Reservoirs and Transmission Pathways of Resistant Indicator Bacteria in the Biotope Pig Stable and along the Food Chain: A Review from a One Health Perspective

The One Health aspect of climate events with impact on foodborne pathogens transmission

The ongoing effects of climate change have exacerbated two significant challenges to global populations: the transmission of foodborne pathogens and antimicrobial resistance (AMR) through the food chain. Using the latest available scientific information this review explores how climate-related factors such as rainfall, floods, storms, hurricanes, cyclones, dust, temperature and humidity impact the spread of the foodborne pathogens Salmonella, E. coli, Campylobacter, Vibrio, Listeria, and Staphylococcus aureus. We explore the complex dynamics between environmental changes and the heightened risk of foodborne diseases, analysing the contribution of wildlife, insects and contaminated environments in the proliferation of AMR and climate change. This review paper combines a thorough analysis of current literature with a discussion on findings from a wide variety of studies to provide a comprehensive overview of how climatic factors contribute to the survival, persistence and transmission of bacterial pathogens in the food chain. In addition, we discuss the necessity for effective mitigation strategies and policies. By providing insights into the interrelationships between climate change and food safety, this review hopes to inform future research and policy development to promote safer and more sustainable food systems and further integration within the One Health approach.

Proteomic profiling of antibiotic-resistant Escherichia coli GW-AmxH19 isolated from hospital wastewater treated with physical plasma

Microorganisms which are resistant to antibiotics are a global threat to the health of humans and animals. Wastewater treatment plants are known hotspots for the dissemination of antibiotic resistances. Therefore, novel methods for the inactivation of pathogens, and in particular antibiotic-resistant microorganisms (ARM), are of increasing interest. An especially promising method could be a water treatment by physical plasma which provides charged particles, electric fields, UV-radiation, and reactive species. The latter are foremost responsible for the antimicrobial properties of plasma. Thus, with plasma it might be possible to reduce the amount of ARM and to establish this technology as additional treatment stage for wastewater remediation. However, the impact of plasma on microorganisms beyond a mere inactivation was analyzed in more detail by a proteomic approach. Therefore, Escherichia coli GW-AmxH19, isolated from hospital wastewater in Germany, was used. The bacterial solution was treated by a plasma discharge ignited between each of four pins and the liquid surface. The growth of E. coli and the pH-value decreased during plasma treatment in comparison with the untreated control. Proteome and antibiotic resistance profile were analyzed. Concentrations of nitrite and nitrate were determined as long-lived indicative products of a transient chemistry associated with reactive nitrogen species (RNS). Conversely, hydrogen peroxide served as indicator for reactive oxygen species (ROS). Proteome analyses revealed an oxidative stress response as a result of plasma-generated RNS and ROS as well as a pH-balancing reaction as key responses to plasma treatment. Both, the generation of reactive species and a decreased pH-value is characteristic for plasma-treated solutions. The plasma-mediated changes of the proteome are discussed also in comparison with the Gram-positive bacterium Bacillus subtilis. Furthermore, no effect of the plasma treatment, on the antibiotic resistance of E. coli, was determined under the chosen conditions. The knowledge about the physiological changes of ARM in response to plasma is of fundamental interest to understand the molecular basis for the inactivation. This will be important for the further development and implementation of plasma in wastewater remediation.

Extended-spectrum β-lactamase-producing Escherichia coli from poultry: A review

Extended-spectrum β-lactamases (ESBLs) are β-lactamase enzymes produced by Gram-negative bacterial pathogens that harbor the ESBL genes. In addition, most ESBL genes are plasmid-mediated and usually encode a broader spectrum of antimicrobial resistance, especially to penicillins, first-generation, second-generation, and third-generation cephalosporins, as well as monobactam, such as aztreonam. Escherichia coli has become an opportunistic pathogen, especially in poultry, and has been implicated in zoonotic diseases that can be transmitted to humans, resulting in public health problems. Poultry can act as carriers of ESBL-producing E. coli (ESBL-EC) bacteria to humans through poultry meat that is contaminated by waste products, feces, and excretions. The ESBL gene CTX-M type was identified as the main cause of infection in humans and was detected in poultry as a cause of infection accompanied by clinical symptoms. Several studies have also shown a link between E. coli and ESBL gene transfer from birds to humans. Controlling the spread of ESBL-EC involves maintaining the cleanliness of poultry products, especially meat, and eliminating contaminant sources from poultry. Likewise, maintaining the environmental cleanliness of poultry slaughterhouses and poultry farms must be taken as a precautionary measure to curtail the increasing spread of ESBL-EC into the environment. This review aimed to explain the spread of ESBL-producing E. coli in poultry.

Occurrence of multidrug resistance associated with extended-spectrum β‑lactamase and the biofilm forming ability of Escherichia coli in environmental swine husbandry

Extended-spectrum beta-lactamase (ESBL) production and biofilm formation are mechanisms employed by Escherichia coli to resist beta-lactam antibiotics. Thus, we aimed to examine antibiotic resistance associated with ESBL production and biofilm formation in E. coli isolates from swine farms in Southern Thailand. In total, 159 E. coli isolates were obtained, with 44 isolates identified as ESBL producers, originating from feces (18.87 %) and wastewater (8.80 %) samples. All ESBL-producing strains exhibited resistance to ampicillin (100 %), followed by the cephalosporin group (97.73 %) and tetracycline (84.09 %). Multidrug resistance was observed in 17 isolates (38.63 %). Among the isolates from feces samples, the blaGES gene was the most prevalent, detected in 90 % of the samples, followed by blaCTX-M9 (86.67 %) and blaCTX-M1 (66.67 %), respectively. In the bacteria isolated from wastewater, both blaGES and blaCTX-M9 genes were the predominant resistance genes, detected in 100 % of the isolates, followed by blaCTX-M1 (64.29 %) and blaTEM (50 %), respectively. Strong biofilm formation was observed in 11 isolates (36.67 %) from feces and 4 isolates (25.57 %) from wastewater samples. Notably, nearly 100 % of ESBL-producing strains isolated from feces tested positive for both pgaA and pgaC genes, which play a role in intracellular adhesion and biofilm production. These findings contribute to the understanding and potential control of ESBL-producing E. coli, and the dissemination of antibiotic resistance and biofilm-related genes in swine farms.

Risk-factor analysis for extended-spectrum beta-lactamase-producing Enterobacterales colonization or infection: Evaluation of a novel approach to assess local prevalence as a risk factor

OBJECTIVE

To explore an approach to identify the risk of local prevalence of extended-spectrum β-lactamase-producing Enterobacterales (ESBL-E) on ESBL-E colonization or infection and to reassess known risk factors.

DESIGN

Case-control study.

SETTING

Johns Hopkins Health System emergency departments (EDs) in the Baltimore-Washington, DC, region.

PATIENTS

Patients aged ≥18 years with a culture growing Enterobacterales between April 2019 and December 2021. Cases had a culture growing an ESBL-E.

METHODS

Addresses were linked to Census Block Groups and placed into communities using a clustering algorithm. Prevalence in each community was estimated using the proportion of ESBL-E among Enterobacterales isolates. Logistic regression was used to determine risk factors for ESBL-E colonization or infection.

RESULTS

ESBL-E were detected in 1,167 of 11,224 patients (10.4%). Risk factors included a history of ESBL-E in the prior 6 months (aOR, 20.67; 95% CI, 13.71-31.18), exposure to a skilled nursing or long-term care facility (aOR, 1.64; 95% CI, 1.37-1.96), exposure to a third-generation cephalosporin (aOR, 1.79; 95% CI, 1.46-2.19), exposure to a carbapenem (aOR, 2.31; 95% CI, 1.68-3.18), or exposure to a trimethoprim-sulfamethoxazole (aOR, 1.54; 95% CI, 1.06-2.25) within the prior 6 months. Patients were at lower risk if their community had a prevalence <25th percentile in the prior 3 months (aOR, 0.83; 95% CI, 0.71-0.98), 6 months (aOR, 0.83; 95% CI, 0.71-0.98), or 12 months (aOR, 0.81; 95% CI, 0.68-0.95). There was no association between being in a community in the >75th percentile and the outcome.

CONCLUSIONS

This method of defining the local prevalence of ESBL-E may partially capture differences in the likelihood of a patient having an ESBL-E.

Biosecurity and Hygiene Procedures in Pig Farms: Effects of a Tailor-Made Approach as Monitored by Environmental Samples

In livestock, the importance of hygiene management is gaining importance within the context of biosecurity. The aim of this study was to monitor the implementation of biosecurity and hygiene procedures in 20 swine herds over a 12-month period, as driven by tailor-made plans, including training on-farm. The measure of adenosine triphosphate (ATP) environmental contents was used as an output biomarker. The presence of livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) and extended-spectrum β-lactamase producing Escherichia coli (ESBL-E. coli) was also investigated as sentinels of antibiotic resistance. A significant biosecurity improvement (p = 0.006) and a reduction in the ATP content in the sanitised environment (p = 0.039) were observed. A cluster including 6/20 farms greatly improved both biosecurity and ATP contents, while the remaining 14/20 farms ameliorated them only slightly. Even if the ESBL-E. coli prevalence (30.0%) after the hygiene procedures significantly decreased, the prevalence of LA-MRSA (22.5%) was unaffected. Despite the promising results supporting the adoption of tailor-made biosecurity plans and the measure of environmental ATP as an output biomarker, the high LA-MRSA prevalence still detected at the end of the study underlines the importance of improving even more biosecurity and farm hygiene in a one-health approach aimed to preserve also the pig workers health.

Staphylococcus aureus and MRSA in Livestock: Antimicrobial Resistance and Genetic Lineages

Animal production is associated with the frequent use of antimicrobial agents for growth promotion and for the prevention, treatment, and control of animal diseases, thus maintaining animal health and productivity. Staphylococcus aureus, in particular methicillin-resistant S. aureus (MRSA), can cause a variety of infections from superficial skin and soft tissue infections to life-threatening septicaemia. S. aureus represents a serious public health problem in hospital and community settings, as well as an economic and animal welfare problem. Livestock-associated MRSA (LA-MRSA) was first described associated with the sequence (ST) 398 that was grouped within the clonal complex (CC) 398. Initially, LA-MRSA strains were restricted to CC398, but over the years it has become clear that its diversity is much greater and that it is constantly changing, a trend increasingly associated with multidrug resistance. Therefore, in this review, we aimed to describe the main clonal lineages associated with different production animals, such as swine, cattle, rabbits, and poultry, as well as verify the multidrug resistance associated with each animal species and clonal lineage. Overall, S. aureus ST398 still remains the most common clone among livestock and was reported in rabbits, goats, cattle, pigs, and birds, often together with spa-type t011. Nevertheless, a wide diversity of clonal lineages was reported worldwide in livestock.

Evaluation of the Occurrence of Staphylococcaceae with Reduced Susceptibility to Cefoxitin in Wild Ungulates in Brandenburg, Germany, Based on Land Use-Related Factors

Interactions between natural and human-used environments have a significant influence on the spread of antimicrobial resistance in wild ecosystems. Despite current knowledge, fundamental questions about the degree of impact of land use-related factors on the spread of antimicrobial-resistant staphylococci in European wild game animal populations have not yet been answered with certainty. In this study, we evaluated the occurrence of Staphylococcaceae showing reduced susceptibility to cefoxitin in nasal swabs of fallow deer (Dama dama), red deer (Cervus elaphus), roe deer (Capreolus capreolus), and wild boar (Sus scrofa) hunted in Brandenburg, Germany. Evaluations were focused on the use of open-source data regarding the extent as well as the degree of land use, especially for settlement or animal husbandry. Results showed that the detection rate of Staphylococcaceae showing a non-wild-type phenotype for cefoxitin differed between animal species of the studied hunting districts. Statistical analyses of results combined with data on land use features revealed that a high density of cattle or poultry in a county may be associated with an increased detection rate in roe deer or wild boar, respectively. Furthermore, positive correlations were determined between the prevalence of non-wild-type Staphylococcaceae in roe deer or fallow deer and the proportional extent of surface water bodies in the corresponding area. The presented approach establishes a general basis for a risk-oriented assessment of the effects of human activities on the epidemiology of transmissible microorganisms in the human-animal-environment interface, including antimicrobial-resistant bacteria. IMPORTANCE Intensive research regarding the impact of land use-related factors on the prevalence and distribution of antimicrobial-resistant Staphylococcaceae in game ungulate populations is necessary for adequately determining risks related to interactions between wild animals, domestic animals, and humans in common geographic locations. This systematic approach for the analysis of the observations in specific hunting districts of Brandenburg, Germany, adds an innovative value to the research strategy of antimicrobial resistance in wild game animals, which is in accordance with current recommendations worldwide. Thus, results and information obtained in this study build a relevant foundation for future risk assessment regarding the safety of game products. Furthermore, the data generated represent an important basis for improving existing guidelines in land use practices and hunting practices. The use of existing open source data collections provided by official governmental and nongovernmental entities increases not only the impact but also the applicability and comparability of information beyond the regional level.

Antibacterial and antibiofilm effects of essential oil components, EDTA and HLE disinfectant solution on Enterococcus, Pseudomonas and Staphylococcus sp. multiresistant strains isolated along the meat production chain

The spread of multidrug resistant (MDR) bacteria and resistance genes along the food chain and the environment has become a global, but silent pandemic. To face this challenge, it is of outmost importance to develop efficient strategies to reduce potential contamination by these agents. In the present study, 30 strains of Enterococcus sp., Staphylococcus sp. and Pseudomonas sp. isolated from various surfaces throughout the meat production chain in a goat and lamb slaughterhouse were characterized as MDR bacteria harboring several antibiotic resistance genes (ARGs). The antimicrobial efficacy of natural essential oil components “EOCs” (carvacrol “CA,” cinnamaldehyde “CIN,” eugenol “EU,” geraniol “GE,” limonene “LI” and thymol “TH”), HLE disinfectant solution (3–6% H₂O₂; 2.2–4.4% lactic acid and 12.5–25 mM EDTA in water) and EDTA was tested against these MDR bacteria. Results showed that Minimum Inhibitory Concentrations (MIC) were compound and strain dependent. In addition, the synergistic effect of these antimicrobials was evaluated at 1/2 MIC. Here our study showed particularly promising results regarding the inhibitory effect at sub-inhibitory concentrations, which were confirmed by the analysis of bacterial growth dynamics over 72 h. Furthermore, the inhibitory effect of EOCs, HLE disinfectant solution and EDTA or their combinations was studied in developing and established biofilms of MDR bacteria obtaining variable results depending on the morphological structure of the tested strain and the phenolic character of the EOCs. Importantly, the combination of EOCs with HLE or EDTA showed particularly positive results given the effective inhibition of biofilm formation. Moreover, the synergistic combinations of EU and HLE/EDTA, TH, CA, GE, LI or CIN + EDTA/HLE caused log reductions in established biofilms of several strains (1–6 log₁₀ CFU) depending on the species and the combination used, with Pseudomonas sp. strains being the most susceptible. Given these results, we propose novel antimicrobial formulations based on the combination of sub-inhibitory concentrations of EOCs and HLE or EDTA as a highly promising alternative to currently used approaches. This novel strategy notably shows great potential to efficiently decrease the emergence and spread of MDR bacteria and ARGs in the food chain and the environment, thus supporting the decrease of resistomes and pathogenesis in clinical and industrial areas while preserving the antibiotic therapeutic action.

EFSA Panel on Biological Hazards (BIOHAZ), Koutsoumanis K, Allende A, Álvarez‐Ordóñez A, Bolton D, Bover‐Cid S, Chemaly M, Davies R, De Cesare A, Herman L, Hilbert F, Lindqvist R, Nauta M, Ru G, Simmons M, Skandamis P, Suffredini E, Argüello‐Rodríguez H, Dohmen W, Magistrali CF, Padalino B, Tenhagen B, Threlfall J, García‐Fierro R, Guerra B, Liébana E, Stella P, Peixe L. Transmission of antimicrobial resistance (AMR) during animal transport

The transmission of antimicrobial resistance (AMR) between food-producing animals (poultry, cattle and pigs) during short journeys (< 8 h) and long journeys (> 8 h) directed to other farms or to the slaughterhouse lairage (directly or with intermediate stops at assembly centres or control posts, mainly transported by road) was assessed. Among the identified risk factors contributing to the probability of transmission of antimicrobial-resistant bacteria (ARB) and antimicrobial resistance genes (ARGs), the ones considered more important are the resistance status (presence of ARB/ARGs) of the animals pre-transport, increased faecal shedding, hygiene of the areas and vehicles, exposure to other animals carrying and/or shedding ARB/ARGs (especially between animals of different AMR loads and/or ARB/ARG types), exposure to contaminated lairage areas and duration of transport. There are nevertheless no data whereby differences between journeys shorter or longer than 8 h can be assessed. Strategies that would reduce the probability of AMR transmission, for all animal categories include minimising the duration of transport, proper cleaning and disinfection, appropriate transport planning, organising the transport in relation to AMR criteria (transport logistics), improving animal health and welfare and/or biosecurity immediately prior to and during transport, ensuring the thermal comfort of the animals and animal segregation. Most of the aforementioned measures have similar validity if applied at lairage, assembly centres and control posts. Data gaps relating to the risk factors and the effectiveness of mitigation measures have been identified, with consequent research needs in both the short and longer term listed. Quantification of the impact of animal transportation compared to the contribution of other stages of the food-production chain, and the interplay of duration with all risk factors on the transmission of ARB/ARGs during transport and journey breaks, were identified as urgent research needs.

MRSA in Humans, Pets and Livestock in Portugal: Where We Came from and Where We Are Going

Over the years, molecular typing of methicillin-resistant S. aureus (MRSA) has allowed for the identification of endemic MRSA strains and pathogenic strains. After reaching a peak of predominance in a given geographic region, MRSA strains are usually replaced by a new strain. This process is called clonal replacement and is observed worldwide. The worldwide spread of hospital-associated MRSA (HA-MRSA), community-associated MRSA (CA-MRSA) and livestock-associated MRSA (LA-MRSA) clones over the last few decades has allowed this microorganism to be currently considered a pandemic. In Portugal, most HA-MRSA infections are associated with EMRSA-15 (S22-IV), New York/Japan (ST5-II) and Iberian (ST247-I) clones. Regarding the strains found in the community, many of them are frequently associated with the hospital environment, namely the Pediatric, Brazilian and Iberian clones. On the other hand, a strain that is typically found in animals, MRSA clonal complex (CC) 398, has been described in humans as colonizing and causing infections. The ST398 clone is found across all animal species, particularly in farm animals where the economic impact of LA-MRSA infections can have disastrous consequences for industries. In contrast, the EMRSA-15 clone seems to be more related to companion animals. The objective of this review is to better understand the MRSA epidemiology because it is, undoubtedly, an important public health concern that requires more attention, in order to achieve an effective response in all sectors.

A scoping review of factors potentially linked with antimicrobial-resistant bacteria from turkeys (iAM.AMR Project)

Antimicrobial resistance (AMR) is a complex problem that is a threat to global public health. Consumption of turkey meat may be an important source of foodborne exposure to resistant bacteria; recent outbreaks of multi-drug-resistant Salmonella Reading in Canada and the USA have implicated raw turkey products. To better understand the epidemiology of AMR in farmed turkey production, a scoping review was conducted. The objectives were to identify (1) modifiable factors potentially associated with antimicrobial-resistant Campylobacter, Enterococcus, Escherichia coli and Salmonella enterica along the farm-to-fork pathway in turkeys, and (2) data gaps with respect to factors potentially associated with AMR and Canadian commercial turkey production. A comprehensive search of the peer-reviewed literature was conducted in 2019 and updated in 2021. Thirteen references were included, reporting 36 factors. Antimicrobial use factors and their potential associations with AMR were most frequently reported (n = 15 factors; 42%), followed by biosecurity (n = 11; 31%) and management practices (n = 10; 28%). This review revealed important data gaps; no factors pertaining to S. enterica or to stages other than the farm (e.g. abattoir, retail) were identified, and only one Canadian reference was identified. These findings will inform priorities for future research and surveillance regarding turkeys and AMR.

A risk-oriented evaluation of biofilm and other influencing factors on biological quality of drinking water for dairy cows

Despite the importance of livestock drinking water quality on animal physiology, welfare, and performance, influences such as biofilm formation on trough surfaces on microbial water quality are rarely researched. The objective of this study was to assess the microbial quality of water offered to lactating dairy cows and identify risk factors for poor water quality. We further aimed to determine the impact of biofilm formation on water quality and evaluate rapid test systems to score the hygiene status of dairy troughs on the farm. A total of 105 troughs located on 24 typical Western German dairy farms were sampled. Samples of livestock drinking water and biofilm were analyzed for aerobic total viable count (TVC), coliform count (CC), Escherichia coli, methicillin-resistant Staphylococcus aureus (MRSA), and other bacteria resistant to 3rd generation cephalosporins (CRB). Surface protein- and adenosine triphosphate (ATP)-rapid tests were evaluated to detect biofilm formation. The influence of 22 selected fixed and variable trough characteristics on impaired livestock drinking water quality was evaluated by calculating odds ratios. The average TVC, CC, and E. coli counts were 4.4 ± 0.06 (mean ± SD), 1.7 ± 0.1, and 0.6 ± 0.1 log10 cfu per mL, respectively. CC was detectable in 94.3% of all water samples and E. coli in 48.6%. MRSA was found in pooled livestock drinking water samples of a single farm and CRB on three farms, suggesting that troughs might function as a reservoir of antibiotic-resistant bacteria, thereby contributing to an exchange of antibiotic-resistant bacteria between animals. Risk factors for the impairment of at least one microbial quality criteria (TVC, CC, or E. coli) increased significantly (P < 0.05) when using high-volume troughs, other trough materials than stainless steel, a lower distance to the milking parlor, heavy visible soiling, biofilm formation, and high ambient and high water temperatures. CC (r = 0.46; P < 0.001) and E. coli (r = 0.31; P < 0.01) of water samples correlated with their equivalent in biofilm and with the results of rapid tests on trough surfaces (0.31 > r > 0.19; P < 0.05). Addressing the identified risk factors could be an approach to ensure sufficient biological quality of livestock drinking water.

Antimicrobial and Antibiotic Resistance from the Perspective of Polish Veterinary Students: An Inter-University Study

The phenomenon of antibiotic resistance is a global problem that affects the use of antibiotics by humans and animal husbandry. One of the primary reasons for the growing phenomenon of antibiotic resistance is the over-prescription of antibiotics by doctors in human medicine and the overuse of antibiotics in industrial animal farming. Adequate education of veterinary medical students on the use of antibiotics in animal husbandry may reduce antibiotic resistance. For this reason, a survey was conducted among students at four primary research and didactic centers teaching veterinary medicine in Poland. The survey aimed to find out the knowledge and attitude of students towards the use of antibiotics and antibiotic resistance. The survey was conducted in May/June 2021. Four hundred and sixty-seven students participated in the study. The study positively verified that antibiotics and antibiotic resistance knowledge increase with successive years of veterinary studies/education. For most students (82.2%), antibiotic resistance is a significant problem, but only 58.7% believe it is global, and one in three respondents heard about the One Health approach.

Staphylococcus aureus in poultry, with special emphasis on methicillin-resistant strain infection: A comprehensive review from one health perspective

Staphylococcus aureus is a Gram-positive coccus normally present on the skin and internal organs of animals, birds, and humans. Under certain conditions, S. aureus could produce septicemia and affection of the skin, joints, and heart, as well as sepsis and death. The pathogenicity of S. aureus is associated with the presence of some virulent surface proteins and the production of some virulent toxins and enzymes. This pathogen is considered one of the most important and worldwide foodborne causes as it is incriminated in most cases of food poisoning. The hazardous use of antibiotics in the veterinary field leads to the development of multidrug-resistant S. aureus strains that can be transmitted to humans. The incidence of methicillin-resistant S. aureus (MRSA) strains has increased globally. These resistant strains have been detected in live animals, poultry, and humans. In addition, retail animal products, especially those of avian origin, are considered the main source of MRSA strains that can be easily transmitted to humans. MRSA infection is regarded as nosocomial or occupational. Humans get infected with MRSA strains through improper handling or preparation of contaminated animals or poultry carcasses or improper cooking with contaminated meat. Live birds also can transmit MRSA to close-contact workers in poultry farms. Transmission of MRSA infection in hospitals is from an infected individual to a healthy one. Prevention and control of MRSA are based on the application of hygienic measures in farms as well as proper processing, handling, and cooking of retail poultry products. The cooperation between veterinary and human practitioners is a must to avoid the possibility of zoonotic transmission. Accordingly, this review focused on the sources and transmission of MRSA infection, virulence and resistance factors, incidence and prevalence in poultry and different products, antibiotic resistance, and prevention and control strategies.

Extended spectrum beta-lactamase-producing Escherichia coli surveillance in the human, food chain, and environment sectors: Tricycle project (pilot) in Indonesia

The World Health Organization (WHO) has been implementing antimicrobial surveillance with a "One Health" approach, known as the Global Surveillance ESBL E. coli Tricycle Project. We describe the implementation of the Tricycle Project (pilot) in Indonesia, focusing on its results, challenges and recommendations. The samples were 116 patients with bloodstream infections caused by ESBL E. coli, 100 rectal swabs collected from pregnant women, 240 cecums of broiler, and 119 environmental samples, using the standardized method according to the guidelines. ESBL-producing E. coli was found in 40 (40%) of the 100 pregnant women, while the proportion of ESBL-producing E. coli was 57.7% among the total E. coli-induced bloodstream infections. ESBL-producing E. coli was isolated from 161 (67.1%) out of 240 broilers. On the other hand, the average concentration of E. coli in the water samples was 2.0 × 108 CFU/100 mL, and the ratio of ESBL-producing E. coli was 12.8% of total E. coli. Unfortunately, 56.7% of questionnaires for patients were incomplete. The Tricycle Project (pilot) identified that the proportion of ESBL-producing E. coli was very high in all types of samples, and several challenges and obstacles were encountered during the implementation of the study in Indonesia. The finding of this study have implication to health/the antimicrobial resistance (AMR) surveillance. We recommend continuing this project and extending this study to other provinces to determine the AMR burden as the baseline in planning AMR control strategies in Indonesia. We also recommend improving the protocol of this study to minimize obstacles in the field.

Novel methods of microbiome analysis in the food industry

The study of the food microbiome has gained considerable interest in recent years, mainly due to the wide range of applications that can be derived from the analysis of metagenomes. Among these applications, it is worth mentioning the possibility of using metagenomic analyses to determine food authenticity, to assess the microbiological safety of foods thanks to the detection and tracking of pathogens, antibiotic resistance genes and other undesirable traits, as well to identify the microorganisms responsible for food processing defects. Metataxonomics and metagenomics are currently the gold standard methodologies to explore the full potential of metagenomes in the food industry. However, there are still a number of challenges that must be solved in order to implement these methods routinely in food chain monitoring, and for the regulatory agencies to take them into account in their opinions. These challenges include the difficulties of analysing foods and food-related environments with a low microbial load, the lack of validated bioinformatics pipelines adapted to food microbiomes and the difficulty of assessing the viability of the detected microorganisms. This review summarizes the methods of microbiome analysis that have been used, so far, in foods and food-related environments, with a specific focus on those involving Next-Generation Sequencing technologies.

Prevalence and Characteristics of Multidrug-Resistant Livestock-Associated Methicillin-Resistant Staphylococcus aureus (LA-MRSA) CC398 Isolated from Quails (Coturnix Coturnix Japonica) Slaughtered for Human Consumption

Simple Summary

Methicillin-resistant Staphylococcus aureus (MRSA) is an important pathogen in both humans and animals worldwide. MRSA associated with livestock is a zoonotic pathogen that has been reported in several animals and, although its infections in humans are rare, this strain is recognized as an occupational hazard for people working in direct contact with livestock. Thus, we aimed to isolate MRSA from quails and to characterize their antimicrobial resistance and genetic lineages. One hundred swab samples were recovered from quails at the slaughterhouse. To investigate the prevalence and antimicrobial resistance of MRSA in poultry, we conducted this study on 100 quails slaughtered for human consumption. The antimicrobial resistance was investigated in all isolates as well as virulence genes and genetic lineages. Twenty-nine MRSA were isolated. The results showed that all MRSA isolates had resistance to multiple antibiotics. All strains were classified as livestock-associated. Most strains belonged to a well-known livestock-associated lineage: CC398.

Abstract

Livestock-associated MRSA (LA-MRSA) is a zoonotic pathogen that has been reported in several animals, and it is often associated with clonal complex (CC) 398. We aimed to isolate MRSA from quails and to characterize their antimicrobial resistance and genetic lineages. One hundred swab samples were recovered from quails at the slaughterhouse. The swabs were inoculated onto CHROMagar™ MRSA agar plates for MRSA isolation. The presence of antimicrobial-resistant genes and virulence factors was investigated by PCR. All strains were typed by MLST, SCCmec-, spa- and agr-typing. From the 100 samples, 29 MRSA were isolated. All strains were resistant to penicillin, cefoxitin, ciprofloxacin, erythromycin and clindamycin and carried the blaZ, mecA, ermB and ermC genes. All strains, except one, showed resistance to tetracycline and harbored the tetM, tetK and tetL genes in different combinations. Twenty strains belonged to ST398 and SCCmec type V, and nine strains belonged to the new ST6831. Twenty-eight out of twenty-nine strains were ascribed to t011 and one to t108. As far as we know, this is the first report of MRSA from quails slaughtered for human consumption. Most strains belonged to ST398-t011, which is the most common LA-MRSA clone found in livestock in Europe.

The global prevalence and trend of human intestinal carriage of ESBL-producing Escherichia coli in the community

OBJECTIVES

Intestinal colonization by ESBL Escherichia coli and its association with community-acquired MDR infections is of great concern. This review determined the worldwide prevalence of human faecal ESBL E. coli carriage and its trend in the community over the past two decades.

METHODS

A systematic literature search was conducted using PubMed, EMBASE and Google Scholar to retrieve articles published between 1 January 2000 and 13 February 2020 that contained data on the prevalence of faecal carriage of ESBL E. coli among healthy individuals. A cumulative (for the whole period) meta-analysis was used to estimate the global and regional pooled prevalence rates. Articles were grouped into study periods of 3 years, and subgroup meta-analyses were undertaken to examine the global pooled prevalence over time.

RESULTS

Sixty-two articles covering 29 872 healthy persons were included in this meta-analysis. The cumulative (2003-18) global pooled prevalence of ESBL E. coli intestinal carriage in the community was 16.5% (95% CI 14.3%-18.7%; P  <  0.001). The pooled prevalence showed an upward trend, increasing from 2.6% (95% CI 1.6%-4.0%) in 2003-05 to 21.1% (95% CI 15.8%-27.0%) in 2015-18. Over the whole period, the highest carriage rate was observed in South-East Asia (27%; 95% CI 2.9%-51.3%), while the lowest occurred in Europe (6.0%; 95% CI 4.6%-7.5%).

CONCLUSIONS

Globally, an 8-fold increase in the intestinal carriage rate of ESBL E. coli in the community has occurred over the past two decades. Prevention of its spread may require new therapeutic and public health strategies.

Bugs That Can Resist Antibiotics but Not Men: Gender-Specific Differences in Notified Infections and Colonisations in Germany, 2010-2019

Data from surveillance networks show that men have a higher incidence rate of infections with anti-microbial-resistant (AMR) pathogens than women. We systematically analysed data of infections and colonisations with AMR pathogens under mandatory surveillance in Germany to quantify gender-specific differences. We calculated incidence-rates (IR) per 100,000 person-years for invasive infections with Methicillin-resistant Staphylococcus aureus (MRSA), and for infections or colonisations with carbapenem-non-susceptible Acinetobacter spp. (CRA), and Enterobacterales (CRE), using the entire German population as a denominator. We limited the study periods to years with complete notification data (MRSA: 2010-2019, CRA/CRE: 2017-2019). We used Poisson regression to adjust for gender, age group, federal state, and year of notification. In the study periods, IR for all notifications were 4.2 for MRSA, 0.90 for CRA, and 4.8 for CRE per 100,000 person--years. The adjusted IR ratio for infections of men compared to women was 2.3 (95% confidence interval [CI]: 2.2-2.3) for MRSA, 2.2 (95%CI: 1.9-2.7) for CRA, and 1.7 (95%CI: 1.6-1.8) for CRE. Men in Germany show about double the risk for infection with AMR pathogens than women. This was also true for colonisations, where data were available. Screening procedures and associated hygiene measures may profit from a gender-stratified approach.

High Levels of Antibiotic Resistance in Isolates From Diseased Livestock

Overuse of antimicrobials in livestock health and production beyond therapeutic needs has been highlighted in recent years as one of the major risk factors for the acceleration of antimicrobial resistance (AMR) of bacteria in both humans and animals. While there is an abundance of reports on AMR in clinical isolates from humans, information regarding the patterns of resistance in clinical isolates from animals is scarce. Hence, a situational analysis of AMR based on clinical isolates from a veterinary diagnostic laboratory was performed to examine the extent and patterns of resistance demonstrated by isolates from diseased food animals. Between 2015 and 2017, 241 cases of diseased livestock were received. Clinical specimens from ruminants (cattle, goats and sheep), and non-ruminants (pigs and chicken) were received for culture and sensitivity testing. A total of 701 isolates were recovered from these specimens. From ruminants, Escherichia coli (n = 77, 19.3%) predominated, followed by Staphylococcus aureus (n = 73, 18.3%). Antibiotic sensitivity testing (AST) revealed that E. coli resistance was highest for penicillin, streptomycin, and neomycin (77-93%). In addition, S. aureus was highly resistant to neomycin, followed by streptomycin and ampicillin (68-82%). More than 67% of E. coli isolates were multi-drug resistant (MDR) and only 2.6% were susceptible to all the tested antibiotics. Similarly, 65.6% of S. aureus isolates were MDR and only 5.5% were susceptible to all tested antibiotics. From non-ruminants, a total of 301 isolates were recovered. Escherichia coli (n = 108, 35.9%) and Staphylococcus spp. (n = 27, 9%) were the most frequent isolates obtained. For E. coli, the highest resistance was against amoxicillin, erythromycin, tetracycline, and neomycin (95-100%). Staphylococcus spp. had a high level of resistance to streptomycin, trimethoprim/sulfamethoxazole, tetracycline and gentamicin (80-100%). The MDR levels of E. coli and Staphylococcus spp. isolates from non-ruminants were 72.2 and 74.1%, respectively. Significantly higher resistance level were observed among isolates from non-ruminants compared to ruminants for tetracycline, amoxicillin, enrofloxacin, and trimethoprim/sulfamethoxazole.

Characterization of Third-Generation Cephalosporin-Resistant Escherichia coli Isolated from Pigs in Cuba Using Next-Generation Sequencing

Resistance to third-generation cephalosporins (3GC) in Escherichia coli has been reported worldwide from humans and animals, but the situation in Cuba is still poorly understood. This study aimed to gain new insights into the phenotypic and genotypic characteristics of third-generation cephalosporin-resistant (3GC-R) E. coli isolated from pigs in Cuba. Rectal swabs from 215 healthy pigs were taken from different municipalities in the western region of Cuba and spread on MacConkey agar supplemented with cefotaxime and ceftazidime. Ninety-six isolates were identified as 3GC-R E. coli and 87.5% of them were resistant to at least three antibiotic classes as determined by the measurement of the minimum inhibitory concentration (MIC) of 14 antibiotics. Twenty-seven different isolates were selected for Illumina next-generation sequencing, and subsequent in silico analysis was performed for the detection of antibiotic resistance and virulence genes, plasmid incompatibility (Inc) groups, multilocus sequence typing (MLST), and core genome MLST (cgMLST). The sequenced isolates contained extended-spectrum β-lactamase genes bla_CTX-M-32 (n = 17), bla_CTX-M-15 (n = 5), and bla_CTX-M-55 (n = 4) as well as with pAmpC gene bla_CMY-2 (n = 2). They also harbored genes for resistance to other clinically important classes of antibiotics, as well as several diverse virulence factors. The 3GC-R E. coli were genetically highly diverse, belonging to 16 different sequence types. IncX1 was the most frequent Inc group. The presence of 3GC-R E. coli in pigs from Cuba containing several different antibiotic resistance mechanisms emphasizes the need for surveillance programs and the establishment of strategies for the prudent use of antibiotics in food-producing animals.

Prevalence of Antibiotic-Resistant Escherichia coli Isolates from Local and Imported Retail Chicken Carcasses

ABSTRACT

The spread of antibiotic resistance among bacterial strains has been associated with consumption of food contaminated with both pathogenic and nonpathogenic bacteria. The objective of this study was to determine the prevalence of antibiotic resistant Escherichia coli isolates in local and imported retail raw chicken meat in Qatar. A total of 270 locally produced (chilled) and imported (chilled or frozen) whole chicken carcasses were obtained from three Hypermarket stores in Qatar. The 216 E. coli isolates recovered from the chicken samples were subjected to antibiotic susceptibility testing with the disk diffusion method. Extended-spectrum β-lactamase (ESBL) production was evaluated with the double disk synergy test. Isolates harboring colistin resistance were identified with a multiplex PCR assay and DNA sequencing. Nearly 89% (192) of the 216 isolates were resistant to at least one of the 18 antibiotics tested. Isolates from local and imported chicken carcasses had relatively higher resistance to sulfamethoxazole (62% of isolates), tetracycline (59.7%), ampicillin and trimethoprim (52.3% each), ciprofloxacin (47.7%), cephalothin (45.4%), and colistin (31.9%). Less resistance was found to amoxicillin-clavulanic acid (6%), ceftriaxone (5.1%), nitrofurantoin (4.2%), piperacillin-tazobactam (4.2%), cefepime (2.3%), meropenem (1.4%), ertapenem (0.9%), and amikacin (0.9%). Nine isolates (4.2%) were ESBL producers, and 137 (63.4%) were multidrug resistant. The percentages of multidrug-resistant, ESBL-producing, and colistin resistant isolates were significantly higher among isolates from local chilled than from imported chilled and frozen chicken samples. Our findings indicate the high prevalence of antibiotic-resistant E. coli in chicken meat sold at retail in Qatar.

HIGHLIGHTS

Extended Spectrum β-Lactamase (ESBL) Producing Escherichia coli in Pigs and Pork Meat in the European Union

The aim of this article is to review the fast and worldwide distribution of ESBL enzymes and to describe the role of the pork production chain as a reservoir and transmission route of ESBL-producing Escherichia coli and ESBLs in the European Union (EU). The use of β-lactam antibiotics in swine production and the prevalence of ESBL producing E. coli in fattening pigs and pork meat across Europe is analyzed. Overall, an increasing trend in the prevalence of presumptive ESBL producing E. coli in fattening pigs in the EU has been observed in the last decade, although with major differences among countries, linked to different approaches in the use of antimicrobials in pork production within the EU. Moreover, the various dissemination pathways of these bacteria along the pork production chain are described, along with factors at farm and slaughterhouse level influencing the risk of introducing or spreading ESBL producing bacteria throughout the food chain.

In silico mapping of microbial communities and stress responses in a porcine slaughterhouse and pork products through its production chain, and the efficacy of HLE disinfectant

The use of shotgun metagenomic sequencing to understand ecological-level spread of microbes and their genes has provided new insights for the prevention, surveillance and control of microbial contaminants in the slaughterhouse environment. Here, microbial samples were collected from products and surrounding areas though a porcine slaughter process; shotgun metagenomic DNA-sequencing of these samples revealed a high community diversity within the porcine slaughterhouse and pork products, in zones originating from animal arrival through to the sale zones. Bacteria were more prevalent in the first zones, such as arrival- and anesthesia-zones, and DNA viruses were prevalent in the scorching-and-whip zone, animal products and sale zone. Data revealed the dominance of Firmicutes and Proteobacteria phyla followed by Actinobacteria, with a clear shift in the relative abundance of lactic acid bacteria (mainly Lactobacillus sp.) from early slaughtering steps to Proteobacteria and then to viruses suggesting site-specific community compositions occur in the slaughterhouse. Porcine-type-C oncovirus was the main virus found in slaughterhouse, which causes malignant diseases in animals and humans. As such, to guarantee food safety in a slaughterhouse, a better decipher of ecology and adaptation strategies of microbes becomes crucial. Analysis of functional genes further revealed high abundance of diverse genes associated with stress, especially in early zones (animal and environmental surfaces of arrival zone with 57,710 and 40,806 genes, respectively); SOS responsive genes represented the most prevalent, possibly associated with genomic changes responsible of biofilm formation, stringent response, heat shock, antimicrobial production and antibiotic response. The presence of several antibiotic resistance genes suggests horizontal gene transfer, thus increasing the likelihood for resistance selection in human pathogens. These findings are of great concern, with the suggestion to focus control measures and establish good disinfection strategies to avoid gene spread and microbial contaminants (bacteria and viruses) from the animal surface into the food chain and environment, which was achieved by applying HLE disinfectant after washing with detergent.

Individual training for farmers based on results from protein and ATP rapid tests and microbiological conventional cultural methods improves hygiene in pig fattening pens

Optimal hygiene management is an essential part of maintaining a high standard of health in conventional pig production systems and for the successful interruption of infection chains. Currently, efficiency assessments on cleaning and disinfection are only performed by visual inspection or are neglected completely. The aim of this study was to evaluate the available methods for on farm monitoring of hygiene, identify critical points in pig pens and use the data obtained for training purposes. In addition to visual inspection by assessing the cleanliness, microbiological swab samples, i.e., aerobic total viable count (TVC), total coliform count, methicillin-resistant Staphylococcus aureus (MRSA), and extended-spectrum β-lactamases-producing bacteria (ESBL), swab samples for ATP as well as protein residues and agar contact plates combined with 3 different culture media, were applied and ranked according to their suitability for livestock farming. Samples were collected on at least 15 critical points from one representative pen on 6 pig fattening farms with various hygiene management practices after cleaning and disinfection. After the first sampling, farmers were trained with their individual results, and sampling was repeated 6 mo after training. Nipple drinkers, feeding tubes (external and inner surface), and troughs (external and inner surface) showed the greatest bacterial loads (TVC: 4.5-6.7 log10 cfu cm-2) and values for ATP and protein residues; therefore, these surfaces could be identified as the most important critical points. Spearman rank correlations (P < 0.01) were found between the different assessment methods, especially for the TVC and ATP (r = 0.82, P < 0.001). For rapid assessment on farms, ATP tests represented an accurate and cost-efficient alternative to microbiological techniques. Training improved cleaning performance as indicated by a lower rating for visual inspection, TVC, ATP, MRSA, and ESBL in the second assessment. The monitoring of cleaning efficiency in pig pens followed by training of the staff constitutes a valuable strategy to limit the spread of infectious diseases and antibiotic-resistant bacteria. Special attention should be paid to the sufficient hygiene of drinkers and feeders.

Association between antibiotic residues, antibiotic resistant bacteria and antibiotic resistance genes in anthropogenic wastewater - An evaluation of clinical influences

The high use of antibiotics in human and veterinary medicine has led to a wide spread of antibiotics and antimicrobial resistance into the environment. In recent years, various studies have shown that antibiotic residues, resistant bacteria and resistance genes, occur in aquatic environments and that clinical wastewater seems to be a hot spot for the environmental spread of antibiotic resistance. Here a representative statistical analysis of various sampling points is presented, containing different proportions of clinically influenced wastewater. The statistical analysis contains the calculation of the odds ratios for any combination of antibiotics with resistant bacteria or resistance genes, respectively. The results were screened for an increased probability of detecting resistant bacteria, or resistance genes, with the simultaneous presence of antibiotic residues. Positive associated sets were then compared, with regards to the detected median concentration, at the investigated sampling points. All results show that the sampling points with the highest proportion of clinical wastewater always form a distinct cluster concerning resistance. The results shown in this study lead to the assumption that ciprofloxacin is a good indicator of the presence of multidrug resistant P. aeruginosa and extended spectrum β-lactamase (ESBL)-producing Klebsiella spec., Enterobacter spec. and Citrobacter spec., as it positively relates with both parameters. Furthermore, a precise relationship between carbapenemase genes and meropenem, regarding the respective sampling sites, could be obtained. These results highlight the role of clinical wastewater for the dissemination and development of multidrug resistance.

Research and Technological Advances Regarding the Study of the Spread of Antimicrobial Resistance Genes and Antimicrobial-Resistant Bacteria Related to Animal Husbandry

The extensive use of antimicrobials in animal farms poses serious safety hazards to both the environment and public health, and this trend is likely to continue. Antimicrobial resistance genes (ARGs) are a class of emerging pollutants that are difficult to remove once introduced. Understanding the environmental transfer of antimicrobial-resistant bacteria (ARB) and ARGs is pivotal for creating control measures. In this review, we summarize the research progress on the spread and detection of ARB and ARG pollution related to animal husbandry. Molecular methods such as high-throughput sequencing have greatly enriched the information about ARB communities. However, it remains challenging to delineate mechanisms regarding ARG induction, transmission, and tempo-spatial changes in the whole process, from animal husbandry to multiple ecosystems. As a result, future research should be more focused on the mechanisms of ARG induction, transmission, and control. We also expect that future research will rely more heavily on metagenomic -analysis, metatranscriptomic sequencing, and multi-omics technologies

Cross-border comparison of antimicrobial resistance (AMR) and AMR prevention measures: the healthcare workers' perspective

Background

Cross-border healthcare may promote the spread of multidrug-resistant microorganisms (MDRO) and is challenging due to heterogeneous antimicrobial resistance (AMR) prevention measures (APM). The aim of this article is to compare healthcare workers (HCW) from Germany (DE) and The Netherlands (NL) on how they perceive and experience AMR and APM, which is important for safe patient exchange and effective cross-border APM cooperation.

Methods

A survey was conducted amongst HCW (n = 574) in hospitals in DE (n = 305) and NL (n = 269), using an online self-administered survey between June 2017 and July 2018. Mann-Whitney U tests were used to analyse differences between answers of German and Dutch physicians (n = 177) and German and Dutch nurses (n = 397) on 5-point Likert Items and Scales.

Results

Similarities between DE and NL were a high awareness about the AMR problem and the perception that the possibility to cope with AMR is limited (30% respondents perceive their contribution to limit AMR as insufficient). Especially Dutch nurses scored significantly lower than German nurses on their contribution to limit AMR (means 2.6 vs. 3.1, p ≤ 0.001). German HCW were more optimistic about their potential role in coping with AMR (p ≤ 0.001), and scored higher on feeling sufficiently equipped to perform APM (p ≤ 0.003), although the mean scores did not differ much between German and Dutch respondents.

Conclusions

Although both German and Dutch HCW are aware of the AMR problem, they should be more empowered to contribute to limiting AMR through APM (i.e. screening diagnostics, infection diagnosis, treatment and infection control) in their daily working routines. The observed differences reflect differences in local, national and cross-border structures, and differences in needs of HCW, that need to be considered for safe patient exchange and effective cross-border APM.

Phenotypic and genotypic characteristics of Escherichia coli with non-susceptibility to quinolones isolated from environmental samples on pig farms

Background

In the last decade, the growth of the pig-farming industry has led to an increase in antibiotic use, including several used in human medicine, e.g. (fluoro)quinolones. Data from several studies suggest that there is a link between the agricultural use of antibiotics and the prevalence of antibiotic-resistant bacteria in the pig farm environment, including (fluoro)quinolone resistance. This poses a threat to human and animal health. Our goal was to phenotypically and genotypically characterize 174 E. coli showing non-susceptibility to quinolones isolated from environmental samples from pig farms. Antimicrobial susceptibility testing (AST) was performed using the disk diffusion method. PCR and sequence analysis were performed to identify chromosomal mutations in the quinolone resistance-determining regions (QRDR) of gyrA and the isolates were screened for the presence of the plasmid-mediated quinolone resistance (PMQR) genes aac-(6')-Ib-cr, qepA, qnrA, qnrB, qnrC, qnrD and qnrS.

Strain relatedness was assessed by phylogenetic classification and multilocus sequence typing (MLST).

Results

Of 174 isolates, 81% (n = 141) were resistant to nalidixic acid, and 19% (n = 33) were intermediately resistant. Overall, 68.4% (n = 119) were multidrug resistant. This study revealed a prevalence of 79.9% (n = 139) for gyrA QRDR mutations, and detected 21.8% (n = 38) isolates with at least one PMQR gene. The two most frequently detected PMQR genes were qnrB and qnrS (13.8% (n = 24) and 9.8% (n = 17, respectively). E. coli belonging to phylogenetic group A (48.3%/n = 84) and group B1 (33.3% /n = 58) were the most frequent. E. coli ST10 (n = 20) and ST297 (n = 20) were the most common STs.

Conclusions

E. coli with non-susceptibility to quinolones are widespread among the environment of Swiss pig farms and are often associated with an MDR phenotype. In several cases these isolates possess at least one PMQR gene, which could spread by horizontal gene transfer. E. coli from pig farms have diverse STs, some of which are associated with human and animal disease.

Electronic supplementary material

The online version of this article (10.1186/s40813-019-0116-y) contains supplementary material, which is available to authorized users.

Achieving Environmentally Sustainable Livestock Production

Livestock production is a major global source of greenhouse gas emissions [...]