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Urinary Tract Infections

Introduction Urinary tract infection (UTI) is one of the most common infectious diseases, both in ambulatory and hospital settings, and is a major cause of antimicrobial use. This is especially relevant in the era of increasing antimicrobial resistance, and in particular, resistance developing in the Gram-negative organisms, which cause most UTI episodes. In many locations, it is increasingly difficult to select an empiric agent for UTI…

Select Gastrointestinal and Hepatobiliary Infections

Esophagitis Esophagitis is an inflammatory mucosal injury disorder that may be caused by infectious agents and local irritants. The inflammation may present with substernal pain, odynophagia, and occasionally dysphagia. The risk factors for esophageal inflammatory disorders may be iatrogenic (i.e., pill esophagitis, chemical injuries) or disease related. Infectious esophagitis often presents with odynophagia in the setting of immunosuppression, recent antibiotics, corticosteroids, or neutropenia. Most infectious esophagitis…

Lower Respiratory Tract Infections

Lower respiratory tract infections (LRTIs) are among the most frequently encountered and difficult to diagnose infectious syndromes. Symptoms of most LRTIs overlap with other clinical conditions, such as congestive heart failure and obstructive lung disease, such asthma and chronic obstructive pulmonary disease (COPD). Diagnostic tests are not specific to LRTIs, and even invasive studies have a low yield in terms of confirming the diagnosis. This means…

Ear, Nose, Throat, and Neck Infections

Infections of the ear, nose, and throat (ENT) run the gamut from annoying but relatively harmless otitis externa to life-threatening infections of the airway. Despite the broad array of syndromes, most of these share a common set of pathogens and similar principles of evaluation and treatment. This chapter will discuss these pathogens and diagnostic tests before discussing anatomically distinct syndromes and specific treatments. Pathogens The anatomic…

Fever and Rash

Overview Generalized rashes with fever are among the most frequent conditions seen by primary care physicians, and are a common reason for patient visits to the emergency department and dermatologists. The majority of cases do not represent an immediate danger, but some patients may have a life-threatening diagnosis, and a prompt and accurate approach is warranted. Diagnosing fever and rash is frequently challenging, because there is…

Fever of Unknown Origin

Introduction Fever is a common complaint encountered by primary caregivers, internists, and surgeons. We all experience fever throughout our lives, and although frequently the cause of fever is never explained, few of us experience a true “classic” fever of unknown origin (FUO). The term FUO should be reserved for patients who experience all of the following: Fever >3 weeks Oral temperature ≥101° F (38.3° C) on…

A Primer on Antimicrobials

Introduction The serendipitous discovery of penicillin by Sir Alexander Fleming in 1928 was one of the greatest medical advances of the 20th century and marks the beginning of the antibiotic era. The term antibiotic originated with Selman Waksman in 1941, who defined it as any small molecule made by a microbe that antagonizes the growth of another microbe. With the widespread clinical use of antibiotics in…

General Principles of Antimicrobial Therapy

Introduction Antimicrobials differ intrinsically from other drugs. Antimicrobials do not aim to affect biologic processes in the patient, but instead inhibit or kill invading pathogens and commensal microorganisms. The properties of these microorganisms are crucial when choosing an antimicrobial regimen, as are the patient and drug characteristics. The pyramid of infectious diseases is a useful learning tool and illustrates the multiple interactions between the host, pathogen(s),…

A Primer on Microbiology

Introduction to Microorganisms That Interact with Humans In this section, we will introduce the main categories of organisms that interact with humans both as part of the human microbiome and those that are able to cause disease. Some organisms are primarily colonizers of humans and exist in a symbiotic relationship, others are primarily pathogens that cause disease, and some are able to do both. The predominant…

Interacting with the Clinical Microbiology Laboratory

Introduction The clinical microbiology laboratory offers an increasingly diverse menu of diagnostic assays, including maintenance of traditional methods first developed in the early 1900s, to implementing increasingly complex molecular assays and, most recently, implementing whole-genome and next-generation sequencing assays for pathogen detection, typing, and assessment of antimicrobial susceptibility. The laboratory is also becoming increasingly automated, from the adoption of automated enzyme immunoassay (EIA) processors, to nucleic…

Burkholderia cepacia Complex and Other Burkholderia Species

Acknowledgment Substantial material from Jane L. Burns’ chapter in the previous edition has been used. The genus Burkholderia was proposed in 1992 for 7 species that previously were included in Pseudomonas homology group II. All are animal or plant pathogens and are considered opportunistic pathogens in healthy humans. Burkholderia spp. are nutritionally diverse water and soil organisms that are catalase producing and non-glucose fermenting. Species can…

General Approach to Infectious Diseases Evaluation

Infections are disorders or diseases caused by microorganisms such as bacteria, viruses, fungi, or parasites. Infections manifest themselves by a myriad of signs and symptoms in a variety of combinations. It is not possible to discuss in a meaningful way the various permutations and combinations of signs and symptoms associated with infectious diseases. However, some signs and symptoms are, rightly or wrongly, widely regarded as cardinal…

Pseudomonas aeruginosa

Microbiology Pseudomonas aeruginosa is a gram-negative bacillus found widely in nature, soil, and water. Classified as an opportunistic pathogen, P. aeruginosa causes disease infrequently in normal hosts but is a major cause of infection in patients with underlying or immunocompromising conditions. The genome of P. aeruginosa , which is especially large for a prokaryote, has provided an understanding of the metabolic and pathogenic mechanisms that underlie…

Moraxella Species

Microbiology Discovered at the end of the 19th century, Moraxella catarrhalis (formerly Micrococcus catarrhalis , Neisseria catarrhalis, and Branhamella catarrhalis ) has undergone several changes of nomenclature and changes in status as either a commensal of the upper respiratory tract or a true pathogenic organism of both the upper and lower respiratory tract. DNA-DNA and ribosomal RNA (rRNA)–DNA hybridization techniques have shown M. catarrhalis to be…

Eikenella, Pasteurella, and Chromobacterium Species

Microbiology Eikenella, Pasteurella, and Chromobacterium species display both common and contrasting characteristics of laboratory properties, epidemiology, and clinical presentations. Eikenella and Pasteurella spp. are nonmotile, whereas C. violaceum is motile and less fastidious than the others. E. corrodens was the only recognized species within the genus Eikenella until recently. E. corradens is associated with human infections and belongs to the family Neisseriaceae along with the genera…

Less Commonly Encountered NonentericGram-Negative Bacilli

Acknowledgment The authors would like to thank Dr. Michael Brady for contributions to this chapter in past editions. Microbiology and Epidemiology Several genera of nonglucose-fermenting gram-negative bacilli are infrequent opportunistic human pathogens. Most are nonfastidious, aerobic, catalase-positive organisms; motility, oxidase activity, and growth on MacConkey agar are variable. Those organisms that grow on MacConkey agar typically produce colorless colonies indicating they do not ferment glucose. Identification…

Aeromonas Species

Description of the Pathogen The genus Aeromonas (from the Greek “Aer”: gas; and “Monas”: unit; meaning “gas producing units”) consists of environmental, facultatively anaerobic, gram-negative bacilli that are predominantly motile as a result of a single polar flagellum. Although at least 36 species have been described in this genus, only A. hydrophila, A. dhakensis, A. caviae, A. veronii biovar sobria, and A. trota are relevant human…

Acinetobacter Species

Acknowledgments We acknowledge the substantial contributions of D.A. Powell, M.J. Marcon, and A. L. Leber to this chapter in previous editions. Microbiology Acinetobacter species are nonmotile, oxidase-negative, catalase-positive, strictly aerobic, gram-negative coccobacilli. Their inability to ferment glucose or to reduce nitrate distinguishes Acinetobacter from the family Enterobacteriaceae. Acinetobacter is a genus of opportunistic pathogens within the Gammaproteobacteria class in the family Moraxellaceae along with the Moraxella…

Yersinia Species

Yersinia species are bacteria in the family Enterobacteriaceae. Of 15 species of Yersinia , only Yersinia enterocolitica , Y. pseudotuberculosis , and Y. pestis are human pathogens. Y. enterocolitica and Y. pseudotuberculosis are enteropathogens transmitted by consumption of contaminated food or water and cause gastrointestinal syndromes that can develop into fatal septicemia in immunocompromised people. Y. pestis is the cause of plague that most commonly manifests…