Application of different DNA extraction procedures, library preparation protocols and sequencing platforms: impact on sequencing results

In this study three DNA extraction procedures, two library preparation protocols and two sequencing platforms were applied to analyse six bacterial cultures and their corresponding DNA obtained as part of a proficiency test. The impact of each variable on sequencing results was assessed using the following parameters: reads quality, assembly and alignment statistics; number of single nucleotide polymorphisms (SNPs), detected applying assembly- and alignment-based strategies; antimicrobial resistance genes (ARGs), identified on de novo assemblies of all sequenced genomes. The investigated nucleic acid extraction procedures, library preparation kits and sequencing platforms do not significantly affect de novo assembly statistics and number of SNPs and ARGs. The only exception was observed for two duplicates, which were associated to one PCR-based library preparation kit. Results from this comparative study can support researchers in the choice toward the available pre-sequencing and sequencing options, and might suggest further comparisons to be performed.

Comparative genomics of Vibrio cholerae O1 isolated from cholera patients in Bangladesh

Whole genome sequencing was utilized to investigate the genomic profile of Vibrio cholerae O1 strains, isolated from symptomatic patients in a low-income urban area of Dhaka, Bangladesh. Comparative genomics using bioinformatics tools were applied to identify major virulence factors, biotype and antimicrobial resistance genes in three V. cholerae O1 strains (VC-1, 2 and 3) isolated from two case patients. A phylogenetic SNP (single nucleotide polymorphism)-based analysis was conducted to infer the relatedness to V. cholerae O1 strains isolated elsewhere. The V. cholerae strains were the El Tor variant carrying ctxB1 (standard classical genotype). SNP-based global phylogeny revealed that the three isolates were strictly clonal and the closest neighbouring genomes were epidemic clones of V. cholerae O1 isolated in 2010 from cholera patients in Pakistan. All strains harboured the integrase gene of the SXT element (int_SXT ), antimicrobial resistance genes for aminoglycosides, phenicol, sulphonamide and trimethoprim except VC-1 that lacked sulphonamide resistance genes. The multilocus sequence typing (MLST) revealed that the strains belonged to sequence type, ST69. The study provides knowledge on current genetic traits of clinical V. cholerae O1 circulating in urban household clusters of Bangladesh which may help in predicting emergence of new pandemic strains in Bangladesh.

SIGNIFICANCE AND IMPACT OF THE STUDY

Vibrio cholerae has frequently experienced genetic changes with rapid evolution of pandemic clones in the Ganges Delta region. Whole genome sequencing can reveal genetic information of current pathogenic V. cholerae in Bangladesh which includes cefotaxime genotypes, virulence factors, altered antimicrobial resistance pattern as well as mobile genetic element compared to global pandemic strains. This study data could be used in planning future surveillance strategies in Ganges Delta region by informing new epidemiology of current outbreak strains.

Phenotypic and genotypic comparison of salmonellae from diarrhoeic and healthy humans and cattle, Nigeria

The sources and modes of transmission of non-typhoidal Salmonella particularly zoonotic transmission are poorly understood in Africa. This study compared phenotypic and genotypic characteristics of Salmonellae isolated from cattle and humans. Faecal samples of diarrhoeic patients (n = 234), and a healthy population (n = 160), beef cattle at slaughter (n = 250), farms (n = 72) and market (n = 100) were cultured for salmonellae and serotyping and antimicrobial susceptibility were determined. Whole-genome sequence typing (WGST) of selected isolates and bioinformatic analysis were used to identify the multilocus sequence type (MLST), plasmid replicons, antimicrobial resistance genes and genetic relatedness by single nucleotide polymorphism (SNP) analysis. The Salmonella isolates, diarrhoeic patients (n = 17), healthy population (n = 13), cattle (abattoir, n = 67; farms, n = 10; market n = 5), revealed 49 serovars; some serovars were common to humans and cattle. Rare serovars were prevalent: Colindale (cattle and humans); Rubislaw and Bredeney (humans); and Dublin, Give, Eastbourne, Hadar, Marseille, Sundsvall, Bergen, Ekotedo, Carno and Ealing (cattle). The sequence types (ST) include ST 584, ST 198, ST 562 and ST 512 for S. Colindale, S. Kentucky S. Rubislaw and S. Urbana, respectively. Clonal cluster shared by cattle and human WGST isolates was not found. Antimicrobial resistance rates were generally low and towards only chloramphenicol, ampicillin, gentamicin, ciprofloxacin, tetracycline and streptomycin, range 2.7% (chloramphenicol) to 8.9% (streptomycin). Multiply resistant isolates included serovars Kentucky, 4,5,12:i:- and Typhimurium. The study presents a baseline description of the prevalence, serotypes, antimicrobial resistance phenotypes and genetic relatedness of Salmonella isolated from healthy and diarrhoeic humans, and cattle at harvest, on farm and at market. Cattle are a reservoir of diverse salmonellae with shared serovars with humans, but WGST does not support zoonotic transmission. Further study with larger samples is recommended to determine whether epidemiological link exists between cattle and humans.

Detection of linezolid resistance due to the optrA gene in Enterococcus faecalis from poultry meat from the American continent (Colombia)

Background

Three Enterococcus isolates obtained from retail chicken collected in 2010-11 as part of the Colombian Integrated Program for Antimicrobial Resistance Surveillance (COIPARS) showed reduced susceptibility towards linezolid (MIC 8 mg/L).

Objectives

This study aimed at characterizing the isolates resistant to linezolid and detecting the resistance mechanism.

Methods

Strains were analysed in 2011-12 without successful detection of the resistance mechanism. All isolates were found negative for the cfr gene and no 23S rRNA mutations were detected. In 2016, with the novel resistance gene optrA being described, the WGS data were re-analysed using in silico genomic tools for confirmation of species, detection of virulence and resistance genes, MLST and SNP analyses and comparison of the genetic environment with the previously published plasmid pE349.

Results

: Three Enterococcus faecalis isolates were found positive for the optrA gene encoding resistance to linezolid and phenicols. Additional screening of 37 enterococci strains from the same study did not detect any further positives. Typing showed that two of the isolates belong to ST59, while the last belongs to ST489. All isolates carry genes encoding resistance to macrolide-lincosamide-streptogramin B, tetracycline and phenicols. In addition, the ST489 isolate also carries genes conferring aminoglycoside resistance and is resistant to quinolones, but no plasmid-mediated gene was detected. The optrA gene regions of the three plasmids showed high similarity to the originally reported optrA -carrying plasmid pE349.

Conclusions

To the best of our knowledge, this is the first description of the optrA gene in E. faecalis isolated from poultry meat in the Americas.

The first attempt of an active integrated laboratory-based Salmonella surveillance programme in the north-eastern region of Nigeria

AIM

To identify the sources of Salmonella contamination, distribution, prevalence and antimicrobial susceptibility patterns, which have significant impact on public and animal health, and international trade.

METHODS AND RESULTS

A total of 1888 samples were collected by stratified random sampling from 2009 to 2011 from cattle, camels, poultry, fish, vegetables and humans. All identified Salmonella isolates were serotyped and tested for antimicrobial susceptibility by MIC determinations. A total of 149 Salmonella isolates comprising 17 different serovars were obtained (7·9% prevalence). Salmonella Hadar (37%), S. Eko (17%), S. Enteritidis (10%), S. Kentucky (7%) and S. Uganda (7%) were isolated from different sources. The occurrence of antimicrobial resistance was generally low, but S. Enteritidis and S. Eko showed variable antimicrobial resistance patterns, while all S. Kentucky isolates were resistant to seven of 17 tested antimicrobials, including ciprofloxacin and nalidixic acid. Three S. Hadar isolates revealed reduced susceptibility to ciprofloxacin and susceptibility to nalidixic acid and harboured the plasmid-mediated quinolone resistance gene qnrS1.

CONCLUSIONS

Salmonella serovars Hadar, Enteritidis and the previously very rarely reported Eko were the major serovars associated with human infections, animal and environmental contamination in the north-eastern region of Nigeria.

SIGNIFICANCE AND IMPACT OF THE STUDY

These serovars constitute a health risk to poultry, environment and human population in the region.

External quality assurance system (EQAS) for identification of mastitis pathogens in Denmark from 2006 to 2011

Bovine mastitis is the most common and costly dairy cattle disease. Mastitis is most frequently caused by bacterial species, and to ensure optimal treatment and control strategies, proper quality assured diagnosis and identification of the causative agent is important. With the aim to assess the capacity to isolate and identify mastitis pathogens at veterinary clinics, an external quality assurance system (EQAS) was annually (from 2006 to 2011) provided for the identification of mastitis pathogens. This study presents the setup of the proficiency test and the obtained results that enabled the organizers to pinpoint areas for improvement and thereby to assist veterinary practices at strengthening their mastitis diagnostics. The proficiency test consisted of 15 milk samples spiked with a pure culture of a mastitis pathogen and distributed to veterinary practices for identification. Applying an internal quality control strain, i.e. including the same strain of Streptococcus agalactiae in all iterations of the proficiency test, served to gauge the bias caused by the year-to-year variation in the selection of test strains. A total of 73% of all uploaded results over the years were correct, with the internal quality control strain exhibiting a statistically significant ascending trend from 54% correct identifications in 2006 to 91% in 2011 (p-value=0.0082; n=13). Even if specifics were not recorded as regards the laboratory methods employed at the veterinary clinics for identification of mastitis pathogens, the results from this study indicate that the practices' application of basic biochemical analyses in this context could be optimized. In addition, dissemination of information on new methods and updated nomenclature appeared to be an area which future efforts with advantage could aim at.

Molecular characterisation of multidrug-resistant Salmonella enterica serovar Typhimurium isolates from Gomel region, Belarus

This study describes the characterisation by pulsed-field gel electrophoresis (PFGE), multilocus variable number tandem repeat analysis (MLVA) typing and antimicrobial resistance profiles of 35 Salmonella enterica serovar Typhimurium isolates, mostly from infections in children who acquired an infection outside hospitals in the Gomel region of Belarus. Thirty-one isolates were highly similar according to PFGE and MLVA typing, were multidrug-resistant, including resistance to ceftiofur, and harboured the bla(CTX-M-5) gene. These results indicate that a common source may have been responsible for most of the infections.

Serotyping, PCR, phage-typing and antibiotic sensitivity testing of Salmonella serovars isolated from urban drinking water supply systems of Nepal

AIMS

To study the occurrence and diversity of Salmonella serovars in urban water supply systems of Nepal.

METHODS AND RESULTS

Occurrence of Salmonella was detected in 42 out of 300 water samples by enrichment culture technique in selenite F broth followed by plating on Salmonella Shigella agar. A total of 54 isolates identified to genus level by standard tests were subsequently confirmed by serotyping, phage typing and PCR detection of virulence genes (inv A and spv C). The predominant serotype was Salmonella Typhimurium, followed by Salm. Typhi, Salm. Paratyphi A and Salmonella Enteritidis. Most of the Salm. Typhi isolates were E1 phage type followed by UVS4, A and UVS1. All isolates of Salm. Paratyphi A and Salm. Enteritidis were an untypable (UT) phage type. The majority of isolates were multi-drug resistant as revealed by Kirby-Bauer disc diffusion technique. Ceftriaxone resistant isolates of Salm. Enteritidis indicated the presence of one of the ESBL genes, blaSHV, whereas the genes blaTEM and blaCTX were absent.

CONCLUSIONS

The microbiological quality of the urban water supply is poor and indicates possibility of fatal outbreaks of enteric fever and related infections in Nepal.

SIGNIFICANCE AND IMPACT OF THE STUDY

The present study will be useful in water borne disease control and prevention strategy formulation in Nepal and in the global context.

Effect of abolishment of the use of antimicrobial agents for growth promotion on occurrence of antimicrobial resistance in fecal enterococci from food animals in Denmark

From 1995 to 2000, a total of 673 Enterococcus faecium and 1,088 Enterococcus faecalis isolates from pigs together with 856 E. faecium isolates from broilers were isolated and tested for susceptibility to four classes of antimicrobial agents used for growth promotion as part of the Danish program of monitoring for antimicrobial resistance. The four antimicrobials were avilamycin, erythromycin, vancomycin, and virginiamycin. Major changes in the use of antimicrobial agents for growth promotion have occurred during the last 6 years in Denmark. The government banned the use of avoparcin in 1995 and of virginiamycin in 1998. Furthermore, the producers have voluntarily stopped all use beginning in 1999. The avoparcin ban in 1995 was followed by a decrease in the occurrence of glycopeptide-resistant E. faecium (GRE) in broilers, from 72.7% in 1995 to 5.8% in 2000. The occurrence of glycopeptide resistance among isolates from pigs remained constant at around 20% from 1995 to 1997. It was shown that, in GRE from pigs, the genes encoding macrolide and glycopeptide resistance were genetically linked and that, following the decrease in the use of tylosin during 1998 and 1999, the occurrence of GRE in pigs decreased to 6.0% in 2000. From 1995 to 1997 the occurrence of erythromycin resistance among E. faecium and E. faecalis isolates from pigs was almost 90%. Use of tylosin decreased considerably during 1998 and 1999, and this decrease was followed by decreases in the occurrence of resistance to 46.7 and 28.1% among E. faecium and E. faecalis isolates from pigs, respectively. Erythromycin resistance among E. faecium isolates from broilers reached a maximum of 76.3% in 1997 but decreased to 12.7% in 2000 concomitantly with more limited use of virginiamycin. Use of virginiamycin increased from 1995 to 1997 and was followed by an increased occurrence of virginiamycin resistance among E. faecium isolates in broilers, from 27.3% in 1995 to 66.2% in 1997. In January 1998 the use of virginiamycin was banned in Denmark, and the occurrence of virginiamycin resistance decreased to 33.9% in 2000. Use of avilamycin increased from 1995 to 1996 and was followed by an increase in avilamycin resistance among E. faecium isolates from broilers, from 63.6% in 1995 to 77.4% in 1996. Since 1996 avilamycin usage has decreased, followed by a decrease in resistance to 4.8% in 2000. Our observations show that it is possible to reduce the occurrence of antimicrobial resistance in a national population of food animals when the selective pressure is removed. Cases in which resistance to vancomycin was linked to resistance to erythromycin were exceptions. In such cases resistance did not decrease until the use of both avoparcin and tylosin was limited.