Have genetic targets for faecal pollution diagnostics and source tracking revolutionized water quality analysis yet?
DNA/RNA analysis
faecal and MST markers
faecal indicator
faecal pollution microbiology
microbial source tracking
systematic review
Journal
FEMS microbiology reviews
ISSN: 1574-6976
Titre abrégé: FEMS Microbiol Rev
Pays: England
ID NLM: 8902526
Informations de publication
Date de publication:
05 07 2023
05 07 2023
Historique:
received:
14
12
2022
revised:
26
05
2023
accepted:
05
06
2023
medline:
27
7
2023
pubmed:
8
6
2023
entrez:
7
6
2023
Statut:
ppublish
Résumé
The impacts of nucleic acid-based methods - such as PCR and sequencing - to detect and analyze indicators, genetic markers or molecular signatures of microbial faecal pollution in health-related water quality research were assessed by rigorous literature analysis. A wide range of application areas and study designs has been identified since the first application more than 30 years ago (>1100 publications). Given the consistency of methods and assessment types, we suggest defining this emerging part of science as a new discipline: genetic faecal pollution diagnostics (GFPD) in health-related microbial water quality analysis. Undoubtedly, GFPD has already revolutionized faecal pollution detection (i.e., traditional or alternative general faecal indicator/marker analysis) and microbial source tracking (i.e., host-associated faecal indicator/marker analysis), the current core applications. GFPD is also expanding to many other research areas, including infection and health risk assessment, evaluation of microbial water treatment, and support of wastewater surveillance. In addition, storage of DNA extracts allows for biobanking, which opens up new perspectives. The tools of GFPD can be combined with cultivation-based standardized faecal indicator enumeration, pathogen detection, and various environmental data types, in an integrated data analysis approach. This comprehensive meta-analysis provides the scientific status quo of this field, including trend analyses and literature statistics, outlining identified application areas, and discusses the benefits and challenges of nucleic acid-based analysis in GFPD.
Identifiants
pubmed: 37286726
pii: 7191838
doi: 10.1093/femsre/fuad028
pmc: PMC10368376
pii:
doi:
Substances chimiques
Wastewater
0
Nucleic Acids
0
Types de publication
Meta-Analysis
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Informations de copyright
© The Author(s) 2023. Published by Oxford University Press on behalf of FEMS.
Références
J Environ Qual. 2016 Jul;45(4):1205-14
pubmed: 27380068
Water Res. 2009 Jul;43(12):3124-32
pubmed: 19476965
Water Res. 2005 Feb;39(4):541-8
pubmed: 15707626
Sci Total Environ. 2018 Sep 1;634:1174-1183
pubmed: 29710623
FEMS Microbiol Rev. 2000 Dec;24(5):555-65
pubmed: 11077149
Front Microbiol. 2018 Oct 30;9:2301
pubmed: 30425684
Sci Total Environ. 2022 Dec 20;853:158509
pubmed: 36063947
Front Microbiol. 2016 Nov 01;7:1692
pubmed: 27847499
Trends Microbiol. 2014 Dec;22(12):697-706
pubmed: 25199597
J Environ Qual. 2005 Mar-Apr;34(2):581-9
pubmed: 15758111
Nature. 2022 Aug;608(7921):15-16
pubmed: 35902752
Appl Environ Microbiol. 2013 May;79(9):2906-13
pubmed: 23435885
PLoS One. 2023 Jan 26;18(1):e0278548
pubmed: 36701383
Appl Environ Microbiol. 2010 Sep;76(17):5802-14
pubmed: 20639358
J Microbiol Methods. 2021 Jan;180:106091
pubmed: 33137355
J Microbiol. 2021 Mar;59(3):259-269
pubmed: 33565053
Environ Sci Technol. 2013 Aug 6;47(15):8548-56
pubmed: 23755882
Clin Chem. 2009 Apr;55(4):611-22
pubmed: 19246619
J Appl Microbiol. 2019 Mar;126(3):701-717
pubmed: 30244503
Water Res. 2013 Nov 15;47(18):6897-908
pubmed: 23992621
Environ Health Perspect. 2021 Jun;129(6):67004
pubmed: 34160249
Nat Commun. 2019 May 16;10(1):2200
pubmed: 31097702
Nat Rev Microbiol. 2008 Oct;6(10):776-88
pubmed: 18794915
J Environ Qual. 2015 Sep;44(5):1392-401
pubmed: 26436257
Nature. 2012 Jun 13;486(7402):207-14
pubmed: 22699609
Water Res. 2020 Sep 1;182:116014
pubmed: 32622131
Water Res. 2007 Aug;41(16):3701-15
pubmed: 17644149
Microb Ecol. 2013 May;65(4):1011-23
pubmed: 23475306
Water Res. 2011 Jul;45(13):3960-8
pubmed: 21640368
Water Res. 2018 Nov 1;144:424-434
pubmed: 30059905
Sci Total Environ. 2022 Jun 1;823:153680
pubmed: 35150684
Environ Health Perspect. 2021 Jun;129(6):67003
pubmed: 34160247
Water Res. 2020 Oct 1;184:116132
pubmed: 32777635
Proc Natl Acad Sci U S A. 2015 Aug 18;112(33):10419-24
pubmed: 26240328
J Hazard Mater. 2020 Nov 5;398:122820
pubmed: 32502801
Sci Total Environ. 2015 Jun 1;517:86-95
pubmed: 25723960
Appl Environ Microbiol. 2008 Feb;74(3):745-52
pubmed: 18065617
Environ Health Perspect. 1986 Nov;69:7-13
pubmed: 3816738
Food Environ Virol. 2022 Jun;14(2):199-211
pubmed: 35508751
Water Res. 2015 May 1;74:34-46
pubmed: 25706222
Front Microbiol. 2021 Aug 06;12:674214
pubmed: 34421839
Appl Environ Microbiol. 2009 May;75(10):3045-54
pubmed: 19329663
Appl Environ Microbiol. 2011 Mar;77(6):2094-102
pubmed: 21278274
Sci Total Environ. 2023 Jan 20;857(Pt 2):159533
pubmed: 36270368
Appl Environ Microbiol. 2006 Aug;72(8):5537-46
pubmed: 16885307
Water Res. 2012 May 1;46(7):2023-41
pubmed: 22348997
Water Res. 2011 Jan;45(3):1358-68
pubmed: 21074236
Am J Public Health Nations Health. 1936 Apr;26(4):406-11
pubmed: 18014410
J Microbiol Methods. 2006 Nov;67(2):310-20
pubmed: 16753236
Nucleic Acids Res. 2006 Feb 01;34(2):659-66
pubmed: 16452296
Int J Environ Res Public Health. 2019 Nov 09;16(22):
pubmed: 31717479
Appl Environ Microbiol. 2009 Sep;75(17):5544-54
pubmed: 19592538
Water Res. 2017 Oct 1;122:62-69
pubmed: 28591662
Environ Res. 2021 Feb;193:110531
pubmed: 33249042
Sci Prog. 2019 Dec;102(4):351-376
pubmed: 31818206
Water Res. 2018 May 15;135:168-186
pubmed: 29471200
Appl Environ Microbiol. 2012 Feb;78(4):922-32
pubmed: 22139002
Environ Microbiol. 2008 Oct;10(10):2598-608
pubmed: 18564182
Appl Environ Microbiol. 2004 Dec;70(12):7396-403
pubmed: 15574941
Environ Sci Technol. 2013;47(23):13611-20
pubmed: 24187936
Front Microbiol. 2021 Jul 14;12:668778
pubmed: 34335498
J Appl Microbiol. 2010 Nov;109(5):1599-608
pubmed: 20629798
Environ Sci Technol. 2017 Aug 15;51(16):9146-9154
pubmed: 28700235
Nat Rev Microbiol. 2021 Aug;19(8):514-527
pubmed: 33785903
Sci Total Environ. 2022 Jul 10;829:154431
pubmed: 35278558
Water Res. 2021 Mar 15;192:116845
pubmed: 33508720
Water Res. 2015 May 15;75:83-94
pubmed: 25765167
WIREs Water. 2018 May-Jun;5(3):e1282
pubmed: 29780584
J Hyg (Lond). 1908 Jan;8(1):92-158
pubmed: 20474353
J Appl Microbiol. 2006 Jul;101(1):44-52
pubmed: 16834590
Appl Environ Microbiol. 2009 Nov;75(22):7261-7
pubmed: 19767474
Sci Total Environ. 2022 Jan 20;805:149877
pubmed: 34818780
J Microbiol Methods. 2020 Jul;174:105947
pubmed: 32442655
Science. 2002 Mar 29;295(5564):2352-3
pubmed: 11923506
J Water Pollut Control Fed. 1969 Aug;41(8):Suppl:R336+
pubmed: 4900708
Environ Sci Technol. 2014 Oct 7;48(19):11453-61
pubmed: 25203917
Water Res. 2018 Jan 1;128:148-156
pubmed: 29101858
Water Res. 2022 Aug 1;221:118827
pubmed: 35820313
Environ Sci Technol. 2017 Jun 20;51(12):7028-7035
pubmed: 28541661
Front Microbiol. 2015 Sep 25;6:1027
pubmed: 26441948
Int J Hyg Environ Health. 2016 Jul;219(4-5):405-11
pubmed: 27079972
Water Res. 2018 Apr 15;133:282-288
pubmed: 29407709
Water Res. 2011 Jan;45(2):439-52
pubmed: 20851449
J Microbiol Methods. 2020 Dec;179:106099
pubmed: 33159993
Front Microbiol. 2021 Jan 11;11:610296
pubmed: 33584574
J Environ Manage. 2020 May 1;261:110220
pubmed: 32148290
Sci Total Environ. 2022 Sep 1;837:155319
pubmed: 35452738
Sci Total Environ. 2015 Feb 15;506-507:287-98
pubmed: 25460962
J Environ Qual. 2017 Jan;46(1):219-226
pubmed: 28177403
J Appl Microbiol. 2009 Nov;107(5):1518-27
pubmed: 19457032
Appl Environ Microbiol. 2006 Jan;72(1):612-21
pubmed: 16391098
Water Res. 2020 Aug 15;181:115926
pubmed: 32417460
Appl Environ Microbiol. 2016 May 31;82(12):3525-3536
pubmed: 27060115
Environ Sci Technol. 2018 May 1;52(9):5076-5084
pubmed: 29570973
Appl Environ Microbiol. 2019 Oct 1;85(20):
pubmed: 31420339
J Contam Hydrol. 2022 Apr;246:103960
pubmed: 35066264
Environ Pollut. 2018 Jan;232:571-579
pubmed: 29032906
Water Res. 2022 Apr 1;212:118114
pubmed: 35091220
Water Res. 2018 Nov 1;144:1-12
pubmed: 30005176
Front Sustain Food Syst. 2020 Feb;3:
pubmed: 32440656
Sci Total Environ. 2022 Nov 20;848:157707
pubmed: 35908692
mBio. 2015 Feb 24;6(2):e02574
pubmed: 25714718
J Microbiol Methods. 2012 Nov;91(2):276-89
pubmed: 22940102
Microbiome. 2017 Aug 16;5(1):86
pubmed: 28810907
Environ Sci Technol. 2012 Sep 18;46(18):10206-13
pubmed: 22913457
FEMS Microbiol Rev. 2005 Nov;29(5):897-910
pubmed: 16219511
Environ Pollut. 2018 Jan;232:1-9
pubmed: 28986079
Appl Environ Microbiol. 2000 Oct;66(10):4571-4
pubmed: 11010920
Water Res. 2019 Nov 1;164:114898
pubmed: 31404902
Appl Environ Microbiol. 1994 Aug;60(8):2963-70
pubmed: 8085832
Environ Health. 2017 May 12;16(1):45
pubmed: 28499453
PLoS One. 2022 Apr 12;17(4):e0266749
pubmed: 35413082
Curr Microbiol. 2020 Apr;77(4):682-687
pubmed: 31811375
Water Res. 2013 Nov 15;47(18):6839-48
pubmed: 23911226
Sci Total Environ. 2022 Oct 20;844:157146
pubmed: 35798098
Appl Environ Microbiol. 2006 Aug;72(8):5610-4
pubmed: 16885315
J Microbiol Methods. 2020 Oct;177:106050
pubmed: 32891632
Nat Microbiol. 2016 Dec 19;2:16242
pubmed: 27991881
Water Res. 2020 Mar 15;171:115440
pubmed: 31955059
J Microbiol Methods. 2012 Mar;88(3):433-5
pubmed: 22285854
Sci Total Environ. 2016 Dec 15;573:1460-1471
pubmed: 27522292
Environ Sci Technol. 2010 Oct 15;44(20):7777-82
pubmed: 20853824
Water Res. 2020 Mar 15;171:115392
pubmed: 31865126
Water Res. 2021 Sep 15;203:117479
pubmed: 34365192
Int J Hyg Environ Health. 2020 Mar;224:113420
pubmed: 31748129
J Water Health. 2010 Sep;8(3):466-78
pubmed: 20375476
Annu Rev Microbiol. 1996;50:645-77
pubmed: 8905094
Water Res. 2007 Aug;41(16):3539-52
pubmed: 17632210
J Appl Microbiol. 2010 Dec;109(6):1853-67
pubmed: 20722877
Water Res. 2009 Nov;43(19):4872-7
pubmed: 19783274
Acta Pathol Microbiol Scand Suppl. 1960;48(Suppl 136):3-124
pubmed: 14409549
J Contam Hydrol. 2004 Apr;69(3-4):195-213
pubmed: 15028391
Nat Rev Microbiol. 2021 Oct;19(10):639-653
pubmed: 34045709
J Environ Qual. 2018 Sep;47(5):1086-1093
pubmed: 30272770
J Water Health. 2012 Sep;10(3):358-70
pubmed: 22960480
Nat Rev Microbiol. 2014 Dec;12(12):789-90
pubmed: 25564681
Nat Rev Microbiol. 2021 Dec;19(12):774-785
pubmed: 34183820
mSystems. 2020 Nov 3;5(6):
pubmed: 33144315
Microbiol Mol Biol Rev. 2019 Oct 2;83(4):
pubmed: 31578217
Environ Sci Technol. 2021 Aug 3;55(15):10451-10461
pubmed: 34291905
Environ Sci Technol. 2018 Sep 4;52(17):9634-9645
pubmed: 30080397
Sci Total Environ. 2019 Feb 1;649:1491-1501
pubmed: 30308917
Water Res. 2019 Jun 1;156:456-464
pubmed: 30952079
J Microbiol Methods. 2012 Jan;88(1):155-61
pubmed: 22108496
J Environ Sci Health A Tox Hazard Subst Environ Eng. 2014;49(14):1685-92
pubmed: 25320855
Environ Sci Technol. 2016 Jul 5;50(13):6803-13
pubmed: 26992352
Environ Sci Technol. 2008 Jul 15;42(14):5229-34
pubmed: 18754373
Epidemiology. 2008 May;19(3):375-83
pubmed: 18379427
Environ Sci Technol. 2003 May 15;37(10):2242-50
pubmed: 12785531
Environ Health. 2010 Oct 31;9:66
pubmed: 21040526
J Appl Microbiol. 2013 Sep;115(3):897-907
pubmed: 23701119
Appl Environ Microbiol. 2012 Oct;78(20):7317-26
pubmed: 22885746
Environ Pollut. 2019 Nov;254(Pt B):113108
pubmed: 31491696
Elementa (Wash D C). 2018;6:
pubmed: 30393748
J Appl Bacteriol. 1983 Oct;55(2):349-57
pubmed: 6654767
Environ Sci Technol. 2021 Sep 7;55(17):11667-11679
pubmed: 34382777
Environ Sci Technol. 2020 Oct 20;54(20):13101-13109
pubmed: 32969642
Appl Environ Microbiol. 2011 Aug 15;77(16):5571-6
pubmed: 21705550
J Virol Methods. 2011 Sep;176(1-2):38-45
pubmed: 21664379
Water Res. 2021 Apr 15;194:116907
pubmed: 33610927
Environ Health. 2017 Oct 2;16(1):103
pubmed: 28969670
Environ Microbiol. 2005 Feb;7(2):249-59
pubmed: 15658992
Sci Total Environ. 2022 Mar 10;811:152060
pubmed: 34861306
J Water Health. 2014 Dec;12(4):824-34
pubmed: 25473992
Environ Sci Process Impacts. 2018 Mar 1;20(3):480-492
pubmed: 29404550
J Water Health. 2005 Dec;3(4):381-92
pubmed: 16459844
Int J Hyg Environ Health. 2020 May;226:113496
pubmed: 32135507
Water Res. 2013 Nov 15;47(18):6873-82
pubmed: 23871252
Water Environ Res. 2017 Feb 1;89(2):127-143
pubmed: 28160781
Water Res. 2017 Nov 1;124:543-555
pubmed: 28806705
Water Res. 2022 Jun 30;218:118534
pubmed: 35537251
Water Res. 2022 Oct 15;225:119162
pubmed: 36191524
Environ Sci Technol. 2006 Aug 1;40(15):4746-53
pubmed: 16913133
Appl Environ Microbiol. 2018 Oct 1;84(20):
pubmed: 30097445
Sci Rep. 2020 Feb 27;10(1):3616
pubmed: 32107444
Environ Sci Technol. 2004 Nov 15;38(22):5932-8
pubmed: 15573591
Water Res. 2015 Mar 1;70:205-13
pubmed: 25540834
Water Sci Technol. 2015;72(11):1962-72
pubmed: 26606090
Appl Environ Microbiol. 2016 Apr 18;82(9):2773-2782
pubmed: 26921430
Front Microbiol. 2021 Aug 12;12:684533
pubmed: 34475855
Water Res. 2016 Sep 15;101:84-94
pubmed: 27258619
Appl Environ Microbiol. 1990 Feb;56(2):307-14
pubmed: 2306085
Water Res. 2011 Apr;45(8):2561-72
pubmed: 21420709
Int J Environ Res Public Health. 2018 Jul 23;15(7):
pubmed: 30041450
Water Res. 2018 Mar 15;131:142-150
pubmed: 29281808
Environ Res. 2020 Nov;190:109982
pubmed: 32745749
J Microbiol Methods. 2021 May;184:106186
pubmed: 33766609
Appl Environ Microbiol. 2002 Dec;68(12):5796-803
pubmed: 12450798
Food Environ Virol. 2014 Dec;6(4):260-8
pubmed: 24952878
Sci Total Environ. 2022 Sep 1;837:155663
pubmed: 35523326
Water Res. 2007 May;41(10):2151-62
pubmed: 17400275
J Environ Qual. 2015 Sep;44(5):1491-502
pubmed: 26436266
Water Res. 2003 Feb;37(4):909-13
pubmed: 12531273
Appl Environ Microbiol. 2014 May;80(10):3086-94
pubmed: 24610857
J Microbiol Methods. 2014 Oct;105:59-66
pubmed: 25038459
Sci Total Environ. 2015 Apr 1;511:676-83
pubmed: 25600418
Water Res. 2014 Oct 1;62:167-79
pubmed: 24954130
Environ Sci Technol. 2010 Aug 15;44(16):6281-8
pubmed: 20704227
Appl Environ Microbiol. 2019 Jul 1;85(14):
pubmed: 31076423
Environ Microbiol. 2018 Sep;20(9):3132-3140
pubmed: 29797757
Environ Sci Technol. 2016 Sep 6;50(17):9524-32
pubmed: 27447291
Appl Environ Microbiol. 2010 Nov;76(22):7608-16
pubmed: 20851970
J Hazard Mater. 2023 Feb 5;443(Pt B):130262
pubmed: 36327846
Water Res. 2021 Jan 1;188:116507
pubmed: 33126000
Water Res. 2021 Jan 1;188:116537
pubmed: 33126005
Environ Sci Technol. 2019 Jul 16;53(14):8271-8281
pubmed: 31268313
Nat Microbiol. 2021 Nov;6(11):1443-1454
pubmed: 34702978
Environ Int. 2019 Sep;130:104703
pubmed: 31295713
PLoS One. 2020 Apr 30;15(4):e0232054
pubmed: 32352994
Environ Sci Technol. 2011 Jul 1;45(13):5652-9
pubmed: 21662992
FEMS Microbiol Rev. 1997 Nov;21(3):213-29
pubmed: 9451814
Microb Biotechnol. 2017 Nov;10(6):1775-1780
pubmed: 28925595
PLoS One. 2019 Jun 6;14(6):e0216827
pubmed: 31170166
Appl Environ Microbiol. 2009 May;75(9):2940-4
pubmed: 19270114
Microorganisms. 2020 Jul 26;8(8):
pubmed: 32722600
Environ Sci Technol. 2011 May 1;45(9):4038-45
pubmed: 21466151
Microbes Environ. 2008;23(2):101-8
pubmed: 21558695
Sci Total Environ. 2017 Jan 1;574:960-968
pubmed: 27668848
Environ Health Perspect. 2006 Jan;114(1):24-8
pubmed: 16393653
Sci Total Environ. 2019 Oct 10;686:158-170
pubmed: 31176815
Sci Total Environ. 2022 Apr 10;816:151534
pubmed: 34780821
Microb Ecol. 2011 May;61(4):955-67
pubmed: 21080161
Front Microbiol. 2021 Jun 14;12:660368
pubmed: 34194406
Mar Pollut Bull. 2013 Jun 15;71(1-2):51-63
pubmed: 23623653
Sci Total Environ. 2021 May 10;768:144278
pubmed: 33736313
Water Res X. 2020 Dec 09;11:100080
pubmed: 33490943
Appl Environ Microbiol. 2017 Mar 31;83(8):
pubmed: 28159789
Sci Total Environ. 2022 Oct 15;843:156964
pubmed: 35764146
Lett Appl Microbiol. 2021 Apr;72(4):458-466
pubmed: 33300161
Anal Biochem. 2002 Apr 15;303(2):186-93
pubmed: 11950218
Water Res. 2016 May 01;94:371-381
pubmed: 27040577
Microbiome. 2018 May 24;6(1):93
pubmed: 29793542
Environ Microbiol Rep. 2021 Jun;13(3):243-245
pubmed: 33904249
Appl Environ Microbiol. 2010 Mar;76(5):1359-66
pubmed: 20061457