Molecular Detection of Colistin Resistance mcr-1 Gene in Multidrug-Resistant Escherichia coli Isolated from Chicken

Zoonotic and antimicrobial-resistant Escherichia coli (hereafter, E. coli) is a global public health threat which can lead to detrimental effects on human health. Here, we aim to investigate the antimicrobial resistance and the presence of mcr-1 gene in E. coli isolated from chicken feces. Ninety-four E. coli isolates were obtained from samples collected from different locations in Bangladesh, and the isolates were identified using conventional microbiological tests. Phenotypic disk diffusion tests using 20 antimicrobial agents were performed according to CLSI-EUCAST guidelines, and minimum inhibitory concentrations (MICs) were determined for a subset of samples. E. coli isolates showed high resistance to colistin (88.30%), ciprofloxacin (77.66%), trimethoprim/sulfamethoxazole (76.60%), tigecycline (75.53%), and enrofloxacin (71.28%). Additionally, the pathotype eaeA gene was confirmed in ten randomly selected E. coli isolates using primer-specific polymerase chain reaction (PCR). The presence of mcr-1 gene was confirmed using PCR and sequencing analysis in six out of ten E. coli isolates. Furthermore, sequencing and phylogenetic analyses revealed a similarity between the catalytic domain of Neisseria meningitidis lipooligosaccharide phosphoethanolamine transferase A (LptA) and MCR proteins, indicating that the six tested isolates were colistin resistant. Finally, the findings of the present study showed that E. coli isolated from chicken harbored mcr-1 gene, and multidrug and colistin resistance. These findings accentuate the need to implement strict measures to limit the imprudent use of antibiotics, particularly colistin, in agriculture and poultry farms.

Genomic characteristics and comparative genomics of Salmonella enterica subsp. enterica serovar Schwarzengrund strain S16 isolated from chicken feces

Background Salmonella enterica subsp. enterica serovar Schwarzengrund (S. Schwarzengrund) is most frequently isolated from commensals humans or poultry. Here we report S. Schwarzengrund strain S16, the first sequenced genome in the Republic of Korea. Additionally, genome sequencing for strain S16 was performed and compared with other S. Schwarzengrund genomes obtained from public database. Results Strain S16 was isolated from chicken feces. The complete genome consists of one chromosome and one plasmid. The genome size is 4,822,755 bp with 4852 coding sequences. Strain S16 was determined as serovar Schwarzengrund by in silico serotyping and typed as sequence type (ST) 96. Forty-six S. Schwarzengrund genomes yielded a pangenome of 7112 genes, core-genome of 3374 genes, accessory-genome of 2906 genes, and unique-genome of 835 genes. Eighty-one genes were unique to strain S16, including hypothetical proteins and transcriptional regulators. Genotypic analysis of antibiotic resistance of strain S16 confirmed resistance to amikacin, ciprofloxacin, sulfamethoxazole, streptomycin, and tetracycline. Unlike other S. Schwarzengrund genomes, strain S16 had a mutation of gyrB. Moreover, similar to other S. Schwarzengrund genomes reported in other countries, strain S16 was harbored for 153 virulence genes including Saf operon and cdtB gene. All the antibiotic resistance genes and virulence genes were present in the core- or accessory-genomes. Conclusions Complete genome of strain S16 was sequenced. Comparative genomic analysis revealed several genes responsible for antibiotic resistance and specific genomic features of strain S16 and identified virulence factors that might contribute to the human and animal pathogenicity of other S. Schwarzengrund genomes.

Prevalence and antibiotic resistance of Salmonella isolated from poultry and its environment in the Mekong Delta, Vietnam

Background and Aim: Salmonella is one of the leading causes of zoonotic and foodborne infectious outbreaks in humans and poultry and its associated environment is a potential reservoir of Salmonella. In recent years, the antibiotic resistance of bacteria, including Salmonella, has been increasing. This study aimed to investigate the prevalence and antibiotic resistance of Salmonella isolated from poultry, its environment, and the pest animals found at poultry farms and households of the Mekong Delta, Vietnam. Materials and Methods: A total of 3,055 samples were collected from the broiler farms and households of the Mekong Delta from 2017 to 2020. Salmonella was isolated using conventional methods (culturing on selective agar – BPLS and biochemical test) and the isolates were examined for antibiotic resistance against 14 antibiotics using the disk diffusion method. Results: Salmonella was isolated from 181 samples (5.92%), which included chicken feces (7.67%), pest animals (5.98%), and environmental samples (4.33%). The environmental samples comprised bedding (5.88%), feed (5.48%), and drinking water (0.70%). The prevalence of Salmonella was the highest in rats (15.63%) and geckos (12.25%) followed by ants (2.83%) and cockroaches (2.44%); however, Salmonella was not isolated from any fly species. Most of the isolates exhibited resistance to 1-9 antibiotics. The isolates were relatively resistant to chloramphenicol (62.98%), tetracycline (55.80%), ampicillin (54.14%), and sulfamethoxazole/trimethoprim (53.04%). Sixty-two multiple resistance patterns were found in the isolates, with ampicillin-cefuroxime-chloramphenicol-tetracycline- sulfamethoxazole/trimethoprim being the most frequent (7.18%). Conclusion: The chickens, husbandry environment, and pest animals at poultry farms and households were found to be important Salmonella sources in the Mekong Delta. Salmonella isolates from these sources also exhibited a wide-ranging resistance to antibiotics as well as several resistance patterns. Hence, biosecurity should be addressed in poultry farms and households to prevent cross-contamination and reduce the spread of Salmonella infections.

Ruminant-Related Risk Factors are Associated with Shiga Toxin–Producing Escherichia coli Infection in Children in Southern Ghana

Livestock can provide benefits to low-income households, yet may expose children to zoonotic enteropathogens that cause illness and negative long-term health outcomes. The aim of this cross-sectional study was to determine whether livestock-related risk factors, including animal ownership, exposure to animal feces, and consumption of animal-source foods, were associated with bacterial zoonotic enteropathogen infections in children 6–59 months old in Greater Accra, Ghana. Stool samples from 259 children and 156 household chickens were analyzed for atypical enteropathogenic Escherichia coli (aEPEC), Campylobacter jejuni/coli (C. jejuni/coli), Salmonella, and Shiga toxin–producing Escherichia coli (STEC) using quantitative polymerase chain reaction (qPCR). aEPEC, C. jejuni/coli, STEC, and Salmonella were detected in 45.6%, 11.6%, 4.3%, and 0.8% of children’s stool samples, respectively. In adjusted logistic regression models, household ownership of goats or sheep was associated with STEC detection in children (odds ratio [95% confidence interval {CI}]: 4.30 [1.32, 14.08]), as were positive detection of STEC in chicken feces (7.85 [2.54, 24.30]) and frequent consumption of fresh cow’s milk (3.03 [1.75, 5.24]). No livestock-related risk factors were associated with aEPEC or C. jejuni/coli infection in children. Our findings suggest that ruminant ownership in southern Ghana may expose children to STEC through household fecal contamination and foodborne routes. The lack of association between livestock risk factors and the more commonly detected pathogens, aEPEC and C. jejuni/coli, warrants further research, particularly to help explain how animal-keeping and sanitation practices affect transmission of fecal pathogens that were highly prevalent in chicken feces.

Parasitoids Collected from Animal Feces in Brazil

The purpose of the paper is to report the species of dipteran parasitoids in poultry feces on farms, buffalo, and cattle in the field in Brazil. The experiments were carried out from April 2006 to December 2007. The pupae were obtained by the flotation method. They were individually placed in gelatin capsules until the emergency of the adult flies or their parasitoids. The specie more frequent was S endius with 7.2%. Were obtained from bovine feces 628 pupae of dipterous in buffalo feces, 3,437 pupae were collected and from chicken feces 2,799 pupae, from which 78, 172 and 504 parasitoids emerged, respectively. The most frequent species in bovine, of buffalo and chicken feces were: Gnathopleura quadridentata Wharton (Hymenoptera: Braconidae) with 25.6%, Spalangia drosophilae Ashmead (Hymenoptera: Pteromalidae) with 21.5% and Pachycrepoideus vindemmiae (Rondani, 1875) with 46.8%, respectively.

Characterization of Extended-Spectrum Cephalosporin (ESC) Resistance in Salmonella Isolated from Chicken and Identification of High Frequency Transfer of blaCMY-2 Gene Harboring Plasmid In Vitro and In Vivo

A total of 136 Salmonella isolates from chicken feces and meat samples of the top 12 integrated chicken production companies throughout Korea were collected. Among the 17 ESC-resistant Salmonella; blaCTX-M-15 was the most prevalent gene and two strains carried blaTEM-1/blaCTX-M-15 and blaCMY-2, respectively. The transferable blaCTX-M-15 gene was carried by IncFII plasmid in three isolates and the blaCMY-2 gene carried by IncI1 plasmid in one isolate. blaCMY-2 gene-harboring strain was selected as the donor based on the high frequency of blaCMY-2 gene transfer in vitro and its transfer frequencies were determined at 10−3 transconjugants per recipient. The transfer of blaCMY-2 gene-harboring plasmid derived from chicken isolate into a human pathogen; enteroinvasive Escherichia coli (EIEC), presented in mouse intestine with about 10−1 transfer frequency without selective pressure. From the competition experiment; blaCMY-2 gene-harboring transconjugant showed variable fitness burden depends on the parent strains. Our study demonstrated direct evidence that the blaCMY-2 gene harboring Salmonella from chicken could frequently transfer its ESC-resistant gene to E. coli in a mouse intestine without antimicrobial pressure; resulting in the emergence of multidrug resistance in potentially virulent EIEC isolates of significance to human health; which can increase the risk of therapeutic inadequacy or failures.

Antimicrobial Resistance Profiles, Virulence Genes, and Genetic Diversity of Thermophilic Campylobacter Species Isolated From a Layer Poultry Farm in Korea

Thermophilic Campylobacter species are among the major etiologies of bacterial enteritis globally. This study aimed at assessing the antimicrobial resistance (AMR) profiles, virulence genes, and genetic diversity of thermophilic Campylobacter species isolated from a layer poultry farm in South Korea. One hundred fifty-three chicken feces were collected from two layer poultry farms in Gangneung, South Korea. The Campylobacter species were isolated by cultural techniques, while PCR and sequencing were used for species confirmation. Antimicrobial susceptibility testing for six antimicrobials [ciprofloxacin (CIP), nalidixic acid (NAL), sitafloxacin (SIT), erythromycin (ERY), tetracycline (TET), and gentamicin (GEN)] was carried out by broth microdilution. Three AMR and nine virulence genes were screened by PCR. Genotyping was performed by flaA-restriction fragment length polymorphism (RFLP) and multilocus sequence typing (MLST). Of the 153 samples, Campylobacter spp. were detected in 55 (35.9%), with Campylobacter jejuni and Campylobacter coli being 49 (89.1%) and six (10.9%), respectively. High-level resistance was observed for CIP (100%), NAL (100%), and TET (C. jejuni, 93.9%; C. coli: 83.3%). No resistance was observed for SIT. The missense mutation (C257T) in gyrA gene was confirmed by sequencing, while the tet(O) gene was similar to known sequences in GenBank. The rate of multidrug-resistant (MDR) strains was 8.2%, and they all belonged to C. jejuni. All Campylobacter isolates possessed five virulence genes (cdtB, cstII, flaA, cadF, and dnaJ), but none possessed ggt, while the rates for other genes (csrA, ciaB, and pldA) ranged between 33.3 and 95.9%. The flaA-RFLP yielded 26 flaA types (C. jejuni: 21 and C. coli: five), while the MLST showed 10 sequence types (STs) for C. jejuni and three STs for C. coli, with CC-607 (STs 3611) and CC-460 (ST-460) being predominant. Among the 10 STs of C. jejuni, three were newly assigned. The findings of this study highlight the increased resistance to quinolones and TET, the virulence potential, and the diverse genotypes among Campylobacter strains isolated from the layer poultry farm.

Comparative viral metagenomics from chicken feces and farm dust in the Netherlands

ABSTRACTLivestock animals housed in close proximity to humans can act as sources or intermediate hosts facilitating animal-to-human transmission of zoonotic diseases. Understanding virus diversity in livestock is important for identifying potential zoonotic threats and for ensuring animal health and safe livestock production. Here, we report viral metagenomic characterization of chicken feces (N=51) and paired farm dust samples (N=13) using metagenomic deep sequencing. Samples were collected at 4-5 time points in three broiler farms in the Netherlands. Viruses in the Parvoviridae and Picornaviridae families were the most prevalent, detected in all feces and dust samples and in all feces and 85% of dust samples, respectively. Virus composition found in chicken feces and corresponding dust samples were similar. Great genomic diversity was identified in Picornaviridae and 46 sequences from five picornavirus genera (Sicinivirus, Megrivirus, Anatvirus, Gallivirus and Avisvirus) were detected. For calicivirus, Basovirus and an unclassified novel chicken calicivirus were identified in 13 fecal and 1 dust samples. Two distinct types of chicken astroviruses were identified. Phylogenetic analyses of identified virus sequences from Picornaviridae, Astroviridae and Caliciviridae suggested that viral sequences obtained from different farms are often more closely related to each other than global reference sequences, and sequences from feces and paired dust samples also clustered together. Importantly, our sequencing methodology enabled the recover viral genome sequences from farm dusts, allowing the tracking of virus chatter between livestock animals and their farm environment. This study, albeit relative sample size, does expand current knowledge of virus communities in chickens and surrounding dusts.IMPORTANCEChickens may harbor various zoonotic pathogens, some of which can cause severe clinical outcomes in animals and humans. Farm dust can act as vector to facilitate zoonoses transmission. Here, we report the metagenomic characterization of virus communities of chicken feces and paired farm dust samples collected at multiple time points during the production cycle in broiler farms in the Netherlands. Parvoviridae and Picornaviridae were most frequently detected. We also identified novel astrovirus and calicivirus sequences that would inform future virus taxonomy classification. This is the first study to characterize virus communities in farmed chickens and paired farm dust samples. We also describe a dust sequencing strategy that can be adapted for future dust metagenomic characterization. Our study could help setting up a surveillance baseline for tracking virus flow between chickens and their farm environment which could guide zoonotic outbreak preparedness and health risk assessment of farm exposure.

Effects of larval rearing substrates on some life-table parameters of Lutzomyia longipalpis sand flies

Sand flies are the insects responsible for transmitting Leishmania parasites, the causative agents of leishmaniasis in humans. However, the effects of sand fly breeding sites on their biology and ecology remain poorly understood. Herein, we studied how larval nutrition associated with putative breeding sites of the sand fly Lutzomyia longipalpis affects their oviposition, development, microbiome, and susceptibility to Leishmania by rearing L. longipalpis on substrates collected from an endemic area for leishmaniasis in Brazil. The results showed that female L. longipalpis select the oviposition site based on its potential to promote larval maturation and while composting cashew leaf litter hindered the development, larvae reared on chicken feces developed rapidly. Typical gut microbial profiles were found in larvae reared upon cashew leaf litter. Adult females from larvae reared on substrate collected in chicken coops were infected with Leishmania infantum, indicating that they were highly susceptible to the parasite. In conclusion, the larval breeding sites can exert an important role in the epidemiology of leishmaniasis.

EFEKTIFITAS BIO-KOMPOS DAN BIO-POC TERHADAP SERANGAN HAMA PENGGEREK BATANG (Ostrinia furnacalis) PADA JAGUNG MANIS

The stem borer (Ostrinia furnacalis Guenee) is one of the main pests of corn. The yield loss due to this pest attack reaches 20-80%. These pests are generally controlled chemically, causing various negative effects from the results of control, therefore environmentally friendly control techniques are needed, such as the use of bio-compost and bio-LOF. Bio-compost is compost combined with a consortium of bacteria Serratia marcecens, Bacillus thuringiensis and Pseudomonas fluorescens. Bio-LOF is a liquid organic fertilizer that is processed using cow feces, cow urine, Glicerida leaves and coconut husk. The research objective is to determine the effectiveness of bio-compost with several concentrations of bio-LOF to control stem borer pests in sweet corn. The research was conducted at experimental land of Payakumbuh Agricultural Polytechnic from January to June 2020. This study used a factorial completely randomized design (4x3) with 3 replications. Factor K, namely K1; Tithonia bio-compost, K2; Hay bio-compost. K3; Manure bio-compost. K4: without bio-compost. Factor D are: D1; Bio-LOF concentration 30%, D2; Bio-LOF 20%. D3: without Bio-LOF. The data obtained were analyzed for variance using a statistical program of 8.0, then continued with the dancun test α 5%. The results showed that the three types of bio-compost combined with bio-LOF could reduce the percentage of O. furnacalis pest attack on the stems and tips of sweet corn cobs. There were 5 treatment combinations with very effective criteria for coefficient of relatively control (CRC), namely. Tithonia bio-compost, Bio-LOF 30%, Hay bio-compost, bio-LOF 30%, chicken feces bio-compost, bio-LOF 30%, Straw bio-compost, Bio-LOF 20%, Without bio-compost, Bio-LOF 30%. The concentration of bio-LOF sprayed on the stems and leaves affects the effectiveness of the control where the 30% bio-LOF concentration had the very effective criteria of control, while the 20% concentration had the effective criteria of control.