Teleclinical Microbiology: An Innovative Approach to Providing Web-Enabled Diagnostic Laboratory Services in Syria

Objectives: Telemedicine can compensate for the lack of health care specialists in response to protracted humanitarian crises. We sought to assess the usability of a teleclinical microbiology (TCM) program to provide diagnostic services in a hard-to-reach region of Syria. Methods: A semimobile station was equipped with conventional micrograph and macrograph digital imaging systems. An electronic platform (Telemicrobiology in Humanitarian Crises, TmHC) was created to facilitate sharing, interpreting, and storing the results. A pilot study was conducted to identify the bacterial species and antimicrobial susceptibility pattern of 74 urinary clinical isolates. An experience survey was conducted to capture the feedback of 8 participants in the program. Results: The TmHC platform (https://sdh.ngo/tmhc/) enabled systematic transmission of the laboratory records and co-interpretation of the results. The isolates were identified as Escherichia coli (n = 61), Klebsiella pneumoniae (n = 12), and Proteus mirabilis(n = 1). All the isolates were multidrug resistant. The performance of our TCM module was rated 4 (satisfying) and 5 (very satisfying) by 6 and 2 users, respectively. Data security of and cost-effectiveness were the main perceived concerns. Conclusions: Although we encountered several context-related obstacles, our TCM program managed to reach a highly vulnerable population of 4 million people confined in the northwest region of Syria.publishedVersio

The Acinetobacter baumannii website (Ab-web): a multidisciplinary knowledge hub, communication platform, and workspace

Acinetobacter baumannii is a Gram-negative bacterium increasingly implicated in hospital-acquired infections and outbreaks. Effective prevention and control of such infections are commonly challenged by the frequent emergence of multidrug-resistant strains. Here we introduce Ab-web (https://www.acinetobacterbaumannii.no), the first online platform for sharing expertise on A. baumannii. Ab-web is a species-centric knowledge hub, initially with ten articles organized into two main sections, ‘Overview’ and ‘Topics’, and three themes, ‘epidemiology’, ‘antibiotic resistance’, and ‘virulence’. The ‘workspace’ section provides a spot for colleagues to collaborate, build, and manage joint projects. Ab-web is a community-driven initiative amenable to constructive feedback and new ideas

Prevalence of plasmid-mediated quinolone resistance in Norwegian and Swedish clinical isolates of Escherchia coli and Klebsiella spp.

The aim of this study was to examine the presence of plasmid-mediated qnr and aac(6')-Ib-cr resistance genes among Escherichia coli and Klebsiella spp. clinical isolates obtained between 2003 and 2005 from Norway and Sweden and showed resistance and/or reduced susceptibility to nalidixic acid and ciprofloxacin, respectively. Prevalence of the qnr (1.6%) and aac(6’)-Ib-cr (14.1%) determinants was low. The qnr-genes were more prevalent in Klebsiella spp. (7.7%) than in E. coli (0.7%). qnrS1 was the most common qnr gene.The qnrS1 genes were located on at least three different plasmid backbones. Nevertheless, the qnrS1-containing area containd matching structures in all the qnrS1-positive isolates

Identification, molecular epidemiology, and antibiotic resistance characterization of Acinetobacter spp. clinical isolates

The papers of the thesis are not available in Munin: 1. Karah, N., B. Haldorsen, K. Hegstad, G. S. Simonsen, A. Sundsfjord, Ø. Samuelsen and the Norwegian Study Group on Acinetobacter: 'Species identification and molecular characterization of Acinetobacter spp. blood culture isolates from Norway', Journal of Antimicrobial Chemotheraphy (2011) 66:738-744. Available at http://dx.doi.org/10.1093/jac/dkq521 2. Karah, N., B. Haldorsen, N. O. Hermansen, Y. Tveten, E. Ragnhildstveit, D. H. Skutlaberg, S. Tofteland, A. Sundsfjord and Ø. Samuelsen: 'Emergence of OXA carbapenemase- and 16S rRNA methylase-producing international clones of Acinetobacter baumannii in Norway', Journal of medical microbiology (2011), 60:515-521. Available at http://dx.doi.org/10.1099/jmm.0.028340-0 3. Karah, N., C. G. Giske, A. Sundsfjord, and Ø. Samuelsen: 'A diversity of OXA-carbapenemases and class 1 integrons among carbapenem-resistant Acinetobacter baumannii clinical isolates from Sweden belonging to different international clonal lineages' (submitted paper to Microbial Drug Resistance). 4. Karah, N., R. Smyth, B. Haldorsen, G. S. Simonsen, A. Sundsfjord, and Ø. Samuelsen: 'Performance of VITEK 2, BD Phoenix, and MALDI-TOF MS systems for species identification of Acinetobacter blood culture isolates' (manuscript

Insights into the genetic contexts of sulfonamide resistance among early clinical isolates of Acinetobacter baumannii

Since the late 1930s, resistance to sulfonamides has been accumulating across bacterial species including Acinetobacter baumannii, an opportunistic pathogen increasingly implicated the spread of antimicrobial resistance worldwide. Our study aimed to explore events involved in the acquisition of sulfonamide resistance genes, particularly sul2, among the earliest available isolates of A. baumannii. The study utilized the genomic data of 19 strains of A. baumannii isolated before 1985. The whole genomes of 5 clinical isolates obtained from the Culture Collection University of Göteborg (CCUG), Sweden, were sequenced using the Illumina MiSeq system. Acquired resistance genes, insertion sequence elements and plasmids were detected using ResFinder, ISfinder and Plasmidseeker, respectively, while sequence types (STs) were assigned using the PubMLST Pasteur scheme. BLASTn was used to verify the occurrence of sul genes and to map their genetic surroundings. The sul1 and sul2 genes were detected in 4 and 9 isolates, respectively. Interestingly, sul2 appeared thirty years earlier than sul1. The sul2 gene was first located in the genomic island GIsul2 located on a plasmid, hereafter called NCTC7364p. With the emergence of international clone 1, the genetic context of sul2 evolved toward transposon Tn6172, which was also plasmid-mediated. Sulfonamide resistance in A. baumannii was efficiently acquired and transferred vertically, e.g., among the ST52 and ST1 isolates, as well as horizontally among non-related strains by means of a few efficient transposons and plasmids. Timely acquisition of the sul genes has probably contributed to the survival skill of A. baumannii under the high antimicrobial stress of hospital settings

CRISPR-based subtyping to track the evolutionary history of a global clone of Acinetobacter baumannii

Acinetobacter baumannii global clone 1 (GC1) is the second most common clone in the global population of A. baumannii isolates and a key cause of hospital-acquired infections. In this study, comparative analysis of the clustered regularly interspaced short palindromic repeats (CRISPR)-based sequence types (CST) was performed to determine the genetic relatedness and track patterns of descent among 187 GC1 isolates, as a complement to the evolutionary inferences from their multilocus sequence types and genome-wide single nucleotide polymorphism (SNP)-based phylogeny. The CST2 cluster, CST2 and all the CSTs descending from CST2, corresponded to GC1 lineage 1. This cluster included 143 of the 187 isolates showing a prevalent geographical distribution worldwide. A well-demarcated group of 13 CSTs, accounting for 33 of the 187 isolates, corresponded to GC1 lineage 2. All the CSTs of this group were characterized by the absence of spacer Ab-18. Many of the GC1 lineage 2 isolates had an epidemiological link to the Middle East and/or were obtained in military healthcare facilities. GC1 lineage 3 was a novel lineage that has so far been limited to Afghanistan, Pakistan and India. Diversification of A. baumannii GC1 into lineages and clades has probably been related to a dynamic expansion after passing a migration bottleneck to enter the hospital environment. We conclude that CRISPR-based subtyping is a convenient method to trace the evolutionary history of particular bacterial clones, such as A. baumannii GC1

Communicable diseases in northwest Syria in the context of protracted armed conflict and earthquakes

The earthquakes in Türkiye and Syria in February, 2023, have caused further devastation in northwest Syria-an area already affected by protracted armed conflict, mass forced displacement, and inadequate health and humanitarian provision. The earthquake damaged infrastructure supporting water, sanitation, and hygiene, and health-care facilities. The disruptions to epidemiological surveillance and ongoing disease control measures resulting from the earthquake will accelerate and expand ongoing and new outbreaks of many communicable diseases including measles, cholera, tuberculosis, and leishmaniasis. Investing in existing early warning and response network activities in the area is essential. Antimicrobial resistance, which had already been an increasing concern in Syria before the earthquake, will also be exacerbated given the high number of traumatic injuries and breakdown of antimicrobial stewardship, and the collapse of infection prevention and control measures. Tackling communicable diseases in this setting requires multisectoral collaboration at the human-animal-environment nexus given the effect of the earthquakes on all these sectors. Without this collaboration, communicable disease outbreaks will further strain the already overburdened health system and cause further harm to the population

Database for the ampC alleles in Acinetobacter baumannii

Acinetobacter baumannii is a troublesome opportunistic pathogen with a high capacity for clonal dissemination. We announce the establishment of a database for the ampC locus in A. baumannii, in which novel ampC alleles are differentiated based on the occurrence of >= 1 nucleotide change, regardless of whether it is silent or missense. The database is openly accessible at the pubmlst platform for A. baumannii (http://pubmlst.org/abaumannii/). Forty-eight distinctive alleles of the ampC locus have so far been identified and deposited in the database. Isolates from clonal complex 1 (CC1), according to the Pasteur multilocus sequence typing scheme, had a variety of the ampC locus alleles, including alleles 1, 3, 4, 5, 6, 7, 8, 13, 14, 17, and 18. On the other hand, isolates from CC2 had the ampC alleles 2, 3, 19, 20, 21, 22, 23, 24, 26, 27, 28, and 46. Allele 3 was characteristic for sequence types ST3 or ST32. The ampC alleles 10, 16, and 25 were characteristic for CC10, ST16, and CC25, respectively. Our study points out that novel gene databases, in which alleles are numbered based on differences in their nucleotide identities, should replace traditional records that use amino acid substitutions to define new alleles

Communicable diseases in northwest Syria in the context of protracted armed conflict and earthquakes

The earthquakes in Türkiye and Syria in February, 2023, have caused further devastation in northwest Syria—an area already affected by protracted armed conflict, mass forced displacement, and inadequate health and humanitarian provision. The earthquake damaged infrastructure supporting water, sanitation, and hygiene, and health-care facilities. The disruptions to epidemiological surveillance and ongoing disease control measures resulting from the earthquake will accelerate and expand ongoing and new outbreaks of many communicable diseases including measles, cholera, tuberculosis, and leishmaniasis. Investing in existing early warning and response network activities in the area is essential. Antimicrobial resistance, which had already been an increasing concern in Syria before the earthquake, will also be exacerbated given the high number of traumatic injuries and breakdown of antimicrobial stewardship, and the collapse of infection prevention and control measures. Tackling communicable diseases in this setting requires multisectoral collaboration at the human–animal–environment nexus given the effect of the earthquakes on all these sectors. Without this collaboration, communicable disease outbreaks will further strain the already overburdened health system and cause further harm to the population

Control and management of multidrug resistant Acinetobacter baumannii : A review of the evidence and proposal of novel approaches

Hospital-acquired infections are on the rise and are a substantial cause of clinical and financial burden for healthcare systems. While infection control plays a major role in curtailing the spread of outbreak organisms, it is not always successful. One organism of particular concern is Acinetobacter baumannii, due to both its persistence in the hospital setting and its ability to acquire antibiotic resistance. A. baumannii has emerged as a nosocomial pathogen that exhibits high levels of resistance to antibiotics, and remains resilient against traditional cleaning measures with resistance to Colistin increasingly reported. Given the magnitude and costs associated with hospital acquired infections, and the increase in multidrug-resistant organisms, it is worth re-evaluating our current approaches and looking for alternatives or adjuncts to traditional antibiotics therapies. The aims of this review are to look at how this organism is spread within the hospital setting, discuss current treatment modalities, and propose alternative methods of outbreak management