Polymerase chain reaction-based active surveillance of MRSA in emergency department patients

Burden of Antimicrobial Resistance in Japan: A Systematic Literature Review and Meta-Analysis

INTRODUCTION

Antimicrobial resistance (AMR) is one of the most serious public health challenges worldwide, including in Japan. However, there is limited evidence assessing the AMR burden in Japan. Thus, this systematic literature review (SLR) and meta-analysis (MA) were conducted to assess the clinical and economic burden of AMR in Japan.

METHODS

Comprehensive literature searches were performed on EMBASE, MEDLINE, the Cochrane Library, and ICHUSHI between 2012 and 2022 following the Preferred Reporting Items for Systematic Reviews and Meta-Analysis guidelines. MA estimated a pooled effect between the two comparative arms (AMR vs. non-AMR). The results were reported in measures of odds ratios (ORs) for in-hospital mortality and in standardized mean differences (SMDs) for length of stay (LOS) and direct medical costs.

RESULTS

Literature searches identified 1256 de-duplicated records, of which 56 observational studies (English, n = 35; Japanese, n = 21) were included. Of note, twenty-two studies (39.3%) compared the AMR group with non-AMR group. In the SLR, in-hospital mortality, LOS, and direct medical costs were higher in the AMR group compared to the non-AMR group. Eight studies were selected for the MA. In the AMR group, the pooled estimate showed a statistically higher in-hospital mortality [random effect (RE)-OR 2.25, 95% CI 1.34-3.79; I2 = 89%; τ2 = 0.2257, p < 0.01], LOS (RE-SMD 0.37, 95% CI  - 0.09-0.84; I2 = 99%; τ2 = 0.3600, p < 0.01), and direct medical cost (RE-SMD 0.53, 95% CI 0.43-0.62; I2 = 0.0%; τ2 = 0.0, p = 0.88) versus the non-AMR group.

CONCLUSION

Our study presents an overview of the clinical and economic burden of AMR in Japan. Patients with AMR infections experience significantly higher in-hospital mortality, LOS, and direct medical costs compared with patients without AMR infections.

Molecular characterization of typing and subtyping of Staphylococcal cassette chromosome SCCmec types I to V in methicillin-resistant Staphylococcus aureus from clinical isolates from COVID-19 patients

Background and Objectives

Methicillin resistance is acquired by the bacterium due to mecA gene which codes for penicillin-binding protein (PBP2a) having low affinity for β-lactam antibiotics. mecA gene is located on a mobile genetic element called staphylococcal cassette chromosome mec (SCCmec). SCCmec genomic island comprises two site-specific recombinase genes namely ccrA and ccrB [cassette chromosome recombinase] accountable for mobility. Currently, SCCmec elements are classified into types I, II, III, IV and V based on the nature of the mec and ccr gene complexes and are further classified into subtypes according to variances in their J region DNA. SSCmec type IV has been found in community-acquired isolates with various genetic backgrounds. The present study was undertaken to categorize the types of SCCmec types and subtypes I, II, III, IVa, b, c, d, and V and PVL genes among clinical MRSA isolates from COVID-19 confirmed cases.

Materials and Methods

Based on the Microbiological and Molecular (mecA gene PCR amplification) confirmation of MRSA isolated from 500 MRSA SCCmec clinical samples, 144 cultures were selected for multiplex analysis. The multiplex PCR method developed by Zhang et al. was adapted with some experimental alterations to determine the specific type of these isolates.

Results

Of the total 500 MRSA, 144 MRSA (60 were CA-MRSA and 84 were HA-MRSA) were selected for characterization of novel multiplex PCR assay for SSCmec Types I to V in MRSA. Molecular characterization of multiplex PCR analysis revealed results compare to the phenotypic results. Of the 60 CA-MRSA; in 56 MRSA strains type IVa was found and significantly defined as CA-MRSA while 4 strains showed mixed gens subtypes. Type II, III, IA, and V were present in overall 84 HA-MRSA. Molecular subtyping was significantly correlated to define molecularly as CA-MRSA and HA-MRSA however 15 (10%) strains showed mixed genes which indicates the alarming finding of changing epidemiology of CA-MRSA and HA-MRSA as well.

Conclusion

We have all witnessed of COVID-19 pandemic, and its mortality was mostly associated with co-morbid conditions and secondary infections of MDR pathogens. Rapid detections of causative agents of these superbugs with their changing epidemiology by investing in typing and subtyping clones are obligatory. We have described an assay designed for targeting SSCmec types and subtypes I, II, III, IVa,V according to the current updated SCCmec typing system. Changing patterns of molecular epidemiology has been observed by this newly described assay.

Utility of a Cell-Direct Polymerase Chain Reaction-Based Nucleic Acid Lateral Flow Immunoassay for Detection of Bacteria in Peripheral Blood Leukocytes of Suspected Sepsis Cases

Background

The detection of the pathogens in the blood is essential for the management of septic patients; however, conventional blood culture takes 2–3 days. Therefore, rapid and convenient methods may be useful to aid clinical decision-making.

Methods

Blood samples with sepsis clinically diagnosed in cases that fulfilled the diagnostic criteria were used and analyzed the utility of a novel bacterial nucleic acid identification test using a cell-direct polymerase chain reaction (cdPCR)-based nucleic acid lateral flow immunoassay (NALFIA) which were named as “DiagnoSep” to detect representative bacteria in peripheral blood leukocytes in patients admitted to our hospital and compared the conventional blood culture results simultaneously taken from the patients.

Results

We analyzed the total 42 samples in the terms of this study and found 18 (42.8%) were positive on cdPCR-NALFIA, and 24 (57.1%) were positive on blood cultures. Although the positive rate was higher with blood cultures, 15 samples showed positive results from both blood cultures and cdPCR-NALFIA, and the identified bacteria agreed for 10 samples. Of the 18 cdPCR-NALFIA-positive cases, the results for 8 samples differed from the results of blood cultures; four of them had an implanted pacemaker or prosthetic joint and were positive for Staphylococcus aureus or Staphylococcus epidermidis on cdPCR-NALFIA.

Conclusion

Blood culture tests are probably the gold standard in identifying causative organisms in sepsis, but the rapid results from cdPCR-NALFIA simultaneously used with blood culture may make it an important auxiliary diagnostic tool for identifying infecting organisms and lead to the improvement of mortality of the septic patients, because these combined results provide the wide information on the possible pathogens in early phase.

Evaluation of agar culture plates to efficiently identify small colony variants of methicillin-resistant Staphylococcus aureus

Background: Small-colony variants of methicillin-resistant Staphylococcus aureus (SCV-MRSA) recently were described as slow-growing, thymidine-dependent strains; typically, SCV-MRSA were isolated from patients receiving sulfamethoxazole-trimethoprim, but detection of these strains frequently was delayed because of their small colony size and slow growth. Bacteremia cases due to SCV-MRSA sometimes become lethal when the initiation of treatment with intravenous anti-methicillin-resistant Staphylococcus aureus (MRSA) drugs starts too late. Methods: Here, we evaluated the use of general MRSA-specific agar plates in Japan, including MS-CFX, X-MRSA, and CHROMagar, for the efficient detection of SCV-MRSA, including the comparative detection efficiencies of these media for stock strains and clinical isolates. Results: Among the three MRSA-specific agar plates that were tested, X-MRSA and CHROMagar showed similar detection efficiencies for both 24 and 48 hrs culturing; in contrast, MS-CFS did not permit the detection of SCV-MRSA in stock strains. For clinical isolates of SCV-MRSA, X-MRSA plates permitted detection of the smallest and slowest-growing colonies of SCV-MRSA at 48 hrs of culturing; in contrast, CHROMagar and MS-CFX sometimes did not identify SCV-MRSA at 24 and 48 hrs. Conclusion: Optimization of media and incubation times will be necessary for efficient identification for SCV-MRSA, which would prevent delays in diagnosis and treatment with anti-MRSA drugs.

Ability of serum procalcitonin to distinguish focus of infection and pathogen types in patients with bloodstream infection

Background

Serum procalcitonin (PCT) is a widely recognized inflammatory marker which can distinguish systemic bacterial infection from other types of infections. The ability of PCT levels to distinguish different pathogens from different focus of infection is contradictory.

Methods

This study included 551 patients with bloodstream infection (BSI) diagnosed with positive blood culture (BC) during Jan 2013 and May 2018. The patients were divided into two groups with or without definite focus of infection. In this study, we analyzed PCT levels induced by Gram-positive bacteria, Gram-negative bacteria and fungal infection. Relationship of time between PCT peak and BC collection, and the impact of antibiotics usage on PCT peak distribution were examined.

Results

For patients without definite focus of infection, the serum PCT values of Gram-negative bacteria were higher than that of Gram-positive bacteria (P<0.05). A cut-off value of 7.54 ng/mL for PCT showed a sensitivity of 88.3%. For patients with definite focus of infection, the serum PCT values of Gram-negative bacteria were significantly higher than Gram-positive bacteria in patients with lower respiratory tract (P=0.003), abdominal (P=0.039), urinary tract infection (P=0.025), but not in patients with upper respiratory tract infection (P=0.664). The PCT values between multidrug-resistant organism (MDRO) and sensitive bacteria were not statistically significant (P>0.05) among all patients. Moreover, among patients who use antibiotics before BC collection, the longer antibiotics used, the higher trend of the proportion for PCT peak distribution after BC collection. The higher proportion of antibiotics combined before BC collection, the lower proportion of PCT peak distribution appeared before BC collection, and the higher the proportion of PCT peak distribution appeared after BC collection.

Conclusions

PCT value is determined by many factors. PCT value is related to not only Gram-positive bacteria or Gram-negative bacteria, but also related to specific pathogens, and specific of infection sites etc. The use of Antibiotics is also an important factor of PCT value.

Spread of seb-Positive Methicillin-Resistant Staphylococcus aureus SCCmec Type II-ST764 Among Elderly Japanese in Nonacute Care Settings

We investigated the prevalence and molecular epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) among 356 residents of nine long-term care facilities (LTCFs) in Japan during 2015 and 2017. In total, 800 specimens were tested and 39 MRSA isolates were recovered from 31 (8.71%) residents. PCR-based open reading frame typing (POT) and pulsed-field gel electrophoresis typing were performed for the 39 MRSA isolates; five of them showing identical pulsotypes, and POT scores were excluded in further analysis. Staphylococcal cassette chromosome mec (SCCmec) typing, multilocus sequence typing, and toxin gene detection were performed for one representative MRSA isolate per resident. Among the 34 unrelated MRSA isolates, 15 (44.1%) and 19 (55.9%) were of SCCmec types II and IV, respectively, and belonged to seven sequence types (STs). Among the 15 SCCmec II isolates, 11 (73.3%), 3, and 1 belonged to ST764 (clonal complex [CC]5), ST5 (CC5), and ST630 (CC8), respectively. Among the 19 SCCmec IV isolates, 13 (68.4%), 3, 2, and 1 belonged to ST1 (CC1), ST474 (CC1), ST8 (CC8), and ST380 (CC8), respectively. Among the 14 CC5 lineage-SCCmec II isolates, one ST5 isolate and 7 of the 11 ST764 isolates (63.6%) carried seb gene, and 14 (87.5%) of 16 CC1 lineage-SCCmec IV isolates had sea gene (p < 0.05). The results indicate that the seb-positive SCCmec type II-ST764 clone has spread in Japanese LTCF environments. As LTCF residents have multiple comorbidities and increased susceptibility to infections, it is necessary to monitor MRSA colonization in LTCFs through periodic screening to prevent dissemination.

Methicillin-resistant Staphylococcus aureus nasal colonization and infection in an intensive care unit of a university hospital in China

Objective This study was performed to determine the prevalence and risk factors associated with nasal methicillin-resistant Staphylococcus aureus (MRSA) colonization upon intensive care unit (ICU) admission and during the ICU stay in mainland China. Methods A prospective observational study was performed in a 50-bed general ICU of a 4300-bed teaching hospital in China from 2011 to 2013. Nasal swabs for MRSA detection were obtained upon ICU admission and at discharge for patients having stayed in the ICU for longer than 3 days. Results In total, 115 patients (4.1%; 95% confidence interval [CI], 3.4-4.9) were already colonized with MRSA on ICU admission, and another 185 patients (10.7%; 95% CI, 9.3-12.2) acquired MRSA during their ICU stay. Development of an MRSA infection was significantly more likely in patients with than without MRSA colonization on ICU admission (odds ratio [OR], 2.8; 95% CI, 1.1-7.3). Patients who acquired MRSA had significantly prolonged lengths of stay in the ICU (23.3 days) and higher hospital bills (135,171 RMB; about 19,590 USD) than those who tested negative for MRSA. Conclusion The MRSA colonization rate among ICU patients in mainland China is high. Patients with MRSA-positive nasal swabs are more likely to develop MRSA infections.

Usefulness of matrix-assisted laser desorption ionization time-of-flight mass spectrometry to identify pathogens, including polymicrobial samples, directly from blood culture broths

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (TOF-MS) is now widely used to detect pathogens in clinical settings in Japan. Here, we report the ability of TOF-MS to detect bacteria from blood culture (BC) broths, and compare the efficacy of TOF-MS to that of conventional culture methods. Bacteria were correctly detected from 63 monomicrobial samples within 80 minutes; results matched those obtained by conventional BC methods, although the conventional methods took 2-3 days. In addition to the 63 monomicrobial samples, another three polymicrobial samples were tested; notably, the infecting bacteria were not correctly identified in two of these three samples. To better assess the TOF-MS detection of polymicrobial samples, we tested various ratios of mixed broth samples, including combinations of the bacteria that we were unable to detect in clinical samples. Combinations of Enterobacter cloacae and Pseudomonas aeruginosa were correctly detected at a culture ratio of 2:1, but not in the 3:1 mixture. These results suggested that TOF-MS is a strong tool for the rapid and correct detection of pathogens from monomicrobial BC samples, though results need to be carefully checked when handling known or suspected polymicrobial samples.

Ability of procalcitonin to diagnose bacterial infection and bacteria types compared with blood culture findings

Procalcitonin (PCT) and C-reactive protein serve as biomarkers of infection in patients with sepsis/bacteremia. The present study assessed the clinical characteristics of 280 patients with suspected sepsis who were admitted to Tohoku Medical and Pharmaceutical University Hospital between January 2012 and December 2013. Among the patients, 133 and 147 were positive and negative for PCT, respectively. Patients who were PCT positive were older and more frequently male, had reduced levels of platelets and albumin, and increased levels of aspartate aminotransferase, alanine aminotransferase, blood urea nitrogen, creatinine, and C-reactive protein. Patients who were PCT positive had significantly higher blood culture positivity compared with those who were PCT negative, and the sensitivity and specificity of PCT for detecting positive blood cultures were 74.5% and 59.1%, respectively. Escherichia coli was detected in PCT-positive patients, whereas Staphylococcus epidermidis and Staphylococcus lugdunensis were frequently detected in PCT-negative patients. Levels of PCT were higher in the patients infected with gram-negative rods than those with gram-positive cocci. Furthermore, extended-spectrum β-lactamase (ESBL)-producing bacteria cases showed higher levels of PCT than those of non-ESBL cases. These results suggest that PCT may be a useful biomarker of sepsis, and it might serve as a strong tool to detect patients with severe gram-negative rod bacteremia including ESBL-producing bacteria cases early due to its relative high sensitivity.