Antibiotic resistance and virulence genes in commensal Escherichia coli and Salmonella isolates from commercial broiler chicken farms

Public Health Risk of Campylobacter spp. Isolated from Slaughterhouse and Retail Poultry Meat: Prevalence and Antimicrobial Resistance Profiles

Campylobacter spp. represents one of the most frequently incriminated pathogens in the evolution of foodborne gastroenteritis in humans worldwide. Alongside Salmonella spp., Yersinia spp., Escherichia coli, and Listeria monocytogenes, these pathogens represent a principal threat to public health because they are vehiculated to humans via food products and many of them have developed alarming resistance to different classes of antimicrobials. Thus, the present study aimed to provide scientifically relevant data on the public health risk represented by Campylobacter spp., contamination of chicken carcasses at the slaughterhouse and retail levels, and the antimicrobial resistance of the isolated strains. A total of 130 samples collected from slaughterhouses (n = 40) and retail stores (n = 90) were analyzed using standardized microbiological methods (ISO 10272-1:2017). Of these, the overall prevalence of Campylobacter spp. was 27.7%, with a prevalence at the slaughterhouse level of 32.5% and at the retail level of 25.5%. Following antimicrobial resistance profile determinations using the Kirby-Bauer disc diffusion assay, the isolated strains showed resistance to the following antimicrobials in descending order: ciprofloxacin (41.6%), tetracycline (25.0%), chloramphenicol (16.6%), gentamicin (11.1%), ertapenem (5.6%), and erythromycin (2.8%). The study results confirm that chicken meat may pose a threat to public health and, moreover, that due to the widespread use of antimicrobials, a large number of strains have developed antimicrobial resistance, leading to difficulties in the treatment of various foodborne diseases.

Effects of multidrug-resistant bacteria and multi-antibiotic combination on intestinal microbiota in mice

Multidrug-resistant bacteria are a clinical and an epidemiological challenge. However, the effects of multidrug-resistant bacteria and multi-antibiotic combination on gut microbiota are unclear. In this study, the effects of multidrug-resistant bacteria and multi-antibiotic combination on intestinal microbiota in mice have been observed by high-throughput sequencing. Resistant Escherichia coli (RP4) and 0.5, 1, and 2 mg/L antibiotics (Amp, Km, and Tet multi-antibiotic combination) could decrease the number of specific operational taxonomic units from 223 in the normal saline control group to 178 in the antibiotic-resistant bacteria group and 34 in the antibiotic group, and antibiotics are the biggest influencing factor. Multidrug-resistant bacteria and multi-antibiotic combination could affect the function of intestinal microbiota, and the effect of multidrug-resistant bacteria was similar to that of multi-antibiotic combination. Small intestine is the main colonization site of antibiotic-resistant bacteria, and Proteobacteria and Bacteroidetes are the major antibiotic-resistance acquired bacteria as determined by transmission electron microscopy and agarose plate screening culture.

Houseflies (Musca domestica) as vectors of multidrug-resistant, ESBL-producing Escherichia coli in broiler poultry farms of North India: implications for antibiotic resistance transmission

The transmission of antibiotic resistance (AR) from farm animals to healthy human communities, beyond the food chain, is often facilitated by biological vectors, notably houseflies (Musca domestica). This study aimed to evaluate the role of M. domestica collected from commercial broiler chicken farms as a carrier of multidrug-resistant (MDR), extended-spectrum β-lactamase (ESBL)-producing Escherichia coli. E. coli were isolated separately from the housefly's external surface (ES) and internal homogenate (IH) to determine the primary AR transmission route within houseflies. Remarkably, 68.6% houseflies harboured E. coli. Isolated E. coli were evaluated for susceptibility to clinically relevant antibiotics and screened for the presence of 22 plasmid-borne AR genes (ARGs) using PCR. Results revealed significant resistance to key antibiotics, with > 70% of isolates resistant to ampicillin and > 50% resistant to tetracycline and nalidixic acid in both ES- and IH-derived E. coli. Notably, a significant prevalence of resistance was observed to third-generation cephalosporins. Additionally, > 80% of E. coli isolates were MDR. A statistically significant difference (unpaired t-test, p < 0.05) was observed in the presence of ESBL-producing E. coli between the houseflies' ES (28.14%) and IH (38.14%). ARGs such as, ampC, tetA, qnrS, strA, strB, and sul3 were frequently detected in both ES- and IH-derived E. coli isolates. Among the ESBL-producing genes, blaCTX-M was the most abundant. Pearson's correlation analysis predicted the ARGs responsible for phenotypic resistance to specific antibiotics. Farm-derived flies harboured a significantly higher number of MDR E. coli (unpaired t-test, p < 0.05) than the ones isolated from flies housing a distant non-farm environment. Conclusively, this study illustrates the role of houseflies as vectors for AR transmission from AR hotspots to human communities.

Risk of Colonization with Multidrug-Resistant Gram-Negative Bacteria Among Travellers and Migrants: A Narrative Review

Globalization in the 21st century has posed several challenges. In particular, the spread of multidrug-resistant bacterial strains, especially Gram-negative bacteria, which are prevalent in certain regions of the world, is one of the most critical issues. This raises concerns about the risks associated with the booming tourism industry and migratory flows. In fact, even transient colonization with multidrug-resistant strains can present significant challenges to individual, family, and public health. Understanding the epidemiology and mechanisms of resistance, associated risk factors and prevention policies is therefore essential to ensure that strategies are in place to limit the global spread of high-risk bacterial clones and thereby protect public health.

Antibiotic residues in poultry products and bacterial resistance: A review in developing countries

Antimicrobial resistance (AMR) is a growing global concern, particularly in poultry farming, where antibiotics are widely used for both disease prevention and growth promotion. This review examines the misuse of antibiotics in poultry production, especially in developing countries, and its contribution to the emergence of antibiotic-resistant bacteria. The findings highlight that factors such as increasing demand for poultry protein, the availability of inexpensive antibiotics, and weak regulatory oversight have led to widespread misuse, accelerating the spread of resistance genes. Although evidence links poultry farming to AMR, significant data gaps remain, especially regarding resistance transmission from poultry to humans. The review underscores the urgent need for stronger regulatory frameworks, phased-out use of antimicrobial growth promoters, and enhanced awareness campaigns to address this issue. Improving the capacity of regulatory bodies and developing more robust national data monitoring systems are essential steps to mitigate the threat of AMR in poultry farming and to protect both animal and human health.

Dissemination of IncC plasmids in Salmonella enterica serovar Thompson recovered from seafood and human diarrheic patients in China

Salmonella Thompson is a prevalent foodborne pathogen and a major threat to food safety and public health. This study aims to reveal the dissemination mechanism of S. Thompson with co-resistance to ceftriaxone and ciprofloxacin. In this study, 181 S. Thompson isolates were obtained from a retrospective screening on 2118 serotyped Salmonella isolates from foods and patients, which were disseminated in 12 of 16 districts in Shanghai, China. A total of 10 (5.5 %) S. Thompson isolates exhibited resistance to ceftriaxone (MIC ranging from 8 to 32 μg/mL) and ciprofloxacin (MIC ranging from 2 to 8 μg/mL). The AmpC β-lactamase gene blaCMY-2 and plasmid-mediated quinolone resistance (PMQR) genes of qnrS and qepA were identified in the 9 isolates. Conjugation results showed that the co-transfer of blaCMY-2, qnrS, and qepA occurred on the IncC plasmids with sizes of ∼150 (n = 8) or ∼138 (n = 1) kbp. Three typical modules of ISEcp1-blaCMY-2-blc-sugE, IS26-IS15DIV-qnrS-ISKpn19, and ISCR3-qepA-intl1 were identified in an ST3 IncC plasmid pSH11G0791. Phylogenetic analysis indicated that IncC plasmids evolved into Lineages 1, 2, and 3. IncC plasmids from China including pSH11G0791 in this study fell into Lineage 1 with those from the USA, suggesting their close genotype relationship. In conclusion, to our knowledge, it is the first report of the co-existence of blaCMY-2, qnrS, and qepA in IncC plasmids, and the conjugational transfer contributed to their dissemination in S. Thompson. These findings underline further challenges for the prevention and treatment of Enterobacteriaceae infections posed by IncC plasmids bearing blaCMY-2, qnrS, and qepA.

Production systems and important antimicrobial resistant-pathogenic bacteria in poultry: a review

Economic losses and market constraints caused by bacterial diseases such as colibacillosis due to avian pathogenic Escherichia coli and necrotic enteritis due to Clostridium perfringens remain major problems for poultry producers, despite substantial efforts in prevention and control. Antibiotics have been used not only for the treatment and prevention of such diseases, but also for growth promotion. Consequently, these practices have been linked to the selection and spread of antimicrobial resistant bacteria which constitute a significant global threat to humans, animals, and the environment. To break down the antimicrobial resistance (AMR), poultry producers are restricting the antimicrobial use (AMU) while adopting the antibiotic-free (ABF) and organic production practices to satisfy consumers' demands. However, it is not well understood how ABF and organic poultry production practices influence AMR profiles in the poultry gut microbiome. Various Gram-negative (Salmonella enterica serovars, Campylobacter jejuni/coli, E. coli) and Gram-positive (Enterococcus spp., Staphylococcus spp. and C. perfringens) bacteria harboring multiple AMR determinants have been reported in poultry including organically- and ABF-raised chickens. In this review, we discussed major poultry production systems (conventional, ABF and organic) and their impacts on AMR in some potential pathogenic Gram-negative and Gram-positive bacteria which could allow identifying issues and opportunities to develop efficient and safe production practices in controlling pathogens.

Antimicrobial resistance profile of Escherichia coli isolated from poultry litter

Antimicrobial resistance is a threat to animal and human health. As a commensal and zoonotic bacterium, Escherichia coli has the potential to be a pathogenic source of antimicrobial resistance. The purpose of this study aimed to investigate the antimicrobial resistance profile of E. coli isolated from litter collected from pens in a broiler chicken experiment. E. coli was isolated from litter samples (n = 68 isolates) of 16 pens housing broilers to d 53 of age. Resistance to 10 antimicrobials was observed by disc diffusion. The presence of 23 antimicrobial and heavy metal resistance genes, O serogroups, and avian pathogenic E. coli (APEC-like) minimal predictor genes were identified through PCR. E. coli isolates presented the greatest resistance to cephalothin (54.4%), tetracycline (27.9%), streptomycin (29.4%), ampicillin (20.6%), colistin (13.2%), sulphonamides (8.8%), and imipenem (1.5%). Multidrug resistance to at least 3 antimicrobials was observed in 22.1% of isolates. The identified O-types of the E. coli isolates were O15, O75, O78, and O91. There was a greater likelihood that the genes groEL, aph(3)IA, silP, sull, aadA, qacEdelta1, iroN, ompTp, and hlyF were present in isolates that exhibited ampicillin resistance (P ≤ 0.05). There was a greater likelihood that the groEL gene was present in isolates resistant to ampicillin, colistin, tetracycline, sulphonamides, or cephalothin (P ≤ 0.05). Further characterizing E. coli antimicrobial resistance is essential and aids in developing effective solutions, thereby furthering the One Health objective.

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

Longitudinal study on the effects of growth-promoting and therapeutic antibiotics on the dynamics of chicken cloacal and litter microbiomes and resistomes

BACKGROUND

Therapeutic and growth-promoting antibiotics are frequently used in broiler production. Indirect evidence indicates that these practices are linked to the proliferation of antimicrobial resistance (AMR), the spread of antibiotic-resistant bacteria from food animals to humans, and the environment, but there is a lack of comprehensive experimental data supporting this. We investigated the effects of growth promotor (bacitracin) and therapeutic (enrofloxacin) antibiotic administration on AMR in broilers for the duration of a production cycle, using a holistic approach that integrated both culture-dependent and culture-independent methods. We specifically focused on pathogen-harboring families (Enterobacteriaceae, Enterococcaceae, and Staphylococcaceae).

RESULTS

Antibiotic-resistant bacteria and antibiotic resistance genes were ubiquitous in chicken cloaca and litter regardless of antibiotic administration. Environment (cloaca vs. litter) and growth stage were the primary drivers of variation in the microbiomes and resistomes, with increased bacterial diversity and a general decrease in abundance of the pathogen-harboring families with age. Bacitracin-fed groups had higher levels of bacitracin resistance genes and of vancomycin-resistant Enterococcaceae (total Enterococcaceae counts were not higher). Although metagenomic analyses classified 28-76% of the Enterococcaceae as the commensal human pathogens E. faecalis and E. faecium, culture-based analysis suggested that approximately 98% of the vancomycin-resistant Enterococcaceae were avian and not human-associated, suggesting differences in the taxonomic profiles of the resistant and non-resistant strains. Enrofloxacin treatments had varying effects, but generally facilitated increased relative abundance of multidrug-resistant Enterobacteriaceae strains, which were primarily E. coli. Metagenomic approaches revealed a diverse array of Staphylococcus spp., but the opportunistic pathogen S. aureus and methicillin resistance genes were not detected in culture-based or metagenomic analyses. Camphylobacteriaceae were significantly more abundant in the cloacal samples, especially in enrofloxacin-treated chickens, where a metagenome-assembled C. jejuni genome harboring fluoroquinolone and β-lactam resistance genes was identified.

CONCLUSIONS

Within a "farm-to-fork, one health" perspective, considering the evidence that bacitracin and enrofloxacin used in poultry production can select for resistance, we recommend their use be regulated. Furthermore, we suggest routine surveillance of ESBL E. coli, vancomycin-resistant E. faecalis and E. faecium, and fluoroquinolone-resistant C. jejuni strains considering their pathogenic nature and capacity to disseminate AMR to the environment. Video Abstract.

Mandated restrictions on the use of medically important antibiotics in broiler chicken production in Canada: implications, emerging challenges, and opportunities for bolstering gastrointestinal function and health– A review

Chicken Farmers of Canada has been progressively phasing out prophylactic use of antibiotics in broiler chicken production. Consequently, hatcheries, veterinarians, and nutritionists have been mandated to contend with less reliance on use of preventive antibiotics. A topical concern is the increased risk of proliferation of enteric pathogens leading to poor performance, increased mortality and compromised welfare. Moreover, the gut harbors several taxa such as Campylobacter and Salmonella capable of causing significant illnesses in humans via contaminated poultry products. This has created opportunity for research and development of dietary strategies designed to modulate gastrointestinal environment for enhanced performance and food safety. Albeit with inconsistent responses, literature data suggests that dietary strategies such as feed enzymes, probiotics/prebiotics and phytogenic feed additives can bolster gut health and function in broiler chickens. However, much of the efficacy data was generated at controlled research settings that vary significantly with the complex commercial broiler production operations due to variation in dietary, health and environmental conditions. This review will summarize implications of mandated restrictions on the preventative use of antibiotics and emerging Canadian broiler production programs to meet processor specifications. Challenges and opportunities for integrating alternative dietary strategies in commercial broiler production settings will be highlighted.

Antimicrobial uses for livestock production in developing countries

Antimicrobial is an indispensable part of veterinary medicine used for the treatment and control of diseases as well as a growth promoter in livestock production. Frequent use of antimicrobials in veterinary practices may lead to the residue in animal originated products and creates some potential problems for human health. The presence of antimicrobial residues in animal originated foods may induce serious health problems such as allergic reaction, antimicrobial resistance (AMR), and lead to carcinogenic and mutagenic effects in the human body. The misuse or abuse of antibiotics in human medicine is thought to be a principal cause of AMR but some antimicrobial-resistant bacteria and their resistant genes originating from animals are also responsible for developing AMR. However, the residual effect of antimicrobials in feed and food products of animal origin is undeniable. In developing countries, the community is unaware of this residual effect due to lack of proper information about antibiotic usage, AMR surveillance, and residue monitoring system. It is imperative to reveal the current situation of antimicrobial use in livestock production and its impacts on public health. Moreover, the safety levels of animal feeds and food products of animal origin must be strictly monitored and public awareness should be developed against the indiscriminate use of antimicrobial in animal production. Therefore, the current review summarizes the literature on antimicrobial use in livestock production and its hazardous residual impacts on the human body in developing countries.

Molecular characterisation of extended-spectrum β-lactamase-producing Escherichia coli and Salmonella isolated from poultry and poultry products in Egypt

Extended-spectrum β-lactamase (ESBL) producing E. coli and salmonellae have spread rapidly worldwide and pose a serious threat to human and animal health. The present study was conduct-ed to determine the prevalence of ESBL-producing E.coli and salmonellae, to perform molecular characterisation of the ESBL-related bla genes, including blaTEM, blaSHV and blaCTX, and the sus-ceptibilities of these bacteria to various antimicrobial agents. From a total of 300 poultry samples, 25 and 20 samples were recognised as Salmonella and E. coli, respectively by microbiological and molecular methods. All E. coli and Salmonella isolates were positive for an ESBL phenotype. Mo-lecular detection for antibiotic resistance gene revealed blaTEM in all isolates of salmonellae and E. coli (100%), while blaSHV was detected in 5 (20%) and 2 (10%) of salmonellae and E. coli isolates, respectively. None of the isolates contained blaCTX gene. Serotyping of Salmonella spp. in chick-ens revealed that S. enteritidis was the major isolates followed by S. Infantis (21.4%), S. Kentucky (14.2%) and S. Typhimurium, S. Kapemba, S. Newport, S. Vejle and S. Magherafelt were detected at 7.1% respectively. S. Infantis was the major isolate detected in chicks (60%), while in ducks S. Typhimurium and S. Blegdam were identified. In ducklings, S. Sinchew, S. Infantis and S. Sekon-di were equally prevalent. Only S. Newmexico was identified in poultry products. E. coli in chick-en were serotyped into O1, O8, O29, O125, O128 and O157. In chicks, O29 and O126 serotypes were detected. In poultry products only O8 was detected. The results indicate that ESBL frequen-cy has reached an alarming level in poultry isolates in Egypt, with TEM enzymes being the pre-dominant β-lactamases detected.

Genome sequences of two multidrug-resistant Escherichia coli strains MEZEC8 and MEZEC10 isolated from livestock in South Africa

OBJECTIVES

The emergence of antimicrobial-resistant livestock-associated Escherichia coli represents a great public health concern. Here we report the draft genome sequences of two multidrug-resistant livestock-associated E. coli strains MEZEC8 and MEZEC10 isolated from sheep in South Africa.

METHODS

Genomic DNA of E. coli strains MEZEC8 and MEZEC10 was sequenced using an Illumina MiSeq platform. Generated reads were trimmed and de novo assembled. The assembled contigs were analysed for antimicrobial resistance genes, chromosomal mutations and extrachromosomal plasmids, and the sequence type (ST) was determined by multilocus sequence typing (MLST). To compare strains MEZEC8 and MEZEC10 with other previously published sequences of E. coli strains, raw read sequences of E. coli from livestock were downloaded from the NCBI's Sequence Read Archive and all sequence files were treated identically to generate a core genome bootstrapped maximum likelihood phylogenetic tree.

RESULTS

Antimicrobial resistance genes were detected in MEZEC8 and MEZEC10 conferring resistance to tetracycline and macrolides. MEZEC10 harboured two extrachromosomal plasmids (pO111 and Incl2), while MEZEC8 did not contain any extrachromosomal plasmids. Strain MEZEC8 belonged to serotype H25:O9 and ST58, whereas strain MEZEC10 belonged to serotype H49:O8 and ST1844.

CONCLUSION

The genome sequences of E. coli strains MEZEC8 and MEZEC10 will serve as a reference point for molecular epidemiological studies of antimicrobial-resistant livestock-associated E. coli in Africa. In addition, this study allows in-depth analysis of genomic structure and will provide valuable information enabling us understand the antimicrobial resistance of livestock-associated E. coli.

Effects of wild blueberry (Vaccinium angustifolium) pomace feeding on gut microbiota and blood metabolites in free-range pastured broiler chickens

There is a need to develop cost-effective approaches to modulate gut microbiota, promote bird health, and prevent infections in pasture-raised broiler chickens. The present study evaluated the efficacy of organic wild blueberry (Vaccinium angustifolium) also called low-bush blueberry pomace (LBBP)-supplemented feed to modulate the chicken gut microbiota, and blood metabolites in order to improve bird health and productivity. Slow-growing broiler chickens were reared on pasture up to 64 D for sampling after 2 wk of treatment during brooding with 0, 1, and 2% LBBP in feed. Intestinal samples were collected at different time-points throughout the trial for bacterial culture and microbial community analysis by 16S rRNA gene sequencing using Illumina MiSeq. Blood sera were also analyzed for metabolites at each sampling time. Of the 14 bacterial phyla, the predominant taxa across all sampling time-points were Firmicutes, Proteobacteria, Bacteroidetes, and Tenericutes, representing >97% of all sequences. Bacteroidetes seemed to be replacing Firmicutes by LBBP supplementation, with the most noticeable effect at day 64 with 1% LBBP. LBBP inclusion enriched Lactobacillus, Bacteroides, and Bifidobacterium, while Escherichia coli, Clostridium_Clostridiaceae, Helicobacter, and Enterococcus showed higher abundances in control birds at the end of trial. Principal co-ordinate analysis showed a clear clustering of the intestinal samples from control and LBBP-treated groups at day 29. Application of LBBP resulted in a decrease (P < 0.05) in cholesterol at day 21, and an increase (P < 0.05) in high-density lipoprotein cholesterol in 14-day-old broilers. Higher (P < 0.05) levels of phosphorus, magnesium, and globulin at day 21 as well as iron and albumin at day 36 were also observed in 1% LBBP-fed birds. Despite limitations consisting essentially of low sampled birds for measurements, this study indicated that dietary supplementation of LBBP could positively influence gut microbiota and blood metabolites that may contribute to the overall health of pasture-raised broiler chickens.

Genome Analysis and Multiplex PCR Method for the Molecular Detection of Coresistance to Cephalosporins and Fosfomycin in Salmonella enterica Serovar Heidelberg

Heidelberg is among the top three Salmonella enterica serovars associated with human foodborne illness in Canada. Traditional culture and antimicrobial susceptibility testing techniques can be time-consuming to identify Salmonella Heidelberg resistant to cephalosporins and fosfomycin. Rapid and accurate detection of such antibiotic-resistant Salmonella Heidelberg isolates is essential to adopt appropriate control measures. In this study, 15 Salmonella Heidelberg strains isolated from feces of Canadian broiler chickens were characterized by whole genome sequencing. Salmonella Heidelberg genomes had an average coverage of greater than 80-fold, an average of 4,761 protein-coding genes, and all belonged to multilocus sequence type ST15. Genome sequences were compared with genomes in the National Center for Biotechnology Information Pathogen Detection database ( www.ncbi.nlm.nih.gov/pathogens/ ), including human outbreak isolates. The Canadian broiler isolates clustered with chicken isolates from the United States and an equine clinical isolate from Ontario, Canada. In agreement with their antimicrobial resistance phenotypes, several chromosomally encoded specific antimicrobial resistance genes including fosA7 and multidrug resistance efflux pump determinants were detected. An AmpC-like β-lactamase gene, bla_CMY-2, linked with a quaternary ammonium compound resistance gene, sugE, on a replicon type IncI1 plasmid was detected in all 15 broiler Salmonella Heidelberg isolates. Of the 205,031 published Salmonella genomes screened in silico, 4,954 (2.4%) contained bla_CMY-2, 8,143 (4.0%) contained fosA7, and 919 (0.4%) contained both resistance genes. The combination of both resistance genes (fosA7 and bla_CMY-2) was detected in 64% of the Heidelberg genomes and in a small proportion of various other serovars. A PCR method was developed to detect Salmonella Heidelberg in pure culture and chicken feces based on specific primers targeting genes conferring fosfomycin (fosA7) and third-generation cephalosporin (bla_CMY-2) resistance as well as the Salmonella-specific invA gene and the universal 16S rRNA genes. The PCR assay was specific and sensitive for bla_CMY-2 and fosA7 harboring Salmonella Heidelberg. However, some other Salmonella serovars containing these two resistance genes could also be detected by the developed PCR method.

Transcriptional profiling of Salmonella enterica serovar Enteritidis exposed to ethanolic extract of organic cranberry pomace

Non-typhoidal Salmonella enterica serovars continue to be an important food safety issue worldwide. Cranberry (Vaccinium macrocarpon Ait) fruits possess antimicrobial properties due to their various acids and phenolic compounds; however, the underlying mechanism of actions is poorly understood. We evaluated the effects of cranberry extracts on the growth rate of Salmonella enterica serovars Typhimurium, Enteritidis and Heidelberg and on the transcriptomic profile of Salmonella Enteritidis to gain insight into phenotypic and transcriptional changes induced by cranberry extracts on this pathogen. An ethanolic extract from cranberry pomaces (KCOH) and two of its sub-fractions, anthocyanins (CRFa20) and non-anthocyanin polyphenols (CRFp85), were used. The minimum inhibitory (MICs) and bactericidal (MBCs) concentrations of these fractions against tested pathogens were obtained using the broth micro-dilution method according to the Clinical Laboratory Standard Institute’s guidelines. Transcriptional profiles of S. Enteritidis grown in cation-adjusted Mueller-Hinton broth supplemented with or without 2 or 4 mg/ml of KCOH were compared by RNASeq to reveal gene modulations serving as markers for biological activity. The MIC and MBC values of KCOH were 8 and 16 mg/mL, respectively, against all tested S. enterica isolates. The MIC value was 4 mg/mL for both CRFa20 and CRFp85 sub-fractions, and a reduced MBC value was obtained for CRFp85 (4 mg/ml). Treatment of S. Enteritidis with KCOH revealed a concentration-dependent transcriptional signature. Compared to the control, 2 mg/ml of KCOH exposure resulted in 89 differentially expressed genes (DEGs), of which 53 and 36 were downregulated and upregulated, respectively. The upregulated genes included those involved in citrate metabolism, enterobactin synthesis and transport, and virulence. Exposure to 4 mg/ml KCOH led to the modulated expression of 376 genes, of which 233 were downregulated and 143 upregulated, which is 4.2 times more DEGs than from exposure to 2 mg/ml KCOH. The downregulated genes were related to flagellar motility, Salmonella Pathogenicity Island-1 (SPI-1), cell wall/membrane biogenesis, and transcription. Moreover, genes involved in energy production and conversion, carbohydrate transport and metabolism, and coenzyme transport and metabolism were upregulated during exposure to 4 mg/ml KCOH. Overall, 57 genes were differentially expressed (48 downregulated and 9 upregulated) in response to both concentrations. Both concentrations of KCOH downregulated expression of hilA, which is a major SPI-1 transcriptional regulator. This study provides information on the response of Salmonella exposed to cranberry extracts, which could be used in the control of this important foodborne pathogen.

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.

Egg Production in Poultry Farming Is Improved by Probiotic Bacteria

Antimicrobial resistance (AMR) is one of the most serious threats for human health in the near future. Livestock has played an important role in the appearance of antibiotic-resistant bacteria, intestinal dysbiosis in farming animals, or the spread of AMR among pathogenic bacteria of human concern. The development of alternatives like probiotics is focused on maintaining or improving production levels while diminishing these negative effects of antibiotics. To this end, we supplied the potential probiotic Enterococcus faecalis UGRA10 in the diet of laying hens at a final concentration of 10⁸ Colony Forming Units per gram (CFU/g) of fodder. Its effects have been analyzed by: (i) investigating the response of the ileum and caecum microbiome; and (ii) analyzing the outcome on eggs production. During the second half of the experimental period (40 to 76 days), hens fed E. faecalis UGRA10 maintained egg production, while control animals dropped egg production. Supplementation diet with E. faecalis UGRA10 significantly increased ileum and caecum bacterial diversity (higher bacterial operational taxonomic unit richness and Faith’s diversity index) of laying hens, with animals fed the same diet showing a higher similarity in microbial composition. These results point out to the beneficial effects of E. faecalis UGRA10 in egg production. Future experiments are necessary to unveil the underlying mechanisms that mediate the positive response of animals to this treatment.

Growth of Salmonella enterica Serovars Typhimurium and Enteritidis in Iron-Poor Media and in Meat: Role of Catecholate and Hydroxamate Siderophore Transporters

Enteritidis and Typhimurium are among the top Salmonella enterica serovars implicated in human salmonellosis worldwide. This study examined the individual and combined roles of catecholate-iron and hydroxamate-iron transporters in the survival in meat of Salmonella Enteritidis and Typhimurium. Catecholate-iron-III (Fe³⁺) and hydroxamate-Fe³⁺ transporter genes fepA, iroN, and fhuACDB were deleted in isolates of these serovars to generate single, double, and triple mutants. Growth rate in high- and low-iron media was compared among mutants, complements, and their wild-type parents. Susceptibility to 14 antibiotics, the ability to produce and utilize siderophores, and survival on cooked chicken breast were evaluated. In iron-poor liquid media, differences were observed between the growth characteristics of mutant Salmonella Enteritidis and Typhimurium. The double Δ iroNΔ fepA and the triple Δ fhuΔ iroNΔ fepA mutants of Salmonella Enteritidis exhibited prolonged lag phases (λ = 9.72 and 9.53 h) and a slow growth rate (μ_max = 0.35 and 0.25 h^-1) similar to that of its Δ tonB mutant (λ = 10.12 h and μ_max = 0.30 h^-1). In Salmonella Typhimurium, double Δ iroNΔ fepA and triple Δ fhuΔ iroNΔ fepA mutations induced a similar growth pattern as its Δ tonB mutant. Double deletions of fepA and iroN reduced the siderophore production and the use of enterobactin as an iron source. In the Δ iroNΔ fepA mutant, but not in Δ fhuΔ iroNΔ fepA, the ferrichrome or deferrioxamine promoted growth for both serovars, confirming the specific role of the FhuACDB system in the uptake and transport of hydroxamate Fe³⁺. Survival of the mutants was also evaluated in a meat assay, and no difference in survival was observed among the mutants compared with wild type. This study showed differences between serovars in the importance of catecholate-iron and hydroxamate-iron uptake on Salmonella growth in iron-restricted media. Data also confirmed that both Salmonella Enteritidis and Typhimurium are well equipped to survive on cooked chicken meat, offering a rich iron condition.

Antimicrobial Resistance in the Food Chain in the European Union

Consumers require safety foods but without losing enough supply and low prices. Food concerns about antimicrobial residues and antimicrobial-resistant (AMR) bacteria are not usually appropriately separated and could be perceived as the same problem. The monitoring of residues of antimicrobials in animal food is well established at different levels (farm, slaughterhouse, and industry), and it is preceded by the legislation of veterinary medicines where maximum residues limits are required for medicines to be used in food animal. Following the strategy of the World Health Organization, one of the proposed measures consists in controlling the use of critical antibiotics. The European Union surveillance program currently includes the animal species with the highest meat production (pigs, chickens, turkeys, and cattle) and the food derived from them, investigating antimicrobial resistance of zoonotic (Salmonella and Campylobacter) and indicator (Escherichia coli and enterococci) bacteria. AMR mechanisms encoded by genes have a greater impact on transfer than mutations. Sometimes these genes are found in mobile genetic elements such as plasmids, transposons, or integrons, capable of passing from one bacterium to another by horizontal transfer. It is important to know that depending on how the resistance mechanism is transferred, the power of dissemination is different. By vertical transfer of the resistance gene, whatever its origin, will be transmitted to the following generations. In the case of horizontal transfer, the resistance gene moves to neighboring bacteria and therefore the range of resistance can be much greater.

Effect of an organic acids based feed additive and enrofloxacin on the prevalence of antibiotic-resistant E. coli in cecum of broilers

Increasing antibiotic resistance is a major public health concern. Fluoroquinolones are used to treat and prevent poultry diseases worldwide. Fluoroquinolone resistance rates are high in their countries of use. The aim of this study was to evaluate the effect of an acids-based feed additive, as well as fluoroquinolone antibiotics, on the prevalence of antibiotic-resistant E. coli. A total of 480 broiler chickens (Ross 308) were randomly assigned to 3 treatments: a control group receiving a basal diet; a group receiving a feed additive (FA) based on formic acid, acetic acid and propionic acid; and an antibiotic enrofloxacin (AB) group given the same diet, but supplemented with enrofloxacin in water. A pooled fecal sample of one-day-old chicks was collected upon arrival at the experimental farm. On d 17 and d 38 of the trial, cecal samples from each of the 8 pens were taken, and the count of E. coli and antibiotic-resistant E. coli was determined.The results of the present study show a high prevalence of antibiotic-resistant E. coli in one-day-old chicks. Supplementation of the diet with FA and treatment of broilers with AB did not have a significant influence on the total number of E. coli in the cecal content on d 17 and d 38 of the trial. Supplementation with FA contributed to better growth performance and to a significant decrease (P ≤ 0.05) in E. coli resistant to ampicillin and tetracycline compared to the control and AB groups, as well as to a decrease (P ≤ 0.05) in sulfamethoxazole and ciprofloxacin-resistant E. coli compared to the AB group. Treatment with AB increased (P ≤ 0.05) the average daily weight compared to the control group and increased (P ≤ 0.05) the number of E. coli resistant to ciprofloxacin, streptomycin, sulfamethoxazole and tetracycline; it also decreased (P ≤ 0.05) the number of E. coli resistant to cefotaxime and extended spectrum beta-lactamase- (ESBL-) producing E. coli in the ceca of broilers.

Antibiotic resistance, serogroups, virulence genes, and phylogenetic groups of Escherichia coli isolated from yaks with diarrhea in Qinghai Plateau, China

Background

Ruminants serve as one of the most important reservoirs for pathogenic Escherichia coli. Infection with E. coli, a foodborne enteropathogen, can lead to asymptomatic infections that can cause life-threatening complications in humans. Therefore, from a clinical and human health perspective, it is important to know which virulence genes, phylogenetic groups, serogroups, and antibiotic resistance patterns are present in E. coli strains in yaks with diarrheic infections.

Methods

Two-hundred and ninety-two rectal swabs were collected from diarrheic yaks in Qinghai Plateau, China. The antimicrobial sensitivity of each resulting isolate was evaluated according to the disk diffusion method, and different PCR assays were performed for the detection of virulence genes and different phylogroups. Additionally, strains were allocated to different serogroups based on the presence of O antigen via the slide agglutination method.

Results

Among the E. coli isolates tested, most of the isolates were multidrug resistant (97%) and harbored at least one virulence gene (100%). We observed ten virulence genes (sfa, eaeA, cnf1, etrA, papC, hlyA, aer, faeG, rfc, and sepA), of which sfa was the most commonly found (96.9%). Significant positive associations between some resistance phenotypes and virulence genes were observed (P < 0.05, OR > 1). The majority of the E. coli isolates belonged to phylogroup A (79.5%), and the others belonged to phylogroups B1 (7.5%), D (4.1%), B2 (5.8%), and F (0.7%). Among all the E. coli strains tested, serogroups O₉₁ and O₁₄₅ were the most prevalent, accounting for 15.4 and 14.4%, respectively.

Conclusions

Our results suggest that yaks with diarrhea serve as a reservoir of pathogenic E. coli carrying various virulence genes and resistance phenotypes. Therefore, clinicians and relevant authorities must ensure the regulatory use of antimicrobial agents and prevent the spread of these organisms through manure to farm workers and food-processing plants.

Occurrence and molecular characteristics of antimicrobial resistance of Escherichia coli from broilers, pigs and meat products in Thailand and Cambodia provinces

Nine hundred and forty-one samples were collected in Sa Keao, Thailand (n = 554) and Banteay Meanchey, Cambodia (n = 387) from July 2014 to January 2015. A total of 667 Escherichia coli isolates (381 isolates from Sa Keao and 286 isolates from Banteay Meanchey) were obtained and examined for antimicrobial susceptibility, class 1 integrons, ESBL genes and horizontal transfer of resistance determinants. Prevalence of E. coli in pig and broiler carcass samples from slaughterhouses and fresh markets was 36-85% in Sa Keao and 11-69% in Banteay Meanchey. The majority of these isolates were multidrug resistant (75.3%). Class 1 integrons were common in both Thai (47%) and Cambodian (62%) isolates, of which four resistance gene cassette arrays including aadA1, dfrA1-aadA1, dfrA12-aadA2 and aadA2-linF were identified. Class 1 integrons in two broiler isolates from Sa Keao (dfrA12-aadA2) and one broiler isolate from Banteay Meanchey (dfrA1-aadA1) were horizontally transferable. Sixteen isolates were confirmed to be ESBL-producing strains with ESBL gene blaCTX-M-15 , broad spectrum β-lactamase gene blaTEM-1 and the AmpC gene blaCMY-2 being detected. The blaTEM-1 gene was most prevalent and located on a conjugative plasmid.

Accuracy of the evaluation method for alkaline agents' bactericidal efficacies in solid, and the required time of bacterial inactivation

An alkaline agent, namely food additive grade calcium hydroxide (FdCa (OH)2) in the powder form, was evaluated for its bactericidal efficacies in chicken feces at pH 13. The point for this evaluation was neutralization of the alkaline agent's pH at the time of bacterial recovery, since otherwise the results are substantially misleading. Without neutralization of the FdCa (OH)2 pH, the spiked bacteria were killed within min at the time of recovery in aqueous phase, but not in the solid form in feces, hence, it has been demonstrated that when bacteria were in solid, it took longer time than in liquid for the alkaline agent to inactivate them down to the acceptable level (≥3 log10 CFU/ml).

Antibiotic susceptibility pattern and analysis of plasmid profiles of Pseudomonas aeruginosa from human, animal and plant sources

Multidrug resistant organisms (MDROs) constitute a major public health threat globally. Clinical isolates of Pseudomonas aeruginosa remains one of the most studied MDROs however there is paucity of information regarding the susceptibility of its animal and plants isolates to antipseudomonas drug in Nigeria. From a total of 252 samples consisting of plants, animals and clinical samples, 54, 24 and 22 P. aeruginosa were isolated from vegetables, animals and clinical sources respectively. All the isolates were identified by standard biochemical methods. Antimicrobial susceptibility testing (AST) of the 100 P. aeruginosa isolates against 7 antipseudomonal drugs was carried out by disk diffusion method, the phenotypic detection of ESBL was done by double disk synergy test (DDST) while plasmid extraction on 20 selected isolates based on their resistance to 2 or more classes of antibiotics was carried out by alkaline lysis method and analysed with Lambda DNA/Hind lll marker respectively. The AST results revealed highest resistance of 91 and 55 % to ceftazidime and carbenicillin respectively while highest susceptibilities of 99 % for piperacillin–tazobactam and imipenem were recorded in overall assay. Fifteen out of 100 isolates specifically (10) from vegetables, (3) clinical and (2) poultry isolates showed synergy towards the beta-lactamase inhibitor indicating production of ESBL by DDST method. Detection of plasmids was among vegetable (n = 4), poultry (n = 4), cow (n = 3) and clinical isolates (n = 1). Plasmid profile for the selected isolates revealed 6 of the strains had one plasmids each while 5 strains possessed 2–4 plasmids and 1 strain had 5 plasmids. The sizes of the plasmid range from <1 to ≥23kbp. Detection of ESBL and Plasmids among the investigated isolates is suggestive of multiple interplay of resistance mechanism among the isolates. Plants and animal isolates of P. aeruginosa harbouring multiple mechanisms of resistance is of concern due to the danger it poses on the public health.

Genomic Microbial Epidemiology Is Needed to Comprehend the Global Problem of Antibiotic Resistance and to Improve Pathogen Diagnosis

Contamination of waste effluent from hospitals and intensive food animal production with antimicrobial residues is an immense global problem. Antimicrobial residues exert selection pressures that influence the acquisition of antimicrobial resistance and virulence genes in diverse microbial populations. Despite these concerns there is only a limited understanding of how antimicrobial residues contribute to the global problem of antimicrobial resistance. Furthermore, rapid detection of emerging bacterial pathogens and strains with resistance to more than one antibiotic class remains a challenge. A comprehensive, sequence-based genomic epidemiological surveillance model that captures essential microbial metadata is needed, both to improve surveillance for antimicrobial resistance and to monitor pathogen evolution. Escherichia coli is an important pathogen causing both intestinal [intestinal pathogenic E. coli (IPEC)] and extraintestinal [extraintestinal pathogenic E. coli (ExPEC)] disease in humans and food animals. ExPEC are the most frequently isolated Gram negative pathogen affecting human health, linked to food production practices and are often resistant to multiple antibiotics. Cattle are a known reservoir of IPEC but they are not recognized as a source of ExPEC that impact human or animal health. In contrast, poultry are a recognized source of multiple antibiotic resistant ExPEC, while swine have received comparatively less attention in this regard. Here, we review what is known about ExPEC in swine and how pig production contributes to the problem of antibiotic resistance.

Antimicrobial Resistance of Escherichia fergusonii Isolated from Broiler Chickens

The objective of this study was to investigate the antibiotic resistance of Escherichia fergusonii isolated from commercial broiler chicken farms. A total of 245 isolates from cloacal and cecal samples of 28- to 36-day-old chickens were collected from 32 farms. Isolates were identified using PCR, and their susceptibility to 16 antibiotics was determined by disk diffusion assay. All isolates were susceptible to meropenem, amikacin, and ciprofloxacin. The most common resistances were against ampicillin (75.1%), streptomycin (62.9%), and tetracycline (57.1%). Of the 184 ampicillin-resistant isolates, 127 were investigated using a DNA microarray carrying 75 probes for antibiotic resistance genetic determinants. Of these 127 isolates, the β-lactamase blaCMY2, blaTEM, blaACT, blaSHV, and blaCTX-M-15 genes were detected in 120 (94.5%), 31 (24.4%), 8 (6.3%), 6 (4.7%), and 4 (3.2%) isolates, respectively. Other detected genes included those conferring resistance to aminoglycosides (aadA1, strA, strB), trimethoprims (dfrV, dfrA1), tetracyclines (tetA, tetB, tetC, tetE), and sulfonamides (sul1, sul2). Class 1 integron was found in 35 (27.6%) of the ampicillin-resistant isolates. However, our data showed that the tested E. fergusonii did not carry any carbapenemase blaOXA genes. Pulsed-field gel electrophoresis revealed that the selected ampicillin-resistant E. fergusonii isolates were genetically diverse. The present study indicates that the monitoring of antimicrobial-resistant bacteria should include enteric bacteria such as E. fergusonii, which could be a reservoir of antibiotic resistance genes. The detection of isolates harboring extended-spectrum β-lactamase genes, particularly blaCTX-M-15, in this work suggests that further investigations on the occurrence of such genes in broilers are warranted.

Inactivation of bacteria on surfaces by sprayed slightly acidic hypochlorous acid water: in vitro experiments

The capacity of slightly acidic hypochlorous acid water (SAHW), in both liquid and spray form, to inactivate bacteria was evaluated as a potential candidate for biosecurity enhancement in poultry production. SAHW (containing 50 or 100 ppm chlorine, pH 6) was able to inactivate Escherichia coli and Salmonella Infantis in liquid to below detectable levels (≤2.6 log10 CFU/ml) within 5 sec of exposure. In addition, SAHW antibacterial capacity was evaluated by spraying it using a nebulizer into a box containing these bacteria, which were present on the surfaces of glass plates and rayon sheets. SAHW was able to inactivate both bacterial species on the glass plates (dry condition) and rayon sheets within 5 min spraying and 5 min contact times, with the exception of 50 ppm SAHW on the rayon sheets. Furthermore, a corrosivity test determined that SAHW does not corrode metallic objects, even at the longest exposure times (83 days). Our findings demonstrate that SAHW is a good candidate for biosecurity enhancement in the poultry industry. Spraying it on the surfaces of objects, eggshells, egg incubators and transport cages could reduce the chances of contamination and disease transmission. These results augment previous findings demonstrating the competence of SAHW as an anti-viral disinfectant.

Identification and prevalence of tetracycline resistance in enterococci isolated from poultry in Ilishan, Ogun State, Nigeria

Background:

Tetracycline is one of the most frequently used antibiotics in Nigeria both for human and animal infections because of its cheapness and ready availability. The use of tetracycline in animal husbandry could lead to horizontal transfer of tet genes from poultry to human through the gut microbiota, especially enterococci. Therefore, this study is designed to identify different enterococcal species from poultry feces in selected farms in Ilishan, Ogun State, Nigeria, determine the prevalence of tetracycline resistance/genes and presence of IS256 in enterococcal strains.

Materials and Methods:

Enterococci strains were isolated from 100 fresh chicken fecal samples collected from seven local poultry farms in Ilishan, Ogun State, Nigeria. The strains were identified by partial sequencing of 16S rRNA genes. Antibiotic susceptibility of the isolates to vancomycin, erythromycin, tetracycline, gentamicin, amoxycillin/claulanate, and of loxacin were performed by disc diffusion method. Detection of tet, erm, and van genes and IS256 insertion element were done by polymerase chain reaction amplification.

Results:

Sixty enterococci spp. were identified comprising of Enterococcus faecalis 33 (55%), Enterococcus casseliflavus 21 (35%), and Enterococcus gallinarium 6 (10%). All the isolates were resistant to erythromycin (100%), followed by tetracycline (81.67%), amoxicillin/clavulanic acid (73.33%), ofloxacin (68.33%), vancomycin (65%), and gentamicin (20%). None of the enterococcal spp. harbored the van and erm genes while tet(M) was detected among 23% isolates and is distributed mostly among E. casseliflavus. IS256 elements were detected only in 33% of E. casseliflavus that were also positive for tet(M) gene.

Conclusion:

This study provides evidence that tetracycline resistance gene is present in the studied poultry farms in Ilishan, Ogun State, Nigeria and underscores the need for strict regulation on tetracycline usage in poultry farming in the studied location and consequently Nigeria.

Genomic Comparison of Non-Typhoidal Salmonella enterica Serovars Typhimurium, Enteritidis, Heidelberg, Hadar and Kentucky Isolates from Broiler Chickens

BACKGROUND

Non-typhoidal Salmonella enterica serovars, associated with different foods including poultry products, are important causes of bacterial gastroenteritis worldwide. The colonization of the chicken gut by S. enterica could result in the contamination of the environment and food chain. The aim of this study was to compare the genomes of 25 S. enterica serovars isolated from broiler chicken farms to assess their intra- and inter-genetic variability, with a focus on virulence and antibiotic resistance characteristics.

METHODOLOGY/PRINCIPAL FINDING

The genomes of 25 S. enterica isolates covering five serovars (ten Typhimurium including three monophasic 4,[5],12:i:, four Enteritidis, three Hadar, four Heidelberg and four Kentucky) were sequenced. Most serovars were clustered in strongly supported phylogenetic clades, except for isolates of serovar Enteritidis that were scattered throughout the tree. Plasmids of varying sizes were detected in several isolates independently of serovars. Genes associated with the IncF plasmid and the IncI1 plasmid were identified in twelve and four isolates, respectively, while genes associated with the IncQ plasmid were found in one isolate. The presence of numerous genes associated with Salmonella pathogenicity islands (SPIs) was also confirmed. Components of the type III and IV secretion systems (T3SS and T4SS) varied in different isolates, which could explain in part, differences of their pathogenicity in humans and/or persistence in broilers. Conserved clusters of genes in the T3SS were detected that could be used in designing effective strategies (diagnostic, vaccination or treatments) to combat Salmonella. Antibiotic resistance genes (CMY, aadA, ampC, florR, sul1, sulI, tetAB, and srtA) and class I integrons were detected in resistant isolates while all isolates carried multidrug efflux pump systems regardless of their antibiotic susceptibility profile.

CONCLUSIONS/SIGNIFICANCE

This study showed that the predominant Salmonella serovars in broiler chickens harbor genes encoding adhesins, flagellar proteins, T3SS, iron acquisition systems, and antibiotic and metal resistance genes that may explain their pathogenicity, colonization ability and persistence in chicken. The existence of mobile genetic elements indicates that isolates from a given serovar could acquire and transfer genetic material. Conserved genes in the T3SS and T4SS that we have identified are promising candidates for identification of diagnostic, antimicrobial or vaccine targets for the control of Salmonella in broiler chickens.

Potential risk for drug resistance globalization at the Hajj

Antibiotics were once considered the miracle cure for infectious diseases. The tragedy would be the loss of these miracles as we witness increased antibiotic resistance throughout the world. One of the concerns during mass gatherings is the transmission of antibiotic resistance. Hajj is one of the most common recurring mass gatherings, attracting millions of people from around the world. The transmission of drug-resistant organisms during the Hajj is not well described. In the current review, we summarize the available literature on the transmission and acquisition of antibiotic resistance during the Hajj and present possible solutions.

IncA/C plasmids: An emerging threat to human and animal health?

Incompatibility group IncA/C plasmids are large, low copy, theta-replicating plasmids that have been described in the literature for over 40 years. However, they have only recently been intensively studied on the genomic level because of their associations with the emergence of multidrug resistance in enteric pathogens of humans and animals. These plasmids are unique among other enterobacterial plasmids in many aspects, including their modular structure and gene content. While the IncA/C plasmid genome structure has now been well defined, many questions remain pertaining to their basic biological mechanisms of dissemination and regulation. Here, we discuss the history of IncA/C plasmids in light of our recent understanding of their population distribution, genomics, and effects on host bacteria.

Antibiotics in Canadian poultry productions and anticipated alternatives

The use of antibiotics in food-producing animals has significantly increased animal health by lowering mortality and the incidence of diseases. Antibiotics also have largely contributed to increase productivity of farms. However, antibiotic usage in general and relevance of non-therapeutic antibiotics (growth promoters) in feed need to be reevaluated especially because bacterial pathogens of humans and animals have developed and shared a variety of antibiotic resistance mechanisms that can easily be spread within microbial communities. In Canada, poultry production involves more than 2600 regulated chicken producers who have access to several antibiotics approved as feed additives for poultry. Feed recipes and mixtures vary greatly geographically and from one farm to another, making links between use of a specific antibiotic feed additive and production yields or selection of specific antibiotic-resistant bacteria difficult to establish. Many on-farm studies have revealed the widespread presence of antibiotic-resistant bacteria in broiler chickens. While some reports linked the presence of antibiotic-resistant organisms to the use of feed supplemented with antibiotics, no recent studies could clearly demonstrate the benefit of antimicrobial growth promoters on performance and production yields. With modern biosecurity and hygienic practices, there is a genuine concern that intensive utilization of antibiotics or use of antimicrobial growth promoters in feed might no longer be useful. Public pressure and concerns about food and environmental safety (antibiotic residues, antibiotic-resistant pathogens) have driven researchers to actively look for alternatives to antibiotics. Some of the alternatives include pre- and probiotics, organic acids and essential oils. We will describe here the properties of some bioactive molecules, like those found in cranberry, which have shown interesting polyvalent antibacterial and immuno-stimulatory activities.

Centrifugal spreader mass and nutrients distribution patterns for application of fresh and aged poultry litter

A spin-type centrifugal spreader was evaluated using fresh and aged poultry litter upon dry mass, product nitrogen (N), phosphorus (P) and potassium (K), incubation study soil available N and particle size distribution patterns. Relative to the aged litter (37% moisture content), the fresh litter (17% moisture content) had greater <1.00 mm particle size fraction weights and atmospheric particulate was launched, which posed as a potential fallout to adjacent fields, waterways and residences. Relative to the aged litter, the broadcast fresh litter resulted in higher coefficients of variation (CV) over its transverse distance, a narrower calculated space distance between passes for uniform spread and lower soil available N concentrations. For nitrogen application over the broadcast transverse distance the fresh litter displayed a high R(2) best fit 4th order polynomial distribution pattern, while the aged litter showed high R(2) best fit 6th order polynomial distribution pattern. A soil incubation study of the fresh and aged broadcast litter resulted in a more variable or lower R(2) best fit 2nd order polynomial distribution pattern. For both the fresh and aged litter, the calculated distance between passes to achieve a uniform mass distribution was greater than that required for the broadcast of soil available N. For the fresh litter, the soil available N and litter P concentration levels strongly correlated (relatively high p and R(2) values) with the <1.00 mm fraction weight, while for the aged litter this relationship was not as significant. In addition to reducing the health risk (i.e. pathogens, antibiotic residues and resistant bacteria) and/or environment issues (particulate fallout onto waterways, adjacent fields and/or residences) our study mass, particulate and N distribution patterns results suggest that poultry litter should be allowed to age before broadcast application is attempted.

Escherichia fergusonii

Escherichia fergusonii was introduced in the genus Escherichia almost 65 years later than Escherichia coli after which the genus was named. From then (1985) onwards mainly case reports on E. fergusonii associated with disease in individuals of veterinary or human origin have been reported and only very few more extensive studies became available. This has resulted in very fragmented knowledge on this organism. The aim of this manuscript is to give an overview of what is known on E. fergusonii today and to stimulate more research on this organism so that better insight can be obtained in the role that E. fergusonii plays in human and animal infections.

Duplex PCR methods for the molecular detection of Escherichia fergusonii isolates from broiler chickens

Escherichia fergusonii is an emerging pathogen that has been isolated from a wide range of infections in animals and humans. Primers targeting specific genes, including yliE (encoding a conserved hypothetical protein of the cellulose synthase and regulator of cellulose synthase island), EFER_1569 (encoding a hypothetical protein, putative transcriptional activator for multiple antibiotic resistance), and EFER_3126 (encoding a putative triphosphoribosyl-dephospho-coenzyme A [CoA]), were designed for the detection of E. fergusonii by conventional and real-time PCR methods. Primers were screened by in silico PCR against 489 bacterial genomic sequences and by both PCR methods on 55 reference and field strains. Both methods were specific and sensitive for E. fergusonii, showing amplification only for this bacterium. Conventional PCR required a minimum bacterial concentration of approximately 10(2) CFU/ml, while real-time PCR required a minimum of 0.3 pg of DNA for consistent detection. Standard curves showed an efficiency of 98.5%, with an R(2) value of 0.99 for the real-time PCR assay. Cecal and cloacal contents from 580 chickens were sampled from broiler farms located in the Fraser Valley (British Columbia, Canada). Presumptive E. fergusonii isolates were recovered by enrichment and plating on differential and selective media. Of 301 total presumptive isolates, 140 (46.5%) were identified as E. fergusonii by biochemical profiling with the API 20E system and 268 (89.0%) using PCR methods. E. fergusonii detection directly from cecal and cloacal samples without preenrichment was achieved with both PCR methods. Hence, the PCR methods developed in this work significantly improve the detection of E. fergusonii.

Antibiotic resistance and diversity of Salmonella enterica serovars associated with broiler chickens

The objective of this study was to analyze the antibiotic resistance phenotype and genotype of Salmonella isolated from broiler production facilities. A total of 193 Salmonella isolates recovered from commercial farms in British Columbia, Canada, were evaluated. Susceptibility to antibiotics was determined with the Sensititre system. Virulence and antibiotic resistance genes were detected by PCR assay. Genetic diversity was determined by pulse-field gel electrophoresis (PFGE) typing. Seventeen serovars of Salmonella were identified. The most prevalent Salmonella serovars were Kentucky (29.0% of isolates), Typhimurium (23.8%), Enteritidis (13.5%), and Hadar (11.9%); serovars Heidelberg, Brandenburg, and Thompson were identified in 7.7, 4.1, and 3.6% of isolates, respectively. More than 43% of the isolates were simultaneously resistant to ampicillin, amoxicillin-clavulanic acid, ceftiofur, cefoxitim, and ceftriaxone. This β-lactam resistance pattern was observed in 33 (58.9%) of the Salmonella Kentucky isolates; 2 of these isolates were also resistant to chloramphenicol, streptomycin, sulfisoxazole, and tetracycline. Genes associated with resistance to aminoglycosides (aadA1, aadA2, and strA), β-lactams (blaCMY-2, blaSHV, and blaTEM), tetracycline (tetA and tetB), and sulfonamide (sul1) were detected among corresponding resistant isolates. The invasin gene (invA) and the Salmonella plasmid virulence gene (spvC) were found in 97.9 and 25.9% of the isolates, respectively, with 33 (71.7%) of the 46 Salmonella Typhimurium isolates and 17 (65.4%) of the 26 Salmonella Enteritidis isolates carrying both invA and spvC. PGFE typing revealed that the antibiotic-resistant serovars were genetically diverse. These data confirm that broiler chickens can be colonized by genetically diverse antibiotic-resistant Salmonella isolates harboring virulence determinants. The presence of such strains is highly relevant to food safety and public health.

Effect of 3',5'-cyclic diguanylic acid in a broiler Clostridium perfringens infection model

In an effort to explore strategies to control Clostridium perfringens, we investigated the synergistic effect of a ubiquitous bacterial second messenger 3',5'-cyclic diguanylic acid (c-di-GMP) with penicillin G in a broiler challenge model. All chicks were inoculated in the crop by gavage on d 14, 15, and 16 with a mixture of 4 C. perfringens strains. Birds were treated with saline (control group) or 20 nmol of c-di-GMP by gavage or intramuscularly (IM) on d 24, all in conjunction with penicillin G in water for 5 d. Weekly samplings of ceca and ileum were performed on d 21 to 35 for C. perfringens and Lactobacillus enumeration. On d 35 of age, the IM treatment significantly (P < 0.05) reduced C. perfringens in the ceca, suggesting possible synergistic activity between penicillin G and c-di-GMP against C. perfringens in broiler ceca. Moreover, analysis of ceca DNA for the presence of a series of C. perfringens virulence genes showed a prevalence of 30% for the Clostridium perfringens alpha-toxin gene (cpa) from d 21 to 35 in the IM-treated group, whereas the occurrence of the cpa gene increased from 10 to 60% in the other 2 groups (control and gavage) from d 21 to 35. Detection of β-lactamase genes (blaCMY-2, blaSHV, and blaTEM) indicative of gram-negative bacteria in the same samples from d 21 to 35 did not show significant treatment effects. Amplified fragment-length polymorphism showed a predominant 92% similarity between the ceca of 21-d-old control birds and the 35-d-old IM-treated c-di-GMP group. This suggests that c-di-GMP IM treatment might be effective at restoring the normal microflora of the host on d 35 after being challenged by C. perfringens. Our results suggest that c-di-GMP can reduce the colonization of C. perfringens in the gut without increasing the selection pressure for some β-lactamase genes or altering the commensal bacterial population.

In vitro and in vivo antibacterial activities of cranberry press cake extracts alone or in combination with β-lactams against Staphylococcus aureus

BACKGROUND

Cranberry fruits possess many biological activities partly due to their various phenolic compounds; however the underlying modes of action are poorly understood. We studied the effect of cranberry fruit extracts on the gene expression of Staphylococcus aureus to identify specific cellular processes involved in the antibacterial action.

METHODS

Transcriptional profiles of four S. aureus strains grown in broth supplemented or not with 2 mg/ml of a commercial cranberry preparation (Nutricran®90) were compared using DNA arrays to reveal gene modulations serving as markers for biological activity. Ethanol extracted pressed cakes from fresh fruits also produced various fractions and their effects on marker genes were demonstrated by qPCR. Minimal inhibitory concentrations (MICs) of the most effective cranberry fraction (FC111) were determined against multiple S. aureus strains and drug interactions with β-lactam antibiotics were also evaluated. Incorporation assays with [(3)H]-radiolabeled precursors were performed to evaluate the effect of FC111 on DNA, RNA, peptidoglycan (PG) and protein biosynthesis.

RESULTS

Treatment of S. aureus with Nutricran®90 or FC111 revealed a transcriptional signature typical of PG-acting antibiotics (up-regulation of genes vraR/S, murZ, lytM, pbp2, sgtB, fmt). The effect of FC111 on PG was confirmed by the marked inhibition of incorporation of D-[(3)H]alanine. The combination of β-lactams and FC111 in checkerboard assays revealed a synergistic activity against S. aureus including strain MRSA COL, which showed a 512-fold drop of amoxicillin MIC in the presence of FC111 at MIC/8. Finally, a therapeutic proof of concept was established in a mouse mastitis model of infection. S. aureus-infected mammary glands were treated with amoxicillin, FC111 or a combination of both; only the combination significantly reduced bacterial counts from infected glands (P<0.05) compared to the untreated mice.

CONCLUSIONS

The cranberry fraction FC111 affects PG synthesis of S. aureus and acts in synergy with β-lactam antibiotics. Such a fraction easily obtained from poorly exploited press-cake residues, may find interesting applications in the agri-food sector and help reduce antibiotic usage in animal food production.