scholarly journals Genomic diversity of class I integrons from antimicrobial resistant strains of Salmonella Typhimurium isolated from livestock, poultry and humans

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0243477
Author(s):  
Sangeeta Rao ◽  
Lyndsey Linke ◽  
Enrique Doster ◽  
Doreene Hyatt ◽  
Brandy A. Burgess ◽  
...  
Keyword(s):  
Multidrug Resistance ◽  
Antimicrobial Resistance ◽  
Host Species ◽  
Critical Role ◽  
Genomic Diversity ◽  
Class I ◽  
Resistance Pattern ◽  
Human Populations ◽  
High Occurrence ◽  
Class I Integrons

Introduction Multidrug resistance (MDR) is a serious issue prevalent in various agriculture-related foodborne pathogens including Salmonella enterica (S. enterica) Typhimurium. Class I integrons have been detected in Salmonella spp. strains isolated from food producing animals and humans and likely play a critical role in transmitting antimicrobial resistance within and between livestock and human populations. Objective The main objective of our study was to characterize class I integron presence to identify possible integron diversity among and between antimicrobial resistant Salmonella Typhimurium isolates from various host species, including humans, cattle, swine, and poultry. Methods An association between integron presence with multidrug resistance was evaluated. One hundred and eighty-three S. Typhimurium isolates were tested for antimicrobial resistance (AMR). Class I integrons were detected and sequenced. Similarity of AMR patterns between host species was also studied within each integron type. Results One hundred seventy-four (95.1%) of 183 S.Typhimurium isolates were resistant to at least one antimicrobial and 82 (44.8%) were resistant to 5 or more antimicrobials. The majority of isolates resistant to at least one antimicrobial was from humans (45.9%), followed by swine (19.1%) and then bovine (16.9%) isolates; poultry showed the lowest number (13.1%) of resistant isolates. Our study has demonstrated high occurrence of class I integrons in S. Typhimurium across different host species. Only one integron size was detected in poultry isolates. There was a significant association between integron presence of any size and specific multidrug resistance pattern among the isolates from human, bovine and swine. Conclusions Our study has demonstrated a high occurrence of class I integrons of different sizes in Salmonella Typhimurium across various host species and their association with multidrug resistance. This demonstration indicates that multidrug resistant Salmonella Typhimurium is of significant public health occurrence and reflects on the importance of judicious use of antimicrobials among livestock and poultry.

Antimicrobial Resistance of Salmonella enterica Isolates from Bulk Tank Milk and Milk Filters in the United States†

2013 ◽  
Vol 76 (1) ◽  
pp. 18-25 ◽  
Author(s):  
J. S. VAN KESSEL ◽  
J. SONNIER ◽  
S. ZHAO ◽  
J. S. KARNS
Keyword(s):  
Antimicrobial Resistance ◽  
Gel Electrophoresis ◽  
Salmonella Enterica ◽  
Pulsed Field Gel Electrophoresis ◽  
Class I ◽  
Bulk Tank Milk ◽  
Pulsed Field ◽  
Extended Spectrum ◽  
Class I Integrons ◽  
Bulk Tank

Salmonella isolates were recovered from bulk tank milk as part of the National Animal Health Monitoring System (NAHMS) Dairy 2002 and 2007 surveys. In-line milk filters were also tested in the 2007 survey. The objective of this study was to determine the prevalence of antimicrobial resistance among Salmonella enterica isolates from bulk milk and milk filters in the NAHMS Dairy 2002 and 2007 surveys and to further characterize resistant isolates. Susceptibilities to 15 antibiotics were determined for 176 Salmonella isolates of 26 serotypes using an automated antimicrobial susceptibility system. Resistant isolates were screened by PCR for the presence of the extended-spectrum β-lactamase (blaCMY) gene and class I integrons and further characterized by pulsed-field gel electrophoresis. Thirty isolates (17.0%) representing six S. enterica serotypes exhibited resistance to at least one antimicrobial agent (serotypes Newport [14 of 14 isolates exhibited resistance], Dublin [7 of 7], Typhimurium [3 of 5], Kentucky [4 of 22], Anatum [1 of 13], and Infantis [1 of 2]). Twenty isolates (11.4%), including all 14 Newport, 3 Dublin, 2 Typhimurium, and 1 Infantis isolate, displayed the typical multidrug-resistant, blaCMY-positive (MDR-AmpC) phenotype which included resistance to ampicillin, chloramphenicol, streptomycin, sulfonamide, and tetracycline, plus resistance to amoxicillin–clavulanic acid and extended-spectrum cephalosporins. Five of the MDR-AmpC isolates carried class I integrons (2.8%). Two-enzyme (XbaI and BlnI) pulsed-field gel electrophoresis discerned clades within serotypes and, together with the resistance profiles, identified strains that appeared to have persisted temporally and geographically. These results suggest that there is a low but appreciable risk of infection with MDR Salmonella from consumption of nonpasteurized milk and dairy products.

Prevalence of Antimicrobial Resistance in Salmonellae Isolated from Market-Age Swine

2001 ◽  
Vol 64 (10) ◽  
pp. 1496-1502 ◽  
Author(s):  
LEIGH A. FARRINGTON ◽  
ROGER B. HARVEY ◽  
SANDRA A. BUCKLEY ◽  
ROBERT E. DROLESKEY ◽  
DAVID J. NISBET ◽  
...  
Keyword(s):  
Veterinary Medicine ◽  
Lymph Node ◽  
Multidrug Resistance ◽  
Antimicrobial Resistance ◽  
Lymph Nodes ◽  
The Other ◽  
Disk Diffusion ◽  
Penicillin G ◽  
Resistance Testing ◽  
Resistance Pattern

Antimicrobial resistance levels were examined for 365 Salmonella isolates recovered from the lymph nodes (n = 224) and cecal contents (n = 141) of market-age swine at slaughter. Antimicrobial resistance testing was performed by disk diffusion using 13 antibiotics common in the treatment of disease in human and veterinary medicine. Although none of the antibiotics tested were used subtherapeutically within the last 5 years on the farms sampled, resistance to chlortetracycline, penicillin G, streptomycin, and sulfisoxazole was common. Penicillin G resistance was significantly more frequent (P = 0.03) and sulfisoxazole resistance was significantly less frequent (P < 0.01) in lymph node versus cecal isolates. Multidrug resistance was observed among 94.7% of the lymph node isolates and 93.5% of the cecal isolates. The most frequent multidrug resistance pattern included three antibiotics—penicillin G, streptomycin, and chlortetracycline. Isolates in somatic serogroup B, and more specifically, Salmonella Agona and Salmonella Schwarzengrund isolates, were often resistant to a greater number of antibiotics than were isolates in the other serogroups. Streptomycin, sulfisoxazole, ampicillin (lymph node isolates), and nitrofurantoin (cecal isolates) resistance levels differed significantly between somatic serogroups. The prevalence of penicillin G-, streptomycin-, and sulfisoxazole-resistant isolates differed significantly between serovars for both lymph node and cecal isolates. Results of this study suggest that a correlation exists between the somatic serogroup or serovar of a Salmonella isolate and its antimicrobial resistance status, which is specific to the antibiotic of interest and the source of the isolate (lymph node versus cecal contents).

scholarly journals Evolution of Multiresistance in Nontyphoid Salmonella Serovars from 1984 to 1998 in Argentina

2002 ◽  
Vol 46 (12) ◽  
pp. 3963-3970 ◽  
Author(s):  
Betina E. Orman ◽  
Silvia A. Piñeiro ◽  
Sonia Arduino ◽  
Marcelo Galas ◽  
Roberto Melano ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Shigella Flexneri ◽  
Variable Region ◽  
Resistance Mechanisms ◽  
Class I ◽  
Pcr Analysis ◽  
Resistance Determinants ◽  
Serovar Typhimurium ◽  
Class I Integrons

ABSTRACT Molecular evolution of multiresistance in nontyphoid Salmonella spp. was investigated with 155 isolates obtained in Argentina from 1984 to 1998. In 74 isolates obtained from 1984 to 1988 resistance was associated with the presence of Tn3, Tn9, class I (In0) and II (Tn7) integrons, and the aac(3)-IIa gene. Extended-spectrum cephalosporin (ESC) resistance in Salmonella spp. emerged in 1989, and 81 isolates resistant to at least one ESC and one aminoglycoside were collected thereafter. Among these, two patterns of antimicrobial resistance mechanisms were found: from 1989 to 1992, resistance was related to the spreading of Tn1331 and bla CTX-M-2, in addition to the persistence of In0 and Tn7. From 1993 to 1998, several integrons were added to the first pattern and three integron groups (IG), namely, IG1 (38% of the isolates), IG2 (51%), and IG3 (11%), were identified. At least two β-lactamase genes were detected in 65% of the isolates (after 1989) by PCR analysis. Furthermore, five β-lactamase genes, bla CTX-M- 2 , bla OXA-9, bla OXA-2, bla TEM-1, and bla PER-2, were found in two isolates. The bla CTX-M-2 gene was found in several complex sulI-type integrons with different rearrays within the variable region of class I integrons, suggesting evolution of these integrons in nontyphoid Salmonella. In conclusion, progressive acquisition and accumulation of plasmid-mediated resistance determinants occurred from 1984 to 1998 in nontyphoid Salmonella isolates of the most prevalent serovars from Argentina. It is suggested that antimicrobial resistance mechanisms in these bacteria may have been the consequence of plasmid exchange between Salmonella enterica serovar Typhimurium and Escherichia coli or Shigella flexneri and/or spreading of mobile elements from the nosocomial environment.

scholarly journals Genomic diversity of Escherichia coli isolates from non-human primates in the Gambia

2020 ◽  
Vol 6 (9) ◽  
Author(s):  
Ebenezer Foster-Nyarko ◽  
Nabil-Fareed Alikhan ◽  
Anuradha Ravi ◽  
Gaëtan Thilliez ◽  
Nicholas M. Thomson ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Host Species ◽  
Type Species ◽  
The Gambia ◽  
Genomic Diversity ◽  
Multi Drug Resistance ◽  
Erythrocebus Patas ◽  
Content Type ◽  
Link Type

Increasing contact between humans and non-human primates provides an opportunity for the transfer of potential pathogens or antimicrobial resistance between host species. We have investigated genomic diversity and antimicrobial resistance in Escherichia coli isolates from four species of non-human primates in the Gambia: Papio papio (n=22), Chlorocebus sabaeus (n=14), Piliocolobus badius (n=6) and Erythrocebus patas (n=1). We performed Illumina whole-genome sequencing on 101 isolates from 43 stools, followed by nanopore long-read sequencing on 11 isolates. We identified 43 sequence types (STs) by the Achtman scheme (ten of which are novel), spanning five of the eight known phylogroups of E. coli . The majority of simian isolates belong to phylogroup B2 – characterized by strains that cause human extraintestinal infections – and encode factors associated with extraintestinal disease. A subset of the B2 strains (ST73, ST681 and ST127) carry the pks genomic island, which encodes colibactin, a genotoxin associated with colorectal cancer. We found little antimicrobial resistance and only one example of multi-drug resistance among the simian isolates. Hierarchical clustering showed that simian isolates from ST442 and ST349 are closely related to isolates recovered from human clinical cases (differences in 50 and 7 alleles, respectively), suggesting recent exchange between the two host species. Conversely, simian isolates from ST73, ST681 and ST127 were distinct from human isolates, while five simian isolates belong to unique core-genome ST complexes – indicating novel diversity specific to the primate niche. Our results are of planetary health importance, considering the increasing contact between humans and wild non-human primates.

scholarly journals Multidrug Resistance Pattern in Escherichia coli: The Evolving Threat of Antimicrobial Resistance in a Developing Country

2013 ◽  
Vol 140 (suppl 1) ◽  
pp. A045-A045 ◽  
Author(s):  
Anthony Azenabor ◽  
Henrietta N. Igbokwe ◽  
Sanjib Bhattacharyya ◽  
Steve M. Gradus ◽  
Manjeet Khubbar ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Multidrug Resistance ◽  
Antimicrobial Resistance ◽  
Developing Country ◽  
Resistance Pattern

scholarly journals Genomic diversity of Escherichia coli isolates from non-human primates in the Gambia

2020 ◽  
Author(s):  
Ebenezer Foster-Nyarko ◽  
Nabil-Fareed Alikhan ◽  
Anuradha Ravi ◽  
Gaëtan Thilliez ◽  
Nicholas Thomson ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Population Structure ◽  
Antimicrobial Resistance ◽  
Genome Sequencing ◽  
Host Species ◽  
The Gambia ◽  
Genomic Diversity ◽  
Whole Genome ◽  
E Coli ◽  
Sequence Types

AbstractIncreasing contact between humans and non-human primates provides an opportunity for the transfer of potential pathogens or antimicrobial resistance between host species. We have investigated genomic diversity, and antimicrobial resistance in Escherichia coli isolates from four species of non-human primate in the Gambia: Papio papio (n=22), Chlorocebus sabaeus (n=14), Piliocolobus badius (n=6) and Erythrocebus patas (n=1). We performed Illumina whole-genome sequencing on 101 isolates from 43 stools, followed by nanopore long-read sequencing on eleven isolates. We identified 43 sequence types (STs) by the Achtman scheme (ten of which are novel), spanning five of the eight known phylogroups of E. coli. The majority of simian isolates belong to phylogroup B2—characterised by strains that cause human extraintestinal infections—and encode factors associated with extraintestinal disease. A subset of the B2 strains (ST73, ST681 and ST127) carry the pks genomic island, which encodes colibactin, a genotoxin associated with colorectal cancer. We found little antimicrobial resistance and only one example of multi-drug resistance among the simian isolates. Hierarchical clustering showed that simian isolates from ST442 and ST349 are closely related to isolates recovered from human clinical cases (differences in 50 and seven alleles respectively), suggesting recent exchange between the two host species. Conversely, simian isolates from ST73, ST681 and ST127 were distinct from human isolates, while five simian isolates belong to unique core-genome ST complexes—indicating novel diversity specific to the primate niche. Our results are of public health importance, considering the increasing contact between humans and wild non-human primates.Impact statementLittle is known about the population structure, virulence potential and the burden of antimicrobial resistance among Escherichia coli from wild non-human primates, despite increased exposure to humans through the fragmentation of natural habitats. Previous studies, primarily involving captive animals, have highlighted the potential for bacterial exchange between non-human primates and humans living nearby, including strains associated with intestinal pathology. Using multiple-colony sampling and whole-genome sequencing, we investigated the strain distribution and population structure of E. coli from wild non-human primates from the Gambia. Our results indicate that these monkeys harbour strains that can cause extraintestinal infections in humans. We document the transmission of virulent E. coli strains between monkeys of the same species sharing a common habitat and evidence of recent interaction between strains from humans and wild non-human primates. Also, we present complete genome assemblies for five novel sequence types of E. coli.Author notesAll supporting data, code and protocols have been provided within the article or through supplementary data files. Nine supplementary figures and six supplementary files are available with the online version of this article.AbbreviationsExPEC, Extraintestinal pathogenic Escherichia coli; ST, Sequence type; AMR, Antimicrobial resistance; MLST, Multi-locus sequence typing; VFDB, Virulence factors database; SNP, single nucleotide polymorphism; SPRI, Solid phase reversible immobilisation.Data summaryThe raw sequences and polished assemblies from this study are available in the National Center for Biotechnology Information (NCBI) Short Read Archive, under the BioProject accession number PRJNA604701. The full list and characteristics of these strains and other reference strains used in the analyses are presented in Table 1 and Supplementary Files 1-4 (available with the online version of this article).

scholarly journals Salmonella enterica isolates from pasture-raised poultry exhibit antimicrobial resistance and class I integrons

2010 ◽  
Vol 109 (6) ◽  
pp. 1957-1966 ◽  
Author(s):  
S.N. Melendez ◽  
I. Hanning ◽  
J. Han ◽  
R. Nayak ◽  
A.R. Clement ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Salmonella Enterica ◽  
Class I ◽  
Class I Integrons

scholarly journals Antimicrobial Resistance in Enterobacteriaceae Bacteria Causing Infection in Trauma Patients: A 5-Year Experience from a Tertiary Trauma Center

2021 ◽  
Author(s):  
Omika Katoch ◽  
Surbhi Khurana ◽  
Purva Mathur ◽  
Rajesh Malhotra
Keyword(s):  
Multidrug Resistance ◽  
Antimicrobial Resistance ◽  
Trauma Center ◽  
Multiple Drug Resistance ◽  
Tertiary Care ◽  
Capital City ◽  
Resistance Pattern ◽  
Retrospective Data ◽  
Disk Diffusion Test ◽  
Klebsiella Spp

Abstract Introduction Multiple drug resistance emergences among bacteria at an alarming rate worldwide are posing a serious threat to the treatment benefits that have been achieved with antibiotics. This crisis is due to the inappropriate and overuse of existing antibiotics. We evaluated the antimicrobial resistance pattern of Enterobacteriaceae pathogens isolated from intensive care units (ICUs), wards, and outpatient department (OPD) patients. Objectives The aim of the study is to determine the antimicrobial resistance pattern in bacteria of Enterobacteriaceae family. Material and Methods This is a retrospective study conducted at a tertiary care level-1 trauma center in the capital city of India. We collected all the retrospective data of 5 years from the laboratory information system software of the microbiology laboratory. The retrospective data included patients’ details, samples detail, organism’s identification, and their antimicrobial susceptibility testing, done by Vitek2 compact system and disk diffusion test according to each year’s Clinical and Laboratory Standards Institute (CLSI) guidelines. This study included the interpretation of zone diameters and minimum inhibitory concentrations of all isolates according to CLSI guidelines, 2018. Results Among all the Enterobacteriaceae, Klebsiella spp. was the most commonly isolated pathogen, followed by Escherichia coli and Enterobacter spp. in ICUs and wards, while in OPD patients E. coli was the most commonly isolated pathogen, followed by Klebsiella spp. and Enterobacter spp. Enterobacteriaceae isolates remained resistant to all classes of cephalosporins in all settings. In addition, β lactam and β-lactamase inhibitor remained less effective. Carbapenems showed less resistance than quinolones and aminoglycosides. Among the different antimicrobial agents, tigecycline proved most effective in all settings; however, it showed more resistance than other studies. Conclusion Tigecycline proved effective among different multidrug resistance bacteria. Multidrug resistance in bacteria leads to prolonged hospital stays as well as makes the treatment less cost effective. Proper and judicious use of antimicrobials is the need of the hour.

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