Dataset Information

Reservoirs of antimicrobial resistance genes in retail raw milk.

ABSTRACT:

Background

It has been estimated that at least 3% of the USA population consumes unpasteurized (raw) milk from animal sources, and the demand to legalize raw milk sales continues to increase. However, consumption of raw milk can cause foodborne illness and be a source of bacteria containing transferrable antimicrobial resistance genes (ARGs). To obtain a comprehensive understanding of the microbiome and antibiotic resistome in both raw and processed milk, we systematically analyzed 2034 retail milk samples including unpasteurized milk and pasteurized milk via vat pasteurization, high-temperature-short-time pasteurization, and ultra-pasteurization from the United States using complementary culture-based, 16S rRNA gene, and metagenomic sequencing techniques.

Results

Raw milk samples had the highest prevalence of viable bacteria which were measured as all aerobic bacteria, coliform, and Escherichia coli counts, and their microbiota was distinct from other types of milk. 16S rRNA gene sequencing revealed that Pseudomonadaceae dominated raw milk with limited levels of lactic acid bacteria. Among all milk samples, the microbiota remained stable with constant bacterial populations when stored at 4?°C. In contrast, storage at room temperature dramatically enriched the bacterial populations present in raw milk samples and, in parallel, significantly increased the richness and abundance of ARGs. Metagenomic sequencing indicated raw milk possessed dramatically more ARGs than pasteurized milk, and a conjugation assay documented the active transfer of bla_CMY-2, one ceftazidime resistance gene present in raw milk-borne E. coli, across bacterial species. The room temperature-enriched resistome differed in raw milk from distinct geographic locations, a difference likely associated with regionally distinct milk microbiota.

Conclusion

Despite advertised "probiotic" effects, our results indicate that raw milk microbiota has minimal lactic acid bacteria. In addition, retail raw milk serves as a reservoir of ARGs, populations of which are readily amplified by spontaneous fermentation. There is an increased need to understand potential food safety risks from improper transportation and storage of raw milk with regard to ARGs. Video Abstract.

SUBMITTER: Liu J

PROVIDER: S-EPMC7320593 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Reservoirs of antimicrobial resistance genes in retail raw milk.

Liu Jinxin J Zhu Yuanting Y Jay-Russell Michele M Lemay Danielle G DG Mills David A DA

Microbiome 20200626 1

<h4>Background</h4>It has been estimated that at least 3% of the USA population consumes unpasteurized (raw) milk from animal sources, and the demand to legalize raw milk sales continues to increase. However, consumption of raw milk can cause foodborne illness and be a source of bacteria containing transferrable antimicrobial resistance genes (ARGs). To obtain a comprehensive understanding of the microbiome and antibiotic resistome in both raw and processed milk, we systematically analyzed 2034 ...[more]

PMID: 32591006

Similar Datasets

Project description:BackgroundDrug resistance genes and their mobile genetic elements are frequently identified from environmental saprophytic organisms. It is widely accepted that the use of antibiotics in animal husbandry selects for drug resistant microorganisms, which are then spread from the farm environment to humans through the consumption of contaminated food products. We wished to identify novel drug resistance genes from microbial communities on retail food products. Here, we chose to study the microbial communities on retail spinach because it is commonly eaten raw and has previously been associated with outbreaks of bacterial infections.ResultsWe created metagenomic plasmid libraries from microbiota isolated from retail spinach samples. We identified five unique plasmids that increased resistance to antimicrobial drugs in the E. coli host. These plasmids were identified in E. coli that grew on plates that contained ampicillin (pAMP), aztreonam (pAZT), ciprofloxacin (pCIP), trimethoprim (pTRM), and trimethoprim-sulfamethoxazole (pSXT). We identified open reading frames with similarity to known classes of drug resistance genes in the DNA inserts of all 5 plasmids. These drug resistance genes conferred resistance to fluoroquinolones, cephalosporins, and trimethoprim, which are classes of antimicrobial drugs frequently used to treat human Gram negative bacterial infections. These results show that novel drug resistance genes are found in microbiota on retail produce items.ConclusionsHere we show that microbiota of retail spinach contains DNA sequences previously unidentified as conferring antibiotic resistance. Many of these novel sequences show similarity to genes found in species of bacteria, which have previously been identified as commensal or saprophytic bacteria found on plants. We showed that these resistance genes are capable of conferring clinically relevant levels of resistance to antimicrobial agents. Food saprophytes may serve as an important reservoir for new drug-resistance determinants in human pathogens.

Project description:Background Staphylococcus aureus is one of the most important foodborne pathogens in the world and the main cause of dairy cow mastitis. Few studies have investigated the epidemic pedigree of S. aureus of bovine origin in Hunan, China. Therefore, we aimed to analyze the capsular polysaccharides (CP), molecular typing, and antibiotic resistance characteristics of S. aureus isolated from raw milk of dairy farms in Hunan Province. Methods Between 2018 and 2022, 681 raw milk samples were collected from dairy cows from farms in Changsha, Changde, Shaoyang, Yongzhou, and Chenzhou in Hunan Province. S. aureus was isolated from these samples, and the isolates were subjected to molecular typing, CP typing, and determination of antibiotic resistance through broth dilution and polymerase chain reaction (PCR). Results From 681 raw milk samples, 76 strains of S. aureus were isolated. The pathogenicity of 76 isolates was determined preliminarily by detecting cp5 and cp8 CP genes. Eighteen types of antimicrobial resistance phenotypes of 76 S. aureus strains were detected by the broth dilution method, and 11 kinds of related resistance genes were amplified by PCR. The S. aureus isolates had CP5 (42.10%) and CP8 (57.89%). S. aureus had a multiple antimicrobial resistance rate of 26.75%. The isolated strains had the highest resistance rate to penicillin (82.89%) and showed varying degrees of resistance to other drugs, but no isolate showed resistance to doxycycline. The 76 isolates all carried two or more antibiotic resistance genes, with a maximum of eight antibiotics resistance genes. FemB was detected in all isolates, but none of isolates carried vanA, ermA, or glrA. The 76 isolates were divided into 22 sequence types (ST) and 20 spa types by MLST and spa typing, and the number of t796-ST7 (n = 15) isolates was the highest, which may be the major epidemic strain of multidrug-resistant S. aureus. Conclusion The present findings indicate the need to increase production of the CP8 S. aureus vaccine in Hunan Province and strengthen resistance monitoring of t796-ST7 isolates with the prevalent molecular type of multi-drug resistant strains. The use of β-lactam, macrolides, and lincosamides should be reduced; doxycycline, sulfonamides, and glycopeptides could be appropriately added to veterinary antibiotics to treat infectious diseases in dairy cows.

Project description:Multidrug-resistant enterococci are considered crucial drivers for the dissemination of antimicrobial resistance determinants within and beyond a genus. These organisms may pass numerous resistance determinants to other harmful pathogens, whose multiple resistances would cause adverse consequences. Therefore, an understanding of the coexistence epidemiology of resistance genes is critical, but such information remains limited. In this study, our first objective was to determine the prevalence of principal resistance phenotypes and genes among Enterococcus faecalis isolated from retail chicken domestic products collected throughout Japan. Subsequent analysis of these data by using an additive Bayesian network (ABN) model revealed the co-appearance patterns of resistance genes and identified the associations between resistance genes and phenotypes. The common phenotypes observed among E. faecalis isolated from the domestic products were the resistances to oxytetracycline (58.4%), dihydrostreptomycin (50.4%), and erythromycin (37.2%), and the gene tet(L) was detected in 46.0% of the isolates. The ABN model identified statistically significant associations between tet(L) and erm(B), tet(L) and ant(6)-Ia, ant(6)-Ia and aph(3')-IIIa, and aph(3')-IIIa and erm(B), which indicated that a multiple-resistance profile of tetracycline, erythromycin, streptomycin, and kanamycin is systematic rather than random. Conversely, the presence of tet(O) was only negatively associated with that of erm(B) and tet(M), which suggested that in the presence of tet(O), the aforementioned multiple resistance is unlikely to be observed. Such heterogeneity in linkages among genes that confer the same phenotypic resistance highlights the importance of incorporating genetic information when investigating the risk factors for the spread of resistance. The epidemiological factors that underlie the persistence of systematic multiple-resistance patterns warrant further investigations with appropriate adjustments for ecological and bacteriological factors.

Project description:The purpose of this study was to determine whether raw milk, unpasteurized dairy products, pork, and beef available for sale in the Kujawsko-Pomorskie and Wielkopolska regions in Poland are contaminated with Campylobacter spp. bacteria and may be a potential source of infection. For isolated strains, antibiotic susceptibility and the presence of genes responsible for virulence were examined. Material for research included 1058 food samples collected between 2014 and 2018 with 454 samples of raw milk and unpasteurized dairy products (milk from vending machines, milk from owners of dairy cows, cheese, milk cream) and 604 samples of raw meat (pork, beef). The results indicated that 9.3% of the samples were positive for Campylobacter spp., and Campylobacter jejuni was predominant in this study. Campylobacter bacteria was not found in milk collected from vending machines, as well as cheese and milk cream samples. Campylobacter was noted in 12.7% of beef samples, 11.8% of raw milk purchased from individual suppliers, and 10.9% of pork samples. Resistance to erythromycin (2.0%), azithromycin (3.1%), gentamicin (4.1%), tetracycline (65.3%), and ciprofloxacin (71.4%) was determined using the disc diffusion method. Furthermore, the prevalence of racR, sodB, csrA, virB11, cdtB, iam, and wlaN genes were examined using the PCR method. The sodB, csrA, and cdtB genes exhibited the highest detection rate, but none of the genes were identified in 100% of the isolates. Statistically significant differences between the presence of virulence marker genes, including for iam, racR, and csrA markers, were noted among different sources of the isolates. Differences in the distribution of iam, wlaN, and virB11 were also shown between C. jejuni and C. coli strains. As a result of the analysis, it has been concluded that unpasteurized milk, beef, and pork could be a sources of Campylobacter pathogens. Moreover, this study revealed virulent properties of Campylobacter isolated from such food products and high resistance rates to fluoroquinolones, which may represent difficulties in campylobacteriosis treatment.

Dataset Information

Reservoirs of antimicrobial resistance genes in retail raw milk.

Background

Results

Conclusion

Publications

Reservoirs of antimicrobial resistance genes in retail raw milk.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets