Distribution of carbapenem resistance determinants among epidemic and non-epidemic types of Acinetobacter species in Japan

We performed a comparative molecular analysis on three types of clinically isolated Acinetobacter spp.: epidemic sequence types (STs) of Acinetobacter baumannii (epidemic ST-AB), non-epidemic sequence types of A. baumannii (non-epidemic ST-AB) and non-baumannii Acinetobacter spp. A total of 87 isolates – 46 A. baumannii, 25 A. pittii and 16 A. nosocomialis – from 43 hospitals were analysed. Of these, 31 A. baumannii isolates were ST1 or ST2 according to the Pasteur Institute multilocus sequence typing scheme and were defined as epidemic ST-AB. The other 15 A. baumannii isolates were defined as non-epidemic ST-AB. The epidemic ST-AB isolates harboured the bla OXA-23-like gene or had an ISAba1 element upstream of bla OXA-51-like, or both, whereas non-epidemic ST-AB and non-baumannii Acinetobacter spp. isolates harboured bla OXA-58-like or metallo-β-lactamase genes, or both. The proportion of multidrug-resistant isolates was significantly higher in the epidemic ST-AB isolates (48 %) than that in the other types of Acinetobacter isolates (5 %) (P<0.05). In addition, epidemic ST-AB isolates exhibited a relatively higher proportion of fluoroquinolone resistance. We demonstrated that, in terms of genotypes and phenotypes of antimicrobial resistance, non-epidemic ST-AB isolates shared more similarity with non-baumannii Acinetobacter spp. isolates than with epidemic ST-AB isolates, regardless of bacterial species. In addition, this study revealed that, even in Japan, where IMP-type metallo-β-lactamase producers are endemic, epidemic ST-AB harbouring bla IMP have not yet emerged.

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A species-wide genetic atlas of antimicrobial resistance in Clostridioides difficile

10.1101/2021.06.14.448453 ◽

2021 ◽

Author(s):

Korakrit Imwattana ◽

César Rodríguez ◽

Thomas V Riley ◽

Daniel R Knight

Keyword(s):

Antimicrobial Resistance ◽

Strong Association ◽

Tetracycline Resistance ◽

Multidrug Resistant ◽

Fluoroquinolone Resistance ◽

Drug Resistant ◽

Genomic Epidemiology ◽

Clostridioides Difficile ◽

Geographical Regions ◽

Sequence Types

Antimicrobial resistance (AMR) plays an important role in the pathogenesis and spread of Clostridioides difficile infection (CDI), the leading healthcare-related gastrointestinal infection in the world. An association between AMR and CDI outbreaks is well documented, however, data is limited to a few 'epidemic' strains in specific geographical regions. Here, through detailed analysis of 10,330 publicly-available C. difficile genomes from strains isolated worldwide (spanning 270 multilocus sequence types (STs) across all known evolutionary clades), this study provides the first species-wide snapshot of AMR genomic epidemiology in C. difficile. Of the 10,330 C. difficile genomes, 4,532 (43.9%) in 89 STs across clades 1 - 5 carried at least one genotypic AMR determinants, with 901 genomes (8.7%) carrying AMR determinants for three or more antimicrobial classes (multidrug-resistant, MDR). No AMR genotype was identified in any strains belonging to the cryptic clades. C. difficile from Australia/New Zealand had the lowest AMR prevalence compared to strains from Asia, Europe and North America (p<0.0001). Based on the phylogenetic clade, AMR prevalence was higher in clades 2 (84.3%), 4 (81.5%) and 5 (64.8%) compared to other clades (collectively 26.9%) (p<0.0001). MDR prevalence was highest in clade 4 (61.6%) which was over three times higher than in clade 2, the clade with the second-highest MDR prevalence (18.3%). There was a strong association between specific AMR determinants and three major epidemic C. difficile STs: ST1 (clade 2) with fluoroquinolone resistance (mainly T82I substitution in GyrA) (p<0.0001), ST11 (clade 5) with tetracycline resistance (various tet-family genes) (p<0.0001) and ST37 (clade 4) with macrolide-lincosamide-streptogramin B (MLSB) resistance (mainly ermB) (p<0.0001) and MDR (p<0.0001). A novel and previously overlooked tetM-positive transposon termed Tn6944 was identified, predominantly among clade 2 strains. This study provides a comprehensive review of AMR in the global C. difficile population which may help in the early detection of drug-resistant C. difficile strains, and prevention of spread world-wide.

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Need for Annual Surveillance of Antimicrobial Resistance in Streptococcus pneumoniae in the United States: 2-Year Longitudinal Analysis

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.45.4.1037-1042.2001 ◽

2001 ◽

Vol 45 (4) ◽

pp. 1037-1042 ◽

Cited By ~ 94

Author(s):

Daniel F. Sahm ◽

James A. Karlowsky ◽

Laurie J. Kelly ◽

Ian A. Critchley ◽

Mark E. Jones ◽

...

Keyword(s):

United States ◽

Streptococcus Pneumoniae ◽

Antimicrobial Resistance ◽

Antimicrobial Agents ◽

The United States ◽

Multidrug Resistant ◽

Fluoroquinolone Resistance ◽

Resistance Patterns ◽

Changing Patterns ◽

Resistance To Penicillin

ABSTRACT Although changing patterns in antimicrobial resistance inStreptococcus pneumoniae have prompted several surveillance initiatives in recent years, the frequency with which these studies are needed has not been addressed. To approach this issue, the extent to which resistance patterns change over a 1-year period was examined. In this study we analyzed S. pneumoniaeantimicrobial susceptibility results produced in our laboratory with isolates obtained over 2 consecutive years (1997–1998 and 1998–1999) from the same 96 institutions distributed throughout the United States. Comparison of results revealed increases in resistant percentages for all antimicrobial agents studied except vancomycin. For four of the agents tested (penicillin, cefuroxime, trimethoprim-sulfamethoxazole, and levofloxacin), the increases were statistically significant (P < 0.05). Resistance to the fluoroquinolone remained low in both years (0.1 and 0.6%, respectively); in contrast, resistance to macrolides was consistently greater than 20%, and resistance to trimethoprim-sulfamethoxazole increased from 13.3 to 27.3%. Multidrug resistance, concurrent resistance to three or more antimicrobials of different chemical classes, also increased significantly between years, from 5.9 to 11%. The most prevalent phenotype was resistance to penicillin, azithromycin (representative macrolide), and trimethoprim-sulfamethoxazole. Multidrug-resistant phenotypes that included fluoroquinolone resistance were uncommon; however, two phenotypes that included fluoroquinolone resistance not found in 1997–1998 were encountered in 1998–1999. This longitudinal surveillance study of resistance inS. pneumoniae revealed that significant changes do occur in just a single year and supports the need for surveillance at least on an annual basis, if not continuously.

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First description of NDM-1-, KPC-2-, VIM-2- and IMP-4-producing Klebsiella pneumoniae strains in a single Chinese teaching hospital

Epidemiology and Infection ◽

10.1017/s0950268814000995 ◽

2014 ◽

Vol 143 (2) ◽

pp. 376-384 ◽

Cited By ~ 27

Author(s):

Y. LIU ◽

L.-G. WAN ◽

Q. DENG ◽

X.-W. CAO ◽

Y. YU ◽

...

Keyword(s):

16S Rrna ◽

Klebsiella Pneumoniae ◽

Teaching Hospital ◽

Multidrug Resistant ◽

The Other ◽

Quinolone Resistance ◽

Resistance Determinants ◽

Carbapenem Resistant ◽

Extended Spectrum ◽

Chinese Teaching

SUMMARYA total of 180 non-duplicate carbapenem-resistant Klebsiella pneumoniae isolates were recovered from patients hospitalized between December 2010 and January 2012 at a Chinese hospital. Eight KPC-2, four NDM-1, one VIM-2, and five KPC-2 plus IMP-4 producers were identified and all were multidrug resistant due to the presence of other resistance determinants, including extended-spectrum β-lactamases (CTX-M-15, SHV-12), 16S rRNA methylases (armA, rmtB) and plasmid-mediated quinolone-resistance determinants (qnrA, B, S, aac(6′)-Ib-cr). Nine K. pneumoniae clones (Kpn-A1/ST395, Kpn-A3/ST11, Kpn-A2/ST134, Kpn-B/ST263, Kpn-C/ST37, Kpn-D/ST39, Kpn-E/ST1151, Kpn-F/ST890, Kpn-G/ST1153) were identified. blaKPC-2 was located on transferable ~65 kb IncL/M (ST395, ST11, ST134, ST39) and ~100 kb IncA/C (ST37, ST1153, ST890) plasmids, respectively. On the other hand, blaNDM-1 was associated with a ~70 kb IncA/C plasmid (ST263). However, non-typable plasmids of ~40 kb containing blaVIM-2 were detected in the ST1151 clone. This work reports the first co-occurrence of four diverse types of carbapenemase of K. pneumoniae clones from a single hospital in China. IncA/C, IncL/M, and other successful plasmids may be important for the dissemination of carbapenemases, producing a complex epidemiological picture.

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Distribution and Antimicrobial Resistance of Salmonella Isolated from Pigs with Diarrhea in China

Microorganisms ◽

10.3390/microorganisms6040117 ◽

2018 ◽

Vol 6 (4) ◽

pp. 117 ◽

Cited By ~ 10

Author(s):

Jin-Hui Su ◽

Yao-Hong Zhu ◽

Tian-Yi Ren ◽

Liang Guo ◽

Gui-Yan Yang ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Metal Tolerance ◽

Heavy Metal Tolerance ◽

Clonal Expansion ◽

Multidrug Resistant ◽

High Similarity ◽

Enteric Diseases ◽

Antimicrobial Resistance Genes ◽

Wide Range ◽

Sequence Types

Salmonella can cause enteric diseases in humans and a wide range of animals, and even outbreaks of foodborne illness. The aim of this study was to investigate the frequency and distribution of serovars, and antimicrobial resistance in Salmonella isolates from pigs with diarrhea in 26 provinces in China from 2014 to 2016. A total of 104 Salmonella isolates were identified and the dominant serovar was S. 4,[5],12:i:- (53.9%). All Salmonella isolates were resistant to trimethoprim-sulfamethoxazole, and many were resistant to ampicillin (80.8%) and tetracycline (76.9%). Among 104 Salmonella isolates, aac(6′)-Ib-cr was the dominant plasmid-mediated quinolone resistance gene (80.8%), followed by qnrS (47.1%). The pulsed-field gel electrophoresis results suggest that the Salmonella isolates from different regions were genetically diverse, and ST34 was the most prevalent. S. 4,[5],12:i:- isolates is the widespread presence of heavy metal tolerance genes. The fact that the same sequence types were found in different regions and the high similarity coefficient of S. 4,[5],12:i:- isolates from different regions indicate the clonal expansion of the isolates, and the isolates carried various antimicrobial resistance genes. The multidrug resistant Salmonella can be widely detected in pigs, which will present a challenge for farm husbandry.

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Population genomics and antimicrobial resistance in Corynebacterium diphtheriae

Genome Medicine ◽

10.1186/s13073-020-00805-7 ◽

2020 ◽

Vol 12 (1) ◽

Author(s):

Melanie Hennart ◽

Leonardo G. Panunzi ◽

Carla Rodrigues ◽

Quentin Gaday ◽

Sarah L. Baines ◽

...

Keyword(s):

Soviet Union ◽

Antimicrobial Resistance ◽

Diphtheria Toxin ◽

Population Genomics ◽

Bacterial Species ◽

Toxin Production ◽

Multidrug Resistant ◽

Corynebacterium Diphtheriae ◽

Toxin Gene ◽

Phylogenetic Structure

Abstract Background Corynebacterium diphtheriae, the agent of diphtheria, is a genetically diverse bacterial species. Although antimicrobial resistance has emerged against several drugs including first-line penicillin, the genomic determinants and population dynamics of resistance are largely unknown for this neglected human pathogen. Methods Here, we analyzed the associations of antimicrobial susceptibility phenotypes, diphtheria toxin production, and genomic features in C. diphtheriae. We used 247 strains collected over several decades in multiple world regions, including the 163 clinical isolates collected prospectively from 2008 to 2017 in France mainland and overseas territories. Results Phylogenetic analysis revealed multiple deep-branching sublineages, grouped into a Mitis lineage strongly associated with diphtheria toxin production and a largely toxin gene-negative Gravis lineage with few toxin-producing isolates including the 1990s ex-Soviet Union outbreak strain. The distribution of susceptibility phenotypes allowed proposing ecological cutoffs for most of the 19 agents tested, thereby defining acquired antimicrobial resistance. Penicillin resistance was found in 17.2% of prospective isolates. Seventeen (10.4%) prospective isolates were multidrug-resistant (≥ 3 antimicrobial categories), including four isolates resistant to penicillin and macrolides. Homologous recombination was frequent (r/m = 5), and horizontal gene transfer contributed to the emergence of antimicrobial resistance in multiple sublineages. Genome-wide association mapping uncovered genetic factors of resistance, including an accessory penicillin-binding protein (PBP2m) located in diverse genomic contexts. Gene pbp2m is widespread in other Corynebacterium species, and its expression in C. glutamicum demonstrated its effect against several beta-lactams. A novel 73-kb C. diphtheriae multiresistance plasmid was discovered. Conclusions This work uncovers the dynamics of antimicrobial resistance in C. diphtheriae in the context of phylogenetic structure, biovar, and diphtheria toxin production and provides a blueprint to analyze re-emerging diphtheria.

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Complete Genome Sequence of Acinetobacter radioresistens Strain LH6, a Multidrug-Resistant Bacteriophage-Propagating Strain

Microbiology Resource Announcements ◽

10.1128/mra.00929-18 ◽

2018 ◽

Vol 7 (5) ◽

Cited By ~ 2

Author(s):

Clay S. Crippen ◽

Steven Huynh ◽

William G. Miller ◽

Craig T. Parker ◽

Christine M. Szymanski

Keyword(s):

Antimicrobial Resistance ◽

Acinetobacter Baumannii ◽

Genome Sequence ◽

Complete Genome Sequence ◽

Related Species ◽

Complete Genome ◽

Multidrug Resistant ◽

Drug Resistant ◽

Content Type ◽

Resistance Determinants

Antimicrobial resistance is a major problem worldwide. Understanding the interplay between drug-resistant pathogens, such as Acinetobacter baumannii and related species, potentially acting as environmental reservoirs is critical for preventing the spread of resistance determinants.

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Genome Sequences of Multidrug-Resistant Salmonella enterica Serovar Dublin Isolates

Microbiology Resource Announcements ◽

10.1128/mra.00698-19 ◽

2019 ◽

Vol 8 (31) ◽

Author(s):

Baha Abdalhamid ◽

Emily L. Mccutchen ◽

Kacie D. Flaherty ◽

Steven H. Hinrichs ◽

Peter C. Iwen

Keyword(s):

Antimicrobial Resistance ◽

Salmonella Enterica ◽

Draft Genome ◽

Multidrug Resistant ◽

Genome Sequences ◽

Content Type ◽

Resistance Determinants ◽

Human Samples ◽

Systemic Infections ◽

Salmonella Enterica Serovar Dublin

Salmonella enterica serovar Dublin, which can cause enteritis and systemic infections in humans, has been associated with antimicrobial resistance. Here, we report draft genome sequences of seven multidrug-resistant S. Dublin isolates from human samples. These sequences will contribute to an understanding of pathogenesis and resistance determinants in this serovar.

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OXA-24 Carbapenemase Gene Flanked by XerC/XerD-Like Recombination Sites in Different Plasmids from Different Acinetobacter Species Isolated during a Nosocomial Outbreak

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01674-09 ◽

2010 ◽

Vol 54 (6) ◽

pp. 2724-2727 ◽

Cited By ~ 73

Author(s):

María Merino ◽

Joshi Acosta ◽

Margarita Poza ◽

Francisca Sanz ◽

Alejandro Beceiro ◽

...

Keyword(s):

Horizontal Transmission ◽

Carbapenem Resistance ◽

Acinetobacter Calcoaceticus ◽

Multidrug Resistant ◽

Clinical Strain ◽

Acinetobacter Species ◽

Gene Comparison ◽

Carbapenemase Gene ◽

Large Outbreak ◽

Culture Sample

ABSTRACT A clinical strain of Acinetobacter calcoaceticus resistant to carbapenems was isolated from a blood culture sample from an inpatient in a hospital in Madrid (Spain) during a large outbreak of infection (affecting more than 300 inpatients), caused by a multidrug-resistant Acinetobacter baumannii clone. The carbapenem resistance in both the A. calcoaceticus and A. baumannii clones was due to a bla OXA-24 gene harbored in different plasmids. The plasmids were fully sequenced, revealing the presence of site-specific recombination binding sites putatively involved in mobilization of the bla OXA-24 gene. Comparison of plasmids contained in the two strains revealed possible horizontal transmission of resistance genes between the Acinetobacter species.

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Occurrence of Pseudomonas spp. in Raw Vegetables: Molecular and Phenotypical Analysis of Their Antimicrobial Resistance and Virulence-Related Traits

International Journal of Molecular Sciences ◽

10.3390/ijms222312626 ◽

2021 ◽

Vol 22 (23) ◽

pp. 12626

Author(s):

Lidia Ruiz-Roldán ◽

Beatriz Rojo-Bezares ◽

Carmen Lozano ◽

María López ◽

Gabriela Chichón ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Insertion Sequence ◽

Multidrug Resistant ◽

Pulsed Field Gel Electrophoresis ◽

Plant Diseases ◽

Resistant Isolate ◽

Ecological Niches ◽

Great Capacity ◽

Pseudomonas Spp ◽

Sequence Types

Pseudomonas is characterized by its great capacity to colonize different ecological niches, but also by its antimicrobial resistance and pathogenicity, causing human, animal, or plant diseases. Raw and undercooked food is a potential carrier of foodborne disease. The aim of this study was to determine the occurrence of Pseudomonas spp. among raw vegetables, analysing their antimicrobial resistance, virulence, and molecular typing. A total of 163 Pseudomonas spp. isolates (12 different species) were recovered from 77 of the 145 analysed samples (53.1%) and were classified into 139 different pulsed-field gel electrophoresis patterns. Low antimicrobial resistance levels, but one multidrug-resistant isolate, were found. Among the 37 recovered P. aeruginosa strains, 28 sequence-types and nine serotypes were detected. Eleven OprD patterns and an insertion sequence (ISPa1635) truncating the oprD gene of one imipenem-resistant strain were found. Ten virulotypes were observed, including four exoU-positive and thirty-one exoS-positive strains. The lasR gene was absent in three ST155 strains and was truncated by different insertion sequences (ISPre2, IS1411, and ISPst7) in other three strains. High biofilm, motility, pigment, elastase, and rhamnolipid production were detected. Our study demonstrated a low occurrence of P. aeruginosa (18%) and low antimicrobial resistance, but a high number of virulence-related traits in these P. aeruginosa strains, highlighting their pathological importance.

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Horizontal transfer of OXA-23-carbapenemase-producing Acinetobacter species in intensive care units at an academic complex hospital, Durban, KwaZulu-Natal, South Africa

Southern African Journal of Infectious Diseases ◽

10.4102/sajid.v32i4.36 ◽

2017 ◽

Vol 32 (4) ◽

pp. 119-126

Author(s):

Khine Swe Swe-Han ◽

Melendhran Pillay ◽

Desmond Schnugh ◽

Koleka P. Mlisana ◽

Kamaldeen Baba ◽

...

Keyword(s):

Intensive Care ◽

Intensive Care Units ◽

Genetic Relatedness ◽

Horizontal Transmission ◽

Laboratory Data ◽

Carbapenem Resistance ◽

Multidrug Resistant ◽

Acinetobacter Species ◽

Pfge Typing ◽

Class D

Introduction: Carbapenemase production is an important mechanism of carbapenem resistance in Acinetobacter species. This study investigated the presence of the carbapenem-hydrolysing class D β–lactamase- encoding genes, blaOXA-23 and blaOXA-58, and their association with the spread of multidrug-resistant (MDR) Acinetobacter species in intensive care units at an academic hospital. Method: Forty-four MDR Acinetobacter species were confirmed using VITEK®2 and Epsilometer tests. The blaOXA-23 and blaOXA-58 genes were detected by polymerase chain reaction (PCR) in twenty-four selected isolates. The blaOXA-23 amplicons were sequenced and compared to the GenBank database. Genotypic relatedness of isolates was determined by pulsed field gel electrophoresis (PFGE). Clinical and laboratory data were analysed. Results: Among the twenty-four isolates, eighteen were carbapenem resistant and six were sensitive. The blaOXA-23 gene, but not blaOXA-58, was detected in the eighteen resistant strains. The blaOXA-23 amplicons showed 100% identity with the GenBank database of blaOXA-23. The MICs of carbapenems against Acinetobacter species carrying the blaOXA-23 gene were 8 to 16 μg/ml. Genetic relatedness was evident among isolates of seven pairs from fourteen patients. Of these patients, twelve were in the same ICUs and two were adjacent to another ICU during the same hospitalisation period. Conclusion: The selected MDR Acinetobacter species carried the blaOXA-23 gene responsible for resistance to carbapenems, while molecular and clinical data analysis suggested horizontal transmission in ICUs. In addition, the PFGE typing of a diverse collection of MDR Acinetobacter species clones showed that isolates were related to no more than two patients, suggesting that no outbreak had occurred.

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