scholarly journals Molecular typing of bacteria for epidemiological surveillance and outbreak investigation / Molekulare Typisierung von Bakterien für die epidemiologische Überwachung und Ausbruchsabklärung

2016 ◽  
Vol 67 (4) ◽  
pp. 199-224 ◽  
Author(s):  
Werner Ruppitsch

SummaryConstant confrontations with microbial threats pose major challenges to human and animal health, agricultural and food production, and public safety. Identifying pathogenic bacteria (species) and tracking strains (by series of well-characterized isolates) to their sources are especially important in outbreak investigations. Compared to the identification of the species, the identification of the source and spread of microbial infections represents a major—and many times futile—challenge. This is due to the multitude of ways microorganisms can occur and spread within healthcare facilities and in the community; how, when, and where they can contaminate the complex nutrition chain, leading to natural and man-made outbreaks.Typing is the characterization of isolates or strains below species or subspecies level. Typing of bacterial isolates is an essential procedure to identify the microbe causing the illness or to track down an outbreak to the suspected source. In the genomic era, the introduction of molecular methods has largely replaced phenotypic methods and “molecular epidemiology” has emerged as a new discipline. The current molecular typing methods can be classified into three categories: (a) PCR-based methods, (b) DNA fragment analysis-based methods, and (c) DNA sequence-based methods, including the new exciting era of high-throughput genome sequencing.

2013 ◽  
Vol 18 (4) ◽  
Author(s):  
A J Sabat ◽  
A Budimir ◽  
D Nashev ◽  
R Sá-Leão ◽  
J M van Dijl ◽  
...  

2017 ◽  
Vol 2 (1) ◽  
pp. 23 ◽  
Author(s):  
Roberto Viau ◽  
Lee M. Kiedrowski ◽  
Barry N. Kreiswirth ◽  
Mark Adams ◽  
Federico Perez ◽  
...  

Molecular typing using repetitive sequenced-based PCR (rep-PCR) and hsp60 sequencing were applied to a collection of diverse Enterobacter cloacae complex isolates. To determine the most practical method for reference laboratories, we analyzed 71 E. cloacae complex isolates from sporadic and outbreak occurrences originating from 4 geographic areas. While rep-PCR was more discriminating, hsp60 sequencing provided a broader and a more objective geographical tracking method similar to multilocus sequence typing (MLST). In addition, we suggest that MLST may have higher discriminative power compared to hsp60 sequencing, although rep-PCR remains the most discriminative method for local outbreak investigations. In addition, rep-PCR can be an effective and inexpensive method for local outbreak investigation.


Author(s):  
Majid Baserisalehi ◽  
Samira Zarezadeh ◽  
Majid Baserisalehi ◽  
Saeed Shoa

Stenotrophomonas maltophilia is an emerging pathogenic non-fermentative Gram-negative Bacillus species. It has caused many nosocomial infections and can be isolated from various hospital wards and healthcare facilities. Research has shown that most of its strains are inherently resistant to many antibiotics and have multidrug resistance. This research intended to determine its occurrence frequency at some Hospitals in shiraz, Iran. The present study was conducted in six months (from early spring to late summer 2019). Clinical samples (Blood, Urine and cerebrospinal fluid (CSF)) collected from 120 patients afflicted with various infections. The samples were transferred to the Laboratory and subjected to microbiological analysis. Identification of the isolates was carried out by phenotypic methods and Stenotrophomonas maltophilia isolates verified using molecular methods. In total, various bacteria were isolated from 84 clinical samples. The isolates were Escherichia coli, Enterobacter aerogenes, Klebsiella pneumoniae, Stenotrophomonas maltophilia, Staphylococcus aureus and Pseudomonas aeruginosa. Stenotrophomonas maltophilia was isolated from 17 (20.2%) positive samples and most of them were isolated from blood samples. Our finding indicated that Stenotrophomonas maltophilia isolated more from blood samples follow by CSF sample. In addition, our finding illustrated that Stenotrophomonas maltophilia can be considered as the common nosocomial agent at hospitals in Shiraz, Iran.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Samuel Lumborg ◽  
Samuel Tefera ◽  
Barry Munslow ◽  
Siobhan M. Mor

AbstractThis study explores the perceived influence of climate change on the health of Hamer pastoralists and their livestock in south-western Ethiopia. A combination of focus group discussions and key informant interviews were conducted with Hamer communities as well as local health workers, animal health workers and non-governmental organisation (NGO) staff. Thematic framework analysis was used to analyse the data. Reductions in rangeland, erratic rainfall, recurrent droughts and loss of seasonality were perceived to be the biggest climate challenges influencing the health and livelihoods of the Hamer. Communities were travelling greater distances to access sufficient grazing lands, and this was leading to livestock deaths and increases in ethnic violence. Reductions in suitable rangeland were also precipitating disease outbreaks in animals due to increased mixing of different herds. Negative health impacts in the community stemmed indirectly from decreases in livestock production, uncertain crop harvests and increased water scarcity. The remoteness of grazing lands has resulted in decreased availability of animal milk, contributing to malnutrition in vulnerable groups, including children. Water scarcity in the region has led to utilisation of unsafe water sources resulting in diarrhoeal illnesses. Further, seasonal shifts in climate-sensitive diseases such as malaria were also acknowledged. Poorly resourced healthcare facilities with limited accessibility combined with an absence of health education has amplified the community’s vulnerability to health challenges. The resilience and ambition for livelihood diversification amongst the Hamer was evident. The introduction of camels, increase in permanent settlements and new commercial ideas were transforming their livelihood strategies. However, the Hamer lack a voice to express their perspectives, challenges and ambitions. There needs to be collaborative dynamic dialogue between pastoral communities and the policy-makers to drive sustainable development in the area without compromising the values, traditions and knowledge of the pastoralists.


Antibiotics ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 829
Author(s):  
Wim Gorssen ◽  
Dominiek Maes ◽  
Roel Meyermans ◽  
Jürgen Depuydt ◽  
Steven Janssens ◽  
...  

The use of antimicrobials in animal production is under public debate, mainly due to the risk of transfer of resistance to pathogenic bacteria in humans. Therefore, measures have been taken during the last few decades to reduce antibiotic usage in animals, for instance, by national monitoring programmes and by improving animal health management. Although some initiatives exist in molecular genetic selection, quantitative genetic selection of animals towards decreased antibiotic usage is an underexplored area to reduce antibiotic usage. However, this strategy could yield cumulative effects. In this study, we derived new phenotypes from on-farm parenteral antibiotic records from commercially grown crossbred finishing pigs used in the progeny test of Piétrain terminal sires to investigate the heritability of antibiotics usage. Parenteral antibiotic records, production parameters and pedigree records of 2238 full-sib pens from two experimental farms in Belgium between 2014 and 2020 were analysed. Heritability estimates were moderate (18–44%) for phenotypes derived from all antibiotic treatments, and low (1–15%) for phenotypes derived from treatments against respiratory diseases only. Moreover, genetic correlations between these new phenotypes and mortality were low to moderate (0.08–0.60) and no strong adverse genetic correlations with production traits were found. The high heritabilities and favourable genetic correlations suggest these new phenotypes, derived from on-farm antibiotics records, to be promising for inclusion in future pig breeding programs to breed for a decrease in antibiotics usage.


2007 ◽  
Vol 28 (7) ◽  
pp. 845-852 ◽  
Author(s):  
G. W. Coombs ◽  
H. Van Gessel ◽  
J. C. Pearson ◽  
M.-R. Godsell ◽  
F. G. O'Brien ◽  
...  

Objective.To describe the control of an outbreak of infection and colonization with the New York/Japan methicillin-resistantStaphylococcus aureus(MRSA) clone in multiple healthcare facilities, and to demonstrate the importance of making an MRSA management policy involving molecular typing of MRSA into a statewide public health responsibility.Setting.A range of healthcare facilities, including 2 metropolitan teaching hospitals and a regional hospital, as well as several community hospitals and long-term care facilities in a nonmetropolitan healthcare region.Interventions.A comprehensive, statewide MRSA epidemiological investigation and management policy.Results.In May 2005, there were 3 isolates referred to the Western Australian Gram-Positive Bacteria Typing and Research Unit that were identified as the New York/Japan MRSA clone, a pandemic MRSA clone with the ability to spread and replace existing clones in a region. Subsequent investigation identified 28 additional cases of infection and/or colonization dating from 2002 onward, including 1 involving a colonized healthcare worker (HCW) who had previously been hospitalized overseas. Of the 31 isolates detected, 25 were linked epidemiologically and via molecular typing to the isolate recovered from the colonized HCW. Four isolates appeared to have been introduced separately from overseas. Although the isolate from the single remaining case patient was genetically indistinct from the isolates that spread within Western Australia, no specific epidemiological link could be established. The application of standard outbreak management strategies reduced further spread.Conclusions.The elimination of the New/York Japan MRSA clone in a healthcare region demonstrates the importance of incorporating MRSA management policy into statewide public health programs. The mainstays of such programs should include a comprehensive and effective outbreak identification and management policy (including pre-employment screening of HCWs, where applicable) and MRSA clone identification by multilocus sequence typing.


1999 ◽  
Vol 20 (11) ◽  
pp. 756-758 ◽  
Author(s):  
Jeffrey D. Klausner ◽  
Carol Zukerman ◽  
Ajit P. Limaye ◽  
Lawrence Corey

AbstractUsing molecular typing methods, we confirmed an outbreak ofStenotrophomonas maltophiliaamong bone marrow transplant patients. The likely source was a healthcare worker who may have washed with moisturizer instead of soap between patients. Hospital epidemiologists need to go beyond antibiograms when evaluating outbreaks and be vigilant about all aspects of hand washing.


2013 ◽  
Vol 62 (5) ◽  
pp. 701-707 ◽  
Author(s):  
Jia-Li Feng ◽  
Jin-Yan Lin ◽  
Xiao-Bing Jiang ◽  
Ou Zhang ◽  
Jiang-Feng Zhu ◽  
...  

Laribacter hongkongensis is a potential emerging pathogen, associated with community-acquired diarrhoea. For epidemiological purposes, different molecular typing methods, such as pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing, have been developed for this pathogen. However, these methods require specialized equipment and costly reagents. More importantly, they are labour-intensive and time-consuming, which is not really suitable for foodborne disease outbreak investigations. In this study, we developed a rapid and reliable method using 22-mer primers specific for the enterobacterial repetitive intergenic consensus sequence (ERIC). PFGE was used for comparison, to evaluate this method. A total of 81 isolates of L. hongkongensis were examined: 79 isolates recovered from food of diverse origins and two strains derived from patients with L. hongkongensis-associated infection. Typing patterns and clustering analysis indicated that the 81 L. hongkongensis isolates were grouped into 21 and 13 genotypes by ERIC-PCR and PFGE, respectively. ERIC-PCR was found as reproducible as PFGE. A high percentage (70.4 %) of isolates yielded distinguishable ERIC-PCR patterns, which were concordant with the results from PFGE. These results suggest that ERIC-PCR is valuable for use in the epidemiological investigation of L. hongkongensis.


2018 ◽  
Vol 6 (15) ◽  
pp. e00295-18
Author(s):  
Alexander Fortuna ◽  
Ricardo Ramnarine ◽  
Aimin Li ◽  
Nahuel Fittipaldi ◽  
Christine Frantz ◽  
...  

ABSTRACT Legionella pneumophila outbreak investigations require the development of reliable typing methods to better understand the genetic relationships of the isolates involved. Here, we report the draft genome sequences of four clinical Legionella pneumophila isolates obtained between 2000 and 2012 in Ontario, Canada.


2014 ◽  
Vol 04 (03) ◽  
pp. 147-152 ◽  
Author(s):  
Tiehao Lin ◽  
Liying Lin ◽  
Fan Zhang

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