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Ballesté E, Pascual-Benito M, Martín-Díaz J, Blanch AR, Lucena F, Muniesa M, Jofre J, García-Aljaro C. Dynamics of crAssphage as a human source tracking marker in potentially faecally polluted environments. WATER RESEARCH 2019; 155:233-244. [PMID: 30851594 DOI: 10.1016/j.watres.2019.02.042] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 02/18/2019] [Accepted: 02/19/2019] [Indexed: 05/26/2023]
Abstract
Recent studies have shown that crAssphage is abundant in human faecal samples worldwide. It has thus been postulated as a potential microbial source tracking (MST) marker to detect human faecal pollution in water. However, an effective implementation of crAssphage in water management strategies will depend on an understanding of its environmental dynamics. In this work, the abundance and temporal distribution of crAssphage was analysed in the effluent of wastewater treatment plants using different sewage treatments, and in two rivers (water and sediments) that differ in pollution impact and flow regime. Additionally, the influence of environmental conditions (temperature and rainfall) on the removal of the marker was studied along a river section, and natural inactivation was assessed by a mesocosms approach. Molecular and culture-based tools were used to compare crAssphage abundance and dynamics with those of bacteria and bacteriophages currently applied as global indicators (E. coli, somatic coliphages, Bacteroides GA17 bacteriophages, and the human-associated MST markers HF183 and HMBif). CrAssphage concentrations in sewage effluent and river samples were similar to those of HF183 and HMBif and higher than other general and/or culture-based indicators (by 2-3 orders of magnitude). Measurement of crAssphage abundance revealed no temporal variability in the effluent, although rainfall events affected the dynamics, possibly through the mobilisation of sediments, where the marker was detected in high concentrations, and an increase in diffuse and point pollution. Another factor affecting crAssphage inactivation was temperature. Its persistence was longer compared with other bacterial markers analysed by qPCR but lower than culturable markers. The results of this study support the use of crAssphage as a human source tracking marker of faecal pollution in water, since it has similar abundances to other molecular human MST markers, yet with a longer persistence in the environment. Nevertheless, its use in combination with infectious bacteriophages is probably advisable.
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Affiliation(s)
- E Ballesté
- Department of Genetics, Microbiology and Statistics, Microbiology Section, Faculty of Biology, University of Barcelona, Diagonal 643, E-08028, Barcelona, Spain.
| | - M Pascual-Benito
- Department of Genetics, Microbiology and Statistics, Microbiology Section, Faculty of Biology, University of Barcelona, Diagonal 643, E-08028, Barcelona, Spain
| | - J Martín-Díaz
- Department of Genetics, Microbiology and Statistics, Microbiology Section, Faculty of Biology, University of Barcelona, Diagonal 643, E-08028, Barcelona, Spain
| | - A R Blanch
- Department of Genetics, Microbiology and Statistics, Microbiology Section, Faculty of Biology, University of Barcelona, Diagonal 643, E-08028, Barcelona, Spain
| | - F Lucena
- Department of Genetics, Microbiology and Statistics, Microbiology Section, Faculty of Biology, University of Barcelona, Diagonal 643, E-08028, Barcelona, Spain
| | - M Muniesa
- Department of Genetics, Microbiology and Statistics, Microbiology Section, Faculty of Biology, University of Barcelona, Diagonal 643, E-08028, Barcelona, Spain
| | - J Jofre
- Department of Genetics, Microbiology and Statistics, Microbiology Section, Faculty of Biology, University of Barcelona, Diagonal 643, E-08028, Barcelona, Spain
| | - C García-Aljaro
- Department of Genetics, Microbiology and Statistics, Microbiology Section, Faculty of Biology, University of Barcelona, Diagonal 643, E-08028, Barcelona, Spain
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Ballesté E, García-Aljaro C, Blanch AR. Assessment of the decay rates of microbial source tracking molecular markers and faecal indicator bacteria from different sources. J Appl Microbiol 2018; 125:1938-1949. [PMID: 30066371 DOI: 10.1111/jam.14058] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Revised: 07/11/2018] [Accepted: 07/28/2018] [Indexed: 01/18/2023]
Abstract
AIMS Evaluate the T90 and compare the decay of different faecal indicator bacteria (FIB) and molecular microbial source tracking (MST) markers of human and animal sources during summer and winter. METHODS AND RESULTS The persistence of Escherichia coli and enterococci and several MST molecular markers targeting host-specific Bifidobacterium and Bacteroidales species (BifHM, BifCW, BifPL, HF183/BFD, Rum2Bac and Pig2Bac) was assessed at the same time using mesocosms. Dialysis bags filled with diluted wastewater from different sources were kept in an outdoor water tank and monitored regularly to assess the inactivation rates. The T90 values of E. coli by culture methods ranged from 1·52 to 5·69 days in summer and 2·06 to 6·19 days in winter, whereas with qPCR 2·29-4·23 days in summer and 4·17-8·09 days in winter. T90 values for enterocci ranged from 1·15 to 3·10 days in summer and from 3·01 to 5·46 days in winter. Significant differences were observed between faecal sources for both markers. For the MST makers similar T90 values were obtained in summer (1·05-1·91 days), whereas higher variability was observed in winter (2·90-6·12 days). CONCLUSIONS Different decay rates were observed for the FIB from the different sources, especially for E. coli in ruminant samples. A higher variability among T90 values of the different MST markers in winter was observed, whereas similar T90 values were detected in summer highlighting the stronger effect of environmental parameters during this season. SIGNIFICANCE AND IMPACT OF THE STUDY The diverse inactivation rates observed in bacteria from different faecal sources have implications when these rates are used to model faecal pollution in water. The use of FIBT90 of different sources is essential to develop reliable predictive models. Since different inactivation of E. coli regarding the source of pollution has been observed, the source of the pollution has to be considered for modelling approaches.
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Affiliation(s)
- E Ballesté
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Catalonia, Spain
| | - C García-Aljaro
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Catalonia, Spain
| | - A R Blanch
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Catalonia, Spain
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Masters NM, Wiegand A, Thompson JM, Vollmerhausen TL, Hatje E, Katouli M. Enterococci populations of a metropolitan river after an extreme flood event: prevalence, persistence and virulence determinants. JOURNAL OF WATER AND HEALTH 2017; 15:684-694. [PMID: 29040072 DOI: 10.2166/wh.2017.284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We investigated the prevalence, persistence and virulence determinants of enterococci populations in water samples collected over three rounds following an extreme flood event in a metropolitan river. Enterococci (n = 482) were typed using the high resolution biochemical fingerprinting method (PhP typing) and grouped into common (C) or single (S) biochemical phenotypes (BPTs). In all, 23 C-BPTs (72.6% of isolates) were found across the sites. A representative isolate of each C-BPT was identified to the species level and tested for the presence of seven virulence genes (VGs), biofilm formation and resistance to 14 antibiotics. The enterococci concentrations in samples collected during the first two rounds were above national recreational water guidelines. By round three, enterococci concentrations decreased significantly (P < 0.05). However, 11 C-BPTs (55.5% of isolates) persisted across all sampling rounds. E. casseliflavus and E. mundtii were the most common enterococci populations comprising of >57% of all isolates. Ten of the 11 most dominant C-BPTs were resistant to multiple antibiotics and harboured one or more VGs. The high prevalence of antibiotic resistance and VGs among enterococci isolates in this catchment not only provides them with niche advantages but also poses a risk to public health.
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Affiliation(s)
- Nicole M Masters
- Genecology Research Centre, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia E-mail:
| | - Aaron Wiegand
- Genecology Research Centre, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia E-mail:
| | - Jasmin M Thompson
- Genecology Research Centre, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia E-mail:
| | - Tara L Vollmerhausen
- Genecology Research Centre, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia E-mail:
| | - Eva Hatje
- Genecology Research Centre, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia E-mail:
| | - Mohammad Katouli
- Genecology Research Centre, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia E-mail:
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Masters NM, Wiegand A, Thompson JM, Vollmerhausen TL, Hatje E, Katouli M. Assessing the population dynamics of Escherichia coli in a metropolitan river after an extreme flood event. JOURNAL OF WATER AND HEALTH 2017; 15:196-208. [PMID: 28362301 DOI: 10.2166/wh.2016.285] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We investigated Escherichia coli populations in a metropolitan river after an extreme flood event. Between nine and 15 of the 23 selected sites along the river were sampled fortnightly over three rounds. In all, 307 E. coli were typed using the PhP typing method and were grouped into common (C) or single (S) biochemical phenotypes (BPTs). A representative from each of the 31 identified C-BPTs was tested for 58 virulence genes (VGs) associated with intestinal and extra-intestinal E. coli, resistance to 22 antibiotics, production of biofilm and cytotoxicity to Vero cells. The number of E. coli in the first sampling round was significantly (P < 0.01) higher than subsequent rounds, whereas the number of VGs was significantly (P < 0.05) higher in isolates from the last sampling round when compared to previous rounds. Comparison of the C-BPTs with an existing database from wastewater treatment plants (WWTPs) in the same catchment showed that 40.6% of the river isolates were identical to the WWTP isolates. The relatively high number of VGs and antibiotic resistance among the C-BPTs suggests possessing and retaining these genes may provide niche advantages for those naturalised and/or persistent E. coli populations which may pose a health risk to the community.
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Affiliation(s)
- Nicole M Masters
- Genecology Research Centre, School of Health and Sports Science, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia E-mail:
| | - Aaron Wiegand
- Genecology Research Centre, School of Health and Sports Science, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia E-mail:
| | - Jasmin M Thompson
- Genecology Research Centre, School of Health and Sports Science, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia E-mail:
| | - Tara L Vollmerhausen
- Genecology Research Centre, School of Health and Sports Science, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia E-mail:
| | - Eva Hatje
- Genecology Research Centre, School of Health and Sports Science, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia E-mail:
| | - Mohammad Katouli
- Genecology Research Centre, School of Health and Sports Science, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia E-mail:
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Gundogdu A, Bolkvadze D, Kilic H. In vitro Effectiveness of Commercial Bacteriophage Cocktails on Diverse Extended-Spectrum Beta-Lactamase Producing Escherichia coli Strains. Front Microbiol 2016; 7:1761. [PMID: 27857711 PMCID: PMC5093111 DOI: 10.3389/fmicb.2016.01761] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 10/20/2016] [Indexed: 12/03/2022] Open
Abstract
The objective of this study is to determine the in vitro susceptibility of Georgian bacteriophage cocktails on multidrug resistant (MDR) extended-spectrum beta-lactamase producing Escherichia coli (ESBL-EC) isolated from patients’ blood and urine cultures. A total of 615 E. coli isolates were included in this study. Phene Plate (PhP)-typing and phylogenetic grouping were used for the typing. Antimicrobial resistance profiles and ESBL production of all isolates were confirmed according to Clinical and Laboratory Standards Institute (CLSI) criteria. The activities of four bacteriophage cocktails (Enko-phage, SES-bacteriophage, Pyo-bacteriophage, and Intesti-bacteriophage) were determined against 142 ESBL-EC using in vitro spot tests. According to this, Enko-phage were active against 87.3% of the tested strains while that ratio was 81.7% for Intesti-bacteriophage, 81.7% for Pyo-bacteriophage, and 59.2% for SES-bacteriophage cocktails. Based on the contingency tests, the phage cocktails were observed to be statistically significantly (p < 0.001) more effective on ESBL-EC strains belonging to phylogenetic groups D and B2. The employed phage cocktails were found to be affective against all tested resistant types. These results are promising especially for the infections that are caused by MDR pathogens that are difficult to treat. As this is a preliminary step to the potential clinical trials to be designed for the country, in vitro confirmation of their success on a MDR ESBL-EC collection should be accepted as an initial action, which is encouraging to consider clinical trials of phage therapy especially in countries which are not introduce phage therapy.
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Affiliation(s)
- Aycan Gundogdu
- Department of Microbiology and Clinical Microbiology, Faculty of Medicine, Erciyes UniversityKayseri, Turkey; Genome and Stem Cell Center (GENKOK), Erciyes UniversityKayseri, Turkey
| | - Darajen Bolkvadze
- Laboratory of Molecular Biology, G. Eliava Institute of Bacteriophages, Microbiology and Virology Tbilisi, Georgia
| | - Huseyin Kilic
- Department of Microbiology and Clinical Microbiology, Faculty of Medicine, Erciyes University Kayseri, Turkey
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Masters N, Christie M, Katouli M, Stratton H. A combination of PhP typing and β-d-glucuronidase gene sequence variation analysis for differentiation of Escherichia coli from humans and animals. Can J Microbiol 2015; 61:409-16. [PMID: 25950195 DOI: 10.1139/cjm-2015-0048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We investigated the usefulness of the β-d-glucuronidase gene variance in Escherichia coli as a microbial source tracking tool using a novel algorithm for comparison of sequences from a prescreened set of host-specific isolates using a high-resolution PhP typing method. A total of 65 common biochemical phenotypes belonging to 318 E. coli strains isolated from humans and domestic and wild animals were analysed for nucleotide variations at 10 loci along a 518 bp fragment of the 1812 bp β-d-glucuronidase gene. Neighbour-joining analysis of loci variations revealed 86 (76.8%) human isolates and 91.2% of animal isolates were correctly identified. Pairwise hierarchical clustering improved assignment; where 92 (82.1%) human and 204 (99%) animal strains were assigned to their respective cluster. Our data show that initial typing of isolates and selection of common types from different hosts prior to analysis of the β-d-glucuronidase gene sequence improves source identification. We also concluded that numerical profiling of the nucleotide variations can be used as a valuable approach to differentiate human from animal E. coli. This study signifies the usefulness of the β-d-glucuronidase gene as a marker for differentiating human faecal pollution from animal sources.
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Affiliation(s)
- N Masters
- Genecology Research Centre, School of Health and Sports Science, University of the Sunshine Coast, Maroochydore, Queensland, Australia
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Masters N, Christie M, Stratton H, Katouli M. Viability and stability of Escherichia coli and enterococci populations in fecal samples upon freezing. Can J Microbiol 2015; 61:495-501. [PMID: 26053765 DOI: 10.1139/cjm-2015-0020] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
We studied the survival of Escherichia coli and enterococci populations in fecal samples of 7 host species after storage at -20 and -80 °C for 30 days. Composite fecal samples were collected from cows, chickens, horses, pigs, dogs, birds, and humans, and bacteria were enumerated before and after storage. Twenty-eight colonies of each bacterial species were typed before and after storage and the strains were assigned to different biochemical phenotypes (BPTs). A significant reduction in the number of E. coli was observed in all samples stored at -20 °C but in only 3 of those samples stored at -80 °C. However, the numbers of enterococci were similar in most stored samples (except cow and birds). The number and the distribution of E. coli and enterococci BPTs in fresh samples did not vary significantly from those stored at either temperature. Furthermore, the population structure of E. coli and enterococci did not change significantly after storage at -80 °C, this was always the case for those samples stored at -20 °C. We conclude that for those studies investigating E. coli or enterococci population structure, short-term storage (≤ 30 days) of fecal samples in a glycerol broth at -80 °C is a preferable option.
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Affiliation(s)
- N Masters
- a GeneCology Research Centre, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - M Christie
- b School of Biomolecular and Physical Sciences, Griffith University, Nathan, Queensland, Australia
| | - H Stratton
- b School of Biomolecular and Physical Sciences, Griffith University, Nathan, Queensland, Australia.,c Smart Water Research Centre, Griffith University, Gold Coast, Queensland, Australia
| | - M Katouli
- a GeneCology Research Centre, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland, Australia.,c Smart Water Research Centre, Griffith University, Gold Coast, Queensland, Australia
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