J. Michael Miller

Microbiology Technical Services, LLC

2018 was a memorable year for infectious diseases and the microbiology laboratory, and this article, albeit through the eyes of only one individual, will review some of the key events and issues that microbiology and infectious diseases encountered in 2018. Some of these were daily “problems,” and some were welcome additions to our diagnostic acume...

The critical nature of the microbiology laboratory in infectious disease diagnosis calls for a close, positive working relationship between the physician/advanced practice provider and the microbiologists who provide enormous value to the healthcare team. This document, developed by experts in laboratory and adult and pediatric clinical medicine, p...

The critical nature of the microbiology laboratory in infectious disease diagnosis calls for a close, positive working relationship between the physician/advanced practice provider and the microbiologists who provide enormous value to the healthcare team. This document, developed by experts in laboratory and adult and pediatric clinical medicine, p...

It is the legal responsibility of the microbiology laboratory to develop and implement specimen management policies that are supported by the medical staff and the antimicrobial stewardship committee. These policies will promote the production of microbiology results that are accurate, significant, and clinically relevant and will reduce the potent...

Epidemiological surveillance for microbes is currently based on either agar culture followed by identification, or genetic amplification. Both techniques are highly skilled-labor intensive, costly, and must be done in central laboratories. The Defined Substrate Utilization ® (DSU ®) format pro-vides an epidemiological series of specific screening f...

In today's competitive health care climate, microbiology laboratories are asked to do more work, often with limited or decreasing resources. Cost-saving strategies, successfully implemented in one or more microbiology laboratories across the globe, are listed. For each cost-saving suggestion, careful evaluation must occur prior to implementation, c...

A widely-perceived requirement for validation of all new specimen collection swabs by the laboratory appears to be the result of misinformation.…

The critical role of the microbiology laboratory in infectious disease diagnosis calls for a close, positive working relationship between the physician and the microbiologists who provide enormous value to the health care team. This document, developed by both laboratory and clinical experts, provides information on which tests are valuable and in...

The critical role of the microbiology laboratory in infectious disease diagnosis calls for a close, positive working relationship between the physician and the microbiologists who provide enormous value to the health care team. This document, developed by both laboratory and clinical experts, provides information on which tests are valuable and in...

Strain-typing technology in support of outbreak identification and resolution has evolved from phenotypic analysis, such as serology and biotypes, to much-more-robust molecular genetic approaches, such as pulsed-field gel electrophoresis (PFGE) and whole-genome sequencing. Whole-genome mapping (WGM) has been recently applied to subtyping analysis,...

Prevention of injuries and occupational infections in U.S. laboratories has been a concern for many years. CDC and the National Institutes of Health addressed the topic in their publication Biosafety in Microbiological and Biomedical Laboratories, now in its 5th edition (BMBL-5). BMBL-5, however, was not designed to address the day-to-day operation...

• The One Health concept integrates human, animal, and environmental health to provide valuable insights when dealing with infectious agents. • Investigating emerging pathogens benefits when the skills and knowledge of those specializing in human and animal infectious diseases are brought together, thus increasing the likelihood of identifying ways...

Renaissance man; a warm, humane person; and outstanding academic physician and scientist, Dr. Winn is remembered vividly as a contributor to understanding of emerging infectious diseases; a contemporary, efficient diagnostic clinical microbiologist; and a treasured educator. Born in Richmond, Virginia, on April 2, 1941, he was a true scholar, gradu...

Clinical microbiologists have a new and unique opportunity to increase our value to health care by broadening how we think about disease processes and asking ourselves what we can do to help resolve a disease, assist in tracking a cause, or even predict an outbreak before it occurs. Human health, animal health (both wildlife and domestic animals),...

Accidental infections acquired in the laboratory environment are not reportable in a formal forum outside the institution, and therefore, there is little opportunity to evaluate such occurrences and learn from them. We evaluated voluntary responses from 88 facilities, 53 large hospitals (>200 beds) or academic institutions, 32 smaller facilities (<...

For the last several years, most clinical microbiologists have heard, talked, and thought about; have been threatened with; or have actually experienced the consolidation of clinical microbiology (CM) services. We present (i) concepts, experiences, and practices that we and others have found to be successful during the operation of consolidated CM...

The Select Agent Rule was established to protect public health and safety and was designed specifically to address the possession, use, and transfer of select agents and toxins. It was published in the Federal Register Friday, 18 March, 2005, and became effective on 18 April, 2005. This rule applies to virtually all laboratories, including clinical...

Neisseria meningitidis is infrequently reported as a laboratory-acquired infection. Prompted by two cases in the United States in 2000, we assessed this risk among laboratorians. We identified cases of meningococcal disease that were possibly acquired or suspected of being acquired in a laboratory by placing an information request on e-mail discuss...

We evaluated the Vitek 2 ID-GNB identification card (bioMérieux, Inc., Durham, N.C.) for its ability to identify members of the family Enterobacteriaceae and other gram-negative bacilli that are isolated in clinical microbiology laboratories. Using 482 enteric stock cultures and 103 strains of oxidase-positive, gram-negative glucose-fermenting and...

I n response to the threat of bioterrorism and following a presidential order, offi-cials at the Centers for Disease Control and Prevention (CDC), Association of Public Health Laboratories (APHL), Federal Bureau of Investigation (FBI), and United States Army Medical Research Institute of Infectious Diseases (USAMRIID) established the Laboratory Res...

The MicroScan Rapid Neg ID3 panel is designed for the identification of Enterobacteriaceae and nonenteric glucose-fermenting and nonfermenting gram-negative bacilli. We evaluated this panel for its ability to identify gram-negative non-Enterobacteriaceae bacteria. A total of 134 strains, representing 26 genera and 42 species, were taken from storag...

Bioterrorism preparedness is clearly a goal for the health care community, working in concert with city, county, state, and federal public health and emergency authorities and in collaboration with law enforcement at the local and federal levels. Opening the channels of communication between all groups involved, obtaining the necessary resources, a...

Nosocomial device-related infections with Gram-positive cocci and their resistance to vancomycin are of increasing occurrence. We examined clinical isolates of relatively avirulent coagulase-negative staphylococci for their resistance to vancomycin and for their capabilities to adhere in vitro to medical grade silicone. Vancomycin resistance was fo...

Human blood components have been shown to enhance biofilm formation by gram-positive bacteria. We investigated the effect of human blood on biofilm formation on the inner lumen of needleless central venous catheter connectors by several gram-negative bacteria, specificallyEnterobacter cloacae, Pseudomonas aeruginosa, andPantoea agglomerans. Results...

Modern medicine has led to dramatic changes in infectious diseases practice. Vaccination and antibiotic therapy have benefited millions of persons. However, constrained resources now threaten our ability to adequately manage threats of infectious diseases by placing clinical microbiology services and expertise distant from the patient and their inf...

Central venous catheter needleless connectors (NCs) have been shown to develop microbial contamination. A protocol was developed for the collection, processing, and examination of NCs to detect and measure biofilms on these devices. Sixty-three percent of 24 NCs collected from a bone marrow transplant center contained biofilms comprised primarily o...

This review presents the current taxonomy of the genera Proteus, Providencia, and Morganella, along with the current methods for the identification of each species within the three genera, incorporating both conventional biochemical and commercial methods. While all of these organisms are ubiquitous in the environment, individual case reports and n...

The MicroScan Rapid Neg ID3 panel (Dade Behring, Inc., West Sacramento, Calif.) is designed for the identification of gram-negative bacilli. We evaluated its ability to accurately identify Enterobacteriaceae that are routinely encountered in a clinical laboratory and glucose nonfermenting gram-negative bacilli. Using 511 stock cultures that were ma...

This review presents the current taxonomy of the genera Proteus, Providencia, and Morganella, along with the current methods for the identification of each species within the three genera, incorporating both conventional biochemical and commercial methods. While all of these organisms are ubiquitous in the environment, individual case reports and n...

Strains traditionally identified as Proteus vulgaris formed three biogroups. Biogroup 1, characterized by negative reactions for indole production, salicin fermentation and aesculin hydrolysis, is now known as Proteus penneri. Biogroup 2, characterized by positive reactions for indole, salicin and aesculin, was shown by DNA hybridization (hydroxyap...

Studies conducted in France and Germany suggest that up to 19% of clinically identified Klebsiella sp. are actually Klebsiella planticola, an environmental species that has been attributed to two cases of septicemia, with a rare isolate of Klebsiella terrigena (0. 4%) being identified. A 1-year survey of newborns on a neonatal ward, also conducted...

To determine the degree to which species identification or strain relatedness assessment of successive blood culture isolates of coagulase-negative staphylococci (CNS) may improve the clinical diagnosis of bloodstream infection (BSI). 400-bed community hospital. Prospective laboratory survey during which all CNS blood culture isolates obtained betw...

The Oxyrase OxyPlate anaerobe incubation system was evaluated for its ability to support the growth of clinically significant anaerobic bacteria previously identified by the Anaerobe Reference Laboratory at the Centers for Disease Control and Prevention. The results were compared with those obtained with conventional anaerobe blood agar plates incu...

Providencia heimbachae was first described in 1986. It has been isolated from penguin feces and an aborted bovine fetus. To date, there has been no reported isolation of this organism from human specimens. We now report the isolation of P. heimbachae from the stool of a 23-year-old woman with idiopathic diarrhea. The identity of the human strain wa...

Clostridium perfringens is a common cause of food-borne illness. The illness is characterized by profuse diarrhea and acute abdominal pain. Since the illness is usually self-limiting, many cases are undiagnosed and/or not reported. Investigations are often pursued after an outbreak involving large numbers of people in institutions, at restaurants,...

Objective: To evaluate the ID 32E bacterial identification system for accuracy in the identification of members of the family Enterobacteriaceae, Pseudomonas aeruginosa, Stenotrophomonas maltophilia, and Acinetobacter baumannii/Iwoffii. Methods: Stock cultures of 497 Enterobacteriaceae and 27 commonly encountered non-enteric Gram-negative rods were...

We describe the isolation and identification of Enterobacter intermedium from the gallbladder of a patient with cholecystitis. There have been only four documented isolations of this organism from humans; it normally occurs in surface water and unpolluted soils. The identification was initially made by a MicroScan Walk/Away system with a Neg Combo...

Because the way specimens are collected and handled may directly affect the outcome of microbiological analysis, appropriate specimen management is critical to ensuring laboratory effectiveness and an acceptable turnaround time. Specific guidelines on specimen collection are necessary for optimal use of microbiology services.

Erwinia persicinus was first described in 1990 after being isolated from a variety of fruits and vegetables, including bananas, cucumbers, and tomatoes. In 1994, it was shown to be the causative agent of necrosis of bean pods. We now report the first human isolate of E. persicinus. The strain was isolated from the urine of an 88-year-old woman who...

The BBL Crystal Anaerobe (ANR) identification system was evaluated, and the results were compared with those from conventional anaerobic methods. We tested 322 clinically significant anaerobic bacteria according to the manufacturer's instructions. The system identified correctly 286 of 322 (88.8%) of the anaerobic bacteria tested. Of these, 263 of...

Erwinia persicinus was first described in 1990 after being isolated from a variety of fruits and vegetables, including bananas, cucumbers, and tomatoes. In 1994, it was shown to be the causative agent of necrosis of bean pods. We now report the first human isolate of E. persicinus . The strain was isolated from the urine of an 88-year-old woman who...

We evaluated the Vitek GNI+ and Becton Dickinson Crystal E/NF identification systems for their ability to accurately identify 619 and 626 strains, respectively, of members of the family Enterobacteriaceae and other glucose-fermenting and non-glucose-fermenting gram-negative rods. All strains tested were taken from a stock collection and passed thre...

We evaluated the Vitek GNI+ and Becton Dickinson Crystal E/NF identification systems for their ability to accurately identify 619 and 626 strains, respectively, of members of the family Enterobacteriaceae and other glucose-fermenting and non-glucose-fermenting gram-negative rods. All strains tested were taken from a stock collection and passed thre...

Enterobacter hormaechei was first identified as a unique species in 1989. Between 29 November 1992 and 17 March 1993, an outbreak of E. hormaechei occurred among premature infants in the intensive care nursery (ICN) at The Hospital of the University of Pennsylvania. The 10 infants whose cultures were positive for E. hormaechei (six were infected an...

To determine the species distribution of coagulase-negative staphylococci (CoNS) in patients with endophthalmitis and to ascertain whether the patient's own flora was a major source of postoperative endophthalmitis following cataract extraction. In a 4-year multicenter prospective study, 524 bacterial isolates were submitted from 225 Endophthalmiti...

We present two cases of rapidly progressing, fatal pneumonia caused by Bacillus cereus. These cases are interesting in that B. cereus, even from blood or sputum specimens, may often be considered a contaminant and receive inadequate attention. Also of interest was the fact that the two patients resided in the same area of the state, were welders by...

Various commercially produced agglutination kits are widely used for the identification of Staphylococcus aureus. These kits detect the presence of protein A and/or clumping factor on S. aureus. The literature has shown that methicillin-resistant S. aureus (MRSA) isolates which are deficient in both clumping factor and protein A may be misidentifie...

A case of postsurgical endophthalmitis caused by Agrobacterium radiobacter in a 70-year-old male is reported. A. radiobacter organisms are normally environmental bacteria but may occasionally be opportunistic pathogens. Infection in this case occurred after the patient was discharged following routine cataract surgery. The infection cleared after e...

To determine the cause(s) of an outbreak of gram-negative bacteremia (GNB) in open-heart-surgery (OHS) patients at hospital A. Case-control and cohort studies and an environmental survey. Nine patients developed GNB with Enterobacter cloacae (6), Pseudomonas aeruginosa (5), Klebsiella pneumoniae (3), Serratia marcescens (2), or Klebsiella oxytoca (...

The growth of Alloiococcus otitis under different atmospheres and nutritional conditions was studied. The growth rates of 25 strains of gram-positive cocci representing five genera on heart infusion agar plates containing 5% rabbit blood and on brucella agar plates with and without sheep blood under aerobic, increased CO2, and anaerobic atmospheres...

In November 1991, an intravenous therapy team was instituted on the medical/surgical wards of a 330-bed acute care Veteran's Affairs Medical Center. Before this, IV insertions/care were performed by house officers and registered nurses. Intravenous-related bacteremias decreased from 4.6/1000 patient discharges to 1.5/1000 patient discharges (P < 0....

We report the use of BioBASE, a computer-enhanced numerical identification software package, as a valuable aid for the rapid identification of unknown enteric bacilli when using conventional biochemicals. We compared BioBASE identification results with those of the Centers for Disease Control and Prevention's mainframe computer to determine the for...

The Oxoid AnaeroGen system was compared with the BBL GasPak for the production of an anaerobic atmosphere and was evaluated for its ability to support the growth of 135 clinically significant anaerobic bacteria. An anaerobe chamber was used as the "gold standard" for supporting the growth of anaerobes. The AnaeroGen requires no catalyst, produces n...

Identification of anaerobic bacteria requires special media and growth conditions that contribute to a higher cost per identification than that for aerobic isolates. Newer rapid methods streamline the identification process, but confirmation to the species level is often difficult. The Presumpto Plate method for the identification of commonly encou...

The EZ Streak urine culture device (Difco Laboratories, Detroit, Mich.) combines the advantages of both the dip-slide and the classic urine culture technique, enabling bacterial enumeration and isolation following a simple inoculation step. Five hundred clean-catch urine specimens submitted by outpatients attending a health maintenance organization...

Bacteriophage typing (BT) (World Health Organization method) has been used at the Centers for Disease Control and Prevention for over 30 years to type isolates of Staphylococcus aureus. Since studies have shown that BT patterns have poor reproducibility and because BT fails to type a high percentage (15 to 20%) of isolates, the Centers for Disease...

We compared the accuracy of the An-IDENT system (bioMerieux Vitek, Inc., Hazelwood, Mo.) and the RapID ANA II system (Innovative Diagnostic Systems, Norcross, Ga.) with that of conventional biochemical tests for the identification of 85 strains of Actinomyces species. In our hands, the overall accuracy of the An-IDENT was 59% and that of the RapID...

The genus Citrobacter was recently determined to contain 11 genetically distinct species. In addition, the International Committee on Systematic Bacteriology no longer recognizes C. diversus and has, instead, validated the name C. koseri in its place. The 11 species are C. freundii, C. koseri, C. amalonaticus, C. farmeri, C. youngae, C. braakii, C....

A 4-year prospective study compared the accuracy of the STAPH-IDENT system (bioMérieux Vitek, Inc., Hazelwood, Mo.) with that of the reference procedure of the Centers for Disease Control and Prevention for the identification of Staphylococcus species, Stomatococcus mucilaginosus, and Micrococcus species. The study compared the results from 1,106 c...

Three extracting reagents were compared for effectiveness in the Ehrlich indole procedure: xylene (the recommended reagent), Hemo-De (a terpene-based product containing d-limonene), and Micro-Clear (an isoparaffinic hydrocarbon). Thirty-three strains representing 12 species of indole-positive aerobes or facultative anaerobes and 50 strains represen...

Nosocomial bloodstream infection is an important cause of morbidity and mortality among neonates. From September 1 through December 5, 1990 (epidemic period), gram-negative bacteremia developed in 26 neonates after their admission to the neonatal intensive care unit (NICU) of Hospital General, a 1000-bed public teaching hospital in Guatemala with a...

To assess the risk of acquisition of Pseudomonas cepacia by person-to-person transmission at cystic fibrosis summer camps, we conducted in 1990 a study at three camps attended by patients with cystic fibrosis who had P. cepacia infection and patients without P. cepacia infection but who were considered susceptible to infection. We obtained sputum o...

To assess the risk of acquisition of Pseudomonas cepacia by person-to-person transmission at cystic fibrosis summer camps, we conducted in 1990 a study at three camps attended by patients with cystic fibrosis who had P. cepacia infection and patients without P. cepacia infection but who were considered susceptible to infection. We obtained sputum o...

Fifty-nine Staphylococcus aureus isolates and 1 isolate of Staphylococcus intermedius were typed by investigators at eight institutions by using either antibiograms, bacteriophage typing, biotyping, immunoblotting, insertion sequence typing with IS257/431, multilocus enzyme electrophoresis, restriction analysis of plasmid DNA, pulsed-field or field...

We compared the API 20E (21 h) (API; bioMérieux Vitek, Hazelwood, Mo.), the Vitek GNI card (4 to 18 h) (Vitek; bioMérieux Vitek), the identification portion of the MicroScan Walk/Away Rapid Neg Combo 3 panel (2 h) (W/A; Baxter Diagnostics, Inc., West Sacramento, Calif.), and the Becton Dickinson Cobas Micro ID-E/NF rotor (21 h) (Cobas; Becton Dicki...

The Biolog Identification System (Biolog, Inc., Hayward, Calif.) was challenged at two separate laboratories with 113 coded isolates, including 33 type strains of staphylococci, 5 strains of Micrococcus spp., and 1 strain of Stomatococcus mucilaginosus. Test parameters between the sites were controlled as much as possible. Discrepancies were arbitr...

A multicenter trial of the Sensititre AP80 panel read on the Sensititre AutoReader (Radiometer America, Westlake, Ohio) for the automated identification of gram-negative bacilli was conducted with 1,023 clinical isolates (879 members of the family Enterobacteriaceae plus 144 nonenteric organisms). Assignment of taxa was based on the computer-assist...

A numerical-code system for the reference identification of Staphylococcus species, Stomatococcus mucilaginosus, and Micrococcus species was established by using a selected panel of conventional biochemicals. Results from 824 cultures (289 eye isolate cultures, 147 reference strains, and 388 known control strains) were used to generate a list of 35...

A cluster of six neonatal cases of coagulase-negative staphylococcal bacteremias occurred in a Los Angeles County neonatal intensive care unit in March 1989. A retrospective cohort study assessed the impact of host-and delivery-related variables, length of hospitalization, duration of antibiotic treatment, performance or duration of invasive proced...

Hospital-acquired infections in the United States contribute to approximately 80,000 deaths per year, with an associated cost of > $4 billion. Some of these infections are associated with outbreaks and clusters occurring within the hospital. The hospital infection control team must respond quickly and decisively to recognize and curtail these outbr...

We evaluated the ability of the Baxter autoSCAN-W/A System (MicroScan Division, Baxter Diagnostics, Inc., West Sacramento, Calif.) to use the rapid (2-h) gram-negative identification panel for accurate identification of members of the family Enterobacteriaceae. At 2 h, 353 of 467 (75.6%) strains in a challenge set of biochemically typical and atypi...