Antimicrobial Resistance and Molecular Characterization of Salmonella Rissen Isolated in China During 2008-2019

Background

This study aimed to provide epidemiological features of Salmonella enterica serovar Rissen, determine antimicrobial susceptibility, virulence gene profiles, and describe the potential association of S. Rissen from different sources in China.

Methods

During 2008-2019, a total of non-repetitive 228 S. Rissen isolates were collected from human, animals and environment in China. The antimicrobial susceptibility test, screening of antimicrobial and virulence genes by PCR, and pulsed-field gel electrophoresis (PFGE) were performed.

Results

Among the 154 isolates from human, the majority of the cases (80.5%) occurred in summer, and S. Rissen was mainly detected in people aged 21-40 (37.7%) and 41-60 (28.6%) years old, and 74 non-human source S. Rissen strains were identified, with pork being the most common source. About 93.4% isolates were resistant to at least one of the 12 tested antimicrobial agents, and high frequencies of resistance were observed for tetracyclines (91.2%), trimethoprim-sulfamethoxazole (74.1%) and ampicillin (67.5%). A total of 171 (75%) isolates were resistant to at least three categories of antimicrobials, and the most common resistance profile was Tetracycline(s)-β-Lactams-Sulfonamides. The resistance rates to chloramphenicol, quinolones and sulfafurazole were significantly higher in strains isolated from human compared to non-human source strains. Among these isolates, the β-Lactams resistance was mainly associated with gene blaTEM (54.7%), sulfonamide resistance with sul2 (45.7%) and sul3 (54.3%), tetracycline resistance with tetA (81.3%). All the isolates harbored virulence genes hilA, sopB, sciN, stn and ssrB, and most of them harbored ssaQ (98.7%), mgtC (98.7%) and invA (98.2%). The majority (91.7%) of S. Rissen isolates showed high similarity (>80%) with each other in PFGE patterns and came from human, animals and environment.

Conclusion

The high frequencies of multidrug resistance and probable clonal dissemination in this serovar call for the necessity of systematic surveillance on S. Rissen in China.

Uropathogens and their antimicrobial-resistant pattern among suspected urinary tract infections patients in eastern Nepal: A hospital inpatients-based study

Background

Urinary tract infections are the primary factors that cause mortality and morbidity in patients with underlying comorbid conditions and are responsible for most hospital admissions worldwide.

Objectives

The study aims to identify the common bacterial uropathogens and determine their antimicrobial susceptibility pattern, including multidrug-resistant/extensively drug-resistant bacteria.

Methods

The descriptive cross-sectional study was conducted among inpatients provisionally suspected of urinary tract infections in the medical ward of Koshi Hospital, Biratnagar, Nepal. Samples were inoculated in a cystine lysine electrolyte-deficient medium, and pure growth of significant bacteria was further subjected Gram staining, biochemical identification, and antimicrobial susceptibility testing as per laboratory standard procedure and Clinical Laboratory Standards Institute guidelines, respectively. Descriptive and inferential statistical analysis was performed to analyze the outcomes and a p-value < 0.05 was considered statistically significant.

Results

A total of 305 patients urine specimens were examined, of which 251 (82.29%) samples resulted in significant bacterial growth in the culture. Escherichia coli (62.94%) was the most predominantly isolated organism, followed by Klebsiella pneumoniae (12.35%), Staphylococcus aureus (9.16%), and Pseudomonas aeruginosa (8.76%). Among antimicrobials, colistin had shown absolute susceptibility (100%) toward gram-negative uropathogens followed by carbapenem and aminoglycosides in a majority of uropathogens. Escherichia coli was found to be the leading drug-resistant bacteria (70%) among uropathogens. The presence of multidrug-resistant/extensively drug-resistant bacteria uropathogens was found to be significantly associated with diabetes mellitus and those with combined antimicrobial therapies. Diabetic patients were twice (OR~2) more likely to colonize and develop uropathogens as compared to non-diabetics.

Conclusion

Escherichia coli was the most common uropathogens followed by Klebsiella pneumoniae in urinary tract infection patients. The polymyxin group (colistin) of antimicrobials was found to be effective in all multidrug-resistant and extensively drug-resistant uropathogens. The study recommends the need of optimized antimicrobial stewardship program to develop effective strategies in the management of urinary tract infections in diverse healthcare settings.

Comparison between clinical evaluations and laboratory findings and the impact of biofilm on antimicrobial susceptibility in vitro in canine otitis externa

BACKGROUND

In canine otitis externa (OE), biofilm-producing bacteria are frequently present but biofilm may be underdiagnosed clinically.

HYPOTHESIS/OBJECTIVES

The study aimed to investigate an association between clinical and cytological findings with bacteriological data from dogs with OE, to establish, through Environmental Scanning Electron Microscope (ESEM) examination, whether the presence of biofilm in vivo can be predicted and to evaluate the impact of biofilm on antimicrobial susceptibility tests.

MATERIALS AND METHODS

Fifty-six dogs showing clinical signs of OE were enrolled. One cotton swab each was collected for ESEM, bacterial culture and susceptibility testing and for cytology. Staphylococcus pseudintermedius (n = 42, 48.8%) and Pseudomonas aeruginosa (n = 26, 30.2%) were tested for their ability to form biofilm. Minimum Inhibitory Concentrations (MIC), Minimal Biofilm Inhibitory Concentrations (MBIC) and Minimal Biofilm Eradication Concentrations (MBEC) towards enrofloxacin, gentamicin, polymyxin B and rifampicin were determined.

RESULTS

Pseudomonas aeruginosa was positively associated with the biofilm clinical evaluation (p < 0.01) and neutrophils (p < 0.05), nuclear streaks (p < 0.01) and rods bacteria (p < 0.01) on cytology. S. pseudintermedius was associated with a low presence of neutrophils. There was a statistical correlation between clinical and cytological biofilm presence (p ≤ 0.01), but none with the biofilm production assay nor ESEM biofilm detection. No differences were found comparing the results of MIC and MBIC. MBEC results showed higher values than MIC and MBIC for all antimicrobials tested (p ≤ 0.001).

CONCLUSIONS AND CLINICAL RELEVANCE

Biofilm presence in OE was often underdiagnosed. Even if there is no specific clinical or cytological pattern related to biofilm, its presence should always be suspected.

Transcriptome analysis of Fenneropenaeus merguiensis in response to Vibrio proteolyticus infection

In recent years, due to the destruction of the culture environment and serious ecological pressure, especially in the process of culture, residual bait, faeces and fishery drug abuse will lead to the accumulation of harmful metabolites such as ammonia nitrogen and nitrite, and biological denitrification is the most economical and effective method to remove the single. Therefore, in this study, a nitrite removal strain XA19 was isolated and screened from a shrimp biofloc culture pond. This strain was identified as a clade of Vibrio proteolyticus because the homology between XA19 and V. proteolyticus WDVP was as high as 99.86% by using 16S rDNA gene sequence analysis and NCBI database comparison. Scanning electron microscopy images showed that V. proteolyticus is short-rod-shaped with a curved body and no budding spores, pods and flagella. Antimicrobial susceptibility test proved that V. proteolyticus was resistant to ampicillin, oxacillin, penicillin, vancomycin and clindamycin. In the median lethal concentration 50 (LC50 ) test, at 7-day post-infection (dpi), LC50 of V. proteolyticus for Fenneropenaeus merguiensis was 1.69 × 104  CFU/mL. Transcriptome sequencing analysis was carried out on hepatopancreas of F. merguiensis at 24 and 48 hpi. A total of 176 differentially expressed genes (DEGs) were screened at 24 hpi, including 104 up-regulated DEGs and 72 down-regulated DEGs, and a total of 52 DEGs were screened at 48 hpi, including 32 up-regulated DEGs and 20 down-regulated DEGs. In the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of DEGs, many immune-related signalling pathways were significantly enriched, including Hippo signalling pathway, phagosome, Toll and Imd signalling pathways and Wnt signalling pathway. In addition, some pathways related to Warburg effect were also enriched, including Glycolysis/Gluconeogenesis, Biosynthesis of amino acids, amino sugar and nucleotide sugar metabolism and so on. In this study, the toxicity and drug sensitivity of V. proteolyticus were systematically studied, and the immune response of hepatopancreas of F. merguiensis to V. proteolyticus infection was preliminarily revealed from the molecular level. The results may provide a reference for the prevention and control of V. proteolyticus.

Analysis of multidrug-resistant determinants of clinically isolated Acinetobacter baumannii CYZ via whole genome sequencing

Acinetobacter baumannii is a multidrug-resistant coccobacillus responsible for severe nosocomial infectious diseases. This study mainly focuses on investigating the antimicrobial resistance features of a clinically isolated strain (A. baumannii CYZ) using the PacBio Sequel II sequencing platform. The chromosomal size of A. baumannii CYZ is 3,960,760 bp, which contains a total of 3803 genes with a G + C content of 39.06%. Functional analysis performed using the Clusters of Orthologous Groups of Proteins (COGs), Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, as well as the Comprehensive Antibiotic Resistance Database (CARD) revealed a complicated set of antimicrobial resistance determinants in the genome of A. baumannii CYZ, which were mainly classified into multidrug efflux pumps and transport systems, β-lactamase relative and penicillin-binding proteins, aminoglycoside modification enzymes, alternation of antibiotic target sites, lipopolysaccharide relative, and other mechanisms. A total of 35 antibiotics were tested for the antimicrobial susceptibility of A. baumannii CYZ, and the organism exhibited a stronger antimicrobial resistance ability. The phylogenetic relationship indicated that A. baumannii CYZ has high homology with A. baumannii ATCC 17978; however, the former also exhibited its specific genome characteristics. Our research results give insight into the genetic antimicrobial-resistant features of A. baumannii CYZ as well as provide a genetic basis for the further study of the phenotype.

Awareness and Knowledge of Antimicrobial Resistance, Antimicrobial Stewardship and Barriers to Implementing Antimicrobial Susceptibility Testing among Medical Laboratory Scientists in Nigeria: A Cross-Sectional Study

Background: Antimicrobial resistance (AMR) is now considered one of the greatest global health threats. This is further compounded by a lack of new antibiotics in development. Antimicrobial stewardship programmes can improve and optimize the use of antibiotics, thereby increasing the cure rates of antibiotic treatment and decreasing the problem of AMR. In addition, diagnostic and antimicrobial stewardships in the pathology laboratories are useful tools to guide clinicians on patient treatment and to stop the inappropriate use of antibiotics in empirical treatment or narrow antibiotics. Medical Laboratory Scientists are at the forefront of performing antibiotics susceptibility testing in pathology laboratories, thereby helping clinicians to select the appropriate antibiotics for patients suffering from bacterial infections. Methods: This cross-sectional study surveyed personal antimicrobial usage, the knowledge and awareness on AMR, and antimicrobial stewardship, as well as barriers to antimicrobial susceptibility testing among medical laboratory scientists in Nigeria using pre-tested and validated questionnaires administered online. The raw data were summarized and exported in Microsoft Excel and further analyzed using IBM SPSS version 26. Results: Most of the respondents were males (72%) and 25-35 years old (60%). In addition, the BMLS degree was the highest education qualification most of the respondents (70%) achieved. Of the 59.2% of the respondents involved in antibiotics susceptibility testing, the disc diffusion method was the most commonly used (67.2%), followed by PCR/Genome-based detection (5.2%). Only a small percentage of respondents used the E-test (3.4%). The high cost of testing, inadequate laboratory infrastructure, and a lack of skilled personnel are the major barriers to performing antibiotics susceptibility testing. A higher proportion of a good AMR knowledge level was observed in male respondents (75%) than females (42.9%). The knowledge level was associated with the respondent's gender (p = 0.048), while respondents with a master's degree were more likely to possess a good knowledge level of AMR (OR: 1.69; 95% CI: 0.33, 8.61). Conclusion: The findings of this study indicate that Nigerian medical laboratory scientists had moderate awareness of AMR and antibiotic stewardship. It is necessary to increase investments in laboratory infrastructure and manpower training, as well as set up an antimicrobial stewardship programme to ensure widespread antibiotics susceptibility testing in hospitals, thereby decreasing empirical treatment and the misuse of antibiotics.

Antibiotic resistance in Helicobacter pylori: From potential biomolecular mechanisms to clinical practice

Increasing rates of Helicobacter pylori resistance are associated with multiple clinical challenges. Bacterial factors linked to H. pylori resistance are mutations, efflux pumps, and biofilms. Gene mutations such as nucleic acid synthesis-related gene mutations, rRNA coding gene mutations, and cell wall synthesis-related gene mutations are the most important mechanisms by which H. pylori evades bactericidal effects. These mechanisms are also closely related to the biological activity of the efflux pump systems and biofilms. Activation of the efflux pump system and biofilm formation both lead to the emergence of MDR strains, further increasing the difficulty of eradication therapy. In this review, the status of antibiotic resistance in H. pylori from different regions and countries is summarized and compared, and H. pylori resistance profiles and their changing trends in the clinic are described. Then, research progress on biomolecular mechanisms underlying antibiotic resistance, diagnostic methods, and treatment strategies are introduced and discussed. Challenges resulting from increasing resistance, potential solutions to combat increasing resistance, and future directions are discussed to help clinicians and researchers better address the emergence and spread of resistant H. pylori strains and optimize drug regimens. With the rate of H. pylori resistance to commonly used antibiotics increasing, more attention should be given to the selection of antibiotics and to monitoring resistance when antibiotics are used for clinical eradication treatment. Individualized precise eradication treatment under the guidance of drug susceptibility testing will become the mainstream method of treatment in the future.

Phenotypical Detection of β-Lactamases in a Multidrug-Resistant and Extensively Drug-Resistant Chryseobacterium indologens: A Rare Human Pathogen With Special References to Risk Factor

Chryseobacterium indologenes is gram-negative bacteria that cause infection in humans. It is less frequently isolated in the laboratory. The development of drug-resistant and its intrinsic ability to resist a wide range of antimicrobials enables them to cause mortality in an immunocompromised patient with a longer hospital stay. Our study objectives are to investigate antimicrobial-resistant patterns, drug-resistant enzymes, and the risk factor analysis associated with multidrug-resistant (MDR), extensively drug-resistant (XDR), and Pan-drug resistant (PDR) within 2 years. Altogether 53 strains of Chryseobacterium indologens were obtained from 5000 specimens that were processed for routine bacterial culture. The bacterial identification was done using conventional techniques (colony morphology, gram staining, flexirubin test, and biochemical tests) as well as the VITEK-2 System to further confirm. The bacterial isolate were processed to observe antimicrobial susceptibility test (AST) using disk diffusion method. MDR XDR and PDR were classified following European Centre for Disease Prevention and Control guidelines. C. indologens strains with beta-lactamases such as extended-spectrum beta-lactamases (ESBL), metallo beta-lactamases (MBL), and Amp-C beta-lactamases (Amp-C) were detected phenotypically. The highest isolation of C. indologens was observed in a sputum sample. In vitro antimicrobial susceptibility test revealed susceptibility to tigecycline followed by levofloxacin, cotrimoxazole, and piperacillin-tazobactam. From 53 isolates of C. indologens, MDR accounts for 56.60% and 22.64% for XDR. Combined antimicrobial therapy and longer hospital stay were found to be the leading risk factor. All 53 C. indologenes strains were detected as MBL. Total ESBL was detected in 16.98% of MBL producer strains and Amp-C was observed in 13.20% of MBL-producing strains. All 3 enzyme co-oproducers were seen in only 5.66% of C. indologens. Although it is rarely encountered in the laboratory, it showed a remarkable effect in patients with underlying predisposing factors and prolonged hospital stays. The presence of betalactamases determined the drug-resistant activity on a wide spectrum of tested antibiotics.

Antimicrobial Profiles and Conventional PCR Assay of Shiga Toxigenic Escherichia coli O157:H7 (STEC) Isolated from Cattle Slaughtered at Bedele Municipal Abattoir, South West Ethiopia

Background

Shiga toxin producing Escherichia coli O157:H7 (STEC) is considered the most prevalent food borne pathogen that has gained increasing attention worldwide in recent years.

Methods

A cross-sectional study was carried out at Bedele Municipal abattoir on cattle that were reported healthy from detailed ante-mortem inspections and having various body conditions scores. A total of 516 samples were collected and examined after enriched in modified peptone water. Following an enrichment, the samples were plated onto MacConkey agar and then onto Eosin methylene blue agar. Finally after a few similar procedures, 14 E. coli O157:H7 (STEC) isolates were confirmed through latex agglutination test. The collected data were analyzed using SPSS version 20 statistical software.

Results

This study finding revealed that the overall prevalence of E. coli O157:H7 out of 516 samples was found to be 2.7%. However, on sample type basis, the prevalence of E. coli O157:H7 from feacal samples, carcass swabs, butcher hand swabs and knife swabs were 4.7%, 3.3%, 1.1% and 1.1%, respectively. It was also found that that the prevalence of E. coli O157:H7 was significantly affected by age groups of slaughtered cattle (p<0.05). Moreover, in vitro antimicrobial susceptibility test result on average showed that almost all of E. coli O157:H7 isolates were highly susceptible to kanamycin and no resistance was shown to ciprofloxacin and gentamicin. Finally, the conventional PCR detection of stx1, st2 and hylA genes revealed that only 21.4% and 14.3% were found to contain stx1 and hylA genes respectively.

Conclusion

To wrap up, this study showed that Shiga toxin producing E. coli O157:H7 (STEC) isolates were found with almost low overall prevalence rate from all sample sources in this study site. Therefore, improving abattoir facilities and slaughter house workers' personal hygiene are recommended to curtail E. coli O157:H7 meat contamination in this abattoir.

Are There Any Changes in the Causative Microorganisms Isolated in the Last Years from Hip and Knee Periprosthetic Joint Infections? Antimicrobial Susceptibility Test Results Analysis

BACKGROUND

PJIs following total hip and knee arthroplasty represent severe complications with broad implications, and with significant disability, morbidity, and mortality. To be able to provide correct and effective management of these cases, an accurate diagnosis is needed. Classically, acute PJIs are characterized by a preponderance of virulent microorganisms, and chronic PJIs are characterized by a preponderance of less-virulent pathogens like coagulase-negative staphylococci or Cutibacterium species. This paper aims to analyze if there are any changes in the causative microorganisms isolated in the last years, as well as to provide a subanalysis of the types of PJIs.

METHODS

In this single-center study, we prospectively included all retrospectively consecutive collected data from patients aged over 18 years that were hospitalized from 2016 through 2022, and patients that underwent a joint arthroplasty revision surgery. A standardized diagnostic protocol was used in all cases, and the 2021 EBJIS definition criteria for PJIs was used.

RESULTS

114 patients were included in our analysis; of them, 67 were diagnosed with PJIs, 12 were acute/acute hematogenous, and 55 were chronic PJIs. 49 strains of gram-positive aerobic or microaerophilic cocci and 35 gram-negative aerobic bacilli were isolated. Overall, Staphylococcus aureus was the most common isolated pathogen, followed by coagulase-negative staphylococci (CoNS). All cases of acute/acute hematogenous PJIs were caused by gram-positive aerobic or microaerophilic cocci pathogens. Both Staphylococcus epidermidis and methicillin-resistant S. aureus were involved in 91.66% of the acute/acute hematogenous PJIs cases. 21.8% of the chronic PJIs cases were caused by pathogens belonging to the Enterobacterales group of bacteria, followed by the gram-negative nonfermenting bacilli group of bacteria, which were involved in 18.4% of the cases. 12 chronic cases were polymicrobial.

CONCLUSION

Based on our findings, empiric broad-spectrum antibiotic therapy in acute PJIs could be focused on the bacteria belonging to the gram-positive aerobic or microaerophilic cocci, but the results should be analyzed carefully, and the local resistance of the pathogens should be taken into consideration.

What's New in Antibiograms? Updating CLSI M39 Guidance with Current Trends

A vast amount of antimicrobial susceptibility test (AST) data is generated from routine testing in diagnostic laboratories for the primary purpose of guiding clinicians in antimicrobial therapy decisions for their patients. However, there is additional value for these data when they are compiled at the local, regional, national, and global levels. Cumulative AST data can be used to prepare antibiograms at the individual health care facility level. These reports can be used to gain insight into appropriate empirical therapy options prior to the availability of AST results on an individual patient's isolate. Different types of cumulative AST data reports can also be compiled at the regional, national, and global levels to estimate susceptibility rates in geographic regions, document trends in evolving microbial populations, and recognize the appearance and spread of emerging antimicrobial resistance threats. The first CLSI M39 Guideline for Analysis and Presentation of Cumulative AST Data was published in 2000. Since that time, there have been changes to AST and reporting recommendations as well as the introduction of advanced informatics technologies to analyze and present data. The 5th edition of M39 has taken into consideration these changes to assist those who analyze, present, and utilize routine antibiograms and other types of cumulative AST data reports as well as those who design information systems for the capturing and analyzing of AST data. Furthermore, antimicrobial stewardship programs (ASPs) have expanded considerably, and uses of the antibiogram by ASPs have been addressed. This minireview will remind users of the basic recommendations for analysis and presentation of antibiograms and provide new suggestions to enhance these reports.

WGS-Based Lineage and Antimicrobial Resistance Pattern of Salmonella Typhimurium Isolated during 2000-2017 in Peru

Salmonella Typhimurium is associated with foodborne diseases worldwide, including in Peru, and its emerging antibiotic resistance (AMR) is now a global public health problem. Therefore, country-specific monitoring of the AMR emergence is vital to control this pathogen, and in these aspects, whole genome sequence (WGS)—based approaches are better than gene-based analyses. Here, we performed the antimicrobial susceptibility test for ten widely used antibiotics and WGS-based various analyses of 90 S. Typhimurium isolates (human, animal, and environment) from 14 cities of Peru isolated from 2000 to 2017 to understand the lineage and antimicrobial resistance pattern of this pathogen in Peru. Our results suggest that the Peruvian isolates are of Typhimurium serovar and predominantly belong to sequence type ST19. Genomic diversity analyses indicate an open pan-genome, and at least ten lineages are circulating in Peru. A total of 48.8% and 31.0% of isolates are phenotypically and genotypically resistant to at least one antibiotic, while 12.0% are multi-drug resistant (MDR). Genotype−phenotype correlations for ten tested drugs show >80% accuracy, and >90% specificity. Sensitivity above 90% was only achieved for ciprofloxacin and ceftazidime. Two lineages exhibit the majority of the MDR isolates. A total of 63 different AMR genes are detected, of which 30 are found in 17 different plasmids. Transmissible plasmids such as lncI-gamma/k, IncI1-I(Alpha), Col(pHAD28), IncFIB, IncHI2, and lncI2 that carry AMR genes associated with third-generation antibiotics are also identified. Finally, three new non-synonymous single nucleotide variations (SNVs) for nalidixic acid and eight new SNVs for nitrofurantoin resistance are predicted using genome-wide association studies, comparative genomics, and functional annotation. Our analysis provides for the first time the WGS-based details of the circulating S. Typhimurium lineages and their antimicrobial resistance pattern in Peru.

Single Cell Raman Spectroscopy Deuterium Isotope Probing for Rapid Antimicrobial Susceptibility Test of Elizabethkingia spp

Nosocomial infection by multi-drug resistance Elizabethkingia spp. is an emerging concern with severe clinical consequences, particularly in immunocompromised individuals and infants. Efficient control of this infection requires quick and reliable methods to determine the appropriate drugs for treatment. In this study, a total of 31 Elizabethkingia spp., including two standard strains (ATCC 13253 and FMS-007) and 29 clinical isolates obtained from hospitals in China were subjected to single cell Raman spectroscopy analysis coupled with deuterium probing (single cell Raman-DIP). The results demonstrated that single cell Raman-DIP could determine antimicrobial susceptibility of Elizabethkingia spp. in 4 h, only one third of the time required by standard broth microdilution method. The method could be integrated into current clinical protocol for sepsis and halve the report time. The study also confirmed that minocycline and levofloxacin are the first-line antimicrobials for Elizabethkingia spp. infection.

Molecular Mechanism of the β-Lactamase Mediated β-Lactam Antibiotic Resistance of Pseudomonas aeruginosa Isolated From a Chinese Teaching Hospital

Pseudomonas aeruginosa can cause infections in the blood, lungs (pneumonia), or other parts of the body after surgery. To investigate the molecular characteristics of β-lactam antibiotic resistance of P. aeruginosa isolated from a hospital population between 2015 and 2017, in this study, the antimicrobial susceptibility and the resistance gene profile of the bacteria were determined. The Pulsed-field gel electrophoresis (PFGE) was used to characterize the clonal relatedness and sequencing and comparative genomic analysis were performed to analyze the structure of the resistance gene-related sequences. As a result, of the 260 P. aeruginosa strains analyzed, the resistance rates for 6 β-lactam antibiotics ranged from 4.6 to 9.6%. A total of 7 genotypes of 44 β-lactamase genes were identified in 23 isolates (8.9%, 23/260). Four transconjugants from different donors carrying bla_CARB-3 exhibited a phenotype of reduced susceptibility to piperacillin–tazobactam, ceftazidime, and cefepime, and 2 transconjugants harboring bla_IMP-45 exhibited a phenotype of reduced susceptibility to carbapenems. bla_CARB positive isolates (n = 12) presented six PFGE patterns, designated groups A to F. Two bla genes (bla_IMP-45 and bla_OXA-1) in PA1609 related to a class 1 integron (intI1-bla_IMP-45-bla_OXA-1-aac(6′)-Ib7-catB3-qacE∆1-sul1) were encoded on a plasmid (pPA1609-475), while the bla_CARB-3 gene of PA1616 also related to a class 1 integron was located on the chromosome. The results suggest that β-lactam antibiotic resistance and clonal dissemination exist in this hospital population. It indicates the necessity for molecular surveillance in tracking β-lactamase-producing strains and emphasizes the need for epidemiological monitoring.

FadACB and smeU1VWU2X Contribute to Oxidative Stress-Mediated Fluoroquinolone Resistance in Stenotrophomonas maltophilia

Pathogenic bacteria experience diverse stresses induced by host cells during infection and have developed intricate systems to trigger appropriate responses. Bacterial stress responses have been reported to defend against these stresses and cross-protect bacteria from antibiotic attack. In this study, we aimed to assess whether oxidative stress affects bacterial susceptibility to fluoroquinolone (FQ) and the underlying mechanism. Stenotrophomonas maltophilia, a species with high genetic diversity, is distributed ubiquitously and is an emerging multidrug-resistant opportunistic pathogen. FQs are among the limited antibiotic treatment options for S. maltophilia infection. The minimum inhibitory concentrations (MICs) of 103 S. maltophilia clinical isolates against ciprofloxacin (CIP) and levofloxacin (LVX) were determined using the agar dilution method in Mueller-Hinton plates with or without menadione (MD), a superoxide generator. The resistance rates for ciprofloxacin and levofloxacin were 40% and 18% in the MD-null group and increased to 91% and 23%, respectively, in the MD-treated group. Of the 103 isolates tested, 54% and 27% had elevated MICs against ciprofloxacin and levofloxacin, respectively, in the presence of MD. The involvement of oxidative stress responses in the MD-mediated FQ resistance was further assessed by mutants construction and viability assay. Among the 16 oxidative stress alleviation systems evaluated, fadACB and smeU1VWU2X contributed to MD-mediated FQ resistance. The antibiotic susceptibility test is an accredited clinical method to evaluate bacterial susceptibility to antibiotics in clinical practice. However, oxidative stress-mediated antibiotic resistance was not detected using this test, which may lead to treatment failure.

Different Antimicrobial Susceptibility Testing Methods to Determine Vancomycin Susceptibility and MIC for Staphylococcus aureus with Reduced Vancomycin Susceptibility

The methods and results obtained using commercialized automation systems used for antimicrobial susceptibility testing are not entirely consistent. Therefore, we evaluated different antimicrobial susceptibility testing methods to determine vancomycin susceptibility and minimum inhibitory concentration (MIC) for Staphylococcus aureus with reduced vancomycin susceptibility (SA-RVS). A total of 128 clinical isolates of S. aureus were tested, including 99 isolates showing an MIC of ≥2 µg/mL using the VITEK2 system (VITEK2). Antimicrobial susceptibility tests were performed using the Sensititre system (Sensititre), Phoenix M50 system (Phoenix), and MicroScan WalkAway 96 Plus system (MicroScan). Vancomycin MICs were determined using the broth microdilution method (BMD) and Etest. Essential agreement and category agreement for each method were compared with BMD results as the reference method. The BMD and Etest showed complete essential agreement (100%). VITEK2, Sensititre, and Phoenix showed high essential agreement (>99%), while MicroScan showed the lowest essential agreement (92.2%). The MIC MICs determined via Etest, VITEK2, and MicroScan tended to be higher than that determined via BMD. When comparing BMD with Etest, the category agreement was 93.8% and minor errors were observed for eight isolates. VITEK2, Sensititre, and Phoenix showed category agreements of 96.1%, 96.1%, and 99.2%, respectively, while MicroScan showed the lowest category agreement of 85.2%. The determination of vancomycin susceptibility and MIC for S. aureus varied among the methods. Caution should be taken when interpreting RVS and intermediate results for S. aureus. For confirmation of SA-RVS results, it would be appropriate to test with BMD or a more reliable testing method.

Trends of Antimicrobial Susceptibility in Clinically Significant Coagulase-Negative Staphylococci Isolated from Cerebrospinal Fluid Cultures in Neurosurgical Adults: a Nine-Year Analysis

Coagulase-negative staphylococci (CoNS) are the main pathogens in health care-associated ventriculitis and meningitis (HCAVM). This study aimed to assess antimicrobial susceptibility. Moreover, the treatment and clinical outcome were described. All neurosurgical adults admitted to one of the largest neurosurgical centers in China with clinically significant CoNS isolated from cerebrospinal fluid cultures in 2012 to 2020 were recruited. One episode was defined as one patient with one bacterial strain. Interpretive categories were applied according to the MICs. The clinical outcomes were dichotomized into poor (Glasgow Outcome Scale 1 to 3) and acceptable (Glasgow Outcome Scale 4 to 5). In total, 534 episodes involving 519 patients and 16 bacteria were analyzed. Over the 9 years, eight antimicrobial agents were used in antimicrobial susceptibility tests, including six in over 80% of CoNS. The range of resistance rates was 0.8% to 84.6%. The vancomycin resistance rate was the lowest, whereas the penicillin resistance rate was the highest. The linezolid (a vancomycin replacement) resistance rate was 3.1%. The rate of oxacillin resistance, representing methicillin-resistant staphylococci, was 70.2%. There were no significant trends of antimicrobial susceptibility over the 9 years for any agents analyzed. However, there were some apparent changes. Notably, vancomycin-resistant CoNS appeared in recent years, while linezolid-resistant CoNS appeared early and disappeared in recent years. Vancomycin (or norvancomycin), the most common treatment agent, was used in 528 (98.9%) episodes. Finally, 527 (98.7%) episodes had acceptable outcomes. It will be safe to use vancomycin to treat CoNS-related HCAVM in the immediate future, although continuous monitoring will be needed. IMPORTANCE Coagulase-negative staphylococci are the main pathogens in health care-associated ventriculitis and meningitis. There are three conclusions from the results of this study. First, according to antimicrobial susceptibility, the rates of resistance to primary antimicrobial agents are high and those to high-level agents, including vancomycin, are low. Second, the trends of resistance rates are acceptable, especially for high-level agents, although long-term and continuous monitoring is necessary. Finally, the clinical outcomes of neurosurgical adults with coagulase-negative staphylococci-related health care-associated ventriculitis and meningitis are acceptable after treatment with vancomycin. Therefore, according to the antimicrobial susceptibility and clinical practice, vancomycin will be safe to treat coagulase-negative staphylococci-related health care-associated ventriculitis and meningitis.

Reservoir of Antibiotic Residues and Resistant Coagulase Negative Staphylococci in a Healthy Population in the Greater Accra Region, Ghana

Antimicrobial resistance threatens infectious disease management outcomes, especially in developing countries. In this study, the occurrence of resistant coagulase-negative staphylococci (rCoNS) and antibiotic residues in urine samples of 401 healthy individuals from Korle-Gonno (KG) and Dodowa (DDW) in Ghana was investigated. MALDI-ToF/MS with gram-staining techniques detected and identified the CoNS. SPE-LC-MS/MS detected and quantified nine commonly used antibiotics in the samples. The results showed 63 CoNS isolates detected in 47 (12%) samples, with S. haemolyticus (78%) and S. epidermidis (8%) being predominant. Most of the isolates (95%) were resistant to at least one antibiotic, with the highest resistance observed against sulphamethoxazole (87%). Resistance profiles in samples from DDW and KG were largely comparable, but with some differences. For instance, DDW isolates were more resistant to gentamicin (p = 0.0244), trimethoprim (p = 0.0045), and cefoxitin (p = 0.0078), whereas KG isolates were more resistant to erythromycin (p = 0.0356). Although the volunteers had not knowingly consumed antibiotics two weeks before sampling, antibiotic residues, ranging between 1.44-17000 ng mL-1 were identified in 22% of urine samples. Samples with antibiotic residues were likely to also contain rCoNS (89%). The most frequent antibiotics detected were tetracycline (63%) and ciprofloxacin (54%). Healthy individuals could thus be reservoirs of antibiotic residues and rCoNS at the community level.

A Rapid Antimicrobial Susceptibility Test for Klebsiella pneumoniae Using a Broth Micro-Dilution Combined with MALDI TOF MS

Background

Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) is a novel method that can be used to identify pathogens and has potential applications in the detection of drug-resistant bacteria.

Purpose

To evaluate the ability of a MALDI-TOF MS-based broth micro-dilution method in detecting the minimum inhibitory concentration (MIC) values of Klebsiella pneumoniae to ceftriaxone and imipenem.

Materials and Methods

Sixty strains of K. pneumoniae with different levels of resistance to carbapenems and cephalosporins were randomly collected. The 0.5 McFarland (Mc) concentration of the bacterial suspension was inoculated in cation-adjusted Mueller-Hinton broth (CAMHB) with a final cell turbidity of 5×10⁵ CFU/mL. The broth was incubated with serial concentrations of antibiotics. After centrifuging the bacterial suspensions, the lysed cells were analyzed by MALDI-TOF MS to identify the growth-promoting or inhibitory effects on K. pneumoniae. The molecular mechanisms of resistance were investigated by PCR and DNA sequencing analysis.

Results

The expression of known resistance genes (blaKPC, blaFOX, blaDHA, blaCTX-M and blaTEM) was detected in the 30 carbapenems-resistant strains. The agreement between the MIC values derived from the MALDI-TOF MS analysis and from the broth micro-dilution method was 61.7% for ceftriaxone and 71.7% for imipenem. According to the Clinical and Laboratory Standards Institute (CLSI) breakpoint of resistance to ceftriaxone and imipenem, the 60 isolates were accurately classified as resistant or susceptible isolates with 100% sensitivity and 100% specificity.

Conclusion

The transmission and infection of multidrug-resistant bacteria could be better managed and treated with the rapid identification of strains and antimicrobial susceptibility. A MALDI-TOF MS-based susceptibility test could be used to identify resistance of K. pneumoniae within a short time-frame. This approach could potentially be used as a supplementary antimicrobial susceptibility test that could be investigated on more bacterial species combined with different antibiotics.

Carbapenem resistance in Acinetobacter baumannii, and their importance in hospital-acquired infections: a scientific review

Carbapenem is an important therapy for serious hospital-acquired infections and for the care of patients affected by multidrug-resistant organisms, specifically Acinetobacter baumannii; however, with the global increase of carbapenem-resistant A. baumannii, this pathogen has significantly threatened public health. Thus, there is a pressing need to better understand this pathogen in order to develop novel treatments and control strategies for dealing with A. baumannii. In this review, we discuss an overview of carbapenem, including its discovery, development, classification and biological characteristics, and its importance in hospital medicine especially in critical care units. We also describe the peculiarity of bacterial pathogen, A. baumannii, including its commonly reported virulence factors, environmental persistence and carbapenem resistance mechanisms. In closing, we discuss various control strategies for overcoming carbapenem resistance in hospitals and for limiting outbreaks. With the appearance of strains that resist carbapenem, the aim of this review is to highlight the importance of understanding this increasingly problematic healthcare-associated pathogen that creates significant concern in the field of nosocomial infections and overall public health.

Antimicrobial sensitivity of Avibacterium paragallinarum isolates from layers in the special region of Yogyakarta, Indonesia

Background and Aim:

Infectious coryza (IC) is an upper respiratory disease of chicken caused by Avibacterium paragallinarum. Its clinical symptoms are swollen face and malodorous sinus exudate. This study was conducted to determine the antimicrobial sensitivity of A. paragallinarum isolates from layers in the Special Region of Yogyakarta, Indonesia.

Materials and Methods:

The samples used in this study were 30 layers that showed IC symptoms. The colony and cell morphology were observed with Gram staining; then, biochemical tests (catalase, oxidase, urease, indole, and motility tests, and carbohydrate fermentation tests using lactose, maltose, mannitol, and sorbitol) were performed to the suspected colony to identify A. paragallinarum. An antibiotic sensitivity test was performed using several antibiotic disks against A. paragallinarum isolates that were cultured on Mueller-Hinton Agar.

Results:

Out of 30 samples, 24 samples (80%) were found positive for A. paragallinarum. All isolates were sensitive to ampicillin (AMP) and amoxicillin (AML) (100%), and chloramphenicol (C) (91.6%). The antibiotics with intermediate sensitivity were enrofloxacin (79.2%), fosfomycin (75%), and ciprofloxacin (54.2%). The isolates were most resistant to erythromycin (100%), followed by tetracycline (87.5%), streptomycin (83.3%), doxycycline and kanamycin (70.8%), and trimethoprim (62.5%).

Conclusion:

Out of the total samples, 24 samples (80%) from layers with IC symptoms were identified biochemically as A. paragallinarum. It was sensitive to AMP, AML, and C.

Tracing Clostridium perfringens strains along the chicken production chain from farm to slaughter by multilocus sequence typing

The current study is undertaken to characterize the prevalence, genotypes distribution, antibiotic resistance and genetic diversity of Clostridium perfringens (C. perfringens) collected from different stages of a chicken production chain. In total, 579 samples from a broiler farm and 378 samples from the slaughterhouse were collected from a large-scale rearing and slaughter one-stop enterprise in Weifang, China, between June and July 2019, of which 30.40% of the samples from farm and 54.50% of samples from slaughterhouse were determined to be positive for C. perfringens, respectively. The contamination of chicken products was relatively serious, with the total positive rate of carcasses at 59.73%; the positive rate of carcass samples was the highest in the evisceration process, which might be the critical point of C. perfringens contamination. A total of 476 isolates of C. perfringens were recovered; and 99.58% of recovered isolates were identified as type A, with the remaining isolates being type G. Antimicrobial susceptibility testing revealed that 97.15% of the isolates showed multiple antibiotic resistance and 67.89% of them were resistant to at least five classes of commonly used antibiotics. Multilocus sequence typing results of 91 representative isolates showed that the isolates can be divided into 74 sequences types (STs); 40.66% of the isolates can be included into seven clonal complexes (CCs). Although most of the isolates were classified as type A, considerable genetic diversity was observed, with the Simpson's diversity index of ST up to 0.9902. Some isolates from farm stage and slaughter stage were distributed in the same ST or CC, indicating that chicken products may be contaminated by the same ST or CC of C. perfringens originated from the farm stage. The high contamination rates of chicken products and the widespread multiple antibiotic resistance of isolates indicated potential public health risks, control measures at rearing and slaughtering stage should be considered to reduce this risk.

Automated Miniaturized Digital Microfluidic Antimicrobial Susceptibility Test Using a Chip-Integrated Optical Oxygen Sensor

We present the first digital microfluidic (DMF) antimicrobial susceptibility test (AST) using an optical oxygen sensor film for in-situ and real-time continuous measurement of extracellular dissolved oxygen (DO). The device allows one to monitor bacterial growth across the entire cell culture area, and the fabricated device was utilized for a miniaturized and automated AST. The oxygen-sensitive probe platinum(II)-5,10,15,20-tetrakis-(2,3,4,5,6-pentafluorophenyl)-porphyrin was embedded in a Hyflon AD 60 polymer and spin-coated as a 100 nm thick layer onto an ITO glass serving as the DMF ground electrode. This DMF-integrated oxygen sensing film was found to cause no negative effects to the droplet manipulation or cell growth on the chip. The developed DMF platform was used to monitor the DO consumption during Escherichia coli (E. coli) growth caused by cellular respiration. A rapid and reliable twofold dilution procedure was developed and performed, and the AST with E. coli ATCC 25922 in the presence of ampicillin, chloramphenicol, and tetracycline at different concentrations from 0.5 to 8 μg mL^-1 was investigated. All sample dispensation, dilution, and mixing were performed automatically on the chip within 10 min. The minimum inhibitory concentration values measured from the DMF chip were consistent with those from the standard broth microdilution method but requiring only minimal sample handling and working with much smaller sample volumes.

Microbiological Concordance in the Management of Diabetic Foot Ulcer Infections with Osteomyelitis, on the Basis of Cultures of Different Specimens at a Diabetic Foot Center in China

OBJECTIVE

This study aimed to assess the microbiological concordance between swab and soft tissue cultures, and corresponding bone specimen cultures from patients with diabetic foot osteomyelitis (DFO). We aimed to analyze the bone specimens' antimicrobial susceptibilities, and to improve clinical management of diabetic foot ulcer infections by using proper antibiotics.

METHODS

The microbial culture results of ulcer swabs, and soft tissue and bone tissue specimens, and the antimicrobial susceptibility tests of bone specimens from patients with DFO were analyzed in a single diabetic foot center.

RESULTS

A total of 60 patients with results from three specimens were included. Staphylococcus aureus was the most common bacterium isolated from the three specimens. The microbiological results for the three specimens were identical in 12 cases, the culture results from swabs and bone tissue specimens were identical in 14 cases, and the results from soft tissue and bone tissue were identical in 46 cases. The concordance of the results of pathogens isolated between soft tissue and bone specimen cultures was higher than that between the swab and bone cultures. Gram-positive bacteria were more sensitive to moxifloxacin, linezolid, and vancomycin, while Gram-negative bacteria were more sensitive to piperacillin/tazobactam, cefoperazone/sulbactam, and carbapenems.

CONCLUSION

Soft tissue culture results have more reliable microbiological concordance to identify DFO bacteria than swab culture results and targeted antibiotic therapy for DFO should be based on antimicrobial susceptibility testing in bone tissue specimen cultures.

In vitro Activity of Lefamulin Against the Common Respiratory Pathogens Isolated From Mainland China During 2017-2019

PURPOSE

Lefamulin is a novel antibiotic approved by the U.S. Food and Drug Administration in 2019 for the treatment of community-acquired bacterial pneumonia (CABP). In this study we evaluated the in vitro antimicrobial activity of lefamulin in order to better understand its antibiogram.

METHODS

The test strains were isolated from patients across China during the period from 2017 to 2019, including 634 strains of respiratory pathogens. The minimum inhibitory concentrations (MICs) of lefamulin and comparators were determined by broth microdilution method.

RESULTS

Lefamulin showed potent activity against Streptococcus pneumoniae and Staphylococcus evidenced by 100% inhibition at 0.25 mg/L, and favorable MIC50/90 (0.125/0.125 mg/L) against S. pneumoniae (penicillin MIC ≥ 2 mg/L), MIC50/90 (≤0.015/0.125 mg/L) against methicillin-resistant S. aureus, and MIC50/90 (≤0.015/0.06 mg/L) against methicillin-resistant S. epidermidis. Lefamulin also had good activity against Streptococcus pyogenes and Streptococcus agalactia (MIC50/90: ≤0.015/≤0.015 mg/L), β-lactamase-producing Haemophilus influenzae (MIC50/90: 0.5/1 mg/L), β-lactamase-negative H. influenzae (MIC50/90: 1/1 mg/L), Moraxella catarrhalis (MIC50/90: 0.25/0.25 mg/L), and Mycoplasma pneumoniae (MIC50/90: 0.03/0.03 mg/L) regardless of resistance to azithromycin. Lefamulin was generally more active than the comparators against the test strains.

CONCLUSION

In summary, lefamulin has good and broad-spectrum coverage of respiratory pathogens (methicillin-sensitive and -resistant Staphylococcus, S. pneumoniae, β-hemolytic Streptococcus, H. influenzae, M. catarrhalis and M. pneumoniae). In vitro activity supports the use of lefamulin in the treatment of CABP in China.

Molecular characterization and antimicrobial susceptibility of bacterial isolates present in tap water of public toilets

BACKGROUND

The present study was carried out to investigate the tap water quality of public toilets in Amritsar, Punjab, India.

METHODS

Water samples from the taps of the public toilets were collected in sterile containers and physicochemical and bacteriological analysis was performed using standard methods. Also, genotypic and phenotypic characterization of the bacterial isolates was performed using different biochemical tests and 16S ribosomal RNA analysis. An antibiotic susceptibility test was performed using antibiotics based on their mode of action. A biofilm assay was performed to assess the adhesion potential of the isolates.

RESULTS

A total of 25 bacterial isolates were identified from the water samples, including Acinetobacter junii, Acinetobacter pittii, Acinetobacter haemolyticus, Bacillus pumilus, Bacillus megaterium, Bacillus marisflavi, Bacillus flexus, Bacillus oceanisediminis, Pseudomonas otitidis, Pseudomonas sp. RR013, Pseudomonas sp. RR021, Pseudomonas sp. RR022, Escherichia coli and Enterobacter cloacae. The results of the antimicrobial susceptibility test revealed that the antibiotics cefodroxil, aztreonam, nitrofurantoin, cefepime, ceftazidime and amoxyclav were found to be mostly ineffective against various isolates. The biofilm assay revealed the weak, moderate and strong biofilm producers among them.

CONCLUSIONS

The tap water in the public toilets was microbially contaminated and needs to be monitored carefully. The antibiotic susceptibility profile showed that of 25 bacterial isolates, 5 were multidrug resistant. Bacterial isolates exhibited strong to weak adhesion potential in the biofilm assay.

A Rapid Flow Cytometric Antimicrobial Susceptibility Assay (FASTvet) for Veterinary Use - Preliminary Data

A rapid flow cytometric antimicrobial susceptibility test for bacteria isolated from companion animals – the FASTvet assay, developed by FASTinov^®, was evaluated. Bacterial strains isolated from different biological samples of companion animals with infectious diseases in progress were obtained from several veterinary clinical laboratories across the country. A total of 115 strains, comprising 65 Gram-negative and 50 Gram positive isolates, were incubated with 13 antimicrobial drugs (ampicillin, amoxicillin-clavulanic acid, piperacillin-tazobactam, cefpodoxime, imipenem, enrofloxacin, gentamicin, amikacin for Gram-negative; penicillin, cefoxitin, enrofloxacin, vancomycin and ampicillin for Gram-positive) at breakpoint concentrations following CLSI protocol (CLSI Vet 01, 2018) for 1 h and analyzed by flow cytometry. The overall categorical agreement was 95.6% in case of Gram-negative and of 96.7% in Gram-positive isolates when compared to microdilution. FASTvet kits contribute to reduce the turnaround time (2 vs. 24 h) with early determination of the antimicrobial susceptibility profile. The correct and rapid choice of the target antibiotic therapy, will have a positive impact on animal care, contributing for preventing antimicrobial resistance. In conclusion, FASTinov^® vet kits showed an excellent performance, both for Gram-negative and Gram-positive isolates encouraging us to enlarge the sample size and planning multicentric studies.

Modern Tools for Rapid Diagnostics of Antimicrobial Resistance

Fast, robust, and affordable antimicrobial susceptibility testing (AST) is required, as roughly 50% of antibiotic treatments are started with wrong antibiotics and without a proper diagnosis of the pathogen. Validated growth-based AST according to EUCAST or CLSI (European Committee on Antimicrobial Susceptibility Testing, Clinical Laboratory Standards Institute) recommendations is currently suggested to guide the antimicrobial therapy. Any new AST should be validated against these standard methods. Many rapid diagnostic techniques can already provide pathogen identification. Some of them can additionally detect the presence of resistance genes or resistance proteins, but usually isolated pure cultures are needed for AST. We discuss the value of the technologies applying nucleic acid amplification, whole genome sequencing, and hybridization as well as immunodiagnostic and mass spectrometry-based methods and biosensor-based AST. Additionally, we evaluate the potential of integrated systems applying microfluidics to integrate cultivation, lysis, purification, and signal reading steps. We discuss technologies and commercial products with potential for Point-of-Care Testing (POCT) and their capability to analyze polymicrobial samples without pre-purification steps. The purpose of this critical review is to present the needs and drivers for AST development, to show the benefits and limitations of AST methods, to introduce promising new POCT-compatible technologies, and to discuss AST technologies that are likely to thrive in the future.

Comparison of Microdilution Method with Agar Dilution Method for Antibiotic Susceptibility Test of Neisseria gonorrhoeae

Introduction

Antimicrobial resistance (AMR) of Neisseria gonorrhoeae (N. gonorrhoeae) becomes a grave public health problem in the world. A strengthened Antimicrobial Resistance Surveillance Program is needed to track the trend of AMR development. However, the lack of a proper antimicrobial susceptibility test (AST) method is a barrier to expand the AMR surveillance in China. Traditional agar dilution (AD) method is laborious and E-test strips have no approval license for clinical use. Herein, a Chinese group modified the microdilution (MD) method for clinical ASTs. The objective of this study is to compare the MD method with the AD method for N. gonorrhoeae AST.

Materials and Methods

A total of 166 clinical isolates were tested for antimicrobial susceptibility of ceftriaxone, spectinomycin, azithromycin, ciprofloxacin, tetracycline, and penicillin using MD and AD method simultaneously. Results of MD method were read manually or automatically. Rates of essential agreement (EA), category agreement (CA), minor error, and very major error were compared.

Results

The total EAs (compared with results read manually) of penicillin, tetracycline, ciprofloxacin, spectinomycin, ceftriaxone, and azithromycin were 90.4%, 97.0%, 85.5%, 100.0%, 94%, and 72.3%; and CAs were 82.5%, 94.0%, 100%, 100%, 95.2%, and 94%, respectively.

Conclusion

We conclude that the MD method might be an alternative for clinical AST of N. gonorrhoeae in China. In particular, MD method has the potency of accurate differentiation of isolates resistant to ceftriaxone or azithromycin, which were empirically recommended for gonococcal treatment, but its quality remained suboptimal, and further improvement is needed for clinical use.

Same-day antimicrobial susceptibility test using acoustic-enhanced flow cytometry visualized with supervised machine learning

Purpose. Antimicrobial susceptibility is slow to determine, taking several days to fully impact treatment. This proof-of-concept study assessed the feasibility of using machine-learning techniques for analysis of data produced by the flow cytometer-assisted antimicrobial susceptibility test (FAST) method we developed.Methods. We used machine learning to assess the effect of antimicrobial agents on bacteria, comparing FAST results with broth microdilution (BMD) antimicrobial susceptibility tests (ASTs). We used Escherichia coli (1), Klebsiella pneumoniae (1) and Staphylococcus aureus (2) strains to develop the machine-learning algorithm, an expanded panel including these plus E. coli (2), K. pneumoniae (3), Proteus mirabilis (1), Pseudomonas aeruginosa (1), S. aureus (2) and Enterococcus faecalis (1), tested against FAST and BMD (Sensititre, Oxoid), then two representative isolates directly from blood cultures.Results. Our data machines defined an antibiotic-unexposed population (AUP) of bacteria, classified the FAST result by antimicrobial concentration range, and determined a concentration-dependent antimicrobial effect (CDE) to establish a predicted inhibitory concentration (PIC). Reference strains of E. coli, K. pneumoniae and S. aureus tested with different antimicrobial agents demonstrated concordance between BMD results and machine-learning analysis (CA, categoric agreement of 91 %; EA, essential agreement of 100 %). CA was achieved in 35 (83 %) and EA in 28 (67 %) by machine learning on first pass in a challenge panel of 27 Gram-negative and 15 Gram-positive ASTs. Same-day AST results were obtained from clinical E. coli (1) and S. aureus (1) isolates.Conclusions. The combination of machine learning with the FAST method generated same-day AST results and has the potential to aid early antimicrobial treatment decisions, stewardship and detection of resistance.

Diagnostic evaluation of a point-of-care test for culture and microbial susceptibility testing in canine dermatological infections in clinical practice

Background and Aim

Empirical antimicrobial therapy is frequently given in superficial bacterial folliculitis (SBF) and otitis externa (OE) in dogs, especially for the initial clinical presentation. Culture and subsequent antimicrobial susceptibility testing (AST) are generally limited to chronic cases with poor response to initial therapy. Several factors contribute to the failure to implement the use of AST in veterinary practice, i.e., long laboratory turnaround time or special requirements for sample shipping. Point-of-care (PoC) testing might reduce laboratory turnaround time and costs and the risk of emergence of multidrug-resistant pathogens. This study evaluated the Speed Biogram™ PoC test in canine SBF and OE compared with conventional methods for culture and AST.

Materials and Methods

Thirty-four canine samples were analyzed: eleven from SBF, seven from bacterial OE, four from mixed OE, six from Malassezia spp. OE, and six negative controls. Sensitivity (Se) and specificity (Sp) of the PoC test and the agreement between the PoC test and conventional methods were evaluated.

Results

Se and Sp of PoC test in discriminating between healthy and unhealthy subjects were 100% (95% confidence interval [CI] 87.66-100.00) and 100% (95% CI 54.1-100.0), respectively. For bacterial identification, the k value was 0.532. Se and Sp of PoC tests for AST were 81.73% (95% CI 72.95-88.63) and 93.10% (95% CI 88.86-96.98), respectively with a total good agreement between tests (mean k=0.714), but major (8/27) and very major (19/27) errors were observed in 55% of bacterial conventional culture-positive samples.

Conclusion

PoC test can identify dogs with SBF and OE, but AST is not sufficiently accurate. The lack of susceptibility testing for methicillin makes this test inappropriate for use in small animal practice.

In Vitro Benznidazole and Nifurtimox Susceptibility Profile of Trypanosoma cruzi Strains Belonging to Discrete Typing Units TcI, TcII, and TcV

We ascertain the in vitro Benznidazole (BZN) and Nifurtimox (NFX) susceptibility pattern of epimastigotes, trypomastigotes, and amastigotes of 21 T. cruzi strains, from patients, reservoir, and triatomine bugs of various geographic origins. Using this panel of isolates, we compute the Epidemiological cut off value (CO_wt). Then, the frequency of the susceptible phenotype (Wild type) towards benznidazole (BZN) and nifurtimox (NFX) within this set of strains belonging to three discrete typing units (DTUs), TcI, TcII, and TcV, was deduced. We observed that the susceptibility status of individual T. cruzi isolates toward BZN and NFX is related to the genetic background and underlying factors that are probably related to the individual life trait history of each strain. Analyzing drug susceptibility in this conceptual framework would offer the possibility to evidence a link between isolates expressing a low susceptibility level (not wild-type) as defined by the CO_wt value and none-curative treatment. It will also permit us to track drug-resistant parasites in the T. cruzi population.

Klebsiella pneumoniae-induced multiple invasive abscesses: A case report and literature review

RATIONALE

Klebsiella pneumoniae infection can induce multiple invasive abscesses, and the invasive infection is severe and life-threatening.

PATIENT CONCERNS

A 69-year-old previously healthy Chinese male presented with fever, chill, backache, and ocular pain.

DIAGNOSIS

The blood culture results indicated Klebsiella pneumoniae of the K1 serotype. Multiple invasive abscesses in liver, lung, eye, soft tissue, and central nervous system were identified by imaging examination. Subsequently, the patient experienced right ocular pain accompanied by visual disturbance. Tyndall sign was strongly positive, and lens opacity was observed by the ophthalmologist.

INTERVENTIONS

Full-dose and long-term treatment with meropenem was performed. Intraventricular injection of glass and anterior chamber puncture with antibiotics were performed twice. The patient also underwent an evacuation of the brain abscess.

OUTCOMES

The patient's headache and lumbar backache were relieved, his ophthalmodynia disappeared, and his vision recovered after nearly 3 months of treatment.

LESSONS

Imaging examination is very important for severe Klebsiella pneumoniae infection. The choice of antibiotics is complex, and the antimicrobial regimen should be adjusted according to the assessment of illness and the therapeutic effect. Surgical intervention must be considered for patients with multiple invasive abscesses.

Rapid antimicrobial susceptibility tests for sepsis; the road ahead

Current methods for antimicrobial susceptibility testing (AST) are too slow to affect initial treatment decisions in the early stages of sepsis, when the prescriber is most concerned to select effective therapy immediately, rather than finding out what will not work 1 or 2 days later. There is a clear need for much faster differentiation between viral and bacterial infection, and AST, linked to earlier aetiological diagnosis, without sacrificing either the accuracy of quantitative AST or the low cost of qualitative AST. Truly rapid AST methods are eagerly awaited, and there are several candidate technologies that aim to improve the targeting of our limited stock of effective antimicrobial agents. However, none of these technologies are approaching the point of care and nor can they be described as truly culture-independent diagnostic tests. Rapid chemical and genomic methods of resistance detection are not yet reliable predictors of antimicrobial susceptibility and often rely on prior bacterial isolation. In order to resolve the trade-off between diagnostic confidence and therapeutic efficacy in increasingly antimicrobial-resistant sepsis, we propose a series of three linked decision milestones: initial clinical assessment (e.g. qSOFA score) within 10 min, initial laboratory tests and presumptive antimicrobial therapy within 1 h, and definitive AST with corresponding antimicrobial amendment within an 8 h window (i.e. the same working day). Truly rapid AST methods therefore must be integrated into the clinical laboratory workflow to ensure maximum impact on clinical outcomes of sepsis, and diagnostic and antimicrobial stewardship. The requisite series of development stages come with a substantial regulatory burden that hinders the translation of innovation into practice. The regulatory hurdles for the adoption of rapid AST technology emphasize technical accuracy, but progress will also rely on the effect rapid AST has on prescribing behaviour by physicians managing the care of patients with sepsis. Early adopters in well-equipped teaching centres in close proximity to large clinical laboratories are likely to be early beneficiaries of rapid AST, while simplified and lower-cost technology is needed to support poorly resourced hospitals in developing countries, with their higher burden of AMR. If we really want the clinical laboratory to deliver a specific, same-day diagnosis underpinned by definitive AST results, we are going to have to advocate more effectively for the clinical benefits of bacterial detection and susceptibility testing at critical decision points in the sepsis management pathway.

A Rapid Antimicrobial Susceptibility Test for Determining Yersinia pestis Susceptibility to Doxycycline by RT-PCR Quantification of RNA Markers

Great efforts are being made to develop new rapid antibiotic susceptibility tests to meet the demand for clinical relevance versus disease progression. This is important especially in diseases caused by bacteria such as Yersinia pestis, the causative agent of plague, which grows rapidly in vivo but relatively slow in vitro. This compromises the ability to use standard growth-based susceptibility tests to obtain rapid and proper antibiotic treatment guidance. Using our previously described platform of quantifying antibiotic-specific transcriptional changes, we developed a molecular test based on changes in expression levels of doxycycline response-dependent marker genes that we identified by transcriptomic analysis. This enabled us to determine the minimal inhibitory concentration of doxycycline within 7 h compared to the 24 h required by the standard CLSI test. This assay was validated with various Y. pestis strains. Moreover, we demonstrated the applicability of the molecular test, combined with a new rapid bacterial isolation step from blood cultures, and show its relevance as a rapid test in clinical settings.

Genetic and phenotypic characterizations of drug-resistant Mycobacterium tuberculosis isolates in Cheonan, Korea

BACKGROUND

Mycobacterium tuberculosis (MTB) causes tuberculosis (TB), which is a fatal disease. Cases of drug-resistant MTB have increased in recent years. In this study, we analyzed 7 sites of MTB DNA sequences, including the rpoB and inhA gene, to investigate the relationship between gene mutations and drug resistance in MTB.

METHODS

Mycobacterium tuberculosis liquid culture samples (197 specimens from 74 cases) were collected between June 2015 and May 2016 and sequenced. The results were compared with those obtained from antibiotic susceptibility tests.

RESULTS

In 65 (87.8%) cases, the antibiotic-resistant phenotype was consistent with genotyping results, whereas in 9 (12.2%) cases, there was no match. Eight mutations were detected in the rpoB gene, which showed the highest mutation rate. Sequencing results indicated that these mutations were present in 12 cases.

CONCLUSION

Previously published data on antibiotic resistance genes are insufficient for effective prevention of multidrug- or extensive drug-resistant TB. Additional studies are needed to characterize the complement of antibiotic resistance genes in MTB.

Sudden death of an Indian peafowl (Pavo cristatus) at a zoo due to non-pigmented Serratia marcescens infection

A 16-year-old female Indian peafowl (Pavo cristatus) died two days after recognition of conjunctivitis in the right eye, anorexia and depression. Gross necropsy revealed a thick pseudomembrane under the eyelid and hydropericardium. Histopathological examination revealed hepatocellular necrosis, sinusoidal and vascular congestion and infiltrated inflammatory cells. Infiltration by inflammatory cells was noted in the epicardium. The lungs had mild interstitial pneumonia with the extensive congestion within the capillaries of the air sacs. Tubular interstitial congestion and necrosis was noted in the kidneys. Bacterial culture and nucleotide sequencing of the inflammatory specimens identified the causative agent as Serratia marcescens, an uncommon bacterium in birds. In summary, this study describes the sudden death of an Indian peafowl due to S. marcescens infection, which is rarely seen in animals.

MOLECULAR IDENTIFICATION AND ANTIMICROBIAL RESISTANCE PATTERN OF SEVEN CLINICAL ISOLATES OF Nocardia spp. IN BRAZIL

Nocardia is a ubiquitous microorganism related to pyogranulomatous infection, which is difficult to treat in humans and animals. The occurrence of the disease is on the rise in many countries due to an increase in immunosuppressive diseases and treatments. This report of cases from Brazil presents the genotypic characterization and the antimicrobial susceptibility pattern using the disk-diffusion method and inhibitory minimal concentration with E-test® strips. In summary, this report focuses on infections in young adult men, of which three cases were cutaneous, two pulmonary, one neurological and one systemic. The pulmonary, neurological and systemic cases were attributed to immunosuppressive diseases or treatments. Sequencing analysis of the 16S rRNA segments (1491 bp) identified four isolates of Nocardia farcinica, two isolates of Nocardia nova and one isolate of Nocardia asiatica. N. farcinica was involved in two cutaneous, one systemic and other pulmonary cases; N. nova was involved in one neurological and one pulmonary case; and Nocardia asiatica in one cutaneous case. The disk-diffusion antimicrobial susceptibility test showed that the most effective antimicrobials were amikacin (100%), amoxicillin/clavulanate (100%), cephalexin (100%) and ceftiofur (100%), while isolates had presented most resistance to gentamicin (43%), sulfamethoxazole/trimethoprim (43%) and ampicillin (29%). However, on the inhibitory minimal concentration test (MIC test), only one of the four isolates of Nocardia farcinica was resistant to sulfamethoxazole/trimethoprim.

Research of the heteroresistance of Pseudomonas aeruginosa to imipenem

Pseudomonas aeruginosa (PA) plays plays an important role in nosocomial infection. To explore the heteroresistance of PA to imipenem (IMP), we detected the sensitivity of 140 strains of PA to IMP using the KB method and VITEK method. Combined with resistance mutation analysis, the heteroresistance of PA to IMP was determined. Whilst, the double disk synergy test and SYBGreen RT-PCR for efflux pump were performed in IMP-heteroresistant PA strains. In this study, we confirmed 20 IMP-heteroresistant strains. The double disk synergy tests suggested that none of 20 heteroresistant PA strains produced metalloenzyme. The SYBGreen quantitative RT-PCR revealed that the MexAB expression level of efflux pump in IMP-heteroresistant PA was significantly higher than that in the IMP-sensitive strains (P<0.05), while there was no significantly different between the MexCD expression between resistant strains and sensitive strains (P<0.05). We believe that the clinicians should pay more attention to the PA heteroresistance to IMP, and the heteroesistance of PA to IMP is related to high expression in the MexAB of PA efflux pump.

Macrolides decrease the minimal inhibitory concentration of anti-pseudomonal agents against Pseudomonas aeruginosa from cystic fibrosis patients in biofilm

BACKGROUND

Biofilm production is an important mechanism for bacterial survival and its association with antimicrobial resistance represents a challenge for the patient treatment. In this study we evaluated the in vitro action of macrolides in combination with anti-pseudomonal agents on biofilm-grown Pseudomonas aeruginosa recovered from cystic fibrosis (CF) patients.

RESULTS

A total of 64 isolates were analysed. The biofilm inhibitory concentration (BIC) results were consistently higher than those obtained by the conventional method, minimal inhibitory concentration, (MIC) for most anti-pseudomonal agents tested (ceftazidime: P = 0.001, tobramycin: P = 0.001, imipenem: P < 0.001, meropenem: P = 0.005). When macrolides were associated with the anti-pseudomonal agents, the BIC values were reduced significantly for ceftazidime (P < 0.001) and tobramycin (P < 0.001), regardless the concentration of macrolides. Strong inhibitory quotient was observed when azithromycin at 8 mg/L was associated with all anti-pseudomonal agents tested in biofilm conditions.

CONCLUSIONS

P. aeruginosa from CF patients within biofilms are highly resistant to antibiotics but macrolides proved to augment the in vitro activity of anti-pseudomonal agents.