Alam et al (2022): Emergence and Evolutionary Response of Vibrio cholerae to Novel Bacteriophage, Democratic Republic of the Congo

I have been reading the paper by Alam et al (2022): "Emergence and Evolutionary Response of Vibrio cholerae to Novel Bacteriophage, Democratic Republic of the Congo".

Epidemiology

In this paper, the authors sequenced the whole genomes of 24 toxigenic V. cholerae O1 strains belonging to the current pandemic lineage (7PET lineage), and isolated in 2015-2017 from patients in the Democratic Republic of the Congo (DRC). They found that the DRC isolates belonged to two clades, which they denoted as I and II.

Bacteriophages

The authors were interested in figuring out how bacteriophages affect evolution of V. cholerae in DRC, since they may contribute to persistance of some strains and demise of other strains.

An interesting finding in this paper was that in 41% of faecal samples from cholera patients, the authors identified a novel ICP1 (Bangladesh cholera phage 1) bacteriophage. This was genetically distinct from ICP1 isolates previously found in Bangaldesh and India. Some of the DRC strains were found from lab. experiments to be resistant to the novel ICP1 phage, but the mechanism for this resistance is not yet clear.

Curiously, V. cholerae clones that were sensitive to the novel ICP1 phage seem to be propagating more successfully in DRC, while clones that were phage-resistant appeared to have died out. The authors suggested that this may reflect a fitness cost of phage resistance, for example, if phage resistance results in lower virulence.

 

 

Irenge et al (2020): Genomic analysis of pathogenic isolates of Vibrio cholerae from easter Democratic Republic of the Congo (2014-2017)

I have been reading the paper by Irenge et al (2020): "Genomic analysis of pathogenic isolates of Vibrio cholerae from eastern Democratic Republic of the Congo (2014-2017)". 

Epidemiology

In this paper, they carried out whole genome sequencing of 78 clinical isolates of V. cholerae associated cholera in eastern DRC between 2014 and 2017. They found that most isolates (73/78) were V. cholerae O1 biotype El Tor with CTX-3 type prophage, and belonged to current pandemic lineage (7PET lineage). Furthermore, they belonged to the T10 sublineage of 7PET found in East Africa, and comprised two sub-clades corresponding to MLST sequence types ST69 and ST515. The isolates had the a large deletion in the VSP-II genomic island; this deletion had previously been seen in several East African isolates.

 Antimicrobial resistance

All V. cholerae isolates displayed resistance in laboratory tests to trimethoprim-sulfamethoxazole and nalidixic acid. Nine V. cholerae O1 isolates displayed decreased susceptibility to ciprofloxacin, whereas 9 O1 and 2 non-O1 isolates were resistant to ampicillin. 

From genome sequencing, they found that all DRC 01 isolates had the SXT/R391 integrative conjugative element ICEVchBan5. Another very interesting finding was that while V. cholerae in Yemen with mutations gyrA(S83I) and parC(S85L) had decreased susceptibility to ciprofloxacin in laboratory tests, relatively few DRC isolates with this combination of mutations showed decreased susceptibility to ciprofloxacin.

Irenge et al 2020: Genome Sequence of a Pathogenic Vibrio cholerae 01 El Tor Strain Defective for the Entire Vibrio Pathogenicity Island 1

I have been reading the paper Irenge et al (2020): "Genome Sequence of a Pathogenetic Vibrio cholerae O1 El Tor Strain Defective for the Entire Vibrio Pathogenicity Island 1, Isolated in the Eastern Democratic Republic of the Congo". 

In this paper they describe a Vibrio cholerae isolate from a cholera patient from DRC, for which they have sequenced the genome. They found that the isolate belonged to the current pandemic lineage (7PET lineage). A previous paper from this team had reported a larger set of V. cholerae 7PET isolates from DRC, that mostly belonged to the T10 sublineage of 7PET. These previous isolates comprised two different clades of a phylogenetic tree, with ST515 and ST69 sequence types respectively. The isolate sequenced in this paper belonged to the ST515 clade, and was very unusual because it had a complete deletion (about 80 kb long) of the Vibrio pathogenicity island 1 (VPI-1). The island extended from gene VC_0774 to VC_0845. This was surprising as the VPI-1 includes the toxin coregulated pilus (TCP) cluster that plays a critical role in colonisation of the host gut.

Al Malki et al (2021): Draft Genome Sequences of Seven Vibrio cholerae Isolates from Adult Patients in Qatar

I have been reading the paper by Al Malki et al (2021): "Draft Genome Sequences of Seven Vibrio cholerae Isolates from Adult Patients in Qatar".

In this paper, the authors sequenced 7 Vibrio cholerae genomes from patients in Qatar. Of these 7 isolates, 6 were isolates from stool and one from blood. Four of the isolates had MLST sequence type ST69, so were likely to belong to the current pandemic lineage (7PET lineage). The other three isolates, including that isolated from blood, had other sequence types, so likely belong to other (non-pandemic) lineages of V. cholerae.

Weill et al (2019): Genomic insights into the 2016-2017 cholera epidemic in Yemen

 I have been reading the paper by Weill et al (2019): "Genomic insights into the 2016-2017 cholera epidemic in Yemen".

In this paper, the authors (which include my group leader Nick Thomson) sequenced the genomes of 42 isolates from 2016-2017 from the Yemen cholera epidemic, as well as 74 additional isolates from South Asia, the Middle East, and Eastern and Central Africa (116 isolates sequenced in total). 

Epidemiology

They showed that the Yemeni isolates belonged to a single sublineage of the current pandemic lineage (7PET lineage), and that this sublineage, named "T13", had originated in South Asia and caused outbreaks in East Africa (e.g. Kenya, Tanzania, Uganda) in 2015-2016 before appearing in Yemen. They point out that prior to the Yemen epidemic, there were large cholera outbreaks across the Horn of Afria, which serves as a major hub of migration into Yemen.

 The Yemeni isolates were different from those that had been previously circulating in the Middle East, such as those from Iraq in 2007 and 2015, and from Iran in 2012 and 2015. Those previous isolates were independently imported from South Asia on two separate occasions. 

Antibiotic resistance

The Yemeni isolates had a narrow lab. phenotype of antimicrobial drug resistance to nalidixic acid, the vibriostatic agent O/129 and nitrofurantoin. Resistance to O/129 is due to the gene dfrA1, which is part of an integratic conjugative element ICEVchInd5/ICEVchBan5 in the Yemeni isolates.

The authors found that the Yemeni isolates were susceptible to polymyxin B, resistance to which is used as a marker of the El Tor biotype (which is a common phenotype in the 7PET lineage).

Cholera toxin subtype

The Yemeni isolates had the cholera toxin subunit B gene variant ctxB7. The ctxB7 allele was first detected in India in 2006, and has been exported outside Asia on three separate occasions: to West Africa in 2008 ("T12 sublineage"), Haiti in 2010, and East Africa around 2013-2014 ("T13 sublineage").

Pathogenwatch

I have added a "collection" of the genomes sequenced by Weill et al to Pathogenwatch, which you can see here (116 genomes). 

 

Mutreja et al (2011): Evidence for several waves of global transmission in the seventh cholera pandemic

I have been reading the paper by Mutreja et al (2011): "Evidence for several waves of global transmission in the seventh cholera pandemic", by Ankur Mutreja, Gordon Dougan, my current group leader Nick Thomson, and their collaborators. 

Epidemiology

In this paper, they sequenced the genomes of 136 Vibrio cholerae isolates, and combined those with 18 previously published V. cholerae genomes, to make a phylogenetic analysis of 154 global isolates. Based on this, they showed that the current pandemic lineage of cholera (7PET lineage) has spread from the Bay of Bengal in at least three independent but overlapping waves with a common ancestor in the 1950s. Wave 1 spread in 1977-1992 and included the South American pandemic in the 1990s, Wave 2 in 1978-1984, and Wave 3 in 1986-1990. 

 Antimicrobial resistance

Wave 2 and 3 isolates have integrative conjugative element of the SXT family (an SXT/R391 ICE) carrying antimicrobial resistance genes, which they estimated to have been gained around 1978-1984. 

Cholera toxin subtype

They found that each wave had a particular cholera toxin (CTX) type.

Lineages of Vibrio cholerae

As well as investigating the spread of the current pandemic lineage (7PET lineage) of V. cholerae, Mutreja et al also put the 7PET lineage in context within the species. From phylogenetic analysis, they showed that the 7PET lineage is one of eight lineages of V. cholerae (L1-L8): 7PET is lineage L2, while the 'Classical' lineage (an earlier pandemic lineage) is lineage L1 in their classification, and isolates from the US Gulf Coast are L3. 

Pathogenwatch

I made a Pathogenwatch 'collection' for the isolates sequenced by Mutreja et al (2011), which you can see here. The collection contains 131 isolates, as I left out 5 relatively low-quality assemblies.

Murase et al 2022: Genomic dissection of the Vibrio cholerae O-serogroup global reference strains

I have been reading a fantastic paper by Murase et al (2022): "Genomic dissection of the Vibrio cholerae O-serogroup global reference strains: reassessing our view of diversity and plasticity between two chromosomes". 

There are about 200 O-serogroups of V. cholerae known, but only serogroups O1 and O139 are found in the current pandemic lineage (7PET lineage). Non-O1, non-O139 serogroups of V. cholerae are relatively poorly studied, but can also contribute to much smaller outbreaks of milder diarrhoeal illness (e.g. by serogroup O75, and by serogroup O37).

Sequencing of serogroup reference strains

In this paper, Murase et al have sequenced and analysed the whole set of V. cholerae O-serogroup reference strains. This included 210 O-serogroups that have been identified, taking the Sakazaki collection, which included 194 V. cholerae strains, 14 V. mimicus strains and 2 V. metoecus strains. Among the reference strains, three strains were identified as Aeromonas sp. and one as V. fluvialis, so these were excluded from further analyses and they just focussed on the remaining 206 strains (including 190 V. cholerae).

O-antigen biosynthetic clusters

Murase et al found that there were 9 strain pairs that had almost identical O-antigen biosynthetic gene clusters, and were also serologically identical. They removed these from the accredited O-antigen reference list (removing the underlined serogroup): O5 and O185, O17 and O198, O18 and O136, O20 and O121, O31 and O84, O68 and O129, O74 and O200, O85 and O163, and O87 and O119.

Interestingly, Murase et al also found that there were 16 pairs of strains with almost identical O-antigen biosynthetic gene clusters on chromosome 1, but different serological patterns. They suggest this is likely due to presence of additional O-antigen biosynthesis genes in those strains at secondary loci on chromosome 2.

Pathogenwatch

 I have added a "collection" to Pathogenwatch for the Murase et al paper, containing 190 V. cholerae genomes, which you can see here.