A review and meta-analysis of non-typhoidal Salmonella in Vietnam: Challenges to the control and antimicrobial resistance traits of a neglected zoonotic pathogen

Non-typhoidal Salmonella (NTS) is a food-borne zoonotic pathogen with important implications for human health. Despite its importance, the burden of NTS infections in Vietnam is unknown. We conducted a systematic review and a meta-analysis to describe the prevalence and phenotypic antimicrobial resistance (AMR) for NTS over time in Vietnam. Following PRISMA guidelines, we identified 72 studies from PubMed and Google Scholar containing data relevant to 'Salmonella', 'Salmonellosis', and 'Vietnam', or 'Viet Nam'. Of those, forty-two papers reporting prevalence of NTS, and twenty-six including data on phenotypic resistance were selected for meta-analysis. The prevalence of NTS ranged from 2% to 5% in humans and from 30% to 41% in samples from animals and the farm/slaughterhouse environment. Between 2000 and 2020 we observed a 27.3% (p = 0.044) increase in absolute terms in prevalence among individuals with enteric diseases and a 12.0% (p = 0.047) increase in aquaculture/seafood samples. The most commonly serovars identified across studies included S. Weltevreden (12.0%), followed by S. Typhimurium (10.1%), S. Derby (6.4%), S. London (5.8%), S. Anatum (4.4%), S. Rissen (3.9%), S. Enteritidis (3.7%), S. Albany (3.3%) and S. 4,[5],12:i:- (3.0%). Over the same period, there was an increasing trend in the pooled AMR prevalence for quinolones (15.6% relative increase), 3rd-, 4th-, and 5th-generation cephalosporins (23.7%), penicillins (16.1%), tetracyclines (12.9%), sulfonamides (8.8%), amphenicol (17.8%), and multidrug resistance (11.4%) (all p ≤ 0.014). A broad range of AMR genes (ARGs) were detected in both human and animal populations. The observed prevalence and AMR trends in Vietnam underscore the need of adopting a One Health strategy encompassing surveillance systems, research initiatives, and awareness campaigns to effectively address the challenges posed by NTS.

Molecular characterization of Campylobacter spp. isolates obtained from commercial broilers and native chickens in Southern Thailand using whole genome sequencing

Chickens are the primary reservoirs of Campylobacter spp., mainly C. jejuni and C. coli, that cause human bacterial gastrointestinal infections. However, genomic characteristics and antimicrobial resistance of Campylobacter spp. in low- to middle-income countries need more comprehensive exploration. This study aimed to characterize 21 C. jejuni and 5 C. coli isolates from commercial broilers and native chickens using whole genome sequencing and compare them to 28 reference Campylobacter sequences. Among the 26 isolates, 13 sequence types (ST) were identified in C. jejuni and 5 ST in C. coli. The prominent ST was ST 2274 (5 isolates, 19.2%), followed by ST 51, 460, 2409, and 6455 (2 isolates in each ST, 7.7%), while all remaining ST (464, 536, 595, 2083, 6736, 6964, 8096, 10437, 828, 872, 900, 8237, and 13540) had 1 isolate per ST (3.8%). Six types of antimicrobial resistance genes (ant(6)-Ia, aph(3')-III, blaOXA, cat, erm(B), and tet(O)) and one point mutations in the gyrA gene (Threonine-86-Isoleucine) and another in the rpsL gene (Lysine-43-Arginine) were detected. The blaOXA resistance gene was present in all isolates, the gyrA mutations was in 95.2% of C. jejuni and 80.0% of C. coli, and the tet(O) resistance gene in 76.2% of C. jejuni and 80.0% of C. coli. Additionally, 203 virulence-associated genes linked to 16 virulence factors were identified. In terms of phenotypic resistance, the C. jejuni isolates were all resistant to ciprofloxacin, enrofloxacin, and nalidixic acid, with lower levels of resistance to tetracycline (76.2%), tylosin (52.3%), erythromycin (23.8%), azithromycin (22.2%), and gentamicin (11.1%). Most C. coli isolates were resistant to all tested antimicrobials, while 1 C. coli was pan-susceptible except for tylosin. Single-nucleotide polymorphisms concordance varied widely, with differences of up to 13,375 single-nucleotide polymorphisms compared to the reference Campylobacter isolates, highlighting genetic divergence among comparative genomes. This study contributes to a deeper understanding of the molecular epidemiology of Campylobacter spp. in Thai chicken production systems.

The characterization and correlation between the phenotypic and genotypic resistance of Campylobacter spp. isolates from commercial broilers and native chickens in the south of Thailand

RESEARCH HIGHLIGHTS

High Campylobacter prevalence in chickens; C. jejuni more prevalent than C. coli.Susceptibility to macrolides but resistance to quinolones/tetracyclines in isolates.Homogeneous resistance patterns within farms; higher in broilers than in native birds.Partial association between phenotypic and genotypic resistance among isolates.

Impact of antimicrobial use on abundance of antimicrobial resistance genes in chicken flocks in Vietnam

Objectives

We investigated longitudinally Vietnamese small-scale chicken flocks in order to characterize changes in antimicrobial resistance gene (ARG) content over their life cycle, and the impact of antimicrobial use (AMU) on an intervention consisting of veterinary advice provision.

Methods

AMU data and faecal samples were collected from 83 flocks (25 farms) at day-old, mid- and late-production (∼4 month cycle). Using high-throughput real-time PCR, samples were investigated for 94 ARGs. ARG copies were related to 16S rRNA and ng of DNA (ngDNA). Impact of AMU and ARGs in day-olds was investigated by mixed-effects models.

Results

Flocks received a mean (standard error, SE) animal daily dose (ADD) of 736.7 (83.0) and 52.1 (9.9) kg in early and late production, respectively. Overall, ARGs/16S rRNA increased from day-old (mean 1.47; SE 0.10) to mid-production (1.61; SE 0.16), further decreasing in end-production (1.60; SE 0.1) (all P > 0.05). In mid-production, ARGs/16S rRNA increased for aminoglycosides, phenicols, sulphonamides and tetracyclines, decreasing for polymyxins β-lactams and genes that confer resistance to mutiple classes (multi-drug resistance) (MDR). At end-production, aminoglycoside resistance decreased and polymyxin and quinolone resistance increased (all P < 0.05). Results in relation to ngDNA gave contradictory results. Neither AMU nor ARGs in day-olds had an impact on subsequent ARG abundance. The intervention resulted in 74.2% AMU reduction; its impact on ARGs depended on whether ARGs/ngDNA (+14.8%) or ARGs/16S rRNA metrics (-10.7%) (P > 0.05) were computed.

Conclusions

The flocks' environment (contaminated water, feed and residual contamination) is likely to play a more important role in transmission of ARGs to flocks than previously thought. Results highlight intriguing differences in the quantification of ARGs depending on the metric chosen.

Modelling the impact of antimicrobial use and external introductions on commensal E. coli colistin resistance in small-scale chicken farms of the Mekong delta of Vietnam

Colistin is a critically important antimicrobial for human medicine, and colistin-resistant Escherichia coli are commonly found in poultry and poultry products in Southeast Asia. Here, we aim at disentangling the within-farm and outside-farm drivers of colistin resistance in small-scale chicken farms of the Mekong delta of Vietnam. Nineteen Vietnamese chicken farms were followed up along a whole production cycle, during which weekly antimicrobial use data were recorded. At the beginning, middle and end of each production cycle, commensal E. coli samples from birds were collected, pooled and tested for colistin resistance. Twelve models were fitted to the data using an expectation-maximization algorithm and compared. We further tested the spatial clustering of the occurrence of resistance importations from external sources using the local Moran's I statistic. In the best model, colistin resistance in E. coli from chickens was found to be mostly affected by importations of resistance, and, to a lesser extent, by the use of antimicrobials in the last 1.73 weeks [0.00; 2.90], but not by the use of antimicrobials in day-olds, nor their colistin resistance carriage from hatchery. The occurrence of external source importations proved to be sometimes spatially clustered, suggesting a role of local environmental sources of colistin resistance.

Antimicrobial resistance in commensal Escherichia coli from humans and chickens in the Mekong Delta of Vietnam is driven by antimicrobial usage and potential cross-species transmission

Objectives

To investigate phenotypic antimicrobial resistance (AMR) in relation to antimicrobial use (AMU) and potential inter-species transmission among Escherichia coli from humans and chickens located in the same households in the Mekong Delta of Vietnam.

Methods

We collected data on AMU and faecal swabs from humans (N = 426) and chickens (N = 237) from 237 small-scale farms. From each sample, one E. coli strain was isolated and tested for its susceptibility against 11 antimicrobials by Sensititre AST. The association between AMR and AMU was investigated by logistic regression modelling. Using randomization, we compared the degree of similarity in AMR patterns between human and chicken E. coli from the same farms compared with isolates from different farms.

Results

The AMU rate was ∼19 times higher in chickens (291.1 per 1000 chicken-days) than in humans (15.1 per 1000 person-days). Isolates from chickens also displayed a higher prevalence of multidrug resistance (63.3%) than those of human origin (55.1%). AMU increased the probability of resistance in isolates from human (ORs between 2.1 and 5.3) and chicken (ORs between 1.9 and 4.8). E. coli from humans and chickens living on same farms had a higher degree of similarity in their AMR patterns than isolates from humans and chicken living on different farms.

Conclusions

We demonstrated the co-influence of AMU and potential transmission on observed phenotypic AMR patterns among E. coli isolates from food-producing animals and in-contact humans. Restricting unnecessary AMU alongside limiting interspecies contact (i.e. increasing hygiene and biocontainment) are essential for reducing the burden of AMR.

Minimum inhibitory concentrations of commercial essential oils against common chicken pathogenic bacteria and their relationship with antibiotic resistance

Aims

We investigated the antibacterial effect of seven essential oils (EOs) and one EO‐containing liquid phytogenic solution marketed for poultry and pigs (‘Product A’) on chicken pathogens, as well as the relationship between minimum inhibitory concentration (MIC) in EOs and antibiotics commonly administered to chicken flocks in the Mekong Delta (Vietnam).

Methods and Results

Micellar extracts from oregano (Origanum vulgare), cajeput (Melaleuca leucadendra), garlic (Allium sativum), black pepper (Piper nigrum), peppermint (Mentha × piperita L.), tea tree (Melaleuca alternifolia), cinnamon (Cinnamomum zeylanicum) EOs and Product A were investigated for their MIC against Avibacterium endocarditidis (N = 10), Pasteurella multocida (N = 7), Ornitobacterium rhinotracheale (ORT) (N = 10), Escherichia coli (N = 10) and Gallibacterium anatis (N = 10). Cinnamon EO had the lowest median MIC across strains (median 0.5 mg/ml [IQR, interquartile range 0.3–2.0 mg/ml]), followed by Product A (3.8 mg/ml [1.9–3.8 mg/ml]), oregano EO (30.4 mg/ml [7.6–60.8 mg/ml]) and garlic 63.1 mg/ml [3.9 to >505.0 mg/ml]. Peppermint, tea tree, cajeput and pepper EOs had all MIC ≥219 mg/ml. In addition, we determined the MIC of the 12 most commonly used antibiotics in chicken flocks in the area. After accounting for pathogen species, we found an independent, statistically significant (p < 0.05) positive correlation between MIC of 10 of 28 (35.7%) pairs of EOs. For 67/96 (69.8%) combinations of EOs and antibiotics, the MICs were correlated. Of all antibiotics, doxycycline was positively associated with the highest number of EOs (peppermint, tea tree, black pepper and cajeput, all p < 0.05). For cinnamon, the MICs were negatively correlated with the MICs of 11/12 antimicrobial tested (all except colistin).

Conclusions

Increases in MIC of antibiotics generally correlates with increased tolerance to EOs. For cinnamon EO, however, the opposite was observed.

Significance and Impact of the Study

Our results suggest increased antibacterial effects of EOs on multi‐drug resistant pathogens; cinnamon EO was particularly effective against bacterial poultry pathogens.

Relationship between clinicopathologic factors and FDG avidity in radioiodine-negative recurrent or metastatic differentiated thyroid carcinoma

BACKGROUND

In this study, we investigated the relationship between clinicopathologic factors, BRAFV600E mutation status and [18F] F-fluoro-2-deoxyglucose (FDG) avidity in patients with radioiodine (RAI)-negative recurrent or metastatic differentiated thyroid cancer (DTC).

METHODS

From 2015 to 2018 all patients with suspected recurrent or metastatic radioiodine-negative DTC patients who underwent FDG positron emission tomography/computed tomography (PET/CT) were retrospectively reviewed. Suspected lesions on FDG PET/CT were biopsied and underwent BRAFV600E mutation testing by immunohistochemistry and real-time PCR. Tumor size, recurrent versus metastatic disease, histopathologic features including classical type versus aggressive subtypes (poorly differentiated, tall cell, columnar cell, hobnail variants) and BRAFV600E mutation status were correlated with the SUVmax of highest hypermetabolic lesions on FDG PET/CT by the univariate analysis using logistic regression.

RESULTS

Sixty-three consecutive patients, 55 (87.3%) female, with median age of 48 (range 17-81) were included. The majority of patients had BRAFV600E mutation and classical subtype, 55/63 (87.3%) and 45/63(71.4%), respectively. Thyroglobulin at the time of suspected recurrence was 262.7 ng/ml (range 16.3-1000) and patients received a median 3 prior RAI treatments. Fifty-four patients (85.7%) had local recurrence. The majority of patients 58/63 (92.1%) had FDG-avid disease on PET/CT. On univariate analysis, tumor size aggressive histopathologic types and distant metastasis are the significant factors for predicting FDG uptake, p = 0.04, p = 0.001 and p = 0.004 respectively. Although FDG uptake of BRAFV600E bearing recurrent/metastatic RAIR DTC lesions was higher than those without the mutation, the difference did not reach statistical significance, SUVmax of 7.11 versus 4.91, respectively, p = 0.2.

CONCLUSION

The majority of recurrent or metastatic RAI-negative DTC have BRAFV600E mutation and detectable disease on FDG PET/CT. FDG avidity of the recurrent or metastatic RAI-negative DTC is independently associated with the aggressive histopathologic features.

Characterizing Antimicrobial Resistance in Chicken Pathogens: A Step towards Improved Antimicrobial Stewardship in Poultry Production in Vietnam

In the Mekong Delta of Vietnam, farmers use large quantities of antimicrobials to raise small-scale chicken flocks, often including active ingredients regarded of “critical importance’” by the World Health Organization. Due to limitations in laboratory capacity, the choice of antimicrobials normally does not follow any empirical criteria of effectiveness. The aim of this study was to highlight non-critically important antimicrobials against which chicken pathogens are likely to be susceptible as a basis for treatment guidelines. Microtiter broth dilution method was performed to determine the minimal inhibitory concentration (MIC) of 12 commonly used antimicrobials for 58 isolates, including Ornithobacterium rhinotracheale (ORT) (n = 22), Gallibacterium anatis (n = 19), and Avibacterium endocarditidis (n = 17). Unfortunately, internationally accepted breakpoints for resistance in these organisms do not exist. We drew tentative epidemiological cut-offs (TECOFFs) for those antimicrobial-pathogen combinations where MIC distributions suggested the presence of a distinct non-wild-type population. Based on the observed results, doxycycline would be the drug of choice for A.endocarditidis (11.8% presumptive non-wild type) and G. anatis infections (5.3% presumptive non-wild type). A total of 13.6% ORT isolates were non-wild type with regards to oxytetracycline, making it the drug of choice against this pathogen. This study illustrates the challenges in interpreting susceptibility testing results and the need to establish internationally accepted breakpoints for veterinary pathogens.

Carriage of the zoonotic organism Streptococcus suis in chicken flocks in Vietnam

Streptococcus suis infections are an emerging zoonotic agent causing severe disease in humans and a major pig pathogen worldwide. We investigated the colonization of S. suis in healthy chickens in different flocks (n = 59) as well as in-contact pigs in farms with S. suis-positive chickens (n = 44) in the Mekong Delta of Vietnam. Streptococcus suis was isolated from 20 (33.9%) chicken flocks and from all pigs investigated. Chicken isolates formed a distinct genotypic cluster compared with pig and human strains, although two chicken isolates (10%) clustered with pig isolates. Chicken isolates had unusually high levels of resistance against tetracycline (100%), clindamycin (100%) and erythromycin (95%); and intermediate resistance against penicillin (35%) and ceftriaxone (15%). Our findings suggest that chickens may potentially represent a source of S. suis infection to in-contact humans and pigs.

Antimicrobial residues, non-typhoidal Salmonella, Vibrio spp. and associated microbiological hazards in retail shrimps purchased in Ho Chi Minh city (Vietnam)

We investigated antimicrobial residues, non-typhoidal Salmonella (NTS), Vibrio spp. and their associated antimicrobial resistance (AMR), in shrimps locally purchased in Ho Chi Minh City (Vietnam). In addition, we investigated the relationship between AMR in NTS, Vibrio spp. and antimicrobial residue in the same sample. A total of 40 samples of shrimp heads/shells from different retail sources was cultured using ISO 6579-1:2017 (NTS) and ISO/TS 21872-1:2007 (Vibrio spp.). Phenotypic antimicrobial susceptibility was investigated using Vitek (NTS, 34 antimicrobials) and disk diffusion (Vibrio spp., 12 antimicrobials). A total of 9 (22.5%) samples contained antimicrobial residue, including tetracyclines, fluoroquinolones, sulfonamides and macrolides (in 7.5%, 7.5%, 2.5% and 2.5% of samples, respectively). Shrimp samples from supermarkets had a higher prevalence of antimicrobial residue than those purchased in street markets (50% vs. 13.3%) (p = 0.049). A total of 30 (75%) samples were contaminated with NTS. All samples contained Vibrio spp., with V. parahaemolyticus being most common (87.5% samples). A total of 58.9% NTS isolates were multidrug resistant. With regards to the highest priority, critically important antimicrobials, the highest resistance corresponded to quinolones (14.4-47.8%), followed by 3rd and 4th generation cephalosporins (3.3-7.8%). Vibrio spp. isolates were characterised by their high resistance against ampicillin (82.7%) and 3rd generation cephalosporins (8.3-16.5%). Extended Spectrum Beta-Lactamase (ESBL) activity was detected in 28.1% V. parahaemolyticus isolates. Half of ESBL-positive V. parahaemolyticus strains harboured bla CTX-M1. We found an association between the presence of residues and the number of resistances for NTS (p = 0.075) and Vibrio spp. isolates (p = 0.093) from the same sample. These findings suggest that the presence of residues may contribute to the selection of AMR in foodborne pathogens in shrimps. Authorities should strengthen policies aiming at restricting inappropriate antimicrobial usage in shrimp farming, and step up monitoring of antimicrobial residues and food-borne pathogens at retail in Vietnam.

Characterization of viral, bacterial, and parasitic causes of disease in small-scale chicken flocks in the Mekong Delta of Vietnam

In the Mekong Delta region of Vietnam, small-scale chicken farming is common. However, high levels of disease or mortality in such flocks impair economic development and challenge the livelihoods of many rural households. We investigated 61 diseased small-scale flocks (122 chickens) for evidence of infection with 5 bacteria, 4 viruses, and helminths. Serological profiles (ELISA) were also determined against 6 of these pathogens. The aims of this study were the following: (1) to investigate the prevalence of different pathogens and to compare the probability of detection of bacterial pathogens using PCR and culture; (2) to investigate the relationship between detection of organisms in birds' tissues and the observed morbidity and mortality, as well as their antibody profile; and (3) to characterize risk factors for infection with specific viral or bacterial pathogens. We used PCR to test for viral (viruses causing infectious bronchitis [IB], highly pathogenic avian influenza [HPAI], Newcastle disease, and infectious bursal disease [IBD]) and bacterial pathogens (Mycoplasma gallisepticum, Pasteurella multocida, Avibacterium paragallinarum, and Ornithobacterium rhinotracheale [ORT]). The latter two were also investigated in respiratory tissues by conventional culture. Colisepticemic Escherichia coli was investigated by liver or spleen culture. In 49 of 61 (80.3%) flocks, at least one bacterial or viral pathogen was detected, and in 29 (47.5%) flocks, more than one pathogen was detected. A. paragallinarum was detected in 62.3% flocks, followed by M. gallisepticum (26.2%), viruses causing IBD (24.6%) and IB (21.3%), septicemic E. coli (14.8%), ORT (13.1%), and HPAI viruses (4.9%). Of all flocks, 67.2% flocks were colonized by helminths. Mortality was highest among flocks infected with HPAI (100%, interquartile range [IQR]: 81.6–100%) and lowest with flocks infected with ORT (5.3%, IQR: 1.1–9.0%). The results indicated slight agreement (kappa ≤ 0.167) between detection by PCR and culture for both A. paragallinarum and ORT, as well as between the presence of cestodes and ORT infection (kappa = 0.317). Control of A. paragallinarum, viruses causing HPAI, IBD, and IB, M. gallisepticum, and gastrointestinal helminths should be a priority in small-scale flocks.

Optimization of the in vitro fertilization protocol for frozen epididymal sperm with low fertilization ability in Ban-A native Vietnamese pigs

The aim of the present study was to improve the penetration during in vitro fertilization (IVF) of a frozen lot of epididymal sperm with a notoriously low fertilization ability of a Ban boar which is a native Vietnamese breed by optimizing different parameters of the IVF system. In Experiment 1, we determined that Pig-fertilization medium was superior medium to Tyrode's albumin lactate pyruvate-polyvinyl alcohol medium for IVF and defined the optimum the sperm concentration (1 × 10⁶  sperm/ml). In Experiment 2, we clarified that partial removal of cumulus cells from cumulus-oocyte complexes by hyaluronidase treatment before IVF enhances sperm penetration, whereas complete cumulus removal reduces penetration. Finally, in Experiment 3 the elevation of concentration of caffeine in Pig-fertilization medium from 2 to 5 mmol/L and the prolongation of the co-culture of gametes from 3 to 5 hr significantly increased the total penetration rate from 15.2% to over 50%. In conclusion, the combination of partial oocyte denudation, an elevated caffeine concentration in Pig-fertilization medium and an extended interval of IVF with using an optimized sperm concentration was a potent way to improve the fertilization results for a frozen epididymal Ban sperm lot with low fertility.

Zoonotic Transmission of mcr-1 Colistin Resistance Gene from Small-Scale Poultry Farms, Vietnam

We investigated the consequences of colistin use in backyard chicken farms in Vietnam by examining the prevalence of mcr-1 in fecal samples from chickens and humans. Detection of mcr-1–carrying bacteria in chicken samples was associated with colistin use and detection in human samples with exposure to mcr-1–positive chickens.

Antimicrobial residues and resistance against critically important antimicrobials in non-typhoidal Salmonella from meat sold at wet markets and supermarkets in Vietnam

Excessive antimicrobial usage and deficiencies in hygiene in meat production systems may result in undesirable human health hazards, such as the presence of antimicrobial drug residues and non-typhoidal Salmonella (NTS), including antimicrobial resistant (AMR) NTS. Recently, Vietnam has witnessed the emergence of integrated intensive animal production systems, coexisting with more traditional, locally-sourced wet markets. To date no systematic studies have been carried out to compare health hazards in beef, pork and chicken in different production systems. We aimed to: (1) estimate the prevalence of antimicrobial residues in beef, pork and chicken meat; (2) investigate the prevalence and levels of NTS contamination; and (3) investigate serovar distribution and AMR against critically important antimicrobials by animal species and type of retail (wet market vs. supermarket) in Vietnam. Fresh pork, beef and chicken meat samples (N=357) sourced from wet markets and supermarkets in Ho Chi Minh City (HCMC), Hanoi and Dong Thap were screened for antimicrobial residues by PremiTest, and were further investigated by Charm II. Samples from HCMC (N=113) were cultured using ISO 6579:2002/Amd 1:2007. NTS bacteria were quantified using a minimum probable number (MPN) technique. NTS isolates were assigned to serovar by Multilocus Sequence Typing (MLST), and were investigated for their phenotypic susceptibility against 32 antimicrobials. A total of 26 (7.3%) samples tested positive by PremiTest (9.5% beef, 4.1% pork and 8.4% chicken meat). Sulfonamides, tetracyclines and macrolides were detected by Charm in 3.1%, 2.8% and 2.0% samples, respectively. Overall, meat samples from wet markets had a higher prevalence of residues than those from supermarkets (9.6% vs. 2.6%) (p=0.016). NTS were isolated from 68.4% samples from HCMC. Chicken samples from wet markets had by far the highest NTS counts (median 3.2 logMPN/g). NTS isolates displayed high levels of resistance against quinolones (52.2%) and β-lactams (49.6%), but low levels against 3rd generation cephalosporins (4.4%) and aminoglycosides (0.8%). The highest adjusted prevalence of multidrug resistance (MDR) corresponded to isolates from chicken meat and pork (OR 8.3 and 1.8, respectively) (baseline=beef). S. Kentucky was the most common serovar identified (11 from chicken, 1 from beef) and 91.7% isolates was MDR. 11/12 isolates corresponded to ST198, a worldwide-disseminated multi-resistant NTS clone. We recommend stepping up policy measures to promote responsible antimicrobial use in animal production, as well as awareness about withdrawal periods to limit the hazard of residues in animal products, and improving slaughtering/hygiene procedures to limit cross-contamination with NTS, particularly in poultry wet markets.

Antimicrobial Resistance in Bacterial Poultry Pathogens: A Review

Antimicrobial resistance (AMR) is a global health threat, and antimicrobial usage and AMR in animal production is one of its contributing sources. Poultry is one of the most widespread types of meat consumed worldwide. Poultry flocks are often raised under intensive conditions using large amounts of antimicrobials to prevent and to treat disease, as well as for growth promotion. Antimicrobial resistant poultry pathogens may result in treatment failure, leading to economic losses, but also be a source of resistant bacteria/genes (including zoonotic bacteria) that may represent a risk to human health. Here we reviewed data on AMR in 12 poultry pathogens, including avian pathogenic Escherichia coli (APEC), Salmonella Pullorum/Gallinarum, Pasteurella multocida, Avibacterium paragallinarum, Gallibacterium anatis, Ornitobacterium rhinotracheale (ORT), Bordetella avium, Clostridium perfringens, Mycoplasma spp., Erysipelothrix rhusiopathiae, and Riemerella anatipestifer. A number of studies have demonstrated increases in resistance over time for S. Pullorum/Gallinarum, M. gallisepticum, and G. anatis. Among Enterobacteriaceae, APEC isolates displayed considerably higher levels of AMR compared with S. Pullorum/Gallinarum, with prevalence of resistance over >80% for ampicillin, amoxicillin, tetracycline across studies. Among the Gram-negative, non-Enterobacteriaceae pathogens, ORT had the highest levels of phenotypic resistance with median levels of AMR against co-trimoxazole, enrofloxacin, gentamicin, amoxicillin, and ceftiofur all exceeding 50%. In contrast, levels of resistance among P. multocida isolates were less than 20% for all antimicrobials. The study highlights considerable disparities in methodologies, as well as in criteria for phenotypic antimicrobial susceptibility testing and result interpretation. It is necessary to increase efforts to harmonize testing practices, and to promote free access to data on AMR in order to improve treatment guidelines as well as to monitor the evolution of AMR in poultry bacterial pathogens.

Colonization of Enteroaggregative Escherichia coli and Shiga toxin-producing Escherichia coli in chickens and humans in southern Vietnam

Background

Enteroaggregative (EAEC) and Shiga-toxin producing Escherichia coli (STEC) are a major cause of diarrhea worldwide. E. coli carrying both virulence factors characteristic for EAEC and STEC and producing extended-spectrum beta-lactamase caused severe and protracted disease during an outbreak of E. coli O104:H4 in Europe in 2011. We assessed the opportunities for E. coli carrying the aggR and stx genes to emerge in ‘backyard’ farms in south-east Asia.

Results

Faecal samples collected from 204 chicken farms; 204 farmers and 306 age- and gender-matched individuals not exposed to poultry farming were plated on MacConkey agar plates with and without antimicrobials being supplemented. Sweep samples obtained from MacConkey agar plates without supplemented antimicrobials were screened by multiplex PCR for the detection of the stx1, stx2 and aggR genes. One chicken farm sample each (0.5 %) contained the stx1 and the aggR gene. Eleven (2.4 %) human faecal samples contained the stx1 gene, 2 samples (0.4 %) contained stx2 gene, and 31 (6.8 %) contained the aggR gene. From 46 PCR-positive samples, 205 E. coli isolates were tested for the presence of stx1, stx2, aggR, wzx_O104 and fliC_H4 genes. None of the isolates simultaneously contained the four genetic markers associated with E. coli O104:H4 epidemic strain (aggR, stx2, wzx_O104 and fliC_H4). Of 34 EAEC, 64.7 % were resistant to 3^rd-generation cephalosporins.

Conclusion

These results indicate that in southern Vietnam, the human population is a more likely reservoir of aggR and stx gene carrying E. coli than the chicken population. However, conditions for transmission of isolates and/or genes between human and animal reservoirs resulting in the emergence of highly virulent E. coli strains are still favorable, given the nature of‘backyard’ farms in Vietnam.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-016-0827-z) contains supplementary material, which is available to authorized users.

Antimicrobial Consumption in Medicated Feeds in Vietnamese Pig and Poultry Production

Antimicrobials are extensively used as growth promoters in animal feeds worldwide, but reliable estimates are lacking. We conducted an internet-based survey of commercial chicken and pig feed products officially approved for sale in Vietnam over the period March-June 2015. Information on the antimicrobial contents in feed products, alongside animal production data, was used to estimate in-feed antimicrobial consumption to produce one kilogram of live animal (chicken, pig), as well as to estimate country-wide antimicrobial consumption through animal feeds. A total of 1462 commercial feed formulations were examined. The survey-adjusted estimated antimicrobial contents were 25.7 and 62.3 mg/kg in chicken and pig feeds, respectively. Overall, it was estimated that 77.4 mg [95% CI 48.1-106.8] and 286.6 mg [95% CI 191.6-418.3] of in-feed antimicrobials were used to raise 1 kg of live chicken and pig, respectively. Bacitracin (15.5% feeds), chlortetracycline (11.4%), and enramycin (10.8%) were the most common antimicrobials present in chicken feed formulations, whereas bacitracin (24.8%), chlortetracycline (23.9%), and florfenicol (17.4%) were the most common in pig feed formulations. Overall, 57% of the total quantitative usage consisted of antimicrobials regarded by WHO of importance for human medicine, including amoxicillin, colistin, tetracyclines, neomycin, lincomycin, and bacitracin. These figures confirm a very high magnitude of in-feed consumption of antimicrobials, especially in pig production. Results from this study should encourage further monitoring of antimicrobials used in animal production, and foster discussion about existing policies on inclusion of antimicrobials in animal feed rations.

Non-Typhoidal Salmonella Colonization in Chickens and Humans in the Mekong Delta of Vietnam

Salmonellosis is a public health concern in both the developed and developing countries. Although the majority of human non‐typhoidal Salmonella enterica (NTS) cases are the result of foodborne infections or person‐to‐person transmission, NTS infections may also be acquired by environmental and occupational exposure to animals. While a considerable number of studies have investigated the presence of NTS in farm animals and meat/carcasses, very few studies have investigated the risk of NTS colonization in humans as a result of direct animal exposure. We investigated asymptomatic NTS colonization in 204 backyard chicken farms, 204 farmers and 306 matched individuals not exposed to chicken farming, in southern Vietnam. Pooled chicken faeces, collected using boot or handheld swabs on backyard chicken farms, and rectal swabs from human participants were tested. NTS colonization prevalence was 45.6%, 4.4% and 2.6% for chicken farms, farmers and unexposed individuals, respectively. Our study observed a higher prevalence of NTS colonization among chicken farmers (4.4%) compared with age‐, sex‐ and location‐ matched rural and urban individuals not exposed to chickens (2.9% and 2.0%). A total of 164 chicken NTS strains and 17 human NTS strains were isolated, and 28 serovars were identified. Salmonella Weltevreden was the predominant serovar in both chickens and humans. NTS isolates showed resistance (20–40%) against tetracycline, chloramphenicol, sulfamethoxazole‐trimethoprim and ampicillin. Our study reflects the epidemiology of NTS colonization in chickens and humans in the Mekong delta of Vietnam and emphasizes the need of larger, preferably longitudinal studies to study the transmission dynamics of NTS between and within animal and human host populations.

Highly Pathogenic Avian Influenza Virus A/H5N1 Infection in Vaccinated Meat Duck Flocks in the Mekong Delta of Vietnam

We investigated episodes of suspected highly pathogenic avian influenza (HPAI)-like illness among 12 meat duck flocks in two districts in Tien Giang province (Mekong Delta, Vietnam) in November 2013. In total, duck samples from 8 of 12 farms tested positive for HPAI virus subtype A/haemagglutinin 5 and neuraminidase 1 (H5N1) by real-time RT-PCR. Sequencing results confirmed clade of 2.3.2.1.c as the cause of the outbreaks. Most (7/8) laboratory-confirmed positive flocks had been vaccinated with inactivated HPAI H5N1 clade 2.3.4 vaccines <6 days prior to onset of clinical signs. A review of vaccination data in relation to estimated production in the area suggested that vaccination efforts were biased towards larger flocks and that vaccination coverage was low [21.2% ducks vaccinated with two shots (range by district 7.4-34.9%)]. The low-coverage data, the experimental evidence of lack of cross-protection conferred by the currently used vaccines based on clade 2.3.4 together with the short lifespan of meat duck flocks (60-70 days), suggest that vaccination is not likely to be effective as a tool for control of H5N1 infection in meat duck flocks in the area.

High levels of antimicrobial resistance among escherichia coli isolates from livestock farms and synanthropic rats and shrews in the Mekong Delta of Vietnam

In Mekong Delta farms (Vietnam), antimicrobials are extensively used, but limited data are available on levels of antimicrobial resistance (AMR) among Escherichia coli isolates. We performed a structured survey of AMR in E. coli isolates (n = 434) from 90 pig, chicken, and duck farms. The results were compared with AMR among E. coli isolates (n = 234) from 66 small wild animals (rats and shrews) trapped on farms and in forests and rice fields. The isolates were susceptibility tested against eight antimicrobials. E. coli isolates from farmed animals were resistant to a median of 4 (interquartile range [IQR], 3 to 6) antimicrobials versus 1 (IQR, 1 to 2) among wild mammal isolates (P < 0.001). The prevalences of AMR among farmed species isolates (versus wild animals) were as follows: tetracycline, 84.7% (versus 25.6%); ampicillin, 78.9% (versus 85.9%); trimethoprim-sulfamethoxazole, 52.1% (versus 18.8%); chloramphenicol, 39.9% (versus 22.5%); amoxicillin-clavulanic acid, 36.6% (versus 34.5%); and ciprofloxacin, 24.9% (versus 7.3%). The prevalence of multidrug resistance (MDR) (resistance against three or more antimicrobial classes) among pig isolates was 86.7% compared to 66.9 to 72.7% among poultry isolates. After adjusting for host species, MDR was ∼8 times greater among isolates from wild mammals trapped on farms than among those trapped in forests/rice fields (P < 0.001). Isolates were assigned to unique profiles representing their combinations of susceptibility results. Multivariable analysis of variance indicated that AMR profiles from wild mammals trapped on farms and those from domestic animals were more alike (R(2) range, 0.14 to 0.30) than E. coli isolates from domestic animals and mammals trapped in the wild (R(2) range, 0.25 to 0.45). The results strongly suggest that AMR on farms is a key driver of environmental AMR in the Mekong Delta.