Validation of Methicillin-Resistant Staphylococcus aureus (MRSA) Risk Factors in Predicting MRSA Community-Acquired Pneumonia at an Academic Medical Center.

Background: The 2019 Infectious Diseases Society of America community-acquired pneumonia (CAP) guidelines recommend antimethicillin- resistant Staphylococcus aureus (MRSA) therapy in patients with CAP based on previously identified risk factors for MRSA with an emphasis on local epidemiology and institutional validation of risk. Thus, we sought to assess the ability of guideline-recognized risk factors to predict MRSA CAP at our institution. Methods: This was a single-center, retrospective cohort study from January 2016 to March 2020. Patients were included if they were >18 years old, diagnosed with CAP, and had a MRSA nasal screen and respiratory culture obtained on admission. Patients were excluded if CAP diagnosis was not met, respiratory cultures were not obtained within 48 hours of antibiotic initiation, or they had cystic fibrosis. Sensitivity, specificity, negative predictive value, positive predictive value, and likelihood ratios (LR) were calculated using Vasser Stats 2019. Pre/post-test odds and pre/post-test probabilities were calculated using Excel 2019. Results: Of 705 screened patients, 221 were included. MRSA prevalence in CAP patients at our institution was 3.6%. History of MRSA isolated from a respiratory specimen had high specificity (98%), high positive LR of 20 (95% CI 5.3-74.8), and high post-test probability of 42.8%. Receipt of IV antibiotics during hospitalization within the past 90 days had a positive LR of 1.9 (95% CI 0.74-4.84). A positive MRSA nasal screen on admission had a positive LR of 6.9 (95% CI 4.0-12.1), negative LR 0.28 (95% CI 0.08-0.93), positive post-test probability of 20.7%, and negative post-test probability of 1.04%. Conclusion: Our study utilized institutional data to validate guideline recognized risk factors for MRSA CAP specifically at our institution. Risk factors including history of MRSA isolated from a respiratory specimen, and positive post-admission MRSA nasal screen were validated as significant risk factors; receipt of IV antibiotics during hospitalization within the past 90 days was not shown to be a risk factor for MRSA CAP based on our institutional data. Validated risk factors may help providers discern which patients with CAP at our institution would benefit most from empiric MRSA treatment.

Development and Validation of Two RT-qPCR Diagnostic Assays for Detecting Severe Acute Respiratory Syndrome Coronavirus 2 Genomic Targets across Two Specimen Types.

Following the outbreak and subsequent pandemic of coronavirus disease 2019 (COVID-19), clinical diagnostic laboratories worldwide sought accurate and reliable testing methodologies. However, many laboratories were and still are hindered by a number of factors, including an unprecedented demand for testing, reagent and laboratory supply shortages and availability of qualified staff. To respond to these concerns, two separate laboratory-developed tests were validated for detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using two different specimen types. In addition, these assays target different genomic regions of SARS-CoV-2, allowing for viral detection and mitigating genetic variation. Lower limit of detection and clinical evaluation studies showed detection of SARS-CoV-2 at 500 cp/mL with nasopharyngeal and saliva samples. These multiplexed RT-qPCR assays, although based on modified CDC, New York State Department of Health, and World Health Organization Emergency Use Authorization tests, allow for higher throughput and rapid turnaround time, benefiting patients, clinicians, and communities as a whole. These cost-effective tests also use readily obtainable reagents, circumventing commercial assay supply chain issues. The laboratory-developed tests described here have improved patient care and are highly adaptable should the need arise at other clinical diagnostic laboratories. Furthermore, the foundation and design of these assays may be modified in the future for detection of COVID-19 variants or other RNA-based viral detection tests.

Impact of a pharmacist-facilitated, evidence-based bundle initiative on Staphylococcus aureus bacteremia management.

OBJECTIVE: To evaluate a pharmacist-facilitated evidence-based bundle (EBB) initiative with infectious disease consultation (IDC) for Staphylococcus aureus bacteremia (SAB). METHODS: This was a before-and-after quasi-experimental study of adult patients with SAB before and after the pharmacist-facilitated EBB initiative, which included IDC, timely definitive antibiotics, source control, echocardiography, and repeat blood cultures. RESULTS: Ninety and 111 patients were included in pre- and post-intervention cohorts, respectively. We observed significant increases in adherence to all 5 (4.4% vs 68.5%, P < 0.001) and 4 (10.0% vs 76.6%, P < 0.001) EBB elements. Time to definitive antibiotics (48 vs 16 hours, P < 0.001), time to IDC (43.5 vs 32 hours, P < 0.001), SAB duration (95 vs 66 hours, P = 0.009), persistent SAB (18.9% vs 9.0%, P = 0.041), and length of stay (14 vs 13 days, P = 0.027) also improved. No statistically significant differences for SAB-related readmission or all-cause mortality were observed. CONCLUSIONS: Our pharmacist-facilitated SAB initiative was associated with improved EBB adherence and clinical outcomes.

The New York State SARS-CoV-2 Testing Consortium: Regional Communication in Response to the COVID-19 Pandemic.

The COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2, created an unprecedented need for comprehensive laboratory testing of populations, in order to meet the needs of medical practice and to guide the management and functioning of our society. With the greater New York metropolitan area as an epicenter of this pandemic beginning in March 2020, a consortium of laboratory leaders from the assembled New York academic medical institutions was formed to help identify and solve the challenges of deploying testing. This report brings forward the experience of this consortium, based on the real-world challenges which we encountered in testing patients and in supporting the recovery effort to reestablish the health care workplace. In coordination with the Greater New York Hospital Association and with the public health laboratory of New York State, this consortium communicated with state leadership to help inform public decision-making addressing the crisis. Through the length of the pandemic, the consortium has been a critical mechanism for sharing experience and best practices in dealing with issues including the following: instrument platforms, sample sources, test performance, pre- and post-analytical issues, supply chain, institutional testing capacity, pooled testing, biospecimen science, and research. The consortium also has been a mechanism for staying abreast of state and municipal policies and initiatives, and their impact on institutional and laboratory operations. The experience of this consortium may be of value to current and future laboratory professionals and policy-makers alike, in dealing with major events that impact regional laboratory services.

Cefiderocol for treatment of an empyema due to extensively drug-resistant Pseudomonas aeruginosa: Clinical observations and susceptibility testing considerations.

Cefiderocol is a novel siderophore cephalosporin antibacterial with activity against carbapenem-resistant Gram-negative bacteria including Pseudomonas aeruginosa. We report a medically complex patient treated with compassionate use cefiderocol for an empyema caused by extensively drug-resistant P. aeruginosa as well as clinical considerations for cefiderocol use based on our findings. We observed a potential discordance in cefiderocol susceptibility testing results depending if disk diffusion or iron-depleted cation-adjusted Mueller Hinton Broth dilution is used. Furthermore, interpretative criteria differ between the Clinical Laboratory Standards Institute and United States Food and Drug Administration for P. aeruginosa, which makes cefiderocol interpretation potentially challenging for clinicians. We may have also observed selective pressure from prior cefiderocol exposure given the respective increases and decreases in MIC values and zone diameters for P. aeruginosa isolates following cefiderocol treatment. Additional data are needed to further describe cefiderocol use, susceptibility testing, and resistance development as real-world clinical use expands.

Determining the Impact of the Opioid Crisis on a Tertiary-Care Hospital in Central New York to Identify Critical Areas of Intervention in the Local Community.

BACKGROUND: Central New York has been afflicted by the heroin epidemic with an increase in overdose deaths involving opioids. OBJECTIVE: The objective of the study was to understand the epidemiology of hospitalizations related to a diagnosis of opioid use (OU). DESIGN: The study was designed as a retrospective analysis of hospitalized patients admitted from January 1, 2008, to December 30, 2018, using ICD-9 and 10 codes for heroin or opiate use, overdose, or poisoning. Setting. The study was conducted in a tertiary-care and teaching hospital located in Central New York. Patients. Hospitalized patients were included as study participants. RESULTS: Opioid use-related admissions increased from .05/100 hospital admissions in 2008 to a peak of 2.9/100 in 2018, a 58-fold increase. There were 49 deaths over the 11-year period for an overall case fatality of 1.2 per 100 OU admissions. The median age for all years was 40 years (SD of 13.7 years), and admissions were largely white caucasians (67.0% of all admissions). The mean length of stay was 8.55 days (SD 12 days), with a range of 1 to 153 days. The most frequent discharge diagnosis was due to infections (15.0% of discharge diagnoses) followed by trauma (5.8% of discharge diagnoses). Methicillin-resistant Staphylococcus aureus was more common in patients with OU (58.1%) than in patients with non-OU (43%) (p < 0.0001 by chi-square with Yates' correction). Spatial analysis was performed by zip code and demonstrated regional hotspots for OU-related admissions. Limitations. The limitations of this study are its retrospective nature and largely numerator-based analysis. The use of ICD codes underrepresents the true burden due to underreporting and failure to code appropriately. This study focuses on patients who are hospitalized for a medical reason with a secondary diagnosis of opioid use and does not include patients who present to the emergency room with an overdose underrepresenting the true burden of the problem. CONCLUSIONS: Our results demonstrate the impact of the opioid epidemic in one tertiary-care center and the need to prepare for the costs and resources to address addiction care for this population.

Molecular Epidemiology of Invasive Staphylococcus aureus Infections and Concordance with Colonization Isolates.

OBJECTIVES: To characterize Staphylococcus aureus isolates recovered from hospitalized children and to determine the concordance between colonizing and invasive isolates. STUDY DESIGN: Children with culture-confirmed, community-onset, invasive S aureus infections were enrolled in this prospective case series from a large children's hospital over a 5-year period. Colonization isolates were obtained from the anterior nares, oropharynx, and inguinal folds and were compared with invasive isolates via repetitive-element, sequence-based polymerase chain reaction testing. Isolates with a ≥96% genetic match were characterized as concordant. RESULTS: A total of 86 S aureus isolates (44 invasive, 42 colonization) were collected from 44 children with invasive infections. Clinical isolates were genetically diverse, 64% of invasive isolates were methicillin-susceptible S aureus (MSSA), and 59% of cases had a colonizing S aureus isolate at the time of hospitalization. Of those who were colonized, at least 1 of their colonization isolates was indistinguishable from the infecting isolate in 88% of cases. Patients with invasive MSSA were significantly more likely to have a concordant MSSA colonization isolate present compared with patients with invasive methicillin-resistant S aureus (MRSA) (61% vs 38%, P < .05). CONCLUSIONS: Invasive MSSA infection was more common than MRSA infection in this pediatric cohort, and patients with MSSA infection were significantly more likely than those with MRSA infection to have concordant colonizing isolates across multiple anatomic sites. These findings warrant larger scale validation and may have important infection control and epidemiologic implications, as unlike MRSA, transmissibility of MSSA largely is ignored in healthcare settings.

Streptococcus anginosus Group Bacterial Infections.

BACKGROUND: The Streptococcus anginosus group (SAG) causes a variety of infections in adults. To better understand the burden of SAG infections and their associated morbidity and mortality, we conducted a retrospective analysis of these infections in adults at a tertiary care center. METHODS: A retrospective review of all cultures positive for SAG in adults and a corresponding review of the patients' medical records were conducted at a tertiary care facility in central New York. Patients with these cultures during the period of January 2007-December 2011 were included. Demographic data, area of residence, clinical features and underlying illnesses, site of infection, length of hospital stay, antibiotic susceptibility and antibiotic therapy were recorded and analyzed. RESULTS: There were 332 SAG cases; most patients were males (59%), mean age of 47 years and 84% lived in urban areas. Overall mortality was 3% with underlying conditions common such as diabetes (25%), hypertension (31%) and immunodeficiency (22%). Most of the infections were related to skin and soft tissue (72%) and polymicrobial (70%) with gram-negative anaerobes and Enterobacteriaceae commonly isolated with SAG. CONCLUSIONS: We present the largest study, thus far, reviewing the clinical presentation, management and outcome of infections due to the SAG of organisms. Notable findings from our study are the low mortality associated with SAG infection, and the propensity to present as a skin and tissue and polymicrobial infection. Our findings will assist clinicians in managing patients with SAG infections and recognizing that S anginosus may be one of several organisms responsible for infection.

Unrecognized viral respiratory tract infections in premature infants during their birth hospitalization: a prospective surveillance study in two neonatal intensive care units.

OBJECTIVE: To determine the frequency and effects of nosocomial respiratory viral infections (RVIs) in premature neonates, including those who may be asymptomatic. STUDY DESIGN: We performed a year-long surveillance for RVIs in infants <33 weeks gestational age admitted to 2 Syracuse neonatal intensive care units. Infants were enrolled within 3 days of neonatal intensive care unit admission and were sampled for RVIs until discharge using a multiplex polymerase chain reaction assay capable of detecting 17 different respiratory viruses or subtypes. RESULTS: Twenty-six of 50 prematurely born infants (52%) tested positive for a respiratory virus at least once during their birth hospitalization. Testing positive for a respiratory virus was significantly associated with longer length of stay (70 days vs 35 days, P = .002) and prolonged ventilatory support (51 vs 13 days, P = .002). Infants who tested positive for a respiratory virus during their birth hospitalization had more than twice the rate of developing bronchopulmonary dysplasia (P < .05). CONCLUSION: Nosocomial RVIs were frequent in our study population, despite the absence of clinical indicators of illness. Length of hospital stay was significantly longer and a diagnosis of bronchopulmonary dysplasia was more common in infants who had respiratory viruses detected.

High fecal hand contamination among wilderness hikers.

Information about hand hygiene and fecal hand contamination among the general public is limited. Hands are an important vector in transmission of various pathogenic bacteria. We found high (31%) prevalence of fecal hand contamination among healthy adults engaged in hiking.

Actinomyces meyeri infection: case report and review of the literature.

Actinomyces meyeri is an uncommon cause of actinomycosis. We present a patient with pneumonia and empyema due to A. meyeri. The patient underwent open thoracotomy with decortication and was discharged home on a twelve-month course of oral penicillin. Review of the English literature revealed thirty-two cases of infection due to A. meyeri. The majority of patients were male, and a significant number had poor dental hygiene and a history of alcoholism. More than other Actinomyces species, A. meyeri causes pulmonary infection and has a predilection for dissemination. Prognosis is favorable with prolonged penicillin therapy combined with surgical debridement, if needed.

Viral etiology of acute febrile respiratory illnesses in hospitalized children younger than 24 months.

BACKGROUND: Respiratory infections are a leading cause of pediatric hospitalizations. This study investigated whether virus-virus or virus-Bordetella co-infections are more frequent or more severe than previously recognized. METHODS: This is a 3-year prospective study of children younger than 24 months hospitalized with a febrile respiratory illness. Viral pathogens were detected using multiplex polymerase chain reaction (PCR), enzyme-linked immunoassays, and/or viral cultures from nasopharyngeal samples. Bordetella infections were detected by PCR. RESULTS: A total of 201 patients were enrolled. Respiratory viruses were detected in 187 (93%) patients, with 52 (28%) multipathogen infections. The most common viruses detected were respiratory syncytial virus and rhinovirus/enterovirus. There were no differences in illness severity when comparing patients infected with one pathogen and those with multipathogen infection. CONCLUSION: Virus co-infection in young children hospitalized with an acute febrile respiratory infection is common but does not appear to be associated with illness severity.

Empyema of preexisting subdural hemorrhage caused by a rare salmonella species after exposure to bearded dragons in a foster home.

An infant had a subdural empyema caused by the rare Salmonella species enterica subspecies houtenae (IV) serotype 44:z4,z23:- after only indirect exposure to exotic reptiles in her foster home. Infants recovering from preexisting subdural hematoma are at risk for development of empyema.

Incidence of invasive community-onset Staphylococcus aureus infections in children in Central New York.

We determined the incidence of invasive community-onset Staphylococcus aureus infections, clinical characteristics, and antibiotic susceptibilities in 128 hospitalized children in central New York. The prevalence of invasive S aureus infections in our institution remained <1% between 1996 and 2006, although the proportion of methicillin-resistant S aureus infections significantly increased.

Nosocomial contamination of laryngoscope handles: challenging current guidelines.

BACKGROUND: Laryngoscope blades are often cleaned between cases according to well-defined protocols. However, despite evidence that laryngoscope handles could be a source of nosocomial infection, neither our institution nor the American Society of Anesthesiologists has any specific guidelines for handle disinfection. We hypothesized that laryngoscope handles may be sufficiently contaminated with bacteria and viruses to justify the implementation of new handle-cleaning protocols. METHODS: Sixty laryngoscope handles from the adult operating rooms were sampled with premoistened sterile swabs. Collection was performed between cases, in operating rooms hosting a broad variety of subspecialty procedures, after the room and equipment had been thoroughly cleaned for the subsequent case. Samples from 40 handles were sent for aerobic bacterial culture, and antimicrobial susceptibility testing was performed for significant isolates. Samples from 20 handles were examined for viral contamination using a polymerase chain reaction assay that detects 17 respiratory viruses. RESULTS: Of the 40 samples sent for culture, 30 (75%) were positive for bacterial contamination. Of these positive cultures, 25 (62.5%) yielded coagulase-negative staphylococci, seven (17.5%) Bacillusspp. not anthracis, three (7.5%) alpha-hemolytic Streptococcusspp., and one each (2.5%) of Enterococcusspp., Staphylococcus aureus(S. aureus), and Corynebacteriumspp. No vancomycin-resistant enterococci, methicillin-resistant S. aureus, or Gram-negative rods were detected. All viral tests were negative. CONCLUSION: We found a high incidence of bacterial contamination of laryngoscope handles despite low-level disinfection. However, no vancomycin-resistant enterococci, methicillin-resistant S. aureus, Gram-negative rods, or respiratory viruses were detected. Our results support adoption of guidelines that include, at a minimum, mandatory low-level disinfection of laryngoscope handles after each patient use.

Pseudomonas aeruginosa acute prostatitis and urosepsis after sexual relations in a hot tub.

We report a case of a previously healthy 38-year-old male with acute prostatitis and concurrent Pseudomonas aeruginosa urosepsis. Pulsed-field gel electrophoresis analysis confirmed that the source of the organism was the patient's newly purchased hot tub, which was filled with water from a stream.

Dipylidium caninum mimicking recurrent enterobius vermicularis (pinworm) infection.

Pinworm infection is a very common diagnosis in young children that is not always confirmed through laboratory evaluation before empiric therapy is prescribed. This article describes a toddler who was treated several times for pinworms because small white worms were seen in her perianal area. Laboratory analysis of parasite material found in her diaper later confirmed a diagnosis of dipylidiasis. Because the signs of dipylidiasis and pinworm infection overlap and the treatments for these parasitic infections are different, the laboratory should clinically confirm suspected persistent or recurrent pinworms.

An outbreak of multidrug-resistant Acinetobacter baumannii-calcoaceticus complex infection in the US military health care system associated with military operations in Iraq.

BACKGROUND: We investigated an outbreak of multidrug-resistant Acinetobacter baumannii-calcoaceticus complex infection among US service members injured in Iraq. METHODS: The investigation was conducted in Iraq and Kuwait, in the 2 military hospitals where the majority of injured service members were initially treated. After initially characterizing the outbreak, we evaluated 3 potential sources of infection for the period March 2003 to December 2004. The evaluation included screening samples that were obtained from the skin of patients for the presence of colonization and assessing the soil and health care environments for the presence of A. baumanii-calcoaceticus complex organisms. Isolates obtained from samples from patients in US Military treatment facilities, as well as environmental isolates, were genotypically characterized and compared using pulsed-field gel electrophoresis. RESULTS: A. baumanii-calcoaceticus complex organisms were present on the skin in only 1 (0.6%) of 160 patients who were screened and in 1 (2%) of 49 soil samples. A. baumanii-calcoaceticus complex isolates were recovered from treatment areas in 7 of the 7 field hospitals sampled. Using pulsed-field gel electrophoresis, we identified 5 cluster groups in which isolates from patients were related to environmental isolates. One cluster included hospitalized patients who had not been deployed to Iraq. Among the clinical isolates, only imipenem, polymyxin B, and colistin demonstrated reliable in vitro antimicrobial activity. Generally, the environmental isolates were more drug susceptible than were the clinical isolates. CONCLUSIONS: Our findings suggest that environmental contamination of field hospitals and infection transmission within health care facilities played a major role in this outbreak. On the basis of these findings, maintaining infection control throughout the military health care system is essential. Novel strategies may be required to prevent the transmission of pathogens in combat field hospitals.