Clonal and plasmidic dissemination of critical antimicrobial resistance genes through clinically relevant ExPEC and APEC-like lineages (ST) in the dairy cattle population of Québec, Canada.

Antimicrobial resistance can be effectively limited by improving the judicious use of antimicrobials in food production. However, its effect on the spread of AMR genes in animal populations is not well described. In the province of Québec, Canada, a new legislation implemented in 2019 has led to an unprecedented reduction in the use of critical antimicrobials in dairy production. We aimed to investigate the potential link between ESBL/AmpC E. coli isolated before and after legislation and to determine the presence of plasmids carrying genes responsible for critical AMR. We collected fecal samples from calves, cows, and manure pit from 87 Québec dairy farms approximately 2 years before and 2 years after the legislation came into effect. The whole genomes of 183 presumptive ESBL/AmpC E. coli isolated after cefotaxime enrichment were sequenced. Their phylogenetic characteristics (MLST, serogroup, cgMLST) and the presence of virulence and resistance genes and replicons were examined. A maximum likelihood phylogenetic tree was constructed based on single nucleotide polymorphism (SNPs). We identified 10 clonal lineages (same cgMLST) and 7 clones (SNPs ≤ 52). Isolates belonging to these clones could be found on different farms before and after the legislation, strongly suggesting a clonal spread of AMR genes in the population during this 4-year period. All isolates were multidrug resistant (MDR), with clone 2 being notable for the presence of macrolide, fluoroquinolone, and third-generation cephalosporin resistance genes. We also identified clinically relevant ExPEC (ST10) and APEC-like lineages (ST117, ST58, ST88) associated with the presence of ExPEC and APEC virulence genes, respectively. Our data also suggests the presence of one epidemic plasmid belonging to the IncY incompatibility group and carrying qnrs1 and blaCTX-M-15. We demonstrated that AMR genes spread through farms and can persist over a 4-year period in the dairy cattle population through both plasmids and E. coli clones, despite the restriction of critical antimicrobial use. MDR ExPEC and APEC-like STs are present in the normal microbiota of cattle (more frequently in calves). These data increase our knowledge on gene dissemination dynamics and highlight the fact that biosecurity measures should be enhanced in this industry to limit such dissemination.

Summary of Known U.S. Injuries and Fatalities Involving Livestock Waste Storage, Handling, and Transport Operations: 1975-2019.

HIGHLIGHTS: Approximately ten cases were documented annually over the 44-year period; 48% were in the last decade and 28% were in the last three years, primarily due to more aggressive surveillance and on-line access to incident reports. A total of 389 incidents involving 459 individuals were documented, of which 59% were fatal; >85% of the victims were male, with an average age of 37. 49 rescue incidents involved a total of 119 secondary victims, indicating that approximately 26% of the victims were secondary victims, including first responders. 20% of all victims, when age was known, were children or youth under the age of 21. ABSTRACT: There is limited published research exploring the frequency and causes of livestock waste-related fatalities and injuries among farm operators and workers. While there has been ongoing surveillance of mortality and morbidity involving agricultural confined space-related incidents, such as grain storage facilities, few resources have been invested in estimating the frequency of livestock waste-related incidents, which are often reported as primarily involving confined spaces. Existing surveillance efforts have historically underreported fatal cases, injuries, and near misses and misclassified these incidents as non-farm related. For nearly 40 years, the Purdue Agricultural Confined Spaces Incident Database (PACSID) has been used to document agricultural confined space-related incidents, of which manure storage and handling activities have accounted for 22% of the cases documented. The specific goal of this study was to address the gap in the current understanding of the frequency and severity of injuries associated with livestock waste storage, handling, and transport by: (1) developing a consistent way to identify, document, and code these cases; (2) summarizing all known U.S. cases, both fatal and non-fatal, currently documented in the PACSID; (3) identifying the most significant risks contributing to livestock waste storage, handling, and transport-related incidents; and (4) providing evidence-based recommendations and mitigation strategies to enhance the effectiveness of current injury prevention measures. The PACSID and other sources were mined for relevant data, and an aggressive effort was made to document additional cases through a variety of surveillance methods. A total of 459 individual U.S. cases from the study period (1975 to 2019) were identified, coded using a uniform coding system, and summarized. Overall, cases were documented in 43 states, with 66% (302 cases) documented in heavily agricultural and, more specifically, historically strong dairy production states. Of the cases reviewed, 59% were fatal, males ages 21 to 30 and dairy farm workers were identified as high-risk populations, 20% were identified as under the age of 21, and 49 incidents involved multiple victims. Farm injury data limitations and underreporting were problematic, especially during the early years of the study period. However, the findings provide a foundation for recommending safer workplace safety and health practices, evaluating existing engineering and regulatory standards, assessing the impacts of current injury prevention efforts, and redesigning farm safety programs, especially those targeting livestock workers, to reduce the frequency and severity of these incidents.

Summary of Injuries and Fatalities Involving Livestock Manure Storage, Handling, and Transport Operations in Seven Central States: 1976-2019.

HIGHLIGHTS A total of 133 cases were documented in a seven-state region, with Iowa reporting 43% of the cases and asphyxiations accounting for 42% of all cases. Most victims were male (>79%) with an average age of 38 years. The overall fatality rate was 57%, and 16% of the victims were under the age of 21. Thirteen incidents involved secondary victims, including eleven incidents involving two, one incident involving three, and one incident involving four. ABSTRACT. Research was conducted to document, classify, analyze, and summarize available injury and fatality data involving facilities and equipment for livestock manure storage, handling, and transport in the seven-state region (Iowa, Kansas, Minnesota, Missouri, Nebraska, North Dakota, and South Dakota) served by the Central States Center for Agricultural Safety and Health (CS-CASH). Data were initially drawn from the Purdue Agricultural Confined Space Incident Database (PACSID), which contained over 2,400 individual U.S. cases of agricultural confined space related entrapment, engulfment, entanglement, asphyxiation, and falls that were documented between 1975 and 2019. Data from these cases have been partially summarized and published, but the findings did not include in-depth analysis of manure-related incidents. Approximately one in five (460) of the 2,400+ cases that were documented over 44 years involved storage, handling, or transport of livestock wastes, including exposure to toxic gases. Of these, 133 cases were documented as having occurred in the targeted seven-state region. Each case was identified and coded according to a protocol developed previously to classify incidents related to livestock manure handling, storage, and transport. Iowa and Minnesota accounted for 79% of the total, with swine operations accounting for 33% of cases when livestock type was known. Of the victims, 79% were male. Ages ranged from 1 to 85, with an average age of 38, and 15% of the victims were age 21 and under. There were 13 incidents for which two or more victims were identified, including one incident involving four victims. It is believed that historical under-reporting of incidents, especially non-fatal incidents, continues to be a barrier to achieving a more comprehensive understanding of the scope and magnitude of the problem. However, the findings are sufficient to be used in cooperation with stakeholders to enhance the content and delivery of evidence-based agricultural safety and health programs, promote safer work practices, and contribute to the development of engineering design standards. The desired outcomes of this research include more effective strategies to protect farmers and farm workers who are at high risk of manure-related injuries. The findings also provide a sufficient baseline to gauge the effectiveness of future injury prevention measures.

Prevalence of Antimicrobial Resistance and Characteristics of Escherichia coli Isolates From Fecal and Manure Pit Samples on Dairy Farms in the Province of Québec, Canada.

Antimicrobial resistance (AMR) is an important burden for public health and veterinary medicine. For Québec (Canada) dairy farms, the prevalence of AMR is mostly described using passive surveillance, which may be misleading. In addition, the presence of extended spectrum ß-lactamase (ESBL)/AmpC producing Escherichia coli is unknown. This observational cross-sectional study used random dairy farms (n = 101) to investigate AMR and extended spectrum ß-lactamase (ESBL)/AmpC producing Escherichia coli. Twenty antimicrobials were tested on E. coli isolates (n = 593) recovered from fecal samples (n = 599) from calves, cows, and the manure pit. Isolates were mostly susceptible (3% AMR or less) to the highest priority critically important antimicrobials in humans. The highest levels of AMR were to tetracycline (26%), sulfisozaxole (23%) and streptomycin (19%). The resistance genes responsible for these resistances were, respectively: tet(A), tet(B), sul1, sul2, sul3, aph(3")-Ib (strA), aph(6)-Id (strB), aadA1, aadA2, and aadA5. ESBL analysis revealed two predominant phenotypes: AmpC (51%) and ESBL (46%) where bla CMY-2 and bla CTX-M ( bla CTX-M-1, bla CTX-M-15, and bla CTX-M-55) were the genes responsible for these phenotypes, respectively. During this study, 85% of farms had at least one ESBL/AmpC producing E. coli. Isolates from calves were more frequently resistant than those from cows or manure pits. Although prevalence of AMR was low for critically important antimicrobials, there was a high prevalence of ESBL/AmpC-producing E. coli on Quebec dairy farms, particularly in calves. Those data will help determine a baseline for AMR to evaluate impact of initiatives aimed at reducing AMR.

Farm-Related Injuries and Fatalities Involving Children, Youth, and Young Workers during Manure Storage, Handling, and Transport.

Objective: Manure storage, handling, and transport facilities and equipment have been associated with life threatening hazards on many livestock farms. These hazards have been documented in prior research as including 1) exposure to toxic manure gases or lack of adequate oxygen in enclosed structures, which can be fatal to both humans and livestock; 2) below and above ground liquid manure storage structures that have the potential risk for drowning and falling; and 3) mechanical hazards associated with manure handling and transport equipment, including entanglement, road collisions, runover, and equipment failure.Methods: Over the past 40 years, Purdue University's Agricultural Safety and Health Program (PUASHP) has collected, documented, and maintained data regarding agricultural-related injuries and fatalities associated with agricultural confined spaces in the United States. As part of ongoing surveillance, a total of 369 fatal and non-fatal cases relating to manure storage, handling and transport equipment, and facilities have been documented. Of these, 89 have involved children, youth, and young farm workers ages (birth-21) documented between 1975 and 2019. The purpose of this study was to summarize these 89 documented cases to better understand contributing factors and to develop recommendations for evidence-based strategies to reduce the frequency and severity of these incidents. Though recognized as not comprehensive for all incidents of this type, the data represent the largest data set known to exist, providing insight into previously unstudied hazards facing children and youth living and working on, and visiting farms as non-workers.Results: Findings in this study include: there has been an increase in the documented frequency of these incidents, which may be due, at least partially, to enhanced or more aggressive surveillance efforts; 57% of the cases were fatal; incidents involving underground or inground manure storage facilities were the most frequent type; incidents involving manure transport vehicles were higher than expected; 33% of the victims were five years of age and younger; and July was the month with the most documented incidents.Conclusions: Recommendations for future injury prevention strategies include incorporation of information on manure-related hazards in curricula targeting children and youth, more aggressive enforcement of child labor laws that currently prohibit the employment of youth to work in manure storage structures or to be involved in their operations, and greater use of physical and administrative controls, including safety signage, fencing, gates, and covers to restrict access to manure storage structures.

Development of methodology to document and code farm-related injuries and fatalities involving manure storage, handling and transport - with summary of 2017 incidents.

As part of ongoing surveillance of fatalities and injuries involving agricultural confined spaces by Purdue University's Agricultural Safety and Health Program, nearly 300 cases involving manure storage, handling, and transport equipment and facilities have been documented over the past 30 years. With the exception of a summary of 77 fatalities published by Beaver and Field1, these cases have not been previously analysed or published due to a lack of resources and the limitations of the Purdue Agricultural Confined Spaces Incident Database (PACSID) which was designed primarily for analysis of grain-related cases. These limitations included differences in terminology used to code case information in the PACSID and dissimilar causative and contributing factors. To develop a consistent and more useful approach to process and analyze data, 28 U.S. manure-related incidents involving 39 victims documented as having occurred in 2017 were examined for type of incident, victim characteristics, primary contributing factors, and nature of injuries. A review of literature was conducted to identify previously reported contributing factors, and a coding rubric was developed and reviewed by a panel of experts. It was determined that the rubric provided a consistent way to code and analyze descriptive information available on each case. A pilot analysis was completed of the 39 cases using the new tool, and results were summarized. The final methodology will be used to analyze all historically documented incidents, as well as future incidents. Findings presented include a review of relevant literature, discussion of the methods used in case documentation, classifications developed from sample data, and a summary of incidents in 2017. Anticipated outcomes include: 1) consistent strategy to document, code, and summarize manure-related incidents; 2) means of classification of key contributing factors; 3) identification of new or emerging trends; and 4) completion of previously documented incidents.

Online Design Aid for Evaluating Manure Pit Ventilation Systems to Reduce Entry Risk.

On-farm manure storage pits contain both toxic and asphyxiating gases such as hydrogen sulfide, carbon dioxide, methane, and ammonia. Farmers and service personnel occasionally need to enter these pits to conduct repair and maintenance tasks. One intervention to reduce the toxic and asphyxiating gas exposure risk to farm workers when entering manure pits is manure pit ventilation. This article describes an online computational fluid dynamics-based design aid for evaluating the effectiveness of manure pit ventilation systems to reduce the concentrations of toxic and asphyxiating gases in the manure pits. This design aid, developed by a team of agricultural engineering and agricultural safety specialists at Pennsylvania State University, represents the culmination of more than a decade of research and technology development effort. The article includes a summary of the research efforts leading to the online design aid development and describes protocols for using the online design aid, including procedures for data input and for accessing design aid results. Design aid results include gas concentration decay and oxygen replenishment curves inside the manure pit and inside the barns above the manure pits, as well as animated motion pictures of individual gas concentration decay and oxygen replenishment in selected horizontal and vertical cut plots in the manure pits and barns. These results allow the user to assess (1) how long one needs to ventilate the pits to remove toxic and asphyxiating gases from the pit and barn, (2) from which portions of the barn and pit these gases are most and least readily evacuated, and (3) whether or not animals and personnel need to be removed from portions of the barn above the manure pit being ventilated.