Complete DNA sequence of a ColBM plasmid from avian pathogenic Escherichia coli suggests that it evolved from closely related ColV virulence plasmids

Longitudinal study of avian pathogenic Escherichia coli (APEC) serogroups associated with disease in Georgia poultry using molecular serology and virulence gene analysis

RESEARCH HIGHLIGHTS

Several emerging APEC serogroups were observed in Georgia poultry populations.An association between APEC serogroups and bird type was observed.The prevalence of different APEC serogroups was influenced by season.A multiplex PCR assay targeting common serogroups of APEC in Georgia poultry was developed.

Molecular characterization, virulence and antimicrobial and biocidal susceptibility of selected bacteria isolated from the cloaca of nestling ospreys (Pandion haliaetus) from Mono Lake, California, USA

In the present study, the presence of the Enterobacterales, Staphylococcus spp., Mammaliicoccus spp., and Enterococcus spp. in cloacal samples of nestling ospreys (Pandion haliaetus), a fish-eating specialist, from Mono Lake, California, USA was examined by a multiphasic approach, including antimicrobial and biocide susceptibility testing, genotyping, and whole genome sequencing of selected isolates. The most commonly detected species was Escherichia coli, followed by Mammaliicoccus sciuri, Staphylococcus delphini, Enterococcus faecalis, Enterococcus faecium, Hafnia alvei, Klebsiella pneumoniae, Citrobacter braakii and single isolates of Edwardsiella tarda, Edwardsiella albertii, Klebsiella aerogenes, Plesiomonas shigelloides and Staphylococcus pseudintermedius. Multi-drug resistance (MDR) was observed in two E. coli isolates and in an Enterococcus faecium isolate. The MDR blaCTX-M-55-positive E. coli belonged to the pandemic clone ST58. The results of the present study suggest that nestling ospreys are exposed to MDR bacteria, possibly through the ingestion of contaminated fish. Ospreys may be good biosentinels for the presence of these microorganisms and antibiotic resistance in the local environment and the risk for other wildlife, livestock and humans.

Virulence-associated genes in faecal and clinical Escherichia coli isolates cultured from broiler chickens in Australia

A healthy chicken's intestinal flora harbours a rich reservoir of Escherichia coli as part of the commensal microbiota. However, some strains, known as avian pathogenic E. coli (APEC), carry specific virulence genes (VGs) that enable them to invade and cause extraintestinal infections such as avian colibacillosis. Although several VG combinations have been identified, the pathogenic mechanisms associated with APEC are ill-defined. The current study screened a subset of 88 E. coli isolates selected from 237 pre-existing isolates obtained from commercial poultry flocks in Australia. The 88 isolates were selected based on their enterobacterial repetitive intergenic consensus (ERIC) and antimicrobial resistance (AMR) profiles and included 29 E. coli isolates cultured from chickens with colibacillosis (referred to as clinical E. coli or CEC) and 59 faecal E. coli (FEC) isolates cultured from clinically healthy chickens. The isolates were screened for the presence of 35 previously reported VGs. Of these, 34 were identified, with iucA not being detected. VGs focG, hlyA and sfa/foc were only detected in FEC isolates. Eight VGs had a prevalence of 90% or above in the CEC isolates. Specifically, astA (100%); feoB (96.6%); iutA, iss, ompT, iroN and hlyF (all 93.1%); and vat (89.7%). The prevalence of these were significantly lower in FEC isolates (astA 79.7%, feoB 77.9%, iutA 52.5%, iss 45.8%, ompT 50.9%, iroN 37.3%, hlyF 50.9% and vat 42.4%). The odds ratios that each of these eight VGs were more likely to be associated with CEC than FEC ranged from 7.8 to 21.9. These eight VGs may be used to better define APEC and diagnostically detect APEC in Australia. Further investigations are needed to identify the roles of these VGs in pathogenicity.

Evaluating the effects of virulence genotype, swarming motility, and multi-locus sequence types of Escherichia coli on layer chicken embryos

AIMS

To determine the effects of swarming motility (SM) and multi-locus sequence types (MLST) on the main effect of virulence genotype of Escherichia coli through an embryos lethality assay between the 12th and 18th days of incubation.

METHODS AND RESULTS

We collected 58 E. coli isolates from asymptomatic commercial hens (n = 42) and lesions of colibacillosis cases (n = 16), then classified their virulence genotype as avirulent, moderately virulent, virulent-healthy, and virulent-colibacillosis categories by the presence of five virulence-associated genes (iroN, ompT, hlyF, iutA, and iss). These isolates were further classified as non-motile, motile, or hyper-motile by SM assay. From the 58 isolates, we selected 29 for ELA and determined their MLST. Each isolate was inoculated into 15 embryonated eggs through the allantoic cavity. We found the avirulent isolates reduced the relative embryo weight compared to virulent-colibacillosis and moderately virulent isolates (37.49 vs. 41.51 and 40.34%, P = 0.03). Among the moderately virulent and virulent-colibacillosis categories, embryo lethality was lower when isolates were non-motile. Yolk retention was unaffected by virulence categories, motility, or MLST.

CONCLUSION

Interaction between virulence genotype and SM substantially influenced the embryo lethality assay of E. coli isolates.

Horizontal transfer characterization of ColV plasmids in blaCTX-M-bearing avian Escherichia coli

Extended-spectrum-β-lactamases (ESBLs)-producing Escherichia coli conferred resistance to most β-lactams, except for carbapenems. To date, the transmission mechanism of blaCTX-M, as the most common ESBLs subtype, in E. coli has received sustained attention around the worldwide, but the research on the pathogenicity of blaCTX-M-bearing E. coli is still scarce. The aims of this study were to discern the spread characteristics of ColV (encoding colicin V) plasmids in blaCTX-M-positive E. coli. The multi-drug resistance traits, phylogroups, and ColV plasmid profilings were screened in 76 blaCTX-M-positive E. coli. Thereafter, the genetic profiles of E. coli G12 and GZM7 were determined by whole genome sequencing, conjugation and S1-pulsed-field gel electrophoresis. The median lethal dose was analyzed in E. coli G12 and TG12A, the ColV-plasmid transconjugant of G12. Of all 76 blaCTX-M-bearing E. coli, 67.11% exhibited resistance to at least 2 drugs in addition to ceftiofur, 14.47% carried ColV-positive plasmids, and 53.95% were phylogroup C. Further studies demonstrated that the blaCTX-M-bearing E. coli G12 was assigned to the predominant lineage O78:H4-ST117 of phylogroup G. In addition, its ColV-positive plasmid simultaneously carried multiple resistance genes, and could be independently transferred to confer partial pathogenicity on its host by plasmid mating. E. coli GZM7 was O53:H9-ST23 of phylogroup C, which belonged to another representative lineage of APEC (avian pathogenic E. coli). Its ColV-positive plasmid could complete conjugation with the help of the other coexisting-resistance conjugative plasmid, although it failed to transfer alone. Our findings highlight the flexibly horizontal transfer of ColV plasmids along with multidrug-resistant genes among blaCTX-M-bearing E. coli poses a threat to poultry health and food safety, which contributes to elucidate the concept of "One Health" and deserves particular concern.

Presence of fimH and iss type 1, 2 and 3 genes in uropathogenic Escherichia coli isolates recovered from an apex medical institute in North India

PURPOSE

To detect the presence of fimH and iss type 1, 2 and 3 genes in uropathogenic Escherichia coli (UPEC) isolates recovered from patients coming to the out patient department (OPD) of our hospital.

METHODS

E. coli isolates recovered from patients who had symptoms of urinary tract infection (UTI) were processed for the presence of fimH and iss genes. DNA was extracted using an in house method after which conventional PCR using forward and reverse primers targeting the four genes was carried out. The amplified products were electrophoresed and visualized in a gel documentation imager. Relevant demographic details of the patients were recorded on a pre-designed pro-forma and antimicrobial susceptibility testing of the isolates was done by disc diffusion method.

RESULTS

fimH was present in 87.5% of UPEC isolates whereas iss type 1 was seen in 7.3%, type 2 in 4.2% and iss type 3 in 71.9% isolates. Age of the patients ranged from 3 months to 82 ​yrs (mean 43.5 SD ​± ​18.20). UTI was more common in females (60.2%) as compared to males patients (39.8%). Dysuria (66.7%) was the most common symptom in the studied subjects and diabetes mellitus (42.6%) the most common co-morbidity. A total of 56.5% patients gave a history of prior antibiotic intake. The UPEC isolates were resistant to most of the antibiotics tested. However all the isolates were sensitive to polymyxin B and colistin. Fosfomycin resistance was seen in 9.5% of the UPEC isolates harbouring fimH gene.

CONCLUSION

This is the first study that highlights the presence of iss type 3 gene in UPEC isolates along with the fimH and iss type 1 and 2 genes. The results of this study can serve as a stepping stone for future in depth research into the significance of the iss genes in causing UTI.

Survey of clinical and commensal Escherichia coli from commercial broilers and turkeys, with emphasis on high-risk clones using APECTyper

Molecular characterization of avian pathogenic Escherichia coli (APEC) is challenging due to the complex nature of its associated disease, colibacillosis, in poultry. Numerous efforts have been made toward defining APEC, and it is becoming clear that certain clonal backgrounds are predictive of an avian E. coli isolate's virulence potential. Thus, APEC can be further differentiated as high-risk APEC based upon their clonal background's virulence potential. However, less clear is the degree of overlap between clinical isolates of differing bird type, and between clinical and gastrointestinal isolates. This study aimed to determine genomic similarities and differences between such populations, comparing commercial broiler vs. turkey isolates, and clinical vs. gastrointestinal isolates. Differences were observed in Clermont phylogenetic groups between isolate populations, with B2 as the dominant group in turkey clinical isolates and G as the dominant group in broiler clinical isolates. Nearly all clinical isolates were classified as APEC using a traditional gene-based typing scheme, whereas 53.4% and 44.1% of broiler and turkey gastrointestinal isolates were classified as APEC, respectively. High-risk APEC were identified among 31.0% and 46.9% of broiler and turkey clinical isolates, compared with 5.7% and 2.9% of broiler and turkey gastrointestinal isolates. As found in previous studies, no specific known virulence or fitness gene sets were identified which universally differentiate between clinical and gastrointestinal isolates. This study further demonstrates the utility of a hybrid APEC typing approach, considering both plasmid content and clonal background, for the identification of dominant and highly virulent APEC clones in poultry production.

Virulence Genotype and Phenotype of Multiple Antimicrobial-Resistant Escherichia coli Isolates from Broilers Assessed from a "One-Health" Perspective

ABSTRACT

Extraintestinal pathogenic Escherichia coli (ExPEC) include several serotypes that have been associated with colibacillosis in poultry and with urinary tract infections (UTIs) and newborn meningitis in humans. In this study, 57 antimicrobial-resistant E. coli from apparently healthy broiler chickens were characterized for their health and safety risks. These isolates belonged to 12 serotypes, and isolates of the same serotype were clonal based on single nucleotide variant analysis. Most of the isolates harbored plasmids; IncC and IncFIA were frequently detected. The majority of the resistant isolates harbored plasmid-mediated resistance genes, including aph(3″)-Ib, aph(6)-Id, blaCMY-2, floR, sul1, sul2, tet(A), and tet(B), in agreement with their resistant phenotypes. The class 1 integron was detected in all E. coli serotypes except O124:H25 and O7:H6. Of the 57 broiler E. coli isolates, 27 were avian pathogenic, among which 18 were also uropathogenic E. coli and the remainder were other ExPEC. The two isolates of serotype O161:H4 (ST117) were genetically related to the control avian pathogenic strains and a clinical isolate associated with UTIs. A strain of serotype O159:H45 (ST101) also was closely related to a UTI isolate. The detected virulence factors included adhesins, invasins, siderophores, type III secretion systems, and toxins in combination with other virulence determinants. A broiler isolate of serotype O7:H18 (ST38) carried the ibeA gene encoding a protein involved in invasion of brain endothelium on a 102-kbp genetic island. This isolate moderately adhered and invaded Caco-2 cells and induced mortality (42.5%) in a day-old-chick infection model. The results of this study suggest that multiple antimicrobial-resistant E. coli isolates recovered from apparent healthy broilers can be pathogenic and act as reservoirs for antimicrobial resistance genes, highlighting the necessity of their assessment in a "One-Heath" context.

HIGHLIGHTS

An Integrated Perspective on Virulence-Associated Genes (VAGs), Antimicrobial Resistance (AMR), and Phylogenetic Clusters of Pathogenic and Non-pathogenic Avian Escherichia coli

Avian pathogenic Escherichia coli (APEC) is an important bacterial pathogen that causes avian colibacillosis and leads to huge economic losses in the poultry industry. Different virulence traits contribute to pathogenesis of APEC infections, and antimicrobial resistance (AMR) has also been an overwhelming issue in poultry worldwide. In the present study, we aimed to investigate and compare the presence of virulence-associated genes (VAGs), AMR, and phylogenetic group's distribution among APEC and avian fecal E. coli (AFEC) strains. E. coli from birds with colisepticemia and yolk sac infection (YSI) (APEC) plus E. coli strains from the feces of healthy birds (AFEC) were compared by the aforementioned traits. In addition, the clonal relatedness was compared using Enterobacterial repetitive intergenic consensus PCR (ERIC-PCR). Although all strains were susceptible to fosfomycin, ceftriaxone, and cefixime, almost all strains (98%) were multi-drug resistant (MDR). All strains (except two) harbored at least three or more VAGs, and the virulence scores tended to be higher in pathogenic strains especially in the colisepticemic group. All phylogenetic groups were found in isolates from YSI, colisepticemia, and the feces of healthy birds; however, the frequency of phylogroups varied according to the source of the isolate. B1 and C phylogroups were statistically more likely to be found among APEC from YSI and colisepticemic E. coli groups, respectively, while phylogroup A was the most frequently occurring phylogroup among AFEC strains. Our findings also revealed that AMR and VAGs are not essentially co-evolved traits as in some instances AMR strains were more prevalent among AFEC. This reflects the divergent evolutionary pathways of resistance acquisition in pathogenic or non-pathogenic avian E. coli strains. Importantly, strains related to phylogenetic group C showed higher virulence score and AMR that requires further attention. To some extent, ERIC-PCR was able to group strains by isolation source, phylogroup, or virulence genes. Further integrated studies along with assessment of more detailed genotypic and phenotypic features could potentially lead to better understanding of virulence, resistance, and evolution of ExPEC.

Longitudinal study on the effect of autogenous vaccine application on the sequence type and virulence profiles of Escherichia coli in broiler breeder flocks

Colibacillosis is one of the most common problems in the poultry industry. Escherichia coli strains on farms are often genetically diverse and therefore commercial vaccines provide little protection to the flocks. Here, we investigated the effect of the autogenous E. coli vaccines on the prevalence of 84 virulence-associated genes in E. coli isolated from four and five consecutive flocks on two broiler breeder farms, respectively. 115 E. coli isolates were sequenced using Illumina technologies, and compared based on both their set of housekeeping genes and their virulence profiles, defined through the composition of virulence genes. Predominantly, phylogenetic analysis showed obvious distinction between the isolates originating from different farms suggesting spatial-dependent transmission of pathogenic strains. We detected 23 sequence types, while 52.58 % of the isolates belonged to two clonal complexes. Analysis of the virulence genes showed highest prevalence (>85 %) of feoB, uspA, uspB, uspG, uspE, fimH, ompA, astA, focA, hlyE, uspC, crl, csgA, ompT and iss, of which 50 % are toxin associated genes, demonstrating the importance of competition in the pathogenesis process. Interestingly, usp genes, which are primarily associated with uropathogenic E. coli strains, were detected in all investigated isolates. The heatmap analysis demonstrated that strains belonging to same phylogenetic groups often share similar virulence profiles, confirming the usefulness of quick tests for phylogenetic typing. However, our results suggest the need to update the list of the minimal predictors used for the identification of avian pathogenic strains. Overall results indicate that continuous application of autogenous vaccines led to lower genetic diversity of E. coli housekeeping genes, but not virulence genes.

Colistin-Resistant mcr-1-Positive Escherichia coli ST131-H22 Carrying bla CTX-M-15 and qnrB19 in Agricultural Soil

The pandemic Escherichia coli sequence type 131 (ST131) carrying plasmid-mediated colistin resistance mcr genes has emerged worldwide causing extraintestinal infections, with lineages belonging to three major clades (A, B, and C). Clade B is the most prevalent in animals, contaminating associated meat products, and can be transmitted zoonotically. However, the bla_CTX–M–15 gene has only been associated with C2 subclade so far. In this study, we performed a genomic investigation of an E. coli (strain S802) isolated from a kale crop in Brazil, which exhibited a multidrug-resistant (MDR) profile to clinically significant antimicrobials (i.e., polymyxin, broad-spectrum cephalosporins, aminoglycosides, and fluoroquinolones). Whole-genome sequencing analysis revealed that the S802 strain belonged to serotype O25:H4, ST131/CC131, phylogenetic group B2, and virotype D5. Furthermore, S802 carried the clade B-associated fimH22 allele, genes encoding resistance to clinically important antimicrobials, metals, and biocides, and was phylogenetically related to human, avian, and swine ST131-H22 strains. Additionally, IncHI2-IncQ1, IncF [F2:A-:B1], and ColE1-like plasmids were identified harboring mcr-1.1, bla_CTX–M–15, and qnrB19, respectively. The emergence of the E. coli ST131-H22 sublineage carrying mcr-1.1, bla_CTX–M–15, and qnrB19 in agricultural soil represents a threat to food and environmental safety. Therefore, a One Health approach to genomic surveillance studies is required to effectively detect and limit the spread of antimicrobial-resistant bacteria and their resistance genes.

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.

Ways to minimize bacterial infections, with special reference to Escherichia coli, to cope with the first-week mortality in chicks: an updated overview

On the commercial level, the poultry industry strives to find new techniques to combat bird's infection. During the first week, mortality rate increases in birds because of several bacterial infections of about ten bacterial species, especially colisepticemia. This affects the flock production, uniformity, and suitability for slaughter because of chronic infections. Escherichia coli (E. coli) causes various disease syndromes in poultry, including yolk sac infection (omphalitis), respiratory tract infection, and septicemia. The E. coli infections in the neonatal poultry are being characterized by septicemia. The acute septicemia may cause death, while the subacute form could be characterized through pericarditis, airsacculitis, and perihepatitis. Many E. coli isolates are commonly isolated from commercial broiler chickens as serogroups O₁, O₂, and O₇₈. Although prophylactic antibiotics were used to control mortality associated with bacterial infections of neonatal poultry in the past, the commercial poultry industry is searching for alternatives. This is because of the consumer's demand for reduced antibiotic-resistant bacteria. Despite the vast and rapid development in vaccine technologies against common chicken infectious diseases, no antibiotic alternatives are commercially available to prevent bacterial infections of neonatal chicks. Recent research confirmed the utility of probiotics to improve the health of neonatal poultry. However, probiotics were not efficacious to minimize death and clinical signs associated with neonatal chicks' bacterial infections. This review focuses on the causes of the increased mortality in broiler chicks during the first week of age and the methods used to minimize death.

Genome evolution and the emergence of pathogenicity in avian Escherichia coli

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

Role of Plasmids in the Ecology and Evolution of "High-Risk" Extraintestinal Pathogenic Escherichia coli Clones

Bacterial plasmids have been linked to virulence in Escherichia coli and Salmonella since their initial discovery. Though the plasmid repertoire of these bacterial species is extremely diverse, virulence-associated attributes tend to be limited to a small subset of plasmid types. This is particularly true for extraintestinal pathogenic E. coli, or ExPEC, where a handful of plasmids have been recognized to confer virulence- and fitness-associated traits. The purpose of this review is to highlight the biological and genomic attributes of ExPEC virulence-associated plasmids, with an emphasis on high-risk dominant ExPEC clones. Two specific plasmid types are highlighted to illustrate the independently evolved commonalities of these clones relative to plasmid content. Furthermore, the dissemination of these plasmids within and between bacterial species is examined. These examples demonstrate the evolution of high-risk clones toward common goals, and they show that rare transfer events can shape the ecological landscape of dominant clones within a pathotype.

Distinguishing Pathovars from Nonpathovars: Escherichia coli

Escherichia coli is one of the most well-adapted and pathogenically versatile bacterial organisms. It causes a variety of human infections, including gastrointestinal illnesses and extraintestinal infections. It is also part of the intestinal commensal flora of humans and other mammals. Groups of E. coli that cause diarrhea are often described as intestinal pathogenic E. coli (IPEC), while those that cause infections outside of the gut are called extraintestinal pathogenic E. coli (ExPEC). IPEC can cause a variety of diarrheal illnesses as well as extraintestinal syndromes such as hemolytic-uremic syndrome. ExPEC cause urinary tract infections, bloodstream infection, sepsis, and neonatal meningitis. IPEC and ExPEC have thus come to be referred to as pathogenic variants of E. coli or pathovars. While IPEC can be distinguished from commensal E. coli based on their characteristic virulence factors responsible for their associated clinical manifestations, ExPEC cannot be so easily distinguished. IPEC most likely have reservoirs outside of the human intestine but it is unclear if ExPEC represent nothing more than commensal E. coli that breach a sterile barrier to cause extraintestinal infections. This question has become more complicated by the advent of whole genome sequencing (WGS) that has raised a new question about the taxonomic characterization of E. coli based on traditional clinical microbiologic and phylogenetic methods. This review discusses how molecular epidemiologic approaches have been used to address these questions, and how answers to these questions may contribute to our better understanding of the epidemiology of infections caused by E. coli. *This article is part of a curated collection.

Genotypic and Phenotypic Characterization of Incompatibility Group FIB Positive Salmonella enterica Serovar Typhimurium Isolates from Food Animal Sources

Salmonella enterica is one of the most common bacterial foodborne pathogens in the United States, causing illnesses that range from self-limiting gastroenteritis to more severe, life threatening invasive disease. Many Salmonella strains contain plasmids that carry virulence, antimicrobial resistance, and/or transfer genes which allow them to adapt to diverse environments, and these can include incompatibility group (Inc) FIB plasmids. This study was undertaken to evaluate the genomic and phenotypic characteristics of IncFIB-positive Salmonella enterica serovar Typhimurium isolates from food animal sources, to identify their plasmid content, assess antimicrobial resistance and virulence properties, and compare their genotypic isolates with more recently isolated S. Typhimurium isolates from food animal sources. Methods: We identified 71 S. Typhimurium isolates that carried IncFIB plasmids. These isolates were subjected to whole genome sequencing and evaluated for bacteriocin production, antimicrobial susceptibility, the ability to transfer resistance plasmids, and a subset was evaluated for their ability to invade and persist in intestinal human epithelial cells. Results: Approximately 30% of isolates (n = 21) displayed bacteriocin inhibition of Escherichia coli strain J53. Bioinformatic analyses using PlasmidFinder software confirmed that all isolates contained IncFIB plasmids along with multiple other plasmid replicon types. Comparative analyses showed that all strains carried multiple antimicrobial resistance genes and virulence factors including iron acquisition genes, such as iucABCD (75%), iutA (94%), sitABCD (76%) and sitAB (100%). In 17 cases (71%), IncFIB plasmids, along with other plasmid replicon types, were able to conjugally transfer antimicrobial resistance and virulence genes to the susceptible recipient strain. For ten strains, persistence cell counts (27%) were noted to be significantly higher than invasion bacterial cell counts. When the genome sequences of the study isolates collected from 1998–2003 were compared to those published from subsequent years (2005–2018), overlapping genotypes were found, indicating the perseverance of IncFIB positive strains in food animal populations. This study confirms that IncFIB plasmids can play a potential role in disseminating antimicrobial resistance and virulence genes amongst bacteria from several food animal species.

Chicken-source Escherichia coli within phylogroup F shares virulence genotypes and is closely related to extraintestinal pathogenic E. coli causing human infections

ExPEC is an important pathogen that causes diverse infection in the human extraintestinal sites. Although avian-source phylogroup F Escherichia coli isolates hold a high level of virulence traits, few studies have systematically assessed the pathogenicity and zoonotic potential of E. coli isolates within phylogroup F. A total of 1,332 E. coli strains were recovered from chicken colibacillosis in China from 2012 to 2017. About 21.7% of chicken-source E. coli isolates were presented in phylogroup F. We characterized phylogroup F E. coli isolates both genotypically and phenotypically. There was a widespread prevalence of ExPEC virulence-related genes among chicken-source E. coli isolates within phylogroup F. ColV/BM plasmid-related genes (i.e. hlyF, mig-14p, ompTp, iutA and tsh) occurred in the nearly 65% of phylogroup F E. coli isolates. Population structure of chicken-source E. coli isolates within phylogroup F was revealed and contained several dominant STs (such as ST59, ST354, ST362, ST405, ST457 and ST648). Most chicken-source phylogroup F E. coli held the property to produce biofilm and exhibited strongly swimming and swarming motilities. Our result showed that the complement resistance of phylogroup F E. coli isolates was closely associated with its virulence genotype. Our research further demonstrated the zoonotic potential of chicken-source phylogroup F E. coli isolates. The phylogroup F E. coli isolates were able to cause multiple diseases in animal models of avian colibacillosis and human infections (sepsis, meningitis and UTI). The chicken-source phylogroup F isolates, especially dominant ST types, might be recognized as a high-risk food-borne pathogen. This was the first study to identify that chicken-source E. coli isolates within phylogroup F were associated with human ExPEC pathotypes and exhibited zoonotic potential.

Three new serine-protease autotransporters of Enterobacteriaceae (SPATEs) from extra-intestinal pathogenic Escherichia coli and combined role of SPATEs for cytotoxicity and colonization of the mouse kidney

Serine protease autotransporters of Enterobacteriaceae (SPATEs) are secreted proteins that contribute to virulence and function as proteases, toxins, adhesins, and/or immunomodulators. An extra-intestinal pathogenic E. coli (ExPEC) O1:K1 strain, QT598, isolated from a turkey, was shown to contain vat, tsh, and three uncharacterized SPATE-encoding genes. Uncharacterized SPATEs: Sha (Serine-protease hemagglutinin autotransporter), TagB and TagC (tandem autotransporter genes B and C) were tested for activities including hemagglutination, autoaggregation, and cytotoxicity when expressed in E. coli K-12. Sha and TagB conferred autoaggregation and hemagglutination activities. TagB, TagC, and Sha all exhibited cytopathic effects on a bladder epithelial cell line. In QT598, tagB and tagC are tandemly encoded on a genomic island, and were present in 10% of UTI isolates and 4.7% of avian E. coli. Sha is encoded on a virulence plasmid and was present in 1% of UTI isolates and 20% of avian E. coli. To specifically examine the role of SPATEs for infection, the 5 SPATE genes were deleted from strain QT598 and tested for cytotoxicity. Loss of all five SPATEs abrogated the cytopathic effect on bladder epithelial cells, although derivatives producing any of the 5 SPATEs retained cytopathic activity. In mouse infections, sha gene-expression was up-regulated a mean of sixfold in the bladder compared to growth in vitro. Loss of either tagBC or sha did not reduce urinary tract colonization. Deletion of all 5 SPATEs, however, significantly reduced competitive colonization of the kidney supporting a cumulative role of SPATEs for QT598 in the mouse UTI model.

Avian-source mcr-1-positive Escherichia coli is phylogenetically diverse and shares virulence characteristics with E. coli causing human extra-intestinal infections

Colisepticemia caused by bloodstream infection of the extraintestinal pathogenic Escherichia coli (ExPEC) has become a serious public health problem. The recent emergence of the colistin-resistant Enterobacteriaceae, especially mcr-1-positive E. coli (MCRPEC) exerts great concern around the world. The molecular epidemiology and zoonosis risk of avian-origin MCRPEC are reported to be substantially lower. Here, we presented a system-wide analysis of emerging trends and zoonotic risk of MCRPEC recovered from avian colibacillosis in China. Our results showed the majority of avian-source MCRPEC isolates were classified as ExPECs. We also found that not only MCRPEC in phylogroups B2 and D, but also several E. coli populations in groups B1 and F possessed high virulence in the two models of avian colibacillosis and three rodent models for ExPEC-associated human infections. The high-virulent MCRPEC clones belong to ST131, as well as ST-types (such as ST48, ST117, ST162, ST501, ST648, and ST2085). Our data suggested the zoonotic risk of MCRPEC appeared to be a close association with ColV/ColBM type virulence plasmids. A comprehensive genomic analysis showed the overlapped of ColV/ColBM plasmids contents between MCRPEC isolates from humans and poultry. Identification of ColV/ColBM plasmids among human MCRPEC isolates revealed the potential transmission of avian-source mcr-1-positive ExPECs to humans. Moreover, the presence of ColV/ColBM plasmid-encoded virulence determinants, could be used as a predictive label for pathogenic MCRPEC. These findings highlighted avian-origin MCRPEC isolates could be recognized as a foodborne pathogen.

PlaScope: a targeted approach to assess the plasmidome from genome assemblies at the species level

Plasmid prediction may be of great interest when studying bacteria of medical importance such as Enterobacteriaceae as well as Staphylococcus aureus or Enterococcus. Indeed, many resistance and virulence genes are located on such replicons with major impact in terms of pathogenicity and spreading capacities. Beyond strain outbreak, plasmid outbreaks have been reported in particular for some extended-spectrum beta-lactamase- or carbapenemase-producing Enterobacteriaceae. Several tools are now available to explore the ‘plasmidome’ from whole-genome sequences with various approaches, but none of them are able to combine high sensitivity and specificity. With this in mind, we developed PlaScope, a targeted approach to recover plasmidic sequences in genome assemblies at the species or genus level. Based on Centrifuge, a metagenomic classifier, and a custom database containing complete sequences of chromosomes and plasmids from various curated databases, PlaScope classifies contigs from an assembly according to their predicted location. Compared to other plasmid classifiers, PlasFlow and cBar, it achieves better recall (0.87), specificity (0.99), precision (0.96) and accuracy (0.98) on a dataset of 70 genomes of Escherichia coli containing plasmids. In a second part, we identified 20 of the 21 chromosomal integrations of the extended-spectrum beta-lactamase coding gene in a clinical dataset of E. coli strains. In addition, we predicted virulence gene and operon locations in agreement with the literature. We also built a database for Klebsiella and correctly assigned the location for the majority of resistance genes from a collection of 12 Klebsiella pneumoniae strains. Similar approaches could also be developed for other well-characterized bacteria.

Spread and Persistence of Virulence and Antibiotic Resistance Genes: A Ride on the F Plasmid Conjugation Module

The F plasmid or F-factor is a large, 100-kbp, circular conjugative plasmid of Escherichia coli and was originally described as a vector for horizontal gene transfer and gene recombination in the late 1940s. Since then, F and related F-like plasmids have served as role models for bacterial conjugation. At present, more than 200 different F-like plasmids with highly related DNA transfer genes, including those for the assembly of a type IV secretion apparatus, are completely sequenced. They belong to the phylogenetically related MOB_F12A group. F-like plasmids are present in enterobacterial hosts isolated from clinical as well as environmental samples all over the world. As conjugative plasmids, F-like plasmids carry genetic modules enabling plasmid replication, stable maintenance, and DNA transfer. In this plasmid backbone of approximately 60 kbp, the DNA transfer genes occupy the largest and mostly conserved part. Subgroups of MOB_F12A plasmids can be defined based on the similarity of TraJ, a protein required for DNA transfer gene expression. In addition, F-like plasmids harbor accessory cargo genes, frequently embedded within transposons and/or integrons, which harness their host bacteria with antibiotic resistance and virulence genes, causing increasingly severe problems for the treatment of infectious diseases. Here, I focus on key genetic elements and their encoded proteins present on the F-factor and other typical F-like plasmids belonging to the MOB_F12A group of conjugative plasmids.

Dose-dependent differential resistance of inbred chicken lines to avian pathogenic Escherichia coli challenge

Avian pathogenic E. coli (APEC) cause severe respiratory and systemic disease. To address the genetic and immunological basis of resistance, inbred chicken lines were used to establish a model of differential resistance to APEC, using strain O1 of serotype O1:K1:H7. Inbred lines 7₂, 15I and C.B12 and the outbred line Novogen Brown were inoculated via the airsac with a high dose (10⁷ colony-forming units, CFU) or low dose (10⁵ CFU) of APEC O1. Clinical signs, colibacillosis lesion score and bacterial colonization of tissues after high dose challenge were significantly higher in line 15I and C.B12 birds. The majority of the 15I and C.B12 birds succumbed to the infection by 14 h post-infection, whilst none of the line 7₂ and the Novogen Brown birds developed clinical signs. No difference was observed after low dose challenge. In a repeat study, inbred lines 7₂ and 15I were inoculated with low, intermediate or high doses of APEC O1 ranging from 10⁵ to 10⁷ CFU. The colonization of lung was highest in line 15I after high dose challenge and birds developed clinical signs; however, colonization of blood and spleen, clinical signs and lesion score were not different between lines. No difference was observed after intermediate or low dose challenge. Ex vivo, the phagocytic and bactericidal activity of lung leukocytes from line 7₂ and 15I birds did not differ. Our data suggest that although differential resistance of inbred lines 7₂, 15I and C.B12 to APEC O1 challenge is apparent, it is dependent on the infectious dose. Research Highlights Lines 15I and C.B12 are more susceptible than line 7₂ to a high dose of APEC O1. Differential resistance is dose-dependent in lines 15I and 7₂. Phagocytic and bactericidal activity is similar and dose independent.

Serological diversity, molecular characterisation and antimicrobial sensitivity of avian pathogenic Escherichia coli (APEC) isolates from broiler chickens in Kashmir, India

The present study has determined the serological diversity, virulence-gene profile and in vitro antibiogram of avian pathogenic Escherichia coli (APEC) isolates from broiler chickens in India suspected to have died of colibacillosis. The virulence-gene profile of APEC was compared with that of the Escherichia coli isolates from faeces of apparently healthy chickens, called avian faecal E. coli (AFEC). In total, 90 representative isolates of APEC and 63 isolates of AFEC were investigated in the present study. The APEC were typed into 19 serogroups, while some isolates were rough and could not be typed. Most prevalent serogroup was O2 (24.44%). Among the eight virulence genes studied, the prevalence of seven genes (iss, iucD, tsh, cva/cvi, irp2, papC and vat) was significantly higher in APEC than in AFEC isolates. However, there was no significant difference between APEC and AFEC isolates for possession of astA gene. The most frequent gene detected among the two groups of organisms was iss, which was present in 98.88% and 44.44% of APEC and AFEC isolates respectively. The in vitro antibiogram showed that the majority (96.6%) of APEC isolates were resistant to tetracycline, while 82.2% were resistant to cephalexin, 78.8% to cotrimoxazole, 68.8% to streptomycin and 63.3% to ampicillin. However, most of them (84.45%) were sensitive to gentamicin. Thus, it is concluded that APEC from the broiler chickens carried putative virulence genes that attributed to their pathogenicity. Furthermore, the majority of APEC isolates were found to be multi-drug resistant, which, in addition to leading treatment failures in poultry, poses a public health threat.

Escherichia coli ST131-H22 as a Foodborne Uropathogen

E. coli ST131 is an important extraintestinal pathogen that can colonize the gastrointestinal tracts of humans and food animals. Here, we combined detection of accessory traits associated with avian adaptation (ColV plasmids) with high-resolution phylogenetics to quantify the portion of human infections caused by ST131 strains of food animal origin. Our results suggest that one ST131 sublineage—ST131-H22—has become established in poultry populations around the world and that meat may serve as a vehicle for human exposure and infection. ST131-H22 is just one of many E. coli lineages that may be transmitted from food animals to humans. Additional studies that combine detection of host-associated accessory elements with phylogenetics may allow us to quantify the total fraction of human extraintestinal infections attributable to food animal E. coli strains.

Escherichia coli sequence type 131 (ST131) has emerged rapidly to become the most prevalent extraintestinal pathogenic E. coli clones in circulation today. Previous investigations appeared to exonerate retail meat as a source of human exposure to ST131; however, these studies focused mainly on extensively multidrug-resistant ST131 strains, which typically carry allele 30 of the fimH type 1 fimbrial adhesin gene (ST131-H30). To estimate the frequency of extraintestinal human infections arising from foodborne ST131 strains without bias toward particular sublineages or phenotypes, we conducted a 1-year prospective study of E. coli from meat products and clinical cultures in Flagstaff, Arizona. We characterized all isolates by multilocus sequence typing, fimH typing, and core genome phylogenetic analyses, and we screened isolates for avian-associated ColV plasmids as an indication of poultry adaptation. E. coli was isolated from 79.8% of the 2,452 meat samples and 72.4% of the 1,735 culture-positive clinical samples. Twenty-seven meat isolates were ST131 and belonged almost exclusively (n = 25) to the ST131-H22 lineage. All but 1 of the 25 H22 meat isolates were from poultry products, and all but 2 carried poultry-associated ColV plasmids. Of the 1,188 contemporaneous human clinical E. coli isolates, 24 were ST131-H22, one-quarter of which occurred in the same high-resolution phylogenetic clades as the ST131-H22 meat isolates and carried ColV plasmids. Molecular clock analysis of an international ST131-H22 genome collection suggested that ColV plasmids have been acquired at least six times since the 1940s and that poultry-to-human transmission is not limited to the United States.

Characterization of avian pathogenic Escherichia coli isolated from free-range helmeted guineafowl

Avian pathogenic Escherichia coli (APEC) isolates from apparently healthy free range helmeted guineafowl were characterized. Most of them had a high frequency of virulence associated genes, multi drug resistance and high pathogenicity. We demonstrated that helmeted guineafowl have potential to transmit antibiotic resistant APEC to other species including humans.

Molecular characterization and antibiotic resistance patterns of avian fecal Escherichia coli from turkeys, geese, and ducks

Background and Aim:

Avian fecal Escherichia coli (AFEC) are considered to be the natural reservoir of pathogenic strains in extraintestinal infections as such characterization of AFEC gives insight into the spread of the potential pathogenic lineage. The aim of the study was to investigate the reservoirs of avian pathogenic E. coli (APEC) from fecal samples of healthy ducks, geese, and turkeys by determining the antibiotic resistance patterns of AFEC isolates from turkeys, geese and ducks and characterization of the isolates using virulence genes, plasmid profiles, and phylogenetic grouping.

Materials and Methods:

The disc diffusion method was used to determine antibiotic resistance of 100 AFEC isolates from turkeys (9), geese (29), and ducks (62) to 8 antibiotics. Molecular characterization of the isolates was done by multiplex polymerase chain reaction to investigate the presence of 12 virulence genes, plasmid profiling, and phylogenetic grouping based on the 16S rRNA sequences.

Results:

Antibiogram profiles indicated maximum resistance to cloxacillin (100%) and bacitracin (100%) for all AFEC isolates and high sensitivity to ciprofloxacin; however, all isolates exhibited multi-drug resistance. The AFEC isolates from turkeys (6) and geese (12) did not contain virulence genes. The frz (3.7%), sitD (29.6%), and fimH (92.5%) were detected in the duck isolates. None of the isolates had the KpsM, iutA, vat, sitA, hlyF, pstB, ompT, uvrY, and sopB genes. Plasmid profiling gave four plasmid profiles with the plasmids ranging from 1.5 to 55 kb. Phylogenetic analysis of 16S rRNA sequences revealed similarities between AFEC isolates from the different poultry species, as the isolates did not cluster according to avian species.

Conclusion:

AFEC isolates are potential reservoirs of APEC as they contain some of the virulence genes associated with APEC. Multidrug resistance is high in AFEC isolated from healthy birds. This is a public health concern.

The ColM Family, Polymorphic Toxins Breaching the Bacterial Cell Wall

Bacteria host an arsenal of antagonism-mediating molecules to combat for ecologic space. Bacteriocins represent a pivotal group of secreted antibacterial peptides and proteins assisting in this fight, mainly eliminating relatives. Colicin M, a model for peptidoglycan-interfering bacteriocins in Gram-negative bacteria, appears to be part of a set of polymorphic toxins equipped with such a catalytic domain (ColM) targeting lipid II. Diversifying recombination has enabled parasitism of different receptors and has also given rise to hybrid bacteriocins in which ColM is associated with another toxin module. Remarkably, ColM toxins have recruited a diverse array of immunity partners, comprising cytoplasmic membrane-associated proteins with different topologies. Together, these findings suggest that different immunity mechanisms have evolved for ColM, in contrast to bacteriocins with nuclease activities.

Characterization of plasmids harboring blaCTX-M and blaCMY genes in E. coli from French broilers

Resistance to extended-spectrum cephalosporins (ESC) is a global health issue. The aim of this study was to analyze and compare plasmids coding for resistance to ESC isolated from 16 avian commensal and 17 avian pathogenic Escherichia coli (APEC) strains obtained respectively at slaughterhouse or from diseased broilers in 2010-2012. Plasmid DNA was used to transform E. coli DH5alpha, and the resistances of the transformants were determined. The sequences of the ESC-resistance plasmids prepared from transformants were obtained by Illumina (33 plasmids) or PacBio (1 plasmid). Results showed that 29 of these plasmids contained the blaCTX-M-1 gene and belonged to the IncI1/ST3 type, with 27 and 20 of them carrying the sul2 or tet(A) genes respectively. Despite their diverse origins, several plasmids showed very high percentages of identity. None of the blaCTX-M-1-containing plasmid contained APEC virulence genes, although some of them were detected in the parental strains. Three plasmids had the blaCMY-2 gene, but no other resistance gene. They belonged to IncB/O/K/Z-like or IncFIA/FIB replicon types. The blaCMY-2 IncFIA/FIB plasmid was obtained from a strain isolated from a diseased broiler and also containing a blaCTX-M-1 IncI1/ST3 plasmid. Importantly APEC virulence genes (sitA-D, iucA-D, iutA, hlyF, ompT, etsA-C, iss, iroB-E, iroN, cvaA-C and cvi) were detected on the blaCMY-2 plasmid. In conclusion, our results show the dominance and high similarity of blaCTX-M-1 IncI1/ST3 plasmids, and the worrying presence of APEC virulence genes on a blaCMY-2 plasmid.

Evolution of Regions Containing Antibiotic Resistance Genes in FII-2-FIB-1 ColV-Colla Virulence Plasmids

Three ColV virulence plasmids carrying antibiotic resistance genes were assembled from draft genome sequences of commensal ST95, ST131, and ST2705 Escherichia coli isolates from healthy Australians. Plasmids pCERC4, pCERC5, and pCERC9 include almost identical backbones containing FII-2 and FIB-1 replicons and the conserved ColV virulence region with an additional ColIa determinant. Only pCERC5 includes a complete, uninterrupted F-like transfer region and was able to conjugate. pCERC5 and pCERC9 contain Tn1721, carrying the tet(A) tetracycline resistance determinant in the same location, with Tn2 (bla_TEM; ampicillin resistance) interrupting the Tn1721 in pCERC5. pCERC4 has a Tn1721/Tn21 hybrid transposon carrying dfrA5 (trimethoprim resistance) and sul1 (sulfamethoxazole resistance) in a class 1 integron. Four FII-2:FIB-1 ColV-ColIa plasmids in the GenBank nucleotide database have a related transposon in the same position, but an IS26 has reshaped the resistance gene region, deleting 2,069 bp of the integron 3'-CS, including sul1, and serving as a target for IS26 translocatable units containing bla_TEM, sul2 and strAB (streptomycin resistance), or aphA1 (kanamycin/neomycin resistance). Another ColV-ColIa plasmid containing a related resistance gene region has lost the FII replicon and acquired a unique transfer region via recombination within the resistance region and at oriT. Eighteen further complete ColV plasmid sequences in GenBank contained FIB-1, but the FII replicons were of three types, FII-24, FII-18, and a variant of FII-36.

Comparative Analysis of Phylogenetic Assignment of Human and Avian ExPEC and Fecal Commensal Escherichia coli Using the (Previous and Revised) Clermont Phylogenetic Typing Methods and its Impact on Avian Pathogenic Escherichia coli (APEC) Classification

The Clermont scheme has been used for subtyping of Escherichia coli since it was initially described in early 2000. Since then, researchers have used the scheme to type and sub-type commensal E. coli and pathogenic E. coli, such as extraintestinal pathogenic E. coli (ExPEC), and compare their phylogenetic assignment by pathogenicity, serogroup, distribution among ExPEC of different host species and complement of virulence and resistance traits. Here, we compare assignments of human and avian ExPEC and commensal E. coli using the old and revised Clermont schemes to determine if the new scheme provides a refined snapshot of isolate classification. 1,996 E. coli from human hosts and poultry, including 84 human neonatal meningitis E. coli isolates, 88 human vaginal E. coli, 696 human uropathogenic E. coli, 197 healthy human fecal E. coli, 452 avian pathogenic E. coli (APEC), 200 retail poultry E. coli, 80 crop and gizzard E. coli from healthy poultry at slaughter and 199 fecal E. coli from healthy birds at slaughter. All isolates were subject to phylogenetic analysis using the Clermont et al. (2000, 2013) schemes and compared to determine the effect of the new classification on strain designation. Most of the isolates’ strain designation remained where they were originally assigned. Greatest designation change occurred in APEC where 53.8% of isolates were reclassified; while classification rates among human strains ranged from 8 to 14%. However, some significant changes were observed for UPEC associated strains with significant (P < 0.05) designation changes observed from A to C and D to E or F phylogenetic types; a similar designation change was noted among NMEC for D to F designation change. Among the APEC significant designation changes were observed from A to C and D to E and F. These studies suggest that the new scheme provides a tighter and more meaningful definition of some ExPEC; while the new typing scheme has a significant impact on APEC classification. A comparison of phylogenetic group assignment by content of virulence, resistance, replicon and pathogenicity island genes in APEC suggests that insertion of pathogenicity islands into the genome appears to correlate closely with revised phylogenetic assignment.

Genome-Wide Survey of Genes Under Positive Selection in Avian Pathogenic Escherichia coli Strains

The ability to obtain bacterial genomes from the same host has allowed for comparative studies that help in the understanding of the molecular evolution of specific pathotypes. Avian pathogenic Escherichia coli (APEC) is a group of extraintestinal strains responsible for causing colibacillosis in birds. APEC is also suggested to possess a role as a zoonotic agent. Despite its importance, APEC pathogenesis still has several cryptic pathogenic processes that need to be better understood. In this work, a genome-wide survey of eight APEC strains for genes with evidence of recombination revealed that ∼14% of the homologous groups evaluated present signs of recombination. Enrichment analyses revealed that nine Gene Ontology (GO) terms were significantly more represented in recombinant genes. Among these GO terms, several were noted to be ATP-related categories. The search for positive selection in these APEC genomes revealed 32 groups of homologous genes with evidence of positive selection. Among these groups, we found several related to cell metabolism, as well as several uncharacterized genes, beyond the well-known virulence factors ompC, lamB, waaW, waaL, and fliC. A GO term enrichment test showed a prevalence of terms related to bacterial cell contact with the external environment (e.g., viral entry into host cell, detection of virus, pore complex, bacterial-type flagellum filament C, and porin activity). Finally, the genes with evidence of positive selection were retrieved from genomes of non-APEC strains and tested as were done for APEC strains. The result revealed that none of the groups of genes presented evidence of positive selection, confirming that the analysis was effective in inferring positive selection for APEC and not for E. coli in general, which means that the study of the genes with evidence of positive selection identified in this study can contribute for the better understanding of APEC pathogenesis processes.

Spread of avian pathogenic Escherichia coli ST117 O78:H4 in Nordic broiler production

Background

Escherichia coli infections known as colibacillosis constitute a considerable challenge to poultry farmers worldwide, in terms of decreased animal welfare and production economy. Colibacillosis is caused by avian pathogenic E. coli (APEC). APEC strains are extraintestinal pathogenic E. coli and have in general been characterized as being a genetically diverse population. In the Nordic countries, poultry farmers depend on import of Swedish broiler breeders which are part of a breeding pyramid. During 2014 to 2016, an increased occurrence of colibacillosis on Nordic broiler chicken farms was reported. The aim of this study was to investigate the genetic diversity among E. coli isolates collected on poultry farms with colibacillosis issues, using whole genome sequencing.

Methods

Hundred and fourteen bacterial isolates from both broilers and broiler breeders were whole genome sequenced. The majority of isolates were collected from poultry with colibacillosis on Nordic farms. Subsequently, comparative genomic analyses were carried out. This included in silico typing (sero- and multi-locus sequence typing), identification of virulence and resistance genes and phylogenetic analyses based on single nucleotide polymorphisms.

Results

In general, the characterized poultry isolates constituted a genetically diverse population. However, the phylogenetic analyses revealed a major clade of 47 closely related ST117 O78:H4 isolates. The isolates in this clade were collected from broiler chickens and breeders with colibacillosis in multiple Nordic countries. They clustered together with a human ST117 isolate and all carried virulence genes that previously have been associated with human uropathogenic E. coli.

Conclusions

The investigation revealed a lineage of ST117 O78:H4 isolates collected in different Nordic countries from diseased broilers and breeders. The data indicate that the closely related ST117 O78:H4 strains have been transferred vertically through the broiler breeding pyramid into distantly located farms across the Nordic countries.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3415-6) contains supplementary material, which is available to authorized users.

Plasmids from Shiga Toxin-Producing Escherichia coli Strains with Rare Enterohemolysin Gene (ehxA) Subtypes Reveal Pathogenicity Potential and Display a Novel Evolutionary Path

Most Shiga toxin-producing Escherichia coli (STEC) strains associated with severe disease, such as hemolytic-uremic syndrome (HUS), carry large enterohemolysin-encoding (ehxA) plasmids, e.g., pO157 and pO103, that contribute to STEC clinical manifestations. Six ehxA subtypes (A through F) exist that phylogenetically cluster into eae-positive (B, C, F), a mix of eae-positive (E) and eae-negative (A), and a third, more distantly related, cluster of eae-negative (D) STEC strains. While subtype B, C, and F plasmids share a number of virulence traits that are distinct from those of subtype A, sequence data have not been available for subtype D and E plasmids. Here, we determined and compared the genetic composition of four subtype D and two subtype E plasmids to establish their evolutionary relatedness among ehxA subtypes and define their potential role in pathogenicity. We found that subtype D strains carry one exceptionally large plasmid (>200 kbp) that carries a variety of virulence genes that are associated with enterotoxigenic and enterohemorrhagic E. coli, which, quite possibly, enables these strains to cause disease despite being food isolates. Our data offer further support for the hypothesis that this subtype D plasmid represents a novel virulence plasmid, sharing very few genetic features with other plasmids; we conclude that these plasmids have evolved from a different evolutionary lineage than the plasmids carrying the other ehxA subtypes. In contrast, the 50-kbp plasmids of subtype E (pO145), although isolated from HUS outbreak strains, carried only few virulence-associated determinants, suggesting that the clinical presentation of subtype E strains is largely a result of chromosomally encoded virulence factors.

IMPORTANCE

Bacterial plasmids are known to be key agents of change in microbial populations, promoting the dissemination of various traits, such as drug resistance and virulence. This study determined the genetic makeup of virulence plasmids from rare enterohemolysin subtype D and E Shiga toxin-producing E. coli strains. We demonstrated that ehxA subtype D plasmids represent a novel E. coli virulence plasmid, and although subtype D plasmids were derived from nonclinical isolates, they encoded a variety of virulence determinants that are associated with pathogenic E. coli In contrast, subtype E plasmids, isolated from strains recovered from severely ill patients, carry only a few virulence determinants. The results of this study reemphasize the plasticity and vast diversity among E. coli plasmids. This work demonstrates that, although E. coli strains of certain serogroups may not be frequently associated with disease, they should not be underestimated in protecting human health and food safety.

pCERC3 from a commensal ST95 Escherichia coli: A ColV virulence-multiresistance plasmid carrying a sul3-associated class 1 integron

The rare sulphonamide resistance gene sul3 was found in the commensal Escherichia coli ST95 strain 22.1-R1 that was isolated in 2010 from the faeces of a healthy Australian adult. The genome of 22.1-R1 was sequenced and a 144,344bp RepFII/FIB plasmid, pCERC3, carrying sul3 was assembled. The sul3 gene is part of a class 1 integron featuring a sul3-containing conserved segment (sul3-CS) that replaced the classic sul1-containing 3'-conserved segment (3'-CS) usually seen in class 1 integrons. The integron contained the cassette array dfrA12-orfF-aadA2-cmlA1-aadA1-qacH, conferring resistance to trimethoprim, streptomycin, spectinomycin, chloramphenicol and quaternary ammonium compound. Two additional antibiotic resistance genes, blaTEM (ampicillin resistance) and tetA(B) (tetracycline) were adjacent to the integron, forming a single resistance region. In pCERC3, the sul3-type class 1 integron was flanked by sequence derived from the tnp and mer modules of Tn21 and was in the same location as In2, the sul1-containing In5-type class 1 integron of Tn21. At one end the sequence extends into Tn2670-derived sequence and then into sequence derived from the plasmid NR1 (R100). Examination of the sequences of eleven more complete sul3-containing plasmids in GenBank confirmed the relationship between sul3-associated integrons and Tn21/Tn2670/NR1. This suggests that the events that formed sul3-associated class 1 integrons occurred within the Tn21/Tn2670 context, most likely in NR1 or a related plasmid. The backbone of pCERC3 is most closely related to the backbones of ColV virulence plasmids and contains a complete ColV operon as well as several virulence associated genes and gene clusters. Hence, pCERC3 is both an antibiotic resistance and virulence plasmid.

The molecular characterisation of Escherichia coli K1 isolated from neonatal nasogastric feeding tubes

BACKGROUND

The most common cause of Gram-negative bacterial neonatal meningitis is E. coli K1. It has a mortality rate of 10-15 %, and neurological sequelae in 30-50 % of cases. Infections can be attributable to nosocomial sources, however the pre-colonisation of enteral feeding tubes has not been considered as a specific risk factor.

METHODS

Thirty E. coli strains, which had been isolated in an earlier study, from the residual lumen liquid and biofilms of neonatal nasogastric feeding tubes were genotyped using pulsed-field gel electrophoresis, and 7-loci multilocus sequence typing. Potential pathogenicity and biofilm associated traits were determined using specific PCR probes, genome analysis, and in vitro tissue culture assays.

RESULTS

The E. coli strains clustered into five pulsotypes, which were genotyped as sequence types (ST) 95, 73, 127, 394 and 2076 (Achman scheme). The extra-intestinal pathogenic E. coli (ExPEC) phylogenetic group B2 ST95 serotype O1:K1:NM strains had been isolated over a 2 week period from 11 neonates who were on different feeding regimes. The E. coli K1 ST95 strains encoded for various virulence traits associated with neonatal meningitis and extracellular matrix formation. These strains attached and invaded intestinal, and both human and rat brain cell lines, and persisted for 48 h in U937 macrophages. E. coli STs 73, 394 and 2076 also persisted in macrophages and invaded Caco-2 and human brain cells, but only ST394 invaded rat brain cells. E. coli ST127 was notable as it did not invade any cell lines.

CONCLUSIONS

Routes by which E. coli K1 can be disseminated within a neonatal intensive care unit are uncertain, however the colonisation of neonatal enteral feeding tubes may be one reservoir source which could constitute a serious health risk to neonates following ingestion.

Origin and Dissemination of Antimicrobial Resistance among Uropathogenic Escherichia coli

Antimicrobial agents of various types have important bearing on the outcomes of microbial infections. These agents may be bacteriostatic or –cidal, exert their impact via various means, originate from a living organism or a laboratory, and appropriately be used in or on living tissue or not. Though the primary focus of this chapter is on resistance to the antimicrobial agents used to treat uropathogenic Escherichia coli (UPEC)-caused urinary tract infections (UTIs), some attention will be given to UPEC’s resistance to silver-containing antiseptics, which may be incorporated into catheters to prevent foreign body-associated UTIs.

Resistance and virulence factors of Escherichia coli isolated from chicken

Chicken meat has become an important part of the human diet and besides contamination by pathogenic Escherichia coli there is a risk of antibiotic resistance spreading via the food chain. The purpose of this study was to examine the prevalence of resistance against eight antibiotics and the presence of 14 virulence factors among 75 Escherichia coli strains isolated from chicken meat in the Czech Republic after classification into phylogenetic groups by the multiplex PCR method. More than half of strains belonged to A phylogroup, next frequently represented was B1 phylogroup, which suggests the commensal strains. The other strains were classified into phylogroups B2 and D, which had more virulence factors. Almost half of all E. coli strains were resistant to at least one of eight-tested antibiotics. A multidrug resistance was observed in 13% of strains. The most prevalent virulence genes were iucD, iss and tsh. None of genes encoding toxins was detected. Most of E. coli strains isolated from chicken meat can be considered as nonpathogenic on the basis of analysis of virulence factors, antibiotic resistance and phylogroups assignment. It can provide a useful tool for prediction of a potential risk from food contaminated by E. coli.

Plasmid-Encoded Iron Uptake Systems

Plasmids confer genetic information that benefits the bacterial cells containing them. In pathogenic bacteria, plasmids often harbor virulence determinants that enhance the pathogenicity of the bacterium. The ability to acquire iron in environments where it is limited, for instance the eukaryotic host, is a critical factor for bacterial growth. To acquire iron, bacteria have evolved specific iron uptake mechanisms. These systems are often chromosomally encoded, while those that are plasmid-encoded are rare. Two main plasmid types, ColV and pJM1, have been shown to harbor determinants that increase virulence by providing the cell with essential iron for growth. It is clear that these two plasmid groups evolved independently from each other since they do not share similarities either in the plasmid backbones or in the iron uptake systems they harbor. The siderophores aerobactin and salmochelin that are found on ColV plasmids fall in the hydroxamate and catechol group, respectively, whereas both functional groups are present in the anguibactin siderophore, the only iron uptake system found on pJM1-type plasmids. Besides siderophore-mediated iron uptake, ColV plasmids carry additional genes involved in iron metabolism. These systems include ABC transporters, hemolysins, and a hemoglobin protease. ColV- and pJM1-like plasmids have been shown to confer virulence to their bacterial host, and this trait can be completely ascribed to their encoded iron uptake systems.

Comparative genomic analysis shows that avian pathogenic Escherichia coli isolate IMT5155 (O2:K1:H5; ST complex 95, ST140) shares close relationship with ST95 APEC O1:K1 and human ExPEC O18:K1 strains

Avian pathogenic E. coli and human extraintestinal pathogenic E. coli serotypes O1, O2 and O18 strains isolated from different hosts are generally located in phylogroup B2 and ST complex 95, and they share similar genetic characteristics and pathogenicity, with no or minimal host specificity. They are popular objects for the study of ExPEC genetic characteristics and pathogenesis in recent years. Here, we investigated the evolution and genetic blueprint of APEC pathotype by performing phylogenetic and comparative genome analysis of avian pathogenic E. coli strain IMT5155 (O2:K1:H5; ST complex 95, ST140) with other E. coli pathotypes. Phylogeny analyses indicated that IMT5155 has closest evolutionary relationship with APEC O1, IHE3034, and UTI89. Comparative genomic analysis showed that IMT5155 and APEC O1 shared significant genetic overlap/similarities with human ExPEC dominant O18:K1 strains (IHE3034 and UTI89). Furthermore, the unique PAI I₅₁₅₅ (GI-12) was identified and found to be conserved in APEC O2 serotype isolates. GI-7 and GI-16 encoding two typical T6SSs in IMT5155 might be useful markers for the identification of ExPEC dominant serotypes (O1, O2, and O18) strains. IMT5155 contained a ColV plasmid p1ColV₅₁₅₅, which defined the APEC pathotype. The distribution analysis of 10 sequenced ExPEC pan-genome virulence factors among 47 sequenced E. coli strains provided meaningful information for B2 APEC/ExPEC-specific virulence factors, including several adhesins, invasins, toxins, iron acquisition systems, and so on. The pathogenicity tests of IMT5155 and other APEC O1:K1 and O2:K1 serotypes strains (isolated in China) through four animal models showed that they were highly virulent for avian colisepticemia and able to cause septicemia and meningitis in neonatal rats, suggesting zoonotic potential of these APEC O1:K1 and O2:K1 isolates.

Human health impacts of antibiotic use in agriculture: A push for improved causal inference

Resistant bacterial infections in humans continue to pose a significant challenge globally. Antibiotic use in agriculture contributes to this problem, but failing to appreciate the relative importance of diverse potential causes represents a significant barrier to effective intervention. Standard epidemiologic methods alone are often insufficient to accurately describe the relationships between agricultural antibiotic use and resistance. The integration of diverse methodologies from multiple disciplines will be essential, including causal network modeling and population dynamics approaches. Because intuition can be a poor guide in directing investigative efforts of these non-linear and interconnected systems, integration of modeling efforts with empirical epidemiology and microbiology in an iterative process may result in more valuable information than either in isolation.

Nucleotide sequences of 16 transmissible plasmids identified in nine multidrug-resistant Escherichia coli isolates expressing an ESBL phenotype isolated from food-producing animals and healthy humans

OBJECTIVES

Nine extended-spectrum β-lactamase (ESBL)-producing Escherichia coli isolated from healthy humans and food-producing animals were found to transfer their cefotaxime resistance marker at high frequency in laboratory conjugation experiments. The objective of this study was to completely characterize 16 transmissible plasmids that were detected in these bacterial isolates.

METHODS

The nucleotide sequences of all 16 plasmids were determined from transconjugants using next-generation sequencing technology. Open reading frames were assigned using Rapid Annotation using Subsystem Technology and analysed by BLASTn and BLASTp. The standard method was used for plasmid multilocus sequence typing (pMLST) analysis. Plasmid structures were subsequently confirmed by PCR amplification of selected regions.

RESULTS

The complete circularized nucleotide sequence of 14 plasmids was determined, along with that of a further two plasmids that could not be confirmed as closed. These ranged in size from 1.8 to 166.6 kb. Incompatibility groups and pMLSTs identified included IncI1/ST3, IncI1/ST36, IncN/ST1, IncF and IncB/O, and those of the same Inc types presented a similar backbone structure despite being isolated from different sources. Eight plasmids contained bla(CTX-M-1) genes that were associated with either ISEcp1 or IS26 insertion sequence elements. Six plasmids isolated from humans and chickens were identical or closely related to the IncI1 reference plasmid, R64.

CONCLUSIONS

These data, based on comparative sequence analysis, highlight the successful spread of blaESBL-harbouring plasmids of different Inc types among isolates of human and food-producing animal origin and provide further evidence for potential dissemination routes.