Clinical Outcomes and Bacterial Characteristics of Carbapenem-resistant Acinetobacter baumannii Among Patients From Different Global Regions

BACKGROUND

Carbapenem-resistant Acinetobacter baumannii (CRAb) is 1 of the most problematic antimicrobial-resistant bacteria. We sought to elucidate the international epidemiology and clinical impact of CRAb.

METHODS

In a prospective observational cohort study, 842 hospitalized patients with a clinical CRAb culture were enrolled at 46 hospitals in five global regions between 2017 and 2019. The primary outcome was all-cause mortality at 30 days from the index culture. The strains underwent whole-genome analysis.

RESULTS

Of 842 cases, 536 (64%) represented infection. By 30 days, 128 (24%) of the infected patients died, ranging from 1 (6%) of 18 in Australia-Singapore to 54 (25%) of 216 in the United States and 24 (49%) of 49 in South-Central America, whereas 42 (14%) of non-infected patients died. Bacteremia was associated with a higher risk of death compared with other types of infection (40 [42%] of 96 vs 88 [20%] of 440). In a multivariable logistic regression analysis, bloodstream infection and higher age-adjusted Charlson comorbidity index were independently associated with 30-day mortality. Clonal group 2 (CG2) strains predominated except in South-Central America, ranging from 216 (59%) of 369 in the United States to 282 (97%) of 291 in China. Acquired carbapenemase genes were carried by 769 (91%) of the 842 isolates. CG2 strains were significantly associated with higher levels of meropenem resistance, yet non-CG2 cases were over-represented among the deaths compared with CG2 cases.

CONCLUSIONS

CRAb infection types and clinical outcomes differed significantly across regions. Although CG2 strains remained predominant, non-CG2 strains were associated with higher mortality. Clinical Trials Registration. NCT03646227.

The metallo-β-lactamases strike back: emergence of taniborbactam escape variants

Metallo-β-lactamases (MBLs) have evolved relatively rapidly to become an international public health threat. There are no clinically available β-lactamase inhibitors with activity against MBLs. This may change with the introduction of cefepime-taniborbactam. Herein, we review three manuscripts (S. I. Drusin, C. Le Terrier, L. Poirel, R. A. Bonomo, et al., Antimicrob Agents Chemother 68:e01168-23, 2024, https://doi.org/10.1128/aac.01168-23; C. Le Terrier, C. Viguier, P. Nordmann, A. J. Vila, and L. Poirel, Antimicrob Agents Chemother 68:e00991-23, 2024, https://doi.org/10.1128/aac.00991-23; D. Ono, M. F. Mojica, C. R. Bethel, Y. Ishii, et al., Antimicrob Agents Chemother 68:e01332-23, 2024, https://doi.org/10.1128/aac.01332-23) in which investigators describe elegant experiments to explore MBL/taniborbactam interactions and modifications to MBLs, in response, to reduce the affinity of taniborbactam. Challenges with MBL inhibition will not disappear; rather, they will evolve commensurate with advancements in medicinal chemistry.

Cefiderocol heteroresistance associated with mutations in TonB-dependent receptor genes in Pseudomonas aeruginosa of clinical origin

The siderophore-cephalosporin cefiderocol(FDC) presents a promising treatment option for carbapenem-resistant (CR) P. aeruginosa (PA). FDC circumvents traditional porin and efflux mediated resistance by utilizing TonB-dependent receptors (TBDRs) to access the periplasmic space. Emerging FDC resistance has been associated with loss of function mutations within TBDR genes or the regulatory genes controlling TBDR expression. Further, difficulties with antimicrobial susceptibility testing (AST) and unexpected negative clinical treatment outcomes have prompted concerns for heteroresistance, where a single lineage isolate contains resistant subpopulations not detectable by standard AST. This study aimed to evaluate the prevalence of TBDR mutations among clinical isolates of P. aeruginosa and the phenotypic effect on FDC susceptibility and heteroresistance. We evaluated the sequence of pirR , pirS , pirA , piuA or piuD from 498 unique isolates collected before the introduction of FDC from 4 clinical sites in Portland, OR (1), Houston, TX (2), and Santiago, Chile (1). At some clinical sites, TBDR mutations were seen in up to 25% of isolates, and insertion, deletion, or frameshift mutations were predicted to impair protein function were seen in 3% of all isolates (n=15). Using population analysis profile testing, we found that P. aeruginosa with major TBDR mutations were enriched for a heteroresistant phenotype and undergo a shift in the susceptibility distribution of the population as compared to susceptible strains with wild type TBDR genes. Our results indicate that mutations in TBDR genes predate the clinical introduction of FDC, and these mutations may predispose to the emergence of FDC resistance.

Priorities and Progress in Gram-positive Bacterial Infection Research by the Antibacterial Resistance Leadership Group: A Narrative Review

The Antibacterial Resistance Leadership Group (ARLG) has prioritized infections caused by gram-positive bacteria as one of its core areas of emphasis. The ARLG Gram-positive Committee has focused on studies responding to 3 main identified research priorities: (1) investigation of strategies or therapies for infections predominantly caused by gram-positive bacteria, (2) evaluation of the efficacy of novel agents for infections caused by methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococci, and (3) optimization of dosing and duration of antimicrobial agents for gram-positive infections. Herein, we summarize ARLG accomplishments in gram-positive bacterial infection research, including studies aiming to (1) inform optimal vancomycin dosing, (2) determine the role of dalbavancin in MRSA bloodstream infection, (3) characterize enterococcal bloodstream infections, (4) demonstrate the benefits of short-course therapy for pediatric community-acquired pneumonia, (5) develop quality of life measures for use in clinical trials, and (6) advance understanding of the microbiome. Future studies will incorporate innovative methodologies with a focus on interventional clinical trials that have the potential to change clinical practice for difficult-to-treat infections, such as MRSA bloodstream infections.

Multiple clonal transmissions of clinically relevant extended-spectrum beta-lactamase-producing Escherichia coli among livestock, dogs, and wildlife in Chile

OBJECTIVES

Extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-E. coli) are a main cause of human deaths associated with antimicrobial resistance (AMR). Despite hundreds of reports of the faecal carriage of ESBL-E. coli in domestic and wild animals, the dynamics of its circulation remains poorly understood.

METHODS

We used whole genome sequencing of 19 ESBL-E. coli previously isolated in the same local setting from dogs, livestock, and a wild rodent in Central Chile to assess potential cross-species transmission of ESBL-E. coli.

RESULTS

Isolates harboured a large number of AMR (n = 95) and virulence (n = 45) genes, plasmids replicons (n = 24), and E. coli sequence types including top extraintestinal pathogenic E. coli ST410, ST58, ST88, and ST617. Almost identical clones (<50 single nucleotide polymorphisms difference, same antibiotic and heavy metal resistance genes, virulence genes, and plasmids) were found in faeces of dogs, cattle, or sheep from the same farm, and in a dog and a wild rodent living in proximity.

CONCLUSIONS

To our knowledge, this is the first report of multiple clonal cross-species transmission of ESBL-E. coli in domestic and potentially wild animals of Latin America. Our results suggest that relatively rare spread of AMR across animal species can still occur by both clonal and plasmid dissemination. Our study highlights the need for establishing preventive measures to limit the circulation of these bacteria among animals in agricultural settings, particularly given the highly pathogenic profile of several E. coli strains detected in these animals.

Trends in Inpatient Antibiotic Use Among Adults Hospitalized During the Coronavirus Disease 2019 Pandemic in Argentina, Brazil, and Chile, 2018-2021

BACKGROUND

High rates of antibiotic use (AU) among inpatients with coronavirus disease 2019 (COVID-19) despite low rates of bacterial coinfection and secondary infection have been reported. We evaluated the impact of the COVID-19 pandemic on AU in healthcare facilities (HCFs) in South America.

METHODS

We conducted an ecologic evaluation of AU in inpatient adult acute care wards in 2 HCFs each in Argentina, Brazil, and Chile. The AU rates for intravenous antibiotics were calculated as the defined daily dose per 1000 patient-days, using pharmacy dispensing records and hospitalization data from March 2018-February 2020 (prepandemic) and March 2020-February 2021 (pandemic). Differences in median AU were compared between the prepandemic and pandemic periods, using the Wilcoxon rank sum test to determine significance. Interrupted time series analysis was used to analyze changes in AU during the COVID-19 pandemic.

RESULTS

Compared with the prepandemic period, the median difference in AU rates for all antibiotics combined increased in 4 of 6 HCFs (percentage change, 6.7%-35.1%; P < .05). In the interrupted time series models, 5 of 6 HCFs had significant increases in use of all antibiotics combined immediately at the onset of the pandemic (immediate effect estimate range, 15.4-268), but only 1 of these 5 HCFs experienced a sustained increase over time (change in slope, +8.13; P < .01). The effect of the pandemic onset varied by antibiotic group and HCF.

CONCLUSIONS

Substantial increases in AU were observed at the beginning of the COVID-19 pandemic, suggesting the need to maintain or strengthen antibiotic stewardship activities as part of pandemic or emergency HCF responses.

High Burden of Intestinal Colonization With Antimicrobial-Resistant Bacteria in Chile: An Antibiotic Resistance in Communities and Hospitals (ARCH) Study

BACKGROUND

Antimicrobial resistance is a global threat, heavily impacting low- and middle-income countries. This study estimated antimicrobial-resistant gram-negative bacteria (GNB) fecal colonization prevalence in hospitalized and community-dwelling adults in Chile before the coronavirus disease 2019 pandemic.

METHODS

From December 2018 to May 2019, we enrolled hospitalized adults in 4 public hospitals and community dwellers from central Chile, who provided fecal specimens and epidemiological information. Samples were plated onto MacConkey agar with ciprofloxacin or ceftazidime added. All recovered morphotypes were identified and characterized according to the following phenotypes: fluoroquinolone-resistant (FQR), extended-spectrum cephalosporin-resistant (ESCR), carbapenem-resistant (CR), or multidrug-resistant (MDR; as per Centers for Disease Control and Prevention criteria) GNB. Categories were not mutually exclusive.

RESULTS

A total of 775 hospitalized adults and 357 community dwellers were enrolled. Among hospitalized subjects, the prevalence of colonization with FQR, ESCR, CR, or MDR-GNB was 46.4% (95% confidence interval [CI], 42.9-50.0), 41.2% (95% CI, 37.7-44.6), 14.5% (95% CI, 12.0-16.9), and 26.3% (95% CI, 23.2-29.4). In the community, the prevalence of FQR, ESCR, CR, and MDR-GNB colonization was 39.5% (95% CI, 34.4-44.6), 28.9% (95% CI, 24.2-33.6), 5.6% (95% CI, 3.2-8.0), and 4.8% (95% CI, 2.6-7.0), respectively.

CONCLUSIONS

A high burden of antimicrobial-resistant GNB colonization was observed in this sample of hospitalized and community-dwelling adults, suggesting that the community is a relevant source of antibiotic resistance. Efforts are needed to understand the relatedness between resistant strains circulating in the community and hospitals.

Heavy Metal Pollution From a Major Earthquake and Tsunami in Chile Is Associated With Geographic Divergence of Clinical Isolates of Methicillin-Resistant Staphylococcus aureus in Latin America

Methicillin-resistant Staphylococcus aureus (MRSA) is a priority pathogen listed by the World Health Organization. The global spread of MRSA is characterized by successive waves of epidemic clones that predominate in specific geographical regions. The acquisition of genes encoding resistance to heavy-metals is thought to be a key feature in the divergence and geographical spread of MRSA. Increasing evidence suggests that extreme natural events, such as earthquakes and tsunamis, could release heavy-metals into the environment. However, the impact of environmental exposition to heavy-metals on the divergence and spread of MRSA clones has been insufficiently explored. We assess the association between a major earthquake and tsunami in an industrialized port in southern Chile and MRSA clone divergence in Latin America. We performed a phylogenomic reconstruction of 113 MRSA clinical isolates from seven Latin American healthcare centers, including 25 isolates collected in a geographic area affected by an earthquake and tsunami that led to high levels of heavy-metal environmental contamination. We found a divergence event strongly associated with the presence of a plasmid harboring heavy-metal resistance genes in the isolates obtained in the area where the earthquake and tsunami occurred. Moreover, clinical isolates carrying this plasmid showed increased tolerance to mercury, arsenic, and cadmium. We also observed a physiological burden in the plasmid-carrying isolates in absence of heavy-metals. Our results are the first evidence that suggests that heavy-metal contamination, in the aftermath of an environmental disaster, appears to be a key evolutionary event for the spread and dissemination of MRSA in Latin America.

Global epidemiology and clinical outcomes of carbapenem-resistant Pseudomonas aeruginosa and associated carbapenemases (POP): a prospective cohort study

BACKGROUND

Carbapenem-resistant Pseudomonas aeruginosa (CRPA) is a global threat, but the distribution and clinical significance of carbapenemases are unclear. The aim of this study was to define characteristics and outcomes of CRPA infections and the global frequency and clinical impact of carbapenemases harboured by CRPA.

METHODS

We conducted an observational, prospective cohort study of CRPA isolated from bloodstream, respiratory, urine, or wound cultures of patients at 44 hospitals (10 countries) between Dec 1, 2018, and Nov 30, 2019. Clinical data were abstracted from health records and CRPA isolates were whole-genome sequenced. The primary outcome was 30-day mortality from the day the index culture was collected. We compared outcomes of patients with CRPA infections by infection type and across geographic regions and performed an inverse probability weighted analysis to assess the association between carbapenemase production and 30-day mortality.

FINDINGS

We enrolled 972 patients (USA n=527, China n=171, south and central America n=127, Middle East n=91, Australia and Singapore n=56), of whom 581 (60%) had CRPA infections. 30-day mortality differed by infection type (bloodstream 21 [30%] of 69, respiratory 69 [19%] of 358, wound nine [14%] of 66, urine six [7%] of 88; p=0·0012) and geographical region (Middle East 15 [29%] of 52, south and central America 20 [27%] of 73, USA 60 [19%] of 308, Australia and Singapore three [11%] of 28, China seven [6%] of 120; p=0·0002). Prevalence of carbapenemase genes among CRPA isolates also varied by region (south and central America 88 [69%] of 127, Australia and Singapore 32 [57%] of 56, China 54 [32%] of 171, Middle East 27 [30%] of 91, USA ten [2%] of 527; p<0·0001). KPC-2 (n=103 [49%]) and VIM-2 (n=75 [36%]) were the most common carbapenemases in 211 carbapenemase-producing isolates. After excluding USA patients, because few US isolates had carbapenemases, patients with carbapenemase-producing CRPA infections had higher 30-day mortality than those with non-carbapenemase-producing CRPA infections in both unadjusted (26 [22%] of 120 vs 19 [12%] of 153; difference 9%, 95% CI 3-16) and adjusted (difference 7%, 95% CI 1-14) analyses.

INTERPRETATION

The emergence of different carbapenemases among CRPA isolates in different geographical regions and the increased mortality associated with carbapenemase-producing CRPA infections highlight the therapeutic challenges posed by these organisms.

FUNDING

National Institutes of Health.

Clinical characteristics, microbiology and outcomes of a cohort of patients treated with ceftolozane/tazobactam in acute care inpatient facilities, Houston, Texas, USA

Background

Ceftolozane/tazobactam is a β-lactam/β-lactamase inhibitor combination with activity against a variety of Gram-negative bacteria, including MDR Pseudomonas aeruginosa. This agent is approved for hospital-acquired and ventilator-associated bacterial pneumonia. However, most real-world outcome data come from small observational cohorts. Thus, we sought to evaluate the utilization of ceftolozane/tazobactam at multiple tertiary hospitals in Houston, TX, USA.

Methods

We conducted a multicentre retrospective study of patients receiving at least 48 h of ceftolozane/tazobactam therapy from January 2016 through to September 2019 at two hospital systems in Houston. Demographic, clinical and microbiological data were collected, including the infecting bacterial isolate, when available. The primary outcome was composite clinical success at hospital discharge. Secondary outcomes included in-hospital mortality and clinical disposition at 14 and 30 days post ceftolozane/tazobactam initiation. Multivariable logistic regression analysis was used to identify predictors of the primary outcome and mortality. Recovered isolates were tested for susceptibility to ceftolozane/tazobactam and underwent WGS.

Results

A total of 263 patients were enrolled, and composite clinical success was achieved in 185 patients (70.3%). Severity of illness was the most consistent predictor of clinical success. Combination therapy with ceftolozane/tazobactam and another Gram-negative-active agent was associated with reduced odds of clinical success (OR 0.32, 95% CI 0.16-0.63). Resistance to ceftolozane/tazobactam was noted in 15.4% of isolates available for WGS; mutations in ampC and ftsI were common but did not cluster with a particular ST.

Conclusions

Clinical success rate among this patient cohort treated with ceftolozane/tazobactam was similar compared with previous experiences. Ceftolozane/tazobactam remains an alternative agent for treatment of susceptible isolates of P. aeruginosa.

Multiomics characterization of methicillin-resistant Staphylococcus aureus (MRSA) isolates with heterogeneous intermediate resistance to vancomycin (hVISA) in Latin America

BACKGROUND

Heterogeneous vancomycin-intermediate Staphylococcus aureus (hVISA) compromise the clinical efficacy of vancomycin. The hVISA isolates spontaneously produce vancomycin-intermediate Staphylococcus aureus (VISA) cells generated by diverse and intriguing mechanisms.

OBJECTIVE

To characterize the biomolecular profile of clinical hVISA applying genomic, transcriptomic and metabolomic approaches.

METHODS

39 hVISA and 305 VSSA and their genomes were included. Core genome-based Bayesian phylogenetic reconstructions were built and alterations in predicted proteins in VISA/hVISA were interrogated. Linear discriminant analysis and a Genome-Wide Association Study were performed. Differentially expressed genes were identified in hVISA-VSSA by RNA-sequencing. The undirected profiles of metabolites were determined by liquid chromatography and hydrophilic interaction in six CC5-MRSA.

RESULTS

Genomic relatedness of MRSA associated to hVISA phenotype was not detected. The change Try38 → His in Atl (autolysin) was identified in 92% of the hVISA. We identified SNPs and k-mers associated to hVISA in 11 coding regions with predicted functions in virulence, transport systems, carbohydrate metabolism and tRNA synthesis. Further, capABCDE, sdrD, esaA, esaD, essA and ssaA genes were overexpressed in hVISA, while lacABCDEFG genes were downregulated. Additionally, valine, threonine, leucine tyrosine, FAD and NADH were more abundant in VSSA, while arginine, glycine and betaine were more abundant in hVISA. Finally, we observed altered metabolic pathways in hVISA, including purine and pyrimidine pathway, CoA biosynthesis, amino acid metabolism and aminoacyl tRNA biosynthesis.

CONCLUSIONS

Our results show that the mechanism of hVISA involves major changes in regulatory systems, expression of virulence factors and reduction in glycolysis via TCA cycle. This work contributes to the understanding of the development of this complex resistance mechanism in regional strains.

1573. Impact of the COVID-19 Pandemic on Antibiotic Use among Hospitalized Adults in Argentina, Brazil, and Chile

Background

Reports showing high rates of antibiotic use (AU) in patients with coronavirus disease 2019 (COVID-19) despite low rates of secondary bacterial infection have emerged from various countries across the globe. We evaluated the impact of the COVID-19 pandemic on AU in healthcare facilities (HCFs) in Argentina, Brazil, and Chile.

Methods

We conducted an ecologic evaluation of AU in inpatient adult acute care wards (excluding maternity wards) in 6 HCFs in Argentina, Brazil, and Chile; 2 HCFs per country. AU data for intravenously administered antibiotics commonly used to treat respiratory infections were collected from pharmacy dispensing records and aggregated to monthly defined daily dose (DDD)/1000 patient days. Graphs were created to depict AU and COVID-19 discharges over time throughout the 36-month study period (03/2018–02/2021). Relative changes in AU for all antibiotics combined and specific classes were calculated by comparing median AU for the 24-month pre-pandemic period (3/2018–2/2020) with the 12-month pandemic period (3/2020–2/2021). Only statistically significant differences (P< 0.05) determined by the Wilcoxon signed-rank test are reported.

Results

Compared to the pre-pandemic period, the use of all included antibiotics combined increased in 4/6 HCFs (6.7–35.1%). In the 4 HCFs that experienced increases in AU, Figure 1 shows that use was high during months when COVID-19 patient surges occurred. In 3/4 of these HCFs, AU remained high despite significant decreases in COVID-19 discharges. Ceftriaxone use increased in 2/6 HCFs (27.1–51.6%). Use of β-lactam antibiotics with activity against Pseudomonas aeruginosa increased in 3/6 HCFs (31.3–82.5%) and decreased in 1/6 HCFs (-18.9%). Vancomycin and linezolid use increased in 3/6 HCFs (36.9–77.1%).

Conclusion

Increases in AU among hospitalized adults were observed in 4 of 6 South American HCFs included in this study. The high rates of broad-spectrum antibiotic use in the HCFs may impact further emergence of antibiotic resistance. Understanding how this increase in antibiotic use compares to rates of bacterial infections during this time period is critical.

Disclosures

Jose M. Munita, MD, BioMerieux: Grant/Research Support|MSD: Grant/Research Support|Pfizer: Grant/Research Support Matias Salomao, MD, Cepheid: Lecture.

1917. Impact of the COVID-19 Pandemic on Antimicrobial Stewardship, Infection Prevention & Control, and Clinical Microbiology Practices in Argentina, Brazil, and Chile

Background

During the coronavirus disease 2019 (COVID-19) pandemic, healthcare facilities (HCFs) were overwhelmed with increasing patient volumes and limited resources. Reports of disruptions in routine practices at HCFs have emerged. We evaluated changes in policies, practices, and programs for antimicrobial stewardship (AMS), infection prevention and control (IPC), and clinical microbiology across six HCF in South America following the onset of the COVID-19 pandemic.

Methods

We conducted a survey in 6 HCFs in Argentina, Brazil, and Chile; 2 HCFs in each country. Data on 5 components (facility characteristics, antibiotic procurement and distribution, AMS activities, IPC activities, and clinical microbiology) were collected from designated specialists within each HCF from March 2018 – February 2021. We compared observations within these 5 components pre-pandemic (March 2018 – February 2020) to during pandemic (March 2020 – February 2021.)

Results

During the pandemic, the number of ICU beds increased across all the 6 HCFs by 57-633%, and the number of ventilators increased by 15-317% in 5 out of the 6 HCFs. Healthcare personnel shortages were observed in all 6 HCFs, notably common for nurses and laboratory personnel (Table 1). Extended use of N95 respirators was reported across all 6 HCFs with 2 doing extended use of gowns and medical masks. The only PPE reused was N95 respirators in 2 HCFs. Difficulties in cohorting patients with multi-drug resistance organism (MDRO) was reported by one of the HCFs. Three HCFs reported shortages in drugs with coverage for MRSA, gram-negative bacteria, and fungal pathogens despite no reports of interruption in AMS activities in these HCFs. Two hospitals reported delays on microbiology results.

Facility characteristics and reported changes during COVID-19 pandemic (March 2020-February 2021)

Conclusion

The COVID-19 pandemic led to substantial increases in ICU beds, number of ventilators, and extended use of PPE suggesting increases in admission of severe patients and suboptimal IPC practices in HCFs in South America. It is unclear if shortages in agents commonly used to treat MDRO was related to overuse or access difficulties. Additional evaluation is needed to determine the impact of these findings on antimicrobial resistance and antimicrobial use.

Disclosures

Matias Salomao, MD, Cepheid: Lecture.

Clinical outcomes and bacterial characteristics of carbapenem-resistant Klebsiella pneumoniae complex among patients from different global regions (CRACKLE-2): a prospective, multicentre, cohort study

BACKGROUND

Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a global threat. We therefore analysed the bacterial characteristics of CRKP infections and the clinical outcomes of patients with CRKP infections across different countries.

METHODS

In this prospective, multicentre, cohort study (CRACKLE-2), hospitalised patients with cultures positive for CRKP were recruited from 71 hospitals in Argentina, Australia, Chile, China, Colombia, Lebanon, Singapore, and the USA. The first culture positive for CRKP was included for each unique patient. Clinical data on post-hospitalisation death and readmission were collected from health records, and whole genome sequencing was done on all isolates. The primary outcome was a desirability of outcome ranking at 30 days after the index culture, and, along with bacterial characteristics and 30-day all-cause mortality (a key secondary outcome), was compared between patients from China, South America, and the USA. The desirability of outcome ranking was adjusted for location before admission, Charlson comorbidity index, age at culture, Pitt bacteremia score, and anatomical culture source through inverse probability weighting; mortality was adjusted for the same confounders, plus region where relevant, through multivariable logistic regression. This study is registered at ClinicalTrials.gov, NCT03646227, and is complete.

FINDINGS

Between June 13, 2017, and Nov 30, 2018, 991 patients were enrolled, of whom 502 (51%) met the criteria for CRKP infection and 489 (49%) had positive cultures that were considered colonisation. We observed little intra-country genetic variation in CRKP. Infected patients from the USA were more acutely ill than were patients from China or South America (median Pitt bacteremia score 3 [IQR 2-6] vs 2 [0-4] vs 2 [0-4]) and had more comorbidities (median Charlson comorbidity index 3 [IQR 2-5] vs 1 [0-3] vs 1 [0-2]). Adjusted desirability of outcome ranking outcomes were similar in infected patients from China (n=246), South America (n=109), and the USA (n=130); the estimates were 53% (95% CI 42-65) for China versus South America, 50% (41-61) for the USA versus China, and 53% (41-66) for the USA versus South America. In patients with CRKP infections, unadjusted 30-day mortality was lower in China (12%, 95% CI 8-16; 29 of 246) than in the USA (23%, 16-30; 30 of 130) and South America (28%, 20-37; 31 of 109). Adjusted 30-day all-cause mortality was higher in South America than in China (adjusted odds ratio [aOR] 4·82, 95% CI 2·22-10·50) and the USA (aOR 3·34, 1·50-7·47), with the mortality difference between the USA and China no longer being significant (aOR 1·44, 0·70-2·96).

INTERPRETATION

Global CRKP epidemics have important regional differences in patients' baseline characteristics and clinical outcomes, and in bacterial characteristics. Research findings from one region might not be generalisable to other regions.

FUNDING

The National Institutes of Health.

Contemporary Clinical and Molecular Epidemiology of Vancomycin-Resistant Enterococcal Bacteremia: A Prospective Multicenter Cohort Study (VENOUS I)

Background

Vancomycin-resistant enterococci (VRE) are major therapeutic challenges. Prospective contemporary data characterizing the clinical and molecular epidemiology of VRE bloodstream infections (BSIs) are lacking.

Methods

The Vancomycin-Resistant Enterococcal BSI Outcomes Study (VENOUS I) is a prospective observational cohort of adult patients with enterococcal BSI in 11 US hospitals. We included patients with Enterococcus faecalis or Enterococcus faecium BSI with ≥1 follow-up blood culture(s) within 7 days and availability of isolate(s) for further characterization. The primary study outcome was in-hospital mortality. Secondary outcomes were mortality at days 4, 7, 10, 12, and 15 after index blood culture. A desirability of outcome ranking was constructed to assess the association of vancomycin resistance with outcomes. All index isolates were subjected to whole genome sequencing.

Results

Forty-two of 232 (18%) patients died in hospital and 39 (17%) exhibited microbiological failure (lack of clearance in the first 4 days). Neutropenia (hazard ratio [HR], 3.13), microbiological failure (HR, 2.4), VRE BSI (HR, 2.13), use of urinary catheter (HR, 1.85), and Pitt BSI score ≥2 (HR, 1.83) were significant predictors of in-hospital mortality. Microbiological failure was the strongest predictor of in-hospital mortality in patients with E faecium bacteremia (HR, 5.03). The impact of vancomycin resistance on mortality in our cohort changed throughout the course of hospitalization. Enterococcus faecalis sequence type 6 was a predominant multidrug-resistant lineage, whereas a heterogeneous genomic population of E faecium was identified.

Conclusions

Failure of early eradication of VRE from the bloodstream is a major factor associated with poor outcomes.

Antimicrobial resistance in wildlife and in the built environment in a wildlife rehabilitation center

Injured and orphaned wildlife are often brought to Wildlife Rehabilitation Centers (WRC) to be cared for by professionals to ultimately be released back to their natural habitats. In these centers, animals may spend months and frequently receive prolonged antibiotic therapy. Therefore, WRC may play a role in the emergence and dissemination of antimicrobial resistance (AMR). The goal of this study was to investigate the presence and antibiotic resistance profiles of Gram-negative bacteria with reduced susceptibility to cephalosporins in both the wildlife admitted to a WRC and in the WRC built environment in Chile. A cross-sectional study was conducted sampling animals undergoing rehabilitation (n = 64) and the WRC environment (n = 160). Isolated bacterial species were identified with MALDI-TOF, and antimicrobial susceptibility determined using the disk diffusion method. Enterobacteriaceae and Pseudomonadaceae were the dominant bacterial families among the environmental (n = 78) and animal (n = 31) isolates. For Enterobacteriaceae, isolates of the most abundant species (E. coli) were classified into 20 antibiotic resistance profiles, with eight of those isolates being resistant to more than nine antibiotics, including imipenem. Isolates of the Pseudomonadaceae family identified 11 isolates with resistance to antibiotics such as carbapenems and quinolones. Even though a cluster analysis based on antibiotic resistance patterns did not show a clear overlap between environmental and animal isolates, it is important to highlight the identification of isolates resistant to carbapenems, which is very relevant from a public health perspective. Further, numerous antibiotic resistance profiles were observed in different bacterial species, indicating not only environmental contamination with a wide diversity of bacteria, but also a wide diversity of resistant bacteria in animals at the WRC. The approach taken by sampling animals and their hospital environment can be useful in understanding AMR dynamics in wildlife rehabilitation settings, as well as the potential dissemination of AMR into the natural environment.

•

The wildlife center was contaminated with wide diversity of resistant bacteria.

•

There was wide diversity of resistant bacteria in wildlife at the center.

•

Resistant isolates to carbapenems were present, which has public health relevance.

•

No clear overlap between wildlife and the center antibiotic resistance patterns.

•

Wildlife rehabilitation should be considered in antimicrobial resistance dynamics.

Multi-country cross-sectional study of colonization with multidrug-resistant organisms: protocol and methods for the Antibiotic Resistance in Communities and Hospitals (ARCH) studies

BACKGROUND

Antimicrobial resistance is a global health emergency. Persons colonized with multidrug-resistant organisms (MDROs) are at risk for developing subsequent multidrug-resistant infections, as colonization represents an important precursor to invasive infection. Despite reports documenting the worldwide dissemination of MDROs, fundamental questions remain regarding the burden of resistance, metrics to measure prevalence, and determinants of spread. We describe a multi-site colonization survey protocol that aims to quantify the population-based prevalence and associated risk factors for colonization with high-threat MDROs among community dwelling participants and patients admitted to hospitals within a defined population-catchment area.

METHODS

Researchers in five countries (Bangladesh, Chile, Guatemala, Kenya, and India) will conduct a cross-sectional, population-based prevalence survey consisting of a risk factor questionnaire and collection of specimens to evaluate colonization with three high-threat MDROs: extended-spectrum cephalosporin-resistant Enterobacteriaceae (ESCrE), carbapenem-resistant Enterobacteriaceae (CRE), and methicillin-resistant Staphylococcus aureus (MRSA). Healthy adults residing in a household within the sampling area will be enrolled in addition to eligible hospitalized adults. Colonizing isolates of these MDROs will be compared by multilocus sequence typing (MLST) to routinely collected invasive clinical isolates, where available, to determine potential pathogenicity. A colonizing MDRO isolate will be categorized as potentially pathogenic if the MLST pattern of the colonizing isolate matches the MLST pattern of an invasive clinical isolate. The outcomes of this study will be estimates of the population-based prevalence of colonization with ESCrE, CRE, and MRSA; determination of the proportion of colonizing ESCrE, CRE, and MRSA with pathogenic characteristics based on MLST; identification of factors independently associated with ESCrE, CRE, and MRSA colonization; and creation an archive of ESCrE, CRE, and MRSA isolates for future study.

DISCUSSION

This is the first study to use a common protocol to evaluate population-based prevalence and risk factors associated with MDRO colonization among community-dwelling and hospitalized adults in multiple countries with diverse epidemiological conditions, including low- and middle-income settings. The results will be used to better describe the global epidemiology of MDROs and guide the development of mitigation strategies in both community and healthcare settings. These standardized baseline surveys can also inform future studies seeking to further characterize MDRO epidemiology globally.

Detection of heterogeneous vancomycin intermediate resistance in MRSA isolates from Latin America

BACKGROUND

Vancomycin is a common first-line option for MRSA infections. The heterogeneous vancomycin-intermediate Staphylococcus aureus (hVISA) phenotype is associated with therapeutic failure. However, hVISA isolates are usually reported as vancomycin susceptible by routine susceptibility testing procedures.

OBJECTIVES

To detect and characterize the hVISA phenotype in MRSA isolates causing infections in nine Latin American countries.

METHODS

We evaluated a total of 1189 vancomycin-susceptible MRSA isolates recovered during 2006-08 and 2011-14. After an initial screening of hVISA using glycopeptide-supplemented agar strategies, the detection of hVISA was performed by Etest (GRD) and Macro-method (MET). Isolates deemed to be hVISA were subjected to population analysis profile/AUC (PAP/AUC) and WGS for further characterization. Finally, we interrogated alterations in predicted proteins associated with the development of the VISA phenotype in both hVISA and vancomycin-susceptible S. aureus (VSSA) genomes.

RESULTS

A total of 39 MRSA isolates (3.3%) were classified as hVISA (1.4% and 5.6% in MRSA recovered from 2006-08 and 2011-14, respectively). Most of the hVISA strains (95%) belonged to clonal complex (CC) 5. Only 6/39 hVISA isolates were categorized as hVISA by PAP/AUC, with 6 other isolates close (0.87-0.89) to the cut-off (0.9). The majority of the 39 hVISA isolates exhibited the Leu-14→Ile (90%) and VraT Glu-156→Gly (90%) amino acid substitutions in WalK. Additionally, we identified 10 substitutions present only in hVISA isolates, involving WalK, VraS, RpoB and RpoC proteins.

CONCLUSIONS

The hVISA phenotype exhibits low frequency in Latin America. Amino acid substitutions in proteins involved in cell envelope homeostasis and RNA synthesis were commonly identified. Our results suggest that Etest-based methods are an important alternative for the detection of hVISA clinical isolates.

Longitudinal assessment of SARS-CoV-2 IgG seroconversionamong front-line healthcare workers during the first wave of the Covid-19 pandemic at a tertiary-care hospital in Chile

Background

Healthcare workers (HCWs) are at high risk of exposure to SARS-CoV-2. Cross-sectional studies have provided variable rates of seroprevalence in HCWs. Longitudinal assessments of the serological response to Covid-19 among HCWs are crucial to understanding the risk of infection and changes in antibody titers over time. We aimed to investigate seroprevalence and risk factors associated with seroconversion in a prospective cohort of HCWs during the peak of the first wave of the Covid-19 pandemic.

Methods

We conducted a longitudinal study among 446 front-line HCWsin a tertiary-care hospital in Chile from April to July 2020. IgG was determined monthly using two different ELISAs in serum samples of HCWs, during the three-month period. In each visit, demographic data, symptoms, risk factors, and exposure risks were also assessed.

Results

The overall seroprevalence at the end of the study period was 24% (95% CI20.2–28.3), with 43% of seropositive HCWs reporting no prior symptoms. Seroconversion rates significantly differed over the study period, from 2.1% to as high as 8.8% at the peak of the epidemic. There were no statistically significant differences observed between HCWs in direct clinical care of patients with Covid-19 and those working in low risk areas. Antibody titers appeared to wane over time.

Conclusions

HCWs were severely affected with a high rate of seroconversion that appeared to mirror the local epidemiological situation. A significant amount of participants underwent an asymptomatic infection, highlighting the need for improved surveillance policies. Antibody titers appear to wane over time; further studies to understand this finding’s impact on the risk of reinfection are warranted.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-021-06208-2.

Perspective on Clinically-Relevant Antimicrobial Resistant Enterobacterales in Food: Closing the Gaps Using Genomics

Antimicrobial resistance is one of the most important public health concerns—it causes 700,000 deaths annually according to the World Health Organization (WHO). Enterobacterales such as E. coli and Klebsiella pneumoniae, have become resistant to many relevant antimicrobials including carbapenems and extended spectrum cephalosporins. These clinically relevant resistant Enterobacterales (CRRE) members are now globally distributed in the environment including different food types (meats, produce, dairy). Unlike known foodborne pathogens, CRRE are not usually part of most food surveillance systems. However, numerous reports of CRRE highlight the importance of these bacteria in food and have been shown to contribute to the overall crisis of antimicrobial resistance. This is especially important in the context of carriage of these pathogens by immuno-compromised individuals. CRRE infections upon consumption of contaminated food could colonize the human gastrointestinal tract and eventually be a source of systemic infections such as urinary tract infections or septicemia. While different aspects need to be considered to elucidate this, whole genome sequencing along with metadata could be used to understand genomic relationships of CRRE obtained from foods and humans, including isolates from clinical infections. Once robust scientific data is available on the role of CRRE in food, countries could move forward to better survey and control CRRE in food.

Risk factors associated with faecal carriage of extended-spectrum cephalosporin-resistant Escherichia coli among dogs in Southeast Brazil

Faecal carriage of extended-spectrum cephalosporin-resistant Escherichia coli (ESC-R E. coli) in dogs has been reported worldwide and can reduce the effectiveness of treatments against bacterial infections. However, the drivers that influence faecal carriage of ESC-R E. coli in dogs are poorly understood. The aims of this study were to estimate the prevalence of ESC-R E. coli among dogs prior to their admission to a veterinary teaching hospital and to identify risk factors associated with the faecal carriage of ESC-R E. coli. Rectal swabs (n = 130) were collected from dogs and screened for ESC-R E. coli using MacConkey agar supplemented with cefotaxime (2 μg/mL). E. coli species was confirmed by MALDI-TOF and screening of extended-spectrum beta-lactamase (ESBL) genes was conducted by multiplex PCR. Questionnaires were completed by each dog's owner to test several human and dog characteristics associated with ESC-R E. coli. The prevalence of faecal carriage of ESC-R E. coli was 9.2 % and 67 % of ESC-R E. coli isolates harboured ESBL genes including CTX-M alone or in combination with TEM. All ESC-R E. coli isolates were resistant to ceftriaxone, cefpodoxime, and cefotaxime and were susceptible to cefoxitin and carbapenems. The likelihood of carrying ESC-R E. coli was 15 times higher (OR = 14.41 [95 % CI: 1.80-38.02], p < 0.01) if the dog was treated with antibiotics 3-12 months prior to sampling and 8 times higher (OR = 7.96 [95 % CI: 2.96-92.07], p < 0.01) if the dog had direct contact with livestock, but 15 times lower (OR = 0.07 [95 % CI: 0.01-0.32], p < 0.01) if the dog was dewormed during the previous year. Our findings confirm the faecal carriage of ESC-R E. coli in subclinical dogs and call for further investigation regarding the impact of deworming on antibiotic-resistant bacteria in companion animals.

Higher Prevalence of Extended-Spectrum Cephalosporin-Resistant Enterobacterales in Dogs Attended for Enteric Viruses in Brazil Before and After Treatment with Cephalosporins

The extensive use of antibiotics is a leading cause for the emergence and spread of antimicrobial resistance (AMR) among dogs. However, the impact of using antibiotics to treat viral infections on AMR remains unknown. In this study, we compared the prevalence of extended-spectrum cephalosporin-resistant Enterobacterales (ESCR-E) between dogs with a suspected infection of canine parvovirus (CPV) and canine distemper (CDV) before and after treatment with third-generation cephalosporins. We found a higher prevalence of ESCR-E faecal carriage in dogs suspected of CPV (37%) and CDV (15%) compared to dogs with noninfectious pathologies (9%) even prior to the start of their treatment. A 7-day course of ceftriaxone or ceftiofur administrated to CPV and CDV-suspected dogs substantially increased their ESCR-E faecal carriage during treatment (85% for CPV and 57% for CDV), and 4 weeks after the treatment ended (89% for CPV and 60% for CDV) when dogs were back in their households. Most of the observed resistance was carried by ESCR-E. coli carrying bla_CTX-M genes. Our results suggest the need to optimize prophylactic antibiotic therapy in dogs treated for a suspected viral infection to prevent ESCR-E emergence and spread in the community.

1453. PBP2, PBP2a and PBP4 Clone-specific Polymorphisms are not Associated to Ceftaroline (CPT) Susceptibility in Chilean Clinical Isolates of Methicillin-Resistant Staphylococcus aureus (MRSA)

Background

CPT is a last-generation cephalosporin active against MRSA due to its affinity for PBP2a. CPT-resistance (CPT-R) is well-described, with mutations in the active transpeptidase domain of PBP2a associated to high-level resistance. The accumulation of changes in the non-penicillin-binding domain of PBP2a has been linked to elevations of the minimal inhibitory concentration (MIC) to CPT to levels around 2-4ug/mL. PBP4 and PBP2 have also been implicated as potentially relevant mecA-independent mechanisms of CPT-R. We recently reported high rates of CPT-non-susceptibility in clinical MRSA strains from Chile. However, the mutational landscape of PBPs in clinical MRSA isolates from Chile and its relation to CPT susceptibility has not been assessed.

Methods

We analyzed 180 MRSA isolates collected from 2000-2018 in Santiago, Chile. Identification was confirmed by MALDI-TOF and methicillin resistance with cefoxitin disk-diffusion. CPT susceptibility was performed by BMD following CLSI-2019 guidance. Whole-genome sequencing was performed for all isolates; the mutational profile of PBPs was determined using reference sequences for PBP2 (AGY89563.1), PBP2a (NG_047938.1) and PBP4 (X91786.1).

Results

All isolates were phenotypically-confirmed MRSA and harbored mecA. The MIC₅₀/MIC₉₀ by BMD was 2/2μg/dL; only 71 (39%) isolates were CPT-susceptible (MIC <1µg/mL). Most isolates belonged to ST5/SCCmecI (70%,126/180), ST105/SCCmecII (10%,18/180) and ST8/SCCmecIV (5%, 9/180). All ST5/SCCmecI isolates carried the mutations in PBP2 (Y156D), PBP2a (M122I and E150K), and PBP4 (T189S, L234H, and T409A); CPT-susceptibility among ST5/SCCmecI was only 22%. On the other hand, all ST105/SCCmecII isolates had mutations in PBP2 (S707L) and PBP4 (T189S, L234H, and T409A) and exhibited a higher CPT-susceptibility rate (67%). All 9 isolates belonging to the ST8/SCCmecIV lineage harbored a non-coding mutation in PBP2a (g-6t) and the previously observed L234H change in PBP4. Importantly, no association between specific polymorphisms and MIC to CPT was found.

Table 1. PBPs mutations compared to CPT MICs by MLST and SCCmec

Conclusion

Changes in the studied PBPs were frequent among MRSA circulating in Chile and were conserved among different genetic backgrounds. However, these changes were not associated with the level of CPT MIC among these isolates.

Disclosures

Cesar A. Arias, MD, MSc, PhD, FIDSA, Entasis Therapeutics (Scientific Research Study Investigator)MeMed (Scientific Research Study Investigator)Merck (Grant/Research Support)

273. Comparative Effectiveness of Ampicillin in the Treatment of Enterococcus faecalis Bloodstream Infections in Patients With Cancer

Background

E. faecalis (Efc) isolates are usually susceptible to ampicillin (AMP). AMP-based regimens are the standard of care for enterococcal infections, although other antibiotics are often used as definitive treatment. We thus compared outcomes of patients with cancer and Efc bacteremia treated with AMP-containing (ACR) and non-AMP-containing antibiotic regimens (NACR).

Methods

A multicenter, prospective, observational cohort study conducted at MD Anderson Cancer Center, Henry Ford Hospital, and Memorial Hermann Health System. Eligible patients were ≥ 18 years old, diagnosed with cancer, and had at least one Efc bloodstream isolate collected from 12/2015 to 12/2018. Patients with polymicrobial infections were excluded. Patients were divided into two groups: i) ACR and ii) NACR. ACR included patients who received AMP at any time during treatment; other antimicrobials were permitted. NACR patients did not receive AMP at any time. The primary outcome compared desirability of outcome ranking (DOOR) between ACR and NACR at day 14. The DOOR consisted of six hierarchical levels: 1 - death; 2 - inpatient without microbiological cure (MC) and with acute kidney injury (AKI); 3 - inpatient without MC and without AKI; 4 - inpatient admitted with MC and with AKI; 5 - inpatient with MC and without AKI; 6 - alive and discharged. Comparison of DOORs between ACR and NACR was performed using inverse probability of treatment weighted (IPTW) ordered logistic regression.

Results

Seventy-one patients were included (ACR, n = 35; NACR, n = 36). No difference was seen in DOORs at day 14 between ACR and NACR (odds ratio [OR] 1.14, 95% Confidence Interval [CI] 0.45 – 2.92, p=0.78). No difference was observed for all-cause mortality at day 14 (OR 0.6, 95% CI 0.09 – 3.77, p=0.58) or day 30 (OR 0.42, 95% CI 0.09 – 1.94, p=0.27). Patients treated with ACR received a lower median duration of other antibiotics at any point during treatment compared to NACR: daptomycin (2 v 4 days) vancomycin (2 v 4 days), and linezolid (1 v 2 days).

Conclusion

Patients with cancer and Efc bloodstream infections had similar outcomes when treated with ACR and NACR. ACR were associated with less use of broad-spectrum antimicrobials. Future research should focus on the ecologic impact of use of NACR.

Disclosures

Marcus Zervos, MD, Melinta Therapeutics (Grant/Research Support) Cesar A. Arias, MD, MSc, PhD, FIDSA, Entasis Therapeutics (Scientific Research Study Investigator)MeMed (Scientific Research Study Investigator)Merck (Grant/Research Support)

Covid-19 in South America: clinical and epidemiological characteristics among 381 patients during the early phase of the pandemic in Santiago, Chile

BACKGROUND

Understanding the characteristics of the Covid-19 pandemic in different geographical regions, ethnic and socioeconomic settings are of emerging importance. This study presents the demographic and clinical features of SARS-CoV-2 infected patients in a large private healthcare center in Santiago, Chile, during the first month of the pandemic.

METHODS

We analyzed the demographics, laboratory and clinical characteristics including severity and outcome of all patients diagnosed with Covid-19 during the first month of the pandemic. SARS-2-CoV infection was confirmed by RT-PCR in nosopharyngeal samples. The primary outcome was a composite of ICU admission or all-cause, in-hospital mortality. Clinical and laboratory parameters of hospitalized patients were analyzed regarding their association with the primary outcome.

RESULTS

From March 3 to April 4, 2020, 3679 individuals were tested for SARS-CoV-2 in our hospital. Of those, 381 had Covid-19 and were included into this analysis. Most patients (99.2%) were Chileans, 12% returning from recent travel. The median age was 39 years (IQR 31-49) and 52% were female. A total of 88 patients (23.1%) were hospitalized; 18 (3.7%) required ICU and/or died. The overall mortality was 0.7%. Increased body mass index (BMI) and elevated C-reactive protein (CRP) were independently associated with ICU care or death.

CONCLUSION

During the first weeks of the pandemic in Chile, most Covid-19 patients were young, with low rates of hospitalization, ICU requirement, and fatality. BMI and CRP on admission were predictors for severity. Our data provide important information on the clinical course and outcome of Covid-19 in a Latin American setting.

Covid-19 in South America: clinical and epidemiological characteristics among 381 patients during the early phase of the pandemic in Santiago, Chile

BACKGROUND

Understanding the characteristics of the Covid-19 pandemic in different geographical regions, ethnic and socioeconomic settings are of emerging importance. This study presents the demographic and clinical features of SARS-CoV-2 infected patients in a large private healthcare center in Santiago, Chile, during the first month of the pandemic.

METHODS

We analyzed the demographics, laboratory and clinical characteristics including severity and outcome of all patients diagnosed with Covid-19 during the first month of the pandemic. SARS-2-CoV infection was confirmed by RT-PCR in nosopharyngeal samples. The primary outcome was a composite of ICU admission or all-cause, in-hospital mortality. Clinical and laboratory parameters of hospitalized patients were analyzed regarding their association with the primary outcome.

RESULTS

From March 3 to April 4, 2020, 3679 individuals were tested for SARS-CoV-2 in our hospital. Of those, 381 had Covid-19 and were included into this analysis. Most patients (99.2%) were Chileans, 12% returning from recent travel. The median age was 39 years (IQR 31-49) and 52% were female. A total of 88 patients (23.1%) were hospitalized; 18 (3.7%) required ICU and/or died. The overall mortality was 0.7%. Increased body mass index (BMI) and elevated C-reactive protein (CRP) were independently associated with ICU care or death.

CONCLUSION

During the first weeks of the pandemic in Chile, most Covid-19 patients were young, with low rates of hospitalization, ICU requirement, and fatality. BMI and CRP on admission were predictors for severity. Our data provide important information on the clinical course and outcome of Covid-19 in a Latin American setting.

Genomic Epidemiology of Vancomycin-Resistant Enterococcus faecium (VREfm) in Latin America: Revisiting The Global VRE Population Structure

Little is known about the population structure of vancomycin-resistant Enterococcus faecium (VREfm) in Latin America (LATAM). Here, we provide a complete genomic characterization of 55 representative Latin American VREfm recovered from 1998-2015 in 5 countries. The LATAM VREfm population is structured into two main clinical clades without geographical clustering. Using the LATAM genomes, we reconstructed the global population of VREfm by including 285 genomes from 36 countries spanning from 1946 to 2017. In contrast to previous studies, our results show an early branching of animal related isolates and a further split of clinical isolates into two sub-clades within clade A. The overall phylogenomic structure of clade A was highly dependent on recombination (54% of the genome) and the split between clades A and B was estimated to have occurred more than 2,765 years ago. Furthermore, our molecular clock calculations suggest the branching of animal isolates and clinical clades occurred ~502 years ago whereas the split within the clinical clade occurred ~302 years ago (previous studies showed a more recent split between clinical an animal branches around ~74 years ago). By including isolates from Latin America, we present novel insights into the population structure of VREfm and revisit the evolution of these pathogens.

1827. Genetic Characterization of Methicillin-Resistant Staphylococcus aureus (MRSA) Isolates Associated with the Development of Reduced Susceptibility to Vancomycin from Latin America

Background

Vancomycin (VAN) is a first-line therapeutic option for severe MRSA infections, especially in Latin America where other options are limited. However, reduced susceptibility to VAN may lead to therapeutic failures. The molecular mechanisms leading the development of VAN-intermediate S. aureus (VISA) and heterogeneous-VISA (hVISA) phenotypes are still unclear. We explored genetic signatures associated with hVISA phenotype in MRSA isolates recovered from bacteremic patients in 9 Latin American countries (2011–2014) in order to develop a genomic platform to identify these isolates.

Methods

From 538 VAN-susceptible MRSA (MIC90 = 1 µg/mL) we identified 30 hVISA isolates using GRD and macromethod E-tests; from these, 3 were confirmed by PAP-AUC. Whole-genome sequencing was performed in all 30 isolates using Illumina platform. Based on previous studies, we selected 46 genes involved in hVISA development. Multiple Blast alignments were performed using genomes of ATCC29213 and N315 (VAN-susceptible), Mu3 (hVISA) and Mu50 (VISA) as references.

Results

A total of 130 changes in 46 predicted proteins belonging to 8 functional categories were determined: 48 changes related to cell wall biogenesis, 22 to DNA/RNA processing, 17 to regulatory systems, 12 to cofactors and enzymes, 11 to membrane biosynthesis, 9 to virulence, 6 to amino acid metabolism, and 5 to transport of nitrogen and putrescine/spermidine. The most common changes identified in all the hVISA were: Y38H in Atl, N16S in PBP4, S160A in RpoB, L14I in WalK and E156G in YvqF, compared with VSSA strains. The proteins with the highest number of changes detected in the isolates confirmed by PAP-AUC were: CapP, DltA, Pbp4, TcaA, LytM (Cell wall biogenesis); MutL, RpoB (DNA/RNA processing); GraS (Regulatory systems); and PgsA (Membrane biosynthesis).

Conclusion

Changes in genes associated with cell wall biogenesis, DNA/RNA processing, regulatory systems, and membrane biosynthesis were the most prevalent in Latin American hVISA strains. Genetic signatures in genes encoding GraR (N197S), RpoB (H481Y, H481N), VraS (I5N), WalK (L14F, R222K) and MrsR (E146K) are potentially associated with this phenotype. These changes could be used to develop a platform for possible identification of hVISA isolates.

Disclosures

All Authors: No reported Disclosures.

622. The Accessory Genome in Enterococcal Bacteremia: Results from the Vancomycin-Resistant Enterococcal Bacteremia Outcomes Study (VENOUS)

Background

Vancomycin-resistant enterococci (VRE) are a major cause of nosocomial bloodstream infections. Enterococci exhibit remarkable genomic plasticity and can recombine through the acquisition of genetic material via mobile genetic elements (MGEs), including resistance genes. The accessory genome plays a major role in the evolution of enterococci within the human host. Thus, dissecting the entire genome (pan-genome) is of paramount importance to characterize the population structure of enterococci causing disease.

Methods

VENOUS is an ongoing prospective, observational study of adults with enterococcal bacteremia. From September 2016 to March 2018, E. faecalis (Efs) and E. faecium (Efm) were collected in 14 hospitals of a single hospital system and a major cancer center in Houston, TX, and a general hospital in Detroit, MI. Short- and long-read genomic sequencing were performed with Illumina MiSeq and Oxford Nanopore Technologies GridION X5, respectively. A proprietary bioinformatics pipeline was utilized for genome assembly and further analyses.

Results

156 Efs and 98 Efm isolates from single patients were analyzed. The average proportion of core genes in each genome was 64.6% (53.0–74.1) and 49.1% (45.2–51.0) for Efs and Efm, respectively. The vanA gene cluster was identified in 5.1% (8/157) of Efs and 57.1% (56/98) of Efm. The plasmid-encoded aac(6′)-Ie-aph(2″)-Ia gene conferring high-level resistance to aminoglycosides was found in 37.6% (59/157) Efs, seven of which also possessed vanA. Long-read sequencing of vanA-harboring plasmids from a subset of VRE revealed that the vanA cluster was carried in plasmids ranging from 31.7 to 132.3 kb. Although the vanA operon was fairly conserved, insertions of MGE were identified in the intergenic regions of vanS/vanH and vanX/vanY. Furthermore, a variety of MGE insertions mediated integration of the vanA operon, including IS1216 and IS256 (figure).

Conclusion

Accessory genes, including AMR genes, comprise a significant proportion of the enterococcal pan-genome, indicating major genetic plasticity within these organisms. Acquired resistance genes seem to have a high degree of recombination and play a substantial role in the expansion of the genomic repertoire in clinical isolates.

Disclosures

Samuel L. Aitken, PharmD, Melinta Therapeutics: Grant/Research Support, Research Grant; Merck, Sharpe, and Dohme: Advisory Board; Shionogi: Advisory Board.

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.

612. Molecular Mechanisms Leading to Ceftolozane–Tazobactam Resistance in Clinical Isolates of Pseudomonas aeruginosa from Five Latin American Countries

Background

Ceftolozane–tazobactam (C/T) is a combination of an antipseudomonal cephalosporin with a known β-lactamase inhibitor, with a potent in vitro activity against P. aeruginosa (Pae), without activity against carbapenemases. Among the mechanisms of resistance to C/T that have emerged, substitutions in the Pseudomonal-derived cephalosporinase (PDC), in AmpR, and in some ESBLs, are the most commonly described. The aim of this study was to identify the molecular mechanisms responsible for the in vitro non-susceptibility (NS) to C/T in a group of clinical Pae strains from Latin America.

Methods

Clinical Pae isolates (n = 508) were collected between January 2016 and October 2017 from 20 hospitals located in Argentina, Brazil, Chile, Colombia, and Mexico. Minimum inhibitory concentrations (MICs) to C/T were determined by standard broth microdilution and interpreted according to CLSI M100 S28 breakpoints. Production of carbapenemases in Pae isolates displaying NS to C/T was assessed by carbaNP® followed by PCR to detect blaKPC, blaNDM-1, blaVIM and blaIMP. Illumina whole-genome sequencing (WGS) was performed for isolates in which NS to C/T was not mediated by carbapenemases. The presence of mutations in PDC, AmpR, oprD and dacB as compared with PAO1, was evaluated.

Results

According to the CLSI breakpoints, 162/508 (32%) Pae isolates demonstrated NS to C/T. Due to the absence of growth, only 151/162 were further processed. Table 1 summarizes the results obtained by carbaNP®, PCR and WGS performed on these isolates. In 53% of the isolates, NS to C/T was explained by the production of at least one carbapenemase, KPC or VIM. WGS revealed that in addition to substitutions in PDC and AmpR, some isolates carried mutations in oprD and dacB (encoding PBP4) genes. The molecular mechanism of resistance in 4/56 isolates is yet to be determined.

Conclusion

Carbapenemase production is the most common mechanism of resistance to C/T detected in this study. VIM and KPC were detected in equal proportions, while none of the isolates was found to carry IMP or NDM. Further studies are warranted to establish the role of the novel substitutions found in PDC and AmpR, as well as the degree to which the mutations found in oprD and dacB contribute to the NS phenotype in some isolates.

Disclosures

All authors: No reported disclosures.

2248. Clinical and Microbiological Outcomes Associated with Real-World Use of Ceftolozane/Tazobactam

Background

Ceftolozane/tazobactam (C/T) is a novel cephalosporin/β-lactamase inhibitor combination for treating Gram-negative infections, particularly Pseudomonas aeruginosa (PA). C/T has been FDA-approved for complicated intra-abdominal and urinary tract infections and has just completed a trial in ventilator nosocomial pneumonia, but real-world outcome data are still emerging.

Methods

Demographic, microbiologic, treatment and outcome data of patients who received C/T for ≥48 hours from January 2016 to August 2018 at multiple centers within a single hospital system were retrospectively collected. Available isolates were analyzed for C/T susceptibility (by Etest) and whole-genome sequencing (WGS). Spades v.3.11.1 was used for assembly, multi-locus sequence typing v2.10 performed for in silico MLST with the PubMLST database and Abricate v0.7 was used for resistance gene screening with the CARD database.

Results

Among 45 patients, 58% were non-white, 53% were female and 13% were immunocompromised. The median age was 64 years (IQR, 50 to 69). At the time of the index event, a high proportion of patients required ICU care (42%) and pressor support (13%) as well as had invasive devices in place (64%). A minority (2.4%) had prior exposure to C/T. Respiratory infections were most common (38%) followed by urinary tract (20%). Concomitant Gram-negative agents were used in 18%. 69% achieved clinical success (i.e., recovery from infection-related signs and symptoms). The in-hospital mortality rate was 16% of which 5 out of 7 were attributed to infection. Microbiology was available for 91% of patients; 84% had PA isolates resistant to at least 3 antipseudomonal classes (Figures 1 and 2). Ten PA isolates were analyzed with WGS (Table 1). C/T resistance arose during therapy in one patient (MIC increase from 1 to 128 µg/mL). WGS showed a substitution in AmpC β-lactamase (A46D) and presence of bla_CARB-2.

Conclusion

Although C/T was used in a critically ill population with highly resistant organisms, cure rates were high and mortality was low. Acquired β-lactamases were not frequently seen among the PA isolates. C/T is a vital therapeutic option, particularly on MDR isolates for which options are limited.

Disclosures

Samuel L. Aitken, PharmD, Melinta Therapeutoics: Grant/Research Support, Research Grant; Merck, Sharpe, and Dohme: Advisory Board; Shionogi: Advisory Board.

Higher MICs (>2 mg/L) Predict 30-Day Mortality in Patients With Lower Respiratory Tract Infections Caused by Multidrug- and Extensively Drug-Resistant Pseudomonas aeruginosa Treated With Ceftolozane/Tazobactam

Background

Ceftolozane/tazobactam (C/T) efficacy and safety in ventilator-associated pneumonia (VAP) is being evaluated at a double dose by several trials. This dosing is based on a pharmacokinetic (PK) model that demonstrated that 3 g q8h achieved ≥90% probability of target attainment (50% ƒT > minimal inhibitory concentration [MIC]) in plasma and epithelial lining fluid against C/T-susceptible P. aeruginosa. The aim of this study was to evaluate the efficacy of different C/T doses in patients with lower respiratory infection (LRI) due to MDR- or XDR-P. aeruginosa considering the C/T MIC.

Methods

This was a multicenter retrospective study of 90 patients with LRI caused by resistant P. aeruginosa who received a standard or high dose (HDo) of C/T. Univariable and multivariable analyses were performed to identify independent predictors of 30-day mortality.

Results

The median age (interquartile range) was 65 (51-74) years. Sixty-three (70%) patients had pneumonia, and 27 (30%) had tracheobronchitis. Thirty-three (36.7%) were ventilator-associated respiratory infections. The median C/T MIC (range) was 2 (0.5-4) mg/L. Fifty-four (60%) patients received HDo. Thirty-day mortality was 27.8% (25/90). Mortality was significantly lower in patients with P. aeruginosa strains with MIC ≤2 mg/L and receiving HDo compared with the groups with the same or higher MIC and dosage (16.2% vs 35.8%; P = .041). Multivariate analysis identified septic shock (P < .001), C/T MIC >2 mg/L (P = .045), and increasing Charlson Comorbidity Index (P = .019) as independent predictors of mortality.

Conclusions

The effectiveness of C/T in P. aeruginosa LRI was associated with an MIC ≤2 mg/L, and the lowest mortality was observed when HDo was administered for strains with C/T MIC ≤2 mg/L. HDo was not statistically associated with a better outcome.

A Multicenter Study To Evaluate Ceftaroline Breakpoints: Performance in an Area with High Prevalence of Methicillin-Resistant Staphylococcus aureus Sequence Type 5 Lineage

Ceftaroline (CPT) is a broad-spectrum agent with potent activity against methicillin-resistant Staphylococcus aureus (MRSA). The sequence type 5 (ST5) Chilean-Cordobés clone, associated with CPT nonsusceptibility, is dominant in Chile, a region with high rates of MRSA infections. Here, we assessed the in vitro activity of CPT against a collection of MRSA isolates collected between 1999 and 2018 from nine hospitals (n = 320) and community settings (n = 41) in Santiago, Chile, and evaluated performance across testing methodologies. We found that our hospital-associated isolates exhibited higher CPT MIC distributions (MIC50 and MIC90 of 2 mg/liter) than the community isolates (MIC50 and MIC90 of 0.5 mg/liter), a finding that was consistent across time and independent of the culture source. High proportions (64%) of isolates were CPT nonsusceptible despite the absence of CPT use in Chile. Across methodologies, the Etest underestimated the MIC relative to the gold standard broth microdilution (BMD) test (MIC50 and MIC90 of 1 and 1.5 mg/liter, respectively). There was low (∼51%) categorical agreement (CA) between Etest and BMD results across CLSI and EUCAST breakpoints. The recent revision of CLSI guidelines abolished "very major error" (VME) from the previous guidelines (81%), which perform similarly to the EUCAST guidelines. The level of concordance between CLSI and EUCAST for BMD testing and Etest was >95%. Disk diffusion performed poorly relative to BMD under CLSI (CA, 55%) and EUCAST (CA, 36%) guidelines. Comparison of EUCAST to CLSI for disk diffusion (with EUCAST used as the reference) showed low agreement (CA, 25%; VME, 70%). In summary, CPT-nonsusceptible MRSA are dominant in clinical settings in Chile. Our results provide data to support the reevaluation of CPT breakpoints and to improve agreement across methodologies and agencies.

A One Health - One World initiative to control antibiotic resistance: A Chile - Sweden collaboration

Controlling antibiotic resistance is a global concern. The One Health initiative has provided a strategy to deal with this problem efficiently within a country. However, due to the global nature of the problem it is paramount not only to focus on specific countries, but to establish ways to avoid the development of antibiotic resistance in different geographical regions. In this letter, we propose a One Health - One World approach that would enable different countries to connect by sharing information about infections, outbreaks and surveillance. We believe such a strategy should be implemented worldwide in order to mitigate the development and dissemination of antibiotic resistance.

Novel Strategies for the Management of Vancomycin-Resistant Enterococcal Infections

PURPOSE OF REVIEW

Vancomycin-resistant enterococci (VRE) are important nosocomial pathogens that commonly affect critically ill patients. VRE have a remarkable genetic plasticity allowing them to acquire genes associated with antimicrobial resistance. Therefore, the treatment of deep-seated infections due to VRE has become a challenge for the clinician. The purpose of this review is to assess the current and future strategies for the management of recalcitrant deep-seated VRE infections and efforts for infection control in the hospital setting.

RECENT FINDINGS

Preventing colonization and decolonization of multidrug-resistant bacteria are becoming the most promising novel strategies to control and eradicate VRE from the hospital environment. Fecal microbiota transplantation (FMT) has shown remarkable results on treating colonization and infection due to Clostridiodes difficille and VRE, as well as to recover the integrity of the gut microbiota under antibiotic pressure. Initial reports have shown the efficacy of FMT on reestablishing patient microbiota diversity in the gut and reducing the dominance of VRE in the gastrointestinal tract. In addition, the use of bacteriophages may be a promising strategy in eradicating VRE from the gut of patients. Until these strategies become widely available in the hospital setting, the implementation of infection control measures and stewardship programs are paramount for the control of this pathogen and each program should provide recommendations for the proper use of antibiotics and develop strategies that help to detect populations at risk of VRE colonization, prevent and control nosocomial transmission of VRE, and develop educational programs for all healthcare workers addressing the epidemiology of VRE and the potential impact of these pathogens on the cost and outcomes of patients. In terms of antibiotic strategies, daptomycin has become the standard of care for the management of deep-seated infections due to VRE. However, recent evidence indicates that the efficacy of this antibiotic is limited, and higher (10-12 mg/kg) doses and/or combination with β-lactams is needed for therapeutic success. Clinical data to support the best use of daptomycin against VRE are urgently needed. This review provides an overview of recent developments regarding the prevention, treatment, control, and eradication of VRE in the hospital setting. We aim to provide an update of the most recent therapeutic strategies to treat deep-seated infections due to VRE.

Laboratory exposure to Coccidioides: lessons learnt in a non-endemic country

Coccidioides is a primary pathogenic fungus, which infects humans through highly infectious arthroconidia, causing substantial morbidity including life-threatening disseminated infections. Due to the low infectious dose, laboratory personnel might become infected during diagnostic procedures. Accordingly, coccidioidomycosis is reported as the most frequent laboratory-acquired systemic mycosis worldwide. This risk is aggravated in non-endemic countries, where the diagnosis may not be suspected. We report on an inadvertent exposure of 44 persons to Coccidioides posadasii in a clinical microbiology laboratory in Chile, the measures of containment after rapid diagnosis with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, and the lessons learnt in a non-endemic setting.

1399. Efficacy of Daptomycin Combination with β-Lactams for Daptomycin-resistant Enterococcus faecium Harboring LiaSR Substitutions

Background

Daptomycin (DAP) is one of the mainstay treatments for Enterococcus faecium infections. However, development of resistance threatens its continued viability as a treatment option. Although the mechanisms of DAP resistance in enterococci are not fully comprehended, they are associated with alterations in cell envelope phospholipids assembly which leads to repulsion of the drug from cell exterior and diversion from the cell septum. Previous data suggest that combination of DAP with β-lactams has the potential to improve patient outcomes. In this investigation, we sought to evaluate combinations of DAP with ampicillin (AMP), ceftaroline (CPT), and ertapenem (ERT).

Methods

E. faecium R497 harboring liaSFR mutations (DAP MIC of 16 mg/L) was evaluated in a simulated endocardial vegetation (SEV) pharmacokinetic and pharmacodynamic model over 336 hours at a starting inoculum of 10⁹ log10 CFU/g of SEV. DAP alone at 10 mg/kg/day or DAP (6, 8, 10 mg/kg/day) in combination with AMP (2 g continuous infusion), CPT 600 mg q12h or ERT 1 g q24h were evaluated. The emergence of DAP resistance was determined daily over the course of the 14-day experiment.

Results

DAP alone was not bactericidal and high-level DAP resistance was observed (MIC increase from 16 to 256 µg/mL) for all DAP alone regimens. Combination of DAP+AMP offered a significant reduction in log₁₀CFU/g amounts (up to 7 log₁₀ CFU/g and to detection limits) in 24 hours in DAP10+AMP model with no further emergence of DAP resistance. Even in DAP 6 mg/kg/day with AMP (2 g), dramatic killing with no further emergence of resistance was observed. Neither CPT nor ERT in combination with DAP was effective against this strain. At higher doses of DAP (14 mg/kg/day) + CPT or ERT, a temporary (0–48 hours) CFU/g reduction was observed followed by regrowth and the further emergence of DAP resistance.

Conclusion

Combination of DAP + AMP offered the most encouraging results against E. faecium R497. A DAP dose sparring effect was noted with DAP + AMP but not with CPT or ERT. The reason for the discrepancy is unknown and is under further investigation. Further evaluation of DAP plus β-lactam therapy is warranted to discover the most optimized DAP and β-lactam therapy to improve patient outcome and prevent the emergence of resistance.

Disclosures

B. Murray, Paratek pharmaceuticals: Consultant and Scientific Advisor, Consulting fee and Speaker honorarium; Forest/Actavis: Grant Investigator, Grant recipient; Cubist/Merck: Grant Investigator, Grant recipient. C. Arias, Merck & Co., Inc.: Grant Investigator, Research support; MeMed: Grant Investigator, Research support; Allergan: Grant Investigator, Research support; M. J. Rybak, Allergan: Consultant, Grant Investigator and Speaker’s Bureau, Research grant and Research support; Achaogen: Consultant, Grant Investigator and Speaker’s Bureau, Consulting fee, Research grant and Research support; Bayer: Consultant, Grant Investigator and Speaker’s Bureau, Consulting fee, Research grant and Research support; Melinta: Consultant, Grant Investigator and Speaker’s Bureau, Consulting fee, Research grant and Research support; Merck: Consultant, Grant Investigator and Speaker’s Bureau, Consulting fee, Research grant and Research support; Theravance: Consultant, Grant Investigator and Speaker’s Bureau, Consulting fee, Research grant and Research support; Sunovian: Consultant, Grant Investigator and Speaker’s Bureau, Consulting fee, Research grant and Research support; Zavante: Consultant, Grant Investigator and Speaker’s Bureau, Consulting fee, Research grant and Research support; NIAID: Consultant, Grant Investigator and Speaker’s Bureau, Consulting fee, Research grant and Research support

1214. High Frequency of Genes Encoding Resistance to Heavy Metals in Methicillin-Resistant Staphylococcus aureus (MRSA) Endemic Lineages From South America

Background

MRSA-USA300 is a community-associated clone that has spread worldwide, becoming the most successful clone in the USA. Since 2005, the MRSA-USA300 Latin-American Variant (USA300-LV) has disseminated in community and hospitals in Northern South America. Phylogenetic analysis revealed that USA300-LV is not derived from the USA300 (NA-USA300) but rather, the two clones diverged from a common ancestor. During their evolution, NA-USA300 strains incorporated the ACME element and USA300-LV acquired a copper and mercury resistance mobile element designated COMER. Interestingly, contamination by heavy metals in South American has been recently highlighted and could be driving the selection of resistant genetic lineages. We investigated the frequency of merA, merB, and copB in genomes of clinical isolates of S. aureus from Latin America (LA).

Methods

The presence of merA/merB and copB encoding mercury and copper resistance, respectively, were investigated in 515 S. aureus sequenced genomes recovered from bacteremic patients in hospitals from nine Latin American hospitals trough BLAST searches.

Results

The prevalence of merAB in S. aureus was 35% (181 out of 515 genomes). Interestingly, among 181 merAB-positive S. aureus, 174 were MRSA (96%). Moreover, 71%, 60%, 59%, and 51% of MRSA genomes from Peru, Ecuador, Colombia, and Venezuela, respectively, harbored mercury resistance genes. Similarly, 65%, 60%, and 22% of MRSA genomes from Ecuador, Colombia, and Venezuela, contained the copB gene. Among 174 MRSA harboring merAB, ST8 and ST5 were the most predominant lineages in (43% and 45% of genomes, respectively). In contrast, among 95 MRSA carrying copB, ST8 was the most frequent lineage (96% of isolates). MRSA from countries with high prevalence of mercury genes showed association with ST5 and ST8. 88% of Colombian and 87% of Ecuadorian MRSA harboring merAB belonged to ST8 lineage, whereas ST5 was predominant in 88% of Peruvian MRSA. In Venezuela, ST5 and ST8 were found in 44% and 33%, respectively, of MRSA positive for merAB.

Conclusion

High levels of mercury in rivers of Colombia, Ecuador and Peru has been reported. Thus, the prevalence of heavy metal resistance genes in MRSA clinical isolates suggest an adaptation of endemic genotypes to heavy metal contamination caused by activities like metal mining.

Disclosures

J. M. Munita, Pfizer: Grant Investigator, Research grant. C. Arias, Merck & Co., Inc.: Grant Investigator, Research support. MeMed: Grant Investigator, Research support. Allergan: Grant Investigator, Research support.

2059. Comparative Evaluation of Ceftaroline Susceptibility Methods in Clinical Isolates of Methicillin-Resistant Staphylococcus aureus (MRSA): Results from a Multicenter Study

Background

Ceftaroline (CPT) is a last generation cephalosporin with activity against MRSA. Recent data raised concerns regarding routine susceptibility testing in clinical laboratories, suggesting a poor performance for detecting nonsusceptible S. aureus (MIC >1 µg/dL) using either disc or gradient strips (Cantón R 2017)

Aim

To evaluate the results of CPT susceptibility testing with Etest^® and disk diffusion (Kirby–Bauer technique [KB]) as compared with broth microdilution (BMD), in clinical isolates of MRSA obtained from different hospitals in Santiago, Chile.

Methods

During 2017, we prospectively collected consecutive clinical strains of MRSA recovered from the blood or other sterile sites in ten tertiary-care hospitals in Santiago, Chile. One isolate per patient was obtained. Identification was confirmed by MALDI-TOF and susceptibility testing of all isolates was performed at a central lab. CPT susceptibility was evaluated by BMD and KB following CLSI 2017 directions. Etest was performed as per manufacturer’s instructions. Categorical agreement (CA), essential agreement (EA) and very major errors (VME) were evaluated. Susceptibilities were analyzed using CLSI established breakpoints

Results

Forty unique MRSA isolates were tested. Using BMD, the MIC₅₀/MIC₉₀ was 2/4 μg/dL, respectively. Moreover, only 18 (45%) isolates were CPT susceptible. Out of the remaining 22 MRSA strains, 8 (20%) were intermediate and 14 (35%) CPT-resistant (CPT-R). Using Etest, the MIC₅₀/MIC₉₀ was 1/2 μg/dL, with 31 (78%) isolates being considered susceptible and the remaining catalogued as intermediate. CPT susceptibility using KB catalogued 38 (95%) isolates as susceptible and only 2 as intermediate. No CPT-R strains were found by Etest or KB. The CA was for Etest and KB, respectively; Etest’s EA was 80%. Worryingly, out of 14 CPT-R isolates by BMD, 6 were deemed susceptible by Etest and 12 by KB, obtaining VME rates of 43 and 87%, respectively

Conclusion

Performance of both Etest and KB to assess CPT susceptibility in MRSA isolates from Chile was poor, with a unacceptably high proportion of VME, and a CA lower than 50% for both techniques. Correlation of CPT susceptibility with the molecular epidemiology of the isolates is currently being performed

Disclosures

All authors: No reported disclosures.

2560. Multispecies Outbreak of KPC-2 Producing Enterobacteriaceae in a Chilean Pediatric Hospital

Background

Carbapenem-resistant Enterobacteriaceae (CRE) are a critical global health problem. We detected a surge of CRE cases in a pediatric hospital in Chile, a country with a low endemicity of KPC-producing organisms. Herein, we describe the molecular epidemiology of this outbreak.

Methods

CRE isolates from clinical specimens and surveillance rectal swabs (obtained using chromID CARBA SMART agar, BioMerieux) of pediatric patients were collected from July 2015 to January 2017. Species identity was confirmed by MALDI-TOF. Carbapenemase genes (bla_KPC, bla_NDM, bla_VIM, bla_IMP, and bla_OXA-48-like) were detected by multiplex PCR, followed by amplification and sequencing of the bla_KPC allele. Conjugation experiments were conducted with representative species as donors and sodium azide-resistant E. coli J53 as recipient. PCR-based plasmid typing (PBRT Diatheva kit) was then performed on donors and recipients. For K. pneumoniae, genetic relatedness was investigated by PFGE, multilocus sequence typing and wzi typing.

Results

Sixty-one CRE clinical and surveillance isolates were obtained from 49 patients aged 17 days to 16 years. bla_KPC-2 was present in 57/62 isolates; no other carbapenemases were found. For 11 patients, multiple cultures were obtained; 4/11 had more than one KPC-harboring species. KPC-harboring isolates displayed ertapenem MICs ranging from 1 to >8 mg/L. Preliminary analyses suggest that bla_KPC-2 is contained within a nonclassical Tn4401 structure (lacking the upstream promoter). Mating experiments indicate that bla_KPC-2 is carried by a conjugative IncN backbone plasmid. Interestingly, K. pneumoniae isolates were nonclonal by PFGE and belonged to multiple STs unrelated to CG258 (ST34, ST36, among others) and different wzi types (37, 154, among others).

Conclusion

We report a multispecies outbreak of KPC-2 producing CRE in children mainly driven by horizontal dissemination of a promiscuous IncN plasmid. The nonclonal, multispecies nature of this outbreak provides insights into the complex dynamics of KPC dissemination in countries like Chile, where the clonal spread of highly successful clones like CG258 is not the predominant dissemination vehicle, and instead HGT-related spread could be playing a more important role.

Disclosures

All authors: No reported disclosures.

1009. Venous 1: A Prospective Multicenter Cohort Study of Enterococcal Bacteremia

Background

Enterococci often cause hospital-associated bloodstream infections in critically ill and immunocompromised patients. Prospective studies to assess the clinical impact of enterococcal bacteremia (EB) are lacking. We conducted a prospective study to investigate the clinical and microbiological factors associated with mortality in EB.

Methods

Adults with EB were prospectively followed in three US tertiary hospitals from September 2016 to March 2018. Individuals with EB for whom follow-up blood culture data within 7 days of index culture were available were included. Microbiologic failure (MF) was defined as clearance of bacteremia ≥4 days after the first blood culture. The main outcome was hospital mortality.

Results

A total of 282 patients were included with 69 (24%) infected with vancomycin-resistant enterococci (VRE). The majority of patients were male (60%) with a median age of 63 years. Median length of hospitalization for VRE patients was longer (25 d) than non-VRE (13 days, P < 0.001). E. faecium corresponded to 77% of VRE isolates, whereas E. faecalis comprised 72% of non-VRE. The average time to first blood culture was 16 days for VRE vs. 4 days for non-VRE (P < 0.001). Patients with VRE were more likely to have hematological malignancy or bone marrow transplant (P < 0.003), whereas patients infected non-VRE were more likely to have solid tumors (P = 0.02). The most common antibiotic used was daptomycin as monotherapy for both VRE and non-VRE with a median dose of 8 mg/kg for both groups. Overall mortality was 25% (43% vs. 20% in VRE vs. non-VRE patients, respectively; P < 0.0001). Factors significantly associated with mortality in univariate analyses included ICU admission, prolonged hospitalization, hematological malignancy, use of immunosuppressive therapy, hemodialysis, neutropenia (<500 cell/mL), Pitt bacteremia score >3, infection with VRE and MF. ICU admission (RR 3.3; 95% CI 1.7–7.5, neutropenia (RR 4.1; 95% CI 1.3–12.9), Pitt bacteremia score >3 (RR 6.8; 95% CI 2.6–18.0), MF (RR 4.7; 95% CI 2.2–10.3) and infection with VRE (RR 4.1; 95% CI 1.1–16.6) remained significantly associated with mortality in multivariate analyses.

Conclusion

The presence of VRE in EB and MF are associated with increased mortality. EB represent a major burden of disease in hospital settings.

Disclosures

C. Arias, Merck & Co., Inc.: Grant Investigator, Research support. MeMed: Grant Investigator, Research support. Allergan: Grant Investigator, Research support.

1221. Genetic Characteristics of Healthcare-Associated Methicillin-Resistant Staphylococcus aureus (HA-MRSA) Belonging to Clonal Complex 5 (CC5) in Latin-America

Background

MRSA are responsible for a high proportion of healthcare-associated infections. HA-MRSA is multidrug resistant, and infections occur most frequently among inpatients, for example, those who have undergone invasive medical procedures or those aged 50 to 60 years and older. Dominance of multidrug-resistant CC5 (Chilean and New York/Japan clones) was prevalent in infections in Latin America with the notable exception of Colombia and Ecuador where USA300-LV isolates dominate. We performed genetic characterization of HA-MRSA-CC5 isolates recovered from infections in nine countries (12 hospitals).

Methods

Species identification of S. aureus and presence of mecA were performed by PCR. We determined MICs to common anti-MRSA antibiotics and performed screening for VISA phenotype. Molecular characterization included detection of lukSF-PV and SCCmec typing. PFGE and MLST were performed in selected MRSA isolates with susceptibility patterns typical of the Chilean (ST5-MRSA-I) and USA300-LV (ST8-MRSA-IV) lineages.

Results

A total of 665 S. aureus isolates were prospectively recovered from 592 patients. A high frequency of methicillin resistance (&gt;40%) was observed in all countries (62%, 55%, 44%, and 40% in BRA, PER, CHI and ARG, respectively). Decreased susceptibility to VAN was not observed and VAN MIC90 was 1 µg/mL. In PER and CHI, the overwhelming majority of isolates (89%) belonged to the Chilean/Cordobes clone (CC5) with susceptibility patterns typical of this lineage (Resistance to β-lactams, MLSB-type, quinolones, and aminoglycosides). The New York/Japan clone (ST5-MRSA-II) was predominant in Brazil, replacing the prevalent hospital-associated Brazilian (ST239-MRSA-III) lineage. Most Argentinian MRSA isolates exhibiting a CA (ST5-IV) pattern, previously described in this country.

Conclusion

A variety of MRSA genetic lineages are circulating in Latin America with geographic clustering and clonal replacement. Dissemination of the CA-USA300-LV has not occurred beyond the northern region of the subcontinent.

Disclosures

J. M. Munita, Pfizer: Grant Investigator, Research grant. C. Arias, Merck & Co., Inc.: Grant Investigator, Research support. MeMed: Grant Investigator, Research support. Allergan: Grant Investigator, Research support.

Whole-Genome Sequencing Accurately Identifies Resistance to Extended-Spectrum β-Lactams for Major Gram-Negative Bacterial Pathogens

Background

There is marked interest in using DNA-based methods to detect antimicrobial resistance (AMR), with targeted polymerase chain reaction (PCR) approaches increasingly being incorporated into clinical care. Whole-genome sequencing (WGS) could offer significant advantages over targeted PCR for AMR detection, particularly for species where mutations are major drivers of AMR.

Methods

Illumina MiSeq WGS and broth microdilution (BMD) assays were performed on 90 bloodstream isolates of the 4 most common gram-negative bacteria causing bloodstream infections in neutropenic patients. The WGS data, including both gene presence/absence and detection of mutations in an array of AMR-relevant genes, were used to predict resistance to 4 β-lactams commonly used in the empiric treatment of neutropenic fever. The genotypic predictions were then compared to phenotypic resistance as determined by BMD and by commercial methods during routine patient care.

Results

Of 133 putative instances of resistance to the β-lactams of interest identified by WGS, only 87 (65%) would have been detected by a typical PCR-based approach. The sensitivity, specificity, and positive and negative predictive values for WGS in predicting AMR were 0.87, 0.98, 0.97, and 0.91, respectively. Using BMD as the gold standard, our genotypic resistance prediction approach had a significantly higher positive predictive value compared to minimum inhibitory concentrations generated by commercial methods (0.97 vs 0.92; P = .025).

Conclusions

These data demonstrate the potential feasibility of using WGS to guide antibiotic treatment decisions for patients with life-threatening infections for an array of medically important pathogens.

The Cefazolin Inoculum Effect Is Associated With Increased Mortality in Methicillin-Susceptible Staphylococcus aureus Bacteremia

Background

Recent studies have favored the use of cefazolin over nafcillin for the treatment of methicillin-susceptible Staphylococcus aureus (MSSA) bacteremia. The clinical influence of the cefazolin inoculum effect (CzIE) in the effectiveness of cephalosporins for severe MSSA infections has not been evaluated.

Methods

We prospectively included patients from 3 Argentinian hospitals with S. aureus bacteremia. Cefazolin minimum inhibitory concentrations (MICs) were determined at standard (10⁵ colony-forming units [CFU]/mL) and high (10⁷ CFU/mL) inoculum. The CzIE was defined as an increase of MIC to ≥16 µg/mL when tested at high inoculum. Whole-genome sequencing was performed in all isolates.

Results

A total of 77 patients, contributing 89 MSSA isolates, were included in the study; 42 patients (54.5%) had isolates with the CzIE. In univariate analysis, patients with MSSA exhibiting the CzIE had increased 30-day mortality (P = .034) and were more likely to have catheter-associated or unknown source of bacteremia (P = .033) compared with patients infected with MSSA isolates without the CzIE. No statistically significant difference between the groups was observed in age, clinical illness severity, place of acquisition (community vs hospital), or presence of endocarditis. The CzIE remained associated with increased 30-day mortality in multivariate analysis (risk ratio, 2.65; 95% confidence interval, 1.10–6.42; P = .03). MSSA genomes displayed a high degree of heterogeneity, and the CzIE was not associated with a specific lineage.

Conclusions

In patients with MSSA bacteremia where cephalosporins are used as firstline therapy, the CzIE was associated with increased 30-day mortality. Clinicians should be cautious when using cefazolin as firstline therapy for these infections.

Gram-Positive Bacterial Infections: Research Priorities, Accomplishments, and Future Directions of the Antibacterial Resistance Leadership Group

Antimicrobial resistance in gram-positive bacteria remains a challenge in infectious diseases. The mission of the Gram-Positive Committee of the Antibacterial Resistance Leadership Group (ARLG) is to advance knowledge in the prevention, management, and treatment of these challenging infections to improve patient outcomes. Our committee has prioritized projects involving methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococci (VRE) due to the scope of the medical threat posed by these pathogens. Approved ARLG projects involving gram-positive pathogens include (1) a pharmacokinetics/pharmacodynamics study to evaluate the impact of vancomycin dosing on patient outcome in MRSA bloodstream infection (BSI); (2) defining, testing, and validating innovative assessments of patient outcomes for clinical trials of MRSA-BSI; (3) testing new strategies for "step-down" antibiotic therapy for MRSA-BSI; (4) management of staphylococcal BSIs in neonatal intensive care units; and (5) defining the impact of VRE bacteremia and daptomycin susceptibility on patient outcomes. This article outlines accomplishments, priorities, and challenges for research of infections caused by gram-positive organisms.

Multicenter Evaluation of Ceftolozane/Tazobactam for Serious Infections Caused by Carbapenem-Resistant Pseudomonas aeruginosa

A multicenter, retrospective study of patients infected with carbapenem-resistant Pseudomonas aeruginosa who were treated with ceftolozane/tazobactam was performed. Among 35 patients, pneumonia was the most common indication and treatment was successful in 26 (74%). Treatment failure was observed in all cases where isolates demonstrated ceftolozane-tazobactam minimum inhibitory concentrations ≥8 μg/mL.

Ceftaroline-Resistant, Daptomycin-Tolerant, and Heterogeneous Vancomycin-Intermediate Methicillin-Resistant Staphylococcus aureus Causing Infective Endocarditis

We report a case of infective endocarditis (IE) caused by ceftaroline-resistant, daptomycin-tolerant, and heterogeneous vancomycin-intermediate methicillin-resistant S. aureus (MRSA). Resistance to ceftaroline emerged in the absence of drug exposure, and the E447K substitution in the active site of PBP2a previously associated with ceftaroline resistance was identified. Additionally, we present evidence of patient-to-patient transmission of the strain within the same unit. This case illustrates the difficulties in treating MRSA IE in the setting of a multidrug-resistant phenotype.