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Perez-Zabaleta, MarielORCID iD iconorcid.org/0000-0003-3873-4977
Publications (10 of 20) Show all publications
Soares, R. R. .., Varg, J. E., Szabó, A., Kluge, M., Petrini, F., Psallida, M., . . . Székely, A. J. (2025). Hyperplex PCR enables highly multiplexed analysis of point mutations in wastewater: Long-term SARS-CoV-2 variant surveillance in Sweden as a case study. Water Research, 274, Article ID 123154.
Open this publication in new window or tab >>Hyperplex PCR enables highly multiplexed analysis of point mutations in wastewater: Long-term SARS-CoV-2 variant surveillance in Sweden as a case study
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2025 (English)In: Water Research, ISSN 0043-1354, E-ISSN 1879-2448, Vol. 274, article id 123154Article in journal (Refereed) Published
Abstract [en]

Wastewater-based surveillance (WBS) allows the analysis of pathogens, chemicals or other biomarkers in wastewater to derive unbiased epidemiological information at population scale. After re-gaining attention during the SARS-CoV-2 pandemic, the field holds promise as a surveillance and early warning system by tracking emerging pathogens with pandemic potential. Expanding the current toolbox of analytical techniques for wastewater analysis, we explored the use of Hyperplex PCR (hpPCR) to analyse SARS-CoV-2 mutations in wastewater samples collected weekly in up to 22 sites across Sweden between October 2022 and December 2023. The samples were tested using a probe panel ranging from 10- to 18-plex, continuously adapted within 1–2 weeks to quantify relevant mutations of concern over time. For cross-validation, the samples were simultaneously analysed with commonly used methods including quantitative PCR (qPCR) and next-generation sequencing (NGS). hpPCR is demonstrated herein to provide (1) systematic single nucleotide specificity with a straightforward probe design, (2) high multiplexity with minimal panel re-optimization requirements and (3) 4–5-week earlier mutation detection relative to NGS with comparable performance of mutation frequency quantification (Pearson r = 0.88, n = 50). Hence, hpPCR is shown to be a powerful complementary tool to the current workflow involving NGS and qPCR by facilitating the assembly of dynamic high-plex panels compatible with high-frequency monitoring of multiple key pathogens and/or variants in WBS.

Place, publisher, year, edition, pages
Elsevier BV, 2025
Keywords
hpPCR, Monitoring, Mutations, Padlock probes, Rolling circle amplification, Wastewater-based surveillance
National Category
Microbiology
Identifiers
urn:nbn:se:kth:diva-359299 (URN)10.1016/j.watres.2025.123154 (DOI)001414049700001 ()39847906 (PubMedID)2-s2.0-85215436690 (Scopus ID)
Note

QC 20250217

Available from: 2025-01-29 Created: 2025-01-29 Last updated: 2025-05-27Bibliographically approved
Perez Zabaleta, M., Berg, C., Latorre-Margalef, N., Owusu-Agyeman, I., Kiyar, A., Botnen, H., . . . Cetecioglu, Z. (2025). Wastewater surveillance of SARS-CoV-2 from aircraft to citywide monitoring. Nature Communications, 16(1), Article ID 5125.
Open this publication in new window or tab >>Wastewater surveillance of SARS-CoV-2 from aircraft to citywide monitoring
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2025 (English)In: Nature Communications, E-ISSN 2041-1723, Vol. 16, no 1, article id 5125Article in journal (Refereed) Published
Abstract [en]

Wastewater monitoring is highly efficient in SARS-CoV-2 surveillance for tracking virus spread through travel, surpassing traditional airport passenger testing. This study explored the links between SARS-CoV-2 contents and variants from aircraft to city, assessing the impact of detected variants from international travellers versus the local population. A total of 969 variants using next-generation sequencing (NGS) were examined to understand the links between—aircraft, Arlanda airport, wastewater treatment plants (WWTPs), and Stockholm city—and compared these to variants detected in Stockholm hospitals from January to May 2023. SARS-CoV-2 contents in WWTPs reflected local infection rates, requiring analysis from multiple plants for an accurate city-wide infection assessment. Variants initially detected in aircraft arriving from China did not spread widely during the study period. RT-qPCR is adequate for the detection of specific variants in wastewater, including Variants Under Monitoring. However, NGS remains a powerful method for identifying novel variants. Wastewater monitoring was more effective than clinical testing in the early detection of specific variants, with notable delays observed in clinical surveillance. Furthermore, a broad range of variants are detected in wastewater that surpasses clinical tests. This underscores the vital role of wastewater-based epidemiology in managing future outbreaks and enhancing global health security.

Place, publisher, year, edition, pages
Springer Nature, 2025
National Category
Infectious Medicine Other Industrial Biotechnology
Identifiers
urn:nbn:se:kth:diva-364432 (URN)10.1038/s41467-025-60490-1 (DOI)40456842 (PubMedID)2-s2.0-105007158676 (Scopus ID)
Note

QC 20250613

Available from: 2025-06-12 Created: 2025-06-12 Last updated: 2025-06-13Bibliographically approved
Perez-Zabaleta, M., Williams, C. & Cetecioglu, Z. (2024). Development and implementation of assays to monitor human adenovirus F40/41 in wastewater: Trends preceding, during, and following the non-A-to-E hepatitis outbreak in Stockholm. Environment International, 190, Article ID 108937.
Open this publication in new window or tab >>Development and implementation of assays to monitor human adenovirus F40/41 in wastewater: Trends preceding, during, and following the non-A-to-E hepatitis outbreak in Stockholm
2024 (English)In: Environment International, ISSN 0160-4120, E-ISSN 1873-6750, Vol. 190, article id 108937Article in journal (Refereed) Published
Abstract [en]

Human adenovirus (HAdV) type F41 has been identified as a possible cause of the non-A-to-E hepatitis outbreak. This study uses wastewater monitoring to track HAdV F40 and F41, supporting clinical investigations and providing insights into the pathogen's role in the outbreak. Given the limited clinical monitoring in Sweden of HAdV-F40/41, this approach also helps estimate the true infection burden of this pathogen during the outbreak. This study developed three qPCR assays for the hexon, penton, and fiber genes of HAdV F40 and F41. The hexon assay was F41-specific, while the fiber assay detected multiple HAdV-F strains. Comprehensive monitoring of HAdV-F40/41 levels in Stockholm's wastewater was conducted over 1.5 years, capturing the period before, during, and after the outbreak. A significant infection wave was observed in spring 2022, with strains beyond lineage 2 contributing to the outbreak. Moreover, simultaneous SARS-CoV-2 surveillance revealed that HAdV-F infections peaked at different times from COVID-19, but the HAdV-F wave aligned with the relaxation of pandemic restrictions. These findings offer valuable insights for future HAdV-F investigations and confirm its role in the non-A-to-E hepatitis outbreak.

Place, publisher, year, edition, pages
Elsevier BV, 2024
Keywords
Human adenovirus F41, Human adenovirus F40, Wastewater-based epidemiology, non-A-to-E hepatitis
National Category
Microbiology in the medical area
Identifiers
urn:nbn:se:kth:diva-352588 (URN)10.1016/j.envint.2024.108937 (DOI)001293302500001 ()39126729 (PubMedID)2-s2.0-85200820269 (Scopus ID)
Note

QC 20240903

Available from: 2024-09-03 Created: 2024-09-03 Last updated: 2024-09-03Bibliographically approved
Wilson, G. J. L., Perez-Zabaleta, M., Owusu-Agyeman, I., Kumar, A., Ghosh, A., Polya, D. A., . . . Richards, L. A. (2024). Discovery of sulfonamide resistance genes in deep groundwater below Patna, India. Environmental Pollution, 356, Article ID 124205.
Open this publication in new window or tab >>Discovery of sulfonamide resistance genes in deep groundwater below Patna, India
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2024 (English)In: Environmental Pollution, ISSN 0269-7491, E-ISSN 1873-6424, Vol. 356, article id 124205Article in journal (Refereed) Published
Abstract [en]

Global usage of pharmaceuticals has led to the proliferation of bacteria that are resistant to antimicrobial treatments, creating a substantial public health challenge. Here, we investigate the emergence of sulfonamide resistance genes in groundwater and surface water in Patna, a rapidly developing city in Bihar, India. We report the first quantification of three sulfonamide resistance genes (sulI, sulII and sulIII) in groundwater (12-107 m in depth) in India. The mean relative abundance of gene copies was found to be sulI (2.4 x 10(-2) copies/16S rRNA gene) > sulII (5.4 x 10(-3) copies/16S rRNA gene) > sulIII (2.4 x 10(-3) copies/16S rRNA gene) in groundwater (n = 15) and surface water (n = 3). A comparison between antimicrobial resistance (AMR) genes and wastewater indicators, particularly tryptophan:fulvic-like fluorescence, suggests that wastewater was associated with AMR gene prevalence. Urban drainage channels, containing hospital and domestic wastes, are likely a substantial source of antimicrobial resistance in groundwater and surface water, including the Ganges (Ganga) River. This study is a reference point for decision-makers in the fight against antimicrobial resistance because it quantifies and determines potential sources of AMR genes in Indian groundwater.

Place, publisher, year, edition, pages
Elsevier BV, 2024
Keywords
Antimicrobial resistance genes, Sulfonamides, Water contamination, Rapidly developing city, Wastewater
National Category
Microbiology
Identifiers
urn:nbn:se:kth:diva-350157 (URN)10.1016/j.envpol.2024.124205 (DOI)001254953900001 ()38797351 (PubMedID)2-s2.0-85194577782 (Scopus ID)
Note

QC 20240723

Available from: 2024-07-23 Created: 2024-07-23 Last updated: 2024-07-23Bibliographically approved
Owusu-Agyeman, I., Perez-Zabaleta, M. & Cetecioglu, Z. (2024). The fate of severe acute respiratory syndrome coronavirus-2 and pepper mild mottle virus at various stages of wastewater treatment process. Ecotoxicology and Environmental Safety, 285, Article ID 117097.
Open this publication in new window or tab >>The fate of severe acute respiratory syndrome coronavirus-2 and pepper mild mottle virus at various stages of wastewater treatment process
2024 (English)In: Ecotoxicology and Environmental Safety, ISSN 0147-6513, E-ISSN 1090-2414, Vol. 285, article id 117097Article in journal (Refereed) Published
Abstract [en]

This study investigated the efficiency of the treatment processes of wastewater treatment plants (WWTPs) to remove severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and pepper mild mottle virus (PMMoV) from the wastewater and sewage sludge, as well as the influence of the mode of operation on the quality of the treated wastewater. SARS-CoV-2 and PMMoV were detected and quantified at different stages of the wastewater and sludge treatment process of three major WWTPs in Stockholm, Sweden. The results showed that primary, biological, and advanced membrane treatment processes are effective in removing SARS-CoV-2 from the wastewater with removal efficiencies of 99–100 % for all WWTPs, while the virus was accumulated in the primary and waste-activated sludges due to higher affinity to biosolids. Operation strategies such as bypass reintroduced the virus into the treated wastewater. The WWTPs achieved relatively low PMMoV removal efficiencies (63–87 %) most probably due to the robust capsid structure of the virus. Anaerobic digestion could not completely remove SARS-CoV-2 and PMMoV from the sludge leading to increased levels of SARS-CoV-2 and PMMoV in dewatered sludge. The study gives an overview of WWTPs’ role in tackling pathogen spread in society in the event of a pandemic and disease breakout.

Place, publisher, year, edition, pages
Elsevier BV, 2024
Keywords
Pepper mild mottle virus, Removal efficiency, Severe Acute Respiratory Syndrome Coronavirus 2, Sludge, Wastewater
National Category
Water Treatment
Identifiers
urn:nbn:se:kth:diva-354275 (URN)10.1016/j.ecoenv.2024.117097 (DOI)001327222800001 ()39332205 (PubMedID)2-s2.0-85204897820 (Scopus ID)
Note

QC 20241023

Available from: 2024-10-02 Created: 2024-10-02 Last updated: 2025-02-10Bibliographically approved
Owusu-Agyeman, I., Plaza, E., Elginoz, N., Atasoy, M., Khatami, K., Perez-Zabaleta, M., . . . Cetecioglu, Z. (2023). Conceptual system for sustainable and next-generation wastewater resource recovery facilities. Science of the Total Environment, 885, 163758, Article ID 163758.
Open this publication in new window or tab >>Conceptual system for sustainable and next-generation wastewater resource recovery facilities
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2023 (English)In: Science of the Total Environment, ISSN 0048-9697, E-ISSN 1879-1026, Vol. 885, p. 163758-, article id 163758Article in journal (Refereed) Published
Abstract [en]

Shifting the concept of municipal wastewater treatment to recover resources is one of the key factors contributing to a sustainable society. A novel concept based on research is proposed to recover four main bio-based products from mu-nicipal wastewater while reaching the necessary regulatory standards. The main resource recovery units of the pro-posed system include upflow anaerobic sludge blanket reactor for the recovery of biogas (as product 1) from mainstream municipal wastewater after primary sedimentation. Sewage sludge is co-fermented with external organic waste such as food waste for volatile fatty acids (VFAs) production as precursors for other bio-based production. A por-tion of the VFA mixture (product 2) is used as carbon sources in the denitrification step of the nitrification/denitrifica-ti on process as an alternative for nitrogen removal. The other alternative for nitrogen removal is the partial nitrification/anammx process. The VFA mixture is separated with nanofiltration/reverse osmosis membrane technol-ogy into low-carbon VFAs and high-carbon VFAs. Polyhydroxyalkanoate (as product 3) is produced from the low -carbon VFAs. Using membrane contactor-based processes and ion-exchange techniques, high-carbon VFAs are recovered as one-type VFA (pure VFA) and in ester forms (product 4). The nutrient-rich fermented and dewatered bio-solid is applied as a fertilizer. The proposed units are seen as individual resource recovery systems as well as a concept of an integrated system. A qualitative environmental assessment of the proposed resource recovery units confirms the positive environmental impacts of the proposed system.

Place, publisher, year, edition, pages
Elsevier BV, 2023
Keywords
Resource recovery, Biogas, Volatile fatty acids, Bioplastics, Environmental sustainability
National Category
Industrial Biotechnology Oceanography, Hydrology and Water Resources
Identifiers
urn:nbn:se:kth:diva-330531 (URN)10.1016/j.scitotenv.2023.163758 (DOI)001003742800001 ()37120021 (PubMedID)2-s2.0-85156256927 (Scopus ID)
Note

QC 20230630

Available from: 2023-06-30 Created: 2023-06-30 Last updated: 2023-06-30Bibliographically approved
Perez-Zabaleta, M., Archer, A., Khatami, K., Jafferali, M. H., Nandy, P., Atasoy, M., . . . Cetecioglu, Z. (2023). Long-term SARS-CoV-2 surveillance in the wastewater of Stockholm: What lessons can be learned from the Swedish perspective?. Science of the Total Environment, 858, Article ID 160023.
Open this publication in new window or tab >>Long-term SARS-CoV-2 surveillance in the wastewater of Stockholm: What lessons can be learned from the Swedish perspective?
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2023 (English)In: Science of the Total Environment, ISSN 0048-9697, E-ISSN 1879-1026, Vol. 858, article id 160023Article in journal (Refereed) Published
Abstract [en]

Wastewater-based epidemiology (WBE) can be used to track the spread of SARS-CoV-2 in a population. This study pre-sents the learning outcomes from over two-year long monitoring of SARS-CoV-2 in Stockholm, Sweden. The three main wastewater treatment plants in Stockholm, with a total of six inlets, were monitored from April 2020 until June 2022 (in total 600 samples). This spans five major SARS-CoV-2 waves, where WBE data provided early warning signals for each wave. Further, the measured SARS-CoV-2 content in the wastewater correlated significantly with the level of positive COVID-19 tests (r = 0.86; p << 0.0001) measured by widespread testing of the population. Moreover, as a proof-of-concept, six SARS-CoV-2 variants of concern were monitored using hpPCR assay, demonstrating that var-iants can be traced through wastewater monitoring.During this long-term surveillance, two sampling protocols, two RNA concentration/extraction methods, two calcula-tion approaches, and normalization to the RNA virus Pepper mild mottle virus (PMMoV) were evaluated. In addition, a study of storage conditions was performed, demonstrating that the decay of viral RNA was significantly reduced upon the addition of glycerol to the wastewater before storage at -80 degrees C. Our results provide valuable information that can facilitate the incorporation of WBE as a prediction tool for possible future outbreaks of SARS-CoV-2 and preparations for future pandemics.

Place, publisher, year, edition, pages
Elsevier BV, 2023
Keywords
Severe acute respiratory syndrome coronavirus 2, (SARS-CoV-2), COVID-19, Wastewater-based epidemiology (WBE), Storage conditions, Sewage surveillance, hpPCR
National Category
Infectious Medicine
Identifiers
urn:nbn:se:kth:diva-323417 (URN)10.1016/j.scitotenv.2022.160023 (DOI)000905229500012 ()36356735 (PubMedID)2-s2.0-85141913926 (Scopus ID)
Note

QC 20230201

Available from: 2023-02-01 Created: 2023-02-01 Last updated: 2023-02-01Bibliographically approved
Khatami, K., Perez-Zabaleta, M. & Cetecioglu, Z. (2022). Pure cultures for synthetic culture development: Next level municipal waste treatment for polyhydroxyalkanoates production. Journal of Environmental Management, 305, 114337-114337, Article ID 114337.
Open this publication in new window or tab >>Pure cultures for synthetic culture development: Next level municipal waste treatment for polyhydroxyalkanoates production
2022 (English)In: Journal of Environmental Management, ISSN 0301-4797, E-ISSN 1095-8630, Vol. 305, p. 114337-114337, article id 114337Article in journal (Refereed) Published
Abstract [en]

Polyhydroxyalkanoates (PHAs), as bio-based plastics, promise a transition from petroleum products to green and sustainable alternatives. However, their commercial production is yet impeded by high production costs. In this study, we assessed synthetic culture in mono and co-culture modes for bacterial PHA production. It was demonstrated that volatile fatty acids (VFAs) derived from food waste and primary sludge are cheap carbon sources for maintaining high production yields in the synthetic cultures. The maximum obtained PHA was 77.54 ± 5.67% of cell dried weight (CDW) (1.723 g/L) from Cupriavidus necator and 54.9 ± 3.66% of CDW (1.088 g/L) from Burkholderia cepacia. The acquired results are comparable to those in literature using sugar substrates. Comparatively, lower PHA productions were obtained from the co-cultivations ranging between 36-45 CDW% (0.39–0.48 g/L). Meanwhile, the 3-hydroxyvalerate content in the biopolymers were increased up to 21%.

Place, publisher, year, edition, pages
Elsevier BV, 2022
National Category
Other Environmental Biotechnology
Identifiers
urn:nbn:se:kth:diva-306797 (URN)10.1016/j.jenvman.2021.114337 (DOI)000741737800004 ()34972045 (PubMedID)2-s2.0-85122106177 (Scopus ID)
Note

QC 20220131

Available from: 2021-12-29 Created: 2021-12-29 Last updated: 2023-09-13Bibliographically approved
Perez-Zabaleta, M., Atasoy, M., Khatami, K., Eriksson, E. & Cetecioglu, Z. (2021). Bio-based conversion of volatile fatty acids from waste streams to polyhydroxyalkanoates using mixed microbial cultures. Bioresource Technology, 323, Article ID 124604.
Open this publication in new window or tab >>Bio-based conversion of volatile fatty acids from waste streams to polyhydroxyalkanoates using mixed microbial cultures
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2021 (English)In: Bioresource Technology, ISSN 0960-8524, E-ISSN 1873-2976, Vol. 323, article id 124604Article in journal (Refereed) Published
Abstract [en]

Production of polyhydroxyalkanoates is an important field in the biorefinery as bio-alternative to conventional plastics. However, its commercialization is still limited by high production cost. In this study, a process with the potential to reduce the production cost of polyhydroxyalkanoates was proposed. Mixed cultures accumulated polyhydroxyalkanoates using volatile fatty acid-rich effluents from waste streams, without pH and temperature control. In addition, the impact of two types of carbon sources was investigated by analyzing the microbial community as well as the polyhydroxyalkanoate accumulation capacity. Mixed cultures successfully adapted to different substrates, consuming the volatile fatty acids in their totality. The phyla Proteobacteria, Bacteroidetes and Firmicutes dominated the bacterial community. The highest polyhydroxyalkanoate content was 43.5% w/w, which is comparable to contents reported from mixed cultures using synthetic carbon sources. The biopolymer consisted of (R)-3-hydroxybutyrate 94.8 ± 1.7% w/w and (R)-3-hydroxyvaletare 5.2 ± 1.7% w/w.

Place, publisher, year, edition, pages
Elsevier, 2021
National Category
Bioprocess Technology
Identifiers
urn:nbn:se:kth:diva-288163 (URN)10.1016/j.biortech.2020.124604 (DOI)000614252300012 ()33387708 (PubMedID)2-s2.0-85098731136 (Scopus ID)
Note

QC 20210331

Available from: 2020-12-30 Created: 2020-12-30 Last updated: 2022-06-25Bibliographically approved
Khatami, K., Perez-Zabaleta, M., Owusu-Agyeman, I. & Cetecioglu, Z. (2021). Waste to bioplastics: How close are we to sustainable polyhydroxyalkanoates production?. Journal of Waste Management, 119, 374-388
Open this publication in new window or tab >>Waste to bioplastics: How close are we to sustainable polyhydroxyalkanoates production?
2021 (English)In: Journal of Waste Management, ISSN 2356-7724, E-ISSN 2314-6052, Vol. 119, p. 374-388Article in journal (Refereed) Published
Abstract [en]

Increased awareness of environmental sustainability with associated strict environmental regulations has incentivized the pursuit of novel materials to replace conventional petroleum-derived plastics. Polyhydroxyalkanoates (PHAs) are appealing intracellular biopolymers and have drawn significant attention as a viable alternative to petrochemical based plastics not only due to their comparable physiochemical properties but also, their outstanding characteristics such as biodegradability and biocompatibility. This review provides a comprehensive overview of the recent developments on the involved PHA producer microorganisms, production process from different waste streams by both pure and mixed microbial cultures (MMCs). Bio-based PHA production, particularly using cheap carbon sources with MMCs, is getting more attention. The main bottlenecks are the low production yield and the inconsistency of the biopolymers. Bioaugmentation and metabolic engineering together with cost effective downstream processing are promising approaches to overcome the hurdles of commercial PHA production from waste streams.

Place, publisher, year, edition, pages
Elsevier BV, 2021
Keywords
PolyhydroxyalkanoatesWaste streamsBioproductionMetabolic engineeringBioaugmentation
National Category
Environmental Management
Research subject
Chemical Engineering
Identifiers
urn:nbn:se:kth:diva-287567 (URN)10.1016/j.wasman.2020.10.008 (DOI)000599766200036 ()33139190 (PubMedID)2-s2.0-85094816822 (Scopus ID)
Note

QC 20201216

Available from: 2020-12-15 Created: 2020-12-15 Last updated: 2025-02-10Bibliographically approved
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ORCID iD: ORCID iD iconorcid.org/0000-0003-3873-4977

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