Laboratory Diagnosis of Lyme Borreliosis.
Abstract SUMMARYLyme borreliosis is caused by a growing list of related, yet distinct, spirochetes with complex biology and sophisticated immune evasion mechanisms. It may result in a range of clinical manifestations involving different organ systems, and can lead to persistent sequelae in a subset of cases. The pathogenesis of Lyme borreliosis is incompletely understood, and laboratory diagnosis, the focus of this review, requires considerable understanding to interpret the results correctly. Direct detection of the infectious agent is usually not possible or practical, necessitating a continued reliance on serol...
Source: Clinical Microbiology Reviews - January 30, 2021 Category: Microbiology Authors: Branda JA, Steere AC Tags: Clin Microbiol Rev Source Type: research

Erratum for Yahav et al., "New β-Lactam-β-Lactamase Inhibitor Combinations".
Erratum for Yahav et al., "New β-Lactam-β-Lactamase Inhibitor Combinations". Clin Microbiol Rev. 2021 Mar 17;34(2): Authors: Yahav D, Giske CG, Gramatniece A, Abodakpi H, Tam VH, Leibovici L PMID: 33504504 [PubMed] (Source: Clinical Microbiology Reviews)
Source: Clinical Microbiology Reviews - January 30, 2021 Category: Microbiology Authors: Yahav D, Giske CG, Gramatniece A, Abodakpi H, Tam VH, Leibovici L Tags: Clin Microbiol Rev Source Type: research

Erratum for Zhang and Duchaine, "SARS-CoV-2 and Health Care Worker Protection in Low-Risk Settings: a Review of Modes of Transmission and a Novel Airborne Model Involving Inhalable Particles".
Erratum for Zhang and Duchaine, "SARS-CoV-2 and Health Care Worker Protection in Low-Risk Settings: a Review of Modes of Transmission and a Novel Airborne Model Involving Inhalable Particles". Clin Microbiol Rev. 2021 Mar 17;34(2): Authors: Zhang XS, Duchaine C PMID: 33504505 [PubMed] (Source: Clinical Microbiology Reviews)
Source: Clinical Microbiology Reviews - January 30, 2021 Category: Microbiology Authors: Zhang XS, Duchaine C Tags: Clin Microbiol Rev Source Type: research

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2): a Systemic Infection.
Abstract SUMMARYTo date, seven identified coronaviruses (CoVs) have been found to infect humans; of these, three highly pathogenic variants have emerged in the 21st century. The newest member of this group, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was first detected at the end of 2019 in Hubei province, China. Since then, this novel coronavirus has spread worldwide, causing a pandemic; the respiratory disease caused by the virus is called coronavirus disease 2019 (COVID-19). The clinical presentation ranges from asymptomatic to mild respiratory tract infections and influenza-like illness to se...
Source: Clinical Microbiology Reviews - January 15, 2021 Category: Microbiology Authors: Synowiec A, Szczepański A, Barreto-Duran E, Lie LK, Pyrc K Tags: Clin Microbiol Rev Source Type: research

Staphylococcus lugdunensis: a Skin Commensal with Invasive Pathogenic Potential.
Abstract SUMMARYStaphylococcus lugdunensis is a species of coagulase-negative staphylococcus (CoNS) that causes serious infections in humans akin to those of S. aureus It was often misidentified as S. aureus, but this has been rectified by recent routine use of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) in diagnostic laboratories. It encodes a diverse array of virulence factors for adhesion, cytotoxicity, and innate immune evasion, but these are less diverse than those encoded by S. aureus It expresses an iron-regulated surface determinant (Isd) system combined with...
Source: Clinical Microbiology Reviews - December 29, 2020 Category: Microbiology Authors: Heilbronner S, Foster TJ Tags: Clin Microbiol Rev Source Type: research

Type I Natural Killer T Cells as Key Regulators of the Immune Response to Infectious Diseases.
Kalergis AM Abstract SUMMARYThe immune system must work in an orchestrated way to achieve an optimal response upon detection of antigens. The cells comprising the immune response are traditionally divided into two major subsets, innate and adaptive, with particular characteristics for each type. Type I natural killer T (iNKT) cells are defined as innate-like T cells sharing features with both traditional adaptive and innate cells, such as the expression of an invariant T cell receptor (TCR) and several NK receptors. The invariant TCR in iNKT cells interacts with CD1d, a major histocompatibility complex class I (MH...
Source: Clinical Microbiology Reviews - December 29, 2020 Category: Microbiology Authors: Gálvez NMS, Bohmwald K, Pacheco GA, Andrade CA, Carreño LJ, Kalergis AM Tags: Clin Microbiol Rev Source Type: research

Erratum for Geno et al., "Pneumococcal Capsules and Their Types: Past, Present, and Future".
Erratum for Geno et al., "Pneumococcal Capsules and Their Types: Past, Present, and Future". Clin Microbiol Rev. 2021 Mar 17;34(2): Authors: Geno KA, Gilbert GL, Song JY, Skovsted IC, Klugman KP, Jones C, Konradsen HB, Nahm MH PMID: 33361144 [PubMed] (Source: Clinical Microbiology Reviews)
Source: Clinical Microbiology Reviews - December 29, 2020 Category: Microbiology Authors: Geno KA, Gilbert GL, Song JY, Skovsted IC, Klugman KP, Jones C, Konradsen HB, Nahm MH Tags: Clin Microbiol Rev Source Type: research

Epidemiology, Pathophysiology, Diagnosis, and Management of Cerebral Toxoplasmosis.
Abstract SUMMARYToxoplasma gondii is known to infect a considerable number of mammalian and avian species and a substantial proportion of the world's human population. The parasite has an impressive ability to disseminate within the host's body and employs various tactics to overcome the highly regulatory blood-brain barrier and reside in the brain. In healthy individuals, T. gondii infection is largely tolerated without any obvious ill effects. However, primary infection in immunosuppressed patients can result in acute cerebral or systemic disease, and reactivation of latent tissue cysts can lead to a deadly outc...
Source: Clinical Microbiology Reviews - November 28, 2020 Category: Microbiology Authors: Elsheikha HM, Marra CM, Zhu XQ Tags: Clin Microbiol Rev Source Type: research

New β-Lactam-β-Lactamase Inhibitor Combinations.
New β-Lactam-β-Lactamase Inhibitor Combinations. Clin Microbiol Rev. 2020 Dec 16;34(1): Authors: Yahav D, Giske CG, Grāmatniece A, Abodakpi H, Tam VH, Leibovici L Abstract SUMMARYThe limited armamentarium against drug-resistant Gram-negative bacilli has led to the development of several novel β-lactam-β-lactamase inhibitor combinations (BLBLIs). In this review, we summarize their spectrum of in vitro activities, mechanisms of resistance, and pharmacokinetic-pharmacodynamic (PK-PD) characteristics. A summary of available clinical data is provided per drug. Four approved BLBLIs are ...
Source: Clinical Microbiology Reviews - November 14, 2020 Category: Microbiology Authors: Yahav D, Giske CG, Grāmatniece A, Abodakpi H, Tam VH, Leibovici L Tags: Clin Microbiol Rev Source Type: research

Human Herpesviruses 6A and 6B in Brain Diseases: Association versus Causation.
Abstract SUMMARYHuman herpesvirus 6A (HHV-6A) and human herpesvirus 6B (HHV-6B), collectively termed HHV-6A/B, are neurotropic viruses that permanently infect most humans from an early age. Although most people infected with these viruses appear to suffer no ill effects, the viruses are a well-established cause of encephalitis in immunocompromised patients. In this review, we summarize the evidence that the viruses may also be one trigger for febrile seizures (including febrile status epilepticus) in immunocompetent infants and children, mesial temporal lobe epilepsy, multiple sclerosis (MS), and, possibly, Alzhei...
Source: Clinical Microbiology Reviews - November 14, 2020 Category: Microbiology Authors: Komaroff AL, Pellett PE, Jacobson S Tags: Clin Microbiol Rev Source Type: research

Progress and Challenges in the Prevention, Diagnosis, and Management of Cytomegalovirus Infection in Transplantation.
Abstract SUMMARYHosts with compromised or naive immune systems, such as individuals living with HIV/AIDS, transplant recipients, and fetuses, are at the highest risk for complications from cytomegalovirus (CMV) infection. Despite substantial progress in prevention, diagnostics, and treatment, CMV continues to negatively impact both solid-organ transplant (SOT) and hematologic cell transplant (HCT) recipients. In this article, we summarize important developments in the field over the past 10 years and highlight new approaches and remaining challenges to the optimal control of CMV infection and disease in tra...
Source: Clinical Microbiology Reviews - October 30, 2020 Category: Microbiology Authors: Limaye AP, Babu TM, Boeckh M Tags: Clin Microbiol Rev Source Type: research

State of the Art in the Culture of the Human Microbiota: New Interests and Strategies.
Abstract SUMMARYThe last 5 years have seen a turning point in the study of the gut microbiota with a rebirth of culture-dependent approaches to study the gut microbiota. High-throughput methods have been developed to study bacterial diversity with culture conditions aimed at mimicking the gut environment by using rich media such as YCFA (yeast extract, casein hydrolysate, fatty acids) and Gifu anaerobic medium in an anaerobic workstation, as well as media enriched with rumen and blood and coculture, to mimic the symbiosis of the gut microbiota. Other culture conditions target phenotypic and metabolic features of b...
Source: Clinical Microbiology Reviews - October 30, 2020 Category: Microbiology Authors: Tidjani Alou M, Naud S, Khelaifia S, Bonnet M, Lagier JC, Raoult D Tags: Clin Microbiol Rev Source Type: research

SARS-CoV-2 and Health Care Worker Protection in Low-Risk Settings: a Review of Modes of Transmission and a Novel Airborne Model Involving Inhalable Particles.
The objective of this review is to identify and appraise the available evidence (clinical trials and laboratory studies on masks and respirators, epidemiological studies, and air sampling studies), clarify key concepts and necessary conditions for airborne transmission, and shed light on knowledge gaps in the field. We find that, except for aerosol-generating procedures, the overall data in support of airborne transmission-taken in its traditional definition (long-distance and respirable aerosols)-are weak, based predominantly on indirect and experimental rather than clinical or epidemiological evidence. Consequently, we p...
Source: Clinical Microbiology Reviews - October 30, 2020 Category: Microbiology Authors: Zhang XS, Duchaine C Tags: Clin Microbiol Rev Source Type: research

Mechanisms of Drug-Induced Tolerance in Mycobacterium tuberculosis.
Abstract SUMMARYSuccessful treatment of tuberculosis (TB) can be hampered by Mycobacterium tuberculosis populations that are temporarily able to survive antibiotic pressure in the absence of drug resistance-conferring mutations, a phenomenon termed drug tolerance. We summarize findings on M. tuberculosis tolerance published in the past 20 years. Key M. tuberculosis responses to drug pressure are reduced growth rates, metabolic shifting, and the promotion of efflux pump activity. Metabolic shifts upon drug pressure mainly occur in M. tuberculosis's lipid metabolism and redox homeostasis, with reduced tricarb...
Source: Clinical Microbiology Reviews - October 20, 2020 Category: Microbiology Authors: Goossens SN, Sampson SL, Van Rie A Tags: Clin Microbiol Rev Source Type: research

Remdesivir against COVID-19 and Other Viral Diseases.
ybniker J Abstract SUMMARYPatients and physicians worldwide are facing tremendous health care hazards that are caused by the ongoing severe acute respiratory distress syndrome coronavirus 2 (SARS-CoV-2) pandemic. Remdesivir (GS-5734) is the first approved treatment for severe coronavirus disease 2019 (COVID-19). It is a novel nucleoside analog with a broad antiviral activity spectrum among RNA viruses, including ebolavirus (EBOV) and the respiratory pathogens Middle East respiratory syndrome coronavirus (MERS-CoV), SARS-CoV, and SARS-CoV-2. First described in 2016, the drug was derived from an antiviral library of...
Source: Clinical Microbiology Reviews - October 20, 2020 Category: Microbiology Authors: Malin JJ, Suárez I, Priesner V, Fätkenheuer G, Rybniker J Tags: Clin Microbiol Rev Source Type: research

Immunopathogenesis of Coronavirus-Induced Acute Respiratory Distress Syndrome (ARDS): Potential Infection-Associated Hemophagocytic Lymphohistiocytosis.
Abstract SUMMARYThe outbreak of coronavirus disease 2019 (COVID-19) in December 2019 in Wuhan, China, introduced the third highly pathogenic coronavirus into humans in the 21st century. Scientific advance after the severe acute respiratory syndrome coronavirus (SARS-CoV) epidemic and Middle East respiratory syndrome coronavirus (MERS-CoV) emergence enabled clinicians to understand the epidemiology and pathophysiology of SARS-CoV-2. In this review, we summarize and discuss the epidemiology, clinical features, and virology of and host immune responses to SARS-CoV, MERS-CoV, and SARS-CoV-2 and the pathogenesis of cor...
Source: Clinical Microbiology Reviews - October 14, 2020 Category: Microbiology Authors: Quan C, Li C, Ma H, Li Y, Zhang H Tags: Clin Microbiol Rev Source Type: research

Performance and Application of 16S rRNA Gene Cycle Sequencing for Routine Identification of Bacteria in the Clinical Microbiology Laboratory.
r S Abstract SUMMARYThis review provides a state-of-the-art description of the performance of Sanger cycle sequencing of the 16S rRNA gene for routine identification of bacteria in the clinical microbiology laboratory. A detailed description of the technology and current methodology is outlined with a major focus on proper data analyses and interpretation of sequences. The remainder of the article is focused on a comprehensive evaluation of the application of this method for identification of bacterial pathogens based on analyses of 16S multialignment sequences. In particular, the existing limitations of similarit...
Source: Clinical Microbiology Reviews - September 13, 2020 Category: Microbiology Authors: Church DL, Cerutti L, Gürtler A, Griener T, Zelazny A, Emler S Tags: Clin Microbiol Rev Source Type: research

Beyond Cytomegalovirus and Epstein-Barr Virus: a Review of Viruses Composing the Blood Virome of Solid Organ Transplant and Hematopoietic Stem Cell Transplant Recipients.
Abstract SUMMARYViral primary infections and reactivations are common complications in patients after solid organ transplantation (SOT) and hematopoietic stem cell transplantation (HSCT) and are associated with high morbidity and mortality. Among these patients, viral infections are frequently associated with viremia. Beyond the usual well-known viruses that are part of the routine clinical management of transplant recipients, numerous other viral signatures or genomes can be identified in the blood of these patients. The identification of novel viral species and variants by metagenomic next-generation sequencing ...
Source: Clinical Microbiology Reviews - August 28, 2020 Category: Microbiology Authors: Zanella MC, Cordey S, Kaiser L Tags: Clin Microbiol Rev Source Type: research

Convalescent Plasma Therapy for COVID-19: State of the Art.
Abstract SUMMARYConvalescent plasma (CP) therapy has been used since the early 1900s to treat emerging infectious diseases; its efficacy was later associated with the evidence that polyclonal neutralizing antibodies can reduce the duration of viremia. Recent large outbreaks of viral diseases for which effective antivirals or vaccines are still lacking has renewed the interest in CP as a life-saving treatment. The ongoing COVID-19 pandemic has led to the scaling up of CP therapy to unprecedented levels. Compared with historical usage, pathogen reduction technologies have now added an extra layer of safety to the us...
Source: Clinical Microbiology Reviews - August 15, 2020 Category: Microbiology Authors: Focosi D, Anderson AO, Tang JW, Tuccori M Tags: Clin Microbiol Rev Source Type: research

The ASM Journals Committee Values the Contributions of Black Microbiologists.
ik AJ PMID: 32737035 [PubMed - as supplied by publisher] (Source: Clinical Microbiology Reviews)
Source: Clinical Microbiology Reviews - August 3, 2020 Category: Microbiology Authors: Schloss PD, Junior M, Alvania R, Arias CA, Baumler A, Casadevall A, Detweiler C, Drake H, Gilbert J, Imperiale MJ, Lovett S, Maloy S, McAdam AJ, Newton ILG, Sadowsky MJ, Sandri-Goldin RM, Silhavy TJ, Tontonoz P, Young JH, Cameron CE, Cann I, Fuller AO, Ko Tags: Clin Microbiol Rev Source Type: research

The Echo of Pulmonary Tuberculosis: Mechanisms of Clinical Symptoms and Other Disease-Induced Systemic Complications.
Abstract SUMMARYClinical symptoms of active tuberculosis (TB) can range from a simple cough to more severe reactions, such as irreversible lung damage and, eventually, death, depending on disease progression. In addition to its clinical presentation, TB has been associated with several other disease-induced systemic complications, such as hyponatremia and glucose intolerance. Here, we provide an overview of the known, although ill-described, underlying biochemical mechanisms responsible for the clinical and systemic presentations associated with this disease and discuss novel hypotheses recently generated by vario...
Source: Clinical Microbiology Reviews - July 4, 2020 Category: Microbiology Authors: Luies L, du Preez I Tags: Clin Microbiol Rev Source Type: research

Coronavirus Disease 2019-COVID-19.
Abstract SUMMARYIn recent decades, several new diseases have emerged in different geographical areas, with pathogens including Ebola virus, Zika virus, Nipah virus, and coronaviruses (CoVs). Recently, a new type of viral infection emerged in Wuhan City, China, and initial genomic sequencing data of this virus do not match with previously sequenced CoVs, suggesting a novel CoV strain (2019-nCoV), which has now been termed severe acute respiratory syndrome CoV-2 (SARS-CoV-2). Although coronavirus disease 2019 (COVID-19) is suspected to originate from an animal host (zoonotic origin) followed by human-to-human transm...
Source: Clinical Microbiology Reviews - June 27, 2020 Category: Microbiology Authors: Dhama K, Khan S, Tiwari R, Sircar S, Bhat S, Malik YS, Singh KP, Chaicumpa W, Bonilla-Aldana DK, Rodriguez-Morales AJ Tags: Clin Microbiol Rev Source Type: research

Infectious Complications of Biological and Small Molecule Targeted Immunomodulatory Therapies.
Abstract SUMMARYThe past 2 decades have seen a revolution in our approach to therapeutic immunosuppression. We have moved from relying on broadly active traditional medications, such as prednisolone or methotrexate, toward more specific agents that often target a single receptor, cytokine, or cell type, using monoclonal antibodies, fusion proteins, or targeted small molecules. This change has transformed the treatment of many conditions, including rheumatoid arthritis, cancers, asthma, and inflammatory bowel disease, but along with the benefits have come risks. Contrary to the hope that these more specific agents ...
Source: Clinical Microbiology Reviews - June 12, 2020 Category: Microbiology Authors: Davis JS, Ferreira D, Paige E, Gedye C, Boyle M Tags: Clin Microbiol Rev Source Type: research

Antimicrobial Resistance Surveillance in Low- and Middle-Income Countries: Progress and Challenges in Eight South Asian and Southeast Asian Countries.
Abstract SUMMARYAntimicrobial resistance (AMR) is a serious global health threat and is predicted to cause significant health and economic impacts, particularly in low- and middle-income countries (LMICs). AMR surveillance is critical in LMICs due to high burden of bacterial infections; however, conducting AMR surveillance in resource-limited settings is constrained by poorly functioning health systems, scarce financial resources, and lack of skilled personnel. In 2015, the United Nations World Health Assembly endorsed the World Health Organization's Global Action Plan to tackle AMR; thus, several countries are st...
Source: Clinical Microbiology Reviews - June 12, 2020 Category: Microbiology Authors: Gandra S, Alvarez-Uria G, Turner P, Joshi J, Limmathurotsakul D, van Doorn HR Tags: Clin Microbiol Rev Source Type: research

Device-Associated Menstrual Toxic Shock Syndrome.
Abstract SUMMARYIn the 1980s, menstrual toxic shock syndrome (mTSS) became a household topic, particularly among mothers and their daughters. The research performed at the time, and for the first time, exposed the American public as well as the biomedical community, in a major way, to understanding disease progression and investigation. Those studies led to the identification of the cause, Staphylococcus aureus and the pyrogenic toxin superantigen TSS toxin 1 (TSST-1), and many of the risk factors, for example, tampon use. Those studies in turn led to TSS warning labels on the outside and inside of tampon boxes an...
Source: Clinical Microbiology Reviews - May 29, 2020 Category: Microbiology Authors: Schlievert PM, Davis CC Tags: Clin Microbiol Rev Source Type: research

Taenia solium Cysticercosis and Its Impact in Neurological Disease.
Abstract SUMMARYTaenia solium neurocysticercosis (NCC) is endemic in most of the world and contributes significantly to the burden of epilepsy and other neurological morbidity. Also present in developed countries because of immigration and travel, NCC is one of few diseases targeted for eradication. This paper reviews all aspects of its life cycle (taeniasis, porcine cysticercosis, human cysticercosis), with a focus on recent advances in its diagnosis, management, and control. Diagnosis of taeniasis is limited by poor availability of immunological or molecular assays. Diagnosis of NCC rests on neuroimaging finding...
Source: Clinical Microbiology Reviews - May 29, 2020 Category: Microbiology Authors: Garcia HH, Gonzalez AE, Gilman RH Tags: Clin Microbiol Rev Source Type: research

Host-Directed Antiviral Therapy.
Abstract SUMMARYAntiviral drugs have traditionally been developed by directly targeting essential viral components. However, this strategy often fails due to the rapid generation of drug-resistant viruses. Recent genome-wide approaches, such as those employing small interfering RNA (siRNA) or clustered regularly interspaced short palindromic repeats (CRISPR) or those using small molecule chemical inhibitors targeting the cellular "kinome," have been used successfully to identify cellular factors that can support virus replication. Since some of these cellular factors are critical for virus replication, b...
Source: Clinical Microbiology Reviews - May 16, 2020 Category: Microbiology Authors: Kumar N, Sharma S, Kumar R, Tripathi BN, Barua S, Ly H, Rouse BT Tags: Clin Microbiol Rev Source Type: research

Antimicrobial Resistance in ESKAPE Pathogens.
Abstract SUMMARYAntimicrobial-resistant ESKAPE ( Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) pathogens represent a global threat to human health. The acquisition of antimicrobial resistance genes by ESKAPE pathogens has reduced the treatment options for serious infections, increased the burden of disease, and increased death rates due to treatment failure and requires a coordinated global response for antimicrobial resistance surveillance. This looming health threat has restimulated interest in the development of new...
Source: Clinical Microbiology Reviews - May 16, 2020 Category: Microbiology Authors: De Oliveira DMP, Forde BM, Kidd TJ, Harris PNA, Schembri MA, Beatson SA, Paterson DL, Walker MJ Tags: Clin Microbiol Rev Source Type: research

Antifungal Susceptibility Testing: Current Approaches.
Abstract SUMMARYAlthough not as ubiquitous as antibacterial susceptibility testing, antifungal susceptibility testing (AFST) is a tool of increasing importance in clinical microbiology laboratories. The goal of AFST is to reliably produce MIC values that may be used to guide patient therapy, inform epidemiological studies, and track rates of antifungal drug resistance. There are three methods that have been standardized by standards development organizations: broth dilution, disk diffusion, and azole agar screening for Aspergillus Other commonly used methods include gradient diffusion and the use of rapid automate...
Source: Clinical Microbiology Reviews - May 2, 2020 Category: Microbiology Authors: Berkow EL, Lockhart SR, Ostrosky-Zeichner L Tags: Clin Microbiol Rev Source Type: research

Intrathecal Antibacterial and Antifungal Therapies.
Abstract SUMMARYIntrathecal administration of anti-infectives is indicated in central nervous system infections by multiresistant pathogens when drugs that can reach adequate cerebrospinal fluid (CSF) concentrations by systemic therapy are not available. Antibiotics that readily pass the blood-brain and blood-CSF barriers and/or that have low toxicity allowing an increase in the daily dosage should not be used for intrathecal therapy. Intrathecal therapy is accompanied by systemic treatment. Antibacterials indispensable for intrathecal therapy include aminoglycosides, colistin, daptomycin, tigecycline, and vancomy...
Source: Clinical Microbiology Reviews - May 2, 2020 Category: Microbiology Authors: Nau R, Blei C, Eiffert H Tags: Clin Microbiol Rev Source Type: research

Burkholderia cepacia Complex Bacteria: a Feared Contamination Risk in Water-Based Pharmaceutical Products.
eia I Abstract SUMMARYBurkholderia cepacia (formerly Pseudomonas cepacia) was once thought to be a single bacterial species but has expanded to the Burkholderia cepacia complex (Bcc), comprising 24 closely related opportunistic pathogenic species. These bacteria have a widespread environmental distribution, an extraordinary metabolic versatility, a complex genome with three chromosomes, and a high capacity for rapid mutation and adaptation. Additionally, they present an inherent resistance to antibiotics and antiseptics, as well as the abilities to survive under nutrient-limited conditions and to metabolize the or...
Source: Clinical Microbiology Reviews - April 18, 2020 Category: Microbiology Authors: Tavares M, Kozak M, Balola A, Sá-Correia I Tags: Clin Microbiol Rev Source Type: research

Caseum: a Niche for Mycobacterium tuberculosis Drug-Tolerant Persisters.
Abstract SUMMARYCaseum, the central necrotic material of tuberculous lesions, is a reservoir of drug-recalcitrant persisting mycobacteria. Caseum is found in closed nodules and in open cavities connecting with an airway. Several commonly accepted characteristics of caseum were established during the preantibiotic era, when autopsies of deceased tuberculosis (TB) patients were common but methodologies were limited. These pioneering studies generated concepts such as acidic pH, low oxygen tension, and paucity of nutrients being the drivers of nonreplication and persistence in caseum. Here we review widely accepted b...
Source: Clinical Microbiology Reviews - April 3, 2020 Category: Microbiology Authors: Sarathy JP, Dartois V Tags: Clin Microbiol Rev Source Type: research

Human Melioidosis.
Abstract SUMMARYThe causative agent of melioidosis, Burkholderia pseudomallei, a tier 1 select agent, is endemic in Southeast Asia and northern Australia, with increased incidence associated with high levels of rainfall. Increasing reports of this condition have occurred worldwide, with estimates of up to 165,000 cases and 89,000 deaths per year. The ecological niche of the organism has yet to be clearly defined, although the organism is associated with soil and water. The culture of appropriate clinical material remains the mainstay of laboratory diagnosis. Identification is best done by phenotypic methods, altho...
Source: Clinical Microbiology Reviews - March 13, 2020 Category: Microbiology Authors: Gassiep I, Armstrong M, Norton R Tags: Clin Microbiol Rev Source Type: research

Imported Malaria in Countries where Malaria Is Not Endemic: a Comparison of Semi-immune and Nonimmune Travelers.
rsen E, Ramharter M Abstract SUMMARYThe continuous increase in long-distance travel and recent large migratory movements have changed the epidemiological characteristics of imported malaria in countries where malaria is not endemic (here termed non-malaria-endemic countries). While malaria was primarily imported to nonendemic countries by returning travelers, the proportion of immigrants from malaria-endemic regions and travelers visiting friends and relatives (VFRs) in malaria-endemic countries has continued to increase. VFRs and immigrants from malaria-endemic countries now make up the majority of malaria patien...
Source: Clinical Microbiology Reviews - March 13, 2020 Category: Microbiology Authors: Mischlinger J, Rönnberg C, Álvarez-Martínez MJ, Bühler S, Paul M, Schlagenhauf P, Petersen E, Ramharter M Tags: Clin Microbiol Rev Source Type: research

Hepatitis B Virus: Advances in Prevention, Diagnosis, and Therapy.
Abstract SUMMARYCurrently, despite the use of a preventive vaccine for several decades as well as the use of effective and well-tolerated viral suppressive medications since 1998, approximately 250 million people remain infected with the virus that causes hepatitis B worldwide. Hepatitis C virus (HCV) and hepatitis B virus (HBV) are the leading causes of liver cancer and overall mortality globally, surpassing malaria and tuberculosis. Linkage to care is estimated to be very poor both in developing countries and in high-income countries, such as the United States, countries in Western Europe, and Japan. In the Unit...
Source: Clinical Microbiology Reviews - February 29, 2020 Category: Microbiology Authors: Nguyen MH, Wong G, Gane E, Kao JH, Dusheiko G Tags: Clin Microbiol Rev Source Type: research

Epidemiology of β-Lactamase-Producing Pathogens.
Epidemiology of β-Lactamase-Producing Pathogens. Clin Microbiol Rev. 2020 Mar 18;33(2): Authors: Bush K, Bradford PA Abstract SUMMARYβ-Lactam antibiotics have been widely used as therapeutic agents for the past 70 years, resulting in emergence of an abundance of β-lactam-inactivating β-lactamases. Although penicillinases in Staphylococcus aureus challenged the initial uses of penicillin, β-lactamases are most important in Gram-negative bacteria, particularly in enteric and nonfermentative pathogens, where collectively they confer resistance to all β-lactam-containi...
Source: Clinical Microbiology Reviews - February 29, 2020 Category: Microbiology Authors: Bush K, Bradford PA Tags: Clin Microbiol Rev Source Type: research

Consolidation of Clinical Microbiology Laboratories and Introduction of Transformative Technologies.
We describe why consolidation of clinical microbiology laboratories will generate quality benefits for many, if not most, aspects of the services separate institutions already provided individually. We also define the important role of innovative and large-scale diagnostic platforms. Such platforms lend themselves particularly well to computational (AI)-driven genomics and bioinformatics applications. These and other diagnostic innovations will allow for better infectious disease detection, surveillance, and prevention with novel translational research and optimized (diagnostic) product and service development opportunitie...
Source: Clinical Microbiology Reviews - February 29, 2020 Category: Microbiology Authors: Vandenberg O, Durand G, Hallin M, Diefenbach A, Gant V, Murray P, Kozlakidis Z, van Belkum A Tags: Clin Microbiol Rev Source Type: research

Mumps: an Update on Outbreaks, Vaccine Efficacy, and Genomic Diversity.
Abstract SUMMARYMumps is an acute viral infection characterized by inflammation of the parotid and other salivary glands. Persons with mumps are infectious from 2 days before through 5 days after parotitis onset, and transmission is through respiratory droplets. Despite the success of mumps vaccination programs in the United States and parts of Europe, a recent increase in outbreaks of mumps virus infections among fully vaccinated populations has been reported. Although the effectiveness of the mumps virus component of the measles-mumps-rubella (MMR) vaccine is suboptimal, a range of contributing factors has led t...
Source: Clinical Microbiology Reviews - February 29, 2020 Category: Microbiology Authors: Lam E, Rosen JB, Zucker JR Tags: Clin Microbiol Rev Source Type: research

Immunomodulatory Strategies in Herpes Simplex Virus Encephalitis.
Abstract SUMMARYHerpes simplex virus 1 (HSV-1) can be responsible for life-threatening HSV encephalitis (HSE). The mortality rate of patients with HSE who do not receive antiviral treatment is 70%, with most survivors suffering from permanent neurological sequelae. The use of intravenous acyclovir together with improved diagnostic technologies such as PCR and magnetic resonance imaging has resulted in a reduction in the mortality rate to close to 20%. However, 70% of surviving patients still do not recover complete neurological functions. Thus, there is an urgent need to develop more effective treatments for a bet...
Source: Clinical Microbiology Reviews - February 15, 2020 Category: Microbiology Authors: Piret J, Boivin G Tags: Clin Microbiol Rev Source Type: research

Emerging Tick-Borne Diseases.
Abstract SUMMARYIncreases in tick-borne disease prevalence and transmission are important public health issues. Efforts to control these emerging diseases are frustrated by the struggle to control tick populations and to detect and treat infections caused by the pathogens that they transmit. This review covers tick-borne infectious diseases of nonrickettsial bacterial, parasitic, and viral origins. While tick surveillance and tracking inform our understanding of the importance of the spread and ecology of ticks and help identify areas of risk for disease transmission, the vectors are not the focus of this document...
Source: Clinical Microbiology Reviews - January 5, 2020 Category: Microbiology Authors: Madison-Antenucci S, Kramer LD, Gebhardt LL, Kauffman E Tags: Clin Microbiol Rev Source Type: research

Performance of Zika Assays in the Context of Toxoplasma gondii, Parvovirus B19, Rubella Virus, and Cytomegalovirus (TORCH) Diagnostic Assays.
Abstract SUMMARYInfections during pregnancy that may cause congenital abnormalities have been recognized for decades, but their diagnosis is challenging. This was again illustrated with the emergence of Zika virus (ZIKV), highlighting the inherent difficulties in estimating the extent of pre- and postnatal ZIKV complications because of the difficulties in establishing definitive diagnoses. We reviewed the epidemiology, infection kinetics, and diagnostic methods used for Toxoplasma gondii, parvovirus B19, rubella virus, and cytomegalovirus (TORCH) infections and compared the results with current knowledge of ZIKV d...
Source: Clinical Microbiology Reviews - December 14, 2019 Category: Microbiology Authors: Voordouw B, Rockx B, Jaenisch T, Fraaij P, Mayaud P, Vossen A, Koopmans M Tags: Clin Microbiol Rev Source Type: research

Chagas Disease in the United States: a Public Health Approach.
Abstract SUMMARYTrypanosoma cruzi is the etiological agent of Chagas disease, usually transmitted by triatomine vectors. An estimated 20 to 30% of infected individuals develop potentially lethal cardiac or gastrointestinal disease. Sylvatic transmission cycles exist in the southern United States, involving 11 triatomine vector species and infected mammals such as rodents, opossums, and dogs. Nevertheless, imported chronic T. cruzi infections in migrants from Latin America vastly outnumber locally acquired human cases. Benznidazole is now FDA approved, and clinical and public health efforts are under way by researc...
Source: Clinical Microbiology Reviews - December 1, 2019 Category: Microbiology Authors: Bern C, Messenger LA, Whitman JD, Maguire JH Tags: Clin Microbiol Rev Source Type: research

Laboratory Diagnosis of Human Brucellosis.
Abstract SUMMARYThe clinical presentation of brucellosis in humans is variable and unspecific, and thus, laboratory corroboration of the diagnosis is essential for the patient's proper treatment. The diagnosis of brucellar infections can be made by culture, serological tests, and nucleic acid amplification assays. Modern automated blood culture systems enable detection of acute cases of brucellosis within the routine 5- to 7-day incubation protocol employed in clinical microbiology laboratories, although a longer incubation and performance of blind subcultures may be needed for protracted cases. Serological tests,...
Source: Clinical Microbiology Reviews - November 16, 2019 Category: Microbiology Authors: Yagupsky P, Morata P, Colmenero JD Tags: Clin Microbiol Rev Source Type: research

The Global Ascendency of OXA-48-Type Carbapenemases.
Abstract SUMMARYSurveillance studies have shown that OXA-48-like carbapenemases are the most common carbapenemases in Enterobacterales in certain regions of the world and are being introduced on a regular basis into regions of nonendemicity, where they are responsible for nosocomial outbreaks. OXA-48, OXA-181, OXA-232, OXA-204, OXA-162, and OXA-244, in that order, are the most common enzymes identified among the OXA-48-like carbapenemase group. OXA-48 is associated with different Tn1999 variants on IncL plasmids and is endemic in North Africa and the Middle East. OXA-162 and OXA-244 are derivatives of OXA-48 and a...
Source: Clinical Microbiology Reviews - November 16, 2019 Category: Microbiology Authors: Pitout JDD, Peirano G, Kock MM, Strydom KA, Matsumura Y Tags: Clin Microbiol Rev Source Type: research

Aspergillus fumigatus and Aspergillosis in 2019.
los G Abstract SUMMARYAspergillus fumigatus is a saprotrophic fungus; its primary habitat is the soil. In its ecological niche, the fungus has learned how to adapt and proliferate in hostile environments. This capacity has helped the fungus to resist and survive against human host defenses and, further, to be responsible for one of the most devastating lung infections in terms of morbidity and mortality. In this review, we will provide (i) a description of the biological cycle of A. fumigatus; (ii) a historical perspective of the spectrum of aspergillus disease and the current epidemiological status of these infec...
Source: Clinical Microbiology Reviews - November 16, 2019 Category: Microbiology Authors: Latgé JP, Chamilos G Tags: Clin Microbiol Rev Source Type: research

The Role of the BCL-2 Family of Proteins in HIV-1 Pathogenesis and Persistence.
Abstract SUMMARYAdvances in HIV-1 therapy have transformed the once fatal infection into a manageable, chronic condition, yet the search for a widely applicable approach to cure remains elusive. The ineffectiveness of antiretroviral therapy (ART) in reducing the size of the HIV-1 latent reservoir has prompted investigation into the mechanisms of HIV-1 latency and immune escape. One of the major regulators of apoptosis, the BCL-2 protein, alongside its homologous family members, is a major target of HIV-1-induced change. Recent studies have now demonstrated the association of this protein with cells that support pr...
Source: Clinical Microbiology Reviews - November 1, 2019 Category: Microbiology Authors: Chandrasekar AP, Cummins NW, Badley AD Tags: Clin Microbiol Rev Source Type: research

A Comprehensive Update on the Problem of Blood Culture Contamination and a Discussion of Methods for Addressing the Problem.
Discussion of Methods for Addressing the Problem. Clin Microbiol Rev. 2019 Dec 18;33(1): Authors: Doern GV, Carroll KC, Diekema DJ, Garey KW, Rupp ME, Weinstein MP, Sexton DJ Abstract SUMMARYIn this review, we present a comprehensive discussion of matters related to the problem of blood culture contamination. Issues addressed include the scope and magnitude of the problem, the bacteria most often recognized as contaminants, the impact of blood culture contamination on clinical microbiology laboratory function, the economic and clinical ramifications of contamination, and, perhaps most importantly, a s...
Source: Clinical Microbiology Reviews - November 1, 2019 Category: Microbiology Authors: Doern GV, Carroll KC, Diekema DJ, Garey KW, Rupp ME, Weinstein MP, Sexton DJ Tags: Clin Microbiol Rev Source Type: research

Tuberculosis Vaccine Development: Progress in Clinical Evaluation.
Abstract SUMMARYTuberculosis (TB) is the leading killer among all infectious diseases worldwide despite extensive use of the Mycobacterium bovis bacille Calmette-Guérin (BCG) vaccine. A safer and more effective vaccine than BCG is urgently required. More than a dozen TB vaccine candidates are under active evaluation in clinical trials aimed to prevent infection, disease, and recurrence. After decades of extensive research, renewed promise of an effective vaccine against this ancient airborne disease has recently emerged. In two innovative phase 2b vaccine clinical trials, one for the prevention of Mycobacte...
Source: Clinical Microbiology Reviews - November 1, 2019 Category: Microbiology Authors: Sable SB, Posey JE, Scriba TJ Tags: Clin Microbiol Rev Source Type: research

Rapid Growth and Metabolism of Uropathogenic Escherichia coli in Relation to Urine Composition.
Abstract SUMMARYUropathogenic Escherichia coli (UPEC) strains cause a majority of urinary tract infections (UTIs). Since UPEC strains can become antibiotic resistant, adjunct or alternate therapies are urgently needed. UPEC strains grow extremely rapidly in patients with UTIs. Thus, this review focuses on the relation between urine composition and UPEC growth and metabolism. Compilation of urinary components from two major data sources suggests the presence of sufficient amino acids and carbohydrates as energy sources and abundant phosphorus, sulfur, and nitrogen sources. In a mouse UTI model, mutants lacking enzy...
Source: Clinical Microbiology Reviews - October 18, 2019 Category: Microbiology Authors: Reitzer L, Zimmern P Tags: Clin Microbiol Rev Source Type: research

Early Events in Coccidioidomycosis.
Abstract SUMMARYSince its description nearly 130 years ago, hundreds of studies have deepened our understanding of coccidioidomycosis, also known as valley fever (VF), and provided useful diagnostic tests and treatments for the disease caused by the dimorphic fungi Coccidioides spp. In general, most of the literature has addressed well-established infections and has described patients who have experienced major complications. In contrast, little attention has been given to the earliest consequences of the pathogen-host interaction and its implications for disease manifestation, progression, and resolution. ...
Source: Clinical Microbiology Reviews - October 18, 2019 Category: Microbiology Authors: Donovan FM, Shubitz L, Powell D, Orbach M, Frelinger J, Galgiani JN Tags: Clin Microbiol Rev Source Type: research