Identification of the main glutamine and glutamate transporters in Staphylococcus aureus and their impact on c-di-AMP production

A Staphylococcus aureus strain deleted for the c‐di‐AMP cyclase gene dacA is unable to survive in rich medium unless it acquires compensatory mutations. Previously identified mutations were in opuD, encoding the main glycine‐betaine transporter, and alsT, encoding a predicted amino acid transporter. Here, we show that inactivation of OpuD restores the cell size of a dacA mutant to near wild‐type (WT) size, while inactivation of AlsT does not. AlsT was identified as an efficient glutamine transporter, indicating that preventing glutamine uptake in rich medium rescues the growth of the S. aureus dacA mutant. In addition, GltS was identified as a glutamate transporter. By performing growth curves with WT, alsT and gltS mutant strains in defined medium supplemented with ammonium, glutamine or glutamate, we revealed that ammonium and glutamine, but not glutamate promote the growth of S. aureus. This suggests that besides ammonium also glutamine can serve as a nitrogen source under these conditions. Ammonium and uptake of glutamine via AlsT and hence likely a higher intracellular glutamine concentration inhibited c‐di‐AMP production, while glutamate uptake had no effect. These findings provide, besides the previously reported link between potassium and osmolyte uptake, a connection between nitrogen metabolism and c‐di‐AMP signalling in S. aureus.

Microbial colonization of intravascular catheter connectors in hospitalized patients

BACKGROUND

Central line-associated bloodstream infections may be due to catheter connector colonization and intraluminal migration of pathogens. We assessed the colonization of the split septum catheter connector system, and subsequently the luer lock catheter connector system.

METHODS

This was a prospective, 2 phase, quality improvement study at a tertiary referral center. Each phase of the study was performed over 3 consecutive days in hospitalized patients receiving an active infusion; first with a split septum lever lock connector and second with a luer lock connector and alcohol port protector. The connectors were inoculated onto blood agar plates and incubated. Plates were assessed for microbial growth after 48-72 hours.

RESULTS

In phase I, 98 (41.9%) of 234 split septum connectors yielded microbial growth. In phase II, 56 (23.1%) of 243 luer lock connectors yielded microbial growth. In phase II only, there was a significant increased rate of contamination in peripheral catheters compared with all other catheters, and the rate of contamination on the acute care wards was significantly higher when compared with the intensive care units.

CONCLUSIONS

Bacterial colonization of the lever lock system was unacceptably high among all catheter types and hospital locations. Transition to luer lock catheter connectors and alcohol port protectors decreased the colonization; however, colonization still remained substantial. Causation of colonization cannot be determined with these results.

Urease is an essential component of the acid response network of Staphylococcus aureus and is required for a persistent murine kidney infection

Staphylococcus aureus causes acute and chronic infections resulting in significant morbidity. Urease, an enzyme that generates NH₃ and CO₂ from urea, is key to pH homeostasis in bacterial pathogens under acidic stress and nitrogen limitation. However, the function of urease in S. aureus niche colonization and nitrogen metabolism has not been extensively studied. We discovered that urease is essential for pH homeostasis and viability in urea-rich environments under weak acid stress. The regulation of urease transcription by CcpA, Agr, and CodY was identified in this study, implying a complex network that controls urease expression in response to changes in metabolic flux. In addition, it was determined that the endogenous urea derived from arginine is not a significant contributor to the intracellular nitrogen pool in non-acidic conditions. Furthermore, we found that during a murine chronic renal infection, urease facilitates S. aureus persistence by promoting bacterial fitness in the low-pH, urea-rich kidney. Overall, our study establishes that urease in S. aureus is not only a primary component of the acid response network but also an important factor required for persistent murine renal infections.

Urease has been reported to be crucial to bacteria in environmental adaptation, virulence, and defense against host immunity. Although the function of urease in S. aureus is not clear, recent evidence suggests that urease is important for acid resistance in various niches. Our study deciphered a function of S. aureus urease both in laboratory conditions and during host colonization. Furthermore, we uncovered the major components of the regulatory system that fine-tunes the expression of urease. Collectively, this study established the dual function of urease which serves as a significant part of the S. aureus acid response while also serving as an enzyme required for persistent kidney infections and potential subsequent staphylococcal metastasis.

Evaluation of the bacterial burden of gel nails, standard nail polish, and natural nails on the hands of health care workers

BACKGROUND

Acrylic nails harbor more bacteria than natural nails, and wear is not recommended for health care workers (HCWs). Little is known about the new and popular gel nail products. This study sought to evaluate the bacterial burden of gel nails, standard nail polish, and natural nails on the hands of HCWs.

METHODS

The study was conducted at 3 health centers. Nails on the dominant hand of 88 HCWs were painted with gel polish and standard polish. Cultures were obtained on days 1, 7, and 14 of wear and before and after hand hygiene with alcohol hand gel.

RESULTS

A total of 741 cultures were obtained. Bacterial burden increased over time for all nail types (P ≤ .0001). Reductions in the bacterial burden of natural nails and standard polish, but not gel polish, (P = .001, P = .0028, and P = .98, respectively) were seen after hand hygiene. All 3 nail types become more contaminated with bacteria over time. Standard polish and natural nails may be more amenable to hand hygiene than gel polish.

CONCLUSIONS

This study did not show an increased number of microorganisms on nails with gel polish; however, gel nails may be more difficult to clean using alcohol hand gel.

1095. The Value of Hardwiring Diagnostic Stewardship in the Electronic Health Record: Electronic Ordering Restrictions for PCR-Based Rapid Diagnostic Testing of Diarrheal Illnesses

Background

In 2015, the microbiology laboratory introduced a multiplex PCR test (FilmArray™ Gastrointestinal Panel (GIP)), replacing traditional stool culture. The GIP is faster and more sensitive than traditional stool culture, detecting 22 common viral, bacterial, and parasitic pathogens; but is significantly more expensive. The antimicrobial stewardship program (ASP) developed guidelines on test use and interpretation, recommending inpatient use only once per admission and not after hospital day 5. C. difficile test results from the GIP were not reported at any time.

Methods

Inpatient GIP use was reviewed over one year and considered inappropriate if performed >3 days after admission or repeated. Noncompliance with ASP recommendations was common; no meaningful pathogens were detected upon review of all inappropriate GIP use. An inpatient GIP electronic order restriction was implemented in April 2017 eliminating the ability to order tests inappropriately. GIP testing outside the restriction could be approved by the microbiology lab director. We captured separate C. difficile testing rates as a counterbalance measure. We used Poisson regression models to compare the rate of GIP and C. difficile tests per month between Period 1 (July 2015–March 2017) and Period 2 (April 2017–March 2018) per 1,000 patient-days (PD).

Results

The restriction resulted in a 26% reduction in GIP ordering rates between the two periods (Table 1, Figure 1). Direct cost savings was approximately $63,000. Table 1 shows changes in C. difficile test ordering rates during Periods 1 and 2. When including GIP tests that were ordered but not completed, potential GIP testing was reduced by 46% for a savings of $131,000 (Figure 2). Only 42 test overrides were approved by the microbiology director since the intervention; of those only two were positive (Cryptosporidium and Norovirus).

Conclusion

Diagnostic stewardship of GIP using guidelines and electronic ordering restrictions can lead to meaningful improvements in test appropriateness and reduction in cost and waste, demonstrating the value of ASP interacting with the microbiology laboratory.

Disclosures

All authors: No reported disclosures.

291. Effect of Previous Antibiotic Exposure on the Yield of Bone Biopsy Culture in Patients With Osteomyelitis

Background

Bone biopsy and culture are gold standards for the diagnosis of osteomyelitis and are key factors in defining the etiology and treatment of osteomyelitis. There is concern that recent antibiotic exposure will decrease the sensitivity of microbiologic cultures.

Methods

A retrospective analysis was performed of patients who underwent bone biopsy for evaluation of osteomyelitis at the University of Nebraska Medical Center from 2014 to 2017. Microbiological culture data were compared with the number of days of antibiotic treatment the patient received prior to biopsy. Days of antibiotic use was divided into quartiles and the Cochran-Armitage test was used to test whether antibiotic exposure was associated with culture yield. Fisher’s exact test and the Mann–Whitney test were used to compare anatomic location, diagnostic method, tobacco use, median WBC, ESR, CRP with culture positivity. Multivariable logistic regression was used to determine independent predictors of culture positivity.

Results

A total of 211 patients were studied. Descriptive statistics: 63% male, 85% Caucasian, median age: 55 years, duration of osteomyelitis prior to biopsy: median 39 days (mean 139 days). Location of osteomyelitis: lower extremity 48%, sacral/pelvic 19%, skull/facial 12%, spine 11%, upper extremity/chest 9%. Within 2 weeks prior to biopsy, the median value of the maximum WBC count, ESR, and CRP was 10.5, 66, and 5.7, respectively. A significant negative linear trend between culture positivity and days of antibiotic exposure (P < 0.0001) was observed (Figure 1). The rate of culture positivity was 85.07% for patients diagnosed with osteomyelitis who did not receive antibiotics and dropped to 78.57%, 73.08%, and 50% for patients who received 1–3 days, 4–14 days, and >14 days of antibiotics, respectively. Other independent predictors of culture positivity included elevated CRP (P = 0.0017) and clinical diagnosis of osteomyelitis (vs. histologic or radiographic) (P = 0.0042).

Conclusion

There is a clear negative linear correlation between pre-bone biopsy antibiotic exposure and culture positivity in patients diagnosed with osteomyelitis. In addition, elevated CRP and method of osteomyelitis diagnosis independently correlate with culture positivity.

Disclosures

All authors: No reported disclosures.

The conserved regulatory RNA RsaE down-regulates the arginine degradation pathway in Staphylococcus aureus

RsaE is a regulatory RNA highly conserved amongst Firmicutes that lowers the amount of mRNAs associated with the TCA cycle and folate metabolism. A search for new RsaE targets in Staphylococcus aureus revealed that in addition to previously described substrates, RsaE down-regulates several genes associated with arginine catabolism. In particular, RsaE targets the arginase rocF mRNA via direct interactions involving G-rich motifs. Two duplicated C-rich motifs of RsaE can independently downregulate rocF expression. The faster growth rate of ΔrsaE compared to its parental strain in media containing amino acids as sole carbon source points to an underlying role for RsaE in amino acid catabolism. Collectively, the data support a model in which RsaE acts as a global regulator of functions associated with metabolic adaptation.

Automated Real-Time Collection of Pathogen-Specific Diagnostic Data: Syndromic Infectious Disease Epidemiology

Background

Health care and public health professionals rely on accurate, real-time monitoring of infectious diseases for outbreak preparedness and response. Early detection of outbreaks is improved by systems that are comprehensive and specific with respect to the pathogen but are rapid in reporting the data. It has proven difficult to implement these requirements on a large scale while maintaining patient privacy.

Objective

The aim of this study was to demonstrate the automated export, aggregation, and analysis of infectious disease diagnostic test results from clinical laboratories across the United States in a manner that protects patient confidentiality. We hypothesized that such a system could aid in monitoring the seasonal occurrence of respiratory pathogens and may have advantages with regard to scope and ease of reporting compared with existing surveillance systems.

Methods

We describe a system, BioFire Syndromic Trends, for rapid disease reporting that is syndrome-based but pathogen-specific. Deidentified patient test results from the BioFire FilmArray multiplex molecular diagnostic system are sent directly to a cloud database. Summaries of these data are displayed in near real time on the Syndromic Trends public website. We studied this dataset for the prevalence, seasonality, and coinfections of the 20 respiratory pathogens detected in over 362,000 patient samples acquired as a standard-of-care testing over the last 4 years from 20 clinical laboratories in the United States.

Results

The majority of pathogens show influenza-like seasonality, rhinovirus has fall and spring peaks, and adenovirus and the bacterial pathogens show constant detection over the year. The dataset can also be considered in an ecological framework; the viruses and bacteria detected by this test are parasites of a host (the human patient). Interestingly, the rate of pathogen codetections, on average 7.94% (28,741/362,101), matches predictions based on the relative abundance of organisms present.

Conclusions

Syndromic Trends preserves patient privacy by removing or obfuscating patient identifiers while still collecting much useful information about the bacterial and viral pathogens that they harbor. Test results are uploaded to the database within a few hours of completion compared with delays of up to 10 days for other diagnostic-based reporting systems. This work shows that the barriers to establishing epidemiology systems are no longer scientific and technical but rather administrative, involving questions of patient privacy and data ownership. We have demonstrated here that these barriers can be overcome. This first look at the resulting data stream suggests that Syndromic Trends will be able to provide high-resolution analysis of circulating respiratory pathogens and may aid in the detection of new outbreaks.

Expanding the Coverage of the Metabolome with Nitrogen-Based NMR

Isotopically labeling a metabolite and tracing its metabolic fate has provided invaluable insights about the role of metabolism in human diseases in addition to a variety of other issues. ¹³C-labeled metabolite tracers or unlabeled ¹H-based NMR experiments are currently the most common application of NMR to metabolomics studies. Unfortunately, the coverage of the metabolome has been consequently limited to the most abundant carbon-containing metabolites. To expand the coverage of the metabolome and enhance the impact of metabolomics studies, we present a protocol for ¹⁵N-labeled metabolite tracer experiments that may also be combined with routine ¹³C tracer experiments to simultaneously detect both ¹⁵N- and ¹³C-labeled metabolites in metabolic samples. A database consisting of 2D ¹H-¹⁵N HSQC natural-abundance spectra of 50 nitrogen-containing metabolites are also presented to facilitate the assignment of ¹⁵N-labeled metabolites. The methodology is demonstrated by labeling Escherichia coli and Staphylococcus aureus metabolomes with ¹⁵N₁-ammonium chloride, ¹⁵N₄-arginine, and ¹³C₂-acetate. Efficient ¹⁵N and ¹³C metabolite labeling and identification were achieved utilizing standard cell culture and sample preparation protocols.

Yield Improvement of the Anti-MRSA Antibiotics WAP-8294A by CRISPR/dCas9 Combined with Refactoring Self-Protection Genes in Lysobacter enzymogenes OH11

The cyclic lipodepsipeptides WAP-8294A are antibiotics with potent activity against methicillin-resistant Staphylococcus aureus (MRSA). One member of this family, WAP-8294A2 (Lotilibcin), was in clinical trials due to its high activity and distinct chemistry. However, WAP-8294A compounds are produced in a very low yield by Lysobacter and only under very stringent conditions. Improving WAP-8294A yield has become very critical for research and application of these anti-MRSA compounds. Here, we report a strategy to increase WAP-8294A production. We first used the CRISPR/dCas9 system to increase the expression of five cotranscribed genes (orf1-5) in the WAP gene cluster, by fusing the omega subunit of RNA polymerase with dCas9 that targets the operon's promoter region. This led to the transcription of the genes increased by 5-48 folds in strain dCas9-ω3. We then refactored four putative self-protection genes (orf6, orf7, orf9 and orf10) by reorganizing them into an operon under the control of a strong Lysobacter promoter, P_HSAF. The refactored operon was introduced into strain dCas9-ω3, and the transcription of the self-protection genes increased by 20-60 folds in the resultant engineered strains. The yield of the three main WAP-8294A compounds, WAP-8294A1, WAP-8294A2, and WAP-8294A4, increased by 6, 4, and 9 folds, respectively, in the engineered strains. The data also showed that the yield increase of WAP-8294A compounds was mainly due to the increase of the extracellular distribution. WAP-8294A2 exhibited potent (MIC 0.2-0.8 μg/mL) and specific activity against S. aureus among a battery of clinically relevant Gram-positive pathogens (54 isolates).

Executive Summary: Management of Adults With Hospital-acquired and Ventilator-associated Pneumonia: 2016 Clinical Practice Guidelines by the Infectious Diseases Society of America and the American Thoracic Society

It is important to realize that guidelines cannot always account for individual variation among patients. They are not intended to supplant physician judgment with respect to particular patients or special clinical situations. IDSA considers adherence to these guidelines to be voluntary, with the ultimate determination regarding their application to be made by the physician in the light of each patient's individual circumstances.These guidelines are intended for use by healthcare professionals who care for patients at risk for hospital-acquired pneumonia (HAP) and ventilator-associated pneumonia (VAP), including specialists in infectious diseases, pulmonary diseases, critical care, and surgeons, anesthesiologists, hospitalists, and any clinicians and healthcare providers caring for hospitalized patients with nosocomial pneumonia. The panel's recommendations for the diagnosis and treatment of HAP and VAP are based upon evidence derived from topic-specific systematic literature reviews.

Take my breath away

A lack of oxygen activates a pathway that causes the bacterial cell wall to break down, which, in turn, aids bacterial biofilm development.

The metalloprotease SepA governs processing of accumulation-associated protein and shapes intercellular adhesive surface properties in Staphylococcus epidermidis

The otherwise harmless skin inhabitant Staphylococcus epidermidis is a major cause of healthcare-associated medical device infections. The species' selective pathogenic potential depends on its production of surface adherent biofilms. The Cell wall-anchored protein Aap promotes biofilm formation in S. epidermidis, independently from the polysaccharide intercellular adhesin PIA. Aap requires proteolytic cleavage to act as an intercellular adhesin. Whether and which staphylococcal proteases account for Aap processing is yet unknown. Here, evidence is provided that in PIA-negative S. epidermidis 1457Δica, the metalloprotease SepA is required for Aap-dependent S. epidermidis biofilm formation in static and dynamic biofilm models. qRT-PCR and protease activity assays demonstrated that under standard growth conditions, sepA is repressed by the global regulator SarA. Inactivation of sarA increased SepA production, and in turn augmented biofilm formation. Genetic and biochemical analyses demonstrated that SepA-related induction of biofilm accumulation resulted from enhanced Aap processing. Studies using recombinant proteins demonstrated that SepA is able to cleave the A domain of Aap at residue 335 and between the A and B domains at residue 601. This study identifies the mechanism behind Aap-mediated biofilm maturation, and also demonstrates a novel role for a secreted staphylococcal protease as a requirement for the development of a biofilm.

Evaluation of the BioFire FilmArray® GastrointestinalPanel in a Midwestern Academic Hospital

The BioFire FilmArray® Gastrointestinal Panel (GIP) was implemented to replace traditional stool culture and enzyme immunoassay (EIA) testing for stool pathogens. The purpose of this study was to evaluate the detection rate, incidence of coinfection, and culture recovery rate of gastrointestinal (GI) pathogens detected by the GIP over a 1-year period. A total of 2257 stools collected from January to December 2015 were tested using the GIP. Clostridium difficile colonization was also evaluated by an antigen/toxin EIA and confirmatory polymerase chain reaction (PCR). The GIP detected one pathogen in 911 (40.4%) specimens. Coinfections were detected in 176 (7.8%) of these specimens. The most frequently detected pathogens were C. difficile (15.2%), norovirus (8.9%), enteropathogenic Escherichia coli (7.1%), enteroaggregative E. coli (3.4%), Campylobacter spp. (2.3%), and sapovirus (2.0%). Each of the remaining GIP targets had a detection rate of ≤1.6%. The recovery of bacteria for public health investigations varied, with rates as high as 77% for Salmonella to as low as 30% for Yersinia enterocolitica. Of stools positive for C. difficile on the GIP that were tested by EIA, only 42.7% (88/206) were found to be producing detectable toxin. Overall, the implementation of the GIP resulted in high detection rates of GI pathogens, including the frequent detection of coinfections. This is a promising test to streamline the testing of agents causing infectious gastroenteritis from multiple tests down to a single order with limited hands-on time. Ongoing studies will need to assess the impact that the GIP has on downstream patient care and public health practices.

Salmonella Bacteremia Among Children in Central and Northwest Nigeria, 2008-2015

BACKGROUND

Etiologic agents of childhood bacteremia remain poorly defined in Nigeria. The absence of such data promotes indiscriminate use of antibiotics and delays implementation of appropriate preventive strategies.

METHODS

We established diagnostic laboratories for bacteremia surveillance at regional sites in central and northwest Nigeria. Acutely ill children aged <5 years with clinically suspected bacteremia were evaluated at rural and urban clinical facilities in the Federal Capital Territory, central region and in Kano, northwest Nigeria. Blood was cultured using the automated Bactec incubator system.

RESULTS

Between September 2008 and April 2015, we screened 10,133 children. Clinically significant bacteremia was detected in 609 of 4051 (15%) in the northwest and 457 of 6082 (7.5%) in the central region. Across both regions, Salmonella species account for 24%-59.8% of bacteremias and are the commonest cause of childhood bacteremia, with a predominance of Salmonella enterica serovar Typhi. The prevalence of resistance to ampicillin, chloramphenicol, and cotrimoxazole was 38.11%, with regional differences in susceptibility to different antibiotics but high prevalence of resistance to readily available oral antibiotics.

CONCLUSIONS

Salmonella Typhi is the leading cause of childhood bacteremia in central Nigeria. Expanded surveillance is planned to define the dynamics of transmission. The high prevalence of multidrug-resistant strains calls for improvement in environmental sanitation in the long term and vaccination in the short term.

Management of Adults With Hospital-acquired and Ventilator-associated Pneumonia: 2016 Clinical Practice Guidelines by the Infectious Diseases Society of America and the American Thoracic Society

It is important to realize that guidelines cannot always account for individual variation among patients. They are not intended to supplant physician judgment with respect to particular patients or special clinical situations. IDSA considers adherence to these guidelines to be voluntary, with the ultimate determination regarding their application to be made by the physician in the light of each patient's individual circumstances.These guidelines are intended for use by healthcare professionals who care for patients at risk for hospital-acquired pneumonia (HAP) and ventilator-associated pneumonia (VAP), including specialists in infectious diseases, pulmonary diseases, critical care, and surgeons, anesthesiologists, hospitalists, and any clinicians and healthcare providers caring for hospitalized patients with nosocomial pneumonia. The panel's recommendations for the diagnosis and treatment of HAP and VAP are based upon evidence derived from topic-specific systematic literature reviews.

Francisella tularensis bacteria associated with feline tularemia in the United States

Tularemia in the United States was examined by reviewing 106 Francisella tularensis isolates, mostly from Nebraska, collected during 1998–2012: 48% of Nebraska cases were cat-associated; 7/8 human cases were caused by subtype A.I. A vaccine is needed to reduce feline-associated tularemia, and cat owners should protect against bites/scratches and limit their pet’s outdoor access.

Resistance to Acute Macrophage Killing Promotes Airway Fitness of Prevalent Community-Acquired Staphylococcus aureus Strains

The incidence of methicillin-resistant Staphylococcus aureus (MRSA) pneumonia in otherwise healthy individuals is increasing. To investigate the mechanism underlying the epidemiological success of predominant community-associated (CA)-MRSA strains, we examined their fitness traits during the initial interaction between bacteria and the host occurring in the lower airway. Using a mouse respiratory infection model, we show that clinical isolates often responsible for CA infections are highly resistant to clearance from healthy airways, whereas S. aureus strains not as prevalent or traditionally associated with hospital-associated infections are relatively susceptible. Mechanistically, the competitive fitness of S. aureus is a result of both agr-dependent and -independent resistance to innate bacterial killing. Furthermore, we show that rather than evasion from neutrophil-dependent bactericidal process, the observed S. aureus fitness in the lower airways is due to its intrinsic resistance to resident alveolar macrophage-mediated intracellular killing. Importantly, we demonstrate that the virulence determinants responsible for bacterial persistence in immune-competent mice are dispensable in mice with predisposing conditions such as influenza infection. Taken together, these novel findings of the improved competence of predominant CA-MRSA strains to survive innate killing in healthy hosts, particularly at the very beginning stage of infection, provide a unique insight into their epidemiological success.

The major autolysin is redundant for Staphylococcus aureus USA300 LAC JE2 virulence in a murine device-related infection model

The major Staphylococcus aureus autolysin, Atl, has been implicated in attachment to surfaces and release of extracellular DNA during biofilm formation under laboratory conditions. Consistent with this, polyclonal antibodies to the amidase and glucosaminidase domains of Atl inhibited in vitro biofilm formation. However, in a murine model of device-related infection the community-associated S. aureus strain USA300 LAC JE2 established a successful infection in the absence of atl These data indicate that Atl activity is not required for biofilm production in this infection model and reveal the importance of characterizing the contribution of biofilm phenotypes to virulence under in vivo conditions.

Generation of a Transposon Mutant Library in Staphylococcus aureus and Staphylococcus epidermidis Using bursa aurealis

Transposon mutagenesis is a genetic process that involves the random insertion of transposons into a genome resulting in the disruption of function of the genes in which they insert. Identification of the insertion sites through DNA sequencing allows for the identification of the genes disrupted and the creation of "libraries" containing a collection of mutants in which a large number of the nonessential genes have been disrupted. These mutant libraries have been a great resource for investigators to understand the various biological functions of individual genes, including those involved in metabolism, antibiotic susceptibility, and pathogenesis. Here, we describe the detailed methodologies for constructing a sequence defined transposon mutant library in both Staphylococcus aureus and S. epidermidis using the mariner-based transposon, bursa aurealis.

Francisella tularensis Subtype A.II Genomic Plasticity in Comparison with Subtype A.I

Although Francisella tularensis is considered a monomorphic intracellular pathogen, molecular genotyping and virulence studies have demonstrated important differences within the tularensis subspecies (type A). To evaluate genetic variation within type A strains, sequencing and assembly of a new subtype A.II genome was achieved for comparison to other completed F. tularensis type A genomes. In contrast with the F. tularensis A.I strains (SCHU S4, FSC198, NE061598, and TI0902), substantial genomic variation was observed between the newly sequenced F. tularensis A.II strain (WY-00W4114) and the only other publically available A.II strain (WY96-3418). Genome differences between WY-00W4114 and WY96-3418 included three major chromosomal translocations, 1580 indels, and 286 nucleotide substitutions of which 159 were observed in predicted open reading frames and 127 were located in intergenic regions. The majority of WY-00W4114 nucleotide deletions occurred in intergenic regions, whereas most of the insertions and substitutions occurred in predicted genes. Of the nucleotide substitutions, 48 (30%) were synonymous and 111 (70%) were nonsynonymous. WY-00W4114 and WY96-3418 nucleotide polymorphisms were predominantly G/C to A/T allelic mutations, with WY-00W4114 having more A+T enrichment. In addition, the A.II genomes contained a considerably higher number of intact genes and longer repetitive sequences, including transposon remnants than the A.I genomes. Together these findings support the premise that F. tularensis A.II may have a fitness advantage compared to the A.I subtype due to the higher abundance of functional genes and repeated chromosomal sequences. A better understanding of the selective forces driving F. tularensis genetic diversity and plasticity is needed.