Frequency of pathogens in routine bacteriological diagnosis in fish and their antimicrobial resistance

Aquaculture is one of the sectors of animal husbandry with the fastest growth rate. However, the increase in the sector’s production chain without proper management can result in factors that favor the development of diseases, especially infectious diseases caused by bacteria. Many factors, such as agriculture or industry resides, improper use of antibiotics in animals or humans, have contributed to increased environmental pressure and the appearance of antibiotic-resistant bacteria, while residues from these drugs can remain in the carcasses and in water a risk to public and environmental health. From that, we identified the bacterial genus/species and their bacterial resistance to antibiotics from samples received from fish disease outbreaks for bacteriosis diagnosis between January 2017 and October 2020. Isolated bacteria were subjected to the Kirby and Bauer sensitivity test for five classes of antibiotics (penicillins, fluoroquinolones, aminoglycosides, amphenicols, and tetracyclines). Of the 181 analyzed outbreaks, 232 bacteria were isolated, including Streptococcus spp., Aeromonas spp., Edwardsiella spp., Plesiomonas shigelloides, Pseudomonas aeruginosa, Chromobacterium violaceum, Flavobacterium spp., Citrobacter spp., Enterococcus spp., Vibrio spp., Enterobacter spp., Chryseobacterium meningosepticum. Of the 232 bacteria, 40 strains were classified as multidrug resistant (MDR), with Plesiomonas shigelloides, Aeromonas spp., and Edwardsiella spp. representing more than half of this number (22/total). With several bacteria demonstrating resistance to Brazilian aquaculture-legalized drugs (tetracycline and florfenicol), it is mandatory to research, not only for alternatives to the use of antibiotics, but also for other drugs effective against the main circulating bacterial pathogens. In addition, vigilance over the occurrence of resistant bacteria is necessary, considering the appearance of zoonotic bacteria with multi-resistant characteristics, becoming a public health concern.

Predictors of aetiology and outcomes of acute gastrointestinal illness in returning travellers: a retrospective cohort analysis

Background Gastrointestinal illness is a major cause of morbidity in travellers and is a common reason for presentation to healthcare services on return. Whilst the aetiology of imported gastrointestinal disease is predominantly infectious, outcomes are variable due to a range of phenomena such as post-infectious irritable bowel syndrome, drug resistance and occult pathology (both infectious and non-infectious). Previous studies have focussed on predictors of aetiology of gastrointestinal disease in travellers; we present a retrospective study combining both aetiological and early outcome data in a large cohort of returned travellers. Method We identified 1450 patients who attended our post-travel walk-in clinic with gastrointestinal symptoms between 2010 and 2016. Demographic, travel, clinical and laboratory data was collected through case note review. Logistic regression analysis to examine correlates of aetiology and outcome were performed in R (CRAN Project 2017). Results Of 1450 patients in our cohort 153 reported bloody diarrhoea and 1081 (74.6%) reported non-bloody diarrhoea. A definitive microbiological diagnosis was made in 310 (20.8%) of which 137 (9.4%) had a parasite identified and 111 (7.7%) had a bacterial cause identified. Factors associated with a parasitological diagnosis included history of travel to South Asia (aOR = 2.55; 95%CI 1.75–3.70, p < 0.0001) and absence of bloody diarrhoea (aOR = 0.22; 95%CI 0.066–0.53, p < 0.005). Factors associated with a bacteriological diagnosis included male gender (aOR = 1.69; 95%CI 1.10–2.62, p < 0.05), an age < 37 years on presentation (aOR = 2.04; 95%CI 1.25–3.43, p < 0.01), white cells on stool microscopy (aOR = 3.52; 95%CI 2.09–5.86, p < 0.0001) and a C-reactive protein level of >5iu/dL (aOR = 4.68; 95%CI 2.91–7.72, p < 0.0001). The majority (1235/1450, 82.6%) reported full symptomatic resolution by the first follow up visit; factors associated with lack of symptomatic resolution included female gender (aOR = 1.45 95%CI 1.06–1.99, p < 0.05), dysenteric diarrhoea (aOR = 2.14 (95%CI 1.38–3.25, p < 0.0005) and elevated peripheral leukocyte count (aOR = 1.58 95%CI 1.02–2.40, p < 0.05). Conclusions In a cohort of returned travellers, we were able to identify multiple factors that are correlated with both aetiology and outcome of imported gastrointestinal syndromes. We predict these data will be valuable in the development of diagnostic and therapeutic pathways for patients with imported gastrointestinal infections.

Usefulness of GeneXpert MTB/RIF in the diagnosis of extra-pulmonary tuberculosis

Background: Diagnosis of extra-pulmonary tuberculosis (TB) is often delayed because of diverse clinical presentations and difficulties in establishing the bacteriological diagnosis. This study aimed to evaluate usefulness of GeneXpert MTB/RIF in the diagnosis of extra-pulmonary TB in Bangladeshi patients. Methods: This cross-sectional study was done in BIRDEM General Hospital, Dhaka, Bangladesh from 2013 to 2016 as a part of Bangladesh Diabetic Somiti (BADAS)-USAID-TB Care-II project. Representative samples from 590 clinically suspected extra-pulmonary TB cases were tested for GeneXpert MTB/RIF along with conventional methods. Results: Total patients were 590 [mean age 43.9 (range 1-95) years] with male predominance (326, 55.3%). Most (513, 86.9%) patients were diabetic and new (574, 97.3%) TB suspects; while 16 (2.7%) patients had past history of TB. Common samples were pleural fluid (125, 21.2%), urine (110, 18.6%), cerebrospinal fluid (CSF) (91, 15.4%), pus (82, 13.9%), tracheal aspirates (57, 9.7%), ascitic fluid (45, 7.6%), gastric lavage (31, 5.3%), broncho-alveolar lavage (BAL) (18, 3.1%), lymph node aspirates (11, 1.9%) and synovial fluid (8, 1.4%). Among 590 samples, 68 (11.5%) were positive for Mycobacterium tuberculosis. Diagnostic yield was common for lymph nodes (4/7, 57.1%), pus (25/82, 30.5%), BAL (4/18, 22.2%), tracheal aspirates (8/57, 14.0%), urine (7/110, 6.4%), CSF (6/91, 6.6%) and pleural fluid (7/125, 5.6%). Of the 68 GeneXpert MTB/RIF positive samples, 52 (76.1%) were rifampicin sensitive, 16 (23.9%) showed intermediate sensitivity and none of the samples was resistant to rifampicin. Conclusions: GeneXpert MTB/RIF appeared as useful tool for diagnosing extra-pulmonary TB. Birdem Med J 2021; 11(2): 121-124

A Highly Sensitive and Specific Probe-Based Real-Time PCR for the Detection of Avibacterium paragallinarum in Clinical Samples From Poultry

Avibacterium paragallinarum (historically called Hemophilus paragallinarum) causes infectious coryza (IC), which is an acute respiratory disease of chickens. Recently, outbreaks of IC have been reported in Pennsylvania (PA) in broilers, layer pullets, and laying hens, causing significant respiratory disease and production losses. A tentative diagnosis of IC can be made based on history, clinical signs, and characteristic gross lesions. However, isolation and identification of the organism are required for a definitive diagnosis. Major challenges with the bacteriological diagnosis of A. paragallinarum include that the organism is difficult to isolate, slow-growing, and can only be successfully isolated during the acute stage of infection and secondary bacterial infections are also common. As there were very limited whole genomes of A. paragallinarum in the public databases, we carried out whole-genome sequencing (WGS) of PA isolates and based on the WGS data analysis; we designed a novel probe-based PCR assay targeting a highly conserved sequence in the recN, the DNA repair protein gene of A. paragallinarum. The assay includes an internal control, with a limit of detection (LOD) of 3.93 genomic copies. The PCR efficiency ranged between 90 and 97%, and diagnostic sensitivity of 98.5% compared with conventional gel-based PCR. The test was highly specific, and no cross-reactivity was observed with other species of Avibacterium and a range of other common poultry respiratory viral and bacterial pathogens. Real-time PCR testing on 419 clinical samples from suspected flocks yielded 94 positives and 365 negatives in agreement with diagnostic bacterial culture-based detection. We also compared the recN PCR assay with a previous HPG-2 based real-time PCR assay which showed a PCR efficiency of 79%.

Predictors of Aetiology and Outcomes of Acute Gastrointestinal Illness in Returning Travellers: a Retrospective Cohort Analysis

Background: Gastrointestinal illness is a major cause of morbidity in travellers and is a common reason for presentation to healthcare services on return. Whilst the aetiology of imported gastrointestinal disease is predominantly infectious, outcomes are variable due to a range of phenomena such as post-infectious irritable bowel syndrome, drug resistance and occult pathology (both infectious and non-infectious). Previous studies have focussed on predictors of aetiology of gastrointestinal disease in travellers; we present a retrospective study combining both aetiological and early outcome data in a large cohort of returned travellers. Method: We identified 1450 patients who attended our post-travel walk-in clinic with gastrointestinal symptoms between 2010 and 2016. Demographic, travel, clinical and laboratory data was collected through case note review. Logistic regression analysis to examine correlates of aetiology and outcome were performed in R (CRAN Project 2017). Results: Of 1450 patients in our cohort 153 reported bloody diarrhoea and 1081 (74.6%) reported non-bloody diarrhoea. A definitive microbiological diagnosis was made in 310 (20.8%) of which 137 (9.4%) had a parasite identified and 111 (7.7%) had a bacterial cause identified. Factors associated with a parasitological diagnosis included history of travel to South Asia (aOR=2.55; 95%CI 1.75-3.70, p<0.0001) and absence of bloody diarrhoea (aOR=0.22; 95%CI 0.066-0.53, p<0.005). Factors associated with a bacteriological diagnosis included male gender (aOR=1.69; 95%CI 1.10-2.62, p<0.05), an age <37 years on presentation (aOR=2.04; 95%CI 1.25-3.43, p<0.01), white cells on stool microscopy (aOR=3.52; 95%CI 2.09-5.86, p<0.0001) and a C-reactive protein level of >5iu/dL (aOR=4.68; 95%CI 2.91-7.72, p<0.0001). The majority (1235/1450, 82.6%) reported full symptomatic resolution by the first follow up visit; factors associated with lack of symptomatic resolution included female gender (aOR=1.45 95%CI 1.06-1.99, p<0.05), dysenteric diarrhoea (aOR=2.14 (95%CI 1.38-3.25, p<0.0005) and elevated peripheral leukocyte count (aOR=1.58 95%CI 1.02-2.40, p<0.05).Conclusions: In a cohort of returned travellers, we were able to identify multiple factors that are correlated with both aetiology and outcome of imported gastrointestinal syndromes. We predict these data will be valuable in the development of diagnostic and therapeutic pathways for patients with imported gastrointestinal infections.

Tuberculosis space-temporal distribution from 2011 to 2016 in the municipality of Maputo, Mozambique

Objective: Carry out a spatial-temporal characterization of the incidence of tuberculosis (TB) in Maputo, Mozambique. Method: a descriptive ecological study of tuberculosis cases reported in an information system. The annual mean incidence rate and the number of TB notification cases in the municipality of Maputo from 2011 to 2016 were analyzed. Descriptive statistics were used with calculations of measures of central tendency (mean) and an application of the Poisson linear regression model. Trimester notifications were stratified by district, clinical form, and age group. The quarterly average temperature of the evaluated area was added as a covariate in the model seasonal. Results: 34,623 TB cases were notified from 2011 to 2016, with a trimester average of 1,443 cases. The average annual incidence was higher in the Kampfumo district, with 909.8 per 100 thousand inhabitants (95% CI 854.1 - 968.2); almost twice as much as the incidence of the municipality of Maputo, 527.8 (95% CI 514, 3-541.6), and the country of Mozambique, 551 (95% CI 356 - 787). The clinical diagnosis of the tested cases was higher concerning the bacteriological diagnosis; 44%, and 35%, respectively. Conclusion: Maputo had similar incidence rates to the country of Mozambique, however, there was a heterogeneity rate by district and a reduction in the number of TB cases in both the general population (not co-infected with HIV) and those over 15 years old, being higher in the first trimester.

Status and problems of bacteriological diagnosis of diphtheria infection in the Russian Federation

The purpose of the work was to assess the state of bacteriological diagnosis of diphtheria infection in Russia in order to establish possible reasons for the decrease in the release of C. diphtheriae. The Reference Center for Monitoring the Pathogens of Measles, Rubella, Mumps, Pertussis and Diphtheria in 2018 in 85 subjects of Russia conducted a questionnaire of laboratories of medical organizations and the Centers for Hygiene and Epidemiology of Rospotrebnadzor, carrying out bacteriological studies for diphtheria infection. It was found that the number of studies conducted over the five-year period decreased by 1.2 times. The tendency to decrease the number of bacteriological studies for diphtheria is observed in the territories of almost all federal districts. In 99% and 29% of cases, the institutions of the FBUZ Centers for Hygiene and Epidemiology and medical organizations (MO) and use in their work documents regulating bacteriological studies for diphtheria infection. In a number of territories, the list of documents used includes documents that are invalid or do not define such studies. Most organizations use dry tampons when examining for diphtheria, however, 13.1% and 53.4% of FBUZ Centers for Hygiene and Epidemiology and medical organizations (respectively) use commercial transport environments, which does not comply with regulatory documentation. Analysis of the quality of work of bacteriological laboratories showed shortcomings at the stage of preparation of media (use of donor blood, or absence of addition of blood and potassium tellurite), Elek tests (addition of horse serum or absence of serum to the medium), setting of incomplete biochemical series (absence of tests for urease and nitrate reductase), absence of standard control strains, incomplete volume of internal laboratory quality control. Given the continuing circulation of the pathogen in various countries of the world and in our country, as well as the possibility of imported cases of infection from endemic regions, the analysis was aimed at drawing the attention of specialists to the problem of improving the quality of laboratory diagnosis of diphtheria in Russia.

Multiple drug resistance of Listeria monocytogenes isolated from aborted women by using serological and molecular techniques in Diwaniyah city/ Iraq

Background and Objectives: The study was sought to detect the effect of Listeria monocytogenes on pregnant Iraqi women at Al-Diwaniya hospitals and determination of virulence genes and antimicrobial susceptibility of isolates. Materials and Methods: 360 specimens including blood, urine, vaginal and endocervical were collected from 90 patients with spontaneous abortions. Blood samples were displayed to immunological study and remaining specimens were subjected to bacteriological diagnosis. PCR was used to determine the virulence factors and antimicrobial resistance genes. Results: Fifteen positive samples (16.6%) of patients and thirteen isolates (14.5%) from patients were recognized based on ELISA and PCR assay respectively. The general isolation of L. monocytogenes strains in cases of abortive women was 13/270 (4.8%). L. monocytogenes strains were highly virulent because of presence of virulence factors associated genes, namely actA, hlyA, plcA and prfA in all strains. Multiple drug resistance (MAR) index values of 15.4% of isolates were >0.2. Conclusion: It is necessary for conducting susceptibility testing and to select the suitable antibiotics and avoid the effects of these bacteria in pregnant women.

Performance Evaluation of the Novodiag Bacterial GE+ Multiplex PCR Assay

ABSTRACT The bacteriological diagnosis of intestinal bacterial infections has historically been based on culture on agar plates. However, culture may lack sensitivity, and some enteropathogens, such as pathovars of Escherichia coli, may escape routine diagnosis. Our goal was to evaluate the analytical performance of the Novodiag Bacterial GE+ kit for the detection of enteropathogenic bacteria in acute community diarrhea. We included 251 stools in this study (198 retrospective and 53 prospective). The analytical performance was calculated using a composite reference standard (CRS) in the absence of a perfect gold standard (lack of sensitivity of culture). The CRS was defined as positive if culture was positive or, in case of a negative culture, if the BD Max extended enteric bacterial panel and/or other real-time PCR (RT-PCR) tests were positive. Of the 251 samples, 200 were positive, and 51 were negative. Overall sensitivities of the Novodiag Bacterial GE+ kit for Campylobacter sp., Salmonella sp., Shigella sp./enteroinvasive E. coli (EIEC), Yersinia enterocolitica, enterohemorrhagic E. coli (EHEC), and enterotoxigenic E. coli (ETEC) ranged from 98.98 to 100%, specificities ranged from 98.08 to 100%, positive predictive values (PPVs) ranged from 88.24 to 100%, and negative predictive values (NVPs) ranged from 99.36 to 100%. The analytical performance of the Novodiag Bacterial GE+ kit is excellent. It can be used as a routine tool in the rapid diagnosis of bacterial gastroenteritis. Despite the eNAT tube dilution of the primary sample, the detection of Salmonella sp. and EHEC was perfect. The kit has the advantage of only detecting pathogenic Y. enterocolitica. Its performance for Campylobacter is very satisfactory.