Outbreak report of polymyxin-carbapenem-resistant Klebsiella pneumoniae causing untreatable infections evidenced by synergy tests and bacterial genomes

Polymyxin-carbapenem-resistant Klebsiella pneumoniae (PCR-Kp) with pan (PDR)- or extensively drug-resistant phenotypes has been increasingly described worldwide. Here, we report a PCR-Kp outbreak causing untreatable infections descriptively correlated with bacterial genomes. Hospital-wide surveillance of PCR-Kp was initiated in December-2014, after the first detection of a K. pneumoniae phenotype initially classified as PDR, recovered from close spatiotemporal cases of a sentinel hospital in Rio de Janeiro. Whole-genome sequencing of clinical PCR-Kp was performed to investigate similarities and dissimilarities in phylogeny, resistance and virulence genes, plasmid structures and genetic polymorphisms. A target phenotypic profile was detected in 10% (12/117) of the tested K. pneumoniae complex bacteria recovered from patients (8.5%, 8/94) who had epidemiological links and were involved in intractable infections and death, with combined therapeutic drugs failing to meet synergy. Two resistant bacterial clades belong to the same transmission cluster (ST437) or might have different sources (ST11). The severity of infection was likely related to patients’ comorbidities, lack of antimicrobial therapy and predicted bacterial genes related to high resistance, survival, and proliferation. This report contributes to the actual knowledge about the natural history of PCR-Kp infection, while reporting from a time when there were no licensed drugs in the world to treat some of these infections. More studies comparing clinical findings with bacterial genetic markers during clonal spread are needed.

for three days, and teicoplanin (400mg IV q12h) for one day, with dosages based on renal clearance.Appendix Table 1 shows patient and CCBH17440 strain data profiles.
Case 2. A previously healthy 25-year-old 85Kg black female with meningoencephalitis, later diagnosed as rhombencephalitis, was admitted to the same bed as the index case on the fifth day after his death.This bed was cleaned regularly and remained unoccupied for four days before this patient occupied it.Ceftriaxone, vancomycin, acyclovir/ganciclovir and later a course of ampicillin was given to this patient to treat her baseline disease.She also received pulse therapy with methylprednisolone (1g IV q24h) for three days but did not respond to the treatment.During the hospital course, she had worsened level of consciousness requiring mechanical ventilation.Four days later, she initiated empirical therapy for VAP with meropenem, polymyxin B, and linezolid for 21 days.On the 21 st day of admission, she was transferred to adult medical-surgical ICU at the same hospital because she developed acute renal failure requiring hemodialysis.Rectal and tracheal colonization with possible XDR and possible PDR K. pneumoniae strains were detected eight and 18 days later, respectively.Further, she received trimethoprim-sulfamethoxazole to treat Stenotrophomonas maltophilia VAP for 12 days, followed by another course of antibiotics comprising polymyxin B, meropenem, amikacin, vancomycin, and caspofungin for clinical sepsis and empirical therapy for CDAD, evolving with copious diarrhea until her death.PDR K. pneumoniae strains were isolated again from urine (≥10 5 CFU) and tracheal aspirate (≥10 6 CFU) (CCBH17428), causing sepsis due to VAP, without response to the combination of polymyxin B (1 million IU q12h), amikacin (1g q24h), vancomycin (1g q12h) and amphotericin B lipid complex (300mg q24) for nine days and levofloxacin (750mg IV q24h) for one day.
Supplementary Table 5. Virulence score and associated genes and features according to the main biological characteristics predicted in the literature, possibly leading to specific stages (yellow, pink and green) of ST437 (red) and ST11 (blue) polymyxin-carbapenemresistant K. pneumoniae infection.Case number in order of strain detection.AMR, antimicrobial resistance; MLST, multilocus sequence typing

Table 1 .
Algorithm 1. K. pneumoniae (Kp) complex isolates, without repetition, according to clinical and surveillance samples and resistance profile to any carbapenems and polymyxins, tertiary federal hospital, December 2014 to August 2015.a Target resistance corresponds to intermediate/resistance profile to any carbapenems (meropenem, imipenem or ertapenem) screening positive for polymyxins resistance.b One strain (CCBH19496) was excluded from the genome analysis due to experimental problems.CR-Kp, carbapenemresistant Kp; ESBL, extended spectrum beta-lactamase; PCR-Kp, polymyxin-carbapenem-resistant K. pneumoniae Supplementary Demographic and clinical characteristics of patients infected by polymyxin-carbapenem-resistant K.

days of previous rectal colonization with colistin- carbapenem-resistant K. pneumoniae and
developed Nosocomial diarrhea

56 days of previous rectal colonization with colistin-carbapenem-resistant K. pneumoniae,
Pneumonia and Pleural effusion, Nosocomial diarrhea Cases reported in order of strains detection; a Including non preserved CR-Kp screening positive for polymyxin resistance.b Reported cases in order of detection of target isolates.c Rectal swab negative for CRE previously or during infection.

Table 4 .
Antimicrobial resistance profile and related genes in clinical ST437 (red) and ST11 (blue) polymyxincarbapenem-resistant K. pneumoniae samples.

fepC/fhuF/ iroD e /iroN e /iutA f /sitA
3irulence score according toLam et al. 20203; b red and blue colors mean the presence of the gene(s) respectively in ST437 and ST11 strains, while color in blank represents the absence of the gene(s).cGenes,protein names and predicted virulence according to the main associated biological characteristics, and references in Supplementary Table5A(Excel file 1).d References: Kawai 2006 13 ; Candan & Aksöz, 2015 14 ; Paczosa et al. 2016 15 .e weak identity of 65% with 100% of coverage.f 99-100% of global identity.g clbS gene absent in all strains.h we did not detect mutations in kpnEFGH genes.AMR, antimicrobial resistance; CG, clonal group; LPS, lipopolysaccharide; MLST, multilocus sequence typing; NE, not evaluable.Case number in order of strain detection.Index strains.Case number in order of strains detection.AMR, antimicrobial resistance; MLST, multilocus sequence typing.samples, according to Plasmidfinder 16 and Platon 17 . a