Comparing gut resistome composition among patients with acute Campylobacter infections and healthy family members

AbstractCampylobacter commonly causes foodborne infections and antibiotic resistance is an imminent concern. It is not clear, however, if the human gut ‘resistome’ is affected by Campylobacter during infection. Application of shotgun metagenomics on stools from 26 cases with Campylobacter infections and 44 healthy family members (controls) identified 406 unique antibiotic resistance genes (ARGs) representing 153 genes/operons, 40 mechanisms, and 18 classes. Cases had greater ARG richness (p < 0.0001) and Shannon diversity (p < 0.0001) than controls with distinct compositions (p = 0.000999; PERMANOVA). Cases were defined by multidrug resistance genes and were dominated by Proteobacteria (40.8%), specifically those representing Escherichia (20.9%). Tetracycline resistance genes were most abundant in controls, which were dominated by Bacteroidetes (45.3%) and Firmicutes (44.4%). Hierarchical clustering of cases identified three clusters with distinct resistomes. Case clusters 1 and 3 differed from controls containing more urban and hospitalized patients. Relative to family members of the same household, ARG composition among matched cases was mostly distinct, though some familial controls had similar profiles that could be explained by a shorter time since exposure to the case. Together, these data indicate that Campylobacter infection is associated with an altered resistome composition and increased ARG diversity, raising concerns about the role of infection in the spread of resistance determinants.

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Tn1403, a Multiple-Antibiotic Resistance Transposon Made Up of Three Distinct Transposons

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01279-06 ◽

2007 ◽

Vol 51 (5) ◽

pp. 1827-1829 ◽

Cited By ~ 31

Author(s):

H. W. Stokes ◽

Liam D. H. Elbourne ◽

Ruth M. Hall

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Antibiotic Resistance Genes ◽

Tetracycline Resistance ◽

Resistance Determinant ◽

Multiple Antibiotic Resistance

ABSTRACT Transposon Tn1403 from a clinical Pseudomonas strain is composed of three transposons, including Tn5393c. A related transposon Tn1404* from a plant-associated Pseudomonas strain lacks Tn5393 but includes a transposon carrying the tet(C) tetracycline resistance determinant. These compound transposons illustrate the role of preexisting transposons in generating clusters of antibiotic resistance genes.

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Antibiotic resistomes discovered in the gut microbiomes of Korean swine and cattle

GigaScience ◽

10.1093/gigascience/giaa043 ◽

2020 ◽

Vol 9 (5) ◽

Cited By ~ 3

Author(s):

Suk-Kyung Lim ◽

Dongjun Kim ◽

Dong-Chan Moon ◽

Youna Cho ◽

Mina Rho

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Antibiotic Resistance Genes ◽

Tetracycline Resistance ◽

Gene Families ◽

Resistance Determinant ◽

Farm Animals ◽

Tetracycline Resistance Genes ◽

Term Evolution

Abstract Background Antibiotics administered to farm animals have led to increasing prevalence of resistance genes in different microbiomes and environments. While antibiotic treatments help cure infectious diseases in farm animals, the possibility of spreading antibiotic resistance genes into the environment and human microbiomes raises significant concerns. Through long-term evolution, antibiotic resistance genes have mutated, thereby complicating the resistance problems. Results In this study, we performed deep sequencing of the gut microbiomes of 36 swine and 41 cattle in Korean farms, and metagenomic analysis to understand the diversity and prevalence of antibiotic resistance genes. We found that aminoglycoside, β-lactam, lincosamide, streptogramin, and tetracycline were the prevalent resistance determinants in both swine and cattle. Tetracycline resistance was abundant and prevalent in cattle and swine. Specifically, tetQ, tetW, tetO, tet32, and tet44 were the 5 most abundant and prevalent tetracycline resistance genes. Their prevalence was almost 100% in swine and cattle. While tetQ was similarly abundant in both swine and cattle, tetW was more abundant in swine than in cattle. Aminoglycoside was the second highest abundant resistance determinant in swine, but not in cattle. In particular, ANT(6) and APH(3′′) were the dominant resistance gene families in swine. β-lactam was also an abundant resistance determinant in both swine and cattle. Cfx was the major contributing gene family conferring resistance against β-lactams. Conclusions Antibiotic resistome was more pervasive in swine than in cattle. Specifically, prevalent antibiotic resistance genes (prevalence >50%) were found more in swine than in cattle. Genomic investigation of specific resistance genes from the gut microbiomes of swine and cattle in this study should provide opportunities to better understand the exchange of antibiotic resistance genes in farm animals.

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Macleaya cordata extracts suppressed the increase of a part of antibiotic resistance genes in fecal microorganism of weaned pigs

Canadian Journal of Animal Science ◽

10.1139/cjas-2017-0200 ◽

2018 ◽

Vol 98 (4) ◽

pp. 884-887

Author(s):

Y. Li ◽

H. Li ◽

Q. Chu ◽

F. Xu ◽

T. Liang ◽

...

Keyword(s):

Antibiotic Resistance ◽

Herbal Medicine ◽

Chinese Herbal Medicine ◽

Resistance Genes ◽

Antibiotic Resistance Genes ◽

Tetracycline Resistance ◽

Weaned Pigs ◽

Tetracycline Resistance Genes ◽

Chinese Herbal ◽

Macleaya Cordata

This study was designed to evaluate the effects of Macleaya cordata extracts (Chinese herbal medicine extracts) and antibiotics combination with chlortetracycline (CTC) on the antibiotic resistance genes in fecal microorganism. Compared with the group without antibiotics, the relative abundances of all six tetracycline resistance genes were increased after 75 mg kg−1 CTC supplementation. Interestingly, M. cordata extracts in feed suppressed the increase of a part of tetracycline resistance genes in fecal microorganism of weaned pigs.

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Diversity of the Tetracycline Mobilome within a Chinese Pig Manure Sample

Applied and Environmental Microbiology ◽

10.1128/aem.01754-16 ◽

2016 ◽

Vol 82 (21) ◽

pp. 6454-6462 ◽

Cited By ~ 6

Author(s):

Sébastien Olivier Leclercq ◽

Chao Wang ◽

Yaxin Zhu ◽

Hai Wu ◽

Xiaochen Du ◽

...

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Efflux Pump ◽

Genetic Resistance ◽

Antibiotic Resistance Genes ◽

Tetracycline Resistance ◽

Animal Manure ◽

Pig Manure ◽

Tetracycline Antibiotics ◽

Tetracycline Resistance Genes

ABSTRACTTetracycline antibiotics are widely used in livestock, and tetracycline resistance genes (TRG) are frequently reported in the manure of farmed animals. However, the diversity of TRG-carrying transposons in manure has still been rarely investigated. Using a culture-free functional metagenomic procedure, combined with large-insert library construction and sequencing, bioinformatic analyses, and functional experiments, we identified 17 distinct TRGs in a single pig manure sample, including two newtetgenes:tet(59), encoding a tetracycline efflux pump, andtet(W/N/W), encoding mosaic ribosomal protection. Our study also revealed six new TRG-carrying putative nonconjugative transposons: Tn5706-like transposon Tn6298, IS200/605-related transposon Tn6303, Tn3family transposon Tn6299, and three ISCR2-related transposons, Tn62300, Tn62301, and Tn62302.IMPORTANCEFertilization of agricultural fields with animal manure is believed to play a major role in antibiotic resistance dissemination in the environment. There is growing concern for the possible spread of antibiotic resistance from the environment to humans since genetic resistance determinants may be located in transposons and other mobile genetic elements potentially transferable to pathogens. Among the various antibiotic resistance genes found in manure, tetracycline resistance genes (TRGs) are some of the most common. The present study provides a detailed snapshot of the tetracycline mobilome in a single pig manure sample, revealing an unappreciated diversity of TRGs and potential TRG mobility vectors. Our precise identification of the TRG-carrying units will enable us to investigate in more details their mobility effectiveness.

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The distribution of antibiotic resistance genes in chicken gut microbiota commensals

Scientific Reports ◽

10.1038/s41598-021-82640-3 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Helena Juricova ◽

Jitka Matiasovicova ◽

Tereza Kubasova ◽

Darina Cejkova ◽

Ivan Rychlik

Keyword(s):

Antibiotic Resistance ◽

Gut Microbiota ◽

Resistance Genes ◽

Intestinal Tract ◽

Antibiotic Resistance Genes ◽

Tetracycline Resistance ◽

Tetracycline Resistance Genes ◽

Gene Coding ◽

Chicken Gut Microbiota ◽

Acquired Antibiotic Resistance

AbstractAntibiotic resistance in bacterial pathogens or several indicator bacteria is commonly studied but the extent of antibiotic resistance in bacterial commensals colonising the intestinal tract is essentially unknown. In this study, we aimed to investigate the presence of horizontally acquired antibiotic resistance genes among chicken gut microbiota members in 259 isolates with known whole genomic sequences. Altogether 124 isolates contained at least one gene coding for antibiotic resistance. Genes coding for the resistance to tetracyclines (detected in 101 isolates), macrolide-lincosamide-streptogramin B antibiotics (28 isolates) and aminoglycosides (25 isolates) were the most common. The most frequent tetracycline resistance genes were tet(W), tet(32), tet(O) and tet(Q). Lachnospiraceae and Ruminococcaceae frequently encoded tet(W). Lachnospiraceae commonly coded also for tet(32) and tet(O). The tet(44) gene was associated with Erysipelotrichaceae and tet(Q) was detected in the genomes of Bacteroidaceae and Porphyromonadaceae. Without any bias we have shown that antibiotic resistance is quite common in gut commensals. However, a comparison of codon usage showed that the above-mentioned families represent the most common current reservoirs but probably not the original host of the detected resistances.

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Identification and antibiotic resistance profiling of bacterial isolates from septicaemic soft-shelled turtles (Pelodiscus sinensis)

Veterinární Medicína ◽

10.17221/65/2016-vetmed ◽

2017 ◽

Vol 62 (No. 3) ◽

pp. 169-177 ◽

Cited By ~ 13

Author(s):

TH Chung ◽

SW Yi ◽

BS Kim ◽

WI Kim ◽

GW Shin

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Present Report ◽

Antibiotic Resistance Genes ◽

Tetracycline Resistance ◽

Edwardsiella Tarda ◽

Pelodiscus Sinensis ◽

Class 1 Integron ◽

Class 1 ◽

M 14

The present study sought to identify pathogens associated with septicaemia in the Chinese soft-shelled turtle (Pelodiscus sinensis) and to characterise antibiotic resistance in these pathogens. Twenty-three isolates recovered from the livers of diseased soft-shelled turtles were genetically identified as Aeromonas hydrophila (n = 8), A. veronii (n = 3), Citrobacter freundii (n = 4), Morganella morganii (n = 3), Edwardsiella tarda (n = 2), Wohlfahrtiimonas chitiniclastica (n = 1), Chryseobacterium sp. (n = 1), and Comamonas sp. (n = 1). Most isolates (n = 21) were resistant to ampicillin whereas a low percentage of isolates was susceptible to aminoglycosides (amikacin, gentamicin, and tobramycin). PCR assays and sequence analysis revealed the presence of the qnrS2 and blaTEM antibiotic resistance genes in all isolates. The blaDHA-1, blaCTX-M-14 and blaCMY-2 genes were harboured by 17.4% (n = 4), 13.5% (n = 3) and 8.7% (n = 2) of the strains, respectively. One or more tetracycline resistance genes were detected in 60.9% (n = 14) of the isolates. Four isolates (17.4%) harboured single or multiple class 1 integron cassettes. Collectively, a variety of bacterial pathogens were involved in the occurrence of septicaemia in Chinese soft-shelled turtles and most of the isolates had multi-antibiotic resistant phenotypes. To our knowledge, the present report is the first to identify W. chitiniclastica and Comamonas sp. as causes of septicaemia in soft-shelled turtles and the first to identify Aeromonas spp. with blaCTX-M-14 and blaDHA-1 resistance genes.

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IS26 Family Members IS257 and IS1216 Also Form Cointegrates by Copy-In and Targeted Conservative Routes

mSphere ◽

10.1128/msphere.00811-19 ◽

2020 ◽

Vol 5 (1) ◽

Cited By ~ 5

Author(s):

Christopher J. Harmer ◽

Ruth M. Hall

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Target Selection ◽

Family Members ◽

Low Frequency ◽

Antibiotic Resistance Genes ◽

Temperature Sensitive ◽

Restrictive Temperature ◽

Content Type ◽

Gram Positive Bacteria

ABSTRACT IS26 has been shown to form cointegrates both by a copy-in mechanism involving one insertion sequence (IS) and a target and by a targeted conservative mechanism involving two ISs. IS26 is the flagship of a group of 65 bacterial ISs in the recently redefined IS6/IS26 family. Here, whether other family members can also use two mechanisms was examined using members of the IS257/IS431 and IS1216 isoform groups, which are associated with antibiotic resistance genes in staphylococci and enterococci, respectively. Transposases Tnp257 and Tnp1216 have 39% and 47% amino acid identities, respectively, with Tnp26 and are 62% identical to one another. Using a novel transposition assay, pUC-based plasmids carrying these ISs integrated into the chromosome of a temperature-sensitive polA Escherichia coli strain grown at the restrictive temperature. In the cointegrates, the plasmid carrying IS257 was flanked by various 8-bp target site duplications, consistent with random target selection. However, in a mating-out assay, only the targeted conservative reaction was detectable at a low frequency in a recA-negative E. coli strain, indicating that IS257 is at least 100-fold less active than IS26. For IS1216, in mating-out assays, both copy-in and targeted conservative cointegrate formation were detectable at frequencies similar to those observed for IS26. Duplication of various 8-bp target sites was detected for the copy-in route. For both IS257 and IS1216, when both of the plasmids carried an IS, the targeted conservative route occurred at a significantly higher frequency than the copy-in route, and only cointegrates formed by the conservative route were detected. IMPORTANCE IS26 differs from other studied ISs in the reactions that it can undertake. The differences make IS26 uniquely suited to its key role in the recruitment and spread of antibiotic resistance genes in Gram-negative bacteria. However, whether other ISs in the IS6/IS26 family can perform the same reactions is not known. IS257/IS431 and IS1216 isoforms found associated with antibiotic resistance genes in the Gram-positive bacteria staphylococci, enterococci, streptococci, and clostridia are related to IS26. However, the way that they move had not been investigated, limiting interpretation of their role in resistance gene dissemination and in the formation of cointegrates and complex resistance regions in staphylococci and enterococci. Here, they are shown to share the broad catalytic capabilities of IS26, demonstrating that it is likely that all members of the redefined IS6/IS26 family of bacterial ISs likewise are able to use both the copy-in and conservative routes.

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Characterization of antibiotic resistance genes in the species of the rumen microbiota

Nature Communications ◽

10.1038/s41467-019-13118-0 ◽

2019 ◽

Vol 10 (1) ◽

Cited By ~ 9

Author(s):

Yasmin Neves Vieira Sabino ◽

Mateus Ferreira Santana ◽

Linda Boniface Oyama ◽

Fernanda Godoy Santos ◽

Ana Júlia Silva Moreira ◽

...

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Animal Health ◽

Antibiotic Resistance Genes ◽

Tetracycline Resistance ◽

Multidrug Resistant ◽

Resistant Bacteria ◽

Ruminal Bacteria ◽

Genes Encoding

AbstractInfections caused by multidrug resistant bacteria represent a therapeutic challenge both in clinical settings and in livestock production, but the prevalence of antibiotic resistance genes among the species of bacteria that colonize the gastrointestinal tract of ruminants is not well characterized. Here, we investigate the resistome of 435 ruminal microbial genomes in silico and confirm representative phenotypes in vitro. We find a high abundance of genes encoding tetracycline resistance and evidence that the tet(W) gene is under positive selective pressure. Our findings reveal that tet(W) is located in a novel integrative and conjugative element in several ruminal bacterial genomes. Analyses of rumen microbial metatranscriptomes confirm the expression of the most abundant antibiotic resistance genes. Our data provide insight into antibiotic resistange gene profiles of the main species of ruminal bacteria and reveal the potential role of mobile genetic elements in shaping the resistome of the rumen microbiome, with implications for human and animal health.

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Intra- and Interspecies Conjugal Transfer of Tn916-Like Elements from Lactococcus lactis In Vitro and In Vivo

Applied and Environmental Microbiology ◽

10.1128/aem.00470-09 ◽

2009 ◽

Vol 75 (19) ◽

pp. 6352-6360 ◽

Cited By ~ 25

Author(s):

Joanna Boguslawska ◽

Joanna Zycka-Krzesinska ◽

Andrea Wilcks ◽

Jacek Bardowski

Keyword(s):

Antibiotic Resistance ◽

Lactococcus Lactis ◽

Resistance Genes ◽

Antibiotic Resistance Genes ◽

Tetracycline Resistance ◽

Raw Milk ◽

M Gene ◽

Transfer Resistance

ABSTRACT Tetracycline-resistant Lactococcus lactis strains originally isolated from Polish raw milk were analyzed for the ability to transfer their antibiotic resistance genes in vitro, using filter mating experiments, and in vivo, using germfree rats. Four of six analyzed L. lactis isolates were able to transfer tetracycline resistance determinants in vitro to L. lactis Bu2-60, at frequencies ranging from 10−5 to 10−7 transconjugants per recipient. Three of these four strains could also transfer resistance in vitro to Enterococcus faecalis JH2-2, whereas no transfer to Bacillus subtilis YBE01, Pseudomonas putida KT2442, Agrobacterium tumefaciens UBAPF2, or Escherichia coli JE2571 was observed. Rats were initially inoculated with the recipient E. faecalis strain JH2-2, and after a week, the L. lactis IBB477 and IBB487 donor strains were introduced. The first transconjugants were detected in fecal samples 3 days after introduction of the donors. A subtherapeutic concentration of tetracycline did not have any significant effect on the number of transconjugants, but transconjugants were observed earlier in animals dosed with this antibiotic. Molecular analysis of in vivo transconjugants containing the tet(M) gene showed that this gene was identical to tet(M) localized on the conjugative transposon Tn916. Primer-specific PCR confirmed that the Tn916 transposon was complete in all analyzed transconjugants and donors. This is the first study showing in vivo transfer of a Tn916-like antibiotic resistance transposon from L. lactis to E. faecalis. These data suggest that in certain cases food lactococci might be involved in the spread of antibiotic resistance genes to other lactic acid bacteria.

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Incidence, Distribution, and Spread of Tetracycline Resistance Determinants and Integron-Associated Antibiotic Resistance Genes among Motile Aeromonads from a Fish Farming Environment

Applied and Environmental Microbiology ◽

10.1128/aem.67.12.5675-5682.2001 ◽

2001 ◽

Vol 67 (12) ◽

pp. 5675-5682 ◽

Cited By ~ 178

Author(s):

Anja S. Schmidt ◽

Morten S. Bruun ◽

Inger Dalsgaard ◽

Jens L. Larsen

Keyword(s):

Antibiotic Resistance ◽

Resistance Gene ◽

Resistance Genes ◽

Antibiotic Resistance Genes ◽

Tetracycline Resistance ◽

Class 1 Integron ◽

Gene Cassettes ◽

Class 1 Integrons ◽

Resistance Determinants ◽

Class 1

ABSTRACT A collection of 313 motile aeromonads isolated at Danish rainbow trout farms was analyzed to identify some of the genes involved in high levels of antimicrobial resistance found in a previous field trial (A. S. Schmidt, M. S. Bruun, I. Dalsgaard, K. Pedersen, and J. L. Larsen, Appl. Environ. Microbiol. 66:4908–4915, 2000), the predominant resistance phenotype (37%) being a combined oxytetracycline (OTC) and sulphadiazine/trimethoprim resistance. Combined sulphonamide/trimethoprim resistance (135 isolates) appeared closely related to the presence of a class 1 integron (141 strains). Among the isolates containing integrons, four different combinations of integrated resistance gene cassettes occurred, in all cases including a dihydrofolate reductase gene and a downstream aminoglycoside resistance insert (87 isolates) and occasionally an additional chloramphenicol resistance gene cassette (31 isolates). In addition, 23 isolates had “empty” integrons without inserted gene cassettes. As far as OTC resistance was concerned, only 66 (30%) out of 216 resistant aeromonads could be assigned to resistance determinant class A (19 isolates), D (n = 6), or E (n = 39); three isolates contained two tetracycline resistance determinants (AD, AE, and DE). Forty OTC-resistant isolates containing large plasmids were selected as donors in a conjugation assay, 27 of which also contained a class 1 integron. Out of 17 successful R-plasmid transfers to Escherichia coli recipients, the respective integrons were cotransferred along with the tetracycline resistance determinants in 15 matings. Transconjugants were predominantly tetApositive (10 of 17) and contained class 1 integrons with two or more inserted antibiotic resistance genes. While there appeared to be a positive correlation between conjugative R-plasmids andtetA among the OTC-resistant aeromonads, tetEand the unclassified OTC resistance genes as well as class 1 integrons were equally distributed among isolates with and without plasmids. These findings indicate the implication of other mechanisms of gene transfer besides plasmid transfer in the dissemination of antibiotic resistance among environmental motile aeromonads.

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