Metagenomic analysis of acquired antibiotic resistance determinants in the gut microbiota of wild boars (Sus scrofa) – preliminary results

AbstractIntroductionLand application of manure that contains antibiotics and resistant bacteria may facilitate the establishment of an environmental reservoir of antibiotic-resistant microbes, promoting their dissemination into agricultural and natural habitats. The main objective of this study was to search for acquired antibiotic resistance determinants in the gut microbiota of wild boar populations living in natural habitats.Material and MethodsGastrointestinal samples of free-living wild boars were collected in the Zemplén Mountains in Hungary and were characterised by culture-based, metagenomic, and molecular microbiological methods. Bioinformatic analysis of the faecal microbiome of a hunted wild boar from Japan was used for comparative studies. Also, shotgun metagenomic sequencing data of two untreated sewage wastewater samples from North Pest (Hungary) from 2016 were analysed by bioinformatic methods. Minimum spanning tree diagrams for seven-gene MLST profiles of 104 E. coli strains isolated in Europe from wild boars and domestic pigs were generated in Enterobase.ResultsIn the ileum of a diarrhoeic boar, a dominant E. coli O112ab:H2 strain with intermediate resistance to gentamicin, tobramycin, and amikacin was identified, displaying sequence type ST388 and harbouring the EAST1 toxin astA gene. Metagenomic analyses of the colon and rectum digesta revealed the presence of the tetQ, tetW, tetO, and mefA antibiotic resistance genes that were also detected in the gut microbiome of four other wild boars from the mountains. Furthermore, the tetQ and cfxA genes were identified in the faecal microbiome of a hunted wild boar from Japan.ConclusionThe gastrointestinal microbiota of the free-living wild boars examined in this study carried acquired antibiotic resistance determinants that are highly prevalent among domestic livestock populations.

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Impact of Feed Supplementation with Antimicrobial Agents on Growth Performance of Broiler Chickens, Clostridium perfringens and Enterococcus Counts, and Antibiotic Resistance Phenotypes and Distribution of Antimicrobial Resistance Determinants in Escherichia coli Isolates

Applied and Environmental Microbiology ◽

10.1128/aem.01086-07 ◽

2007 ◽

Vol 73 (20) ◽

pp. 6566-6576 ◽

Cited By ~ 103

Author(s):

Moussa S. Diarra ◽

Fred G. Silversides ◽

Fatoumata Diarrassouba ◽

Jane Pritchard ◽

Luke Masson ◽

...

Keyword(s):

Escherichia Coli ◽

Antibiotic Resistance ◽

Antimicrobial Resistance ◽

Broiler Chickens ◽

Antimicrobial Agents ◽

Growth Promoters ◽

Feed Supplementation ◽

E Coli ◽

Resistance Determinants ◽

Class 1

ABSTRACT The effects of feed supplementation with the approved antimicrobial agents bambermycin, penicillin, salinomycin, and bacitracin or a combination of salinomycin plus bacitracin were evaluated for the incidence and distribution of antibiotic resistance in 197 commensal Escherichia coli isolates from broiler chickens over 35 days. All isolates showed some degree of multiple antibiotic resistance. Resistance to tetracycline (68.5%), amoxicillin (61.4%), ceftiofur (51.3%), spectinomycin (47.2%), and sulfonamides (42%) was most frequent. The levels of resistance to streptomycin, chloramphenicol, and gentamicin were 33.5, 35.5, and 25.3%, respectively. The overall resistance levels decreased from day 7 to day 35 (P < 0.001). Comparing treatments, the levels of resistance to ceftiofur, spectinomycin, and gentamicin (except for resistance to bacitracin treatment) were significantly higher in isolates from chickens receiving feed supplemented with salinomycin than from the other feeds (P < 0.001). Using a DNA microarray analysis capable of detecting commonly found antimicrobial resistance genes, we characterized 104 tetracycline-resistant E. coli isolates from 7- to 28-day-old chickens fed different growth promoters. Results showed a decrease in the incidence of isolates harboring tet(B), bla TEM, sulI, and aadA and class 1 integron from days 7 to 35 (P < 0.01). Of the 84 tetracycline-ceftiofur-resistant E. coli isolates, 76 (90.5%) were positive for bla CMY-2. The proportions of isolates positive for sulI, aadA, and integron class 1 were significantly higher in salinomycin-treated chickens than in the control or other treatment groups (P < 0.05). These data demonstrate that multiantibiotic-resistant E. coli isolates can be found in broiler chickens regardless of the antimicrobial growth promoters used. However, the phenotype and the distribution of resistance determinants in E. coli can be modulated by feed supplementation with some of the antimicrobial agents used in broiler chicken production.

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Antibiotic survey ofLactococcus lactisstrains to six antibiotics by Etest, and establishment of new susceptibility-resistance cut-off values

Journal of Dairy Research ◽

10.1017/s0022029907002543 ◽

2007 ◽

Vol 74 (3) ◽

pp. 262-268 ◽

Cited By ~ 21

Author(s):

Ana Belén Flórez ◽

Morten Danielsen ◽

Jenni Korhonen ◽

Joanna Zycka ◽

Atte von Wright ◽

...

Keyword(s):

Antibiotic Resistance ◽

Inhibitory Concentration ◽

Tetracycline Resistance ◽

Large Collection ◽

Bacterial Strains ◽

Resistance Determinants ◽

Resistant Strains ◽

Geographical Locations ◽

S Genes ◽

Acquired Antibiotic Resistance

In order to establish cut-off values forLactococcus lactisto six antibiotics to distinguish susceptible and intrinsically resistant strains from those having acquired resistances, the minimum inhibitory concentration (MIC) of tetracycline, erythromycin, clindamycin, streptomycin, chloramphenicol and vancomycin was determined in 93 differentLc. lactisstrains using the Etest. These bacterial strains were originally isolated from dairy and animal sources in widely separated geographical locations. Cut-offs were defined on the basis of the distribution of the MICs frequency of the studied antibiotics, which in the absence of acquired determinants should approach to a normal statistical distribution. In general, the new cut-off values proposed in this study are higher than previously defined (European Commission, 2005. The EFSA Journal 223, 1–12). Based on these new values, all the strains tested were susceptible to erythromycin, chloramphenicol and vancomycin, and 79 susceptible to all six antibiotics. However, 11 strains (around 12%) were considered resistant to tetracycline (six of which had been identified after screening of a large collection of lactococci strains for tetracycline resistance) and five (5·4%) resistant to streptomycin. Of these, two fish isolates proved to be resistance to both tetracycline and streptomycin. From the tetracycline resistant strains,tet(M) and mosaictet(L/S) genes were amplified by PCR, demonstrating they harboured acquired antibiotic resistance determinants.

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Antibiotic resistance determinants in the interplay between food and gut microbiota

Genes & Nutrition ◽

10.1007/s12263-011-0226-x ◽

2011 ◽

Vol 6 (3) ◽

pp. 275-284 ◽

Cited By ~ 51

Author(s):

Chiara Devirgiliis ◽

Simona Barile ◽

Giuditta Perozzi

Keyword(s):

Antibiotic Resistance ◽

Gut Microbiota ◽

Resistance Determinants

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Commensal Escherichia coli of healthy humans: a reservoir for antibiotic-resistance determinants

Journal of Medical Microbiology ◽

10.1099/jmm.0.022475-0 ◽

2010 ◽

Vol 59 (11) ◽

pp. 1331-1339 ◽

Cited By ~ 112

Author(s):

Jannine K. Bailey ◽

Jeremy L. Pinyon ◽

Sashindran Anantham ◽

Ruth M. Hall

Keyword(s):

Escherichia Coli ◽

Antibiotic Resistance ◽

Resistance Genes ◽

Resistant Strain ◽

Healthy Adults ◽

Susceptible Strain ◽

E Coli ◽

Resistance Determinants ◽

Healthy Humans ◽

Depth Analysis

This study examined in detail the population structure of Escherichia coli from healthy adults with respect to the prevalence of antibiotic resistance and specific resistance determinants. E. coli isolated from the faeces of 20 healthy adults not recently exposed to antibiotics was tested for resistance to ten antibiotics and for carriage of integrons and resistance determinants using PCR. Strain diversity was assessed using biochemical and molecular criteria. E. coli was present in 19 subjects at levels ranging from 2.0×104 to 1.7×108 c.f.u. (g faeces)−1. Strains resistant to one to six antibiotics were found at high levels (>30 %) in only ten individuals, but at significant levels (>0.5 %) in 14. Resistant isolates with the same phenotype from the same individual were indistinguishable, but more than one susceptible strain was sometimes found. Overall, individuals harboured one to four E. coli strains, although in 17 samples one strain was dominant (>70 % of isolates). Eighteen strains resistant to ampicillin, sulfamethoxazole, tetracycline and trimethoprim in 15 different combinations were observed. One resistant strain was carried by two unrelated individuals and a susceptible strain was shared by two cohabiting subjects. Two minority strains were derivatives of a more abundant resistant strain in the same sample, showing that continuous evolution is occurring in vivo. The trimethoprim-resistance genes dfrA1, dfrA5, dfrA7, dfrA12 or dfrA17 were in cassettes in a class 1 or class 2 integron. Ampicillin resistance was conferred by the bla TEM gene, sulfamethoxazole resistance by sul1, sul2 or sul3 and tetracycline resistance by tetA(A) or tetA(B). Chloramphenicol resistance (cmlA1 gene) was detected only once. Phylogenetic groups A and B2 were more common than B1 and D. Commensal E. coli of healthy humans represent an important reservoir for numerous antibiotic-resistance genes in many combinations. However, measuring the true extent of resistance carriage in commensal E. coli requires in-depth analysis.

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Were Polish wild boars exposed to Schmallenberg virus?

Journal of Veterinary Research ◽

10.1515/jvetres-2017-0019 ◽

2017 ◽

Vol 61 (2) ◽

pp. 151-155 ◽

Cited By ~ 1

Author(s):

Julia Kęsik-Maliszewska ◽

Artur Jabłoński ◽

Magdalena Larska

Keyword(s):

Positive Result ◽

Wild Boar ◽

Clinical Disease ◽

Schmallenberg Virus ◽

Rt Pcr ◽

Free Living ◽

Hunting Season ◽

Wild Boars ◽

Two Samples ◽

High Incidence

AbstractIntroduction: A novel to Europe Schmallenberg virus (SBV) causes clinical disease manifested by reproduction disorders in farm ruminants. In free-living ruminants, SBV antibodies as well as the virus were detected. Recent studies also revealed SBV antibodies in wild boars. The study investigates SBV antibodies occurring in wild boars in Poland at the peak of recent virus epidemics in the country.Material and Methods: Samples collected from 203 wild boars culled during the 2012/2013 and 2013/2014 hunting season were serologically tested using multi-species cELISA. Attempted neutralisation tests failed due to poor serum quality. RT-PCR was implemented in seropositive and doubtful animals.Results: Two samples collected from wild boar in the winter of 2013 gave a positive result in ELISA, while another two from the 2012/2013 hunting season were doubtful. No SBV RNA was detected in spleen and liver tissues.Conclusion: Low SBV seroprevalence in wild boars, despite high incidence of SBV infections occurring simultaneously in wild ruminants, suggests that boars are unlikely to be a significant reservoir of the virus in the sylvatic environment in Poland.

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A Preliminary Study on Antimicrobial Susceptibility of Staphylococcus spp. and Enterococcus spp. Grown on Mannitol Salt Agar in European Wild Boar (Sus scrofa) Hunted in Campania Region—Italy

Animals ◽

10.3390/ani12010085 ◽

2021 ◽

Vol 12 (1) ◽

pp. 85

Author(s):

Francesca Paola Nocera ◽

Gianmarco Ferrara ◽

Emanuela Scandura ◽

Monica Ambrosio ◽

Filomena Fiorito ◽

...

Keyword(s):

Antibiotic Resistance ◽

Wild Boar ◽

Diffusion Method ◽

Resistant Bacteria ◽

Mannitol Salt Agar ◽

Campania Region ◽

Wild Boars ◽

Nasal Cavities ◽

Enterococcus Spp ◽

Staphylococcus Spp

The importance of wild boar lies in its role as a bioindicator for the control of numerous zoonotic and non-zoonotic diseases, including antibiotic resistance. Mannitol Salt Agar (MSA) is a selective medium used for isolation, enumeration, and differentiation of pathogenic staphylococci. Other genera such as Enterococcus spp. are also salt tolerant and able to grow on MSA. The present study focused on the identification, by matrix assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF-MS), of bacteria grown on MSA isolated from the nasal cavities of 50 healthy wild boars hunted in Campania Region (southern Italy) in the year 2019. In addition, the antimicrobial resistance phenotype of the isolated strains was determined by disk diffusion method. Among genus Staphylococcus, coagulase-negative Staphylococcus (CoNS) were the most common isolated species, with Staphylococcus xylosus as the most prevalent species (33.3%). Furthermore, Enterococcus spp. strains were isolated, and Enterococcus faecalis was the species showing the highest frequency of isolation (93.8%). For staphylococci, high levels of resistance to oxacillin (93.3%) were recorded. Differently, they exhibited low frequencies of resistance to tested non-β-lactams antibiotics. Among enterococci, the highest resistances were observed for penicillin (93.7%), followed by ampicillin (75%), and ciprofloxacin (68.7%). Interestingly, 43.7% of the isolated strains were vancomycin-resistant. In conclusion, this study reports the phenotypic antibiotic resistance profiles of Staphylococcus spp. and Enterococcus spp. strains isolated from nasal cavities of wild boars hunted in Campania Region, highlighting that these wild animals are carriers of antibiotic resistant bacteria.

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Pets becoming established in the wild: free–living Vietnamese potbellied pigs in Spain

Animal Biodiversity and Conservation ◽

10.32800/abc.2013.36.0209 ◽

2013 ◽

Vol 36 (2) ◽

pp. 209-215

Author(s):

M. Delibes–Mateos ◽

◽

A. Delibes ◽

Keyword(s):

Wild Boar ◽

Sus Scrofa ◽

Species Abundance ◽

Crop Damage ◽

Wild Boar Population ◽

Natural Habitats ◽

Free Living ◽

In The Wild ◽

Google Search ◽

Adequate Management

Vietnamese potbellied (VPB) pigs (Sus scrofa) are a common pet in North America and Europe, but their recent decrease in popularity has increased their abandonment. Our main aim was to identify potential cases of free–living VPB pigs in Spain through an in–depth Google search. We identified 42 cases of free–living VPB pigs distributed throughout the country. The number of free–living VPB pigs reported increased by year but the species abundance still seems to be low. Signs of VPB pig reproduction and possible hybrids between VPB pigs and wild boar or feral pigs have been also reported. Free–living VPB pigs could erode the gene pool of the Spanish wild boar population and exacerbate the damage (e.g. crop damage or spread of diseases) already caused by wild board. Urgent evaluation and adequate management of wild VPB pig sightings is needed to prevent their establishment in natural habitats.

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Comparative genome analysis of Erysipelothrix rhusiopathiae isolated from domestic pigs and wild boars suggests host adaptation and selective pressure from the use of antibiotics

Microbial Genomics ◽

10.1099/mgen.0.000412 ◽

2020 ◽

Vol 6 (8) ◽

Author(s):

Robert Söderlund ◽

Nicoletta Formenti ◽

Stefania Caló ◽

Mario Chiari ◽

Mate Zoric ◽

...

Keyword(s):

Wild Boar ◽

Host Adaptation ◽

Extracellular Proteins ◽

Gene Variants ◽

Erysipelothrix Rhusiopathiae ◽

Content Type ◽

Wild Boars ◽

Domestic Pigs ◽

Resistance Determinants ◽

Capsule Production

The disease erysipelas caused by Erysipelothrix rhusiopathiae (ER) is a major concern in pig production. In the present study the genomes of ER from pigs (n=87), wild boars (n=71) and other sources (n=85) were compared in terms of whole-genome SNP variation, accessory genome content and the presence of genetic antibiotic resistance determinants. The aim was to investigate if genetic features among ER were associated with isolate origin in order to better estimate the risk of transmission of porcine-adapted strains from wild boars to free-range pigs and to increase our understanding of the evolution of ER. Pigs and wild boars carried isolates representing all ER clades, but clade one only occurred in healthy wild boars and healthy pigs. Several accessory genes or gene variants were found to be significantly associated with the pig and wild boar hosts, with genes predicted to encode cell wall-associated or extracellular proteins overrepresented. Gene variants associated with serovar determination and capsule production in serovars known to be pathogenic for pigs were found to be significantly associated with pigs as hosts. In total, 30 % of investigated pig isolates but only 6 % of wild boar isolates carried resistance genes, most commonly tetM (tetracycline) and lsa(E) together with lnu(B) (lincosamides, pleuromutilin and streptogramin A). The incidence of variably present genes including resistance determinants was weakly linked to phylogeny, indicating that host adaptation in ER has evolved multiple times in diverse lineages mediated by recombination and the acquisition of mobile genetic elements. The presented results support the occurrence of host-adapted ER strains, but they do not indicate frequent transmission between wild boars and domestic pigs. This article contains data hosted by Microreact.

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Whole-genome analysis of antimicrobial-resistant Escherichia coli in human gut microbiota reveals its origin and flexibility in transmitting mcr-1

10.1101/2021.02.19.431933 ◽

2021 ◽

Author(s):

Yichen Ding ◽

Woei-Yuh Saw ◽

Linda Wei Lin Tan ◽

Don Kyin Nwe Moong ◽

Niranjan Nagarajan ◽

...

Keyword(s):

Antibiotic Resistance ◽

Gut Microbiota ◽

Resistance Gene ◽

Meat Products ◽

Colistin Resistance ◽

Human Gut ◽

Antibiotic Resistant ◽

Raw Meat ◽

E Coli ◽

Human Gut Microbiota

AbstractMultidrug resistant (MDR) Escherichia coli strains that carry extended-spectrum β-lactamases (ESBLs) or colistin resistance gene mcr-1 have been identified in the human gut at an increasing incidence worldwide. In this study, we sampled and characterized MDR Enterobacteriaceae from the gut microbiota of healthy Singaporeans and show that the prevalence of ESBL-producing and mcr-positive Enterobacteriaceae is 26.6% and 7.3%, respectively. Whole-genome sequencing of 37 E. coli isolates identified 25 sequence types and assigned them into six different phylogroups, suggesting that the human intestinal MDR E. coli strains are highly diverse. In addition, we found that E. coli isolates belonging to phylogroup D, B2 and F carry a higher number of virulence genes, whereas isolates of phylogroup A, B1 and E carry fewer virulence factor genes but are frequent carriers of florfenicol resistance gene floR and colistin resistance gene mcr-1. Comparison of the seven mcr-1-positive E. coli isolates revealed that mcr-1 is carried by conjugative plasmids or embedded in composite transposons, which could potentially mobilize mcr-1 to other pathogenic Enterobacteriaceae strains or MDR plasmids. Finally, we found that 12 out of the 37 MDR E. coli isolates in this study show high similarity to ESBL-producing E. coli isolates from raw meats from local markets, suggesting a potential transmission of MDR E. coli from meat products to the human gut microbiota. Our findings show diverse antibiotic resistance and virulence profiles of intestinal E. coli and call for better countermeasures to block the transmission of MDR E. coli via the food chain.ImportanceThe human gut can harbor both antibiotic resistant and virulent E. coli which may subsequently cause infections. In this study, the antibiotic resistance and virulence traits of antibiotic-resistant E. coli isolates from human gut microbiota of healthy subjects were investigated. The isolated E. coli strains carry a diverse range of antibiotic resistance mechanisms and virulence factor genes, are highly diverse to each other, and are likely to originate from raw meat products from the local markets. Of particular concern are seven E. coli isolates which carry colistin resistance gene mcr-1. This gene can be mobilized into other pathogens and MDR plasmids, thereby spreading resistance to the last-resort antibiotic colistin. Our findings also suggest that raw meat could serve as important source to transmit MDR bacteria into the human gut microbiota.

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Urine Microbial Landscape in Children with Urinary Tract Infections in Ryazan and Ryazan Region

Doctor Ru ◽

10.31550/1727-2378-2021-20-10-48-53 ◽

2021 ◽

Vol 20 (10) ◽

pp. 48-53

Author(s):

N.A. Belykh ◽

◽

S.V. Tereschenko ◽

N.A. Anikeeva ◽

S.S. Kantutis ◽

...

Keyword(s):

Escherichia Coli ◽

Antibiotic Resistance ◽

Urinary Tract ◽

Klebsiella Pneumoniae ◽

Urinary Tract Infections ◽

Patient Specific ◽

E Coli ◽

Resistance Determinants ◽

Study Results ◽

Tract Infections

Study Objective: To study a spectrum of uropathogens and their sensitivity to antimicrobials in urinary tract infections (UTIs) in children in Ryazan and Ryazan Region. Study Design: retrospective study. Materials and Methods. We conducted a retrospective local laboratory monitoring of urinary microflora and analysed its sensitivity to antimicrobials in 111 patients aged 2 months to 17 years old who were undergoing traditional UI therapy in 2020. The study group comprised 75 (67.6%) girls and 36 (32.4%) boys. Pathogen isolation and type identification were performed using urine specimens collected in sterile disposable plastic containers prior to antimicrobial therapy. Material was delivered for analysis within 2 hours from collection. For testing of pathogen sensitivity to antimicrobials, we used the phenotyping diffusion test and an analytical test for carbapenems inactivation. Study Results. Prevailing causative agents of UIs were Escherichia coli (50.4%) and Klebsiella pneumoniae (14.4%). Resistance determinants were found in 9.0% and 2.7% of Е. соli and K. pneumoniae urological strains, respectively. The main mechanism of resistivity was production of wide spectrum plasmid β-lactamases. The highest activity in E. coli was demonstrated by generation III–IV cephalosporins, aminoglycosides, fosfomicin (100%), nitrofurantoin (91.3%), and aminopenicillins (76.1–86.9%). For K. pneumoniae, generation III–IV cephalosporins and aminoglycosides were most potent (100%). All resistant pathogens were sensitive to cefoperazone sulbactam, meropenem, imipenem, aminoglycosides (100%); tigecycline, nitrofurantoin, and fosfomicin were most potent against E. coli. Conclusion. Children with UIs in Ryazan Region had mostly gram-negative bacteria in their urine (85.6%), Enterobacteralеs (81.1%) being a prevailing type. Antimicrobials resistance determinants were quite rare (17.8%) in these urine isolates; all of them were class A ЕSBL producers. These characteristic features of antibiotic resistance of uropathogenic enterobacteria strains allow using β-lactam antibiotics in empiric initial treatment and emphasising the need in patient-specific selection of antimicrobials. Keywords: antibacterial therapy, antibiotic resistance, children, urinary tract infections, Escherichia coli, Klebsiella pneumoniae.

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