Rapid Progression of Invasive Listeria monocytogenes Infection in a Patient With Cirrhosis and Primary Sclerosing Cholangitis on Ustekinumab.

We present the case of a 62-year-old immunocompromised man with ulcerative colitis, primary sclerosing cholangitis, and cirrhosis treated with azathioprine and ustekinumab who quickly developed invasive Listeria monocytogenes infection after incidental identification on routine paracentesis. The infection rapidly progressed from bacterial peritonitis to bacteremia and meningitis within three days. Treatment with ampicillin and trimethoprim/sulfamethoxazole was successful. We highlight the increased risk of invasive listeriosis in immunocompromised individuals, including those on biologic therapies, and the importance of considering Listeria as a pathogen from sterile sites even in asymptomatic patients.

Recurrent Neisseria cinerea bacteremia secondary to cardiovascular implantable electronic device infection.

We present the first case of cardiac implantable electronic device (CIED) infection due to Neisseria cinerea in a 64-year-old woman from Panama. She had a history of splenectomy, aortic valve stenosis requiring transcatheter aortic valve replacement (TAVR), and permanent pacemaker placement. She presented with relapsing N. cinerea bacteremia over a 3-month period. Transesophageal echocardiography revealed a lead vegetation in the superior vena cava. She was successfully treated with pacemaker removal and 2 weeks of IV antibiotic therapy. N. cinerea is an aerobic gram-negative commensal diplococcus typically found in the human nasopharynx. Infection in humans is rare with few case reports in the literature.

Clinical Use of a 16S Ribosomal RNA Gene-Based Sanger and/or Next Generation Sequencing Assay to Test Preoperative Synovial Fluid for Periprosthetic Joint Infection Diagnosis.

Preoperative pathogen identification in patients with periprosthetic joint infection (PJI) is typically limited to synovial fluid culture. Whether sequencing-based approaches are of potential use in identification of pathogens in PJI, and if so which approach is ideal, is incompletely defined. The objective of the study was to analyze the accuracy of a 16S rRNA (rRNA) gene-based PCR followed by Sanger sequencing and/or targeted metagenomic sequencing approach (tMGS) performed on synovial fluid for PJI diagnosis. A retrospective study was conducted, analyzing synovial fluids tested between August 2020 and May 2021 at a single center. Subjects with hip, knee, shoulder, and elbow arthroplasties who had synovial fluid aspirated and clinically subjected to sequence-based testing and conventional culture were studied. A total of 154 subjects were included in the study; 118 had noninfectious arthroplasty failure (NIAF), while 36 had PJI. Clinical sensitivity and specificity for diagnosis of PJI were 69% and 100%, respectively, for the sequencing-based approach and 72% and 100%, respectively, for conventional culture (P = 0.74). The combination of both tests was more sensitive (83%) than culture alone (P = 0.04). Results of sequencing-based testing led to changes in treatment in four of 36 (11%) PJI subjects. Microbial identification was achieved using Sanger and next generation sequencing in 19 and 6 subjects, respectively. When combined with culture, the described 16S rRNA gene sequencing-based approach increased sensitivity compared to culture alone, suggesting its potential use in the diagnosis of PJI when synovial fluid culture is negative. IMPORTANCE Periprosthetic joint infection (PJI) is a dreadful complication of joint replacement. Noninvasive identification of infectious pathogens has been traditionnally limited to culture-based testing of synovial fluid which has poor sensitivity. Sanger and Next-generation sequencing (NGS) may be used for synovial fluid testing in PJI, but experience in routine practice is sparse. We used a targeted metagenomic sequencing approach for routine testing of synovial fluid involving NGS when Sanger sequencing had failed or was likely to fail. The objective of this study was to analyze the approach's performance for diagnosis of PJI in comparison to culture for testing synovial fluid. Overall, the sequencing-based approach was not superior to culture for diagnosis of PJI, but yielded positive results in some culture-negative samples.

Pathogen Detection in Infective Endocarditis Using Targeted Metagenomics on Whole Blood and Plasma: a Prospective Pilot Study.

Initial microbiologic diagnosis of infective endocarditis (IE) relies on blood cultures and Bartonella and Coxiella burnetii serology. Small case series and one prospective study have preliminarily reported application of metagenomic sequencing on blood or plasma for IE diagnosis. Here, results of a prospective pilot study evaluating targeted metagenomic sequencing (tMGS) for blood-based early pathogen detection and identification in IE are reported. Subjects diagnosed with possible or definite IE at a single institution were prospectively enrolled with informed consent from October 2020 to July 2021. Blood was drawn and separated into whole blood and plasma. Both specimen types were subjected to nucleic acid extraction and PCR targeting the V1-V3 region of the 16S ribosomal RNA gene, followed by next-generation sequencing on an Illumina MiSeqTM platform. 35 subjects, 28 (80%) with definite and 7 (20%) with possible IE were enrolled, including 6 (17%) with blood culture-negative endocarditis (BCNE). Overall, 20 whole blood (59%) and 16 plasma (47%) samples tested positive (P = 0.47). When results of whole blood and plasma testing were combined, a positive tMGS result was found in 23 subjects (66%). tMGS identified a potential pathogen in 5 of 6 culture-negative IE cases. Although further study is needed, the results of this pilot study suggest that blood-based tMGS may provide pathogen identification in subjects with IE, including in culture-negative cases.

Antibiotic susceptibility testing of Staphylococcus aureus using the Biolog OmniLog® system, a metabolic phenotyping assay.

Use of the Biolog OmniLog® phenotyping system for antibiotic susceptibility testing (AST) was evaluated using 51 clinical isolates of Staphylococcus aureus. MIC testing by broth microdilution was compared to results generated using the OmniLog® system for oxacillin, daptomycin, vancomycin, gentamicin, linezolid, and tetracycline. There was >90% essential and categorical agreement between methods for all antibiotics, except gentamicin, which had 83.6% essential agreement, although very major errors occurred with linezolid (n = 3) and daptomycin (n = 1). Precision was satisfactory, with 5 triplicate measurements in agreement. A quantitative threshold allowed automated interpretation of MICs yielding results comparable to manual interpretation; oxacillin, gentamicin, and tetracycline resistance could be identified at a median of 7.13, 5.25, and 7.25 hours, respectively. Limitations include the small number of isolates, and especially resistant isolates tested, and the focus on a single species. Overall, the OmniLog® system was a precise method for AST of S. aureus, although accuracy was imperfect.

Speciation patterns and processes in the zooplankton of the ancient lakes of Sulawesi Island, Indonesia.

Although studies of ancient lake fauna have provided important insights about speciation patterns and processes of organisms in heterogeneous benthic environments, evolutionary forces responsible for speciation in the relatively homogenous planktonic environment remain largely unexplored. In this study, we investigate possible mechanisms of speciation in zooplankton using the freshwater diaptomids of the ancient lakes of Sulawesi, Indonesia, as a model system. We integrate phylogenetic and population genetic analyses of mitochondrial and nuclear genes with morphological and genome size data. Overall, our results support the conclusion that colonization order and local adaptation are dominant at the large, island scale, whereas at local and intralacustrine scales, speciation processes are regulated by gene flow among genetically differentiated and locally adapted populations. In the Malili lakes, the diaptomid populations are homogenous at nuclear loci, but show two highly divergent mitochondrial clades that are geographically restricted to single lakes despite the interconnectivity of the lake systems. Our study, based on coalescent simulations and population genetic analyses, indicates that unidirectional hybridization allows gene flow across the nuclear genome, but prevents the introgression of mitochondria into downstream populations. We suggest that hybridization and introgression between young lineages is a significant evolutionary force in freshwater plankton.

The evolutionary history of sarco(endo)plasmic calcium ATPase (SERCA).

Investigating the phylogenetic relationships within physiologically essential gene families across a broad range of taxa can reveal the key gene duplication events underlying their family expansion and is thus important to functional genomics studies. P-Type II ATPases represent a large family of ATP powered transporters that move ions across cellular membranes and includes Na(+)/K(+) transporters, H(+)/K(+) transporters, and plasma membrane Ca(2+) pumps. Here, we examine the evolutionary history of one such transporter, the Sarco(endo)plasmic reticulum calcium ATPase (SERCA), which maintains calcium homeostasis in the cell by actively pumping Ca(2+) into the sarco(endo)plasmic reticulum. Our protein-based phylogenetic analyses across Eukaryotes revealed two monophyletic clades of SERCA proteins, one containing animals, fungi, and plants, and the other consisting of plants and protists. Our analyses suggest that the three known SERCA proteins in vertebrates arose through two major gene duplication events after the divergence from tunicates, but before the separation of fishes and tetrapods. In plants, we recovered two SERCA clades, one being the sister group to Metazoa and the other to Apicomplexa clade, suggesting an ancient duplication in an early eukaryotic ancestor, followed by subsequent loss of one copy in Opisthokonta, the other in protists, and retention of both in plants. We also report relatively recent and independent gene duplication events within invertebrate taxa including tunicates and the leech Helobdella robusta. Thus, it appears that both ancient and recent gene duplication events have played an important role in the evolution of this ubiquitous gene family across the eukaryotic domain.

The ancient lakes of Indonesia: towards integrated research on speciation.

Ancient lakes have provided considerable insights into the drivers of speciation and adaptive radiation in aquatic organisms. Most studies of species-flocks, however, focus only on a single group of organisms, and few have attempted to integrate geological, limnological, ecological, and genetic drivers of speciation on multiple species-flocks at various trophic levels. As such, there is a need for a comprehensive model system for research on speciation in aquatic environments where multiple radiations are investigated at various levels of biological organization (e.g., individual, population, and ecosystem) and placed in light of geographical and geological setting. The ancient Malili Lakes of Sulawesi, Indonesia, are ideal candidates for such a model, and represent the only hydrologically connected ancient lakes in the world. These lakes are characterized by ultra-oligotrophy and unique physicochemical conditions that govern the composition and production of planktonic communities. At higher trophic levels, there are three recurring trends: (1) low taxonomic richness and simple community structures, (2) adaptive radiations with trophic specialization, and (3) remarkably high endemism with evolutionary innovations throughout the lakes and species-flocks. Furthermore, the restricted geographic distributions of species-flocks within the Malili Lakes indicate that each lake constitutes a unique environment, and dispersal among lakes is limited, despite close contemporary connectivity. These observations suggest that ecological and evolutionary processes are regulated from the bottom up, and speciation is primarily facilitated by interspecific and intraspecific competition for limited resources. The Malili Lakes represent an outstanding natural model for integrative research into speciation as they offer the opportunity to explore the roles of geography, dispersal, and selection in the radiation of aquatic organisms.

Ancient lakes revisited: from the ecology to the genetics of speciation.

Explosive speciation in ancient lakes has fascinated biologists for centuries and has inspired classical work on the tempo and modes of speciation. Considerable attention has been directed towards the extrinsic forces of speciation--the geological, geographical and ecological peculiarities of ancient lakes. Recently, there has been a resurgence of interest in the intrinsic nature of these radiations, the biological characteristics conducive to speciation. While new species are thought to arise mainly by the gradual enhancement of reproductive isolation among geographically isolated populations, ancient lakes provide little evidence for a predominant role of geography in speciation. Recent phylogenetic work provides strong evidence that multiple colonization waves were followed by parallel intralacustrine radiations that proceeded at relatively rapid rates despite long-term gene flow through hybridization and introgression. Several studies suggest that hybridization itself might act as a key evolutionary mechanism by triggering major genomic reorganization/revolution and enabling the colonization of new ecological niches in ancient lakes. These studies propose that hybridization is not only of little impediment to diversification but could act as an important force in facilitating habitat transitions, promoting postcolonization adaptations and accelerating diversification. Emerging ecological genomic approaches are beginning to shed light on the long-standing evolutionary dilemma of speciation in the face of gene flow. We propose an integrative programme for future studies on speciation in ancient lakes.