Clinical Microbiology Laboratory Research Articles

Recent Trends in Antimicrobial Resistance among Anaerobic Clinical Isolates.

Anaerobic bacteria are normal inhabitants of the human commensal microbiota and play an important role in various human infections. Tedious and time-consuming, antibiotic susceptibility testing is not routinely performed in all clinical microbiology laboratories, despite the increase in antibiotic resistance among clinically relevant anaerobes since the 1990s. β-lactam and metronidazole are the key molecules in the management of anaerobic infections, to the detriment of clindamycin. β-lactam resistance is usually mediated by the production of β-lactamases. Metronidazole resistance remains uncommon, complex, and not fully elucidated, while metronidazole inactivation appears to be a key mechanism. The use of clindamycin, a broad-spectrum anti-anaerobic agent, is becoming problematic due to the increase in resistance rate in all anaerobic bacteria, mainly mediated by Erm-type rRNA methylases. Second-line anti-anaerobes are fluoroquinolones, tetracyclines, chloramphenicol, and linezolid. This review aims to describe the up-to-date evolution of antibiotic resistance, give an overview, and understand the main mechanisms of resistance in a wide range of anaerobes.

The Current Policy Debate around the Regulation of LDTs: What It Means for Infectious Disease Testing and Where It May Be Headed

The debate over federal regulation of diagnostic tests is not new, but scientific advances, societal developments, and global events over the past decade have accelerated efforts by the Food and Drug Administration (FDA) and members of Congress to revise the regulatory oversight of these devices, including laboratory-developed tests (LDTs). Despite years of congressional hearings and public meetings, legislation in the House and Senate, draft guidance from the FDA, and debate in the stakeholder community, LDT regulation remains unchanged, and the path forward remains unclear. LDTs play an essential role in infectious disease (ID) management and treatment, and changes in their regulation will have far-reaching implications for diagnostic laboratories. LDTs are widely used by clinical microbiology laboratories for the diagnosis and monitoring of a myriad infectious diseases, and until three years ago, such testing was conducted largely out of the spotlight. The COVID-19 pandemic changed this by bringing ID tests into the forefront. As the 118th Congress gets under way, the regulation and oversight of diagnostic tests, including LDTs, remains at the forefront of health care policy discussions on Capitol Hill and with the FDA. Change is coming, and it is important that clinical microbiologists, ID physicians, and other laboratorians have a seat at the table when such changes are being discussed.

Antimicrobial susceptibility testing of Bacteroides species by disk diffusion: The NordicAST Bacteroides study

ObjectivesAntimicrobial susceptibility testing (AST) of anaerobic bacteria has until recently been done by MIC methods. We have carried out a multi-centre evaluation of the newly validated EUCAST disk diffusion method for AST of Bacteroides spp. MethodsA panel of 30 Bacteroides strains was assembled based on reference agar dilution MICs, resistance gene detection and quantification of cfiA carbapenemase gene expression. Nordic clinical microbiology laboratories (n = 45) performed disk diffusion on Fastidious Anaerobe Agar with 5% mechanically defibrinated horse blood (FAA-HB) for piperacillin-tazobactam, meropenem and metronidazole. ResultsA total of 43/45 (95.6%) laboratories carried out disk diffusion per protocol. Intraclass correlation coefficients were 0.87 (0.80–0.93) for piperacillin-tazobactam, 0.95 (0.91–0.97) for meropenem and 0.89 (0.83–0.94) for metronidazole. For metronidazole, one media lot yielded smaller zones and higher variability than another. Piperacillin-tazobactam and meropenem zone diameters correlated negatively with cfiA expression. A meropenem zone diameter of <28 mm in B. fragilis indicated presence of cfiA. Piperacillin-tazobactam had the most false susceptible results. Categorical errors for this antimicrobial were particularly prevalent in cfiA-positive strains, and piperacillin-tazobactam had the highest number of comments describing zone reading difficulties. ConclusionsInter-laboratory agreement by disk diffusion was good or very good. The main challenges were media-related variability for metronidazole and categorical disagreement with the reference method for piperacillin-tazobactam in some cfiA-positive strains. An area of technical uncertainty specific for such strains may be warranted.

Direct-from-Blood Detection of Pathogens: a Review of Technology and Challenges.

Blood cultures have been the staple of clinical microbiology laboratories for well over half a century, but gaps remain in our ability to identify the causative agent in patients presenting with signs and symptoms of sepsis. Molecular technologies have revolutionized the clinical microbiology laboratory in many areas but have yet to present a viable alternative to blood cultures. There has been a recent surge of interest in utilizing novel approaches to address this challenge. In this minireview, I discuss whether molecular tools will finally give us the answers we need and the practical challenges of incorporating them into the diagnostic algorithm.

From bottle to bedside: Implementation considerations and antimicrobial stewardship considerations for bloodstream infection rapid diagnostic testing.

Antimicrobial stewardship (AMS) programs have been quick to adopt novel molecular rapid diagnostic technologies (mRDTs) for bloodstream infections (BSIs) to improve antimicrobial management. As such, most of the literature demonstrating the clinical and economic benefits of mRDTs for BSI is in the presence of active AMS intervention. Leveraging mRDTs to improve antimicrobial therapy for BSI is increasingly integral to AMS program activities. This narrative review discusses available and future mRDTs, the relationship between the clinical microbiology laboratory and AMS programs, and practical considerations for optimizing the use of these tools within a health system. Antimicrobial stewardship programs must work closely with their clinical microbiology laboratories to ensure that mRDTs are used to their fullest benefit while remaining cognizant of their limitations. As more mRDT instruments and panels become available and AMS programs continue to expand, future efforts must consider the expansion beyond traditional settings of large academic medical centers and how combinations of tools can further improve patient care.

Under-Reporting Cases and Deaths from Melioidosis: A Retrospective Finding in Songkhla and Phatthalung Province of Southern Thailand, 2014-2020.

Melioidosis, caused by Burkholderia pseudomallei, is a notifiable disease associated with a high mortality rate in Thailand. The disease is highly endemic in northeast Thailand, while its prevalence in other parts of the country is poorly documented. This study aimed at improving the surveillance system for melioidosis in southern Thailand, where the disease was believed to be underreported. Two adjacent southern provinces, Songkhla and Phatthalung, were selected as the model provinces to study melioidosis. There were 473 individuals diagnosed with culture-confirmed melioidosis by clinical microbiology laboratories at four tertiary care hospitals in both provinces from January 2014 to December 2020. The median age was 54 years (IQR 41.5-64), 284 (60%) of the patients were adults ≥50 years of age, and 337 (71.2%) were male. We retrospectively analyzed 455 patients treated at either Songklanarind Hospital, Hatyai Hospital, Songkhla Provincial Hospital, or Phatthalung Provincial Hospital, of whom 181 (39.8%) patients died. The median duration from admission to death was five days (IQR 2-17). Of the 455 patients, 272 (57.5%) had at least one clinical risk factor, and 188 (39.8%) had diabetes. Two major clinical manifestations, bacteremia and pneumonia, occurred in 274 (58.1%) and 166 (35.2%) patients, respectively. In most cases, 298 (75%) out of 395 local patients were associated with rainfall. Over the seven years of the study, the average annual incidence was 2.87 cases per 100,000 population (95% CI, 2.10 to 3.64). This study has confirmed that these two provinces of southern Thailand are endemic to melioidosis; even though the incidence rate is much lower than that of the Northeast, the mortality rate is comparably high.

Evaluation of the NG-Test CARBA 5 Lateral Flow Assay with an IMP-27-Producing Morganella morganii and Other Morganellaceae.

An isolate of Morganella morganii (MMOR1) that tested susceptible to 3rd/4th-generation cephalosporins and intermediate to meropenem was characterized as positive for NDM and IMP carbapenemases by NG-Test CARBA 5. Our objective was to further investigate this result, given the inconsistent susceptibility profile and unusual epidemiological profile for our region. The MMOR1 isolate was retested for antimicrobial susceptibilities and characterized for carbapenemase production. MMOR1 tested susceptible to ceftazidime, ceftriaxone, cefepime, aztreonam, and ertapenem, and intermediate to meropenem and imipenem. The isolate tested positive by carbapenem inactivation method (CIM) and CIM+EDTA (eCIM) testing, indicating metallo-β-lactamase production. The isolate tested negative for all carbapenemase genes on Xpert Carba-R, but positive for IMP on repeat testing of NG-Test CARBA 5. Whole-genome sequencing revealed MMOR1 contained blaIMP-27, but no other carbapenemase genes. Additional testing with NG-Test CARBA 5 revealed a false-positive NDM band when the assay was overloaded with test inoculum. Supplementary isolates were tested with an overloaded inoculum (n = 6 M. morganii; n = 1 P. mirabilis; n = 1 IMP-27-producing P. rettgeri; n = 1 IMP-1-producing E. coli; n = 1 K. pneumoniae), and two non-carbapenemase-producing carbapenem non-susceptible M. morganii also generated a false-positive NDM band; though, this was not universal among this species. A dual IMP+/NDM+ M. morganii is an unusual result that should prompt additional investigation, especially in nonendemic regions and when the susceptibility profile is incompatible. IMP-27 is not detected by Xpert Carba-R but is variably detected by NG-Test CARBA 5. The microorganism inoculum used for NG-Test CARBA 5 must be carefully controlled for accurate results. IMPORTANCE The detection of carbapenemase-producing carbapenem-resistant Enterobacterales (CP-CRE) is an important function of the clinical microbiology laboratory, where positive identifications have immediate implications for infection control and surveillance strategies in the inpatient setting and can inform appropriate selection of therapy among the various novel anti-CP-CRE agents. NG-Test CARBA 5 is a relatively new lateral flow assay used for detection of carbapenemases in CP-CRE. Here, we describe the characterization of a Morganella morganii isolate that generated a false-positive NDM carbapenemase detection by this assay, and perform bacterial test inoculum experiments with additional isolates to further investigate a cause of false-positive results using the NG-Test CARBA 5. While a lateral flow assay like the NG-Test CARBA 5 is a very desirable test format for clinical laboratories, there are pitfalls to avoid when performing this test and interpreting results, including recognizing an overloaded test assay, which could lead to false-positive results.

Clinical Performance Evaluation of a Rapid Real-Time PCR Assay for Monkeypox Diagnosis: a Retrospective and Comparative Study.

In an increasingly globalized and interconnected world, the outbreak of an infectious disease in one country can become a worrying health emergency for the whole world. A current example is the 2022 monkeypox virus (mpox) outbreak affecting multiple areas across the world. In this context, strategies to interrupt transmission as soon as possible by identifying cases, clusters, and sources of infection should be developed around the world to prevent these crises. The aim of this retrospective and collaborative study was to perform external clinical validation of the VIASURE monkeypox virus real-time PCR detection kit (CerTest Biotec, Spain) with ready-to-use reagents designed for the rapid detection of mpox. A total of 165 samples with suspected infection were used for this analysis. The standard procedures of the clinical microbiology laboratory of the Miguel Servet University Hospital, using the RealStar Orthopoxvirus PCR kit v1.0 (Altona Diagnostics) and bidirectional Sanger sequencing (STAB VIDA, Caparica, Portugal), were considered reference techniques. Furthermore, a subset of 67 mpox-negative samples and 13 mpox-positive samples were routinely tested for clinical diagnosis of other rash/ulcerative pathologies. Accuracy testing resulted in appropriate clinical validation values, as follows: sensitivity, 1 (95% confidence interval [CI], 0.97 to 1); specificity, 1 (95% CI, 0.98 to 1); positive predictive value, 1 (95% CI, 0.93 to 1); negative predictive value, 1 (95% CI, 0.95 to 1). The strength of agreement between assays was almost perfect. The added value is the useful support for the specific diagnosis of mpox infections due to the diagnostic specificity data obtained. IMPORTANCE Given that a large number of mpox outbreaks have been reported worldwide since 2022 in countries in which the disease is not endemic, the main concern for clinicians and global health systems should be to develop effective, available, and easy-to-implement diagnostic strategies to interrupt mpox transmission as soon as possible. This retrospective study demonstrates the satisfactory clinical parameters of a commercially available molecular diagnostic kit for routine testing for mpox in clinical diagnostic laboratories.

A Correlation between the Number of Airborne Bacteria and Fungi using the Settle Plate Method with Temperature and Relative Humidity at the Clinical Microbiology Laboratory of Dr. Soetomo Regional General Hospital Surabaya, Indonesia

Air is an important part of human life. However, air can be contaminated with microorganisms such as airborne bacteria and fungi. Temperature and relative humidity in a room can have an impact on the quantity of airborne bacteria and fungi. This study aims to figure out the correlation between the number of airborne bacteria and fungi with temperature and relative humidity. In 15 rooms of Microbiology laboratory, NA and SDA Petri plates were placed, after incubation, the number of colonies in each plate was counted. Pearson test was conducted with SPSS to determine the correlation between temperature and relative humidity to the number of airborne bacteria and fungi. The highest number of airborne bacteria was in the reading room (352 CFU/m3), while the lowest number was in the laundry room (13 CFU/m3) and the highest number of airborne fungi was in the Mycology room (156 CFU/m3), while there were no airborne fungi found in the urine and laundry rooms. Based on the results of the Pearson test, it was found that the value of p = 0.668 (p&gt; 0.5) showed that there was no correlation between temperature and the number of airborne bacteria and fungi. Based on the results of the Pearson test, the value of p = 0.745 (p&gt; 0.5) showed that there was no correlation between relative humidity and the number of airborne bacteria and fungi. There is no correlation between temperature and relative humidity with the number of airborne bacteria and fungi.

Vogesella urethralis-induced aspiration pneumonia and bacteremia in an elderly man: a first case report and literature review

BackgroundVogesella species are common aquatic Gram-negative rods that were first reported in 1997. Vogesella urethralis bacterium was first isolated from human urine in 2020. Only two cases of disease caused by Vogesella species have been reported with no case of Vogesella urethralis-caused disease being reported as yet. Herein, we report a case of aspiration pneumonia and bacteremia caused by Vogesella urethralis.Case presentationAn 82-year-old male patient was admitted with dyspnea, increased sputum production, and hypoxia. Gram-negative rods were isolated from the blood and sputum cultures of the patient. He was diagnosed with aspiration pneumonia and bacteremia. Initially, Vogesella urethralis was wrongly identified as Comamonas testosteroni based on fully automated susceptibility testing; however, additional 16S rRNA gene sequencing identified the causative as Vogesella urethralis. The patient was treated with piperacillin and tazobactam. Unfortunately, he developed aspiration pneumonia again and died during hospitalization.ConclusionsSince no database exists for rare bacteria in traditional clinical microbiology laboratories, 16S rRNA gene sequence analysis is useful. We report the first case of Vogesella urethralis-induced aspiration pneumonia and bacteremia.

Rapid automated antifungal susceptibility testing system for yeasts based on growth characteristics.

Fungal pathogens are a major threat to public health, as they are becoming increasingly common and resistant to treatment, with only four classes of antifungal medicines currently available and few candidates in the clinical development pipeline. Most fungal pathogens lack rapid and sensitive diagnostic techniques, and those that exist are not widely available or affordable. In this study, we introduce a novel automated antifungal susceptibility testing system, Droplet 48, which detects the fluorescence of microdilution wells in real time and fits growth characteristics using fluorescence intensity over time. We concluded that all reportable ranges of Droplet 48 were appropriate for clinical fungal isolates in China. Reproducibility within ±2 two-fold dilutions was 100%. Considering the Sensititre YeastOne Colorimetric Broth method as a comparator method, eight antifungal agents (fluconazole, itraconazole, voriconazole, caspofungin, micafungin, anidulafungin, amphotericin B, and 5-flucytosine) showed an essential agreement of >90%, except for posaconazole (86.62%). Category agreement of four antifungal agents (fluconazole, caspofungin, micafungin, and anidulafungin) was >90%, except for voriconazole (87.93% agreement). Two Candida albicans isolates and anidulafungin showed a major discrepancy (MD) (2.60%), and no other MD or very MD agents were found. Therefore, Droplet 48 can be considered as an optional method that is more automated and can obtain results and interpretations faster than previous methods. However, the optimization of the detection performance of posaconazole and voriconazole and promotion of Droplet 48 in clinical microbiology laboratories still require further research involving more clinical isolates in the future.

Reliability of a terbinafine agar containing method for the screening of dermatophyte resistance.

The increase in terbinafine resistance worldwide due to Trichophyton indotineae underlies the need for surveillance networks, deploying easy to perform methods to correctly identify resistant isolates and thereby reduce their spread. In the present study, we evaluated the performances of the terbinafine containing agar method (TCAM). Different technical parameters, such as culture medium (RPMI agar [RPMIA] or Sabouraud dextrose agar [SDA]) and inoculum size, were evaluated. Our study showed that terbinafine susceptibility determined using the TCAM was reliable and independent of the inoculum or medium used. We then performed a multicenter, blinded study. Five isolates of T. indotineae and 15 of genotype I or II of T. interdigitale, including five terbinafine-resistant isolates (four T. indotineae, one T. interdigitale) were sent to eight clinical microbiology laboratories. Each laboratory analyzed the 20 isolates' terbinafine susceptibility by the TCAM using both culture media. TCAM allowed all participants to correctly determine the terbinafine susceptibility of analyzed isolates without prior training. All participants agreed that the dermatophyte tested, regardless of species or genotype, grew better on SDA than on RPMIA medium but accumulated fungal growth after 14 days eventually minimized the effect of this difference. In conclusion, TCAM is a reliable, easy to perform screening method for assessing terbinafine resistance. However, despite good performances, TCAM is a qualitative method and minimal inhibitory concentrations must be determined by the EUCAST standardized method to follow the evolution of terbinafine resistance levels.

Retrospective and Comparative Study of Three Molecular Assays for the Macrolide Resistance Detection in Mycoplasma genitalium Positive Urogenital Specimens.

The capacity of Mycoplasma genitalium to develop resistance to macrolides makes detection of macrolide resistance genes by rapid real-time PCR assays increasingly necessary in clinical diagnostic laboratories so as to initiate appropriate treatment as rapidly as possible. The aim of this retrospective and comparative study was to conduct the clinical evaluation of three commercially available kits for macrolide resistance detection. A total of 111 M. genitalium positive samples analyzed in the Clinical Microbiology Laboratory of the Miguel Servet University Hospital, Zaragoza (Spain) were used. After M. genitalium molecular confirmation, the three assays under study were evaluated and discrepant results were resolved via sequencing. The clinical sensitivity for resistance detection was 83% (95% confidence interval, 69% to 93%) for the ResistancePlus® MG panel kit (SpeeDx Pty Ltd., Sydney, Australia), 95% (84% to 99%) for AllplexTM MG & AziR Assay (Seegene®, Seoul, Korea), and 97% (88% to 99%) for the VIASURE macrolide resistance-associated mutations (23SrRNA) Real time PCR detection kit (Certest Biotec, Zaragoza, Spain). The clinical specificity was 100% (94% to 100%) for Allplex and VIASURE assays and 95% (86% to 99%) for SpeeDx assay. The results arising from this study are cause for strong consideration for the implementation of rapid real-time PCR assays in clinical diagnosis laboratories to eliminate treatment failure and transmission as soon as possible.

Basic competence for etiological diagnosis of lower respiratory tract infection after application of metagenomic next-generation sequencing

In addition to clinical manifestations, medical history, and imaging, the diagnosis of low respiratory tract infection (LRTI) depends mainly on the ability of the clinical microbiology laboratory to detect the pathogens. However, conventional culture may be time-consuming, the sensitivity of microscopy is low, and nucleic acid-based targeted tests (e.g., PCR) could only cover limited range of pathogens. The use of mNGS technology has improved the diagnostic rate of LRTI, but the conventional microbiology detection has been neglected to some extent. This review addressed the appropriate use of these methods with the aim of strengthening the ability of traditional microbiology methods in LRTI diagnosis after mNGS application.

Prevalence and Phenotypic Detection of Carbapenem-Resistant Enterobacter Species from the Clinical Specimens of a Tertiary Care Hospital in Bangladesh

Background: Carbapenem-resistant Enterobacter (CRE) is an emerging threat spread rapidly around the world in the past few years, posing substantial hazards to human health. Objective: The study was conducted to evaluate the prevalence of carbapenem resistance and to detect carbapenemase producers phenotypically from patients of a major tertiary care hospital, in Bangladesh. Methods: Prospective cross-sectional study was conducted from July 2018 to June 2019, at the Dhaka Medical College hospital. Patients admitted to different wards, and intensive care units, visited the outpatient department, and samples received in the microbiology department were included in this study. A total of 350 clinical samples were collected, inoculated, and incubated in accordance to the standard protocol. Identification was done using the standard biochemical method. Antimicrobial susceptibility testing of commonly used antibiotics including imipenem was done using Kirby Bauer disk diffusion method. All the clinical isolates of Enterobacter were screened for carbapenem resistance as per CLSI guidelines. Such strains were then subjected to phenotypic confirmation of carbapenemase production by the Modified Hodge test. All isolates that gave a positive screening test were further evaluated for Metallo-β lactamase (MBL) production. MBL was further detected by Combined Disc Test (CD) using a combination of Imipenem and Imipenem-EDTA and double disc synergy (DDS) test. Result: A total of 350 clinical specimens were analyzed, of which 224 (65.14%) isolates yielded growth. Among them, 28 (12.28%) Enterobacter were isolated of which 12 (42.86%) were found to be Imipenem resistant (14.25%) and were labeled 'Carbapenem-resistant Enterobacter" or CRE. Minimum inhibitory concentration (MIC) was determined among the carbapenem-resistant clinical isolates. Modified Hodge test (MHT) performed on the 12 carbapenem-resistant isolates showed 9 (75%) isolates to be carbapenemase enzyme producers. Nine out of twelve carbapenem-resistant isolates are Metallo-beta-lactamase producers detected by combined disc test (CDT) and eight (66.67%) MBL producers detected by DDS test. Conclusion: The finding from this study revealed a high prevalence of carbapenem resistance among isolated Enterobacter species in hospital settings as well as community levels. As there are limited treatment regimens, therefore, the timely and accurate detection of carbapenem-resistant Enterobacter species is essential for the clinical treatment and prevention of infections. Simple phenotypic methods like MHT can be used for the rapid detection of carbapenemases, and these are expected to be used routinely in clinical microbiology laboratories. Update Dent. Coll. j: 2023; 13(1): 17-22

NON-TYPHOIDAL SALMONELLA: A HOSPITAL BASED STUDY FROM SOUTH INDIA

Background &amp; objectives: The objective of this study was to evaluate the prevalence of Non-typhoidal Salmonella and to nd their antibiotic susceptibility pattern in a tertiary care hospital in South India. A signicant global health issue is the steadily rising percentage of Non-typhoidal Salmonella (NTS) infections in people. A descriptive study was conducted at Methods: a tertiary care teaching hospital in South India. Culture and sensitivity of stool samples of clinically suspected patients were done in the Microbiology laboratory from Sree Gokulam Medical College and Research Foundation. All samples were inoculated onto appropriate culture plates. Colonies suspected as Salmonella were identied by standard laboratory methods, initially by manual biochemical tests and by the VITEK-2 automated systems (bioMérieux) and nal serotyping by polyvalent antisera. 3 of the Salmonella isolates were sent to CMC, Vellore, India for serotyping. Antibiotic susceptibility tests were performed by Kirby Bauer's disc diffusion method on Mueller-Hinton agar and results were interpreted as per the CLSI guidelines (2022). Signed informed consent was obtained from all participants. Tests were performed in the clinical Microbiology Laboratory under the Department of Microbiology, Sree Gokulam Medical College and Research Foundation, Venjaramoodu, Trivandrum. Of the 244 mot Results: ion samples, Non-typhoidal Salmonella isolated were from 20 motion samples. The predominant serotype isolated was Salmonella Typhimurium (S. Typhimurium) in 16(80%) followed by Salmonella enteritidis in 3(15%) and Salmonella C2 in 1(5%) isolates. It was noticed by an increasing trend of resistance to Ampicillin, Chloramphenicol, Cephalosporins (Third generation) and Quinolones over this 18 month study. Based on this study, Conclusions: faecal prevalence of NTS (8.20%) were increasing among motion samples. Majority of isolates were from females (75%) with a mean age group belonging to Adults (46-60yrs). Except for Ampicillin and Cotrimoxazole, NTS isolates exhibited high rates of resistance to rst-line antibiotics. The gradual but consistent increase in resistance to Ampicillin, Fluoroquinolones, third generation Cephalosporins may restrict future treatment 1 options. Hence periodic monitoring of NTS infections, serotype distribution and antimicrobial resistance trend is recommended .

DETECTION OF CARBAPENEMASE PRODUCING GRAM NEGATIVE BACILLI WITH SIMPLIFIED CARBAPENEM INACTIVATION METHOD (SCIM)

This study reports the Simplied carbapenem inactivation method to detect carbapenemase-producing gram negative bacilli in a simple and accurate manner. This method is based on Modied Carbapenem inactivation method with the improvement of experimental procedure. Instead of incubating the antibiotic disc in the organism culture media, the organism to be tested and smeared directly onto the antibiotic disk in the sCIM. This method is suitable for routine use in most clinical microbiology lab for detection of carbapenemase-producing gram negative bacilli.

Aminopenicillins vs non-aminopenicillins for treatment of enterococcal lower urinary tract infections

Aminopenicillins (APs) achieve urinary concentrations that exceed typical minimum inhibitory concentrations for enterococcal lower urinary tract infection (UTI). The local clinical microbiology laboratory discontinued routine susceptibilities on enterococcal urine isolates, and reports that 'APs are predictably reliable for uncomplicated enterococcal UTI'. The objective of this study was to compare outcomes of APs with non-APs (NAPs) for enterococcal lower UTIs. This was an institutional-review-board-approved, retrospective cohort of adults hospitalized with symptomatic enterococcal lower UTIs from 2013 to 2021. The primary endpoint was composite clinical success at 14 days, defined as resolution of symptoms without new symptoms and no repeat culture growth of the index organism. A non-inferiority analysis was utilized with a 15% margin, and logistic regression evaluated characteristics associated with 14-day failure. In total, 178 subjects were included: 89 AP patients and 89 NAP patients. Vancomycin-resistant enterococci (VRE) were identified in 73 (82%) AP patients and 76 (85%) NAP patients (P=0.54); in total, 34 (38.2%) AP patients and 66 (74.2%) NAP patients had confirmed Enterococcus faecium (P<0.001). Amoxicillin (n=36, 40.5%) and ampicillin (n=36, 40.5%) were the most commonly used APs, and linezolid (n=41, 46%) and fosfomycin (n=30, 34%) were the most commonly used NAPs. Fourteen-day clinical success rates for APs and NAPs were 83.1% and 82.0%, respectively [1.1% difference, 97.5% confidence interval (CI) -0.117 to 0.139]. Among the E. faecium subgroup, 14-day clinical success was observed in 27/34 (79.4%) AP patients and 53/66 (80.3%) NAP patients (P=0.916). On logistic regression, APs were not associated with 14-day clinical failure (adjusted odds ratio 0.84, 95% CI 0.38-1.86). APs were non-inferior to NAPs for treating enterococcal lower UTIs, and may be considered irrespective of susceptibility results.

Time series model for a proportion of antimicrobial resistance rate

BackgroundAntimicrobial resistance acts as a global problem in many regions of the world. The prevention and treatment of modern medicine are becoming ineffective. Governments all over the world are working effortlessly to overcome this problem and there is a requirement for extra care by the government and healthcare delivery systems to strengthen antimicrobial policy and standardize treatment guidelines. ObjectiveThis study aims to forecast the antimicrobial resistance rate for the future and simultaneously to bring awareness of new time-series proportion models available to model the rate/proportion data in the field of clinical and public health by taking an example of antimicrobial resistance rate data. MethodsData on Escherichia coli isolated from blood cultures showing variable susceptibility to different antimicrobial agents has received from a clinical microbiology laboratory of tertiary care hospital, Manipal, Karnataka, between the years June 2015 and December 2019. Beta auto-regressive moving average model is used to forecast the antimicrobial resistance rate data. To help non-statisticians an R shiny app named BARMA. app has been developed for the same. ResultsA resistance rate of a total of 55-time points was used to forecast the resistance rate of E.coli to the antimicrobial Amoxicillin-clavulanic acid. On average, the forecasted resistance rate is 57% (50%–65%). ConclusionForecasting of antimicrobial resistance rate can help to alert healthcare policymakers to have appropriate precautionary measures and to attain the sustainable development goals (SDGs).

Genomics of Invasive Cutibacterium acnes Isolates from Deep-Seated Infections.

Cutibacterium acnes, formerly known as Propionibacterium acnes, is a commensal of the human pilosebaceous unit but also causes deep-seated infection, especially in the context of orthopedic and neurosurgical foreign materials. Interestingly, little is known about the role of specific pathogenicity factors for infection establishment. Here, 86 infection-associated and 103 commensalism-associated isolates of C. acnes were collected from three independent microbiology laboratories. We sequenced the whole genomes of the isolates for genotyping and a genome-wide association study (GWAS). We found that C. acnes subsp. acnes IA1 was the most significant phylotype among the infection isolates (48.3% of all infection isolates; odds ratio [OR] = 1.98 for infection). Among the commensal isolates, C. acnes subsp. acnes IB was the most significant phylotype (40.8% of all commensal isolates; OR = 0.5 for infection). Interestingly, C. acnes subsp. elongatum (III) was rare overall and did not occur at all in infection. The open reading frame-based GWAS (ORF-GWAS) did not show any loci with a strong signal for infection association (no P values of ≤0.05 after adjustment for multiple testing; no logarithmic OR [logOR] of ≥|2|). We concluded that all subspecies and phylotypes of C. acnes, possibly with the exception of C. acnes subsp. elongatum, are able to cause deep-seated infection given favorable conditions, most importantly related to inserted foreign material. Genetic content appears to have a small effect on the likelihood of infection establishment, and functional studies are needed to understand the individual factors contributing to deep-seated infections caused by C. acnes. IMPORTANCE Opportunistic infections emerging from human skin microbiota are of ever-increasing importance. Cutibacterium acnes, being abundant on the human skin, may cause deep-seated infections (e.g., device-associated infections). Differentiation between invasive (i.e., clinically significant) C. acnes isolates and sole contaminants is often difficult. Identification of genetic markers associated with invasiveness not only would strengthen our knowledge related to pathogenesis but also could open ways to selectively categorize invasive and contaminating isolates in the clinical microbiology lab. We show that in contrast to other opportunistic pathogens (e.g., Staphylococcus epidermidis), invasiveness is apparently a broadly distributed ability across almost all C. acnes subspecies and phylotypes. Thus, our work strongly supports an approach in which clinical significance is judged from clinical context rather than by detecting specific genetic traits.