Dynamics of bla_KPC-2 Dissemination from Non-CG258 Klebsiella pneumoniae to Other Enterobacterales via IncN Plasmids in an Area of High Endemicity

Carbapenem-resistant Enterobacterales (CRE) pose a significant threat to global public health. The most important mechanism for carbapenem resistance is the production of carbapenemases. Klebsiella pneumoniae carbapenemase (KPC) represents one of the main carbapenemases worldwide. Complex mechanisms of bla_KPC dissemination have been reported in Colombia, a country with a high endemicity of carbapenem resistance. Here, we characterized the dynamics of dissemination of bla_KPC gene among CRE infecting and colonizing patients in three hospitals localized in a highly endemic area of Colombia (2013 and 2015).

ABSTRACT

Carbapenem-resistant Enterobacterales (CRE) pose a significant threat to global public health. The most important mechanism for carbapenem resistance is the production of carbapenemases. Klebsiella pneumoniae carbapenemase (KPC) represents one of the main carbapenemases worldwide. Complex mechanisms of bla_KPC dissemination have been reported in Colombia, a country with a high endemicity of carbapenem resistance. Here, we characterized the dynamics of dissemination of bla_KPC gene among CRE infecting and colonizing patients in three hospitals localized in a highly endemic area of Colombia (2013 and 2015). We identified the genomic characteristics of KPC-producing Enterobacterales recovered from patients infected/colonized and reconstructed the dynamics of dissemination of bla_KPC-2 using both short and long read sequencing. We found that spread of bla_KPC-2 among Enterobacterales in the participating hospitals was due to intra- and interspecies horizontal gene transfer (HGT) mediated by promiscuous plasmids associated with transposable elements that was originated from a multispecies outbreak of KPC-producing Enterobacterales in a neonatal intensive care unit. The plasmids were detected in isolates recovered in other units within the same hospital and nearby hospitals. The gene “epidemic” was driven by IncN-pST15-type plasmids carrying a novel Tn4401b structure and non-Tn4401 elements (NTE_KPC) in Klebsiella spp., Escherichia coli, Enterobacter spp., and Citrobacter spp. Of note, mcr-9 was found to coexist with bla_KPC-2 in species of the Enterobacter cloacae complex. Our findings suggest that the main mechanism for dissemination of bla_KPC-2 is HGT mediated by highly transferable plasmids among species of Enterobacterales in infected/colonized patients, presenting a major challenge for public health interventions in developing countries such as Colombia.

INTRODUCTION

Carbapenem-resistant Enterobacterales (CRE) currently pose a significant threat to global public health because the resulting infections are associated with high morbidity and mortality and very limited treatment options (1). In addition, the widespread transmission of carbapenem resistance via mobile genetic elements remains a main reason for concern (2). The most important mechanism for carbapenem resistance is the production of carbapenemases. Indeed, the Klebsiella pneumoniae carbapenemase (KPC) constitutes the most common class A beta-lactamase enzyme. KPC circulates worldwide and, along with New Delhi metallo-β-lactamase (NDM class B), Verona integron-encoded metallo-β-lactamase (VIM class B), imipenemase metallo-β-lactamases (IMP class B), and oxacilinase-48 (OXA-48 class D), is the most common carbapenemase identified worldwide (3, 4).

Since the first case of KPC identified in a K. pneumoniae clinical isolate from North Carolina in 1996 (5), international spread has occurred, and multiple outbreaks have been reported worldwide. In particular, a single clonal group (CG), designated CG258, has been responsible for the majority of infections, with two principal sequence types (STs) ST258 and ST512 (a single locus variant of ST258) representing the majority of bla_KPC-containing K. pneumoniae. CG258 is responsible for >80% of outbreak isolates in the United States and about 90% of infections in Israel (6–9). The allelic variants bla_KPC-2 and bla_KPC-3 are the predominant genes associated with K. pneumoniae in Europe (Greece and Italy), Middle East (Israel), South America (Colombia and Argentina), and North America (especially the United States) (6–13). The bla_KPC gene is often located on the mobile transposon Tn4401 and also on diverse plasmids, including broad-host-range plasmids of the incompatibility groups IncA/C, IncL/M, and IncN (14). Outbreaks of KPC-producing Enterobacterales caused by transferable plasmids have also been reported, specifically, by “promiscuous” plasmids of incompatibility group N (IncN) that harbor the bla_KPC-2 gene (15).

In South America, the first detection of bla_KPC on a conjugative plasmid was reported in Colombia (16), and since then, the country has become a region where strains producing carbapenemases are endemic (17). In Colombia, outbreaks of KPC-producing K. pneumoniae were initially attributed to strains belonging to clonal group CG258 (12, 13). Previous published data also suggested cocirculation of K. pneumoniae CG258 strains carrying bla_KPC-3 and non-CG258 (from different STs) harboring bla_KPC-2 (18, 19). However, a recent comprehensive genomic study indicated that the likely emergence of carbapenem resistance in Colombian hospitals was driven by the horizontal transfer of promiscuous plasmids harboring bla_KPC-2 among Gram-negative bacteria instead of clonal dissemination of CG258 strains (19).

Here, we characterized the dynamics of transmission of bla_KPC genes among CRE infecting and colonizing patients in an area of endemicity in Colombia around the city of Medellín, encompassing more than 2 million inhabitants. We provide evidence that the major mechanism for the spread of carbapenemase resistance (bla_KPC-2) is the horizontal gene transfer (HGT) mediated by highly transferable plasmids, leading to a high endemicity of carbapenem resistance among Enterobacterales.

RESULTS

Infection/colonization by KPC-producing Enterobacterales in neonates and adults.

Between July 2013 and August 2015, 185 CRE clinical isolates of infected and colonized patients were collected from three hospitals serving the Medellin metropolitan area and adjacent communities (Central area of Colombia). Among the recovered organisms, 131 (70.8%) were positive for bla_KPC (based on PCR), with 125 (95,4%) and 6 (4.6%) isolates carrying bla_KPC-2, and bla_KPC-3, respectively. These isolates were obtained from a group of 110 patients, encompassing 58 (53%) adults, 51 (46%) newborns, and one infant patient (1%) (see Data Set S1 in the supplemental material).

Among adult patients, 27 (47%) were colonized and 31 (43%) were considered infected. A total of 6 infected patients were previously colonized by KPC-producing Enterobacterales. More than half of the patients were males (56.9%, n = 33) and the majority were older (median age of 61 years; interquartile range [IQR] = 48 to 79 and 70 years; IQR = 56 to 81 years in colonized and infected patients, respectively). In the infected patients, KPC-producing Enterobacterales were most frequently isolated from urine and respiratory samples (32.3 and 25.8%, respectively). Overall, patients exhibited several underlying conditions, among which diabetes (34.5%), chronic obstructive pulmonary disease (20.7%), and chronic kidney disease (20.7%) were the most common. A total of 14 (24.1%) patients had previous antibiotic exposure. The most frequent antibiotics were cephalosporins (13.8%), beta-lactam/beta-lactamase inhibitor combination and carbapenems (10.3% for each) (see Table S1 in the supplemental material).

Among newborns, 46 (90.2%) were colonized, and 5 (9.8%) were infected by KPC-producing Enterobacterales. In colonized newborns, the mean length of hospital stay before sampling was 12 days (IQR = 5 to 30 days). A total of 26.1% (n = 12) were premature, and 36.9% (n = 17) had been previously exposed to antibiotics, mainly to aminoglycosides (26.1%), aminopenicillins (26.1%), and cephalosporins (23.9%). Several patients were colonized by up to 2 (n = 7) or 3 (n = 1) different species of Enterobacterales (see Table S2).

A total of 48 neonates (45 colonized and 3 infected) were involved in an outbreak that occurred during the study period in the neonatal intensive care unit (NICU) in hospital 1. Indeed, on 7 March 2014, 11 cases of CRE colonization in newborns were detected in the weekly surveillance cultures. Overall, 82 and 7 newborns, respectively, were colonized and infected by CRE and linked to the outbreak, which was declared over on 30 December 2014. Subsequently, five sporadic cases of colonization by carbapenem-resistant Enterobacter cloacae were detected between January and August 2015.

Non-CG258 K. pneumoniae in the outbreak setting shared an IncN plasmid.

Of the 57 isolates previously identified as carbapenem-resistant K. pneumoniae, 51 (89.5%) and 6 (10.5%) were positive for bla_KPC-2 and bla_KPC-3, respectively (see Data Set S1). Of these, 29 isolates were selected for WGS (n = 23/bla_KPC-2, n = 6/bla_KPC-3) based on initial characterization by rep-PCR/DiversiLab. The majority (n = 25) were identified as K. pneumoniae, 3 were identified as Klebsiella quasipneumoniae, and 1 was identified as Klebsiella variicola.

The KPC-2-producing K. pneumoniae isolates involved in the neonatal outbreak in hospital 1 (in 2014), exhibited a variety of genetic backgrounds that were not related to CG258. One main lineage was ST502 (n = 10) harboring capsular type wzi 50. Other isolates belonged to ST140 (n = 2), ST36 (n = 1), and ST101 (n = 1) exhibiting different capsular types (wzi 306, 394, and 29, respectively) and virulence factors. Despite the major differences in genetic backgrounds the isolates harbored a similar IncN plasmid replicon type and carried bla_SHV, sul1, fosA, and aac(6′)-Ib-cr conferring, respectively, β-lactam, sulfonamide, fosfomycin, and aminoglycoside/quinolone resistance (Fig. 1 and Table 1). In addition, the bla_KPC-2 gene was located on a novel Tn4401b transposon, which was flanked by a GATCT target site duplication and modified by the insertion of the Tn5403 element which was flanked by 34-bp inverted repeats into the ISKpn6 element (see Fig. S1 in the supplemental material).

FIG 1.

Phylogenetic tree showing the genetic relationships among isolates of Klebsiella spp. (n = 29), E. coli (n = 12), and Enterobacter cloacae complex (n = 20) harboring bla_KPC. The results were generated by RAxML and visualized by the iTOL program. For species assignation, “K.va” indicates Klebsiella variicola, “K.qu” indicates Klebsiella quasipneumoniae, “K.pn” indicates Klebsiella pneumoniae, “E.col” indicates Escherichia coli, “E.ch” indicates Enterobacter chengduensis, “E.as” indicates Enterobacter asburiae, “E.ko” indicates Enterobacter kobei, “E.clo” indicates Enterobacter cloacae, and “E.ho” indicates Enterobacter hormaechei. Isolates were characterized by ST and year of isolation. We show whether the isolate was recovered from an infected/colonized patient, a neonate or an adult patient, and from a outbreak/nonoutbreak. We indicate the bla_KPC variant, transposable element carrying bla_KPC, capsular type (wzi typing), IncN replicon plasmid identified in the different species of Enterobacterales harboring bla_KPC and virulence determinants identified in Klebsiella spp.

TABLE 1.

Molecular characteristics of 72 KPC-producing Enterobacterales isolates sequenced by Illumina platform

Species	STa	Hospital	No. of isolates	Patient type	Variant of blaKPC-2	Transposon isoformb	Additional resistance genes	Plasmid replicon typec
Klebsiella spp.
K. pneumoniae	ST502	1	10	Neonate	blaKPC-2	Novel Tn4401b	blaSHV-62, sul1, aac(6′)-Ib-cr, fosA	IncN, IncR
	ST140	1	2	Neonate	blaKPC-2	Novel Tn4401b	blaSHV-1, sul1, aac(6′)-Ib-cr, str(A,B), oqx(A,B), fosA	IncN, IncFIA, IncFII
	ST101	1	1	Neonate	blaKPC-2	Novel Tn4401b	blaSHV-1, sul1, aac(6′)-Ib-cr, aph(3″)-Ib, aph(6′)-Id, str(A,B), oqx(A,B), catA1, tet(D), fosA	IncN, IncFIB, IncFIB(K), IncFII, IncFII(K)
	ST36	1	1	Neonate	blaKPC-2	Novel Tn4401b	blaSHV-11, sul1, aac(6′)-Ib-cr, str(A,B), oqx(A,B)	IncN, IncR, IncFIB, IncFII
	ST17	1	1	Adult	blaKPC-2	Novel Tn4401b	blaSHV-11, sul1, aac(6′)-Ib-cr, oqx(A,B), tet(D), fosA	IncN, IncFIB(K), IncFII
		2	1	Adult	blaKPC-3	Tn4401a	blaSHV-11, sul1, sul2, aadA2, oqx(A,B), erm(B), cmIA1, tet(B,D), fosA, dfrA15	IncFIB(K), IncFIB(pQIL), IncFII, IncFII(K)
		3	1	Adult	blaKPC-3	ND	blaSHV-11, sul1, oqx(A,B), catA1, tetD, fosA	IncHI1B, IncFIB
	ST15	1	1	Adult	blaKPC-2	Novel Tn4401b	sul1, aac(6′)-Ib-cr, aadA1, oqx(A,B), qnrB19, mph(A), tet(A), fos(A)	IncN, ColpVC, IncFIB(K), IncFII(K), IncI1
	ST433	1	1	Adult	blaKPC-2	Non-Tn4401	blaSHV-11, sul(1,2), aac(6′)-Ib-cr, aadA16, oqx(A,B), qnrB6, fosA5, arr3, dfrA27	IncN, ColRNAI, IncFIB(K), IncFII(K), IncX3
	ST964	1	1	Adult	blaKPC-2	Tn4401b	blaSHV-1, aac(3″)-IIa, aph(3″)-Ib, aph(6′)-Id, oqx(A,B), qnrB19, fosA	IncFIA, IncFIB(K), IncFII(K)
	ST25	1	1	Adult	blaKPC-2	Tn4401b	blaSHV-1, oqx(A,B), fosA	ND
	ST258	1	1	Adult	blaKPC-3	Tn4401b	blaSHV-28, sul(1,3), aac(3)-IVa, aac(6′)-Ib, aph(4)-Ia, aad(A2,A24), oqx(A,B), catA1, cmlA1, fosA, dfrA12	ColRNAI, IncR, IncFIB(K), IncFII(K), Incl2
	ST512	1	3	Adult	blaKPC-3	Tn4401a	blaSHV-11, sul1, aac(6′)-Ib, aph(3)-Ia, aadA2, oqx(A,B), catA1, fosA, dfrA12	ColRNAI, IncFIB(K), IncFIB(pQIL), IncFII(K), IncX3
K. variicola		1	1	Adult	blaKPC-2	Novel Tn4401b	blaLEN25, sul1, aac(6′)-Ib-cr, oqx(A,B).	IncN, IncFIB(K), IncFII(K)
K. quasipneumoniae		1	1	Adult	blaKPC-2	Tn4401b	blaOKP-A-5, sul1, oqx(A,B), fosA	IncR, IncFII(K)
		2	1	Adult	blaKPC-2	Novel Tn4401b	blaOKP-A-5, sul1, aac(6′)-Ib-cr, oqx(A,B), fosA	IncN, IncR, IncFII(K)
		2	1	Adult	blaKPC-2	Tn4401b	blaOKP-B-3, sul2, rmtG, oqx(A,B), qnrB19, fosA	IncL/M(pMU407), IncHI1B, IncFIB, IncFII
E. coli	ST349	1	4	Neonate	blaKPC-2	Novel Tn4401b	blaOXA-1, sul1, aac(6′)-Ib-cr, aadA1, catA1, tet(B)	IncN, IncFIB
	ST131	1	2	Adult	blaKPC-2	Novel Tn4401b	blaSHV-5, sul1, sul3, aac(3)-IV, aac(6′)-Ib-cr, aph(4)-Ia, aad(A1,A2), cmIA1	IncN, IncHI2, IncHI2A, IncFIB, IncFII, IncI1
		1	1	Adult	blaKPC-2	Non-Tn4401	sul(1,2), aac(3)-IId, aph(3″)-Ib, aph(3)-IId, aadA16, qnrB6, tet(A), arr3, dfrA12, dfrA27	IncN, IncFIA, IncFIB, IncFII
	ST1236	1	1	Adult	blaKPC-2	Non-Tn4401	blaTEM-1A	ColRNAI, IncY
	ST405	2	1	Adult	blaKPC-2	ND	blaCMY-2, sul(1,2), aac(3)-IId, aadA5, aph(3″)-Ib, aph(6′)-Id, str(A,B), mph(A), tet(A), dfrA17	IncFIB, IncFII, IncI1
	ST8217	2	1	Adult	blaKPC-2	Tn4401 b	blaCTX-M-12, sul(1,2), aadA1, rmtG, qnrB19, mdf(A)	IncL/M(pMU407), IncHI1B, IncFIB, IncFII, IncI1
	ST127	2	1	Adult	blaKPC-2	Tn4401b	aac(3″)-IIa, str(A,B), qnrB19	IncN2, IncFII
	ST101	3	1	Adult	blaKPC-2	Tn4401b	sul(2,3), aad(A1,A2), str(A,B), qnrB19, cmIA1, floR, tet(A), tet(M), dfrA12	IncL/M(pMU407), IncN2, IncFIB, IncX1
Enterobacter cloacae complex
E. hormaechei	ST1396*	1	1	Neonate	blaKPC-2	Non-Tn4401	blaACT-7, sul1, aac(6′)-Ib-cr, aph(3″)-Ib, aadA16, qnrB6, fosA, arr-3, dfrA27	IncN, IncFIB(K)
	ST116	1	4	Neonate	blaKPC-2	ND	blaACT-7, sul2, aph(3″)-Ib, aph(6)-Id, str(A,B), tet(D), fos(A), dfrA14	IncFIB, IncFII
	ST66	1	2	Neonate	blaKPC-2	ND	blaACT-7, blaACT-16, fosA, aph(6′)-Id	IncFIB, IncFII
	ST141	1	1	Neonate	blaKPC-2	ND	blaACT-7	IncFIB(K), IncFII
	ST510	1	2	Neonate	blaKPC-2	Tn4401b	blaACT-7, sul(1,2), aac(3)-IId, aadA2, mph(A), tet(D), fosA, dfrA12	IncFII, IncL/M, IncX5
	ST200	2	1	Adult	blaKPC-2	Tn4401b	blaACT-16, blaCTX-M12, sul(1,2), aac(3)-IId, aac(6′)-Ian, aph(3″)-Ib, aph(6′)-Id, aadA2, qnrE1, mph(A), catA2, tet(D), fosA, dfrA12, mcr-9	IncN2, IncHI2, IncHI2A, IncFIB, IncFII, IncX5
E. asburiae	ST252	1	1	Neonate	blaKPC-2	Non-Tn4401	blaACT-3, blaACT-7, sul1, aac(6′)-Ib-cr, aadA16, qnrE1, qnrB6, fosA, arr3, dfrA27	IncN, IncFIB(K)
E. cloacae	ST456	1	2	Adult	blaKPC-2	Tn4401b	blaCMH-3, sul1, aac(6′)-Ib-cr, aac(6′)-Ib3 aac(6′)-II, aadA1 aadA2, mphA, fosA, dfrA1, dfrA12	ND
		2	1	Adult	blaKPC-2	Tn4401b	blaCMH-3, blaCTX-M-12, sul(1,2), aac(6′)-Ib-cr, aac(3)-IId, aac(6′)-Ib3, aac(6′)-II, aadA1, aadA2, rmtG, qnrB19, mph(A), tet(D), fosA, dfrA(1,12)	IncL/M
		3	1	Adult	blaKPC-2	Tn4401b	blaCHM-3, blaCTX-M-12, sul1, aac(3)-IId, aac(6′)-Ib3, aac(6′)-II, aad(A1,A2), aac(6′)-Ib-cr, mph(A), tet(D), fosA, dfr(A1,A12)	ND
E. kobei	ST32	1	2	Adult	blaKPC-2	Tn4401b	blaACT-9, aph(3″)-Ib aph(6)-Id, aacA4, fosA	IncN2
		1	1	Adult	blaKPC-2	Tn4401b	blaACT-9, sul1, aac(3″)-IIa, aac(3)-VIa, aph(3″)-Ib aph(6)-Id, aadA1, qnrB19, tet(A), fosA, mcr-9	IncN2
E. chengduensis	ST414	2	1	Adult	blaKPC-2	Tn4401b	blaACT-6, aac(3″)-IIa, aph(3″)-Ib, aph(6′)-Id, qnrB19, fosA	IncN2
Citrobacter spp.
C. portucalensis		1	1	Adult	blaKPC-2	Tn4401b	blaCMY-77, sul(1,2), aac(6′)-Ib-cr, aad(A2,A16), qnrB19, qnrB6, mph(A), tet(D), arr-3, dfrA12 dfrA27	IncN, lncHI1A(CIT), IncHL1B(CIT), IncX5
C. freundii	ST215	1	1	Adult	blaKPC-2	Tn4401b	blaCMY-110, sul1, aac(6′)-Ib-cr, aadA16, qnrB6, arr-3, dfrA27	IncN, RepA
	ST169	2	1	Adult	blaKPC-2	Tn4401b	blaCMY-65, qnrB38	Col440l, lncFlB(pHCM2), IncX5
	ST504*	2	1	Adult	blaKPC-2	Tn4401b	blaCMY-65, blaCTX-M15, sul1, aac(3″)-IIa, aac(6′)-Ib-cr, ant(2″)-Ia, aph(3″)-Ib, aph(6′)-Id, aadA1, qnrB60, qnrB38, mph(A), erm(B), catB3, cmlA1	IncN2, IncFII(K), RepA
	ST22	2	1	Adult	blaKPC-2	Tn4401b	blaCMY-48, sul(1,2), aac(3″)-IIa, aac(6′)-Ian, aph(3″)-Ib, aph(3′)-Ia aph(6′)-Id, aad(A10,A1), qnrB19, tet(B), tet(D), dfrA1	IncN2, RepA
Serratia marcescens		1	4	Adult	blaKPC-2	Tn4401 b	blaSRT-2, blaCTX-M-12, sul(1,2), aac(3″)-IIa, aac(6′)-Ic, qnrB19 aac(6′)-Ib-cr, tet(41)	IncA/C, IncA/C2, IncN2, IncR, IncHl1A(CIT), IncHL1B(CIT), IncP6
		3	1	Neonate	blaKPC-2	Tn4401b	sul(1,2), aac(3″)-IIa, aac(6′)-Ic, aac(6′)-Ian, aph(3″)-Ib, aph(3′)-Ia, aph(6′)-Id, aadA10, catA1, dfrA1	IncA/C2, IncN2
		3	1	Adult	blaKPC-2	Tn4401b	blaSRT-2, blaCTX-M-12, sul1, aac(6′)-II, aac(6′)-Ic, ant(2″)-Ia, aadA5	IncL/M

^a*, new sequence type (ST).

^bND, not detected.

^cThe IncN plasmid replicon type is indicated in boldface.

We also detected bla_KPC-2 in non-CG258 K. pneumoniae (ST15, -17, -25, -433, and -964; Fig. 1) from colonized and infected adults in the participating hospitals (2013 to 2015). Some isolates that belonged to ST15 and ST17 (C1-205 and C1-01) carried bla_KPC-2 on the novel Tn4401b. Of note, we found similar resistance genes and plasmid replicons (IncN) to that found in isolates that had been involved in the NICU outbreak (Fig. 1 and Table 1). In particular, a K. pneumoniae ST433 (C1-201-2) isolate carried bla_KPC-2 on a non-Tn4401 genetic element (NTE_KPC) of Tn3 elements-Δbla_TEM-bla_KPC-2-ΔTn1721, previously described (20). This isolate carried five plasmid replicons, including IncN and genes conferring resistance to several antibiotics, including sulfonamides, rifampin, trimethoprim, aminoglycosides, and quinolones (Table 1).

Furthermore, K. variicola (C1-76) and K. quasipneumoniae (C2-116) isolates recovered from colonized adults at hospital 1 and hospital 2, also carried the bla_KPC-2 on the novel Tn4401b. We also identified the IncN plasmid replicon and resistance determinants similar to those isolates from the neonatal outbreak (Fig. 1 and Table 1). Overall, our results suggest that the spread of bla_KPC-2 across different clones of K. pneumoniae non-CG258, K. variicola, and K. quasipneumoniae strains was due to the same IncN type conjugative plasmid that carried the gene bla_KPC-2 into the modified Tn4401b via insertion of a Tn5403 element. This plasmid seems to have the ability to broadly disseminate between hospitals.

Simultaneous circulation of K. pneumoniae CG258 harboring bla_KPC-3 favors dissemination of carbapenem resistance.

Phylogenetic analyses showed four CG258 K. pneumoniae isolates that harbored bla_KPC-3. They belonged to ST512 (C1-184-1, C1-169-2, and C1-168) and ST258 (C1-78). All of them contained the wzi 154 capsular type and were recovered from infected and colonized adult patients from a single hospital (Fig. 1). In the ST258 isolate, bla_KPC-3 was located on a Tn4401b transposon, and we were able to identify virulence factors, such as type 3 fimbriae, yersiniabactin, and colibactin, as well as five plasmid replicons, including IncI2 (Fig. 1 and Table 1). A BLAST analysis indicated high similarity to an Incl2 plasmid previously described in US isolates and to a K. pneumoniae isolate from Colombia (COL-Kpn48) (19, 21) (see Fig. S2). In contrast, the bla_KPC-3 of ST512 isolates was located on a Tn4401a transposon and contained only the type 3 fimbriae (Fig. 1). We also identified a set of four plasmid replicons that were shared, including the IncFIB(pQIL) plasmid replicon (two isolates, C1-168 and C1-169-2) (Table 1). Of note, the IncFIB(pQIL) plasmid is similar to a ST512 strain previously associated with an outbreak in the city of Medellin (19). Thus, our findings suggest that carbapenem-resistant K. pneumoniae CG258 isolates are also circulating concomitantly with non-CG258 K. pneumoniae, favoring the dissemination of carbapenem resistance.

Interspecies transmission of IncN plasmids carrying bla_KPC-2 carbapenemase.

During the sampling period, we collected 74 isolates from species other than K. pneumoniae carrying bla_KPC-2 in colonized/infected neonates and adults (see Data Set S1). In total, 43 of these isolates were selected for WGS based on initial characterization by rep-PCR/DiversiLab. The organisms identified were Escherichia coli (n = 12, 7 STs), Enterobacter cloacae complex (including Enterobacter hormaechei [n = 11, 5 STs, 1 new ST], Enterobacter cloacae [n = 4, 1 ST], Enterobacter kobei [n = 3, 1ST], Enterobacter asburiae [n = 1, 1 ST], and a recently described species of Enterobacter chengduensis [n = 1, 1 ST] [22]) (Fig. 1), Citrobacter freundii (n = 4, 3 STs, 1 new ST), Citrobacter portucalensis (n = 1), and Serratia marcescens (n = 6) (see Fig. S3).

Most isolates carried genes conferring resistance to several antibiotics, including amynoglycosides, sulfonamides, tetracyclines, trimethroprim, quinolones, phenicols, fosfomycin, and β-lactams (Table 1). Notably, two isolates of Enterobacter cloacae complex (E. kobei ST32 and E. hormaechei ST200) harbored the mcr-9 gene, related to resistance to polymyxins (23) (Table 1). Of note, the genetic environment of mcr-9 was similar to the one found in the chromosome of E. hormaechei strain S5 (accession number CP031571.1) recovered in the United States in 2015 (24) (see Fig. S4).

The bla_KPC-2 gene was located on the Tn4401b isoform in 25/43 isolates sequenced. The remaining isolates carried the novel Tn4401b, including six E. coli isolates (ST349 [n = 4] and ST131 [n = 2]) (Fig. 1). The non-Tn4401 element (NTE_KPC) found in K. pneumoniae ST433 (see above) was also detected in two E. coli isolates (ST131 and ST1236). In E. hormaechei ST1396 and E. asburiae ST252, NTE_KPC was identified with a insertion of Tn5403 into the tnpA(Tn3). Of note, these isolates shared the IncN plasmid replicon (Table 1). In E. coli ST405 (n = 1) and E. hormaechei ST116 (n = 4), ST66 (n = 2), and ST141 (n = 1), bla_KPC-2 was not detected in the genome, suggesting the loss of the plasmid or bla_KPC gene during storage or subculture processing prior to sequencing.

Taken together, our results support interspecies dissemination of bla_KPC-2 among Enterobacterales driven by promiscuous plasmids, predominantly of the incompatibility N group (IncN) carrying a novel Tn4401b structure and non-Tn4401 elements (NTE_KPC).

Characterization of IncN plasmids involved in dissemination of bla_KPC-2.

We evaluated the transferability of bla_KPC-2 by mating assays, selecting one K. pneumoniae ST15 (C1-205) isolate carrying the bla_KPC-2 on the novel Tn4401b and IncN plasmid replicon type as donor. We readily transferred bla_KPC-2 into E. coli J53 with a conjugation efficiency of 1 × 10⁻² per donor cells. We selected the transconjugant (E. coli Tc_C1-205) and other Enterobacterales (C1-70, C1-83, C1-93, C1-94, C1-143, C1-134, C1-205, and C2-116) to characterize the genetic location of bla_KPC-2. Our results indicated that all isolates had bla_KPC2 located on an ∼56-Kb plasmid (see Fig. S5).

To reconstruct the complete plasmid sequence, we selected one K. pneumoniae ST502 isolate (C1-94) and sequenced the genome using the MinION platform (long-read sequencing). The 56,321-bp plasmid was designated pIncN_C1-94_KPC and determined to be ST15 at the pMLST (Fig. 2a). We confirmed that the plasmid carried the novel Tn4401b associated with a class 1 integron and other resistance genes [sul1, qacEDelta1, aac(6′)Ib-cr]. Subsequently, we used this plasmid sequence to determine its presence in each isolate using the Illumina data (short read). We identified the plasmid in the transconjugant strain (E. coli Tc_C1-205) and 24 Enterobacterales isolates (Fig. 2a). Our findings support the notion that pIncN_C1-94-KPC mediated the initial neonatal outbreak, spreading to other units within the same hospital, and was circulating simultaneously in other regional hospitals into different Enterobacterales.

FIG 2.

(a) BLAST Ring Image Generator (BRIG 0.95 and BLASTN v2.2.29) alignment of 24 sequenced bla_KPC-2-carrying Enterobacterales and the Tc_C1-205 transconjugant harboring the annotated pIncN_C1-94_KPC (accession number “contig_241_1” within WGS genome SAMN07291374; inside ring). Each isolate and the Tc_C1-205 transconjugant are indicated by a ring of different color (left panel). The outer ring shows resistance genes, as well as the structural genes of pIncN_C1-94_KPC indicated by different colors (right panel). The novel transposon Tn4401 (blue dotted line) harboring an insertion of Tn5403 (red dotted line) into ISkpn6 is also shown. (b) BLAST Ring Image Generator (BRIG 0.95 and BLASTN v2.2.29) of six sequenced bla_KPC-2-carrying Enterobacterales isolates using plasmid pEC881 as reference (accession number CP019026.1) from an E. coli recovered in Cali, Colombia, 2013 (inside ring). Each isolate is indicated by a ring of different color (left panel). The outer ring shows the resistance and structural genes indicated by different colors (right panel). The NTE_KPC element (green dotted line) harboring an insertion of Tn5403 (red dotted line) into tnpA(Tn3) in C1-174 and C1-186 isolates is also shown.

We also detected a second IncN plasmid in some isolates that carried the bla_KPC-2 on non-Tn4401 elements (NTE_KPC) (C1-169-1, C1-201-2, C1-186, and C1-174). This plasmid was similar to a completely sequenced pEC881_KPC plasmid (accession number CP019026.1) from an E. coli strain recovered in Cali, Colombia, in 2013 (20) (Fig. 2b). Likewise, we identified the backbone of this plasmid in Citrobacter portucalensis (C1-154) and C. freundii ST215 (C1-185) isolates recovered from adults at hospital 1 (Fig. 2b).

DISCUSSION

In this study, we characterized the dynamics of dissemination of bla_KPC-2 in different genera and species of Enterobacterales in hospitals serving an area of endemicity in Colombia with more than 2 million inhabitants. We show that broad dissemination of bla_KPC is facilitated by intra- and interspecies HGT mediated by promiscuous plasmids associated with transposable elements. This mechanism of spread led initially to a multispecies outbreak of KPC-2-producing Enterobacterales in a neonatal care unit. Subsequently, the bla_KPC-2-carrying plasmids were detected in Enterobacterales recovered from adult units in the same hospital and nearby hospitals over 3 years. The gene “epidemic” was driven by IncN-pST15-type plasmids carrying a novel Tn4401b structure and non-Tn4401 elements (NTE_KPC).

Previous studies (18, 19) had suggested that dissemination of bla_KPC-2 among K. pneumoniae non-CG258 in Colombia was mainly due to HGT, as well as its dissemination in other Enterobacterales (25, 26). Our study, using and extended and comprehensive evaluation of Enterobacterales recovered from colonized and infected patients in a high-endemicity area of Colombia, supports that concept and shows the efficient and expanding spread of carbapenem resistance, occurring mainly from hospitalized patients with the possibility of “spillover” to the community maintaining high circulation of these genes. Consistent with previous observations, K. pneumoniae isolates belonging to CG258 and carrying bla_KPC-3 also circulated simultaneously with other genetic backgrounds (mostly harboring bla_KPC-2). This phenomenon has created a “perfect storm” for dissemination of carbapenem resistance in Colombia (19).

Interestingly, multiple species of KPC-2-producing Enterobacterales (n = 24) were recovered in the NICU outbreak and adult units from hospital 1 and, subsequently, in nearby hospitals. The isolates exhibited heterogeneous genetic backgrounds but had in common the location of bla_KPC-2 gene within a novel Tn4401b element which harbors an insertion of Tn5403 transposon into the ISKpn6 (Fig. 1 and see Fig. S1). The Tn5403 element was previously identified as a “helper” element that participated in the transfer of nonconjugative plasmids, found in isolates of K. pneumoniae recovered from polluted aquatic environments (27). It was also found in isolates of Raoultella ornithinolytica, a microorganism widely distributed in aquatic environments, insects, and fish (28). Of note, Tn5403 only contains genes related to transpositions function and is known to transpose by replicative transposition. The element seems to play as “disruptive” or “reorganizing” force via transposition within plasmids from clinical isolates (29). Thus, it is tempting to speculate that this novel Tn4401b structure could have originated through the introduction of Tn5403 element mediated by homologous recombination between environmental and human-adapted hospital isolates.

Our analysis of short- and long-read whole-genome sequencing revealed that the novel Tn4401b element was harbored within the pIncN_C1-94_KPC plasmid, which was identified in the 24 Enterobacterales isolates described above (Fig. 2a), showing a high conjugation efficiency, as has been previously described in IncN-type plasmids (30–32). An additional non-Tn4401 element “carrier” of bla_KPC-2 (NTE_KPC) was also identified in different species of Enterobacterales from neonates and adults (Table 1), harbored in a plasmid similar to the IncN pEC881_KPC reported previously (20) (Fig. 2b). Thus, these two IncN plasmids played a key role in the transmission interspecies of bla_KPC-2 in some of the participating hospitals. Presumably, transposition of Tn5403 occurred and facilitated plasmid rearrangements (29).

Our findings are in agreement with previous studies (15, 32–37) by showing that the interspecies spread of bla_KPC-2 through plasmids adds an additional layer of complexity to the molecular investigation of multispecies outbreaks and strongly suggest conjugation capacity and high plasticity of IncN ST15 plasmids in the gastrointestinal environment within a patient. Thus, the data in the study indicated that dissemination of the bla_KPC-2 gene started in July 2013 in a K. pneumoniae ST17 isolate from an infected adult patient localized in non-ICU in hospital 1 that carried the bla_KPC2 within the novel Tn4401b into pIncN_C1-94_KPC plasmid. This plasmid seems to be the source of the subsequent outbreaks in the neonatal unit.

Figure 3 attempts to reconstruct the events of dissemination of bla_KPC2 of the outbreak. Our data suggest that, in the beginning of the outbreak (March 2014), the clonal dissemination of bla_KPC2 by non-CG258 lineage of K. pneumoniae ST502 occurred, followed by emergence of KPC-2-producing E. coli ST349 by acquisition of the pIncN_C1-94_KPC plasmid (Fig. 2a) and subsequent spread to other species of Enterobacterales (March to December 2014). In parallel, an E. coli ST131 recovered from an adult patient in non-ICU setting carried the bla_KPC-2 on NTE_KPC within a plasmid highly similar to pECC881_KPC (Fig. 2b). After the outbreak was controlled (2015), we detected sporadic cases in neonates colonized by E. asburiae ST252 (C1-174) and E. hormaechei ST1396 (C1-186) carrying bla_KPC-2 in the same plasmid pEC881_KPC, with some variations in the region containing the bla_KPC2. Also, in the adult unit C. freundii ST215 (C1-185) and C. portucalensis (C1-154) were identified carrying the backbone of pEC881_KPC, albeit carrying a Tn4401b (Fig. 2b), suggesting gene rearrangement likely through transposition and homologous recombination. Likewise, one isolate of K. quasipneumoniae (C2-116) recovered from an adult patient in hospital 2 (January 2015), harbored the pIncN_C1-94_KPC plasmid.

FIG 3.

Timeline of the outbreak and dissemination of bla_KPC2 among different Enterobacterales in hospitals located in Medellin and surrounding areas (2013 to 2015). The neonates are in orange, adult from hospital 1 in brown and adult from hospital 2 in dark blue. The asterisk indicates the place of stay in ICU (red) and non-ICU (light blue) at the time of sampling. The type of plasmid identified in the isolates are indicated with black and green ring. Those that exhibited variations within mobile elements are indicated with a green arrow pointing to the right.

Another important finding in our study is the identification of a group of closely related E. cloacae ST456 isolates (n = 4) carrying bla_KPC-2 on Tn4401b (Fig. 1), a finding only previously reported in Norway (38). Of note, E. kobei ST32 and E. hormaechei ST200 isolates recovered from infected and colonized adult patients carried the mcr-9 gene within a genetic environment similar to a previous isolate described in USA (Fig. S2). The mcr-9 was described initially in Salmonella enterica and E. coli (23, 39), and later in Enterobacter spp. and Klebsiella pneumoniae and has been associated with carbapenemase-encoding genes (bla_NDM-1, bla_VIM-1, bla_VIM-4, and bla_OXA-48) in the United States, China, and European countries (24, 40, 41). In South America, it has recently been described in K. quasipneumoniae associated with bla_NDM-1 in Argentina (42). To our knowledge, this is the first report of Enterobacter spp. harboring mcr-9 and bla_KPC-2. However, at the time of isolation, the organisms were susceptible to colistin therefore it is likely that the mcr-9 gene was not expressed, a finding consistent with previous reports (43). Of note, mcr-9 had not been previously reported in Colombia.

Some limitations of the study include the limited number of hospitals in the region and that we were not able to resolve all plasmid sequences by long-read sequencing. Seven isolates of E. hormaechei involved in the NICU outbreak could have lost the bla_KPC gene or the plasmid that contained it during storage or subculture processing prior to sequencing. Therefore, it was not possible to define the genetic environment of bla_KPC gene in those isolates. However, we used the analysis of those genomes in the study to describe aspects related to the outbreak in NICU from hospital 1.

In conclusion, the KPC carbapenemase epidemic in an area of high endemicity in Colombia is driven by the horizontal transfer of promiscuous plasmids harboring bla_KPC-2 among members of the Enterobacterales. This phenomenon has resulted in the occurrence of multispecies outbreak and high-level of genetic diversity of KPC-producing Enterobacterales. Our findings provided evidence of an epidemic of plasmid carrying bla_KPC rather than clonal expansion of successful genetic lineage. Interrupting plasmid transmission is a challenge for public health interventions in developing countries.

MATERIALS AND METHODS

Strain selection and clinical and epidemiological characterization.

We conducted a prospective surveillance study of CRE in three tertiary-care hospitals in Colombia between 2013 and 2015. Hospital 1 is located in Medellín and, hospitals 2 and 3 are located in surrounding areas (202, 143, and 146 beds, respectively). All hospitals have functional intensive care units (ICU) for adults and two of them have neonatal intensive care units (NICU).

We isolated Enterobacterales from infected or colonized patients. Colonization was defined as a CRE recovered from a surveillance rectal culture (only in two hospitals) or a clinical sample without associated symptoms or disease. Infection was defined by a compatible clinical syndrome with confirmation by the infectious disease services and/or infection control committee, retrospectively. Rectal swabs were cultured on a selective chromogenic medium (chromID CARBA; bioMérieux). The collected Enterobacterales exhibited nonsusceptibility to at least one carbapenem (imipenem, meropenem or ertapenem). Multiple CRE isolates from an individual patient, in the same or different specimens, were also included.

Surveillance rectal swabs were collected in the following patients: (i) individuals with previous stay in the ICU, (ii) patients who received broad-spectrum antibiotic treatment (piperacillin-tazobactam, cefepime, quinolones, or carbapenems) within 90 days before admission, (iii) immunosuppressed patients due to hematologic disease or cancer, (iv) patients who underwent kidney transplantation, (v) use of a long-term urinary catheter or surgical wound drainage, (vi) suspected infection at a different institution, and (vii) hemodialysis and peritoneal dialysis. Clinical and demographic data from colonized and infected patients (i.e., age, sex, colonization or infection by more than one CRE, ICU admission, antibiotic use, use of invasive medical devices, underlying diseases, and comorbidities) were collected from electronically medical records and recorded in a Microsoft Access Database. This study was approved by the Institutional Review Board (IRB) of each participating hospital.

Bacterial identification, antibiotic susceptibility testing, and detection of the bla_KPC gene.

Identification and antimicrobial susceptibility of Enterobacterales were performed by using the automated Vitek-2 system (bioMérieux Marcy-l’Étoile, France). The antimicrobial agents tested included ertapenem, imipenem, meropenem, cefotaxime, ceftazidime, ceftriaxone, cefepime, gentamicin, amikacin, and ciprofloxacin. MICs results were interpreted following the Clinical and Laboratory Standards Institute (CLSI) breakpoints (44).

All isolates classified as carbapenem-resistant were tested by PCR for the presence of the bla_KPC gene using primers and assays previously described (5). Klebsiella pneumoniae ATCC BAA-1705 and Klebsiella pneumoniae ATCC BAA-1706 were used as positive and negative controls for the PCR assay, respectively. DNA sequencing was performed on PCR amplification products and the results were compared and aligned with reference sequence using the online BLAST database for detection of variants of the bla_KPC gene.

Whole-genome sequencing.

A total of 72 isolates of CRE carrying bla_KPC were selected for whole-genome sequencing (WGS) based on initial characterization by rep-PCR/DiversiLab (bioMérieux Marcy-l’Étoile, France) and choosing representatives strains of major clonotypes. Genomic DNA was extracted with the GeneJET Genomic DNA purification kit (Thermo Fisher Scientific, Waltham, MA). DNA libraries were prepared using a NexteraXT DNA sample preparation kit and multiplexed with a NexteraXT index primer kit on the Illumina platform (Illumina, San Diego, CA). Genomic libraries were sequenced on a MiSeq sequencer to obtain 250-bp paired-end reads using kit v2 and v3 (Illumina). The readings were processed to eliminate low quality bases and contamination with sequences of adapters and later assembled by de novo assembly. Cleaning and assembly were carried out using CLC Genomics Workbench assembler, version 8.5. The genomes were annotated using the RAST server (http://rast.nmpdr.org).

In order to reconstruct a fully closed plasmid sequence from a Klebsiella pneumoniae isolate carrying the bla_KPC-2 and isolated from hospital 1, we used the MinION (Oxford Nanopore Technologies, Oxford, UK) platform to obtain long-read sequences. Genomic DNA was extracted using the DNeasy blood and tissue kit (Qiagen), and MinION libraries were prepared using the SQK-LSK208 kit according to the manufacturer´s protocol. We used both Illumina and MinION reads to fully generate the plasmid sequence. The BLAST Ring Image Generator (BRIG) (45) was used to align the assembled reads of the sequenced clinical isolates and the transconjugant Tc_C1-205 strain to the bla_KPC-2 carrying K. pneumoniae C1-94 plasmid (pIncN_C1-94_KPC) (accession number “contig_241_1” within WGS genome SAMN07291374). In addition, we aligned the assembled reads of some isolates sequenced to the reference plasmids carrying bla_KPC included pEC881_KPC (accession number CP019026.1) and pBK15692 (accession number NC_022520).

In silico MLST, genome annotation, virulence factors, and capsular typing.

The assemblies were typed on the web server of the Center for Genomic Epidemiology using the multilocus sequence typing (MLST; MLST 2.0 server; https://cge.cbs.dtu.dk/services/MLST/) (46). The determination of resistance elements, the plasmid replicon, and plasmid multilocus sequence type (pMLST) were identified using Resfinder 2.1 (https://cge.cbs.dtu.dk/services/ResFinder/), Plasmidfinder 2.1 (https://cge.cbs.dtu.dk/services/PlasmidFinder/), and pMLST 2.0, (https://cge.cbs.dtu.dk/services/pMLST/), respectively (47, 48), using an identity percentage higher than 95% and a coverage cutoff greater than 90%. The Tn4401 isoforms were determined by BLASTn comparing the region surrounding each bla_KPC gene to the sequences of the Tn4401 isoforms as described previously (49).

In addition, we identified virulence genes and capsular typing (wzi sequencing) of isolates of K. pneumoniae using the Institut Pasteur’s Klebsiella BigsDB site (http://bigsdb.pasteur.fr/klebsiella/klebsiella.html).

Phylogenetic analyses.

The phylogenetic reconstruction of the isolates was carried out by detecting single nucleotide polymorphisms (SNP) against reference genomes specific to each family of Enterobacterales: Klebsiella spp (accession number NZ_LAKK01000012.1), Escherichia coli (accession number CP010876.1), Citrobacter freundii (accession number NZ_CP011612.1), Enterobacter complex (accession number NRIS01000001.1), and Serratia marcescens (accession number NZ_HG326223.1). We also included the following reference genomes as an external group: E. coli K-12 MG1655 (accession number NC_000913), Escherichia fergusonii ATCC 35469 (accession number NC_011740.1), and Salmonella enterica CT18 (accession number NC_003198.1). An SNP matrix was constructed and used to reconstruct the phylogeny of the strains with RAxML (50). We used the general time reversal model with a GAMMA distribution and the Lewis correction for the parameters to determine the best phylogenetic reconstruction by maximum likelihood because the SNP matrix constitutes a matrix without invariant characters. We performed 20 runs and chose the one with the best score. In addition, 100 bootstraps were made to support the reconstructions. The trees obtained were visualized by iTOL (51).

Transferability of the bla_KPC gene and plasmid analysis.

We selected one isolate of K. pneumoniae (C1-205) from hospital 1 carrying the bla_KPC gene (according to short-read WGS-base analysis) and used it as donor in a conjugation experiment, with sodium azide-resistant E. coli strain J53 as the recipient. The experiments were performed as previously described (37). Briefly, donor and recipient were grown overnight with agitation at 37°C in tryptic soy broth (TSB). Cultures were transferred into fresh TSB (ratio 1:100) and incubated with agitation for approximately 5 h at 37°C, until the culture reached exponential growth (i.e., an optical density at 600 nm of 0.5 to 0.6). Donor and recipient cultures were mixed at a 1:10 ratio in fresh TSB and incubated at 37°C without agitation for 20 h. The conjugation mixture was diluted in phosphate-buffered saline, and dilutions were plated on tryptic soy agar (TSA) containing imipenem (4 μg/ml) and azide (150 μg/ml) for selection of transconjugants. The conjugation efficiency was calculated by dividing the number of transconjugant by donor cells. Antimicrobial susceptibility testing and PCR amplification of bla_KPC gene were subsequently performed to confirm the transconjugant Tc_C1-205.

To confirm the localization of bla_KPC-2 gene on a plasmid, we selected eight isolates of different Enterobacterales of hospitals 1 and 2 carrying bla_KPC genes (C1-70, C1-83, C1-93, C1-94, C1-143, C1-134, C1-205, and C2-116) based on short-read WGS analysis and the E. coli transconjugant (Tc_C1-205). S1 digestion and pulsed-field gel electrophoresis was performed using the previously described protocol (52, 53), followed by Southern hybridization using a digoxigenin (DIG) DNA-labeled bla_KPC probe (DIG-High Prime DNA labeling and detection starter kit II; Roche, Germany), following the manufacturer’s instructions. A transconjugant (Tc_C1-205) was sequenced on the Illumina MiSeq platform (Illumina), and the reads were assembled de novo using CLC Genomics Workbench assembler (v8.5) with default parameters, and the contigs were mapped against Escherichia coli J53 reference genome (accession number AICK01). Identification of plasmids associated with transfer of the bla_KPC gene was performed with BLASTn, using the unmapped contig harboring bla_KPC in E. coli Tc_C1-205 (accession number SAMN12815781).

Data availability.

The sequence data for the isolates included in this study were submitted to the NCBI GenBank database under BioProject number PRJNA391501.