Evaluation of antimicrobial susceptibility tests for Acinetobacter and Pseudomonas species using disks containing a high dose of meropenem.

The emergence and dissemination of carbapenem-resistant species of Acinetobacter and Pseudomonas have become a serious health concern. Routine antimicrobial disk susceptibility tests in clinical laboratories cannot distinguish between isolates that are highly carbapenem-resistant and those that are moderately carbapenem-resistant. The present study describes antimicrobial susceptibility tests using disks containing high doses (1000 µg) of meropenem. The diameters of inhibition zones were significantly negatively correlated with the MICs of Pseudomonas and Acinetobacter species for meropenem (R2: 0.93 and 0.91, respectively) and imipenem (R2: 0.75 and 0.84, respectively). Double disk synergy tests using clavulanic acid or sodium mercaptoacetate can detect ESBL or MBL producers. Susceptibility tests using disks containing high doses of meropenem can easily detect highly carbapenem-resistant isolates in a quantitative manner. These disks may be useful in bacteriological laboratories because of their technical ease, stability, and relatively low cost.

Detection of SARS-CoV-2 omicron variants by immunochromatographic kit.

An immunochromatographic kit using antibodies against recombinant N protein of an omicron B.1.1.529 of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was developed to detect SARS-CoV-2 omicron variants. The kit detected omicron variants (BA.1.18, BA.1.1, BA.2, BA.2.12.1, BA.2.75, BA.4.1, BA.4.6, BE.1, BA.5.2.1, XE, BF.7, BF.7.4.1, XBB.1, XBB.1.5 and BQ.1.1) as well as Wuhan strain and a delta variant.

Antibodies against spike protein of SARS-CoV-2 variants in bovine whey IgG enriched fraction.

Bovine whey IgG enriched fraction contains IgG antibodies against bacterial and viral pathogens, including antibodies against the spike protein [amino acids (aa) 1-1274] of SARS-CoV-2 Wuhan strain (2019-nCoV WHU01). To date, 13 SARS-CoV-2 variants have been identified, including gamma, delta, kappa, and omicron, which contain 10, eight, seven, and over 30 mutations in the spike protein, respectively. We investigated whether bovine whey IgG enriched fraction contains antibodies against spike proteins of these variants, specifically recombinant partial length spike proteins (aa 177-512, aa 509-685, aa 177-324, aa 250-410 and aa 387-516) of these variants. Direct enzyme-linked immunosorbent assays revealed bovine whey IgG enriched fraction contained antibodies against all recombinant spike proteins of these variants with highest reactivity against aa 177-512 region of omicron spike protein. These results indicate bovine whey IgG enriched fraction contains antibodies against spike proteins of several SARS-CoV-2 variants, including omicron.

Assessment of an immunochromatographic kit for detection of severe acute respiratory syndrome coronavirus 2 and influenza viruses.

An immunochromatographic kit was developed to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza viruses (A and B) on two detection positions of a single strip. The sensitivity and specificity for SARS-CoV-2 were 97.4 % and 100 %, respectively, and those for influenza viruses were 100 %, respectively.

Development of an immunochromatographic kit to detect severe acute respiratory syndrome coronavirus 2.

BACKGROUND: The novel severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is responsible for the worldwide coronavirus disease-19 (COVID-19) pandemic, starting in late 2019. The standard diagnostic methods to detect SARS-CoV-2 are PCR-based genetic assays. Antigen-antibody-based immunochromatographic assays are alternative methods of detecting this virus. Rapid diagnosis kits to detect SARS-CoV-2 are urgently needed. STUDY DESIGN: Three monoclonal antibodies against SARS-CoV-2 nucleocapsid (N) protein were used to develop an antigen-antibody-based immunochromatographic kit to detect SARS-CoV-2. These assays were evaluated using　 nasopharyngeal swab specimens collected from patients suspected of having COVID-19. RESULTS: These assays detected recombinant SARS-CoV-2 N protein at concentrations >0.2 ng/mL within 10 min after protein loading, but did not detect the N proteins of Middle East respiratory syndrome coronavirus (MERS-CoV), human coronaviruses OC43 (HCoV-OC43) and 299E (HCoV-229E) and other pathogens causing respiratory infections. Nasopharyngeal swab specimens obtained 1～3, 4～9, and ≥ 10 days after symptom onset from COVID-19 patients diagnosed by RT-PCR showed positivity rates of 100 %, >80 %, and <30 %, respectively. CONCLUSIONS: Kits using this immunochromatographic assay may be a rapid and useful tool for point-of-care diagnosis of COVID-19 when samples are obtained from patients 1～9 days after symptom onset.

Presence of antibodies against SARS-CoV-2 spike protein in bovine whey IgG enriched fraction.

Bovine whey IgG enriched fraction contains antibodies against various human bacterial pathogens. It contains antibodies against some viral antigens, including human respiratory syncytial virus and influenza virus. We investigated whether the IgG enriched fraction has cross-reactivity with IgG antibodies against SARS-CoV-2 spike (S) and nucleocapsid (N) proteins. The full-length and partial-length SARS-CoV-2 S, N, a recombinant protein of the receptor binding domain (RBD) and nine peptides covering the receptor binding motif (RBM) of S were prepared. Direct enzyme-linked immunosorbent assays were conducted using these recombinant proteins and peptides as coating antigens and revealed the IgG enriched fraction contained antibodies against partial-length S [amino acids (aa) 177-512, 288-512, 348-578, 387-516 and 408-664], full-length N (aa 1-419) and partial-length N (aa 1-120, 111-220, 1-220 and 210-419), two RBD peptides, covering aa 427-446 and 502-520 of S, and recombinant RBD of S. These results indicate IgG enriched fraction contains antibodies against SARS-CoV-2.

Evaluation of a new selective agar medium for detection of carbapenem-resistant Enterobacteriaceae.

CRE-JU is a novel selective agar for carbapenem-resistant Enterobacteriaceae that contains ceftazidime, cloxacillin, meropenem, and vancomycin. This study evaluated the ability of 63 carbapenem-resistant isolates and 53 non-carbapenem-resistant Enterobacteriaceae strains clinically isolated in Japan, Myanmar, Nepal, and Vietnam to grow on CRE-JU. CRE-JU showed 92.1% sensitivity and 100% specificity for detecting carbapenem-resistant Enterobacteriaceae compared with dug susceptibility profiles.

Assessment of a newly developed immunochromatographic assay for NDM-type metallo-ß-lactamase producing Gram-negative pathogens in Myanmar.

BACKGROUND: To detect carbapenemase-producing Gram-negative bacteria in bacterial laboratories at medical settings, a new immunochromatographic assay for New Delhi metallo-ß-lactamases (NDMs) was developed. METHODS: The immunochromatographic assay for New Delhi metallo-ß-lactamases producers was developed using rat monoclonal antibodies against NDMs. The assessment was performed using 350 isolates of Gram-negative bacteria, including Acinetobacter baumannii (51 isolates), Enterobacteriaceae (163 isolates), and Pseudomonas aeruginosa (136 isolates) obtained from 2015 to 2017 in medical settings in Myanmar. Of them, 302 isolates were resistant to carbapenems, including imipenem and/or meropenem. The blaNDM genes were identified by PCR and sequencing. RESULTS: Of the 350 clinical isolates tested, 164 (46.9%) (60 isolates of Escherichia coli, 51 isolates of Klebsiella pneumoniae, 25 isolates of Enterobacter cloacae, 23 isolates of P. aeruginosa, and 5 isolates of A. baumannii) were positive on this assay, and all the positive isolates harbored genes encoding NDM-1, - 4, - 5 and - 7. The remaining 186 (53.1%) isolates negative on the assay did not harbor genes encoding NDMs. The assay had a specificity of 100% and a sensitivity of 100%. The assessment revealed that more than 90% of carbapenem-resistant Enterobacteriaceae produced NDMs. CONCLUSIONS: The immunochromatographic assay is an easy-to-use and reliable kit for detection of NDMs-producing Gram-negative bacteria. The assay revealed that NDM-producing Enterobacteriaceae isolates are wide-spread in medical settings in Myanmar.

Development of a New Semi-Selective Lysine-Ornithine-Mannitol-Arginine-Charcoal Medium for the Isolation of Pantoea Species from Environmental Sources in Japan.

Although Pantoea species are widely distributed among plants, water, soils, humans, and animals, due to a lack of efficient isolation methods, the clonality of Pantoea species is poorly characterized. Therefore, we developed a new semi-selective medium designated 'lysine-ornithine-mannitol-arginine-charcoal' (LOMAC) to isolate these species. In an inclusive and exclusive study examining 94 bacterial strains, all Pantoea strains exhibited yellow colonies on LOMAC medium. The performance of the medium was assessed using Pantoea-spiked soils. Percent average agreement relative to the Api20E biochemical test was 97%. A total of 24 soil spot samples and 19 plant types were subjected to practical trials. Of the 91 yellow colonies selected on LOMAC medium, 81 were correctly identified as Pantoea species using the biochemical test. The sequencing of 16S rRNA (rrs) and gyrB from these isolates confirmed that Pantoea agglomerans, P. vagans, P. ananatis, and P. deleyi were present in Japanese fields. A phylogenetic analysis using rrs enabled only the limited separation of strains within each Pantoea spp., whereas an analysis using gyrB revealed higher variability and enabled the finer resolution of distinct branches. P. agglomerans isolates were divided into 3 groups, 2 of which were new clades, with the other comprising a large group including biocontrol strains. P. vagans was also in one of the new clades. The present results indicate that LOMAC medium is useful for screening Pantoea species. The use of LOMAC medium will provide new opportunities for identifying the beneficial properties of Japanese Pantoea isolates.

An improved carbapenem inactivation method, CIMTrisII, for carbapenemase production by Gram-negative pathogens.

The modified carbapenem inactivation method (mCIM) is a simple phenotypic screening method for detecting carbapenemase production by Enterobacteriaceae and Pseudomonas aeruginosa. We recently developed another modified carbapenem inactivation method (CIMTris), in which carbapenemase is extracted from bacteria with Tris-HCl buffer, to detect carbapenemase production by Acinetobacter and Pseudomonas species. This study describes an improved carbapenem inactivation method, CIMTrisII, for detecting carbapenemase production by Gram-negative pathogens, including Enterobacteriaceae, Acinetobacter and Pseudomonas species. CIMTrisII was different from CIMTris in the concentration of Meropenem disks (5-µg MEM disks vs. 10-µg MEM disks), the inoculum volume of the bacteria (a 5-µl loopful vs. a 10 µl loopful) and the incubation time (1 vs. 2 h). CIMTrisII showed an overall sensitivity of 99.3 % and an overall specificity of 95.0 % for tested isolates. In comparison, CIMTris showed a sensitivity of 96.1 % and a specificity of 96.3 %, and mCIM showed a sensitivity of 67.1 % and a specificity of 100 %. CIMTrisII is thus deemed useful for detecting carbapenemase production by Gram-negative pathogens.

[Development and Evaluation of a New Selective Culture Medium, KBM Anaero RS-GNR, for Detection of Anaerobic Gram Negative Rods].

The laboratory culture methods for isolating drug-resistant pathogens has been the gold standard in medical microbiology, and play pivotal roles in the overall management of infectious diseases. Recently, several reports have emphasized the development of antibiotics-resistance among anaerobic gram-negative rods, especially Genus Bacteroides and Prevotella. Therefore, a selective culture method to detect these pathogens is needed. We developed here the new selective culture medium, termed "KBM Anaero RS-GNR," for detecting anaerobic Gram-negative rods. Growth capability and selectivity of the agar medium were assessed by using the pure culture suspensions of more than 100 bacterial strains as well as the 13 samples experimentally contaminated with these bacterial strains. This new medium, "KBM Anaero RS-GNR," successfully showed the selective isolation of anaerobic Gram-negative rods. Compared with commercially available medium, "PV Brucella HK Agar, " which is also designed to detect anaerobic Gram-negative rods, there was no significant difference of the overall detection efficiency between two media. However, "KBM Anaero RS-GNR" showed superior to selectivity for anaerobic Gram-negative rods, especially from the samples contaminated with Candida species. Thus, the culture method using KBM Anaero RS-GNR is relevant for isolation of anaerobic Gram-negative rods especially from clinical specimens.

[Utility of the Rapid Staining with the Use of Microwave for Detection of Genus Mycobacterium].

Recently, many laboratories use fluorescence microscopy for rapid screening of clinical specimens for detection of Genus Mycobacterium. The success of the stain depends on the staining temperature at which the fluorescent dye could uniformly penetrate the cell wall through waxy lipid barrier of the mycobacterial organism. Therefore, this process requires a precise heating control. In this study, to control the temperature during fluorescent auramine- rhodamine staining, we explored the potential use of microwave. The efficiency of microwave irradiation during the staining process was evaluated by using a Mycobacterium avium-containing sputum of which the smear slide was irradiated with several different conditions in combination of time and wattage. As a result, 1) the liquid temperature of the stain correlated well with wattage of microwave irradiation. 2) The tubercle bacilli were easily visualized as brilliant fluorescent bacilli in an orange color when it was set at the best condition of 600 W and 10 sec irradiation. 3) The sensitivity of microscopy with this staining method (MW method) was higher than those of conventional staining methods such as Ziehl-Neelsen staining and standard auramine-rhodamine staining, demonstrating that MW method can be applicable to the sputum slides which contained a few bacilli. Thus, we established the new staining method that is rapid and easy to perform in clinical laboratories. Since the MW method has not yet been utilized in order to conduct fluorescence microscopy for sputum smears, advancement on this method will make a vast change in testing of acid fast bacilli.

Associations between co-detected respiratory viruses in children with acute respiratory infections.

Viruses are the major etiological agents of acute respiratory infections (ARIs) in young children. Although respiratory virus co-detections are common, analysis of combinations of co-detected viruses has never been conducted in Japan. Nineteen respiratory viruses or subtypes were surveyed using multiplex real-time PCR on 1,044 pediatric (patient age < 6 years) ARI specimens collected in Osaka City, Japan between January 2010 and December 2011. In total, 891 specimens (85.3%) were virus positive (1,414 viruses were detected), and 388 of the virus-positive specimens (43.5%, 388/891) were positive for multiple viruses. The ratio of multiple/total respiratory virus-positive specimens was high in children aged 0-35 months. Statistical analyses revealed that human bocavirus 1 and human adenovirus were synchronously co-detected. On the other hand, co-detections of human parainfluenza virus type 1 (HPIV-1) with HPIV-3, HPIV-3 with human metapneumovirus (hMPV), hMPV with respiratory syncytial virus A (RSV A), hMPV with influenza virus A (H1N1) 2009 (FLUA (H1N1) 2009), RSV A with RSV B, and human rhinovirus and FLUA (H1N1) 2009 were exclusive. These results suggest that young children (<3 years) are highly susceptible to respiratory viruses, and some combinations of viruses are synchronously or exclusively co-detected.

Development of the novel chromogenic screening medium for methicillin-resistant Staphylococcus aureus.

MRSA-chrom, a novel chromogenic screening agar medium for methicillin-resistant Staphylococcus aureus (MRSA), was developed. There were all MRSA strains recovered in 24h as a specific blue-colored colony among 130 microbes including 42 MRSA strains. MRSA-chrom showed the highest detection ratio among 4 commercially available selective media using 50 clinical specimens.

Detection and genetic characterization of human enteric viruses in oyster-associated gastroenteritis outbreaks between 2001 and 2012 in Osaka City, Japan.

Enteric viruses are an important cause of viral food-borne disease. Shellfish, especially oysters, are well recognized as a source of food-borne diseases, and oyster-associated gastroenteritis outbreaks have on occasion become international occurrences. In this study, 286 fecal specimens from 88 oyster-associated gastroenteritis outbreaks were examined for the presence of 10 human enteric viruses using antigenic or genetic detection methods in order to determine the prevalence of these infections. All virus-positive patients were over 18 years old. The most common enteric virus in outbreaks (96.6%) and fecal specimens (68.9%) was norovirus (NoV), indicating a high prevalence of NoV infection associated with the consumption of raw or under-cooked oysters. Five other enteric viruses, aichiviruses, astroviruses, sapoviruses, enteroviruses (EVs), and rotavirus A, were detected in 30.7% of outbreaks. EV strains were characterized into three rare genotypes, coxsackievirus (CV) A1, A19, and EV76. No reports of CVA19 or EV76 have been made since 1981 in the Infectious Agents Surveillance Report by the National Infectious Diseases Surveillance Center, Japan. Their detection suggested that rare types of EVs are circulating in human populations inconspicuously and one of their transmission modes could be the consumption of contaminated oysters. Rapid identification of pathogens is important for the development of means for control and prevention. The results of the present study will be useful to establish an efficient approach for the identification of viral pathogens in oyster-associated gastroenteritis in adults.

A novel chromogenic screening medium for isolation of enterohemorrhagic Escherichia coli.

EHEC-chrom, a novel chromogenic screening agar medium for enterohemorrhagic Escherichia coli (EHEC) , was developed. A total of 52 EHEC strains, which were studied for the inclusivity study, grew and formed blue-green colored colonies on EHEC-chrom. When 43 gram-negative bacteria other than EHEC were inoculated for the exclusivity study, 10 strains grew and formed colorless colonies. A total of 28 gram-positive bacteria failed to grow and 1 yeast strain grew as colorless colonies. EHEC-chrom was compared with CHROMagar™ STEC, XM-EHEC agar and CT-MacConkey base agar with a specific sugar (CT-SorbitolMAC, CT-rhamnoseMAC and CT-sorboseMAC) as commercially available selective agar using 100 food samples artificially contaminated with low levels (<10 logCFU/25g) of EHEC. Numbers of samples from which EHEC was recovered by using EHEC-chrom, CHROMagar™ STEC, XM-EHEC agar and CT-MacConkey base agar with specific sugar were 62, 58, 59 and 60, respectively. Our results suggested EHEC-chrom was a useful alternative for EHEC screening in food.

Detection of five rash-associated viruses using multiplex real-time PCR during 2006-2011.

Many viruses have been reported to be associated with rash development. Multiplex real-time PCR was used to investigate the presence of 5 viruses associated with rashes: measles virus (MV), rubella virus (RV), human parvovirus B19 (PVB19), human herpes virus 6 (HHV-6), and HHV-7. A total of 187 clinical specimens from 169 patients with erythema were collected between January 2006 and December 2011. Virus-positive specimens were as follows: MV (n = 23), PVB19 (n = 8), RV (n = 2), HHV-6 (n = 5), HHV-7 (n = 1), MV and PVB19 (n = 1), and HHV-6 and HHV-7 (n = 1). All of the MV-positive specimens were collected in 2007 and the strains whose sequence were available (21/24, 87.5%) were of genotype D5. The results indicate that multiplex real-time PCR might be a useful screening method for detecting and differentiating rash-associated viruses in clinical specimens.

Increase of GII.2 norovirus infections during the 2009-2010 season in Osaka City, Japan.

During the 2009-2010 season, a significant numerical increase of genotype GII.2 norovirus (NoV)-associated outbreaks was observed in Osaka City, Japan. The most common genotype in that season was GII.2 (44.6%), followed by GII.4 (39.2%). Mostly, GII.2 strains were associated with outbreaks in children and with person-to-person contact. The National Infectious Disease Surveillance Center reported that GII.2 NoV infections were widespread in Japan in that season. Comparative phylogenetic analysis of RNA-dependent RNA polymerase (RdRp) and capsid sequences revealed that this GII.2 epidemic resulted from two genetic strains. The first, GII.2p2 strains, had an identical genotype in the RdRp and capsid genes. GII.2p2 strains in the 2009-2010 season were a different genetic cluster from the strains of spring 2004, the previous epidemic of GII.2 NoV, but showed no unique amino acid change. The second, GII.2 chimera virus (GII.2p16), had GII.16 RdRp and GII.2 capsid genotypes, suggesting prior recombination at the junction of ORF1 and ORF2. GII.2p16 strains had four significant amino acid changes in the P2 subdomain, suggesting antigenic changes. Before the 2009-2010 season, GII.2 chimera viruses had been observed only sporadically. This spreading of GII.2p16 strains in the 2009-2010 season might be the first epidemic of GII.2 chimera virus. This study revealed that the NoV epidemic in the 2009-2010 season differed considerably from the prior season, when GII.4 was predominant. Furthermore, GII.2 strains persisted in human populations by drastic recombination and gradual accumulation of mutations, indicating a prevalent pattern of non-GII.4 genotypes with genetic evolution.