Table 2.
Included studies, separated by pathogen stratum
| Publication | WHO REGION Country Coverage (type of surveillance) $ |
Start year End year approx. duration |
Target species (sample material) |
No. isolates: -study total -belonging to stratum -stratum WGS |
Sequencing technology and lab (central, decentral, external) |
Typing methods | Availability* of epidemiological information | Epidemiological information integrated with genetic differences (threshold) to infer clusters or transmission pathways | Public availability of sequence data | |||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Age | Gender | Diagnosis | Outcome | HAI/ CAI | Ward, clinic | Travel | Hosp. history | |||||||||
| Stratum 1: Carbapenem-resistant or carbapenemase-producing Enterobacterales | ||||||||||||||||
| Afolayan, 2021 [20] |
AFRICAN Nigeria Subnational (sentinel, tertiary care hospitals) |
2016 2018 36 m |
Antimicrobial-resistant Klebsiella spp. (clinical: blood, CSF, urine) |
141 11 11 |
Illumina de novo central |
MLST, SNP | ✓ | ✓ | ✓ | ✗ | ✓ | ✓ | ✗ | ✗ |
Time of isolate recovery; others for visualisation (ESBL-Kp: 1–3 SNPs) |
Yes |
| Milenkov, 2021 [46] |
AFRICAN Madagascar Subnational (sentinel, maternity wards) |
2018 2019 9 m |
ESBL- producing Enterobacterales (screening) |
170 1 1 |
Illumina + ONT de novo central |
MLST, SNP | ✓ | ✓ | ✓ | ✗ | ✗ | ✗ | ✗ | ✗ |
Unclear; isolate origin for visualisation (ESBL-Ec: <10 SNPs) |
Yes |
| Karlowsky, 2021 [35] |
AMERICAS Canada National (comprehensive, tertiary care hospitals) |
2007 2018 144 m |
ESBL-positive Escherichia coli and Klebsiella pneumoniae (clinical) |
812 23 23 |
Illumina de novo central |
MLST | ✓ | ✓ | ✗ | ✗ | ✗ | ✓ | ✗ | ✗ | NR (NA) | Yes |
| Saavedra, 2021 [51] |
AMERICAS Colombia National (comprehensive, NRL) |
2013 2017 60 m |
Carbapenem-resistant Klebsiella pneumoniae (clinical) |
425 425 425 |
Illumina de novo central |
MLST, SNP | ✓ | ✓ | ✓ | ✗ | ✗ | ✗ | ✗ | ✗ | Unclear (NR) | Yes |
| Bulens, 2023 [23] |
AMERICAS USA Subnational (sentinel, MuGSI) |
2012 2015 36 m |
Carbapenem-resistant Enterobacterales (clinical) |
1499 1499 12 |
Illumina de novo central |
MLST | ✓ | ✓ | ✓ | ✓ | ✓ | ✗ | ✓ | ✓ | NR (NA) | No |
| Lapp, 2023 [39] |
AMERICAS USA Subnational (comprehensive, MuGSI and statewide CRE surveillance) |
2016 2018 36 m |
Carbapenem-resistant (blaKPC-carrying) Enterobacterales (clinical) |
255 255 255 |
Illumina de novo decentral |
MLST, SNP | ✓ | ✓ | ☑ | ✗ | ✗ | ✓ | ✗ | ✓ |
Comorbidities, geographic (≤ 5, 10, and 15 SNVs) |
Yes |
| Al-Farsi, 2020 [21] |
EAST MEDITERRANEAN Oman National (comprehensive) |
2015 2015 10 m |
Escherichia coli with reduced susceptibility to carbapenems (clinical and screening) |
35 35 35 |
Illumina de novo central |
MLST, cgMLST, wgMLST, SNP | ✓ | ✓ | ✓ | ✓ | ✗ | ✓ | ☑ | ✓ |
Hospital, ward, isolation date, hospitalisation and travel history (Ec: ≤10 SNPs) |
Yes |
| Sonnevend, 2022 [55] |
EAST MEDITERRANEAN United Arab Emirates National (sentinel) |
2018 2019 9 m |
Carbapenem-resistant Enterobacterales (clinical and screening) |
504 504 504 |
Illumina de novo central |
MLST, cgMLST | ✓ | ✓ | ✗ | ✗ | ✗ | ✓ | ✗ | ✗ |
Hospital (Kp: ≤15 allelic differences) |
Yes |
| Do Nascimento, 2017 [28] |
EUROPE UK Subnational (comprehensive) |
2015 2016 18 m |
Enteroaggregative Escherichia coli (clinical: faecal samples) |
155 1 1 |
Illumina mapping central |
MLST | ✓ | ✓ | ✗ | ✗ | ✗ | ✗ | ☑ | ✗ | NR (NA) | Yes |
| Roer, 2017 [50] |
EUROPE Denmark National (comprehensive) |
2014 2015 24 m |
Third-generation cephalosporin-resistant Escherichia coli (blood culture) |
552 5 5 |
Illumina de novo central |
MLST, SNP | ✓ | ✓ | ✓ | ✗ | ✗ | ✗ | ✗ | ✗ |
Unclear; isolate origin for visualisation (Ec: ≤10 SNPs) |
No |
| Hammerum, 2020 [32] |
EUROPE Denmark National (comprehensive) |
2016 2019 44 m |
OXA-244-producing Escherichia coli (clinical and screening) |
24 24 24 |
Illumina de novo central |
MLST, cgMLST | ✓ | ✓ | ✗ | ✗ | ✗ | ✓ | ✓ | ✓ |
Travel and hospitalisation history, place of sampling and residence, (Ec: ≤10 allelic differences) |
Yes |
| Taylor, 2021 [56] |
EUROPE UK Subnational (sentinel) |
2016 2016 6 m |
Amikacin-resistant Enterobacterales (clinical and screening) |
271 135 135 |
Illumina de novo central |
MLST | ✓ | ✓ | ✓ | ✗ | ✗ | ✗ | ☑ | ✗ | NR (NA) | No |
| Canada-Garcia, 2022 [24] |
EUROPE Spain National (sentinel) |
2019 2019 4 m |
Carbapenemase-producing Klebsiella pneumoniae and Escherichia coli (clinical) |
403 403 403 |
Illumina de novo central |
MLST, SNP, cgMLST | ✓ | ✓ | ✗ | ✗ | ✗ | ✗ | ✗ | ✗ |
Unclear (Kp: ≤10 SNPs, ≤ 5 allelic differences) |
Yes |
| Hans, 2023 [33] |
EUROPE Germany National (comprehensive) |
2013 2019 84 m |
NDM-5-producing Escherichia coli (clinical and screening) |
329 329 222 |
Illumina de novo central |
MLST, cgMLST, SNP | ✓ | ✓ | ✗ | ✗ | ✗ | ☑ | ✗ | ✗ |
Geography (Ec: ≤100 SNPs) |
Yes |
| Ljungquist, 2023 [43] |
EUROPE Norway National (comprehensive) |
2015 2021 84 m |
Carbapenemase-producing Enterobacterales (clinical and screening) |
389 389 389 |
Illumina de novo central |
MLST, cgMLST | ✓ | ✓ | ✗ | ✗ | ✗ | ✗ | ✓ | ✗ | Hospital, travel history (NR) | Yes |
| Raffelsberger, 2023 [49] |
EUROPE Norway Subnational (comprehensive) |
2015 2016 19 m |
ESBL-producing Escherichia coli and Klebsiella pneumoniae (screening) |
4999 2 2 |
Illumina de novo external |
MLST, SNP | ✓ | ✓ | ✓ | ✗ | ✗ | ✗ | ✓ | ✓ |
NR (Ec: ≤17 SNPs) |
Yes |
| Nagaraj, 2021 [47] |
SOUTH EAST ASIA India National (sentinel) |
2013 2019 84 m |
Carbapenem resistant Klebsiella pneumoniae (clinical) |
344 280 280 |
Illumina de novo NR |
MLST, SNP | ✓ | ✓ | ✓ | ✗ | ✓ | ✓ | ✗ | ✗ | Hospital, inpatient/outpatient, age (Kp: ≤3 SNPs) | Yes |
| Marimuthu, 2017 [44] |
WEST PACIFIC Singapore National (comprehensive) |
2013 2015 17 m |
Carbapenem-resistant Enterobacteriaceae (clinical and screening) |
430 430 206 |
Illumina de novo central |
MLST, SNP | ✓ | ✓ | ✓ | ✓ | ✗ | ✓ | ✓ | ✓ |
Hospital (Ec: ≤58 SNPs, Kp: ≤151 SNPs) |
Yes |
| Sherry, 2019 [52] |
WEST PACIFIC Australia Subnational (comprehensive) |
2012 2016 60 m |
Carbapenemase-producing Enterobacterales (clinical and screening) |
361 361 361 |
Illumina de novo central |
MLST, SNP | ✓ | ✓ | ✗ | ✗ | ✓ | ✓ | ✓ | ✓ |
“Data from concurrent epidemiologic investigations” (Hospital, hospitalisation and travel history) (≤ 23 SNPs) |
Yes |
| Argimon, 2020 [22] |
WEST PACIFIC Philippines National (sentinel) |
2013 2014 24 m |
Carbapenemase- and/or ESBL-producing Klebsiella pneumoniae and Escherichia coli (clinical) |
805 ~ 420 ~ 420 |
Illumina de novo central |
MLST, SNP | ✓ | ✗ | ✗ | ✗ | ✓ | ✓ | ✗ | ✗ | Hospital, ward isolation date, HAI/CAI, age (threshold unclear) | Yes |
| Carlos, 2021 [25] |
WEST PACIFIC Philippines National (sentinel) |
2015 2017 36 m |
Carbapenem-, extended spectrum beta-lactam-, and cephalosporin-resistant Klebsiella pneumoniae (clinical) |
259 139 139 |
Illumina de novo central |
MLST, SNP | ✓ | ✓ | ✗ | ✗ | ✓ | ✓ | ✗ | ✗ |
Hospital, ward, sampling time, age, HAI/CAI (threshold unclear) |
Yes |
| Lane, 2021 [38] |
WEST PACIFIC Australia Subnational (comprehensive) |
2016 2018 36 m |
Carbapenemase-producing Enterobacterales (clinical and screening) |
402 402 402 |
Illumina de novo central |
MLST, SNP | ✓ | ✓ | ✓ | ✓ | ✗ | ✓ | ✓ | ✓ |
Hospital, hospitalisation and travel history and eventual additional outbreak investigation (threshold unclear) |
Yes |
| Forde, 2023 [30] |
WEST PACIFIC Australia Subnational (comprehensive) |
2017 2021 50 m |
Carbapenemase-producing Enterobacterales (clinical and screening) |
2660 293 293 |
Illumina de novo central |
MLST, SNP | ✓ | ✗ | ✗ | ✗ | ✓ | ✓ | ✗ | ✗ |
Hospital, HAI/CAI (≤ 5 SNPs/Mb) |
Yes |
| Ko, 2023 [37] |
WEST PACIFIC China National (sentinel) |
2019 2020 12 m |
Carbapenemase-producing Escherichia coli (clinical) |
31 31 13 |
ONT de novo NR |
MLST, cgMLST | ✓ | ✓ | ✗ | ✗ | ✗ | ✗ | ✗ | ✗ | Unclear (NR) | No |
| Li, 2023 [42] |
WEST PACIFIC China Subnational (sentinel) |
2017 2022 72 |
Carbapenem-resistant Klebsiella pneumoniae (clinical) |
662 662 101 |
Illumina de novo external |
MLST, SNP | ✓ | ✓ | ✗ | ✗ | ✗ | ✗ | ✗ | ✗ |
Unclear, age, sex, isolation region and year for visualisation (NR) |
Yes |
| Stratum 2: Carbapenem-resistant or carbapenemase-producing Acinetobacter spp. | ||||||||||||||||
| Perovic, 2022 [48] |
AFRICAN South Africa Subnational (sentinel) |
2017 2019 30 m |
Acinetobacter baumannii complex (focus on colistin resistant) (blood culture) |
4822 1786 38 |
Illumina de novo central |
MLST, SNP | ✓ | ✓ | ✓ | ✓ | ✗ | ✓ | ✗ | ✓ |
Hospital and age for visualisation (NR) |
Yes |
| Adams, 2020 [19] |
AMERICAS Argentina National (sentinel, NRL) |
2014 2017 48 m |
NDM-producing Acinetobacter spp. (clinical) |
40 40 40 |
Illumina de novo NR |
MLST, SNP | ✓ | ✓ | ✗ | ✗ | ✗ | ✓ | ✗ | ✗ |
Hospital but no cluster definition (threshold unclear) |
Yes |
| Iovleva, 2022 [34] |
AMERICAS USA Subnational (comprehensive for study network) |
2017 2018 14 m |
Carbapenem-resistant Acinetobacter baumannii (clinical and screening) |
155 155 115 |
Illumina + ONT de novo central |
MLST, SNP | ✓ | ✓ | ✓ | ✓ | ✗ | ✓ | ✗ | ✗ |
Hospital, study site (≤ 10 SNPs) |
Yes |
| Taylor, 2021 [56] |
EUROPE UK Subnational (sentinel) |
2016 2016 6 m |
Amikacin- resistant Acinetobacter baumannii (clinical and screening) |
271 16 16 |
Illumina de novo central |
MLST | ✓ | ✓ | ✓ | ✗ | ✗ | ✗ | ☑ | ✗ | NR (NA) | No |
| Argimon, 2020 [22] |
WEST PACIFIC Philippines National (sentinel) |
2013 2014 24 m |
Carbapenemase-producing Acinetobacter baumannii (clinical) |
805 108 108 |
Illumina de novo central |
MLST, SNP | ✓ | ✗ | ✗ | ✗ | ✓ | ✓ | ✗ | ✗ | Hospital, ward isolation date, HAI/CAI, age (threshold unclear) | Yes |
| Chilam, 2021 [26] |
WEST PACIFIC Philippines National (sentinel) |
2013 2014 24 m |
Acinetobacter baumannii (focus on carbapenem-resistant) (clinical) |
5254 445 117 |
Illumina de novo central |
MLST, SNP | ✓ | ✓ | ✓ | ✗ | ✓ | ✓ | ✗ | ✗ |
Hospital (threshold unclear) |
Yes |
| Sherry, 2021 [53] |
WEST PACIFIC Australia Subnational (unclear) |
2017 2017 2 m |
Carbapenem-resistant Acinetobacter spp. (clinical) |
408 2 2 |
Illumina de novo central |
MLST, SNP | ✓ | ✓ | ✗ | ✗ | ✓ | ✓ | ✗ | ✓ | Hospitalisation history, wards, admission dates (≤ 25 SNPs) | Yes |
| Forde, 2023 [30] |
WEST PACIFIC Australia Subnational (comprehensive) |
2017 2021 50 m |
Carbapenem-resistant Acinetobacter baumannii (clinical and screening) |
2660 35 35 |
Illumina de novo central |
MLST, SNP | ✓ | ✗ | ✗ | ✗ | ✓ | ✓ | ✗ | ✗ |
Hospital, HAI/CAI (≤ 5 SNPs/Mb) |
Yes |
| Stratum 3: Methicillin-resistant Staphylococcus aureus | ||||||||||||||||
| Lee, 2017 [40] |
AMERICAS USA Subnational (comprehensive, Ten primary care clinics) |
2007 2015 108 m |
Staphylococcus aureus (MRSA and MSSA) (clinical and screening) |
144 71 71 |
Illumina mapping NR |
MLST, SNP | ✓ | ✓ | ✓ | ✗ | ✗ | ✗ | ✗ | ✗ |
Place of sampling (NR) |
Yes |
| Guthrie, 2020 [31] |
AMERICAS Canada Subnational (sentinel) |
2010 and 2016 24 m |
Methicillin-Resistant Staphylococcus aureus (clinical) |
426 426 426 |
Illumina mapping central |
MLST, SNP | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✗ | ✗ | Age, hospital, HAI/CAI (≤ 10 SNPs) | Yes |
| Di Gregorio, 2023 [27] |
AMERICAS South America International (sentinel) |
2019 2019 7 m |
Staphylococcus aureus (MRSA and MSSA) (blood culture) |
443 182 165 |
Illumina de novo central |
MLST, SNP | ✓ | ✓ | ✓ | ✗ | ✓ | ✗ | ✗ | ✗ | Country, HAI/CAI (threshold unclear) | Yes |
| Toleman, 2019 [57] |
EUROPE UK Subnational (comprehensive) |
2012 2013 12 m |
Methicillin-resistant Staphylococcus aureus (MRSA) (blood culture) |
425 425 425 |
Illumina de novo central |
MLST, SNP | ✓ | ✓ | ✗ | ✗ | ✓ | ✗ | ✗ | ✗ | NR | Yes |
| Enger, 2022 [29] |
EUROPE Norway National (comprehensive) |
2008 2016 108 m |
Methicillin-resistant Staphylococcus aureus (clinical and screening) |
475 475 108 |
Illumina de novo central |
MLST, SNP | ✓ | ✓ | ✓ | ✗ | ✓ | ✗ | ☑ | ✓ | Birth country and HAI/CAI for visualisation (NR) | Yes |
| van der Mee-Marquet, 2022 [58] |
EUROPE France Subnational (sentinel) |
2021 2021 8 m |
Staphylococcus aureus (MRSA and MSSA) (blood culture) |
53 5 5 |
Illumina NR | MLST, (SNP unclear) | ✓ | ✓ | ✓ | ✓ | ✗ | ✓ | ✗ | ✗ | NR | No |
| Masim, 2021 [45] |
WEST PACIFIC Philippines National (sentinel) |
2013 2014 24 m |
Methicillin-resistant Staphylococcus aureus (clinical) |
6211 3549 118 |
Illumina de novo external |
MLST, SNP | ✓ | ✓ | ✗ | ✗ | ✓ | ✓ | ✗ | ✗ | Unclear (NR) | Yes |
| Sherry, 2021 [53] |
WEST PACIFIC Australia Subnational (unclear) |
2017 2017 2 m |
Methicillin-resistant Staphylococcus aureus (clinical and screening) |
408 88 88 |
Illumina de novo central |
MLST, SNP | ✓ | ✓ | ✗ | ✗ | ✓ | ✓ | ✗ | ✓ |
Hospitalisation history, wards, admission dates (≤ 15 SNPs) |
Yes |
| Sherry, 2022 [54] |
WEST PACIFIC Australia Subnational (comprehensive) |
2017 2018 14 m |
Methicillin-resistant Staphylococcus aureus (clinical and screening) |
2275 811 811 |
Illumina de novo central |
MLST, SNP | ✓ | ✓ | ✗ | ✗ | ✓ | ✓ | ✗ | ✓ | Hospitalisation history, wards, admission dates (≤ 15 SNPs) | Yes |
| Yamaguchi, 2022 [59] |
WEST PACIFIC Japan National (comprehensive) |
2010 2018 56 m** |
Methicillin-resistant Staphylococcus aureus (clinical: skin and pus) |
1770 1770 92 |
Illumina de novo external |
MLST, SNP | ✓ | ✓ | ✗ | ✗ | ✗ | ✗ | ✗ | ✗ | Unclear (NR) | Yes |
| Forde, 2023 [30] |
WEST PACIFIC Australia Subnational (comprehensive) |
2017 2021 50 m |
Methicillin-resistant Staphylococcus aureus (clinical and screening) |
2660 620 620 |
Illumina de novo central |
MLST, SNP | ✓ | ✗ | ✗ | ✗ | ✓ | ✓ | ✗ | ✗ |
Hospital, HAI/CAI (≤ 5 SNPs/Mb) |
Yes |
| Stratum 4: Vancomycin-resistant Enterococci | ||||||||||||||||
| Kleinman, 2023 [36] |
AMERICAS Canada National (sentinel) |
2013 2018 72 m |
Vancomycin-resistant Enterococcus ST1478 (blood culture) |
115 115 115 |
Illumina de novo central |
MLST, SNP | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✗ | ✓ |
Patient movement data (hospital, ward) (< 20 SNVs) |
No |
| Lee, 2020 [41] |
WEST PACIFIC Australia National (sentinel) |
2015 2017 36 m |
Vancomycin-resistant Enterococcus faecium (blood culture) |
1025 537 537 |
Illumina de novo central |
MLST, SNP | ✓ | ✓ | ✗ | ✓ | ✗ | ✗ | ✗ | ✗ | Unclear (NR) | Yes |
| Sherry, 2021 [53] |
WEST PACIFIC Australia Subnational (unclear) |
2017 2017 2 m |
vanA vancomycin- resistant Enterococcus faecium (clinical and screening) |
408 64 64 |
Illumina de novo central |
MLST, SNP | ✓ | ✓ | ✗ | ✗ | ✓ | ✓ | ✗ | ✓ |
Hospitalisation history, ward, admission dates (≤ 25 SNPs) |
Yes |
| Sherry, 2022 [54] |
WEST PACIFIC Australia Subnational (comprehensive) |
2017 2018 14 m |
vanA vancomycin- resistant Enterococcus faecium (clinical and screening) |
2275 346 346 |
Illumina de novo central |
MLST, SNP | ✓ | ✓ | ✗ | ✗ | ✓ | ✓ | ✗ | ✓ | Hospitalisation history, wards, admission dates (≤ 25 SNPs) | Yes |
| Forde, 2023 [30] |
WEST PACIFIC Australia Subnational (comprehensive) |
2017 2021 50 m |
Vancomycin-resistant enterococci (clinical and screening) |
2660 433 433 |
Illumina de novo central |
MLST, SNP | ✓ | ✗ | ✗ | ✗ | ✓ | ✓ | ✗ | ✗ |
Hospital, HAI/CAI (≤ 5 SNPs/Mb) |
Yes |
Abbreviations: bp = base pair; cg = core genome; CSF = cerebrospinal fluid; Ec = Escherichia coli; HAI/ CAI = hospital- /community- acquired infection; Hosp. history = hospitalisation history; Kp = Klebsiella pneumoniae; m = month; med = medium; MLST = multi-locus sequence typing; MuGSI = Multi-site Gram-negative Surveillance Initiative; NR = not reported; PFGE = pulsed field gel electrophoresis; SCCmec = staphylococcal cassette chromosome mec; SNP = single nucleotide polymorphism; target = target pathogen (i.e. MRSA); target WGS = target pathogens submitted for WGS; VNTR = variable number tandem repeat; WGS = whole genome sequencing; WHO = World Health Organization
$ “Sentinel” refers to surveillance in a selected sample of sites that do not cover all areas in the national or sub-national region; “comprehensive” refers to surveillance that is potentially including all sites within the covered area
*✓ Available; ☑ Available but reportedly < 80% complete; ✗ Not reported/not available
**Intermittent periods from 2010 to 2018: 2010 (February to September), 2012 (February 2012 to January 2013), 2014 (January to December), 2016
(January to December), and 2018 (January to December)