High- #Risk #International #Clones of #Carbapenem-Nonsusceptible #Pseudomonas aeruginosa Endemic to #Indonesian #ICUs: Impact of a Multifaceted Infection Control Intervention Analyzed at the Genomic Level (MBio, abstract)

[Source: MBio, full page: (LINK). Abstract, edited.]

High-Risk International Clones of Carbapenem-Nonsusceptible Pseudomonas aeruginosa Endemic to Indonesian Intensive Care Units: Impact of a Multifaceted Infection Control Intervention Analyzed at the Genomic Level

Andreu Coello Pelegrin, Yulia Rosa Saharman, Aurélien Griffon, Mattia Palmieri, Caroline Mirande, Anis Karuniawati, Rudyanto Sedono, Dita Aditianingsih, Wil H. F. Goessens, Alex van Belkum, Henri A. Verbrugh, Corné H. W. Klaassen, Juliëtte A. Severin

Peter Gilligan, Editor

DOI: 10.1128/mBio.02384-19



Infection control effectiveness evaluations require detailed epidemiological and microbiological data. We analyzed the genomic profiles of carbapenem-nonsusceptible Pseudomonas aeruginosa (CNPA) strains collected from two intensive care units (ICUs) in the national referral hospital in Jakarta, Indonesia, where a multifaceted infection control intervention was applied. We used clinical data combined with whole-genome sequencing (WGS) of systematically collected CNPA to infer the transmission dynamics of CNPA strains and to characterize their resistome. We found that the number of CNPA transmissions and acquisitions by patients was highly variable over time but that, overall, the rates were not significantly reduced by the intervention. Environmental sources were involved in these transmissions and acquisitions. Four high-risk international CNPA clones (ST235, ST823, ST375, and ST446) dominated, but the distribution of these clones changed significantly after the intervention was implemented. Using resistome analysis, carbapenem resistance was explained by the presence of various carbapenemase-encoding genes (blaGES-5, blaVIM-2-8, and blaIMP-1-7-43) and by mutations within the porin OprD. Our results reveal for the first time the dynamics of P. aeruginosa antimicrobial resistance (AMR) profiles in Indonesia and additionally show the utility of WGS in combination with clinical data to evaluate the impact of an infection control intervention. (This study has been registered at www.trialregister.nl under registration no. NTR5541).



In low-to-middle-income countries such as Indonesia, work in intensive care units (ICUs) can be hampered by lack of resources. Conducting large epidemiological studies in such settings using genomic tools is rather challenging. Still, we were able to systematically study the transmissions of carbapenem-nonsusceptible strains of P. aeruginosa (CNPA) within and between ICUs, before and after an infection control intervention. Our data show the importance of the broad dissemination of the internationally recognized CNPA clones, the relevance of environmental reservoirs, and the mixed effects of the implemented intervention; it led to a profound change in the clonal make-up of CNPA, but it did not reduce the patients’ risk of CNPA acquisitions. Thus, CNPA epidemiology in Indonesian ICUs is part of a global expansion of multiple CNPA clones that remains difficult to control by infection prevention measures.

Keywords: Antibiotics; Drugs Resistance; Carbapenem; Pseudomonas aeruginosa; ICU; Nosocomial outbreaks; Indonesia.


A 7-year #surveillance of the #drug #resistance in #Klebsiella pneumoniae from a primary #healthcare center (Ann Clin Microbiol Antimicrob., abstract)

[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]

Ann Clin Microbiol Antimicrob. 2019 Nov 9;18(1):34. doi: 10.1186/s12941-019-0335-8.

A 7-year surveillance of the drug resistance in Klebsiella pneumoniae from a primary health care center.

Li G1, Zhao S1, Wang S1, Sun Y1, Zhou Y1, Pan X2.

Author information: 1 Department of Clinical Laboratory, Affiliated Dongyang Hospital of Wenzhou Medical University, Dongyang, Zhejiang, China. 2 Department of Biomedical Sciences Laboratory, Affiliated Dongyang Hospital of Wenzhou Medical University, No. 60 Wuningxi Road, Dongyang, Zhejiang, China. panfengyuwuzu@163.com.




The increased prevalence of Klebsiella pneumoniae infections and resistance rates are a current cause for concern. However, data for resistance rates in K. pneumoniae strains from primary hospitals and the resistance distribution among the different isolate sample sources are scarce.


All the K. pneumoniae strains were isolated from patients who visited a primary health care center located in Central Zhejiang Province from January 2011 to December 2017. The specimens included blood, sputum, cervical secretions and urine. The species were identified by the Vitek 2 Compact Bacterial Identification and Monitoring System or VITEK-MS and the extended spectrum β-lactamase (ESBL) and drug resistance profiles were identified using the AST-GN13 Gram negative susceptibility card (VITEK-2). The genotype of strains from urine sources was analyzed by detecting TEM and SHV genes. Finally, the drug resistance rates among the isolates from different sample sources were analyzed using the Chi square test with SPSS software.


A total of 5319 K. pneumoniae strains were isolated in this study. Among the 20 antimicrobial drugs studied, the resistance rates of K. pneumoniae strains varied from 1.4% (ertapenem) to 23.1% (nitrofurantoin). The antibiotic resistance rates varied significantly among the isolate samples sources for all, with the highest rates for all antibiotics except for nitrofurantoin found in urine samples. In addition, the ESBL-positive rate in urine samples was 27.1%, significantly higher than that of cervical secretions (20.2%), blood (16.5%) and sputum (15.2%). Compared to the ESBL-negative strains, higher resistance rates were detected in the ESBL-positive strains. The most common genotype of isolates from urine was SHV (28%, 23/82), following by TEM (14.6%, 12/82).


The highest resistance rates of K. pneumoniae strains to most antibiotics found in urine samples are partly due to the ESBLs, indicating that a special attention should be paid in the treatment of urinary tract infection.

KEYWORDS: Drug resistance; ESBL; Klebsiella pneumoniae; Urine

PMID: 31706307 DOI: 10.1186/s12941-019-0335-8

Keywords: Antibiotics; Drugs Resistance; UTI; China; Nosocomial outbreaks.


#Comparison of #infection #control practices in a #Dutch and #US #hospital using the infection #risk scan (#IRIS) method (Am J Infect Control, abstract)

[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]

Am J Infect Control. 2019 Nov 5. pii: S0196-6553(19)30856-9. doi: 10.1016/j.ajic.2019.09.020. [Epub ahead of print]

Comparison of infection control practices in a Dutch and US hospital using the infection risk scan (IRIS) method.

Willemsen I1, Jefferson J2, Mermel L3, Kluytmans J4.

Author information: 1 Department of Microbiology and Infection Control, Amphia Hospital, Breda, the Netherlands. Electronic address: iwillemsen@amphia.nl. 2 Department of Epidemiology & Infection Control, Rhode Island Hospital, Providence, RI, USA. 3 Department of Epidemiology & Infection Control, Rhode Island Hospital, Providence, RI, USA; Department of Medicine, Warren Alpert Medial School of Brown University, Providence, RI, USA. 4 Department of Microbiology and Infection Control, Amphia Hospital, Breda, the Netherlands; Julius Center for Health Sciences and Primary Care, UMC Utrecht, Utrecht University, Utrecht, the Netherlands.




The infection risk scan (IRIS) is a tool to measure the quality of infection control (IC) and antimicrobial use in a standardized way. We describe the feasilibility of the IRIS in a Dutch hospital (the Netherlands, NL) and a hospital in the United States (US).


Cross-sectional measurements were performed. Variables included a hand hygiene indicator, environmental contamination, IC preconditions, personal hygiene of health care workers, use of indwelling medical devices, and use of antimicrobials.


IRIS was performed in 2 wards in a US hospital and 4 wards in a Dutch hospital. Unjustified use of medical devices: none in the US hospital, 2.2% in the Dutch hospital; inappropriate use of antibiotics: 11.7% (US), 19% (NL); items considered not clean: 10% (US); 36% (NL); shortcomings preconditions: 6 of 20 (US), 6 of 40 (NL); health care workers with rings, watches, or long sleeves: 34 of 43 (US), none in the NL hospital; and hand hygiene actions per patient/day: 41 (US) and 10 (NL). US data judged against the Dutch guidelines and vice versa revealed remarkable differences.


We showed the feasibility of using the IRIS in a US hospital. The method provided insight in IC local performance. This method could be the first step to standardize the measurement of the quality of IC and antimicrobial use. However, if the IRIS is used for benchmarking between hospitals in different regions, this should be done in the context of regional guidelines and policies.

Copyright © 2019 Association for Professionals in Infection Control and Epidemiology, Inc. Published by Elsevier Inc. All rights reserved.

KEYWORDS: Antimicrobial resistance; Benchmarking; Guidelines; Infection prevention

PMID: 31703820 DOI: 10.1016/j.ajic.2019.09.020

Keywords: Antibiotics; Drugs Resistance; IPC; HCWs; Nosocomial Outbreaks; USA; Netherlands.


#Risk of #transmission via #medical #employees and importance of routine #infection-prevention #policy in a #nosocomial #outbreak of #MERS: a descriptive analysis from a tertiary care hospital in South #Korea (BMC Pulm Med., abstract)

[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]

BMC Pulm Med. 2019 Oct 30;19(1):190. doi: 10.1186/s12890-019-0940-5.

Risk of transmission via medical employees and importance of routine infection-prevention policy in a nosocomial outbreak of Middle East respiratory syndrome (MERS): a descriptive analysis from a tertiary care hospital in South Korea.

Ki HK1, Han SK2, Son JS3, Park SO4.

Author information: 1 Division of infectious diseases, Department of Internal Medicine, School of Medicine, Konkuk University, Konkuk University Medical Centre, 120-1 Neungdong-ro (Hwayang-dong), Gwangjin-gu, Seoul, 05029, Republic of Korea. 2 Department of Emergency Medicine, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, 108 Pyung-Dong, Jongno-Gu, Seoul, 110-746, Republic of Korea. 3 Division of Infectious Diseases, Department of Internal Medicine, Kyung Hee University Hospital at Gangdong, 892, Dongnam-ro, Gangdong-gu, Seoul, Republic of Korea. 4 Department of Emergency Medicine, School of Medicine, Konkuk University, Konkuk University Medical Centre, 120-1 Neungdong-ro (Hwayang-dong), Gwangjin-gu, Seoul, 05029, Republic of Korea. empso@kuh.ac.kr.




In 2015, South Korea experienced an outbreak of Middle East respiratory syndrome (MERS), and our hospital experienced a nosocomial MERS infection. We performed a comprehensive analysis to identify the MERS transmission route and the ability of our routine infection-prevention policy to control this outbreak.


This is a case-cohort study of retrospectively analysed data from medical charts, closed-circuit television, personal interviews and a national database. We analysed data of people at risk of MERS transmission including 228 in the emergency department (ED) and 218 in general wards (GW). Data of personnel location and movement, personal protection equipment and hand hygiene was recorded. Transmission risk was determined as the extent of exposure to the index patient: 1) high risk: staying within 2 m; 2) intermediate risk: staying in the same room at same time; and 3) low risk: only staying in the same department without contact.


The index patient was an old patient admitted to our hospital. 11 transmissions from the index patient were identified; 4 were infected in our hospital. Personnel in the ED exhibited higher rates of compliance with routine infection-prevention methods as observed objectively: 93% wore a surgical mask and 95.6% washed their hands. Only 1.8% of personnel were observed to wear a surgical mask in the GW. ED had a higher percentage of high-risk individuals compared with the GW (14.5% vs. 2.8%), but the attack rate was higher in the GW (16.7%; l/6) than in the ED (3%; 1/33). There were no transmissions in the intermediate- and low-risk groups in the ED. Otherwise 2 patients were infected in the GW among the low-risk group. MERS were transmitted to them indirectly by staff who cared for the index patient.


Our study provide compelling evidence that routine infection-prevention policies can greatly reduce nosocomial transmission of MERS. Conventional isolation is established mainly from contact tracing of patients during a MERS outbreak. But it should be extended to all people treated by any medical employee who has contact with MERS patients.

TRIAL REGISTRATION: NCT02605109 , date of registration: 11th November 2015.

KEYWORDS: Hand hygiene; Infection control; Isolation; Middle East respiratory syndrome coronavirus; Nosocomial infection

PMID: 31666061 DOI: 10.1186/s12890-019-0940-5

Keywords: MERS-CoV; Hand hygiene; IPCs; Nosocomial Outbreaks; S. Korea.


#Contamination of #hospital #surfaces with #respiratory #pathogens in #Bangladesh (PLOS One, abstract)

[Source: PLoS One, full page: (LINK). Abstract, edited.]


Contamination of hospital surfaces with respiratory pathogens in Bangladesh

Md. Zakiul Hassan , Katharine Sturm-Ramirez, Mohammad Ziaur Rahman, Kamal Hossain, Mohammad Abdul Aleem, Mejbah Uddin Bhuiyan, Md. Muzahidul Islam, Mahmudur Rahman, Emily S. Gurley


Published: October 28, 2019 / DOI: https://doi.org/10.1371/journal.pone.0224065



With limited infection control practices in overcrowded Bangladeshi hospitals, surfaces may play an important role in the transmission of respiratory pathogens in hospital wards and pose a serious risk of infection for patients, health care workers, caregivers and visitors. In this study, we aimed to identify if surfaces near hospitalized patients with respiratory infections were contaminated with respiratory pathogens and to identify which surfaces were most commonly contaminated. Between September-November 2013, we collected respiratory (nasopharyngeal and oropharyngeal) swabs from patients hospitalized with respiratory illness in adult medicine and paediatric medicine wards at two public tertiary care hospitals in Bangladesh. We collected surface swabs from up to five surfaces near each case-patient including: the wall, bed rail, bed sheet, clinical file, and multipurpose towel used for care giving purposes. We tested swabs using real-time multiplex PCR for 19 viral and 12 bacterial pathogens. Case-patients with at least one pathogen detected had corresponding surface swabs tested for those same pathogens. Of 104 patients tested, 79 had a laboratory-confirmed respiratory pathogen. Of the 287 swabs collected from surfaces near these patients, 133 (46%) had evidence of contamination with at least one pathogen. The most commonly contaminated surfaces were the bed sheet and the towel. Sixty-two percent of patients with a laboratory-confirmed respiratory pathgen (49/79) had detectable viral or bacterial nucleic acid on at least one surface. Klebsiella pneumoniae was the most frequently detected pathogen on both respiratory swabs (32%, 33/104) and on surfaces near patients positive for this organism (97%, 32/33). Surfaces near patients hospitalized with respiratory infections were frequently contaminated by pathogens, with Klebsiella pneumoniae being most common, highlighting the potential for transmission of respiratory pathogens via surfaces. Efforts to introduce routine cleaning in wards may be a feasible strategy to improve infection control, given that severe space constraints prohibit cohorting patients with respiratory illness.


Citation: Hassan MZ, Sturm-Ramirez K, Rahman MZ, Hossain K, Aleem MA, Bhuiyan MU, et al. (2019) Contamination of hospital surfaces with respiratory pathogens in Bangladesh. PLoS ONE 14(10): e0224065. https://doi.org/10.1371/journal.pone.0224065

Editor: Sarah Tschudin-Sutter, University Hospital Basel, SWITZERLAND

Received: February 11, 2019; Accepted: October 4, 2019; Published: October 28, 2019

This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.

Data Availability: All relevant data are within the paper and its Supporting Information files.

Funding: Emily S Gurley received the funding award. The Grant No. is GR-00720 (cooperative agreement number 5U01CI000628). The study was funded by the Centers for Disease Control and Prevention (CDC), Atlanta (https://www.cdc.gov/). US CDC provided technical support in the study design, data collection and analysis and preparation of the manuscript

Competing interests: The authors have declared that no competing interests exist

Keywords: Infectious diseases; Nosocomial outbreaks; Klebsiella pneumoniae; Bangladesh.


Characterization of #phenotypic and #genotypic traits of #carbapenem-resistant #Acinetobacter baumannii clinical isolates recovered from a tertiary care #hospital in #Taif, #Saudi Arabia (Infect Drug Resist., abstract)

[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]

Infect Drug Resist. 2019 Oct 3;12:3113-3124. doi: 10.2147/IDR.S206691. eCollection 2019.

Characterization of phenotypic and genotypic traits of carbapenem-resistant Acinetobacter baumannii clinical isolates recovered from a tertiary care hospital in Taif, Saudi Arabia.

El-Badawy MF1,2, Abdelwahab SF1,3, Alghamdi SA4, Shohayeb MM1,5.

Author information: 1 Division of Pharmaceutical Microbiology, Department of Pharmaceutics and Industrial Pharmacy, College of Pharmacy, Taif University, Taif 21974, Kingdom of Saudi Arabia. 2 Department of Microbiology and Immunology, Faculty of Pharmacy, Misr University for Science and Technology, 6th of October City 12568, Egypt. 3 Department of Microbiology and Immunology, Faculty of Medicine, Minia University, Minia 61511, Egypt. 4 Medical Genetics, Clinical Laboratory Department, College of Applied Medical Sciences, Taif University, Taif 21974, Kingdom of Saudi Arabia. 5 Department of Microbiology and Biotechnology, Faculty of Pharmacy, Delta University for Science and Technology, Gamasa 35712, Egypt.




Acinetobacter baumannii (A. baumannii) is a common nosocomial pathogen, which developed multi-drug-resistance to different classes of antibiotics including carbapenems. This study examined ten common carbapenemase genes among 32 carbapenem-resistant A. baumannii clinical isolates recovered from Taif, Saudi Arabia.


Isolates were phenotypically identified to the genus level by Vitek®2 and API 20NE®. The species level was confirmed by the amplification of bla OXA-51. The susceptibility for 21 different antibiotics was performed by Vitek 2 and modified Kirby-Bauer method. Isolates were genetically screened for 10 carbapenemases. Phylogenetic relatedness between isolates was determined by ERIC-PCR.


Genotypically identified A. baumannii represented 100% of the total phenotypically identified Acinetobacter spp. All the carbapenem-resistant isolates were sensitive to polymyxin B and colistin. Among the other antibiotics, ampicillin/sulbactam and tigecycline were the most effective agents. 90.8% of the isolates were resistant to all ten investigated β-lactams. bla OXA-51, bla IPM, bla NDM and bla OXA-23 were detected in 100%, 87.5%, 62.5% and 59.4% of isolates, respectively. Also, bla VIM and bla OXA-40 were less prevalent and were detected in 9.3% and 3.1% of the isolates, respectively. In addition, bla KPC, bla OXA-48, bla OXA-58, bla OXA-181 were not detected in any isolate. The A. baumannii isolates were categorised into ten genotypes on the basis of the detected carbapenemase genes and ERIC-PCR revealed a remarkable clonal diversity among these isolates.


Class A and class D carbapenemase genes were the most commonly detected among carbapenem resistant A. baumannii (CRAB) clinical isolates.

© 2019 El-Badawy et al.

KEYWORDS: A. baumannii; ERIC-PCR; blaOXA-51; carbapenemases; carbapenems

PMID: 31632100 PMCID: PMC6781848 DOI: 10.2147/IDR.S206691

Keywords: Antibiotics; Drugs Resistance; Carbapenem; Acinetobacter baumannii; Nosocomial outbreaks; Saudi Arabia.


#Clinical Manifestations of #Nipah Virus-Infected #Patients Who Presented to the #Emergency Department During an #Outbreak in #Kerala State in #India, May 2018 (Clin Infect Dis., abstract)

[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]

Clin Infect Dis. 2019 Oct 18. pii: ciz789. doi: 10.1093/cid/ciz789. [Epub ahead of print]

Clinical Manifestations of Nipah Virus-Infected Patients Who Presented to the Emergency Department During an Outbreak in Kerala State in India, May 2018.

Chandni R1, Renjith TP1, Fazal A1, Yoosef N1, Ashhar C1, Thulaseedharan NK1, Suraj KP1, Sreejith MK1, Sajeeth Kumar KG1, Rajendran VR1, Remla Beevi A2, Sarita RL3, Sugunan AP4, Arunkumar G5, Mourya DT6, Murhekar M7.

Author information: 1 Government Medical College, Kozhikode, Kerala, India. 2 Directorate of Medical Education, Thiruvananthapuram, Kerala, India. 3 Directorate of Health Services, Thiruvananthapuram, Kerala, India. 4 Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Port Blair, Andaman & Nicobar Islands, India. 5 Manipal Institute of Virology, Manipal Academy of Higher Education (Institute of Eminence Deemed to be University), Manipal, Karnataka, India. 6 ICMR-National Institute of Virology, Pune, Maharashtra, India. 7 ICMR-National Institute of Epidemiology, Chennai, Tamil Nadu, India.




An outbreak of Nipah virus (NiV) disease occurred in the Kozhikode district of Kerala State in India in May 2018. Several cases were treated at the emergency medicine department (ED) of the Government Medical College, Kozhikode (GMCK). The clinical manifestations and outcome of these cases are described.


The study included 12 cases treated in the ED of GMCK. Detailed clinical examination, laboratory investigations, and molecular testing for etiological diagnosis were performed.


The median age of the patients was 30 years and the male to female ratio was 1.4:1.0. All the cases except the index case contracted the infection from hospitals. The median incubation period was 10 days, and the case fatality ratio was 83.3%. Ten (83.3%) patients had encephalitis and 9 out of 11 patients whose chest X-rays were obtained had bilateral infiltrates. Three patients had bradycardia and intractable hypotension requiring inotropes. Encephalitis, acute respiratory distress syndrome, and myocarditis were the clinical prototypes, but there were large overlaps between these. Ribavirin therapy was given to a subset of the patients. Although there was a 20% reduction in NiV encephalitis cases treated with the drug, the difference was not statistically significant. The outbreak ended soon after the introduction of total isolation of patients and barrier nursing.


The outbreak of NiV disease in Kozhikode in May 2018 presented as encephalitis, acute respiratory distress and myocarditis or combinations of these. The CFR was high. Ribavirin therapy was tried but no evidence for its benefit could be obtained.

Twelve cases of Nipah virus disease were treated in the emergency department of a referral hospital in Kozhikode, India, in May 2018. The case fatality ratio was 83.3%. Ten cases each had encephalitis and acute respiratory distress syndrome and 3 had myocarditis. Transmission was mostly nosocomial.

© The Author(s) 2019. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail: journals.permissions@oup.com.

KEYWORDS: Kerala-India; Nipah clinical manifestations Kozhikode; Nipah epidemic; Nipah virus; encephalitis

PMID: 31627214 DOI: 10.1093/cid/ciz789

Keywords: Nipah Virus; India; Kerala; ARDS; Encephalitis; Myocarditis; Nosocomial outbreaks.