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Urinary antigen tests are a widely used rapid diagnostic method for Legionella pneumonia. However, conventional urinary antigen tests are unable to detect anything other than Legionella pneumophila serogroup 1. The Ribotest Legionella (Ribotest) can detect all serogroups by using antibodies recognizing L. pneumophila ribosomal protein L7/L12 in addition to the conventional L. pneumophila serogroup 1 lipopolysaccharide. The aim of this study was to evaluate the performance of Ribotest against conventional urinary antigen tests, including the detection of Legionellaceae other than L. pneumophila. We investigated the detection sensitivity of various kits using in-vitro culture-soluble antigen extracts of ATCC strains and 22 clinical isolates collected from multiple medical facilities in the Kinki region of Japan. For L. pneumophila serogroup 1, four kits, including Ribotest, had a detection sensitivity of 105 CFU/mL, with only Check Legionella having a sensitivity of 106 CFU/mL. L. pneumophila non-serogroup 1 and Legionellaceae of other species were undetectable by the four conventional kits, whereas Ribotest could detect them with a sensitivity of 105–108 CFU/mL. The Ribotest was also able to detect other species such as Legionella hackeliae , Legionella feeleii , Legionella anisa, Fluoribacter bozemanae , and Fluoribacter dumoffii , but the detection sensitivity of L. hackeliae and L. feeleii was 108 CFU/mL, which was much lower than that of the other strains. The Ribotest has high potential to be applied as a rapid diagnostic method for pneumonia caused by other species of Legionella and Fluoribacter. [ABSTRACT FROM AUTHOR]

The ability to predict which patients with a history of coronavirus disease (COVID-19) will exhibit a high antibody titer is necessary for more efficient screening of potential convalescent plasma donors. We aimed to identify factors associated with a high immunoglobulin G (IgG) titer in Japanese convalescent plasma donors after COVID-19. This cross-sectional study included volunteers undergoing screening for convalescent plasma donation after COVID-19. Serum anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) S-protein IgG antibodies were measured using a high-sensitivity chemiluminescence enzyme immunoassay. IgG antibodies were measured in 581 patients, 534 of whom had full information of selected independent variables. Multiple linear regression analysis revealed that increasing age (1.037 [1,025, 1.048]), days from symptom onset to sampling (0.997 [0.995, 0.998]), fever (1.664 [1.226, 2.259]), systemic corticosteroid use during SARS-CoV-2 infection (2.382 [1.576, 3.601]), and blood type AB (1.478 [1.032, 2.117]) predict antibody titer. Older participants, those who experienced fever during infection, those treated with systemic corticosteroids during infection, those from whom samples were obtained earlier after symptom onset, and those with blood type AB are the best candidates for convalescent plasma donation. Therefore, these factors should be incorporated into the screening criteria for convalescent plasma donation after SARS-CoV-2 infection. [ABSTRACT FROM AUTHOR]

The worldwide spread of organisms with antimicrobial resistance is of concern, especially the trend of significantly increasing carbapenemase-producing Enterobacterales (CPE). In this study, we investigated the annual trend of intestinal CPE carriage rates in inpatients and healthy adults in a primary care hospital in Tenri, Japan. We collected 551 samples of feces from inpatients in our institution and 936 samples from healthy people living in Tenri city from December 2012 to April 2015. All samples were cultured on MacConkey agar plates containing 4 μg/mL ceftazidime for screening test. The colonies grown on the screening medium were detected for carbapenemase genes (bla IMP-1 , bla IMP-2 , bla VIM , bla KPC , bla GES , bla NDM , and bla OXA-48 groups) by multiplex PCR, and CPE were identified by MALDI-TOF MS. Plasmid replicon typing and pulsed-field gel electrophoresis (PFGE) were performed on PCR-positive strains. The CPE carriage rate was 1.6% (9/551) in the inpatient group and 0% (0/936) in the healthy adults group. The numbers of strains positive for the carbapenemase gene were 4 for Enterobacter cloacae , 2 for Klebsiella pneumoniae , 1 for Citrobacter freundii , 1 for Raoultella ornithinolytica and 1 for Escherichia coli. In all CPE strains, the carbapenemase gene was bla IMP-6 and the plasmid replicon type was IncN. The 4 E. cloacae strains showed a similar pattern in PFGE. In the same city in Japan, CPE intestinal carriers were detected only in the inpatient group in this study but not in a healthy adults, suggesting that the spread of asymptomatic CPE carriers was confined to inpatients. [ABSTRACT FROM AUTHOR]

Obligate anaerobes exist as resident flora in various sites in humans, but they are also emphasized as endogenous causative microorganism of infections. We performed surveillance to understand the trend of drug susceptibility in obligate anaerobic bacteria in the Kinki area of Japan. In the experiment, we used 156 obligate anaerobe isolates collected from 13 institutions that participated in the Study of Bacterial Resistance Kinki Region of Japan. MALDI Biotyper was used to identify the collected strains, and among the 156 test strains, those that could be identified with an accuracy of Score Value 2.0 or more included 6 genera, 30 species, and 144 strains (Bacteroides spp. 77 strains, Parabacteroides sp. 2 strains, Prevotella spp. 29 strains, Fusobacterium spp. 14 strains, Porphyromonas spp. 2 strains, and Clostridioides difficile 20 strains), and they were assigned as subject strains for drug susceptibility testing. The drug susceptibility test was carried out by broth microdilution method using Kyokuto Opt Panel MP ANA (Kyokuto Pharmaceutical Industrial Co., Ltd., Tokyo, Japan) and judged according to CLSI criteria. As a result, Bacteroides and Parabacteroides species showed good sensitivities to tazobactam-piperacillin, imipenem, metronidazole and chloramphenicol, and low sensitivities to ampicillin, cefoperazone and vancomycin. Prevotella species showed good sensitivities to sulbactam-ampicillin, tazobactam-piperacillin, cefmetazole, imipenem, doripenem and metronidazole. Susceptibility rates to other drugs were slightly different depending on the bacterial species. Both Fusobacterium spp. and Porphyromonas spp. showed high sensitivities to many drugs. C. difficile was highly sensitive to vancomycin and metronidazole, having MIC 90 s of 0.5 μg/mL and ≤2 μg/mL, respectively. [ABSTRACT FROM AUTHOR]

Abstract A monovalent rotavirus vaccine (RV1) was introduced to the national immunization program in Kenya in July 2014. There was increased detection of uncommon G3P[6] strains that coincided temporally with the timing of this vaccine introduction. Here, we sequenced and characterized the full genomes of two post-vaccine G3P[6] strains, RVA/Human-wt/KEN/KDH1951/2014/G3P[6] and RVA/Human-wt/KEN/KDH1968/2014/G3P[6], as representatives of these uncommon strains. On full-genomic analysis, both strains exhibited a DS-1-like genotype constellation: G3-P[6]-I2-R2-C2-M2-A2-N2-T2-E2-H2. Phylogenetic analysis revealed that all 11 genes of strains KDH1951 and KDH1968 were very closely related to those of human G3P[6] strains isolated in Uganda in 2012–2013, indicating the derivation of these G3P[6] strains from a common ancestor. Because the uncommon G3P[6] strains that emerged in Kenya are fully heterotypic as to the introduced vaccine strain regarding the genotype constellation, vaccine effectiveness against these G3P[6] strains needs to be closely monitored. Highlights • Characterization of uncommon human G3P[6] strains isolated in Kenya. • G3P[6] strains emerged in Kenya in 2014, just after the RV1 vaccine introduction. • Post-vaccine G3P[6] strains exhibited a DS-1-like genotype constellation. • Kenyan G3P[6] strains are fully heterotypic to the introduced RV1 vaccine strain. • Vaccine effectiveness against these G3P[6] strains needs to be closely monitored. [ABSTRACT FROM AUTHOR]

An unusual rotavirus strain, DB2015-066 with the G10P[14] genotype (RVA/Human-wt/THA/DB2015-066/2015/G10P[14]), was detected in a stool sample from a child hospitalized with acute gastroenteritis in Thailand. Here, we sequenced and characterized the full-genome of the strain DB2015-066. On whole genomic analysis, strain DB2015-066 was shown to have a unique genotype constellation: G10-P[14]-I2-R2-C2-M2-A3-N2-T6-E2-H3. The backbone genes of this strain (I2-R2-C2-M2-A3-N2-T6-E2-H3) are commonly found in rotavirus strains from artiodactyls such as cattle. Furthermore, phylogenetic analysis indicated that each of the 11 genes of strain DB2015-066 could be of artiodactyl (likely bovine) origin. Thus, strain DB2015-066 appeared to be derived from through zoonotic transmission of a bovine rotavirus strain. Of note, the VP7 gene of strain DB2015-066 was located in G10 lineage-6 together with ones of bovine and bovine-like rotavirus strains, away from the clusters comprising other G10P[14] strains in G10 lineage-2/4/5/9, suggesting the occurrence of independent bovine-to-human interspecies transmission events. Our observations provide important insights into the origins of rare G10P[14] strains, and into dynamic interactions between artiodactyl and human rotavirus strains. [ABSTRACT FROM AUTHOR]

The 7-valent pneumococcal conjugate vaccine (PCV7) was introduced among children in Japan in 2010. There are no long-term multicenter surveillance studies of antimicrobial resistance in S. pneumoniae before and after the introduction of PCV7. Therefore, we examined chronological trends in antimicrobial resistance among 4534 strains of S. pneumoniae isolated from both children and adults in the Kinki region of Japan during 2001–2015. High-level penicillin and third-generation cephalosporin resistance in S. pneumoniae increased among both children and adults during the period before the introduction of PCV7 (2001–2010). Besides penicillin and cephalosporin, pneumococcal carbapenem and macrolide resistance increased among children. The rate of resistance to these antibiotics was higher among children than among adults. The introduction of PCV7 decreased the rate of non-susceptibility to β-lactam antibiotics and the rate of multidrug resistant S. pneumoniae among children, but not among adults. [ABSTRACT FROM AUTHOR]

Recently, carbapenemase-producing Enterobacteriaceae (CPE) have been spreading worldwide and have become a threat in healthcare systems. We investigated the isolation frequency and molecular epidemiological characteristics of CPE isolated from clinical samples collected at a primary care hospital over the four years of 2010–2013 in Japan. CPE were detected in 17 (0.34%) of 4875 isolates by the broth microdilution method, sodium mercaptoacetate inhibition test, and modified Hodge test using meropenem disks. The frequency of CPE isolates was 0.09% in 2010, 0.17% in 2011, 0.16% in 2012 and 0.82% in 2013. Isolates positive for carbapenemase included Klebsiella pneumoniae (0.92%), Escherichia coli (0.12%), Enterobacter cloacae (0.80%), Klebsiella oxytoca (0.55%), Enterobacter aerogenes (0.81%) and Proteus mirabilis (0.08%). Antimicrobial susceptibility testing showed low MICs for piperacillin-tazobactam, amikacin, ciprofloxacin and levofloxacin, and only one multidrug-resistant strain. The carbapenemase genotype of all strains was IMP-6, and 94% of the strains were simultaneous CTX-M-2 producers. Two K. pneumoniae and 3 E. coli isolates showed the same pulsed-field gel electrophoresis group. Multilocus sequence typing detected no international high-risk clone types. Plasmid replicon typing detected IncN from all CPE strains, and IncF and IncFIB were simultaneously detected in 24% and 18%, respectively. All patients with detected CPE were inpatients, and many were elderly long-term hospitalized patients or had a history of prior vancomycin or levofloxacin antibiotic administration. The rapid spread of CPE is a concern in Japan. Preventive measures must be implemented against the spread of CPE after considering the epidemiological trend of CPE detection, antibiograms, and risk factors. [ABSTRACT FROM AUTHOR]

Infectious diseases caused by extended-spectrum β-lactamase (ESBL)-producing Escherichia coli are prevalent because of nosocomial infection. In addition, colonization of ESBL-producing E. coli in the intestinal tract of community dwellers due to the contamination of meat or environmental water is assumed to be one of the sources, but the causes have not been clarified. To analyze these factors, we investigated the difference in clonal groups using a combination of phylogenetic groups and multilocus sequence typing of ESBL-producing E. coli , which were obtained from the feces of an inpatient group in our hospital and a community-dwelling group living in a Japanese city. The carriage rate of ESBL-producing E. coli in the inpatient group was 12.5% (32/257), similar to that of 8.5% (42/496) in the community dwellers (P = 0.082). Of the ESBL clonal groups detected from the community dwellers, 52% (22/42) were clonal groups, including D-ST1485, D-ST70, D-ST2847, B2-ST550, B2-ST3510, A-ST93, A-ST580, A-ST716 and B1-ST2787, that have not been detected from human pathogens, meat, companion animals and environmental water, whereas all clonal groups detected from the inpatients were those that had already been reported. The rate of fluoroquinolone-resistant ESBL clonal groups colonizing the intestinal tract of the inpatient group rose as the number of hospital days increased. These results indicated that different factors were related to colonization of ESBL-producing E. coli in the feces of the inpatient group and the community-dwelling group. [ABSTRACT FROM AUTHOR]

Human rotavirus strains having the unconventional G4P[6] genotype have been sporadically identified in diarrheic patients in different parts of the world. However, the whole genome of only one human G4P[6] strain from Africa (central Africa) has been sequenced and analyzed, and thus the exact origin and evolutionary pattern of African G4P[6] strains remain to be elucidated. In this study, we characterized the full genome of an African G4P[6] strain (RVA/Human-wt/KEN/KCH148/2019/G4P[6]) identified in a stool specimen from a diarrheic child in Kenya. Full genome analysis of strain KCH148 revealed a unique Wa-like genogroup constellation: G4-P[6]-I1-R1-C1-M1-A1-N1-T7-E1-H1. NSP3 genotype T7 is commonly found in porcine rotavirus strains. Furthermore, phylogenetic analysis showed that 10 of the 11 genes of strain KCH148 (VP7, VP4, VP6, VP1-VP3, NSP1, and NSP3-NSP5) appeared to be of porcine origin, the remaining NSP2 gene appearing to be of human origin. Therefore, strain KCH148 was found to have a porcine rotavirus backbone and thus is likely to be of porcine origin. Furthermore, strain KCH148 is assumed to have been derived through interspecies transmission and reassortment events involving porcine and human rotavirus strains. To our knowledge, this is the first report on full genome-based characterization of a human G4P[6] strain from east Africa. Our observations demonstrated the diversity of human G4P[6] strains in Africa, and provide important insights into the origin and evolutionary pattern of zoonotic G4P[6] strains on the African continent. • Characterization of an unconventional human G4P[6] strain isolated in Kenya. • This is the second African human G4P[6] strain whose full genome has been characterized. • Ten of the 11 genes of the G4P[6] strain appeared to be of porcine and porcine-like origin. • Evidence for interspecies transmission and reassortment events involving porcine and human strains. • There is diversity of zoonotic G4P[6] strains in Africa. [ABSTRACT FROM AUTHOR]

We assessed use of the MicroScan ESBL confirmation panel (Dade Behring, Tokyo, Japan) for the detection of eight Enterobacteriaceae-producing extended-spectrum β-lactamases (ESBL) species. Of 137 bacterial strains isolated from patients in 32 hospitals in the Kinki area of Japan, 91 produced ESBL and comprised 60 bacteria (of E. coli, K. oxytoca, and K. pneumoniae) targeted by the NCCLS ESBL test and 31 non-target bacteria such as chromosomal AmpC-producing bacteria (e.g., Serratia marcescens, Enterobacter spp.). Sensitivity and specificity of the MicroScan panel for the target bacteria were 92% and 93%, respectively; sensitivity and specificity for non-target bacteria were 52% and 100%, respectively. There were 20 ESBL-positive strains that were not inhibited by clavulanic acid in the MicroScan panel (3 of 32 ESBL-producing E. coli strains, 1 of 24 K. pneumoniae, 1 of 4 K. oxytoca, 8 of 13 E. cloacae, and 7 of 14 S. marcescens), and most of them were bacteria not targeted by the NCCLS test. In 19 of the 20 strains, the synergy effect of clavulanic acid was observed in the modified-double-disk synergy test using only the cefepime-disk. Because these strains had high MICs of ≥ 16 μg/ml for cephamycins such as cefoxitin and cefmetazole, these strains might produce high levels of AmpC in addition to ESBL. The MicroScan ESBL confirmation panel showed excellent performance in detecting target, but not other bacteria. Addition of cefepime and clavulanic acid to the MicroScan panel may significantly improve detection of non-target bacteria. [Copyright &y& Elsevier]

An unusual rotavirus strain with the G3P[10] genotype (RVA/Human-wt/THA/MS2015-1-0001/2015/G3P[10]) was identified in a stool sample from a hospitalized child aged 11 months with severe gastroenteritis in Thailand. In the current study, we sequenced and characterized the full genome of strain MS2015-1-0001. On full-genomic analysis, strain MS2015-1-0001 exhibited the following genotype configuration: G3-P[10]-I8-R3-C3-M3-A9-N3-T3-E3-H6, which is identical or closely related to those of bat and bat-like rotavirus strains (MYAS33-like). Furthermore, phylogenetic analysis revealed that all 11 genes of strain MS2015-1-0001 appeared to be of bat origin. Our findings provide evidence for bat-to-human interspecies transmission of rotaviruses and important insights into dynamic interactions between human and bat rotavirus strains. • Characterization of a rare human G3P[10] strain isolated in Thailand. • Each of the 11 genes of the G3P[10] strain appeared to be of bat origin. • Direct evidence for bat-to-human zoonotic transmission of rotaviruses. [ABSTRACT FROM AUTHOR]