Wednesday, March 29, 2023
| Carbapenemases (no. isolates) | Geographic location (no. isolates) | Sequence types (no. isolates) |
|---|---|---|
| KPCs (50) | ||
| KPC-2 (35) | Argentina (4), Brazil (5), Colombia (8), Greece (1), Guatemala (4), Israel (2), Puerto Rico (2), United States (4), Venezuela (1), Vietnam (4) | ST10 (3), ST46 (2), ST69 (2), ST95 (3), ST131 (7), ST349 (1), ST405 (3), ST410 (3), ST538 (1), ST540 (1), ST607 (1), ST617 (1), ST648 (1), ST1193 (1), ST1196 (1), ST2172 (1), ST2279 (1), ST3580 (1) |
| KPC-3 (14) | Colombia (1), Israel (1), Italy (8), United States (4) | ST12 (1), ST73 (1), ST131 (7), ST141 (1), ST191 (1), ST617 (1), ST973 (1), ST1148 (1) |
| KPC-18 (1) | United States (1) | ST131 (1) |
| NDMs (66) | ||
| NDM-1 (19) | Egypt (3), Guatemala (2), Kuwait (1), Morocco (4), Philippines (1), Romania (1), Russia (3), Serbia (1), Thailand (2), Vietnam (1) | ST38 (1), ST44 (1), ST69 (1), ST95 (1), ST131 (4), ST167 (3), ST345 (1), ST361 (1), ST617 (2), ST1193 (1), ST1434 (1), ST1470 (1), ST4553 (1), |
| NDM-4 (1) | Vietnam (1) | ST405 (1) |
| NDM-5 (40) | Canada (1), Egypt (16), Italy (2), Jordan (4), Lebanon (1), Thailand (8), United Kingdom (2), Vietnam (6) | ST131 (1), ST156 (1), ST167 (11), ST361 (4), ST405 (3), ST410 (12), ST448 (2), ST648 (4), ST2003 (2) |
| NDM-6 (1) | Guatemala (1) | ST38 (1) |
| NDM-7 (5) | Philippines (4), Vietnam (1) | ST156 (2), ST410 (1), ST448 (1), ST5229 (1) |
| OXA-48–like (96) | ||
| OXA-48 (40) | Austria (1), Belgium (2), Egypt (3), Georgia (3), Israel (1), Lebanon (2), Mexico (1), Morocco (2), Saudi Arabia (1), Spain (2), Thailand (1), Tunisia (1), Turkey (15), United Kingdom (1), Vietnam (4) | ST10 (2), ST12 (1), ST34 (1), ST38 (8), ST58 (1), ST131 (2), ST224 (1), ST349 (1), ST354 (6), ST361 (1), ST405 (4), ST410 (2), ST624 (1), ST648 (1), ST1431 (1), ST11260 (6) |
| OXA-181 (48) | Egypt (6), Germany (1), Jordan (15), Kuwait (1), Lebanon (1), Malaysia (1), South Africa (2), Taiwan (1), Thailand (2), Turkey (18) | ST46 (1), ST131 (1), ST167 (2), ST205 (1), ST354 (1), ST410 (21), ST648 (1), ST1284 (18), ST1487 (1), ST6802 (1) |
| OXA-232 (5) | Malaysia (1), Mexico (3), Thailand (1) | ST127 (1), ST131 (1), ST361 (3) |
| OXA-244 (3) | Egypt (3) | ST58 (1), ST648 (1), ST1722 (1) |
| VIMs (4) | ||
| VIM-1 (2) | Greece (1), Spain (1) | ST88 (1), ST404 (1) |
| VIM-23 (2) | Mexico (2) | ST410 (2) |
| IMPs (2) | ||
| IMP-59 (2) | Australia (2) | ST357 (2) |
| Two carbapenemases (11) | ||
| NDM-1 + VIM-1 (1) | Egypt (1) | ST131 (1) |
| NDM-1 + OXA-181 (2) | Egypt (2) | ST46 (2) |
| NDM-5 + OXA-48 (1) | Egypt (1) | ST167 (1) |
| NDM-5 + OXA-181 (5) | Egypt (3), South Korea (1), Vietnam (1) | ST410 (4), ST448 (1) |
| NDM-5 + OXA-232 (2) | United Kingdom (2) | ST2083 (2) |
Table. Global molecular epidemiology of 229 carbapenemase-producing Escherichia coli isolates, 36 countries, 2015–2017*
*KPC, Klebsiella pneumoniae carbapenemase; NDM, New Delhi metallo-β-lactamase; OXA, oxacillinase; ST, sequence type ; VIM, Verona integron‒encoded metallo-β-lactamase.
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This activity is intended for infectious disease clinicians, epidemiologists, public health officials, geneticists, internists, and other clinicians who treat and manage patients with or at risk for carbapenemase-producing Escherichia coli.
The goal of this activity is to describe the geographic distribution of different carbapenemase genes (including associations with dominant sequence types, clades, and underlying mobile genetic elements), other β-lactamases, antibiotic resistance genes, and virulence factors, based on short read whole genome sequencing of 229 carbapenemase-producing Escherichia coli (2015-17) from 36 countries (including 20 lower- and middle-income countries).
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We describe the global molecular epidemiology of 229 carbapenemase-producing Escherichia coli in 36 countries during 2015–2017. Common carbapenemases were oxacillinase (OXA) 181 (23%), New Delhi metallo-β-lactamase (NDM) 5 (20%), OXA-48 (17%), Klebsiella pneumoniae carbapenemase 2 (15%), and NDM-1 (10%). We identified 5 dominant sequence types (STs); 4 were global (ST410, ST131, ST167, and ST405), and 1 (ST1284) was limited to Turkey. OXA-181 was frequent in Jordan (because of the ST410-B4/H24RxC subclade) and Turkey (because of ST1284). We found nearly identical IncX3-bla OXA-181 plasmids among 11 STs from 12 countries. NDM-5 was frequent in Egypt, Thailand (linked with ST410-B4/H24RxC and ST167-B subclades), and Vietnam (because of ST448). OXA-48 was common in Turkey (linked with ST11260). Global K. pneumoniae carbapenemases were linked with ST131 C1/H30 subclade and NDM-1 with various STs. The global carbapenemase E. coli population is dominated by diverse STs with different characteristics and varied geographic distributions, requiring ongoing genomic surveillance.
Carbapenems are effective options available for treating serious infections caused by multidrug-resistant (MDR) Enterobacterales bacteria[1]. The emergence of carbapenem resistance is a major public health concern, and the World Health Organization has identified carbapenem-resistant Enterobacterales as critical-priority bacteria[2].
Carbapenemases are important causes of carbapenem resistance[3]. Carbapenemase genes can be transferred between Enterobacterales species. The most common carbapenemases among Enterobacterales are Klebsiella pneumoniae carbapenemases (KPCs), imipenemases (IMPs), Verona integron–encoded metallo-β-lactamases (VIMs), New Delhi metallo-β-lactamases (NDMs), and oxacillinase (OXA) 48–like enzymes. Escherichia coli is the second most common carbapenemase-producing Enterobacterales species[4,5].
Because E. coli is mainly responsible for human community-associated infections[6], it evades conventional hospital-based infection-prevention measures[7]. E. coli is an important One Health (i.e., human, animal, environmental health) reservoir for antimicrobial resistance (AMR) genes[8]. Tracking global mobile genetic elements and E. coli clones associated with carbapenemase genes is a public health priority[9] and aids in designing management and prevention strategies.
Comprehensive epidemiology data about carbapenemase-producing E. coli is limited to institutional, regional, or countrywide surveys[10]. We used short-read whole-genome sequencing (WGS) to describe the molecular characteristics and international distribution of carbapenemase-producing E. coli. We describe the geographic distribution of different carbapenemase genes (including their associations with dominant sequence types [STs], clades and underlying mobile genetic elements), other β-lactamases, AMR genes, and virulence factors.
