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Meat inspection is important to ensure food safety and protect public health. Visual inspection of slaughtered carcasses for pathological changes should be supported by bacteriological analysis to determine whether the entire carcass or parts of it should be condemned. The aim of this study was to determine the bacterial species present in different sample types from condemned broiler carcasses. Furthermore, we investigated the genetic characteristics, zoonotic potential, and relatedness of Escherichia coli, the predominant bacterial species isolated from the carcasses. A total of 400 broiler carcasses condemned because of cellulitis (100), scratches (100), hepatitis (100), and healthy control carcasses (100) were selected. Samples of meat, pathological lesion, and bone marrow of each carcass were obtained for microbial analysis. From the analyzed samples, 469 bacterial isolates were recovered with E. coli accounting for 45.8%, followed by Aeromonas spp. (27.9%), in particular A. veronii. The highest rate of bacterial isolation was observed in carcasses condemned with cellulitis, whereas carcasses with hepatitis had the lowest rate of bacterial isolation. Forty-four E. coli isolates originating from different sample types were selected for whole genome sequencing. A clonal relationship was shown between E. coli from different sample types of the same carcass condemned with cellulitis and scratches. A major clade of E. coli was found in carcasses condemned with cellulitis with isolates containing mdf(A), tet(A), and blaTEM-1B genes that confer resistance to macrolides, tetracycline, and ampicillin, respectively. E. coli in this clade all belonged to ST117 and clustered with E. coli isolates previously collected from dead chickens and carcasses condemned due to cellulitis in Denmark, Finland, and the United Kingdom. Bacterial evaluation results of carcasses condemned with cellulitis, scratches (moderate to severe skin lesion), and acute hepatitis confirmed the need fo

Polycyclic aromatic hydrocarbons (PAH) are present and pervasive in the environment. Handling of the foods by the vendors is therefore likely to introduce PAHs into the meals. Quantification of PAH was made using HPLC-FID and consumption data by face–face interviews with 188 regular consumers for the vendors. Data obtained were iterated 10,000 times using palisade @risk software and results presented at 95th percentile level of consumption showing the worst case scenario. Dietary risk assessment of 12-priority PAHs was carried out on the components of two staple foods in Ghana. Naphthalene was detected in all food samples at concentrations ranging from 1.7 to 6.5 mg kg −1 at 95th percentile consumption level. Benzo(a)pyrene and dibenz-a,h-anthracene were detected in fried chicken samples with the stochastic concentrations of 1.2E–02 mg kg −1 and 3.2E–03 mg kg −1, respectively, at the 95th percentile level of consumption. Incremental life cancer risk values fell within the deminis value of ≤10 −6 to 10 −4 except at the 95th percentile level of consumption of chicken, hot pepper sauce, and soup components of the meals which were higher (10 −3). The 95th percentile level of consumption of fried rice meal as well as the 50th and 95th percentile level of consumption of the fufu meal had a hazard index above 1, indicating consumers may be suffering the non-carcinogenic effects due to PAH in the respective meals. The study, therefore, showed that high consumption levels of the street vended foods are likely to cause dietary risk to the health of its consumers.

Background: Acinetobacter baumannii are of major human health importance because they cause life-threatening nosocomial infections and often are highly resistant to antimicrobials. Specific multidrug-resistant A. baumannii lineages are implicated in hospital outbreaks globally. We retrospectively investigated a suspected outbreak of carbapenem-resistant A. baumannii (CRAB) colonizing patients in an intensive care unit (ICU) of a tertiary hospital in Southwest Nigeria where genomic surveillance of Acinetobacter has hitherto not been conducted. Methods: A prospective observational study was conducted among all patients admitted to the ICU between August 2017 and June 2018. Acinetobacter species were isolated from rectal swabs and verified phenotypically with the Biomerieux Vitek 2 system. Whole genome sequencing (WGS) was performed on the Illumina platform to characterize isolates from a suspected outbreak during the study period. Phylogenetic analysis, multilocus sequence typing, and antimicrobial resistance gene prediction were carried out in silico. Results: Acinetobacter isolates belonging to the A. baumannii complex were recovered from 20 (18.5%) ICU patients. Single nucleotide polymorphism (SNP) analysis and epidemiological information revealed a putative outbreak clone comprising seven CRAB strains belonging to the globally disseminated international clone (IC) 2. These isolates had ≤2 SNP differences, identical antimicrobial resistance and virulence genes, and were all ST1114/1841. Conclusion: We report a carbapenem-resistant IC2 A. baumannii clone causing an outbreak in an ICU in Nigeria. The study findings underscore the need to strengthen the capacity to detect A. baumannii in human clinical samples in Nigeria and assess which interventions can effectively mitigate CRAB transmission in Nigerian hospital settings.

Salmonella enteritidis is a major foodborne pathogen worldwide. In this study, a total of 276 S. enteritidis isolates, collected between 2016 and 2017 from human, food and farm/slaughterhouse samples, were studied to enhance the understanding of the epidemiology of human salmonellosis in Singapore. Results showed all 276 isolates belonged either to ST1925 (70.3%) or ST11 (29.7%), with ST11 being significantly more frequent in extra-intestinal isolates and chicken isolates. Food isolates, most of which were from poultry, showed the highest prevalence of resistance (33–37%) against beta-lactams or beta-lactams/beta-lactamase inhibitor combination (ampicillin, piperacillin and ampicillin/sulbactam). The analysis showed the detection of genes associated with resistance to aminoglycoside genes (99.6%), tetracycline (55.1%), and beta-lactams (14.9%) of all isolates. Nine types of plasmids were found in 266 isolates; the most common incompatibility group profiles were IncFIB(S)-IncFII(S)-IncX1 (72.2%) and IncFIB(S)-IncFII(S) (15.8%). Most plasmid harbouring isolates from chicken (63.6%, 14/22) and from human (73.8%, 175/237) shared the same plasmid profile (IncFIB(S)-IncFII(S)-IncX1). SNP analysis showed clustering of several isolates from poultry food products and human isolates, suggesting phylogenetic relatedness among these isolates. Lastly, this study provides important epidemiological insights on the application of phenotypic and next-generation sequencing (NGS) tools for improved food safety and public health surveillance and outbreak investigation of S. enteritidis.

Extraintestinal pathogenic Escherichia coli (ExPEC) is a globally distributed pathogen, with uropathogenic E. coli (UPEC) and sepsis-associated E. coli (SEPEC) pathotypes particularly involved in human and companion animal disease, while avian pathogenic pathotype (APEC) severely impact poultry health and production. Similarities between APEC from poultry/meat and human ExPEC suggest that some APEC lineages may have zoonotic potential. ExPEC sequence type 73 (ST73) and its clonal complex (CC) are increasing causes of urinary tract infections and sepsis, but its role in zoonotic disease is less well understood. Here, we analyzed the genome sequences of 25 E. coli isolates from Brazil (11 APEC and 14 UPEC) from two time periods, from poultry producing areas and hospitals in the same geographical regions. Isolates were compared to 558 publicly available ST73/CC73 global sequences. Brazilian APEC harbored virulence factors associated with UPEC/SEPEC such as sfa, cnf1, vat, usp, hlyA, iron acquisition and protectins/serum resistance systems, while lacking some common APEC markers and widespread multidrug resistance. Analysis of core genome MLST and SNP phylogenetic trees indicated evolutionary relationships between subgroups of the Brazilian APEC to two contemporary Brazilian UPEC isolates from the same region, and one Brazilian UPEC available from another study. Phylogenies showed a non-host, geographical, or pathotype specificity, with APEC isolates clustering closely with international human UPEC, SEPEC. The remaining Brazilian UPEC grouped within human clusters. Collectively, this suggests a zoonotic potential for subgroups of Brazilian APEC from the ST73 lineage that could contaminate poultry products and subsequently cause human infection.

Soil-transmissible helminthes (STH) infections are among the most common sanitation-related public health problems in poor periurban settlements of tropical regions of low- A nd middle-income countries. In Ghana, research studies documenting the incidence rate, intensity, and occupational risk factors of STH infections among adults are scanty. A prospective cohort study of 261 waste handlers was conducted to investigate this. Stool samples were collected after 90 and 180 days of treatment with albendazole (400 mg per dose). The geometric mean intensity of STH among waste handlers after 180 days of treatment was 2.8 eggs/gram (light intensity), with an incidence rate of 1.5%. The proportion of waste handlers with light intensity STH infections was 4.8%. The odds of STH infection among female waste handlers were 80% lower when compared with male waste handlers (aOR = 0.2; 95% CI: 0.0-0.8). Waste handlers who used rubber gloves when working were 80% (aOR = 0.2: 95% CI: 0.2-1.9) protected from STH infections compared with those who did not use gloves. Infections with STH among the 261 waste handlers significantly correlated with the type of waste handling activities (LR χ2 = 15.3; p=0.033) with the highest proportion of infection found among transporters, 2 (40%). Waste handlers should receive periodic antihelminthic treatment, at least once every six months, practice adequate hand hygiene, and use suitable personal protective equipment during work.

Animals are considered important sources of ESBL/AmpC-producing bacteria in humans. We analyzed indications of transfer of ESBL/AmpC genes between pigs and pig farmers in Vietnam by analyzing whole genome sequences of 114 ESBL/AmpC-producing E. coli isolated from the two hosts, and performed conjugation experiments and plasmid profiling to confirm that such transfer could have happened. ESBL-encoding genes detected in pigs and pig farmers included blaCTX–M-55, blaCTX-M-27, blaCTX-M-65, blaCTX-M-15, blaCTX-M-14, blaCTX-M-3, blaCTX-M-24, and blaCARB-2, and AmpC β-lactamases included blaCMY-2, blaDHA-1, and blaCMY-42. The most frequent ESBL gene, blaCTX-M-55, was carried on plasmid with replicons types IncF, IncX, IncH, IncN, IncR, and IncP. The insertion transposases downstream of the blaCTX-M-55 gene were different in plasmids carried by different strains. The second most detected gene, blaCTX-M-27, is found in a stable genetic arrangement with the same flanking transposons seen across strains, and the gene was located on similar conjugal IncF plasmid types, suggesting a horizontal spread of these plasmids. In three strains, we observed a novel blaCTX-M-27 harboring IncF type of plasmid which had not been reported before. Its closest reference in NCBI was the non-ESBL Salmonella Typhimurium plasmid pB71 that might have experienced an insertion of blaCTX-M-27. Our data also point to an emergence of plasmids co-carrying ESBL genes, mcr genes, quinolones and other antimicrobials resistance determinants, and such plasmids require special attention. Plasmids phylogeny confirmed that the blaCTX-M-55 encoding plasmids varied considerably, while those encoding blaCTX-M-27 were closely related. Plasmids harboring both ESBL genes were confirmed to be conjugative and not to differ in transfer efficacy. The isolates carrying the plasmids, even those with plasmids of similar types, showed wide genetic variation with high number of SNPs, suggesting horizontal spread of plasmids in

Antimicrobial resistance is a global public health concern, and resistance genes in Salmonella, especially those located on mobile genetic elements, are part of the problem. This study used phenotypic and genomic methods to identify antimicrobial resistance and resistance genes, as well as the plasmids that bear them, in Salmonella isolates obtained from poultry in Nigeria. Seventy-four isolates were tested for susceptibility to eleven commonly used antimicrobials. Plasmid reconstruction and identification of resistance and virulence genes were performed with a draft genome using in silico approaches in parallel with plasmid extraction. Phenotypic resistance to ciprofloxacin (50.0%), gentamicin (48.6%), nalidixic acid (79.7%), sulphonamides (71.6%) and tetracycline (59.5%) was the most observed. Antibiotic resistance genes (ARGs) detected in genomes corresponded well with these observations. Commonly observed ARGs included sul1, sul2, sul3, tet (A), tet (M), qnrS1, qnrB19 and a variety of aminoglycoside-modifying genes, in addition to point mutations in the gyrA and parC genes. Multiple ARGs were predicted to be located on IncN and IncQ1 plasmids of S. Schwarzengrund and S. Muenster, and most qnrB19 genes were carried by Col (pHAD28) plasmids. Seventy-two percent (19/24) of S. Kentucky strains carried multidrug ARGs located in two distinct variants of Salmonella genomic island I. The majority of strains carried full SPI-1 and SPI-2 islands, suggesting full virulence potential

We analyzed and compared genomes of Extended Spectrum Beta-Lactamase (ESBL)-producing Escherichia coli from pigs and pig farm workers at 116 farms in Vietnam. Analyses revealed the presence of blaCTX-M-55, blaCTX-M-27, blaCTX-M-15, blaCTX-M-14, blaCTX-M-3, blaCTX-M-65, blaCTX-M-24, blaDHA-1, and blaCMY2 in both hosts. Most strains from pigs contained quinolones (qnr) and colistin resistance genes (mcr-1 and mcr-3). Isolates predominantly harbored more than one plasmid replicon and some harbored plasmid replicons on the same contigs as the ESBL genes. Five strains from farm workers of ST38 (2), ST69 (1), and ST1722 (2) were classified as either uropathogenic E. coli (UPECHM)/extraintestinal pathogenic E. coli (ExPECJJ) or UPECHM, and the remaining were genetically distinct commensals. A high heterogeneity was found among the ESBL-producing E. coli from pigs and workers, with most isolates belonging to unrelated phylogroups, serogroups, and sequence types with >4046 Single-Nucleotide Polymorphisms-(SNPs). In comparing the genomes of pig isolates to those from humans, it appeared that ESBL-producing E. coli in workers did not predominantly originate from pigs but were rather host-specific. Nevertheless, the occurrence of ESBL-producing E. coli carrying plasmid-mediated colistin and quinolone resistance genes in pigs could represent a potential source for horizontal transmission to humans through food rather than direct contact.

A large-scale food poisoning outbreak happened at a school canteen in Ninh Binh Province, Vietnam, in 2018, resulting in the hospitalization of 352 students with clinical symptoms indicative of a staphylococcal food poisoning. A subsequent laboratory investigation detected Staphylococcus aureus in two food items—deep-fried shrimp and chicken floss—at up to 103 CFU/mL, and staphylococcal enterotoxins (SEs) in chicken floss at ≥0.211 ng SEs/g. S. aureus was also isolated from patients’ vomit and stool samples, and kitchen workers’ stool samples, as well as in frozen chicken meat, but not on the kitchen workers’ hand surfaces, suggesting the cause of this food poisoning outbreak was S. aureus contamination of the chicken meat. Molecular characterization revealed the S. aureus strains isolated from all samples were closely related; all belonged to sequence type (ST) ST6 and spa type t701 and carried both sea and sec genes. This SE-producing strain was resistant to penicillin and tetracycline, while still susceptible to oxacillin, erythromycin, gentamicin, methicillin, and vancomycin. Since S. aureus food poisonings are often underreported, our investigation added to the sparse qualitative and quantitative data of pathogenic S. aureus monitoring and surveillance in Vietnam, providing needed knowledge to guide preventative measures for future outbreaks

Antimicrobial resistance constitutes a global challenge to public health. The common addition of Zn, Cu and other metals to animal feed and the widespread presence of metal ions in livestock and their receiving environments may be a factor that facilitates the proliferation of antimicrobial resistance via co-selection of antimicrobial resistance genes (ARGs) and metal resistance genes (MRGs). However, the extent of co-selection is not yet fully understood. In this study, we used a metagenomic approach to profile ARGs, MRGs and mobile genetic elements (MGEs) known to constitute potential ARG and MRG vectors of transmission, and we determined the concentration of metal ions to assess the interrelationships between the occurrence of ARGs, MRGs and metal concentrations in samples from pig farms in China. Samples analyzed included fresh pig feces, soils fertilized with treated slurry, and sediments from aquatic environments, where effluent from treated slurry was discharged. Resistance genes to tetracycline and zinc were the most commonly observed ARGs and MRGs for all three types of samples. Significant correlations were observed between the abundance of ARGs and MRGs, and between ARGs/MRGs and MGEs, and between metal and ARGs/MGEs as documented by Pearson's correlation analysis (r > 0.9, P < 0.001). Further network analysis revealed significant co-occurrence between specific ARGs and MRGs, between ARGs/MRGs and MGEs, and between specific metals (Zn, Cr, and Mn) and ARGs and MGEs. Collectively, our findings demonstrate a high level of co-occurrence of antimicrobial and metal resistance genes in slurry from pig farms and their surrounding environments. The results suggest that metals added to pig feed might facilitate co-selection of ARGs and MGEs in the pig production environments, thereby resulting in a bigger pool of mobile ARGs.

In northen Vietnam, shrimp farming has in several provinces changed from extensive to intensive production. This change has brought a number of socio-cultural, economic and environmental challenges, including disease outbreaks and an increase in the application of antimicrobials and chemical compounds to prevent and treat diseases. This qualitative study sought to explore shrimp farmers' practices and experiences and the contextual influencers that impact on shrimp farmers' management of ponds in Nghe An and Quang Ninh provinces in Northern Vietnam. In-depth interviews and focus group discussions were conducted with 15 farm owners in each province, and with selected aquaculture technicians employed by the Vietnamese government. Participant observation was carried out during farm visits to gain insight into management practices and preventive and curative treatment. The results showed that farmers were uncertain about how to respond to disease and relied on trial-and-error experiments with antimicrobial products, as well as Chinese products without the auxiliary labels in Vietnamese. Low levels of trust towards government guidance, lead many farmers to be guided by the private and commercial stakeholders with which farmers had more regular contact. Even in this relation, a degree of mistrust was found. The farmers' summed-up their situation as “praying in four directions” [có bệnh thì vái tứ phương] or “playing a game with the Gods” [đánh bạc với trời]. Intensive shrimp farming may be highly profitable, but also a precarious enterprise. We discuss our empirical findings against three analytical concepts. Firstly chronic liminality, defined as an enduring uncertain livelihood situation. Secondly, cultural capital representing farmers' engagement with “know-how” of modern technology of intensive shrimp farming, and globalization. Finally the concept of agency, is applied to discuss farmers diverse actions aimed at gaining control over diseases. Applying these concep

Antimicrobial resistance is a global public health concern, and resistance genes in Salmonella, especially those located on mobile genetic elements, are part of the problem. This study used phenotypic and genomic methods to identify antimicrobial resistance and resistance genes, as well as the plasmids that bear them, in Salmonella isolates obtained from poultry in Nigeria. Seventyfour isolates were tested for susceptibility to eleven commonly used antimicrobials. Plasmid reconstruction and identification of resistance and virulence genes were performed with a draft genome using in silico approaches in parallel with plasmid extraction. Phenotypic resistance to ciprofloxacin (50.0%), gentamicin (48.6%), nalidixic acid (79.7%), sulphonamides (71.6%) and tetracycline (59.5%) was the most observed. Antibiotic resistance genes (ARGs) detected in genomes corresponded well with these observations. Commonly observed ARGs included sul1, sul2, sul3, tet (A), tet (M), qnrS1, qnrB19 and a variety of aminoglycoside-modifying genes, in addition to point mutations in the gyrA and parC genes. Multiple ARGs were predicted to be located on IncN and IncQ1 plasmids of S. Schwarzengrund and S. Muenster, and most qnrB19 genes were carried by Col (pHAD28) plasmids. Seventy-two percent (19/24) of S. Kentucky strains carried multidrug ARGs located in two distinct variants of Salmonella genomic island I. The majority of strains carried full SPI-1 and SPI-2 islands, suggesting full virulence potential.

Staphylococcus aureus is an opportunistic pathogen leading to food poisoning as well as human infections. The present study examined the prevalence and characterization of antimicrobial-resistant S. aureus in sushi from 42 outlets and in pork products from eight outlets in Beijing, China. The total bacterial counts were between 3.0 and 8.9 log CFU/g (mean 5.5 ± 1.5 log CFU/g) in sushi products and 4.8 to 7.4 log CFU/g (mean 5.6 ± 0.8 log CFU/g) in pork products. The mean counts of coliforms were 2.7 and 2.9 log CFU/g in sushi and pork, respectively. Staphylococcus aureus was isolated from seven sushi outlets (13 isolates) and two pork outlets (2 isolates) with average counts below 2 log CFU/g in all cases. A total of 15 S. aureus isolates were further characterized. Six lineages of S. aureus were present, including ST398 (n = 5), ST25 (n = 4), ST15 (n = 2), ST59 (n = 2), ST8 (n = 1) and ST2631 (n = 1). Thirteen isolates contained the scn virulence marker, whereas four and eight isolates contained the virulence marker edinB and enterotoxin genes, respectively. Characterization of antimicrobial resistance profiles documented resistances to ampicillin (n = 15), penicillin (n = 14), ceftazidime (n = 6), erythromycin (n = 4), tetracycline (n = 3), clindamycin (n = 3), and gentamicin (n = 1). Three MRSA isolates were obtained, one from pork (ST398) and two from one sushi outlet (ST59). They were all resistant to at least three classes of antimicrobials and two of them contained the scn gene and enterotoxin genes. Twelve sushi isolates and one of the pork isolates contained the scn gene, indicating that they were of human origin. This emphasizes the potential importance of transmission through foods of antimicrobial-resistant S. aureus including MRSA. We also showed that S. aureus exhibited geographical variation with regards to ST profiles, antimicrobial-resistance and virulence genes when comparing isolates from sushi products sold in Beijing and Copenhagen, Denmark.