Clinical Bacteriology Research Articles

Bacterial infections epidemiology and factors associated with multidrug resistance in the northern region of Ghana

Bacterial infections caused by multidrug resistant organisms are a major global threat. There is still a knowledge gap on this situation in the Northern Region of Ghana. This study determined the prevalence and resistance profile of bacterial infections. It also identified factors associated with multidrug resistance in the study area. This was a retrospective cross-sectional design and it analyzed data from the samples received at the Tamale Zonal Public Health Reference Laboratory from June 2018 to May 2022. The data were analyzed using the R software version 4.2.0. Univariate and multivariable binary logistic regression analyses were used to determine the factors associated with multidrug resistance. The samples included all specimen types possible. The specimens were collected for the purpose of clinical bacteriology diagnostics. Overall a total of 1222 isolates were obtained. The three (3) main bacteria responsible for infections were: Klebsiella spp. (27%), Moraxella spp. (22%), Escherichia spp. (16%). High resistance levels were found against the tested antibiotics and about 41.60% of the bacterial strains isolated were multidrug resistant. Hospitalization was associated with multidrug resistance in univariate (COR 1.96; 95% CI 1.43–2.71; P-value < 0.001) and multivariable analyses (AOR 1.78; 95% CI 1.28–2.49; P-value < 0.001). There is the need for further research on the molecular epidemiology of antibiotic resistance genes in the study area to effectively control the spread of multidrug resistant pathogens. In addition, efforts to build the capacity of health professionals on infection prevention and control as well as diagnostic and antimicrobial stewardship needs urgent attention.

Role of gene sequencing for the diagnosis, tracking and prevention of bacterial infections

Gene sequencing is the inevitable future of diagnostic microbiology. Of the various molecular assays available, sequencing is the promising technique for detecting culture-negative infections due to uncultivable bacteria namely culture-negative endocarditis, meningitis, brain abscess, keratitis, urinary tract infections, empyema, septic arthritis and septicaemia. Sequencing also helps to predict full resistance profile of bacteria and its virulence traits. Sequencing is an emerging and powerful technique to perform the epidemiological studies in an outbreak situation. This review focuses on the common applications of sequencing in clinical bacteriology including isolate characterisation, antimicrobial resistance and virulence factor profiling, establishing the source of infections and tracking the disease transmission.

Restoring non-COVID-19 clinical research and surveillance in Oyo state, Nigeria during the SARS-CoV-2pandemic.

Many sub-Saharan African patients receive clinical care from extramurally-supported research and surveillance. Dur- ing the COVID-19 pandemic, pausing these activities reduces pa- tient care, surveillance, and research staff employment, increasing pandemic losses. In Oyo State, Nigeria, we paused a multi-country invasive salmonellosis surveillance initiative and a rural clinical bac- teriology project. Working with research partners raises health facility con- cerns about SARS-CoV-2 transmission risks and incurs infection pre- vention costs, so we developed and implemented re-opening plans to protect staff and patients and help health facilities deliver care. Our reopening plan included appointing safety and per- sonal protective equipment (PPE) managers from existing project staff cadres, writing new standard operating procedures, implement- ing extensive assessed training, COVID-19 testing for staff, procuring and managing PPE, and providing secondary bacteraemia blood culture support for COVID-19 patients in State isolation facilities. Surveillance data showed that the pandemic reduced care access and negatively affected patient unsupervised antibacterial use. The re-opening plan repurposed human and material resources from national and international extramurally-supported programs to mitigate these effects on public health. A structured reopening plan restarted care, surveil- lance, and infection prevention and control.

Validation of Three MicroScan® Antimicrobial Susceptibility Testing Plates Designed for Low-Resource Settings.

Easy and robust antimicrobial susceptibility testing (AST) methods are essential in clinical bacteriology laboratories (CBL) in low-resource settings (LRS). We evaluated the Beckman Coulter MicroScan lyophilized broth microdilution panel designed to support Médecins Sans Frontières (MSF) CBL activity in difficult settings, in particular with the Mini-Lab. We evaluated the custom-designed MSF MicroScan Gram-pos microplate (MICPOS1) for Staphylococcus and Enterococcus species, MSF MicroScan Gram-neg microplate (MICNEG1) for Gram-negative bacilli, and MSF MicroScan Fastidious microplate (MICFAST1) for Streptococci and Haemophilus species using 387 isolates from routine CBLs from LRS against the reference methods. Results showed that, for all selected antibiotics on the three panels, the proportion of the category agreement was above 90% and the proportion of major and very major errors was below 3%, as per ISO standards. The use of the Prompt inoculation system was found to increase the MIC and the major error rate for some antibiotics when testing Staphylococci. The readability of the manufacturer’s user manual was considered challenging for low-skilled staff. The inoculations and readings of the panels were estimated as easy to use. In conclusion, the three MSF MicroScan MIC panels performed well against clinical isolates from LRS and provided a convenient, robust, and standardized AST method for use in CBL in LRS.

MASS-SPECTROMETRIC STUDIES OF HELMINTHS: INFORMATION TECHNOLOGIES FOR IDENTIFICATION OF PARASITIC INFECTION CAUSES

Mass spectrometry is currently used to identify bacteria, mycobacteria and some fungi. Unlike clinical bacteriology, MALDI-TOF MS is practically not used for the identification of human and animal parasites. Homogenate protein profiles were obtained using Microflex LT MALDI-TOF MS (Bruker Daltonics Germany) with Flex Control software, visualized using Flex analysis 3.3 software (Bruker Daltonics). Analysis of protein extracts of nematodes showed spectra with high intensity peaks in the range of 2–20 kDa. Slight differences in the mass spectrometric spectra of Ascaris lumbricoides and Ascaris suum in the same range, which characterizes nematode species, confirm the results obtained in full-genome analysis of helminth data that the causative agent of human ascariasis is an evolutionarily close relative of swine ascarids. In the high ranges of mass spectrometric analysis of Dirofilaria immitis and Dirofilaria repens, significantly frequent peaks were observed, which probably characterize the whole genus of nematodes. In the range above 6000 kDa, the spectra differed in representative peaks, which allowed to differentiate one species from another in protein profile. A comparative analysis of the mass spectrometric peaks of helminths D.repens, D. immitis using R medium (MALDIquant). On the cluster of dendrograms of averaged mass spectra, it was found that for two individuals of D. repens, as well as for two individuals of D. immitis, the sections of the dendrograms coincide with a high degree of probability. For D. immitis, the coincidence rate was 100%, for D. repens 70%. The results obtained can form the basis for the creation of a library of protein profiles with the aim of accelerated and objective dirofilaria differentiation.

Patterns of antimicrobial, multidrug and methicillin resistance among Staphylococcus spp. isolated from canine specimens submitted to a diagnostic laboratory in Tennessee, USA: a descriptive study

BackgroundMultidrug- and methicillin-resistant staphylococci are both veterinary and public health concerns due to their zoonotic potential. Therefore, the objective of this study was to investigate patterns of antimicrobial, multidrug, and methicillin resistance among four Staphylococcus spp. commonly isolated from canine clinical specimens submitted to the Clinical Bacteriology Laboratory at the University of Tennessee College of Veterinary Medicine (UTCVM).MethodsResults of antimicrobial susceptibility testing and mecA polymerase chain reaction (PCR) for isolates of four common Staphylococcus spp. isolates were obtained from the Bacteriology Laboratory at the UTCVM between 01/01/2006 and 12/31/2017. Cochran-Armitage trend test was used to assess temporal trends of antimicrobial resistance (AMR), multidrug resistance (MDR), and methicillin resistance. Kappa test of agreement was used to assess agreement between the results of PCR and disk diffusion tests.ResultsMost of the 7805 isolates were S. pseudintermedius (6453 isolates), followed by S. coagulans (860), S. aureus (330), and S. schleiferi (162). Among S. pseudintermedius isolates, 45.5% were MDR, and 30.8% were methicillin-resistant (MRSP). There was a significant temporal increase in MRSP (p = 0.017). Chloramphenicol resistance increased among both MRSP and methicillin-susceptible (MSSP) isolates (p < 0.0001). Among S. aureus isolates, 40.9% were MDR, 37.4% were methicillin-resistant (MRSA), and the proportion of MRSA isolates increased significantly (p = 0.0480) over time. There was an increasing temporal trend in the proportion of MDR isolates among MSSP (p = 0.0022), but a decrease among MRSP (p < 0.0001) and MRSA (p = 0.0298). S. schleiferi had the highest percentage (56.9%) of methicillin-resistant isolates. Oxacillin disk diffusion was superior to cefoxitin for the detection of mecA-mediated resistance and had almost perfect agreement with mecA PCR assay for S. pseudintermedius (95.4% agreement, kappa (κ) = 0.904; p < 0.0001), S. coagulans (95.6%, κ = 0.913; p < 0.0001) and S. schleiferi (97.7%, κ = 0.945; p < 0.0001). However, cefoxitin disk diffusion was superior to oxacillin disk diffusion and had almost perfect agreement with mecA PCR assay for S. aureus (95.3%, κ = 0.834; p < 0.0001).ConclusionsThe levels of resistance and increasing temporal trends are concerning. These findings have implications for treatment decisions and public health due to the zoonotic potential of staphylococci. Continued surveillance and use of antibiograms to guide clinical decisions will be critical.

Blood culture surveillance in a secondary care hospital in Benin: epidemiology of bloodstream infection pathogens and antimicrobial resistance

BackgroundAlthough global surveillance of antimicrobial resistance (AMR) is considered key in the containment of AMR, data from low- and middle-income countries, especially from sub-Saharan Africa, are scarce. This study describes epidemiology of bloodstream infections and antimicrobial resistance rates in a secondary care hospital in Benin.MethodsBlood cultures were sampled, according to predefined indications, in BacT/ALERT FA Plus and PF Plus (bioMérieux, Marcy-l’Etoile, France) blood culture bottles (BCB) in a district hospital (Boko hospital) and to a lesser extent in the University hospital of Parakou. These BCB were incubated for 7 days in a standard incubator and twice daily inspected for visual signs of growth. Isolates retrieved from the BCB were processed locally and later shipped to Belgium for reference identification [matrix-assisted laser desorption/ionization time-of-flight spectrometry (MALDI-TOF)] and antibiotic susceptibility testing (disk diffusion and E-tests).ResultsFrom October 2017 to February 2020, 3353 BCB were sampled, corresponding to 3140 blood cultures (212 cultures consisting of > 1 BCB) and 3082 suspected bloodstream infection (BSI) episodes. Most of these cultures (n = 2471; 78.7%) were sampled in children < 15 years of age. Pathogens were recovered from 383 (12.4%) cultures, corresponding to 381 confirmed BSI. 340 of these pathogens were available and confirmed by reference identification. The most common pathogens were Klebsiella pneumoniae (n = 53; 15.6%), Salmonella Typhi (n = 52; 15.3%) and Staphylococcus aureus (n = 46; 13.5%). AMR rates were high among Enterobacterales, with resistance to third-generation cephalosporins in 77.6% of K. pneumoniae isolates (n = 58), 12.8% of Escherichia coli isolates (n = 49) and 70.5% of Enterobacter cloacae isolates (n = 44). Carbapenemase production was detected in 2 Escherichia coli and 2 Enterobacter cloacae isolates, all of which were of the New Delhi metallo-beta lactamase type. Methicillin resistance was present in 22.4% of S. aureus isolates (n = 49).ConclusionBlood cultures were successfully implemented in a district hospital in Benin, especially among the pediatric patient population. Unexpectedly high rates of AMR among Gram-negative bacteria against commonly used antibiotics were found, demonstrating the clinical and scientific importance of clinical bacteriology laboratories at this level of care.

Causas de morte e condenação de órgãos no abate de ovinos em sistema de confinamento no Sul do Rio Grande do Sul

ABSTRACT: In Brazil the second largest sheep herd is in Rio Grande do Sul and in recent years the demand for meat consumption of this specie has increased. Intensive farming systems have made considerable progress in this region with the objective of increasing the production of sheep for slaughter and obtaining a uniform batch to ensure better quality of sheep meat to consumers. However, the agglomeration and stress that animals go through can lead to the occurrence of illnesses and economic loss to producers. The objectives of this paper were to determine the main causes of death that affected sheep in a feedlot system, to establish forms of control and prophylaxis of diagnosed illnesses, and to estimate the economic losses resulting from them. The objective was also to determine the causes of condemnation of organs or carcasses in the slaughterhouses that processed the sheep were sent, and to estimate the losses in this productive sector. For this, a follow-up work was carried out in an establishment located in the city of São Lourenço do Sul, Rio Grande do Sul, from October 2020 to September 2021. The dead sheep at the feedlot were necropsied, and the diagnosis was made based on clinical signs, pathology, and bacteriology. The main diseases diagnosed were parasitic enteritis (15.4%), pneumonia (13%), and listeriosis (9.6%). In the slaughterhouse study, the lesions that led to the highest number of condemnations were hydatidosis (29.9%), renal congestion (26.2%), and renal ischemia (25.8%). The economic losses estimated for the death of sheep in 2021 was R$17,480.00, significantly lower than the approximate losses in 2019 and 2020 of R$50,000.00 and R$54,000.00, respectively. This highlights the importance of technical assistance to reduce these losses due to mortality in sheep raised in a feedlot system. It was also observed the kidneys of the sheep were the organs most frequently selected for condemnation. The economic value of the kidneys sold as disposed waste was eight time lower than that the value of kidneys suitable for consumption.

Limited added value of negative pressure wound therapy compared with calcium alginate dressings for second intention healing in a noncontaminated and contaminated equine distal limb wound model.

Distal limb wounds in horses often show aberrant healing due to a slow inflammatory response. In human medicine, negative pressure wound therapy (NPWT) is used for the treatment of chronic wounds with a similar inflammatory response. To compare the effect of NPWT to calcium alginate dressings on the healing of (non) contaminated equine distal limb wounds. Controlled experiment. Circular wounds were created on the left and right dorsomedial metacarpus of 10 horses. In five horses, the wounds were contaminated with Staphylococcus aureus and Pseudomonas aeruginosa. In all horses, one limb was treated with NPWT, the other with calcium alginate dressings. Treatments were applied during nine days for noncontaminated wounds and six days for contaminated wounds. Noninvasive (clinical assessment, bacteriology swabs, thermographic images and wound dimensions) and invasive (biopsies for histology and growth factor analysis) measurements were taken regularly for 71 and 29days respectively. Effects of selected parameters on continuous dependent variables were analysed using ANOVA, while for discrete dependent variables, logistic regression was applied. In noncontaminated wounds, there was significantly less wound retraction in the early healing stages when treated with NPWT (mean difference [95% CI]=19.2% [13.3%-25.1%]; P=.005), although wound size was not significantly different between NPWT and control wounds at later healing stages. Noncontaminated control wounds had a significantly higher neutrophil influx (OR [95% CI]=1.99 [1.49-2.66]; P<.001) and lower macrophage influx (OR [95% CI]=0.75 [0.60-0.93]; P=.008) compared with NPWT-treated wounds. Bacterial load and the presence of growth factors did not differ between treatments in noncontaminated wounds. In contaminated wounds, no differences between treatments were observed in wound size, histological parameters, bacterial load or growth factor concentration. Sample size is small. No long-term advantage was detected with NPWT compared with calcium alginate dressings in noncontaminated or contaminated equine distal limb wounds healing by second intention.

Psychometrics of health-related quality of life questionnaires in bronchiectasis: a systematic review and meta-analysis

IntroductionUnderstanding the psychometric properties of health-related quality of life (HRQoL) questionnaires can help inform selection in clinical trials. Our objective was to assess the psychometric properties of HRQoL questionnaires in bronchiectasis using a systematic review and meta-analysis of the literature.MethodsA literature search was conducted. HRQoL questionnaires were assessed for psychometric properties (reliability, validity, minimal clinically important difference (MCID) and floor/ceiling effects). Meta-analyses assessed the associations of HRQoL with clinical measures and responsiveness of HRQoL in clinical trials.Results166 studies and 12 HRQoL questionnaires were included. The Bronchiectasis Health Questionnaire (BHQ), Leicester Cough Questionnaire (LCQ), Chronic Obstructive Pulmonary Disease (COPD) Assessment Test (CAT) and Medical Outcomes Study 36-item Short-Form Health Survey (SF-36) had good internal consistency in all domains reported (Cronbach's α≥0.7) across all studies, and the Quality of Life-Bronchiectasis (QOL-B), St George's Respiratory Questionnaire (SGRQ), Chronic Respiratory Disease Questionnaire (CRDQ) and Seattle Obstructive Lung Disease Questionnaire (SOLQ) had good internal consistency in all domains in the majority of (but not all) studies. BHQ, SGRQ, LCQ and CAT had good test–retest reliability in all domains reported (intraclass correlation coefficient ≥0.7) across all studies, and QOL-B, CRDQ and SOLQ had good test–retest reliability in all domains in the majority of (but not all) studies. HRQoL questionnaires were able to discriminate between demographics, important markers of clinical status, disease severity, exacerbations and bacteriology. For HRQoL responsiveness, there was a difference between the treatment and placebo effect.ConclusionsSGRQ was the most widely used HRQoL questionnaire in bronchiectasis studies and it had good psychometric properties; however, good psychometric data are emerging on the bronchiectasis-specific HRQoL questionnaires QOL-B and BHQ. Future studies should focus on the medium- to long-term test–retest reliability, responsiveness and MCID in these HRQoL questionnaires which show potential in bronchiectasis.

Swine Erysipelas; It’s Epidemiology, Diagnosis, Treatment and Control and Preventive Measures, Comprehensive Review

Erysipelas is an infectious disease seen mainly in growing pigs and characterized clinically by fever, arthritis, skin lesions and sudden death. The disease may be acute, subacute, or chronic. Swine erysipelas is a disease caused by a specific micro organ Erysipelothrix rhusiopathiae whic h is a zoonotic ubiquitous gram-positive bacterium that causes erysipelas in swine, mammals, birds and erysipeloid in humans. People in contact with animals, animal products or animal wastes are at greatest risk. The acute form of swine erysipelas may have been confused for other diseases in pigs which are characterized by acute symptoms such as sudden death (for example, African swine fever). It can be diagnosed by its clinical signs, necropsy findings, bacteriology, antimicrobial response, molecular and serological examinations. It is recommended to increase awareness of the disease among animal and human practitioners as treatment is easy and available and vaccination is possible. However, the disease is still unknown to local veterinarians, clinical doctors, meat inspectors, butchers and laboratory personnel. Proper hygiene, regular pork inspection, use of protective wear among people working/ in contact with animals should be promoted. The disease causes high economic loss in pig rearing areas and influences the public health being a severe zoonotic disease. So the objective of this review is to create a better understanding of the disease for proper control and prevention of the disease

Analysis of trends of post-analytical quality indicators in Clinical Bacteriology laboratory: A pilot study from a tertiary care teaching hospital in Uttarakhand, India

ContextImplementation of quality management system (QMS) which encompasses various quality indicators (QIs), can serve as a stepping stone for continuous improvement & help in achieving globally accepted quality standards in a diagnostic laboratory. AimsTo generate preliminary data on trends of post-analytical QIs in Bacteriology section. Settings and designA pilot study was conducted at a tertiary care teaching hospital located in Rishikesh, Uttarakhand. Methods and materialData of the following four quality indicators pertaining to aerobic culture and sensitivity testing of various clinical samples received in Clinical Bacteriology laboratory was compiled and retrospectively analysed: (i) Rate of reporting errors; (ii) Rate of re-dos; (iii) Percentage of reports correlating with clinical diagnosis; (iv) Percentage of adherence to safety precautions by employees working in diagnostics. Statistical analysis usedDescriptive statistics like mean and frequency distribution plots. ResultsThe mean reporting error rate was 0.12 per 1000 tests. It was consistently low from July 2018 to May 2019, after which an overall increasing trend was observed. The mean rate of re-dos was 2.79 per 1000 tests. An overall decreasing trend was observed with maximum rates during the months of December 2017 and January 2018. On an average only 7.86% of the reports co-related with clinical diagnosis. Almost 100% adherence to safety precautions was observed with the exception of two instances of needle stick injuries (NSIs). ConclusionsCommitment of laboratory personnel in adopting, maintaining and analysing QMS data will lead to further strengthening of our existing healthcare system.

The utility of Amies charcoal bacteriology swabs for storage of canine urine prior to culture.

To determine the usefulness of bacteriology swabs as a storage method of canine urine samples and the effect on quantitative bacterial culture. Two hundred fourteen canine urine samples were collected by cystocentesis. The reference aliquot was placed in a sterile tube and processed for quantitative bacterial culture within 6hours. A bacteriology swab was then immersed in the urine for 5seconds and returned to the charcoal Amies media container. The urine samples in the sterile tube and bacteriology swab were stored at room temperature for 48 hours and processed for quantitative bacterial culture. Thirty-seven of the samples were positive on reference culture with a total of 42 bacterial isolates. Samples stored in sterile tube and bacteriology swab had identical sensitivity and specificity for detection of bacteriuria (94.7% and 100%, respectively) with very good agreement (κ=0.92; 95% CI 0.81 to 1.00). Agreement between the bacterial species of the reference sample and the bacteriology swab was higher (κ=0.85; 95% CI 0.71 to 0.99) than compared to the sterile tube (κ=0.78; 95% CI 0.62 to 0.94), but the overlapping confidence intervals mean improved agreement cannot be inferred. Bacteriology swabs stored in Amies charcoal transport media should be considered an alternative method to preserve canine urine sample when immediate processing for quantitative bacterial culture is not possible. The sensitivity of culturing plain urine, stored for 48 hours in a sterile tube, for detection of bacteriuria, was higher than previously reported.

Microbiological Profile and Drug-Resistance Pattern of Pathogens Among Patients Who Visited the University of Gondar Comprehensive Specialized Hospital, Ethiopia.

BackgroundThe emergence of antimicrobial resistance (AMR) is a public health threat in developing countries including Ethiopia; and there is a paucity of information regarding antimicrobial resistance patterns of commonly isolated pathogens, particularly in the study area. Hence, this study aimed to assess the microbiological profiles and resistance patterns of pathogens among patients who visited a tertiary hospital in the study setting.MethodsThis study was based on secondary data sources from the hospital microbiology database and culture reports between September 2019 and August 2020 at the University of Gondar comprehensive specialized hospitals, Ethiopia. Data about socio-demographic characteristics and clinical parameters, types of specimens collected, culture results, and antibiotic resistance pattern were collected manually by using a data abstraction format from the department of clinical bacteriology registration book and electronic database.ResultsA total of 5328 culture results were included in the final analysis. Bacterial growth was documented only in 803 (15.1%) samples. From the positive culture results documented, the highest positivity rate was reported from abscess (47.8%) followed by blood (26.2%) and urine (15.1%) samples. Among the bacterial isolates S. aureus (32.5%), Klebsiella species (17.9%), E. coli (14.8%) and Streptococcus species (7.4%) were the commonly identified organisms. Of the 803 bacterial isolates, about 672 (83.6%) isolates were resistant to at least one antibiotic and 19.7% isolates were MDR.ConclusionThis study showed that Staphylococcus aureus, Klebsiella pneumonia species, and Escherichia coli were the commonest isolated pathogens. Antimicrobial resistance among common isolates was high for most routinely used antibiotics, and some reserved drugs like carbapenems and fourth-generation cephalosporin. Thus, this study may have implications on patient management, drug procurement, local treatment guideline development, and rational use of antibiotics. Furthermore, this finding could also help to facilitate the implementation of antimicrobial stewardship and infection prevention and control interventions within the hospital.

NGS-Based S. aureus Typing and Outbreak Analysis in Clinical Microbiology Laboratories: Lessons Learned From a Swiss-Wide Proficiency Test.

Whole genome sequencing (WGS) enables high resolution typing of bacteria up to the single nucleotide polymorphism (SNP) level. WGS is used in clinical microbiology laboratories for infection control, molecular surveillance and outbreak analyses. Given the large palette of WGS reagents and bioinformatics tools, the Swiss clinical bacteriology community decided to conduct a ring trial (RT) to foster harmonization of NGS-based bacterial typing. The RT aimed at assessing methicillin-susceptible Staphylococcus aureus strain relatedness from WGS and epidemiological data. The RT was designed to disentangle the variability arising from differences in sample preparation, SNP calling and phylogenetic methods. Nine laboratories participated. The resulting phylogenetic tree and cluster identification were highly reproducible across the laboratories. Cluster interpretation was, however, more laboratory dependent, suggesting that an increased sharing of expertise across laboratories would contribute to further harmonization of practices. More detailed bioinformatic analyses unveiled that while similar clusters were found across laboratories, these were actually based on different sets of SNPs, differentially retained after sample preparation and SNP calling procedures. Despite this, the observed number of SNP differences between pairs of strains, an important criterion to determine strain relatedness given epidemiological information, was similar across pipelines for closely related strains when restricting SNP calls to a common core genome defined by S. aureus cgMLST schema. The lessons learned from this pilot study will serve the implementation of larger-scale RT, as a mean to have regular external quality assessments for laboratories performing WGS analyses in a clinical setting.

Improving Confirmatory Testing for the Antimicrobial Resistance Surveillance Network in Ethiopia

Background: In July 2017, the Ethiopian Public Health Institute (EPHI) launched an antimicrobial resistance (AMR) surveillance network at 4 sentinel laboratories. The National Clinical Bacteriology and Mycology Laboratory (NRL) at EPHI performs monthly confirmatory testing on a subset of isolates submitted by these sites. We assessed the existing confirmatory testing program to identify gaps and develop solutions, including a monitoring and evaluation (M&amp;E) system. Methods: We assembled a technical working group (TWG) of key stakeholders. Laboratory site visits included workflow observation, process mapping, document review, and technologist interviews. Proposed solutions to observed gaps were drafted in formats consistent with their intended application. Feedback from the TWG was incorporated into final drafts. Available AMR network staff members were trained remotely, and they will train remaining staff. Results: Table 1 describes major gaps and solutions identified. Conclusions: Confirmatory testing provides a mechanism to evaluate laboratory testing proficiency, target improvements, and estimate surveillance data quality, yet standardized methods were lacking. Our efforts highlight key components of confirmatory testing programs and provide a model for use in laboratories with similar needs.Funding: NoneDisclosures: None

Improving Report Generation and Delivery System of Microbiological Investigations at MRI – Sri Lanka with Concern to Turn-Around-Time, An Intervention Study

&lt;p&gt;Background: Clinical Bacteriology Laboratory (CBL) of the Medical Research Institute (MRI) is a National Reference Laboratory in Sri Lanka. The service improvement research project aimed at improving the report generation and delivery system. &lt;br /&gt;Methods: The mixed-method applied to study the process. Gap identification and designing of the intervention used a qualitative approach. Quantitative methods measured the effectiveness of the improvements. A package of interventions based on total quality management (TQM) principles designed with all stakeholder participation. &lt;br /&gt;Results: Delay in sample transport resulted from poor communication, lack of established mechanism and weak coordination between the transport unit and wards. The paper-based report generation process was disorganized, unreliable and error-prone. Additionally, the report delivery to Hospitals revolved on the incoming ambulance or government postal service a tied-up, poorly coordinated system. The interventions promoted coordinated communication. WHONET, a free windows based Laboratory Information System and database software, developed by the World Health Organization for microbiology laboratories installed to generate reliable and accurate automated reports. Reports in PDF format delivered to end-users by secured email. Timeliness, accuracy, quality and uniformity of reports improved. Improvement in post-intervention turn-around-time was statistically significant (p&amp;lt;0.05). &lt;br /&gt;Conclusion: The interventions based on TQM principles improved the process of report generation and delivery. Laboratory automation is a feasible and effective solution in the local setting. The end-user satisfaction perceived to be high on the improvements.&lt;/p&gt;

Genotypic to Phenotypic Resistance Discrepancies Identified Involving β-Lactamase Genes, blaKPC, blaIMP, blaNDM-1, and blaVIM in Uropathogenic Klebsiella pneumoniae.

IntroductionKlebsiella pneumoniae carbapenemase (KPC) belongs to the Group-A β-lactamases that incorporate serine at their active site and hydrolyze various penicillins, cephalosporins, and carbapenems. Metallo-beta-lactamases (MBLs) are group-B enzymes that contain one or two essential zinc ions in the active sites and hydrolyze almost all clinically available β-lactam antibiotics. Klebsiella pneumoniae remains the pathogen with the most antimicrobial resistance to KPC and MBLs.MethodsThis research investigated the blaKPC, and MBL genes, namely, blaIMP, blaVIM, and blaNDM-1 and their phenotypic resistance to K. pneumoniae isolated from urinary tract infections (UTI) in Bangladesh. Isolated UTI K. pneumoniae were identified by API-20E and 16s rDNA gene analysis. Their phenotypic antimicrobial resistance was examined by the Kirby-Bauer disc diffusion method, followed by minimal inhibitory concentration (MIC) determination. blaKPC, blaIMP, blaNDM-1, and blaVIM genes were evaluated by polymerase chain reactions (PCR) and confirmed by sequencing.ResultsFifty-eight K. pneumoniae were identified from 142 acute UTI cases. Their phenotypic resistance to amoxycillin-clavulanic acid, cephalexin, cefuroxime, ceftriaxone, and imipenem were 98.3%, 100%, 96.5%, 91.4%, 75.1%, respectively. Over half (31/58) of the isolates contained either blaKPC or one of the MBL genes. Individual prevalence of blaKPC, blaIMP, blaNDM-1, and blaVIM were 15.5% (9), 10.3% (6), 22.4% (13), and 19% (11), respectively. Of these, eight isolates (25.8%, 8/31) were found to have two genes in four different combinations. The co-existence of the ESBL genes generated more resistance than each one individually. Some isolates appeared phenotypically susceptible to imipenem in the presence of blaKPC, blaIMP, blaVIM, and blaNDM-1 genes, singly or in combination.ConclusionThe discrepancy of genotype and phenotype resistance has significant consequences for clinical bacteriology, precision in diagnosis, the prudent selection of antimicrobials, and rational prescribing. Heterogeneous phenotypes of antimicrobial susceptibility testing should be taken seriously to avoid inappropriate diagnostic and therapeutic decisions.

Swine Erysipelas; It’s Epidemiology, Diagnosis, Treatment and Control and Preventive Measures, Comprehensive Review

Erysipelas is an infectious disease seen mainly in growing pigs and characterized clinically by fever, arthritis, skin lesions and sudden death. The disease may be acute, subacute, or chronic. Swine erysipelas is a disease caused by a specific micro organ Erysipelothrix rhusiopathiae whic h is a zoonotic ubiquitous gram-positive bacterium that causes erysipelas in swine, mammals, birds and erysipeloid in humans. People in contact with animals, animal products or animal wastes are at greatest risk. The acute form of swine erysipelas may have been confused for other diseases in pigs which are characterized by acute symptoms such as sudden death (for example, African swine fever). It can be diagnosed by its clinical signs, necropsy findings, bacteriology, antimicrobial response, molecular and serological examinations. It is recommended to increase awareness of the disease among animal and human practitioners as treatment is easy and available and vaccination is possible. However, the disease is still unknown to local veterinarians, clinical doctors, meat inspectors, butchers and laboratory personnel. Proper hygiene, regular pork inspection, use of protective wear among people working/ in contact with animals should be promoted. The disease causes high economic loss in pig rearing areas and influences the public health being a severe zoonotic disease. So the objective of this review is to create a better understanding of the disease for proper control and prevention of the disease.

A Feasible Laboratory-Strengthening Intervention Yielding a Sustainable Clinical Bacteriology Sector to Support Antimicrobial Stewardship in a Large Referral Hospital in Ethiopia.

Background: Access to clinical bacteriology in low resource settings (LRS) is a key bottleneck preventing individual patient management of treatable severe infections, detection of antimicrobial resistance (AMR), and implementation of effective stewardship interventions. We sought to demonstrate the feasibility of a practical bundle of interventions aimed at implementing sustainable clinical bacteriology services at Tikur Anbessa Specialized Hospital in Addis Ababa, Ethiopia, and report on cost and intensity of supervision.Methods: Starting in Dec 2015, an intervention based on the CLSI QMS01-A guideline was established, consisting of (i) an initial needs assessment, (ii) development of key standard operating procedures, (iii) adaptation of processes for LRS, (iv) training and supervision of laboratory staff via consultant visits and existing online resources, and (v) implementation of a practical quality systems approach. A guiding principle of the bundle was sustainability of all interventions post implementation.Outcomes and challenges: An initial investment of ~US$ 26,200 for laboratory reagents, and a total of 50 visit-days per year from three Canadian and Norwegian microbiologists were committed. Twelve SOPs, including antimicrobial susceptibility testing, were adapted, and an automated blood culture platform was donated (bioMerieux). In the first 18 months of implementation of the intervention, the average volume of specimens analyzed in the lab went from 15/day to 75/day. The number of blood cultures tested increased from an average of 2/day to over 45/day. Antimicrobial susceptibility testing was introduced and cumulative antibiograms were generated for the institution. Quality control was implemented for all procedures and quality assurance tools implemented included external quality assurance and proficiency testing of six technologists with longitudinal follow-up. The laboratory is on the path toward SLIPTA accreditation by the African Society for Laboratory Medicine. Reagent costs, staff training and retention, and engagement of clinical personnel with the lab proved to be manageable challenges. Key external challenges include in-country supply-chain management issues, lack of competition among distributors, and foreign-currency exchange distortions.Conclusions: Using a relatively low-intensity intervention based on existing training tools and accreditation schemes, we demonstrate that establishment of reasonable-quality clinical bacteriology is not only within reach but also a critical step toward assessing the burden of AMR in settings like this one and implementing effective stewardship strategies.