Identification of Mycobacterium abscessus using the peaks of ribosomal protein L29, L30 and hemophore-related protein by MALDI-MS proteotyping

Mycobacteroides (Mycobacterium) abscessus, which causes a variety of infectious diseases in humans, is becoming detected more frequently in clinical specimens as cases are spreading worldwide. Taxonomically, M. abscessus is composed of three subspecies of M. abscessus subsp. abscessus, M. abscessus subsp. bolletii, and M. abscessus subsp. massiliense, with different susceptibilities to macrolides. In order to identify rapidly these three subspecies, we determined useful biomarker proteins, including ribosomal protein L29, L30, and hemophore-related protein, for distinguishing the subspecies of M. abscessus using the matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) profiles. Thirty-three clinical strains of M. abscessus were correctly identified at the subspecies-level by the three biomarker protein peaks. This study ultimately demonstrates the potential of routine MALDI-MS-based laboratory methods for early identification and treatment for M. abscessus infections.

Characterization of pig tonsils as niches for the generation of Streptococcus suis diversity

Streptococcus suis is a gram-positive bacterium that causes meningitis, septicemia, endocarditis, and other disorders in pigs and humans. We obtained 42 and 50 S. suis isolates from lesions of porcine endocarditis and palatine tonsils, respectively, of clinically healthy pigs in Japan; we then determined their sequence types (STs) by multilocus sequence typing (MLST), cps genotypes, serotypes, and presence of classical major virulence-associated marker genes (mrp, epf, and sly). The 42 isolates from endocarditis lesions were assigned to a limited number of STs and clonal complexes (CCs). On the other hand, the 50 isolates from tonsils were diverse in these traits and seemingly in the degree of virulence, suggesting that tonsils can accommodate a variety of S. suis isolates. The goeBURST full algorithm using tonsil isolates obtained in this study and those retrieved from the database showed that major CCs as well as many other clusters were composed of isolates originating from different countries, and some of the STs were very similar to each other despite the difference in country of origin. These findings indicate that S. suis with not only different but also similar mutations in the genome have survived in tonsils independently across different geographical locations. Therefore, unlike the lesions of endocarditis, the tonsils of pigs seemingly accommodate various S. suis lineages. The present study suggests that S. suis acquired its diversity by natural mutations during colonization and persistence in the tonsils of pigs.

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.

Klebsiella pneumoniae co-harbouring bla NDM-1 , armA and mcr-10 isolated from blood samples in Myanmar

Background. The spread of Enterobacteriaceae coproducing carbapenemases, 16S rRNA methylase and mobile colistin resistance proteins (MCRs) has become a serious public health problem worldwide. This study describes two clinical isolates of Klebsiella pneumoniae coharbouring bla IMP-1, armA and mcr-10.Methods. Two clinical isolates of K. pneumoniae resistant to carbapenems and aminoglycosides were obtained from two patients at a hospital in Myanmar. Their minimum inhibitory concentrations (MICs) were determined by broth microdilution methods. The whole-genome sequences were determined by MiSeq and MinION methods. Drug-resistant factors and their genomic environments were determined.Results. The two K. pneumoniae isolates showed MICs of ≥4 and ≥1024 µg ml-1 for carbapenems and aminoglycosides, respectively. Two K. pneumonaie harbouring mcr-10 were susceptible to colistin, with MICs of ≤0.015 µg ml-1 using cation-adjusted Mueller-Hinton broth, but those for colistin were significantly higher (0.5 and 4 µg ml-1) using brain heart infusion medium. Whole-genome analysis revealed that these isolates coharboured bla NDM-1, armA and mcr-10. These two isolates showed low MICs of 0.25 µg ml-1 for colistin. Genome analysis revealed that both bla NDM-1 and armA were located on IncFIIs plasmids of similar size (81 kb). The mcr-10 was located on IncM2 plasmids of sizes 220 or 313 kb in each isolate. These two isolates did not possess a qseBC gene encoding a two-component system, which is thought to regulate the expression of mcr genes.Conclusion. This is the first report of isolates of K. pneumoniae coharbouring bla NDM-1, armA and mcr-10 obtained in Myanmar.

Emergence of colistin-resistant Acinetobacter modestus harboring intrinsic phosphoethanolamine transferase EptA

OBJECTIVES

Colistin-resistant Gram-negative pathogens have become a serious worldwide medical problem. This study was designed to reveal effects of an intrinsic phosphoethanolamine transferase from Acinetobacter modestus on Enterobacterales.

METHODS

A strain of colistin resistant A. modestus was isolated from a sample of nasal secretions taken from a hospitalized pet cat in 2019 in Japan. The whole genome was sequenced by next generation sequencing, and transformants of Escherichia coli, Klebsiella pneumoniae and Enterobacter cloacae harboring the phosphoethanolamine transferase encoding gene from A. modestus were constracted. Lipid A modification in E. coli transformants was analyzed using electrospray ionization mass spectrometry.

RESULTS

Sequencing of the entire genome revealed that the isolate harbored a phosphoethanolamine transferase encoding gene, eptA_AM, on its chromosome. Transformants of E. coli, K. pneumoniae and E. cloacae harboring both the promoter and eptA_AM gene from A. modestus had 32-fold, 8-fold and 4-fold higher MICs for colistin, respectively, than transformants with control vector. The genetic environment surrounding eptA_AM in A. modestus was similar to the environments surrounding eptA_AM in Acinetobacter junii and Acinetobacter venetianus. Electrospray ionization mass spectrometry analysis revealed that EptA_AM modifies lipid A in Enterobacterales.

CONCLUSIONS

This is the first report to describe the isolation of a strain of A. modestus in Japan and to show that its intrinsic phosphoethanolamine transferase, EptA_AM, contributes to colistin resistance in Enterobacterales and A. modestus.

Emergence of carbapenem-resistant Pseudomonas alcaligenes and Pseudomonas paralcaligenes clinical isolates with plasmids harbouring bla IMP-1 in Japan

Introduction. The emergence of carbapenem-resistant Pseudomonas species producing metallo-β-lactamase (MBL) has become a serious medical problem worldwide. IMP-type MBL was firstly detected in 1991 in Japan. Since then, it has become one of the most prevalent types of MBLs.Hypothesis/Gap statement. Avirulent species of Pseudomonas, such as Pseudomonas alcaligenes, function as reservoirs of drug resistance-associated genes encoding carbapenemases in clinical settings.Methodology. Active surveillance for carbapenem-resistant Gram-negative pathogens was conducted in 2019 at a hospital in Tokyo, Japan. Of the 543 samples screened for carbapenem-resistant isolates, 2 were species of Pseudomonas. One was from a stool sample from a medical staff member, and the other was from a stool sample from a hospitalized patient.Results. Whole-genome sequencing showed that the former isolate was a strain of P. alcaligenes, and the latter was a strain of Pseudomonas paralcaligenes, a species close to P. alcaligenes. Both isolates were resistant to all carbapenems and harboured bla _IMP-1 genes encoding IMP-1 MBL, which conferred resistance to carbapenems. The bla _IMP-1 genes of P. alcaligenes and P. paralcaligenes were located on the plasmids, pMRCP2, 323125 bp in size, and pMRCP1333, 16592 bp in size, respectively. The sequence of 82 % of pMRCP2 was 92 % similar to the sequence of a plasmid of P. aeruginosa PA83, whereas the sequence of 79 % of pMRCP1333 was >95 % similar to the sequence of a plasmid of Achromobacter xylosoxidans FDAARGOS 162. The genomic environments surrounding the bla _IMP-1 of pMRCP2 and pMRCP1333 differed completely from each other.Conclusions. These results indicate that the two isolates acquired bla _IMP-1 from different sources and that P. alcaligenes and P. paralcaligenes function as vectors and reservoirs of carbapenem-resistant genes in hospitals.

Pseudomonas paralcaligenes sp. nov., isolated from a hospitalized patient

A Gram-stain-negative, aerobic, rod-shaped, non-endospore-forming bacterium, designated as strain MRCP1333^T, was isolated from a faecal sample from a hospital patient in Japan. MRCP1333^T grew at temperatures of 15-40 °C (optimum 25-35 °C), with 1.0-3.0 % (w/v, 171-513 mM) NaCl [optimum 1-2 % (w/v), 171-342 mM], and at pH 6.0-9.5 (optimum pH 7.0-8.0). The results of phylogenetic analysis based on the sequences of the 16S rRNA gene and the 53 genes encoding the bacterial ribosome protein subunits indicated that MRCP1333^T represented a member of the Pseudomonas aeruginosa group, most closely related to Pseudomonas alcaligenes. Whole-genome comparisons, using average nucleotide identity, digital DNA-DNA hybridization and average amino acid identity, confirmed that MRCP1333^T represented a distinct species in the P. aeruginosa group. Phenotypic characterization tests demonstrated utilization by this strain of citrate, glycerol, and d-malic acid, the ability to reduce nitrite to nitrogen and the ability of this strain to grow in the presence of minocycline and tetrazolium blue, distinguishing this strain from P. alcaligenes and other closely related species of the P. aeruginosa group. The major fatty acids of MRCP1333^T were summed feature 8 (C_18 : 1ω7c/C_18 : 1ω6c; 38.4 %), summed feature 3 (C_16 : 1ω7c/C_16 : 1ω6c; 21.1 %) and C_16 : 0 (20.6 %). The DNA G+C content of MRCP1333^T was 66.5 mol%. Genetic and phenotypic evidence indicated that MRCP1333^T should be classified as representing a novel species, for which the name Pseudomonas paralcaligenes sp. nov. is proposed. The type strain is MRCP1333^T (=LMG 32254^T,=JCM 34250^T).

Plasmids Harboring a Tandem Duplicate of blaVIM-24 in Carbapenem-Resistant ST1816 Pseudomonas aeruginosa in Japan

The aim of this study was to clarify the biological and clinical significance of a tandem duplicate of bla_VIM-24 in Pseudomonas aeruginosa ST1816 isolates. Thirteen ST1816 isolates carrying a plasmid harboring bla_VIMs were obtained from two medical settings in Japan between 2016 and 2019. Complete sequencing revealed that, of the 13 plasmids, four had a tandem duplicate of bla_VIM-24. These four plasmids harbored a replicon, a relaxase gene, and T4SS genes belonging to IncP-9, MOB_F, and MPF_T, respectively. All four plasmids transferred to PAO1 by filter mating. Cefepime marginally affected the growth of PAO1, carrying a pUCP19 harboring the tandem duplicate. Western blotting analysis showed that the relative intensity of VIM-24 metallo-β-lactamase produced by a PAO1 transformant containing a tandem duplicate was 2.6-fold higher than that produced by a PAO1 transformant containing a single copy. These results suggest that the tandem duplicate of bla_VIM-24 in plasmids may confer resistance against cefepime, enabling P. aeruginosa ST1816 strains to proliferate in hospitals in Japan.

Case report: Whole genome sequence of Clostridium perfringens JUM001 causing acute emphysematous cholecystitis

A strain of Clostridium perfringens was isolated from the bile sample of a patient with emphysematous cholecystitis who underwent a laparoscopic cholecystectomy, followed by treatment with meropenem and recovery. Metagenomic analysis of the bile sample showed that 99.73% of the bile microbiota consisted of C. perfringens, indicating that C. perfringens JUM001 was the causative pathogen of acute emphysematous cholecystitis in this patient. Complete genome sequencing showed that C. perfringens JUM001 contained a circular chromosome of 3,231,023 bp and two circular plasmids, pJUM001-1 of 49,289 bp and pJUM001-2 of 47,855 bp. JUM001 was found to possess a typing toxin gene, plc, but no other typing toxin genes, indicating that its toxinotype is type A. The plasmids pJUM001-1 and pJUM001-2 belonged to the pCP13-like and pCW3-like families of plasmids, respectively, which are characteristic conjugative and archetypical plasmids of C. perfringens. Phylogenetic analysis showed that JUM001 was closely related to C. perfringens strain JXNC-DD isolated from a dog in China. To our knowledge, this is the first report of whole-genome sequences of a clinical isolate of C. perfringens causing acute emphysematous cholecystitis.

Spread of Carbapenem-Resistant Klebsiella pneumoniae Clinical Isolates Producing NDM-Type Metallo-β-Lactamase in Myanmar

A total of 38 isolates of carbapenem-resistant Klebsiella pneumoniae harboring blaNDM were obtained during surveillance of 10 hospitals in Myanmar. Of these 38 isolates, 19 (50%) harbored genes encoding 16S rRNA methylases, such as armA or rmtB. The K. pneumoniae strains tested belonged to 17 sequence types (STs), including the high-risk clonal lineages ST101 and ST147. The ST101 and ST147 isolates carried IncFII plasmids harboring blaNDM-5 and IncFIB(pQil) plasmids harboring blaNDM-1, respectively. These results indicate that IncFII plasmids harboring blaNDM-5 and IncFIB(pQil) plasmids harboring blaNDM-1 have been spreading in K. pneumoniae ST101 and ST147 isolates, respectively, in Myanmar. IMPORTANCE The emergence of carbapenem-resistant K. pneumoniae has become a serious problem in medical settings worldwide. The present study demonstrated that carbapenem-resistant K. pneumoniae strains have been spreading in medical settings in Myanmar. In particular, plasmid genes encoding NDMs and 16S rRNA methylases have been spreading in K. pneumoniae high-risk clones.

Bile Collected From the Normal Gallbladder of Patients During Surgery Has Simple Bacterial Flora

Background

Bile inhibits bacterial growth because it is rich in bacteriostatic compounds such as bile acids. Analytical techniques using a high-intensity sequencer recently revealed bacterial flora in the bile of normal gallbladders in brain-dead patients. Therefore, we performed a microbial flora analysis of bile collected from pathologically normal gallbladders surgically removed from patients with hepatobiliary pancreatic diseases and normal liver function.

Methods

Bacterial DNA was extracted from bile samples and analyzed using 16S rRNA sequencing.

Results

The culture results of all 12 bile samples were negative. However, the results of the 16S ribosome gene analysis suggested the presence of bacterial flora in all samples. The phyla Firmicutes, Proteobacteria, Actinobacteria, and, more specifically, the genera Anaerobacillus, Delftia, Bacillus, Ralstonia, Ochrobactrum, Acidovorax, and Curvibacter were detected in all 12 samples. The results of the 16S rRNA gene profile analysis revealed that Anaerobacillus and Delftia accounted for 58.62%-87.63% of the bacteria identified in each sample.

Conclusion

In a bacterial flora analysis targeting the 16S ribosomal gene, a specific bacterial flora was detected in bile collected from the pathologically normal gallbladders of patients with hepatobiliary pancreatic diseases. Although a diverse bacterial flora was previously reported in the bile of brain-dead patients, the present results revealed a simple bacterial flora with no diversity in the bile samples.

Three novel species of the Bacillus cereus group isolated from clinical samples in Japan

Three Gram-positive bacterial strains, BML-BC004, BML-BC017 and BML-BC059, isolated from blood samples from three inpatients in Japan, were identified as members of Bacillus cereus using matrix-assisted laser desorption ionization time-of-flight MS. The 16S rRNA gene sequences of these three strains were more than 97.1 % similar to 18 type strains belonging to the B. cereus group. Whole-genome comparisons, using average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH), confirmed that the three strains represented three individual distinct species belonging to the B. cereus group. A phylogenetic tree showed that BML-BC004, BML-BC017 and BML-BC059 were located close to B. luti, B. mobilis and B. paramycoides, respectively. Based on these phylogenetic and phenotypic data, including values below the threshold for ANI and dDDH, the three strains should be classified as representing three different novel species of the B. cereus group: Bacillus sanguinis sp. nov., with type strain BML-BC004^T (=DSM 111102^T=JCM 34122^T), Bacillus paramobilis sp. nov., with type strain BML-BC017^T (=DSM 111100^T=JCM 34124^T) and Bacillus hominis sp. nov., with type strain BML-BC059^T (=DSM 111101^T=JCM 34125^T).

Emergence of a multidrug-resistant plasmid encoding bla NDM-1, bla OXA-420 and armA in a clinical isolate of Acinetobacter variabilis in Japan

Acinetobacter variabilis (formerly genospecies 15 sensu Tjernberg and Ursing) has been isolated from humans and animals and was proposed to be a novel species in 2015. A multidrug-resistant A. variabilis isolate, RYU24, was obtained in 2012 from an inpatient in Okinawa, Japan, with no record of overseas travel. The isolate was resistant to carbapenems, aminoglycosides and ciprofloxacin, with minimum inhibitory concentrations (MICs) of 32 µg ml^-1 for imipenem and meropenem; > 1024 µg ml^-1 for amikacin, arbekacin, gentamicin and tobramycin; and 8 µg ml^-1 for ciprofloxacin. The isolate was found to harbour a 68-kbp plasmid carrying bla _NDM-1, which encodes New Delhi metallo-β-lactamase-1 (NDM-1); bla _OXA-420, which encodes an OXA-58-like carbapenemase and; armA, which encodes ArmA 16S rRNA methylase conferring pan-aminoglycoside resistance. To our knowledge, this is the first report of a plasmid harbouring the three major drug-resistance genes, bla _NDM-1, bla _OXA-420 and armA.

Molecular characterisation of carbapenem-resistant Pseudomonas aeruginosa clinical isolates in Nepal

OBJECTIVES

The emergence of carbapenem-resistant Pseudomonas aeruginosa has become a serious worldwide medical problem. The aim of this study was to determine the genetic and epidemiological properties of carbapenem-resistant P. aeruginosa strains isolated from hospitals in Nepal.

METHODS

A total of 43 carbapenem-resistant P. aeruginosa isolates obtained from patients in two hospitals in Nepal between 2018 and 2020 were analysed. Their whole genomes were sequenced by next-generation sequencing. A phylogenetic tree was constructed from single nucleotide polymorphism (SNP) concatemers. Multilocus sequence typing (MLST) was performed and antimicrobial resistance genes were identified.

RESULTS

Of the 43 isolates, 17 harboured genes encoding carbapenemases, including IMP-1, IMP-26, KPC-2, NDM-1, VIM-2 and VIM-5, and 12 harboured genes encoding 16S rRNA methylases, including RmtB4 and RmtF2. The carbapenem-resistant P. aeruginosa isolated in Nepal belonged to various sequence types (STs), including ST235 (5 isolates), ST244 (7 isolates), ST274 (1 isolate), ST357 (10 isolates), ST654 (3 isolates), ST664 (1 isolate), ST773 (1 isolate), ST823 (3 isolates), ST1047 (8 isolates), ST1203 (2 isolates) and ST3453 (2 isolates).

CONCLUSION

To the best of our knowledge, this is the first molecular epidemiological analysis of carbapenem-resistant P. aeruginosa clinical isolates from Nepal. The findings strongly suggest that P. aeruginosa isolates producing carbapenemases and 16S rRNA methylases have spread throughout medical settings in Nepal.

Basis of the persistence of capsule-negative Streptococcus suis in porcine endocarditis inferred from comparative genomics

The capsule (cap) of Streptococcus suis is an anti-phagocytic element and is one of the major virulence factors. However, we have found cap-positive and cap-negative isolates in porcine endocarditis. Here, we compared genome sequences of multiple cap-negative isolates with those of a cap-positive isolate from a single endocarditis. Cap-positive and cap-negative isolates from the same pig were phylogenetically closest compared with those from other pigs. Some of cap-negative isolates from the same pig showed different mutations in capsular polysaccharide synthesis (cps) genes, suggesting that these isolates arisen in pigs after infection. Different mutations in whole-genomes were also found among isolates with identical mutations in cps genes, indicating that mutations in cps genes and the whole-genome occurred independently. Since cap-negative isolates are rarely found in lesions of other diseases, these results suggest that endocarditis lesions may simply favored cap-negative mutants to survive the niches, leading to their persistence in the lesions.

Pseudomonas allokribbensis sp. nov. and Pseudomonas gozinkensis sp. nov., Two New Species Isolated from a Volcanic Island, Izu Oshima, Japan

The genomes of two Pseudomonas strains, IzPS23^T and IzPS32d^T isolated from soil samples of Izu Oshima were compared to Pseudomonas type strains. Whole-genome sequence analysis revealed both belong to the Pseudomonas fluorescens lineage. The average nucleotide identity values of the whole-genome sequences of IzPS23^T and IzPS32d^T compared with other type strains showed high correlations with Pseudomonas kribbensis (93.1%) and Pseudomonas glycinae (93.5%), respectively. Genome-to-genome distances between the whole-genome sequences of IzPS23^T and IzPS32d^T showed correlations with Pseudomonas kribbensis (51.0%) and Pseudomonas glycinae (53.2%), respectively. Genotypic and phenotypic analysis indicated the two strains were novel species, and were named Pseudomonas allokribbensis (IzPS23^T = CECT 9961^T, = LMG 31525^T) and Pseudomonas gozinkensis (IzPS32d^T = CECT 9962^T, = LMG 31526^T), respectively.

Emergence of clinical isolates of Pseudomonas asiatica and Pseudomonas monteilii from Japan harbouring an acquired gene encoding a carbapenemase VIM-2

Pseudomonas asiatica and Pseudomonas monteilii, belonging to the Pseudomonas putida phylogenetic group, are occasionally isolated from clinical samples, partly because they are often misidentified as P. putida in clinical laboratories. There are five reports describing carbapenem-resistant clinical isolates of these species. Carbapenem-resistant strains of P. asiatica and P. monteilii were isolated from stool samples. These isolates were sequenced using Illumina MiSeq and reidentified using average nucleotide identity (ANI) based on comparisons of their whole-genome sequences using the OrthoANI algorithm. The clonal relatedness of the isolates was assessed by pulse-field gel electrophoresis (PFGE). The size of plasmids conveying bla _VIM-2 was examined by Southern blotting. A total of six carbapenem-resistant clinical isolates of P. asiatica (two isolates) and P. monteilii (four isolates) were obtained from stool samples from five patients in a Japanese hospital. All isolates harboured blaVIM-2. The two isolates of P. asiatica had a different pattern in the PFGE analysis, with both having a 23 kb plasmid. Of the four isolates of P. monteilii with similar patterns in the PFGE analysis, three had 320 kb plasmids and one had a 240 kb plasmid. The genetic environments of the 320/240 kb and 23 kb plasmids differed. The results strongly indicated that carbapenem-resistant P. asiatica and P. monteilii producing metallo-β-lactamase are emerging in Japan. This is the first report of carbapenem-resistant P. asiatica and P. monteilii in Japan.

Analysis of appendectomy samples identified dysbiosis in acute appendicitis

Appendicitis is the most common cause of sudden-onset abdominal pain requiring surgery. Culture-independent techniques have revealed that the complex intestinal bacterial ecology is associated with various diseases. To evaluate differences in patient characteristics and gut microbiota distribution in patients with appendicitis, we enrolled 12 patients who underwent appendectomy for appendicitis (appendicitis group) and 13 patients who underwent ileocecal resection or right hemicolectomy for colon cancer (control group). Microbiota were analyzed using next-generation sequencing of surgical specimens from appendix swab samples collected postoperatively. Overall differences in the structure of the gut microbiota were evaluated using the α- and β-diversity indices, which were calculated using the weighted or unweighted UniFrac distance. Changes in the gut microbial distribution were taxonomically evaluated at the phylum and genus levels. The α-diversity of observed species was significantly different between patients with and without inflammation of the appendix. The appendiceal microbiome of patients with appendicitis exhibited the highest unweighted UniFrac distances. There were no significant differences at the phylum level. Ruminococcus (p=0.02) and f_erysipelotrichaceae_g_clostridium (p=0.005) were increased in the control group compared with the appendicitis group. This pilot study provides the first report of the correlation of the gut microbiota with the pathogenesis of appendicitis evaluated using mucus-origin sampling.

Emergence and spread of VIM-type metallo-β-lactamase-producing Pseudomonas aeruginosa clinical isolates in Japan

OBJECTIVES

The aim of this study was to determine the genetic and epidemiological properties of Pseudomonas aeruginosa strains producing VIM-type metallo-β-lactamases isolated from patients in Japan.

METHODS

A total of 1860 clinical isolates of carbapenem-resistant P. aeruginosa were obtained from patients hospitalised in Japan from 2012-2018. Carbapenem-resistant P. aeruginosa isolates were screened for bla_VIM genes by PCR. Antimicrobial susceptibility was determined by the broth microdilution method. The whole genomes of these isolates were sequenced using a next-generation sequencer, and phylogenetic analysis was performed using single nucleotide polymorphism concatemers. Multilocus sequence typing (MLST) was performed and drug resistance genes were identified using whole-genome sequence data.

RESULTS

Of 1860 isolates, 25 bla_VIM-positive isolates were screened in nine medical settings in Japan. The population of VIM-producing P. aeruginosa significantly increased between 2012 and 2018. All 25 bla_VIM-positive isolates were resistant to imipenem, meropenem and ciprofloxacin but were susceptible to colistin. The isolates harboured bla_VIM-1, bla_VIM-2, bla_VIM-24, bla_VIM-60 or the novel variant bla_VIM-66 and belonged to four different sequence types (STs), including ST179, ST233, ST235 and ST1816. The 11 isolates harbouring bla_VIM-24, bla_VIM-60 or bla_VIM-66 were obtained from a single hospital, all belonging to ST1816. VIM-24, VIM-60 and VIM-66 had an amino acid substitution (Arg228Leu) compared with VIM-2.

CONCLUSIONS

The number of P. aeruginosa strains producing VIM-type MBLs has increased in medical settings in Japan. Pseudomonas aeruginosa ST1816 producing VIM enzymes with Arg228Leu substitution have emerged and evolved in a medical setting in Japan.

Re-identification of strains deposited as Pseudomonas aeruginosa, Pseudomonas fluorescens and Pseudomonas putida in GenBank based on whole genome sequences

The taxonomic classification of Pseudomonas species has been revised and updated several times. This study utilized average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) cutoff values of 95 and 70 %, respectively, to re-identify the species of strains deposited in GenBank as P. aeruginosa, P. fluorescens and P. putida. Of the 264 deposited P. aeruginosa strains, 259 were correctly identified as P. aeruginosa, but the remaining five were not. All 28 deposited P. fluorescens strains had been incorrectly identified as P. fluorescens. Four of these strains were re-identified, including two as P. kilonensis and one each as P. aeruginosa and P. brassicacearum, but the remaining 24 could not be re-identified. Similarly, all 35 deposited P. putida strains had been incorrectly identified as P. putida. Nineteen of these strains were re-identified, including 12 as P. alloputida, four as P. asiatica and one each as P. juntendi, P. monteilii and P. mosselii. These results strongly suggest that Pseudomonas bacteria should be identified using ANI and dDDH analyses based on whole genome sequencing when Pseudomonas species are initially deposited in GenBank/DDBJ/EMBL databases.

Pseudomonas izuensis sp. nov., a novel species isolated from Izu Oshima, Japan

An aerobic, Gram-stain-negative, rod-shaped bacterial strain, IzPS43_3003^T, was isolated from Izu Oshima, an active volcanic island located 22 km east of the Izu Peninsula, Japan. The sequence of its 16S rRNA gene indicated that IzPS43_3003^T belongs to the Pseudomonas fluorescens lineage, with its sequence being most similar to that of Pseudomonas vancouverensis DhA-51^T (99.79 %). Phylogenetic analysis based on whole genome sequences showed that IzPS43_3003^T was a member of the Pseudomonas jessenii subgroup. The average nucleotide identity values and genome-to genome distances between the whole genome sequences of IzPS43_3003^T and other type strains showed that the highest correlations were with Pseudomonas moorei DSM 12647^T (87.3 and 33.5% respectively). These genotypic and phenotypic analyses indicated that IzPS43_3003^T belongs to a novel species, Pseudomonas izuensis sp. nov. Its type strain is IzPS43_3003^T (=LMG 31527^T,=CECT 9963^T).

Pseudomonas yangonensis sp. nov., isolated from wound samples of patients in a hospital in Myanmar

Strains of a Gram-negative, aerobic, rod-shaped, non-spore-forming bacterium, designated MY50^T, MY63 and MY101, were isolated from wound samples of three hospitalized patients in Yangon, Myanmar. Strains MY50^T, MY63 and MY101 grew at temperatures of 4-44 °C, in media containing 1.0-7.0 % (w/v) NaCl and at pH 6.0-9.5. Phylogenetic analysis based on 16S rRNA gene and whole genome sequences showed that these strains belonged to the genus Pseudomonas and were part of the Pseudomonas oleovorans group and located close to Pseudomonas guguanensis and Pseudomonas mendocina. Whole-genome comparisons, using average nucleotide identity and digital DNA-DNA hybridization analyses, confirmed that strains MY50^T, MY63 and MY101 were the same strain and they were a distinct species in the P. oleovorans group. Results of phenotypic characterization tests demonstrated that utilization of p-hydroxy-phenylacetic acid, glycerol, l-pyroglutamic acid and quinic acid could distinguish these strains from other species of the P. oleovorans group. These genetic and phenotypic characteristics suggest that they should be classified as representing a novel species, under the proposed name Pseudomonas yangonensis sp. nov. The type strain is MY50^T (=LMG 31602^T,=JCM 33396^T), with a DNA G+C content of 62.82 mol%.

Genome analysis-based reclassification of Pseudomonas fuscovaginae and Pseudomonas shirazica as later heterotypic synonyms of Pseudomonas asplenii and Pseudomonas asiatica, respectively

This study was conducted to clarify the taxonomic status of the species Pseudomonas fuscovaginae and Pseudomonas shirazica . Whole genome sequences for the type strains of P. fuscovaginae and P. shirazica were compared against the closely related type strains of the Pseudomonas putida group and the Pseudomonas fluorescens group species. Average nucleotide identity and digital DNA–DNA hybridization values between P. fuscovaginae LMG 2158T and Pseudomonas asplenii ATCC 23835T were 98.4 and 85.5 %, and between P. shirazica VM14T and Pseudomonas asiatica RYU5T were 99.3 and 95.3 %. These values were greater than recognized thresholds for bacterial species delineation, indicating that they belong to the same genomospecies, respectively. Therefore, P. fuscovaginae and P. shirazica should be reclassified as later heterotypic synonyms of P. asplenii and P. asiatica , respectively.

Pseudomonas atagosis sp. nov., and Pseudomonas akappagea sp. nov., New Soil Bacteria Isolated from Samples on the Volcanic Island Izu Oshima, Tokyo

During the exploration of microbial natural resources, two strains of Pseudomonas, PS14^T and PS24^T, were isolated from samples taken from Izu Oshima, a volcanic island located 120 km southwest of central Tokyo. Phylogenetic analysis based on 16S rRNA gene sequences showed that PS14^T was most similar to Pseudomonas baetica a390^T (99.6%) and Pseudomonas helmanticensis OHA11^T (99.5%), and that PS24^T was most similar to Pseudomonas qingdaonensis JJ3^T (98.8%) and Pseudomonas lutea OK2^T (98.7%). The major fatty acids of these two strains were C_16:0 and C_17:0 cyclo, summed feature 3 (C_16:1 ω6c and/or C_16:1 ω7c), and summed feature 8 (C_18:1 ω7c and/or _18:1 ω6c). The phylogenetic analyses, DNA-DNA hybridization results and phenotypic traits indicated that PS14^T and PS24^T constitute two novel species, Pseudomonas atagosis sp. nov. (type strain PS14^T = CECT 9940^T, = LMG 31496^T) and Pseudomonas akappagea sp. nov. (type strain PS24^T = CECT 9941^T, = LMG 31497^T), respectively. The sequence data of the draft genomes of PS14^T and PS24^T were deposited in the GenBank database under accession numbers VXCA00000000 and VXCP00000000, respectively, and the sequence data of their 16S rRNA genes were deposited in the GenBank database under accession numbers MN396717 and MN382268, respectively.

Molecular epidemiology of multidrug-resistant Acinetobacter baumannii isolates from hospitals in Myanmar

OBJECTIVE

The aim of this study was to clarify the genetic and epidemiological properties of multidrug-resistant Acinetobacter baumannii in medical settings in Myanmar.

METHODS

A total of 45 A. baumannii clinical isolates were obtained in medical settings in Myanmar. The whole genomes were sequenced by a next generation sequencer, and the phylogenetic tree was constructed from single nucleotide polymorphism concatemers. Multilocus sequence types were deduced and drug resistance genes were identified.

RESULTS

Thirty-eight MDR Acinetobacter baumannii isolates were obtained from seven hospitals in Myanmar. The majority of MDR A. baumannii isolates belonged to ST2. Of the 38 isolates, 5 harbored bla_NDM-1, and 28 did armA or armA2 CONCLUSIONS: A. baumannii ST2 producing 16S rRNA methylase ArmA has been spreading in medical settings in Myanmar.

Pseudomonas juntendi sp. nov., isolated from patients in Japan and Myanmar

A Gram-negative, aerobic, rod-shaped, non-spore-forming bacterium, designated as strain BML3^T, was isolated from a sputum sample of a hospital patient in Japan. Strain BML3^T grew at temperatures from 4 to 40 °C, in 1.0-7.0 % (w/v) NaCl and at pH 6.0-9.0. Results of phylogenetic analysis based on the sequences of housekeeping genes, including the 16S rRNA gene and rpoB, rpoD and gyrB, showed that strain BML3^T was part of the Pseudomonas putida group and located close to Pseudomonas asiatica, Pseudomonas monteiliiand P. putida . Whole-genome comparisons, using average nucleotide identity and digital DNA-DNA hybridization, confirmed strain BML3^T to be a distinct species among the P. putida group. Phenotypic characterization tests demonstrated that the utilization of phenylmercuric acetate could distinguish this strain from other closed species of the P. putida group. Based on genetic and phenotypic evidence, strain BML3^T should be classified as a novel species, for which the name Pseudomonas juntendi sp. nov. is proposed. The type strain is BML3^T (=DSM 109244^T,=JCM 33395^T), with a DNA G+C content of 62.66 mol %.

Effects of storage temperature, storage time, and Cary-Blair transport medium on the stability of the gut microbiota

How long fecal samples can withstand a period of refrigeration or room temperature, and the appropriate preservative, are largely unknown. Cary-Blair transport medium has been used for many years because it is inexpensive and prevents bacterial overgrowth. However, its effectiveness for metagenomic analyses has never been tested. We found that the microbial compositions using a 16S rRNA sequence of samples left at 4°C for 3 or 7 days or at 25°C for 1, 3, or 7 days differed significantly from samples stored at -80°C in no-preservative method. Whereas samples stored in Cary-Blair medium remained unchanged for longer periods. The relative abundances of phylum Bacteroidetes and Actinobacteria, changed significantly at 25°C, whereas Cary-Blair medium inhibited the reduction in Bacteroidetes and the increase in Actinobacteria. The bacterial survival counts were significantly lower in the RNAlater samples than in the Cary-Blair samples under aerobic and anaerobic culture conditions. In conclusion, storage time and storage temperature significantly affect the gut microbial composition in fecal samples. Given the low cost, inhibitory effect on bacterial changes, and potential utility in bacterial isolation, Cary-Blair medium containers are suitable for large-scale or hospital-based microbiome studies, especially if direct freezing at -80°C is unavailable.

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.

Pseudomonas asiatica sp. nov., isolated from hospitalized patients in Japan and Myanmar

A novel Gram-negative, aerobic, rod-shaped, non-spore-forming bacterial strain, RYU5^T, was isolated from a stool sample of an inpatient at a hospital in Okinawa, Japan. The optimal growth temperature of RYU5^T was 30 °C. Phylogenetic analysis based on the sequences of housekeeping genes, including the 16S rRNA, rpoB, rpoD and gyrB genes, showed that RYU5^T was a member of the Pseudomonas putida group and was located close to Pseudomonas monteilii and P. putida. Whole-genome comparisons, using average nucleotide identity and digital DNA-DNA hybridization, confirmed that strain RYU5^T should be classified as a novel species of Pseudomonas. Phenotypic characterization tests showed that utilization of d-mannose, d-serine, l-arabinose and d-fructose could distinguish this strain from other related species of the genus Pseudomonas. Based on genetic and phenotypic evidence, strain RYU5^T should be classified as a novel species, for which the name Pseudomonas asiatica sp. nov. is proposed. The type strain is RYU5^T (=DSM 107182^T, =JCM 32716^T), with a DNA G+C content of 62.25 mol%.

Complete Genome Sequence of Streptococcus ruminantium sp. nov. GUT-187T (=DSM 104980T =JCM 31869T), the Type Strain of S. ruminantium, and Comparison with Genome Sequences of Streptococcus suis Strains

Streptococcus ruminantium sp. nov. of type strain GUT-187^T, previously classified as Streptococcus suis serotype 33, is a recently described novel streptococcal species. This study was designed to determine the complete genome sequence of S. ruminantium GUT-187^T using a combination of Oxford Nanopore and the Illumina platform, and to compare this sequence with the genomes of 27 S. suis representative strains. The genome of GUT-187^T was 2,090,539 bp in size, with a GC content of 40.01%. This genome contained 1,961 predicted protein coding DNA sequences (CDSs); of these, 1,685 (85.9%) showed similarity with S. suis CDSs. Of the remaining 276 CDSs, 81 (29.3%) showed some degree of similarity with CDSs of other streptococcal species. The genome of GUT-187^T contained no intact prophage. The numbers of prophages and CRISPR spacers, as well as the presence or absence of genes encoding CRISPR-associated proteins, differed in S. ruminantium and S. suis. A phylogenetic analysis indicates that GUT-187^T may be outgroup to the S. suis strains in our sample, thereby justifying its classification as distinct species. Gene mapping indicated 10.2 times of massive genome rearrangements in average occurred between S. ruminantium and S. suis. There was no significant statistical difference in clusters of orthologous group distribution between S. ruminantium and S. suis.

Development of PCR for identifying Streptococcus parasuis, a close relative of Streptococcus suis

Streptococcus parasuis has recently been removed taxonomically from Streptococcus suis, a zoonotic pathogen. S. parasuis has been detected in healthy pigs and in diseased pigs, which suggests that S. parasuis is involved in the normal microbiota of pigs and has potential pathogenicity. However, the pathogenicity of S. parasuis in pigs is unclear because of the lack of appropriate detection methods that discriminate S. parasuis from S. suis. In this study, we developed a PCR method that is specific for S. parasuis. The detection limit of the PCR was 350 CFU per reaction. Bacteria isolated from the saliva of eight pigs were collected and examined by PCR. Sixty-four isolates positive for PCR were obtained from the samples of all pigs. Thirteen of the 64 isolates were genetically confirmed as S. parasuis, and biologically and biochemically had nearly the same features of known S. parasuis strains, which suggested that strains positive for PCR were S. parasuis. Among the 64 isolates, 28 isolates were serotypes 20, 22, or 26 in the S. suis serotyping scheme. The remaining 36 isolates were untypeable, which suggested the presence of novel serotypes or a capsule-negative form. Therefore, the PCR method described in this study is a useful tool for identifying S. parasuis, and can be used in etiological studies on this bacterium.

Defining the taxonomic status of Streptococcus suis serotype 33: the proposal for Streptococcus ruminantium sp. nov

To clarify the taxonomic classification of Streptococcus suis serotype 33, we performed biochemical and molecular genetic analyses using isolates (GUT-183, GUT-184, GUT-185, GUT-186, GUT-187T, GUT-188, GUT-189, GUT-190, GUT-191, GUT-192 and GUT-193) from bovine endocarditis. A comparative sequence analysis showed 99.2-100 % sequence similarity among the reference strain of S. suis serotype 33 and our isolates for the 16S rRNA gene. These similarities were higher than those between the isolate GUT-187T and S. suis and other streptococci. Comparison of sodA genes also showed high degrees of similarities among the reference strain of S. suis serotype 33 and our isolates (99.7-100 %), which were higher than those between the GUT-187T and S. suis and other streptococci. DNA-DNA relatedness among three isolates (GUT-186, GUT-187T, the reference strain of S. suis serotype 33) was over 76.7 %. In contrast, the relatedness between GUT-187T and the other streptococcal species (S. suis, Streptococcus parasuis, Streptococcus acidominimus and Streptococcus porci) was 8.4-24.9 %. Phylogenetic analyses showed that the isolates did not affiliate closely to any known species of the genus Streptococcus. Moreover, GUT-187T could be distinguished from S. suis and other closely related species of genus Streptococcus using biochemical tests. On the basis of the phenotypic and molecular genetic data, we propose that the isolates of S. suis serotype 33 should be classified into the genus Streptococcus, Streptococcus ruminantium sp. nov. with the type strain GUT-187T (=DSM 104980T=JCM 31869T).

Comparative Genome Analyses of Streptococcus suis Isolates from Endocarditis Demonstrate Persistence of Dual Phenotypic Clones

Many bacterial species coexist in the same niche as heterogeneous clones with different phenotypes; however, understanding of infectious diseases by polyphenotypic bacteria is still limited. In the present study, encapsulation in isolates of the porcine pathogen Streptococcus suis from persistent endocarditis lesions was examined. Coexistence of both encapsulated and unencapsulated S. suis isolates was found in 26 out of 59 endocarditis samples. The isolates were serotype 2, and belonged to two different sequence types (STs), ST1 and ST28. The genomes of each of the 26 pairs of encapsulated and unencapsulated isolates from the 26 samples were sequenced. The data showed that each pair of isolates had one or more unique nonsynonymous mutations in the cps gene, and the encapsulated and unencapsulated isolates from the same samples were closest to each other. Pairwise comparisons of the sequences of cps genes in 7 pairs of encapsulated and unencapsulated isolates identified insertion/deletions (indels) ranging from one to 104 bp in different cps genes of unencapsulated isolates. Capsule expression was restored in a subset of unencapsulated isolates by complementation in trans with cps expression vectors. Examination of gene content common to isolates indicated that mutation frequency was higher in ST28 pairs than in ST1 pairs. Genes within mobile genetic elements were mutation hot spots among ST28 isolates. Taken all together, our results demonstrate the coexistence of dual phenotype (encapsulated and unencapsulated) bacterial clones and suggest that the dual phenotypes arose independently in each farm by means of spontaneous mutations in cps genes.

Development of loop-mediated isothermal amplification to detect Streptococcus suis and its application to retail pork meat in Japan

We here developed a novel loop-mediated isothermal amplification (LAMP) method to detect Streptococcus suis in raw pork meat. This method, designated LAMPSS, targeted the recombination/repair protein (recN) gene of S. suis and detected all serotypes of S. suis, except those taxonomically removed from authentic S. suis, i.e., serotypes 20, 22, 26, 32, 33, and 34. The specificity of LAMPSS was confirmed and its detection limit was 5.4cfu/reaction. Among the 966 raw pork meat samples examined, including sliced pork, minced pork, and the liver, tongue, heart, and small intestine, 255 samples tested positive with LAMPSS. The rate of contamination was higher in the organs than in pork. No significant difference was observed in the total bacterial count between LAMPSS-positive and -negative samples. The number of shops that provided LAMPSS-positive pork was slightly higher in those that sold swine organs and pork than in those that sold only pork, suggesting that cross contamination occurred from the organs to pork. Among the 255 which tested positive for LAMPSS, only 47 samples tested positive for the previously described LAMP specific for S. suis serotype 2. Two isolates of S. suis serotype 2, belonging to sequence type 28, which is potentially hazardous to humans, as well as those of some other serotypes were obtained from 19 out of 47 samples by combining LAMP with a replica plating method. These results suggest that LAMPSS will be a useful tool for the surveillance of raw pork meat in the retail market.

Reappraisal of the taxonomy of Streptococcus suis serotypes 20, 22 and 26: Streptococcus parasuis sp. nov

In order to clarify the taxonomic position of serotypes 20, 22 and 26 of Streptococcus suis , biochemical and molecular genetic studies were performed on isolates (SUT-7, SUT-286T, SUT-319, SUT-328 and SUT-380) reacted with specific antisera of serotypes 20, 22 or 26 from the saliva of healthy pigs as well as reference strains of serotypes 20, 22 and 26. Comparative recN gene sequencing showed high genetic relatedness among our isolates, but marked differences from the type strain S. suis NCTC 10234T, i.e. 74.8–75.7 % sequence similarity. The genomic relatedness between the isolates and other strains of species of the genus Streptococcus , including S. suis, was calculated using the average nucleotide identity values of whole genome sequences, which indicated that serotypes 20, 22 and 26 should be removed taxonomically from S. suis and treated as a novel genomic species. Comparative sequence analysis revealed 99.0–100 % sequence similarities for the 16S rRNA genes between the reference strains of serotypes 20, 22 and 26, and our isolates. Isolate STU-286T had relatively high 16S rRNA gene sequence similarity with S. suis NCTC 10234T (98.8 %). SUT-286T could be distinguished from S. suis and other closely related species of the genus Streptococcus using biochemical tests. Due to its phylogenetic and phenotypic similarities to S. suis we propose naming the novel species Streptococcus parasuis sp. nov., with SUT-286T ( = JCM 30273T = DSM 29126T) as the type strain.