Clinical Bacteriology Research Articles

Erik Waaler (1903–1997): one of the founders of rheumatological immunology who discovered rheumatoid factor

Erik Waaler was born at Hamar, Norway on 22 February 1903 and died in Bergen on 3 March 1997 (figure 1). He graduated from the Medical Faculty, University of Oslo,...

P165 Correlation of clinical profile and respiratory bacteriology of adult patients in a cystic fibrosis unit in Argentina

P165 Correlation of clinical profile and respiratory bacteriology of adult patients in a cystic fibrosis unit in Argentina

The Mini-Lab: accessible clinical bacteriology for low-resource settings

The Mini-Lab: accessible clinical bacteriology for low-resource settings

Diet Modulates the High Sensitivity to Systemic Infection in Newborn Preterm Pigs.

Background: Preterm infants are born with an immature immune system, limited passive immunity, and are at risk of developing bacteremia and sepsis in the postnatal period. We hypothesized that enteral feeding, with or without added immunoglobulins, improves the clinical response to systemic infection by coagulase negative staphylococci.Methods: Using preterm cesarean delivered pigs as models for preterm infants, we infused live Staphylococcus epidermidis (SE, 5 × 109 colony forming units per kg) systemically 0–3 days after birth across five different experiments. SE infection responses were assessed following different gestational age at birth (preterm vs. term), enteral milk diets (bovine colostrum, infant formula with or without added porcine plasma) and with/without systemic immunoglobulins. Pigs infected with SE were assessed 12–48 h for clinical variables, blood bacteriology, chemistry, hematology, and gut dysfunction (intestinal permeability, necrotizing enterocolitis lesions).Results: Adverse clinical responses and increased mortality were observed in preterm vs. term pigs, when infected with SE just after birth. Feeding bovine colostrum just after birth improved blood SE clearance and clinical status (improved physical activity and intestinal structure, fewer bone marrow bacteria), relative to pigs fed infant formula. A few days later, clinical responses to SE bacteremia (hematology, neutrophil phagocytic capacity, T cell subsets) were less severe, and less affected by different milk diets, with or without added immunoglobulins.Conclusion: Prematurity increases the sensitivity of newborn pigs to SE bacteremia, potentially causing sepsis. Sensitivity to systemic SE infection decreases rapidly in the days after preterm birth. Both age and diet (parenteral nutrition, colostrum, milk, formula) may influence gut inflammation, bacterial translocation and systemic immune development in the days after birth in preterm newborns.

Clinical Features, Bacteriology, and Antibiotic Treatment Among Patients with Presumed Naja Bites in Vietnam

Clinical and bacteriological features of cobra (Naja) bites are still relatively unknown in Vietnam. This study aimed to characterize the clinical and bacteriological characteristics of local wounds in patients with presumed Naja spp bite, as well as their antibiotic treatment. A cross-sectional study was performed on presumed Naja bite patients who were admitted to Bach Mai Hospital in Hanoi, Vietnam. In vitro bacterial isolation, blood tests, and lesion measure were conducted, and antibiotic susceptibilities of localized bite wounds were assessed. The Mann-Whitney test was used to examine the difference in clinical characteristics between patients experiencing presumed Naja atra bites and Naja kaouthia bites. Data are presented as percentages or median with interquartile range, as appropriate. Statistical significance was accepted at P<0.05. Among 46 patients, all had typical clinical features of Naja bite. The median bite-to-hospital time was 6 h (interquartile range 4.0-11.3). The dominant organisms isolated from local wounds were Morganella morganii (11/36) and Enterococcus faecalis (25/36). All cultures were susceptible to ciprofloxacin. No difference was found with regard to pain, swelling circumference, swelling spread, or necrotic area between patients bitten by presumed Naja atra and Naja kaouthia (P>0.05). Wound necrosis and infection were important clinical issues in presumed Naja spp snake bites. Morganella morganii and Enterococcus faecalis were dominant in local wound swabs of such cases. Ciprofloxacin should be an effective first-line antibiotic for patients with presumed Naja bite.

Implementation of the WASPLab™ and first year achievements within a university hospital.

In essence, automation can be driven by several of the following incentives: increased processing capacity of the laboratory, better costs control through processes standardization, optimized traceability, or improved workflows to reduce turnaround times (TAT). This project aims at presenting an overview of the project management and change management with a focus on the major challenges addressed by lab staff and laboratory leadership during the different phases of the implementation of the WASPLab™ in a routine clinical bacteriology laboratory. This paper reports our experience and reviews changes in the bacteriology laboratory at Geneva University Hospitals when shifting to the WASPLab™. Practically, the whole automation process was segmented into different packages (specimen type-based segmentation) allowing sequential validation, staff training, and routine implementation. Such process allowed reaching 90% of the identified "automatable" samples within 1year, including personal training, documentation for accreditation supported by publications, without interrupting routine operations. In addition, we implemented a validated automated solution for antimicrobial disk diffusion susceptibility testing. Structured supervision and accurate monitoring of all the activities related to the automation project including key partners such as IT support, technical committee, and after-sales service guaranteed a swift and timely achievement of the project allowing the improvement of the workflow in routine bacteriology within 1year.

Piloting Clinical Bacteriology in the Ebola Virus Disease Care Response to Detect Intercurring Bloodstream Infections and Inform Appropriate Antibiotic Treatment

Piloting Clinical Bacteriology in the Ebola Virus Disease Care Response to Detect Intercurring Bloodstream Infections and Inform Appropriate Antibiotic Treatment

Report of the Korean Association of External Quality Assessment Service on Clinical Bacteriology and Mycology (2016)

Report of the Korean Association of External Quality Assessment Service on Clinical Bacteriology and Mycology (2016)

Microbiology of urine samples obtained through suprapubic bladder aspiration: A 10-year epidemiological snapshot

Purpose Suprapubic bladder aspiration is an invasive procedure in which a needle is used to obtain a urine sample directly from the bladder. Its advantages are sensitivity (detection of significant bacteriuria is close to 100%), suitability for cultivation of anaerobic bacteria, and low risk of contamination. Our purpose was to characterize the microbiology and epidemiology of urine samples obtained through this procedure in the Clinical Center of the University of Szeged’s Institute of Clinical Microbiology between 2008 and 2017. Materials and methods Over the 10-year period, patient data were collected and suprapubic bladder aspirations were performed, and the samples are processed in accordance with routine laboratory procedures in clinical bacteriology. Results Of 187 urine samples obtained from 148 patients, 32.6% (n = 61) were culture-positive (defined as 102 colony forming units/ml or more). Conclusions This method should be considered an important sampling procedure in the differential diagnostics of upper urinary tract infections, particularly in children &lt;2 years of age, and in older people, hospitalized patients.

INFECCIONES POR BACTERIAS ANAEROBIAS: CRITERIOS DE MANEJO CLÍNICO Y PROCEDIMIENTOS MICROBIOLÓGICOS DE DIAGNÓSTICO

The increase of infections with anaerobic bacteria, the resistance of these organisms to limited treatment options for the empirical data, and the recent and little knowledge we have about these bodies, leads the doctor not to suspect that it is in most cases, compared to a possible infectious agent which involves an anaerobic germ, delaying diagnosis and timely initiation of appropriate antibiotic therapy, explaining the sudden increase in morbidity and mortality, and the vulnerability of patients. This creates an urgent need in the hospitals to develop updated and standardize protocols, guidelines management of infections caused by anaerobic bacteria and consistent with available resources to secure and optimize the processes involved in search and retrieval of these demanding germs, and it will allow all the medical and paramedical staff proper management of these events in order to improve the service and the patient safety. The purpose of this study is to standardize an updated protocol of clinical and anaerobic bacteriology to unify the criteria for selection, collection and proper transportation of clinical samples, which ensures the viability of the specimen and the recovery of anaerobic organisms in order to obtain their identification and susceptibility to antibiotics.

External Quality Assessment of Bacterial Identification and Antimicrobial Susceptibility Testing in African National Public Health Laboratories, 2011–2016

Background: In 2002, the World Health Organization (WHO) launched a regional microbiology external quality assessment (EQA) programme for national public health laboratories in the African region, initially targeting priority epidemic-prone bacterial diseases, and later including other common bacterial pathogens. Objectives: The aim of this study was to analyse the efficacy of an EQA programme as a laboratory quality system evaluation tool. Methods: We analysed the proficiency of laboratories’ performance of bacterial identification and antimicrobial susceptibility testing (AST) for the period 2011–2016. The National Institute for Communicable Diseases of South Africa provided technical coordination following an agreement with WHO, and supplied EQA samples of selected bacterial organisms for microscopy (Gram stain), identification, and antimicrobial susceptibility testing (AST). National public health laboratories, as well as laboratories involved in the Invasive Bacterial Diseases Surveillance Network, were enrolled by the WHO Regional Office for Africa to participate in the EQA programme. We analysed participants’ results of 41 surveys, which included the following organisms sent as challenges: Streptococcus pneumonia, Haemophilus influenzae, Neisseria meningitidis, Salmonella Typhi, Salmonella Enteritidis, Shigella flexneri, Staphylococcus aureus, Streptococcus agalactiae, Streptococcus anginosus, Enterococcus faecium, Serratia marcescens, Acinetobacter baumannii, and Enterobacter cloacae. Results: Eighty-one laboratories from 45 countries participated. Overall, 76% of participants obtained acceptable scores for identification, but a substantial proportion of AST scores were not in the acceptable range. Of 663 assessed AST responses, only 42% had acceptable scores. Conclusion: In the African Region, implementation of diagnostic stewardship in clinical bacteriology is generally suboptimal. This report illustrates that AST is poorly done compared to microscopy and identification. It is critically important to make the case for implementation of quality assurance in AST, as it is the cornerstone of antimicrobial resistance surveillance reporting and implementation of the Global Antimicrobial Resistance Surveillance System.

BacPipe: A Rapid, User-Friendly Whole-Genome Sequencing Pipeline for Clinical Diagnostic Bacteriology.

SummaryDespite rapid advances in whole genome sequencing (WGS) technologies, their integration into routine microbiological diagnostics has been hampered by the lack of standardized downstream bioinformatics analysis. We developed a comprehensive and computationally low-resource bioinformatics pipeline (BacPipe) enabling direct analyses of bacterial whole-genome sequences (raw reads or contigs) obtained from second- or third-generation sequencing technologies. A graphical user interface was developed to visualize real-time progression of the analysis. The scalability and speed of BacPipe in handling large datasets was demonstrated using 4,139 Illumina paired-end sequence files of publicly available bacterial genomes (2.9–5.4 Mb) from the European Nucleotide Archive. BacPipe is integrated in EBI-SELECTA, a project-specific portal (H2020-COMPARE), and is available as an independent docker image that can be used across Windows- and Unix-based systems. BacPipe offers a fully automated “one-stop” bacterial WGS analysis pipeline to overcome the major hurdle of WGS data analysis in hospitals and public-health and for infection control monitoring.

Antibiotic resilience: a necessary concept to complement antibiotic resistance?

Resilience is the capacity of systems to recover their initial state or functions after a disturbance. The concepts of resilience and resistance are complementary in ecology and both represent different aspects of the stability of ecosystems. However, antibiotic resilience is not used in clinical bacteriology whereas antibiotic resistance is a recognized major problem. To join the fields of ecology and clinical bacteriology, we first review the resilience concept from ecology, socio-ecological systems and microbiology where it is widely developed. We then review resilience-related concepts in microbiology, including bacterial tolerance and persistence, phenotypic heterogeneity and collective tolerance and resistance. We discuss how antibiotic resilience could be defined and argue that the use of this concept largely relies on its experimental measure and its clinical relevance. We review indicators in microbiology which could be used to reflect antibiotic resilience and used as valuable indicators to anticipate the capacity of bacteria to recover from antibiotic treatments.

Comparison of the Copan WASPLab incorporating the BioRad expert system against the SIRscan 2000 automatic for routine antimicrobial disc diffusion susceptibility testing

ObjectivesThis study investigated the agreement at the categorical level between the Copan WASPLab incorporating the BioRad expert system against the SIRscan 2000 automatic for antimicrobial disc diffusion susceptibility testing. MethodsThe 338 clinical strains (67 Pseudomonas aeruginosa, 19 methicillin-resistant Staphylococcus aureus, 75 methicillin-sensitive S. aureus and 177 Enterobacterales isolates) analysed in this study were non-duplicate isolates obtained from consecutive clinical samples referred to the clinical bacteriology laboratory at Geneva University Hospitals between June and August 2019. For the WASPLab the inoculum suspension was prepared in strict accordance with the manufacturer's instruction (Copan WASP srl, Brescia, Italy) by adding 2 mL of the 0.5 McFarland primary suspension used for the SIRscan analysis into a sterile tube filled with 4 mL of sterile saline (1:3 dilution). The inoculum (2 × 30 μL loop/spreader) was spread over the entire surface of Mueller–Hinton agar plates according to the AST streaking pattern defined by Copan. The antibiotic discs were dispensed by the WASP and inoculated media were loaded on conveyors for transfer to the automatic incubators. The plates were incubated for 16 h, and several digital images were acquired. Inhibition zone diameters were automatically read by the WASPLab and were adjusted manually whenever necessary. For the SIRscan 2000 automatic, the antimicrobial disc diffusion susceptibility testing was performed according to the EUCAST guidelines. The gradient strip method was used to resolve discrepancies. ResultsThe overall categorical agreement between the compared methods reached 99.1% (797/804; 95% CI 98.2%–99.6%), 99.5% (1029/1034; 95% CI 98.9%–99.8%), and 98.8% (2798/2832; 95% CI 98.3%–99.1%) for P. aeruginosa, S. aureus and the Enterobacterales, respectively. ConclusionsWASPLab incorporating the BioRad expert system provides a fully automated solution for antimicrobial disc diffusion susceptibility testing with equal or better accuracy than other available phenotypic methods.

Diagnostic Bacteriology in District Hospitals in Sub-Saharan Africa: At the Forefront of the Containment of Antimicrobial Resistance.

This review provides an update on the factors fuelling antimicrobial resistance and shows the impact of these factors in low-resource settings. We detail the challenges and barriers to integrating clinical bacteriology in hospitals in low-resource settings, as well as the opportunities provided by the recent capacity building efforts of national laboratory networks focused on vertical single-disease programmes. The programmes for HIV, tuberculosis and malaria have considerably improved laboratory medicine in Sub-Saharan Africa, paving the way for clinical bacteriology. Furthermore, special attention is paid to topics that are less familiar to the general medical community, such as the crucial role of regulatory frameworks for diagnostics and the educational profile required for a productive laboratory workforce in low-resource settings. Traditionally, clinical bacteriology laboratories have been a part of higher levels of care, and, as a result, they were poorly linked to clinical practices and thus underused. By establishing and consolidating clinical bacteriology laboratories at the hospital referral level in low-resource settings, routine patient care data can be collected for surveillance, antibiotic stewardship and infection prevention and control. Together, these activities form a synergistic tripartite effort at the frontline of the emergence and spread of multi-drug resistant bacteria. If challenges related to staff, funding, scale, and the specific nature of clinical bacteriology are prioritized, a major leap forward in the containment of antimicrobial resistance can be achieved. The mobilization of resources coordinated by national laboratory plans and interventions tailored by a good understanding of the hospital microcosm will be crucial to success, and further contributions will be made by market interventions and business models for diagnostic laboratories. The future clinical bacteriology laboratory in a low-resource setting will not be an “entry-level version” of its counterparts in high-resource settings, but a purpose-built, well-conceived, cost-effective and efficient diagnostic facility at the forefront of antimicrobial resistance containment.

English

Antimicrobials have been playing an important role in preventing illness and death associated with infections due to bacteria. However, the emergence and spread of resistance by pathogens have decreased the effectiveness of the commonly prescribed antimicrobials. Intestinal Escherichia coli are among bacterial pathogens that are endowed with such resistance traits because they are important source and reservoir of genes that encode antimicrobial resistance. To determine the antimicrobial resistance profile of fecal isolates of E. coli from diarrheic patients. Stool samples were collected consecutively from 100 individuals who visited Selam Health Center during the study period, April to June 2018. Samples were collected and transported under sterile condition to the National Clinical Bacteriology and Mycology reference Laboratory, Ethiopian Public Health Institute. The samples were streaked on MacConkey agar and incubated overnight at 37°C. E. coli isolates were further confirmed using conventional biochemical tests. Antimicrobial susceptibility status was determined using the disk diffusion method on Mueller Hinton agar as recommended by the Clinical Laboratory Standard Institute. The raw data was compiled and entered to spreadsheet and analysis was done using SPSS Version 20 with p-value ≤0.05 considered statistically significant. Out of the 100 patients, 43 were female and the rest were male. Confirmed E. coli were isolated from 73 individuals. Antimicrobial susceptibility testing showed that E. coli isolated in this study were highly resistant to trimethoprim-sulfamethoxazole 49 (67.1%) and amoxicillin-clavulanic acid 47(64.4 %). No isolates showed resistance to gentamicin and tobramicin. Of all the isolates, 11(15.1%) were multidrug resistant. No association was observed between antimicrobial resistance status and sex of individuals included in this study. However, there was an association between age and resistance patterns. Resistance to commonly prescribed antibiotics among E. coli isolated in this study was high and a considerable proportions of the strains were multidrug resistant. This is an indication for an alarming rate of resistance of intestinal E. coli to first line antimicrobials. To reduce the problem, regular monitoring and education for the community are very important. Key words: Escherichia coli, antibiotic susceptibility, multidrug resistant, Ethiopia, biochemical tests, disk diffusion.

Role of Tumor Necrosis Factor alpha promoter polymorphisms in interferon related side effects in chronic hepatitis B patients under interferon alpha 2b treatment

Objective(s). Interferon alpha therapy is associated with series of adverse effects leading premature discontinuation of treatment. Here we aimed to determine the effects of Tumor necrosis alpha promoter polymorphisms on interferon related side effects during interferon alpha 2b treatment in chronic hepatitis B patients&#x0D; Material and Method(s). This observational study enrolled 50 chronic hepatitis B patients, who were treated with interferon alpha 2b 10 tiw plus lamivudine 100mg/day at Selçuk University Meram Medical Faculty Department of Infectious Diseases and Clinical Bacteriology between 2006-2007. Patients were followed-up with complete blood count, transaminases and amylase monthly at out patient clinics of our department. All patients were asked to fill a questionnaire to evaluate the interferon related side effects at every visit. Tumor necrosis factor alpha -238 and -308 polymorphisms were investigated with PCR-Restriction fragment length polymorphisms.&#x0D; Result(s) and Conclusion Arthralgia was present in 93.8% of patients. Exhaustion, loss of appetite, mount dryness and fever are the leading complaints of the patients. Median complaint scores were 9, 9.5, 11 and 5 at 4th, 12th, 24th and 48th week visits, respectively. Thrombocytopenia and leucopenia were detected in 8 (16%) and 5 (10%) patients, respectively. One-third of the patients reported depressive mood however, depression was diagnosed in 5 (10%) patients. TNF alpha promoter 238GG and 308GG allele was present in 42/50 and 43/50 patients, respectively. No association was found between TNF promoter allele and certain patient-reported side effect, complaint score, hematological and psychological adverse effects. TNF alpha promoter polymorphisms do not contribute to occurrence of IFN alpha treatment related side effects.

Neonatal Sepsis: Clinical Spectrum, Bacteriological Profile and Antibiotic Sensitivity Patterns in Neonatal Intensive Care Unit in a Tertiary Care Hospital

Neonatal Sepsis: Clinical Spectrum, Bacteriological Profile and Antibiotic Sensitivity Patterns in Neonatal Intensive Care Unit in a Tertiary Care Hospital

Factors associated with lung cytology as obtained by non-endoscopic broncho-alveolar lavage in group-housed calves

BackgroundRespiratory infections are the main indication for antimicrobial use in calves. As in humans and horses, studying inflammation of the deep airways by lung cytology raises the possibility of preventing respiratory disease and targeting its treatment in the future. Whether lung cytology findings coincide with clinical signs and lung ultrasonographic findings is currently unknown. Therefore, the objective of the present study was to determine the association of lung cytology with clinical signs, lung consolidation and broncho-alveolar lavage fluid (BALf) characteristics (including bacteriology).A total of 352 indoor group-housed calves aged between 1 and 6 months from 62 conveniently selected commercial herds were included in this cross-sectional study. Clinical examination, thoracic ultrasound and bacteriology and cytology on non-endoscopic broncho-alveolar lavage (nBAL) samples were performed.ResultsPneumonia, defined as presence of ultrasonographic lung consolidations ≥1 cm in depth, affected 42.4% of the calves. Mean BALf neutrophil percentage was 36.6% (SD 23.8; R 0–97.4) and only a positive induced tracheal cough reflex (P = 0.04), standing posture (P = 0.03) increased breathing rate (P = 0.02) and isolation of Pasteurella multocida (P = 0.005), were associated with increased neutrophil percentage. No significant associations between lung ultrasonographic findings and cytology results were present, except for presence of basophils in BALf and consolidation of > 3 cm in depth (OR = 2.6; CI = 1.2–5.6; P = 0.01). Abnormal lung sounds were associated with detection of eosinophils in BALf (OR = 2.8; CI = 1.0–8.1; P = 0.05). Total nucleated cell count (TNCC) (P < 0.001) was positively and macrophage percentage (P = 0.02) negatively associated with volume of lavage fluid recovered. Macroscopic blood staining of BALf increased TNCC (P = 0.002) and lymphocyte percentage (P = 0.001).ConclusionsOnly a limited number of clinical signs and ultrasonographic findings were associated with nBAL cytology. BALf cytology offers additional and distinct information in calves aiding in detection and prevention of respiratory conditions. In this population, selected from herds not reporting any recent respiratory illness, a high number of calves had ultrasonographic lung consolidation and high neutrophil percentage in BALf, suggesting that subclinical disease presentations frequently occur.

Development of an all-in-one transportable clinical bacteriology laboratory: feedback from testing a Mini-Lab prototype

Development of an all-in-one transportable clinical bacteriology laboratory: feedback from testing a Mini-Lab prototype