A framework was developed to characterize the antimicrobial use/antimicrobial resistance complex in livestock systems in Indonesia, Vietnam, and Thailand. Farm profitability, disease prevention, and mortality rate reduction were identified as drivers toward antimicrobial use in livestock systems. It revealed that antimicrobial use was high in all sectors studied, and that routine preventative use was of particular importance to broiler production systems. Misleading feed labeling was identified as a hurdle to the collection of accurate antimicrobial use data, with farmers being unaware of the antimicrobials contained in some commercial feed. Economic analysis found that the cost of antimicrobials was low relative to other farm inputs, and that farm profitability was precariously balanced. High disease and poor prices were identified as potential drivers toward economic loss. The research indicates that antimicrobial use in small-scale poultry production systems improves feed conversion ratios and overall productivity. However, data were limited to quantify adequately these potential gains and their impacts on the food supply. During the study, all countries embraced and implemented policies on better management of antimicrobial use in livestock and surveillance of antimicrobial resistance. Future policies need to consider farm-level economics and livestock food supply issues when developing further antimicrobial use interventions in the region.

The study aimed to examine the prevalence and genetic characteristics of ESBL-production and colistin resistance in Salmonella and Escherichia coli from pigs and pork in the border area among Thailand, Cambodia, Lao PDR, and Myanmar. Salmonella (n = 463) and E. coli (n = 767) isolates were collected from pig rectal swab from slaughterhouses (n = 441) and pork from retail markets (n = 368) during October 2017 and March 2018. All were determined for susceptibility to colistin and cephalosporins, ESBL production and mcr and ESBL genes. Salmonella was predominantly found in Cambodia (65.8%). Serovars Rissen (35.6%) and Anatum (15.3%) were the most common. The E. coli prevalence in pork was above 91% in all countries. Colistin-resistance rate in E. coli (10.4%) was significantly higher than Salmonella (2.6%). ESBL-producing Salmonella (1.9%) and E. coli (6.3%) were detected. The bla_CTX-M-55 and bla_CTX-M-14 were identified. The mcr-1 gene was detected in Salmonella (n = 12) and E. coli (n = 68). The mcr-1/bla_CTX-M-55 and mcr-3/bla_CTX-M-55 co-concurrence was observed in one Salmonella and three E. coli isolates, respectively. In conclusion, pigs and pork serve as carriers of colistin and new generation cephalosporins resistance. Testing for resistance to last line antibiotics should be included in national AMR surveillance program using One Health approach.

A total of 594 Vibrio parahaemolyticus isolates from cultivated oysters (n = 361) and estuarine water (n = 233) were examined for antimicrobial resistance (AMR) phenotype and genotype and virulence genes. Four hundred forty isolates (74.1%) exhibited resistance to at least one antimicrobial agent and 13.5% of the isolates were multidrug-resistant strains. Most of the V. parahaemolyticus isolates were resistant to erythromycin (54.2%), followed by sulfamethoxazole (34.7%) and trimethoprim (27.9%). The most common resistance genes were qnr (77.8%), strB (27.4%) and tet(A) (22.1%), whereas bla_TEM (0.8%) was rarely found. Four isolates (0.7%) from oysters (n = 2) and estuarine water (n = 2) were positive to tdh, whereas no trh-positive isolates were observed. Significantly positive associations among AMR genes were observed. The SXT elements and class 1, 2 and 3 integrons were absent in all isolates. The results indicated that V. parahaemolyticus isolates from oysters and estuarine water were potential reservoirs of resistance determinants in the environment. This increasing threat of resistant bacteria in the environment potentially affects human health. A ‘One Health’ approach involved in multidisciplinary collaborations must be implemented to effectively manage antimicrobial resistance.

Metabolite profiles from biological samples suffer from both technical variations and subject-specific variants. To improve the quality of metabolomics data, conventional data processing methods can be employed to remove technical variations. These methods do not consider sources of subject variation as separate factors from biological factors of interest. This can be a significant issue when performing quantitative metabolomics in clinical trials or screening for a potential biomarker in early-stage disease, because changes in metabolism or a desired-metabolite signal are small compared to the total metabolite signals. As a result, inter-individual variability can interfere subsequent statistical analyses. Here, we propose an additional data processing step using linear mixed-effects modelling to readjust an individual metabolite signal prior to multivariate analyses. Published clinical metabolomics data was used to demonstrate and evaluate the proposed method. We observed a substantial reduction in variation of each metabolite signal after model fitting. A comparison with other strategies showed that our proposed method contributed to improved classification accuracy, precision, sensitivity and specificity. Moreover, we highlight the importance of patient metadata as it contains rich information of subject characteristics, which can be used to model and normalize metabolite abundances. The proposed method is available as an R package lmm2met.

Background: Tilapia is a primary aquaculture fish in Thailand, but little is known about the occurrence of antimicrobial resistance (AMR) inAeromonas hydrophila,Salmonellaspp., andVibrio choleraecolonizing healthy tilapia intended for human consumption and the co-occurrence of these AMR bacteria in the cultivation water.Methods: This study determined the phenotype and genotype of AMR, extended-spectrumβ-lactamase (ESBL) production, and virulence factors ofA. hydrophila,Salmonellaspp., andV. choleraeisolated from hybrid red tilapia and cultivation water in Thailand. Standard culture methods such as USFDA’s BAM or ISO procedures were used for the original isolation, with all isolates confirmed by biochemical tests, serotyping, and species-specific gene detection based on PCR.Results: A total of 278 isolates consisting of 15A. hydrophila, 188Salmonellaspp., and 75V. choleraeisolates were retrieved from a previous study. All isolates ofA. hydrophilaandSalmonellaisolates were resistance to at least one antimicrobial, with 26.7% and 72.3% of the isolates being multidrug resistant (MDR), respectively. AllA. hydrophilaisolates were resistant to ampicillin (100%), followed by oxytetracycline (26.7%), tetracycline (26.7%), trimethoprim (26.7%), and oxolinic acid (20.0%). The predominant resistance genes inA. hydrophilaweremcr-3(20.0%), followed by 13.3% of isolates havingfloR,qnrS,sul1,sul2, anddfrA1. Salmonellaisolates also exhibited a high prevalence of resistance to ampicillin (79.3%), oxolinic acid (75.5%), oxytetracycline (71.8%), chloramphenicol (62.8%), and florfenicol (55.3%). The most common resistance genes in theseSalmonellaisolates wereqnrS(65.4%),tetA(64.9%),bla_TEM(63.8%), andfloR(55.9%). AllV. choleraeisolates were susceptible to all antimicrobials tested, while the most common resistance gene wassul1(12.0%). One isolate ofA. hydrophilawas positive forint1, while all isolates ofSalmonellaandV. choleraeisolates were negative for integrons andint_SXT. None of the bacterial isolates in this study were producing ESBL. The occurrence ofmcr-3(20.0%) in these isolates from tilapia aquaculture may signify a serious occupational and consumer health risk given that colistin is a last resort antimicrobial for treatment of Gram-negative bacteria infections.Conclusions: Findings from this study on AMR bacteria in hybrid red tilapia suggest that aquaculture as practiced in Thailand can select for ubiquitous AMR pathogens, mobile genetic elements, and an emerging reservoir ofmcrand colistin-resistant bacteria. Resistant and pathogenic bacteria, such as resistance to ampicillin and tetracycline, or MDRSalmonellacirculating in aquaculture, together highlight the public health concerns and foodborne risks of zoonotic pathogens in humans from cultured freshwater fish.