Poultry Sources Research Articles

Plasmid Profile and ERIC–PCR Characterization of Salmonella Infantis Isolates Recovered from Poultry Sources

BACKGROUND: Pseudomonas aeruginosa is considered one of the most common bacterial pathogens causing nosocomial infections in human cases. However, the pathogenesis of this bacterium in companion birds is poorly understood. OBJECTIVES: The aim of the present study was to isolate P. aeruginosa from pet birds with respiratory illness manifestations referred to the clinic of the University of Tehran. Moreover, the antimicrobial susceptibility of the recovered P. aeruginosa isolates carrying MexAB-OprM efflux pump was evaluated. METHODS: Selective media and biochemical tests were used to isolate and identify P. aeruginosa isolates from 126 companion birds. The species-specific polymerase chain reaction (PCR) based on the 16S rRNA gene was applied to confirm P. aeruginosa. In addition, the sensitivity of isolates to 20 antimicrobial agents was assessed by an antimicrobial susceptibility test. Multiplex PCR was used to detect genes associated with MexAB-OprM efflux pump by specific primers in recovered P. aeruginosa isolates. RESULTS: All seven isolates identified as P. aeruginosa in culture by biochemical tests were confirmed utilizing species-specific PCR. The results of the antimicrobial susceptibility test demonstrated multidrug resistance (MDR) among the isolates with the highest resistance to neomycin, kanamycin, rifampicin, and vancomycin (100% of iso-lates) followed by colistin (57% of isolates). The mexA and oprM genes were detected in all isolates by multiplex PCR, while the mexB gene was not amplified in any of the seven isolates. CONCLUSIONS: We found P. aeruginosa isolates in sick birds and observed MDR in these isolates. Therefore, companion birds could be considered a potential public health concern, especially for owners and veterinary staff.

Core Genome MLST for Source Attribution of Campylobacter coli

Campylobacter species are among the leading foodborne bacterial agents of human diarrheal illness. The majority of campylobacteriosis has been attributed to Campylobacter jejuni (85% or more), followed by Campylobacter coli (5–10%). The distribution of C. jejuni and C. coli varies by host organism, indicating that the contribution to human infection may differ between isolation sources. To address the relative contribution of each source to C. coli infections in humans, core genome multilocus sequence type with a 200-allele difference scheme (cgMLST200) was used to determine cgMLST type for 3,432 C. coli isolated from food animals (n = 2,613), retail poultry meats (n = 389), human clinical settings (n = 285), and environmental sources (n = 145). Source attribution was determined by analyzing the core genome with a minimal multilocus distance methodology (MMD). Using MMD, a higher proportion of the clinical C. coli population was attributed to poultry (49.6%) and environmental (20.9%) sources than from cattle (9.8%) and swine (3.2%). Within the population of C. coli clinical isolates, 70% of the isolates that were attributed to non-cecal retail poultry, dairy cattle, beef cattle and environmental waters came from two cgMLST200 groups from each source. The most common antibiotic resistance genes among all C. coli were tetO (65.6%), blaOXA–193 (54.2%), aph(3′)-IIIa (23.5%), and aadE-Cc (20.1%). Of the antibiotic resistance determinants, only one gene was isolated from a single source: blaOXA–61 was only isolated from retail poultry. Within cgMLST200 groups, 17/17 cgMLST200-435 and 89/92 cgMLST200-707 isolates encoded for aph(3’)-VIIa and 16/16 cgMLST200-319 harbored aph(2’)-If genes. Distribution of blaOXA alleles showed 49/50 cgMLST200-5 isolates contained blaOXA–498 while blaOXA–460 was present in 37/38 cgMLST200-650 isolates. The cgMLST200-514 group revealed both ant(6)-Ia and sat4 resistance genes in 23/23 and 22/23 isolates, respectively. Also, cgMLST200-266 and cgMLST200-84 had GyrAT86I mutation with 16/16 (100%) and 14/15 (93.3%), respectively. These findings illustrate how cgMLST and MMD methods can be used to evaluate the relative contribution of known sources of C. coli to the human burden of campylobacteriosis and how cgMLST typing can be used as an indicator of antimicrobial resistance in C. coli.

Maternal Dietary Protein Patterns During Pregnancy and the Risk of Infant Eczema: A Cohort Study.

Background: Previous studies have suggested that maternal dietary protein was associated with allergic diseases in offspring, but few studies have evaluated the influence of dietary protein patterns. This study aimed to explore the prospective association between maternal dietary protein patterns during pregnancy and the risk of infant eczema.Methods: A total of 713 mother-child pairs from a prospective cohort in Guangzhou, China were recruited. Maternal dietary protein was estimated using a validated face-to-face food frequency questionnaire at 20–28 weeks' gestation from 2017 to 2018. Dietary protein patterns were calculated based on the sources of protein. The data of infant eczema was assessed at 6 months of age using the symptom questionnaire of eczema. Logistic regression was carried out to examine the associations between maternal dietary protein patterns and infant eczema.Results: The cumulative incidence of infant eczema at 6 months of age was 51.19%. Mothers of infants with eczema consumed more protein from poultry source during pregnancy than mothers of infants without eczema, while no statistical differences were observed in maternal intakes of protein from cereals and tubers, vegetables, fruits, red meat, fish and seafood, eggs, dairy, soybean, and nuts and seeds. Four dietary protein patterns were identified and termed poultry, plant, dairy and eggs, and red meat and fish. The cumulative incidence of eczema was 61.2, 45.8, 48.0, 51.4% for these four patterns, respectively. Compared to the poultry dietary pattern, the plant pattern and the dairy and eggs pattern were associated with a reduced risk of infant eczema, and the adjusted odds ratios (95% confidence interval) were 0.572 (0.330–0.992), 0.478 (0.274–0.837), respectively. No such association was observed for the red meat and fish dietary protein pattern.Conclusion: This is the first study that focused on the association between maternal dietary protein during pregnancy from a whole-diet perspective and infant eczema. Compared with the poultry dietary protein pattern, the maternal plant pattern and the dairy and eggs pattern during pregnancy were associated with a reduced risk of infant eczema.

Characterization of Campylobacter jejuni isolated from dogs and humans using flaA-SVR fragment sequencing in Ismailia, Egypt

IntroductionDogs are known as asymptomatic carriers forCampylobacter jejuni. The number of pet dogs is increasing in Egypt in the last decade. ObjectiveThis study aimed to investigate the frequency ofC. jejuni infection in dogs and humans, molecular typing of associated virulence genes, and flaA-SVR gene using sequencing. Methodology152 unpaired fecal swabs from dogs (n = 72) and humans (80) were examined for the presence of C. jejuni and Campylobacter 23S rRNA, and the pathogenicity genes including mapA genes, virB11, flaA, wlaN, iam, tetO, and aadA genes. Sequencing of the flaA- amplicon was also performed for the representative isolates. ResultsThe isolation rate ofC. jejuni was 20.8 % and 31.2 %, respectively in dogs and humans, and all isolates were tested positive for 23S rRNA and mapA genes. C. jejuni harbor virB11 and wlaN (20 %, 0%), iam (10 %, 20 %), tetO and aadA1 (40 %, both), and flaA (40 %, 20 %) in human and dog strains, respectively. The flaA-SVR sequences revealed high identity between human and dog isolates (94.8 %), but revealed 18 substitutions in the amino acid sequence, and showed that the dog and human C. jejuni were close to strains isolated from human and poultry sources. Conclusionthis study demonstrated the comparative sequence analysis ofC. jejuni flaA-SVR fragment in dogs and some Egyptians, which indicated a high identity percentage between them. The results suggest that C. jejuni reservoirs dogs is an alarming public health concern and effective hygienic measures are necessary for house-holding pets to prevent C. jejuni zoonosis in Egypt’s community.

Campylobacter jejuni ST50, a pathogen of global importance: A comparative genomic analysis of isolates from Australia, Europe and North America.

Campylobacter jejuni is the leading cause of bacterial gastroenteritis globally, and infections are often transmitted through consumption of raw or undercooked poultry. Campylobacter jejuni ST50 is among the top ten sequence types (STs) reported in the collected isolates listed at PubMLST records from poultry, food and clinical sources for Asia, Europe, North America, Oceania and South America. This study was designed to determine the most commonly reported C.jejuni STs globally using the PubMLST database and assess similarities between genomes of C.jejuni ST50 isolates from geographically distinct locations. To gain a better understanding of C.jejuni diversity, we compared draft genome sequences of 182 ST50 isolates recovered from retail or caecal poultry samples in Oceania, Europe and North America that were collected over a period of 9years (2010 to 2018). Overall, phylogenetic analysis revealed that isolates from geographically distinct locations tended to cluster based on the continent where the sample was collected. Among ST50 isolates from Europe and North America, we identified resistance determinants associated with phenotypic resistance to beta-lactams (EU: 55%; GB: 43.1%), tetracyclines (CA: 77.3%; EU: 37.5%; GB: 9.8%; US: 43.5%) and fluoroquinolones (EU: 60.0%; GB: 15.7%); no resistance determinants were identified in isolates from Australia. In general, the majority of the virulence genes, with rare exceptions such as wlaN, cj1138, hddA and rfbC, were evenly distributed throughout the genomes of all ST50 isolates in this study. Genomic-based characterization of C.jejuni ST50 isolates from poultry on three continents highlighted that geographically distinct isolates have evolved independently but only represent a glimpse into the diversity of C.jejuni.

Metallo-\u03b2-lactamase and AmpC genes in Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa isolates from abattoir and poultry origin in Nigeria

BackgroundGram-negative bacteria (GNB) including Escherichia coli, Pseudomonas aeruginosa, and Klebsiella pneumoniae represent the most relevant reservoir of resistance genes such as metallo-β-lactamase (MBL) and AmpC genes that give them the undue advantage to resist antimicrobial onslaught. This study aimed to investigate the occurrence of MBL (blaIMP-1, blaIMP-2, blaVIM-1, blaVIM-2) and AmpC (blaFOX, blaDHA, blaCMY, blaACC) resistance genes in aforementioned GNB collected from abattoir and poultry sources in Nigeria.ResultsIn total, 370 isolates were collected from abattoir tables (n = 130), anal region of cows (n = 120), and the cloacae of poultry birds (n = 120). The test isolates showed high rate of resistance to cephalosporins and carbapenems. The MBLs were phenotypically detected in 22 E. coli, 22 P. aeruginosa, and 18 K. pneumoniae isolates using combined disc test (CDT). However, only 11 E. coli, 24 P. aeruginosa, and 18 Klebsiella pneumoniae isolates were phenotypically confirmed to be AmpC producers using cefoxitin-cloxacillin double disk synergy test (CC-DDST). MBL encoding genes (particularly the blaIMP-1 genes and blaIMP-2 genes) were detected by polymerase chain reaction (PCR) in 12 (54.6%) E. coli, 15 (83.3%) K. pneumoniae, and 16 (72.7%) P. aeruginosa isolates. AmpC genes (particularly the blaCMY genes and blaFOX genes) were found in a total of 5 (29.4%) E. coli isolates, 5 (27.8%) isolates of K. pneumoniae, and 10 (41.7%) isolates of P. aeruginosa.ConclusionsOur study showed the circulation of MBL and AmpC genes in GNB from abattoir and poultry origin in Nigeria. Adoption of regular control policies is necessary to reduce the spread of these species as soon as possible, especially in poultry and slaughterhouses.

Antimicrobial Resistance Profile and ExPEC Virulence Potential in Commensal Escherichia coli of Multiple Sources.

We recently described the genetic antimicrobial resistance and virulence profile of a collection of 279 commensal E. coli of food-producing animal (FPA), pet, wildlife and human origin. Phenotypic antimicrobial resistance (AMR) and the role of commensal E. coli as reservoir of extra-intestinal pathogenic Escherichia coli (ExPEC) virulence-associated genes (VAGs) or as potential ExPEC pathogens were evaluated. The most common phenotypic resistance was to tetracycline (76/279, 27.24%), sulfamethoxazole/trimethoprim (73/279, 26.16%), streptomycin and sulfisoxazole (71/279, 25.45% both) among the overall collection. Poultry and rabbit were the sources mostly associated to AMR, with a significant resistance rate (p > 0.01) to quinolones, streptomycin, sulphonamides, tetracycline and, only for poultry, to ampicillin and chloramphenicol. Finally, rabbit was the source mostly associated to colistin resistance. Different pandemic (ST69/69*, ST95, ST131) and emerging (ST10/ST10*, ST23, ST58, ST117, ST405, ST648) ExPEC sequence types (STs) were identified among the collection, especially in poultry source. Both ST groups carried high number of ExPEC VAGs (pandemic ExPEC STs, mean = 8.92; emerging ExPEC STs, mean = 6.43) and showed phenotypic resistance to different antimicrobials (pandemic ExPEC STs, mean = 2.23; emerging ExPEC STs, mean = 2.43), suggesting their role as potential ExPEC pathogens. Variable phenotypic resistance and ExPEC VAG distribution was also observed in uncommon ExPEC lineages, suggesting commensal flora as a potential reservoir of virulence (mean = 3.80) and antimicrobial resistance (mean = 1.69) determinants.

Genetic characterisation of a subset of Campylobacter jejuni isolates from clinical and poultry sources in Ireland.

Campylobacter spp. is a significant and prevalent public health hazard globally. Campylobacter jejuni is the most frequently recovered species from human cases and poultry are considered the most important reservoir for its transmission to humans. In this study, 30 Campylobacter jejuni isolates were selected from clinical (n = 15) and broiler (n = 15) sources from a larger cohort, based on source, virulence, and antimicrobial resistance profiles. The objective of this study was to further characterise the genomes of these isolates including MLST types, population structure, pan-genome, as well as virulence and antimicrobial resistance determinants. A total of 18 sequence types and 12 clonal complexes were identified. The most common clonal complex was ST-45, which was found in both clinical and broiler samples. We characterised the biological functions that were associated with the core and accessory genomes of the isolates in this study. No significant difference in the prevalence of virulence or antimicrobial resistance determinants was observed between clinical and broiler isolates, although genes associated with severe illness such as neuABC, wlaN and cstIII were only detected in clinical isolates. The ubiquity of virulence factors associated with motility, invasion and cytolethal distending toxin (CDT) synthesis in both clinical and broiler C. jejuni genomes and genetic similarities between groups of broiler and clinical C. jejuni reaffirm that C. jejuni from poultry remains a significant threat to public health.

Ecoepidemiology and Potential Transmission of Vibrio cholerae among Different Environmental Niches: An Upcoming Threat in Egypt.

Cholera is a negative public health event caused by Vibrio cholerae. Although V. cholerae is abundant in natural environments, its pattern and transmission between different niches remain puzzling and interrelated. Our study aimed to investigate the occurrence of nonpathogenic V. cholerae in the natural environment during endemicity periods. It also aimed to highlight the role of molecular ecoepidemiology in mapping the routes of spread, transmission, and prevention of possible future cholera outbreaks. V. cholerae was detected in different aquatic environments, waterfowl, and poultry farms located along the length of the Nile River in Giza, Cairo, and Delta provinces, Egypt. After polymerase chain reaction amplification of the specific target outer membrane gene (Omp W) of suspected isolates, we performed sequence analysis, eventually using phylogenetic tree analysis to illustrate the possible epidemiological relationships between different sequences. Data revealed a significant variation in the physicochemical conditions of the examined Nile districts related to temporal, spatial, and anthropogenic activities. Moreover, data showed an evident association between V. cholerae and the clinically diseased Synodontis schall fish. We found that the environmental distress triggered by the salinity shift and elevated temperature in the Middle Delta of the Nile River affects the pathogenesis of V. cholerae, in addition to the characteristics of fish host inhabiting the Rosetta Branch at Kafr El-Zayat, El-Gharbia province, Egypt. In addition, we noted a significant relationship between V. cholerae and poultry sources that feed on the Nile dikes close to the examined districts. Sequence analysis revealed clustering of the waterfowl and broiler chicken isolates with human and aquatic isolated sequences retrieved from the GenBank databases. From the obtained data, we hypothesized that waterfowl act as a potential vector for the intermediate transmission of cholera. Therefore, continuous monitoring of Nile water quality and mitigation of Nile River pollution, in addition to following good managemental practices (GMPs), general hygienic guidelines, and biosecurity in the field of animal production and industry, might be the way to break this cyclic transmission between human, aquatic, and animal sectors.

Isolation, host specificity and genetic characterization of Campylobacter specific bacteriophages from poultry and swine sources

The isolation and characterization of 304 Campylobacter specific bacteriophage isolates from broiler and swine sources is reported in this study. Genome size characterization determined by PFGE classified these isolates,called CAM1-CAM304, within the campylophages group II (n = 18) and group III (n = 286). Host range analyses showed a high host specificity and similar lytic spectrum among isolates of the same group. Campylophages of group II infected C. jejuni, C. coli and even a C. fetus strain whereas those of group III only infected C. jejuni strains. The most promising 59 campylophage candidates were selected according to their lytic activity and their genetic diversity was analyzed by RFLP using SmiI and HhaI endonucleases for group II and III campylophages, respectively. Moreover, RAPD-PCR technique was for the first time assessed in the genetic characterization of campylophages and it was shown to be effective only for those of group II. Bacteriophage isolates grouped in a same genotype displayed different host ranges, therefore, 13 campylophages of group II and eight of group III were differentiated considering all the approaches assayed. An in-depth analysis of these bacteriophages will be performed to confirm their promising potential for the biocontrol of Campylobacter within the farm to fork process.

Growth Performance of Smooth Marron (Cherax cainii) Fed Different Dietary Protein Sources

Fish farming including freshwater crayfish still has a dependency on the availability of fish meal as the main source of protein in feed. The purpose of this study was to evaluate alternative protein sources including poultry by-products, feather meal, lupine flour, soybean meal and meat, and bone meal for smooth marron (Cherax cainii) freshwater crayfish feed. A total of 150 juvenile marrons (9.09 ± 0.21 g) were kept for 90 days and distributed into 15 rearing tanks consisting of five treatments with three replications. The results indicated that there was no significant difference in the increase in biomass, survival rate, moulting rate (weight), feed efficiency ratio, and feed digestibility (P> 0.05). However, marron juvenile fed with a protein source of poultry by-products meal had the highest specific growth rate (0.31 ± 0.05 g / day). In addition, marron fed with fish meal protein resulted a significant increase in carapace length (P <0.05). Based on the digestibility test, it was found that the digestibility level of the feed ranged from 76.39 ± 0.01 - 79.11 ± 0.01% and replacement of fish meal had no significant effect on dry matter digestibility (P> 0.05). Overall, the results of this study indicate that the general growth performance of marron is not affected by the replacement of fish meal in the feed. Alternative protein materials can be used as a protein source to replace fish meal in marron feed so that the use of fish meal can be reduced.

Whole-Genome Sequencing Analysis of Salmonella Enterica Serotype Enteritidis Isolated from Poultry Sources in South Korea, 2010-2017.

Salmonella enterica subsp. enterica serotype Enteritidis (SE) is recognized as a major cause of human salmonellosis worldwide, and most human salmonellosis is due to the consumption of contaminated poultry meats and poultry byproducts. Whole-genome sequencing (data were obtained from 96 SE isolates from poultry sources, including an integrated broiler supply chain, farms, slaughterhouses, chicken transporting trucks, and retail chicken meats in South Korea during 2010–2017. Antimicrobial resistance and virulence genes were investigated using WGS data, and the phylogenetic relationship of the isolates was analyzed using single-nucleotide polymorphism (SNP) typing and core genome multilocus sequence typing (cgMLST). All isolates carried aminoglycoside resistance genes, aac(6’)-Iaa, and 56 isolates carried multiple antimicrobial resistance genes. The most frequent virulence gene profile, pef-fim-sop-inv.-org-sip-spa-sif-fli-flg-hil-ssa-sse-prg-pag-spv, was found in 90 isolates. The SNP analysis provided a higher resolution than the cgMLST analysis, but the cgMLST analysis was highly congruent with the SNP analysis. The phylogenetic results suggested the presence of resident SE within the facility of processing plants, environments of slaughterhouses, and the integrated broiler supply chain, and the phylogenetically related isolates were found in retail meats. In addition, the SE isolates from different origins showed close genetic relationships indicating that these strains may have originated from a common source. This study could be valuable reference data for future traceback investigations in South Korea.

Evaluation of rBapB, rOmpC and rOmpA proteins of Salmonella Typhimurium as vaccine candidates for control of zoonotic salmonellosis in poultry

Background: Non-typhoidal salmonellosis is an important zoonotic infection worldwide, and a leading cause of food poisoning in humans caused by mainly Salmonella Typhimurium and Salmonella Enteritidis from poultry sources is the leading cause of zoonotic infections. Vaccination of birds is considered to be effective tool in controlling zoonotic salmonellosis. There is a continuous search to find suitable vaccine candidates for development of reliable vaccine. The aim of the present study was to evaluate the use of cocktail of recombinant biofim associated protein B (BapB), Outer membrane protein A (OmpA) and outer membrane C (OmpC) for immunization of birds to elucidate its protection against virulent Salmonella Typhimurium. Methods and materials: The three recombinant proteins were prepared after cloning and expressing the respective genes and were characterized by SDS-PAGE and Western blot analyses. The protein preparations were tested as vaccine candidate in layer birds by comparing the immune response, protection and organ clearance against commercial vaccine and control. One hundred birds were divided into 5 groups (rBapB + adjuvant, rBapB + rOmpA + adjuvant rOmpC, rOmpA + rOmpC + adjuvant, commercial vaccine and PBS control) and immunized with 150 μg dose i/m. The kinetics of antibody production against the recombinant proteins were monitored by ELISA and the CMI response was measured by the flow cytometry analysis of the CD4+ or CD8+ of PBM cells. Results: The cocktail of recombinant proteins i.e., BapB, OmpC, OmpA proved to be good immunogens, which induced a significantly higher humoral immune response than control. The protective index (based on faecal shedding of organism) of cocktail of recombinant proteins ranged between 50 and 85.7% as observed for 3 weeks after challenge. The rBapB + rOmpA + rOmpC cocktail group yielded higher humoral and cell-mediated immune response against both S. Typhimurium and S. Enteritidis in comparision to rOmpA + rOmpC cocktail group. Therefore, the protein preparations conferred satisfactory protection against challenge infections with virulent strains of S. Typhimurium as evidenced by limited faecal shedding and minimal detection of Salmonella from edible tissues. Conclusion: The study indicate that the cocktail of expressed rBapB, rOmpA and rOmpC in prokaryotic expression system afforded a satisfactory protective response and organ clearance against virulent S. Typhimurium and S. Enteritidis challenge in birds.

A Multidrug-Resistant Salmonella Infantis Clone is Spreading and Recombining in the United States.

Recently, there have been reports worldwide of a multidrug-resistant, emergent Salmonella Infantis (ESI) clone with a large megaplasmid (pESI), often containing the extended-spectrum beta-lactamase gene blaCTX-M-65. This clone also has a gyrA mutation conferring fluoroquinolone resistance, further limiting treatment options. In the United States, this clone has also been found in poultry sources, indicating a likely source of human illnesses. We conducted short-read sequencing of Salmonella enterica isolated from retail meats as part of routine surveillance by the National Antimicrobial Resistance Monitoring System (NARMS). We analyzed the resulting data temporally and geographically to determine when and where the ESI clone has spread in the United States. We found the ESI clone was first found in retail meats in Tennessee in 2014, but by 2019 was throughout the United States and comprised 29% of all Salmonella isolated from retail chickens, and 7% from retail turkey. Of these isolates, 85.0% were within 20 single nucleotide polymorphisms (SNPs) of those causing human illnesses. Long-read sequencing data indicated substantial recombination in the pESI plasmid resulting in the presence of 0-10 resistance genes, despite all their chromosomes being within 31 SNPs of one another. This work demonstrates the rapid spread of this clone of Salmonella Infantis in poultry in the United States, with the potential for increased burden of human illness attributed to this multidrug-resistant pathogen.

Toxinotyping and molecular characterization of antimicrobial resistance in Clostridium perfringens isolated from different sources of livestock and poultry

The present study was designed to understand the presence of antimicrobial resistance among the prevalent toxinotypes of Clostridium perfringens recovered from different animals of Tamil Nadu, India. A total of 75 (10.76%) C. perfringens were isolated from 697 multi-species fecal and intestinal content samples. C. perfringens type A (90.67%), type C (2.67%), type D (4%) and type F (2.67%) were recovered. Maximum number of isolates were recovered from dog (n = 20, 24.10%) followed by chicken (n = 19, 5.88%). Recovered isolates were resistant to gentamicin (44.00%), erythromycin (40.00%), bacitracin (40.00%), and tetracycline (26.67%), phenotypically and most of the isolates were found to be resistant to multiple antimicrobials. Genotypic characterization revealed that tetracycline (41.33%), erythromycin (34.66%) and bacitracin (17.33%) resistant genes were present individually or in combination among the isolates. Combined results of phenotypic and genotypic characterization showed the highest percentage of erythromycin resistance (26.66%) among the isolates. None of the isolates showed amplification for lincomycin resistance genes. The correlation matrix analysis of genotypic resistance showed a weak positive relationship between the tetracycline and bacitracin resistance while a weak negative relationship between the tetracycline and erythromycin resistance. The present study thus reports the presence of multiple-resistance genes among C. perfringens isolates that may be involved in the dissemination of resistance to other bacteria present across species. Further insights into the genome can help to understand the mechanism involved in gene transfer so that measures can be taken to prevent the AMR spread.

Source attributed case-control study of campylobacteriosis in New Zealand

BackgroundFollowing an initial reduction in human campylobacteriosis in New Zealand after the implementation of poultry food chain-focused interventions during 2006–2008, further decline has been relatively small.We report a year-long study of notified campylobacteriosis cases, incorporating a case control study combined with a source attribution study. The purpose was to generate up-to-date evidence on the relative contributions of different sources of campylobacteriosis in New Zealand. MethodsThe study approach included:• A case-control study of notified cases (aged six months or more) sampled in a major urban centre (Auckland, every second case) and a mixed urban/rural area (Manawatū/Whanganui, every case), between 12 March 2018 and 11 March 2019.• Source attribution of human campylobacteriosis cases sampled from these two regions over the study period by modelling of multilocus sequence typing data of Campylobacter jejuni and C. coli isolates from faecal samples of notified human cases and relevant sources (poultry, cattle, sheep). ResultsMost cases (84%) were infected with strains attributed to a poultry source, while 14% were attributed to a cattle source. Approximately 90% of urban campylobacteriosis cases were attributed to poultry sources, compared to almost 75% of rural cases.Poultry consumption per se was not identified as a significant risk factor. However specific risk factors related to poultry meat preparation and consumption did result in statistically significantly elevated odds ratios. ConclusionsThe overall findings combining source attribution and analysis of specific risk factors indicate that poultry meat remains a dominant pathway for exposure and infection.

Snapshot Study of Whole Genome Sequences of Escherichia coli from Healthy Companion Animals, Livestock, Wildlife, Humans and Food in Italy.

Animals, humans and food are all interconnected sources of antimicrobial resistance (AMR), allowing extensive and rapid exchange of AMR bacteria and genes. Whole genome sequencing (WGS) was used to characterize 279 Escherichia coli isolates obtained from animals (livestock, companion animals, wildlife), food and humans in Italy. E. coli predominantly belonged to commensal phylogroups B1 (46.6%) and A (29%) using the original Clermont criteria. One hundred and thirty-six sequence types (STs) were observed, including different pandemic (ST69, ST95, ST131) and emerging (ST10, ST23, ST58, ST117, ST405, ST648) extraintestinal pathogenic Escherichia coli (ExPEC) lineages. Eight antimicrobial resistance genes (ARGs) and five chromosomal mutations conferring resistance to highest priority critically important antimicrobials (HP-CIAs) were identified (qnrS1, qnrB19, mcr-1, blaCTX-M1,15,55, blaCMY-2, gyrA/parC/parE, ampC and pmrB). Twenty-two class 1 integron arrangements in 34 strains were characterized and 11 ARGs were designated as intI1 related gene cassettes (aadA1, aadA2, aadA5, aad23, ant2_Ia, dfrA1, dfrA7, dfrA14, dfrA12, dfrA17, cmlA1). Notably, most intI1 positive strains belonged to rabbit (38%) and poultry (24%) sources. Three rabbit samples carried the mcr-1 colistin resistance gene in association with IS6 family insertion elements. Poultry meat harbored some of the most prominent ExPEC STs, including ST131, ST69, ST10, ST23, and ST117. Wildlife showed a high average number of virulence-associated genes (VAGs) (mean = 10), mostly associated with an ExPEC pathotype and some predominant ExPEC lineages (ST23, ST117, ST648) were identified.

Establishment and Spatial Distribution of Anthropogenic Ammonia Emission Inventory in Zhejiang Province

The ammonia emissions inventory of Zhejiang Province was established in 2017 using the activity data of various ammonia emission sources, emission factors, and an estimation method. Ammonia emissions for each source and city in Zhejiang Province were analyzed. The spatial distribution and intensity of ammonia emissions in 2017 were mapped using ArcGIS software. The total anthropogenic ammonia emissions in Zhejiang Province in 2017 were 122.00 kt. The farmland ecosystem was the major source of total ammonia emissions (36.06 kt), and nitrogen fertilizer applications was the largest contributor in this category (87.12%), followed by the livestock and poultry source (29.44%). The waste and human-activity sources were the two major non-agricultural sources, accounting for 44.07% and 28.49%, respectively. Hangzhou City had the highest ammonia emissions in 2017, accounting for 17.83% of the total ammonia emissions in Zhejiang Province. However, the ammonia emission intensity in Jiaxing City was the highest, reaching 3.82 t ·km-2. The spatial distribution map revealed that ammonia emissions in the northern and southeastern Zhejiang were relatively higher, while ammonia emission intensity was higher in the northern and northeastern region.

High Frequency of Multidrug-Resistant (MDR) Atypical Enteropathogenic Escherichia coli (aEPEC) in Broilers in Hungary.

Escherichia coli (EC) strains belong to several pathotypes capable of infecting both humans and animals. Some of them have zoonotic potential and can sporadically cause epidemic outbreaks. Our aim was to screen for the distribution of these pathotypes in broilers and their related products. Therefore, E. coli strains were isolated (n = 118) from poultry intestine (n = 57), carcass (n = 57), and wastewater (n = 4) samples from one slaughterhouse with own reared poultry source and the National Reference Laboratory (NRL) poultry E. coli collection (n = 170) from the year 2017 was also studied. All 288 E. coli strains were screened by PCR for pathotype-specific genes stx, eae, st-lt, aggR, ipaH, and for further EPEC-specific virulence genes (bfp, EAF, tir, perA, ler). Altogether 35 atypical enteropathogenic E. coli (aEPEC) strains from the slaughterhouse and 48 aEPEC strains from the NRL collection were found. Regarding the phylogenetic groups of aEPEC, all four main groups were represented but there was a shift toward the B2 group (25%) as compared with the non-EPEC isolates (3%). The aEPEC isolates belonged to serogroups O14, O108, and O45. Multidrug resistance (MDR) was abundant in aEPEC strains (80 out of 83 aEPEC) with a diverse resistance pattern (n = 56). Our results of this study indicate that the high frequency of aEPEC in broilers and on their carcass surface, with frequent MDR to several antibiotic groups, raises the possibility that these strains pose a zoonotic risk to humans.

Molecular Characterization and Antibiotic Resistant Profiles of Campylobacter Species Isolated From Poultry and Diarrheal Patients in Southeastern China 2017-2019.

Campylobacter is a zoonotic pathogen that causes foodborne diarrheal illness globally. To better understand health risks in Southeastern China, Campylobacter spp. were surveyed in humans and representative poultry products over 3 years. One hundred and ninety-five representative isolates (n = 148, Campylobacter jejuni; n = 45, Campylobacter coli; n = 2 Campylobacter hyointestinalis) were examined for genetic relatedness and antimicrobial susceptibility. Nearly all Campylobacter isolates (99.0%, 193/195) were resistant to at least one class of antimicrobials, and 45.6% (89/195) of the isolates exhibited multidrug resistance. Genotypic analysis revealed high diversity among tested strains. Multilocus sequence typing (MLST) displayed 120 sequence types (STs) including 42 novel STs being added to the PubMLST international database. Sixty-two STs belonged to 16 previously characterized clonal complexes (CCs), of which CC-21, CC-45, CC-464, CC-574, CC-353, and CC-828 were most frequently identified. In addition, pulsed-field gel electrophoresis (PFGE) fingerprinting resulted in 66 PFGE SmaI patterns among the 125 isolates, with eight patterns shared between human and poultry sources. Subtyping data did not correlate with antimicrobial resistance phenotypes. Taken together, this large-scale surveillance study highlights high antimicrobial resistance and molecular features of Campylobacter isolates in Southeastern China.