Molecular Epidemiology of Carbapenem-Resistant Klebsiella aerogenes in Japan.

Information regarding Klebsiella aerogenes haboring carbapenemase in Japan is limited. A comprehensive nationwide survey was conducted from September 2014 to December 2022, and 67 non-duplicate strains of carbapenem-resistant K. aerogenes were isolated from 57 healthcare facilities in Japan. Through genetic testing and whole-genome sequencing, six strains were found to possess carbapenemases, including imipenemase (IMP)-1, IMP-6, New Delhi metallo-ß-lactamase (NDM)-1, and NDM-5. The strain harboring blaNDM-5 was the novel strain ST709, which belongs to the clonal complex of the predominant ST4 in China. The novel integron containing blaIMP-1 featured the oxacillinase-101 gene, which is a previously unreported structure, with an IncN4 plasmid type. However, integrons found in the strains possessing blaIMP-6, which were the most commonly identified, matched those reported domestically in Klebsiella pneumoniae, suggesting the prevalence of identical integrons. Transposons containing blaNDM are similar or identical to the transposon structure of K. aerogenes harboring blaNDM-5 previously reported in Japan, suggesting that the same type of transposon could have been transmitted to K. aerogenes in Japan. This investigation analyzed mobile genetic elements, such as integrons and transposons, to understand the spread of carbapenemases, highlighting the growing challenge of carbapenem-resistant Enterobacterales in Japan and underscoring the critical need for ongoing surveillance to control these pathogens.

Disseminated tuberculosis with paradoxical reactions caused by a Mycobacterium tuberculosis strain belonging to the Indo-Oceanic lineage: An imported case in Japan.

Tuberculosis remains a major public health concern. Millions of tuberculosis cases and associated deaths have been reported worldwide. The Indo-Oceanic lineage Mycobacterium tuberculosis is common in Southeast Asia and causes extrapulmonary lesions. Only a few case studies on this lineage with genetic analysis using whole-genome sequencing have been reported in the literature. We present a case of disseminated tuberculosis, characterized by a variety of extrapulmonary lesions and paradoxical reactions, caused by the Indo-Oceanic lineage M. tuberculosis in a woman in Myanmar. A 22-year-old Burmese woman had arthritis in the right knee, with unknown aetiology, and was referred to our hospital. Computed tomography of the trunk revealed multiple nodular shadows in both lungs; swollen mediastinal lymph nodes; and small, low-density areas in the spleen. M. tuberculosis was detected in the sputum sample, joint aspirate, subcutaneous tumor, and exudate. She experienced a variety of paradoxical reactions together with aggressive tuberculosis dissemination in all areas of the body. Whole-genome sequencing of the DNA of MTB obtained from sputum and the right cervical subcutaneous abscess confirmed the Indo-Oceanic lineage of M. tuberculosis, the predominant strain in Myanmar. The Indo-Oceanic lineage M. tuberculosis causes disseminated tuberculosis all over the body including the periungual region. When patients show unusual symptoms, physicians should consider the introduction of new strains from foreign countries. Genetic analyses of the strains are recommended to define and confirm the lineages.

Role of the Healthcare Surface Environment in Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Transmission and Potential Control Measures.

The healthcare environment serves as one of the possible routes of transmission of epidemiologically important pathogens, but the role of the contaminated environment on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission remains unclear. We reviewed survival, contamination, and transmission of SARS-CoV-2 via environmental surfaces and shared medical devices as well as environmental disinfection of SARS-CoV-2 in healthcare settings. Coronaviruses, including SARS-CoV-2, have been demonstrated to survive for hours to days on environmental surfaces depending on experimental conditions. The healthcare environment is frequently contaminated with SARS-CoV-2 RNA in most studies but without evidence of viable virus. Although direct exposure to respiratory droplets is the main transmission route of SARS-CoV-2, the contaminated healthcare environment can potentially result in transmission of SARS-CoV-2 as described with other coronaviruses such as SARS and Middle East respiratory syndrome coronaviruses. It is important to improve thoroughness of cleaning/disinfection practices in healthcare facilities and select effective disinfectants to decontaminate inanimate surfaces and shared patient care items.

Chromobacterium haemolyticum Pneumonia Associated with Near-Drowning and River Water, Japan.

We report a severe case of Chromobacterium haemolyticum pneumonia associated with near-drowning and detail the investigation of the pathogen and river water. Our genomic and environmental investigation demonstrated that river water in a temperate region can be a source of C. haemolyticum causing human infections.

Prolonged presence of SARS-CoV-2 in a COVID-19 case with rheumatoid arthritis taking iguratimod treated with ciclesonide.

We report a coronavirus disease 2019 (COVID-19) case with rheumatoid arthritis taking iguratimod. The patient who continued iguratimod therapy without dose reduction was treated with ciclesonide had an uneventful clinical course, but prolonged detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was observed after resolution of symptoms. The effects of disease-modifying antirheumatic drugs (DMARDs) and ciclesonide on clinical course and viral shedding remain unknown and warrant further investigation.

Germicidal Activity against Carbapenem/Colistin-Resistant Enterobacteriaceae Using a Quantitative Carrier Test Method.

Susceptibility to germicides for carbapenem/colistin-resistant Enterobacteriaceae is poorly described. We investigated the efficacy of multiple germicides against these emerging antibiotic-resistant pathogens using the disc-based quantitative carrier test method that can produce results more similar to those encountered in health care settings than a suspension test. Our study results demonstrated that germicides commonly used in health care facilities likely will be effective against carbapenem/colistin-resistant Enterobacteriaceae when used appropriately in health care facilities.

Enhanced terminal room disinfection and acquisition and infection caused by multidrug-resistant organisms and Clostridium difficile (the Benefits of Enhanced Terminal Room Disinfection study): a cluster-randomised, multicentre, crossover study.

BACKGROUND: Patients admitted to hospital can acquire multidrug-resistant organisms and Clostridium difficile from inadequately disinfected environmental surfaces. We determined the effect of three enhanced strategies for terminal room disinfection (disinfection of a room between occupying patients) on acquisition and infection due to meticillin-resistant Staphylococcus aureus, vancomycin-resistant enterococci, C difficile, and multidrug-resistant Acinetobacter. METHODS: We did a pragmatic, cluster-randomised, crossover trial at nine hospitals in the southeastern USA. Rooms from which a patient with infection or colonisation with a target organism was discharged were terminally disinfected with one of four strategies: reference (quaternary ammonium disinfectant except for C difficile, for which bleach was used); UV (quaternary ammonium disinfectant and disinfecting ultraviolet [UV-C] light except for C difficile, for which bleach and UV-C were used); bleach; and bleach and UV-C. The next patient admitted to the targeted room was considered exposed. Every strategy was used at each hospital in four consecutive 7-month periods. We randomly assigned the sequence of strategies for each hospital (1:1:1:1). The primary outcomes were the incidence of infection or colonisation with all target organisms among exposed patients and the incidence of C difficile infection among exposed patients in the intention-to-treat population. This trial is registered with ClinicalTrials.gov, NCT01579370. FINDINGS: 31 226 patients were exposed; 21 395 (69%) met all inclusion criteria, including 4916 in the reference group, 5178 in the UV group, 5438 in the bleach group, and 5863 in the bleach and UV group. 115 patients had the primary outcome during 22 426 exposure days in the reference group (51·3 per 10 000 exposure days). The incidence of target organisms among exposed patients was significantly lower after adding UV to standard cleaning strategies (n=76; 33·9 cases per 10 000 exposure days; relative risk [RR] 0·70, 95% CI 0·50-0·98; p=0·036). The primary outcome was not statistically lower with bleach (n=101; 41·6 cases per 10 000 exposure days; RR 0·85, 95% CI 0·69-1·04; p=0·116), or bleach and UV (n=131; 45·6 cases per 10 000 exposure days; RR 0·91, 95% CI 0·76-1·09; p=0·303) among exposed patients. Similarly, the incidence of C difficile infection among exposed patients was not changed after adding UV to cleaning with bleach (n=38 vs 36; 30·4 cases vs 31·6 cases per 10 000 exposure days; RR 1·0, 95% CI 0·57-1·75; p=0·997). INTERPRETATION: A contaminated health-care environment is an important source for acquisition of pathogens; enhanced terminal room disinfection decreases this risk. FUNDING: US Centers for Disease Control and Prevention.

The Role of Patient Care Items as a Fomite in Healthcare-Associated Outbreaks and Infection Prevention.

Patient-care items can serve as a source or reservoir for healthcare-associated pathogens in hospitals. We reviewed healthcare- associated outbreaks from medical equipment and provide infection prevention recommendations. Multiple healthcare-associated outbreaks via a contaminated patient-care item were identified, including infections with multidrug-resistant organisms. The type of patient care items implicated as a fomite causing healthcare-associated infections (HAIs) has changed over time. Patient populations at risk were most commonly critically ill patients in adult and neonatal intensive care units. Most fomite related healthcare-associated outbreaks were due to inappropriate disinfection practices. Repeated healthcare-associated outbreaks via medical equipment highlight the need for infectious disease professionals to understand that fomites/medical devices may be a source of HAIs. The introduction of new and more complex medical devices will likely increase the risk that such devices serve as a source of HAIs. Assuring appropriate cleaning and disinfection or sterilization of medical equipment is necessary to prevent future fomite-associated outbreaks.

A Prolonged Outbreak of KPC-3-Producing Enterobacter cloacae and Klebsiella pneumoniae Driven by Multiple Mechanisms of Resistance Transmission at a Large Academic Burn Center.

Klebsiella pneumoniae carbapenemase (KPC)-producing Enterobacter cloacae has been recently recognized in the United States. Whole-genome sequencing (WGS) has become a useful tool for analysis of outbreaks and for determining transmission networks of multidrug-resistant organisms in health care settings, including carbapenem-resistant Enterobacteriaceae (CRE). We experienced a prolonged outbreak of CRE E. cloacae and K. pneumoniae over a 3-year period at a large academic burn center despite rigorous infection control measures. To understand the molecular mechanisms that sustained this outbreak, we investigated the CRE outbreak isolates by using WGS. Twenty-two clinical isolates of CRE, including E. cloacae (n = 15) and K. pneumoniae (n = 7), were sequenced and analyzed genetically. WGS revealed that this outbreak, which seemed epidemiologically unlinked, was in fact genetically linked over a prolonged period. Multiple mechanisms were found to account for the ongoing outbreak of KPC-3-producing E. cloacae and K. pneumoniae This outbreak was primarily maintained by a clonal expansion of E. cloacae sequence type 114 (ST114) with distribution of multiple resistance determinants. Plasmid and transposon analyses suggested that the majority of blaKPC-3 was transmitted via an identical Tn4401b element on part of a common plasmid. WGS analysis demonstrated complex transmission dynamics within the burn center at levels of the strain and/or plasmid in association with a transposon, highlighting the versatility of KPC-producing Enterobacteriaceae in their ability to utilize multiple modes to resistance gene propagation.

Genomic Analysis of Multidrug-Resistant Escherichia coli from North Carolina Community Hospitals: Ongoing Circulation of CTX-M-Producing ST131-H30Rx and ST131-H30R1 Strains.

Escherichia coli sequence type 131 (ST131) predominates globally among multidrug-resistant (MDR) E. coli strains. We used whole-genome sequencing (WGS) to investigate 63 MDR E. coli isolates from 7 North Carolina community hospitals (2010 to 2015). Of these, 39 (62%) represented ST131, including 37 (95%) from the ST131-H30R subclone: 10 (27%) from its H30R1 subset and 27 (69%) from its H30Rx subset. ST131 core genomes differed by a median of 15 (range, 0 to 490) single-nucleotide variants (SNVs) overall versus only 7 within H30R1 (range, 3 to 12 SNVs) and 11 within H30Rx (range, 0 to 21). The four isolates with identical core genomes were all H30Rx. Epidemiological and clinical characteristics did not vary significantly by strain type, but many patients with MDR E. coli or H30Rx infection were critically ill and had poor outcomes. H30Rx isolates characteristically exhibited fluoroquinolone resistance and CTX-M-15 production, had a high prevalence of trimethoprim-sulfamethoxazole resistance (89%), sul1 (89%), and dfrA17 (85%), and were enriched for specific virulence traits, and all qualified as extraintestinal pathogenic E. coli The high overall prevalence of CTX-M-15 appeared to be possibly attributable to its association with the ST131-H30Rx subclone and IncF[F2:A1:B-] plasmids. Some phylogenetically clustered non-ST131 MDR E. coli isolates also had distinctive serotypes/fimH types, fluoroquinolone mutations, CTX-M variants, and IncF types. Thus, WGS analysis of our community hospital source MDR E. coli isolates suggested ongoing circulation and differentiation of E. coli ST131 subclones, with clonal segregation of CTX-M variants, other resistance genes, Inc-type plasmids, and virulence genes.

Healthcare Outbreaks Associated With a Water Reservoir and Infection Prevention Strategies.

Hospital water may serve as a reservoir of healthcare-associated pathogens, and contaminated water can lead to outbreaks and severe infections. The clinical features of waterborne outbreaks and infections as well as prevention strategies and control measures are reviewed. The common waterborne pathogens were bacteria, including Legionella and other gram-negative bacteria, and nontuberculous mycobacteria, although fungi and viruses were occasionally described. These pathogens caused a variety of infections, including bacteremia and invasive and disseminated diseases, particularly among immunocompromised hosts and critically ill adults as well as neonates. Waterborne outbreaks occurred in healthcare settings with emergence of new reported reservoirs, including electronic faucets (Pseudomonas aeruginosa and Legionella), decorative water wall fountains (Legionella), and heater-cooler devices used in cardiac surgery (Mycobacterium chimaera). Advanced molecular techniques are useful for achieving a better understanding of reservoirs and transmission pathways of waterborne pathogens. Developing prevention strategies based on water reservoirs provides a practical approach for healthcare personnel.

'No touch' technologies for environmental decontamination: focus on ultraviolet devices and hydrogen peroxide systems.

PURPOSE OF REVIEW: This article reviews 'no touch' methods for disinfection of the contaminated surface environment of hospitalized patients' rooms. The focus is on studies that assessed the effectiveness of ultraviolet (UV) light devices, hydrogen peroxide systems, and self-disinfecting surfaces to reduce healthcare-associated infections (HAIs). RECENT FINDINGS: The contaminated surface environment in hospitals plays an important role in the transmission of several key nosocomial pathogens including methicillin-resistant Staphylococcus aureus, vancomycin-resistant Enterococcus spp., Clostridium difficile, Acinetobacter spp., and norovirus. Multiple clinical trials have now demonstrated the effectiveness of UV light devices and hydrogen peroxide systems to reduce HAIs. A limited number of studies have suggested that 'self-disinfecting' surfaces may also decrease HAIs. SUMMARY: Many studies have demonstrated that terminal cleaning and disinfection with germicides is often inadequate and leaves environmental surfaces contaminated with important nosocomial pathogens. 'No touch' methods of room decontamination (i.e., UV devices and hydrogen peroxide systems) have been demonstrated to reduce key nosocomial pathogens on inoculated test surfaces and on environmental surfaces in actual patient rooms. Further UV devices and hydrogen peroxide systems have been demonstrated to reduce HAI. A validated 'no touch' device or system should be used for terminal room disinfection following discharge of patients on contact precautions. The use of a 'self-disinfecting' surface to reduce HAI has not been convincingly demonstrated.

Review of fungal outbreaks and infection prevention in healthcare settings during construction and renovation.

Hospital construction and renovation activities are an ever-constant phenomenon in healthcare facilities, causing dust contamination and possible dispersal of fungal spores. We reviewed fungal outbreaks that occurred during construction and renovation over the last 4 decades as well as current infection prevention strategies and control measures. Fungal outbreaks still occur in healthcare settings, especially among patients with hematological malignancies and those who are immunocompromised. The causative pathogens of these outbreaks were usually Aspergillus species, but Zygomycetes and other fungi were occasionally reported. Aspergillus most commonly caused pulmonary infection. The overall mortality of construction/renovation-associated fungal infection was approximately 50%. The minimal concentration of fungal spores by air sampling for acquisition of fungal infections remains to be determined. Performing infection control risk assessments and implementing the recommended control measures is essential to prevent healthcare-associated fungal outbreaks during construction and renovation.

Next-Generation Sequencing and Comparative Analysis of Sequential Outbreaks Caused by Multidrug-Resistant Acinetobacter baumannii at a Large Academic Burn Center.

Next-generation sequencing (NGS) analysis has emerged as a promising molecular epidemiological method for investigating health care-associated outbreaks. Here, we used NGS to investigate a 3-year outbreak of multidrug-resistant Acinetobacter baumannii (MDRAB) at a large academic burn center. A reference genome from the index case was generated using de novo assembly of PacBio reads. Forty-six MDRAB isolates were analyzed by pulsed-field gel electrophoresis (PFGE) and sequenced using an Illumina platform. After mapping to the index case reference genome, four samples were excluded due to low coverage, leaving 42 samples for further analysis. Multilocus sequence types (MLST) and the presence of acquired resistance genes were also determined from the sequencing data. A transmission network was inferred from genomic and epidemiological data using a Bayesian framework. Based on single-nucleotide variant (SNV) differences, this MDRAB outbreak represented three sequential outbreaks caused by distinct clones. The first and second outbreaks were caused by sequence type 2 (ST2), while the third outbreak was caused by ST79. For the second outbreak, the MLST and PFGE results were discordant. However, NGS-based SNV typing detected a recombination event and consequently enabled a more accurate phylogenetic analysis. The distribution of resistance genes varied among the three outbreaks. The first- and second-outbreak strains possessed a blaOXA-23-like group, while the third-outbreak strains harbored a blaOXA-40-like group. NGS-based analysis demonstrated the superior resolution of outbreak transmission networks for MDRAB and provided insight into the mechanisms of strain diversification between sequential outbreaks through recombination.

First confirmed case of spondylodiscitis with epidural abscess caused by Parvimonas micra.

Parvimonas micra was renamed species as within Gram-positive anaerobic cocci and rarely causes severe infections in healthy people. We report the first confirmed case of spondylodiscitis with epidural abscess caused by P. micra in a healthy women. The patient has a pain in low back and anterior left thigh. Magnetic resonance imaging and computed tomography detected the affected lesion at the L2 and L3 vertebral bodies. All isolates from the surgical and needle biopsy specimens were identified as P. micra by 16S rRNA and MALDI-TOF. In this case, P. micra showed high sensitivity to antimicrobial therapy. She was successfully treated with debridement and sulbactam/ampicillin, followed by oral metronidazole for a total of 10 weeks. The causative microorganisms of spondylodiscitis are not often identified, especially anaerobic bacteria tend to be underestimated. On the other hand, antimicrobial therapy for spondylodiscitis is usually prolonged. Accordingly, we emphasize the importance of performing accurate identification including anaerobic bacteria.

Microbiological and molecular epidemiological analyses of community-associated methicillin-resistant Staphylococcus aureus at a tertiary care hospital in Japan.

Molecular characterization of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) is generally conducted referred to staphylococcal cassette chromosome mec (SCCmec) type IV or V. CA-MRSA is now a cause of concern since such strains have been isolated not only from individuals in a community but also from patients in healthcare settings. The aim of this study was to analyze microbiological and molecular epidemiological features of CA-MRSA strains at a Japanese tertiary care hospital using PCR based-open reading frame typing (POT). This technique allows for molecular classification into CA-MRSA (POT-CA) and hospital-associated (HA-) MRSA (POT-HA) with clonal discrimination. Clinical MRSA isolates obtained from consecutive patients between October 1, 2012 and September 30, 2013 at the hospital were analyzed in combination with the clinical definition for CA-MRSA by the Centers for Disease Control and Prevention and POT. Of 219 isolates (76 clonal groups), 64 (29.3%) were clinical-HA/POT-CA isolates (22 clonal groups). Some clones of them accumulated in this hospital and might be involved in nosocomial transmission. Virulent factors of the isolates were analyzed, and only one (1.6%) Panton-Valentine leukocidin gene positive isolate but no arginine catabolic mobile element genes positive isolate were found in clinical-HA/POT-CA. Additionally, clinical-HA/POT-CA isolates showed higher antimicrobial susceptibility than clinical-HA/POT-HA, especially to minocycline, doxycycline, and amikacin. The most frequent genotype of molecular CA-MRSA was multi-locus sequence type 5-SCCmecIV, previously not detected in Japan. Although CA-MRSA at this hospital showed low virulence and higher antimicrobial susceptibility, the risk of nosocomial infection from them should be recognized, requiring stricter infection control measures.

A case of culture-negative endocarditis due to Streptococcus tigurinus.

Culture-negative endocarditis remains a diagnostic and therapeutic challenge despite recent medical advances. Streptococcus tigurinus, a novel member of the Streptococcus mitis group, was first identified in Zurich. S. tigurinus possesses virulence determinants and causes invasive infections. We report a case of culture-negative endocarditis with serious complications due to S. tigurinus, which was identified by 16S ribosomal RNA gene sequence analysis of excised valve tissue specimens. This technique is useful for identification of the causative microorganism in patients with culture-negative endocarditis and may facilitate early diagnosis and appropriate antimicrobial treatment.

High frequency of Acinetobacter soli among Acinetobacter isolates causing bacteremia at a tertiary hospital in Japan.

Acinetobacter baumannii is generally the most frequently isolated Acinetobacter species. Sequence analysis techniques allow reliable identification of Acinetobacter isolates at the species level. Forty-eight clinical isolates of Acinetobacter spp. were obtained from blood cultures at Tohoku University Hospital. These isolates were identified at the species level by partial sequencing of the RNA polymerase ß-subunit (rpoB), 16S rRNA, and gyrB genes. Then further characterization was done by using the PCR for detection of OXA-type ß-lactamase gene clusters, metallo-ß-lactamases, and carO genes. Pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing were also performed. The most frequent isolate was Acinetobacter soli (27.1%). Six of the 13 A. soli isolates were carbapenem nonsusceptible, and all of these isolates produced IMP-1. PFGE revealed that the 13 A. soli isolates were divided into 8 clusters. This study demonstrated that A. soli accounted for a high proportion of Acinetobacter isolates causing bacteremia at a Japanese tertiary hospital. Non-A. baumannii species were identified more frequently than A. baumannii and carbapenem-nonsusceptible isolates were found among the non-A. baumannii strains. These results emphasize the importance of performing epidemiological investigations of Acinetobacter species.

Twelve-year survey (2001-2012) of the antimicrobial susceptibility of Streptococcus pneumoniae isolates from otorhinolaryngology clinics in Miyagi Prefecture, Japan.

INTRODUCTION: Streptococcus pneumoniae is one of the most common bacteria causing otorhinolaryngological infections, such as acute otitis media and upper respiratory tract infection. Our group surveyed the drug susceptibility profile of S. pneumoniae isolates from otorhinolaryngology patients. MATERIALS AND METHODS: A total of 41,069 S. pneumoniae isolates were detected at Miyagi Medical Association Health Center between May 2001 and December 2012. Specimens were obtained from patients at 40 otorhinolaryngology outpatient clinics in Miyagi Prefecture, Japan. The minimum inhibitory concentrations (MICs) of 8 antimicrobial agents were measured using the broth microdilution method according to Clinical and Laboratory Standards Institute guidelines. RESULTS: In children aged 0-2 years old, the MIC50 values of penicillins decreased after 2010 (PCG: 1 µg/ml (2010) to 0.06 µg/ml (2012); ABPC: 1 µg/ml (2010) to 0.25 µg/ml (2012)). The prevalence of penicillin-resistant S. pneumoniae (PRSP) decreased from 35.2% (2010) to 14.6% (2012) in rhinorrhea specimens and from 43.4% (2010) to 14.3% (2012) in otorrhea specimens. Susceptibility to cephems (ceftriaxone and cefditoren) and carbapenems (panipenem) also showed improvement after 2010. For macrolides (clarithromycin) and lincosamides (clindamycin), MIC50 values increased in all age groups during the study period, and a high level of resistance was seen until 2012. There were no marked changes of susceptibility to fluoroquinolones (LVFX) during the study period. CONCLUSION: Improvement of susceptibility of S. pneumoniae to ß-lactams occurred after 2010 in Miyagi Prefecture, Japan.