Genotypic analysis of virulence genes and antimicrobial profile of diarrheagenic Escherichia coli isolated from diseased lambs in Iran

Antibiotic resistance profiling and phylotyping of human-diarrheagenic Escherichia coli pathotypes detected from diarrheic and non-diarrheic calves in Iran

BACKGROUND

Escherichia coli (E. coli) serves as a common indicator of gut microbiota and is utilized for monitoring antimicrobial resistance determinants in food-producing animals. This study aimed to investigate antimicrobial resistance patterns in virulence gene-positive E. coli isolates obtained from 340 healthy and diarrheic calves.

METHODS AND RESULTS

A total of 340 fecal swab samples were obtained from diarrheic (n = 170) and healthy (n = 170) calves for 12 months from different farms in Kerman, Iran. The samples were phenotypically analyzed to detect E. coli isolates and antibiotic resistance. Also, antimicrobial resistance genes, diarrheagenic E. coli pathotypes, and phylogenetic background were screened by PCR. Fifteen percent (51/340) of E. coli isolates were positive for at least one of the examined virulence genes (VGs); the prevalence of VGs in E. coli isolates from healthy calves (36/170; 21.17%) was higher than that in diarrheic cases (15/170; 8.82%). Out of the 51 VG-positive isolates, six pathotypes including Shiga toxin-producing E. coli (STEC; 27.45%), enterotoxigenic E. coli (ETEC; 23.52%), enterohemorrhagic E. coli (EHEC; 19.6%), necrotoxigenic E. coli (NTEC; 19.6%), enteropathogenic E. coli (EPEC; 15.68%), enteroinvasive E. coli (EIEC; 1.96%) and three hybrid pathotypes including ETEC/STEC, ETEC/EHEC, and STEC/EIEC were detected among the strains. Antimicrobial resistance (AR) was observed in 98.03% of the VG-positive isolates, which was the same for both healthy and diarrheic calves. The maximum prevalence rate of AR was found against trimethoprim/sulfamethoxazole (49.01%; 3/51), while the minimum prevalence rate was against gentamycin (5.88%; 25/51). Among the VG-positives, phylotype A was found to be the most prevalent followed by B1 and D phylotypes.

CONCLUSIONS

The prevalence of VG-positive E. coli isolates was higher in healthy calves compared to diarrheic cases. AR was widespread among VG-positive isolates. These findings suggest that calves may serve as potential reservoirs of antimicrobial-resistant hybrid pathotypes of E. coli.

Investigation of antibiotic resistance, virulence genes, and biofilm formation of Escherichia coli isolated from sheep feces in Shiraz industrial slaughterhouse, South of Iran

Background

With the increase in human population, the consumption of livestock products such as sheep meat has also increased. Sheep are the reservoir and shedder of Escherichia coli that can be transmitted to humans. Aims: Characterization of fecal E. coli isolated from sheep in slaughterhouse.

Methods

Stool specimens were collected from 30 apparently healthy sheep from different flocks in Shiraz industrial slaughterhouse. The resistance of E. coli isolates against 10 antibiotics was determined by disk diffusion method. The presence of three major extended spectrum beta-lactamase (ESBL) genes and five tetracycline resistance genes as well as seven virulence genes were investigated by polymerase chain reaction (PCR) technique. Using the microtiter plate method, the biofilm formation ability of E. coli isolates was investigated.

Results

The highest frequency of resistance was to amoxicillin (100%) followed by tetracycline (25%). All E. coli isolates were susceptible to gentamicin and nitrofurantoin, and only one isolate was resistant to the tested third-generation cephalosporins. Multidrug resistance phenotype was observed in 16.7% of the isolates. bla TEM (25%) was the most prevalent ESBL gene and tetA (62.5%) was the most prevalent tetracycline resistance gene in the isolates. crl, csgA, fimH, and bcsA genes were present in all isolates, and the prevalence of papC and afa genes was 95.8% and 83.3%, respectively. In total, 62.5% of the isolates were biofilm producers.

Conclusion

According to the concept of One Health, the presence of virulent antibiotic-resistant biofilm producing strains of E. coli in sheep is a risk to public health.

Expression analysis of TLR signaling pathway genes under lipopolysaccharide-induced and E. coli F17-infected sheep intestinal epithelial cells

Escherichia coli (E. coli) F17 is one of the main pathogens causing diarrhea in young livestock. The specific F17 fimbriae and lipopolysaccharide (LPS) in the surface components of E. coli F17 induces immune activation via interacting with the intestinal epithelial cells (IECs)-expressed innate immune toll-like receptors (TLRs) signaling pathway. In this study, the expression patterns of eight canonical genes from the TLR signaling pathway (IL-6, IL-8, IL-1β, TLR4, MyD88, CD14, TNF-α and TRAF6) were analyzed in LPS-induced IECs, E. coli F17-infected IECs and ileum tissue of E. coli F17-infected lambs. The results showed that increased expression levels of all the studied genes were observed following post-LPS-induced and E. coli F17-infected treatment, with TLR4 having the highest up-regulated expression multiple (compared to NC, fold change = 17.94 and 20.11, respectively), and CD14 having the lowest up-regulated expression multiple (fold change = 2.68 and 1.59, respectively), and higher expression levels of all the studied TLR signaling pathway genes were observed in ileum tissue of E. coli F17 antagonistic (AN) lambs than in E. coli F17 sensitive (SE) lambs. Furthermore, when compared to LPS-induced IECs, E. coli F17-infected IECs showed a more pronounced increase in the expression of IL6, TLR4 and TNF-α, indicating the different roles of these genes in the IECs resistance to E. coli F17 infection. Our results demonstrate that the TLR signaling pathway likely promotes immune activation and provide the first evidence that TLRs have a significant potential to protect against E. coli F17 infections.

Prevalence of Shiga toxin-producing Escherichia coli and Salmonellae and some associated hematologic and biochemical profile alterations in lambs

Lamb enteritis constitutes an economic burden on sheep production worldwide. We aimed to estimate the prevalence of Shiga toxin-producing Escherichia coli (STEC) and Salmonellae among diarrheic lambs at Kafrelsheikh Governorate, Egypt and to detect the associated clinical, hematologic, biochemical, and antioxidant parameters. Fifty diarrheic and twenty apparently healthy control lambs were examined clinically, and hematologically. Diarrheic lambs had a significant elevated body temperature, respiratory and pulse rate, most of hemogram para-meters, total proteins and albumin, oxidative stress markers malonaldiahyde and nitric oxide levels, liver enzymes, urea and creatinine than control group. On the other hand, these diarrheic lambs had significant reduction in total leukocyte count and lymphocytes, antioxidant biomarkers super oxide dismutase activities and reduced glutathione than control lambs. E. coli and Salmonella spp. were isolated from 32.00% and 16.00% of diseased lambs, respectively. Serotyping and biochemical tests of examined samples identified 16 E. coli isolates belonged to 10 different serotypes; O6, O8, O26:H11, O75, O84:H21, O103:H2, O114:H4, O121:H7, O128:H2 and O163:H2. All isolates are STEC as they harbor either Shiga-toxin 1 or Shiga-toxin 2 genes or both. One isolate carries intimin gene (eaeA) and classified as EHEC; O26:H11. The obtained nine isolates of Salmonella carry enterotoxin (Stn) genes, eight of them carry hyper-invasive locus (hilA) gene, all isolates belonged to six serotypes; S. Enteritidis, S. Heidelberg, S. Tsevie, S. Typhimurium, S. Essen, and S. Infantis. Lamb diarrhea was prevalent in the studied area and might constitute a veterinary and public health threat. Alteration in hemato-biochemical para-meters and oxidative-anti-oxidant balance could help adopt appropriate treatment regimens.

Potential Zoonotic Pathovars of Diarrheagenic Escherichia coli Detected in Lambs for Human Consumption from Tierra del Fuego, Argentina

Diarrheagenic Escherichia coli (DEC) pathovars impact childhood health. The southern region of Argentina shows the highest incidence of hemolytic uremic syndrome (HUS) in children of the country. The big island of Tierra del Fuego (TDF) in Argentina registered an incidence of five cases/100,000 inhabitants of HUS in 2019. This work aimed to establish the prevalence of STEC, EPEC, and EAEC in lambs slaughtered in abattoirs from TDF as well as to characterize the phenotypes and the genotypes of the isolated pathogens. The prevalence was 26.6% for stx+, 5.7% for eae+, and 0.27% for aagR+/aaiC+. Twelve STEC isolates were obtained and belonged to the following serotypes: O70:HNT, O81:H21, O81:HNT, O102:H6, O128ab:H2, O174:H8, and O174:HNT. Their genotypic profiles were stx_1c (2), stx_1c/ehxA (3), stx_2b/ehxA (1), stx_1c/stx_2b (2), and stx_1c/stx₂/ehxA (4). Six EPEC isolates were obtained and corresponded to five serotypes: O2:H40, O32:H8, O56:H6, O108:H21, and O177:H25. All the EPEC isolates were bfpA- and two were ehxA+. By XbaI-PFGE of 17 isolates, two clusters were identified. By antimicrobial susceptibility tests, 8/12 STEC and 5/6 EPEC were resistant to at least one antibiotic. This work provides new data to understand the ecology of DEC in TDF and confirms that ovine are an important carrier of these pathogens in the region.

A One Health Perspective for Defining and Deciphering Escherichia coli Pathogenic Potential in Multiple Hosts

E. coli is one of the most common species of bacteria colonizing humans and animals. The singularity of E. coli 's genus and species underestimates its multifaceted nature, which is represented by different strains, each with different combinations of distinct virulence factors. In fact, several E. coli pathotypes, or hybrid strains, may be associated with both subclinical infection and a range of clinical conditions, including enteric, urinary, and systemic infections. E. coli may also express DNA-damaging toxins that could impact cancer development. This review summarizes the different E. coli pathotypes in the context of their history, hosts, clinical signs, epidemiology, and control. The pathotypic characterization of E. coli in the context of disease in different animals, including humans, provides comparative and One Health perspectives that will guide future clinical and research investigations of E. coli infections.

Antimicrobial resistance patterns and phylogenetic analysis of Shiga toxin-producing Escherichia coli strains from goats using both Clermont phylogenetic schemes

Foodborne transmission of Shiga toxin-producing Escherichia coli (STEC) poses a threat to public health. The Clermont typing schemes (previous and revised) have been used widely to phylotype E. coli. The present study was conducted to compare the relationship of the Clermont phylogenet-ic schemes in STEC strains isolated from goats and antibiotic resistance patterns in the southeast of Iran. Overall 52 strains carrying the stx gene were used for subsequent analysis. All strains were determined by analysing the genomic DNA with a PCR-based method using the two Clermont et al. (2000, 2013) schemes. Extended spectrum beta-lactamase (ESBL) producing strains were con-firmed by the double disk-diffusion method. STEC strains were also tested for susceptibility to 20 antimicrobials agents. In the original Clermont method, the prevalent phylogroups were B1 (69.2%) and A (28.8%). The significant phylogenetic groups of strains according to the revised Clermont method were B1 (82.7%), A (13.5%) and unknown (3.8%). However, STEC strains underwent changes as noted from A to B1 (17.3%), B1 to unknown (3.8%), B1 to A (1.9%) and D to B1 (1.9%) groupings. Of the 52 stx-positive strains, two ESBL producing strains were detected. Susceptibility data showed that the most frequent resistance phenotype was related to cefazolin (90.4%), streptomycin (88.5%), ampicillin (86.5%) and oxytetracycline (82.7%) respectively. Alt-hough the overall frequency of the reassigned phylotypes was not significant, most changes oc-curred within the A phylotype. Therefore, implementation of the new method on isolates belong-ing to the A phylotype in the old method seems to be necessary to obtain accurate results.

Molecular characterization of pathogenic Escherichia coli isolated from diarrheic and in-contact cattle and buffalo calves

Escherichia coli field isolates from calves were characterized and categorized into the most significant diarrheagenic pathotypes using polymerase chain reaction (PCR) assays with different specific primers. The used PCR systems were designed to detect sequences representing the group-specific virulence genes encoding fimbriae f5 (K99), Shiga toxins (stx₁ and stx₂), heat-stable enterotoxins (st), heat-labile enterotoxins (lt), intimin (eae), hemolysin (hylA), and EAEC heat-stable enterotoxin (astA). In the present work, a total of 150 E. coli field isolates were recovered from 150 fecal swabs collected from 100 diarrheic and 50 apparently healthy in-contact cattle and buffalo calves under 3 months old. Out of these 150 isolated E. coli, 106 isolates from 77 diarrheic and 29 in-contact calves harbored one or more of the investigated virulence genes. The pathotyping of the isolates could classify them into shigatoxigenic E. coli (STEC), enteropathogenic E. coli (EPEC), enterotoxigenic E. coli (ETEC), and enteroaggregative E. coli (EAEC) with a 30.7, 2.7, 12.7, and 7.3% distribution, respectively. Meanwhile, the detection rates of f5, stx₁, stx₂, st, lt, eae, hylA, and astA genes were 17.3, 27.3, 6.7, 10, 37.3, 17.7, 9.3, and 20.7%, respectively. These virulence genes were found either single or in different combinations, such as stx/eae, stx/st/f5, eae/st/f5, or st/lt/f5. Four attaching-effacing shigatoxigenic E. coli isolates (AE-STEC) harboring stx/eae were retrieved from diarrheic calves. Although none of the stx-or eae-positive isolates was verified as O157:H7, STEC isolates detected in apparently healthy calves have potential pathogenicity to humans highlighting their zoonotic importance as reservoirs. Atypical combinations of ETEC/STEC and ETEC/EPEC were also detected in percentages of 14.7 and 2.7%, respectively. Most of these atypical combinations were found more in buffalo calves than in cattle calves. While STEC and EPEC isolates were detected more in cattle calves than in buffalo calves, ETEC isolates were the same in the two species. The pathogenic E. coli infection in calves was recorded to be higher in the first weeks of life with the largest numbers of virulence factor-positive isolates detected at the age of 4 weeks. Histopathological examination of five intestinal samples collected from four dead buffalo calves revealed typical attaching and effacing (AE) lesion which was correlated with the presence of intimin encoding virulence gene (eae). Other lesions characterized by hemorrhagic enteritis, shortening and fusion of intestinal villi and desquamation of the lining epithelium of intestinal mucosa had also been detected.

The First Isolation and Molecular Characterization of Shiga Toxin-Producing Virulent Multi-Drug Resistant Atypical Enteropathogenic Escherichia coli O177 Serogroup From South African Cattle

Atypical enteropathogenic E. coli (aEPEC) is a group of diarrhoeagenic Escherichia coli with high diversity of serogroups, which lack the bundle-forming pili (BFP) and genes encoding for shiga toxins. The aim of this study was to isolate, identify and determine virulence and antibiotic resistance profiles of aEPEC O177 strains from cattle feces. A total of 780 samples were collected from beef and dairy cattle and analyzed for the presence of E. coli O177. One thousand two hundred and seventy-two (1272) presumptive isolates were obtained and 915 were confirmed as E. coli species. Three hundred and seventy-six isolates were positively confirmed as E. coli O177 through amplification of rmlB and wzy gene sequences using multiplex PCR. None of these isolates harbored bfpA gene. A larger proportion (12.74%) of the isolates harbored hlyA gene while 11.20, 9.07, 7.25, 2.60, and 0.63% possessed stx₂, stx₁, eaeA, stx_2a, and stx_2d, respectively. Most of E. coli O177 isolates carried stx₂/hlyA (9.74%). Furthermore, 7.40% of the isolates harbored stx₁/stx₂ while 7.09% possessed stx₁/stx₂/hlyA genes. Only one isolate harbored stx₁/stx₂/hly/eaeA/stx_2a/stx_2d while 5.11% of the isolates harbored all the four major virulence genes stx₁/stx₂/hlyA/eaeA, simultaneously. Further analysis revealed that the isolates displayed varied antimicrobial resistance to erythromycin (63.84%), ampicillin (21.54%), tetracycline (13.37%), streptomycin (17.01%), kanamycin (2.42%), chloramphenicol (1.97%), and norfloxacin (1.40%). Moreover, 20.7% of the isolates exhibited different phenotypic multi-drug resistance patterns. All 73 isolates harbored at least one antimicrobial resistance gene. The aadA, streA, streB, erm, and tetA resistance genes were detected separately and/or concurrently. In conclusion, our findings indicate that environmental isolates of aEPEC O177 strains obtained from cattle in South Africa harbored virulence and antimicrobial resistance gene determinants similar to those reported in other shiga-toxin producing E. coli strains and suggest that these determinants may contribute to the virulence of the isolates.

Characterization of bacterial community changes and antibiotic resistance genes in lamb manure of different incidence

Bacterial enteritis is the most important disease in lamb for breeding greatly affects the growth of animals. Changes in the community of intestinal flora can cause the disorder of the colonic environment induced diarrhea. This study aimed to investigate the relationship between the incidence of bacterial enteritis and the number of intestinal microbiome, then the prevalence of drug-resistant genes was detected. Fecal samples were collected at five fattening sheep farms with different incidence of bacterial enteritis, pathogenic bacteria were isolated and identified, drug sensitivity tests were performed. Then, changes in number and structure of intestinal flora were compared by 16S rDNA V3-V4 region high-throughput sequencing, and the ARGs were detected using high-throughput real-time PCR. Our results revealed that the microbial communities were positively correlated with the incidence of bacterial enteritis in different farms. Bacterial communities were higher in YJ (with highest incidence of diarrhea) than any other farms. However, the ARGs seemed not to be more affected by the incidence of bacterial enteritis, but one of the significant findings to emerge from this study is that MCR-1 and NDM are detected in manure. This study has provided an insight of the changes occurring in intestinal flora and AGRs in fattening sheep farms with diverse incidence of bacterial enteritis.

Molecular investigation of the colicinogenic Escherichia coli strains that are capable of inhibiting E. coli O157:H7 in vitro

Background

Escherichia coli O157:H7 is a highly virulent human pathogen with severe consequences following infection, which claims many lives worldwide. A suggested method for controlling this bacterium is the competitive elimination through using probiotic bacteria that prevent its colonization. Some nonpathogenic E. coli strains that produce antibacterial colicins are among these probiotic bacteria. We aimed to isolate and characterize the colicinogenic E. coli strains from diarrheic and healthy sheep that inhibit E. coli O157:H7, which could be used as possible probiotic sources. A total of 292 E. coli isolates (146 from each diarrheic and healthy sheep) were screened for the presence of colicin and virulence genes. The phylogenetic group/subgroup determination was performed by PCR. In vitro evaluation of inhibitory effect of colicinogenic isolates on E. coli O157:H7 was done phenotypically.

Results

The frequency of diarrhea associated colicinogenic E. coli isolates was significantly higher than those isolated from healthy sheep. An association between ETEC and the genes coding for colicin-V & colicin-Iab in diarrheic E. coli isolates was observed. Moreover, there was an association between ipaH and Colicin-V encoding genes. Furthermore, E. coli isolates showing bacteriocinogeny while possessing no virulence genes had a frequency of 97.67 and 11.94% in healthy and diarrheic isolates, respectively. Of these strains, five isolates (3.42%) from diarrheic and twenty-five isolates (17.12%) from healthy sheep inhibited O157:H7 strain. Additionally, colicin E1 and colicin Iab genes were more prevalent in B1 phylogroup.

Conclusions

These results signified that healthy sheep could be considered as a potential source for anti-O175:H7 bacterial isolates.

ECOR phylotyping and determination of virulence genes in Escherichia coli isolates from pathological conditions of broiler chickens in poultry slaughter-houses of southeast of Iran

Avian pathogenic Escherichia coli (APEC) are responsible for wide ranges of extra-intestinal diseases in poultry including colibacillosis, cellulitis, coligranuloma and yolk sac infection. Numbers of virulence are considered important in the pathogenicity of these diseases. The aims of the present study were phylogenetic typing and virulence genes detection in Escherichia coli isolates from colibacillosis and cellulitis of broiler chickens in poultry slaughterhouses of Shahrbabak region, Kerman, Iran. A total number of eighty three E. coli isolates were taken from broiler chickens with colibacillosis and thirty four isolates were taken from carcasses with cellulitis in the industrial slaughterhouses. Biochemically confirmed E. coli isolates were subjected to polymerase chain reaction assay to determine phylogenetic groups and presence of pap C, sfa/focDE, iucD, afaIB-C, hlyA, fimH and crl virulence genes. Colibacillosis isolates were belonged to A (54.21%), B1 (7.22%), B2 (6.03%) and D (32.53%) phylogroups. Whereas, the isolates from cellulitis cases were belonged to three main phylogroups; A (55.88%), B1 (5.88%) and D (38.24%). Statistical analysis showed a specific association between the presence of crl virulence gene and phylogroups of A and D in colibacillosis isolates. The results showed that the isolates from both diseases in broiler chickens could be assigned to various phylogenetic groups (mainly A(. Also, the virulence genes profile of cellulitis E. coli is completely different from that of colibacillosis in this region.