Methicillin-resistant Staphylococcus aureus bacteremia with elevated vancomycin minimum inhibitory concentrations

This case-control study of 25 cases with methicillin-resistant Staphylococcus aureus (MRSA) bacteremia with vancomycin minimum inhibitory concentration (MIC) ≥ 2 µg/mL and 391 controls (MIC < 2 µg/mL) characterized the clinical characteristics, treatments, and outcomes associated with elevated vancomycin MIC. Elevated vancomycin MIC was associated with baseline hemodialysis, prior MRSA colonization, and metastatic infection.

Robust clinical detection of SARS-CoV-2 variants by RT-PCR/MALDI-TOF multitarget approach

The coronavirus disease 2019 (COVID-19) pandemic has sparked the rapid development of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnostics. However, emerging variants pose the risk for target dropout and false-negative results secondary to primer/probe binding site (PBS) mismatches. The Agena MassARRAY® SARS-CoV-2 Panel combines reverse-transcription polymerase chain reaction and matrix-assisted laser desorption/ionization time-of-flight mass-spectrometry to probe for five targets across N and ORF1ab genes, which provides a robust platform to accommodate PBS mismatches in divergent viruses. Herein, we utilize a deidentified data set of 1262 SARS-CoV-2-positive specimens from Mount Sinai Health System (New York City) from December 2020 to April 2021 to evaluate target results and corresponding sequencing data. Overall, the level of PBS mismatches was greater in specimens with target dropout. Of specimens with N3 target dropout, 57% harbored an A28095T substitution that is highly specific for the Alpha (B.1.1.7) variant of concern. These data highlight the benefit of redundancy in target design and the potential for target performance to illuminate the dynamics of circulating SARS-CoV-2 variants.

Modified methicillin-resistant Staphylococcus aureus detected in neonatal intensive care patients

Objectives

As part of an active MRSA surveillance programme in our neonatal ICU, we identified nares surveillance cultures from two infants that displayed heterogeneity in methicillin resistance between isolated subclones that lacked mecA and mecC.

Methods

The underlying mechanism for the modified Staphylococcus aureus (MODSA) methicillin-resistance phenotype was investigated by WGS.

Results

Comparison of finished-quality genomes of four MODSA and four MSSA subclones demonstrated that the resistance changes were associated with unique truncating mutations in the gene encoding the cyclic diadenosine monophosphate phosphodiesterase enzyme GdpP or a non-synonymous substitution in the gene encoding PBP2.

Conclusions

These two cases highlight the difficulty in identifying non-mecA, non-mecC-mediated MRSA isolates in the clinical microbiology laboratory, which leads to difficulties in implementing appropriate therapy and infection control measures.

Lemierre's syndrome associated with hypervirulent Klebsiella pneumoniae: A case report and genomic characterization of the isolate

We describe a case of Lemierre’s syndrome (LS) caused by a hypervirulent strain of Klebsiella pneumoniae in a 63-year-old female with hypertension, hyperlipidemia, and diabetes mellitus, who presented with right neck pain and fevers. Computerized tomography of the neck and chest revealed an occluded right internal jugular vein secondary to thrombosis and septic emboli in lungs. Blood cultures grew K. pneumoniae. The patient was treated with ampicillin-sulbactam and then transitioned to amoxicillin-clavulanate to complete a 6-week course of antibiotics, and a 3-month course of rivaroxaban. String test of the K. pneumoniae isolate was positive at 2 cm. Whole genome sequencing identified several genes associated with the hypervirulent strain, notably the genes encoding for aerobactin (iucA and iucB) and salmochelin (iroB) iron acquisition systems. LS can rarely be caused by K. pneumoniae. Clinicians should monitor for known complications, such as septic emboli in patients with LS.

Deciphering the introduction and transmission of SARS-CoV-2 in the Colombian Amazon Basin

BACKGROUND

The SARS-CoV-2 pandemic has forced health authorities across the world to take important decisions to curtail its spread. Genomic epidemiology has emerged as a valuable tool to understand introductions and spread of the virus in a specific geographic location.

METHODOLOGY/PRINCIPAL FINDINGS

Here, we report the sequences of 59 SARS-CoV-2 samples from inhabitants of the Colombian Amazonas department. The viral genomes were distributed in two robust clusters within the distinct GISAID clades GH and G. Spatial-temporal analyses revealed two independent introductions of SARS-CoV-2 in the region, one around April 1, 2020 associated with a local transmission, and one around April 2, 2020 associated with other South American genomes (Uruguay and Brazil). We also identified ten lineages circulating in the Amazonas department including the P.1 variant of concern (VOC).

CONCLUSIONS/SIGNIFICANCE

This study represents the first genomic epidemiology investigation of SARS-CoV-2 in one of the territories with the highest report of indigenous communities of the country. Such findings are essential to decipher viral transmission, inform on global spread and to direct implementation of infection prevention and control measures for these vulnerable populations, especially, due to the recent circulation of one of the variants of concern (P.1) associated with major transmissibility and possible reinfections.

261. A Single-Center Case Series of Methicillin-Resistant S. aureus Bacteremia with Elevated Minimal Inhibitory Concentrations to Vancomycin

Background

Methicillin-resistant Staphylococcus aureus (MRSA) is a serious nosocomial pathogen, and is listed as a “High Priority Pathogen” by the WHO due to concerns of antimicrobial resistance and lack of novel therapeutics. Even in vancomycin-susceptible MRSA, increased rates of treatment failure occur in the setting of an increased minimum inhibitory concentration (MIC) to vancomycin, which is considered the gold-standard of therapy. We performed a case series of 25 patients infected with MRSA with an elevated MIC to vancomycin. Additionally, we describe the use of combination therapy with beta-lactams for the management of these highly complex cases.

Methods

We conducted a retrospective case series of 25 patients hospitalized at MSH between 8/2014–5/2019 who were treated for MRSA bacteremia where the isolate had an MIC ≥ 2. Data was centralized into the REDCap program. Clonal typing of bacteria and analysis of clinical features were performed in SAS and R.

Results

In total, 25 patients developed MRSA bacteremia with a vancomycin MIC ≥ 2. The majority of cases involved infection from vascular access, arteriovenous fistula/graft, and septic joint/osteomyelitis. All 25 patients were initially treated with vancomycin, with modification of therapy varying widely depending on clinician. The most common vancomycin-alternative was daptomycin (14/25 patients, alone and in combination). Combination therapy with vancomycin or daptomycin and a beta-lactam was used in 9 cases (36% of cases). Average number of days to clearance was 18.3 (range 1–69 days). Univariate and multivariate analyses revealed significant correlation MRSA bacteremia with vancomycin MIC ≥ 2 and admission from a nursing home or skilled nursing facility (p=0.02), history of MRSA colonization (p=0.006), and persistent bacteremia (bacteremia &gt;7 days)(p&lt; .0.001).

Conclusion

With few novel therapeutics under development, management of MRSA bacteremia with a rising MIC to vancomycin is a clinical challenge for practitioners. In our case series we found that treatment is largely patient and practitioner-dependent, and far from standardized. Further definition of the clinical risk factors for development and novel therapeutic strategies will enable understanding of how to best manage these challenging infections.

Disclosures

All Authors: No reported disclosures

SARS-CoV-2 Transmission among Marine Recruits during Quarantine

BACKGROUND

The efficacy of public health measures to control the transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has not been well studied in young adults.

METHODS

We investigated SARS-CoV-2 infections among U.S. Marine Corps recruits who underwent a 2-week quarantine at home followed by a second supervised 2-week quarantine at a closed college campus that involved mask wearing, social distancing, and daily temperature and symptom monitoring. Study volunteers were tested for SARS-CoV-2 by means of quantitative polymerase-chain-reaction (qPCR) assay of nares swab specimens obtained between the time of arrival and the second day of supervised quarantine and on days 7 and 14. Recruits who did not volunteer for the study underwent qPCR testing only on day 14, at the end of the quarantine period. We performed phylogenetic analysis of viral genomes obtained from infected study volunteers to identify clusters and to assess the epidemiologic features of infections.

RESULTS

A total of 1848 recruits volunteered to participate in the study; within 2 days after arrival on campus, 16 (0.9%) tested positive for SARS-CoV-2, 15 of whom were asymptomatic. An additional 35 participants (1.9%) tested positive on day 7 or on day 14. Five of the 51 participants (9.8%) who tested positive at any time had symptoms in the week before a positive qPCR test. Of the recruits who declined to participate in the study, 26 (1.7%) of the 1554 recruits with available qPCR results tested positive on day 14. No SARS-CoV-2 infections were identified through clinical qPCR testing performed as a result of daily symptom monitoring. Analysis of 36 SARS-CoV-2 genomes obtained from 32 participants revealed six transmission clusters among 18 participants. Epidemiologic analysis supported multiple local transmission events, including transmission between roommates and among recruits within the same platoon.

CONCLUSIONS

Among Marine Corps recruits, approximately 2% who had previously had negative results for SARS-CoV-2 at the beginning of supervised quarantine, and less than 2% of recruits with unknown previous status, tested positive by day 14. Most recruits who tested positive were asymptomatic, and no infections were detected through daily symptom monitoring. Transmission clusters occurred within platoons. (Funded by the Defense Health Agency and others.).

PathoSPOT genomic epidemiology reveals under-the-radar nosocomial outbreaks

Background

Whole-genome sequencing (WGS) is increasingly used to map the spread of bacterial and viral pathogens in nosocomial settings. A limiting factor for more widespread adoption of WGS for hospital infection prevention practices is the availability of standardized tools for genomic epidemiology.

Methods

We developed the Pathogen Sequencing Phylogenomic Outbreak Toolkit (PathoSPOT) to automate integration of genomic and medical record data for rapid detection and tracing of nosocomial outbreaks. To demonstrate its capabilities, we applied PathoSPOT to complete genome surveillance data of 197 MRSA bacteremia cases from two hospitals during a 2-year period.

Results

PathoSPOT identified 8 clonal clusters encompassing 33 patients (16.8% of cases), none of which had been recognized by standard practices. The largest cluster corresponded to a prolonged outbreak of a hospital-associated MRSA clone among 16 adults, spanning 9 wards over a period of 21 months. Analysis of precise timeline and location data with our toolkit suggested that an initial exposure event in a single ward led to infection and long-term colonization of multiple patients, followed by transmissions to other patients during recurrent hospitalizations.

Conclusions

We demonstrate that PathoSPOT genomic surveillance enables the detection of complex transmission chains that are not readily apparent from epidemiological data and that contribute significantly to morbidity and mortality, enabling more effective intervention strategies.

Staphylococcus aureus Bacteremia in Patients Infected With COVID-19: A Case Series

Background

Previous viral pandemics have shown that secondary bacterial infections result in higher morbidity and mortality, with Staphylococcus aureus being the primary causative pathogen. The impact of secondary S. aureus bacteremia on mortality in patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remains unknown.

Methods

This was a retrospective observational case series of patients with coronavirus disease 2019 (COVID-19) who developed secondary S. aureus bacteremia across 2 New York City hospitals. The primary end point was to describe 14-day and 30-day hospital mortality rates of patients with COVID-19 and S. aureus bacteremia. Secondary end points included predictors of 14-day and 30-day hospital mortality in patients with COVID-19 and S. aureus bacteremia.

Results

A total of 42 patients hospitalized for COVID-19 with secondary S. aureus bacteremia were identified. Of these patients, 23 (54.8%) and 28 (66.7%) died at 14 days and 30 days, respectively, from their first positive blood culture. Multivariate analysis identified hospital-onset bacteremia (≥4 days from date of admission) and age as significant predictors of 14-day hospital mortality and Pitt bacteremia score as a significant predictor of 30-day hospital mortality (odds ratio [OR], 11.9; 95% CI, 2.03-114.7; P = .01; OR, 1.10; 95% CI, 1.03-1.20; P = .02; and OR, 1.56; 95% CI, 1.19-2.18; P = .003, respectively).

Conclusions

Bacteremia with S. aureus is associated with high mortality rates in patients hospitalized with COVID-19. Further investigation is warranted to understand the impact of COVID-19 and secondary S. aureus bacteremia.

SARS-CoV-2 spread across the Colombian-Venezuelan border

INTRODUCTION

Venezuela and Colombia both adopted measures of containment early in response to the COVID-19 pandemic. However, Venezuela's ongoing humanitarian crisis has decimated its health care system, and forced millions of Venezuelans to flee through its porous border with Colombia. The extensive shared border, and illegal cross-border transit through improvised trails between the two countries are major challenges for public health authorities. We report the first SARS-CoV-2 genomes from Venezuela, and present a snapshot of the SARS-CoV-2 epidemiologic landscape in the Colombian-Venezuelan border region.

METHODS

We sequenced and assembled viral genomes from total RNA extracted from nasopharyngeal (NP) clinical specimens using a custom reference-based analysis pipeline. Three assemblies obtained were subjected to typing using the Phylogenetic Assignment of Named Global Outbreak LINeages 'Pangolin' tool. A total of 376 publicly available SARS-CoV-2 genomes from South America were obtained from the GISAID database to perform comparative genomic analyses. Additionally, the Wuhan-1 strain was used as reference.

RESULTS

We found that two of the SARS-CoV-2 genomes from Venezuela belonged to the B1 lineage, and the third to the B.1.13 lineage. We observed a point mutation in the Spike protein gene (D614G substitution), previously reported to be associated with increased infectivity, in all three Venezuelan genomes. Additionally, three mutations (R203K/G204R substitution) were present in the nucleocapsid (N) gene of one Venezuelan genome.

CONCLUSIONS

Genomic sequencing demonstrates similarity between SARS-CoV-2 lineages from Venezuela and viruses collected from patients in bordering areas in Colombia and from Brazil, consistent with cross-border transit despite administrative measures including lockdowns. The presence of mutations associated with increased infectivity in the 3 Venezuelan genomes we report and Colombian SARS-CoV-2 genomes from neighboring borders areas may pose additional challenges for control of SARS-CoV-2 spread in the complex epidemiological landscape in Latin American countries. Public health authorities should carefully follow the progress of the pandemic and its impact on displaced populations within the region.

Introductions and early spread of SARS-CoV-2 in the New York City area

New York City (NYC) has emerged as one of the epicenters of the current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. To identify the early transmission events underlying the rapid spread of the virus in the NYC metropolitan area, we sequenced the virus that causes coronavirus disease 2019 (COVID-19) in patients seeking care at the Mount Sinai Health System. Phylogenetic analysis of 84 distinct SARS-CoV-2 genomes indicates multiple, independent, but isolated introductions mainly from Europe and other parts of the United States. Moreover, we found evidence for community transmission of SARS-CoV-2 as suggested by clusters of related viruses found in patients living in different neighborhoods of the city.

552. Within-Host Evaluation of Colonization During Active Methicillin-Resistant S. aureus Bacteremia

Background

Staphylococcus aureus is a common commensal pathogen and a frequent cause of bacteremia, with nasal and blood isolates from single patients matching >80% of the time. Based on our prior work on paired single-patient isolates,¹ our aim was to collect a contemporary set of colonizing isolates from those with methicillin-resistant S. aureus (MRSA) bloodstream infections (BSIs), evaluate the within-host diversity by whole-genome sequencing (WGS), and detail the clinical features linked to colonization.

Methods

Adult patients with MRSA BSIs were screened for MRSA in the anterior nares from July 2018 to March 2019. Blood isolates underwent WGS, and spa and agr function screens were performed on three unique nasal isolates per patient. Clinical data from the electronic medical records underwent uni- and multivariate analyses on clinical features and outcomes.

Results

Of 55 unique patients with MRSA BSIs, screening of 45 subjects revealed that 67% were colonized with MRSA. The majority (64%) were males, 32% had prior colonization, and the most common infection sources were vascular access (27%), skin (24%), and unknown (24%). For those with nasal colonization, blood isolates were composed of 57% clonal complex (CC)5/t002, 33% CC8/t008, and 10% other. 81% of nasal isolates matched the blood, with 20% of nasal isolates harboring diverse spa types and 23% carried agr mutants. During this time frame, WGS found one transmission event involving a colonized subject. Colonization was associated with male gender (OR=4.52 95% CI [1.05–19.49]; P = 0.04) and prior hospital admission within the last 3 months (OR=6.12 95% CI [1.44–26.09]; P = 0.01) in multivariate analysis, with no differences in outcomes.

Conclusion

Colonization is an important component of invasive MRSA disease, and we found high rates of colonization with a predominance of the CC5. We also noted significant diversity and high proportion of agr mutants. At-risk groups included males and those with prior hospitalization. Combined molecular and clinical analyses can define the intrahost and interhost transmission dynamics of MRSA, and enables the development of targeted approaches in order to curtail disease.

1. Altman, D. R. et al. Genome Plasticity of agr-defective Staphylococcus aureus during clinical infection. Infect. Immun.(2018).

Disclosures

All authors: No reported disclosures.

2129. When Is Methicillin-resistant Staphylococcus aureus not Methicillin-resistant Staphylococcus aureus?

Background

As part of active surveillance in our NICU for methicillin-resistant Staphylococcus aureus (MRSA), two isolates representing modified S. aureus (MODSA), which are Methicillin resistant but lacking mecA or C were identified. Our current microbiology laboratory workflow for screening for MRSA involves plating isolates on chromoID agar (bioMérieux, Marcy-l’Etoile, France) as well as on sheep blood agar (SBA). Β hemolytic colonies on SBA that are catalase and coagulase positive are set up for confirmation and antimicrobial susceptibility testing on the Vitek 2 (bioMérieux, Marcy-l’Etoile, France).

Methods

These 2 isolates (from Baby 1 and Baby 2) tested positive for green colonies on the chromoagar plates. The Vitek 2 subsequently identified both these isolates as MRSA. However, for research purposes, all positive NICU MRSA isolates are tested via whole-genome sequencing (WGS). Both isolates were identified by WGS as methicillin-susceptible Staphylococcus aureus (MSSA). We subsequently went back and performed additional workup on these isolates. Isolates were plated on SBA and chromagar again and incubated for 24 hours. 2 colonies of different morphologies from the chromagar plates and 3 from the SBA were randomly selected and subcultured to chromagar and SBA for a total of 5 subcultures. Each of the subcultures was tested using staphaurex, mannitol salt agar and the Cepheid Xpert MRSA assay and all were confirmed to be Staphylococcus aureus.

Results

All 10 isolates tested negative by the Cepheid Xpert MRSA assay for MRSA. Phenotypic testing was set up again for all ten isolates using the vitek GP panel, as well as cefoxitin disk, and oxacillin E test using Mueller–Hinton agar supplemented with 2% NaCl as per CLSI methods. See table attached for results.

Conclusion

In conclusion, these two cases highlight the difficulty in identifying non-MecA, non-MecC-mediated MRSA isolates in the clinical microbiology laboratory. This is particularly important as more laboratories rely on testing for MecA by PCR for surveillance testing. These 2 cases were further complicated by heterogeneous sub-populations of Staphylococcus aureus. Failure to recognize these variant forms of MRSA can lead to difficulties in implementing appropriate therapy and infection control measures. Improved methodologies are needed.

Disclosures

All authors: No reported disclosures.

Tempo and mode of gene duplication in mammalian ribosomal protein evolution

Gene duplication has been widely recognized as a major driver of evolutionary change and organismal complexity through the generation of multi-gene families. Therefore, understanding the forces that govern the evolution of gene families through the retention or loss of duplicated genes is fundamentally important in our efforts to study genome evolution. Previous work from our lab has shown that ribosomal protein (RP) genes constitute one of the largest classes of conserved duplicated genes in mammals. This result was surprising due to the fact that ribosomal protein genes evolve slowly and transcript levels are very tightly regulated. In our present study, we identified and characterized all RP duplicates in eight mammalian genomes in order to investigate the tempo and mode of ribosomal protein family evolution. We show that a sizable number of duplicates are transcriptionally active and are very highly conserved. Furthermore, we conclude that existing gene duplication models do not readily account for the preservation of a very large number of intact retroduplicated ribosomal protein (RT-RP) genes observed in mammalian genomes. We suggest that selection against dominant-negative mutations may underlie the unexpected retention and conservation of duplicated RP genes, and may shape the fate of newly duplicated genes, regardless of duplication mechanism.