Interlaboratory comparison of Pseudomonas aeruginosa phage susceptibility testing.

Standardized approaches to phage susceptibility testing (PST) are essential to inform selection of phages for study in patients with bacterial infections. There is no reference standard for assessing bacterial susceptibility to phage. We compared agreement between PST performed at three centers: two centers using a liquid assay standardized between the sites with the third, a plaque assay. Four Pseudomonas aeruginosa phages: PaWRA01ø11 (EPa11), PaWRA01ø39 (EPa39), PaWRA02ø83 (EPa83), PaWRA02ø87 (EPa87), and a cocktail of all four phages were tested against 145 P. aeruginosa isolates. Comparisons were made within measurements at the two sites performing the liquid assay and between these two sites. Agreement was assessed based on coverage probability (CP8), total deviation index, concordance correlation coefficient (CCC), measurement accuracy, and precision. For the liquid assay, there was satisfactory agreement among triplicate measurements made on different days at site 1, and high agreement based on accuracy and precision between duplicate measurements made on the same run at site 2. There was fair accuracy between measurements of the two sites performing the liquid assay, with CCCs below 0.6 for all phages tested. When compared to the plaque assay (performed once at site 3), there was less agreement between results of the liquid and plaque assays than between the two sites performing the liquid assay. Similar findings to the larger group were noted in the subset of 46 P. aeruginosa isolates from cystic fibrosis. Results of this study suggest that reproducibility of PST methods needs further development.

In Vivo Emergence of Dual Resistance to Rifampin and Levofloxacin in Osteoarticular Cutibacterium avidum.

Cutibacterium avidum is an emerging causative agent of orthopedic device-related infections (ODRIs). There are no guidelines for the antimicrobial treatment of C. avidum ODRI, but oral rifampin is frequently used in combination with a fluoroquinolone following intravenous antibiotics. We describe the in vivo emergence of combined resistance to rifampin and levofloxacin in a C. avidum strain isolated from a patient with early-onset ODRI treated with debridement, antibiotic treatment, and implant retention (DAIR) using rifampin combined with levofloxacin as the oral treatment. Whole-genome sequencing of C. avidum isolates before and after antibiotic exposure confirmed strain identity and identified new mutations in rpoB and gyrA, leading to amino acid substitutions previously reported to be associated with resistance to rifampin (S446P) and fluoroquinolones (S101L), respectively, in other microbial agents, in the posttherapy isolate. Aside from the molecular insights reported here, this study highlights potential limitations of the combination of oral rifampin and levofloxacin in patients undergoing a DAIR procedure for C. avidum ODRI and the potential need to evaluate specific optimal therapy for emerging ODRI pathogens. IMPORTANCE In this study, we report for the first time the in vivo emergence of dual resistance to levofloxacin and rifampin in C. avidum isolated from a patient who received both antibiotics orally in the setting of a salvage debridement and implant retention of an ODRI. Aside from the molecular insights reported here, this study highlights potential limitations of the combination of oral rifampin and levofloxacin in patients undergoing these surgical procedures and the potential need to evaluate specific optimal therapy for emerging ODRI pathogens.

Core Genome Multilocus Sequence Typing and Antibiotic Susceptibility Prediction from Whole-Genome Sequence Data of Multidrug-Resistant Pseudomonas aeruginosa Isolates.

Over the past decade, whole-genome sequencing (WGS) has overtaken traditional bacterial typing methods for studies of genetic relatedness. Further, WGS data generated during epidemiologic studies can be used in other clinically relevant bioinformatic applications, such as antibiotic resistance prediction. Using commercially available software tools, the relatedness of 38 clinical isolates of multidrug-resistant Pseudomonas aeruginosa was defined by two core genome multilocus sequence typing (cgMLST) methods, and the WGS data of each isolate was analyzed to predict antibiotic susceptibility to nine antibacterial agents. The WGS typing and resistance prediction data were compared with pulsed-field gel electrophoresis (PFGE) and phenotypic antibiotic susceptibility results, respectively. Simpson's Diversity Index and adjusted Wallace pairwise assessments of the three typing methods showed nearly identical discriminatory power. Antibiotic resistance prediction using a trained analytical pipeline examined 342 bacterial-drug combinations with an overall categorical agreement of 92.4% and very major, major, and minor error rates of 3.6, 4.1, and 4.1%, respectively. IMPORTANCE Multidrug-resistant Pseudomonas aeruginosa isolates are a serious public health concern due to their resistance to nearly all or all of the available antibiotics, including carbapenems. Utilizing molecular approaches in conjunction with antibiotic susceptibility prediction software warrants investigation for use in the clinical laboratory workflow. These molecular tools coupled with antibiotic resistance prediction tools offer the opportunity to overcome the extended turnaround time and technical challenges of phenotypic susceptibility testing.

Development and Evaluation of a Core Genome Multilocus Sequencing Typing (cgMLST) Scheme for Serratia marcescens Molecular Surveillance and Outbreak Investigations.

Serratia marcescens can cause a range of severe infections and contributes to nosocomial outbreaks. Although whole-genome sequencing (WGS)-based typing is the standard method for molecular surveillance and outbreak investigation, there is no standardized analytic scheme for S. marcescens core genome multilocus sequence typing (cgMLST). Here, the development and evaluation of a S. marcescens cgMLST scheme is reported with the goal of enabling a standardized methodology and typing nomenclature. Four hundred ninety-one high-quality S. marcescens WGS data sets were extracted from public databases and-using the genomic sequence of NCBI reference strain S. marcescens Db11 (NZ_HG326223.1) as a starting point-all Db11 genes present in ≥97% data sets used to create a cgMLST scheme. The novel scheme was evaluated using WGS data from 24 outbreak investigations (n = 175 isolates) distributed over three continents. Analysis of Db11 genes within the 491 data sets identified 2,692 target genes present in ≥97% of genomes (mean, 99.1%; median, 99.9%). These genes formed the novel cgMLST scheme, covering 47.8% of nucleotides in the Db11 genome. Analyzing 175 isolates from 24 outbreaks using the novel scheme gave comparable results to previous typing efforts for both general groupings and allelic distances within clusters. In summary, a novel cgMLST scheme for S. marcescens was developed and evaluated. The scheme and its associated nomenclature will improve standardization of typing efforts for molecular surveillance and outbreak investigation, allowing better understanding of S. marcescens genomic epidemiology and facilitating interlaboratory comparisons.

Corrigendum: Pharmacokinetic assessment of staphylococcal phage K following parenteral and intra-articular administration in rabbits.

[This corrects the article DOI: 10.3389/fphar.2022.840165.].

Preliminary Reproducibility Evaluation of a Phage Susceptibility Testing Method Using a Collection of Escherichia coli and Staphylococcus aureus Phages.

BACKGROUND: Increasing antimicrobial resistance combined with a lagging pipeline of novel antimicrobial compounds have resulted in a resurgence of interest in phage therapy. To select optimal phage or phage combinations for patients for whom phage therapy is considered, assessment of activity of a panel of phages against the patients' bacterial isolate(s) should ideally be performed. Classical phage susceptibility testing methods (i.e., agar overlay) may be laborious, with expertise outside of normal training and competency of medical laboratory science staff needed. CONTENT: Adaptive Phage Therapeutics™ leveraged a commercially available phenotyping system (Biolog OmniLog®) to generate the PhageBank Susceptibility Test™, which uses a custom data analysis pipeline (PhageSelect™) to measure the delay in reaching log-phase metabolic activity ("hold time") when a given isolate is challenged with a specific phage. The goal of this study was to preliminarily assess reproducibility of this approach by testing 2 bacterial species at 2 sites, APT and an academic site. Nineteen Escherichia coli phages were tested against 18 bacterial isolates, and 21 Staphylococcus aureus phages, against 11 bacterial isolates. Result comparisons were statistically excellent for E. coli (κ = 0.7990) and good/fair for S. aureus (κ = 0.6360). SUMMARY: The described method provides good/fair to excellent statistical reproducibility for assessment of phage susceptibility of 2 commonly encountered bacterial species.

Antibiotic susceptibility testing of Staphylococcus aureus using the Biolog OmniLog® system, a metabolic phenotyping assay.

Use of the Biolog OmniLog® phenotyping system for antibiotic susceptibility testing (AST) was evaluated using 51 clinical isolates of Staphylococcus aureus. MIC testing by broth microdilution was compared to results generated using the OmniLog® system for oxacillin, daptomycin, vancomycin, gentamicin, linezolid, and tetracycline. There was >90% essential and categorical agreement between methods for all antibiotics, except gentamicin, which had 83.6% essential agreement, although very major errors occurred with linezolid (n = 3) and daptomycin (n = 1). Precision was satisfactory, with 5 triplicate measurements in agreement. A quantitative threshold allowed automated interpretation of MICs yielding results comparable to manual interpretation; oxacillin, gentamicin, and tetracycline resistance could be identified at a median of 7.13, 5.25, and 7.25 hours, respectively. Limitations include the small number of isolates, and especially resistant isolates tested, and the focus on a single species. Overall, the OmniLog® system was a precise method for AST of S. aureus, although accuracy was imperfect.

Acinetobacter baumannii Genomic Sequence-Based Core Genome Multilocus Sequence Typing Using Ridom SeqSphere+ and Antimicrobial Susceptibility Prediction in ARESdb.

Whole-genome sequencing (WGS) is rapidly replacing traditional typing methods for the investigation of infectious disease outbreaks. Additionally, WGS data are being used to predict phenotypic antimicrobial susceptibility. Acinetobacter baumannii, which is often multidrug-resistant, is a significant culprit in outbreaks in health care settings. A well-characterized collection of A. baumannii was studied using core genome multilocus sequence typing (cgMLST). Seventy-two isolates previously typed by PCR-electrospray ionization mass spectrometry (PCR/ESI-MS) provided by the Antimicrobial Resistance Leadership Group (ARLG) were analyzed using a clinical microbiology laboratory developed workflow for cgMLST with genomic susceptibility prediction performed using the ARESdb platform. Previously performed PCR/ESI-MS correlated with cgMLST using relatedness thresholds of allelic differences of ≤9 and ≤200 allelic differences in 78 and 94% of isolates, respectively. Categorical agreement between genotypic and phenotypic antimicrobial susceptibility across a panel of 11 commonly used drugs was 89%, with minor, major, and very major error rates of 8%, 11%, and 1%, respectively.

Pharmacokinetic Assessment of Staphylococcal Phage K Following Parenteral and Intra-articular Administration in Rabbits.

The therapeutic value of phage as an alternative to antibiotics for the treatment of bacterial infections is being considered in the wake of mounting antibiotic resistance. In this study, the pharmacokinetic properties of Staphylococcus aureus phage K following intravenous and intra-articular administration were investigated in a rabbit model. Using a traditional plaque assay and a novel quantitative PCR assay to measure phage levels in specimens over time, it was found that intra-articularly administered phage enters the systemic circulation; that phage may be detected in synovial fluid up to 24 h following the intra-articular, but not intravenous, administration; and that qPCR-based enumeration is generally more sensitive than plaque enumeration, with fair to moderate correlation between the two methods. Findings presented should inform the design of phage therapy experiments and therapeutic drug monitoring in preclinical and human phage studies.

Macrolide Resistance in Mycoplasma pneumoniae, Midwestern United States, 2014 to 2021.

The epidemiology of macrolide resistance in Mycoplasma (Mycoplasmoides) pneumoniae in the United States is incompletely described. Using a PCR assay targeting common mutations associated with macrolide resistance in M. pneumoniae (23S rRNA gene, A2063G/A2064G), the frequency of macrolide resistance was estimated to be 10% based on analysis of 114 samples tested from January 2014 to September 2021 at Mayo Clinic Laboratories. Seasonality data showed the highest rates of M. pneumoniae infection in the fall/early winter.

Contribution of Uremia to Ureaplasma-Induced Hyperammonemia.

Lung transplant recipients (LTRs) are vulnerable to hyperammonemia syndrome (HS) in the early postoperative period, a condition typically unresponsive to nonantibiotic interventions. HS in LTRs is strongly correlated with Ureaplasma infection of the respiratory tract, although it is not well understood what makes LTRs preferentially susceptible to HS compared to other immunocompromised hosts. Ureaplasma species harbor highly active ureases, and postoperative LTRs commonly experience uremia. We hypothesized that uremia could be a potentiating comorbidity, providing increased substrate for ureaplasmal ureases. Using a novel dialyzed flow system, the ammonia-producing capacities of four isolates of Ureaplasma parvum and six isolates of Ureaplasma urealyticum in media formulations relating to normal and uremic host conditions were tested. For all isolates, growth under simulated uremic conditions resulted in increased ammonia production over 24 h, despite similar endpoint bacterial quantities. Further, transcripts of ureC (from the ureaplasmal urease gene cluster) from U. urealyticum IDRL-10763 and ATCC-27816 rose at similar rates under uremic and nonuremic conditions, with similar endpoint populations under the two conditions (despite markedly increased ammonia concentrations under uremic conditions), indicating that the difference in ammonia production by these isolates is due to increased urease activity, not expression. Lastly, uremic mice infected with an Escherichia coli strain harboring a U. urealyticum serovar 8 gene cluster exhibited higher blood ammonia levels compared to nonuremic mice infected with the same strain. Taken together, these data show that U. urealyticum and U. parvum produce more ammonia under uremic conditions compared to nonuremic conditions. This implies that uremia is a plausible contributing factor to Ureaplasma-induced HS in LTRs. IMPORTANCE Ureaplasma-induced hyperammonemia syndrome is a deadly complication affecting around 4% of lung transplant recipients and, to a lesser extent, other solid organ transplant patients. Understanding the underlying mechanisms will inform patient management, potentially decreasing mortality and morbidity. Here, it is shown that uremia is a plausible contributing factor to the pathophysiology of the condition.

"Answers in hours": A prospective clinical study using nanopore sequencing for bile duct cultures.

BACKGROUND: Surgical site infection is a major source of morbidity in patients undergoing pancreatic head resection and is often from organisms in intraoperative bile duct cultures. As such, many institutions use prolonged prophylactic antibiotics and tailor based on bile duct cultures. However, standard cultures take days, leaving many patients unnecessarily on prolonged antibiotics. Nanopore sequencing can provide data in hours and, thus, has the potential to improve antibiotic stewardship. The present study investigates the feasibility of nanopore sequencing in intraoperative bile samples. METHODS: Patients undergoing pancreatic head resection were included. Intra-operative bile microbial profiles were determined with standard cultures and nanopore sequencing. Antibiotic recommendations were generated, and time-to-results determined for both methods. Organism yields, resistance patterns, antibiotic recommendations, and costs were compared. RESULTS: Out of 42 patients, 22 (52%) had samples resulting in positive standard cultures. All positive standard cultures had microbes detected using nanopore sequencing. All 20 patients with negative standard cultures had negative nanopore sequencing. Nanopore sequencing detected more bacterial species compared to standard cultures (10.5 vs 4.4, p < 0.05) and more resistance genotypes (10.3 vs 2.7, p < 0.05). Antimicrobial recommendations based on nanopore sequencing provided coverage for standard cultures in 27 out of 44 (61%) samples, with broader coverage recommended by nanopore sequencing in 13 out of 27 (48%) of these samples. Nanopore sequencing results were faster (8 vs 98 hours) than standard cultures but had higher associated costs ($165 vs $38.49). CONCLUSION: Rapid microbial profiling with nanopore sequencing is feasible with broader organism and resistance profiling compared to standard cultures. Nanopore sequencing has perfect negative predictive value and can potentially improve antibiotic stewardship; thus, a randomized control trial is under development.

Considerations for the Use of Phage Therapy in Clinical Practice.

Increasing antimicrobial resistance and medical device-related infections have led to a renewed interest in phage therapy as an alternative or adjunct to conventional antimicrobials. Expanded access and compassionate use cases have risen exponentially but have varied widely in approach, methodology, and clinical situations in which phage therapy might be considered. Large gaps in knowledge contribute to heterogeneity in approach and lack of consensus in many important clinical areas. The Antibacterial Resistance Leadership Group (ARLG) has convened a panel of experts in phage therapy, clinical microbiology, infectious diseases, and pharmacology, who worked with regulatory experts and a funding agency to identify questions based on a clinical framework and divided them into three themes: potential clinical situations in which phage therapy might be considered, laboratory testing, and pharmacokinetic considerations. Suggestions are provided as answers to a series of questions intended to inform clinicians considering experimental phage therapy for patients in their clinical practices.

Activity of Omadacycline in Rat Methicillin-Resistant Staphylococcus aureus Osteomyelitis.

Omadacycline, vancomycin, and rifampin, as well as rifampin combination therapies, were evaluated in an experimental rat model of methicillin-resistant Staphylococcus aureus (MRSA) osteomyelitis. All treatment groups had less MRSA recovered than saline-treated animals. The emergence of rifampin resistance was observed in 3 of 16 animals with rifampin monotherapy and none with rifampin combination therapy. After treatment, the median tibial bacterial loads were 6.04, 0.1, 4.81, and 5.24 log10 CFU/g for saline-, rifampin-, vancomycin-, and omadacycline-treated animals, respectively. Omadacycline or vancomycin administered with rifampin yielded no detectable MRSA. Omadacycline administered with rifampin deserves evaluation in humans as a potential treatment for osteomyelitis.

Core Genome Multilocus Sequence Typing and Prediction of Antimicrobial Susceptibility Using Whole-Genome Sequences of Escherichia coli Bloodstream Infection Isolates.

In total, 50 Escherichia coli bloodstream isolates from the clinical laboratory and 12 E. coli isolates referred for pulsed-field gel electrophoresis (PFGE) were sequenced, assessed for clonality using core genome multilocus sequence typing (cgMLST), and evaluated for genomic susceptibility predictions using ARESdb. Results of sequence typing using whole-genome sequencing (WGS)-based MLST and sequence type (ST)-specific PCR were identical. Overall categorical agreement between genotypic (ARESdb) and phenotypic susceptibility testing for 62 isolates and 11 antimicrobial agents was 91%. Among the referred isolates, high major error rates were found for ceftazidime, cefepime, and piperacillin-tazobactam.

Intraoperative bile duct cultures in patients undergoing pancreatic head resection: Prospective comparison of bile duct swab versus bile duct aspiration.

BACKGROUND: Postoperative surgical site infection is a major source of morbidity after pancreatic head resections, and data suggest bacterobilia as a leading cause. Some centers use intraoperative bile duct cultures to guide postoperative antimicrobial prophylaxis. This prospective study evaluates culture differences between traditional bile duct swab versus bile duct aspiration intraoperative samples. METHODS: Prospective patients undergoing pancreatic head resection with both bile duct swab and bile duct aspiration were included. Cultures were reviewed for organism characteristics. Any growth of organisms was considered a positive culture. Bile duct swab yield and characteristics were compared with bile duct aspiration. Postoperative surgical site infection complications were compared to bile duct culture results. RESULTS: Fifty patients were included. Bile duct aspiration resulted in a significantly higher median number of organisms compared to bile duct swab (6 vs 3; P < .001). There were no differences in the number of patients (37 vs 33) having positive bile duct aspiration and bile duct swab cultures (P = .385). Anaerobic cultures (not possible with bile duct swab) were positive in 21 patients with bile duct aspiration. A total of 37 (74%) patients had preoperative biliary stenting, which highly associated (P < .001) with positive cultures. Bile duct culture organisms correlated with postoperative surgical site infection in 12/17 (71%) patients. CONCLUSION: Use of bile duct aspiration improves intraoperative bile duct culture organism yield over bile duct swab and may improve tailoring of antibiotics in patients undergoing pancreatic head resection.

Comparative Transcriptomic Analysis of Staphylococcus aureus Associated with Periprosthetic Joint Infection under in Vivo and in Vitro Conditions.

Transcriptomic analysis can provide insight as to how Staphylococcus aureus adapts to the environmental niche of periprosthetic joint infection (PJI), a challenging clinical infection. Here, in vivo RNA expression of eight S. aureus PJIs was compared with expression of the corresponding isolates in planktonic culture using a total RNA-sequencing approach. Expression varied among isolates, with a common trend showing increased expression of several ica-independent biofilm formation genes, including sdr, fnb, ebpS, and aaa; genes encoding enzymes and toxins, including coa, nuc, hlb, and hlgA/B/C; and genes facilitating acquisition of iron via the iron-binding molecule siderophore B (snb) and heme consumption protein (isd) pathways in PJI. Several antimicrobial resistance determinants were detected; although their presence correlated with phenotypic susceptibility of the associated isolates, no difference in expression between in vivo and in vitro conditions was identified.

Clinical Evaluation of a Real-Time PCR Assay for Simultaneous Detection of Helicobacter pylori and Genotypic Markers of Clarithromycin Resistance Directly from Stool.

Helicobacter pylori infection is mainly diagnosed noninvasively, with susceptibility testing traditionally requiring endoscopy. Treatment is empirical, with clarithromycin-based triple therapy recommended where resistance rates are below 15%. Rising rates of clarithromycin resistance, resulting in high clarithromycin-based therapy failure rates, are seen worldwide, but U.S. data are limited. We developed a real-time PCR assay for simultaneous detection of H. pylori and genotypic markers of clarithromycin resistance directly from stool specimens. The assay was validated by testing 524 stool samples using an H. pylori stool antigen test as the reference method for detection accuracy and Sanger sequencing to confirm genotypic susceptibility results. A separate set of 223 antigen-positive stool samples was tested and retrospective medical record review conducted to define clinical utility. PCR resulted in 88.6% and 92.8% sensitivity in the validation and clinical study sets, respectively. Sequencing confirmed correct detection of clarithromycin resistance-associated mutations in all positive validation samples. The PCR-predicted clarithromycin resistance rate was 39% in the clinical data set overall and 31% in treatment-naive patients; the clarithromycin-based triple therapy eradication rate in treatment-naive patients was 62%. The clarithromycin-based triple therapy success was lower when resistance was predicted by PCR (41%) than when no resistance was predicted (70%; P = 0.03). PCR results were positive in 98% of antigen-positive stools from patients tested for eradication. The described PCR assay can accurately and noninvasively diagnose H. pylori, provide genotypic susceptibility, and test for eradication. Our findings support the need for susceptibility-guided therapy in our region if a clarithromycin-based regimen is considered.

Yersinia occitanica is a later heterotypic synonym of Yersinia kristensenii subsp. rochesterensis and elevation of Yersinia kristensenii subsp. rochesterensis to species status.

The taxonomic position of Yersinia kristensenii subsp. rochesterensis and Yersinia occitanica was re-evaluated by genomic analysis. Average nucleotide identity (ANI), digital DNA-DNA hybridization values, and phylogenetic analyses of the type strains indicate that Y. kristensenii subsp. rochesterensis and Y. occitanica are the same genospecies. Additionally, the overall genomic relatedness index (OGRI) values reveal that Y. kristensenii subsp. rochesterensis should be elevated to species status as Yersinia rochesterensis sp. nov.