COPLA, a taxonomic classifier of plasmids Redondo-Salvo, Santiago; Bartomeus-Peéalver, Roger; Vielva, Luis ...
BMC bioinformatics,
07/2021, Letnik:
22, Številka:
1
Journal Article
Recenzirano
Odprti dostop
Plasmids are mobile genetic elements, key in the dissemination of antibiotic resistance, virulence determinants and other adaptive traits in bacteria. Obtaining a robust method for plasmid ...classification is necessary to better understand the genetics and epidemiology of many pathogens. Until now, plasmid classification systems focused on specific traits, which limited their precision and universality. The definition of plasmid taxonomic units (PTUs), based on average nucleotide identity metrics, allows the generation of a universal plasmid classification scheme, applicable to all bacterial taxa. Here we present COPLA, a software able to assign plasmids to known and novel PTUs, based on their genomic sequence. We implemented an automated pipeline able to assign a given plasmid DNA sequence to its cognate PTU, and assessed its performance using a sample of 1000 unclassified plasmids. Overall, 41% of the samples could be assigned to a previously defined PTU, a number that reached 63% in well-known taxa such as the Enterobacterales order. The remaining plasmids represent novel PTUs, indicating that a large fraction of plasmid backbones is still uncharacterized. COPLA is a bioinformatic tool for universal, species-independent, plasmid classification. Offered both as an automatable pipeline and an open web service, COPLA will help bacterial geneticists and clinical microbiologists to quickly classify plasmids.
To reveal the occurrence and mechanisms for dispersal of antibiotic resistance (AbR) among the microbial assemblages inhabiting impacted coastal environments, we performed a weekly, two-year duration ...time-series study at two urban beaches between 2014 and 2016. We combined quantitative PCR and multiplex PCR/reverse line blot techniques to track patterns in the occurrence of 31 AbR genes, including genes that confer resistance to antibiotics that are critically important antimicrobials for human medicine. Patterns in the abundance of these genes were linked to specific microbial groups and environmental parameters by coupling qPCR and 16S rRNA amplicon sequencing data with network analysis. Up to 100-fold increases in the abundance of several AbR genes, including genes conferring resistance to quinolones, trimethoprim, sulfonamides, tetracycline, vancomycin and carbapenems, occurred following storm-water and modelled wet-weather sewer overflow events. The abundance of AbR genes strongly and significantly correlated with several potentially pathogenic bacterial OTUs regularly associated with wastewater infrastructure, such as Arcobacter, Acinetobacter, Aeromonas and Cloacibacterium. These high-resolution observations provide clear links between storm-water discharge and sewer overflow events and the occurrence of AbR in the coastal microbial assemblages inhabiting urban beaches, highlighting a direct mechanism for potentially significant AbR exposure risks to humans.
•Storm-water events augment antibiotic resistance genes in coastal receiving waters.•Several antibiotic resistance genes remain elevated 1–2 weeks following rainfall.•Beach swimmers could be exposed to antibiotic resistant microbes and their genes.
•27 Salmonella outbreaks were linked to beef consumption during 2012–2019.•Ground beef contributed disproportionately to the number of beef-attributed illnesses.•8 of 9 outbreaks caused by ...antimicrobial-resistant strains were multidrug-resistant.•Outbreaks highlight where interventions can be applied along farm–fork continuum.
The Centers for Disease Control and Prevention (CDC) has identified nontyphoidal Salmonella as one of the top five pathogens contributing to foodborne illnesses in the United States. Beef continues to be a common source of Salmonella outbreaks, despite the implementation of interventions at slaughter and processing facilities to reduce contamination of beef. We described Salmonella outbreaks linked to beef in the United States during 2012–2019, examined trends, and identified potential targets for intervention and prevention strategies. We queried CDC’s Foodborne Disease Outbreak Surveillance System (FDOSS) for all foodborne nontyphoidal Salmonella outbreaks linked to beef as the single contaminated ingredient or implicated food, with the date of first illness onset from 2012 to 2019. Information on antimicrobial resistance (AR) for outbreak-related isolates was obtained from CDC’s National Antimicrobial Resistance Monitoring System (NARMS). We calculated the number of outbreaks, outbreak-related illnesses, hospitalizations, and deaths overall, by beef processing category and Salmonella serotype. During 2012–2019, 27 Salmonella outbreaks were linked to beef consumption, resulting in 1103 illnesses, 254 hospitalizations, and two deaths. The most common category of beef implicated was nonintact raw, ground beef (12 outbreaks, 44%), followed by intact raw (six outbreaks, 22%). Ground beef was responsible for the most illnesses (800, 73%), both of the reported deaths, and was the source of the largest outbreak. AR data were available for 717 isolates from 25 (93%) outbreaks. Nine (36%) of these outbreaks had isolates resistant to one or more of the antibiotics tested by NARMS, of which eight (89%) contained multidrug-resistant isolates. Several outbreaks reported highlight challenges faced during investigations, areas where further research may be warranted, and opportunities to prevent future outbreaks along the farm-to-fork continuum.
Increasing azithromycin treatment failure in sexually transmitted Mycoplasma genitalium infection, is linked to macrolide resistance and second-line treatment relies on the fluoroquinolone, ...moxifloxacin. We recently detected fluoroquinolone and macrolide resistance-associated mutations in 15% and 43%, respectively, of 143 initial M. genitalium PCR-positive specimens. For a subset of 33 Western Sydney Sexual Health Centre patients, clinical information and results of sequence analysis of M. genitalium macrolide and fluoroquinolone target genes - the 23S rRNA gene, and parC and gyrA, respectively - were used to examine whether mutations were associated with treatment failure. Macrolide resistance-associated mutations correlated with microbiological (p = 0.013) and clinical (p = 0.024) treatment failure, and fluoroquinolone resistance-associated mutations with microbiological moxifloxacin treatment failure (p = 0.005). We describe the first reported cases of clinical and microbiological moxifloxacin treatment failure. Failure of first- and second-line antibiotic treatment of M. genitalium infection is occurring and likely to increase with current treatment strategies.
Genomic characterization of an Escherichia coli O157:H7 strain linked to leafy greens–associated outbreaks dates its emergence to late 2015. One clade has notable accessory genomic content and a ...previously described mutation putatively associated with increased arsenic tolerance. This strain is a reoccurring, emerging, or persistent strain causing illness over an extended period.
A multidrug-resistant Salmonella enterica serotype Anatum strain reported in Taiwan was isolated in the United States from patients and from seafood imported from Asia. Isolates harbored 11 ...resistance determinants, including quinolone and inducible cephalosporin resistance genes. Most patients had traveled to Asia. These findings underscore the need for global One Health resistance surveillance.
Abstract
Background
Antimicrobial resistance in nontyphoidal Salmonella (NTS) can limit treatment options. We assessed the contribution of international travel to antimicrobial-resistant NTS ...infections.
Methods
We describe NTS infections that were reported to the Foodborne Diseases Active Surveillance Network during 2018–2019 and screened for genetic resistance determinants, including those conferring decreased susceptibility to first-line agents (ciprofloxacin, ceftriaxone, or azithromycin). We used multivariable logistic regression to assess the association between resistance and international travel during the 7 days before illness began. We estimated the contribution of international travel to resistance using population-attributable fractions, and we examined reported antimicrobial use.
Results
Among 9301 NTS infections, 1159 (12%) occurred after recent international travel. Predicted resistance to first-line antimicrobials was more likely following travel; the adjusted odds ratio varied by travel region and was highest after travel to Asia (adjusted odds ratio, 7.2 95% confidence interval, 5.5–9.5). Overall, 19% (95% confidence interval, 17%–22%) of predicted resistance to first-line antimicrobials was attributable to international travel. More travelers than nontravelers receiving ciprofloxacin or other fluoroquinolones had isolates with predicted resistance to fluoroquinolones (29% vs 9%, respectively; P < .01).
Conclusions
International travel is a substantial risk factor for antimicrobial-resistant NTS infections. Understanding risks of resistant infection could help target prevention efforts.
International travelers were more likely to have nontyphoidal Salmonella infections resistant to first-line antibiotics compared with nontravelers. Surveillance using whole-genome sequencing for tracking resistant strains, including those associated with travel, can help inform prevention efforts and treatment guidelines.
Infantis carrying extended spectrum β-lactamase
on a pESI-like megaplasmid has recently emerged in United States poultry. In order to determine the carriage rate and gene content variability of this ...plasmid in U.S.
Infantis, whole genome sequences of
isolates from humans and animals in the U.S. and internationally containing the pESI-like plasmid were analyzed. The U.S. Department of Agriculture Food Safety and Inspection Service (FSIS) identified 654 product sampling isolates containing pESI-like plasmids through hazard analysis and critical control point (HACCP) verification testing in 2017 and 2018. The Centers for Disease Control and Prevention identified 55 isolates with pESI-like plasmids in 2016-2018 through the National Antimicrobial Resistance Monitoring System. Approximately 49% of pESI-like plasmids from FSIS verification isolates and 71% from CDC NARMS contained
. Pan-plasmid genome analysis was also performed. All plasmids contained
and more than 95% contained 172 other conserved genes; 61% contained
. In a hierarchical clustering analysis, some plasmids from U.S. animal sources clustered together and some plasmids from South America clustered together, possibly indicating multiple plasmid lineages. However, most plasmids contained similar genes regardless of origin. Carriage of the pESI-like plasmid in U.S. appears to be limited to
Infantis and carriage rates increased from 2017 to 2018.
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