Mobile elements carrying ermF and tetQ genes in gram-positive and gram-negative bacteria

Metagenomic profiling of antibiotic resistance genes and their associations with the bacterial community along the Kanda River, an urban river in Japan

Antibiotic resistance genes (ARGs) present in urban rivers have the potential to disseminate antibiotic-resistant bacteria into other environments, posing significant threats to both ecological and public health. Although metagenomic analyses have been widely employed to detect ARGs in rivers, our understanding of their dynamics across different seasons in diverse watersheds remains limited. In this study, we performed a comprehensive genomic analysis of the Kanda River in Japan at 11 sites from upstream to estuary throughout the year to assess the spread of ARGs and their associations with bacterial communities. Analysis of 110 water samples using the 16S rRNA gene revealed variations in bacterial composition corresponding to seasonal changes in environmental parameters along the river. Shotgun metagenomics-based profiling of ARGs in 44 water samples indicated higher ARG abundance downstream, particularly during the summer. Weighted gene co-expression network analysis (WGCNA) linking bacterial lineages and ARGs revealed that 12 ARG subtypes co-occurred with 128 amplicon sequence variants (ASVs). WGCNA suggested potential hosts for ErmB, ErmF, ErmG, tetQ, tet (W/N/W), aadA2, and adeF, including gut-associated bacteria (e.g., Prevotella, Bacteroides, Arcobacter) and indigenous aquatic microbes (e.g., Limnohabitans and C39). In addition, Pseudarcobacter (a later synonym of Arcobater) was identified as a host for adeF, which was also confirmed by single cell genomics. This study shows that ARG distribution in urban rivers is affected by seasonal and geographical factors and demonstrates the importance of monitoring rivers using multiple types of genome sequencing, including 16S rRNA gene sequencing, metagenomics, and single cell genomics.

Deeper Exploration of Gut Microbiome: Profile of Resistome, Virome and Viral Auxiliary Metabolic Genes of Three Ethnic Indian Groups

The current study explored the resistomes and viromes of three Indian ethnic populations: Jaisalmer, Khargone, and Ladakh. These three groups had different dietary habits and antibiotic consumption rates. A resistome analysis indicated that compared to the Jaisalmer (n = 10) group, the burden of antibiotic resistance genes in the gut microbiome was higher in the Khargone (n = 12) and Ladakh (n = 9) groups. However, correlational analysis factoring in food habits, healthcare, and economic status was not statistically significant due to the limited number of samples. A considerable number of antibiotic resistance genes (ARGs) were present in well-known gut commensals such as Bifidobacteriaceae, Acidomonococcaceae, etc., as retrieved directly by mapping to the Resfinder database using the Groot tool. Further, the raw reads were assembled using MEGAHIT, and putative bacteriophages were retrieved using the VIBRANT tool. Many of the classified bacteriophages of the virome revealed that bacteria belonging to the families Bifidobacteriaceae and Enterocococcaceae were their hosts. The prophages identified in these groups primarily contained auxiliary metabolic genes (AMGs) for primary amino acid metabolism. However, there were significantly fewer AMGs in the Ladakh group than in the Jaisalmer group (p < 0.05). None of the classified bacteriophages or prophages contained ARGs. This indicates that phages do not normally carry antibiotic resistance genes.

A novel conjugative transposon carrying an autonomously amplified plasmid

Tetracyclines serve as broad-spectrum antibiotics to treat bacterial infections. The discovery of new tetracycline resistance genes has led to new questions about the underlying mechanisms of resistance, gene transfer, and their relevance to human health. We tracked changes in the abundance of a 55-kbp conjugative transposon (CTn214) carrying tetQ, a tetracycline resistance gene, within a Bacteroides fragilis metagenome-assembled genome derived from shotgun sequencing of microbial DNA extracted from the ileal pouch of a patient with ulcerative colitis. The mapping of metagenomic reads to CTn214 revealed the multi-copy nature of a 17,044-nt region containing tetQ in samples collected during inflammation and uninflamed visits. B. fragilis cultivars isolated from the same patient during periods of inflammation harbored CTn214 integrated into the chromosome or both a circular, multi-copy, extrachromosomal region of the CTn214 containing tetQ and the corresponding integrated form. The tetracycline-dependent mechanism for the transmission of CTn214 is nearly identical to a common conjugative transposon found in the genome of B. fragilis (CTnDOT), but the autonomously amplified nature of a circular 17,044-nt region of CTn214 that codes for tetQ and the integration of the same sequence in the linear chromosome within the same cell is a novel observation. Genome and transcriptome sequencing of B. fragilis cultivars grown under different concentrations of tetracycline and ciprofloxacin indicates that tetQ in strains containing the circular form remains actively expressed regardless of treatment, while the expression of tetQ in strains containing the linear form increases only in the presence of tetracycline.IMPORTANCEThe exchange of antibiotic production and resistance genes between microorganisms can lead to the emergence of new pathogens. In this study, short-read mapping of metagenomic samples taken over time from the illeal pouch of a patient with ulcerative colitis to a Bacteroides fragilis metagenome-assembled genome revealed two distinct genomic arrangements of a novel conjugative transposon, CTn214, that encodes tetracycline resistance. The autonomous amplification of a plasmid-like circular form from CTn214 that includes tetQ potentially provides consistent ribosome protection against tetracycline. This mode of antibiotic resistance offers a novel mechanism for understanding the emergence of pathobionts like B. fragilis and their persistence for extended periods of time in patients with inflammatory bowel disease.

Prevalence of antimicrobial resistant genes in Bacteroides spp. isolated in Oita Prefecture, Japan

INTRODUCTION

Bacteroides spp. are the most common anaerobic bacteria isolated from the human gastrointestinal tract. Several resistant genes are present in Bacteroides spp. However, most studies have focused on the prevalence of the cfiA gene in Bacteroides fragilis alone. We assessed the susceptibility to antimicrobial agents and the prevalence of cepA, cfiA, cfxA, ermF, nim, and tetQ genes in Bacteroides strains isolated from clinical specimens in our hospital.

METHODS

We isolated 86 B. fragilis and 58 non-fragilis Bacteroides strains from human clinical specimens collected from January 2011 to November 2021. Resistance against piperacillin (PIPC), cefotaxime (CTX), cefepime (CFPM), meropenem (MEPM), clindamycin, and minocycline was determined.

RESULTS

The resistant rates of penicillins and cephalosporins in non-fragilis isolates were significantly higher than those in B. fragilis isolates. In B. fragilis isolates, the resistant rates of PIPC, CTX, and CFPM in cfxA-positive isolates were significantly higher than those in cfxA-negative isolates (71% vs. 16%, 77% vs. 19%, and 77% vs. 30%, respectively). Thirteen B. fragilis isolates harbored the cfiA gene, two of which were resistant to MEPM. Six of the 13 cfiA-positive B. fragilis isolates were heterogeneously resistant to MEPM.

CONCLUSION

It is important to evaluate the use of MEPM as empirical therapy for Bacteroides spp. infections, considering the emergence of carbapenem resistance during treatment, existence of MEPM-resistant strains, and heterogeneous resistance.

Short-Term Impact of Oxytetracycline Administration on the Fecal Microbiome, Resistome and Virulome of Grazing Cattle

Antimicrobial resistance (AMR) is an important public health concern around the world. Limited information exists about AMR in grasslands-based systems where antibiotics are seldom used in beef cattle. The present study investigated the impacts of oxytetracycline (OTC) on the microbiome, antibiotic resistance genes (ARGs), and virulence factor genes (VFGs) in grazing steers with no previous exposure to antibiotic treatments. Four steers were injected with a single dose of OTC (TREAT), and four steers were kept as control (CONT). The effects of OTC on fecal microbiome, ARGs, and VFGs were assessed for 14 days using 16S rRNA sequencing and shotgun metagenomics. Alpha and beta microbiome diversities were significantly affected by OTC. Following treatment, less than 8% of bacterial genera had differential abundance between CONT and TREAT samples. Seven ARGs conferring resistance to tetracycline (tet32, tet40, tet44, tetO, tetQ, tetW, and tetW/N/W) increased their abundance in the post-TREAT samples compared to CONT samples. In addition, OTC use was associated with the enrichment of macrolide and lincosamide ARGs (mel and lnuC, respectively). The use of OTC had no significant effect on VFGs. In conclusion, OTC induced short-term alterations of the fecal microbiome and enrichment of ARGs in the feces of grazing beef cattle.

Prevotella: An insight into its characteristics and associated virulence factors

Prevotella species, a gram-negative obligate anaerobe, is commonly associated with human infections such as dental caries and periodontitis, as well as other conditions such as chronic osteomyelitis, bite-related infections, rheumatoid arthritis and intestinal diseases like ulcerative colitis. This generally harmless commensal possesses virulence factors such as adhesins, hemolysins, secretion systems exopolysaccharide, LPS, proteases, quorum sensing molecules and antibiotic resistance to evolve into a well-adapted pathogen capable of causing successful infection and proliferation in the host tissue. This review describes several of these virulence factors and their advantage to Prevotella spp. in causing inflammatory diseases like periodontitis. In addition, using genome analysis of Prevotella reference strains, we examined other putative virulence determinants which can provide insights as biomarkers and be the targets for effective interventions in Prevotella related diseases like periodontitis.

Dog/cat-origin quinolone-resistant Streptococcus agalactiae isolates with point mutations in quinolone resistance-determining regions: Relatedness with clonal complex 10

OBJECTIVE

We aimed to investigate dog/cat-origin quinolone-resistant Streptococcus agalactiae isolates with point mutations in quinolone resistance-determining regions (QRDRs) and to define the relatedness between quinolone-resistant isolates and their microbiological features of capsular genotype, sequence type (ST)/clonal complex (CC), and antimicrobial resistance (AMR) gene.

METHODS

With dog/cat-origin 22 isolates, type strain, and human-origin 6 isolates, we performed antimicrobial susceptibility testing by agar plate dilution method using levofloxacin, ciprofloxacin, and moxifloxacin. We also determined amino acid sequences in QRDRs of gyrA/gyrB/parC/parE genes and their point mutations. We conducted capsular genotyping, multilocus sequence typing, and AMR genotyping in our previous investigations. Correlations between quinolone-resistant population and their microbiological features were examined.

RESULTS

We found dog/cat-origin seven (31.8%) quinolone-resistant isolates harboring minimum inhibitory concentrations (MICs) of levofloxacin 16-32 μg/mL, ciprofloxacin 32 μg/mL, and moxifloxacin 2-4 μg/mL: human three isolates indicated MICs of levofloxacin 16-64 μg/mL, ciprofloxacin 32 μg/mL, and moxifloxacin 2-16 μg/mL. Point mutations Ser81Leu in gyrA and Ser79Phe/Ser79Tyr/Asp83Asn/Gly128Asp in parC were observed among these resistant isolates: mutations Leu495Ile/Val503Ile in parE was found among quinolone-nonresistant isolates. There was a significant correlation between dog/cat-origin quinolone-resistant population and ST10 (p = 0.023)/CC10 (p = 0.021).

CONCLUSION

To our best knowledge, this is the first report assessing dog/cat-origin quinolone-resistant S. agalactiae. Our observations could be applied in future, by veterinarians while treating dogs and cats with clinical symptoms/signs suggestive of streptococcal infections.

Biofilm production ability and associated characteristics of Streptococcus agalactiae isolates from companion animals and humans

OBJECTIVE

We evaluated biofilm production ability (BPA) of Streptococcus agalactiae isolates from companion animals/humans and clarified the relationship between BPA populations and other microbiological features.

METHODS

Companion animal-/human-origin isolates were collected with host information. We measured BPA using crystal violet staining, via virulence-associated gene profiling (hylB-pavA-pilB-spb1-srtC1-brpA), capsular genotyping, multilocus sequence typing, and antimicrobial resistance (AMR) phenotyping/genotyping. Significant difference in BPA of isolates from different hosts was assessed. We analyzed the association between BPA populations and the virulence genotypes, capsular genotypes, sequence types/clonal complexes, and AMR phenotypes/genotypes. Inhibitory effect of berberine on BPA was evaluated.

RESULTS

Five, twenty-six, and twenty-six isolates belonged to strong, moderate, and weak biofilm producers, whereas seventeen showed no biofilm production. We defined strong, moderate, or weak biofilm producers as the producer group (n = 57) to conduct a comparative analysis between the producer and non-producer populations. There was a significant correlation between the producer population and vaginal specimen. We found significant associations between the producer group and presence (57.9%) of pilB and between the non-producer population and presence (70.6%) of spb1. There was no association between the producer group and capsular genotypes, sequence types/clonal complexes, and AMR phenotypes/genotypes (except for a significant correlation between the producer group and AMR to minocycline). We confirmed inhibitory effect of berberine at sub-minimum inhibitory concentrations (MICs) against the type strain on BPA.

CONCLUSION

Our observations suggest that S. agalactiae harboring pilB is more capable of producing biofilms, with berberine inhibitory effect at sub-MICs on BPA.

Comparison of HPLC–DAD and LC–MS Techniques for the Determination of Tetracyclines in Medicated Feeds Using One Extraction Protocol

Four antibiotics, oxytetracycline, tetracycline, doxycycline, and chlortetracycline were separated and quantified in medicated feed. Tetracyclines from feed samples were extracted with 0.01 M citric buffer and acetonitrile (pH 3.0) and further purified with 0.45 µm syringe filters. The purified extract was separated on commercial RP-C18 column and analyzing using liquid chromatograph (LC) with two different detectors: diode array detector (DAD) and mass spectrometry (MS). These methods provided average recoveries from 72.2 to 101.8% for high pressure liquid chromatography (HPLC) with diode array detection and from 45.6 to 87.0% for liquid chromatography with mass spectrometry. The limit of detection in medicated feed ranged from 4.2 to 10.7 mg kg−1 for HPLC–DAD and 5.6 to 10.8 mg kg−1 for LC–MS. Our experiment showed that using the same extraction mixture we do not obtain the same recovery values for the analyzed compounds using two different detection techniques such as DAD and MS.

Metagenomics of antimicrobial and heavy metal resistance in the cecal microbiome of fattening pigs raised without antibiotics

This study aimed to detect the cecal microbiome, antimicrobial resistance (AMR) and heavy metal resistance genes (MRGs) in fattening pigs raised under antibiotic-free (ABF) conditions compared with ordinary industrial pigs (control, C) using whole-genome shotgun sequencing. ABF pigs showed the enrichment of Prevotella (33%) and Lactobacillus (13%), whereas Escherichia coli (40%), Fusobacterium and Bacteroides (each at 4%) were notably observed in the C group. Distinct clusters of cecal microbiota of ABF and C pigs were revealed; however, microbiota of some C pigs (C1) appeared in the same cluster as ABF and were totally separated from the remaining C pigs (C2). For AMR genes, the highest abundance tet(Q) (35.7%) and mef(A) (12.7%) were markedly observed in the ABF group whereas tet(Q) (26.2%) and tet(W) (10.4%) were shown in the C group. tet(Q) was positively correlated to Prevotella in ABF and C1 samples. In the C2 group, the prominent tet(W) was positively correlated to Fusobacterium and Bacteroides Pigs have never received tetracycline but pregnant sows used chlortetracycline once 7 d before parturition. Chromosomal Cu and Zn resistance genes were also shown in both groups regardless the received Cu and Zn feed additives. A higher abundance of multi-metal resistance genes was observed in the C group (44%) compared with the ABF group (41%). In conclusion, the microbiome clusters in some C pigs were similar to that in ABF pigs. High abundant tetracycline resistance genes interrelated to major bacteria were observed in both ABF and C pigs. MRGs were also observed.IMPORTANCE: Owing to the increased problem of AMR in farm animals, raising farm animals without antibiotics is one method that could solve this problem. Our study showed that only some tetracycline and macrolide resistance genes, tet(Q), tet(W) and mef(A), were markedly abundant in ABF and C groups. The tet(Q) and tet(W) genes interrelated to different predominant bacteria in each group, showing the potential role of major bacteria as reservoirs of AMR genes. In addition, chromosomal Cu and Zn resistance genes were also observed in both pig groups, not depending on the use of Cu and Zn additives in both farms. The association of MRGs and AMR genotypes and phenotypes together with the method to re-sensitize bacteria to antibiotics should be studied further to unveil the cause of high resistance genes and solve the problems.

Intracellular invasion ability of Streptococcus agalactiae among non-invasive isolates from human adults and companion animals in Japan

OBJECTIVE

This study evaluated the cell invasion ability (CIA) of Streptococcus agalactiae isolates from humans and companion animals and clarified the relationship between CIA populations and their microbiological features.

METHODS

Human-origin and companion animal-origin isolates were collected along with host information. We measured CIA using human-lineage colon cancer epithelium (Caco-2) and keratinocyte (HaCaT) cell lines, via virulence-associated gene profiling (bca-rib-bac-lmb-cylE-hylB-pavA-pilB-spb1-srtC1-brpA), capsular genotyping, multilocus sequence typing, and antimicrobial resistance (AMR) phenotyping/genotyping. Significant differences in data regarding CIA into epithelium and keratinocytes and those of isolates from different hosts were assessed. We analyzed the association of CIA populations with the virulence genotypes, capsular genotypes, sequence types/clonal complexes, and AMR phenotypes/genotypes.

RESULTS

A comparative analysis was performed between human (n = 15) and canine (n = 17) non-invasive isolates. There was a difference in CIA data between Caco-2 and HaCaT cells using human and animal isolates. For percent invasion ability into Caco-2 cells, we designated values ≥ 0.1 as high-frequency CIA and values < 0.1 as low-frequency CIA. Fourteen isolates harbored high-frequency and 18 isolates harbored low-frequency strains. There was no association between the high-frequency population and the virulence genotypes, capsular genotypes, sequence types/clonal complexes, and AMR phenotypes/genotypes.

CONCLUSION

This is the first report assessing the invasion ability of S. agalactiae into HaCaT and Caco-2 cells. Our observations suggest that S. agalactiae is more capable of entering Caco-2 rather than HaCaT.

Comparison between Invasive and Non-Invasive Streptococcus agalactiae Isolates from Human Adults, Based on Virulence Gene Profiles, Capsular Genotypes, Sequence Types, and Antimicrobial Resistance Patterns

This study assessed whether invasive group B Streptococcus (GBS) isolates were similar to non-invasive isolates from adult patients. Invasive and non-invasive GBS isolates were collected from three hospitals and two laboratory centers between January 2015 and October 2019. The isolates were identified by 16S rRNA amplicon sequencing and amplification of the GBS-specific dltS gene. The virulence gene profiles, capsular genotypes, sequence types (STs)/clonal complexes (CCs), and antimicrobial resistance (AMR) phenotypes/genotypes were determined for the 72 invasive and 50 non-invasive isolates that were comparatively analyzed. We observed a significantly decreased rate of rib detection in the invasive isolates compared to that in the non-invasive isolates (77.8% vs. 92.0%, P < 0.05). Additionally, we found significant differences in the prevalence of CC1 (23.6% vs. 46.0%, P < 0.05) and CC26 (12.5% vs. 2.0%, P < 0.05) between invasive and non-invasive populations. However, there were no significant differences in the comparative data of the virulence gene profiles, capsular genotypes, other STs/CCs, and AMR phenotypes/genotypes between the two populations. These findings suggest that both invasive and non-invasive isolates share similar features in terms of virulence gene profile, capsular genotype, ST/CC, and AMR genotype/phenotype (except for the rates of rib detection and CC1/CC26 prevalence).

Antimicrobial susceptibility patterns of anaerobic bacteria identified from clinical specimens of diseased dogs and cats

We aimed to clarify antimicrobial susceptibility patterns of anaerobes from diseased companion animals. Bacterial identification was based on the Japanese 2012 guidelines for the testing of anaerobic bacteria. AST was performed using the broth microdilution method. The anaerobe-containing samples collected from 2014 to 2018 included blood (anaerobe recovery rate, 5.0%), bile (9.4%), joint fluids (0.6%), pleural effusions (42.6%), ascites (64.1%), cerebrospinal fluids (3.0%), and punctures (75.0%). The anaerobes identified included Bacteroides spp. (33.2%), Peptostreptococcus spp. (19.6%), Prevotella spp. (13.6%), Propionibacterium spp. (10.3%), Clostridium spp. (9.3%), and Fusobacterium spp. (7.5%). Bacteroides fragilis group isolates were resistant to penicillin G (100%), ampicillin (100%), cefmetazole (63.6%), ceftizoxime (90.0%), and clindamycin (40.0%). Our observations demonstrated antimicrobial susceptibility in anaerobes isolated from Japanese companion animals.

Fate and transport of antibiotics and antibiotic resistance genes in runoff and soil as affected by the timing of swine manure slurry application

Land application of swine manure slurry is a common practice to supplement nutrients to soil for crop production. This practice can introduce antibiotic residues and antibiotic resistance genes (ARGs) into the environment. Field testing is critical in identifying manure management practices effective in minimizing the environmental impacts of manure-borne antibiotic and ARGs. The objective of this study was to determine how the timing of swine manure application relative to rainfall events impacts the fate and transport of antibiotics and ARGs in surface runoff and manure-amended soil. Swine manure slurry was either broadcast or injected on test plots in the field. A set of three 30-min simulated rainfall events, 24 h apart, were initiated on manured plots 1 day, 1 week, 2 weeks, or 3 weeks after the manure application. Results showed that an interval longer than 2 weeks between application and rainfall often significantly reduced the levels of antibiotics and ARGs tested in runoff with the exception of tet(X). For soil samples from broadcast plots, concentrations of two of the three antibiotics tested (lincomycin and tiamulin) decreased substantially in the first two weeks after manure application. In contrast, concentrations of most of the ARGs tested (tet(Q), tet(X), and erm(A)) in soil did not change significantly during the test period. Information obtained from the study can be beneficial in designing manure management practices and estimating the environmental loading of antibiotics and ARGs resulting from manure application.

Comparative diversity of microbiomes and Resistomes in beef feedlots, downstream environments and urban sewage influent

Background

Comparative knowledge of microbiomes and resistomes across environmental interfaces between animal production systems and urban settings is lacking. In this study, we executed a comparative analysis of the microbiota and resistomes of metagenomes from cattle feces, catch basin water, manured agricultural soil and urban sewage.

Results

Metagenomic DNA from composite fecal samples (FC; n = 12) collected from penned cattle at four feedlots in Alberta, Canada, along with water from adjacent catchment basins (CB; n = 13), soil (n = 4) from fields in the vicinity of one of the feedlots and urban sewage influent (SI; n = 6) from two municipalities were subjected to Illumina HiSeq2000 sequencing. Firmicutes exhibited the highest prevalence (40%) in FC, whereas Proteobacteria were most abundant in CB (64%), soil (60%) and SI (83%). Among sample types, SI had the highest diversity of antimicrobial resistance (AMR), and metal and biocide resistance (MBR) classes (13 & 15) followed by FC (10 & 8), CB (8 & 4), and soil (6 & 1). The highest antimicrobial resistant (AMR) gene (ARG) abundance was harboured by FC, whereas soil samples had a very small, but unique resistome which did not overlap with FC & CB resistomes. In the beef production system, tetracycline resistance predominated followed by macrolide resistance. The SI resistome harboured β-lactam, macrolide, tetracycline, aminoglycoside, fluoroquinolone and fosfomycin resistance determinants. Metal and biocide resistance accounted for 26% of the SI resistome with a predominance of mercury resistance.

Conclusions

This study demonstrates an increasing divergence in the nature of the microbiome and resistome as the distance from the feedlot increases. Consistent with antimicrobial use, tetracycline and macrolide resistance genes were predominant in the beef production system. One of the feedlots contributed both conventional (raised with antibiotics) and natural (raised without antibiotics) pens samples. Although natural pen samples exhibited a microbiota composition that was similar to samples from conventional pens, their resistome was less complex. Similarly, the SI resistome was indicative of drug classes used in humans and the greater abundance of mercury resistance may be associated with contamination of municipal water with household and industrial products.

Electronic supplementary material

The online version of this article (10.1186/s12866-019-1548-x) contains supplementary material, which is available to authorized users.

Chronic impacts of oxytetracycline on mesophilic anaerobic digestion of excess sludge: Inhibition of hydrolytic acidification and enrichment of antibiotic resistome

We evaluated the chronic impact of oxytetracycline (OTC) on performance and antibiotic resistance development during the mesophilic anaerobic digestion (AD) of antibiotic-containing biomass. Mesophilic AD was conducted in a completely stirred tank reactor by constantly feeding municipal excess sludge spiked with increasing concentrations of OTC (0-1000 mg L^-1) under a solid retention time of 20 days over a period of 265 days. Results showed that methane generation of mesophilic AD was inhibited when the OTC concentration in digested sludge was increased to around 18,000 mg kg^-1 (OTC dose, 1000 mg L^-1), due to the inhibition of fermenting and acidogenic bacteria. Metagenomic sequencing and high-throughput quantitative PCR analysis demonstrated that tetracycline resistance genes were the most dominant type (38.47-43.76%) in the resistome, with tetG, tetX, tetM, tetR, tetQ, tetO, and tetL as the dominant resistant subtypes throughout the whole experimental period. The relative abundance of these tet genes increased from 2.10 × 10^-1 before spiking OTC (OTC concentration in digested sludge, 8.97 mg kg^-1) to 2.83 × 10^-1 (p < 0.05) after spiking OTC at a dose of 40 mg L^-1 (OTC concentration in digested sludge, 528.52 mg kg^-1). Furthermore, mobile genetic elements, including integrons, transposons, and plasmids, were also enriched with the increase in OTC dose. Based on partial canonical correspondence analysis, the contributions of horizontal (mobile element alteration) and vertical (bacterial community shift) gene transfer to antibiotic resistome variation were 29.35% and 21.51%, respectively. Thus, considering the inhibition of hydrolytic acidification and enrichment of antibiotic resistome, mesophilic AD is not suggested to directly treat the biomass containing OTC concentration higher than 200 mg L^-1.

Effects of chlortetracycline on the fate of multi-antibiotic resistance genes and the microbial community during swine manure composting

Excessive use of antibiotics in breeding industry leads to accumulation of antibiotic residuals and antibiotic resistance genes (ARGs) in environment from improperly treated livestock excrements. Four commonly used veterinary antibiotics including chlortetracycline (CTC), sulfamerazine (SMZ), enrofloxacin (ENR) and erythromycin (ERY) were monitored in the swine manure composting. Co-resistance and cross-resistance effects among relative ARGs, correlations between ARGs and bacterial community under multiple antibiotics residual during the composting were investigated in this research. With CTC addition up to 20 mg/kg, more than 99% of CTC removal was achieved after composting, and most of the other antibiotics can be thoroughly removed as well. The variations in ARGs during the composting were strongly correlated to the compositions of the microbial community, Bacteroides and Sporosarcina were main ARGs carriers in the thermophlic phase. Clostridium Ⅺ, Clostridium sensu stricto, and Pseudoxanthomonas, might spread ARGs in cooling and maturing stage. Most of the tested ARGs in swine manure can be effectively reduced through composting, thus makes the compost products safe for soil fertilization.

Human Activity Determines the Presence of Integron-Associated and Antibiotic Resistance Genes in Southwestern British Columbia

The dissemination of antibiotic resistant bacteria from anthropogenic sources into the environment poses an emerging public health threat. Antibiotic resistance genes (ARGs) and gene-capturing systems such as integron-associated integrase genes (intI) play a key role in alterations of microbial communities and the spread of antibiotic resistant bacteria into the environment. In order to assess the effect of anthropogenic activities on watersheds in southwestern British Columbia, the presence of putative antibiotic resistance and integrase genes was analyzed in the microbiome of agricultural, urban influenced, and protected watersheds. A metagenomics approach and high-throughput quantitative PCR (HT qPCR) were used to screen for elements of resistance including ARGs and intI. Metagenomic sequencing of bacterial genomic DNA was used to characterize the resistome of microbial communities present in watersheds over a 1-year period. There was a low prevalence of ARGs relative to the microbial population (<1%). Analysis of the metagenomic sequences detected a total of 60 elements of resistance including 46 ARGs, intI1, and groEL/intI1 genes and 12 quaternary ammonium compounds (qac) resistance genes across all watershed locations. The relative abundance and richness of ARGs was found to be highest in agriculture impacted watersheds compared to urban and protected watersheds. A downstream transport pattern was observed in the impacted watersheds (urban and agricultural) during dry months. Similar to other reports, this study found a strong association between intI1 and ARGs (e.g., sul1), an association which may be used as a proxy for anthropogenic activities. Chemical analysis of water samples for three major groups of antibiotics was below the detection limit. However, the high richness and gene copy numbers (GCNs) of ARGs in impacted sites suggest that the effects of effluents on microbial communities are occurring even at low concentrations of antimicrobials in the water column. Antibiotic resistance and integrase genes in a year-long metagenomic study showed that ARGs were driven mainly by environmental factors from anthropogenized sites in agriculture and urban watersheds. Environmental factors such as land-use and water quality parameters accounted for 45% of the variability observed in watershed locations.

Impact of sequencing depth on the characterization of the microbiome and resistome

Developments in high-throughput next generation sequencing (NGS) technology have rapidly advanced the understanding of overall microbial ecology as well as occurrence and diversity of specific genes within diverse environments. In the present study, we compared the ability of varying sequencing depths to generate meaningful information about the taxonomic structure and prevalence of antimicrobial resistance genes (ARGs) in the bovine fecal microbial community. Metagenomic sequencing was conducted on eight composite fecal samples originating from four beef cattle feedlots. Metagenomic DNA was sequenced to various depths, D1, D0.5 and D0.25, with average sample read counts of 117, 59 and 26 million, respectively. A comparative analysis of the relative abundance of reads aligning to different phyla and antimicrobial classes indicated that the relative proportions of read assignments remained fairly constant regardless of depth. However, the number of reads being assigned to ARGs as well as to microbial taxa increased significantly with increasing depth. We found a depth of D0.5 was suitable to describe the microbiome and resistome of cattle fecal samples. This study helps define a balance between cost and required sequencing depth to acquire meaningful results.

Dissipation of antimicrobial resistance genes in compost originating from cattle manure after direct oral administration or post-excretion fortification of antimicrobials

Dissipation of antimicrobial resistance genes (ARG) during composting of cattle manure generated through fortification versus administration of antimicrobials in feed was compared. Manure was collected from cattle fed diets containing (kg^-1) dry matter (DM): (1) 44 mg chlortetracycline (CTC), (2) a mixture of 44 mg each of chlortetracycline and sulfamethazine (CTCSMZ), (3) 11 mg tylosin (TYL) or (4) Control, no antimicrobials. Manures were composted for 30 d with a single mixing after 16 d to generate the second heating cycle. Quantitative PCR (qPCR) was used to measure 16S rDNA and tetracycline (tet), erythromycin (erm) and sulfamethazine (sul) genes. Temperature peaks ranged from 48 to 68°C across treatments in the first composting cycle, but except for the control, did not exceed 55°C in the second cycle. Copy numbers of 16S rDNA decreased (P < 0.05) during composting, but were not altered by antimcrobials. Except tet(L), all ARG decreased by 0.1-1.6 log₁₀ g DM^-1 in the first cycle, but some genes (tet[B], tet[L], erm[F], erm[X]) increased (P < 0.05) by 1.0-3.1 log₁₀ g DM^-1 in the second. During composting, levels of tet(M) and tet(W) in CTC, erm(A), erm(B) and erm(X) in TYL, and sul(1) in CTCSMZ remained higher (P < 0.05) in fed than fortified treatments. The dissipation of ARG during composting of manure fortified with antimicrobials differs from manure generated by cattle that are administered antimicrobials in feed, and does not always align with the dissipation of antimicrobial residues.

Fate of antibiotic resistance genes and their associations with bacterial community in livestock breeding wastewater and its receiving river water

Large amounts of antibiotics are currently used in livestock breeding, which is the main driving factor contributing to the occurrence, spread and proliferation of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in the environment. In this study, high-throughput sequencing based metagenomic approaches were employed to characterize the tempo-spacial changes of antibiotic resistome, bacterial community and their correlations in pig farming wastewater and its receiving river. A total of 194 ARG subtypes within 14 ARG types were detectable in all the samples, and their total relative abundance increased in the river water after receiving wastewater discharge, while decreased in the downstream river water. Network analysis showed that 25.26% ARGs within the same type or among the different types showed higher incidences of non-random co-occurrence. The wastewater discharge evidently increased bacterial diversity and induced bacterial community shift in the receiving river water. The genera of Treponema, Prevotella, Pseudomonas, Bacteroides, Oscillibacter and Acholeplasma dominated in the wastewater samples and almost disappeared in the receiving river water, but bacterial pathogens Clostridium difficile and Arcobacter butzleri still occurred in the receiving water. Correlation analysis and host analysis consistently showed that the changes in the abundances of several key genera like Prevotella and Treponema were significantly and positively correlated with the antibiotic resistome alteration. Variation partitioning analysis indicated that bacterial community played a more important role in the resistome alteration than mobile genetic elements. This study may help to understand the correlations among antibiotic resistome, microbiota and environmental conditions in the wastewater-receiving river water.

The Intestinal Microbiome in Infectious Diseases: The Clinical Relevance of a Rapidly Emerging Field

The field of infectious disease is undergoing a paradigm shift as the intestinal microbiome is becoming understood. The aim of this review is to inform infectious disease physicians of the potential relevance of the intestinal microbiome to their practice. We searched Medline using both index and text words relating to infectious diseases, microbiome, and probiotics. Relevant articles published up through 2017 were reviewed within Rayyan. The review illustrates pathophysiologic concepts linking the microbiome and infectious diseases; specifically, the intestinal microbiome’s relevance to early immune development, the microbiome and enteric infections, the microbiome’s relevance in compromised hosts, and antimicrobial resistance. Within each subject, there are specific examples of diseases and at-risk patient populations where a role for the microbiome has been strongly established. This provides an overview of the significance of the intestinal microbiome to microbiology, pediatric and adult infectious diseases with an underpinning of concepts useful for the practicing clinician.

Streptococcus anginosus (milleri) Group Strains Isolated in Poland (1996-2012) and their Antibiotic Resistance Patterns

Streptococcus anginosus, Streptococcus intermedius and Streptococcus constellatus form a group of related streptococcal species, namely the Streptococcus Anginosus Group (SAG). The group, previously called "milleri" had been rarely described until 1980/1990 as source of infections. Nowadays SAG bacteria are often described as pathogens causing predominantly purulent infections. The number of infections is highly underestimated, as SAG strains are often classified in the microbiology laboratory as less virulent "viridans streptococci" Epidemiological situation regarding SAG infections in Poland has been unrecognized, therefore we performed a retrospective analysis of strains isolated between 1996 and 2012. Strains suspected of belonging to SAG were re-identified using an automated biochemical approach (Vitek2) and MALDI-TOF MS. We performed first analysis of antibiotic resistance among SAG strains isolated in Poland using automated methods (Vitek2), disk diffusion tests and E-Tests. We also performed PCR detection of resistance determinants in antibiotic resistant strains. Clonal structure of analyzed strains was evaluated with PFGE and MLVF methods. All three species are difficult to distinguish using automated diagnostic methods and the same is true for automated MIC evaluation. Our analysis revealed SAG strains are rarely isolated in Poland, predominantly from purulent infections. All isolates are very diverse on the genomic level as estimated by PFGE and MLVF analyses. All analyzed strains are sensitive to penicillin, a substantial group of strains is resistant to macrolides and the majority of strains are resistant to tetracycline.

The gut resistome is highly dynamic during the first months of life

AIM

We investigated the longitudinal development of several antibiotic resistance genes (ARGs) of the infant gut resistome during the first months after birth.

MATERIALS & METHODS

Fecal samples from 120 infants collected at the ages of 5, 13 and 31 weeks were analyzed and subjected to qPCR for the detection of several ARGs.

RESULTS

The prevalence of ARGs significantly increased for ermB, tetM and tetQ, while it decreased for aac(6')-aph(2'). Birth mode and breastfeeding significantly affected tetQ prevalence. Correlations to bacterial taxa suggest that fluctuations in some ARGs are (partly) attributed to shifts in bacteroides colonization rates.

CONCLUSION

Acquisition of ARGs in the gut microbiota occurs shortly after birth and resistome composition fluctuates over the course of several months, reflecting changes in microbial community structure.

Heterogeneity in resistant fecal Bacteroides fragilis group collected from healthy people

Normal nonpathogenic flora would represent a constant lake of resistance genes potentially transferable to human pathogens. To assess the prevalence of resistance genes and genetic variability of Bacteroides fragilis group (BFG) from normal flora, 177 Bacteroides isolates obtained from the fecal samples of healthy individuals. These isolates were subjected to antibiotic susceptibility testing and pulsed field gel electrophoresis (PFGE). The isolates were further tested for the presence of ermF, tetQ and bft genes by PCR. Our results indicated the presence of different clonal strains (1 common type and 57 single types) among the resistant isolates. The resistance rate for the six antibiotics in this study was between 1% and 95%. Most of the isolates (99%) were susceptible to metronidazole. ermF and tetQ were detected in all erythromycin and tetracycline resistant isolates. None of the isolates were carried bft gene. These data suggest dissemination of heterogenic clonal groups in healthy persons and resistance to 5 high commonly used antibiotics.

Tetracycline and Phenicol Resistance Genes and Mechanisms: Importance for Agriculture, the Environment, and Humans

Recent reports have speculated on the future impact that antibiotic-resistant bacteria will have on food production, human health, and global economics. This review examines microbial resistance to tetracyclines and phenicols, antibiotics that are widely used in global food production. The mechanisms of resistance, mode of spread between agriculturally and human-impacted environments and ecosystems, distribution among bacteria, and the genes most likely to be associated with agricultural and environmental settings are included. Forty-six different tetracycline resistance () genes have been identified in 126 genera, with (M) having the broadest taxonomic distribution among all bacteria and (B) having the broadest coverage among the Gram-negative genera. Phenicol resistance genes are organized into 37 groups and have been identified in 70 bacterial genera. The review provides the latest information on tetracycline and phenicol resistance genes, including their association with mobile genetic elements in bacteria of environmental, medical, and veterinary relevance. Knowing what specific antibiotic-resistance genes (ARGs) are found in specific bacterial species and/or genera is critical when using a selective suite of ARGs for detection or surveillance studies. As detection methods move to molecular techniques, our knowledge about which type of bacteria carry which resistance gene(s) will become more important to ensure that the whole spectrum of bacteria are included in future surveillance studies. This review provides information needed to integrate the biology, taxonomy, and ecology of tetracycline- and phenicol-resistant bacteria and their resistance genes so that informative surveillance strategies can be developed and the correct genes selected.

Identification and antimicrobial susceptibility of obligate anaerobic bacteria from clinical samples of animal origin

The etiology of veterinary infectious diseases has been the focus of considerable research, yet relatively little is known about the causative agents of anaerobic infections. Susceptibility studies have documented the emergence of antimicrobial resistance and indicate distinct differences in resistance patterns related to veterinary hospitals, geographic regions, and antibiotic-prescribing regimens. The aim of the present study was to identify the obligate anaerobic bacteria from veterinary clinical samples and to determinate the in vitro susceptibility to eight antimicrobials and their resistance-associated genes. 81 clinical specimens obtained from food-producing animals, pets and wild animals were examined to determine the relative prevalence of obligate anaerobic bacteria, and the species represented. Bacteroides spp, Prevotella spp and Clostridium spp represented approximately 80% of all anaerobic isolates. Resistance to metronidazole, clindamycin, tetracycline and fluoroquinolones was found in strains isolated from food-producing animals. Ciprofloxacin, enrofloxacin and cephalotin showed the highest resistance in all isolates. In 17%, 4% and 14% of tetracycline-resistant isolates, the resistance genes tetL, tetM and tetW were respectively amplified by PCR whereas in 4% of clindamycin-resistant strains the ermG gene was detected. 26% of the isolates were positive for cepA, while only 6% harbored the cfxA (resistance-conferring genes to beta-lactams). In this study, the obligate anaerobic bacteria from Costa Rica showed a high degree of resistance to most antimicrobials tested. Nevertheless, in the majority of cases this resistance was not related to the resistance acquired genes usually described in anaerobes. It is important to address and regulate the use of antimicrobials in the agricultural industry and the empirical therapy in anaerobic bacterial infections in veterinary medicine, especially since antibiotics and resistant bacteria can persist in the environment.

Identification of ribosomal RNA methyltransferase gene ermF in Riemerella anatipestifer

Riemerella anatipestifer is a major bacterial pathogen of waterfowl, globally responsible for avian septicaemic disease. As chemotherapy is the predominant method for the prevention and treatment of R. anatipestifer infection in poultry, the widespread use of antibiotics has favoured the emergence of antibiotic-resistant strains. However, little is known about R. anatipestifer susceptibility to macrolide antibiotics and its resistance mechanism. We report for the first time the identification of a macrolide resistance mechanism in R. anatipestifer that is mediated by the ribosomal RNA methyltransferase ermF. We identified the presence of the ermF gene in 64/206 (31%) R. anatipestifer isolates from different regions in China. An ermF deletion strain was constructed to investigate the function of the ermF gene on the resistance to high levels of macrolides. The ermF mutant strain showed significantly decreased resistance to macrolide and lincosamide, exhibiting 1024-, 1024-, 4- and >2048-fold reduction in the minimum inhibitory concentrations for erythromycin, azithromycin, tylosin and lincomycin, respectively. Furthermore, functional analysis of ermF expression in E. coli XL1-blue showed that the R. anatipestifer ermF gene was functional in E. coli XL1-blue and conferred resistance to high levels of erythromycin (100 µg/ml), supporting the hypothesis that the ermF gene is associated with high-level macrolide resistance. Our work suggests that ribosomal RNA modification mediated by the ermF methyltransferase is the predominant mechanism of resistance to erythromycin in R. anatipestifer isolates.

In silico analysis of antibiotic resistance genes in the gut microflora of individuals from diverse geographies and age-groups

The spread of antibiotic resistance, originating from the rampant and unrestrictive use of antibiotics in humans and livestock over the past few decades has emerged as a global health problem. This problem has been further compounded by recent reports implicating the gut microbial communities to act as reservoirs of antibiotic resistance. We have profiled the presence of probable antibiotic resistance genes in the gut flora of 275 individuals from eight different nationalities. For this purpose, available metagenomic data sets corresponding to 275 gut microbiomes were analyzed. Sequence similarity searches of the genomic fragments constituting each of these metagenomes were performed against genes conferring resistance to around 240 antibiotics. Potential antibiotic resistance genes conferring resistance against 53 different antibiotics were detected in the human gut microflora analysed in this study. In addition to several geography/country-specific patterns, four distinct clusters of gut microbiomes, referred to as ‘Resistotypes’, exhibiting similarities in their antibiotic resistance profiles, were identified. Groups of antibiotics having similarities in their resistance patterns within each of these clusters were also detected. Apart from this, mobile multi-drug resistance gene operons were detected in certain gut microbiomes. The study highlighted an alarmingly high abundance of antibiotic resistance genes in two infant gut microbiomes. The results obtained in the present study presents a holistic ‘big picture’ on the spectra of antibiotic resistance within our gut microbiota across different geographies. Such insights may help in implementation of new regulations and stringency on the existing ones.

Occurrence of antimicrobials and antimicrobial resistance genes in beef cattle storage ponds and swine treatment lagoons

Livestock manure treatment and storage structures are potential environmental sources of antimicrobials and antimicrobial resistance genes (ARGs). In this study, the occurrence of antimicrobials and ARGs was investigated in the water and the sludge compartments of beef cattle storage ponds and swine lagoons. Analysis was focused on two families of antimicrobials (sulfonamide and tetracycline) and the corresponding ARGs (sul1, sul2, tetO, tetQ and tetX). Results showed that the pseudo-partitioning coefficients of tetracyclines were higher than those of sulfonamides, suggesting different distributions of these two classes of antimicrobials between water and sludge. The ARGs tested were detected in nearly all ponds and lagoons, with the highest relative abundance in sul2 at 6.3×10(-1) copies per 16S rRNA gene. A positive correlation was observed between total sul genes and total sulfonamides in water while the correlation was negative in sludge. No significant correlation was found between total tet genes and total tetracyclines in either water or sludge, but significant correlations were observed for certain individual tet genes. Ammonia concentrations strongly correlated with all ARGs except tetX. This study provided quantitative information on the occurrence of antimicrobials and ARGs in the liquid and solid compartments of typical manure treatment and storage structures.

Intracellular and extracellular antimicrobial resistance genes in the sludge of livestock waste management structures

The sludge compartment in livestock waste management structures is a potential hotbed for the emergence and proliferation of antimicrobial resistance among bacteria. Little is known about the distribution of antimicrobial resistance genes (ARGs) between the intracellular and extracellular DNA pools in the sludge. The overall objective of this study was to assess the significance of extracellular ARGs to the total ARGs in the sludge of livestock waste management structures. In this study, sludge samples were collected from four cattle manure storage ponds and three swine waste treatment lagoons and analyzed for genetic indicators of resistance. Intracellular DNA (iDNA) and extracellular DNA (eDNA) in the sludge were separately extracted using an optimized protocol. ARGs [sul(I), sul(II), tet(O), tet(Q), and tet(X)] in both the iDNA and eDNA extracts were quantified using quantitative polymerase chain reaction (qPCR), and antimicrobials, including sulfonamides and tetracyclines, were measured using liquid chromatography tandem mass spectrometry. Results showed that eDNA constituted less than 1.5% of the total DNA in sludge. All ARGs tested were detected in nearly all eDNA and iDNA samples. Furthermore, every gram of dry sludge contained from 1.7 × 10(3) to 4.2 × 10(8) copies of extracellular ARG and from 3.2 × 10(7) to 3.2 × 10(10) copies of intracellular ARG. Chlortetracycline concentrations ranged between 187 and 2674 μg/g of sludge wet weight (ww), while sulfonamide concentrations were lower than 6.3 μg/g of sludge ww. The detection of ARGs in eDNA extracts suggests that transformation is a potential mechanism in ARG proliferation in the sludge of livestock waste management structures.

Scarce detection of mobile erm genes associated with tetQ in Bacteroides and Parabacteroides from Costa Rica

The frequency of finding of clindamycin-resistant anaerobic bacteria in clinical samples has doubled from 2008 to 2010 in Costa Rica. To determine whether this increase is due to dissemination of erm genes aided by tetQ elements, we analyzed 100 isolates of Bacteroides or Parabacteroides from a regional hospital, a national hospital, and the community. Antimicrobial susceptibilities were recorded with a broth micro-dilution method and erm genes were detected by PCR and Southern blotting. In addition, plasmid isolation and mating experiments were performed to clarify the location and mobility of the detected erm genes. Resistance to clindamycin was by far more frequent in the regional hospital (72%) than in the national hospital (29%) and the community (26%). Resistance to tetracycline was even more common, with the community (85%) outweighing the hospitals (71-72%). While MIC of clindamycin were higher in the hospitals than in the community (P < 0.05), the opposite was seen for tetracycline (P < 0.0001). Of the sought-after genes, only ermG (n = 2), ermA (n = 1), and ermF (n = 1) were detected in the hospitals and ermF in the community (n = 2). In opposition to the low frequency of finding of erm genes, 71% of the isolates were positive for tetQ. None of the detected genes were encoded on plasmids. Only three isolates from the hospitals transferred their erm genes laterally. By contrast, 13 hospital isolates and two community isolates transferred tetQ. Despite the widespread finding of tetracycline-resistant tetQ-positive bacteria, mobile erm genes were rare in our bacterial collection. We conclude that the detected erm genes are likely not included in typical conjugative transposons of Bacteroides and Parabacteroides.

Genetic analysis of mobile tetQ elements in oral Prevotella species

Prevotella species are members of the bacterial oral flora and are opportunistic pathogens in polymicrobial infections of soft tissues. Antibiotic resistance to tetracyclines is common in these bacteria, and the gene encoding this resistance has been previously identified as tetQ. The tetQ gene is also found on conjugative transposons in the intestinal Bacteroides species; whether these related bacteria have transmitted tetQ to Prevotella is unknown. In this study, we describe our genetic analysis of mobile tetQ elements in oral Prevotella species. Our results indicate that the mobile elements encoding tetQ in oral species are distinct from those found in the Bacteroides. The intestinal bacteria may act as a reservoir for the tetQ gene, but Prevotella has incorporated this gene into an IS21-family transposon. This transposon is present in Prevotella species from more than one geographical location, implying that the mechanism of tetQ spread between oral Prevotella species is highly conserved.

Tetracycline resistance genes in activated sludge wastewater treatment plants

The development and proliferation of antibiotic resistance in pathogenic, commensal, and environmental microorganisms is a major public health concern. The extent to which human activities contribute to the maintenance of environmental reservoirs of antibiotic resistance is poorly understood. In the current study, wastewater treatment plants (WWTPs) were investigated as possible sources of tetracycline resistance via qualitative PCR and quantitative PCR (qPCR). Various WWTPs and two freshwater lakes were surveyed for the presence of an array of 10 tetracycline resistance determinants (tet(R)): tet(A)-(E), tet(G), tet(M), tet(O), tet(Q), tet(S). All WWTP samples contained more different types of tet(R) genes, as compared to the lake water samples. Gene copy numbers of tet(G) and tet(Q) in these samples were quantified via qPCR and normalized to both the volume of original sample and to the amount of DNA extracted per sample (a proxy for bacterial abundance). Concentrations of tet(Q) were found to be highest in wastewater influent while tet(G) concentrations were highest in activated sludge. Investigation of the effects of UV disinfection on wastewater effluent showed no reduction in the number of detectable tet(R) gene types.

Tetracycline resistance mediated by tet(W), tet(M), and tet(O) genes of Bifidobacterium isolates from humans

MICs of tetracyclines were determined for 86 human Bifidobacterium isolates and three environmental strains. The tet(O) gene was found to be absent in these isolates. tet(W) and tet(M) were found in 26 and 7%, respectively, of the Bifidobacterium isolates, and one isolate contained both genes. Chromosomal DNA hybridization showed that there was one chromosomal copy of tet(W) and/or tet(M).

Determinants of resistance in Bacteroides fragilis strains according to recent Brazilian profiles of antimicrobial susceptibility

Susceptibility profiles of 99 Bacteroides fragilis strains for 9 antimicrobial agents were defined by using an agar dilution method. The isolates were uniformly susceptible to imipenen and metronidazole. All isolates were resistant to ampicillin. The resistance rates to amoxicillin/clavulanate, cefoxitin, cefotaxime, chloramphenicol, clindamycin and tetracycline were 3.0, 12.1, 15.1, 1.0, 18.2 and 75.7%, respectively. Sixteen strains showed reduced susceptibility to metronidazole (MIC 2-4 mg/L) but none had nim genes using PCR. All strains were also investigated for the presence of cepA, cfiA, cfxA, ermF and tetQ genes by PCR methodology and 92.9, 4.9, 24.2, 2 and 64.6% of the strains were respectively found positive. These results reflect the importance of surveys of susceptibility profiles and the relevance of detecting major genetic determinants to monitor the dissemination of these genes.

Quantitative real-time PCR using TaqMan and SYBR Green for Actinobacillus actinomycetemcomitans, Porphyromonas gingivalis, Prevotella intermedia, tetQ gene and total bacteria

Accurate quantification of bacterial species in dental plaque is needed for microbiological diagnosis of periodontal diseases. The present study was designed to assess the sensitivity, specificity and quantitativity of the real-time PCR using the GeneAmp Sequence Detection System with two fluorescence chemistries. TaqMan probe with reporter and quencher dye, and SYBR Green dye were used for sources of the fluorescence. Primers and probes were designed for Actinobacillus actinomycetemcomitans, Porphyromonas gingivalis, Prevotella intermedia and total bacteria based on the nucleotide sequences of the respective 16S ribosomal RNA genes. Since spread of antibiotic resistance genes is one of the crucial problems in periodontal therapy, quantitative detection of tetQ gene, which confers resistance to tetracycline, was included in the examination. The detection of P. gingivalis, P. intermedia and A. actinomycetemcomitans was linear over a range of 10-10(7) cells (10-10(7) copies for tetQ gene), while the quantitative range for total bacteria was 10(2)-10(7) cells. Species-specific amplifications were observed for the three periodontal bacteria, and there was no significant difference between the TaqMan and SYBR Green chemistry in their specificity, quantitativity and sensitivity. The SYBR Green assay, which was simpler than TaqMan assay in its manipulations, was applied to the clinical plaque samples. The plaque samples were obtained from eight patients (eight periodontal pockets) before and 1 week after the local drug delivery of minocycline. Although the number of P. gingivalis, P. intermedia and A. actinomycetemcomitans markedly decreased after the antibiotic therapy in most cases, higher copy numbers of the tetQ gene were detectable. The real-time PCR demonstrated sufficient sensitivity, specificity and quantitativity to be a powerful tool for microbiological examination in periodontal disease, and the quantitative monitoring of antibiotic resistance gene accompanied with the antibiotic therapy should be included in the examination.

Presence and antibiotic resistance of Porphyromonas gingivalis, Prevotella intermedia, and Prevotella nigrescens in children

BACKGROUND/AIMS

Only limited information exists about the prevalence in children of pathogens associated with periodontitis. The aim of the present study was to determine by culture whether 8-11-year-old children carry Porphyromonas gingivalis, Prevotella intermedia, and/or P. nigrescens in samples from the gingiva and/or the buccal mucosa taken before, and after caries treatment and oral hygiene instruction. A second aim was to assess the proportion of subjects who had gram-negative anaerobes carrying the tet(Q) and erm(F) genes, suggesting antibiotic resistance to tetracycline or erythromycin.

METHOD

A total of 150 children provided gingival and buccal swab bacterial samples that were cultured for P. gingivalis, P. intermedia, and P. nigrescens. The species was verified using DNA-DNA hybridization with species-specific probes made from the variable region of the 16S rRNA sequences. Antibiotic-resistant genes, tet(Q) and erm(F), were identified using specific DNA-DNA hybridization with specific DNA probes.

RESULTS

A total of 116 isolates of black-pigmented bacteria were cultured from 47 (31%) of 150 children. Five isolates were identified as P. gingivalis, 29 as P. intermedia, 33 as P. nigrescens, and 49 as other species. In general, the bacteria were not culturable at more than one time period. We found that 55% of these 47 children harbored black pigmented bacteria that carried either one or both of the two antibiotic-resistant genes studied (tet(Q), and erm(F)).

CONCLUSION

The present study demonstrated that children not exposed to regular dental treatment carry bacteria outside the gingival sulcus that have been associated with periodontitis, and that standard treatment procedures may not clear the presence of the putative pathogens. In addition, antibiotic-resistant genes are common in identifiable gram-negative anaerobes, including putative pathogens.

Distribution of mef(A) in gram-positive bacteria from healthy Portuguese children

We screened 615 gram-positive isolates from 150 healthy children for the presence of the erm(A), erm(B), erm(C), erm(F), and mef(A) genes. The mef(A) genes were found in 20 (9%) of the macrolide-resistant isolates, including Enterococcus spp., Staphylococcus spp., and Streptococcus spp. Sixteen of the 19 gram-positive isolates tested carried the other seven open reading frames (ORFs) described in Tn1207.1, a genetic element carrying mef(A) recently described in Streptococcus pneumoniae. The three Staphylococcus spp. did not carry orf1 to orf3. A gram-negative Acinetobacter junii isolate also carried the other seven ORFs described in Tn1207.1. A Staphylococcus aureus isolate, a Streptococcus intermedius isolate, a Streptococcus sp. isolate, and an Enterococcus sp. isolate had their mef(A) genes completely sequenced and showed 100% identity at the DNA and amino acid levels with the mef(A) gene from S. pneumoniae.

Distribution of erm(F) and tet(Q) genes in 4 oral bacterial species and genotypic variation between resistant and susceptible isolates

BACKGROUND

Bacteroides forsythus, Porphyromonas gingivalis and Prevotella intermedia are Gram-negative anaerobic bacteria that are currently considered potential periopathogens. Prevotella nigrescens has recently been separated from P. intermedia and its rôle in periodontitis is unknown. The erm(F) gene codes for an rRNA methylase, conferring resistance to macrolides, lincosamides and streptogramin B (MLSB), and the tet(Q) gene for a ribosomal protection protein, conferring resistance to tetracycline. The presence of these resistance genes could impair the use of antibiotics for therapy.

PURPOSE

The aim of this study was to determine the carriage of erm(F) and tet(Q), and genetic variability of 12 Porphyromonas gingivalis, 10 Prevotella intermedia, 25 Prevotella nigrescens and 17 Bacteroides forsythus isolates from 9 different patient samples.

METHODS

We used polymerase chain reaction (PCR) for detecting antibiotic resistance genes, and pulsed-field gel electrophoresis (PFGE) for detecting genetic variability among the isolates.

RESULTS

Thirty-one (48%) isolates were resistant to both erythromycin and tetracycline and carried the erm(F) and tet(Q) genes, eight (13%) were tetracycline resistant and carried the tet(Q) gene, 9 (14%) were erythromycin resistant and carried the erm(F) gene, and 12 (19%) isolates did not carry antibiotic resistance genes. PFGE was used to compare isolates from the same patient and isolates from different patient samples digested with XbaI. No association was found between antibiotic resistance gene carriage and PFGE patterns in any species examined. All isolates of the same species from the same patient had highly related or identical PFGE patterns. Isolates of same species from different patients had unique PFGE pattern for each species tested.

CONCLUSION

All isolates of the same species from any one patient were genetically related to each other but distinct from isolates from other patients, and 66% of the patients carried antibiotic resistant isolates, which could impair antibiotic therapy.

Tetracycline antibiotics: mode of action, applications, molecular biology, and epidemiology of bacterial resistance

Tetracyclines were discovered in the 1940s and exhibited activity against a wide range of microorganisms including gram-positive and gram-negative bacteria, chlamydiae, mycoplasmas, rickettsiae, and protozoan parasites. They are inexpensive antibiotics, which have been used extensively in the prophlylaxis and therapy of human and animal infections and also at subtherapeutic levels in animal feed as growth promoters. The first tetracycline-resistant bacterium, Shigella dysenteriae, was isolated in 1953. Tetracycline resistance now occurs in an increasing number of pathogenic, opportunistic, and commensal bacteria. The presence of tetracycline-resistant pathogens limits the use of these agents in treatment of disease. Tetracycline resistance is often due to the acquisition of new genes, which code for energy-dependent efflux of tetracyclines or for a protein that protects bacterial ribosomes from the action of tetracyclines. Many of these genes are associated with mobile plasmids or transposons and can be distinguished from each other using molecular methods including DNA-DNA hybridization with oligonucleotide probes and DNA sequencing. A limited number of bacteria acquire resistance by mutations, which alter the permeability of the outer membrane porins and/or lipopolysaccharides in the outer membrane, change the regulation of innate efflux systems, or alter the 16S rRNA. New tetracycline derivatives are being examined, although their role in treatment is not clear. Changing the use of tetracyclines in human and animal health as well as in food production is needed if we are to continue to use this class of broad-spectrum antimicrobials through the present century.