Culture-based study on the development of antibiotic resistance in a biological wastewater system treating stepwise increasing doses of streptomycin

Class 1 In-Tn5393c array contributed to antibiotic resistance of non-pathogenic Pseudoxanthomonas mexicana isolated from a wastewater bioreactor treating streptomycin

The emergence of antibiotic resistance in retort to environmental pollutants during wastewater treatment still remains elusive. Here, we first to investigate the emergence of antibiotic resistance in an environmental non-pathogenic bacterium, Pseudoxanthomonas mexicana isolated from a lab-scale bioreactor treating wastewater containing streptomycin. The molecular mechanism of antibiotic resistance development was evaluated in its genomic, transcriptional, and proteomic levels. The streptomycin resistant (SR) strain showed strong resistance to streptomycin (MIC > 600 μg/mL) as well to sulfamethoxazole, ampicillin, and kanamycin (≥250 μg/mL). A 13.4 kb class-1-integron array consisting of a new arrangement of gene cassette (IS6100-sul1-aadA2-catB3-aacA1-2-aadB-int1-IS256-int) linked with Tn5393c transposon was identified in the SR strain, which has only been reported in clinical pathogens so far. iTRAQ-LC-MS/MS proteomics revealed 22 up-regulated proteins in the SR strain growing under 100 mg L^-1 streptomycin, involving antibiotic resistance, toxin production, stress response, and ribosomal protein synthesis. At the mRNA level, elevated expressions of ARGs (strA, strB, and aadB) and 30S-ribosomal protein genes (rpsA and rpsU) were observed in the SR strain. The results highlighted the genomic plasticity and multifaceted regulatory mechanism employed by P. mexicana in adaptation to high-level streptomycin during biological wastewater treatment.

Cross-regional scale pollution of freshwater biofilms unveiled by antibiotic resistance genes

A comprehensive global profile of the distribution of ARGs in freshwater biofilms is lacking. We utilized metagenomic approaches to reveal the diversity, abundance, transferability and hosts of ARGs in 96 freshwater biofilm samples from 38 sampling sites across four countries. The abundant ARGs were associated with bacitracin, multidrug, polymyxin macrolide-lincosamide-streptogramin (MLS) aminoglycoside, β-lactam, chloramphenicol, sulfonamide and tetracycline resistance, consistent with the spectrum of antibiotics commonly used in human or veterinary medicine. As expected, the resistome in freshwater biofilm habitats was significantly influenced by geographical location and human footprint. Based on the co-occurrence pattern revealed by network analysis, mdtC, kdpE, and emrB were proposed as ARG indicators in freshwater biofilms that can be used to evaluate the abundance of 46 other co-occurring ARG subtypes quantitatively. Metagenomic assembly analysis revealed that the identified ARGs were hosted by more than 46 bacterial phyla, including various pathogens, which greatly expands the knowledge of resistome diversity in freshwater biofilms. Our study points to the central roles of biofilms in harbouring ARGs. The results could enhance understanding the distribution of ARGs in freshwater habitats, thereby strengthening the global environmental risk assessment and management of ARGs.

Response of antibiotic resistance to the co-exposure of sulfamethoxazole and copper during swine manure composting

Heavy metals driven co-selection of antibiotic resistance in soil and water bodies has been widely concerned, but the response of antibiotic resistance to co-existence of antibiotics and heavy metals in composting system is still unknown. Commonly used sulfamethoxazole and copper were individually and jointly added into four reactors to explore their effects on antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), heavy metal resistance genes (MRGs) and bacterial community structure. The abundance of total ARGs and MGEs were notably decreased by 68.64%-84.95% and 91.27-97.38%, respectively, after the composting. Individual addition of sulfamethoxazole, individual addition of copper, simultaneously addition of sulfamethoxazole and copper increased the abundance of ARGs and MGEs throughout the composting period. Co-exposure of sulfamethoxazole and copper elevated the total abundance of ARGs by 1.17-1.51 times by the end of the composting compared to individual addition of sulfamethoxazole or copper. Network analysis indicated that the shifts in potential host bacteria determined the ARGs variation. Additionally, MGEs and MRGs had significant effects on ARGs, revealing that horizontal gene transfer and heavy metals induced co-resistance could promote ARGs dissemination.

Lipopeptide production by Serratia marcescens SmSA using a Taguchi design and its application in enhanced heavy oil recovery

Biosurfactant production at reactor level by Serratia marcescens SmSA was optimized and evaluated to enhance the heavy oil recovery on carbonate rocks. Temperature, agitation, and carbon/nitrogen (C/N) ratio were evaluated to optimize biosurfactant production by using a Taguchi (L9) design. The best conditions (C/N ratio: 6, 25 °C, and agitation: 100 rpm) were used to scale up the biosurfactant production with a 3-L bioreactor. The best aeration for biosurfactant production was 0.66 volume of air per volume of liquid per minute (vvm), producing the lowest surface tension (26 mN/m) in 14 h, with a biosurfactant yield of 14.26 g/L as a crude product and 2.85 g/L as a purified product, and a critical micelle concentration of 280 mg/L. The biosurfactant was characterized as a lipopeptide, and it was stable under extreme conditions: pH (2-12), salinity up to 200 g/L, and temperature up to 150 °C confirmed by thermogravimetric analysis. Enhanced oil recovery test was carried out with a carbonate core and heavy oil under reservoir conditions, obtaining an additional recovery of 8%, due to reduced interfacial tension and modified wettability of the rock. These findings highlight the potential application of S. marcescens SmSA biosurfactant in enhanced oil recovery.

Dynamics of class 1 integrons in aerobic biofilm reactors spiked with antibiotics

Class 1 integrons are strongly associated with the dissemination of antibiotic resistance in bacteria. However, little is known about whether the presence of antibiotics affects the abundance of integrons and antibiotic resistance genes during biological wastewater treatment. To explore the roles of class 1 integrons in spreading antibiotic resistance genes in environmental compartments, the dynamics of integrons were followed in biofilm reactors treating synthetic wastewater respectively spiked with streptomycin (STM) and oxytetracycline (OTC). The relative abundance of the integron-integrase gene (intI1) increased 12 or 29-fold respectively when treated with STM or OTC, under incrementally increasing dosage regimes from 0 to 50 mg L^-1. Significant increases in intI1 abundance initially occurred at an antibiotic dose of 0.1 mg L^-1. At the beginning of the experiment, 51% to 64% of integrons carried no gene cassettes. In STM and OTC spiked systems, there was a significant increase in the proportion of integrons that contained resistance gene cassettes, particularly at intermediate and higher antibiotic concentrations. Gene cassettes encoding resistance to aminoglycosides, trimethoprim, beta-lactam, erythromycin, and quaternary ammonium compounds were all detected in the treated systems. Three tetracycline resistance genes (tetA, tetC, tetG) were significantly correlated with the abundance of intI1 (p < 0.01), despite no tet resistance being present as a gene cassette. Genome sequencing of isolates showed synteny between the tet resistance genes and intI1, mediated through linkage to transposable elements including Tn3, IS26 and ISCR3. Class 1 integrons appeared to be under positive selection in the presence of antibiotics, and might have actively acquired new gene cassettes during the experiment.

Novel Transposon Tn6433 Variants Accelerate the Dissemination of tet(E) in Aeromonas in an Aerobic Biofilm Reactor under Oxytetracycline Stresses

Little is known about the mechanisms that disseminate antibiotic resistance genes (ARGs) in wastewater microbial communities under antibiotic stress. The role of horizontal transfer mechanisms in dissemination of ARGs in an aerobic biofilm reactor under incremental oxytetracycline doses from 0 to 50 mg/L was studied. Aeromonas strains were the most common culturable bacteria in the reactor, with tet(E) as the most prevalent ARGs (73.3%) being possibly responsible for the oxytetracycline resistance phenotype. Genomic sequencing demonstrated that tet(E) was mainly carried by a Tn3 family transposon named Tn6433, whose incidence increased from 14.6% to 75.0% across the treatments. Tn6433 carrying tet(E) was initially detected in Aeromonas chromosomes at an oxytetracycline dose of 1 mg/L but subsequently detected on plasmids pAeca1-a variants (pAeca1-a, pAeca1-b, and pAeme6) and pAeca2 under higher oxytetracycline stress. The core region of the Tn6433-tet(E) structure was highly conserved, consisting of a transposition and resolution module, a class 1 integron, core passenger genes, and a Tn1722/Tn501-like transposon. Such a structure was found on both the chromosome and plasmids, suggesting that Tn6433 mediated the transposition of tet(E) from the chromosome to plasmid pAeca2 under increasing stresses. Bacteria carrying the transferable plasmid pAeca1-a were dominant in high antibiotic treatments, suggesting that Tn6433 disseminated tet(E), conferring selective advantages to recipients of this ARG.

Metagenomic and metatranscriptomic analyses reveal activity and hosts of antibiotic resistance genes in activated sludge

Wastewater treatment plants (WWTPs) are a source and reservoir for subsequent spread of various antibiotic resistance genes (ARGs). However, little is known about the activity and hosts of ARGs in WWTPs. Here, we utilized both metagenomic and metatranscriptomic approaches to comprehensively reveal the diversity, abundance, expression and hosts of ARGs in activated sludge (AS) from three conventional WWTPs in Taiwan. Based on deep sequencing data and a custom-made ARG database, a total of 360 ARGs associated with 24 classes of antibiotics were identified from the three AS metagenomes, with an abundance range of 7.06 × 10^-1-1.20 × 10^-4 copies of ARG/copy of 16S rRNA gene. Differential coverage binning analysis revealed that >22 bacterial phyla were the putative hosts of the identified ARGs. Surprisingly, genus Mycobacterium and family Burkholderiaceae were observed as multi-drug resistant harboring 14 and 50 ARGs. Metatranscriptome analysis showed 65.8% of the identified ARGs were being expressed, highlighting that ARGs were not only present, but also transcriptionally active in AS. Remarkably, 110 identified ARGs were annotated as plasmid-associated and displayed a close to two-fold increased likelihood of being transcriptionally expressed compared to those ARGs found exclusively within bacterial chromosomes. Further analysis showed the transcript abundance of aminoglycoside, sulfonamide, and tetracycline resistance genes was mainly contributed by plasmid-borne ARGs. Our approach allowed us to specifically link ARGs to their transcripts and genetic context, providing a comprehensive insight into the prevalence, expression and hosts of ARGs in AS. Overall, results of this study enhance our understanding of the distribution and dissemination of ARGs in WWTPs, which benefits environmental risk assessment and management of ARB and ARGs.

Thermophilic anaerobic digestion reduces ARGs in excess sludge even under high oxytetracycline concentrations

The feasibility of thermophilic anaerobic digestion (AD) for the attenuation of antibiotic resistance genes (ARGs) in biomass wastes under high antibiotic concentrations remains unclear. In this study, a thermophilic completely stirred digester (55 °C) was fed with municipal excess sludge spiked with increasing concentrations of oxytetracycline (OTC) (0-1000 mg/L) over a period of 280 days. Results showed that thermophilic AD could maintain stable methane production (338.40 ± 26.26 mL/d/gVS) even at an OTC dose of 1000 mg/L with the sludge phase OTC concentration reaching around 24,000 mg/kg. More important, the abundance of resistome detected by high-throughput quantitative PCR in the substrate was reduced (p < 0.01) by 55.54%-86.27% by thermophilic AD over the whole period. Partial canonical correspondence and network analyses showed that the reduction of ARGs was achieved mainly through two ways: eliminating the original hosts of ARGs in the substrate (from 41.74% ± 2.60% in the substrate to 12.08% ± 1.02% in digested sludge), and blocking the horizontal proliferation of ARGs in the digested sludge by reducing the abundance of mobile genetic elements and restricting their horizontal exchange within a small number of thermophilic genera. This study showed that thermophilic AD is feasible for the attenuation of ARGs in biomass even containing high level of OTC.

Genome Sequencing and Comparative Analysis of Stenotrophomonas acidaminiphila Reveal Evolutionary Insights Into Sulfamethoxazole Resistance

Stenotrophomonas acidaminiphila is an aerobic, glucose non-fermentative, Gram-negative bacterium that been isolated from various environmental sources, particularly aquatic ecosystems. Although resistance to multiple antimicrobial agents has been reported in S. acidaminiphila, the mechanisms are largely unknown. Here, for the first time, we report the complete genome and antimicrobial resistome analysis of a clinical isolate S. acidaminiphila SUNEO which is resistant to sulfamethoxazole. Comparative analysis among closely related strains identified common and strain-specific genes. In particular, comparison with a sulfamethoxazole-sensitive strain identified a mutation within the sulfonamide-binding site of folP in SUNEO, which may reduce the binding affinity of sulfamethoxazole. Selection pressure analysis indicated folP in SUNEO is under purifying selection, which may be owing to long-term administration of sulfonamide against Stenotrophomonas.