Antimicrobial drug resistance in Taiwan

Characterization of Carbapenem-Resistant K. Pneumoniae Isolated from Intensive Care Units of Zagazig University Hospitals

The advent of carbapenem-resistant Klebsiella pneumoniae (CRKP) poses a significant challenge to public health, as carbapenems are typically employed as a last resort to treat nosocomial infections caused by such organisms, especially in intensive care units (ICUs). This study aims to characterize the CRKP isolated from patients admitted to the Zagazig University Hospitals (ZUHs) ICU in Egypt. About 56.2%, 41.0%, and 32.4% of the isolates indicated the presence of bla_NDM, bla_OXA-48, and bla_KPC, respectively. Carbapenemase-encoding genes were found in many isolates, and bla_NDM was the most predominant gene. Nevertheless, this situation has become a heavy burden in developing countries, including Egypt, and is associated with substantial morbidity, mortality, and increased healthcare expenses.

Extensively drug-resistant Haemophilus influenzae - emergence, epidemiology, risk factors, and regimen

Background

Concern about Haemophilus influenzae infection has been increasing over recent decades. Given the emergence of H. influenzae with severe drug resistance, we assessed the prevalence of as well as risk factors and potential therapies for extensively drug-resistant (XDR) H. influenzae infection in Taiwan.

Results

In total, 2091 H. influenzae isolates with disk diffusion-based antibiotic susceptibility testing from 2007 to 2018 were enrolled. H. influenzae strains resistant to ampicillin, chloramphenicol, levofloxacin, and trimethoprim-sulfamethoxazole tended to be isolated from patient wards (≧41%), whereas those resistant to amoxicillin-clavulanate, cefotaxime, and cefuroxime were more likely to be isolated from intensive care units (approximately 50%). XDR H. influenzae was first identified in 2007, and its incidence did not significantly change thereafter. Overall prevalence of single, multiple, and extensively drug-resistant H. influenzae over 2007–2018 was 21.5% (n = 450), 26.6% (n = 557), and 2.5% (n = 52), respectively. A stepwise logistic regression analysis revealed that blood culture (odds ratio: 4.069, 95% confidence intervals: 1.339–12.365, P = 0.013) was an independent risk factor for XDR H. influenzae infection. No nosocomial transmission of XDR H. influenzae observed. Antibiotic susceptibility testing results demonstrated that cefotaxime was effective against 78.8% (n = 41) of the XDR strains.

Conclusions

The presence of XDR H. influenzae strains was identified in Taiwan, and cefotaxime was efficacious against most of these strains.

Current Crises and Potential Conflicts in Asia and the Pacific: Challenges Facing Global Health or Global Public Health by a Different Name

Since 1945, the reasons for major crises and how the world responds to them have changed every 10-15 years or sooner. Whereas these crises vary greatly across global regions, their economic, environmental, ecological, social, and disease aspects are increasingly under the influence of widely integrated global changes and forces arising primarily from: climate extremes; rapid unsustainable urbanization; critical biodiversity losses; and emergencies of scarcity in water, food, and energy. These slow-moving but increasingly severe crises affect larger populations across many borders and lead to the emergence of increasing population-based, preventable public health emergencies related to water, sanitation, food, shelter, energy, and related health illnesses, and ultimately global health security. This report explores the impact of these crises on Asia and the Pacific region, and their potential for regional conflict.

In vitro activity of cefoperazone and cefoperazone-sulbactam against carbapenem-resistant Acinetobacter baumannii and Pseudomonas aeruginosa

Background

This study aimed to investigate the in vitro activity of cefoperazone–sulbactam against carbapenem-resistant Acinetobacter baumannii and Pseudomonas aeruginosa, and to evaluate the antibiotic resistance mechanisms of these bacteria.

Materials and methods

In total, 21 isolates of carbapenem-resistant P. aeruginosa and 15 isolates of carbapenem-resistant A. baumannii with different pulsed-field gel electrophoresis types were collected for assessment of the in vitro antibacterial activities of cefoperazone and cefoperazone–sulbactam and the associated resistance mechanisms of the bacteria.

Results

For carbapenem-resistant P. aeruginosa, the minimum inhibitory concentration (MIC) value and antibiotic susceptibility rate were similar for cefoperazone and cefoperazone–sulbactam (at 1:1 and 2:1 ratios). In contrast, for carbapenem-resistant A. baumannii, the MIC values, including the MIC range, MIC that inhibited 50% of isolates (MIC₅₀) and MIC that inhibited 90% of isolates (MIC₉₀), were reduced after treatment with sulbactam and cefoperazone. We screened resistance genes, including VIM-2, OXA-2 and OXA-10, in 21 carbapenem-resistant P. aeruginosa isolates. Only one (4.8%) of the isolates showed expression of VIM-2, and neither the OXA-2 nor the OXA-10 gene was detected. However, 20 (95.2%) isolates among the carbapenem-resistant P. aeruginosa isolates selected for oprD sequencing showed the phenomenon of nucleotide substitution or deletion. Among 15 carbapenem-resistant A. baumannii isolates, we found that ten (66.7%) isolates had concomitant expression of the OXA-23 and ISAba1-OXA-23 genes, and six (40.0%) isolates had expression of the OXA-24-like gene. All 15 isolates had OXA-51-like gene expression, and only 1 (6.7%) isolate had ISAba1-OXA-51-like gene expression. None of the isolates contained the IMP-1, IMP-8, KPC, NDM, VIM-1 or OXA-48 genes.

Conclusion

The in vitro antibacterial activity of cefoperazone against carbapenem-resistant A. baumannii can be enhanced by adding sulbactam to cefoperazone, but the addition does not affect carbapenem-resistant P. aeruginosa. This significant difference can be explained by the different resistance mechanisms of carbapenem-resistant A. baumannii and P. aeruginosa.

Bacterial diversity among four healthcare-associated institutes in Taiwan

Indoor microbial communities have important implications for human health, especially in health-care institutes (HCIs). The factors that determine the diversity and composition of microbiomes in a built environment remain unclear. Herein, we used 16S rRNA amplicon sequencing to investigate the relationships between building attributes and surface bacterial communities among four HCIs located in three buildings. We examined the surface bacterial communities and environmental parameters in the buildings supplied with different ventilation types and compared the results using a Dirichlet multinomial mixture (DMM)-based approach. A total of 203 samples from the four HCIs were analyzed. Four bacterial communities were grouped using the DMM-based approach, which were highly similar to those in the 4 HCIs. The α-diversity and β-diversity in the naturally ventilated building were different from the conditioner-ventilated building. The bacterial source composition varied across each building. Nine genera were found as the core microbiota shared by all the areas, of which Acinetobacter, Enterobacter, Pseudomonas, and Staphylococcus are regarded as healthcare-associated pathogens (HAPs). The observed relationship between environmental parameters such as core microbiota and surface bacterial diversity suggests that we might manage indoor environments by creating new sanitation protocols, adjusting the ventilation design, and further understanding the transmission routes of HAPs.

Molecular Characterization of Klebsiella pneumoniae Clinical Isolates with Elevated Resistance to Carbapenems

Background:

Emergence of carbapenems-resistant K. pneumoniae represents a serious challenge for antimicrobial therapy.

Objective:

The aim of this research is to determine different mechanisms mediating the emergence of K. pneumoniae isolates with high-level carbapenem resistance.

Method:

A total of 80 K. pneumoniae isolates were purified from sputum and urine specimens. The minimum inhibitory concentrations (MICs) of imipenem and meropenem were determined by broth microdilution method. Carbapenemases were detected by Modified Hodge test and PCR. Additionally, the copy numbers of the identified genes (bla_VIM-1, bla_NDM-1 and bla_OXA-48) were quantified by RT-PCR. The outer membrane proteins OmpK35 and OmpK36 of the resistant isolates were analyzed.

Results:

Eight isolates were resistant to carbapenems; six of these isolates possessed elevated MICs to imipenem and meropenem (≥16 µg/ml). Carbapenem resistant isolates harbored bla_NDM-1 (n=5), bla_VIM-1 (n=4) and bla_OXA-48 (n=1) with some isolates had multiple carbapenemases genes. Six isolates with high MICs to imipenem contained multi-copies of the carbapenemases genes along with the lack of OmpK35. Isolates with intermediate resistance to carbapenems (MIC; 4-8 µg/ml) did not exhibit multiple carbapenemases but lacked the OmpK35. Random amplified polymorphic DNA exhibited three different patterns and indicated that five isolates encoded the same pattern P1.

Conclusion:

This study elucidated that multiple carbapenemases genes, high copy number of carbapenemases and loss of the porin OmpK35 could collectively contribute to the emergence of K. pneumoniae isolates with high resistance to carbapenems. Hence, more restrictions should be applied on the use of carbapenems to reduce the emergence of the resistant clones.

Dynamic change of surface microbiota with different environmental cleaning methods between two wards in a hospital

Terminal disinfection and daily cleaning have been performed in hospitals in Taiwan for many years to reduce the risks of healthcare-associated infections. However, the effectiveness of these cleaning approaches and dynamic changes of surface microbiota upon cleaning remain unclear. Here, we report the surface changes of bacterial communities with terminal disinfection and daily cleaning in a medical intensive care unit (MICU) and only terminal disinfection in a respiratory care center (RCC) using 16s ribosomal RNA (rRNA) metagenomics. A total of 36 samples, including 9 samples per sampling time, from each ward were analysed. The clinical isolates were recorded during the sampling time. A large amount of microbial diversity was detected, and human skin microbiota (HSM) was predominant in both wards. In addition, the colonization rate of the HSM in the MICU was higher than that in the RCC, especially for Moraxellaceae. A higher alpha-diversity (p = 0.005519) and a lower UniFrac distance was shown in the RCC due to the lack of daily cleaning. Moreover, a significantly higher abundance among Acinetobacter sp., Streptococcus sp. and Pseudomonas sp. was shown in the RCC compared to the MICU using the paired t test. We concluded that cleaning changes might contribute to the difference in diversity between two wards.

Antimicrobial resistance (AMR) and plant-derived antimicrobials (PDAms) as an alternative drug line to control infections

Infectious diseases caused by antimicrobial-resistant microbes (ARMs) and the treatment are the serious problems in the field of medical science today world over. The development of alternative drug line to treat such infectious diseases is urgently required. Researches on ARMs revealed the presence of membrane proteins responsible for effusing the antibiotics from the bacterial cells. Such proteins have successfully been treated by plant-derived antimicrobials (PDAms) synergistically along with the commercially available antibiotics. Such synergistic action usually inhibits the efflux pump. The enhanced activity of plant-derived antimicrobials is being researched and is considered as the future treatment strategy to cure the incurable infections. The present paper reviews the advancement made in the researches on antimicrobial resistance along with the discovery and the development of more active PDAms.

Carbapenem and cefoxitin resistance of Klebsiella pneumoniae strains associated with porin OmpK36 loss and DHA-1 β-lactamase production

Clinical isolates of carbapenem-resistant Klebsiella pneumoniae (K. pneumoniae) strains are being increased worldwide. Five pan-resistant K. pneumoniae strains have been isolated from respiratory and ICU wards in a Chinese hospital, and reveal strong resistance to all β-lactams, fluoroquinolones and aminoglycosides. Totally 27 β-lactamase genes and 2 membrane pore protein (porin) genes in 5 K. pneumoniae strains were screened by polymerase chain reaction (PCR). The results indicated that all of 5 K. pneumoniae strains carried blaTEM-1 and blaDHA-1 genes, as well as base deletion and mutation of OmpK35 or OmpK36 genes. Compared with carbapenem-sensitive isolates by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), the resistant isolates markedly lacked the protein band of 34-40 kDa, which might be the outer membrane proteins of OmpK36 according to the electrophoresis mobility. In addition, the conjugation test was confirmed that blaDHA-1 mediated by plasmids could be transferred between resistant and sensitive strains. When reserpine (30 μg/mL) and carbonyl cyanide m-chlorophenylhydrazone (CCCP) (50 μg/mL) were added in imipenem and meropenem, the MICs had no change against K. pneumoniae strains. These results suggest that both DHA-1 β-lactamase and loss or deficiency of porin OmpK36 may be the main reason for the cefoxitin and carbapenem resistance in K. pneumoniae strains in our hospital.

Comparison of genospecies and antimicrobial resistance profiles of isolates in the Acinetobacter calcoaceticus-Acinetobacter baumannii complex from various clinical specimens

This study was conducted to compare the prevalences of antimicrobial resistance profiles of clinical isolates in the Acinetobacter calcoaceticus-Acinetobacter baumannii complex from sterile and nonsterile sites and to further study the relationship of antimicrobial resistance profiles and genospecies by amplified rRNA gene restriction analysis (ARDRA). A total of 1,381 isolates were tested with 12 different antibiotics to show their antimicrobial susceptibility profiles. A total of 205 clinical isolates were further analyzed by ARDRA of the intergenic spacer (ITS) region of the 16S-23S rRNA gene. It was found that the overall percentage of isolates from nonsterile sites (urine, sputum, pus, or catheter tip) that were resistant to the 12 antibiotics tested was significantly higher than that of isolates from sterile sites (cerebrospinal fluid [CSF], ascites fluid, and bloodstream) (46% versus 22%; P < 0.05). After ARDRA, it was found that 97% of the 62 isolates resistant to all antibiotics tested were the A. baumannii genospecies, which was identified in only 31% of the isolates susceptible to all antibiotics tested. More genospecies diversity was identified in the isolates susceptible to all antibiotics tested, including genospecies of 13TU (34%), genotype 3 (29%), and A. calcoaceticus (5%). Furthermore, as 91% (10/11) of the isolates from CSF were susceptible to all antibiotics tested, the A. calcoaceticus-A. baumannii complex isolates with multidrug resistance could be less invasive than the more susceptible isolates. This study also indicated current emergence of carbapenem-, fluoroquinolone-, aminoglycoside-, and cephalosporin-resistant A. calcoaceticus-A. baumannii complex isolates in Taiwan.

A novel computational method identifies intra- and inter-species recombination events in Staphylococcus aureus and Streptococcus pneumoniae

Advances in high-throughput DNA sequencing technologies have determined an explosion in the number of sequenced bacterial genomes. Comparative sequence analysis frequently reveals evidences of homologous recombination occurring with different mechanisms and rates in different species, but the large-scale use of computational methods to identify recombination events is hampered by their high computational costs. Here, we propose a new method to identify recombination events in large datasets of whole genome sequences. Using a filtering procedure of the gene conservation profiles of a test genome against a panel of strains, this algorithm identifies sets of contiguous genes acquired by homologous recombination. The locations of the recombination breakpoints are determined using a statistical test that is able to account for the differences in the natural rate of evolution between different genes. The algorithm was tested on a dataset of 75 genomes of Staphylococcus aureus and 50 genomes comprising different streptococcal species, and was able to detect intra-species recombination events in S. aureus and in Streptococcus pneumoniae. Furthermore, we found evidences of an inter-species exchange of genetic material between S. pneumoniae and Streptococcus mitis, a closely related commensal species that colonizes the same ecological niche. The method has been implemented in an R package, Reco, which is freely available from supplementary material, and provides a rapid screening tool to investigate recombination on a genome-wide scale from sequence data.

The extent to which recombination occurs in natural populations is either unknown or controversial but it is widely accepted that recombination plays a crucial role in the evolution of many bacterial species. Numerous methods have been developed for the investigation of recombination events, but most of them require expensive computations and are applicable only to a limited number of genomes or to short nucleotide sequences. Here we present a new algorithm designed to identify recombination events affecting a group of adjacent genes. The procedure is based on the comparison of gene sequences and requires as input the matrix of gene conservation of a test genome against a group of reference genomes. The method is fast, and has minimal computational requirements. Therefore, it can be applied to datasets composed of a large number of complete genomes, and can be easily adapted to analyze data directly from high-throughput sequencing projects. We applied the algorithm to a dataset of S. aureus and streptococcal genomes and we found evidence of yet undetected inter and intra-species recombination events, suggesting that the use of Reco will shed new light on the evolution of bacterial species, and provide important information to improve classification criteria of bacterial species.

Vestuário de profissionais de saúde como potenciais reservatórios de microrganismos: uma revisão integrativa

Objetivou-se identificar na literatura, artigos sobre a ocorrência de contaminação por microrganismos, em jalecos, aventais e uniformes dos profissionais de saúde, e a similaridade com aqueles associados às Infecções Relacionadas à Assistência à Saúde, considerando o perfil de resistência aos antimicrobianos. Realizou-se busca por artigos nas seguintes bases de dados: MEDLINE, LILACS e SCOPUS, publicados entre 2000 e 2010. Foram selecionados nove artigos. Os estudos evidenciaram a contaminação dos jalecos, aventais e uniformes. Nos estudos analisados, verificou-se a presença de bactérias, principalmente, nos bolsos, punhos e região abdominal. Quanto ao perfil de sensibilidade, verificou-se recuperação de Staphylococcus aureus meticilina resistente, seguidos dos Gram negativos resistentes aos antimicrobianos. Identificou-se semelhança entre as cepas isoladas no vestuário dos profissionais de saúde e aquelas relacionadas à ocorrência de infecções. Assim, jalecos, aventais e uniformes devem ser considerados na cadeia de disseminação de microrganismos resistentes.

Molecular characterisation of multiple drug-resistant Acinetobacter baumannii isolates in southern Taiwan

The purpose of this study was to develop a multiplex polymerase chain reaction (mt-PCR) assay for synchronous detection of carbapenem resistance genes and/or pandrug resistance genes in clinical isolates of multidrug-resistant Acinetobacter baumannii (MDR-AB) and to investigate the association between the genetic make-up and a drug-resistant pattern. In total, 213 MDR-AB isolates were collected. All clinical isolates underwent antimicrobial susceptibility testing and were analysed for the presence of oxacillinase genes (bla(OXA-23), bla(OXA-24), bla(OXA-51)-like and bla(OXA-58)), class A and C β-lactamase genes (bla(TEM-1) and bla(AmpC), respectively), and an integron-associated antibiotic resistance gene (int1) by an in-house-designed mt-PCR assay. Of the 213 isolates, 73.87% harboured both bla(TEM-1) and bla(AmpC) and 83.92% carried at least three oxacillinase genes. Moreover, 64.82% of the isolates were significant in that they had two β-lactamase genes and three oxacillinase genes (P<0.001), indicating the complexity of the genetic make-up of carbapenem-resistant A. baumannii. The bla(OXA-51)-like allele was detected in the majority of these A. baumannii isolates (97.49%), whereas bla(OXA-23) was rarely prevalent in these isolates. In multivariate logistic regression, the presence of bla(OXA-23) and bla(TEM-1) had a statistically significant association with imipenem resistance [bla(OXA-23), P=0.004, odds ratio (OR)=10.52, 95% confidence interval (CI) 2.12-52.17; bla(TEM-1), P=0.005, OR=6.14, 95% CI 1.74-21.62]. These results suggest that detecting bla(OXA-23) and bla(TEM-1) genes could be used to predict imipenem resistance in MDR-AB isolates. A mt-PCR for detecting carbapenem resistance genes and pandrug resistance genes of A. baumannii isolates was developed to provide an assay to quickly screen for potential imipenem-resistant A. baumannii in the clinic.

The Inhibition Effect of TiO2/Ag Thin Film on Acinetobacter baumannii

The nosocomial infections caused by opportunistic pathogen Acinetobacter baumannii was increasing in recent years. It was known that the attachment of A. baumannii on solid surface was a key factor for infection. This study was conducted to evaluate the inhibitory effect of titanium dioxide (TiO2)/Ag thin film on A. baumannii. In this study, TiO2 thin films were firstly prepared by using the modified impregnation method, then TiO2/Ag thin films were prepared by using the spin-coating with 5000 ppm Ag+. The TiO2/Ag thin film was analyzed by field-emission scanning electron micrographs and X-ray diffractometer. The nano-size and Anatase crystal structure were confirmed. Twenty clinical A. baumannii isolates were examined for the bactericidal effect of TiO2/Ag thin film either in the dark or under visible light activation for 20 min. The inhibition efficiencies of TiO2/Ag thin film under visible light on these 20 isolates ranged from 41% to 90%. The effects of TiO2/Ag thin film in the dark were slightly lower than visible light-activated group. Our results suggested that coating of TiO2/Ag on solid surface in hospital environment might be helpful for the prevention of nosocomial A. baumannii infection.