Microbiology Laboratory Research Articles

Consensus for antifungal stewardship in China (2024 edition).

Invasive fungal disease (IFD) has become a serious threat to human health in China and around the world, with high mortality and morbidity. Currently, the misdiagnosis rate of IFD is extremely high, compounded with the low quality of prescription antifungals and the high incidence of adverse events associated with IFD treatment, resulting in lengthy hospitalization, low clinical response, and high disease burden, which have become serious challenges in clinical practice. Antifungal stewardship (AFS) can not only significantly increase the early diagnosis rate of IFD, reduce inappropriate utilization of antifungal drugs, improve patient prognosis, but can also improve therapeutic safety and reduce healthcare expenses. Thus, it is urgent to identify key AFS metrics suitable for China's current situation. Based on metrics recommended by international AFS consensuses, combined with the current situation of China and the clinical experience of authoritative experts in various fields, several metrics were selected, and experts in the fields of respiratory diseases, hematology, intensive care units (ICUs), dermatology, infectious diseases, microbiology laboratory and pharmacy were invited to assess AFS metrics by the Delphi method. Consensus was considered to be reached with an agreement level of ≥80% for the metric. Consensus was reached for 24 metrics, including right patient metrics (n=4), right time metrics (n=3), and right use metrics (n=17). Right use metrics were further subdivided into drug choice (n=8), drug dosage (n=4), drug de-escalation (n=1), drug duration (n=2), and drug consumption (n=2) metrics. Forty-six authoritative experts assessed and reviewed the above metrics, and a consensus was reached with a final agreement level of ≥80% for 22 metrics. This consensus is the first to propose a set of AFS metrics suitable for China, which helps to establish AFS standards in China and is also the first AFS consensus in Asia, and may improve the standard of clinical diagnosis and treatment of IFD, and guide hospitals to implement AFS, ultimately promoting the rational use of antifungal drugs and improving patient prognosis.

Culture of Cultures: A Small Step Towards Augmenting Diagnostic Stewardship.

Laboratories with a well-established diagnostic stewardship program for culture and the antimicrobial susceptibility test (C-AST) play a key role in guiding clinicians to institute specific targeted therapy. Blood culture is one of the most critical investigations performed at a microbiology laboratory. Therefore, it is particularly important to develop a robust diagnostic stewardship model for the blood culture laboratory division. Aiming at this hypothesis, this hospital-based clinical audit carried out within the Department of General Medicine, centered on the critical domain of antimicrobial stewardship (AMSP). The audit's primary objective was to systematically evaluate prevailing practices and pinpoint areas necessitating refinement in the administration of antimicrobial agents. Employing a meticulous approach involving exhaustive data scrutiny and feedback mechanisms, the audit unearthed strategic opportunities to optimize prescription patterns, curtail unwarranted antimicrobial utilization, and fortify adherence to established guidelines. The subsequent execution of targeted interventions, encompassing educational initiatives and routine performance feedback, culminated in a noteworthy enhancement of antimicrobial prescribing practices. These outcomes unequivocally underscore the efficacy of the audit in cultivating a milieu of judicious antimicrobial utilization, thereby augmenting patient care and mitigating antibiotic resistance within the department.

Overuse of antibiotics for urinary tract infections in pregnant refugees, Lebanon.

To determine whether adding urine culture to urinary tract infection diagnosis in pregnant women from refugee camps in Lebanon reduced unnecessary antibiotic use. We conducted a prospective, cross-sectional study between April and June 2022 involving pregnant women attending a Médecins Sans Frontières sexual reproductive health clinic in south Beirut. Women with two positive urine dipstick tests (i.e. a suspected urinary tract infection) provided urine samples for culture. Bacterial identification and antimicrobial sensitivity testing were conducted following European Committee on Antimicrobial Susceptibility Testing guidelines. We compared the characteristics of women with positive and negative urine culture findings and we calculated the proportion of antibiotics overprescribed or inappropriately used. We also estimated the cost of adding urine culture to the diagnostic algorithm. The study included 449 pregnant women with suspected urinary tract infections: 18.0% (81/449) had positive urine culture findings. If antibiotics were administered following urine dipstick results alone, 368 women would have received antibiotics unnecessarily: an overprescription rate of 82% (368/449). If administration was based on urine culture findings plus urinary tract infection symptoms, 144 of 368 women with negative urine culture findings would have received antibiotics unnecessarily: an overprescription rate of 39.1% (144/368). The additional cost of urine culture was 0.48euros per woman. A high proportion of pregnant women with suspected urinary tract infections from refugee camps unnecessarily received antibiotics. Including urine culture in diagnosis, which is affordable in Lebanon, would greatly reduce antibiotic overprescription. Similar approaches could be adopted in other regions where microbiology laboratories are accessible.

Heroic history of the Institute of Epidemiology and Microbiology (1941–1945) and the main achievements of the present time

The aim of this article was to show the labor valour during the Great Patriotic War of the employees of the first research institute in Irkutsk, which began its history in 1912, as well as their success of the present time. The oldest scientific institution in the Irkutsk region was originally created on the initiative of the Siberian Medical Society as a laboratory and was transformed into the Chemical and Bacteriological Institute in 1918, and in 1930 it became the Institute of Epidemiology and Microbiology of the People’s Commissariat of Public Health of Russia.By the beginning of the Great Patriotic War, the institute had an epidemiological department and a microbiological laboratory that carried out epidemiological surveillance and diagnosis of a wide range of infections in Siberia. During the war years, the manufacturing sector with the production of vaccines and serums acquired particular importance. By the end of the war, 285 employees worked at the institute, 32 of them had higher education. During the war years, the production of vaccines against typhoid, paratyphoid, dysentery, diphtheria, tuberculosis, and smallpox was significantly increased. Serums against tetanus and measles, and a dysentery bacteriophage were produced. At the same time, research projects and thesis works were carried out. The employees of the institute received national and departmental awards, commendations, honorary distinctions, and rewards for their scientific work and production excellence.Currently, the institute continues the glorious traditions of the past and demonstrates truly heroic efforts in the development of virology and microbiology, working in priority areas of medical and biological science. Of course, the works of scientists of the present time will be appreciated only by descendants, as is now happening with the assessment of the work of the Institute of Epidemiology and Microbiology during the Great Patriotic War.

Immune response to SARS-CoV-2 vaccine administered to patients with solid cancers under systemic treatment: A prospective, monocentric study (Immunocovid-19).

e23093 Background: Despite vaccination, COVID-19 could still cause severe disease in immunocompromised patients (pts). While subsequent vaccine doses increase immune response in the general population, few data concerning cancer pts under systemic treatment are reported. Methods: This study will be conducted on blood samples from 1000 pts admitted to Reggio Emilia AUSL-IRCCS Cancer Center and undergoing systemic therapies who received ≥ 2 vaccine doses. The samples will be analyzed at Clinical Microbiology and Chemistry Laboratories of Reggio Emilia AUSL-IRCCS. We will perform antibody IgM-IgG serology by means of COVID-19 VIRCLIA® Monotest and anti-spike antibodies evaluation using LIAISON® SARS CoV-2 Trimerics IgG. We will also investigate cell immune response (B and T lymphocyte counts) and analyze specific lymphocyte subsets on the first 200 pts treated with chemo- (CT) or immunotherapy (IO). Then, we will evaluate the T-cell response on the first 50 pts and those with an inadequate anti-spike serologic response through the T-SPOT.COVID test. Statistical analyses will be conducted by the Clinical Studies and Statistical Unit Staff. Results: Here, we report preliminary data on the first 240 pts enrolled and treated with CT (55.4%), IO (26.3%), or other therapies (18.3%). Most of the pts were male (58%), had metastatic cancer (82%), and no previous COVID-19 infection (60%). 84% of pts were affected by gastrointestinal, lung, urogenital and breast cancer. We stratified pts in three groups according to the time from the last vaccine dose (0-6/6-12/ > 12 months). We showed no significant decrease in cellular and humoral immune response over time from the last vaccine dose, independent of the specific treatment received, also if CT (Table 1). Furthermore, clinical characteristics as gender, treatment, and primary tumor site appear not to influence immune response, even if a trend to a higher response in pts previously affected by COVID-19 has been observed. The T-SPOT.COVID test performed on the first 27 pts showed that 19% had no T-cell activation, even with good IgG response. Conclusions: This feasible and cost-effective study has a potential impact on public health. Although these are preliminary data, the immune response to COVID-19 vaccines remains good after 12 months from the last dose administered in cancer pts. The enrollment is ongoing, and we could provide relevant information on the influence of clinical factors on the immune response and identify specific subgroups that could benefit from different vaccine approaches. [Table: see text]

Microbiological Evaluation of Commercial Hand Sanitisers Available in Pakistan Using European Standard and Membrane Filtration Method.

To evaluate the antibacterial efficacy of various commercially available alcohol-based hand sanitisers (ABHS) using European standard (EN 1500) method and perform ABHS testing with membrane filtration method. A Cross-sectional observational study. Place and Duration of the Study:Quality Control Section of the Microbiology Laboratory, The Aga Khan University Hospital, Karachi, Pakistan, from February to April 2023. Efficacy of 14 commercially and widely accessible hand sanitisers was defined as reducing micro-organism growth. It was determined using the EN 1500 European standard test and membrane filtration method. Majority (92.8%) ABHS showed a significant bacterial reduction except one ABHS tested with the EN 1500 method. Only six ABHS products were tested through the membrane filtration method because high viscosity of hand sanitisers was causing damage to filter membranes. Continued vigilance in evaluating hand sanitiser's efficacy through robust testing methods is essential to ensure public health and prevent the dissemination of misleading products that may compromise hand hygiene practices. Hand sanitisers, European standard, Membrane filtration method, Antibacterial efficacy.

Isolation, Identification and Antimicrobial Susceptibility of some Bacterial Species Isolated from Dental Plaque

Dental plaque is a sticky bacterial film that develops on teeth producing plaque as a result. If it ‘is not removed with regular dental cleanings and daily brushing, it can initiate oral health issues such as gum diseases and dental caries. This study aimed to determine the prevailing bacterial species found in some patients’ dental plaque cases and dental caries and to analyze the antimicrobial susceptibility of the obtained bacteria. A total of 60samples of dental plaque were taken from patients who attended the health centres in Baghdad with different ages using cotton swabs. All gained swabs were transported to the microbiology laboratory and cultured on culture media. According to standard laboratory diagnosis protocols, primary diagnosis was performed. VITE 2Compact Automated-System (GP (and (GN (diagnosis cards used according to manufacturer company constructions (BioMérieux)to confirm the diagnosis. Antibiotic susceptibility test was done by using antibiotic disks according to Kirby-Bauer method. Out of 60samples, forty-two (70%) samples showed growth on culture media, while 18(30%) showed no growth, most of the isolates, 29(69.0%) were Gram-positive bacteria represented by Streptococcus mutans, Staphylococcus aureus, and only 13(30.9%) of isolates were Gram-negative includes Klebsiella pneumonia and Escherichia coli.According to the antibiotic susceptibility test results, Gram-positive bacteria showed high resistance against amoxicillin, Cefotaxim and erythromycin with percentages of 86.2%-and 89.6%respectively. Gram-negative bacteria showed high resistance against amoxicillin and erythromycin with percentages of 76.9%and 69.2%against Cefotaxim

Coagulase-Negative Staphylococcus (CoNS) Susceptibility Pattern Towards Antibiotics in Infection Patients at RSUP Dr. Mohammad Hoesin Palembang

Introduction. Coagulase Negative Staphylococcus (CoNS) is a bacterial species commonly causing infection in humans upon entrance into bloodstream. Antibiotics remain the therapeutic modality of choice in eradicating CoNS bacteria. Increasing incidence of antimicrobial resistance has made it difficult to administer the right treatment. In addition, CoNS susceptibility patterns differ between regions and with time. This study aimed to determine the susceptibility pattern of CoNS towards various antibiotics in infection patients at RSUP Dr. Mohammad Hoesin Palembang. Methods. This study was a descriptive, observational study using the data from blood cultures of CoNS bacteria undergoing antimicrobial susceptibility test (AST) in the Clinical Microbiology Laboratory, and utilizing demographic and clinical data from the Medical Records Installation from July 1, 2021 to December 31, 2021. Results. There were 123 isolates from patient blood cultures which underwent AST. The most frequently identified bacterial species were Staphylococcus hominis ssp hominis, Staphylococcus epidermidis, Staphylococcus haemolyticus, and Staphylococcus saprophyticus. AST results showed that on average, CoNS were susceptible to tigecycline (100%), nitrofurantoin (98.4−100%), linezolid (86.1−100%), and vancomycin (80.6−100%). CoNS were most resistant to benzylpenicillin (100%), oxacillin (85.5−97.2%), and erythromycin (75−97.2%). Conclusion. CoNS were resistant towards several available antibiotics in RSUP Dr. Mohammad Hoesin Palembang.

A STUDY ON IN VITRO ACTIVITY OF FOSFOMYCIN AGAINST ENTEROBACTERIACAE UROPATHOGEN ALONG WITH MICROBIOLOGICAL PROFILE AND ANTIBIOGRAM OF UROPATHOGENS

Background:Urinary tract infection (UTI) is one of the most common infection throughout the world that may affect both the lower and the upper urinary tracts. Aims & Objective:The present study was done to determine various organisms causing Urinary tract infections and to analyse antimicrobial sensitivity patterns of those isolates. Materials and Methods:This prospective study was conducted from April 2020 to March 2021at SIMS& RH, Tumkur. All urine samples were received in Microbiology laboratory for routine microbiology investigations were inoculated on Blood agar and MacConkey agar culture media using calibrated wire loop . Urinary isolates with significant bacteriuria were further processed by conventional biochemical tests and antimicrobial susceptibility testing was done as per standard methods. Results: A total of 697 urine samples were processed in that 324 (46.48%) samples were shown as significant growth of bacteria. Most of the cases seen in (67.28%) female and under age group of 21-30(22.22%).The predominantly Gram-negative bacteria (85.18%) were isolated followed by Gram positive bacteria(10.49%) and Candida spp(4.32%). The Gram negative bacteria showed high sensitivity to Ampicillin sulbactum (88.27%) followed by Amikacin (87.24%). All Gram-positive bacteria isolates is showed sensitivity to Vancomycin (100%).We found that 235( 92.88%) Enterobacteriaceace isolates were is susceptible for Fosfomycin. Conclusion:. Antibiotic resistance has become a major clinical problem worldwide and has increased over the years.Hence antibiotic susceptibility testing should be done to diagnose and treat the drug resistant UTI cases. Fosfomycin may be given empirically in patients with uncomplicated urinary tract infection due to Enterobacteriaceace.

Minimal inhibitory concentration (MIC) of sodium hypochlorit against bacterial isolate from equipment in the microbiology laboratory

Microbiology laboratory equipment is susceptible to bacterial contamination and therefore has the potential to become a medium for the spread of disease and infection. The existence of a less than sterile microbiological analysis process in the STIKes Karsa Husada Garut Microbiology Laboratory causes bacterial contamination of laboratory equipment such as bacterial analysis that does not comply with standards or the use of less than sterile equipment. To control the spread of contaminants, a decontamination process is required using a chemical disinfectant, namely sodium hypochlorite. Measuring the effectiveness of a disinfectant by looking at or can be determined by the Minimum Inhibitory Concentration (MIC). The aim of this research was to determine the effectiveness of sodium hypochlorite disinfectant in inhibiting the growth of microorganisms in bacterial isolates from the STIKes Karsa Husada Garut Microbiology Laboratory equipment. The data analysis used was analyzed descriptively. The results of this research are the Minimum Inhibitory Concentration (MIC) of sodium hypochlorite disinfectant on bacterial isolates from the STIKes Karsa Husada Garut Microbiology Laboratory equipment at a concentration of 4%. So it can be concluded that sodium hypochlorite disinfectant with a concentration of 4% is effective in inhibiting the growth of microorganisms.

Clean your own house first: Integrating Sustainability into Microbiology Labs.

Clean your own house first: Integrating Sustainability into Microbiology Labs.

Clinical Utility of Blood Culture Identification 2 Panel in Flagged Blood Culture Samples from the Intensive Care Unit of a Tertiary Care Hospital.

The availability of rapid diagnostic platforms for positive blood cultures has accelerated the speed at which the clinical microbiology laboratory can identify the causative organism and facilitate early appropriate antimicrobial therapy. There is a paucity of data regarding the clinical utility of the blood culture identification 2 (BCID2) panel test and its correlation with phenotypic drug susceptibility testing (DST) in flagged blood culture bottles from intensive care units (ICUs) in countries such as India, which have high rates of multidrug-resistant gram-negative bacteria (MDR-GNB). We conducted a retrospective observational study in a tertiary care ICU on 200 patients above 18 years of age in whom a BCID2 test was ordered when blood cultures flagged positive. We found 99% concordance between BCID2 and cultures in the identification of bacteria and yeasts and 96.5% concordance between phenotypic and genotypic DST. Furthermore, BCID2 was available about 1.5 days earlier than conventional ID and DST and played a key role in tailoring antimicrobials in 82.5% of the patients. Polymyxin-based therapy was discontinued earlier after an empiric dose in 138 patients (69%) based on BCID2 reports. In critically ill patients with monomicrobial bacteremia, BCID2 rapidly identifies bacteria and antimicrobial resistance (AMR) genes and is significantly faster than conventional culture and sensitivity testing. Antibiotics were escalated in more than a third of patients and de-escalated in almost a fifth on the same day. We recommend that all ICUs routinely incorporate the test in their antibiotic decision-making process and in antimicrobial stewardship. Vineeth VK, Nambi PS, Gopalakrishnan R, Sethuraman N, Ramanathan Y, Chandran C, et al. Clinical Utility of Blood Culture Identification 2 Panel in Flagged Blood Culture Samples from the Intensive Care Unit of a Tertiary Care Hospital. Indian J Crit Care Med 2024;28(5):461-466.

Bacteriological profile of community peritonitis in adults at Mohammed VI university hospital

A good analysis of intraperitoneal bacteriological results constitutes the basis of therapeutic consideration. The objective of this work is to report the main epidemiological and bacteriological characteristics of community-acquired peritonitis in adults at the Mohammed VI University Hospital of Marrakech. This is a retrospective descriptive study carried out in the microbiology laboratory of Arrazi hospital at Mohammed VI University Hospital in Marrakech over a period of seven years from January 1, 2017 to December 31, 2023 including all community peritonitis documented in our hospital. The cytobacteriological study was carried out according to conventional methods. During the study period (2017-2023), 503 documented peritonitis were collected, The profile of the incriminated germs was dominated by Escherichia coli (48.9%) followed by Streptococci (18.3%), 8% of Pseudomonas aeruginosa and 18.5% for other Enterobacteria. Our results showed that E coli becomes increasingly resistant to the combination of amoxicillin acid clavulanic which is the antibiotic commonly used in our context, this leads us to review the antibiotics prescribed probabilistically in our context for the management of peritonitis community.

Colistin, the last resort antibiotic: challenges in the implementation of its routine susceptibility testing

Background: colistin has become a critical antibiotic for lifethreatening multidrug resistance Gram-negative infections, particularly carbapenemase-producing bacteria. Detecting colistin resistance in routine microbiology laboratories is crucial for combating these fatal infections poses a challenge. Especially in developing countries, there is a need for a cost-effective, rapid, and user-friendly diagnostic method. Objective: implementing the various available methods for colistin testing is a significant challenge in resource-limited settings due to logistic difficulties and the need for technical expertise. Materials and Methods: this study shares experiences and insights gained while implementing in-vitro colistin susceptibility testing in a high-load bacteriology laboratory of a tertiary care center in Delhi, India. The following test methods for colistin susceptibility testing were incorporated in the routine antimicrobial susceptibility testing of our laboratory: Colistin Agar Test, Colistin Broth Disk Elution Test, Broth Microdilution susceptibility testing. Results: inconsistent growth patterns were observed in the colistin agar dilution Minimum Inhibitory Concentration (MIC) method, which could be resolved only after the preparation of fresh plates containing that specific concentration of colistin. The contamination issue of plates on use over a few days was addressed by pouring agar containing various concentrations of colistin in cottonplugged glass tubes. In the colistin broth disk elution test, due to the non-availability of screw-capped 10 mL glass tubes, MacCornety bottles (30 mL) were used. Subcultures were performed from the turbid wells to rule out the growth of contaminants when encountering discordant MIC values or skipped wells on the colistin broth microdilution test. Conclusions: despite several technical issues in in-vitro colistin susceptibility testing, we have successfully implemented it in our laboratory. Our experiences can offer guidance to laboratories that are still in the process of implementing it.

Phytochemical Profile and Antibacterial Activity of Nigella Sativa against Biofilm-producing Bacteria Uropathogens

This study explores the antibacterial effects of Nigella sativa seeds on bacteria obtained from clinical samples. The aim was to assess the antibacterial properties of both aqueous and methanolic extracts of Nigella sativa seeds against E. coli, S. aureus, and P. aeruginosa. The three samples were collected from the Microbiology Laboratory of Modibbo Adamawa Medical Centre and were reconfirmed using culture, microscopy, and some biochemical tests. The seed samples of N. sativa were procured from herbal point Yola, Adamawa State, Nigeria. The phytochemical assay of the extracts revealed the presence of flavonoids, alkaloids, tannins, phenols, cardiac glycosides, steroids, saponins, and terpenoids in both extracts. The highest antibacterial activity against S. aureus, E. coli, and P. aeruginosa was demonstrated by the aqueous extract of N. sativa seeds, with inhibition zone diameters of 19.30 ±0.61 mm, 8.10 ±2.17 mm, and 12.00 ±0.29 mm, respectively. However, the methanol extract exhibited slightly greater activity against E. coli and P. aeruginosa, with inhibition zone diameters of 12.10 ±0.38 mm and 13.80 ±0.40 mm, respectively. Both methanol and aqueous extracts showed minimum inhibitory concentrations (MICs) of 25 mg/mL against S. aureus and E. coli. Similarly, for P. aeruginosa, the MIC was 25 mg/mL for methanol extract and 50 mg/mL for aqueous extract. The minimum bactericidal concentration (MBC) for both extracts against S. aureus and E. coli was determined to be 25 mg/mL. However, for P. aeruginosa, the MBC was 25 mg/mL for the aqueous extract and 50 mg/mL for the methanol extract. The study indicates that N. sativa seed extract possesses antibacterial properties against S. aureus and P. aeruginosa, underscoring its potential as an effective medicinal antibacterial agent.

An exception-reporting approach for wound swab culture: effect on post-report antibiotic initiation.

Wound swab culture is a high-volume test performed in clinical microbiology laboratories. In this analysis, we have shown that an alternative approach to reporting positive wound swab cultures has resulted in a large reduction in post-report antibiotic initiation, suggesting that the current standard method of reporting generates considerable unnecessary antibiotic use. If these findings are replicated elsewhere, wider adoption of this reporting would represent an opportunity for many clinical microbiology laboratories to have a significant impact on community antimicrobial stewardship.

Invasive pneumococcal disease surveillance in Canada, 2021-2022.

Invasive pneumococcal disease (IPD, Streptococcus pneumoniae) has been a nationally notifiable disease in Canada since 2000. The use of conjugate vaccines has caused a shift in the distribution of serotypes over time. This report is a summary of the demographics, serotypes and antimicrobial resistance of IPD isolates collected in Canada in 2021 and 2022. The National Microbiology Laboratory (NML) of the Public Health Agency of Canada in Winnipeg, Manitoba collaborates with provincial and territorial public health laboratories to conduct national surveillance of IPD. There were 1,999 isolates reported in 2021 and 3,775 isolates in 2022. Serotype was determined by the Quellung reaction or whole-genome sequencing (WGS). Antimicrobial susceptibilities were determined by WGS methods, broth microdilution, or data shared by collaborators in the Canadian Antimicrobial Resistance Alliance program at the University of Manitoba. Population-based IPD incidence rates were obtained through the Canadian Notifiable Disease Surveillance System. The incidence of IPD in Canada was 5.62 cases per 100,000 population in 2021, decreasing from the peak of 10.86 cases per 100,000 population in 2018. Serotypes with increasing trends (p<0.05) between 2018 and 2022 included: 4 (6.1%-12.4%), 9V (1.0%-5.1%) and 12F (4.8%-5.4%). The overall prevalence of PCV13 serotypes increased over the same period (31.2%-41.5%, p<0.05) while the prevalence of non-vaccine types decreased significantly (27.3%-21.5%, p<0.0001). The highest rates of antimicrobial resistance in 2021 and 2022 were seen with clarithromycin (21%, 2021; 24%, 2022) and erythromycin (22%, 2021; 24%, 2022). Multidrug-resistant IPD continued to increase from 2018 to 2022 (6.7%-12.6%, p<0.05). The number of cases of IPD continued to decrease in 2021 in comparison to previous years, however, 2022 saw a return to pre-COVID-19 levels. Disease due to PCV13 serotypes 3, 4, 9V and 19F, as well as non-PCV13 serotypes 12F and 20, is increasing in prevalence. Surveillance of IPD to monitor changing serotype distribution and antimicrobial resistance is essential.

Invasive group A streptococcal disease surveillance in Canada, 2021-2022.

Invasive group A streptococcal (iGAS, Streptococcus pyogenes) disease has been a nationally notifiable disease in Canada since 2000. This report summarizes the demographics, emm types, and antimicrobial resistance of iGAS isolates collected in Canada in 2021 and 2022. The Public Health Agency of Canada's National Microbiology Laboratory collaborates with provincial and territorial public health laboratories to conduct national surveillance of invasive S. pyogenes. Emm typing was performed using the Centers for Disease Control and Prevention emm sequencing protocol or extracted from whole-genome sequencing data. Antimicrobial susceptibilities were determined using Kirby-Bauer disk diffusion according to Clinical and Laboratory Standards Institute guidelines or predicted from whole-genome sequencing data based on the presence of resistance determinants. Overall, the incidence of iGAS disease in Canada was 5.56 cases per 100,000 population in 2021, decreasing from the peak of 8.6 cases per 100,000 population in 2018. A total of 2,630 iGAS isolates were collected during 2022, representing an increase from 2021 (n=2,179). In particular, there was a large increase in isolates collected from October to December 2022. The most predominant emm type overall in 2021 and 2022 was emm49, at 21.5% (n=468) and 16.9% (n=444), respectively, representing a significant increase in prevalence since 2018 (p<0.0001). The former most prevalent type, emm1, increased from 0.5% (n=10) in 2021 to 4.8% (n=125) in 2022; similarly, emm12 increased from 1.0% (n=22) in 2021 to 5.8% (n=151) in 2022. These two types together accounted for almost 25% of isolates collected in late 2022 (October to December). Antimicrobial resistance rates in 2021 and 2022 included: 14.9%/14.1% erythromycin resistance, 4.8%/3.0% clindamycin resistance, and <1% chloramphenicol resistance. The increase of iGAS isolates collected in Canada is an important public health concern. Continued surveillance of iGAS is critical to monitor expanding emm types and antimicrobial resistance patterns.

Nasal carriage rate, associated factors, and antimicrobial susceptibility patterns of methicillin resistance Staphylococcus aureus among pre-clinical undergraduate students at the College of Health and Medical Sciences, Haramaya University, Ethiopia

BackgroundStaphylococcus aureus nasal carriage has been linked to higher rates of infection and morbidity. People with Methicillin-resistant Staphylococcus aureus can be a potential source of infection for others. University students living together in crowded conditions increase their risk of acquiring infections. The prevalence of S. aureus, particularly Methicillin-resistant Staphylococcus aureus nasal carriage, in Ethiopian university students is sparse.ObjectiveThis study aimed to determine the nasal carriage rate, associated factors, and antimicrobial susceptibility patterns of methicillin-resistant Staphylococcus aureus among pre-clinical students at the College of Health and Medical Sciences, Haramaya University, Ethiopia, from 1 July to 30 August 2022.MethodsAn institutional-based cross-sectional study was conducted among 270 randomly selected pre-clinical Health and Medical Sciences students. Data on associated factors were collected using pre-tested, structured questionnaires. A nasal swab was taken from each participant and sent to the microbiology laboratory via Amies transport media in a cold chain. There, it was cultivated using conventional techniques. The isolated colonies were found to be S. aureus, and its antimicrobial susceptibility was performed using the Kirby–Bauer disk diffusion method on Muller–Hinton agar. Methicillin-resistant Staphylococcus aureus expressing using cefoxitin based on CLSI breakpoint. Data were entered into Epi-Data version 4.4.2.1 and exported to the Statistical Package for Social Sciences (SPSS) software version 25 for analysis. Pearson’s chi-square test was performed to predict the associations between variables. A p-value less than 0.05 was regarded as statistically significant.ResultMethicillin-resistant Staphylococcus aureus nasal carriage was 5.9% (95% CI: 3.09–8.7) of cases of S. aureus nasal colonization, which was found to be 12.96% (95% CI: 8.85–16.96). Methicillin-resistant Staphylococcus aureus nasal colonization was significantly associated with the history of cigarette smoking (p = 0.000), intake of khat (p = 0.042), nose-picking habit (p = 0.003), history of sharing personal goods (p = 0.021), and history of hospitalizations (p = 0.00). All of the Methicillin-resistant Staphylococcus aureus isolates were resistant to ampicillin and cefoxitin.ConclusionBased on the findings, a considerable proportion of healthy students harbored Methicillin-resistant Staphylococcus aureus strains associated with behavioral factors. Furthermore, these isolates showed high resistance to cefoxitin and ampicillin. Hence, it is crucial to regularly test pre-clinical students to prevent endogenous infections and the spread of Methicillin-resistant Staphylococcus aureus.

Carbapenem-resistant gram-negative bacterial infections and risk factors for acquisition in a Kenyan intensive care unit

BackgroundCarbapenem-resistant Gram-negative bacteria (CR-GNB) are a critical public health threat globally; however, there are inadequate surveillance data, especially in intensive care units (ICU), to inform infection prevention and control in many resource-constrained settings. Here, we assessed the prevalence of CR-GNB infections and risk factors for acquisition in a Kenyan ICU.MethodsA hospital-based cross-sectional study design was adopted, recruiting 162 patients clinically presenting with bacterial infection after 48 h of ICU admission, from January to October 2022 at the Nairobi West Hospital, Kenya. Demographics and clinical data were collected by case report form. The type of sample collected, including blood, tracheal aspirate, ascitic tap, urine, stool, and sputum depended on the patient’s clinical presentation and were transported to the hospital Microbiology laboratory in a cool box for processing within 2 h. The samples were analyzed by cultured and BD Phoenix system used for isolates’ identity and antimicrobial susceptibility.ResultsCR-GNB infections prevalence was 25.9% (42/162), with Klebsiella pneumoniae (35.7%, 15/42) and Pseudomonas aeruginosa (26.2%, 11/42) predominating. All isolates were multidrug-resistant (MDR). P. aeruginosa and A. baumannii were 100% colistin-resistant, while K. pneumoniae (33.3%) was tigecycline-resistant. History of antibiotics (aOR = 3.40, p = 0.005) and nasogastric tube (NGT) use (aOR = 5.84, p = < 0.001) were the risk factors for infection.ConclusionOur study highlights high MDR- and CR-GNB infections in ICU, with prior antibiotic exposure and NGT use as risk factors, and diminishing clinical value of colistin and tigecycline. In this study setting and beyond, strict implementation of antimicrobial stewardship programs and adherence to infection prevention and control through monitoring, evaluation and feedback are warranted to curb CR-GNB infections, especially among the risk groups.