Okonkwo, Valentine and Cholet, Fabien and Ijaz, Umer Z. and Koottatep, Thammarat and Pussayanavin, Tatchai and Polpraset, Chongrak and Sloan, William T. and Connelly, Stephanie and Smith, Cindy J. (2023) intI1 gene abundance from septic tanks in Thailand using validated intI1 primers. Applied and Environmental Microbiology, 89 (11): e01071-23. ISSN 0099-2240
AI Summary:
The study monitored household and healthcare septic tanks in Thailand using the intI1 gene abundance as a proxy for antimicrobial resistance (AMR). The results showed that intI1 gene abundance was greatest in influent, followed by effluent, and lowest in sludge. The study also found that while septic tanks remove some intI1, they remain a source of AMR to the surrounding environment.AI Topics:
Antimicrobial resistance (AMR) poses a serious global health threat, and wastewater treatment (WWT), including septic tanks, is a source of AMR. In Thailand, antibiotics are unregulated, and septic tanks are commonly used. Yet, their impact on the spread or mitigation of AMR is unknown. We monitored household and healthcare conventional septic tanks (CST) and household solar septic tanks (SST) in Thailand using the class 1 integron-integrase (intI1) gene abundance as a proxy for AMR. A systematic review of the literature found 65 intI1 primers. We evaluated the coverage and specificity of each, including a new MGB TaqMan primer-probe, against clinical and environmental intI1, intI1-like, and non-intI1 databases. The three best primers were selected, laboratory validated for DNA and mRNA quantification, and used to quantify septic tank intI1 gene abundance. No primer set could distinguish between intI1 and intI1-like sequences. While primer choice did not affect gene abundance of the same sample (P-value > 0.05), sometimes when comparing the same samples quantified by different primers, statistical differences were observed for one but not the other primer set. This may lead to different interpretations of AMR risk. Irrespective of primers or reactor type intI1 gene abundance was greatest in influent > effluent > sludge. intI1 gene abundance was lowest in the effluent of the SST-household < CST-household < CST-healthcare. 31% to 42% of intI1 was removed by the CST-household tank, indicating while septic tanks remove some intI1 they remain a source to the surrounding environment. Toward the goal of achieving standardization across studies, we recommend the F3-R3 primer for intI1 quantification.
Okonkwo, Valentine
Author
Okonkwo, Valentine and Cholet, Fabien and Ijaz, Umer Z. and Koottatep, Thammarat and Pussayanavin, Tatchai and Polpraset, Chongrak and Sloan, William T. and Connelly, Stephanie and Smith, Cindy J. (2023) intI1 gene abundance from septic tanks in Thailand using validated intI1 primers. Applied and Environmental Microbiology, 89 (11): e01071-23. ISSN 0099-2240
See full publications listCholet, Fabien
Author
Cholet, Fabien and Vignola, Marta and Quinn, Dominic and Ijaz, Umer Z. and Sloan, William T. and Smith, Cindy J. (2025) Microbial ecology of drinking water biofiltration based on 16S rRNA sequencing: a meta-analysis. Water Research, 281: 123684. ISSN 0043-1354
Cholet, Fabien and Agogué, Hélène and Ijaz, Umer Z. and Lachaussée, Nicolas and Pineau, Philippe and Smith, Cindy J. (2024) Low-abundant but highly transcriptionally active uncharacterised Nitrosomonas drive ammonia-oxidation in the Brouage mudflat, France. Science of the Total Environment, 946: 174312. ISSN 0048-9697
Shi, Xiang and Pereira, Ryan and Uzma and Savage, Laurie and Poursat, Baptiste and Quinn, Dominic and Kostrytsia, Anastasiia and Cholet, Fabien and Smith, Cindy J. and Gauchotte-Lindsay, Caroline and Sloan, William T. and Ijaz, Umer and Vignola, Marta (2024) Microbial stratification and DOM removal in drinking water biofilters: implications for enhanced performance. Water Research, 262: 122053. ISSN 0043-1354
See full publications listIjaz, Umer
Author
Cholet, Fabien and Vignola, Marta and Quinn, Dominic and Ijaz, Umer Z. and Sloan, William T. and Smith, Cindy J. (2025) Microbial ecology of drinking water biofiltration based on 16S rRNA sequencing: a meta-analysis. Water Research, 281: 123684. ISSN 0043-1354
Saleem, Farrukh and Ameer, Aqsa and Afzal, Farhan and Usman, Muhammad and Irshad, Hamid and Sattar, Sadia and Ijaz, Umer Zeeshan and Javed, Sundus (2025) A cross-sectional survey of poultry management systems, practices and antimicrobial use in relation to disease outbreak in Pakistan. BMC Research Notes, 18: 144. ISSN 1756-0500
Badar, Ayesha and Aqueel, Rhea and Nawaz, Ali and Ijaz, Umer Zeeshan and Malik, Kauser Abdulla (2025) Microbiota transplantation for Cotton Leaf Curl Disease suppression - core microbiome and transcriptome dynamics. Communications Biology, 8 (1): 380. ISSN 2399-3642
See full publications listKoottatep, Thammarat
Author
Okonkwo, Valentine and Cholet, Fabien and Ijaz, Umer Z. and Koottatep, Thammarat and Pussayanavin, Tatchai and Polpraset, Chongrak and Sloan, William T. and Connelly, Stephanie and Smith, Cindy J. (2023) intI1 gene abundance from septic tanks in Thailand using validated intI1 primers. Applied and Environmental Microbiology, 89 (11): e01071-23. ISSN 0099-2240
See full publications listPussayanavin, Tatchai
Author
Okonkwo, Valentine and Cholet, Fabien and Ijaz, Umer Z. and Koottatep, Thammarat and Pussayanavin, Tatchai and Polpraset, Chongrak and Sloan, William T. and Connelly, Stephanie and Smith, Cindy J. (2023) intI1 gene abundance from septic tanks in Thailand using validated intI1 primers. Applied and Environmental Microbiology, 89 (11): e01071-23. ISSN 0099-2240
See full publications listPolpraset, Chongrak
Author
Okonkwo, Valentine and Cholet, Fabien and Ijaz, Umer Z. and Koottatep, Thammarat and Pussayanavin, Tatchai and Polpraset, Chongrak and Sloan, William T. and Connelly, Stephanie and Smith, Cindy J. (2023) intI1 gene abundance from septic tanks in Thailand using validated intI1 primers. Applied and Environmental Microbiology, 89 (11): e01071-23. ISSN 0099-2240
See full publications listSloan, William
Author
Cholet, Fabien and Vignola, Marta and Quinn, Dominic and Ijaz, Umer Z. and Sloan, William T. and Smith, Cindy J. (2025) Microbial ecology of drinking water biofiltration based on 16S rRNA sequencing: a meta-analysis. Water Research, 281: 123684. ISSN 0043-1354
Gupta, Rohit and Murray, Cameron and Sloan, William T. and You, Siming (2025) Predicting the methane production of microwave-pretreated anaerobic digestion of food waste: a machine learning approach. Energy. ISSN 0360-5442 (In Press)
Alghafli, Khaled and Shi, Xiaogang and Sloan, William and Ali, Awad M. (2025) Investigating the role of ENSO in groundwater temporal variability across Abu Dhabi Emirate, United Arab Emirates using machine learning algorithms. Groundwater for Sustainable Development, 28: 101389. ISSN 2352-801X
See full publications listConnelly, Stephanie
Author
Okonkwo, Valentine and Cholet, Fabien and Ijaz, Umer Z. and Koottatep, Thammarat and Pussayanavin, Tatchai and Polpraset, Chongrak and Sloan, William T. and Connelly, Stephanie and Smith, Cindy J. (2023) intI1 gene abundance from septic tanks in Thailand using validated intI1 primers. Applied and Environmental Microbiology, 89 (11): e01071-23. ISSN 0099-2240
Vignola, Marta and Lenselink, Jeanine and Quinn, Dominic and Ijaz, Umer Zeeshan and Pereira, Ryan and Sloan, William T. and Connelly, Stephanie and Moore, Graeme and Gauchotte-Lindsay, Caroline and Smith, Cindy J. (2023) Differential utilisation of dissolved organic matter compound fractions by different biofilter microbial communities. AQUA: Water Infrastructure, Ecosystems and Society, 72 (10). pp. 1837-1851. ISSN 2709-8028
See full publications listSmith, Cindy
Author
Cholet, Fabien and Vignola, Marta and Quinn, Dominic and Ijaz, Umer Z. and Sloan, William T. and Smith, Cindy J. (2025) Microbial ecology of drinking water biofiltration based on 16S rRNA sequencing: a meta-analysis. Water Research, 281: 123684. ISSN 0043-1354
Fantinelli Franco, Fabiane and Malik, Muhammad and Manjakkal, Libu and Roshanghias, Ali and Smith, Cindy and Gauchotte-Lindsay, Caroline (2024) Optimising carbon structures in laser-induced graphene electrodes using design of experiments for enhanced electrochemical sensing characteristics. ACS Applied Materials and Interfaces, 16 (47). pp. 65489-65502. ISSN 1944-8244
Fantinelli Franco, Fabiane and Malik, Muhammad Hassan and Manjakkal, Libu and Roshanghias, Ali and Smith, Cindy J. and Gauchotte-Lindsay, Caroline (2024) Optimizing carbon structures in laser-induced graphene electrodes using design of experiments for enhanced electrochemical sensing characteristics. ACS Applied Materials and Interfaces, 16 (47). pp. 65489-65502. ISSN 1944-8244
See full publications listAvailable under License Creative Commons Attribution.
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