Whole genome sequencing analysis on antibiotic-resistant Escherichia coli isolated from pig farms in Banten Province, Indonesia.

IMPORTANCE: The emergence and rapid increase in the incidence of multidrug-resistant (MDR) bacteria in pig farms has become a serious concern and reduced the choice of effective antibiotics. OBJECTIVE: This study analyzed the phylogenetics and diversity of antibiotic resistance genes (ARGs) and molecularly identified the source of ARGs in antibiotic-resistant Escherichia coli isolated from pig farms in Banten Province, Indonesia. METHODS: Forty-four antibiotic-resistant E. coli isolates from fecal samples from 44 pig farms in Banten Province, Indonesia, were used as samples. The samples were categorized into 14 clusters. Sequencing was performed using the Oxford Nanopore Technologies MinION platform, with barcoding before sequencing with Nanopore Rapid sequencing gDNA-barcoding (SQK-RBK110.96) according to manufacturing procedures. ARG detection was conducted using ResFinder, and the plasmid replicon was determined using PlasmidFinder. RESULTS: Three phylogenetic leaves of E. coli were identified in the pig farming cluster in Banten Province. The E. coli isolates exhibited potential resistance to nine classes of antibiotics. Fifty-one ARGs were identified across all isolates, with each cluster carrying a minimum of 10 ARGs. The ant(3'')-Ia and qnrS1 genes were present in all isolates. ARGs in the E. coli pig farming cluster originated mainly from plasmids, accounting for an average of 89.4%. CONCLUSIONS AND RELEVANCE: The elevated potential for MDR events, coupled with the dominance of ARGs originating from plasmids, increases the risk of ARG spread among bacterial populations in animals, humans, and the environment.

Metagenomic insights into isolable bacterial communities and antimicrobial resistance in airborne dust from pig farms.

This study aims to investigate bacterial communities and antimicrobial resistance (AMR) in airborne dust from pig farms. Airborne dust, pig feces and feed were collected from nine pig farms in Thailand. Airborne dust samples were collected from upwind and downwind (25 meters from pig house), and inside (in the middle of the pig house) of the selected pig house. Pig feces and feed samples were individually collected from the pen floor and feed trough from the same pig house where airborne dust was collected. A direct total bacteria count on each sampling plate was conducted and averaged. The ESKAPE pathogens together with Escherichia coli, Salmonella, and Streptococcus were examined. A total of 163 bacterial isolates were collected and tested for MICs. Pooled bacteria from the inside airborne dust samples were analyzed using Metagenomic Sequencing. The highest bacterial concentration (1.9-11.2 × 103 CFU/m3) was found inside pig houses. Staphylococcus (n = 37) and Enterococcus (n = 36) were most frequent bacterial species. Salmonella (n = 3) were exclusively isolated from feed and feces. Target bacteria showed a variety of resistance phenotypes, and the same bacterial species with the same resistance phenotype were found in airborne dust, feed and fecal from each farm. Metagenomic Sequencing analysis revealed 1,652 bacterial species across all pig farms, of which the predominant bacterial phylum was Bacillota. One hundred fifty-nine AMR genes of 12 different antibiotic classes were identified, with aminoglycoside resistance genes (24%) being the most prevalent. A total of 251 different plasmids were discovered, and the same plasmid was detected in multiple farms. In conclusion, the phenotypic and metagenomic results demonstrated that airborne dust from pig farms contained a diverse array of bacterial species and genes encoding resistance to a range of clinically important antimicrobial agents, indicating the significant role in the spread of AMR bacterial pathogens with potential hazards to human health. Policy measurements to address AMR in airborne dust from livestock farms are mandatory.

Prevalence and Genetic Characterization of Porcine Respiratory Coronavirus in Korean Pig Farms.

Porcine respiratory coronavirus (PRCV) is a member of the species Alphacoronavirus 1 within the genus Alphacoronavirus of the family Coronaviridae. A few studies have been conducted on the prevalence of PRCV since its first identification in 1997, but there have been no recent studies on the prevalence and genetic characterization of the virus in Korea. In this study, the seroprevalence of PRCV was determined in Korean pig farms using a commercially available TGEV/PRCV differential enzyme-linked immunosorbent assay kit. The farm-level seroprevalence of PRCV was determined to be 68.6% (48/70), similar to previous reports in Korea, suggesting that PRCV is still circulating in Korean pig herds nationwide. Among the 20 PRCV-seropositive farms tested in this study, PRCV RNAs were detected in 17 oral fluid samples (28.3%) from nine farms (45.0%), while TGEV RNAs were not detected in any sample. To investigate the genetic characteristics of Korean PRCV strains, genetic and phylogenetic analyses were conducted on PRCV spike gene sequences obtained in this study. The three Korean PRCV strains (KPRCV2401, KPRCV2402, and KPRCV2403) shared 98.5-100% homology with each other and 96.2-96.6% and 91.6-94.5% homology with European and American strains, respectively. A 224-amino acid deletion was found in the S gene of both Korean and European PRCVs but not in that of American PRCVs, suggesting a European origin for Korean PRCVs. Phylogenetic analysis showed that Korean PRCVs are more closely related to European PRCVs than American PRCVs but clustered apart from both, suggesting that Korean PRCV has evolved independently since its emergence in Korean PRCVs. The results of this study will help expand knowledge on the epidemiology and molecular biology of PRCV currently circulating in Korea.

Salivary and serum haptoglobin, adenosine deaminase, and immunoglobulin G in growing pigs.

BACKGROUND: Identification of animals in need of medical treatment is important in porcine health management, where analytical samples applicable at farm level could be utilized. Several biomarkers are measurable in saliva, which is less stressful to collect than blood. Saliva sampling is easy to learn and repeatable, making it suitable for monitoring purposes. Previous research suggests that porcine health biomarkers are dependent on production stage and gender, and that combining biomarkers improves diagnostic sensitivity. However, proper monitoring of biomarkers during the complete production cycle has not been studied. We aimed to describe the dynamics of salivary and serum haptoglobin (Hp), adenosine deaminase (ADA), and immunoglobulin G (IgG) in four production stages (suckling, early growing, late growing, finishing), on commercial Finnish pig farms using a total of 117 piglets. The relationship between gender and biomarker dynamics was investigated, as well as the relationships between these biomarkers in saliva and serum. RESULTS: The highest salivary concentrations of Hp, ADA and IgG were measured in suckling piglets. The differences between production stages were generally larger in saliva than for the corresponding serum biomarkers. All correlation coefficients between salivary biomarkers were positive in each production stage and the strength of the correlation varied from 0.245 to 0.762. No similar trend was observed regarding correlation coefficients either between serum biomarkers or between salivary and serum biomarkers. Gender was associated with some biomarker concentrations. CONCLUSIONS: The biomarker dynamics supported previous findings that collection of analytical samples should be conducted in age-matched populations. Positive and even strong relationships between salivary biomarkers indicate the potential to use especially saliva for health monitoring. Our results also suggest the importance of considering gender effects when assessing some salivary or serum biomarkers.

An economic assessment of alternative antimicrobial use scenarios on pig farms.

This paper explores the theoretical economic outcome of management changes that result in different levels of antimicrobial use (AMU) in two types of UK pig farm. A static farm economic pig production model (FEPM) was used on a representative 'Top-third' most profitable farm and a representative 'Mid-range' profitable farm. Three AMU theoretical management scenarios were investigated; (a) management changes leading to a reduction of AMU by 35% (AMU35); (b) more extensive management changes leading to a reduction of AMU by 95% (AMU95); and (c) implementing depopulation of the herd (AMU Depop). A sensitivity analysis was conducted to determine the effect of increases or decreases in pig revenue and feed price on farm gross margin under these scenarios. Over a single year, the AMU35 scenario was estimated to have a small positive impact (+3%) on both farm types. The other two AMU reduction scenarios had higher AMU reduction on farms but required higher variable cost and hence they resulted in lower farm profitability. There was a substantial reduction (up to -50%) in farm gross margin under these two AMU reduction scenarios in the modeled short-term time-period. The impact of the alternative AMU scenarios was slightly higher on a farm representing the 'Top-third' farm type, reducing farm gross margin further by 7% compared to the 'Mid-range' farm. Nevertheless, both farm types stay profitable under all three AMU scenarios. The results showed that in the modeled short-term implementing management changes that result in a reduction of on-farm AMU by 35% had a good economic outcome. In practice, the other two scenarios would be considered as longer-term strategies. Although both require higher initial costs to implement, the improved biosecurity and hygiene will benefit from lower disease occurrence for a longer term. Farm gross margins were, however, found to be highly sensitive to changes on market prices especially increasing feed prices. An increase of more than 15% in feed price moved a profitable farm into a loss-making farm. It will be economically challenging for uptakes of these, or similar, AMU reduction scenarios on farms if the market prices become un-favorable to pig farmers.

Predominance of the Blastocystis subtype ST5 among free-living sympatric rodents within pig farms in China suggests a novel transmission route from farms.

Blastocystis is a parasitic protist that can infect humans and various domestic and wild animals. However, there is limited research on the prevalence of this parasite among rodents, particularly those living in pig farm settings. Therefore, to investigate the occurrence, molecular characterization, and zoonotic potential of Blastocystis among rodents within pig farm environments, we conducted an investigation of 227 rodents and shrews from 34 pig farms located in Henan, Shaanxi, and Shanxi provinces of China using nested PCR of the SSU rRNA gene of Blastocystis. The potential transmission and public health implications were also assessed from a One Health perspective. Blastocystis was detected in 86 (37.9%) fecal samples. The highest infection rate was observed among Ruttus norvegicus (73.7%, 42/58), followed by Ruttus tanezumi (30.1%, 41/136), and Mus musculus (12.0%, 3/25). However, it was not detected among individuals with Apodemus agrarius (n = 1) and Crocidura shantungensis (n = 7). Five known zoonotic Blastocystis subtypes (ST1-ST5) were identified, with ST4 (51.2%, 44/86) and ST5 (40.7%, 35/86) being the predominant ones, followed by ST1 (3.5%, 3/86), ST3 (3.5%, 3/86), and ST2 (1.2%, 1/86). ST4 was prevalent among R. norvegicus (83.3%, 35/42), while ST5 dominated R. tanezumi (70.7%, 29/41). Furthermore, ST5 exhibited the widest distribution at pig farm level, accounting for 65.0% (13/20) of Blastocystis-positive pig farms. This investigation presents the first documented Blastocystis infection in R. tanezumi and M. musculus, highlighting the predominant presence of the zoonotic ST5 subtype in rodents for the first time. The results demonstrate that sympatric rodents can serve as natural reservoirs for Blastocystis and play a role in its transmission. These findings provide information on the dynamics of rodent transmission and emphasize the potential public health threat posed by zoonotic Blastocystis subtypes spillover from pig farms.

Simultaneous Electrochemical Detection of Cu2+ and Zn2+ in Pig Farm Wastewater.

In recent years, the rapid development of pig farming has led to a large quantity of heavy metal-polluted wastewater. Thus, it was desirable to develop a simple heavy metal detection method for fast monitoring of the wastewater from the pig farms. Therefore, there was an urgent need to develop a simple method for rapidly detecting heavy metal ions in pig farm wastewater. Herein, a simple electrochemical method for simultaneous detection of Cu2+ and Zn2+ was developed and applied to pig farm wastewater. With a glassy carbon electrode and anodic stripping voltammetry, simultaneous detection of Cu2+ and Zn2+ in water was achieved without the need for complicated electrode modification. Furthermore, it was found that the addition of Cd2+ can enhance the response current of the electrode to Zn2+, which increased the signal by eight times. After systematic optimization, the limit of detection (LOD) of 9.3 µg/L for Cu2+ and 45.3 µg/L for Zn2+ was obtained. Finally, it was successfully applied for the quantification of Cu2+ and Zn2+ with high accuracy in pig farm wastewater. This work provided a new and simple solution for fast monitoring of the wastewater from pig farms and demonstrated the potential of electrochemical measurement for application in modern animal husbandry.

Estimating the time of infection for African swine fever in pig farms in Korea.

African swine fever (ASF) is a highly contagious and lethal disease with characteristics of hemorrhagic fever. ASF outbreaks in pig farms significantly damage the entire pork industry. Understanding the transmission dynamics of ASF is crucial to effectively respond. Notably, it is important to know when the infection started on the outbreak farm. This study aimed at establishing a procedure for estimating the time of infection on pig farms affected by the ASF outbreak in Korea. The protocol for sampling to detect ASF virus infection, the estimation of the time interval between infection and detection, and the estimation of the infection stage parameters for the simulation model were described. After infection, fattening sheds (9.8 days in median) had the longest detection time compared with pregnant (8.6 days) or farrowing sheds (8.0 days). The intervals were 8.8 days for farrow-to-finisher farms, 7.0 days for farrow-to-weaning farms, and 9.5 days for fattening farms. The findings of this study provide valuable insights into ASF outbreaks in pig farms thus, improving the disease control ability.

Nitrogen removal characteristics of heterotrophic nitrification-aerobic denitrification bacterium Acinetobacter ZQ-A1 and community characteristics analysis of its application in pig farm wastewater.

A heterotrophic nitrifying aerobic denitrifying (HN-AD) strain ZQ-A1 with excellent denitrification performance, identified as Acinetobacter, was isolated from simultaneous nitrification and denitrification (SND) craft. ZQ-A1 was capable of removing NH4+, NO2-, and NO3-; the 21-hour removal rates were 84.84%, 87.13%, and 92.63%. ZQ-A1 has the ability to treat mixed nitrogen sources. In addition, ZQ-A1 can be well applied to actual sewage. According to the analysis of microbial community characteristics, the relative abundance of Acinetobacter in the experimental group increased from 0.06% to 2.38%, which is an important reason for the removal rate of NH4+ exceeding 99% within 30 days. The results of KEGG function prediction showed that with the addition of ZQ-A1, the relative abundance of pathways related to bacterial metabolism, such as tricarboxylic acid cycle metabolism, was higher. The research expanded the thinking of HN-AD bacteria in actual production and laid a foundation for its application in sewage treatment.

Pathogenicity and Pathological Characteristics of African Swine Fever Virus Strains from Pig Farms in South Korea from 2022 to January 2023.

Since the first African swine fever (ASF) outbreak occurred at a pig farm in South Korea in September 2019, as of 31 January 2023, 31 ASF cases have occurred at pig farms, while 2799 ASF virus (ASFV)-infected wild boars have been identified. The circulation of ASFV in wild boar populations poses a high risk of spillover to pig farms in the country. However, information on the changes in the pathogenicity of Korean ASFV strains from wild boars is not available. Investigating the pathogenicity of ASFV strains from pig farms is the only way to predict their alterations. In a previous study, no changes in the pathogenicity of ASFV strains circulating during 2019-2021 were identified through animal experiments. In this study, we chose two ASFV strains with potentially reduced pathogenicity among ten viruses obtained from pig premises from 2022 to January 2023 and estimated their pathogenicities and pathological characteristics. All the inoculated pigs died 8-10 days post-inoculation after showing pyrexia, depression, anorexia, and recumbency together with the common pathological lesions of enlarged hemorrhagic lymph nodes and splenomegaly with infarction. These results support that the pathogenicity among ASFV isolates in South Korea still remained unchanged during the study period.

How Does Epidemic Prevention Training for Pig Breeding Affect Cleaning and Disinfection Procedures Adoption? Evidence from Chinese Pig Farms.

African Swine Fever (ASF) is a highly infectious disease, severely affecting domestic pigs and wild boar. It has significantly contributed to economic losses within the pig farming industry. As a critical component of biosecurity measures, the selection of cleaning and disinfection (C&D) procedures is a dynamic and long-term decision that demands a deeper knowledge base among pig farmers. This study uses a binary logit model to explore the effect of epidemic prevention training on the adoption of C&D procedures among pig farmers with irregular and regular C&D procedures based on micro-survey data obtained from 333 pig farmers from Sichuan. The endogeneity issue was handled using propensity score matching, resulting in solid conclusions. In addition, the critical mediating impact of biosecurity cognition was investigated using a bootstrap analysis. The empirical study demonstrated that epidemic prevention training encourages pig farmers to adopt C&D procedures, with biosecurity cognition significantly mediating. Furthermore, epidemic prevention training was more likely to promote the adoption of C&D procedures among pig farmers with shorter breeding experiences and those having breeding insurance. Our study emphasized the importance of implementing epidemic prevention training to improving pig farmers' biosecurity cognition and promoting the adoption of C&D procedures. The results included suggested references for preventing ASF and the next epidemic of animal diseases.

Trends in the management of organic swine farm waste by composting: A systematic review.

Pig farming contributes to the economic development of nations and supplies human food demand; however, it generates a large amount of organic waste which, if not managed properly, becomes a risk to the environment and human and animal health. Considering the relevance of composting and its usefulness for the use of waste, this study aimed to determine the global trends in the management of composting manure, mortality and other organic waste produced on pig farms over the last five years (2017-2022). Systematic search involved four databases: ISI Web of Science, Scopus, Ebsco and Scielo. Of the total findings, 56 articles were included in the review, further classified into 14 categories for their respective analysis: co-substrates/additives, microbial communities, antibiotic resistance, heavy metals, polycyclic aromatic hydrocarbons, microbiological/parasitological quality, phytopathogens, nitrogen transformation, bioinoculants, comparison/combination with other waste management techniques, factors affecting composting, swine mortality and plant growth promotion/phytotoxicity. The review exemplified the importance of swine mortality composting as an alternative for organic matter management in pig farms, considering that the process also includes manure, vegetable waste and wood chips, among others. Controlled factors throughout the process are a requirement to obtain a stable product with physicochemical and microbiological quality that complies with national and international regulations and that will be useful and safe for application on crops, ensuring environmental, animal, and human health.

Serotyping and Antimicrobial Resistance Profiling of Multidrug-Resistant Non-Typhoidal Salmonella from Farm Animals in Hunan, China.

Non-typhoidal Salmonella (NTS) is a foodborne pathogen and a prevalent causative agent for disease outbreaks globally. The Salmonella enterica serovar 4,[5],12:i:- (S.4,[5],12:i:-) belongs to the monophasic variant of Salmonella typhimurium, which is of current global concern. In this study, the epidemiology and genomic characterization of S. 4,[5],12:i:- isolates from 17 livestock farms in Hunan Province between 2019 and 2020, as well as their susceptibility to 14 antimicrobial agents, were profiled. Twelve Salmonella serotypes were identified using the White-Kauffmann-Le Minor scheme, and whole-genome sequencing analyses were conducted based on these isolates. Overall, 107 Salmonella strains were isolated, of which 73% (78/107) were multidrug resistant. Resistance to tetracycline (85.05%) was found to be the most prevalent, followed by the oqxAB and aac(6')-Ib-cr genes. S. typhimurium (monophasic) 4,[5],12:i:- was the most common serotype, followed by S. typhimurium and S. derby. Most antimicrobial-resistant strains were isolated from pigs, indicating that they could be important reservoirs of resistant non-typhoidal Salmonella strains. The presence of similar genetic environments in S. 4,[5],12:i:- indicates both vertical and horizontal transmission of resistance plasmids, which may promote the spread of drug resistance genes. Appropriate measures should be taken to curb the prevalence of S. 4,[5],12:i:-.

Genetic Profile of African Swine Fever Viruses Circulating at Pig Farms in South Korea during the Outbreaks between 2022 and April 2023.

Fifteen pig farms were affected by African swine fever (ASF) in South Korea during the outbreaks between 2022 and April 2023. The ASF virus (ASFV) genome was directly extracted from the blood and tissue samples of 15 ASFV-positive pig farms to analyze the genetic characteristics. Phylogenetic analysis revealed that the 15 strains belonged to p72 genotype II and CD2v serogroup 8, which were the central variable region (CVR) I variants of the B602L gene. Fourteen strains were intergenic region (IGR) II variants, containing an additional tandem repeat sequence (TRS), between I73L and I329R, with the exception of one strain from an ASFV-infected pig farm reported on 22 January 2023, which was an IGR I variant. In addition, a single-nucleotide polymorphism (SNP) was detected at position 107 from the start of the IGR between A179L and A137R in six isolates. The findings of this study suggest that the sources of the virus at the pig farms from which these variants originated differed from those of other pig farms.

Carbon and water footprint analysis of pig farm buildings in Northeast China using building-information-modeling enabled assessment.

Environmental impact evaluation of buildings is critical for further analysis and optimization of pig farms for sustainable pork production. This study is the first attempt to quantify the carbon and water footprints of a standard intensive pig farm building using building information modeling (BIM) and operation simulation model. The model was constructed with carbon emission and water consumption coefficients, and a database was built. The results showed that the operational stage of pig farm accounted for most of the carbon footprint (49.3-84.9 %) and water footprint (65.5-92.5 %). Building materials production ranked second in carbon (12.0-42.5 %) and water footprints (4.4-24.9 %), and pig farm maintenance ranked third in carbon (1.7-5.7 %) and water footprints (0.7-3.6 %). Notably, the mining and production stages of building materials contributed the largest carbon and water footprints of pig farm construction. Masonry materials have a significant impact on the overall carbon and water footprints of the pig farm. Pig farm using aerated concrete could reduce 41.1 % of the total carbon footprint and 58.9 % of the total water footprint compared to that using coal gangue sintered brick and autoclaved fly ash brick. This study presented a BIM-enabled method for carbon and water footprint analysis of pig farms and illustrated how the model can be used to facilitate the low carbon design of agricultural buildings.

Tahibacter harae sp. nov., isolated from pig farm soil in Guangdong, PR China.

In the process of exploring the microbial diversity of pig farms, a Gram-stain-negative, aerobic, rod-shaped, non-spore-forming, non-motile bacterial strain, designated P2KT, was isolated from soil sample collected at a pig farm, Guangdong Province, PR China. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain P2KT belonged to the genus Tahibacter, with the highest sequence similarity to Tahibacter aquaticus PYM5-11T (98.6%) and Tahibacter caeni BUT-6T (98.3 %). The genome size of strain P2KT was 6.0 Mb with a DNA G+C content of 68.3 mol%. Average nucleotide identity values between strain P2KT and the type strains of the genus Tahibacter were 81.1-81.6 %. The digital DNA-DNA hybridization values between P2KT and these relative species were 24.5-25.6%. The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, an unknown aminolipids, two unknown lipids and three unknown phospholipids. The major respiratory quinone of strain P2KT was ubiquinone Q-8, and the main fatty acids (>10.0 % of total fatty acids) of strain P2KT were iso-C15:0, iso-C16:0 and summed feature 9 (C16:0 10-methyl and/or iso-C17:1 ω9c). Based on phenotypic and genotypic data, strain P2KT represents a novel species within the genus Tahibacter, for which the name Tahibacter harae sp. nov. is proposed, with the type strain P2KT (=GDMCC 1.3107T=JCM 35231T).

Scheme of Effective Epidemiological Investigations in Trichinella Outbreaks on Pig Farms.

Trichinellosis is a parasitic, zoonotic disease caused by larvae of the genus Trichinella. Infection occurs via the consumption of raw or undercooked meat containing this parasite. Symptoms of the disease manifest as intestinal disorders, followed by facial swelling, fever, muscle pain and other symptoms, eventually leading to neurological and cardiac complications and even death. In Europe, trichinellosis is most often associated with the consumption of meat from wild boars, pigs and horses. In recent years, wild boars that are hunted illegally and not tested for Trichinella spp. have been the most common cause of trichinellosis in humans; however, there have also been cases where infected pigs have been the source of infection. When trichinellosis is suspected in humans, epidemiological measures are taken to identify the source. Similarly, an epidemiological investigation should be initiated whenever Trichinella spp. has been detected in pigs. However, commonly used actions do not provide sufficient data to determine the source of infection for pigs and to prevent further transmission. Therefore, in this article, we propose a scheme for effective epidemiological investigations into Trichinella outbreaks on pig farms that can help trace the transmission mechanisms of the parasite and that takes into account currently available testing tools. The proposed pathway can be easily adopted for epidemiological investigations in routine veterinary inspection work.

The risk of pig and chicken farming for carriage and transmission of Escherichia coli containing extended-spectrum beta-lactamase (ESBL) and mobile colistin resistance (mcr) genes in Thailand.

South-East Asian countries report a high prevalence of extended-spectrum cephalosporin- (ESC-) and colistin-resistant Escherichia coli (Col-R-Ec). However, there are still few studies describing the molecular mechanisms and transmission dynamics of ESC-R-Ec and, especially, Col-R-Ec. This study aimed to evaluate the prevalence and transmission dynamics of Ec containing extended spectrum beta-lactamases (ESBL) and mobile colistin resistance (mcr) genes using a 'One Health' design in Thailand. The ESC-R-Ec and Col-R-Ec isolates of human stool samples (69 pig farmers, 155 chicken farmers, and 61 non-farmers), rectal swabs from animals (269 pigs and 318 chickens), and the intestinal contents of 196 rodents were investigated. Resistance mechanisms and transmission dynamics of Ec isolates (n=638) were studied using short and long read sequencing. We found higher rates of ESBL-Ec isolates among pig farmers (n=36; 52.2%) than among chicken farmers (n=58; 37.4 %; P<0.05) and the control group (n=61; 31.1 %; P<0.05). Ec with co-occurring ESBL and mcr genes were found in 17 (6.0 %), 50 (18.6 %) and 15 (4.7 %) samples from humans, pigs and chickens, respectively. We also identified 39 (13.7 %) human samples with non-identical Ec containing ESBL and mcr. We found higher rates of ESBL-Ec, in particular CTX-M-55, isolates among pig farmers than among non-pig farmers (P<0.01). 'Clonal' animal-human transmission of ESBL-Ec and Ec with mcr genes was identified but rare as we overall found a heterogenous population structure of Ec. The Col-R-Ec from human and animal samples often carried mcr-1.1 on conjugative IncX4 plasmids. The latter has been identified in Ec of many different clonal backgrounds.

Distribution and migration of antibiotic resistance genes, as well as their correlation with microbial communities in swine farm and its surrounding environments.

The prevalence and correlation of antibiotic resistance genes (ARGs) in pig farm wastewater treatment plants (WWTPs) and surrounding environment were investigated using metagenomics and real time quantitative PCR (q-PCR). The hosts of ARGs were also studied in this study. The abundance of ARGs decreased significantly in the anoxic/oxic (A/O) process and disinfection tank of WWTPs. New ARGs emerged in wastewater that passed though the anaerobic reactor. The abundances of ARGs in the soils and water near pig farm were 10- and 35-fold higher than those in the control, respectively. The abundance of ARGs in wells near pig farm were an order of magnitude higher than that in the control. Similarly, a high abundance of ARGs was detected in swine manure. After composting, most of the ARGs were eliminated, but sul1 increased 10.5-fold. A high-throughput analysis revealed that the pig farm altered the microbial community structure in the surrounding environment, with 52% and 37% of the operational taxonomic units (OTUs) endemic to the soil and water samples near pig farm in comparison with these data in the control, respectively. The phyla Proteobacteria, Choroflexi, and Actinobacteriota dominated the water and soil samples. In addition, three pathogenic genera were found in the surrounding soil and water samples. A metagenomic analysis identified 14 types of ARGs (>1%), with the highest proportion of multidrug ARGs at 47%. A total of 28 subtypes of ARGs were detected (>1%), with macB the most prevalent. The correlation analysis revealed that several key phyla, including Proteobacteria, Actinobacteria and Acidobacteria, were the main potential hosts and posed a positive correlation with the ARGs. Efflux pumps (60-66%) were the primary resistance mechanism, and each resistance mechanism was distributed in similar proportions in the microbial community.

Occurrence and Genomic Characterization of mcr-1-Harboring Escherichia coli Isolates from Chicken and Pig Farms in Lima, Peru.

Resistance to colistin generated by the mcr-1 gene in Enterobacteriaceae is of great concern due to its efficient worldwide spread. Despite the fact that the Lima region has a third of the Peruvian population and more than half of the national pig and poultry production, there are no reports of the occurrence of the mcr-1 gene in Escherichia coli isolated from livestock. In the present work, we studied the occurrence of E. coli carrying the mcr-1 gene in chicken and pig farms in Lima between 2019 and 2020 and described the genomic context of the mcr-1 gene. We collected fecal samples from 15 farms in 4 provinces of Lima including the capital Lima Metropolitana and recovered 341 E. coli isolates. We found that 21.3% (42/197) and 12.5% (18/144) of the chicken and pig strains were mcr-1-positive by PCR, respectively. The whole genome sequencing of 14 mcr-1-positive isolates revealed diverse sequence types (e.g., ST48 and ST602) and the presence of other 38 genes that confer resistance to 10 different classes of antibiotics, including beta-lactamase blaCTX-M-55. The mcr-1 gene was located on diverse plasmids belonging to the IncI2 and IncHI1A:IncHI1B replicon types. A comparative analysis of the plasmids showed that they contained the mcr-1 gene within varied structures (mikB-mcr1-pap2, ISApl1-mcr1-pap2, and Tn6330). To the best of our knowledge, this is the first attempt to study the prevalence of the mcr-1 gene in livestock in Peru, revealing its high occurrence in pig and chicken farms. The genetic diversity of mcr-1-positive strains suggests a complex local epidemiology calling for a coordinated surveillance under the One-Health approach that includes animals, retail meat, farmers, hospitals and the environment to effectively detect and limit the spread of colistin-resistant bacteria.