Prevalence of Antibiotic Resistance Genes in Multidrug-Resistant Enterobacteriaceae on Portuguese Livestock Manure

Abstract

The exposure of both crop fields and humans to antibiotic-resistant bacteria in animal excreta is an emergent concern of the One Health initiative. This study assessed the contamination of livestock manure from poultry, pig, dairy farms and slaughterhouses in Portugal with resistance determinants. The resistance profiles of 331 Enterobacteriaceae isolates to eight β-lactam (amoxicillin, cefoxitin, cefotaxime, cefpirome, aztreonam, ceftazidime, imipenem and meropenem) and to five non-β-lactam antibiotics (tetracycline (TET), trimethoprim/sulfamethoxazole (SXT), ciprofloxacin (CIP), chloramphenicol (CHL) and gentamicin) was investigated. Forty-nine integron and non-β-lactam resistance genes were also screened for. Rates of resistance to the 13 antibiotics ranged from 80.8% to 0.6%. Multidrug resistance (MDR) rates were highest in pig farm samples (79%). Thirty different integron and resistance genes were identified. These were mainly associated with resistance to CHL (catI and catII), CIP (mainly, qnrS, qnrB and oqx), TET (mainly tet(A) and tet(M)) and SXT (mostly dfrIa group and sul3). In MDR isolates, integron presence and non-β-lactam resistance to TET, SXT and CHL were positively correlated. Overall, a high prevalence of MDR Enterobacteriaceae was found in livestock manure. The high gene diversity for antibiotic resistance identified in this study highlights the risk of MDR spread within the environment through manure use.

Fecal cultivable aerobic microbiota of dairy cows and calves acting as reservoir of clinically relevant antimicrobial resistance genes

“…Netthisinghe et al [27] showed high concentrations of ARG-producing bacteria in the feeding area of farms, where there is a higher concentration of fecal deposition when compared with other areas. Kyselková et al [28] and Amador et al [29] reported the presence of ARGs and genetic elements, including those detected in this study, in bacteria from fecal samples from dairy farms. Antimicrobial-resistant Gram-negative bacteria were detected in the feces of healthy lactating dairy cattle in different countries [30].…”

Manure as a Potential Hotspot for Antibiotic Resistance Dissemination by Horizontal Gene Transfer Events

“…The tet gene family, involved in the active efflux of tetracycline compounds, ribosomal protection or the enzymatic modification of antimicrobial agents [58], has been reported as one of the most frequently detected ARGs in animal manure [21,25]. After manure application, tet gene levels in the soil are increased significantly and manure application amended with tetracyclines promotes the accumulation of tet genes and modifies the soil bacterial composition [54,55,59,60]. These genes are often embedded in plasmids (isolated from manure and animal bacteria) [61,62] and inserted in transposons, which facilitates their dissemination [54].…”

Developing Irrigation Management at District Scale Based on Water Monitoring: Study on Lis Valley, Portugal

“…Water quality monitoring in the district is a very important procedure to know the local reality over time and allow adjustments to be as effective as possible, as highlighted by [38,54,55]. (ii) The organic load of livestock applied to the soil in certain areas of the district makes the emerging microbiological risk significant [56]. (iii) The downstream part of the district has hydrogeological characteristics of significant salinity, which is a risk factor for soil due to capillary rise or drainage water reuse [57].…”

“…Poor water quality leads to multiple risk problems, requiring protection, adaptation, or mitigation measures: (i) Judicious use of manure as soil fertilizer, which should be appropriately composted in farms and slaughterhouses treatment plants [58]. Cautions should be reinforced when applied to horticultural crops, or crop handling, to protect environmental and public health problems due to microbes and other contaminants like antibiotics [56]. (ii) Choice of irrigation technology should take into account irrigation water quality and should be adjusted according to the risk assessment for the farmer and the consumer of the product.…”