Impacts of florfenicol on the microbiota landscape and resistome as revealed by metagenomic analysis

Abstract Background Drug-resistant fish pathogens can cause significant economic loss to fish farmers. Since 2012, florfenicol has become an approved drug for treating both septicemia and columnaris diseases in freshwater fish. Due to the limited drug options available for aquaculture, the impact of the therapeutical florfenicol treatment on the microbiota landscape as well as the resistome present in the aquaculture farm environment needs to be evaluated. Results Time-series metagenomic analyses were conducted to the aquatic microbiota present in the tank-based catfish production systems, in which catfish received standard therapeutic 10-day florfenicol treatment following the federal veterinary regulations. Results showed that the florfenicol treatment shifted the structure of the microbiota and reduced the biodiversity of it by acting as a strong stressor. Planctomycetes, Chloroflexi, and 13 other phyla were susceptible to the florfenicol treatment and their abundance was inhibited by the treatment. In contrast, the abundance of several bacteria belonging to the Proteobacteria, Bacteroidetes, Actinobacteria, and Verrucomicrobia phyla increased. These bacteria with increased abundance either harbor florfenicol-resistant genes (FRGs) or had beneficial mutations. The florfenicol treatment promoted the proliferation of florfenicol-resistant genes. The copy number of phenicol-specific resistance genes as well as multiple classes of antibiotic-resistant genes (ARGs) exhibited strong correlations across different genetic exchange communities (p < 0.05), indicating the horizontal transfer of florfenicol-resistant genes among these bacterial species or genera. Florfenicol treatment also induced mutation-driven resistance. Significant changes in single-nucleotide polymorphism (SNP) allele frequencies were observed in membrane transporters, genes involved in recombination, and in genes with primary functions of a resistance phenotype. Conclusions The therapeutical level of florfenicol treatment significantly altered the microbiome and resistome present in catfish tanks. Both intra-population and inter-population horizontal ARG transfer was observed, with the intra-population transfer being more common. The oxazolidinone/phenicol-resistant gene optrA was the most prevalent transferred ARG. In addition to horizontal gene transfer, bacteria could also acquire florfenicol resistance by regulating the innate efflux systems via mutations. The observations made by this study are of great importance for guiding the strategic use of florfenicol, thus preventing the formation, persistence, and spreading of florfenicol-resistant bacteria and resistance genes in aquaculture.

Download Full-text

The Prevalence and Characterization of Extended-Spectrum β-Lactamase- and Carbapenemase-Producing Bacteria from Hospital Sewage, Treated Effluents and Receiving Rivers

International Journal of Environmental Research and Public Health ◽

10.3390/ijerph17041183 ◽

2020 ◽

Vol 17 (4) ◽

pp. 1183 ◽

Cited By ~ 3

Author(s):

Luhua Zhang ◽

Xinyue Ma ◽

Li Luo ◽

Nan Hu ◽

Jiayao Duan ◽

...

Keyword(s):

Resistance Genes ◽

Wastewater Treatment Plants ◽

Bacterial Species ◽

Resistant Bacteria ◽

Antibiotic Resistant ◽

Carbapenem Resistant ◽

High Prevalence ◽

Treated Effluents ◽

Hospital Sewage

Hospital sewage plays a key role in the dissemination of antibiotic-resistant genes (ARGs) by serving as an environmental antimicrobial resistance reservoir. In this study, we aimed to characterize the cephalosporin- and carbapenem-resistant isolates from hospital sewage and receiving rivers. The results showed that ESBL (blaCTX-M) and carbapenemase genes (blaNDM and blaKPC) were widely detected in a number of different bacterial species. These resistance genes were mainly harbored in Enterobacteriaceae, followed by Acinetobacter and Aeromonas isolates. More attention should be given to these bacteria as important vectors of ARGs in the environment. Furthermore, we showed that the multidrug resistance phenotype was highly prevalent, which was found in 85.5% Enterobacteriaceae and 75% Acinetobacter strains. Notably, the presence of carbapenemase genes in isolates from treated effluents and receiving rivers indicates that the discharges of wastewater treatment plants could be an important source for high-risk resistance genes propagation to the environment. In conclusion, this study shows a high prevalence of ESBL- and carbapenemase-producing bacteria in hospital sewage and receiving rivers in China. These findings have serious implications for human health, and also suggest the need for more efforts to control the dissemination of resistant bacteria from hospital sewage into the environment.

Download Full-text

Bacteriophage selection against a plasmid-encoded sex apparatus leads to the loss of antibiotic-resistance plasmids

Biology Letters ◽

10.1098/rsbl.2011.0384 ◽

2011 ◽

Vol 7 (6) ◽

pp. 902-905 ◽

Cited By ~ 41

Author(s):

Matti Jalasvuori ◽

Ville-Petri Friman ◽

Anne Nieminen ◽

Jaana K. H. Bamford ◽

Angus Buckling

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Bacterial Species ◽

Low Frequency ◽

Antibiotic Resistance Genes ◽

Resistant Bacteria ◽

Bacterial Cells ◽

Antibiotic Resistant ◽

Resistance Plasmids ◽

Resistant Mutants

Antibiotic-resistance genes are often carried by conjugative plasmids, which spread within and between bacterial species. It has long been recognized that some viruses of bacteria (bacteriophage; phage) have evolved to infect and kill plasmid-harbouring cells. This raises a question: can phages cause the loss of plasmid-associated antibiotic resistance by selecting for plasmid-free bacteria, or can bacteria or plasmids evolve resistance to phages in other ways? Here, we show that multiple antibiotic-resistance genes containing plasmids are stably maintained in both Escherichia coli and Salmonella enterica in the absence of phages, while plasmid-dependent phage PRD1 causes a dramatic reduction in the frequency of antibiotic-resistant bacteria. The loss of antibiotic resistance in cells initially harbouring RP4 plasmid was shown to result from evolution of phage resistance where bacterial cells expelled their plasmid (and hence the suitable receptor for phages). Phages also selected for a low frequency of plasmid-containing, phage-resistant bacteria, presumably as a result of modification of the plasmid-encoded receptor. However, these double-resistant mutants had a growth cost compared with phage-resistant but antibiotic-susceptible mutants and were unable to conjugate. These results suggest that bacteriophages could play a significant role in restricting the spread of plasmid-encoded antibiotic resistance.

Download Full-text

Antimicrobial Susceptibility Profiles and Resistance Genes in Genus Aeromonas spp. Isolated from the Environment and Rainbow Trout of Two Fish Farms in France

Microorganisms ◽

10.3390/microorganisms9061201 ◽

2021 ◽

Vol 9 (6) ◽

pp. 1201

Author(s):

Niki Hayatgheib ◽

Ségolène Calvez ◽

Catherine Fournel ◽

Lionel Pineau ◽

Hervé Pouliquen ◽

...

Keyword(s):

Resistance Genes ◽

Antibiotic Use ◽

Resistant Bacteria ◽

Aquatic Environments ◽

Fish Farms ◽

Antibiotic Resistant ◽

Resistant Strains ◽

Trout Farms ◽

Susceptibility Profiles ◽

The Impact

This study presents the occurrence and abundance of Aeromonas antibiotic-resistant bacteria (ARB) and genes (ARGs) isolated from water, biofilm and fish in two commercial trout farms before and one week after flumequine treatment. Wild (WT) and non-wild (NWT) strains were determined for quinolones (flumequine, oxolinic acid and enrofloxacin), oxytetracycline (OXY), florfenicol (FFN), trimethoprim-sulfamethoxazole (TMP) and colistin (COL), and pMAR (presumptive multi-resistant) strains were classified. Forty-four ARGs for the mentioned antibiotics, β-lactams and multi-resistance were quantified for 211 isolates. BlaSHV-01, mexF and tetE were the dominant ARGs. A greater occurrence and abundance of tetA2, sul3, floR1, blaSHV-01 and mexF were observed for NWT compared to WT. The occurrence of pMAR and NWT Aeromonas for quinolones, OXY, FFN, TMP, COL and ARGs depended on the Aeromonas origin, antibiotic use and the presence of upstream activities. Our results revealed the impact of a flumequine treatment on Aeromonas present on a fish farm through an increase in NWT and pMAR strains. The link between fish and their environment was shown by the detection of identical ARB and ARGs in the two types of samples. There appears to be a high risk of resistance genes developing and spreading in aquatic environments.

Download Full-text

Withdraw of prophylactic antimicrobials does not change resistome in pigs

10.21203/rs.2.18011/v1 ◽

2019 ◽

Author(s):

Maria Fernanda Loayza Villa ◽

Alejandro Torres ◽

Lixin Zhang ◽

Gabriel Trueba

Keyword(s):

Antibiotic Resistance ◽

Antimicrobial Resistance ◽

Resistance Genes ◽

Resistant Bacteria ◽

Productive Performance ◽

Fitness Costs ◽

Antibiotic Resistant ◽

Human Microbiota ◽

Antimicrobial Resistance Genes ◽

The Impact

Abstract Background: The use of antimicrobials in the animal industry has increased the prevalence of antibiotic resistant bacteria and antimicrobial-resistance genes which can be transferred to human microbiota through the food chain or the environment. To reduce the influx of antibiotic-resistance to the human microbiota, restrictions on antimicrobials (in food animals) have been implemented in different countries. We investigated the impact of an antimicrobial restriction on the frequency of antimicrobial-resistant bacteria in pigs (PCI 1050) from an Ecuadorian farm. Results: No differences in antimicrobial resistant coliforms or antimicrobial resistance genes (richness and abundance) were found when we compared animals fed with or without antibiotics. Nevertheless, the absence of antimicrobials in pigs didn’t impact the productive performance of animals. Conclusion: Fitness costs of antimicrobial resistance in bacteria within intestinal microbiota of animals seems to be overestimated. Avoiding antimicrobials as prophylactics in pigs fed is not enough to control maintenance and spread of antimicrobial resistance.

Download Full-text

Detection of antibiotic-resistant bacteria and their resistance genes from houseflies

Veterinary World ◽

10.14202/vetworld.2020.266-274 ◽

2020 ◽

Vol 13 (2) ◽

pp. 266-274 ◽

Cited By ~ 3

Author(s):

Sharmin Akter ◽

Abdullah Al Momen Sabuj ◽

Zobayda Farzana Haque ◽

Md. Tanvir Rahman ◽

Md. Abdul Kafi ◽

...

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Bacterial Species ◽

Animal Health ◽

Antibiotic Resistance Genes ◽

Diffusion Method ◽

Resistant Bacteria ◽

Antibiotic Resistant Bacteria ◽

Salmonella Spp ◽

Antibiotic Resistant

Background and Aim: Houseflies (Musca domestica) are synanthropic insects which serve as biological or mechanical vectors for spreading multidrug-resistant bacteria responsible for many infectious diseases. This study aimed to detect antibiotic-resistant bacteria from houseflies, and to examine their resistance genes. Materials and Methods: A total of 140 houseflies were captured using sterile nylon net from seven places of Mymensingh city, Bangladesh. Immediately after collection, flies were transferred to a sterile zipper bag and brought to microbiology laboratory within 1 h. Three bacterial species were isolated from houseflies, based on cultural and molecular tests. After that, the isolates were subjected to antimicrobial susceptibility testing against commonly used antibiotics, by the disk diffusion method. Finally, the detection of antibiotic resistance genes tetA, tetB, mcr-3, mecA, and mecC was performed by a polymerase chain reaction. Results: The most common isolates were Staphylococcus aureus (78.6%), Salmonella spp., (66.4%), and Escherichia coli (51.4%). These species of bacteria were recovered from 78.3% of isolates from the Mymensingh Medical College Hospital areas. Most of the isolates of the three bacterial species were resistant to erythromycin, tetracycline, penicillin and amoxicillin and were sensitive to ciprofloxacin, ceftriaxone, chloramphenicol, gentamicin, and azithromycin. Five antibiotic resistance genes of three bacteria were detected: tetA, tetB, mcr-3, and mecA were found in 37%, 20%, 20%, and 14% isolates, respectively, and no isolates were positive for mecC gene. Conclusion: S. aureus, Salmonella spp., and E. coli with genetically-mediated multiple antibiotic resistance are carried in houseflies in the Mymensingh region. Flies may, therefore, represent an important means of transmission of these antibiotic-resistant bacteria, with consequent risks to human and animal health.

Download Full-text

Impact of Antibiotic-Resistant Bacteria on Immune Activation and Clostridioides difficile Infection in the Mouse Intestine

Infection and Immunity ◽

10.1128/iai.00362-19 ◽

2020 ◽

Vol 88 (4) ◽

Cited By ~ 1

Author(s):

James W. Keith ◽

Qiwen Dong ◽

Matthew T. Sorbara ◽

Simone Becattini ◽

Jonathan K. Sia ◽

...

Keyword(s):

Colonic Mucosa ◽

Bacterial Species ◽

Intestinal Lumen ◽

Resistant Bacteria ◽

Colonization Resistance ◽

Antibiotic Resistant ◽

Content Type ◽

Clostridioides Difficile ◽

Wide Range ◽

The Impact

ABSTRACT Antibiotic treatment of patients undergoing complex medical treatments can deplete commensal bacterial strains from the intestinal microbiota, thereby reducing colonization resistance against a wide range of antibiotic-resistant pathogens. Loss of colonization resistance can lead to marked expansion of vancomycin-resistant Enterococcus faecium (VRE), Klebsiella pneumoniae, and Escherichia coli in the intestinal lumen, predisposing patients to bloodstream invasion and sepsis. The impact of intestinal domination by these antibiotic-resistant pathogens on mucosal immune defenses and epithelial and mucin-mediated barrier integrity is unclear. We used a mouse model to study the impact of intestinal domination by antibiotic-resistant bacterial species and strains on the colonic mucosa. Intestinal colonization with K. pneumoniae, Proteus mirabilis, or Enterobacter cloacae promoted greater recruitment of neutrophils to the colonic mucosa. To test the hypothesis that the residual microbiota influences the severity of colitis caused by infection with Clostridioides difficile, we coinfected mice that were colonized with ampicillin-resistant bacteria with a virulent strain of C. difficile and monitored colonization and pathogenesis. Despite the compositional differences in the gut microbiota, the severity of C. difficile infection (CDI) and mortality did not differ significantly between mice colonized with different ampicillin-resistant bacterial species. Our results suggest that the virulence mechanisms enabling CDI and epithelial destruction outweigh the relatively minor impact of less-virulent antibiotic-resistant intestinal bacteria on the outcome of CDI.

Download Full-text

Withdraw of prophylactic antimicrobials does not change the pigs’ resistome

10.1101/716597 ◽

2019 ◽

Author(s):

Loayza-Villa Fernanda ◽

Torres Alejandro ◽

Zhang Lixin ◽

Trueba Gabriel

Keyword(s):

Antimicrobial Resistance ◽

Resistance Genes ◽

Commensal Bacteria ◽

Resistant Bacteria ◽

Human Pathogens ◽

Fitness Costs ◽

Antibiotic Resistant Bacteria ◽

Antibiotic Resistant ◽

Antimicrobial Resistance Genes ◽

The Impact

AbstractThe use of antimicrobials in the animal industry has increased the prevalence of antimicrobial resistant commensal bacteria in food products derived from animals, which could be associated with antimicrobial resistance in human pathogens. To reduce the influx of antibiotic resistant bacteria (and genes) to the human microbiota, restrictions on antimicrobials (in food animals) have been implemented in different countries. We investigated the impact of antimicrobial restriction in the frequency of antimicrobial resistant bacteria in pigs. No differences in antimicrobial resistance or antimicrobial resistance genes (richness or abundance) was found when we compared animals fed with and without antibiotics. Fitness costs of antimicrobial resistance in bacteria (in the field) seems to be overestimated.

Download Full-text