Chicken as reservoir for extraintestinal pathogenic Escherichia coli in humans, Canada

The occurrence of Salmonella, extended-spectrum β-lactamase producing Escherichia coli and carbapenem resistant non-fermenting Gram-negative bacteria in a backyard poultry flock environment

Increase in the number of small-scale backyard poultry flocks in the USA has substantially increased human-to-live poultry contact, leading to increased public health risks of the transmission of multi-drug resistant (MDR) zoonotic and food-borne bacteria. The objective of this study was to detect the occurrence of Salmonella and MDR Gram-negative bacteria (GNB) in the backyard poultry flock environment. A total of 34 backyard poultry flocks in Washington State (WA) were sampled. From each flock, one composite coop sample and three drag swabs from nest floor, waterer-feeder, and a random site with visible faecal smearing, respectively, were collected. The samples were processed for isolation of Salmonella and other fermenting and non-fermenting GNB under ceftiofur selection. Each isolate was identified to species level using MALDI-TOFF and tested for resistance against 16 antibiotics belonging to eight antibiotic classes. Salmonella serovar 1,4,[5],12:i:- was isolated from one (3%) out of 34 flocks. Additionally, a total of 133 ceftiofur resistant (Cef^R ) GNB including Escherichia coli (53), Acinetobacter spp. (45), Pseudomonas spp. (22), Achromobacter spp. (8), Bordetella trematum (1), Hafnia alvei (1), Ochrobactrum intermedium (1), Raoultella ornithinolytica (1), and Stenotrophomonas maltophilia (1) were isolated. Of these, 110 (82%) isolates displayed MDR. Each flock was found positive for the presence of one or more Cef^R GNB. Several MDR E. coli (n = 15) were identified as extended-spectrum β-lactamase (ESBL) positive. Carbapenem resistance was detected in non-fermenting GNB including Acinetobacter spp. (n = 20), Pseudomonas spp. (n = 11) and Stenotrophomonas maltophila (n = 1). ESBL positive E. coli and carbapenem resistant non-fermenting GNB are widespread in the backyard poultry flock environment in WA State. These GNB are known to cause opportunistic infections, especially in immunocompromised hosts. Better understanding of the ecology and epidemiology of these GNB in the backyard poultry flock settings is needed to identify potential risks of transmission to people in proximity.

Escherichia coli strains of chicken and human origin: Characterization of antibiotic and heavy-metal resistance profiles, phylogenetic grouping, and presence of virulence genetic markers

Multiple antibiotic-resistant extra-intestinal pathogenic Escherichia coli (ExPEC) strains represent a serious health care problem both for poultry and humans. Recently isolates with combined resistance to both antibiotics and heavy metals have been increased worldwide, with growing concern for possible co-selection of antimicrobial resistant genes. In the present study we characterized, at a phenotypic and genetic level, 80 E. coli isolates: forty independent isolates were collected from manure samples of healthy chickens and 40 from independent human extra-intestinal infections (ExPEC strains). The results obtained indicated that i) compared to chicken, human isolates presented a broader spectrum of antibiotic resistance and virulence potentials; ii) although at a lower extent, ExPEC-associated virulence genes were also present in chicken isolates, suggesting they may be potentially pathogens; iii) that arsenic (As) and zinc (Zn) tolerance genetic determinants were significantly more prevalent among chicken and human isolates respectively, while those responsible for tolerance to cadmium (Cd), silver (Ag) and copper (Cu) were equally distributed among the two groups of strains; iv) a very strong correlation was found between chicken gentamicin (GM) resistance and cadmium (Cd) tolerance. Elucidating the role of heavy metals in the selection and spread of highly pathogenic E. coli strains (co-selection) is of primary importance to lower the potential risk of infections in poultry and humans. The control of bacterial zoonotic agents, that commonly occur in livestock and that may be transmitted, directly or via the food chain, to human populations, could be of relevant interest.

Extraintestinal Foodborne Pathogens

In general, foodborne diseases present themselves with gastrointestinal symptoms caused by bacterial, viral, and parasitic pathogens well established to be foodborne. These pathogens are also associated with extraintestinal clinical manifestations. Recent studies have suggested that Escherichia coli and Klebsiella pneumoniae, which both cause common extraintestinal infections such as urinary tract and bloodstream infections, may also be foodborne. The resolution and separation of these organisms into pathotypes versus commensals by modern genotyping methods have led to the identification of key lineages of these organisms causing outbreaks of extraintestinal infections. These epidemiologic observations suggested common- or point-source exposures, such as contaminated food. Here, we describe the spectrum of extraintestinal illnesses caused by recognized enteric pathogens and then review studies that demonstrate the potential role of extraintestinal pathogenic E. coli (ExPEC) and K. pneumoniae as foodborne pathogens. The impact of global food production and distribution systems on the possible foodborne spread of these pathogens is discussed.

Epidemiology and genotypic characterisation of dissemination patterns of uropathogenic Escherichia coli in a community

To characterise the dissemination patterns of uropathogenic Escherichia coli (UPEC) in a community, we conducted a study utilising molecular and fundamental descriptive epidemiology. The subjects, consisted of women having community-acquired acute urinary tract infection (UTI), were enrolled in the study from 2011 to 2012. UPEC isolates were subjected to antibacterial-susceptibility testing, O serogrouping, phylotyping, multilocus-sequence typing with phylogenetic-tree analysis and pulsed-field-gel electrophoresis (PFGE). From the 209 unique positive urinary samples 166 UPEC were isolated, of which 129 were fully susceptible to the tested antibiotics. Of the 53 sequence types (STs), the four most prevalent STs (ST95, ST131, ST73 and ST357) accounted for 60% of all UPEC strains. Antimicrobial resistance was less frequently observed for ST95 and ST73 than for the others. A majority of rare STs and a few common STs constituted the diversity pattern within the population structure, which was composed of the two phylogenetically distinct clades. Eleven genetically closely related groups were determined by PFGE, which accounted for 42 of the 166 UPEC isolates, without overt geo-temporal clustering. Our results indicate that a few major lineages of UPEC, selected by unidentified factors, are disseminated in this community and contribute to a large fraction of acute UTIs.

Multilocus sequence typing of Escherichia coli isolates from urinary tract infection patients and from fecal samples of healthy subjects in a college community

Community-acquired urinary tract infections (UTIs) are one of the most common bacterial infections worldwide. Escherichia coli is the most common cause of community-acquired UTI. In general, UTI results from E. coli in the intestine that enters the bladder via the urethra. However, whether these E. coli strains that cause UTI represent members of the intestinal commensal E. coli or a distinct subgroup of pathogenic E. coli remains unestablished. Here, we analyzed E. coli isolates from fecal samples of healthy volunteers and urine samples of UTI patients obtained from a university-affiliated health center. The E. coli isolates were genotyped by multilocus sequence typing (MLST). From May to October 2018, we analyzed 89 E. coli isolates from 76 (75%) rectal swabs from 113 unique healthy volunteers. We also analyzed 106 (27%) E. coli isolates from 398 unique urine samples collected between August and October 2018. Fecal and urine E. coli isolates each contained 31 distinct sequence types (STs). Nine STs were shared by fecal and urine E. coli isolates, which accounted for approximately 50% of urine isolates typed by MLST. Among the shared genotypes, ST10 and ST131 were significantly more frequently found in fecal samples, whereas ST95 and ST127 were significantly more frequently recovered from UTI samples. ST73 was found only among urine samples. These E. coli genotypes clustered and fluctuated over time. These observations suggest that E. coli genotypes found to cause UTI transiently colonize the intestine and that their primary reservoir may reside outside of the human intestine.

Antibiogram and recent incidence of multi-drug resistant carbapenemase producing Escherichia coli isolated from paediatric patients

Objective:

To gauge the recent breadth of MDR E. coli along with antibiogram of carbapenemase producing (CP) E. coli among children from an institute which receives patients from all over Punjab.

Methods:

The bacterial strains of E. coli isolated from various specimens of patients were collected from April 2017 to August 2018 and processed using standard biochemical tests and API 20E system (bioMerieux). Phenotypic screening for CP E. coli was done by the modified Hodge test, whereas antibiotic susceptibility testing was done with Kirby-Bauer disc diffusion technique.

Results:

Total of 6,468 bacterial strains were isolated, out of which 1,552 (24%) were E. coli. Carbapenem resistance was observed in 245 (16%) strains, amongst which 113 (46%) were confirmed to be CP. E. coli isolated from males were higher as compared to females (p<0.05). Majority of the organisms were isolated from blood (37.2%) samples. The hospital discharged about 65% of patients, while 23% left against medical advice. Overall MDR amongst E. coli was 93.26%. Colistin sulphate (15.9%) and nitrofurantoin (16.8%) showed the most efficacy followed by amikacin (15%) and fosfomycin (10.6%).

Conclusion:

The isolation of high number of MDR E. coli amongst the paediatric patients is worrisome, which could serve as a potential source of horizontal genes transfer to other genera.

Schizandrin attenuates inflammation induced by avian pathogenic Escherichia coli in chicken type II pneumocytes

Avian pathogenic Escherichia coli (APEC) is a kind of highly pathogenic parenteral bacteria, which adheres to chicken type II pneumocytes through pili, causing inflammatory damage of chicken type II pneumocytes. Without affecting the growth of bacteria, anti-adhesion to achieve anti-inflammatory effect is considered to be a new method for the treatment of multi-drug-resistant bacterial infections. In this study, the anti-APEC activity of schizandrin was studied in vitro. By establishing the model of chicken type II pneumocytes infected with APEC-O78, the adhesion number, the expression of virulence genes, the release of lactate dehydrogenase (LDH), levels of tumor necrosis factor (TNF)-α, interleukin (IL)-1β, IL-6, IL-8 and activation of nuclear factor-κB (NF-κB) and mitogen-activated protein kinase (MAPK) signaling pathways were detected. The results showed that schizandrin reduced the release of LDH and the adherence of APEC on chicken type II pneumocytes. Moreover, schizandrin markedly decreased the levels of IL-1β, IL-8, IL-6, and TNF-α, the mechanism responsible for these effects was attributed to the inhibitory effect of schizandrin on NF-κB and MAPK signaling activation. In conclusion, our findings revealed that schizandrin could reduce the inflammatory injury of chicken type II pneumocytes by reducing the adhesion of APEC-O78 to chicken type II pneumocytes. The results indicate that schizandrin can be a potential agent to treat inflammation caused by avian colibacillosis.

Non-viable chicken embryos: an overlooked niche harbouring a significant source of multidrug resistant bacteria in the poultry production

Antimicrobial resistance (AMR) is a global issue, posing a grave threat to the public, animal, and environmental health. The AMR surveillance at the level of the hatchery is crucial to develop an AMR control strategy in the poultry industry. The objective of this study was to investigate the AMR profiles of bacteria isolated from yolk material of non-viable broiler chicken embryos at hatch from commercial hatcheries in western Canada. Antimicrobial susceptibility testing was done using the Kirby–Bauer disk diffusion method focusing on Escherichia coli (n = 170) and Enterococcus (n = 256) species, which are commonly used as indicators of AMR evolution. E. coli isolates were resistant to tetracycline, ampicillin, amoxycillin-clavulanic acid, triple sulpha, ceftiofur, gentamycin, and spectinomycin at the rate of 52.9%, 50.6%, 40.0% 31.8%, 29.4%, 29.4%, 21.8% respectively. Among those, 37.1% of E. coli were multidrug resistant. The descending order of antimicrobial resistance of E. faecalis was; tetracycline (61.9%), ceftiofur (46.2%), bacitracin (43.9%), erythromycin (31.4%) and tylosin (27.4%). Multidrug resistance was detected in 40.4% of E. faecalis isolates, and 85.7% of E. faecium isolates. To the best of our knowledge, this is the first report on AMR surveillance of non-viable chicken embryos. Overall, the present study revealed that non-viable chicken embryos, an overlooked niche for AMR surveillance, harbour multidrug-resistant E. coli, and enterococci that can be a substantial source of superbugs in the environment. Our data also highlight the urgency of including non-viable chicken embryos in AMR surveillance programme to understand AMR dissemination and its control.

Isolation and characterization of pathogenic Escherichia coli bacteriophages from chicken and beef offal

OBJECTIVE

This study was conducted to isolate and characterize lytic bacteriophages for pathogenic Escherichia coli from chicken and beef offal, and analyze their capability as biocontrol for several foodborne pathogens. Methods done in this research are bacteriophage isolation, purification, titer determination, application, determination of host range and minimum multiplicity of infection (miMOI), and bacteriophage morphology.

RESULTS

Six bacteriophages successfully isolated from chicken and beef offal using EPEC and EHEC as host strain. Bacteriophage titers observed between 10⁹ and 10¹⁰ PFU mL^-1. CS EPEC and BL EHEC bacteriophage showed high efficiency in reduction of EPEC or EHEC contamination in meat about 99.20% and 99.04%. The lowest miMOI was 0.01 showed by CS EPEC bacteriophage. CI EPEC and BL EPEC bacteriophage suspected as Myoviridae family based on its micrograph from Transmission Electron Microscopy (TEM). Refers to their activity, bacteriophages isolated in this study have a great potential to be used as biocontrol against several foodborne pathogens.

Extended-spectrum β-lactamase-producing Escherichia coli in human-derived and foodchain-derived samples from England, Wales, and Scotland: an epidemiological surveillance and typing study

BACKGROUND

Extended-spectrum β-lactamase-producing Escherichia coli isolates (ESBL-E coli) cause more than 5000 cases of bacteraemias annually in the UK. The contribution of the food chain to these infections is debated. We aimed to identify the most important reservoirs of ESBL-E coli that colonise and infect humans to identify strategic intervention points.

METHODS

Sampling for ESBL-E coli was done between Aug 1, 2013, and Dec 15, 2014. We used selective media to seek ESBL-E coli in routinely submitted samples from human faeces, and prospectively collected samples from sewage, farm slurry, and retail foodstuffs in London, East Anglia, northwest England, Scotland, and Wales. We sequenced recovered isolates and compared these isolates with 293 bloodstream and 83 veterinary surveillance ESBL-E coli isolates from the same regions.

FINDINGS

2157 (11%) of 20 243 human faeces samples contained ESBL-E coli, including 678 (17%) of 3995 in London. ESBL-E coli also were frequent in sewage and retail chicken (104 [65%] of 159 meat samples), but were rare in other meats and absent from plant-based foods (0 of 400 fruit and vegetable samples). Sequence type (ST) 131 dominated among ESBL-E coli from human blood (188 [64%] of 293 isolates), faeces (128 [36%] of 360), and sewage (14 [22%] of 65) with STs 38 and 648 also widespread; CTX-M-15 was the predominant ESBL in these lineages (319 [77%] of 416). By contrast, STs 602, 23, and 117-mostly with CTX-M-1 ESBL-dominated among food and veterinary isolates (68 [31%] of 218), with only two ST131 organisms recovered. ST10 occurred in both animals and humans, being frequent in surveillance bovines (11 [22%] of 51 cattle) and representing 15 (4%) of 360 human faecal isolates (but only three [1%] of 293 from bacteraemias); however, both human and animal ST10 isolates were diverse in serotype.

INTERPRETATION

Most human bacteraemias with ESBL-E coli in the UK involve internationally prevalent human-associated STs, particularly ST131; non-human reservoirs made little contribution to invasive human disease. Any interventions that seek to target food or livestock can affect the numbers of human infections caused by ESBL-E coli; prevention of the spread of resistant lineages among humans is more vital.

FUNDING

NIHR Policy Research.

Escherichia coli from Commercial Broiler and Backyard Chickens Share Sequence Types, Antimicrobial Resistance Profiles, and Resistance Genes with Human Extraintestinal Pathogenic Escherichia coli

Escherichia coli recovered from poultry, and extraintestinal pathogenic E. coli (ExPEC), responsible for most cases of urinary tract infection (UTI) and bloodstream infection (BSI) in humans, may share genetic characteristics, suggesting that poultry are a potential source of ExPEC. Here, we compared E. coli isolated from commercial broiler and backyard chickens (n = 111) with ExPEC isolated from patients with community- or hospital-acquired UTI or BSI (n = 149) from Southeast Brazil. Isolates were genotyped by multilocus sequence typing, tested for susceptibility to antimicrobial agents, and screened for β-lactamase genes. We found that 10 genotypes were shared among poultry and human isolates: sequence type (ST) 10, ST48, ST58, ST88, ST90, ST93, ST131, ST602, ST617, and ST1018. Thirty-five (23%) ExPEC and 35 (31%) poultry E. coli isolates belonged to the shared STs. ST58 and ST88 isolates from human and poultry sources shared identical antimicrobial resistance profiles. bla_TEM-1 was the most prevalent β-lactamase gene, identified in 65 (92%) of 71 ExPEC and 29 (67%) of 43 poultry E. coli that tested positive for β-lactamase genes. Commercial broiler chicken isolates shared the extended-spectrum β-lactamase (ESBL) genes bla_CTX-M-2, bla_CTX-M-8, and bla_SHV-2 with human isolates; backyard chicken isolates lacked ESBL genes. In conclusion, several genotypic and phenotypic characteristics were shared between human and poultry E. coli; this suggests that there is potential for transmission of E. coli and antimicrobial resistance genes from poultry to humans, perhaps through environmental contamination, direct contact, or consumption. Additional research is needed to understand the potential direction and pathways of transmission.

Molecular Characterization of Multidrug-Resistant Escherichia coli Isolates from Edible Offal in Korea

HIGHLIGHTS

Edible offal is significantly contaminated by antimicrobial-resistant Escherichia coli. E. coli from edible offal is harboring various antimicrobial resistance and virulence genes. Improvements in hygienic conditions of edible offal production is required.

Characterization and rapid identification of phylogroup G in Escherichia coli, a lineage with high virulence and antibiotic resistance potential

The phylogeny of the Escherichia coli species, with the identification of seven phylogroups (A, B1, B2, C, D, E and F), is linked to the lifestyle of the strains. With the accumulation of whole genome sequence data, it became clear that some strains belong to a group intermediate between the F and B2 phylogroups, designated as phylogroup G. Here, we studied the complete sequences of 112 strains representative of the G phylogroup diversity and showed that it is composed of one main sequence type complex (STc)117 and four other STcs (STc657, STc454, STc738 and STc174). STc117, which phylogeny is characterized by very short internal branches, exhibits extensive O diversity, but little H-type and fimH allele diversity, whereas the other STcs are characterized by a main O, H and fimH type. STc117 strains possess many traits associated with extra-intestinal virulence, are virulent in a mouse sepsis model and exhibit multi-drug resistance such as CTX-M production. Epidemiologic data on 4,524 Australian and French strains suggest that STc117 is a poultry-associated lineage that can also establish in humans and cause extra-intestinal diseases. We propose an easy identification method that will help to trace this potentially virulent and resistant phylogroup in epidemiologic studies.

Extended-Spectrum β-Lactamase and AmpC β-Lactamase-Producing Escherichia coli Isolates from Chickens Raised in Small Flocks in Ontario, Canada

Food-producing animals are recognized to play a role in the epidemiology of antimicrobial resistance in Canada. However, the presence of resistant organisms in particular groups of animals, such as chickens raised in small-holder flocks, has not been studied. The purpose of this study was, therefore, to identify and characterize Escherichia coli possessing broad-spectrum β-lactamase genes among a collection of third-generation cephalosporin-resistant isolates recovered from 205 small flocks in southern Ontario. Extended-spectrum β-lactamase (ESBL; CTX-M-1) positive strains were isolated from 26 out of 205 flocks (12.7%), whereas 39 strains possessing AmpC (CMY-2) were grown from 31 out of 205 flocks (15.1%). Pulsed-field gel electrophoresis (PFGE) revealed that the isolates were genetically heterogeneous. Further testing by multi-locus sequence typing confirmed that none of the PFGE-defined clusters belonged to ST131. Our results suggest that the dissemination of this resistance in bacteria isolated from chickens in small-holder flocks may be associated with the spread of plasmids rather than particular E. coli clones and that these isolates do not possess the ESBL types most commonly associated with human infections (CTX-M-15).

Prevalence of antibiotic-resistant E. coli in broilers challenged with a multi-resistant E. coli strain and received ampicillin, an organic acid-based feed additive or a synbiotic preparation

The aim of this study was to evaluate the effect of ampicillin, an organic acid-based feed additive and a synbiotic preparation on the prevalence of antibiotic-resistant E. coli in the ceca of broilers. A total of 2000 broiler chickens (Ross 708) were randomly assigned to 5 groups with 8 replicates. The negative control group was the only group that was not subjected to avian pathogenic E. coli challenge, while all the other 4 groups received a multi-resistant E. coli strain that was resistant to ampicillin, cephalexin, and nalidixic acid as an oral challenge. The second group served as a challenge control, and the third group received the antibiotic ampicillin via water for 5 d. The fourth group received a feed additive based on organic acids and cinnamaldehyde, and the fifth group received a synbiotic preparation via feed and water. On day 17 and 38 of the trial, cecal samples from 3 birds from each of the 40 pens were obtained, and the E. coli counts and abundances of antibiotic-resistant E. coli were determined. Oral challenge with an avian pathogenic E. coli strain did not influence the performance, and there was no significant difference in growth performance between groups. The total E. coli count was lower (P < 0.05) in the group supplemented with the synbiotic than in the challenge control group on day 38 of the trial. Administration of an antibiotic for 5 d led to a significant increase in the abundance of E. coli strains resistant to ampicillin, amoxicillin-clavulanic acid, cefoxitin, and ceftriaxone. There was no increase in the abundance of antibiotic-resistant E. coli observed in the groups that received feed supplemented with an organic acid/cinnamaldehyde-based feed additive or a synbiotic. Moreover, the effects of the tested feed additives on the prevalence of resistant E. coli are demonstrated by the lower ceftriaxone minimal inhibitory concentration values for this group than for the antibiotic group. Additionally, the synbiotic group exhibited lower ceftriaxone minimal inhibitory concentration values than the antibiotic group.

Antimicrobial Resistance and Potential Pathogenicity of Escherichia coli Isolates from Healthy Broilers in Québec, Canada

Antimicrobial resistance (AMR) is a global health issue, particularly when it affects critically important antimicrobials such as third-generation cephalosporins (3GC). The objective of this study was to characterize Escherichia coli isolates from healthy chickens in Québec in farms where ceftiofur has been administered to chickens in ovo over a long period with regard to their AMR, multidrug resistance (MDR), potential virulence, clonality, and possession of plasmids of the incompatibility groups carrying extended-spectrum beta-lactamases (ESBLs)/AmpC genes. More than 62% of indicator isolates were MDR with resistance observed for each of the nine classes of antimicrobials tested by disk diffusion. 3GC resistance was encoded by the bla_CMY-2 gene (26.7% in indicator isolates), whereas bla_CTX-M was only detected in isolates selected after supplementation with ceftriaxone (3 bla_CTX-M-1 isolates). Examination of bla_CMY-2-positive isolates by pulsed-field gel electrophoresis showed clustering of isolates originating from different floors of the livestock building within farms. The bla_CMY-2 gene was carried on replicon plasmids FIB, I1, K/B, and B/O, whereas bla_CTX-M-1 gene was located on I1 as demonstrated by transformation experiments; some of these plasmids cotransferred nonsusceptibility against tetracycline or sulfonamides. In addition, six isolates, of which three were AmpC-producers, were defined as potential human extraintestinal pathogenic E. coli. In summary, this study showed that ESBLs/AmpC-producing E. coli isolates from apparently healthy chickens in Québec, Canada predominantly possess bla_CMY-2 rather than bla_CTX-M maybe because of the in ovo use of ceftiofur to prevent omphalitis and may be spread through clones or plasmids, and that some of these isolates could be capable of infecting humans.

Pathogenic potential and the role of clones and plasmids in beta-lactamase-producing E. coli from chicken faeces in Vietnam

BACKGROUND

Antimicrobial resistance (AMR) in food-producing animals is a global public health issue. This study investigated AMR and virulence profiles of E. coli isolated from healthy chickens in Vietnam. E. coli were isolated from fecal samples collected in five chicken farms located in the provinces of Hoa Binh, Thai Nguyen and Bac Giang in the North of Vietnam. These isolates were examined by disk diffusion for their AMR, PCR for virulence and AMR genes, pulsed-field gel electrophoresis for relatedness between blaCMY-2/blaCTX-M-positive isolates, electroporation for transferability of blaCMY-2 or blaCTX-M genes and sequencing for mutations responsible for ciprofloxacin resistance.

RESULTS

Up to 99% of indicator isolates were multidrug resistant. Resistance to third-generation cephalosporins (3GC) was encoded by both blaCTX-M and blaCMY-2 genes; blaCTX-M genes being of genotypes blaCTX-M-1, - 14, - 15, - 17, - 57 and - 87, whereas ciprofloxacin resistance was due to mutations in the gyrA and parC genes. Some isolates originating from farms located in different provinces of Vietnam were found to be closely related, suggesting they may have been disseminated from a same source of contamination. Plasmids may also have played a role in the diffusion of 3GC-resistance as the blaCMY-2 gene was located on plasmids A/C and I1, and the blaCTX-M gene variants were carried by I1, FIB, R and HI1. Plasmids carrying the blaCMY-2/blaCTX-M genes also co-transferred resistance to other antimicrobials. In addition, isolates potentially capable of infecting humans, of which some produced blaCMY-2/blaCTX-M, were identified in this study.

CONCLUSIONS

Both clones and plasmids could be involved in the dissemination of 3GC-resistant E. coli within and between chicken farms in Vietnam. These results demonstrate the necessity to monitor AMR and control antimicrobial use in poultry in Vietnam.

Phenotypic and genotypic characteristics of Escherichia coli with non-susceptibility to quinolones isolated from environmental samples on pig farms

Background

In the last decade, the growth of the pig-farming industry has led to an increase in antibiotic use, including several used in human medicine, e.g. (fluoro)quinolones. Data from several studies suggest that there is a link between the agricultural use of antibiotics and the prevalence of antibiotic-resistant bacteria in the pig farm environment, including (fluoro)quinolone resistance. This poses a threat to human and animal health. Our goal was to phenotypically and genotypically characterize 174 E. coli showing non-susceptibility to quinolones isolated from environmental samples from pig farms. Antimicrobial susceptibility testing (AST) was performed using the disk diffusion method. PCR and sequence analysis were performed to identify chromosomal mutations in the quinolone resistance-determining regions (QRDR) of gyrA and the isolates were screened for the presence of the plasmid-mediated quinolone resistance (PMQR) genes aac-(6')-Ib-cr, qepA, qnrA, qnrB, qnrC, qnrD and qnrS.

Strain relatedness was assessed by phylogenetic classification and multilocus sequence typing (MLST).

Results

Of 174 isolates, 81% (n = 141) were resistant to nalidixic acid, and 19% (n = 33) were intermediately resistant. Overall, 68.4% (n = 119) were multidrug resistant. This study revealed a prevalence of 79.9% (n = 139) for gyrA QRDR mutations, and detected 21.8% (n = 38) isolates with at least one PMQR gene. The two most frequently detected PMQR genes were qnrB and qnrS (13.8% (n = 24) and 9.8% (n = 17, respectively). E. coli belonging to phylogenetic group A (48.3%/n = 84) and group B1 (33.3% /n = 58) were the most frequent. E. coli ST10 (n = 20) and ST297 (n = 20) were the most common STs.

Conclusions

E. coli with non-susceptibility to quinolones are widespread among the environment of Swiss pig farms and are often associated with an MDR phenotype. In several cases these isolates possess at least one PMQR gene, which could spread by horizontal gene transfer. E. coli from pig farms have diverse STs, some of which are associated with human and animal disease.

Electronic supplementary material

The online version of this article (10.1186/s40813-019-0116-y) contains supplementary material, which is available to authorized users.

Diversity of CTX-M-positive Escherichia coli recovered from animals in Canada

Historically, extended-spectrum cephalosporin resistance in bacteria from animals in Canada has been attributed to the SHV and CMY β-lactamase families. This pattern is beginning to change with the emergence of the bla_CTX-M gene family among Escherichia coli recovered from various animal species. Here we analyze and compare whole genome sequences of bla_CTX-M-positive E. coli isolates (n = 173) from dogs, chicken, swine, horses and beef cattle in Canada. Ten bla_CTX-M variants were identified with bla_{CTX-M-1,-14, -15, -27} and bla_CTX-M-55 being identified in most animal species. These variants occurred across many sequence types, suggesting that mobile genetic elements mediate the spread of bla_CTX-M. The variants bla_{CTX-M-14, -15, -27} and bla_CTX-M-55 are associated with the global spread of bla_CTX-M in human clinical isolates and their presence could be indicative of transfer between humans and animals. These variants were also the principal variants identified among sequence type 131 isolates, which were not associated with any other species than dogs. These isolates carried the same bla_CTX-M variants as E. coli isolates found in humans. Close contact may promote the transmission of these isolates between humans and companion animals.

Virulence factors, prevalence and potential transmission of extraintestinal pathogenic Escherichia coli isolated from different sources: recent reports

Extraintestinal pathogenic E. coli (ExPEC) are facultative pathogens that are part of the normal human intestinal flora. The ExPEC group includes uropathogenic E. coli (UPEC), neonatal meningitis E. coli (NMEC), sepsis-associated E. coli (SEPEC), and avian pathogenic E. coli (APEC). Virulence factors (VF) related to the pathogenicity of ExPEC are numerous and have a wide range of activities, from those related to bacteria colonization to those related to virulence, including adhesins, toxins, iron acquisition factors, lipopolysaccharides, polysaccharide capsules, and invasins, which are usually encoded on pathogenicity islands (PAIs), plasmids and other mobile genetic elements. Mechanisms underlying the dynamics of ExPEC transmission and the selection of virulent clones are still poorly understood and require further research. The time shift between colonization of ExPEC and the development of infection remains problematic in the context of establishing the relation between consumption of contaminated food and the appearance of first disease symptoms. What appears to be most difficult is to prove that ExPEC strains cause disease symptoms and to examine the mechanism of transition from the asymptomatic colonization of the intestines to the spreading of the bacteria outside the digestive system. A significant problem for researchers who are trying to ascribe ExPEC transmission to food, people or the environment is to draw the distinction between colonization of ExPEC and infection. Food safety is an important challenge for public health both at the production stage and in the course of its processing and distribution. Examination of the genetic similarity of ExPEC strains will allow to determine their origin from different sources. Many levels of genotyping have been proposed in which the typing of strains, plasmids and genes is compared in order to obtain a more complete picture of this complex problem. The aim of our study was to characterize E. coli strains isolated from humans, animals and food for the presence of bacterial genes encoding virulence factors such as toxins, and iron acquisition systems (siderophores) in the context of an increasing spread of ExPEC infections.

Genotypes and Antimicrobial Susceptibility Profiles of Hemolytic Escherichia coli from Diarrheic Piglets

Hemolytic Escherichia coli are important pathogens in neonatal and weaned pigs. In this study, we analyzed 95 hemolytic E. coli isolated from intestinal contents or fecal samples of diarrheic piglets in 15 states of the United States between November 2013 and December 2014. Phenotypic antimicrobial susceptibility was determined through Sensititre BOFO6F plates for all the strains. They were all resistant to clindamycin, penicillin, tiamulin, tilmicosin, and highly resistant to oxytetracycline (91.6%), chlortetracycline (78.9%), ampicillin (75.8%), and sulfadimethoxine (68.4%). 86.2% of them were multidrug resistant. Whole genome sequencing (WGS) showed that 55 strains were enterotoxigenic E. coli (ETEC) and 40 strains were non-ETEC, and the strains belonged to 22 known and 2 novel sequence types (STs). ST100 and ST10 were the main and predominant STs in ETEC strains, whereas the non-ETEC strains were diverse with ST23 and ST761 as the main STs. Antibiotic resistance gene/mutation profiling of the genomes confirmed the results of antimicrobial susceptibility test. Notably, significant differences were found in the susceptibility to enrofloxacin between ETEC and non-ETEC (58.2% vs. 5.0%) and gentamicin (32.7% vs. 7.5%). ampH, ampC2, and ampC1 were the most common beta-lactamase genes in all E. coli strains, and extended-spectrum beta-lactamase (ESBL) genes were rare in these isolates. This study provides new insights into antibiotic resistance and genotypes of intestinal pathogenic E. coli associated with swine disease in the United States, and support the utility of WGS in accurate prediction of resistance to most antibiotics.

Discovery of mcr-1-Mediated Colistin Resistance in a Highly Virulent Escherichia coli Lineage

Resistance to last-line polymyxins mediated by the plasmid-borne mobile colistin resistance gene (mcr-1) represents a new threat to global human health. Here we present the complete genome sequence of an mcr-1-positive multidrug-resistant Escherichia coli strain (MS8345). We show that MS8345 belongs to serotype O2:K1:H4, has a large 241,164-bp IncHI2 plasmid that carries 15 other antibiotic resistance genes (including the extended-spectrum β-lactamase bla _CTX-M-1) and 3 putative multidrug efflux systems, and contains 14 chromosomally encoded antibiotic resistance genes. MS8345 also carries a large ColV-like virulence plasmid that has been associated with E. coli bacteremia. Whole-genome phylogeny revealed that MS8345 clusters within a discrete clade in the sequence type 95 (ST95) lineage, and MS8345 is very closely related to the highly virulent O45:K1:H4 clone associated with neonatal meningitis. Overall, the acquisition of a plasmid carrying resistance to colistin and multiple other antibiotics in this virulent E. coli lineage is concerning and might herald an era where the empirical treatment of ST95 infections becomes increasingly more difficult.IMPORTANCE Escherichia coli ST95 is a globally disseminated clone frequently associated with bloodstream infections and neonatal meningitis. However, the ST95 lineage is defined by low levels of drug resistance amongst clinical isolates, which normally provides for uncomplicated treatment options. Here, we provide the first detailed genomic analysis of an E. coli ST95 isolate that has both high virulence potential and resistance to multiple antibiotics. Using the genome, we predicted its virulence and antibiotic resistance mechanisms, which include resistance to last-line antibiotics mediated by the plasmid-borne mcr-1 gene. Finding an ST95 isolate resistant to nearly all antibiotics that also has a high virulence potential is of major clinical importance and underscores the need to monitor new and emerging trends in antibiotic resistance development in this important global lineage.

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.

A Population-Based Surveillance Study of Shared Genotypes of Escherichia coli Isolates from Retail Meat and Suspected Cases of Urinary Tract Infections

Community-acquired urinary tract infection caused by Escherichia coli is one of the most common infectious diseases in the United States, affecting approximately seven million women and costing approximately 11.6 billion dollars annually. In addition, antibiotic resistance among E. coli bacteria causing urinary tract infection continues to increase, which greatly complicates treatment. Identifying sources of uropathogenic E. coli and implementing prevention measures are essential. However, the reservoirs of uropathogenic E. coli have not been well defined. This study demonstrated that poultry sold in retail stores may serve as one possible source of uropathogenic E. coli. This finding adds to a growing body of evidence that suggests that urinary tract infection may be a food-borne disease. More research in this area can lead to the development of preventive strategies to control this common and costly infectious disease.

There is increasing evidence that retail food may serve as a source of Escherichia coli that causes community-acquired urinary tract infections, but the impact of this source in a community is not known. We conducted a prospective, population-based study in one community to examine the frequency of recovery of uropathogenic E. coli genotypes from retail meat samples. We analyzed E. coli isolates from consecutively collected urine samples of patients suspected to have urinary tract infections (UTIs) at a university-affiliated health service and retail meat samples from the same geographic region. We genotyped all E. coli isolates by multilocus sequence typing (MLST) and tested them for antimicrobial susceptibility. From 2016 to 2017, we cultured 233 E. coli isolates from 230 (21%) of 1,087 urine samples and 177 E. coli isolates from 120 (28%) of 427 retail meat samples. Urine samples contained 61 sequence types (STs), and meat samples had 95 STs; 12 STs (ST10, ST38, ST69, ST80, ST88, ST101, ST117, ST131, ST569, ST906, ST1844, and ST2562) were common to both. Thirty-five (81%) of 43 meat isolates among the 12 STs were from poultry. Among 94 isolates in the 12 STs, 26 (60%) of 43 retail meat isolates and 15 (29%) of 51 human isolates were pan-susceptible (P < 0.005). We found that 21% of E. coli isolates from suspected cases of UTIs belonged to STs found in poultry. Poultry may serve as a possible reservoir of uropathogenic E. coli (UPEC). Additional studies are needed to demonstrate transmission pathways of these UPEC genotypes and their food sources.

IMPORTANCE Community-acquired urinary tract infection caused by Escherichia coli is one of the most common infectious diseases in the United States, affecting approximately seven million women and costing approximately 11.6 billion dollars annually. In addition, antibiotic resistance among E. coli bacteria causing urinary tract infection continues to increase, which greatly complicates treatment. Identifying sources of uropathogenic E. coli and implementing prevention measures are essential. However, the reservoirs of uropathogenic E. coli have not been well defined. This study demonstrated that poultry sold in retail stores may serve as one possible source of uropathogenic E. coli. This finding adds to a growing body of evidence that suggests that urinary tract infection may be a food-borne disease. More research in this area can lead to the development of preventive strategies to control this common and costly infectious disease.

Virulence potential of commensal multidrug resistant Escherichia coli isolated from poultry in Brazil

There is an increasing number of reports worldwide about multidrug resistance (MDR) with potential of ExPEC in commensal E. coli. The present study evaluated the potential ExPEC in selected 44 MDR E.coli isolates, collected from livestock. ExPEC isolates were characterized by analysis of five main groups of virulence genes (papA and/or papC, sfa and/or foc, afa and/or dra, kpsMT II and iutA). We also determined the increased virulence potential analyzing other 29 virulence genes, the epidemiology of these isolates. Additionally, fifteen ExPEC isolates were selected to evaluate the adhesion and invasion capacity in vitro using Caco-2 cells. Based on the analysis of the five main virulence genes, 72.7% (32/44) strains were classified as ExPEC. The presence of each gene was iutA 88.6%, KpsMT II 70.4%, papC 25%, sfa/focDE 4.5%; afa/draBC genes were not found. All E. coli isolates were classified into: phylogenetic groups A (34%), B1 (10%), B2 (20%), and D (36%). MLST revealed 7 different STs among isolates, including a new ST identified (ST5687). The in vitro assay in Caco-2 cells showed that all isolates were capable to adhere or invade the epithelial cells, although this occurred at variable levels. The ExPEC isolate LO122 reached similar levels of invasion to the positive control strain Salmonella Typhimurium LT2. These results showed that the apparently commensal microbiota of poultry harbors MDR ExPEC isolates with high adhesion and invasion potential.

EFFECTIVENESS OF MENIRAN (PHYLLANTHUS NIRURI LINN) AS ANTIBACTERIAL FOR RESISTANCE ANTIBIOTICS PREVENTION OF ENTEROTOXIN ESCHERICHIA COLI

ABSTRACT               Escherichia coli (E. coli) can be isolated from the environment both inside and outside the hospes body. There were 89 serotypes in which 21% showed resistance to various antibiotics, such as E. coli enterotoxin. Alternative efforts were needed as a substitute for antibiotics, one of them through the use of medicinal plants, such as meniran (Phyllanthus niruri Linn).  Meniran plant is an immunomodulator that serves to repair the immune system of the body. The research was done through several stages: isolation and identification of  E. coli enterotoxin from several broiler farms in East Java using the polymerase chain reaction (PCR) method, E. coli resistance test against some antibiotics, making meniran extract and activation test against E. coli enterotoxin The study was divided into five treatments: T0+ (group of chickens were infected by E. coli enterotoxin), T0- (control group, not infected), T1 (infected by E. coli enterotoksin + 20% meniran extract), T2 (infected by E. coli enterotoksin + 25% extract meniran), T3 (infected by E. coli enterotoxin + 30% extract meniran). Data were analyzed by ANOVA (Analysis of Variance). The results were showed that all of  E. coli DNA isolates which tested by the PCR method was showed positive reactions at 600 bp. In the next stage, that E. coli enterotoxin are resistance to some antibiotics, such as Amoxicillin, Amphicillin, Erythromycin, Cephalosporins, Tetracycline, Cloxacillin and Gentamicin. Furthermore, 30% Phyllanthus niruri linn extract  effective as an antibacterial for the prevention of antibiotic resistance from E. coli enterotoxin. 

Draft Genomic Sequencing of Six Potential Extraintestinal Pathogenic Escherichia coli Isolates from Retail Chicken Meat

Potential extraintestinal pathogenic Escherichia coli strains DP254, WH333, WH398, F356, FEX675, and FEX725 were isolated from retail chicken meat products. Here, we report the draft genome sequences for these six E. coli isolates, which are currently being used in food safety research.

Lethality Prediction for Escherichia Coli O157:H7 and Uropathogenic E. coli in Ground Chicken Treated with High Pressure Processing and Trans-Cinnamaldehyde

Pathogenic Escherichia coli, intestinal (O157:H7) as well as extraintestinal types (for example, Uropathogenic E. coli [UPEC]) are commonly found in many foods including raw chicken meat. The resistance of E. coli O157:H7 to UPEC in chicken meat under the stresses of high hydrostatic Pressure (HHP, also known as HPP-high pressure processing) and trans-cinnamaldehyde (an essential oil) was investigated and compared. UPEC was found slightly less resistant than O157:H7 in our test parameter ranges. With the addition of trans-cinnamaldehyde as an antimicrobial to meat, HPP lethality enhanced both O157:H7 and UPEC inactivation. To facilitate the predictive model development, a central composite design (CCD) was used to assess the 3-parameter effects, that is, pressure (300 to 400 MPa), trans-cinnamaldehyde dose (0.2 to 0.5%, w/w), and pressure-holding time (15 to 25 min), on the inactivation of E. coli O157:H7 and UPEC in ground chicken. Linear models were developed to estimate the lethality of E. coli O157:H7 (R² = 0.86) and UPEC (R² = 0.85), as well as dimensionless nonlinear models. All models were validated with data obtained from separated CCD combinations. Because linear models of O157:H7 and UPEC had similar R² and the significant lethality difference of CCD points was only 9 in 20; all data were combined to generate models to include both O157:H7 and UPEC. The results provide useful information/tool to predict how pathogenic E. coli may survive HPP in the presence of trans-cinnamaldehyde and to achieve a great than 5 log CFU/g reduction in chicken meat. The models may be used for process optimization, product development and to assist the microbial risk assessment.

PRACTICAL APPLICATION

The study provided an effective means to reduce the high hydrostatic pressure level with incorporation of antimicrobial compound to achieve a 5-log reduction of pathogenic E. coli without damaging the raw meat quality. The developed models may be used to predict the high pressure processing lethality (and process optimization), product development (ingredient selection), and to assist the microbial risk assessment.

Risk factors for acquisition of multidrug-resistant Escherichia coli and development of community-acquired urinary tract infections

We examined risk factors associated with the intestinal acquisition of antimicrobial-resistant extraintestinal pathogenic Escherichia coli (ExPEC) and development of community-acquired urinary tract infection (UTI) in a case-control study of young women across Canada. A total of 399 women were recruited; 164 women had a UTI caused by E. coli resistant to ⩾1 antimicrobial classes and 98 had a UTI caused by E. coli resistant to ⩾3 antimicrobial classes. After adjustment for age, student health service (region of Canada) and either prior antibiotic use or UTI history, consumption of processed or ground chicken, cooked or raw shellfish, street foods and any organic fruit; as well as, contact with chickens, dogs and pet treats; and travel to Asia, were associated with an increased risk of UTI caused by antimicrobial resistant E. coli. A decreased risk of antimicrobial resistant UTI was associated with consumption of apples, nectarines, peppers, fresh herbs, peanuts and cooked beef. Drug-resistant UTI linked to foodborne and environmental exposures may be a significant public health concern and understanding the risk factors for intestinal acquisition of existing or newly emerging lineages of drug-resistant ExPEC is important for epidemiology, antimicrobial stewardship and prevention efforts.

Genome Sequences of Five Multidrug-Resistant Escherichia coli Sequence Type 117 Isolates Recovered from Dairy Calves

Escherichia coli sequence type 117 (ST117) strains have been recovered from poultry with colibacillosis, as well as from urinary tract infections and fatal septic infections in humans. To further investigate ST117 isolates recovered from nonpoultry food animals, we sequenced the genomes of five ST117 isolates from dairy calves in Pennsylvania.

Molecular epidemiology of infectious diseases

Molecular epidemiology (ME) is a branch of epidemiology developed by merging molecular biology into epidemiological studies. In this paper, the authors try to discuss the ways that molecular epidemiology studies identify infectious diseases' causation and pathogenesis, and unravel infectious agents' sources, reservoirs, circulation pattern, transmission pattern, transmission probability, and transmission order. They bring real-world examples of research works in each area to make each study design more understandable. They also address some research areas and study design aspects that need further attention in future. They close with some thoughts about future directions in this field and emphasize on the need for training competent molecular epidemiology specialists that are capable of dealing with rapid advances in the field.

The Prevalence of Extended-Spectrum Beta-Lactamase-Producing Multidrug-Resistant Escherichia Coli in Poultry Chickens and Variation According to Farming Practices in Punjab, India

BACKGROUND

Agricultural use of antimicrobials in subtherapeutic concentrations is increasing in response to the rising demand for food animal products worldwide. In India, the use of antimicrobials in food animal production is unregulated. Research suggests that many clinically important antimicrobials are used indiscriminately. This is the largest study to date in India that surveys poultry production to test for antimicrobial resistance and the occurrence of extended-spectrum β-lactamases (ESBLs) modulated by farming and managerial practices.

OBJECTIVES

Our goal was to survey poultry production for resistance to eleven clinically relevant antimicrobials and phenotypic occurrence of ESBLs as modulated by farming and managerial practices.

METHODS

Eighteen poultry farms from Punjab were surveyed, and 1,556 Escherichia coli isolates from 530 birds were tested for susceptibility to 11 antimicrobials using the disk diffusion method and validated using VITEK 2 (bioMérieux, Marcy-L’Étoile, France). Samples from 510 of these birds were phenotypically tested for ESBL production using the combination disk method and confirmed using VITEK 2. Generalized linear mixed models were used to infer differences in resistance profiles associated with different farming practices and facility types.

RESULTS

Resistance profiles were significantly different between broiler and layer farms. Broiler farms were 2.2 [ampicillin (AMP), p=0.017] to 23 [nalidixic acid (NX), p<0.001] times more likely to harbor resistant E. coli strains than layer farms. Adjusting for farm type (broiler vs. layer), the odds of resistance (although not statistically significant) to all antimicrobials except nitrofurantoin (NIT) were higher in independent facilities (IUs) as compared to contracted facilities (CFs). Increased prevalence of multidrug resistance (MDR; 94% compared to 60% in layers), including prevalence of ESBL-producing strains (87% compared to 42% in layers), was observed in broiler farms.

CONCLUSIONS

Our findings suggest that unregulated use of clinically relevant antimicrobials in Indian broiler and layer farms may contribute to the emergence of resistance and support the need to curb the nontherapeutic use of medically important antimicrobials in food animal production. https://doi.org/10.1289/EHP292.

Chromosomal location of the fosA3 and blaCTX-M genes in Proteus mirabilis and clonal spread of Escherichia coli ST117 carrying fosA3-positive IncHI2/ST3 or F2:A-:B- plasmids in a chicken farm

The aim of this study was to investigate the spread and location of the fosA3 gene among Enterobacteriaceae from diseased broiler chickens. Twenty-nine Escherichia coli and seven Proteus mirabilis isolates recovered from one chicken farm were screened for the presence of plasmid-mediated fosfomycin resistance genes by PCR. The clonal relatedness of fosA3-positive isolates, the transferability and location of fosA3, and the genetic context of the fosA3 gene were determined. Seven P. mirabilis isolates with three different pulsed-field gel electrophoresis (PFGE) patterns and five E. coli isolates belonging to sequence type 117 (ST117) and phylogenetic group D were positive for fosA3 and all carried the bla_CTX-M gene. In E. coli, the genetic structures IS26-ISEcp1-bla_CTX-M-65-IS26-fosA3-1758 bp-IS26 and IS26-ISEcp1-bla_CTX-M-3-bla_TEM-1-IS26-fosA3-1758 bp-IS26 were present on transferable IncHI2/ST3 and F2:A-:B- plasmids, respectively. However, fosA3 was located on the chromosome of the seven P. mirabilis isolates. IS26-ISEcp1-bla_CTX-M-65-IS26-fosA3-1758 bp-IS26 and IS26-bla_CTX-M-14-611 bp-fosA3-1222 bp-IS26 were detected in three and four P. mirabilis isolates, respectively. Minicircles that contained both fosA3 and bla_CTX-M-65 were shared between E. coli and P. mirabilis. This is the first report of the fosA3 gene integrated into the chromosome of P. mirabilis isolates with the bla_CTX-M gene. The emergence and clonal spread of avian pathogenic E. coli ST117 with the feature of multidrug resistance and high virulence are a serious problem.

Comparison by multilocus variable-number tandem repeat analysis and antimicrobial resistance among atypical enteropathogenic Escherichia coli strains isolated from food samples and human and animal faecal specimens

AIM

This study assessed whether multilocus variable-number tandem repeat analysis (MLVA) and antimicrobial susceptibility testing discriminated diarrhoeagenic atypical enteropathogenic Escherichia coli (aEPEC) from aEPEC indigenous to domestic animals or healthy people.

METHODS AND RESULTS

MLVA genotyping of 142 aEPEC strains isolated from foods and faecal samples of domestic animals and humans revealed 126 distinct MLVA profiles that distributed to four clusters, yielding a Simpson's index of diversity (D) of 99·8%. Cluster 2 included 87% of cattle isolates and 67% of patient isolates. The plurality (15/34, 44%) of strains from healthy humans mapped to Cluster 1, while half (18/41, 44%) of the swine strains belonged to Cluster 4. Testing for antimicrobial susceptibility revealed that 52 strains (37%) of aEPEC were resistant to one or more agents; only 10 strains (7%) exhibited resistance to more than three agents. Strains isolated from swine or food exhibited a wider variety of resistance phenotypes than bovine or human strains.

CONCLUSIONS

MLVA assigned the aEPEC isolates from cattle and patients to Cluster 2, distinct from aEPEC from other sources. Hog yards may be a larger source of drug-resistant strains than are cattle ranches.

SIGNIFICANCE AND IMPACT OF THE STUDY

MLVA suggests that human diarrhoeagenic aEPEC are derived from cattle and are distinct from strains carried by healthy people and other animals. Cattle appear to be reservoirs of human diarrhoeagenic aEPEC.

Phylogenetic diversity, antimicrobial susceptibility and virulence characteristics of phylogroup F Escherichia coli in Australia

Unlike Escherichia coli strains belonging to phylogroup B2, the clinical significance of strains belonging to phylogroup F is not well understood. Here we report on a collection of phylogroup F strains recovered in Australia from faeces and extra-intestinal sites from humans, companion animals and native animals, as well as from poultry meat and water samples. The distribution of sequence types was clearly non-random with respect to isolate source. The antimicrobial resistance and virulence trait profiles also varied with the sequence type of the isolate. Phylogroup F strains tended to lack the virulence traits typically associated with phylogroup B2 strains responsible for extra-intestinal infection in humans. Resistance to fluoroquinolones and/or expanded-spectrum cephalosporins was common within ST648, ST354 and ST3711. Although ST354 and ST3711 are part of the same clonal complex, the ST3711 isolates were only recovered from native birds being cared for in a single wildlife rehabilitation centre, whereas the ST354 isolates were from faeces and extra-intestinal sites of dogs and humans, as well as from poultry meat. Although ST354 isolates from chicken meat in Western Australia were distinct from all other ST354 isolates, those from poultry meat samples collected in eastern Australia shared many similarities with other ST354 isolates from humans and companion animals.

Reservoirs of Extraintestinal Pathogenic Escherichia coli

Several potential reservoirs for the Escherichia coli strains that cause most human extraintestinal infections (extraintestinal pathogenic E. coli; ExPEC) have been identified, including the human intestinal tract and various non-human reservoirs, such as companion animals, food animals, retail meat products, sewage, and other environmental sources. Understanding ExPEC reservoirs, chains of transmission, transmission dynamics, and epidemiologic associations will assist greatly in finding ways to reduce the ExPEC-associated disease burden. The need to clarify the ecological behavior of ExPEC is all the more urgent because environmental reservoirs may contribute to acquisition of antimicrobial resistance determinants and selection for and amplification of resistant ExPEC. In this chapter, we review the evidence for different ExPEC reservoirs, with particular attention to food and food animals, and discuss the public health implications of these reservoirs for ExPEC dissemination and transmission.

Thymus transcriptome reveals novel pathways in response to avian pathogenic Escherichia coli infection

Avian pathogenic Escherichia coli (APEC) can cause significant morbidity in chickens. The thymus provides the essential environment for T cell development; however, the thymus transcriptome has not been examined for gene expression in response to APEC infection. An improved understanding of the host genomic response to APEC infection could inform future breeding programs for disease resistance and APEC control. We therefore analyzed the transcriptome of the thymus of birds challenged with APEC, contrasting susceptible and resistant phenotypes. Thousands of genes were differentially expressed in birds of the 5-day post infection (dpi) challenged-susceptible group vs. 5 dpi non-challenged, in 5 dpi challenged-susceptible vs. 5 dpi challenged-resistant birds, as well as in 5 dpi vs. one dpi challenged-susceptible birds. The Toll-like receptor signaling pathway was the major innate immune response for birds to respond to APEC infection. Moreover, lysosome and cell adhesion molecules pathways were common mechanisms for chicken response to APEC infection. The T-cell receptor signaling pathway, cell cycle, and p53 signaling pathways were significantly activated in resistant birds to resist APEC infection. These results provide a comprehensive assessment of global gene networks and biological functionalities of differentially expressed genes in the thymus under APEC infection. These findings provide novel insights into key molecular genetic mechanisms that differentiate host resistance from susceptibility in this primary lymphoid tissue, the thymus.

Modeling the Inactivation of Intestinal Pathogenic Escherichia coli O157:H7 and Uropathogenic E. coli in Ground Chicken by High Pressure Processing and Thymol

Disease causing Escherichia coli commonly found in meat and poultry include intestinal pathogenic E. coli (iPEC) as well as extraintestinal types such as the Uropathogenic E. coli (UPEC). In this study we compared the resistance of iPEC (O157:H7) to UPEC in chicken meat using High Pressure Processing (HPP) in with (the hurdle concept) and without thymol essential oil as a sensitizer. UPEC was found slightly more resistant than E. coli O157:H7 (iPEC O157:H7) at 450 and 500 MPa. A central composite experimental design was used to evaluate the effect of pressure (300–400 MPa), thymol concentration (100–200 ppm), and pressure-holding time (10–20 min) on the inactivation of iPEC O157:H7 and UPEC in ground chicken. The hurdle approach reduced the high pressure levels and thymol doses imposed on the food matrices and potentially decreased food quality damaged after treatment. The quadratic equations were developed to predict the impact (lethality) on iPEC O157:H7 (R² = 0.94) and UPEC (R² = 0.98), as well as dimensionless non-linear models [Pr > F (<0.0001)]. Both linear and non-linear models were validated with data obtained from separated experiment points. All models may predict the inactivation/lethality within the same order of accuracy. However, the dimensionless non-linear models showed potential applications with parameters outside the central composite design ranges. The results provide useful information of both iPEC O157:H7 and UPEC in regard to how they may survive HPP in the presence or absence of thymol. The models may further assist regulatory agencies and food industry to assess the potential risk of iPEC O157:H7 and UPEC in ground chicken.

Polyphosphate Kinase Mediates Antibiotic Tolerance in Extraintestinal Pathogenic Escherichia coli PCN033

Extraintestinal pathogenic Escherichia coli (ExPEC) causes a variety of acute infections in its hosts, and multidrug-resistant strains present significant challenges to public health and animal husbandry. Therefore, it is necessary to explore new drug targets to control E. coli epidemics. Previous studies have reported that ppk mutants of Burkholderia pseudomallei and Mycobacterium tuberculosis are more susceptible than the wild types (WTs) to stress. Therefore, we investigated the stress response to antibiotics mediated by polyphosphate kinase (PPK) in ExPEC strain PCN033. We observed that planktonic cells of a ppk knockout strain (Δppk) were more susceptible to antibiotics than was WT. However, biofilm-grown Δppk cells showed similar susceptibility to that of the WT and were more tolerant than the planktonic cells. During the planktonic lifestyle, the expression of genes involved in antibiotic tolerance (including resistance-conferring genes, and antibiotic influx, and efflux genes) did not change in the Δppk mutant without antibiotic treatment. However, the resistance-conferring gene bla and efflux genes were upregulated more in the WT than in the Δppk mutant by treatment with tazobactam. After treatment with gentamycin, the efflux genes and influx genes were upregulated and downregulated, respectively, more in the WT than in the Δppk mutant. The expression of genes involved in biofilm regulation also changed after treatment with tazobactam or gentamycin, and which is consistent with the results of the biofilm formation. Together, these observations indicate that PPK is important for the antibiotic stress response during the planktonic growth of ExPEC and might be a potential drug target in bacteria.

Inactivation of Uropathogenic Escherichia coli in Ground Chicken Meat Using High Pressure Processing and Gamma Radiation, and in Purge and Chicken Meat Surfaces by Ultraviolet Light

Extraintestinal pathogenic Escherichia coli, including uropathogenic E. coli (UPEC), are common contaminants in poultry meat and may cause urinary tract infections after colonization of the gastrointestinal tract and transfer of contaminated feces to the urethra. Three non-thermal processing technologies used to improve the safety and shelf-life of both human and pet foods include high pressure processing (HPP), ionizing (gamma) radiation (GR), and ultraviolet light (UV-C). Multi-isolate cocktails of UPEC were inoculated into ground chicken which was then treated with HPP (4°C, 0-25 min) at 300, 400, or 500 MPa. HPP D10, the processing conditions needed to inactivate 1 log of UPEC, was 30.6, 8.37, and 4.43 min at 300, 400, and 500 MPa, respectively. When the UPEC was inoculated into ground chicken and gamma irradiated (4 and -20°C) the GR D10 were 0.28 and 0.36 kGy, respectively. The UV-C D10 of UPEC in chicken suspended in exudate and placed on stainless steel and plastic food contact surfaces ranged from 11.4 to 12.9 mJ/cm(2). UV-C inactivated ca. 0.6 log of UPEC on chicken breast meat. These results indicate that existing non-thermal processing technologies such as HPP, GR, and UV-C can significantly reduce UPEC levels in poultry meat or exudate and provide safer poultry products for at-risk consumers.

Characterization of an rmtB-carrying IncI1 ST136 plasmid in avian Escherichia coli isolates from chickens

The rmtB gene, one of the 16S rRNA methylase genes whose products confer high-level resistance to aminoglycosides, is most prevalent among Enterobacteriaceae strains. In this study, eight non-duplicate rmtB-carrying avian Escherichia coli strains from a farm in China were isolated and characterized, and further examined by phylogenetic grouping, conjugation experiments and PCR-based replicon typing. In addition, the genetic environment of rmtB was investigated by cloning and sequencing. Six rmtB-carrying E. coli were identified as phylogroup A, sequence type (ST) 156 (A-ST156), with two assigned to D-ST117; however, all of them carried the same IncI1 ST136 plasmid. The genetic environment of the rmtB gene in these eight plasmids was the same, as shown by PCR mapping. A multidrug-resistant region carrying blaTEM-1, rmtB, a class 1 integron cassette array (intI1-dfrA12-orfF-aadA2-qacEΔ1-sul1) and aacC2 was characterized on the conjugative IncI1 ST136 plasmid. Co-location of the rmtB gene with a class 1 integron cassette array and aacC2 on the conjugative plasmid will facilitate its maintenance and dissemination.

Characteristics of CTX-M Extended-Spectrum β-Lactamase-Producing Escherichia coli Strains Isolated from Multiple Rivers in Southern Taiwan

Extended-spectrum β-lactamase (ESBL)-producing Escherichia coli sequence type ST131 has emerged as the leading cause of community-acquired urinary tract infections and bacteremia worldwide. Whether environmental water is a potential reservoir of these strains remains unclear. River water samples were collected from 40 stations in southern Taiwan from February to August 2014. PCR assay and multilocus sequence typing (MLST) analysis were conducted to determine the CTX-M group and sequence type, respectively. In addition, we identified the seasonal frequency of ESBL-producing E. coli strains and their geographical relationship with runoffs from livestock and poultry farms between February and August 2014. ESBL-producing E. coli accounted for 30% of the 621 E. coli strains isolated from river water in southern Taiwan. ESBL-producing E. coli ST131 was not detected among the isolates. The most commonly detected strain was E. coli CTX-M group 9. Among the 92 isolates selected for MLST analysis, the most common ESBL-producing clonal complexes were ST10 and ST58. The proportion of ESBL-producing E. coli was significantly higher in areas with a lower river pollution index (P = 0.025) and regions with a large number of chickens being raised (P = 0.013). ESBL-producing E. coli strains were commonly isolated from river waters in southern Taiwan. The most commonly isolated ESBL-producing clonal complexes were ST10 and ST58, which were geographically related to chicken farms. ESBL-producing E. coli ST131, the major clone causing community-acquired infections in Taiwan and worldwide, was not detected in river waters.

Nontherapeutic Use of Antimicrobial Agents in Animal Agriculture: Implications for Pediatrics

Antimicrobial resistance is one of the most serious threats to public health globally and threatens our ability to treat infectious diseases. Antimicrobial-resistant infections are associated with increased morbidity, mortality, and health care costs. Infants and children are affected by transmission of susceptible and resistant food zoonotic pathogens through the food supply, direct contact with animals, and environmental pathways. The overuse and misuse of antimicrobial agents in veterinary and human medicine is, in large part, responsible for the emergence of antibiotic resistance. Approximately 80% of the overall tonnage of antimicrobial agents sold in the United States in 2012 was for animal use, and approximately 60% of those agents are considered important for human medicine. Most of the use involves the addition of low doses of antimicrobial agents to the feed of healthy animals over prolonged periods to promote growth and increase feed efficiency or at a range of doses to prevent disease. These nontherapeutic uses contribute to resistance and create new health dangers for humans. This report describes how antimicrobial agents are used in animal agriculture, reviews the mechanisms of how such use contributes to development of resistance, and discusses US and global initiatives to curb the use of antimicrobial agents in agriculture.

Molecular characterization of bacteremic Escherichia coli isolates in Romania

The increasing prevalence of invasive infections caused by antibiotic resistant Escherichia coli strains in Romanian patients, already mentioned in the European reports, requires better knowledge of their specific traits. Thus, a set of 38 E. coli blood isolates, collected between 2010 and 2012 at one of the local hospitals participating into the European Antimicrobial Resistance Surveillance Network, was investigated retrospectively with respect to the phylogenetic origin, extraintestinal virulence-associated markers (i.e. fimH, papC, papG alleles, sfa/foc, afa/dra, hly, cnf1, sat, iucC, fyuA, ibeA), and beta-lactamase encoding genes (i.e. bla CTX-M, bla TEM, and bla SHV alleles). The isolates with extended-spectrum beta-lactamase (ESBL) phenotypes were further characterized using PCR-based replicon typing and multilocus sequencing typing. For ST131 members, pulsed-field gel electrophoresis (PFGE) and PCR-based detection of fimH30 allele were performed. Overall, the isolates were more likely members of the major phylogenetic group A (53 %) and to a lesser extent of groups B2 (29 %), D (10 %), and B1 (8 %). All but three of the virulence markers sought (i.e. papGI, hly, cnf1) were detected with prevalence ranging from 3 % (i.e. ibeA, papGIII) to 87 % (fimH). As expected, the most complex genotypes (four to seven virulence markers) defined the isolates derived from phylogenetic groups B2 and D. ESBL producers were bla CTX-M-15-positive, mostly of phylogroup A (67 %), harboured IncF multireplicon plasmids, and belonged to six sequence types (i.e. ST10, ST131, ST167, ST410, ST540, ST1275). Members of ST10 clonal complex (i.e. ST10, ST167) were the most common. The ST131 isolates belonged to H30 subclone and displayed 74 % similarity at PFGE analysis.

First detection of extended-spectrum cephalosporin- and fluoroquinolone-resistant Escherichia coli in Australian food-producing animals

This study aimed to define the frequency of resistance to critically important antimicrobials (CIAs) [i.e. extended-spectrum cephalosporins (ESCs), fluoroquinolones (FQs) and carbapenems] among Escherichia coli isolates causing clinical disease in Australian food-producing animals. Clinical E. coli isolates (n=324) from Australian food-producing animals [cattle (n=169), porcine (n=114), poultry (n=32) and sheep (n=9)] were compiled from all veterinary diagnostic laboratories across Australia over a 1-year period. Isolates underwent antimicrobial susceptibility testing to 18 antimicrobials using the Clinical and Laboratory Standards Institute disc diffusion method. Isolates resistant to CIAs underwent minimum inhibitory concentration determination, multilocus sequence typing (MLST), phylogenetic analysis, plasmid replicon typing, plasmid identification, and virulence and antimicrobial resistance gene typing. The 324 E. coli isolates from different sources exhibited a variable frequency of resistance to tetracycline (29.0-88.6%), ampicillin (9.4-71.1%), trimethoprim/sulfamethoxazole (11.1-67.5%) and streptomycin (21.9-69.3%), whereas none were resistant to imipenem or amikacin. Resistance was detected, albeit at low frequency, to ESCs (bovine isolates, 1%; porcine isolates, 3%) and FQs (porcine isolates, 1%). Most ESC- and FQ-resistant isolates represented globally disseminated E. coli lineages (ST117, ST744, ST10 and ST1). Only a single porcine E. coli isolate (ST100) was identified as a classic porcine enterotoxigenic E. coli strain (non-zoonotic animal pathogen) that exhibited ESC resistance via acquisition of bla_CMY-2. This study uniquely establishes the presence of resistance to CIAs among clinical E. coli isolates from Australian food-producing animals, largely attributed to globally disseminated FQ- and ESC-resistant E. coli lineages.