Resistomes and microbiome of meat trimmings and colon content from culled cows raised in conventional and organic production systems

Comparative microbiome analysis of beef cattle, the feedyard environment, and airborne particulate matter as a function of probiotic and antibiotic use, and change in pen environment

Introduction

Intensive beef cattle production systems are frequently implicated as a source of bacteria that can be transferred to nearby humans and animals via effluent water, manure used as fertilizer, or airborne particulate matter. It is crucial to understand microbial population dynamics due to manure pack desiccation, antibiotic usage, and antibiotic alternatives within beef cattle and their associated feedyard environment. Understanding how bacterial communities change in the presence of antibiotics can also improve management practices for reducing the spread of foodborne bacteria.

Methods

In this study, we aimed to compare the microbiomes within cattle feces, the feedyard environment and artificially produced airborne particulate matter as a function of pen change and treatment with tylosin or probiotics. We utilized 16S rRNA sequencing to compare bacterial communities among sample types, study days, and treatment groups.

Results

Bacterial community diversity varied as a function of sampling day and pen change (old or new) within fecal and manure pack samples. Manure pack samples from old pens and new pens contained diverse communities of bacteria on days 0 and 84; however, by day 119 of the study these taxonomic differences were less evident. Particulate matter samples exhibited significant differences in community diversity and predominant bacterial taxa compared to the manure pack they originated from. Treatment with tylosin did not meaningfully impact bacterial communities among fecal, environmental, or particulate matter samples; however, minor differences in bacterial community structure were observed in feces from cattle treated with probiotics.

Discussion

This study was the first to characterize and compare microbial communities within feces, manure pack, and airborne particulate matter from the same location and as a function of tylosin and probiotic treatment, and pen change. Although fecal and environmental samples are commonly used in research studies and other monitoring programs to infer public health risk of bacteria and antimicrobial resistance determinants from feedyard environments, our study suggests that these samples may not be appropriate to infer public health risk associated with airborne particulate matter.

Effect of Antimicrobial Use in Conventional Versus Natural Cattle Feedlots on the Microbiome and Resistome

Antimicrobial use (AMU) in the livestock industry has been associated with increased levels of antimicrobial resistance. Recently, there has been an increase in the number of "natural" feedlots in the beef cattle sector that raise cattle without antibiotics. Shotgun metagenomics was employed to characterize the impact of AMU in feedlot cattle on the microbiome, resistome, and mobilome. Sequenced fecal samples identified a decline (q < 0.01) in the genera Methanobrevibacter and Treponema in the microbiome of naturally vs. conventionally raised feedlot cattle, but this difference was not (q > 0.05) observed in catch basin samples. No differences (q > 0.05) were found in the class-level resistome between feedlot practices. In fecal samples, decreases from conventional to natural (q < 0.05) were noted in reads for the antimicrobial-resistant genes (ARGs) mefA, tet40, tetO, tetQ, and tetW. Plasmid-associated ARGs were more common in feces from conventional than natural feedlot cattle. Interestingly, more chromosomal- than plasmid-associated macrolide resistance genes were observed in both natural and conventional feedlots, suggesting that they were more stably conserved than the predominately plasmid-associated tetracycline resistance genes. This study suggests that generationally selected resistomes through decades of AMU persist even after AMU ceases in natural production systems.

Nanopore Sequencing Assessment of Bacterial Pathogens and Associated Antibiotic Resistance Genes in Environmental Samples

As seen in earlier and present pandemics, monitoring pathogens in the environment can offer multiple insights on their spread, evolution, and even future outbreaks. The present paper assesses the opportunity to detect microbial pathogens and associated antibiotic resistance genes, in relation to specific pathogen sources, by using nanopore sequencing in municipal waters and wastewaters in Romania. The main results indicated that waters collecting effluents from a meat processing facility exhibit altered communities' diversity and abundance, with reduced values (101-108 and 0.86-0.91) of Chao1 and, respectively, Simpson diversity indices and Campylobacterales as main order, compared with other types of municipal waters where the same diversity index had much higher values of 172-214 and 0.97-0.98, and Burkholderiaceae and Pseudomonadaceae were the most abundant families. Moreover, the incidence and type of antibiotic resistance genes were significantly influenced by the proximity of antibiotic sources, with either tetracycline (up to 45% of total reads) or neomycin, streptomycin and tobramycin (up to 3.8% total reads) resistance incidence being shaped by the sampling site. As such, nanopore sequencing proves to be an easy-to-use, accessible molecular technique for environmental pathogen surveillance and associated antibiotic resistance genes.

Distribution of Extremely Heat-Resistant Escherichia coli in the Beef Production and Processing Continuum

Understanding the dynamics of stress-resistant Escherichia coli (E. coli) across the meat production and processing continuum is important for tracking sources of such microbes and devising effective modes of control. The Locus of Heat Resistance (LHR) is a ∼14-19 Kb genetic element imparting extreme heat resistance (XHR) in Enterobacteriaceae. It has been hypothesized that thermal and antimicrobial interventions applied during meat processing may select for LHR⁺E. coli. Thus, our goal was to study the prevalence and molecular biology of LHR⁺E. coli among lots of beef cattle (n = 3) from production through processing. Two hundred thirty-two generic E. coli isolated from the same animals through seven stages of the beef processing continuum (cattle in feedyards to packaged strip loins) were examined. LHR⁺E. coli were rare (0.6%; 1 of 180) among the early stages of the beef continuum (feces and hides at feedlot, feces and hides at harvest, and preevisceration carcasses), whereas the prevalence of LHR⁺E. coli on final carcasses and strip loins was remarkably higher. Half (14 of 28) of the final carcass E. coli possessed the LHR, while 79.2% (19 of 24) of the strip loin E. coli did. Eighty-five percent (29 of 34) of the LHR⁺E. coli presented with the XHR phenotype. The selection or enrichment of LHR⁺E. coli from harvest steps to the final products appeared unlikely as the LHR⁺E. coli isolates were effectively controlled by antimicrobial interventions typically used during beef processing. Further, whole-genome sequencing of the isolates suggested LHR⁺E. coli are persisting in the chilled processing environment and that horizontal LHR transfer among E. coli isolates may take place.

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.