Acquisition of resistance to ceftazidime-avibactam during infection treatment in Pseudomonas aeruginosa through D179Y mutation in one of two blaKPC-2 gene copies without losing carbapenem resistance

Ceftazidime/Avibactam (CAZ/AVI) is frequently used to treat KPC-producing Pseudomonas aeruginosa (KPC-PA) and Enterobacterales. CAZ/AVI resistance is driven by several mechanisms. In P. aeruginosa this mainly occurs through alteration of AmpC, porins, and/or efflux pump overexpression, whereas in Enterobacterales it frequently occurs through D179Y substitution in the active site of KPC enzyme. This aminoacid change abolishes AVI binding to the KPC active site, hence inhibition is impaired. However, this substitution also decreases KPC-mediated resistance to carbapenems (“see-saw” effect). The goal of this work was to characterize the in vivo acquisition of CAZ/AVI resistance through D179Y substitution in a KPC-PA isolated from a hospitalized patient after CAZ/AVI treatment. Two KPC-PA isolates were obtained. The first isolate, PA-1, was obtained before CAZ/AVI treatment and was susceptible to CAZ/AVI. The second isolate, PA-2, was obtained after CAZ/AVI treatment and exhibited high-level CAZ/AVI resistance. Characterization of isolates PA-1 and PA-2 was performed through short and long-read whole genome sequencing analysis. The hybrid assembly showed that PA-1 and PA-2A had a single plasmid of 54,030 bp, named pPA-1 and pPA-2 respectively. Each plasmid harbored two copies of the bla_KPC-containing Tn4401b transposon. However, while pPA-1 carried two copies of bla_KPC-2, pPA-2 had one copy of bla_KPC-2 and one copy of bla_KPC-33, the allele with the D179Y substitution. Interestingly, isolate PA-2 did not exhibit the “see-saw” effect. The bla_KPC-33 allele was detected only through hybrid assembly using a long-read-first approach. The present work describes a KPC-PA isolate harboring a plasmid-borne CAZ/AVI resistance mechanism based on two copies of bla_KPC-2-Tn4401b and D179Y mutation in one of them, that is not associated with loss of resistance to carbapenems. These findings highlight the usefulness of a fine-tuned combined analysis of short and long-read data to detect similar emerging resistance mechanisms.

666. Molecular Epidemiology of Methicillin-Resistant Staphylococcus aureus in Chile between 1999-2018

Background

The global spread of methicillin-resistant Staphylococcus aureus (MRSA) is associated with distinct genetic lineages that predominate in specific geographical regions. Available evidence suggests the Chilean-Cordobes clone (ChC), an ST5-SCCmecI lineage, has largely predominated in Chilean hospitals since its first description in the late 1990’s. Although the circulation of other MRSA lineages, including community-associated clones, has been well documented, the dynamics of clonal replacement over time has not been explored. Therefore, we aimed to study the molecular epidemiology and dynamics of clonal replacement using a large collection of clinical MRSA strains recovered from Chile during the last two decades.

Methods

We used whole-genome sequencing (WGS) and core-based phylogenomic analysis to identify genetic lineages and explore their relationship in 798 MRSA isolates obtained between 1999-2018 from two tertiary-care Chilean hospitals.

Results

Overall, the most frequently identified clones were the ST5-SCCmecI ChC (n=476, 60%), followed by ST105-SCCmecII (n=119, 15%), ST72-SCCmecIV (n=74, 9%), and ST8-SCCmecII (n=26, 3%). Phylogenomic reconstruction demonstrated 7 major clades: Clade I (CC30); Clade II (CC22); Clade III (CC97); Clade IV (CC8); Clade V (ST72); Clade VI (CC5/ST225 and ST105) and Clade VII (CC5/ST5-SCCmecI) (Fig. 1). The ChC clone remained the most frequent MRSA lineage throughout the study period (Fig. 2). However, its relative abundance decreased from >90% of isolates in 1999 to ca. 40% in 2018. This decrease began around 2005 and was associated with a progressive expansion of the ST105-SCCmecII and ST72-SCCmecIV lineages (Fig. 2). A Bayesian molecular clock analysis established the most recent common ancestor in 1964 (95% HPD interval=1961.975-1966.218) and corroborated a CC5 expansion event starting in Chile in 1999 (Fig. 3). Interestingly, our analyses revealed two branches within the ST5-SCCmecI lineage: one predominating in 1999-2006, and a more recent branch (related to the ST105-SCCmecII clone) that emerged around 2008.

Figure 1. Core genome phylogenomic reconstruction of the 798 MRSA isolates.

The seven major clades are represented by colored sections. The Clade I (purple section) was composed of isolates belonging to the CC30. Clade II (cyan section) includes four isolates of CC22. Clade III (red section) is composed of isolates of CC97. Clade IV (blue section) grouped isolates of different ST239 and ST8, belonging to the CC8. Clade V (orange section) includes isolates of ST72. Clade VI (yellow section) includes isolates of ST225 and ST105, both belonging to CC5. Clade VII (green section) is mostly composed of isolates of ST5-SCCmecI. The inner ring shows the ST of the isolates; the external ring shows the staphylococcal chromosomal cassette mec (SCCmec) type.

Figure 2. Relative frequency of MRSA clones from 1999 to 2018.

The genomes were grouped according to their isolation dates. Most frequent MRSA clones are represented by colored sections.

Figure 3. Maximum clade credibility tree from the molecular clock analysis of the 798 MRSA genomes.

A Bayesian molecular clock analysis was performed with BEAST using the isolation date of each genome as a calibrator. The colored strip showed the most frequent clones. The red dot shows a major event of divergence in 2008.

Conclusion

The ChC clone remains the most prevalent MRSA in Chile. However, our data is consistent with the evolution of this clone and a progressive replacement of with ST105 and ST72 genetic lineages.

Disclosures

Lorena Diaz, PhD , Nothing to disclose Cesar A. Arias, M.D., MSc, Ph.D., FIDSA, Entasis Therapeutics (Grant/Research Support)MeMed Diagnostics (Grant/Research Support)Merk (Grant/Research Support)

556. Phylogenomic Epidemiology of Methicillin-Resistant Staphylococcus aureus (MRSA) Chilean-Cordobes Clone in Latin America

Background

The MRSA Chilean-Cordobes (ChC) clone belongs to the clonal complex 5 (CC5) and typically carries SCCmec I. The ChC clone predominated widely throughout several countries of Latin America (LA), but during the mid-2000s a CA-MRSA CC8 LA variant (USA300-LV) quickly replaced the ChC in Colombia and Ecuador. Most notably, this replacement was not observed in Peru or Chile. Here, we aimed to understand the phylogenomic relatedness of the CC5 ChC clone obtained from different countries of LA.

Methods

We sequenced and analyzed the genomes of 115 MRSA isolates obtained between 2011–2014 from bloodstream infections in 6 LA countries (Argentina, Brazil, Colombia, Chile, Peru, and Venezuela). All isolates were confirmed as ChC clone by pulsed-field gel electrophoresis (PFGE). We used core genome-based phylogenomic reconstructions and molecular clock analysis to infer the relationships and time of divergence between clades.

Results

Whole-genome-based multilocus sequence typing determined that 110/115 isolates belonged to ST5 and carried SCCmec I. The phylogenomic reconstruction showed ChC isolates clustered into 4 major clades distinctly segregated by country of origin (Figure 1). Interestingly, isolates recovered from Chile divided into 2 different clades that segregate according to the city of origin (Santiago [SCL] or Concepción [CON]), suggesting these clades evolved independently. Molecular clock analyses suggested all clades share a common ancestor with the divergence of the Chilean clades occurring earlier (Figure 2). Of note, analysis of heavy metal genes suggested the divergence between Chilean isolates was characterized by the loss of a mercury resistance gene cluster, which is present in an 88% of CON isolates, but only in 28% of SCL (Figure 2).

Conclusion

MRSA isolates belonging to the ChC clone from 6 LA countries clustered in 4 clades according to the geographical region of isolation. This segregation suggests divergent adaptations that may respond to different selective pressures. Heavy metal resistance could play a role in the ability of the MRSA ChC to disseminate in specific geographical locations.

Disclosures

All authors: No reported disclosures.

1597. Evaluation of Ceftaroline Resistance (CPT-R) in Chile Across Time and a Comparison of CLSI vs. EUCAST Breakpoints in Methicillin-Resistant Staphylococcus aureus (MRSA)

Background

CPT-R in MRSA is associated with clonal complex (CC) 5 lineages. Chile, with wide dissemination of the CC5 Chilean-Cordobes clone, has high MRSA rates. In 2019, CLSI revised the breakpoints (BPs) keeping susceptible (S, minimum inhibitory concentration [MIC mg/L] ≤1), added susceptible dose-dependent (SDD, MIC 2–4), removed intermediate (MIC 2); resistant (R) is now MIC ≥8. EUCAST S is MIC ≤ 1, but R differentiates among pneumonia (MIC > 1) and nonpneumonia (NP) isolates (MIC > 2). We evaluated CPT-R across time and agreement between agencies for broth microdilution (BMD), E-test and Disk Diffusion (DD)

Methods

Hospital- (HA; n = 320, 10 centers) and community-associated (CA, n = 37) clinical MRSA isolates collected between 1999 and 2018 were confirmed with MALDI-TOF, cefoxitin DD, and mecA PCR. CPT susceptibilities were evaluated by BMD, E-test and DD (5 and 30 mg) across revised and old CLSI or EUCAST BPs. We determined essential and categorical agreement (EA, CA), very major, major, and minor errors (VME, ME, MiE)

Results

The MIC50/MIC90 of HA-MRSA with BMD was 2/2 mg/L (64% of isolates considered CPT non-susceptible) and 0.5/0.5 mg/L for CA-MRSA. MIC50/MIC90 was 1/1.5 with E-test. Strains collected in 1999–2008 (n = 161) and 2009–2018 (n = 159) both had a MIC50/MIC90 of 2/2. The EA of E-test with BMD was 82%; results of CA-VME-ME-MiE were 51-0-0-48% using the new CLSI BPs or 51-81-0-45% using EUCAST or old CLSI BPs. For BMD, CA-VME-ME-MiE between new CLSI and EUCAST was 95-0-0-5 with 100% CA for E-test. Under NP EUCAST BPs, R isolates increase from 5 to 21% by BMD and 0 to 8% by E-test. CA-VME-ME-MiE between new CLSI and NP EUCAST BPs for BMD is 79-0-0-21 and for E-test is 91-0-0-8. For DD vs. BMD, CA-VME-ME-MiE is 55-0-1-44 with new CLSI BPs, 53-63-1-43 with old CLSI and 36-6-35-51 with EUCAST. With EUCAST DD (5 μg CPT) as reference vs. CLSI DD (30ug CPT), CA-VME-ME-MiE is 25-70-0-38.

Conclusion

CPT nonsusceptibility is frequent in the CC5 HA-MRSA clone circulating in Chile across time. All methods had poor performance against BMD, but revision of CLSI BPs decreased error rates. E-test under called the MIC. CLSI DD (under called nonsusceptibility) and EUCAST DD (overcalled resistance) are drastically discordant. Respiratory isolates evaluated under NP BPs increased rates of resistance.

Disclosures

All authors: No reported disclosures.

1592. In Vitro Activity of Ceftolozane/Tazobactam (C/T) Against Enterobacteriaceae and Pseudomonas aeruginosa Circulating in Chile

Background

The widespread dissemination of carbapenem-resistant (CR) P. aeruginosa and Enterobacteriaceae has created a major global public health crisis. C/T is a recently approved therapeutic which consists of the combination of a novel cephalosporin (ceftolozane) and tazobactam (a β-lactamase inhibitor). C/T has shown good activity against a wide range of multidrug-resistant (MDR) Gram negatives, being particularly interesting as an alternative for MDR P. aeruginosa. We aimed to determine the activity of C/T against clinical strains of Enterobacteriaceae and P. aeruginosa recovered in 4 large clinical centers from Chile.

Methods

We analyzed 434 isolates of Enterobacteriaceae (347 E. coli, 66 K. pneumoniae, 21 Enterobacter cloacae complex) and 57 P. aeruginosa collected during 2017 from 4 tertiary care institutions in Santiago, Chile. Identification was performed as per each local clinical microbiology lab. Susceptibility testing was performed by broth microdilution using customized Sensititre plates (Trek). Carba-NP was performed to screen for carbapenemase production. Susceptibilities were analyzed as per 2019 CLSI breakpoints.

Results

The MIC50/90 for C/T against Enterobacteriaceae and P. aeruginosa were 1/4 μg/mL and 2/16 μg/mL, respectively. In Enterobacteriaceae, susceptibility to C/T reached 92% in E. coli (Figure 1A), 91% in E. cloacae complex (Figure 1B) and 70% in K. pneumoniae (Figure 1C). Remarkably, C/T remained active against 58% (33/57) of CR Enterobacteriaceae (Figure 2A). Among Carba-NP-negative CR isolates (46%, 26/57), susceptibility to C/T was 54% (Figure 3 A–C). In P. aeruginosa, the overall susceptibility to C/T was 81% (Figure 1D), maintaining activity against 69% (25/36) of CR strains (Figure 2B). Importantly, susceptibility to C/T in CR P. aeruginosa isolates with a negative Carba-NP (67%, 24/36) was 83% (20/24) (Figure 3D).

Conclusion

In this multicenter study, we observed that C/T was highly active against clinical isolates of Enterobacteriaceae and P. aeruginosa. Of note, C/T remained active against a large proportion of CR clinical strains. Moreover, the activity of C/T was particularly high against CR P. aeruginosa isolates with a negative Carba-NP.

Disclosures

All authors: No reported disclosures.