Mitigation of nontuberculous mycobacteria in hospital water: challenges for infection prevention.

PURPOSE OF REVIEW: The purpose of this review is to summarize recent literature on nontuberculous mycobacteria in water of healthcare systems. Despite improvement in identification techniques and emergence of infection prevention and control programs, nontuberculous mycobacteria remain present in hospital water systems, causing outbreaks and pseudo-outbreaks in healthcare settings. RECENT FINDINGS: Waterborne outbreaks and pseudo-outbreaks of nontuberculous mycobacteria continue to affect hospitals. Improvements in methods of identification and investigation, including MALDI-TOF and whole genome sequencing with evaluation of single nucleotide polymorphisms, have been used successfully in outbreak and pseudo-outbreak investigations. Recent studies have shown control of outbreaks in immunocompromised patients through the use of sterile water for consumption, as well as control of pseudo-outbreaks by using sterile water for procedures. Construction activities have been implicated in outbreaks and pseudo-outbreaks of nontuberculous mycobacteria. Water management programs are now required by the Joint Commission, which will likely improve water risk mitigation. SUMMARY: Improvement in detection and identification of nontuberculous mycobacteria has led to increasing recognition of waterborne outbreaks and pseudo-outbreaks. Water management programs are of vital importance in infection prevention.

Mycobacterium chimaera left ventricular assist device infections.

A global outbreak of invasive Mycobacterium chimaera infections after cardiac surgery has recently been linked to bioaerosols from contaminated heater-cooler units. The majority of cases have occurred after valvular surgery or aortic graft surgery and nearly half have resulted in death. To date, infections in patients with left ventricular assist devices (LVADs) have not been characterized in the literature. We report two cases of device-associated M. chimaera infection in patients with continuous-flow LVADs and describe challenges related to diagnosis and management in this population.

Expanded Gram-Negative Antimicrobial Prophylaxis Reduces Surgical Site Infections in Hip Arthroplasty.

BACKGROUND: A first-generation cephalosporin is the recommended antibiotic prophylaxis for implants. However, this standard does not address the increasing prevalence and virulence of gram-negative pathogens infecting patients. We found that gram-negative bacilli caused 30% of our surgical site infections (SSIs) following hip procedures, whereas only 10% of knee SSIs were caused by gram-negative bacilli. To address this, we instituted Expanded Gram-Negative Antimicrobial Prophylaxis (EGNAP) for our hip arthroplasty patients. The purpose of this study is to measure the effect of EGNAP on the SSI rates following primary total hip arthroplasty. METHODS: The study consisted of 10,084 total patients. Before July 2012, all patients were administered 1 g of cefazolin. After July 2012, our protocol was adjusted by adding the EGNAP with either gentamicin or aztreonam to hip patients (group 1) and not to the knee arthroplasty patients (group 2). RESULTS: Group 1 consisted of the 5389 primary hip arthroplasty patients. Of these patients, 4122 (before July 2012) did not receive weight-based high-dose gentamicin and 1267 (after July 2012) did. Before the introduction of EGNAP, group 1 SSI rate was 1.19% (49/4122). After July 2012 when EGNAP was added, the overall group 1 SSI rate decreased to 0.55% (7/1267) (P = .05). During the study period, there was not a significant difference in SSI rate of knee arthroplasty (group 2): 1.08% vs 1.02% (P = .999). CONCLUSIONS: The addition of EGNAP for hip arthroplasty is a safe and effective method to decrease SSIs. LEVEL OF EVIDENCE: III. Case-control study.

Is routine antibiotic prophylaxis cost effective for total joint replacement patients?

The routine use of amoxicillin antibiotic prophylaxis prior to dental procedures for patients with total joint prostheses in place remains controversial. This analysis shows that the practice may not be cost-effective for patients in whom the risk of infection with dental work is low. However, specific data quantifying the risk and the impact prophylactic antibiotics can have is needed. Patients and physicians will need to continue to consider their use on an individual basis and should consider the risk of infection as well as the risk of adverse drug reaction when making treatment decisions.

Risk Factors for Infection Following Total Knee Arthroplasty: A Series of 3836 Cases from One Institution.

Higher PJI rates may be related to identifiable risk factors, which may or may not be modifiable. Identifying risk factors preoperatively provides opportunities for modification and potentially decreasing the incidence of PJI. The purposes of this study were to: (1) retrospectively identify and quantify risk factors for PJI following primary TKA, and (2) to classify those significant risk factors as either non-modifiable or modifiable for intervention prior to surgery. Optimization of modifiable risk factors such as Staphylococcus aureus colonization, and tobacco use prior to primary TKA may decrease the incidence of periprosthetic joint infection after primary TKA, thereby reducing morbidity and the costs associated with treating those infections.

Extended-Infusion versus standard-infusion piperacillin-tazobactam for sepsis syndromes at a tertiary medical center.

Piperacillin-tazobactam (PTZ) is frequently used as empirical and targeted therapy for Gram-negative sepsis. Time-dependent killing properties of PTZ support the use of extended-infusion (EI) dosing; however, studies have shown inconsistent benefits of EI PTZ treatment on clinical outcomes. We performed a retrospective cohort study of adult patients who received EI PTZ treatment and historical controls who received standard-infusion (SI) PTZ treatment for presumed sepsis syndromes. Data on mortality rates, clinical outcomes, length of stay (LOS), and disease severity were obtained. A total of 843 patients (662 with EI treatment and 181 with SI treatment) were available for analysis. Baseline characteristics of the two groups were similar, except for fewer female patients receiving EI treatment. No significant differences between the EI and SI groups in inpatient mortality rates (10.9% versus 13.8%; P = 0.282), overall LOS (10 versus 12 days; P = 0.171), intensive care unit (ICU) LOS (7 versus 6 days; P = 0.061), or clinical failure rates (18.4% versus 19.9%; P = 0.756) were observed. However, the duration of PTZ therapy was shorter in the EI group (5 versus 6 days; P < 0.001). Among ICU patients, no significant differences in outcomes between the EI and SI groups were observed. Patients with urinary or intra-abdominal infections had lower mortality and clinical failure rates when receiving EI PTZ treatment. We did not observe significant differences in inpatient mortality rates, overall LOS, ICU LOS, or clinical failure rates between patients receiving EI PTZ treatment and patients receiving SI PTZ treatment. Patients receiving EI PTZ treatment had a shorter duration of PTZ therapy than did patients receiving SI treatment, and EI dosing may provide cost savings to hospitals.

Factors associated with loss to follow-up in outpatient parenteral antimicrobial therapy: A retrospective cohort study.

We assessed factors associated with increased risk to loss of follow-up with infectious diseases staff in OPAT patients. Discharge to subacute healthcare facilities is strongly associated with loss to follow-up. We did not identify sociodemographic disparities. Poor communication between OPAT providers and subacute healthcare facilities remains a serious issue.

Characterization of Y chromosome diversity in newfoundland and labrador: evidence for a structured founding population.

The population of Newfoundland and Labrador (NL) is largely derived from settlers who migrated primarily from England and Ireland in the 1700s-1800s. Previously described as an isolated founder population, based on historical and demographic studies, data on the genetic ancestry of this population remains fragmentary. Here we describe the largest investigation of patrilineal ancestry in NL. To determine the paternal genetic structure of the population, 1,110 Y chromosomes from an NL-based cohort were analyzed using 5,761 Y-specific SNPs. We identified 160 distinct terminal haplogroups, the majority of which (71.4%) belong to the R1b haplogroup. When compared with global reference populations, the NL population haplogroup composition and frequencies primarily resemble those observed in English and Irish ancestral source populations. There is also evidence of genetic contributions from Basque, French, Portuguese, and Spanish fishermen and early settlers who frequented NL. Interestingly, the observed population structure shows geographical and religious clustering that can be associated with the settlement of the ancestral source populations from predominantly Protestant, England, and Catholic, Ireland respectively. For example, the R1b-M222 haplogroup, seen in people of Irish descent, is found clustered in the Irish-settled Southeast region of NL. The clustering and expansion of Y haplogroups in conjunction with the geographical and religious clusters illustrate that limited subsequent in-migration, geographic isolation, and societal factors have contributed to the genetic substructure of the NL population and its designation as a founder population.

Risk factors for treatment failure of polymyxin B monotherapy for carbapenem-resistant Klebsiella pneumoniae infections.

Polymyxins are reserved for salvage therapy of infections caused by carbapenem-resistant Klebsiella pneumoniae (CRKP). Though synergy has been demonstrated for the combination of polymyxins with carbapenems or tigecycline, in vitro synergy tests are nonstandardized, and the clinical effect of synergy remains unclear. This study describes outcomes for patients with CRKP infections who were treated with polymyxin B monotherapy. We retrospectively reviewed the medical records of patients with CRKP infections who received polymyxin B monotherapy from 2007 to 2011. Clinical, microbiology, and antimicrobial treatment data were collected. Risk factors for treatment failure were identified by logistic regression. Forty patients were included in the analysis. Twenty-nine of 40 (73%) patients achieved clinical cure as defined by clinician-documented improvement in signs and symptoms of infections, and 17/32 (53%) patients with follow-up culture data achieved microbiological cure. End-of-treatment mortality was 10%, and 30-day mortality was 28%. In a multivariate analysis, baseline renal insufficiency was associated with a 6.0-fold increase in clinical failure after adjusting for septic shock (odds ratio [OR] = 6.0; 95% confidence interval [CI] = 1.22 to 29.59). Breakthrough infections with organisms intrinsically resistant to polymyxins occurred in 3 patients during the treatment. Eighteen of 40 (45%) patients developed a new CRKP infection a median of 23 days after initial polymyxin B treatment, and 3 of these 18 infections were polymyxin resistant. The clinical cure rate achieved in this retrospective study was 73% of patients with CRKP infections treated with polymyxin B monotherapy. Baseline renal insufficiency was a risk factor for treatment failure after adjusting for septic shock. Breakthrough infections with organisms intrinsically resistant to polymyxin B and development of resistance to polymyxin B in subsequent CRKP isolates are of concern.

De novo mutations in FOXP1 in cases with intellectual disability, autism, and language impairment.

Heterozygous mutations in FOXP2, which encodes a forkhead transcription factor, have been shown to cause developmental verbal dyspraxia and language impairment. FOXP2 and its closest homolog, FOXP1, are coexpressed in brain regions that are important for language and cooperatively regulate developmental processes, raising the possibility that FOXP1 may also be involved in developmental conditions that are associated with language impairment. In order to explore this possibility, we searched for mutations in FOXP1 in patients with intellectual disability (ID; mental retardation) and/or autism spectrum disorders (ASD). We first performed array-based genomic hybridization on sporadic nonsyndromic ID (NSID) (n = 30) or ASD (n = 80) cases. We identified a de novo intragenic deletion encompassing exons 4-14 of FOXP1 in a patient with NSID and autistic features. In addition, sequencing of all coding exons of FOXP1 in sporadic NSID (n = 110) or ASD (n = 135) cases, as well as in 570 controls, revealed the presence of a de novo nonsense mutation (c.1573C>T [p.R525X]) in the conserved forkhead DNA-binding domain in a patient with NSID and autism. Luciferase reporter assays showed that the p.R525X alteration disrupts the activity of the protein. Formal assessments revealed that both patients with de novo mutations in FOXP1 also show severe language impairment, mood lability with physical aggressiveness, and specific obsessions and compulsions. In conclusion, both FOXP1 and FOXP2 are associated with language impairment, but decrease of the former has a more global impact on brain development than that of the latter.

The effects of human population structure on large genetic association studies.

Large-scale association studies hold substantial promise for unraveling the genetic basis of common human diseases. A well-known problem with such studies is the presence of undetected population structure, which can lead to both false positive results and failures to detect genuine associations. Here we examine approximately 15,000 genome-wide single-nucleotide polymorphisms typed in three population groups to assess the consequences of population structure on the coming generation of association studies. The consequences of population structure on association outcomes increase markedly with sample size. For the size of study needed to detect typical genetic effects in common diseases, even the modest levels of population structure within population groups cannot safely be ignored. We also examine one method for correcting for population structure (Genomic Control). Although it often performs well, it may not correct for structure if too few loci are used and may overcorrect in other settings, leading to substantial loss of power. The results of our analysis can guide the design of large-scale association studies.

The Effectiveness of Ultraviolet Smart D60 in Reducing Contamination of Flexible Fiberoptic Laryngoscopes.

OBJECTIVE: To compare the effectiveness of disinfection protocols utilizing a ultraviolet (UV) Smart D60 light system with Impelux™ technology with a standard Cidex ortho-phthalaldehyde (OPA) disinfection protocol for cleaning flexible fiberoptic laryngoscopes (FFLs). METHODS: Two hundred FFLs were tested for bacterial contamination after routine use, and another 200 FFLs were tested after disinfection with one of four methods: enzymatic detergent plus Cidex OPA (standard), enzymatic detergent plus UV Smart D60, microfiber cloth plus UV Smart D60, and nonsterile wipe plus UV Smart D60. Pre- and post-disinfection microbial burden levels and positive culture rates were compared using Kruskal-Wallis ANOVA and Fisher's two-sided exact, respectively. RESULTS: After routine use, approximately 56% (112/200) of FFLs were contaminated, with an average contamination level of 9,973.7 ± 70,136.3 CFU/mL. The standard reprocessing method showed no positive cultures. The enzymatic plus UV, microfiber plus UV, and nonsterile wipe plus UV methods yielded contamination rates of 4% (2/50), 6% (3/50), and 12% (6/50), respectively, with no significant differences among the treatment groups (p > 0.05). The pre-disinfection microbial burden levels decreased significantly after each disinfection technique (p < 0.001). The average microbial burden recovered after enzymatic plus UV, microfiber plus UV, and nonsterile wipe plus UV were 0.40 CFU/mL ± 2, 0.60 CFU/mL ± 2.4, and 12.2 CFU/mL ± 69.5, respectively, with no significant difference among the treatment groups (p > 0.05). Micrococcus species (53.8%) were most frequently isolated, and no high-concern organisms were recovered. CONCLUSION: Disinfection protocols utilizing UV Smart D60 were as effective as the standard chemical disinfection protocol using Cidex OPA. LEVEL OF EVIDENCE: NA Laryngoscope, 133:3512-3519, 2023.

Planetary Mapping Using Deep Learning: A Method to Evaluate Feature Identification Confidence Applied to Habitats in Mars-Analog Terrain.

The goals of Mars exploration are evolving beyond describing environmental habitability at global and regional scales to targeting specific locations for biosignature detection, sample return, and eventual human exploration. An increase in the specificity of scientific goals-from follow the water to find the biosignatures-requires parallel developments in strategies that translate terrestrial Mars-analog research into confident identification of rover-explorable targets on Mars. Precisely how to integrate terrestrial, ground-based analyses with orbital data sets and transfer those lessons into rover-relevant search strategies for biosignatures on Mars remains an open challenge. Here, leveraging small Unmanned Aerial System (sUAS) technology and state-of-the-art fully convolutional neural networks for pixel-wise classification, we present an end-to-end methodology that applies Deep Learning to map geomorphologic units and quantify feature identification confidence. We used this method to assess the identification confidence of rover-explorable habitats in the Mars-analog Salar de Pajonales over a range of spatial resolutions and found that spatial resolutions two times better than are available from Mars would be necessary to identify habitats in this study at the 1-σ (85%) confidence level. The approach we present could be used to compare the identifiability of habitats across Mars-analog environments and focus Mars exploration from the scale of regional habitability to the scale of specific habitats. Our methods could also be adapted to map dome- and ridge-like features on the surface of Mars to further understand their origin and astrobiological potential.

PharmVar Tutorial on CYP2D6 Structural Variation Testing and Recommendations on Reporting.

The Pharmacogene Variation Consortium (PharmVar) provides nomenclature for the highly polymorphic human CYP2D6 gene locus and a comprehensive summary of structural variation. CYP2D6 contributes to the metabolism of numerous drugs and, thus, genetic variation in its gene impacts drug efficacy and safety. To accurately predict a patient's CYP2D6 phenotype, testing must include structural variants including gene deletions, duplications, hybrid genes, and combinations thereof. This tutorial offers a comprehensive overview of CYP2D6 structural variation, terms, and definitions, a review of methods suitable for their detection and characterization, and practical examples to address the lack of standards to describe CYP2D6 structural variants or any other pharmacogene. This PharmVar tutorial offers practical guidance on how to detect the many, often complex, structural variants, as well as recommends terms and definitions for clinical and research reporting. Uniform reporting is not only essential for electronic health record-keeping but also for accurate translation of a patient's genotype into phenotype which is typically utilized to guide drug therapy.

The Newfoundland and Labrador mosaic founder population descends from an Irish and British diaspora from 300 years ago.

The founder population of Newfoundland and Labrador (NL) is a unique genetic resource, in part due to its geographic and cultural isolation, where historical records describe a migration of European settlers, primarily from Ireland and England, to NL in the 18th and 19th centuries. Whilst its historical isolation, and increased prevalence of certain monogenic disorders are well appreciated, details of the fine-scale genetic structure and ancestry of the population are lacking. Understanding the genetic origins and background of functional, disease causing, genetic variants would aid genetic mapping efforts in the Province. Here, we leverage dense genome-wide SNP data on 1,807 NL individuals to reveal fine-scale genetic structure in NL that is clustered around coastal communities and correlated with Christian denomination. We show that the majority of NL European ancestry can be traced back to the south-east and south-west of Ireland and England, respectively. We date a substantial population size bottleneck approximately 10-15 generations ago in NL, associated with increased haplotype sharing and autozygosity. Our results reveal insights into the population history of NL and demonstrate evidence of a population conducive to further genetic studies and biomarker discovery.

PRKCB is associated with calcineurin inhibitor-induced renal dysfunction in heart transplant recipients.

OBJECTIVES: Single nucleotide polymorphisms (SNPs) in the transforming growth factor-ß1 gene (TGFB1) have been inconsistently associated with calcineurin inhibitor (CNI)-induced renal dysfunction following cardiac transplantation. The impact of genetic variants related to the renin-angiotensin-aldosterone system (RAAS) and natriuretic peptides, which are implicated in CNI nephrotoxicity, is unknown. The primary objective of this study was to validate the association between two common variants in TGFB1 (rs1800470, rs1800471) and postcardiac transplant renal function. The secondary objective was to investigate the effect of candidate genes related to the RAAS, natriuretic peptides, and other elements involved in the intracellular signaling of these pathways. METHODS: We conducted a retrospective cohort study of 158 heart transplant recipients treated with CNIs, and evaluated the association between select SNPs and the estimated glomerular filtration rate as calculated by the Modification of Diet in Renal Disease simplified formula. A total of 273 SNPs distributed in 44 genes were tested. RESULTS: No association was observed between TGFB1 variants and renal function. One polymorphism in the protein kinase C-ß gene (PRKCB; rs11074606), which is implicated in the RAAS intracellular signaling, was significantly associated with post-transplant estimated glomerular filtration rate after adjusting for possible confounders (P=0.00049). This marker is in linkage disequilibrium with two variants located in putative regulatory regions of the gene (rs2283541, rs1013316). CONCLUSION: Our results suggest that PRKCB may be a potential predictor of CNI-induced nephrotoxicity in heart transplant recipients, and could therefore be a promising candidate to identify patients who are most susceptible to this adverse drug reaction.

The persistence of Staphylococcus aureus decolonization after mupirocin and topical chlorhexidine: implications for patients requiring multiple or delayed procedures.

Preoperative screening and decolonization of methicillin-sensitive and methicillin-resistant Staphylococcus aureus (MSSA and MRSA, respectively) are advocated to reduce surgical site infections. We determined the rate and duration of decolonization in patients undergoing elective orthopedic surgery. Patients undergoing elective orthopedic surgery were seen in our preoperative testing program (PAT) and had their anterior nares cultured for MRSA and MSSA. All patients were treated with intranasal mupirocin and a topical chlorhexidine solution. A cohort of patients returned to PAT before a subsequent elective procedure and were recultured. All culture results and time between PAT visits were recorded, and the rates of successful initial and persistent decolonization were determined. Six hundred ten patients visited PAT 1290 times. Overall, 94 (70.1%) of 134 patients with initially MRSA- or MSSA-positive cultures remained decolonized at a mean time of 156 days (SD=140), whereas 40 patients (29.9%) were not decolonized by the time of repeat testing at a mean time of 213 days (SD=187). At repeat testing, there were 2 newly MRSA-positive and 35 newly MSSA-positive patients. Staphylococcus aureus decolonization with intranasal mupirocin and topical chlorhexidine was effective but not persistent in a significant proportion of patients. A small number of previously uncolonized patients became colonized. Staphylococcus aureus screening and decolonization protocols must be repeated before any readmission, regardless of prior colonization status.

Assessment of risk factors associated with outpatient parenteral antimicrobial therapy (OPAT) complications: A retrospective cohort study.

Objective: To characterize factors associated with increased risk of outpatient parenteral antimicrobial therapy (OPAT) complication. Design: Retrospective cohort study. Setting: Four hospitals within NYU Langone Health (NYULH). Patients: All patients aged ≥18 years with OPAT episodes who were admitted to an acute-care facility at NYULH between January 1, 2017, and December 31, 2020, who had an infectious diseases consultation during admission. Results: Overall, 8.45% of OPAT patients suffered a vascular complication and 6.04% suffered an antimicrobial complication. Among these patients, 19.95% had a 30-day readmission and 3.35% had OPAT-related readmission. Also, 1.58% of patients developed a catheter-related bloodstream infection (CRBSI). After adjusting for key confounders, we found that patients discharged to a subacute rehabilitation center (SARC) were more likely to develop a CRBSI (odds ratio [OR], 4.75; P = .005) and to be readmitted for OPAT complications (OR, 2.89; P = .002). Loss to follow-up with the infectious diseases service was associated with increased risks of CRBSI (OR, 3.78; P = .007) and 30-day readmission (OR, 2.59; P < .001). Conclusions: Discharge to an SARC is strongly associated with increased risks of readmission for OPAT-related complications and CRBSI. Loss to follow-up with the infectious diseases service is strongly associated with increased risk of readmission and CRBSI. CRBSI prevention during SARC admission is a critically needed public health intervention. Further work must be done for patients undergoing OPAT to improve their follow-up retention with the infectious diseases service.

Cost-effectiveness of a Staphylococcus aureus screening and decolonization program for high-risk orthopedic patients.

We conducted a Markov decision analysis to assess the cost savings associated with a preoperative Staphylococcus aureus screening and decolonization program on 365 hip and knee arthroplasties and 287 spine fusions. A 2-way sensitivity analysis was also used to calculate the needed reduction in surgical site infections to make the program cost saving. If cost of treating an infected hip or knee arthroplasty is equal to the cost of a primary knee arthroplasty, then the screening program needs to result in a 35% reduction in the revision rate, or a relative revision rate of 65% for patients in the screening program, to be cost saving. For spine fusions, the reduction in the revision rate to make the program cost saving is only 10%. Universal Staphylococcus aureus screening and decolonization for hip and knee arthroplasty and spinal fusion patients needs to result in only a modest reduction in the surgical site infection rate to be cost saving.

Rate and consequences of missed Clostridioides (Clostridium) difficile infection diagnosis from nonreporting of Clostridioides difficile results of the multiplex GI PCR panel: experience from two-hospitals.

INTRODUCTION: It is common among microbiology laboratories to blind the Clostridioides difficile (C. difficile) BioFire FilmArray GI Panel result in fear of overdiagnosis. METHODS: We examined the rate of missed community-onset C. difficile infection (CDI) diagnosis and associated outcomes. Adult patients with FilmArray GI Panel positive for C. difficile on hospital admission who lacked dedicated C. difficile testing were included. RESULTS: Among 144 adults with a FilmArray Panel positive for C. difficile, 18 did not have concurrent dedicated C. difficile testing. Eight patients were categorized as possible, 5 as probable and 4 as definite cases of missed CDI diagnosis. We observed associated delays in initiation of appropriate therapy, intensive care unit admissions, hospital readmissions, colorectal surgery and death/discharge to hospice. Five out of 17 lacked risk factors for CDI. CONCLUSION: The practice of concealing C. difficile FilmArray GI Panel results needs to be reconsidered in patients presenting with community-onset colitis.