fluoroquinolone resistant salmonella enterica subspecies enterica serovar paratyphi  (Pasteur Institute)

Journal: Microbial Genomics

Article Title: Phylogenomic investigation of an outbreak of fluoroquinolone-resistant Salmonella enterica subsp. enterica serovar Paratyphi A in Phnom Penh, Cambodia

doi: 10.1099/mgen.0.000972

Figure Lengend Snippet: Epidemic curve of all 516 blood-culture-confirmed cases of Paratyphi A identified between 2008 and 2021 at both the MBL-IPC and SHCH. The epidemic curve is annotated with clinical fluoroquinolone-resistance screening results. Clinical fluoroquinolone-resistance screening was performed using nalidixic acid (NAL; 30 µg) disc diffusion until the end of 2009, when the preferred predictor was updated by EUCAST to PEF (5 µg) disc diffusion. The patient catchment area of both the MBL-IPC and SHCH (Phnom Penh and the surrounding provinces) has remained similar throughout the study period.

Article Snippet: In early 2020, the Medical Biology Laboratory of the Pasteur Institute of Cambodia isolated an unusually high number of fluoroquinolone-resistant Salmonella enterica subspecies enterica serovar Paratyphi A strains during its routine bacteriological surveillance activities in Phnom Penh, Cambodia.

Techniques: Diffusion-based Assay

Journal: Microbial Genomics

Article Title: Phylogenomic investigation of an outbreak of fluoroquinolone-resistant Salmonella enterica subsp. enterica serovar Paratyphi A in Phnom Penh, Cambodia

doi: 10.1099/mgen.0.000972

Figure Lengend Snippet: Antibiotic resistance rates of 146 Paratyphi A strains isolated during the 2020 Phnom Penh outbreak at both the MBL-IPC ( N =32) and SHCH ( N =114)

Article Snippet: In early 2020, the Medical Biology Laboratory of the Pasteur Institute of Cambodia isolated an unusually high number of fluoroquinolone-resistant Salmonella enterica subspecies enterica serovar Paratyphi A strains during its routine bacteriological surveillance activities in Phnom Penh, Cambodia.

Techniques: Isolation

Journal: Microbial Genomics

Article Title: Phylogenomic investigation of an outbreak of fluoroquinolone-resistant Salmonella enterica subsp. enterica serovar Paratyphi A in Phnom Penh, Cambodia

doi: 10.1099/mgen.0.000972

Figure Lengend Snippet: Phylogenetic network showing patterns of descent among the 32 Paratyphi A strains isolated by the MBL-IPC in relation to the Phnom Penh hospital or clinic where patients presented. The median-joining network is based on 40 SNP differences detected across the whole core genome. Each circle represents a unique haplotype, and the size of the circle is proportional to the number of isolates sharing that type. Haplotypes represent variations of a genome in a bacterial population that evolves through the gradual accumulation of mutations. Hatch marks on the branches represent the number of mutational steps between haplotypes. Colour codes represent different hospitals and clinics, as shown in the key.

Article Snippet: In early 2020, the Medical Biology Laboratory of the Pasteur Institute of Cambodia isolated an unusually high number of fluoroquinolone-resistant Salmonella enterica subspecies enterica serovar Paratyphi A strains during its routine bacteriological surveillance activities in Phnom Penh, Cambodia.

Techniques: Isolation

Journal: Microbial Genomics

Article Title: Phylogenomic investigation of an outbreak of fluoroquinolone-resistant Salmonella enterica subsp. enterica serovar Paratyphi A in Phnom Penh, Cambodia

doi: 10.1099/mgen.0.000972

Figure Lengend Snippet: Time-tree of 288 Paratyphi A lineage 2.3 isolates detailing relatedness, geographical origin, chromosomal gyrA resistance mutations and the classification of all analysed strains. The maximum clade credibility beast2 tree is based on 920 SNP differences detected across the whole core genome of the isolate panel and was visualized using iTOL v6.5.3 . Paratype (sub-)lineages are annotated on the tree branches. Tip labels of Cambodian isolates are coloured red. The labels highlighted with a pink background represent the studied 2020 MBL-IPC Phnom Penh outbreak isolates. The timing of the transmission event that introduced Paratyphi A lineage 2.3 into Cambodia is annotated as a red star in the phylogeny. The leaves on the tree are coloured according to the geographical origin of the isolates: we classified countries into United Nations sub-regions to limit the number of colours in the phylogeny. The different sub-regions are illustrated in the map using light colours, while countries included in the studied panel belonging to that sub-region are displayed in dark colours. Vector map data of administrative boundaries of countries was obtained from Natural Earth and visualized using qgis v.2.18.13 . The gyrA resistance conferring mutations detected in sequence isolates are visualized in the ring around the time-tree. Six discussed independent gyrA -S83F acquisition events are annotated on the tree using arrows.

Article Snippet: In early 2020, the Medical Biology Laboratory of the Pasteur Institute of Cambodia isolated an unusually high number of fluoroquinolone-resistant Salmonella enterica subspecies enterica serovar Paratyphi A strains during its routine bacteriological surveillance activities in Phnom Penh, Cambodia.

Techniques: Transmission Assay, Plasmid Preparation, Sequencing

Journal: Microbial Genomics

Article Title: Phylogenomic investigation of an outbreak of fluoroquinolone-resistant Salmonella enterica subsp. enterica serovar Paratyphi A in Phnom Penh, Cambodia

doi: 10.1099/mgen.0.000972

Figure Lengend Snippet: Overview of all Paratyphi A sub-lineage 2.3.1 gyrA -S83F /gyrA -D87G acquisition events Isolates sequenced in this study are highlighted in bold. The timing of acquisition events was inferred by estimating the t MRCA of all sequenced isolates that descended from an ancestor strain that acquired the resistance-conferring mutation. The uncertainty around the timing is reflected in the 95 % HPD interval. As isolates ERR1877997 and ERR1878006 represent singletons, the timing of acquisition event 5/6 is reflected by the isolation year of these isolates (2014 and 2015, respectively). Note the ERR1878006 gyrA mutation was incorrectly called as gyrA -S83F in another publication [ 6 ].

Article Snippet: In early 2020, the Medical Biology Laboratory of the Pasteur Institute of Cambodia isolated an unusually high number of fluoroquinolone-resistant Salmonella enterica subspecies enterica serovar Paratyphi A strains during its routine bacteriological surveillance activities in Phnom Penh, Cambodia.

Techniques: Mutagenesis, Isolation

Journal: Microbial Genomics

Article Title: Phylogenomic investigation of an outbreak of fluoroquinolone-resistant Salmonella enterica subsp. enterica serovar Paratyphi A in Phnom Penh, Cambodia

doi: 10.1099/mgen.0.000972

Figure Lengend Snippet: The demographic history of Cambodian Paratyphi A sub-lineage 2.3.1. (a) All 113 sequenced 2.3.1 isolates annotated with their gyrA resistance conferring mutations. (b) Bayesian Skyline plot that shows changes in the bacterial effective population size ( N e ) through time since 1999, based on 95 SNP differences detected across the whole core genome of the sequenced 2.3.1 isolate panel ( n =113). This plot allows us to discuss relative increases or decreases to the bacterial population size through time. The central dashed line represents the median bacterial population size with its 95 % central posterior density (CPD) interval represented by the upper and lower lines. Note the y -axis is on a log scale.

Article Snippet: In early 2020, the Medical Biology Laboratory of the Pasteur Institute of Cambodia isolated an unusually high number of fluoroquinolone-resistant Salmonella enterica subspecies enterica serovar Paratyphi A strains during its routine bacteriological surveillance activities in Phnom Penh, Cambodia.

Techniques: