and qseA) of 10⁸ CFU/ml APEC-O78 were significantly increased compared with those of 10⁷ CFU/ml, and the mRNA expressions of four virulence genes (hlyE, tsh, iss, and luxS) of 10⁸ CFU/ml APEC-O78 were higher than those of 10⁹ CFU/ml (p < 0.05) after incubation for 6 h. These results suggested that AI-2-mediated QS is involved in the cell damage induced by APEC-O78, indicating AI-2 may be one new potential target for preventing chicken colibacillosis.

Characterization and antimicrobial resistance patterns of Escherichia coli isolated from feces of healthy broiler chickens

ABSTRACT: Avian pathogenic Escherichia coli (APEC) strains are isolated from lesions of poultry presenting colibacillosis, which is a disease that causes either systemic or localized clinical signs. Such strains share many characteristics with E. coli strains that cause extra-intestinal illness in humans. There is not a consensus on how to define the APEC pathotype with regard to the presence of virulence traits. On the other hand, in the past few years, five minimal predictors for APEC detection were proposed. The E. coli isolates in this work were tested through polymerase chain reaction (PCR) to the five proposed minimal predictors and cva C. The strains presenting them were categorized as potential APEC. The APEC and non-APEC categories showed high resistance (> 50%) to cephalotin, erythromycin, streptomycin, sulphametoxazol/trimethoprim, ampicillin, and amoxicillin. Potential APEC strains were significantly more resistant to cephalotin (p < 0.05) and neomcycin (p < 0.01) than non-APEC. These latter were significantly more resistant to tetracycline (p < 0.01) than the potential APEC strains. These results demonstrate that feces of poultry present E. coli strains with resistant features, showing or not the potential of causing colibacillosis in poultry. Because APEC and extra-intestinal illness in humans may be similar, these resistant strains are of interest to public health.

CARACTERIZAÇÃO FILOGENÉTICA MOLECULAR E RESISTÊNCIA ANTIMICROBIANA DE Escherichia coli ISOLADAS DE CAPRINOS NEONATOS COM DIARREIA

Resumo A diarreia neonatal determina alterações significativas na conversão alimentar, resultando na queda da produtividade de caprinos. A resistência antimicrobiana em bactérias caracteriza-se como importante problema de saúde pública, assim, a Escherichia coli pode ser caracterizada como importante patógeno por expressar mecanismos de virulência responsáveis por significativas afecções clínicas em seres humanos e animais. O presente estudo avaliou a presença de E. coli em 117 amostras fecais de caprinos e analisou a resistência antimicrobiana dos isolados. Colônias sugestivas foram submetidas a testes bioquímicos, seguido de determinação do grupo genotípico e análise filogenética; posteriormente foram submetidas à prova de suscetibilidade a antimicrobianos. Foram identificados isolados de E. coli, Salmonella spp, Shigella sonnei e Enterobacter aerogenes. Isolados de E. coli foram classificados filogeneticamente em B2 (9/39), D (19/39), B1 (7/39) e A (4/29). Os fatores de virulência identificados foram K99 (04/39) e Stx (02/39). À prova de suscetibilidade antimicrobiana, os isolados foram sensíveis a Cloranfenicol, Estreptomicina, Amoxicilina e Ciprofloxacina, sendo todos resistentes à Lincomicina, Vancomicina e Penicilina. Os resultados reforçam a necessidade de estabelecimento de protocolos criteriosos para o uso de antimicrobianos, medida fundamental para o aprimoramento da sanidade dos rebanhos caprinos brasileiros.

Virulence Genes Content and Antimicrobial Resistance in Escherichia coli from Broiler Chickens

A total of 121 E. coli strains were isolated from broiler chickens (96 extraintestinal pathogenic (ExPEC) strains from diseased broiler chickens and 25 avian fecal E. coli (AFEC) from healthy ones). Ten of the isolates (6 from diseased chickens and 4 from healthy birds) were serogrouped and 25 were examined for 4 virulence markers (tsh, papC, colV, and iss genes) as well as for their antimicrobial resistance. Five strains were nontypable and the rest were serotyped as follows: O86:K61 (2/5), O78:K80 (1/5), and O128:K67 (1/5) were recovered from diseased chickens, while O111:K58 strain (1/4) was isolated from healthy ones. The iss gene was found in 72.2% of the examined ExPEC strains in contrast to zero percentages (0%) in the AFEC strains, which may serve as a good marker for distinguishing APEC and its knocking out may help in creation of candidate vaccine that may prove sucess in elimination of infections in broiler chickens. Antimicrobial resistance patterns revealed a complete resistance to gentamicin, pefloxacin, amoxicillin, and enrofloxacin among examined strains followed by varying degrees of resistance for the rest of tested agents. The highest resistance was recorded against norfloxacin, in 24 isolates (96%), in contrast to the lowest resistance was recorded against colistin sulphate, in 14 strains (56%). These findings suggest the need for the prudent use of antimicrobials with broiler chickens and act as a warrant for the possibility of avian sources to transmit these resistant isolates to humans.

Inhibitory effects of α-cyperone on adherence and invasion of avian pathogenic Escherichia coli O78 to chicken type II pneumocytes

Avian pathogenic Escherichia coli (APEC) are extra-intestinal pathogenic E. coli, and usually cause avian septicemia through breaching the blood-gas barrier. Type II pneumocytes play an important role of maintaining the function of the blood-gas barrier. However, the mechanism of APEC injuring type II pneumocytes remains unclear. α-cyperone can inhibit lung cell injury induced by Staphylococcus aureus. In order to explore whether α-cyperone regulates the adherence and invasion of APEC-O78 to chicken type II pneumocytes, we successfully cultured chicken type II pneumocytes. The results showed that α-cyperone significantly decreased the adherence of APEC-O78 to chicken type II pneumocytes. In addition, α-cyperone inhibited actin cytoskeleton polymerization induced by APEC-O78 through down regulating the expression of Nck-2, Cdc42 and Rac1. These results provide new evidence for the prevention of colibacillosis in chicken.

Genotypic Analyses ofEscherichia coliIsolated from Chickens with Colibacillosis and Apparently Healthy Chickens in Japan

A genotypic comparison using pulsed-field gel electrophoresis (PFGE), amplified ribosomal restriction analysis (ARDRA) as well as PCRs targeting virulence associated genes reported elsewhere in avian pathogenic Escherichia coli(APEC) was made between E. coli strains isolated from chickens with colibacillosis and those from the feces of apparently healthy chickens in Japan. The majority (67%) of clinical isolates belonged to a certain phylogenetic ARDRA but not PFGE cluster, with virulence-related genes carried by ColV plasmid being markedly prevalent. The result suggests that APEC strains originated from the same "ancestor" in the course of E. coli evolution.

Prevalence of avian pathogenic Escherichia coli (APEC) clone harboring sfa gene in Brazil

Escherichia coli sfa+ strains isolated from poultry were serotyped and characterized by polymerase chain reaction (PCR) and amplified fragment length polymorphism (AFLP). Isolates collected from 12 Brazilian poultry farms mostly belonged to serogroup O6, followed by serogroups O2, O8, O21, O46, O78, O88, O106, O111, and O143. Virulence genes associated were: iuc 90%, fim 86% neuS 60%, hly 34%, tsh 28%, crl/csg 26%, iss 26%, pap 18%, and 14% cnf. Strains from the same farm presented more than one genotypic pattern belonging to different profiles in AFLP. AFLP showed a clonal relation between Escherichia coli sfa+ serogroup O6. The virulence genes found in these strains reveal some similarity with extraintestinal E. coli (ExPEC), thus alerting for potential zoonotic risk.

Clonality and virulence traits of Escherichia coli associated with haemorrhagic septicaemia in turkeys

Fifty-five clinical isolates of avian pathogenic Escherichia coli (APEC) from seven outbreaks of acute haemorrhagic septicaemia in turkeys were characterized by serotyping, plasmid profiling including restriction analysis with HindIII, ribotyping with EcoRI and HindIII, multilocus sequence typing (MLST) and virulence profiling. A clonal relationship was demonstrated for each outbreak according to serotype, plasmid profiling, ribotyping, and MLST. In addition, isolates demonstrated highly similar virulence profiles, as all isolates were positive for F11 pili and possessed genes encoding aerobactin (iucD), increased serum survival (iss), temperature-sensitive haemagglutinin (tsh) and colicin V plasmid operon genes (cva/cvi). However, only 20% of the isolates produced colicin V and 42% exhibited serum resistance. All strains with O group O111 and a single O18ac strain (demonstrating non-clonal DNA profiles) were positive for enteroaggregative heat-stabile toxin (EAST1), while isolates of a single outbreak all possessed the enteroaggregative toxin gene (astA). All isolates were negative for genes encoding verocytotoxins (vtx/stx), iron-repressible protein (irp2), P-fimbria (papC), invasion plasmid antigen (ipaH), attaching and effacing gene (eae), enterohaemolysin (ehxA), and enterotoxins LT, STIa (ST(p)) and STIb (ST(h)). In conclusion, highly similar virulence profiles were demonstrated for isolates of E. coli associated with a single well-defined lesion type of colibacillosis in turkeys; acute haemorrhagic septicaemia. The isolates obtained, however, demonstrated a different phylogenetic background, underlining the importance of using well-defined strain collections for characterization of APEC pathotypes.

The importance of sample size in the determination of a flock-level antimicrobial resistance profile for Escherichia coli in broilers

Determining herd- or flock-specific antimicrobial resistance profiles is important to guide therapeutic use of antimicrobials and to assess risk factors for the development and spread of antimicrobial resistance. As such, it is of utmost importance to optimize the sampling strategy for the determination of herd-specific antimicrobial resistance profiles. However, the multitude of prevalences measured at the same time as well as the presence of variation both at the level of the animal and the bacterial population of concern make it impossible to use conventional sample size determination methods. In this article, the use of bootstrapping techniques for sample size determination was explored. In particular, one-stage and two-stage bootstrap samplings were used to determine the optimal number of animals and the optimal number of isolates within one animal. Results show that focus should be on the number of animals sampled rather than on the number of isolates tested within one animal.

Escherichia coli phylogenetic group determination and its application in the identification of the major animal source of fecal contamination

BACKGROUND

Escherichia coli strains are commonly found in the gut microflora of warm-blooded animals. These strains can be assigned to one of the four main phylogenetic groups, A, B1, B2 and D, which can be divided into seven subgroups (A0, A1, B1, B22, B23, D1 and D2), according to the combination of the three genetic markers chuA, yjaA and DNA fragment TspE4.C2. Distinct studies have demonstrated that these phylo-groups differ in the presence of virulence factors, ecological niches and life-history. Therefore, the aim of this work was to analyze the distribution of these E. coli phylo-groups in 94 human strains, 13 chicken strains, 50 cow strains, 16 goat strains, 39 pig strains and 29 sheep strains and to verify the potential of this analysis to investigate the source of fecal contamination.

RESULTS

The results indicated that the distribution of phylogenetic groups, subgroups and genetic markers is non-random in the hosts analyzed. Strains from group B1 were present in all hosts analyzed but were more prevalent in cow, goat and sheep samples. Subgroup B23 was only found in human samples. The diversity and the similarity indexes have indicated a similarity between the E. coli population structure of human and pig samples and among cow, goat and sheep samples. Correspondence analysis using contingence tables of subgroups, groups and genetic markers frequencies allowed the visualization of the differences among animal samples and the identification of the animal source of an external validation set. The classifier tools Binary logistic regression and Partial least square--discriminant analysis, using the genetic markers profile of the strains, differentiated the herbivorous from the omnivorous strains, with an average error rate of 17%.

CONCLUSIONS

This is the first work, as far as we are aware, that identifies the major source of fecal contamination of a pool of strains instead of a unique strain. We concluded that the analysis of the E. coli population structure can be useful as a supplementary bacterial source tracking tool.

ÍNDICE DE PATOGENICIDADE, PRODUÇÃO DE HEMOLISINA E SOROGRUPO DE AMOSTRAS DE ESCHERICHIA COLI ISOLADAS DE AVES DE POSTURA COMERCIAL

RESUMO Este estudo avaliou o índice de patogenicidade, a produção de hemolisina e a determinação de sorogrupos de cepas deEscherichia coli isoladas de fígado de aves de postura comercial com um dia de idade. Para este estudo, foram analisados 32 lotes, dos quais 15 foram positivos para o isolamento de E. coli no fígado, totalizando vinte e quatro amostras. A patogenicidade dos isolados foi determinada por inoculação no saco aéreo de pintinhos e classificada como alta, intermediária, baixa ou não-patogênica. Os sorogrupos foram identificados utilizando um conjunto de antissoros anti-O (O1 a O180). A produção de hemolisina foi determinada por semeadura em ágar sangue de galinha (8%) e em placas de ágar sangue de carneiro (8%). Do total de amostras estudadas, 17 (70,83%) foram classificadas como não patogênica, 6 (25%) como de baixa patogenicidade e 1 (4,17%) de alta patogenicidade. Foram identificados 14 sorogrupos diferentes: O1, O2, O5, O8, O15, O18, O22, O36, O64, O70, O75, O115, O132, O141. Cinco cepas não tiveram o sorogrupo identificado. Com relação ao teste de produção de hemolisina, todas as cepas foram consideradas negativas, tanto para o teste realizado com ágar sangue de galinha quanto para o de carneiro. Os resultados obtidos neste estudo demonstram a importância de se identificar as cepas prevalentes deE. colinas diferentes regiões produtoras, podendo ser utilizados em estudos epidemiológicos.

Virulence factors of avian pathogenic Escherichia coli (APEC)

Avian pathogenic Escherichia coli (APEC) strains cause a great diversity of diseases in birds and are responsible for great economic losses in the avian industry. To date, several studies have been carried out to better understand the APEC pathogenesis for a possible development of tools which could prevent the economics losses caused by these strains. This review discusses the virulence factors described do date to be expressed by these strains and the advances made to understand and identify virulence determinants present in APEC.

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

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.

Rapid detection of virulence-associated genes in avian pathogenic Escherichia coli by multiplex polymerase chain reaction

Based on recently published prevalence data of virulence-associated factors in avian pathogenic Escherichia coli (APEC) and their roles in the pathogenesis of colibacillosis, we developed a multiplex polymerase chain reaction (PCR) as a molecular tool supplementing current diagnostic schemes that mainly rely on serological examination of strains isolated from diseased birds. Multiple isolates of E. coli from clinical cases of colibacillosis known to possess different combinations of eight genes were used as sources of template DNA to develop the multiplex PCR protocol, targeting genes for P-fimbriae (papC), aerobactin (iucD), iron-repressible protein (irp2), temperature-sensitive hemagglutinin (tsh), vacuolating autotransporter toxin (vat), enteroaggregative toxin (astA), increased serum survival protein (iss), and colicin V plasmid operon genes (cva/cvi). In order to verify the usefulness of this diagnostic tool, E. coli strains isolated from fecal samples of clinically healthy chickens were also included in this study, as were uropathogenic (UPEC), necrotoxigenic, and diarrhegenic E. coli strains. The application of the multiplex PCR protocol to 14 E. coli strains isolated from septicemic poultry showed that these strains harbored four to eight of the genes mentioned above. In contrast, those isolates that have been shown to be nonpathogenic for 5-wk-old chickens possessed either none or, at most, three of these genes. We found only one enterohemorrhagic (EHEC), one enteropathogenic (EPEC), and two enterotoxic (ETEC) E. coli strains positive for irp2, and another two ETEC strains positive for astA. As expected, UPEC isolates yielded different combinations of the genes iss, papC, iucD, irp2, and a sequence similar to vat. However, neither the colicin V operon genes cva/cvi nor tsh were amplified in UPEC isolates. The multiplex PCR results were compared with those obtained by DNA-DNA-hybridization analyses to validate the specificity of oligonucleotide primers, and the protocol was concluded to be a useful, sensitive, and rapid assay system to detect avian pathogenic E. coli and differentiate them from nonpathogenic strains and those belonging to other pathotypes.

Phenotypic Characterization ofipaH+ Escherichia coli Strains Associated with Yolk Sac Infection

Seventy-six Escherichia coli serotypes possessing the ipaH gene typical of enteroinvasive E. coli (EIEC) strains were characterized. Biochemical identification of our strains shows positive reactions for lactose fermentation (100% of strains), lysine decarboxylase (98.7% of strains) and motility (67.1% of strains), properties that do not correspond with those described to the EIEC group. The serotypes agree with an initial classification. In this, some common O antigens identified among ipaH+ strains were O2 (n=20), OR (n=11) and non-determined O? (n=10). The O2:NM serotype was the most common. Sixty-six percent (n=50) of the ipaH+ E. coli strains were colicin producers, of them, 26 (34%) produced Col V and other colicins, 13 (17%) produced colicins other than Col V, and 11 (14.5%) produced Col V only. Trimethoprim/Sulfa (72%), ampicillin (64.5%), enrofloxacin (55.3%), and ciprofloxacin (47.4%) were the major antimicrobial resistance frequencies observed. Twenty-five different multiresistance patterns were observed, where sixty-six strains (86.8%) were included. A MIC test showed that most of the strains were sensitive to low gentamicin and kanamycin concentrations, whereas most of the strains were resistant to tetracycline. An invasiveness assay showed that the predominant alterations caused to HEp-2 cells were changes in shape and staining, and in most of the specimens, a partial monolayer detachment was also seen. Fifteen strains invaded more than 30% of the monolayer cells, causing the formation of intercellular bridges or filipoidal-like protrusions. The results suggest the existence of specific clone complexes derived from EIEC strains adapted to the avian host. To our knowledge, this is the first study that demonstrates the presence of extraintestinal invasive E. coli (ExIEC) strains.

Avian pathogenicEscherichia colitransmission from broiler breeders to their progeny in an integrated poultry production chain

Early cases of colibacillosis with omphalitis, yolk sac infection and increased mortality were observed in five broiler chicken flocks (A1, A2, A3, A4 and B1) from two broiler breeder flocks A and B, respectively. Avian pathogenic Escherichia Coli (APEC) serotype O78, Fim/Tsh/Iuc pathotype, were isolated from flocks A, A1, A2, A3 and A4, and APEC serotype O139, pathotype Fim/Iuc, from flocks B and B1. APEC O78 strains isolated from broiler chicks A1, A2, A3 and A4, originating from breeder flock A, had the same antibiotic resistance pattern as APEC O139 strains isolated from broiler chicks B1 and breeder B. The random amplified polymorphic DNA technique performed on APEC strains revealed two distinct clusters of genetic similarity: cluster I consisted of some APEC O78 and cluster II of APEC O139. These results indicated that a transmission of APEC strains from adults A and B to their respective progeny could occur.

Virulence-associated traits in avian Escherichia coli: Comparison between isolates from colibacillosis-affected and clinically healthy layer flocks

Colibacillosis appears to be of increasing importance in layer flocks. The aim of this study was to determine characteristics of avian pathogenic Escherichia coli associated with the occurrence of colibacillosis outbreaks at flock level. Forty E. coli strains originating from layers from healthy flocks ('control isolates'), consisting of 25 caecal and 15 extra-intestinal isolates, were compared with 40 strains isolated from layers originating from colibacillosis-affected flocks ('outbreak isolates'), consisting of 20 caecal and 20 extra-intestinal isolates. The examined characteristics were adhesins, invasivity in T84 cell culture, serum resistance, iron uptake, colicin production, and toxinogenicity. The following traits were significantly more often detected in the outbreak isolates than in the control isolates: tsh, iss, iucA, iutA, irp2, fyuA, iroC, cvaC, colicin and colicin V production. A comparison of the extra-intestinal outbreak isolates and the caecal control isolates yielded the same results as when the caecal isolates, extra-intestinal isolates and total number of isolates of the outbreak and the control group were compared. When comparing the caecal and extra-intestinal isolates within the control and within the outbreak group, no significant differences were detected. The O78 and O2 groups showed significant differences with other O-types and NT strains for prevalence of most of the same characteristics. The combination of type 1 fimbriae, tsh, serum resistance, iss, traT, iucA, fyuA, iroC and colicin or colicin V production was significantly more often present in extra-intestinal outbreak isolates than in extra-intestinal control isolates. Only the combination of serum resistance, fyuA and colicin production was present in all outbreak isolates, with a significantly lower prevalence in the control isolates. None of the characteristics or combinations examined were exclusive to the outbreak isolates.

Adhesion properties, fimbrial expression and PCR detection of adhesin-related genes of avian Escherichia coli strains

Forty-nine avian pathogenic Escherichia coli (APEC) strains obtained from chickens suffering from septicemia (24), swollen head syndrome (14) and omphalitis (11), isolated from individuals in different regions of Brazil and from different outbreaks, were studied for their adhesion to trachea epithelial cells, fimbrial expression and hemagglutination capacity to different erythrocyte types. These results were compared with their content of fimbriae-related genes as detected by polymerase chain reaction (PCR) using specific pair of primers. The aim of these assays was to determine the importance of expression of adhesins in the pathogenic strains and to evaluate the presence of adhesin genes either previously described or not yet recognized for APEC strain. Thirty commensal strains isolated from poultry showing no signs of any of the above diseases were used to compare the results with the pathogenic isolates. The PCR assay demonstrated that septicaemic and swollen head syndrome strains had the highest number of adhesion-related genes of recognized importance in pathogenicity. Using different media for growth conditions, 40 different D-mannose resistant haemagglutination patterns were observed in this study, what indicates the expression of a great variability of surface agglutinins in these bacterial strains. Our results also showed that adhesion, whether D-mannose resistant (MRA) or D-mannose sensitive (MSA), is a characteristic observed in both pathogenic and commensal strains. Several strains with positive adherence had no genetic sequences related to the studied adhesin genes what indicates that our APEC strains probably possess a genome with adhesins genes besides those describe elsewhere and that have not yet been described.

Molecular epidemiology of avian pathogenic Escherichia coli (APEC) isolated from colisepticemia in poultry

The molecular biology and epidemiology of 150 avian pathogenic Escherichia coli strains (APEC) isolated from septicemic poultry in Germany was investigated by serotyping, pulsed field gel electrophoresis (PFGE), and polymerase chain reaction (PCR). Only 49.6% of the isolates could be grouped to serogroups O1, O2, and O78. Macrorestriction analyses data revealed two large clonal groups (clusters I and II) among the APEC strains with a similarity of 60.9% to each other. An association between restriction pattern and serogroup or origin of the strains was only present in a few subgroups of each clusters I and II, but was not evident. In contrast, our data revealed distinct combinations of virulence-associated genes in that 51.2% of the O2-strains harboured a combination of the genes fyuA, irp2, iucD, tsh, vat, fimC, and colV and 36.4% of the O78-strains possessed the same gene combination with exception of vat. With 34 different gene combinations the non-O1, -O2, -O78 isolates revealed a higher variability in their virulence gene pattern than O1-, O2-, and O78-strains with 6, 13, and 9 patterns, respectively. Our data indicate only a limited association between the virulence gene pattern and the serogroup of APEC strains and question the sensitivity of O-typing for APEC identification without the application of further diagnostic tools. Although a limited number of APEC clones exist, horizontal gene transfer seems to be common in these pathogens. These findings strengthen further research on the population structure of APEC and may be the reason for the lack of clear definition of this common E. coli pathotype.

Serotyping and Virulence Genes Detection in Escherichia coli Isolated from Fertile and Infertile Eggs, Dead-in-Shell Embryos, and Chickens with Yolk Sac Infection

Escherichia coli is a common avian pathogen mainly associated with extraintestinal infections such as yolk sac infection (YSI). The aim of this study was to determine the serotypes and the presence of some virulence genes of E. coli strains isolated from different samples in a vertically integrated poultry operation in Mexico. Two hundred sixty-seven E. coli isolates from different samples were serotyped using rabbit serum against the 175 somatic (O) and 56 flagellar (H) antigens of the typing schema. Virulence genes were determined by colony blot hybridization, using DNA probes for st, eae, agg1, agg2, bfp, lt, cdt, slt, and ipaH diarrhea-associated virulence factors. The serogroup of 85% of the strains was determined; O19 (12%), 084 (9%), 08 (6%), and 078 (5%) were the most common. Using the complete antigenic formula (O and H), O19:NM (n = 31) was the serotype most frequently isolated from dead-in-shell embryos and in broilers that had died on the fourth, fifth, sixth, and seventh days after hatch. One hundred ten strains (41.2%) hybridized with one or more of the used probes. Of these, ipaH (72%), eae (30%), and cdt (27%) were the most common. Considering the origin of the respective isolates, 40% of the broiler farm strains were positive for at least one probe. Results show that some avian E. coli strains isolated in Mexico are included in avian pathogenic E. coli serotypes not previously reported, suggesting that they could be specific for this geographic area. The wide distribution of the ipaH gene among nonmotile strains suggests that this invasiveness trait could be important in YSI pathogenesis. On the other hand, some other genes could contribute to E. coli virulence during YSI.

Determination of the clonal structure of avian Escherichia coli strains by isoenzyme and ribotyping analysis

Forty-nine avian Escherichia coli strains isolated from different outbreak cases of septicemia (24), swollen head syndrome (14) and omphalitis (11), and 20 strains isolated from poultry with no signs of the mentioned illnesses, for a total of 69 strains, were typed by isoenzyme profile and ribotyping analysis by restriction fragment length polymorphism (RFLP). Isoenzyme analysis discriminated better among strains (0-0.07 degree of genetic dissimilarity) than ribotyping analysis (0- 0.02 degree of genetic dissimilarity). The enzyme profiles of the E. coli isolates allowed the identification of 33 clones that were organized into six main clusters (A-F). Cluster A comprised 87% of the pathogenic strains and had no commensal strains, while commensal strains were assigned to clusters B-F. The ribotyping analysis resulted in a more heterogenous distribution of strains but most of those that cause the same type of infection were kept close together. Taken as a whole, these results demonstrate that pathogenic clones are more similar to one another when compared with commensal strains and suggest a correlation between the genetic background and the pathogenic characteristics of avian pathogenic E. coli strains.

Clonal relationships among avian Escherichia coli isolates determined by enterobacterial repetitive intergenic consensus (ERIC)-PCR

Forty-nine avian Escherichia coli isolates isolated from different outbreak cases of septicemia (24 isolates), swollen head syndrome (14 isolates) and omphalitis (11 isolates), and 30 commensal isolates isolated from poultry with no signs of illness were characterized by enterobacterial repetitive intergenic consensus (ERIC)-PCR technique and their serotypes were determined. The ERIC-PCR profile allowed the typing of the 79 isolates into 68 ERIC-types and grouped the isolates into four main clusters (A-D), with the omphalitis isolates being grouped with the commensals and separated from the septicaemia and swollen head syndrome. These results indicate that ERIC-PCR is a technique that could replace other molecular characterization techniques such as random amplification of polymorphic DNA (RAPD)-PCR and restriction fragment length polymorphism (RFLP), reinforce previous observations that omphalitis isolates are just opportunistic agents, and are consistent with many reports that specific genotypes are responsible for causing specific diseases. Most of the isolates were either nontypable or rough, supporting the need for alternative methods for typing these isolates.