Genomic diversity of antimicrobial-resistant and Shiga toxin gene-harboring non-O157 Escherichia coli from dairy calves

Biswas, Debabrata; Kim, Seon Woo; Springer, Hayley R.; Hovingh, Ernest; Kessel, Jo Ann S. Van; Haley, Bradd J.

doi:10.1016/j.jgar.2023.02.022

Cited by 5 publications

(6 citation statements)

References 19 publications

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“…Indeed, the proportion of positive samples in BTM was very low (3.4% of stx-positive samples), while the proportion on the RMF of the same herds were significantly higher (41.3% of stx-positive samples), as well as in calf feces. These differences were not unexpected [11,27,38,39,42], and may be explained in the following way:…”

Section: Stec Prevalence In the Different Matricesmentioning

confidence: 85%

“…The presence of STEC in calf has been reported in few studies [39][40][41], but at best of our knowledge, this approach was never thought as a way to identify potential vector animals within and between herds, and a potential critical point for control measures. The availability of new commercial molecular assays allows to identify non-O157 serotypes in milk and milk products which simplify and make more efficient the detection process.…”

Section: Aims Of the Pilot Studymentioning

confidence: 99%

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How to Improve Surveillance Program for Shiga Toxin-Producing E. coli (STEC): Gap Analysis and Pilot Study

Sora,

Zaghen,

Zecconi

2024

Preprint

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Several pathotypes of enteric E. coli have been identified. The group represented by Shiga toxin-producing E. coli (STEC) is of particular interest. Raw milk and raw milk products are significant sources of STEC infection in humans; therefore, identifying pathogens at the herd level is crucial for public health. Most national surveillance programs focus solely on raw milk and raw milk cheeses that are ready for retail sale, neglecting the possibility of evaluating the source of contamination directly at the beginning of the dairy chain. In order to assess the viability of new molecular methodologies applied to raw milk filters enabling the identification of the presence of STEC serotypes in milk production and apply the same methods to identify the presence of these pathogens in calf feces we analyzed, through a commercial real-time PCR assay, a total of 290 samples coming from 18 different dairy herds; 88 bulk tank milk (BTM), 104 raw milk filters (RMF) and 98 calves’ feces samples. In total 3.4% of BTM, 41.4% of RMF and 73.4% of calves’ feces tested positive for stx presence, supporting our hypothesis that BTM is not a suitable matrix to assess the STEC presence at herd level, underestimating it. Our conclusion is that the surveillance program needs critical and extensive improvements such as RMF and calves’ feces analysis implementation in order to be more efficient in detecting and preventing STEC infections. The epidemiology of these infections and the characteristics of the pathogen clearly show how a One Health approach will be pivotal to improve our capabilities to control the spread of these infections.

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Section: Stec Prevalence In the Different Matricesmentioning

confidence: 85%

Section: Aims Of the Pilot Studymentioning

confidence: 99%

How to Improve Surveillance Program for Shiga Toxin-Producing E. coli (STEC): Gap Analysis and Pilot Study

Sora,

Zaghen,

Zecconi

2024

Preprint

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“…Therefore, these differences were expected [ 11 , 28 , 37 , 42 , 43 ] and may be explained as follows: Milk: 25 mL of raw milk are sampled from the bulk tank, which is capable of holding 150–10,000 liters of milk at 4 °C, which results in a poor detection level, particularly when the prevalence of STEC-positive cows is very low and/or when milking practices are optimal. Milk Filters: with this type of sample, it is easier to find positivity because the main task of the filter is to block and retain any type of fecal or litter debris coming from the milking routine, and all the milk passes through the filter; therefore, there is no dilution effect.…”

Section: Discussionmentioning

confidence: 99%

“…The presence of STEC in calves has been reported in a few studies [ 37 , 38 , 39 ], but, to the best of our knowledge, this approach was never thought to be a way to identify potential vector animals within and between herds and a potential critical point for control measures. The availability of new commercial molecular assays allows identification of non-O157 serotypes in milk and milk products, simplifying and making the detection process more efficient.…”

Section: Introductionmentioning

confidence: 99%

How to Improve Surveillance Program for Shiga Toxin-Producing E. coli (STEC): Gap Analysis and Pilot Study

Sora,

Zaghen,

Zecconi

2024

Pathogens

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Several pathotypes of enteric E. coli have been identified. The group represented by Shiga toxin-producing E. coli (STEC) is of particular interest. Raw milk and raw milk products are significant sources of STEC infection in humans; therefore, identifying pathogens at the herd level is crucial for public health. Most national surveillance programs focus solely on raw milk and raw milk cheeses that are ready for retail sale, neglecting the possibility of evaluating the source of contamination directly at the beginning of the dairy chain. To assess the viability of the application of new molecular methodologies to STEC identification in raw milk filters and in calf feces, we analyzed 290 samples from 18 different dairy herds, including 88 bulk tank milk (BTM), 104 raw milk filters (RMF), and 98 calf feces samples. In total 3.4% of BTM, 41.4% of RMF, and 73.4% of calves’ feces were positive for stx, supporting our hypothesis that BTM is not a suitable matrix to assess the presence of STEC at herd level, underestimating it. Our conclusion is that the surveillance program needs critical and extensive improvements such as RMF and calves’ feces analysis implementation to be more efficient in detecting and preventing STEC infections. The epidemiology of these infections and the characteristics of the pathogen clearly show how a One Health approach will be pivotal in improving our capabilities to control the spread of these infections.

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“…Multidrug-resistant (MDR) Escherichia coli are frequently isolated from dairy cow and calf feces, unpasteurized cow's milk, and culled dairy cow beef and are a major component of the suite of antimicrobial-resistant bacteria (ARB) carried by young calves [1][2][3]. A minority of these E. coli are enterohemorrhagic (EHEC) Shiga toxin-encoding strains that can cause moderate to severe gastrointestinal disease, septicemia, hemolytic uremia syndrome (HUS), chronic sequelae, and possibly death [4,5]. However, E. coli is highly diverse, with many suites of virulence and fitness factors (VFFs) that can cause both mild to severe gastrointestinal and extra-intestinal infections, such as urinary tract infections (UTIs) and meningitis [6].…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Analysis of Escherichia coli Isolated from Dairy Animals Identifies Virulence Factors and Genes Enriched in Multidrug-Resistant Strains

Haley,

Kim,

Salaheen

et al. 2023

Antibiotics

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The gastrointestinal tracts of dairy calves and cows are reservoirs of antimicrobial-resistant bacteria (ARB), which are present regardless of previous antimicrobial therapy. Young calves harbor a greater abundance of resistant bacteria than older cows, but the factors driving this high abundance are unknown. Here, we aimed to fully characterize the genomes of multidrug-resistant (MDR) and antimicrobial-susceptible Escherichia coli strains isolated from pre-weaned calves, post-weaned calves, dry cows, and lactating cows and to identify the accessory genes that are associated with the MDR genotype to discover genetic targets that can be exploited to mitigate antimicrobial resistance in dairy farms. Results indicated that both susceptible and resistant E. coli isolates recovered from animals on commercial dairy operations were highly diverse and encoded a large pool of virulence factors. In total, 838 transferrable antimicrobial resistance genes (ARGs) were detected, with genes conferring resistance to aminoglycosides being the most common. Multiple sequence types (STs) associated with mild to severe human gastrointestinal and extraintestinal infections were identified. A Fisher’s Exact Test identified 619 genes (ARGs and non-ARGs) that were significantly enriched in MDR isolates and 147 genes that were significantly enriched in susceptible isolates. Significantly enriched genes in MDR isolates included the iron scavenging aerobactin synthesis and receptor genes (iucABCD-iutA) and the sitABCD system, as well as the P fimbriae pap genes, myo-inositol catabolism (iolABCDEG-iatA), and ascorbate transport genes (ulaABC). The results of this study demonstrate a highly diverse population of E. coli in commercial dairy operations, some of which encode virulence genes responsible for severe human infections and resistance to antibiotics of human health significance. Further, the enriched accessory genes in MDR isolates (aerobactin, sit, P fimbriae, and myo-inositol catabolism and ascorbate transport genes) represent potential targets for reducing colonization of antimicrobial-resistant bacteria in the calf gut.

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Genomic diversity of antimicrobial-resistant and Shiga toxin gene-harboring non-O157 Escherichia coli from dairy calves

Cited by 5 publications

References 19 publications

How to Improve Surveillance Program for Shiga Toxin-Producing E. coli (STEC): Gap Analysis and Pilot Study

How to Improve Surveillance Program for Shiga Toxin-Producing E. coli (STEC): Gap Analysis and Pilot Study

How to Improve Surveillance Program for Shiga Toxin-Producing E. coli (STEC): Gap Analysis and Pilot Study

Genome-Wide Analysis of Escherichia coli Isolated from Dairy Animals Identifies Virulence Factors and Genes Enriched in Multidrug-Resistant Strains

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