Emergent emm4 group A Streptococcus evidences a survival strategy during interaction with immune effector cells

The major gram-positive pathogen group A Streptococcus (GAS) is a model organism for studying microbial epidemics as it causes waves of infections. Since 1980, several GAS epidemics have been ascribed to the emergence of clones producing increased amounts of key virulence factors such as streptolysin O (SLO). Herein, we sought to identify mechanisms underlying our recently identified temporal clonal emergence amongst emm4 GAS, given that emergent strains did not produce augmented levels of virulence factors relative to historic isolates. Through the creation and analysis of isoallelic strains, we determined that a conserved mutation in a previously undescribed gene encoding a putative carbonic anhydrase was responsible for the defective in vitro growth observed in the emergent strains. We also identified that the emergent strains survived better inside macrophages and killed macrophages at lower rates relative to the historic strains. Via creation of isogenic mutant strains, we linked the emergent strain "survival" phenotype to the downregulation of the SLO encoding gene and upregulation of the msrAB operon which encodes proteins involved in defense against extracellular oxidative stress. Our findings are in accord with recent surveillance studies which found high ratio of mucosal (i.e., pharyngeal) relative to invasive infections amongst emm4 GAS. Inasmuch as ever-increasing virulence is unlikely to be evolutionary advantageous for a microbial pathogen, our data furthers understanding of the well described oscillating patterns of virulent GAS infections by demonstrating mechanisms by which emergent strains adapt a "survival" strategy to outcompete previously circulating isolates.

Increasing Incidence of Streptococcus anginosus Group Intracranial Infections Associated With Sinusitis, Otitis Media, and Mastoiditis in Children

BACKGROUND

The Streptococcus anginosus group (SAG) pathogens have the potential to cause head and neck space infections, including intracranial abscesses. Several centers noted an increase in intracranial abscesses in children during the SARS-CoV-2 pandemic, prompting a Centers for Disease Control and Prevention health alert in May 2022. We examined the epidemiology of pediatric intracranial abscesses at a tertiary care center with a focus on SAG pre- and post-pandemic.

METHODS

Cases of intracranial abscesses of any microbiologic etiology admitted from January 2011 to December 2022 were identified using International Classification of Diseases 10 codes. Subjects were cross-referenced with culture results from the microbiology laboratory at Texas Children's Hospital. Cases included were those associated with either otitis media, mastoiditis or sinusitis and medical records were reviewed.

RESULTS

A total of 157 cases were identified and 59.9% (n = 94) were caused by SAG. The incidence of all sinogenic/otogenic intracranial infections (P = 0.002), and SAG-specific infections (P = 0.004), increased from 2011 to 2022. SAG infection was more often associated with multiple surgeries, and these subjects were more likely to require craniotomy or craniectomy. Among sinogenic abscesses, S. intermedius was the most common pathogen, while among otogenic cases, S. pyogenes predominated. From March 2020 to Dec 2022, 9/49 cases tested positive for SARS-CoV-2 (18.4%); characteristics of infection were not significantly different among cases with and without SARS-CoV-2.

CONCLUSIONS

Over the last decade, intracranial complications of sinusitis/otitis have been increasing, specifically those caused by SAG; this trend, however, predated the SARS-CoV-2 pandemic. SAG was associated with a greater need for surgical intervention, specifically neurosurgery. Further work is necessary to determine the cause for these rising infections.

LiaR-dependent gene expression contributes to antimicrobial responses in group A Streptococcus

The ability to sense and respond to host defenses is essential for pathogen survival. Some mechanisms involve two-component systems (TCS) that respond to host molecules, such as antimicrobial peptides (AMPs) and activate specific gene regulatory pathways to aid in survival. Alongside TCSs, bacteria coordinate cell division proteins, chaperones, cell wall sortases and secretory translocons at discrete locations within the cytoplasmic membrane, referred to as functional membrane microdomains (FMMs). In Group A Streptococcus (GAS), the FMM or "ExPortal" coordinates protein secretion, cell wall synthesis and sensing of AMP-mediated cell envelope stress via the LiaFSR three-component system. Previously we showed GAS exposure to a subset of AMPs (α-defensins) activates the LiaFSR system by disrupting LiaF and LiaS co-localization in the ExPortal, leading to increased LiaR phosphorylation, expression of the transcriptional regulator SpxA2, and altered GAS virulence gene expression. The mechanisms by which LiaFSR integrates cell envelope stress with responses to AMP activity and virulence are not fully elucidated. Here, we show the LiaFSR regulon is comprised of genes encoding SpxA2 and three membrane-associated proteins: a PspC domain-containing protein (PCP), the lipoteichoic acid-modifying protein LafB and the membrane protein insertase YidC2. Our data show phosphorylated LiaR induces transcription of these genes via a conserved operator, whose disruption attenuates GAS virulence and increases susceptibility to AMPs in a manner primarily dependent on differential expression of SpxA2. Our work expands understanding of the LiaFSR regulatory network in GAS and identifies targets for further investigation of mechanisms of cell envelope stress tolerance contributing to GAS pathogenesis.

Gestational diabetes augments group B Streptococcus infection by disrupting maternal immunity and the vaginal microbiota

Group B Streptococcus (GBS) is a pervasive perinatal pathogen, yet factors driving GBS dissemination in utero are poorly defined. Gestational diabetes mellitus (GDM), a complication marked by dysregulated immunity and maternal microbial dysbiosis, increases risk for GBS perinatal disease. Using a murine GDM model of GBS colonization and perinatal transmission, we find that GDM mice display greater GBS in utero dissemination and subsequently worse neonatal outcomes. Dual-RNA sequencing reveals differential GBS adaptation to the GDM reproductive tract, including a putative glycosyltransferase (yfhO), and altered host responses. GDM immune disruptions include reduced uterine natural killer cell activation, impaired recruitment to placentae, and altered maternofetal cytokines. Lastly, we observe distinct vaginal microbial taxa associated with GDM status and GBS invasive disease status. Here, we show a model of GBS dissemination in GDM hosts that recapitulates several clinical aspects and identifies multiple host and bacterial drivers of GBS perinatal disease.

Invasive Group A Streptococcus in Infants Less Than 1-year of Age From 2012 to 2022: A Single-Center Experience

The incidence of invasive Group A Streptococcus (iGAS) has varied throughout the COVID-19 pandemic. We reviewed iGAS infections in infants ≤1 year from 2012 to 2022. Twenty-five percent of cases occurred in the last quarter of 2022. Pneumonia (21.8%) was the most common presentation. Twenty-one patients (65.6%) were successfully transitioned to oral antibiotics.

Identification of distinct impacts of CovS inactivation on the transcriptome of acapsular group A streptococci

Group A streptococcal (GAS) strains causing severe, invasive infections often have mutations in the control of virulence two-component regulatory system (CovRS) which represses capsule production, and high-level capsule production is considered critical to the GAS hypervirulent phenotype. Additionally, based on studies in emm1 GAS, hyperencapsulation is thought to limit transmission of CovRS-mutated strains by reducing GAS adherence to mucosal surfaces. It has recently been identified that about 30% of invasive GAS strains lacks capsule, but there are limited data regarding the impact of CovS inactivation in such acapsular strains. Using publicly available complete genomes (n = 2,455) of invasive GAS strains, we identified similar rates of CovRS inactivation and limited evidence for transmission of CovRS-mutated isolates for both encapsulated and acapsular emm types. Relative to encapsulated GAS, CovS transcriptomes of the prevalent acapsular emm types emm28, emm87, and emm89 revealed unique impacts such as increased transcript levels of genes in the emm/mga region along with decreased transcript levels of pilus operon-encoding genes and the streptokinase-encoding gene ska. CovS inactivation in emm87 and emm89 strains, but not emm28, increased GAS survival in human blood. Moreover, CovS inactivation in acapsular GAS reduced adherence to host epithelial cells. These data suggest that the hypervirulence induced by CovS inactivation in acapsular GAS follows distinct pathways from the better studied encapsulated strains and that factors other than hyperencapsulation may account for the lack of transmission of CovRS-mutated strains. IMPORTANCE Devastating infections due to group A streptococci (GAS) tend to occur sporadically and are often caused by strains that contain mutations in the control of virulence regulatory system (CovRS). In well-studied emm1 GAS, the increased production of capsule induced by CovRS mutation is considered key to both hypervirulence and limited transmissibility by interfering with proteins that mediate attachment to eukaryotic cells. Herein, we show that the rates of covRS mutations and genetic clustering of CovRS-mutated isolates are independent of capsule status. Moreover, we found that CovS inactivation in multiple acapsular GAS emm types results in dramatically altered transcript levels of a diverse array of cell-surface protein-encoding genes and a unique transcriptome relative to encapsulated GAS. These data provide new insights into how a major human pathogen achieves hypervirulence and indicate that factors other than hyperencapsulation likely account for the sporadic nature of the severe GAS disease.

Temporal dynamics of genetically heterogeneous extended-spectrum cephalosporin-resistant Escherichia coli bloodstream infections

Extended-spectrum cephalosporin-resistant Escherichia coli (ESC-R-Ec) is an urgent public health threat with sequence type clonal complex 131 (STc131), phylogroup B2 strains being particularly concerning as the dominant cause of ESC-R-Ec infections. To address the paucity of recent ESC-R-Ec molecular epidemiology data in the United States, we used whole-genome sequencing (WGS) to fully characterize a large cohort of invasive ESC-R-Ec at a tertiary care cancer center in Houston, Texas, collected from 2016 to 2020. During the study time frame, there were 1,154 index E. coli bloodstream infections (BSIs) of which 389 (33.7%) were ESC-R-Ec. Using time series analyses, we identified a temporal dynamic of ESC-R-Ec distinct from ESC-susceptible E. coli (ESC-S-Ec), with cases peaking in the last 6 months of the calendar year. WGS of 297 ESC-R-Ec strains revealed that while STc131 strains accounted for ~45% of total BSIs, the proportion of STc131 strains remained stable across the study time frame with infection peaks driven by genetically heterogeneous ESC-R-Ec clonal complexes. bla CTX-M variants accounted for most β-lactamases conferring the ESC-R phenotype (89%; 220/248 index ESC-R-Ec), and amplification of bla CTX-M genes was widely detected in ESC-R-Ec strains, particularly in carbapenem non-susceptible, recurrent BSI strains. Bla CTX-M-55 was significantly enriched within phylogroup A strains, and we identified bla CTX-M-55 plasmid-to-chromosome transmission occurring across non-B2 strains. Our data provide important information regarding the current molecular epidemiology of invasive ESC-R-Ec infections at a large tertiary care cancer center and provide novel insights into the genetic basis of observed temporal variability for these clinically important pathogens. IMPORTANCE Given that E. coli is the leading cause of worldwide ESC-R Enterobacterales infections, we sought to assess the current molecular epidemiology of ESC-R-Ec using a WGS analysis of many BSIs over a 5-year period. We identified fluctuating temporal dynamics of ESC-R-Ec infections, which have also recently been identified in other geographical regions such as Israel. Our WGS data allowed us to visualize the stable nature of STc131 over the study period and demonstrate a limited but genetically diverse group of ESC-R-Ec clonal complexes are detected during infection peaks. Additionally, we provide a widespread assessment of β-lactamase gene copy number in ESC-R-Ec infections and delineate mechanisms by which such amplifications are achieved in a diverse array of ESC-R-Ec strains. These data suggest that serious ESC-R-Ec infections are driven by a diverse array of strains in our cohort and impacted by environmental factors suggesting that community-based monitoring could inform novel preventative measures.

Hyperphosphorylation of the Group A Streptococcal Control of Virulence Regulator Increases Promoter Occupancy Specifically at Virulence Factor-Encoding Genes

The control of virulence two-component gene regulatory system (CovRS) is critical to the pathogenesis of many medically important streptococci. In emm1 group A streptococci (GAS), CovR directly binds the promoters of numerous GAS virulence factor-encoding genes. Elimination of CovS phosphatase activity increases CovR phosphorylation (CovR~P) levels and abrogates GAS virulence. Given the emm type-specific diversity of CovRS function, in this study we used chromatin immunoprecipitation sequencing (ChIP-seq) to define global CovR DNA occupancy in the wild-type emm3 strain MGAS10870 (medium CovR~P) and its CovS phosphatase-negative derivative 10870-CovS-T284A (high CovR~P). In the wild-type emm3 strain, 89% of the previously identified emm1 CovR binding sites present in the emm3 genome were also enriched; additionally, we ascertained unique CovR binding, primarily to genes in mobile genetic elements and other sites of interstrain chromosomal differences. Elimination of CovS phosphatase activity specifically increased CovR occupancy at the promoters of a broad array of CovR repressed virulence factor-encoding genes, including those encoding the key GAS regulator Mga and M protein. However, a limited number of promoters had augmented enrichment at low CovR~P levels. Differential motif searches using sequences enriched at high versus low CovR~P levels revealed two distinct binding patterns. At high CovR~P, a pseudopalindromic AT-rich consensus sequence (WTWTTATAAWAAAAWNATDA) consistent with CovR binding as a dimer was determined. Conversely, sequences specifically enriched at low CovR~P contained isolated ATTARA motifs suggesting an interaction with a monomer. These data extend understanding of global CovR DNA occupancy beyond emm1 GAS and provide a mechanism for previous observations regarding hypovirulence induced by CovS phosphatase abrogation. IMPORTANCE Given its key role in pathogenesis of Gram-positive bacteria, CovR is one of the most important members of the OmpR/PhoB family of transcriptional regulators. Herein we extend recent GAS CovR global binding analyses done in emm1 to a non-emm1 strain, which is important considering the known inter-emm-type heterogeneity in GAS CovRS function. Our data provide mechanistic understanding for variation in CovRS function between emm types and the profound hypovirulence of CovS phosphatase-negative strains in addition to indicating differential targeting by phosphorylated and nonphosphorylated CovR isoforms at specific CovR binding sites. These findings advance knowledge regarding how a key bacterial virulence regulator impacts pathogenesis and add to the growing appreciation of the function of nonphosphorylated OmpR/PhoB family members.

Clinical Epidemiology and Antimicrobial Resistance Patterns of Infections Due to Salmonella Species in Children, Houston, TX. 2016-2021: A Retrospective Study

BACKGROUND

Salmonellosis continues to be a major public health issue and high rates of infection are reported among young children. The contemporary clinical epidemiology of pediatric Salmonella spp. infections in the US is not well characterized.

METHODS

We performed a retrospective observational study in a large hospital network in Houston, TX. We included all patients 18 years or younger identified as having a positive culture for Salmonella spp. from any body site during the years 2016-2021. The patient's medical record was accessed and detailed demographic, clinical and microbiological information were collected.

RESULTS

We identified a total of 110 pediatric patients with Salmonella spp. infections between 2016 and 2021. The highest frequency (69%) of infections was observed among children 0-5 years old. Bloody diarrhea was most frequently reported for children 0-1 years old. Although the highest number of salmonellosis was among infants smaller than 1 year, the percentage of bacteremia in this age group was the lowest (15%). Serotype Infantis was the most common (21%) and was less likely to cause Salmonella bacteremia. Among the Salmonella spp. isolates that had antimicrobial susceptibility performed 5 showed resistance to one or more antibiotics including 1 extensively drug-resistant S. ser. Typhi originating from Pakistan.

CONCLUSION

Our findings suggest distinct clinical characteristics of Salmonella infections in the pediatric population. Consistent identification of isolates to the sub-species level along with serotyping seems critical to identify emerging lineages with increased virulence. Special consideration should be given to empiric treatment for patients who have recently returned from the Indian subcontinent.

High-Yield Deterministic Focused Ion Beam Implantation of Quantum Defects Enabled by In Situ Photoluminescence Feedback

Focused ion beam implantation is ideally suited for placing defect centers in wide bandgap semiconductors with nanometer spatial resolution. However, the fact that only a few percent of implanted defects can be activated to become efficient single photon emitters prevents this powerful capability to reach its full potential in photonic/electronic integration of quantum defects. Here an industry adaptive scalable technique is demonstrated to deterministically create single defects in commercial grade silicon carbide by performing repeated low ion number implantation and in situ photoluminescence evaluation after each round of implantation. An array of 9 single defects in 13 targeted locations is successfully created-a ≈70% yield which is more than an order of magnitude higher than achieved in a typical single pass ion implantation. The remaining emitters exhibit non-classical photon emission statistics corresponding to the existence of at most two emitters. This approach can be further integrated with other advanced techniques such as in situ annealing and cryogenic operations to extend to other material platforms for various quantum information technologies.

Increases in group A streptococcal infections in the pediatric population in Houston, TX, 2022

Beginning in October 2022, we observed a substantial increase in the total number of cases of invasive GAS disease (iGAS) in the pediatric population in Houston, TX. Emm12 GAS strains were disproportionately represented but the overall proportion of iGAS infections observed during the current spike was similar to pre-pandemic years.

Dynamic Periodicity of Extended-Spectrum Cephalosporin Resistant Bloodstream Escherichia coli Infections Driven by Non-CC131 Strains

Extended-spectrum cephalosporin resistant (ESC-R) Escherichia coli (ESC-R- Ec ) is an urgent public health threat with clonal complex (CC) 131, phylogroup B2 strains being particularly concerning as the dominant cause of ESC-R- Ec infections. To address the paucity of recent ESC-R- Ec molecular epidemiology data in the United States (US), we used whole genome sequencing (WGS) to fully characterize a large cohort of invasive ESC-R- Ec at a tertiary care cancer center in Houston, Texas collected from 2016-2020. During the study timeframe, there were 1154 index E. coli bloodstream infections (BSIs) of which 389 (33.7%) were ESC-R. Using time series analyses, we identified a temporal dynamic of ESC-R E. coli BSIs ( Ec -BSIs), distinct from ESC-susceptible Ec -BSIs, with cases peaking in the last 6 months of the calendar year. WGS of 297 ESC-R Ec -BSI strains revealed that while CC131 strains accounted for ∼45% of total infections, the proportion of CC131 strains remained stable across the time-period, and infection peaks were driven by genetically diverse, non-CC131 isolates. Bla _CTX-M variants accounted for most β-lactamases conferring the ESC-R phenotype (89%; 220/248 index ESC-R Ec -BSIs), and amplification of bla _CTX-M genes was widely detected in ESC-R Ec -BSI strains, particularly in carbapenem non-susceptible strains and in strains causing recurrent BSIs. Bla _{CTX- M-55} was significantly enriched within phylogroup A strains, and we identified bla _CTX-M-55 plasmid-to-chromosome transmission occurring across non-B2 strains. Our data provide important information regarding the current molecular epidemiology of invasive ESC-R E. coli and provide novel insights into the genetic basis of observed temporal variability for these clinically important pathogens.

IMPORTANCE

Given that E. coli is the leading cause of ESC-R Enterobacterales infection, we sought to assess the current molecular epidemiology of ESC-R- Ec using a WGS based analysis of many BSIs over a several year period. We identified a clear temporal dynamic of ESC-R- Ec infections, which has also recently been identified in other geographical regions such as Israel. Our WGS data allowed us to visualize the stable nature of CC131 over the study period and demonstrate that non-CC131 strains drove the infection peaks. Additionally, we provide the first widespread assessment of β-lactamase gene copy number in ESC-R- Ec infections and delineate mechanisms by which such amplifications are achieved in a diverse array of ESC-R- Ec strains. These data suggest that even for a tertiary care center, serious ESC-R- Ec infections are driven by a diverse array of strains and impacted by environmental factors suggesting that community-based monitoring could inform novel preventative measures.

2004. Contemporary Clinical Epidemiology of Pediatric Shigella spp. Infections in Houston, TX, 2016-2021

Background

Infections due to Gram-negative pathogens that cause gastrointestinal illnesses are a significant cause of morbidity in children. The contemporary clinical and epidemiological features of pediatric Shigella spp. infections in urban cities in the United States are not well described.

Methods

We used a retrospective cohort of patients (0-18 years of age) from a network of hospitals in Houston, TX. Only patients with Shigella spp. isolated from clinical samples dated from 2016 to 2021 were included in the study. Demographic, clinical, and microbiological data and susceptibility profile were extracted from the medical record.

Results

We identified a total of 73 pediatric patients with Shigella spp. Infections. The median age at presentation was 5 years. Hospital admission occurred in 32 % of infections with a median length of stay of 1 day (Table 1). Of cases with available clinical data, 80% of patients with Shigella spp. infections reported fever (Table 2). Of note, 62% of patients developed bloody diarrhea (Table 2). The majority of patients infected with Shigella flexneri (4/7) reported a history of international travel. Seizures were observed in 5 patients. No episodes of bacteremia were identified. Among patients with an identified exposure, daycare attendance and contact with individuals experiencing similar symptoms were the most common (Table 2). The majority of Shigella species were S. sonnei (90.4%) (Table 3). Resistance to trimethoprim-sulfamethoxazole (TMP-SMX) was common (45/68, 66%) among Shigella spp. isolates tested. No resistance to third generation cephalosporins was observed. (Table 3). Although azithromycin was the most common antibiotic used for treatment, susceptibility testing for this antibiotic was not performed in any of the cases.

Conclusion

Infections due to Shigella spp. are a significant burden among pediatric patients in a major metropolitan health care system (Houston, TX). Bloody diarrhea was the most common presentation, although the presence of Shiga-toxin-positive isolates was unknown. The observed high frequency of resistance to TMP-SMX and emergence of multi-drug resistant Shigella spp. in other countries warrants continued surveillance.

Disclosures

Cesar A. Arias, MD, PhD, Entasis Phramceuticals: Grant/Research Support|MeMed Diagnostics: Grant/Research Support|Merck: Grant/Research Support.

1543. Validation of a Nitrocefin-based Rapid Test for the Detection of the Cefazolin Inoculum Effect in Pediatric Patients with Methicillin-Susceptible Staphylococcus aureus Acute Osteomyelitis

Background

The cefazolin (Cz) inoculum effect (CzIE) defined as a Cz MIC ≥ 16 µg/mL at high inoculum (10⁷ CFU/mL) in MSSA isolates has been associated with poor outcomes in adult patients with bacteremia. Recently, it was associated with higher rates of progression to chronic osteomyelitis in pediatric patients with acute MSSA osteomyelitis, independent of the treatment choice. Thus, its detection could be important for management of certain MSSA infections. Broth microdilution at high inoculum is the gold standard for the detection of the CzIE. Yet, this method is lengthy (3–5 days), cumbersome, and expensive. We developed a nitrocefin-based rapid test (∼3h) which can identify the CzIE among MSSA isolates and that can be incorporated in the laboratory workflow. Previously, this rapid test was validated in MSSA isolates from adult patients with bacteremia. Here, we aimed to validate it in isolates from pediatric patients with acute MSSA osteomyelitis

Methods

We included 206 MSSA isolates from the same number pediatric patients from Houston, TX (2011–2018). All patients were diagnosed with acute MSSA osteomyelitis. The CzIE was determined using broth microdilution at high inoculum with a cutoff of Cz MIC ≥ 16 µg/mL. Whole genome sequence analysis was performed using Illumina Hi-Seq. BlaZ type was determined according to predicted BlaZ residues at position 119 and 207. The nitrocefin rapid test was performed following the published protocol (Rincon et al., JCM, 2021). Performance metrics were calculated for the complete data set and for specific BlaZ types.

Results

The prevalence of the CzIE was 33%. Compared to the gold standard, the nitrocefin rapid test had a sensitivity of 81% and a specificity of 93% (Table 1). The false negative and false positive rate of 9.2% and 13.8%, respectively, with an overall accuracy of 89%. There were no false positive results among blaZ negative strains. Among type A BlaZ MSSA, the sensitivity was 96.7%, and the specificity was 80%, while in type C BlaZ, they were 70.5% and 92.8%, respectively.

Performance metrics of the Nitrocefin-based Rapid Test in 206 MSSA isolates from pediatric patients with acute MSSA osteomyelitis compared to the Gold Standard of Broth Microdilution at high Inoculum.

Conclusion

The nitrocefin-based rapid test was able to correctly detect the CzIE in isolates from pediatric patients with MSSA acute osteomyelitis, with an overall accuracy of 89%. Implementation of this test may contribute to therapeutic decisions in deep-seated MSSA infections.

Disclosures

Sheldon L. Kaplan, MD, MeMed: Grant/Research Support|Pfizer: Grant/Research Support Jonathon C. McNeil, MD, Agency for Healthcare Research and Quality: Grant/Research Support|Allergan: Provided reagents for unrelated research|Nabriva: Site investigator for multicenter clinical trial Cesar A. Arias, MD, PhD, Entasis: Grant/Research Support|MeMed Diagnostics Ltd: Grant/Research Support|Merck: Grant/Research Support.

Reduced Ceftaroline Susceptibility among Invasive MRSA Infections in Children: a Clinical and Genomic Investigation

Ceftaroline represents an attractive therapy option for methicillin-resistant Staphylococcus aureus (MRSA). Little data is available, however, regarding the frequency of reduced susceptibility (RS) to ceftaroline among pediatric MRSA infections. We screened invasive MRSA isolates at a tertiary children's hospital for ceftaroline RS. Ceftaroline RS occurred in 2.9% of isolates and only among health care associated infections. Ceftaroline RS isolates were more often clindamycin-resistant. Sequencing data indicated the predominance of the CC5 lineage among ceftaroline RS isolates.

Staphylococcus aureus Colonization in Healthy Children during the First Year of the Severe Acute Respiratory Syndrome Coronavirus 2 Pandemic

The early severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic was temporally associated with a reduction in many childhood infections, although the impact on bacterial colonization is unknown. We longitudinally assessed Staphylococcusaureus colonization prior to and through the first year of the pandemic. We observed a decline in methicillin-resistant Staphylococcus aureus colonization associated with SARS-CoV-2 prevention mandates.

Use of whole-genome sequencing to detect transmission of group A Streptococcus in Houston, TX

We used a combination of local, comprehensive strain surveillance and bacterial whole-genome sequencing to identify potential transmission events of group A streptococcus (GAS) in Houston, TX, USA. We identified pharyngeal and skin and soft tissue sources of infection as having important roles in community GAS transmission, including invasive diseases.

CovS inactivation reduces CovR promoter binding at diverse virulence factor encoding genes in group A Streptococcus

The control of virulence gene regulator (CovR), also called caspsule synthesis regulator (CsrR), is critical to how the major human pathogen group A Streptococcus fine-tunes virulence factor production. CovR phosphorylation (CovR~P) levels are determined by its cognate sensor kinase CovS, and functional abrogating mutations in CovS can occur in invasive GAS isolates leading to hypervirulence. Presently, the mechanism of CovR-DNA binding specificity is unclear, and the impact of CovS inactivation on global CovR binding has not been assessed. Thus, we performed CovR chromatin immunoprecipitation sequencing (ChIP-seq) analysis in the emm1 strain MGAS2221 and its CovS kinase deficient derivative strain 2221-CovS-E281A. We identified that CovR bound in the promoter regions of nearly all virulence factor encoding genes in the CovR regulon. Additionally, direct CovR binding was observed for numerous genes encoding proteins involved in amino acid metabolism, but we found limited direct CovR binding to genes encoding other transcriptional regulators. The consensus sequence AATRANAAAARVABTAAA was present in the promoters of genes directly regulated by CovR, and mutations of highly conserved positions within this motif relieved CovR repression of the hasA and MGAS2221_0187 promoters. Analysis of strain 2221-CovS-E281A revealed that binding of CovR at repressed, but not activated, promoters is highly dependent on CovR~P state. CovR repressed virulence factor encoding genes could be grouped dependent on how CovR~P dependent variation in DNA binding correlated with gene transcript levels. Taken together, the data show that CovR repression of virulence factor encoding genes is primarily direct in nature, involves binding to a newly-identified DNA binding motif, and is relieved by CovS inactivation. These data provide new mechanistic insights into one of the most important bacterial virulence regulators and allow for subsequent focused investigations into how CovR-DNA interaction at directly controlled promoters impacts GAS pathogenesis.

Tight regulation of virulence factor production is a critical, but poorly understood aspect of bacterial pathogenesis. The OmpR/PhoB family member control of virulence regulator (CovR) is the master virulence factor controller in group A Streptococcus (GAS), a bacterium which commonly causes a diverse array of human infections. Mutations in the cognate kinase of CovR, CovS, are commonly observed among invasive GAS isolates, but the functional impact of CovS on global CovR function is unknown. Herein, we defined CovR global DNA binding locations, identified a consensus CovR binding motif, and determined how inactivation of the CovR cognate sensor kinase, CovS, impacts CovR-DNA interaction. Our findings show that CovR-repressed virulence factor encoding genes are directly regulated by CovR and that CovS inactivation markedly reduces CovR binding at CovR-repressed promoters. Given the widespread nature of CovR homologues in streptococci and other Gram-positive pathogens, these findings extend understanding of mechanisms by which OmpR/PhoB family members impact the ability of bacteria to cause serious infections.

Hematopoietic stem and progenitor cells improve survival from sepsis by boosting immunomodulatory cells

New therapeutic strategies to reduce sepsis-related mortality are urgently needed, as sepsis accounts for one in five deaths worldwide. Since hematopoietic stem and progenitor cells (HSPCs) are responsible for producing blood and immune cells, including in response to immunological stress, we explored their potential for treating sepsis. In a mouse model of Group A Streptococcus (GAS)-induced sepsis, severe immunological stress was associated with significant depletion of bone marrow HSPCs and mortality within approximately 5–7 days. We hypothesized that the inflammatory environment of GAS infection drives rapid HSPC differentiation and depletion that can be rescued by infusion of donor HSPCs. Indeed, infusion of 10,000 naïve HSPCs into GAS-infected mice resulted in rapid myelopoiesis and a 50–60% increase in overall survival. Surprisingly, mice receiving donor HSPCs displayed a similar pathogen load compared to untreated mice. Flow cytometric analysis revealed a significantly increased number of myeloid-derived suppressor cells in HSPC-infused mice, which correlated with reduced inflammatory cytokine levels and restored HSPC levels. These findings suggest that HSPCs play an essential immunomodulatory role that may translate into new therapeutic strategies for sepsis.

704. Contemporary Salmonella spp. Infections in Houston, TX (2019 and 2020) and Emergence of Cephalosporin Resistance

Background

Salmonella spp. Infections are a significant cause of morbidity in children in the United States. Contemporary clinical and microbiological characteristics of pediatric Salmonella infections in urban cities are not well described.

Methods

We used a retrospective chart review of records (0-18 years of age) from a network of hospitals (n=11) in Houston, TX. Only patients with Salmonella spp. isolated from clinical samples in 2019 and 2020 were included. Demographic, clinical, and microbiological data were extracted from the medical record.

Results

A total of 35 pediatric cases of Salmonella spp infection were identified over the two-year period. Median age was 1.6 years with over one-third (13/35, 37.1%) under one year (Table 1). Nearly half (15/35, 42.9%) of patients required hospitalization with a median length of stay of 2 days. From cases with available clinical data (n=31), most common symptoms were fever (22/31, 71%) and bloody diarrhea (21/31, 67.7%) (Table 2). Bacteremia was detected in 17.1% (6/35) of cases (Table 3). Exposure history was elicited in 29% (9/31) of cases with foreign travel being most common risk factor (Table 2). All speciated isolates were Salmonella enterica with the majority (24/29, 82.8%) subspecies enterica. Of 24 samples with serotype information, the most common was infantis (Table 3). A single isolate was resistant to all antibiotics tested except meropenem (Table 3) and was recovered from a patient after travel to Pakistan. Nearly half of patients (15/31, 48.4%) received definitive therapy with a third generation cephalosporin antibiotic. Complications were rare and included septic arthritis/osteomyelitis (n=1), UTI (n=3), coagulopathy (n=1), and hepatitis (n=1).

Conclusion

Salmonella spp. Infections were common in the Houston metropolitan area over the 2-year period and occurred primarily in young children. Foreign travel seems to be a major risk factor for acquisition of this infection in children. For the first time, the identification of a multi-drug resistant Salmonella isolate suggests that this phenotype is likely to increase and highlights the importance of ongoing surveillance.

Disclosures

Anthony R. Flores, MD, MPH, PhD, Nothing to disclose Cesar A. Arias, M.D., MSc, Ph.D., FIDSA, Entasis Therapeutics (Grant/Research Support)MeMed Diagnostics (Grant/Research Support)Merk (Grant/Research Support)

1248. A Machine-Learning Approach to Predict the Cefazolin Inoculum Effect in Methicillin-Susceptible Staphylococcus aureus

Background

The cefazolin (Cz) inoculum effect (CzIE), defined as an increase in the Cz MIC to ≥16 µg/mL at high inoculum (107 CFU/mL), has been associated with poor outcomes in MSSA bacteremia and osteomyelitis. The CzIE is associated with the BlaZ β-lactamase, encoded by blaZ and regulated by BlaR (antibiotic sensor) and BlaI (transcriptional repressor). Here, we aimed to obtain a machine-learning (ML) model to predict the presence of the CzIE based on the nucleotide sequence of the entire bla operon and its regulatory components.

Methods

Using whole genome sequencing, we analyzed the nucleotide sequences of the entire bla operon in 436 MSSA isolates recovered from blood, soft-tissue infections or pneumonia in adults (training-testing cohort, prevalence of the CzIE: 46%). Also, 32 MSSA recovered from pediatric patients with osteomyelitis with the CzIE were included as validation cohort. The CzIE was determined by broth microdilution at high inoculum. K-mer counts were obtained from the bla operon sequences of the isolates from the testing-training cohort, and then used in a ML pipeline which i) discards uninformative K-mers, ii) identifies optimal hyper-parameters and, iii) performs training of the model using 70% of the sequences as training set and 30% as testing set. The pipeline tested 11 different K-mer sizes and 2 models: Logistic Regression (LR) and Support Vector Machine (SVM). Finally, the model with best predictive ability was applied to the sequences of the MSSA osteomyelitis isolates (validation cohort).

Results

The ML approach had high specificity ( >90%), accuracy ( >80%) and ROC-AUC values ( >0.7) for detecting the CzIE in the testing set of isolates (Figure 1), independently of the type of model or the K-mer size used. The best predictive ability was with LR using K-mers of 17 nucleotides, with an accuracy of 84%, specificity of 96%, and sensitivity of 70% in the testing set (Figure 2). In the validation cohort, the model was capable to correctly identify all the strains exhibiting the CzIE (100% sensitivity).

Conclusion

The ML approach is a promising genomic application to detect the CzIE in MSSA isolates of a variety of sources, bypassing phenotypic testing. Further validation is needed to evaluate its possible utility in clinical settings.

Disclosures

Jonathon C. McNeil, MD, Agency for Healthcare Research and Quality (Research Grant or Support)Allergan (Grant/Research Support)Nabriva (Grant/Research Support, Other Financial or Material Support, Site PI for a multicenter trial) Anthony R. Flores, MD, MPH, PhD, Nothing to disclose Sheldon L. Kaplan, MD, Pfizer (Research Grant or Support) Cesar A. Arias, M.D., MSc, Ph.D., FIDSA, Entasis Therapeutics (Grant/Research Support)MeMed Diagnostics (Grant/Research Support)Merk (Grant/Research Support) Lorena Diaz, PhD , Nothing to disclose

1141. Effect of the SARS-CoV-2 Pandemic on Staphylococcus aureus Colonization in Healthy Children

Background

Staphylococcus aureus is a common colonizer of the skin and mucus membranes. Several investigators have reported reductions in a number of childhood infections temporally associated with social distancing/masking mandates intended to curb the SARS-CoV-2 pandemic. No data are available regarding the impact of these measures on bacterial colonization. We report preliminary results from an ongoing longitudinal S. aureus colonization study initiated just prior to the pandemic.

Methods

Healthy children < 18 years were recruited from 2 Houston-area primary care clinics from Nov 2019- Feb 2020. Subjects had anterior nares and axillary cultures obtained and completed questionnaires. Additional questionnaires and cultures were performed every three months for 1 year. Identified S. aureus were subjected to antimicrobial susceptibility testing as well as PCR for genes associated with tolerance to antiseptics (qacA/B, smr). Beginning in March 2020, social distancing and masking mandates were initiated. Temporary restrictions on non-essential research activities were enacted and follow-up encounters were not resumed until June 2020; subjects completed follow-up by Feb 2021. Comparison of colonization rates pre- and post-SARS-CoV-2 pandemic were performed.

Results

168 children were enrolled and 75.6% completed at least 2 follow-up encounters. 51.2% were colonized at least once by S. aureus and 8.1% had MRSA colonization (Figure 1). Those with MRSA colonization were older than those without (9.6 vs. 5.8 years, p=0.04). The frequency of S. aureus colonization was stable during the study period; however, rates of MRSA colonization declined beginning in summer 2020 (Figure 2 and 3, p=0.04). There was no difference in self-reported masking/social distancing practices or any traditional MRSA risk factors among those with and without MRSA colonization in the 6-12 month follow-up period.

Conclusion

Overall S. aureus nasal and axillary colonization in children remained relatively constant in the pre- and post-SARS-CoV-2 pandemic. A temporal association with social distancing/masking mandates and reduced MRSA colonization was observed. These findings suggest the potential impacts aggressive infection control practices may have on community MRSA colonization.

Disclosures

Jonathon C. McNeil, MD, Agency for Healthcare Research and Quality (Research Grant or Support)Allergan (Grant/Research Support)Nabriva (Grant/Research Support, Other Financial or Material Support, Site PI for a multicenter trial) Anthony R. Flores, MD, MPH, PhD, Nothing to disclose

698. Contemporary Clinical Epidemiology of Pediatric Shigella and Campylobacter Infections in Houston, TX, 2019 and 2020

Background

Infections due to Gram-negative, diarrheal pathogens are a significant cause of morbidity in children. Clinical features of pediatric Shigella and Campylobacter infections in urban cities in the United States are not well described.

Methods

We used a retrospective chart review of records (0-18 years of age) from a network of hospitals in Houston, TX. Only patients with Shigella spp. or Campylobacter spp. isolated from clinical samples in 2019 and 2020 were included. Demographic, clinical, and microbiological data were extracted from the medical record.

Results

We identified a total of 59 and 16 pediatric patients with Shigella spp. and Campylobacter spp. infections, respectively. Hospital admission occurred in 27.1% (16/59) of Shigella and 25% (4/16) of Campylobacter. Length of stay ranged between 1 and 2 days for both pathogens (Table 1). Of cases with available clinical data, Shigella infections were more likely to report fever during their illness compared to Campylobacter (80% versus 45.4%) (Table 2). Seizures were observed in 4 Shigella infected patients. No episodes of Shigella or Campylobacter bacteremia were identified. Among patients with an identified exposure, daycare attendance and contact with individuals experiencing similar symptoms were most common (Table 2). The vast majority of Shigella species were S. sonnei (96.6%) and all Campylobacter were C. jejuni (Table 3). Resistance to trimethoprim-sulfamethoxazole (TMP-SMX) was common (40/55, 72.7%) among Shigella isolates tested. No resistance to fluoroquinolones or third generation cephalosporins in any of the Shigella spp. isolates was observed. Susceptibility testing was not performed in Campylobacter due to lack of isolates. The most frequent antibiotic used was azithromycin (in 73.3% and 75% of patients with Shigella and Campylobacter, respectively). Major complications included urinary tract infection (n=1), rectal prolapse (n=1) and splenomegaly (n=1).

Conclusion

Infections due to Shigella and Campylobacter were a significant burden among pediatric patients between 2019 and 2020 in Houston, TX. The observed high frequency of resistance to TMP-SMX and emergence of multi-drug resistant Shigella in other countries warrants continued surveillance.

Disclosures

Anthony R. Flores, MD, MPH, PhD, Nothing to disclose Cesar A. Arias, M.D., MSc, Ph.D., FIDSA, Entasis Therapeutics (Grant/Research Support)MeMed Diagnostics (Grant/Research Support)Merk (Grant/Research Support)

Identification of epidemic scarlet fever group A Streptococcus strains in the paediatric population of Houston, TX, USA

Scarlet fever (SF) has recently been associated with group A streptococcal (GAS) strains possessing multidrug resistance and specific streptococcal exotoxins. We screened a local surveillance collection of GAS emm12 strains in Houston, TX, USA for antimicrobial resistance and identified a single isolate matching the antimicrobial resistance pattern previously reported for SF clones. Using whole-genome sequencing and combining genome sequence data derived from national surveillance databases, we identified additional emm12 GAS clones similar to those associated with prior SF outbreaks, emphasizing the need for continued surveillance for epidemic emergence in the USA.

The Indirect Impact of the SARS-CoV-2 Pandemic on Invasive Group a Streptococcus, Streptococcus Pneumoniae and Staphylococcus Aureus Infections in Houston Area Children

Masking and social distancing have been adopted to mitigate the severe acute respiratory syndrome coronavirus 2 pandemic. We evaluated the indirect impact of severe acute respiratory syndrome coronavirus 2 prevention strategies on invasive Staphylococcus aureus, Streptococcus pneumoniae (pneumococcus) and Group A Streptococcus in Houston area children. We observed a decline in invasive pneumococcal disease and invasive Group A Streptococcus temporally associated with social distancing/masking/school closures.

Recognizing a MIS-Chievous Cause of Acute Viral Gastroenteritis

Historically, children evaluated for vomiting and diarrhea secondary to viral enteritis have symptoms lasting 2-4 days and respond to supportive care, including oral rehydration and anti-emetics if required. Recently, within a 14-day timespan, we encountered three children with severe diarrhea who rapidly became dehydrated and went into hypotensive shock. Although SARS-CoV-2 molecular tests were negative by nasopharyngeal swab, all were later found to have MIS-C. This small case series underscores features reported in previous larger studies and emphasizes the rapid clinical evolution of this condition. We highlight the importance of early recognition of cardinal laboratory findings characteristic of MIS-C (i.e., lymphopenia, markedly elevated acute phase reactants, and hypoalbuminemia). We also show serologic evidence that the pathophysiological mechanism of SARS-CoV-2 related diarrhea may differ from other causes of dehydrating vomiting and diarrhea, with no serologic evidence of villus cell injury.

1200. Risk of group A streptococcal Transmission Among the Pediatric Population in the Houston Area

Background

Disease due to group A Streptococcus (GAS) occurs frequently in children and usually manifests as pharyngitis or superficial skin infections. However, invasive disease (iGAS) such as necrotizing fasciitis or streptococcal toxic shock syndrome is responsible for significant morbidity and mortality. National-level surveillance at the Centers for Disease Control and Prevention (CDC) estimates >10,000 cases and ~1,500 deaths due to iGAS occur annually in the US. Much interest revolves around the ability to detect potential transmission events (PTEs) of GAS disease using surveillance data as such information may change recommendations for chemoprophylaxis of close contacts. Studies by the CDC have shown a secondary attack rate from 66.1 to 102 /100,000, primarily occurring among older adults with co-morbidities. However, previous studies were limited in that the GAS surveillance was limited to iGAS disease.

Methods

Retrospective study using a comprehensive GAS passive surveillance system. GAS isolates and associated metadata were obtained from 2 hospital systems in the Texas Medical Center from 2017-2019. Molecular emm typing of GAS isolates was performed using the CDC protocol. PTEs were defined based on GAS disease isolates originating from the same zip code, occurring within 30 days of each other, and of the same emm type.

Results

A total of 1291 isolates were included in the study – 94 PTEs were identified representing 168 individual GAS isolates of which 74 were defined as index cases. The 4 most common GAS emm types identified among PTEs were emm1 (43/94, 45.7%), emm12 (30/94, 31.9%), emm4 (6/94, 6.4%), and emm6 (5/94, 5.3%). Index cases most frequently resulted in a single PTE (n=74) with an average number of PTEs per index case of 1.3 (range 1 to 3 PTEs). From index cases, 10 GAS isolates were derived from invasive disease (10/74, 13.5%) and 6 from skin and soft tissue infections (SSTI; 6/74, 8.1%). A substantial proportion of PTEs resulted in iGAS (9/94, 9.5%) and SSTI (10/94, 10.6%).

Conclusion

Using comprehensive local surveillance, we were able to identify several potential GAS transmission events. Further analysis – including whole genome sequencing on index and PTE isolates – is needed to better define transmission events.

Disclosures

Jonathon C. McNeil, MD, Nabriva (Research Grant or Support, I serve as the site investigator on a multicenter clinical trial sponsored by Nabriva)

Genome-wide analysis of in vivo CcpA binding with and without its key co-factor HPr in the major human pathogen group A Streptococcus

Catabolite control protein A (CcpA) is a master regulator of carbon source utilization and contributes to the virulence of numerous medically important Gram‐positive bacteria. Most functional assessments of CcpA, including interaction with its key co‐factor HPr, have been performed in nonpathogenic bacteria. In this study we aimed to identify the in vivo DNA binding profile of CcpA and assess the extent to which HPr is required for CcpA‐mediated regulation and DNA binding in the major human pathogen group A Streptococcus (GAS). Using a combination RNAseq/ChIP‐seq approach, we found that CcpA affects transcript levels of 514 of 1667 GAS genes (31%) whereas direct DNA binding was identified for 105 GAS genes. Three of the directly regulated genes encode the key GAS virulence factors Streptolysin S, PrtS (IL‐8 degrading proteinase), and SpeB (cysteine protease). Mutating CcpA Val301 to Ala (strain 2221‐CcpA‐V301A) abolished interaction between CcpA and HPr and impacted the transcript levels of 205 genes (40%) in the total CcpA regulon. By ChIP‐seq analysis, CcpAV301A bound to DNA from 74% of genes bound by wild‐type CcpA, but generally with lower affinity. These data delineate the direct CcpA regulon and clarify the HPr‐dependent and independent activities of CcpA in a key pathogenic bacterium.

Adhesin genes and biofilm formation among pediatric Staphylococcus aureus isolates from implant-associated infections

Background

Microbial surface component recognizing adhesive matrix molecules (MSCRAMMs) facilitate Staphylococcus aureus adherence to host tissue. We hypothesized that S. aureus isolates from implant-associated infections (IAIs) would differ in MSCRAMM profile and biofilm formation in vitro compared to skin and soft tissue infection (SSTI) isolates.

Methods

Pediatric patients and their isolates were identified retrospectively. IAI and SSTI isolates were matched (1:4). Pulsed field gel electrophoresis was performed to group isolates as USA300 vs. non-USA300. Whole genome sequencing was performed and raw sequence data were interrogated for presence of MSCRAMMs (clfA, clfB, cna, ebh, efb, fnbpA, fnbpB, isdA, isdB, sdrC, sdrD, sdrE), biofilm-associated (icaA,D,B,C), and Panton-Valentine leukocidin (lukSF-PV) genes, accessory gene regulator group, and multilocus sequence types. In vitro biofilm formation was assessed for 47 IAI and 47 SSTI isolates using a microtiter plate assay. Conditional logistic regression was performed for analysis of matched data (STATA11, College Station, TX).

Results

Forty-seven IAI and 188 SSTI isolates were studied. IAI isolates were more often methicillin susceptible S. aureus and non-USA300 vs. SSTI isolates [34 (72%) vs. 79 (42%), p = 0.001 and 38 (81%) vs. 57 (30%) p <0.001, respectively]. Greater than 98% of isolates carried clfA, clfB, efb, isdA, isdB, and icaA,D,B,C while cna was more frequently found among IAI vs. SSTI isolates (p = 0.003). Most isolates were strong biofilm producers.

Conclusions

S. aureus IAI isolates were significantly more likely to be MSSA and non-USA300 than SSTI isolates. Carriage of MSCRAMMs and biofilm formation did not differ significantly between isolates. Evaluation of genetic polymorphisms and gene expression profiles are needed to further delineate the role of adhesins in the pathogenesis of IAIs.

Group A Streptococcus Transcriptome Analysis

Global gene expression analyses in bacteria have undergone a dramatic transformation. Prior to the development of high-throughput sequencing technologies, real-time PCR or microarray studies were the mainstay of assessing differences in gene expression in bacteria. Real-time PCR remains a critical tool for targeted gene expression analyses. However, microarray studies have given way to the plethora of advantages in RNA sequencing (RNA-seq) for the determination of global gene expression (i.e., transcriptome). Increased accessibility to high-throughput sequencing and user-friendly bioinformatics data analysis software have made RNA-seq technology use more widespread. Here, we provide comprehensive methods to perform RNA sequencing of Streptococcus pyogenes strains grown in vitro in standard laboratory media, including cell growth, RNA extraction, ribosomal RNA depletion, and library construction. Considerations for library sequencing and data analysis are also provided.

Unexpected relationships between frequency of antimicrobial resistance, disease phenotype and emm type in group A Streptococcus

Despite universal susceptibility to β-lactams, resistance to second-line antimicrobials (e.g. erythromycin) is increasingly common among group A Streptococcus (GAS). To better understand the frequency of regional GAS antimicrobial resistance, we screened a previously described GAS strain collection from Houston, TX, USA, for resistance to commonly used antimicrobials. A total of 100/929 (10.8 %) showed resistance to at least one antimicrobial. Tetracycline resistance was identified in 52 (5.6 %) GAS strains. The cumulative frequency of erythromycin and clindamycin resistance [macrolide (M) and macrolide-lincosamide-streptogramin (MLS) phenotypes] was greatest among invasive GAS strains (9.9 %) compared to that of strains derived from any other infection type (5.9 %, P=0.045). We identified emm types 11, 75, 77 and 92 as the only emm types with high (e.g. >50 %) within-emm type resistance and contributing to the majority (24/26; 92 %) of erythromycin/clindamycin resistance in invasive GAS. High-frequency resistance emm types were also significantly overrepresented in invasive GAS strains as indicated by invasive index. We performed whole-genome sequencing to define genetic elements associated with resistance among emm types 11, 75, 77 and 92. Diverse mobile elements contributed to GAS resistance including transposons, integrative conjugative elements, prophage and a plasmid. Phylogenetic analysis suggests recent clonal emergence of emm92 GAS strains. Our findings indicate that less frequently encountered GAS emm types disproportionately contribute to resistance phenotypes, are defined by diverse mobile genetic elements and may favour invasive disease.

855. Evolution of Group B Streptococcal Capsular Type V Invasive Infections in Neonates and Young Infants: A Whole Genome Sequencing Study

Background

Since 1970 group B Streptococcus (GBS) has been a frequent cause of sepsis or meningitis in young infants. Capsular polysaccharide type V was first recognized in 1990 and has increased to the point where it now causes ~15% of GBS infections. GBS type V strains are almost entirely sequence type 1 (ST1) in adult infections. To understand the emergence of type V GBS, we compared infant strains before 1990 to more contemporary isolates from young infants and adults.

Methods

Thirty-five strains isolated from blood or CSF of infants <90 days of age (Houston, 1979–1996) were compared with the following previously sequenced type V, ST1 strains: (1) 14 from infant blood or CSF from Center for Disease Control and Prevention (CDC) (2015–2017), (2) 193 blood ST1 isolates from adults (Houston, 1992–2013), and (3) 516 invasive isolates from the CDC (2015–2017). Isolates were sequenced using an Illumina MiSeq instrument followed by molecular typing, antimicrobial resistance gene determination, and phylogenetic analysis. Antimicrobial susceptibility testing (AST) was performed using disk diffusion and E-test.

Results

The majority (29/35) of Houston young infant strains were ST1. Type V GBS strains isolated prior to 1990 were more likely to be of ST-2 or ST-26 (5/10) compared with those from 1990 or later (24/25 and 14/14 CDC infant invasive type V). Tetracycline resistance was identified in 83% (29/35) while macrolide resistance (MR) occurred in only 23% (8/35) of the strains. Compared with early neonatal isolates, MR was significantly more frequent among contemporary neonatal (12/14, 86%, P < 0.0001) and adult (502/710, 71%, P < 0.0001) ST1 GBS. Phylogenetic analysis showed two distinct clades defined, in part, by MR. A high-frequency MR (340/360, 94%) clade was defined by the presence of erm(B) on Tn3872 while the low-frequency MR clade (159/350, 45%) was more diverse in mobile elements contributing to MR. The majority (27/29) of early neonatal ST1 GBS strains were observed in the low-frequency MR clade.

Conclusion

Infant invasive disease due to type V GBS before 1990 consisted of more diverse STs but is now almost exclusively ST1. Differences in the frequency of MR between early neonatal and contemporary type V ST1 GBS suggest MR may, at least in part, have driven the expansion of type V ST1 GBS.

Disclosures

All Authors: No reported Disclosures.

Capsule-Negative emm Types Are an Increasing Cause of Pediatric Group A Streptococcal Infections at a Large Pediatric Hospital in Texas

BACKGROUND

Bacterial infections caused by group A Streptococcus (GAS) are common in childhood. Few study reports have provided data on pediatric-specific trends in the epidemiology and bacterial strain characteristics of GAS infections.

METHODS

We prospectively collected GAS isolates from the clinical microbiology laboratory at Texas Children's Hospital between July 1, 2013, and June 30, 2017. Patient characteristics and GAS disease categories were determined through chart review. GAS isolates were obtained from patients in either the inpatient or outpatient setting, and cases were defined as pharyngeal disease, skin and soft-tissue infection (SSTI), or invasive disease on the basis of predefined criteria. All isolates were emm typed to determine trends over time.

RESULTS

We identified 930 cases over the 4-year period, including 432 (46.4%) pharyngeal, 235 (25.3%) SSTI, and 263 (28.3%) invasive disease types. The most frequently encountered emm types were emm1 (21.4%), emm12 (15.7%), emm89 (14.6%), emm4 (9.2%), and emm3 (8.2%). We observed significant changes over the 4-year period in the relative frequency of infections caused by emm1 (-17.7%; P = .046), emm4 (8.7%; P = .023), or emm6 (-7.9%; P = .024). Using bioinformatic analyses and targeted gene sequencing, we also discovered that all GAS emm28 and emm87 types harbored mutations that rendered them incapable of producing capsule. The relative frequency of GAS disease cases caused by capsule-negative GAS emm types (emm4, emm22, emm28, emm87, and emm89) increased over the 4-year period (32.2%-44.4%), although the difference was statistically significant for only nonpharyngeal disease types (27.1%-43.9%; P = .038).

CONCLUSIONS

Our data suggest an evolving epidemiology of GAS in the Houston pediatric population characterized by an increase in the frequency of capsule-negative emm types.

Hypervirulent group A Streptococcus emergence in an acaspular background is associated with marked remodeling of the bacterial cell surface

Inactivating mutations in the control of virulence two-component regulatory system (covRS) often account for the hypervirulent phenotype in severe, invasive group A streptococcal (GAS) infections. As CovR represses production of the anti-phagocytic hyaluronic acid capsule, high level capsule production is generally considered critical to the hypervirulent phenotype induced by CovRS inactivation. There have recently been large outbreaks of GAS strains lacking capsule, but there are currently no data on the virulence of covRS-mutated, acapsular strains in vivo. We investigated the impact of CovRS inactivation in acapsular serotype M4 strains using a wild-type (M4-SC-1) and a naturally-occurring CovS-inactivated strain (M4-LC-1) that contains an 11bp covS insertion. M4-LC-1 was significantly more virulent in a mouse bacteremia model but caused smaller lesions in a subcutaneous mouse model. Over 10% of the genome showed significantly different transcript levels in M4-LC-1 vs. M4-SC-1 strain. Notably, the Mga regulon and multiple cell surface protein-encoding genes were strongly upregulated–a finding not observed for CovS-inactivated, encapsulated M1 or M3 GAS strains. Consistent with the transcriptomic data, transmission electron microscopy revealed markedly altered cell surface morphology of M4-LC-1 compared to M4-SC-1. Insertional inactivation of covS in M4-SC-1 recapitulated the transcriptome and cell surface morphology. Analysis of the cell surface following CovS-inactivation revealed that the upregulated proteins were part of the Mga regulon. Inactivation of mga in M4-LC-1 reduced transcript levels of multiple cell surface proteins and reversed the cell surface alterations consistent with the effect of CovS inactivation on cell surface composition being mediated by Mga. CovRS-inactivating mutations were detected in 20% of current invasive serotype M4 strains in the United States. Thus, we discovered that hypervirulent M4 GAS strains with covRS mutations can arise in an acapsular background and that such hypervirulence is associated with profound alteration of the cell surface.

Identification of a chimeric emm gene and novel emm pattern in currently circulating strains of emm4 Group A Streptococcus

Group A Streptococcus (GAS) is classified on the basis of the sequence of the gene encoding the M protein (emm) and the patterns into which emm types are grouped. We discovered a novel emm pattern in emm4 GAS, historically considered pattern E, arising from a fusion event between emm and the adjacent enn gene. We identified the emm–enn fusion event in 51 out of 52 emm4 GAS strains isolated by national surveillance in 2015. GAS isolates with an emm–enn fusion event completely replaced pattern E emm4 strains over a 4-year span in Houston (2013–2017). The novel emm–enn gene fusion and new emm pattern has potential vaccine implications.

Neonatal Bacteremia and Cutaneous Lesions Caused by Photorhabdus luminescens: A Rare Gram-Negative Bioluminescent Bacterium

Photorhabdus luminescens is a rare bacterium that causes human disease. In this report, we describe the case of a neonate with Photorhabdus luminescens bacteremia, including clinical presentation and treatment; we also report a literature review of rare human diseases.

Clinical Manifestations and Bacterial Genomic Analysis of Group A Streptococcus Strains That Cause Pediatric Toxic Shock Syndrome

We report here 18 cases of pediatric group A streptococcal toxic shock syndrome, associated clinical findings, and bacterial molecular genetic characteristics discovered through whole-genome sequencing. This comparative whole-genome sequencing revealed unique gene content (speK) and polymorphisms (dpiB) in emm87 group A Streptococcus, the relative contributions of which, in combination with the host response, in the development of streptococcal toxic shock syndrome remain to be elucidated.

Cluster of Fatal Group A Streptococcal emm87 Infections in a Single Family: Molecular Basis for Invasion and Transmission

Hypervirulent disease due to group A Streptococcus (GAS) can result from strains with mutations that enhance virulence gene expression but reduce subsequent transmission. We used whole-genome sequencing to investigate intrafamilial spread among 4 siblings of infection due to a hypervirulent GAS strain that resulted in a fatality. All invasive and pharyngeal GAS isolates had an identical mutation in a gene encoding a key regulatory protein that yielded a hyperinvasive phenotype. These data challenge the prevailing theory of reduced transmission induced by mutations that lead to hypervirulent GAS by showing that spread of hypervirulent GAS may lead to clusters of invasive disease.

Unique Footprint in the scl1.3 Locus Affects Adhesion and Biofilm Formation of the Invasive M3-Type Group A Streptococcus

The streptococcal collagen-like proteins 1 and 2 (Scl1 and Scl2) are major surface adhesins that are ubiquitous among group A Streptococcus (GAS). Invasive M3-type strains, however, have evolved two unique conserved features in the scl1 locus: (i) an IS1548 element insertion in the scl1 promoter region and (ii) a nonsense mutation within the scl1 coding sequence. The scl1 transcript is drastically reduced in M3-type GAS, contrasting with a high transcription level of scl1 allele in invasive M1-type GAS. This leads to a lack of Scl1 expression in M3 strains. In contrast, while scl2 transcription and Scl2 production are elevated in M3 strains, M1 GAS lack Scl2 surface expression. M3-type strains were shown to have reduced biofilm formation on inanimate surfaces coated with cellular fibronectin and laminin, and in human skin equivalents. Repair of the nonsense mutation and restoration of Scl1 expression on M3-GAS cells, restores biofilm formation on cellular fibronectin and laminin coatings. Inactivation of scl1 in biofilm-capable M28 and M41 strains results in larger skin lesions in a mouse model, indicating that lack of Scl1 adhesin promotes bacterial spread over localized infection. These studies suggest the uniquely evolved scl1 locus in the M3-type strains, which prevents surface expression of the major Scl1 adhesin, contributed to the emergence of the invasive M3-type strains. Furthermore these studies provide insight into the molecular mechanisms mediating colonization, biofilm formation, and pathogenesis of group A streptococci.

Role of Operative or Interventional Radiology-Guided Cultures for Osteomyelitis

BACKGROUND AND OBJECTIVE

Acute hematogenous osteomyelitis (AHO) is a severe infection in children. Drainage of purulent collections in bones provides specimens for culture as well as therapeutic benefit. Interventional radiology (IR)-guided procedures may serve as a less invasive means of culture in select patients. We examined the impact of IR and surgically obtained cultures in the diagnosis and management of AHO.

METHODS

A retrospective review of cases of AHO was performed from 2011 to 2014. Patients with chronic disease, orthopedic hardware, puncture wounds, or an infected contiguous focus were excluded.

RESULTS

A total of 250 cases met inclusion criteria. Blood cultures were positive in 107 of 231 cases (46.3%), and 123 of 150 patients had positive cultures (82%) obtained by orthopedic surgery. Of these 123 patients, 62 (50.4%) had organisms identified only through operating room (OR) cultures. Of the 66 patients who had cultures obtained by IR, 34 (51.5%) had positive IR cultures. For those with positive IR cultures, 18 (52.9%) had negative blood cultures. Among the 80 patients with negative blood culture and positive OR/IR culture, the results changed antibiotic therapy in 68 (85%) patients.

CONCLUSIONS

IR or OR culture was the only means of identifying a pathogen in 80 of 216 cases (37%), and in >80% changed medical management. IR can be used effectively to obtain bone cultures in children with AHO not requiring open surgical drainage. Further research is needed to better understand the optimal utilization of IR and OR culture in pediatric AHO.

Application of Whole-Genome Sequencing to an Unusual Outbreak of Invasive Group A Streptococcal Disease

Whole-genome analysis was applied to investigate atypical point-source transmission of 2 invasive group A streptococcal (GAS) infections. Isolates were serotype M4, ST39, and genetically indistinguishable. Comparison with MGAS10750 revealed nonsynonymous polymorphisms in ropB and increased speB transcription. This study demonstrates the usefulness of whole-genome analyses for GAS outbreaks.

Adhesin competence repressor (AdcR) from Streptococcus pyogenes controls adaptive responses to zinc limitation and contributes to virulence

Altering zinc bioavailability to bacterial pathogens is a key component of host innate immunity. Thus, the ability to sense and adapt to the alterations in zinc concentrations is critical for bacterial survival and pathogenesis. To understand the adaptive responses of group A Streptococcus (GAS) to zinc limitation and its regulation by AdcR, we characterized gene regulation by AdcR. AdcR regulates the expression of 70 genes involved in zinc acquisition and virulence. Zinc-bound AdcR interacts with operator sequences in the negatively regulated promoters and mediates differential regulation of target genes in response to zinc deficiency. Genes involved in zinc mobilization and conservation are derepressed during mild zinc deficiency, whereas the energy-dependent zinc importers are upregulated during severe zinc deficiency. Further, we demonstrated that transcription activation by AdcR occurs by direct binding to the promoter. However, the repression and activation by AdcR is mediated by its interactions with two distinct operator sequences. Finally, mutational analysis of the metal ligands of AdcR caused impaired DNA binding and attenuated virulence, indicating that zinc sensing by AdcR is critical for GAS pathogenesis. Together, we demonstrate that AdcR regulates GAS adaptive responses to zinc limitation and identify molecular components required for GAS survival during zinc deficiency.

Streptococcus mitis strains causing severe clinical disease in cancer patients

The genetically diverse viridans group streptococci (VGS) are increasingly recognized as the cause of a variety of human diseases. We used a recently developed multilocus sequence analysis scheme to define the species of 118 unique VGS strains causing bacteremia in patients with cancer; Streptococcus mitis (68 patients) and S. oralis (22 patients) were the most frequently identified strains. Compared with patients infected with non–S. mitis strains, patients infected with S. mitis strains were more likely to have moderate or severe clinical disease (e.g., VGS shock syndrome). Combined with the sequence data, whole-genome analyses showed that S. mitis strains may more precisely be considered as >2 species. Furthermore, we found that multiple S. mitis strains induced disease in neutropenic mice in a dose-dependent fashion. Our data define the prominent clinical effect of the group of organisms currently classified as S. mitis and lay the groundwork for increased understanding of this understudied pathogen.

A naturally occurring single amino acid replacement in multiple gene regulator of group A Streptococcus significantly increases virulence

Single-nucleotide polymorphisms (SNPs) are the most common source of genetic variation within a species; however, few investigations demonstrate how naturally occurring SNPs may increase strain virulence. We recently used group A Streptococcus as a model pathogen to study bacteria strain genotype-patient disease phenotype relationships. Whole-genome sequencing of approximately 800 serotype M59 group A Streptococcus strains, recovered during an outbreak of severe invasive infections across North America, identified a disproportionate number of SNPs in the gene encoding multiple gene regulator of group A Streptococcus (mga). Herein, we report results of studies designed to test the hypothesis that the most commonly occurring SNP, encoding a replacement of arginine for histidine at codon 201 of Mga (H201R), significantly increases virulence. Whole transcriptome analysis revealed that the H201R replacement significantly increased expression of mga and 54 other genes, including many proven virulence factors. Compared to the wild-type strain, a H201R isogenic mutant strain caused significantly larger skin lesions in mice. Serial quantitative bacterial culture and noninvasive magnetic resonance imaging also demonstrated that the isogenic H201R strain was significantly more virulent in a nonhuman primate model of joint infection. These findings show that the H201R replacement in Mga increases the virulence of M59 group A Streptococcus and provide new insight to how a naturally occurring SNP in bacteria contributes to human disease phenotypes.

Molecular characterization of an invasive phenotype of group A Streptococcus arising during human infection using whole genome sequencing of multiple isolates from the same patient

Invasive group A streptococcal (GAS) strains often have genetic differences compared to GAS strains from nonsterile sites. Invasive, "hypervirulent" GAS strains can arise from a noninvasive progenitor following subcutaneous inoculation in mice, but such emergence has been rarely characterized in humans. We used whole genome analyses of multiple GAS isolates from the same patient to document the molecular basis for emergence of a GAS strain with an invasive phenotype during human infection. In contrast to previous theories, we found that elimination of production of the cysteine protease SpeB was not necessary for emergence of GAS with an invasive, "hypervirulent" phenotype.

Reduced expression of claudin-2 is associated with high histological grade and metastasis of feline mammary carcinomas

Claudins (CLDNs) are a family of tight junction (TJ) proteins that play an important role in maintaining cell polarity, in controlling paracellular ion flux and in regulating cell proliferation and differentiation. There is a growing body of evidence that associates changes in CLDN expression with the development of human breast cancer. In the present study CLDN-2 expression was examined immunohistochemically in samples of normal feline mammary tissue (n = 5) and mammary carcinomas (n = 52), including metastatic lesions (n = 29). Seventy-seven percent of carcinomas showed reduced CLDN-2 expression compared with that observed in normal mammary gland. Reduced expression of CLDN-2 was significantly associated with a high histological grade of carcinoma (P = 0.011), with 88.6% of grade II/III carcinomas showing decreased expression. Furthermore, CLDN-2 down-regulation was significantly associated with metastatic disease (P = 0.0027), with 93.1% of cases with signs of metastasis showing decreased expression of this protein. CLDN-2 may constitute a molecular marker for identification of a subgroup of feline mammary carcinomas characterized by high histological grade and the development of metastasis.

Differential virulence gene expression of group A Streptococcus serotype M3 in response to co-culture with Moraxella catarrhalis

Streptococcus pyogenes (group A Streptococcus, GAS) and Moraxella catarrhalis are important colonizers and (opportunistic) pathogens of the human respiratory tract. However, current knowledge regarding colonization and pathogenic potential of these two pathogens is based on work involving single bacterial species, even though the interplay between respiratory bacterial species is increasingly important in niche occupation and the development of disease. Therefore, to further define and understand polymicrobial species interactions, we investigated whether gene expression (and hence virulence potential) of GAS would be affected upon co-culture with M. catarrhalis. For co-culture experiments, GAS and M. catarrhalis were cultured in Todd-Hewitt broth supplemented with 0.2% yeast extract (THY) at 37°C with 5% CO₂ aeration. Each strain was grown in triplicate so that triplicate experiments could be performed. Bacterial RNA was isolated, cDNA synthesized, and microarray transcriptome expression analysis performed. We observed significantly increased (≥4-fold) expression for genes playing a role in GAS virulence such as hyaluronan synthase (hasA), streptococcal mitogenic exotoxin Z (smeZ) and IgG endopeptidase (ideS). In contrast, significantly decreased (≥4-fold) expression was observed in genes involved in energy metabolism and in 12 conserved GAS two-component regulatory systems. This study provides the first evidence that M. catarrhalis increases GAS virulence gene expression during co-culture, and again shows the importance of polymicrobial infections in directing bacterial virulence.

Group A Streptococcus emm gene types in pharyngeal isolates, Ontario, Canada, 2002-2010

Determination of emm variations may help improve vaccine design.

Group A Streptococcus (GAS) is a human-adapted pathogen that causes a variety of diseases, including pharyngitis and invasive infections. GAS strains are categorized by variation in the nucleotide sequence of the gene (emm) that encodes the M protein. To identify the emm types of GAS strains causing pharyngitis in Ontario, Canada, we sequenced the hypervariable region of the emm gene in 4,635 pharyngeal GAS isolates collected during 2002–2010. The most prevalent emm types varied little from year to year. In contrast, fine-scale geographic analysis identified inter-site variability in the most common emm types. Additionally, we observed fluctuations in yearly frequency of emm3 strains from pharyngitis patients that coincided with peaks of emm3 invasive infections. We also discovered a striking increase in frequency of emm89 strains among isolates from patients with pharyngitis and invasive disease. These findings about the epidemiology of GAS are potentially useful for vaccine research.