The clinically important anaerobic, human pathogenic Bacteroides species and their antibiotic resistance levels in Central and Southeast Europe

Abstract The Bacteroides and Parabacteroides species are important obligate anaerobic bacteria that are significant constituents of normal flora (microbiota), and opportunistic pathogens with special biological background. They are highly resistant to antibiotics and monitoring their resistance levels is important for their empiric therapy. Several antibiotic resistance studies were conducted in the USA and Europe and we have data for the region involved in this study showing comparable trends. Multidrug-resistant strains are emerging among Bacteroides too, where the proper antibiotic tests and treatments may be life-saving.

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Pheromone killing of multidrug-resistantEnterococcus faecalisV583 by native commensal strains

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1500553112 ◽

2015 ◽

Vol 112 (23) ◽

pp. 7273-7278 ◽

Cited By ~ 31

Author(s):

Michael S. Gilmore ◽

Marcus Rauch ◽

Matthew M. Ramsey ◽

Paul R. Himes ◽

Sriram Varahan ◽

...

Keyword(s):

Antibiotic Resistance ◽

Cross Talk ◽

Metabolic Pathways ◽

Multidrug Resistant ◽

Mobile Elements ◽

Competitive Growth ◽

Gi Tract ◽

Subsequent Infection ◽

Native Flora ◽

Resistant Strains

Multidrug-resistantEnterococcus faecalispossess numerous mobile elements that encode virulence and antibiotic resistance traits as well as new metabolic pathways, often constituting over one-quarter of the genome. It was of interest to determine how this large accretion of mobile elements affects competitive growth in the gastrointestinal (GI) tract consortium. We unexpectedly observed that the prototype clinical isolate strain V583 was actively killed by GI tract flora, whereas commensal enterococci flourished. It was found that killing of V583 resulted from lethal cross-talk between accumulated mobile elements and that this cross-talk was induced by a heptapeptide pheromone produced by nativeE. faecalispresent in the fecal consortium. These results highlight two important aspects of the evolution of multidrug-resistant enterococci: (i) the accretion of mobile elements inE. faecalisV583 renders it incompatible with commensal strains, and (ii) because of this incompatibility, multidrug-resistant strains sharing features found in V583 cannot coexist with commensal strains. The accumulation of mobile elements in hospital isolates of enterococci can include those that are inherently incompatible with native flora, highlighting the importance of maintaining commensal populations as means of preventing colonization and subsequent infection by multidrug-resistant strains.

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Antibiotic Resistance and Virulence Gene Characteristics of Methicillin-Resistant Staphylococcus aureus (MRSA) Isolated from Healthy Edible Marine Fish

International Journal of Microbiology ◽

10.1155/2020/9803903 ◽

2020 ◽

Vol 2020 ◽

pp. 1-9

Author(s):

Justine Fri ◽

Henry A. Njom ◽

Collins N. Ateba ◽

Roland N. Ndip

Keyword(s):

Staphylococcus Aureus ◽

Antibiotic Resistance ◽

Marine Fish ◽

Control Strategies ◽

Virulence Gene ◽

Multidrug Resistant ◽

Methicillin Resistant ◽

Vancomycin Mics ◽

Resistant Strains ◽

Mrsa Strains

Thirty-three (33) isolates of methicillin-resistant Staphylococcus aureus (MRSA) from healthy edible marine fish harvested from two aquaculture settings and the Kariega estuary, South Africa, were characterised in this study. The phenotypic antimicrobial susceptibility profiles to 13 antibiotics were determined, and their antibiotic resistance determinants were assessed. A multiplex PCR was used to determine the epidemiological groups based on the type of SCCmec carriage followed by the detection of staphylococcal enterotoxin-encoding genes sea-sed and the Panton Valentine leucocidin gene (pvl). A high antibiotic resistance percentage (67–81%) was observed for Erythromycin, Ampicillin, Rifampicin, and Clindamycin, while maximum susceptibility to Chloramphenicol (100%), Imipenem (100%), and Ciprofloxacin (94%) was recorded. Nineteen (58%) of the MRSA strains had Vancomycin MICs of ≤2 μg/mL, 4 (12%) with MICs ranging from 4–8 μg/mL, and 10 (30%) with values ≥16 μg/mL. Overall, 27 (82%) isolates were multidrug-resistant (MDR) with Erythromycin-Ampicillin-Rifampicin-Clindamycin (E-AMP-RIP-CD) found to be the dominant antibiotic-resistance phenotype observed in 4 isolates. Resistance genes such as tetM, tetA, ermB, blaZ, and femA were detected in two or more resistant strains. A total of 19 (58%) MRSA strains possessed SCCmec types I, II, or III elements, characteristic of healthcare-associated MRSA (HA-MRSA), while 10 (30%) isolates displayed SCCmec type IVc, characteristic of community-associated MRSA (CA-MRSA). Six (18%) of the multidrug-resistant strains of MRSA were enterotoxigenic, harbouring the see, sea, or sec genes. A prevalence of 18% (6/33) was also recorded for the luk-PVL gene. The findings of this study showed that marine fish contained MDR-MRSA strains that harbour SCCmec types, characteristic of either HA-MRSA or CA-MRSA, but with a low prevalence of enterotoxin and pvl genes. Thus, there is a need for continuous monitoring and implementation of better control strategies within the food chain to minimise contamination of fish with MDR-MRSA and the ultimate spread of the bug.

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Comprehensive Genome Analysis of Carbapenem-Resistant Strains of Raoultella Species, an Emerging Multidrug-Resistant Bacterium in Hospitals

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01367-19 ◽

2019 ◽

Vol 63 (12) ◽

Cited By ~ 1

Author(s):

Xiao Yu ◽

Beiwen Zheng ◽

Jing Zhang ◽

Hao Xu ◽

Tingting Xiao ◽

...

Keyword(s):

Antibiotic Resistance ◽

Antibiotic Resistance Genes ◽

Genomic Analysis ◽

Multidrug Resistant ◽

Control Measures ◽

Carbapenem Resistant ◽

Multidrug Resistant Bacterium ◽

The World ◽

Resistant Strains

ABSTRACT We report the characterization of six carbapenem-resistant Raoultella spp. (CRRS) in our hospital and a genomic analysis of 58 publicly available isolates. CRRS isolates are sporadically identified around the world, and different transposons carrying carbapenemases were the resistant mechanisms. Mobile genetic elements play an important role in acquiring antibiotic resistance genes from the hospital. An improved understanding of these transposon and targeted control measures will be very valuable to prevent CRRS dissemination.

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Characterisation of antibiotic resistance ofSalmonellaisolated from dog treats in Japan

Epidemiology and Infection ◽

10.1017/s0950268819000153 ◽

2019 ◽

Vol 147 ◽

Author(s):

S. Yukawa ◽

I. Uchida ◽

Y. Tamura ◽

S. Ohshima ◽

T. Hasegawa

Keyword(s):

Antibiotic Resistance ◽

Nalidixic Acid ◽

Salmonella Enterica ◽

Antimicrobial Agents ◽

Multidrug Resistant ◽

Surveillance Data ◽

Potential Source ◽

Human Salmonellosis ◽

The Usa

AbstractDog treats might be contaminated withSalmonella. In Canada and the USA, outbreaks of human salmonellosis related to exposure to animal-derived dog treats were reported. Consequently, surveillance data onSalmonellacontamination of dog treats have been gathered in many countries, but not in Japan. In the current study, we investigated whether dog treats in Japan were contaminated withSalmonella. Overall, 303 dog treats (of which 255 were domestically produced) were randomly collected and the presence ofSalmonellainvestigated. Seven samples were positive forSalmonella entericasubsp.enterica. Among these isolates, three were identified as serovar 4,5,12:i:–; two were serovar Rissen; and two were serovar Thompson. All serovar 4,5,12:i:– and Thompson isolates were resistant to one or more drugs. Two serovar Rissen isolates were fully susceptible to all tested antimicrobial agents. AllSalmonellaisolates were susceptible to cefotaxime, ciprofloxacin and nalidixic acid. The geneblaTEMwas detected in two serovar 4,5,12:i:– isolates. TheblaCTX−MandblaCMYgenes were not detected in any isolates. This study demonstrated that dog treats in Japan could constitute a potential source of dog and humanSalmonellainfections, including multidrug-resistantSalmonellaisolates.

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Microevolution of acquired colistin resistance in Enterobacteriaceae from ICU patients receiving selective decontamination of the digestive tract

10.1101/2020.04.26.059691 ◽

2020 ◽

Author(s):

Axel B. Janssen ◽

Denise van Hout ◽

Marc J.M. Bonten ◽

Rob J.L. Willems ◽

Willem van Schaik

Keyword(s):

Digestive Tract ◽

Response Regulator ◽

Multidrug Resistant ◽

Selective Decontamination ◽

Opportunistic Pathogens ◽

Colistin Resistance ◽

Gram Negative ◽

Routine Surveillance ◽

Resistant Strains ◽

Prophylactic Use

AbstractColistin is an antibiotic that targets the lipopolysaccharides present in the membranes of Gram-negative bacteria. It is used as last-resort drug to treat infections with multidrug-resistant strains. Colistin is also used in selective decontamination of the digestive tract (SDD), a prophylactic therapy used in patients hospitalised in intensive care units (ICUs) to selectively eradicate opportunistic pathogens in the oropharyngeal and gut microbiota. In this study, we aimed to unravel the mechanisms of acquired colistin resistance in Gram-negative opportunistic pathogens obtained from SDD-treated patients.Routine surveillance of 428 SDD-treated patients resulted in thirteen strains with acquired colistin resistance (Escherichia coli n=9; Klebsiella aerogenes, n=3; Enterobacter asburiae, n=1) from five patients. Genome sequence analysis showed that these isolates represented multiple distinct colistin-resistant clones, but that within the same patients, colistin-resistant strains were clonally related. We identified previously described mechanisms that lead to colistin resistance, i.e. a G53 substitution in the response regulator PmrA/BasR, and the acquisition of the mobile colistin resistance gene mcr-1.1, but we also observed novel variants of basR with an 18-bp deletion, and a G19E substitution in the sensor histidine kinase BasS. We experimentally confirmed these variants to contribute to reduced colistin susceptibility. In a single patient, we observed that colistin resistance in a single E. coli clone evolved through two unique variants in basRS.We show that prophylactic use of colistin during SDD can select for colistin resistance in species that are not intrinsically colistin-resistant. This highlights the importance of continued surveillance for the emergence of colistin resistance in patients treated with SDD.

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Is there any association between antibiotic resistance and virulence genes in Enterococcus isolates?

Medical Science and Discovery ◽

10.36472/msd.v6i12.327 ◽

2019 ◽

Vol 6 (12) ◽

pp. 310-315

Author(s):

Nergis Aşgın ◽

Emre Taşkın

Keyword(s):

Antibiotic Resistance ◽

Virulence Genes ◽

Multidrug Resistant ◽

Automated System ◽

High Frequencies ◽

Resistant Strains ◽

Vancomycin Resistant ◽

High Level

Objective: In this study, we aim to determine the frequency of antibiotic resistance and five virulence genes in Enterococcus species and the relationship between antibiotic resistance and virulence genes. Material and Methods: A total of 86 Enterococcus strains isolated from inpatients between 2015 and 2016 were included. Identification and antibiotic susceptibilities of strains were determined using a BD Phoenix fully automated system. The presence of virulence-associated genes (esp, gel E, asa1, hyl, and cyl) were investigated by using PCR method. Results: Of the 86 Enterococcus strains, 53 (61.6%) and 33 (38.4%) were Enterococcus faecium and Enterococcus faecalis, respectively. Vancomycin and high-level gentamicin resistance (HLGR) in E. faecalis strains were 0.6% and 60.6%, respectively. Furthermore, 52 of the 53 E. faecium strains were both vancomycin-resistant and HLGR. The frequency of esp, gel E, asa1, cyl, and hyl was 91.9%, 60.5%, 54.7%, 43%, and 26.7%, respectively. The asa 1, cyl, and gel E genes were detected at high frequencies in vancomycin-susceptible and non-HLGR strains, whereas hyl gene was detected at high frequencies in vancomycin-resistant and HLGR strains. Conclusion: Virulence genes were more frequent in vancomycin-susceptible and non-HLGR Enterococcus strains than in the resistant strains. Although infections caused by multidrug-resistant strains are difficult to treat, it should be considered that susceptible strains have more virulence genes. This may reduce the in vivo efficacy of drugs and lead to treatment failures. Therefore, in addition to the in vitro susceptibilities of drugs, clinical efficacy should be monitored.

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Whole-genome comparative analysis at the lineage/sublineage level discloses relationships between Mycobacterium tuberculosis genotype and clinical phenotype

PeerJ ◽

10.7717/peerj.12128 ◽

2021 ◽

Vol 9 ◽

pp. e12128

Author(s):

Andrea Monserrat Negrete-Paz ◽

Gerardo Vázquez-Marrufo ◽

Ma. Soledad Vázquez-Garcidueñas

Keyword(s):

Antibiotic Resistance ◽

Mycobacterium Tuberculosis ◽

Clinical Phenotype ◽

Effective Strain ◽

Pulmonary Involvement ◽

Multidrug Resistant ◽

Nucleotide Polymorphisms ◽

Mtbc Strain ◽

Resistant Strains ◽

Phylogenetic Lineages

Background Human tuberculosis (TB) caused by members of the Mycobacterium tuberculosis complex (MTBC) is the main cause of death among infectious diseases worldwide. Pulmonary TB (PTB) is the most common clinical phenotype of the disease, but some patients develop an extrapulmonary (EPTB) phenotype in which any organ or tissue can be affected. MTBC species include nine phylogenetic lineages, with some appearing globally and others being geographically restricted. EPTB can or not have pulmonary involvement, challenging its diagnosis when lungs are not implicated, thus causing an inadequate treatment. Finding evidence of a specific M. tuberculosis genetic background associated with EPTB is epidemiologically relevant due to the virulent and multidrug-resistant strains isolated from such cases. Until now, the studies conducted to establish associations between M. tuberculosis lineages and PTB/EPTB phenotypes have shown inconsistent results, which are attributed to the strain predominance from specific M. tuberculosis lineages/sublineages in the samples analyzed and the use of low-resolution phylogenetic tools that have impaired sublineage discrimination abilities. The present work elucidates the relationships between the MTBC strain lineages/sublineages and the clinical phenotypes of the disease as well as the antibiotic resistance of the strains. Methods To avoid biases, we retrieved the raw genomic reads (RGRs) of all (n = 245) the M. tuberculosis strains worldwide causing EPTB available in databases and an equally representative sample of the RGRs (n = 245) of PTB strains. A multiple alignment was constructed, and a robust maximum likelihood phylogeny based on single-nucleotide polymorphisms was generated, allowing effective strain lineage/sublineage assignment. Results A significant Odds Ratio (OR range: 1.8–8.1) association was found between EPTB and the 1.1.1, 1.2.1, 4.1.2.1 and ancestral Beijing sublineages. Additionally, a significant association between PTB with 4.3.1, 4.3.3, and 4.5 and Asian African 2 and Europe/Russia B0/W148 modern Beijing sublineages was found. We also observed a significant association of Lineage 3 strains with multidrug resistance (OR 3.8; 95% CI [1.1–13.6]), as well as between modern Beijing sublineages and antibiotic resistance (OR 4.3; 3.8–8.6). In this work, it was found that intralineage diversity can drive differences in the immune response that triggers the PTB/EPTB phenotype.

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Resistance diagnostics as a public health tool to combat antibiotic resistance: A model-based evaluation

10.1101/452656 ◽

2018 ◽

Cited By ~ 1

Author(s):

David McAdams ◽

Kristofer Wollein Waldetoft ◽

Christine Tedijanto ◽

Marc Lipsitch ◽

Sam P. Brown

Keyword(s):

Public Health ◽

Antibiotic Resistance ◽

Point Of Care ◽

Fitness Cost ◽

Opportunistic Pathogens ◽

Targeted Interventions ◽

Drug Choice ◽

Informed Treatment ◽

Resistant Strains ◽

Improve Treatment Efficacy

AbstractRapid point-of-care resistance diagnostics (POC-RD) are a key tool in the fight against antibiotic resistance. By tailoring drug choice to infection genotype, doctors can improve treatment efficacy while limiting costs of inappropriate antibiotic prescription. Here we combine epidemiological theory and data to assess the potential of RD innovations in a public health context, as a means to limit or even reverse selection for antibiotic resistance. POC-RD can be used to impose a non-biological fitness cost on resistant strains, by enabling diagnostic-informed treatment and targeted interventions that reduce resistant strains’ opportunities for transmission. We assess this diagnostic-imposed fitness cost in the context of a spectrum of bacterial population biologies, and find that the expected impact varies from selection against resistance for obligate pathogens to marginal public health improvements for opportunistic pathogens with high ‘bystander’ antibiotic exposure during asymptomatic carriage (e.g. the pneumococcus). We close by generalizing the notion of RD-informed strategies to incorporate carriage surveillance information, and illustrate that coupling transmission-control interventions to the discovery of resistant strains in carriage can potentially select against resistance in a broad range of opportunistic pathogens.

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Enterobacteriaceae Antibiotic Resistance in Ready-to-Eat Foods Collected from Hospital and Community Canteens: Analysis of Prevalence

Journal of Food Protection ◽

10.4315/0362-028x.jfp-17-317 ◽

2018 ◽

Vol 81 (3) ◽

pp. 424-429 ◽

Cited By ~ 1

Author(s):

SARA VINCENTI ◽

MATTEO RAPONI ◽

ROMINA SEZZATINI ◽

GABRIELE GIUBBINI ◽

PATRIZIA LAURENTI

Keyword(s):

Antibiotic Resistance ◽

Microbiological Quality ◽

Multidrug Resistant ◽

Food Samples ◽

Intrinsic Resistance ◽

Antibiotic Resistant ◽

Contemporary World ◽

Hygiene Practices ◽

Resistant Strains ◽

Cold Food

ABSTRACT Foodborne diseases and antibiotic resistance are serious widespread health problems in the contemporary world. In this study, we compared the microbiological quality of ready-to-eat (RTE) foods found in community canteens versus hospital canteens in Rome, Italy, focusing on detection and quantification of Enterobacteriaceae and the antibiotic resistance of these bacteria. Our findings show a remarkable difference in Enterobacteriaceae contamination between RTE foods distributed in community canteens (33.5% of samples) and those distributed in hospital canteens (5.3% of samples). This result highlights greater attention to good manufacturing practices and good hygiene practices by the food operators in hospitals compared with food operators in community canteens. As expected, a higher percentage of cold food samples (70.9%) than of hot food samples (10.8%) were positive for these bacteria. Excluding the intrinsic resistance of each bacterial strain, 92.3% of the isolated strains were resistant to at least one antibiotic, and about half of the isolated strains were classified as multidrug resistant. The prevalence of multidrug-resistant strains was 50% in the community samples and 33.3% in hospital canteens. Our results indicate that approximately 38% of RTE foods provided in community canteens is not compliant with microbiological food safety criteria and could be a special risk for consumers through spread of antibiotic-resistant strains. Hygienic processing and handling of foods is necessary for both hospital and community canteens.

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Draft Genome Sequences of Nonclinical and Clinical Enterobacter cloacae Isolates Exhibiting Multiple Antibiotic Resistance and Virulence Factors

Genome Announcements ◽

10.1128/genomea.01218-17 ◽

2017 ◽

Vol 5 (45) ◽

Cited By ~ 3

Author(s):

Mitali Mishra ◽

Shashank Patole ◽

Harapriya Mohapatra

Keyword(s):

Antibiotic Resistance ◽

Efflux Pump ◽

Draft Genome ◽

Enterobacter Cloacae ◽

Multidrug Resistant ◽

Multiple Antibiotic Resistance ◽

Opportunistic Pathogens ◽

Genome Sequences ◽

Content Type ◽

Therapeutic Drugs

ABSTRACT Enterobacter spp. have been implicated as opportunistic pathogens which over the years have gained resistance toward most of the available therapeutic drugs. We sequenced two multidrug-resistant Enterobacter cloacae isolates harboring multiple efflux pump genes. These isolates exhibited strain-specific modulation of efflux pump protein expression.

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