Emerging multidrug resistance in community-associated Staphylococcus aureus involved in skin and soft tissue infections and nasal colonization.

Background: Staphylococcus aureus is a major pathogen causing significant morbidity and mortality worldwide. The emergence of MDR S. aureus strains in the community setting has major implications in disease management. However, data regarding the occurrence and patterns of MDR community-associated S. aureus sub-clones is limited. Objectives: To use whole-genome sequences to describe the diversity and distribution of resistance mechanisms among community-associated S. aureus isolates. Methods: S. aureus isolates from skin and soft tissue infections (SSTIs) and nasal colonization were collected from patients within 10 primary care clinics from 2007 to 2015. The Illumina Miseq platform was used to determine the genome sequences for 144 S. aureus isolates. Phylogenetic and bioinformatics analyses were performed using in silico tools. The resistome was assembled and compared with the phenotypically derived antibiogram. Results: Approximately one-third of S. aureus isolates in the South Texas primary care setting were MDR. A higher proportion of SSTI isolates were MDR in comparison with nasal colonization isolates. Individuals with MDR S. aureus SSTIs were more likely to be African American and obese. Furthermore, S. aureus populations are able to acquire and lose antimicrobial resistance genes. USA300 strains were differentiated by a stable chromosomal mutation in gyrA conferring quinolone resistance. The resistomes were highly predictive of antimicrobial resistance phenotypes. Conclusions: These findings highlight the high prevalence and epidemiological factors associated with MDR S. aureus strains in the community setting and demonstrate the utility of next-generation sequencing to potentially quicken antimicrobial resistance detection and surveillance for targeted interventions.

A prospective observational cohort study in primary care practices to identify factors associated with treatment failure in Staphylococcus aureus skin and soft tissue infections.

BACKGROUND: The incidence of outpatient visits for skin and soft tissue infections (SSTIs) has substantially increased over the last decade. The emergence of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) has made the management of S. aureus SSTIs complex and challenging. The objective of this study was to identify risk factors contributing to treatment failures associated with community-associated S. aureus skin and soft tissue infections SSTIs. METHODS: This was a prospective, observational study among 14 primary care clinics within the South Texas Ambulatory Research Network. The primary outcome was treatment failure within 90 days of the initial visit. Univariate associations between the explanatory variables and treatment failure were examined. A generalized linear mixed-effect model was developed to identify independent risk factors associated with treatment failure. RESULTS: Overall, 21% (22/106) patients with S. aureus SSTIs experienced treatment failure. The occurrence of treatment failure was similar among patients with methicillin-resistant S. aureus and those with methicillin-susceptible S. aureus SSTIs (19 vs. 24%; p = 0.70). Independent predictors of treatment failure among cases with S. aureus SSTIs was a duration of infection of ≥7 days prior to initial visit [aOR, 6.02 (95% CI 1.74-19.61)] and a lesion diameter size ≥5 cm [5.25 (1.58-17.20)]. CONCLUSIONS: Predictors for treatment failure included a duration of infection for ≥7 days prior to the initial visit and a wound diameter of ≥5 cm. A heightened awareness of these risk factors could help direct targeted interventions in high-risk populations.

The automated clinical microbiology laboratory: fact or fantasy?

Automated chemistry laboratories dependent on robotic processes are the standard in both academic and large community hospital settings. Diagnostic microbiology manufacturers are betting that robotics will be used for specimen processing, plate reading, and organism identification in the near future. These systems are highly complex and have large footprints and hefty price tags. However, they are touted as being more efficient, rapid, and accurate than standard processes. Certain features, such as image collection, are highly innovative. Hospital administrators may be swayed to institute these new systems because of the promise of the need for fewer skilled workers, higher throughput, and greater efficiency. They also may be swayed by the fact that workers with the requisite clinical microbiology skills are becoming more difficult to find, and this technology should allow fewer skilled workers to handle larger numbers of cultures. In this Point-Counterpoint, Nate Ledeboer, Medical Director, Clinical Microbiology and Molecular Diagnostics, Dynacare Laboratories, and Froedtert Hospital, Milwaukee, WI, will explain why he believes that this approach will become widespread, while Steve Dallas of the University of Texas Health Science Center San Antonio explains why he thinks that this automation may not become widely used.

A Case of New Delhi Metallo-ß-Lactamase-Producing Enterobacter and a Review of Cases in the United States From January 2009 to September 2022.

Antimicrobial resistance is a growing problem. Novel resistance mechanisms continue to emerge, and the pipeline of antimicrobial development struggles to keep up. Antimicrobial stewardship and proper infection control are key in preventing the spread of these infections. A case of a carbapenem-resistant Enterobacter cloacae complex urinary isolate was identified in an 81-year-old male patient at the San Antonio Veterans Affairs hospital, Texas, USA. The patient was placed on isolation, and further testing of the isolate to other antibiotics requested. The purpose of this study is to analyze the details of reports of such cases and to review at-risk populations and appropriate treatment for resistant organisms.

Diverse Role of blaCTX-M and Porins in Mediating Ertapenem Resistance among Carbapenem-Resistant Enterobacterales.

Among carbapenem-resistant Enterobacterales (CRE) are diverse mechanisms, including those that are resistant to meropenem but susceptible to ertapenem, adding further complexity to the clinical landscape. This study investigates the emergence of ertapenem-resistant, meropenem-susceptible (ErMs) Escherichia coli and Klebsiella pneumoniae CRE across five hospitals in San Antonio, Texas, USA, from 2012 to 2018. The majority of the CRE isolates were non-carbapenemase producers (NCP; 54%; 41/76); 56% of all NCP isolates had an ErMs phenotype. Among ErMs strains, E. coli comprised the majority (72%). ErMs strains carrying blaCTX-M had, on average, 9-fold higher copies of blaCTX-M than CP-ErMs strains as well as approximately 4-fold more copies than blaCTX-M-positive but ertapenem- and meropenem-susceptible (EsMs) strains (3.7 vs. 0.9, p < 0.001). Notably, carbapenem hydrolysis was observed to be mediated by strains harboring blaCTX-M with and without a carbapenemase(s). ErMs also carried more mobile genetic elements, particularly IS26 composite transposons, than EsMs (37 vs. 0.2, p < 0.0001). MGE- ISVsa5 was uniquely more abundant in ErMs than either EsMs or ErMr strains, with over 30 more average ISVsa5 counts than both phenotype groups (p < 0.0001). Immunoblot analysis demonstrated the absence of OmpC expression in NCP-ErMs E. coli, with 92% of strains lacking full contig coverage of ompC. Overall, our findings characterize both collaborative and independent efforts between blaCTX-M and OmpC in ErMs strains, indicating the need to reappraise the term "non-carbapenemase (NCP)", particularly for strains highly expressing blaCTX-M. To improve outcomes for CRE-infected patients, future efforts should focus on mechanisms underlying the emerging ErMs subphenotype of CRE strains to develop technologies for its rapid detection and provide targeted therapeutic strategies.

Development of doxycycline MIC and disk diffusion interpretive breakpoints and revision of tetracycline breakpoints for Streptococcus pneumoniae.

A study was performed to derive susceptibility testing interpretive breakpoints for doxycycline with Streptococcus pneumoniae and to reassess breakpoints for tetracycline using the requirements defined in Clinical and Laboratory Standards Institute (CLSI) document M23-A3. Tetracycline and doxycycline MICs and disk diffusion zone sizes were determined on 189 isolates selected from the 2009-2010 CDC Active Bacterial Core surveillance strain collection according to the testing methods described in CLSI documents M07-A8 and M02-A10. Tetracycline and doxycycline MICs and zones were compared to each other directly, and the reproducibility of MICs and zone diameters for both drugs was determined. Scattergrams of tetracycline MICs versus corresponding zone diameters and doxycycline MICs versus zones were prepared, and analysis indicated that the present CLSI tetracycline MIC and disk breakpoints did not fit the susceptibility data for doxycycline. Doxycycline was 1 to 3 dilutions more potent than tetracycline, especially in strains harboring the tetM resistance determinant. tetM was detected in ≥ 90% of isolates having tetracycline MICs of ≥ 4 µg/ml and in ≥ 90% with doxycycline MICs of ≥ 1. Limited pharmacokinetic/pharmacodynamic (PK/PD) data coupled with application of the error-rate bounded method of analysis suggested doxycycline-susceptible breakpoints of either ≤ 0.25 µg/ml or ≤ 0.5 µg/ml, with intermediate and resistant breakpoints 1 and 2 dilutions higher, respectively. The disk diffusion zone diameter correlates were susceptible at ≥ 28 mm, intermediate at 25 to 27 mm, and resistant at ≤ 24 mm. Revised lower tetracycline MIC breakpoints were suggested as susceptible at ≤ 1 µg/ml, intermediate at 2 µg/ml, and resistant at ≥ 4 µg/ml. Suggested tetracycline disk diffusion zones were identical to those of doxycycline.

Sensitivity and Specificity of a Novel Colony Characteristic for Determination of Methicillin-Resistant Staphylococcus aureus.

PURPOSE: To assess colony morphology of Staphylococcus aureus isolates for target shape (T1) and its utility in the identification of methicillin-resistant S. aureus (MRSA). METHODS: Staphylococcus species isolated from blood cultures were studied for colony morphology characteristics. A polymerase chain reaction (PCR) test was performed on positive blood culture bottles for the detection of S. aureus and methicillin resistance. Colony morphology was read at 24 and 48 hours and defined as follows: target shaped (T1) - an elevated colony center encircled by a pale zone, which is surrounded by a single ring of peripheral enhancement giving a 'target' appearance; dome-shaped (T2) with an elevated center lacking the 'target' appearance. RESULTS: At 48 hours, 73.7% of MRSA and 59.5% of coagulase-negative staphylococci (CoNS) showed T1 morphology. T1 morphology has a sensitivity of 73.68% and specificity of 93.55% amongst S. aureus for identification of methicillin resistance and a high positive predictive value (95.45%) at 48 hours. CONCLUSION: T1 morphology has a modest sensitivity with specificity and positive predictive value amongst S. aureus for identification of methicillin resistance at 48 hours. It can be potentially used for the identification of MRSA, especially in resource-limited settings and wherein a molecular test is not repeated if PCR testing has already identified methicillin-sensitive S. aureus (MSSA) on a recent specimen on the same patient.

Malassezia Hepatic Abscess in a Neonate.

Malassezia sp. require exogenous lipid for growth and can cause disseminated infection in neonates requiring intravenous lipid infusions. Usually, Malassezia infection in neonates presents as fungemia or hematogenous dissemination into bone or lungs. We present a presumed case of Malassezia liver abscess associated with lipid infusion via a mispositioned umbilical venous catheter.

High-throughput microarray for antimicrobial susceptibility testing.

We describe the development of a novel, high-throughput, nano-scale microarray platform for antimicrobial susceptibility testing (AST). The platform allows to process 480 samples at 50 nL volume on a single chip, analyze by fluorescence read-out with an easy dunk-and-rinse step, and the ability to process multiple samples and chips simultaneously. We demonstrate the applicability of this chip for culturing community acquired methicillin resistant Staphylococcus aureus (CA-MRSA), and perform AST against clinical isolates of CA-MRSA. The chip platform holds promise for an impact in microbial biotechnology as an attractive high-throughput, lower sample volume and quicker alternative to conventional AST such as the traditional broth microdilution or the newer automated systems.

Treatment of streptococcal pharyngitis with once-daily compared with twice-daily amoxicillin: a noninferiority trial.

BACKGROUND: Two relatively small previous studies comparing once-daily amoxicillin with conventional therapy for group A streptococcal (GAS) pharyngitis reported similar rates of bacteriologic success for each treatment group. The purpose of this study was to further evaluate once-daily amoxicillin for GAS pharyngitis in a larger study. METHODS: In a single pediatric practice, from October through May for 2 consecutive years (2001-2003), we recruited children 3 to 18 years of age who had symptoms and signs suggestive of GAS pharyngitis. Patients with a positive rapid test for GAS were stratified by weight (<40 kg or >or=40 kg) and then randomly assigned to receive once-daily (750 mg or 1000 mg) or twice-daily (2 doses of 375 mg or 500 mg) amoxicillin for 10 days. We determined bacteriologic failure rates for GAS in the pharynx from subsequent swabs taken at 14 to 21 (visit 2) and 28 to 35 (visit 3) days after treatment initiation. We conducted a randomized, controlled, investigator-blinded, noninferiority trial to evaluate whether amoxicillin given once daily would have a bacteriologic failure rate no worse than that of amoxicillin given twice daily within a prespecified margin of 10%. GAS isolates were characterized to distinguish bacteriologic failures from new acquisitions. Adverse events were described and adherence was evaluated by review of returned daily logs and dosage bottles. RESULTS: Of 2139 potential study patients during the 2-year period, we enrolled 652 patients, 326 into each treatment group. Children in the 2 groups were comparable with respect to all demographic and clinical characteristics except that children <40 kg more often presented with rash in each treatment group. At visit 2, failure rates were 20.1% (59 of 294) for the once-daily group and 15.5% (46 of 296) for the twice-daily group (difference, 4.53%; 90% confidence interval [CI], -0.6 to 9.7). At visit 3, failure rates were 2.8% (6 of 216) for the once-daily group and 7.1% (16 of 225) for the twice-daily group (difference, -4.33; 90% CI, -7.7 to -1.0). Gastrointestinal and other adverse events occurred in the once-daily treatment group with a frequency comparable to that in the twice-daily treatment group. Presumed allergic reactions occurred in 0.9% (6 of 635). More than 95% (516 of 541) of patients complied with 10 days of therapy with no significant differences between groups. CONCLUSIONS: We conclude that amoxicillin given once daily is not inferior to amoxicillin given twice daily. Gastrointestinal and other events did not occur significantly more often in the once-daily treatment group. From the data in this large, investigator-blinded, controlled study, once-daily amoxicillin appears to be a suitable regimen for treatment of GAS pharyngitis.

Comparative whole genome sequencing of community-associated methicillin-resistant Staphylococcus aureus sequence type 8 from primary care clinics in a Texas community.

STUDY OBJECTIVE: Our understanding of the molecular dynamics driving the community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) epidemic at the whole genome level is limited. We sought to assess the use of whole genome sequencing (WGS) to evaluate the genomic diversity and genotypic prediction of antimicrobial resistance of CA-MRSA isolates from patients in South Texas. DESIGN: Comparative whole genome sequencing. ISOLATES: Thirteen clinical CA-MRSA isolates recovered from patients presenting with skin and soft tissue infections to nine primary care clinics in the South Texas Ambulatory Research Network between 2010 and 2013. MEASUREMENTS AND MAIN RESULTS: Comparative WGS was performed on the 13 MRSA sequence type 8 clinical isolates. We compared the resistome of genes encoding for antibiotic resistance with a phenotypically derived antibiogram using standard antimicrobial susceptibility testing. The strains differed by an average of 72 single nucleotide polymorphisms (SNPs) per isolate in the core genome compared with FPR3757 (USA300, reference strain). There were a total of 623 unique SNPs in the core genome (range 47-88 SNPs per isolate). We identified 19 nonsynonymous SNPs in genes encoding proven or putative S. aureus virulence determinants in the core genome. There was complete concordance between genotypic evidence for antimicrobial resistance and the phenotypically derived antibiogram. CONCLUSION: Overall, although these CA-MRSA isolates were similar on the level of clonal type, clinical syndrome, and geographic area, the strains were diverse at the genome level. Furthermore, our findings provide important proof-of-concept information for using WGS as a potential front-end screening tool for antimicrobial resistance predictions.

Extrapharyngeal group A Streptococcus infection: diagnostic accuracy and utility of rapid antigen testing.

BACKGROUND: Antigen tests have been well-studied and are widely used in pediatric practice for rapid detection of group A Streptococcus (GAS) infections in the throat, but they have not been examined sufficiently for the detection of infection of skin sites, such as the perineal region or impetiginous lesions. METHODS: During the 3-year period 1999 to 2002, we evaluated 239 patients with suspected GAS skin infection, in 5 pediatric practices, using 3 Dacron swabs for each site. The first swab was tested in the pediatric office laboratory with an antigen detection kit. For the first 91 patients, the Abbott Test Pack Plus antigen detection test (ADT) was used. The Abbott Signify Strep A ADT was used to test subsequent patients. The second swab was tested with BD Directigen 1-2-3 ADT in the hospital laboratory. The third swab was placed in modified Stuart's transport medium for comparison of recovery of GAS from culture in broth or on agar. A positive culture served as the reference standard. Test performance and test accuracy were determined for each ADT. RESULTS: Of the 247 ADTs and cultures performed on 239 patients, 91 with suspected skin infection were tested with the Test Pack Plus test, 149 with the Signify Strep A test and 247 with the Directigen test. Eighty-six (35%) cultures were positive, 73 from perineal sites (54 rectal, 13 vaginal, 6 penile) and 13 from impetiginous lesions. There was 100% concordance for the 86 cultures positive for GAS in a comparison between dry Dacron swabs and swabs that had been placed in modified Stuart's transport medium. Test Pack Plus and Signify Strep A ADTs had similar performance characteristics for skin infections: sensitivity, 92 and 88%; specificity, 99 and 97%; positive predictive value, 96 and 94%; and negative predictive value, 97 and 93%. Directigen ADT had sensitivity 78%, specificity 100%, positive predictive value 100% and negative predictive value 89%. Accuracy for the tests varied from 92 to 97%. CONCLUSION: Tests designed to detect GAS carbohydrate antigen in patients with pharyngitis can be used rapidly and accurately to detect GAS antigen in patients with cutaneous lesions suspected of GAS infection.

Treatment failure and costs in patients with methicillin-resistant Staphylococcus aureus (MRSA) skin and soft tissue infections: a South Texas Ambulatory Research Network (STARNet) study.

OBJECTIVE: To measure the incidence of treatment failure and associated costs in patients with methicillin-resistant Staphylococcus aureus skin and soft tissue infections (SSTIs). METHODS: This was a prospective, observational study in 13 primary care clinics. Primary care providers collected clinical data, wound swabs, and 90-day follow-up information. Patients were considered to have "moderate or complicated" SSTIs if they had a lesion ≥5 cm in diameter or diabetes mellitus. Treatment failure was evaluated within 90 days of the initial visit. Cost estimates were obtained from federal sources. RESULTS: Overall, treatment failure occurred in 21% of patients (21 of 98) at a mean additional cost of $1,933.71 per patient. In a subgroup analysis of patients who received incision and drainage, those with moderate or complicated SSTIs had higher rates of treatment failure than those with mild or uncomplicated SSTIs (36% vs. 10%; P=.04). CONCLUSIONS: One in 5 patients presenting to a primary care clinic for a methicillin-resistant S. aureus SSTI will likely require additional interventions at an associated cost of almost $2,000 per patient. Baseline risk stratification and new treatment approaches are needed to reduce treatment failures and costs in the primary care setting.