BACKGROUND: Understanding the epidemiology of carbapenem-resistant A. baumannii complex (CRAB) and the patients impacted is an important step toward informing better infection prevention and control practices and improving public health response. METHODS: Active, population-based surveillance was conducted for CRAB in 9 U.S. sites from January 1 to December 31, 2019. Medical records were reviewed, isolates were collected and characterized including antimicrobial susceptibility testing and whole genome sequencing. RESULTS: Among 136 incident cases in 2019, 66 isolates were collected and characterized; 56.5% were from cases who were male, 54.5% were from persons of Black or African American race with non-Hispanic ethnicity, and the median age was 63.5 years. Most isolates, 77.2%, were isolated from urine, and 50.0% were collected in the outpatient setting; 72.7% of isolates harbored an acquired carbapenemase gene (aCP), predominantly blaOXA-23 or blaOXA-24/40; however, an isolate with blaNDM was identified. The antimicrobial agent with the most in vitro activity was cefiderocol (96.9% of isolates were susceptible). CONCLUSIONS: Our surveillance found that CRAB isolates in the U.S. commonly harbor an aCP, have an antimicrobial susceptibility profile that is defined as difficult-to-treat resistance, and epidemiologically are similar regardless of the presence of an aCP.
Downstream next-generation sequencing (NGS) of the syphilis spirochete Treponema pallidum subspecies pallidum (T. pallidum) is hindered by low bacterial loads and the overwhelming presence of background metagenomic DNA in clinical specimens. In this study, we investigated selective whole-genome amplification (SWGA) utilizing multiple displacement amplification (MDA) in conjunction with custom oligonucleotides with an increased specificity for the T. pallidum genome and the capture and removal of 5'-C-phosphate-G-3' (CpG) methylated host DNA using the NEBNext Microbiome DNA enrichment kit followed by MDA with the REPLI-g single cell kit as enrichment methods to improve the yields of T. pallidum DNA in isolates and lesion specimens from syphilis patients. Sequencing was performed using the Illumina MiSeq v2 500 cycle or NovaSeq 6000 SP platform. These two enrichment methods led to 93 to 98% genome coverage at 5 reads/site in 5 clinical specimens from the United States and rabbit-propagated isolates, containing >14 T. pallidum genomic copies/µL of sample for SWGA and >129 genomic copies/µL for CpG methylation capture with MDA. Variant analysis using sequencing data derived from SWGA-enriched specimens showed that all 5 clinical strains had the A2058G mutation associated with azithromycin resistance. SWGA is a robust method that allows direct whole-genome sequencing (WGS) of specimens containing very low numbers of T. pallidum, which has been challenging until now. IMPORTANCE Syphilis is a sexually transmitted, disseminated acute and chronic infection caused by the bacterial pathogen Treponema pallidum subspecies pallidum. Primary syphilis typically presents as single or multiple mucocutaneous lesions and, if left untreated, can progress through multiple stages with various clinical manifestations. Molecular studies often rely on direct amplification of DNA sequences from clinical specimens; however, this can be impacted by inadequate samples due to disease progression or timing of patients seeking clinical care. While genotyping has provided important data on circulating strains over the past 2 decades, WGS data are needed to better understand strain diversity, perform evolutionary tracing, and monitor antimicrobial resistance markers. The significance of our research is the development of an SWGA DNA enrichment method that expands the range of clinical specimens that can be directly sequenced to include samples with low numbers of T. pallidum.
Syphilis , Treponema pallidum , Animals , High-Throughput Nucleotide Sequencing , Metagenomics , Rabbits , Syphilis/microbiology , Treponema pallidum/genetics , Whole Genome Sequencing
Background: We estimated SARS-CoV-2 Delta- and Omicron-specific effectiveness of two and three mRNA COVID-19 vaccine doses in adults against symptomatic illness in US outpatient settings. Methods: Between October 1, 2021, and February 12, 2022, research staff consented and enrolled eligible participants who had fever, cough, or loss of taste or smell and sought outpatient medical care or clinical SARS-CoV-2 testing within 10 days of illness onset. Using the test-negative design, we compared the odds of receiving two or three mRNA COVID-19 vaccine doses among SARS-CoV-2 cases versus controls using logistic regression. Regression models were adjusted for study site, age, onset week, and prior SARS-CoV-2 infection. Vaccine effectiveness (VE) was calculated as (1 - adjusted odds ratio) × 100%. Results: Among 3847 participants included for analysis, 574 (32%) of 1775 tested positive for SARS-CoV-2 during the Delta predominant period and 1006 (56%) of 1794 participants tested positive during the Omicron predominant period. When Delta predominated, VE against symptomatic illness in outpatient settings was 63% (95% CI: 51% to 72%) among mRNA two-dose recipients and 96% (95% CI: 93% to 98%) for three-dose recipients. When Omicron predominated, VE was 21% (95% CI: -6% to 41%) among two-dose recipients and 62% (95% CI: 48% to 72%) among three-dose recipients. Conclusions: In this adult population, three mRNA COVID-19 vaccine doses provided substantial protection against symptomatic illness in outpatient settings when the Omicron variant became the predominant cause of COVID-19 in the United States. These findings support the recommendation for a third mRNA COVID-19 vaccine dose.
COVID-19 , Outpatients , Adult , Humans , COVID-19 Testing , COVID-19 Vaccines , COVID-19/prevention & control , SARS-CoV-2/genetics , RNA, Messenger/genetics
We present the chromosome sequences of a Naegleria fowleri isolate from a human primary amebic meningoencephalitis (PAM) case. The genome sequences were assembled from Illumina HiSeq and PacBio sequencing data and verified with the optical mapping data. This led to the identification of 37 contigs representing 37 chromosomes in N. fowleri.
As the COVID-19 pandemic overwhelmed health care systems around the world, new strategies to mitigate its spread and provide patients access to health care have been employed. Although a critical component of this strategy, telemedicine is not a perfect solution for many scenarios and is often limited. Overall, telemedicine has been an invaluable tool to improve access to care and minimize the risk of person-to-person transmission of COVID-19.
The genus Chryseobacterium in the family Weeksellaceae is known to be polyphyletic. Amino acid identity (AAI) values were calculated from whole-genome sequences of species of the genus Chryseobacterium, and their distribution was found to be multi-modal. These naturally-occurring non-continuities were leveraged to standardise genus assignment of these species. We speculate that this multi-modal distribution is a consequence of loss of biodiversity during major extinction events, leading to the concept that a bacterial genus corresponds to a set of species that diversified since the Permian extinction. Transfer of nine species (Chryseobacterium arachidiradicis, Chryseobacterium bovis, Chryseobacterium caeni, Chryseobacterium hispanicum, Chryseobacterium hominis, Chryseobacterium hungaricum,, Chryseobacterium pallidum and Chryseobacterium zeae) to the genus Epilithonimonas and eleven (Chryseobacterium anthropi, Chryseobacterium antarcticum, Chryseobacterium carnis, Chryseobacterium chaponense, Chryseobacterium haifense, Chryseobacterium jeonii, Chryseobacterium montanum, Chryseobacterium palustre, Chryseobacterium solincola, Chryseobacterium treverense and Chryseobacterium yonginense) to the genus Kaistella is proposed. Two novel species are described: Kaistella daneshvariae sp. nov. and Epilithonimonas vandammei sp. nov. Evidence is presented to support the assignment of Planobacterium taklimakanense to a genus apart from Chryseobacterium, to which Planobacterium salipaludis comb nov. also belongs. The novel genus Halpernia is proposed, to contain the type species Halpernia frigidisoli comb. nov., along with Halpernia humi comb. nov., and Halpernia marina comb. nov.
Chryseobacterium/classification , Phylogeny , Amino Acids/chemistry , Extinction, Biological
Ganglioneuromas (GNs) are benign, differentiated tumors that are derived from neural crest sympathogonia. They can be found anywhere in the body along autonomic ganglia. These tumors are seen most often in individuals over 10 years of age and are usually asymptomatic. However, GNs can grow large and cause symptoms due to mass effect. GNs are rarely located within the suprarenal gland and are benign tumors that are often diagnosed late in their course due to mass effect or found incidentally on imaging studies. We describe a case of a 22-year-old female who presented to clinic with vague abdominal pain. She underwent an extensive workup which ultimately revealed a rare presentation of a left suprarenal GN that required surgical removal. She underwent an extensive workup which ultimately revealed a left suprarenal GN that required surgical removal. The patient underwent laparotomy and surgical excision of the mass and made a full recovery.
Purpose of Review: Post dural puncture headache (PDPH) is a known and relatively common complication which may occur in the setting of patients undergoing lumbar punctures (LP) for diagnostic or therapeutic purposes, and is commonly treated with an epidural blood patch (EBP). There have been few publications regarding the long-term safety of EBP for the treatment of PDPH. Recent Findings: The aim of this pilot study was to examine any association of chronic low back pain (LBP) in patients who experienced a PDPH following a LP, and were treated with an EBP. A total of 49 patients were contacted and completed a survey questionnaire via telephone. There was no increased risk of chronic LBP in the dural puncture group receiving EBP (percentage difference 1% [95% CI -25% - 26%], RR: 0.98 [95% CI 0.49 - 1.99]) compared to the dural puncture group not receiving EBP. There were no significant differences in the severity and descriptive qualities of pain between the EBP and non-EBP groups. Both groups had higher prevalence of back pain compared to baseline. Summary: Our findings suggest that dural puncture patients undergoing EBP do not experience low back pain with increased frequency compared to dural puncture patients not undergoing EBP. Higher prevalence of LBP compared to baseline and compared to general population was seen in both groups. However, this pilot study is limited by a small sample size and no definitive conclusion can be drawn from this observation. The findings of this study should spur further prospective research into identifying potential associations between LP, EBP and chronic low back pain.
Low Back Pain , Post-Dural Puncture Headache , Blood Patch, Epidural , Humans , Low Back Pain/etiology , Pilot Projects , Post-Dural Puncture Headache/epidemiology , Post-Dural Puncture Headache/etiology , Post-Dural Puncture Headache/therapy , Spinal Puncture/adverse effects
Background: Post dural puncture headache (PDPH) is a known complication which may occur in the setting of patients undergoing lumbar punctures (LP) for diagnostic or therapeutic purposes. The gold standard for treating a PDPH is an epidural blood patch (EBP). There have been few publications evaluating the long-term outcomes of PDPH treated with EBP. The aim of this pilot study was to examine the incidence of chronic headaches in dural puncture patients who received EBP versus those who did not. Methods: A retrospective case control study was performed at a single large center institution. Forty-nine patients who had intentional dural puncture were identified on chart review and completed a survey questionnaire via phone interview: twenty-six of these patients required a subsequent EBP, while twenty-three did not. The primary outcomes were the development and prevalence of chronic headaches after the procedures. There was no statistically significant difference in the prevalence of current headaches between the EBP group and Non-EBP group (54% vs. 52% p = 0.91). There were no significant differences in the rates of severity and descriptive qualities of headache between the EBP and non-EBP groups. There was higher incidence of tinnitus in the PDPH patients. Summary: This pilot study demonstrates that patients who received an EBP for treatment of a PDPH following LP are no more likely to experience chronic headaches compared to patients who do not receive an EBP. However, both the EBP group and Non-EBP group had high incidence of chronic headaches which may be related to dural puncture or a baseline trait of this cohort given the recall bias. There is a suggestion that tinnitus could be a long-term residual symptom of PDPH treated with EBP.
Post-Dural Puncture Headache , Blood Patch, Epidural , Case-Control Studies , Humans , Pilot Projects , Post-Dural Puncture Headache/epidemiology , Post-Dural Puncture Headache/etiology , Post-Dural Puncture Headache/therapy , Retrospective Studies
Whooping cough (pertussis), primarily caused by Bordetella pertussis, has resurged in the United States, and circulating strains exhibit considerable chromosome structural fluidity in the form of rearrangement and deletion. The genus Bordetella includes additional pathogenic species infecting various animals, some even causing pertussis-like respiratory disease in humans; however, investigation of their genome evolution has been limited. We studied chromosome structure in complete genome sequences from 167 Bordetella species isolates, as well as 469 B. pertussis isolates, to gain a generalized understanding of rearrangement patterns among these related pathogens. Observed changes in gene order primarily resulted from large inversions and were only detected in species with genomes harboring multicopy insertion sequence (IS) elements, most notably B. holmesii and B. parapertussis While genomes of B. pertussis contain >240 copies of IS481, IS elements appear less numerous in other species and yield less chromosome structural diversity through rearrangement. These data were further used to predict all possible rearrangements between IS element copies present in Bordetella genomes, revealing that only a subset is observed among circulating strains. Therefore, while it appears that rearrangement occurs less frequently in other species than in B. pertussis, these clinically relevant respiratory pathogens likely experience similar mutation of gene order. The resulting chromosome structural fluidity presents both challenges and opportunity for the study of Bordetella respiratory pathogens.IMPORTANCE Bordetella pertussis is the primary agent of whooping cough (pertussis). The Bordetella genus includes additional pathogens of animals and humans, including some that cause pertussis-like respiratory illness. The chromosome of B. pertussis has previously been shown to exhibit considerable structural rearrangement, but insufficient data have prevented comparable investigation in related species. In this study, we analyze chromosome structure variation in several Bordetella species to gain a generalized understanding of rearrangement patterns in this genus. Just as in B. pertussis, we observed inversions in other species that likely result from common mutational processes. We used these data to further predict additional, unobserved inversions, suggesting that specific genome structures may be preferred in each species.
Despite high vaccine coverage, pertussis cases in the United States have increased over the last decade. Growing evidence suggests that disease resurgence results, in part, from genetic divergence of circulating strain populations away from vaccine references. The United States employs acellular vaccines exclusively, and current Bordetella pertussis isolates are predominantly deficient in at least one immunogen, pertactin (Prn). First detected in the United States retrospectively in a 1994 isolate, the rapid spread of Prn deficiency is likely vaccine driven, raising concerns about whether other acellular vaccine immunogens experience similar pressures, as further antigenic changes could potentially threaten vaccine efficacy. We developed an electrochemiluminescent antibody capture assay to monitor the production of the acellular vaccine immunogen filamentous hemagglutinin (Fha). Screening 722 U.S. surveillance isolates collected from 2010 to 2016 identified two that were both Prn and Fha deficient. Three additional Fha-deficient laboratory strains were also identified from a historic collection of 65 isolates dating back to 1935. Whole-genome sequencing of deficient isolates revealed putative, underlying genetic changes. Only four isolates harbored mutations to known genes involved in Fha production, highlighting the complexity of its regulation. The chromosomes of two Fha-deficient isolates included unexpected structural variation that did not appear to influence Fha production. Furthermore, insertion sequence disruption of fhaB was also detected in a previously identified pertussis toxin-deficient isolate that still produced normal levels of Fha. These results demonstrate the genetic potential for additional vaccine immunogen deficiency and underscore the importance of continued surveillance of circulating B. pertussis evolution in response to vaccine pressure.
Adhesins, Bacterial/genetics , Bordetella pertussis/genetics , Bordetella pertussis/immunology , Genome, Bacterial , Genomics , Virulence Factors, Bordetella/genetics , Adhesins, Bacterial/biosynthesis , Gene Duplication , Genomics/methods , Humans , Mutation , Phylogeny , Polymorphism, Single Nucleotide , Sequence Deletion , Virulence Factors, Bordetella/biosynthesis , Whole Genome Sequencing , Whooping Cough/immunology , Whooping Cough/microbiology
Despite high pertussis vaccine coverage, reported cases of whooping cough (pertussis) have increased over the last decade in the United States and other developed countries. Although Bordetella pertussis is well known for its limited gene sequence variation, recent advances in long-read sequencing technology have begun to reveal genomic structural heterogeneity among otherwise indistinguishable isolates, even within geographically or temporally defined epidemics. We have compared rearrangements among complete genome assemblies from 257 B. pertussis isolates to examine the potential evolution of the chromosomal structure in a pathogen with minimal gene nucleotide sequence diversity. Discrete changes in gene order were identified that differentiated genomes from vaccine reference strains and clinical isolates of various genotypes, frequently along phylogenetic boundaries defined by single nucleotide polymorphisms. The observed rearrangements were primarily large inversions centered on the replication origin or terminus and flanked by IS481, a mobile genetic element with >240 copies per genome and previously suspected to mediate rearrangements and deletions by homologous recombination. These data illustrate that structural genome evolution in B. pertussis is not limited to reduction but also includes rearrangement. Therefore, although genomes of clinical isolates are structurally diverse, specific changes in gene order are conserved, perhaps due to positive selection, providing novel information for investigating disease resurgence and molecular epidemiology.IMPORTANCE Whooping cough, primarily caused by Bordetella pertussis, has resurged in the United States even though the coverage with pertussis-containing vaccines remains high. The rise in reported cases has included increased disease rates among all vaccinated age groups, provoking questions about the pathogen's evolution. The chromosome of B. pertussis includes a large number of repetitive mobile genetic elements that obstruct genome analysis. However, these mobile elements facilitate large rearrangements that alter the order and orientation of essential protein-encoding genes, which otherwise exhibit little nucleotide sequence diversity. By comparing the complete genome assemblies from 257 isolates, we show that specific rearrangements have been conserved throughout recent evolutionary history, perhaps by eliciting changes in gene expression, which may also provide useful information for molecular epidemiology.
Chromosomes, Bacterial/genetics , Evolution, Molecular , Gene Expression Profiling , Gene Expression Regulation, Bacterial/genetics , Genome, Bacterial , Bordetella pertussis , Conserved Sequence , Gene Order/genetics , Genes, Bacterial/genetics , Genetic Linkage , Genetic Variation/genetics , Phylogeny
Vaccine formulations and vaccination programs against whooping cough (pertussis) vary worldwide. Here, we report the complete genome sequences of two divergent Bordetella pertussis reference strains used in the production of pertussis vaccines.
Amblyomma americanum is an abundant tick in the southeastern, midwestern, and northeastern United States. It is a vector of multiple diseases, but limited genomic resources are available for it. We sequenced the complete mitochondrial genome of a single female A. americanum collected in Georgia using the Illumina platform. The consensus sequence was 14,709 bp long, and the mean coverage across the assembly was >12,000×. All expected tick genomic features were present, including two "Tick-Box" motifs, and in the expected order for the Metastriata. Heteroplasmy rates were low compared to the most closely related tick for which data are available, Amblyomma cajennense. The phylogeny derived from the concatenated protein coding and rRNA genes from the 33 available tick mitochondrial genomes was consistent with those previously proposed for the Acari. This is the first complete mitochondrial sequence for A. americanum, which provides a useful reference for future studies of A. americanum population genetics and tick phylogeny.
Genome, Mitochondrial , Ticks/genetics , Animals , Female , Phylogeny , Polymorphism, Genetic , Species Specificity
Strains of Neisseria gonorrhoeae with mosaic penA genes bearing novel point mutations in penA have been isolated from ceftriaxone treatment failures. Such isolates exhibit significantly higher MIC values to third-generation cephalosporins. Here we report the in vitro isolation of two mutants with elevated MICs to cephalosporins. The first possesses a point mutation in the transpeptidase region of the mosaic penA gene, and the second contains an insertion mutation in pilQ.
Cephalosporins/pharmacology , Fimbriae Proteins/genetics , Neisseria gonorrhoeae/drug effects , Neisseria gonorrhoeae/genetics , beta-Lactamases/genetics , Anti-Bacterial Agents/pharmacology , Drug Resistance, Multiple, Bacterial , Erythromycin/pharmacology , Gonorrhea/drug therapy , Gonorrhea/microbiology , Humans , Microbial Sensitivity Tests , Molecular Sequence Data , Mutation , Neisseria gonorrhoeae/isolation & purification , Penicillin-Binding Proteins/genetics , Treatment Failure
Bacillus cereus strains, such as G9241, causing anthrax-like illnesses have recently been discovered. We report the genome sequence of a clinical strain, B. cereus BcFL2013, which is similar to G9241, recovered from a patient in Florida.
