Klebsiella pneumoniae ST307 with blaOXA-181, South Africa, 2014-2016

Abstract

Klebsiella pneumoniae sequence type (ST) 307 is an emerging global antimicrobial drug-resistant clone. We used whole-genome sequencing and PCR to characterize K. pneumoniae ST307 with oxacillinase (OXA) 181 carbapenemase across several private hospitals in South Africa during 2014-2016. The South Africa ST307 belonged to a different clade (clade VI) with unique genomic characteristics when compared with global ST307 (clades I-V). Bayesian evolution analysis showed that clade VI emerged around March 2013 in Gauteng Province, South Africa, and then evolved during 2014 into 2 distinct lineages. K. pneumoniae ST307 clade VI with OXA-181 disseminated over a 15-month period within 42 hospitals in 23 cities across 6 northeastern provinces, affecting 350 patients. The rapid expansion of ST307 was most likely due to intrahospital, interhospital, intercity, and interprovince movements of patients. This study highlights the importance of molecular surveillance for tracking emerging antimicrobial clones.

Keywords: Enterobacteriaceae; Klebsiella pneumoniae; ST307; South Africa; antimicrobial resistance; bacteria; carbapenemases; genomic surveillance; outbreak; sequence type.

Figure 1

Locations of Klebsiella pneumoniae with ST307 oxacillinase 48–like in South Africa during January 2014–December 2016, as identified at Ampath Molecular Diagnostic Reference Center (PTA). EC, Eastern Cape Province; FS, Free State Province; GT-other, other cities in Gauteng Province; JHB, Johannesburg, Gauteng Province; LP, Limpopo Province; MP, Mpumalanga Province; NW, North West Province; PTA, Pretoria, Gauteng Province; ST, sequence type.

Figure 2

Geographic distribution of Klebsiella pneumoniae sequence type 307 with oxacillinase 181 in northeastern South Africa, January 2014–December 2016. A) South Africa; B) Gauteng Province; C) Limpopo Province; D) Mpumalanga Province. Map source: http://d-maps.com.

Figure 3

Bayesian phylogenetic analysis of global Klebsiella pneumoniae sequence type (ST) 307 isolates. The ST307 genomes included 88 from South Africa (this study) and 620 international isolates from 19 countries (downloaded from the US National Center for Biotechnology Information whole genome shotgun database). ST307 has 6 distinct clades, as indicated on branches. CTX-M, active on cefotaxime first isolated in Munich; KPC, Klebsiella pneumoniae carbapenemase; NDM, New Delhi metallo-β-lactamases; OXA, active on oxacillin; QRDR, quinolone resistance determinants.

Figure 4

Bayesian evolution analysis of Klebsiella pneumoniae sequence type (ST) 307 in South Africa hospitals, January 2014–December 2016. A and B indicate the 2 distinct lineages that evolved within Gauteng Province. Highlighted areas depict the provinces from which isolates were obtained, and colored dots at the tips of areas represent the cities from which the isolates were obtained (e.g., for Gauteng Province, Pretoria is red, Johannesburg is green). Dark blue dots at branch points indicate posterior probability >70%, and dot size is proportional to posterior probability values. Hospital locations are indicated as follows; all are private except for Tshwane tertiary hospital: A1, Alberton; J1–J10, Johannesburg; P1–P8, Pretoria; B1–3, Benoni; BO1, Boksburg; BR1, Brakpan; C1–C2, Centurion; EC1, Eastern Cape Province; FS1, Free State Province; K1, Krugersdorp; K2, Kempton Park; LP1–2, Limpopo Province; MP1–6, Mpumalanga Province; NW1, North West Province; S1, Springs; TTH, Tshwane (tertiary hospital). Box 1 shows intrahospital spread: highly related ST307 isolates were obtained from patient I51 and patient I68 in hospital P5. Box 2 shows interhospital spread: patient I14 was transferred from hospital P1 to hospital P4; 3 months later, highly related ST307 was isolated from patient K43 at hospital P4. Box 3 shows intercity and interprovince spread: patient I2 from Springs, patient K61 from Heidelberg, and patient K22 from North West Province, all with highly related ST307 isolates, had previously received medical care at hospital J2 in Johannesburg. HPD, highest posterior density interval; POP, outpatient.