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Schuetz AN, Theel ES, Cole NC, Rothstein TE, Gordy GG, Patel R. Testing for Helicobacter pylori in an era of antimicrobial resistance. J Clin Microbiol 2024; 62:e0073223. [PMID: 38193664 PMCID: PMC10865822 DOI: 10.1128/jcm.00732-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024] Open
Abstract
Antimicrobial resistance in Helicobacter pylori has reached alarming levels and is compromising traditional empiric treatment of H. pylori. Antimicrobial susceptibility testing is routinely performed for infectious diseases when there is a risk of resistance and is now recommended to guide therapy for H. pylori. This mini-review overviews the current diagnostics for H. pylori with a focus on tests that enable susceptibility-guided treatment, including molecular tests performed directly on stool and endoscopically collected specimens.
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Affiliation(s)
- Audrey N. Schuetz
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Elitza S. Theel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Nicolynn C. Cole
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Tanner E. Rothstein
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Garrett G. Gordy
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Division of Public Health, Infectious Diseases, and Occupational Medicine, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
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Mushtaq A, Chen DJ, Strand GJ, Dylla BL, Cole NC, Mandrekar J, Patel R. Corrigendum to "Clinical significance of coryneform Gram-positive rods from blood identified by MALDI-TOF mass spectrometry and their susceptibility profiles - a retrospective chart review" [Diagn Microbiol Infect Dis 2016;85(3):372-376]. Diagn Microbiol Infect Dis 2019; 94:106. [PMID: 30857915 DOI: 10.1016/j.diagmicrobio.2019.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ammara Mushtaq
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Derrick J Chen
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Gregory J Strand
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Brenda L Dylla
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Nicolynn C Cole
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Jayawant Mandrekar
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN 55905, USA
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA; Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
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Bhatti MM, Rucinski SL, Schwab JJ, Cole NC, Gebrehiwot SA, Patel R. Eight-Year Review of Bordetella pertussis Testing Reveals Seasonal Pattern in the United States. J Pediatric Infect Dis Soc 2017; 6:91-93. [PMID: 26621328 DOI: 10.1093/jpids/piv079] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 10/25/2015] [Indexed: 12/14/2022]
Abstract
Review of Bordetella pertussis polymerase chain reaction testing from 2007 through 2014 revealed a yearly spike in positivity rates during the summer throughout the United States. Paradoxically, the highest test volumes occurred outside of this time frame, which provides an opportunity for improved test utilization.
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Affiliation(s)
- Micah M Bhatti
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology
| | - Stefanea L Rucinski
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology
| | - Jeramy J Schwab
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology
| | - Nicolynn C Cole
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology
| | - Senait A Gebrehiwot
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology.,Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota
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Mushtaq A, Greenwood-Quaintance KE, Cole NC, Kohner PC, Ihde SM, Strand GJ, Harper LW, Virk A, Patel R. Differential Antimicrobial Susceptibilities of Granulicatella adiacens and Abiotrophia defectiva. Antimicrob Agents Chemother 2016; 60:5036-9. [PMID: 27216060 PMCID: PMC4958207 DOI: 10.1128/aac.00485-16] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 05/16/2016] [Indexed: 12/13/2022] Open
Abstract
MICs of 25 Abiotrophia defectiva and 109 Granulicatella adiacens isolates were determined by broth microdilution. Using CLSI breakpoints, the susceptibilities of A. defectiva and G. adiacens isolates were, respectively, 24% and 34% to penicillin, 92% and 22% to ceftriaxone, 48% and 3% to cefepime, 72% and 87% to meropenem, 92% and 10% to cefotaxime, 100% and 97% to levofloxacin, 92% and 80% to clindamycin, and 24% and 50% to erythromycin. All isolates were susceptible to vancomycin. In the penicillin-susceptible subgroup, all A. defectiva isolates were susceptible to ceftriaxone; however, 62% of G. adiacens isolates were ceftriaxone nonsusceptible.
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Affiliation(s)
- Ammara Mushtaq
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Kerryl E Greenwood-Quaintance
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Nicolynn C Cole
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Peggy C Kohner
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Sherry M Ihde
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Gregory J Strand
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Lance W Harper
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Abinash Virk
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Robin Patel
- 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
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Mushtaq A, Chen DJ, Strand GJ, Dylla BL, Cole NC, Mandrekar J, Patel R. Clinical significance of coryneform Gram-positive rods from blood identified by MALDI-TOF mass spectrometry and their susceptibility profiles - a retrospective chart review. Diagn Microbiol Infect Dis 2016; 85:372-376. [PMID: 27179368 DOI: 10.1016/j.diagmicrobio.2016.04.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 04/20/2016] [Indexed: 11/16/2022]
Abstract
With the advent of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), most Gram-positive rods (GPRs) are readily identified; however, their clinical relevance in blood cultures remains unclear. Herein, we assessed the clinical significance of GPRs isolated from blood and identified in the era of MALDI-TOF MS. A retrospective chart review of patients presenting to the Mayo Clinic, Rochester, MN, from January 1, 2013, to October 13, 2015, was performed. Any episode of a positive blood culture for a GPR was included. We assessed the number of bottles positive for a given isolate, time to positivity of blood cultures, patient age, medical history, interpretation of culture results by the healthcare team and whether infectious diseases consultation was obtained. We also evaluated the susceptibility profiles of a larger collection of GPRs tested in the clinical microbiology laboratory of the Mayo Clinic, Rochester, MN from January 1, 2013, to October 31, 2015. There were a total of 246 GPRs isolated from the blood of 181 patients during the study period. 56% (n = 101) were deemed contaminants by the healthcare team and were not treated; 33% (n = 59) were clinically determined to represent true bacteremia and were treated; and 8% (n = 14) were considered of uncertain significance, with patients prescribed treatment regardless. Patient characteristics associated with an isolate being treated on univariate analysis included younger age (P = 0.02), identification to the species level (P = 0.02), higher number of positive blood culture sets (P < 0.0001), lower time to positivity (P < 0.0001), immunosuppression (P = 0.03), and recommendation made by an infectious disease consultant (P = 0.0005). On multivariable analysis, infectious diseases consultation (P = 0.03), higher number of positive blood culture sets (P = 0.0005) and lower time to positivity (P = 0.03) were associated with an isolate being treated. 100, 83, 48 and 34% of GPRs were susceptible to vancomycin, meropenem, penicillin and ceftriaxone, respectively.
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Affiliation(s)
- Ammara Mushtaq
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Derrick J Chen
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Gregory J Strand
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Brenda L Dylla
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Nicolynn C Cole
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Jayawant Mandrekar
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN 55905, USA
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA; Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA.
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Peel TN, Cole NC, Dylla BL, Patel R. Matrix-assisted laser desorption ionization time of flight mass spectrometry and diagnostic testing for prosthetic joint infection in the clinical microbiology laboratory. Diagn Microbiol Infect Dis 2014; 81:163-8. [PMID: 25533615 DOI: 10.1016/j.diagmicrobio.2014.11.015] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 11/13/2014] [Accepted: 11/24/2014] [Indexed: 11/18/2022]
Abstract
Identification of pathogen(s) associated with prosthetic joint infection (PJI) is critical for patient management. Historically, many laboratories have not routinely identified organisms such as coagulase-negative staphylococci to the species level. The advent of matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS) has enhanced clinical laboratory capacity for accurate species-level identification. The aim of this study was to describe the species-level identification of microorganisms isolated from periprosthetic tissue and fluid specimens using MALDI-TOF MS alongside other rapid identification tests in a clinical microbiology laboratory. Results of rapid identification of bacteria isolated from periprosthetic joint fluid and/or tissue specimens were correlated with clinical findings at Mayo Clinic, Rochester, Minnesota, between May 2012 and May 2013. There were 178 PJI and 82 aseptic failure (AF) cases analyzed, yielding 770 organisms (median, 3/subject; range, 1-19/subject). MALDI-TOF MS was employed for the identification of 455 organisms (59%) in 197 subjects (123 PJIs and 74 AFs), with 89% identified to the species level using this technique. Gram-positive bacteria accounted for 68% and 93% of isolates in PJI and AF, respectively. However, the profile of species associated with infection compared to specimen contamination differed. Staphylococcus aureus and Staphylococcus caprae were always associated with infection, Staphylococcus epidermidis and Staphylococcus lugdunensis were equally likely to be a pathogen or a contaminant, whereas the other coagulase-negative staphylococci were more frequently contaminants. Most streptococcal and Corynebacterium isolates were pathogens. The likelihood that an organism was a pathogen or contaminant differed with the prosthetic joint location, particularly in the case of Propionibacterium acnes. MALDI-TOF MS is a valuable tool for the identification of bacteria isolated from patients with prosthetic joints, providing species-level identification that may inform culture interpretation of pathogens versus contaminants.
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Affiliation(s)
- Trisha N Peel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA; Department of Surgery, St Vincent's Hospital Melbourne, University of Melbourne, Melbourne, VIC, Australia.
| | - Nicolynn C Cole
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Brenda L Dylla
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA; Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, MN, USA.
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Vasoo S, Mason EL, Gustafson DR, Cunningham SA, Cole NC, Vetter EA, Steinmann SP, Wilson WR, Patel R, Berbari EF, Henry NK. Desulfovibrio legallii prosthetic shoulder joint infection and review of antimicrobial susceptibility and clinical characteristics of Desulfovibrio infections. J Clin Microbiol 2014; 52:3105-10. [PMID: 24850351 PMCID: PMC4136176 DOI: 10.1128/jcm.00083-14] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 04/11/2014] [Indexed: 11/20/2022] Open
Abstract
We describe a case of shoulder hemiarthroplasty infection with Desulfovibrio legallii. Antimicrobial susceptibilities of 36 Desulfovibrio isolates are presented. Metronidazole and carbapenems exhibited reliable activity, although piperacillin-tazobactam did not. Eleven previous cases of Desulfovibrio infection are reviewed; most arose from a gastrointestinal tract-related source.
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Affiliation(s)
- Shawn Vasoo
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Erin L Mason
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Daniel R Gustafson
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Scott A Cunningham
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Nicolynn C Cole
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Emily A Vetter
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Scott P Steinmann
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, Minnesota, USA
| | - Walter R Wilson
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Robin Patel
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Elie F Berbari
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Nancy K Henry
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA Division of Pediatric Infectious Diseases, Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota, USA
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Selinger CP, Ellul P, Smith PA, Cole NC. Oesophageal stent insertion for palliation of dysphagia in a District General Hospital: experience from a case series of 137 patients. QJM 2008; 101:545-8. [PMID: 18443004 DOI: 10.1093/qjmed/hcn045] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Endoscopic oesophageal stent insertion is a widely used procedure to alleviate dysphagia caused by malignant strictures of the oesophagus and gastric cardia. It can, however, be associated with significant complications, mortality and morbidity. AIM AND METHOD This retrospective case note study was undertaken to assess success rates, complications and mortality of oesophageal stenting when undertaken in a UK District General Hospital (DGH) setting. Patients who underwent oesophageal stenting for malignant disease from January 2000 to January 2006 were included. RESULTS Of the 137 patients studied, oesophageal adenocarcinoma was present in 57% of patients, squamous cell oesophageal carcinoma in 37% and gastric adenocarcinoma in 6%. Indications for stent insertion were: presence of non-resectable tumours (65%), co-morbidities that contraindicated surgery (25%), refusal by patients for surgery for potentially resectable disease (6%) and a need for enhanced oral nutrition prior to surgery (4%). Prior to stenting 86.4% of patients suffered from advanced dysphagia. A significant improvement in symptoms was seen in 94% of patients. Discharge from hospital was within 48 h in 45% of cases. Chest pain was experienced by 13.9% of patients and serious acute stent-related complications (perforation or bleeding) occurred in 5.8% of patients. Overall 41.6% of patients had at least one complication. Mortality was 4.4% at 7 days and 24.8% at 30 days. CONCLUSION Oesophageal stent insertion proved to be an effective palliation of dysphagia in group studied. It is a relatively safe procedure with a low rate of serious acute complications (5.8%) and can be done as a short stay in many patients.
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Affiliation(s)
- C P Selinger
- Penine Acute NHS Trust, Greater Manchester, England.
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