Publications by authors named "Scott A Cunningham"

61 Publications

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

Surgery 2021 Jul 2. Epub 2021 Jul 2.

Division of Hepatobiliary and Pancreas Surgery, Department of Surgery, Mayo Clinic, Rochester, MN. Electronic address:

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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.surg.2021.06.013DOI Listing
July 2021

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

J Mol Diagn 2021 Aug 5;23(8):986-999. Epub 2021 Jun 5.

Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota; Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota. Electronic address:

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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jmoldx.2021.05.011DOI Listing
August 2021

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

J Clin Microbiol 2021 04 20;59(5). Epub 2021 Apr 20.

Division of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA

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 and genotypic markers of clarithromycin resistance directly from stool specimens. The assay was validated by testing 524 stool samples using an 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%;  = 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 , 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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/JCM.03040-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8091827PMC
April 2021

is a later heterotypic synonym of subsp. and elevation of subsp. to species status.

Int J Syst Evol Microbiol 2021 Feb;71(2)

Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Rochester, Minnesota, USA.

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

Download full-text PDF

Source
http://dx.doi.org/10.1099/ijsem.0.004626DOI Listing
February 2021

Plasmid Acquisition Alters Vancomycin Susceptibility in Clostridioides difficile.

Gastroenterology 2021 02 14;160(3):941-945.e8. Epub 2020 Nov 14.

Division of Gastroenterology and Hepatology, Department of Medicine, Rochester, Minnesota; Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota. Electronic address:

The increasing incidence of primary and recurring Clostridioides difficile infections (CDI), which evade current treatment strategies, reflects the changing biology of C difficile. Here, we describe a putative plasmid-mediated mechanism potentially driving decreased sensitivity of C difficile to vancomycin treatment. We identified a broad host range transferable plasmid in a C difficile strain associated with lack of adequate response to vancomycin treatment. The transfer of this plasmid to a vancomycin-susceptible C difficile isolate decreased its susceptibility to vancomycin in vitro and resulted in more severe disease in a humanized mouse model. Our findings suggest plasmid acquisition in the gastrointestinal tract to be a possible mechanism underlying vancomycin treatment failure in patients with CDI, but further work is needed to characterize the mechanism by which plasmid genes determine vancomycin susceptibility in C difficile.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1053/j.gastro.2020.10.046DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7878333PMC
February 2021

Molecular epidemiology of methicillin-susceptible in infants in a neonatal intensive care unit.

Infect Control Hosp Epidemiol 2020 12 16;41(12):1402-1408. Epub 2020 Sep 16.

Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo ClinicRochester, Minnesota.

Objective: To investigate the molecular epidemiology of methicillin-susceptible Staphylococcus aureus (MSSA) in infants in a neonatal intensive care unit (NICU) using whole-genome sequencing.

Design: Investigation of MSSA epidemiology in a NICU.

Setting: Single-center, level IV NICU.

Methods: Universal S. aureus screening was done using a single swab obtained from the anterior nares, axilla, and groin area of infants in the NICU on a weekly basis. Core genome multilocus sequence type (cgMLST) analysis was performed on MSSA isolates detected over 1 year (2018-2019).

Results: In total, 68 MSSA-colonized infants were identified, and cgMLSTs of 67 MSSA isolates were analyzed. Overall, we identified 11 cgMLST isolate groups comprising 39 isolates (58%), with group sizes ranging from 2 to 10 isolates, and 28 isolates (42%) were unrelated to each other or any of the isolate groups. Cases of infants colonized by MSSA were scattered throughout the 1-year study period, and isolates belonging to the same cgMLST group were typically detected contemporaneously, over a few weeks or a few months. Overall, 13 infants (19.7%) developed MSSA infections: bacteremia (n = 3), wound infection (n = 5), conjunctivitis (n = 4), and cellulitis (n = 1). We detected no association between these clinically manifest infections and specific cgMLST groups.

Conclusions: Although MSSA isolates in infants in a NICU showed high diversity, most were related to other isolates, albeit within small groups. cgMLST facilitates an understanding of the complex transmission dynamics of MSSA in NICUs, and these data can be used to inform better control strategies.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1017/ice.2020.355DOI Listing
December 2020

Staphylococcus aureus whole genome sequence-based susceptibility and resistance prediction using a clinically amenable workflow.

Diagn Microbiol Infect Dis 2020 Jul 11;97(3):115060. Epub 2020 Apr 11.

Division of Clinical Microbiology, Mayo Clinic, Rochester, MN; Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, MN. Electronic address:

We used graphical user interface-based automated analytical tools from Next Gen Diagnostics (Mountain View, CA) and 1928 Diagnostics (Gothenburg, Sweden) to analyze whole genome sequence (WGS) data from 102 unique blood culture isolates of Staphylococcus aureus to predict antimicrobial susceptibly, with results compared to those of phenotypic susceptibility testing. Of 916 isolate/antibiotic combinations analyzed using the Next Gen Diagnostics tool, there were 9 discrepancies between WGS predictions and phenotypic susceptibility/resistance, including 8 for clindamycin and 1 for minocycline. Of 612 isolate/antibiotic combinations analyzed using the 1928 Diagnostics tool, there were 13 discrepancies between WGS predictions and phenotypic susceptibility/resistance, including 9 for clindamycin, 3 for trimethoprim-sulfamethoxazole, and 1 for rifampin. Trimethoprim-sulfamethoxazole was not assessed by Next Gen Diagnostics, and minocycline was not assessed by 1928 Diagnostics. There was complete concordance between phenotypic susceptibility/resistance and genotypic prediction of susceptibility/resistance using both analytical platforms for oxacillin, vancomycin, and mupirocin, as well as by the Next Gen Diagnostics analytical tool for levofloxacin (the 1928 Diagnostics tool did not assess levofloxacin). These results suggest that, from a performance standpoint, with some caveats, automatic bioinformatics tools may be acceptable to predict susceptibility and resistance to a panel of antibiotics for S. aureus.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.diagmicrobio.2020.115060DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8094441PMC
July 2020

Core genome MLST and resistome analysis of Klebsiella pneumoniae using a clinically amenable workflow.

Diagn Microbiol Infect Dis 2020 May 21;97(1):114996. Epub 2020 Jan 21.

Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, MN; Division of Clinical Microbiology, Mayo Clinic, Rochester, MN.

Whole genome sequencing (WGS) is replacing traditional microbiological typing methods for investigation of outbreaks in clinical settings. Here, we used a clinical microbiology laboratory core genome multilocus sequence typing (cgMLST) workflow to analyze 40 isolates of K. pneumoniae which are part of the Antimicrobial Resistance Leadership Group (ARLG) isolate collection, alongside 10 Mayo Clinic K. pneumoniae isolates, comparing results to those of pulsed-field gel electrophoresis (PFGE). Additionally, we used the WGS data to predict phenotypic antimicrobial susceptibility (AST). Thirty-one of 40 ARLG K. pneumoniae isolates belonged to the same PFGE type, all of which, alongside 3 isolates of different PFGE types, formed a large cluster by cgMLST. PFGE and cgMLST were completely concordant for the 10 Mayo Clinic K. pneumoniae isolates. For AST prediction, the overall agreement between phenotypic AST and genotypic prediction was 95.6%.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.diagmicrobio.2020.114996DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7422488PMC
May 2020

Yersinia kristensenii subsp. rochesterensis subsp. nov., isolated from human feces.

Int J Syst Evol Microbiol 2019 Aug 28;69(8):2292-2298. Epub 2019 May 28.

Division of Infectious Diseases, Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota, USA.

A single bacterial isolate, EPLC-04, was isolated from human feces and identified as representing a member of the genus Yersinia on the basis of phenotypic characteristics, matrix assisted laser desorption ionization time-of-flight mass spectrometry and partial 16S rRNA gene sequencing. The isolate's phenotypic profile differed from that described for the most closely related species, Yersinia kristensenii, by exhibiting lipase production and lacking pyrazinamidase activity. Multiple genetic targets, including the complete (1465 bp) 16S rRNA gene sequence and partial sequences of groEL (539 bp), gyrB (935 bp), glnA (525 bp) and recA (535 bp) indicated that the isolate exhibited 98.91, 92.16, 90.81, 92.78 and 89.01 % identity with Yersinia aldovae, 98.98, 91.99, 90.17, 89.77 and 89.55 % identity with Yersinia intermedia, and 99.66, 98.11, 98.50, 98.49 and 98.51 % identity with Y. kristensenii, respectively. Phylogenetic reconstructions based on the combination of the four housekeeping genes indicated that the isolate formed a unique branch, supported by a bootstrap value of 100 %. Digital DNA-DNA homology and 16S rRNA gene sequencing identified EPLC-04 as representing Y. kristensenii. However, the unique phenotypic traits and results of phylogenetic analysis indicate that it represents a novel subspecies of Y. kristensenii. The name Yersinia kristenseniisubsp. rochesterensis subsp. nov. is proposed for this novel taxon (type strain EPLC-04=ATCC BAA-2637, DSMZ 28595).
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1099/ijsem.0.003464DOI Listing
August 2019

Lack of correlation of virulence gene profiles of Staphylococcus aureus bacteremia isolates with mortality.

Microb Pathog 2019 Aug 15;133:103543. Epub 2019 May 15.

Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA; Division of Infectious Diseases, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA. Electronic address:

Purpose: Whole genome sequencing (WGS) analysis of Staphylococcus aureus is increasingly used in clinical practice. Although bioinformatics tools used in WGS analysis readily define the S. aureus virulome, the clinical value of this type of analysis is unclear. Here, virulence genes in S. aureus bacteremia (SAB) isolates were evaluated by WGS, with superantigens (SAgs) further evaluated by conventional PCR and functional assays, and results correlated with mortality.

Methods: 152 SAB isolates collected throughout 2015 at a large Minnesota medical center were studied and associated clinical data analyzed. Virulence genes were identified from previously-reported WGS data (https://doi.org/10.1371/journal.pone.0179003). SAg genes sea, seb, sec, sed, see, seg, seh, sei, sej, and tst were also assessed by individual PCR assays. Mitogenicity of SAgs was assessed using an in vitro proliferation assay with splenocytes from HLA-DR3 transgenic mice.

Results: Of the 152 SAB isolates studied, 106 (69%) were methicillin-susceptible S. aureus (MSSA). The number of deaths attributed and not attributed to SAB, and 30-day survivors were 24 (16%), 2 (1%), and 128 (83%), respectively. From WGS data, both MSSA and MRSA had high proportions of adhesion (>80%) and immune-evasion (>70%) genes. There was no difference in virulomes between survivor- and non-survivor-associated isolates. Although over 60% of SAB isolates produced functional SAgs, there were no differences in the distribution or prevalence of SAg genes between survivor- and non-survivor-associated isolates.

Conclusion: In this study of one year of SAB isolates from a large medical center, the S. aureus virulome, as assessed by WGS, and also for SAgs using individual PCRs and phenotypic characterization, did not impact mortality.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.micpath.2019.103543DOI Listing
August 2019

Molecular Approach to Diagnosis of Cardiovascular Implantable Electronic Device Infection.

Clin Infect Dis 2020 02;70(5):898-906

Division of Infectious Diseases Mayo Clinic College of Medicine and Science, Rochester, Minnesota.

Background: Sonicate fluid (SF), a solution derived from vortexing and sonication of explanted cardiovascular implantable electronic devices (CIEDs), is a higher-yield specimen compared with swabs or tissues for culture-based detection of microorganisms associated with CIED infection. Despite this, SF culture fails to identify a causative organism in ~50% of cases. We aimed to evaluate the diagnostic performance of 16S ribosomal RNA gene (rRNA) polymerase chain reaction (PCR)/sequencing of SF and compare it with that of SF culture.

Methods: We identified 322 SF specimens from extracted CIEDs and reviewed clinical data for each patient. Subjects were classified as having or not having CIED infection. Cases were subcategorized as culture negative if no significant growth was reported from SF cultures and as culture positive if an organism was detected above predefined thresholds. 16S rRNA PCR/sequencing was performed, with the organisms identified reported according to Clinical and Laboratory Standards Institute guidelines for sequence data interpretation.

Results: A total of 278 SF samples corresponded to infected cases, of which 160 were culture positive and 118 culture negative. The remaining 44 were from noninfected cases, of which 2 were culture positive. Compared with SF culture, the sensitivity of 16S rRNA PCR/sequencing was higher (64% vs 57.5%, P = .003). 16S rRNA PCR/sequencing detected a potential pathogen in 28 of 118 culture-negative cases, identifying staphylococci in the majority (18/28).

Conclusions: 16S rRNA PCR/sequencing has higher sensitivity to detect bacteria in SF from extracted CIEDs than does SF culture.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/cid/ciz266DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7931840PMC
February 2020

Whole-genome sequencing for methicillin-resistant Staphylococcus aureus (MRSA) outbreak investigation in a neonatal intensive care unit.

Infect Control Hosp Epidemiol 2018 12 4;39(12):1412-1418. Epub 2018 Oct 4.

1Division of Pediatric Infectious Diseases,Department of Pediatric and Adolescent Medicine,Mayo Clinic,Rochester,Minnesota.

Objective: To evaluate whole-genome sequencing (WGS) as a molecular typing tool for MRSA outbreak investigation.

Design: Investigation of MRSA colonization/infection in a neonatal intensive care unit (NICU) over 3 years (2014-2017).

Setting: Single-center level IV NICU.PatientsNICU infants and healthcare workers (HCWs).

Methods: Infants were screened for MRSA using a swab of the anterior nares, axilla, and groin, initially by targeted (ring) screening, and later by universal weekly screening. Clinical cultures were collected as indicated. HCWs were screened once using swabs of the anterior nares. MRSA isolates were typed using WGS with core-genome multilocus sequence typing (cgMLST) analysis and by pulsed-field gel electrophoresis (PFGE). Colonized and infected infants and HCWs were decolonized. Control strategies included reinforcement of hand hygiene, use of contact precautions, cohorting, enhanced environmental cleaning, and remodeling of the NICU.

Results: We identified 64 MRSA-positive infants: 53 (83%) by screening and 11 (17%) by clinical cultures. Of 85 screened HCWs, 5 (6%) were MRSA positive. WGS of MRSA isolates identified 2 large clusters (WGS groups 1 and 2), 1 small cluster (WGS group 3), and 8 unrelated isolates. PFGE failed to distinguish WGS group 2 and 3 isolates. WGS groups 1 and 2 were codistributed over time. HCW MRSA isolates were primarily in WGS group 1. New infant MRSA cases declined after implementation of the control interventions.

Conclusion: We identified 2 contemporaneous MRSA outbreaks alongside sporadic cases in a NICU. WGS was used to determine strain relatedness at a higher resolution than PFGE and was useful in guiding efforts to control MRSA transmission.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1017/ice.2018.239DOI Listing
December 2018

Clinical and Molecular Correlates of Escherichia coli Bloodstream Infection from Two Geographically Diverse Centers in Rochester, Minnesota, and Singapore.

Antimicrob Agents Chemother 2018 10 24;62(10). Epub 2018 Sep 24.

Division of Infectious Diseases, Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA

bacteremia is caused mainly by sequence type complex 131 (STc131) and two clades within its fluoroquinolone-resistance-associated 30 subclone, 30R1 and 30Rx. We examined clinical and molecular correlates of bacteremia in two geographically distinct centers. We retrospectively studied 251 unique bloodstream isolates from 246 patients (48 from the Mayo Clinic, Rochester, MN [MN], and 198 from Tan Tock Seng Hospital, Singapore [SG]), from October 2013 through March 2014. Isolates underwent PCR for phylogroup, STc, type, and virulence gene profiles, and medical records were reviewed. Although STc131 accounted for 25 to 27% of all bacteremia isolates at each site, its extended-spectrum-β-lactamase (ESBL)-associated 30Rx clade was more prominent in SG than in MN (15% versus 4%; = 0.04). In SG only, patients with STc131 (versus other STc isolates) were more likely to receive inactive initial antibiotics (odds ratio, 2.8; = 0.005); this was true specifically for patients with 30Rx (odds ratio, 7.0; = 0.005). 30Rx comprised 16% of community-onset bacteremia episodes in SG but none in MN. In SG, virulence scores were higher for 30Rx than for 30R1, non-30 STc131, and non-STc131 isolates ( < 0.02 for all comparisons). At neither site did mortality differ by clonal status. The ESBL-associated 30Rx clade was more prevalent and more often of community onset in SG, where it predicted inactive empirical treatment. The clonal distribution varies geographically and has potentially important clinical implications. Rapid susceptibility testing and clonal diagnostics for 30/30Rx might facilitate earlier prescribing of active therapy.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/AAC.00937-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6153841PMC
October 2018

Eight Years of Clinical Legionella PCR Testing Illustrates a Seasonal Pattern.

J Infect Dis 2018 07;218(4):669-670

Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota.

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/infdis/jiy201DOI Listing
July 2018

Molecular epidemiology of Staphylococcus aureus bacteremia in a single large Minnesota medical center in 2015 as assessed using MLST, core genome MLST and spa typing.

PLoS One 2017 2;12(6):e0179003. Epub 2017 Jun 2.

Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, United States of America.

Staphylococcus aureus is a leading cause of bacteremia in hospitalized patients. Whether or not S. aureus bacteremia (SAB) is associated with clonality, implicating potential nosocomial transmission, has not, however, been investigated. Herein, we examined the epidemiology of SAB using whole genome sequencing (WGS). 152 SAB isolates collected over the course of 2015 at a single large Minnesota medical center were studied. Staphylococcus protein A (spa) typing was performed by PCR/Sanger sequencing; multilocus sequence typing (MLST) and core genome MLST (cgMLST) were determined by WGS. Forty-eight isolates (32%) were methicillin-resistant S. aureus (MRSA). The isolates encompassed 66 spa types, clustered into 11 spa clonal complexes (CCs) and 10 singleton types. 88% of 48 MRSA isolates belonged to spa CC-002 or -008. Methicillin-susceptible S. aureus (MSSA) isolates were more genotypically diverse, with 61% distributed across four spa CCs (CC-002, CC-012, CC-008 and CC-084). By MLST, there was 31 sequence types (STs), including 18 divided into 6 CCs and 13 singleton STs. Amongst MSSA isolates, the common MLST clones were CC5 (23%), CC30 (19%), CC8 (15%) and CC15 (11%). Common MRSA clones were CC5 (67%) and CC8 (25%); there were no MRSA isolates in CC45 or CC30. By cgMLST analysis, there were 9 allelic differences between two isolates, with the remaining 150 isolates differing from each other by over 40 alleles. The two isolates were retroactively epidemiologically linked by medical record review. Overall, cgMLST analysis resulted in higher resolution epidemiological typing than did multilocus sequence or spa typing.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0179003PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5456361PMC
September 2017

Cardiothoracic Transplant Recipient Mycoplasma hominis: An Uncommon Infection with Probable Donor Transmission.

EBioMedicine 2017 May 19;19:84-90. Epub 2017 Apr 19.

Division of Pulmonary and Critical Care Medicine, Department of Medicine, Rochester, MN 55905, USA. Electronic address:

The role of infection with Mycoplasma hominis following cardiothoracic organ transplantation and its source of transmission have not been well-defined. Here, we identify and describe infection with M. hominis in patients following cardiothoracic organ transplantation after reviewing all cardiothoracic transplantations performed at our center between 1998 and July 2015. We found seven previously unreported cases of M. hominis culture positive infection all of whom presented with pleuritis, surgical site infection, and/or mediastinitis. PCR was used to establish the diagnosis in four cases. In two instances, paired single lung transplant recipients manifested infection, and in one of these pairs, isolates were indistinguishable by multilocus sequence typing (MLST). To investigate the prevalence of M. hominis in the lower respiratory tract, we tested 178 bronchoalveolar lavage (BAL) fluids collected from immunocompromised subjects for M. hominis by PCR; all were negative. Review of the literature revealed an additional 15 cases of M. hominis in lung transplant recipients, most with similar clinical presentations to our cases. We recommend that M. hominis should be considered in post-cardiothoracic transplant infections presenting with pleuritis, surgical site infection, or mediastinitis. M. hominis PCR may facilitate early diagnosis and prompt therapy. Evaluation for possible donor transmission should be considered.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ebiom.2017.04.026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5440619PMC
May 2017

Comparison of Whole-Genome Sequencing Methods for Analysis of Three Methicillin-Resistant Staphylococcus aureus Outbreaks.

J Clin Microbiol 2017 06 12;55(6):1946-1953. Epub 2017 Apr 12.

Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA

Whole-genome sequencing (WGS) can provide excellent resolution in global and local epidemiological investigations of outbreaks. A variety of sequencing approaches and analytical tools have been used; it is not clear which is ideal. We compared two WGS strategies and two analytical approaches to the standard method of SmaI restriction digestion pulsed-field gel electrophoresis (PFGE) for typing Forty-two isolates from three outbreaks and 12 reference isolates were studied. Near-complete genomes, assembled with paired-end and long-mate-pair (8 kb) libraries were first assembled and analyzed utilizing an in-house assembly and analytical informatics pipeline. In addition, paired-end data were assembled and analyzed using a commercial software package. Single nucleotide variant (SNP) analysis was performed using the in-house pipeline. Two assembly strategies were used to generate core genome multilocus sequence typing (cgMLST) data. First, the near-complete genome data generated with the in-house pipeline were imported into the commercial software and used to perform cgMLST analysis. Second, the commercial software was used to assemble paired-end data, and resolved assemblies were used to perform cgMLST. Similar isolate clustering was observed using SNP calling and cgMLST, regardless of data assembly strategy. All methods provided more discrimination between outbreaks than did PFGE. Overall, all of the evaluated WGS strategies yielded statistically similar results for typing.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/JCM.00029-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5442552PMC
June 2017

Multicenter Performance Assessment of Carba NP Test.

J Clin Microbiol 2017 06 12;55(6):1954-1960. Epub 2017 Apr 12.

Division of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA

Eighty Gram-negative bacilli (54 and 26 nonfermenting Gram-negative bacilli) obtained from multiple institutions in the United States were distributed in a blinded manner to seven testing laboratories to compare their performance of a test for detection of carbapenemase production, the Carba NP test. The Carba NP test was performed by all laboratories, following the Clinical and Laboratory Standards Institute (CLSI) procedure. Site-versus-site comparisons demonstrated a high level of consistency for the Carba NP assay, with just 3/21 site comparisons yielding a difference in sensitivity ( < 0.05). Previously described limitations with carbapenemases and carbapenemases associated with were noted. Based on these data, we demonstrate that the Carba NP test, when implemented with the standardized CLSI methodology, provides reproducible results across multiple sites for detection of carbapenemases.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/JCM.00244-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5442553PMC
June 2017

Genotypic analysis of from patients with Whipple disease in the Americas.

J Clin Pathol 2017 Oct 6;70(10):891-895. Epub 2017 Apr 6.

Infectious Diseases Pathology Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.

, the agent of Whipple disease, causes a rare bacterial disease that may be fatal if not treated. The classical form of the disease includes diarrhoea, weight loss, arthritis, endocarditis and neurological manifestations. Genotyping studies done in Europe, Africa and Asia showed high genetic diversity with no correlation between genotypes and clinical features, but contributed to a better understanding of the epidemiology of the disease. More than 70 genotypes have been described. No similar assessment of in the USA and the Caribbean has been performed. In this study, we describe genetic analysis of DNA from histopathological samples obtained from 30 patients from the Americas with Whipple disease and compare the genotypes with those previously identified. Complete genotypes were obtained from 18 patients (60%). Only 4 genotypes were previously described, and 14 were newly reported, confirming the diversity of strains.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1136/jclinpath-2017-204382DOI Listing
October 2017

Phenotypic and Molecular Antimicrobial Susceptibility of Helicobacter pylori.

Antimicrob Agents Chemother 2017 04 24;61(4). Epub 2017 Mar 24.

Division of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA

Failure to eradicate infection is often a result of antimicrobial resistance, which for clarithromycin is typically mediated by specific point mutations in the 23S rRNA gene. The purpose of this study was to define current patterns of antimicrobial susceptibility in isolates derived primarily from the United States and to survey them for the presence of point mutations in the 23S rRNA gene and assess the ability of these mutations to predict phenotypic clarithromycin susceptibility. Antimicrobial susceptibility testing was performed using agar dilution on 413 isolates submitted to Mayo Medical Laboratories for susceptibility testing. For a subset of these isolates, a 150-bp segment of the 23S rRNA gene was sequenced. A total of 1,970 MICs were reported over the 4-year study period. The rate of clarithromycin resistance was high (70.4%), and elevated MICs were frequently observed for metronidazole (82.4% of isolates had an MIC of >8 μg/ml) and ciprofloxacin (53.5% of isolates had an MIC of >1 μg/ml). A total of 111 archived isolates underwent 23S rRNA gene sequencing; we found 95% concordance between genotypes and phenotypes ( = 0.9802). Resistance to clarithromycin was most commonly due to an A2143G mutation (82%), followed by A2142G (14%) and A2142C (4%) mutations. Clinical isolates derived primarily from the United States demonstrated a high rate of clarithromycin resistance and elevated metronidazole and ciprofloxacin MICs. The relative distribution of point mutations at positions 2143 and 2142 in the 23S rRNA gene in clarithromycin-resistant was similar to that reported from other parts of the world; these mutations predict phenotypic resistance to clarithromycin.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/AAC.02530-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5365656PMC
April 2017

Ureaplasma urealyticum Causes Hyperammonemia in an Experimental Immunocompromised Murine Model.

PLoS One 2016 18;11(8):e0161214. Epub 2016 Aug 18.

Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, United States of America.

Hyperammonemia syndrome is an often fatal complication of lung transplantation which has been recently associated with Ureaplasma infection. It has not been definitely established that Ureaplasma species can cause hyperammonemia. We established a novel immunocompromised murine model of Ureaplasma urealyticum infection and used it to confirm that U. urealyticum can cause hyperammonemia. Male C3H mice were pharmacologically immunosuppressed with mycophenolate mofetil, tacrolimus and oral prednisone for seven days, and then challenged intratracheally (IT) and/or intraperitoneally (IP) with 107 CFU U. urealyticum over six days, while continuing immunosuppression. Spent U. urealyticum-free U9 broth was used as a negative control, with uninfected immunocompetent mice, uninfected immunosuppressed mice, and infected immunocompetent mice serving as additional controls. Plasma ammonia concentrations were compared using Wilcoxon ranks sum tests. Plasma ammonia concentrations of immunosuppressed mice challenged IT/IP with spent U9 broth (n = 14) (range 155-330 μmol/L) were similar to those of normal mice (n = 5), uninfected immunosuppressed mice (n = 5), and U. urealyticum IT/IP challenged immunocompetent mice (n = 5) [range 99-340 μmol/L, p = 0.60]. However, immunosuppressed mice challenged with U. urealyticum IT/IP (n = 20) or IP (n = 15) had higher plasma ammonia concentrations (range 225-945 μmol/L and 276-687 μmol/L, respectively) than those challenged IT/IP with spent U9 broth (p<0.001). U. urealyticum administered IT/IP or IP causes hyperammonemia in mice pharmacologically immunosuppressed with a regimen similar to that administered to lung transplant recipients.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0161214PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4990232PMC
July 2017

Erratum for Norgan et al., Carbapenem- and Colistin-Resistant Enterobacter cloacae from Delta, Colorado, in 2015.

Antimicrob Agents Chemother 2016 08 22;60(8):5106. Epub 2016 Jul 22.

Division of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA Division of Infectious Diseases, Mayo Clinic, Rochester, Minnesota, USA.

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/AAC.01219-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4958225PMC
August 2016

Antimicrobial Susceptibility and Clonality of Clinical Ureaplasma Isolates in the United States.

Antimicrob Agents Chemother 2016 08 22;60(8):4793-8. Epub 2016 Jul 22.

Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA

Ureaplasma urealyticum and Ureaplasma parvum are pathogens involved in urogenital tract and intrauterine infections and also in systemic diseases in newborns and immunosuppressed patients. There is limited information on the antimicrobial susceptibility and clonality of these species. In this study, we report the susceptibility of 250 contemporary isolates of Ureaplasma (202 U. parvum and 48 U. urealyticum isolates) recovered at Mayo Clinic, Rochester, MN. MICs of doxycycline, azithromycin, ciprofloxacin, tetracycline, erythromycin, and levofloxacin were determined by broth microdilution, with MICS of the last three interpreted according to CLSI guidelines. Levofloxacin resistance was found in 6.4% and 5.2% of U. parvum and U. urealyticum isolates, respectively, while 27.2% and 68.8% of isolates, respectively, showed ciprofloxacin MICs of ≥4 μg/ml. The resistance mechanism of levofloxacin-resistant isolates was due to mutations in parC, with the Ser83Leu substitution being most frequent, followed by Glu87Lys. No macrolide resistance was found among the 250 isolates studied; a single U. parvum isolate was tetracycline resistant. tet(M) was found in 10 U. parvum isolates, including the single tetracycline-resistant isolate, as well as in 9 isolates which had low tetracycline and doxycycline MICs. Multilocus sequence typing (MLST) performed on a selection of 46 isolates showed high diversity within the clinical Ureaplasma isolates studied, regardless of antimicrobial susceptibility. The present work extends previous knowledge regarding susceptibility to antimicrobial agents, resistance mechanisms, and clonality of Ureaplasma species in the United States.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/AAC.00671-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4958210PMC
August 2016

An Immunocompromised Child with Bloodstream Infection Caused by Two Escherichia coli Strains, One Harboring NDM-5 and the Other Harboring OXA-48-Like Carbapenemase.

Antimicrob Agents Chemother 2016 06 23;60(6):3270-5. Epub 2016 May 23.

Wayne State University and Detroit Medical Center, Detroit, Michigan, USA

We describe a 16-year-old neutropenic patient from the Middle East with bloodstream infection caused by two carbapenemase-producing Escherichia coli isolates that we characterized by whole-genome sequencing. While one displayed meropenem resistance and was blaNDM positive, the other demonstrated meropenem susceptibility yet harbored blaOXA181 (which encodes a blaOXA48-like enzyme). This report highlights the challenge of laboratory detection of blaOXA48-like enzymes and the clinical implications of genotypic resistance detection in carbapenemase-producing Enterobacteriaceae.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/AAC.03118-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4879384PMC
June 2016

Evaluation of the Check-Points Check MDR CT103 and CT103 XL Microarray Kits by Use of Preparatory Rapid Cell Lysis.

J Clin Microbiol 2016 05 17;54(5):1368-71. Epub 2016 Feb 17.

Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA

Using a rapid bacterial lysis method, the Check MDR CT103 and CT103 XL microarrays demonstrated accuracies of 98.1% and 94.2%, respectively, for detection of known resistance genes in 108 multidrug-resistant Gram-negative bacilli. In 45 isolates, 49 previously unrecognized extended-spectrum β-lactamase or plasmid AmpC targets were detected and confirmed by conventional PCR.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/JCM.03302-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4844729PMC
May 2016

Carbapenem- and Colistin-Resistant Enterobacter cloacae from Delta, Colorado, in 2015.

Antimicrob Agents Chemother 2016 05 22;60(5):3141-4. Epub 2016 Apr 22.

Division of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA Division of Infectious Diseases, Mayo Clinic, Rochester, Minnesota, USA

Resistance to carbapenems in Enterobacteriaceae is a clinical problem of growing significance. Difficulty in treating multidrug-resistant Gram-negative organisms with conventional antibiotics has led to a renewed and increasing use of polymyxin compounds, such as colistin. Here, we report the isolation of carbapenem- and colistin-resistant Enterobacter cloacae from a polymicrobial lower extremity wound in an ambulatory patient. Whole-genome sequencing demonstrated the presence of chromosomal blaIMI-1 and blaAmpC, as well as numerous efflux pump genes.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/AAC.03055-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4862446PMC
May 2016

Draft Genome Sequences of Nine Pseudomonas aeruginosa Strains, Including Eight Clinical Isolates.

Genome Announc 2015 Oct 8;3(5). Epub 2015 Oct 8.

Department of Surgery, Mayo Clinic, Rochester, Minnesota, USA Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA

We report on nine draft genomes of Pseudomonas aeruginosa isolates, assembled using a hybrid paired-end and Nextera mate-pair library approach. Eight are of clinical origin, and one is the ATCC 27853 strain. We also report their multilocus sequence types.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/genomeA.01154-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4599088PMC
October 2015

Reply to Idelevich and Beck.

Clin Infect Dis 2016 Jan 22;62(2):269-70. Epub 2015 Sep 22.

Laboratory Medicine and Pathology Infectious Diseases.

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/cid/civ826DOI Listing
January 2016

In Vitro Activities of Ceftazidime-Avibactam, Aztreonam-Avibactam, and a Panel of Older and Contemporary Antimicrobial Agents against Carbapenemase-Producing Gram-Negative Bacilli.

Antimicrob Agents Chemother 2015 Dec 21;59(12):7842-6. Epub 2015 Sep 21.

Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA

Among 177 carbapenemase-producing Gram-negative bacilli (108 KPC, 32 NDM, 11 IMP, 8 OXA-48, 4 OXA-181, 2 OXA-232, 5 IMI, 4 VIM, and 3 SME producers), aztreonam-avibactam was active against all isolates except two NDM producers with elevated MICs of 8/4 and 16/4 mg/liter; ceftazidime-avibactam was active against all KPC-, IMI-, SME-, and most OXA-48 group-producing isolates (93%) but not metallo-β-lactamase producers. Among older and contemporary antimicrobials, the most active were colistin, tigecycline, and fosfomycin, with overall susceptibilities of 88%, 79%, and 78%, respectively.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/AAC.02019-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4649150PMC
December 2015
-->