scholarly journals Divergent evolution of Corynebacterium diphtheriae in India: An update from National Diphtheria Surveillance network

PLoS ONE ◽  
2021 ◽  
Vol 16 (12) ◽  
pp. e0261435
Author(s):  
Naveen Kumar Devanga Ragupathi ◽  
Dhiviya Prabaa Muthuirulandi Sethuvel ◽  
Dhivya Murugan ◽  
Ranjini Ranjan ◽  
Vikas Gautam ◽  
...  
Keyword(s):  
Molecular Data ◽  
Divergent Evolution ◽  
Biochemical Tests ◽  
Toxigenic Strain ◽  
Surveillance Network ◽  
Typing Method ◽  
Epidemiological Analysis ◽  
Surveillance Programme ◽  
Corynebacterium Diphtheria ◽  
Sequence Types

Diphtheria is caused by a toxigenic bacterium Corynebacterium diphtheria which is being an emerging pathogen in India. Since diphtheria morbidity and mortality continues to be high in the country, the present study aimed to study the molecular epidemiology of C. diphtheriae strains from India. A total of 441 diphtheria suspected specimens collected as part of the surveillance programme between 2015 and 2020 were studied. All the isolates were confirmed as C. diphtheriae with standard biochemical tests, ELEK’s test, and real-time PCR. Antimicrobial susceptibility testing for the subset of isolates showed intermediate susceptibility to penicillin and complete susceptible to erythromycin and cefotaxime. Isolates were characterized using multi locus sequence typing method. MLST analysis for the 216 C. diphtheriae isolates revealed major diversity among the sequence types. A total of 34 STs were assigned with majority of the isolates belonged to ST466 (30%). The second most common ST identified was ST405 that was present in 14% of the isolates. The international clone ST50 was also seen. The identified STs were grouped into 8 different clonal complexes (CC). The majority belongs to CC5 followed by CC466, CC574 and CC209, however a single non-toxigenic strain belongs to CC42. This epidemiological analysis revealed the emergence of novel STs and the clones with better dissemination properties. This study has also provided information on the circulating strains of C. diphtheriae among the different regions of India. The molecular data generated through surveillance system can be utilized for further actions in concern.

scholarly journals Occurrence and Determination of Antimicrobial Resistant Escherichia coli Isolates in Fish and Vegetables as Indicator Organism of Faecal Contamination in Dar es Salaam, Tanzania

2021 ◽  
Vol 2021 ◽  
pp. 1-9
Author(s):  
Francis Mwanza ◽  
Erick Vitus Gabriel Komba ◽  
Dominic Mukama Kambarage
Keyword(s):  
Escherichia Coli ◽  
Genetic Diversity ◽  
Genetic Relatedness ◽  
Diffusion Method ◽  
Urban Farming ◽  
Biochemical Tests ◽  
Typing Method ◽  
Organic Fertiliser ◽  
E Coli ◽  
Fish Samples

Escherichia coli such as E. coli O157:H7, a non-sorbitol-fermenting (NSF) E. coli, is an essential human pathogen among other common zoonotic pathogens carried by animals especially cattle. They are discharged through cattle faeces into the environment. With the increasing practice of urban farming, livestock manure is used as organic fertiliser in either fish ponds or vegetable gardens. This practice increases the risk of transmission of such pathogens to humans. This study aimed at determining the occurrence, antimicrobial resistance profiles, and genetic relatedness of E. coli isolates from manure, vegetables, and fish. Microbiological standard methods were used to isolate and identify E. coli isolates from manure, vegetable, and fish samples. Confirmed isolates on biochemical tests were tested for resistance against six antibiotics using the disc diffusion method. Enterobacterial repetitive intergenic consensus polymerase chain reaction (ERIC-PCR) typing method was used to generate fingerprints and determine the genetic relatedness of the E. coli isolates. Of 156 samples including 89 manure, 53 vegetables, and 16 fish, 36 (23.1%) samples were positive for E. coli from where a total of 48 E. coli different isolates were recovered that were subjected to antimicrobial susceptibility testing and genetic relatedness. Of these isolates, 25 (52.1%) were resistant to at least one antimicrobial agent and 12 (48.0%) showed multidrug resistance. ERIC-PCR profiles of E. coli isolates from manure, vegetables, and fish showed genetic diversity with genetic relatedness ranging from 74.5% to 100%. Nine phylogenetic clusters (I–IX) determined at 90% threshold level of genetic relatedness were identified among the isolates. This study determined the occurrence, antimicrobial resistant patterns, and genetic diversity of antimicrobial-resistant E. coli isolates from different sources. This study showed the potential of microbial health risk to humans through contamination, and hence, it is necessary to monitor and improve husbandry practices in urban farming.

scholarly journals Standardised surveillance of Clostridium difficile infection in European acute care hospitals: a pilot study, 2013

2016 ◽  
Vol 21 (29) ◽  
Author(s):  
Sofie M van Dorp ◽  
Pete Kinross ◽  
Petra Gastmeier ◽  
Michael Behnke ◽  
Axel Kola ◽  
...  
Keyword(s):  
Clostridium Difficile ◽  
Acute Care ◽  
Acute Care Hospitals ◽  
Molecular Data ◽  
European Countries ◽  
Hospital Data ◽  
Hospital Discharges ◽  
Surveillance Network ◽  
And Control ◽  
Microbiological Data

Clostridium difficile infection (CDI) remains poorly controlled in many European countries, of which several have not yet implemented national CDI surveillance. In 2013, experts from the European CDI Surveillance Network project and from the European Centre for Disease Prevention and Control developed a protocol with three options of CDI surveillance for acute care hospitals: a ‘minimal’ option (aggregated hospital data), a ‘light’ option (including patient data for CDI cases) and an ‘enhanced’ option (including microbiological data on the first 10 CDI episodes per hospital). A total of 37 hospitals in 14 European countries tested these options for a three-month period (between 13 May and 1 November 2013). All 37 hospitals successfully completed the minimal surveillance option (for 1,152 patients). Clinical data were submitted for 94% (1,078/1,152) of the patients in the light option; information on CDI origin and outcome was complete for 94% (1,016/1,078) and 98% (294/300) of the patients in the light and enhanced options, respectively. The workload of the options was 1.1, 2.0 and 3.0 person-days per 10,000 hospital discharges, respectively. Enhanced surveillance was tested and was successful in 32 of the hospitals, showing that C. difficile PCR ribotype 027 was predominant (30% (79/267)). This study showed that standardised multicountry surveillance, with the option of integrating clinical and molecular data, is a feasible strategy for monitoring CDI in Europe.

scholarly journals Molecular Epidemiology of Invasive Listeriosis due toListeria monocytogenesin a Spanish Hospital over a Nine-Year Study Period, 2006–2014

2015 ◽  
Vol 2015 ◽  
pp. 1-10 ◽  
Author(s):  
Jaime Ariza-Miguel ◽  
María Isabel Fernández-Natal ◽  
Francisco Soriano ◽  
Marta Hernández ◽  
Beatrix Stessl ◽  
...  
Keyword(s):  
Genetic Relatedness ◽  
Growth Patterns ◽  
Phenotypic Characteristics ◽  
Genetic Studies ◽  
Epidemiological Analysis ◽  
Spanish Hospital ◽  
Northwestern Spain ◽  
High Degree ◽  
Sequence Types ◽  
Invasion Assays

We investigated the pathogenicity, invasiveness, and genetic relatedness of 17 clinicalListeria monocytogenesstains isolated over a period of nine years (2006–2014). All isolates were phenotypically characterised and growth patterns were determined. The antimicrobial susceptibility ofL. monocytogenesisolates was determined in E-tests. Invasion assays were performed with epithelial HeLa cells. Finally,L. monocytogenesisolates were subtyped by PFGE and MLST. All isolates had similar phenotypic characteristics (β-haemolysis and lecithinase activity), and three types of growth curve were observed. Bacterial recovery rates after invasion assays ranged from 0.09% to 7.26% (1.62 ± 0.46). MLST identified 11 sequence types (STs), and 14 PFGE profiles were obtained, indicating a high degree of genetic diversity. Genetic studies unequivocally revealed the occurrence of one outbreak of listeriosis in humans that had not previously been reported. This outbreak occurred in October 2009 and affected three patients from neighbouring towns. In conclusion, the molecular epidemiological analysis clearly revealed a cluster (three human cases, all ST1) of not previously reported listeriosis cases in northwestern Spain. Our findings indicate that molecular subtyping, in combination with epidemiological case analysis, is essential and should be implemented in routine diagnosis, to improve the tracing of the sources of outbreaks.

scholarly journals Isolation of Human Lineage, Fluoroquinolone-Resistant and Extended-β-Lactamase-Producing Escherichia coli Isolates from Companion Animals in Japan

Antibiotics ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 1463
Author(s):  
Toyotaka Sato ◽  
Shin-ichi Yokota ◽  
Tooru Tachibana ◽  
Satoshi Tamai ◽  
Shigeki Maetani ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Companion Animals ◽  
Clinical Settings ◽  
Chain Reaction ◽  
Epidemiological Analysis ◽  
E Coli ◽  
Global Concern ◽  
Polymerase Chain ◽  
Sequence Types ◽  
M 14

An increase in human and veterinary fluoroquinolone-resistant Escherichia coli is a global concern. In this study, we isolated fluoroquinolone-resistant E. coli isolates from companion animals and characterized them using molecular epidemiological analysis, multiplex polymerase chain reaction to detect E. coli ST131 and CTX-M type extended-spectrum β-lactamases (ESBL), and multi-locus sequence typing analysis. Using plain-CHROMagar ECC, 101 E. coli isolates were isolated from 34 rectal swabs of dogs and cats. The prevalence of resistance to fluoroquinolone and cefotaxime was 27.7% and 24.8%, respectively. The prevalence of fluoroquinolone-resistant isolates (89.3%) was higher when CHROMagar ECC with CHROMagar ESBL supplement was used for E. coli isolation. The prevalence of cefotaxime resistance was also higher (76.1%) when 1 mg/L of ciprofloxacin-containing CHROMagar ECC was used for isolation. The cefotaxime-resistant isolates possessed CTX-M type β-lactamase genes (CTX-M-14, CTX-M-15, or CTX-M-27). Seventy-five percent of fluoroquinolone-resistant isolates were sequence types ST131, ST10, ST1193, ST38, or ST648, which are associated with extensive spread in human clinical settings. In addition, we isolated three common fluoroquinolone-resistant E. coli lineages (ST131 clade C1-M-27, C1-nM27 and ST2380) from dogs and their respective owners. These observations suggest that companion animals can harbor fluoroquinolone-resistant and/or ESBL-producing E. coli, in their rectums, and that transmission of these isolates to their owners can occur.

scholarly journals Carbapenemases and extended-spectrum β-lactamases producing Enterobacteriaceae isolated from Tunisian and Libyan hospitals

2016 ◽  
Vol 10 (07) ◽  
pp. 718-727 ◽  
Author(s):  
Najla Mathlouthi ◽  
Charbel Al-Bayssari ◽  
Allaaeddin El Salabi ◽  
Sofiane Bakour ◽  
Salha Ben Gwierif ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Susceptibility Testing ◽  
Test Method ◽  
Bacterial Isolates ◽  
Biochemical Tests ◽  
E Coli ◽  
Extended Spectrum ◽  
Encoding Genes ◽  
Sequence Types ◽  
Esbl Producers

Introduction: The aim of the study was to investigate the prevalence of extended-spectrum β-lactamase (ESBL) and carbapenemase production among clinical isolates of Enterobacteriaceae recovered from Tunisian and Libyan hospitals. Methodology: Bacterial isolates were recovered from patients in intensive care units and identified by biochemical tests and MALDI-TOF. Antibiotic susceptibility testing was performed by disk diffusion and the E-test method. ESBL and carbapenemase activities were detected using standard microbiological tests. Antibiotic resistance-encoding genes were screened by PCR and sequencing. Clonal relationships between Klebsiella pneumoniae strains were carried out using multi-locus sequence typing (MLST). Results: A total of 87 isolates were characterized, with 51 and 36, respectively, identified as E. coli and K. pneumoniae. Overall the resistance prevalence was high for aminoglycosides (> 60%), fluoroquinolones (> 80%), and extended-spectrum cephalosporins (> 94%), and was low for imipenem (11.4%). Among this collection, 58 strains (66.6%) were ESBL producers and 10 K. pneumoniae strains (11.4%) were carbapenemase producers. The antibiotic resistance-encoding genes detected were blaCTX-M-15 (51.7%), blaTEM-1 (35.6%), several variants of blaSHV (21.8%), and blaOXA-48 (11.4%). The MLST typing of K. pneumoniae isolates revealed the presence of multiple clones and three novel sequence types. Also, close relationships between the OXA-48-producing strains from Tunisia and Libya were demonstrated. Conclusions: This study is the first paper describing the emergence of carbapenemase- and ESBL-producing Enterobacteriaceae, sensitive to colistin, isolated in Tunisia and Libya. Active surveillance and testing for susceptibility to colistin should be implementing because resistance to colistin, mainly in Klebsiella, has been recently reported worldwide.

scholarly journals Serotyping, MLST, and Core Genome MLST Analysis of Salmonella enterica From Different Sources in China During 2004–2019

2021 ◽  
Vol 12 ◽  
Author(s):  
Shigan Yan ◽  
Wencheng Zhang ◽  
Chengyu Li ◽  
Xu Liu ◽  
Liping Zhu ◽  
...  
Keyword(s):  
Salmonella Enterica ◽  
Core Genome ◽  
Foodborne Pathogen ◽  
Food Poisoning ◽  
Human Infection ◽  
Temporal And Spatial Distribution ◽  
Typing Method ◽  
Bacterial Typing ◽  
Mlst Analysis ◽  
Sequence Types

Salmonella enterica (S. enterica) is an important foodborne pathogen, causing food poisoning and human infection, and critically threatening food safety and public health. Salmonella typing is essential for bacterial identification, tracing, epidemiological investigation, and monitoring. Serotyping and multilocus sequence typing (MLST) analysis are standard bacterial typing methods despite the low resolution. Core genome MLST (cgMLST) is a high-resolution molecular typing method based on whole genomic sequencing for accurate bacterial tracing. We investigated 250 S. enterica isolates from poultry, livestock, food, and human sources in nine provinces of China from 2004 to 2019 using serotyping, MLST, and cgMLST analysis. All S. enterica isolates were divided into 36 serovars using slide agglutination. The major serovars in order were Enteritidis (31 isolates), Typhimurium (29 isolates), Mbandaka (23 isolates), and Indiana (22 isolates). All strains were assigned into 43 sequence types (STs) by MLST. Among them, ST11 (31 isolates) was the primary ST. Besides this, a novel ST, ST8016, was identified, and it was different from ST40 by position 317 C → T in dnaN. Furthermore, these 250 isolates were grouped into 185 cgMLST sequence types (cgSTs) by cgMLST. The major cgST was cgST235530 (11 isolates), and only three cgSTs contained isolates from human and other sources, indicating a possibility of cross-species infection. Phylogenetic analysis indicated that most of the same serovar strains were putatively homologous except Saintpaul and Derby due to their multilineage characteristics. In addition, serovar I 4,[5],12:i:- and Typhimurium isolates have similar genomic relatedness on the phylogenetic tree. In conclusion, we sorted out the phenotyping and genotyping diversity of S. enterica isolates in China during 2004–2019 and clarified the temporal and spatial distribution characteristics of Salmonella from different hosts in China in the recent 16 years. These results greatly supplement Salmonella strain resources, genetic information, and traceability typing data; facilitate the typing, traceability, identification, and genetic evolution analysis of Salmonella; and therefore, improve the level of analysis, monitoring, and controlling of foodborne microorganisms in China.

scholarly journals Phenotypic profile of priority multiresistant Аcinetobacter baumannii sequence types (ST 1167, ST 944, ST 208)

2022 ◽  
Vol 98 (6) ◽  
pp. 639-647
Author(s):  
O. S. Fedotova ◽  
Yu. A. Zakharova ◽  
A. V. Ostapchuk ◽  
U. A. Bazhanova ◽  
A. A. Zakharov
Keyword(s):  
Test Panel ◽  
Biochemical Tests ◽  
Phenotypic Properties ◽  
Genetic Method ◽  
Phenotypic Profile ◽  
Typing Methods ◽  
Phenotypic Methods ◽  
Multiresistant Strains ◽  
Hospital Acquired ◽  
Sequence Types

Introduction. About 1,000,000 cases of infections caused by Acinetobacter spp. per year are registered globally, making up 1.8% of all the cases of hospital-acquired infections. In compliance with long-term studies carried out in in this country and abroad, Acinetobacter baumannii is a clinically important representative of the Acinetobacter genus. Intraspecific typing of microorganisms is an integral part of a clinical microbiologist's contribution to scoring the outbreaks of purulent-septic infections within the sphere of HAI surveillance. Most of the practicing microbiological laboratories cannot use genotypic typing methods because of their high costs.Objective. Developing a test panel for intraspecific identification of A. baumannii sequence types (ST 1167, ST 944, ST 208) based on their phenotypic properties.Materials and methods. Intraspecific membership of 74 A. baumannii strains obtained from four multipurpose health settings of a large industrial centre was studied using a genetic method (multilocus sequence typing) and a suite of phenotypic methods (biochemical tests, biofilmogenous capacity, growth inhibition zones to antibacterial drugs, sensitivity to aniline dyes, disinfectants and Acinetobacter bacteriophage) was studied.Results. Phenotypic features of three predominant A. baumannii sequence types (ST 1167, 944, 208) were determined.Discussion. An efficacious economy set of differentiating tests allowing identification of intraspecific features of A. baumannii multiresistant strains was сreated.Conclusion. The test panel will enable the laboratories that cannot use sequencing methods to conduct intraspecific differentiation of common A. baumannii sequence types as part of microbiological monitoring.

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