Microbial contamination pathways in a poultry abattoir provided clues on the distribution and persistence of Arcobacter spp.

The consumption of contaminated poultry meat is a significant threat for public health, as it implicates in foodborne pathogen infections, such as those caused by Arcobacter. The mitigation of clinical cases requires the understanding of contamination pathways in each food process and the characterization of resident microbiota in the productive environments, so that targeted sanitizing procedures can be effectively implemented. Nowadays these investigations can benefit from the complementary and thoughtful use of culture- and omics-based analyses, although their application in situ is still limited. Therefore, the 16S-rRNA gene-based sequencing of total DNA and the targeted isolation of Arcobacter spp. through enrichment were performed to reconstruct the environmental contamination pathways within a poultry abattoir, as well as the dynamics and distribution of this emerging pathogen. To that scope, broiler's neck skin and caeca have been sampled during processing, while environmental swabs were collected from surfaces after cleaning and sanitizing. Metataxonomic survey highlighted a negligible impact of fecal contamination and a major role of broiler's skin in determining the composition of the resident abattoir microbiota. The introduction of Arcobacter spp. in the environment was mainly conveyed by this source rather than the intestinal content. Arcobacter butzleri represented one of the most abundant species and was extensively detected in the abattoir by both metataxonomic and enrichment methods, showing higher prevalence than other more thermophilic Campylobacterota. In particular, Arcobacter spp. was recovered viable in the plucking sector with high frequency, despite the adequacy of the sanitizing procedure.IMPORTANCEOur findings have emphasized the persistence of Arcobacter spp. in a modern poultry abattoir and its establishment as part of the resident microbiota in specific environmental niches. Although the responses provided here are not conclusive for the identification of the primary source of contamination, this biogeographic assessment underscores the importance of monitoring Arcobacter spp. from the early stages of the production chain with the integrative support of metataxonomic analysis. Through such combined detection approaches, the presence of this pathogen could be soon regarded as hallmark indicator of food safety and quality in poultry slaughtering.

Accumulation of resistance genes in Salmonella Typhimurium transmitted between poultry and dairy farms increases the risk to public health.

Salmonella Typhimurium is a zoonotic pathogen that poses a major threat to public health. This generalist serotype can be found in many hosts and the environment where varying selection pressures may result in the accumulation of antimicrobial resistance determinants. However, the transmission of this serotype between food-producing hosts, specifically between poultry layer flocks and nearby dairy herds, was never demonstrated. We investigated an outbreak at a dairy in Israel to determine the role of nearby poultry houses to be sources of infection. The 2-month outbreak resulted in a 47% mortality rate among 15 calves born in that period. Routine treatment of fluid therapy, a nonsteroidal anti-inflammatory, and cefquinome was ineffective, and control was achieved by the introduction of vaccination of dry cows against Salmonella (Bovivac S, MSD Animal Health) and a strict colostrum regime. Whole genome sequencing and antimicrobial sensitivity tests were performed on S. Typhimurium strains isolated from the dairy (n = 4) and strains recovered from poultry layer farms (n = 10). We identified acquired antimicrobial-resistant genes, including the blaCTX-M-55 gene, conferring resistance to extended-spectrum cephalosporins, which was exclusive to dairy isolates. Genetic similarity with less than five single nucleotide polymorphism differences between dairy and poultry strains suggested a transmission link. This investigation highlights the severe impact of S. Typhimurium on dairy farms and the transmission risk from nearby poultry farms. The accumulation of potentially transferable genes conferring resistance to critically important antimicrobials underscores the increased public health risk associated with S. Typhimurium circulation between animal hosts.IMPORTANCESalmonella Typhimurium is one of the major causes of food-borne illness globally. Infections may result in severe invasive disease, in which antimicrobial treatment is warranted. Therefore, the emergence of multi-drug-resistant strains poses a significant challenge to successful treatment and is considered one of the major threats to global health. S. Typhimurium can be found in a variety of animal hosts and environments; however, its transmission between food-producing animals, specifically poultry layers flocks and dairy herds, was never studied. Here, we demonstrate the transmission of the pathogen from poultry to a nearby dairy farm. Alarmingly, the multi-drug-resistant strains collected during the outbreak in the dairy had acquired resistance to extended-spectrum cephalosporins, antibiotics critically important in treating Salmonellosis in humans. The findings of the study emphasize the increased risk to public health posed by zoonotic pathogens' circulation between animal hosts.

Potential of ZnO nanoparticles for multi-drug resistant Escherichia coli having CRISPR-Cas from poultry market in Lahore.

BACKGROUND AND OBJECTIVES: Apart from known factors such as irrational use of antibiotics and horizontal gene transfer, it is now reported that clustered regularly interspaced short palindromic repeats (CRISPR) are also associated with increased antimicrobial resistance. Hence, it is critical to explore alternatives to antibiotics to control economic losses. Therefore, the present study aimed to determine not only the association of CRISPR-Cas system with antibiotic resistance but also the potential of Zinc Oxide nanoparticles (ZnO-NPs) for avian pathogenic Escherichia coli (APEC) isolated from poultry market Lahore. MATERIALS AND METHODS: Samples (n = 100) were collected from live bird markets of Lahore, and isolates were confirmed as Escherichia coli (E. coli) using the Remel One fast kit, and APEC was identified using PCR. The antibiotic resistance pattern in APEC was determined using the minimum inhibitory concentration (MIC), followed by genotypic confirmation of antibiotic-resistant genes using the PCR. The CRISPR-Cas system was also identified in multidrug-resistant (MDR) isolates, and its association with antibiotics was determined using qRT-PCR. The potential of ZnO-NPs was evaluated for multidrug-resistant (MDR) isolates by MIC. RESULTS: All isolates of APEC were resistant to nalidixic acid, whereas 95% were resistant to chloramphenicol and 89% were resistant to streptomycin. Nineteen MDR APEC were found in the present study and the CRISPR-Cas system was detected in all of these MDR isolates. In addition, an increased expression of CRISPR-related genes was observed in the standard strain and MDR isolates of APEC. ZnO-NPs inhibited the growth of resistant isolates. CONCLUSIONS: The findings showed the presence of the CRISPR-Cas system in MDR strains of APEC, along with the potential of ZnO-NPs for a possible solution to proceed. This highlights the importance of regulating antimicrobial resistance in poultry to reduce potential health consequences.

The activity of hyaD contributed to the virulence of avian Pasteurella multocida.

Fowl cholera is an infectious disease that affects both poultry and wild birds, characterized by hemorrhagic and septicemic symptoms, caused by Pasteurella multocida (P. multocida), and leading to substantial economic losses in the poultry sector. The development of genetic engineering vaccines against avian P. multocida encountered early-stage challenges due to the limited availability of effective gene editing tools. Presently, NgAgoDM-enhanced homologous recombination stands as a potent technique for achieving efficient gene knockout in avian P. multocida. Hence, this study employed NgAgoDM-enhanced homologous recombination to target and knockout hyaE (239-359aa), hyaD, hexABC, and hexD, denoted as ΔhyaE (239-359aa), ΔhyaD, ΔhexABC, and ΔhexD, respectively. Additionally, we generated a hyaD recovery strain with two point mutations, designated as mhyaD. Thus, this study systematically examined the impact of capsular synthetic gene clusters on the pathogenicity of P. multocida. Moreover, the study demonstrated the critical role of hyaD activity in the virulence of avian P. multocida. This study offers novel insights for enhancing attenuated vaccines further.

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

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

In-silico insights of ESBL variants and tracking the probable sources of ESBL-producing Escherichia coli in a small-scale poultry farm.

Commercial broiler farms face challenges of extended spectrum beta-lactamase (ESBL)-producing Escherichia coli transmitted from both vertical and horizontal routes. Understanding the dynamics of ESBL-E. coli transmission in compromised biosecurity settings of small-scale rural poultry farms is essential. This study aimed to elucidate the probable transmission pathways of ESBL-E. coli in such settings, employing phylogenetic analysis and molecular docking simulations to explore the catalytic properties of ß-lactamase variants. Sampling was conducted on a small-scale poultry farm in West Bengal, India, collecting 120 samples at three intervals during the broiler production cycle. E. coli isolates underwent resistance testing against eight antimicrobials, with confirmation of ESBL production. Genotypic analysis of ESBL genes and sequencing were performed, alongside molecular docking analyses and phylogenetic comparisons with publicly available sequences. Among 173 E. coli isolates, varying resistance profiles were observed, with complete resistance to cefixime and high resistance to amoxicillin and tetracycline. The incidence of ESBL-E. coli fluctuated over the production cycle, with dynamic changes in the prevalence of blaCTX-M-type and blaSHV-type genes. Phylogenetic analysis indicated partial clonal relationships with human clinical strains and poultry strains from the Indian subcontinent. Molecular docking confirmed the catalytic efficiencies of these ESBL variants. The study highlights probable vertical transmission of ESBL-E. coli and emphasizes drinking water as a potential source of horizontal transmission in small-scale poultry farms. Strict biosecurity measures could prevent the spread of antimicrobial-resistant bacteria in birds and their products in a small scale poultry farm.

Preliminary snapshot reveals a relationship between multidrug-resistance and biofilm production among enterobacteriaceae isolated from fecal samples of farm-raised poultry in ceará, Brazil.

Antimicrobial resistance and biofilm formation by microbial pathogens pose a significant challenge to poultry production systems due to the persistent risk of dissemination and compromise of bird health and productivity. In this context, the study aimed to investigate the occurrence of different multiresistance phenotypes and the biofilm-forming ability of Enterobacteriaceae isolated from broiler chicken excreta in poultry production units in Ceará, Brazil. Samples were collected from three distinct broiler breeding facilities and subjected to isolation, identification, antibiotic susceptibility testing, phenotypic screening for ß-lactamases enzymes, and biofilm formation evaluation. Seventy-one strains were identified, being Escherichia coli (37 %) and Proteus mirabilis (32 %), followed by Klebsiella pneumoniae (11 %), Providencia stuartii (9 %), Klebsiella aerogenes (6 %), Alcaligenes faecalis (4 %), and Salmonella sp. (1 %). A significant proportion (87 %) of multiresistant strains were detected. For the phenotypic evaluation of ß-lactamases production, strains with resistance to second and third-generation cephalosporins and carbapenems were tested. About 4 of 6 and 10 of 26 were positive for inducible chromosomal AmpC ß-lactamase and extended-spectrum ß-lactamase (ESBL), respectively. Regarding biofilm formation, it was observed that all MDR strains were capable of forming biofilm. In this sense the potential of these MDR bacteria to develop biofilms becomes a significant concern, representing a real threat to both human and animal health, as biofilms offer stability, antimicrobial protection, and facilitate genetic transfer.

Evaluation of virulence determinants and cell surface properties associated with biofilm formation in methicillin-resistant Staphylococcus aureus (MRSA) and extended spectrum beta-lactamase (ESBL) Escherichia coli from livestock and poultry origin.

Antibiotic resistance poses a persistent threat to modern medicine due to the emergence of novel antibiotic-resistant strains. Therefore, a timely understanding of antibiotic resistance and the virulence biology of pathogenic bacteria, particularly those of public health significance, is crucial for implementing effective mitigation strategies. This study aimed to investigate the virulence profiles of ten S. aureus isolates (NDa to NDj) and ten E. coli isolates (ND1 to ND10) originating from livestock and poultry, and to assess how various cell surface properties and biofilm formation abilities influence antibiotic resistance phenotypes. Antibiotic resistance profiling through phenotypic (AST) and genotypic methods (PCR) confirmed that NDa to NDe were methicillin-resistant S. aureus (MRSA) and ND1 to ND5 were extended-spectrum ß-lactamase (ESBL) producing E. coli isolates. Virulence properties such as hemolytic activity, coagulase activity, and nuclease activity were found to be independent of the antibiotic resistance phenotype in S. aureus. In contrast, biofilm formation phenotype was observed to influence antibiotic resistance phenotypes, with MRSA and ESBL E. coli isolates demonstrating higher biofilm formation potency. Chemical and enzymatic analysis of S. aureus and E. coli biofilms revealed proteins and polysaccharides as major components, followed by nucleic acids. Furthermore, cell surface properties such as auto-aggregation and hydrophobicity were notably higher in isolates with strong to medium biofilm-forming capabilities (ESBL and MRSA isolates), corroborated by genomic confirmation of various genes associated with biofilm, adhesion, and colonization. In conclusion, this study highlights that surface hydrophobicity and biofilm formation ability of MRSA (NDa to NDe) and ESBL E. coli (ND1 to ND5) isolates may influence antibiotic resistance phenotypes.

Isolation, identification, and molecular characterization of potential keratinolytic fungus sp. from Southern Assam: relevance to poultry wastes and its biological management.

Feather waste is a highly prevalent form of keratinous waste that is generated by the poultry industry. The global daily production of feather waste has been shown to approach 5 million tons, typically being disposed of through methods such as dumping, landfilling, or incineration which contribute significantly to environmental pollutions. The proper management of these keratinous wastes is crucial to avoid environmental contamination. The study was carried out to isolate the keratinolytic fungi from the poultry disposal sites of different region of North-East India to evaluate its potential in bioremediation of the feathers wastes. Out of 12 fungal strains isolated from the sites, the fungus showing the highest zone of hydrolysis on both the skim milk and keratin agar medium was selected for the study and the molecular identification of the isolate was performed through DNA sequence analysis by amplifying the internal transcribed spacer (ITS) region. The sequence results showed higher similarity (above 95%) with Aspergillus spp. and was named Aspergillus sp. Iro-1. The strain was further analyzed for its feather degrading potential which was performed in submerged conditions under optimized conditions. The study showed that the strain could effectively degrade the feathers validated through weight loss method, and the structural deformations in the feathers were visualized through scanning electron microscopy (SEM). Aspergillus sp. Iro-1 was obtained from the southern region of Assam. It would be of great importance as the implementation of this sp. can help in the bioremediation of feathers wastes in this region. This is the first study of identification of feather degrading fungus from southern part of Assam (Barak).

Salmonella Hadar linked to two distinct transmission vehicles highlights challenges to enteric disease outbreak investigations.

In 2020, an outbreak of Salmonella Hadar illnesses was linked to contact with non-commercial, privately owned (backyard) poultry including live chickens, turkeys, and ducks, resulting in 848 illnesses. From late 2020 to 2021, this Salmonella Hadar strain caused an outbreak that was linked to ground turkey consumption. Core genome multilocus sequence typing (cgMLST) analysis determined that the Salmonella Hadar isolates detected during the outbreak linked to backyard poultry and the outbreak linked to ground turkey were closely related genetically (within 0-16 alleles). Epidemiological and traceback investigations were unable to determine how Salmonella Hadar detected in backyard poultry and ground turkey were linked, despite this genetic relatedness. Enhanced molecular characterization methods, such as analysis of the pangenome of Salmonella isolates, might be necessary to understand the relationship between these two outbreaks. Similarly, enhanced data collection during outbreak investigations and further research could potentially aid in determining whether these transmission vehicles are truly linked by a common source and what reservoirs exist across the poultry industries that allow Salmonella Hadar to persist. Further work combining epidemiological data collection, more detailed traceback information, and genomic analysis tools will be important for monitoring and investigating future enteric disease outbreaks.

Chlamydia psittaci detected at a live poultry wholesale market in central China.

BACKGROUND: We investigated the presence of Chlamydia psittaci in poultry and the environment in live poultry wholesale markets in Changsha during 2021-2022 and conducted a phylogenetic analysis to understand its distribution in this market. METHODS: In total, 483 samples were analyzed using real-time polymerase chain reaction and 17 C. psittaci-positive samples using high-throughput sequencing, BLAST similarity, and phylogenetic analysis. RESULTS: Twenty-two out of 483 poultry and environmental samples were positive for C. psittaci (overall positivity rate: 4.55%) with no difference in positivity rates over 12 months. Chlamydia psittaci was detected at 11 sampling points (overall positivity rate: 27.5%), including chicken, duck, and pigeon/chicken/duck/goose shops, with pigeon shops having the highest positivity rate (46.67%). The highest positivity rates were found in sewage (12.5%), poultry fecal (7.43%), cage swab (6.59%), avian pharyngeal/cloacal swab (3.33%), and air (2.29%) samples. The ompA sequences were identified in two strains of C. psittaci, which were determined to bear genotype B using phylogenetic analysis. Thus, during monitoring, C. psittaci genotype B was detected in the poultry and environmental samples from the poultry wholesale market in Changsha. CONCLUSIONS: To address the potential zoonotic threat, C. psittaci monitoring programs in live poultry markets should be enhanced.

Use of a commercial tissue dissociation system to detect Salmonella-contaminated poultry products.

Successful detection of bacterial pathogens in food can be challenging due to the physical and compositional complexity of the matrix. Different mechanical/physical and chemical methods have been developed to separate microorganisms from food matrices to facilitate detection. The present study benchmarked a commercial tissue digestion system that applies both chemical and physical methods to separate microorganisms from tissues against stomaching, a standard process currently utilized by commercial and regulatory food safety laboratories. The impacts of the treatments on the physical properties of the food matrix were characterized along with the compatibility of the methods with downstream microbiological and molecular detection assays. The results indicate the tissue digestion system can significantly reduce the average particle size of the chicken sample relative to processing via a stomacher (P < 0.001) without adversely affecting either real-time PCR (qPCR) or plate counting assays, which are typically used to detect Salmonella. Furthermore, inoculated chicken treated with the GentleMACS resulted in a significant increase (P < 0.003) in the qPCR's detection capabilities relative to stomached controls. Cohen kappa (κ) coefficient and McNemar's test indicate the plating assays and PCR results agree with measurements obtained via the 3 M Molecular Detection System as defined in the MLG standard (κ > 0.62; P > 0.08). Collectively, the results demonstrate that the technique enables detection of pathogens in meat at lower levels of contamination using current industry standard technologies.

Prevalence and serotype of poultry salmonellosis in Africa: a systematic review and meta-analysis.

Salmonellosis represents a significant economic and public health concern for the poultry industry in Africa, leading to substantial economic losses due to mortality, reduced productivity, and food safety problems. However, comprehensive information on the burden of poultry salmonellosis at the continental level is scarce. To address this gap, a systematic review and meta-analysis were conducted to consolidate information on the prevalence and circulating serotypes of poultry salmonellosis in African countries. This involved the selection and review of 130 articles published between 1984 and 2021. A detailed systematic review protocol was structured according to Cochrane STROBE and PRISMA statement guideline. From the 130 selected articles from 23 different African countries, the overall pooled prevalence estimate (PPE) of poultry salmonellosis in Africa was found to be 14.4% (95% CI = 0.145-0.151). Cameroon reported the highest PPE at 71.9%. The PPE was notably high in meat and meat products at 23%. The number of research papers reporting poultry salmonellosis in Africa has shown a threefold increase from 1984 to 2021. Salmonella Enteritidis and Typhimurium were the two most prevalent serotypes reported in 18 African countries. Besides, Salmonella Kentucky, Virchow, Gallinarum, and Pullorum were also widely reported. Western Africa had the highest diversity of reported Salmonella serotypes (141), in contrast to southern Africa, which reported only 27 different serotypes. In conclusion, poultry salmonellosis is highly prevalent across Africa, with a variety of known serotypes circulating throughout the continent. Consequently, it is crucial to implement strategic plans for the prevention and control of Salmonella in Africa.RESEARCH HIGHLIGHTS The pooled sample prevalence of poultry salmonellosis in Africa is high (14.4%).The highest PPE was recorded in meat and meat products.Salmonella serotypes of zoonotic importance were found in all sample types.Salmonella Enteritidis and Typhimurium are common serotypes spreading in Africa.

Isolation and characterization of enterococci from poultry reveals high incidence of Enterococcus thailandicus in Victoria, Australia.

AIMS: Antibiotic resistance is a global health crisis. Roughly two-thirds of all antibiotics used are in production animals, which have the potential to impact the development of antibiotic resistance in bacterial pathogens of humans. There is little visibility on the extent of antibiotic resistance in the Australian food chain. This study sought to establish the incidence of antibiotic resistance among enterococci from poultry in Victoria. METHODS AND RESULTS: In 2016, poultry from a Victorian processing facility were swabbed immediately post-slaughter and cultured for Enterococcus species. All isolates recovered were speciated and tested for antibiotic susceptibility to 12 antibiotics following the Clinical Laboratory Standards Institute guidelines. A total of 6 farms and 207 birds were sampled and from these 285 isolates of Enterococcus were recovered. Eight different enterococcal species were identified as follows: E. faecalis (n = 122; 43%), E. faecium (n = 92; 32%), E. durans (n = 35; 12%), E. thailandicus (n = 23; 8%), E. hirae (n = 10; 3%), and a single each of E. avium, E. gallinarum, and E. mundtii. Reduced susceptibility to older classes of antibiotics was common, in particular: erythromycin (73%), rifampin (49%), nitrofurantoin (40%), and ciprofloxacin (39%). Two vancomycin-intermediate isolates were recovered, but no resistance was detected to either linezolid or gentamicin. CONCLUSIONS: The relatively high numbers of a recently described species, E. thailandicus, suggest this species might be well adapted to colonize poultry. The incidence of antibiotic resistance is lower in isolates from poultry than in human medicine in Australia. These results suggest that poultry may serve as a reservoir for older antibiotic resistance genes but is not driving the emergence of antimicrobial resistance in human bacterial pathogens. This is supported by the absence of resistance to linezolid and gentamicin.

Co-existence of two plasmids harboring transferable resistance-nodulation-division pump gene cluster, tmexCD1-toprJ1, and colistin resistance gene mcr-8 in Klebsiella pneumoniae.

BACKGROUND: The emergence of plasmid-mediated mobile colistin resistance (mcr) gene poses a great challenge to the clinical application of polymyxins. To date, mcr-1 to mcr-10 have been found in animals, humans, and the environment. Among them, mcr-8 was first identified in Klebsiella pneumoniae (K. pneumoniae) of swine origin, and then mcr-8.1 to mcr-8.5 were successively identified. Notably, K. pneumoniae is the major host of the mcr-8 gene in both animals and humans. This study aims to explore the characteristics of K. pneumoniae strains carrying the mcr-8 gene and tmexCD1-toprJ1 gene cluster and investigate the correlation between these two antibiotic resistance genes. METHODS: The isolates from the poultry farms and the surrounding villages were identified by mass spectrometer, and the strains positive for mcr-1 to mcr-10 were screened by polymerase chain reaction (PCR). The size of the plasmid and the antimicrobial resistance genes carried were confirmed by S1-nuclease pulsed-field gel electrophoresis (S1-PFGE) and Southern hybridization, and the transferability of the plasmid was verified by conjugation experiments. Antimicrobial susceptibility testing (AST) and whole genome sequencing (WGS) were used to characterize the strains. RESULTS: Two K. pneumoniae isolates (KP26 and KP29) displaying polymyxin resistance were identified as mcr-8 gene carriers. Besides that, tigecycline-resistant gene cluster tmexCD1-toprJ1 was also found on the other plasmid which conferred strain resistance to tigecycline. Through epidemiological analysis, we found that the mcr-8 gene has dispersed globally, circulating in the human, animals, and the environment. Furthermore, our analysis suggests that the coexistence of mcr-8 and tmexCD1-toprJ1 on a single plasmid might evolved through plasmid recombination. CONCLUSIONS: Although the mcr-8 and tmexCD1-toprJ1 gene clusters in the two strains of K. pneumoniae in this study were on two different plasmids, they still pose a potential threat to public health, requiring close monitoring and further study.

Molecular characterization and prevalence of ß-lactamase-producing Enterobacterales in livestock and poultry slaughterhouses wastewater in Iran.

Beta-lactamase-producing Enterobacterales bacteria cause severe hard-to-treat infections. Currently, they are spreading beyond hospitals and becoming a serious global health concern. This study investigated the prevalence and molecular characterization of extended-spectrum ß-lactamase and AmpC-type ß-lactamase-producing Enterobacterales (ESBL-PE, AmpC-PE) in wastewater from livestock and poultry slaughterhouses in Ardabil, Iran. A total of 80 Enterobacterales bacteria belonging to 9 species were identified. Among the isolates, Escherichia coli (n = 21/80; 26.2%) and Citrobacter spp. (n = 18/80; 22.5%) exhibited the highest frequency. Overall, 18.7% (n = 15/80) and 2.5% (n = 2/80) of Enterobacterales were found to be ESBL and AmpC producers, respectively. The most common ESBL producer isolates were E. coli (n = 9/21; 42.8%) and Klebsiella pneumoniae (n = 6/7; 85.7%). All AmpC-PE isolates belonged to E. coli strains (n = 2/21; 9.5%). In this study, 80% of ESBL-PE and 100% of AmpC-PE isolates were recovered from poultry slaughterhouse wastewater. All ESBL-PE and AmpC-PE isolates were multidrug-resistant. In total, 93.3% of ESBL-PE isolates harbored the blaCTX-M gene, with the blaCTX-M-15 being the most common subgroup. The emergence of ESBL-PE and AmpC-PE in wastewater of food-producing animals allows for zoonotic transmission to humans through contaminated food products and contaminations of the environment.

Susceptibility of pESI positive Salmonella to treatment with biocide chemicals approved for use in poultry meat processing as compared to Salmonella without the pESI plasmid.

Salmonella is a common cause of human foodborne illness, which is frequently associated with consumption of contaminated or undercooked poultry meat. Serotype Infantis is among the most common serotypes isolated from poultry meat products globally. Isolates of serotype Infantis carrying the pESI plasmid, the most dominant strain of Infantis, have been shown to exhibit oxidizer tolerance. Therefore, 16 strains of Salmonella with and without pESI carriage were investigated for susceptibility to biocide chemical processing aids approved for use in US poultry meat processing: peracetic acid (PAA), cetylpyridinium chloride (CPC), calcium hypochlorite, and sodium hypochlorite. Strains were exposed for 15 s to simulate spray application and 90 min to simulate application in an immersion chiller. All strains tested were susceptible to all concentrations of PAA, CPC, and sodium hypochlorite when applied for 90 min. When CPC, calcium hypochlorite, and sodium hypochlorite were applied for 15 s to simulate spray time, strains responded similarly to each other. However, strains responded variably to exposure to PAA. The variation was not statistically significant and appears unrelated to pESI carriage. Results highlight the necessity of testing biocide susceptibility in the presence of organic material and in relevant in situ applications.

Emergence and Comparative Genome Analysis of Salmonella Ohio Strains from Brown Rats, Poultry, and Swine in Hungary.

Rats are particularly important from an epidemiological point of view, because they are regarded as reservoirs for diverse zoonotic pathogens including enteric bacteria. This study is the first to report the emergence of Salmonella serovar Ohio in brown rats (Rattus norvegicus) and food-producing animals in Hungary. We first reveal the genomic diversity of the strains and their phylogenomic relationships in the context of the international collection of S. Ohio genomes. This pathogen was detected in 4.3% (4/92) of rats, captured from multiple sites in Hungary. A whole-genome-based genotype comparison of S. Ohio, Infantis, Enteritidis, and Typhimurium strains showed that 76.4% (117/153) of the virulence and antimicrobial resistance genes were conserved among these serovars, and none of the genes were specific to S. Ohio. All S. Ohio strains lacked virulence and resistance plasmids. The cgMLST phylogenomic comparison highlighted a close genetic relationship between rat and poultry strains of S. Ohio from Hungary. These strains clustered together with the international S. Ohio genomes from aquatic environments. Overall, this study contributes to our understanding of the epidemiology of Salmonella spp. in brown rats and highlights the importance of monitoring to minimize the public health risk of rodent populations. However, further research is needed to understand the route of infection and evolution of this serovar.

Microbiome analyses of poultry feeds: Part II. Comparison of different poultry feeds.

Within the realm of poultry feed mill operations, the persistent concern over microbial feed quality necessitates the establishment of a robust baseline for enhancing and sustaining the standards of commercial feeds. This dual-phase investigation, comprising Parts I, was previously published, and the current study presented here as Part II aimed to illuminate this baseline using 16S rRNA gene sequencing. In Part II, nine distinct commercial poultry feeds formulated as starters, growers, starter/growers, or supplements, the selected feeds underwent genomic DNA extraction, amplification with custom dual-indexed primers, and subsequent Illumina MiSeq sequencing. Through data analysis in QIIME2-2021.4 and R Studio, the study unveils alpha (Kruskal-Wallis) and beta (ANOSIM) diversity, taxonomic differences (ANCOM), and core microbiomes (core_members), deeming main and pairwise effects statistically significant at p < 0.05 and Q < 0.05. Notably, the investigation identified 30% common core microbial members across the nine feed types, shedding light on potential foodborne poultry pathogens such as Helicobacter and Campylobacter. Probiotic-associated feeds exhibited distinct microbial communities, emphasizing the need to explore their impact on the early poultry gastrointestinal tract (GIT) further.

Microbiome analyses of poultry feeds: Part I. Comparison of five different DNA extraction methods.

Given extensive variability in feed composition, the absence of a dedicated DNA extraction kit for poultry feed underscores the need for an optimized extraction technique for reliable downstream sequencing analyses. This study investigates the impact of five DNA extraction techniques: Qiagen QIAamp DNA Stool Mini Kit (Qiagen), modified Qiagen with Lysing Matrix B (MQ), modified Qiagen with celite purification (MQC), polyethylene glycol (PEG), and 1-Day Direct. Genomic DNA amplification and Illumina MiSeq sequencing were conducted. QIIME2-2021.4 facilitated data analysis, revealing significant diversity and compositional differences influenced by extraction methods. Qiagen exhibited lower evenness and richness compared to other methods. 1-Day Direct and PEG enhanced bacterial diversities by employing bead beating and lysozyme. Despite similar taxonomic resolution, the Qiagen kit provides a rapid, consistent method for assessing poultry feed microbiomes. Modified techniques (MQ and MQC) improve DNA purification, reducing bias in commercial poultry feed samples. PEG and 1-Day Direct methods were effective but may require standardization. Overall, this study underscores the importance of optimized extraction techniques in poultry feed analysis, with potential implications for future standardization of effective methods.