Nationwide surveillance of antimicrobial susceptibility of 509 rapidly growing mycobacteria strains isolated from clinical specimens in Japan

AbstractThis study aimed to identify effective treatments against rapidly growing mycobacteria (RGM) infections by investigating the minimum inhibitory concentrations (MIC) of 24 antimicrobial agents and their molecular mechanisms of resistance. In total, 509 clinical RGM isolates were identified by analyzing the sequences of three housekeeping genes (hsp65, rpoB, and sodA), and their susceptibilities to 24 antimicrobial agents were tested. We also performed sequencing analysis of antimicrobial resistance genes (rrl, rrs, gyrA, and gyrB). To identify Mycobacteroides abscessus group subspecies, we performed PCR-based typing and determined the sequevar of erm(41). We identified 15 RGM species, most of which were susceptible to amikacin and linezolid. Among these species, arbekacin and sitafloxacin had the lowest MIC among the same class of antimicrobials. The MIC of rifabutin for M. abscessus subsp. abscessus (MAB) was lower than that for M. abscessus subsp. massiliense (MMA). The proportion of MAB isolates with MIC ≤ 2 mg/L for rifabutin was significantly higher than that of MMA [MAB: 50/178 (28.1%) vs. MMA: 23/130 (17.7%); p = 0.041]. In summary, our study revealed the antimicrobial susceptibility profile of 15 RGM species isolated in Japan and indicated that arbekacin, sitafloxacin, and rifabutin may be possible therapeutic options for RGM infections.

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Nationwide surveillance of antimicrobial susceptibility of 509 rapidly growing mycobacteria strains isolated from clinical specimens in Japan

10.21203/rs.3.rs-269825/v1 ◽

2021 ◽

Author(s):

Keisuke Kamada ◽

Atsushi Yoshida ◽

Shigekazu Iguchi ◽

Yuko Arai ◽

Yutaka Uzawa ◽

...

Keyword(s):

Antimicrobial Susceptibility ◽

Molecular Mechanisms ◽

Antimicrobial Agents ◽

Housekeeping Genes ◽

Sequencing Analysis ◽

Mechanisms Of Resistance ◽

Rapidly Growing Mycobacteria ◽

Antimicrobial Susceptibility Profile ◽

Antimicrobial Resistance Genes ◽

Nationwide Surveillance

Abstract This study aimed to identify effective treatments against rapidly growing mycobacteria (RGM) infections by investigating the minimum inhibitory concentrations (MIC) of 24 antimicrobial agents and their molecular mechanisms of resistance. In total, 509 clinical RGM isolates were identified by analyzing the sequences of three housekeeping genes (hsp65, rpoB, and sodA), and their susceptibilities to 24 antimicrobial agents were tested. We also performed sequencing analysis of antimicrobial resistance genes (rrl, rrs, gyrA, gyrB). To identify Mycobacteroides abscessus group subspecies, we performed PCR-based typing and determined the sequevar of erm(41). We identified 15 RGM species, most of which were susceptible to amikacin and linezolid. Among these species, arbekacin and sitafloxacin had the lowest MIC among the same class of antibiotics. The MIC of rifabutin for M. abscessus subsp. abscessus (MAB) was lower than that for M. abscessus subsp. massiliense (MMA). The number of MAB isolates with MIC ≤ 2 mg/L for rifabutin was significantly higher than that of MMA [MAB: 50/178 (28.1%) vs. MMA: 23/130 (17.7%); p = 0.041]. In summary, our study revealed the antimicrobial susceptibility profile of 15 RGM species isolated in Japan and indicated that arbekacin, sitafloxacin, and rifabutin may be possible therapeutic options for RGM infections.

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Antimicrobial Susceptibility and Mechanisms of Resistance in Shigella and Salmonella Isolates from Children under Five Years of Age with Diarrhea in Rural Mozambique

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01282-08 ◽

2009 ◽

Vol 53 (6) ◽

pp. 2450-2454 ◽

Cited By ~ 43

Author(s):

Inácio Mandomando ◽

Dinis Jaintilal ◽

Maria J. Pons ◽

Xavier Vallès ◽

Mateu Espasa ◽

...

Keyword(s):

Antibiotic Resistance ◽

Nalidixic Acid ◽

Antimicrobial Susceptibility ◽

Molecular Mechanisms ◽

Antimicrobial Agents ◽

Shigella Flexneri ◽

Colorimetric Method ◽

Multidrug Resistant ◽

Mechanisms Of Resistance ◽

First Line

ABSTRACT The antimicrobial susceptibility and mechanisms of resistance of 109 Shigella and 40 Salmonella isolates from children with diarrhea in southern Mozambique were assessed. The susceptibility to seven antimicrobial agents was tested by disk diffusion, and mechanisms of resistance were searched by PCR or colorimetric method. A high proportion of Shigella isolates were resistant to chloramphenicol (Chl) (52%), ampicillin (Amp) (56%), tetracycline (Tet) (66%), and trimethoprim-sulfamethoxazole (Sxt) (84%). Sixty-five percent of the isolates were multidrug resistant. Shigella flexneri isolates were more resistant than those of Shigella sonnei to Amp (66% versus 0.0%, P < 0.001) and Chl (61% versus 0.0%, P < 0.001), whereas S. sonnei isolates presented higher resistance to Tet than S. flexneri isolates (93% versus 64%, P = 0.02). Resistance among Salmonella isolates was as follows: Tet and Chl, 15% each; Sxt, 18%; and Amp, 25%. Only 3% of Salmonella isolates were resistant to nalidixic acid (Nal), and none to ciprofloxacin or ceftriaxone (Cro). Among Salmonella isolates, multiresistance was found in 23%. Among Shigella isolates, antibiotic resistance was related mainly to the presence of oxa-1-like β-lactamases for Amp, dfrA1 genes for Sxt, tetB genes for Tet, and Chl acetyltransferase (CAT) activity for Chl. Among Salmonella isolates, resistance was conferred by tem-like β-lactamases for Amp, floR genes and CAT activity for Chl, tetA genes for Tet, and dfrA1 genes for Sxt. Our data show that Shigella isolates are resistant mostly to the most available, inexpensive antibiotics by various molecular mechanisms but remain susceptible to ciprofloxacin, Cro, and Nal, which is the first line for empirical treatment of shigellosis in the country.

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Antimicrobial susceptibility profile of enterobacteria isolated from wild grey-breasted parakeets (Pyrrhura griseipectus)

Pesquisa Veterinária Brasileira ◽

10.1590/1678-5150-pvb-6696 ◽

2021 ◽

Vol 41 ◽

Author(s):

Antonio Jackson F. Beleza ◽

William Cardoso Maciel ◽

Arianne S. Carreira ◽

Adson R. Marques ◽

Fabio P. Nunes ◽

...

Keyword(s):

Antibiotic Resistance ◽

Multidrug Resistance ◽

Antimicrobial Susceptibility ◽

Endemic Species ◽

Antimicrobial Agents ◽

Bacterial Species ◽

Cloacal Swab ◽

Illegal Trade ◽

Hafnia Alvei ◽

Antimicrobial Susceptibility Profile

ABSTRACT: The grey-breasted parakeet (Pyrrhura griseipectus) is an endangered psittacine species that have been affected by illegal trade and deforestation. Currently, this endemic species is only found in three areas in Ceará state, in Brazil. This study aimed to investigate the frequency and diversity of Enterobacteriaceae in wild adult grey-breasted parakeets and determine their susceptibility to antimicrobial agents. Cloacal swab samples were collected from 27 individuals and environmental swabs (drag swabs) from five nests used by these birds. Twenty-seven strains from nine species of Enterobacteriaceae were recovered from cloacal swabs, and the most prevalent bacteria strains were Hafnia alvei (22%) and Pantoea agglomerans (22%). From environmental nest samples, seven strains from three bacterial species were isolated, being the P. agglomerans the most frequent species (100%). Twenty-two of the 27 isolates (81.4%) exhibited antibiotic resistance, varying from one to eight of the 12 antimicrobials commonly used. Resistance to amoxicillin was the most prevalent (70.4%), followed by azithromycin (22.2%) and ceftriaxone (18.5%). None of the strains were resistant to gentamicin, tobramycin, ciprofloxacin or tetracycline. The H. alvei was the main species presenting multidrug resistance, including resistance against meropenem, which is an important finding. These results could provide interesting information on the health of these endangered wild grey-breasted parakeets. They could also indicate that the obtained isolates are part of a group of bacteria that are typical components of the enteric microbiota of birds, which present elevated rates of resistance to amoxicillin.

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Genomic analysis reveals fifty years of antimicrobial resistance evolution in husbandry Escherichia coli from China

10.21203/rs.3.rs-484138/v1 ◽

2021 ◽

Author(s):

Lu Yang ◽

Yingbo Shen ◽

Junyao Jiang ◽

Xueyang Wang ◽

Dongyan Shao ◽

...

Keyword(s):

Escherichia Coli ◽

Antimicrobial Resistance ◽

Large Scale ◽

Antimicrobial Agents ◽

Bacterial Genome ◽

Careful Consideration ◽

Meat Production ◽

Antimicrobial Use ◽

Sequencing Analysis ◽

Antimicrobial Resistance Genes

Abstract Antimicrobial agents have been used in meat production for decades and its consumption is considered an key driver for the emergence and dissemination of antimicrobial resistance (AMR). However, large-scale studies on AMR changes in animal isolates since the introduction of antimicrobial usage remain scarce. We applied whole genome sequencing analysis to 982 animal-derived Escherichia coli collected in China from 1970s to 2019 and found increasing trends for the presence of numerous antimicrobial resistance genes (ARGs), including those conferring resistance to critically important agents for veterinary (florfenicol and norfloxacin) and human medicine (colistin, cephalosporins, and meropenem). Extensive diversity and increasing complexity of ARGs and their associated mobile genetic elements (MGEs) such as plasmids were also observed. The plasmids, IncC, IncHI2, IncK, IncI, IncX and IncF played a key role as highly effective vehicles for disseminating ARGs. Correlation analysis also revealed an association between antimicrobial production and emergence of ARGs at a spatial and temporal level. Prohibiting or strictly curtailing antimicrobial use in animals will potentially negate the current trends of AMR as the bacterial genome is highly changeable and using different drugs of the same class, or even unrelated classes, may co-select for MGEs carrying a plethora of co-existing ARGs. Therefore, limiting or ceasing antimicrobial use in animals to control AMR requires careful consideration.

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Antimicrobial Resistance Genes in Porcine Pasteurella multocida Are Not Associated with Its Antimicrobial Susceptibility Pattern

Antibiotics ◽

10.3390/antibiotics9090614 ◽

2020 ◽

Vol 9 (9) ◽

pp. 614

Author(s):

Máximo Petrocchi-Rilo ◽

César-B. Gutiérrez-Martín ◽

Esther Pérez-Fernández ◽

Anna Vilaró ◽

Lorenzo Fraile ◽

...

Keyword(s):

Resistance Genes ◽

Antimicrobial Susceptibility ◽

Pasteurella Multocida ◽

Antimicrobial Agents ◽

Tetracycline Resistance ◽

Susceptibility Pattern ◽

Antimicrobial Susceptibility Pattern ◽

Tetracycline Resistance Genes ◽

Antimicrobial Resistance Genes ◽

Western Spain

Forty-eight Pasteurella multocida isolates were recovered from porcine pneumonic lungs collected from farms in “Castilla y León” (north-western Spain) in 2017–2019. These isolates were characterized for their minimal inhibition concentrations to twelve antimicrobial agents and for the appearance of eight resistance genes: tetA, tetB, blaROB1, blaTEM, ermA, ermC, mphE and msrE. Relevant resistance percentages were shown against tetracyclines (52.1% for doxycycline, 68.7% for oxytetracycline), sulphamethoxazole/trimethoprim (43.7%) and tiamulin (25.0%), thus suggesting that P. multocida isolates were mostly susceptible to amoxicillin, ceftiofur, enrofloxacin, florfenicol, marbofloxacin and macrolides. Overall, 29.2% of isolates were resistant to more than two antimicrobials. The tetracycline resistance genes (tetA and tetB) were detected in 22.9% of the isolates, but none were positive to both simultaneously; blaROB1 and blaTEM genes were found in one third of isolates but both genes were detected simultaneously in only one isolate. The ermC gene was observed in 41.7% of isolates, a percentage that decreased to 22.9% for msrE; finally, ermA was harbored by 16.7% and mphE was not found in any of them. Six clusters were established based on hierarchical clustering analysis on antimicrobial susceptibility for the twelve antimicrobials. Generally, it was unable to foresee the antimicrobial susceptibility pattern for each family and the association of each particular isolate inside the clusters established from the presence or absence of the resistance genes analyzed.

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Mechanism of Resistance to Several Antimicrobial Agents in Salmonella Clinical Isolates Causing Traveler's Diarrhea

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.48.10.3934-3939.2004 ◽

2004 ◽

Vol 48 (10) ◽

pp. 3934-3939 ◽

Cited By ~ 34

Author(s):

Roberto Cabrera ◽

Joaquím Ruiz ◽

Francesc Marco ◽

Inés Oliveira ◽

Margarita Arroyo ◽

...

Keyword(s):

Amino Acid ◽

Antimicrobial Resistance ◽

Nalidixic Acid ◽

Molecular Mechanisms ◽

Antimicrobial Agents ◽

Mechanisms Of Resistance ◽

Traveler’S Diarrhea ◽

Genes Encoding ◽

Dihydrofolate Reductases ◽

Traveler's Diarrhea

ABSTRACT The evolution of antimicrobial resistance in Salmonella isolates causing traveler's diarrhea (TD) and their mechanisms of resistance to several antimicrobial agents were analyzed. From 1995 to 2002, a total of 62 Salmonella strains were isolated from stools of patients with TD. The antimicrobial susceptibility to 12 antibiotics was determined, and the molecular mechanisms of resistance to several of them were detected as well. The highest levels of resistance were found against tetracycline and ampicillin (21 and 19%, respectively), followed by resistance to nalidixic acid (16%), which was mainly detected from 2000 onward. Molecular mechanisms of resistance were analyzed in 16 isolates. In these isolates, which were resistant to ampicillin, two genes encoding β-lactamases were detected: oxa-1 (one isolate) and tem-like (seven isolates [in one strain concomitantly with a carb-2]). Resistance to tetracycline was mainly related to tetA (five cases) and to tetB and tetG (one case each). Resistance to chloramphenicol was related to the presence of the floR and cmlA genes and to chloramphenicol acetyltransferase activity in one case each. Different genes encoding dihydrofolate-reductases (dfrA1, dfrA12, dfrA14, and dfrA17) were detected in trimethoprim-resistant isolates. Resistance to nalidixic acid was related to the presence of mutations in the amino acid codons 83 or 87 of the gyrA gene. Further surveillance of the Salmonella spp. causing TD is needed to detect trends in their resistance to antimicrobial agents, as we have shown in our study with nalidixic acid. Moreover, such studies will lead to better treatment and strategies to prevent and limit their spread.

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The Antimicrobial Susceptibility of Porphyromonas gingivalis: Genetic Repertoire, Global Phenotype, and Review of the Literature

Antibiotics ◽

10.3390/antibiotics10121438 ◽

2021 ◽

Vol 10 (12) ◽

pp. 1438

Author(s):

Georg Conrads ◽

Tim Klomp ◽

Dongmei Deng ◽

Johannes-Simon Wenzler ◽

Andreas Braun ◽

...

Keyword(s):

Porphyromonas Gingivalis ◽

Resistance Genes ◽

Antimicrobial Susceptibility ◽

Rural Areas ◽

Antimicrobial Agents ◽

International Standards ◽

Periodontal Pathogen ◽

International Studies ◽

Antimicrobial Resistance Genes ◽

Amoxicillin Clavulanate

The in vitro antimicrobial susceptibility of 29 strains of the major periodontal pathogen Porphyromonas gingivalis and three P. gulae (as an ancestor) to nine antibiotics (amoxicillin, amoxicillin/clavulanate, clindamycin, metronidazole, moxifloxacin, doxycycline, azithromycin, imipenem, and cefoxitin) was evaluated by E-testing of minimal inhibitory concentration (MIC) according to international standards. The results were compared with 16 international studies reporting MICs from 1993 until recently. In addition, 77 currently available P. gingivalis genomes were screened for antimicrobial resistance genes. E-testing revealed a 100% sensitivity of P. gingivalis and P. gulae to all antibiotics. This was independent of the isolation year (1970 until 2021) or region, including rural areas in Indonesia and Africa. Regarding studies worldwide (675 strains), several method varieties regarding medium, McFarland inoculation standards (0.5–2) and incubation time (48–168 h) were used for MIC-testing. Overall, no resistances have been reported for amoxicillin + clavulanate, cefoxitin, and imipenem. Few strains showed intermediate susceptibility or resistance to amoxicillin and metronidazole, with the latter needing both confirmation and attention. The only antibiotics which might fail in the treatment of P. gingivalis-associated mixed anaerobic infections are clindamycin, macrolides, and tetracyclines, corresponding to the resistance genes erm(B), erm(F), and tet(Q) detected in our study here, as well as fluoroquinolones. Periodical antibiotic susceptibility testing is necessary to determine the efficacy of antimicrobial agents and to optimize antibiotic stewardship.

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Antimicrobial Susceptibility Profile of Extended Spectrum Beta- lactamases Producing Enterobacteriaceae isolated from clinical samples refereed to the National Bacteriology and Mycology Reference Laboratory, Ethiopia

10.21203/rs.2.20224/v1 ◽

2020 ◽

Author(s):

Abebe Aseffa Negeri ◽

Eyasu Tigabu Seyoum ◽

Dejenie Shiferaw Taklu ◽

Estifanos Tsige ◽

Dawit Assefa ◽

...

Keyword(s):

Antimicrobial Susceptibility ◽

Antimicrobial Agents ◽

Multidrug Resistant ◽

Clinical Samples ◽

Reference Laboratory ◽

Beta Lactamases ◽

E Coli ◽

Antimicrobial Susceptibility Profile ◽

Extended Spectrum Beta Lactamases ◽

Culture Positive

Abstract Background Extended-spectrum beta-lactamases (ESBL) producing Enterobacteriaceae are prevalent worldwide and they are unique challenges for treatment and control of bacterial infectious diseases. ESBL genes not only confer resistance to oximino-cephalosporins and aztreonum but also, they are multidrug-resistant to other commonly available antimicrobial agents used in clinical practice.Objective To determine the prevalence and antimicrobial susceptibility profile of ESBL producing Enterobacteriaceae isolated from clinical samples referred to the national clinical bacteriology and mycology reference laboratory.Materials and Methods A cross-sectional study was conducted on Enterobacteriaceae culture- positive clinical samples that were referred to the national bacteriology and mycology reference laboratory from August 2018 to July 2019. Bacterial isolation was performed according to the inoculation and incubation conditions of each clinical specimen and identifications of the isolates were performed using standardized biochemical tests for gram-negative bacteria. Antimicrobial susceptibility profiles of these cultures were determined using the disk diffusion method on Muller Hinton agar according to the recommendation by Clinical and Laboratory Standard Institute (CLSI). ESBL production was detected using CLSI Screening and confirmation test. A double-disk synergy test was used for confirmation.Results Out of 371 culture positive for Enterobacteriaceae , 240 (64.7%) were positive for ESBL production, and the most prevalent species were Klebsiella sp 131(54.6%) followed by E. coli 79 (32.9%). Of 131 ESBL positive Klebsiella spp, 95 (72.5%) were obtained from blood samples and among 79 E. coli isolates, 51 (64.6%) of the strains were isolated from urine samples. All ESBL positive isolates were resistant to ampicillin and all generation of cephalosporins. In addition, 100% of them were multidrug resistant. There were also high proportions of resistant ESBL positive isolates to other classes of antimicrobial agents. Less resistance rates were documented for carbapenems drugs and amikacin from the class of aminoglycosides.Conclusion ESBL producing Enterobacteriaceae we reported in this study was not only highly prevalent but also they are multidrug resistant to most clinically available antimicrobial agents including carbapenems. Therefore, public awareness and regular monitoring

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Antimicrobial Resistance Genes Associated with Salmonella enterica Serovar Newport Isolates from Food Animals

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00842-07 ◽

2007 ◽

Vol 52 (1) ◽

pp. 353-356 ◽

Cited By ~ 26

Author(s):

Aaron M. Lynne ◽

Bobbie S. Rhodes-Clark ◽

Kimberly Bliven ◽

Shaohua Zhao ◽

Steven L. Foley

Keyword(s):

Antimicrobial Resistance ◽

Resistance Genes ◽

Salmonella Enterica ◽

Genetic Basis ◽

Antimicrobial Agents ◽

Multiple Resistance ◽

Sequencing Analysis ◽

Antimicrobial Resistance Genes ◽

Dna Sequencing Analysis ◽

Multiple Resistance Genes

ABSTRACT Salmonella enterica serotype Newport is an important cause of salmonellosis, with strains increasingly being resistant to multiple antimicrobial agents. The increase is associated with the acquisition of multiple resistance genes. This study characterizes the genetic basis of resistance of serotype Newport isolates collected from veterinary sources by PCR and DNA sequencing analysis.

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Identification, Genotyping and Antimicrobial Susceptibility Testing of Brucella spp. Isolated from Livestock in Egypt

Microorganisms ◽

10.3390/microorganisms7120603 ◽

2019 ◽

Vol 7 (12) ◽

pp. 603 ◽

Cited By ~ 3

Author(s):

Aman Ullah Khan ◽

Waleed S. Shell ◽

Falk Melzer ◽

Ashraf E. Sayour ◽

Eman Shawkat Ramadan ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Antimicrobial Susceptibility ◽

Molecular Mechanisms ◽

Antimicrobial Agents ◽

Susceptibility Testing ◽

Brucella Melitensis ◽

Rpob Gene ◽

Antimicrobial Susceptibility Testing ◽

Animal Populations ◽

Microbiological Methods

Brucellosis is a highly contagious zoonosis worldwide with economic and public health impacts. The aim of the present study was to identify Brucella (B.) spp. isolated from animal populations located in different districts of Egypt and to determine their antimicrobial resistance. In total, 34-suspected Brucella isolates were recovered from lymph nodes, milk, and fetal abomasal contents of infected cattle, buffaloes, sheep, and goats from nine districts in Egypt. The isolates were identified by microbiological methods and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). Differentiation and genotyping were confirmed using multiplex PCR for B. abortus, Brucella melitensis, Brucella ovis, and Brucella suis (AMOS) and Bruce-ladder PCR. Antimicrobial susceptibility testing against clinically used antimicrobial agents (chloramphenicol, ciprofloxacin, erythromycin, gentamicin, imipenem, rifampicin, streptomycin, and tetracycline) was performed using E-Test. The antimicrobial resistance-associated genes and mutations in Brucella isolates were confirmed using molecular tools. In total, 29 Brucella isolates (eight B. abortus biovar 1 and 21 B. melitensis biovar 3) were identified and typed. The resistance of B. melitensis to ciprofloxacin, erythromycin, imipenem, rifampicin, and streptomycin were 76.2%, 19.0%, 76.2%, 66.7%, and 4.8%, respectively. Whereas, 25.0%, 87.5%, 25.0%, and 37.5% of B. abortus were resistant to ciprofloxacin, erythromycin, imipenem, and rifampicin, respectively. Mutations in the rpoB gene associated with rifampicin resistance were identified in all phenotypically resistant isolates. Mutations in gyrA and gyrB genes associated with ciprofloxacin resistance were identified in four phenotypically resistant isolates of B. melitensis. This is the first study highlighting the antimicrobial resistance in Brucella isolated from different animal species in Egypt. Mutations detected in genes associated with antimicrobial resistance unravel the molecular mechanisms of resistance in Brucella isolates from Egypt. The mutations in the rpoB gene in phenotypically resistant B. abortus isolates in this study were reported for the first time in Egypt.

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