Heterozygous, Polyploid, Giant Bacterium, Achromatium, Possesses an Identical Functional Inventory Worldwide across Drastically Different Ecosystems

Achromatium is large, hyperpolyploid and the only known heterozygous bacterium. Single cells contain approximately 300 different chromosomes with allelic diversity far exceeding that typically harbored by single bacteria genera. Surveying all publicly available sediment sequence archives, we show that Achromatium is common worldwide, spanning temperature, salinity, pH, and depth ranges normally resulting in bacterial speciation. Although saline and freshwater Achromatium spp. appear phylogenetically separated, the genus Achromatium contains a globally identical, complete functional inventory regardless of habitat. Achromatium spp. cells from differing ecosystems (e.g., from freshwater to saline) are, unexpectedly, equally functionally equipped but differ in gene expression patterns by transcribing only relevant genes. We suggest that environmental adaptation occurs by increasing the copy number of relevant genes across the cell’s hundreds of chromosomes, without losing irrelevant ones, thus maintaining the ability to survive in any ecosystem type. The functional versatility of Achromatium and its genomic features reveal alternative genetic and evolutionary mechanisms, expanding our understanding of the role and evolution of polyploidy in bacteria while challenging the bacterial species concept and drivers of bacterial speciation.

595. Characteristics of Antimicrobials Which Affect Parenteral Antibiotic Therapy Outcomes

Background Outpatient parenteral antibiotic therapy (OPAT) has reduced length of stay, decreased nosocomial infections, and improved patient satisfaction/outcomes. Factors for choosing candidates and regimens for OPAT include: type of infection, organisms, antibiotic side effects, number of antibiotics and frequency of administration. This study sought to evaluate if antibiotic type, frequency, and duration, are associated with complications, and particularly if vancomycin is associated with an increase rate of complication. Methods Retrospective chart review of Zablocki VA Medical Center patients, Milwaukee, WI discharged from 2013-2017 on OPAT evaluated types of infection, antimicrobial regimens, number of antibiotics, duration, frequency, adverse events and outcomes. Primary outcome analyzed was whether or not there was a complication. Complication defined as antibiotic change/dose adjustment, PICC line complication, or additional clinic/hospital visit Results 294 cases identified during study period. 286 (95.7%) were male. Most common antibiotics were vancomycin (78; 26.53%), daptomycin (42;14.9%) ertapenem (81, 27.55%), cefazolin (24;8.16%) and ceftriaxone (50;17%). Staphylococcus and Streptococcus were the most common organisms at 42.86% and 22.79% respectively. Univariate analysis of the most common antibiotics, maximum frequency and duration are summarized in table 1. A multivariable found cephalosporins were associated with no complication (OR 2.23, CI 1.20-4.35), and Vancomycin (OR 0.20, CI 0.11-0.36) and Gentamicin (OR 0.06, CI 0.06-0.58) were significantly associated with complication. Antibiotic frequency, duration, bacterial speciation were associated with no complication when controlling for antibiotic type Table 1 Conclusion Antibiotics given for longer durations or require more frequent monitoring like vancomycin may have higher rates of complications. This study supports the hypothesis that vancomycin and aminoglycosides are associated with complications even when controlling for duration and frequency; cephalosporins are associated with no complication. New, safer antibiotics like long acting lipoglycopeptides may provide alternatives to Vancomycin to diminish the burden on ancillary OPAT staff who deal with OPAT complications. Disclosures All Authors: No reported disclosures

Normal Respiratory Flora as a Cause of Community-Acquired Pneumonia

Background Intensive studies have failed to identify an etiologic agent in >50% cases of community-acquired pneumonia (CAP). Bacterial pneumonia follows aspiration of recognized bacterial pathogens (RBPs) such as Streptococcus pneumoniae, Haemophilus influenzae, and Staphylococcus aureus after they have colonize the nasopharynx. We hypothesized that aspiration of normal respiratory flora (NRF) might also cause CAP. Methods We studied 120 patients hospitalized for CAP who provided a high-quality sputum specimen at, or soon after admission, using Gram stain, quantitative sputum culture, bacterial speciation by matrix-assisted laser desorption ionization time-of-flight, and viral polymerase chain reaction. Thresholds for diagnosis of bacterial infection were ≥105 colony-forming units (cfu)/mL sputum for RBPs and ≥106 cfu for NRF. Results Recognized bacterial pathogens were found in 68 of 120 (56.7%) patients; 14 (20.1%) of these had a coinfecting respiratory virus. Normal respiratory flora were found in 31 (25.8%) patients; 10 (32.2%) had a coinfecting respiratory virus. Infection by ≥2 RBPs occurred in 10 cases and by NRF together with RBPs in 13 cases. Among NRF, organisms identified as Streptococcus mitis, which share many genetic features of S pneumoniae, predominated. A respiratory virus alone was found in 16 of 120 (13.3%) patients. Overall, an etiologic diagnosis was established in 95.8% of cases. Conclusions Normal respiratory flora, with or without viral coinfection, appear to have caused one quarter of cases of CAP and may have played a contributory role in an additional 10.8% of cases caused by RBPs. An etiology for CAP was identified in >95% of patients who provided a high-quality sputum at, or soon after, the time of admission.

Heterozygous, polyploid, giant bacterium, Achromatium, possesses an identical functional inventory worldwide across drastically different ecosystems

Achromatium is large, hyperpolyploid and the only known heterozygous bacterium. Single cells contain ca. 300 different chromosomes with allelic diversity typical of entire bacterial communities. Surveying all publicly available sediment sequence archives, we show Achromatia are common worldwide, spanning temperature, salinity, pH, and depth ranges normally resulting in bacterial speciation. Nevertheless, Achromatia display no ecotypic phylogenetic signal and contain a, globally identical, complete functional inventory. Achromatia cells from differing ecosystems (e.g. freshwater vs. saline) are, unexpectedly, equally functionally equipped but differ in gene expression patterns by transcribing only relevant genes. We suggest environmental adaptation occurs by increasing the copy number of relevant genes across the cell’s hundreds of chromosomes, without losing irrelevant ones, thus maintaining the ability to survive in any ecosystem type. The functional versatility of Achromatium, and its genomic features, reveal alternative genetic and evolutionary mechanisms, expanding our understanding of the role and evolution of polyploidy in bacteria while challenging the bacterial species concept and drivers of bacterial speciation.

Genomic determinants of speciation and spread of the Mycobacterium tuberculosis complex

Models on how bacterial lineages differentiate increase our understanding of early bacterial speciation events and the genetic loci involved. Here, we analyze the population genomics events leading to the emergence of the tuberculosis pathogen. The emergence is characterized by a combination of recombination events involving core pathogenesis functions and purifying selection on early diverging loci. We identify the phoR gene, the sensor kinase of a two-component system involved in virulence, as a key functional player subject to pervasive positive selection after the divergence of the Mycobacterium tuberculosis complex from its ancestor. Previous evidence showed that phoR mutations played a central role in the adaptation of the pathogen to different host species. Now, we show that phoR mutations have been under selection during the early spread of human tuberculosis, during later expansions, and in ongoing transmission events. Our results show that linking pathogen evolution across evolutionary and epidemiological time scales points to past and present virulence determinants.

Genomic determinants of speciation and spread of the Mycobacterium tuberculosis complex

ABSTRACTBACKGROUNDModels on how bacterial lineages differentiate increase our understanding on early bacterial speciation events and about the genetic loci involved. Here, we analyze the population genomics events leading to the emergence of the tuberculosis pathogen.RESULTSThe emergence is characterized by a combination of recombination events involving core pathogenesis functions and purifying selection on early diverging loci. We identify the phoR gene, the sensor kinase of a two-component system involved in virulence, as a key functional player subject to pervasive positive selection after the divergence of the MTBC from its ancestor. Previous evidence showed that phoR mutations played a central role in the adaptation of the pathogen to different host species. Now we show that phoR have been under selection during the early spread of human tuberculosis, during later expansions and in on-going transmission events.CONCLUSIONSOur results show that linking pathogen evolution across evolutionary and epidemiological timescales point to past and present virulence determinants.

Evaluating factors that dictate struvite stone composition: A multi-institutional clinical experience from the EDGE Research Consortium

Introduction: Struvite stones account for 15% of urinary calculi and are typically associated with urease-producing urinary tract infections and carry significant morbidity. This study aims to characterize struvite stones based on purity of stone composition, bacterial speciation, risk factors, and clinical features.Methods: Retrospective data was collected from patients diagnosed with infection stones between 2008 and 2012. Stone analysis, perioperative urine cultures, bacterial speciation, and clinical data were collected and analyzed. The purity of struvite stones was determined. Statistical comparisons were made among homogeneous and heterogeneous struvite stones.Results: From the four participating centres, 121 struvite stones were identified. Only 13.2% (16/121) were homogenous struvite. Other components included calcium phosphate (42.1%), calcium oxalate (33.9%), calcium carbonate (27.3%), and uric acid (5.8%). Partial or full staghorn calculi occurred in 23.7% of cases. Ureaseproducing bacteria were only present in 30% of cases. Proteus, E. coli, and Enterococcus were the most common bacterial isolates from perioperative urine, and percutaneous nephrolithotomy was the most common modality of treatment. Only 40% of patients had a urinalysis that was nitrite-positive, indicating that urinalysis alone is not reliable for diagnosing infection stones. The study’s limitation is its retrospective nature; as such, the optimal timing of cultures with respect to stone analysis or treatment was not always possible, urine cultures were often not congruent with stone cultures in the same patient, and our findings of E. coli commonly cultured does not suggest causation.Conclusions: Struvite stones are most often heterogeneous in composition. Proteus remains a common bacterial isolate; however, E. coli and Enterococcus were also frequently identified. This new data provides evidence that patients with struvite stones can have urinary tract pathogens other than urease-producing bacteria, thus challenging previous conventional dogma.